Bibliography

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%T HELP
%K glookbib, query, search, about, instructions, FAQ
%X on using this bibliography search program -
   `glookbib' searches for entries using ALL of the given keywords exactly
   so adding more words will narrow the search.  If you first find little
   or nothing, use fewer and more general search terms.
   Terms must be spelt correctly - English (UK) spelling is preferred.
   Try singular in preference to plural.
   Do NOT include      and or * + ) (        etc.


%T John W. Backus
%D 3/12/1924 - 17/3/2007
%K Backus, John, biography, Fortran, obituary, zz0307
%X The B in BNF.  1977 Turing award.
   [Also search for: Backus].
   "... `You need the willingness to fail all the time,' he said. `You have to
   generate many ideas and then you have to work very hard only to discover
   that they don't work. And you keep doing that over and over until you find
   one that does work.'"
   -- [<A HREF="http://www.nytimes.com/2007/03/19/obituaries/20cnd-backus.html">obit@NYT</A>]['07],
   Nature [<A HREF="http://dx.doi.org/10.1038/446998a">doi:10.1038/446998a</A>]['07]
   and [<A HREF="http://en.wikipedia.org/wiki/John_Backus">wikipedia</A>]['07].

%T Niels Bohr
%D 1885-1962
%K Bohr, quantum, physics, physicist, quote, quotable, expert, experts,
   expertise, specialist
%X "An expert is a person who has made all the mistakes that can be made in
   a very narrow field<!-- from jnc on arc rejoinders '05 -->."

%T Edgar F. Codd
%D 1923-2003
%K Codd, relational databases, DBMS, normal form, normalisation, SQL,
   biography, obituary, zz0403
%X See his  1 9 7 0  paper.
   Aug. 23, 1923 (Portland, England) -- April 18, 2003 (Williams Island, Fla)
   obit:[<A HREF="http://www.bayarea.com/mld/mercurynews/news/local/5676133.htm" TARGET="EXTERNAL">Mercury News</A>][20/4/'03]

%T Peter Cook
%D 1937-1995
%K Cook, Pete, Dud, comedy, comedian, humour, humor, entertainment, biography
%X Born Torquay 17 Nov 1937,
   died (gastrointestinal haemorrhage) London 9 Jan 1995, aged 57.
   Pembroke College Cambridge.
   Beyond The Fringe
     (with Alan Bennett, Jonathan Miller, Dudley Moore, Edinburgh Festival '60)
   TV:   Not Only ... But Also (Pete and Dud, 1965-71)
   Film: The Wrong Box (1966)
         Bedazzled (1967)
         Monte Carlo or Bust (1969)
         The Rise and Rise of Michael Rimmer (1970)     (other films)
   Nightclub: `The Establishment'
   Involved with `Private Eye' magazine 1963-.
   m. Wendy Snowdon,  Judy Huxtable (1973),  Lin Chong Cook (1989).
   [Also see:  Tragically I was an only twin]

%T Seymour Cray
%D 1925-1996
%K Cray, Cray1, Cray2, super computers, supercomputer, computer architecture
%X Cray, born 28 Sept 1925, died 5 Oct 1996 aged 71
   from head injuries sustained in a car accident.

%T Francis Crick
%D 1916-2004
%K Crick, MolBio, DNA, double helix, Nobel prize, NobelPrize
%X DNA's double helix structure with Watson, but also see Rosalind Franklin.

%T Gorge Dantzig
%D 1914-2005
%K simplex method, linear programming
%X 8/11/1914-13/5/2005

%T Edsger Wybe Dijkstra
%D 1930-2002
%K computer science, program verification, proof, correctness, obituary,
   biography, zz0802
%X [<A HREF="http://www.cs.utexas.edu/users/UTCS/notices/dijkstra/ewdobit.html" TARGET="external">notice</A>][8/2002]
   [<A HREF="http://www.cs.utexas.edu/users/EWD" TARGET="external">works</A>][8/2002]

%T Richard Doll
%D 1912-2005
%K smoking, medicine, health, lung cancer, epidemiologist, epidemiology
%X "Only 60 years ago, smoking was generally regarded as innocuous. Now it is
   recognized as the main cause of lung cancer, the world's commonest cancer.
   More than any other person, Richard Doll was responsible for this remarkable
   transformation in attitude, as well as for the now widely accepted view that
   much cancer (not just of the lung) is, at least in principle, avoidable.
   Doll, who died on 24 July 2005 aged 92, was the world's foremost
   epidemiologist and had a wide influence on the progress of the subject...."
   [<A HREF="http://dx.doi.org/10.1038/438041a" TARGET="external">doi:10.1038/438041a</A>]['05]

%T Peter Elias
%D 1923-2001
%K information theory, coding
%X [<A HREF="http://people.cornell.edu/pages/jc353/peter_elias.htm">cornell</A>]['04]

%T Paul Erdos
%D 1913-1996
%K mathematics, Hungary
%X Dr Paul Erdos  born Hungary 1913,
   died 20 Sept 1996 aged 83   [- The Age Fri 4 Oct 96]

%A Stephen Jay Gould
%D 1941-2002
%K Darwinian evolution

%T Hypatia
%D 370-415
%K Hypatia, biography, mathematics, maths, science
%X from D. Burton History of Mathematics: An Introduction, 3rd Edition, 1995:
   Hypatia (370-415) was distinguished in mathematics, medicine, and philosophy
   and is reported to have written a commentary on the first six books of
   Diophantus' _Arithmetica_, as well as a treatise on Apollonius's _Conic
   Sections_.  From her father she had obtained a knowledge of the astronomical
   discoveries of Claudius Ptolemy, and she edited the _Almagest_ of this
   great astronomer.  She was also the unquestioned leader of the neo-Platonic
   school of philosophy and took part in the last attempt to oppose the
   Christian religion.  As a living symbol of the old culture, she was destined
   to be a pawn in a struggle for political mastery of Alexandria.
      Hypatia lectured at the Museum on mathematics and philosophy, and her
   classes attracted many distinguished listeners.  Among these was the
   philosopher Synesius of Cyrene, who was later to become bishop of
   Ptolemais.  In the letters of Synesius that have come down to us, he always
   spoke of Hypatia in the highest terms, calling her "mother, sister,
   reverend teacher," and praising both her learning and her virtue.
   In spite of support from Synesius and other Christians, the Christian
   leaders regarded Hypatia's neo-Platonic philosophy
   as heretical.  Her position was further threatened by her friendship with
   Orestes, Roman governor of the city and the only countervailing force to
   Cyril, bishop of Alexandria.  The followers of Cyril spread rumors that
   Hypatia was drawing large crowds to her lecture hall, where under the guise
   of scholarship, she was expounding paganism - and that moreover, her
   influence over Orestes was the only obstacle to a reconciliation between
   the governor and himself.  As she returned one day from her classes,
   Hypatia was waylaid by a mob of religious zealots, slashed by sharp oyster
   shells, and finally torn limb from limb, her remains delivered to the
   flames.  With the death of Hypatia, the long and glorious history of Greek
   mathematics was at an end.
   via: Michael Kinyon <!-- email: mkinyon@peabody.iusb.indiana.edu -->(12/'94)

%T Norman Neill Greenwood
%D 19/1/1925-14/11/2011
%K Greenwood, Professor chemistry, chemist, obit, obituary,
   Mossbauer spectroscopy
%X obit@[<A HREF="http://www.leeds.ac.uk/secretariat/obituaries/2012/greenwood_norman.html">Leeds Uni.</A>]['13],
   [<A HREF="http://www.guardian.co.uk/science/2012/nov/27/norman-greenwood">Grauniad</A>]['13],
   [<A HREF="http://www.thetimes.co.uk/tto/opinion/obituaries/article3615585.ece">Times</A>]['13],
   [<A HREF="https://en.wikipedia.org/wiki/Norman_Greenwood">wikip</A>]['24],
   [<A HREF="https://royalsocietypublishing.org/doi/10.1098/rsbm.2019.0015">RoyalSoc</A>]['24].

%T M. Karnaugh
%D 1924-
%K Karnaugh, biography, map, mathematics, computing, circuit design, science
%X According to Ken Rosen's discrete mathematics textbook,
   Maurice Karnaugh was born in 1924, attended CCNY (BS) and Yale (MS, PhD),
   worked for AT&T from 1952 until 1970, when he became a researcher at IBM.
   He has contributed to applications of digital techniques in computing and
   telecommunications and is currently interested in knowledge-based systems
   and heuristic search methods.
   From: <!-- email: grossman@vela.acs.oakland.edu --> (Jerry Grossman, 11/'94)
         Organization: Oakland University, Rochester, Michigan, U.S.A.

%A N. Mandela
%T Long Walk to Freedom - The Autobiography of Nelson Mandela.
%I Little, Brown and Cp.
%D 1995
%K Mandela, autobiography, auto biography, politics, South Africa
%X reviewed in The Age, Saturday 28/1/95, $35

%A Benoit Mandelbrot
%D 1924-2010
%K Mandelbrot, set, fractal, fractals, dimension
%X 1924 -14 Oct 2010   (age 85.11).
   (See [<A HREF="http://dx.doi.org/10.1126/science.1199471">doi:10.1126/science.1199471</A>]['10].)

%A Donald Michie
%D 1923-2007
%K Michie, artificial intelligence, AI, UK
%X obit by M.Boden in Nature: [<A HREF="http://dx.doi.org/10.1038/448765a">doi:10.1038/448765a</A>][16/8/'07],
   dm@[<A HREF="http://www.aiai.ed.ac.uk/~dm/">ed ac uk</A>]['10].

%A Patrick Moore
%D 1923-2012
%K Moore, Sir Patrick, astronomy, astronomer, The Sky at Night, BBC, TV
%X Sir Patrick Moore, 4/3/1923 - 9/12/2012, 89.
   '... Sir Patrick presented the first edition of The Sky at Night on
   24 April 1957. He last appeared in an episode broadcast on Monday. ...'
   -- [<A HREF="http://www.bbc.co.uk/news/uk-20657939">bbc</A>]['12].
   [<A HREF="http://www.guardian.co.uk/science/2012/dec/09/sir-patrick-moore">Grdn</A>]['12].
   '... Then there was the occasion that he visited Utah with a television
   crew. "Welcome to the Mormon state," said a humourless citizen. "We are
   quite different from the rest of America. You will find no swearing or
   drinking or wild women here."
   "It's hardly worth coming, is it?: replied Moore. ...'
   -- [<A HREF="http://www.telegraph.co.uk/news/obituaries/science-obituaries/9732840/Sir-Patrick-Moore.html">DT</A>]['12].

%A Prof. Sidney Morgenbesser
%D 1921-2004
%K Morgenbesser, philosopher, humourist
%X 1950s, J. L. Austin: "... no language employs a double +ve to make a -ve."
          S.M.:  "Yeah, yeah."
   Asked if he agreed with Mao's view that a statement can be both true and
      false at the same time.   SM: "Well I do and I don't."
   On the philosophy of pragmatism: "It sounds good in theory, but
      it'll never work in practice."
   On his modest publishing: "Moses wrote one book. Then what did he do?"
   @ U. Columbia from 1954 until retired 1990,
   b.22/9/1921, d.2/8/2004   -- from obit, by A. Gumbel, Independent, Aug '04.

%T K. Popper
%D 1902-1994
%K Popper, Karl, biography, philosophy of science
%X Karl Popper From David Walker on Popper, The Age, 22/9/94:
   We can never establish an idea beyond doubt.  And yet we can measure the
   strength of any "scientific" idea by requiring it to make predictions which,
   if wrong, would show that idea to be untenable.

%T Arthur L. Samuel
%D 1901-1990
%K Samuel, board game playing, checkers, AI, machine learning, IBM, IBM701
%X [also search for: checkers]
   [<A HREF="http://infolab.stanford.edu/pub/voy/museum/samuel.html">obit</A>]['07].

%T Claude Shannon
%D 1917-2001
%K Shannon, mathematical theory of communication, information theory, IT,
   communications, encode, code, cryptography, obituary, zz0301
%X died 26 Feb 2001
   [<A HREF="http://www.bell-labs.com/news/2001/february/26/1.html" TARGET="external">www</A>][26/2/2001].

%A Lloyd Shapely
%D 1923-2016
%K Shapely, obit, maths, game theory, stable marriage problem, UCCA, zz0416,
   1962, 2012 Nobel prize, NobelPrize
%X "Lloyd Stowell Shapley made profound contributions to almost every area of
   game theory ... His findings have been applied to all sorts of settings, from
   politics to hospitals. His whimsically titled 1962 paper - 'On College
   Admissions & the Stability of Marriage' - published in The Amer. Math.
   Monthly & co-authored with the late mathematician David Gale, won S. the
   2012 Nobel prize in economics, which I shared with him. ..."
   -- A.E.Roth, [<A HREF="http://dx.doi.org/10.1038/532178a">doi:10.1038/532178a</A>][4/2016].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Graph/Stable/">stable-marriage</A>].)

%T Ray Solomonoff
%D 1926-2009
%K Solomonoff, obit, AI, II, algorithmic, information, probability, theory, AIT,
   complexity
%X obit@[<A HREF="http://www.nytimes.com/2010/01/10/science/10solomonoff.html">NYT</A>]['10].
   rjs@[<A HREF="http://world.std.com/~rjs/">std</A>]['11] & publns.

%T Chris Wallace (C. S.)
%D 1933-2004
%K Wallace, CSW, minimum message length, MML, computer science, Australia, MDL,
   CSWallace, CSSE, Monash, obit, description, information theory, zz1004
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">C S Wallace's publications</A>]['24] -- searchable database.
   (Obit by Gopal Gupta was at www.csse.monash.edu.au/~gopal/csw.html [2004].)

%T John Archibald Wheeler
%K Wheeler, physics, quantum, obit, delayed choice experiment, wave, particle
%X JAW@[<A HREF="https://en.wikipedia.org/wiki/John_Archibald_Wheeler">wikip</A>]['16].

%T Sir Frank Whittle
%D 1907-1996
%K Whittle, biography, aircraft, turbo-jet engine, Gloster
%X 1 June 1907  Born in Coventry.
      Oct 1932  Granted a patent for the turbo-jet engine.
          1937  `Power Jets' tests its first jet engine.
   15 May 1941  Jet propelled Gloster-Whittle E28/39 first flew.
   Achieved 370mph (595kph) at 25,000 feet shortly after - faster than
   the Spitfire or any other propeller driven aircraft.
   Gloster Meteor saw active service towards the end of WWII.
   Whittle's invention was neglected before and after the war in the UK.
   The report says `death announced on 10 August 1996, aged 89'.
   - from the Daily Telgraph and Guardian, in The Age 23/8/96.



%T Accuracy, Precision
%K accuracy, precision, defn, definition
%X "The accuracy of a measurement system is the degree of closeness of
      measurements of a quantity to that quantity's actual (true) value.
   The precision of a measurement system ... is the degree to which repeated
      measurements under unchanged conditions show the same results."
   -- [<A HREF="http://en.wikipedia.org/wiki/Accuracy_and_precision">wikip</A>]['13].

%T Acetylation
%K Acetylation, defn, definition
%X "... process of introducing an acetyl group into a compound, specifically,
   the substitution of an acetyl group for an active hydrogen atom. A reaction
   involving the replacement of the hydrogen atom of a hydroxyl group with an
   acetyl group (CH3 CO) yields a specific ester, the acetate. ...
   ... post-translational modification of proteins, for example, histones, p53,
   and tubulins. ... In histone acetylation & deacetylation, the histones are
   acetylated and deacetylated on lysine residues in the N-terminal tail as part
   of gene regulation. ...""
   [<A HREF="http://en.wikipedia.org/wiki/Acetylation">wikip</A>]['09].

%T Almost Tree
%K almost tree, almostTree, defn, definition
%X A graph G is 'almost-tree(k)' if every 'block', B, of G
   has |E(B)| <= |V(B)|+k.
   (I.e., each (biconn.) block is only a little (k) more than a tree itself.)
   G is 'almost-tree' if it is almost-tree(k) for some constant k.
   [Also search for: block defn].

%T Ancestral
%K ancestral, ancestralGraph, defn, definition
%X "Ancestral graphs are mixed gs. used with three(!) kinds of edges:
   directed edges... , bidirected edges ... , & undirected edges ... ,
   required to satisfy some additional constraints:
   . If there is an edge from u to v, with an arrowhead at v [ie either directed
     from u to v or bidirected], then there does not exist a path from v to u
     consisting of undirected edges and/or directed edges oriented consistently
     with the path.
   . If v is an endpoint of an undirected edge, then it is not also the
     endpoint of an edge with an arrowhead at v. ..."
   -- AG@[<A HREF="https://en.wikipedia.org/wiki/Ancestral_graph">wikip</A>]['18].
   [Also search for: chainGraph].

%T ANCOVA
%K ANCOVA, defn, definition
%X ANalysis of COVAriance
   "ANCOVA allows you to remove from a dependent var. (y) irrelevant or error
   variance that can not be predicted from your independent var. (x). Hence, by
   accounting for the 3rd var., you are more able to obtain a accurate picture
   of the proportion of variance in y that x is capable of accounting for; in
   other words, your power is increased."
   [<A HREF="http://www.uwsp.edu/psych/cw/statmanual/ancovaoverview.html">uwsp</A>]['05]

%T ANOVA
%T ANOVA, defn, definition
%X ANalysis Of VAriation
   "In an analysis of variance the variation in the response measurements is
   partitoned into components that corr. to different sources of variation.
   The goal in this procedure is to split the total variation in the data into
   a portion due to random error and portions due to changes in the values of
   the independent variable(s)."
   -- [<A HREF="http://www.itl.nist.gov/div898/handbook/prc/section4/prc431.htm">nist</A>]['05]

%T AR, ARMA
%K AR, autoregressive moving average, auto regressive, defn, definition
%X ARMA Auto Regressive Moving Average in time-series analysis.
   [Also see: Box Jenkins c197x]

%T argmin
%K argmin, argmax, definition, defn
%X e.g. if A[1], A[2], ... A[n] is an array of n numbers then
   argmin<SUB>i</SUB>{A[i]=v} is the index of the 1st elt having the value v.
   argmax<SUB>x in R</SUB> f(x) is the value of x, in R, that maximizes f(x).

%T assignment problem
%K Assignment problem, defn, definition
%X "... the assignment problem (or linear assignment problem) is given two sets,
   A & T, of equal size, & a weight fn C: AxT->R. Find a bijection f: A->T s.t.
   the cost  fn: SUM_{a in  A} C_{a, f(a)} is minimized. ..."
   -- AP@[<A HREF="https://en.wikipedia.org/wiki/Assignment_problem">wikip</A>]['22].
   (Often spec. by an nxn matrix, seek a perm of cols to minimse the trace.
   Is used in  g r a p h  m'tching.)

%T Automaton
%K automaton, automata, finite state, FA, FSA, deterministic, DFA, DFSA, non,
   nondeterministic, NFA, NFSA, NDFA, NDFSA, definition, defn
%X . A FA is [S,A,T] where S is a finite set of states one being the start
     state and some possibly being acceptance states, A is an alphabet, and
     T is a finite set of transitions (arcs, edges) each labelled with
     a letter from the alphabet.
   . A NFA (as opposed to DFA) is a FA where we allow 2 or more transitions
     out of a state to have the same label, & we (may) allow null-transitions.
   (Also see Mealy machine and Moore machine.)

%T Avogadro's constant
%K Avogadro's constant, Avogadros, defn, definition
%X The # of atoms in a sample whose bulk mass in grams equals the
   relative atomic mass of the element.
   P.Andreas et al. [<A HREF="http://arxiv.org/abs/1010.2317">arXiv</A>](2010)
   measured the # of atoms in a sphere of silicon-28 to calculate Avogadro's
   constant to nine sig.figs.: 6.02214084(18) x 10**23 / mol.

%T backpropagation
%K Backpropagation, backprop, NN, ANN, defn, definition
%X "... backprop. computes the gradient of the loss fn wrt the wts of the n/wk
   for a single input-output example, & does so efficiently, unlike a naive
   direct comp'n of the gradient wrt each wt individually. ... makes it feasible
   to use gradient methods for training multilayer networks ... works by
   computing the gradient of the loss fn wrt each wt by the chain rule,
   computing the gradient one layer at a time, iterating backward from the last
   layer ..."
   -- backprop@[<A HREF="https://en.wikipedia.org/wiki/Backpropagation">wikip</A>]['22].

%T Bagging and Boosting
%K bagging, boosting, definition, defn
%X Bagging algorithm:
   Definition: bootstrap sample: uniformly sample m instances
               of the training set with replacement
   1. Generate T boostrap samples
   2. Build a classifier for each bootstrap sample, C_1, C_2, ..., C_T
   3. A final classifier C_* is built by choosing as its output the
   output of the majority of C_1,...,C_T. Ties are broken arbitrarily.
      ------
   Boosting algorithm:
   I is the classifier function
   S is the training data of size m
   1. Set instance weights to 1
   2. for i = 1 to T (the number of trials)
       { 3. C_i = I( S )
         4. epsilon_i = 1/m Sum_{over instances where C_i is in error} weight_i
            (average of error)
         5. if error > 0.5 set S to be a bootstrap sample and goto 3.
            (if this keeps on happening then we have a big problem!)
         6. beta_i = epsilon_i / (1 - epsilon_i)
         7. for each x_j in S, if C_i( x_j ) is correct, update
              weight( x_j ) = weight( x_j ) * beta_i
         8. normalise weights so total over S is m
       }
   9. C_*( x ) = arg max_{over y}  Sum_{over C_i(x) = y } log 1/beta_i
      (Each classifier in the sequence is has weight beta_i which is
      a function of how it performed on the data)
   via rohan 12/1999

%T Beta distribution
%K beta, definition, defn
%X               Gamma(a+b)
   f(x|a,b) = ----------------- . x**(a-1) . (1-x)**(b-1),    x in [0,1].
              Gamma(a).Gamma(b)
   NB. Uniform if a=b=1.  Beta dist'n is conjugate prior for binomial dist'n.
   Also see the Dirichlet distribution.

%T Beta function
%K Beta function, definition, defn
%X Beta(a,b) = Gamma(a).Gamma(b)/Gamma(a+b)         (see beta distribution).

%T Biconnected
%K biconnected, k connected, kConnected, defn, definition
%X A graph, G, is 'biconnected' is it is connected and removing
   any vertex leaves it connected.
     (NB. Biconnected == '2-connected' (2-vertex-connected) *except*
      that K2 = <{u,v}, {(u,v)}> is taken to be biconn. but *sometimes*
      not to be 2-connected -- wikip.)
 * A 'biconnected component' of a graph is a maximal subgraph of G that is b..
 * G is 'k-vertex-connected' (or just 'k-connected') if
   it is connected and removing any k-1 vertices leaves it so.
     (So for all u and v, there are k "independent" paths from u to v
      ... if G is not K2.)
 * G is 'k-edge-connected' if
   it is connected and removing any k-1 edges leaves it so.

%T Bipartite
%K Bipartite, defn, definition
%X A graph is b. iff its vertices are in 2 disjont sets, U and V,
   s.t. every edge is of the form (u,v), u in U, v in V.
   A graph is b. iff it is two colourable.
   A graph is b. iff it does not contain an odd cycle.

%T Block
%K block, defn, definition
%X A 'block' of a graph, G, is either
   a maximal biconnected subgraph of G, a 'bridge', or an isolated vertex.

%T Bridge
%K bridge, defn, definition
%X A 'bridge' (or a 'cut edge') in a graph, G, is
   an edge whose removel disconnects G  -- wikip.

%T Bugs
%K Bug, bugs, Hemiptera, Heteroptera, defn, definition
%X "Hemiptera is an order of insects most often known as the true bugs
   (cf. bug), comprising around 50,000-80,000 species of cicadas, aphids,
   planthoppers, leafhoppers, shield bugs, and others. ... share a common
   arrangement of sucking mouthparts. Sometimes, the name true bugs is applied
   more narrowly still to insects of the suborder Heteroptera only. ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Hemiptera">wikip</A>]['13].

%T CAGE (Cap-analysis g' e')
%K CAGE, defn, definition
%X In Bioinformatics:
   "Cap-analysis gene expression (CAGE) Basic and Analysis Databases store an
   original resource produced by CAGE, which measures expression levels of
   transcription starting sites by sequencing large amounts of transcript 5'
   ends, termed CAGE tags. ... avg length is 20bp"
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gkj034">doi:10.1093/nar/gkj034</A>]['06].

%T Carmichael numbers
%K Carmichael number, carmicael, definition, defn
%X "In number theory, a Carmichael number is a composite number n, which in
   modular arith. satisfies the congruence reln: b^(n-1) = 1 (mod n) ..."
   -- CN@[<A HREF="https://en.wikipedia.org/wiki/Carmichael_number">wikip</A>]['22].

%T Catalan numbers
%K Catalan number, definition, defn
%X The # of  (i) (strict) binary trees having n internal nodes and n+1 leaves,
   (ii) ways of dividing an (n+2)-gon into triangles by joining vertices by
   straight lines.
                       1   2n          n: 0 1 2 3  4  5
   n >= 0,  cat(n) = -----(  )    cat(n): 1 1 2 5 14 42 ...
                     (n+1)  n     Named after Eugene Charles Catalan.
   (See C@[<A HREF="https://en.wikipedia.org/wiki/Catalan_number">wikip</A>]['18].)

%T Centerpoint
%K centerpoint, centrepoint, centre, center point, defn, definition, Tukey,
   depth, median
%X "... Given a set of pts in d-dim. space, a centerpoint of the set is a
   pt such that any hyperplane that goes through that pt divides the set of
   pts in two roughly equal subsets: the smaller part should have at least a
   1/(d+1) fraction of the points. ... Every non-empty set of points (with no
   duplicates) has at least one centerpoint. ... Closely related [to] Tukey
   depth of a point (min # pts on one side of h-plane thru the pt), and
   Tukey median ... O(n^(d-1) + n log n) time[Chan04]."
   -- [<A HREF="http://en.wikipedia.org/wiki/Centerpoint_%28geometry%29">wikip</A>]['13].
   [Also search for: geometric median] (not the same thing).

%T Chain
%K chain, chainGraph, defn, definition
%X "A chain graph is a graph which may have both directed & undirected
   edges, but without any *directed* cycles (i.e., if we start at any vertex
   & move along the g. respecting the dirns of any arrows, we cannot return
   to the vertex we started from if we have passed an arrow) ..." -- wikip.
   (NB. Apparently not the same as PDAG:
   e.g. < {a,b,c}, {a->b, a->c, b-c} > is both a PDAG and a chainGraph, but
        < {a,b,c}, {a->b, b-c,  a-c} > is a PDAG but is not a chainGraph --
        think a->b-c-a.)
   [Also search for: PDAG]  and  [also search for: Frydenberg c1990],
   [also search for: ancestralGraph], [also search for: essentialGraph], and
   [also search for: chainGraph].

%T Chi Squared
%K chisquared, definition, defn
%X a p-variate normal distribution for x=(x1, x2, ..., xp) is
   p(x) = (2.pi)^(-p/2) . |s|^(-1/2) . exp( -(x-m)' . s^(-1) . (x-m)/2 )
   where m=(m1,...,mp) and s is the (co-)variance matrix.
   The chi-squared distribution as the probability mass outside
   a contour of the multivariate normal.  For the p-variate normal dist'n
   the pr mass outside the contour defined by
     chi0^2 = (x-m)' . s^(-1) . (x-m)
   is given by the chi^2 integral of p degrees of freedom
     INTEGRAL[chi0^2..oo] pr(chi^2 | p) d chi^2
   where chi^2 distribution of q degrees of freedom is
     pr(chi^2 | q) = 1/(2^(q/2).Gamma(q/2)) . (chi^2)^((q-2)/2) . exp(-chi^2/2)
   - see Box and Jenkins 1970 pp260

%T ChIP
%K ChIP, Chromatin ImmunoPrecipitation, ChIP chip, ChIPchip, ChIP seq, ChIPseq,
   definition, defn
%X ChIP-chip (ChIP on chip):
     Chromatin ImmunoPrecipiation (ChIP) analyses of protein-DNA
     interactions typically rely on DNA microarray (chip) hybridization
     quantification (Chip-chip),  c2008.
     [<A HREF="http://en.wikipedia.org/wiki/ChIP-chip">@wikip</A>]['08].
   ChIP-Seq (ChIP-sequencing):
     "ChIP-Seq combines chromatin immunoprecipitation (ChIP) with massively
     parallel DNA sequencing to identify binding sites of DNA-assoc. proteins.
     ... to determine how transcription factors & other chromatin-assoc.
     proteins influence phenotype-affecting mechanisms."
     [<A HREF="http://en.wikipedia.org/wiki/Chip-Sequencing">@wikip</A>]['08].

%T chordal
%K chordal, defn, definition
%X An undirected graph is chordal (aka triangulated) if it contains
   no chordless cycle of length greater than 3.
   [Also search for: simplicial defn].

%T Chromatin
%K Chromatin, defn, definition
%X "... complex combination of DNA, RNA, and protein that makes up chromosomes.
   ... major components of chromatin are DNA and histone proteins ..."
   [<A HREF="http://en.wikipedia.org/wiki/Chromatin">wikip</A>]['09].
   [also search for: methylation]  [and for: acetylation].

%T Clique
%K clique, maximal, definition, defn
%X A 'clique' of an undirected graph, G, is a set of vertices s.t. the
   induced subgraph is complete.
   A 'maximal clique' is a clique that is not a subset of a larger.
   . The 'clique problem' (does G have a clique of size >= k?) is NPC.
   . The maximum (NB. ...mum) clique problem is NPC.
   Also see: (maximal|maximum) independent set.

%T Clustering Coefficient
%K Clustering Coefficient, definition, defn
%X The c.c. of a vertex, v, in a directed graph, G, is
   # edges between vertices in N divided by |N|.(|N|-1)
   where N = {v' | v' adjacent to v}.  (Similarly for undir. G.)
   The c.c. of the whole graph, G, is the mean vertex-c.c..
   [Also search for: graphModel].

%T Combinations
%K combinations, nCr, n choose r, nChooseR, defn, definition
%X (n) = nCr = n!/(k!(n-k)!),  n choose r,  ways of choosing r things from n.
   (r)

%T Conductance
%K Conductance, Cheeger inequality, graph, defn, definition
%X "In graph theory the conductance of a graph G=(V,E) measures how 'well-knit'
   the graph is: It controls how fast a random walk on G converges to a uniform
   distribution. The cond. of a g. is often called the Cheeger const. ...
   The conductance of a cut (S,S') is
      psi(S) = SUM_{i in S, j in S'} a_ij / min(a(S), a(S'))
      where [a_ij] is the adj.matrix of G,
            a(S) = SUM_{i in S} SUM_{j in V} A_ij, and
            a(S)=SUM{i in S, j in V} a_ij.
      (A cut of a graph is a partion of V into S and S'.)
  The conductance of G
      phi(G) = min_{S subset V} psi(S).
   -- [<A HREF="https://en.wikipedia.org/wiki/Conductance_(graph)">wikip</A>]['16].

%T Conjugate Prior
%K conjugate priors, bayesian statistics, stats, definition, defn
%X A prior distribution such that the posterior distribution has the same form.
   (E.g. Conjugate prior for the *mean* of a Normal distribution is Normal.)
   See e.g. Gelman et al 1995, or Bernardo + Smith 1994.

%T Continuum hypothesis
%K Continuum hypothesis, countable, aleph, defn, definition
%X "... the continuum hypothesis (abbreviated CH) is a hypothesis about the
   possible sizes of infinite sets. It states that
     there is no set whose cardinality is strictly between that of
     the integers and the real numbers,
   or equivalently, that
     any subset of the real numbers is finite, is countably infinite, or
     has the same cardinality as the real numbers. ..."
   -- CH@[<A HREF="https://en.wikipedia.org/wiki/Continuum_hypothesis">wikip</A>]['23].

%T contravariantly recursive data type
%K contravariantly, contravariant, data type, datatype, negative,
   defn, definition
%X Negative [data t] isn't the usual term; we mostly call them 'contravariantly
   recursive' data types, due to CT influence.  Anyways the thing to note
   is that the value appears recursively, on the left of an arrow, e.g.,
      data Foo = Foo (Foo -> Bool)   -- contravariantly recursive
      data Foo = Foo (Bool -> Foo)   -- covariantly recursive
   -- Stefan O'Rear, stefanor at cox dot net, h@skell.list, [4/'07]

%T convolutional neural network
%K Convolutional, convolutionalNN, defn, definition
%X CNN@[<A HREF="https://en.wikipedia.org/wiki/Convolutional_neural_network">wikip</A>]['24].

%T Covariance
%K Covariance, defn, definition
%X "... the covariance between two real-valued random variables X and Y, with
    expected values E(X)=mu and E(Y)=nu is defined as: cov(X,Y)=E((X-mu)(Y-nu))
    ...  equiv. to  cov(X,Y)=E(XY)-mu*nu
    If X and Y are independent, then their covariance is zero. ..."
    -- [<A HREF="http://en.wikipedia.org/wiki/Covariance">wikip.</A>][11/'05]
    [Also search for: ANCOVA defn]

%T CpG
%K CpG, CpG island, islands, defn, definition
%X "CpG sites are regions of DNA where a cytosine nucleotide occurs next to a
   guanine nucleotide in the linear seq. of bases along its length.
   "CpG" stands for cytosine and guanine separated by a phosphate, which links
   the 2 nucleosides together in DNA. The "CpG" notation is used to distinguish
   a cytosine followed by guanine from a cytosine base paired to a guanine....
   CpG dinucleotides have long been observed to occur with a much lower freq. in
   the seq. of vertebrate genomes than ... random chance. ...
   ... regions of the DNA which have a higher conc. of CpG sites, known as CpG
   islands. ~ 1/2 of all genes in mammalian g. have CpG i. assoc. with the start
   of the gene. ..."
   --[<A HREF="http://en.wikipedia.org/wiki/CpG">wikip.</A>][4/'07]
   [Also search for: Methylation defn].

%T Cross Validation
%K cross validation, crossvalidation, kfold, definition, defn
%X In k-fold cross-validation, you divide the data into k subsets of
   (approximately) equal size. You train the net k times, each time leaving
   out one of the subsets from training, but using only the omitted subset to
   compute whatever error criterion interests you. If k equals the sample
   size, this is called "leave-one-out" cross-validation. "Leave-v-out" is a
   more elaborate and expensive version of cross-validation that involves
   leaving out all possible subsets of v cases.
      Note that cross-validation is quite different from the "split-sample" or
   "hold-out" method that is commonly used for early stopping in NNs. In the
   split-sample method, only a single subset (the validation set) is used to
   estimate the generalization error, instead of k different subsets; i.e.,
   there is no "crossing". While various people have suggested that
   cross-validation be applied to early stopping, the proper way of doing so is
   not obvious  [...] Form -
    <A HREF="http://www.faqs.org/faqs/ai-faq/neural-nets/part3/section-12.html"
     TARGET="external">A.N.N. FAQ</A>
   [Via r o h a n  2/'00]

%T Cyclotomic
%K cyclotomic polynomial, defn definition, totient
%X "... the nth cyclotomic polynomial, for any +ve int. n, is the unique
   irreducible polynomial with int. coefficients that is a divisor of
   x^n-1 and is not a divisor of x^k-1 for any k < n. Its roots are all
   nth primitive roots of unity ...
      p_n(x) = PI_{1<=k<=n,gcd(k,n)=1} (x-e^{2.pi.k/n}) ...
   The c.polynomials are monic ps. with int. coeffs. that are irreducible over
   the field of the rational numbers. Except for n=1 or 2, they are
   palindromics of even degree. ..."
   -- CP@[<A HREF="https://en.wikipedia.org/wiki/Cyclotomic_polynomial">wikip</A>]['21].

%T d-separation
%K d separation, dSeparation, direction dependent separation, definition, defn
%X in the context of Bayesian networks...
   (Defn 2.3, p42, bai, kk and an '04) "A set of nodes E d-separates 2 other
   sets of nodes, X and Y, if every path from a node in X to a node in Y
   is blocked given E."

%T DAG
%K DAG, DAGs, definition, defn
%X DAG = directed acyclic graph
   (In the case of Bayesian networks, 1 DAG == many TOMs in general,
   and one SEC == many DAGs in general.)

%T de Bruijn Graph
%K DeBruijn, de Bruijn, graph, definition, defn
%X Given an alphabet {a,b,...} of m symbols, the n-dim. deB. graph is a
   directed graph s.t.
      V = {(a**n, a**(n-1)b, ... }, i.e. all 'n' words, and
      E = {(p,q) | p = xw, q = wy, for symbols x & y, and 'n-1' word w}.
   Hence an edge represents an 'n+1' word, xwy.
   (DeB graphs became "big" in sequence assembly als. ~ c199x / c200x.)
   Also see [<A HREF="http://en.wikipedia.org/wiki/De_Bruijn_graph">wikip</A>]['09].

%T Decomposition
%K decomposition, definition, defn
%X *Of a graph: There are at least(!),
       simplicial decomp., recursively simplicial d.,
       tree d., modular d., of a graph.
       [Also search for: simplicial]  and  [also search for: Diestel graph].
   *Of a matrix: e.g., LU decomposition/factorization, ..., of a matrix.

%T Derangement
%K derangement, definition, defn
%X "a permutation of the elts of a set, s.t. no elt appears in its original
   posn. ... a derangement is a perm'n that has no fixed points."
   -- d@[<A HREF="https://en.wikipedia.org/wiki/Derangement">wikip</A>]['22].

%T Dirichlet distribution
%K Dirichlet distribution, dirichelet, beta, definition, defn
%X                         Gamma(a1+...+at)
   f(x1..xt|a1..at) = --------------------------- x1**(a1-1) . ... . xt**(at-1)
                      Gamma(a1) . ... . Gamma(at)
   where x1, ..., xt >= 0, and  x1+...+xt = 1  -- NB.
   Generalizes the Beta distribution (t=2) to t >= 2 dimensions;
   conjugate prior to the multinomial distribution.
   Also see D@[<A HREF="https://en.wikipedia.org/wiki/Dirichlet_distribution">wikip</A>]['18].

%T Discrete Logarithm
%K Discrete Logarithm, log, defn, definition
%X "Let G be any group. Denote its g.op. by multiplication & its identity elt
   by 1. Let b be any elt of G. For any +ve int. k, the expression b^k denotes
   the product of b with itself k times ... Let a also be an elt of G. An int.
   k that solves the eqn b^k=a is termed a discrete log (or simply log, in this
   context) of a to the base b. One writes k=log_b(a). ...  d.log is considered
   to be comp. intractable [in general]. ... efficient q.alg. due to Shor ..."
   -- DL@[<a HREF="https://en.wikipedia.org/wiki/Discrete_logarithm">wikip</A>]['21].

%T Domain
%K Domain, proteinDomain, defn, definition
%X "A protein domain is a conserved part of a given p.seq. & (tertiary) struct.
   that can evolve, function, & exist indep. of the rest of the p.chain. Each
   domain forms a compact 3D struct. & often can be indep. stable & folded. ...
      The concept of the domain was first proposed in 1973 by Wetlaufer [as]
      stable units of protein structure that could fold autonomously. ...
      [other defns as] units of: compact structure, function and evolution,
      folding. ..."
   -- PD@[<A HREF="https://en.wikipedia.org/wiki/Protein_domain">wikip</A>][7/2017].
   [Also search for: superSecondary defn].

%T Dominate, Maximal
%K dominate, dominates, dominated, maximal, point, points, 2D, definition, defn
%X The point (x,y) dominates the point (v,w) iff x > v and y > w.
   A point p=(x,y) in a set S is maximal iff it is not dominated by
   another point in S.                [See e.g. Kapoor c2000]

%T Dominating set
%K dominating set, defn, definition
%X "a dominating set for a graph G=(V,E) is a subset D of V s.t.
   every vertex not in D is adjacent to at least one member of D ...
   Dominating sets are closely related to independent sets ... any
   maximal indep. set in a g. is nec. also a minimal dominating set ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Dominating_set">wikip</A>]['15].
   [Also search for: independent set].

%T double factorial
%K Double Factorial, doubleFactorial, definition, defn
%X (!!).  For odd int N,  N!! = N.(N-2). ... .1,  e.g., 5!! = 5.3.1 = 15.
   !! is sometimes defined for even int K = 2k,  K!! = (2**K)k!   (0!! = 1.)

%T doubly stochastic matrix
%K doubly, defn, definition
%X a matrix of "nonnegative real numbers, each of whose rows and
   columns sums to 1"
   -- DSM@[<A HREF="https://en.wikipedia.org/wiki/Doubly_stochastic_matrix">wukip</A>]['24].

%T Duchenne smile
%K Duchenne smile, smiles, zygomatic, obicularus orus, definition, defn
%X "... authentic or so-called Duchenne smiles (a Duchenne smile occurs when
   both the zygomatic major and obicularus orus facial muscles fire, and human
   beings identify these as 'genuine' smiles)." -- Bl@nchflower & Osw@ld c2004

%T Endogenous / Exogenous variables
%K endogenous, exogenous, variable, statistical model, definition, defn
%X Exogenous variable: one that is not caused by another variable in the model.
     i.e. an external, independent "input".
   Endogenous Variable: one caused by other variable(s) in the model.
     i.e. a dependent "output".  NB Can also cause other endogenous variables.

%T Ergodic
%K ergodic, ergodicity, source, chain, chains, definition, defn
%X From Welsh 'Codes and Cryptography', p83, Clarendon 1988 :-
     We define a source Src over an alphabet Sigma to be 'ergodic'
     if it is (i) stationary and also (ii) below.
     For any sequence S=(S1, ..., Sm) and any output X=(X1, X2, ...) of Src,
     define the 'frequency' f[N](S,X) is the number of times S occurs
     in the first N terms of X.
     (ii) lim[N->infinity] (f[N](S,X))/N  =  P(X1=S1, ..., Sm)
   e.g. (p84):
     With probability 1/3 a source emits a random string of 0's and 1's;
     with probability 2/3, it emits a random string of 1's and 2's.  Show
     that this source is *not* ergodic.
   From Feller 'An Intro to Prob Theory and Its Applic'ns' p393, 1950 & 1968:-
     ... [Markov] chains whose states are ergodic (that is, they are
     aperiodic and persistent with finite mean recurrence times. ...).

%T Essential
%K essential, essentialGraph, defn, definition
%X "Essential graphs are graphs in which there are directed arcs & edges
   (not directed [i.e. und...] arcs). The essential g. corr. to a given B.n/wk
   is the g. in which the directed arcs corr. to the arcs of the B.n/wk whose
   orientation cannot be changed without changing the probabilistic relations
   encoded.  Edges represent the arcs that can be inverted."
   -- [<A HREF="https://library.bayesia.com/pages/viewpage.action?pageId=2392545">ba'es'a</A>]['18].
   [Also search for: chainGraph].

%T Eukaryote, Prokaryote
%K Eukaryotic,Prokaryotic, eukaryotes,prokaryotes, organelle, defn, definition
%X Eukaryotes have a cell nucleus and organelles, prokaryotes don't!-)
   Organelles: nucleus, ribosome (make protein), mitochondria (energy),
               chloroplast (photsynthesis), endoplasmic reticulum,
               Golgi apparatus, lysosome.

%T Eulerian circuit
%K graph, graphs, circuit, circuits, loop, loops, cycle, cycles, path, paths,
   Euler, definition, defn, Chinese Postman Problem
%X A graph has a E.C. iff there is a circuit which visits each *edge*
   exactly once.  (Also see Hamiltonian circuit).
    . An undirected, *connected* graph has an E.C. iff
      it has no vertex of odd degree -- Euler.
   & for a dir. connected graph, iff for all v, in-degree = out-degree -- E.
   ([Also search for: Chinese Postman Problem] --each edge trav AT LEAST once.)
   (BTW, Eulerian paths get a look-in in DNA sequence assembly.)

%T Exact cover
%K exact cover, set, defn, definition
%X Given a set X, and a collection S, of subsets of X, an
   'exact cover' is a subset S* of S s.t. each member of X
   is contained in exactly one member of S*
   -- [<A HREF="http://en.wikipedia.org/wiki/Exact_cover">wikip</A>]['14].
   NP-complete, of course.
   A generalisation where "exactly one" becomes "at most one".
   (The 'exact' because of the 'exactly one member of S*',
   else S* is just a 'set cover' of X.)
   [Also search for: Knuth DLX].

%T Factorization
%K factorization, factorisation, defn, definition
%X "In graph theory, a factor of a graph G is a spanning subgraph,
   i.e., a subg. that has the same vertex set as G.  A k-factor of a graph
   is a spanning k-regular subg., & a k-factorization partitions the edges
   of the graph into disjoint k-factors. A graph G is said to be k-factorable
   if it admits a k-factorization. ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Graph_factorization">wikip</A>]]['18].

%T Feedforward, Feedback
%K feed, forward, forwards, back, backward, backwards, control,
   definition, defn
%X Box and Jenkins, book 1970, p4:
     [...] The reason control is necessary is that there are inherent
     disturbances or noise in the process. When we can measure these
     disturbances, it may be possible to make compensatory changes in
     some other variable.  This is referred to as 'feedforward control'.
     Alternatively, or in addition, we may be able to use the deviation
     from target or ''error signal'' of the output characteristic
     itself to calculate the appropriate compensatory changes.
     This is called 'feedback control'.

%T Fibonacci word
%K Fibonacci word, definition, defn
%X S[0]=0, S[1]=01, ..., S[n]=S[n-1]++S[n-2].
   So S[2]=010, S[3]=01001, S[4]=01001010, ..., etc..
   Extends to the 'infinite Fibonacci word'.
   (See [<A HREF="http://en.wikipedia.org/wiki/Fibonacci_word">wikip</A>]['10].)

%T Frechet
%K Frechet, definition, defn
%X "... the Frechet distance is a measure of similarity between curves that
   takes into account the location and ordering of the points along the curves.
   It is named after Maurice Frechet. ... imagine a man traversing a finite
   curved path while walking his dog on a leash, with the dog traversing a
   separate one. Assume that the dog varies her speed to keep as much slack in
   her leash as possible: the F.dist. between the two curves is the length of
   the shortest leash sufficient for both to traverse their separate paths. ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Fr%C3%A9chet_distance">wikip</A>]['18].

%T Gamma distribution
%K Gamma distribution, definition, defn
%X                            a
   prob density is  f(x) = -------- (a.x)**(r-1).exp(-a.x),  r>0, a>0, x>0.
                           Gamma(r)

%T Gamma Function
%K Gamma function, definition, defn
%X Gamma(x) = INTEGRAL[0..infin]{ t**(x-1).exp(-t) dt }
   Generalizes factorial,  Gamma(n) = (n-1)!,  Gamma(1/2) = sqrt(pi),
   Gamma(1) = 1,  Gamma(x) = (x-1).Gamma(x-1), x > 0, continuous x.

%T Geometric Median
%K Geometric Median, centre, center, defn, definition, multidimensional, 1D, nD,
   1median
%X In n-dimension Euclidean space, R^n,
   "The GM = argmin_[y in R^n] { ||x_i - y||_2 }.  Does not depend on
   the [choice] of orthogonal Cartesian coordinates ...
   ... If y is distinct from all the given pts [y satisfies]
   SUM[j=1..m] ((x_j - y) / ||x_j-y||) = 0. ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Geometric_median">wikip</A>]['13].
   [Also search for: centerpoint] (not the same thing).

%T Girth
%K Girth, defn, definition
%X "the girth of a graph is the length of a shortest cycle
   contained in the graph."  And no cycles => girth = infinity.
   -- [<A HREF="http://en.wikipedia.org/wiki/Girth_(graph_theory)">wikip</A>]['14].

%T GPCR
%K GPCR, defn, definition
%C GPCR "G protein-coupled receptor"
   -- GPCR@[<A HREF="https://en.wikipedia.org/wiki/G_protein-coupled_receptor">wikip</A>]['20].

%T Graphical Model
%K graphical model, graphicalModel, defn, definition
%X "A log-linear model is graphical if whenever the model contains all
   two-factor terms generated by a high-order interaction the model also
   contains the higher-order interaction" -- FPj (2014) after Christensen97.
   (Also see GM@[<A HREF="https://en.wikipedia.org/wiki/Graphical_model">wikip</A>]['19].)

%T Group
%K group, semigroup, monoid, ring, field, defn, definition
%X SEMIGROUP: binary op '.' is associative.
   MONOID: binary operation '.', assoc. x.(y.z)=(x.y).z, id 'i', i.x=x.i=x.
   GROUP:  binary operation '.', assoc. x.(y.z)=(x.y).z, id 'i', i.x=x.i=x,
           inverse 'inv(x)' s.t. x.inv(x)=inv(x).x=i.
   RING:   two binary ops +, '.', + assoc., commutative, id '0', inverse '-x',
           '.' assoc., id '1', '.' is left- & right-distrib. over '+'.
   FIELD:  two binary ops +, '.', '+' assoc., commutative, id '0', inverse '-x',
           '.' assoc., commutative, id '1', inv(x) '1/x' if x!=0,
           '.' is left- & r-distrib. over '+'.
   [<A HREF="https://en.wikipedia.org/wiki/Semigroup">Semigroup</A>],
   [<A HREF="https://en.wikipedia.org/wiki/Monoid">Monoid</A>],
   [<A HREF="https://en.wikipedia.org/wiki/Group_(mathematics)">Group</A>],
   [<A HREF="https://en.wikipedia.org/wiki/Ring_(mathematics)">Ring</A>],
   [<A HREF="https://en.wikipedia.org/wiki/Field_(mathematics)">Field</A>]['23] -- wikip.

%T Hamiltonian
%K Hamiltonian, defn, definition
%X "In quantum mechanics, the Hamiltonian of a system is an operator corr. to
   the total energy of that sys. inc. both kinetic & potential energy. ..."
   -- HQ@[<A HREF="https://en.wikipedia.org/wiki/Hamiltonian_(quantum_mechanics)">wikip</A>]['23],
      HM@[<A HREF="https://en.wikipedia.org/wiki/Hamiltonian_mechanics">wikip</A>]['24].

%T Hamiltonian circuit
%K graph, graphs, circuit, circuits, loop, loops, cycle, cycles, path, paths,
   definition, defn
%X A graph has a H.C. if there is a circuit which visits each vertex
   exactly once.  (NB. need not use all edges.)  (Also see Eulerian circuit.)
   . Determining if there is a H.C., and/or finding one, are NP complete.
   A H.C. is sometimes also called a 'spanning circuit', similarly s.path.
   (May also be interested in the shortest H.C..)

%T Hellinger distance
%K Hellinger distance, definition, defn
%X "... given 2 probability measures P and Q that are absolutely continuous
   in respect to a 3rd prob. measure, l, the square of the Hellinger distance
   between P & Q is defined as
      H**2(P,Q) = 0.5 INTEGRAL {sqrt(dP/dl) - sqrt(dQ/dl)}**2 dl "
   --[<A HREF="http://en.wikipedia.org/wiki/Hellinger_distance">wikip</A>]['08].
   (H**2(p,q) = 0.5 INTEGRAL {sqrt(p) - sqrt(q)}**2 dx   in simple cases.)
   V.like the KL dist. for many distributions, always bounded, not a metric.

%T Hilbert space
%K Hilbert space, defn, definition
%X A H.s. is a vector space with an inner product, < x, y >,  s.t.
   the norm, |x| = sqrt( < x, x > ), makes it a complete metric space
   (complete ~ convergent series, metric ~ triangle ineq. etc.).

%T Histone
%K Histone, Histones, defn, definition
%X "... the chief protein components of chromatin. They act as spools around
   which DNA winds, and they play a role in gene regulation. ...
   6 classes ... core h. H2A, H2B, H3, H4, and  linker h. H1, H5. ...
   H3 & H4 h. have long tails protruding from the nucleosome which can be
   covalently modified at several places. Modifications of the tail inc.
   methylation, acetylation, ..."
   [<A HREF="http://en.wikipedia.org/wiki/Histone">wikip</A>]['09].

%T Homology
%K Homology, homologous, homolog,  orthology, orthologous, ortholog,
   paralogy, paralogous, paralog,  xenology,  xenologous,  xenolog,
   similarity, MolBio, defn, definition
%X In Biology
   ... *homology* is similarity due to shared ancestry between a pair of
   structures, or genes, in different taxa. A common [eg] of h.structures is
   the forelimbs of vertebrates ...
   Homologous sequences are *orthologous* if they were separated by
   a speciation event ...  Homologous sequences are *paralogous* if
   they were separated by a gene duplication event ...
   Homologs resulting from horizontal gene transfer between two organisms
   are termed *xenologs*. ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Homology_(biology)">wikip</A>][9/'09].

%T Hybrid
%K hybrid, hybridGraph, mixedGraph, defn, definition
%X A 'hybrid graph' can contain both directed and undirected edges.
   [Also search for: chainGraph]  and  [also search for: PDAG].

%T IID
%K IID, definition, defn
%X independent and identically distributed

%T I-Map
%K iMap, iMaps, maps, independence, definition, defn
%X "Bayesian networks which have the Markov property [all dependencies
   explicitly shown by arcs] are also called Independence-maps
   (or I-maps for short), ..."   "... we shall prefer ... minimal I-maps..."
   -- BAI book, Korb and Nicholson, '04.

%T incidence matrix
%K incidence matrix, definition, defn
%X The (unoriented) incidence matrix of a graph G = < V, E > is
   a |V|x|E| matrix, having one row per vertex, & one column per edge.
   The column of edge (u,v) is trans([0,...,0,1,0,...,0,1,0,...0])
   with two 1s, in rows u and v.
   In an oriented i.m., the two 1s become +1 and -1.
   (See [<A HREF="http://en.wikipedia.org/wiki/Incidence_matrix">wikip</A>][7/'10].)

%T Independent set,  maximal independent set
%K independent set, stable, maximal, MIS, vertex cover, defn, definition
%X An 'independent set' or 'stable set', I, of a graph, G, is a set of vertices
   no two of which are adjacent.  (So any edge has at most one vertex in I.)
   A 'maximal indep. set' is an IS that is not a proper subset of another.
    . The decision problem (does G have an IS of size >= k?) is NPC.
    . The maximum (NB. ...mum) indep. set problem is NPC.
   NB. G has a MIS of size k iff the complement-graph has a clique of size k.
   NB. The complement of an MIS is a maximal vertex cover (of the edges).
   Also see: (maximal|maximum) clique.

%T Induced
%K induced, subgraph, defn, definition
%X H is an 'induced subgraph' of G iff
     (i)  H is a subgraph of G, and
     (ii) uv is an edge of H iff uv is an edge of G.
   (NB. In a (non-induced) subg., uv in H => uv in G.  Not necc. <= .)

%T Inner product
%K inner, dot, scalar, product, defn, definition
%X generalises dot product, x.y, on a vector space, e.g.
     for two reals < x, y > = x*y
     for R**n      < (x1, ..., xn), (y1, ..., yn) > = c1*y1+...+xn*yn
     fns on [a,b]  < f, g > = INTEGRAL[a,b] f g dx
   have < x+y,v > = < x,v > + < y,v >,  < ax, v > = a < x,v >,
        < x,y > = < y,x >  (or, = complex_conj(< y,x >)),
        < x,x > >= 0,                   < x,x > = 0 iff x=0.
   Note for unit vec u, x.u = size of the component of x in the u direction.

%T inverse
%K inverse, matrix
%X M.inv(M) = I,  e.g., |a b| * | d -b|           = |1 0|
                        |c d|   |-c  a| / (ad-bc)   |0 1|;  NB det=ad-bc.
   e.g., 3x3:
     |a11 a12 a13|       | |a22 a23|  -|a12 a13|  |a12 a13| |
   A=|a21 a22 a23|,      | |a32 a33|   |a32 a33|  |a22 a23| |
     |a31 a32 a33|       | -|a21 a23| |a11 a13| -|a11 a13|  |
                    A^-1=|  |a31 a33| |a31 a33|  |a21 a23|  | / det(A)
                         | |a21 a22|  -|a11 a12|  |a11 a12| |
                         | |a31 a32|   |a31 a32|  |a21 a22| |
   -- [<A HREF="http://mathworld.wolfram.com/MatrixInverse.html">3x3</A>]['07].

%T Islam
%K Islam, Shia, Shi'a, Shi'ite, Shiite, Sunni, defn
%X Islam@[<A HREF="http://en.wikipedia.org/wiki/Islam">wikip</A>]['14];
     Sunni@[<A HREF="http://en.wikipedia.org/wiki/Sunni_Islam">wikip</A>]['14]
        est 75-90% Muslims;
     Shia@[<A HREF="http://en.wikipedia.org/wiki/Shia_Islam">wikip</A>]['14]
        est 10-20% Muslims, 90%+ of Iran, 65%+ of Iraq.
   (Calendar: 1AH = 622CE.)

%T Isoform
%K Isoform, defn, definition
%X geneIsoform@[<A HREF="https://en.wikipedia.org/wiki/Gene_isoform">wikip</A>]['20,
   proteinIsoform@[<A HREF="https://en.wikipedia.org/wiki/Protein_isoform">wikip</A>]['20].

%T Jacobian
%K Jacobian, defn, definition
%X given F : R^n -> R^m,
   J = |d F1 / d x1 ... d F1 / d xn|
       | ...        .    ...       |
       | ...         .   ...       |
       |d Fm / d x1 ... d Fm / d xn|,    --an m x n matrix.
   [<A HREF="http://en.wikipedia.org/wiki/Jacobian">J@wikip</A>]['07].

%T JIF
%K JIF, journalIF, defn, definition
%X "the two-year JIF is the ratio between the # of citations received in that
   year for publications in that j. that were published in the two preceding
   years & the total # of 'citable items' published in that j. during the two
   preceding years."
   -- JIF@[<A HREF="https://en.wikipedia.org/wiki/Impact_factor">wikip</A>]['22].
   Also see June 1994 ISI/[<A HREF="https://clarivate.com/webofsciencegroup/essays/impact-factor/">clar'vate</A>].

%T k-core component
%K k-core component, components, defn, definition
%X A k-core component of a graph is a maximal weakly connected subgraph
   in which every vertex has degree >=k.

%T Kirchhoff's theorem
%K Kirchhoff, kirchoff, kirchof, kirchhof, theorem, Laplacian matrix,
   arborescence, definition, defn
%X    (Useful re enumerating spanning trees of a graph G.)
   Theorem: The # of spanning trees of a graph, G, is (v1 ... v[n-1)/n,
   where the v[i] are the non-zero Eigen values of the Laplacian matric of G.
   ... Equivalently the # of spanning trees = to the abs.value (determinant)
   of any cofactor of the Laplacian matrix of G. ...
   . The Laplacian matrix of G is the degree matrix (diagonal) of G minus
     the adjacency matrix of G.
   (An arbor. is a dir.rooted tree, s.t. all edges pt away from the root.)
   -- [<A HREF="http://en.wikipedia.org/wiki/Matrix_tree_theorem">wikip</A>]['12].
   [Also search for: enumerate Eulerian circuits].

%T Laplacian
%K Laplacian, operator, definition, defn
%X For a function, f : R^n -> R,
   laplacian(f) = SUM[i=1..n]{ d^2 f / dx[i]^2 };  the trace of f's Hessian.
   Written as Delta f, or del^2 f, or del.del f.
   (The discrete Laplacian (operator|matrix) is defined on graphs.)

%T Levy probability distribution
%K Levy, stable, defn, definition
%X Prob dens fn,  f(x|c) = sqrt(c/2pi).exp(-c/2x) / x*(3/2),  cts x>=0,
   c>0 is a "scale" parameter.  It is stable (as are the normal & Cauchy).
   Mean & var'ce infinite. Mode c/3. Cumm distn fn, F(x|c) = erfc(sqrt(c/2x)).
   -- [<A HREF="http://en.wikipedia.org/wiki/Levy_distribution">@wikip</A>]['07]

%T Line Graph
%K line graph, adjoint, interchange graph, defn, definition
%X Given an undirected graph, G, the line graph, L(G), of G is a graph s.t.
      if uv=(u,v) is an edge in G then uv is a vertex in L(G), and
      if vw=(v,w) is another edge in G, then (uv,vw) is an edge in L(G).
   (Also a directed G version,  and a very special "complete" case
    is the order 'k' and 'k+1' de Bruijn graphs.)
   Also see [<A HREF="http://en.wikipedia.org/wiki/Line_graph">wikip</A>]['09].

%T Linear Programming
%K Linear Programming, LP, defn, definition
%X "Linear programming (LP) is a math.method to achieve the best outcome
   (eg max.profit or min.cost) given a linear objective fn & linear inequality
   constraint ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Linear_programming">wikip</A>]['11].
   [Also search for: LinearProgramming].

More formally, linear programming is a technique for the optimization of a linear objective function, subject to linear equality and linear inequality constraints. Its feasible region is a convex polyhedron,

%T Logistic
%K Logistic Function, Logistic Regression, sigmoid, sigmoidal functions,
   S-shaped, definition, defn
%X Logistic   Y = alpha/(1+exp(beta(gamma + X)))
     Y tends to  0  as X tends to -infinity,
     Y tends to alpha as X tends to +infinity;
   alpha=1 can be used to model a gradual change, with X, of a  pr from 0 to 1.
   Point of inflexion where  X=-gamma, Y=alpha/2.
   beta determines how rapid the change from lo to high is.
     --
   Simple, special case is  Y = 1/(1+exp(-x)), sigmoid, as in ANNs
     Y tends to 0 as x tends to -infinity
     Y = 1/2 if x=0
     Y tends to 1 as x tends to +infinity
   Sometimes scaled so that range is [-1,+1].
     --
   Logistic Regression: x[i] inputs discr. or cts, y output dependant discr.,
     pr(y) ~ theta = exp(a+b1*x1+b2*x2+...) / (1+exp(a+b1*x1+b2*x2+...)
   it is a case of a 'generalized linear model'.
   [Also see: logit defn]

%T Logit
%K logit, defn, definition
%X 1. logit(p) = log(p/(1-p)) = log(p) - log(1-p)
        tends to -inf as p -> 0;  -> +inf as p -> 1,
   2. link fn in logistic regression, model of Y given (x1, ..., xn) :
        logit( Pr(Y=1|x1...xn) ) = a + b1*x1 + b2*x2 + ... + bn*xn
      [Also see: logistic regression defn]

%T Loopless
%K loopless, defn, definition
%X "In computational combinatorics, a loopless algorithm or loopless imperative
   alg. is an imperative alg. that generates successive combinatorial objects,
   such as partitions, permutations, & combinations, in constant time & the
   first object in linear time. ..."
   -- loopless@[<A HREF="https://en.wikipedia.org/wiki/Loopless_algorithm">wikip</A>]['18].

%T Mahalanobis distance
%K Mahalanobis distance, defn, definition
%X mean mu = (mu_1, ..., mu_N)^T, co-variance matrix S,
   if x = (x_1, ..., x_N)^T then DM(x) = sqrt((x-mu)^T S^-1 (x-mu))
   -- [<A HREF="http://en.wikipedia.org/wiki/Mahalanobis_distance">wikip</A>]['13].
   (So it is a kind-of 'number of standard deviations from mu' distance
   that takes correlations into account.)

%T Markov blanket
%K Markov Blanket, markovblanket, defn, definition
%X 1. In a Bayesian network (a DAG), the MB of a variable (Vertex) v consists of
      v's parents, v's children & the other parents of v's children [KK8/2014].
      To calculate a probability distribution over possible values of v,
      it is sufficient to know the values of the variables in the MB.
   2. In an undirected graph, the MB of variable v is the set of v's neighbours.

%T Matching
%K Matching, perfect, defn, definition
%X A 'matching' of a graph, G, is a set of pairwise disjoint edges.
   A 'perfect matching' is a matching that includes all vertices of G.

%T Maximal, Minimal
%K maximal, minimal, defn, definition
%X (P, <=) is a partially ordered set;  S is a subset of P;
   x in S is a maximal (minimal) element of S if
   y in S and x <= y   (y <= x)  implies x=y  (ditto).
   (Informally, 'maximal' means there are 'none bigger'.)

%T Mealy machine
%K Mealy machine, finite state, FSM, automaton, definition, defn
%X A finite state machine that produces an output for each transition (edge,
   arc). The output Q depends on both the current state S and the input I, e.g.
            i/q         means in state S, for input i,
        S-------->S'    move to S' and output q.
   G.H.Mealy. A method for synthesizing sequential circuits.
   Bell System Technical J., pp.1045-1079, 34(5), 1955.
   (Also see Moore machine, and automaton.)

%T MCS
%K MCS, MCIS, MCES, common subgraph, sub graph, definition, defn
%X MCS: Maximum Common Subgraph problem
    . MCIS: Maximum Common Induced Subg. (induced by vertex corr.),
    . MCES: Maximum Common Edge Subgraph.
   Both versions can allow connected, or disconnected ...-subgraphs.
   [Also search for: MCS Modular product].

%T MeDIP
%K MeDIP, seq, mDIP, definition, defn
%X "Methylated DNA immunoprecipitation (MeDIP or mDIP)"
   [<A HREF="http://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation">wikip</A>]['09].
   [Also search for: Methylation defn].

%T Mersenne prime
%K Mersenne prime, primes, defn, definition
%X A Mersenne number is of the form M[n] = 2^n-1; n composite => M[n] composite.
   A Mersenne prime  is of the form M[p] = 2^p-1.
   -- [<A HREF="http://en.wikipedia.org/wiki/Mersenne_prime">wikip</A>]['13],
   2^57,885,161 - 1 is a M. prime of 17,425,170 digits
   -- [<A HREF="http://www.mersenne.org/">gimps</A>][25/1/'13].

%T Methylation
%K Methylation, methyl, methyltransferase, 5 methylcytosine, defn, definition
%X ... attachment or subs'n of a methyl group (CH3) ...
   In biochem. the replacement of a hydrogen atom with the methyl group. ...
   DNA methylation in vertebrates typically occurs at CpG sites [...CG...] ...
   C->5-methylcytosine. ... catalyzed by the enzyme DNA methyltransferase. ...
   Protein methylation typically takes place on arginine or lysine residues
   -- [<A HREF="http://en.wikipedia.org/wiki/Methylation">wikip</A>]['08].
   [Also search for: CpG defn].

%T Minor of a graph
%K Minor, graph, defn, definition
%X "... undirected graph H is called a minor of the graph G if H can be formed
   from G by deleting edges and vertices and by contracting edges. ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Graph_minor">wikip</A>]['15].
   And,
   "an edge contraction is an operation which removes an edge from a graph
   while simultaneously merging the two vertices that it previously joined."
   -- [<A HREF="http://en.wikipedia.org/wiki/Edge_contraction">wikip</A>]['15].
   (An edge 'subdivision' is (x,y) -> (x,z) and (z,y) for a new vertex z.)

%T Module
%K module, modular, defn, definition
%X Of a graph:
   "X is a module if, for each vertex v not in X, either every member of X
   is a non-neighbor of v or every member of X is a neighbor of v. ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Modular_decomposition">wikip</A>]['18].
   (E.g., each "part" of a complete bipartite graph, K_{m,n}, is a module.)
   And, 'modular decomposition' of a graph into subsets [modules] of vertices.
   Also see 'decomposition'.

%T Modular Product
%T Modular Product, graph, association, compatibility, MCS, defn, definition
%X The 'modular product' of two graphs, G = (U,E) and H = (V,F), is a graph
   GH = (UxV, E') where (u,v) and (u',v') are adjacent in GH iff
     (i)  u and u' are adjacent in G,     and v and v' are adjcent in H, or
     (ii) u and u' are not adjacent in G, and v and v' are. adjcent in H
   A maximum clique in GH ~ a maximum common subgraph (MCS) of G and H.
   -- [<A HREF="http://en.wikipedia.org/wiki/Modular_product_of_graphs">wikip</A>].
   (i.e., G and H "agree" on GH.)
   'Modular product graph' AKA 'association graph' and 'compatibility graph'.

%T Monty Hall
%M Monty Hall problem, Three Prisoners, defn, definition
%X "Suppose you're on a game show, & you are given the choice of 3 doors.
   Behind one door is a car, the others, goats. You pick a door, say #1, & the
   host, who *knows* what is behind each door, opens another door, say #3,
   which has a goat. He says to you: 'Do you want to pick door #2?'
   Is it to your advantage to switch your choice of doors?" - C.F.Whitaker"
   Ans:  Yes!  Switching improves your odds from 1/3 to 2/3.
        1 2 3 pr    stick  switch
        C G G 1/3     C      G
        G C G 1/3     G      C
        G G C 1/3     G      C
   -- [<A HREF="http://en.wikipedia.org/wiki/Marilyn_vos_Savant">wikip</A>]['10].
   "The 3 Prisoners problem (M.Gardner's Mathematical Games 1959) is equiv.
   to the MHproblem. ... 3 condemned prisoners, a random one has been secretly
   chosen to be pardoned. One of the prisoners begs the warden to tell him the
   name of one of the others who will be executed, arguing that this reveals no
   info. about his own fate but increases his chances of being pardoned from 1/3
   to 1/2. The warden obliges, (secretly) flipping a coin to decide which name
   to provide if the prisoner who is asking is the one being pardoned. The Q is
   whether knowing the warden's ans. changes the prisoner's chances of being
   pardoned. This problem ~ MHproblem; the prisoner asking the Q still has a 1/3
   pr. of being pardoned but his unnamed cohort [therefore] has a 2/3 chance."
   -- [<A HREF="http://en.wikipedia.org/wiki/Monty_Hall_problem">wikip</A>]['10].

%T Moore machine
%K Moore machine, finite state, FSM, automaton, definition, defn
%X A finite state machine that produces an output for each state, e.g.
                i              means in state S, for input i,
        [S/q]------->[S'/q']   move to S' and output q'.
   (Also see Mealy machine, and automaton.)

%T Morphisms
%K morphism, catamorphism, anamorphism, hylomorphism, paramorphism,
   definition, defn
%X catamorphism on a type T is a fn T->U that destructs an obj of type T
     calls itself rec' on any comp'ts of T that are of type T and combines
     this rec' result with the other cmpnts of T to a U.
   anamorphism  on a type T is a fn U->T that destructs the U, on the cmpnts
     of type U it applies recn to convert them to Ts, then combines the
     results with other cmpnts to a T, using the constructor fns of T.
   hylomorphism, given a way to construct a list and destruct one, compose the
     two opns into one that captures recn via a list.
   paramorphism almost catamorphism, not only deals with rec' result of the
     parts (e.g. tail) but also the parts (tail) themselves.
   cata~κατα~downwards; ana~ανα~up; hylo~υλη~matter; para~παρα~parallel-with;
   -- after Αugusteijn, Adv. F.P., c1998.

%T mutual information
%K mutual information, definition, defn
%X For discrete vars X and Y,
      I(X; Y) = sum_x sum_y p(x & y) log(p(x & y) / (p(x) p(y))),
      >= 0, is zero if X and Y are indept.
   Replace sums by integrals for cts vars.

%T nonparametric
%K nonparametric, parametric, definition, defn
%X "Nonparametric stats. is the branch of stats. that is not based solely on
   parameterized families of probs. distns (common examples of parameters are
   the mean and variance). Nonparametric stats. is based on either being
   distribution-free or having a specified distn but with the distn's params.
   unspecified. ... The statistician Larry Wasserman has said that 'it is
   difficult to give a precise definition of nonparametric inference.' ..."
   -- NonP@[<A HREF="https://en.wikipedia.org/wiki/Nonparametric_statistics">wikip</A>]['18].

%T norm
%K norm, defn, definition
%X a norm of a vector, |x| (sometimes written ||x||),  satisfies
     |x| >= 0  and |x| = 0 iff x=0  -- i.e. +ve definite,
     |ax| = a|x|,  |x+y| <= |x|+|y|  -- triangle ineq..
   For an inner-product vector space  |x| = sqrt( < x,x > ) = length of x
   is the natural norm.
   More generally the p-norm, p=1,2,... :  |x|[p] = {SUM[i] |x[i]|**p}**(1/p)
   1_norm=|x1|+...+|xn|,  2_norm(x)=sqrt(x.x),... (aka L1-norm, L2-norm...).

%T Octonion
%K Octonion, octonions, 8D, octonian
%X "... 'O' a normed division algebra over the real numbers ... eight dimensions
   ... noncommutative & nonassociative ... are 'alternative' [i.e., x(xy)=(xx)y
   & (yx)x=y(xx)] ... discovered in 1843 by John T. Graves ..."
   -- O@[<A HREF="https://en.wikipedia.org/wiki/Octonion">wikip</A>]['22].
   [Also search for: quaternion].

%T Ontology
%K Onology, defn, definition
%X Greek: on - being, thing, 'object', i.e. in existence, being, 'what there is'
     logos - the 'word' (as in the bible), speech of, study of, knowledge of -;
     ontos - genetive of on.
   Hence ontology ontos-logos -> the 'logos of on' -
     the study of on - study of (existing) objects.
   e.g. methodology (the study of method), ornitology - the study of birds, ...
   ... 3 most common ontologies: taxonomies (trees), thesaurus (ie. objects
   and their ties/relations), formal logical systems  -- hws ['05]
   [<A HREF="http://www.ontology.org/" TARGET="EXTERNAL">ontology.org</A>]['04]

%T oriented graph
%K oriented, defn, definition
%X "An oriented graph is a directed graph in which
    at most one of (x,y) and (y,x) may be arcs."
   -- OG@[<A HREF="https://en.wikipedia.org/wiki/Graph_(mathematics)">wikip</A>]['15].

%T Outerplanar Graph
%K outerplanar, outer planar, defn, definition
%X An 'outerplanar' graph can be embedded in the plane so that the vertices
   lie on a circle & the edges lie inside the circle & do not intersect.
   (An outerplanar graph is planar.)

%T Orthogonal, Orthonormal functions
%K Orthogonal, Orthonormal, definition, defn
%X f() and g() are
   orthogonal  if Integral[a,b] (f(x).g(x)) dx = 0, and
   orthonormal if Integral[a,b] (f(x))**2 dx = 1 in addition and similarly g().
   (NB. normal as in normalised.)
   Naturally extend (pair-wise) to more than two functions.

%T Outer product
%K outer product, defn, definition
%X for vectors x and y, a matrix:  (x outerproduct y)[i,j] = x[i] * y[j]

%T Oxymoron
%K oxymoron, contradiction in terms, defn, definition
%X "... Wilfred Owen's poem The Send-off refers to soldiers leaving for the
   front line, who 'lined the train with faces grimly gay.' The oxymoron grimly
   gay highlights the contradiction between how the soldiers feel & how they
   act: though they put on a brave face & act cheerfully, they feel grim. ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Oxymoron">wikip</A>]['14].
   "... contradiction in terms refers to a combination of words whose meanings
   are in conflict with one another. Examples are 'liquid ice', 'settled
   science', & 'square circle'. If the contradiction is intentional
   (rhetorical or poetic), then one can speak of an oxymoron."
   -- [<A HREF="http://en.wikipedia.org/wiki/Contradictio_in_terminis">wikip</A>]['14].

%T PDAG
%K PDAG, partiallyDAG, partialDAG, semiDAG, defn, definition
%X A partially directed acyclic graph (PDAG) is a hybrid graph
   whose directed subgraph contains no cycles.
   (NB. Apparently not the same as chainGraph,
   e.g. < {a,b,c}, {a->b, a->c, b-c} > is both a PDAG and a chainGraph, but
        < {a,b,c}, {a->b, b-c,  a-c} > is a PDAG but is not a chainGraph --
        think a->b-c-a.)
   [Also search for: chainGraph].

%T Planar Graph
%K planar graph, graphs, defn, definition
%X ... a graph that can be drawn on a plane surface with no edges crossing.
   A finite graph is planar iff it does not contain a subgraph
   that is a subdivision of K5 or K3,3  -- Kuratowski.
     (Subdivision allows split an edge (x,y) into (x,z) & (z,y) for a new z.)
   For a planar graph with v vertices and e edges:
     if v > 3 then e < 3v-6, and
     if v > 3 and there are no cycles of length 3, then e < 2v-4  --wikip.

%T PPM
%K PPM, prediction by partial matching, match, context, defn, definition
%X A broad technique for data (text) compression based around an adaptively
   built, variable depth suffix tree, or equivalent data structure.
   There are many(!) variations on how to balance predictions from long
   contexts that been been seen rarely against those from short contexts
   that have been seen frequently.
   [Also search for: ppm compression].

%T Procrustes transformation
%K Procrustes, defn, definition
%X "A Procrustes transformation is a geometric trans. that involves only
   translation, rotation, uniform scaling, or a combination of these trans.
   Hence, it may change the size or posn, but not the shape of a geometric
   object. ..."
   -- PT@[<A HREF="https://en.wikipedia.org/wiki/Procrustes_transformation">wikip</A>]['22].

%T Quadratic Assignment
%K Quadratic Assignment, QAP, defn, definition
%X "Given 2 sets, P (the "facilities") and L (the "locations"), of equal size,
   and a weight fn, w : P x P -> R, and a distance fn, d : L x L -> R,
   find the bijection, f : P -> L (the "assignment"), s.t. the cost fn:
   SUM[a,b in P] { w[a,b] . d[f(a),f(b)] }  is minimized."
   -- [<A HREF="http://en.wikipedia.org/wiki/Quadratic_assignment_problem">wikip</A>]['09].
   (NP-hard.-()

%T Quadratic Programming
%K Quadratic Programming, QuadraticProgramming, QP, defn, definition
%X Optimization of a quadratic fn, f(X), of several variables, X, subject to
   linear constraints on them.
     f(X) = (1/2) transpose(X) Q X + transpose(C) X,  & in|eq' of the form...
     A X <= B, and/or  E X =  D.
   -- [<A HREF="http://en.wikipedia.org/wiki/Quadratic_programming">wikip</A>]['11].
   [Also search for: QuadraticProgramming] and
   [also search for: LinearProgramming].

%T Quasipolynomial
%K Quasipolynomial, QP, quasi, defn, definition
%X As in Quasipolynomial time complexity, 2^O((log n)^c), for a constant c.
   If c=1 then 2^O(log n) ~ 2^(k log n) ~ 2^log(n^k) ~ n^k, i.e., polynomial.
   If c > 1 then worse than polynomial, but better than exponential in n.

%T Quaternion
%K Quaternion, quaternions, division-algebra, defn, definition
%X Quaternions,  H = {a1+bi+cj+dk | a,b,c,d in R}, i**2=j**2=k**2=ijk=-1.
      x | 1  i  j  k
      --|-----------   noncommutative
      1 | 1  i  j  k
      i | i -1  k -j
      j | j -k -1  i
      k | k  j -i -1
      --------------
   (a+bi+cj+dk)(A+Bi+Cj+Dk)
      = aA-bB-cC-dD + (aB+bA+cD-dC)i + (aC-bD+cA+dB)j + (aD+bC-cB+dA)k.
   Associative, p(qr) = (pq)r,  but noncommutative.
   Conjugate: if q=a+bi+cj+dk, conjugate(q) = q* = a-bi-cj-dk;  (pq)*=(q*)(p*).
   Norm:      ||q|| = sqrt(q q*) = sqrt(a**2 + b**2 + c**2 + d**2).
   Inverse:   q**(-1) = q* / ||q||**2.     NB. p(q**-1) != (q**-1)p in general.
   Devised by Hamilton (1843).
   -- [<A HREF="http://en.wikipedia.org/wiki/Quaternion">wikip</A>]['11].
   [Also search for: octonion].

%T Rank-Select Directory
%K rank select directory, defn, definition, RSD, DRSD, dictionary, directories,
   queries, dictionaries, data structure
%X A collection data-structure, S, that supports
     1. rank(x,S) = |{y in S s.t. y <= x}|, and
     2. select(i) returns the ith smallest element in S.
   Esp. in the case where elementType = String.  Useful in a compressed index.
   May be 'static', or 'dynamic' when elements can be added (and deleted).
   (Also see SDS@[<A HREF="https://en.wikipedia.org/wiki/Succinct_data_structure">wikip</A>]['19].)

%T Receiver Operating Characteristics
%K Receiver Operating Characteristics, ROC, characteristic, curve, curves,
   false positives, negatives, true, sensitivity, specificity, coverage,
   tradeoff, misclassification, definition, defn
%X Receiver Operating Curves (e.g., in Medicine)
      Consider a diagnostic test which returns a real value.
      If True Negatives (TN) have a normal dist' that overlaps
      with True Positives (TP) then which cut-point should be
      chosen that decides whether someone is positive or negative?
      The ROC curve is the plot of TP (sensitivity) against False Positive
      45-degree straight-line curves indicate a worthless test.
   NB. TP = sensitivity = fraction of positives identified
       FP = 1-specificity where spec' = fraction of claimed +ves that are real.
       (FP can = 1 if positives are a small proportion of population.)
       Awkward terminology.
   Receiver Operating Curves (in Data Mining)
      Applications of inductive learning algorithms to real-world
      data mining problems have shown repeatedly that using accuracy
      to compare classifiers is not adequate because the underlying
      assumptions rarely hold. We present a method for the comparison
      of classifier performance that is robust to imprecise
      class distributions and misclassification costs. The ROC
      convex hull method combines techniques from ROC analysis,
      decision analysis and computational geometry, and adapts them
      to the particulars of analyzing learned classifiers.
      The method is efficient and incremental, minimizes the management
      of classifier performance data, and allows for clear visual
      comparisons and sensitivity analyses.
      From <A HREF="http://www.croftj.net/~fawcett/ROCCH/" TARGET="external">[www]</A>[1999].
   An interesting historical note:
      You may be wondering where the name "Receiver Operating Characteristic"
      came from. ROC analysis is part of a field called
      "Signal Detection Theory" developed during World War II for the analysis
      of radar images. Radar operators had to decide whether a blip on the
      screen represented an enemy target, a friendly ship, or just noise.
      Signal detection theory measures the ability of radar receiver operators
      to make these important distinctions. Their ability to do so was called
      the Receiver Operating Characteristics. It was not until the 1970's that
      signal detection theory was recognized as useful for interpreting medical
      test results.
      From <A HREF="http://gim.unmc.edu/dxtests/roc3.htm" TARGET="external">[www]</A>[1999].
   -- via rohan [12/1999].
   (Also see ROC@[<A HREF="http://en.wikipedia.org/wiki/Receiver_operating_characteristic">wikip</A>]['10].)

%T Recurrent Neural Network
%K Recurrent, RNN, RecurrentNN, definition, defn
%X "A recurrent neural network (RNN) is a class of ANN where
   connections between nodes can create a cycle ..."
   -- RNN@[<A HREF="https://en.wikipedia.org/wiki/Recurrent_neural_network">wikip</A>].
   (As opposed to a feedforward ANN.)
   [Also search for: transformerNN].

%T Red Queen Hypothesis
%K Red Queen Hypothesis, biol, definition, defn
%X "It takes all the running you can do, to keep in the same place."
   -- The Red Queen in Lewis Carroll's 'Through the Looking Glass.'
   1. 'A species must run (evolve) to stay in the same place (survive).'
      See van-Valen 1973.
   2. 'Coevolution of host and parasite(s) may => sexual reproduction reduces
      risk to offspring.'   See Bell c1982, Hamilton c1982 and c1993.

%T Refer
%K refer, bibliography, bib, groff, nroff, troff, file format, definition, defn,
   lookbib, invert, indxbib,  glookbib, ginvert, gindxbib,
%X program and file-format used by the troff document formatting package
     %A an Author
     %T title of article or book
     %J journal or conference containing the article
       %W city of conference
     %B book containing the article
     %I publisher (issuer)
       %C city where published
     %S series e.g. LNCS
     %V volume
     %N issue number within volume
     %P page(s) e.g. 12-23
     %M month JAN, FEB, ...
     %D date e.g. 2003
     %O other e.g. also available as tech' rep' xyz
     %K keywords
     %X abstract
     %Q author if the author is not a person (no A fields)
   There are more fields;  see J. F. Ossanna, Nroff/Troff User's Guide.
   (Also see groff@[<A HREF="https://www.gnu.org/software/groff/">gnu</A>]['18].)

%T reinforcement learning
%K Reinforcement learning, MDP, defn, definition
%X "... the focus is on finding a balance between exploration (of uncharted
   territory) & exploitation (of current knowledge) ..."
   -- RL@[<A HREF="https://en.wikipedia.org/wiki/Reinforcement_learning">wikip</A>]['22].

%T ReLU
%K ReLu, rectifier, rectified, softplus, smoothReLU, defn, definition
%X "... f(x) = max(0, x) ... This activation fn ... In 2011 it was found to
   enable better training of deeper NNs ..."
   "... f(x) ln(1+e^x) ... softplus or smoothReLU ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Rectifier_(neural_networks)">wikip</A>]['22].
   [Also search for: ReLU NN].

%T resequencing
%K resequencing, resequence, definition, defn
%X "Resequencing of candidate genes or other genomic regions of interest in
   patients & controls is a key step in detection of mutations associated with
   various congenital diseases. Resequencing techniques can be divided into
   those which test for known mutations (genotyping) & those which scan for any
   mutation in a given target region (variation analysis). Typical mutations
   being tested are substitution (SNP), insertion & deletion mutations."
   -- NCBI [<A HREF="http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/TechResequencing.shtml">www</A>]['08].

%T rotation
%K rotation, defn, definition
%X   |ux vx wx|   origin fixed, 3D rotation matrix A, (1,0,0)->(ux,uy,uz) etc,
   A=|uy vy wy|   x y z axes -> u v w axes, det(A)=1, orthogonal i.e.,
     |uz vz wz|   trans(A)=inv(A), 3 degrees of freedom.
   Also, Euler axis + rotation; Euler rotations; Quaternions.
   -- [<A HREF="http://en.wikipedia.org/wiki/Rotation_representation_%28mathematics%29">wikip</A>]['10].

%T Running Mean
%K RunningMean, defn, definition, stability, unstable
%X The simple calculation of the mean may be numerically unstable.
   The running mean is more stable:
      m' = (i*m + x[i+1])/(i+1) = m + (x[i+1]-m)/(i+1),
   where m is the "old" mean of x[1..i], and m' is the "new" mean of x[1..i+1].

%T SEC
%K SEC, SECs, definition, defn
%X in the context of Byesian networks,   SEC = statistical equivalence class.
   Thm 6.1 Verma and Pearl 199O (p.164 bai kk & an '04) "Any 2 causal models
   over the same variables that have the same skeleton and the same
   v-structures are Markov equivalent."
   i.e. for any parameterization of one, there is some param'n of t'other
   that gives the same prob' dist'n.     One SEC == many DAGs in general.
   (And one DAG == many TOMs, in general.)

%T significance test
%K significance level, test, testing, Pvalue, defn, definition
%X "... significance level of a test is the maximum probability, assuming the
   null hypothesis, that the statistic would be observed. Hence, the
   significance level is the probability that the null hypothesis will be
   rejected in error when it is true (a decision known as a Type I error, or
   "false positive"). The significance of a result is also called its p-value;
   the smaller the p-value, the more significant the result is said to be. ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Significance_test">wikip</A>]['07]
   "... p-value is the probability of obtaining a result at least as extreme as
   a given data pt, assuming the data pt was the result of chance alone. ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/P-value">wikip</A>]['07]

%T Simplicial
%K simplicial, recursively simplicial, defn, definition
%X "... A simplicial vertex v [of an undirected graph] is one whose
   neighbours form a clique ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Vertex_(graph_theory) ">wikip</A>]['18].
   (Note, hence v belongs to exactly one (maximal) clique of G.)
   Re chordal graphs:-
   An (undirected) graph G = < V, E > is 'recursively simplicial' if it has
   at least one simplicial vertex, v, and G[V\{v}] is recursively simplicial.
   G is chordal iff it is recursively simplicial  [Beeri et al 1983].
   [Also search for: chordal defn].

%T Simpson's Paradox
%K Simpson's Paradox, Simpsons, Reversal of Inequalities, definition, defn,
   probability
%X         a/b < A/B,
           c/d < C/D, and
   (a+c)/(b+d) > (A+C)/(B+D).
   e.g. a=1, b=5, A=2, B=8, c=6, d=8, C=4, D=5
              Men    Women
   History    1/5  < 2/8,    a higher fraction of women is accepted,
   Geography  6/8  < 4/5,    ditto,
   University 7/13 > 6/13    but overall a higher fraction of men is accepted!
   ... more women are applying for jobs [History] that are harder to get. ...
   [<A HREF="http://plato.stanford.edu/entries/paradox-simpson/">www</A>]['05]

%T Soundex
%K Soundex, name, names, sound similar, defn, definition
%X lossy coding system for names,
   names that sound similar (Smith, Smyth) get the same code
   e.g. [<A HREF="http://www.archives.gov/research_room/genealogy/census/soundex.htm" TARGET="EXTERNAL">www</A>][10.'04]
   1 B,F,P,V;  2 C,G,J,K,Q,S,X,Z;  3 D,T;  4 L;  5 M,N;  6 R
   ignore A,E,I,O,U,H,W,Y.  ...

%T star graph
%K star, defn, definition
%X "a star S_k is the complete bipartite graph K_1,k: a tree with one internal
   node & k leaves (but, no internal nodes and k+1 leaves when k <= 1).
   Alternatively, some authors define S_k to be the tree of order k with max
   diameter 2; in which case a star of k > 2 has k-1 leaves."
   -- star@[<A HREF="https://en.wikipedia.org/wiki/Star_(graph_theory)">wikip</A>]['15].

%T stdin, stdout, stderr
%K stdin, stdout, stderr, redirection, defn, definition
%X stdin  - standard  input stream (0),
   stdout - standard output stream (1),
   stderr - standard  error stream (2).
   Redirect stdin from file inF, stdout to outF, and errors to errF:
   prog  < inF  > outF  2> errF

%T Steiner Tree
%K Steiner Tree, defn, definition
%X "(Euclidean S. T.) Given N pts in the plane ... connect them by lines of
   min. total length s.t. any 2 pts may be interconnected by line segments
   either directly *or* via *other* points & line segments. ..."
      [i.e. like min span' tree but can add new points]
   "(S. T. in graphs) Given a weighted graph G(V,E,w) & a subset of its vertices
   S subseteq V, find a tree of min. wt which *includes* all vertices in S. ...
   Most versions of S. T. [are] NPC."
   -- [<A HREF="http://en.wikipedia.org/wiki/Steiner_tree">wikip</A>]['09].

%T Straight
%K straight, straightLine, straightLineProgram, SLP, defn, definition
%X "In maths, more specifically in computational algebra, an [SLP] for a finite
   group G = < S > is a finite seq. L of elts of G such that every elt of L
   either belongs to S, is the inverse of a preceding elt, or the product of two
   preceding elts. An SLP L is said to compute a group elt g in G if g  in L,
   where g is encoded by a word in S and its inverses. ...
   Babai & Szemeredi (1984) ... prove that every elt of a finite group G has an
   SLP of length O(log^2 |G|) in every generating set. ..."
   -- SLP@[<A HREF="https://en.wikipedia.org/wiki/Straight-line_program">wikip</A>]['18].
   [Also search for: Szemeredi c1984].

%T Structural Risk Minimization
%K SRM, minimisation, empirical, expected, VC dimension, shatters, Vapnik,
   definition, defn
%X Given a risk (penalty) function, Q(z,a), for datum z and model a,
   e.g. number of items misclassified or squared error, or ... etc. .
   Empirical risk, Remp(a) = {Q(z1,a) + ... + Q(zl,a)}/l,
      measured penalty on the training data-set  z1, z2,...,zl.
   Expected  risk,    R(a) = INTEGRAL Q(z,a) dP(z)  risk on future data
      (seems to be a problem 'cos P() unknown but there is a useful bound).
   For a set of real valued fns, L, bounded of range D, and of VC dim'n h.
   With prob' 1-n,  R(a) <= Remp(a) + phi(l/h, (-ln n)/l).
   -- [<A HREF="http://www.esat.kuleuven.ac.be/sista/natoasi/vapnik.pdf" TARGET="external">Vapnik.pdf</A>][7/'02]

%T Strongly connected component
%K strongly connected component, strong, defn, definition
%X A directed graph, G, is strongly connected if there is a path from every
   vertex of G to every other vertex of G.
   A strongly connected component is a maximal strongly connected subgraph of G.
   [Also search for: Tarjan c1972].

%T Subdivision
%K subdivision, division, graph, defn, definition
%X A graph G' is a subdivision of G if some edge(s) of G is (are)
   subdivided in G' by the addition of vertices along the edge(s),
   e.g., in G: u-----v  ->  in G': u--w--x--v.
   [Also search for: planar defn].

%T SuperSecondary Structure
%K SuperSecondary, super secondary, structuralMotif, defn, definition
%X "In a chain-like biological molecule, such as a protein or nucleic acid,
   a structural motif is a supersecondary structure, which also appears in a
   variety of other molecules. ...
      In proteins, a str.motif describes the connectivity between s.s.elts.  ...
      Note that, while the spatial sequence[?] of elts may be identical in all
      instances of a motif, they may be encoded in any order within the
      underlying gene. In addition to s.s.elts, protein str.motifs often include
      loops of variable length and unspecified structure. ..."
   -- SM@[<A HREF="https://en.wikipedia.org/wiki/Structural_motif">wikip</A>][7/2017].
      "A supersecondary struct. is a compact 3D p.struct. of several adjacent[?]
      elts of a sec.struct. that is smaller than a pr.domain or a subunit. ..."
   -- SSS@[<A HREF="https://en.wikipedia.org/wiki/Supersecondary_structure">wikip</A>][7/2017].
   --and--
   "Secondary structure elements are observed to combine in specific geometric
   arrangements known as motifs or supersecondary structures. ..."
   -- SSS@[<A HREF="http://www.cryst.bbk.ac.uk/PPS95/course/6_super_sec/super.html">bbk.ac.uk</A>][7/2017].
   --and--
   "Secondary structure elts are observed to combine in specific geometric
   arrangements known as motifs or super-secondary structures. ..."
   -- SSS@[<A HREF="https://swissmodel.expasy.org/course/text/chapter2.htm">expasy.org</A>][7/2017].
      "There is a blurred distinction between "super-secondary structure" &
      'tertiary structure'. The introduction of the term 's.s.structure' was
      necessary when it became clear that certain arrangements of two or three
      sec.structs. are present in many different protein structs., even with
      completely different seqs..  Note that some proteins do not consist of an
      assembly of these super-secondary motifs. ..."
   -- Tert@[<A HREF="https://swissmodel.expasy.org/course/text/chapter4.htm">expasy.org</A>][7/2017].
   [Also search for: proteinDomain defn].

%T Taxonomy
%K Taxonomy, taxa, Linnaean, phylogeny, defn, definition,
   domain, kingdom, phylum, class, order, family, genus, species
%X Living things classified under:
   domain -> kingdom -> phylum -> class -> order -> family -> genus -> species.

%T Tensor
%K Tensor, defn, definition, covector
%X "... an algebraic object that describes a multilinear relationship between
   sets of algebraic objects related to a vector space. ... A tensor may be
   represented as an array (potentially multidimensional). ..."
   -- Tensor@[<A HREF="https://en.wikipedia.org/wiki/Tensor">wikip</A>]['22].
   "... raising & lowering indices are operations on tensors which change their
   type. Raising & lowering indices are a form of index manipulation in tensor
   expressions. ... vectors are elts of a vector space V over a field K ...
   The dual space is the space of linear functionals mapping V->K. Concretely,
   in matrix notation these can be thought of as row vectors ...
   A (0,0) tensor is a number in the field F. A (1,0) tensor is
   a vector.  A (0,1) tensor is a covector. ..."
   -- RandLI@[<A HREF="https://en.wikipedia.org/wiki/Raising_and_lowering_indices">wikip</A>]['23].
   (Also see TF@[<A HREF="https://en.wikipedia.org/wiki/Tensor_field">wikip</A>]['22].)

%T That v. Which
%K that, which, defn, definition, use, usage, restrictive, defining
%X . Restrictive:  We saw two puppies this morning, one a day old and
        one a week old.  The one *that* was born yesterday is tiny.
   . Non-restrictive:  We saw a puppy and a kitty this morning.
        The puppy, *which* was born yesterday, was tiny.        -- after wikip.
   But some think that to make the distinction is to be pedantic.

%T TOM
%K TOM, TOMs, definition, defn
%X in Bayesian networks: TOM = Totally Ordered Model
   1 DAG == many TOMs, in general  (and one SEC == many DAGs in general).

%T Transformer Neural Network
%K Transformer, TransformerNN, GPT, defn, definition
%X "A Transformer is a deep learning architecture that relies on the attention
   mechanism ... requiring less training time compared to prev. recurrentNN ..."
   -- Tr@[<A HREF="https://en.wikipedia.org/wiki/Transformer_(machine_learning_model)">wikip</A>]['23].
   (BTW, c2022, GPT="generative pre-trained transformer".)
   [Also search for: RecurrentNN], RNN.

%T Transitive Reduction
%K transitive reduction, definition, defn
%X "The transitive reduction of a [di-graph] binary relation R on a set X is a
   minimal relation R' on X such that the transitive closure of R' is the same
   as the transitive closure of R.  If the transitive closure of R is
   antisymmetric and finite, then R' is unique. However, neither existence nor
   uniqueness of transitive reductions is guaranteed in general."
   [<A HREF="http://en.wikipedia.org/wiki/Transitive_reduction">wikip</A>]['08].

%T Translation, transcription
%K transcription, translation, MolBio, DNA, RNA, mRNA, tRNA, intron, exon,
   gene structure, genes, definition, defn
%X <A HREF="/~lloyd/tildeStrings/Notes/DNA-RNA-protein.html">[notes]</A>

%T Transition, transversion
%K Transition, Transversion, MolBio, DNA, defn, definition
%X Transition:   purine to purine (A < - > G), or pyrimidine to py. (C < - > T).
   Transversion: purine to pyrimidine, and v.v..
   The latter have greater effects, and are less common, than the former.

%T Treeidth
%K Treewidth, defn, definition
%X "... the treewidth of an undirected graph is an int. which specifies,
   informally, how far the graph is from being a tree. ... the largest vertex
   set in a tree decomposition of the g., in terms of the size of the largest
   clique in a chordal completion of the g., in terms of the maximum order of a
   haven describing a strategy for a pursuit-evasion game on the g., or in terms
   of the maximum order of a bramble, a coll'n of connected subgs. that all
   touch each other. ..."
   -- TW@[<A HREF="https://en.wikipedia.org/wiki/Treewidth">wikip</A>]['22].

%T Unimodular
%K unimodular matrix, total, totally, defn, definition
%X "... a unimodular matrix M is a square integer matrix with determinant +1 or
   -1. Equivalently, it is an integer matrix that is invertible over the ints.
   form a group GL[n](Z). ...
   A totally unimodular matrix (TU matrix) is a [not necc. square] matrix for
   which every square non-singular submatrix is unimodular. ... "
   -- [<A HREF="http://en.wikipedia.org/wiki/Unimodular_matrix">wikip</A>]['11].

%T Universal
%K universal, defn, definition
%X "In data compression, a universal code for integers is a prefix code that
   maps the +ve ints. onto binary codewords, [s.t.] that whatever the true
   probability distn on ints, as long as the distn is monotonic (i.e.,
   p(i) >= p(i+1) ...), the expected lengths of the codewords are within a
   const. factor of the expected lengths that the optimal code for that
   prob.distn would have assigned.
   A universal code is asymptotically optimal if the ratio between actual &
   optimal expected lengths is bounded by a function of the information entropy
   of the code that, in addition to being bounded, approaches 1 as entropy
   approaches infinity. ..."
   -- UC@[<A HREF="https://en.wikipedia.org/wiki/Universal_code_(data_compression)">wikip</A>]['18].
   [Also seatrch for: intCode].

%T V-structure
%K v structure, Vstructure, Vstructures, structures, definition, defn
%X for Bayesian networks, a pattern between a child and 2 unconnected parents
   e.g. A     B  or  A     C  or  B     C   not A---->B   nor
         .   .        .   .        .   .         .   .    A-->B-->C
           .            .            .             .
           v            v            v             v      A   B-->C
           C            B            A             C      etc.     [see SEC]


%T Stop Words
%X From: C. J. van Rijsbergen. Information Retrieval. p18-19. TABLE 2.1
   a small example list of `stop words'
   ----------------------------------------------------------------------------
   A               CANNOT          INTO            OUR             THUS
   ABOUT           CO              IS              OURS            TO
   ABOVE           COULD           IT              OURSELVES       TOGETHER
   ACROSS          DOWN            ITS             OUT             TOO
   AFTER           DURING          ITSELF          OVER            TOWARD
   AFTERWARDS      EACH            LAST            OWN             TOWARDS
   AGAIN           EG              LATTER          PER             UNDER
   AGAINST         EITHER          LATTERLY        PERHAPS         UNTIL
   ALL             ELSE            LEAST           RATHER          UP
   ALMOST          ELSEWHERE       LESS            SAME            UPON
   ALONE           ENOUGH          LTD             SEEM            US
   ALONG           ETC             MANY            SEEMED          VERY
   ALREADY         EVEN            MAY             SEEMING         VIA
   ALSO            EVER            ME              SEEMS           WAS
   ALTHOUGH        EVERY           MEANWHILE       SEVERAL         WE
   ALWAYS          EVERYONE        MIGHT           SHE             WELL
   AMONG           EVERYTHING      MORE            SHOULD          WERE
   AMONGST         EVERYWHERE      MOREOVER        SINCE           WHAT
   AN              EXCEPT          MOST            SO              WHATEVER
   AND             FEW             MOSTLY          SOME            WHEN
   ANOTHER         FIRST           MUCH            SOMEHOW         WHENCE
   ANY             FOR             MUST            SOMEONE         WHENEVER
   ANYHOW          FORMER          MY              SOMETHING       WHERE
   ANYONE          FORMERLY        MYSELF          SOMETIME        WHEREAFTER
   ANYTHING        FROM            NAMELY          SOMETIMES       WHEREAS
   ANYWHERE        FURTHER         NEITHER         SOMEWHERE       WHEREBY
   ARE             HAD             NEVER           STILL           WHEREIN
   AROUND          HAS             NEVERTHELESS    SUCH            WHEREUPON
   AS              HAVE            NEXT            THAN            WHEREVER
   AT              HE              NO              THAT            WHETHER
   BE              HENCE           NOBODY          THE             WHITHER
   BECAME          HER             NONE            THEIR           WHICH
   BECAUSE         HERE            NOONE           THEM            WHILE
   BECOME          HEREAFTER       NOR             THEMSELVES      WHO
   BECOMES         HEREBY          NOT             THEN            WHOEVER
   BECOMING        HEREIN          NOTHING         THENCE          WHOLE
   BEEN            HEREUPON        NOW             THERE           WHOM
   BEFORE          HERS            NOWHERE         THEREAFTER      WHOSE
   BEFOREHAND      HERSELF         OF              THEREBY         WHY
   BEHIND          HIM             OFF             THEREFORE       WILL
   BEING           HIMSELF         OFTEN           THEREIN         WITH
   BELOW           HIS             ON              THEREUPON       WITHIN
   BESIDE          HOW             ONCE            THESE           WITHOUT
   BESIDES         HOWEVER         ONE             THEY            WOULD
   BETWEEN         I               ONLY            THIS            YET
   BEYOND          IE              ONTO            THOSE           YOU
   BOTH            IF              OR              THOUGH          YOUR
   BUT             IN              OTHER           THROUGH         YOURS
   BY              INC             OTHERS          THROUGHOUT      YOURSELF
   CAN             INDEED          OTHERWISE       THRU            YOURSELVES
   ----------------------------------------------------------------------------
   The book is available on the WWW at
   <A HREF="http://www.dcs.gla.ac.uk/">gla</A>][under publications, 3/'96].


%T Windows 2000
%D 1999
%K Microsoft, MS, Gates, windows, 2000, win2k, win2000, y2k,
   2K, y2000, millenium bug, funny, ha ha, haha, zz0399
%X 4/3/1999: Microsoft announcement out of Redmond WA today
   to the effect that Windows-2000, originally scheduled
   for distribution in the second quarter of next year,
   has been delayed and will now be released in early 1901.


%A Alf-Christian Achilles
%T Bibliography
%D 1994
%K bibliography, BibBib, bib, Computer Science, CSci, CS, computing,
   Karlsruhe, www, HREF, URL, ftp
%X *** closed down abot 2023 ***
   <A HREF="http://liinwww.ira.uka.de/bibliography/index.html">http://liinwww.ira.uka.de/bibliography/index.html</A> [4/'95]
   The old URL will continue to work by means of redirection, which
   should be transparent to clients:
   <A HREF="http://www.ira.uka.de/ftp/ira/bibliography/">bibliography</A>
   BTW,     ftp://ftp.ira.uka.de/pub/bibliography/bibliography.dsc.gz is also
   <A HREF="ftp://ftp.ira.uka.de/pub/bibliography/bibliography.dsc.gz">bib-bib</A> ~ 130K
   a bibliography of online bibliographies.
   Alf-Christian Achilles,
   Lehrstuhl Informatik fuer Ingenieure, und Naturwissenschaftler,   (8/'94)
   University of Karlsruhe, D-76128 Karlsruhe, Germany
   tel: +49 721 608-4335;  fax: +49 721 69 86 75
   <!-- email: achilles of ira.uka.de --> .

%T Computing Research Repository (ACM);  ACM digital library
%D 1998
%K CRR, ACM, LANL, technical report, TR, bib, bibliography,
   computer, CS, CSci, www, HREF, http, zz0998
%X ACM, Los ALomos and CSTR:
   [<A HREF="https://dl.acm.org/">dl.acm.org</A>]['23].
   Was <A HREF="http://www.acm.org/corr/">[web]</A>[9/1998].

%T CORE
%K bibliography, open university, access, repository, scientific,
   research, papers, literature
%X "... CORE is a not-for-profit service delivered by The Open University ..."
   -- [<A HREF="https://core.ac.uk/">core.ac.uk</A>][2024].

%T Computer Science Technical Reports
%D 1994
%K CSTR, Cornell, Computer Science, CS, CSci, technical report server, TR,
   computing, distributed, bib, bibliography, www, HREF, http
%X [<A HREF="https://hdl.handle.net/1813/5602">2003+</A>]['24],
   [<A HREF="https://hdl.handle.net/1813/5603">1968-2002</A>]['24],
    at [<A HREF="http://www.cs.cornell.edu/">Cornell CSci home</A>]['24].
   (was: <A HREF="http://cs-tr.cs.cornell.edu/">CSTR server</A>.)

%T Glimpse
%D 1994
%K Glimpse, Arizona, Computer Science, CS, CSci, bib, bibliography,
   computing, www, HREF, http
%X was: <A HREF="http://glimpse.cs.arizona.edu/">[about Glimpse]</A> [7/'97]
        <A HREF="http://glimpse.cs.arizona.edu:1994/bib/">bibliography</A> (Glimpse)
   about 240,000 citations as of 8/'94, but "not found" as of 2024.

%A R. Golding
%T Refdbms: a distributed bibliographic database manager
%D 1994 ?
%K bib, c1994 c199x, bibliography, BibBib, computer, graphics, systems,
   computing, www, HREF, FTP
%X History: [<A HREF="https://www.usenix.org/legacy/publications/library/proceedings/sf94/full_papers/golding.pdf">www</A>][2024].
   <A HREF="ftp://ftp.cse.ucsc.edu/pub/refdbms/refdbms.README.html">Refdbms</A>
   via: achilles of ira.uka.de  Fri Aug  5 18:00:14 1994

%A ?
%T BibNet: Automatized maintenance of a remote bibliography via email
%D 1994 ?
%K Bibnet, BibTex, net, bib, bibliography, computing, www, HREF, FTP
%X FAQ@[<A HREF="https://netlib.org/bibnet/faq.html">www</A>][2024].
   <A HREF="ftp://netlib.att.com/netlib/bibnet/readme.Z">BibNet</A>
   via: achilles of ira.uka.de  Fri Aug  5 18:00:14 1994


%A M. Chartier
%T The alarming rise of predatory conferences
%J Eos
%V 103
%M SEP
%D 2022
%K news, views, c2022, c202x, c20xx, zz1124, CFP, fake, academia, scam,
   publications
%X "For-profit confs. that masquerade as legit, academic events but lack
   trusted sel'n & peer review processes are becoming more common. ..."
   -- [<A HREF="https://doi.org/10.1029/2022EO220449">doi:10.1029/2022EO220449</A>]['14].

%T Int. Workshop on the ACL2 Theorem Prover and its Applications
%K ACL, ACL2, wShop,CFP,theorem,proving,proof,www,HREF,http, zz0725, zz0726
%X [<A HREF="https://www.cs.utexas.edu/~moore/acl2/workshops.html">series</A>] Mar 1999, ... May 2020, ... May 2025 ...

%T Australasian Computer Science Week
%K ACSW, Australia, Australian,
   computing,CSci,CFP,conf,www,HREF,http, zz0225, zz0126
%X [<A HREF="https://acsw.core.edu.au/">core.edu.au</A>]
   2025 Feb 10-14, Brisbane, deadline ???

%T Int. Symp. on Artificial Intelligence and Mathematics
%K ISAIM, AIM,  AI, II,  conf,CFP,www,http,HREF, zz1025, zz1027
%X NB. biennial
   [<A HREF="https://isaim2024.cs.ou.edu/">8-10 Jan 2024</A>] Ft Lauderdale, deadline 17 Oct 2023
   [Also search for: AIS conf CFP].

%T Australian Joint Conf. on Artificial Intelligence
%K AJCAI,  CFP,conf,AI,II,http,HREF,www, zz0725, zz0726
%X [<A HREF="https://ajcai2024.org/">25-29 Nov 2024</A>], Melbourne, deadline 15 Jul 2024

%T Int. Workshop on Artificial Intelligence and Statistics
%K AIS,   AI,II,stats,wShop,conf,CFP,http,HREF,www
%X [<A HREF="https://aistats.org/aistats2025/">3-5 May 2025</A>] Thailand, deadline 3 Oct 2024
   Also see [<A HREF="https://aistats.org/">aistats.org</A>]['24].
   [Also search for: AIM conf CFP]

%T Bioinformatics Australia Conference
%K ABACBS, BA,  CFP,conf,MolBio,www,http, zz0825, zz0826
%X [<A HREF="https://www.abacbs.org/">abacbs.org</A>]['24].
   * 4-6 Nov 2024, Sydney, deadline 26 Aug 2024

%T Int. Conf. on Automated Deduction
%K CADE,  CFP,conf,www,HREF,http,logic,  zz0225, zz0226
%X See [<A HREF="http://cadeinc.org/">cadeinc.org</A>]['24].
   * 28 July - 2 Aug 2025, Stuttgart, deadline 17 Feb 2025

%T Int. Conf. on Compiler Construction
%K CC,  CFP,conf,programming languages,,http,www,HREF, zz1024, zz1025
%X [<A HREF="https://conf.researchr.org/home/CC-2025">1-2 Mar 2025</A>] Las Vegas, deadline 3 Nov 2024

%T COCOON
%K Cocoon, Computing and Combinatorics Conference,
   conf,CFP,www,HREF,http,algorithms,  zz0425,zz0426
%X [<A HREF="http://www.wikicfp.com/cfp/program?id=523">Cocoon</A>]['24]
   * 30th, 23-25 Aug 2024, Shangai, deadline 1 April 2024

%T IEEE Comp. Soc. Bioinformatics Conf. (CSB)
%K CSB,  CSB2003, 2003,  MolBio, conf, CFP, http, HREF, www
%X [<A HREF="http://conferences.computer.org/bioinformatics/">2003</A>] August 11-14, Stanford
      deadline 1 April 2003

%T Data Compression Conference
%K DCC, CFP,Snowbird,Utah,compress,conf,CSci,www,HREF,http, zz1025,zz1026
%X [<A HREF="https://datacompressionconference.org/">18-21 March 2025</A>] Snowbird, deadline 11 Oct 2024

%T European Conf. on Computational Biology
%K ECCB, bioinformatics,MolBio,  conf,CFP,www,HREF,http, zz0326, zz0125
%X see ISMB33 2025  (ISMB/ECCB)
   [<A HREF="https://eccb2024.fi">16-20 Sept 2024</A>] Turku .fi, deadline 14 March 2024

%T European Conf. on Machine Learning (ECML)
%K ECML,  CFP,conf,AI,Euro,EEC,www,HREF,http, zz0225, zz0226, zz0227
%X [<A HREF="ecmlpkdd.org">ecmlpkdd.org</A>]['24].
   * 9-13 Sep 2024, Vilnius, deadline 15 March 2024

%T European Symposium on Algorithms
%K ESA,Algo,Europe, conf,CFP,algorithm,CSci,www,HREF,http, zz0425, zz0526
%X [<A HREF="https://algo-conference.org/">algo-conference.or</A>]['24].
   * 15-19 Sept 2025, Warsaw, deadline ?? April 2025

%T Int. Symp. on Functional and Logic Programming (FLOPS)
%K FLOPS, conf,CFP,Japan,.jp,FP,LP,www,HREF,http, zz1025, zz1026
%X [<A HREF="https://conf.researchr.org/home/flops-2024">2024 May 15-17</A>], Kumamoto, deadline 6 Dec 2023
   [<A HREF="https://conf.researchr.org/home/flops-2022">2022 May 10-12</A>], Kyoto, deadline 14 Nov 2021
   ... ?every 2 years? ...

%T Haskell Workshop
%K Haskell, Symposium, wShop,conf,FP,CFP,http,www,HREF, zz0525, zz0526
%X [<A HREF="https://www.haskell.org/haskell-symposium/">haskell-symposium</A>]['24].
   * 2025 Singapore
   * 2024 Milan
   [<A HREF="http://haskell.org/haskell-symposium/2023">8-9 Sep 2023</A>], Seattle, deadline 1 June 2023
   [[Also see ICFP]]

%T Int. Conf. on Data Mining
%K ICDM,  CFP,Conf,IEEE,KD,AI,www,HREF,http,  zz0625, zz0626
%X [<A HREF="https://www.icdm2024.org/">9-12 Dec 2024</A>] AbuDhabi, deadline 14 June 2024

%T Int. Conf. on Functional Programming (ICFP)
%K ICFP, CFP,conf,FP,theory,lambda calculus,http,HREF,www,zz0225,zz0226
%X [<A HREF="https://icfpconference.org/">ICFP</A>]['24]
   * 2-7 Sept 2024, Milan, deadline 8 Feb 2024

%T Int Conf Machine Learning
%K ICML,  conf,AI,II,CFP,www,HREF,http, zz1224,zz0125, zz0126
%X [<A HREF="https://icml.cc/">ICML</A>]['24]
   * 13-19 July 2025, Vancouver, deadline 9 Jan 2024

%T Int. Conf. Logic Programming
%K ICLP,  conf,CFP,LP,www,HREF,http,  zz0425, zz0426
%X [<A HREF="https://logicprogramming.org/conferences/">ICLP</A>]['24]
   * 11-17 Oct 2024, Dallas, deadline 8 July 2024

%T Int. Coll. on Theoretical Aspects of Computing
%K ICTAC,  CFP,conf,TCS,theory,www,HREF,http, zz0525,zz0625, zz0526
%X 21st [<A HREF="https://ictac2024.cs.ait.ac.th/">25-29 Nov 2024</A>] Bangkok, deadline 14 June 2024

%T Int. Symp. on the Implementation & Application of Functional Languages
%K IFL,  CFP,conf,wShop,FP,programming,www,HREF,http, zz0725,zz0825, zz0726
%X [<A HREF="https://ifl-symposia.org/">IFL</A>]['24].
   * 26-29 Aug 2024, Nijmegen, deadline 4 Aug 2024

%T Int. Conf. Inductive Logic Programming
%K ILP,  CFP,conf,LP,AI,www,HREF,http,  zz0225, zz0226
%X [<A HREF="http://ilp.fe.up.pt/">2004 Sep 6-8</A>] Porto, .pt, deadline 3 May '04
   [<A HREF="http://www.rgai.hu/ilp2003/">2003 Sep 29 - Oct 1</A> Hungary

%T Int. Conf. on Intelligent Systems for Molecular Biology
%K ISMB, ISCB, MolBio,conf,CFP,bioinformatics,II,www,HREF,http, zz0125,zz0126
%X [<A HREF="https://www.iscb.org/ismb">ISMB</A>]['24]
   * 20-24 July 2025, Liverpool, deadline 23 Jan 2025 (proc.), inc. ECCB24

%T Int. Symp. on Trends in Functional Programming (ISTFP)
%K ISTFP,TFP,  CFP,conf,FP,www,HREF,http, zz1124, zz1125,zz1225
%X [<A HREF="https://www.trendsfp.com/">TFP</A>]['24].
   * 13-16 Jan 2025, Oxford, deadline 13 Nov 2024

%T Maximum Entropy and Bayesian Methods Workshop
%K MaxEnt,  CFP,wShop,conf,Bayes,Bayesian,inference,zz0325,zz0326
%X [<A HREF="https://maxent2024.ugent.be/">1-5July 2024</A>] Ghent, deadline 15 March 2024.

%T Int. Symp. on Practical Aspects of Declarative Languages
%K PADL,  CFP,conf,programming,FP,LP,www,HREF,http, zz0925,zz1025, zz0926
%X [<A HREF="https://popl25.sigplan.org/home/PADL-2025">20-21 Jan 2025</A>] Denver, deadline 18 Oct 2024
   [Also search for: conf CFP FP].

%T Workshop on Partial Evaluation and Program Manipulation
%K PEPM,  wShop,CFP,www,FP,HREF,http, zz1025, zz1026, zz1026
%X [<A HREF="https://popl25.sigplan.org/home/pepm-2025">19-25 Jan 2025, Denver, deadline 14 Oct 2024.

%T Principles of Programming Languages
%K POPL,  conf,CFP,www,HREF,http,CSci,  zz0625,zz0725, zz0626
%X [<A HREF="https://www.sigplan.org/Membership/">POPL</A>]['24].
   * 19-25 Jan 2025, Denver, deadline 11 July 2024

%T Int. Symp. Principles and Practice of Declarative Programming
%K PPDP,  CFP,conf,FP,LP,sigplan, zz0525, zz0526
%X [<A HREF="https://ppdp2024.github.io/">9-11 Sept 2024</A>] Milan, deadline 13 May 2024

%T RECOMB: Int. Conf. on Computational Molecular Biology
%K Recomb,  MolBio,conf,CFP,www,HREF,http,bioinformatics, zz0925,zz1025, zz0926
%X [<A HREF="https://recomb.org/">RECOMB</A>]['24].
   * 26-29 Apr 2025, Seoul, deadline 16 Oct 2024

%T Rocky Mountain Bioinformatics Conf.  (Rocky, Aspen, Colorado)
%K ROCKY,  conf,CFP,MolBio,www,HREF,http,  zz1025, zz1026
%X not held in 2023, see late 2024 ???
   [<A HREF="https://www.iscb.org/rocky2022">2022 Dec 8-10</A>], deadline 17 Oct 2022

%T Annual ACM Symposium on Theory of Computing
%K STOC, computer science, CSci, computing, conf,CFP,conference,www,HREF,http,
   zz1024, zz1124, zz1025
%X [<A HREF="https://acm-stoc.org/">STOC</A>]['24].
   * 23-27 June 2025, Prague, deadline 4 Nov 2024

%T Int. Conf. on Uncertainty in Artificial Intelligence
%K UAI,  CFP,conf,AI,CSci,computing,conference,www,HREF,http,  zz0125,zz0225
%X Assoc for Uncertainty in AI [<A HREF="https://www.auai.org/">AUAI</A>]['24].
   * ? 2025 ?
   * 15-19 July 2024, Barcelona, deadline 8 Jan 2024.


%T Aliweb
%D 1994
%K Aliweb, internet, search engine, SE, www, HREF, http
%X <A HREF="http://web.nexor.co.uk/public/aliweb/aliweb.html">Aliweb home (UK)</A>
   (been u/s for a while - 12/94)
   <A HREF="http://www.cs.indiana.edu/aliweb/search">Mirror at IU USA</A>

%T Alta Vista
%D 1996
%K AltaVista, Dec, digital, search engine, SE, www, HREF, http
%X <A HREF="http://altavista.digital.com/">[here]</A>  [2/'96]
   Telstra's Australian mirror:-
   <A HREF="http://www.altavista.yellowpages.com.au/cgi-bin/telstra?">[oz]</A>
   but the Telstra site is at least a few days behind in its index (10/96).

%T Anzwers
%D 1997
%K Anzwers, answers, Australia, NZ, search engine, SE, www, HREF, http
%X <A HREF="http://www.anzwers.com.au/">[web]</A>[12/'97].

%A G. Weinberg
%T Duck Duck Go
%D 2011
%K Duck Duck Go, DuckDuckGo, search engine, SE, www, HREF, http, zz0613,
   anonymously, tracking (not)
%X [<A HREF="https://duckduckgo.com/">duckduckgo</A>][2013].

%T Excite
%D 1996
%K Excite, search engine, SE, www, HREF, http
%X <A HREF="http://excite.com/">[excite]</A> [5/'97]

%T Google
%D 1999
%K google, googol, search engine, SE, www, HREF, http, zz0499
%X <A HREF="http://www.google.com/">google</A> [4/1999].
   A page is "important" (regardless of a query) if
      1. other pages of high importance point to it,
      2. lots of other pages point to it.
   Returns important pages, that match query, and have terms "close" together.
   [Also search for: PageRank].

%T Harvest
%D 1995
%K Harvest, gatherer, broker, internet, search engine, SE, www, HREF, http
%X <A HREF="http://harvest.cs.colorado.edu/">[about Harvest]</A>
   <A HREF="http://www.town.hall.org/Harvest/brokers/www-home-pages/query.html">[Query]</A>  [10/95]

%T htdig
%A Andrew Scherpbier
%D 1995
%K HTDIG, internet search engine, web, SE, www, HREF, http, zz0499
%X A free search engine available, with full source code under
   the GNU general public licence, and originally developed at
   San Diego State University.  Needs C and C++ and Unix.
   [<A HREF="http://www.htdig.org/">htdig.org</A>] [3/1999]

%T ICE
%D 1997
%K ICE, Perl, web, SE, search engine, index, indexong, www, HREF, http, zz0899
%X web-site indexing kit in Perl
   <A HREF="http://www.objectweaver.de/ice/">objectweaver.de</A>[8/'99]
   <A HREF="http://ice.cornell-iowa.edu/">ice.cornell-iowa.edu</A>[8/'99]
   <A HREF="http://www.pi.informatik.tu-darmstadt.de/~neuss/ice/ice.html"
     >darmstadt</A> (old) ['97]

%T Infoseek
%D 1996
%K Infoseek, search engine, SE, www, HREF. http
%X <A HREF="http://www.infoseek.com/">[infoseek]</A> [5/'97]

%T Lycos
%D 1994
%K Lycos, internet, search engine, SE, www, HREF, http
%X <A HREF="http://www.lycos.com/">lycos.com  search form</A> [10/'96]
   <A HREF="http://lycos.cs.cmu.edu/lycos-form.html">Lycos search-form</A>
   <A HREF="http://query2.lycos.cs.cmu.edu/cgi-bin/pursuit">Lycos2 search form</A>
   <A HREF="http://lycos.cs.cmu.edu/">Lycos home page</A>  

%T MetCrawler
%D 1995
%K MetaCrawler, meta crawler, search engine, SE, www, HREF, http, zz0895
%X <A HREF="http://www.cs.washington.edu/research/projects/ai/metacrawler/www/">metacrawler</A> [8/'95]

%T Nutch
%K Nutch, internet, search engine, SE, www, HREF, http, zz1103
%X [<A HREF="http://www.nutch.org/">nutch.org</A>][11/'03]
   as of 2003, it is a *plan*, to build an *open-source* web search engine;
   coincidentally(?) google plans to "float" soon.

%T Open Text
%D 1995
%K OpenText, internet, search engine, SE, www, HREF, http
%X <A HREF="http://index.opentext.net/indexb.html">[pinstripe]</A>[5/1998]
      seem to have abandoned the general search-engine market and gone
      to a business-only index.
   <A HREF="http://www.opentext.com/omw/simplesearch">search engine</A>[1997]
      <A HREF="http://www.opentext.com/">opentext.com</A>
      SURFERS BEWARE: THEY ARE SELLING KEY WORDS to guarantee a top listing!
      $1000 / search term / month,  words in top 100 may cost more $

%A B. Pinkerton
%T WebCrawler
%D 1994
%K WebCrawler, wwwC, w3C, WC, internet, search engine, SE, www, HREF, http
%X <A HREF="http://webcrawler.com/">Web Crawler</A>                   [9/'95]
   <A HREF="http://webcrawler.cs.washington.edu/WebCrawler/WebQuery.html">Old Crawler</A>

%T W3 Search Engines
%D 1994
%K W3 search engine, SE, internet, www, HREF, http
%X <A HREF="http://cuiwww.unige.ch/meta-index.html">W3 Search Engines</A>

%A O. McBryan
%T World Wide Web Worm
%D 1994
%K World Wide Web Worm, wwww, w4, search engine, SE, internet, www, HREF, http
%X <A HREF="http://www.cs.colorado.edu/home/mcbryan/WWWW.html">WWWW home</A>


%T All Prior Art
%A A. Reben
%D 2016
%K all prior art, c2016, c201x, c20xx, zz0516, patent troll, patents, trolls,
   patent system, patented, 3D printed soap, law, fun, funny, ha ha, haha,
   HREF, www, http
%X "All Prior Art is a project attempting to algorithmically create & publicly
   publish all possible new prior art, thereby making the published concepts not
   patent-able. The concept is to democratize ideas, provide an impetus for
   change in the patent system, & to preempt patent trolls. The system works by
   pulling text from the entire database of US issued & published (un-approved)
   patents & creating prior art from the patent language. While most inventions
   generated will be nonsensical, the cost to computationally create & publish
   millions of ideas is nearly zero - which allows for a higher probability of
   possible valid prior art. ..."
   -- [<A HREF="http://allpriorart.com/about/">www</A>]['16].
   [Also search for: postmodernism generator].

%T Gerry Anderson Appreciation Society
%K Anderson, Fanderson, fan club, puppet, puppetry, super marionation, FAB,
   supermarionation, film, TV, Supercar, Fireball XL5, Stingray, Thunderbirds,
   Captain Scarlet, Joe 90, Joe90, Secret Service, UFO, Space, Space1999,
   Precinct, fun, funn, www, HREF, http, zz0397
%X <A HREF="http://www.fanderson.org.uk">[web]</A> [3/2023]
   <A HREF="http://www.kikgraphics.demon.co.uk/fanderson.html">[web]</A> [1998]
   <A HREF="http://www.aiai.ed.ac.uk/~bat/GA/fanderson.html">[web]</A> [1997]
   Fanderson, PO Box 93, Wakefield, West Yorkshire WF1 1XJ, England   [3/'97]

%A P. Greenspun
%T Butterflies
%D 1995
%K butterfly, insect, images, jpg, jpeg, fun, funn, www, HREF, http
%X [<A HREF="http://www.photo.net/photo/butterflies/">www</A>][7/'01]
   [<A HREF="http://www-swiss.ai.mit.edu/philg/photo/butterflies/">was</A>]['95]

%T Cambridge Coffee Pot
%D 1994
%K Coffee pot, silly, www, HREF, http
%X <A HREF="http://www.cl.cam.ac.uk/coffee/coffee.html">Coffee pot</A>

%T Cats and Robots
%D 1996
%K cat, cats, robot, robots, intelligent, fun, funn, funny, ha ha,
   www, HREF, http, zz0696
%X <A HREF="/~lloyd/tildeMisc/1996.Cats.html">Cat</A>

%T Centennial Light Bulb
%D 2001
%K light bulb, electric, centenial, century 1901, 2001, fun, funn, www,
   Livermore Pleasanton fire station, HREF, http, zz0701
%X This 4-Watt hand-blown electric bulb with a "carbide filament"
   has supposedly been burning since 1901 -
   Was [<A HREF="http://205.187.115.100/" TARGET="external">www</A>][7/'01]
    - [<A HREF="mailto:bulb@lpfire.org">email</A>] the bulb!

%T Christmas
%D 1994
%K Christmas, Xmas, father, santa claus klaus, www, HREF, http
%X <A HREF="http://north.pole.org/">North Pole<IMG SRC="/~lloyd/tildeImages/Misc/Xmas.holly.gif"></A>

%T CMU Coke Machine
%D 2007
%K Coke, Coca Cola, silly, www, HREF, http
%X [<A HREF="http://www.bennetyee.org/ucsd-pages/coke.html">list@bennetyee.org</A>][2007]
   [<A HREF="http://www-cse.ucsd.edu/users/bsy/coke.html">list@ucsd</A>][1998]
   [<A HREF="http://www.cs.cmu.edu/afs/cs.cmu.edu/user/bsy/www/coke.html">list@cmu</A>][1996]
   [<A HREF="http://porsche.boltz.cs.cmu.edu:8001/htbin/coke2">CMU coke</A>][1994]

%T Covered Bridges
%D 1994
%K covered bridge, Pennsylvania, Philadelphia, USA, fun, funn, www, HREF, http
%X <A HREF="http://william-king.www.drexel.edu/top/bridge/CB1.html">Bridges</A>
   <A HREF="http://129.25.48.205/top/bridge1/CB1.html">Bridges</A> [- old link]
   (Drexel University)

%T Cybergrrl
%D 1995
%K Cybergrrl, cybergirl, cyber girl, women, gender, fun, funn, www, HREF, http,
   Aliza Sherman
%X [<A HREF="http://www.cybergrrl.com/">Cybergrrl</A>][10/'95] dormant?['18],
   used to be http://www.interport.net/~asherman/ many moons ago.
   (See AS@[<A HREF="http://en.wikipedia.org/wiki/Aliza_Sherman">wikip</A>]['15]
        or [<A HREF="http://alizasherman.com/">alizasherman.com</A>]['18].)

%A Doctor Fun
%D 1994
%K Doctor Fun, Dr, cartoon, comic, funny, www, HREF, http
%X was: sunsite.unc.edu/Dave/Dr-Fun/latest.jpg,
        sunsite.unc.edu/Dave/drfun.html   2003.

%T Essay Marking
%D 1998
%K English, Grammar, Spelling, exam, mark, marks, www, HREF, http, zz1198,
   fun, funn, funny, bot, bots, autonomous, agent, agents,
   education, courseware, vapour ware
%X <A HREF="/~lloyd/tildeMisc/1998.Essay.html">[web]</A>[10/1998]

%T Flight Simulator
%D 1998
%K flight, simulator, sim, air combat, ACM, flightsim, www, HREF, http
%X <A HREF="http://pw1.netcom.com/~rrainey/index.html">~rrainey</A> [5/1999]
   ACM 4.8 has IEEE 1278 Distributed Interactive Simulation (DIS) protocol.

%T Formula One
%D 1994
%K Formula one, F1, Grand Prix, GP, car, race, racing, sport, automotive,
   entertainment, fun, funn, www, HREF, http
%X [<A HREF="http://www.fia.com/" TARGET="external">fia.com</A>][7/'01]
   [<A HREF="http://www.fia.com/FreePress/FIA_F1_Guide/F1_Calendar.html" TARGET="external">F1 Calendar</A>][7/'01]

%A The Goon Show
%D 1994
%K Goons, entertainment, media, radio, fun funn, www, HREF, http
%X [<A HREF="http://www.goon.org/" TARGET="external">goon.org</A>][7/'01, 3/'23]
   [<A HREF="http://minnie.tuhs.au/Goons/index.html">Goon Show Archive</A>][4/'01]
   [<A HREF="http://minnie.cs.adfa.oz.au/Goons/index.html">Goon Show Archive</A>]['94]

%T Human Powered Vehicles
%D 1995
%K Human powered vehicle, HPV, fun, funn, www, HREF, http, zz0695
%X <A HREF="http://www.ihpva.org/">Human Powered Vehicle Archive</A>
   <A HREF="http://www.ihpva.org/source-guide.html">Human Powered Vehicle Archive Source Guide</A>
   - Claas van der Linde  <!-- email: vanderlinde@sgcl1.unisg.ch -->  [6/'95]

%T Decavitator
%D 1994
%K Human powered vehicle, boat, boating, hydrofoil, HPV,
   fun, funn, www, HREF, http
%X <A HREF="http://lancet.mit.edu/decavitator/Decavitator.html">Decavitator</A>
   27 Oct 1991: 18.5 knots (9.53m/s) over 100 metres.
   31 Dec 1992: DuPont prize.    Boat in Museum of Science in Boston, Mass.

%E A. Davison
%T Humour The Computer
%I MIT press
%D 1995
%P 226
%K ha ha, humour, humor, book, HTC, funny, www, HREF, http, zz0796
%X $13.95 US;  isbn:262540754;
   gets a poor review in Comp Rev p227 May 96.
   Was   www.cs.mu.oz.au/~ad/humour/HTCreading.html   1995.

%T Information Super-Highway
%M APR
%D 1990
%K internet, superhighway, infobahn, pigeon, OSI, packet, message,
   1st, April, April1, funny, www, HREF, http
%X <A HREF="/~lloyd/tildeMisc/1990.pigeon.html">super highway</A>

%T Land-Rover
%D 1994
%K Land-Rover, LandRover, Range Rover, automotive, automobile, car,
   four wheel drive, all, 4WD, 4x4, 4X4, fun, funn, www, HREF, http
%X <A HREF="/~lloyd/4/LandRover/">Land-Rover</A>

%A Lego
%K Lego, LegoLand, lugnet, toy, toys, fun, funn, www, HREF, http, zz0999
%X <A HREF="http://www.lugnet.com/">lugnet.com</A> (Lego Builders) [9/'99, '23]
   <A HREF="http://www.lego.com/">lego.com</A> [1998]
   <A HREF="http://legowww.homepages.com/">Lego at .com</A> [5/'95]
   <A HREF="http://legowww.itek.norut.no/">Lego at .no </A> ['94]

%T Kylie Minogue
%D 1994
%K Minogue, Kylie, oz, au, entertainment, pop, music, fun, funn,
   www, HREF, http
%X KM@[<A HREF="https://en.wikipedia.org/wiki/Kylie_Minogue">wikip</A>]['23].
   The unofficial-site below closed down in February 2001 - Tony Henshall.
     <A HREF="http://www.confidence-uk.com/kylie/">Kylie</A> [10/'97]
     <A HREF="http://kylie.telescope.org/">Kylie</A> [2/'97]
     <A HREF="http://www.telescope.org/kylie/">Kylie</A> [4/'95]
     <A HREF="http://www.eia.brad.ac.uk/kylie/index.html">original</A> ['94]
     <IMG SRC="/~lloyd/tildeImages/Film/Kylie.gif">
     Is this voyeurism?  Is it cyberstalking?
     I am slightly surprised that the site has lasted so long
     and has not been closed down over copyright.
   But there is now an official site ...
     <A HREF="http://www.kylie.com/">[www.kylie.com]</A>[10/'97]
    (<A HREF="http://www.deconstruction.co.uk/kylie/">[2/'97]</A>)

%T Private Eye
%D 1995
%K Private Eye, satire, satirical, political, politics, mag, magazine, media,
   England, UK, fun, funn, www, HREF, http, zz0795
%X [<A HREF="http://www.private-eye.co.uk" TARGET="external">www</A>][7/'01, '23]
   was [<A HREF="http://www.intervid.co.uk/intervid/eye/gateway.html" TARGET="external"><IMG SRC="/~lloyd/tildeImages/Cartoons/Private.Eye.gif" ALIGN="middle">the Eye</A>]['95]


%A anon ?
%T Rabbit's Thesis
%K Research, PhD, thesis, funny
%X <A HREF="/~lloyd/tildeMisc/1997.thesis.html">[thesis]</A>

%T America's Cup
%D 1994
%K sail, sailing, yacht, yachting, race, boat, America's, Americas, cup, AC95,
   sport, fun, funn, www, HREF, http, zz0517
%X [<A HREF="https://www.americascup.com/">www</A>]['17] (#35: 26/5-27/6 2017).
   Was [<A HREF="http://www.americascup.org/" TARGET="external">www</A>][7/'01],
       [<A HREF="http://www.ac95.org">AC 1995</A>].

%T Sydney - Hobart Yacht Race
%D 1994
%K sail, sailing, yacht, yachting, annual, race, sport, fun, funn,
   www, HREF, http
%X was [<A HREF="http://s2h.tas.gov.au/" TARGET="external">www</A>][7/'01]
   was [<A HREF="http://info.tas.gov.au/shyr/index.html">Sydney-Hobart</A>]['94]
   Start: 1.00 pm Boxing Day  (annual event)

%T Spam
%A Hormel
%K Spam, Hormel, FAQ, 1937, luncheon meat, ham, pork, pig,
   www, fun, funn, HREF, http, zz1098
%X Hormel invented Spam in Austin, Minnesota, USA, 1937.
   Apparently it's pork shoulder, ham and spices.
   1998: claim 5 billion cans have been sold.
   See <A HREF="http://www.spam.com/">www.spam.com</A> [10/1998]

%A J. Cho
%T Spam Ku; Tranquil Reflections on Luncheon Loaf.
%I Harper_Perennial
%M OCT
%D 1998
%P 96
%K spam, haiku, spamku, senryu, book, text, fun, funn, funny, ha ha, hahah,
   www, HREF, http, zz1098
%X isbn:0060952784;  about us$7;
   *Was* www.spamhaiku.com/   12/2003,
         pemtropics.mit.edu/~jcho/spam/   10/1998.

%T Standards
%K standards, quality, fun, funn, funny, zz0297
%X <A HREF="/~lloyd/tildeMisc/1997.10pc.html">[here]</A> [2/'97]
   from Bill Waite.

%T Trabant
%D 1996
%K Trabant, Trabi, East Germany, eastern, plastic, car,
   fun, funn, silly, www, HREF, http, zz1096
%X [<A HREF="http://www.team.net/www/ktud/trabi.html">Trabi-web</A>]['96, '23].
   In addition to the history there are pictures from the '70s, '60s
   which show You the life with Trabant in Hungary and other
   interesting bits.
   - <A HREF="mailto:npal of enet.hu">Paul Negyesi</A> [10/'96]

%T Travels with Samantha
%D 1994
%K Samantha, travel, slide show, fun, funn, www, HREF, http, Greenspun
%X [<A HREF="http://philip.greenspun.com/samantha/">www</A>]['17, '23].
   Was [<A HREF="http://www.photo.net/samantha/slide-show.html">Travels</A>]['01]
       [<A HREF="http://www-swiss.ai.mit.edu/samantha/slide-show.html">Travels</A>]['94].

%T SpellingLand
%D 1994
%K Spelling, Aaron, Melrose-Place, Beverly Hills, 90210, The Heights,
   Models Inc, entertainment, media, TV, soap, soapie, silly, www, HREF, http
%X was metaverse.com/modelsinc/ 2/1995
   <IMG SRC="/~lloyd/tildeImages/TV/Models.small.gif">
   Mega-corp' seems to have done-in the unofficial site.

%T Wallace and Gromit
%D 1994
%K fun, funn, TV, cartoon, www, HREF, http
%X <IMG SRC="/~lloyd/tildeImages/Cartoons/W+G.Gromit.gif"> <IMG SRC="/~lloyd/tildeImages/Cartoons/W+G.Wallace.gif">
   Surely there must be a W+G (www) site somewhere - tell me if you know.

%A J. Butler
%T Scotch Malt Whisky
%K whisky, alcohol, Scotland, fun, funn, www, HREF, http
%X [<A HREF="http://www.dcs.ed.ac.uk/home/jhb/whisky/">Virtual Whisky</A>][1998,2001,2023]
   [<A HREF="http://www.dcs.ed.ac.uk/staff/jhb/whisky/">Virtual Whisky</A>][1994]

%T US University Professors
%D 1998
%K fun, funny, haha, joke, universities, quality, poll
%X Relayed from Bill Waite at Colorado:
      U.S. News & World Report says that a poll of university
      professors found that 94% of the respondents thought that
      they were better at their jobs than their average colleague.
      U.S. News & World Report 16 Dec 96 p26
   Well, what do they expect? EVERYONE knows the USA is perfect.(-csw 8/1998)


%T Jstor
%D 2001
%K Jstor, org, Jstore, journal, jrnl, stor, store, archive, repository,
   JRSS, www, HREF, http, zz0401
%X [<A HREF="http://www.jstor.org/">www</A>][4/01]
   Quite good on statistical journals.  Gets papers typically after 2-5 years.

%T Galaxy
%D 1994
%K Galaxy, index, wwwIndex, www, HREF, http
%X <A HREF="http://www.einet.net/galaxy.html">Galaxy at einet</A>

%A O. McBryan
%T Mother of all bulletin boards
%D 1994
%K mother, index, guide, wwwIndex, virtual, online, www, HREF, http
%X <A HREF="http://www.cs.colorado.edu/homes/mcbryan/public_html/bb/summary.html">Mother of all bulletin boards</A>

%T Virtual Libraries
%D 1994
%K virtual library, index, guide, wwwIndex, online, www, HREF, http
%X <A HREF="http://www.w3.org/pub/DataSources/bySubject/Virtual_libraries/Overview.html">Virtual Libraries</A> [10/'96]

%T The Virtual Library
%D 1994
%K Virtual Library, vlib org, Encyclopaedia, index, online,
      BioScience, BioSciences, Bio, Biol, Biology, MolBio,
      Computing, computer science, CS, CSci,
   www, wwwIndex, home, page, information, HREF, URL, http
%X [<A HREF="http://vlib.org/" TARGET="EXTERNAL">vlib.org</A>][2003]
      [<A HREF="http://vlib.org/Computing">Computing</A>][2023]

%T WWW.AU
%D 1995
%K WWW, AU, aus, com, oz, Australia, Australian, internet,
   index, wwwIndex, search engine, SE, www, HREF, http
%X <A HREF="http://www.sofcom.com.au/WWW.AU/">Australian Site Index</A>

%T FreePages
%K free pages, commercial, com, co, England, uk,
   index, wwwIndex, www, HREF, http, zz0396
%X <A HREF="http://www.freepages.co.uk/">[web page]</A>   [3/'96]

%T Yahoo - a Guide to WWW
%D 1994
%K Yahoo, index, guide, virtual, online, impressive,
   index, wwwIndex, search engine, SE, www, HREF, http
%X <A HREF="http://www.yahoo.com/">they went commercial</A> [4/'95]
   <A HREF="http://akebono.stanford.edu/yahoo/">original URL</A>

%T Yellow Pages
%D 1995
%K wwwIndex, commercial, company, business, www, HREF, http, zz0595
%X <A HREF="http://www.yellow.com/">YP</A> [5/'95]


%T Applied Bioinformatics
%I Open Mind Journals
%K Applied Bioinformatics, OMJ, jrnl, MolBio, http, HREF, www
%X [<A HREF="http://www.openmindjournals.com/bioinformatics.html" TARGET="external">www</A>][8/'02]
     editor Dr Allen Rodrigo -- 2002
     [<A HREF="http://www.openmindjournals.com/Bio_Archive_Top.htm" TARGET="external">archive</A>][8/'02]

%T The Computer Journal
%D 1995
%K Computer Journal, jrnl, COMPJ, computing, society, British, UK,
   computer science, CS, CSci, research, academic, publishing,  www, HREF, http
%X [<A HREF="http://comjnl.oxfordjournals.org/">[COMPJ</A>]['05]
      online ISSN 1460-2067, print ISSN 0010-4620  ['05]
   [<A HREF="http://www.oup.co.uk/computer_journal/">Journal</A>][2/'96]
     Abstracts online and searchable.
   old URLS:
     <A HREF="http://www.dcs.gla.ac.uk/other/computer_journal/">Journal</A>
     <A HREF="http://www.dcs.gla.ac.uk/other/computer_journal/journal_contents/">contents</A>

%T Journal of Bioinformatics
%K Journal Bioinformatics, Biology, CABIOS, MolBio, jrnl, molecular biology,
   www, HREF, http, zz1297
%X was CABIOS
   [<A HREF="http://bioinformatics.oupjournals.org/" TARGET="external">at oupjournals.org</A>][10/'00]
   [<A HREF="http://www.oup.co.uk/bioinformatics/" TARGET="external">at OUP</A>][9/'00]
   [<A HREF="/~lloyd/tildeMisc/1998.BioInf.html" TARGET="external">local</A>]['98]

%T Journal of Functional and Logic Programming
%D 1995...
%I European Association for Programming Languages and Systems
%K JFLP, FP, LP, jrnl, EAPLS, www, http, HREF, zz0902
%X [<A HREF="http://danae.uni-muenster.de/lehre/kuchen/JFLP/">JFLP</A>][10/'02]

%T Journal of Functional Programming
%D 1989...
%K Journal Functional Programming, jrnl, JFP, FP, lambda calculus,
   programming languages, http, HREF, www
%X [<A HREF="http://journals.cambridge.org/action/displayJournal?jid=JFP">at CUP</A>][2014],
   [<A HREF="http://titles.cambridge.org/journals/journal_catalogue.asp?mnemonic=jfp" TARGET="external">at CUP</A>][8/'02],
   [<A HREF="http://www.dcs.gla.ac.uk/jfp/" TARGET="external">at glasgow</A>][8/'02].
   Print, issn:0956-7968; Online issn:1469-7653.

%T Nature
%K Nature, biology, science, magazine, journal, jrnl, commercial, media,
   www, HREF, http, zz1095
%X <A HREF="http://www.nature.com/">[web page]</A>   (slow)
   - wasteful graphics;  '95 on

%T New Scientist
%K New Scientist, UK, science, magazine, journal, jrnl, commercial, media,
   www, HREF, http, zz1095
%X <A HREF="http://www.newscientist.com/">[web page]</A> (slow)
   - silly big Img map; why do they bother?
   wwweb column  -  `netropolitan', email: edit@news.newsci.ipc.co.uk
                     give  Netropolitan  in the subject line
   about '95 on.


%A Lloyd Allison
%T Home page
%D 1994
%K computer science, computing, CS, CSci, Monash, bibliography, bib,
   person, www, home page, HREF, http
%X [<A HREF="https://users.monash.edu.au/~lloyd/">LA home</A>]['23].
   [<A HREF="https://users.monash.edu.au/~lloyd/tildeBIB/">Bibliography</A>]'23].
   Disclaimer: use information at own risk, no liability accepted.

%A Ralph Nader
%T Essential Information
%D 1997
%K consumer protection, social issues, consumerism, politics, law, legal,
   business, antitrust, anti-trust, Microsoft, micro-soft, MS,
   topical, person, EI, www, HREF, http, org, zz1097
%X <A HREF="http://www.essential.org/EI.html">[web]</A>[10/'97]
   `Appraising Microsoft' Conference November 1997


%T A Mighty Girl
%D 2016
%K A Mighty Girl, mightygirl, girls, women, web, www, HREF, URL, http,
   role models, books, toys, zz0916
%X "... collection of books, toys, movies, and music for parents, teachers, and
   others dedicated to raising smart, confident, and courageous girls and, of
   course, for girls themselves ..."   (via BA.)
   -- [<A HREF="http://www.amightygirl.com/">www</A>][2016].

%T Australian Computer Society
%K ACS org .au, Australia
%X [<A HREF="http://www.acs.org.au/">acs.org.au</A>]['05]
   [Also see: CORE au]

%T Australian Genomic Information Centre
%D 1996
%K MolBio, Australia, genome, Biolgy, Biol, Bio, genetics,
   science, www, site, home page, HREF, URL, http, zz0496
%X "... ANGIS was closed at the end of 2009."
   -- [<A HREF="https://en.wikipedia.org/wiki/ANGIS">wikip</A>]['23].
   [<A HREF="http://www.angis.su.oz.au">[ANGIS web page]</A>][3/'96]

%T Australian National University
%D 1994
%K ANU, university, Canberra, ACT, Australia,
   Research School of Biological Sciences, RSBS, Biology, Bio Informatics,
      MolBio, Bio, Biol, Biology, science, Complex Systems, genetics,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://life.anu.edu.au/">ANU BioInformatics</A>

%T Australian Tax Office
%K ATO, tax, taxes, taxation, income, reform, GST, superannuation,
   super, superann, business, number, ABN, company, law, file, TFN,
   gov, au, www, site, page, HREF, URL, http
%X <A HREF="http://www.ato.gov.au">www.ato.gov.au</A> [4/2000]
   <A HREF="http://www.business.gov.au">www.business.gov.au</A> [4/2000]

%T The 1901 Census for England and Wales
%K Census, UK, England, Wales, Scotland, 1901, familysearch, records,
   genealogy
%X [<A HREF="http://www.1901census.nationalarchives.gov.uk/">1901census.nationalarchives.gov.uk</A>][2005]
   There is a charge to see individual records.
   "The 1881 and 1891 censuses are also available online
   [<A HREF="http://www.nationalarchives.gov.uk/census/">www.nationalarchives.gov.uk/census/</A>].
   You can also purchase CD-Roms with a name index to the 1881 census."
   Scotland: [<A HREF="http://www.scotlandspeople.gov.uk/">scotlandspeople.gov.uk</A>][2005]

%T CORE: COmputing Research and Education
%D 2004
%K CORE, Australian, .au, ACSC, computer science, CS, CSci, Comp Sci, ACSA,
   Australia, www,HREF,http
%X [<A HREF="http://www.core.edu.au/">core.edu.au</A>]['05] (Monash member c2005)
   [Also see: ACS au]

%T CSIRO
%D 1994
%K CSIRO, commonwealth, scientific, science, organization, Australia,
   mineral products, mine, mining, site, page, www, HREF, http
%X <A HREF="http://www.dmp.csiro.au">Division of Mineral Products</A>
   email: jluker@dmp.csiro.au  (11/'94)

%T Federal Department of Communications and the Arts
%D 1995
%K Government, gov, Australia, au, dca, InterNet, regulation, law, media,
   www, HREF, http, zz0895
%X <A HREF="http://www.dca.gov.au/">Dept. Comms. and the Arts</A>
   <A HREF="http://www.dca.gov.au/pubs.html">Publications</A>

%T Walter and Eliza Hall Institute, Melbourne
%D 1994
%K Hall, Victoria, Australia, WEHI, MolBio, Bio, Biol, Biology, science,
   institute, organization, www, site, page, information, HREF, URL, http,
   SRS, DNA, sequence, sequences
%X <A HREF="http://www.wehi.edu.au/">Walter and Eliza Hall home</A>
   <A HREF="http://srs.wehi.edu.au/srs/srsc">[seq' retrieval system]</A>

%T La Trobe University
%D 1994
%K LaTrobe, university, Melbourne, Victoria, Australia,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.latrobe.edu.au/">LA Trobe home</A>

%T Libraries
%K library, membership, jrnls, journals, scientific, research, books, ebooks,
   free, cheap, open, public, access, electronic, ejrnls, eresources, texts,
   HREF, www, http, arxiv, biorxiv, citeseer, Jstor, Plan S, PlanS, PLoS,
   pubmed, Sci Hub, SciHub, unpaywall, wikipedia, scholar, preprint server,
   paywall, paywalls, file sharing, pirate, Alexandra Elbakyan, copyright
%X National Library of Au[<A HREF="https://www.nla.gov.au/">www</A>]['20],
 * State Library of Vic[<A HREF="https://www.slv.vic.gov.au/search-discover/free-journals-databases-ebooks">www</A>]['19],
     Jstor, ProQuest, pressreader, 
     [<A HREF="https://login.ezproxy.slv.vic.gov.au/login?url=https://search.proquest.com/compscijour/fromDatabasesLayer?accountid=13905">more</A>]['19].
 * Cambridge U. Library [<A HREF="https://www.lib.cam.ac.uk/">www</A>]['20].
 ---------------------------------------------------------------------------
 * arxiv.org[<A HREF="https://arxiv.org/">www</A>]['19] preprint server,
     comp.sci[<A HREF="https://arxiv.org/corr">www</A>]['19],
     archive/cs[<A HREF="https://arxiv.org/archive/cs">www</A>]['19].
 * biorxiv[<A HREF="https://www.biorxiv.org/">www</A>]['19].
 * citeseer [<A HREF="http://citeseer.ist.psu.edu/">www</A>]['20].
 * Jstor[<A HREF="https://www.jstor.org/">www</A>]['20]
     "access to more than 12 million ac. jrnl articles, books ...".
 * PLoS [<A HREF="https://plos.org/">www</A>]['20] "an open access publ.".
 * pubmed[<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/">www</A>]['19].
 * Sci-Hub[<A HREF="https://sci-hub.tw/">www</A>]['20] (pirate access)
     (NB. *not* Sci-HuBeta).
 * unpaywall[<A HREF="http://unpaywall.org/">www</A>]['19] 
     "An open database of 25,621,121 free articles."
 * wikipedia[<A HREF="https://en.wikipedia.org/">www</A>]['19],
     ?wikipedia-library[<A HREF="https://wikipedialibrary.wmflabs.org/">www</A>]['19]
       "You have made a min. of 500 edits ... at least 10 ... last month"?,
     on open-access[<A HREF="https://en.wikipedia.org/wiki/Open_access">www</A>]['19],
     on Plan-S[<A HREF="https://en.wikipedia.org/wiki/Plan_S">www</A>]['20]
       "an initiative for open-access science publishing",
     on Sci-Hub[<A HREF="https://en.wikipedia.org/wiki/Sci-Hub">www</A>]'20].
 ---------------------------------------------------------------------------
 * google.scholar[<A HREF="https://scholar.google.com/">www</A>]['19].
 * [Also search for: research open access].

%T Melbourne University
%D 1994
%K Melbourne, university, Victoria, Australia, www, site, HREF, http
%X <A HREF="http://www.unimelb.edu.au/">Melbourne University</A>
      <A HREF="http://www.cs.mu.oz.au/">Comp Sci</A>

%T Monash University, Australia 3168
%D 1994
%K Monash, university, Clayton, Melbourne, Victoria, Australia,
   Department of Computer Science, CS, CSci, FCIT, FaCIT, computing,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.csse.monash.edu.au/">School Comp Sci & SW Eng</A>[1998]
   <A HREF="http://www.cs.monash.edu.au/">Dept of Comp' Sci'</A>[..1997]
   <A HREF="http://www.monash.edu.au/">Monash University</A>.

%T Monash Library Search
%K Voyager, Sesame, Sesame2, SesameII,
   Hargrave, book, books, search, www, HREF, http
%X <A HREF="http://www.lib.monash.edu.au/">[home]</A>      [4/1999]
   <A HREF="http://library.monash.edu.au/">[catalogue]</A> [4/1999]
   <A HREF="http://library.monash.edu.au/cgi-bin/Swebrecon?DB=local&PAGE=hbSearch">[author/title/subject search]</A> [4/1999]
   old: <A HREF="http://www.lib.monash.edu.au/wwwlib/">[wwweb]</A> [1997]

%T National Library of Australia
%D 1995
%K National, library, NLA, Australia, ACT, Canberra, government, organization,
   www, HREF, http, TROVE, archive, archives, pictures, images
%X [<A HREF="http://www.nla.gov.au/">NLA</A>][1995]
      [<A HREF="http://trove.nla.gov.au/">TROVE</A>][2011]

%T National Tertiary Education Union
%D 1997
%K NTEU, unions, university, www, HREF, http
%X <A HREF="http://www.edunions.labor.net.au/nteu/">[web]</A> [4/'97]

%T NTEU Monash Branch
%D 1997
%K NTEU, Monash University, Australia, edu, au, staff union,
    enterprise bargaining, zz0298
%X <A HREF="http://www-personal.monash.edu.au/~greg/monnteu.htm">[web]</A>[2/1998]

%T James Cook University
%D 1994
%K Queensland, jcu, university, Australia, Computer Science, CS, CSci,
   computing, www, site, page, information, HREF, URL, http
%X <A HREF="http://www.cs.jcu.edu.au/">CS JCU home</A>
   email: postmaster@cs.jcu.edu.au

%T Simprotect
%D 2023
%K Simprotect, zz0623, SIM card, protect, illegal, mobile phone transfer,
   porting, identity theft, criminal, fraud, scam, banking, Australia, OIAC,
   www, HREF, http
%X [<A HREF="https://www.simprotect.org.au/">simprotect</A>]['23],
   [<A HREF="https://www.simprotect.org.au/protecting-yourself">protecting</A>]['23].
   [<A HREF="https://www.idcare.org/fact-sheets/credit-reports-australia">credit-reports</A>]['23].

%T Charles Sturt University
%D 1995
%K Sturt, University, Australia, site, page, information,
   www, HREF, http
%X <A HREF="http://www.csu.edu.au/">CSU home</A>

%T University of Sydney
%D 1997
%K Sydney, Basser Dept Computer Science, Comp Sci, CSci,
   www, site, page, HREF, URL, http
%X <A HREF="http://www.cs.su.oz.au/">[web]</A>[11/1997]

%T University of Western Australia
%D 1994
%K WA, UWA, university, Nedlands, Perth, 6009, Australia, Computer Science,
   CS, CSci, computing, www, site, page, information, HREF, URL, http
%X <A HREF="http://www.cs.uwa.edu.au/">CS UWA home</A>

%T National Parks, Western Australia
%D 1996
%K WA, gov, au, west, Australian, conservation and land management, CALM, park,
   www, site, HREF, http, zz0996
%X <A HREF="http://www.calm.wa.gov.au/national_parks/index.html">[NatParks]</A>
   <A HREF="http://www.calm.wa.gov.au/">[CALM]</A>
   [9/'96]

-------------------------------------------------------------------------------

%T Birkbeck College, London University
%D 1994
%K Birkbeck, University of London, England, UK, Europe,
   Computer Science, CS, CSci, computing, database languages,
   Crystallography, MolBio, Bio, Biol, Biology, protein, MHC,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://web.dcs.bbk.ac.uk/">Birkbeck home</A>
   <A HREF="http://www.cryst.bbk.ac.uk/">Cryst Birkbeck home</A>

%T The British Library
%D 1995
%K British Library, BL, National, museum, history, Magna Carta,
   London, England, UK, Europe, online, institution,  www, site, HREF, http
%X <A HREF="http://www.bl.uk/">[www.bl.uk</A> [12/1998]
   <A HREF="http://icarus.bl.uk/">[Portico]</A> [10/'96]
   <A HREF="http://icarus.bl.uk/nbs/catalist.html">catalogues</A> [10/'96]
   ... external access is for the most part subject to commercial terms ...

%T University of Cambridge, England
%D 1993
%K Cambridge, university, England, UK, Europe,
   Computer Laboratory, Lab, CL, CS, CSci, computer science, computing,
   TR, Pegasus,    School Biological Sciences, Bio, Biol, Biology,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.cl.cam.ac.uk/">Comp. Lab. home</A>
      <A HREF="ftp://ftp.cl.cam.ac.uk/papers/index.html">published papers</A>
      <A HREF="ftp://ftp.cl.cam.ac.uk/papers/reports/index.html">tech repts</A>
      <A HREF="http://www.cl.cam.ac.uk/users/mjcg/Research94/Research94.html">postgrad' info'</A> [5/'95]
   <A HREF="http://www.bio.cam.ac.uk/">Biol. Sci.</A>

%T Cambridge University Press
%K CUP, press, books, publisher, publishing, www, HREF, http
%X <A HREF="http://www.cup.cam.ac.uk/">CUP</A>

%T Sanger Centre
%K Cambridge, Sanger Centre, Center, organization,
   England, UK, Europe, British Medical Research Council, BMRC, MRC,
   European BioInformatics Institute, EBI, Bio Informatics,
   MolBio, Bio, Biol, Biology, science,
   www, site, page, information, HREF, URL, http
%X [<A HREF="http://www.sanger.ac.uk/">Sanger home</A>]
     [<A HREF="http://www.sanger.ac.uk/Software/">Software/</A>][10/'00]
   [<A HREF="http://www.ebi.ac.uk/">EBI home</A>][Sept '94 ?]
   (see also EMBL)

%T University of Wales College at Cardiff
%D 1994
%K Cardiff, university, Wales, UK, Europe,
   Department of Computing Mathematics, Maths, Computer Science, CS, CSci,
      COMMA, course, lecture, notes courseware, C, CC, X-Windows, AI,
   interesting, impressive,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.cs.cf.ac.uk/">Comp Sci</A>
   <A HREF="http://www.cs.cf.ac.uk/Teaching/">CS Lecture Notes</A>[3/'97]

%T Daresbury Laboratory
%D 1994
%K Daresbury, organization, England, UK, Europe, High Energy Physics,
   Computing, BioInformatics, Informatics, Bio, Biol, Biology, science,
   SEQNET, EMBnet, MolBio, CBMT, Collaborative Biomolecular Tools, Software,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.dl.ac.uk/">Daresbury home</A>
   <A HREF="http://www.dl.ac.uk/SEQNET/home.html">SEQNET</A>
   <A HREF="http://www.dl.ac.uk/CBMT/HOME.html">CBMT home</A> and subpages
   Collaborative  BioMolecular Tools is  a new venture in making software
   easier to develop and more reusable.  It's founded on the premise that
   the Biomolecular community is collaborative by nature and would like
        *A Biomolecular C++ class library
        *A library of filters/scripts (e.g. *.csh, *.tcl, *.com, etc)
        *GUI components (e.g. tcl/tk, and possibly some GUI's)
        *Reference data for file formats and other standards
        *CIF's and their use both in crystallography and elsewhere
        *Reference data (e.g. Atomic data, Amino Acid properties)
   <!-- email: ajb@s-crim1.dl.ac.uk     (8/'94) --> .

%T Edinburgh University, Scotland
%K Edinburgh, university, Scotland, UK, Europe,
   DCS, Computer Science, CS, CSci, computing,
      functional programming, FP, Standard ML, SML,
      Laboratory for Foundations of CS, LFCS,  CCS, pi calculus pi-calculus,
   DAI, Artificial Intelligence, AI,
   Cognitive Science, cogsci,
   TR, report, reports, www, site, page, information, HREF, URL, http
%X [<A HREF="http://www.inf.ed.ac.uk/" TARGET="EXTERNAL">Informatics</A>][11/'03]
     [<A HREF="http://www.inf.ed.ac.uk/research/cisa/" TARGET="EXTERNAL">Centre for Intelligent Systems and their Applications</A>][11/'03]
     [<A HREF="http://www.inf.ed.ac.uk/research/lfcs/" TARGET="EXTERNAL">Lab' for Foundations of Computer Science</A>][11/'03]
     ...

%T Glasgow University
%D 1993
%K Glasgow, university, Scotland, UK, Europe,
   Computer Science, CS, CSci, computing,
      Functional Programming language, FP, Haskell, Gofer,
   www, site, page, information, HREF, URL, FTP
%X <A HREF="http://www.dcs.gla.ac.uk/">DCS Glasgow</A>
   <A HREF="http://www.dcs.gla.ac.uk/fp/">functional programming</A>    [2/'96]
 old links:
   <A HREF="http://www.dcs.glasgow.ac.uk/">DCS Glasgow</A>
   <A HREF="ftp://ftp.dcs.glasgow.ac.uk/pub/glasgow-fp/glasgow-fp.html">Glasgow FP</A>

%T Royal Holloway College, London University
%D 1998
%K Holloway and Bedford New, RH, RHBNC, RHNBC, London, England, UK, Europe,
   Department of Computer Science, Support Vector Machines, Method, SVM,
   www, site, page, HREF, http
%X <A HREF="http://www.cs.rhbnc.ac.uk/">CompSci</A> [6/2000]
      <A HREF="http://www.clrc.rhbnc.ac.uk/research/SVM/">Support Vector Machines</A>[6/2000]
   <A HREF="http://www.rhbnc.ac.uk/">College</A> [7/1998]

%T Imperial College, London University
%D 1994
%K Imperial, college, university, IC, London, England, UK, Europe,
   Department of Computing, DOC, CS, CSci, computer science,
      functional programming, FP, logic, LP, Hope, Hope+, language, archive,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.doc.ic.ac.uk/">Dept. Computing, Imperial home</A>
   <A HREF="http://src.doc.ic.ac.uk/">SunSITE N. Europe Archive</A>
      <A HREF="http://src.doc.ic.ac.uk/public/ic.doc/ALA/papers/R.Paterson/">Hope by Ross Paterson</A>
      There is even a html Form to run Hope.

%T London and South East Centre for High Performance Computing Archive
%D 1994
%K London, organization, SEL SE HPC, centre, center, England, UK, Europe,
   computing, archive, bib, bibliography,
   functional programming, FP,
   parallel concurrent, multi-processor, NN, ANN,
   www, site, page, information, HREF, URL, http, ftp
%X <A HREF="http://www.lpac.ac.uk/SEL-HPC/Articles/index.html">HPC Archive</A>
   <A HREF="http://www.lpac.ac.uk/SEL-HPC/Articles/FuncArchive.html">FP arch'</A>
   <A HREF="http://www.lpac.ac.uk/SEL-HPC/Articles/FuncAdd.html">add articles</A>
   <A HREF="http://www.lpac.ac.uk/SEL-HPC/Articles/">other archives</A>
   Jonathan M. D. Hill    (7/'94)

%T Manchester University, England.
%D 1994
%K Manchester, university, England, UK, Europe,
   Department of Computer Science, computing, CS, CSci, MU, MU5,
   data flow dataflow,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.cs.man.ac.uk/">Comp. Sci. Manchester</A>

%T The Numerical Algorithms Group Ltd
%D 1994
%K NAG, computing, computer, Oxford, England, UK, Europe,
   numerical algorithm, Fortran, Fortran90, F90,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.nag.co.uk:70/">NAG home</A>

%T National Institute for Medical Research
%D 1994
%K National, nimr, mrc, institute, organization, England, UK, Europe,
   medicine, medical, council, bio, biol, biology, MolBio, science,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.nimr.mrc.ac.uk/">Medical Research Council (UK)</A>
   The Home Page includes information about MRC Institutes and Units,
   Interdisciplinary Research Centres, and about other UK Research
   Councils.  Hyperlinks are provided where available.
   Frank Norman,  (1/'95)
      Deputy Librarian, National Institute for Medical Research,
      The Ridgeway, Mill Hill, London NW7 1AA
   <A HREF="http://nimsn41.nimr.mrc.ac.uk/">NIMR</A> (under const'n 9/'94)

%T Open University
%D 1995
%K Open University, TV, distance education, England, UK, Europe,
   www, HREF, http,
%X <A HREF="http://www.open.ac.uk/">Open University</A>

%T Oxford University
%D 1994
%K Oxford, university, England, UK, Europe,
   Computing Laboratory, comlab, cl, CSci, CS, computer science,
      Programming Research Group, PRG, TR,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.comlab.ox.ac.uk/">O. U. Comp Lab home</A>
   <A HREF="http://www.comlab.ox.ac.uk/oucl/publications/">Comp Lab publns</A>
   <A HREF="http://www.comlab.ox.ac.uk/oucl/publications/tr.html">PRG TRs</A>

%T Oxford University Press
%D 1995
%K Oxford, press, publisher, publishing, books, OUP, www, HREF, http
%X [<A HREF="http://www.oup.co.uk/">OUP</A>]['95]

%T University College, London
%D 1994
%K UCL, university, London, England, UK, Europe,
   Computer Science, CS, CSci,
      tour, tourist, guide, interactive, map, interesting, impressive,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.cs.ucl.ac.uk/">Comp. Sci. UCL home</A>
   See the tour of London.

%A M. Amos
%T Warwick University
%D 1994
%K Warwick, university, England, UK, Europe,
   Computer Science, CSci, CS, computing, Genetic Algorithm, GEARS, GA,
   www, site, page, information, HREF, URL, http
%X references were obtained from the extensive collection of bibliographies
   that form part of the GEARS (GEnetic Algorithms Research Students)
   mailing list archive. The GEARS archive may be accessed either
   <A HREF="http://www.dcs.warwick.ac.uk/~martyn/ga.html">GEARS (2/95)</A>
   <A HREF="ftp://ftp.dcs.warwick.ac.uk/">dcs warwick ftp</A>
       (137.205.224.1) /pub/gaphd/Bibliographies
   via: Martyn Amos = martyn@dcs.warwick.ac.uk =  Parallel Computation Group,
        email: martyn@alife.santafe.edu  =  Department of Computer Science,
          (Santa Fe Institute)   =  University of Warwick, Coventry, UK

%T University of York
%D 1994
%K York, university, England, UK, Europe,
   Computer Science, CSci, CS, computing, functional programming, FP,
   www, site, page, information, HREF, URL, http
%X [<A HREF="http://www.york.ac.uk/">York home page</A>][2/'03]
      [<A HREF="http://www.cs.york.ac.uk/">Comp Sci</A>][2/'03]

-------------------------------------------------------------------------------

%T Genethon
%D 1994
%K Genethon, Human Genome Centre, Center, organization, France, Europe,
   MolBio, Biol, Biology, science, Bio Informatics, BioInformatics,
   DNA, genetics, protein, HUGO,
   www, site, page, information, HREF, URL, http
%X [<A HREF="http://www.genethon.fr/">Genethon home</A>][5/'03]
      [<A HREF="http://www.genethon.fr/php/index_us.php">english</A>][5/'03]

%A N. Pioch
%T WebMuseum network
%D 1994
%K Paris, France, Europe, FR, Telecom, organization, enst,
   Louvre, tour, tourist, art gallery, painting, impressionist,
   interesting, impressive,
   www, site, page, information, HREF, URL, http, zz0895
%X <IMG SRC="/~lloyd/tildeImages/Art/Manet.Olympia.small.gif" ALIGN="right">[<A HREF="http://www.ibiblio.org/wm/">ibiblio.org</A>]['00]
   [<A HREF="http://sunsite.doc.ic.ac.uk/wm/">Imperial Coll UK</A>]['00]
   [<A HREF="http://www.netspot.unisa.edu.au/wm/">Univ. of S.A.</A>]['95 not '00 ?]
   [<A HREF="http://mistral.enst.fr/">ENST home</A>] (original)
   Used to be "just" the Louvre tour,
   now it's generalizing [8/'95]
   <BR CLEAR="all">

%T Pasteur Institute
%D 1995
%K Pasteur Institute, France, Europe, MolBio, biology, bio, biol, science,
   page, site, information, www, URL, HREF, http, zz0595
%X <A HREF="http://www.pasteur.fr/">French</A>
   <A HREF="http://www.pasteur.fr/welcome-uk.html">English</A>
   <A HREF="http://www.pasteur.fr/other/biology/francais/rubriques-fr.html">topics (French)</A>
   <A HREF="http://www.pasteur.fr/other/biology/english/rubriques-uk.html">topics (English)</A>
   Catherine LETONDAL <!-- email: letondal@pasteur.fr --> [5/'95]

-------------------------------------------------------------------------------

%T Universitat Bielefeld
%D 1994
%K Bielefeld, Germany, Europe, de, University, techfak,
      Fuellen, biocomputing course, MolBio, BioMoo,
   www, site, page, information, HREF, URL
%X [<A HREF="http://www.techfak.uni-bielefeld.de/">uni-bielefeld.de</A>][5/'03]
      [<A HREF="http://www.techfak.uni-bielefeld.de/techfakengl.html">english</A>][5/'03]
      [<A HREF="http://cweb.uni-bielefeld.de/agbi/home/">bioinformatics</A>][5/'03]

%T German National Centre for Computer Science,
   GMD Machine Learning Archive
%D 1994
%K GMD, Germany, Deutschland, Europe, center, centre, organization, archive,
   artificial intelligence, AI, machine learning, inductive inference, II,
   computing, Esprit, MLT, MLnet, Golem, ILP, ILPnet,
   www, site, page, information, HREF, URL, FTP
%X <A HREF="ftp://ftp.gmd.de:/MachineLearning">GMD Machine Learning</A>
   email: ml-archive@gmd.de

%T European Molecular Biology Laboratory,
   Heidelberg
%D 1994
%K Heidelberg, organization, EMBL, Germany, Europe,
   MolBio, Biol, Biology, science, Bio Informatics, BioInformatics,
   DNA, gene, genetics, protein, genome, HUGO, software,
   www, site, page, information, HREF, URL, http, FTP
%X <A HREF="http://www.embl-heidelberg.de/">EMBL home</A>
      ftp server under "network and www services":
      <A HREF="file://ftp.embl-heidelberg.de/">FTP EMBL</A>

%T Lehrstuhl Informatik fuer Ingenieure und Naturwissenschaftler,
   University of Karlsruhe,
%D 1994
%K Karlsruhe, university, Germany, Deutschland, Europe, ira, uka, de,
   computing, www, site, page, information, HREF, URL, ftp
%X <A HREF="http://www.ira.uka.de/">Informatik</A>

%T Max Planck Institut fuer Informatik
%D 1994
%K Max Planck, institute, Saarbrucken, Germany, Europe,
   Computer Science, CS, CSci, computing, Institute for, mpi,
      Programming Logics, Logic, LP,  M. Hanus,
   www, site, page, information, HREF, URL
%X <A HREF="http://www.mpi-sb.mpg.de/">MPI home</A>

-------------------------------------------------------------------------------

%T Chalmers University of Technology - University of Gothenburg.
%K Goteborg, Chalmers, university, Sweden, SE, Europe,
   Computer Science, CS, CSci, computing,
      Functional Programming, language, FP, Lazy ML, LML, Haskell,
   www, site, page, information, http, HREF, URL
%X [<A HREF="http://www.chalmers.se/Home-E.html">Chalmers home</A>][12/'03]
   [<A HREF="http://www.gu.se/English/default.html">Goteborg home</A>][12/'03]
      [<A HREF="http://www.cse.chalmers.se/doit/doiteng/">CSci Chalmers</A>][12/'03]
   [<A HREF="http://www.hum.gu.se/gu/gu.html">Goteborg home</A>]['94]
      [<A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A>]['94]

-------------------------------------------------------------------------------

%T Swiss Institute of Bioinformatics
%K ISB SIB, Swiss, Switzerland, ch, Europe, MolBio, bioinformatics, genome,
   swiss prot, protein, swissprot, prosite, ExPASy, database data base,
   www, site, page, URL, http, HREF
%X [<A HREF="http://www.isb-sib.ch/">isb-sib</A>][8/'00]
   [<A HREF="http://www.expasy.ch/">ExPASy</A>] Expert prot' anal' sys
     [<A HREF="http://www.expasy.ch/sprot/">s-prot</A>]
     [<A HREF="http://www.expasy.ch/prosite/">prosite</A>]
       [<A HREF="http://expasy.proteome.org.au/sprot/">s-prot (.au)</A>]

%T Basel University
%K Basel, university, Switzerland, Swiss, ch, Europe,
   Biocomputing, Computing, BioInformatics, Informatics, embnet,
      MolBio, Bio, Biol, Biology, science, software, Archive, bionet,
   newsgroup, www, site, page, information, URL, http, HREF
%D 1994
%X [<A HREF="http://www.ch.embnet.org/">ch.embnet.org</A>][5/'03]

%T University of Geneva
%D 1994
%K Geneva, university, Switzerland, Swiss, ch, Europe,
   Centre Universitaire d' Informatique, CUI, unige, computing,
      programming language, PL, languages, list,
   www, site, page, information, HREF, URL
%X <A HREF="http://cuiwww.unige.ch/">CUI home</A>
      see the programming-language list (huge):
      <A HREF="http://cuiwww.unige.ch/langlist">language list</A>

%T CERN
%D 1994
%K Geneva, CERN, organization, Switzerland, Swiss, ch, Europe,
      High Energy Particle Physics, science, Centre, Center,
   www, site, page, information, HREF, URL
%X <A HREF="http://www.cern.ch/">CERN home</A> - birthplace of www.

%T International Organization for Standardization
%D 2001
%K ISO, IEC, Organisation, Standardisation, Standards, programming language,
   ISO9899, 9899 1999, C, CC, gcc, ISO7185, 7185 1990, Pascal,
   web, site, home, page, information, www, http, HREF, ch, IOS, zz0601
%X [<A HREF="https://www.iso.org/">www</A>]['23]
   [<A HREF="https://www.iso.org/standards.html">standards</A>]['23].
   Was [<A HREF="http://www.iso.ch/">www</A>][6/'01]
       [<A HREF="http://www.iso.ch/iso/en/prods-services/catalogue/intstandards/CatalogueListPage.CatalogueList">standards</A>].
      (look under IT (35), Languages (35.060) )
   e.g. 1999 C standard ISO/IEC 9899:1999
   e.g. 1990 Pascal standard ISO 7185:1990
  and [<A HREF="http://www.standards.com.au/">standards.com.au</A>][6/'01]
	AS 3955-1991 == ISO/IEC 9899 1990  [yes 1991 and 1990]
	Draft DR 99511 CP on `C' == ISO/IEC 9899:1998  (drafts are free)

-------------------------------------------------------------------------------

%A Yasuhiko Higaki
%T Chiba University
%D 1994
%K Chiba, university, Japan, jp, Asia,
   music, renaissance, consort, instrument, sound, snd, audio,
   interesting, www, site, page, information, HREF, URL, http
%X <A HREF="http://www.hike.te.chiba-u.ac.jp/">Elec Eng Chiba home</A>
   <A HREF="http://www.hike.te.chiba-u.ac.jp/cons1/">Renaissance consort</A>

-------------------------------------------------------------------------------

%T University of Arizona
%D 1994
%K Arizona, university, USA,
   Computer Science, CS, CSci, computing,
      Icon, SR, string, symbolic, programming language,
   www, site, page, information, HREF, URL, http, FTP
%X <A HREF="http://www.arizona.edu/">Arizona home</A>
   <A HREF="http://www.cs.arizona.edu/">Comp. Sci. Arizona home</A>
      see Icon and Snobol in the FTP area

%T BioMolecular Engineering Research Center
%D 1994
%K Boston, USA, bmerc, center, centre, MolBio, bio, biol, biology, science,
   www, HREF, http
%X <A HREF="http://bmerc-www.bu.edu/">BMERC</A> at Boston University

%T Brigham Young University
%D 1994
%K Brigham Young, university, BYU, Utah, USA,
   Computer Science, CS, CSci, computing,
      course, lecture, notes, courseware, online,
         P. Windley, Concepts of Programming Languages, Paradigms,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.cs.byu.edu/">CS BYU home</A>
      see the Dept resources, online class information:
      <A HREF="http://www.cs.byu.edu/info/online.html">Online course information</A>

%T University of California, Berkeley
%D 1994
%K California, Berkeley, university, ucb, USA,
      Museum of Paleontology, science, Dinosaur, interesting,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.berkeley.edu/">Berkeley home</A>

%T University of California, Irvine
%D 1994
%K California, Irvine, university, UCI, USA,
   Computer Science, CS, CSci, ICS, computing,
   Artificial Intelligence, AI, machine learning, repository, MLR, FOCL, HYDRA,
   www, site, page, information, HREF, URL, http
%X The Machine Learning group of the Department of Information and
   Computer Science at the University of California - Irvine:
   <A HREF="http://www.ics.uci.edu/AI/ML/Machine-Learning.html">UCI.M.Learn</A>
   From here you can access UCI's repository of databases for machine learning
   research, digests of the Machine Learning List, programs (FOCL, Occam, and
   HYDRA) developed at UCI, and papers by authors from UCI.
   correspondence to Tim Hume, UC, Irvine       (7/'94)
   email: hume@ics.uci.edu

%T University of California at San Francisco
%D 1993
%K California, San Francisco, UCSF, university, USA,
   The Visible Embryo Project, embryology, bio, biol, biology, science,
      visualisation, visualization, mpeg,
   interesting, impressive, www, site, page, information, HREF, URL, http
%X <A HREF="http://visembryo.ucsf.edu/">Visible Embryo</A> is the home page
   for the Visible Embryo Project and has a MPEG movie of a reconstructed
   embryo. (Resolution had to be dropped to fit the MPEG format).
   via: <!-- email: toni@athe.wustl.edu --> (Toni Kazic)      (7/'94)

%T University of California at Santa Cruz
%D 1994
%K California, Santa Cruz, UCSC, university, USA,
   computer engineering information science, cse, CS, CSci, computing,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.ucsc.edu/">UCSC home</A>
   <A HREF="http://www.cse.ucsc.edu/">CSE UCSC home</A>

%T Computer Science, Carnegie Mellon University
%D 1994
%K Carnegie Mellon University, CMU, USA,
   CSci, Computer Science, computing,
      programming language research, languages,
      Artificial Intelligence, AI, machine learning, repository, archive,
   Statistics, stats, StatLib, inductive inference,
   www, site, page, information, HREF, URL, http, FTP
%X <A HREF="http://www.cmu.edu/">CMU home</A>
   <A HREF="http://www.cs.cmu.edu/scs/scs.html">School of Comp Sci</A>
     <A HREF="http://www.cs.cmu.edu/csd/index.html">Dept. of Comp Sci</A>
       Anonymous ftp: ftp.cs.cmu.edu [128.2.206.173]   cd /user/ai
       <A HREF="ftp://ftp.cs.cmu.edu/user/">CSci ftp</A>
       <A HREF="http://www.cs.cmu.edu/groups/pop/pop.html">Princ' of P' L'</A>
       <A HREF="http://www.cs.cmu.edu/groups/ml/ml.html">Mach' Learning</A>
       <A HREF="http://www.cs.cmu.edu/Web/Groups/AI/html/repository.html">CMU A.I. Repository</A>
   <A HREF="http://lib.stat.cmu.edu/">StatLib Index</A>

%T University of Colorado
%D 1994
%K Colorado, Boulder, university, USA, Computer Science, CS, CSci, computing,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.cs.colorado.edu/">CS Colorado home</A>

%T Cornell University
%D 1994
%K Cornell, university, USA, Computer Science, CS, CSci, computing,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.cs.cornell.edu/">Cornell CSci home</A>

%T Federal Aviation Authority (USA)
%D 1997
%K FAA, fear of flying, planes, air safety, government, gov, regulation,
   US, USA, www, site, page, HREF, URL, http, zz0297
%X <A HREF="http://www.faa.gov/">FAA</A> [2/'97]

%T Harvard University
%D 1994
%K Harvard, university, USA, www, site, page, information, HREF, URL, http
%X <A HREF="http://golgi.harvard.edu/harvard.html">Harvard home</A>

%T The John Hopkins University
%D 1993
%K Hopkins, John Hopkins University, USA,
   BioInformatics, Bio Informatics, science,
      MolBio, Biol, Biology, DNA, protein, gene, genome, HUGO, HGN, gdb, OWL,
   www, site, page, information, HREF, URL, http
%X [<A HREF="http://gdbwww.gdb.org/">GDB</A>][5/'03]
   Johns Hopkins University Computational Biology system at gopher:
   gopher.gdb.org [see HGN 5(3):8 (September 1993)].
   [see HGN 5(6):1-3 (March 1994)].
   <!-- email: MARTINSA@IRAVX2.HSRD.ORNL.GOV --> (7/'94)

%T Indiana University
%D 1994
%K Indiana, university, USA,
   Music, internet,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.music.indiana.edu/">Music Indiana home</A>
   Pointers to lots of internet resources on music.

%T Iowa State University
%D 1994
%K Iowa, university, USA,
   Chemical Engineering,
      MolBio, Pedro, Pedros, Pedro's, research tools,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.public.iastate.edu/">Iowa home</A>
   <A HREF="http://www.public.iastate.edu/~pedro/homepage.html">Pedro home</A>
   <A HREF="http://www.public.iastate.edu/~pedro/research_tools.html">Pedro's research tools</A>

%T Lawrence Livermore National Laboratory
%D 1995
%K Lawrence Livermore, LLNL, organization, USA, www, site, HREF, http
      genome, hugo, MolBio, biology, computing, science
%X [<A HREF="http://www.llnl.gov/">llnl.gov</A>][5/'03]
      [<A HREF="http://bbrp.llnl.gov/bbrp/bbrp.homepage.html">llnl.gov/brp</A>][5/'03]

%T Library of Congress
%D 1994
%K Library Congress, organization, USA, www, site, HREF, http
%X <A HREF="http://lcweb.loc.gov/homepage/lchp.html">Library</A>

%T Massachusetts Institute of Technology
%D 1994
%K Massachusetts, MIT, university, USA,
   Artificial Intelligence Laboratory, AI,
   Computer Science, CS, CSci, computing,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.ai.mit.edu/">A.I. MIT home</A>
   <A HREF="http://www.lcs.mit.edu/">CSci MIT home</A>

%A T. Munzner
%A S. Levy
%A M. Phillips
%T University of Minnesota, Visualization
%D 1994
%K Minnesota, University of Minnesota, UMN, USA,
   Geomview, Geometry Centre Center, graphics, visualization, visualization,
   computing, www, site, page, information, HREF, URL, http
%X <A HREF="http://www.geom.umn.edu/docs/software/viz/geomview/geomview.html">visualization</A>
   visualization package
   via: <!-- email: toni@athe.wustl.edu --> (Toni Kazic)      (7/'94)

%T National Aeronautics and Space Administration
%D 1994
%K National Aeronautics, organization, NASA, AMES, USA,
   www, site, page, information, HREF, URL, http,
   Biocomputation Center, Centre, biocomp, biocomputing, biology,
   RNR visualization, graphics
%X <A HREF="http://www.arc.nasa.gov/">NASA Ames home</A>
   <A HREF="http://biocomp.arc.nasa.gov/">biocomp.arc.nasa.gov</A>
   <A HREF="http://www.nas.nasa.gov/RNR/Visualization/annotatedURLs.html">visualization</A>
      Web tour of visualization work, software and demos
      via: <!-- email: toni@athe.wustl.edu --> (Toni Kazic)      (7/'94)

%T The National Center for Genome Resources
%W Santa Fe, NM
%D 1994
%K National Center Genome, centre, Santa Fe, USA, science, MolBio,
   DNA, HUGO, map, mapping, ncgr, GSDB, SIGMA, www, site, page, HREF, http
%X <A HREF="http://www.ncgr.org">Genome Resources</A>
   This server currently includes pages for both the Genome Sequence Data
   Base (GSDB) and SIGMA (System for Integrated Genome Map Assembly).
   The National Center for Genome Resources, 1800 Old Pecos Trail,
   Santa Fe, NM 87505, USA.   tel: (505) 982-7840   fax: (505) 982-7690
   email: ncgr@ncgr.org

%T National Center for BioInformatics,
   National Library of Medicine,
   National Institutes of Health, USA.
%D 1994
%K National Institutes of Health, institute, Washington, USA, NCBI, NLM, NIH,
   MolBio, Biol, Biology, science, Computing, Computational, Bio Informatics,
   center, centre, gene, genetics, GenBank, Blast, genome, HUGO, profiles,
   scientists, bib, bibliography, Entrez, MedLine,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.nih.gov/">NIH home</A>
   <A HREF="http://www.nlm.nih.gov/">NLM home</A>
   <A HREF="http://www.ncbi.nlm.nih.gov/">NCBI home</A>
      see  Searching GenBank / Entrez Browser / MedLine
   <A HREF="http://www.ncbi.nlm.nih.gov/BRB/Bib/index.html">NCBI staff bib</A>
   <A HREF="http://www.profiles.nlm.nih.gov/">Profiles in Science</A> [9/1998]

%T New York University
%D 1994
%K New-York, NYU, university, USA,
   Medicine, Medical, science, Bio, Biol, Biology,  NIH Guide, NIH-Guide,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://www.med.nyu.edu/nih-guide.html">NIH-Guide</A>
   <A HREF="http://www.med.nyu.edu/">med.nyu home</A>
   via: Ross Smith,  Research Computing Resource,                  (7/'94)
        Department of Cell Biology, NYU-MC
        <!-- email: SMITH@MCCLB0.MED.NYU.EDU --> .

%T Santa Fe
%D 1994
%K Santa Fe Institute, SantaFe, USA,
   Artificial Life, ALife, AI, complex systems, computing,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://alife.santafe.edu/">Santa Fe home</A>

%T Smithsonian Institution
%D 1995
%K Smithsonian, Washington DC, USA, museum, institute, www, HREF, http
%X <A HREF="http://www.si.edu/">Smithsonian</A>
   <A HREF="http://ceps.nasm.edu:2020/NASMpage.html">Nat'l Air and Space</A>

%T Stanford University
%K Stanford, university, USA,
   Computer Science, CS, CSci, computing,
      SIFT, netnews, net news, enews, filter, server, filtering,
   www, site, page, information, HREF, URL, http
%X The Stanford Netnews Filtering Service:
   <A HREF="http://woodstock.stanford.edu:2000/">Stanford News Filter</A>
   will allow you to construct filters to search Usenet on a
   regular basis for keywords of your choice,and you receive a synopsis of the
   hits via e-mail for you to pursue.
   via: R. Andrew Harper Center for Scientific Computing, Tietotie 6,
        P.O. Box 405,  (8/'94) SF-02101 Espoo Finland,
        <!-- email: harper@convex.csc.fi --> .
        <!-- Molbio/software: harper@nic.funet.fi --> .

%T University of Texas at San Antonio,
%W San Antonio, Texas 78249 , USA
%D 1994
%K Texas, UTSA, University of Texas, San Antonio, USA,
   Computer Science, CS, CSci, computing,
      High Performance Computing and Software Laboratory, HPCSL, HPC, parallel,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://rabbit.cs.utsa.edu/Welcome.html">CS.UTSA</A>
   The technical reports can also be accessed through anonymous ftp:
   dragon.cs.utsa.edu (129.115.10.42), under pub directory.
   <A HREF="ftp://dragon.cs.utsa.edu/pub/">HPCSL FTP</A>
   email: hpcs@dragon.cs.utsa.edu    (7/'94)

%E B. H. Dunford-Shore
%E F. Fabrizio
%E J. Holcomb
%E W. Wise
%E T. Kazic
%T Washington University, IBC, St. Louis, USA
%D 1993
%K Washington, Saint St. Louis, university, wustl, USA,
   Institute of Biomedical Computing, IBC,
      MolBio, biology, biol, bio, biochem, science,
      HHS, klotho, biochemical compound, database,
   www, site, page, information, HREF, URL, http
%X <A HREF="http://ibc.wustl.edu/klotho/">Klotho</A> gets you to Klotho.
   For the IBC home page, on which David is going to mount the HHS stuff:
   <A HREF="http://ibc.wustl.edu/">IBC home</A>.
   We have pointers to NCBI etc from there (Remote Biomedical HTTP etc).
   Also check out the Hopkins site; see OWL.
   via: <!-- email: toni@athe.wustl.edu --> (Toni Kazic)      (7/'94)

%T University of Washington, Seattle
%K Washington, university, Seattle, USA,
   Computer Science and Engineering, CS, CSci, computing,
      Weird Programming Language, Languages, Cecil,
   Genetics, Joe Felsenstein,
      MolBio, bio, biol, evolution, transition, transversion,
      PHYLIP, software, bibliography of population genetics, bionet,
   www, site, information, HREF, URL, FTP
%X [<A HREF="http://www.cs.washington.edu/">CSci Washington home</A>]['07] Sleepless in Seattle,
      [<A HREF="http://www.cs.washington.edu/research/research-samples/weird.html">Weird Programming Languages</A>]['94]
   [<A HREF="http://evolution.genetics.washington.edu/">Evoln genetics</A>]['07]

%T The Marine Biology Laboratory, Woods Hole
%D 1994
%K Woods Hole, MBL, USA, marine biology, bio, biol, MolBio, organization,
   institute,  science, www, site, page, information, HREF, URL, http
%X <A HREF="http://www.mbl.edu/">MBL home</A>

%T Yale University
%K Yale, university, USA,
   Computer Science, CS, CSci, computing,
      functional programming, FP, Haskell, hbc, Gofer, implementation,
      Linda, parallel, concurrent, language,
   www, site, page, information, HREF, URL, http, FTP
%X [<A HREF="http://www.cs.yale.edu/">CSci Yale</A>][12/'03]
   [<A HREF="http://www.cs.yale.edu/HTML/YALE/CS/FrontDoor.html">CSci Yale</A>]['94]
   [<A HREF="http://www.cs.yale.edu/HTML/YALE/CS/haskell/yale-fp.html">FP Yale</A>]['94]
   email: haskell-request@cs.yale.edu          (8/'94)

-------------------------------------------------------------------------------

%T British High Commission, Australia
%D 1997
%K British, Britain, BIS, BISA, UK, England, Europe, embassy, visa, permit,
   site, gov, au, www, HREF, http
%X <A HREF="http://www.uk.emb.gov.au/">[web]</A>[12/'97]

-------------------------------------------------------------------------------

%T The Global Network Academy
%D 1994
%K Global, GNA, virtual university, school, course, courseware, online,
   www, page, information, HREF, URL, http
%X <A HREF="http://uu-gna.mit.edu:8001/uu-gna/index.html">Global Network Academy</A>

%T IEEE
%D 1995
%K IEEE, computing, institute, organization, www, HREF, http
%X <A HREF="http://www.ieee.org/">IEEE</A>

%T Linux
%D 1994
%K Linux, Unix, computing, computer operating system, intel, pentium,
   OS, OP, Sys, PC, WINE, microsoft windows emulator, ms, win95, win98,
   www, URL, HREF, http
%X <A HREF="http://www.linux.org/">Linux home page</A>[8/1994]

%T Open Software Foundation
%D 1994
%K Open, OSF, computer, computing, organization, www, URL, HREF, http
%X <A HREF="http://riwww.osf.org:8001/">OSF Research Institute</A>

%T X-Windows
%D 1999
%K X windows, Xwindows, XX, window, org, consortium, system, X11,
   gui, www, URL, http, HREF, zz0499
%X <A HREF="http://www.x.org/">www.x.org</A> [4/1999]

-------------------------------------------------------------------------------

%T The Age Newspaper
%D 1994
%K Age, Melbourne, Victoria, Australia, theage, commercial,  news, paper,
   press, newspaper, media, Computer edition, Wright, Mitchell, cybersurf,
   www, HREF, http
%X <A HREF="http://www.theage.com.au/">The Age www</A>                   [9/95]
   Computer Age (Tuesday)
      Cybersurf column  email: cybersurf@theage.com.au                  (8/'94)
      Lisa Mitchell     email: lmitch@theage.com.au
      Charles Wright    email: charles@theage.com.au

%T Australian Personal Computer
%D 1995
%K APC, magazine, computing, PC, commercial, media, online, www, HREF, http
%X <A HREF="http://www.com.au/">APC</A> [2/'95]

%T The Guardian
%D 1994
%K Guardian, Grauniad, commercial,  news paper, press, newspaper, media,
   England, UK, Europe, www, HREF, http
%X <A HREF="http://www.guardian.co.uk/">Grauniad</A>
   searchable archives as of 11/'94

%T Le Monde diplomatique
%D 1997
%K Le Monde, LeMonde, commercial, press, media, news paper, newspaper,
   France, French, Europe, www, HREF, http, zz1097
%X <A HREF="http://www.monde-diplomatique.fr/md/en/index.html">[web]</A>
   [10/'97]

%T UK Press Association
%D 1995
%K Press Association, press, newspaper, news paper, commercial, media,
   England, UK, Europe, www, HREF, http
%X <A HREF="http://www.padd.press.net/">Press Assoc</A>
   email: www@padd.press.net

%T The Sydney Morning Herald
%D 1995
%K Sydney Morning Herald, press, news paper, newspaper, commercial, media,
   Australia, oz, www, HREF, http
%X <A HREF="http://www.smh.com.au/index.html">home page</A>
   <A HREF="http://www.smh.com.au/search/index.html">search archives</A>
   mostly stuff with a computing angle as of 7/95

%T The Daily Telegraph
%D 1994
%K Telegraph, electronic, ET, commercial, news paper, newspaper, media,
   England, UK, Europe, www, HREF, http
%X <A HREF="http://www.telegraph.co.uk">Telegraph</A> (form to register)
   fairly comprehensive version of the paper-paper
   email: et@telegraph.co.uk

%T Times Higher Education Supplement
%D 1995
%K Times, THES, commercial, newspaper, news paper, press, media,
   England, UK, Europe, www, HREF, http
%X <A HREF="http://www.timeshigher.newsint.co.uk/">[THES]</A>

%T New York Times
%D 1998
%K New York Times, news paper, newspaper, commercial, media, press,
   US, USA, America, NY, NYtimes, www, HREF, http
%X <A HREF="http://www.nytimes.com/">[NYtimes]</A>[9/1998]

%T CNN
%D 1996
%K CNN, US, USA, cable, news, press, media, www, HREF, http, zz1196
%X <A HREF="http://www.cnn.com/">[web]</A> [11/'96]

%T Feature Photo
%D 1995
%K FeaturePhoto, feature photo, picture, pictures, photographs,
   news, press, media, commercial, www, HREF, http, zz1295
%X <A HREF="http://www.featurephoto.com/">[busy site]</A>

%T San Francisco Examiner
%D 1994
%K electric examiner, SF, California, USA, commercial, news paper,
   press, newspaper, media, www, HREF, http
%X <A HREF="http://sfgate.com/examiner/">SF (USA) Examiner</A>
   (under development as of 11/'94)

-------------------------------------------------------------------------------

%T Adobe Systems Inc.
%D 1994
%K Adobe, acrobat, pdf, computer, computing, commercial, www, HREF, http
%X <A HREF="http://www.adobe.com/">www.adobe.com</A>

%T Apache
%D 1997
%K Apache, world wide web, server, servers, www, HREF, http, zz0797
%X public domain http server
   <A HREF="http://www.syd.dit.csiro.au/tools/apache/">[Au mirror]</A> [7/'97]
   <A HREF="http://www.apache.org/">[Apache]</A>

%T Digital Equipment Corporation
%D 1994
%K Digital, DEC, SRC, computer, computing, commercial, www, HREF, http
%X <A HREF="http://www.research.digital.com/">DEC research</A>
   <A HREF="http://www.research.digital.com/SRC/home.html">Systems Research Center</A>

%T IBM T. J. Watson Research Center
%D 1995
%K IBM, Watson, centre, Yorktown Heights, computing, commercial,
   www, HREF, http
%X <A HREF="http://www.watson.ibm.com/watson/">IBM T. J. Watson</A>

%T Intel
%D 1995
%K Intel, computer, computing, commercial, 386, 486, pentium, www, HREF, http
%X <A HREF="http://www.intel.com/">Intel</A>

%T Eastman Kodak Company
%D 1995
%K Kodak, image processing, imaging, photography, photoCD, photo CD, PCD,
   media, commercial, www, HREF, http
%X <A HREF="http://www.kodak.com/">Kodak</A>

%T Netscape
%D 1996
%K Netscape, documentation, developers, JavaScript, Live Connect, LiveConnect,
   browser, navigator, world wide web, commercial, site, www, HREF, http
%X <A HREF="http://developer.netscape.com/">[web]</A> ['97]

%T Silicon Graphics
%D 1994
%K Silicon, SGI, computer, computing, commercial, 3D, 3-D,
   VRML, VRML2, virtual reality markup language, cosmo player, cosmoplayer,
   mineset, mine set, data mining, datamining,   www, HREF, http
%X [<A HREF="http://www.sgi.com">SGI</A>]
   [<A HREF="http://www.sgi.com/software/">Software</A>][8/'00]
     [<A HREF="http://www.sgi.com/software/cosmo/">Cosmo VRML</A>][7/97][8/'00]
     [<A HREF="http://www.sgi.com/software/mineset/">MineSet</A>][8/'00] -- not supported is of '02

%T Tandem Computers
%D 1995
%K Tandem, parallel, computer, computing, commercial, www, HREF, http
%X <A HREF="http://www.tandem.com/">Tandem</A>

%T Thinking Machines
%D 1994
%K Thinking, parallel, computer, computing, commercial, connection machine,
   CM2, CM5, www, HREF, http
%X <A HREF="http://www.think.com/">thinking</A>

-------------------------------------------------------------------------------

%A Australian Broadcasting Corporation
%D 1995
%K ABC, oz, TV, television, radio, media, organization, site,
   www, HREF, http, zz0895, topical,
   hotchips, hot chips, quantum, behind the news, btn
%X <A HREF="http://www.abc.net.au/default.htm">A.B.C.</A>
   <A HREF="http://www.abc.net.au/quantum/default.htm">Quantum</A>
   <A HREF="http://www.abc.net.au/hotchips/default.htm">Hot Chips</A>
   <A HREF="http://www.abc.net.au/btn/default.htm">Behind the News</A>

%T Australian Consumers' Association (ACA)
%D 1995
%K ACA, consumer, choice, commercial, www, HREF, http
%X <A HREF="http://www.sofcom.com.au/ACA/">ACA</A>

%T DERA - Defence Evaluation and Research Agency (UK)
%D 1999
%K DERA, England, United Kingdom, Great Britain, Europe, gov, government,
   www dra hmg gb, HREF, http, site, zz0499,
   Ella, Algol 68 Algol68, a68, a682c, a68toc
%X DERA, Ively Road, Farnborough, Hampshire, GU14 OLX, UK
   <A HREF="http://www.dra.hmg.gb/dera.htm">www.dra.hmg.gb</A> [4/1999]
   <A HREF="ftp://ftp.dra.hmg.gb/">ftp.dra.hmg.gb</A> anon ftp [4/1999]
      Algol68 to C:
      <A HREF="ftp://ftp.dra.hmg.gb/pub/ella/">ftp.dra.hmg.gb/pub/ella/</A>

%T Gallup Poll
%D 1995
%K Gallup, poll, opinion, survey, commercial, www, HREF, http
%X <A HREF="http://www.gallup.com">Gallup</A>

%T Popular Mechanics
%D 1995
%K popular mechanics, automotive, car, cars, planes, magazine, media,
   www, HREF, http
%X <A HREF="http://popularmechanics.com/">Popular Mechanics</A>

%T STA Travel
%D 1996
%K STA Travel, statravel, aus, oz, com, www, HREF, http, zz0696
%X <A HREF="http://www.statravelaus.com.au/">STA Travel</A>

%T Telstra Corporation
%D 1995
%K Telstra, telecom, telecommunications, communications, Australia, au,
   telephone, white pages, yellowpages, yellow, yp,
   commercial, business, www, HREF, http
%X <A HREF="http://www.telstra.com.au/">Telstra home page</A>
   <A HREF="http://www.whitepages.com.au/">White Pages</A>
   <A HREF="http://www.yellowpages.com.au/">[yellow pages]</A>
   <A HREF="http://www.yellowpages.com.au/yp/text/">[yp text version]</A>

%T US Patent and Trademark Office
%K patent, patents, USA, org, organization, gov, www, HREF, http, zz0396
%X <A HREF="http://www.uspto.gov/">[web page]</A>                       [3/'96]

%T VICNET
%D 1995
%K VicNet, Vic Net, Victoria, State, Australia, Government, public, au,
   site, www, HREF, http, zz0695
%X <A HREF="http://www.vicnet.net.au/">VicNet</A>

%T Visa Card
%D 1994
%K Visa, credit card, bank, banking, finance, commercial, www, HREF, http
%X <A HREF="http://www.visa.com/visa/">Visa</A>



%T GNU - Free Software Foundation
%K GNU, free software foundation, FSF, copyright, copyleft, IP,
   general public license, GPL, lesser, LGPL, site, www, HREF, http
%X [<A HREF="http://www.gnu.org/" TARGET="external">gnu.org</A>][6/2000]
     [<A HREF="http://www.gnu.org/copyleft/gpl.html" TARGET="external">GPL</A>] - general
     [<A HREF="http://www.gnu.org/copyleft/lesser.html" TARGET="external">LGPL</A>] - lesser

%T Gnome
%K GNU, Gnome, office desktop environment, desk top, windows, MS, office2000,
   FSF, free, www, HREF, http
%X [<A HREF="http://www.gnome.org/">gnome.org</A>][10/2000]
   [Hint, see also:  star office]



%T IP number network index
%D 1997
%K IP address, internet, networks, numbers, identity, name, names, zz0197
%X <A HREF="http://xray.chm.bris.ac.uk:8000/IP/indexpage.html">[here]</A>
   A series of indices giving the network name and identity of all IP
   network numbers - now completed and including Class C networks.
   From:
   <A HREF="mailto:crossley@siva.bris.ac.uk">John Crossley</A> [1/'97]


%T Intelligent Tools for Problem Solving in Bioinformatics and Medicine
%J Int. J. of Artificial Intelligence Tools
%K 2004, CFP, jrnl, special issue, MolBio, zz0904
%X [<A HREF="http://www.eunite.org/eunite/news/CfP_JAIT2.pdf">deadline 1 Oct 2004</A>][7/'04]

%T Special Issue on Machine Learning on Bioinformatics
%J IEEE/ACM Trans. on Computational Biology and Bioinformatics
%K 2004, CFP, jrnl, special issue, MolBio,Biol,AI,II,www,HREF,http,  zz0804
%X [<A HREF="http://www.csd.uwo.ca/faculty/ling/SI_ML_Bio/SI_ML_Bio.htm" TARGET="EXTERNAL">uwo.ca</A>][7/'04], deadline 1 Sept 2OO4 (for 2005)


%T Mars Pathfinder
%D 1997
%K Mars, jpl, rover, pictures, space exploration, NASA, solar system,
   www, HREF, http, zz0797
%X <A HREF="http://mpfwww.jpl.nasa.gov">NASA</A>
   <A HREF="http://sparkli.tip.csiro.au/mars/">CSIRO Au mirror</A>
   <A HREF="http://mars.sgi.com">SGI mirror</A>
   <A HREF="http://www.sun.com/mars">Sun mirror</A>  [7/'97]

%T Higher Education Review
%D 1997
%K HER, HERE, West Report, Australia, university, www, HREF, zz0597
%X <A HREF="http://www.deet.gov.au/divisions/hed/hereview/"
   >[DEET Higher Ed' review]</A> [5/'97]
   <A HREF="http://www.edunions.labor.net.au/nteu/heissues.html"
   >[Ed' Unions]</A> [4/'97]

%T Eternity Puzzle
%D 1999
%K puzzle, million pounds, millionaire, jig saw, jigsaw, prize, competition,
   topical, www, HREF, http, zz1099
%X <A HREF="http://www.eternity-puzzle.co.uk/">official</A> [10/1999]
   <A HREF="http://www.mathpuzzle.com/eternity.html">mathpuzzle.com</A> [10/1999]


%T Abbreviations
%K abbreviation, apostrophe, full stop, stops, fullstop, words, contraction,
   ie, eg, cf
%X [<A HREF="http://www.phon.ucl.ac.uk/home/dick/tta/wordpunc/wordpunc.htm">www.phon.ucl.ac.uk/home/dick/...</A>][10/'04]...
    "Apostrophes of omission   Mary's here.
     Possessive apostrophes    Mary's house.
     Very occasionally 's is possible for plurals, ... "mind your p's and q's"
     Apostrophes of omission ... a contraction
       I don't think he's very happy. ...  In every case, the apostrophe
       is written in the place where the full form has a vowel ...
       One minor exception ... o'clock ... a historical relic.
     Full stops in abbreviations ...
       E. Sussex for East Sussex, Prof. for Professor, B.C. for Before Christ
       Abbreviated Latin words...
         i.e. id est,  e.g. exempli gratia,  a.m.,  cf. conferre.
     [But] abbreviations that include the last letter as well as
     the first do not take a full stop; Dr for Doctor  Mr for Mister ...
     Units ... 200 kg for 200 kilograms ... 90 mph ..."
   [<A HREF="http://intarch.ac.uk/news/housestyle/pres.html">intarch.ac.uk</A>][10/'04]
     [Figure->Fig.] "...Plurals follow the same rule as their
     singular counterparts.  e.g. Drs  Figs. ..."  [note "."]
   Both the Macquarie and F.T.Woods cite ... omitting the stop when the
     final letter is shown (=> 'Dr' and 'Drs', 'Prof.' but 'Profs'!)
     Woods (1978) cites Fowler but claims that OUP, which publ. Fowler, doesn't
     follow him.  Woods also says that words in common use don't need the stop
     e.g. 'pub', 'cab' and 'zoo', but 'exam.' or 'maths.' (counter to his Fowler
     rule).  Note that slovenly writin' requires an apostrophe, regar'less of
     whether the last letter is given. [--ajh 10/'O4].

%T The Directory
%D 1995
%K Academic jobs, university, education, job, position, appointment,
   www, HREF, http, zz0695
%X <A HREF="http://www.thedirectory.aone.net.au/" TARGET="external">1998</A> no jobs online
   <A HREF="http://www.mel.aone.net.au/thedirectory/" TARGET="external">1995</A>

%T Jobs.ac.uk
%D 1998
%K Academic jobs, university, education, job, position, appointment,
   online, search, England, UK, Europe, www, HREF, http, zz0398
%X <A HREF="http://jobs.ac.uk/" TARGET="external">[jobs.ac.uk]</A>[3/1998]

%T Maxima, a Computer Algebra System
%D 2008
%K Maxima, doe, mit, computer algebra system, package, software, Maple,
   symbolic, math, maths, calculus, integration, ODE solver, 3D plotting
%X [<A HREF="http://maxima.sourceforge.net/"  TARGET="external">2008</A>].

%J Journal of Experimental Algorithmics
%D 1995
%I ACM
%K algorithm, data structure, CSci, computing, JEA, jrnl, ACM,
   online, on line, www, HREF, http, zz1195
%X archival, online-only journal covering discrete algorithms and data
   structures such as combinatorial optimization, computational biology,
   computational geometry, graph manipulation, graphics, heuristics, network
   design, parallel processing, routing, searching and sorting, scheduling,
   and VLSI design.  Submissions will typically include an article, a suite of
   programs, a collection of test data, and computational results.
   First issue in 1Q 1996.   Articles are solicited, by
   Bernard Moret  (email: editor@jea.acm.org)  of UNew Mexico/CS.
   For other details see jea.acm.org: <A HREF="http://www.jea.acm.org" TARGET="external">[web]</A> <A HREF="ftp://ftp.jea.acm.org" TARGET="external">[ftp]</A>
   [email: acmjea@saratoga.cs.unm.edu,    comp.theory, 11/2/95.]

%T Amnesty International
%K Amnesty, politics, political, refugee, human rights
%X <A HREF="http://www.traveller.com/~hrweb/ai/aidoc.html" TARGET="external">[AI]</A>      [9/95]

%T WSU Computer Animations
%D 1994
%K animation, multimedia, mpeg, mpg, computer, computing, www, HREF, http
%X <A HREF="http://www.eecs.wsu.edu/IRL/ANIM/Anim.html" TARGET="external">WSU anim archive</A>

%T The Neanderthal Museum
%K anthropology, neander, neanderthal, early man, origin, origins, human
%X <A HREF="http://www.neanderthal.de/" TARGET="external">[web]</A>[7/1999]

%A M. Greenhalgh
%T Art History
%D 1994
%K Art, arts, history, gallery, images, painting, picture, print, prints,
   etching, classical, sculpture, architecture,  impressive, ANU,
   www, site, HREF, http
%X <A HREF="http://rubens.anu.edu.au/" TARGET="external">A.N.U. Art History</A><IMG SRC="/~lloyd/tildeImages/Art/ANU.art.hist.gif">
   Prints: about 2800 images 15C to 19C mainly
   Classical Architecture: 2500 images
   Sculpture: 3000 images (by Dec '94)

%T DIVA
%D 1994
%K Art, arts, visual, gallery, painting, picture, image, images,
   Monash, Australia, www, HREF, http
%X <A HREF="http://www.monash.edu.au/diva/intro.html" TARGET="external">Diva</A>
   <!-- email: Jennifer.Durran@arts.monash.edu.au ('94) --> .

%T Journal of Artificial Intelligence Research
%D 1994
%K artificial intelligence, AI, computer, computing, electronic, science, CS,
   CSci, jrnl, online, JAIR, www, HREF, http, zz0595
%X <A HREF="http://www.cs.washington.edu/research/jair/home.html" TARGET="external">JAIR</A>
   published electronically and in print.         ['94]
   JAIR: Experimental Comments Facility:
   <A HREF="http://www.cs.washington.edu/research/jair/table-of-contents-vol2.html" TARGET="external">vol 2</A>
   - Peter Turney   email: peter@ai.iit.nrc.ca    [5/'95]

%T Knowledge and Information Systems: An International Journal
%I SpringerVerlag
%D 1999
%K artificial intelligence, jrnl, electronic, KAIS, AI, II,
   machine learning, base, zz0298
%X Starting early in 1999, Springer-Verlag will publish a new quarterly
   journal (above) [...] both electronic as well as print form.
   <A HREF="/~lloyd/tildeMisc/1998.KAIS.html" TARGET="external">[more here]</A>

%T Tierra
%D 1995
%K Artificial Life, AL, Tierra, AI, computing, zz0595, www, HREF, http, ftp
%X Tierra Working Group Report
   <A HREF="http://www.krl.caltech.edu/pub/avida/NetTierraWG.html" TARGET="external">www http</A> [5/'95]
   <A HREF="ftp://ftp.krl.caltech.edu/pub/avida/NetTierraWG" TARGET="external">FTP</A> [5/'95]
   The Tierra Workshop took place on March 24-26, 1995.
   From   email: brown@rigel.krl.caltech.edu (C. Titus Brown)

%T Australian Web Servers
%D 1994
%K Australia, states, sites, map, web, www, HREF, http
%X <A HREF="http://www.csu.edu.au/links/ozmap.html" TARGET="external">OZ map</A>

%T Autism, Asperger's
%D 2004
%K Autism, autistic, Asperger's, Aspergers, syndrome, www,HREF,http
%X [<A HREF="http://www.autism.org/">autism.org</A>][10/'04]
   [<A HREF="http://www.asperger.org/">asperger.org</A>][10/'04]
   --"Asperger's syndrome was first described by a German doctor, Hans
   Asperger, in 1944 (1 year after Leo Kanner's first paper on autism)...."

%A L. Allison
%T Computing for Molecular Biology
%D 1994
%K Biology, Biol, Bio, MolBio, computer, computing, science, CS, CSci, theory,
   alignment, multiple, evolutionary, family, phylogenetic, tree, trees,
   www, HREF, http
%X [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Computing for Molecular Biology</A>].

%T International Society for Computational Biology
%D 1998
%K MolBio, ISCB, ISMB, PSB, home page, site, www, HREF, http, zz0798
%X <A HREF="http://www.iscb.org/" TARGET="external">[home page]</A>[7/98]

%A Computational Molecular Biology
%J Jrnl Combinatorial Optimization
%D 1999 ???
%K jrnl, CFP, MolBio, JCO, 1998, zz0198
%X <A HREF="/~lloyd/tildeMisc/1998.JCO.html" TARGET="external">[here]</A>
   submit by 15 Aug 1998; Extended to 31 Aug 1998

%A Discrete Applied Mathematics, Computational Molecular Biology (series)
%D 1998
%K MolBio, DAM, CMB, Biol, CFP, series, www, HREF, http, zz0898
%X <A HREF="/~lloyd/tildeMisc/1998.DAMCMB.html" TARGET="external">[information]</A>

%T Commercial Biomedical Site
%D 1995
%K Biology, bio, biol, MolBio, medicine, medical, science, commercial,
   gemini, co, com, www, HREF, http, zz0595
%X <A HREF="http://www.gemini.co.uk/gemini/biopages/" TARGET="external">here</A>
   Dupont NEN, BioWhittaker, Dynatech, Muratech, BIS
   Abbott Diagnostics Division is already with us and you may be interested
   in the discovery of a new hepatitis virus GBV-C - or the application of
   LCR to Chlamydia testing.
   - email: pmassoc@tcp.co.uk  [5/'95]

%T Bio-XML
%K Biology, BioXML, MolBio, www, http, HREF, bio-ontology, bioontology, ontologies,
   biological, biol, Systems Biology Markup Language, SBML, mark-up, workbench, SBW
%X Systems Biology Mark-up Language (SBML) and Systems Biology Workbench:
      [<A HREF="http://www.cds.caltech.edu/erato/" TARGET="external">home</A>][11/'01]
      Markup Language: [<A HREF="http://www.cds.caltech.edu/erato/sbml/docs/index.html" TARGET="external">www</A>][11/'01]
      Workbench:       [<A HREF="http://www.cds.caltech.edu/erato/sbw/docs/index.html"  TARGET="external">www</A>][11/'01]

%T Theoretical Biophysics, Illinois
%D 1994
%K Biophysics, MolBio, Science, molecular dynamics, uiuc, www, HREF, http
%X [<A HREF="http://www.ks.uiuc.edu/">ks.uiuc.edu</A>][5/'03]

%T Bioinformatics
%K Bioinformatics, Computational Biology, Biol, MolBio, PSB, ISCB,
   International Society, courses, subjects, courseware,
   topical, www, HREF, http, zz0300
%X PSB:  <A HREF="http://ribozyme.vadms.wsu.edu/~vadms/classes/PSB/PSB-edu.html">www</A> c1996/'97
   ISCB: <A HREF="http://www.iscb.org/training.html">training</A>
   J. Bioinformatics: [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/reprint/14/7/549">14(7)</A>]['05]
      [<A HREF="http://dx.doi.org/10.1093/bioinformatics/14.7.549">doi:10.1093/bioinformatics/14.7.549</A>]['05]
      was [<A HREF="http://www3.oup.co.uk/bioinformatics/hdb/Volume_14/Issue_07/html/btb119_gml.html">14(7)</A>]['00]
   Sloan Foundation:  <A HREF="http://www.sloan.org/programs/scitech_page1.htm">www</A> report
   Russ Altman: <A HREF="http://smi-web.stanford.edu/people/altman/bioinformatics.html">www</A>, Bioinf' at Stanford
     - via Larry Hunter [3/2000]
  [<A HREF="/~lloyd/tildeStrings/Notes/Teaching.html">condensed</A>]

%T BioJava
%D 2000
%K Biology, bioinformatics, open source, Bio Java, Biol, biological, tools,
   MolBio, www, HREF, http, zz0700
%X <A HREF="http://www.biojava.org/" TARGET="external">biojava.org</A> [6/00]

%T Malaria Foundation International
%K biology, MolBio, malaria, Plasmodium Falciparum, p.falciparum,
   gene, genome, CHR, chromosomes, chromosome, www, HREF, http, zz0900
%X [<A HREF="http://www.malaria.org/" TARGET="external">malaria.org</A>][8/'00]
   [<A HREF="http://www.sanger.ac.uk/Projects/P_falciparum/ftp.shtml" TARGET="external">Sanger Centre P.falciparum</A>][9/'00]
     [<A HREF="ftp://ftp.sanger.ac.uk/pub/pathogens/malaria2/EMBL_files" TARGET="external">chr1 chr3 chr4</A>][9/'00]
   [<A HREF="http://www.tigr.org/tdb/edb/pfdb/pfdb.html" TARGET="external">TIGR</A>][9/'00]
     [<A HREF="http://www.tigr.org/tdb/edb/pfdb/Pf2.html" TARGET="external">chr2</A>][9/'00]
     [<A HREF="ftp://ftp.tigr.org/pub/data/p_falciparum/" TARGET="external">chr2 chr10 chr11 chr14</A>][9/'00]
   [<A HREF="http://sequence-www.stanford.edu/group/malaria/index.html" TARGET="external">Stanford</A>][9/'00]
     [<A HREF="http://baggage.stanford.edu/group/malaria/download.html" TARGET="external">chr12</A>][9/'00]
   [<A HREF="http://www.wehi.edu.au/MalDB-www/" TARGET="external">WEHI</A>][2/'01]
     [<A HREF="http://www.wehi.edu.au/MalDB-www/chr2list.htm" TARGET="external">c2 annotations</A>][2/'01]

%A E. Birney
%T Wise2
%D 1999
%K Biology, MolBio, GeneWise, Wise, Wise2, gene, find, finding,
   www, HREF, http
%X [<A HREF="http://www.sanger.ac.uk/Software/Wise2/" TARGET="external">Software/wise2/</A>][10/2000]
   [<A HREF="http://www.sanger.ac.uk/Software/" TARGET="external">Software/</A>][10/2000]

%T Amazon Bookstore
%D 1996
%K books, book shop, store, US, USA, www, HREF, http, zz1196
%X <A HREF="http://www.amazon.com/" TARGET="external">[web]</A> [11/'96]

%T Cameras
%K camera, gphoto, gfoto, photo, photography, digital, Olympus, Kodak,
   Linux, www, HREF, http, zz0799
%X <A HREF="http://www.gphoto.org/" TARGET="external">gphoto.org</A> [7/1999]

%T Internet Cello Society
%D 1995
%K Cello, classical music, arts, entertainment, www, HREF, http
%X <A HREF="http://tahoma.cwu.edu:2000/~michelj/" TARGET="external">Cello</A>

%T Checkers, Chinook
%D 1995
%K checkers, chequers, AI, computer, computing, game, games,
   play, playing, www, HREF, http
%X email: jonathan@cs.ualberta.ca (Jonathan Schaeffer) [4/'95]
   The World Checkers Champion, Chinook, is now accessible via the WWW:
   <A HREF="http://web.cs.ualberta.ca/~chinook" TARGET="external">Chinook</A>
   From the home page, you can test your checker skill against
   Chinook, read about Chinook's World Championship matches,
   find out more about the game of checkers, etc.

%A J. McCormack
%T Computer Art
%D 1994
%K Computer art, CompArt, arts, image, images, gif, animation, mpg, mpeg, mov,
   multimedia, graphics, computing, science, CS, CSci, jonmc, Monash,
   www, HREF, http
%X <A HREF="/~jonmc" TARGET="external">Jonmc's home page</A>

%T Bletchley Park
%K Computer, history, computing, Bombe, Enigma, Colossus, Lorenz, encryption,
   cypher, cyphers, cryptology, code breaker, breaking, military codes,
   codebreaker, world war two, ww2, wwII, Ultra, Alan Turing,
   c193x, c194x, c19xx, Milton Keynes, UK, www, HREF, http, zz0699
%X Where the `Ultra' code-breaking work went on to read WW2 German military
   messages encrypted using various cyphers, including the `Enigma' machine.
   [<A HREF="http://www.bletchleypark.org.uk/" TARGET="external">web</A>] [10/2004]
   [<A HREF="http://www.codesandciphers.org.uk/" TARGET="external">codesandciphers.org.uk</A>]['04]

%T The Retrocomputing Museum
%D 1995
%K Computer, history, computing, retro, programming languages,
   computer science, CS, CSci, www, HREF, http
%X <A HREF="ftp://locke.ccil.org/pub/retro/retromuseum.html" TARGET="external">RETRO</A>

%T Charles Babbage Institute
%D 1995
%K Computer, history, cbi, computing, CS, CSci, www, HREF, http
%X <A HREF="http://cbi.itdean.umn.edu/cbi/welcome.htm" TARGET="external">CBI</A>
   <A HREF="http://fs1.itdean.umn.edu/cbi/cbihome.htm" TARGET="external">CBI</A> - old URL

%A J. A. N. Lee
%T History of Computing
%D 1994
%K Computer, history, computing, image, images of, picture, gif,
   science, www, HREF, http
%X <A HREF="http://info.cs.vt.edu/~history/index.html" TARGET="external">History of Computing</A>

%A Mike Muuss
%T Historic Computer Images
%K Computer, history, computers, computing, image, images of, pictures,
   science, gif, jpg, jpeg, www, HREF, http
%X [<A HREF="https://ftp.arl.army.mil/ftp/historic-computers/">History</A>]['23],
   [<A HREF="http://ftp.arl.mil/~mike/comphist/">History</A>][12/'03],
   [<A HREF="http://ftp.brl.mil/ftp/historic-computers/" TARGET="external">Historic Images</A>][1994].

%T Computer Museum
%D 1995
%K Computer, history, computing, Oxford, www, HREF, http, zz0695
%X <A HREF="http://www.comlab.ox.ac.uk/archive/other/museums/computing.html" TARGET="external">here</A> [6/'95]

%T High Performance Computing
%K Computing, HPC, VPAC, APAC, cluster, beowulf, MPI, MP, SMP, scalable,
   parallel, concurrent, site, org, www, HREF, http, zz1000
%X [<A HREF="http://www.vicpac.org/" TARGET="external">VPAC</A>][9/'00]
   [<A HREF="http://www.beowulf.org/" TARGET="external">beowulf</A>][9/'00]
   [<A HREF="http://www.mcs.anl.gov/mpi/" TARGET="external">MPI msg passing interface</A>][9/'00]
   [<A HREF="http://www.openmp.org/" TARGET="external">MP  shared memory</A>][9/'00]

%T ACM Programming Competition
%K Programming Contest, ACM, inter collegiate, intercollegiate, 1999, 2000,
   south pacific, www, HREF, http
%X <A HREF="/~lloyd/tildeMisc/ACM-comp.html" TARGET="external">[more...]</A>

%T First Course Language List (The Reid Report).
%D 2002
%K programming language, PL, computer science, major, majors, first course,
   Dick Reid, report, 1999, survey, CS1, CSC1, CSE1, Level1, languages, year
%X [<A HREF="http://www.csee.wvu.edu/~vanscoy/reid.htm" TARGET="external">wvu.edu</A>][10/'02] (#23 2/2002)
   [<A HREF="http://www.csc.calpoly.edu/~mliu/TeachJava/collegeList.html" TARGET="external">csc.calpoly.edu/~mliu/... #20, 8/'99 list</A>][10/'02]
   [<A HREF="ftp://ftp.cps.msu.edu:pub/arch/CS1_Langauge_List.Z" TARGET="external">Michigan</A>]['99]
   -- via Linda M / P

%T Psyche
%D 1995
%K Consciousness, Psyche, journal, jrnl, online, virtual, mind,
   www, HREF, http, zz0695
%X Was [<A HREF="http://psyche.cs.monash.edu.au/" TARGET="external">Psyche</A>'['95].

%T Copyright
%K Copyright, copy, copy-right, author, owner, copying, reproduce,
   reproduction, protection, publish, publishing, ownership, scanning,
   law, legal, ethics, australia, council, Berne convention,
   www, HREF, http, zz1098
%X Australian Copyright Council
     <A HREF="http://www.copyright.org.au/info10.htm" TARGET="external">[introduction]</A> [1996]
     <A HREF="http://www.copyright.org.au/" TARGET="external">[copyright.org.au]</A> [1998]
   USA
     US Copyright <A HREF="http://lcweb.loc.gov/copyright/" TARGET="external">Office</A> [1998]
     Copyright Clearance <A HREF="http://www.copyright.com/" TARGET="external">Center</A> [1998]
     Stanford University Libraries <A
       HREF="http://fairuse.stanford.edu/" TARGET="external">[fair-use]</A> [1998]
   <A HREF="ftp://rtfm.mit.edu/pub/usenet/news.answers/law" TARGET="external">news.answers.law/(c)</A> [1994]

%T Beyond the Frame
%D 1997
%K copyright, Le Monde, France, copy-right, law, legal, France,
   photo, image, images,  www, HREF, http, zz1097
%X <A HREF="http://www.monde-diplomatique.fr/md/en/1997/07/photo.html" TARGET="external">www</A>
   Interesting article on copyright of images


%T Data Mining Group
%D 2000
%K Data Mining, DMG,  PMML, predictive model markup language, XML,
   www, HREF, http
%X [<A HREF="http://www.dmg.org/" TARGET="external">dmg.org</A>][9/'00]
   Predictive Model Markup Language (PMML) is an XML-based language which
      provides a quick and easy way for companies to define predictive
      models and share models between compliant vendors' applications
      [<A HREF="http://www.dmg.org/html/pmml_v1_1.html" TARGET="external">PMML 1.1</A>]['00]
   [search hint, try: inductive inference]

%T National Center for Data Mining (USA)
%D 2000
%K Data Mining, NCDM, centre, stats, statistics,
   PMML, predictive model markup language, DSTP, data space transfer protocol,
   Psockets,     www, HREF, http, zz0900
%X National Center for Data Mining, University of Illinois-Chicago
   [<A HREF="http://www.ncdm.uic.edu/" TARGET="external">NCDM</A>][9/'00]
      [<A HREF="http://www.ncdm.uic.edu/dstp/" TARGET="external">DSTP</A>][9/'00]
   [search hint, try: inductive inference]
   [search hint, try: machine learning]

%T CRAN: The Comprehensive R Archive Network
%D 2000
%K Data Mining, CRAN, R, RR, S, SS, Splus, GNU, software,
   www, HREF, http, zz0900
%X R, also known as "GNU S", is a language and environment for
   statistical computing and graphics.
   R is available as Free Software under the terms of the
   Free Software Foundation's GNU General Public License in source code form.
   [<A HREF="http://lib.stat.cmu.edu/R/CRAN/" TARGET="external">www</A>][2'01]
   [<A HREF="http://www.stat.cmu.edu/R/CRAN/" TARGET="external">www</A>][9'00]

%T Omega Project for Statistical Computing
%D 2000
%K Data Mining, stats, statistics, Omega, R, RR, SS, Splus, Java,
   Omegahat, RJava, interface,  www, HREF, http, zz0900
%X We have provided an R package which allows R users to create
   Java objects and call Java methods interactively from R.
   The Omega project began in July, '98...
   [<A HREF="http://www.omegahat.org/" TARGET="external">www</A>][9/'00]
   [Search hint, try: RR]

%T SPSS
%K Data Mining, stats, statistics, SPSS, www, HREF, http
%X [<A HREF="http://www.spss.com/" TARGET="external">spss.com</A>][9/'00]
   [<A HREF="http://www.spss.com/datamine/" TARGET="external">/datamine</A>][9/'00]
   (see Clementine)

%T Rulequest
%D 2000
%K Data Mining, Rulequest, Ross Quinlan, See5, C5, C4, decision tree, trees,
   software, www, HREF, http
%X [<A HREF="http://www.rulequest.com/" TARGET="external">www</A>][9/'00]

%A A. Pryke
%T The Data Mine
%D 1995
%K Data Mining, TheDataMine, inductive inference, II, computing, CSci,
   www, HREF, http, zz0895
%X [<A HREF="http://www.cs.bham.ac.uk/~anp/TheDataMine.html" TARGET="external">TheDataMine</A>[[9/'00]
   Andy Pryke A.N.Pryke@cs.bham.ac.uk [8/'95]

%T Clementine
%I SPSS
%D 2003
%K advert, Clementine, stats, statistics, commercial, .com, data mining,
   datamining, software, statistical
%X [<A HREF="http://www.spss.com/PDFs/CLMCATINS-0802.pdf">CLMCATINS-0802.pdf</A>][4/'03]
   [<A HREF="http://www.spss.com/SPSSBI/Clementine/">spss.com/...</A>][4/'03]
   [<A HREF="http://www.spss.com/">spss.com</A>][4/'03]
   And ... "Clementine is based on a visual programming interface which links
   data access, manipulation and visualisation together with machine learning
   (decision tree induction and neural networks). Trained rules and networks
   can be exported as C source code. It uses a graphical 'building block'
   approach to develop applications. Clementine can access data from files or
   databases, provides a graphical interface for data manipulation and data
   visualization, and has a number of machine learning algorithms.
   It contains the C5.0 algorithm for creating decision trees, and
   allows for using boosting. Clementine also has a standard which
   allows users to write code to use the Clementine interface on programs
   written outside of Clementine."  -- [<A HREF="http://www.cald.cs.cmu.edu/software.html">cs.cmu.edu/...</A>][5/'03]

%T Clustan
%K data mining, ClustanGraphics, cluster, clustering, software,
   k-means, kmeans, www, HREF, http
%X via  D e a n  M c K e n z i e  2/'02
   [<A HREF="http://www.clustan.com/" TARGET="external">www</A>][2/'02]
   not forgetting an important application...
   [<A HREF="http://www.whiskyclassified.com/" TARGET="external">www</A>][2/'02]

%T Zherlock - a general data analysis tool
%D 2003
%K data mining, software, www, HREF, http
%X [<A HREF="http://www.zherlock.org/">zherlock.org</A>][5/'03]
   ... intuitive GUI, it should also be easy for the method developer
   to rapidly implement new algorithms. This can be accomplished by
   writing a plugin for Zherlock in your favourite programming language. ...
   ... The bad news is that Zherlock still is in the implementation
   phase! But things are happening, and at the moment, you can download
   a pre-beta-version  [5/'03]


%A Digital Object Identifier System (DOI)
%D 2002
%K Digital Object Identifier, DOI, DOIlink, document, paper, papers, number,
   address, crossref, persistent, link, links, location, http, HREF, www,
   online
%X The Digital Object Identifier (DOI(r)) is a system for identifying and
   exchanging intellectual property in the digital environment. ...
   [<A HREF="http://www.doi.org/" TARGET="external">doi.org</A>][11/'02]
   Use http://dx.doi.org/pp.ppp/ssssssssss (if the publisher is uptodate!)
          i.e. doi_proxy/prefix/suffix
   [<A HREF="http://www.press.umich.edu/jep/04-02/davidson.html" TARGET="EXTERNAL">about</A>][10/'04]

%A Disabilities and Internet Access
%D 1997
%K disabled, vision impaired, sight, blind, deaf, internet,
   site, design, www, HREF, http, zz0797
%X NSW Attorney General's Department has some guidelines:
   <A HREF="http://www.agd.nsw.gov.au/standards.html" TARGET="external">[NSW AG]</A> [7/'97]

%D DVD
%D 1999
%K DVD, digital versatile disc, video disc, DVD, DeCSS, disk, encryption,
   crack, cracking, Content Scrambling System, CSS, attack, attacks,
   Livid, MPAA, www, HREF, http, topical, zz1199
%X <A HREF="http://crypto.gq.nu/" TARGET="external">crypto.gq.nu</A>[11/1999]
      claims code is weak, open to attack, and indeed opened.
   <A HREF="http://crypto.gq.nu/livid.html" TARGET="external">.../livid.html</A>[11/1999]
      links and reports.
   <A HREF="/~lloyd/tildeMisc/Local/199911DVD.html" TARGET="external">[local]</A>[11/1999]

%T Dyslexia
%K dyslexia, dyslexic, association, spell, spelling, text to speech,
   FAQ, www, HREF, http
%X <A HREF="http://www.interdys.org/" TARGET="external">[International Dys' Assoc]</A>
   <A HREF="http://www.bda-dyslexia.org.uk/" TARGET="external">[British Dys' Assoc']</A>
      98 London Rd., Reading RG1 5AU, UK

%T textHELP
%I Lorien Systems
%D 1997
%K dyslexia, dyslexic, texthelp, text help, text to speech, www, HREF, http
%X <A HREF="http://www.texthelp.com/" TARGET="external">[texthelp]</A> [11/'97]

%T Earthquake Information
%D 1994
%K Earthquake, quake, world, geology, science, www, HREF, http
%X <A HREF="http://www.civeng.carleton.ca/cgi-bin/quakes" TARGET="external">Quakes</A>

%T GreenPeace
%D 1995
%K Environment, org, organization, green peace, www, HREF, http, zz0795
%X <A HREF="http://www.greenpeace.org/" TARGET="external">Greenpeace</A>

%T FAX
%D 1995
%K Fax, faq, InterNet, www, HREF, http, zz0895
%X <A HREF="http://www.io.org/~fsc/infores/faqs/fax-faq.html" TARGET="external">FAQ</A> [8/'95]
   <A HREF="http://linux1.balliol.ox.ac.uk/fax/faxsend.html" TARGET="external">Oxford</A> [8/'95]

%T Flightgear
%D 1998
%K flight simulators, simulator, flying, game, games,
   open source, free, www, HREF, http, zz1001
%X [<A HREF="http://www.flightgear.org/">flightgear.org</A>][10/'01]

%A L. Allison
%T Functional Programming
%D 1994
%K functional, FP, programming, language, computer, computing,
   lambda, www, HREF, http
%X <A HREF="/~lloyd/tildeFP/" TARGET="external">Functional Programming page</A>

%A J. Farrell
%T Functional Programming
%D 1994
%K functional, FP, programming, language, computer, computing, science,
   CS, CSci, www, HREF, http
%X <A HREF="ftp://coral.cs.jcu.edu.au/web/FP/home.html" TARGET="external">JF's FP page</A>

%A M. Hanus
%T Functional Logic Programming
%D 1996
%K functional, logic, programming language, FP, LP, FLP,
   computer, science, CS, CSci, www, HREF, http, zz0296
%X [<A HREF="http://www.informatik.uni-kiel.de/~mh/FLP/" TARGET="external">here</A>][10/'03]
   [<A HREF="http://www-i2.informatik.rwth-aachen.de/hanus/FLP/" TARGET="external">here</A>][2/'96]

%A S. Kimball
%A P. Mattis
%T GIMP
%D 1997
%K Graphics, multimedia, software, GNU, Gimp, image, photo shop, photoshop,
   photograph, processing, manipulation, www, HREF, http, zz0797
%X <A HREF="http://www.gimp.org/">[gimp.org]</A> [6/'00]
   <A HREF="http://www.xcf.berkeley.edu/~gimp/" TARGET="external">[gimp]</A> [7/'97]

%T Project Gutenberg
%D 1994
%K Gutenberg, Gutenburg, virtual, online, text, texts, book, books, library,
   Arts, literature, interesting, www, HREF, http
%X <A HREF="http://med-amsa.bu.edu/Gutenberg/Welcome.html" TARGET="external">Gutenberg home</A>
   Fact; Fiction; Music includes Beethoven's 5th, zipped midi file.
   <!-- email: emair@bu.edu ('94) --> .

%T Haiku - Microsoft error messages
%D 2000
%K Haiku, micro soft, errors, message, BSOD, abend, bug, disc, crash, reboot,
   windows xp, haikus, art, mind, brain, fun, funny, ha ha, haha, silly,
   www, HREF, http
%X <A HREF="Local/2000-MSpoet.html">[here]</A>

%T USA Holocaust Memorial Museum
%D 1994
%K Holocaust, genocide, history, world war 2, WW2, www, HREF, http
%X <A HREF="http://www.ushmm.org/" TARGET="external">Museum</A>

%T HTML
%K HTML, HTML1, HTML2, HTML3, HTML4, HTML+, XML, XHTML, SVG, CSS, MathML,
   hyper text markup language, hypertext, mark up, www, HREF, http, zz0595
%X <A HREF="http://www.w3.org/TR/" TARGET="external">www.w3.org/TR/</A> [1999]
   <A HREF="http://www.w3.org/TR/REC-html40/" TARGET="external">HTML-4</A> rec' [4/1998]
   <A HREF="http://www.w3.org/TR/REC-xml" TARGET="external">XML 1.0</A> rec' [2/1998]
   LA's <A HREF="/~lloyd/tilde/InterNet/HTML.html" TARGET="external">HTML stuff</A>

%T HTML Tidy
%D 1999
%K HTML, tidy, HTMLtidy, tidying up, pretty print, prettyprint, improve,
   MS, microsoft, Word, word2000, www, HREF, http, ASP, zz1199
%X <A HREF="http://www.w3.org/People/Raggett/tidy/" TARGET="external">[www]</A>[11/1999]
   Builds a parse tree "from the source file, then pretty prints the
   parse tree using the current layout options."

%T Image Compression
%D 1995
%K image compression, gif, jpg, jpeg, www, HREF, ftp
%X from <!-- email: arjan@stud.uni-sb.de --> Arne Jansen [3/'95]
   try <A HREF="ftp.ncsa.uiuc.edu/" TARGET="external">ftp.ncsa</A>
       /misc/file.formats/graphics.formats

%T ILP Newsletter
%D 1994
%K inductive logic programming, ILP, Artificial Intelligence, AI, II,
   computer, computing, science, CS, Sci, www, HREF, http
%X <A HREF="http://www-ai.ijs.si/ilpnet.html" TARGET="external">ILP Newsletter</A>

%T International Standard Book Number (ISBN)
%K isbn, isbn13, isbns, book, numbers, books, www, HREF, http, zz0408
%X Int: [<A HREF="http://isbn-international.org/" TARGET="external">isbn-international.org</A>]['08]
   AU:  [<A HREF="http://www.thorpe.com.au/isbn/" TARGET="external">www</A>]['08]
   UK:  [<A HREF="http://www.isbn.nielsenbookdata.co.uk/" TARGET="external">www</A>]['8]
   USA: [<A HREF="http://www.isbn.org/" TARGET="external">www</A>]['08]
        [<A HREF="http://www.isbn.org/converterpub.asp" TARGET="external">10->13</A>]
   On ...X:  "In the case of the check digit, the last digit of the ISBN, the
   upper case X can appear. The method of determining the check digit for the
   ISBN is the modulus 11 with the weighting factors 10 to 1. The Roman numeral
   X is used in lieu of 10 where ten would occur as a check digit."

%T Center for Intelligent Information Retrieval
%D 1995
%K Information retrieval, IR, centre, CIIR, text, umass,
    www, HREF, http, zz0595
%X <A HREF="http://ciir.cs.umass.edu/" TARGET="external">CIIR</A>

%T Java
%D 1995
%K Java, hot, hotjava, interactive, browser, WebRunner, web, runner, Oak,
   sun, www, HREF, http
%X <A HREF="http://java.sun.com/" TARGET="external">Java</A>
   <A HREF="http://www.javasoft.com/" TARGET="external">javasoft.com</A> [10/95]

%T Java3D
%D 2006
%K Java 3D, VR, VRML, computer graphics, www, HREF, http, zz1297
%X [<A HREF="http://www.j3d.org/">j3d.org</A>]['06]
   [<A HREF="java.sun.com/products/java-media/3D/">java3d@sun</A>]['06]
   [<A HREF="http://java3d.sdsc.edu/" TARGET="external">java3d</A>][12/'97]
   Java 3D: comined effort by  Intel, SGI, Apple, Sun --1997
   Sun's Java3D due early/mid 1998

%T Law
%D 1995
%K Law, legal information, Australia, www, HREF, http, zz0895
%X <A
   HREF="http://spirit.com.au/~dan/law/" TARGET="external">Australian Legal Information</A> -
     Daniel Austin  dan@spirit.com.au [8/'95]
   <A HREF="http://www.yahoo.com/Government/Law/Countries/Australia" TARGET="external">Yahoo on oz law</A> [8/'95]

%T Law Journal
%D 1998
%K Law, legal information, US, USA, internet, www, HREF, http, zz0398
%X <A HREF="http://www.ljx.com/" TARGET="external">[LJX]</A>
   <A HREF="http://www.ljx.com/internet/" TARGET="external">[LJX/internet]</A> [3/1998]

%T As You Like It (Ars Longa Grp Ltd)
%D 1995
%K literature, books, library, arts, online, www, HREF, http
%X <A HREF="http://www.portal.com/~skip/ayli.html" TARGET="external">As You Like It</A>
   copyright-expired books online

%T NIST Digital Library of Mathematical Functions
%D 2007
%K math, maths, function, numerical analysis, Gamma, Bessel, Hypergeometric,
   Legendre, Zeta, beta, www, HREF, http
%X [<A HREF="http://dlmf.nist.gov/" TARGET="EXTERNAL">www</A>]['07]

%T History of Mathematics at St. Andrews
%D 1994
%K mathematics, history, maths, mathematicians, science, biography,
   www, HREF, http
%X <A HREF="http://www-groups.dcs.st-and.ac.uk/~history" TARGET="external">history</A>
   email: bs@st-andrews.ac.uk (Ben Soares  12/'94)

%T Mathpuzzle.com
%D 1999
%K Mathematics puzzle, puzzles, math, maths, mathematical,
   www, HREF, http, zz1099
%X <A HREF="http://www.mathpuzzle.com/" TARGET="external">mathpuzzle.com</A> [10/1999]

%T MicroSoft XP
%D 2002
%K MicroSoft, MS, XP, MSXP, windows, operating system, licence, conditions,
   product activation, EULA, end user licence agreement, law, legal,
   product user rights, PUR, registration, reinstallation,
   privacy, www, http, HREF, zz0202
%X [<A HREF="http://www.arachnoid.com/boycott/">XP problems</A>][2/'02]
   ... You acknowledge and agree that Microsoft may automatically check
   the version of the Product and/or its components that you are
   utilizing and may provide upgrades or fixes to the Product that
   will be automatically downloaded to your Workstation Computer. ...
   [Also see: Registration Wizard]

%T MicroSoft's Registration Wizard
%D 1995
%K MicroSoft, MS, windows95, registration wizard, scandal, espionage,
   dirty trick tricks, computing, commercial, rumor, rumour,
   www, HREF, http, zz0595
%X <A HREF="/~lloyd/tildeMisc/1995.RegWiz.html" TARGET="external">here</A>

%T Internet Movie DataBase
%D 1994
%K Movie, movies, film, films, arts, entertainment, media, data base,
   imdb, uk, us, Cardiff, www, HREF, http, ftp
%X sign of the times - went commercial on 17/3/96
      [<A HREF="https://www.imdb.com">imdb.com</A>]['23]
      [<A HREF="http://uk.imdb.com/" TARGET="external">UK</A>['96]
      [<A HREF="http://us.imdb.com/" TARGET="external">US</A>['96]
      <A HREF="http://www.moviedatabase.com/" TARGET="external">[front door]</A> [10/'96].
   DataBase previously known as Cardiff Movie DataBase.
      <A HREF="http://ballet.cit.gu.edu.au/Movies/" TARGET="external">Australia</A>
      <A HREF="http://www.leo.org/Movies/" TARGET="external">Germany</A>
      <A HREF="http://www.csl.sony.co.jp/Movies/" TARGET="external">Japan</A>
      <A HREF="http://cezanne.daum.co.kr/Movies/" TARGET="external">Korea</A>
      <A HREF="http://www.gem.co.za/Movies/" TARGET="external">South Africa</A>
      <A HREF="http://www.cm.cf.ac.uk/Movies/" TARGET="external">UK</A>
      <A HREF="http://www.msstate.edu/Movies/" TARGET="external">USA</A>
   Send email with subject HELP FAQ to <A HREF="mailto:movie@ibmpcug.co.uk">movie@ibmpcug.co.uk</A>
   for information on The Internet Movie Database.
   <!-- email: cn@ibmpcug.co.uk (Colin Needham) -->       [6/'95]

%T Buena Vista Pictures
%D 1994
%K Movie, movies, film, films, arts, entertainment, media, Touchstone,
   Walt Disney, Hollywood, commercial, www, HREF, http
%X <A HREF="http://www.movies.com/" TARGET="external">[Buena Vista]</A> [2/'97]
   <A HREF="http://bvp.wdp.com/BVPM/" TARGET="external">[old URL]</A>     ['94]

%T MCA Universal
%D 1994
%K Movie, movies, film, films, arts, entertainment, media, commercial,
   www, HREF, http
%X <A HREF="http://www.mca.com/" TARGET="external">www.mca.com</A> [2/'97]

%T Sony Pictures
%D 1995
%K Movie, movies, film, films, arts, entertainment, media, commercial,
   www, HREF, http
%X <A HREF="http://www.spe.sony.com/Pictures/" TARGET="external">Sony Pictures</A> [2/'97]
   <A HREF="http://www.sony.com/" TARGET="external">Sony</A>

%T MultiMedia
%D 1994
%K multimedia, index, wwwIndex, unige, audio, aif, mpeg, computer, computing,
   FAQ, FAQs, zz0595, www, HREF, http
%X <A HREF="http://viswiz.gmd.de/MultimediaInfo/" TARGET="external">MultiMedia Info</A> [5/'95]
   was at:
   <A HREF="http://cuiwww.unige.ch/OSG/MultimediaInfo/" TARGET="external">MultiMedia UniGe</A> ['94]

%T Multimedia, Tech' Uni' Berlin
%D 1995
%K multimedia, MMC, Berlin, www, HREF, http, zz0695
%X MMC (Multimedia Collaboration) is a videoconferencing system developed,
   which runs on a wide variety of platforms.
   <A HREF=" http://www.prz.tu-berlin.de/docs/html/MMC/" TARGET="external">http://www.prz.tu-berlin.de/docs/html/MMC/</A>
   Nicolai Leymann    email: nicolai@prz.tu-berlin.de   [6/'95]

%T Early Music
%D 1995
%K music, early, arts, entertainment, www, HREF, http
%X <A HREF="http://www.catalog.com/virtual/jr/earlym.html" TARGET="external">early music</A>
   Still in early stages of development, but some info and links are there.
   Let me know if anyone has gifs related to early music that I could include.
   Justin Renquist    email: justinr@sirius.com  (1/'95)

%T MIDI
%D 1994
%K Music, MIDI, arts, digital, synthesizer, www, HREF, http
%X <A HREF="http://www.eeb.ele.tue.nl/midi/index.html" TARGET="external">MIDI</A>

%T MIDI analogue synthesizers
%D 1995
%K Music, MIDI, analogue synthesizers, www, HREF, http
%X <A HREF="http://www.me.chalmers.se/~thed/analog.html" TARGET="external">Synths</A> [3/'95]

%T Virtual Radio
%D 1994
%K Music, Radio, vradio, music, arts, entertainment, media, www, HREF, http
%X <A HREF="http://www.microserve.net:80/vradio" TARGET="external">VRadio</A>

%T CDnow
%D 1996
%K music, shop, store, CD, compact discs, com, entertainment,
   www, HREF, http, zz1196
%X CD shop:- <A HREF="http://www.cdnow.com/" TARGET="external">[web]</A> [11/'96]

%T UCLA and (2002) Columbia Law Library Music Copyright Infringement
   Online Archive
%D 2002
%K UCLA, Columbia, music, copyright, plagiarism, law, legal, case, cases,
   midi file, files, www, HREF, http
%X © @ [<A HREF="http://cip.law.ucla.edu/" TARGET="EXTERNAL">ucla</A>]['11].
   [<A HREF="http://library.law.columbia.edu/music_plagiarism/" TARGET="external">front door</A>][1/'03],
      [<A HREF="http://library.law.columbia.edu/music_plagiarism/index2.html" TARGET="external">index</A>][1/'03],
      [<A HREF="http://library.law.columbia.edu/music_plagiarism/titles_authors.html" TARGET="external">titles</A>][1/'03].

%T British National Corpus
%D 1995
%K natural language, NL, AI, text, texts, words, English, BNC, www, HREF, http
%X Extracts from 4124 modern British English texts of all kinds, both
   spoken and written.  Each text is segmented into orthographic sentence
   units, and each word automatically assigned a part of speech code. There
   are six and a quarter million sentences, and over 100 million words.
   -  British National Corpus, Oxford University Computing Services,
      13 Banbury Road, Oxford OX2 6NN, England
      <A HREF="http://info.ox.ac.uk/bnc" TARGET="external">BNC home page</A>
      tel +44 (1865) 273 280,  fax +44 (1865) 273 275
      email: natcorp@oucs.ox.ac.uk   [5/'95]

%T WordNet
%D 1995
%K natural language, NL, AI, text, word net, Princeton, words, www, HREF, http
%X <A HREF="http://www.cogsci.princeton.edu/%7Ewn/" TARGET="external">[wordnet]</A>       [2/'96]

%T Ig Nobel Prizes
%D 1997
%K Ig Nobel prize, igNobel, ignoble, noble, Science, spam, funny, silly,
   Annals Improbable Research, hot AIR, www, HREF, http, zz1097
%X [<A HREF="https://www.improbable.com/">improbable.com</A>][2021].
   WAS  [www dot improb dot com]  but since taken over.
   Communications: Sanford Wallace of Cyber Promotions, spam, spam, spam...
   [<A HREF="/~lloyd/tildeMisc/1994.IgNobel.html" TARGET="external">1994 Prizes</A>]

%T Microsoft and Open Source
%D 2001
%K Open Source, topical, Microsoft, MS, hotmail, opensource,
   free BSD, freeBSD, zz0601
%X [<A HREF="/~lloyd/tildeMisc/2001/2001-MS-BSD.html">more...</A>]

%T Mac on Linux
%D 2002
%K Operating Systems, Apple, Mac, MOL, maconlinux org,
   OS, OS9, OSX, OS10, cross platform, emulation
%X [<A HREF="http://www.maconlinux.org/" TARGET="external">maconlinux</A>][4/'02]


%T Ontology
%D 2007
%K ontology, ontologies, SUMO, Suggested Upper Merged Ontology, standard,
   OWL, Web Ontology Language, OWL DL, OWLDL, w3, w3c,  www, HREF, http
%X [<A HREF="http://www.ontologyportal.org/">SUMO@ontologyportal.org</A>]['07]
      Suggested Upper Merged Ontology (SUMO)...
      ...has been mapped to all of the WordNet lexicon.
   [<A HREF="http://www.w3.org/TR/owl-ref/">OWL@w3.org</A>];'07]
      ...Web Ontology Language (OWL) ...semantic markup language... for www.

%T GORP - Great Outdoor Recreation Pages
%D 1995
%K outdoor recreation, commercial, walking, camping, hiking, zz0795,
   gorp, com, www, HREF, http
%X <A HREF="http://www.gorp.com/" TARGET="external">www.gorp.com</A>

%T Pentium MMX Bug
%D 1997
%K Pentium, MMX, bug, error, fault, computer, computing, Intel,
   technology, hardware, 586, zz1197
%X Intel have done it again ...
   ... a certain sequence of instructions fed into the MMX (graphics) chip
   will cause the Pentium to freeze and require rebooting.
   It "shouldn't happen under normal circumstances" is the official
   Intel line, but bets are on for the number of weeks before viruses
   taking "advantage" of this "feature" appear!
   - LA 11/1997
   See also the Pentium division bug, 1994.

%T Pentium Bug
%M NOV
%D 1994
%K Pentium, bug, error, fault, computer, computing, technology, hardware,
   divide, division, floating point, 486, 586, Intel,  www, HREF, http
%X <A HREF="/~lloyd/tildeMisc/1994.Pentium.bug.html" TARGET="external">bug</A>
   <A HREF="http://www.mathworks.com/Pentium/README.html" TARGET="external">Mathworks collection (12/'94)</A>

%T Principia Cybernetica
%D 1995
%K philosophy, mind, free will, AI, cybernetics, systemic, computing,
   online, www, HREF, http
%X <A HREF="http://pespmc1.vub.ac.be/" TARGET="external">Principia Cybernetica</A>

%T Processing.org
%D 2006
%K processing, computer graphics, 2D, 3D, Java
%X beta, 4/2005
   [<A HREF="http://processing.org/">www</A>]['06]

%T National Museum of Photography, Film and Television
%D 1996
%K photo, film, films, movie, movies, TV, tele, telly, museums, NMPFT,
   archive, archives, institute, BFI, NFA, Bradford, national, British, BBC,
   ITV, Great Britain, GB, England, UK, Europe, EC, www, HREF, http, zz0996
%X <A HREF="http://www.nmsi.ac.uk/nmpft/" TARGET="external">[NMPFT]</A>[9/'96]
   online material is a "bit thin" as of 9/96
   also  National Film Archive,
         British Film Institute, 21 Stephen St., London SIP IPL
         tel: 0171 255 1444,  fax: 0171 436 7950
   and   BBC Written Archive, Caversham Park, Reading, KG4 8TZ
         (tel: 01734. 472 742,  Xts. 280 and 282,   fax: 01734 461 145)

%T RealAudio
%D 1995
%K radio, RealAudio, real audio, on demand, broadcast, broad casting,
   sound, multimedia, www, HREF, http, zz0895
%X <A HREF="http://www.realaudio.com/" TARGET="external">www.realaudio.com</A> [8/'95]
   real time audio broadcasting using 14.4K modems and standard phone lines
   - they say.

%T Robot Auto Racing Simulation (RARS)
%D 1995
%K robotics, auto, car, race, racing, robot, RARS, www, HREF, http
%X <A HREF="/~lloyd/tildeMisc/1995.RARS.html" TARGET="external">RARS</A>

%T SANE: Scanners Are Now Easy
%D 2001
%K SANE, scanner, scanners, scanning, scan, photo, photos, photographs,
   image, images, video, v4l, v4l2, Unix, Linux, HP, zz0801
%X [<A HREF="http://sane-v4l2.inodes.org/">v4l2</A>][11/'02]
   [<A HREF="http://www.mostang.com/sane/">sane</A>][8/2001]

%T Australian Schools on the InterNet
%D 1995
%K School, schools, Australia, K12, inter net, web, www, HREF, http
%X <A HREF="http://www.ufo.com.au/AusWired/Chalk/Schools.html" TARGET="external">here</A>
    Luke Howard  email: lukeh@ufo.com.au  [4/'95]

%T Australian Science Archives Project
%D 1994
%K science, history, scientist, technology, medicine, biography,
   ASAP, ASAPweb, www, HREF, http
%X <A HREF="http://coombs.anu.edu.au/SpecialProj/ASAP/ASAPHome.html" TARGET="external">ASAP home</A>
   <A HREF="http://coombs.anu.edu.au/SpecialProj/ASAP/asap_information.html" TARGET="external">about ASAP</A>

%T The Science Museum, London
%D 1995
%K Science, museum, technology, institution, London, England, UK, Europe,
   www, HREF, http, zz0595
%X <A HREF="http://www.nmsi.ac.uk/Welcome.html" TARGET="external">Welcome page</A>
   <A HREF="http://www.nmsi.ac.uk/Index/Index.html" TARGET="external">Index and Search</A>
   <A HREF="http://www.nmsi.ac.uk/galleries/computing.html" TARGET="external">galleries/computing</A>

%T Exploratorium
%D 1994
%K Science, museum, California, San Francisco, USA, fun, funn, www, HREF, http
%X <A HREF="http://www.exploratorium.edu/" TARGET="external">Exploratorium</A>

%T Solar System
%D 1995
%K solar system, space, nine planets, nineplanets, planet, astronomy,
   science, www, HREF, http
%X <A HREF="http://seds.lpl.arizona.edu/nineplanets/nineplanets/nineplanets.html" TARGET="external">Nineplanets</A>

%T Sport
%D 1994
%K sport, news, entertainment, mit, www, HREF, http
%X <A HREF="http://tns-www.lcs.mit.edu/cgi-bin/sports" TARGET="external">Sport</A>

%T Olympic Games
%K sport, entertainment, Olympics, www, HREF, http
%X <A HREF="http://www.atlanta.olympic.org/" TARGET="external">Atlanta 1996</A>

%T Stock Market
%K stockmarket, stocks, shares, share prices, www, HREF, http
%X <A HREF="http://www.moneyworld.co.uk/stocks/" TARGET="external">moneyworld UK</A> [12/97]

%T The World Lecture Hall
%D 1994
%K Teaching, education, course, notes, virtual, online, courseware, index,
   www, HREF, http
%X <A HREF="http://wwwhost.cc.utexas.edu/world/instruction/index.html" TARGET="external">Here</A>
   A big collection of www notes for many subjects.

%T British Broadcasting Corporation
%D 1994
%K television, TV, media, BBC, beeb, club, UK, Europe, www, HREF, http
%X <A HREF="http://www.bbcnc.org.uk/" TARGET="external">BBC networking club</A>

%T TB / HIV Research Laboratory at Brown U.
%D 1994
%K Tuberculosis, TB, HIV, Aids, infectious disease,
   medicine, science, Biology, Bio, Biol, MolBio,  www, HREF, http
%X <A HREF="http://www.brown.edu/Research/TB-HIV_Lab/" TARGET="external">TB HIV Lab at Brown University</A>
   The TB/HIV Research Laboratory is dedicated to research into the
   prevention and treatment of two infectious diseases of global importance -
   human immunodeficiency virus (HIV) and tuberculosis (TB).
   email: Gabriel_Meister@Postoffice.Brown.EDU  (12/'94)

%T Unicode
%K Unicode, UTF8, UTF-8, web, Greek letters, characters, set, sets, www, HREF, http
%X 1. Look at [<A HREF="http://www.hclrss.demon.co.uk/unicode/greek.html">www</A>][11/'01] α, β, γ...
      There's no need even to change the charset of the page -
      the ampersand-hash, `&#', says that it is Unicode.
   2. There is a Unicode compliant vim around. Look at the vim home
      page. I typed those using "yudit", which is a Unicode-oriented editor.
      It has a menu to select input language, then I typed in romanized Greek,
   - Jim Breen [11/2001]
   [<A HREF="http://www.unicode.org/">Unicode.org</A>][2/'02]

%T United Kingdom
%K United Kingdom, UK, Great Britain, GB, England, Scotland, Wales,
   Northern Ireland, Ulster, Rhuddlan, 1284, 1707, 1801, 1921, 1927
%X I don't know how authoritative this is, but the CIA Factbook says:
   [conventional long form: United Kingdom of Great Britain & Northern Ireland
    conventional short form: United Kingdom
    abbreviation: UK
    England has existed as a unified entity since the 10th century;
    the union between England and Wales was enacted under the Statute
    of Rhuddlan in 1284; in the Act of Union of 1707, England and Scotland
    agreed to permanent union as Great Britain; the legislative union of
    Great Britain and Ireland was implemented in 1801, with the adoption
    of the name the `United Kingdom of Great Britain and Ireland';
    the Anglo-Irish treaty of 1921 formalized a partition of Ireland;
    six northern Irish counties remained part of the United Kingdom as
    Northern Ireland and the current name of the country, `the United Kingdom
    of Great Britain and Northern Ireland', was adopted in 1927.]
   Both the Home Office and EU websites use the
   `United Kingdom of Great Britain and Northern Ireland' formula.
   So Great Britain is really England, Scotland and Wales.
   It would appear that `uk' is a better domain name than `gb'  -  Jim [10/'00]

%T Living Worlds
%D 1997
%K virtual reality, VRML, VRML2, livingworlds, world, www, HREF, http
%X <A HREF="http://www.livingworlds.com/" TARGET="external">[web]</A>[10/1997]

%T Virtual Reality Modeling Language (VRML)
%D 1994
%K virtual reality, VR, VRML, markup, Inventor, OOGL, Labyrinth, graphics,
   3D, Web, WebSpace, WebForce, computing, www, HREF, http
%X <A HREF="http://vrml.wired.com/" TARGET="external">VRML forum</A>  (4/'95)
   <A HREF="http://www.eit.com/vrml/" TARGET="external">VRML technical forum</A>  (4/'95)
   <A HREF="/~lloyd/tildeMisc/1995.WebSpace.html" TARGET="external">WebSpace and WebForce announcement</A> (4/'95)
   The VRML repository - browsers and viewers for Mac and PC:
     <A HREF="http://www.sdsc.edu/vrml/" TARGET="external">[sdsc.edu]</A>[7/1998]
   Weblynx Ultimate Virtual World Library on VRML projects
     <A HREF="http://weblynx.com.au/virtual.htm" TARGET="external">[weblynx.com.au]</A>[7/1998]
   Gallery of Virtual 3D Worlds shows VRML examples
     <A HREF="http://www.aesthetic.com/vrmlGallery/vrmlGallery_se.html" TARGET="external">[aesthetic.com]</A>[2/1998]
   The Virtual Cities Repository lists 3D computer models of cities
     <A HREF="http://aleph.afuu.fr/AN/test.html" TARGET="external">[aleph.afuu.fr]</A>[7/1998]

%T World War II Air Force Cartoon Journals
%D 1995
%K war, ww2, wwII, Rarey, www, HREF, http
%X <A HREF="http://www.nbn.com/home/rareybird/index.html" TARGET="external">here</A>

%T Andy Warhol
%D 1994
%K Warhol, art, arts, gallery, museum, www, HREF, http
%X <A HREF="http://www.warhol.org/warhol" TARGET="external">Andy Warhol museum Pittsburgh USA</A>

%T White House
%D 1994
%K WhiteHouse, Clinton, Gore, vice, president, politics, USA, www, HREF, http
%X <A HREF="http://www.whitehouse.gov/" TARGET="external">White House</A>
   <A HREF="http://www.whitehouse.gov/White_House/Family/html/First_Family.html" TARGET="external">First Family<IMG SRC="/~lloyd/tildeImages/People/Clinton.small.gif"></A>
   <A HREF="http://www.whitehouse.gov/White_House/EOP/First_Lady/html/HILLARY_Home.html" TARGET="external">Hilary Rodham Clinton home page</A>
   <A HREF="http://www.whitehouse.gov/White_House/EOP/OVP/html/GORE_Home.html" TARGET="external">Al Gore home page</A>

%A C. Tong
%T Women of Science at the Marine Biology Laboratory, Woods Hole
%D 1994
%K women, woman, gender, girl, girls, science, bio, biol, biology, MolBio, mbl,
   McClintock, www, HREF, http
%X [<A HREF="http://comm.archive.mbl.edu/publications/women_index.html">www</A>]['16]
   [<A HREF="http://hermes.mbl.edu/publications/women_index.html">www</A>]['14]
   [<A HREF="http://www.mbl.edu/publications/women_index.html">www</A>]['07]
   [<A HREF="http://www.mbl.edu/inside/what/news/publications/women_index.html">www</A>][5/'03]
   [<A HREF="http://hermes.mbl.edu/women_of_science/women.html" TARGET="external">www</A>][7/'01]
   [<A HREF="http://www.mbl.edu/html/WOMEN/intro.html" TARGET="external">Here</A>][/'94]

%A E. Spertus
%T Women and Computer Science
%K women, woman, gender, girl, girls, computer science, computing, CS, CSci,
   mit, www, HREF, http
%X [<A HREF="https://ellenspertus.com/" TARGET="EXTERNAL">ellenspertus.com</A>][2022].
   [<A HREF="http://people.mills.edu/spertus/Gender/gender.html"  TARGET="external">www</A>][2007]
   [<A HREF="http://www.mills.edu/ACAD_INFO/MCS/SPERTUS/Gender/gender.html" TARGET="external">www</A>][1998]
   [<A HREF="http://www.ai.mit.edu/people/ellens/gender.html" TARGET="external">www</A>][1994]

%A E. Freeman
%A S. Hupfer
%T TAP: The Ada Project
%K women, woman, gender, girl, girls, computer science, computing, CS, CSci,
   Ada Lovelace, www, HREF, http, yale
%X [<A HREF="http://www.women.cs.cmu.edu/ada/">cmu</A>][2014]
   [<A HREF="http://tap.mills.edu/" TARGET="external">www</A>][2002]
   [<A HREF="http://www.cs.yale.edu/~tap/tap.html" TARGET="external">www</A>][1999]
   [<A HREF="http://www.cs.yale.edu/HTML/YALE/CS/HyPlans/tap/tap.html" TARGET="external">www</A>][1994]
   <IMG SRC="/~lloyd/tildeImages/People/Ada.gif">

%T VisLab, Visualisation
%D 1995
%K visualization, computer graphics, GUI, scientific, data,
   VisLab, Sydney, usyd,  www, HREF, http
%X <A HREF="http://www.usyd.edu.au/su/vislab/" TARGET="external">VisLab</A>

%T T_Vision
%D 1995
%K visualization, TVision, T_Vision, Terra, planet, earth, view,
   computer graphics, www, HREF, http, zz0795
%X Earth vis' project, can fly around and zoom in to objects
   just a few cm in size.  Runs on big sgi machines.
   <A HREF="http://www.artcom.de/projects/terra/" TARGET="external">Terra</A> [7/'95]

%T Web Browsers
%D 2001
%K web browser, konqueror, conqueror, KDE,  Microsoft, MS Explorer,
   Mozilla,  Netscape, AOL, navigator,  Opera, Opera5,
   HTML, HTML4, XML, www, HREF, http, zz0701
%X [<A HREF="http://www.konqueror.org/" TARGET="external">konqueror.org</A>][7/'01]
      KDE as per Linux
   [<A HREF="http://www.mozilla.org/" TARGET="external">mozilla</A>][7/'01]
      open source
   [<A HREF="http://developer.netscape.com/" TARGET="external">netscape</A>][7/'01]
   [<A HREF="http://www.opera.com/" TARGET="external">opera.com</A>][7/'01]
      Linux, Solaris, Mac, Windows,  small, under 3MB (plus Java)
      (US$10, or free with ad's)

%W WWW  W3.org
%K WWW, W3, org, world wide web, HTML, XML, HREF, http
%X <A HREF="http://www.w3.org/" TARGET="external">[www]</A> [11/1999]
   <A HREF="http://www.w3.org/TR/" TARGET="external">[/TR/]</A> rec's [11/1999]

%A M. Podlipec
%T XAnim
%D 1994
%K XAnim, anim, animation, mpg, mpeg, qtm, mov, quick time, computing,
   viewer, program,  www, HREF, http
%X <A HREF="http://www.portal.com/~podlipec/home.html" TARGET="external">XAnim home page</A>


%A E. M. Forster
%T The Machine Stops
%D 1909
%K book, c1909, c190x, c19xx, zz0715, SciFi, novel, short story, internet,
   human, reality, AI
%X "... a science fiction short story (12,300 words) by E. M. Forster.
   After initial publication in The Oxford & Cambridge Review (Nov. 1909)
   ... The story is particularly notable for predicting new technologies such
   as instant messaging & the Internet. ... set in a post-apocalyptic world
   where humanity lives underground & relies on a giant m/c to provide
   their needs. ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/The_Machine_Stops">wikip</A>]['15].
   Penguin classic, 2011; uk us isbn:0141195983; uk us isbn13:978-0141195988.

%A K. Capek
%T Rossum's Universal Robots
%D 1920
%O Rossumovi UniverzalnÃ Roboti
%K play, SciFi, robot, AI, c1920, c192x, c19xx, zz0124, Karel Capek, RUR,
   android
%X introduced the word "robot" to the English language & to SciFi as a whole
   (Also see [<A HREF="https://doi.org/10.1126/science.adm9749">doi:10.1126/science.adm9749</A>]['24].)

%A O. G. Selfridge
%T Pandemonium: A paradigm for learning
%J Proc. of a Symp. at the Nat. Physical Lab.
%V 1
%M NOV
%D 1958
%K conf, c1958, c195x, c19xx, zz1116, AI, II, NN, ANN, Pandemonium, parallel,
   machine learning, demon, demons, aspect-oriented programming, NLP
%X "... The basic motif behind our model is the notion of
   parallel processing.  ..."
   -- scan@[<A HREF="https://aitopics.org/download/classics:504E1BAC">aitopics</A>]['22].
   (Also see, "... Selfridge wrote important early papers on neural networks &
   pattern recognition & machine learning, & his 'Pandemonium' paper (1959) is
   generally recognized as a classic in AI. ... introduced the notion of
   'demons' that record events as they occur, recognize patterns in those events
   & may trigger subsequent events according to patterns they recognize. Over
   time, this idea gave rise to aspect-oriented programming...."
   -- OGS@[<A HREF="https://en.wikipedia.org/wiki/Oliver_Selfridge">wikip</A>]['16].)
   ? in Mechanisation of Thought Processes: Symp. Held at the National
   Physical Lab. on 24th, 25th, 26th & 27th Nov 1958, vol.2 ?

%A J. Weizenbaum
%T On the impact of the computer on society: How does one insult a machine?
%J Science
%V 176
%N 4035
%M MAY
%D 1972
%K jrnl, c1972, c197x, c19xx, zz0823, AI, society, Weizenbaum, Turing test,
   artificial intelligence, risk, risks, chatBot, technology, ethics,
   CSci, CompSci
%X -- [<A HREF="https://doi.org/10.1126/science.176.4035.609">doi:10.1126/science.176.4035.609</A>]['23].
   Also see,
   "... W. argued that his fellow comp.scientists should try to view their
   activities from the standpoint of a member of the public. Whereas C.S.
   wonder how to get their technology to work & use 'electronic wizardry' to
   make it safe, W. argued that ordinary people would ask 'is it good?' &
   'do we need these things?' ..."
   -- [<A HREF="https://www.science.org/doi/full/10.1126/science.adk0176">8/2023</A>]['23].

%A B. R. Gaines
%T Behaviour/structure transformations under uncertainty
%J Int. J. Man-Machine Studies
%V 8
%P 337-365
%D 1976
%K jrnl, IJMMS, c1976, c197x, c19xx, formal language, inductive inference,
   infer, II, AI, learn, grammar, probabilistic, finite-state, FSA, machine,
   FSM, automaton, PFSA, PFSM
%X "... analyses the problem of determining a structure for an automaton,
   optimal in some sense, from observations of its behaviour which are
   themselves uncertain. ... An implemented algorithm for this modelling process
   is then described with examples of its application to: probabilistic sources;
   sampled deterministic sources; grammatical inference; human behaviour; and
   program derivation from traces."
   --- [<A HREF="https://doi.org/10.1016/S0020-7373(76)80005-3">doi:10.1016/S0020-7373(76)80005-3</A>].
   (Ref in:  G e o r g e f f   &   W a l l a c e  '84.)
   [Also search for: infer finite state automaton].

%A A. Newell
%A H. A. Simon
%T Computer science as empirical inquiry: symbols and search
%J CACM
%V 19
%N 3
%P 113-?
%M MAR
%D 1976
%K jrnl, CACM, c1976, c197x, c19xx, AI, GOFAI, symbolic,
   artificial intelligence, computing
%X via enews <!-- email: chandler at helix.nih.gov --> (1/'95).

%A P. Cheeseman
%T A Problem Solving System with Learning
%I Dept. Comp. Sci., Monash University, .au
%D 1979
%K PhD thesis, artificial intelligence, AI, c1979, c197x, c19xx
%X '... received his B.S. degree in Physics and Mathematics with honors
   from Melbourne University (Australia) in 1971, his M.Phil. in
   Applied Mathematics from Waikato University (New Zealand) in 1973, and
   his PhD degree in AI from Monash Uni.
   (Australia) in 1979. His Ph.D thesis title was
   "A Problem Solving System with Learning".'
   [<A HREF="http://ic.arc.nasa.gov/ic/projects/bayes-group/people/cheeseman/">nasa</A>]['05].

%A B. G. Buchanan
%A E. H. Shortliffe
%T Uncertainty and evidential support
%P ?-?
%B Rule Based Expert Systems: The MYCIN Experiment of the
   Stanford Heuristic Programming project
%I AddisonWesley
%D 1984
%K MYCIN, AI, rule, rules, evidence, system, c1984, c198x, c19xx, medical
%X ref in  M u s e n.

%A H. J. Berliner
%D 1984
%T Search vs knowledge: An analysis from the domain of games
%P 105-117
%B Artificial and Human Intelligence
%E Elithorn, A.
%E Banerji, R.
%I Elsevier Science Publishers, New York
%K AHI, AI, game, play, playing, search, tree, plie, ply, plies, depth
%X [try keywords   `game', `game tree' or `search tree'  in bib'searches]
   From: fawcett at nynexst.com (Tom Fawcett)  (7/94)

%A W. J. Clancey
%T Heuristic classification
%J Artificial Intelligence
%V 27
%P 289-350
%D 1985
%K jrnl, AI, MYCIN, PUFF, rule based, c1985, c198x, c19xx
%X ref in M u s e n.
   [Also search for: classification].

%A M. E. Lesk
%T Automatic sense disambiguation using machine readable dictionaries:
   how to tell a pine cone from an ice cream cone
%J Proc. of the 5th annual int. conf. on Systems documentation
%W New York
%I ACM
%P 24-26
%D 1986
%K conf, SIGDOC, c1986, c198x, c19xx, zz0518, MLesk, MELesk, algorithm,
   word sense, wordSense, NLP, context, ambiguity
%X pdf@[<A HREF="https://doi.org/10.1145/318723.318728">doi:10.1145/318723.318728</A>]['18].
   Also see,  "... based on the assumption that words in a given
   'neighborhood' (section of text) will tend to share a common topic.
   A simplified version of the Lesk alg. is to compare the dictionary
   defn of an ambiguous word with the terms contained in its neighborhood. ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Lesk_algorithm">wikip</A>]['18].

%A M. Henrion
%T Propagating uncertainty in Bayesian networks by probabilistic logic sampling
%J UAI
%P 149-163
%D 1986
%K conf, UAI, UAI2, c1986, c198x, c19xx, network, stochastic, sample, generate
%X "... current algorithms for propagating updates are either restricted to
   singly connected networks (Chow trees), as the scheme of Pearl & Kim, or
   they are liable to exponential complexity when dealing with multiply
   connected networks. Probabilistic logic sampling is a new scheme employing
   stochastic simulation which can make probabilistic inferences in large,
   multiply connected networks, with an arbitrary degree of precision
   controlled by the sample size. A prototype implementation, named Pulse, is
   illustrated, which provides efficient methods to estimate conditional
   probabilities, perform systematic sensitivity analysis, & compute evidence
   weights to explain inferences."

%A K.-C. Chang
%A R. Fung
%T Symbolic probabilistic inference with both discrete and continuous variables
%I IEEE Trans. Systems, Man and Cybernetics
%V 25
%N 6
%P 910-916
%M JUN
%D 1995
%K jrnl, IEEE, c1995, c199x, c19xx, general, mixed Bayesian network, dowe, nets,
   machine learning, real, continuous, discrete, inverse, networks
%X " ... SPI ... both discrete and continuous variables (SPI-DC) ..."
   -- [<A HREF="http://dx.doi.org/10.1109/21.384253">doi:10.1109/21.384253</A>]['00].
   [Also search for: Shachter mixed c1990].

%A C. Adami
%T Learning and complexity in genetic auto-adaptive systems
%J Physica D
%V 80
%N ?
%P 154-?
%D 1995
%K auto adaptive, Tierra, Avida, artificial life, AL, genetic algorithm, GA,
   learn, phase transition, disorder, chaos, fractal
%X  We describe and investigate the learning capabilities displayed by a
    population of self-replicating segments of computer code subject to random
    mutation: the tierra environment.  We find that learning is achieved
    through phase transitions that adapt the population to the environment it
    encounters, with a learning rate characterized by external parameters such
    as mutation rate and population size.  Our results suggest that most
    effective learning is achieved close to the transition to disorder, and
    that learning curves of evolutionary systems are fractal.
  Organization: Avida Artificial Life group
  email: brown at krl.caltech.edu (C. Titus Brown)               (7/94)
  <A HREF="http://www.krl.caltech.edu/avida/">AVIDA</A>
  anonymous ftp: ftp.krl.caltech.edu (131.215.79.21) see /pub/avida/

%A J. Pearl
%T Causal diagrams for empirical research
%J Biometrika
%V 82
%P 669-710
%D 1995
%K jrnl, diagram, causal model, c1995, c199x, c19xx, zz0905, graphical models,
   network, d-separation, dSeparation, nonparametric, AI, II, cause, effect
%X NB. Paper pp.669-688, discussion pp.688-702, rejoinder pp.702-710.
   "... graphical models can be used as a math. language for integrating
   statistical & subject-matter info.. ... develops a principled,
   nonparametric framework for causal inference, in which diagrams are queried
   to determine if the assumptions available are sufficient for identifying
   causal effects from nonexperimental data. If so the diagrams can be queried
   to produce math. expressions for causal effects in terms of observed
   distributions; otherwise, the diagrams can be queried to suggest additional
   obs. or aux. experiments from which the desired inferences can be obtained."
   -- [<A HREF="http://bayes.cs.ucla.edu/R218-B.pdf">pdf</A>]['05].

%A Charniak
%T Statistical Language Learning
%I MITpress
%D 1994 ish ?
%K text, book, AI, natural language processing, NL, NLP, statistics, stats,
   machine learn, c199x, c19xx
%X isbn:0-262-03216-3
   a useful survey of basic techniques in statistical language
   modelling.  Much of this research has appeared either in dissertations
   or obscure (to me at least) conference proceedings.  Charniak has
   done a good job of collecting and collating basic material
   into a readable book at the graduate and advanced undergraduate level.
  Mark Johnson
  Cognitive and Linguistic Sciences, Box 1978,       (7/'94)
  Brown University, Providence, RI 02912, USA
  email: mj at cs.brown.edu

%A W. Buntine
%T Generalized subsumption and its application to induction and redundancy
%J Artificial Intelligence
%V 36
%P 149-176
%M ?
%D 1988
%K AI, inductive inference, II, c1988, c198x, c19xx

%A D. C. Dennett
%T When philosophers encounter Artificial Intelligence
%J Daedalus
%V 117
%N 1(AI)
%P 283-295
%D 1988
%K jrnl, c1998, c198x, c19xx, zz1023, philosophy, AI, mind, frame problem
%X -- [<A HREF="https://www.jstor.org/stable/20025148">jstor:20025148</A>]['23].
   Also see DD@[<A HREF="https://en.wikipedia.org/wiki/Daniel_Dennett">wikip</A>]['23].

%A J. R. Quinlan
%T Induction of decision trees
%J Machine Learning
%V 1
%N 1
%P 81-106
%M MAR
%D 1986
%K DTree, ID3, supervised classification, decision tree,
   inductive inference, II, expert system, c1986, c198x, c19xx, zz1115
%X "The technology for building knowledge-based systems by inductive inference
   from examples has been demonstrated successfully in several practical
   applications. This paper summarizes an approach to synthesizing DTs that has
   been used in a variety of systems, & it describes one such system, ID3, in
   detail. Results from recent studies show ways in which the methodology can be
   modified to deal with information that is noisy &/or incomplete. A reported
   shortcoming of the basic alg. is discussed & two means of overcoming it are
   compared. ... concludes with illustrations of current research directions."
   -- [<A HREF="http://dx.doi.org/10.1023/A:1022643204877">doi:10.1023/A:1022643204877</A>]['15].
   [Also search for: C45]  and   [Also search for: DTree].

%A G. F. Cooper
%T The computational complexity of probabilistic inference using
   Bayesian belief networks
%J Artificial Intelligence
%V 42
%N 2-3
%P 393-405
%M MAR
%D 1990
%K jrnl, AI, network, c1990, c199x, c19xx, NPH, NP hard, probability,
   knowledge representation, machine learning, II
%X "...show that probabilistic inference using belief networks is NP-hard. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0004-3702(90)90060-D">doi:10.1016/0004-3702(90)90060-D</A>]['05] [30 refs]

%A J. R. Quinlan
%T Learning logical definitions from relations
%J Machine Learning
%V 5
%N 3
%P 239-266
%M ?
%D 1990
%K rule, rules, DTree
%X [Also search for: DTree].

%A A. J. Hendriks
%A D. M. Lyons
%T A methodology for creating and adapting reactive systems
%J Int. J. on AI Tools
%V 2
%N 2
%P ?-?
%D 1993
%K robot, robots, AI, jrnl

%A S. Harnad
%T The symbol grounding problem
%J Physica D
%V 42
%N ?
%P 335-346
%M ?
%D 1990
%K AI, c1990, c199x, c19xx, zz1124, philosophy
%X "... How can the semantic interpretation of a formal symbol system be made
   intrinsic to the system, rather than just parasitic on the meanings in our
   heads? ..."
   -- [<A HREF="http://arxiv.org/abs/cs/9906002v1">arxiv:cs/9906002v1</A>]['24],
      [<A HREF="https://doi.org/10.1016/0167-2789(90)90087-6">doi:10.1016/0167-2789(90)90087-6</A>]['24].

%A P. Kuner
%A B. Ueberreiter
%T Pattern recognition by graph matching-combinatorial versus continuous
   optimization
%J Int. J. Pattern Recognition and Artificial Intelligence
%V 2
%N 3
%P 527-542
%M ?
%D 1988
%K IJPRAI, AI, jrnl
%X via <!-- email: rangarajan-anand@cs.yale.edu --> Anand Rangarajan (11/'94)

%A R. Shachter
%A W. Del Favero
%A B. D'Ambrosia
%T Symbolic probabilistic inference: A probabilistic perspective
%J AAAI
%P ?-?
%D 1990
%K conf, AAAI, SPI, mixed Bayesian networks, network, general,
   c1990, c199x, c19xx

%A T. S. Verma
%A J. Pearl
%T Equivalence and synthesis of causal models
%J Proc. 6th Conf. on Uncertainty in AI
%I Elsevier
%P 255-270 (often as 220-227)
%D 1990
%K conf, UAI, c1990, c199x, c19xx, model, Bayesian net, nets, networks, cause,
   effect, statistical equivalence class, SEC, pattern, Vstructure
%X "...DAGs to model the qualitative structure of causal theories, allowing the
   params. to be est. from observational data. 2 causal models are equiv. if
   there is no experiment which could distinguish one from the other. A
   canonical representation for causal models is presented which yields an
   efficient graphical criterion for deciding equivalence, & provides a
   theoretical basis for extracting causal structures from empirical data. This
   rep'n is then extended to the more general case of an embedded causal model,
   that is, a DAG in which only a subset of the vars. are observable. The
   canonical representation presented here yields an efficient alg. for
   determining when 2 embedded causal models reflect the same dependency
   information. This alg. leads to a model theoretic defn of causation in terms
   of statistical dependencies."   -- in isbn:0444892648.
   "two network structures are independence equivalent if and only if they have
   the same structure ignoring arc directions and the same v structures"

%A S. L. Lauritzen
%T Propagation of probabilities, means and variances in mixed graphical
   association models
%J J. Amer. Stat. Soc.
%V 87
%N 420
%P 1098-1108
%M DEC
%D 1992
%K jrnl, JASS, c1992, c199x, c19xx, mean, variance, model, Bayesian network,
   networks, mixed, discrete, continuous, HUGIN
%X "... local comp. of exact prob., means & variances for mixed qualitative &
   quantitative vars.. ...based upon distributions having the property that the
   conditional distribution of the quantitative vars., given the qualitative,
   is multi-variate Gaussian. The computational architecture is set up by
   forming a tree of belief universes, & the calc'ns are then performed by
   local message passing between universes. The asymmetry between the
   quantitative & qualitative vars sets some additional limitations for the
   specification & propagation structure. Approx. methods when ..."

%A K. G. Olesen
%T Causal probabilistic networks with both discrete and continuous variables
%J IEEE Trans. on Pattern Analysis and Machine Intell.
%V 15
%N 3
%P 275-279
%M MAR
%D 1993
%K jrnl, c1993, c199x, c19xx, mixed, Bayesian, network, discrete, continuous,
   HUGIN, Lauritzen
%X "An extension of the expert system shell known as handling uncertainty by
   general influence networks (HUGIN) to include [cts vars], in the form of
   linear additive normally distributed variables, is presented. ...foundation
   of the method was developed by [L], whereas this report primarily focus on
   implementation aspects. ...several advantages over purely discrete sys.. ...
   more natural model of the domain in question, knowledge acquisition is eased,
   & the complexity of belief revision is most often reduced considerably."
   -- [<A HREF="http://dx.doi.org/10.1109/34.204909">doi:10.1109/34.204909</A>]['05].

%E Josephson
%E Josephson
%T Abduction: Computation, Philosophy, Technology
%I CUP
%D 1994
%K AI, CUP, book, text, c1994, c199x, c19xx
%X Cambridge University Press
   <!-- email: chandra@cis.ohio-state.edu --> (B Chandrasekaran   11/'94)

%A B. Chandrasekaran
%T Functional representation and causal processes
%J Advances in Computers
%V 38
%I AcademicPress
%D 1994
%P 73-143
%K cause, causal resoning, AI
%X <!-- email: chandra@cis.ohio-state.edu --> (B Chandrasekaran   11/'94)

%E R. C. Schank
%E A. Kass
%E C. K. Riesbeck
%T Inside Case-Based Explanation
%I Lawrence Erlbaum Assoc., Hillsdale, NJ.
%D 1994
%K book, text, AI, computing, CSci, abduction, causal model models reasoning
%X You can contact the editors at   email: kass at ils.nwu.edu
   Ashwin Ram (12/'94) <!-- email: ashwin.ram@cc.gatech.edu --> .

%E G. Piatetsky-Shapiro
%E W. J. Frawley
%T Knowledge Discovery in Databases
%I MIT-Press
%D 1991
%K database, data base, data mining, book, text,  CSci, computing
%X isbn:0-262-66070-9
   from Prof. William W. Armstrong <!-- email: arms@cs.ualberta.ca --> [2/95]
   also: Cecil Lee   <!-- email: cecil@technet.sg -->  [6/'95]

%E G. Schreiber
%E B. Wielinga
%E J. Breuker
%T KADS: A Principled Approach to Knowledge-Based System Development
%I AcademicPress
%S Knowledge-Based Systems Book Series
%V 11
%D 1993
%K book, text, c1993, c199x, c19xx, AI, ontology
%X (also see c2000)  isbn:0126290407.

%A C. Adami
%T On modeling life
%J Artificial Life
%V 1
%D 1994
%P 428-?
%O Proc. Artificial Life IV, MITpress, 1994, p. 269
%K Avida, artificial life, AL, computing, jrnl, zz0595
%X via: Titus Brown    email: brown at krl.caltech.edu  [5/'95]

%A C. Adami
%A C. T. Brown
%T Evolutionary learning in the 2D artificial life system Avida
%J Proc. Artificial Life IV
%I MITpress
%P 377-?
%D 1994
%K Avida, artificial life, AL, computing, conf, zz0595
%X via: Titus Brown    email: brown at krl.caltech.edu  [5/'95]

%A C. Adami
%A C. T. Brown
%A M. Haggerty
%T Abundance distributions in artificial life and stochastic models:
   "age and area" revisited
%J 3rd European Conference on Artificial Life,
%W Grenada, Spain
%P ?-?
%M JUN
%D 1995 (to appear)
%K ECAL, ECAL3, ECAL95, Avida, artificial life, AL, computing, conf, zz0595
%X via: Titus Brown    email: brown at krl.caltech.edu  [5/'95]

%A A. Sloman
%T Semantics in an intelligent control system
%J Phil. Trans. of the Royal Society: Physical Sciences and Engineering
%V 349
%N 1689
%P 43-58
%D 1994
%K inference, information, CSci, computing, AI, jrnl, PTRS, zz0695
%X <A HREF="ftp://ftp.cs.bham.ac.uk/pub/dist/cog_affect/">FTP</A>
   <A HREF="http://www.cs.bham.ac.uk/~axs/cog_affect">WWW</A>
   in the file called Aaron.Sloman_semantics.ps.Z
   There's another paper extending some of the ideas, in the file
   Sloman.turing90.ps.Z
   - Aaron Sloman (<A HREF="http://www.cs.bham.ac.uk/~axs">www home page</A>)
     School of Computer Science, The University of Birmingham, B15 2TT, England
     email: A.Sloman at cs.bham.ac.uk  OR A.Sloman at bham.ac.uk      [6/'95]

%E L. Steels
%E R. A. Brooks
%T The 'Artificial Life' Route to 'Artificial Intelligence'. Building
   Situated Embodied Agents
%I Lawrence Erlbaum Ass., New Haven.
%D 1993
%K intelligent agent, agents, AI, computing, book
%X via Martin "Lolly" Lorenz <!-- email: martinl@ai.univie.ac.at --> [6/'95]

%A L. Steels
%T The Homo Cyber Sapiens, the Robot Homonidus Intelligens, and
   the 'artificial life' approach to artificial intelligence
%J Proc. Burda Symp. on Brain-Computer-Interfaces
%W Munich
%P ?-?
%M FEB
%D 1995
%K intelligent agent, agents, AI, computing, conf
%X via Martin "Lolly" Lorenz <!-- email: martinl@ai.univie.ac.at --> [6/'95]

%E L. Steels
%T The Biology and Technology of Autonomous Agents
%I Springer
%S NATO ASI Series F
%V 144
%D 1995
%K intelligent agent, agents, AI, computing, book, zz0695
%X via Martin "Lolly" Lorenz <!-- email: martinl@ai.univie.ac.at --> [6/'95]

%A S. A. Umpleby
%T The Cybernetics of Conceptual Systems
%I Inst. for Advanced Studies, Stumpergasse 56, A-1060 Vienna, Austria
%M JUL
%D 1994
%K analogy
%X [<A HREF="http://www.csu.edu.au/ci/vol03/paper4/node7.html">ref</A>][10/'02]
   [<A HREF="http://gwis.gwu.edu/~umpleby/Conceptual_Systems.txt">www</A>][?]

%A D. Hofstadter
%Q The Fluid Analogies Research Group(?)
%T Fluid Concepts and Creative Analogies: Computer Models of the
   Fundamental Mechanisms of Thought
%I BasicBooks
%D 1995
%K book, text, analogy, like, similar, way, program, copy cat, copycat,
   c1995, c199x, c19xx
%X [<A HREF="http://www.psych.indiana.edu/people/homepages/hofstadter.html">home</A>][10/'02]
   [<A HREF="http://www.csu.edu.au/ci/vol03/paper4/node7.html">ref</A>][10/'02]

%A N. Friedman
%A M. Goldszmidt
%T Learning Bayesian networks with local structure
%J UAI
%P 252-262
%E 1996
%K conf, UAI, UAI96, CUAI, AI, learning, network, causal, CPD, dowe, dtree,
   CPT, decision trees, dld, node, nodes, classification tree, inverse, zz0104,
   CTree, Bnet, net, asymmetric, c1996, c199x, c19xx
%X "... examine a novel addition to the known methods for learning Bayesian
   networks from data that improves the quality of the learned networks. Our
   approach explicitly represents and learns the local structure in the
   conditional probability tables (CPTs), that quantify these networks. This
   increases the space of possible models, enabling the representation of CPTs
   with a variable number of parameters that depends on the learned local
   structures. The resulting learning procedure is capable of inducing models
   that better emulate the real complexity of the interactions present in the
   data. We describe the theoretical foundations and practical aspects of
   learning local structures, as well as an empirical evaluation of the
   proposed method. This evaluation indicates that learning curves
   characterizing the procedure that exploits the local structure converge
   faster than these of the standard procedure. Our results also show that
   networks learned with local structure tend to be more complex (in terms of
   arcs), yet require less parameters." [<A HREF="http://www.cs.huji.ac.il/~nirf/Abstracts/FrG3.html">paper</A>][01/'04] [11 pages]
   [I.e. Can use a decision- (classification-) tree in a net's (local) node.]
   -- [<A HREF="http://www.cs.huji.ac.il/~nirf/">~nirf</A>][3/'04],
      [<A HREF="http://robotics.stanford.edu/~moises/">~moises</A>][1/'04].
   [Also search for: network local structure].

%A L. P. Kaelbling
%A M. L. Littman
%A A. W. Moore
%T Reinforcement learning: A survey
%J J. of AI Res.
%V 4
%P 237-285
%D 1996
%K jrnl, JAIR, survey, intro, c1996, c199x, c19xx, zz0822,
   reinforcement learning, AI
%a -- cs/9605103@[<A HREF="https://arxiv.org/abs/cs/9605103">arXiv</A>]['22],
      [<A HREF="https://doi.org/10.1613%2Fjair.301">doi:10.1613/jair.301</A>]['22].
   Also see RL@[<A HREF="https://en.wikipedia.org/wiki/Reinforcement_learning">wikip</A>]['22].

%A J. B. D. Marshall
%A D. R. Hofstadter
%T Beyond copycat: Incorporating self-watching into a computer model of
   high-level perception and analogy-making
%J 1996 Midwest Artif. Intell. and Cog. Sci. Conf.
%E M. Gasser
%D 1996
%K conf, AI, copycat, metacat, analogy, c1996, c199x, c19xx
%X [<A HREF="http://www.psych.indiana.edu/people/homepages/hofstadter.html">Hofs'</A>][10/'02]
   [<A HREF="http://www.cs.indiana.edu/event/maics96/Proceedings/Marshall/marshall.html">paper</A>][10/'02]

%A D. R. Hofstadter
%A J. B. D. Marshall
%T From Copycat to Metacat: Developing a Self-Watching Framework for
   Analogy-Making
%E T. Veale
%J Proc. of the Mind II: Computational Models of Creative Cognition Conference
%W Dublin City University
%D 1997
%O TR 115, Indiana University, Center for Research on Concepts and
   Cognition, 1997.
%K conf, CopyCat, MetaCat, meta cat, analogy
%X [<A HREF="http://www.psych.indiana.edu/people/homepages/hofstadter.html">home</A>][10/'02].

%A C. E. Sluzki
%T The Eigen-Values of Stories: In Homage to Heinz von Foerster
%J Conf. Cybernetics and Circularity: A Conf. on the Seeds of
   Cybernetics in the Work of Heinz von Foerster,
   Annual meeting of the American Society for Cybernetics,
%W U. Illinois, Chicago
%P ?-?
%M MAY
%D 1995
%K story, therapy
%X [<A HREF="http://www.csu.edu.au/ci/vol03/paper4/node7.html">ref</A>][10/'02]

%A Z. Pawlak
%A J. W. Grzymala-Busse
%A R. Slowinski
%A W. Ziarko
%T Rough sets
%J CACM
%V 38
%N 11
%P 88-95
%D 1995
%K jrnl, CACM, rough set, sets, indiscernibility relation, fuzzy, AI
%X "Rough set theory, introduced by Zdzislaw Pawlak in the early 1980s, is a
   new math. tool to deal with vagueness and uncertainty. This approach seems
   to be of fundamental importance to [AI] and cognitive sciences, esp. in the
   areas of ML, knowledge acquisition, decision analysis, KD from DBs, expert
   sys., decision support sys., inductive reasoning, and pattern recognition."
   [<A HREF="http://doi.acm.org/10.1145/219717.219791">doi:10.1145/219717.219791</A>]['05], 25 refs.

%A C. K. Chow
%A C. N. Liu
%T Approximating discrete probability distributions with dependence trees
%J IEEE Trans. on Inf. Theory
%V IT-14
%N 3
%P 462-467
%M MAY
%D 1968
%K jrnl, c1968, c196x, c19xx, IT14, IEEE, first order, dependence tree,
   Bayesian network, net, nets
%X fast algorithm from matrix of pairwise mutual information
   by using a maximum spanning tree (MST).
   "... to approx. optimally an n-dimensional discrete prob. dist. by a product
   of 2nd-order dists., or the dist. of the 1st-order tree dependence. The
   problem is to find an optimum set of n-1 1st order dependence relationship
   among the n vars.. ... the procedure [here] yields an approx. of a min.
   difference in information. ... shown that when this proc. is applied to
   empirical obss. from an unknown dist. of tree dependence, the proc. is the
   maximum-likelihood estimate of the distribution."
   -- pdf@[<A HREF="http://www.cs.toronto.edu/~roweis/csc2515/readings/chowliu.pdf">tor'nto</A>]['06],
      pdf@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.133.9772&rep=rep1&type=pdf">c'teseer</A>]['18],
      [<A HREF="https://doi.org/10.1109/TIT.1968.1054142">doi:10.1109/TIT.1968.1054142</A>]['18] (subscr'n}.

%A B. R. Gaines
%T Axioms for adaptive behaviours
%J Int. J. Man-Machine Studies
%V 4
%P 169-199
%D 1971
%K AI, jrnl, IJMMS
%X from  R a m a n 's   thesis '97

%A D. Michie
%T On Machine Intelligence
%I Wiley
%D 1974
%K book, text, c1974, c197x, c19xx, Donald Michie, AI
%X 1st ed 1974.  2nd ed 1986.
   dm@[<A HREF="http://www.aiai.ed.ac.uk/~dm/">ed ac uk</A>]['10].

%A F. J. Monyanski (sp?)
%A T. L. Booth
%T Inference of finite state probabilistic grammars
%J IEEE Trans Computers
%V C-26
%N 6
%P 521-536
%D 1977
%K jrnl, IEEE, infer, inferring, finite state, machine, automaton,
   FSA, PFSA, FSM, inductive, II, grammar, language
%X from  R a m a n's  thesis '97
   [Also search for: infer finite state automaton].

%A A. W. Biermann
%A J. A. Feldman
%T On the synthesis of finite-state machines from samples of their behaviour
%J IEEE Trans Computers
%V 21
%P 591-597
%D 1972
%K jrnl, IEEE, c1972, c197x, c19xx, infer, inferring, inductive inference, II,
   machine, automaton, FSA, FSM, PFSA, grammar, language, AI, k-tails, kTails,
   ktail, tails, tail, string, word
%X from  R a m a n' s   thesis '97.
   [Also search for: infer finite state automaton].

%A J. Oncina
%A P. Garci
%T Inferring regular languages in polynomial updated time
%J Pattern Recognition: 4th Spanish Symp.
%P 49-61
%I World Scientific
%D 1992
%K conf, infer, finite state, machine, automaton, FSA, FSM, grammar, language,
   learn, learning
%X from  R a m a n' s  thesis  '97
   [Also search for: infer finite state automaton].

%A S. Y. Itoga
%T A new heuristic for inferring regular grammars
%J IEEE Trans. Patterns Analysis and Machine Int.
%V 3
%N 2
%P 191-197
%M FEB
%D 1981
%K c1981, c198x, c19xx, jrnl, IEEE, infer, inference, finite state, machine,
   automaton, automata, FSA, FSM, regular grammar, language, string, strings,
   problem, Feldman, Wharton
%X From  R a m a n' s  thesis '97.
   Abs at 21868935@[<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/21868935">pubmed</A>]['17].
   [Also search for: infer finite state automaton].

%A T. Joachims
%T Text categorization with support vector machines: learning with many
   relevant features
%J European Conf. Mach. Learning, ECML98
%M APR
%D 1998
%P ??-??
%K Conf, ECML, ECML98, machine, method, SVM, IDF, TR 23, TR23,
   Reuters, Reuters21578, ModApte, Ohsumed, Rocchio, C4.5,
   supervised classification, zz0798, c1998, c199x, c19xx
%O TR 23, Univ. Dortmund, Lehrstuhl Informatik III, ?'97?
%X Features are numbers of occurences of words
   after removal of stop words, e.g. 10000 dimensions or more.
   Claims to generally beat naive Bayes, Rocchio, k-nearest neighbour and C4.5
   on Reuters-21578 corpus assigning doc's to 90 categories and
   Ohsumed corpus assigning doc's to one or more of 23 MeSH disease categories.
   NB. claims even worst attributes contain much information for this problem.
   6 pages. 11 refs.
   <A HREF="http://www-ai.informatik.uni-dortmund.de/">Dortmund</A>[7/1998].
   [Also search for: support vector SVM].

%A V. N. Vapnik
%T Statistical Learning Theory
%I JohnWiley
%M SEP
%D 1998
%P 768
%K book, text, machine learning, AI, support vector method, machine, SVM, NN,
   structural risk minimization, SRM, ANN, c1998, c199x, c19xx,
   inductive inference, II, zz0998
%X uk us isbn:0471030031;  A$133 (7/'98).

%A A. J. Smola
%A B. Scholkopf
%T On a kernel-based method for pattern recognition, regression, approximation,
   and operator inversion
%J Algorithmica
%V 22
%P 211-231
%D 1998
%O GMD TR 1064, April '97
%K jrnl, c1998, c199x, c19xx, zz0210, support vector, SVM, AI, kernel, machine,
   regularization, Greene's, Greenes functions
%X "... a Kernel based framework for Pattern Recognition, Regression Est.
   fn Approx. & multiple Operator Inversion. Previous approaches such as
   ridge-regression, SVM and regression by Smoothing Kernels are included as
   special cases. We will show connections between the cost-fn & some properties
   up to now believed to apply to SVMs only. The optimal solution of all the
   problems described above can be found by solving a simple quadratic prog.
   problem. ... closes with a proof of the equiv. between SV-kernels & Greene's
   fns of regularization operators"
   -- [<A HREF="http://www.kernel-machines.org/papers/smosch97.ps.gz">TR</A>]['10].

%A Y. LeCun
%A L. Bottou
%A Y. Bengio
%A P. Haffner
%T Gradient-based learning applied to document recognition
%J Proc. of the IEEE
%V 86
%N 11
%P 2278-2324
%M NOV
%D 1998
%K jrnl, c1998, c199x, c19xx, zz0822, ANN, NN, convolutional, training,
   multilayer, deep, back propagation, backprop, gradient, character recognition
%X "... reviews various methods applied to handwritten character recognition &
   compares them on a std handwritten digit recognition task. CNNs, which are
   specifically designed to deal with the variability of 2D shapes, are shown to
   outperform all other techniques. ..."
   -- [<A HREF="https://doi.org/10.1109/5.726791">doi:10.1109/5.726791</A>]['22].
   (Also see CNN@[<A HREF="https://en.wikipedia.org/wiki/Convolutional_neural_network">wikip</A>]['22].)
   [Also search for: convolutional NN]  &  [also search for: training deep NN].

%A V. N. Vapnik
%T The Nature of Statistical Learning Theory (Stat's for Eng. and Inf. Sci.)
%I SpringerVerlag
%D 1999
%P 304
%K book, text, structural, empirical, risk minimization, ERM, SRM, SVM
%X 1999 2nd edn.  isbn:0387987800.  About us$32.

%A H. Moravec
%T Robot: Mere Machine to Transcendent Mind
%I OUP N.Y.
%D 1998
%K book, text, mind, artificial intelligence, AI, consciousness, Turing test,
   OUP, c1998, c199x, c19xx, zz0499, robot, robots, robotics, HAL, computer,
   future, human, versus, prediction, zzPrediction, zz0140
%X 1st ed 1998; pb us$59; uk us isbn:0195136306; uk us isbn13:978-0195136302.
   Reviewed in Scientific American, Feb 99, p.83.
   *** Apparently predicts: lizard-scale intelligence by 2010,
                            human-scale processing    by 2040. ***
   Hope I'm still around to check up on these predictions.
   [Also search for: computer AI HAL] and [also search for: zzPrediction].

%T Vision-Based Vehicle Guidance
%E I. Masaki
%I SpringerVerlag
%S Perception-Engineering
%D 1992
%K book, text, car, machine vision, visual, guide, drive, AI,
   automatic control, autonomous, road, driving, obstacle avoidance,
   Navlab, Harunobo, c1992, c199x, c19xx, zz0599
%X isbn:0-387-97553-5; and  isbn:3-540-97553-5;
    1. survey,  2. CMU Navlab,  3. Algorithms,  4. Visual Control fuzzy,
    5. local processing 3D,     6. Object Detection,  7. Road Signs,
    8. Driver's Associate,  9. Robot Harunobu-4,  10. on-road,
   11. Lane Boundaries,    12. Optical Flow,      13. Obstacle Avoidance,
   14. parallel arch',     15. Vertical Line Stereo

%A T. Ito
%A S. Kawakatsu
%T An extracting method of the optical flow for an anticollision system
%B Vision-Based Vehicle Guidance.
%I SpringerVerlag
%P 255-267
%D 1992
%K optical flow, collision, obstacle, avoidance
%X chapter 12 of Vision Based Vehicle Guidance, I Masaki (ed)

%A G. F. Cooper
%A E. Herskovits
%T A Bayesian method for the induction of probabilistic networks from data
%J Machine Learning
%I Springer Sci. & Business Media B.V. (prev. Kluwer Acad. Publ. B.V.)
%V 9
%P 309-347
%M OCT
%D 1992
%K jrnl, K2, model, AI, learn, c1992, c199x, c19xx, Bayesian network
%X "...B. method for constructing probabilistic n. from DBs.. ...focus on
   constructing B. belief networks. Potential applications include computer-
   assisted hypothesis testing, automated scientific discovery, and automated
   construction of probabilistic expert systems. We extend the basic method to
   handle missing data and hidden (latent) variables. We show how to perform
   probabilistic inference by averaging over the inferences of multiple belief
   networks. Results ... preliminary evaluation of an alg. for cons. a belief
   network from a database of cases. Finally, we relate the methods in this
   paper to previous work, and we discuss open problems."
   pdf: [<A HREF="http://dx.doi.org/10.1023/A:1022649401552">doi:10.1023/A:1022649401552</A>]['05]

%A D. Fensel
%A R. Straatman
%T The essence of problem-solving methods: Making assumptions for
   efficiency reasons
%J Int. J. Human-Computer Studies
%P 181-215
%V 48
%N 2
%M FEB
%D 1998
%K jrnl, IJHCS, AI, II, method, reason, knowledge-based systems, system,
   c1998, c199x, c19xx, zz0904, solver, learning
%X "...present the following view on problem-solving methods [PSMs] for
   knowledge-based systems: PSMs describe an efficient reasoning strategy for
   achieving a goal by introducing assumptions about the available domain
   knowledge & the required functionality.  Assumptions, dynamic reasoning
   behavior, & functionality are the three elements necessary to characterize a
   PSM. ... we elaborate this argument & introduce a framework for
   characterizing & developing such efficient problem solvers."
   [<A HREF="http://www.ubka.uni-karlsruhe.de/cgi-bin/psview?document=/1998/wiwi/11&search=/1998/wiwi/11">uni-karlsruhe.de</A>][9/'04]
   issn:10715819.

%A T. Bruton
%T Computer Controlled Model Car
%I School of Computer Science & Software Engineering,
   Monash University, Australia
%R BCSE Honours Thesis
%D 1999
%K remote control, autonomous, self driving, vehicle, vehicles, car, cars,
   robot, vision, camera, radio, project, report, toy, model, automobile,
   drive, guidance, c1999, c199x, c19xx
%X [<A HREF="/hons/projects/1999/Tim.Bruton/">www</A>]['99],
   includes a movie from the car driving a circuit.

%A B. D'Ambrosio
%T Inference in Bayesian networks
%J AI Magazine
%P 21-36
%V 20
%N 2
%D 1999
%K AI, network, net, dAmbrosio, update, loop, junction, c1999, c199x, c19xx,
   introduction
%X <!-- r o d o   has --> summer 1999.

%A A. Broggi
%A M. Bertozzi
%A A. Fascioli
%A G. Conte
%T Automatic vehicle guidance
%I WorldScientific
%D 1999
%K ARGO, book, text, vehicles, collison, obstacle, avoidance, car,
   cars, AI, zz0100
%X isbn:9810237200;   US$67; stg42
   [<A HREF="http://www.argo.ce.unipr.it/ARGO/english/">www</A>][11/'02]

%A A. Broggi
%A M. Bertozzi
%A A. Fascioli
%T The 2000 km Test of the ARGO Vision-Based Autonomous Vehicle
%J IEEE Intelligent Sys.
%P 55-64
%D 1999
%K ARGO, vehicles, collison, obstacle, avoidance, car, cars, AI,
   MilleMiglia in Automatico, mille miglia, c1999, c199x, zz1102
%X This paper presents the vision system used by the ARGO autonomous vehicle
   to sense the surrounding environment and the basics of the algorithm used
   to detect lane markings in real-time. The system, based on a pair of
   low-cost b/w cameras, can autonomously steer the vehicle thanks to a
   stepping motor installed on the steering column. This paper also presents a
   discussion and a critical analysis of the 'MilleMiglia in Automatico', an
   extensive test of the ARGO vehicle that took place in the first week of
   June 98, when ARGO drove autonomously for about 2000 km on Italian public
   roads in real traffic conditions. The experience gained during this trip is
   described and the main problems of the vision system discussed. Jan-Feb 1999
   [<A HREF="http://www.argo.ce.unipr.it/ARGO/english/">www</A>][11/'02]

%T Principles of Data Mining and Knowledge Discovery
%E J. M. Zytkow
%E J. Rauch
%I SpringerVerlag
%S LNAI/ LNCS
%V 1704
%M SEP
%W Prague
%D 1999
%K proc, conf, PKDD, PGDD99, PKDD1999, AI, KD, zz0300
%X isbn:3540664904;  au$105.

%A D. Floreano
%A J.-D. Nicoud
%A F. Mondada
%T Advances in Artificial Life
%D 1999
%I SpringerVerlag
%X LNAI
%V 1674
%P 737
%O Proc. 5th Euro. Conf. ECAL '99
%K proc, conf, AI, ALife, LNAI, ECAL5, ECAL99, ECAL1999, zz0500
%X ECAL 99 Lausanne Switzerland Sept 13-17 1999; uk us isbn:3540664521. au$117.

%A S. Russell
%A P. Norvig
%T Artificial Intelligence a Modern Approach
%I PrenticeHall
%S AI
%D 1995
%K book, text, c1995, c199x, c19xx, L3REF, AI, machine learning,
   Bayesian, causal, belief network, networks, net, nets, zz1000
%X 8 sections, 27 chapters.  Used in 3rd yr A.I. '99... .
   1. AI;               2. Problem solving;       3. Knowledge and reasoning;
   4. acting logically; 5. uncertainty;           6. learning;
   7. communication (agents);   8. Conclusions.
   Section 5, chapter 15 includes Bayesian nets.
   2nd ed c2003, pb, uk us isbn:0131038052; uk us isbn13:978-0130803023.

%A W. T. B. Uther
%A M. M. veleso
%T The lumberjack algorithm for learning linked decision forests
%J 6th Pacific Rim Int. Conf. A.I.
%P 156-166
%M AUG
%D 2000
%S LNAI
%V 1886
%K conf, PRICAI, PRICAI2000, PRICAI6, forest, tree, trees, Dforest,
   Dtree, Dgraph, AI, c2000, c200x, c20xx, zz1200
%X ... subconcept multiple times ...
   can handle repeated internal structure (cf a D' tree) thus
   generalising the D' graph's handling of repeated terminal structure.
   The search problem is hard.

%A N. Cristianini
%A J. Shawe-Taylor
%T An Introduction to Support Vector Machines (and Other
   Kernel-Based Learning Methods)
%I CUP
%P 204
%D 2000
%K book, text, SVM, AI, machine learning, machine, kernel based, zz0300,
   c2000, c200x, c20xx,
%X isbn:0-521-78019-5.  (hb)  About £30.
   1. Learning methodology;          2. Linear learning machines;
   3. Kernel induced feature spaces; 4. Generalisation theory;
   5. Optimisation theory;           6. Support vector machines;
   7. Implementation techniques;     8. Applications of SVMs.
   [<A HREF="http://uk.cambridge.org/engineering/catalogue/0521780195/default.htm">CUP</A>][3/'01],
   [<A HREF="http://www.support-vector.net/">www</A>][3/'01],
   [<A HREF="mailto:N.Cristianini@cs.rhul.ac.uk">author 1</A>][3/'01].

%A D. Wu
%T Stochastic inversion transduction grammars, with application to
   segmentation, bracketing, and alignment of parallel corpora
%J IJCAI 95
%P 1328-1335
%M AUG
%D 1995
%K Dekai, conf, IJCAI, IJCAI95, natural language processing, NLP, CFG, zz0301
%X We introduce (1) a novel stochastic inversion transduction grammar
   formalism for bilingual language modeling of sentence-pairs, and
   (2) the concept of bilingual parsing with potential application to
   a variety of parallel corpus analysis problems. ...
   [<A HREF="http://www.cs.ust.hk/~dekai/">www</A>][3/'01] also see '97
   (via  A. C l a r k)

%A D. Wu
%T Stochastic inversion transduction grammars and bilingual parsing of
   parallel corpora
%J Computational Linguistics
%V 23
%N 3
%P 377-404
%M SEP
%D 1997
%O Parallel Text Processing: Alignment and Use of Traslation Corpora,
   Veronis (ed), Kluwer, V13, 2000
%K Dekai, jrnl, natural language processing, NLP, translation, parse,
   CFG, zz0301
%X We introduce (1) a novel stochastic inversion transduction grammar
   formalism for bilingual language modeling of sentence-pairs, and (2)
   the concept of bilingual parsing with a variety of parallel corpus
   analysis applications. ...
   [<A HREF="http://www.cs.ust.hk/~dekai/">www</A>][3/'01]
   (via  A. C l a r k)

%A C. J. C. Burges
%T A tutorial on support vector machines for pattern recognition
%J Data Mining and Knowledge Discovery
%I KluwerAcademic
%V 2
%N 2
%P 121-167
%D 1998
%K jrnl, support vector machine, SVM, separable, non separable, kernel,
   kernels, polynomial, Gaussian radial basis function kernels,
   VC dimension, structural risk minimization, SRM, zz0302
%X ... VC dimension and structural risk minimization. ...
   separable and non-separable data ... kernel mapping technique ...
   homogeneous polynomial and Gaussian radial basis function kernels.
   [<A HREF="http://www.kluweronline.com/issuetoc.htm/1384-5810+2+2+1998">paper</A>][3/'02](must subscribe/ pay)
   author: Bell Labs;  burges at lucent.com

%A J. Darlington
%A Yike Guo
%A J. Sutiwaraphun
%A Hing Wing To
%T Parallel induction algorithms for data mining
%J IDA
%I SpringerVerlag
%S LNCS
%V 1280
%D 1997
%P 437-445
%K parallel, IDA, IDA1997, data mining, inductive inference,
   classification, decision tree, trees, C4.5, C4, C45, C5, DTree, zz0602
%X In the last decade, there has been an explosive growth in the generation
   and collection of data.  Nonetheless, the quality of information inferred
   from this voluminous data has not been proportional to its size.  One of
   the reasons for this is that the computational complexities of the
   algorithms used to extract information from the data are normally
   proportional to the number of input data items resulting in prohibitive
   execution time on large data sets. Parallelism is one solution to this
   problem. In this paper we present preliminary results on experiments in
   parallelising C4.5, a classification-rule learning system using
   decision-trees as a model representation, which has been used as a base
   model for investigating methods for parallelising induction algorithms.
   The experiments assess the potential for improving the execution time by
   exploiting parallelism in the algorithm.
   -- [<A HREF="http://link.springer.de/link/service/series/0558/bibs/1280/12800437.htm">springer_link</A>][6/'02] [authors at Imp. Coll. Lond'n].

%A R. B. Dannenberg
%T An On-line algorithm for real-time accompaniment
%J Proc. of the 1984 Int. Computer Music Conf.
%I Computer Music Association
%P 193-198
%M JUN
%D 1985
%K conf, music, model, models, c1985, c198x, c19xx
%X [<A HREF="http://www-2.cs.cmu.edu/~rbd/">www</A>][7/'02]

%A R. B. Dannenberg
%T Music representation issues, techniques, and systems
%J Computer Music Jrnl
%P 20-30
%V 17
%N 3
%D 1993
%K jrnl, system, computer, c1993, c199x, c19xx
%X [<A HREF="http://www-2.cs.cmu.edu/~rbd/">www</A>][7/'02]
   [<A HREF="http://mitpress.mit.edu/e-journals/Computer-Music-Journal/">jrnl</A>][7/'02].

%A R. B. Dannenberg
%T Machine tongues XIX: Nyquist, a language for composition and sound synthesis
%J Computer Music Jrnl.
%P 50-60
%V 21
%N 3
%D 1977
%K jrnl, system, computer
%X [<A HREF="http://www-2.cs.cmu.edu/~rbd/">www</A>][7/'02]
   [<A HREF="http://mitpress.mit.edu/e-journals/Computer-Music-Journal/">jrnl</A>][7/'02]

%A R. B. Dannenberg
%T Abstract time warping of compound events and signals
%J Computer Music Jrnl.
%P 61-70
%V 21
%N 3
%D 1997
%K jrnl, c1997, c199x, c19xx, system, computer, music, warps, warp, match,
   series, sequence
%X [<A HREF="http://www-2.cs.cmu.edu/~rbd/">www</A>][7/'02]
   [<A HREF="http://mitpress.mit.edu/e-journals/Computer-Music-Journal/">jrnl</A>][7/'02].

%A R. B. Dannenberg
%T The implementation of Nyquist, a sound synthesis language
%J Computer Music Jrnl.
%P 71-82
%V 21
%N 3
%D 1997
%K jrnl, system, computer, music
%X [<A HREF="http://www-2.cs.cmu.edu/~rbd/">www</A>][7/'02]
   [<A HREF="http://mitpress.mit.edu/e-journals/Computer-Music-Journal/">jrnl</A>][7/'02]

%A D. Maxwell Chickering
%A D. Heckerman
%A C. Meek
%T A Bayesian approach to learning Bayesian networks with local structure
%J Proc. 13th Conf. on Uncertainty in AI (UAI97)
%P 80-89
%D 1997
%O TR 97 07, Ms.Res., Aug. 1997
%K conf, UAI, network, dTree, trees, graph, graphs, CPD, CPT, local, node,
   nodes, c1997, c199x, c19xx
%X "...several researchers have investigated techniques for using data to learn
   [BNs] containing compact representations for the conditional probability
   distributions (CPDs) [CPTs] stored at each node. [most] has concentrated on
   using decision-tree representations for the CPDs.  [and] typically apply
   non-Bayesian (or asymptotically B.) scoring functions such as MDL to
   eval. the goodness-of-fit of networks to the data.
   ... investigate a Bayesian approach to learning Bayesian networks that
   contain the more general decision-graph representations of the CPDs. ..."
   [<A HREF="http://research.microsoft.com/research/pubs/view.aspx?tr_id=167">msr</A>]['05]

%A J. Patrick
%A A. K. Raman
%T The sk-strings method for inferring PFSA
%J Workshop on Automata Induction, Grammatical Inference, and
   Language Acquisition, ICML-14
%W Nashville
%M JUL
%D 1997
%K wShop, ICML, ICML97, c1997, c199x, c19xx, string, PFSM, probabilistic, HMM,
   SKstrings, infer, machine, finite state, automaton, automata
%X auths @ u. syd.
   [<A HREF="http://www.cs.iastate.edu/~honavar/mlworkshop.html">program</A>]['05].
   [Also search for: infer finite state automaton].

%A P. E. Agre
%T Toward a critical technical practice: Lessons learned in trying to reform AI
%P ?-?
%B Bridging the Great Divide: Social Science, Technical Systems, and
   Cooperative Work
%E Geof Bowker, et al
%I Erlbaum
%D 1997
%K AI, c1997, c199x, c19xx, zz0413, criticism
%X (via AlanD.)  A *version* at
   [<A HREF="http://polaris.gseis.ucla.edu/pagre/critical.html">www</A>]['13].

%A R. B. Dannenberg
%A Derenyi
%T Combining instrument and performance models for high-quality music synthesis
%J Jrnl. of New Music Research
%P 211-238
%V 27
%N 3
%D 1998
%K jrnl, system, computer, model. c1998, c199x, c19xx
%X [<A HREF="http://www-2.cs.cmu.edu/~rbd/">www</A>][7/'02]

%A P. Desain
%A H. Honing
%T Music, Mind and Machine: Studies in Computer Music,
   Music Cognition and Artificial Intelligence.
%I i.d.b., Ltd., N.Y.
%D 1992 ?
%X HENKJAN at NL.UVA.LET.ALF - '92.   isbn:9051701497.

%A C. Boutilier
%A N. Friedman
%A M. Goldszmidt
%A D. Koller
%T Context-specific independence in Bayesian networks
%J Uncertainty in A. I.
%P 115-123
%D 1996
%K conf, AI, network, machine learning, tree, trees, dtree, decision, inverse,
   CPT, Bnet, UAI, UAI96, c1996, c199x, c19xx
%X ... tree-structured CPTs ...
   (Also see [<A HREF="http://www.allisons.org/ll/Publications/2006AI/">CaMML</A>].)

%A J. Pearl
%T Causality: Models Reasoning and Inference
%I CUP
%P 384
%D 2000
%K book, text, CUP, causal model, models, AI, inductive, II, probability,
   c2000, c200x, c20xx
%X "1. Intr. to probs., graphs, & causal models; 2. A theory of inferred
   causation; 3. Causal diagrams & the identification of causal effects;
   4. Actions, plans, & direct effects; 5. Causality & structural models in the
   social sci.; 6. Simpson's paradox, confounding, & collapsibility;
   7. Structural & counterfactual models; 8. Imperfect experiments: bounds &
   counterfactuals; 9. Probability of causation: interpretation &
   identification; Epilogue: the art & science of cause and effect."
   hb stg30;  uk us isbn:0521773628.

%A P. Becuzzi
%A M. Coppola
%A S. Ruggieri
%A M. Vanneschi
%T Parallelisation of C4.5 as a particular divide and conquer computation
%J Proc. of the 3rd Workshop on High Performance Data Mining
%I SpringerVerlag
%S LNCS
%V 1800
%P ?-?
%M MAY
%D 2000
%K conf, HPDM, HPDM3, parallel, C4.5, C45, C5,
   classification, decision, tree, trees, DTree
%X [<A HREF="http://www-kdd.cnuce.cnr.it/publications.html">preprints</A>][10/'02].
   [Also search for: parallel classification tree].

%A G. Schreiber
%A H. Akkermans
%A A. Anjewierden,  R. de Hoog,  N. Shadbolt,  W. Van de Velde and B. Wielinga
%T Knowledge Engineering and Management: The CommonKADS Methodology
%I MITpress
%D 2000
%K book, text, Guus, KADS, commonKADS, AI, c2000, c200x, c20xx, xxOSP, zOSP04,
   knowledge management, analysis, OM2, ontology
%X [<A HREF="http://www.commonkads.uva.nl/">commonkads.uva.nl</A>][8/'04];
   us isbn:0262193000.

%A S. Ruggieri
%T Efficient C4.5
%J IEEE Trans. Knowledge and Data Eng.
%V 14
%N 2
%P 438-444
%M MAR-APR
%D 2002
%K jrnl, IEEE, TKDE, classification, algorithm, C4.5, C45, C5, EC4.5,
   decision tree, trees, fast, efficient, DTree, zz1002
%X Dipt. di Inf., Pisa Univ., Italy
   ...evaluation of the runtime behavior of C4.5 ...have implemented a
   more efficient version of the algorithm, called EC4.5; up to 5x faster. ...
   1. ...computes the local threshold using the algorithm of C4.5,
      which, in particular, sorts cases by means of the quicksort method.
   2. ...counting sort method.
   3. ...local threshold using a main-memory version of the
      RainForest algorithm, which does not need sorting.
   [<A HREF="http://www.di.unipi.it/~ruggieri/main.html">home</A>][10/'02]
   [<A HREF="http://www-kdd.cnuce.cnr.it/publications.html">preprints</A>][10/'02]
   {via Andre O'}.

%A L. Breiman
%T Random forests
%J Mach. Learning
%V 45
%N 1
%P 5-32
%M OCT
%D 2001
%K jrnl, c2001, c200x, c20xx, zz0518, decision tree, Dtree, AI, II,
   random forest, forests, randomForest, ensemble, Adaboost
%X "Random forests are a combination of tree predictors such that each tree
   depends on the values of a random vector sampled indep. & with the same
   distn for all trees in the forest. The generalization error for forests
   converges a.s. to a limit as the # of trees in the forest becomes large. ...
   depends on the strength of the individual trees in the forest & the
   correlation between them. Using a random selection of features to split each
   node yields error rates that compare favorably to Adaboost (Y. Freund & R.
   Schapire, Machine Learning: Proc. 13th Int. conf., 148-156), but are more
   robust with respect to noise. Internal estimates monitor error, strength, &
   correlation & these are used to show the response to increasing the # of
   features used in the splitting. Internal estimates are also used to measure
   variable importance. These ideas are also applicable to regression."
   -- [<A HREF="https://doi.org/10.1023/A:1010933404324">doi:10.1023/A:1010933404324</A>]['18].
   [Also search for: II random forest].
   (Also see RF@[<A HREF="https://en.wikipedia.org/wiki/Random_forest">wikip</A>]['18].)

%A X. Zeng
%A D. S. Yeung
%T Sensitivity analysis of multilayer perceptron to input and weight
   perturbations
%J IEEE Trans. on Neural Networks
%V 12
%N 6
%P 1358-1366
%M NOV
%D 2001
%K jrnl, ANN, weight, node, perecptrons, artificial neural network
%X via E.M.

%A A. Skowron
%T Rough sets and boolean reasoning
%B Granular Computing
%I Physica-Verlag, .de
%P 95-124
%D 2001
%K chapter, rough set, AI, c2001, c200x, c20xx, fuzzy, AI
%X "interest in RS theory & its appls., worldwide. The theory has been followed
   by the development of several software systems that implement RS ops., in
   particular for solving KD & data mining tasks. RSs are applied in domains,
   such as, for instance, medicine, finance, telecommunication, vibration
   analysis, conflict resolution, intelligent agents, pattern recognition,
   control theory, signal analysis, process industry, marketing, etc. ...
   basic notions & discuss methodologies for analyzing data & surveys some
   appls..  ... we present appls. of RS methods for feature selection,
   feature extraction, discovery of patterns & their appls. for decomp. of
   large data tables as well as the relationship of RSs with assoc. rules..."
   [<A HREF="http://portal.acm.org/citation.cfm?id=761989">abs</A>]['05]
   [Also search for: rough sets],   isbn:3790813877.

%A Feng-Hsiung Hsu
%T Behind Deep Blue: Building the Computer That Defeated the
   World Chess Champion
%I PrincetonUP
%P 298
%M NOV
%D 2002
%K book, Kasparov, world champion, computer chess, AI, artificial intelligence,
   play, game, program, IBM zz0103, c2002, c200x, c20xx
%X about us$28.  isbn:0691090653.

%A A. McCabe
%T An artificially intelligent sports tipper (MAIT)
%J 15th Australian Joint Conf. on Artificial Intelligence
%P ?-?
%M DEC
%D 2002
%K AI02, AI, conf, NN, ANN, rugby, football, footy, soccer, AFL, sport, sports,
   AI15, match, game, results, tip, tipping, tipper, c2002, c200x, c20xx,
   tipster, MAIT, zz0503
%X ... an artificially intelligent model for predicting the outcome of
   particular sporting contests. It is intended as an interesting case study
   of using neural networks for predicting probabilistic events in a sporting
   scenario. The model used is a multi-layer perceptron and it is presented
   with a number of features representing the performance of various sporting
   teams. The system performed quite well and successfully predicted the winner
   in over 70% of the matches. Results also include a study of which features
   are most useful, the results of "live" testing and a comparison of MAIT
   versus other common tipping heuristics.
   [<A HREF="http://www.mymait.com/Paper2/">paper</A>][5/'03]
   [<A HREF="http://www.cs.jcu.edu.au/~alan/">home@jcu.edu.au</A>][5/'03]

%A L. N. de Castro
%A J. Timmis
%T Artificial Immune Systems: A New Computational Intelligence Paradigm
%I SpringerVerlag
%P 357
%M NOV
%D 2002
%K AI, AIS, system, book, text, introduction, survey, c2002, c200x, c20xx,
   nervous, endocrine
%X 1. Introduction.    2. Fundamentals of the Immune System
   3. A Framework for Engineering Artificial Immune Systems
   4. A Survey of Artificial Immune Systems
   5. The Immune System in Context with Other Biological Systems
   6. AIS in Context with other Computational Intelligence Techniques
   7. Case Studies.    8. Conclusions and Future Trends.  isbn:1852335947.
   -- [<A HREF="http://www.cs.kent.ac.uk/people/staff/jt6/aisbook/">@cs.kent.ac.uk</A>]['04],  Euro50.
   &  [<A HREF="http://www.dca.fee.unicamp.br/~lnunes/">auth1</A>]['04]

%A T. Weigel
%A B. Nebel
%T KiRo - an autonomous table soccer player
%J Proc. Int. RoboCup Symp. '02
%W Fukuoka, Japan
%P ?-?
%D 2002
%K conf, bar, table football, foot ball, footy, soccer, foosball, fussball,
   Lowen, kicker roboter, AI, c2002, c200x, c20xx, zz0904, robot, robotics,
   robots
%X "...presents the table soccer game as a new domain for the research in the
   fields of robotics and artificial intelligence. A system capable of playing
   table soccer on a competitive level and in a fully autonomous way is
   described. It can serve a human both as a teammate and an opponent but also
   allows for matches between two artificial players..."
   -- [<A HREF="ftp://ftp.informatik.uni-freiburg.de/documents/papers/ki/weigel-etal-robocup-02-kiro.pdf">pp.pdf@uni-freiburg.de</A>][9/'04],
      [<A HREF="http://www.informatik.uni-freiburg.de/~weigel/">weigel</A>][9/'04],
      [<A HREF="http://www.informatik.uni-freiburg.de/~nebel/">nebel</A>][9/'04].
   (Also see [<A HREF="http://www.table-soccer.org">ITSF</A>]['13],
    and [<A HREF="http://en.wikipedia.org/wiki/Table_football">wikip</A>]['13].)
   [Also search for: foosball].

%A V. Lifschitz
%T Answer set programming and plan generation
%J Artificial Intelligence
%V 138
%P 39-54
%D 2002
%K jrnl, AI, ASP, logic, LP, program, plans, c2002, c200x, c20xx, SMODELS, DLV
%X "... represent a given comp. problem by a LP whose answer sets correspond
   to solutions ... use an answer set solver, such as SMODELS or DLV, to find
   an answer set for this program. ... frame problem ..."
   [<A HREF="http://www.cs.utexas.edu/users/vl/papers/asppg.ps">ps@utexas</A>]['05]

%A S. Colton
%T Automated Theory Formation in Pure Mathematics
%I SpringerVerlag
%D 2002
%K book, text, c2002, c200x, c20xx, maths, AI, automatic, theorem proving,
   theory, proof
%X uk us isbn:1852336099.
   SC@[<A HREF="http://www.doc.ic.ac.uk/~sgc/">IC</A>]['13].
   [Also search for: theorem proving].

%A E. Alpaydin
%T Machine Learning
%I MIT press
%P 400
%D 2004
%K book, text, AI, artificial intelligence, II, c2004, c200x, c20xx, zz0105,
   reinforcement
%X hb, us$50; isbn:0262012111.
   (Also see RL@[<A HREF="https://en.wikipedia.org/wiki/Reinforcement_learning">wikip</A>]['22].)

%A T. Wilkins
%A A. Nicholson
%A T. I. Dix
%T Probabilistic prediction-based replanning architecture for a UAV
%J Proc. of Intelligent Autonomous Vehicles Conf.
%W Portugal
%P ?-?
%D 2004
%K conf, TIDix, AI, planning, replan, autonomous vehicle, c2004, c200x, c20xx,
   pilotless, robot, plane, drone, aircraft, flight, IAV2004, IAV, Aerosonde
%X [<A HREF="ftp://ftp.csse.monash.edu.au/pub/annn/IAV2004.ps">pp.ps@monash</A>]['05]
  auths@csse mon@sh '05.

%A G. Forman
%T A pitfall and solution in multi-class feature selection for text
   classification
%J Proc. 21st Int. Conf. on Machine Learning
%W Banff
%P ?-?
%D 2004
%K conf, ICML, ICML21, c2004, c200x, c20xx, features, information gain,
   difficult classes
%X "IG ...proven method for high-dimensional feature sel.. We found that it and
   other existing methods failed to produce good results on an industrial text
   classification problem. On investigating the root cause, we find that a
   large class of feature scoring methods suffers a pitfall: they can be
   blinded by a surplus of strongly predictive features for some classes, while
   largely ignoring features needed to discriminate difficult classes. In this
   paper we demonstrate this pitfall hurts performance even for a relatively
   uniform text classification task. Based on this understanding, we present
   solutions inspired by round-robin scheduling that avoid this pitfall without
   resorting to costly wrapper methods. Empirical evaluation on 19 datasets
   shows substantial improvements."
   -- [<A HREF="http://www.machinelearning.org/proceedings/papers/107.pdf">.pdf</A>]['04].

%A R. Gilad-Bachrach
%A A. Navot
%A N. Tishby
%T Margin based feature selection - theory and algorithms
%K conf, ICML, ICML21, c2004, c200x, c20xx, features, select, Simba, Relief,
   classifier, classification
%X "...choosing a small set out of a given set of features that capture the
   relevant properties of the data. In the context of supervised classn.
   problems the relevance is determined by the given labels on training data.
   A good choice of features is a key for building compact & accurate class'rs.
   ...introduce a margin based feature seln criterion & apply it to measure the
   quality of sets of features. Using margins we devise novel seln algs. for
   multi-class class'n problems & provide theoretical generalization bound. We
   also study the well known Relief algorithm & show that it resembles a
   gradient ascent over our margin criterion. ... new algorithm to various
   datasets & show that our new Simba alg. ... outperforms Relief."
   [<A HREF="http://www.machinelearning.org/proceedings/papers/100.pdf">.pdf</A>]['04]

%A I. Tsochantaridis
%A T. Hofmann
%A T. Joachims
%A Y. Altun
%T Support vector machine learning for interdependent and structured
   output spaces
%J Proc. 21st Int. Conf. on Machine Learning
%W Banff
%P ?-?
%D 2004
%K conf, c2004, c200x, c20xx, SVM light, SVMlight, functional dependencies,
   ICML, ICML21, space
%X "Learning general functional dependencies is one of the main goals in machine
   learning. Recent progress in kernel-based methods has focused on designing
   flexible & powerful input reps.. ... addresses the complementary issue of
   problems involving complex outputs such as multiple dependent output vars. &
   structured o/p spaces. ... generalize multiclass SVM learning in a
   formulation that involves features extracted jointly from inputs & outputs.
   The resulting optimization problem is solved efficiently by a cutting plane
   algorithm that exploits the sparseness & structural decomposition of the
   problem. [show] versatility & effectiveness ... on problems ranging from
   supervised grammar learning & named-entity recognition, totaxonomic text
   classification & sequence alignment."
   [<A HREF="http://www.machinelearning.org/proceedings/papers/76.pdf">pdf</A>]['04]
   [<A HREF="http://www.cs.cornell.edu/People/tj/publications/tsochantaridis_etal_04a.pdf">pdf</A>]['04]
   [<A HREF="http://svmlight.joachims.org/svm_struct.html">svm_struct.html</A>]['04]

%A E. Gabrilovich
%A S. Markovitch
%T Text categorization with many redundant features: Using aggressive
   feature selection to make SVMs competitive with C4.5
%J Proc. 21st Int. Conf. on Machine Learning
%W Banff
%P ?-?
%D 2004
%K conf, c2004, c200x, c20xx, ICML, ICML21, SVM, features, classification
%X "... usually represent docs. as bags of words & consequently have to deal
   with huge numbers of features. ... majority of these features are[!] relevant
   for classification, & that the performance of text categorization with SVM
   peaks when no feature selection is performed. We describe a class of text
   categorization problems that are characterized with many redundant features.
   Even though most of these features are relevant, the underlying concepts can
   be concisely captured using only a few features, while keeping all of them
   has substantially detrimental effect on categorization accuracy. ... novel
   measure that captures feature redundancy, & use it to analyze a large
   collection of datasets. We show that for problems plagued with numerous
   redundant features the performance of C4.5 is significantly superior to that
   of SVM, while aggressive feature selection allows SVM to beat C4.5 by a
   narrow margin."
   -- [<A HREF="http://www.machinelearning.org/proceedings/papers/198.pdf">pdf</A>]['04].

%A D. Clarke
%A D. W. Albrecht
%A P. E. Tischer
%T An investigation into applying support vector machines to pixel
   classification in image processing
%J Proc. of the 17th Australian Joint Conf. on Advances in AI
%I SpringerVerlag
%S LNAI
%V 3339
%P 140-151
%M DEC
%D 2004
%K conf, AI04, IP, c2004, c200x, c20xx, SVM, SVMs, machine, pixels
%X "... SVMs to classification in [IP]. ... classifying whether pixels have
   been corrupted by impulsive noise, as this is 1 of the simpler
   classification tasks in [IP]. ... straightforward application of SVMs to
   this problem led to a number of difficulties, such as long training times,
   performance that was sensitive to the balance of classes in the training
   data, and poor classification performance overall. ... remedies for some of
   these problems, inc. ... image filters to suppress variation in the training
   data. ... develop a 2-stage c. process which used SVMs in the 2nd stage...."
   -- [<A HREF="http://www.google.com.au/url?sa=t&ct=res&cd=5&url=http%3A//www.springerlink.com/index/L2NM5704Y5U9VN91.pdf&ei=W7cWQ9CtHKK6YID79doJ">paper</A>]['05], isbn:3540240594.
   [Also search for: classification image processing].

%A A. Goldenberg
%A A.Moore
%T Tractable learning of large Bayes net structures from sparse data
%J Proc. 21st Int. Conf. on Machine Learning
%W Banff
%P ?-?
%D 2004
%K conf, c2004, c200x, c20xx, ICML, ICML21, Bayesian network, nets, structure,
   huge, frequent item set, sets
%X "... Is it useful to attempt to learn a BN structure with 100s of 1000s of
   nodes? How should such structure search proceed practically? [and] how can
   Frequent Sets ...which are extremely popular in the area of descriptive data
   mining, be turned into a probabilistic model? Large sparse datasets with
   100s of 1000s of records and attributes appear in social networks,
   warehousing, ... . The complexity of structural search made learning of
   factored probabilistic models on such datasets unfeasible. We propose to use
   Frequent Sets to significantly speed up the structural search. Unlike
   previous approaches, we not only cache n-way sufficient statistics, but also
   exploit their local structure. We also present an empirical evaluation of our
   algorithm applied to several massive datasets."
   [<A HREF="http://www.machinelearning.org/proceedings/papers/257.ps">.ps</A>]['04], auths @ CMU.

%A V. Zykov
%A E. Mytilinaios
%A B. Adams
%A H. Lipson
%T Robotics: Self-reproducing machines  (brief communication)
%J Nature
%V 435
%P 163-164
%M MAY
%D 2005
%K automata, automaton, machine, reproduction, c2005, c200x, c20xx, zz0505,
   cube, cubes, magnet, magnets, robot, robots
%X "A set of modular robot cubes accomplish a feat fundamental to biol. sys..
   Self-reproduction is central to biol. life for long-term sustainability &
   evolutionary adaptation. Although these traits would also be desirable in
   many engineered systems, the principles of self-reproduction have not been
   exploited in machine design. Here we create simple machines that act as
   autonomous modular robots & are capable of physical self-reproduction using
   a set of cubes."
   -- [<A HREF="http://dx.doi.org/10.1038/435163a">doi:10.1038/435163a</A>]['05].

%A G. I. Webb
%A J. Boughton
%A Z. Wang
%T Not so naive Bayes: Aggregating one-dependence estimators
%J Machine Learning
%I Springer
%V 58
%N 1
%P 5-24
%D 2005
%K jrnl, c2005, c200x, c20xx, GIWebb, estimator, AODE, AI, II, regression,
   super-parent, aggregate, aggregated, SPODE
%X "Of numerous proposals to improve the accuracy of naive B. by weakening its
   attr. indep. assumption, both LBR & Super-Parent TAN have demonstrated
   remarkable error performance. However, both techniques obtain this outcome
   at a considerable computational cost. We present a new approach to weakening
   the attr. indep. assumption by averaging all of a constrained class of
   classifiers. In extensive experiments this technique delivers comparable
   prediction accuracy to LBR & Super-Parent TAN with substantially improved
   computational efficiency at test time relative to the former & at training
   time relative to the latter. The new alg. is shown to have low variance & is
   suited to incremental learning."
   -- [<A HREF="http://dx.doi.org/10.1007/s10994-005-4258-6">doi:10.1007/s10994-005-4258-6</A>]['07].
   [Also search for: naive Bayes].

%A J. Cerquides
%A L. de Mantaras
%T Robust Bayesian linear classifier ensembles
%J ECML
%P 72-83
%D 2005
%K conf, ECML, c2005, c200x, c20xx, ensemble, average, model averaging, BMA,
   AODE, deMantaras, constrained optimization, aggregation
%X "... Usually probilistic classifiers restrict the set of possible models
   that can be learnt in order to lower computational complexity costs. ...
   where incorrect modelling assumptions are possibly made, uniform averaging
   sometimes performs even better than bayesian model averaging. ... develop 2
   algs. for learning maximum a posteriori weights for linear mixtures, based
   on EM and on constrained opt. ... empirically show that the maximum a
   posteriori linear mixture weights improve accuracy significantly over
   uniform aggregation."
   [<A HREF="http://dx.doi.org/10.1007/11564096_12">doi:10.1007/11564096_12</A>]['06]
   [<A HREF="http://www.iiia.csic.es/~mantaras/RR-IIIA-2005-03.pdf">pdf</A>]['06]
   AODE - averaged one dependence estimators.

%A A. Konar
%T Computational Intelligence: Principles, Techniques and Applications
%I SpringerVerlag
%D 2005
%K book, c2005, c200x, c20xx, AI, II, artificial intelligence
%X hb, us$80; eu$86; isbn:3540208984.
   A -ve review: [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm073">doi:10.1093/comjnl/bxm073</A>]['07].

%A C. M. Bishop
%T Pattern Recognition and Machine Learning
%I Springer
%D 2006
%K book, text, c2006, c200x, c20xx, Markov random field, fields
%X ... Chris Bishop introduces Markov random fields in the context of
   graphical model (p.383). ... image de-noising is discussed ...
   -- JRittscher, CStewart. uk us isbn:0387310738; uk us isbn13:978-0387310732.

%A R. Kurzwell
%T The Singularity Is Near: When Humans Transcend Biology
%I Penguin
%P 672
%D 2006
%K book, text, c2006, c200x, c20xx, zz1009, artificial intelligence, AI, robot,
   HAL, singularity, robotics, cyborg, spiritual machines, future, futurology,
   mind, techno, speculation, predictions, human, computer, robots
%X Are 'Blade Runner', 'Terminator', and Kurzwell plausible, or not?
   1st ed 2006; pb us$13; uk us isbn:0143037889; uk us isbn13:978-0143037880.
   [Also search for: computer AI HAL].
   [Also search for: human singularity AI].

%A P. Miettinen
%A T. Mielikaine
%A A. Gionis
%A G. Das
%A H. Mannila
%T The discrete basis problem
%J PKDD
%I SpringerVerlag
%P 335-336
%D 2006
%O IEEE Trans. Knowl. Data Eng. 20(10), pp.1348-1362, 2008
%K conf, PKDD, c2006, c200x, c20xx, zz0413, ASSO algorithm, binary, Boolean,
   matrix, factorization, BMF, decomposition, reconstruction accuracy
%X "Matrix decomposition methods represent a data m. as a product of two smaller
   matrices: one containing basis vectors that represent meaningful concepts in
   the data, & another describing how the obs.data can be expressed as
   combinations of the basis vectors. Decomposition methods have been studied
   extensively, but many methods return real-valued matrices. If the original
   data is binary, the interpretation of the basis vectors is hard. We describe
   a matrix decomposition formulation, the Discrete Basis Problem. The problem
   seeks for a Boolean decomposition of a binary matrix, thus allowing the user
   to easily interpret the basis vectors. We show that the problem is comp.
   difficult & give a simple greedy alg. for solving it. ... experimental
   results for the alg.. ... gives intuitively appealing basis vectors. [But]
   cts d.methods often give better reconstr.accuracies. We discuss [why]."
   -- [<A HREF="http://dx.doi.org/10.1007/11871637_33">doi:10.1007/11871637_33</A>]['13],
      uk us isbn:3540453741; uk us isbn13:978-3540453741;
   auth1@[<A HREF="http://www.mpi-inf.mpg.de/~pmiettin/">mpg</A>]['13].
      (Given b.matrix A which is n x m,
       find factors B (n x k), and C (k x m), to "minimise" |A xor B*C|
       "... Asso computes the empirical probabilities of seeing
       1 in row i if it's seen in row j into m x m matrix ..."
       X = (x_ij), x_ij = a_i . a_j / (a_j . a_j).
       Cols of B (& rows of C) sel. from (rounded) cols of X,
       "gain", greedy, no backtracking.)
   [Also search for: matrix decomposition], maybe include [boolean].

%A Y. Yang
%A G. I. Webb
%A J. Cerquide
%A K. Korb
%A J. Boughton
%A K-M. Ting
%T To select or to weigh: A comparative study of model selection and
   model weighing for SPODE ensembles
%J Proc. 17th Euro. Conf. on Machine Learning (ECML'06)
%I SpringerVerlag
%S LNCS
%V 4212
%D 2006
%K conf, c2006, c200x, c20xx, ECML06, II, AI, super parent, SPODE, AODE,
   ensemble, KBKorb
%X "An ensemble of Super-Parent-One-Dependence Estimators (SPODEs) ...
   ... achieving sig. higher class'n accuracy at a moderate cost in class'n
   efficiency.  ...  [present] theoretical & empirical study comparing model
   selection & model weighing for ensembling SPODEs. The focus is on maximizing
   the ensemble's classification accuracy while minimizing its comp. time. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/11871842_50">doi:10.1007/11871842_50</A>]['07].
   [Also search for: naive Bayes].

%A D. R. Hofstadter
%T I Am a Strange Loop
%I BasicBooks
%P 384
%M MAR
%D 2007
%K book, c2007, c200x, c20xx, mind, model, self, consciousness, reflexive,
   paradox, zz0507
%X $26.95, stg.14.99; isbn:0465030785; isbn13:978-0465030781.

%A S. Colton
%T Computational Discovery in Pure Mathematics
%B Communicable Scientific Discovery
%E S. Dzeroski
%E L. Todorowski
%I SpringerVerlag
%S LNAI
%V 4660
%D 2007
%K conf, c2007, c200x, c20xx, zz0915, maths, theorem proving
%X In: 2007; us$40; uk us isbn:354073919X; uk us isbn13:978-3540739197.
   [Also search for: theorem proving].

%A G. Sandini
%A G. Metta
%A D. Vernon
%T The iCub cognitive human robot: An open-system research platform for
   enactive cognition
%J Proc. PerMIS '08 the 8th Workshop on Performance Metrics for
   Intelligent Systems
%P 50-56
%D 2008
%K AI, robot, iCub, c2008, c200x, c20xx, zz0315, robotics, robotcub, AI
%X "... a humanoid robot for research in embodied cognition. At 104cm tall, the
   iCub has the size of a three & half year old child. It will be able to crawl
   on all fours & sit up to manipulate objects. Its hands have been designed to
   support sophisticate manipulation skills. The iCub is distributed as Open
   Source following the GPL/FDL licenses. The entire design is available for
   download from the project homepage & repository (http://www.robotcub.org).
   In the following, we will concentrate on the description of the hardware &
   software systems. ..."
   -- [<A HREF="http://dx.doi.org/10.1145/1774674.1774683">doi:10.1145/1774674.1774683</A>]['15].
   Also see [<A HREF="http://icub.org/">icub.org</A>]['15], cuter than a Terminator.

%A M. Schmidt
%A H. Lipson
%T Distilling free-form natural laws from experimental data
%J Science
%V 324
%N 5923
%P 81-85
%M APR
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1016, Eureqa, eureka, eureqa, eurequa, AI, II,
   inference, inferring, laws, law, rules, rules, equation, equations,
   symbolic regression, automatic, robot, learn, learning, model,
   science, scientist
%X "... A key challenge to finding analytic relations automatically is defining
   algorithmically what makes a correlation in observed data important and
   insightful. We propose a principle for the identification of nontriviality.
   We demonstrated this approach by automatically searching motion-tracking data
   captured from various physical systems, ranging from simple harmonic
   oscillators to chaotic double-pendula. Without any prior knowledge about
   physics, kinematics, or geometry, the alg. discovered Hamiltonians,
   Lagrangians, and other laws of geometric and momentum conservation. The
   discovery rate accelerated as laws found for simpler systems were used to
   bootstrap explanations for more complex systems, gradually uncovering the
   'alphabet' used to describe those systems."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1165893">doi:10.1126/science.1165893</A>]['16].
   (Cornell lab [<A HREF="http://www.creativemachineslab.com/eureqa.html">www</A>]['16],
    commercialised [<A HREF="http://www.nutonian.com/">www</A>]['16](dead '22?),
    Eureqa@[<A HREF="https://en.wikipedia.org/wiki/Eureqa">wikip</A>]['16],
    auth2@[<A HREF="https://scholar.google.com/citations?user=F_Go4V4AAAAJ&hl=en">sch'lar</A>]['22].)
    [Also search for: Eureqa AI]  and  [also search for: robot scientist].

%A M. Schmidt
%A H. Lipson
%T Symbolic regression of implicit equations
%J Genetic Programming Theory and Practice
%V 7
%P 73-85
%D 2009
%K c2009, c200x, c20xx, zz1016,  Eureqa, eureka, eurequa, AI, II,
   symbolic regression, implicit equations, learning, geneticProgramming,
   implicit derivatives
%X "Traditional Symbolic Regression applications are a form of supervised
   learning, where a label y is provided for every [vec] x & an explicit
   symbolic relationship of the form y=f(x) is sought. ... explores the use of
   symbolic regn to perform unsupervised learning by searching for implicit
   relns of the form f(x,y)=0. Implicit relationships are more general & more
   expressive than explicit equns in that they can also represent closed
   surfaces, as well as cts & discontinuous multi-dimensional manifolds. However
   searching these types of equns is particularly challenging because an error
   metric is difficult to define. We studied several direct & indirect
   techniques, & present a successful method based on implicit derivatives. Our
   experiments identified implicit relationships found in a variety of datasets,
   such as equns of circles, elliptic curves, spheres, equns of motion, & energy
   manifolds."
   -- [<A HREF="http://dx.doi.org/10.1007/978-1-4419-1626-6_5">doi:10.1007/978-1-4419-1626-6_5</A>]['16],
   uk us isbn13:978-1-4419-1653-2.
    [Also search for: Eureka AI] and [also search for: geneticProgramming].

%A J. Huang
%A C. Guestrin
%A L. Guibas
%T Fourier theoretic probabilistic inference over permutations
%J J. Mach. Learning Res.
%V 10
%P 997-1070
%M MAY
%D 2009
%K JMLR, eJrnl, c2009, c200x, c20xx, zz0413, permutation, perm, AI, II, compact,
   probability, ranking, rankings, voting, orderings, association
%X "... voting, ranking, & data assoc.. Representing uncertainty over perms. is
   challenging, since there are n! possibilities, & typical compact & factorized
   prob.distn reps., such as graphical models, cannot capture the mutual
   exclusivity constraints assoc. with perms.. ... use the "low-frequency" terms
   of a Fourier decomposition to represent distributions over perms. compactly.
   We present Kronecker conditioning, a novel approach for maintaining &
   updating these distns directly in the Fourier domain, allowing for polynomial
   time bandlimited approxns. Low order F.-based approxs., however, may lead to
   fns that do not corr. to valid distns. [So] present a quadratic program
   defined directly in the F.domain for projecting the approxn onto a
   relaxation of the polytope of legal marginal distns. We demonstrate the
   effectiveness ... on a real camera-based multi-person tracking scenario."
   -- [<A HREF="http://jmlr.csail.mit.edu/papers/v10/huang09a.html">jmlr</A>]['13].

%A R. Kowalski
%T Computational Logic and Human Thinking: How to be Artificially Intelligent
%I CUP
%P 332
%M JUL
%D 2011
%K book, text, CUP, c2011, c201x, c20xx, zz1011, artificial intelligence, AI,
   decision theory, language of thought, LoT, logic
%X 1st ed 2011; hb us$99; uk us isbn:0521194822; uk us isbn13:978-0521194822.
   "... draws upon related developments in various fields from philosophy to
   psychology & law. It pays special attention to the integration of logic
   with decision theory, & the use of logic to improve the clarity &
   coherence of communication in natural languages such as English. ...
   essential reading for teachers & researchers who may be out of touch with
   the latest developments in computational logic. ... also be useful in any
   u/grad course that teaches practical thinking, problem solving or
   communication skills. ..."
   (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/Examples/">e.g.</A>].)

%A D. Mackenzie
%T A flapping of wings
%J Science
%V 335
%N 6075
%P 1430-1433
%M MAR
%D 2012
%K news, c2012, c201x, c20xx, flying, flapping, wing, ornithopter, small,
   robot, robotic, Festo, smartbird, AeroVironment, nano hummingbird, Phoenix,
   AI, drone, drones
%X "... the wings begin to flap while it is still in his hands. Then he tosses
   the bird forward - and with a whir, SmartBird takes off. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.335.6075.1430">doi:10.1126/science.335.6075.1430</A>]['12].

%A C. Doctrow
%A C. Stross
%T The Rapture of the Nerds: A tale of the singularity, posthumanity, and
   awkward social situations
%I TorBooks
%P 352
%M SEP
%D 2012
%K book, AI, singularity, c2012, c201x, c20xx, convergence, sf, nerd, virtual,
   post singularity, Wales, versus, human, Huw, welshman, transcendence, scifi,
   Cory Doctrow, zz0514
%X 1st ed 2012; hb us$17; uk us isbn:0765329107; uk us isbn13:978-0765329103.
   "Welcome to the fractured future, at the dusk of the 21C.  Earth has a
   population of ~ a billion hominids. For the most part, they are happy with
   their lot, living in a preserve at the bottom of a gravity well. Those who
   are unhappy have emigrated, joining one or another of the swarming
   densethinker clades that fog the inner solar system with a dust of molecular
   machinery so thick that it obscures the sun. The splintery metaconsciousness
   of the solar-system has largely sworn off its pre-post-human cousins dirtside
   but its minds sometimes wander ... and when that happens, it casually spams
   Earth's networks with plans for cataclysmically disruptive technologies that
   emulsify whole industries, cultures, and spiritual systems. ..."
   [Also search for: human singularity AI].

%A A. Pease
%A S. Colton
%A J. Charnley
%T Automated theory formation: The next generation
%J IFCOLOG J. Proc. in Computational Logic, Special Issue on Theory Exploration
%D 2013 to appear
%K conf, c2013, c201x, c20xx, ImperialCollege, automatic, maths, theorem prover,
   theory, automatic, proving, proof
%X SC@[<A HREF="http://www.doc.ic.ac.uk/~sgc/">IC</A>]['13].
   [Also search for: theorem proving].

%A X. Hinaut
%A P. F. Dominey
%T Real-time parallel processing of grammatical structure in the fronto-striatal
   system: A recurrent network simulation study using reservoir computing
%J PLoS One
%V 8
%N 2
%P e52946
%M FEB
%D 2013
%K jrnl, eJrnl, c2013, c201x, c20xx, zz0813, iCub, AI, natural language, brain,
   mind, sentence, grammar, processing, words, BA47, frontal cortex, prefrontal,
   striatum, simulation, ANN, RNN, reservoir computing
%X "Sentence processing takes place in real-time. Prev. words in the sentence
   can influence the processing of the current word in the timescale of hundreds
   of millisec.. Recent neurophysiological studies in humans suggest that the
   fronto-striatal system (frontal cortex, & striatum - the major input locus of
   the basal ganglia) plays a crucial role in this process. ... We simulate
   prefrontal area BA47 as a recurrent n/wk that receives on-line input about
   word categories during sentence processing, with plastic connections between
   cortex & striatum. We exploit the homology between the cortico-striatal sys.
   & reservoir computing, where recurrent frontal cortical n/wks are the
   reservoir, & plastic cortico-striatal synapses are the readout. The system is
   trained on sentence-meaning pairs ... The model learns an extended set of
   grammatical constructions, & [can] generalize to novel constructions. It
   demonstrates how early in the sentence, a parallel set of predictions are
   made concerning the meaning, which are then confirmed or updated as the
   processing of the input sentence proceeds. It demonstrates how on-line
   responses to words are influenced by previous words in the sentence, & by
   prev. sentences in the discourse ... This demonstrates that a recurrent
   n.n/wk can decode grammatical structure from sentences in real-time ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0052946">doi:10.1371/journal.pone.0052946</A>]['13],
   auth2@[<A HREF="http://pfdominey.perso.sfr.fr/">sfr</A>]['13].

%A T. Hanser
%A C. Barber
%A E. Rosser
%A J. D. Vessey
%A S. J. Webb
%A S. Werner
%T Self organising hypothesis networks: a new approach for representing and
   structuring SAR knowledge
%J J. of Cheminformatics
%V 6
%P 21
%D 2014
%O 6th Joint Sheffield Conf. on Chemoinformatics
%K conf, c2014, c201x, c20xx, zz0115, LhasaLtd, AI, SOHN, chemical compound,
   Structure Activity Relationship, SAR, quantitative, QSAR
%X "... To combine models at the knowledge level, we propose to decouple the
   learning phase from the knowledge application phase using a pivot repn
   (lingua franca) based on the concept of hypothesis. A hypothesis is a simple
   & interpretable knowledge unit. Regardless of its origin, knowledge is broken
   down into a collection of hypotheses. These h. are subsequently organised
   into hierarchical network. ..."
   "... A hypothesis defines the scope of a class of compounds sharing a SAR
   trend for a given endpoint. From a classification viewpoint, a hypothesis
   defines a class of compounds in the chemical space that fully or partially
   separates the endpoint classes. ... structural hypotheses can represent a
   class of compounds containing a given functional group or more generally a
   structural pattern. ... hypotheses may be based on physico-chemical or
   pharmacophoric properties of the structure. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1758-2946-6-21">doi:10.1186/1758-2946-6-21</A>]['15].
   [Also search for: chemical compound SAR].

%A Y. LeCun
%A Y. Bengio
%A G. Hinton
%T Deep learning
%J Nature
%V 521
%N 7533
%P 436-444
%M MAY
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0715, intro, machine, deep, learning, AI, II,
   training, ANN, ANNs, nets, layers, big data, Lecun
%X "DL allows computational models that are composed of multiple processing
   layers to learn representations of data with mult. levels of abstn. ...
   dramatically improved the state-of-the-art in speech recognition, visual
   object recog., object detection & many other domains such as drug discovery &
   genomics. Deep learning discovers intricate structure in large data sets by
   using the backpropagation alg. to indicate how a m/c should change its
   internal params. that are used to compute the repn in each layer from the
   repn in the prev. layer. Deep convolutional nets ... processing images,
   video, speech & audio, whereas recurrent nets have shone light on seq. data
   such as text & speech."
   -- [<A HREF="http://dx.doi.org/10.1038/nature14539">doi:10.1038/nature14539</A>]['15].
      Also see, "... Various deep learning architectures such as deep neural
      networks, convolutional deep neural networks, ... Alternatively, deep
      learning has been characterized as a buzzword, or a rebranding of
      neural networks. ..."
      -- [<A HREF="https://en.wikipedia.org/wiki/Deep_learning">wikip</A>]['15].
   [Also search for: training deep ANN].

%A Z. Ghahramani
%T Probabilistic machine learning and artificial intelligence
%J Nature
%V 521
%N 7533
%P 452-459
%M MAY
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0715, AI, machine learning, II, probability,
   uncertainty, model
%X "How can a m/c learn from experience? Prob. modelling provides a framework
   for understanding what learning is, & has therefore emerged as one of the
   principal theor. & practical approaches for designing m/cs that learn from
   data acquired through experience. The prob. f/wk, which describes how to
   represent & manipulate uncertainty about models & predictions, has a central
   role in scientific data analysis, m/c learning, robotics, cognitive sci. &
   art.int.. This Review provides an introduction to this f/wk, & discusses some
   of the state-of-the-art advances in the field, namely, probabilistic
   programming, Bayesian optimization, data compn & automatic model discovery."
   -- [<A HREF="http://dx.doi.org/10.1038/nature14541">doi:10.1038/nature14541</A>]['15].

%A M. Ford
%T Rise of the Robots: Technology and the Threat of a Jobless Future
%I BasicBooks
%P 352
%M MAY
%D 2015
%K book, AI, c2015, c201x, c20xx, zz1015, human, robot, automation, job,
   work, employment, risks, prediction
%X "... Artificial intelligence is already well on its way to making
   'good jobs' obsolete: many paralegals, journalists, office workers, and even
   computer programmers are poised to be replaced by robots and smart software.
   As progress continues, blue and white collar jobs alike will evaporate ..."
   1st ed 2015; hb us$16; uk is isbn:0465059996; uk us isbn13:978-0465059997.

%A J. Markoff
%T Machines of Loving Grace: The Quest for Common Ground Between Humans and
   Robots
%I Ecco
%P 400
%M AUG
%D 2015
%K book, AI, c2015, c201x, c20xx, zz1015, human, robot, automation
%X "... offers a sweeping history of the complicated and evolving relationship
   between humans and computers. ..."
   1st ed 2015; hb us$18; uk us isbn:0062266683; uk us isbn13:978-0062266682.

%A D. A. Mindell
%T Our Robots, Ourselves: Robotics and the Myths of Autonomy
%I Viking
%P 272
%I OCT
%D 2015
%K book, AI, c2015, c201x, c20xx, zz1015, human, robot, automation
%X "... takes us to extreme environments - high atmosphere, deep ocean, and
   outer space - to reveal where the most advanced robotics already exist. ...
   But these tools of air, sea, and space also forecast the dangers, ethical
   quandaries, and unintended consequences of a future in which robotics and
   automation suffuse our everyday lives. ..."
   1st ed 2015; hb us$19; uk us isbn:0525426973; uk us isbn13:978-0525426974.

%A B. M. Lake
%A R. Salakhutdinov
%A J. B. Tenenbaum
%T Human-level concept learning through probabilistic program induction
%J Science
%V 350
%N 6266
%P 1332-1338
%M DEC
%D 2015
%K jrnl, c2015, c201x, c20xx, zz1215, AI, machine, learning, II, induction,
   concepts, examples, character recognition, generalization
%X "People ... can often generalize successfully from just a single example, yet
   machine learning algs. typically require tens or hundreds of examples ...
   People can also use learned concepts in richer ways than conventional algs. -
   for action, imagination, & explanation. We present a computational model that
   captures these human learning abilities for a large class of simple visual
   concepts: handwritten characters from the world's alphabets. The model
   represents concepts as simple programs that best explain observed examples
   under a Bayesian criterion. On a challenging one-shot classn task, [it]
   achieves human-level performance while outperforming recent deep learning
   approaches. We also present several 'visual Turing tests' probing the model's
   creative generalization abilities, which in many cases are indistinguishable
   from human behavior."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aab3050">doi:10.1126/science.aab3050</A>]['15].
   [Also search for: induction programming], for example.

%A J.-F. Bonnefon
%A A. Shariff
%A I. Rahwan
%T The social dilemma of autonomous vehicles
%J Science
%V 352
%N 6293
%P 1573-1576
%M JUN
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0716, AI, car, cars, self driving, automobile,
   vehicle, autonomous, robot, ethics, vehicle, pedestrian, safety, risk, risks
%X "... Defining the algorithms that will help AVs make these moral decisions is
   a formidable challenge. We found that participants in six Amazon Mechanical
   Turk studies approved of utilitarian AVs (that is, AVs that sacrifice their
   passengers for the greater good) & would like others to buy them, but they
   would themselves prefer to ride in AVs that protect their passengers at all
   costs. The study participants disapprove of enforcing utilitarian regulations
   for AVs & would be less willing to buy such an AV. Accordingly, regulating
   for utilitarian algs. may paradoxically increase casualties by postponing the
   adoption of a safer technology."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaf2654">doi:10.1126/science.aaf2654</A>]['16].

%A G. M. Del Corso
%A F. Romani
%T An adaptive matrix factorization approach for personalized recommender
   systems
%J arXiv
%M JUL
%D 2016
%K TR, c2016, c201x, c20xx, zz0816, matrix, factorization, recommender system,
   MovieLens, movies, recommendation, AI
%X "... A promising approach is the one based on the low-rank nonnegative matrix
   factorization of A where items and users are represented in terms of a few
   vectors. ... we propose an alg. based on the nonnegative matrix F. approach
   for predicting the missing entries. Numerical test have been performed to
   est. the accuracy in predicting the missing entries & in the recommendations
   provided & we have compared our technique with others in the literature. We
   have tested the alg. on the MovieLens databases containing ratings of users
   on movies."
   -- 1607.07607@[<A HREF="http://arxiv.org/abs/1607.07607">arXiv</A>]['16].
   [Also search for: matrix factorization].

%A H. Lipson
%A M. Kurman
%T Driverless: Intelligent Cars and the Road Ahead
%I MITpress
%P 328
%M OCT
%D 2016
%K book, c2016, c201x, c20xx, zz0916, driverless car, cars, automobile, autos,
   autonomous, google, self driving, road transport
%X "In the year 2014, Google fired a shot heard all the way to Detroit.
   Google's newest driverless car had no steering wheel and no brakes. ..."
   1st ed 2016; hb us$30; uk us isbn:0262035227; uk us isbn13:978-0262035224.

%A D. Castelvecchi
%T Can we open the black box of AI?
%J Nature
%V 538
%B 7623
%P 20-23
%M OCT
%D 2016
%K news, views, c2016, c201x, c20xx, zz1016, artificial neural network, net,
   AI, ANN, NN, black box, deep learning, reason, why, explaining, Eureqa
%X "Artificial intelligence is everywhere. But before scientists trust it,
   they first need to understand how machines learn. ... deciphering the
   black box has become exponentially harder and more urgent. ... neural
   networks are surprisingly easy to fool with images that to people look like
   random noise, or abstract geometric patterns. ... if AI is to give answers
   that humans can easily interpret, 'there's a world of problems for which
   deep learning is just not the answer.' ... '[but] A model produced by Eureqa
   usually has a dozen parameters. A neural network has millions.' ..."
   -- [<A HREF="http://dx.doi.org/10.1038/538020a">doi:10.1038/538020a</A>]['16].

%A K. Grace
%A J. Salvatier
%A A. Dafoe
%A B. Zhang
%A O. Evans
%T When will AI exceed human performance? Evidence from AI experts
%J arXiv
%M JUN
%D 2017
%K TR, c2017, c201x, c20xx, zz0617, AI, artificial intelligence, human, versus,
   HAL, Terminator, singularity, robots, computing, technology, performance,
   ability, society, social consequences, jobs, work, automation, profession,
   futurology, prediction, zzPrediction, zz0124, zz0127, zz0149, zz0153
%X "... we report the results from a large survey of machine learning
   researchers on their beliefs about progress in AI. Researchers predict AI
   will outperform humans in many activities in the next ten years, such as
   translating languages (by 2024), writing high-school essays (by 2026),
   driving a truck (by 2027), working in retail (by 2031), writing a bestselling
   book (by 2049), and working as a surgeon (by 2053). Researchers believe there
   is a 50% chance of AI outperforming humans in all tasks in 45 years and of
   automating all human jobs in 120 years, with Asian respondents expecting
   these dates much sooner than North Americans. These results will inform
   discussion amongst researchers and policymakers about anticipating and
   managing trends in AI."
   -- 1705.08807@[<A HREF="https://arxiv.org/abs/1705.08807">arXiv</A>]['17].
   [Also search for: zzPrediction] for other predictions.
     (Some would say that LLmodels had achieved 'translation' and
     'high-school essays' by 2023.   [Also search for: LLmodel AI].)

%A C. Finn
%A P. Abbeel
%A S. Levine
%T Model-agnostic meta-learning for fast adaptation of deep networks
%J arXiv
%M JUL
%D 2017
%K TR, c2017, c201x, c20xx, zz0820, ANN, model agnostic, meta learning
%X "We propose an alg. for meta-learning that is model-agnostic, in the sense
   that it is compatible with any model trained with gradient descent &
   applicable to a variety of different learning problems, inc. class'n,
   regres'n, & reinf.learning. The goal of meta-l. is to train a model on a
   variety of ... such that a small # of gradient steps with a small amount of
   training data from a new task will produce good generalization performance
   on that task. ...  demonstrate that this approach leads to state-of-the-art
   performance on two few-shot image class'n benchmarks, produces good results
   on few-shot reg'n, & accelerates fine-tuning for policy gradient reinf.
   learning with n.n/wk policies."
   -- [<A HREF="https://arxiv.org/abs/1703.03400">arXiv</A>]['20].


%A M. Tegmark
%T Life 3.0: Being Human in the Age of Artificial Intelligence
%I Knopf
%P 384
%D 2017
%K book, text, c2017, c201x, c20xx, zz0917, AI, Artificial Intelligence, robots,
   robot, android, human versus, convergence, prediction zzPrediction,
   Life3.0, Life3
%X 1st ed 2017; hb us$18; uk us isbn:1101946598; uk us isbn13:978-1101946596.
   "... Should we fear an arms race in lethal autonomous weapons? Will machines
   eventually outsmart us at all tasks, replacing humans on the job market and
   perhaps altogether? Will AI help life flourish like never before or give us
   more power than we can handle?  What sort of future do you want? ..."
   [Also search for: human versus AI].

%A D. George
%A et al
%T A generative vision model that trains with high data efficiency and
   breaks text-based CAPTCHAs
%J Science
%V ?
%N ?
%P ?-?
%M OCT
%D 2017
%K jrnl, c2017, c201x, c20xx, zz1017, AI, CAPTCHA, test, human,
   contour continuity, reCAPTCHA
%X "... drawing inspiration from systems neuroscience, we introduce a
   probabilistic generative model for vision in which message-passing based
   inference handles recognition, segmentation & reasoning in a unified way. The
   model demonstrates excellent generalization & occlusion-reasoning
   capabilities, & outperforms deep neural networks on a challenging scene text
   recognition benchmark while being 300-fold more data efficient. [&] the model
   fundamentally breaks the defense of modern text-based CAPTCHAs by
   generatively segmenting characters without CAPTCHA-specific heuristics. Our
   model emphasizes aspects like data efficiency & compositionality that may be
   important in the path toward general artificial intelligence."
   -- [<A HREF="https://doi.org/10.1126/science.aag2612">doi:10.1126/science.aag2612</A>]['17].
   (Also see the abc[<A HREF="http://www.abc.net.au/news/science/2017-10-27/captcha-cracking-artificial-intelligence-machine-learning/9080608">27/10/2017</A>].)

%A D. Silver
%A et al ...
%A D. Hassabis
%T Mastering chess and shogi by self-play with a general reinforcement learning
   algorithm
%J arXiv
%M DEC
%D 2017
%K TR, c2017, c201x, c20xx, zz1217, Chess, Shogi, game, playing, program, AI,
   deep learning, reinforcement learning, AlphaGo Zero, AlphaZero, ANN, NN
%X "... we generalise [AlphaGo Zero's] approach into a single AlphaZero
   alg. that can achieve, tabula rasa, superhuman performance in many
   challenging domains. Starting from random play, & given no domain knowledge
   except the game rules, AlphaZero achieved within 24 hours a superhuman level
   of play in the games of chess & shogi (Japanese chess) as well as Go, &
   convincingly defeated a world-champion program in each case."
   -- 1712.01815@[<A HREF="https://arxiv.org/abs/1712.01815">arXiv</A>]['17].
   (Also see RL@[<A HREF="https://en.wikipedia.org/wiki/Reinforcement_learning">wikip</A>]['22].)
   [Also search for: AlphaGo].

%A J. Dressel
%A H. Farid
%T The accuracy, fairness, and limits of predicting recidivism
%J Sci. Adv.
%V 4
%N 1
%P eaao5580
%M JAN
%D 2018
%K jrnl, COMPAS, program, law, legal, justice, courts, gaol, jail, reoffender,
   reoffending, criminal, recidivism, parole, c2018, c201x, c20xx, zz0118,
   stats, AI, II, software, Dtree, controversial
%X "Algs. for predicting recidivism are commonly used to assess a criminal
   defendant's likelihood of committing a crime. ... used in pretrial, parole, &
   sentencing decisions. Proponents ... argue that big data & advanced machine
   learning make these analyses more accurate & less biased than humans. We show
   however that the widely used commercial risk assessment s/w COMPAS is no more
   accurate or fair than predictions made by people with little or no criminal
   justice expertise. [&] show that a simple linear predictor provided with only
   two features is nearly equivalent to COMPAS with its 137 features."
   -- [<A HREF="https://doi.org/10.1126/sciadv.aao5580">doi:10.1126/sciadv.aao5580</A>]['18].
   ((Also see: COMPAS Classification software,
   "The COMPAS Classification software is a management support tool that
   can be interfaced with existing jail management systems to provide critical
   inmate management ... Classification - Decision Tree Primary Classification
   and Reclassification Instruments ..."
   [<A HREF="http://www.equivant.com/solutions/inmate-classification">www</A>][1/2018].))

%A S. Cyphers
%A et al ...
%A T. J. Webb
%T Intel nGraph: An intermediate representation, compiler, and executor for
   deep learning
%J arXiv
%M JAN
%D 2018
%K TR, c2018, c201x, c20xx, zz0218, deep learning,NN, ANN, Intel, nGraph,
   neon, TensorFlow, MXNet
%X "... Building on our experience creating neon (a fast deep learning library
   on GPUs), we developed Intel nGraph, a soon to be open-sourced C++ library to
   simplify the realization of optimized deep learning performance across
   frameworks & hardware platforms. Initially-supported frameworks include
   TensorFlow, MXNet, & Intel neon framework. Initial backends are Intel
   Architecture CPUs (CPU), the Intel(R) Nervana Neural Network Processor(R)
   (NNP), & NVIDIA GPUs. Currently supported compiler optimizations include
   efficient memory management & data layout abstraction. ... we describe our
   overall architecture & its core components. In the future, we envision
   extending nGraph API support to a wider range of frameworks, hardware (inc.
   FPGAs & ASICs), & compiler optimizations (training v. inference
   optimizations, multi-node & multi-device scaling via efficient sub-graph
   partitioning, & HW-specific compounding of operations)."
   -- 1801.08058@[<A HREF="https://arxiv.org/abs/1801.08058">arXiv</A>]['18].

%A S. M. A. Eslami
%A et al ...
%A D. Hassabis
%T Neural scene representation and rendering
%J Science
%V 360
%N 6394
%P 1204-1210
%M JUN
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0618, DeepMind, google, NN, ANN,
   artificial, computer vision, GQN, Generative Query, scene representation,
   sensory, 3D, AI
%X "Scene representation - the process of converting visual sensory data into
   concise descriptions ... we introduce the Generative Query Network (GQN), a
   framework within which machines learn to represent scenes using only their
   own sensors. The GQN takes as input images of a scene taken from different
   viewpoints, constructs an internal representation, and uses this
   representation to predict the appearance of that scene from previously
   unobserved viewpoints. The GQN demonstrates representation learning without
   human labels or domain knowledge, paving the way toward machines that
   autonomously learn to understand the world around them."
   -- [<A HREF="https://doi.org/10.1126/science.aar6170">doi:10.1126/science.aar6170</A>]['18].
   (?run for the hills?)

%A S. Li
%A et al ...
%A H. Lipson
%T Particle robotics based on statistical mechanics of loosely coupled
   components
%J Nature
%V 567
%P 361-365
%M MAR
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0319, robotics, robot, swarm, distributed, AI,
   behaviour, movement
%X "... demonstrate a robotic system whose overall behaviour can be successfully
   controlled by exploiting statistical mechanics phenomena. We achieve this by
   incorporating many loosely coupled 'particles', which are incapable of
   independent locomotion & do not possess individual identity or addressable
   position. In the proposed system, each particle is permitted to perform only
   uniform volumetric oscillations that are phase-modulated by a global signal.
   Despite the stochastic motion of the robot & lack of direct control of its
   individual components, we demonstrate physical robots composed of up to two
   dozen particles & simulated robots with up to 100,000 particles capable of
   robust locomotion, object transport & phototaxis (movement towards a light
   stimulus). ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-1022-9">doi:10.1038/s41586-019-1022-9</A>]['19].

%T Turing award
%M MAR
%D 2019
%K news, views, c2018, c201x, c0xx, zz0419, AI, deep learning, NN, ANN,
   neural net, nets, Hinton, Bengio, LeCun
%X Geoffrey Hinton, Yoshua Bengio and Yann LeCun won the 2018(!) Turing award
   for work on "deep learning".
   -- bbc[<A HREF="https://www.bbc.com/news/technology-47721129">27/3/2019</A>],
      AMT@[<A HREF="https://amturing.acm.org/">acm</A>]['19].
   Also see DL@[<A HREF="https://en.wikipedia.org/wiki/Deep_learning">wikip</A>]['19].

%A I. McEwan
%T Machines Like Me: A Novel
%I Penguin
%P 352
%M APR
%D 2019
%K book, c2019, c201x, c20xx, zz0419, SciFi, novel, robot, robots, android
%X 1st ed 2019; hb stg.13, uk isbn:1787331660, uk isbn13:978-1787331662;
                hb us$18;  us isbn:0385545118; us isbn13:978-0385545112.
   "Machines Like Me takes place in an alternative 1980s London. Charlie,
   drifting through life and dodging full-time employment, is in love with
   Miranda, a bright student who lives with a terrible secret. When Charlie
   comes into money, he buys Adam, one of the first synthetic humans and - with
   Miranda's help - he designs Adam's personality. The near-perfect human that
   emerges is beautiful, strong, and clever. It isn't long before a love
   triangle soon forms, and these three beings confront a profound moral
   dilemma. ..."

%T Independent Report on the London Metropolitan Police Service's Trial of
   Facial Recognition Software
%A P. Fussey
%A D. Murray
%Q The Human Rights, Big Data and Technology Project
%M JUL
%D 2019
%K TR, c2019, c201x, c20xx, zz0719, society, human rights, live, face, facial,
   recognition, LFR, CCTV, algorithm, big data, Neoface, MPS, police, policing,
   London, UK, Scotland Yard, bias, discrimination, race, racial profiling,
   legal, law, legality, state, controversial
%X "Between 2016 and 2019 the Metropolitan Police Service (MPS) conducted a
   total of 10 test deployments, trialling live facial recognition (LFR)
   technology during policing operations ... Overall, [it] generated 46 matches
   (p.10) ... Adjudicating officers judged 16 (38.1%) of these 42 ...matches to
   be 'non-credible' ... Of the remaining 22 stops, 14 (63.64%) were verified as
   incorrect matches following an identity check. Eight (36.36%) were verified
   as correct matches following an identity check. This means that across all
   six observed trials, and from all computer-generated alerts, face recognition
   matches were verifiably correct on eight occasions (eight of 42 matches,
   19.05%). ..."
   -- pdf@[<A HREF="https://48ba3m4eh2bf2sksp43rq8kk-wpengine.netdna-ssl.com/wp-content/uploads/2019/07/London-Met-Police-Trial-of-Facial-Recognition-Tech-Report.pdf">www</A>]['19].
   (Also see [<A HREF="https://www.essex.ac.uk/news/2019/07/03/met-police-live-facial-recognition-trial-concerns">U_Ess'x</A>][3/7/2019],
    [<A HREF="https://www.theguardian.com/technology/2019/jul/03/police-face-calls-to-end-use-of-facial-recognition-software">The_G</A>][4/7/2019],
    [<A HREF="https://www.bbc.com/news/business-48842750">bbc</A>][5/7/2019], &
    [<A HREF="https://www.bbc.com/news/technology-49030595">bbc</A>][18/7/2019].)
   [Also search for: facial recognition].

%T The work of the Biometrics Commissioner and the Forensic Science Regulator.
   Nineteenth Report of Session 2017-19
%R HC1970
%Q House of Commons Science and Technology Committee
%M JUL
%D 2019
%K TR, HC1970, c2019, c201x, c20xx, zz0719, face, facial recognition,
   human rights, police, UK, parliament, government, law, legal, privacy
%X "... It is now seven years since the 2012 High Court ruled that the
   indefinite retention of innocent people's custody images was unlawful
   and yet the practice is continuing. A system was meant to have
   been put in place where any custody images were kept for six years and
   then reviewed ... We call on the Government to issue a moratorium on the
   current use of facial recognition technology and no further trials should
   take place until a legislative framework has been introduced and guidance on
   trial protocols, & an oversight & evaluation system, has been established."
   -- pdf@[<A HREF="https://publications.parliament.uk/pa/cm201719/cmselect/cmsctech/1970/1970.pdf">.uk</A>][17/7/2019].
   Also see [<A HREF="https://www.bbc.com/news/technology-49030595">bbc</A>][18/7/2019].
   [Also search for: facial recognition].

%A M. Scanagatta
%A A. SalmerÃ³n
%A F. Stella
%T A survey on Bayesian network structure learning from data
%J Progress in AI
%P 1-15
%M MAY
%D 2019
%K jrnl, eJrnl, Bayesian network, Bnet, c2019, c201x, c20xx, zz0719, learning,
   II, AI
%X "...  In this survey, we review the most relevant structure learning
   algorithms that have been proposed in the literature. We classify them
   according to the approach they follow for solving the problem and we also
   show alternatives for handling missing data and continuous variable. An
   extensive review of existing software tools is also given."
   -- [<A HREF="https://doi.org/10.1007/s13748-019-00194-y">doi:10.1007/s13748-019-00194-y</A>]['19].
   [*Sadly, a lack of experiments comparing the performance of methods.*]
   [Also search for: Bayesian network].

%A S. Russell
%T Human Compatible: Artificial Intelligence and the Problem of Control
%I Viking
%P 352
%M OCT
%D 2019
%K book, text, c2019, c201x, c20xx, zz1019, AI, versus, human, robot,
   convergence, HAL, Terminator, superintelligence, superintelligent
%X 1st ed 2019, hb us$28; uk is isbn:0525558616; uk us isbn13:978-0525558613.
   "... In the popular imagination, superhuman artificial intelligence is an
   approaching tidal wave that threatens not just jobs and human relationships,
   but civilization itself. Conflict between humans and machines is seen as
   inevitable and its outcome all too predictable.  In this groundbreaking book,
   distinguished AI researcher Stuart Russell argues that this scenario can be
   avoided, but only if we rethink AI from the ground up. ..."
   [Also search for: human versus AI].

%A M. Hutson
%T Core progress in AI has stalled in some fields
%J Science
%V 368
%N 6494
%P 927
%M MAY
%D 2020
%K jrnl, AI, c2020, c202x, c20xx, zz0520, progress, II, ANN, NN, neural network,
   controversial, recommendation system
%X "... Researchers have evaluated 81 pruning algs., programs that make neural
   networks, a type of AI, more efficient by trimming unneeded connections. All
   claimed superiority in slightly different ways. But when the researchers
   tried to evaluate them side by side, there was no clear evidence of
   performance improvements over a 10-year period. There are other signs of
   shaky progress across AI. A 2019 meta-analysis of information retrieval
   algs. used in search engines concluded the 'high-water mark ... was actually
   set in 2009.' ..."
   -- [<A HREF="https://doi.org/10.1126/science.368.6494.927">doi:10.1126/science.368.6494.927</A>]['20].

%A D. Castelvecchi
%T Mathematicians welcome computer-assisted proof in 'grand unification' theory
%J Nature
%M JUN
%D 2021
%K news, views, c2021, c202x, c20xx, zz0323, LEAN, maths proof assistant, Xena
%X "Proof-assistant software handles an abstract concept at the cutting edge of
   research, revealing a bigger role for software in mathematics."
    -- [<A HREF="https://doi.org/10.1038/d41586-021-01627-2">doi:10.1038/d41586-021-01627-2</A>]['23].
   (Also see, C. Loh, 'The Lean Proof Assistant', 2022
      [<A HREF="https://doi.org/10.1007/978-3-031-14649-7_1">doi:10.1007/978-3-031-14649-7_1</A>]['23], and
   Lean@[<A HREF="https://en.wikipedia.org/wiki/Lean_(proof_assistant)">wikip</A>]['23].)
  [Also search for: maths proof assistant] & [also search for: theorem proving].

%A Minkyu Shin
%A Jin Kim
%A Minkyung Kim
%T Human learning from Artificial Intelligence: Evidence from human go players'
   decisions after AlphaGo
%J Proc. of the Annual Meeting of the Cognitive Sci. Soc.
%M JUL
%D 2021
%K conf, c2021, c202x, c20xx, zz0323, ANN, AI, AlphaGo, Go, human, game
%X "... examining human decision-making in the board game Go. Our analysis of
   1.3 million move decisions made by professional Go players suggests that
   people learned to make decisions like AI after they observe reasoning
   processes of AI, rather than mere actions of AI. Follow-up analyses compared
   the decision quality of two groups of players: those who had access to AI
   programs & those who did not. In line with the initial results, decision
   quality sig. improved for the players with AI access after they gained access
   to reasoning processes of AI, but not for the players without AI access. Our
   results demonstrate that humans can learn from AI even in a complex domain
   where the computation process of AI is also complicated."
   -- [<A HREF="https://scholars.cityu.edu.hk/en/publications/publication(1cee781f-57f0-4452-8361-04ae1597aeed).html">www</A>]['23].
   [Also search for: AI Go game].

%A L. P. Kaelbling
%T The foundation of efficient robot learning
%J Science
%V 369
%N 6506
%P 915-916
%M AUG
%D 2020
%K news, views, c2020, c202x, c20xx, zz0820, AI, machine learning, intro,
   robotic, robotics, robots, realWorld
%X "The past 10 y. have seen enormous breakthroughs[*] in mach.l., resulting
   in game-changing applications in comp.vision & lang.proc.. The field of
   intell. robotics ... has not yet been revolutionized by these breakthroughs.
   A critical difficulty is that the nec. learning depends on data that can only
   come from acting in a variety of real-world environments. Such data are
   costly to acquire because there is enormous variability in the situations a
   general-purpose robot must cope with. It will take a combination of new
   alg.techniques, inspiration from natural syss, & multiple levels of
   m.learning to revolutionize robotics with general-purpose intell.. ..."
   -- [<A HREF="https://doi.org/10.1126/science.aaz7597">doi:10.1126/science.aaz7597</A>]['20].
   [*][Also search for: progress AI 6494].

%A A. E. Eiben
%A et al ...
%A A. F. Winfield
%T Towards autonomous robot evolution
%J Software Engineering for Robotics (RoboSoft)
%I Springer
%P 29-51
%D 2021
%O RoboSoft, London, Nov. 2019
%K conf, RoboSoft, c2021, c202x, c20xx, zz0222, robot, robotics, evolving,
   AI, UniYork, UYork, York, reproduce, autonomous, SWE
%X "We outline a perspective on the future of evolutionary robotics ... a new
   paradigm, second-order SWE, where instead of directly developing a system for
   a given application, we develop an evolutionary system that will develop the
   target system for us. Importantly, this also holds for the h/w; with a
   complete evolutionary robot system, both the s/w & the h/w are evolved. ..."
   -- [<A HREF="https://doi.org/10.1007/978-3-030-66494-7_2">doi:10.1007/978-3-030-66494-7_2</A>]['21]. (online Dec 2020.)
   Also see project@[<A HREF="https://www.york.ac.uk/robot-lab/are/">UniYork</A>]['22].
   (In: us$122; uk us isbn:3030664937; uk us isbn13:9783030664930.
   "... The origin of this book is a 2-day event, entitled RoboSoft,
   that took place in Nov. 2019. ...")

%A Boyuan Chen
%A et al
%T Full-body visual self-modeling of robot morphologies
%J arXiv
%M NOV
%D 2021
%K TR, c2021, c202x, c20xx, zz0722, Lipson, robot, AI, self modelling,
   awareness
%X "...  'self-models' allow robots to consider outcomes of multiple possible
   future actions, without trying them out in physical reality. Recent progress
   in fully data-driven self-modeling has enabled machines to learn their own
   forward kinematics directly from task-agnostic interaction data ... we
   propose that instead of directly modeling forward-kinematics, a more useful
   form of self-modeling is one that could answer space occupancy queries,
   conditioned on the robot's state. ..."
   -- 2111.06389@[<A HREF="https://arxiv.org/abs/2111.06389">arXiv</A>]['22].
   (Also see last auth@[<A HREF="https://www.me.columbia.edu/faculty/hod-lipson">www</A>]['22].)

%A P. R. Wurman
%A et al
%T Outracing champion Gran Turismo drivers with deep reinforcement learning
%J Nature
%V 602
%P 223-228
%M FEB
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0222, AI, game, eSports, eSport, Gran Turisimo,
   car racing simulation, outplaying, beating humans, PlayStation
%X "... demo. the capabilities of our agent, Gran Turismo Sophy, by winning a
   head-to-head competition [v.] four of the world's best G.T. drivers. By
   describing how we trained championship-level racers, we demo. the
   possibilities & challenges of using these techniques to control complex
   dynamical systems in domains where agents must respect imprecisely defined
   human norms."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-04357-7">doi:10.1038/s41586-021-04357-7</A>]['22].
   (Also see RL@[<A HREF="https://en.wikipedia.org/wiki/Reinforcement_learning">wikip</A>]['22].)

%A S. J. Nightingale
%A H. Farid
%T I-synthesized faces are indistinguishable from real faces and more
   trustworthy
%J PNAS
%V 119
%P e2120481119
%N 8
%M FEB
%D 2022
%K jrnl, PNAS, c2022, c202x, c20xx, zz0222, AI, web, internet, face, faces,
   trust, artificial, StyleGAN, StyleGAN2, generative adversarial network, GAN,
   synthetic, fake
%X "... Our evaluation of the photorealism of AI-synthesized faces indicates
   that synthesis engines have passed through the uncanny valley & [can]
   creat[e] faces that are indistinguishable - & more trustworthy - than real
   faces."
   -- [<A HREF="https://doi.org/10.1073/pnas.2120481119">doi:10.1073/pnas.2120481119</A>]['22].

%A S. Reed
%A et al
%T A generalist agent (Gato)
%M MAY
%D 2022
%K TR, AI, c2022, c202x, c20xx, zz0522, DeepMind, GATO, general
%X "... building a single generalist agent beyond the realm of text outputs. The
   agent, which we refer to as Gato, works as a multi-modal, multi-task,
   multi-embodiment generalist policy. The same n/wk with the same weights can
   play Atari, caption images, chat, stack blocks with a real robot arm & much
   more, deciding based on its context whether to output text, joint torques,
   button presses, or other tokens. ... we describe the model & the data, &
   document the current capabilities of Gato."
   -- 2205.06175@[<A HREF="https://arxiv.org/abs/2205.06175">arXiv</A>]['22].

%T Measuring Goodhart's Law
%M APR
%D 2022
%K TR, news, blogpost, c2022, c202x, c20xx, zz0723, OpenAI, AI, robot, chatBot,
   training, reward model, chatGPT, GPT 3, GPT3, natural language model, ANN, NN
%X "... we train a model to predict these human preferences, known as a reward
   model, and use the reward model's predictions as a proxy objective. But it's
   important to keep track of how well the true objective is being
   optimized. ..."
   -- [<A HREF="https://openai.com/blog/measuring-goodharts-law/">www</A>]['22].
   [Also search for: OpenAI]  (not really "open").
   Also see [<A HREF="https://openai.com">OpenAI</A>]['22] &
   "... non-profit OpenAI Incorporated (OpenAI Inc.) and its
    for-profit subsidiary corp. OpenAI Limited Partnership (OpenAI LP).
    ... considered a competitor to DeepMind ... founded in San Francisco
     in late 2015 by Elon Musk, Sam Altman, & others, ... [&] OpenAI LP received
     a US$1 billion investment from Microsoft ..."
   -- OpenAI@[<A HREF="https://en.wikipedia.org/wiki/OpenAI">wikip</A>]['22,'23].
   [Also search for: natural language NN].

%A A. Hundt
%A et al
%T Robots enact malignant stereotypes
%J 2022 ACM Conf. on Fairness, Accountability, and Transparency
%I ACM
%P 743-756
%M JUN
%D 2022
%K conf, c2022, c202x, c20xx, zz0722, OpenAI, CLIP, NLP, robot, AI, bias,
   stereotype, bias, discrimination, fairness, safety, images
%X "Stereotypes, bias, & discrimination have been extensively documented in
   machine learning (ML) ... we evaluate how ML bias manifests in robots that
   physically & autonomously act within the world. We audit one of several
   recently published CLIP-powered robotic manipulation methods, presenting it
   with objects that have pictures of human faces ... experiments definitively
   show robots acting out toxic stereotypes with respect to gender, race, &
   sci.-discredited physiognomy, at scale. Furthermore, the audited methods
   are less likely to recognize women & people of color. ..."
   -- [<A HREF="https://doi.org/10.1145/3531146.3533138">doi:10.1145/3531146.3533138</A>]['22].

%A V. Rotaru
%A et al
%T Event-level prediction of urban crime reveals a signature of
   enforcement bias in US cities
%J NatureHumanBehaviour
%M JUN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0722, AI, crime, prediction, racial, bias,
   policing, police, law enforcement, state surveillance, USA
%X "... we show that, while predictive models may enhance state power through
   criminal surveillance, they also enable surveillance of the state by tracing
   systemic biases in crime enforcement. We introduce a stochastic inference
   alg. that forecasts crime by learning spatio-temporal dependencies from event
   reports, with a mean area under the [ROC] curve of ~90% in Chicago for crimes
   predicted per week within ~1,000ft. ... enable us to study perturbations of
   crime patterns that suggest that the response to increased crime is biased by
   neighbourhood socio-economic status, draining policy resources from
   socio-economically disadvantaged areas, as demo. in eight major US cities."
  -- [<A HREF="https://doi.org/10.1038/s41562-022-01372-0">doi:10.1038/s41562-022-01372-0</A>]['22].

%A C. de Pascali
%A et al ...
%A B. Mazzolai
%T 3D-printed biomimetic artificial muscles using soft actuators that contract
   and elongate
%J ScienceRobotics
%V 7
%N 68
%M JUL
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0722, dePascali, robot, robotic, robotics,
   GRACE, artificial, muscle, actuator, hand, hands, mimic, biomimetic
%X "... we present a class of pneumatic artificial muscles, named GeometRy-based
   Actuators that Contract & Elongate (GRACE). The GRACEs consist of a
   single-material pleated membrane & do not need any strain-limiting elts. They
   can contract & extend by design, as described by a math. model, & can be
   realized at different dimensional scales & with different materials &
   mechanical performances, enabling a wide range of lifelike movements. ..."
   -- [<A HREF="https://doi.org/10.1126/scirobotics.abn4155">doi:10.1126/scirobotics.abn4155</A>]['22].

%A S. Kapoor
%A A. Narayanan
%T Leakage and the reproducibility crisis in ML-based science
%J arXiv
%M JUL
%D 2022
%K TR, c2022, c202x, c20xx, zz0822, stats, leakage, deep AI, NN, ANN, science,
   reproducibility, scientific research, controversial, exaggerated, overblown,
   overstated, training data, test data, overfitting, statistical,
   error, errors, model
%X "... show that data leakage is indeed a widespread problem & has led to
   severe reproducibility failures. Specifically, through a survey of lit. in
   research ... we find 17 fields where errors have been found, collectively
   affecting 329 papers & in some cases leading to wildly overoptimistic
   conclusions. Based on our survey, we present a fine-grained taxonomy of 8
   types of leakage that range from textbook errors to open research problems.
   ... we undertake a reproducibility study in a field where complex ML models
   are believed to vastly outperform older statistical models such as Logistic
   Regression (LR): civil war prediction. We find that all papers claiming the
   superior performance of complex ML models compared to LR models fail to
   reproduce due to data leakage, & complex ML models don't perform
   substantively better than decades-old LR models. ..."
   -- 2207.07048@[<A HREF="https://arxiv.org/abs/2207.07048">arXiv</A>]['22].
   Also see, E. Gibney, 'Could machine learning fuel a reproducibility crisis in
   science?', Nature, 608, pp.250-251, Aug. 2022
   -- [<A HREF="https://doi.org/10.1038/d41586-022-02035-w">doi:10.1038/d41586-022-02035-w</A>]['22].

%A B. J. Kagan
%A et al ...
%A K. J.Friston
%T In vitro neurons learn and exhibit sentience when embodied in a
   simulated game-world
%J Neuron
%V ?
%M OCT
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1022, DishBrain, human, rodent, neuron,
   NN, ANN, BNN, game, Pong
%X "Integrating neurons into digital systems may enable performance infeasible
   with silicon alone. Here, we develop DishBrain ... neurons in a structured
   environment. In vitro NNs from human or rodent origins are integrated with
   in silico computing ... cultures are embedded in a simulated game-world,
   mimicking the arcade game 'Pong' ... we find apparent learning within five
   minutes of real-time gameplay ..."
   -- [<A HREF="https://doi.org/10.1016/j.neuron.2022.09.001">doi:10.1016/j.neuron.2022.09.001</A>]['22] online Oct 2022.

%A G. Blanc
%A J. Lange
%A Mingda Qiao
%A Li-Yang Tan
%T Properly learning decision trees in almost polynomial time
%J JACM
%V 69
%N 6
%P #39 (1-19)
%M NOV
%D 2022
%K jrnl, JACM, c2022, c202x, c20xx, zz1222, AI, II, decision tree, DTree,
   binary, influential variable, OSSS, Servedio
%X "We give an n^{O(log log n)}-time membership query alg. for properly &
   agnostically learning DTs under the uniform dist'n over {+/-1}^n. [It] shares
   similarities with practical heuristics for learning DTs ... we prove a new
   structural result for DTs that strengthens a theorem of O'Donnell, Saks,
   Schramm, & Servedio. While the OSSS theorem says that every DT has an
   influential variable, we show how every DT can be 'pruned' so that every
   variable in the resulting tree is influential."
   -- [<A HREF="https://doi.org/10.1145/3561047">doi:10.1145/3561047</A>]['22].
   [Also search for: DTree].

%A Minkyu Shin
%A Jin Kim
%A Bas van Opheusden
%A T. L. Griffiths
%T Superhuman Artificial Intelligence can improve human decision-Making by
   increasing novelty
%J PNAS
%M MAR
%D 2023
%K jrnl, PNAS, c2023, c202x, c20xx, zz0323, AlphaGo, AI, Go, game
%X "... analyzing more than 5.8 million move decisions made by professional
   Go players over the past 71 y (1950 to 2021). ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.2214840120">doi:10.1073/pnas.2214840120</A>]['23].
   [Also search for: AI Go game].

%A T. Walsh
%T Artificial Intelligence. Faking It
%I LaTrobe Uni Press
%P 248
%D 2023
%K AI, book, text, c2023, c202x, c20xx, zz1123, philosophy, deep, chatGPT,
   chatbot, large language model, LarLangM, intelligence, reasoning, risk, risks
%X 1st ed 2023; hb us$53; uk us isbn:1803994592; uk us isbn13:978-1803994598.
   "... You know what intelligence is from being intelligent yourself. But
   artificial intelligence isn't going to be like your human intelligence. For
   one, AI isn't going to have all your weaknesses. It isn't going to think as
   slow as you do. Nor is it going to be as forgetful. And it might not be
   hindered by your emotions, like anxiety and fear. ..."

%A K. Grace
%A et al
%T Thousands of AI authors on the future of AI
%J arXiv
%M JAN
%D 2024
%K TR, c2024, c202x, c20xx, zz0124, AI, versus, human, extinction, risk, risks,
   LarLangM, chatGPT, prediction, zzPrediction, zz0127, zz0137, zz0147
%X "... 2,778 researchers ... The aggregate forecasts give at least a 50% chance
   of AI systems achieving several milestones by 2028, inc. autonomously
   constructing a payment processing site from scratch, creating a song
   indistinguishable from a new song by a popular musician, & autonomously
   downloading & fine-tuning a large language model. If science continues
   undisrupted, the chance of unaided machines outperforming humans in every
   possible task was est. at 10% by 2027, and 50% by 2047. ... Between 38% & 51%
   of respondents gave at least a 10% chance to advanced AI leading to outcomes
   as bad as human extinction. ... "
   -- [<A HREF="https://arxiv.org/abs/2401.02843">arxiv:2401.02843</A>]['24].

%T AI now beats humans at basic tasks - new benchmarks are needed, says
   major report
%J Nature
%V 628
%M APR
%D 2024
%K news, views, c2024, c202x, c20xx, zz0424, AI, human versus AI, GPT3,
   performance, comparison, benchmark
%X -- [<A HREF="https://doi.org/10.1038/d41586-024-01087-4">doi:10.1038/d41586-024-01087-4</A>]['24].
   Also see GPQA@[<A HREF="https://arxiv.org/abs/2311.12022">arxiv:2311.12022</A>]['24].
   [Also search for: human versus AI].

%A N. D. Lawrence
%T The Atomic Human: Understanding Ourselves in the Age of AI
%I AllenLane
%M SEP
%D 2024
%K c2024, c202x, c20xx, zz0924, book, text, AI, chatGPT, human
%X "A vital perspective is missing from the discussions we're having about
   Artificial Intelligence - what does it mean for our identity? ..."
   1st ed 2024; hb us#53; uk us isbn:0241625246; uk us isbn13:978-0241625248.
 

%A A. S. St Leger
%A A. L. Cochrane
%A F. Moore
%T Factors associated with cardiac mortality in developed countries with
   particular reference to the consumption of wine
%J Lancet
%V 1
%N 8124
%P 1017-1020
%M MAY
%D 1979
%K jrnl, Lancet, c1979, c197x, c19xx, zz0120, French paradox, MeDi, wine,
   moderate, alcohol, positive, zzAlcohol, drink, drinking, consumption,
   human health, heart disease, Cadiovascular, risk, risks, cause, stats,
   StLeger
%X "Deaths from ischaemic heart-disease in 18 developed countries are not
   strongly assoc. with health-service factors such as doctor and nurse density.
   There is a -ve assoc. with gross national product per capita & a +ve but
   inconsistent assoc. with saturated & monounsaturated fat intake. The
   principal finding is a strong & specific -ve assoc. between ischaemic
   heart-disease deaths & alcohol consumption. This is shown to be wholly
   attributable to wine consumption."
   -- [<A HREF="https://doi.org/10.1016/s0140-6736(79)92765-x">doi:10.1016/s0140-6736(79)92765-x</A>]['19].
   (Also see [<A HREF="https://www.bbc.com/future/article/20191021-is-wine-good-for-you">bbc</A>][22/10/'19].)
   [Also search for: zzAlcohol].

%A R. Doll
%T One for the heart
%J British Medical J.
%V 315
%N 7123
%P 1664-1668
%M DEC
%D 1997
%K jrnl, BMJ, c1997, c199x, c19xx, Adult, Age Factors, Aged, Alcohol Drinking,
   zzAlcohol, positive,  Beer, Cadiovascular, heart, alcohol, Wine, health,
   medical, Disease, Female, Health Policy, Humans, Male, age
%X Moderate alcohol consumption for persons over 45 reduces risk of
   heart disease & premature death.  This applies to all types of alcohol.
   -- [<A HREF="http://bmj.bmjjournals.com/cgi/content/full/315/7123/1664">jrnl</A>]['05].
   [Also search for: zzAlcohol].

%A M. J. Thun
%A R. Peto
%A A. D. Lopez
%A J. H. Monaco
%A S. J. Henley
%A C. W. Heath
%A R. Doll
%T Alcohol consumption and mortality among middle-aged and elderly U.S. adults
%J The New England J. of Medicine
%V 337
%N 24
%P 1705-1714
%M DEC
%D 1997
%K Adult, Aged, Aged 80 and Over, Alcohol Drinking, Cardiovascular
   Disease, Cause of Death, Female, Humans, Liver Cirrhosis, Male, Middle
   Aged, Mortality, Multivariate Analysis, Neoplasms, Proportional Hazards,
   Models, Prospective Studies, Risk Factors, Smoking, United States, USA,
   jrnl, zzAlcohol, positive, health, c1007, c199x, c19xx
%X Moderate alcohol consumption may lower risk of death in middle-aged
   and elderly: Mortality generally lowest among men and woman reporting
   one drink daily.  Deaths from breast cancer higher among women reporting
   at least one drink daily.  This applies to all types of alcohol.
   -- [<A HREF="http://content.nejm.org/cgi/content/short/337/24/1705">jrnl</A>]['05]
   [Also search for: zzAlcohol].

%A C. A. Moore
%A M. J. Khoury
%A Y. Liu
%T Does light-to-moderate alcohol consumption during pregnancy increase
   the risk for renal anomalies among offspring?
%J Pediatrics
%V 99
%N 4
%P e11
%M APR
%D 1997
%K jrnl, c1997, c199x, c19xx, zzAlcohol, negative, Abnormalities Multiple,
   Alcohol Drinking, Case-Control Studies, Confounding Factors [Epidemiology],
   Ethanol, Female, Humans, Infant Newborn, Kidney, Maternal Exposure,
   Odds Ratio, Pregnancy, Risk Factors, factor, birth, health
%X Moderate alcohol consumption may increase risk of giving birth to a
   child with renal agenesis or hypoplasia.  All alcohol types included.
   -- [<A HREF="http://pediatrics.aappublications.org/cgi/content/abstract/99/4/e11">jrnl</A>]['05]
   [Also search for: zzAlcohol].

%A U. Keil
%A L. E Chambless
%A A. Doring
%A B. Filipiak
%A J. Stieber
%T The relation of alcohol intake to coronary heart disease and
   all-cause mortality in a beer-drinking population
%J Epidemiology
%V 8
%N 2
%P 150-156
%M MAR
%D 1997
%K jrnl, c1997, c199x, c19xx, zzAlcohol, beer, moderate, positive,
   Drinking, Cohort Studies, Comparative Study, Coronary Disease,
   Female, Follow-Up Studies, Humans, Incidence, Male, Middle Aged,
   Poisson, Proportional Hazards Models, Risk, Socioeconomic Factors,
   health, Survival Rate, United States USA
%X "...mortality HRRs for the different alcohol groups compared with nondrinkers
   show a U-shaped curve, with the lowest HRR of 0.46 (95% CI = 0.20-0.80) for
   the 20-39.9 gm per day alcohol group and an HRR of 1.04 (95% CI = 0.54-2.00)
   for the > or = 80 gm per day alcohol group. In women, the total mortality HRR
   for those drinking up to 19.9 gm per day as compared with nondrinkers
   was 0.46 (95% CI = 0.22-0.96)."
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9229206&dopt=Abstract">PubMed</A>](Abstract)['05]
   [Also search for: zzAlcohol].

%A M.J. Eckardt
%A S.E. File,  G.L. Gessa,  K.A. Grant
%A C.  Guerri, P.L. Hoffman, H.  Kalant, G.F. Koob, T.K. Li, B.  Tabakoff
%T Effects of moderate alcohol consumption on the central nervous system
%J Alcohol Clin. Exp. Res.
%V 22
%N 5
%P 998-1040
%M AUG
%D 1998
%K jrnl, c1998, c199x, c19xx, zzAlcohol, negative, health, birth, pregnancy,
   effects, moderate, alcohol, central, nervous, system
%X Genetic and gender factors plays an important role. A number of studies
   found measurable diminution in neuropsychologic parameters in habitual
   consumers, whereas others have not. Some studies have also noted positive
   effects on cognitive performance in the aging human. Consumption of ethanol
   during pregnancy at levels considered to be in the moderate range can
   generate fetal alcohol effects (behavioral, cognitive anomalies) in
   the offspring.
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=98392870">pubmed</A>]['05]
   [Also search for: zzAlcohol].

%A J.  Muntwyler
%A C.H. Hennekens
%A J.E. Buring
%A J.M. Gaziano
%T Mortality and light to moderate alcohol consumption after myocardial
   infarction
%J Lancet
%V 352
%N 9144
%P 1882-1885
%M DEC
%D 1998
%K jrnl, c1998, c199x, c19xx, zzAlcohol, positive, heart, health, disease
   mortality, moderate, alcohol, consumption, myocardial, infarction, risk
%X Of 90,150 men in the Physicians' Health Study enrollment cohort who provided
   information on alcohol intake and who had no history of cancer, stroke, or
   liver disease, 5358 had a previous myocardial infarction. During a mean
   follow-up of 5 years, 920 men died. Result: Men with previous myocardial
   infarction who consume small to moderate amounts of alcohol have a lower
   total mortality.
   [Also search for: zzAlcohol].

%A T.K. Jensen
%A N.H.I. Hjollund
%T T.B. Henriksen
%A T.  Scheike
%A H.  Kolstad
%A A.  Giwercman
%A E.  Ernst
%A J.P. Bonde
%A N.E. Skakkebaek
%A J.  Olsen
%T Does moderate alcohol consumption affect fertility? Follow up study among
   couples planning first pregnancy
%J British Medical Journal
%V 317
%N 7157
%P 505-510
%M AUG
%D 1998
%K jrnl, BMJ, c1998, c199x, c19xx, zzAlcohol, negative, health, conception,
   conceive, consumption, fertility, first, pregnancy
%X In the six cycles of follow up 64% of women with a weekly alcohol intake of
   less than five drinks and 55% of women with a higher intake conceived. A
   woman's alcohol intake is associated with decreased fecundability even among
   women with a weekly alcohol intake corresponding to five or fewer drinks.
   Alcohol consumption is discouraged for women trying to become pregnant.
   -- [<A HREF="ttp://bmj.bmjjournals.com/cgi/content/full/317/7157/505">jrnl</A>]['05]
   [Also search for: zzAlcohol].

%A M. P. Zeegers
%A F. E. Tan
%A A. P. Verhagen
%A M. P. Weijenberg
%A P. A. van den Brandt
%T Elevated risk of cancer of the urinary tract for alcohol drinkers:
   a meta-analysis
%J Cancer Causes & Control
%V 10
%N 5
%P 445-451
%M AUG
%D 1999
%K jrnl, alcohol consumption, urinary tract cancer, c1999, c199x, c19xx,
   zzAlcohol, negative, health
%X association between alcohol consumption and urinary tract cancer. Even
   though studies differed in methodology, the results were rather consistent.
   -- [<A HREF="http://dx.doi.org/10.1023/A:1008938520686">doi:10.1023/A:1008938520686</A>]['05]
   [Also search for: zzAlcohol].

%A I. R. White
%T The level of alcohol consumption at which all-cause mortality is least
%J J. of Clinical Epidemiology
%V 52
%N 10
%P 967-975
%M OCT
%D 1999
%K jrnl, alcohol consumption, mortality, nadir, risk, risks, health,
   c1999, c199x, c19xx, zzAlcohol, medical, optimum, optimal, death
%X Moderate consumers of alcohol have lower mortality than either nondrinkers
   or heavy drinkers. review aimed to quantify the level of alcohol consumption
   (termed the nadir) at which the lowest mortality occurs.
   20 cohort studies reported analyses of all-cause mortality for at least 3
   categories of alcohol consumption, giving a total of 60,224 deaths among men
   and 74,824 deaths among women. The nadir in each study was estimated for men
   and women separately in units per week, where 1 unit is 9 g of alcohol. The
   estimated nadirs varied substantially between countries. Combined nadirs were
   estimated for U.S. men (overall nadir 7.7 units per week, 95% confidence
   interval [CI] 6.4-9.1), U.K. men (12.9 units per week, 95% CI 10.8-15.1),
   and U.S. women (2.9 units per week, 95% CI 2.0-4.0). The nadirs were not
   found to be increased in studies of older persons and apply for
   ages 50 to 80 years.
   [Also search for: zzAlcohol].

%A A. Romelsjo
%A A. Leifman
%T Association between alcohol consumption and mortality, myocardial
   infarction, and stroke in 25 year follow up of 49,618 young Swedish men
%J BMJ
%V 319
%N 7213
%P 821-822
%M SEP
%D 1999
%K jrnl, alcohol consumption, positive, mortality, myocardial infarction,
   stroke, cardiovascular diseases, c1999, c199x, c19xx, zzAlcohol,
   heart attack, health
%X This study is based on 49,618 Swedish men conscripted between 1 July 1969
   and 30 June 1970 and born between 1949 and 1952, and reinterviewed 25 years
   later. Compared with abstainers, alcohol consumers had higher unadjusted
   relative risks for mortality, myocardial infarction, and stroke. ...
   ...clear association between level of alcohol use at conscription and risk of
   subsequent hospitalisation or death with a diagnosis of alcoholism, alcohol
   psychosis, or alcohol intoxication, with a significant relative risk of 5.71
   for consumers of >= 15 g ethanol/day, indicating a stability over time. The
   results also indicate a cardioprotective effect of alcohol use in relatively
   young men, in whom myocardial infarction is rare. Possible biological
   mechanisms include an increase in high density lipoprotein cholesterol, a
   decrease in platelet coagulability, and a decrease in plasma fibrinogen
   associated with alcohol intake.
   -- [<A HREF="http://bmj.bmjjournals.com/cgi/content/full/319/7213/821">bmj</A>]['05]
   [Also search for: zzAlcohol].

%A K. Tsumura
%A T. Hayashi
%A C. Suematsu
%A G. Endo
%A S. Fujii
%A K. Okada
%T Daily alcohol consumption and the risk of type 2 diabetes in Japanese men:
   the Osaka Health Survey
%J Diabetes Care
%V 22
%N 9
%P 1432-1437
%M SEP
%D 1999
%K jrnl, alcohol consumption, diabetes, glucose, hypertension, diabetic, Japan,
   c1999, c199x, c19xx, zzAlcohol, health, medical, risk, risks
%X Investigates the relationship between daily alcohol consumption and the risk
   of type 2 diabetes in a large Japanese cohort. The relationship between daily
   alcohol consumption and the risk of type 2 diabetes among lean men and among
   men with a higher BMI was paradoxical. ...
   ... Among men with a BMI > or =22.1 kg/m2, moderate alcohol consumption was
   associated with a reduced risk of type 2 diabetes, but among lean men
   (BMI < or = 22.0 kg/m2), heavy alcohol consumption was associated with an
   increased risk of type 2 diabetes.
   -- [<A HREF="http://care.diabetesjournals.org/cgi/reprint/22/9/1432">jrnl</A>]['05]
   [Also search for: zzAlcohol].

%A M. Bobak
%A Z. Skodova
%A M. Marmot
%T Effect of beer drinking on risk of myocardial infarction: population based
   case-control study
%J BMJ
%V 320
%N 7246
%P 1378-1379
%M MAY
%D 2000
%K jrnl, BMJ, c2000, c200x, c20xx, zzAlcohol, moderate, positive, beer, risk,
   alcohol consumption, Czech, heart, attack, disease, health, medical, risks
%X "... lowest risk of myocardial infarction was found among men who drank
   almost daily or daily and who drank 4-9 L of beer a week. There was a
   suggestion that the protective effect was lost in men who drank twice a day
   or more. This is similar to results of studies of other beverages."
   -- [<A HREF="http://bmj.bmjjournals.com/cgi/content/full/320/7246/1378">jrnl</A>]['05]
   [Also search for: zzAlcohol].

%A U. A. Ajani
%A J. M. Gaziano
%A P. A. Lotufo, S. Liu, C.H.Hennekens, J.E.Buring, J.E.Manson
%T Alcohol consumption and risk of coronary heart disease by diabetes status
%J Circulation
%V 102
%P 500-505
%D 2000
%K jrnl, c2000, c200x, c20xx, zzAlcohol, positive, moderate consumption,
   health, medical, risk, risks, diabetic
%X "...results suggest that light to moderate alcohol consumption is associated
   with similar risk reductions in CHD among diabetic and nondiabetic mena
   -- [<A HREF="http://circ.ahajournals.org/cgi/content/abstract/102/5/500">jrnl</A>]['05]
   [Also search for: zzAlcohol].

%A H. D. Sesso
%A M. J. Stampfer
%A B.Rosner, C.H.Hennekens, J.E.Manson, J.M.Gaziano
%T Seven-year changes in alcohol consumption and subsequent risk of
   cardiovascular disease in men
%J Arch. Intern. Med.
%V 160
%P 2605-2612
%D 2000
%K jrnl, c2000, c200x, c20xx, zzAlcohol, moderate, positive,
   health, medical, heart, male, risk
%X "... among men with initially low alcohol consumption (less  than 1 drink
   per week), ... moderate increase in alcohol consumption may lower their CVD
   risk. The possible reduction in CVD risk from increasing alcohol intake did
   not extend to men initially consuming greater than 1 drink per week. Given
   the potential risks and benefits associated with alcohol consumption,
   physician counseling of patients must be individualized in the context of
   the primary prevention of CVD."
   -- [<A HREF="http://archinte.ama-assn.org/cgi/content/abstract/160/17/2605">jrnl</A>]['05]
   [Also search for: zzAlcohol].

%A K. Nanchahal
%A W. D. Ashton
%A D. A Wood
%T Alcohol consumption, metabolic cardiovascular risk factors and
   hypertension in women
%J Int. J. Epidemiology
%V 29
%P 57-64
%D 2000
%K jrnl, c2000, c200x, c20xx, zzAlcohol, positive, moderate, heart, disease,
   CHD, gender, health, medical, female, risk, risks
%X " ... inverse association between alcohol intake and CHD in women, assoc.
   with favourable changes in lipid and lipoprotein risk factors. Women
   consuming 1-14 units/week had a reduction in CHD risk, but there was an
   increased prevalence of hypertension among those consuming [more than] 15
   units/week. These data suggest that, in terms of the reduced risk of CVD,
   women should be advised to restrict their alcohol consumption to [at most]
   14 units/week."
   -- [<A HREF="http://ije.oupjournals.org/cgi/content/abstract/29/1/57">jrnl</A>]['05]
   [Also search for: zzAlcohol].

%A L. Abramson
%A A. Williams
%A H. M. Krumholz
%A V. Vaccarino
%T Moderate alcohol consumption and risk of heart failure among older persons
%J J. American Med. Assoc.
%V 285
%N 15
%P 1971-1977
%M APR
%D 2001
%K jrnl, JAMA, moderate alcohol, c2001, c200x, c20xx, medical, health, risk,
   risks, zzAlcohol, positive
%X Moderate alcohol consumption has a positive effect on health. Moderate
   alcohol consumptions are associated with a decreasing risk of heart failure
   among older persons. This applies to any type of alcohol.
   -- [<A HREF="http://jama.ama-assn.org/cgi/content/abstract/285/15/1971">jama</A>]['05]
   [Also search for: zzAlcohol].

%A A. Kokavec
%A S. F. Crowe
%T The effect of a moderate level of white wine consumption on the
   hypothalamic-pituitary-adrenal axis before and after a meal
%J Pharmacology Biochemistry and Behavior
%V 70
%N 2-3
%P 243-250
%M OCT-NOV
%D 2001
%K jrnl, alcohol, white wine, Hypothalamic-pituitary-adrenal axis,
   Cortisol, Steroid hormones, Dehydroepiandrosterone sulfate, Sodium,
   Potassium, Electrolytes, Fasting, c2001, c200x, c20xx, zzAlcohol , health
%X Moderate white wine consumption ... (1) significantly
   reduces salivary cortisol irrespective of the prior nutritional status of
   the individual, (2) under fasting conditions significantly reduces salivary
   DHEAS at 135 min, and (3) when consumed alone after a meal significantly
   increases salivary DHEAS immediately. Furthermore, when a moderate amount of
   white wine is consumed prior to food a further decrease in DHEAS was
   demonstrated.
   -- [<A HREF="http://dx.doi.org/10.1016/S0091-3057(01)00606-2">doi:10.1016/S0091-3057(01)00606-2</A>]['05]
   [Also search for: zzAlcohol].

%A A. Sierksma
%A M. S. van der Gaag
%A G. Schaafsma
%A C. Kluft
%A M. Bakker
%A H. F. J. Hendriks
%T Moderate alcohol consumption and fibrinolytic factors of pre- and
   postmenopausal women
%J Nutrition Research
%V 21
%N 1-2
%P 171-181
%M JAN-FEB
%D 2001
%K moderate alcohol consumption, fibrinolytic factors, pre- postmenopausal,
   red wine, jrnl, menopause, women, c2001, c200x, c20xx, zzAlcohol, health
%X Moderate alcohol (red wine) consumption affects fibrinolytic factors in
   postmenopausal women but much less so in premenopausal women using oral
   contraceptives. The response of fibrinolytic activity in postmenopausal
   women after moderate alcohol consumption appears similar to the response
   described earlier for middle-aged men.
   -- [<A HREF="http://dx.doi.org/10.1016/S0271-5317(00)00257-8">doi:10.1016/S0271-5317(00)00257-8</A>]['05]
   [Also search for: zzAlcohol].

%A W. Huang
%A C. Qui
%A B. Winblad
%A L. Fratiglioni
%T Alcohol consumption and incidence of dementia in a community sample
   aged 75 years and older
%J J. of Clinical Epidemiology
%V 55
%N 10
%P 959-964
%M OCT
%D 2002
%K jrnl, Dementia, Alzheimer's disease, Alcohol consumption, Incidence, Age,
   Population-based study, c2002, c200x, c20xx, zzAlcohol, positive, health,
   age, aged
%X Light to moderate drinking might protect against dementia and
   Alzheimer's disease among old people.
   -- [<A HREF="http://dx.doi.org/10.1016/S0895-4356(02)00462-6">doi:10.1016/S0895-4356(02)00462-6</A>]['05]
   [Also search for: zzAlcohol].

%A J. Ilich
%A R. Brownbill
%A L. Tamborini
%A Z. Crncevic-Orlic
%T To drink or not to drink: How are alcohol, caffeine and past smoking
   related to bone mineral density in elderly women?
%J J. of the Amercian College of Nutrition
%V 21
%N 6
%P 536-544
%M DEC
%D 2002
%K jrnl, bone mineral density, calcium, alcohol, caffeine, past smoking,
   postmenopausal, menopause, c2002, c200x, c20xx, zzAlcohol, positive,
   coffee, zzCoffee, woman, health, medical, risk, risks, osteoporosis
%X Small/moderate alcohol consumption acts positively on bone mineral density,
   whereas caffeine and past smoking affect it negatively.
   PMID: 12480799 [PubMed - indexed for MEDLINE]
   -- [<A HREF="http://www.jacn.org/cgi/content/abstract/21/6/536">jrnl</A>]['05]
   [Also search for: zzAlcohol]  and  [also search for: zzCoffee].

%A P. Pignatelli
%A L. Lenti
%A F. M. Pulcinelli, R. Catasca, G. Saccani, G. Germano, A. Marcoccia,
%A M. Assunta Silvertri, A. Ghiselli, F. Violi
%T Red and white wine differently affect collagen-induced platelet aggregation
%J Pathophysiology of Haemostasis and Thrombosis
%V 32
%N 5-6
%P 356-358
%M SEP-DEC
%D 2002
%K jrnl, Platelets, flavonoids, wine, c2002, c200x, x20xx, zzAlcohol, positive,
   health, heart disease
%X Red wine has a stronger antithrombotic activity than white wine.
   -- [<A HREF="http://dx.doi.org/10.1159/000073599">doi:10.1159/000073599</A>]['05]
   PMID: 13679675 [PubMed - indexed for MEDLINE]
   [Also search for: zzAlcohol].

%A L. Djousse
%A J. F. Dorgan, Y. Zhang, A. Schatzkin
%A M. Hood, R. B. D'Agostino, D. L. Copenhafer, B.E. Kreger, R.C. Ellision
%T Alcohol consumption and risk of lung cancer: the Framingham Study
%J J. of the Nat. Cancer Inst.
%V 94
%N 24
%P 1877-1882
%M DEC
%D 2002
%K jrnl, c2002, c200x, c20xx, zzAlcohol, neutral, alcohol consumption,
   lung cancer, cohort study, smoking, tobacco, heakth, medical, risk,
   risks, disease
%X Light or moderate drinking has no significant association with the risk
   of lung cancer.  PMID: 12488481 [PubMed - indexed for MEDLINE].
   -- [<A HREF="http://jncicancerspectrum.oupjournals.org/cgi/content/full/jnci;94/24/1877">jrnl</A>]['05].
   (Also see [<A HREF="http://www.framinghamheartstudy.org/">F.H.study</A>]['12].)
   [Also search for: zzAlcohol].

%A A.F. Dixon
%A J.B. Dixon
%A P.E. O'Brien
%T Cardiovascular benefit of light to moderate alcohol consumption
%J Australian Family Physician
%V 32
%N 8
%P 649-52
%M AUG
%D 2003
%K jrnl, zzAlcohol, positive, c2003, c200x, c20xx, heart, health, medical,
   Alcohol, Drinking, Cardiovascular Diseases, Diabetes, risk, risks
%X Individuals drinking at least once per week and less than four times a
   day have a reduced mortality rate, in particular, cardiovascular mortality
   rate drops 30-40%. Also shows reduced incidence of stroke, type 2 diabetes,
   myocardial infarction and congestive heart failure.
   -- [<A HREF="http://www.racgp.org.au/document.asp?id=10308">jrnl</A>]['05]
   -- [<A HREF="http://www.racgp.org.au/afp/downloads/pdf/august2003/20030805dixon.pdf">pdf</A>]['05]
   [Also search for: zzAlcohol].

%A K.J. Mukamal
%A R.A. Kronmal
%A M.A.Mittleman,  D.H.O'Leary,  J.F.Polak,  M.Cushman,  D.S.Siscovick
%T Alcohol consumption and carotid atherosclerosis in older adults: The
   cardiovascular health study
%J Arteriosclerosis, Thrombosis, and Vascular Biology:
   J. of the American Heart Assoc.
%V 23
%N 12
%P 2252-2259
%M DEC
%D 2003
%K jrnl, zzAlcohol, positive, health, c2003, c200x, c20xx, moderate alcohol,
   consumption, carotid, artery, atherosclerosis, intima-media, thickness,
   epidemiology
%X Amongst older adults, 1 to 6 drinks per week was associated with less
   carotid atherosclerosis and consumption of 14 or more drinks was associated
   with greater atherosclerosis.
   -- [<A HREF="http://dx.doi.org/10.1161/01.ATV.0000101183.58453.39">doi:10.1161/01.ATV.0000101183.58453.39</A>]['05]
   -- [<A HREF="http://atvb.ahajournals.org/cgi/reprint/23/12/2252">jrnl</A>]['05]
   [Also search for: zzAlcohol].

%A S. Carlsson
%A N. Hammar
%A V.Grill,  J.Kaprio
%T Alcohol consumption and the incidence of type 2 diabetes
%J Diabetes Care
%V 26
%N 10
%P 2785
%M OCT
%D 2003
%K jrnl, zzAlcohol, positive,c2003, c200x, c20xx, moderate alcohol consumption,
   Type 2 Diabetes, diabetic, health, medical, risk, risks
%X "Moderate alcohol consumption (5-29.9g/d men, 5-19.9g/d women)...
   reduced incidence of type 2 diabetes v. low consumption (less than 5 g/day)
   ... (relative risk 0.7, 95% CI 0.5-1.0 mean, 0.6,, 0.3-1.1 w.) ...
   ... Moderate consumption of alcohol reduces the risk of type 2 diabetes in
   women, while binge drinking and high school consumption increases the risk."
   -- [<A HREF="http://care.diabetesjournals.org/cgi/content/abstract/26/10/2785">jrnl</A>]['05]
   [Also search for: zzAlcohol].

%A A. P. Whelan
%A W. H. Sutherland
%A M. P. McCormick
%A D. J. Yeoman
%A S. A. de Jong
%A M. J. Williams
%T Effects of white and red wine on endothelial function in subjects with
   coronary artery disease
%J Internal Medicine J.
%V 34
%N 5
%P 224-228
%M MAY
%D 2004
%K jrnl, pharmacology,   Coronary Arteriosclerosis, physiopathology,   Coronary
   Arteriosclerosis, therapy,   Endothelium Vascular, drug effects,   Wine,
   c2004, c200x, c20xx, zzAlcohol, health, risk, risks, medical, anti oxidants,
   alcohol consumption, positive
%X About Wine, positive. Data suggest that wine acutely improves endothelial
   function in patients with CAD. This improved endothelial function might
   contribute to a reduced risk of cardiovascular events.
   -- [<A HREF="http://www.blackwell-synergy.com/links/doi/10.1111/j.1444-0903.2004.00507.x/abs/">abs</A>]['05]
   [Also search for: zzAlcohol].

%A J. K. Tofferi
%A A. J. Taylor
%A I. M. Feuerstein
%A P. G. O'Malley
%T Alcohol intake is not associated with subclinical coronary atherosclerosis
%J Am Heart J.
%V 148
%N 5
%P 803-809
%M NOV
%D 2004
%K Alcohol consumption, jrnl, Drinking, Calcinosis, Coronary Arteriosclerosis,
   health, etiology, Coronary Disease, c2004, c200x, c20xx, zzAlcohol, heart
%X Alcohol intake does not appear to be inversely related to subclinical CAC,
   implying that previous observations of a protective effect of alcohol on
   clinical CAD may involve factors related to plaque stability rather than
   atherogenesis.
   [Also search for: zzAlcohol].

%A K. Albertsen
%A Andersen AM
%T Alcohol consumption during pregnancy and the risk of preterm delivery
%J Am J. Epidemiol
%V 159
%P 155-161
%M AUG
%D 2004
%K jrnl, pregnancy, risk factors, Alcohol, Preterm, birth, premature, baby,
   health, c2004, c200x, c20xx, zzAlcohol, health, medical risks,
   alcohol consumption, negative
%X All alcohol, negative mostly. Consumption of 7 or more drinks per week was
   associated with an increased risk of pre-term delivery in woman having their
   1st child. Pre-term delivery was not affected by type of alcohol intake.
   Consuming less than 4 alcoholic drinks per week does not increase risk of
   pre-term delivery.
   -- [<A HREF="http://aje.oupjournals.org/cgi/content/full/159/2/155">jrnl</A>]['05]
   [Also search for: zzAlcohol].

%A L. Letenneur
%T Risk of dementia and alcohol and wine consumption: a review of recent results
%J Biol. Res.
%V 37
%N 2
%P 189-193
%D 2004
%K jrnl, zzAlcohol, positive, c2004, c200x, c20xx. zz0818, human health, brain,
   dementia, Alzheimers disease, alcohol consumption, wine, moderate drinking
%X "... there was a negative association only with AD. after adjustment
   (OR = 0.55; p < 0.05). The inverse relationship between moderate wine
   drinking & incident dementia was explained neither by known predictors of
   dementia nor by medical, psychological or socio-familial factors. These
   results were confirmed from data of the Rotterdam study. Light-to-moderate
   drinking (one to three drinks per day) was sig. associated with a lower risk
   of any dementia (hazard ratio 0.58 [95% CI 0.38-0.90]) & vascular dementia
   (hazard ratio 0.29 [0.09-0.93]). No evidence that the relation between
   alcohol & dementia varied by type of alcoholic beverage was found. ..."
   -- [<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/15455646">pubm'd</A>]['18].
   [Also search for: zzAlcohol].

%A M. Inoue1
%A S. Tsugane
%T Impact of alcohol drinking on total cancer risk: data from a
   large-scale population-based cohort study in Japan
%J British J. Cancer
%V 92
%P 182-187
%D 2005
%K jrnl, c2005, c200x, c20xx, zzAlcohol, negative, alcohol consumption,
   health, medical, risk, risks
%X "...cohort study of alcohol consumption & total cancer incidence & mortality
   in 73,281 subjects (35,007 men & 38,274 women) aged 40-59 y.o. at baseline
   over a 10-year follow-up period. ...  men, the lowest risk of developing
   cancer was observed among occasional drinkers, & a linear positive assoc.
   with increased ethanol intake was noted ... . The positive relation was
   sim. for cancer incidence & mortality, but was more striking among current
   smokers & alcohol-related cancers.  ... few women were regular drinkers
   . ... suggest that increased ethanol intake linearly elevates the risk of
   cancer, & that nearly 13% of cancers among males in this study were due to
   heavy drinking (300 g per week of ethanol), to which smoking substantially
   contributed. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/sj.bjc.6602277">doi:10.1038/sj.bjc.6602277</A>]['05]
   [Also search for: zzAlcohol].

%A M. S.V. Elkind
%A R. Sciacca
%A B. Boden-Albala
%A T. Rundek
%A M. C. Paik
%A R. L. Sacco
%T Moderate alcohol consumption reduces risk of ischemic stroke: The northern
   Manhattan study
%J Stroke
%V 37
%N 1
%P 13-19
%M JAN
%D 2006
%K c2006, c200x, c20xx, zzAlcohol, medicine, alcohol, positive, health,
   drink, drinking, IS, strokes, stats
%X "... Mean age among participants (n=3176) was 69.1+/-10.3 years; 62.8% were
   women, 20.8% were non-Hispanic white, 24.5% non-Hispanic black, & 52.4% were
   Hispanic. No alcohol in the previous year was present in 62.3%, & 32.5% drank
   moderately. After adjusting for other risk factors compared with those who
   did not drink in the past year, moderate drinkers had a reduced risk of IS
   (0.67; 95% CI, 0.46 to 0.99) & IS, myocardial infarction, or vascular death
   (0.74; 95% CI, 0.59 to 0.94). Results were similar when never-drinkers were
   used as referent group. Reduction in risk was seen for nonatherosclerotic IS
   subtypes & results stratified by age sex & race-ethnicity were similar. ..."
   -- [<A HREF="http://dx.doi.org/10.1161/01.STR.0000195048.86810.5b">doi:10.1161/01.STR.0000195048.86810.5b</A>]['07]
   [Also search for: zzAlcohol].

%A C. Winkler
%A B. Wirleitner
%A K.Schroecksnadel,  H.Schennach,  D.Fuchs
%T Beer down-regulates activated peripheral blood mononuclear cells in vitro
%J Int. Immunopharmacology
%V 6
%N 3
%P 390-395
%M MAR
%D 2006
%K jrnl, zzAlcohol, positive, health, c2006, c200x, c20xx, alcohol consumption,
   ale, drinking, medical, stats
%X "Moderate consumption of alcoholic beverages is suggested to reduce
   cardiovascular risk. Within this context, most attention is drawn to
   antioxidant ingredients of wine, but also beer was found to be beneficial.
   [...] Data suggest that the immunosuppressive capacity of beer may relate
   to its anti-inflammatory nature."
   -- [<A HREF="http://dx.doi.org/10.1016/j.intimp.2005.09.002 ">doi:10.1016/j.intimp.2005.09.002</A>]['06]
   [Also search for: zzAlcohol].

%A K. M. Fillmore
%A W. C. Kerr
%A T.Stockwell,  T.Chikritzhs,  A.Bostrom
%T Moderate alcohol use and reduced mortality risk: systematic error in
   prospective studies
%J Addiction Research and Theory
%V 14
%N 2
%P 101-132
%M MAY
%D 2006
%K jrnl, zzAlcohol, negative, health, medicine, c2006, c200x, c20xx,
   alcohol consumption, drinking, stats, bias, mortality, risk, risks
%X [<A HREF="http://nurseweb.ucsf.edu/www/fffillk.htm">F</A>]['06]
     [<A HREF="http://www.stakes.fi/nat/nat02/4/english/fillm.htm">TR c2002</A>]['06]
     inc. appendix of many studies.
   -- [<A HREF="http://www.arg.org/kerr.html">Kerr</A>]['06]
   [Also search for: zzAlcohol].

%A R. Corder
%A et al
%T Health: Endothelin-1 synthesis reduced by red wine
%J Nature
%V 414
%P 863-864
%M DEC
%D 2006
%K jrnl, zzAlcohol, positive, health, c2006, c200x, c20xx, alcohol consumption,
   endothelin1, ET-1, ET1, procyanidin, procyanidins, qmul,
   heart, coronary, risk, risks, red wine
%X "Stat. evidence of reduced coronary heart disease in areas of high wine
   consumption has led to the widespread belief that wine affords a protective
   effect. Although moderate drinking of any a. helps to reduce the incidence
   of coronary heart disease, there is no clear evidence that red wine confers
   an additional benefit. Here we show that red wines strongly inhibit the
   synthesis of endothelin-1, a vasoactive peptide that is crucial in the
   development of coronary atherosclerosis. Our findings indicate that
   components specific to red wine may help to prevent coronary heart disease."
   -- [<A HREF="http://dx.doi.org/10.1038/414863a">doi:10.1038/414863a</A>]['06] NB. red wine
   -- [<A HREF="http://www.whri.qmul.ac.uk/staff/corder.html">auth1</A>]['06]
   [Also search for: zzAlcohol].



%A Y. Li
%A W. Xu
%A M. W. McBurney
%A V. D. Longo
%T SirT1 inhibition reduces IGF-I/IRS-2/Ras/ERK1/2 signaling and protects
   neurons
%J Cell Metabolism
%V 8
%N 1
%P 38-48
%M JUL
%D 2008
%K jrnl, zzAlcohol, health, c2008, c200x, c20xx, ambiguous, resveratrol,
   sirtuins, sirtuin, SirT1, IGF, IGFI, IRS2, Ras, ERK1, ERK2, neuron, aging
%X "Sirtuins are known to protect cells & extend life span, but our previous
   studies indicated that S.cerevisiae Sir2 can also increase stress
   sensitivity & limit life-span extension. ... evidence for a role of the
   mammalian Sir2 ortholog SirT1 in the sensitization of neurons to oxidative
   damage. SirT1 inhibition increased acetylation & decreased phosphorylation of
   IRS-2; it also reduced activation of the Ras/ERK1/2 pathway, suggesting that
   SirT1 may enhance IGF-I signaling in part by deacetylating IRS-2. Either the
   inhibition of SirT1 or of Ras/ERK1/2 was associated with resistance to
   oxidative damage. Markers of oxidized proteins & lipids were reduced in the
   brain of old SirT1-deficient mice, but[!] the life span of the homozygote
   knockout mice was reduced under both normal & calorie-restricted conditions.
   These results are consistent with findings in S.cerevisiae & other model
   systems, suggesting that mammalian sirtuins can play both protective &
   proaging roles."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cmet.2008.05.004">doi:10.1016/j.cmet.2008.05.004</A>]['08].
   [NB. red wine contains resveratrol which seems to increase SirT1].
   [Also search for: zzAlcohol].

%A K. J. Pearson
%A et al
%T Resveratrol delays age-related deterioration and mimics transcriptional
   aspects of dietary restriction without extending life span
%J Cell Metabolism
%V ?
%N ?
%P ?-?
%M ?
%D 2008
%K jrnl, zzAlcohol, health, positive, c2008, c200x, c20xx, ambiguous,
   resveratrol, diet, delay, aging, red wine
%X "... resveratrol mimics effects of DR [dietary restriction] in lower
   organisms. In mice, we find that resveratrol induces gene expression patterns
   in multiple tissues that parallel those induced by DR & every-other-day
   feeding. Moreover, resveratrol-fed elderly mice show a marked reduction in
   signs of aging, including reduced albuminuria, decreased inflammation, &
   apoptosis in the vascular endothelium, increased aortic elasticity, greater
   motor coordination, reduced cataract formation, & preserved bone mineral
   density. However, mice fed a standard diet did not live longer when treated
   with resveratrol beginning at 12 months of age. Our findings indicate that
   resveratrol treatment has a range of beneficial effects in mice but does not
   increase the longevity of ad libitum-fed animals when started midlife."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cmet.2008.06.011">doi:10.1016/j.cmet.2008.06.011</A>]['08].
   [NB. red wine contains resveratrol].
   [Also search for: zzAlcohol].


%A M. Schutze
%A et al ...
%A M. M. Bergmann
%T Alcohol attributable burden of incidence of cancer in eight European
   countries based on results from prospective cohort study
%J BMJ
%V 342
%P d1584
%M APR
%D 2011
%K BMJ, jrnl, zzAlcohol, health, negative, c2011, c201x, c20xx, zz0411, cancer,
   cancers, alcohol consumption, drinking
%X "... attributable fractions for consumption higher than the rec.upper limit
   (2 drinks a day for men with about 24g alcohol, one for women with about
   12g a.) & the est.total annual # of cases of alcohol attrib. cancer.
      If we assume causality, among men & women, 10% (95% CI 7 to 13%) &
   3% (1 to 5%) of the incidence of total cancer was attributable to former &
   current alcohol consumption in the selected European countries. For selected
   cancers the figures were 44% (31 to 56%) & 25% (5 to 46%) for upper
   aerodigestive tract, 33% (11 to 54%) & 18% (-3 to 38%) for liver, 17% (10 to
   25%) & 4% (-1 to 10%) for colorectal cancer for men & women, resp., & 5.0%
   (2 to 8%) for female breast cancer. A substantial part of the alcohol
   attributable fraction in 2008 was assoc. with alcohol consumption higher than
   the recommended upper limit: 33,037 of 178,578 alcohol related cancer cases
   in men & 17,470 of 397,043 alcohol related cases in women.  ..."
   -- [<A HREF="http://dx.doi.org/10.1136/bmj.d1584">doi:10.1136/bmj.d1584</A>]['11].
   [Also search for: zzAlcohol].

%A T. C. St Laurent
%A M. Arseneault
%A F. Longpre
%A C. Ramassamy
%T Tyrosol and hydroxytyrosol, two main components of olive oil, protect
   N2a cells against amyloid-beta-induced toxicity. Involvement of the
   NF-kB signaling
%J Curr. Alzheimer Res.
%V 8
%N 5
%P 543-551
%M AUG
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0120, StLaurent, Tyrosol, Tyr, hydroxytyrosol,
   white wine, alcohol, consumption, zzAlcohol, positive, drinking, Olive oil,
   MeDi, Alzheimers, human health, risk, risks, StLaurent
%X "... Several studies have reported that adherence to the Mediterranean
   diet (MeDi) was assoc. with a reduction in incident of dementia. The
   beneficial effect of MeDi may be the result of the association of some
   individual and non-identified food components and high consumption of
   olive oil. ... identified two individual food components of the MeDi as
   neuroprotective agent against Abeta and their potential involvement in the
   beneficial effect of the MeDi for the prevention of AD."
   -- [<A HREF="https://doi.org/10.2174/156720511796391845">doi:10.2174/156720511796391845</A>]['19],
      [<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/21605049">pubm'd</A>]['19].
    (Also see, "... We found in white wine two compounds common to extra
    virgin olive oil, which is recognised as a healthy food, more or less
    in the same amount,' Bertelli says. These compounds, tyrosol and
    hydroxytyrosol, have also been found to be protective against Alzheimer's
    disease ..."
    -- [<A HREF="https://www.bbc.com/future/article/20191021-is-wine-good-for-you">bbc</A>][22/10/'19].)
   [Also search for: zzAlcohol].

%A R. D. Semba
%A et al
%T Resveratrol levels and all-cause mortality in older community-dwelling adults
%J JAMA Internal Medicine
%V ?
%P ?-?
%M MAY
%D 2014
%K jrnl, medicine, c2014, c201x, c20xx, zz0514, health, red wine, alcohol,
   zzAlcohol, consumption, Chianti, Italy, InCHIANTI, neutral, chocolate,
   resveratol, aging, ageing, mediterranean diet, mortality, longevity,
   lifespan
%X "... Prospective cohort study, the Invecchiare in Chianti (InCHIANTI) Study
   ('Aging in the Chianti Region'), 1998 to 2009 conducted in 2 villages in the
   Chianti area in a popn-based sample of 783 community-dwelling men & women 65y
   or older. ... Mean (95% CI) log total urinary resveratrol metabolite conc.
   were 7.08 (6.69-7.48) nmol/g of creatinine. During 9y of follow-up, 268
   (34.3%) of the participants died. From the lowest to the highest quartile of
   baseline total urinary resveratrol metabolites, the proportion ... who died
   from all causes was 34.4%, 31.6%, 33.5%, & 37.4%, resp. (P=.67). ... in the
   lowest quartile had a hazards ratio for mortality of 0.80 (95% CI, 0.54-1.17)
   compared with those in the highest q. of total urinary res. in a
   multivariable Cox proportional hazards model that adjusted for potential
   confounders. Res.levels were not sig. assoc. with serum CRP, IL-6, IL-1beta,
   TNF, prevalent or incident cardiovascular disease, or cancer. ...
   In older community-dwelling adults, total urinary res.metabolite conc. was
   not assoc. with inflammatory markers, cardiovascular disease, or cancer or
   predictive of all-cause mortality. Res.levels achieved with a Western diet
   did not have a substantial influence on health status & mortality risk of the
   popn in this study."  [online May 2014.]
   -- [<A HREF="http://dx.doi.org/10.1001/jamainternmed.2014.1582">doi:10.1001/jamainternmed.2014.1582</A>]['14],
      auth1@[<A HREF="http://www.jhsph.edu/faculty/directory/profile/1092/Semba/Richard">jhsph</A>].
   (Also see [<A HREF="http://www.bbc.com/news/health-27371546">bbc</A>][13/5/2014].)
   [Also search for: Resveratrol]  and  [also search for: zzAlcohol].

%A Y. Cao
%A W. C. Willett
%A E. B. Rimm
%A M. J. Stampfer
%A E. L. Giovannucci
%T Light to moderate intake of alcohol, drinking patterns, and risk of cancer:
   results from two prospective US cohort studies
%J BMJ
%D 2015
%V 351
%P h4238
%M AUG
%D 2015
%K jrnl, BMJ, c2015, c201x, c200xx, zz0815, alcohol, zzAlcohol, human, HPFS,
   moderate, light, drinking, smoking, men, women, cancer, risks,
   weak negative, health
%X "... 88,084 women & 47,881 men participating in the Nurses' Health Study
   (from 1980) & Health Profs. Follow-up Study (from 1986), followed until 2010.
   ... 19,269 & 7571 (exc. non-advanced prostate cancers) incident cancers were
   documented among women & men, resp., over 3,144,853 person years. Compared
   with non-drinkers, light to moderate drinkers had relative risks of total
   cancer of 1.02 (95% ci 0.98-1.06) & 1.04 (1.00-1.09; Ptrend=0.12) for alcohol
   intake of 0.1-4.9 & 5-14.9 g/day among women, resp..  Corr. values for men
   were 1.03 (0.96-1.11), 1.05 (0.97-1.12), & 1.06 (0.98-1.15; Ptrend=0.31) for
   alcohol intake of 0.1-4.9, 5-14.9, & 15-29.9 g/day, resp.. Associations for
   light to moderate drinking & total cancer were similar among ever or never
   smokers, although alcohol consumption above moderate levels (in particular
   >= 30 g/day) was more strongly assoc. with risk of total cancer among ever
   smokers than never smokers. For a priori defined alcohol related cancers in
   men, risk was not appreciably increased for light & moderate drinkers who
   never smoked (Ptrend=0.18). However, for women, even an alcohol consumption
   of 5-14.9 g/day was assoc. with increased risk of alcohol related cancer
   (relative risk 1.13 (95% ci 1.06-1.20)), driven by breast cancer. More
   frequent & heavy episodic drinking was not further assoc. with risk of total
   cancer after adjusting for total alcohol intake. ...
   Light to moderate drinking is assoc. with minimally increased risk of overall
   cancer. For men who have never smoked, risk of alcohol related cancers is not
   appreciably increased for light & moderate drinking (up to two drinks/day).
   However, for women who have never smoked, risk of alcohol related cancers
   (mainly breast cancer) increases even within the range of up to one alcoholic
   drink a day."  [37 refs.]
   -- [<A HREF="http://dx.doi.org/10.1136/bmj.h4238">doi:10.1136/bmj.h4238</A>][18/8/'15],
      [<A HREF="http://www.bmj.com/content/351/bmj.h4238">www</A>][18/8/'15].
   [Also search for: zzAlcohol].

%A Y. Gepner
%A et al ...
%A I. Shai
%T Effects of initiating moderate alcohol intake on cardiometabolic risk in
   adults with type 2 diabetes: A 2-year randomized, controlled trial
%J Ann. Intern. Med.
%V 163
%N 8
%P 569-579
%M OCT
%D 2015
%K jrnl, c2015, c201x, c200xx, zz0116, alcohol, zzAlcohol, human,
   moderate, light, drinking, type 2, type2, diabetes, guidelines, risks,
   weak positive, red wine, health, Mediterranean diet
%X "... Patients were randomly assigned to 150 mL of mineral water, white wine,
   or red wine with dinner for 2 years. Wines & mineral water were provided.
   All groups followed a Mediterranean diet without caloric restriction. ...
   suggests that initiating moderate wine intake, especially red wine, among
   well-controlled diabetics as part of a healthy diet is apparently safe &
   modestly decreases cardiometabolic risk. The genetic interactions suggest
   that ethanol plays an important role in glucose metabolism, & red wine's
   effects also involve nonalcoholic constituents."
   -- [<A HREF="http://dx.doi.org/10.7326/M14-1650">doi:10.7326/M14-1650</A>]['16].
   [Also search for: zzAlcohol].
   (Also see bbc[<A HREF="http://www.bbc.com/news/magazine-35255577">8/1/16</A>].)

%A T. Stockwell
%A J. Zhao
%A S. Panwar
%A A. Roemer
%A T. Naimi
%A T. Chikritzhs
%T Do "moderate" drinkers have reduced mortality risk? A systematic review and
   meta-analysis of alcohol consumption and all-cause mortality
%J J. of Studies on Alcohol and Drugs
%V 77
%N 2
%P 185-198
%M MAR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0316, zzAlcohol, moderate, alcohol, consumption,
   negative, health, drink, drinking, abstain, risk, risks, mortality, death
%X "... After adjustment for abstainer biases and quality-related study
   characteristics, no sig. redn in mortality risk was observed for low-volume
   drinkers (RR = 0.97, 95% CI [0.88, 1.07]). Analyses of higher-quality
   bias-free studies also failed to find reduced mortality risk for low-volume
   alcohol drinkers. Risk estimates for occasional drinkers were similar to
   those for low- and medium-volume drinkers. ..."
   -- [<A HREF="http://dx.doi.org/10.15288/jsad.2016.77.185">doi:10.15288/jsad.2016.77.185</A>]['16].
   [Also search for: zzAlcohol].

%A J. Connor
%A R. Kydd
%A B. Maclennan
%A K. Shield
%A J. Rehm
%T Alcohol-attributable cancer deaths under 80-years of age in New Zealand
%J Drug and Alcohol Review
%V 36
%N 3
%P 415-423
%M JUN
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0716, drink, drinking, alchohol, consumption,
   zzAlcohol, negative, human health, risk, risks, cancer, disease, Maori
%X "Cancer deaths made up 30% of all alcohol-attributable deaths in NZs aged
   15-79 years in 2007, more than all other chronic diseases combined. We aimed
   to est. alcohol-attributable cancer mortality & years of life lost by cancer
   site & identify differences between Maori & non-Maori New Zealanders. ...
   A.consumption was responsible for 4.2% of all c.deaths under 80 years of age
   in 2007. An avg. of 10.4 years of life was lost per person; 12.7 years for
   Maori & 10.1 years for non-Maori. Half of the deaths were attributable to
   avg. consumption of < 4 std drinks per day. Breast cancer comprised 61% of
   alcohol-attributable cancer deaths in women, & more than one-third of breast
   cancer deaths were attributable to avg. consumption of < 2 std drinks per
   day. Mortality data from 2012 produced very similar findings. ..."
   -- [<A HREF="http://dx.doi.org/10.1111/dar.12443">doi:10.1111/dar.12443</A>]['16].
   [Also search for: zzAlcohol].

%A S. Bell
%A et al
%A H. Hemingway
%T Association between clinically recorded alcohol consumption and initial
   presentation of 12 cardiovascular diseases: population based cohort study
   using linked health records
%J BMJ
%V 356
%P j909
%M MAR
%D 2017
%K rnl, BMJ, c2017, c201x, c20xx, zz0616, drink, drinking, moderate, alchohol,
   consumption, zzAlcohol, positive, human health, risk, risks, heart disease
%X "... 1,937,360 adults (51% women), aged >=30 who were free from
   cardiovascular disease at baseline. ... Non-drinking was associated with an
   increased risk of unstable angina (hazard ratio 1.33, 95% c.i. 1.21 to 1.45),
   myocardial infarction (1.32, 1.24 to 1.41), unheralded coronary death (1.56,
   1.38 to 1.76), heart failure (1.24, 1.11 to 1.38), ischaemic stroke (1.12,
   1.01 to 1.24), peripheral arterial disease (1.22, 1.13 to 1.32), and
   abdominal aortic aneurysm (1.32, 1.17 to 1.49) compared with moderate
   drinking ... Heavy drinking (exceeding guidelines) conferred an increased
   risk of presenting with unheralded coronary death ..."
   -- [<A HREF="https://doi.org/10.1136/bmj.j909">doi:10.1136/bmj.j909</A>]['17].
   [Also search for: zzAlcohol].

%A A. Topiwala
%A et al ...
%A K. P. Ebmeier
%T Moderate alcohol consumption as risk factor for adverse brain outcomes and
   cognitive decline: longitudinal cohort study
%J BMJ
%P j2353
%V 357
%M JUN
%D 2017
%K jrnl, BMJ, c2017, c201x, c20xx, zz0616, drink, drinking, alchohol,
   consumption, moderate, zzAlcohol, negative, human health, risk, risks,
   brain, hippocampus
%X "... Observational cohort study with weekly alcohol intake & cognitive
   performance measured repeatedly over 30 years (1985-2015). ... 550 men &
   women with mean age 43.0 (SD 5.4) at study baseline, none were 'alcohol
   dependent' according to the CAGE screening questionnaire, & all safe to
   undergo MRI of the brain at follow-up. ...  Higher a.consumption over the 30
   year follow-up was assoc. with increased odds of hippocampal atrophy in a
   dose dept fashion. While those consuming over 30 units a week were at the
   highest risk compared with abstainers (odds ratio 5.8, 95% c.i. 1.8 to 18.6;
   P <= 0.001), even those drinking moderately (14-21 units/week) had three
   times the odds of right sided hippocampal atrophy (3.4, 1.4 to 8.1; P=0.007).
   There was no protective effect of light drinking (1- <7 units/week) over
   abstinence. ...  Alcohol consumption, even at moderate levels, is assoc.
   with adverse brain outcomes ..."
   -- [<A HREF="https://doi.org/10.1136/bmj.j2353">doi:10.1136/bmj.j2353</A>]['17].
   [Also search for: zzAlcohol].

%A C. Holst
%A et al
%T Alcohol drinking patterns and risk of diabetes: A cohort study of
   70,551 men and women from the general Danish population
%J Diabetologia
%V ?
%P 1-10
%M JUL
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0717, diabetes, moderate alcohol consumption,
   drink, drinking, human health, risk, risks, sugar, zzAlcohol, positive
%X "Alcohol consumption is inversely associated with diabetes, but little is
   known about the role of drinking patterns. We examined the assoc. between
   alcohol drinking patterns & diabetes risk in men & women from the general
   Danish population. ... Danish Health Examination Survey 2007-2008. Of the
   76,484 survey participants, 28,704 men and 41,847 women ... consumption of
   alcohol over 3-4 days per week is assoc. with the lowest risk of diabetes,
   even after taking avg. weekly a.consumption into account."  (online 27/7.)
   -- [<A HREF="http://dx.doi.org/10.1007/s00125-017-4359-3">doi:10.1007/s00125-017-4359-3</A>]['17].
   [Also search for: zzAlcohol].

%A A. M. Wood
%A et al ...
%A J. Danesh
%T Risk thresholds for alcohol consumption: combined analysis of
   individual-participant data for 599,912 current drinkers in 83 prospective
   studies
%J The Lancet
%V 391
%N 10129
%P 1513-1523
%M APR
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0418,  moderate alcohol consumption,
   drink, drinking, human health, risk, risks, zzAlcohol, negative
%X "... studied individual-participant data from 599,912 current drinkers
   without previous cardiovascular disease. ...  Alcohol consumption was roughly
   linearly associated with a higher risk of stroke (HR per 100 g per week
   higher consumption 1.14, 95% CI, 1.10-1.17), coronary disease excluding
   myocardial infarction (1.06, 1.00-1.11), heart failure (1.09, 1.03-1.15),
   fatal hypertensive disease (1.24, 1.15-1.33); and fatal aortic aneurysm
   (1.15, 1.03-1.28). By contrast, increased alcohol consumption was
   log-linearly associated with a lower risk of myocardial infarction (HR 0.94,
   0.91-0.97). In comparison to those who reported drinking > 0- <= 100 g per
   week, those who reported drinking > 100- <= 200 g per week, > 200- <= 350
   g per week, or > 350 g per week had lower life expectancy at age 40 years of
   approximately 6 months, 1-2 years, or 4-5 years, respectively. ...
   the threshold for lowest risk of all-cause mortality was about 100 g/week.
   For cardiovascular disease subtypes other than myocardial infarction, there
   were no clear risk thresholds below which lower alcohol consumption stopped
   being associated with lower disease risk. ..."
   -- [<A HREF="https://doi.org/10.1016/S0140-6736(18)30134-X">doi:10.1016/S0140-6736(18)30134-X</A>]['18].
   [Also search for: zzAlcohol].

%T Alcohol use and burden for 195 countries and territories, 1990-2016:
   A systematic analysis for the Global Burden of Disease Study 2016
%Q GBD 2016 Alcohol Collaborators
%J The Lancet
%V ?
%P ?-?
%M AUG
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0818, moderate alcohol, zzAlcohol, negative,
   consumption, drink, drinking, human health, risks, DALY, DALYs
%X "... 694 data sources of individual & popln-level alcohol consumption,
   along with 592 prospective & retrospective studies on the risk of alcohol
   use, we produced ests. of the prevalence of current drinking, abstention,
   the distribution of a.consumption among current drinkers in std drinks
   daily (defined as 10g of pure ethyl a.), & a.-attributable deaths & DALYs.
   ... Globally, alcohol use was the 7th leading risk factor for both deaths &
   DALYs in 2016, accounting for 2.2% (95% uncertainty interval [UI] 1.5-3.0) of
   age-standardised female deaths & 6.8% (5.8-8.0) of age-standardised male
   deaths. Among the popln aged 15-49 years, alcohol use was the leading
   risk factor globally in 2016, with 3.8% (95% UI 3.2-4.3) of female deaths &
   12.2% (10.8-13.6) of male deaths attributable to alcohol use. For the
   popln aged 15-49 years, female attributable DALYs were 2.3% (95% UI
   2.0-2.6) & male attributable DALYs were 8.9% (7.8-9.9). The three leading
   causes of attributable deaths in this age group were tuberculosis (1.4%
   [95% UI 1.0-1.7] of total deaths), road injuries (1.2% [0.7-1.9]), &
   self-harm (1.1% [0.6-1.5]). For poplns aged 50 years & older, cancers
   accounted for a large proportion of total alcohol-attributable deaths in
   2016, constituting 27.1% (95% UI 21.2-33.3) of total alcohol-attributable
   female deaths & 18.9% (15.3-22.6) of male deaths. The level of alcohol
   consumption that minimised harm across health outcomes was zero (95% UI
   0.0-0.8) std drinks per week."  (online Aug 2018)
   -- [<A HREF="https://doi.org/10.1016/S0140-6736(18)31310-2">doi:10.1016/S0140-6736(18)31310-2</A>]['18].

%A T. J. Hydes
%A et al ...
%A N. Sheron
%T A comparison of gender-linked population cancer risks between alcohol and
   tobacco: how many cigarettes are there in a bottle of wine?
%J BMC Public Health
%V 19
%P #316
%M MAR
%D 2019
%K jrnl, ejrnl, c2019, c201x, c20xx, zz0120, moderate, alcohol, negative,
   zzAlcohol, drinking, gender, men, women, health, risk, risks
%X "... One bottle of wine per week is assoc. with an increased absolute
   lifetime cancer risk for non-smokers of 1.0% (men) & 1.4% (women). The
   overall absolute increase in cancer risk for one bottle of wine per week
   equals that of five (men) or ten cigarettes per week (women). Gender
   differences result from levels of moderate drinking leading to a 0.8%
   absolute risk of breast cancer in female non-smokers. ..."
   -- [<A HREF="https://doi.org/10.1186/s12889-019-6576-9">doi:10.1186/s12889-019-6576-9</A>]['19].
   [Also search for: zzAlcohol].

%A I. Y. Millwood
%A et al ...
%A Zhengming Chen
%T Conventional and genetic evidence on alcohol and vascular disease aetiology:
   a prospective study of 500,000 men and women in China
%J The Lancet
%V 393
%N 10183
%P 1831-1843
%M MAY
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0120, moderate, alcohol, negative,
   zzAlcohol, drinking, heart disease, attack, stroke
%X "The prospective China Kadoorie Biobank enrolled 512,715 adults between
   June 25, 2004, and July 15, 2008, from ten areas of China ... 161,498
   participants were genotyped for two variants that alter alcohol metabolism,
   ALDH2-rs671 and ADH1B-rs1229984. ... Genetic epidemiology shows that the
   apparently protective effects of moderate alcohol intake against stroke are
   largely non-causal. Alcohol consumption uniformly increases blood pressure
   and stroke risk, and appears in this one study to have little net effect on
   the risk of myocardial infarction."
   -- [<A HREF="https://doi.org/10.1016/S0140-6736(18)31772-0">doi:10.1016/S0140-6736(18)31772-0</A>]['19].
     (Also see,
      "... found that the more people drank, the more likely they were to
     experience high blood pressure and stroke - and there was no reduced
     risk among people who drank one to two units per day. There was no
     association either way with heart attacks. As a result, while there
     was a clear link between alcohol consumption and stroke risk, something
     in alcohol may protect us against heart attacks.  ..."
     -- [<A HREF="https://www.bbc.com/future/article/20191021-is-wine-good-for-you">bbc</A>][22/10/'19], so some +ve and some -ve.)
   [Also search for: zzAlcohol].

%P P. Sarich
%A et al ...
%A M. F. Weber
%T Alcohol consumption, drinking patterns and cancer incidence in an
   Australian cohort of 226,162 participants aged 45 years and over
%J Brit. J. of Cancer
%V 124
%P 513-523
%MOCT
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0621, alcohol, negative, zzAlcohol,
   moderate drinking, cancer, risk, risks, human, medicine
%X "... Increasing levels of alcohol intake were assoc. with increased risk of
   cancers of the upper aerodigestive tract (1.19; 1.10-1.29), mouth & pharynx
   (1.18; 1.08-1.29), oesophagus (1.22; 1.04-1.43), colorectum (1.09;
   1.04-1.15), colon (1.13; 1.06-1.20), liver (1.22; 1.04-1.44) & breast (1.11;
   1.02-1.21). Breast cancer risk was marginally assoc. with drinking pattern,
   with higher risk when intake was concentrated on 1-3 days/week compared to
   the same amount spread over 4-7 days (P_interactionâ=â0.049)."
   -- [<A HREF="https://doi.org/10.1038/s41416-020-01101-2">doi:10.1038/s41416-020-01101-2</A>]['21].

%A A. Topiwala
%A et al
%T No safe level of alcohol consumption for brain health: observational
   cohort study of 25,378 UK Biobank participants
%J medrXiv
%M MAY
%D 2021
%K TR, c2019, c201x, c20xx, zz0120, moderate, alcohol, negative, zzAlcohol,
   drinking, human health, risks, blood pressure, brain, beer, wine, spirits
%X "... Alcohol consumption was negatively linearly assoc. with global brain
   grey matter volume (beta=-0.1, 95% CI=-0. 11 to -0.09, p<2x10^{-16}). ...
   Widespread negative assoc. were observed with white matter microstructure ...
   Higher blood pressure & body mass index increased risk of alcohol-related
   harm ... Binging on alcohol had additive -ve effects on brain structure on
   top of the abs. volume consumed (daily compared to never binging: beta=-0.19,
   95% CI= -0.30 to -0.08, p<0.01). No evidence was found for differential
   effects of drinking wine, beer or spirits. ..."
   -- [<A HREF="https://doi.org/10.1101/2021.05.10.21256931">doi:10.1101/2021.05.10.21256931</A>]['21],
      [<A HREF="https://www.medrxiv.org/content/10.1101/2021.05.10.21256931v1.full.pdf">www</A>].
   [Also search for: zzAlcohol].

%A A. Topiwala
%A et al
%T Alcohol consumption and telomere length: Mendelian randomization clarifies
   alcohol's effects
%J Molec. Psychi.
%V ?
%M JUL
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0822, alcohol consumption, zzAlcohol, drinking,
   negative, telomere, telomeres, length, short, human, health, risks
%K "... Two-sample MR used data from 472,174 participants in a recent
   genome-wide assoc. study (GWAS) of telomere length. ... suggested a causal
   relationship between alcohol traits, more strongly for AUD, & t.length.
   Higher genetically-predicted AUD (inverse variance-weighted (IVW) b=-0.06,
   95% (CI): -0.10 to -0.02, p=0.001) was assoc. with shorter t.length. ..."
   -- [<A HREF="https://doi.org/10.1038/s41380-022-01690-9">doi:10.1038/s41380-022-01690-9</A>]['22].
   [Also search for: zzAlcohol].

%A D. de Andrade
%A et al
%T Investigating the relationship between inaccurate blood alcohol concentration
   estimates, harm and other negative consequences
%J Drug and Alcohol Review
%M NOV
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1222, alcohol consumption, drinking, zzAlcohol,
   drunkeness, BAC, human health, harm, risks, Australia, Queensland, uniQld
%X "... Patrons with a low BAC were more likely to overestimate their BAC, while
   patrons with higher BACs were more likely to underest. their BAC. Moderately
   intoxicated patrons had the most precise BAC estimations. Patrons with a high
   BAC & who underestimated their intoxication level were more likely to have
   been recently ejected from licensed venues, compared to accurate estimators
   or over-estimators."
   -- [<A HREF="https://doi.org/10.1111/dar.13569">doi:10.1111/dar.13569</A>]['22].
   One for the season.  [Also search for: zzAlcohol].

%T Canada's Guidance on Alcohol and Health: Final Report
%I Canadian Centre on Substance Use and Addiction (CCSA)
%M JAN
%D 2023
%K report, c2023, c202x, c20xx, zz0123, negative, zzAlcohol, advice, drinking,
   alcohol consumption, human health, harm, risks, study, Canada
%X "... Using these different thresholds, this project's estimates make it
   possible to put forward a clear continuum of risk whereby the risk for those
   who consume 2 std drinks or less per week is low, it is moderate for those
   who consume between 3 & 6 std drinks per week, & it is increasingly high for
   those who consume above 6 std drinks per week, with increasing risk conferred
   by every additional drink. ..."
   -- [<A HREF="https://ccsa.ca/sites/default/files/2023-01/Canada%27s%20Guidance%20on%20Alcohol%20and%20Health%20Final%20Report_l.pdf">www</A>]['23].
   [Also search for: zzAlcohol].


%A L. Pisano
%T Liber Abaci (Book of the Abacus)
%D 1202
%K Fibonacci, book, c1202, c120x, c12xx
%X Leonardo Pisano was known for most of his life as Fibonacci...
   His father's name was Bonacio which means "simpleton",
   and F' means blockhead!
    -- From  B e r n s t e i n "Against the..." [c1996].
   See T. H. G a r l a n d  "Fascinating Fibonaccis" [c1987].

%A C. Hierholzer
%T Ueber die moglichkeit, einen linienzug ohne wiederholung und ohne
   unterbrechung zu umfahren
%J Mathematische Annalen
%V 6
%N 1
%P 30-32
%D 1873
%O 'The possibility to avoid a continuous line without repetition and
   without interruption' - ggl translation.
%K jrnl, c1873, c187x, c18xx, zz0515, Eulerian circuit, circuits, cycle, cycles,
   path, paths, tour, tours, trail, trails, algorithm, maths, graph
%X [<A HREF="http://dx.doi.org/10.1007/BF01442866">doi:10.1007/BF01442866</A>]['15].
   See, "... more efficient than Fleury's alg. ... Choose any starting vertex v,
      & follow a trail of edges from that vertex until returning to v. ... The
      tour formed in this way is a closed tour, but may not cover all the
      vertices & edges of the initial graph. ... As long as there exists a
      vertex u that belongs to the current tour but that has adjacent edges not
      part of the tour, start another trail from u, following unused edges until
      returning to u, & join the tour formed in this way to the prev. tour.
      overall alg. takes linear time."
   -- E@[<A HREF="http://en.wikipedia.org/wiki/Eulerian_path">wikip</A>]['15].
   [Also search for: Eulerian cycle algorithm].

%A M. Fleury
%T Deux problemes de geometrie de situation
%J J. de mathematiques elementaires
%V 2
%P 257-261
%D 1883
%K jrnl, c1883, c188x, c18xx, zz0515, Eulerian circuit, circuits, cycle, cycles,
   path, paths, trail, trails, Fleury, algorithm, maths, graph
%X See, "... alg. starts at a vertex of odd degree, or, if the graph has none,
   it starts with an arb. chosen vertex. At each step it chooses the next edge
   in the path to be one whose deln would not disconnect the g., unless there
   is no such e., in which case it picks the remaining e. left at the current
   vertex. It then moves to the other endpoint of that vertex & deletes the
   chosen edge. ... If we are to re-run Tarjan's linear time bridge-finding alg.
   after the removal of every edge, Fleury's alg. will have a time complexity
   of O(|E|^2). ... A dynamic bridge-finding alg. of Thorup (2000) allows this
   to be improved to O(|E|log^3|E| log log|E|) but this is still sig. slower
   than alternative algs.. ..."
   -- E@[<A HREF="http://en.wikipedia.org/wiki/Eulerian_path">wikip</A>]['15].
   [Also search for: Eulerian cycle algorithm].

%A A. D. Booth
%T A signed binary multiplication technique
%J Q. Jrnl Mech. Appl. Math.
%V 4
%N 2
%P 236-240
%D 1951
%K jrnl, c1951, c195x, c19xx, zz0624, integer multiplication, algorithm,
   multiplier
%X "A technique is described whereby binary numbers of either sign may be
   multiplied together by a uniform process which is independent of any
   foreknowledge of the signs of these numbers."
   -- [<A HREF="https://doi.org/10.1093/qjmam/4.2.236">doi:10.1093/qjmam/4.2.236</A>]['24].
   [Also search for: fast integer multiplication].
   Also see BA@[<A HREF="https://en.wikipedia.org/wiki/Booth%27s_multiplication_algorithm">wikip</A>]['24].

%A D. A. Huffman
%T A method for the construction of minimum-redundancy codes
%J Proc. Inst. Radio Eng.
%V 40
%N 9
%P 1098-1101
%M SEP
%D 1952
%K jrnl, prefix, code, coding, data compression, compress, Huffman code,
   binary code, tree, c1952, c195x, c19xx
%X [Also search for: binary code tree].

%A H. Steinhaus
%T Sur la division pragmatique (On fair division)
%J Econometrica
%V 17, Suppl. Report of the Washington Mtg
%P 315-319
%V 16
%N 1
%P 101-104
%M JUL
%D 1949
%K jrnl, c1948, 194x, c19xx, zz0623, fair division, cake, cut, cutting,
   slice, slices, slicing, resource allocation, fairly, last diminisher,
   divide, choose
%X "Le principe de division en deux moities, que l'on peut designer par
   la regle "l'un divise, 1'autre choisit," est bien connu; on pretend meme
   qu'il existe dans la tradition juridique anglaise ..."
   -- 1907319@[<A HREF="https://www.jstor.org/stable/1907319">Jstor</A>]['23].
   Also see DaC@[<A HREF="https://en.wikipedia.org/wiki/Divide_and_choose">wikip</A>['23]
  and LastD@[<A HREF="https://en.wikipedia.org/wiki/Last_diminisher">wikip</A>]['23] for more than two slices.

%A G. B. Dantzig
%A D. R. Fulkerson
%A S. M. Johnson
%T Solution of a large-scale traveling-salesman problem
%J Op. Res.
%V 2
%P 393-410
%D 1954
%K jrnl, OR, c1954, c195x, c19xx, zz1221, travelling salesman problem, TSP,
   salesperson, algorithm, cutting plane method
%X -- 166695@[<A HREF="https://www.jstor.org/stable/166695">Jstor</A>]['21].
   Reprinted with an intro by V.Chvatal and W.Cook in
   '50 Years of Integer Programming 1958-2008',
   M. Junger et al. (eds.), Springer, 2010,
   -- [<A HREF="https://doi.org/10.1007/978-3-540-68279-0_1">doi:10.1007/978-3-540-68279-0_1</A>]['21],
      [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.606.2752&rep=rep1&type=pdf">c'tseer</A>]['21].
   [Also search for: travelling salesman].

%A D. A. Huffman
%T The synthesis of sequential switching circuits
%J J. of the Franklin Institute
%V 257
%N 3-4
%P 161-190 and 275-303
%D 1954
%O TR 274, MIT, Res. Lab. of Electronics.
%K jrnl, circuit, logic, c1954, c195x, c19xx, TR 274, TR274, RLE
%X [<A HREF="http://hdl.handle.net/1721.1/4804">TR 274</A>][4/'04]
   Also see  M e a l y,  M o o r e.

%A H. W. Kuhn
%T The Hungarian method for the assignment problem
%J Naval Res. Logist. Quart.
%V 2
%N 1-2
%P 83-97
%M MAR
%D 1955
%K jrnl, c1955, c195x, c19xx, Munkres, maths, bipartite, graph, graphs, match,
   maximum weighted matching, assignment problem, algorithm, primal dual, cost,
   workers, tasks, matrix, bipartite graph, perfect matching, Hungarian method,
   Hungarians, Konig, Egervary
%X "Assuming that numerical scores are available for the performance of each of
   n persons on each of n jobs, the 'assignment problem' is the quest for an
   assignment of persons to jobs so that the sum of the n scores so obtained is
   as large as possible. ... shown that ideas latent in the work of two
   Hungarian math... may be exploited ..."
   -- [<A HREF="https://doi.org/10.1002/nav.3800020109">doi:10.1002/nav.3800020109</A>]['21],
   ("The Hungarian method is a combinatorial optimization alg. that solves the
   assignment problem in polynomial time & which anticipated later primal-dual
   methods. ... We are given a nonnegative nxn matrix, where the element in the
   i-th row & j-th column represents the cost of assigning the j-th job to the
   i-th worker. We have to find an assignment of the jobs to the workers that
   has minimum cost. ..."
   -- HAlg@[<A HREF="https://en.wikipedia.org/wiki/Hungarian_algorithm">wikip</A>]['16].)
   [Also search for: bipartite graph matching] and
   [also search for: graph Hungarian method].
   (Also see Munkres c1957.)

%A G. H. Mealy
%T A method for synthesizing sequential circuits
%J Bell System Technical J.
%P 1045-1079
%V 34
%N 5
%M SEP
%D 1955
%K jrnl, mealy machine, machines, automaton, automata, circuit, finite state,
   c1955, c195x, c19xx, FSM, FSA
%X A finite state machine that produces an output for each transition (edge,
   arc).  The output Q depends on both the current state S and the input I.
   e.g.      i/q         means in state S, for input i,
         S-------->S'    output q and move to S'.
   Also see  M o o r e,  H u f f m a n.

%A E. F. Moore
%T Gedanken experiments on sequential machines
%B Automata Studies
%S Ann. Math. Studies
%V 341
%A C. E. Shannon
%E J. McCarthy
%P 129-153
%I Princeton U. P.
%D 1956
%K Moore machine, c1956, c195x, c19xx, circuit, circuits, FSA, FSM
%X Also see  H u f f m a n,  M e a l y.

%A L. R. Ford
%A D. R. Fulkerson
%T Maximal flow through a network
%J Canadian J. of Mathematics
%V 8
%P 399-404
%D 1956
%K jrnl, c1956, c195x, c19xx, maximum flow, max, flows, maxFlow, min cut,
   minCut, problem, theorem, augmenting path, maths, graph, graphs, networks,
   algorithm
%X "... As long as there is a path from the source (start node) to the
   sink (end node), with available capacity on all edges in the path, we send
   flow along one of these paths. Then we find another path, & so on. A path
   with available capacity is called an augmenting path. ..." -- wikip [08].
   -- [<A HREF="http://www.rand.org/pubs/papers/P605/">TR,c1954,$13.50</A>]['08].
   (Also see MFMC@[<A HREF="https://en.wikipedia.org/wiki/Max-flow_min-cut_theorem">wikip</A>]['20]
    and FFA@[<A HREF="https://en.wikipedia.org/wiki/Ford%E2%80%93Fulkerson_algorithm">wikip</A>]['21].)
   [Also search for: Edmonds Karp c1972].

%A J. Munkres
%T Algorithms for the assignment and transportation problems
%J J. Soc. Indust. Appl. Math.
%V 5
%P 32-38
%D 1957
%K jrnl, c1957, c195x, c19xx, Kuhn, algorithm, maths, graph, graphs, bipartite,
   matrix, perfect, maximum weighted matching, assignment, problem,
   Hungarian method, Hungarians
%X "... present algs for the soln of the general assignment & transportation
   problems. In Sec.1, a statement of the alg. for the assignment problem
   appears, along with a proof for the correctness of the alg.. ..."
   -- [<A HREF="https://www.jstor.org/stable/2098689">Jstor</A>]['21].
   (Bipartite graph, part 1 and part 2 of size n,
   find a matching s.t. every vertex i in part 1 ~ some vertex j in part 2,
   and so that we max (or min) total cost.     Polynomial time alg., O(n**4):
   -- HAlg@[<A HREF="http://en.wikipedia.org/wiki/Hungarian_algorithm">wikip</A>]['08].)
   [Also search for: graph Hungarian method]
   (Also see Kuhn c1955.)

%A R. Bellman
%T On a routing problem
%J Quarterly of Applied Mathematics
%V 16
%N 1
%P 87-90
%D 1958
%K jrnl, c1958, c195x, c19xx, maths, graph, graphs, path, paths, short,
   shortest, weighted, network, all pairs, APSP, dynamic programming, DPA,
   algorithm, Ford
%X "An attempt to determine an optimal route from one point to another, given a
   set of N cities, with every two linked by a road, and the times required to
   transverse these roads. The times are not directly proportional to the
   distances because of the varying quality of roads and quantities of traffic.
   The functional equation technique of dynamic programming, combined with
   approximation in policy space, yields an iterative algorithm which converges
   after at most (N-1) iterations."
   -- P1000.html@[<A HREF="http://www.rand.org/pubs/papers/P1000.html">rand</A>]['16],
      scan@[<A HREF="http://www.dtic.mil/dtic/tr/fulltext/u2/606258.pdf">dtic</A>]['16].
   [Also search for: Ford paths c1962] and
   [also search for: graph shortest path algorithm].

%A M. B. Roy
%T Theorie des graphes. Transitivite et connexite
%J C. R. Acad. Sci. Paris
%V 249
%P 216-218
%M JUL
%D 1959
%K jrnl, c1959, c195x, c19xx, zz0423, all pairs shortest paths, APSP, pair,
   path, closure, Warshall, maths, graph
%X -- [<A HREF="https://gallica.bnf.fr/ark:/12148/bpt6k3201c/f222.image">gallica.bnf.fr</A>]['23].
   (Also see WF@[<A HREF="https://en.wikipedia.org/wiki/Floyd%E2%80%93Warshall_algorithm">wikip</A>]['23].)
   [Also search for: shortest paths graph].

%A M. O. Rabin
%A D. Scott
%T Finite automata and their decision problems
%J IBM J. Res. and Dev.
%V 3
%N 2
%D 1959
%K jrnl, c1959, c195x, c19xx, zz0823, FSM, FSA, DFA, NDFA, NFA. DFM, NDFM,
   non, deterministic, nonDeterministic, finite state automaton, machine,
   powerset construction, subset construction, problem, algorithm, language
%X "Finite automata are considered ... as instruments for classifying finite
   tapes. Each one-tape a. defines a set of tapes, a two-tape a. defines a set
   of pairs of tapes, etc. The structure of the defined sets is studied. Various
   generalizations of the notion of an a. are introduced & their reln to the
   classical a. is determined. Some decision problems concerning a. are shown to
   be solvable by effective algs.; others turn out to be unsolvable by algs.."
   -- [<A HREF="https://doi.org/10.1147/rd.32.0114">doi:10.1147/rd.32.0114</A>]['23].
   Also see PSC@[<A HREF="https://en.wikipedia.org/wiki/Powerset_construction">wikip</A>]['23].

%A D. A. Pope
%A M. L. Stein
%T Multiple precision arithmetic
%J CACM
%V 3
%P 652-654
%D 1960
%K jrnl, CACM, c1960, c196x, c19xx, zz0624, integer, computer arithmetic,
   division, BigInt, algorithm
%X -- [<A HREF="https://doi.org/10.1145/367487.367499">doi:10.1145/367487.367499</A>]['24].
   [Also search for: computer arithmetic].

%A M. Held
%A R. M. Karp
%T A dynamic programming approach to sequencing problems
%J Proc. 1961 16th ACM nat. mtg
%P 71.201-71.204
%M JAN
%D 1961
%K conf, c1961, c196x, c19xx, zz0720, travelling salesman problem, TSP, DPA,
   scheduling, problem, algorithm, Held, Karp, Bellman
%X "... explores a DP approach to the soln of three sequencing problems: a
   scheduling problem involving arbitrary cost fns, the TSP, and an assembly
   line balancing problem. ..."
   -- [<A HREF="https://doi.org/10.1145/800029.808532">doi:10.1145/800029.808532</A>]['20].
   [Also search for: travelling salesman problem DPA].
   (Also see TSP@[<A HREF="https://en.wikipedia.org/wiki/Held%E2%80%93Karp_algorithm">wikip</A>]['20].)

%A C. A. R. Hoare
%T Algorithm 65: FIND
%J CACM
%V 4
%P 321-322
%D 1961
%K jrnl, CACM, Find, selection, select, percentile, percentiles, median,
   problem, algorithm, quartile, quickselect, partition, quartiles,
   c1961, c196x, c19xx
%X aka "quickselect", avg O(n)-time, O(n^2) worst case.
   Also see  B l u m  et al  '73.
   [<A HREF="http://doi.acm.org/10.1145/366622.366647">doi:10.1145/366622.366647</A>]['05].
   [Also search for: median selection problem].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Sort/Select/">selection</A>].)

%A C. Schensted
%T Longest increasing and decreasing subsequences
%J Canad. J. Math.
%V 13
%P 179-191
%D 1961
%K jrnl, c1961, c196x, c19xx, zz1217, longest increasing subsequence,
   ascending, LASS, problem, LISS
%X "... finite seqs. of ints.. Typical of the problems we shall treat is the
   determination of the # of sequences of length n, consisting of the ints.,
   1,2,...,m, which have a longest increasing subsequence of length a.
   Throughout the first part of the paper we will deal only with seqs. in which
   no numbers are repeated. In the second part we will extend the results to
   include the possibility of repetition. Our results will be stated in terms of
   standard Young tableaux."
   -- [<A HREF="https://doi.org/10.4153/CJM-1961-015-3">doi:10.4153/CJM-1961-015-3</A>]['17].
   [Also search for: LASS problem].

%A S. Warshall
%T A theorem on boolean matrices
%J JACM
%V 9
%N 1
%P 11-12
%M JAN
%D 1962
%K jrnl, JACM, c1962, c196x, c19xx, Warshall, Floyd, Roy, algorithm,
   all pairs shortest paths, pair, path, APSP, closure, maths, graph
%X -- [<A HREF="https://doi.org/10.1145/321105.321107">doi:10.1145/321105.321107</A>]['23].
   AKA Roy (1959) & Floyd-Warshall algorithm.
   [Also search for: shortest paths graph].

%A R. Bellman
%T Dynamic programming treatment of the travelling salesman problem
%J JACM
%V 9
%N 1
%P 61-?
%M JAN
%D 1962
%K jrnl, JACM, c1962, c196x, c19xx, zz0720, travelling salesman problem, TSP,
   DPA, algorithm, Held, Karp, Bellman
%X -- [<A HREF="https://doi.org/10.1145/321105.321111">doi:10.1145/321105.321111</A>]['20].
   [Also search for: travelling salesman problem DPA].
   (Also see TSP@[<A HREF="https://en.wikipedia.org/wiki/Held%E2%80%93Karp_algorithm">wikip</A>]['20].)

%A D. Gale
%A L. S. Shapley
%T College admissions and the stability of marriage
%J Amer. Math. Monthly
%V 69
%P 9-15
%M JAN
%D 1962
%O a RAND report 1961
%K jrnl, c1962, c196x, c19xx, stable marriage problem, bipartite, maths, graph,
   matching, match, stability, unstable, university, college, school, admission,
   admissions, rank, rankings, preference, preferences, deferred acceptance,
   cooperative game theory, Roth
%X "Intro.: The problem ... A college ... n applicants of which it can
   admit a quota of only q. ..."
   -- [<A HREF="http://www.jstor.org/stable/2312726">Jstor</A>]['12].
   (Also a RAND report, 1961,
      "A procedure for assigning applicants to colleges which removes all
      uncertainties &, assuming there are enough applicants, assigns to each
      coll. precisely its quota. To determine the existence of stable
      assignments, the auths. discuss whether it is possible, for any pattern
      of prefs., to find a stable set of marriages. It is shown that the
      extn of the 'deferred acceptance' procedure to the problem of coll. admn.
      yields not only a stable but an optimal assignment of applicants."
      -- [<A HREF="http://www.rand.org/pubs/papers/P2240.html">www</A>]['12].)
   [Also search for: stable marriage].
      Lloyd Shapley & Alvin Roth won the 2012 Nobel prize for economics
      for their work on optimal matches (David Gale died in 2008).
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Graph/Stable/">stable-marriage</A>].)

%A A. Karatsuba
%A Yu. Ofman
%T Multiplication of many-digital numbers by automatic computers
%J Proc. USSR Acad. Scis
%V 145
%P 293-294
%D 1962
%O Translation in the acad. j. Physics-Doklady, 7 (1963), pp. 595-596
%K conf, c1962, c196x, c19xx, zz0621, fast, integer arithmetic, multiplication,
   algorithm, BigInt
%X Discovered 1960 published 1962, it's the n^{log_2(3)} recursive alg.,
   mentioned by Knuth in AoCP vol.2, & beats the O(n^2) "school alg.".
   -- K_alg@[<A HREF="https://en.wikipedia.org/wiki/Karatsuba_algorithm">wikip</A>]['21].
   [Also search for: Toom Cook integer multiplication] and
   [also search for: fast integer multiplication].
   Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Arithmetic/">more</A>]['24].

%A A. Toom
%A S. Cook
%T Toom Cook multiplication
%D 1963
%K TR, c1963, c196x, c19xx, zz0621, Toom, Cook, fast, integer, computer,
   arithmetic, multiplication, BigInt, Toom3
%X "... Given two large integers, a & b, Toom-Cook splits up a & b into k
   smaller parts each of length l, & performs operations on the parts. As k
   grows, one may combine many of the mult. sub-ops, thus reducing the overall
   complexity of the alg.. ..."
   -- TC@[<A HREF="https://en.wikipedia.org/wiki/Toom%E2%80%93Cook_multiplication">wikip</A>]['21].
   Toom3, where k=3, "can do a size-3N mult. for the cost of five size-N mult."
   Generalization of Karatsuba alg. (1962, in which k=2).
   [Also search for: Karatsuba integer multiplication] and
   [also search for: Toom Cook integer multiplication].
   Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Arithmetic/">more</A>]['24].

%A B. R. Heap
%T Permutations by interchanges
%J COMPJ
%V 6
%N 3
%P 293-298
%M OCT
%D 1963
%K COMPJ, jrnl, permutation, permute, generator, perm, swap, interchange,
   algorithm, generate, combinatorial object, c1963, c196x, c19xx
%X "Methods for obtaining all poss. perms. of a # of objects, in which each
   p. differs from its predecessor only by the interchange of two of the objects
   are discussed. Details of two programs which produce these perms. are given,
   one allowing a specified posn to be filled by each of the objects in a
   predet. order, the other needing the min. of storage space in a computer."
   -- [<A HREF="https://doi.org/10.1093/comjnl/6.3.293">doi:10.1093/comjnl/6.3.293</A>]['23].

%A R. Graham
%T Bounds for certain multiprocessing anomalies
%J Bell System Tech. J.
%V 45
%P 1563-1581
%D 1966
%K jrnl, c1966, c196x, c19xx, make span, makespan, job shop scheduling,
   jobs, jobshop, machines, schedule, list
%X pdf@[<A HREF="http://www.math.ucsd.edu/~ronspubs/66_04_multiprocessing.pdf">ucsd</A>]['11], and
      "... given n jobs J1, J2, ..., Jn of varying sizes, which need to be
      scheduled on m identical mcs, while trying to minimize the makespan. The
      makespan is the total length of the schedule (... when all the jobs have
      finished processing)."
      -- [<A HREF="http://en.wikipedia.org/wiki/Makespan">wikip</A>]['11].

%A M. A. Kronrod
%T An optimal ordering algorithm without a field of operation
%J Dokl. Akad. Nauk USSR
%V 186
%N 6
%P 1256-1258
%D 1969
%K jrnl, c1969, c196x, c19xx, zz0818, sort, sorting, merge, merging, in-situ,
   insitu, inPlace, space, algorithm
%C -- dan34705@[<A HREF="http://mi.mathnet.ru/eng/dan34705">mathnet.ru</A>]['18].
   [Also search for: insitu merge].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Sort/Insitu/">inSitu</A>].)

%A V. Strassen
%T Gaussian elimination is not optimal
%J Numer. Math.
%V 13
%P 354-356
%D 1969
%K jrnl, c1969, c196x, c19xx, fast matrix multiplication, matrix, product,
   inverse, matrices, arrays, algorithm
%X "Below we will give an alg. which computes the coeffs. of the product of two
   square matrices A & B of order n from the coeffs. of A & B with less than
   4.7 - n log 7 arithmetical ops. (all logs. in this paper are for base 2, thus
   log 7 ~ 2.8; the usual method requires ~ 2n^3 arithmetical ops.). The alg.
   induces algs. for inverting a matrix of order n, solving a system of n linear
   equns in n unknowns, computing a determinant of order n etc. all requiring
   less than (const n log 7) arithmetical ops.. ..."
   -- [<A HREF="https://doi.org/10.1007/BF02165411">doi:10.1007/BF02165411</A>]['22].
   [Also search for: fast matrix multiplication algorithm].
   (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/Algol68/">source-code</A>].)

%A R. M. Burstall
%T A program for solving word sum puzzles
%J COMPJ
%V 12
%N 1
%P 48-51
%M FEB
%D 1969
%K COMPJ, jrnl, puzzle, game, cryptarithm, cryptic arithmetic, cryptarithmetic,
   c1969, c196x, c19xx
%X [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_12/Issue_01/120048.sgm.abs.html">paper</A>][9/'01],
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_12/Issue_01/">issue</A>][9/'01].

%A B. H. Bloom
%T Space/time trade-offs in hash coding with allowable errors
%J CACM
%V 13
%N 7
%M JUL
%D 1970
%K jrnl, CACM, c1970, c197x, c19xx, zz0223, Bloom filter, hash, hashing, error,
   membership test, superimposed code
%X "... problem considered is that of testing a series of messages one-by-one
   for membership in a given set of messages. Two new hash-coding methods are
   examined & compared with a particular conventional hash-coding method. The
   computational factors considered are [space & time] ... reduction in space is
   accomplished by exploiting the possibility that a small fraction of errors of
   commission may be tolerable in some applications ..."
   -- [<A HREF="https://doi.org/10.1145/362686.362692">doi:10.1145/362686.362692</A>]['23].
   Also see BF@[<A HREF="https://en.wikipedia.org/wiki/Bloom_filter">wikip</A>]['23], and
    "A Bloom filter can be considered a kind of superimposed code"
    -- Sup'code@[<A HREF="https://en.wikipedia.org/wiki/Superimposed_code">wikip</A>]['23].
   [Also search for: Bloom filter]  and  [also search for: superimposed code].

%A J. H. Ellis
%T The possibility of non-secret digital encryption
%I CESG Research Report
%M JAN
%D 1970
%K TR, c1970, c197x, c19xx, zz0417, public key encryption, channel,
   key, security, cryptography, communication network, Diffie, Hellman, Merkle,
   Ellis, Cocks, Williamson, CESG, GCHQ
%X "[1] The possibility of Non-Secret digital encryption.
        J.H.Ellis, CESG Research Report, Jan 1970;
    [2] A note on non-secret encryption. C.C.Cocks, Nov 1973"
   -- [<A HREF="http://cryptocellar.org/cesg/secenc.pdf">pdf</A>]['17], was
   "... [<A HREF="http://cryptocellar.web.cern.ch/cryptocellar/cesg/possnse.pdf">pdf</A>][retrieved 2015-08-28] ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Diffie-Hellman_key_exchange">wikip</A>]['17].
   (See
    "...At GCHQ, by 1975 James Ellis had proved that a symmetric secret-key
    system is unnecessary and Clifford Cocks with Malcolm Williamson showed
    how such 'public-key cryptography' could be achieved. Until then it was
    believed that secure communication was impossible without exchange of a
    secret key, with key distribution as a major impediment. With these
    discoveries the essential principles were known but were kept secret until
    1997. ..."
    -- bbc[<A HREF="http://www.bbc.com/news/uk-england-gloucestershire-11475101">5/10/2010</A>].)
   [Also search for: public key encryption].

%A D. G. Corneil
%A C. C. Gotlieb
%T An efficient algorithm for graph isomorphism
%J JACM
%V 17
%N 1
%P 51-64
%M JAN
%D 1970
%K jrnl, c1970, c197x, c19xx, maths, graph isomorphism, graphs
%X [<A HREF="http://doi.acm.org/10.1145/321556.321562">doi:10.1145/321556.321562</A>], [10 refs].
   (An often efficient conjectured algorithm, in fact.)
   (The conjecture is said to be false.)
   [Also search for: maths graph isomorphism].

%A R. J. Ord-Smith
%T Generation of permutation sequences: part 1
%J COMPJ
%P 152-155
%V 13
%N 2
%M MAY
%D 1970
%K COMPJ, jrnl, permute, perm, OrdSmith, generator, algorithm,
   c1970, c197x, c19xx
%X -- [<A HREF="http://dx.doi.org/10.1093/comjnl/13.2.152">doi:10.1093/comjnl/13.2.152</A>]['05],
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_13/Issue_02/130152.sgm.abs.html">paper</A>][9/'01],
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_13/Issue_02/">issue</A>][9/'01].

%A R. J. Ord-Smith
%T Generation of permutation sequences: part 2
%J COMPJ
%P 136-139
%V 14
%N 2
%M MAY
%D 1971
%K COMPJ, jrnl, c1971, c197x, c19xx, permute, perm, OrdSmith, generator,
   algorithm
%X [<A HREF="http://dx.doi.org/10.1093/comjnl/14.2.136">doi:10.1093/comjnl/14.2.136</A>]['05],
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_14/Issue_02/140136.sgm.abs.html">paper</A>][9/'01],
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_14/Issue_02/">issue</A>][9/'01].

%A D. Shanks
%T Class number, a theory of factorization and genera
%J Proc. Symp. Pure Math., Prov., R.I.
%I AMS
%V 20
%P 415-440
%D 1971
%K conf, maths, c1971, c197x, c19xx, zz0920, baby step giant step algorithm,
   discrete logarithm, log, Dlog, order, group, factorization, factor,
   integer factorisation, factoring, genera, prime, primes
%X -- conf@[<A HREF="https://doi.org/10.1090/pspum/020">doi:10.1090/pspum/020</A>]['23],
   or see, "... a meet-in-the-middle alg. for comp. the discrete logarithm or
           order of an elt in a finite abelian group due to Daniel Shanks ..."
   or see BSGS@[<A HREF="https://en.wikipedia.org/wiki/Baby-step_giant-step">wikip</A>]['20] inc. the algorithm,
   Also see DL@[<A HREF="https://en.wikipedia.org/wiki/Discrete_logarithm">wikip</A>]['20].
   [Also search for: discrete logarithm].

%A J. M. Yohe
%T Algorithm 428: Hu-Tucker minimum redundancy alphabetic coding method
%J CACM
%V 15
%N 5
%P 360-362
%M MAY
%D 1972
%K jrnl, CACM, c1972, c197x, c19xx, data compression, Huffman, code,
   binary codes, tree, Hu, Tucker, ordered, algorithm
%X "... implements the Hu-Tucker method of variable length, min.redundancy
   alphabetic binary encoding. The symbols of the alphabet are considered to be
   an ordered forest of n terminal nodes. Two nodes in an ordered forest are
   said to be tentative-connecting if the sequence of nodes between the two
   given nodes is either empty or consists entirely of nonterminal nodes."
   -- [<A HREF="http://dx.doi.org/10.1145/355602.361319">doi:10.1145/355602.361319</A>]['13].
   [Also search for: binary code tree].

%A A. V. Aho
%A M. R. Garey
%A J. D. Ullman
%T The transitive reduction of a directed graph
%J SIAM J. Comput.
%V 1
%N 2
%P 131-137
%D 1972
%K jrnl, c1972, c197x, c19xx, transitive reduction, directed graph, digraph,
   maths, graphs, algorithm
%X "We consider economical representations for the path info. in a di.graph.
   A di.graph G^t is said to be a transitive reduction of the di.graph G
   provided that (i) G^t  has a directed path from vertex u to vertex v iff
   G has a directed path from u to v, & (ii) there is no graph with fewer arcs
   than G^t  satisfying condition (i). Though di.graphs with cycles may have
   > 1 such representation, we select a natural canonical representative as the
   trans. redn for such graphs. ... the time complexity of the best alg. for
   finding the trans.redn of a graph is the same as the time to compute the
   transitive closure of a graph or to perform Boolean matrix multiplication."
   -- [<A HREF="http://dx.doi.org/10.1137/0201008">doi:10.1137/0201008</A>]['08].

%A R. M. Karp
%A R. E. Miller
%A A. L. Rosenberg
%T Rapid identification of repeated patterns in strings, trees and arrays
%J Proc. 4th annual ACM symp. on Theory of Computing
%W Denver
%P 125-136
%D 1972
%K conf, pattern, string, tree, array, c1972, c197x, c19xx, match, matching,
   KMR72, search, searching, substring, subarray, subtree, sequence
%X "... look at a number of matching problems & devise general techniques for
   attacking [them]. ... describe a strategy for constructing efficient al's
   for solving 2 types of matching problems. We use this strategy to develop
   explicit algorithms for these 2 problems applied to strings (where the
   patterns are substrings) & arrays (where the patterns are subarrays or
   blocks). ...also alg's for these & related problems for trees, where the
   patterns are subtrees. Certain special cases of these algorithms are also
   discussed. Although we do not claim that these algorithms are optimal, we
   analyze each algorithm to estimate its computational cost. This provides
   some basis for choosing which alg' is most desirable in any given situation."
   -- [<A HREF="http://doi.acm.org/10.1145/800152.804905">doi:10.1145/800152.804905</A>]['09],
      [<A HREF="http://portal.acm.org/citation.cfm?id=804905">paper@acm.org</A>]['04].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/">strings</A>].)

%A R. Tarjan
%T Depth-first search and linear graph algorithms
%J SIAM J. Comput.
%V 1
%N 2
%P 146-160
%M JUN
%D 1972
%K jrnl, SIAM, c1972, c197x, c19xx, maths, graph, graphs, depth first traversal,
   biconnected, strong, strongly connected, component, components, maximum,
   maximal, algorithm
%X "The value of depth-first search or 'backtracking' as a technique for solving
   problems is illustrated by two examples. An improved version of an alg. for
   finding the strongly connected components of a directed graph & an alg. for
   finding the biconnected components of an undirect g. are presented. The space
   & time requirements of both algs. are bounded by k1 V + k2 E + k3 for some
   consts k1, k2, & k3, where V is the # of vertices & E is the # of edges ..."
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.327.8418">c'teseer</A>]['15],
      pdf@[<A HREF="http://www.csee.wvu.edu/~xinl/library/papers/comp/Tarjan_siam1972.pdf">wvu</A>]['15].
   Also see, "...The crux of the alg. comes in determining whether a node is the
      root of a strongly connected component. ... each node is given a depth
      search index, v.index, which numbers the nodes consecutively in the order
      in which they are discovered. [&] each node is assigned a value,
      v.lowlink, that satisfies v.lowlink := min {v'.index : v' is reachable
      from v}. Therefore v is the root of a strongly connected component iff if
      v.lowlink=v.index.  The value v.lowlink is computed during the depth 1st
      search s.t. it is always known when needed. ..."
   -- T@[<A HREF="http://en.wikipedia.org/wiki/Tarjan's_strongly_connected_components_algorithm">@wikip</A>]['08].

%A J. Nievergelt
%A E. M. Reingold
%T Binary search trees of bounded balance
%J SIAM J. on Comput.
%V 2
%N 1
%D 1973
%K jrnl, c1973, c197x, c19xx, zz1024, bounded, search, weight balanced tree,
   data structure, dataStructure, algorithm
%X "A new class of binary search trees, called t. of bounded balance, is intro..
   ... are easy to maintain in their form despite insertions & deletions of
   nodes, & the search time is only moderately longer than in completely
   balanced trees. Trees of bounded balance differ from other classes of binary
   search trees in that they contain a param. which can be varied so the
   compromise between short search time & infrequent restructuring can be chosen
   arbitrarily."
   -- [<A HREF="https:doi.org/10.1137/0202005">doi:10.1137/0202005</A>]['24].
   [Also search for: balanced search tree].

%A G. Ehrlich
%T Loopless algorithms for generating permutations, combinations, and other
   combinatorial configurations
%J JACM
%V 20
%N 1
%P 500-513
%M JUL
%D 1973
%K jrnl, JACM, c1973, c197x, c19xx, zz1118, loopless algorithm, combinatorial,
   generator, generate, enumerate, enumeration, permutation, combination,
   partition, Gray code
%X "The purpose of this work is to find a method for building loopless algs. for
   listing combinatorial items, like partitions, permutations, combinations,
   Gray code, etc..  Algs. for the above sequence are detailed in full."
   -- [<A HREF="https://doi.org/10.1145/321765.321781">doi:10.1145/321765.321781</A>]['18].
   [Also search for: loopless].

%A C. Bron
%A J. Kerbosch
%T Algorithm 457: Finding all cliques of an undirected graph
%J CACM
%V 16
%N 9
%P 575-577
%M SEP
%D 1973
%K jrnl, CACM, c1973, c197x, c19xx, ACM, find, finding, maximal, all, clique,
   maths, graph, graphs, algorithm, complete
%X "... A maximal complete subgraph (clique) is a complete subgraph that is not
   contained in any other complete subgraph. ... present two backtracking algs.,
   using a branch-and-bound technique to cut off branches that cannot lead to a
   clique.  ..."
   -- pdf@[<A HREF="http://doi.acm.org/10.1145/362342.362367">doi:10.1145/362342.362367</A>]['05],
   &  [<A HREF="http://en.wikipedia.org/wiki/Bron-Kerbosch_algorithm">wikip</A>]['10].

%A A. T. Berztiss
%T A backtrack procedure for isomorphism of directed graphs
%J JACM
%V 20
%N 3
% 365-377
%M JUL
%D 1973
%K jrnl, JACM, c1973, c197x, c19xx, maths, graph, isomorphism
%X "A reasonably efficient procedure for testing pairs of directed gs. for
   isomorphism is important in info.retrieval & other application fields in
   which structured data have to be matched. One such procedure, a backtrack
   procedure based on a representation of directed graphs by linear formulas,
   is described. A procedure for finding a partial subdigraph of a digraph that
   is isomorphic to a given digraph is also described."
   -- [<A HREF="http://doi.acm.org/10.1145/321765.321766">doi:10.1145/321765.321766</A>]['10].
   [Also search for: maths graph isomorphism].

%A J. E. Hopcroft
%A R. M. Karp
%T An n**(5/2) algorithm for maximum matchings in bipartite graphs
%J SIAM J. Comput.
%V 2
%N 4
%P 225-231
%D 1973
%K jrnl, c1973, c197x, c19xx, maths, bipartite, graph, graphs, maximum match,
   matching, assignment, problem, algorithm
%X "... shows how to construct a maximum matching in a bipartite graph with
   n vertices & m edges in a number of comp. steps prop. to (m+n)sqrt(n)."
   -- [<A HREF="https://doi.org/10.1137/0202019">doi:10.1137/0202019</A>]['21].
   (Also see, "...a matching M in G is a set of pairwise non-adjacent edges ..."
   -- HK@[<A HREF="http://en.wikipedia.org/wiki/Hopcroft-Karp_algorithm">wikip</A>]['08].)

%A J. M. Pollard
%T Theorems of factorization and primality testing
%J Math. Proc. of the Cambridge Phil. Soc.
%V 76
%N 3
%P 521-528
%D 1974
%K conf, c1974, c197x, c1`9xx, zz0124, prime, integer, factorisation, factoring,
   factorization
%X "... the problem of obtaining theor. estimates for the # of arithmetical
   op'ns required to factorize a large int. n or test it for primality. ..."
   -- [<A HREF="https://doi.org/10.1017/S0305004100049252">doi:10.1017/S0305004100049252</A>]['24].
   Also see Pp1@[<A HREF="https://en.wikipedia.org/wiki/Pollard%27s_p_%E2%88%92_1_algorithm">wikip</A>]['24].
   [Also search for: integer factorisation].

%A R. A. Finkel
%A J. L. Bentley
%T Quad trees a data structure for retrieval on composite keys
%J Acta Informatica
%V 4
%P 1-9
%M MAR
%D 1974
%K jrnl, c1974, c197x, c19xx, zz0722, quad tree, Qtree, quadTree, data, key,
   retrieval, insertion, deletion, search, nearest, closest, neighbour, vector,
   binning, algorithm
%X "The quad tree is a data struct. appropriate for storing info. to be
   retrieved on composite keys. We discuss the specific case of 2D retrieval,
   although the structure is easily generalised to arbitrary dimensions.
   Algs. are given both for staightforward insertion & for a type of balanced
   insertion into quad trees. Empirical analyses show that the avg. time for
   insertion is logarithmic with the tree size. ..."
   -- [<A HREF="https://doi.org/10.1007/BF00288933">doi:10.1007/BF00288933</A>]['22].
   Also see QT@[<A HREF="https://en.wikipedia.org/wiki/Quadtree">wikip</A>]['22].
   [Also search for: KDtree].

%A J. P. Fillmore
%A S. G. Williamson
%T On backtracking: a combinatorial description of the algorithm
%J SIAM J Comput.
%V 3
%N 1
%P 41-55
%M MAR
%D 1974
%K jrnl, c1974, c197x, c19xx, maths, backtrack, search, isomorph rejection,
   permutation, generator, isomorph rejection, G-invariant partitions,
   n queens, nqueens, 8 queens, soma cube
%X "A basic alg. for solving many discrete problems is the so-called
   'backtracking' alg.. The basic problem is that of generating the elts of a
   subset S_0 of a finite set in an efficient manner. If a group G acts on S_0,
   then one might wish to obtain only nonisomorphic elements of S_0.  ... the
   basic b.alg. is described in terms of chains of partitions on the set S. The
   corr. isomorph rejection problem is described in terms of G-invariant chains
   of partitions on S. Examples & flow charts are given."
   -- [<A HREF="http://dx.doi.org/10.1137/0203004">doi:10.1137/0203004</A>]['10].
   [Also search for: isomorph rejection].

%A R. Tarjan
%T A note on finding the bridges of a graph
%J IPL
%V 2
%N 6
%P 160-161
%M APR
%D 1974
%K jrnl, IPL, c1974, c197x, c19xx, zz0515, bridge, finding, maths, graph,
   algorithm, connected, connectivity
%X "... If there is a path from a vertex v to a vertex w in G but every path
   from v to w contains edge e then e is said to be a 'bridge' of G. ...
   finding all bridges of G requires O(V+E) time with this alg.. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0020-0190(74)90003-9">doi:10.1016/0020-0190(74)90003-9</A>]['15].
   [Also search for: graph bridge algorithm].
   (Useful in finding Eulerian circuits or trails (paths) in a graph.)

%A V. Arlazarov
%A I. Zuev
%A A. Uskov
%A I. Faradzev
%T An algorithm for the reduction of finite non-oriented graphs to
   canonical form
%J Zh. Vycheil. Mat. Mat. Fiz.
%V 14
%N 3
%P 737-743
%D 1974
%K jrnl, c1974, c197x, c19xx, maths, graph, isomorphism, canonical, labelling,
   permutation, canonization, labeling
%X (Ref in  M c K a y c1976,  who implies that it uses backtracking,
   and pruning, probably using the aut.grp of the graph.)
   [Also search for: canonical labelling maths graph], and
   [also search for: maths graph isomorphism].

%A A. Proskurowski
%T Search for a unique incidence matrix of a graph
%J BIT Numerical Mathematics
%V 14
%N 2
%P 209-226
%M JUN
%D 1974
%K jrnl, BIT, c1974, c197x, c19xx, maths, graph, graphs, incidence, adjacency,
   maximal, matrix, rowmim, minimal, maximum, canonical, labeling, labelling,
   isomorphism, canonization, automorphism
%X "... problem of isomorphism of simple graphs without selfloops & gives a
   proposal for a canonical repn of graphs & an efficient deterministic proc. to
   find this representation. ... Sec.1 defines the topological & computational
   language used & presents the isom.problem. ... [main results in] sec.2,
   [then] the ALGOL-version of the alg. & an analysis of its efficiency ..."
   -- pdf@[<A HREF="http://www.springerlink.com/content/n106325p84j54113/">springerlink</A>]['10],
   [<A HREF="http://dx.doi.org/10.1007/BF01932948">doi:10.1007/BF01932948</A>]['10].
   [Also search for: maths graph isomorphism] and
   [also search for: maths graph canonical labelling].

%A H. N. Gabow
%T Implementation of Algorithms for Maximum Matching on NonBipartite Graphs
%I Stanford Uni.
%D 1974
%K PhD thesis, c1974, c197x, c19xx, maths, graph, match, non-bipartite,
   algorithm

%A R. W. Floyd
%A R. L. Rivest
%T Expected time bounds for selection
%J CACM
%V 18
%N 3
%P 165-172
%M MAR
%D 1975
%K jrnl, CACM, c1975, c197x, c19xx, zz0718, median, select, selection, problem,
   algorithm 489, algorithm489, CSD 349, CSD349, bound
%X "A new seln alg. ... v.efficient on  average,  both theor, & practically.
   The # of comparisons used to select the i-th smallest of n numbers is
   n+min(i,n-i)+o(n). A lower bound within 9 percent of the above formula is
   also derived."  (Note, "... on  average ...")
   -- [<A HREF="https://doi.org/10.1145/360680.360691">doi:10.1145/360680.360691</A>]['18],
      pdf@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.309.8475&rep=rep1&type=pdf">citese'r</A>['18].
   (*ALSO see 'Algorithm 489, SELECT', CACM, p.173, same issue
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.309.7108&rep=rep1&type=pdf">citese'r</A>['18].*)
   [Also seach for: median selection problem] and
   [also search for: Kiwiel select c2005].

%A G. Manacher
%T A new linear-time ``on-line'' algorithm for finding the
   smallest initial palindrome of a string
%J JACM
%P 346-351
%V 22
%N 3
%M JUL
%D 1975
%K jrnl, JACM, palindromes, strings, sequence, c1975, c197x, c19xx
%X Initial palindrome of S is a `w' s.t. S = w+w'+u, where w'=reverse(w).
   -- [<A HREF="http://doi.acm.org/10.1145/321892.321896">paper.pdf@doi.acm.org/10.1145/321892.321896</A>]['03].

%A D. C. Schmidt
%A L. E. Druffel
%T A fast backtracking algorithm to test directed graphs for isomorphism using
   distance matrices
%J JACM
%V 23
%N 3
%P 433-445
%D 1976
%K jrnl, JACM, c1976, c197x, c19xx, maths, graph, graphs, isomorphism,
   distance matrix, backtrack
%X "A backtracking alg. for testing a pair of digraphs for isomorphism ...
   The information contained in the distance matrix representation of a graph is
   used to establish an initial partition of the graph's vertices. This distance
   matrix information is then applied in a backtracking proc. to reduce the
   search tree of possible mappings. While the alg. is not guaranteed to run in
   polynomial time, it performs efficiently for a large class of graphs."
   pdf: [<A HREF="http://doi.acm.org/10.1145/321958.321963">doi:10.1145/321958.321963</A>]['08].
   [Also search for: maths graph isomorphism].

%A W. Diffie
%A M. Hellman
%T New directions in cryptography
%J IEEE Trans. on Info. Theory
%V 22
%N 6
%P 644-654
%M NOV
%D 1976
%K jrnl, CACM, ca978, c197x, c19xx, zz0417, public key encryption, channel,
   key, security, cryptography, communication network, Diffie, Hellman, Merkle,
   Ellis, Cocks, Williamson, GCHQ
%X "Two kinds of contemporary developments in cryptography are examined.
   Widening applications of teleprocessing have given rise to a need for new
   types of cryptographic systems, which minimize the need for secure key
   distribution channels and supply the equivalent of a written signature. This
   paper suggests ways to solve these currently open problems. It also discusses
   how the theories of communication and computation are beginning to provide
   the tools to solve cryptographic problems of long standing."
   -- [<A HREF="http://dx.doi.org/10.1109/TIT.1976.1055638">doi:10.1109/TIT.1976.1055638</A>]['17].
   (Also see D-H@[<A HREF="https://en.wikipedia.org/wiki/Diffie%E2%80%93Hellman_key_exchange">wikip</A>]['17], and
   the bbc[<A HREF="http://www.bbc.com/news/business-39341663">24/4/2017</A>].
   Also,
    "...At GCHQ, by 1975 James Ellis had proved that a symmetric secret-key
    system is unnecessary and Clifford Cocks with Malcolm Williamson showed
    how such 'public-key cryptography' could be achieved. Until then it was
    believed that secure communication was impossible without exchange of a
    secret key, with key distribution as a major impediment. With these
    discoveries the essential principles were known but were kept secret until
    1997. ..."
    -- bbc[<A HREF="http://www.bbc.com/news/uk-england-gloucestershire-11475101">5/10/2010</A>].)
   [Also search for: public key encryption].

%A N. E. Gibbs
%A W. G. Poole
%A P. K. Stockmeyer
%T A comparison of several bandwidth and profile reduction algorithms
%J Trans. on Math. Software
%I ACM
%V 2
%N 4
%P 322-330
%D 1976
%K TOMS, c1976, c197x, c19xx, matrix, matrices, sparse, manipulation, package,
   store, storing, data structure, algorithm, CSC, CCS, CSR, CRS, columns,
   rows, format
%X pdf@[<A HREF="http://dx.doi.org/10.1145/355705.355707">doi:10.1145/355705.355707</A>]['16].
   Also see SM@[<A HREF="https://en.wikipedia.org/wiki/Sparse_matrix">wikip</A>]['16].
   [Also search for: sparse matrix], optionally include 'algorithm'.

%A H. N. Gabow
%T An efficient implementation of Edmonds' algorithm for maximum matching on
   graphs
%J JACM
%V 23
%N 2
%P 221-234
%M APR
%D 1976
%K jrnl, JACM, c1976, c197x, c19xx, maths, graph, edge, edges, Edmond, Edmonds,
   matching, problem, edges, assignment, algorithm
%X "A matching on a graph is a set of edges, no 2 of which share a vertex. A
   maximum matching contains the greatest number of edges possible. ...presents
   an efficient implementation of Edmonds' alg. for finding a MM. ... time is
   proportional to V**3, where V is the # of vertices; previous implementations
   of Edmonds' alg. have computation time proportional to V**4. The impl. is
   based on a system of labels that encodes the structure of alternating paths."
   -- [<A HREF="http://doi.acm.org/10.1145/321941.321942">doi:10.1145/321941.321942</A>]['07].
   [Also search for: maths graph maximum matching].

%A G. Collins
%A D. Musser
%T Analysis of the Pope-Stein division algorithm
%J IPL
%V 6
%N 5
%P 151-155
%M OCT
%D 1977
%K jrnl, IPL, c1977, c197x, c19xx, zz0624, integer division, BigInt,
   computer arithmetic, algorithm
%X -- [<A HREF="https://doi.org/10.1016/0020-0190(77)90012-6">doi:10.1016/0020-0190(77)90012-6</A>],
   or [<A HREF="http://digital.library.wisc.edu/1793/57558">wisc</A>]['24].
   [Also search for: BigInt division].

%A R. C. Read
%A D. G. Corneil
%T The graph isomorphism disease
%J J. of Graph Theory
%V 1
%N 4
%P 339-363
%D 1977
%K jrnl, c1977, c197x, c19xx, zz1115, maths, graph, isomorphism, algorithm,
   graphs, intro, survey, history, NPC
%X "The g.i. problem - to devise a good alg. for determining if two graphs are
   isomorphic - is of considerable practical importance, & is also of theor.
   interest due to its relationship to the concept of NP-completeness. No
   efficient (i.e., polynomial-bound) alg. for g.i. is known, & it has been
   conjectured that no such alg. can exist. Many papers on the subject have
   appeared, but progress has been slight; in fact, the intractable nature of
   the problem & the way that many graph theorists have been led to devote much
   time  to it, recall those aspects of the four-color conjecture which prompted
   Harary to rechristen it the 'four-color disease.' ... surveys the present
   state of the art of i.testing, discusses its relationship to NP-completeness,
   & indicates some of the difficulties inherent in this particularly elusive &
   challenging problem. A comprehensive bib. of papers relating to the g.i.
   problem is given."
   -- [<A HREF="http://dx.doi.org/10.1002/jgt.3190010410">doi:10.1002/jgt.3190010410</A>]['15].
   [Also search for: graph isomorphism].

%A L. T. Pardo
%T Stable sorting and merging with optimal space and time bounds
%J SIAM J. Comput.
%V 6
%N 2
%P 351-372
%D 1977
%K jrnl, c1977, c197x, c19xx, zz0818, sort, sorting, merge, merging, in situ,
   insitu, inPlace, stable, algorithm, space
%X "... two algs. for stable merging & stable sorting of files. The algs. have
   optimal worst case time bounds, the merge is linear & the sort is of order
   (n log n). Extra storage requirements are also optimal, since both algs. make
   use of a fixed # of pointers. Files are handled only by means of the
   primitives exchange & comparison of records & basic pointer transformations."
   -- [<A HREF="https://doi.org/10.1137/0206025">doi:10.1137/0206025</A>]['18].
   [Also search for: insitu merge].

%A H. T. Kung
%A F. Luccio
%A F. P. Preparata
%T On finding the maxima of a set of vectors
%J JACM
%V 22
%N 4
%P 469-477
%M OCT
%D 1977
%K jrnl, JACM, c1977, c197x, c19xx, maximal, vector, point, points, set, sets,
   dominate, dominator, minima, minimal, computational geometry
%X "... d dimensions ... # of comparisons C[d](n) ...
   Trivial that C[1](n) = n-1 and C[d](n) <= O(n^2) for d>=2.  Show that
   (i) C[d](n) =  O(n log n)       for d=2 and 3, and
       C[d](n) <= O(n(log n)^(d-2)) for d > 3.
  (ii) C[d](n) >= ceil(log n) for d >= 2.
   pdf:[<A HREF="http://doi.acm.org/10.1145/321906.321910">doi:10.1145/321906.321910</A>]['06]
   [A pt is maximal iff it is not dominated by another pt, where (for d=2)
   (x,y) dominates (v,w) iff x > v and y > w.  (Dominates is a partial order.)]
   Alg 3.1, finds maxima of a set, V, of d-dim vectors:-
     1 Arrange elts of V as a seq v1,...,vn s.t. v1[1] > ... > vn[1].
     2 i:=1; T[0]:=empty.   (T[0],T[1],... are sets of (d-1)-dim vectors)
     3 if v[i][2..d] < T[i-1] then T[i]:=T[i-1]
       else T[i]:=maxima( T[i-1] + {v[i][2..d]} )
     4 if i=n then stop else {i:=i+1; goto 3}
     where "u < T" means there is a w in T s.t. u <= w.
   Thm 3.1. The vector v[i] is maximal iff v[i][2..d] in T[n].
   [Also search for: maxima dominate].

%A R. C. Merkle
%T Secure communications over insecure nhannels
%J CACM
%V 21
%N 4
%P 294-299
%M APR
%D 1978
%K jrnl, CACM, ca978, c197x, c19xx, zz0417, public key encryption, channel,
   key, security, cryptography, communication network, Diffie Hellman
%X "According to traditional conceptions of cryptographic security, it is
   necessary to transmit a key, by secret means, before encrypted massages can
   be sent securely. This paper shows that it is possible to select a key over
   open communications channels in such a fashion that communications security
   can be maintained. A method is described which forces any enemy to expend an
   amount of work which increases as the square of the work required of the two
   communicants to select the key. The method provides a logically new kind of
   protection against the passive eavesdropper. It suggests that further
   research on this topic will be highly rewarding, both in a theoretical and
   a practical sense."
   -- [<A HREF="http://dx.doi.org/10.1145/359460.359473">doi:10.1145/359460.359473</A>]['17].
   (Also see D-H@[<A HREF="https://en.wikipedia.org/wiki/Diffie%E2%80%93Hellman_key_exchange">wikip</A>]['17] and
    the bbc[<A HREF="http://www.bbc.com/news/business-39341663">24/4/2017</A>].)
   [Also search for: public key encryption].

%A E. C. Horvath
%T Stable sorting in asymptotically optimal time and extra space
%J JACM
%V 25
%N 2
%P 177-199
%M APR
%D 1978
%K jrnl, JACM, c1978, c197x, c19xx, zz0818, stable, sort, sorting, merge,
   merging, algorithm, in-situ, insitu, inPlace, space, Kronrod, contiguent
%X "... Section 1 shows that a stable sorting alg. may be derived directly from
   a stable merging alg., & thereafter this paper is restricted to stable
   merging algs..  Sec.2 defines the concept of a contiguent, & shows that a
   contiguent-forming alg. may be used as the basis for a stable merging alg..
   A class of contiguent-forming algs. which exhibit a space/time tradeoff is
   presented. In the extremes, one alg. in the class gives rise to a stable
   merge requiring O(N) time & O(N log N) bits of extra space, another alg.
   requires O(N log N) time & O(log N) bits of extra space to merge.
   Sec.3 describes the Stable Kronrod Merge, which requires O(N) time & O(log N)
   bits of extra space, but is not applicable to all cases.  Sec.4, however,
   shows how the Stable Kronrod Merge may be combined with contiguent-forming
   alg. to yield a generally applicable class of stable merging algs..  One
   alg. in the class is shown to require O(N) time & O(log N) bits of extra
   space to merge ..."
   -- [<A HREF="http://dx.doi.org/10.1145/322063.322064">doi:10.1145/322063.322064</A>]['18].
   [Also search for: insitu merge].

%A J. H. Goodnight
%T A tutorial on the SWEEP operator
%J Statistical Computing
%I Amer. Stat. Assoc.
%V 33
%N 3
%P 149-?
%M AUG
%D 1979
%K c1979, c197x, c19xx, zz0708, stats, sweep operator, least squares, LSQ,
   linear regression, Gaussian elimination
%X [<A HREF="http://www.jstor.org/stable/2683825">@Jstor</A>]['08],
   via E M and D S.

%A S. L. Mitchell
%T Linear algorithms to recognize outerplanar and maximal outerplanar graphs
%J IPL
%V 9
%N 5
%P 229-232
%M DEC
%D 1979
%K jrnl, IPL, c1979, c197x, c19xx, maths, graph, graphs, outerplanar, algorithm
%X "Graph recognition; analysis of algorithms; maximal outerplanar graphs"
   [<A HREF="http://dx.doi.org/10.1016/0020-0190(79)90075-9">doi:10.1016/0020-0190(79)90075-9</A>]['08].

%A P. Downey
%A B. Leong
%A R. Sethi
%T Computing sequences with addition chains
%J SIAM J. Comput.
%V 10
%N 3
%D 1981
%K jrnl, c1981, c198x, c19xx, zz1124, AdditionChain, addition chain, sequence
%X "Given a seq. of +ve ints., n_1,...,n_m, what is the smallest # of additions
   needed to compute all m ints. starting with 1? This generalization of the
   addition chain (m=1) problem will be called the addition-seq. problem. We
   show that the seq. {2^0, 2^1, ... 2^(n-1), 2^n-1} can be computed with
   n+2.13.sqrt(n)+log(n) additions, & that n+sqrt(n)-2 is a lwb. This lwb result
   is applied to show that the addition-seq. problem is NPC."
   -- [<A HREF="https://doi.org/10.1137/0210047">doi:10.1137/0210047</A>]['24].

%A J. K. Wong
%T Some simple in-place merging algorithms
%J BIT Numer. Maths.
%V 21
%N 2
%P 157-166
%M JUN
%D 1981
%K jrnl, c1981, c198x, c19xx, zz0818, in situ, insitu, merge, merging, space,
   algorithm
%X "... family[1] merges stably in O(k.n) time and O(n^{1/k}) additional space
   with a limiting case running in O(n log n) time & constant space. The second
   family merges unstably in O(k.n) time & O(log^k n) space with a limiting case
   running in O(nG(n)) time & constant space. Here G(n) is the least k s.t.
   F(k) >= n where F(0)=1 & F(i)=2^{F(iâ1)} for i >= 1. Each alg. gives rise to
   a corresponding merge sort."
   -- [<A HREF="https://doi.org/10.1007/BF01933160">doi:10.1007/BF01933160</A>]['18].
   [Also search for: insitu merge].

%A W. Baur
%A V. Strassen
%T The complexity of partial derivatives
%J Theor. Comp. Sci.
%V 12
%N 1
%P 317-330
%M FEB
%D 1983
%K jrnl, TCS, c1983, c198x, c19xx, zz1023, partial derivative, gradient,
   Baur Strassen theorem, numerical algorithm, complexity, discriminant,
   matrix inversion, arithmetic circuit complexity, reverse mode
%X "Let L denote the nonscalar complexity in k(x_1,...,x_n). We prove
   L(f,f'_1,...,f'_n) <= 3L(f). Using this we determine the complexity of single
   power sums, single elementary symmetric fns, the resultant & the discriminant
   as root fns, up to order of magnitude. Also we linearly reduce matrix
   inversion to computing the determinant."
   -- [<A HREF="https://doi.org/10.1016/0304-3975(83)90110-X">doi:10.1016/0304-3975(83)90110-X</A>]['23].
   [Also search for: partial derivative algorithm] and
   [also search for: reverse mode].
   (Also see ArithCC@[<A HREF="https://en.wikipedia.org/wiki/Arithmetic_circuit_complexity">wikip</A>]['23].)

%A N. Karmarkar
%A R. M. Karp
%T The differencing method of set partitioning
%I U.C.Berkeley
%R CSD-83-113
%M DEC
%D 1983
%X TR 113, TR113, CSD-83-113, c1983, c198x, c19xx, set partitioning, partition,
   number, numbers, difference, differences, algorithm, heuristic, NP, NPC
%X pdf@[<A HREF="http://techreports.lib.berkeley.edu/accessPages/CSD-83-113.html">ber...</A>]['10].
  (Given a (multi)set, S, of N +ve ints, partition S into S1 and S2,
   s.t. the sum of numbers in S1 and in S2 are the same -- if possible.
   Or optimise: minimise the difference.)

%A R. E. Tarjan
%T An improved algorithm for hierarchical clustering using strong components
%J IPL
%V 17
%N 1
%P 37-41
%D 1983
%K IPL, jrnl, c1983, c198x, c19xx, cluster, component, maths, graph, graphs,
   zz0706

%A H. N. Gabow
%A R. E. Tarjan
%T A linear-time algorithm for a special case of disjoint set union
%J Proc. 15th ACM Symp. on Theory of Computing (STOC)
%P 246-251
%D 1983
%K conf, STOC, c1983, c198x, c19xx, linear, union find, tree, min, LCA,
   nearest common ancestor, reducibility, data structure, dataStructure, DS
%X "... linear-time alg. for the special case of the disjoint set union problem
   in which the structure of the unions (defined by a union tree) is known in
   advance. The alg. executes an intermixed seq. of m union & find ops. on n
   elts in 0(m+n) time & 0(n) space ... a slight but theoretically sig.
   improvement over the fastest known alg. for the general problem, which runs
   in 0(m &agr;(m+n,n) + n) time & 0(n) space, where &agr; is a functional
   inverse of Ackermann's fn. Used as a subroutine, the alg. gives similar
   improvements in the efficiency of alg. for solving a # of other problems,
   inc. 2-processor scheduling, the off-line min problem, matching on convex
   graphs, finding nearest common ancestors off-line, testing a flow graph for
   reducibility, & finding 2 disjoint directed spanning trees. The alg. obtains
   its efficiency by combining a fast alg. for the general problem with table
   look-up on small sets, & requires a random access machine ... . ...extends to
   the case in which single-node additions to the union tree are allowed. The
   extended alg. is useful in finding maximum cardinality matchings on
   nonbipartite graphs."
   -- pdf@[<A HREF="http://dx.doi.org/10.1145/800061.808753">doi:10.1145/800061.808753</A>]['08].
   [Also search for: union find].

%A A. Sanfeliu
%A K. S. Fu
%T A distance measure between attributed relational graphs for pattern
   recognition
%J IEEE Trans. Systems, Man, and Cybernetics
%V 13
%P 353-362
%D 1983
%K jrnl, c1983, c198x, c19xx, graph edit distance, GED, maths, graphs, similar,
   similarity
%X "A method to determine a dist.measure between two nonhierarchical attributed
   relational graphs ... based on the compn of the minimum # of modifications
   required to transform an input g. into the reference one. ... include node
   insertion, node deletion, branch insertion, branch deletion, node label
   substitution and branch label substitution. ..."
   --- [<A HREF="https://doi.org/10.1109/TSMC.1983.6313167">doi:10.1109/TSMC.1983.6313167</A>]['22].
   [Also search for: graph edit distance GED].

%A R. E. Tarjan
%A J. van Leeuwen
%T Worst-case analysis of set union algorithms
%J JACM
%V 31
%N 2
%P 245-281
%M JAN
%D 1984
%K jrnl, JACM, c1984, c198x, c19xx, zz0614, vanLeeuwen, disjoint set, sets,
   union find, problem, algorithm, data structure, dataStructure, DS,
   path compression
%X "... analyzes the asymptotic worst-case running time of a number of variants
   of the well-known method of path compression for maintaining a collection of
   disjoint sets under union. We show that two one-pass methods proposed by van
   Leeuwen & van der Weide are asymptotically optimal, whereas several other
   methods, including one proposed by Rein & advocated by Dijkstra, are slower
   than the best methods."
   -- [<A HREF="http://dx.doi.org/10.1145/62.2160">doi:10.1145/62.2160</A>]['14].
   (Also see d.set@[<A HREF="http://en.wikipedia.org/wiki/Disjoint-set_data_structure">wikip</A>].)
   [Also search for: union find]  and  [also search for: disjoint set].

%A D. D. Sleator
%A R. E. Tarjan
%T Self adjusting binary search trees
%J JACM
%V 32
%N 3
%M JUL
%D 1985
%P 660?
%K jrnl, data structure, DS, binary search tree, c1985, c198x, c19xx,
   dataStructure, DS, binary-tree

%A J. H. Reif
%A L. G. Valiant
%T A logarithmic time sort for linear size networks
%J JACM
%M JAN
%D 1987
%P 60-67
%V 34
%N 1
%K sort, parallel sorting, algorithm, concurrent, linear, size, network,
   log n time
%X randomized algorithm
   N node network constant valence
   O(log N)   N items on an N-node cube connected cycles graph.
   for some constant k, for large enough alpha,
   terminates in k*alpha*log(N) time with probability 1-1/N^alpha

%A R. Tarjan
%T Enumeration of the elementary circuits of a directed graph
%J SIAM J. Comput.
%V 2
%N 3
%M SEP
%D 1973
%P 211-216
%K SJC, algorithm, backtrack, circuit, cycle, digraph, maths, graph, simple,
   loop, c1973, c197x, c19xx
%X time O(V.E.(C+1))   V vertices  E edges  C elementary circuits

%A J. Earley
%T High level operations in automatic programming
%I Dept. of Elec. Engr. & Comp. Sci. and the Electronics Res. Lab., UCB
%M OCT
%D 1973
%K TR, strength reduction, program differentiation, c1973, c197x, c19xx
%X ref in  P a i g e and S c h w a r t z c1977.

%A J. Earley
%T High level iterators and a method for automatically designing
   data structure representation
%I Dept. of Elec. Engr. & Comp. Sci., and the Electronic Res. Lab., UCB
%M FEB
%D 1974
%K TR, strength reduction, differentiation program, c1974, c197x, c19xx,
   iterator inversion, DS, algorithm
%X ref in  P a i g e  and  S c h w a r t z c1977

%A R. Shostak
%T Deciding linear inequalities by computing loop residues
%J JACM
%V 28
%N 4
%M OCT
%D 1981
%P 769-779
%K theorem proving,  decision procedure, linear programming, inequation, CSP,
   linear inequality, real feasibility, constraint satisfaction, algorithm,
   LinearProgramming, automatic, c1981, c198x, c19xx
%X real feasibility satisfiability of sets of linear inequalities
   of form x <= y+c   quick  by loops of certain graphs residues
   then sets of arbitrary inequalities.
   [Also search for: LinearProgramming] and [also search for: theorem proving].

%A J. L. Bentley
%T Multidimensional binary search trees used for associative searching
%J CACM
%V 18
%N 9
%P 509-517
%M SEP
%D 1975
%K jrnl, CACM, tree, nearest neighbour, neighbour, nn, quad tree, search,
   multi dimension, c1975, c197x, c19xx
%X ref in greensp@n 2OOO.

%A D. B. Johnson
%T Finding all the elementary circuits of a directed graph
%J SIAM J. Comput.
%V 4
%N 1
%M MAR
%D 1975
%P 77-84
%K SJC, c1975, c197x, c19xx, algorithm, circuit, elementary, simple cycle,
   loop, digraph, maths, graphs, enumerate, enumeration
%X time O((n+e)(c+1)),   space O(n+e),
   n vertices,   e edges,   c elementary cycles.

%A A. Schonhage
%A M. Paterson
%A N. Pippenger
%T Finding the median
%J J. of Computer and Sys. Sciences
%V 13
%N 2
%P 184-199
%M OCT
%D 1976
%K jrnl, JCSS, c1976, c197x, c19xx, selection, problem, percentile, percentiles,
   median, quartile, quartiles, ith, kth, algorithm, select, hyperpair,
   hyperpairs
%X "An algorithm is described which determines the median of N elements
   using in the worst case a number of comparisons asymptotic to 3N."
   -- [<A HREF="https://doi.org/10.1016/S0022-0000(76)80029-3">doi:10.1016/S0022-0000(76)80029-3</A>]['18].
   Also see  B l u m  et al '73, and Paterson  '96 ?or '97?, and D o r '95.
   [Also search for: median selection problem].

%A I. Munro
%A P. Spira
%T Sorting and searching in multisets
%J SIAM J. Comput.
%V 5
%D 1976
%P 1-8
%K SJC, set, sets, multiset, sort, sorting, search, searching, intersection,
   empty, algorithm, multi set, sets

%A N. Pippenger
%T Sorting and selecting in rounds
%J SIAM J. Comput.
%V 16
%N 6
%P 1032-1038
%M DEC
%D 1987
%K SJC, sort, select, min, max, percentile, percentiles, median, merge,
   parallel algorithm

%A M. Blum
%A R. Floyd
%A V. Pratt
%A R. Rivest
%A R. Tarjan
%T Time bounds for selection
%J J. Computer and System Science
%V 7
%N 4
%P 448-461
%M AUG
%D 1973
%K jrnl, JCSS, c1973, c197x, c19xx, sort, select, selection, pick, find, min,
   max, percentile, percentiles, median, quartile, quartiles, fast, algorithm,
   first, second, third, ith, kth, i-th, nth, n-th, problem
%X "The number of comparisons required to select the i-th smallest of n numbers
   is shown to be at most a linear fn of n  by analysis of a  new selection
   alg. - PICK.  Specifically, no more than 5.4305 n comparisons are ever
   required. This bound is improved for extreme values of i, & a new lower bound
   on the requisite number of comparisons is also proved."
   -- [<A HREF="http://dx.doi.org/10.1016/S0022-0000(73)80033-9">doi:10.1016/S0022-0000(73)80033-9</A>]['13].
   O(n), 5.4305n comparisons to select i-th element  in the worst case!
   Uses b-th of the d-th elements, eg. median of group medians.
   Given S = s1, ..., sn and i:
   1. (a) divide s into n/c columns of length c and sort each column.
      (b) T := select the d-th smallest element of each column, |T|=n/c,
          m := b-th smallest elt of T
   2. Compare m to all other elts of S
   3. If rank of m = i then stop
      otherwise if rank m > i then discard elts >=m
                otherwise discard elts <= m
   Also see  P a t e r s o n  '96  ?or '97?
   [Also search for: median selection problem].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Sort/Select/">selection</A>].)

%A R. S. Boyer
%A J. S. Moore
%T A fast string search algorithm
%J CACM
%M OCT
%D 1977
%V 20
%N 10
%P 762-772
%K pattern, substring, searching, find, sub string, complexity, time,
   text editing, jrnl, CACM, c1977, c197x, c19xx
%X finds a search string in time, at  worst, patlen+strlen
   [Also search for: string search algorithm].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/">Strings</A>].)

%A J. W. Cooley
%A J. W. Tukey
%T An algorithm for the machine calculation of complex Fourier series
%J Math. Comp.
%V 19
%P 297-301
%D 1965
%K jrnl, maths, c1965, c196x, c19xx, zz0820, Fast Fourier Transform, FFT, DFT,
   series, algorithm, Yates, Good, history
%X "An efficient method for the calculation of the interactions of a 2^m
   factorial experiment was introduced by Yates & is widely known by his name.
   The generalization to 3^m was given by Box et al.[1]. Good[2] generalized
   these methods & gave elegant algs. for which one class of applications is the
   calculation of Fourier series. ..."
   -- [<A HREF="https://doi.org/10.1090/S0025-5718-1965-0178586-1">doi:10.1090/S0025-5718-1965-0178586-1</A>]['20].
   (Also see FFT@[<A HREF="https://en.wikipedia.org/wiki/Fast_Fourier_transform">wikip</A>]['20] and
             DFT@[<A HREF="https://en.wikipedia.org/wiki/Discrete_Fourier_transform">wikip</A>]['20].)

%A J. A. Nelder
%A R. Mead
%T A simplex method for function minimization
%J COMPJ
%V 7
%N 4
%P 308-313
%M JAN
%D 1965
%K jrnl, COMPJ, c1965, c196x, c19xx, zz0420, functionMin, function,
   minimization, minimum, minimisation, algorithm, Simplex
%X "A method is described for the minimization of a fn of n variables, which
   depends on the comparison of fn values at the (n+1) vertices of a general
   simplex, followed by the replacement of the vertex with the highest value by
   another point. The simplex adapts itself to the local landscape, & contracts
   on to the final minimum. The method is shown to be effective &
   computationally compact. A proc. is given for the estimation of the Hessian
   matrix in the neighbourhood of the minimum, needed in statistical estimation
   problems."
   -- [<A HREF="https://doi.org/10.1093/comjnl/7.4.308">doi:10.1093/comjnl/7.4.308</A>]['20],
      and correction
      [<A HREF="https://doi.org/10.1093/comjnl/8.1.27">doi:10.1093/comjnl/8.1.27</A>]['20].
   [Also search for: functionMin].

%A D. R. Fulkerson
%A O. A. Gross
%T Incidence matrices and interval graphs
%J Pacific J. Math.
%V 15
%P 835-855
%D 1965
%K jrnl, c1965, c196x, c19xx, PJM, jrnl, matrix, interval, maths, graph, C1P,
   consecutive ones property
%X ref' from Karp, Mapping the genome ... STOC '93.

%A P. M. Spira
%A A. Pan
%T On finding and updating spanning trees and shortest paths
%J SIAM J. Comput.
%V 4
%P 375-380
%D 1975
%K jrnl, tree, dynamic, minimum, MST, update, incremental, construction
%X ref in  E p p s t e i n  TR-92-04.

%A K. S. Booth
%A G. S. Leuker
%T Testing for the consecutive ones property, interval graphs, and graph
   planarity using PQ-tree algorithms
%J J. Comput. Sys. Sci.
%V 13
%N 3
%P 335-379
%M DEC
%D 1976
%K jrnl, c1976, c197x, c19xx, C1P, planar graph, maths, graphs, interval, one,
   ones, 1s, PQ tree, dataStructure, DS, trees, PQtree, chord, chordal,
   chordality, permutation, Lueker, Leuker, JCSS, algorithm, MolBio, genetic,
   map, mapping, RSM, sequence reconstruction
%X *** PQ-tree is a data structure which represents the permutations of a set U
   *** in which various subsets of U occur consecutively.
   Efficient algorithms given for manipulating PQ-trees.
   Alg's then given test for consec 1s property and planarity.
   Consec 1s extended to a test for interval graphs using
   a recently discovered fast recognition alg for chordal graphs.
   All algorithms run in O(n) time where n is size of input.

%A G. S. Leuker
%A K. S. Booth
%T A linear time algorithm for deciding interval graph isomorphism
%J JACM
%V 26
%N ??
%P 183-195
%M ???
%D 1976
%K interval graph, maths, graphs, c1976, c197x, c19xx

%A B. Paige
%A J. T. Schwartz
%T Expression continuity and the formal differentiation of algorithms
%J 4th Ann. Symp. on the Principles of Prog. Langs.
%P 58-71
%D 1977
%K conf, POPL, ACM, Sigplan, algorithm, program, programs, c1977, c197x, c19xx,
   strength reduction, compilation, set, sets, theoretic, POPL4, optimisation,
   optimization, SETL
%X "This paper explores the technique of 'strength reduction' or 'formal
   differentation' in a set theoretic context, as recently introduced by
   Earley [c1973, c1974]. We give pragmatic rules for the recognition &
   treatment of reasonably general cases in which the optimization is
   applicable, & consider some of the problems which arise in actually
   attempting to install this optimization as part of a compiling system."
   [<A HREF="http://doi.acm.org/10.1145/512950.512957">doi:10.1145/512950.512957</A>][10/'04]
   (P & S of the prog lang SETL)

%A K. S. Booth
%T Isomorphism testing for graphs, semigroups and finite
   automata are polynomially equivalent problems
%J SIAM J. Comput.
%V 7
%N 3
%M AUG
%D 1978
%K SJC, jrnl, c1978, c197x, c19xx, maths, graph,  regular graph, maths, group,
   semigroup,  finite automata, isomorphism, problem, polynomial reduction, NP,
   NPC, complexity

%A F. Chin
%A D. Houck
%T Algorithms for updating minimum spanning trees
%J J. Comput. Syst. Sci.
%V 16
%P 333-334
%D 1978
%K jrnl, JCSS, update, dynamic, incremental, construction, tree, MST,
   c1978, c197x, c19xx
%X ref in  E p p s t e i n  TR-92-04.

%A L. Babai
%T Moderately exponential bound for graph isomorphism
%J Proc. Conf. on Foundations of Computational Theory  FCT 21
%M AUG
%D 1981
%I SpringerVerlag
%S LNCS
%K c1981, c198x, c19xx,  problem, complexity, maths, graph isomorphism,
   conf, FCT 21, FCT21
%X [Also search for: maths graph isomorphism].

%A J. Eve
%A R. Kurki-Suonio
%T On computing the transitive closure of a relation
%J Acta Informatica
%V 8
%P 303-314
%D 1977
%K maths, graph, component, transitive closure, relation, algorithm,
   best case, c1977, c197x, c19xx
%X improves on Tarjan algorithm
   O(V^3) worst case worse than existing algorithms but
   O(V^2) best cases better than others

%A S. Even
%A O. Goldreich
%T The minimum length generator sequence problem is NP-hard
%J J. Algorithms
%V 2
%P 311-313
%M SEP
%D 1981
%K jrnl, P, NP, NPC, NPH, complexity class, set, base, generators,
   maths, group, groups, permutation, c1981, c198x, c19xx, word problem
%X (1) given a set of generators of a permutation group G,
       and a target permutation P,
       find the length of a shortest generator sequence for P.
   (2) find the min uper bound on the length of generator
       sequences for any element of G.
   reduce them to 3XC
   -- [<A HREF="http://dx.doi.org/10.1016/0196-6774(81)90029-8">doi:10.1016/0196-6774(81)90029-8 </A>]['07].
   [Also search for: group generator sequence].

%A M. J. Fischer
%A L. J. Stockmeyer
%T Fast on-line integer multiplication
%J ACM Symposium on Theory of Computing
%P 67-72
%D 1973
%K conf, STOC, on line, online, integer multiply, multiplication, big ints,
   complexity, algorithm, big, large, c1973, c197x, c19xx, computer arithmetic,
   operation
%X A Turing machine does * on-line if gets low order digits first and produces
   k digit before reading k+1 digits.
   Give a technique to convert off-line alg to on-line; new alg O(f(n)*log n).
   Apply to Schonhage Strassen alg to get
   O(n * (log n)^2 log log n)   on-line alg.
   Also applied to  product of polynomials over finite ring,
   recognition of palindromes O(n*log n) on line, multiplication by a constant.
   convolutions
   -- [<A HREF="http://portal.acm.org/citation.cfm?id=804037">acm</A>][4/'04].
   [Also search for: fast integer multiplication].

%A Chiba
%A et al
%T Drawing plane graphs nicely
%J Acta Informatica
%V 22
%P 187-201
%D 1985
%K plane graph, draw, drawing, display, nice, pretty print, layout, format,
   planar
%X ref picked from v-news so authors incomplete: Chiba et al
   can't vouch for it.
   [Also search for: graph drawing].

%A G. N. Frederickson
%T Data structures for on-line updating of minimum spanning trees with
   applications.
%J SIAM J. Comput.
%P 781-798
%V 14
%D 1985
%K jrnl, c1985, c198xm c19xx, MST, dynamic, update, tree, incremental,
   construction, dataStructure, DS
%X ref in  E p p s t e i n  TR-92-04.

%A M. R. Garey
%A D. S. Johnson
%A G. L. Miller
%A C. H. Papadimitriou
%T The complexity of colouring circular arcs and chords
%I Bell Labs
%D 1979 ???
%K maths, graph colouring, algorithm, NP, NPC, c19xx, c197x
%X prove  word problem for products of symmetric groups,
          circular arc graph colouring problem,
          circle graph colouring problem
   are NPcomplete  NPC.
   For any fixed k, problem of determining whether a given circular arc graph
   is k colourable is in polynomial time.

%A Z. Galil
%T Efficient algorithms for finding maximum matching in graphs
%J Computing Surveys
%V 18
%N 1
%M MAR
%D 1986
%P 23-38
%K survey, intro, c1986, c198x, c19xx, maths, graph, graphs, match,
   maximum matching, assignment problem, algorithm, augmenting path,
   general, bipartite
%X "... techniques used for designing the most efficient algs. for finding a
   maximum cardinality or weighted matching in (general or bipartite) gs.. It
   also lists some open problems concerning possible improvements in existing
   algs. & the existence of fast parallel algs. for these problems." [54 refs].
   -- [<A HREF="https://doi.org/10.1145/6462.6502">doi:10.1145/6462.6502</A>]['08].
   [Also search for: graph assignment problem].

%A G. Robins
%T The ISI grapher
%I Information Sciences Institute
%D 1988
%K ISI, graph, graphics, draw, pretty print, layout, format, nicely,
   plane, planar, plain
%X Software:  200K of CommonLisp code
   draws graphs nicely
   runs on Symbolics, TI Explorer, Mac II, Sun
   gabriel@vaxb.isi.edu
   Gabriel Robins, ISI, 4676 Admiralty Way, Marina Del Ray, Ca 90292 6695
   announced via enews

%A A. Blumer
%A J. Blumer
%A A. Ehrenfeucht
%A D. Haussler
%A M. T. Chen
%A J. Seiferas
%T The smallest automaton recognising the subwords of a text
%J Theoretical Computer Science
%D 1985
%V 40
%P 31-55
%K search, automaton, FSA, FSM, subword, substring, DAWG, c1985, c198x, c19xx,
   TCS, directed acyclic, DAWGs, DAG, word, maths, graph, TCS, repeated string,
   repeat, words, suffix tree, prefix

%A G. E. Collins
%A M. Mignotte
%A F. Winkler
%T Arithmetic in basic algebraic domains
%J In Computer Algebra: Symbolic and Algebraic Computation,
   Computing Suppl. 4. Vienna
%I Springer
%P 189-220
%D 1982
%K conf, c1982, c198x, c19xx, zz0624, maths, computer arithmetic, ints, BigInt,
   integer, numbers, domain, base conversion, algorithm, change
%X "... arith. Ops, essentially addition, multiplication, exponentiation,
   division, gcd calculation & evaluation, on the basic algebraic domains. ...
   the best known algs, from a computational point of view, are presented. The
   basic domains considered here are the rational ints, the rational numbers,
   integers modulo m, Gaussian integers, polynomials, rational functions,
   power series, finite fields & P-adic numbers. Bounds on the maximum, minimum
   & avg. Computing time (t+, t-, t*) for the various algorithms are given.
   -- [<A HREF="https://doi.org/10.1007/978-3-7091-7551-4_13">doi:10.1007/978-3-7091-7551-4_13</A>]['24],
   or [<A HREF="https://www3.risc.jku.at/publications/download/risc_229/paper_55.pdf">www</A>]['24].
   Also see PN#BC@[<A HREF="https://en.wikipedia.org/wiki/Positional_notation#Base_conversion">wikip</A>]['24].

%A A. Shamir
%T A polynomial time algorithm for breaking the basic Merkle-Hellman
   cryptosystem
%J Proc 23rd annual symposium on Foundations of Computer Science
%D 1982
%P 145-152
%K FCS, FoCS, FOCS23, FOCS82, P, c1982, c198x, c19xx,
   public key encryption, knapsack problem, code, cypher, cryptography
%X broke basic knapsack public key system.
   [Also search for: public key encryption].

%A R. L. Rivest
%T Partial-match retrieval algorithms
%J SIAM J. Comput.
%V 5
%N 1
%P 19-50
%D 1976
%K jrnl, algorithm, nearest neighbour, nn, c1976, c197x, c19xx, hash, hashing,
   neighbourhood, algorithm
%X "We examine the efficiency of hash-coding & tree-search algs. for retrieving
   from a file of k-letter words all words which match a partially-specified
   input query word (e.g., retrieving all six-letter English words of the form
   S**R*H where '*' is a 'don't care' character).  We precisely characterize
   those balanced hash-coding algs. with minimum avg # of lists examined. Use of
   the first few letters of each word as a list index is shown to be one such
   optimal alg.. A new class of combinatorial designs (called assoc. block
   designs) provides better hash fns with a greatly reduced worst-case # of
   lists examined, yet with optimal avg behavior maintained. Another efficient
   variant involves storing each word in several lists.  Tree-search algs. are
   shown to be approximately as efficient as hash-coding algs., on the avg. In
   general, these algs. require time about O(n^((k-s)/k)) to respond to a query
   word with s letters spec., given a file of nk-letter words. Previous algs.
   either required time O(s.n/k) or else used exorbitant amounts of storage."
   -- [<A HREF="https://doi.org/10.1137/0205003">doi:10.1137/0205003</A>]['23],
   [Also search for: hashing neighbourhood].

%A R. Rivest
%A A. Shamir
%A L. Adleman
%T On digital signatures and public key cryptosystems
%J CACM
%V 21
%P 120-126
%D 1978
%K RSA, public key, encryption, encrypt, code, signature, cryptography,
   c1978, c197x, c19xx, jrnl, CACM, cryptosystem, encryption
%X based on factoring product of 2 very large primes
   [Also search for: public key encryption].

%A D. Gries
%A J. Misra
%T A linear sieve algorithm for finding prime numbers
%J CACM
%V 21
%N 12
%M DEC
%D 1978
%P 999-1003
%K sieve of Eratosthenese, algorithm, primes, number, c1978, c197x, c19xx
%X all primes in [1..n], O(n) if multiplication of ints <= n is O(1).

%A Z. Galil
%A J. Seiferas
%T Time-space-optimal string matching
%J JCSS
%V 26
%P 280-294
%D 1983
%N 3
%M JUN
%K search, algorithm, sub string, match, search, find, linear time, space
%X linear time and constant amount of local space
   these are minimum bounds and are attained
   Also see  B o y e r, M o o r e

%A A. K. Griffith
%T Empirical exploration of the performance of the alpha beta tree-searching
   heuristic
%J IEEE Trans. on Computers
%V C-25
%N 1
%M JAN
%D 1976
%P 6-10
%K TOCS, alpha, beta, alpha-beta, tree search,
   prune, pruning, c1976, c197x, c19xx

%A S. W. Golomb
%A L. D. Baumert
%T Backtrack programming
%J JACM
%V 12
%N 4
%M OCT
%D 1965
%P 516-524
%K backtracking, nondeterminism, combinatorial problem, n queens, n-queens,
   nqueens, queen, back track, non determinism, comma free code,
   sum free set, sets, c1965, c196x, c19xx
%X early specification of backtrack technique.
   examples: n-queens, 8queens
             comma free codes
             sum free sets

%A J. Hopcroft
%A W. Paul
%A L. Valiant
%T On time versus space
%J JACM
%V 24
%N 2
%M APR
%D 1977
%P 332-337
%K turing machine, time, space, complexity, tradeoff, trade off
%X Shows every det' multitape TM of time complexity t(n)
   can be simulated by a det' TM of tape complexity t(n)/log t(n).
   Consequently for tape constructable t(n), the class of langs recognizable by
   TMs of time complexity t(n) is strictly contained in the class recognized
   by TMs of tape complexity t(n).
   In particular context-sensitive langs cannot be recognized in linear time
   by det' TMs.

%A P. Pritchard
%T Another look at the longest ascending subsequence problem
%J Acta Informatica
%V 16
%N 1
%P 87-91
%M AUG
%D 1981
%O TR 16, Dept. of Computer Science, Uni. of Qld, Aug, 1980
%M AUG
%D 1980
%K TR16, c1980, c198x, c19xx, LASS, LAS, program transformation, one, monotonic,
   longest, descending, ascending, increasing, decreasing, multi pass,
   multipass, problem, algorithm
%X Turns multi-pass algorithm into 1-pass; gives an O(n log(n)) algorithm.
   A sequence of length > M**2 contains a monotonic subseq of length > M.
   Monotonic means ascending or descending.
   -- [<A HREF="http://dx.doi.org/10.1007/BF00289592">doi:10.1007/BF00289592</A>]['06].
   [Also search for: LASS problem].

%A G. H. Golub
%A C. F. Van Loan
%T An analysis of the total least squares problem
%J SIAM J. Numerical Analysis
%V 17
%N 6
%P 883-893
%M DEC
%D 1980
%K jrnl, c1980, c198x, c19xx, vanLoan, line, fit, fitting, approximation, LSQ,
   TLS, RMS, square, error, linear regression
%X "Total least squares (TLS) ... fitting that is appropriate when there are
   errors in both the obs. vector $b (mxl)$ & in the data matrix $A (mxn)$. ...
   discussed by several authors & amounts to fitting a 'best' subspace to the
   pts $(a^{T}_{i},b_{i}), i=1,\ldots,m,$ where $a^{T}_{i}$ is the $i$-th row of
   $A$. ... a singular value decomposition analysis of the TLS problem is
   presented. The sensitivity ... as well as its relationship to ordinary least
   squares regression is explored. An alg. for solving the TLS problem is
   proposed that utilizes the singular value decomposition & which provides a
   measure of the underlying problem's sensitivity."
   -- pdf@[<A HREF="http://www.jstor.org/stable/2156807">Jstor</A>]['13],
      pdf@[<A HREF="http://www.cs.cornell.edu/cv/ResearchPDF/Analysis.total.least.squares.prob.pdf">crnll</A>]['13].

%A R. N. Horspool
%T Practical fast searching in strings
%J SPE
%V 10
%P 501-506
%D 1980
%K SPE, jrnl, c1981, c198x, c19xx, sub string, search, find, pattern match,
   good, text editing, algorithm, Boyer Moore, Knuth Morris Pratt, fast
%X Boyer Moore method outperforms even special search hardware instructions.
   However for very short strings special purpose instructions are fastest.
   Codes up algorithms and gets statistics on them.
   [Also search for: string search algorithm]. (Also see:  S m i t   '82)
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/">Strings</A>].)

%A D. E. Knuth
%A M. F. Plass
%T Breaking paragraphs into lines
%J SPE
%V 11
%N 11
%P 1119-1184
%M NOV
%D 1981
%K jrnl, SPE, c1981, c198x, c19xx, paragraph, line, breaks, break, total fit,
   document layout, pagination, markup, rendering, dynamic programming, DPA,
   typesetting, publishing, algorithm
%X "...problem of dividing the text of a para. into lines of approx. equal
   length. ... method considers the para. as a whole, so that the final
   appearance of a given line might be influenced by the text on succeeding
   lines. A system based on 3 simple primitive concepts called boxes, glue, &
   penalties provides the ability to deal satisfactorily with a wide variety of
   typesetting problems in a unified framework, using a single alg. that
   determines optimum breakpoints. The alg. avoids backtracking by a judicious
   use of the techniques of dynamic programming. Extensive computational
   experience confirms that the approach is both efficient & effective in
   producing high-quality output. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.4380111102">doi:10.1002/spe.4380111102</A>]['08].
   [Also search for: Plass c1981].

%A H. Riesel
%T Prime Numbers and Computer Methods for Factorization
%I Birkhauser
%D 1985
%K text, book, c1985, c198x, c19xx, factor, primes, number, primality,
   integer factorization, factoring, factorisation, algorithm
%X 2012 reprint of 1994 edn;
   pb us$98; uk us isbn:1461266815; uk us isbn13:978-1461266815.
   [Also search for: integer factorisation]  and  [also search for: primality].

%A R. D. Silverman
%T The multiple polynomial quadratic sieve
%J Mathematics of Computation
%V 48
%N 177
%P 329-339
%M JAN
%D 1987
%K jrnl, c1987, c198x, c19xx, MPQS, prime, primes, factor, factorisation,
   factorization, Eratosthenese, algorithm, integer, quadratic sieve,
%X [Also search for: integer factorisation].

%A D. Kozen
%T Lower bounds for natural proof systems
%J 18th Annual Symposium on Foundations of Computer Science
%M OCT
%D 1977
%I IEEE
%P 254-266
%K FOCS, FOCS18, FOCS77, FCS, NP, NPC, Pspace, logic, bound
%X 2 decidable logical theories are presented, one complete for
   deterministic polynomial time, P, one complete for polynomial space.
   Both have natural proof systems. A lower space bound of
   n/log(n) is shown for the proof system of the P complete theory and
   a lower bound of 2^(c n/log(n)) is shown for the other.

%A D. E. Knuth
%A R. W. Moore
%T An analysis of alpha-beta pruning
%J Artificial Intelligence
%P 293-326
%V 6
%D 1975
%K AI, alpha beta, prune, pruning, tree search, heuristic, c1975, c197x, c19xx,
   game, games, trees

%A R. M. Karp
%A M. Held
%T Finite-state processes and dynamic programming
%J SIAM J. Appl. Math.
%V 13
%N 3
%P 693-718
%D 1967
%K SIAM, SJAM, jrnl, DPA, algorithm, FSM, FSA, c1967, c196x, c19xx

%A S. Winograd
%T A new algorithm for inner product
%J IEEE Trans. Comput.
%V C17
%N 7
%P 693-694
%M JUL
%D 1968
%K jrnl, c1968, c196x, c19xx, zz0624, matrix multiplication, inner product,
   algorithm
%X "... a new way of computing the inner product of two vectors ... In
   particular, we obtain that the product of two nxn matrices can be performed
   using roughly (n^3)/2 multiplications instead of the usual n^3 ..."
   -- [<A HREF="https://doi.org/10.1109/TC.1968.227420">doi:10.1109/TC.1968.227420</A>]['24].
   [Also search for: Strassen 1969].

%A R. M. Karp
%T Reducibility among combinatorial problems
%B Complexity of Computer Computations
%E R. E. Miller
%E J. W. Thatcher
%I PlenumPress
%D 1972
%P 85-103
%K P, NP, NPC, PNPproblem, complexity, time, c1972, c197x, c19xx
%X [Also search for: PNPproblem].

%A R. L. Rivest
%T On the optimality of Elias's algorithm for performing best-match searches
%J IFIP74
%I Elsevier North-Holland
%P 678-681
%D 1974
%K conf, IFIP, IFIP74, nearest neighbour, NN, Elias

%A D. E. Knuth
%A J. L. Szwarcfiter
%T A structured program to generate all topological sorting arrangements
%J IPL
%V 2
%D 1974
%P 153-157
%K jrnl, IPL, c1974, c197x, c19xx, sort, topological sort, combinatorial,
   permutation, algorithm, DAG, generator

%A B. S. Kaliski
%A R. L. Rivest
%A A. T. Sherman
%T Is the data encryption standard a group? (preliminary abstract)
%J Advances in Cryptology -  Eurocrypt 85
%I SpringerVerlag
%S LNCS
%V 219
%M APR
%D 1985
%P 81-95
%K DES, Code, cypher, crack, decode, maths, group, cryptography
%X if DES were a group, can break it in 2^28
   not known if des is a group
   statistical test suggest des is probably not a group

%A T. Lengauer
%A R. E. Tarjan
%T A fast algorithm for finding dominators in a flow graph
%I Computer Science Dept., Stanford University
%R CS-78-650
%M MAR
%D 1978
%K TR, c1978, c197x, c19xx, dominate, dominates, dominator, maxima, maximal,
   vertex, flow graph
%X simple version O(E log N) time    E edges N vertices or nodes
   better version O(E alpha(E,N))    where alpha is Ackermann ^ -1.
   Let G=(V,E,r) be a flow graph.
   A vertex v DOMINATES another vertex w != v in G if every path from r to w
   contains v.
   [Also search for: maxima dominate].

%A E. M. Luks
%T Isomorphism of graphs of bounded valence can be tested in polynomial time
%J 21st IEEE Symp. on Foundations of Computer Science
%P 42-49
%D 1980
%O J. Comp and Sys. Sci., 25(1), pp.42-65, Aug., '82.
%K conf, c1980, c198x, c19xx, FOCS, FOCS21, FOCS80, maths, graph isomorphism,
   problem, algorithm, divide and conquer, P, NP, NPC, bounded degree, valence,
   fan out, color, colour automorphism
%X "Suppose we are given a set of generators for a group G of permutations of a
   colored set A. The color automorphism problem for G involves finding
   generators for the subgroup of G which stabilizes the color classes. It is
   shown that testing isomorphism of graphs of bounded valance is polynomial-
   -time reducible to the color automorphism problem for groups with composition
   factors of bounded order. The algorithm for the latter problem involves 3
   divide-&-conquer maneuvers. The problem is solved sequentially on the
   G-orbits. An orbit is broken into a minimal system of imprimitivity blocks.
   At that point, the hypothesis on G guarantees the presence of a subgroup P of
   "small" index which acts a p-group on the blocks. Divide-&-conquer is then
   used on the group, trading the problem on G for a small # of similar problems
   on P. In the trivalent case p=2, P=G & the analysis requires only elementary
   notions. For higher valence, the justification requires some new observations
   about primitive permutation groups."
   JCSS: [<A HREF="http://dx.doi.org/10.1016/0022-0000(82)90009-5">doi:10.1016/0022-0000(82)90009-5</A>]['08] [26 refs],
   auth@[<A HREF="http://ix.cs.uoregon.edu/~luks/">uOregon</A>]['10].
   [Also search for: maths graph isomorphism].

%A D. Lichtenstein
%A M. Sipser
%T Go is Pspace hard
%J IEEE CH1397
%D 1978
%K Go, game, Pspace, complexity

%A E. Bonomi
%A J-L. Luttoni
%T The N-city travelling salesman problem: Statistical mechanics and the
   Metropolis algorithm
%J SIAM Review
%V 26
%N 4
%M OCT
%D 1984
%P 551-568
%K travelling salesman, salesperson, TSP, sales man person, P, NP, NPC,
   approximate, heuristic, traveling, c1984, c198x, c19xx
%X [Also search for: travelling salesman problem].

%A E.M. Reingold
%T On the optimality of some set algorithms
%J JACM
%V 19
%D 1972
%P 649-59
%K set union, set, sets, algorithm, c1972, c197x, c19xx
%X via enews

%A G. L. Miller
%T On the n^log(n) isomorphism technique
%D 77??
%I Dept of Mathematics, MIT
%K maths, group, graph, quasigroup, latin square, Steiner system,
   isomorphism, algorithm
%X Tarjan has given an algorithm for deciding group (order n)
   isomorphism in O(n^(log(n)+O(1)))  when groups given as
   multiplication tables.
   Show this generalizes to quasigroups, latin squares, steiner systems
   and many graphs generated by these objects.

%A L. G. Khachian
%T A polynomial algorithm in linear programming
%J Soviet Mathematics Doklady
%V 20
%P 191-194
%D 1979
%K jrnl, complexity, polynomial time, P, ellipsoid, c1979, c197x, c19xx,
   LinearProgramming, linear programming, algorithm
%X Previously thought to be a NPC problem.
   (Got into the Guardian and into the Age p14 3/11/1979.
   "Within a few days, newspapers worldwide were saying that Khachian had
   solved the tr@veling s@lesman problem, which wasn't true - New Sci'ist '87)
   Also see  K a r m a r k a r.
   [Also search for: LinearProgramming].

%A G. L. Miller
%T Graph isomorphism, general remarks
%J JCSS
%V 18
%P 128-142
%D 1979
%K jrnl, JCSS, c1979, c197x, c19xx, maths, graph, isomorphism, graphs,
   problem, valence
%X complexity of graph isomorphism is an open question.
   Some results about the structure of the problem
   especially about valence of graphs.
   [<A HREF="http://doi.acm.org/10.1145/800105.803404">doi:10.1145/800105.803404</A>]['10].
   [Also search for: maths graph isomorphism].

%A S. Fortune
%A J. Hopcroft
%T A note on Rabin's nearest-neighbor algorithm
%J IPL
%V 8
%N 1
%P 20-23
%M JAN
%D 1979
%K jrnl, IPL, c1979, c197x, c19xx, nearest neighbour algorithm, probabilistic,
   hash, hashing, closest pair, points
%X "... finding the closest pair of a set of pts in Euclidean space. The running
   time of [R's] alg. using the worst-case expected-time measure is linear. This
   compares with time O(n log n) for the best of the known deterministic algs.
   ... most of the speedup of R's alg. is due to the hashing, & not to the
   probabilistic nature of the basic alg. ..."
   -- [<A HREF="https://doi.org/10.1016/0020-0190(79)90085-1">doi:10.1016/0020-0190(79)90085-1</A>]['23].

%A D. G. McVitie
%A L. B. Wilson
%T Stable marriage assignment for unequal sets
%J BIT
%V 10
%P 295-309
%D 1970
%K jrnl, stable marriage algorithm, problem, match, matching, preference,
   c1970, c197x, c19xx
%X (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Graph/Stable/">stable-marriage</A>].)

%A B. W. Kernighan
%A S. Lin
%T An efficient heuristic procedure for partitioning graphs
%J Bell Syst. Tech. J.
%N 2
%V 49
%P 291-307
%M FEB
%D 1970
%K jrnl, c1970, c197x, c19xx, maths, graph, graphs, partition, partitioning,
   algorithm, heuristic, layout, cut
%X pdf@[<A HREF="http://m.bell-labs.com/who/bwk/partitioning.pdf">bell</A>]['10],
   pdf@[<A HREF="http://www.cs.princeton.edu/~bwk/btl.mirror/new/partitioning.pdf">pr'nceton</A>]['10].
  ("Let G(V,E) be a graph, & let V be the set of nodes & E the set of edges.
   The alg. attempts to find a partition of V into 2 disjoint subsets A & B of
   equal size, such that the sum of the weights of the edges between nodes in A
   & B, T, is minimized. ... The alg. attempts to find an optimal series of
   interchange operations between elements of A & B which maximizes ... & then
   executes the ops, producing a partition of the graph to A & B.[1]"
   -- KLalg@[<A HREF="https://en.wikipedia.org/wiki/Kernighan%E2%80%93Lin_algorithm">wikip</A>]['10].)

%A D. G. McVitie
%A L. B. Wilson
%T The stable marriage problem
%J CACM
%V 14
%N 7
%M JUL
%D 1971
%P 486-492
%K jrnl, stable marriage algorithm, problem, match, matching, preference,
   c1971, c197x, c19xx
%X used in university entrance allocation of students to universities. UCCA
   Algorithm uses recursion reminiscent of continuations.
   -- [<A HREF="http://doi.acm.org/10.1145/362619.362631">doi:10.1145/362619.362631</A>]['05].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Graph/Stable/">stable-marriage</A>].)

%A D. M. Perlman
%T Isomorph rejection on power sets
%J SIAM J. Comput.
%V 3
%N 3
%P 177-183
%M SEP
%D 1974
%K jrnl, c1974, c197x, c19xx, isomorph rejection, power set, symmetry, group,
   backtrack, backtracking, back track, permutation, generator, maths, group,
   algorithm, coset representative
%X "If X is a finite set and G a finite group acting on X, then an action of
   G on P(X), the set of all subsets of X, is induced in a natural way. An
   efficient generating alg. is described which, when incorporated into a
   backtrack procedure, produces a system of distinct representatives for the
   action of G on P(X)."
   -- [<A HREF="http://dx.doi.org/10.1137/0203013">doi:10.1137/0203013</A>]['10].
   [Also search for: isomorph rejection].

%A V. R. Pratt
%T Every prime has a succinct certificate
%J SIAM J. Comput.
%V 4
%N 3
%M SEP
%D 1975
%P 214-220
%K jrnl, prime, number, certificate, verify, NP, NPC, primes, primality,
   check, test, testing, c1975, c197x, c19xx
%X "To prove that a number n is composite, it suffices to exhibit the working
   for the multn of a pair of factors. This working, represented as a string, is
   of length bounded by a polynomial in log2 n. We show that the same property
   holds for the primes. It is noteworthy that almost no other set is known to
   have the property that short proofs for membership or nonmembership exist for
   all candidates without being known to have the property that such proofs are
   easy to come by. It remains an open problem whether a prime n can be
   recognized in only (log2^alpha)(n) opns of a Turing m/c for any fixed
   alpha. The proof system used for certifying primes is as follows.
   Axiom. $(x,y,1).
   Inference Rules.
      R1: (p,x,a),q |- (p,x,qa) provided
               x^((p - 1)/q) not_equiv 1 (mod p), and q|(p-1).
      R2: (p,x,p-1) |- p provided x^(p-1) equiv 1 (mod p).
   Theorem 1. 'p is a theorem' equiv 'p is a prime'.
   Theorem 2. 'p is a theorem' superset p' has a proof of ceil(4 log2 p) lines'.
   -- [<A HREF="http://dx.doi.org/10.1137/0204018">doi:10.1137/0204018</A>]['10].
   [Also search for: primality].

%A P. Pritchard
%T A sublinear additive sieve for finding prime numbers
%J CACM
%V 24
%N 1
%M JAN
%D 1981
%P 18-23
%K jrnl, c1981, c198x, c19xx, prime, number, primes, sieve of Eratosthenese,
   algorithm
%X Finds primes in range 2 to N,
   theta(N/log log N) additions.
   (Also see Dunten, Jones, Sorenson 1996).

%A T. Granlund
%A P. L. Montgomery
%T Division by invariant integers using multiplication
%J PLDI '94 Proc. of the ACM SIGPLAN conf
%D 1994
%K conf, c1994, c199x, c19xx, zz0314, computer arithmetic, operation, integer,
   division, divide, div, alpha, mips, risc, sparc, algorithm, fast
%X "Integer division remains expensive on today's processors as the cost of
   integer multiplication declines. We present code seqs. for divn by arbitrary
   nonzero int.consts. & run-time invariants using int.multn. The algs. assume a
   two's complement architecture. Most also require that the upper half of an
   integer product be quickly accessible. We treat unsigned divn, signed divn
   where the quotient rounds towards zero, signed divn where the quotient rounds
   towards -infinity, & divn where the result is known a priori to be exact. We
   give some implementation results using the C compiler GCC."
   -- [<A HREF="http://dx.doi.org/10.1145/773473.178249">doi:10.1145/773473.178249</A>]['14].
   (Also see Newton-Raphson division
    NRD@[<A HREF="http://en.wikipedia.org/wiki/Newton%E2%80%93Raphson_division#Newton.E2.80.93Raphson_division">wikip</A>]['14].)

%A T. Akutsu
%A M. Halldrosson
%T On the approximation of largest common point sets and
   largest common subtrees
%J Proc. 5th Ann. Int. Symp. on Algorithms and Computation
%I SpringerVerlag
%S LNCS
%V 834
%P 405-413
%D 1994
%K conf, c1994, c199x, c19xx, largest, maximum, common, subtree, subtrees,
   point set, points, sets, sub tree
%X from a ref.

%A D. Coppersmith
%T An approximate Fourier transform useful in quantum factoring
%I IBM
%R RC 19642 7/12/'94
%D 1994
%K TR, c1994, c199x, c19xx, zz0323, quantum computing, Fourier Transform, QFT,
   Shor, Shors, algorithm, factoring, integer, integers, factors
%X "We define an approx. version of the Fourier transform on 2L elts, which is
   computationally attractive in a certain setting, & which may find application
   to the problem of factoring ints with a q.computer as is currently under
   investigation by Peter Shor. (1994 IBM Internal Report)
   -- [<A HREF="https://doi.org/10.48550/arXiv.quant-ph/0201067">arXiv</A>]['23].
   Also see, "... The best QFT algs. known (as of late 2000) require only
   O(n log n) gates to achieve an efficient approx'n. ...
   the QFT acts on a quantum state |x>=SUM_{i=0..N-1}(x_i |i>) and maps
   it to a q.state SUM_{i=0..N-1}(y_i |i>) according to the formula:
   y_k=(1/sqrt(N))SUM_{n=0..N-1}(x_n w^{nk}_N), k=0,1..,N-1.  ...
   w^n_N is a rotation ..."
   -- QFT@[<A HREF="https://en.wikipedia.org/wiki/Quantum_Fourier_transform">wikip</A>]['23].
   [Also search for: quantum Shor algorithm].

%A R. Grone
%A R. Merris
%T The Laplacian spectrum of a graph II
%J SIAM J. on Discrete Mathematics
%V 7
%N 2
%P 221-229
%D 1994
%K jrnl, c1994, c199x, c19xx, maths, graph, graphs, discrete, Laplacian matrix,
   spectrum, spectral, majorization, Eigenvalue, Eigenvalues
%X "Let G be a graph. Denote by D(G) the diagonal matrix of its vertex degrees
   & by A(G) its adjacency matrix. Then L(G)=D(G)-A(G) is the Laplacian matrix
   of G. The 1st section ...devoted to properties of Laplacian integral graphs,
   those for which the Laplacian spectrum consists entirely of integers. The
   second ...relates the degree seq. & the Laplacian spectrum through
   majorization. The third ...introduces the notion of a d-cluster, using it to
   bound the multiplicity of d in the spectrum of L(G)."
   -- [<A HREF="http://dx.doi.org/10.1137/S0895480191222653">doi:10.1137/S0895480191222653</A>]['08].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Laplacian_matrix">wikip</A>]['08].)

%A D. Eppstein
%T Offline algorithms for dynamic minimum spanning tree problems
%J J. Algorithms
%V 17
%P 237-250
%D 1994
%O Tech. Rep. 92-04, ICS, UCI, '92;
   2nd Worksh. Alg. and Data Struct., LNCS 519, 392-399, '91.
%K jrnl, trees, MST, update, updating, off-line, geometric, planar point set
%X ... graph subject to edge weight modifications.  Seq' of MSTs is
   computed off-line, *after* the seq of mod's is known. ...
   O(log n) work per mod' where n = # of vertices. ...
   solves offline geometric MST problem for planar point set subject
   to insertion and del'n; ... O((log n)**2) work per mod for the
   Euclidean metric and O(log n log log n) for the rectilinear metric.
   -- [<A HREF="http://www.ics.uci.edu/~eppstein/pubs/Epp-TR-92-04.pdf">TR 92 04</A>][11/'02],
   &  [<A HREF="http://www.ics.uci.edu/~eppstein/pubs/all.html">pubs</A>][11/'02].

%A B. Dunten
%A J. Jones
%A J. Sorenson
%T A space efficient fast prime number sieve
%J IPL
%V 59
%P 79-84
%M JUL
%D 1996
%K jrnl, IPL, c1996, c199x, c19xx, prime, primes, sieve of Eratosthenese,
   algorithm, sublinear, zz0996
%X [Also search for: Pritchard 1981].

%A M. O. Rabin
%T Probabilistic algorithms
%B Algorithms and Complexity
%E J. F. Traub
%I AcademicPress
%D 1976
%P 21-39
%K probabilistic, prime, number, Miller, primality, primes, witness, test,
   testing, algorithm,  c1976, c197x, c19xx
%X [Also search for: primality].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Primes/">primality</A>].)

%A M. O. Rabin
%T Probabilistic algorithm for testing primality
%J J. of Number Theory
%V 12
%P 128-138
%D 1980
%K jrnl, c1980, c198x, c19xx, prime, number, numbers, primes, primality,
   factors, witness, test, testing, Miller, probabilistic, algorithm, algorithms
%X "We present a practical probabilistic alg. for testing large numbers of
   arbitrary form for primality. [It] has the feature that when it determines a
   number composite then the result is always true, but when it asserts that a
   number is prime there is a provably small probability of error. The alg. was
   used to generate large numbers asserted to be primes of arbitrary and special
   forms, inc. v.large numbers asserted to be twin primes. Theor.foundations as
   well as details of implementation and experimental results are given."
   -- [<A HREF="http://dx.doi.org/10.1016/0022-314X(80)90084-0">doi:10.1016/0022-314X(80)90084-0</A>]['11].
   [Also search for: primality].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Primes/">primality</A>].)

%A S. S. Reddi
%T Alternate solutions to the cigarette smoker's problem without conditionals
%J IPL
%V 6
%N 1
%P 22-24
%M FEB
%D 1977
%K jrnl, IPL, c1977, c197x, c19xx, fork, conditional

%A D. H. Redelmeier
%T Counting polyominoes: yet another attack
%J Discrete Mathematics
%V 36
%D 1981
%P 191-203
%K polyominoe, pentominoe, enumerate, enumeration, c1981, c198x, c19xx
%X up to n=24 in 10 months of computer time
   [Also search for: polyomino].

%A E. Robertson
%A I. Munro
%T NP-completeness, puzzles and games
%J Utilas Mathematica
%V 13
%D 1978
%P 99-116
%K NP, NPC, complexity, instant insanity

%A J. S. Rohl
%T Programming improvements to Fike's algorithm for generating permutations
%J COMPJ
%P 156-159
%V 19
%N 2
%D 1976
%K jrnl, COMPJ, c1976, c197x, c19xx, permute, permutation, Fike, Jeff Rohl,
   JSRohl, enumerate, enumeration, generator
%X "... Fike describes an elegant new algorithm for generating permutations &
   gives two procedures implementing this algorithm. In this paper we give
   improved versions with comparative measurements on two machine/compiler
   systems. ... show that on one of the systems rec. proc. is the fastest."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/19.2.156">doi:10.1093/comjnl/19.2.156</A>]['08].

%A J. S. Rohl
%T Generating permutations by choosing
%J COMPJ
%V 21
%N 4
%P 302-305
%D 1978
%K jrnl, COMPJ, permute, permutation, algorithm, n queens, n-queens, 8-queens,
   c1978, c197x, c19xx, enumerate, enumeration, generate, generator, recursion,
   JSRohl, nqueens
%O correction V22 N2 p191 '79
%X "...give a simple, general algorithm which will produce arrangements of
   n marks taken r at a time where the marks may or may not be distinct.
   Various procedures based on the algorithm are presented, some producing the
   arrangements in lexicographical order, some not. The algorithm is easy to
   use as the basis for a solution to some comb'l problem as an example shows."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/21.4.302">doi:10.1093/comjnl/21.4.302</A>]['05].

%A J. S. Rohl
%T Recursion via Pascal
%I CUP
%D 1984
%K book, text, CUP, c1984, c198x, c19xx, good, recursion, removal, recursive,
   programming, algorithms, L3Ref, L2Ref, combinatorics, combinatorial,
   permutations, Towers of Hanoi, trees, Btree, Btrees, JSRohl
%X pb, uk us isbn:0521269342; uk us isbn13:978-0521269346;
   hb, uk us isbn:0521263298; uk us isbn13:978-0521263290.

%A A. Schonhage
%T Storage modification machines
%J SIAM J. Comput.
%V 9
%N 3
%M AUG
%D 1980
%P 490-508
%K jrnl, 1980, c198x, c19xx, SJC, complexity, SMM, fast, integer multiply,
   multiplications
%X show existence of an SMM that performs integer multiplication
   in linear time.

%A A. Schonhage
%A V. Strassen
%T Schnelle multiplikation grosser zahlen
%J Computing
%V 7
%P 281-292
%D 1971
%K jrnl, fast integer multiplication, multiply, algorithm, c1971, c197x, c19xx,
   computer arithmetic, BigInt, operation, convolution, FFT
%X Multiply two N digit binary numbers in O(N lg N lg lg N) steps  time.
      "An algorithm is given for computing the product of two N-digit binary
      numbers by O(N lgN lg lgN) steps. Two ways of implementing the alg are
      considered: multitape TMs & logical nets (with step=binary logical elt.)"
   -- pdf@[<A HREF="http://link.springer.com/article/10.1007/BF02242355">Springer</A>]['13].
   Also see arith@[<A HREF="https://en.wikipedia.org/wiki/Computational_complexity_of_mathematical_operations">wikip</A>]['21] and
    * SS_alg@[<A HREF="https://en.wikipedia.org/wiki/Sch%C3%B6nhage%E2%80%93Strassen_algorithm">wikip</A>]['21].
   [Also search for: fast integer multiplication].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Arithmetic/">more</A>].)

%A A. Schonhage
%A A. F. W. Grotefeld
%A E. Vetter
%T Fast Algorithms: A multitape Turing machine implementation
%I BI-Wissenschaftsverlag
%P 297
%D 1994
%K book, text, c1994, c199x, c19xx, computer algorithm, multiplication,
   large numbers, machines, multi-tape, algorithmic complexity, analysis,
   long integer arithmetic, BigInt, multi-precision, zz1097
%X "... describes an efficient implementation of long integer arithmetic and
   other multi-precision algorithms including a fast version of
   Schonhage-Strassen mutiplication. ..."
   [Also search for: Schonhage Strassen 1971].
   In H@rgrave, M0n@sh MOS511.2 S371.1F  - via alanf.  isbn:3411168919.
   -- [<A HREF="http://www.informatik.uni-bonn.de/~schoe/tp/TPbook.html">www</A>][6/'08].
   [Also search for: fast integer multiplication].

%A J. G. Herriot
%T Algorithm 472 Procedures for natural spline interpolation
%J Collected Algorithms from CACM
%V 16
%N 12
%P 763-768
%M DEC
%D 1973
%K approximation, natural, cubic, spline, splines, smooth curve, curves, ACM,
   c1973, c197x, c19xx
%X [<A HREF="http://doi.acm.org/10.1145/362552.362558">doi:10.1145/362552.362558</A>]['05]

%A A. B. Susts
%T Random number generators
%D 1960 ???
%K RNG, pseudo PRNG
%X source unknown

%A L. J. Stockmeyer
%A A. K. Chandra
%T Intrinsically difficult problems
%J Scientific American
%V 240
%N 5
%M MAY
%D 1979
%P 124-133
%K c1979, c197x, c19xx, news, views, intro, survey, N, P, NP, NPC,
   PNPproblem, complexity
%X [Also search for: PNPproblem].

%A G. de v. Smit
%T A comparison of three string matching algorithms
%J SPE
%V 12
%P 57-66
%D 1982
%M JAN
%K c1982, c198x, c19xx, jrnl, SPE, good text, sub string, substring, pattern,
   search, algorithm, find, match, matching, Knuth Morris Pratt, Boyer Moore,
   speed, time, complexity
%X 1. straightforward algorithm
   2. Knuth Morris Pratt
   3. Boyer Moore       -- usually best by far
   Also see  H o r s p o o l '80.
   [Also search for: string search algorithm].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/">Strings</A>].)

%A R. Sedgewick
%T Permutation generation methods
%J Computing Surveys
%V 9
%N 2
%M JUN
%D 1977
%P 137-164
%K jrnl, c1977, c197x, c19xx, permutations, generator, combinatorial algorithm,
   lexicographical order, random permutations, recursion

%A N. Suzuki
%A D. Jefferson
%T Verification of Presburger array programs
%J JACM
%V 27
%N 1
%M JAN
%D 1980
%P 191-205
%K program verification, correctness, proof

%A R. E. Shostak
%T On the sup-inf method for proving Presburger formulas
%J JACM
%V 24
%N 4
%M OCT
%D 1977
%P 529-543
%K theorem proving, program proof, verification, sup, inf, linear programming

%A R. E. Shostak
%T A practical decision procedure for arithmetic with function symbols
%J JACM
%V 26
%N 2
%M APR
%D 1979
%P 351-360
%K jrnl, JACM, c1979, c197x, c19xx, theorem proving, presburger arithmetic,
   verification
%X ?On p.353 seems it is not a decision procedure?
   [Also search for: theorem proving].

%A J. T. Schwartz
%T Fast probabilistic algorithms for verification of polynomial identities
%J JACM
%V 27
%N 4
%M OCT
%D 1980
%P 701-717
%K algorithm, equality

%A R. Solovay
%A V. Strassen
%T A fast Monte-Carlo test for primality
%J SIAM J. Comput.
%V 6
%N 1
%M MAR
%D 1977
%P 84-85
%K c1977, c197x, c19xx, prime, number, primality, test, random, Monte Carlo,
   Las Vegas, probabilistic algorithm
%X [Also search for: Rabin primality].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Primes/">primality</A>].)

%A J. D. Swift
%T Isomorph rejection in exhaustive search techniques
%J Proc. 10th Symposium in Appl. Math. of the American Math. Soc.
%M APR
%D 1958
%P 195-200
%K conf, c1958, c195x, c19xx, backtrack, symmetry, coset, maths, group,
   permutation algorithm, algorithm
%X [Also search for: isomorph rejection].

%A A. Shamir
%T On the security of DES
%J CRYPTO 85
%D 1985
%P 280-281
%K DES, code, cypher, cryptography

%A Philip of Macedon
%D 382-336 B.C.
%K divide and rule, conquer, binary recursion, divide et impera, origin, quote
%X whose ruling philosophy is  commonly described in high school textbooks as:
   (divide et impera = divide and rule)   [?source?]

%A J. Tarhio
%A E. Ukkonen
%T A greedy approximation algorithm for constructing shortest common
   superstrings
%J Theoretical Computer Science
%V 57
%D 1988
%P 131-145
%K TCS, LCS, SCS, SCSS, DNA, super string, sequence assembly, MolBio
%X Note  superSTRING not supersequence,   problem is NP-complete,
   approximate algorithm time O(m.n) for m strings of total length n
   they prove (n-k)>=(n-kmin)/2  or  k <= (n+kmin)/2
   where k=length of approx' SCSS and kmin is the len of scss.
   In all examples k <= 2.kmin   but not proven.

%A B. Weide
%T A survey of analysis techniques for discrete algorithms
%J Computing Surveys
%V 9
%N 4
%M DEC
%D 1977
%P 291-313
%K complexity, NP, NPC, approximation

%A B. D. McKay
%T Computing automorphisms and canonical labellings of graphs
%J Int. Conf. on Combinatorial Mathematics
%I SpringerVerlag
%S LNCS
%V 686
%P 223-232
%D 1977
%K conf, c1977, c197x, c19xx, maths, group, graph, automophism, isomorphism,
   canonical labelling, form, relabelling, relabel, canonization, algorithm,
   nauty, labeling
%X (Early- / pre- nauty.)
   "A new alg. is presented for the related problems of canonically labelling a
   graph or digraph and of finding its automorphism group. The automorphism
   group is found in the form of a set of less than n generators, where n is the
   # of vertices. An implementation is reported which is sufficiently conserving
   of time & space for it to be useful for graphs with over a 1000 vertices."
   -- [<A HREF="http://dx.doi.org/10.1007/BFb0062536">doi:10.1007/BFb0062536</A>]['10].
   [Also search for: canonical labelling maths graph], and
   [also search for: McKay c1981].

%A B. D. McKay
%T Practical graph isomorphism
%J Congressus Numerantium
   (10th. Manitoba Conference on Numerical Mathematics and Computing)
%V 30
%P 45-87
%D 1981
%K conf, c1981, c198x, c19xx, zz0903, Nauty, algorithm, maths, graph, graphs,
   canonical, labelling, labeling, automorphism group, canonization, generators
%X ... canonically labelling a graph ... generators for its
   automorphism group. ...               [at A N U as of '03]
   [<A HREF="http://cs.anu.edu.au/~bdm/nauty/PGI/">pdf</A>]['08],
   [<A HREF="http://cs.anu.edu.au/~bdm/papers/pgi.pdf">.pdf</A>][9/'03],
      [Also, J P Bern@rdy: As an exercise ... implemented (it in Haskell)
       -- haskell mail list, 23 Sept '03.  Look for "HGAL" at Haskell.org ]
   [Also search for: maths graph isomorphism] and
   [also search for: nauty maths graph].

%A D. Wood
%T The towers of Brahma and Hanoi revisited
%J J. Recreational Mathematics
%V 14
%N 1
%D 1981-82
%P 17-24
%K algorithm, tower
%X [see also  reve's puzzle]

%A J. R. Ullman
%T An algorithm for subgraph isomorphism
%J JACM
%V 23
%N 1
%P 31-42
%M JAN
%D 1976
%K jrnl, JACM, c1976, c197x, c19xx, Ullman, U76, P, NP, NPC, maths, graph,
   graphs, subgraph, isomorphism, isomorphic, algorithm
%X "Subgraph isomorphism can be determined by means of a brute-force tree-search
   enumeration proc.. ... new alg. is introduced that attains efficiency by
   inferentially eliminating successor nodes in the tree search. To assess the
   time actually taken by the new alg., subgraph isomorphism, clique detection,
   graph isomorphism, and directed graph isomorphism experiments have been
   carried out with random and with various nonrandom graphs. A parallel
   asynchronous logic-in-memory implementation of a vital part of the alg. is
   also described, although this h/w has not actually been built. The h/w
   implementation would allow very rapid determination of isomorphism."
   -- pdf@[<A HREF="http://doi.acm.org/10.1145/321921.321925">doi:10.1145/321921.321925</A>]['08].
      (Given H and G, ?H < G? is NPC.  But if H is *fixed*, the
      problem is polynomial in |G|, the polyn. depending on H.)
   (See [<A HREF="http://www.allisons.org/ll/AlgDS/Graph/Subgraph-Isomorphism/">algorithm</A>].)
   [Also search for: subgraph isomorphism].

%A L. G. Valiant
%T Relative complexity of checking and evaluating
%J IPL
%V 5
%N 1
%M MAY
%D 1976
%P 20-23
%K complexity, P, NP

%A J. W. Grossman
%A R. S. Zeitman
%T An inherently iterative computation of Ackermann's function (note)
%J Theoretical Computer Science
%V 57
%N 2-3
%M MAY
%D 1988
%P 327-330
%K TCS, Ackermann, recursion

%A A. V. Aho
%A M. J. Corasick
%T Efficient String Matching: An Aid to Bibliographic Search
%J CACM
%V 18
%N 6
%P 333-340
%M JUN
%D 1975
%K text, string, pattern, search, match, matching
%X finite automata for string substring sub  match matching algorithm
   multiple overlapping strings

%A Apostolico
%A Giancarlo
%T The Boyer-Moore-Galil String Searching ...
%J SIAM J. Comput.
%V 15
%N 1
%D 1986
%K SJC, text, sub string, substring, pattern, find, search, match,
   matching, algorithm, Boyer Moore Galil
%X see  B o y e r,  M o o r e
   [Also search for: string search algorithm].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/">Strings</A>].)

%A B. Commentz-Walter
%T A string matching algorithm that is fast on the average
%B Automata, Languages and Programming
%E H. A. Maurer
%I SpringerVerlag
%S LNCS
%N 71
%D 1979
%P 118-132
%K text, sub string, substring, find, search, searching, pattern,
   match, matching

%A M. C. Harrison
%T Implementation of the substring test by hashing
%J CACM
%V 14
%N 12
%P 777-779
%M DEC
%D 1971
%K jrnl, CACM, c1971, c197x, c19xx, text, sub string, substring, search,
   find, fast, hash, hashing, pattern match, matching, algorithm
%X Also see  Karp  &  Rabin, '87.

%A Galil
%T On Improving the Worst Case Running Time of the Boyer-Moore ...
%J PROC ICALP
%B LNCS 62
%P 241-250
%D 1978
%K conf, c1978, c197x c19xx, sub string, substring, pattern, find, match,
   matching, search, algorithm, Boyer Moore
%X [Also search for: string search algorithm].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/">Strings</A>].)

%A Apostolico
%A Preparata
%T Structural properties of the string statistics problem
%J JCSS
%V 31
%D 1985
%P 394-411
%K jrnl, JCSS, c1985, c198x, c19xx,  string, pattern, match, matching, stats

%A G. D. Knott
%T A numbering system for binary trees
%J CACM
%V 20
%N 2
%P 113-115
%M FEB
%D 1977
%K jrnl, CACM, c1977, c197x, c19xx, tree, generate, enumerate, enumeration,
   generation
%X pdf: [<A HREF="http://dx.doi.org/10.1145/359423.359434">doi:10.1145/359423.359434</A>]['12].

%A A. Proskurowski
%T On the generation of binary trees
%J JACM
%V 27
%N 1
%M JAN
%D 1980
%P 1-2
%K jrnl, JACM, c1980, c198x, c19xx, code, tree, traversal, ordering, enumerate,
   enumeration, generate
%X see also Knuth V1 section 2.3.4.5.
   pdf: [<A HREF="http://dx.doi.org/10.1145/322169.322170">doi:10.1145/322169.322170</A>]['12].

%A M. Solomon
%A R. A. Finkel
%T A note on enumerating binary trees
%J JACM
%V 27
%N 1
%P 3-5
%M JAN
%D 1980
%K jrnl, JACM, c1980, c198x, c19xx,  tree, generate, generator, enumeration,
   enumerate, combinatorics
%X pdf at [<A HREF="http://dx.doi.org/10.1145/322169.322171">doi:10.1145/322169.322171</A>]['12].

%T Computer Algebra: Symbolic and Algebraic Computation
%E B. Buchberger
%E G. E. Collins
%E R. Loos
%I SpringerVerlag
%P 293
%D 1983
%K text, book, conf, c1983, c198x, c19xx
%X uk us isbn:321181776X; uk us isbn13:978-3211817766.

%A J.H. Davenport
%A Y. Siret
%A E. Tournier
%T Computer Algebra
%I AcademicPress
%D 1988
%K text, book

%A F. K. Hwang
%T Latin squares and superqueens
%J Journal of Combinatorial Theory series A
%V 34
%N 1
%M JAN
%D 1983
%P 110-114
%K latin square, super queen, torus, n-queens, pandiagonal, Knut Vik design,
   n queens, nqueens

%A A. O. L. Atkin
%A L. Hay
%A R. G. Larson
%T Enumeration and construction of pandiagonal latin squares of prime order
%J Computers and Mathematics with Applications
%V 9
%N 2
%P 267-292
%D 1983
%K CMA, latin square, pandiagonal, cyclic, semi-cyclic, enumerate, enumeration,
   generate
%X enumeration and algebraic description for n <= 13.
   for n=5, 7, 11 there are n-3 squares up to == (renaming of entries)
   for n=13 there are 12,386 inequivalent squares, 10 cyclic in all directions,
   1560 cyclic in 1 direction,
   methods given to construct all squares for n > 11 and prime.

%A D. Gusfield
%T An efficient algorithm for the optimal stable marriage
%J JACM
%V 34
%N 3
%M JUL
%D 1987
%P 532-543
%K stable marriage, problem, match, matching, c1987, c198x, c19xx
%X minimises total pain does not favour men or women  O(n^4).
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Graph/Stable/">stable-marriage</A>].)

%A D. Gusfield
%A R. W. Irving
%T The Stable Marriage Problem: Structure and Algorithms
%I MITpress
%D 1989
%P 240
%K book, text, maths, graph matching, match, bipartite,
   problem, computer algorithm, CS, CSci, c1989, c198x, c19xx
%X us isbn:0262071185;  H@rgrave Mos 511.5 G982S.
   UK ed 2003; isbn:0262515520; isbn13:978-0262515528.
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Graph/Stable/">stable-marriage</A>].)

%A A. Lempel
%A J. Ziv
%T On the complexity of finite sequences
%J IEEE Trans. Inf. Theory
%V IT-22
%P 783-795
%M NOV
%D 1976
%K jrnl, text, data compression, sequence, string, random,
   randomness, LempelZiv, ZivLempel, c1976, c197x, c19xx
%X "Roughly speaking, the complexity of a finite fully specified
   sequence is a measure of the extent to which the given sequence
   resembles a random one." [p75]
   Scan S = s1 s2 ... sn from left to right,  add a new word to
   memory for every new substring of consec' [chars].
   e.g. S = 0 0 0 1 1 0 1 0 0 1 0 0 0 1 0 1
              ---
      '' => 0.0 0 1.1 0.1 0 0.1 0 0 0.1 0 1  complexity = min |history|
            ---   # #   ~~~~~ ~~~~~
                    +++ +++
                    =====             =====
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. Ziv
%A A. Lempel
%T A universal algorithm for sequential data compression
%J IEEE Trans. Inf. Theory
%V IT-23
%P 337-343
%M MAY
%D 1977
%K jrnl, text, data compression, compress, code, coding, encoding,
   sequence, string, algorithm, LempelZiv, ZivLempel, c1977, c197x, c19xx
%X ... encoding future segments of the source-output via maximum-length
   copying from a buffer containing the recent past output.  The
   transmitted codeword consists of the buffer address and the length
   of the copied segment. ...
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. Ziv
%A A. Lempel
%T Compression of individual sequences via variable rate encoding
%J IEEE Trans. Inf. Theory
%P 530-536
%M SEP
%D 1978
%K jrnl, data compress, compression, code, coding, encoding,
   sequence, string, algorithm, LempelZiv, ZivLempel, c1978, c197x, c19xx
%X also see the '77 paper.

%A A. George
%A J. W. H. Liu
%T An implementation of a pseudoperipheral node finder
%J TOMS
%I ACM
%V 5
%N 3
%M SEP
%D 1979
%P 284-295
%K band, banded matrix, peripheral node, nodes, maths, graph,
   heuristic, algorithm, eccentricity
%X Heuristic for putting a graph or matrix in banded form
   Graph G = < X, E >
   Eccentricity of a node  l(x)=max{d(x,y) | y in X}
   Diameter of G = max{l(x) | x in X}
   A node is peripheral if its eccentricity = diameter of graph
   Used to find "starting" nodes for many numerical algorithms.

%A L. Babai
%A L. Kucera
%T Canonical labelling of graphs in linear average time
%J FOCS
%I IEEE
%P 39-46
%M OCT
%D 1979
%K conf, FOCS, c1979, c197x, c19xx, maths, graph, canonical labelling,
   renumbering, canonization, labeling, isomorphism
%X (NB. 'average time', not worst case.)
   "Canonical labelling of graphs [CL] can be used, e.g., to test isomorphism.
   We prove that a simple vertex classification procedure results after only
   2 refinement steps in a CL of random gs. with probability 1-exp(-cn). With a
   slight mod., [get] a linear time CL alg. with only exp(-cn log n/log log n)
   probability of failure. An additional depth-first search yields a CL of all
   gs. in linear average time. "
   -- [<A HREF="http://dx.doi.org/10.1109/SFCS.1979.8">doi:10.1109/SFCS.1979.8</A>]['10], co$ts.
   (Also see canonization@[<A HREF="http://en.wikipedia.org/wiki/Graph_canonization">wikip</A>]['15].)
   [Also search for: canonical labelling maths graph].

%A J. Cooley
%A P. Lewis
%A P. Welch
%T The finite Fourier transform
%J IEEE Trans. on Audio and Electroacoustics
%V 17
%N 2
%P 77-85
%M JUN
%D 1969
%K jrnl, c1969, c196x, c19xx, zz0820, finite Fourier transform, fast, FFT,
   discrete, DFT, algorithm
%X "... The convolution & term-by-term product op'ns are defined & their equiv.
   ops. in transform space are given. A discussion of the transforms of
   stretched & sampled fns leads to a sampling theorem for finite seqs.. Finally
   these results are used to give a simple derivation of the fast Fourier
   transform algorithm."
   -- [<A HREF="https://doi.org/10.1109/TAU.1969.1162036">doi:10.1109/TAU.1969.1162036</A>]['20].
   (Also see DFT@[<A HREF="https://en.wikipedia.org/wiki/Discrete_Fourier_transform">wikip</A>]['20].)
   [Also search for: FFT algorithm].

%A T. C. Hu
%A W. T. Torres
%T Shortcut in the decomposition algorithm for shortest paths in a network
%J IBM J. Res. Develop.
%M JUL
%D 1969
%P 387-390
%V 13
%N 4
%K shortest paths, path, minimum distance, closure, block, window, algorithm

%A J. Y. Yen
%T Finding the lengths of all shortest paths in n-node nonnegative distance
   complete networks using 1/2N^3 additions and N^3 comparisons
%J JACM
%V 19
%N 3
%M JUL
%D 1972
%P 423-424
%K jrnl, JACM, c1972, c197x, c19xx, shortest path, paths, APSP,
   minimum distance, closure, algorithm, maths, graph
%X -- [<A HREF="https://doi.org/10.1145/321707.321712">doi:10.1145/321707.321712</A>]['23].

%A J. Y. Hu
%T On Hu's decomposition algorithm for shortest paths in a network
%J Operations Research
%V 19
%N 4
%P 983-985
%D 1971
%K OR, OpRes, shortest path, paths, Hu
%X m blocks, each with u nodes, overlaps have v nodes
   time ~  mu^3 + (m^2+6m-7)u^2v + (2m^2+10m-20)uv^2 + (m^2+6m-14)v^3
   if n~mu and u~2v
   this is O( mu^3 + m^2u^2 + m^2u^3 + m^2u^3 )  or  O( m^2 u^3 )  or O(n^2 u)

%A J. Liu
%A A. Sherman
%T Comparative analysis of the Cuthill-McKee and Reverse Cuthill-McKee
   ordering algorithms for sparse matrices.
%J SIAM J. Num. Anal.
%V 13
%N ?
%P 198-213
%D 1976
%K jrnl, SIAM, matrix, band, banded, diagonal, diagonals
%X To perm rows and cols to get matrix into a banded form.
   Ref in  B e r r y  et al '96

%A I. S. Duff
%T Survey of sparse matrix research
%J Proceedings IEEE
%V 65
%N 4
%P 500-535
%M APR
%D 1977
%K jrnl, sparse, band, bands, banded, triangular, block, blocks,
   Kron tearing, matrix, matrices, algorithm, diagonal, diagonals,
   diagonalise, c1977, c197x, c19xx

%A H. N. Gabow
%T Two algorithms for generating weighted spanning trees in order
%J SIAM J. on Computing
%V 6
%N 1
%P 139-150
%D 1977
%K jrnl, minimum, cost, spanning tree, trees, generate, c1977, c197x, c19xx,
   MST

%A R. M. Karp
%T Note: a characterization of the minimum cycle mean in a digraph
%J Discrete Mathematics
%V 23
%P 309-311
%D 1978
%K maths, graph, arc, path, cycle, negative
%X minimum cycle mean < 0  =>  negative cycle exists
   O(n.E) time algorithm

%A T. C. Hu
%A F. Ruskey
%T Circular cuts in a network
%J Mathematics of Operations Research
%V 5
%N 3
%M AUG
%D 1980
%P 422-434
%K MOR, OR, OpRes, network, maths, graph, max flow, min cut
%X nodes V1, V2, ...  with weights w1, ...
   arcs connect Vi and Vj have capacity bij
   Problem: pick a subset of nodes containing V1 s.t.
      total weight of subset is less than a given constant
      and the total arc capacity needed to separate the subset
      from the rest of the network is a min.
   special cases are = max-flow-min-cut  and the 0-1 knapsack problems

%A J. S. Rohl
%A T. D. Gedeon
%T The Reve's puzzle
%J COMPJ
%V 29
%N 2
%D 1986
%P 187-188
%K jrnl, reve, reves puzzle, recursion, towers of Hanoi, c1986, c198x, c19xx,
   COMPJ, JSRohl
%X "The Towers of Hanoi problem, explored in many recent Journal papers, is
   extended to consider a related problem, The Reve's Puzzle. It is shown that
   The Reve's Puzzle is a generalisation of the Towers of Hanoi problem and a
   number of questions concerning the elegance of the algorithms are posed."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/29.2.187">doi:10.1093/comjnl/29.2.187</A>]['05].

%A J. E. Hopcroft
%A J. K. Wong
%T Linear time algorithm for isomorphism of planar graphs (Preliminary Report)
%J Proc. 6th Ann. Symp. on Theory of Computing
%I ACM
%P 172-184
%D 1974
%K conf, c1974, c197x, c19xx, planar, maths, graph, isomorphism, graphs,
   STOC STC STOC74 STOC6
%X "... arbitrary planar graphs & improved to O(|V|log|V|) steps by Hopcroft &
   Tarjan. [here] the time bound for planar g. isomorphism is improved to
   O(|V|). [and] the alg. can be easily extended to partition a set of planar
   graphs into equivalence classes of isomorphic graphs in time linear in the
   total number of vertices in all graphs in the set. A random access model of
   computation ...is assumed. Although the proposed alg. has a linear asymptotic
   growth rate, at the present stage of development it appears to be inefficient
   on account of a rather large constant. ..."
   [<A HREF="http://doi.acm.org/10.1145/800119.803896">doi:10.1145/800119.803896</A>]['08].
   [Also search for: graph isomorphism bounded degree].

%A M. Fontet
%T A linear algorithm for testing isomorphism of planar graphs
%J ICALP
%P 411-424
%D 1976
%K conf, ICALP, c1976, c197x, c19xx, maths, graph isomorphism, plane, planar
%X (i) via enews, and (ii) in DBLP as of 2OO8 with
   Max Fontet: Test d'isomorphie d'hypergraphes planaires,
   Automata Theory and Formal Languages pp.93-98, 1975.

%A D. J. Rose
%A R. E. Tarjan
%A G. S. Lueker
%T Algorithmic aspects of vertex elimination on graphs
%J SIAM J. Comput.
%V 5
%N 2
%P 266-283
%D 1976
%K jrnl, c1976, c197x, c19xx, zz0618, maths, graph, graphs, vertex elimination,
   fill-in, fillin, Gaussian elimination, sparse symmetric, linear, ordering,
   chordal, minimal triangulation, algorithm, undirected, directed
%X "We consider a graph-theoretic elimination process which is related to
   performing Gaussian elimination on sparse symmetric +ve definite systems of
   linear equns. We give a new linear-time alg. to calculate the fill-in
   produced by any elimination ordering, & we give two new related algs. for
   finding orderings with special properties. One alg., based on breadth-first
   search, finds a perfect elimination ordering, if any exists, in O(n+e) time,
   if the problem g. has n vertices & e edges. An extension of this alg. finds a
   minimal (but not necessarily minimum) ordering in O(ne) time. We conjecture
   that the problem of finding a minimum ordering is NP-complete."
   -- [<A HREF="https://doi.org/10.1137/0205021">doi:10.1137/0205021</A>]['18],
      Finds a use in 'optimal decomp by ...', H.-G. Leimer, 1993.
   [Also search for: minimal triangulation]  and  [also search for: Rose c1972].
     (BTW also, R.&T., 'Alg ... on *directed* graphs', SIAM J Appl Maths, 34(1),
     1978, [<A HREF=" http://www.jstor.org/stable/2100866">Jstor</A>]['18], and
     TR@[<A HREF="http://i.stanford.edu/pub/cstr/reports/cs/tr/75/531/CS-TR-75-531.pdf">stanf.</A>]['18].)

%A M. Stadel
%T A remark on the time complexity of the subtree problem
%J Computing
%V 19
%N 4
%P 297-302
%M DEC
%D 1978
%K c1978, c197x, c19xx, sub tree, subtree, trees, isomorphism, bounded degree
%X "... shown that the subtree problem may be solved in the general case in
   time O(n^2.5) and in the case of bounded degree in time O(n^2)
   (n denotes the length of the input).
 * [Q: Is T1 ~ a subtree of T2?]
   -- [<A HREF="http://dx.doi.org/10.1007/BF02252027">doi:10.1007/BF02252027</A>]['08].

%A D. W. Matula
%T Subtree isomorphism in O(n**(5/2))
%J Annals of Discrete Mathematics
%V 2
%P 91-106
%D 1978
%K c1978, c197x, c19xx, sub tree, subtree, trees, isomorphism
%X from a ref.

%A J. L. Bentley
%A B. W. Weide
%A A. C. Yao
%T Optimal expected time algorithms for closest point problems
%J TOMS
%I ACM
%V 6
%N ?
%P 563-580
%D 1980
%K Voronoi diagram, algorithm
%O Proc. 16th Ann. Allerton Conf. on Comm. Control and Comp. 843-851 1978.
%X describes a O(n) *average* time algorithm for 2d Voronoi diagram, provided
   points come from a uniform distribution.
   Generalises to n dimensions and any distribution that is bounded below on
   a region.
   Via enews

%A R. P. Brent
%T A linear algorithm for data compression
%J ACSC 10
%K conf, ACSC10, c1987, c198x, c19xx, data, compress, compression, code
%D 1987
%O Australian Computer Journal 19(2), May 1987, pp.64-68.
%X "... finds maximal common substrings in the input data using a simple
   hashing scheme, & repeated substrings are encoded using Huffman coding. Time
   & space requirements are proportional to the size of the input data. A
   modification which uses a bounded buffer is also described. The algorithm is
   simpler than comparable linear-time algorithms & gives excellent compression
   ratios on both text & binary files."
   See [<A HREF="http://wwwmaths.anu.edu.au/~brent/pub/pubsall.html">@ANU</A>]['07], inc. pdf.

%A P. Tischer
%T Data compression ?
%J ACSC 10
%P ??-??
%D 1987
%K ACSC, ACSC10, data, compress, compression, code

%A E. M. Reingold
%A J. Nievergelt
%A N. Deo
%T Combinatorial Algorithms: Theory and Practice
%I PrenticeHall
%D 1977
%K text, book
%X includes  O(log(n)) time to count bits in a word

%A H. Mannila
%A E. Ukkonen
%T A simple linear-time algorithm for in-situ merging
%J IPL
%V 18
%N 4
%P 203-208
%D 1984
%K jrnl, IPL, c1984, c198x, c19xx, sort, sorting, merge, merging,
   in situ, in-situ, insitu, inPlace, linear time, algorithm
%X "A simple alg. for merging two ordered lists in bounded workspace is
   given. [It] is developed by 1st finding an intuitively clear
   divide-&-conquer alg. with sublinear workspace, & then removing the
   workspace."
   -- [<A HREF="https://doi.org/10.1016/0020-0190(84)90112-1">doi:10.1016/0020-0190(84)90112-1</A>]['19].
   [Also search for: insitu merge].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Sort/Insitu/">in-situ</A>].)

%A J. M. Pallo
%T Enumerating, ranking and unranking binary trees
%J COMPJ
%V 29
%N 2
%D 1986
%K jrnl, COMPJ, c1986, c198x, c19xx, enumerate, enumeration, generate, count,
   ranking, binary, tree, trees, rank
%X "We introduce weight sequences, which are sequences of positive integers
   characterising binary trees, in order to generate lexicographically binary
   trees as a list. Algs. are developed to determine the posn of a given weight
   seq., and to generate the weight seq. of a given posn. We also use weight
   seqs. in order to study a transformation on binary trees. Furthermore, we
   make a link with term rewriting systems."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/29.2.171">doi:10.1093/comjnl/29.2.171</A>]['12]  (via AK).

%A Rui Feng Zhu
%A T. Takaoka
%T A technique for two-dimensional pattern matching
%J CACM
%V 32
%N 9
%M SEP
%D 1989
%P 1110-1120
%K pattern, search, find, match, matching, 2D, two dimensions, bit map
%X exact 2D pattern matching,
   pattern[1..P1,1..P2],  text[1..N1,1..N2]
   two methods
   (a) combination of Rabin Karp  and  the Knuth, Morris, Pratt 1D algorithm
       O(N1*N2+P1*P2) time  avg and worst  - optimal
       O(N1*N2+P1*P2) space on-line.
   (b) O(N1*N2*log(P2)/P2+P1*P2) time on avg

%A G. L. Miller
%A J. H. Reif
%T Parallel tree contraction
%J Adv. in Comp. Res.
%V 5
%P 47-72
%D 1989
%K jrnl, c1989, c198x, c19xx, zz0722, trees, problem, algorithm, expression,
   subexpression elimination, rake
%X "... introduces parallel tree contraction: a new bottom-up technique for
   constructing parallel algs. on trees. ... [solve] expression evaluation &
   subexp'n elimination. ... we show these applications only require time &
   processors on a randomized PRAM or processors on a deterministic PRAM. ..."
   -- pdf@[<A HREF="http://www.cs.cmu.edu/~guyb/paralg/papers/MillerReif89.pdf">cmu</A>]['22].
   (Also see TC@[<A HREF="https://en.wikipedia.org/wiki/Tree_contraction">wikip</A>]['22].)

%A A. Lingas
%T Subgraph isomorphism for biconnected outerplanar graphs in cubic time
%J Theor. Comp. Sci.
%V 63
%N 3
%P 295-302
%M MAR
%D 1989
%O Proc. 3rd Symp. on Theoretical Aspects of Comp. Sci., Jan. 1986, Orsay,
   and TR R-86-10, ida.liu.se.
%K jrnl, TCS, c1989, c198x, c19xx, DPA, maths, graph, graphs, biconnected,
   outerplanar
%X "A dynamic programming alg. for determining whether a biconnected outerplanar
   graph is isomorphic to a subgraph of another biconnected outerplanar graph
   is presented. The algorithm runs in cubic time."
   -- [<A HREF="http://dx.doi.org/10.1016/0304-3975(89)90011-X">doi:10.1016/0304-3975(89)90011-X</A>]['08].
   (Horvath et al ['06]: "A bicon. outerp. G has a unique Hamiltonian cycle
    which bounds the outer face of a planar embedding [and] can be computed
    efficiently [Lingas '89].")
   [Also search for: subgraph isomorphism].

%A G. Gonnet
%A J. I. Munro
%T Heaps on Heaps
%J SIAM J. Comput.
%V 15
%N 4
%P 964-971
%D ????
%O ICALP 82
%K heap, sort, binary search
%X uses a binary search over the path to a leaf node.
   via enews

%A L. Greengard
%A V. Rokhlin
%T A fast algorithm for particle simulations
%J J. of Computational Physics
%V 73
%N 2
%M DEC
%D 1987
%P 325-348
%K c1987, c198x, c19xx, n-body, n body problem, gravity, forces, quadtree,
   quad tree, Qtree
%X "An algorithm is presented for the rapid evaluation of the potential & force
   fields in systems involving large #s of particles whose interactions are
   Coulombic or gravitational in nature. ..."
   -- [<A HREF="https://doi.org/10.1016/0021-9991(87)90140-9">doi:10.1016/0021-9991(87)90140-9</A>]['22].
   Quadtree data struct used to achieve O(n) time.  via enews
   Also see QT@[<A HREF="https://en.wikipedia.org/wiki/Quadtree">wikip</A>]['22].

%A L.F. Greengard
%T The Rapid Evaluation of Potential Fields in Particle Systems
%I MITpress
%D 1988.
%K n-body, n body, problem
%X isbn:026207110X.
   Systems with over a million bodies are now being solved using
   these techniques.

%A D. S. Johnson
%A M. Yannakakis
%A C. H. Papadimitriou
%T On generating all maximal independent sets
%J IPL
%V 27
%N 3
%P 119-123
%M MAR
%D 1988
%K IPL, jrnl, c1988, c198x, c19xx, maximal independent set, maths, graph,
   graphs, MIS, sets, enumerate, enumeration, enumerating, generate, generating,
   polynomial delay, algorithm
%X "... generates all maximal independent sets of a g. in lex. order, with only
   polynomial delay between the output of 2 successive independent sets.
   We also show that there is no polynomial-delay alg. for generating all MISs
   in reverse lexicographic order, unless P=NP."  [!]  [8 refs].
   [<A HREF="http://dx.doi.org/10.1016/0020-0190(88)90065-8">doi:10.1016/0020-0190(88)90065-8</A>]['08].

%A N. L. Cramer
%T A representation for the adaptive generation of simple programs
%J Int. Conf. on Genetic Algorithms and Their Applications
%D 1985
%M JUL
%P 183-187
%K GA, genetic algorithm, machine learning, search, c1985, c198x, c19xx
%X ... used to produce two input, one output multiplication functions.

%A J. L. Szwarcfiter
%A P. E. Lauer
%T A search strategy for the elementary cycles of a directed graph
%J BIT
%V 16
%D 1976
%P 192-204
%K maths ,graph, cycle, loop, elementary, simple
%X They do it in time O(n + m*(c + 1)), where n,m and c are the numbers of
   vertices, edges and cycles, respectively.
   Brendan McK@y.  bdm of anucsd.oz.au  or  bdm659 of csc1.anu.oz.au ['90].

%A B. Monien
%A I. H. Sudborough
%T Bandwidth constrained NP-complete problems
%J 13th Symposium on the Theory of Computing
%I ACM
%D 1981
%P 207-217
%K STC, STC13, STC81, conf, c1981, c198x, c19xx, NP, NPC, complete,
   three, 3 satisfiability, independent set, vertex cover, dominating set,
   colourability
%X 3-satisfiability, independent set and vertex cover,
   simple max cut, partition into triangles, 3-dimensional matching,
   exact cover by 3 sets, dominating set, graph Grundy number,
   3 colourability, directed and undirected Hamiltonian circuit,
   bandwidth minimization, feedback vertex set and feedback arc set.

%A B.-C. Huang
%A M. A. Langston
%T Practical in-place merging
%J CACM
%V 31
%N 3
%P 348-352
%M MAR
%D 1988
%K jrnl, CACM, c1988, c198x, c19xx, in situ, insitu, merge, merging
%X "We present a novel, yet straightforward linear-time alg. for merging 2
   sorted lists in a fixed amount of additional space. Const. of proportionality
   ests. & empirical testing reveal that this proc. is reasonably competitive
   with merge routines free to squander unbounded additional memory, making it
   particularly attractive whenever space is a critical resource."
   -- [<A HREF="https://doi.org/10.1145/42392.42403">doi:10.1145/42392.42403</A>]['18],
      pdf@[<A HREF="http://akira.ruc.dk/~keld/teaching/algoritmedesign_f04/Artikler/04/Huang88.pdf">ruc.dk</A>]['18].
   [Also search for: insitu merge], also see (stable) H & L 1992.
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Sort/Insitu/">in-situ</A>].)

%A P. K. Pearson
%T Fast hashing of variable length strings
%J CACM
%V 33
%N 6
%M JUN
%D 1990
%K CACM, jrnl, perfect, hash, hashing, string, c1990, c199x, c19xx
%X He discusses use of hash functions of the form:
      h = 0; n = length(string);
      for i = 1 through n do
         h = Table [ h XOR string [i]];
      enddo; return h;
   where Table is a 256-byte array.  Each character in the string hashed
   costs an XOR operation and an indexed read from memory (above the costs
   of reading the character).  This function can "sometimes be modified to
   produce a minimal perfect hashing function over a modest list of words."

%A B. Jackson
%T Shortest circuit covers and postman tours in graphs with a
   nowhere zero 4-flow
%J SIAM J. on Computing
%V 19
%N 4
%P 659-665
%M AUG
%D 1990
%K jrnl, short, cover, tour, maths, graph, c1990, c199x, c19xx

%A Bing-Chao Huang
%A M. A. Langston
%Y Fast stable merging and sorting in constant extra space.
%J COMPJ
%V 35
%N 6
%P 643-650
%D 1992
%O Int. Conf. Computing and Information, Toronta May 1989, p71-79
%K merge, merging, in place, in-place, O(1), constant extra, space, algorithm,
   in situ insitu, in-situ, stable, sort, sorting,
   jrnl, COMPJ, ICCI, c1992, c199x, c19xx
%X claim good constant of proportionality too
   "...we presented a novel, yet straightforward linear-time algorithm for
   merging two sorted lists in a fixed amount of additional space. Constant of
   proportionality estimates & empirical testing reveal that this procedure is
   reasonably competitive with merge routines free to squander unbounded
   additional memory, making it particularly attractive whenever space is a
   critical resource. [here] devise a relatively simple strategy by which this
   efficient merge can be made stable, & extend our results in a nontrivial way
   to the problem of stable sorting by merging. [give] upper bounds on our
   algorithms' constants of proportionality, suggesting that in some
   environments (most notably external file processing) their modest run-time
   premiums may be more than offset by the dramatic space savings achieved."
   -- [<A HREF="https://doi.org/10.1093/comjnl/35.6.643">doi:10.1093/comjnl/35.6.643</A>]['18].
   [Also search for: insitu merge],  also see (unstable) H & L 1988.
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Sort/Insitu/">in-situ</A>].)

%A F. J. Urbanek
%T An O(log(n)) algorithm for computing the nth element of the solution
   of a difference equation.
%J IPL
%V 11
%N 2
%P 66-67
%M OCT
%D 1980
%K log n time, fibonacci, fast, difference equation, fibonaci,
   recurrence relation, jrnl, IPL, c1980, c198x, c19xx
%X | Fn+1 Fn   | = | 1  1 |
   | Fn   Fn-1 |   | 1  0 |
   now exponentiate RHS in log n steps
   see Gries and Levin same issue!
   *** [Also search for: fast Fibonacci recurrence].

%A D. Gries
%A G. Levin
%T Computing Fibonacci numbers (and similarly defined functions) in log time
%J IPL
%V 11
%N 2
%P 68-69
%M OCT
%D 1980
%K jrnl, IPL, log n time, fibonacci, fast, difference equation, fibonaci,
   recurrence relation, jrnl, IPL, c1980, c198x, c19xx
%X see Urbanek same issue!
   *** [Also search for: fast Fibonacci recurrence].

%A M. Sharir
%T Some observations concerning formal differentiation of set theoretic
   expressions
%J TOPLAS
%V 4
%N 2
%P 196-225
%M APR
%D 1982
%K jrnl, TOPLAS, differentiation, program algorithm, c1982, c198x, c19xx,
   strength reduction
%X [<A HREF="http://doi.acm.org/10.1145/357162.357166">TOPLAS '82</A>]10/'04]
   Also see  E a r l e y c1973 (c1974), and P a i g e & S c h w a r t z c1977.

%A R. Paige
%A S. Koenig
%T Finite differencing of computable expressions
%T TOPLAS
%V 4
%N 3
%P 402-454
%M JUL
%D 1982
%K jrnl, TOPLAS, differentiation, program, algorithm, c1982, c198x, c19xx,
   differentiable expression, optimisation, strength reduction
%X 'Finite differencing is a program optimization method that generalizes
   strength reduction, and provides an efficient implementation for a host of
   program transformations including "iterator inversion." Finite differencing
   is formally specified in terms of more basic transformations shown to
   preserve program semantics. Estimates of the speedup that the technique
   yields are given. A full illustrative example of alg. derivation is
   presented.'
   -- [<A HREF="http://doi.acm.org/10.1145/357172.357177">doi:10.1145/357172.357177</A>][10/'04]
   Also see  S h a r i r  c1982.

%A D. Gries
%T A note on a standard strategy for developing loop invariants and loops
%J IPL
%V 2
%N 1
%P 207-214
%M DEC
%D 1982
%K jrnl, IPL, c1982, c198x, c19xx, maximum sum interval, subarray, section,
   1D, 2D, square, rectangle, weight, problem. algorithm, verification,
   stepwise refinement, loop invariant, c1982, c198x, c19xx
%X -- [<A HREF="https://doi.org/10.1016/0167-6423(83)90015-1">doi:10.1016/0167-6423(83)90015-1</A>]['24].
   eg: given a seq' of numbers s1...sn find s[i..j] of max' sum
       NB. some #s may be negative.
   eg, 2D: given a boolean matrix find the largest square of true elements
   (Also see MSP@[<A HREF="https://en.wikipedia.org/wiki/Maximum_subarray_problem">wikip</A>]['24].)

%A N. Karmarkar
%T A new polynomial-time algorithm for linear programming
%J Combinatorica
%V 4
%P 373-395
%D 1984
%K jrnl, complexity, P, LinearProgramming, interior point,
   Khachian, c1984, c198x, c19xx
%X auth @ AT&T Bell Labs; issn:02099683.
   [Also search for: LinearProgramming].

%A G. Turan
%T On the succinct representation of graphs
%J Discrete Applied Mathematics
%V 8
%N 3
%P 289-294
%M JUL
%D 1984
%K jrnl, c1984, c198x, c19xx, unlabelled, unlabeled, planar, maths, graph,
   graphs, information, content, compress, compressed, data structure,
   dataStructure, DS, complexity, compression, encoding
%X "It is shown that unlabelled planar graphs can be encoded in 12n bits, and
   an asymptotically optimal representation is given for labeled planar graphs."
   p.290: "G a class of graphs, ... G[n] graphs on n vertices [in] G."
   p.290: "There is a repn of unlabelled planar graphs satisfying l(n) <= 12n."
   p.291: "There is a repn of labelled planar graphs satisfying
          l(n) = n ceil(log2 n) + 12n."
   -- [<A HREF="http://dx.doi.org/10.1016/0166-218X(84)90126-4">doi:10.1016/0166-218X(84)90126-4</A>]['08].
   [planar "4 bits / edge, ... loops & mult. edges"    -- see V i a n a, c2008.]
   [For planar G, if n=|V| > 3, e < 3v-6   ( < 2v-4 if no cycles of length 3).]
   [Also search for: complexity graph]  and  [also search for: compress graph].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/Graph/">graphs</A>].)

%A Adler
%A Karmarkar
%A Resende
%A Veiga
%T An implementation of Karmarkar's algorithm for linear programming
%J Math. Prog.
%V 44
%P 297-335
%D 1989
%K LinearProgramming, linear programming, problem, algorithm, Karmarkar,
   jrnl, c1989, c198x, c19xx
%X via enews
   [Also search for: LinearProgramming].

%A Adler
%A Karmarker
%A Resende
%A Viega
%D 1989
%T Data Structures and Programming Techniques for the implementation of
   Karmarkar's Algorithm
%J ORSA J. Computing
%V 1
%N 4
%P 84-106
%K LinearProgramming, linear programming, problem, algorithm, Karmarkar,
   jrnl, c1989, c198x, c19xx, dataStructure, DS
%X via enews
   [Also search for: LinearProgramming].

%A A. George
%A J. Liu
%T Computer Solution of Large Sparse Positive Definite Systems
%I PrenticeHall
%D 1981
%K book, text, c1981, c198x, c19xx, linear programming, problem, algorithm,
   Karmarkar, book, matrix, matrices, reverse Cuthill McKee, RCM, band, bands,
   banded, diagonals, eccentricity, node, vertex, graph
%X via enews;  also  B e r r y  et al '96.
   [Also search for: sparse matrix].

%A Gill
%A Murray
%A Saunders
%A Tomlin
%A Wright
%D 1986
%T On Projected Newton Barrier Methods for Linear Programming, and an
   Equivalence to Karmarkar's Projective Method
%J Math. Prog.
%V 36
%P 183
%K LinearProgramming, linear programming, problem, algorithm, Karmarkar
%X via enews
   [Also search for: LinearProgramming].

%A Lustig
%A Marsten
%A Shanno
%D 1989
%T Computational Experience with a Primal-Dual Interior Point Method for Linear
   Programming
%R Ga. Tech. Technical Report J-89-11.
%K LinearProgramming, linear programming, problem, algorithm, Karmarkar,
   primal dual
%X via enews
   [Also search for: LinearProgramming].

%A Lustig
%A Marsten
%A Shanno
%D 1990
%T On Implementing Mehrotra's Predictor-Corrector Interior Point Method for
   Linear Programming
%R Princeton Technical Report SOR 90-03.
%K LinearProgramming, linear programming, problem, algorithm,
   Karmarkar, predictor corrector
%X via enews
   [Also search for: LinearProgramming].

%A Marsten
%A Subramanian
%A Saltzman
%A Lustig
%A Shanno
%D 1990
%T Interior Point Methods for Linear Programming: Just Call
   Newton, Lagrange, and Fiacco and McCormick!
%J Interfaces
%V 20
%N 4
%P 105-116
%K LinearProgramming, linear programming, problem, algorithm, Karmarkar
%X via enews
   [Also search for: LinearProgramming].

%A E. W. Dijkstra
%T A note on two problems in connexion with graphs
%J Numerische Mathematik
%V 1
%P 269-271
%D 1959
%K weighted, graph, graphs, all pairs shortest paths, APSP, path, minimal,
   minimum, problem, algorithm, weight, closure, spanning tree, connection,
   SSSP, 1D DPA, c1959, c195x, c19xx, maths, connection
%X -- [<A HREF="https://doi.org/10.1007/BF01386390">doi:10.1007/BF01386390</A>]['23].
   [Also search for: SSSP algorithm].

%A K. Esselink
%T The order of Appel's algorithm
%J IPL
%V 41
%P 141-147
%D 1992
%K Appel, many body, n-body, n body, particle, problem, gravity, gravitational,
   simulation, simulate
%X says algorithm of Appel for n-body problem is O(n) not(n log(n)).

%A W. F. Lunnon
%T Counting polyominoes
%B Computers in Number Theory
%E A. O. L. Atkin
%E B. J. Birch
%P 347-352
%I AcademicPress
%D 1971
%K pentominoe, polyominoe, combinatorics, enumerate, enumeration, generate,
   count, c1971, c197x, c19xx
%X for 18 squares,  192,622,052  non-equivalent polyominoes.

%A W. F. Lunnon
%T Counting hexagonal and triangular polyoninoes
%B Graph Theory and Computing
%E R. C. Read
%I AcademicPress
%D 1972
%K pentominoe, polyominoe, triangular, hexagonal, grid, lattice,
   combinatorics, count, generate, enumerate, enumeration

%A W. F. Lunnon
%T Symmetry of cubical and general polyominoes
%B Graph Theory and Computing
%E R. C. Read
%I AcademicPress
%D 1972
%P 101-108
%K pentomino, polyominoe, combinatrics, count, generate, enumerate
%X number of p's in 2 and 3D with different symmetries, to units=6.

%A F. Gavril
%T Algorithms for minimum coloring, maximum clique, minimum covering by
   cliques, and maximum independent set of a chordal graph
%J SIAM J. Comput.
%V 1
%N 2
%P 180-187
%D 1972
%K jrnl, c1972, c197x, c19xx, zz0818, maths, graph, chordal, algorithm,
   colouring, clique, covering, independent, Rose, R orientation, rOrientation
%X "... Given a chordal graph, we present, ways for constructing efficient
    algs. for finding a minimum coloring, a minimum covering by cliques, a
   maximum clique, & a maximum independent set. The proofs are based on a
   theorem of D.Rose[3] that a finite g. is chordal iff it has some special
   orientation called an R-orientation. In the last part of this paper we prove
   that an infinite g. is chordal iff it has an R-orientation."
   -- [<A HREF="https://doi.org/10.1137/0201013">doi:10.1137/0201013</A>]['18].

%A W. F. Lunnon
%T A map-folding problem
%J Math. Comp.
%V 22
%P 193-199
%D 1968
%K map, maps, fold, folding, combinatorics, count, generate, enumerate
%X do not have

%A W. F. Lunnon
%T Map-folding revisited
%J Math. Comp.
%V ???
%P ???-???
%D 19??
%K map, maps, fold, folding, combinatorics, count, generate, enumerate,
   enumeration, c197x, c19xx
%X to appear in the ref I have, about 71 or 72 ?   do not have

%A W. F. Lunnon
%T Multidimensional map-folding
%J COMPJ
%V 14
%P 75-80
%D 1971
%K map, maps, fold, folding, combinatorics, count, generate, enumerate,
   enumeration, c1971, c197x, c19xx
%X do not have

%A W. F. Lunnon
%T The IU function: size of a free distributive lattice
%B Combinatorial Mathematics
%E D. J. Welsh
%I AcademicPress
%P 173-181
%D 1971

%A N. Tomizawa
%T On some techniques useful for solution of transportation network problems
%J Networks
%V 1
%N 2
%P 173-194
%D 1971
%K jrnl, c1971, c197x, c19xx, zz0823, maths, graph, network, primal dual,
   Hungarian method, algorithm, bipartite, matching, assignment, problem
%X "... an efficient alg. for solving transportation problems. The improvement
   over the existing algs. of the 'primal-dual' type ... negative-cost arcs are
   removed so that the Dijkstra's alg. may be applied. Esp., the alg. requires
   at most n^3 additions & comparisons when applied to an n-by-n assignment
   problem ..."
   -- [<A HREF="https://doi.org/10.1002/net.3230010206">doi:10.1002/net.3230010206</A>]['23].
   [Also search for: graph Hungarian method].
   Also see HAlg@[<A HREF="https://en.wikipedia.org/wiki/Hungarian_algorithm">wikip</A>]['23].

%A W. F. Lunnon
%T A postage-stamp problem
%J COMPJ
%V 12
%P 377-380
%D 1969
%K postage stamp, combinatorics, count, generate, enumerate

%A A. Shamir
%T Factoring numbers in O(logn) arithmetic steps
%J IPL
%V 8
%N 1
%P 28-32
%M JAN
%D 1978
%K jrnl, c1971, c197x, z9xx, zz0123, integer, factorisation, factorization,
   factoring, algorithm, primes
%X "A non-trivial factor of a composite # n can be found by performing arith.
   steps in a # proportional to the # of bits in n, & thus there are extremely
   short straight-line factoring programs. However, this theoretical result does
   not imply that natural numbers can be factored in polynomial time in the
   Turing-m/c model of complexity, since the numbers operated on can be as big
   as 2 to the power c n-squared, thus requiring exponentially many bit ops."
   -- [<A HREF="https://doi.org/10.1016/0020-0190(79)90087-5">doi:10.1016/0020-0190(79)90087-5</A>]['23].
   [Also search for: integer factorisation].

%A W. F. Lunnon
%T Four combinatorial problems
%J ???
%I Atlas Computer Laboratory
%V ??
%M JAN
%D 1971
%P 35-38
%K pentominoe, polyominoe, map fold maps folding, Dedekind's problem,
   postage stamp stamps, combinatorics, count, generate, enumerate,
   c1971, c197x, c19xx, zz0122
%X "This article is a brief review of four problems we have attacked in the past
   few years. They all share the following characteristics: they are intuitively
   appealing and easy to pose; but they are (it seems) impossible to solve in
   any meaningful sense, and the only effective computational approach to them
   is direct enumeration; the functions f(n) involved grow exponentially, and
   with them the computing time required; but the computer space required is
   very small. ..."
   -- paper@[<A HREF="http://www.chilton-computing.org.uk/acl/literature/acl/p017.htm">www</A>]['22].

%A W. F. Lunnon
%T Counting multidimensional polyominoes
%J COMPJ
%V 18
%N 4
%P 366-367
%M NOV
%D 1975
%K pentominoe, polyominoe, combinatorics, multi dimensional, count,
   generate, enumerate, enumeration
%X dimension d
   n=17, d=2, 50,107,908 non-equivalent properly 2-D polyominoes

%A J. S. Madachy
%T Pentominoes - some solved and unsolved problems
%J J. Rec. Maths
%V 2
%N 3
%M JUL
%D 1969
%P 181-188
%K pentominoe, polyominoe, combinatorics, tile tiles, tiling, count, generate,
   enumerate, enumeration
%X # up to n=15 squares;   some tilings too.

%A H. L. Morgan
%T The generation of a unique machine description for chemical structures - a
   technique developed at chemical abstracts service
%J J. Chem. Doc.
%V 5
%N 2
%P 107-113
%M MAY
%D 1965
%K jrnl, c1965, c196x, c19xx, zz1220, maths, graph, color refinement algorithm,
   CRP, problem, isomorphism, colour, colouring, naive vertex classification,
   chemical compound, molecule
%X -- [<A HREF="https://doi.org/10.1021/c160017a018">doi:10.1021/c160017a018</A>]['20].
   ("begins with a uniform coloring of the Vs of 2 graphs G & H and refines the
   V-coloring step by step ... if two Vs have identical colors but differently
   colored n'hoods (with the multiplicities of colors counted), then these Vs
   get new different colors [etc] ... [but color-ref.] sometime fails to
   distinguish non-isomorphics graphs. ..." -- Arvind et al 2O15.
   "The Color Refinement alg. can be viewed as the 1-D version of ... the
   Weisfeiler-Leman alg." -- Grohe&Neuen 2020.)
   [Also search for: Weisfeiler Leman algorithm].

%A J. G. Fletcher
%T A program to solve the pentomino problem by the recursive use of macros
%J CACM
%V 8
%N 10
%M OCT
%D 1965
%P 621-623
%K pentominoe, polyominoe, combinatrics, tile, tiles, tiling
%X fit the 12 pentominoes into a 60 square plane area
   3 x 20   2 solutions (non-equivalent under rotation and reflection)
   4 x 15   368 solutions
   5 x 12   1010 solutions
   6 x 10   2339 solutions
   two  5 x 6 boxes 2 solutions
   8 x 8 box with 2 x 2 hole in centre  65 solutions.

%A F. Harary
%A E. M. Palmer
%A R. C. Read
%T On the cell-growth problem for arbitrary polygons
%J Discrete Maths.
%V 11
%P 371-389
%D 1975
%K pentominoe, polyominoe, cell, cells, growth, polygon, combinatorics,
   triangle, square, hexagon, n-gon, count, generate, enumerate, enumeration

%A A. Motoyama
%A H. Hosoya
%T King and domino polynomials for polyomino graphs
%J J. Math. Physics
%V 18
%D 1977
%P 1485-1490
%K polyominoe, pentomino, domino, lattice, grid, count, generate, enumerate

%A D. M. Sunday
%T A very fast substring search algorithm
%J CACM
%V 33
%P 132-142
%D 1990
%K text, sub string, substring, find, search, match, matching, skip,
   c1990, c199x, c19xx
%X uses the skipping technique on pairs of characters --
   -- see  B o y e r,  M o o r e,  c1977
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/">Strings</A>].)

%A G. H. Gonnet
%T Handbook of Algorithms and Data Structures
%I AddisonWesley
%D 1984
%K algorithm, data structure, dataStructure, DS, ADS, L3Ref, L4Ref,
   book, text, c1984, c198x, c19xx
%X 1st ed 1984; uk us isbn:020114218X; uj us isbn13:978-0201142181.
   [Also search for: Gonnet c1991].

%A J. E. Hopcroft
%A J. D. Ullman
%T Set merging algorithms
%J SIAM J. Comput.
%V 2
%N 4
%M DEC
%D 1973
%P 294-303
%K jrnl, c1973, c197x, c19xx, set, merge, merging, union find, member, subset,
   partition, disjoint set, minimum spanning tree, MST, data structure,
   dataStructure, DS
%X considers problem of merging sets formed from n items
   s.t. name of set containing an item is known.
   Two different algorithms & data structure given.
   Time bounded by const*nG(n)
   where G(n) is a fn whose asympototic growth < any finite # of logs of n.
   [Also search for: union find].

%A G. M. Adel'son-Vel'skii
%A E. M. Landis
%T An algorithm for the organization of information
%J Soviet Mathematics Doklady
%V 3
%P 1259-1263
%D 1962
%K height balanced tree, binary search tree, AVL, AVL tree, trees,
   dataStructure, DS, jrnl, Adelson Velskii, Landis, c1962, c196x, c19xx
%X (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Tree/#AVL">AVL-tree</A>]['16].)

%A M. Kwan
%T Graphic programming using odd and even points
%J Chinese Math.
%V 1
%P 273-277
%D 1962
%K jrnl, c1962, c196x, c19xx, maths, graph, graphs, tour, tours, circuit,
   circuits, cycle, chinese postman problem, point, Eulerian
%X Find a minimum length closed walk that traverses each edge AT LEAST once.
   Finding an optimal solution in a graph with both directed & undirected edges
   is NPC.
   cf. [also search for: Eulerian cycle] or E.path.

%A L. R. Ford jr
%A D. R. Fulkerson
%T Flows in Networks
%I PrincetonUP
%D 1962
%K c1962, c196x, c19xx, maths, graph, graphs, network, maximum flow, flows,
   path, paths, problem, algorithm
%X rev ed 2010; pb us$37; uk us isbn:0691146675; uk us isbn13:978-0691146676.
   [Also search for: Ford Fulkerson] and [also search for: graph maximum flow].

%A C. A. R. Hoare
%T Quicksort
%J COMPJ
%V 5
%N 1
%P 10-15
%D 1962
%K jrnl, COMPJ, quick sort, quicksort, sorting, partition, algorithm,
  c1962, c196x, c19xx
%X see also C.A.R.Hoare Alg 63 Partition, Alg 64 Quicksort CACM V4 p321
   "A description is given of a new method of sorting in the random-access
   store of a computer. The method compares very favourably with other known
   methods in speed, in economy of storage, and in ease of programming. Certain
   refinements of the method, which may be useful in the optimization of inner
   loops, are described in the second part of the paper."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/5.1.10">doi:10.1093/comjnl/5.1.10</A>]['05],
      [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_05/Issue_01/050010.sgm.abs.html">paper@oup.co.uk</A>]['04].
   [Also search for: Hoare c196x].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Sort/">Sorting</A>].)

%A R. C. Prim
%T Shortest connection networks and some generalizations
%J Bell Systems Technical J.
%P 1389-1401
%M NOV
%D 1957
%K jrnl, Prims, maths, graph, graphs, network, minimum spanning tree, MST,
   algorithm, c1957, c195x, c19xx
%X (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Graph/Undirected/">Graphs</A>].)

%A R. Fletcher
%A C. M. Reeves
%T Function minimization by conjugate gradients
%J COMPJ
%V 7
%N 2
%P 149-154
%D 1964
%K jrnl, COMPJ, c1964, c196x, c19xx, zz0223, function, minimisation, minimise,
   gradient, numerical, algorithm, functionMin
%X "A quadratically convergent gradient method for locating an unconstrained
   local minimum of a fn of several variables is described. Particular
   advantages are its simplicity & its modest demands on storage, space for only
   three vectors being required. An ALGOL procedure is presented, & the paper
   includes a discussion of results obtained by its used on various test fns."
   -- [<A HREF="https://doi.org/10.1093/comjnl/7.2.149">doi:10.1093/comjnl/7.2.149</A>]['23].
   [Also search for: function minimisation].

%A M. J. D. Powell
%T An efficient method for finding the minimum of a function of several
   variables without calculating derivatives
%J COMPJ
%V 7
%N 2
%P 155-162
%D 1964
%K jrnl, COMPJ, c1964, c196x, c19xx, zz0223, function, minimisation, minimise,
   gradient, numerical, algorithm, functionMin
%X "A simple variation of the well-known method of minimizing a fn of several
  variables by changing one parameter at a time is described. ... is such that
   when the procedure is applied to a quadratic form, it causes conjugate
   directions to be chosen, so the ultimate rate of convergence is fast when the
   method is used to minimize a general fn. A further variation completes the
   method, & its ensures that the convergence rate from a bad approximation to a
   minimum is always efficient. Practical applications of the procedure have
   proved to be very satisfactory, & numerical examples are given in which fns
   of up to twenty variables are minimized."
   -- [<A HREF=" https://doi.org/10.1093/comjnl/7.2.155">doi:10.1093/comjnl/7.2.155</A>]['23].
   [Also search for: function minimisation].

%A R. E. Goldschmidt
%T Applications of Division by Convergence
%I MIT
%M JUN
%D 1964
%K MSc, c1964, c196x, c19xx, zz0621, fast, integer, arithmetic, division, div,
   Goldschmidt division, div
%X pdf@[<A HREF="http://dspace.mit.edu/bitstream/handle/1721.1/11113/34136725-MIT.pdf">mit</A>]['21.
   Also see, "... uses an iterative process of repeatedly multiplying both the
      dividend & divisor by a common factor F_i, chosen such that the divisor
      converges to 1. This causes the dividend to converge to the sought
      quotient Q. ..."
   -- G_div in div@[<A HREF="https://en.wikipedia.org/wiki/Division_algorithm">wikip</A>]['21].
   (< Q, R >:=N/D, N=numerator(dividend), D=denominator (divisor),
                   Q=quotient, R=remainder".)

%A J. W. J. Williams
%T Algorithm 232 Heapsort
%J CACM
%V 7
%N 6
%M JUN
%D 1964
%P 347-348
%K jrnl, CACM, heap sort, heapsort, sorting, algorithm, c1964, c196x, c19xx
%X theta(N log N) time
   -- [<A HREF="http://doi.acm.org/10.1145/512274.512284">doi:/10.1145/512274.512284</A>]['06].
   [Also search for: Floyd heap].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Sort/">Sorting</A>].)

%A R. W. Floyd
%T Algorithm 245: Treesort
%J CACM
%V 7
%N 12
%P 701
%M DEC
%D 1964
%K jrnl, CACM, c1964, c196x, c19xx, zz0517, sort, sorting, binary, heap,
   heapify
%X theta(N) time
   -- [<A HREF="https://doi.org/10.1145/355588.365103">doi:10.1145/355588.365103</A>]['17].

%A R. Durstenfeld
%T Algorithm 235: Random permutation
%J CACM
%V 7
%N 7
%P 420
%M JUL
%D 1964
%K jrnl, CACM, c1964, c196x, c19xx, zz0713, random permutation, permutations,
   perm, algorithm, shuffle
%X It applies N-1 random swaps to a given array, p[0..N-1], of N elements:
      for i := N-1 step -1 to 1 do p.swap(i, random(0, i)) od,
   where i <= random(i, j) <= j.
   -- [<A HREF="http://dx.doi.org/10.1145/364520.364540">doi:10.1145/364520.364540</A>]['13].

%A W. D. Maurer
%T An improved hash code for scatter storage
%J CACM
%V 11
%N 1
%P 35-38
%M JAN
%D 1968
%K jrnl, CACM, c1968, c196x, c19xx,  hash, hashing, code, collision,
   quadratic search, probe, probing

%A R. Morris
%T Scatter storage techniques
%J CACM
%V 11
%N 1
%M JAN
%D 1968
%P 38-44
%K jrnl, CACM, c1968, c196x, c19xx, hash, hashing, code, linear, random, probe,
   probing, chain, chaining, collision

%A J. B. Kruskal
%T On the shortest spanning subtree of a graph and the travelling salesman
   problem
%J Proc. Am. Math. Soc.
%V 7
%N 1
%P 48-50
%M FEB
%D 1956
%K Kruskals, maths, graph, graphs, network, minimum spanning tree, MST,
   travelling sales man, salesperson, person, problem, TSM, TSP, algorithm,
   jrnl, c1956, c195x, c19xx, traveling
%X (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Graph/Undirected/">Graphs</A>].)

%A R. M. Karp
%A M. O. Rabin
%T Efficient randomized pattern-matching algorithms
%J IBM J. Res. Dev.
%V 31
%N 2
%P 249-260
%M MAR
%D 1987
%K string, substring, search, pattern, match, matching, hash, hashing,
   algorithm, randomised, c1987, c198x, c19xx
%X very simple and almost always linear-time.
   Also see  H a r r i s o n '71,  and  B o y e r, M o o r e '77.
   [Also search for: substring search hashing].

%A D. E. Knuth
%A J. H. Morris
%A V. R. Pratt
%T Fast pattern matching in strings
%J SIAM J. Comput.
%V 6
%N 2
%P 323-350
%M JUN
%D 1977
%K jrnl, text, sub string, substring, find, match, search, pattern, matching,
   algorithm, c1977, c197x, c19xx
%X linear time in string length.    [Also see:  B o y e r,  M o o r e  1977]
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/">Strings</A>.])

%A S. van Huffel
%A J. Vandewalle
%T The Total Least Squares Problem: Computational Aspects and Analysis
%I SIAM
%S Frontiers in Appl. Math.
%V 9
%P 300
%D 1991
%K book, text, TLS, LSQ, RMS, approximation, error, noise, vanHuffel
%X us$50; isbn:0898712750; isbn13:978-0898712759.
   [Also search for: total least squares].
   [<A HREF="http://www.ec-securehost.com/SIAM/FR09.html">details</A>][11/'03].

%A G. H. Gonnet
%A R. Baeza-Yates
%T Handbook of Algorithms and Data Structures in Pascal and C
%I AddisonWesley
%P 424
%D 1991
%K book, text, good, c1991, c199x, c19xx, good, algorithm, data structure,
   dataStructure, DS, source code, L3Ref, L4Ref
%X 2nd ed 1991; uk us isbn:0201416077; uk us isbn13:978-0201416077;
   a very useful book.

%A P. D. Smith
%T Experiments with a very fast substring search algorithm
%J SPE
%V 21
%N 10
%P 1065-1074
%M OCT
%D 1991
%K jrnl, SPE, c1991, c199x, c19xx, text, sub string, substring, find,
   string, strings, search, pattern match, matching
%X (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/">Strings</A>].)

%A D. R. Morrison
%T PATRICIA - practical algorithm to retrieve information coded in
   alphanumeric
%J JACM
%V 15
%N 4
%P 514-534
%M OCT
%D 1968
%K jrnl, JACM, patricia tree, trees, trie, tries, data structure, dataStructure,
   DS, string, text, search, searching, compact suffix tree, crit bit, radix,
   prefix, c1968, c196x, c19xx
%X Patricia - acronym, look at paper's title.    A Patricia Tree is a
   trie with the constraint that single-descendant nodes are eliminated.
   -- [<A HREF="http://doi.acm.org/10.1145/321479.321481">doi:10.1145/321479.321481</A>]['06].
   [AKA radix tree, crit-bit tree].

%A A. Hume
%A D. Sunday
%T Fast string searching
%J SPE
%V 21
%N 11
%P 1221-1248
%M NOV
%D 1991
%K jrnl, SPE, c1991, c199x, c19xx, text, sub string, substring, search, find,
   pattern match, matching, algorithm
%X [Also search for: string search algorithm].

%A G. Davies
%A S. Bowsher
%T Algorithms for pattern matching
%J SPE
%V 16
%N 6
%P 575-601
%M JUN
%D 1986
%K jrnl, SPE, text, sub string, substring, pattern, find, match, matching,
   search, algorithm

%A L. Lovasz
%A M. Plummer
%T Matching Theory
%I NorthHolland
%D 1986
%K book, text, match, matching, graph, graphs, vertex, c1986, c198x, c19xx,
   maths, edge, incident, problem
%X "[given] A (weighted) graph G=(V,E), find the largest-size set of edges S
   from E such that each vertex in V is incident to at most one edge of S."
   -- [<A HREF="http://www2.toki.or.id/book/AlgDesignManual/BOOK/BOOK4/NODE164.HTM#matching">toki.or.id</A>][9/'05]

%A R. A. Baeza-Yates
%T Improved string matching
%J SPE
%V 19
%N 3
%P 257-271
%M MAR
%D 1989
%K text, strings, sub string, substring, pattern, find, search, match,
   matching, algorithm, jrnl, SPE, c1989, c198x, c19xx

%A O. Petersson
%A A. Moffat
%T A framework for adaptive sorting
%B Algorithm Theory - SWAT '92
%E O. Murmi
%E E. Ukkonen
%I SpringerVerlag
%S LNCS
%V 621
%P 422-433
%M JUL
%D 1992
%O 3rd Scandinavian Workshop on Algorithm Theory, Helsinki, 1992
%K conf, sort, sorting, adaptive, presort, sorted, sortedness, algorithm,
   SWAT, SWAT3, SWAT92
%X 15 refs.  M0n@sh, H@rgrave, Mos 517.59 S283/3

%A M. C. Golumbic
%T Algorithmic Graph Theory and Perfect Graphs
%I AcademicPress
%P 340
%D 1980
%K c1980, c198x, c19xx, interval graph, maths, graphs, text, book
%X 2nd ed.; uk us isbn:0444515305; uk us isbn13:978-0444515308.

%A M. C. Golumbic
%T Interval Graphs and Related Topics
%J Discrete Mathematics
%V 55
%P 113-121
%D 1985
%K c1985, c198x, c19xx, interval graph, maths, graphs, DM
%X via enews

%A M. B. Cozzens
%T Higher and Multi-dimensional Analogues of Interval Graphs, Ph.D. thesis
%I Dept. of Mathematics, Rutgers University, New Jersey
%D 1981
%K interval graph, maths, graphs, PhD thesis
%X via enews

%A F. S. Roberts
%T Discrete Mathematical Models
%I PrenticeHall
%D 1976
%K c1976, c197x, c19xx, interval graph, maths, graphs, text, book
%X via enews

%A F. S. Roberts
%T Graph Theory and its Applications to Problems of Society
%S NSF-CBSM Monograph No. 29
%I SIAM Publications
%D 1978
%K interval graph, maths, graphs, text, book
%X via enews

%A D. B. Johnson
%T Efficient algorithms for shortest paths in sparse networks
%J JACM
%V 24
%N 1
%P 1-13
%M JAN
%D 1977
%K jrnl, JACM, c1977, c197x, c19xx, Johnson's algorithm, all pairs, APSP,
   single source, shortest path, SSSP, paths, network, maths, sparse, graph
%X single source non-negative arcs:
      O( min( n^(1+1/k) + e, (n+e) log n))   n nodes, e edges, k>0 a fixed int
      O(e) on dense graphs.
   Single source all-pairs unrestricted graphs
      O(min( n^(2+1/k) +ne,  n^2 log n + ne log n)).
   -- [<A HREF="https://doi.org/10.1145/321992.321993">doi:10.1145/321992.321993</A>]['21].
   Also see alg@[<A HREF="https://en.wikipedia.org/wiki/Johnson%27s_algorithm">wikip</A>]['21].
   [Also search for: maths graph shortest path].

%A T. A. Williams
%A G. P. White
%T A note on Yen's algorithm for finding the length of all shortest paths
   in n-node non-negative distance networks
%J JACM
%V 20
%N 3
%M JUL
%D 1973
%P 389-390
%K jrnl, JACM, c1973, c197x, c19xx, Yen, algorithm, all pairs, shortest path,
   APSP, paths, maths, sparse graph
%X "... An error in Yen's algorithm is pointed out, and an
   alternative is offered which will produce correct results."
   -- [<A HREF="https://doi.org/10.1145/321765.321769">doi:10.1145/321765.321769</A>]['21].
   [Also search for: maths graph shortest path].

%A B. Srinivasan
%A V. K. Rao
%T On the shortest path algorithms for sparse graphs
%R 3
%D 1982
%I Divn. Computer Applications, Asian Inst. Technology, Bangkok

%A J. J. McGregor
%T Backtrack search algorithms and the maximal common subgraph problem
%J SPE
%V 12
%N 1
%P 23-34
%M JAN
%D 1982
%K jrnl, SPE, c1982, c198x, c19xx, Maximal Common Subgraph problem, MCS, graph,
   maths, backtrack, backtracking, chemical compound, similarity
%X "Backtrack algs. are applicable to a wide variety of problems. An efficient
   but readable version of such an alg. is presented & its use in the problem of
   finding the maximal common subgraph of 2 gs. is described. Techniques
   available in this application area for ordering & pruning the backtrack
   search are discussed. ... has been used successfully as a component of a
   program for analysing chemical reactions & enum. the bond changes which have
   taken place."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.4380120103">doi:10.1002/spe.4380120103</A>]['10].

%A M. L. Fredman
%A R. E. Tarjan
%T Fibonacci heaps and their uses in improved network optimization algorithms
%J JACM
%V 34
%N 3
%P 596-615
%M JUL
%D 1987
%K jrnl, JACM, c1987, c198x, c19xx, Fibonacci heap, heaps, priority q, queue,
   maths, graph, graphs, shortest paths, path, SSSP, dataStructure, DS
%X "... arbitrary deletion from an n-item heap in O(log n) amortized time and
   all other standard heap operations in O(1) amortized time. ... "
   -- [<A HREF=" http://doi.acm.org/10.1145/28869.28874">doi:10.1145/28869.28874</A>]['06].
   An application is to make Dijkstra's (1959) single source shortest paths
   alg O(|E|+|V|.log|V|)-time   (- T h o r u p '99), which is
   good for sparse graphs, and optimal in a comparison model.
   [Also search for: pairing heap]  and  [also search for: SSSP algorithm].

%A D. Jablonowski
%A V. A. Guarna jr
%T GMB: A tool for manipulating and animating graph data structures
%J SPE
%V 19
%N 3
%P 283-301
%M MAR
%D 1989
%K jrnl, c1989, c198x, c19xx, SPE, GMB, maths, graph, graphs, draw, drawing,
   layout, display, plot, plotting, Guarna
%X via enews

%A L. A. Rowe
%A M. Davis
%A E. Messinger
%A C. Meyer
%A C. Spirakis
%A A. Tuan
%T A browser for directed graphs
%J SPE
%V 17
%N 1
%P 61-76
%M JAN
%D 1987
%K maths, graph, graphs, draw, drawing, display, layout, plot, plotting
%X via enews
   [Also search for: graph drawing].

%A F.N. Paulisch
%A W.F. Tichy
%T EDGE: An extendible graph editor
%J SPE
%V 20
%N 1
%M JUN
%D 1990
%P 64-88
%K jrnl, SPE, EDGE, graph, graphs, tree, trees, draw, drawing, plot, plotting,
   maths, display, edit
%X via enews

%A R. Tamassia
%A G. Di Battista
%A C. Batini
%T Automatic Graph Drawing and Readability of Diagrams
%J IEEE Transactions On Systems, Man, And Cybernetics
%V 18
%N 1
%M JAN/FEB.
%D 1988
%P 61-79
%K TOSMC, maths, graph, graphs, tree, trees, draw, drawing, plot, plotting,
   display
%X via enews
   [Also search for: graph drawing].

%A K. Sugiyama
%A S. Tagawa
%A M. Toda
%T Methods for Visual Understanding of Hierarchical System Structures
%J IEEE Transactions On Systems, Man, And Cybernetics
%V SMC-11
%N 2
%M FEB
%D 1981
%P 109-125
%K TOSMC, tree, trees, draw, drawing, plot, plotting, display
%X via enews

%A L. B. Protsko
%A P. G. Sorenson
%A J. P. Tremblay
%A D. A. Schaefer
%T Towards the Automatic Generation on Software Diagrams
%J IEEE Transactions On Software Engineering
%V 17
%N 1
%M JAN
%D 1991
%P 10-21
%K TOSE, tree, trees, draw, drawing, plot, plotting, display
%X via enews

%A J. Q. Walker_II
%T A Node-positioning Algorithm for General Trees
%J SPE
%V 20
%N 7
%M JUL
%D 1990
%P 685-705
%K Walker, node, position, graph, graphs, tree, trees,
   draw, drawing, plot, plotting, layout, pretty print, format, display
%X via enews

%A C. Batini
%A E. Nardelli
%A R. Tamassia
%T A Layout Algorithm for Data Flow Diagrams
%J IEEE Transactions On Software Engineering
%V SE-12
%N 4
%M APR
%D 1986
%P 538-546
%K TOSE, graph, graphs, tree, trees, draw, drawing, plot, plotting, display
%X via enews
   [Also search for: graph drawing].

%A K.J. Supowit
%A E. Reingold
%T The Complexity of Drawing Trees Nicely
%J Acta Informatica
%D 1983
%P 377-392
%K tree, trees, draw, drawing, plot, plotting, display, layout
%X via enews
   [Also search for: graph drawing].

%A E. Reingold
%A J.S. Tilford
%T Tidier Drawing of Trees
%J IEEE Transactions On Software Engineering
%V SE-7
%N 2
%M MAR
%D 1981
%P 223-228
%K TOSE, tree, trees, draw, drawing, plot, plotting, display
%X via enews

%A J.G. Vaucher
%T Pretty-Printing of Trees
%J SPE
%V 10
%D 1980
%P 553-561
%K pretty print, printing, tree, trees, draw, drawing, plot, plotting, display,
   layout
%X via enews

%A G. Brightwell
%A P. Winkler
%T Counting linear extensions is #P-complete
%J Proc 23rd ACM Symp. on Theory of computing
%P 175-181
%D 1991
%K conf, extension, DAG, DAGs, count, number, enumeration, c1991, c199x, c19xx,
   ACM, partial order, partially ordered, topological sort, poset, TOM, TOMs,
   total order, totally, enumerate
%X "... counting the number of linear extensions of a given
   partially ordered set is #P complete. ..."
   -- [<A HREF="http://doi.acm.org/10.1145/103418.103441">doi.acm.org/10.1145/103418.103441</A>][2/'04].

%A Thomas M. J. Fruchterman
%A E.k. M. Reingold
%T Graph drawing by force-directed placement
%I SPE
%V 21
%N 11
%M NOV
%D 1991
%P 1129-1164
%K graph, graphs, draw, drawing, plot, plotting, layout, display,
   force directed, pretty print, format
%X via enews
   [Also search for: graph drawing].

%A H. W. Lenstra
%A C. Pomerance
%T A rigorous time bound for factoring integers
%J JAMS
%V 5
%N 5
%P 483-516
%M JUL
%D 1992
%K jrnl, c1992, c199x, c19xx, zz0123, factorisation, factorization, factoring,
   integer, prime, primes, class group relations algorithm, GRH, Schnorr, Seysen
%X "... probabilistic alg. is exhibited that factors any +ve int. into prime
   factors in expected time at most L_n[1/2, 1+o(1)] for n->inf, where
   L_n[a,b]=exp(b(log n)^a(log log x)^{1-a)). ..."
   -- [<A HREF="https://doi.org/10.1090/S0894-0347-1992-1137100-0">doi:10.1090/S0894-0347-1992-1137100-0</A>]['23].
   (Also see IF@[<A HREF="https://en.wikipedia.org/wiki/Integer_factorization">wikip</A>]['23].)

%A I. Rivin
%A R. Zabih
%T A dynamic programming solution to the n-queens problem
%J IPL
%D 1992 ???
%V 41
%N 5
%P ???-???
%K n-queens, nqueens, n queens problem, combinatorics, DP, DPA, algorithm
%X via enews.

%A R. A. Vowels
%T Division by 10
%J Australian Comp. J.
%V 24
%N 3
%P 81-85
%M AUG
%D 1992
%K jrnl, ACJ, c1992, c199x, c19xx, zz0621, fast, integer, arithmetic, division,
   by constant, constants, div, divisor, ten, div10 decimal, numeral, toString
%X "Division of a binary int. & a binary floating-point mantissa by 10 can be
   performed with shifts & adds, yielding a sig. improvement in h/w execution
   time, & in s/w execution time if no h/w div instn is available. Several algs.
   are given, appropriate to specific m/c word sizes, h/w & h/w instns available
   & depending on whether a remainder is required. The int. div algs. presented
   here contain a new strategy that produces the correct quotient directly,
   without the need for the supplementary correction required of previously-
   -published algs.. The algs. are competitive in time with binary coded decimal
   (BCD) div by 10. Both the int. & flpt algs. are an order of magnitude faster
   than conventional division."
   -- pdf@[<A HREF="https://50years.acs.org.au/content/dam/acs/50-years/journals/acj/ACJ-V24-N03-199208.pdf">www</A>]['21].

%A S. Minton
%A M. D. Johnston
%A A. B. Philips
%A P. Laird
%T Minimizing conflicts: A heuristic repair method for constraint satisfaction
   and scheduling problems
%J Artificial Intelligence
%V 58
%P 161-205
%D 1992
%K AI, n queens, nqueens, n-queens, combinatorics
%X via enews;     From the abstract:
   "We demonstrate empirically that on the n-queens problem, a technique
   based on this approach performs orders of magnitude better than
   traditional backtracking techniques."

%A E. B. Escott
%T Procede expeditif pour calculer un terme tres eloigne dans la serie de
   Fibonacci
   (Fast algorithm for calculating remote terms in the Fibonacci series)
%J L'Intermediaire des Mathematiciens
%V 7
%P 172-175
%D 1900
%K Fibonacci, recurrence relation, linear, series, fast, log, remote term,
   recursion, c1900, c190x, c19xx
%X From: Jeffrey Shallit,  shallit AT graceland.uwaterloo.ca  '93.
   [Also search for: fast Fibonacci recurrence].

%A J. C. P. Miller
%A D. J. Spencer Brown
%T An algorithm for evaluation of remote terms in a linear recurrence sequence
%J COMPJ
%V 9
%P 188-190
%D 1966
%K Fibonacci, recurrence relation, series, fast, log, c1966, c196x, c19xx,
   series, difference equation, calculate, jrnl, COMPJ, Gries, Levin, Urbanek,
   term, value
%X "A method is described for computing terms U[n] given by a linear recurrence
   relation from initial conditions near n=0, whereby, values for large n may
   be obtained without computing all intermediate values. The total number of
   operations is of order log n."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/9.2.188">doi:10.1093/comjnl/9.2.188</A>]['14],
      [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_09/Issue_02/090188.sgm.abs.html">paper@compj</A>]['04].
   From: Jeffrey Shallit,  shallit AT graceland.uwaterloo.ca   '93.
   *** [Also search for: fast Fibonacci recurrence].

%A M. D. Atkinson
%T The cyclic towers of Hanoi
%J IPL
%V 13
%N 3
%P 118-119
%D 1981
%K jrnl, IPL, tower, Hanoi, Reve, Reves, Reve's puzzel, recursion
%X via enews

%A D. E. Knuth
%A P. B. Bendix
%T Simple word problems in universal algebra
%B Computational Problems in Abstract Algebra
%E J. Leech
%P 263-297
%D 1970
%I Pergamon
%K c1970, c197x, c19xx, maths, group, groups, algorithm, word problem, algebra,
   coset
%X via enews.
   (See [<A HREF="http://en.wikipedia.org/wiki/Knuth-Bendix_completion_algorithm">wikip</A>]['09].)

%A J. Edmonds
%A R. M. Karp
%T Theoretical improvements in algorithmic efficiency for network flow problems
%J JACM
%V 19
%N 2
%P 248-264
%M APR
%D 1972
%K jrnl, JACM, c1972, c197x, c19xx, zz1021, maths, graph, graphs, network, flow,
   flows, max, maximum, Hitchcock transportation, augmenting path, min,
   minimum cost, problem, algorithm, Hungarian method, Ford Fulkerson
%X "... new algs. for the maximum flow problem, the Hitchcock transportation
   problem, & the general minimum-cost flow problem. ... the Ford-Fulkerson
   labeling method ... We show that, if each flow augmentation is made along an
   augmenting path having a min. # of arcs, then a max. flow in an n-node n/wk
   will be obtained after no more than ~(n a-n) augmentations; & then ...
   a max. flow will be determined within at most 1+logM/(M-1) if(t,S) augm's,
   where f*(t,s) is the value of the max. flow & M is the max. # of arcs across
   a cut. Next a new alg. is given for the min.-cost flow problem ..."
   -- [<A HREF="https://doi.org/10.1145/321694.321699">doi:10.1145/321694.321699</A>]['21] or
      [<A HREF="https://doi.org/10.1007/3-540-36478-1_4">doi:10.1007/3-540-36478-1_4</A>]['21].
   (Also see HAlg@[<A HREF="https://en.wikipedia.org/wiki/Hungarian_algorithm">wikip</A>]['21], and
    "... max. flow in a flow network in O(|V|.|E|^2) time. ..."
    -- E_and_K@[<A HREF="https://en.wikipedia.org/wiki/Edmonds%E2%80%93Karp_algorithm">wikip</A>]['21].)
    [Also search for: Tomizawa graph].

%A S. Kleene
%T General recursive functions of natural numbers
%J Math. Ann.
%V 112
%P 729-745
%D 1936
%X via enews

%A T. Bell
%A D. Kulp
%T Longest-match string searching for Ziv-Lempel compression
%J SPE
%V 23
%N 2
%P 757-771
%M JUL
%D 1993
%K jrnl, SPE, c1993, c199x, c19xx, longest match, search, Ziv Lempel, LZ, ZL,
   data, file, compress, algorithm

%A M. Dyer
%A R. Kannan
%T On Barvinok's algorithm for counting lattice points in fixed dimension
%J Maths of Op. Res.
%V 22
%P 545-549
%D 1993
%K jrnl, c1993, c199x, c19xx, zz0214, integral, integer, simplex, convex,
   polyhedron, count, point, points, Barvinok
%X "We describe a simplification of a recent polynomial-time alg. of
   A.I.Barvinok for counting the number of lattice points in a polyhedron in
   fixed D. ... show that only very elementary properties of exponential sums
   are needed to develop a polynomial-time alg.."
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.39.949">c'teseer</A>]['14],
      ps@[<A HREF="http://www.cs.cmu.edu/afs/cs.cmu.edu/user/kannan/public/www/Papers/barvinok.ps.Z">cmu</A>]['14].

%A H.-G. Leimer
%T Optimal decomposition by clique separators
%J Discrete Maths.
%V 113
%N 1-3
%M APR
%D 1993
%K jrnl, c1993, c199x, c19xx, zz0618, maths, graph, decomposition, clique,
   separator, algorithm, maximal prime subgraph, subgraphs
%X "... [Tarjan's 1985 O(mn)-time] alg. is modified, so that
   no new maximal prime subgraphs are generated, i.e. so that a graph is
   decomposed exactly into its maximal prime subgs. which is the
   unique minimal derived system of prime subgraphs."
   -- [<A HREF="https://doi.org/10.1016/0012-365X(93)90510-Z">doi:10.1016/0012-365X(93)90510-Z</A>]['18].
   (L's alg. esp. depends on Rose, Tarjan & Lueker 1976, and on Tarjan 1985.)
   [Also search for: graph decomposition] and [also search for: Tarjan c1985].

%A D. Pearson
%A V. V. Vazirani
%T Efficient sequential and parallel algorithms for maximal bipartite sets
%J J. of Algorithms
%V 14
%N 2
%P 171-179
%M MAR
%D 1993
%K jrnl, c1993, c199x, c19xx, maximal bipartite set, MBS, sets, subgraph,
   linear time, algorithm, maths, graph, graphs, maximum, cardinality, MBS
%X "A maximal bipartite set (MBS) in an undirected graph G = (V, E) is a
   maximal collection of vertices B subset of, or equal to, V whose induced
   subgraph is bipartite. ... present efficient sequential (linear time) &
   parallel (NC) algorithms for constructing an MBS."
   "... lin time, seq. alg greedily adds vertices as long as they do not
   introduce an odd-length cycle. [seems] to be no way to parallelize ...
   [and] parallel alg ... different approach."
   [<A HREF="http://dx.doi.org/10.1006/jagm.1993.1008">doi:10.1006/jagm.1993.1008</A>]['08].

%A M. Steel
%A T. Warnow
%T Kaikoura tree theorems: Computing the maximum agreement subtree
%J IPL
%V 48
%N 2
%P 77-82
%N NOV
%D 1993
%K jrnl, IPL, MolBio, c1993, c199x, c19xx, maximum, largest, agreement, subtree,
   MAST, problem, subtrees, common, sub tree, evolutionary
%X "... given a set S = {S1, S2,..., Sn} & 2 trees P & Q leaf-labelled by the
   elts. of S, find a maximum cardinality subset S0 of S s.t. P|S0 = Q|S0.
   ... arises in evolutionary tree construction ... . A superpolynomial time
   alg. for finding a max. agreement subt. of 2 binary trees was found by
   Kubicka et al. ... we will present an O(n**4.5 log n + V) alg. to determine
   the largest agr. subt. of 2 trees on n leaves, where V is the max. # of
   nodes in the trees. For ... trees of max. degree k, there are 2 algs
   presented: one has running time O(k! n**2 + V) ...other...
   O(k**2.5 n**2 log n + V). ... also apply when the trees are constrained to
   be rooted; in this case a max. agreement subtree is also constrained to be
   rooted. Each of the algs. we present can be modified to produce a max.
   agreement subt., rather than computing only the size. ..."
   [<A HREF="http://dx.doi.org/10.1016/0020-0190(93)90181-8">doi:10.1016/0020-0190(93)90181-8</A>]['08].

%A S. K. Park
%A K. W. Miller
%T Random number generators: Good ones are hard to find
%J CACM
%V 31
%N 10
%P 1192-1201
%M OCT
%D 1988
%K jrnl, CACM, c1988, c198x, c19xx, random number generator, RNG,
   pseudo PRNG, algorithm
%X via enews

%A J. L. Bentley
%A M. D. McIlroy
%T Engineering a sort function
%J SPE
%V 23
%N ?
%P 1249-1265
%M ?
%D 1993
%K jrnl, SPE, sort, sorting, algorithm, quick, quicksort, speed,
   time complexity, c1993, c199x, c19xx, zz0603
%X M at Dartmouth.

%A G. Marsaglia
%T Remarks on choosing and implementing random number generators
%J CACM
%V 36
%N 7
%P 105-110
%M JUL
%D 1993
%K jrnl, CACM, c1993, c199x, c19xx, random number generator, RNG, pseudo PRNG,
   algorithm
%X via enews

%A J. Tarhio
%A E. Ukkonen
%T Approximate Boyer-Moore string matching
%J SIAM J. Comput.
%V 22
%N 2
%P 243-260
%P APR
%D 1993
%O TR A-1990-3 Dept. Computer Science, University of Helsinki MAR '90
%K jrnl, c1993, c199x, c19xx, SJC, match, search, k-mismatch, kmismatch,
   mismatch, change, substitution, indel, insert, delete, Boyer Moore,
   sub string, substring, pattern, find, matching, search, algorithm
%X |pattern|=m, |text|=n, <= k mismatches, |alphabet|=c
   give O(kn{1/(m-k) + (k/c)}) algorithm, and
   a related algorithm for <= k differences (indel and/or change).
   Claim fast in practice.
   -- [<A HREF="http://dx.doi.org/10.1137/0222018">doi:10.1137/0222018</A>]['08].

%A J. Hopcroft
%A R. Tarjan
%T Efficient planarity testing
%J JACM
%V 21
%N 4
%D 1974
%K jrnl, ACM, JACM, planar graph, graphs, test, algorithm, c1974, c197x, c19xx,
   maths, linear
%X "...describes an efficient alg. to determine whether an arbitrary graph G
   can be embedded in the plane. ... may be viewed as an iterative version of a
   method originally proposed by Auslander and Parter and correctly formulated
   by Goldstein. The alg. used depth-first search and has O(V) time and space
   bounds, where V is the number of vertices in G. An ALGOL implementation of
   [it] succesfully tested graphs with as many as 900 vertices in < than 12s."
   [<A HREF="http://doi.acm.org/10.1145/321850.321852">doi:10.1145/321850.321852</A>]['05]
   via enews sequential alg, linear time.  See N. Deo JACM 23(1) '76
   '...does not look for K5 or K3,3 minors, but attempts to find an embedding of
   the graph. If no such embedding is found, the graph is nonplanar.' -KM '05.

%A D. T. Gillespie
%T A general method for numerically simulating the stochastic time evolution of
   coupled chemical reactions
%J J. Computational Phys.
%V 22
%N 4
%P 403-434
%M DEC
%D 1976
%K jrnl, c1976, c197x c19xx, zz0520, Doob, Gillespie's algorithm, stochastic,
   simulation, reaction, pandemic, epidemic, infection, transmission
%X "An exact method is presented for numerically calculating, within the
   framework of the stochastic formulation of chemical kinetics, the time
   evolution of any spatially homogeneous mixture of molecular species which
   interreact through a specified set of coupled chemical reaction channels. The
   method is a compact computer-oriented, Monte Carlo simulation procedure. ..."
   -- [<A HREF="https://doi.org/10.1016/0021-9991(76)90041-3">doi:10.1016/0021-9991(76)90041-3</A>]['20].
   Also see, "In probability theory, the Gillespie algorithm (or occasionally
     the Doob-Gillespie algorithm) generates a statistically correct trajectory
     (possible solution) of a stochastic equation. ..."
     -- G'sA@[<A HREF="https://en.wikipedia.org/wiki/Gillespie_algorithm">wikip</A>]['20].

%A N. Deo
%T Notes on Hopcroft and Tarjan's planarity algorithm
%J JACM
%V 23
%N 1
%D 1976
%K JACM, jrnl, planar graph, maths, graphs, test, testing, c1976, c197x, c19xx
%X via enews,
   notes and corrections on Hopcroft and Tarjan JACM 21(4) '74.

%A P. L. Montgomery
%T Speeding up the Pollard and elliptic curve methods of factorization
%J Mathematics of Computation
%V 48
%D 1987
%P 243-264
%K c1987, c198x, c19xx, prime, factor, factors, algorithm, integer,
   factorisation, ecm
%X via enews
   [Also search for: integer factorisation].

%A J. Pollard
%T A Monte Carlo method for factorization
%J BIT
%V 15
%P 331-334
%D 1975
%P 331-334
%K c1975, c197x, c19xx, prime, factor, factors, integer, factorisation,
   algorithm, prime, smooth, Monte-Carlo
%X "... describe briefly a novel factorization method involving prob. ideas."
   -- [<A HREF="https://doi.org/10.1007/BF01933667">doi:10.1007/BF01933667</A>]['24].
   via enews.  Good if factors < 10^6.
   Also see Pp1@[<A HREF="https://en.wikipedia.org/wiki/Pollard%27s_p_%E2%88%92_1_algorithm">wikip</A>]['24].
   [Also search for: integer factorisation].

%A H. Lenstra
%T Factoring integers with elliptic curves
%J Annals Math.
%V 126
%P 649-673
%D 1987
%K c1987, c198x, c19xx, prime, factor, factors, integer, factorisation,
   algorithm, factorization, elliptic curve method, ecm, GEECM
%X -- at Jstor [<A HREF="https://doi.org/10.2307/1971363">doi:10.2307/1971363</A>]['23].
   Also see, "... sub-exponential running time, alg. for int. factorization ...
      the third-fastest known ... still the best alg. for divisors <= 50 to
      60 digits ..."
   -- LEC@[<A HREF="https://en.wikipedia.org/wiki/Lenstra_elliptic-curve_factorization">wikip</A>]['23].
   [Also search for: integer factorisation].

%A R. Jonker
%A A. Volgenant
%T A shortest augmenting path algorithm for dense and sparse
   linear assignment problems
%J Computing
%V 38
%P 325-240
%D 1987
%K jrnl, c1987, c198x, c19xx, zz1021, maths, graph, graphs, augmenting path,
   linear assignment problem, algorithm
%X "... a shortest augmenting path alg. for the linear assignment problem. It
   contains new initialization routines & a special implementation of Dijkstra's
   shortest path method. For both dense & sparse problems computational
   experiments show this alg. to be uniformly faster than the best algs. from
   the lit.. A Pascal implementation is presented."
   -- [<A HREF="https://doi.org/10.1007/BF02278710">doi:10.1007/BF02278710</A>]['21].
   [Also search for: maths graph assignment problem].
   (Also see HAlg@[<A HREF="https://en.wikipedia.org/wiki/Hungarian_algorithm">wikip</A>]['21].)

%A S. Dvorak
%A B. Durian
%T Stable linear time sublinear space merging
%J COMPJ
%V 30
%N 4
%P 372-375
%D 1987
%K sort, sorting, merge, merging, in situ, insitu, in-situ, algorithm,
   jrnl, COMPJ, c1989, c198x, c19xx
%X "A new method for stable merging of two segments A(1..m), A(m+1..m) into
   A(1..n) in O(n) time is presented. ...no restrictions on n or m & the alg'
   requires O(n[half]) [LA: sqrt(n)] workspace. ...procedure is given in Pascal
   together with results of time measurements on samples of random integers."
   [<A HREF="http://dx.doi.org/10.1093/comjnl/30.4.372">doi:10.1093/comjnl/30.4.372</A>]['05].
   [Also search for: insitu merge].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Sort/Insitu/">in-situ</A>].)

%A D. Coppersmith
%A S. Winograd
%T Matrix multiplication via arithmetic progressions
%J Annual ACM Symposium on Theory of Computing
%V 9
%P 251-280
%D 1987
%O J. of Symbolic Computation, 9(3), pp.251-280, March '90.
%K conf, c1987, c198x, c19xx, zz0508, progression, fast matrix multiplication,
   matrices, algorithm, complexity, trilinear, Salem-Spencer theorem
%X "We present a new method for accelerating matrix multiplication
   asymptotically. This work builds on recent ideas of Volker Strassen, by using
   a basic trilinear form which is not a matrix product. We make novel use of
   the Salem-Spencer Theorem, which gives a fairly dense set of integers with no
   three-term arithmetic progression. Our resulting matrix exponent is 2.376."
   -- pdf@[<A HREF="http://doi.acm.org/10.1145/28395.28396">doi:10.1145/28395.28396</A>]['08], and
      JSC('90)@[<A HREF="http://dx.doi.org/10.1016/S0747-7171(08)80013-2">doi:10.1016/S0747-7171(08)80013-2</A>]['11].
   [i.e. for nxn matrices, time is O(n**2.367).] ?theor, not a practical alg???
   [Also search for: fast matrix multiplication algorithm].
   (Also see D. Coppersmith & S. Winograd, "On the Asymptotic Complexity of
     Matrix Multiplication," SIAM J. of Comput., 11(3), pp.472-492, Aug. '82.)

%A J. Kobler
%A U. Schoning
%A J. Toran
%T The Graph Isomorphism Problem: Its Structural Complexity
%I Birkhauser, Boston
%D 1993
%K maths, graphs, P, NP, NPC, text, book, c1993, c199x, c19xx,
   computational complexity
%X uk us isbn:1461267129; uk us isbn13:978-1461267126.
   [Also search for: Toran c2004] and
   [also search for: graph isomorphism].

%A D. S. Hirschberg
%A S. S. Seiden
%T A bounded-space tree traversal algorithm
%J IPL
%V 47
%N 4
%P 215-219
%M SEP
%D 1993
%K bounded space, IPL, jrnl, c1993, c199x, c19xx
%X 13 refs.

%A K. Bowden
%T Kron's method of tearing on a transputer array
%J COMPJ
%V 33
%N 5
%P 453-459
%D 1990
%K Kron, matrix, matrices, tear, tearing, system, subsystem, decomposition,
   block, diagonal, Diaoptics, MIMD, parallel, concurrent, multiprocessor
%X 8 refs.

%A G. Kron
%T Diaoptics: The Piecewise Solution of Large-Scale Systems
%I MacDonald, London
%D 1963
%K Kron, matrix, matrices, tear, tearing, system, subsystem, decomposition,
   block, diagonal, book, text
%X from paper by  B o w d e n   in   C o m p j  '90.

%A R. K. Ahuja
%A T. L. Magnanti
%A J. B. Orlin
%T Some recent advances in network flows
%J SIAM Review
%V 33
%P 175-219
%D 1991
%K survey, intro, c1991, c199x, c19xx, network, flow, max, flows
%X "... Several techniques have proven to be very successful in permitting
   researchers to make these recent contributions: (i) scaling of the problem
   data; (ii) improved analysis of algorithms, especially amortized worst-case
   performance and the use of potential functions; and (iii) enhanced data
   structures. This survey illustrates some of these techniques and their
   usefulness in developing faster network flow algorithms ..."
   [Also search for: Ahuja c1993].

%A R. K. Ahuja
%A T. L. Magnanti
%A J. B. Orlin
%T Network Flows: Theory, Algorithms, and Applications
%I PrenticeHall
%P 864
%D 1993
%K text, book, c1993, c199x, c19xx, max, maximum, graph, graphs, net work, flow,
   maths, algorithm, application
%X 1st ed 1993, us$140; uk us isbn:013617549X; uk us isbn13:978-0136175490.
   Ahuja and Orlin also had a survey in (I think) SIAM Review, about 2y ago.
   From: M. Saltzm@n, Clemson U., Math Sci. 11/93
   [Also search for: Ahuja c1991].

%A M. Berger
%A I. Rigoutsos
%T An algorithm for point clustering and grid generation
%J IEEE Trans. Systems, Man and Cybernetics.
%V 21
%N 5
%M SEP/OCT
%D 1991
%P 1278-1286
%K SMC, TSMC, partition, cluster, points, enclosing rectangles, 2D, 3D
%X special purpose clustering alg' and its application to automatic grid
   generation, a technique used to solve partial differential equns.  13 refs.

%A A. Farago
%A T. Linder
%A G. Lugosi
%T Fast nearest-neighbour search in dissimilarity spaces
%J IEEE Trans. Pattern Analysis and Machine Intelligence
%V 15
%N 9
%M SEP
%D 1993
%K nearest neighbour, similarity, dissimilarity, cluster, clustering,
   algorithm
%X This paper provides an exact probabilistic analysis of this family
   of algorithms, proving its O(1) asymptotic average complexity measured
   in the number of dissimilarity calculations.   13 refs.

%A National Research Council, Panel on Probability and Algorithms
%T Probability and Algorithms
%I National Academy Press, Washington D.C., USA.
%D 1992
%K text, book, NRC, probabilistic, algorithm, random, randomised, randomized
%X H@rgrave Mos517.1 N277P

%A R. Sedgewick
%T Algorithms in C
%I AddisonWesley
%D 1990
%K book, text, c1990, c199x, c19xx, algorithm, data structure, dataStructure,
   DS, ADS, L2Ref L3Ref, cc
%X uk us isbn:0201514257;   later edition '97 became multiple volumes.
   [Also search for: Sedgewick book].

%A R. Sedgewick
%T Algorithms in C, 3rd edn, parts 1-4
%I AddisonWesley
%M DEC
%P 720
%D 1997
%K book, text, c1997, c199x, c19xx, algorithm, data structure, ADS, structures,
   dataStructure, DS, sort, search, L2Ref, L3Ref, cc, zz0801
%X Vol 1, parts 1-4: fundamentals; data structures; sorting; searching.
   3rd ed 1997, pb; uk us isbn:0201314525; uk us isbn13:978-0201314526.
   [Also search for: Sedgewick book].

%A R. Schaffer
%A R. Sedgewick
%T The analysis of Heapsort
%J J. of Algorithms
%V 15
%P 76-100
%D 1993
%K jrnl, c1993, c199x, c19xx, sort, sorting, Heap, Heap-sort, HeapSort, time,
   complexity, average case, algorithm
%X via enews.

%A U. Manber
%A G. Myers
%T Suffix arrays: a new method for on-line string searches
%J SIAM J. Comput.
%V 22
%N 5
%P 935-948
%M OCT
%D 1993
%O Proc. of the 1st annual ACM-SIAM Symp. on Discrete algorithms,
   pp.319-327, 1990
%K jrnl, SJC, suffix, prefix, array, tree, trees, online, string search,
   searching, match, matching, find, index, algorithm, data structure,
   substring, pattern, text, dataStructure, DS, c1993, c199x, c19xx, Udi,
   longest common prefix, LCP, strings, algorithm
%X "A new & conceptually simple [DS] ... for on-line string searches ...
   [construction] reduced to sort and search paradigm ...
   Typically uses 3 to 5 times less space than a suffix tree.
   The query, ? is W a substring of S ?, can be answered in O(|W|+log|S|) which
   is competitive with (& in some cases slightly better than[?]) S.trees. ...
   The worst case time to build a S.array. is O(|S| log|S|),  v. O(|S|)
   for a S.tree, but there is an O(|S|) expected time alg to build an S.array
   regardless of the alphabet size."
   [<A HREF="http://locus.siam.org/SICOMP/volume-22/art_0222058.html">SIAM</A>]['05]
   Also see [<A HREF="http://portal.acm.org/citation.cfm?id=320218">symp.pdf@acm.org</A>]['04] in, isbn:0898712513.
   (p.322: "Our sorting alg'm uses similar ideas to those in [KMR72]."
    K a r p,  M i l l e r,  R o s e n b e r g, c1972.)
    [[NB. sorting the suffixes using, for each suffix S{i}, the posn in the
      h-order of S{i} as its primary key & the posn of S{i+h} in the same order
      as its secondary key, yields the 2h-order. ... So <= log n passes.]]
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/Suffix/">Suffix</A>].)

%A J. Teuhola
%A T. Raita
%T Application of finite-state model to text compression
%J COMPJ
%V 36
%V 7
%P 607-614
%D 1993
%K finite state machine, models, FSM, FSA, Markov, HMM, text, data compression,
   compress, jrnl, COMPJ, c1993, c199x, c19xx, dynamic Markov Compression, DMC
%X clones states; alphabet > 2  ie. text
   "The bit-oriented [FSM] applied in Dynamic Markov Compression (DMC)) is here
   generalized to a larger alphabet. The [FSM] is built adaptively during
   compression, by applying 2 types of mod.s to the [mc] structure: state
   cloning & shortcut creation. The [mc] size is kept tolerable by an escape
   transition mechanism. Similar to DMC, the new method is combined with
   arithmetic coding, based on the maintained transition frequencies. The
   experiments show that the new approach produces notably better compression
   gains for different sorts of texts in natural and formal languages. In some
   cases the results are better than for any comp. tech. found in the lit.."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/36.7.607">doi:10.1093/comjnl/36.7.607</A>]['05],
      [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_36/Issue_07/360607.sgm.abs.html">paper@oup.co.uk</A>]['04].

%A T. B. Cooper
%A J. H. Kingston
%T The solution of real instances of the timetabling problem
%J COMPJ
%V 36
%V 7
%P 645-653
%D 1993
%K school, time table, tables, tabling, time-table, time-tabling, timetable,
   scheduling, jrnl, COMPJ
%X 21 refs

%A J. L. Spouge
%T Computation of the gamma, digamma and trigamma functions
%J SIAM J. Numer. Anal.
%V 31
%N 3
%P ??-??
%M JUN
%D 1994
%K SJNA, n!, factorial, Stirling, Stirling's approximation, c1994, c199x, c19xx,
   gamma, digamma, trigamma, function
%X Paper claims fast and accurate.

%A L. G. Valiant
%T The Complexity of Computing the Permanent
%J Theoretical Computer Science
%V 8
%P 189-201
%D 1979
%K TCS, jrnl, c1979, c197x, c19xx, P, NP, NPH, NPC

%A Jerrum
%A Sinclair
%T ???
%J SIAM J. Computing
%V ??
%P ??-??
%D 1989
%K permanent, matrix, P, NP, NPC, NPH, approximate, approximation, algorithm,
   randomised, randomized

%A Jerrum
%A Vazirani
%T ???
%J Proc. 33rd Ann. Symposium on Foundations of Computer Science (FOCS)
%P ??-??
%D 1992
%K permanent, matrix, P, NP, NPC, NPH, approximate, approximation, algorithm,
   randomised, randomized

%A Karmarkar
%A Karp
%A et al
%T ???
%J SIAM J. Computing
%V 22
%P ??-??
%D 1993
%K permanent, matrix, P, NP, NPC, NPH, approximate, approximation, algorithm,
   randomised, randomized

%A D. B. Johnson
%T A note on Dijkstra's shortest path algorithm
%J JACM
%V 20
%N 3
%P 385-388
%M JUL
%D 1973
%K jrnl, JACM, c1973, c197x, c19xx, single source, SSSP, algorithm,
   all destinations, shortest path problem, paths, maths, graph, Dijkstra
%X -- [<A HREF="https://doi.org/10.1145/321765.321768">doi:10.1145/321765.321768</A>]['23].
   [Also search for: SSSP algorithm].

%A D. Avis
%A K. Fukuda
%T Reverse search for enumeration
%J Discr. Appl. Maths.
%V 65
%N 1-3
%P 21-46
%M MAR
%D 1996
%O 1st Int. Colloquium on Graphs and Optimization (GOI), 1992
%K jrnl, c1996, c199x, c19xx, zz0914, reverse search, enumeration, enumerate,
   listing, triangulation, maths, graph, spanning tree, induced subgraph,
   topological ordering, sort, 01 integer programming, problem
%X "The rev.search technique has been recently intro. ... efficient enum. of
   vertices of polyhedra & arrangements. [Here] develop this idea in a general
   framework & show its broader applicns to various problems in OR,
   combinatorics, & geometry. ... propose new algs. for listing
     (i) all triangulations of a set of n pts in the plane.
     (ii) all cells in a hyperplane arrangement in R^n.
     (iii) all spanning trees of a g.,
     (iv) all Eucl. (noncrossing) trees spanning a set of n pts in the plane.
     (v) all connected induced subgraphs of a g., &
     (vi) all top.orderings of an acyclic g..
   Finally, we propose a new alg. for the 0-I int. prog. problem which can be
   considered as an alt. to the branch-&-bound alg.."
   -- [<A HREF="http://dx.doi.org/10.1016/0166-218X(95)00026-N">doi:10.1016/0166-218X(95)00026-N</A>]['14].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Recn/Subgraph/">SubGraphs</A>].)

%T The development of the number field sieve
%E A. K. Lenstra
%E H. W. Lenstra
%I Springer
%S LNM
%V 1554
%D 1993
%K conf, c1993, c199x, c19xx, zz0123, factorization, factorisation, factoring,
   number field sieve, NFS, GNFS, algorithm, integers, integer, prime, primes,
   Lenstra, Pollard
%X uk us isbn13:978-3540570134.
   "The [NFS] is an algo. for finding the prime factors of large integers. It
   depends on algebraic number theory. Proposed by John Pollard in 1988, the
   method was used in 1990 to factor the ninth Fermat #, a 155-digit int.. The
   alg. is most suited to #s of a special form, but there is a promising variant
   that applies in general. This volume contains six research papers that
   describe the operation of the [NFS], from both theoretical & practical
   perspectives. Pollard's original manuscript is included. [&] there is an
   annotated bibliography of directly related literature."
   -- [<A HREF="https://doi.org/10.1007/BFb0091534">doi:10.1007/BFb0091534</A>]['23].
   (Also see NFS@[<A HREF="https://en.wikipedia.org/wiki/General_number_field_sieve">wikip</A>]['23].)
   [Also search for: integer factorisation].

%A T. Akutsu
%T A polynomial time algorithm for finding a largest common subgraph of
   almost trees of bounded degree
%J IEICE Trans. Fundamentals Electronics, Commns & Comp. Scis. E76-A
%P 1488-1493
%D 1993
%K jrnl, c1993, c199x, c19xx, dynamic programming, maximum common subgraph, MCS,
   MCES, biconnected components, almost tree, maths, graph, chemical compound
%X "... finding a largest common subgraph of graphs ... known that the problem
   is NP-hard even if graphs are restricted to planar gs. of vertex degree <= 3.
 * BTW, a graph is called an 'almost tree' if |E(B)| <= |V(B)|+K holds for
   every block B where K is a const.. [Here] a polynomial time alg. for ...
   two graphs which are connected, almost trees & of bounded vertex degree. The
   alg. is an extension of a subtree isomorphism alg. which is based on dynamic
   prog.. Moreover, it is shown that the degree bound is essential. That is, the
   problem ... of two connected almost trees is proved to be NP-hard for any
   K >= 0 if degree is not bounded. The 3D matching problem, a well known NPC
   problem, is reduced to the problem."
   -- pdf@[<A HREF="http://ci.nii.ac.jp/naid/110003215627/en">nii</A>]['10],
   auth@[<A HREF="http://www.kuicr.kyoto-u.ac.jp/coe_db-bin/KUICR_info_e.pl?user=akutsu">kyoto-u</A>]['10].
   (R a y m o n d + W i l l e t t  say it solves the MCES problem.
   The above 'almost tree' condition is quite restrictive.  ?Block? )

%A J. Sorenson
%T Two fast GCD Algorithms
%J J. Algorithms
%V 16
%N 1
%P 110-144
%M JAN
%D 1994
%K JA, c1994, c199x, c19xx, GCD, greatest common divisor algorithm
%X theta( n^2 / log n ) bit operations for two n-bit integers.

%A Per Brinch Hansen
%T Multiple length division revisited: a tour of the minefield
%J SPE
%V 24
%N 6
%P 579-601
%M JUN
%D 1994
%K jrnl, SPE, c1994, c199x, c19xx, long, division, divn, arithmetic, algorithm,
   mine-field, mine field

%A N. Korte
%A R. H. Mohring
%T An incremental linear-time algorithm for recognizing interval graphs
%J SIAM J. Comput.
%V 18
%P 68-81
%D 1989
%K SJC, jrnl, linear time, interval graph, maths, mohring, moehring
%X ref' from Karp, Mapping the genome ... STOC '93

%A S. Lin
%A B. W. Kernighan
%T An effective heuristic for the travelling salesman problem
%J Oper. Res.
%V 21
%N 2
%P 498-516
%D 1973
%K jrnl, c1973, c197x, c19xx, OpR, OpRes, OR, TSP, sales man, person,
   two opt, twoOpt, 2opt, heuristic, salesperson, traveling
%X The (i,j) reversal of a permutation  a1,a2...ai...aj...an  is
   a1...ai-1,aj...ai,aj+1...an.  Make neighbourhood of all such
   reversals of current perm'; pick best; ...
   (Not guaranteed optimal of course.) From a ref'.
   [Also search for: travelling salesman problem].
   (Also see TSP@[<A HREF="https://en.wikipedia.org/wiki/Held%E2%80%93Karp_algorithm">wikip</A>]['20].)

%A J. Hopcroft
%A R. Tarjan
%T Algorithm 447: Efficient algorithms for graph manipulation
%J CACM
%V 16
%N 6
%P 372-378
%M JUN
%D 1973
%K jrnl, CACM, c1973, c197x, c19xx, zz0914, maths, graphs, algorithm, 447,
   partition, partitioning, connected component, biconnected components,
   simple path, paths
%X "Efficient algs. are presented for partitioning a graph into connected
   components, biconnected components & simple paths. The alg. for partitioning
   of a g. into simple paths of iterative & each iteration produces a new path
   between two vertices already on paths. (The start v. can be specified
   dynamically.) If V is the # of vertices & E is the # of edges, each alg.
   requires time & space proportional to max(V,E) when executed on a random
   access computer."
   -- [<A HREF="http://dx.doi.org/10.1145/362248.362272">doi:10.1145/362248.362272</A>]['14].
   (Also see Gpartn@[<A HREF="https://en.wikipedia.org/wiki/Graph_partition">wikip</A>]['20].)
   [Also search for: graph partition].

%A M. L. Fredman
%T On computing the length of longest increasing subsequences
%J Discr. Maths
%V 11
%N 1
%P 29-35
%D 1975
%K jrnl, c1975, c197x, c19xx, zz0215, longest ascending subsequence, LAS, LASS,
   problem, algorithm
%X "Let S = x1, x2, ...,  xn be a sequence of n distinct elements from a
   linearly ordered set. We consider the problem of determining the length of
   the longest increasing subsequences of S. An alg. which performs this task is
   described & is shown to perform n log n - n log log n + O(n) comparisons in
   its worst case. This worst case behavior is shown to be best possible."
   -- [<A HREF="http://dx.doi.org/10.1016/0012-365X(75)90103-X">doi:10.1016/0012-365X(75)90103-X</A>]['15].
   [Also search for: LASS problem].

%A J. A. Chisman
%T The clustered traveling salesman problem
%J Comp. and Op. Res.
%V 2
%N 2
%P 115-119
%M SEP
%D 1975
%K jrnl, c1975, c197x, c19xx, clustered travelling salesman problem, CTSP, TSP,
   cluster, traveling
%X "The traveling salesman problem is expanded to include the sitn where a group
   of cities (cluster) must be visited contiguously in an optimal, unspecified
   order. Given several sets of clusters within the problem, a method is
   developed for optimizing simultaneously the ordering of cities within each
   cluster & the ordering of clusters. A real-world warehousing problem is shown
   to fit this formulation."  [11 refs].
   -- [<A HREF="http://dx.doi.org/10.1016/0305-0548(75)90015-5">doi:10.1016/0305-0548(75)90015-5</A>]['12].
   [Also search for: travelling salesman].

%A A. M. Garsia
%A M. L. Wachs
%T A new algorithm for minimum cost binary trees
%J SIAM J. Comput.
%V 6
%N 4
%P 622-642
%D 1977
%K jrnl, c1977, c197x, c19xx, zz0220, minimum cost binary tree, optimum,
   search trees, Huffman code, linearithmic, Garsia Wachs, algorithm, Hu-Tucker
%X "A new alg. for constructing minimum cost binary trees in O(n log n) time is
   presented. [It] is similar to the well-known Hu-Tucker alg.. Our proof of
   validity is based on finite variational methods & is therefore quite
   different & somewhat simpler than the proof for the H.-T. alg. Our proof
   also yields some additional information about the structure of min. cost b.
   trees. This permits a linear time implementation ... in a special case."
   -- [<A HREF="https://doi.org/10.1137/0206045">doi:10.1137/0206045</A>]['20].
   Also see GW@[<A HREF="https://en.wikipedia.org/wiki/Garsia%E2%80%93Wachs_algorithm">wikip</A>]['20].
   ("An alg. is said to run in quasilinear time (aka log-linear time) if
   T(n)=O(n log^k(n)) for some +ve const. k; linearithmic is the case k=1."
   TC@[<A HREF="https://en.wikipedia.org/wiki/Time_complexity">wikip</A>]['20].)
   (Also see R.S.Bird JFP [<A HREF="https://doi.org/10.1017/S0956796819000194">doi:10.1017/S0956796819000194</A>][21/1/'20].)
   [Also search for: binary code tree].

%A Bein
%A Kamburowski
%A Stallmann
%T Optimal reduction of two-terminal directed acyclic graphs
%J SIAM J. Comput.
%V 21
%N ?
%P 112-1129 ???
%M ?
%D 1992
%K SJC, jrnl, directed, acyclic, maths, graph, DAG, graphs, theory,
   two terminal, series parallel
%X They "measure" how nearly a dag is series-parallel by finding the minimum
   number of "node" reductions that must be used, in addition to series and
   parallel arc reductions, to reduce the dag to a single arc.
 via: David J. Michael  IBM Software Solutions, Cary, NC   (8/'94)
      tel: (919) 469-6510    (email:davidm OF vnet.ibm.com).

%A L. Szirmay-Kalos
%T Dynamic Layout Algorithm to Display General Graphs
%B Graphics Gems IV
%E P. Heckbert
%P 505-517
%I AcademicPress
%D 1994
%K c1994, c199x, c19xx, Szirmay Kalos, cartography, layout, format, graph,
   graphs, visualization, physically-based methods, display
%X Gives code that finds aesthetic arrangements for a graph.
   This could be used to graphically display data structures.
   Contains C++ code.
   FTP: code in princeton.edu pub/Graphics/GraphicsGems/GemsIV/GGemsIV.tar.Z
   via: cgatti@cscs.ch (Claudio Gatti)   (8/'94).

%A M. H. MacGregor
%A W. D. Grover
%T Optimized k-shortest-paths algorithm for facility restoration
%J SPE
%V 24
%N 9
%P 823-834
%M SEP
%D 1994
%K jrnl, SPE, shortest, path, paths, maths, graph

%A T. Nishizeki
%A N. Chiba
%T Planar Graphs: Theory and Practice
%J Annals of Discrete Math
%V 32
%N ?
%P ?-?
%M ?
%D 1988
%K maths, graph, planarity
%X via <!-- email: wevrick@pickard.mast.queensu.ca --> (Daniel Wevrick 12/'94).

%A L. Kou
%A G. Markowsky
%A L. Berman
%T A fast algorithm for Steiner trees
%J Acta Informatica
%V 15
%N ?
%P 141-145
%M ?
%D 1981
%K jrnl, c1981, c198x, c19xx, Steiner, tree, algorithm, CS, CSci, computing
%X From <!-- email: pmanyem@eos.ncsu.edu --> (Prabhu Manyem,   2/'95)

%A V. Estivill-Castro
%A D. Wood
%T A survey of adaptive sorting algorithms
%J ACM Comput. Surveys
%V 24
%N 4
%M DEC
%D 1992
%P 441-476
%K jrnl, ACM, presort, adaptive, sort, sorting, algorithm, c1992, c199x, c19xx
%X reviewed in Comp. Rev. 35(10) p532-533 Oct '94
   [<A HREF="http://www.csd.uwo.ca/tech-reports/333/" >www</A>][8/'02]
   [<A HREF="http://doi.acm.org/10.1145/146370.146381">acm</A>][8/'02]

%A H. Saran
%A V. Vazirani
%T Finding k-cuts within twice the optimal
%J FOCS
%D 1991
%P 743-751
%K maths, graph theory, k cut cuts, kcut, kcuts, FOCS, FOCS91, conf
%X email: Olivier.Goldschmidt@imag.fr   [4/'95]
   see also  Goldschmidt  Math of Operations Research  1994

%A O. Goldschmidt
%A D. S. Hochbaum
%T A polynomial algorithm for the k-cut problem for fixed k
%J Math. of Operations Research
%V 19
%N 1
%M FEB
%D 1994
%K maths, graph theory, k cut cuts, kcut, kcuts, Op Res, OpRes, OR, jrnl
%X An earlier version of the paper appeared in FOCS 1988.  In the same paper,
   we show that the problem is NP-hard for general N.
   For N fixed, the problem is solvable in polynomial time.
   email: Olivier.Goldschmidt@imag.fr   [4/'95]

%A Ding-Zhu Du
%T On greedy heuristics for Steiner minimum trees
%J Algorithmica
%V 13
%N 4
%P 381-386
%M APR
%D 1995
%K jrnl, c1995, c199x, c19xx, tree, maths, graph, cost, algorithm, CSci

%A R. C. Singleton
%T Mixed radix fast Fourier tranforms
%B Programs for Digital Signal Processing
%I IEEE Press
%P ?-?
%D 1979
%K Fourier, transform, algorithm, radix, prime, CSci, zz0895
%X - Daniel P. Johnson,   Honeywell Technology Center
   <!-- email: drdan@src.honeywell.com --> [7/'95]

%A D. Bini
%A V. Pan
%T Polynomial and Matrix Computations, Volume 1:  Fundamental Algorithms
%I Birkhauser
%C Boston
%P 436
%D 1994
%K book, text, c1994, c199x, c19xx, Fourier, transform, algorithm,
   mixed radix, CSci, zz0895
%X hb; us isbn:0817637869; isbn13:978-0817637866.
   - via Steve Tate  <!--  email: srt at cs.unt.edu --> [7/'95]

%A K. Mulmuley
%T Lower bounds for parallel linear programming and other problems
%J Annual ACM Symp. on Theory of Computing
%P 603-614
%D 1994
%K conf, TOC, ACM, theory, complexity, P, NC, RNC, c1994, c199x, c19xx
%X ... lin' prog' ... network flow ... cannot be decided efficiently in
   parallel in a det' or randomized fashion, using finite precision
   arithmetic...  comparison, indirect ref's, branching op's but no bit
   manipulation ...     isbn:0897916638.
   -- [<A HREF="http://doi.acm.org/10.1145/195058.195413">doi:doi.acm.org/10.1145/195058.195413</A>][3/'04].
   [Also search for: LinearProgramming].

%A A. Amir
%T An alphabet independent approach to two-dimensional pattern matching
%J SIAM J. Comput.
%V 23
%N 2
%P 313-323
%M APR
%D 1994
%K two dimensional, 2D, pattern matching, match, image processing, IP,
   SJC, jrnl, zz0895
%X review in Comp. Rev. p263 May '95
   see also Zhu and Takaoka CACM '89

%A R. E. Blahut
%T Fast Algorithms for Digital Signal Processing
%I AddisonWesley
%D 1985
%K book, text, computing, Fourier, transform, FT, DSP
%X Bob Williamson  <!-- email: Bob.Williamson@anu.edu.au --> [8/'95]

%A C. M. Rader
%T Discrete Fourier transforms when the number of data samples is prime
%J Proc. IEEE
%V 56
%P 1107-1108
%D 1968
%K FT, digital signal processing, radix, prime, DSP
%X Bob Williamson  <!-- email: Bob.Williamson@anu.edu.au --> [8/'95]

%A Cornuejols
%A Nemhauser
%T Tight bounds for Christofides' traveling salesman heuristic
%J Math. prog.
%V 14
%P 116-121
%D 1978
%K c1978, c197x, c19xx, travelling, salesperson, sales, man, problem, TSP,
   TSM, zz0895
%X - David Williamson <!-- email: dpw@watson.ibm.com -->  [8/95]
   [Also search for: travelling salesman problem].

%A D. B. Johnson
%A T. Mizoguchi
%T Selecting the Kth element in X + Y and X1 + X2 + ... + Xm
%J SIAM J Computing
%V 7
%N 2
%P 147-153
%M MAY
%D 1978
%K jrnl, selection, c1978, c197x, c19xx, select, multiset, multisets, median,
   selection, problem, algorithm
%X O(n log n)-time to find kth order stat. in X+Y = {x[i]+y[j] | 1 <= i,j <= n}
   [Also search for: Johnson c1978]  and
   [also search for: median selection problem].

%A R. L. Rivest
%A L. Adleman
%A M. L. Dertouzos
%T On data banks and privacy homomorphisms
%J Foundations of Secure Computation
%D 1978
%K c1978, c197x, c19xx, zz0415, homomorphic encryption, DBMS, security,
   privacy, cloud computing, RSA, data
%X pdf@[<A HREF="http://luca-giuzzi.unibs.it/corsi/Support/papers-cryptography/RAD78.pdf">unibs.it</A>]['15].
   Also see HE@[<A HREF="http://en.wikipedia.org/wiki/Homomorphic_encryption">wikip</A>]['15].
   [Also search for: homomorphic encryption].

%A D. B. Johnson
%A S. D. Kashdan
%T Lower bounds for selection in X+Y and other multisets
%J JACM
%V 25
%N 4
%P 556-570
%M OCT
%D 1978
%K jrnl, JACM, c1978, c197x, c19xx, multiset, select, selection, problem,
   lower bound, complexity, median, gap, gaps, difference, differences,
   algorithm
%X "...known that the structure in the multiset X+Y, for X & Y multisets of n
   real #s, enables selection to be performed more quickly than m other sets of
   size O(n^2). ... a LOWER BOUND of Omega(max(n, K^(1/2) log K)) is given for
   selecting the Kth elt in X+X, & thus in X+Y, for K selecting the 1st through
   the median element. Selection of gaps, that is, consecutive differences in a
   sorted order, is shown to be Omega(n log n) for all K. These results hold
   also when inputs are restricted to integers. The problem of selection on X+X
   can be generalized to selection on the set of multisets of size m chosen from
   X, where the multlsets are ranked on the sums of their elements. When m & n
   grow, selection of the Kth largest multiset of size m is NP-hard when inputs
   are expressed in binary notation. If subsets of X are characterized as paths,
   circuits, or spanning trees of an edge-weighted graph, then selection of the
   Kth largest such subset of X remains NP-hard. It is not possible to show
   these problems to be NP-hard when inputs are expressed m unary, since algs.
   exist which run in time polynomml m the sums of the values of the inputs."
   -- [<A HREF="http://doi.acm.org/10.1145/322092.322097">doi:10.1145/322092.322097</A>]['07].
   [Also search for: median selection problem].

%A R. Mathon
%T A note on the graph isomorphism counting problem
%J IPL
%V 8
%N 3
%P 131-136
%M MAR
%D 1979
%K jrnl, IPL, c1979, c197x, c19xx, zz0416, maths, graph, automorphism,
   #GA, counting, size, number, problem, count, uToronto, uniToronto
%X "... to show that the problem of recognising whether or not 2 graphs are
   isom. & the problem of counting all isomorphisms between the graphs are
   polynmomial time equivalent. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0020-0190(79)90004-8">doi:10.1016/0020-0190(79)90004-8</A>]['16].
   (Also see, "... counting the automorphisms [of G] is
   polynomial-time equivalent to graph isomorphism ..."
   --  GA@[<A HREF="https://en.wikipedia.org/wiki/Graph_automorphism">wikip</A>]['16].)
   [Also search for: maths graph isomorphism].

%A F. P. Preparata
%A M. I. Shamos
%T Computational Geometry: an Introduction
%I SpringerVerlag
%S Texts and Monographs in Comp. Sci.
%P 390
%D 1985
%K book, text, c1985, c198x, c19xx, search, searching, convex hull, rectangle
%X us$76, uk us isbn:0387961313.
   [<A HREF="http://euro.ecom.cmu.edu/people/faculty/mshamos/">auth2@cmu</A>]['06]

%A T. Leighton
%T Tight bounds on the complexity of parallel sorting
%J IEEE Transactions on
%V C-34
%N 4
%P 344-354
%M APR
%D 1985
%K conf, sort, columnSort, c1985, c198x, c19xx, sorting, parallel, algorithm,
   complexity, bound,
%X "... prove tight upper and lower bounds on the # of processors, info.
   transfer, wire area, & time needed to sort N numbers in a bounded-degree
   fixed-connection n/w. ... results are: 1) the const'n of an N-node degree-3
   n/w capable of sorting N numbers in O(log N) word steps; 2) a proof that any
   n/w capable of sorting N(7 log N)-bit numbers in T bit steps requires area A
   where AT**2=y(N**2 log**2 N); & 3) the const'n of a "small-constant-factor"
   bounded-degree n/w that sorts N y(log N)-bit numbers in T=y(log N) bit steps
   with A = y(N2) area."
   -- [<A HREF="http://dx.doi.org/10.1109/TC.1985.5009385">doi:10.1109/TC.1985.5009385</A>]['09],
   [also search for: columnSort].

%A P. Flajolet
%A G. N. Martin
%T Probabilistic counting algorithms for data base applications
%J JCSS
%V 31
%P 182-209
%D 1985
%K jrnl, JCSS, c1985, c198x, c19xx, counting, count, counts, distinct elements,
   values, streaming, estimate, algorithm
%X "... est the # of distinct elts ... in a single pass ...small additional
   storage ... and only a few ops per elt scanned. ..."
   (Also see streaming@[<A HREF="http://en.wikipedia.org/wiki/Streaming_algorithm">wikip</A>]['12].)

%A R. Irving
%T An efficient algorithm for the 'stable roommates' problem
%J J. Algorithms
%V 6
%N 4
%P 577-595
%M DEC
%D 1985
%K jrnl, c1985, c198x, c19xx, zz0623, stable roommates problem, SRP, algorithm,
   roommate, marriage, match, graph, matching, pairs, pairing
%X "... The stable roommates problem involves a single set of even cardinality
   n, each member of which ranks all the others in order of preference. A stable
   matching is now a partition of this single set into pairs so that no two
   unmatched members both prefer each other to their partners under the
   matching. In this case, there are problem instances for which no stable
   matching exists. However, the present paper describes an O(n^2) alg. that
   will determine, for any instance of the problem, whether a stable matching
   exists, & if so, will find such a matching."
   -- [<A HREF="https://doi.org/10.1016/0196-6774(85)90033-1">doi:10.1016/0196-6774(85)90033-1</A>]['23].
   Also see SRP@[<A HREF="https://en.m.wikipedia.org/wiki/Stable_roommates_problem">wikip</A>]['23].
   [Also search  for: stable marriage problem].

%E E. L. Lawler
%E J. K. Lenstra
%E A. H. G. Rinnooy Kan
%E D. B. Shmoys
%T The Traveling Salesman Problem
%I Wiley
%P 476
%M SEP
%D 1985
%K book, text, c1985, c198x, c19xx, sales man, person, salesperson, travelling,
   TSP, TSM, zz0895, maths, graph, graphs, vertex, vertices, visit, problem
%X - via David Williamson <!-- email: dpw@watson.ibm.com -->  [8/95]
   hb; uk us isbn:0471904139; uk us isbn13:978-0471904137.
   (Also see TSP@[<A HREF="https://en.wikipedia.org/wiki/Held%E2%80%93Karp_algorithm">wikip</A>]['20].)

%A K. G. Murty
%T An algorithm for ranking all the assignments in order of increasing cost
%J Operations Res.
%V 16
%P 682-687
%D 1986
%K jrnl, c1986, c198x, c19xx, OR, OpRes, c1986, c198x, c19xx, rank, ranking,
   assignment

%A K. J. Supowit
%T Decomposing a set of points into chains, with applications to permutation
   and circle graphs
%J IPL
%V 21
%P 249-252
%D 1985
%K jrnl, IPL, graph, graphs, algorithm, colouring, coloring, clique, cover,
   maths, independent set, sets, CSci, zz0995
%X (i) minimum coloring,
   (ii)finding the size of the maximum clique,
   (iii)minimum covering by cliques,
   (iv) finding the size of the maximum independent set.
   Supowit presented O(n \ log n) algorithms for all these problems
   - Amitava <!-- datta@neumann.une.edu.au -->  [9/'95]

%A P. Barrett
%T Implementing the Rivest Shamir and Adleman public key encryption algorithm
   on a standard digital signal processor
%J CRYPTO 86
%P 311-323
%O LNCS, vol.263, 1987
%D 1986
%K conf, c1986, c198x, c19xx, zz0314, PGP, reduction, mod, modulo, modular,
   computer arithmetic, integer, operation, fast
%X "A description of the techniques employed at Oxford U. to obtain a high speed
   implementation of the RSA encryption alg. on an 'off-the-shelf' digital
   signal processing chip. Using these techniques a 2.5 sec. (avg) encrypt time
   (for 512 bit exponent & modulus) was achieved on a first generation DSP (The
   T.I. TMS 32010) & times < 1 sec. are achievable on 2nd gen.parts. [&] the
   techniques of alg. development employed lead to a provably correct
   implementation."
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-47721-7_24">doi:10.1007/3-540-47721-7_24</A>]['14],
      BR@[<A HREF="http://en.wikipedia.org/wiki/Barrett_reduction">wikip</A>]['14],
      NR_div@[<A HREF="http://en.wikipedia.org/wiki/Newton-Raphson_division">wikip</A>]['14]..
   [Also search for: public key encryption].

%A L. L. Larmore
%A D. S. Hirschberg
%T A fast algorithm for optimal length-limited Huffman codes
%J JACM
%V 37
%N 3
%P 464-473
%M JUL
%D 1990
%K jrnl, c1990, c199x, c19xx, ACM, package-merge, data compression, coding,
   limit, Huffman, binary code, CSci
%X see Katajainen, Moffat and Turpin 1995

%A E. Nuutila
%T An efficient transitive closure algorithm for cyclic digraphs
%J IPL
%V 52
%P 207-213
%D 1994
%K IPL, jrnl, c1994, c199x, c19xx, directed graph, maths, graphs, algorithm,
   digraph, strong component, components, Esko, STACK_TC, STACKTC, zz0706
%X [<A HREF="http://www.cs.hut.fi/~enu/ps/ipl-comptc.ps">.ps</A>]['06]
   Also see thesis c1995.

%A G. Farr
%T On problems with short certificates
%J Acta Informatic
%M MAY
%D 1994
%K jrnl, c1994, c199x, c19xx, zz1124, GFarr, NP, forcing, complete
%X "We consider languages in NP whose certificate size is bounded by a fixed,
   slowly growing fn (say f(n)) of the input size. The classes f(n)-NP ...
   are defined in order to classify such langs.. We show that several natural
   problems, involving Boolean satisfiability, graph colouring & Hamiltonian
   circuits, are complete for f(n)-NP. ..."
   -- [<A HREF="https://doi.org/10.1007/BF01178668">doi:10.1007/BF01178668</A>]['24].

%A R. Hassin
%A S. Rubinstein
%T Approximations for the maximum acyclic subgraph problem
%J IPL
%V 51
%N 3
%P 133-140
%M AUG
%D 1994
%K IPL, c1994, c199x, c19xx, minimum feedback arc set, maximum acyclic subgraph,
   largest, maths, graph, near, nearly, DAG, approximation algorithm, edge, arcs
%X "... G=(V,A) ... main result is an O(|A|+d[max]**3) algorithm that produces
   a soln with at least a fraction 1/2+w(1/sqrt(d[max]) of the # of arcs in an
   optimal soln. Here, d[max] is the maximum vertex degree in G.
   -- [<A HREF="http://dx.doi.org/10.1016/0020-0190(94)00086-7">doi:10.1016/0020-0190(94)00086-7</A>].
   Via GF & [<A HREF="http://www.csc.kth.se/~viggo/wwwcompendium/">~viggo</A>]['09]:
      Finding the maximum set of arcs A' such that G'=(V,A') is acyclic is
      approximable within 2/(1+Omega(1/sqrt Delta)) where Delta is the maximum
      degree and, it is APX-complete, and if |E|=Theta(|V|^2) it admits a PTAS.
   [Also search for: minimum feedback arc set].

%A S. Khuller
%A U. Vishkin
%T Biconnectivity approximations and graph carvings
%J JACM
%V 41
%N 2
%P 214-235
%M MAR
%D 1994
%K jrnl, JACM, c1994, c199x, c19xx, two, vertex, maths, graphs, subgraphs,
   theory, minimum spanning 2 edge connected subgraph, carving,
   approximation, tree, biconnected
%X "A spanning tree in a graph is the smallest connected spanning subgraph.
   Given a graph, how does one find the smallest (i.e., least number of edges)
   2-connected spanning subg. (connectivity refers to both edge & vertex
   connectivity, if not specified)?  Unfortunately ...[is] NP-hard. We consider
   the problem of finding a better approx. to the smallest 2-connected subgraph,
   by an efficient alg.. For 2-edge connectivity, our alg. guarantees a soln
   that is no more than 3/2 times the optimal. For 2-vertex connectivity, our
   alg. guarantees a solution that is no more than 5/3 times the optimal.
   The previous best approximation factor is 2 for each of these problems. The
   new algs. (& their analyses) depend upon a structure called a carving of a
   graph, which is of independent interest. We show that approximating the
   optimal soln to within an additive constant is NP-hard as well. We also
   consider the case where the graph has edge weights. For this case, we show
   that an approx'n factor of 2 is possible in polynomial time for finding a
   k-edge connected spanning subgraph. This improves an approx'n factor of 3
   for k=2, due to Frederickson & JaJa['81], & extends it for any k (with an
   increased running time though)."
   [<A HREF="http://doi.acm.org/10.1145/174652.174654">doi:10.1145/174652.174654</A>]['07]
   Defn: [G is "k edge (vertex) connected" if G remains connected on
          removing any set, S, of edges (vertices) where |S| < k.]

%A A. Yu. Kitaev
%T Quantum measurements and the Abelian stabilizer problem
%J arXiv
%M NOV
%D 1995
%K TR, c1995, c199x, c19xx, zz0324, hidden subgroup problem, HSGP,
   quantum computing, quantum Fourier transform, factoring, eigenvalue,
   unitary operator, group
%X "We present a polynomial quantum alg. for the Abelian stabilizer problem
   which includes both factoring & the discrete logarithm. Thus we extend famous
   Shor's results. Our method is based on a procedure for measuring an
   eigenvalue of a unitary operator. Another application of this procedure is a
   polynomial quantum Fourier transform alg. for an arbitrary finite Abelian
   group. The paper also contains a rather detailed introduction to the theory
   of q.comp'n."
   -- [<A HREF="https://arxiv.org/abs/quant-ph/9511026">arxiv:quant-ph/9511026</A>]['34].
   Also see HSGP@[<A HREF="https://en.wikipedia.org/wiki/Hidden_subgroup_problem">wikip</A>]['24].
   [Also search for: hidden subgroup problem HSGP].

%A E. Nuutila
%T Efficient Transitive Closure Computation in Large Digraphs
%J Acta Polytechnica Scandinavica
%S Mathematics and Computing in Engineering Series
%W Helsinki
%N 74
%P 124
%D 1995
%K PhD thesis, c1995, c199x, c19xx, directed graph, maths, graphs, algorithm,
   digraph, strong component, components, Esko, STACK_TC, STACKTC, zz0706
%X "... 2 new transitive closure algs. that are based on detecting the strong
   components are presented. Worst-case analysis and simulation experiments
   show that the new algorithms are more efficient than the previous algs. that
   are based on strong component detection. The algs. use Tarjan's alg. for
   strong component detection. Also, 2 improved versions of Tarjan's alg. are
   presented.  ...  Simulation experiments show that the interval rep. is
   superior to the commonly used adjacency list rep.. ... indicate that the
   interval rep. requires typically at most a space linear to the # of vertices
   ... . ... also indicate that with the interval rep. and the new algs., the
   transitive closure can be computed typically in time linear to the size of
   the input graph."   -- Published by the Finnish Academy of Technology;
   isbn:9516664512; issn:12372404, UDC 681.3.
   [<A HREF="http://www.cs.hut.fi/~enu/thesis.html">thesis.ps</A>]['06]
   [<A HREF="http://www.cs.hut.fi/~enu/tc.html">more</A>]['06]
   Also see IPL c1994.

%A M. A. Hitz
%A E. Kaltofen
%T Integer division in residue number systems
%J IEEE Trans. Computers
%V 44
%N 8
%P 983-989
%M AUG
%D 1995
%K jrnl, algorithm, fast, int, ints, divide, modulo, c1995, c199x, c19xx,
   arithmetic
%X [<A HREF="http://www4.ncsu.edu/~kaltofen/bibliography/95/HiKa95.ps.gz">.ps.gz</A>][4/'04]
   [<A HREF="http://www4.ncsu.edu/~kaltofen/bibliography/">kaltofen</A>][4/'04]

%A H. Prodinger
%T Multiple Quickselect -- Hoare's Find algorithm for several elements
%J IPL
%V 56
%N 3
%P 123-129
%M NOV
%D 1995
%K jrnl, IPL, c1995, c199x, c19xx, find, select, selection problem, median,
   quartiles, time, complexity, passes, comparisonsLent, Mahmoud, zz0803
%X ...``Find'' algorithm ... select p specified order stat's j1, j2, ..., jp
   from ... n elements simultaneously. ...give precise formulae for both the
   avg # of passes & the avg # of comparisons. Averaging again over all poss'
   subsets of p elements, we get results of Lent and Mahmoud as corollaries.
   -- [<A HREF="http://dx.doi.org/10.1016/0020-0190(95)00150-B">doi:10.1016/0020-0190(95)00150-B</A>][8/'03],
      [<A HREF="http://www.wits.ac.za/helmut/abstract/abs_103.htm">@home</A>][8/'03].
   [Also search for: median selection problem].

%A J. Katajainen
%A A. Moffat
%A A. Turpin
%T A fast and space-economical algorithm for length-limited coding
%J Int. Symp. Algorithms and Computation
%W Cairns, Australia
%M DEC
%D 1995
%P ?-?
%K conf, data compression, limit, code, Larmore, Hirschberg, CSci, zz0995
%X Find a good code when the max' length of a code word is limited to L;
   n symbols, frequency of s[i] is p[i], L at least ceiling(log2(n)).
   The package-merge alg' of Larmore and Hirschberg generates length-limited
   code in O(nL) time and O(n) space. Here show how to reduce space to O(L**2).
   NB. for practical purposes L is theta(log(n)).
   Also see Turpin and Moffat CompJ 38(5) '95

%A A. Turpin
%A A. Moffat
%T Practical length-limited coding for large alphabets
%J COMPJ
%V 38
%N 5
%P 339-347
%D 1995
%K COMPJ, jrnl, data compression, limit, code, coding,
   package-merge, c1995, c199x, c19xx, zz1295
%X ... describe an experiment on an alphabet of over 1 million symbols,
   for which length-limited codes can be constructed in 11Mb of memory and
   about 20 seconds of CPU time.  (SPARC 10 / 402)    [27 refs]
   [<A HREF="http://dx.doi.org/10.1093/comjnl/38.5.339">doi:10.1093/comjnl/38.5.339</A>]['05]
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_38/Issue_05/380339.sgm.abs.html">paper@oup.co.uk</A>]['04]

%A I. Ahmad
%A M. K. Dhodhi
%T On the m-way graph partitioning problem
%J COMPJ
%V 38
%N 3
%D 1995
%P 237-244
%K jrnl, COMPJ, mWay, maths, graph, partition, cut, layout, weight,
   genetic algorithm, GA, zz1095
%X Given a graph with weights on both edges and nodes, partition the nodes
   into m disjoint, equal size subsets so that the sum of the weights of the
   edges not within the same partition is minimized.
   Tests include interesting cases to about 19 nodes and random graphs to
   150 nodes with degree in the `teens'.                             20 refs
   [Also search for: graph partition].

%A D. S. Johnson
%A C. R. Aragon
%A L. A. Mcgeoch
%A C. Schevon
%T Optimization by simulated annealing: an experimental evaluation; Part I,
   graph partitioning
%J Oper. Res.
%V 37
%P 865-892
%D 1989
%K JOR, jrnl, simulated annealing, SA, maths, graph, partition, layout, cut
%X ref in  Ahmad and Dhodi '95

%A A. Datta
%A H-P. Lenhof
%A C. Schwarz
%A M. Smid
%T Static and dynamic algorithms for k-point clustering problems
%J J. Algorithms
%V 19
%N 3
%P 474-503
%M NOV
%D 1995
%K jrnl, cluster, static, dynamic, CS, CSci, zz1195
%X given n points in d-space, find a subset of the
   points of size k that minimizes some closeness measure
   e.g. diameter, perimeter, circumradius

%A P. Luders
%A R. Ernst
%A S. Stille
%T An approach to automatic display layout using combinatorial optimization
   algorithms
%J SPE
%V 25
%N 11
%P 1183-1202
%M NOV
%D 1995
%K SPE, jrnl, gui, force directed, graph layout, hypertext, zz1295
%X 17 refs

%A A. Symvonis
%T Optimal stable merging
%J COMPJ
%V 38
%N 8
%P 681-690
%D 1995
%K  jrnl, COMPJ, c1995, c199x, c19xx, merge, merging, in situ, insitu,
   algorithm, time, space, complexity
%X "... stably merge 2 sequences A & B of sizes m & n, m[le]n, respectively,
   with O(m+n) assignments, O(mlog(n/m+1)) comparisons & using only a constant
   amount of additional space. [...] matches all known lower bounds & closes an
   open problem posed by Duzinski & Dydek in '81. Our algorithm is based on
   the unstable algorithm of Mannila & Ukkonen. All techniques we use have
   appeared in the lit' in more complicated forms [uncombined]. [...] also
   present a stable algorithm that requires a linear number of comparisons &
   assignments which we consider to be the simplest alg' for in-place merging."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/38.8.681">doi:10.1093/comjnl/38.8.681</A>]['05].
   [Also search for: insitu merge].

%A J. Cheriyan
%A T. Hagerup
%T A randomized maximum-flow algorithm
%J SIAM J. Comput.
%V 24
%N 2
%P 203-226
%M APR
%D 1995
%K jrnl, SIAM, randomized algorithm, max flow, zz0796
%X good review by D.M.Campbell in Comp Rev p268 May 96
   improves Sleator-Tarjan  O(mn log n)  to  O(mn + (n log n)**2) high prob'

%A T. Fukuda
%A Y. Morimoto
%A S. Morishita
%A T. Tokuyama
%T Interval finding and its application to data mining
%J Proc. 7th Int. Symp. on Algorithms and Computation
%I SpringerVerlag
%S LNCS
%V 1178
%P 55-64
%M DEC
%D 1996
%O IEICE Trans. on Fundamentals of Electronics, Communications and
   Computer Sciences, Vol.E80-A, No.4, pp.620-626, April '97
%K conf, intervals, c1996, c199x, c19xx, interval, search, searching,
   computational geometry
%X "... investigate inverse problems of the interval query problem in applic'n
   to data mining. Let I be the set of all intervals on U = {1, 2,... , n}.
   Consider an objective function f(I), conditional functions u[i](I) on I, and
   define an opt'n problem of finding the interval I maximizing f(I) subject to
   u[i](I) > Ki for given real numbers K[i] (i = 1, 2,... , h). We propose
   efficient algorithms to solve the above opt'n problem if the objective fn is
   either additive or quotient, and the conditional functions are additive,
   where a fn f is additive if f(I) = Sigma[i] iIf^(i) extending a fn f^ on
   U, and quotient if it is represented as a quotient of 2 additive functions.
   We use computational-geometric methods such as convex hull, range searching,
   and multidimensional divide-and-conquer."   uk us isbn13:978-3540620488.
   -- [<A HREF="http://dx.doi.org/10.1007/BFb0009481">doi:10.1007/BFb0009481</A>]['06](subscrn).

%A D. Zeilberger
%A J. Noonan
%T The enumeration of permutations with a prescribed number of
   forbidden subsequences
%J Advances in Appl. Math.
%P 381-407
%V 17
%D 1996
%K jrnl, perm, permutation, generator, enumerate, enumeration, forbidden, bad,
   subsequence, c1996, c199x, c19xx
%X [<A HREF="http://www.mathe2.uni-bayreuth.de/axel/papers/noonan:the_enumeration_of_permutations_with_a_prescribed_number_of_forbidden_patterns.ps.gz">.ps.gz</A>][2/'04].

%A A. Moffat
%A G. Eddy
%A O. Petersson
%T Splaysort: fast, versatile, practical
%J SPE
%V 26
%N 7
%P 781-798
%M JUL
%D 1996
%K SPE, jrnl, splay sort, sorting, adaptive, adapt, algorithm, splay tree,
   presort, sortedness, sorted, CSci, zz0796, c1996, c199x, c19xx
%X has a linear space overhead but adapts to "all common measures of
   sortedness".

%A J. I. Munro
%A V. Raman
%T Fast stable in-place sorting with O(n) data moves
%J Algorithmica
%V 16
%N 2
%P 151-160
%M AUG
%D 1996
%O Proc. 11th FST & TCS Conf.m LNCS 560, pp.266-277, 1991
%K jrnl, c1996, c199x, c19xx, zz0896, sort, sorting, algorithm, in situ, insitu
%X "Until recently, it was not known whether it was possible to stably sort
   (ie. keeping equal elts in their initial order) an array of n elts using only
   O(n) data movements & O(1) extra space. In [10], an alg. was given to perform
   this task in O(n^2) comparisons in the worst case. ... develop a new alg. for
   the problem that performs only O(n^{1+eps}) comparisons (0 < eps < 1 is any
   fixed const.) in the worst case. This bound on the # of comparisons matches
   (asymptotically) the best known bound for the same problem with the stability   constraint dropped."
   -- [<A HREF="https://doi.org/10.1007/BF01940644">doi:10.1007/BF01940644</A>]['18],
   or the 1991_conf[<A HREF="https://doi.org/10.1007/3-540-54967-6_74">doi:10.1007/3-540-54967-6_74</A>]['18].
   [Also search for: insitu merge].

%A J. Ellis
%A M. Markov
%T In situ, stable merging by way of the perfect shuffle
%J COMPJ
%V 43
%N 1
%P 40-53
%D 2000
%K jrnl, COMPJ, c2000, c200x, c20xx, zz0400, insitu, merge, merging, mergesort,
   sort, space, shufflemerge
%X "... no more than O(log**2(n)) bits of extra memory ...
   alg' is recursive and uses a logarithmic number of variables.
   Thus it uses more than `absolutely minimum storage', i.e. O(log(n)) bits...
   We note that ... worst case ... requiring time Omega(n.log(n)),...
   variant ... uses a generalized shuffle (probably not possible in-situ?) ...
   average case time O(n.log(log(m))) where m is the length of
   the shorter input ...  We present evidence indicating the Shufflemerge,
   although almost certainly not asymptotically linear (time), might be
   of value in practice..."
   -- [<A HREF="https://doi.org/10.1093/comjnl/43.1.40">doi:10.1093/comjnl/43.1.40</A>]['05].
   [Also search for: insitu merge].

%A G. Kant
%T Drawing planar graphs using the canonical ordering
%J Algorithmica
%V 16
%N 1
%P 4-32
%M JUL
%D 1996
%K jrnl, maths, graph drawing, graphs, layout, display, planar, zz0896
%X special issue on graph drawing; see other papers in same issue
   [Also search for: graph drawing].

%A M. K. Coleman
%A D. S. Parker
%T Aesthetics-based graph layout for human consumption
%J SPE
%V 26
%N 12
%P 1415-1438
%M DEC
%D 1996
%K jrnl, SPE, graph drawing, graphs, layout, display, zz1100
%X ref from an hons project report
   [Also search for: graph drawing].

%A M. Junger
%A P. Mutzel
%T Maximum planar subgraphs and nice embeddings: practical layout tools
%J Algorithmica
%V 16
%N 1
%P 33-59
%M JUL
%D 1996
%K jrnl, maths, graph drawing, graphs, planar, subgraph, embedding,
   layout, display
%X special issue on graph drawing
   [Also search for: graph drawing].

%A P. Eades
%A S. Whitesides
%T The realization problem for Euclidean minimum spanning trees is NP-hard
%J Algorithmica
%V 16
%N 1
%P 60-82
%M JUL
%D 1996
%K jrnl, maths, graph drawing, graphs, layout, display, NP, NPhard,
   realisation, complexity
%X special issue on graph drawing
   [Also search for: graph drawing].

%A P. Bose
%A W. Lenhart
%A G. Liotta
%T Characterizing proximity trees
%J Algorithmica
%V 16
%N 1
%P 83-110
%M JUL
%D 1996
%K jrnl, graph drawing, graphs, nearest, near, close, layout,
   display, tree, c1996, c199x, c19xx
%X special issue on graph drawing

%A J. Pach
%A F. Shahrokhi
%A M. Szegedy
%T Applications of the crossing number
%J Algorithmica
%V 16
%N 1
%P 111-117
%M JUL
%D 1996
%K jrnl, graph drawing, graphs, layout, display, crossings
%X special issue on graph drawing
   [Also search for: graph drawing].

%A F. Shahrokhi
%A L. A. Szekely
%A O. Sykora
%A I. Vrt'o
%T Drawing graphs on surfaces with few crossings
%J Algorithmica
%V 16
%N 1
%P 118-131
%M JUL
%D 1996
%K jrnl, graph drawing, graphs, layout, display, Vrto, crossing
%X special issue on graph drawing
   [Also search for: graph drawing].

%A A. Itai
%A M. Rodeh
%T Finding a minimum circuit in a graph
%J SIAM J. Comput.
%V 7
%N 4
%P 413-423
%M NOV
%D 1978
%K SIAM, jrnl, comput, maths, graphs, triangle, shortest, path
%X an almost min circuit (at most 1 extra edge) can be found in O(n**2) time.
   A direct alg' for a min circuit O(ne) time.
   Refined to O(n**2) average time alg'.
   Alternatively ~ find a triangle in an aux' graph:
      1. O(e**1.5)   (O(N) for planar graph)
      2. O(n**5/3) on average
      3. O(n**log 7)
   Digraphs - O(n**2 log n)

%A R. Davidson
%A D. Harel
%T Drawing graphs nicely using simulated annealing
%J ACM Trans. Graphics
%V 15
%N 4
%P 301-331
%M OCT
%D 1996
%K jrnl, graph, draw, drawing, layout, nice, SA, zz0297
%X 29 refs
   [Also search for: graph drawing].

%A D. Harel
%A M. Sardas
%T An incremental drawing algorithm for planar graphs
%J Algorithmica
%V ?
%N ?
%P ?
%M ?
%D to appear
%K jrnl, graph, draw, layout, nice
%X ref' in D a v i d s o n  and  H a r e l   Oct'  96
   [Also search for: graph drawing].

%T Graph Drawing
%E G. Goos
%E J. Hartmanis
%E J. van Leeuwen
%I SpringerVerlag
%S LNCS
%V 1190
%P 409
%O Symp. Graph Drawing GD96, Berkeley, Sept 1996
%D 1996
%K graph, graphs, c1996, c199x, c19xx, book, text, conf, layout, zz0697
%X uk us isbn:3540624953.
%X post conf papers, uk us isbn:3540624953; uk us isbn13:978-3540624950.

%T Recent Advances in Total Least Squares Techniques and
   Errors-Variables Modeling
%E S. van Huffel
%I SIAM
%M FEB
%P 377
%D 1997
%K book, c1997, c199x, c19xx, conf, TLS, LSW, RMS, error, fit, fitting,
   approximation, vanHuffel
%X Proc. of the 2nd Int. Workshop on Total Least Squares (TLS) and
   Errors-in-Variables (EIV) Modeling, Leuven, Belgium, Aug '96.
   us$75; us isbn:0898713935.
   [Also search for: total least squares].
   [<A HREF="http://www.ec-securehost.com/SIAM/PR93.html">details</A>][11/'03].

%A I. Fudos
%A C. M. Hoffman
%T A graph-constructive approach to solving systems of geometric constraints
%J ACM Trans. Graphics
%V 16
%N 2
%P 179-216
%M APR
%D 1997
%K jrnl, ACM, ToG, ToGs, computer graphics, constraint programming,
   geometry, layout, over, under, well, constrained
%X p182: Given a set V of n points and lines and a set E of pairwise
         constraints among them, find an intuitive solution that satisfies
   the given constraints.  A pairwise constraint can be one of:
   point to line distance and line to line angle,
   non-zero point to point distance.
   p214: We have presented a quadratic alg ...
         The bottom-up analysis alg' of Bouma et al [1995]
   has been augmented with a top-down decomposition alg' ...

%A D. Comer
%T The ubiquitous B-tree
%J Comp. Surveys
%V 11
%N 2
%P 121-137
%D 1979
%K jrnl, btree, trees, btrees, data structure, dataStructure, DS,
   height balanced, c1979, c197x, c19xx
%X Cited by   S e d g w i c k, Algs in C, '90, 1st ed p.273,
   also by    W i r t h  A+DS  '86, p.268.

%A M. Sharir
%T A strong connectivity algorithm and its applications to data flow analysis
%J Computers and Maths with Applications
%V 7
%N 1
%P 67-72
%D 1981
%K jrnl, c1981, c198x, c19xx, zz0515, strongly connected, components,
   maths graph, Kosaraju's algorithm, Hecht
%X "... a new linear [time] alg. for constructing all strongly connected
   components of a directed g., & show how to apply it in iterative soln of
   data-flow analysis problems, to obtain a simple alg. which improves the
   Hecht-Ullman alg.."
   -- [<A HREF="http://dx.doi.org/10.1016/0898-1221(81)90008-0">doi:10.1016/0898-1221(81)90008-0</A>]['15].
   Also see "...Kosaraju's alg. uses two passes of depth first search. ... It
      is named after S. Rao Kosaraju, who described it (but did not publish his
      results) in 1978; Sharir later published it in 1981."
   -- SCC@[<A HREF="http://en.wikipedia.org/wiki/Strongly_connected_component">wikip</A>]['15].
   [Also search for: strongly connected graph].

%A A. K. Lenstra
%A H. W. Lenstra jr.
%A L. Lovasz
%T Factoring polynomials with rational coefficients
%J Mathematische Annalen
%V 261
%P 515-534
%D 1982
%K jrnl, c1982, c198x, c19xx, zz0321, LLL algorithm, polynomial, factoring,
   factors, vector, lattice basis reduction, nearly orthogonal, orthogonalise
%X "... present a polynomial-time alg. to solve ...: given a non-zero polynomial
   f in Q(X) in one variable with rational coeffs., find the decomposition of f
   into irreducible factors in Q(X). It is well known that this is equiv. to
   factoring primitive polynomials feZ[X] into irreducible factors in Z[X]. Here
   we call f in Z[X] primitive if the GCD of its coeffs. (the content of f)
   is 1.  Our alg. performs well in practice, cf.(8). Its running time, measured
   in bit operations, is O(n^{1/2}+n^9(log(|f|)^3)."
    -- [<A HREF="https://doi.org/10.1007%2FBF01457454">doi:10.1007%2FBF01457454</A>]['21].
   Also see, "The Lenstra-Lenstra-Lovasz (LLL) lattice basis red'n alg. ...
   calculates an LLL-reduced (short, nearly orthogonal) lattice basis in
   time O(d^5 n log^3 B) ..."
   -- LLL@[<A HREF="https://en.wikipedia.org/wiki/Lenstra%E2%80%93Lenstra%E2%80%93Lov%C3%A1sz_lattice_basis_reduction_algorithm">wikip</A>]['21].
   [Also search for: lattice basis] and [also search for: Gram Schmidt].

%A C. Pomerance
%T Analysis and comparison of some integer factoring algorithms
%B Computational Methods in Number Theory, Part I
%E H. W. Lenstra, Jr.
%E R. Tijdeman
%I Math. Centre Tract 154, Amsterdam
%P 89-139
%D 1982
%K c1982, c198x, c19xx, zz0218, factoring, number theory, algorithm, integer,
   factoring, factorization, factorisation, algorithm, quadratic sieve
%X [Also search for: integer factorization].
   (Also see QS@[<A HREF="https://en.wikipedia.org/wiki/Quadratic_sieve">wikip</A>]['18].)

%A D. H. West
%T Approximate solution of the quadratic assignment problem
%J ACM Trans. Math. Softw.
%V 9
%N 4
%P 461-466
%M DEC
%D 1983
%K jrnl, TOMS, c1983, c198x, c19xx, quadratic assignment, travelling salesman,
   traveling, TSP
%X TSP is a special case.

%A L. Babai
%A W. M. Kantor
%A E. M. Luks
%T Computational complexity and the classification of finite simple groups
%J FOCS 24
%P 162-171
%D 1983
%K conf, FOCS, FOCS24, c1983, c198x, c19xx, maths, graph, isomorphism, valency,
   group, theory, NP, P, classification finite simple groups, CFSG
%X "... A1. A polynomial time alg. to test simplicity & find composition factors
   of a given perm.group (COMP).  A2. A poly.time alg. to find elts of given
   prime order p in a perm.group of order divisible by p.  A3. A poly.time
   reduction of the problem of finding Sylow subgroups of perm.groups (SYLFIND)
   to finding the intersection of two cosets of perm.groups (INT). [So] one can
   find Sylow subgroups of solvable groups & of groups with bounded nonabelian
   composition factors in polynomial time.  A4. A poly.time alg. to solve
   SYLFIND for finite simple groups.  A5. An ncd/log d alg. for isomorphism
   (ISO) of graphs of valency less than d & a consequent improved moderately
   exponential general graph isomorphism test in exp(c sqrt n log n) steps.
   A6. A moderately exponential, n,c sqrt n alg. for INT. Combined with A3, we
   obtain an nc sqrt n alg. for SYLFIND as well. All these problems have strong
   links to each other. ISO easily reduces to INT. A subcase of SYLFIND was
   solved in poly.time & applied to bounded valence ISO in [Lul]. Now, SYLFIND
   is reduced to INT. Interesting special cases of SYLFIND belong to
   NP intersection coNP & are not known to have subexp. solns. All the results
   stated depend on the classification of finite simple groups. We note that no
   previous ISO test had no(d) worst case behavior for graphs of valency < d.
   It appears that unless there is another radical breakthrough in ISO, indep.of
   the previous one, the simple groups classn is an indispensable tool for
   further developments."
   -- [<A HREF="http://dx.doi.org/10.1109/SFCS.1983.10">doi:10.1109/SFCS.1983.10</A>]['10].
   [Also search for: maths graph isomorphism].

%A L. Babai
%A E. M. Luks
%T Canonical labeling of graphs
%J Symp. on Theory of Comp.
%I ACM
%P 171-183
%D 1983
%K conf, STOC, STOC15, c1983, c198x, c19xx, zz0115, maths, graph, canonical,
   labelling, labeling, canonization, renumbering
%X "We announce an algebraic approach to the problem of assigning canonical
   forms to graphs. We compute canonical forms & the assoc. canonical labelings
   (or renumberings) in polynomial time for graphs of bounded valence, in
   moderately exponential, exp(n 1/2 + &ogr;(1)), time for general graphs, in
   subexponential, (n log n), time for tournaments & for 2-(&ngr;,&kgr;,&lgr;)
   block designs with &kgr;,&lgr; bounded & (n log log n) time for &lgr;-planes
   (symmetric designs) with &lgr; bounded. We prove some related problems
   NP-hard & indicate some open problems."
   -- [<A HREF="http://dx.doi.org/10.1145/800061.808746">doi:10.1145/800061.808746</A>]['15].
   (Also see canonization@[<A HREF="http://en.wikipedia.org/wiki/Graph_canonization">wikip</A>]['15].)
   [Also search for: maths graph canonical labelling].

%A H. N. Gabow
%A J. L. Bentley
%A R. E. Tarjan
%T Scaling and related techniques for geometry problems
%J Proc. of the Symposium on Theory of Computing (STOC)
%P 135-143
%D 1984
%K conf, c1984, c198x, c19xx, zz0613, 1D RMQ, algorithm, range minimum query,
   maximum, cartesian tree, lowest common ancestor, LCA, post office, problem
%X "3 techniques in computational geometry are explored: Scaling solves a
   problem by viewing it at increasing levels of numerical precision; activation
   is a restricted type of update operation, useful in sweep algs.; the
   Cartesian tree is a data struct. for problems involving maximums & minimums.
   These techniques solve the minimum spanning tree problem in Rk1 and Rk???
   in O(n(lg n)rlg lg n) time & O(n) space, where for Rk??? and k ??? 3,
   r &equil; k???2; for Rk1, r &equil; 1, 2, 4 for k &equil; 3, 4, 5 and
   r &equil; k for k > 5. Other problems solved include Rk1 and Rk all nearest
   neighbors, post office & maximum spanning tree; Rk maxima, Rk rectangle
   searching problems, & Zkp all nearest neighbors (1 ??? p ??? ???)."
   -- [<A HREF="http://dx.doi.org/10.1145/800057.808675">doi:10.1145/800057.808675</A>]['13].
   [Also search for: RMQ range].

%A L. Babai
%T On Lovasz lattice reduction and the nearest lattice point problem
%J Combinatorica
%V 6
%P 1-13
%M MAR
%D 1986
%K jrnl, c1986, c198x, c19xx, zz1120, lattice, algorithm, diophantine,
   integer linear programming, closest vector problem, CVP, nearest
%X "Answering a Q. of Vera Sos, we show how Lovasz' lattice redn can be used to
   find a pt of a given lattice, nearest within a factor of c^d (c=const.) to a
   given pt in R^d. ... two straightforward fast heuristic procs achieve this
   goal when applied to a lattice given by a L...reduced basis. The verification
   of one of them requires proving a geometric feature of L...reduced bases:
   ac^d_1 lwb on the angle between any member of the basis & the hyperplane
   generated by the other members, where c_1 = sqrt(2)/3. ... obtain a soln to
   the nonhomogeneous simultaneous diophantine approx. problem, optimal within a
   factor of C^d. [&] improve the Grotschel-Lovasz-Schrijver version of
   H.W.Lenstra's integer linear programming alg.. The algs., when applied to
   rational input vectors, run in polynomial time."
   -- [<A HREF="https://doi.org/10.1007/BF02579403">doi:10.1007/BF02579403</A>]['20].
   Also see LP@[<A HREF="https://en.wikipedia.org/wiki/Lattice_problem">wikip</A>]['20].
   [Also search for: lattice CVP].

%A S. Dvorak
%A B. Durian
%T Unstable linear time O(1) space merging
%J COMPJ
%V 31
%N 3
%D 1988
%P 279-282
%K sort, sorting, merge, merging, in situ, insitu, in-situ, algorithm,
   jrnl, COMPJ, c1988, c198x, c19xx, complexity
%X gives code       "...unstable merging of 2 neighbouring segments in an 1-[D]
   array is presented. The algorithm runs in O(1) space & in linear time. It is
   based on stable merging, but its working area is not chosen outside merged
   segments; instead it occupies the end of one of them. Despite the fact that
   there are no restrictions on segment sizes, the algorithm is the fastest in
   its class of those published so far."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/31.3.279">doi:10.1093/comjnl/31.3.279</A>]['05].
   [Also search for: insitu merge].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Sort/Insitu/">in-situ</A>].)

%A A. W. Appel
%A G. J. Jacobson
%T The world's fastest Scrabble program
%J CACM
%V 31
%N 5
%P 572-578
%M MAY
%D 1988
%K jrnl, cacm, automaton, directed acyclic word graph, DAWG, words, zz0304,
   data structure, game, games, c1988, c198x, c19xx
%X "An efficient backtracking algorithm makes possible a very fast program to
   play the Scrabble (r) brand crossword game. The efficiency is achieved by
   creating a data structures before the backtracking search begins that serves
   both to focus the search and to make each step of the search fast." 11 refs.
   [<A HREF="http://doi.acm.org/10.1145/42411.42420">.pdf</A>][3/'04]

%A Maw-Shang Chang
%T Efficient algorithms for the domination problems on interval and
   circular-arc graphs
%J SIAM J. Comput.
%V 27
%N 6
%P 1671-1694
%M DEC
%D 1998
%K c1998, c199x, c19xx, zz0899, jrnl, SIAM, algorithm, dominator, dominate,
   maxima, maths, graph
%X review in ACM Comp Rev p169 MAR '99.
   [Also search for: maxima dominate].

%A C. Burnikel
%A J. Ziegler
%T Fast recursive division
%J im Stadtwald, D-Saarbrucken
%M OCT
%D 1998
%K TR, c1998, c199x, c19xx, zz0621, fast, integer, computer arithmetic,
   division, div, BigInt
%X "... 2 K(n) + O(n log n) time to divide a 2n-digit number by an n-digit
   number where K(n) is the Karatsuba mult alg. time ..."
   -- [<A HREF="https://pure.mpg.de/rest/items/item_1819444_4/component/file_2599480/content">mpg.de</A>]['21],
      [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.47.565&rep=rep1&type=pdf">c'teseer</A>]['21].
   [Also search for: fast integer arithmetic].
   Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Arithmetic/">more</A>].

%A E. Chow
%A M. A. Heroux
%T An object-oriented framework for block preconditioning
%J ACM Trans. Math. Software
%V 24
%N 2
%P 159-183
%M JUN
%D 1998
%K jrnl, ACM, TMS, OO, OOP, matrix, matrices, diagonal, solve, solution,
   blocks, algorithm, zz0899
%X review in ACM Comp Rev p169 MAR '99
   Solve Ax=b for matrix A and vectores x and b.
   To help, seek M s.t. M^-1 approximates A^-1 so (M^-1)Ax=(M^-1)b.

%A P. Crescenzi
%T Strictly-upward drawings of ordered search trees
%J Theor. Comp. Sci.
%V 203
%N 1
%P 51-67
%M AUG
%D 1998
%K jrnl, TCS, tree, draw, drawing, plot, layout

%A K. Loudon
%T Mastering Algorithms with C
%I OReilly
%P 560
%D 1999
%K book, text, c1999, c199x, c19xx, algorithm, L3Ref, computer programming
%X pb us$29; uk us isbn:1565924533; uk us isbn13:978-1565924536.
   "... linked lists, stacks, queues, sets, hash tables, trees and B-trees,
   searching, heaps and priority queues, graphs, sorting and searching
   algorithms, numerical methods, data compression, Huffman coding, LZ77,
   data encryption, DES, RSA, graph algorithms, minimum spanning trees,
   geometric algorithms, and convex hulls. ..."

%A Z. Galil
%A G. F. Italiano
%A N. Sarnak
%T Fully dynamic planarity testing with applications
%J JACM
%V 46
%N 1
%P 28-91
%M JAN
%D 1999
%K JACM, jrnl ACM, c1999, c199x, c19xx, planar, maths, graph, graphs, test,
   biconnectivity, triconnectivity, zz0899
%X ... compressed certificates for planarity, bi and tri-connectivity ...
   application ... (i) insert edge if graph remains planar,
   (ii) delete and edge,  (iii) test if edge can be added and stay planar.
   Support these on O(n**2/3)-time  (insertion is "amortized").

%A M. D. McIlroy
%T A killer adversary for quicksort
%J SPE
%V 29
%P 1-4
%D 1999
%K jrnl, SPE, anti, sort, sorting, quick-sort, worst case time complexity,
   quadratic, speed, c1999, c199x, c19xx, zz0603
%X Quick sort can be made to go quadratic by constructing input on the fly.
   in reponse to the seq' of items compared. ...
   ... works against any implementation of quicksort, even a randomizing
   one that satisfies certain very mild and realistic assumptions.
   -- pdf@[<A HREF="http://www.cs.dartmouth.edu/~doug/mdmspe.pdf">dartm.</A>][6/'03].

%A P. Ferragina
%A R. Grossi
%T The string B-tree: A new data structure for string search in external
   memory and its application
%J JACM
%V 46
%N 2
%P 236-280
%M MAR
%D 1999
%K jrnl, JACM, c1999, c199x, c19xx, zz0899, string B-tree, trees, Btree, Btrees,
   search, searching, free text retrieval, index, indexing, suffix, prefix,
   dataStructure, DS
%X "... same worst-case complexity as B-trees they manage [search for]
   unbounded-length strings and perform much more powerful search operations
   such as the ones supported by suffix trees. ..."
   -- [<A HREF="http://dx.doi.org/10.1145/301970.301973">doi:10.1145/301970.301973</A>]['99].

%A M. Thorup
%T Undirected single-source shortest paths with positive integer weights in
   linear time
%J JACM
%V 46
%N 3
%P 362-394
%M MAY
%D 1999
%K jrnl, JACM, c1999, c199x, c19xx, algorithm, path, maths, graph, weighted,
   SSSP, Dijkstra, atomic heap, heaps, zz1199
%X Deterministic linear-time, i.e. O(|E|), and linear-space algorithm.
   NB. for +ve int weights. Good introductory survey from Dijkstra (1959) on.
    ... The alg. avoids the sorting bottleneck [for finding closest
   unvisited vertex] by building a hierarchical bucketing structure,
   identifying vertex pairs that may be visited in any order.
      The alg. is of theoretical interest only, *but* claims there
   is an implementable variation that is O(inv_Ackerman(|V|,|E|).|E|)
   i.e. very nearly O(|E|) in practice.
   -- [<A HREF="https://doi.org/10.1145/316542.316548">doi:10.1145/316542.316548</A>]['23].
   [Also search for: SSSP algorithm].

%T Combinatorial Pattern Matching
%E M. Crochemore
%A M. Paterson
%I SpringerVerlag
%S LNCS
%V 1645
%W Warwick Uni., UK
%M JUL
%D 1999
%K proc, conf, CPM, c1999, c199x, c19xx, CPM99, CPM1999, zz0300
%X uk us isbn:3540662782.

%A B. Mohar
%T The Laplacian spectrum of graphs
%J Graph Theory, Combinatorics and Applications
%V 2
%E Y. Alvi
%E et al
%I Wiley
%D 1991
%P 871-898
%K conf?, graph, c1991, c199x, c19xx, Laplace, Laplacian, spectrum, spectral,
   maths, Eigenvalue, Eigenvalues, lambda, Fiedler ordering,
   envelope minimization, Fiedler vector
%X "...a survey of known results about the spectrum of the Laplacian matrix of
   graphs with special emphasis on the second smallest Laplacian eigenvalue
   lambda and its relation to numerous graph invariants, including connectivity,
   expanding properties, isoperimetric number, maximum cut, independence number,
   genus, diameter, mean distance, and bandwidth-type parameters of a graph.
   Some new results and generalizations are added."
   Ref in  B e r r y  et al '96.
   [<A HREF="http://www.fmf.uni-lj.si/~mohar/Papers/Spec.pdf">pdf@lj</A>]['08].

%A B. Mohar
%T Laplace Eigen-values of graphs - a survey
%J Disc. Math.
%V 109
%N 1-3
%P 171-183
%M NOV
%D 1992
%K jrnl, c1992, c199x, c19xx, Eigenvalue, Eigenvalues, value, graph, vector,
   Fiedler ordering, maths, Laplacian, sparse matrix, band, bands, banded
%X "Several applications of Laplace eigenvalues of graphs in graph theory and
   combinatorial optimization are outlined."
   [<A HREF="http://dx.doi.org/10.1016/0012-365X(92)90288-Q">doi:10.1016/0012-365X(92)90288-Q</A>]['08].
   ref in  B e r r y  et al '96.

%A N. Robertson
%A P. D. Seymour
%T Graph Minors .XIII. The Disjoint Paths Problem
%J J. Comb. Theory, series B
%V 63
%N 1
%P 65-110
%M JAN
%D 1995
%K jrnl, c1995, c199x, c19xx, zz0415, maths, graph, path, minor, check
%X "We describe an alg., which for fixed k >= 0 has running time O(|V(G)|**3),
   to solve the following problem: Given a graph G & k pairs of vertices of G,
   decide if there are k mutually vertex-disjoint paths of G joining the pairs."
   -- [<A HREF="http://dx.doi.org/10.1006/jctb.1995.1006">doi:10.1006/jctb.1995.1006</A>]['15].
   (Also see, "For every fixed graph H, it is possible to test whether
               H is a minor of an input graph G in polynomial time"
    -- [<A HREF="http://en.wikipedia.org/wiki/Graph_minor">wikip</A>]['15].)

%A G. Carpento
%A M. Dell'Amico
%A P. Toth
%T CDT: A subroutine for the exact solution of large-scale,
   asymmetric traveling salesman problems
%J ACM Trans. Math. Softw.
%V 21
%N 4
%P 410-415
%M DEC
%D 1995
%K jrnl, TOMS, c1995, c199x, c19xx, travelling, TSP, problem, maths, graph,
   graphs
%X [Also search for: travelling salesman problem].

%A T. Feder
%A R. Motwani
%T Clique partitions, graph compression and speeding up algorithms
%J Jrnl. Comp. and Sys. Sci.
%P 261-272
%V 51
%N 2
%M OCT
%D 1995
%O Proc 23rd ACM Symp. on Theory of Computing, pp.123-133, '91.
%K JCSS, jrnl, c1995, c199x, c19xx, maths, graph, graphs, bipartite, biclique,
   clique, cliques, partition, compress, compression, algorithm
%X "We first consider the problem of partitioning the edges of a graph G into
   bipartite cliques s.t. the total order of the cliques is minimized, where the
   order of a clique is the # of vertices in it. It is shown that the problem is
   NPC. We then prove the existence of a partition of small total order in a
   sufficiently dense graph & devise an efficient alg. to compute such a
   partition. ... our alg. exhibits a trade-off between the total order of the
   partition & the running time. Next, we define the notion of a compression of
   a graph G & use the result on graph partitioning to efficiently compute an
   optimal compression for graphs of a given size. An interesting application of
   the graph compression result arises from the fact that several graph algs.
   can be adapted to work with the compressed representation of the input graph,
   thereby improving the bound on their running times, particularly on dense
   graphs. This makes use of the trade-off result we obtain from our
   partitioning alg.. The algs. analyzed include those for matchings, vertex
   connectivity, edge connectivity & shortest paths. In each case, we improve
   upon the running times of the best-known algs."   -- from a ref.
   -- [<A HREF="http://theory.stanford.edu/~rajeev/postscripts/compress.ps.gz">.ps.gz@stanf</A>]['08].
   [p1 "...a 'compression' G* of a graph G ... (a) G* is a graph with m* edges,
   where m* < #edges in G, (b) it is comp. easy to convert G into G* and v.."]
   pdf : [<A HREF="http://dx.doi.org/10.1006/jcss.1995.1065">doi:10.1006/jcss.1995.1065</A>].
   Conf. pdf: [<A HREF="http://doi.acm.org/10.1145/103418.103424">doi:10.1145/103418.103424</A>]['08].
   [Also search for: compress graph]  and  [also search for: graph partition].

%A F. Alizadeh
%T Interior point methods in semidefinite programming with applications to
   combinatorial optimization
%J SIAM J. Optim.
%V 5
%P 13-51
%D 1995
%K jrnl, c1995, c199x, c19xx, Semidefinite Programming, SDP, optimisation,
   method
%X "... SDP problem, i.e., the optimization problem of a linear fn of a
   symmetric matrix subject to linear equality constraints & the additional
   condition that the matrix be positive semidefinite.... Next an interior pt
   alg. is presented that converges to the optimal soln in polynomial time. ..."
   -- [<A HREF="https://doi.org/10.1137/0805002">doi:10.1137/0805002</A>]['22].
   ps@[<A HREF="http://rutcor.rutgers.edu/~alizadeh/MYPAPERS/sdp.ps.gz">rutgers</A>]['08],
   auth@[<A HREF="http://rutcor.rutgers.edu/~alizadeh/">rutgers</A>]['08].
   And SDP@[<A HREF="https://en.wikipedia.org/wiki/Semidefinite_programming">wikip</A>]['22].
   (S.D.prog: minimise a linear fn subject to the constraint that
   an affine comb'n of symmetric matrices is +ve semidefinite.)
   [Also search for: SemiDefinite programming].

%A B. T. Messmer
%A H. Bunke
%T Subgraph isomorphism in polynomial time
%D 1995
%K TR, c1995, c199x, c19xx, subgraph isomorphism, maths, graph
%X "... for systems which differentiate between graphs that are a priori known,
   so-called model graphs, & unknown graphs, so-called input graphs. The
   problem to be solved is to find a subgraph isomorphism from an input graph,
   which is given on-line, to any of the model graphs. The new method is based
   on an *intensive* preprocessing step in which the model graphs are used to
   create a decision tree. ...
   *If* we neglect the time needed for preprocessing, the comp.complexity of
   the new subgraph isomorphism alg. is only quadratic in the # of input graph
   vertices. ... However, the d.tree ... may grow exponentially ..."
   -- [<A HREF="ftp://ftp.iam.unibe.ch/pub/TechReports/1995/iam-95-003.ps.gz">ftp .ps.gz</A>]['08].
   [Also search for: subgraph isomorphism].

%A K. Keeler
%A J. Westbrook
%T Short encodings of planar graphs and maps
%J Discrete Applied Mathematics
%V 58
%N 3
%P 239-252
%D 1995
%K jrnl, c1995, c199x, c19xx, planar, maths, graph, graphs, map, information,
   compress, structure, structures, data compression, succinct, brief, encoding,
   the Simpsons
%X "... space-efficient encoding schemes for planar graphs & maps. Our results
   improve on the constants of previous schemes & can be achieved with simple
   encoding algs.. They are near-optimal in number of bits per edge."
   -- [<A HREF="http://dx.doi.org/10.1016/0166-218X(93)E0150-W">doi:10.1016/0166-218X(93)E0150-W</A>]['08].
   "free of loops & of degree 1 Vs, in 3E bits" -- also see V i a n a, c2008.
   [Also search for: compress graph].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/Graph/">graphs</A>].)
      [And, in 'The Simpsons and Their Math. Secrets' (2013), p.109, S.Singh
       reports that KK is a writer for 'The Simpsons' TV cartoon comedy.
       [Also search for: Singh Simpsons book].]

%A M. Farach
%A T. M. Przytycka
%A M. Thorup
%T Computing the agreement of trees with bounded degrees
%J Proc. Third Annual European Symp. on Algorithms
%I SpringerVerlag
%S LNCS
%V 979
%P 381-393
%D 1995
%K conf, MolBio, c1995, c199x, c19xx, largest, maximum, agreement, subtree,
   subtrees, sub tree, evolutionary, MAST, bounded, degree, branching
%X "... where trees are rooted & of bounded degree, [typically] binary. ...
 . algorithm which computes the MAST of k trees on n species where some
   tree has max. degree d in time O(kn**3+n**d)  ...
      improves the Amir & Keselman FOCS '94 O(kn**(d+1) + n**(2d)) bound. ...
 . algorithm which computes the MAST of 2 trees with degree bound d in time
   O(n (sqrt d) log**3 n)  ...
     [cf] Farach & Thorup FOCS '94 O(nc**sqrt(log n)+ n sqrt(d) log n) bound.
   Thus, for d a constant, we get an O(n log**3 n) bound, replacing the
   previous O(nc**sqrt(log n)) bound."   (isbn:3540603131.)
   -- pdf@[<A HREF="http://dx.doi.org/10.1007/3-540-60313-1_157">doi:10.1007/3-540-60313-1_157</A>]['08].

%A S. D. Monson
%A N. J. Pullman
%A R. Rees
%T A survey of clique and biclique coverings and factorizations of
   (0, 1)-matrices
%J Bull. Inst. Combin. Appl.
%V 14
%P 17-86
%D 1995
%K c1995, c199x, c19xx, zz0413, boolean, binary, matrices, covering,
   factorisation, factoring, algorithm, decomposition, BMF
%X [<A HREF="http://www.ams.org/mathscinet-getitem?mr=1330781">ams</A>]['13], MR1330781 (96f:05150) 05C70 (05C35 15A24).
   Auth2, NJP@[<A HREF="http://en.wikipedia.org/wiki/Norman_J._Pullman">wikip</A>]['13] and @[<A HREF="http://www.mast.queensu.ca/~gregoryd/pullman/">queensu</A>]['13] (1931-1999).

%A L. Arge
%T The buffer tree: A new technique for optimal I/O-algorithms
%J Proc. Workshop on Algs. and Data Structs
%I SpringerVerlag
%S LNCS
%V 955
%P 334-345
%D 1995
%K wShop, c1995, c199x, c19xx, buffer tree, trees, bufferTree, algorithm,
   data structure, dataStructure, DS, cache, locality, memory, IO
%X "... technique for transforming an internal-memory tree DS into an external-
   -memory structure. ... can be used to develop a search tree like structure,
   a priority queue, a (1D) range tree & a segment tree, & give egs of how these
   structures can be used to develop efficient I/O algs.. All our algs. are
   either extremely simple or straightforward generalizations of known internal-
   -memory algs. - given the developed external DSs. We believe that algs. ...
   of practical interest due to rel. small constants in the asymptotic bounds."
   [p9: Ops. on the structure ... lazy ...  When a [node's] buffer [of ops] is
        full [push contents] one level down ...]
   -- pdf@[<A HREF="http://www.brics.dk/RS/96/28/BRICS-RS-96-28.pdf">@brics.dk</A>]['08] or,
   Springer [<A HREF="http://dx.doi.org/10.1007/3-540-60220-8_74">doi:10.1007/3-540-60220-8_74</A>]['08]; uk us isbn13:978-3540602200.
   [Also search for: buffer tree].

%A D. Dor
%A U. Zwick
%T Selecting the median
%J Proc. sixth annual ACM-SIAM symp. on Discrete Algorithms (SODA)
%P 28-37
%M JAN
%D 1995
%O SIAM J. Comput., 28(5), pp.1722-1758, 1999
%K conf, SODA, c1995, c199x, c19xx, zz0818, median, select, selection, problem,
   algorithm
%X "Improving the standing result of Schonhage, Paterson and Pippenger [1976]
   we show that the median of a containing N elts can be found using at most
   2.95N comparisons."
   -- pdf@[<A HREF="https://www.cs.unc.edu/~plaisted/comp550/fast.median.finding.pdf">unc</A>]['18],
      [<A HREF="https://doi.org/10.1137/S0097539795288611">doi:10.1137/S0097539795288611</A>]['18] (SIAM J. C. 1999),
      [<A HREF="https://dl.acm.org/citation.cfm?id=313660">acm</A>]['18].
   [Also search for: median selection problem].

%A R. Motwani
%A P. Raghavan
%T Randomized Algorithms
%I CUP
%P 496
%D 1995
%K book, text, CUP, c1995, c199x, c19xx, randomized algorithm, randomised
%X 1st ed 1995; hb us$71; uk us isbn:0521474655; uk us isbn13:978-0521474658.
   "...  The first part of the text presents basic tools such as probability
   theory & prob. analysis that are frequently used in alg. applications.
   ... examples are also given ...  the second part of the book ... focuses on
   an important area to which randomized algs. can be applied ...
   written primarily as a text for advanced undergraduates and graduate ..."
   [Also search for: Randomized Algorithm].

%A A. O. Olagunju
%T A generalised base conversion algorithm
%J J. Elisha Mitchell Sci. Soc.
%V 111
%N 2
%P 132-136
%D 1995
%K jrnl, c1995, c199x, c19xx, zz0624, integer, computer arithmetic,
   base conversion
%X -- [<A HREF="https://www.jstor.org/stable/24335418">jstor:24335418</A>]['24].
   [Also search for: integer base conversion].

%A D. Dor
%A U. Zwick
%T Finding the alpha.n-th largest element
%J Combinatorica
%V 16
%N 1
%P 41-58
%M MAR
%D 1996
%K jrnl, c1996, c199x, c19xx, zz0818, median, select, selection,
   problem, algorithm
%X "...an alg. for selecting the alpha.n-th largest elt (where 0 < alpha < 1),
   from a totally ordered set of N elts, using at most (1+(1+o(1))H(alpha))Â·n
   comparisons where H(alpha) is the binary entropy fn & the o(1) stands for a
   fn that tends to 0 as alpha tends to 0. For small values of alpha this is
   almost the best possible as there is a lower bound of about (1+H(alpha))Â·n
   comparisons. The alg. obtained beats the global 3n upper bound of Schonhage,
   Paterson & Pippenger [1976] for alpha < 1/3."
   -- [<A HREF="https://doi.org/10.1007/BF01300126">doi:10.1007/BF01300126</A>]['18].
   [Also search for: median selection problem].

%A R. Chang
%T On the query complexity of clique size and maximum satisfiability
%J Jrnl. Comp. and Sys. Sci.
%P 298-313
%V 53
%N 2
%M OCT
%D 1996
%K JCSS, jrnl, cliques, maths, graph, graphs, Max Sat, MaxSat
%X from a ref.

%A C. Pomerance
%T A tale of two sieves
%J Notices of the AMS
%P 1473
%M DEC
%D 1996
%K c1996, c199x, c19xx, zz0218, maths, prime numbers, integer, factorisation,
   factorization, factoring, quadratic, number field, sieve, number theory,
   primes, algorithm, Pollard
%X "... In 1970 it was barely possible to factor 'hard' 20-digit numbers. In
   1980, in the heyday of the Brillhart-Morrison continued fraction factoring
   alg., factoring of 50-digit numbers was becoming commonplace. In 1990 my own
   quadratic sieve factoring alg. had doubled the length of the numbers that
   could be factored, the record having 116 digits. By 1994 the quadratic sieve
   had factored the famous 129-digit RSA challenge number that had been
   estimated in Martin Gardner's 1976 Scientific American column to be safe for
   40 quadrillion years (though other estimates around then were more modest).
   But the quadratic sieve is no longer the champion. It was replaced by
   Pollard's number field sieve in the spring of 1996 ..."
   -- [<A HREF="http://www.ams.org/notices/199612/pomerance.pdf">www</A>]['18].
   [Also search for: integer factorisation].

%A F. C. M. Lau
%A P. K. W. Cheng
%A S. S. H. Tse
%T An algorithm for the 2-median problem on two-dimensional meshes
%J COMPJ
%P 101-108
%V 44
%N 2
%D 2001
%K compj, jrnl, 2median, median2, two-median, 2D, mesh,
   location theory, c2001, c200x, c20xx, zz0801
%X p-median problem: Locate p identical facilities such that the
      sum of the distance between every client in the network and
      its nearest facility is minimized.  NP-hard for general networks.
   Paper gives an O(m.n**2.q)-time algorithm, for p=2, on an m*n mesh.
     (Mesh is undirected; all edges of length 1; clients and facilities
      at vertices; all clients have demand 1; can have multiple clients
      at a vertex; a facility can serve any # of clients;
      facilities can be located at any vertices.)

%A J.-D. Boissonnat
%A M. Yvinec
%A H. Bronniman (translator)
%T Algorithmic Geometry
%I CUP
%P 541
%D 2001
%K book, text, c2001, c200x, c20xx, algorithm, combinatorial geometry
%X ... geometric data structures, algorithmic data structuring techniques and
   results from combinatorial geometry. ...
   pb; uk us isbn:0521565294; uk us isbn13:978-0521565295.

%A L. Xiang
%A K. Ushijima
%T On O(1) time algorithms for combinatorial generation
%J COMPJ
%V 44
%N 4
%P 292-302
%D 2001
%K jrnl, COMPJ, algorithm, combinatorial object, objects, generate, generating,
   generator, McKay, loopless program, c2001, c200x, c20xx, zz1001
%X [<A HREF="http://dx.doi.org/10.1093/comjnl/44.4.292">doi:10.1093/comjnl/44.4.292</A>]['05],
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_44/Issue_04/440292.sgm.abs.html">www</A>][10/'01].
   Loopless programs produce the `next' object from the current one
   (and may in fact contain loops!).

%A R. W. P. Luk
%T Compact morphic directed acyclic word graphs
%J COMPJ
%V 44
%N 5
%P 425-434
%D 2001
%K graph, DAWG, MDAWG, string, factor, suffix, automaton, COMPJ, jrnl, zz1101,
   maths, factors, words, DAWGs
%X 14 refs.
   [<A HREF="http://dx.doi.org/10.1093/comjnl/44.5.425">doi:10.1093/comjnl/44.5.425</A>]['05],
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_44/Issue_05/440425.sgm.abs.html">www</A>][11/'01].

%A T. H. Cormen
%A C. E. Leiserson
%A R. L. Rivest
%A C. Stein
%T Introduction to Algorithms
%I MITpress
%P 1180
%D 2001
%K book, text, c2001, c200x, c20xx, algorithm, L3REF, L4REF, zz1201,
   computer programming
%X 3rd ed 2009, pp.1312;
     pb us$62; uk us isbn:0262033844; uk us isbn13:978-0262033848.
     "... new chapters, on van Emde Boas trees and multithreaded algs., & ...
     to the ch. on recurrences (now called "D.-and-C."). ... improved
     [<A HREF="http://www.allisons.org/ll/AlgDS/Dynamic/">dynamic-prog.</A>]
     and greedy algs. and a new notion of edge-based flow in the material
     on flow networks. ..."
   2nd ed 2001, pp.1180; pb, uk us isbn:0262531968;  hb, uk us isbn:0262032937.
   1st ed 1990.
   Uses Pascal like pseudo-code.   [Also search for: algorithm book].

%A E. Bingham
%A H. Mannila
%T Random projection in dimensionality reduction: applications to image and
   text data
%J KDD
%P 245-250
%M AUG
%D 2001
%K conf, c2001, c200x, c20xx, zz0323, approximate, similar, search, retrieval,
   locality sensitive hashing, hash, projections, neighbourhood
%X "Random projections have recently emerged as a powerful method for
   dimensionality red'n ... Our application areas are the processing of both
   noisy & noiseless images, & information retrieval in text documents ..."
   -- [<A HREF="https://doi.org/10.1145/502512.502546">doi:10.1145/502512.502546</A>]['23].
   [Also search for: hashing neighbourhood].

%A W. Myrvold
%A F. Ruskey
%T Ranking and unranking permutations in linear time
%J IPL
%V 79
%N 6
%P 281-284
%M SEP
%D 2001
%K jrnl, IPL, c2001, c200x, c20xx, zz0713, permutation, permutations, rank,
   ranking, unranking, function, enumerate, enumeration, generator, mapping,
   integers, algorithm, inversion vector, factoradic
%X "A ranking fn for the perms on n symbols assigns a unique integer in the
   range [0, n!-1] to each of the n! perms. The corr. unranking fn is the
   inverse: given an int between 0 & n!-1, the value of the fn is the perm
   having this rank. We present simple ranking & unranking algs for perms that
   can be computed using O(n) arithmetic operations."
  (NB. The order put on the perms is NOT the usual lexicographical order.)
   -- [<A HREF="http://dx.doi.org/10.1016/S0020-0190(01)00141-7">doi:10.1016/S0020-0190(01)00141-7</A>]['13], and
   ps@[<A HREF="http://www.cs.uvic.ca/~wendym/my_pubs/RankPerm.ps.gz">uvic</A>]['13].
      (Given p=[p_0 p_1...p_(n-1)], its inv_Vec v=[v_0 v_i...v_(n-1)], where
       v_i is the # of p_j s.t. p_j > p_i and i > j.  == "factoradic" rep'n.)
   [Also search for: ranking permutations].

%A D. H. Besset
%T Object-Oriented Implementation of Numerical Methods:
   An Introduction with Java and Smalltalk
%I MorganKaufmann
%P 792
%D 2001
%K book, text, c2001, c200x, c20xx, numerical algorithms, algorithm, methods,
   math, maths, OO, OOP
%X us$64, uk us isbn:1558606793; uk us isbn13:978-1558606791.
   (Also see [<A HREF="http://commons.apache.org/math/">commons.../math</A>]['07].)

%A G. Chaudhry
%A T. H. Cormen
%A L. F. Wisniewski
%T Columnsort lives! An efficient out-of-core sorting program
%J Proc. 13th annual ACM Symp. on Parallel Algorithms and Architectures
%I ACM
%P 169-178
%D 2001
%K conf, columnSort, c2001, c200x, c20xx, sorting, column sort, columnSort,
   algorithm, now, parallel, nowSort, mesh, grid, farm, multiprocessor,
   workstations, Leighton
%X "...parallel out-of-core sorting alg. ...based on Leighton's['85] columnsort
   ... show how to relax some of the steps of the original columnsort alg. to
   permit a faster out-of-core implementation. Our alg. requires only 4 passes
   over the data, & a 3-pass implementation is possible. Although there is a
   limit on the # of records that can be sorted - as a fn of the memory used
   per processor - this upper limit need not be a severe restriction, & it
   increases superlinearly with the per-processor memory. ... out-of-core
   multiprocessor sorting alg. whose output is in the order assumed by the
   Parallel Disk Model. ... competitive with that of NOW-Sort, ... sort large
   amounts of data quickly on a cluster of workstations." [11 refs].
   -- [<A HREF="http://doi.acm.org/10.1145/378580.378627">doi:10.1145/378580.378627</A>]['09], isbn:1581134096.

%A R. Sedgewick
%T Algorithms in C, Parts 1-5 (2 Vols.): Fundamentals, Data Structures,
   Sorting, Searching, and Graph Algorithms
%I AddisonWesley
%D 2001
%K book, text, c2001, c200x, c20xx, sort, search, algorithm, data structure,
   dataStructure, DS, maths, graph, Sedgewick, Sedgwick
%X 2 volumes; 3rd ed; uk us isbn:0201756080; uk us isbn13:978-0201756081.
   [Also search for: Sedgewick book].

%A A. Aggarwal
%A T. Tokuyama
%T Consecutive interval query and dynamic programming on intervals
%J Disc. Appl. Math.
%V 85
%N 1
%P 1-24
%M JUN
%D 1998
%K jrnl, DPA, maths, algorithm, convex, concave, Monge, matrix search,
   sequential partition, maximum clique covering, interval graph, query,
   c1998, c199x, c19xx, zz0202
%X Given a set of n points (nodes) on a line and a set of m weighted intervals
   defined on the nodes, we consider a particular dynamic programming (DP)
   problem on these intervals. If the weight function of the DP has convex or
   concave property, we can solve this DP problem efficiently by using
   matrix searching in Monge matrices, together with a new query data
   structure, which we call the consecutive query structure. We invoke our
   algorithm to obtain fast algorithms for
    . sequential partition of a graph and for
    . maximum K-clique of an interval graph.
   [<A HREF="http://www.elsevier.com/gej-ng/10/16/23/47/17/show/toc.htt">issue</A>][2/'02]
   [<A HREF="http://www.mathformath.com/">mathformath</A>][2/'02]

%A G. H. Golub
%A C. F. van Loan
%T Matrix Computations
%I NorthOxford Acad.
%P 728
%D 1983
%K book, text, matrices, matrix, algorithm, algorithms, numerical methods,
   Gaussian elimination, orthogonalization, Eigenvalues, Lanczos, zz0502
%X 3rd ed c1996, us$39; us isbn:0801854148; us isbn13:978-0801854149.
   (?1st ed; uk isbn:0946536058; uk isbn13:978-0946536054.?  via Rod W.)

%A G. Gallo
%A M. D. Grigoriadis
%A R. E. Tarjan
%T A fast parametric maximum flow algorithm and applications
%J SIAM J. Comput.
%V 18
%N 1
%D 1989
%K jrnl, c1989, c198x, c19xx, zz0423, maths, graph, max flow, problem,
   algorithm, dense, densest subgraph
%X "The classical max flow problem sometimes occurs in settings in which the
   arc capacities are not fixed but are fns of a single param., & the goal is to
   find the value of the param. s.t. the corr. max flow or min cut satisfies
   some side condn. ... it is shown that the recent MFalg of Goldberg & T. can
   be extended to solve an important class of such parametric MFPs, at the cost
   of only a const. factor in its worst-case time bound. Faster algs. for a
   variety of combinatorial optimization problems follow from the result."
   -- [<A HREF="https://doi.org/10.1137/0218003">doi:10.1137/0218003</A>]['23].
   (Also see https://en.wikipedia.org/wiki/Dense_subgraph">wikip</A>]['23].)
   [Also search for: dense subgraph problem].

%A D. Perrin
%T Finite automata
%J Handbook of Theoretical Comp. Sci.
%I MITpress
%E J. van Leeuwen
%P 3-57
%V A
%D 1990
%K book, c1990, c199x, c19xx, DAWG, DAWGs, automaton, state, automaton, FSA, HMM
%X pb, us isbn:0262720140; us isbn13:978-0262720144.

%A R. A. Horn
%A C. R. Johnson
%T Matrix Analysis
%P 575
%I CUP
%D 1990
%K book, text, CUP, c1990, c199x, c19xx, matrix analysis, matrices, numerical
%X 1st ed c1990, pb us$37; uk us isbn:0521386322; uk us isbn13:978-0521386326.

%A H. L. Bodlaender
%T Polynomial algorithms for graph isomorphism and chromatic index on partial
   k-trees
%J J. of Algorithms
%V 11
%N 4
%P 631-643
%M DEC
%D 1990
%K jrnl, c1990, c199x, c19xx, algorithms, maths, graph, partial k tree, width,
   trees, kTree, treewidth
%X "... show that graph isomorphism & chromatic index are solvable in
   polynomial time when restricted to the class of graphs with treewidth<=k
   (k a constant) (or equivalently, the class of partial k-trees)."  [23 refs].
   -- [<A HREF="http://dx.doi.org/10.1016/0196-6774(90)90013-5">doi:doi:10.1016/0196-6774(90)90013-5</A>]['08].
   [ 1. A complete graph with k vertices is a k-tree.
     2. If G=(V,E) is a k-tree, and not(w in V), and v1,...,vk is a clique
        then H=(V+{v}, E+{(v[i],v)|1<=i<=k}) is a k-tree
     3. All k-trees can be formed from 1 and 2.
     A graph is a 'partial k-tree' iff it is a subgraph of a k-tree.]
   [Also search for: maths graph isomorphism].

%A S. B. Maurer
%A A. Ralston
%T Discrete Algorithmic Mathematics
%I AddisonWesley
%P 772
%D 1991
%K book, text, c1991, c199x, c19xx, maths, comp sci, CSci, counting
%X 3rd ed c2004; hb; uk us isbn:1568811667; uk us isbn13:978-1568811666.
   via Rod W.

%A L. Pursell
%A S. Y. Trimble
%T Gram-Schmidt orthogonalization by Gauss elimination
%J The American Math. Monthly
%V 98
%N 6
%P 544-549
%M JUN-JUL
%D 1991
%K jrnl, AMS, maths, c1991, c199x, c19xx, zz0223, orthogonalisation,
   orthogonalize, normal, orthogonalise, orthonormal, vector, lattice, basis,
   Gram, Schmidt, algorithm, GramSchmidt
%X -- Jstor@[<A HREF="https://doi.org/10.2307/2324877">doi:10.2307/2324877</A>]['23].
   Also see, "a method for orthonormalizing a set of vectors in an inner product
   space, most commonly the Euclidean space R^n ... The GS process takes a
   finite, lin. indep. set of vectors S={v1,...,vk} for k <= n & generates an
   ortho. set S'={u1,...,uk} that spans the same k-dim. subspace of R^n as S."
   -- GS@[<A HREF="https://en.wikipedia.org/wiki/Gram%E2%80%93Schmidt_process">wikip</A>]['23].
   [Also search for: lattice basis] and [also search for: LLL algorithm].

%A C. H. Papadimitriou
%A M. Yannakakis
%T Optimization, approximation, and complexity classes
%J J. Comput. System Sci.
%V 43
%P 425-440
%D 1991
%K jrnl, c1991, c199x, c19xx, MINIMUM VERTEX COVER, MINIMUM DOMINATING SET,
   MINIMUM FEEDBACK ARC SET, MAXIMUM INDEPENDENT SET,
   MAXIMUM K-COLORABLE SUBGRAPH, MAXIMUM CUT, MAXIMUM DIRECTED CUT,
   MINIMUM SET COVER, MAXIMUM SATISFIABILITY, MAXIMUM K-SATISFIABILITY,
   MAXIMUM NOT-ALL-EQUAL 3-SATISFIABILITY, graph algorithm, NP, NPC, class, JCSS
%X "We define a natural variant of NP, MAX NP, and also a subclass called
   MAX SNP. These are classes of optimization problems, and in fact contain
   several natural, well-studied ones. We show that problems in these classes
   can be approximated with some bounded error. ..."
   -- pdf@[<A HREF="http://doi.acm.org/10.1145/62212.62233">doi:10.1145/62212.62233</A>]['09].
   Via GF & [<A HREF="http://www.csc.kth.se/~viggo/wwwcompendium/">~viggo</A>]['09].

%A M. Agrawal
%A N. Kayal
%A N. Saxena
%T Primes is in P
%I Dept. Comp. Sci. & Eng., Indian Inst. of Tech., Kanpur
%M AUG
%D 2002
%O Annals of Maths, 160(2), pp.781-793, Sept. '04
%K TR, primality, prime, number, primes, AKS test, testing, computer algorithm,
   AKS, India, young students, polynomial time, P, NP, complexity, feasible,
   RSA cryptography, public key, encryption, do not panic,
   c2002, c200x, c20xx, zz0802,
%X "... present a deterministic polynomial-time algorithm
   that determines whether an input number n is prime or composite. ..."
   -- [<A HREF="http://www.cse.iitk.ac.in/users/manindra/primality.ps">paper</A>][8/'02].
   (Also See Ann. of Maths, Sept. 2004,
    [<A HREF="https://doi.org/10.4007/annals.2004.160.781">doi:10.4007/annals.2004.160.781</A>]['18] .)
     prime(n :int)
       if n is of the form a**b, a in N and b > 1 then return COMPOSITE
       end_if;
       r := 2;
       while r < n do
         if gcd(n, r) not_eq 1 then return COMPOSITE end_if;
         if r is prime then
           let q be the largest prime factor of r-1;
           if q >= 4*sqrt(r)*log(n) and n**((r-1)/q) not_equiv 1 (mod r) then
             break;
           end_if
         end_if;
         r := r+1
       end_while;
       for a := 1 to 2*sqrt(r)*log(n) do
         if (x-a)**n not_equiv (x**n-a)  (mod x**r-1, n) then
           return COMPOSITE
         end_if
       end_for;
       return PRIME
   ----------------------------------
   "We present an unconditional deterministic polynomial-time algorithm that
   determines whether an input number is prime or composite."
   "... The asymptotic time complexity of the alg. is O~(log^(21/2) n). ..."
   -- Annals Maths, 2004.
   (Public-key cryptographers should not panic, yet. No <I>practical</I> gain
   over the probabilistic method, although the idea might lead to ... what?)
   [Also search for: primality]  (& [also search for: integer factorisation]).
  (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Primes/">primality</A>].)

%A M. Paterson
%T Progress in selection
%J Scandinavian Workshop on Algorithm Theory
%P 368-379
%D 1996
%O LNCS vol.1097, Spr'nger
%K conf, c1996, c199x, c19xx, selection, problem, algorithm, percentile,
   percentiles, median, quartile, quartiles, ith, kth, select, zz0803, problem,
   intro, survey
%X "There has been recent progress in the selection problem, and in
   median-finding in particular, after a lull of ten years. This paper
   reviews some ancient and modern results on this problem, and suggests
   possibilities for future research."
   -- [<A HREF="https://doi.org/10.1007/3-540-61422-2_146">doi:10.1007/3-540-61422-2_146</A>]['18],
      [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.55.1195&rep=rep1&type=pdf">c'teseer</A>]['18],
      [<A HREF="http://www.dcs.warwick.ac.uk/~leslie/alcompapers/selection.ps">.ps</A>][8/'03].
   ? '96 or '97 ?  [at  W a r w i c k,  U K].
   * Also see  B l u m  et al '73.
   [Also search for: median selection problem].

%A J. K. P. Kuan
%A P. H. Lewis
%T Fast k nearest neighbour search for R-tree family
%J Proc. First Int. Conf. on Information, Communications, and Signal Processing
%P 924-928
%W Singapore
%D 1997
%K conf, R-tree, Rtree, knn, MINMAXDIST, MINDIST, dimensions, distance
%X A simplified k nearest neighbour (knn) search for the R-tree family is
   proposed in this paper. This method is modified from the technique
   developed by Roussopoulos et al. The main approach aims to eliminate
   redundant searches when the data is highly correlated. We also describe how
   MINMAXDIST calculations can be avoided using MINDIST as the only distance
   metric which gives a significant speed up. Our method is compared with
   Roussopoulos et al.'s knn search on Hilbert R-trees in different dimensions,
   and shows that an improvement can be achieved on clustered image databases
   which have large numbers of data objects very close to each other. However,
   our method only achieved a marginally better performance of pages accessed
   on randomly distributed databases and random queries far from clustered
   objects, but has less computation intensity.
   [<A HREF="http://eprints.ecs.soton.ac.uk/archive/00000841/">paper</A>][10/'02]

%A L. Mico
%A J. Oncina
%A R. C. Carrasco
%T A fast branch and bound nearest neighbour classifier in metric spaces
%J Pattern Recognition Letters
%V 17
%P 731-739
%D 1996
%K jrnl, nn, knn, space, neighbor, TLAESA, Tree LAESA, AESA
%X [<A HREF="http://www.dlsi.ua.es/~mico/publicaciones.html">ref</A>][10/'02]

%A D. A. Christie
%T Sorting permutations by block-interchanges
%J IPL
%V 60
%N 4
%P 165-169
%M NOV
%D 1996
%K jrnl, IPL, c1996, c199x, c19xx, sort, sorted, sorting, permutation, strings,
   block interchange, edit distance, swap, exchange, move, moves, similarity,
   algorithm
%X "... introduce an operation, called block-interchange, in which 2 substrings,
   or blocks, swap positions in the perm.. We demonstrate a polynomial-time
   alg. for calculating the block-interchange distance of a perm. (i.e. the
   min. # of block-interchanges required to transform the perm. to the id.).
   ... determine the block-interchange diameter of the symmetric group."
   [<A HREF="http://dx.doi.org/10.1016/S0020-0190(96)00155-X">doi:10.1016/S0020-0190(96)00155-X</A>]['09].
   [Also search for: strings block moves].

%A M. X. Goemans
%A D. P. Williamson
%T Primal-dual approximation algorithms for feedback problems in planar graphs
%J Proc. 5th Int. Conf. on Integer Prog. and Combinatorial Optimization
%I SpringerVerlag
%S LNCS
%V 1084
%P 147-161
%D 1996
%O Combinatorica, 17, pp.1-23, 1997
%K conf, c1996, c199x, c19xx, maths, graph, feedback arc set, nearly, near DAG,
   almost, algorithm, MINIMUM FEEDBACK VERTEX SET, MINIMUM FEEDBACK ARC SET,
   MINIMUM EDGE DELETION K-PARTITION, maximum acyclic subgraph, approximation
%X NB. *Planar*.
   "Given a subset of cycles of a graph, we consider the problem of finding a
   minimum-weight set of vertices that meets all cycles in the subset. ...
   generalizes a # of problems, inc. the minimum-weight feedback vertex set
   problem in both directed & undirected graphs, the subset feedback vertex set
   problem, & the graph bipartization problem ... . We give a 9/4-approximation
   alg. for the general problem in planar graphs, given that the subset of
   cycles obeys certain properties. This results in 9/4-app.alg. for the
   aforementioned feedback and bipartization problems in planar graphs. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/PL00009810">doi:10.1007/PL00009810</A>],
   & pdf ~ auth1@[<A HREF="http://www-math.mit.edu/~goemans/publ.html">mit.edu</A>]['09].
   Via GF & [<A HREF="http://www.csc.kth.se/~viggo/wwwcompendium/">!viggo</A>]['09] --
      Given G=(V,A), return a subset A' of A s.t. A' contains at least
      one arc from every directed cycle in G.
   [Also search for: minimum feedback arc set].

%A K. L. Clarkson
%A D. Eppstein
%A G. L. Miller
%A C. Sturtivant
%A S.-H. Teng
%T Approximating center points with iterated Radon points
%J Int. J. Comput. Geom. & Appl.
%V 6
%N 3
%P 357-377
%M SEP
%D 1996
%O ACM Symp. on Comp. Geom., SanDiego, CA, 1993
%K jrnl, c1996, c199x, c19xx, centerpoint, centrepoint, center, center, point,
   radon, Tukey depth, median, algorithm, multiDimensional, high breakdown
%X "... practical & provably good Monte Carlo alg. for approx. center pts. Let
   P be a set of n pts in R^d. A pt c in R^d is a b-center pt of P if every
   closed halfspace containing c contains at least bn pts of P. Every pt set
   has a 1/(d+1)-center pt; our alg. finds an Omega(1/d^2)-center pt with high
   prob.. ... has a small const. factor & is the first approx. center pt alg.
   whose complexity is subexponential in d. ... can be optimally parallelized
   to require O(log^2 d log log n) time. ... has been used in mesh partitioning
   methods & can be used in the construction of high breakdown estimators for
   multivariate datasets in stats.. ... potential to improve results in practice
   for constructing weak epsilon-nets. ... a variant's time bound is fully
   polynomial in d & linear in n, & show how to combine our approach with
   previous techniques to compute high quality center pts more quickly."
   -- 97h:65010@[<A HREF="http://www.ams.org/mathscinet-getitem?mr=97h:65010">ams</A>]['13].
   [Also search for: centerpoint].

%A J. Aoe
%A K. Morimoto
%A M. Shishibori
%A K-H. Park
%T A trie compaction algorithm for a large set of keys
%J IEEE Trans. Knowledge and Data Engineering
%V 8
%N 3
%P 476-491
%D 1996
%K jrnl, c199, c199x, c19xx, DAWG, DAWGs, dataStructure, DS, word, words,
   string, key
%X "A trie structure is frequently used for various applications, such as
   natural language dictionaries, database systems, & compilers. However, the
   total number of states (& transitions between them) of a trie becomes large
   so that space cost may not be acceptable for a huge key set. In order to
   resolve this disadvantage, this paper presents a new scheme, called
   "two-trie," that enables us to perform efficient retrievals, insertions, &
   deletions for the key sets. The essential idea is to construct two tries for
   both front & rear compressions of keys, which is similar to a DAWG (Directed
   Acyclic Word-Graph). The approach differs from a DAWG in that the two-trie
   approach presented can uniquely determine information corresponding to keys
   while a DAWG cannot. For an efficient implementation of the two-trie, two
   types of data structures are introduced. The theoretical & experimental
   observations show that the method presented is more practical than existing
   ones considering the use of dynamic key sets, storing information of keys, &
   compression of transitions."
   [<A HREF="http://csdl.computer.org/comp/trans/tk/1996/03/k0476abs.htm">abs</A>][3/'04] ?r u a subscriber?

%A H. L. Bodlaender
%T A linear-time algorithm for finding tree-decompositions of small treewidth
%J SIAM J. Comput.
%V 25
%N 6
%P 1305-1317
%D 1996
%O Proc. 25th annual ACM symp. on Theory of comp. (STOC), pp 226 234, 1993
%K jrnl, STOC, c1996, c199x, c19xx, zz1218, maths, graph, tree, path,
   decomposition, bounded, treewidth, width, algorithm
%X "... for const k a linear-time alg. that, given a graph $G = (V,E)$,
   determines whether the treewidth of G is at most k &, if so, finds a
   tree-decomposition of G with treewidth at most k. A consequence is that every
   minor-closed class of graphs that does not contain all planar graphs has a
   linear-time recognition alg.. [&] a similar result holds when we look instead
   for path-decompositions with pathwidth at most some constant k."
   -- [<A HREF="https://doi.org/10.1137/S0097539793251219">doi:10.1137/S0097539793251219</A>]['18].
   [Also search for: graph decomposition].

%A M. Crochemore
%A R. Verin
%T Direct construction of compact directed acyclic word graphs
%J 8th Annual Symp., CPM 97
%W Aarhus, Denmark
%S LNCS
%V 1264
%P 116-129
%D 1997
%K CMP, CMP97, c1997, c199x, c19xx, DAWG, DAWGs, maths, graph, words,
   string, strings
%X "The Directed Acyclic Word Graph (DAWG) is an efficient data structure used
   to treat and analyze repetitions in texts, especially in DNA genomic
   sequences. Here, we consider the Compact Directed Acyclic Word Graph of a
   word. We give the first direct algorithm to construct it. It runs in time
   linear in the length of the string on a fixed alphabet. Our implementation
   requires half the memory space used by ordinary DAWGs".
   isbn:3540632204.
   [<A HREF="http://www-igm.univ-mlv.fr/~mac/REC/97-CPM.html">.ps</A>][3/'04]

%A D. Bailey
%A P. Borwein
%A S. Plouffe
%T On the rapid computation of various polylogarithmic constants
%J Maths of Computation
%V 66
%N 218
%P 903-913
%M APR
%D 1997
%K jrnl, c1997, c199x, c19xx, BBP, algorithm, polylogarithmic constants,
   constant, digits of pi, digit, transcendental number, numbers, calculate,
   calculating, formula, digit extraction
%X "... computation of the d-th digit of certain transcendental numbers in
   various bases. These algs. can be easily implemented (multiple precision
   arith. is not needed), require virtually no memory, & feature run times that
   scale nearly linearly with the order of the digit desired. ...",   e.g.,
   pi = SUM[i=0..] { 4/(8*i+1) - 2/(8*i+4) - 1/(8*i+5) - 1/(8*i+6) } / (16**i)
   (NB. the part in {...} is not an integer.)
   -- [<A HREF="http://dx.doi.org/10.1090/S0025-5718-97-00856-9">doi:10.1090/S0025-5718-97-00856-9</A>]['09],
   pdf@[<A HREF="http://www.ams.org/mcom/1997-66-218/S0025-5718-97-00856-9/S0025-5718-97-00856-9.pdf">ams</A>]['09],
   pdf@[<A HREF="crd.lbl.gov/~dhbailey/dhbpapers/digits.pdf">lbl</A>]['09],
   and [<A HREF="http://en.wikipedia.org/wiki/BBP_algorithm">wikip</A>]['09].

%A D. E. Knuth
%T The Art of Computer Programming, Volume 1: Fundamental Algorithms
%I AddisonWesley
%P 672
%D 1997
%K book, text, c1997, c199x, c19xx, computing, program, programs, Mix,
   algorithm, boxed set, volumes
%X us$70 -> us$45; 3rd ed; uk us isbn:0201896834; uk us isbn13:978-0201896831;
  '98 also vols 1-3 boxed set,
  us$190->us$117; uk us isbn:0201485419; uk us isbn13:978-0201485417;

%A D. E. Knuth
%T The Art of Computer Programming, Volume 2: Seminumerical Algorithms
%I AddisonWesley
%P 784
%D 1997
%K book, text, c1997, c199x, c19xx, computing, program, programs, BigInt,
   base conversion, algorithm, semi-numerical, positional number systems
%X us$70 -> us$46; 3rd ed; uk us isbn:0201896842; uk us isbn13:978-0201896848;
   Inc. Positional number systems sec.4.1

%A P. Ramanan
%T Tight Omega(n lg n) lower bound for finding a longest increasing subsequence
%J Int. J. of Computer Mathematics
%V 65
%N 3-4
%P 161-164
%D 1997
%K jrnl, c1997, c199x, c19xx, longest ascending subsequence, LASS, problem
%X "The longest increasing subsequence problem is as follows: Given a sequence
   A = (a1, ..., an), of n real numbers, find a longest increasing subsequence
   of A. There is a well-known O(n lg n)-time comparison tree alg. for solving
   this problem. Also, a tight Omega(n lg n) lwb in the comparison tree model is
   known. We prove a tight Omega(n lg n) lower bound in the more powerful
   algebraic decision tree model. The above lwbs also apply to the apparently
   simpler problem of finding the length of a longest increasing subsequence."
 * [Also search for: LASS problem].

%A T. Miyazaki
%T The complexity of McKay's canonical labelling algorithm
%J Groups and Computation, II
%I AMS
%S DIMACS (Discret. Math. and Theor. Comp. Sci.)
%V 28
%P 239-256
%D 1997
%K c1997, c199x, c19xx, maths, graph, automorphism, isomorphism, exponential,
   time, nauty, McKay, labelling, labeling
%X "... time complexity of McKay's alg. ... The alg. is based on a type of
   backtrack search, & it performs pruning by discovered automorphisms & by
   hashing partial info. of vertex labelings. ... implemented in the nauty
   package. We obtain colorings of Furer's graphs that allow the alg. to compute
   their canonical forms in polynomial time. We then prove an exponential LWB of
   the alg. for connected 3-regular graphs of color-class size 4 using Furer's
   construction. [experiments] also indicate the same exponential LWB."
   -- .ps@[<A HREF="http://www.cs.trincoll.edu/~miyazaki/rutgers.ps">trincoll.edu</A>]['10].
   [Also search for: canonical labelling maths graph].

%A T. Jebelean
%T Practical integer division with Karatsuba complexity
%J ISSAC
%P 339-341
%D 1997
%K conf, c1997, c199x, c19xx, zz0624, fast integer division,
   computer arithmetic, algorithm, BigInt
%X "Combining Karatsuba multiplication with a technique developed by Krandick
   for computing the high-order part of the quotient, we obtain an int. div.
   alg. which is only two times slower, on avg., than K.multiplication. The main
   idea is to delay part of the dividend update until this can be done by
   multiplication between large balanced operands. An implementation under
   saclib is faster than classical mult'n at 40 words, & becomes two times
   faster at 250 words."
   -- [<A HREF="https://doi.org/10.1145/258726.258836">doi:10.1145/258726.258836</A>]['24].

%A D. E. Knuth
%T The Art of Computer Programming, Volume 3: Sorting and Searching
%I AddisonWesley
%P 800
%D 1998
%K book, text, c1998, c199x, c19xx, computing, program, programs, sort,
   algorithm, data structure, dataStructure, DS, table, tables, hash, hashing,
   permutation
%X 2nd ed 1998; uk us isbn:0201896850; uk us isbn13:978-0201896855.

%A S. Arora
%A C. Lund
%A R. Motwani
%A M. Sudan
%A M. Szegedy
%T Proof verification and the hardness of approximation problems
%J JACM
%V 45
%N 3
%P 501-555
%D 1998
%K jrnl, JACM, c1998, c199x, c19xx, zz0419, PCP theorem, complexity, hardness,
   NP, NPC, NPH, randomized, hardness, approximation algorithm, optimization,
   optimisation, probablistic verifier, MAX SNP, Papadimitriou, Yannakakis,
   probabilistically checkable proof, NEXP
%X "We show that every language in NP has a probablistic verifier that checks
   membership proofs for it using logarithmic # of random bits & by examining a
   const. # of bits in the proof. If a string is in the language, then there
   exists a proof s.t. the verifier accepts with prob. 1 (i.e., for every choice
   of its random string). For strings not in the language, the verifier rejects
   every provided 'proof' with prob. >= 1/2. ... builds upon & improves a recent
   result of Arora & Safra [1998] whose verifiers examine a nonconst. # of bits
   in the proof (though this # is a v.slowly growing fn of the input length).
   ... [so] we prove that no MAX SNP-hard problem has a polynomial time
   approximation scheme, unless NP=P. The class MAX SNP was defined by
   Papadimitriou & Yannakakis [1991] & hard problems for this class include
   vertex cover, maximum sat., max. cut, metric TSP, Steiner trees & shortest
   superstring. We also improve upon the clique hardness results of Feige et al
   [1996] & Arora & Safra [1998] & show that there exists a +ve &egr; such s.t.
   the maximum clique size in an N-vertex graph to within a factor of N&egr; is
   NP-hard."
   -- [<A HREF="https://doi.org/10.1145/278298.278306">doi:10.1145/278298.278306</A>]['19].
   Also see,
   "... An alternative [formulation is] the max. fraction of satisfiable
   constraints of a constraint satisfaction problem is NP-hard to approx. within
   some constant factor. ..."
   -- PCP@[<A HREF="https://en.wikipedia.org/wiki/PCP_theorem">wikip</A>]['19].
   [Also search for: probablistic algorithm].

%A B. D. McKay
%T Isomorph-free exhaustive generation
%J J. Algorithms
%V 26
%N 2
%P 306-324
%M FEB
%D 1998
%K jrnl, c1998, c199x, c19xx, isomorphism, rejection, isomorph, generate,
   symmetry, combinatorial objects, representative, representatives,
   equivalence, nauty, enumeration, enumerate, class, BDMcKay, geng
%X "... very general technique for generating families of combinatorial objects
   without isomorphs. It applies to almost any class of objects for which an
   inductive construction process exists. In one form of our technique, no
   explicit isomorphism testing is required. In the other form, isomorph testing
   is restricted to within small subsets of the entire set of objects. A variety
   of different e..g.s are presented, inc. the generation of graphs with some
   hereditary property, ... Latin rectangles & balanced incomplete block
   designs. ... can also be used to perform unbiased stat.  analysis, inc.
   approx.counting, of sets of objects too large to generate exhaustively."
   -- [<A HREF="http://dx.doi.org/10.1006/jagm.1997.0898">doi:10.1006/jagm.1997.0898</A>]['10],
   &  [<A HREF="http://cs.anu.edu.au/~bdm/papers/orderly.ps.gz">.ps.gz</A>]['05].
   [Also search for: isomorphism rejection].

%A E. Cela
%T The Quadratic Assignment Problem: Theory and Algorithms
%I Springer
%D 1998
%K book, text, c1998, c199x, c19xx, zz1109, Quadratic Assignment Problem, QAP,
   L5Ref, optimisation, optimization, algorithm, OR
%X "The QAP is a classical combinatorial opt. problem with numerous applications
   in facility location, scheduling, manufacturing, VLSI design, statistical
   data analysis, etc. The QAP is an extremely hard problem from both
   theoretical & practical pts of view: 1) The QAP is NP-hard to solve to
   optimality & to approximate within a constant approximation ratio, &
   2) instances of size larger than 22 are still considered intractable. ..."
   1st ed 1998; hb us$185; uk us isbn:0792348788; uk us isbn13:978-0792348788.

%A M. Matsumoto
%A T. Nishimura
%T Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random
   number generator
%J ACM Trans. on Modeling and Computer Simulation
%V 8
%N 3
%D 1998
%K c1998, c199x, c19xx, pseudo random number generator, RNG, PRNG, algorithm,
   Mersenne twister, TGFSR, modelling
%X "A new alg. called Mersenne Twister (MT) ... generating uniform pseudorandom
   numbers. For a particular choice of parameters ... provides a super
   astronomical period of 2**19937-1 and 623-dimensional equidistribution up
   to 32-bit accuracy, while using a working area of only 624 words. ...
   The distribution up to v bits accuracy for 1 <= v <= 32 is also shown to be
   good. ...  Its merits are due to the efficient algs. that are unique to
   polynomial calculations over the two-element field."
   -- [<A HREF="http://doi.acm.org/10.1145/272991.272995">doi:10.1145/272991.272995</A>]['09].
   and MT@[<A HREF="http://en.wikipedia.org/wiki/Mersenne_twister">wikip</A>]['09].

%A S. Arora
%T Polynomial time approximation schemes for Euclidean traveling salesman and
   other geometric problems
%J JACM
%V 45
%N 5
%P ?-?
%M SEP
%D 1998
%K jrnl, JACM, c1998, c199x, c19xx, zz1020, Euclidean traveling salesman, ETSP,
   TSP, geometric, metric, problem, approximation algorithm,
   Minimum Steiner Tree, kTSP
%X "... a polynomial time approximation scheme for Euclidean TSP in fixed
   dimensions. For every fixed c>1 & given any n nodes in R^2, a randomized
   version of the scheme finds a (1+1/c)-approx. to the optimum ...tour in
   O(n(log n)^{O(c)}) time. When the nodes are in R^d, the running time incr. to
   O(n(log n)^{(O(sqrt(c)))^{d-1}}). For every fixed c, d the running time is
   n.poly(log(n)), that is nearly linear in n. The alg. can be derandomized, but
   this increases the running time by a factor O(n^d). The prev. best approx.
   alg. for the problem (due to Christofides) achieves a 3/2-aprox. in
   polynomial time. We also give similar approx. schemes for some other NP-hard
   Euclidean problems: Minimum Steiner Tree, k-TSP, & k-MST. (The running times
   of the alg. for k-TSP & k-MST involve an additional multiplicative factor k.)
   The prev. best approx. algs. for all these problems achieved a const.-factor
   approx.. We also give efficient approx. schemes for Euclidean Min-Cost
   Matching, a problem that can be solved exactly in polynomial time.  All our
   algs. also work, with almost no modification, when distance is measured using
   any geometric norm (such as L_p for p>=1 or other Minkowski norms). They also
   have simple parallel (i.e., NC) implementations."
   -- [<A HREF="https://doi.org/10.1145/290179.290180">doi:10.1145/290179.290180</A>]['20].
   Also see TSP@[<A HREF="https://en.wikipedia.org/wiki/Travelling_salesman_problem">wikip</A>]['20].

%A D. J. Bernstein
%T Detecting perfect powers in essentially linear time
%J Math. Comp.
%I AMS
%V 67
%P 1253-1283
%D 1998
%K jrnl, c1998, c199x, c19xx, zz0124, algorithm, detect, power
%X "... gives complete details of an alg. to compute approx. k^th roots; [&]
   uses this in an alg. that, given an int. n > 1, either writes n as a perfect
   power or proves that is not a perfect power; [&] proves, using Loxton's
   theorem on multiple linear forms in logs, that this perfect-power
   decomposition alg. runs in time (log n)^{1+o(1)}"
   -- [<A HREF="https://doi.org/10.1090/S0025-5718-98-00952-1">doi:10.1090/S0025-5718-98-00952-1</A>]['24].
   (This is used in Shor's alg.)

%A K. Beyer
%A J. Goldstein
%A R. Ramakrishnan
%A U. Shaft
%T When is ``nearest neighbour'' meaningful?
%J Proc. 7th Int. Conf. Data Theory
%W Jerusalem
%I Springer
%S LNCS
%V 1540
%P 217-235
%M JAN
%D 1999
%K conf, ICDT, neighbor, dimensions, dimensionality, distance, quote, quotable,
   clustering, zz1102
%X ...show that under a broad set of conditions (much broader than
   independent and identically distributed dimensions), as dimensionality
   increases, the distance to the nearest data point approaches the distance
   to the farthest data point.  ... real and arificial data ...
   this effect can occur for as few as  * 10-15 dimensions *. ...
   should not be interpreted to mean that high-dimensional indexing
   is never meaningful ...  [but] database literature to evaluate
   high-dimensional indexing techniques is flawed ...
   [<A HREF="http://link.springer.de/link/service/series/0558/papers/1540/15400217.pdf">paper</A>][10.'02]

%A D. Peleg
%A V. Rubinovich
%T A near tight lower bound on the time complexity of distributed
   minimum spanning tree construction
%J SIAM J. of Computing
%V 30
%N 5
%P 1427-1442
%D 2000
%O IEEE Foundations of Comp. Sci. (FOCS) Symp., '99
%K jrnl, c2000, c200x, c20xx, MST, trees, weighted graph, maths, graphs,
   complexity
%X "...lower bound of Omega(D+sqrt n/log n) on the time required for the
   distributed construction of a minimum-weight spanning tree (MST) in weighted
   n-vertex networks of diameter D=Omega(log n), in the bounded message model.
   This establishes the asymptotic near-optimality of existing time-efficient
   distributed algorithms for the problem, whose complexity is
   O(D + sqrt n log^* n)."
   [<A HREF="http://dx.doi.org/10.1137/S0097539700369740">doi:10.1137/S0097539700369740</A>]['07].
   [Also search for: maximum sum interval].

%A R. G. Downey
%A M. R. Fellows
%T Parameterized Complexity
%P 530
%I SpringerVerlag
%D 1999
%K book, text, c1999, c199x, c19xx, parametric complexity,
   fixed parameter tractable, tractability, FPT, graph, vertex cover problem
%X euro75; uk us isbn:038794883X.
   [Also see [<A HREF="http://en.wikipedia.org/wiki/Parameterized_complexity">wikip.</A>]['05]:
   "... interesting to see whether we can find an algorithm which is
   exponential only in k, and not in the input size. ...
   ... e.g., there is an alg. which solves the vertex cover problem
   in O(k n + 1.29**k)-time, where n is the # of vertices and k is the
   size of the vertex cover. This proves that vertex cover is
   fixed-parameter tractable with respect to this parameter [k]."

%A R. Impagliazzo
%A R. Paturi
%T Complexity of k-SAT
%J IEEE Conf. on Computational Complexity
%P ?-?
%D 1999
%K conf, c1999, c199x, c19xx, xx0707, NPC, SAT, kSat, 3SAT, k CNF, kCNF, 3CNF,
   exponential time hypothesis, ETH, satisfiability, NP, NPC
%X "... k-SAT is to det, if the given k-CNF fas a satisfiable soln. ...  Define
    s[k] (for k>=3) to be the infinum of {delta | exists O(2**(delta.n))} alg
    for solving k-SAT.  Define ETH (exp. time hypothesis) for k-SAT as follows:
    for k >= 3, s[k] > 0.  [i.e.] k-SAT does not have a subexp-time alg.. ...we
    show that s[k] is an increasing seq. assuming ETH for k-SAT. Let s[infinity]
    be the limit of s[k] ...  we show s[k] <= (1-d/(e.k))s[infinity] for some
    const d > 0."
    [<A HREF="http://www-cse.ucsd.edu/users/russell/mohan3-99.ps">ps@ucsd</A>]['07]
    [<A HREF="http://dx.doi.org/10.1109/CCC.1999.766282">doi:10.1109/CCC.1999.766282</A>]['07] subscr?

%A D. Eppstein
%T Subgraph isomorphism in planar graphs and related problems
%J J. Graph Algorithms and Applications
%V 3
%N 3
%P 1-27
%D 1999
%K jrnl, c1999, c199x, c19xx, zz0211, planar, graph, maths,
   subgraph isomorphism, algorithm
%X "We solve the subgraph isomorphism problem in planar graphs in linear time,
   for any pattern of constant size. Our results are based on a technique of
   partitioning the planar graph into pieces of small tree-width, and applying
   dynamic programming within each piece. The same methods can be used to solve
   other planar graph problems including connectivity, diameter, girth, induced
   subgraph isomorphism, and shortest paths."
   -- [<A HREF="http://arxiv.org/abs/cs/9911003v1">arxiv</A>][2/11],
   &  [<A HREF="http://www.ics.uci.edu/~eppstein/">auth</A>]['11].
      (Problem is NPC, but if G is planar, and H is *fixed*,
      then ?H < G? is solved in time linear in |G|.)
   [Also search for: subgraph isomorphism].

%A Chung-Piaw Teo
%A J. Sethuraman
%A Wee-Peng Tan
%T Gale-Shapley stable marriage problem revisited: Strategic issues and
   applications
%J Proc. 7th Int. IPCO Conf. on Integer Prog. and Comb. Opt.
%I SpringerVerlag
%P 429-438
%D 1999
%K conf, c1999, c199x, c19xx, zz0915, cheat, cheating, dynamic, preference,
   stable match, matching, bipartite, male, female, optimal, partner,
   Singapore, schools, admission
%X "... derive the optimal cheating strategy & show that it is not always poss.
   for a woman to recover her w.-optimal stable partner from the men-optimal
   stable matching mechanism when she can only cheat by permuting her prefs.. In
   fact, we show, using simulation, that the chances that a w. can benefit from
   cheating are slim. In the 2nd part ... consider a two-sided matching market
   found in Singapore. We study the matching mechanism used by the Min. of Edn
   (MOE) in the placement of primary 6 students in secondary schools, & discuss
   why the current method has limited success in accommodating the prefs. of the
   students, & the specific needs of the schools (in terms of the 'mix' of
   admitted students). Using insights from the 1st part ... show that stable
   matching mechanisms are more appropriate in this matching market & explain
   why the strategic behavior of the student's need not be a major concern."
   -- pdf@[<A HREF="http://www.columbia.edu/~js1353/pubs/tst-ms01.pdf">col'mbia</A>]['15].
   uk us isbn:3-540-66019-4.
   [Also search for: stable marriage problem].

%A R. Shamira
%A D. Tsur
%T Faster subtree isomorphism
%J J. of Algorithms
%V 33
%N 2
%P 267-280
%M NOV
%D 1999
%K jrnl, c1999, c199x, c19xx, subtree, sub tree, trees, isomorphism
%X "... Given trees H & G, find a subtree of G which is isomorphic to H or
   decide that there is no such subtree. We give an O((k**1.5 / log k)n)-time
   alg. ... where k & n are the # of vertices in H & G, resp.. This improves
   over the O(k**1.5 n) algs. of Chung & Matula. We also give a randomized
   (Las Vegas) O(k**1.376 n)-time alg. for the decision problem."
   [<A HREF="http://dx.doi.org/10.1006/jagm.1999.1044">doi:10.1006/jagm.1999.1044</A>]['08].

%A D. Gusfield
%T Exact matching
%I UCDavis
%D 1997 ?
%K TR, c199x, c19xx, string, search, algorithm, Z algorithm Zalgorithm
%X See pdf@[<A HREF="http://web.cs.ucdavis.edu/~gusfield/cs224f09/znotes.pdf">notes</A>][2018]
   in [<A HREF="http://web.cs.ucdavis.edu/~gusfield/cs224f09/">notes</A>][2009].
   (Also in G's book c1997.)
   [Also search for: string search algorithm].

%A N. Mastronardi
%A P. Lemmerling
%A S. van Huffel
%T Fast structured total least squares algorithm for solving the basic
   deconvolution problem
%J SIAM J. on Matrix Analysis and Applications
%V 22
%N 2
%P 533-553
%D 2000
%K jrnl, SIAM, c2000, c200x, c20xx, fit, fitting, approximation, noise, TLS,
   LSQ, square, RMS, vanHuffel
%X "...develop a fast algorithm for the basic deconvolution problem. First
   [...] the kernel problem to be solved in the basic deconvolution problem
   is a so-called structured total least squares problem. Due to the low
   displacement rank of the involved matrices and the sparsity of the
   generators, we are able to develop a fast algorithm. We apply [it] on a
   deconvolution problem [...] in a medical application in renography. [...]
   show the increased [...] performance of our algorithm as compared to
   [others] for solving this type of [...] problem. In addition, Monte-Carlo
   simulations indicate the superior statistical performance of the [...]
   estimator compared to other estimators such as the ordinary TLS estimator."
   -- [<A HREF="http://epubs.siam.org/sam-bin/dbq/article/34581">paper</A>][11/'03].
   [Also search for: total least squares TLS].

%A F. Moreno-Seco
%A L. Mico
%A J. Oncina
%T A fast approximately k-nearest-neighbour search algorithm for
   classification tasks.
%J Adv. in Pattern Recognition
%I Springer
%S LNCS
%V 1876
%P 823-831
%D 2000
%K c2000, c200x, c20xx, approximate, search, kNN, neighbor, task
%X [<A HREF="http://www.dlsi.ua.es/~mico/publicaciones.html">ref</A>][10/'02]

%A V. Geffert
%A et al
%A Asymptotically efficient in-place merging
%J TCS
%V 237
%N 1-2
%P 159-181
%M APR
%D 2000
%K jrnl, TCS, c2000, c200x, c20xx, zz1023, in-situ, insitu, stable, merge,
   merging
%X "Two linear-time algs. for in-place/ merging are presented. Both algs.
   perform at most m(t+1)+n/2^t+o(m) comparisons, where m & n are the sizes of
   the input seqs., m <= n, & t=floor(log_2(m/n)). The 1st alg. is for
   unstable merging & it carries out no more than 3(n+m)+o(m) elt moves. The 2nd
   alg. is for stable merging & it accomplishes at most 5n+12m+o(m) moves."
   -- [<A HREF="https://doi.org/10.1016/S0304-3975(98)00162-5">doi:10.1016/S0304-3975(98)00162-5</A>]['23].
   [Also search for: insitu merge].

%A S. Kapoor
%T Dynamic maintenance of maxima of 2-d point sets
%J SIAM J. Comput.
%V 29
%N 6
%P 1858-1877
%M APR
%D 2000
%K jrnl, set, c2000, c200x, c20xx, maximal points, dynamic maintenance,
   balanced trees, plane, insert, delete, maximal, computational geometry,
   minimal, dominate, dominator, dominated, 2D, vector
%X     Defn: "p is a maximal point iff it is not dominated by another point."
   "...efficient scheme for the dynamic maintenance of the set of maxima of a
   2D set of pts. Using the fact that the maxima can be stored in a staircase
   structure, we use a technique in which we maintain approximations to the
   staircase structure. We 1st describe how to maintain the maxima in O(log n)
   time per insertion & deletion when there are n insertions & deletions.
   O(log n) is charged per change for reporting changes to the staircase
   structure which stores the maxima. O(n) space is used. We also show another
   scheme which requires a total of O(n log n + r) time when r maximal pts are
   listed. We finally consider extensions to higher dimensions."
   -- [<A HREF="http://dx.doi.org/10.1137/S0097539798348365">doi:10.1137/S0097539798348365</A>]['06].
   [Also search for: maxima dominate].

%A X. He
%A M. Kao
%A H. Lu
%T A fast general methodology for information-theoretically optimal encodings
   of graphs
%J SIAM J. on Computing
%V 30
%N 3
%P 838-846
%D 2000
%K jrnl, c2000, c200x, c20xx, maths, graph, graphs, compress, data, compression,
   encode, information, planar, triconnected, biconnected, triangulation,
   coding, labeled, labelled
%X "... propose a fast methodology for encoding gs. with info.-theor. min. # of
   bits.  ... a g. with property pi is called a pi-graph. If pi satisfies
   certain properties, then an n-node m-edge pi-graph G can be encoded by a
   binary string X s.t. (1) G & X can be obtained from each other in O(n log n)
   time, & (2) X has at most beta(n)+o(beta(n)) bits for any cts superadditive
   fn beta(n) s.t. there are at most 2^beta(n)+o(beta(n)) distinct n-node
   pi-graphs.   [combinations of] (1) G is a planar graph or a plane graph;
   (2) directed or undirected; (3) triangulated, triconnected, biconnected,
   connected or not ...; (4) nodes labeled with labels from {1,..., ell_1} for
   ell_1 <= n; (5) edges labeled with labels from {1, ..., ell_2} for
   ell_2 <= m; & (6) each node (resp., edge) of G has at most ell_3=O(1)
   self-loops (resp., ell_4=O(1) multiple edges). Moreover, ell_3 & ell_4 are
   not required to be O(1) for the cases of pi being a plane triangulation.
   These eg.s are novel applications of small cycle separators of planar gs. &
 * are the only nontrivial classes of gs., other than rooted trees, with known
 * polynomial-time info.-theor. optimal coding schemes."  [18 refs].
   -- [<A HREF="http://dx.doi.org/10.1137/S0097539799359117">doi:10.1137/S0097539799359117</A>]['08].
   [Also search for: compress graph].

%A R. Myers
%A R. C. Wilson
%A E. R. Hancock
%T Bayesian graph edit distance
%J IEEE Trans. Pattern Analysis and Machine Intell.
%V 22
%N 6
%P 628-635
%M JUN
%D 2000
%K jrnl, c2000, c200x, c20xx, maths, graph edit distance, GED, graphs,
   similarity, similar, match, matching, Sanfeliu, Fu, Wilson, Hancock
%X "... novel framework for comparing & matching corrupted relational graphs.
   ... develops the idea of edit-distance originally introduced for graph-
   -matching by Sanfeliu & Fu. We show how the Levenshtein d. can be used to
   model the prob.distn for structural errors in graph-matching... This
   prob.distn is used to locate matches using MAP label updates. We compare the
   resulting graph-matching alg. with that recently reported by Wilson &
   Hancock. The use of edit-d. offers an elegant alternative to the
   exhaustive compilation of label dictionaries. Moreover, the method is
   polynomial rather than exponential in its worst-case complexity. We support
   our approach with an experimental study on synthetic data & illustrate its
   effectiveness on an uncalibrated stereo correspondence problem. ..."
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/34.862201">doi:10.1109/34.862201</A>]['08] ($19).
   [Also search for: graph edit distance GED].

%A H. N. Gabow
%T Path-based depth-first search for strong and biconnected components
%J IPL
%V 74
%N 3-4
%M MAY
%D 2000
%K jrnl, IPL, c2000, c200x, c20xx, strong, biconnected, component, graph
%X -- [<A HREF="http://dx.doi.org/10.1016/S0020-0190(00)00051-X">doi:10.1016/S0020-0190(00)00051-X</A>]['10],
   ps.gz@[<A HREF="http://www.cs.colorado.edu/~hal/Papers/ipl.ps.gz">colo</A>]['10].
   (A cite says  A k u t s u (93) uses it to decompose a g. into its
   bicon. cmpnts in linear time.)
 * (A biconnected component of a graph is a maximal edge-induced subg. that
   cannot be disconnected by removing one vertex.)

%A M. A. Greenspan
%A G. Godin
%A J. Talbot
%T Acceleration of binning nearest neighbor methods
%J Vision Interface 2000
%W Montreal
%P ?-?
%M MAY
%D 2000
%K conf, nn, neighbour, k-d tree, KDtree, bin, binning, Elias
%X ... based on triangle inequality ... works well for small point sets ...
   compared with k-d tree and Elias bin sets.  ... accelerate k-d tree for
   large point stes about 20% ... space better.
   [<A HREF="http://www.ece.queensu.ca/hpages/faculty/greenspan/MyWebPage/papers/gre00.pdf">paper</A>][10/'02]
   [<A HREF="http://www.ece.queensu.ca/hpages/faculty/greenspan/MyWebPage/Pubs.htm">ref</A>][10/'02]

%A M. Thorup
%T Near-optimal fully-dynamic graph connectivity
%J Proc. 32nd annual ACM symp. on Theory of computing
%P 343-350
%D 2000
%K conf, STOC, STOC00, c2000, c200x, c20xx, zz0515, maths, graph, connected,
   component, bridge, bridges, algorithm
%X "... near-optimal bounds for fully-dynamic g.connectivity which is the most
   basic non-trivial fully-dynamic g.problem. Connectivity queries are supported
   in O(log n/log log log n) time while the updates are supported in
   O(log n(log log n)^3) expected amortized time. The prev. best update time was
   O((log n)^2). Our new bound is only doubly-logarithmic factors from a general
   cell probe lower bound of Omega(log n/log log n). Our alg. runs on a pointer
   m/c, & uses only std AC^0 instns. ... make some comparatively trivial
   observations improving some deterministic bounds. The space bound of the
   prev. O((log n)^2) connectivity alg. is improved from O(m + n log n) to O(m).
   The prev. time complexity of fully-dynamic 2-edge & biconnectivity is
   improved from O((log n)^4) to O((log n)^3 log log n)."
   -- pdf@[<A HREF="http://dx.doi.org/10.1145/335305.335345">doi:10.1145/335305.335345</A>]['15].
   [Also search for: graph bridge algorithm].

%A D. Knuth
%T Dancing links
%J Millenial Perspectives in Computer Science
%I Palgrave
%P 187-214
%D 2000
%O Proc. 1999 Oxford-Microsoft Symp. in Honour of Sir Tony Hoare,
   Palgrave, pp.187-214, 1999
%K symp, c2000, c200x, c20xx, zz0914, dancing links, link, DLX, exact cover,
   search, algorithm, puzzle, solution, constraint satisfaction problem,
   n queens, Nqueens, polyomino, tiling, depth first, backtrack, backtracking
%X "... two tricks to accelerate depth-first search algs. for a class
   of comb'l puzzle problems, such as tiling a tray by a fixed set of
   polyominoes. The 1st trick is to implement each assumption of the search
   with reversible local ops. on doubly linked lists. [So] every step
   of the search affects the data incrementally.  The 2nd trick is to add a
   ghost square that represents the identity of each polyomino. This puts the
   rule that each p. be used once on the same footing as the rule that each
   square be covered once. The coding simplifies to a more abstract form which
   is equiv. to 0-1 integer programming. More sig. for the total comp'n time,
   the search can naturally switch between placing a fixed polyomino or covering
   a fixed square at different stages, according to a combined heuristic.
   Finally ... reports excellent performance for his alg. for some familiar
   puzzles. These include tiling a hexagon by 19 hexiamonds & the N queens
   problem for N up to 18."  (isbn13:978-0333922309)
   -- 0011047@[<A HREF="http://arxiv.org/abs/cs/0011047">arXiv</A>]['14].
   (Matrix 'A' of 0s and 1s, row=set, column=element.
    1. If the matrix A is empty, the problem is solved, terminate successfully;
    2. Otherwise choose a column c (deterministically);
    3. Choose a row r such that A_r,c = 1 (nondet [i.e., try all]);
    4. Include row r in the partial solution;
    5. For each column j s.t. A_r,j = 1 do
          for each row i s.t. A_i,j = 1 do delete row i from matrix A od;
          delete column j from matrix A
       od;
    6. Repeat this algorithm recursively on the reduced matrix A.
    ... circular doubly linked lists of the 1s in the matrix ... a list of
    1s for each row & each col.. Each '1' links to 1s L & R, & up & down.
    -- DLX@[<A HREF="http://en.wikipedia.org/wiki/Knuth%27s_Algorithm_X">wikip</A>]['14].)
   (Note, a 'tiling' is an example of an 'exact cover' of a set.)

%A H. Bunke
%A Xiaoyi Jiang
%T Graph matching and similarity
%J Intell. Sys. and Interf.
%I Springer
%P 281-304
%D 2000
%K c2000, c200x, c20xx, zz0122, maths, graph edit distance, GED, matching,
   match, two, similar, similarity, inexact
%X "Many graphical interfacing problems relay on g.matching. ... we explore &
   illustrate how g.matching can be performed using powerful,'intelligent'
   algs., to improve std methods."
   -- [<A HREF="https://doi.org/10.1007/978-1-4615-4401-2_10">doi:10.1007/978-1-4615-4401-2_10</A>]['22].
   (Also see Gmatch@[<A HREF="https://en.wikipedia.org/wiki/Graph_matching">wikip</A>]['22].)
   [Also search for: graph edit distance GED].

%A J. W. Raymond
%A E. J. Gardiner
%A P. Willett
%T RASCAL: Calculation of graph similarity using maximum common edge subgraphs
%J COMPJ
%V 45
%N 6
%P 631-644
%D 2002
%K compj, jrnl, c2002, c200x, c20xx, MCE, MCES, subgraph, graph, graphs,
   similar, distance, Chemistry, Chem, chemical compound, molecule, molecules,
   compounds, match, matching, approximate, search, edges, Kikust,
   Kikusts heuristic, labeled, labelled
%X "A new graph similarity calculation procedure is introduced for comparing
   labeled graphs. Given a minimum similarity threshold, the procedure consists
   of an initial screening process to determine whether it is possible for the
   measure of similarity between the 2 graphs to exceed the minimum
   threshold, followed by a rigorous maximum common edge subgraph (MCES)
   detection algorithm to compute the exact degree and composition of
   similarity. The proposed MCES algorithm is based on a maximum clique
   formulation of the problem and is a significant improvement over other
   published algorithms. It presents new approaches to both lower and upper
   bounding as well as vertex selection."
   [<A HREF="http://dx.doi.org/10.1093/comjnl/45.6.631">doi:10.1093/comjnl/45.6.631</A>]['05]
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_45/Issue_06/450631.sgm.abs.html">paper</A>][12/'02]

%A R. Mak
%T Java Number Cruncher: The Java Programmer's Guide to Numerical Computing
%I PrenticeHall
%P 480
%D 2002
%K book, text, c2002, c200x, c20xx, numerical algorithms, algorithm, methods,
   math, maths
%X pb, us$47, us isbn:0130460419; us isbn13:9780130460417;
   (Also see [<A HREF="http://commons.apache.org/math/">commons.../math</A>]['07].)

%A S. Heinz
%A J. Zobel
%A H. E. Williams
%T Burst tries: A fast, efficient data structure for string keys
%J ACM Trans. on Info. Sys
%V 20
%N 2
%P 192-223
%M APR
%D 2002
%K jrnl, c2002, c200x, c20xx, data structures, dataStructure, DS, search,
   searching, indexing, burst, trie, tries, burstTrie, string, strings,
   key, keys
%X "... efficient management of large sets of distinct strings in memory. [eg]
   index const'n for text DBs a record is held for each distinct word in the
   text, containing the word itself & information such as counters. We propose
   a new DS, the burst trie, that has sig. advantages ...: it uses about the
   same memory as a binary search tree; it is as fast as a trie; & while not
   as fast as a hash table, a burst trie maintains the strings in sorted or
   near-sorted order. ... explore the params. that govern their performance. ...
   ... burst trie is particularly effective for the skewed freq. distn common
   in text collections, & dramatically outperforms all other DSs ... while
   maintaining sort order."
   [<A HREF="http://doi.acm.org/10.1145/506309.506312">doi:10.1145/506309.506312</A>]['08].
   [Also search for: burst sort].

%A R. Wickremesinghe
%A L. Arge
%A J. S. Chase
%A J. Scott Vitter
%T Efficient sorting using registers and caches
%J J. Experimental Algorithmics
%V 7
%P 9
%D 2002
%O Proc. 4th Int. Workshop on Alg. Eng. (WAE2000), Saarbrucken
%K jrnl, c2002, c200x, c20xx, merge sort, Rmerge, sorting, algorithm, register,
   cache conscious
%X "... complex memory systems. Common m/c models for alg. analysis do not
   reflect many of the features ..., e.g., large register sets, lockup-free
   caches, cache hierarchies, associativity, cache line fetching, & streaming
   behavior. [We] explore the effect of memory system features on sorting ...
   new cache-conscious sorting alg., R-MERGE,  ..." [22 refs], 12 pages.
   pdf@[<A HREF="http://doi.acm.org/10.1145/944618.944627">doi:/10.1145/944618.944627</A>]['09],
   pdf@[<A HREF="http://www.cs.duke.edu/~jsv/Papers/catalog/node229.html">duke.edu</A>]['09].
   [Also search for: sort cache conscious].

%A M. S. Charikar
%T Similarity estimation techniques from rounding algorithms
%J Proc. 34th annual ACM Symp. on Theory of Computing
%P 380-388
%D 2002
%K conf, simhash, c2002, c200x, c20xx, locality, sensitive, hash, hashing,
   close, similar, set similarity, neighbour, neighbourhood, algorithm, sketch,
   fingerprinting
%X "A locality sensitive hashing scheme is a distribution on a family F of hash
   fns operating on a collection of objects, s.t. for 2 objects x, y,
   Prh&egr;F[h(x) = h(y)] = sim(x,y), where sim(x,y) &egr; [0,1] is some
   similarity fn defined on the collection of objects. Such a scheme leads to a
   compact representation of objects so that similarity of objects can be
   est. from their compact sketches, ...  Min-wise independent permutations
   provide an elegant construction of such a locality sensitive hashing scheme
   for a collection of subsets with the set similarity measure
   sim(A,B) = \frac{|A &Pgr; B|}{|A &Pgr B|}. ..." [42 refs].
   pdf: [<A HREF="http://doi.acm.org/10.1145/509907.509965">doi:10.1145/509907.509965</A>]['08].
   [Also search for: hashing neighbourhood].

%A Karl Hasselstrom
%T Fast Division of Large Integers. A Comparison of Algorithms,
   Master's Thesis
%I Comp. Sci., Royal Inst. of Tech., Stockholm
%M FEB
%D 2003
%K MSc, c2003, c200x, c20xx, zz1020, fast, integer division algorithm,
   arithmetic, BigInt
%X -- [<A HREF="https://treskal.com/s/masters-thesis.pdf">www</A>]['20],
   Also see
   Divn@[<A HREF="https://en.wikipedia.org/wiki/Division_algorithm">wikip</A>]['20].
   [Also search for: integer arithmetic algorithm].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Arithmetic/">more</A>].)

%A R. Sinha
%A J. Zobel
%T Efficient trie-based sorting of large sets of strings
%J 26th Australasian Computer Science Conference (ACSC)
%P 11-18
%M FEB
%D 2003
%K conf, ACSC, ACSC2003, sorting, trie, string, burstsort, burst, sort, trie,
   tries, burstTrie, radix, algorithm, MSD, set, string,
   RMIT, zz0203, c2003, c200x, c20xx
%X ... for sets of around 30,000,000 strings, our improved burstsort algorithm
   is nearly twice as fast as the previous best sorting algorithm.
   pdf@[<A HREF="http://www.cs.mu.oz.au/~jz/fulltext/acsc03sz.pdf">mu</A>]['08].
   [Also search for: burst sort].

%A R. Sedgewick
%T Algorithms in Java, Parts 1-5 (2 Vols.): Fundamentals, Data Structures,
   Sorting, Searching, and Graph Algorithms
%I AddisonWesley
%D 2003
%K book, text, c2003, c200x, c20xx, sort, search, algorithm, data structure,
   dataStructure, DS, OO, OOP, computer programming, Sedgewick, Sedgwick
%X 2 vols., uk us isbn:0201775786; uk us isbn13:978-0201775785.
   [also search for: Sedgewick book]

%A M. Kurowski
%T Simple and efficient floor-planning
%J IPL
%V 86
%N 3
%P 113-119
%M MAY
%D 2003
%K jrnl, IPL, floor plan, optimisation, optimization, plane,
   problem, algorithm, zz0703
%X new [...] O(n)-time [alg' for] the floor-plan of a given plane
   near-triangulation. We use modules which are the union of two rectangles
   and are T-, L- or I-shaped. Our algorithm has the following advantages:
   The number of T-shaped modules is at most (n-2)/2, all T-shaped modules are
   uniformly directed, the size of the picture is at most n*n-1. ...
   [<A HREF="http://dx.doi.org/10.1016/S0020-0190(02)00490-8">doi:10.1016/S0020-0190(02)00490-8</A>][7/'03]

%A A. Gibbons
%A A. Pagourtzis
%A I. Potapov
%A W. Rytter
%T Coarse-grained parallel transitive closure algorithm: Path decomposition
   technique
%J COMPJ
%V 46
%N 4
%P 391-400
%M JUL
%D 2003
%K jrnl, COMPJ, zz0703, c2003, c200x, c20xx, parallelism, fine grain,
   systolic algorithm, Guibas Kung Thompson GKT, techniques
%Xa"...relation between fine-grained & coarse-grained distributed computations
   of a class of problems related to the generic transitive closure problem..."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/46.4.391">doi:10.1093/comjnl/46.4.391</A>]['05],
      [<A HREF="http://www.oup.co.uk/computer_journal/current/460391.sgm.abs.html">abs</A>][7/'03].

%A J. M. Pallo
%T Right-arm rotation distance between binary trees
%J IPL
%V 87
%N 4
%P 173-177
%M AUG
%D 2003
%K jrnl, IPL, tree, similarity, rotations, zz0703
%X ...transformation on binary trees, named right-arm rotation, ... special
   instance of the [usual] rotation transformation. Only rotations at nodes
   of the right arm of the trees are allowed. Using ordinal tools, we give
   an efficient algorithm for computing the right-arm rotation distance between
   two binary trees, i.e., the minimum number of right-arm rotations necessary
   to transform one tree into the other.
   ... whether the general rotation distance d(T,T') is in polynomial time
   remains an open problem...
   [<A HREF="http://dx.doi.org/10.1016/S0020-0190(03)00283-7">doi:10.1016/S0020-0190(03)00283-7</A>][7/'03]

%A M. Fulmek
%T Enumeration of permutations containing a prescribed number of
   occurrences of a pattern of length three
%J Advances in Appl. Math.
%P 607-632
%V 30
%N 4
%M MAY
%D 2003
%K jrnl, c2003, c200x, c20xx, perm, permutation, generator, enumerate,
   enumeration, algorithm, pattern, jumps, Noonan, Zeilberger, Krattenthaler
%X "...permutations containing exactly k occurrences of a pattern of length 3.
   This enumeration has received a lot of interest recently, & there are a lot
   of known results. [...] presents an alternative approach to the problem,
   which yields a proof for a formula which so far only was conjectured (by
   Noonan & Zeilberger). This approach is based on bijections from permutations
   to certain lattice paths with "jumps," which were first considered by
   Krattenthaler."
   -- [<A HREF="http://dx.doi.org/10.1016/S0196-8858(02)00501-8">doi:10.1016/S0196-8858(02)00501-8</A>][2/'04].

%A M. R. Fellows
%A C. McCartin
%T On the parametric complexity of schedules to minimize tardy tasks
%J Theoretical Comp. Sci.
%V 298
%N 2
%P 317-324
%M APR
%D 2003
%K jrnl, TCS, c2003, c200x, c20xx, schedule, task, parametric complexity,
   parameterized, FPT
%X "Given a set T of tasks, each of unit length and having an individual
   deadline d(t) in Z+, a set of precedence constraints on T, and a positive
   integer k<=|T|, we can ask "Is there a one-processor schedule for T that
   obeys the precedence constraints and contains no more than k late tasks?"
   This is a well-known NP-complete problem.  ...  in the case where the set of
   precedence constraints can be modelled by a partial order of bounded width,
   we show that both these problems are fixed parameter tractable."
   [<A HREF="http://dx.doi.org/10.1016/S0304-3975(02)00811-3">doi:10.1016/S0304-3975(02)00811-3</A>]['05]

%A J. Cheetham
%A F. Dehne
%A A.Rau-Chaplin,  U.Stege,  P.J.Taillon
%T Solving large FPT problems on coarse grained parallel machines
%J J. Computer and System Sciences
%V 67
%N 4
%P 691-706
%M MAR
%D 2003
%K jrnl, JCSS, c2003, c200x, c20xx, parameterized complexity, k-vertex cover,
   fixed-parameter tractability, FPT, kernelization
%X "... to the k-Vertex Cover problem which has important applications in,
   for example, the analysis of multiple sequence alignment..."
   "... The 2 fundamental algorithmic techniques for solving FPT problems are
   kernelization & bounded-tree search..."
   [<A HREF="http://users.cs.dal.ca/~arc/publications/1-22/paper.pdf">pdf</A>]['05]

%A Li Sheng
%T 2-Role assignments on triangulated graphs
%J TCS
%V 304
%N 1-3
%P 201-214
%M JUL
%D 2003
%K jrnl, TCS, c2003, c200x, c20xx, zz0419, role assignment problem, 2role,
   roleAssignment, social network, graph, maths, algorithm, indifference,
   triangulated
%X "... G graph ... a k-role assignment is a fn mapping each vertex into a role,
   a +ve integer 1,2,...,k, so that if x & y have the same role, then the sets
   of roles assigned to their neighbors are the same. A graph is called a
   triangulated graph [chordal] if ... provide a 'greedy' alg. for finding a
   2-role assignment on a connected, non-bipartite triangulated graph with at
   most one pendant vertex [leaf]. We characterize indifference graphs that have
   a 2-role assignment."
   -- [<A HREF="https://doi.org/10.1016/S0304-3975(03)00084-7">doi:10.1016/S0304-3975(03)00084-7</A>]['19].
   [Also search for: role assignment problem].

%A W.-M. Chen
%A H.-K. Hwang
%A T.-H. Tsai
%T Efficient maxima-finding algorithms for random planar samples
%J Discrete Maths and Theoretical Comp. Sci.
%V 6
%N 1
%P 107-122
%D 2003
%K jrnl, DMTCS, c2003, c200x, c20xx, maxima, maximal, dominate, dominating,
   point, points, sample, planar, 2D
%X "... a simple classification of several known algs. for finding the maxima,
   [&] several new algs.; among these are two efficient algs. -- one with
   expected complexity n+O(sqrt(n log n)) when the pt samples are issued from
   some planar regions & another more efficient than existing ones."
   ... points uniformly ... [66 refs].
   -- [<A HREF="http://www.dmtcs.org/dmtcs-ojs/index.php/dmtcs/article/view/181">www</A>]['14]
    & [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.10.3314">cites'r</A>]['14].
   [Also search for: maxima dominate].

%A H. T. Lau
%T A Numerical Library in Java for Scientists and Engineers
%I ChapmanAndHall
%P 1088
%D 2003
%K book, text, c2003, c200x, c20xx, numerical algorithm, algorithms, methods,
   optimization, math, maths
%X "Reference provides Java-based numeric procedures for use in scientific
   computation. Presents procedural descriptions for linear algebra, ordinary
   and partial differential equations, optimization, parameter estimation,
   mathematical physics & other tools ..."
   hb, us$105, uk us isbn:1584884304; uk us isbn13:978-1584884309.
   (Also see [<A HREF="http://commons.apache.org/math/">commons.../math</A>]['07].)

%A J. Zhou
%A K. A. Ross
%T Buffering accesses to memory-resident index structures
%J Proc. VLDB Conf.
%P ?-?
%M SEP
%D 2003
%K conf, c2003, c200x, c20xx, buffer tree, trees, bufferTree, data structures,
   dataStructure, DS, access, indexing, L1, L2, cache, conscious, memory
%X "... buffer accesses to mem.-resident tree-struct. indexes ...
   several alternative designs ... improve cache perf. ..."
   [sec.6.5: non-random probes ... speed up from buffering is smaller (fig.12)]
   [pdf@[<A HREF="http://www.cs.columbia.edu/%7Ekar/pubsk/buffer.pdf">columbia</A>]['08].
   [Also search for: buffer tree].

%A T. H. Cormen
%A C. E. Leiserson
%A R. L. Rivest
%A C. Stein
%T Introduction to Algorithms and Java
%I McGrawHill
%D 2003
%K book, text, c2003, c200x, c20xx, intro, data structures, L3Ref, algorithm
%X hb us$104; uk is isbn:0072970545; uk us isbn13:978-0072970548.
   [Also search for: algorithm book].

%A S. S. Skiena
%A M. Revilla
%T Programming Challenges
%I Springer
%P 368
%D 2003
%K book, text, c2003, c200x, c20xx, computer programming, algorithms,
%X 1st ed 2003; pb us$39; uk us isbn:0387001638; uk us isbn13:978-0387001630.
   [Also search for: algorithm book].

%A R. Schindler
%T P != NP for infinite time Turing machines
%J Monatshefte fur Mathematik
%V 139
%N 4
%P 335-340
%D 2003
%K jrnl, c2003, c200x, c20xx, P, NP, NPC, PNPproblem, complexity,
   infinite time Turing machine, hypercomputation
%X pdf@[<A HREF="http://wwwmath.uni-muenster.de/logik/Personen/rds/pnenp.pdf">uni-m</A>]['10].

%A R. Sinha
%A J. Zobel
%T Cache-conscious sorting of large sets of strings with dynamic tries
%J ACM J. of Experimental Algorithmics
%V 9
%P 1-31
%D 2004
%K jrnl, c2004, c200x, c20xx, burst sort, burstsort, sorting, algorithm,
   string, set, trie, tries, cache, conscious, aware, miss, misses
%X "... new sorting algorithm for strings, burstsort, based on dynamic
   construction of a compact trie in which strings are kept in buckets. It is
   simple, fast, and efficient. We experimentally compare burstsort to existing
   string-sorting algorithms ...  burstsort is almost twice as fast as any
   previous algorithm due primarily to a lower rate of cache miss."
      "... A container [leaf of the trie] is a small set of strings stored in
   a simple DS such as an array or a bin. search t.. ... A container is burst
   whenever it contains more than a fixed # L of strings. ..."  [20 refs].
   pdf@[<A HREF="http://www.cs.rmit.edu.au/~jz/fulltext/alenex03.pdf">rmit</A>]['09],
   [<A HREF="http://doi.acm.org/10.1145/1005813.1041517">doi:10.1145/1005813.1041517</A>]['09],
   [Also search for: burst sort],  [and for: burst trie].

%A V. V. Vazirani
%T Approximation Algorithms
%I Springer
%P 256
%D 2004
%K book, text, c2004, c200x, c20xx, L4Ref, algorithm
%X 2004 hb us$40; uk us isbn:3540653678; uk us isbn13:978-3540653677.

%A M. Ettinger
%A P. Hoyer
%A E. Knill
%T The quantum query complexity of the hidden subgroup problem is polynomial
%J IPL
%V 91
%P 43-48
%M JUL
%D 2004
%K jrnl, c2004, c200x, c20xx, zz0324, IPL, hidden subgroup problem, HSGP, group,
   maths, quantum computing
%X "...a q.alg. which identifies with certainty a hidden subgroup of an
   arbitrary finite group G in only a polynomial (in log|G|) # of calls to the
   oracle. This is exponentially better than the best classical alg.. However
   our q.alg. requires exponential time, as in the classical case. Our alg.
   utilizes a new technique for constructing error-free algs. for non-decision
   problems on q.computers."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2004.01.024">doi:10.1016/j.ipl.2004.01.024</A>]['24],
      [<A HREF="https://arxiv.org/abs/quant-ph/0401083">arxiv:quant-ph/0401083</A>]['24].
   Also see  HSGP@[<A HREF="https://en.wikipedia.org/wiki/Hidden_subgroup_problem">wikip</A>]['24].
   [Also search for: hidden subgroup problem HSGP].

%A J. Dean
%A S. Ghemawat
%T MapReduce: Simplified data processing on large clusters
%J Sixth Symp. on Operating System Design and Implementation
%P 10-10
%M DEC
%D 2004
%K conf, OSDI, c2004, c200x, c20xx, mapReduce, MR, map reduce, google labs,
   distributed, parallel, cluster, clusters
%X "... processing & generating large data sets. Users specify a map fn that
   processes a key/value pair to generate a set of intermediate key/value pairs,
   & a reduce fn that merges all intermediate values associated with the same
   intermediate key. ...  Programs written in this functional style are
   automatically parallelized & executed on a large cluster of commodity m/cs.
   ... Our implementation of MapReduce runs on a large cluster ... typical
   MapReduce computation processes many terabytes of data on thousands of m/cs."
   -- paper@[<A HREF="http://labs.google.com/papers/mapreduce.html">labs.google.com</A>].
   [Also search for: mapReduce MR].

%A J. M. Boyer
%A W. J. Myrvold
%T On the cutting edge: Simplified O(n) planarity by edge addition
%J J. Graph Algorithms and Applications
%V 8
%N 3
%P 241-273
%D 2004
%K jrnl, c2004, c200x, c20xx, planar graph, maths, graphs, planarity testing,
   test, algorithm
%X "... new O(n)-time methods for planar embedding & Kuratowski subgraph
   isolation that were inspired by the Booth-Lueker PQ-tree impln of the
   Lempel-Even-Cederbaum vertex addition method. ... improve upon our conf.
   formulation & upon the Shih-Hsu PC-tree, both of which perform comprehensive
   tests of planarity conditions embedding the edges from a vertex to its
   descendants in a "batch" vertex addition operation. These tests are simpler
   than but analogous to the templating scheme of the PQ-tree. Instead, we take
   the edge to be the fundamental unit of addition to the partial embedding
   while preserving planarity. This eliminates the batch planarity condn testing
   in favor of a few localized decisions of a path traversal process, & it
   exploits the fact that subgraphs can become biconnected by adding a single
   edge. Our method is presented using only graph constructs, but our defn of
   external activity, path traversal process & theor. analysis of correctness
   can be applied to optimize the PC-tree as well."
   [<A HREF="http://www.cs.brown.edu/sites/jgaa/accepted/2004/BoyerMyrvold2004.8.3.pdf">pdf</A>]['08].

%A A. Sapir
%T The tower of Hanoi with forbidden moves
%J COMPJ
%V 47
%N 1
%P 20-24
%M JAN
%D 2004
%K jrnl, compj, towers, Hanoi, c2004, c200x, c20xx
%X "...variant of the classical [...] problem, where limitations on the
   possible moves among the pegs are imposed. Each variant corresponds to a
   di-graph whose vertices are the pegs, & an edge from one vertex to another
   designates the ability of moving a disk from the first peg to the other,
   provided that the rules concerning the disk sizes are obeyed. There are 5
   non-isomorphic graphs on three vertices, which are strongly connected - a
   sufficient condition for the existence of a solution to the problem. We
   provide optimal algorithms for the problem for all these graphs, & find the
   number of moves each requires."
   [<A HREF="http://dx.doi.org/10.1093/comjnl/47.1.20">doi:10.1093/comjnl/47.1.20</A>]['05]
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_47/Issue_01/470020.sgm.abs.html">www</A>][1/'04]

%A V. Kolmogorov
%A R. Zabih
%T What energy functions can be minimized via graph cuts?
%I IEEE Trans Patt. Anal. and Mach. Intell.
%V 26
%N 2
%P 177-189
%M FEB
%D 2004
%K jrnl, c2004, c200x, c20xx, graph, network, cut, cuts, energy function,
   binary variables, minimise, minimize, optimise, optimize,
   minimum cut, maximum flow
%X "... give a characterization of the energy fns that can be minimized by graph
   cuts. Our results are restricted to fns of binary vars.. However, our work
   generalizes many prev. constructions & is easily applic. to vision problems
   that involve large #s of labels, such as stereo, motion, image restoration,
   & scene reconstruction.  We give a precise characterization of what energy
   fns can be min. using graph cuts, among the energy fns that can be written as
   a sum of terms containing 3 or fewer binary vars.. We also provide a general-
   -purpose construction to minimize such an energy fn. Finally, we give a
   nec.condition for any energy fn of binary vars. to be min. by GCs ..."
   (auths @ CS, Cornell, 2004.)

%A M. J. Freedman
%A K. Nissim
%A B. Pinkas
%T Efficient private matching and set intersection
%J Int. Conf. on the Theory and Appl'ns of Cryptographic Techniques
   EUROCRYPT 2004: Advances in Cryptology
%P 1-19
%M MAY
%D 2004
%K conf, c2004, c200x, c20xx, zz1122, private set intersection, PSI
%X "... computing the intersection of private datasets of two parties, where the
   datasets contain lists of elts taken from a large domain. ... For lists of
   length k, we obtain O(k) communication o'head & O(k ln ln k) comp'n. ..."
   -- [<A HREF="https://doi.org/10.1007/978-3-540-24676-3_1">doi:10.1007/978-3-540-24676-3_1</A>['22].
   (Also see PSI@[<A HREF="https://en.wikipedia.org/wiki/Private_set_intersection">wikip</A>]['22].)
   [Also search for: private set intersection PSI].

%A J. Toran
%T On the hardness of graph isomorphism
%J SIAM J. Computing
%V 33
%N 5
%P 1093-1108
%D 2004
%K jrnl, c2004, c200x, c20xx, zz0115, maths, graph, isomorphism,
   canonical, renumbering, labelling, labeling, computational complexity
%X "We show that the graph isomorphism problem is hard under DLOGTIME uniform
   AC{^0} many-one reductions for the complexity classes NL, PL (probabilistic
   logarithmic space) for every logarithmic space modular class {Mod}_kL & for
   the class DET of problems NC{^1} reducible to the determinant. These are the
   strongest known hardness results for the g.iso. problem & imply a randomized
   logarithmic space redn from the perfect matching problem to g.iso.. We also
   investigate hardness results for the graph automorphism problem."
   -- [<A HREF="http://dx.doi.org/10.1137/S009753970241096X">doi:10.1137/S009753970241096X</A>]['15].
   [Also search for: graph isomorphism].

%A T. M. Chan
%T An optimal randomized algorithm for maximum Tukey depth
%J SODA
%P ?-?
%D 2004
%K conf, SODA, SODA04, c2004, c200x, c20xx, zz0613, Tukey, depth, median,
   centerpoint, centrepoint, center, centre, point, halfspace, location
%X "... 1st optimal alg. to compute the max. Tukey depth (aka location or
   halfspace depth) for a non-degenerate pt set in the plane. ... is randomized
   & requires O(n log n) expected time for n data pts. In a higher fixed dim.
   d >= 3, the expected time bound is O(n^(d-1)), which is probably optimal as
   well. The result is obtained using an interesting variant of the author's
   randomized optn technique, capable of solving "implicit"
   linear-programming-type problems; some other applications ... mentioned."
   -- pdf@[<A HREF="http://dl.acm.org/citation.cfm?id=982853">acm</A>]['13].
   [Also search for: geometric median] (not the same thing).

%A D. J. Pearce
%A P. H. J. Kelly
%T A dynamic algorithm for topologically sorting directed acyclic graphs
%J Proc. 3rd Int. Workshop on Efficient and Experimental Algorithms
%S LNCS
%V 3059
%P 383-398
%D 2004 ???
%K wShop, WEA04, WEA3, maths, graph, DAG, topological sort, c2004, c200x, c20xx,
   incremental algorithms, update, updating, zz0505, sparse, dense
%X "...how to maintain the topological order of a ...(DAG) in the presence of
   edge insertions and deletions. ... new alg. &, although this has marginally
   inferior time complexity compared with the best previously known result,
   we find that its simplicity leads to better performance in practice.
   ...empirical comparison against 3 alternatives over a large number of random
   DAGs. ...our algorithm is the best for sparse graphs and, surprisingly, that
   an alternative with poor theoretical complexity performs marginally better
   on dense graphs."  auth @ ic.ac.uk
   -- pdf@[<A HREF="http://www.doc.ic.ac.uk/~phjk/Publications/DynTopoSortWEA2004.pdf">IC</A>]['05].

%A M. Datar
%A N. Immorlica
%A P. Indyk
%A V. S. Mirrokni
%T Locality-sensitive hashing scheme based on p-stable distributions
%J Proc. 20th annual symp. on Comp. geom.
%P 253-262
%M JUN
%D 2004
%K conf, c2004, c200x, c20xx, zz0323, hash, hashing, approximate, neighbourhood,
   LSH, similar, search
%X "We present a novel Locality-Sensitive Hashing scheme for the Approximate
   Nearest Neighbor Problem under lp norm ..."
   -- [<A HREF="https://doi.org/10.1145/997817.997857">doi:10.1145/997817.997857</A>]['23].
   [Also search for: hashing neighbourhood].

%A K. Marriott
%A P. Moulder
%A L. Hope
%A C. Twardy
%T Layout of Bayesian networks
%J Proc. of the 28th Australasian Comp. Sci. Conf.
%I ACS
%W Newcastle, NSW
%P 97-106
%M JAN
%D 2005
%K conf, ACSC28, network, zz0405, display, CTwardy
%X isbn:1920682201;  issn:14451336.

%A D. Eppstein
%T All maximal independent sets and dynamic dominance for sparse graphs
%J Proc. 16th annual ACM-SIAM symp. on Discrete Algorithms
%P 451-459
%D 2005
%K conf, c2005, c200x, c20xx, sparse, graph, graphs, maximal independent set,
   MIS, enumerate, enumeration, constant, subquadratic, per output, sets,
   maxima, dominated, dominate, maths, reverse search, algorithm
%X "... algs, based on Avis & Fukuda's reverse search paradigm, for listing all
   maximal indep. sets in a sparse graph in polynomial time & delay per output.
   For Bounded Degree graphs, our algs. take constant time per set generated;
   for minor-closed graph families, the time is O(n) per set, & for more general
   sparse graph families we achieve subquadratic time per set. We also describe
   new data structures for maintaining a dynamic vertex set S in a sparse or
   minor-closed graph family, & querying the number of vertices not dominated
   by S; for minor-closed graph families the time per update is constant, while
   it is sublinear for any sparse graph family. We can also maintain a dynamic
   vertex set in an arbitrary m-edge graph & test the independence of the
   maintained set in time O(sqrt m) per update. We use the domination data
   structures as part of our enumeration algs.."
   -- [<A HREF="http://portal.acm.org/citation.cfm?id=1070494">pdf@acm</A>]['08].
   [Also search for: maxima dominate].

%A P. Kaski
%T Algorithms for Classification of Combinatorial Objects
%I Dept of Comp. Sci. and Eng., Helsinki U. of Tech. (Espoo)
%M JUN
%D 2005
%K DSci, thesis, object, combinatorics, c2005, c200x, c20xx, maths, systems,
   Steiner triple system, k-regular graphs, one factorization, graph, design,
   whist tournament, tournaments, isomorph, isomorphism, rejection,
   representative, equivalence, class
%X "... examines algorithms for classification of combinatorial objects up to
   isomorphism. ... The main result of this thesis is a classification of the
   Steiner triple systems of order 19. The other results obtained include the
   nonexistence of a resolvable 2-(15, 5, 4) design, a classification of the
   one-factorizations of k-regular graphs of order 12 for k <= 6 and k = 10, 11,
   a classification of the near-resolutions of 2-(13, 4, 3) designs
   together with the associated thirteen-player whist tournaments, and a
   classification of the Steiner triple systems of order 21 with a nontrivial
   automorphism group."  [via R.T.], isbn:9512277271. isbn:9512277115, print.
   -- [<A HREF="http://lib.tkk.fi/Diss/2005/isbn9512277271/">abs+.pdf</A>]['05].
   [Also search for: isomorph rejection].

%A V. Deolalikar
%A J. D. Hamkins
%A R. Schindler
%T P != NP intersection co-NP for infinite time Turing machines
%J J. of Logic and Computation
%V 15
%N 5
%P 577-592
%D 2005
%K jrnl, c2005, c200x, c20xx, infinite time Turing machine, hypercomputation,
   P, NP, coNP, NPC, PNPproblem
%X "Extending results of Schindler, Hamkins & Welch, we establish in the
   context of infinite time TMs that P is properly contained in NP {cap} co-NP.
   For higher analogues of these classes, we exhibit +ve & -ve results."
   -- pdf@[<A HREF="http://dx.doi.org/10.1093/logcom/exi022">doi:10.1093/logcom/exi022</A>]['10].
   [Also search for: PNPproblem].

%A K. Sorensen
%A G. K. Janssens
%T An algorithm to generate all spanning trees of a graph in order of
   increasing cost
%J Pesqui. Oper.
%V 25
%N 2
%P 219-229
%M MAY / AUG
%D 2005
%K minimum spanning tree, MST, enumerate, enumeration, c2005, c200x, c20xx,
   Murty
%X "A MST of an undirected g. can be easily obtained using classical algs. by
   Prim or Kruskal. A # of algs. have been proposed to enumerate all spanning
   trees of an undirected g.. Good time & space complexities are the major
   concerns of these algs.. Most  algs. generate STs using some fundamental cut
   or circuit. In the generation process, the cost of the T is not taken into
   consideration. ... an alg. to generate STs rees of a g. in order of
   increasing cost. By generating STs in order of increasing cost, new
   opportunities appear. ... possible to determine the 2nd smallest or, in
   general, the  k-th smallest ST. The smallest ST satisfying some additional
   constraints can be found by checking at each generation whether these
   constraints are satisfied. Our alg. is based on  an alg. by Murty('67),
   which enumerates all solutions of an assignment problem in order of
   increasing cost. Both time and space complexities are discussed."
   -- [<A HREF="http://www.scielo.br/pdf/pope/v25n2/25707.pdf">www</A>]['12],
      [<A HREF="http://dx.doi.org/10.1590/S0101-74382005000200004">doi:10.1590/S0101-74382005000200004</A>]['12],
    ? [<A HREF="http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0101-74382005000200001&lng=en&nrm=iso">www</A>]['05]?.

%A V. Estivill-Castro
%A M. Fellows
%A M. Langston
%A F. Rosemond
%T FPT is P-time extremal structure I
%J Algorithms and Complexity in Durham 2005
%E H. Broersma
%E M. Johnson
%E S. Szeider
%I King's Coll. Publications, Texts in Algorithmics
%V 4
%P 1-41
%D 2005
%K TR, c2005, c200x, c20xx, parameterized complexity,
   fixed parameter tractability, FPT, Ptime
%X [<A HREF="http://www.cit.gu.edu.au/~s2130677/techreports/EstFelLanRos.pdf">pdf</A>]['05].

%A D. Shapira
%A J. A. Storer
%T In place differential file compression
%J COMPJ
%V 48
%N 6
%P 677-691
%M NOV
%D 2005
%K jrnl, COMPJ, c2005, c200x, c20xx, inPlace, diff, difference, JAStorer,
   zz1105
%X "... where a target file T of size n is compressed with respect to a source
   file S of size m using no additional space in addition to the that used to
   replace S by T; that is, it is possible to encode using m + n + O(1) space
   & decode using MAX(m,n) + O(1) space (so that when decoding the source file
   is overwritten by the decompressed target file). ... known to be NP-hard
   ...  consider practical in-place algorithms ..."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxh128">doi:10.1093/comjnl/bxh128</A>]['05].

%A H. Cohn
%A R. Kleinberg
%A B. Szegedy
%A C. Umans
%T Group-theoretic algorithms for matrix multiplication
%J 46th Annual IEEE Symp. on Foundations of Comp. Sci.
%I IEEE
%P 379-388
%D 2005
%K conf, FOCS, FOCS05, c2005, c200x, c20xx, zz0508, maths, group theory,
   algorithm, fast matrix multiplication, matrices, product, conjecture,
   Cohn, Umans
%X "We further develop the group-theoretic approach to fast matrix
   multiplication introduced by Cohn and Umans, and for the first time use it
   to derive algorithms asymptotically faster than the standard algorithm. We
   describe several families of wreath product groups that achieve matrix
   multiplication exponent less than 3, the asymptotically fastest of which
   achieves exponent 2.41. We present two conjectures regarding specific
   improvements, one combinatorial and the other algebraic. Either one would
   imply that the exponent of matrix multiplication is 2."
   -- [<A HREF="http://arxiv.org/abs/math/0511460v1">arXiv:math/0511460v1</A>]['08],
      [<A HREF="http://doi.ieeecomputersociety.org/10.1109/SFCS.2005.39">doi:10.1109/SFCS.2005.39</A>]['08].
   [Also search for: fast matrix multiplication algorithm].

%A O. Regev
%T On lattices, learning with errors, random linear codes, and cryptography
%J Proc. of the 37th Annual ACM Symp. on Theory of Comput.
%I ACM
%P 84-93
%D 2005
%K conf, c2005, c200x, c20xx, zz0224, lattice based, code, cryptography,
   GapSVP, SIVP
%X "Our main result is a red'n from worst-case lattice problems such as GapSVP
   & SIVP to a certain learning problem. ... This, we believe, gives a strong
   indication that these problems are hard. Our red'n, however, is quantum.
   Hence, an efficient soln to the learning problem implies a q.alg. for GapSVP
   & SIVP. A main open question is whether this red'n can be made classical
   (i.e., nonquantum). ..."
   -- [<A HREF="https://doi.org/10.1145/1568318.1568324">doi:10.1145/1568318.1568324</A>]['24] and
      pdf@[<A HREF="https://cims.nyu.edu/~regev/papers/qcrypto.pdf">nyu.edu</A>]['24].
   [Also search for: lattice based cryptography].

%A K. C. Kiwiel
%T On Floyd and Rivest's SELECT algorithm
%J TCS
%V 347
%N 1-2
%P 214-238
%M NOV
%D 2005
%K jrnl, TCS, c2005, c200x, c20xx, zz0718, median, select, selection, problem,
   algorithm
%X "We show that several versions of Floyd & Rivest's alg. SELECT for finding
   the k-th smallest of n elts require at most n+min(k,nâk)+o(n) comparisons on
   avg & with high probability. This rectifies the analysis of F & R, & extends
   it to the case of nondistinct elts. Our computational results confirm that
   SELECT may be the best alg. in practice."
   -- [<A HREF="https://doi.org/10.1016/j.tcs.2005.06.032">doi:10.1016/j.tcs.2005.06.032</A>]['18] (open '18).
   [Also seach for: median selection problem] and
   [also search for: Floyd select c1975].

%A M. G. Maas
%A J. Nowak
%T A new method for approximate indexing and dictionary lookup with one error
%J IPL
%V 96
%N 5
%P 185-191
%M DEC
%D 2005
%K jrnl, IPL, c2005, c200x, c20xx, indexing, error, mismatch, mismatches,
   approximate
%X "... index for approx. pattern matching. ... still a challenge in comb. patt.
   matching. We present a new data structure that allows to report all matches
   in worst-case time O(|Sigma|m+occ), which is linear in the patt. len. m & the
   # of occurrences occ for alphabets of const. size |Sigma|.  ... uses
   O(n|Sigma|log n) extra space on avg. & with high prob., where n is the len.
   of the text (indexing) or the # of strings to index (dict. lookup)."
   [<A HREF="http://dx.doi.org/10.1016/j.ipl.2005.08.001">doi:10.1016/j.ipl.2005.08.001</A>]['08].
   [Also search for: approximate indexing].

%A D. E. Knuth
%T Art of Computer Programming, Volume 4, Fascicle 4: Generating All Trees
   -- History of Combinatorial Generation
%I AddisonWesley
%D 2006
%K book, text, c2006, c200x, c20xx, zz0715, tree, combinatorics, generate,
   generator, generating
%X 1st ed 2006; pb us$16; uk us isbn:0321335708; uk us isbn13:978-0321335708.
   "Finally, after a wait of more than 35 years, the 1st part of Vol.4 is at
   last ready for publication. ... This latest fascicle covers the generation
   of all trees."

%A J. F. Korsch
%T Skarbek's algorithm for t-Ary trees
%J COMPJ
%V 49
%N 3
%P 351-357
%M MAY
%D 2006
%K COMPJ, jrnl, c2006, c200x, c20xx, zz0506, nAry, tAry, tree, trees, generate
%X "... generating all n node t-ary trees in linked rep. by providing a context
   & generalizing Skarbek's alg. for generating binary trees. It initially
   appeared that Skarbek's alg. could not be generalized to even 3-ary trees,
   which motivated the author to previously develop an alg. for generating all
   n node t-ary trees in linked representation based on a particular listing of
   integer sequences representing the trees. The context for the generalization
   of Skarbek's alg. turns out to also be a particular listing of integer
   sequences representing the trees. The paper also gives 2 constant average
   time implementations. The 1st generates the next tree from its predecessor
   given in linked representation while the 2nd retains additional information
   about the predecessor beyond just its linked representation."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxk003">doi:10.1093/comjnl/bxk003</A>]['06]

%A S. Eun Bae
%A T. Takaoka
%T Improved algorithms for the K-maximum subarray problem
%J COMPJ
%V 49
%N 3
%P 358-374
%M MAY
%D 2006
%K COMPJ, jrnl, c2006, c200x, c20xx, max, maximum sum interval, intervals,
   array, matrix, subarray, submatrix, contiguous, rectangular, algorithm
%X "The maximum subarray problem is to find the contiguous array elements
   having the largest possible sum. We extend this problem to find K maximum
   subarrays. For general K maximum subarrays where overlapping is allowed,
   Bengtsson and Chen presented O(min{K+n log**2 n, n sqrt K})-time alg. for
   1-D case, which finds unsorted subarrays. Our alg. finds K max. subarrays in
   sorted order with improved complexity of O((n + K) log K). For the 2-D case,
   we introduce 2 techniques that establish O(n^3) and subcubic time."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxl007">doi:10.1093/comjnl/bxl007</A>]['06].
   (Also see MSA@[<A HREF="https://en.wikipedia.org/wiki/Maximum_subarray_problem">wikip</A>]['19].)

%A W. Duckworth
%T Large k-separated matchings
%J 31st Australasian Conf. on Combinatorial Math. and Combinatorial Computing
%W Alice Springs
%M JUL
%D 2006
%K conf, c200x, c200x, c20xx, matching, maths, graph, graphs, ANUni
%X [<A HREF="http://wwwmaths.anu.edu.au/~duckworb/">home</A>]['07]
   (smnrs @ MSI ANU '07)

%A Sang-il Oum
%A P. Seymour
%T Approximating clique-width and branch-width
%J J. Combinatorial Theory, Ser. B
%V 96
%N 4
%P 514-528
%M JUL
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0515, maths, graph, clique width, cliqueWidth,
   branch width, branchWidth, rank width, rankWidth
%X "We construct a polynomial-time alg. to approx. the branch-width of certain
   symmetric submodular fns, & give two applications. The first is to graph
   'clique-width.' ... a measure of the difficulty of decomposing a graph in a
   kind of tree-structure, & if a graph has clique-width at most k then the
   corr. decomposition of the g. is called a 'k-expression.' We find (for fixed
   k) an O(n^9 log n)-time alg.  ... Another application is to the area of
   matroid branch-width. For fixed k, we find an O(n^3.5)-time alg. that, with
   input an n-element matroid in terms of its rank oracle, either outputs a
   branch-decomposition of width at most 3k-1 or a witness that the matroid has
   branch-width at least k+1. ..."
   "... we define the 'rank-width' of a graph to be the branch-width of a
   symmetric submodular function determined by a graph ..." [p.516]
   -- [<A HREF="http://dx.doi.org/10.1016/j.jctb.2005.10.006">doi:10.1016/j.jctb.2005.10.006</A>]['15].

%A V. G. Deineko
%A B. Klinz
%A G. J. Woeginger
%T Exact algorithms for the Hamiltonian cycle problem in planar graphs
%C Operations Res.
%V 34
%N 3
%P 269-274
%M MAY
%D 2006
%K jrnl, c2006, c200x, c20xx, OR, OpRes, zz0707, maths, graph, algorithm,
   cycles, NP, NPC, complete, complexity, algorithmic, subexponential, Dorn
%X "We construct an exact alg. for the Hamiltonian c. [[each vertex]] problem in
   planar gs. with worst-case time-complexity O(c**sqrt(n)) where c is some
   fixed const [indep of] the instance. [and] we show that under the exponential
   time hypothesis the time-c. cannot be improved to O(c**o(srqt(n)))".
   [<A HREF="http://dx.doi.org/10.1016/j.orl.2005.04.013">doi:10.1016/j.orl.2005.04.013</A>]['07]

%A S. Dasgupta
%A C. H. Papadimitriou
%A U. Vazirani
%T Algorithms
%I McGrawHill
%P 336
%D 2006
%K book, text, c2006, c200x, c20xx, L2Ref, L3Ref, algorithms
%X pb us$32, uk us isbn:0073523402; uks us isbn13:978-0073523408.

%A F. Dorn
%A F. V. Fomin
%A D. M. Thilikos
%T Fast subexponential algorithm for non-local problems on graphs of bounded
   genus
%J SWAT 2006
%I SpringerVerlag
%S LNCS
%V 4059
%P 172-183
%D 2006
%K conf, c2006, c200x, c20xx, maths, graph, NP, NPC, complete, complexity,
   algorithmic, Hamiltonian cycle, cycles, length, subexponential, zz0707,
   Deineko
%X "...general technique for designing fast subexp. algs. for several graph
   problems whose instances are restricted to graphs of bounded genus. We use it
   to obtain time 2**{O(sqrt{n})} algs. for a wide family of problems such as
   Hamiltonian Cycle, Sigma-embedded Graph Travelling Salesman Problem,
   Longest Cycle, & Max Leaf Tree.  ... combine planarizing techniques with
   dynamic programming on special type branch decompositions. Our techniques can
   also be used to solve parameterized problems. Thus, for example, we show how
   to find a cycle of length p (or to conclude that there is no such a cycle) on
   graphs of bounded genus in time 2**{O(sqrt{p})}.n**{O(1)}."
   -- [<A HREF="http://dx.doi.org/10.1007/11785293_18">doi:10.1007/11785293_18</A>]['07].

%A M. A. Weiss
%T Data Structures and Algorithm Analysis in C++
%I AddisonWesley
%P 586
%D 2006
%K book, text, c2006, c200x, c20xx, cc, Cplusplus, structure, dataStructure, DS,
   algorithms, L2Ref, L3Ref
%X 3rd ed 2006, pb us$89; uk us isbn:032144146X; uk us isbn13:978-0321441461.
   (Also search for: Weiss book).

%A K. Terasawa
%A Y. Tanaka
%T Spherical LSH for approximate nearest neighbor search on unit hypersphere
%J Workshop on Algs. and Data Structs. (WADS)
%I Springer
%S LNCS
%V 4619
%P 27-38
%D 2007
%K conf, c2007, c200x, c20xx, zz0823, sphere, spherical, locality, sensitive,
   hash, LSH, hashing, neighbourhood
%X "... presents a variant of the LSH alg., focusing on the special case of
   where all pts in the dataset lie on the surface of the unit hypersphere in a
   d-dim. Euclidean space. The LSH scheme is based on a family of hash fns that
   preserves locality of points. ..."
   -- [<A HREF=" https://doi.org/10.1007/978-3-540-73951-7_4">doi:10.1007/978-3-540-73951-7_4</A>]['23].
   [Also search for: locality sensitive hashing].

%A P. J. Ballester
%A W. G. Richards
%T Ultrafast shape recognition for similarity search in molecular databases
%J Proc Royal Soc. A
%V ?
%P ?
%D 2007
%K jrnl, PRSS, c2007, c200x, c20xx, 3D, shape, shapes, match, similar, zz0307,
   molecule, molecules, matching, database
%X "... new approach based on moments of distance distributions is able to
   recognize molecular shape at least 3 orders of magnitude faster than current
   methodologies. Such an ultrafast method permits the identification of
   similarly shaped compounds within the largest molecular databases. [And] the
   problematic requirement of aligning molecules for comparison is circumvented,
   as the proposed distributions are independent of molecular orientation. Our
   methodology could be also adapted to tackle similar hard problems in other
   fields, such as designing content-based Internet search engines for 3-D
   geom. objects or performing fast similarity comp's between proteins. ..."
   [<A HREF="http://dx.doi.org/10.1098/rspa.2007.1823">doi:10.1098/rspa.2007.1823</A>]['07]
   auths@uniOxford ['07]

%A D. L. Applegate
%A R. E. Bixby
%A V. Chvatal
%A W. J. Cook
%T The Traveling Salesman Problem: A Computational Study
%I PrincetonUP
%S Princeton Series in Applied Mathematics
%P 606
%D 2007
%K book, text, c2007, c200x, c20xx, sales man, salesperson, maths, graph,
   graphs, travelling, algorithm
%X hb, us isbn:0691129932; us isbn13:978-0691129938.
   [Also search for: travelling salesman].

%T The Traveling Salesman Problem and Its Variations
   (Combinatorial Optimization)
%E G. Gutin
%E A. P. Punnen
%I Springer
%P 830
%D 2007
%K book, c2007, c200x, c20xx, maths, graph, graphs, sales man, salesperson,
   travelling
%X pb, uk us isbn:0387444599; uk us isbn13:978-0387444598.

%A S. Gregory
%T An algorithm to find overlapping community structure in networks
%J PKDD
%I SpringerVerlag
%S LNCS
%V 4702
%P 91-102
%D 2007
%K conf, PKDD, PKDD07, c2007, c200x, c20xx, network, maths, graph, graphs,
   community, zz1107, Girvan, Newman, between, betweenness centrality,
   hierarchical clustering
%X "...vast majority of [algs] only find disjoint communities, but in many
   real-world networks communities overlap to some extent. ...new alg. for
   discovering overlapping communities in n/ws, by extending Girvan & Newman's
   well-known alg. based on the betweenness centrality measure. Like the
   original alg., ours performs hierarchical clustering - partitioning a n/w
   into any desired number of clusters - but allows them to overlap. Experiments
   confirm good performance on randomly gen. n/ws based on a known overlapping
   community structure, & interesting results have also been obtained on a
   range of real-world networks."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-74976-9">doi:10.1007/978-3-540-74976-9</A>]['07].
   (Also see ComStr@[<A HREF="https://en.wikipedia.org/wiki/Community_structure">wikip</A>]['20].)
   [Also search for: network community].

%A D. Spielman
%T Theory and applications of graph spectra
%J FOCS
%D 2007
%K tutorial, tute, FOCS, c2007, c200x, c20xx, Laplacian, matrix, maths, graph,
   graphs, eigenvectors, eigenvalues, spectum, spectral, intro, survey
%X "... study the eigenvalues & eigenvectors of the Laplacian & normalized
   Laplacian matrices of graphs.  Our first goal will be to provide intution as
   to why these eigenvectors & eigenvalues should reveal combinatorial
   structure.  We will examine applications of eigenvectors & eigenvalues to
   drawing, ranking, partitioning, clustering & coloring problems in graphs.
   We will also discuss connections to random walks in graphs, & how they
   inspire applications of graph spectra in machine learning & image
   segmentation.  We will conclude with a discussion of the theory & practice of
   computing eigenvalues & eigenvectors, & how results from spectral graph
   theory may be applied to accelerate those computations.  We will supply
   examples you can try at home using either Matlab or Python."
   [<A HREF="http://cs-www.cs.yale.edu/homes/spielman/sgta/">notes@yale</A>]['08],
   [<A HREF="http://focs2007.org/tutorial_presentations/">.ppt@focs</A>]['08].

%A M. Furer
%T Faster integer multiplication
%J 39th ACM Symp. on Theory of Computing
%P 57-66
%M JUN
%D 2007
%K conf, STOC, c2007, c200x, c20xx, zz0713, fast integer multiplication,
   complexity, algorithm, computer arithmetic, BigInt, operation
%X "For more than 35 years, the fastest known method for integer multiplication
   has been the Schonhage-Strassen alg running in time O(n log n log log n).
   Under certain restrictive conditions, there is a corr. Omega(n log n)
   lower bound. All this time, the prevailing conjecture has been that the
   complexity of an optimal int mult alg is Theta(n log n). We present a major
   step towards closing the gap from above by presenting an alg running in time
   n log(n 2^O(log* n)). The running time bound holds for multitape Turing
   machines. The same bound is valid for the size of boolean circuits."
   -- [<A HREF="http://dx.doi.org/10.1145/1250790.1250800">doi:10.1145/1250790.1250800</A>]['13],
    & pdf@[<A HREF="http://www.cse.psu.edu/~furer/Papers/mult.pdf">psu</A>]['13] (free).
   [Also search for: fast integer multiplication].

%A D. Conte
%A P. Foggia
%A M. Vento
%T Challenging complexity of maximum common subgraph detection algorithms:
   A performance analysis of three algorithms on a wide database of graphs
%J J. of Graph Algorithms and Applications
%V 11
%N 1
%P 99-143
%D 2007
%K jrnl, c2007, c200x, c20xx, maths, graph, graphs, largest,
   maximum common subgraph, shared, MCS, problem, algorithm
%X "... MCS is a, well known NPC problem for which optimal & suboptimal
   algs.  are known .... Nevertheless, until now no effort has been done for
   characterizing their performance. The lack of a large DB of graphs makes the
   task of comparing the performance of different graph matching algs. difficult
   & often the selection of an alg. is made on the basis of a few experimental
   results available. [here] 3 optimal & well-known algs. for MCS detection are
   described. Moreover a large DB containing various categories of pairs of
   graphs (e.g. random gs., meshes, bounded valence gs.), is presented, & the
   performance of the 3 algs. is evaluated on this DB."
   -- pdf@[<A HREF="http://www.emis.de/journals/JGAA/accepted/2007/ConteFoggiaVento2007.11.1.pdf">emis.de</A>]['08].

%T Handbook of Approximation Algorithms and Metaheuristics
%E T. F. Gonzalez
%I ChapmanHall
%S CRC
%D 2007
%K book, text, c2007, c200x, c20xx, zz0408, approximation algorithm,
   metaheuristic, inapproximability, approximability, sensitivity analysis,
   stability, combinatorial optimization, maths, graph, problem
%X "... methodologies to design and analyze efficient approximation algs. for a
   large class of problems, and to establish inapproximability results for
   another class of problems. It also discusses local search, neural networks,
   and metaheuristics, as well as multiobjective problems, sensitivity analysis,
   and stability. After laying this foundation, the book applies the
   methodologies to classical problems in combinatorial optimization,
   computational geometry, and graph problems. ..."
   pb, us$94, uk us isbn:1584885505; uk us isbn13:978-1584885504.

%A A. Amir
%A J. Fischer
%A M. Lewenstein
%T Two-dimensional range minimum queries
%J 18th Annual Symp. Combinatrial Pattern Matching
%I SpringerVerlag
%S LNCS
%V 4580
%P 286-294
%M JUL
%D 2007
%K conf, CPM, c2007, c200x, c20xx, zz1009, range minimization query, RMQ, 2D,
   minimum, minimisation, smallest, element, matrix, array, higher dimension,
   two, twoD
%X "... for a static (m x n)-matrix of size N=mn which may be preprocessed,
   ... queries of the form 'where is the posn of a min. elt in an axis-parallel
   rectangle?'  Unlike the 1D version of this problem which can be solved in
   provably optimal time & space, the higher-D case has received much less
   attention. The only result we are aware of is due to Gabow, Bentley & Tarjan
   ... in O(NlogN) preprocessing time & space & O(logN) query time. We present
   a class of algs. which can solve the 2D RMQ-problem with O(kN) additional
   space, O(N log**[k+1] N)  preprocessing time & O(1) query time for any k>1,
   [where log**[k] N is log...k...log N]. The soln converges towards an
   alg. with O(N log* N) preprocessing time & space and O(1) query time. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-73437-6_29">doi:10.1007/978-3-540-73437-6_29</A>]['09].
   [Also search for: range minimization query] and
   [also search for: range query].

%A N. Askitis
%A R. Sinha
%T HAT-trie: a cache-conscious trie-based data structure for strings
%J Proc. 13th Australasian Conf. on Comp. Sci.
%V 62
%P 97-105
%D 2007
%K conf, ACSC, ACSC13, ACSC07, c2007, c200x, c20xx, hat trie, hatTrie, tries,
   burst, dataStructure, DS, string, strings, indexing
%X "Tries ... fastest ... for managing strings ...but are space-intensive. The
   burst-trie is almost as fast but reduces space by collapsing trie-chains
   into buckets. This is not however, a cache-conscious approach & can lead to
   poor performance on current processors. ... introduce the HAT-trie, a cache-
   -conscious ... carefully combining existing components. We evaluate perf. ...
   ... shown to be the most efficient trie-based DS for ... variable-length
   strings in-memory while maintaining sort order."
   -- pdf@[<A HREF="https://dl.acm.org/doi/pdf/10.5555/1273749.1273761">ACM</A>]['22],
      was crpit.com/confpapers/CRPITV62Askitis.pdf ['08].
   [Also search for: burst trie].

%A S. J. Puglisi
%A W. F. Smyth
%A A. H. Turpin
%T A taxonomy of suffix array construction algorithms
%J ACM Computing Surveys
%V 39
%N 2
%D 2007
%K survey, c2007, c200x, c20xx, suffix array, complexity, algorithm, string,
   strings, search, indexing
%X "Manber & Myers ['90, '93] proposed suffix arrays as a space-saving alt. to
   s.trees & described the 1st algs. for s.array construction & use. ...
   ... s.array construction algs. have proliferated in bewildering abundance.
   ... attempts to provide simple high-level descriptions of these numerous
   algs. that highlight both their distinctive features & their commonalities,
   while avoiding as much as possible the complexities of implementation
   details. New hybrid algs. are also described. We provide comparisons of the
   algs.' worst-case time complexity & use of additional space [and] results of
   recent experimental test runs on many of their implementations." [49 refs].
   [<A HREF="http://doi.acm.org/10.1145/1242471.1242472">10.1145/1242471.1242472</A>]['07]. (auths 1 & 3 @ rmit, '08),
   auth1@[<A HREF="http://goanna.cs.rmit.edu.au/~sjp/">rmit</A>]['09].
   [Also search for: suffix array],  [or for: suffix array complexity].

%A H. D. Mittelmann
%T Recent benchmarks of optimization software
%J 22nd European Conf. on Operational Res.
%W Prague
%P ?-?
%D 2007
%K conf, EURO XXII, c2007, c200x, c20xx, benchmark, linear programming,
   software, CPLEX, ILOG
%X [<A HREF="http://plato.asu.edu/talks/hamilton.pdf">ASU</A>]['07],
   auth@[<A HREF="http://plato.asu.edu/">ASU</A>]['13].
   (Also see CPLEX@[<A HREF="http://en.wikipedia.org/wiki/CPLEX">wikip</A>]['13].)

%A T. Junttila
%A P. Kaski
%T Engineering an efficient canonical labeling tool for large and sparse graphs
%J 9th SIAM Workshop on Algorithm Engineering and Experiments
%D 2007
%K wShop, ALENEX07, c2007, c200x, c20xx, zz0416, BLISS, algorithm,
   maths, graph, sparse, isomporphism, canonical labeling, labelling
%X "... Within the general framework of backtracking algs. based on
   individualization & refinement, data structures, subroutines, & pruning
   heuristics especially for fast handling of large & sparse gs. are developed.
   Experiments indicate that the alg. implementation in most cases clearly
   outperforms existing state-of-the-art tools."
   -- [<A HREF="http://dx.doi.org/10.1137/1.9781611972870.13">doi:10.1137/1.9781611972870.13</A>]['16].
   (Also see
   GA@[<A HREF="https://en.wikipedia.org/wiki/Graph_automorphism">wikip</A>]['16].)
   [Also search for: maths graph isomorphism].

%A M. Mares
%A M. Straka
%T Linear-time ranking of permutations
%J European Symp. of Algorithms
%I SpringerVerlag
%P 187-193
%D 2007
%K conf, ESA, c2007, c200x, c20xx, zz0713, permutation, permutations, rank,
   lexicographic, ranking, ordering, generator, function, unranking, mapping,
   algorithm
%X "A lexicographic ranking fn for the set of all perms of n ordered symbols
   translates perms to their ranks in the lexicographic order of all perms. This
   is frequently used for indexing data structures by perms. We present algs for
   computing both the ranking fn & its inverse using O(n) arithmetic ops."
      ("... based on an observation that once we assume that our computation
       model is capable of performing basic arithmetic on #s of the order
       of magnitude of the resulting rank ..."  [i.e., bit tricks.])
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-75520-3_18">doi:10.1007/978-3-540-75520-3_18</A>]['13].
  (NB. The usual *lexicographical* order.)
   [Also search for: ranking permutations].

%A P. Flajolet
%A E. Fusy
%A O. Gandouet
%A F. Meunier
%T Hyperloglog: The analysis of a near-optimal cardinality estimation algorithm
%J Int. Conf. Analysis of Algs. (AOFA)
%D 2007
%K conf, c2007, c200x, c20xx, zz0923, hyperloglog, count distinct problem,
   streaming algorithm, data stream, counting, estimating, approximate
%X "... HYPERLOGLOG performs a single pass over the data & produces an est. of
   the cardinality s.t. the relative accuracy (the std error) is typically
   about 1.04/sqrt(m). ..."
   -- [<A HREF="http://algo.inria.fr/flajolet/Publications/FlFuGaMe07.pdf">www</A>]['23].  Also
   see HLL@[<A HREF="https://en.wikipedia.org/wiki/HyperLogLog">wikip</A>]['23],
   and CDP@[<A HREF="https://en.wikipedia.org/wiki/Count-distinct_problem">wikip</A>]['23].

%E R. G. Downey
%E M. R. Fellows
%E M. A. Langston
%T The Computer Journal special issue on parameterized complexity:
   Foreword by the guest editors
%J COMPJ
%V 51
%N 1
%P 1-6
%M JAN
%D 2008
%K jrnl, COMPJ, c2008, c200x, c20xx, fixed parameter, tractability, FPT,
   zz0108, instance, parametrised
%X "Parameterized c. studies a generalization of the notion of polynomial time
   where, in addition to the overall input size, n, one also considers the
   effects on computational complexity of a secondary measurement, the
   parameter. The central notion of the field is fixed-parameter tractability
   (FPT), which refers to solvability in time f(k)n^c, where f is some fn (
   usually exponential) of the param. k, & c is a const.. The subject unfolds in
   2 basic complementary projects & assoc. math. toolkits: (1) How to design
   (& improve) FPT algs., for parameterized problems that admit them & (2) How
   to gather evidence that a parameterized problem probably does not admit an
   FPT algorithm. ..."
   [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm111">doi:10.1093/comjnl/bxm111</A>]['08]

%A D. Marx
%T Parameterized complexity and approximation algorithms
%J COMPJ
%V 51
%N 1
%P 60-78
%M JAN
%D 2008
%K jrnl, COMPJ, c2008, c200x, c20xx, algorithm, FPT, instance parameter
%X [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm048">doi:10.1093/comjnl/bxm048</A>]['08], [116 refs].

%A C. Sloper
%A J. Arne Telle
%T An overview of techniques for designing parameterized algorithms
%J COMPJ
%V 51
%N 1
%P 122-136
%M JAN
%D 2008
%K jrnl, COMPJ, c2008, c200x, c20xx, algorithm, FPT, branching, kernelization,
   induction, win/win, winwin, survey, FPT
%X "A survey of the most important & general techniques in parameterized
   alg. design is given. Each tech. is explained with a meta-alg., its use is
   illustrated by e.g.s, & it is placed in a taxonomy under the 4 main headings
   of branching, kernelization, induction & win/win."
   [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm038">doi:10.1093/comjnl/bxm038</A>]['08]  [36 refs].

%T Approximation and Online Algorithms,
   revised papers 5th Int. Workshop, WAOA '07, Eilat, Oct. 11-12
%E C. Kaklamanis
%E M. Skutella
%I SpringerVerlag
%S LNCS
%V 4927
%P 289
%D 2008
%K wShop, WAOA 07, approximation, online, algorithm, c2008, c200x, c20xx
%X pb eu.45; uk us isbn:3540779175; uk us isbn13:978-3540779179.

%T Reliable Implementation of Real Number Algorithms: Theory and Practice:
   Int. Seminar Dagstuhl Castle, Germany, 2006 (Revised Papers)
%I SpringerVerlag
%M JAN
%D 2008
%K symp, c2008, c200x, c20xx, algorithm, real numbers, number,
   computer arithmetic
%X 1st ed, 2008, us$65; uk us isbn:3540855203; uk us isbn13:978-3540855200.

%A A. De
%A P. P. Kurur
%A C. Saha
%A R. Saptharishi
%T Fast integer multiplication using modular arithmetic
%J SIAM J. Comput.
%V 42
%N 2
%P 685-699
%D 2008
%K conf, STOC, c2008, c200x, c20xx, zz0713, fast integer multiplication,
   Furer, complexity, algorithm, BigInt
%X "... an N log(N 2^O(log* N)) time alg. to multiply two N-bit ints that uses
   modular arithmetic for intermediate computations instead of arith. over
   complex #s as in Furer's alg., which also has the same & so far the best
   known complexity. The prev. best alg. using modular arithmetic (by Schonhage
   & Strassen) has complexity O(N log N loglog N). The advantage of using
   modular arith as opposed to complex number arith is that we can completely
   evade the task of bounding the truncation error due to finite approximations
   of complex #s, which makes the analysis relatively simple. Our alg is based
   upon Furer's alg, but uses FFT over multivariate polynomials along with an
   est of the least prime in an arith progression to achieve this improvement in
   the modular setting. It can also be viewed as a p-adic version of F's alg"
   -- [<A HREF="http://dx.doi.org/10.1137/100811167">doi:10.1137/100811167</A>]['13],
    & [<A HREF="http://arxiv.org/abs/0801.1416">arXiv</A>]['13] (free).
   [Also search for: fast integer multiplication].

%T Encyclopedia of Algorithms
%E M.-Y. Kao
%I Springer
%P 1166
%D 2008
%K book, text, c2008, c200x, c20xx, L4Ref, L5Ref
%X 1st ed 2008, hb, us$276; uk us isbn:0387307702; uk us isbn13:978-0387307701.
   [Also search for: Handbook Algorithms].

%A P. Crescenzi
%A M. Di Ianni
%A F. Greco
%A G. Rossi
%A P. Vocca
%T Making role assignment feasible: A polynomial-time algorithm for computing
   ecological colorings
%J Graph-Theoretic Concepts in Computer Science
%P 90-100
%D 2008
%O LNCS vol. 5344
%K conf, GTCCS, c2008, c200x, c20xx, zz0419, role assignment problem,
   graph, maths, algorithm
%X "... study the problem of ecologically coloring a graph. ... an ecological
   coloring of a graph is a role assignment to the nodes of the graph, s.t. two
   nodes surrounded by the same set of roles must be assigned the same role ...
   prove that, for any simple undirected graph G with n_G distinct
   neighborhoods and for any integer k with 1â<=âkâ<=ân_G , G admits an
   ecological coloring which uses exactly k roles, and that this coloring can be
   computed in polynomial time. ..."
   -- [<A HREF="https://doi.org/10.1007/978-3-540-92248-3_9">doi:10.1007/978-3-540-92248-3_9</A>]['19].
   [Also search for: role assignment problem].

%A Y.-H. Hsieh
%A C.-C. Yu
%A B.-F. Wang
%T Optimal algorithms for the interval location problem with range constraints
   on length and average
%J Algorithmica
%V 5
%N 2
%P 281-290
%M APR
%D 2008
%K jrnl, c2008, c200x, c20xx, algorithm, interval, biased, density, sequence
%X "Let A be a seq. of n real numbers, L1 & L2 be two integers s.t. L1 <= L2,
   & R1 & R2 be two real numbers such that R1 <= R2. An interval of A is
   feasible if its length is between L1 & L2 & its avg. is between R1 & R2.
   ... study the following problems: finding all feasible intervals of A,
   counting all feasible intervals of A, finding a maximum cardinality set of
   non-overlapping feasible intervals of A, locating a longest feasible interval
   of A, & locating a shortest feasible interval of A. ... motivated from the
   problem of locating CpG islands in biomolecular seqs.. ... we firstly show
   that all the problems have an Omega(n log n)-time lwb in the comparison
   model. Then, we use geometric approaches to design optimal algs. for the
   problems. All the presented algs. run in an on-line manner & use O(n) space."
   -- [<A HREF="http://dx.doi.org/10.1109/TCBB.2007.70217">doi:10.1109/TCBB.2007.70217</A>]['08].
   [Also search for: biased interval].

%A S. S. Skiena
%T The Algorithm Design Manual
%I Springer
%P 752
%D 2008
%K book, text, c2008, c200x, c20xx, algorithms, L3Ref, L4Ref, computer,
   programming, program, source, interview, problem, problems
%X 2nd ed 2010; pb us$72; uk us isbn:1849967202; uk us isbn13:978-1849967204;
   2nd ed 2008; hb us$64; uk us isbn:1848000693; uk us isbn13:978-1848000698.
      '... Contains a highly unique catalog of the 75 most important
      algorithmic problems. [And] includes new "war stories" and "interview
      problems", relating experiences from real-world applications. ...'
   [Also search for: Handbook Algorithms].

%A J. Edmonds
%T How to Think About Algorithms
%I CUP
%P 472
%M MAY
%D 2008
%K book, text, CUP, c2008, c200x, c20xx, algorithm, computer programming, SWE,
   design, programs, recursion
%X 1st ed 2008l pb us$38; uk us isbn:0521614104; uk us isbn13:978-0521614108.
   "... presents insights, notations, & analogies to help the novice describe
   & think about algorithms like an expert. By looking at both the big picture
   & easy step-by-step methods for developing algorithms, the author helps
   students avoid the common pitfalls. He stresses paradigms such as loop
   invariants & recursion to unify a huge range of algorithms into a few meta-
   -algs. Part of the goal is to teach the students to think abstractly. ..."

%A P. T. Darga
%A K. A. Sakallah
%A I. L. Markov
%T Faster symmetry discovery using sparsity of symmetries
%J Proc. 45th Design Automation Conf.
%I ACM
%P 149-154
%M JUN
%D 2008
%K DAC08, conf, c2008, c200x, c20xx, zz0416, SAUCY, algorithm,
   maths, graph, automorphism, symmetry, sparse
%X "... existing tools suffer quadratic [?] runtime in the # of symmetries
   explicitly returned & are of limited use on very large, sparse, symmetric
   graphs. ... introduces a new symmetry-discovery alg. which exploits the
   sparsity present not only in the input but also the output, i.e., the
   symmetries themselves. By avoiding quadratic runtime on large graphs, it
   improves state-of-the-art runtimes from several days to less than a second."
   -- pdf@[<A HREF="http://dx.doi.org/10.1145/1391469.1391509">doi:10.1145/1391469.1391509</A>]['16];  uk us isbn13:978-1-60558-115-6.
   (Also see
   GA@[<A HREF="https://en.wikipedia.org/wiki/Graph_automorphism">wikip</A>]['16].)
   [Also search for: maths graph isomorphism] and
   [also search for: maths graph automorphism].

%A M. Thill
%T A more precise rounding algorithm for rational numbers
%J Computing
%V 82
%P 189-198
%M JUN
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0124, algorithm, maths, continued fractions,
   intermediate, fraction, mediant rounding, rational, number
%X "... the current state of art in theory of continued fractions, intermediate
   fractions & their rel'n to the best rational approx. of the 1st & 2nd
   kind. ..."
   -- [<A HREF=" https://doi.org/10.1007/s00607-008-0006-7">doi:10.1007/s00607-008-0006-7</A>]['24] (an erratum 17/8/'08).
   (Also see CFs@[<A HREF="https://en.wikipedia.org/wiki/Continued_fraction">wikip</A>]['24].)

%A R. J. Vanderbei
%T Linear Programming: Foundations and Extensions
%I SpringerVerlag
%S Int. Series in Operations Res. & Management Sci.
%V 114
%M NOV
%D 2008
%K book, text, c2008, c200x, c20xx, linear programming, simplex, algorithm,
   convex, integer, quadratic
%X 3rd ed 2008; hb us$70; uk us isbn:0387743871; uk us isbn13:978-0387743875.
   "... emphasizes constrained optimization, ... linear programming & then
   proceeding to convex analysis, network flows, integer programming, quadratic
   programming, & convex optimization. ... business applications & non-business
   ... focus on solving practical problems, ... C programs to implement the
   major algs. covered. ..."
   [Also search for: LinearProgramming].

%A P. Flajolet
%A R. Sedgewick
%T Analytic Combinatorics
%I CUP
%P 824
%M JAN
%D 2009
%K book, text, CUP, c2009, c200x, c20xx, zz0812, algorithms, Comp Sci, CSci,
   combinatorial, counting, theory, discrete structures
%X 1st ed 2009; hb us$73; uk us isbn:0521898064; uk us isbn13:978-0521898065.
   "... the maths underlying the analysis of discrete structures, which has
   emerged over the past several decades as an essential tool in the
   understanding of properties of computer programs & sci.models with
   applications in physics, biology & chemistry. ... treatment of a large #
   of classical applications is an essential aspect of the presentation. ..."
   pdf & auth1@[<A HREF="http://algo.inria.fr/flajolet/Publications/books.html">inria</A>]['12].  (via Torsten.)

%A H. Petersen
%A S. Grabowski
%T Range mode and range median queries in constant time and sub-quadratic space
%J IPL
%V 109
%N 4
%P 225-228
%M JAN
%D 2009
%K jrnl, IPL, c2009, c200x, c20xx, 1D, range query, median, function, algorithm
%X "Given a list of n items and a fn defined over sub-lists, we study the space
   required for computing the fn for arbitrary sub-lists in constant time.  For
   the fn mode we improve the previously known space bound O(n^2 / log n) to
   O(n^2 log log n / log^2 n) words.  For median the space bound is improved to
   O(n^2 log log^2 n / log^2 n) words from O(n^2 log(k)n / log n), where k is
   an arbitrary constant and log(k) is the iterated logarithm."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2008.10.007">doi:10.1016/j.ipl.2008.10.007</A>]['12].
   [Also search for: range query].

%A H. W. Lenstra
%A C. Pomerance
%T Primality testing with Gaussian periods
%I Dartmouth
%D 2009
%P 46
%K TR, c2009, c200x, c20xx, primality, algorithm, prime, number, test, testing
%X "... deterministic algorithm ... O((log n)**6 . (2+log log n)**c)-time ..."
   -- ver.20090807 pdf@[<A HREF="http://www.math.dartmouth.edu/~carlp/aks080709.pdf">dartm'th</A>]['11].
   [Also search for: primality]  and  [also search for: AKS primality].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Primes/">primality</A>].)

%A M. Bona
%A R. Flynn
%T The average number of block interchanges needed to sort a permutation and
   a recent result of Stanley
%J IPL
%V 109
%N 16
%P 927-931
%M JUL
%D 2009
%K jrnl, IPL, c2009, c200x, c20xx, zz0809, block interchange, move, moves, swap,
   swaps, exchange, sort, sorting, algorithm, sorted, permutation
%X "We use an interesting recent result of probabilistic flavor concerning the
   product of 2 perms. consisting of 1 cycle each to find an explicit formula
   for the avg. # of block interchanges needed to sort a perm. of length n."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2009.04.019">doi:/10.1016/j.ipl.2009.04.019</A>]['09].

%A N. Askitis
%A R. Sinha
%T OzSort: Sorting over 246GB for a penny
%J ACM SIGMOD ?
%P ?-?
%M APR
%D 2009
%O also 'Sorting 100GB for less than 87 kJoules', Sinha & Askitis, same place
%K sorting, OzSort, pSort, sort, c2009, c200x, c20xx, penny sort, pennySort,
   joule sort, jouleSort, joules, competition, benchmark, indy, daytona,
   on disc, out of core, outOfCore, Melbourne
%X "OzSort is a fast & stable external sorting s/w ... optimized for the
   requirements of the PennySort (Indy) benchmark. ... sorts a file containing
   records of 100bytes each, with keys of length 10bytes, where a key starts
   from the 1st byte of each record & whose byte-length characters are gen.
   unif.@random. ... over 246GB in less than 2150.9 secs.; ...  used a computer
   that costs US$439.85 & provides a time budget >= .... The # of records that
   could be s. within the time budget was 2,463,105,024. OzSort can also be
   extended to cater to the Daytona class & be able to sort records & keys of
   varying sizes."
   -- auth1@[<A HREF="http://www.naskitis.com/">naskitis.com</A>]['09],
      auth2@[<A HREF="http://ranjan.sinha.googlepages.com/home">googlep's</A>]['09],
   also see [<A HREF="http://sortbenchmark.org/">sortbenchmark.org</A>]['09].

%A C. Gentry
%T Fully homomorphic encryption using ideal lattices
%J STOC
%V 9
%P 169-178
%M MAY
%D 2009
%K conf, STOC, c2009, c200x, c20xx, zz1121, fully homomorphic encryption,
   lattice, FHE
%X "We propose a fully homomorphic encryption scheme -- i.e., a scheme that
   allows one to evaluate circuits over encrypted data without being able to
   decrypt. ... an encryption scheme that permits eval'n of arbitrary circuits
   we call a scheme that can evaluate its (augmented) decryption circuit
   bootstrappable.  Next, we describe a public key encryption scheme using
   ideal lattices that is almost bootstrappable. ..."
   -- [<A HREF="https://doi.org/10.1145/1536414.1536440">doi:10.1145/1536414.1536440</A>]['21],
   pdf@[<A HREF="https://www.cs.cmu.edu/~odonnell/hits09/gentry-homomorphic-encryption.pdf">cmu</A>]['21].
   [Also search for: homomorphic encryption].

%A M. Stevens
%A A. Sotirov
%A J. Appelbaum
%A A. Lenstra
%A D. Molnar
%A D. A. Osvik
%A B. de Weger
%T Short chosen-prefix collisions for MD5 and the creation of a rogue CA
   certificate
%J CRYPTO
%I SpringerVerlag
%S LNCS
%V 5677
%P 55-69
%D 2009
%K conf, c2009, c200x, c20xx, zz0612, MD5, computer security, SSL certificate,
   hash functions, block, hashes, cryptography, collision, rogue, fake, false,
   breaking, hacking, attack, attacking, hashclash, SHA-1, SHA1
%X (After 'On Collisions for MD5', Marc Stevens, M.thesis, Eindhoven U.T., 2007;
   before 'Attacks on Hash Functions and Applications', PhD thesis, 2012.)
   auth1@[<A HREF="http://marc-stevens.nl/research/">www</A>]['12].
   (Also see MD5@[<A HREF="http://en.wikipedia.org/wiki/Md5">wikip</A>]['12].)

%A L. Fortnow
%T The status of the P versus NP problem
%J CACM
%V 52
%N 9
%P 78-86
%M SEP
%D 2009
%K cacm, review, intro, survey, c2009, c200x, c20xx, zz0310, NP, NPC, complete,
   PNPproblem, problem, complexity, hard, problems
%X "... we don't expect the P versus NP problem to be resolved in the
   near future ..."  [39 refs].
   -- [<A HREF="http://dx.doi.org/10.1145/1562164.1562186">doi:10.1145/1562164.1562186</A>]['10].
   [Also search for: PNPproblem].

%A J. M. Lucas
%T An improved kernel size for rotation distance in binary trees
%J IPL
%V 110
%N 12-13
%P 481-484
%M JUN
%D 2010
%K jrnl, IPL, c2010, c201x, c20xx, zz0510, binary tree, edit distance, rotation,
   rotations, convex polygon triangulation, kernelization, Cleary, St. John
%X "Kernelization ... By pre-processing a problem instance, and converting it
   into an equivalent smaller instance, one can substantially lower the time
   needed to obtain a solution. ... They showed that the original two trees can
   be reduced to an equivalent pair of trees each containing at most 5k nodes.
   ... we show an improved bound on the size of the kernel. Using the
   equivalence of binary trees and convex polygon triangulations, we show that
   the kernel size is bounded by 2k."  [30 refs].
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2010.04.022">doi:10.1016/j.ipl.2010.04.022</A>]['10].

%T 5th Int. Conf., Fun with Algorithms
%E P. Boldi
%E L. Gargano
%M JUN
%D 2010
%K conf, FUN, proc, proceedings, c2010, c201x, c20xx, zz0713, algorithms
%X isbn13:978-3642131219.
  -- index@[<A HREF="http://link.springer.com/book/10.1007/978-3-642-13122-6/">sprngr</A>]['13].

%A A. Elmasry
%T The longest almost-increasing subsequence
%J IPL
%V 110
%N 16
%P 655-658
%M JUL
%D 2010
%K jrnl, IPL, c2010, c201x, c20xx, longest almost increasing subsequence,
   ascending, LASS, problem
%X "Given a seq. of n elts, we introduce the notion of an almost-increasing
   subseq. as the longest subseq. that can be converted to an increasing
   subseq. by possibly adding a value, that is at most a fixed const., to each
   of the elts. We show how to optimally construct such subseq. in O(n log k)
   time, where k is the length of the output subseq.."  [18 refs].
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2010.05.022">doi:10.1016/j.ipl.2010.05.022</A>]['10].
 * [Also search for: LASS problem].

%A P. Miettinen
%T Sparse boolean matrix factorization
%J ICDM
%P 935-940
%D 2010
%K conf, ICDM, c2010, c201x, c20xx, zz0813, BMF, decomposition, sparse,
   sparsity, factor, matrix, factorisation, algorithm
%X "... finding a good B. decomposition is known to be computationally hard,
   with even many sub-problems being hard to approx.. Many real-world data sets
   are sparse, & it is often required that also the factor matrices are sparse.
   ... has motivated many new matrix decomposition methods & many modifications
   of the existing methods. ... studies how BMF behave with sparse data: can we
   assume some sparsity on the factor matrices, & does the sparsity help with
   the comp'y hard problems. The answer ... is shown to be positive."
   -- [<A HREF="http://dx.doi.org/10.1109/ICDM.2010.93">doi:10.1109/ICDM.2010.93</A>]['13].

%A N. Moller
%A T. Granlund
%T Improved division by invariant integers
%J IEEE Trans. Comput.
%M JUN
%D 2010
%K jrnl, c2010, c201x, c20xx, zz0621, fast, integer, arithmetic, division, div,
   algorithm
%X "... problem of dividing a two-word int. by a single-word int., together with
   a few extensions & applications. Due to lack of efficient division instns in
   current processors, the division is performed as a mult. using a precomputed
   single-word approxn of the reciprocal of the divisor, followed by a couple of
   adjustment steps. ..."
   -- [<A HREF="https://doi.org/10.1109/TC.2010.143">doi:10.1109/TC.2010.143</A>]['21] and
    pdf@[<A HREF="https://gmplib.org/~tege/division-paper.pdf">gmplib</A>]['21].
   Also see arith@[<A HREF="https://en.wikipedia.org/wiki/Computational_complexity_of_mathematical_operations">wikip</A>]['21] and
   div@[<A HREF="https://en.wikipedia.org/wiki/Division_algorithm#NewtonâRaphson_division">wikip</A>]['21].

%A H. Katebi
%A K. A. Sakallah
%A I. L. Markov
%T Symmetry and satisfiability: An update
%J Proc. Satisfiability Symposium
%P ?-?
%M JUL
%D 2010
%K SAT10, conf, c2010, c201x, c20xx, zz0416, SAUCY, SAUCY2.1, algorithm,
   SAT, SAT09, SAT2009,  maths, graph, automorphism, symmetry, sparse
%X "... explore further connections between symmetry & satisfiability & demo.
   the existence of intractable SAT instances that exhibit few or no symmetries.
   Specifically, we describe a highly scalable symmetry detection alg. based on
   a decision tree that combines elements of group-theoretic computation &
   SAT-inspired backtracking search, & provide results of its appln on the
   SAT 2009 competition benchmarks. For SAT instances with sig. symmetry we also
   compare SAT runtimes with & w/o the addn of symmetry-breaking constraints."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-14186-7_11">doi:10.1007/978-3-642-14186-7_11</A>]['16].
   (Also see
   GA@[<A HREF="https://en.wikipedia.org/wiki/Graph_automorphism">wikip</A>]['16].)
   [Also search for: maths graph isomorphism] and
   [also search for: maths graph automorphism].

%A D. M. Kane
%A J. Nelson
%A D. P. Woodruff
%T An optimal algorithm for the distinct elements problem
%J PODS
%P ?-?
%D 2010
%K conf, PODS, c2010, c201x, c20xx, count, counting, distinct, elements,
   streaming, stream, algorithm, norm, space
%X "... 1st optimal alg. for est. the # of distinct elts in a data stream,
   closing a long line of theor.research on this problem begun by Flajolet &
   Martin in their seminal paper in FOCS 1983. ... applications to query
   optimization, Internet routing, network topology, & data mining. For a stream
   of indices in {1,...,n}, our alg. computes a (1+/-epsilon)-approx. using an
   optimal O(1/epsilon^-2+log(n)) bits of space with 2/3 success probability,
   where 0 < epsilon < 1 is given. This prob. can be amplified by indep. repn.
   ... processes each stream update in O(1) worst-case time, and can report an
   est. at any pt midstream in O(1) worst-case time, thus settling both the
   space & time complexities simultaneously.  [and] alg. to est. the Hamming
   norm of a stream, a generalization of the # of distinct elts, which is useful
   in data cleaning, packet tracing, & [DB] auditing. Our alg. uses nearly
   optimal space, & has optimal O(1) update and reporting times."
   -- [<A HREF="http://dx.doi.org/10.1145/1807085.1807094">doi:10.1145/1807085.1807094</A>]['12].
   [Also search for: count distinct elements].

%A R. Sedgewick
%T Algorithms (4th ed)
%I AddisonWesley
%P 976
%M MAR
%D 2011
%K book, text, c2011, c201x, c20xx, zz0911, algorithm, data structure,
   dataStructure, DS
%X 4th ed 2011; hb us$61; uk us isbn:032157351X; uk us isbn13:978-0321573513.
      Ch1 Fundamentals, Ch2 Sorting, Ch3 Searching,
      Ch4 Graphs,       Ch5 Strings, Ch6 Context,
   [also search for: Sedgewick book].
   ((Also see [<A HREF="http://www.allisons.org/ll/AlgDS/">AlgDS</A>].))

%A D. P. Williamson
%A D. B. Shmoys
%T The Design of Approximation Algorithms
%I CUP
%P 520
%M APR
%D 2011
%K book, text, c2011, c201x, c20xx, zz0611, OR, algorithm, approximation,
   NPC, NPhard, scheduling, optimization problems, SemiDefinite, randomization,
   computer programming
%X 1st ed 2011; hb us$52; uk us isbn:0521195276; uk us isbn13:978-0521195270.
   "Discrete optimization ... such as scheduling, facility location, and network
   design; ... most such problems are NP-hard. Thus unless P=NP, there are no
   efficient algs. to find optimal solns to such problems. ... approximation
   algs.: efficient algs. that find provably near-optimal solns. ... inc. greedy
   and local search algs., dynamic programming, linear and semidefinite
   programming, and randomization. ..."
   [Also search for: SemiDefinite programming].

%A A. Singh
%A D. Garg
%T Implementation and performance analysis of exponential tree sorting
%J Int. J. of Comp. Applications
%V 24
%N 3
%P ?-?
%M JUN
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0118, integer, sort, sorting, algorithm,
   expected time, Andersson, exponential tree
%X "The trad.alg. for sorting gives a bound of O(n log n) expected time without
   randomization & O(n) with randomization. Recent researches have optimized
   lower bound for deterministic algs. for int.sorting [1-3]. Andersson has
   given the idea of Exponential tree which can be used for sorting [4].
   Andersson, Hagerup, Nilson & Raman have given an alg. which sorts n integers
   in O(n log log n) expected time but uses O(m) space [4, 5]. Andersson has
   given improved alg. which sort integers in O(n log log n) expected time &
   linear space but uses randomization [2, 4]. Yijie Han has improved further to
   sort integers in O(n log log n) expected time & linear space but passes
   integers in a batch i.e. all integers at a time [6]. These algs. are very
   complex to implement. In this paper we discussed a way to implement the
   exponential tree sorting & later compare results with traditional sorting
   technique."
   -- pdf@[<A HREF="http://www.ijcaonline.org/volume24/number3/pxc3873876.pdf">www</A>]['18].
   (*NB. "expected time", not "worst-case time".*)

%A M. J. Atallah
%A T. W. Duket
%T Pattern matching in the Hamming distance with thresholds
%J IPL
%V 111
%N 14
%P 674-677
%M JUL
%D 2011
%K jrnl, IPL, c2011, c201x, c20xx, zz0611, sequence, continuous, float, reals,
   similarity, Hamming distance, pattern, substring, search, match, matching,
   threshold, threshholds
%X "It has long been known that pattern matching in the Hamming distance metric
   can be done in O(min(|S|, sqrt(m/log m)n log m) time, where n is the length
   of the text, m is the length of the pattern, & S is the alphabet. The
   classic alg. for this is due to Abrahamson & Kosaraju. [here] consider the
   following gen'n, motivated by the situation where the entries in the text &
   pattern are analog, or distorted by additive noise, or imprecisely given for
   some other reason: in any alignment of the pattern with the text, two aligned
   symbols a & b contribute +1 to the similarity score if they differ by no
   more than a given threshold theta otherwise they contribute zero. We give an
   O(min(|S|, sqrt(m/log m)n log m) time alg. for this more general version of
   the problem; the classic Hamming distance matching problem is the special
   case of theta=0."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2011.04.004">doi:10.1016/j.ipl.2011.04.004</A>]['11].

%A C. Gentry
%A S. Halevi
%T Implementing Gentry's fully-homomorphic encryption scheme
%J EUROCRYPT
%D 2011
%I SpringerVerlag
%K conf, c2011, c201x, c20xx, zz0415, homomorphic encryption, privacy, data,
   protection, cloud computing
%X '... We tested our implementation with lattices of several dimensions,
   corr.to several security levels. From a "toy" setting in dimension 512, to
   "small," "medium," and "large" settings in dimensions 2048, 8192, and 32768,
   respectively. The public-key size ranges in size from 70 Megabytes for the
   "small" setting to 2.3 Gigabytes for the "large" setting. The time to run one
   bootstrapping operation (on a 1-CPU 64-bit machine with large memory) ranges
   from 30sec. for the "small" setting to 30min. for the "large" setting.'
   -- [<A HREF="http://eprint.iacr.org/2010/520">iacr</A>]['15].
   Also see,
   "[H.E.] a form of encryption that allows compn on ciphertexts, generating an
   encrypted result which, when decrypted, matches the result of the ops as if
   they had been performed on the plaintext. ..."
   -- HE@[<A HREF="http://en.wikipedia.org/wiki/Homomorphic_encryption">wikip</A>]['15].
   [Also search for: homomorphic encryption].

%A P. Bille
%A I. Li Gortz
%T The tree inclusion problem: In linear space and faster
%J ACM Trans. on Algorithms
%P #38
%M JUL
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0321, tree inclusion, subtree,
   problem, algorithm
%X "Given two rooted, ordered, & labeled trees P & T the tree inclusion problem
   is to determine if P can be obtained from T by deleting nodes in T. ... has
   recently been recognized as an important query primitive in XML databases.
   Kilpelainen & Mannila ['95] presented the first polynomial-time alg. using
   quadratic time & space. Since then several improved results have been
   obtained for special cases when P & T have a small # of leaves or small
   depth. However, in the worst case these algs. still use quadratic time &
   space. Let n_S, l_S, & d_S denote the # of nodes, the # of leaves, & the
   depth of a tree S in P, T. . . . show that the tree inc. problem can be
   solved in space O(n_T) & time:
   O(min(l_P n_T, l_P l_T log log n_T + n_T, (n_P n_T)/(log n_T + n_T log n_T)).
   This improves or matches the best known time complexities while using only
   linear space instead of quadratic. ... important in practical applications,
   such as XML databases, where the space is likely to be a bottleneck."
   -- [<A HREF="https://doi.org/10.1145/1978782.1978793">doi:10.1145/1978782.1978793</A>]['21] and
      0608124@[<A HREF="https://arxiv.org/abs/cs/0608124">arXiv</A>]['21].

%A Bing Jian
%A B. C. Vamuri
%T Robust point set registration using Gaussian mixture models
%J IEEE Trans. Patt. Analysis and Mach. Intell.
%V 33
%N 8
%P 1633-1645
%M AUG
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0820, point set registration, defn, sets,
   point cloud, alignment, match, matching, transformation, Wahba problem, pose,
   RANSAC
%X "... present a unified framework for the rigid and nonrigid point set
   registration problem in the presence of sig. amounts of noise ... represent
   the input point sets using GMMs ..."
   -- [<A HREF="https://doi.org/10.1109/TPAMI.2010.223">doi:10.1109/TPAMI.2010.223</A>]['20],
    & code@[<A HREF="https://github.com/bing-jian/gmmreg">gith'b</A>]['20].
 [*Also see PSR@[<A HREF="https://en.wikipedia.org/wiki/Point_set_registration">wikip</A>]['20].*]
   [Also search for: point set].

%A B. A. Burton
%T Searching a bitstream in linear time for the longest substring of any
   given density
%J Algorithmica
%V 61
%N 3
%P 555-579
%M NOV
%D 2011
%K jrnl, c2011, c2011, c20xx, zz0213, algorithm, bit stream, density, bias,
   biased, density, substring, interval
%X "Given an arbitrary bitstream ... problem of finding the longest substr.
   whose ratio of ones to zeroes equals a given value. The central result of
   this paper is an alg. ... linear time. ... involves (i) reformulating the
   problem as a constrained walk through a sparse matrix, [&] (ii) developing a
   data struct. for this s.matrix that allows us to perform each step of the
   walk in amortised const.time. [&] give a linear time alg. to find the longest
   substring whose ratio of ones to zeroes is bounded below by a given value.
   Both problems have practical relevance to crypto. & bioinf.."
   -- [<A HREF="http://dx.doi.org/10.1007/s00453-010-9424-y">doi:10.1007/s00453-010-9424-y</A>]['13],
   BAB@[<A HREF="http://www.maths.uq.edu.au/~bab/">U.Qld</A>]['11].
   [Also search for: density substring].

%A W.-M. Chen
%A H.-K. Hwang
%A T.-H. Tsai
%T Maxima-finding algorithms for multidimensional samples: A two-phase approach
%J Computational Geometry: Theory and Applications
%V 45
%N 1-2
%P 33-53
%K JAN
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0314, maxima, dominate, dominating, point,
   points, sample, algorithm
%X "Simple, two-phase algs. are devised for finding the maxima of
   multidimensional pt samples, one of the very first problems studied in
   comp.geometry. The algs. are easily coded & modified for practical needs.
   The expected complexity of some measures related to the performance of the
   algs. is analyzed. We also compare the efficiency of the algs. with a few
   major ones used in practice, & apply our algs. to find the maximal layers &
   the longest common subsequences of multiple sequences. "
   -- [<A HREF="http://dx.doi.org/10.1016/j.comgeo.2011.08.001">doi:10.1016/j.comgeo.2011.08.001</A>]['14].
   [Also search for: maxima dominate].

%A H. Hassanieh
%A P. Indyk
%A D. Katabi
%A E. Price
%T Simple and practical algorithm for sparse Fourier transform
%J SODA
%P ?-?
%M JAN
%D 2012
%K conf, SODA, c2012, c201x, c20xx, zz0212, fast, faster, sparse, FFT,
   Fourier transform, numerical computing, methods, algorithm, frequency,
   frequencies
%X "... given a complex vector x of length n, and a parameter k, est. the k
   largest (in magnitude) coefficients of the Fourier transform of x. The
   problem is of key interest in several areas, including signal processing,
   audio/image/video compression, and learning theory. We propose a new alg. for
   this problem. [It] leverages techniques from digital signal processing,
   notably Gaussian and Dolph-Chebyshev filters. ... is structurally simpler
   than its predecessors. [So] we are able to extend considerably the range of
   sparsity, k, for which [it] is faster than FFT ..."
   -- pdf@[<A HREF="http://groups.csail.mit.edu/netmit/sFFT/">mit</A>]['12].

%A A. Bjorklund
%A T. Husfeldt
%A P. Kaski
%A M. Koivisto
%T The traveling salesman problem in bounded degree graphs
%J ACM Trans. Algs.
%V 8
%N 2
%P ?-?
%M APR
%D 2012
%K TALG, ACM, c2012, c201x, c20xx, zz0914, traveling salesman problem, TSM,
   algorithm, travelling, salesperson, TSP, maths, graph, bounded, degree,
   Held, Karp, Ryser, matrix, permanent
%X "We show that the TSP in bounded-degree g. can be solved in time
   O((2-e)n), where e > 0 depends only on the degree bound but not on the # of
   cities, n. ... variant of the classical D.P. soln due to Bellman, &, indep.,
   Held & Karp. In the case of bounded integer wts on the edges, we also give a
   polynomial-space alg. with running time O((2-e)n) on bounded-degree g.. [&]
   present an analogous analysis of Ryser's alg. for the permanent of matrices
   with a bounded number of nonzero entries in each column."
   -- [<A HREF="http://dx.doi.org/10.1145/2151171.2151181">doi:10.1145/2151171.2151181</A>]['14].
   [Also search for: travelling salesman problem].

%A S. T. Klein
%A D. Shapira
%T The string-to-dictionary matching problem
%J COMPJ
%I OUP
%V 55
%N 11
%P 1347-1356
%M NOV
%D 2012
%K jrnl, COMPJ, c2012, c201x, c20xx, zz1112, string to dictionary matching,
   problem, search, compressed, Tunstall
%X "... in which a string is searched for in all the poss. concatenations of
   the elts of a given dictionary, with applications to compressed matching in
   variable to fixed-length encodings, such as Tunstall's. Two algs. based on
   suffix trees are suggested, the one focusing on the dict., the other on the
   pattern to be searched for. ... then extended to deal also with patterns that
   include gaps. Experiments on natural lang. text suggest that compressed
   search might use less comparisons for long enough patterns, in spite of a
   potentially large number of encodings."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxs004">doi:10.1093/comjnl/bxs004</A>]['12].

%A A. Griewank
%T Who invented the reverse mode of differentiation?
%J Documenta Math.
%P 389-400
%D 2012
%K c2012, c201x, c20xx, zz1023, reverse mode, partial derivative, cheap,
   gradient, optimisation, automatic differentiation, numerical algorithm,
   backprop, ANN, smooth optimisation, Linnainmaa, reverse mode, ISMP
%X "... there have been many incarnations of this reversal technique, which has
   been suggested by several people from various ï¬elds since the late 1960s, if
   not earlier ..."  (13 refs)
   -- pdf@[<A HREF="https://www.math.uni-bielefeld.de/documenta/vol-ismp/52_griewank-andreas-b.pdf">uni-b...</A>]['23].
   [Also search for: Baur Strassen].

%A M. Kubica
%A T. Kulczynski
%A J. Radoszewski
%A W. Rytter
%A T. Walen
%T A linear time algorithm for consecutive permutation pattern matching
%J IPL
%V 113
%N 12
%D 2013
%P 430-433
%K jrnl, IPL, c2013, c201x, c20xx, zz0917, CPPM, consecutive permutation,
   OPPM, order preserving, pattern matching, problem, algorithm, sequence
%X "... 2 seqs x & w of length m are order-isomorphic (of the same 'shape') if
   w[i] <= w[j] iff x[i] <= x[j] for each i, j in [1,m]. We present a simple
   linear time alg. for checking if a given seq. y of length n contains a factor
   which is order-isomorphic to a given pattern x. A factor is a subseq. of
   consec. symbols of y, so we call our problem the consec.perm.pattern
   matching. The (general) perm. pattern matching problem is related to general
   subseqs. & is known to be NP-complete. We show that the situation for
   consec.subseqs. is sig. different & present an O(n+m) time alg. under a
   natural assumption that the symbols of x can be sorted in time O(m),
   otherwise the time is O(n+m log m). ... use a modification of the classical
   Knuth-Morris-Pratt string matching alg.."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2013.03.015">doi:10.1016/j.ipl.2013.03.015</A>]['17].

%A B. D. McKay
%A A. Piperno
%T Practical graph isomorphism, II
%J arXiv
%M JAN
%D 2013
%K TR, c2013, c201x, c20xx, zz0115, maths, graph, isomorphism, canonical,
   renumbering, labelling, labeling, traces, nauty, bliss, conauto
%X "We report the current state of the g. iso. problem from the practical pt of
   view. After describing the general principles of the refinement-
   -individualization paradigm & proving its validity, we explain how it is
   implemented in several of the key programs. ... bring the description of the
   best known program nauty up to date & describe an innovative approach called
   Traces that outperforms the competitors for many difficult g.classes.
   Detailed comparisons against saucy, Bliss & conauto are presented. "
   -- 1301.1493@[<A HREF="http://arxiv.org/abs/1301.1493">arXiv</A>]['15].

%A E. N. Argyriou
%A M.A. Bekos
%A A. Symvonis
%T Maximizing the total resolution of graphs
%J COMPJ
%V 56
%N 7
%P 887-900
%M JUL
%D 2013
%K jrnl, COMPJ, c2013, c201x, c20xx, zz0713, graph, draw, drawing, crossings,
   crossing, angular, resolution
%X "...  In the graph drawing lit., the resolution of a drawing is either
   measured based on the angles formed by consecutive edges incident on a common
   vertex (angular resn) or by the angles formed at edge crossings (crossing
   resn). ... introduce the notion of 'total resolution', that is, the min. of
   the angular & crossing resn. To the best of our knowledge, this is the 1st
   time where the problem of maximizing the TR of a g. over all its drawings is
   studied. The main contrib. ... consists of drawings of asymptotically optimal
   total resn for complete gs. (circular drawings) & for complete bipartite
   gs. (two-layered drawings).  [&] present & experimentally evaluate a
   force-directed-based alg. that constructs drawings of large total resn."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxs088">doi:10.1093/comjnl/bxs088</A>]['13].
   [Also search for: graph drawing].

%A S. T. Klein
%T On the connection between Hamming codes, Heapsort and other methods
%J IPL
%V 113
%N 17
%P 617-620
%M AUG
%D 2013
%K jrnl, IPL, essay, c2013, c20x, c20xx, zz0713, Hamming code, error correcting,
   Heap sort, heapSort, subset sum problem, sums
%X "A connection between Hamming codes & Heapsort is shown, namely, that they
   can both be derived, the 1st from straightforward error correcting codes &
   the 2nd from a simple sorting method, using almost identical derivation
   processes. It is then demo. that the same process can work for other
   well-known methods. This might trigger similar derivations in the future."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2013.05.013">doi:10.1016/j.ipl.2013.05.013</A>]['13].
   [Also search for: subset sum problem].

%A J. Sherman
%T Nearly maximum flows in nearly linear time
%J arXiv
%M APR
%D 2013
%K arXiv, TR, c2013, c201x, c20zz, zz0214, maths, graph, max flow, maxFlow,
   networks, problem
%X "... new approach to the maximum flow problem in undirected, capacitated
   graphs using alpha-congestion-approximators: easy-to-compute fns that approx.
   the congestion required to route single-commodity demands in a graph to
   within a factor of alpha. ... similar in spirit to that used by Spielman &
   Teng (STOC 2004) for solving Laplacian systems, & we summarize our approach
   as trying to do for L_inf-flows what they do for L_2-flows. ..."
   -- 1304.2077@[<A HREF="http://arxiv.org/abs/1304.2077">arXiv</A>]['14].

%A J. A. Kelner
%A Y. Tat Lee
%A L. Orecchia
%A A. Sidford
%T An almost-linear-time algorithm for approximate max flow in undirected
   graphs, and its multicommodity generalizations
%J arXiv
%M APR
%D 2013
%K arXiv, TR, c2013, c201x, c20xx, zz0214, maths, graph, max flow, maxFlow,
   networks, problem, maximum flows, Sherman
%X "... new framework for approx. solving flow problems in capacitated,
   undirected graphs & apply it to provide asymptotically faster algs. for the
   max s-t flow & max concurrent multicommodity flow problems. ... n vertices &
   m edges, it allows us to find an epsilon-approx max s-t flow in time
   O(m^(1+o(1))epsilon^-2) ... algorithms utilize several new technical tools
   that we believe may be of independent interest: - We give a non-Euclidean
   generalization of gradient descent & provide bounds on its performance. ...
   -We give the first almost-linear-time construction of an O(mo(1))-competitive
   oblivious routing scheme ...  note that independently Jonah Sherman produced
   an almost linear time alg. for maximum flow & we thank him for coordinating
   submissions. "
   -- 1304.2338@[<A HREF="http://arxiv.org/abs/1304.2338">arXiv</A>]['14].

%A M. L. Schmid
%T A note on the complexity of matching patterns with variables
%J IPL
%V 113
%N 19-21
%P 729-733
%M SEP-OCT
%D 2013
%K jrnl, IPL, c2013, c201x, c20xx, zz0813, string, pattern, variable, matching,
   NPC, maths, graph
%X "A word matches a pattern with variables (i.e., a string that contains
   terminal symbols & variable symbols) if & only if it can be obtained from the
   patt. by subs. the vars. by terminal words. To decide for a given word
   whether or not it matches a patt. with vars. is an NP-complete problem, which
   has been indep. discovered & investigated in different areas of theor. comp.
   sci. & which has applications in various contexts. ... we show that the
   problem of matching patterns with vars. remains NP-complete even if every
   var. has at most two occurrences. [&] show that if patterns can be rep. as
   special kinds of planar graphs, then they can be matched in polynomial time."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2013.06.011">doi:10.1016/j.ipl.2013.06.011</A>]['13].

%A M. Blaser
%T Fast matrix multiplication
%J Theory of Comp.
%S Graduate Surveys 5
%M DEC
%D 2013
%K c2013, c201x, c20xx, zz1022, fast, matrix multiplication, tensor, tensors,
   algorithm, bilinear
%X "... overview of the history of fast algs. for m.m. [&] look at some other
   fundamental problems in algebraic complexity like polynomial eval'n. ...
   we have to treat tensors in a very concrete way (which might annoy people
   coming from maths), occasionally prove basic results from combinatorics, &
   solve rec. inequalities explicitly (because we want to annoy people with a
   b/g in theoretical CS, too)."  (60 pages)
   -- [<A HREF="https://doi.org/10.4086/toc.gs.2013.005">doi:10.4086/toc.gs.2013.005</A>]['22].
   [Also search for: fast matrix multiplication algorithm].

%A H. Zenil
%A F. Soler-Toscano
%A K. Dingle
%A A. A. Louisd
%T Correlation of automorphism group size and topological properties with
   program-size complexity evaluations of graphs and complex networks
%J Physica A: Stat. Mechanics and its Applications
%V 404
%P 341-358
%M JUN
%D 2014
%K jrnl, PhysicaA, c2014, c201x, c20xx, zz0416, maths, graph, complexity,
   automorphism, compress, Block Decomposition, BDM, Barabasi
%X "We show that num. approx. of Kolmogorov complexity (KK) of graphs & n/wks
   capture some group-theoretic & topological properties of empirical n/wks,
   ranging from metabolic to social n/wks, & of small synthetic n/wks that we
   have produced. That KK & the size of the group of automorphisms of a graph
   are correlated opens up interesting connections to problems in computational
   geometry, & thus connects several measures & concepts from complexity
   science. We derive these results via two different K.complexity approximation
   methods applied to the adjacency matrices of the graphs & n/wks. The methods
   used are the traditional lossless compression approach to K.complexity, & a
   normalised version of a Block Decomposition Method (BDM) based on algorithmic
   probability theory."
   -- [<A HREF="http://dx.doi.org/10.1016/j.physa.2014.02.060">doi:10.1016/j.physa.2014.02.060</A>]['16],
   * or 1306.0322@[<A HREF="http://arxiv.org/abs/1306.0322">arXiv</A>]['16].
   (Also see
   GA@[<A HREF="https://en.wikipedia.org/wiki/Graph_automorphism">wikip</A>]['16].)
   [Also search for: maths graph automorphism].

%A S. Maxwell
%A M. R. Chance
%A M. Koyuturk
%T Efficiently enumerating all connected induced subgraphs of a large
   molecular network
%J Alg. for Comp. Biol.
%W Tarragona, Spain
%P 171-182
%M JUL
%D 2014
%K conf, c2014, c201x, c20xx, enumerate, enumeration, vertex, subgraph, molecule
%X uk us isbn13:978-3319079523.
   "... propose & evaluate an alg. that reduces the computations necessary to
   enum. subgraphs that maximize an objective fn given a monotonically
   decreasing bounding fn."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-319-07953-0_14">doi:10.1007/978-3-319-07953-0_14</A>]['14].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Recn/Subgraph/">SubGraphs</A>].)
   [Also search for: enumerate subgraph graph].

%A D. Mukhopadhyay
%A S. C. Nandy
%T Efficient multiple-precision integer division algorithm
%J IPL
%V 114
%N 3
%P 152-157
%M MAR
%D 2014
%K jrnl, IPL, c2014, c201x, c20xx, zz1213, integer, division, algorithm,
   Huang, multiple precision, BigInt, arithmetic, long, Smith, quotient,
   remainder
%X "Design & implementation of division alg. is one of the most complicated
   problems in multi-precision arithmetic. Huang et al.[1] proposed an efficient
   multi-precision int. divn alg., & experimentally showed that it is about
   3x faster than the most popular algs. proposed by Knuth[2] & Smith[3].
   [We] report a bug in the alg. of Huang et al.[1], & suggests the nec.
   corrections. The theoretical correctness proof of the proposed alg. is also
   given. The resulting alg. remains as fast as that of[1]." (online 2013.)
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2013.10.005">doi:10.1016/j.ipl.2013.10.005</A>]['24].
   [Also search for: BigInt division].
   Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Arithmetic/">more</A>].

%A P. Rzazewski
%T Exact algorithm for graph homomorphism and locally injective graph
   homomorphism
%J IPL
%V 114
%N 7
%P 387-391
%M JUL
%D 2014
%K jrnl, IPL, c2014, c201x, c20xx, zz0314, maths, graph, graphs, homomorphism,
   H(2,1) labeling, labelling, theory, algorithm
%X "For graphs G & H, a homomorphism from G to H is a fn f: V(G) -> V(H),
   which maps vertices adjacent in G to adj.vertices of H. A h. is locally
   injective if no two vertices with a common neighbor are mapped to a single
   vertex in H. Many cases of g.h. & locally injective g.h. are NPC, so there
   is little hope to design polynomial-time algs. for them. ... present an alg.
   for g.h. & locally injective h. working in time O^*((b+2)^|V(G)|),
   where b is the bandwidth of the complement of H." [18 refs] (online 3/2014.)
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2014.02.012">doi:10.1016/j.ipl.2014.02.012</A>]['14].

%A F. Le Gall
%T Powers of tensors and fast matrix multiplication
%J ISSAC '14
%M JUL
%D 2014
%K conf, ISSAC, ISSAC14, c2014, c201x, c20xx, zz0415, matrix multiplication,
   product, power, fast, algorithm, LeGall, Coppersmith, tensor, matrices
%X "... a method to analyze the powers of a given trilinear form (a special kind
   of algebraic constn also called a tensor) & obtain upper bounds on the
   asymptotic complexity of matrix mult.. Compared with existing approaches,
   this method is based on convex optimization, & thus has polynomial-time
   complexity. As an applicn, we use this method to study powers of the
   construction given by Coppersmith and Winograd [J. of Symbolic Compn, 1990]
   & obtain the upper bound omage < 2.3728639 on the exponent of square matrix
   multiplication, which slightly improves the best known upper bound."
   -- [<A HREF="http://dx.doi.org/10.1145/2608628.2608664">doi:10.1145/2608628.2608664</A>]['15],
      1401.7714@[<A HREF="http://arxiv.org/abs/1401.7714">arXiv</A>]['15].
   (But note, not the practical choice of alg..)
   [Also search for: fast matrix multiplication algorithm].

%A D. Lemire
%A O. Kaser
%T Strongly universal string hashing is fast
%J COMPJ
%V 57
%N 11
%P 1624-1638
%M NOV
%D 2014
%K jrnl, COMPJ, c2014, c201x, c20xx, zz1114, strong, strongly, universal,
   hash, algorithm, hashing, string, strings
%X "We present fast strongly universal string hashing families: they can process
   data at a rate of 0.2 CPU cycle/byte. Maybe surprisingly, we find that these
   families - though they require a large buffer of random numbers - are often
   faster than popular hash fns with weaker theor. guarantees. [&] conventional
   wisdom is that hash fns with fewer multiplications are faster. Yet we find
   that they may fail to be faster due to operation pipelining. ... experimental
   results on several processors inc. low-power processors. ... include hash fns
   designed for processors with the carry-less multiplication instn set.  [&]
   prove, using accessible proofs, the strong universality of our families."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxt070">doi:10.1093/comjnl/bxt070</A>]['14].

%A F. Jarvis
%T Algebraic Number Theory
%I Springer
%S Undergrad. Math. Ser.
%D 2014
%K book, text, maths, c2014, c201x, c20xx, zz0513, number theory, integers,
   primes, field, fields, rings, ideals, lattices, cyclotomic, Zeta, RSA,
   number, quadratic, sieve, Noetherian, factorisation, factorization
%X "1. Unique Factorisation in the Natural Numbers; 2. Number Fields; ..."
   "We are so used to working with the natural numbers from infancy onwards that
   we take it for granted that natural numbers may be factorised uniquely into
   prime numbers. [eg], 360=2^3.3^2.5 is the p.factor'n of 360. However, we
   should notice that there are already senses in which this factorisation is
   not really unique; we can write 360=2x3x5x2x3x2, or even
   360=(-2)x5x3x(-3)x2x2. Nevertheless, we can see that all these factorisations
   are 'essentially the same', in a way which we could make precise, & we will
   do so later."
   -- [<A HREF="https://doi.org/10.1007/978-3-319-07545-7_1">doi:10.1007/978-3-319-07545-7_1</A>['23], via KL.
   [Also search for: integer factorisation],  maybe include "sieve".
   (Also see GNFS@[<A HREF="https://en.wikipedia.org/wiki/General_number_field_sieve">wikip</A>]['23].)

%A T. Hufeldt
%T Graph colouring algorithms
%J arXiv
%D 2015
%O Ch.13, 'Topics in Chromatic Graph Theory',
   L. W. Beineke & R. J. Wilson (eds.),
   Encyclopedia of Mathematics & its Applications 156, CUP,
   ISBN 978-1-107-03350-4, 2015, pp.277-303
%K chapter, c2015, c201x, c20xx, zz0515, graph, grphs, colouring, algorithm
%X "... focus is on vertex-colouring algs. that work for general classes of
   g. with worst-case performance guarantees in a sequential model of
   compn. The presentation aims to demonstrate the breadth of available
   techniques and is organized by algorithmic paradigm."
   uk us isbn13:978-1107033504.

%A M. Grohe
%A P. Schweitzer
%T Isomorphism testing for graphs of bounded rank width
%J arXiv
%P 48
%M MAY
%D 2015
%K TR, c2015, c201x, c20xx, zz0515, maths, graph, isomorphism, algorithm,
   bounded rank width, rankWidth, clique, cliqueWidth
%X "... alg. that, for every fixed k, decides isomorphism of graphs of rank
   width at most k in polynomial time. As the clique width of a g. is bounded in
   terms of its rank width, we also obtain a polynomial time iso.test for g.
   classes of bounded clique width."  [33 refs]
   -- 1505.03737@[<A HREF="http://arxiv.org/abs/1505.03737">arXiv</A>]['15].
   [Also search for: rankWidth graph].

%A M. Tepper
%A G. Sapiro
%T Compressed nonnegative matrix factorization is fast and accurate
%J arXiv
%M MAY
%D 2015
%K TR, c2015, c201x, c20xx, zz0515, nonnegative matrix factorization, NMF, NnMF,
   SNMF, factorisation, algorithm
%X "... propose to use structured random compression, that is, random
   projections that exploit the data structure, for two NMF variants: classical
   & separable. In separable NMF (SNMF) the left factors are a subset of the
   cols. of the input matrix. We present suitable formulations for each problem,
   dealing with different representative algs. within each one. We show that the
   resulting compressed techniques are faster than their uncompressed variants
   ... The proposed structured random projections for SNMF allow to deal with
   arb. shaped large matrices, beyond the std limit of tall-&-skinny m. ..."
   -- 1505.04650@[<A HREF="http://arxiv.org/abs/1505.04650">arXiv</A>]['15].

%A C. Chauve
%A J. Courtiel
%A Y. Ponty
%T An unambiguous and complete dynamic programming algorithm for tree alignment
%J arXiv
%M MAY
%D 2015
%K TR, c2015, c201x, c20xx, zz0615, ordered tree, alignment, DP, trees,
   similarity, edit distance, treeEdit
%X "... inquiry into the multiplicity of optimal solns [&] the existence of
   potentially interesting sub-optimal solns, naturally motivates the q. of
   exploring the space of all, optimal & sub-optimal, tree alignments. ...
   well-known DP-based techniques ... but they require completeness &
   unambiguity of the DP scheme, i.e. the existence of a score-preserving
   bijection between the search space & the set of possible derivations of the
   DP scheme. ... we present the 1st unambiguous & complete DP alg. for the
   al. of a pair of ordered rooted trees. [It] optimally aligns two trees of
   size n_1 and n_2 in Theta(n_1 n_2 max(n_1,n_2)^2) time in the worst-case ...
   Assuming uniformly-drawn random trees ... it has avg-case time & space
   complexities in Theta(n_1 n_2)."  [sub. SPIRE 2015.]
   -- 1505.05983@[<A HREF="http://arxiv.org/abs/1505.05983">arXiv</A>]['15].
   (Note "ordered tree".)
   [Also search for: treeEdit].

%A N. Antulov-Fantulin
%A A. Lancic
%A T. Smuc
%A H. Stefancic
%A M. Sikic
%T Identification of patient zero in static and temporal networks: Robustness
   and limitations
%J Phys. Rev. Lett.
%V 114
%P e248701
%M JUN
%D 2015
%K eJrnl, c2015, c201x, c20xx, zz0715, viral, epidemiology, patient, infection,
   spread, start, first, origin, disease, outbreak, health, epidemic, network
%X "Detection of patient zero can give new insights to epidemiologists about the
   nature of 1st transmissions into a popn. ... study the statistical inference
   problem of detecting the source of epidemics from a snapshot of spreading on
   an arb. n/w structure. By using exact analytic calculations & Monte Carlo
   estimators, we demo. the detectability limits for the
   susceptible-infected-recovered model, which primarily depend on the spreading
   process characteristics. Finally, we demo. the applicability of the approach
   in a case of a simulated sexually transmitted infection spreading over an
   empirical temporal n/w of sexual interactions."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.114.248701">doi:10.1103/PhysRevLett.114.248701</A>]['15].

%A A. Elmrasy
%T Counting inversions adaptively
%J IPL
%V 115
%N 10
%P 769-772
%M OCT
%D 2015
%K jrnl, IPL, c2015, c201x, c20xx, zz0715, counting, inversion, inversions,
   sequence, algorithm, ordering, adaptive
%X "... seq. X of n elts, where the # of inversions in X is Inv. We give a
   simple linear-time transn that reduces the problem of counting the invs. in
   X to that of counting invs. within disjoint subseqs. of X of O(1+(Inv/n)^2)
   elts each. ... apply our transn for counting invs. adaptively in
   O(n lg(Inv/n)) time. Alternatively, if the elts are integers, we achieve a
   running time of O(n sqrt(lg(Inv/n))) the Word-RAM model of compn.." [14 refs]
      (An 'inversion' is a pair of elts in the wrong order,
       i.e., x_i & x_j  s.t.  i < j and x_i > x_j.)
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2015.05.003">doi:10.1016/j.ipl.2015.05.003</A>]['15].

%A P. Brach
%A M. Cygan
%A J. Lacki
%A P. Sankowski
%T Algorithmic complexity of power law networks
%J arXiv
%M JUL
%D 2015
%K TR, c2015, c201x, c20xx, zz0715, power law bounded network, shifted, graph,
   algorithm, complexity, time
%X "... experimentally observed that the majority of real-world networks follow
   power law degree distn. ... study the alg. complexity of such 'typical'
   networks. ...[1] define a deterministic condition for checking whether a
   graph has a power law degree distn & experimentally validate it on real-world
   n/wks. ... [2] give a novel theoretical explanation why many algs. run faster
   on real-world data than what is predicted by alg. worst-case analysis. We
   show how to exploit the power law degree distn to design faster algs. for a
   # of classical P-time problems inc. transitive closure, maximum matching,
   determinant, PageRank & matrix inverse. [&] deal with the problems of
   counting triangles & finding maximum clique. ...  we show that the randomness
   assumption can be replaced with a simple condn on the degrees of adjacent
   vertices ... able to solve the maximum clique problem in polynomial time,
   although in general power law networks the problem is NP-complete. "
   -- 1507.02426@[<A HREF="http://arxiv.org/abs/1507.02426">arXiv</A>]['15].
   (NB. complexity of various algorithms *on* power-law networks.)

%A F. V. Fomin
%A A. Golovnev
%A A. S. Kulikov
%A I. Mihajlin
%T Tight bounds for subgraph isomorphism and graph homomorphism
%J arXiv
%M JUL
%D 2015
%K TR, c2015, c201x, c20xx, zz0715, maths, graph, subgraph, isomorphism
%X "We prove that unless Exponential Time Hypothesis (ETH) fails, deciding if
   there is a homomorphism from graph G to graph H cannot be done in time
   |V(H)|^o(|V(G)|). Combined with the reduction of Cygan, Pachocki, & Socala,
   our result rules out (subject to ETH) a possibility of |V(G)|^o(|V(G)|)-time
   alg. deciding if graph H is a subgraph of G. For both problems our lwbs
   asymptotically match the running time of brute-force algs. trying all poss.
   mappings of one graph into another. Thus, our work closes the gap in the
   known complexity of these fundamental problems. "
   -- 1507.03738@[<A HREF="http://arxiv.org/abs/1507.03738">arXiv</A>]['15].
   [Also search for: subgraph isomorphism].

%A K. Claessen
%A J. Duregard
%A M. H. Palka
%T Generating constrained random data with uniform distribution
%J J. Functional Programming
%V 25
%P e8 (pp.31)
%M JUL
%D 2015
%K jrnl, eJrnl, JFP, c2015, c201x, c20xx, zz0715, FP, generate, random,
   test data, cases, examples, constraint, probability distribution
%X "... technique for automatically deriving test data generators from a given
   executable predicate rep. the set of values we are interested in generating.
   The distn of these generators is uniform over values of a given size. To make
   the gen. efficient, we rely on laziness of the predicate, allowing us to
   prune the space of values quickly. In contrast, implementing test data
   gens. by hand is labour intensive & error prone. [&] handwritten gens. often
   have an unpredictable distn of values, risking that some values are arb.
   underrepresented. We also present a variation of the technique that has
   better performance, but where the distn is skewed in a limited, albeit
   predictable way. ..."
      (E.g. "... Fig.1 Data type & type checker for simply typed l-calculus.
       The Type in the Ap nodes represents the type of the argument term. ...")
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796815000143">doi:10.1017/S0956796815000143</A>]['15].

%A B. Neggazi
%A M. Haddad
%A H. Kheddouci
%T A new self-stabilizing algorithm for maximal p-star decomposition of
   general graphs
%J IPL
%V 115
%N 11
%P 892-898
%M NOV
%D 2015
%K jrnl, IPL, c2015, c201x, c20xx, zz0715, maths, graph, star, stars
%X "... propose a polynomial self-stabilizing alg. for maximal graph decomp.
   into p-stars. Given an arbitrary graph G & a +ve int. p >= 1, this decompn
   provides disjoint components of G, s.t. each component induces a p-star in G.
   Under the unfair distributed scheduler, the alg. converges within
   O(del^2 E) moves where E is the # of edges & del is max. node degree in G."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2015.05.010">doi:10.1016/j.ipl.2015.05.010</A>]['15]  (27 refs, online July 2015).
   [Also search for: star graph].

%A F. Serratosa
%T Computation of graph edit distance: Reasoning about optimality and speed-up
%J Image and Vision Computing
%V 40
%P 38-48
%M AUG
%D 2015
%K jrnl, c2017, c201x, c20xx, zz1122, graph edit distance, GED, matching,
   bipartite, image processing, Hungarian, Jonker Volgenant, algorithm, maths
%X "Bipartite g.matching has been demonstrated to be one of the most efficient
   algorithms to solve error-tolerant g.matching. ... a cost matrix between the
   whole nodes of both gs. & solving the nodes' correspondence through a linear
   assignment method (for instance, Hungarian or Jonker-Volgenant methods). ...
   we compare the three versions ..."
   -- [<A HREF="https://doi.org/10.1016/j.imavis.2015.06.005">doi:10.1016/j.imavis.2015.06.005</A>]['22].
   (Also see GM@[<A HREF="https://en.wikipedia.org/wiki/Graph_matching">wikip</A>]['22].)
   [Also search for: graph edit distance GED].

%A A. N. Zehmakan
%T Bin packing problem: Two approximation algorithms
%J arXiv
%M AUG
%D 2015
%O Int. J. in Foundations of Comp. Sci. & Tech. (IJFCST), July 2015, 5(4)
%K IJFCST, c2015, c201x, c20xx, zz0815, bin packing problem,
   approximation algorithm
%X "... NP-hard nature, several approximation algs. ... It is proved that the
   best alg. for the BPP has the approxn ratio 3/2 & the time order O(n), unless
   P=NP. ... first, a 3/2-approxn alg. is presented, then a modification to FFD
   alg. is proposed to decrease time order to linear. Finally, these suggested
   approxn algs. are compared with some other[s] ... The experimental results
   show the suggested algs. perform efficiently. ... methods which not only
   enjoy the best theor. criteria, but also perform considerably efficient in
   practice."
   -- 1508.01376@[<A HREF="http://arxiv.org/abs/1508.01376">arXiv</A>]['15].

%A E. Liebman
%A B. Chor
%A P. Stone
%T Representative selection in nonmetric datasets
%V 29
%N 8
%P 807-838
%M 2015
%K jrnl, c2015, c201x, c20xx, zz0916, nonmetric, space, data, representatives,
   examples, points, close, distance, measure, threshhold,
   medoid, medoids, subset, music
%X "... problem of representative selection: choosing a subset of data points
   from a dataset that best represents its overall set of elts. This subset
   needs to inherently reflect the type of info. contained in the entire set,
   while minimizing redundancy. For such purposes, clustering might seem like a
   natural approach. However, existing clustering methods are not ideally suited
   for rep. seln, esp. when dealing with nonmetric data, in which only a
   pairwise similarity measure exists. ... propose delta-medoids, a novel
   approach that can be viewed as an extension of the k-medoids alg. & is
   specifically suited for sample representative seln from nonmetric data. We
   empirically validate [it] in two domains: music analysis & motion analysis.
   We also show some theoretical bounds on the performance of delta-medoids &
   the hardness of representative seln in general."
   -- [<A HREF="http://dx.doi.org/10.1080/08839514.2015.1071092">doi:10.1080/08839514.2015.1071092</A>]['16],
    & 1502.07428@[<A HREF="http://arxiv.org/abs/1502.07428">arXiv</A>]['16].

%A J. Calvo-Zaragoza
%A J. Oncina
%A C. De la Higuera
%T Computing the expected edit distance from a string to a PFA
%J 21st Int. Conf. Implementation and Application of Automata
%P 39-50
%D 2016
%K conf, c2016, c201x, c20xx, zz0220, string, strings, FSA, FSM, PFSA, PFSM,
   PFA, median, expected, mean, average, distribution, edit distance
%X "... compare  a  witness  string with a distribution. One possibility is to
   compute the prob. of the string for that distn. [or] giving a more global
   view, is to compute the expected edit dist. from a string randomly drawn to
   the witness string. This # is often used to measure the performance of a
   prediction, the goal then being to return the median string, or the string
   with smallest exp. dist.. To be able to measure this, computing the dist.
   between a hypothesis & that distn is necessary. This paper proposes two
   solns for computing this value, when the distn is defined with a
   probabilistic finite state automaton. The 1st is exact but [cost] can be
   exponential in the length of the input string, ... the 2nd is a F_{pras}."
   -- [<A HREF="https://grfia.dlsi.ua.es/repositori/grfia/pubs/342/distance-string-pfa.pdf">www</A>]['20].

%A D. J. Pearce
%T A space-efficient algorithm for finding strongly connected components
%J IPL
%V 116
%N 1
%P 47-52
%M JAN
%D 2016
%K jrnl, IPL, c2015, c201x, c20xx, zz1115, maths, graph, algorithm, space,
   strongly connected component
%X "Tarjan's alg. for finding the strongly connected components of a directed
   g. is widely used & acclaimed. His original alg. required at most v(2+5w)
   bits of storage, where w is the m/c's word size, whilst Nuutila &
   Soisalon-Soininen reduced this to v(1+4w). Many real world applications
   routinely operate on v.large graphs where the storage requirements of such
   algs. is a concern. ... novel improvement on T's alg. which reduces the space
   requirements to v(1+3w) bits in the worst case. [&] our alg. has been
   independently integrated into the widely-used SciPy library for sci. comp.."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2015.08.010">doi:10.1016/j.ipl.2015.08.010</A>]['15] (online 10/2015).

%A G. van den Hove
%T On the origin of recursive procedures
%J COMPJ
%V 58
%N 11
%P 2892-2899
%M NOV
%D 2015
%K jrnl, COMPJ, c2015, c201x, c20xx, zz1115, computing, history, recursion,
   imperative computer programming languages, concepts, vanDenHove
%X "We investigate the origin of recursive procs. in imperative prog. langs..
   We attempt to set the record straight, & to identify the trend that led to
   recursive procs., by means of an analysis of the related concepts & of the
   most reliable available documents, as far as known to us. We show that not
   all of those who were involved in defining these concepts in these documents
   were fully aware of the implications of their proposals. Our aim is not
   primarily historical, but to contribute to a clarification of some of the
   concepts related to recursion. In particular, we demonstrate that recursive
   proc. declarations & recursive proc. activations are logically disjoint
   concepts."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxu145">doi:10.1093/comjnl/bxu145</A>]['15].
   [Also search for: programming language semantics].

%A K. Kawarabayashi
%T Graph isomorphism for bounded genus graphs in linear time
%J arXiv
%M NOV
%D 2015
%K TR, c2015, c201x, c20xx, zz1115, maths, graph, isomorphism, planar,
   genus, bound
%X "For every integer g, isomorphism of graphs of Euler genus at most g can be
   decided in linear time. This improves prev. known algs. whose time complexity
   is n^O(g) (shown in early 1980's), and in fact, this is the first
   fixed-parameter tractable alg. for the g.i. problem for bounded genus graphs
   in terms of the Euler genus g. ... also generalizes the seminal result of
   Hopcroft & Wong in 1974, which says that the g.i. problem can be decided in
   linear time for planar graphs.  Our proof is quite lengthly & complicated,
   but if we are satisfied with an O(n^3) time alg. for the same problem, the
   proof is shorter & easier.
   -- 1511.02460@[<A HREF="http://arxiv.org/abs/1511.02460">arXiv</A>]['15].
      (The genus of a graph is the minimal integer n s.t. the g. can be drawn
       without crossing itself on a sphere with n handles (i.e. an oriented
       surface of genus n). -- wikip.)
   [Also search for: graph isomorphism].

%A L. Babai
%T Graph isomorphism in quasipolynomial time
%J arXiv
%M DEC
%D 2015
%O Proc. 48th Annual ACM SIGACT Symp. on Theory of Comp. (STOC),
   pp.684-697, 2016
%K TR, conf, STOC, c2015, c201x, c20xx, zz0116, zz0517, maths, graph, string,
   isomorphism, algorithm, graphs, group, coset intersection, quasipolynomial,
   complexity, Luks, local certificate, unaffected stabilizers, Helfgott
%X "We show that the Graph Isomorphism (GI) problem & the related problems of
   String Isomorphism (under group action) (SI) & Coset Intersection (CI) can be
   solved in quasipolynomial (exp((log n)O(1))) time. The best prev. bound for
   GI was exp(O(sqrt(n log n) where n is the # of vertices (Luks, 1983); for the
   other two problems, the bound was similar, exp(O~(sqrt n)), where n is the
   size of the permutation domain (Babai, 1983). The alg. builds on Luks's SI
   framework & attacks the barrier configurations for Ls's alg. by group
   theoretic 'local certificates' & combinatorial canonical partitioning
   techniques. We show that in a well-defined sense, Johnson graphs are the only
   obstructions to effective canonical partitioning"
   -- 1512.03547@[<A HREF="http://arxiv.org/abs/1512.03547">arXiv</A>]['15].
   (Excitement in 2015, will it stand scrutiny?)
   (Also see STOC 2016 [<A HREF="http://dx.doi.org/10.1145/2897518.2897542">doi:10.1145/2897518.2897542</A>]['16].)
   ("...  On Jan 4 I announced that Harald Helfgott pointed out an error in the
   analysis of my Graph Isomorphism test. The error invalidated my previous
   claim of quasipolynomial efficiency. ... On Jan 7 I discovered a replacement
   for the recursive call in the 'Split-or-Johnson' routine that had caused the
   problem. With this modification, I claim that the Graph Isomorphism test
   runs in quasipolynomial time (now really) ..."
   -- LB@[<A HREF="http://people.cs.uchicago.edu/~laci/update.html">www</A>][9/1/2017].)
   [Also search for: maths graph isomorphism].

%A T. Kopelowitz
%A E. Porat
%T Breaking the variance: Approximating the Hamming distance in
   tilde_O(1/epsilon) time per alignment
%J FOCS
%M DEC
%D 2015
%K FOCS, conf, c2015, c201x, c20xx, zz1215, Hamming distance, pattern,
   all locations, sliding, strings, text
%X "... computing the Hamming dist. between a given pattern of length m & each
   locn in a text of length n ... Unfortunately, there is evidence that for a
   text T of size n & a pattern P of size m, one cannot compute the exact H.
   dist. for all locns in T in time which is less than tilde_O(m sqrt(n)).
   However, Karloff showed that if one is willing to suffer a 1+/-epsilon
   approxn, then it is possible to solve the problem with high prob., in
   tilde_O(n/epsilon^2) time. ... strongly believed that obtaining an alg. for
   solving the approxn version cannot be done much faster as a function of
   1/epsilon. We show here that this belief is false by introducing a new
   tilde_O(n epsilon) time alg. that succeeds with high prob.. The main idea
   ... which is common in sparse recovery problems, is to reduce the variance of
   a specific randomized experiment by (approx.) separating heavy hitters
   from non-heavy hitters. However, while known SRTs work very well on vectors,
   they do not seem to apply here, where we are dealing with mismatches between
   pairs of characters. We introduce two main algorithmic ingredients. 1. a new
   sparse recovery method that applies for pair inputs (such as in our setting).
   2. is a new construction of hash/projection fns, which allows to count the
   # of projections that induce mismatches between two chars exponentially
   faster than brute force. ..."
   -- 1512.04515@[<A HREF="http://arxiv.org/abs/1512.04515">arXiv</A>]['15].

%A D. Lemire
%A L. Boystov
%T Decoding billions of integers per second through vectorization
%J SPE
%V 45
%P 1-29
%M ?
%D 2015
%K jrnl, SPE, c2015, c201x, c20xx, zz1118, integer code, decode
%X "... arrays of integers. Encoding &, most importantly, decoding of these
   arrays consumes considerable CPU time. ... researchers have exploited the
   superscalar nature of modern processors &  single-instruction,  multiple-data
    (SIMD) instructions. Nevertheless, we introduce a novel vectorized scheme
   called SIMD-BP128*  that improves over previously proposed vectorized
   approaches. It is nearly twice as fast as the previously fastest schemes on
   desktop processors (varint-G8IU & PFOR). At the same time, SIMD-BP128* saves
   up to 2 bits/int. For even better compression, we propose another new
   vectorized scheme (SIMD-FastPFOR) that has a compression ratio within 10% of
   a state-of-the-art scheme (Simple-8b) while being two times faster during
   decoding."
   -- [<A HREF="https://doi.org/10.1002/spe.2203">doi:10.1002/spe.2203</A>]['18],
      1209.2137@[<A HREF="https://arxiv.org/abs/1209.2137">arXiv</A>][2012].
   [Also search for: Lemire].

%A T. Portegys
%T General graph identification by hashing
%J arXiv
%M DEC
%D 2015
%K TR, c2015, c201x, c20xx, zz0116, maths, graph, equality, hash, hashing, MD5,
   isomorphism
%X "A method for identifying graphs using MD5 hashing is presented. This allows
   fast g. equality comparisons & can also be used to facilitate g.iso. testing.
   The graphs can be labeled or unlabeled. ... identifies vertices by hashing
   the g. configuration in their neighborhoods. With each v. hashed, the
   entire g. can be identified by hashing the v. hashes."
   -- 1512.07263@[<A HREF="http://arxiv.org/abs/1512.07263">arXiv</A>]['15].
   [Also search for: graph isomorphism].

%A S. Curtis
%A S.-C. Mu
%T Calculating a linear-time solution to the densest-segment problem
%J JFP
%V 25
%N e22
%P 32pp
%M DEC
%D 2015
%K jrnl, FJP, c2015, c201x, c20xx, zz0116, densest segment problem, MDS,
   maximum, algorithm, density, width, weight, interval, list, FP
%X "The problem of finding a densest segment of a list is similar to the
   well-known maximum segment sum problem, but its soln is surprisingly
   challenging. We give a general spec. of such problems, & formally develop a
   linear-time online soln, using a sliding-window style alg.. The development
   highlights some elegant properties of densities, involving partitions that
   are decreasing & all right-skew."
   -- [<A HREF="http://dx.doi.org/10.1017/S095679681500026X">doi:10.1017/S095679681500026X</A>]['16].

%A A. Shrivastava
%A C. P. Rangan
%T Stable marriage problem with ties and incomplete bounded length preference
   list under social stability
%J arXiv
%P 9pp
%M JAN
%D 2016
%O ? 6th Int. Conf. on Comp. Sci. & Info. Tech. (CCSIT-2016) ?
%K TR, c2016, c201x, c20xx, zz0116, stable marriage problem, incomplete,
   preference, list, ties, weakly, socially stable matching, match, algorithm,
   NRMP, Scottish medical
%X "... variant of socially stable marriage problem where preference lists may
   be incomplete, may contain ties & may have bounded length. In real world
   application like NRMP & Scottish medical matching scheme such restrictions
   arise v.frequently where set of agents (man/woman) is v.large & providing a
   complete & strict order pref. list is practically in-feasible. In presence of
   ties in pref.lists, the most common soln is weakly socially stable matching.
   It is a fact that in an instance, weakly stable matching can have different
   sizes. This motivates the problem of finding a maximum cardinality weakly
   socially s.m.. ... we find max.size weakly socially s.m. for an instance of
   Stable Marriage problem with Ties & Incomplete bounded length pref.list with
   Social Stability. ... is the known fact, any larger instance of this problem
   is NP-hard."
   -- 1601.03523@[<A HREF="http://arxiv.org/abs/1601.03523">arXiv</A>]['16].
   [Also search for: stable marriage problem].


%A Y. Can
%A H. Kassim
%A G. Fischer
%T New Boolean equation for orthogonalizing of Disjunctive Normal Form based on
   the method of orthogonalizing difference-building
%J J. Electron. Test.
%V 32
%P 197-208
%M MAR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0622, Orthogonal Disjunctive Normal Form, DNF,
   ODNF, circuit, circuits, testing
%X "... a new Boolean equation for the orthogonalization of Boolean fns
   respectively of Ternary-Vector-Lists of disjunctive normal form ... provides
   the math. soln of orthogonalization for the first time. ..."
   -- [<A HREF="https://doi.org/10.1007/s10836-016-5572-6">doi:10.1007/s10836-016-5572-6</A>]['22].

%A M. Amani
%A K. A. Lai
%A R. E. Tarjan
%T Amortized rotation cost in AVL trees
%J IPL
%V 116
%N 5
%P 327-330
%M MAY
%D 2016
%K jrnl, IPL, c2016, c201x, c20xx, zz0116, AVL tree, data structure,
   dataStructure, DS, height balanced
%X "Resolved open problem on performance of AVL trees in terms of rotations.
   n mixed insertions & deletions can cause Theta(n log n) rotations.
   We show a class of AVL trees that allow such expensive operations."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2015.12.009">doi:10.1016/j.ipl.2015.12.009</A>]['16].
   [Also search for: AVL tree].

%A T. Hocevar
%A J. Demsar
%T Combinatorial algorithm for counting small induced graphs and orbits
%J arXiv
%M JAN
%D 2016
%K TR, c2016, c201x, c20xx, zz0216, maths, graph, network, orbit, graphlet,
   small, induced, subgraph, enumerate, enumeration, count, counting, frequent
%X "Graphlet analysis is an approach to n/w analysis that is particularly
   popular in bioinformatics. We show how to set up a system of linear equations
   that relate the orbit counts & can be used in an alg. that is sig. faster
   than the existing approaches based on direct enumeration of graphlets. ...
   requires existence of a vertex with certain properties; we show that such
   vertex exists for graphlets of arbitrary size, except for complete graphs &
   C4, which are treated separately. Empirical analysis of running time agrees
   with the theoretical results.
   -- 1601.06834@[<A HREF="http://arxiv.org/abs/1601.06834">arXiv</A>]['16].
   (Also see:
      T.Hocevar, J.Demsar, A combinatorial approach to graphlet counting,
      Bioinformatics, 30(4), 559-565, 2014,
      [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btt717">doi:10.1093/bioinformatics/btt717</A>]['16].)
   [Also search for: count subgraph].

%A L. Blin
%A M. Potop-Butucaru
%A S. Rovedakis
%A S. Tixeuil
%T A new self-stabilizing minimum spanning tree construction with loop-free
   property
%J COMPJ
%V 59
%N 2
%P 225-243
%M FEB
%D 2016
%K jrnl, COMPJ, c2016, c201x, c20xx, zz0216, distributed, parallel, MST,
   minimum spanning tree, UniParis, Sorbonne
%X "... (MST) construction is a classical problem in Distributed Computing for
   creating a globally minimized structure distributedly. Self-stabilization is
   versatile technique for fwd recovery that permits to handle any kind of
   transient faults in a unified manner. The loop-free property provides
   interesting safety assurance in dynamic n/wks where edge-cost changes during
   operation of the protocol. ... a new self-stabilizing MST protocol that
   improves on prev. known approaches in several ways. First, it makes fewer
   system hypotheses as the size of the n/wk (or an upper bound on the size)
   need not be known to the participants. Secondly, it is loop-free in the
   sense that it guarantees that a spanning tree struct. is always preserved
   while edge costs change dynamically & the protocol adjusts to a new MST.
   Finally, time complexity matches the best known results, while space
   complexity results show that this protocol is the most efficient to date."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxv110">doi:10.1093/comjnl/bxv110</A>]['16].

%A A. Droschinsky
%A N. M. Kriege
%A P. Mutzel
%T Faster algorithms for the maximum common subtree isomorphism problem
%J arXiv
%M FEB
%D 2016
%K TR, c2016, c201x, c20xx, zz0316, maximum common subtree, isomorphism, MCSI,
   algorithm
%X "The max. common subtree isomorphism problem asks for the largest possible
   isomorphism between subtrees of two given input trees. ... a natural
   restn of the max. c. subgraph problem, which is NP-hard in general graphs.
   Confining to trees renders polynomial time algs. possible & is of fundamental
   importance for approaches on more general graph classes. ... We consider the
   general case, where trees are neither rooted nor ordered & the iso. is max.
   w.r.t. a weight fn on the mapped vertices & edges. For trees of order n &
   max. degree D ... achieves a running time of O(n^2 D) by exploiting the
   struct. of the matching instances arising as subproblems. [so] outperforms
   the best previously known approaches. [&] show that for trees of bounded
   degree the time complexity of the problem is O(n^2). For ... unbounded degree
   we show that a further red'n of the running time would directly improve the
   best known approach to the assignment problem. Combining a polynomial-delay
   alg. for the enumeration of all MCS isomorphisms with central ideas of our
   new alg. leads to an improvement of its running time from O(n^6+Tn^2) to
   O(n^3+TnD), where n is the order of the larger tree, T is the # of different
   solns., & D is the min. of the max. node degrees of the input trees. ...
   experimental evaluation on synthetic & real-world instances."
   -- 1602.07210@[<A HREF="http://arxiv.org/abs/1602.07210">arXiv</A>]['16].

%A T. Calders
%A D. Van Assche
%T PROMETHEE is not quadratic: An O(qn log(n)) algorithm
%J arXiv
%M MAR
%D 2016
%K TR, c2016, c201x, c20xx, zz0316, algorithm, PROMETHEE, preference ranking,
   rank, criteria, criterion preference
%X "It is generally believed that the preference ranking method PROMETHEE has a
   quadratic time complexity. ... present an exact alg. that computes
   PROMETHEE's net flow scores in time O(q n log(n)), where q represents the #
   of criteria & n the # of alternatives. [It] is based on 1st sorting the
   alternatives after which the unicriterion flow scores of all alts. can be
   computed in one scan over the sorted list of alts. while maintaining a
   sliding window. ... works with the linear & level criterion preference fns.
   ... is exact &, due to the sub-q. time complexity, vastly extends the
   applicability of the PROMETHEE method. Experiments show that ... PROMETHEE
   can scale up to millions of tuples."
   -- 1603.00091@[<A HREF="http://arxiv.org/abs/1603.00091">arXiv</A>]['16].

%A L. Dhulipala
%A I. Kabiljo
%A B. Karrer
%A G. Ottaviano
%A S. Pupyrev
%A A. Shalita
%T Compressing graphs and indexes with recursive graph bisection
%J arXiv
%M MAR
%D 2016
%K TR, c2016, c201x, c20xx, zz0316, maths, graph, compress, compression, web,
   reorder, reordering, locality, index, Chierichetti
%X "Graph reordering ... increase the locality of the representations of graphs,
   which can be helpful in several applications. ... technique can be used to
   improve compression of gs. & inverted indexes. We extend the recent theor.
   model of Chierichetti et al. (KDD 2009) for g.comp., & show how it can be
   employed for compression-friendly reordering of social n/wks & web graphs &
   for assigning document identifiers in inverted indexes. We design &
   implement a novel theor. sound reordering alg. that is based on recursive
   graph bisection. Our experiments show a sig. improvement of the compression
   rate of graph & indexes over existing heuristics. [It] is relatively simple
   & allows efficient parallel & distributed implementations, which is demo. on
   graphs with billions of vertices & hundreds of billions of edges."
   -- 1602.08820@[<A HREF="http://arxiv.org/abs/1602.08820">arXiv</A>]['16].
   [Also search for: compress graph].

%A P. Eirinakis
%A M. Williamson
%A K. Subramani
%T On the Shoshan-Zwick algorithm for the all-pairs shortest path problem
%J arXiv
%M MAR
%D 2016
%K TR, c2016, c201x, c20xx, zz0416, all pairs shortest path problem, APSP,
   graph, distance, paths, Shoshan Zwick, algorithm
%X "The Shoshan-Zwick alg. solves the ... problem in undirected graphs with
   integer edge costs in the range {1,2,...,M}. It runs in O(~M.n^w) time,
   where n is the # of vertices, M is the largest int. edge cost, & w < 2.3727
   is the exponent of matrix multn. It is the fastest known alg. for this
   problem. ... points out the erroneous behavior of the S.-Z. alg. & revises
   [it] to resolve the issues that cause this behavior. [&] discusses impln
   aspects of the S.-Z. alg. using currently-existing sub-cubic m.multn algs.."
   -- 1603.08627@[<A HREF="http://arxiv.org/abs/1603.08627">arXiv</A>]['16].
   [Also search for: matrix multiplication].

%A O. Gold
%A M. Sharir
%T Dynamic time warping: Breaking the quadratic barrier
%J arXiv
%M JUL
%D 2016
%O ACM Trans. Algs., 14(4), pp.1-17, Oct. 2018
%K TR, c2016, c201x, c20xx, zz0716, time warps, DTW, warping, algorithm, DPA,
   geometric edit distance, GED, similarity, dynamic programming, complexity,
   1D, 3D, RD, sequence, points, L1, warp
%X "Dynamic Time Warping (DTW) is one of the basic similarity measures between
   curves or general temporal sequences (e.g., time series) that are rep. as
   seqs. of pts in some metric space (X,dist). ... is massively used in many
   practical fields of comp.sci., & computing the DTW between two seqs. is a
   classical problem in P. ... the best-known alg. for computing DTW is a
   long-standing DPA that requires quadratic runtime, which is believed to be
   optimal, even for the 1-D case X=R, ... we break the nearly 50 years old
   quadratic time bnd ... by presenting a deterministic alg. that runs in
   O(n^2 log log log n / log log n) time. [It] can be extended to work also for
   higher dimensional spaces R^d, for any constant d, when the underlying
   dist.-metric is polyhedral (e.g., L_1)."
   -- 1607.05994@[<A HREF="http://arxiv.org/abs/1607.05994">arXiv</A>]['16],
      [<A HREF="https://doi.org/10.1145/3230734">doi:10.1145/3230734</A>]['22].
   Also see DTW@[<A HREF="https://en.wikipedia.org/wiki/Dynamic_time_warping">wikip</A>]['22].
   [Also search for: sequence similarity algorithm complexity] and
   [also search for: geometric edit distance].

%A I. Abraham
%A S. Chechik
%A S. Krinninger
%T Fully dynamic all-pairs shortest paths with worst-case update-time revisited
%J arXiv
%M JUL
%D 2016
%K TR, c2016, c201x, c20xx, zz0716, all-pairs shortest paths, APSP, path, maths,
   graph, dynamic, algorithm
%X "... classic problem of dynamically maintaining shortest paths between all
   pairs of nodes of a directed weighted graph. ... insertions & deletions of
   nodes & their incident edges. We give worst-case guarantees on the time
   needed to process a single update ([v.] related results, the update time is
   not amortized over a sequence of updates).  Our main result is a simple
   randomized alg. that for any parameter c > 1 has a worst-case update time of
   O(cn^{2+2/3} log^{4/3}(n)) & answers distance queries correctly with
   probability 1-1/n^c, [v.] an adaptive online adversary if the graph contains
   no -ve cycle. The best deterministic alg. is by Thorup [STOC 2005] with a
   worst-case update time of O~(n^{2+3/4}) & assumes non-negative weights. This
   is the first improvement for this problem for more than a decade.
   Conceptually, our alg. shows that randomization along with a more direct
   approach can provide better bounds."
   -- 1607.05132@[<A HREF="http://arxiv.org/abs/1607.05132">arXiv</A>]['16].
   [Also search for: graph shortest paths algorithm].

%A N. Kurosawa
%T Quicksort with median of medians is considered practical
%J arXiv
%P 6pp.
%M AUG
%D 2016
%K TR, c2016, c201x, c20xx, zz0816, algorithm, sort, sorting, quicksort, median
%X "The linear pivot selection alg., known as median-of-medians, makes the worst
   case complexity of quicksort be O(n ln n). Nevertheless, it has often been
   said that [it] is too expensive to use in quicksort. ... show that we can
   make the quicksort with this kind of pivot selection approach be efficient."
   -- 1608.04852@[<A HREF="http://arxiv.org/abs/1608.04852">arXiv</A>]['16].

%A I. O. Zavadskyi
%T A family of fast exact pattern matching algorithms
%J arXiv
%M AUG
%D 2016
%K TR, c2016, c201x, c20xx, zz0916, string, search, algorithm, Sunday
%X "A family of comparison-based exact pattern matching algs. ... utilize
   multi-dimensional arrays in order to process more than one adjacent text
   window in each iteration of the search cycle. ... leads to a lower avg time
   complexity by the cost of space. ... perform well for short patterns &
   middle size alphabets. ... outperform the Boyer-Moore-Horspool alg., either
   in the original version or with Sunday's Quick search modification, in a wide
   area of pattern length - alphabet size plane. ..."
   -- 1608.08346@[<A HREF="http://arxiv.org/abs/1608.08346">arXiv</A>]['16].
   [Also search for: string search algorithm].

%A A. Droschinsky
%A N. Kriege
%A P. Mutzel
%T Finding largest common substructures of molecules in quadratic time
%J arXiv
%M OCT
%D 2016
%K TR, c2016, c201x, c20xx, zz1016,  molecule, maximum common subgraph problem,
   MCS, MCSG, chemical structure
%X ".... Most drugs are small molecules, which can naturally be interpreted as
   graphs. Hence, the task is formalized as maximum common subgraph problem.
   Albeit the vast majority of molecules yields outerplanar graphs this problem
   remains NP-hard.  ... a variation of the problem of high practical relevance,
   where the rings of molecules must not be broken, i.e., the block & bridge
   structure of the input graphs must be retained by the common subgraph. We
   present an alg. for finding a max. common connected induced subgraph of two
   given outerplanar graphs subject to this constraint. ... runs in time
   O(delta n^2) in outerplanar gs. on n vertices with maximum degree delta. ...
   leads to a quadratic time complexity in molecular graphs, which have bounded
   degree. The experimental comparison on synthetic and real-world datasets
   shows that our approach is highly efficient in practice & outperforms
   comparable state-of-the-art algs.."
   -- 1610.08739@[<A HREF="https://arxiv.org/abs/1610.08739">arXiv</A>]['16].
   [Also search for: maximum common subgraph].

%A D. Harvey
%A J. van der Hoeven
%T Faster integer multiplication using plain vanilla FFT primes
%J arXiv
%M NOV
%D 2016
%K TR, c2016, c201x, c20xx, zz0317, fast integer multiplication, computer,
   arithmetic, algorithm, primes, vanDerHoeven, BigInt
%X "Assuming a conjectural upper bound for the least prime in an arithmetic
   progression, we show that n-bit integers may be multiplied in
   O(n log n 4^(log^* n)) bit operations."
   -- 1611.07144@[<A HREF="https://arxiv.org/abs/1611.07144">arXiv</A>]['16].
   [Also search for: fast integer multiplication].

%A A. Rubinstein
%T Detecting communities is hard, and counting them is even harder
%J arXiv
%M NOV
%D 2016
%K TR, c2016, c201x, c20xx, zz1216, network, friendship, community, near clique
%X "We consider the algorithmic problem of community detection in networks.
   Given an undirected friendship graph G=(V,E), a subset S of V is an
   (a,b)-community if: (i) Every member of the community is friends with an
   a-fraction of the community; (ii) Every non-member is friends with at most a
   b-fraction of the community. ... Arora et al [AGSS12] gave a quasi-polynomial
   time alg. for enumerating all the ... we prove that, assuming the
   Exponential Time Hypothesis (ETH), quasi-polynomial time is in fact necessary
   - and even for a much weaker approximation desideratum. ..."
   -- 1611.08326@[<A HREF="https://arxiv.org/abs/1611.08326">arXiv</A>]['16].
   [Also search for: network community].

%A J. A. Grochow
%A C. Moore
%T Matrix multiplication algorithms from group orbits
%J arXiv
%M DEC
%D 2016
%K TR, c2016, c201x, c20xx, zz1216, matrix multiplication, algorithm, fast
%X "We show how to construct highly symmetric algs. for matrix mult.. ...
   consider algs. which decompose the m. mult. tensor into a sum of rank-1
   tensors, where the decomposition itself consists of orbits under some finite
   group action. We show how to use the representation theory of the corr. group
   to derive simple constraints on the decomposition, which we solve by hand for
   n=2,3,4,5, recovering Strassen's alg. (in a particularly symmetric form) &
   new algs. for larger n. While these new algs. do not improve the known upper
   bounds on tensor rank or the m. mult. exponent, they are beautiful in their
   own right, & we point out modifications of this idea that could plausibly
   lead to further improvements. Our constructions also suggest further patterns
   that could be mined for new algs., inc. a tantalizing connection with
   lattices."
   -- 1612.01527@[<A HREF="https://arxiv.org/abs/1612.01527">arXiv</A>]['16].
   [Also search for: matrix multiplication].

%A J. Tarhio
%A J. Holub
%A E. Giaquinta
%T Technology beats algorithms (in exact string matching)
%J arXiv
%M DEC
%D 2016
%K TR, c22016, c201x, c20xx, zz1216, string, substring, match, matching, search,
   algorithm, SIMD, SSE2, AVX2
%X "More than 120 algs. have been developed for exact string matching within the
   last 40 years. We show by experiments that the naive alg. exploiting SIMD
   instructions of modern CPUs (with symbols compared in a special order) is
   the fastest one for patterns of length up to about 50 symbols and extremely
   good for longer patterns and small alphabets. The alg. compares 16 or 32
   characters in parallel by applying SSE2 or AVX2 instns, respectively. [&]
   it uses loop peeling to further speed up the searching phase. We tried
   several orders for comparisons of pattern symbols and the increasing order of
    their probabilities in the text was the best.
   -- 1612.01506@[<A HREF="https://arxiv.org/abs/1612.01506">arXiv</A>]['16].
   [Also search for: string search algorithm].

%A R. Cramer
%A L. Ducas
%A C. Peikert
%A O. Regev
%T Recovering short generators of principal ideals in cyclotomic rings
%J Int. Conf. on the Theory & Appl. of Cryptographic Techniques
%I Springer
%S LNCS
%V 9666
%P 559-585
%D 2016
%K conf, c2016, c201x, c20xx, zz0224, cyclotomic ring, lattice based, ideal,
   short, generator, encryption, cryptography, algorithm,
   shortest vector problem, SVP
%X "... we clarify the situation by giving a rigorous proof that the log-unit
   lattice is indeed efficiently decodable, for any cyclotomic of prime-power
   index ... as a 2nd main contr'n we obtain an efficient alg. that, given any
   generator of a principal ideal (in a p.-power cyclotomic), finds a
   2^{_O(sqrt(n))}-approx. shortest vector in the ideal. Combining this with
   the result of Biasse & Song yields a q.polynomial-time alg. for the
   2^{_O(sqrt(n))-approx. Shortest Vector Problem on principal ideal lattices."
   -- [<A HREF="https://doi.org/10.1007/978-3-662-49896-5_20">doi:10.1007/978-3-662-49896-5_20</A>]['24].
   [Also search for: lattice based cryptography].

%A W. Cook
%T Shortest possible tour to nearly every pub in the United Kingdom
%D 2016+/-
%K TR, c2016, c201x, c20xx, zz1221, pub crawl, UK, travelling salesman problem,
   UK49687, TSP, salesperson, pubs, PNPproblem
%X "... In Feb. 2018, the Washington Post reported that it would take at least
   1,000 years for a computer to find an optimal route to only 22 pts. So we
   were excited a couple of years ago when we computed the shortest possible
   walk to 24,727 pubs. A ton of math & 10 months of time on a fast computer
   brought home the tour. The comp'n even received fun coverage in The Guardian
   (Oct. 21, 2016), ..."
   -- crawl@[<A HREF="http://www.math.uwaterloo.ca/tsp/uk">uwaterloo</A>]['21].
   (The G [<A HREF="https://www.theguardian.com/travel/2016/oct/21/worlds-longest-pub-crawl-maths-team-plots-route-between-every-pub-in-uk">www</A>][22/10/2016].)
   (Collected ~ 25,000 pubs in 2015, 49,687 by 2016.  NB W. not S. Cook.)
   [Also search for: TSP travelling].

%A A. Brieden
%A P. Gritzmann
%A F. Klemm
%T Electoral district design via constrained clustering
%J arXiv
%M MAR
%D 2017
%K TR, c2017, c201x, c20xx, zz0317, electoral districts, electorate,
   redistribution, politics, elections, voting
%X "... studies the electoral district design problem where municipalities of a
   state have to be grouped into districts of nearly equal popn while obeying
   certain politically motivated requirements. ... a general framework for
   electoral district design that is based on the close connection of
   constrained geometric clustering & diagrams. ... computationally efficient &
   flexible enough to pursue various conflicting juridical demands for the shape
   of the districts. We demonstrate the practicability of our methodology for
   electoral districting in Germany."
   -- 1703.02867@[<A HREF="https://arxiv.org/abs/1703.02867">arXiv</A>]['17].
   [The USA should use this alg..]

%A T. Hyla
%A J. Pejas
%T Elliptic curve multiset hash
%J COMPJ
%V 60
%N 4
%P ?-?
%M MAR
%D 2017
%K jrnl, COMPJ, c2017, c201x, c20xx, zz0417, multiset, multi set, hash,
   hashing, elliptic curve, ECHM, homomorphic, BLAKE2
%X "A multiset hash fn associates a hash value to arbitrary collections of
   objects with possible repetitions. Such a hash fn is said to be homomorphic,
   or incremental, when the hash of the union of two collns is easy to compute
   from the hashes of the two collns themselves: it is usually their sum under a
   suitable group operation. ... tend to be much longer than usual hash fns at
   the same security level (e.g. to achieve a collision resistance of 2^128,
   they are several thousand bits long, as opposed to 256 bits for usual hash
   fns), and they are also quite slow. ... we introduce the Elliptic Curve
   Multiset Hash (ECMH), which combines a usual bit string-valued hash fn like
   BLAKE2 with an efficient encoding into binary elliptic curves to overcome
   both difficulties. On the one hand, the size of ECMH digests is essentially
   optimal: 2m-bit hash values provide O(2^m) collision resistance. On the other
   hand, we demonstrate a highly-efficient s/w implementation of ECMH, which our
   thorough empirical evaluation shows to be capable of processing over
   3 million set elts per sec. on a 4 GHz Intel Haswell m/c at the 128 bit
   security level ..."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxw053">doi:10.1093/comjnl/bxw053</A>]['17].

%A I. Garcia-Marco
%A et al
%T On the complexity of partial derivatives
%J arXiv
%M MAY
%D 2017
%O STOC '17
%K TR, c2017, c201x, c20xx, zz1023, algorithm, partial derivative
%X "... we consider this complexity measure as a computational problem: for an
   input polynomial given as the sum of its nonzero monomials, what is the
   complexity of computing the dimension of its space of partial derivatives?
   We show that this problem is #P-hard & we ask whether it belongs to #P. ...
   a polynomial-time computable lower bound on the dimension of the span of
   partial derivatives, & from this method we derive closed-form lwbs. ..."
   -- [<A HREF="https://arxiv.org/abs/1607.05494">srxiv:1607.05494</A>]['23].

%A S. Bougleux
%A B. Gauzere
%A L. Brun
%T A Hungarian algorithm for error-correcting graph matching
%J 11th IAPR-TC-15 Int. Wshop on Graph-Based Rep'n in Pattern Recognition
%P 118-127
%M MAY
%D 2017
%K conf, c2017, c201x, c20xx, zz1122, maths, graph, edit distance, GED, match,
   matching, bipartite, Hungarian algorithm
%X "Bipartite g. matching algs. become more & more popular to solve
   error-correcting g. matching problems & to approximate the g. edit dist. of
   two gs.. However, the memory requirements & execution times of this method
   are resp. proportional to (n+m)^2 & (n+m)^3 where n & m are the order of the
   g.. Subsequent developments reduced these complexities. However, these
   improvements are valid only under some constraints on the params. of the g.
   edit dist.. We propose ... a new formulation of the bipartite g. matching
   alg. designed to solve efficiently the assoc. g. edit dist. problem. The
   resulting alg. requires O(nm) memory space & O(min(n,m)^2 max(n,m))
   execution times."
   -- [<A HREF="https://www.archives-ouvertes.fr/hal-01540920/document">hal-01540920</A>]['22],
      [<A HREF="https://doi.org/10.1007/978-3-319-58961-9_11">doi:10.1007/978-3-319-58961-9_11</A>]['22].
   [Also search for: graph edit distance GED].

%A K. Iwama
%A J. Teruyama
%T Improved average complexity for comparison-based sorting
%J arXiv
%M MAY
%D 2017
%K TR, c2017, c201x, c20xx, zz0517, sort, sorting, MergeInsertion, algorithm
%X "... studies the avg complexity on the # of comparisons for sorting algs.
   Its info.-theoretic lower bound is (n lg n - 1.4427n+O(log n)). For many
   efficient algs, the first (n lg n) term is easy to achieve & our focus is on
   the (-ve) const. factor of the linear term. The current best value is -1.3999
   for the MergeInsertion sort. Our new value is -1.4106, narrowing the gap by
   some 25%. An important building block of our alg. is 'two-elt insertion,'
   which inserts two #s A & B, A < B, into a sorted seq. T. This insertion
   alg. is still sufficiently simple for rigorous math. analysis & works well
   for a certain range of the length of T for which the simple binary insertion
   does not, thus allowing us to take a complementary approach with the binary
   insertion."
   -- [<A HREF="https://arxiv.org/abs/1705.00849">arXiv</A>]['17].

%A S. Jo
%A S. Joannou
%A D. Okanohara
%A R. Raman
%A S. Rao Satti
%T Compressed bit vectors based on variable-to-fixed encodings
%J COMPJ
%V 60
%N 5
%P 761-775
%M APR
%D 2017
%K jrnl, COMPJ, c2017, c201x, c20xx, zz0517, bit vector, compressed, sparse,
   rank, select
%X "We consider practical implementations of compressed bitvectors, which
   support rank & select operations on a given bit-string, while storing the
   bit-string in compressed form. ... flexible and promising soln to the problem
   of supporting rank & select on moderately compressible bit-strings, such as
   those encountered in real-world applications."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxw103">doi:10.1093/comjnl/bxw103</A>]['17].

%A R. Curticapean
%A H. Dell
%A D. Marx
%T Homomorphisms are a good basis for counting small subgraphs
%J arXiv
%M MAY
%D 2017
%O STOC 2017
%K TR, c2017, c201x, c20xx, zz0617, graph, maths, subgraph, count, enumerate,
   enumeration, counting, homomorphism
%X "We introduce graph motif parameters, a class of g. parameters that depend
   only on the freqs. of const-size induced subgraphs. Classical works by Lovasz
   show that many interesting quantities have this form, inc., for fixed graphs
   H, the # of H-copies (induced or not) in an input graph G, & the # of
   homomorphisms from H to G.  ... obtain faster algs. for counting subgraph
   copies of fixed graphs H in host graphs G: For graphs H on k edges, we show
   how to count subgraph copies of H in time k^O(k).n^(0.174k+o(k)) by a
   surprisingly simple alg.. This improves upon prev. known running times, such
   as O(n^(0.91k+c)) time for k-edge matchings or O(n^(0.46k+c)) time for
   k-cycles. [&] we prove a general complexity dichotomy for evaluating g.motif
   parameters: Given a class C of such params, we consider the problem of
   evaluating 'f in C' on input g. G, parameterized by the # of induced subgs.
   that f depends upon. For every rec. enum. class C, we prove the above problem
   to be either FPT or #W[1]-hard, with an explicit dichotomy criterion. This
   allows us to recover known dichotomies for counting subgs., induced subgs., &
   homomorphisms in a uniform & simplified way, together with improved lwbs.
   ... extend g.motif params. to colored subgs. & prove a complexity trichotomy:
   For vertex-colored gs. H & G, where H is from a fixed class Hc, we want to
   count color-preserving H-copies in G. We show that this problem is either
   polynomial-time solvable or FPT or #W[1]-hard, & that the FPT cases indeed
   need FPT time under reasonable assumptions."
   -- 1705.01595@[<A HREF="https://arxiv.org/abs/1705.01595">arXiv</A>]['17].
   [Also search for: enumerate subgraph] and [also search for: count subgraph].

%A M. Baek
%A T. Knudsen
%T Linear hashing is awesome
%J arXiv
%M JUN
%D 2017
%K TR, conf, FOCS16, c2017, c201x, c20xx, zz0617, linear, hash, hashing,
   chaining, Dietzfelbinger
%X "We consider the hash function h(x)=((ax+b)mod p)mod n where a, b are chosen
   uniformly at random from {0, 1, ..., pâ1}. We prove that when we use h(x) in
   hashing with chaining to insert n elts into a table of size n the
   expected length of the longest chain is O^tilde(n^(1/3)). The proof also
   generalises to give the same bound when we use the multiply-shift hash fn
   by Dietzfelbinger et al. [J. of Alg. '97].
   -- 1706.02783@[<A HREF="https://arxiv.org/abs/1706.02783">arXiv</A>]['17].

%A M. Mitzenmacher
%A T. Morgan
%T Reconciling graphs and sets of sets
%J arXiv
%M JUL
%D 2017
%K TR, c2017, c201x, c20xx, zz0717, set, graph, reconcile, reconciliation
%X "We explore a generalization of set reconciliation, where the goal is to
   reconcile sets of sets. Alice & Bob each have a parent set consisting of s
   child sets, each containing at most h elements from a universe of size u.
   They want to reconcile their sets of sets in a scenario where the total
   number of differences between all of their child sets (under the minimum
   difference matching between their child sets) is d. We give several
   algorithms for this problem, & discuss applications to reconciliation
   problems on graphs, databases, & collections of documents. We specifically
   focus on graph reconciliation, providing protocols based on sets of sets
   reconciliation for random graphs from G(n,p) & for forests of rooted trees."
   -- 1707.05867@[<A HREF="https://arxiv.org/abs/1707.05867">arXiv</A>]['17].

%A S. Gupta
%A S. Roy
%A S. Saurabh
%A M. Zehavi
%T Balanced stable marriage: How close is close enough?
%J arXiv
%M JUL
%D 2017
%K TR, c2017, c201x, c20xx, zz0817, balanced stable marriage, problem,
   dissatisfaction, equal
%X "... the output cannot be an arbitrary stable matching, but one that balances
   between the dissatisfaction of the two parties, men & women. We study
   Balanced Stable Marriage from the viewpoint of Parameterized Complexity. Our
   'above guarantee parameterizations' are arguably the most natural
   parameterizations of the problem at hand. Indeed, our p. precisely fit the
   scenario where there exists a s.m. that both parties would accept, that is,
   where the satisfaction of each party is 'close' to the best it can hope for.
   [&] our p. accurately draw the line between tractability & intractability wrt
   the target value."
   -- 1707.09545@[<A HREF="https://arxiv.org/abs/1707.09545">arXiv</A>]['17].
   [Also search for: stable marriage problem].

%A N. Blum
%T A solution of the P versus NP problem
%J arXiv
%M AUG
%D 2017
%K TR, c2017, c201x, c20xx, zz0817, algorithm, complexity, P, NP, NPC,
   PNPproblem, Berg Ulfberg, Amano Maruoka, Andreev, Andreevs, network, monotone
%X "Berg and Ulfberg and Amano and Maruoka have used CNF-DNF-approximators to
   prove exponential lower bounds for the monotone network complexity of the
   clique function and of Andreev's function. We show that these approximators
   can be used to prove the same lower bound for their non-monotone network
   complexity. This implies P not equal NP."
   -- 1708.03486@[<A HREF="https://arxiv.org/abs/1708.03486">arXiv</A>][11/8/2017].
   [But will it hold up?!].                [Also search for: PNPproblem].
   About three weeks:
      "The proof is wrong. I shall elaborate precisely what the
      mistake is. For doing this, I need some time. I shall put
      the explanation on my homepage"
   -- 1708.03486@[<A HREF="https://arxiv.org/abs/1708.03486">arXiv</A>][30/8/17].

%A S. L. S. Mergen
%A V. P. Moreira
%T DuelMerge: Merging with fewer moves
%J COMPJ
%V 60
%N 9
%P 1271-1278
%M SEP
%D 2017
%K jrnl, COMPJ, c2017, c201x, c20xx, zz0917, duelmerge, algorithm, merge,
   merging, sorting, stable, moves
%X "... duelmerge, a stable merging alg. that is asymptotically optimal in the
   # of comparisons & performs O(n log2(n)) moves. Unlike other partition-based
   algs., we only allow blocks of equal sizes to be swapped, which reduces the
   # of moves required. We performed experiments comparing duelmerge [v.] a # of
   baselines inc. recmerge, the standard merging soln for programming languages
   such as C, & some more recent approaches. The results show that our proposed
   alg. performs fewer moves than other stable solns. Experiments employing
   duelmerge within MergeSort confirmed our positive results in terms of moves,
   comparisons & runtime."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxw105">doi:10.1093/comjnl/bxw105</A>]['17].
   (NB. "*stable* merging".)  [Also search for: merge algorithm].

%A D. Kane
%A R. Williams
%A The orthogonal vectors conjecture for branching programs and formulas
%J arXiv
%M SP
%D 2017
%K TR, c2017, c201x, c20xx, zz1122, orthogonal vectors conjecture, OVC, vector,
   problem, OVP
%X "... Orthogonal Vectors (OV) problem, we wish to determine if there is an
   orthogonal pair of vectors among n Boolean vectors in d dimensions. The OV
   Conjecture (OVC) posits that OV requires ni^{2-o(1)} time to solve, for all
   d=omega(log n). Assuming the OVC, optimal time lower bounds have been proved
   for many prominent problems in P. We prove that OVC is true in several
   computational models of interest ..."
   -- 1709.05294@[<A HREF="https://arxiv.org/abs/1709.05294">arXiv</A>]['22].

%A Hao Chen
%A K. Laine
%A P. Rindal
%T Fast private set intersection from homomorphic encryption
%J ACM SIGSAC Conf. on Comp. and Comm. Security
%P 1243-1255
%M OCT
%D 2017
%K conf, c2017, c201x, c20xx, zz1122, private set intersection, PSI,
   homomorphic encryption
%X "... allows two parties to compute the intersection of their sets without
   revealing anything except the intersection. We use fully homomorphic
   encryption to construct a fast PSI protocol with a small comm'n overhead that
   works particularly well when one of the two sets is much smaller than the
   other, & is secure against semi-honest adversaries. ... Our protocol has
   comm'n complexity linear in the size of the smaller set, & logarithmic in the
   larger set. ..."
   -- [<A HREF="https://doi.org/10.1145/3133956.3134061">doi:10.1145/3133956.3134061</A>]['22],
      [<A HREF="https://eprint.iacr.org/2017/299">www</A>]['22].
   (Also see PSI@[<A HREF="https://en.wikipedia.org/wiki/Private_set_intersection">wikip</A>]['22].)
   [Also search for: private set intersection PSI].

%A D. Lemire
%A N. Kurz
%A C. Rupp
%T Stream VByte: Faster byte-oriented integer compression
%J IPL
%V 130
%P 1-6
%M FEB
%D 2018
%K jrnl, IPL, c2018, c201x, c20xx, zz1017, integer, integers, ints, VByte,
   G8IU, varint-GB, compress, data, compression, algorithm, SIMD
%X "... a novel byte-oriented compression technique that separates the control
   stream from the encoded data. Like varint-G8IU, Stream VByte is well suited
   for SIMD instructions. We show that Stream VByte decoding can be up to twice
   as fast as varint-G8IU decoding over real data sets. In this sense, Stream
   VByte establishes new speed records for byte-oriented integer compression,
   at times exceeding the speed of the memcpy function. On a 3.4 GHz Haswell
   processor, it decodes more than 4 billion differentially-coded integers per
   second from RAM to L1 cache."  (online 10/2017.)
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2017.09.011">doi:10.1016/j.ipl.2017.09.011</A>]['17].
   Also search for: Lemire].

%A F. L. Traversa
%A P. Cicotti
%A F. Sheldon
%A M. Di Ventra
%T Evidence of an exponential speed-up in the solution of hard
   optimization problems
%J arXiv
%M OCT
%D 2017
%K TR, c2017, c201x, c20xx, zz1017, NPC, hard, NPhard, constraint, programming,
   SAT, Max-SAT, MaxSAT, optimization, circuit, circuits, algorithm
%X "... we map the optimization problem into a boolean circuit made of specially
   designed, self-organizing logic gates, which can be built with (non-quantum)
   electronic components; the equilibrium points of the circuit represent the
   approximation to the problem at hand. Then, we solve its associated
   non-linear ordinary differential equations numerically, towards the
   equilibrium points. We demonstrate this exponential gain by comparing a
   sequential MatLab implementation of our solver with the winners of the 2016
   Max-SAT competition on a variety of hard optimization instances. We show
   empirical evidence that our solver scales linearly with the size of the
   problem, both in time & memory ..."
   -- [<A HREF="https://arxiv.org/abs/1710.09278">arXiv</A>]['17].

%A K. Papadopoulos
%A D. Christofides
%T A fast algorithm for the gas station problem
%J IPL
%V 131
%P 55-59
%M MAR
%D 2018
%K jrnl, IPL, c2018, c201x, c20xx, zz1217, gas, petrol, fuel, station,
   garage, travelling, trip, route, problem, graph, cheapest, algorithm,
   Khuller, Malekian, Mestre
%X "In the gas station problem we want to find the cheapest path between two
   vertices of an n-vertex graph. Our car has a specific fuel capacity & at each
   vertex we can fill our car with gas, with the fuel cost depending on the
   vertex. Furthermore, we are allowed at most D stops for refuelling. In this
   short paper we provide an alg. solving the problem in steps improving an
   earlier result by Khuller, Malekian & Mestre."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2017.11.009">doi:10.1016/j.ipl.2017.11.009</A>]['17].

%A E. Karstadt
%A O. Schwartz
%T Matrix multiplication, a little faster
%J Proc. 29th ACM Symp. on Parallelism in Algs. and Arch.
%P 101-110
%M JUL
%D 2017
%K conf, SPAA17, c2017, c201x, c20xx, zz0820, fast, matrix multiplication,
   algorithm
%X "... The leading coeff. of Strassen-Winograd's alg. was believed to be
   optimal for m.mult. algs. with 2x2 base case, due to a [lwb] of Probert
   (1976).  Surprisingly, we obtain a faster m.m.alg., with the same base case
   size & asymptotic complexity as S.-W.'s alg., but with the coeff. reduced
   from 6 to 5. To this end, we extend Bodrato's (2010) method for m.squaring,
   & transform matrices to an alternative basis. ... apply our technique to
   other S.-like algs., improving their arithmetic & communication costs by
   sig. const. factors."
   -- [<A HREF="https://doi.org/10.1145/3087556.3087579">doi:3087556.3087579</A>]['20].
   [Also search for: fast matrix multiplication].


%A Hao Hu
%A R. Sotirov
%T On solving the quadratic shortest path problem
%J arXiv
%M AUG
%D 2017
%K TR, c2017, c201x, c20xx, zz0323, quadratic shortest path problem, QSPP
%X "The quadratic shortest path problem is the problem of finding a path in a
   directed graph such that the sum of interaction costs over all pairs of arcs
   on the path is minimized ... We also present computational results on solving
   the QSPP using a branch & bound alg.. [It] computes a semidefinite
   programming bound in each node of the search tree, & solves instances with
   up to 1300 arcs in less than an hour (!)."
   -- 1708.06580@[<A HREF="https://arxiv.org/abs/1708.06580">arXiv</A>]['23].

%A I. Chillotti
%A N. Gama
%A M. Georgieva
%A M. Izabachene
%T Faster packed homomorphic operations and efficient circuit bootstrapping
   for TFHE
%J Int. Conf. Theory and Applic. of Cryptography & Info. Security
%M NOV
%D 2017
%P 377-408
%K conf, c2017, c201x, c20xx, zz1121, homomorphic encryption, FHE, TFHE library,
   RingGSW, TRGSW, GSW, leveled, levelled
%X "... present several methods to improve the evaluation of h. fns in TFHE,
   both for fully & for leveled h.encryption. We propose two methods to
   manipulate packed data, in order to decrease the ciphertext expansion &
   optimize the evaluation of look-up tables & arbitrary fns in RingGSW based
   homomorphic schemes. ..."
   -- [<A HREF="https://doi.org/10.1007/978-3-319-70694-8_14">doi:10.1007/978-3-319-70694-8_14</A>]['21].
   * Also see pdf@[<A HREF="https://eprint.iacr.org/2017/430.pdf">iacr</A>]['21].
   [Also search for: homomorphic encryption].

%A D. Harvey
%A J. van der Hoeven
%T Faster integer and polynomial multiplication using
   cyclotomic coefficient rings
%J arXiv
%M DEC
%D 2017
%K TR, c2017, c201x, c20xx, zz1217, fast, integer, arithmetic, multiplication,
   BigInt, polynomial, algorithm, vanDerHoeven
%X "... computes the product of two n-bit integers in
   O(n log n (4 sqrt 2)^(log^* n)) bit operations. Previously, the best known
   bound was O(n log n 6^(log^* n)). We also prove that for a fixed prime p,
   polynomials in F_p[X] of degree n may be multiplied in O(n log n 4^(log^* n))
   bit ops; the prev. best bound was O(n log n 8^(log^* n))."
   -- 1712.03693@[<A HREF="https://arxiv.org/abs/1712.03693">arXiv</A>]['17].
   [Also search for: fast integer multiplication].

%A J. Alman
%A V. V. Williams
%T Further limitations of the known approaches for matrix multiplication
%J arXiv
%M DEC
%D 2017
%O 9th Innovations in Theor. Comp. Sci. Conf. (ITCS 2018)
%K TR, c2017, c201x, c20xx, zz0118, fast, matrix multiplication, algorithm
%X "... showing that all known matrix multiplication running times since 1986
   can be achieved from a single very natural tensor - the structural tensor Tq
   of addition modulo an integer q.  (2)We show that if one applies a
   generalization of the known techniques (arbitrary zeroing out of tensor
   powers to obtain independent matrix products in order to use the asymptotic
   sum inequality of Schonhage) to an arbitrary monomial degeneration of Tq,
   then there is an explicit lower bound, depending on q, on the bound on the
   matrix mult. exponent w that one can achieve. We also show upper bounds on
   the value alpha that one can achieve, where alpha is such that
   n x n^alpha x n matrix mult. can be computed in n2+o(1) time.  (3)We show
   that our lower bound on w approaches 2 as q goes to infinity. This suggests
   a promising approach to improving the bound on Ï: for variable q, ..."
   -- 1712.07246@[<A HREF="https://arxiv.org/abs/1712.07246">arXiv</A>]['17].
   [Also search for: fast matrix multiplication algorithm].

%A K. Bringmann
%T A near-linear pseudopolynomial time algorithm for subset sum
%J Proc. 28th Annual ACM-SIAM Symp. on Discrete Algorithms (SODA)
%I SIAM
%P 1073-1084
%D 2017
%K conf, SODA, c2017, c201x, c20xx, zz0222, algorithm, subset sum problem,
   SSP, perfect
%X "Given a set Z of n +ve integers & a target value t, the SuBSETSuM problem
   asks whether any subset of Z sums to t. ... we present a simple & elegant
   randomized alg. running in time ~O(n+1). This improves upon a classic alg. &
   is likely to be near-optimal, since it matches conditional lower bounds from
   SetCover & k-Clique.  We then use [it] & additional tricks to improve the
   best known polynomial space soln from time ~O(n^3t) & space ~O(n^2) to time
   ~O(nt) & space ~O(n.log(t)), assuming the Extended Riemann Hypothesis.
   Unconditionally, we obtain time ~O(nt^{1+e}) & space ~O(nt^e) for any const.
   e>0."
   -- 1610.04712@[<A HREF="https://arxiv.org/abs/1610.04712">arXiv</A>][22],
      [<A HREF="https://doi.org/10.1137/1.9781611974782.69">doi:10.1137/1.9781611974782.69</A>]['22].
   (Also see SSP@[<A HREF="https://en.wikipedia.org/wiki/Subset_sum_problem">wikip</A>]['22].
   And, "perfect sum problem": print all subsets having the given sum -- misc.)
   [Also search for: subset sum problem].

%A D. J. Bernstein
%A N. Heninger
%A p. Lou
%A L. Valenta
%T Post-quantum RSA
%J Post-Quantum Cryptography. PQCrypto
%I Springer
%S LNCS
%V 10346
%D 2017
%K conf, c2017, c201x, c20xx, zz0323, integer factorisation, factorization,
   pqRSA, Grover, GEECM, quantum computing
%X "... proposes RSA params. for which (1) key generation, encryption,
   decryption, signing, & verification are feasible on today's computers while
   (2) all known attacks are infeasible, even assuming highly scalable q.
   computers. ... introduces a new alg. to generate a batch of primes. As part
   of the attack analysis, ... introduces a new q.factorization alg. that
   is often much faster than Shor's alg. & much faster than pre-quantum
   factorization algs.. Initial pqRSA implementation results are provided."
   -- 2017/351@[<A HREF="https://eprint.iacr.org/2017/351">iacr</A>]['23].
   Also see GAlg@[<A HREF="https://en.wikipedia.org/wiki/Grover%27s_algorithm">wikip</A>]['23].
   [Also search for: integer factorisation], maybe inc. quantum.

%A R. Heckel
%A M. Simchowitz
%A K. Ramchandran
%A M. J. Wainwright
%T Approximate ranking from pairwise comparisons
%J arXiv
%M JAN
%D 2018
%K TR, c2018, c201x, c20xx, zz0118, rank, approximate ranking, algorithm,
   sorting, top k, topK, score, comparison, pairwise
   of pre-specified sizes according to their scores, which includes
   identification of the top-k items as the most prominent special case. The
   score of a given item is defined as the probability that it beats a randomly
   chosen other item. Finding an exact ranking typically requires a
   prohibitively large # of comparisons, but in practice, approx. rankings are
   often adequate. ... study the problem of finding approx. rankings from
   pairwise comparisons. We analyze an active ranking alg. that counts the # of
   comparisons won, & decides whether to stop or which pair of items to compare
   next, based on confidence intervals computed from the data collected in
   prev. steps. We show that this alg. succeeds in recovering approx. rankings
   using a # of comparisons that is close to optimal up to logarithmic factors.
   We also present numerical results, showing that in practice, approx. can
   drastically reduce the number of comparisons required to estimate a ranking."
   -- 1801.01253@[<A HREF="https://arxiv.org/abs/1801.01253">arXiv</A>]['18].

%A M. Grohe
%A G. Rattan
%A G. J. Woeginger
%T Graph similarity and approximate isomorphism
%J arXiv
%M FEB
%D 2018
%K TR, c2018, c201x, c20xx, zz0318, approximate graph isomporphism, maths,
   graphAlignment, similarity, matching, Frobenius distance, weighted, SIM,
   WSIM, QAP, problem, algorithm, SemiDefinite
%X The graph similarity problem, also known as approximate graph isomorphism or
   graph matching problem, has been extensively studied in the [ML]  community,
   but has not received much attention in the algorithms community: Given two
   graphs G, H of the same order n with adjacency matrices A_G, A_H, a
   well-studied measure of similarity is the Frobenius distance
   dist(G,H):=min_pi ||A^pi_G - A_H||_F, where pi ranges over all perms. of the
   vertex set of  G  ... The (weighted) graph similarity problem, denoted by
   SIM (WSIM), is the problem of computing this distnce or two graphs of same
   order. This problem is closely related to the notoriously hard quadratic
   assignment problem (QAP), which is known to be NP-hard even for severely
   restricted cases.  ... We show that WSIM is NP-hard as long as one of the
   matrices has unbounded rank or negative eigenvalues: hence, the realm of
   tractability is restricted to positive semi-definite matrices of bounded
   rank. Our main result is a polynomial time alg. for the special case where
   one of the matrices has a bounded clustering number, a parameter arising from
   spectral graph drawing techniques."
   -- 1802.08509@[<A HREF="https://arxiv.org/abs/1802.08509">arXiv</A>]['18].
   [Also search for: graph isomorphism] and
   [also search for: maximum common subgraph] and
   [also search for: graphAlignment].

%A T. Kavitha
%T The popular roommates problem
%J arXiv
%M MAR
%D 2018
%K TR, c2018, c201x, c20xx, zz0418, popular roommates problem, room mate,
   roommate, matching, dominant, matchings, matching, preference, NPH
%X "... in a roommates instance with strict preference lists. While popular
   matchings always exist in a bipartite instance, they need not exist in a
   roommates instance. The complexity of the popular matching problem in a
   roommates instance has been an open problem for several years and here we
   show it is NP-hard. A sub-class of max-size popular matchings called dominant
   matchings has been well-studied in bipartite graphs. We show that the
   dominant matching problem in a roommates instance is also NP-hard and this is
   the case even when the instance admits a stable matching."
   -- 1804.00141@[<A HREF="https://arxiv.org/abs/1804.00141">arXiv</A>]['18].
   [Also search for: stable marriage].  Note, 'NPH'.
   (Also see Gupta roommates c2018 !)

%A S. Gupta
%A P. Misra
%A S. Saurabh
%A M. Zehavi
%T Popular matching in roommates setting is NP-hard
%J arXiv
%M MAR
%D 2018
%K TR, c201x, c20xx, zz0418, popular roommates problem, room mate,
   roommate, matching, NPC
%X "An input to the Popular Matching problem, in the roommates setting, consists
   of a graph G and each vertex ranks its neighbors in strict order, known as
   its preference. In the Popular Matching problem the objective is to test
   whether there exists a matching Mâ such that there is no matching M where
   more people are happier with M than with Mâ. In this paper we settle the
   computational complexity of the Popular Matching problem in the roommates
   setting by showing that the problem is NP-complete. Thus, we resolve an open
   question that has been repeatedly, explicitly asked over the last decade."
   -- [<A HREF="https://arxiv.org/abs/1803.09370">arXiv</A>]['18].  Note 'NPC'.
   (Also see Kavitha roommates c2018 !)

%A A. Polak
%T Why is it hard to beat O(n^2) for longest common weakly increasing
   subsequence?
%J IPL
%V 132
%P 1-5
%M APR
%D 2018
%K jrnl, IPL, c2018, c201x, c20xx, zz0418, LCWIS, LCIS, LCS, problem,
   Longest Common Weakly Increasing Subsequence, algorithm, SETH
%X "... we show that LCWIS cannot be solved in O(n^(2-eps)) time unless the
   Strong Exponential Time Hypothesis (SETH) is false.  The ideas which we
   developed can also be used to obtain a lower bound based on a safer
   assumption of SETH, i.e. a version of SETH which talks about circuits instead
   of less expressive CNF formulas."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2017.11.007">doi:10.1016/j.ipl.2017.11.007</A>]['18].

%A M. Kowaluk
%A A. Lingas
%T Are unique subgraphs not easier to find?
%J IPL
%V 134
%P 57-61
%M JUN
%D 2018
%K jrnl, IPL, c2018, c201x, c20xx, zz0418, maths, graph, subgraph, instance,
   motif, unique
%X "Consider a pattern graph H with l edges, and a host graph G which may
   contain several occurrences of H. ... We show a counterexample to this
   too strong claim and correct it by providing an O~((l(d-1)+2)^l) bound on the
   multiplicative factor instead, where d is the max. # of occurrences of H that
   can share the same edge in the input host graph. We provide also an analogous
   correction in the induced case when occurrences of induced subgs. isomorphic
   to H are sought."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2018.02.010">doi:10.1016/j.ipl.2018.02.010</A>]['18].

%A K. Kurita
%A K. Wasa
%A A. Conte
%A H. Arimura
%A T. Uno
%T Efficient enumeration of subgraphs and induced subgraphs with bounded girth
%J arXiv
%M JUN
%D 2018
%K TR, c2018, c201x, c20xx, zz0618, enumerate, enumeration, subgraph, graph,
   algorithm, girth
%X "The girth of a graph is the length of its shortest cycle. Due to its
   relevance in graph theory, n/wk analysis ... we consider the problem of
   listing connected subgraphs with bounded girth. As a large girth is index of
   sparsity, this allows to extract sparse structures from the input g.. We
   propose two algs., for enumerating respectively vertex induced subgs. & edge
   induced subgs. with bounded girth, both running in O(n) amortized time per
   soln & using O(n^3) space. [&] the algs. can be easily adapted to relax the
   connectivity requirement & to deal with weighted graphs. As a byproduct, the
   2nd alg. can be used to answer the well known question of finding the
   densest n-vertex graph(s) of girth k."
   -- 1806.04307@[<A HREF="https://arxiv.org/abs/1806.04307">arXiv</A>]['18].
   [Also search for: enumerate subgraph].

%A A. Sakharov
%A T. Sakharov
%T The Viterbi algorithm for subsets of stochastic context-free languages
%J IPL
%V 135
%N ?
%P 68-72
%K jrnl, IPL, c2018, c201x, c20xx, zz0718, Viterbi algorithm, CFG, language,
   DPA, most probable path
%X "The time complexity of finding the most probable derivation for stochastic
   context-free grammars is cubic in the size of the input. The Viterbi alg.
   solves the same task in linear time for stochastic regular languages. We
   present two modified versions of this alg.. One finds the most probable path
   & builds a parse tree for stochastic one-counter languages in quadratic time
   of the size of the input. The other finds the most probable derivation for
   stochastic linear languages, also in quadratic time."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2018.03.005">doi:10.1016/j.ipl.2018.03.005</A>]['18].
   [Also search for: DPA].

%A E. Tang
%T A quantum-inspired classical algorithm for recommendation systems
%J arXiv
%M JUL
%D 2018
%K TR, c2018, c201x, c20xx, zz0119, quantum computing, classical algorithm,
   inspired, computer, recommendation systems, recommender, completing, matrix,
   rank, Tang, QML, Kerenidis, Prakash
%X "A recommendation system suggests products to users based on data about user
   preferences. It is typically modeled by a problem of completing an mÃn matrix
   of small rank k. We give the first classical alg. to produce a recommendation
   in O(poly(k)polylog(m,n)) time, which is an exponential improvement on prev.
   alg. that run in time linear in m & n. Our strategy is inspired by a quantum
   alg. by Kerenidis & Prakash: like the q.alg., instead of reconstructing
   a user's full list of prefs., we only seek a randomized sample from the
   user's preferences. Our main result is an alg. that samples high-weight
   entries from a low-rank approx. of the input matrix in time indep. of m & n,
   given natural sampling assumptions on that input matrix. [So] we show that
   K. & P.'s q.m/c learning (QML) alg., one of the strongest candidates for
   provably exponential speedups in QML, does not in fact give an exp. speedup
   over classical alg.."
   -- 1807.04271@[<A HREF="https://arxiv.org/abs/1807.04271">arXiv</A>]['19].
   (Also see editorial N@ture [<A HREF="https://doi.org/10.1038/d41586-018-07801-3">www</A>][18/12/'18].)
   [Also search for: quantum inspired].

%A A. Ilic
%A M. Basic
%T Path matrix and path energy of graphs
%J arXiv
%M OCT
%D 2018
%K TR, c2018, c201x, c20xx, zz1018, maths, graph, algorithm, path matrix,
   energy, Shikare
%X "Given a graph G, we associate a path matrix P whose (i,j) entry represents
   the maximum # of vertex disjoint paths between the vertices i & j, with zeros
   on the main diagonal. ... we resolve four conjectures from [M.M.Shikare,
   P.P.Malavadkar, S.C.Patekar, I.Gutman, 'On Path Eigenvalues & Path
   Energy of Graphs', MATCH Commun. Math. Comput. Chem. {79, 2018, 387-398.] on
   the path energy of graphs & finally present efficient O(|E||V|^3) alg. for
   computing the path matrix used for verifying computational results."
   -- 1810.04870@[<A HREF="https://arxiv.org/abs/1810.04870">arXiv</A>]['18].

%A N. Tatti
%T Strongly polynomial efficient approximation scheme for segmentation
%J IPL
%V 142
%P ?-?
%M FEB
%D 2019
%K jrnl, IPL, c2018, c201x, c20xx, zz1018, segment, sequence, segmentation,
   Seg, MaxSeg, algorithm
%X "Partitioning a sequence of length n into k coherent segments (Seg) ...
   Seg can be solved exactly in time using a classic dynamic program. ...
   first solving a slightly different segmentation problem (MaxSeg), where the
   quality of the segmentation is the maximum penalty of an individual segment.
   ... able to obtain a strongly polynomial alg.. [&] consider a cumulative
   version of Seg, where we are asked to discover the optimal segmentation for
   each prefix of the input seq.. We propose a strongly polynomial alg. that
   yields (1+e) approximation in time O(nk^2/e). ... consider a cumulative
   version of MaxSeg, & show that we can solve the problem in time O(nk log k)."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2018.09.007">doi:10.1016/j.ipl.2018.09.007</A>]['18] (online 10/'18).
   [Also search for: segmentation].

%A S. Assadi
%A M. Kapralov
%A S. Khanna
%T A simple sublinear-time algorithm for counting arbitrary subgraphs via edge
   sampling
%J arXiv
%M NOV
%D 2018
%K TR, c2018, c201x, c20xx, zz1118, maths, graph, subgraph, count, counting,
   estimate, subgraphs, triangle, clique, star
%X "... given a input graph G(V,E) & a target graph H; the goal is to estimate
   the # of occurrences of H in G. Our focus here is on designing sublinear-time
   algs. for approximately counting occurrences of H in G in the setting where
   the alg. is given query access to G. ...bridge this gap between subgraph
   counting & subgraph enumeration by designing a sublinear-time alg. that can
   est. the # of any arbitrary subgraph H in G, denoted by #H, to within a
   (1+/-e)-approximation w.h.p. in O((m^{Ï(H)}/#H)âpoly(log n, 1/e) time. Our
   alg. is allowed the std set of queries for general graphs, namely degree
   queries, pair queries & neighbor queries, plus an additional edge-sample
   query that returns an edge chosen uniformly at random. ..."
   -- 1811.07780@[<A HREF="https://arxiv.org/abs/1811.07780">arXiv</A>]['18].
   [Also search for: count subgraph].

%A N. Tatti
%A P. Miettinen
%T Boolean matrix factorization meets consecutive ones property
%J arXiv
%M JAN
%D 2019
%O SIAM Int. Conf. on Data Mining (SDM19), 2019, to appear
%K TR, c2019, c201x, c20xx, zz0119, Boolean matrix factorisation, BMF,
   algorithm, decomposition, OBMF, consecutive ones property, cyclic, symmetric
%X "... study a problem of Boolean matrix factorization where we additionally
   require that the factor matrices have consecutive ones property (OBMF). A
   major applicn of this optimization problem comes from graph visualization:
   std techniques for visualizing gs. are circular or linear layout, where nodes
   are ordered in circle or on a line. A common problem ... is clutter due to
   too many edges. The std approach to deal with this is to bundle edges
   together & represent them as ribbon. We also show that we can use OBMF for
   edge bundling combined with circular or linear layout techniques. ... not
   only this problem is NP-hard but we cannot have a polynomial-time alg.
   that yields a multiplicative approx. guarantee (unless P=NP). On the +ve
   side, we develop a greedy alg. ... look for the best 1-rank factorization.
   Since even obtaining 1-rank factorization is NP-hard, we propose an iterative
   alg. ... fix one side & and find the other, reverse the roles, & repeat. ...
   step can be done in linear time using pq-trees. ... extend the problem to
   cyclic ones property & symmetric factorizations. ... algs. find high-quality
   factorizations & scale well."
   -- 1901.05797@[<A HREF="https://arxiv.org/abs/1901.05797">arXiv</A>]['19].

%A A. Dumitrescu
%T Finding a mediocre player
%J arXiv
%M JAN
%D 2019
%K TR, c2019, c201x, c20xx, zz0219, mediocre, player, algorithm, pick, find,
   rank, ranking, median, Yao, 1974
%X "Consider a totally ordered set S of n elements; [eg] a set of tennis players
   & their rankings. ... Following Frances Yao (1974), an elt (player) is said
   to be (i,j)-mediocre if it is neither among the top i nor among the bottom j
   elts of S. More than 40 years ago, Yao suggested a stunningly simple alg.
   for finding an (i,j)-mediocre elt: Pick i+j+1 elts arbitrarily & select the
   (i+1)-th largest among them. She also asked: 'Is this the best alg.?' No one
   seems to have found such an alg. ever since. We first provide a deterministic
   alg. that beats the worst-case comparison bound in Yao's alg. for a large
   range of values of i ... We then repeat the exercise for randomized algs; the
   avg. # of comparisons of our alg. beats the avg. comparison bound in Yao's
   alg. for another large range of values of i ... the improvement is most
   notable in the symmetric case i=j. [&] the tight bound obtained in the
   analysis of Yao's alg. allows us to give a definite answer for this class of
   algs.. In summary, we answer Yao's question as follows: (i) 'Presently not'
   for deterministic algs. & (ii) 'Definitely not' for randomized algs. (In
   fairness, it should be said however that Yao posed the question in the
   context of deterministic algs..)
   -- 1901.09017@[<A HREF="https://arxiv.org/abs/1901.09017">arXiv</A>]['19].
   (The problem is a little like the select (the med-ian) problem.
    A mediocre value could be used as the pivot in queeksort.)

%A D. Harvey
%A J. Van Der Hoeven
%T Integer multiplication in time O(n log n)
%J HALarchive
%M MAR
%D 2019
%K TR, c2019, c201x, c20xx, zz0419, fast, integer, multiplication, arithmetic,
   algorithm, BigInt, nLogN, hal02070778, 02070778
%X "... Schonhage and Strassen conjectured in 1971 that the true complexity of
   int.multn lies in Theta(n log n), & ... established their famous upper bound
   M(n)=O(n log n log log n).  In 2007 their result was sharpened by Furer
   to M(n)=O(n log(n) K^{log^â n}) for some unspec. const. K>1, where
   log^â(n) denotes the iterated log, i.e., log^*(n)=min{k>=0: log^{k}(x)<=1}.
   Prior to the present work, the record stood at M(n)=O(n log n 4^{log^*n}).
   The main result of this paper is a verification of the upper bound in
   S&S's conjecture, thus completely closing the remaining 4^{log^*(n)} gap..."
   -- [<A HREF="https://hal.archives-ouvertes.fr/hal-02070778/document">www</A>]['19].
   Also see the abc[<A HREF="https://www.abc.net.au/news/2019-04-10/a-new-way-to-multiply-big-numbers/10985746">10/4/2019</A>],
      arith@[<A HREF="https://en.wikipedia.org/wiki/Computational_complexity_of_mathematical_operations">wikip</A>]['21]
   (and iteratedLog@[<A HREF="https://en.wikipedia.org/wiki/Iterated_logarithm">wikip</A>]['19]).
   [Also search for: fast integer multiplication].

%A A. Rubinstein
%A Z. Song
%T Reducing approximate longest common subsequence to approximate edit distance
%J arXiv
%M APR
%D 2019
%K TR, c2019, c201x, c20xx, zz0419, approximate, approximation, algorithm,
   reduction, LCS, LCSS, Koucky, Saks, strings, longest common subsequence,
   edit distance
%T "Given a pair of strings, the problems of computing their LCS & ED have been
   extensively studied for decades. For exact algs., LCS & ED (with character
   insertions & dels.) are equivalent; the state of the art running time is
   (almost) quadratic & this is tight under plausible fine-grained complexity
   assumptions. But for approximation algs. the picture is different: there is a
   long line of works with improved approximation factors for ED, but for LCS
   (with binary strings) only a trivial 1/2-approximation was known. ... we give
   a reduction from approximate LCS to approximate ED, yielding the first
   efficient (1/2+e)-approximation alg. for LCS for some constant e > 0."
   -- 1904.05451@[<A HREF="https://arxiv.org/abs/1904.05451">arXiv</A>][10/4/2019].
   (Also see Koucky and Saks 1904.05459@[<A HREF="https://arxiv.org/abs/1904.05459">arXiv</A>][10/4/2019].)
   [Also search for: edit distance algorithm] and
   [also search for: LCS algorithm] and
   [also search for: strings approximation algorithm].

%A R. S. Bird
%T How to find a fake coin
%J JFP
%V 29
%P c8
%M APR
%D 2019
%K programming pearl, JFP, FP, c2019, c201x, c20xx, zz0519, fake coin, coins,
   weigh, heavy, light, puzzle, problem
%X "... There are n coins, all identical in appearance, one of which *may* be
   fake. The fake coin, if it exists, is either lighter or heavier than the
   fair coin ..."
   -- [<A HREF="https://doi.org/10.1017/S0956796819000030">doi:10.1017/S0956796819000030</A>]['19].

%A H. A. Helfgott
%T An improved sieve of Eratosthenes
%J Math. Comp.
%V ?
%P ?-?
%M APR
%D 2019
%K jrnl, AMS, c2019, c201x, c20xx, zz0519, Eratosthenes, sieve, algorithm,
   prime, primes, Galway
%X "We show how to carry out a sieve of E. up to N in space
   (N^{1/3} (log N)^{2/3}) and time O(N log N). ... the usual versions of the
   sieve take space about O(sqrt N) and time at least linear on N. We can also
   apply our sieve to any subinterval of [1,N] of length Omega(N^{1/3}) in time
   close to linear on the length of the interval. Before, such a thing was
   possible only for subintervals of [1,N] of length Omega(sqrt N).
   Just as in (Galway, 2000), the approach here is related to Diophantine
   approximation, & also has close ties to Voronoi's work on the Dirichlet
   divisor problem. The advantage of the method here resides in the fact that,
   because the method we will give is based on the sieve of E., we will also be
   able to use it to factor ints, & not just to produce lists of consec.primes."
   -- [<A HREF="https://doi.org/10.1090/mcom/3438">doi:10.1090/mcom/3438</A>]['19],
   &  1712.09130@[<A HREF="https://arxiv.org/abs/1712.09130">arXiv</A>]['17].
   [Also search for: sieve Eratosthenes].

%A L. Babai
%T Canonical form for graphs in quasipolynomial time. Preliminary Report
%J Proc. 51st Annual ACM SIGACT Symp. on Theory of Comp.
%P 1237-1246
%M JUN
%D 2019
%K conf, STOC, c2019, c201x, c20xx, zz1222, maths, graph, canonical labelling,
   form, isomorphism
%X "We outline how to turn the author's quasipolynomial-time g.isomorphism test
   into a construction of a canonical form within the same time bound. The proof
   involves a nontrivial mod'n of the central symmetry-breaking tool, the
   construction of a canonical relational structure of logarithmic arity on the
   ideal domain based on local certificates."
   -- [<A HREF="https://doi.org/10.1145/3313276.3316356">doi:10.1145/3313276.3316356</A>]['22].
   [Also search for: graph canonical].

%A R. Gluck
%A T. Yokoyama
%T Constructing a binary tree from its traversals by reversible recursion and
   iteration
%J IPL
%V 147
%P 32-37
%M JUL
%D 2019
%K jrnl, IPL, c2019, c201x, c20xx, zz0719, reversible, computing, computation,
   trees, traversal, inverse, inversion, algorithm, recursion,
   program, programming
%X "We cast two algs. to generate the inorder & preorder of the labels of a
   binary tree in the context of reversible computing nearly three decades after
   they were first examined in the light of program inversion. The reversible
   traversals directly define the inverse algs. that reconstruct the binary tree
   & have the same linear time & space requirements as the traversals. A
   reversible while-language is extended with reversible recursion."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2019.03.002">doi:10.1016/j.ipl.2019.03.002</A>]['19].

%A M. Bozorg
%A S. Salehkaleybar
%A M. Hashemi
%T Seedless graph matching via tail of degree distribution for correlated
   Erdos-Renyi graphs
%J arXiv
%M JUL
%D 2019
%K TR, c2019, c201x, c20xx, zz0719, maths, graph, isomorphism, match, matching,
   correspondence, morphism, seed, sparse, algorithm
%X "... recovering the node-to-node corr. between two correlated graphs. A
   prev. work theoretically showed that recovering is feasible in sparse
   E-R graphs if & only if the probability of having an edge between a pair of
   nodes in one of the graphs & also between the corr. nodes in the other graph
   is in the order of Omega(log(n)/n), where n is the # of nodes. ... we propose
   a graph matching alg. which obtains correct matching with high prob. in E-R
   graphs for the region of Theta(log(n)/n) without using a seed set of
   pre-matched node pairs as an input. [It] assigns structurally innovative
   features to high-degree nodes based on the tail of empirical degree distn of
   their neighbor nodes. Then, it matches the high-degree nodes according to
   these features, & finally obtains a matching for the remaining nodes. We
   evaluate the performance of proposed alg. in the regions of Theta(log(n)/n)
   & Theta(log^2(n)/n). Experiments show that it outperforms prev. works in both
   regions."
   -- 1907.06334@[<A HREF="https://arxiv.org/abs/1907.06334">arXiv</A>]['19].
   [Also search for: graph isomorphism].

%A J. Lenchner
%T On a Generalization of the Marriage Problem
%J arXiv
%M JUL
%D 2019
%K TR, c2019, c201x, c20xx, zz0719, Hall, symmetric, stable, marriage, Theorem,
   maximal weighted bipartite matching, maths, graph, graphs
%X "We present a generalization of the marriage problem underlying Hall's famous
   Marriage Theorem to what we call the Symmetric Marriage Problem, a problem
   that can be thought of as a special case of Maximal Weighted Bipartite
   Matching. We show that there is a solution to the Symmetric Marriage Problem
   if and only if a variation on Hall's Condition holds on each of the
   bipartitions. We prove both finite and infinite versions of this result and
   provide applications."
   -- [<A HREF="https://arxiv.org/abs/1907.05870">arXiv</A>]['19].

%A A. Golinski
%A F. Wood
%A T. Rainforth
%T Amortized Monte Carlo integration
%X arXiv
%M JUL
%D 2019
%O Int. Conf. on Mach. Learning (ICML)
%K conf, TR, c2019, c201x, c20xx, zz0719, Monte Carlo integration, quadtrature,
   algorithm, Bayesian inference, posterior, ICML
%X "Current approaches to amortizing Bayesian inference focus solely on
   approximating the posterior distribution. Typically ... used to calculate
   expectations for one or more target fns - a computational pipeline which is
   inefficient when the target function(s) are known upfront. ... introduc[e]
   AMCI, a method for amortizing Monte Carlo integration directly. AMCI operates
   similarly to amortized inference but produces three distinct amortized
   proposals, each tailored to a different component of the overall expectation
   calculation. At runtime, samples are produced separately from each amortized
   proposal, before being combined to an overall estimate of the expectation. We
   show that while existing approaches are fundamentally limited in the level of
   accuracy they can achieve, AMCI can theoretically produce arbitrarily small
   errors for any integrable target fn using only a single sample from each
   proposal at runtime. We further show that it is able to empirically
   outperform the theoretically optimal self-normalized importance sampler on a
   # of example problems. Furthermore, AMCI allows not only for amortizing over
   datasets but also amortizing over target functions."
   -- 1907.08082@[<A HREF="https://arxiv.org/abs/1907.08082">arXiv</A>]['19].

%A A. M. Lovett
%A B. Sandlund
%T A simple algorithm for minimum cuts in near-linear time
%J arXiv
%M AUG
%D 2019
%K TR, c2019, c201x, c20xx, zz0919, maths, graph, minimum, min cut, minCut,
   algorithm
%X "We consider the minimum cut problem in undirected, weighted graphs. We give
   a simple alg. to find a minimum cut that 2-respects (cuts two edges of) a
   spanning tree T of a graph G. ... can be used in place of the complicated
   subrtn given in Karger's near-linear time min. cut alg. (JACM, 2000). We give
   a self-contained version of K's alg. with the new proc., which is easy to
   state & relatively simple to implement. It produces a min. cut on an m-edge,
   n-vertex graph in O(m log^3 n) time with high probability. This performance
   matches that achieved by K., thereby matching the current state of the art."
   -- 1908.11829@[<A HREF="https://arxiv.org/abs/1908.11829">arXiv</A>]['19].

%A T. Mieno
%A et al ...
%A M. Takeda
%T Minimal unique substrings and minimal absent words in a sliding window
%J arXiv
%M SEP
%D 2019
%K TR, c2019, c201x, c20xx, zz0919, short, minimal unique substring, MUS,
   minimal absent word, MAW, missing, nullomer, string, strings, sequence,
   algorithm, Crochemore
%X "A substring u of a string T is called a minimal unique substring (MUS) of
   T if u occurs exactly once in T and any proper substring of u occurs at least
   twice in T. A string w is called a minimal absent word (MAW) of T if w does
   not occur in T and any proper substring of w occurs in T. ... study computing
   MUSs and MAWs in a sliding window over a given string T. ... show how the set
   of MUSs can change in a sliding window over T, and present an O(n log s)-time
   and O(d)-space alg. to compute MUSs in a s.window of width d over T, where s
   is the maximum # of distinct chars. in every window. We then give tight upper
   & lower bounds on the maximum # of changes in the set of MAWs in a s.window
   over T. Our bounds improve on the prev.results in [Crochemore et al., 2017]."
   -- 1909.02804@[<A HREF="https://arxiv.org/abs/1909.02804">arXiv</A>]['19].
   (Note 'minimal' not 'minimum'.)
   [Also search for: unique substring].

%A S. Gharibian
%A O. Parekh
%T Almost optimal classical approximation algorithms for a quantum
   generalization of Max-Cut
%M SEP
%D 2019
%K TR, c2019, c201x, c20xx, zz0919, maths, graph, max cut, maxCut,
   approximation algorithm, quantum model, interaction, anti-ferromagnetic
%X "... study classical product state approx. algs. for a physically motivated
   quantum generalization of Max-Cut, known as the q. Heisenberg model. This
   model is notoriously difficult to solve exactly, even on bipartite g., in
   stark contrast to the classical setting of Max-Cut. ... show, for any
   interaction graph, how to classically and efficiently obtain approx. ratios
   0.649 (anti-ferromagnetic XY model) and 0.498 (anti-ferromagnetic Heisenberg
   XYZ model). These are almost optimal; we show that the best possible ratios
   achievable by a product state for these models is 2/3 and 1/2, respectively."
   -- 1909.08846@[<A HREF="https://arxiv.org/abs/1909.08846">arXiv</A>]['19].

%A Huanblao Zhu
%A W. Stuetzle
%T A simple and efficient method to compute a single linkage dendrogram
%J arXiv
%M NOV
%D 2019
%K TR, c2019, c201x, c201xx, zz1119, algorithm, single linkage, link,
   dendrogram, spanning tree, MST, Prim
%X "... A possible approach is to: (i) Form an edge weighted graph G over the
   data, with edge wts reflecting dissimilarities. (ii) Calc. the MST T of G.
   (iii) Break the longest edge of T thereby splitting it into subtrees TL, TR.
   (iv) Apply the splitting process recursively to the subtrees. This approach
   has the attractive feature that Prim's alg. for MST construction calculates
   distances as needed, & hence there is no need to ever store the inter-point
   distance matrix. The recursive partitioning alg. requires us to determine the
   vertices (& edges) of TL & TR. We show how this can be done easily &
   efficiently using information generated by Prim's alg. without any additional
   computational cost."
   -- 1911.00223@[<A HREF="https://arxiv.org/abs/1911.00223">arXiv</A>]['19].
   [Also search for: single link].

%A P. Bille
%A et al ...
%A E. Rotenberg
%T Space efficient construction of Lyndon arrays in linear time
%J arXiv
%M NOV
%D 2019
%K TR, c2019, c201x, c20xx, zz1119, Lyndon array, algorithm, construct
%X "We present the first linear time alg. to construct the 2n-bit version of
   the Lyndon array using only o(n) bits of working space. A simpler variant
   of this algorithm computes the plain (nlgn-bit) version of the Lyndon array
   using only o(1) words of additional working space. All previous algs. are
   either not linear, or use at least (n lg n) bits of additional working space.
   Also in practice, our new als. outperform the previous best ones by an
   order of magnitude, both in terms of time and space."
   -- 1911.03542@[<A HREF="https://arxiv.org/abs/1911.03542">arXiv</A>]['19].
   [Also search for: Lyndon word string].

%A M. Groff
%T The polynomial transform
%J arXiv
%M DEC
%D 2019
%K TR, c2019, c201x, c20xx, zz1219, polynomial transform, discrete, DFT,
   algorithm, finite field
%T "We explore a new form of DFT, which we call the Polynomial Transform. It
   functions over finite fields,or DFTs, of size m3 for m prime and of the form
   3l+1 for some natural l. It uses only O(m3) arithmetic operations on numbers
   of size log m, and takes total time N K log N, for N = Theta(m3 log m)."
   -- 1912.01155@[<A HREF="https://arxiv.org/abs/1912.01155">arXiv</A>]['19].

%A A. Conte
%A A. Marino
%A R. Grossi
%A T. Uno
%A L. Versari
%T Proximity search for maximal subgraph enumeration
%J arXiv
%M JAN
%D 2020
%K TR, c2019, c201x, c20xx, zz0120, graph, graphs, subgraph, subgraphs, maths,
   solution, algorithm, enumerate, enumeration, generate
%X "... subgraphs of an input graph that satisfy a given property & are maximal
   under inclusion. ... a seemingly novel technique, proximity search, to list
   these subgs. in polynomial delay each. These include Maximal Bipartite Subg.,
   Maximal k-Degenerate Subg. (for bounded k), Maximal Induced Chordal Subgs.,
   & Maximal Induced Trees. Using known techniques, such as reverse search, the
   space of sought solns induces an implicit directed graph called 'solution
   graph': however, the latter can give rise to exponential out-degree, thus
   preventing polynomial delay. The novelty of our alg. ... consists in
   providing a technique for generating a better soln graph ... While traversing
   the soln graph incur in space proportional to the # of solns to keep track of
   visited ones, we further propose a technique to induce a parent-child
   relationship & achieve polynomial space when suitable conditions are met."
   -- 1912.13446@[<A HREF="https://arxiv.org/abs/1912.13446">arXiv</A>]['10].
   [Also search for: enumerate subgraph].


%A R. Dondi
%A G. Mauri
%A I. Zoppis
%T Complexity issues of string to graph approximate matching
%J arXiv
%M JAN
%D 2020
%K TR, c2020, c202x, c20xx, zz0120, graph, maths, string, match, matching,
   approximate, problem
%X "The problem of matching a query string to a directed graph, whose vertices
   are labeled by strings ... we present results on the complexity of the
   approximate matching problem, where edit operations are symbol substitutions
   & are allowed only on the graph labels or both on the graph labels & the
   query string. We introduce a variant of the problem that asks whether there
   exists a path in a graph that represents a query string with any number of
   edit operations & we show that is is NPC ... . Moreover, we show
   that the variants of approximate string matching to graph we consider are not
   fixed-parameter tractable, when the parameter is the number of edit
   operations, even for graphs that have distance one from a DAG. The reduction
   for this latter result allows us to prove the inapproximability of the
   variant where edit operations can be applied both on the query string &
   on graph labels."
   -- 2001.01961@[<A HREF="https://arxiv.org/abs/2001.01961">arXiv</A>]['20].

%A T. Bingmann
%A P. Sanders
%A M. Schimek
%T Communication-efficient string sorting
%J arXiv
%M JAN
%D 2020
%K TR, c2020, c202x, c20xx, zz0220, sort, sorting, string, strings, algorithm,
   parallel, distributed, bandwidth, multiway merge, merging
%X "There has been surprisingly little work on algs. for sorting strings on
   distributed-memory parallel machines. We develop efficient algs. for this
   problem based on the multi-way merging principle. These algs. inspect only
   chars. that are needed to determine the sorting order. [&] communication
   volume is reduced by also communicating (roughly) only those chars. & by
   communicating repetitions of the same prefixes only once. Experiments on up
   to 1280 cores reveal that these algs. are often more than five times faster
   than prev. algs."
   -- 2001.08516@[<A HREF="https://arxiv.org/abs/2001.08516">arXiv</A>]['20].

%A Duc Hung Pham
%A K. V. Palem
%A M. V. Panduranga Rao
%T A polynomial time parallel algorithm for graph isomorphism using a
   quasipolynomial number of processors
%J arXiv
%M FEB
%D 2020
%K TR, c2020, c202x, c20xx, zz0220, graph, graphs, isomorphism, maths, parallel,
   algorithm, color refinement, WL, quasipolynomial, processor, Babai
%X "... Babai made a breakthrough in 2015 ... Based on Babai's alg., we prove
   that GI can further be solved by a parallel alg. that runs in polynomial time
   using a quasipolynomial # of processors. We achieve that result by
   identifying the bottlenecks in B's algs. & parallelizing them. In particular,
   we prove that color refinement can be computed in parallel logarithmic time
   using a polynomial # of proc., & the k-dimensional WL refinement can be
   computed in parallel polynomial time using a quasipolynomial # of ps.. Our
   work suggests that Graph Isomorphism & GI-complete problems can be computed
   efficiently in a parallel computer, & provides insights on speeding up
   parallel GI programs in practice."
   -- 2002.04638@[<A HREF="https://arxiv.org/abs/2002.04638">arXiv</A>]['20].
   [Also search for: maths graph isomorphism].

%A Y. Masumura
%A T. Oki
%A Y. Yamaguchi
%T Dynamic programming approach to the generalized minimum Manhattan network
   problem
%J arXiv
%M APR
%D 2020
%K TR, c2020, c202x, c20xx, zz0420, algorithm, DPA, maths, graph,
   generalized minimum Manhattan network, GMMN
%X "... (GMMN): given a set P of pairs of two pts in the Euclidean plane R^2,
    ... find a minimum-length geometric n/wk which consists of axis-aligned
   segments & contains a shortest path in the L1 metric (a so-called Manhattan
   path) for each pair in P. ... generalizes several NP-hard n/wk design
   problems that admit constant-factor approxn algs., such as the rectilinear
   Steiner arborescence (RSA) problem, & it is open whether so does the GMMN
   problem. ... Schnizler (2015) focused on the intersection graphs of the
   rectangles defined by the pairs in P, & gave a polynomial-time DPA for the
   GMMN problem whose input is restricted s.t. both the treewidth & the maximum
   degree of its intersection g. are bounded by consts. [we] attempt to remove
   the degree bound, we provide a polynomial-time alg. for the star case, &
   extend it to the general tree case based on an improved DP approach."
   -- 2004.11166@[<A HREF="https://arxiv.org/abs/2004.11166">arXiv</A>]['20].

%A S. L. S. Mergen
%T UnfairDuelMerge: Merging with even fewer moves
%J COMPJ
%V 63
%N 5
%P 701-708
%M MAY
%D 2020
%K jrnl, COMPJ, c2020, c202x, c20xx, zz0520, in situ, insitu, merge, merging,
   UnfairDuelMerge, Unfair Duel Merge, DuelMerge
%X "... recent development in in-place merging is a minimum storage alg.
   (DuelMerge) that requires half the # of moves in avg., when compared to other
   partition-based algs.. ... achieved by limiting the exchange to blocks with
   equal sizes, & using a particularly suited exchange method. The alg. proposed
   [here] (UnfairDuelMerge) reduces the # of moves even further, by limiting the
   exchange to blocks where the left side is one elt larger than the right side,
   & using the floating hole technique to perform the exchange. As its
   predecessor, the alg. is stable, in-place & the merge is asymptotically
   performed with a O(n log_n n) [???] runtime. A formal description ... is
   provided, as well as an analysis of stability, memory cost & time complexity.
   Experimental results show that the proposed alg. outperforms other
   partition-based solutions when applied directly to merge ordered seqs. & when
   used within MergeSort."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxz015">doi:10.1093/comjnl/bxz015</A>]['20].
   [Also search for: insitu merge].

%A G. E. Pibiri
%A R. Venturini
%T Practical trade-offs for the prefix-sum problem
%J arXiv
%M JUN
%D 2020
%K TR, c2020, c202x, c20xx, zz0620, prefix sum problem, dataStructure, DS
%X "Given an integer array A, the prefix-sum problem is to answer sum(i) queries
   that return the sum of the elts in A[0..i], knowing that the ints in A can be
   changed. It is a classic problem in data structure design with a wide range
   of applications in computing from coding to DBs. ... propose & compare
   several & practical solns to this problem, showing that new trade-offs
   between the performance of queries & updates can be achieved on modern h/w."
   -- 2006.14552@[<A HREF="https://arxiv.org/abs/2006.14552">arXiv</A>]['20].

%A N. Cotumaccio
%A N. Prezza
%T On indexing and compressing finite automata
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0720, FSA, FSM, DFA, DFSA, NFA, NFSA, automaton,
   machine, index, indexing, compress, BWT
%X "An index for a finite automaton is a powerful [DS] that supports locating
   paths labeled with a query pattern, thus solving pattern matching on the
   underlying regular language. ... we solve the long-standing problem of
   indexing arb. fin.automata. Our soln consists in finding a partial
   co-lexicographic order of the states & proving, as in the total order case,
   that states reached by a given string form one interval on the partial order,
   thus enabling indexing. ... lwb stating that such an interval requires O(p)
   words to be represented, p being the order's width ... show that p determines
   the complexity of several fundamental problems on fin.automata: (i) Letting
   sigma be the alphabet size, we provide an encoding for NFAs using
   ceil(log sigma)+2ceil(log p)+2 bits per transition & a smaller encoding for
   DFAs ... generalizing the Burrows-Wheeler transform to arbitrary automata.
   ..."
   -- 2007.07718@[<A HREF="https://arxiv.org/abs/2007.07718">arXiv</A>]['20].

%A L. Kowalik
%A K. Majewski
%T The asymmetric travelling salesman problem in sparse digraphs
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0720, TSP, ATSP, maths, graph, directed, graphs,
   directed Hamiltonicity, algorithm
%X "Asymmetric Travelling Salesman Problem (ATSP) and its special case Directed
   Hamiltonicity are among the most fundamental problems in CS. The DPA running
   in time O^*(2^n) developed almost 60 years ago by Bellman, Held & Karp, is
   still the state of the art for both of these problems. ... We present two new
   det. algs.: the first running in time O(2^{0.441(d-1)n}) & polynomial space,
   & the second in exponential space with running time of O^*(t(d)^{n/2}) for
   a function t(d) <= d."
   -- 2007.12120@[<A HREF="https://arxiv.org/abs/2007.12120">arXiv</A>]['20].
   [Also search for: travelling salesman problem].
   (Also see TSP@[<A HREF="https://en.wikipedia.org/wiki/Held%E2%80%93Karp_algorithm">wikip</A>]['20].)

%A G. Beniamini
%A N. Cheng
%A O. Holtz
%A E. Karstadt
%A O. Schwartz
%T Sparsifying the operators of fast matrix multiplication algorithms
%J arXiv
%M AUG
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, matrix multiplication algorithm
%X "... Many sub-cubic algs. have large leading coeffs., rendering them
   impractical. Karstadt & Schwartz (SPAA17, JACM20) demonstrated how to reduce
   these coeffs. by sparsifying an alg's bilinear operator. Unfortunately, the
   ... finding optimal spars. is NP-Hard. We obtain three new methods to this
   end ... These methods have an exponential worst case running time, but run
   fast in practice & improve the performance of many fast m.mult. algs.. Two of
   [them] are guaranteed to produce leading coeffs. that, under some assumptions
   are optimal."
   -- 2008.03759@[<A HREF="https://arxiv.org/abs/2008.03759">arXiv</A>]['20].
   [Also search for: fast matrix multiplication algorithm].

%A D. Harvey
%T An exponent one-fifth algorithm for deterministic integer factorisation
%J arXiv
%M OCT
%D 2020
%K TR, c2020, c202x, c20xx, zz1020, prime number, factorisation, factorization,
   factoring, composite, integer, algorithm
%X "Hittmeir recently presented a deterministic alg. that provably computes the
   prime factorisation of a +ve integer N in N^{2/9+o(1)} bit operations. Prior
   to this breakthrough, the best known complexity bound for this problem was
   N^{1/4+o(1)}, a result going back to the 1970s. ... we push H's techniques
   further, obtaining a rigorous, deterministic factoring alg. with complexity
   N^{1/5+o(1)}."
   -- 2010.05450@[<A HREF="https://arxiv.org/abs/2010.05450">arXiv</A>]['20].
   [Also search for: integer factorisation].

%A Yuansi Chen
%T An almost constant lower bound of the isoperimetric coefficient in the
   KLS conjecture
%J arXiv
%M NOV
%D 2020
%K TR, c2020, c202x, c20xx, zz0321, Burgain, KLS conjecture, convex,
   high dimension, geometry
%T "We prove an almost constant lower bound of the isoperimetric coefficient in
   the KLS conjecture. The lwb has the dimension dependency d-od(1). When the
   dimension is large enough, our lwb is tighter than the prev. best bound which
   has the dimension dependency d-1/4. Improving the current best lwb of the
   isoperimetric coefficient in the KLS conjecture has many implications, inc.
   improvements of the current best bounds in Bourgain's slicing conjecture & in
   the thin-shell conjecture, better concentration inequalities for Lipschitz
   fns of log-concave measures and better mixing time bounds for MCMC sampling
   algs. on log-concave measures."
   -- 2011.13661@[<A HREF="https://arxiv.org/abs/2011.13661">arXiv</A>]['21].
   (Also see news@[<A HREF="https://www.quantamagazine.org/statistics-postdoc-tames-decades-old-geometry-problem-20210301/">www</A>]['21].)

%A R. C. Hillyard
%A Y. Liaozheng
%A K. R. Sai Vineeth
%T Huskysort
%J arXiv
%M DEC
%D 2020
%K TR, c2020, c202x, c20xx, zz1220, sort, sorting, algorithm, access, accesses,
   Huskysort, Timsort
%X "... a more appropriate yardstick for the performance of sorting algs. is
   based on the total # of array accesses that are required (the 'work'). For a
   sort that is based on divide-&-conquer (inc. iterative variations on that
   theme), we can divide the work into linear, i.e. O(N), work & linearithmic,
   i.e. O(N log N), work. ... may be able to reduce the total # of array
   accesses ... This paper describes an approach to sorting which reduces the #
   of expensive comparisons in the linearithmic phase as much as possible by
   substituting inexpensive comparisons. In Java, the two system sorts are
   dual-pivot quicksort (for primitives) & Timsort for objects. We demonstrate
   that a combination of these two algs. can run sig. faster than either alg.
   alone for the types of objects which are expensive to compare. We call this
   improved sorting alg. Huskysort."
   -- 2012.00866@[<A HREF="https://arxiv.org/abs/2012.00866">arXiv</A>]['20].
   [Also search for: sort algorithm].

%A D. Neuen
%T Isomorphism testing for graphs excluding small topological subgraphs
%J arXiv
%D DEC
%D 2020
%K TR, c2020, c202x, c20xx, zz1220, maths, graph, isomorphism
%X "We give an isomorphism test that runs in time 'n^polylog(h)' on all n-vertex
   graphs excluding some h-vertex vertex graph as a topological subg.. Previous
   results state that isomorphism for such graphs can be tested in time
   'n^polylog(n)' (Babai, STOC 2016) & 'n^f(h)' for some fn f (Grohe & Marx,
   SIAM J. Comp., 2015).  Our result also unifies & extends prev. isomorphism
   tests for graphs of maximum degree d running in time 'n^polylog(d)'
   (FOCS 2018) & for graphs of Hadwiger # h running in time 'n^polylog(h)'
   (FOCS 2020).
   -- 2011.14730@[<A HREF="https://arxiv.org/abs/2011.14730">arXiv</A>]['20].
   [Also search for: graph isomorphism].

%A D. Lemire
%A C. Bartlett
%A O. Kaser
%A Z. Merali
%T Integer division by constants: optimal bounds
%J arXiv
%M DEC
%D 2020
%K TR, c2020, c202x, c20xx, zz1220, fast, integer, division, divide, arithmetic,
   div, constant, algorithm
%X "... Optimizing compilers accelerate software by replacing the division of n
   by d with the div'n of c*n (or c*n+c) by m for convenient integers c & m
   chosen so that they approx. the reciprocal: c/m ~= 1/d. Such techniques are
   esp. advantageous when m is chosen to be a power of two & when d is a const.
   so that c & m can be precomputed. The literature contains many bounds on the
   distance between c/m & the divisor d. Some of these bounds are optimally
   tight, while others are not. Using accessible mathematics, we present opt.
   tight bounds for quotient & remainder computations."
   -- 2012.12369@[<A HREF="https://arxiv.org/abs/2012.12369">arXiv</A>]['20].
   [Also search for: integer arithmetic].

%A B. Dudek
%A P. Gawrychowski
%A K. Pokorski
%T Strictly in-place algorithms for permuting and inverting permutations
%J arXiv
%M JAN
%D 2021
%K TR, c2021, c202x, c20xx, zz0121, permutation, algorithm, in situ, inSitu,
   inPlace, space, storage, Fich, Guspiel
%X "... problem of permuting an array of length n according to a given perm'n
   in place, that is, using only a small # of bits of extra storage ... Our
   first contribution is a strictly in-place generalisation of the method of
   Fich et al. that works in O_e(n^{1+e}) time, for any e>0. Then, we build on
   this generalisation to obtain a strictly in-place alg. for inverting a given
   perm. on n elts working in the same complexity. ..."
   -- 2101.03978@[<A HREF="https://arxiv.org/abs/2101.03978">arXiv</A>]['21].

%A J. Morris
%A Fang Song
%T Simple vertex coloring algorithms
%J arXiv
%M FEB
%D 2021
%K TR, c2021, c202x, c20xx, zz0321, maths, graph, vertex colouring algorithm
%X "Given a graph G with n vertices and maximum degree D, it is known that G
   admits a vertex coloring with D+1 colors s.t. no edge of G is monochromatic.
   This can be seen constructively by a simple greedy alg., which runs in time
   O(n.D). Very recently, a seq. of results ... we give a simple alg. for
   (1+eps)D-coloring. ..."
   -- 2102.07089@[<A HREF="https://arxiv.org/abs/2102.07089">arXiv</A>]['21].

%A V. Reis
%A T. Rothvoss
%T The subspace flatness conjecture and faster integer programming
%I arXiv
%M MAR
%D 2023
%K TR, c2023, c202x, x20xx, zz0924, linear, fast, integer programming,
   algorithm, reverse Minkowski, Dadush, maths
%O IEEE FOCS 2023, doi:10.1109/FOCS57990.2023.00060
%X "... & the Subspace Flatness Conjecture by Dadush (2012) ... We settle this
   conjecture up to a const. in the exponent ... obtain a (log(2n))^O(n)-time
   randomized alg. to solve integer programs in n variables. Another implication
   of our main result is a near-optimal flatness constant of O(n log^3(2n))."
   -- [<A HREF="https://arxiv.org/abs/2303.14605">arxiv:2303.14605</A>]['24].
   (Also see <A HREF="https://dl.acm.org/doi/10.1145/3677384">www</A>]['24].)

%A S. Gorantala
%A et al ...
%A B. Gipson
%T A general purpose transpiler for fully homomorphic encryption
%x arXiv
%M JUN
%D 2021
%K TR, c2021, c202x, c20xx, zz0621, homomorphic encryption, data,
   FHE, XLS SDK, TFHE
%X "... we present a fully homomorphic encryption transpiler that allows
   developers to convert high-level code (e.g., C++) that works on unencrypted
   data into high-level code that operates on encrypted data. Thus, our
   transpiler makes transformations possible on encrypted data. [It] builds on
   Google's open-source XLS SDK & uses an off-the-shelf FHE library, TFHE
   to perform low-level FHE operations. ..."
   -- 2106.07893@[<A HREF="https://arxiv.org/abs/2106.07893">arXiv</A>]['21].

%A N. Kamiyama
%T The envy-free matching problem with pairwise preferences
%J IPL
%V 172
%P ?-?
%M DEC
%D 2021
%K jrnl, IPL, c2021, c202x, c20xx, zz0721, match, envy free matching, EFM,
   problem, preference, 106148
%X "... consider the situation where each agent has a pref. over a subset of
   items & exactly one item is matched to each agent. The envy-freeness of a
   matching guarantees that no one has envy for the others. We consider an
   envy-free matching in the sit'n where each agent has a pref. that is defined
   based on comparisons of any two acceptable items. We prove that in this sit'n
   the problem of checking the existence of an EFM is generally hard."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2021.106158">doi:10.1016/j.ipl.2021.106158</A>]['21].
   [Also search for: matching preference].

%A C. Brosse
%A V. Limouzy
%A A. Mary
%T Polynomial delay algorithm for minimal chordal completions
%J arXiv
%M JUL
%D 2021
%K TR, c2021, c202x, c20xx, zz0721, maths, graph, tree, decomposition, minimal,
   chordal completion, Carmeli
%X "... the problem of listing all the minimal chordal completions of a g..
   ... Carmeli et al proved that all minimal c.completions or equiv. all proper
   tree decompositions of a g. can be listed in incremental polynomial time ...
   [we] provid[e] a polynomial delay alg. to solve this problem which, moreover,
   uses polynomial space. Our alg. relies on Proximity Search ... we introduce a
   new general method called canonical path reconstruction to design polynomial
   delay & polynomial space algs. based on proximity search."
   -- 2107.05972@[<A HREf="https://arxiv.org/abs/2107.05972">arXiv</A>]['21].

%A M. A. Bender
%A B. C. Kuszmaul
%A W. Kuszmaul
%T Linear probing revisited: Tombstones mark the death of primary clustering
%J arXiv
%M JUK
%D 2021
%O ? FOCS, Feb 2022 ?
%K TR, c2021, c202x, c20xx, zz0122, linear hashing, hash table, data structure,
   DS, dataStucture, probing, tombstone, insertion, deletion
%X "... widely believed & taught, however, that linear probing should
   never be used at high load factors; this is because primary-clustering
   effects cause insertions at load factor 1â1/x to take expected time
   Theta(x^2) (rather than the ideal Theta(x)). The dangers of primary
   clustering, first discovered by Knuth in 1963, have been taught to
   generations of comp.scientists, & have influenced the design of some of many
   widely used hash tables. We show that primary clustering is not a foregone
   conclusion. We demonstrate that small design decisions in how delns are
   implemented have dramatic effects on the asymptotic performance of insertions
   so that, even if a hash table operates continuously at a load factor
   1âTheta(1/x), the expected amortized cost per operation is ~O(x). ..."
   -- 2107.01250@[<A HREF="https://arxiv.org/abs/2107.01250">arXiv</A>]['22].

%A L. Gourves
%A A. Harutyunyan
%A M. Lampis
%A N. Melissinos
%T Filling crosswords is very hard
%J arXiv
%M SEP
%D 2021
%K TR, c2021, c202x, c20xx, zz0921, crossword, puzzle, filling, algorithm
%X "We revisit a classical crossword filling puzzle which already appeared in
   Garey & Jonhson's book. ... given a grid with n vertical & horizontal slots
   & a dictionary with m words & are asked to place words from the d. in the
   slots so that shared cells are consistent. We attempt to pinpoint the source
   of intractability of this problem by taking into account the structure of the
   grid graph, which contains a vertex for each slot & an edge if two slots
   intersect. Our main approach is to consider the case where this graph has a
   tree-like structure. Unfortunately, if we impose the common rule that words
   cannot be reused, we show that the problem remains NP-hard even under very
   severe structural restrictions. The problem becomes slightly more tractable
   if word reuse is allowed, as we obtain an m^{tw} alg. in this case, where tw
   is the treewidth of the grid graph. However, even in this case, we show that
   our alg. cannot be improved. ..."
   -- 2109.11203@[<A HREF="https://arxiv.org/abs/2109.11203">arXiv</A>]['21].
   [Also search for: crossword].

%A A. Bjorklund
%A T. Husfeldt
%A P. Kaski
%T The shortest even cycle problem is tractable
%J arXiv
%M NOV
%D 2021
%K TR, c2021, c202x, c20xx, zz1112, maths, graph, even cycle problem, algorithm
%X "Given a directed graph, we show how to efficiently find a shortest
   (directed, simple) cycle on an even # of vertices. As far as we know, no
   polynomial-time alg. was previously known for this problem. In fact, finding
   any even cycle in a directed g. in polynomial time was open for more than two
   decades until Robertson, Seymour, & Thomas (... 1999) &, indep., McCuaig
   (... 2004 ...) gave an efficiently testable structural characterisation of
   even-cycle-free directed g.. ..."
   -- 2111.02992@[<A HREF="https://arxiv.org/abs/2111.02992">arXiv</A>]['21].

%A C. Mathieu
%A H. Zhou
%T A simple algorithm for graph reconstruction
%J arXiv
%M DEC
%D 2021
%K TR, c2021, c202x, c20xx, zz1221, graph reconstruction algorithm, maths,
   distance query, queries, distances2graph
%X "How efficiently can we find an unknown graph using distance queries between
   its vertices? We assume that the unknown g. is connected, unweighted, & has
   bounded degree. The goal is to find every edge in the g.. ... admits a
   reconstruction alg. based on multi-phase Voronoi-cell decomposition & using
   O~(n^{3/2}) dist. queries. ... we analyze a simple reconstruction alg.. We
   show that, on random Delta-regular gs., [it] uses O~(n) dist.queries. As
   by-products, we can reconstruct those gs. using O(log^2(n)) queries to an
   all-distances oracle or O~(n) queries to a betweenness oracle, & we bound the
   metric dim'n of those gs. by log^2(n).  Our reconstruction alg. has a
   v.simple structure, & is highly parallelizable. On general gs. of bounded
   degree, [it] has subquadratic query complexity."
   -- 2112.04549@[<A HREF="https://arxiv.org/abs/2112.04549">arXiv</A>]['21].

%A Sang Won Bae
%T Faster counting empty convex polygons in a planar point set
%J IPL
%V 175
%P #106221
%M APR
%D 2022
%K IPL, jrnl, c2021, c202x, c20xx, zz1221, algorithm, count, counting, polygon,
   empty, point set, sets, 2D
%X "... present two algs: one counts the # of all convex empty polygons in time
   O(T) & the other counts the # of convex empty m-gons for all 3 <= m <= k in
   time O(kT), where T denotes the # of empty triangles in S. Note that T varies
   from Omega(n^2) to O(n^3), while its expected value is known to be Theta(n^2)
   when n input pts are chosen uniformly & independently at random from a
   convex, bounded body."  (online Dec 2O21.)
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2021.106221">doi:10.1016/j.ipl.2021.106221</A>]['21].

%A L. Fortnow
%T Fifty years of P vs. NP and the possibility of the impossible
%J CACM
%V 65
%N 1
%P ?-?
%M JAN
%D 2022
%K jrnl, CACM, c2022, c202x, c20xx, zz1221, algorithm, complexity, NP, NPC,
   PNPproblem, news, views, intro, survey, hard, problems, RSA
%X "On May 4, 1971, computer scientist/mathematician Steve Cook introduced the
   P vs. NP problem to the world in his paper, 'The Complexity of Theorem
   Proving Procedures.' More than 50 years later, the world is still trying to
   solve it. In fact, I addressed the subject 12 y. ago in a Comm. article,
   'The Status of the P versus NP Problem.' The P vs. NP problem, & the theory
   behind it, has not changed dramatically since that 2009 article, but the
   world of computing most certainly has. ... I have chosen to view advances in
   computing, optimization, & m.learning through a P vs. NP lens. ..."
   -- [<A HREF="https://doi.org/10.1145/3460351">doi:10.1145/3460351</A>]['21], online 12/'21, via ajm.
   [Also search for: PNPproblem]  and  [also search for: Cook NPC].

%A A. Aho
%A J. Ullman
%T Abstractions, their algorithms, and their compilers
%J CACM
%V 65
%N 2
%P 76-91
%M FEB
%D 2022
%K jrnl, CACM, c2022, c202x, c20xx, zz0222, algorithms, TuringAward
%X "Computational Thinking, which centers around devising abstractions for
   problems so they can be solved with computational steps and efficient algs.,
   is a concept that serves not only comp. sci. (CS) but progressively more of
   science and everyday life. ..."
   -- [<A HREF="https://doi.org/10.1145/3490685">doi:doi.org/10.1145/3490685</A>]['22].

%A R. Hundt
%T Quantum Computing for Programmers
%I CUP
%P 350
%M MAR
%D 2022
%K book, text, c2022, c202x, c20xx, zz0222, quantum computing, programming,
   algorithm
%X 1st ed 2022; euro61; uk us isbn:1009098179; uk us isbn13:9781009098175.
   "... Over 25 fundamental algs are explained with full math derivations &
   classical code for simulation, using an open-source code base ... in Python &
   C++. After presenting the basics of q.computing ... focuses on algs & the
   infrastructure to simulate them efficiently, beginning with q.teleportation,
   superdense coding, & Deutsch-Jozsa.  Coverage of advanced algs. includes the
   q.supremacy experiment, q. Fourier transform, phase est., Shor's alg.,
   Grover's alg. with derivatives, q.random walks, & the Solovay-Kitaev alg. for
   gate approxn. ..."

%A D. Harvey
%A J. van der Hoeven
%T Polynomial multiplication over finite fields in time O(n log n)
%J JACM
%V 69
%N 2
%P #12 pp.1-40
%M APR
%D 2022
%K jrnl, JACM, c2022, c202x, c20xx, zz0322, fast, polynomial, integer,
   multiplication, algorithm, finite field
%X "Assuming a widely believed hyp. concerning the least prime in an arith.
   progression, we show that polynomials of degree less than n over a finite
   field F_q with q elts can be multiplied in time O(n log q log(n log q))
   uniformly in q. Under the same hyp., we show how to multiply two n-bit ints.
   in time O(n log n); this alg. is somewhat simpler than the unconditional
   alg. from the companion paper. Our results hold in the Turing m/c model with
   a finite # of tapes."
   -- [<A HREF="https://doi.org/10.1145/3505584">doi:10.1145/3505584</A>]['22] (online MAR 2022).
   [Also search for: fast integer multiplication].

%A K. Fox
%A Xinyi Li
%T Approximating the geometric edit distance
%J Algorithmica
%V 84
%P 2395-2413
%M APR
%D 2022
%K jrnl c2022, c202x, c20xx, zz0822, geometric edit distance, GED,
   approximation, algorithm, 3D, point, vector, points, sequence
%X "... we describe the 1st strictly sublinear approx. near-linear time alg.
   for computing the GED of 2 pt seqs in const. dimensional Euclidean space.
   Specifically, we present a randomized O(n log^2 n) time O(sqrt(n))-approx
   alg.. Then, we generalize our result to give a randomized  alpha-approx.
   alg. for any alpha in [sqrt(n), sqrt(n/log n)), running in time
   O(n^2/(a^2 log n)). Both algs. are Monte Carlo & return approximately optimal
   solns with high probability."
   -- [<A HREF="https://doi.org/10.1007/s00453-022-00966-4">doi:10.1007/s00453-022-00966-4</A>]['22].
   [Also search for: geometric edit distance].

%A Li Chen
%A et al ...
%A S. Sachdeva
%T Maximum flow and minimum-cost flow in almost-linear time
%J arXiv
%M APR
%D 2022
%K TR, c2022, c202x, c20xx, zz1022, maths, graph, maximum flow, algorithm,
   max, min cost, network
%X "... alg. that computes exact maximum flows & minimum-cost flows on directed
   graphs with m edges & polynomially bounded integral demands, costs, &
   capacities in m^{1+o(1)} time. ... builds the flow through a seq. of
   m^{1+o(1)} approx. undirected minimum-ratio cycles, each of which is computed
   & processed in amortized m^{o(1)} time using a new dynamic graph data struct.
   Our framework extends to algs. running in m^{1+o(1)} time for computing flows
   that minimize general edge-separable convex fns to high accuracy. This gives
   almost-linear time algs. for several problems including entropy-regularized
   optimal transport, matrix scaling, p-norm flows, & p-norm isotonic regression
   on arbitrary directed acyclic graphs."
   -- 2203.00671@[<A HREF="https://arxiv.org/abs/2203.00671">arXiv</A>]['22].
   [Also search for: graph maximum flow].

%A Takehiro Ito
%A et al
%T Reforming an envy-free matching
%J arXiv
%M JUL
%D 2022
%K TR, c2022, c202x, c20xx, zz0722, envy free matching, match
%X "... envy-free matching when each agent is assigned a single item. Given an
   envy-free m., we consider an op. to exchange the item of an agent with an
   unassigned item preferred by the agent that results in another envy-free m..
   We repeat this op. as long as we can. We prove that the resulting envy-free
   matching is uniquely determined up to the choice of an initial envy-free m.,
   & can be found in polynomial time. We call the resulting matching a reformist
   envy-free m., & then we study a shortest seq. to obtain the reformist
   envy-free m. from an initial envy-free m.. We prove that a shortest seq. is
   computationally hard to obtain even when each agent accepts at most four
   items & each item is accepted by at most three agents. On the other hand, we
   give polynomial-time algs. when each agent accepts at most three items or
   each item is accepted by at most two agents...."
   -- 2207.02641@[<A HREF="https://arxiv.org/abs/2207.02641">arXiv</A>]['22].
   [Also search for: envy free matching].


%A J. Wassenberg
%A M. Blacher
%A J. Giesen
%A P. Sanders
%T Vectorized and performance-portable quicksort
%J SPE
%V ?
%m AUG
%d 2022
%K jrnl, SPE, c2022, c202x, c20xx, zz0922, sort, sorting, quicksort, algorithm,
   GPU, parallel, vectorized, vectorised, fast, vqsort, ips4o, SVE, RISCV
%X "Recent works showed that implementations of quicksort using vector CPU
   inst'ns can outperform the non-vectorized algs. ... [But] these impl'ns are
   typically single-threaded, implemented for a particular inst'n set, &
   restricted to a small set of key types. We lift these three restrictions: our
   proposed vqsort alg. integrates into the state-of-the-art parallel sorter
   ips^4o, with a geometric mean speedup of 1.59. ... works on 7 inst'n sets
   (inc. SVE & RISC-V V) across 4 platforms. It also supports floating-pt &
   16-128 bit integer keys. To the best of our knowledge, this is the fastest
   sort for large arrays of non-tuple keys on CPUs, up to 20 times as fast as
   the sorting algs. implemented in std libraries. ... focuses on the practical
   engineering aspects enabling the speed & portability ... [&] we introduce
   compact & transpose-free sorting nwks for in-register sorting of small arrays
   & a vector-friendly pivot sampling strategy that is robust against
   adversarial input."
   -- [<A HREF="https://doi.org/10.1002/spe.3142">doi:10.1002/spe.3142</A>]['22], online Aug 2022.
   [Also search for: sorting parallel].

&A A. Fawzi
%A et al
%T Discovering faster matrix multiplication algorithms with
   reinforcement learning
%J Nature
%V 610
%K OCT
%D 2022
%K c2022, c202x, c20xx, zz1022, fast, small, 3x3, 4x4, matrix multiplication,
   algorithm, DeepMind, alphazero, alphatensor, ANN, NN
%X "... we report a deep reinforcement learning approach based on AlphaZero for
   discovering efficient & provably correct algs. for the mult'n of arbitrary
   matrices. ... AlphaTensor, is trained to play a single-player game where the
   objective is finding tensor decompositions within a finite factor space. ...
   discovered algs. that outperform the state-of-the-art complexity for many
   matrix sizes. Particularly relevant is the case of 4x4 matrices in a f.f,
   where [it] improves on Strassen's two-level algorithm ..."
   -- [<A HREF="https://www.nature.com/articles/s41586-022-05172-4">doi:s41586-022-05172-4</A>]['22].
   (Interesting certainly, but open to being overhyped.
   Also see MM@[<A HREF="https://en.wikipedia.org/wiki/Matrix_multiplication">wikip</A>]['22].)
   [Also search for: fast matrix algorithm multiplication].

%A M. Kauers
%A J. Moosbauer
%T The FBHHRBNRSSSHK-algorithm for multiplication in Z_2^(5x5) is still not the
   end of the story
%J arXiv
%M OCT
%D 2022
%K TR, c2022, c202x, c20xx, zz1122, small, fast matrix multiplication,
   algorithm, DeepMind, alphatensor, humans
%X "In response to a recent Nature article which announced an alg. for mult.
   5x5-matrices over Z_2 with only 96 mults., two fewer than the prev. record,
   we present an alg. that does the job with only 95 mults..
   -- 2210.04045@[<A HREF="https://arxiv.org/abs/2210.04045">arXiv</A>]['22].
   (Also see [<A HREF="https://analyticsindiamag.com/meet-the-researchers-who-beat-deepmind-at-matrix-multiplication/">www</A>]['22].)
   [Also search for: fast matrix multiplication algorithm].

%A A. Bernstein
%A D. Nanongkai
%A C. Wulff-Nilsen
%T Negative-weight single-source shortest paths in near-linear time
%J arXiv
%M OCT
%D 2022
%K TR, c2022, c202x, c20xx, zz0123, negative weight, shortest path, graph,
   algorithm, maths, shortest path, SSSP, negative weight, Fakcharoenphol, Rao
%X "... randomized alg. that computes single-source shortest paths (SSSP) in
   ~O(m log^8(n) log W) time when edge wts are integral & can be negative. ...
   -- 2203.03456@[<A HREF="https://arxiv.org/abs/2203.03456">arXiv</A>]['23].
   (Also see [<A HREF="https://www.quantamagazine.org/finally-a-fast-algorithm-for-shortest-paths-on-negative-graphs-20230118">q'mag</A>][18/1/'23] and
   also see, 'Historic algorithms help unlock shortest-path problem
   Breakthrough', CACM, SEP 2023 [<A HREF="https://doi.org/10.1145/3607866">doi:10.1145/3607866</A>]['23].)
   [Also search for: SSSP algorithm].

%A V. Skala
%T Summation problem revisited -- more robust computation
%J arXiv
%M NOV
%D 2011
%O Recent Advances in Comp. Sci. Conf, 2013
%K conf, c2013, c201x, c20xx, zz1122, sum, summing, underflow, numerical, ESSA
%X "... even simple summation of values is not precise due to the floating pt
   representation use. ... presents a practical alg. for summation of values
   convenient for medium & large data sets. ... simple, easy to implement. Its
   computational complexity is O(N) [v.] the Exact Sign Summation Alg. (ESSA)
   approach with O(N^2) run-time complexity. ... esp. convenient for cases when
   exponent data differ sig. & many small values are summed with higher values."
   -- 2211.04402@[<a HREF="https://arxiv.org/abs/2211.04402">arXiv</A>]['22].

%A R. Anton
%A N. Mihalache
%A F. Vigneron
%T Fast evaluation of real and complex polynomials
%J arXiv
%M NOV
%D 2022
%K TR, c2022, c202x, c20xx, zz1122, evaluate, polynomial, algorithm.
   Horner's rule, numerical
%X "We propose an alg. for quickly evaluating polynomials. It pre-conditions a
   complex poly. P of degree d in time O(d log d), with a low multiplicative
   const. ... Subsequent evaluations of P computed with a fixed precision of p
   bits are performed in avg arithmetic complexity O(sqrt(d(p + log d)) & memory
   O(dp). ... alg. performs asymptotically as O(sqrt(d log d)) per evaln ..."
   -- 2211.06320@[<A HREF="https://arxiv.org/abs/2211.06320">arXiv</A>]['22].
   (There's a surprise.)

%A J. Townsend
%A J.-W. van de Meent
%T Verified reversible programming for verified lossless compression
%J arXiv
%M NOV
%D 2022
%K TR, c2022, c202x, c20xx, zz1122, reversible programming, program, compress,
   Flipper, Agda
%X "Lossless compression implementations typically contain two programs, an
   encoder & a decoder, which are required to be inverse to one another. We
   observe that a sig. class of compression methods, based on asymmetric
   numeral systems (ANS), have shared structure between the encoder & decoder
   -- the decoder program is the 'reverse' of the encoder program -- allowing
   both to be simultaneously specified by a single, reversible fn. ..."
   -- 2211.09676@[<A HREF="https://arxiv.org/abs/2211.09676">arXiv</A>]['22].
   (Also see flipper@[<A HREF="https://github.com/j-towns/flipper">g'thub</A>]['22].)

%A F. Le Gall
%A S.Seddighin
%T Quantum meets fine-grained complexity: Sublinear time quantum algorithms for
   string problems
%J Algorithmica
%M DEC
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1222, quantum computing, algorithm, strings,
   LeGall, LCS, LCSS, LPS, Ulam distance, LASS
%X "Longest common substring (LCS), longest palindrome substring (LPS), & Ulam
   distance (UL) are 3 fundamental string problems that can be classically
   solved in near linear time. ... we present sublinear time q.algs. for these
   problems along with q.lwbs. ... shed light on a v. surprising fact: Although
   the classic solns for LCS & LPS are almost identical (via suffix trees),
   their q. computational complexities are different. While we give an exact
   ~O(sqrt n) time alg. for LPS, we prove that LCS needs at least time
   ~Omega(n^{2/3}) even for 0/1 strings."
   -- [<A HREF="https://doi.org/10.1007/s00453-022-01066-z">doi:10.1007/s00453-022-01066-z</A>]['22].
   (Ulam dist. is a special case of ED where no char. is allowed to appear more
   than once in a string.  [Also search for: longest ascending subsequence].)

%A G. Barequet
%A M. ShalahÂ 
%T Improved upper bounds on the growth constants of polyominoes and polycubes
%J Algorithmica
%V 84
%PÂ 3559-3586
%M DEC
%D 2022
%O Theoretical Informatics (LATIN 2020)
%K conf, c2022, c202x, c20xx, zz0123, combinatorics, polyominoe, polycube,
   upper bound
%X "... A d-dim. polycube is a face-connected set of cells onÂ Z^d. LetÂ A_d(n)
   denote the # of d-dim. polycubes (distinct up to translations) withÂ n cubes,
   andÂ l_d denote their growth const. lim_{n->inf}A_d(n+1)/A_d(n) ...
   1. We prove thatÂ l_2 <= 4.5252, 2. l_d <= (2d-2)e+o(1) for d>=2 ...
   3. We implement an iterative process in 3D, improving further the upb onÂ l_3
   toÂ 9.3835."
   -- [<A HREF="https://doi.org/10.1007/s00453-022-00948-6">doi:10.1007/s00453-022-00948-6</A>]['23].
   [Also search for: polyominoe].

%A Xi Chen
%A Yaonan Jin
%A T. Randolph
%A R. A. Servedio
%T Subset sum in time 2^{n/2}/poly(n)
%J arXiv
%M JAN
%D 2023
%K TR, c2023, c202x, c20xx, zz0123, subset sum problem, representation method
%X "A major goal in the area of exact exponential algs. is to give an alg. for
   the (worst-case) n-input Subset Sum problem that runs in time
   O(2^{1/2-c)n}) for some const. c>0. ... we give a SS alg. with worst-case
   running time O(2*{n/2}.n^{-g}) for a const. g>0.5023 in std word RAM or
   circuit RAM models. ..."
   -- 2301.07134@[<A HREF="https://arxiv.org/abs/2301.07134">arXiv</A>]['23].
   [Also search for: subset sum problem].

%A J. B. Orlin
%A L. Vegh
%T Directed shortest paths via approximate cost balancing
%J JACM
%V 70
%N 1
%P #3, 1-33
%M FEB
%D 2023
%K jrnl, JACM, c2023, c202x, c20xx, zz0223, directed graph, maths, algorithm,
   all pairs, shortest path, APSP, paths
%X "We present an O(nm) alg. for all-pairs shortest paths computations in a
   directed g. with n nodes, m arcs, & nonnegative integer arc costs. This
   matches the complexity bound attained by Thorup for the all-pairs problems
   in undirected graphs."
   -- [<A HREF="https://doi.org/10.1145/3565019">doi:10.1145/3565019</A>]['23].
   [Also search for: all pairs shortest paths].

%A I. H. Toroslu
%T The Floyd-Warshall all-pairs shortest paths algorithm for disconnected and
   very sparse graphs
%J SPE
%V ?
%M FEB
%D 2023
%K jrnl, SPE, c2023, c202x, c20xx, zz0223, all pairs, shortest path, APSP,
   paths, closure, graph, maths, algorithm
%X "...  However, for graphs without any negative weighted edges, using
   Dijkstra's shortest path alg. for every vertex as a source v. to produce
   all-pairs shortest paths works sig. better than the F.-W. alg., esp. for
   large graphs. [&] for graphs with -ve weighted edges, with no -ve cycle, in
   general Johnson's alg. also performs better ... show a simple improvement on
   the F.-W. alg. that will increases its efficiency, esp. for very sparse
   graphs ..."
   -- [<A HREF="https://doi.org/10.1002/spe.3188">doi:10.1002/spe.3188</A>]['23].
   [Also search for: all pairs shortest paths].

%A D. Das
%A et al ...
%A Barna Saha
%T Weighted edit distance computation: Strings, trees and Dyck
%J arXiv
%M FEB
%D 2023
%K TR, c2023, c202x, c20xx, zz0223, string, strings, tree, trees, edit distance,
   algorithm, weighted
%X "... we propose the first O(n+poly(k))-time alg. that computes weighted
   string edit distance exactly, thus bridging a fundamental gap between our
   understanding of unweighted & weighted ED. We then generalize this result to
   weighted tree & Dyck EDs, which lead to a deterministic alg. that improves
   upon the previous work for unweighted tree ED."
   -- 2302.04229@[<A HREF="https://arxiv.org/abs/2302.04229">arXiv</A>]['23].
   ('k' being the bound on the distance. NB 'weighted'.)
   [Also search for: Ukkonen c1983] and
   [also search for: edit distance algorithm].

%A O. Danvy
%T The tortoise and the hare algorithm for finite lists, compositionally
%J TOPLAS
%V 45
%N 1
%M MAR
%D 2023
%K jrnl, TOPLAS, c2023, c202x, c20xx, zz0323, algorithm, cycle, palindrome,
   tortoise, hare, there and back again, TABA, forth, finite list, lists, FP,
   fold, recursion
%X "... when the fast pointer reaches the end of a finite list, the slow pointer
   points to the middle of this list. In the early 2000's, this property was
   found to make it possible to program a palindrome detector ... Concretely,
   compositionality means that programs that use a fast & a slow pointer can be
   expressed with an ordinary fold function for lists and ..."
   -- [<A HREF="https://doi.org/10.1145/3564619">doi:10.1145/3564619</A>]['23].

%A A. A. Rescigno
%A U. Vaccaro
%T Bounds and algorithms for generalized superimposed codes
%J IPL
%V 182
%P #106365
%M AUG
%D 2023
%K briefComm, IPL, c2023, c202x, c20xx, zz0223, superimposed code, Zatocode,
   Zatocoding, cover free family, coverFree, strongly selective,
   disjunct matrix, Bloom filter
%X "We introduce a class of generalized superimposed codes that include several
   cases already studied in the literature. We give bounds on their size &
   algs. for their construction."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2023.106365">doi:10.1016/j.ipl.2023.106365</A>]['23].
   And, "A Bloom filter can be considered a kind of superimposed code"
   -- Sup'code@[<A HREF="https://en.wikipedia.org/wiki/Superimposed_code">wikip</A>]['23].
   [Also search for: superimposed code].

%A P. Ganapathi
%A R. Chowdhury
%T A unified framework to discover permutation generation algorithms
%J COMPJ
%V 66
%N 3
%P 603-614
%M MAR
%D 2023
%K jrnl, COMPJ, c2023, c202x, c20xx, zz0323, permutation, permute, generator,
   algorithm
%X "We present two simple, intuitive & general algorithmic frameworks that can
   be used to design a wide variety of perm. gen. algs.. ... can be used to
   produce 19 existing perm. alg., inc. the well-known algs. of Heap, Wells,
   Langdon, Zaks, Tompkins & Lipski. ... design two new sorting-based perm. gen.
   algs., one of which is optimal."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxab181">doi:10.1093/comjnl/bxab181</A>]['23].
   [Also search for: permutation generator algorithm].

%A R. Lewis
%T A comparison of Dijkstra's algorithm using Fibonacci heaps, binary heaps, and
   self-balancing binary trees
%J arXiv
%M MAR
%D 2023
%K TR, c2023, c202x, c20xx, zz0323, maths graph, shortest path, paths, heap
%X "... describes the shortest path problem in weighted graphs & examines the
   differences in efficiency that occur when using D.'s alg. with a Fibonacci
   heap & ...  Using C++ implementations of these algs. variants ... the fastest
   method is not always the one that has the lowest asymptotic complexity.
   Reasons for this are discussed & backed with empirical evidence."
   -- 2303.10034@[<A HREF="https://doi.org/10.48550/arXiv.2303.10034">arXiv</A>]['23].

%A T. Lanciano
%A A. Miyauchi
%A A. Fazzone
%A F. Bonchi
%T A survey on the densest subgraph problem and its variants
%J arXiv
%M MAR
%D 2023
%K TR, c2023, c202x, c20xx, zz0423, densest subgraph problem, algorithm,
   maths, graph, dense, density, intro, survey
%X "... in a given graph, a subset of vertices whose induced subgraph maximizes
   a measure of density. ... Recent years have witnessed a revival of research
   interest on this problem with several interesting contributions, inc. some
   groundbreaking results, published in 2022 & 2023. ..."
   -- 2303.14467@[<A HREF="https://doi.org/10.48550/arXiv.2303.14467">arXiv</A>]['23].
   Also see DSP@[<A HREF="https://en.wikipedia.org/wiki/Dense_subgraph">wikip</A>]['23].
   [Also search for: dense subgraph problem].

%A K. Bringmann
%A A. Cassis
%A N. Fischer
%T Negative-weight single-source shortest paths in near-linear time: Now faster!
%J arXiv
%M APR
%D 2023
%K TR, c2-23, c202x, c20xx, zz0423, negative weight, shortest path, graph,
   algorithm, maths, shortest paths, SSSP, negative weight, minimum cycle
%X "... A recent breakthrough result by Bernstein, Nanongkai & Wulff-Nilsen ...
   we improve the running time to O(m log^2(n) log(nW)loglog(n)) ... an
   improvement by nearly six log-factors.  ... As side results, we obtain an
   alg. to compute the minimum cycle mean in the same running time as well as a
   new const'n for computing Low-Diameter Decompositions in directed graphs."
   -- 2304.05279@[<A HREF="https://arxiv.org/abs/2304.05279">arXiv</A>]['23].
   (Also see, 'Historic algorithms help unlock shortest-path problem
   Breakthrough', CACM, SEP 2023 [<A HREF="https://doi.org/10.1145/3607866">doi:10.1145/3607866</A>]['23].)
   [Also search for: SSSP algorithm].

%A O. Serang
%T Median of heaps: linear-time selection by recursively constructing
   binary heaps
%K arXiv
%M APR
%D 2023
%K TR, c2023, c202x, c20xx, zz0423, selection, algorithm, problem, find,
   median heap, kth, data structure, struct
%X "The first worst-case linear-time alg. for sel'n was discovered in 1973;
   however, linear-time binary heap const'n was first published in 1964. Here we
   describe another worst-case linear sel'n alg., which is simply implemented &
   uses binary heap const'n as its principal engine. [It] is implemented in
   place, & shown to perform similarly to in-place median of medians."
   -- [<A HREF="https://arxiv.org/abs/2304.12313">arxiv:2304.12313</A>]['23].
   [Also seach for: median selection problem].

%A B. Doerr
%A et al
%T How well does the Metropolis algorithm cope with local optima?
%J arXiv
%M APR
%D 2023
%O Proc. GECCO 2023
%K TR, conf, c2023, c202x, c20xx, zz0423, Metropolis algorithm, Monte Carlo,
   monteCarlo, Las Vegas, lasVegas, stochastic, optimisation, optimization,
   CLIFF benchmark, optima, optimum, elitist, EAs
%X "The Metropolis algorithm (MA) is a classic stochastic local search ...
   avoids getting stuck in local optima by occasionally accepting inferior
   solutions. ... conduct a math. runtime analysis of the MA on the CLIFF
   benchmark. Apart from one local optimum, cliff fns are monotonically
   increasing towards the global optimum. ... Even with the optimal temp.
   ... the MA optimizes most cliff fns less efficiently than simple elitist
   evolutionary algorithms (EAs), ..."
   -- [<A HREF="https://arxiv.org/abs/2304.10848">arxiv:2304.10848</A>['23].
   [Also search for: Metropolis algorithm].

%A A. Abboud
%A et al
%T Can you solve closest string faster than exhaustive search?
%J arXiv
%M MAY
%D 2023
%K TR, c2023, c202x, c20xx, zz0623, closest string problem, algorithm, strings,
   set, continuous, discrete, representative, remotest
%X "We study the fundamental problem of finding the best string to represent a
   given set, in the form of the Closest String problem: Given a set
   X subset A^d of n strings, find the string x^* minimizing the radius of the
   smallest Hamming ball around x^* that encloses all the strings in X. ...
   In the cts Closest String problem, the goal is to find the soln string x^*
   anywhere in A^d ... prove that it cannot be improved to time
   O(2^{(1âe)d}poly(nd)), for any e > 0, unless the Strong Exponential Time
   Hypothesis fails. In the discrete Closest String problem, x^* is required to
   be in the input set X. ... quadratic time ... the discrete Closest String
   problem can be solved faster than exhaustive search. ..."
   -- 2305.16878@[<A HREF="https://arxiv.org/abs/2305.16878">arXiv</A>]['23].
   [Also search for: closest string problem].

%A Xiaodong Jia
%A A. Kumar
%A Gang Tan
%T A derivative-based parser generator for visibly pushdown grammars
%J TOPLAS
%V 45
%N 2
%P 1-68
%M MAY
%D 2023
%K jrnl, TOPLAS, c2023, c202x, c20xx, zz0623, pushdown grammar, parsing,
   ANTLR, Bison, parser, grammar
%X "... The generated parser accepts ambiguous grammars & produces a parse
   forest cont. all valid parse trees for an input string in linear time ..."
   -- [<A HREF="https://doi.org/10.1145/3591472">doi:10.1145/3591472</A>]['23].
   [Also search for: parser generator].

%A A. Bakshi
%A et al
%T A near-linear time algorithm for the Chamfer distance
%J arXiv
%M JUL
%D 2023
%K TR, c2023, c202x, c20xx, zz0723, point set, points, sets, Chamfer distance,
   approximate algorithm, dissimilarity, earth mover
%X "For any two pt sets A,B subset R^d of size up to n, the Chamfer dist.
   from A to B is defined as CH(A,B) = SUM_{a in A} min_{b in B} d_X(a,b)
   where d_X is the underlying dist. measure (e.g., the Euclidean or Manhattan
   dist.). ... admits a straightforward O(d.n^2)-time brute force alg ...
   present the 1st (1+e)-approx. alg. ... runs in time O(n d log(N)/e^2) & is
   implementable ..."
   -- 2307.03043@[<A HREF="https://arxiv.org/abs/2307.03043">arXiv</A>]['23].

%A D. Cussen
%A J. D. Ullman
%T Matrix multiplication using only addition
%J arXiv
%M JUL
%D 2023
%K TR, c2023, c202x, c20xx, zz0723, fast, matrix multiplication algorithm,
   multiplier, chip, GPU
%X "Matrix multiplication consumes a large fraction of the time taken in many
   machine-learning algs.. ... we demonstrate a method of performing matrix
   mult. without a scalar mult. circuit. In many cases of practical interest,
   only a single addn & a single on-chip copy op. are needed to replace a
   mult.. ... possible to design a matrix-mult. chip that, because it does not
   need time, space- & energy-consuming mult. circuits, can hold many more
   processors, & thus provide a net speedup."
   -- 2307.01415@[<A HREF="https://arxiv.org/abs/2307.01415">arXiv</A>]['23].
   [Also search for: matrix multiplication algorithm].

%A D. Walker
%T Algorithms for 3D Hilbert encoding and decoding
%J arXiv
%M AUG
%D 2023
%K TR, c2023, c202x, c20xx, zz0823, space filling, 3D, cube, curve, curves,
   path, paths, locality, location, ordering, algorithm, Hilbert, Lindenmayer,
   Lsystem
%X "... presents algs. & pseudocode for encoding & decoding 3D Hilbert
   orderings, which have application in a number of areas because of their
   locality properties. ... A 3D Hilbert ordering of depth r passes once through
   each location (x,y,z) in a MxMxM data cube, where M=2^r & x,y, & z are int.
   indices from 0 to M-1. Successive locations in a Hilbert ordering differ by
   addition or subtraction of one of the basis vectors (1,0,0), (0,1,0), &
   (0,0,1) ..."  [6 refs]
   -- 2308.05673@[<A HREF="https://arxiv.org/abs/2308.05673">arXiv</A>]['23].

%A D. Chakraborty
%A S. Das
%A A. Khan
%A A. Subramanian
%T Fair rank aggregation
%J arXiv
%M AUG
%D 2023
%K TR, c2023, c202x, c20xx, zz0823, rank, ranks, ranking, fair, Kendall tau,
   block, strict, strong, fairness
%X"...  rank aggregation problem deals with combining multiple rankings into a
   single aggregate r.. ...  Given any r., we provide a fast & exact alg. for
   finding the closest fair r. for the Kendall tau metric under block-fairness.
   We also provide an exact alg. for finding the closest fair r. for the Ulam
   metric under strict-fairness, when there are only O(1) # of groups. ..."
   -- [<A HREF="https://arxiv.org/abs/2308.10499">arxiv:2308.10499</A>]['23].

%A B. Dudek
%A P. Gawrychowski
%A T. Starikovskaya
%T Sorting signed permutations by reversals in nearly-linear time
%J arXiv
%M AUG
%D 2023
%K TR, MolBio, c2023, c202x, c20xx, zz0923, sorting, signed, permutation,
   reversal
%X "... we show how to leverage the results on dynamic graph connectivity to
   obtain a surprisingly simple O((n log^2 n)/log log n) time alg. ..."
   -- [<A HREF="https://arxiv.org/abs/2308.15928">arxiv:2308.15928</A>]['23].
   [Also search for: sorting reversals] see Pevzner etc.,
   there are 'signed' and 'unsigned' problems.

%A A. Abboud
%A K. Bringmann
%A N. Fischer
%A M. Kunnemann
%T The time complexity of fully sparse matrix multiplication
%J arXiv
%M SEP
%D 2023
%K TR, c2023, c202x, c20xx, zz0923, sparse matrix multiplication, dense,
   algorithm, maths, graph, all-edge triangle
%X "... matrices with m_in nonzeros in the input & m_out nonzeros in the output?
   ... a new alg. that reduces sparse matrix mult. to dense (but smaller)
   rectangular matrix mult.. Our running time thus depends on the optimal
   exponent omega(a,b,c) of multiplying dense naÃnb by n^bxn^c matrices. ...
   In particular, in terms of the input plus output size m=m_in+m_out our alg.
   runs in time O(m^1.3459). Even for Boolean m., this improves over the
   previous ..."
   -- [<A HREF="https://arxiv.org/abs/2309.06317">arxiv:2309.06317</A>]['23].
   [Also search for: matrix multiplication algorithm].

%A E. Demaine
%A Y. Kirkpatrick
%A R. Lin
%T Graph threading
%J arXiv
%M SEP
%D 2023
%K TR, c2023, c202x, c20xx, zz0923, maths, graph, algorithm, thread, threading
%X "... we study the problem of threading a single string through a set of tubes
   so that pulling the string forms a desired g.. ... given a connected graph
   (where edges represent tubes & vertices represent junctions where they meet),
   we give a polynomial-time alg. to find a minimum-length closed walk (rep. a
   threading of string) that induces a connected g. of string at every junction.
   ... based on a surprising reduction to minimum-weight perfect matching. ..."
   -- [<A HREF="https://arxiv.org/abs/2309.10122">arxiv:2309.10122</A>]['23].

%A N. Fischer
%T Deterministic sparse pattern matching via the Baur-Strassen theorem
%J arXiv
%M OCT
%D 2023
%K TR, c2023, c202x, c20xx, zz1023, constellation problem, algorithm, pattern,
   point set, subset, points, transformations
%X "... problem of testing whether a set of pts P can be moved into (or close
   to) another set Q under some prescribed group of transformations. [eg] Given
   two sets of at most n ints. P, Q subset [N], determine whether there is some
   shift s such that P shifted by s is a subset of Q ... can be solved in
   near-linear time O(n log n) by a Monte Carlo randomized alg. ... [A] question
   left open by these previous works is whether Constellation is in det.
   near-linear time (i.e., with only polylogarithmic overhead).  We answer this
   question positively by giving an ... n.(log N)^{O(1))} det. alg ..."
   -- [<A HREF="https://arxiv.org/abs/2310.11913">arxiv:2310.11913</A>]['23].
   [Also search for: Baur Strassen].

%A D. Lemire
%T Exact short products from truncated multipliers
%J COMPJ
%M OCT
%D 2023
%K jrnl, COMPJ, c2023, c202c, c20xx, zz1123, truncated, multiplier,
   arithmetic, multiplication, algorithm, integer, leading digits
%X "We sometimes need to compute the most sig. digits of the product of small
   ints. with a multiplier requiring much storage, e.g. a large int.
   (e.g.5^100) or an irrational number (pi). We only need to access the most
   sig. digits of the multiplier - as long as the ints are sufficiently small.
   We provide an efficient alg. to compute the range of ints. given a truncated
   multiplier & a desired # of digits."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxad077">doi:10.1093/comjnl/bxad077</A>]['23].
   [Also search for: integer multiplication algorithm].

%A D. Aggarwal
%A T. Espitau
%A S. Peters
%A N. Stephens-Davidowitz
%T Recursive lattice reduction - A framework for finding short lattice vectors
%J arXiv
%M NOV
%D 2023
%K TR, c2023, c202x, c20xx, zz1223, short lattice vector, shortest
%X "... the framework works by recursively searching for dense sublattices of
   dense sublattices (or their duals). Eventually, the proc. encounters a rec.
   call on a lattice L with relatively low rank k, at which point we simply use
   a known alg. to find a short non-zero vector in L. ..."
   -- [<A HREF="https://arxiv.org/abs/2311.15064">arxiv:2311.15064</A>]['23].
   [Also search for: short lattice vector].

%A J. T. Fineman
%T Single-source shortest paths with negative real weights in O~(mn^{8/9}) time
%J arXiv
%M NOV
%D 2023
%K TR, c2023, c202x, c20xx, zz1123, shortest paths, randomised, algorithm,
   graph, negative, weight, Shimbel
%X "... a randomized alg. for ... single-source shortest paths on directed gs.
   with real (both +ve & -ve) edge weights. Given an input g. with n vertices
   & m edges, ... completes in O~(mn^{8/9}) time with high probability. For
   real-weighted g., ... constitutes the first asymptotic improvement over the
   classic O(mn)-time alg. variously attributed to Shimbel, Bellman, Ford, &
   Moore."
   -- [<A HREF="https://arxiv.org/abs/2311.02520">arxiv:2311.02520</A>]['23].

%A M. Grohe
%A D. Neuen
%A P. Schweitzer
%T A faster isomorphism test for graphs of small degree
%J SIAM J. Comput.
%V 52
%N 6
%P ?-?
%M DEC
%D 2023
%O FOCS59 2018
%K conf, FOCS, c2023, c202x, c20xx, zz1223, maths, graph isomorphism, algorithm
%X "... Babai [2016] gave a quasipolynomial-time g.isomorphism test. ... we give
   an improved isomorphism test for g. of small degree: [it] runs in time
   n^{O((log d)^c)}, where n is the # of vertices of the input gs., d is the
   maximum degree of the input gs., & c is an absolute const.. The best prev.
   iso.test for gs. of maximum degree d due to Babai, Kantor, & Luks runs in
   time n^{O(d/log d)}."
   -- [<A HREF="https://doi.org/10.1137/19M1245293">doi:10.1137/19M1245293</A>]['23].
   [Also search for: graph isomorphism].

%A J. Alman
%A V. V. Williams
%T Limits on all known (and some unknown) approaches to matrix multiplication
%J SIAM J. Comput.
%V 52
%N 6
%P ?-?
%M DEC
%D 2023
%O FOCS59 2018
%K conf, FOCS, c2023, c202x, c20xx, zz1223, matrix multiplication, algorithm
%X "... The two main approaches are the Laser method of Strassen, & the group
   theoretic approach of Cohn & Umans. We define a generalization based on
   zeroing outs which subsumes these two approaches, which we call the Solar
   method, & an even more general method based on monomial degenerations, which
   we call the Galactic method ..."
   -- [<A HREF="https://doi.org/10.1137/19M124695X">doi:10.1137/19M124695X</A>]['23].
   [Also search for: matrix multiplication].

%A J. Chuzhoy
%A S. Khanna
%T A faster combinatorial algorithm for maximum bipartite matching
%K arXiv
%M DEC
%D 2023
%K TR, c2023, c202x, c20xx, zz1223, maths, graph, maximum, bipartite, matching,
   algorithm
%X "... Hopcroft & Karp (1973) shows that MBM can be solved in O(m sqrt n) time
   on a g. with n vertices & m edges. For the case of v.dense g., a fast matrix
   mult. based approach gives a running time of O(n^{2.371}) ...  Madry
   introduced a new approach based on continuous techniques achieving much
   faster runtime in sparse g.. ... Chen et al. (2022) that gives an m^{1+o(1)}
   time alg. ... are cts techniques essential to obtaining fast algs. for the
   BM problem? Our work makes progress on this q. by presenting a new, purely
   combinatorial alg. for BM, that runs in O~(m^{1/3}n^{5/3}) time ..."
   -- [<A HREF="https://arxiv.org/abs/2312.12584">arxiv:2312.12584</A>]['23].
   [Also search for: maximum bipartite matching].

%A S. Bruch
%T Foundations of vector retrieval
%J arXiv
%M JAN
%D 2024
%K TR, c2024, c202x, c20xx, zz0124, algorithm, search, vectors, retrieval,
   similar, query, intro
%X "... Finding vectors that are more similar to a query vector. This monograph
   is concerned with the q. above & covers fundamental concepts along with
   advanced data structures & algs. for vector retrieval. ..."
   -- [<A HREF="https://arxiv.org/abs/2401.09350">arxiv:2401.09350</A>]['24].

%A S. Kale
%A et al
%T A modern approach to electoral delimitation using the quadtree data structure
%J arXiv
%M FEB
%D 2024
%K TR, c2024, c202x, c20xx, zz0224, politics, electorate, electoral, boundary,
   district, redistribution, gerrymander, delimitation, political, election
%X "... study & analyse the performance of existing delimitation algs. & further
   propose a potential soln, along with its merits, that involves using a
   computational model based on the quadtree data structure to automate the
   districting process by optimizing objective population criteria. ..."
   -- [<A HREF="https://arxiv.org/abs/2402.09336">arxiv:2402.09336</A>]['24].
   [Also search for: gerrymander].

%A N. Cotumaccio
%T Enhanced graph pattern matching
%J arXiv
%M FEB
%D 2024
%K TR, c2024, c202x, c20xx, zz0324, maths, graph pattern, match, stats
%X "Pattern matching queries on strings can be solved in linear time by ...
   (KMP) alg.. In 1973, Weiner introduced the suffix tree of a string & showed
   that the seemingly more difficult problem of computing matching statistics
   can also be solved in liner time. PM queries on graphs are inherently more
   difficult: under the Orthogonal Vector hypothesis, the g. PM problem cannot
   be solved in subquadratic time [TALG 2023]. The complexity of g. PM can be
   parameterized by the topological complexity of the considered g., which is
   captured by a param. p [JACM 2023]. ... we show that, as in the string
   setting, computing matching statistics on g. is as difficult as solving
   standard PM queries. ... introduce a notion of longest common prefix (LCP)
   array for arbitrary gs.."
   -- [<A HREF="https://arxiv.org/abs/2402.16205">arxiv:2402.16205</A>]['24].

%A T. Lecroq
%T A fast implementation of the good-suffix array for the Boyer-Moore string
   matching algorithm
%J arXiv
%M FEB
%D 2024
%K TR, c2024, c202x, c20xx, zz0324, good, suffix, string, search, pattern,
   matching, strings
%X "... The good-suffix table is tricky to compute in linear time. Text book
   solns perform redundant operations. Here we present a fast implementation for
   this good-suffix table based on a tight analysis of the pattern. Experimental
   results show two versions of this new implementation are the fastest in
   almost all tested situations."
   -- [<A HREF="https://arxiv.org/abs/2402.16469">arxiv:2402.16469</A>]['24].

%A B. Das
%A et al
%T Linear space data structures for finite groups with constant query-time
%J Algorithmica
%V 86
%P 1979-2025
%M MAR
%D 2024
%K jrnl. c2024, c202x, c20xx, zz0624, maths, finite group, multiplication query,
   nonAbelian, data structure, algorithm
%X "... We design a constant query-time data structure that can store any finite
   group using O(n) words where n is the order of the group. Since our [DS]
   achieves the information theoretic LWB & answers queries in const. time, it
   is optimal in both space usage & query-time. A crucial step in the process is
   essentially to design linear space & constant query-time [DSs] for nonabelian
   simple groups. The [DS] for nonabelian simple groups are designed using a
   lemma that we prove using the Class'n Theorem for Finite Simple Groups."
   -- [<A HREF="https://doi.org/10.1007/s00453-024-01212-9">doi:10.1007/s00453-024-01212-9</A>]['24].
   [Also search for: maths finite group].

%A K. M. Swenson
%T A simple and efficient algorithm for sorting signed permutations by reversals
%J arXiv
%M APR
%d 2024
%K TR, MolBio, c2024, c202x, c20xx, zz0424, sort, sorting by reversals
%X "In 1937, biologists Sturtevant & Tan posed a comp. Q: transform a chromosome
   rep. by a permutation of genes, into a second perm'n, using a minimum-length
   seq. of reversals, each inverting the order of a contiguous subset of elts.
   Solutions to this problem, applied to Drosophila chrs, were computed by hand.
   The first algorithmic result was a heuristic that was published in 1982. In
   the 1990s a more biologically relevant version of the problem, where the elts
   have signs that are also inverted by a reversal, finally received serious
   attention by the CS community. ... eventually resulted in the 1st polynomial
   time alg. for Signed Sorting by Reversals. Since then, a dozen more articles
   have been dedicated to simplifying the theory & developing algs. with
   improved running times. The current best alg., which runs in
   O(n log^2(n)/log log(n)) time, fails to meet what some consider to be the
   likely lower bound of O(n log n). ... we present the 1st alg. that runs in
   O(n log n) time in the worst case. [It] is fairly simple to implement, & the
   running time hides very low constants."
   -- [<A HREF="https://arxiv.org/abs/2403.20165">arxiv:2403.20165</A>]['24].
   [Also search for: sorting reversals].

%A L. Ganassali
%T The graph alignment problem: fundamental limits and efficient algorithms
%J arXiv
%M APR
%D 2024
%K thesis, c2024, c202x, c20xx, zz0424, maths, graph, alignment, matching,
   similarity, graphAlignment, algorithm
%X "... graph alignment problem, the noisy version of the g.isomorphism problem,
   which aims to find a matching between the nodes of two graphs which preserves
   most of the edges. Focusing on the planted version where the g. are random,
   we are interested in understanding the fundamental information-theoretical
   limits for this problem, as well as designing & analyzing algs. that are able
   to recover the underlying alignment in the data. For these algs., we give
   some high prob. guarantees on the regime in which they succeed or fail."
   -- [<a HREF="https://arxiv.org/abs/2404.12418">arxiv:2404.12418</A>]['24].
   [Also search for: graphAlignment]  &  [also seach for: graph isomorphism].

%A J. A. Perez
%T Hardware addition over finite fields based on Booth-Karatsuba algorithm
%J COMPJ
%M MAY
%D 2024
%K jrnl, COMPJ, c2024, c202x, c20xx, zz0624, addition, computer arithmetic,
   modular, add, adder, algorithm, large, integer, BigInt, Zn, Z_n
%X "... we present an addition alg. on Z/mZ of big-integer numbers based on ...
   using an alternative to trad. h/w implementation for binary addition based on
   FULL-ADDER cells, allowing the red'n of space complexity compared with other
   techniques, such as carry-lookahead, letting us calculate a modular addition
   in an optimal order complexity of O(n) without adding more complexity due to
   reduction operations."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxae034">doi:10.1093/comjnl/bxae034</A>]['24].
   [Also search for: computer arithmetic integer].

%A V. Bhargava
%A et al
%T Multivariate multipoint evaluation over all finite fields
%J JACM
%V 13
%N 3
%P 1-32
%M JUN
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0624, multi point, finite field, evaluating,
   polynomial, maths, algorithm, Bombieri Vinogradov
%X "... evaluating a multivariate polynomial, given as a coef. vector,
   simultaneously at multiple evaln pts. ... there exists a deterministic alg.
   for ... over any finite field F that outputs the evaluations of an m-variate
   p. of degree less than d in each variable at N pts in time
   (d^m+N)^{1+o(1)}.poly(m,d,log|F|) for all m in N, & all suff. large d in N.
   ... [&] a 2nd alg. for ... that is completely elementary &, in particular,
   avoids the use of the Bombieri-Vinogradov theorem. [But] requires a mild
   assumption that the field size is bounded by an exponential tower in d of
   bounded height. ... solves the ... problem over a finite field F in [same]
   time provided that the size of ... F is at most (exp(exp(exp(...(exp(ð))))),
   where the height of this tower of exponentials is fixed."
   -- [<A HREF="https://doi.org/10.1145/3652025">doi:10.1145/3652025</A>]['24].
   (Also see PolyE@[<A HREF="https://en.wikipedia.org/wiki/Polynomial_evaluation">wikip</A>]['24].)

%A F. Romano
%T A square root algorithm faster than Newton's method for multiprecision
   numbers, using floating-point arithmetic
%J arXiv
%M JUN
%D 2024
%K TR, c2024, c202x, c20xx, zz0624, square root, sqrt, algorithm, integer,
   computer arithmetic
%X "... an optimized version of classical Bombelli's alg. for computing int.
   square roots ... floating-point arithmetic is used to compute the initial
   guess of each digit of the root, following similar ideas to those used in
   "The Art of Computer Programming" Vol. 2, p. 4.3.1 for divn. ...
   compared with that of the alg. provided by the Java std lib., which uses the
   Newton's method. From tests, the algorithm presented here turns out to be
   much faster.
   -- [<A HREF="https://arxiv.org/abs/2406.07751">arxiv:2406.07751</A>]['24].
   (Also see iSqrt@[<A HREF="https://en.wikipedia.org/wiki/Integer_square_root">wikip</A>]['24].)

%A M. Koucky
%A J. Matejka
%T SquareSort: a cache-oblivious sorting algorithm
%J arXiv
%M JUL
%D 2024
%K TR, c2024, c202x, c20xx, zz0724, SquareSort, sort, sorting, algorithm,
   blocksize, cache, FunnelSort
%X "... introduce a new simple sorting alg. in that model which has
   asymptotically optimal IO complexity O((n/B)log_{M/B}(n)), where n is the
   instance size, M size of the cache & B size of a memory block. This is the
   same as the complexity of the best known cache-oblivious sorting alg.
   FunnelSort."
   -- [<A HREF="https://arxiv.org/abs/2407.14801">arxiv:2407.14801</A>]['24].
   [Also search for: sorting cache].

%A M. Schmellenkamp
%A et al
%T Detecting and explaining (in)equivalence of context-free grammars
%J arXiv
%M JUL
%D 2024
%K TR, c2024, c202x, c20xx, zz0824, parse, parsing, context free grammar, CFG,
   difference, equivalence
%X "We propose a scalable framework for deciding, proving, & explaining
   (in)equivalence of context-free grammars. We present an implementation of the
   framework & evaluate it on large data sets collected within educational
   support systems. Even though the equivalence problem for CFGs is undecidable
   in general ..."
   -- [<A HREF="https://arxiv.org/abs/2407.18220">arxiv:2407.18220</A>]['24].

%A K. Bringmann
%A N. Fischer
%A V. Nakos
%T Beating Bellman's algorithm for subset sum
%J arXiv
%M OCT
%D 2024
%K TR, c2024, c202x, c20xx, zz1124, subset sum problem,
%X "... Since [1957], it has been an important q. whether Bellman's seminal
   alg. can be improved. ... we positively resolve this q. & design an alg. that
   outperforms B's alg. in all regimes. [It] runs in time O~(|S(X,T)|.sqrt(n))
   thus improving the time complexity by a factor of nearly sqrt(n) ..."
     (given a set X of n non-neg ints, a target t, S(X) is the set of
     all subset-sums, problem: ?is t in S(X)? It's NP-hard.)
   -- [<A HREF="https://doi.org/10.48550/arXiv.2410.21942">arxiv:2410.21942</A>]['24].
   [Also search for: subset sum problem].

%A A. Elmasry
%T Breaking the Bellman-Ford shortest-path bound
%J arXiv
%M OCT
%D 2024
%K TR, c2024, c202x, c20xx, zz1124, algorithm, single source, paths,
   DPA, surprising
%X "... running time of our alg. is therefore O(sqrt(n).m+n.sqrt(m log n))."
   [n vertices, m edges]
   -- [<A HREF="https://arxiv.org/abs/2410.23383v1">arxiv:2410.23383v1</A>]['24].


%A B. A. Galler
%A M. J. Fisher
%T An improved equivalence algorithm
%J CACM
%V 7
%N 5
%P 301-303
%M MAY
%D 1964
%K jrnl, CACM, c1964, c196x, c19xx, zz0613, disjoint set forest, equivalence,
   union find, data structure, datastructure, DS
%X "An alg. for assigning storage on the basis of EQUIVALENCE, DIMENSION &
   COMMON declarations is presented. [It] is based on a tree structure, & has
   reduced computation time by 40% over a prev. published alg. by identifying
   all equiv.classes with one scan of the EQUIVALENCE declarations. The method
   is applicable in any problem in which it is necessary to identify equivalence
   classes, given the element pairs defining the equivalence relation."
   -- [<A HREF="http://dx.doi.org/10.1145/364099.364331">doi:10.1145/364099.364331</A>]['13].
   (Also see disj.set@[<A HREF="http://en.wikipedia.org/wiki/Disjoint-set_data_structure">wikip</A>]['13].)
   [Also search for: union find].

%A R. Bayer
%A E. M. McCreight
%T Binary B-trees for virtual memory
%J Proc ACM SIGFIDET Workshop, San Diego
%P 219-235
%D 1971
%K conf, c1971, c197x, c19xx, btree, tree, btrees, search, dataStructure, DS
%X [Also search for: Bayer btree].

%A R. Bayer
%A E. M. McCreight
%T Organization and maintenance of large ordered indexes
%J Acta Informatica
%V 1
%N 3
%P 173-189
%M SEP
%D 1972
%K jrnl, c1972, c197x, c19xx, l2ref, l3ref, B-tree, btree, trees, btrees,
   balanced, tree, index, data structure, dataStructure, DS, disc, backing,
   storage, large, huge, zz0806
%X "Organization & maintenance of an index for a dynamic random access file is
   considered. ... index must be kept on some pseudo random access backup store
   like a disc or a drum. ... allows retrieval, insertion, & deletion of keys
   in time proportional to logk(I) where I is the size of the index & k is a
   device dependent natural number such that the performance of the scheme
   becomes near optimal. Storage utilization is at least 50% but generally much
   higher. The pages of the index are organized in a special data-structure,
   so-called B-trees. The scheme is analyzed, performance bounds are obtained,
   & a near optimal k is computed. Experiments have been performed with indexes
   up to 100000 keys. An index of size 15000 (100000) can be maintained with an
   avg. of 9 (at least 4) transactions/sec. on an IBM 360/44 with a 2311 disc"
   -- [<A HREF="http://dx.doi.org/10.1007/BF00288683">doi:10.1007/BF00288683</A>]['06],
      [<A HREF="http://portal.acm.org/citation.cfm?coll=GUIDE&dl=GUIDE&id=944347#">?reprint?</A>]['06].

%A R. Bayer
%A E. M. McCreight
%T Symmetric binary B-trees: data structure and maintenance algorithms
%J Acta Informatica
%V 1
%N 4
%M DEC
%D 1972
%P 290-306
%K jrnl, c1972, c197x, c19xx, b-tree, btree, btrees, balanced trees,
   data structure, dataStructure, DS
%X "A class of binary trees is described for maintaining ordered sets of data.
   Random insertions, deletions, & retrievals of keys can be done in time
   proportional to log N where N is the cardinality of the data-set. Symmetric
   B-Trees are a modification of B-trees described previously by Bayer &
   McCreight. This class of trees properly contains the balanced trees."
   -- [<A HREF="http://dx.doi.org/10.1007/BF00289509">doi:10.1007/BF00289509</A>]['06].

%A M. H. Overmars
%A J. van Leeuwen
%T Dynamic multi-dimensional data structures
%J Acta Informatica
%V 17
%D 1982
%P 267-285
%K jrnl, c1982, c198x, c19xx, quad-tree, pseudo-quad-tree, DS, dataStructure,
   quad tree
%X based on Quad- and k-d trees
   this ref via enews.

%A M. H. Overmars
%T The design of dynamic data structures
%S LNCS
%V 156
%I SpringerVerlag
%D 1983
%K DS, dataStructure, quad-tree, pseudo-quad-tree, quad tree
%X this ref via enews.

%A J. M. Smith
%A D. C. P. Smith
%T Database abstractions: aggregations
%J CACM
%M Jun
%D 1977
%V 20
%N 6
%P 405-413
%K data, abstraction, data base

%A P. M. Stocker
%A P. A. Dearnley
%T Self-organising data management systems
%J COMPJ
%V 16
%N 2
%P 100-105
%D 1973
%K COMPJ, jrnl, self organising, dynamic, DBMS, c1973, c197x, c19xx
%X "A framework for a data management system is formulated; the proposed system
   differs appreciably from current systems because it is intended to serve a
   different purpose. This purpose is the management of a database in which
   much of the data is accessed infrequently and where a rapid response time is
   a less important factor than cost."
   -- [<A HREF="http://dx.doi.org/0.1093/comjnl/16.2.100">doi:0.1093/comjnl/16.2.100</A>]['05].

%A P. van Emde Boas
%A R. Kaas
%A E. Zijlstra
%T Design and implementation of an efficient priority queue
%J Mathematical Systems Theory
%V 10
%N 1
%P 99-127
%D 1977
%K jrnl, c1977, c197x, c19xx, priority queue, queues, data structure,
   dataStructure, DS, mergeable heap
%X "... data structure, based upon a hierarchically decomposed tree, which
   enables us to manipulate on-line a priority queue whose priorities are
   selected from the interval 1,...,n with a worst case processing time of
   O(log log n) per instn. ... can be used to obtain a mergeable heap whose time
   requirements are about as good. ... explained based upon an implementation
   of the struct. in a PASCAL program contained in the paper."
   -- [<A HREF="http://dx.doi.org/10.1007/BF01683268">doi:10.1007/BF01683268</A>]['13].
   [Also search for: priority queue dataStructure].

%A J. Vuillemin
%T A data structure for manipulating priority queues
%J CACM
%V 21
%N 4
%P 309-315
%M APR
%D 1978
%K jrnl, CACM, c1978, c197x, c19xx, mergeable heap, heaps, binary tree, insert,
   delete, union, update, search highest priority, dataStructure, DS
%X [Also search for: priority queue dataStructure].

%A H. Edelsbrunner
%T Dynamic data structures for orthogonal intersection queries
%T Report F59
%I Inst. Information Process., Graz Univ. Technology, Austria
%D 1980
%K TR F59, IPL, c1980, c198x, c19xx, zz1114, intervalTree, interval tree, trees,
   data structure, intervals, range, intersection query, search, algorithm,
   geometry, geometric objects
%X pdf@[<A HREF="https://www.cs.duke.edu/~edels/Publications/GeoDS/">duke.edu</A>]['14].
   Also see H.Edelsbrunner and H.A.Maurer,
   'On the intersection of Orthogonal objects,' IPL 13(4,5), pp.177-181, 1981
   -- [<A HREF="http://dx.doi.org/10.1016/0020-0190(81)90053-3">doi:10.1016/0020-0190(81)90053-3</A>]['14].
   (Also see I.Tree@[<A HREF="http://en.wikipedia.org/wiki/Interval_tree">wikip</A>]['14].)

%A E. M. McCreight
%T Priority search trees
%J SIAM J. Comput.
%V 14
%N 2
%P 257-276
%D 1985
%K jrnl, c1985, c198x, c19xx, computational geometry, search tree, 2D,
   priority queue, intersection, interval, rectangle, storage allocation,
   containment, dynamic, linear intervals, interval, concrete complexity,
   dataStructure, DS
%X "Let D be a dynamic set of ordered pairs [x,y] over the set 0,1, ...,k-1 of
   integers. Consider the following operations applied to D: (1) Insert (delete)
   a pair [x,y] into (from) D.  (2) Given test integers x0,x1, and y1, among
   all pairs [x,y] in D such that x0 <= x <= x1 and y <= y1, find a pair whose
   x is minimal (or maximal).  (3) Given test integers x0 and x1, among all
   pairs [x,y] in D such that x0 <= x <= x1, find a pair whose y is minimal.
   (4) Given test integers x0, x1, and y1, enumerate those pairs [x,y] in D
   s.t. x0 <= x <= x1 and y <= y1. Using a new data structure that we call a
   priority search tree, of which 2 variants are introduced, operations (1),
   (2), and (3) can be implemented in O(log n) time, where n is the cardinality
   of D. Operation (4) is performed in at most O(log n + s) time, where s is the
   number of pairs enumerated. The priority search tree occupies O(n) space.
   PST algorithms can be used effectively as subroutines in diverse applic'ns.
   With them one can answer questions of intersection or containment in a
   dynamic set of linear intervals. They can be used in combination with a
   well-known plane-sweep technique, to implement off-line algorithms for
   enumerating all intersecting pairs of rectangles. Priority search trees can
   also be used to implement best-/first-fit storage allocation."
   -- [<A HREF="http://dx.doi.org/10.1137/0214021">doi:10.1137/0214021</A>]['06],
      [<A HREF="/~lloyd/tildeMisc/Local/1985mccreight.pdf">local</A>].

%A Douglas Jones
%T An empirical comparison of priority-queue and event-set implementations
%J CACM
%V 29
%N 4
%P 300-311
%M APR
%D 1986
%K skew heap, heaps, splay tree, priority queues, event set, dataStructure, DS
%X via enews.

%A M. Fredman
%A R. Sedgewick
%A R. Sleator
%A R. Tarjan
%T The pairing heap: A new form of self-adjusting heap
%A Algorithmica
%V 1
%N 1
%P 111-129
%M JAN
%D 1986
%K jrnl, c1986, c198x, c19xx, heaps, heap ordered multiway trees,
   dataStructure, DS
%X also see  S t a s k o  &  V i t t e r  c1987.

%A M. D. Atkinson
%A J.-R. Sack
%A N. Santoro
%A T. Strothotte
%T Min-max heaps and generalized priority queues
%J CACM
%V 29
%N 10
%P 996-1000
%M OCT
%D 1986
%K jrnl, CACM, c1986, c198x, c19xx, zz0408, heap, queue, minmax, findmin,
   findmax, insert, deletemin, deletemax, findmedian, dataStructure, DS
%X "4 simple implementation of double-ended PQs .... a min-max heap, can be
   built in linear time; in contrast to conventional heaps, it allows both
   FindMin and FindMax to be performed in constant time; Insert, DeleteMin, &
   DeleteMax operations can be performed in log. time.  Min-max heaps can be
   generalized to support other similar order-statistics operations efficiently
   (e.g., constant time FindMedian and logarithmic time DeleteMedian);
   furthermore, the notion of min-max ordering can be extended to other
   heap-ordered structures, such as leftist trees."
   -- pdf@[<A HREF="http://dx.doi.org/10.1145/6617.6621">doi:10.1145/6617.6621</A>]['08].

%A J. T. Stasko
%A J. S. Vitter
%T Pairing heaps: experiments and analysis
%J CACM
%V 30
%N 3
%P 234-249
%M MAR
%D 1987
%K jrnl CACM, heap, c1987, c198x, c19xx, dataStructure, DS, two pass, twopass,
   auxiliary
%X "...recently been introduced as a new DS for priority queues. Pairing heaps
   are extremely simple to implement & seem to be very efficient in practice,
   but they are difficult to analyze theoretically, & open problems remain. ...
   been conjectured that they achieve the same amortized time bounds as
   Fibonacci heaps, namely, O(log n) time for delete & delete_min & O(1) for all
   other operations, where n is the size of the priority queue at the time of
   the operation. We provide empirical evidence that supports this conjecture.
   The most promising alg. in our simulations is a new variant of the twopass
   method, called auxiliary twopass. We prove that, assuming no decrease_key
   operations are performed, it achieves the same amortized time bounds as
   Fibonacci heaps." -- [<A HREF="http://doi.acm.org/10.1145/214748.214759">doi:10.1145/214748.214759</A>],
   [also search for: pairing heap].

%A B. Chazelle
%T A functional approach to data structures and its use in multidimensional
   searching
%J SIAM J. Comput.
%V 17
%N 3
%P 427-462
%M JUN
%D 1988
%K jrnl, c1988, c198x, c19xx, search, rectangle, computational geometry, 2D,
   range search, query, count, counting, intersection search, tree, problem,
   dataStructure, DS
%X -- [<A HREF="http://www.cs.princeton.edu/~chazelle/pubs/FunctionalDataStructures.pdf">pdf@princeton</A>]['06].

%A P.-A. Larson
%T Dynamic hash tables
%J CACM
%V 31
%N 4
%P 446-457
%M APR
%D 1988
%K jrnl, CACM, c1988, c198x, c19xx, zz0914, hash, hashing, table, tables,
   linear, spiral, double, collisions, dataStructure, DS
%X "Linear hashing & spiral storage are two dynamic hashing schemes originally
   designed for external files. ... shows how to adapt these two methods for
   hash tables stored in main memory. The necessary d.structs. & algs. are
   described, ... Linear h. is found to be both faster & easier to implement
   than spiral storage. Two alt. techniques are considered: a simple unbalanced
   binary tree & double hashing with periodic rehashing into a larger table. The
   retrieval time of linear h. is similar to double h. & substantially faster
   than a binary tree, except for v. small trees. The loading times of double
   h. (with periodic reorganization), a binary tree, & linear h. are similar.
   Overall, linear h. is a simple & efficient technique for applications where
   the cardinality of the key set is not known in advance."
   -- [<A HREF="http://dx.doi.org/10.1145/42404.42410">doi:10.1145/42404.42410</A>]['14].

%A M. Fredman
%A M. Saks
%T The cell probe complexity of dynamic data structures
%J Proc. 21st Annual ACM Symp. on Theory of Comp.
%I ACM
%P 345-354
%M MAY
%D 1989
%K conf, c1989, c198x, c19xx, zz0613, union find, disjoint set forest,
   data structure dataStructure, DS, complexity
%X "... Theorem 5. Any CPROBE(logn) implementation of the set union problem
   requires &OHgr;(m&agr;(m,n)) time to execute m Find's and n-1 Union's,
   beginning with n singleton sets. N.Blum[2] has given a logn/loglogn alg.
   (worst case time per op.) for the set union problem. This alg. is also
   optimal in the CPROBE(polylogn) model. ..."
   -- [<A HREF="http://dx.doi.org/10.1145/73007.73040">doi:10.1145/73007.73040</A>]['13].
   (Also see disj.set@[<A HREF="http://en.wikipedia.org/wiki/Disjoint-set_data_structure">wikip</A>]['13].)
   [Also search for: union find].

%A W. Pugh
%T Skip lists: A probabilistic alternative to balanced trees
%J CACM
%V 33
%N 6
%P 668-676
%M JUN
%D 1990
%K jrnl, CACM, skip list, data structure, tree, c1990, c199x, c19xx,
   insertion, deletion, balance, uniMaryland, dataStructure, DS
%X [<A HREF="ftp://ftp.cs.umd.edu/pub/skipLists/skiplists.pdf">pdf</A>]['05]
   [<A HREF="http://www.cs.umd.edu/~pugh/">~pugh</A>]['05]
   "Although a skip list may not be balanced, the probability of a skip list
   being substantially unbalanced is insignificant. Algorithms for insertion
   and deletion in skip lists are simpler and faster than equivalent algorithms
   for balanced trees."
   Also see [<A HREF="http://256.com/sources/skip/">G. W@tson's code</A>]['05]

%A G. N. Frederickson
%A S. Rodger
%T A new approach to the dynamic maintenance of maximal points in a plane
%J Discrete and Computational Geometry
%V 5
%N 4
%P 365-374
%M JUL
%D 1990
%K jrnl, c1990, c199x, c19xx, 2D, point, set, sets, dynamic contour search tree,
   maxima, maximal, dominate, dominator, dataStructure, DS
%X "A pt p[i]=(x[i],y[i]) in the x-y plane is maximal if there is no pt
   p[j]=(x[j],y[j]) s.t. x[j] > x[i] and y[j] > y[i].  [[i.e. j dominates i.]]
   We present a simple data structure, a dynamic contour search tree, which
   contains all the points in the plane & maintains an embedded linked list of
   maximal points so that m maximal pts are accessible in O(m)-time. Our
   data structure dynamically maintains the set of pts so that insertions
   take O(log n) time, a speedup of O(logn) over previous results, & deletions
   take O((log n)^2)-time."
   -- [<A HREF="http://dx.doi.org/10.1007/BF02187797">doi:10.1007/BF02187797</A>]['05].
   [Also search for: maxima dominate].

%A W. T. Wipke
%A D. Rogers
%T Tree-structured maximal common subgraph searching. An example of
   parallel computation with a single sequential processor
%J Tetrahedron Computer Methodology
%V 2
%N 3
%P 177-202
%D 1989
%K c1989, c198x, c19xx, maximal common subgraph, MCS, MCES, MCS1,
   chemical compound
%X "... selection of starting materials for synthesis of a target molecule. This
   alg. achieves parallelism of up to 20-fold with a single processor by using a
   unique storage tree. ... requires only 79% of the storage req. by a
   sequential organization & the storage tree requires only 28% of the bonds to
   be represented. The alg. continues to improve rel.to the seq. org. as the #
   of compounds in the library increases. The efficiency of the alg. was eval.
   with 4 queries for 10 different sized libraries, ordered in various ways..."
   -- [<A HREF="http://dx.doi.org/10.1016/0898-5529(89)90046-8">doi:10.1016/0898-5529(89)90046-8</A>]['10].
   (Tree based index, data struct., of chem. substructs..)

%A H. Cameron
%T Balance in AVL trees and space cost of brother trees
%J Theor. Comp. Sci.
%V 127
%P 199-228
%M MAY
%D 1994
%K AVL, height balanced tree, brother tree, tree, trees, TCS, jrnl
   dataStructure, DS, c1994, c199x, c19xx
%X [Also search for: AVL tree].

%A L. Li
%T Java: Data Structures and Programming
%I SpringerVerlag
%M MAR
%D 1998
%P 440
%K book, text, c1998, c199x, c19xx, DS, Java, structure, algorithm,
   object oriented programming language, OO, OOP, zz0698
%X hb, uk us isbn:354063763X; uk us isbn13:978-3540637639; dm89.90, au$74.75;
   lists, trees, graphs, networks, CD-rom included.

%A E. Horowitz
%A S. Sahni
%A S. Anderson-Freed
%T Fundamentals of Data Structures in C
%I W.H.Freem'n
%P 626
%D 1993
%K book, text, cc, L2Ref, algorithms, programming
%X 2nd ed c2007, pb, uk us isbn:0929306406; uk us isbn13:978-0929306407.
   1st ed c1984, hb, uk us isbn:0914894226; uk us isbn13:978-0914894223.
   via Kim M.

%A R. L. Kruse
%A C. L. Tondo
%A B. Leung
%T Data Structures and Program Design in C
%I PrenticeHall
%D 1997
%K book, text, c1997, c199x, c19xx, algorithms, cc, L1Ref,
   computer programming, c, cc
%X pb, uk us isbn:013288366X; uk us isbn13:978-0132883665.
   prescribed in cse-1303 '98.

%A M. A. Weiss
%T Data Structures and Algorithm Analysis in Java
%I AddisonWesley
%P 576
%M OCT
%D 1998
%K book, text, algorithms, structure, c1998, c199x, c19xx, L3Ref, L4Ref, L5Ref
%X 2nd ed 2006; hb us$95; uk us isbn:0321370139; uk us isbn13:978-0321370136.
   "...either an advanced DS course or a 1st-year grad. course..."
   1st ed 1998; hb us$114; uk us isbn:0201357542; uk us isbn13:978-0201357547.
   [<A HREF="http://www.cs.fiu.edu/~weiss/">auth</A>]['05].

%A R. L. Kruse
%A A. J. Ryba
%T Data Structures and Program Design in C++
%I PrenticeHall
%P 717
%D 1999
%K book, text, c1999, c199x, c19xx, algorithms, cc, cplusplus, zz0799
%X tb, uk us isbn:0137689950; uk us isbn13:978-0137689958. us$63

%A T. Standish
%T Data Structures, Algorithms and Software Principles in C
%I W. H. Freem'n
%D 1995
%K book, text, cc, L1Ref, L2Ref, computer programming
%X via Kim M'

%A Kingston
%T Algorithms and Data Structures
%I AddisonWesley
%D 1990
%K book, text, L2Ref, L3Ref, programming
%X via Kim M'

%A R. Giegerich
%A S. Kurtz
%T A comparison of imperative and purely functional suffix tree constructions
%J Sci. of Comp. Programming
%V 25
%N 2-3
%P 187-218
%D 1995
%K jrnl, SCP, functional programming, FP, tree, trees, c1995, c199x, c19xx,
   lazy, string, strings, dataStructure, DS
%X [<A HREF="ftp://ftp.uni-bielefeld.de/pub/papers/techfak/pi/ToAppearInSCP25No2-3.ps.gz">.ps.gz</A>][5/'04]
   [<A HREF="http://www.techfak.uni-bielefeld.de/~kurtz/publications.html">~kurtz</A>][5/'04]
   [<A HREF="http://www.techfak.uni-bielefeld.de/ags/pi/Agpi/publications.html">uni-bielefeld</A>][5/'04].

%A M. A. Weiss
%T Data Structures and Algorithm Analysis in C
%I AddisonWesley
%P 511
%D 1997
%O ``D S and A A'' [not in C], Benjamin_Cummings, '92
%K book, text, L2Ref, L3Ref, c1997, c199x, c19xx, computer programming,
   algorithms, data structure, list, tree, C, cc, gcc
%X us$111; 600pp,
   2nd ed c1997, hb, uk us isbn:0201498405; uk us isbn13:978-0201498400.
   [<A HREF="http://www.cs.fiu.edu/~weiss/">auth</A>]['05],
   [also search for: Weiss book].

%A G. Huet
%T Functional pearl: The zipper
%J JFP
%V 7
%N 5
%P 549-554
%D 1997
%K JFP, c1997, c199x, c19xx, zz0716, FP, data structure, dataStructure, DS,
   list, tree, focus, attention, traverse, traversal, Xmonad, zipping, zipper
%X "Almost every programmer has faced the problem of representing a tree
   together with a subtree that is the focus of attention, where that focus may
   move left, right, up or down the tree. The Zipper is Huet's nifty name for a
   nifty data structure which fulfills this need. I wish I had known of it when
   I faced this task, because the solution I came up with was not quite so
   efficient or elegant as the Zipper."
   -- [<A HREF="https://dx.doi.org/10.1017/s0956796897002864">doi:10.1017/s0956796897002864</A>]['16].
   Also see zipper@[<A HREF="https://en.wikipedia.org/wiki/Zipper_(data_structure)">wikip</A>]['16].

%A A. Manousaka
%A Y. Manolopoulos
%T Fringe analysis of 2-3-trees with a lazy parent split
%J COMPJ
%V 43
%N 5
%P 420-429
%D 2000
%K COMPJ, jrnl, LPS, 2 3 tree, trees, 23tree, 23trees, Btree, Btrees,
   concurrent, lock, locking, database, zz0301, c2000, c200x c20xx
%X ... parent splits postponed until a future access of the latter node.
   ... 2-3 trees with LPS have slightly better performance, more keys in
   the fringe, ...  [16 refs],
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/43.5.420">doi:10.1093/comjnl/43.5.420</A>]['05].
   [Also search for: 23tree].

%A V. Koltun
%T Segment intersection searching problems in general settings
%J Annual Symp. on Computational Geometry
%P 197-206
%D 2001
%K conf, c2001, c200x, c20xx, segment, arc, arcs, triangular windowing problem
%X "... segment intersection searching amidst (possibly intersecting) algebraic
   arcs in the plane.  ... preprocess n arcs in O(n^2+epsilon)-time ...
   data struct size O(n^2+epsilon) ... s.t. the k arcs intersecting a seg. can
   be counted in O(log n) time ...
   ...efficient data structure for the triangular windowing problem, which is a
   generalization of triangular range searching. As another application, the
   1st substantially sub-quadratic algorithm for a red-blue intersection
   counting problem is derived. We also describe simple data structures for
   segment intersection searching among disjoint arcs, & ray shooting among
   algebraic arcs."
   [<A HREF="http://doi.acm.org/10.1145/378583.378667">doi:10.1145/378583.378667</A>]['06]

%A M. A. Weiss
%T Data Structures and Problem Solving Using Java
%I AddisonWesley
%P 928
%M AUG
%D 2001
%K book, text, structure, algorithm, algorithms, c2001, c200x, c20xx,
   L1Ref, L2Ref, computer programming
%X "... text for a 2-semester sequence in computer science introduces DS & AA
   ... Big-Oh, ... paradigms, ...".  us$102,
   2nd ed c2001, hb, uk us isbn:0201748355; uk us isbn13:978-0201748352.
   [<A HREF="http://www.cs.fiu.edu/~weiss/">auth</A>]['05]

%A J. Scott Vitter
%T External memory algorithms and data structures: Dealing with massive data
%J ACM Computing Surveys
%V 33
%N 2
%P 209-271
%M JUN
%D 2001
%K jrnl, c2001, c200x, c20xx, survey, algorithm, data structure, DS, batched,
   online, data mining, IO, transparent parallel I/O programming, TPIE,
   external memory, large, huge, dataset, datasets, zz0607
%X "... solving batched and online problems efficiently in external memory. ...
   ... include distribution and merging. ... sorting, however, disk striping
   can be nonoptimal with respect to I/O, so to gain further improvements we
   discuss distribution and merging techniques ... dictionary lookup and range
   searching. The two important classes of indexed data structures are based
   upon extendible hashing & B-trees.  ... filtering & bootstrapping ..."
   -- [<A HREF="http://doi.acm.org/10.1145/384192.384193">doi:10.1145/384192.384193</A>]['07].

%A R. Raman
%A V. Raman
%A S. S. Rao
%T Succinct dynamic data structures
%I SpringerVerlag
%S LNCS
%V 2125
%P 426-437
%D 2001
%K conf, c2001, c200x, c20xx, succinct, compressed, data structure, index,
   vector ints, array, dynamic, insert, delete, rank, select, partial sum, sums,
   sparse bit map, bitmap, bitmaps, insertion , deletion, dataStructure, DS
%X "... succinct data structs. to represent (i) a seq. of values to support
   partial sum & select queries & update ... & (ii) a dynamic array [of] a
   seq. of elts which supports insertion, deletion & access of an elt at any
   given index.  For the partial sums problem on n non-neg. ints. of k bits each
   we support update ops in O(b) time & sum in O(logb n) time, for any param. b,
   lg n/lglg n <= b <= n**eps for any fixed +ve eps < 1. The space used is
   kn+o(kn) bits & the time bounds are optimal. When b=lgn/lglgn or k=1 (i.e.,
   .. a bit-vector), we can also support the select op. in the same time as the
   sum op., but the update time becomes amortised.  For the dynamic array
   problem, we give 2 structs. both using o(n) bits of extra space where n is
   the # of elts in the array: one supports lookup in const. worst case time &
   updates in O(n**eps) worst case time, & the other supports all ops. in
   O(lgn/lglgn) amortized time. The time bnd of both ... structs. are optimal."
    -- [<A HREF="http://dx.doi.org/10.1007/3-540-44634-6_39">doi:10.1007/3-540-44634-6_39</A>]['10],
   pdf@[<A HREF="http://www.imsc.res.in/~vraman/pub/wads_01.pdf">res.in</A>]['10].
   [Also search for: succinct data structure], and
   [also search for: rank select data structure].

%A L. Arge
%A M. Bender
%A E. Demaine
%A B. Holland-Minkley
%A J. I. Munro
%T Cache-oblivious priority-queue and graph algorithms
%J Proc. 34th ACM Symposium on Theory of Computation
%P 268-276
%I ACM
%D 2002
%K conf, c2002, c200x, c20xx, graphs, cache-oblivious algorithm, cache aware,
   Pqueue, PQ, insert, delete, deleteMin
%X "... develop an optimal cache-oblivious priority queue data structure,
   supporting insertion, deletion, & deletemin ops in O(1 / B log(M/BN) / B)
   amortized memory transfers, where M & B are the memory & block transfer sizes
   of any 2 consecutive levels of a multilevel memory hierarchy. In a cache-
   -oblivious DS, M & B are not used in the description of the structure. The
   bounds match the bounds of several previously developed external-memory
   (cache-aware) priority queue data structures, which all rely crucially on
   knowledge about M & B. Priority queues are a critical component in many of
   the best known external-memory graph algs., & using our cache-oblivious [PQ]
   we develop several cache- oblivious graph algorithms."  [38 refs]
   -- [<A HREF="http://doi.acm.org/10.1145/509907.509950">doi:10.1145/509907.509950</A>]['07]; uk us isbn:1581134959.

%A P. Bozanis
%A A. Nanopoulos
%A Y. Manolopoulos
%T LR-tree: A logarithmic decomposable spatial index method
%J COMPJ
%V 46
%N 3
%P 319-331
%M MAY
%D 2003
%K jrnl, COMPJ, LR-Tree, LRtree, LRtrees, R-Tree, Rtree, Rtrees, space, index,
   search, data structure, dataStructure, DS, c2003, c200x, c20xx, zz0603
%X [<A HREF="http://dx.doi.org/10.1093/comjnl/46.3.319">doi:10.1093/comjnl/46.3.319</A>]['05]
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_46/Issue_03/460319.sgm.abs.html">abs</A>][5/'03]

%A R. Giegerich
%A S. Kurtz
%A J. Stoye
%T Efficient implementation of lazy suffix trees
%J SPE
%V 33
%N 11
%P 1035-1049
%D 2003
%K jrnl, SPE, c2003, c200x, c20xx, suffix tree, prefix, string, strings, space,
   zz0204
%X "...efficient implementation of a write-only top-down construction for
   suffix trees. ...new, space-efficient representation... 12 bytes per input
   character in the worst case and 8.5 bytes... on average..."
   [<A HREF="http://dx.doi.org/10.1002/spe.535">doi:10.1002/spe.535</A>][2/'04]

%A M. T. Goodrich
%A R. Tamassia
%T Data Structures and Algorithms in Java
%I Wiley
%P 656
%M JAN
%D 2004
%K book, text, c2004, c200x, c20xx, structure, algorithm, computer programming
%X 3rd ed c2003, us$100, hb, uk us isbn:0471644528; uk us isbn13:978-0471644521.

%A G. F. Georgakopoulos
%A D. J. McClurkin
%T Generalized template splay: A basic theory and calculus
%J COMPJ
%P 10-19
%V 47
%N 1
%M JAN
%D 2004
%K jrnl, compj, tree, trees, Sleator, Tarjan, self-adjusting, multi-way,
   amortized cost, c2004, c200x, c20xx
%X "...generalize the technique of classic splay trees of Sleator & Tarjan,
   showing that almost all template-based rules for self-adjusting a multi-way
   tree have logarithmic amortized cost & other properties of splay trees, such
   as 'static optimality', the 'static finger' & 'working set' properties. We
   achieve this by defining in a new way (through 'progress factors') a
   potential on a weighted tree, & by introducing a new technique (which we
   call '[plusmn] calculus') for calculating the changes in potential."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/47.1.10">doi:10.1093/comjnl/47.1.10</A>]['05]
   -- [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_47/Issue_01/470010.sgm.abs.html">www</A>][1/'04]

%A L. Arge
%A G. Stolting Brodal
%A R. Fagerberg
%A M. Laustsen
%T Cache-oblivious planar orthogonal range searching and counting
%J Proc. 21st Symp. on Computational Geometry
   (session: Geometric algorithms in alternate computational models)
%W Pisa
%I ACM
%P 160-169
%D 2005
%K conf, c2005, c200x, c20xx, 2D, planar, range query, sided, data structure,
   geometry, geometric, algorithm,  multilevel memory, aware
%X "... the first cache-oblivious [DS] for planar orthogonal range counting, &
   improve on previous results for cache-oblivious planar orthogonal range
   searching. ... uses O(N log2 N) space & answers queries using O(logB N)
   memory transfers, where B is the block size of any memory level in a
   multilevel memory hierarchy. Using bit manipulation techniques, the space
   can be further reduced to O(N). The structure can also be modified to support
   more general semigroup range sum queries in O(logB N) memory transfers, using
   O(N log2 N) space for 3-sided queries & O(N log2**2 N/log2 log2 N) space for
   4-sided queries.Based on the O(N log N) space range counting structure, we
   develop a data structure that uses O(N log2 N) space & answers 3-sided range
   queries in O(logB N+T/B) memory transfers, where T is the number of reported
   points. Based on this structure, we present a general 4-sided range searching
   structure that uses O(N log2**2 N/log2 log2 N) space & answers queries in
   O(logB N + T/B) memory transfers." isbn:1581139918; [28 refs].
   -- pdf@[<A HREF="http://doi.acm.org/10.1145/1064092.1064119">doi:10.1145/1064092.1064119</A>]['07].

%A H. Samet
%T Foundations of Multidimensional and Metric Data Structures
%I MorganKaufmann
%D 2006
%P 1024
%K book, text, c2006, c200x, c20xx, Multidimensional, Metric, Data Structures,
   computer graphics, cgi, 2D, 3D, computational geometry, spatial indexing
%X 1st ed 2006, hb us$56; uk us isbn:0123694469; uk us isbn13:978-0123694461.

%A R. Raman
%A V. Raman
%T S. R. Satti
%T Succinct indexable dictionaries with applications to encoding k-ary trees,
   prefix sums and multisets
%J TOPLAS
%I ACM
%P 3
%N 4
%P article #43
%M NOV
%D 2007
%K jrnl, TOPLAS, c2007, c200x, c20xx, succinct, compressed, data structure,
   index, dictionary, rank, select, insert, delete, partial sum, sums, multiset,
   set, frequency, tree, sparse bit map, bitmap, Fich, Miltersen, Pagh
%X "... storing a set S subsetof {0,...,m-1} for some int. m while supporting
   the ops. rank(x), which returns the # of elts in S that are < x if x in S,
   and -1 otherwise; & select(i) ... . We give a d.struct. ... both ops. in
   O(1) time on the RAM model & requires B(n,m)w+o(n)+O(lglg m) bits to store a
   set of size n, where B(n,m)=floor(lg(m/n) is the min. # of bits required to
   store any n-elt subset from a universe of size m. Previous dictionaries
   taking this space only supported (yes/no) membership queries in O(1) time. In
   the cell probe model we can remove the O(lg lg m) additive term in the space
   bnd, answering a Q. raised by Fich & Miltersen [1995] & Pagh [2001]. ... "
   -- [<A HREF="http://doi.acm.org/10.1145/1290672.1290680">doi:10.1145/1290672.1290680</A>]['10].
   [Also search for: succinct data structure], and
   [also search for: rank select data structure].

%A E. K. Lee
%A C. U. Martel
%T When to use splay trees
%J SPE
%V 37
%N 15
%P 1559-1575
%D 2007
%K jrnl, SPE, c2007, c200x, c20xx, data structure, DS, search, splay tree,
   cache, architecture, speed, time, zz1107
%X "... new empirical results for splay trees. ... understanding of how
   cache performance affects query execution time. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.813">doi:10.1002/spe.813</A>]['07].

%A M. Patrascu
%T Succincter
%J 49th IEEE Symp. on Foundations of Comp. Sci.
%P 305-313
%D 2008
%K conf, FOCS, FOCS49, FOCS08, c2008, c200x, c20xx, zz0610, succinct,
   data structures, redundancy, time, space, trade off, structure, succincter,
   locally decodable arithmetic coding
%X "We can rep'nt an array of n values from {0,1,2} using ceil(n log2(3)) bits
   ... but then we cannot retrieve a single element efficiently. Instead, we can
   encode every block of t elements using ceil(t log2(3)) bits, & bound the
   retrieval time by t. ... a linear trade-off between the redundancy of the
   rep'n & the query time. ... folk wisdom is that [by wasting] 1-bit/block, the
   encoding is so constrained that it cannot help the query in any way. Thus,
   the only thing a query can do is to read the entire block & unpack it.
   We break this limitation & show how to use recn to improve redundancy. It
   turns out that if a block is encoded with 2 (!) bits of r., we can decode a
   single elt, & answer many other interesting queries, in time logarithmic in
   the block size. ... allows us to revisit classic problems in s. data struct.,
   & give surprising new upper bounds. We also construct a locally-decodable
   version of arithmetic coding."
   -- pdf@[<A HREF="http://people.csail.mit.edu/mip/papers/succinct/succinct.pdf">mit</A>]['10],
      [<A HREF="http://people.csail.mit.edu/mip/">auth</A>]['10].
   [Also search for: succinct data structure].

%A N. R. Brisaboa
%A S. Ladra
%A G. Navarro
%T Directly addressable variable-Length codes
%J Proc 16th Int. Symp. on String Processing and Information Retrieval
%P 122-130
%I SpringerVerlag
%S LNCS
%V 5721
%D 2009
%K conf, c2009, c200x, c20xx, succinct, compressed, data structure, structures,
   sparse, bit map, bitmap, partial sum, sums, inverted index, code,
   vector of mostly small ints
%X "We introduce a symbol reordering technique that implicitly synchronizes
   variable-length codes, s.t. it is possible to directly access the i-th
   codeword without need of any sampling method. The technique is practical and
   has many applications to the representation of ordered sets, sparse bitmaps,
   partial sums, and compressed data structures for suffix trees, arrays, and
   inverted indexes, to name just a few. We show experimentally that the
   technique offers a competitive alternative to other data structures that
   handle this problem."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-03784-9_12">doi:10.1007/978-3-642-03784-9_12</A>]['10].
   [Also search for: succinct data structure].

%A P. Ribeiro
%A F. Silva
%A G-tries: an efficient data structure for discovering network motifs
%J Proc. ACM Symp. on Applied Computing
%W Sierre, Switzerland
%I ACM
%P 1559-1566
%D 2010
%K conf, c2010, c201x, c20xx, gTrie, gTries, trie, graph, network, motif,
   subgraph, subgraphs, data structure
%X "... propose a novel specialized data struct. ... g-trie, [for] collections
   of subgraphs. ... idea is akin to a prefix tree in the sense that we take
   advantage of common topology by constructing a multiway tree where the
   descendants of a node share a common substruct.. We give algs. to construct a
   g-trie, to list all stored subgraphs, & to find occurrences on another graph
   of the subgraphs stored in the g-trie. We evaluate the implementation of this
   structure & its assoc. algs. on a set of representative benchmark biol. n/wks
   [] to find n/w motifs. ... we compare their performance with other known
   n/w motif algs. also implemented in the same common platform. ... show that
   indeed, g-tries are a feasible, adequate & very efficient data structure for
   n/w motifs discovery, clearly outperforming previous algs. & DSs."
   uk us isbn13:978-1-60558-639-7.
   -- [<A HREF="http://doi.acm.org/10.1145/1774088.1774422">doi:10.1145/1774088.1774422</A>]['10].

%A T. M. Moosaa
%A M. S. Rahma
%T Indexing permutations for binary strings
%J IPL
%V 110
%N 18-19
%P 795-798
%M SEP
%D 2010
%K jrnl, IPL, c2010, c201x, c20xx, zz0810, binary, string, permutation, index,
   permutations
%X "Given a pattern P of length m and a text T of length n, the permutation
   matching problem asks whether any perm. of P occurs in T. Indexing a string
   for perm. matching seems to be quite hard in spite of the existence of a
   simple non-indexed soln. It is an open question whether there exists an
   index data struct. for this problem with o(n**2) time & space complexity even
   for a binary alphabet. ... we settle this q. by reducing the problem to the
   (min,+) convolution problem & thereby achieving an O(n**2/log n) time data
   struct. for a binary string capable of answering perm. queries in O(m) time.
   The space requirement of the data structure is also improved to be linear."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2010.06.012">doi:10.1016/j.ipl.2010.06.012</A>]['10].

%A J. Katajainena
%A S. S. Rao
%T A compact data structure for representing a dynamic multiset
%J IPL
%V 110
#N 23
%P 1061-1066
%M NOV
%D 2010
%K jrnl, IPL, c2010, c201x, c20xx, zz1010, compact, succinct, data structure,
   multiset, multi set, dataStructure, DS
%X "... maintaining a dynamic multiset that uses (On lg lg n / lg n) bits &
   O(1) words, in addition to the space required by the n elts stored, supports
   searches in O(lg n) worst-case time & updates in O(lg n) amortized time.
   Compared to earlier d.structs., we improve the space requirements from
   O(n) bits to O(n lg lg n / lg n) bits, but the running time of updates is
   amortized, not worst-case."  [11 refs].
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2010.08.007">doi:10.1016/j.ipl.2010.08.007</A>]['10].

%A M. Shapiro
%A N. Preguica
%A C. Masquero
%A M. Zawirski
%T Conflict-free replicated data types
%J 13th Symp. on Stabilization, Safety and Security in Distributed Sys.
%I SpringerVerlag
%O LNCS vol.6976
%P 386-400
%M OCT
%D 2011
%K conf, SSS, c2011, c201x, c20xx, zz0112, CRDT, CRDTs, type, data structure,
   consistency, eventual, strong, EC, SEC
%X "Replicating data under Eventual Consistency (EC) allows any replica to
   accept updates without remote synchronisation. This ensures performance &
   scalability in large-scale distributed sys. (e.g., clouds). However,
   published EC approaches are ad-hoc & error-prone. Under a formal Strong
   Eventual Consistency (SEC) model, we study sufficient condns for convergence.
   A data type that satisfies these conditions is called a Conflict-free
   Replicated Data Type (CRDT). Replicas of any CRDT are guaranteed to converge
   in a self-stabilising manner, despite any number of failures. ... formalises
   two popular approaches (state- & operation-based) & their relevant sufficient
   condns. We study a number of useful CRDTs, such as sets with clean semantics,
   supporting both add & remove ops., & consider in depth the more complex Graph
   data type. CRDT types can be composed to develop large-scale distributed
   applications, & have interesting theoretical properties."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-24550-3_29">doi:10.1007/978-3-642-24550-3_29</A>]['12].

%A K. Headley
%A M. A. Hammer
%T The random access zipper: Simple, purely-functional sequences
%J arXiv
%M AUG
%D 2016
%K TR, c2016, c201x, c20xx, zz0816, FP, data structure, dataStructure, DS,
   zipper, RAZ, update
%X "We introduce the Random Access Zipper (RAZ), a simple, purely-functional
   data structure for editable sequences. A RAZ combines the structure of a
   z. with that of a tree: like a z., edits at the cursor require constant time;
   by leveraging tree structure, relocating the edit cursor in the seq. requires
   logarithmic time. While existing data structures provide these time bounds,
   none do so with the same simplicity & brevity of code as the RAZ. The
   simplicity of the RAZ provides the opportunity for more programmers to extend
   the structure to their own needs ..."
   -- 1608.06009@[<A HREF="http://arxiv.org/abs/1608.06009">arXiv</A>]['16].
   [Also search for: FP zipper].

%A S. Edelkamp
%A A. Elmasry
%A J. Katajainen
%T Heap construction - 50 years later
%J COMPJ
%V 60
%N 5
%P 657-674
%M APR
%D 2017
%K jrnl, COMPJ, c2017, c201x, c20xx, zz0517, algorithm, data structure, binary,
   heap, sort, sorting, heapify
%X "... constructing a binary heap in an array using only a small amount of
   additional space. Let N denote the size of the input, M the capacity of the
   cache, & B the width of the cache lines of the underlying computer, all
   measured as numbers of elts. We show that there exists an in-place
   heap-construction alg. that runs in theta(N) worst-case time & performs at
   most 1.625N+o(N) elt comparisons, 1.5N+o(N) elt moves, N/B+O(N/MÂ·lgN) cache
   misses, & 1.375N+o(N) branch mispredictions. The same bound for the # of elt
   comparisons was derived & conjectured to be optimal by Gonnet & Munro;
   however, their alg. requires theta(N) pointers. For a tuning parameter S, the
   idea is to divide the input into a top tree of size theta(N/S) s.t. each of
   its leaves root a bottom tree of size theta(S). When S=theta(lgN/lglgN), we
   can convert the bottom trees into heaps one by one by packing the extra space
   needed in a few words, & subsequently use Floyd's sift-down procedure to
   adjust the heap order at the upper levels. ..."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxw085">doi:10.1093/comjnl/bxw085</A>]['17].
   [Also search for: Williams heap] and [also search for: Floyd heap].

%A R. Hinze
%T On constructing 2-3 trees
%J JFP
%V 28
%P e19
%M OCT
%D 2018
%K jrnl, JFP, FP, c2018, c201x, c20xx, zz1118, 2-3 tree, 23tree, data structure,
   incremental
%X "We consider the task of constructing 2-3 trees. Given a seq. of elts we seek
   to build a 2-3 tree - in linear time - that contains the elts in symmetric
   order. We discuss three approaches: top-down, bottom-up, & incremental. The
   incremental approach is more flexible than the other two in that it allows us
   to interleave the construction work with other ops., e.g., queries."
   -- [<A HREF="https://doi.org/10.1017/S0956796818000187">doi:10.1017/S0956796818000187</A>]['18].
   [Also search for: 23tree].

%A R. E. Tarjan
%A U. Zwick
%T Optimal resizable arrays
%J SIAM J. Comput.
%V 53
%N 5
%P ?-?
%M OCT
%D 2024
%O Optimal resizable arrays, arxiv, NOV 2022
   [<A HREF="https://arxiv.org/abs/2211.11009">arXiv:2211.11009</A>]['22]
%K jrnl, c2024, c202x, c20xx, zz1024, resize, resizeable, grow, shrink, space,
   array, data structure
%X "... We distinguish between the space needed for storing a resizable array,
   & accessing its items, & the temp. space that may be needed while growing or
   shrinking the a.. For every int. r>=2, we show that N+O(N^{1/r}) space is
   suff. for storing & accessing an array of size N, if N+O(N^{1-1/r}) space
   can be used briefly during grow & shrink operations. Accessing an item by
   index takes O(1) worst-case time, while grow & shrink operations take O(r)
   amortized time. ..."
   -- [<A HREF="https://doi.org/10.1137/23M1575792">doi:10.1137/23M1575792</A>]['24].


%A L. G. Valiant
%T Parallelism in comparison problems
%J SIAM J. Comput.
%V 4
%N 3
%M SEP
%D 1975
%P 348-355
%K parallel algorithm, comparison, sort, merge, sorting, merging, tournament,
   complexity
%X worst case time complexity of algorithms for multiprocessor computers
   binary comparisons as the basic operation
   Problems: max, sort, merge sorted lists.
   data size n >= k processors
   Speedups of at least O(k/log log k) can be achieved wrt comparison
   operations,
   the max algorithm is shown optimal.

%A W. D. Hillis
%A G. L. Steele
%T Data parallel algorithms
%J CACM
%M DEC
%D 1986
%V 29
%N 12
%P 1170-1183
%K parallel algorithm, computer, machine, connection machine
%X algorithms appropriate for fine-grained parallel computers with general
   communication.  All use O(N) processors on problems of size N to solve
   usually in time O(log N).
   64K and 16K-processor ! machines used.
   Each has 4K bits of memory.
   SIMD machine, not MIMD, processors have state bit.
  Examples: Sum array of numbers; all partial sums of an array;
   count and enumerate active processors; radix sort; parse a regular language;
   SKI functional applicative programming language parallel combinator
   reduction; find end of linked list; all partial sums
   of linked list; zip two lists; region labelling.

%A A. H. Karp
%T Programming for Parallelism
%J Computer
%V 20
%N 5
%P 43-57
%M MAY
%D 1987
%K parallel processor, computer, machine, hardware, architecture,
   general purpose, MIMD, survey

%A P. C. Burkimsher
%T Combinator reduction in a shared memory multiprocessor
%J COMPJ
%P 214-222
%M JUN
%D 1987
%V 30
%N 3
%X A parallel combinator reduction machine for a shared memory multiprocessor
   is described: Prism.
   Graphical representation and decentralised scheduling algorithm is
   independent of number of processors.
   Lazy evaluation, extract parallelism at lowest expression level
   called microparallelism.
   Typical programs do not exhibit sufficient mp.
   Modified to do simultaneous evaluation of list elements.
   Improved and can use up to four (4) processors.
   Direct shared memory ideal for parallelism at this scale.
   Concludes that approach good for direct shared memory machines
      but lazy and lists => parallelism greatly restricted.
      So,  sets and eager evaluation may be better.
%K parallel machine, functional, applicative, implementation, language,
   micro, microparallelism, fine grained, lazy, need, list, set, evaluation

%E J. Wing
%E M. Herlihy
%E M. R. Barbacci
%T Proc. from the second workshop on large-grained parallelism
%M NOV
%D 1987
%W Hidden Valley, Pennylvania
%I Carnegie Mellon University
%R CMU/SEI-87-SR-5
%X Extended Abstracts only
   R. Agrawal  Using a network of computer workstations as a loosely coupled
               microprocessor
   S. R. Ahuja, J. R. Ensor, D. N. Horn Parallelism in the Rapport multimedia
               conferencing system
   R. Alonso, L. Cova, K. Kyrimis. Process Scheduling in loosely coupled
               computer networks
   M. R. Barbacci, C. B. Weinstock, J. M. Wing. Durra : language support for
               large-grained parallelism
   R. Bisiani, A. Forin. Agora : heterogeneous and multilanguage parallel
               programming
   F. Bitz, J. A. Webb. Simulation and performance evaluation of heterogeneous
               parallel robotic systems
   D. L. Bryan. Run-time monitoring of tasking behaviour using a specification
               language
   R. Bubenik, W. Zwaenepoel. Eager evaluation in a program development
               environment
   E. C. Cooper, M. B. Jones. An object-oriented approach to remote procedure
               call stub generation fro heterogeneos environments
   C. Diegert. Coupling a network computing resource to a VLSI placement
               problem
   A. K. Elmagarmid. Transaction processing in heterogeneous distributed
               databases
   S. A. Friedberg. Hierarchical process composition
   Jean-Luc Gaudiot, Liang-Teh Lee. Large-grained data-driven approach to
               multiprocessor programming
   T. B. Gendreau. Scheduling in distributed systems
   J. I. Glasgow, G. H. MacEwan, D. B. Skillicorn. Expressing large-grained
               parallelism using operator nets
   A. S. Grimshaw, J. W. S. Liu, M. D. Thomas. Mentat : a prototype macro
               data flow system
   M. P. Herlihy, J. M. Wing. Avalon : language support for reliable
               distributed systems
   N. C. Hutchinson. Emerald : a language to support distributed programming
   D. S. Lane. Modelling time dependent behaviour in parallel software systems
   P. J. Leach. LPG2 position paper.
   I. Lee. A programming system for heterogeneous distributed environment
   P. Le Guernic, A. Benveniste. The synchronous language Signal
   D. E. Long. Optimistic algorithms for replicated data management
   M. S. McKendry The FileNet System
   M. K. Molloy. Requirements for the performance evaluation of parallel systems
   K. T. Narayana. Proving real-time communicating sequential processes correct
   D. Notkin. Research in parallelism at the University of Washington
   C. Pu. Supertransactions
   E. S. Roberts, J. R. Ellis. parmake and dp
   M. Satyanarayanan, J. K. Kistler, E. H. Siegel. Coda : a resilient
                 distributed file system
   L. Shrira. Mercury MIT
   J. A. Stankovic, D. Towsley, G. Rommel. Scheduling parallel programs on a
                 distributed system
   M. Sullivan. Marionette : support for highly parallel distributed programs
   J. Van Zandt   The Pharros project
   W. E. Weihi. Research in distributed systems
   C. T. Wilkes, R. J. LeBlanc. Programming language features for resilience
                 and availibility
   J. M. Wrabetz. A coarse-grained distributed multiprocessing system
   H. Wupper, J. Vytopil. Static typing of temporal and reliability attributes
                 in distributed systems

%A D. L. Waltz
%T Applications of the connection machine
%J Computer
%V 20
%N 1
%M JAN
%D 1987
%P 85-97
%K parallel machine, hypercube, connection machine
%X an ultra fine grained hypercude 16K - 64K processors
   reviewed in Computing Reviews Jan 1988 p 61-62

%A T. P. Blumer
%A P. D. Sidhu
%T Mechanical verification and automatic implementation of communication
   protocols
%J IEEE Trans. Softw. Eng.
%V SE-12
%N 8
%P 827-843
%M AUg
%D 1986
%K communication protocol
%X protocol, specified as a finite state machine
   verifier - reachability, completeness, freedom from deadlock
   compiler to C
   Reviewed Computing Reviews Jan 1988 p 62

%A B. Krautrachue
%A T. Lewis
%T Grain size determination for parallel processing
%J IEEE softw.
%V 5
%N 1
%P 23-32
%M jan
%D 1988
%K parallel, process, granularity


%A J. C. Browne
%A S. J. Kim
%Z U. Texas
%T A General Approach to the Mapping of Parallel Computations upon
   Multiprocessor Architectures
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 1-8
%K Computational Complexity, MIMD, partitioning, linear cluster merging
%X dominant request tree, homogeneous versus heterogeneous mapping,
   Sieve of Eratosthenes on iPSC, Gaussian elimination on Sequent Balance,
   molecular dynamics,

%A Joseph JaJa
%A Shing-Chong Chang
%Z U. Maryland
%T Parallel Algorithms for River Routing
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 9-13
%K Computational Complexity, CREW-PRAM, VLSI, separation problem,
   planar net wiring, routability metric,
%X Extended abstract.

%A Kazuo Sugihara
%A Ichiro. Suzuki
%T Nearly Optimal Clock Synchronization under Unbounded Message
   Transmission Time
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 14-17
%K Computational Complexity, network of processes, message passing,
%X Extended abstract.

%A Joseph JaJa
%A Shing-Chong Chang
%Z U. Maryland
%T Parallel Algorithms for Channel Routing in the Knock-Knee Model
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 18-25
%K CREW-PRAM, VLSI, diagonal diagram, partition grid,
   layer assignment,

%A Y. M. Huang
%A M. Sarrafzadeh
%Z NW U.
%T Parallel Algorithm for Minimum Dual-Cover with Application to
   CMOS Layout
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 26-33
%K VLSI, PRAM, planar graphs, series parallel (SP) graphs,
   dual Euler trail (DET), optimal dual cover, graph separator theory,
   trailhunt, tree separation,

%A Richard M. Fujimoto
%Z U. Utah
%T Lookahead in Parallel Discrete Event Simulation
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 34-41
%K BBN Butterfly, logical processes,
   deadlock avoidance, detection, recovery, performance metrics,
   speedup, null message ratio, deadlock ratio, message avalanche,
   queueing network, FCFS, PRIO, PREEMPT, PRIORITY, communication

%A David E. Foulser
%Z Yale U.
%T A Blocked Jacobi Method for the Symmetric Eigenproblem
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 42-46
%K Numeric Algorithms, blocked classical Jacobi (BCJ),
   block Brewnt-Luk symmetric Eigensolvers, hypermatrix adaptation

%A G. R. Gao
%A S. J. Thomas
%Z McGill
%T An Optimal Parallel Jacobi-Like Solution Method
   for the Singular Value Decomposition
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 47-53
%K Numeric Algorithms, SVD, nearest neighbor, ring topology,
   divide and exchange, single sided computation, hypercube, perfect shuffle,
   iPSC, Matlab
%X Simulator was used.

%A V. Visvanathan
%A P. Sadayappan
%T Modeling and Optimal Scheduling of Parallel Sparse Gaussian Estimation
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 54-61
%X Numeric Algorithms, Directed Acyclic Graphs (DAGs),
   Minimally Constrained Task Graphs (MCTG), Gaussian Elimination (GE),
   idealized concurrent read exclusive write (CREW),
   clique property, common children property,
   algorithm for level assignment (ALA),

%A Sridhar Madala
%A James B. Sinclair
%Z Rice U.
%T Performance of Parallel Partitioning Algorithms
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 62-68
%K parallel algorithm, task graph, Rice, RPPT
%X Non-Numeric Algorithms, task graphs, distribution driven simulation,
   merge, Rice Parallel Processing Testbed (RPPT), divide and conquer,
   independent path (IP) method, type I iterative approximation,
   independent paths normal approximation (IPN), example:
   parallel mergesort, partitioning structure

%A Virendra K. Janakiram
%A Dharma P. Agrawal
%A Ravi Mehrotra
%Z NCSU, Raleigh, NC
%T A Randomized Parallel Branch and Bound Algorithm
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 69-75
%K Non-Numeric Algorithms, b and b tree, MANIP, model, theorem, speedup,
   simulation, MPSIM PRAM-CREW, rsbb algorithm, knapsack problem,
%X Little interprocessor communication.

%A Sakti Pramanik
%A Myoung Ho Kim
%Z Michigan State
%T Generalized Parallel Processing Model for Database Systems
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 76-83
%K parallel algorithm, database, data base
%X Non-Numeric Algorithms, match retrieval search algorithms,
   single and multiple query (queries) with hits and relations,
   throughput maximization, minimum response time,
   Fieldwise eXclusive (FX) model, hashing, generalized disk modulo method
   (GDM)

%A Sanjay Ranka
%A Sartaj Sahni
%Z U. Minn.
%T Image Template Matching on SIMD Hypercube Multicomputers
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 84-91
%K parallel algorithm, computer, SIMD, image processing, IP
%X Image Analysis & Geometry, hypercube multicomputers,
   image template matching, SIMD and MIMD computers,
   one and two dimensional convolution,
   data manipulation, memory access, C1D, C2D, circulation,
   grid embedding,
   See following companion MIMD paper.

%A Sanjay Ranka
%A Sartaj Sahni
%Z U. Minn.
%T Image Template Matching on MIMD Hypercube Multicomputers
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 92-99
%K parallel algorithm, computer, MIMD, image processing, IP
%X Image Analysis & Geometry, hypercube multicomputers,
   medium grain template matching, SIMD and MIMD computers,
   one and two dimensional convolution,
   data manipulation, memory access, Kirsch templates, C2D,
   grid embedding, NCUBE, CRAY2

%A Ivan Stojmenovic
%Z U. Miami
%T Computational Geometry on a Hypercube
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 100-103
%K hyper cube, image processing, IP, convex hull, Voronoi
%X Image Analysis & Geometry, convex hull, Voronoi diagram,
   intersection problem, ECDF searching, maximal elements, dominance counting,
   parallel prefix, broadcast, merging slopes technique, CREW PRAM,
   planar point locating, closest points,

%A Quentin F. Stout
%Z U. Mich.
%T Constant-Time Geometry on PRAMs
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 104-107
%K parallel computer, PRAM, image processing, IP
%X Image Analysis & Geometry, parallel random access machines, CRCW, CRDW,
   collision detection, convex hull,
   detecting write (DW) versus concurrent write (CW) or exclusive write (EW),
   Preliminary version printed.

%A David R. O'Hallaron
%A Radhakisan S. Baheti
%Z GE R&D Center, Schenectady, NY
%T Parallel Implementation of a Kalman Filter on the Warp Computer
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 108-111
%K systolic array, mapping, sample time, W2 language,

%A H. F. Ho
%A G. H. Chen
%A S. H. Lin
%Z Taiwan
%A J. P. Sheu
%T Solving Linear Programming on Fixed-Size Hypercubes
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 112-116
%K simplex method, pipelined broadcasting

%A Floyd B. Hanson
%Z Argonne NL
%T Parallel Computation for Stochastic Dynamic Programming:
   Row Versus Column Code Orientation
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 117-119
%K dynamic programming algorithm, DPA, stochastic, random
%X Applications, Bellman's curse of dimensionality,
   optimal control of nonlinear, continuous time dynamical systems,
   vector processors/computers, machine computational model method
   Alliant FX/8, concurrent outer-vector inner (COVI) model, Fortran,

%A G. H. Atwood
%Z U. Alberta
%T Parallel Langrangian Interpolation
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 120-123
%K Lagrange, interpolate, numerical, parallel algorithm, computing
%X Applications, divided differences, polynomial, Newtonian interpolation,
   evaluation, derivation, theory, PRAM, shared memory architecture,
   The case presented by this paper is a bit weak.  It could be improved
   perhaps it was too shortened.

%A Winsre E. Alexander
%A Seong-Mo Park
%A Jung H. Kim
%T A New Approach to the Implementation of Multidimensional
   Signal Processing Algorithms
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 124-127
%K N dimensional state space (N-D),
   discrete, linear, shift-invariant (DLSI), VLSI, pipelining

%A Vipin Kumar
%A V. Nageshwara Rao
%A K. Kamesh
%Z U. Texas
%T Parallel Depth First Search on a Ring Architecture
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 128-132
%K depth first search (DFS), iso-efficiency

%A Gary D. Hachtel
%A Peter H. Moceyunas
%Z U. Colorado
%T Parallel Algorithms for Answering the Tautology Question
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 133-140
%K conf, Artificial Intelligence, AI, Encore multimax, iPSC,
   unit parallel efficiency, speed up, divide and conquer,
   COFACTOR, DPUP, GRAIL, dynamic processor assignment

%A Michael Greenberg
%A Janice E. Cuny
%Z U. Mass.
%T Parallelism in Knowledge Base Systems with Inheritance
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 141-145
%K Artificial Intelligence, AI, memory access, MIMD, metric

%A Stephen D. Simmes
%A Charles J. Turner
%Z SAIC, Tucson
%T Associative Memories on the Connection Machine
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 146-150
%K Artificial Intelligence, AI, Hopfield, CM-1, CM1, Hamming distance metric,
   asynchronous and synchronous update, image processing example

%A Manuel E. Bermudez
%A George Logothetis
%A Richard Newman-Wolfe
%Z U. FL.
%T Parallel Generation of LR Parsers
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 151-155
%K Artificial Intelligence, AI, push down automata, PDA, SLR(1), SLR1, FOLLOW

%A Ashok Goel
%A P. Sadayappan
%A John R. Josephson
%Z OSU
%T Concurrent Design of Composite Explanatory Hypotheses
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 156-160
%K Artificial Intelligence, AI, synthesis, abductive inference, abduction

%A J. Armstrong
%Z Convex
%T Algorithm and Performance Notes for Block LU Factorization
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 161-164
%K conf, c1988, c198x, c19xx, Numeric Algorithms, Gaussian elimination,
   dense systems, matrix, vector, algorithm, decomposition, Fortran,
   numerical, linear algebra

%A D. C. S. Allison
%A S. Harimoto
%A L. T. Watson
%Z Virginia Poly
%T The Granularity of Parallel Homotopy Algorithms for Polynomial Systems
   of Equations
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 165-168
%K Numeric Algorithms, linear algebra, homogenization, HOMPACK

%A Shie-Tung Peng
%A Moon S. Jun
%Z U. Maryland, Baltimore
%T A New VLSI 2-D Systolic Array for Matrix Multiplication and Its Applications
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 169-172
%K Numeric Algorithms, partition, shortest weight path, mapping
%X Short architectural description included.

%A Shie-Tung Peng
%A Thomas F. Hudson
%Z U. Maryland, Baltimore
%T Parallel Algorithms for Multiplying Very Large Integers
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 173-176
%K EREW, PRAM, FFT
%X Numeric Algorithms, exclusive read write (EREW PRAM),
   parallel random access memory, fast fourier transform (FFT),
   addition, global shared memory, ring-of-integers, complex field,

%A Gita Alaghband
%Z U. Colorado, Denver
%T A Parallel Pivoting Algorithm on a Shared Memory Multiprocessor with
   Controlled Fill-in
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 177-180
%K Numeric Algorithms, LU decomposition, MIMD, linear systems,
%X proposed HEP use

%A M. Whelan
%A Gao R. Guang
%A T. K. Yum
%Z Philips Labs, NY
%T Optimal Decomposition of Matrix Multiplication on Multiprocessor
   Architectures
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 181-185
%K Numeric Algorithms, computation communication overlap, partitioning,
   simulation, speedup

%A Mukesh Singhal
%Z OSU
%T Performance Analysis of an Optimistic Concurrency Control Algorithm
   in Replicated Database Systems
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 186-189
%K parallel algorithms, data base
%X Non-Numeric Algorithms, Thomas Write Rule (TWR),
   approximate, iterative performance model, update-commit, validation,
   response time, suspend queue,

%A Oscar H. Ibarra
%A Ting-Chuen Pong
%A Stephen M. Sohn
%Z U. Minn
%T Hypercube Algorithms for Some String Comparison Problems
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 190-193
%K Non-Numeric Algorithms, NCUBE, minimum length time warp problem,
   longest common subsequence, LCS, LCSS, edit distance, alignment,
   Levenshtein distance, block partitioning, SIMD

%A Yijie Han
%A Yoshihide Igaraski
%T Time Lower Bounds for Sorting on Multi-Dimensional Mesh-Connected
   Processor Arrays
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 194-197
%K Non-Numeric Algorithms, chain theorem, snake-like indexing,
   region cardinality

%A E. Altmann
%A T. A. Marsland
%A T. Breitkreutz
%Z U. Alberta
%T Accounting for Parallel Tree Search Overheads
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 198-201
%K Non-Numeric Algorithms, loosely coupled, vertex cover problem,
   synchronization loss, MANIP, configurations, message passing

%A Peter Varman
%A Kshitij Doshi
%Z Rice U.
%T Sorting with Linear Speedup on a VLSI Network
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 202-206
%K sort, sorting, parallel, concurrent, computer
%X Non-Numeric Algorithms, pipelined packet switch interconnection
   of processors and memories, communications graph (CG), hypercube,
   conflict free routing, coarse merge, mapping,

%A V. Nageshwara Rao
%A Vipin Kumar
%Z U. Texas
%T Concurrent Insertions and Deletions in a Priority Queue
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 207-211
%K Non-Numeric Algorithms, BBN Butterfly, heap, path, window,
   concurrent access, branch and bound

%A Sanjay Ranka
%A Sartaj Sahni
%Z U. Minn.
%T Convolution on SIMD Mesh Connected Multicomputers
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 212-217
%K Image Analysis & Geometry, convolution, mesh multicomputer, shift,
   memory, pairing
%X Authors want it known that these algorithms do not assume any broadcasting.

%A Guy E. Blelloch
%A James J. Little
%Z MIT
%T Parallel Solutions to Geometric Problems on the Scan-Model of Computation
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 218-222
%K Image Analysis & Geometry, connection machine, SIMD, vector model,
   k-D tree algorithm, line drawing, line-of-sight, convex hull, segments,
   recursive splitting
%X Authors emphasize they don't want CREW P-RAM models (many times).

%A Xiaqing Qu
%A Xiaobo Li
%Z U. Alberta
%T Parallel Template Matching Algorithms
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 223-226
%K Image Analysis & Geometry, SIMD, hypercube interconnection
%X one (single) permute multiply phase, local address computation,

%A S. K. Nandy
%A R. Moona
%A S. Rajagopalan
%Z India Inst. Science, Bangalore, India
%T Linear Quadtree Algorithms on the Hypercube
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 227-229
%K Image Analysis & Geometry, neighbor finding, NFA, boundary following, BFA,
   block embedding

%A J. B. G. Roberts
%A J. S. Ward
%Z Royal Signals and Radar Est., Malvern, England
%T Optimising a Reconfigurable MIMD Transputer Machine for Line-of-Sight
   Calculations on Large Digital Maps
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 230-234
%K Image Analysis & Geometry, OCCAM, CSP
%X reconfigurable transputer processor (RTP), SuperNode, 72 x 72 crossbar,
   visibility, shading, 256 KB per PE in prototype, T880, look up,

%A Raad Fatoohi
%A Chester E. Grosch
%T Implementation and Analysis of a Navier-Stokes Algorithm on
   Parallel Computers
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 235-242
%K SIMD, MIMD, MPP, Cray-2, FLEX/32, ADI scheme,
   relaxation, performance, instruction, operation count

%A Mark E. Braaten
%Z GE R&D
%T Solution of Viscous Fluid Flows on a Distributed Memory Concurrent Computer
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 243-250
%K Navier Stokes equations, 2-D laminar flow, CFD,
   computational dynamics, iPSC

%A Herb Schwetman
%A Stephen Burdick
%Z MCC
%T Parallelizing an Electron Transport Monte Carlo Simulator (MOCASIN 2.0)
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 251-256
%K drift diffusion, PPL, Sequent C, MESFET,
   timing, speedup, scattering

%A Eric Lander
%A Jill P. Mesirov
%A Washington Taylor, IV
%T Protein Sequence Comparison on a Data Parallel Computer
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn' State
%C University Park, Penn'
%M AUG
%D 1988
%P 257-263
%K MolBio, biochemistry, connection machine, CM, CM-2, CM2
%X subsequence scoring matching metrics, data mapping, inner loops, timing
   protein alignment, edit distance, string sequence match matching
   LA has

%A Craig B. Stunkel
%Z CSL, U. Ill.
%T Linear Optimization Via Message-Based Parallel Processing
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 264-271
%K iPSC, simplex method, row, column partitioning, search,
   global minimum, maximum, extrema, communication, computation overlap

%A Marc D. Diamond
%A Jim Newhouse
%A Jeff Kimbel
%Z FMC, Minn.
%T Results of a Multiprocessor Implementation for Sequential Decision Processes
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 272-281
%K dynamic programming, simplex, decision graph,
   informed model, minimax, timed Markov, termination/initiation,
   deadlock/race conditions

%A Greg N. Frederickson
%A Ravi Janardan
%T Space-Efficient and Fault-Tolerant Message Routing in Outerplanar Networks
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 282-289
%K Graph Theory, interval routing, multiple node and edge faults
%X Preliminary version published.

%A C. S. George Lee
%A P. R. Chang
%Z Purdue
%T A Decomposition Approach for Balancing Large-Scale
   Acyclic Data Flow Graphs
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 290-294
%K Graph Theory, (ADFG, DFG), Coordinate Rotation DIgital Computer, CORDIC,
   queueing, ILEG, ILCE

%A M. Y. Chan
%Z U. Texas at Dallas
%T Dilation-2 Embeddings of Grids into Hypercubes
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 295-298
%K Graph Theory, 2-Dimensions, 2D, coloring

%A S. Vishwanathan
%A M. A. Sridhar
%Z U. So. Carolina
%T Some Results on Graph Coloring in Parallel
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 299-303
%K Graph Theory, Brooks coloring, c-index, chromatic number

%A A. Lingas
%T Subgraph isomorphism for connected graphs of bounded valence and
   bounded separator is in NC
%J Proc. of the 1988 Int. Conf. on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%P 304-307
%M AUG
%D 1988
%O TR LiTH-IDA-R-89-07, Dept Comp. & Inf. Sci., Linkoping U., Sweden
%K conf, c1988, c198x, c19xx, Graph Theory, CRCW, PRAM, SEP
%X "It is shown that the problem of subgraph isomorphism for connected graphs of
   bounded valence & bounded separator admits a deterministic parallel algorithm
   running in poly-log time and using a polynomial number of processors."

%A R. E. Cypher
%A J. L. C Sanz
%T Optimal Sorting Algorithm on Reduced Architectures
%J Proc. of the 1988 International Conference on Parallel Processing
%V III, Algorithms and Applications
%I Penn State
%C University Park, Penn
%M AUG
%D 1988
%P 308-311
%K Computational Complexity, priority, CRCW, PRAM, cubesort

%A Xiaojun Guan
%A M. A. Langston
%T Time-space optimal parallel merging and sorting
%J International Conference on Parallel Processing
%D 1989
%P III-1 - III-7
%K parallel, merge, sort, EREW, PRAM

%A R. Cole
%T Parallel merge sort
%J SIAM J. Comput.
%V 1
%N 4
%P 770-785
%M AUG
%D 1988
%K parallel, concurrent, merge, sort, sample, CREW, EREW, PRAM
%X merge sort on CREW PRAM, n processors O(log n) time
   same O time but more involved on EREW PRAM

%A R. E. Ladner
%A M. J. Fischer
%T Parallel prefix computation
%J JACM
%V 27
%N 4
%M OCT
%D 1980
%P 831-838
%K prefix, sum, product, parallel, concurrent
%X given  x1, x2, ..., xn
   and an associative operation *
   compute  x1*x2*...*xk for all k s.t.   1 .le. k .le. n.
   A circuit of depth roof(log2(n))+2  and  size .le. 14n
   is found.

%A R. J. Cole
%T An optimally efficient selection algorithm
%J IPL
%V 26
%P 295-299
%M JAN
%D 1988
%K EREW, PRAM, parallel, select, selection, median
%X linear number of operations and
   O(log(n) log*(n)) time.
   Modification on CRCW PRAM
   needs linear # ops and O(log(n) log*(n)/log(log(n))) time.

%A C. U. Martel
%A D. Gusfield
%T A fast parallel quicksort algorithm
%J IPL
%V 30
%M JAN
%D 1989
%P 97-102
%K CRCW PRAM, parallel, quick sort, sorting, quicksort
%X O(log(n)) time using n processors.

%A Shi, Hanmao
%T Parallel Sorting on Multiprocessor Computers
%I Dept of Comp Sci, U of Alberta.
%D 19??
%K parallel, sort, sorting, algorithm
%X 1990 ish
   A new algorithm  called PSRS "Parallel Sorting
   by Regular Sampling " is developed.(include coding)
   Parallel Quicksort. The result is that it
   demonstrates a successful linear speedup parallel sort
   workable on parallel multiprocessors with a large number
   of processors.
   MSc Thesis via enews

%A S. G. Akl
%T Parallel Sorting Algorithm
%D 1985
%K parallel, sort, sorting, algorithm
%X The Design and Analysis of Parallel Algorithm - Akl
   maybe a book ? via enews.

%A Hirschberg
%T Fast Parallel Sorting Algorithm
%J CACM
%V 21
%N 8
%M AUG
%D 1978
%K parallel, sort, sorting, algorithm
%P 657-661
%X via enews


%A S. Lakshmivarahan
%T Parallel Sorting Algorithm
%J Advances in Computers
%D 1984
%K parallel, sort, sorting, algorithm
%P 295-354
%X via enews

%A Preparata
%T New Parallel Sorting Schemes
%J IEEE Trans on Computers
%V C-27
%D 1978
%K parallel, sort, sorting, algorithm
%P 669-673
%X via enews

%A K. E. Batcher
%T Sorting networks and their application
%J Proc. of the AFIP
%D 1968
%K parallel, sort, sorting, algorithm
%P 307-314
%X via enews

%A M. Kumar
%T An Efficient Implementation of Batcher' Odd-Even
   Merge Algorithm and Its Application in Parallel Sorting Schemes.
%J IEEE Trans on Computers
%V C-32
%N 3
%M MAR
%D 1983
%K parallel, sort, sorting, algorithm
%P 254-264
%X   via enews

%A G. Baudet
%A Stevenson
%T Optimal Sorting Algorithms for Parallel Computers
%J IEEE Trans on Computers
%V C-27
%N 1
%M JAN
%D 1978
%K parallel, sort, sorting, algorithm
%P 84-87
%X   via enews

%A B. Wagar
%T Hyperquicksort : A fast Sorting Algorithm for Hypercubes
%B Hypercube Multiprocessors, M. T. Heath
%I SIAM
%P 292-299
%D 1987
%K parallel, sort, sorting, algorithm
%X   via enews

%A M. J. Quinn
%T Parallel Sorting Algorithms for tightly coupled Multiprocessor
%J Parallel computing
%V 6
%P 349-357
%D 1988
%K parallel, sort, sorting, algorithm
   via enews

%A D. Rotem  et al
%T Distributed Sorting
%J IEEE Trans on Computers
%V 34
%N 4
%P 372-375
%D 1985
%K parallel, sort, sorting, algorithm
%X   via enews

%A D. J. Evans
%A N. Y. Yousif
%T The Parallel Neighbour Sort and Two-way merge algorithm
%J Parallel Computing
%V 3
%P 85-90
%D 1986
%K parallel, sort, sorting, algorithm
%X   via enews

%A M. Cole
%T Algorithmic Skeletons: Structure Management of Parallel Computations
%I MITpress
%D 1989
%K parallel, concurrent, program, programming, algorithm, paradigm,
   divide and conquer, multi processor, multi-processor, book, text

%A H. T. Kung
%T Computational models of parallel computers
%P ??-??
%B Scientific Applications of Multi-Processors
%E R. J. Elliot
%E C. A. R. Hoare
%I PrenticeHall
%D 1989
%K parallel, concurrent, program, programming, algorithm, paradigm,
   divide and conquer, multi processor, book, text

%A Galil
%T A constant-time optimal parallel string-matching algorithm
%J STOC '92
%D 1992
%P ??-??
%K conf, c1992, c199x, c19xx, STOC, STOC92, STOC-92, string, match, matching,
   search, parallel
%X via enews

%A E. A. Albacea
%T Basic parallel algorithmic techniques for shared memory machines
%J Australian Comp. J.
%V 27
%N 2
%P 51-61
%M MAY
%D 1995
%K ACJ, jrnl, PRAM, parallel, computer, CSci, zz0695

%A I. Foster
%T Designing and Building Parallel Programs
%I AddisonWesley
%D 1995
%K book, text, c1995, c199x, c19xx, algorithm, program, computing

%A G. Golub
%A J. M. Ortega
%T Scientific Computing: An Introduction with Parallel Computing
%I AcademicPress
%D 1993
%K book, text, c1993, c199x, c19xx, algorithm, program, computing

%A M. Amor
%A F. Arguello
%A J. Lopez
%A O. Plata
%A E. L. Zapata
%T A data-parallel formulation for divide and conquer algorithms
%J COMPJ
%V 44
%N 4
%P 303-320
%D 2001
%K jrnl, COMPJ, c2001, c200x, c20xx, algorithm, parallel, concurrent,
   distributed, zz1001, mapping vector, vectors, index digit permutation,
   space filling curve
%X [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_44/Issue_04/440303.sgm.abs.html">www</A>][10/'01].

%A H. Attiya
%A J. Welch
%T Distributed Computing Fundamentals, Simulations, and Advanced Topics
%I Wiley
%D 2004
%K book, text, c2004, c200x, c20xx, parallel, algorithms, algorithm, computers,
   communication, coordination, synchronization, simulation, topic, Byzantine,
   election, mutual exclusion
%X 2nd ed 2004; uk us isbn:0471453242.
   [<A HREF="http://www.cs.technion.ac.il/~hagit/DC/">auth</A>]['05].

%A Z. Brakerski
%A B. Patt-Shamir
%T Distributed discovery of large near-cliques
%J Proc. 23rd Int Conf. on Distributed computing
%P 206-220
%I SpringerVerlag
%D LNCS
%V ?
%D 2009
%K conf, c2009, c200x, c20xx, maths, graph, near clique, (not quasi), cliques,
   distributed, parallel, algorithm
%X "Given an undirected g. & 0 <= eps <= 1, a set of nodes is called eps-near
   clique if all but an eps fraction of the pairs of nodes in the set have a
   link between them. ... a fast synchronous network alg. that uses small
   messages & finds a near clique. ... present a constant-time alg. that finds,
   with constant probability of success, a linear size eps-near clique if there
   exists an (eps**3)-near clique of linear size in the g.. ... uses messages of
   O(log n) bits. The failure probability can be reduced to n**-Omega(1) in
   O(log n) time factor, & the alg. also works if the g. contains a clique of
   size Omega(n/log**alpha log n) for some alpha in (0,1). .. based on a new
   idea of adapting property testing algs. to the distributed setting."
   -- pdf@[<A HREF="http://portal.acm.org/citation.cfm?id=1813192">acm</A>]['10].

%A V. K. Garg
%T Removing sequential bottleneck of Dijkstra's algorithm for the shortest path
   problem
%J arXiv
%M DEC
%D 2018
%K TR, c2018, c201x, c20xx, zz0119, algorithm, parallel, shortest path, paths,
   maths, graph, DAG, Crauser, Mehlhorn, Meyer, Sanders
%X "... present 4 algs ... SP1, SP2, SP3 & SP4. SP1 & SP2 reduce the # of heap
   operations in D's alg.. For directed acyclic graphs, or directed unweighted
   graphs they have the optimal complexity of O(e) where e is the # of edges
   in the graph which is better than that of D's alg.. For general graphs, their
   worst case complexity matches that of D's alg. for a sequential
   implementation but allows for greater parallelism. Algs SP3 & SP4 allow for
   even more parallelism but with higher work complexity. Alg. SP3 requires
   O(n+e(max(log(n),D))) work where n is the # of vertices & D is the maximum
   in-degree of a node. Alg. SP4 has the most parallelism. It requires O(ne)
   work. ..."
   -- 1812.10499@[<A HREF="https://arxiv.org/abs/1812.10499">arXiv</A>]['19].

%A P. Ganapathi
%A R. Chowdhury
%T Parallel divide-and-conquer algorithms for bubble sort, selection sort and
   insertion sort
%J COMPJ
%V 65
%N 10
%P 2709-2719
%M OCT
%D 2022
%O ? "Published: 02 Aug. 2021" ?
%K COMPJ, jrnl, c2022, c202x, c20xx, zz1022, parallel sorting algorithm, sort,
   sorting
%X "We present efficient parallel recursive divide-and-conquer algs. for bubble
   sort, selection sort, & insertion sort. ... have excellent data locality &
   are highly parallel. The computational complexity of our insertion sort is
   O(n^{log_2^3) in contrast to O(n^2) of std insertion sort."  [33 refs]
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxab107">doi:10.1093/comjnl/bxab107</A>]['22].


%A N. Metropolis
%A A. W. Rosenbluth
%A M. N. Rosenbluth
%A A. H. Teller
%A E. Teller
%T Equations of state calculations by fast computing machines
%J J. Chem. Phys.
%V 21
%N 6
%P 1087-1092
%M JUN
%D 1953
%K jrnl, Metropolis Hastings algorithm, defn, Gibbs sampling, method, state,
   c1953, c195x, c19xx, simulated annealing, Monte Carlo integration,
   MonteCarlo, process, stochastic search, Edward
%X A general method, suitable for fast computing machines, for investigating
   such properties as eqns of state for substances consisting of interacting
   individual molecules is described. The method consists of a modified Monte
   Carlo integration over configuration space. Results for the 2-D rigid sphere
   system have been obtained on the Los Alomos MANIAC & are presented here.
   These results are compared to the free volume eqn of state & to the four-term
   virial coefficient expansion.
   * Sufficient condition: # of possible transitions from each
   * state is constant & every transition is reversible.
   -- [<A HREF="https://doi.org/10.1063/1.1699114">doi:10.1063/1.1699114</A>]['21] & later
      the Rosenbluths, JCP, 22, pp.881-884, 1954 [<A HREF="https://doi.org/10.1063/1.1740207">www</A>]['24].
   Also see Marshall Rosenbluth interview,
   [<A HREF="https://www.aip.org/history-programs/niels-bohr-library/oral-histories/28636-1">www</A>]['21],
   i.e., another example of Stigler's law.
   [Also search for: Metropolis Hastings] and [also search for: Monte Carlo].

%A E. C. Freuder
%T A sufficient condition for backtrack-free search
%J JACM
%V 29
%N 1
%M Jan
%D 1982
%P 24-32
%K constraint satisfaction problem, consistency, backtrack, back track
%X constraint satisfaction problem
   find values for a set of variables subject to a set of constraints
   structure of constraints gives a graph which has width
   guides order to do search in.
   Interested in vertical order of search - order to choose variables in.

%A W. K. Hastings 
%T Monte Carlo sampling methods using Markov chains and their applications
%J Biometrika
%V 57
%N 1
%P 97-109
%M APR
%D 1970
%K jrnl, simulated annealing, SA, defn, Gibbs sampling, estimation, random,
   sample, algorithm, Metropolis, Monte Carlo, MCMC, method, stats,
   c1970, c197x, c19xx
%X "A generalization of the sampling method introduced by Metropolis et al.
   (1953) is presented along with an exposition of ..."
   -- [<A HREF="https://www.jstor.org/stable/2334940">jstor:2334940</A>]['24],
      [<A HREF="https://doi.org/10.1093/biomet/57.1.97">doi:10.1093/biomet/57.1.97</A>]['24].
   [Also search for: Metropolis Hastings].

%A E. C. Freuder
%T Synthesizing constraint expressions
%J CACM
%V 21
%N 11
%M Nov
%D 1978
%P 958-966
%K constraint satisfaction problem

%A D. E. Knuth
%T Estimating the efficiency of backtrack programs
%J Math. Comput.
%V 29
%M Jan
%D 1975
%P 121-136
%K backtrack,  back track, combinatorial, search problem, puzzle,
   efficiency, estimate, complexity

%A R. Dechter
%T Learning while searching in constraint-satisfaction problems
%I Cognitive Systems laboratory, Computer Science Department, UCLA
%D ????
%K constraint satisfaction problems, dead end, dead-end

%A M. R. Williams
%T Heuristic procedures (if they work - leave them alone)
%J SPE
%V 4
%P 237-240
%D 1974
%K heuristic, graph colouring

%A R. J. Walker
%T An enumerative technique for a class of combinatorial problems
%J Proc. of the Tenth Symposium in Applied Mathematics
   of the American Mathematical Society
%M Apr
%D 1958
%P 91-94
%K AMS, backtrack, permutation, n-queens, n queens, nqueens, nqueens
%X numbers of solutions up to n=19

%A P. J. Haynes
%T Discussion and correspondence. A note on the towers of Hanoi
%J COMPJ
%V 20
%N 3
%P 282-285
%K Hanoi, iterative, non-recursive

%A S. Geman
%A D. Geman
%T Stochastic relaxation, Gibbs distributions, and the Bayesian restoration
   of images
%J IEEE Trans. Pattern Analysis and Machine Intel,
%V PAMI-6
%N 6
%P 721-741
%M NOV
%D 1984
%K jrnl, Gibbs sampling, defn, c1984, c198x, c19xx, stochastic, random field,
   posterior, simulated annealing, image restoriation, processing
%X "We make an analogy between images & statistical mechanics systems ...
   assignment of an energy fn in the physical sys. determines its Gibbs
   dist'n ... Gradual temp. redn in the physical sys. isolates low energy
   states ('annealing') or what is the same thing, the most probable states
   under the G.distribution. ..."
   -- [<A HREF="https://doi.org/10.1109/TPAMI.1984.4767596">doi:10.1109/TPAMI.1984.4767596</A>]['24].
   (Also see GS@[<A HREF="https://en.wikipedia.org/wiki/Gibbs_sampling">wikip</A>]['24].)
   [Also search for: Gibbs sampling] & [also search for: Metropolis Hastings].

%A M.-P. Delest
%T Algebraic languages and polyominoe enumeration
%J Theoretical Computer Science
%V 34
%N 1-2
%P 169-206
%M Nov
%D 1984
%K TCS, jrnl, c1984, c198x, c19xx, polyominoe, pentominoe
%X The number of convex polyominoes with perimeter 2n+8 is
   (2n+11) 4^n - (2n+1) C(n,2n)
   43 refs.

%A H. S. Stone
%A J. M. Stone
%T Efficient search techniques - an empirical study pf the N-queens problem
%J IBM J. of Research and Development
%K n queens, n-queens, ibm_rd, nqueens
%V 31
%N 4
%M Jul
%D 1987
%P 464-474

%A J. S. Rohl
%T A faster lexicographical N queens algorithm
%J IPL
%V 17
%N 5
%P 231-233
%M Dec
%D 1983
%K ipl, jrnl, c1983, c198x, c19xx, n-queens, n queens, nqueens

%A M. Reichling
%T A simplified solution of the N queens' problem
%J IPL
%K ipl, n-queens, n queens, nqueens
%V 25
%N 4
%M Jun
%D 1987
%P 253-255

%A C. Clay
%T A new solution to the N <= 8 queens problem
%J SIGPLAN Notices
%K programming languages
%V 21
%N 8
%M Aug
%D 1986
%P 28-30
%K homour, humor, n-queens, n queens, nqueens

%A R. Silver
%A M. Wells
%A S.-Inn Wu
%A M. Hug
%T A concurrent N <= 8 queens' algorithm using Modcap
%J SIGPLAN Notices
%K programming languages, n-queens, n queens, nqueens
%V 21
%N 9
%M Sep
%D 1986
%P 63-76

%A Russell M. Clapp
%A Trevor N. Mudge
%A Richard A. Volz
%T Solutions to the n queens problem using tasking in Ada
%J SIGPLAN Notices
%K programming languages, Ada, n-queens, nqueens
%V 21
%N 12
%M Dec
%D 1986
%P 99-110

%A A. Corana
%A et al
%T Minimizing multimodal functions of continuous variables with the
   simulated annealing algorithm
%J ACM Trans. on Math. Software
%V 13
%N 3
%P 262-280
%M SEP
%D 1987
%K jrnl, TOMS, c1987, c198x, c19xx, function, variable, optimization,
   nonlinear, non-linear, problem
%X Difficult unconstrained non-linear models.
   Also see: [<A HREF="http://www-unix.mcs.anl.gov/otc/Guide/faq/nonlinear-programming-faq.html">www</A>]['05]

%A M. E. Goldsby
%T Solving the N <= 8 queens problem with CSP and Modula-2
%J SIGPLAN Notices
%K programming languages, n-queens, nqueens
%V 22
%N 2
%M Feb
%D 1987
%P 43-52

%A B. Abramson
%A M. M. Young
%T Construction through decomposition: A divide-and-conquer algorithm for
   the N-queens problem
%J J. Parallel & Distributed Computing
%V ???
%P 649-662
%M JUN
%D 1989
%K JPDC, fjcc, fjcc86, n queens, n-queens, divide and conquer, yung, nqueens
%O Proceedings of the 1986 Fall Joint Computer Conference, Dallas, Texas,
   Nov 1986, Harold S. Stone (ed), pp.620-628
%X jrnl ref from an article,  conf' ref from enews

%A B. A. Nadel
%T Representation-Selection for Constraint Satisfaction Problems: A Case
   Study Using n-queens
%R DCS-TR-182
%I Rutgers University, Laboratory for Computer Science Research
%K AI03, AA17, CSP, n queens, n-queens, nqueens

%A R. W. Topor
%T Fundamental solutions of the eight queens problem
%J BIT
%V 22
%N 1
%D 1982
%P 42-52
%K n queens, n-queens, symmetry, group, nqueens

%A J. Gallagher
%T Simulating coroutining for the 8 queens problem
%J Logic Programming Newsletter
%K LP, lpn, n-queens, n queens, nqueens
%N 3
%M Summer
%D 1982
%P 10-11

%A T. W.-S. Plum
%T Random search on the 8-queens problem
%J SPE
%K n-queens, n queens, nqueens
%V 4
%N 3
%M July-September
%D 1974
%P 251-253

%A R. L. Wexelblat
%T Editorial
%J SIGPLAN Notices
%V 21
%N 3
%D March 1986
%P 1
%K AI03, AA17, n queens, n-queens, Problem H03 ADA, nqueens
%X SIGPLAN is having a contest to determine the
   best solution for the N <= 8 Queens problem using
   concurrency in ADA in a substantive manner.
   Deadline for submissions is June, 1986.

%A E. C. Freuder
%T A sufficient condition for backtrack-bounded search
%J JACM
%V 32
%N 4
%M Oct
%D 1985
%P 755-761
%K backtrack, non-determinism, bounded, complexity
%X a reference in a paper

%A A. K. Chandra
%T Independent permutations, as related to a problem of Moser and
   a theorem of Polya
%J J. of Combinatorial Theory
%V 16
%P 111-120
%D 1974
%K JCT, n-queens, n queens, superqueen, nqueens
%X examples
   1. max number of nodes in a d-cube of side n such that no n of these nodes
      are colinear.
   2. n non-capturing super-queens (wrap around) on an n x n board.

%A A. Hedayat
%T A complete solution to the existence and nonexistence of Knut Vik
   designs and orthogonal Knut Vik designs
%J J. of Combinatorial Theory (A)
%V 22
%P 331-337
%D 1977
%K JCT, pandiagonal, latin square, diagonal, super diagonal, torus,
   n queens, n-queens, nqueens
%X solution iff n not a multiple of 2 or 3.

%A R. M. Haralick
%A G. L. Elliott
%T Increasing tree search efficiency for constraint satisfaction problems
%J Artificial Intelligence
%V 14
%P 263-313
%D 1980
%K jrnl, c1980, c198x, c19xx, back track, backtrack, forward checking,
   backmarking
%X "... explore the # of tree search operations required to solve binary
   constraint satisfaction problems.  We show analytically & experimentally
   that the two principles of first trying the places most likely to fail &
   remembering what has been done to avoid repeating the same mistake twice
   improve the std backtracking search.  We experimentally show that a lookahead
   proc. called forward checking (to anticipate the future) which employs the
   most likely to fail principle performs better than std backtracking,
   Ullman's, Waltz's, Mackworth's, & Haralick's discrete relaxation in all
   cases tested, & better than Gaschnig's backmarking in the larger problems."
   --- pdf@[<A HREF="http://haralick.org/journals/haralick_elliot.pdf">haralick.org</A>]['14].

%A H. D. Shapiro
%T Generalized Latin squares on the torus
%J Discrete Mathematics
%V 24
%P 63-77
%D 1978
%K torus, linear, latin square, line, generator, n queens, n-queens, nqueens
%X generator (a,b) generates lines of N points: {(x,y), (x+a,y+b), ... }  mod N
   L is a LS over a set of generators iff each line is a permutation of 0..N-1.
   eg. ordinary LS is a LS over (0,1), (1,0)
       pan diagonal LS is LS over (0,1), (1,0), (1,1), (1,-1)
   shows there is a LS over a set of generators iff there is a linear
   latin square over them: L(i,j)=ki+lj

%A Y. Davidor
%T Genetic Algorithms and Robotics
%I World Scientific
%D 1990
%P 150
%K genetic algorithm, optimisation, search, blind, random, heuristic
%X isbn:981-02-0217-2
   ordered for Hargrave oct 90

%A L.B. Booker
%A D.E. Goldberg
%A J.H. Holland
%T Classifier Systems and Genetic Algorithms
%J Artificial Intelligence
%V 40
%N 1-3
%M SEP
%D 1989
%P 235-282
%K GA

%E L. Davis
%T Genetic Algorithms and Simulated Annealing
%I MorganKaufmann
%D 1987
%K GA, SA

%A J. Doyne Farmer
%A N. Packard
%A A. Perelson
%T The Immune System, Adaptation, and Machine Learning
%J Physica
%V 22D
%D 1986
%P 187-204
%K GA, genetic algorithms

%A D. Goldberg
%T The Genetic Algorithm Approach: Why, How, and  What Next
%B Adaptive and Learning Systems.
%E Kumpati Narendra
%I Plenum
%D 1986
%K GA

%A D. Goldberg
%T Genetic Algorithms in Search, Optimization and Machine Learning
%I AddisonWesley
%D 1989
%K GA

%A J. Holland
%T Escaping Brittleness
%B Machine Learning
%V 2
%E R. Michalski
%E J. Carbonell
%E T. Mitchell
%I MorganKaufmann
%D 1986
%K GA, genetic algorithms

%A John Holland
%T Adaptation in Natural and Artificial Systems
%I University of Michigan Press
%D 1975
%K GA, genetic algorithms
%X Describes the basic algorithms and gives examples.
   [Note: last time I (kurt@Think.COM) checked
   the University of Michigan Press still had copies in stock for
   approximately $15.  Their Phone Number is (313) 764-4394).]

%A J. Holland
%T Adaptation
%B Progress in Theoretical Biology
%E R. Rosen
%E F. Snell
%I AcademicPress
%D 1976
%K MolBio, text, book

%A J. Holland
%A K. Holyoak
%A R. Nisbett
%A P. Thagard
%T Induction
%I MITpress
%D 1986
%K GA, genetic algorithms

%A Carla Reiter
%T Toy Universes
%J Science
%V 86
%M JUN
%D 1986
%P 55-59
%K GA, genetic algorithms

%A D. Schuurmans
%A R. Chai
%A L. Shu
%T Learning Using  Classifier Systems: A Survey
%J Proceedings of CIPS Edmonton '87: Intelligent Integration
%M NOV
%D 1987
%P 386-391
%K GA, genetic algorithms

%J Machine Learning
%V 3
%N 2/3
%K GA
%X special issue is dedicated to genetic algorithms.

%J Int. Conf. on Genetic Algorithms
%D 1985-...
%K GA
%X The first two 1985, 1987 are published by Lawrence Erlbaum and Associates,
   Publishers, 365 Broadway, Hillsdale, NJ, 07642.  The third
   1989 is published by MorganKaufmann Publishers, 2929 Campus Drive,
   San Mateo, CA, 94403.

%T Optimization
%E Nemhauser
%E Rinnooy Kan
%E Todd
%S Handbooks in Operations Research and Management Science
%V 1
%I NorthHolland
%D 1989
%X book, text, nonlinear, non, linear, optimization, programming
%X "Very broad-reaching, with large bibliography; a good reference, and
   worth checking first. Expensive, though, and tough reading for beginners."
   -- [<A HREF="http://www-unix.mcs.anl.gov/otc/Guide/faq/nonlinear-programming-faq.html">www</A>]['05]

%A A. Andersson
%T A note on searching in a binary tree
%J SPE
%V 21
%N 10
%P 1125-1128
%M OCT
%D 1991
%K SPE, jrnl, c1991, c199x, c19xx, binary search tree, searching, lookup,
   two-way, comparisons
%X Algorithm searches a binary tree using two-way comparisons.
   The # of comparisons used is only one more than when using
   three-way comparisons.

%A W. -P. Hwang
%A C. -L. Wang
%T Using procedural parameters and continuations in combinatorial searches
%J SPE
%V 24
%N 4
%P 377-386
%M APR
%D 1994
%K SPE, jrnl, c1994, c199x, c19xx, procedure, formal, parameter, continuation,
   search, backtrack
%X [12 refs].

%A D. Dolev
%A Y. Harari
%A N. Linial
%A N. Nisan
%A M. Parnas
%T Neighborhood preserving hashing and approximate queries
%J Proc. fifth annual ACM-SIAM symp. on Discrete algorithms
%P 251-259
%D 1994
%K conf, c1994, c199x, c19xx, SIAM, retrieval, hash, hashing, approximate,
   similar, similarity, query, near, neighbourhood, close, query,
   mismatch, search, lookup
%X pdf: [<A HREF="http://portal.acm.org/citation.cfm?id=314501">@acm</A>]['08].
   [Also search for: hashing neighbourhood] and [also search for: simhash].

%A C. Faloutsos
%A King-Ip Lin
%T FastMap: a fast algorithm for indexing, data-mining and visualization of
   traditional and multimedia datasets
%J ACM SIGMOD
%P 163-174
%M MAY
%D 1995
%K conf, c1995, c199x, c19xx, zz0323, FastMap, indexing, search
%X "A very promising idea for fast searching in traditional & multimedia
   databases is to map objects into pts in k-d space, using k feature-extraction
   fns ... describe a fast alg. to map objects into pts in some k-D space (k is
   user-defined), s.t. the dissimilarities are preserved ..."
   -- [<A HREF="https://doi.org/10.1145/568271.223812">doi:10.1145/568271.223812</A>]['23].
   [Also search for: approximate indexing].

%A A. Flammenkamp
%T Progress in the no-three-in-line problem II
%J J. of Comb. Theory, ser. A
%V 81
%N 1
%P 108-113
%M JAN
%D 1998
%K jrnl, c1998, c199x, c19xx, zz0424, three in a line, row, problem, grid,
   lattice, puzzle, combinatorics, Z3, rot4, CapSet
%X "First solns to the no-three-in-line problem for n=33, 37, 39, 41, 43, 45,
   48, 50, 52 & for certain symmetry classes for n=26, 42, 44 are presented. All
   configurations with n <= 16 have been generated. Further, the significance of
   a new symmetry class for configurations which are almost as symmetric as
   those in class rot4 is demonstrated."
   -- [<A HREF="https://doi.org/10.1006/jcta.1997.2829">doi:10.1006/jcta.1997.2829</A>]['24].
   Also see No3@[<A HREF="https://en.wikipedia.org/wiki/No-three-in-line_problem">wikip</A>]['24].
   [Also search for: Nqueens problem]  and  [also search for: CapSet].

%A G. S. Brodal
%A S. Venkatesh
%T Improved bounds for dictionary look-up with one error
%J IPL
%V 75
%N 1-2
%P 57-59
%M JUL
%D 2000
%K IPL, jrnl, c2000, c200x, c20xx, one error, mismatch, mismatches, dQuery,
   substitution, approximate, index, indexing, search, searching, lookup, Yao,
   string, sequence, bound
%X "Given a dictionary S of n binary strings each of length m, we consider the
   problem of designing a data structure for S that supports d-queries; given a
   binary query string q of length m, a d-query reports if there exists a string
   in S within Hamming distance d of q. We construct a data structure for the
   case d=1, that requires space O(n log m) and has query time O(1) in a cell
   probe model with word size m. This generalizes & improves the previous bounds
   of Yao & Yao for the problem in the bit probe model. The data struct. can be
   constructed in randomized expected time O(nm)."
   [<A HREF="http://dx.doi.org/10.1016/S0020-0190(00)00079-X">doi:10.1016/S0020-0190(00)00079-X</A>]['08].
   [Also search for: approximate indexing].

%A A. N. Arslan
%A O. Egecioglu
%T Dictionary look-up within small edit distance
%J Proc. 8th Annual Int. Conf. on Computing and Combinatorics
%P 127-136
%D 2002
%I SpringerVerlag
%S LNCS
%V 2387
%K conf, c2002, c200x, c20xx, error, mismatch, mismatches, substitution,
   approximate, index, indexing, search, searching, lookup, string, sequence
%X "Let W be a dictionary consisting of n binary strings of length m each,
   represented as a trie. The usual d-query asks if there exists a string in W
   within Hamming dist. d of a given binary query string q.  [Give] alg. to
   determine if there is a member in W within edit dist. d of a given query
   string q of length m.  The method takes time O(dm**(d+1)) in the RAM model,
   independent of n, & requires O(dm) additional space."
   [<A HREF="http://www.cs.ucsb.edu/~omer/DOWNLOADABLE/dictionary02.ps">.ps@ucsb</A>]['08].
   [<A HREF="http://dx.doi.org/10.1007/3-540-45655-4_15">doi:10.1007/3-540-45655-4_15</A>]['08].
   [Also search for: approximate indexing].

%A A. Chakrabarti
%A O. Regev
%T An optimal randomised cell probe lower bound for approximate
   nearest neighbour searching
%J Proc. 45th Annual IEEE Symp. on Foundations of Comp. Sci.
%P 473-482
%M OCT
%D 2004
%K conf, search, problem, c2004, c200x, c20xx, approximation, DartmouthCollege,
   NN, neighbours, close, similar, zz0605
%X "... ANN search problem on the Hamming cube {0, 1}/sup d/. We show that a
   randomised cell probe alg. that uses polynomial storage & word size
   d/sup O(1)/ requires a worst case query time of
   /spl Omega/ (log log d/ log log log d). The approx'n factor may be as loose
   as 2/sup log 1 - /spl eta//d for any fixed /spl eta/ > 0. This generalises an
   earlier result (Chakrabarti et al., '99) on the deterministic complexity of
   the same problem &, more importantly, fills a major gap in the study of this
   problem since all earlier lower bounds either did not allow randomisation
   according to Chakrabarti et al. ('99) and Liu ('03) or did not allow approx.
   according to Borodin et al. ('99), Barkol & Rabani ('00), & Jayram et al.
   ('03). We also give a cell probe alg. which proves that our lower bound is
   optimal. ..."
   [<A HREF="http://dx.doi.org/10.1109/FOCS.2004.12">doi:10.1109/FOCS.2004.12</A>]['05]
   AC gave seminar to CSSE Monash 6/'05.
   Also see [<A HREF="http://eccc.uni-trier.de/eccc-reports/2003/TR03-070/">TR03-070</A>]]'05].

%A Wei Dong
%A C. Moses
%A Kai Li
%T Efficient k-nearest neighbor graph construction for generic similarity
   measures
%J Proc. 20th int. conf. on World wide web
%P 577-586
%M MAR
%D 2011
%K conf, c2011, c201x, c20xx, zz0323, similar, similarity, search, retrieval,
   kNN, kNNG, nearest, neighbour, neighbourhood
%X "K-Nearest Neighbor Graph (K-NNG) construction ... collaborative filtering,
   similarity search, ... We present NN-Descent, a simple yet efficient alg.
   for approximate K-NNG construction ... it is especially suitable for
   large-scale applications where data structures need to be distributed over
   the n/wk. ..."
   -- [<A HREF="https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=103ac7f316bf8cdad3133b4ce2bbd28d091e7974">c'teseer</A>]['23].
   Also see kNN@[<A HREF="https://en.wikipedia.org/wiki/K-nearest_neighbors_algorithm">wikip</A>]['23].

%A D. Austin
%T Game. SET. Polynomial
%J Amer. Math. Soc. (AMS)
%M AUG
%D 2016
%K AMS, c2016, c201x, c20xx, zz0424, maths, game, SET, cap set, CapSet,
   no three in a line, row, Z3, Pellegrino
%X "A recent Feature Column explored some mathematical ideas that appear while
   playing the card game SET ..."
   -- [<A HREF="https://www.ams.org/publicoutreach/feature-column/fc-2016-08">www</A>]['24].
   Also see  CapSet@[<A HREF="https://en.wikipedia.org/wiki/Cap_set">wikip</A>]['24].
   [Also search for: CapSet].

%A K. Pratt
%T Closed-form expressions for the n-Queens problem and related problems
%J arXiv
%M SEP
%D 2016
%K TR, c2016, c201x, c20xx, zz1016, n queens problem, nQueens, Latin square,
   permanent, matrix
%X "...  derive simple closed-form expressions for the n-queens problem & three
   related problems in terms of permanents of (0,1) matrices. These formulas are
   the first of their kind. [&] provide the first method for solving these
   problems with polynomial space that has a nontrivial time complexity bound.
   We then show how a closed-form for the # of Latin squares of order n follows
   from our method. Finally, we prove lower bounds. In particular, we show that
   the permanent of Schur's complex valued matrix is a lower bound for the
   toroidal semi-queens problem, or equivalently, the number of transversals
   in a cyclic Latin square."
   -- 1609.09585@[<A HREF="https://arxiv.org/abs/1609.09585">arXiv</A>]['16].


%A S. Rajapaksa
%A L. Allison
%A P. J. Stuckey
%A M. Garcia de la Banda
%A A. S. Konagurthu
%T The divergence time of protein structures modelled by Markov matrices and
   its relation to the divergence of sequences
%J arXiv
%M AUG
%D 2023
%K TR, c2023, c202x, c20xx, zz0723, MolBio, protein, sequence alignment,
   similarity, time, evolution, related, LAllison, ArunK, Sandun,
   midnight, twilight zone
%X "A complete time-parameterized statistical model quantifying the divergent
   evolution of protein structures in terms of the patterns of conservation of
   their secondary structures is inferred from a large collection of protein
   3D structure alignments. This provides a better alternative to
   time-parameterized sequence-based models of protein relatedness, that have
   clear limitations dealing with twilight and midnight zones of sequence
   relationships ..."
   -- [<A HREF="https://arxiv.org/abs/2308.06292">arxiv:2308.06292</A>]['23].

%A P. R. Amarasinghe
%A L. Allison
%A P. J Stuckey
%A M. Garcia de la Banda
%A A. M. Lesk
%A A. S. Konagurthu
%T Getting 'φψχal' with proteins: minimum message length inference
   of joint distributions of backbone and sidechain dihedral angles
%J Bioinformatics
%V 39
%N s.1
%P i357-i367
%M JUN
%D 2023
%O ISMB/ECCB 23-27 July 2023, Lyon France
%K jrnl, MolBio, Piyumi, c2023, c202x, c20xx, zz0723, phipsichial, ISMB, ECCB,
   protein structure, angle, mixture, von Mises, vonMises, Dunbrack,
   rotamer library, backbone, side chain, sidechain, statistical model,
   MML, mdl, LAllison, AMLesk, ArunK
%X "... We model the joint distribution of the observed mainchain & sidechain
   dihedral angles ... by a mixture of a product of von Mises probability
   distributions. ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btad251">doi:10.1093/bioinformatics/btad251</A>]['23].
   Also see AK & [<A HREF="https://lcb.infotech.monash.edu/~karun/Site/Home.html">LCB</A>][2023].
   [Also search for: MolBio MML].

%A D. Sumanaweera
%A L. Allison
%A A. S. Konagurthu
%T Bridging the Gaps in Statistical Models of Protein Alignment
%J Bioinformatics
%V 38
%N s.1
%P i229-i237
%M JUL
%D 2022
%O ISMB July 2022, Madison, USA
%K conf, ISMB, MolBio, c2022, c202x, c20xx, zz0722, LAllison, ArunK, Dinithi,
   sequence alignment, gap, indel, model, substitution, PAM, BLOSUM, MML, MDL
%X "... To overcome this gap, this article demonstrates how a complete stat.
   model quantifying the evolution of pairs of aligned proteins can be
   constructed using a time-parameterized substitution matrix &
   a time-parameterized alignment state machine. Methods to derive all
   parameters of such a model from any benchmark collection of aligned protein
   seqs. are described here. This has not only allowed us to generate a unified
   stat.model for each of the nine widely used subst.matrices (PAM, JTT, BLOSUM,
   JO, WAG, VTML, LG, MIQS & PFASUM), but also resulted in a new unified model,
   MMLSUM. Our underlying methodology measures the Shannon info. content using
   each model to explain losslessly any given collection of alignments, which
   has allowed us to quantify the performance of all the above models on six
   comprehensive alignment benchmarks. Our results show that MMLSUM results in a
   new & clear overall best performance ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btac246">doi:10.1093/bioinformatics/btac246</A>]['22],
    & 2010.00855@[<A HREF="https://arxiv.org/abs/2010.00855">arXiv</A>]['20].

%A S. Rajapaksa
%A D. Sumanaweera
%A A. M. Lesk
%A L. Allison
%A P. Stuckey
%A M. Garcia de la Banda
%A P. Stuckey
%A D. Abramson
%A A. S. Konagurthu
%T On the Reliability and Limits of Protein Sequence Alignments
%J Bioinformatics
%V 38
%N s.1
%P i255-i263
%M JUL
%D 2022
%O ISMB July 2022, Madison, USA
%K conf, ISMB, MolBio, c2022, c202x, c20xx, zz0722, sequence alignment,
   protein, structure, sequence, proximity, twilight, midnight, zone,
   AMLesk, LAllison, ArunK, Sandun
%X "... Using techniques not prev. applied to these questions, by weighting
   every possible seq. alignment by its posterior prob. we derive a formal
   math. expectation, & develop an efficient alg. for computation of the
   distance between alternative alignments ... By analyzing the seqs. &
   structures of 1 million protein domain pairs, we report the variation of the
   expected distance between seq.-based & structure-based alignments, as a fn
   of (Markov time of) seq. divergence. Our results clearly demarcate the
   'daylight', 'twilight' & 'midnight' zones for interpreting residue-residue
   correspondences from seq. information alone."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btac247">doi:10.1093/bioinformatics/btac247</A>]['22].

%A L. Allison
%T Subclasses of Class Function used to Implement Transformations of
   Statistical Models
%J arXiv
%M JUL
%D 2022
%K TR, c2022, c202x, c20xx, zz0722, type, class, function, FP, subclass, MDL,
   model, MML, OOP, AI, inference, II, continuous, inverse, transform,
   transformed, LAllison
%X "A library of s/w for inductive inference guided by the Minimum Message
   Length (MML) principle was created previously. It contains various
   (object-oriented-) classes & subclasses of statistical Model & can be used to
   infer Models from given data sets in machine learning problems. Here
   transformations of statistical Models are considered & implemented within the
   library so as to have desirable properties from the object-oriented
   programming & mathematical points of view. The subclasses of class Function
   needed to do such transformations are defined."
   -- 2207.04218@[<A HREF="https://arxiv.org/abs/2207.04218">arXiv</A>]['22].
      [<A HREF="https://doi.org/10.48550/arXiv.2207.04218">doi:10.48550/arXiv.2207.04218</A>]['22].

%A S. Rajapaksa
%A D. Sumanaweera
%A M. Garcia de la Banda
%A P. Stuckey
%A D. Abramson
%A L. Allison
%A A. Lesk
%A A. Konagurthu
%Y On identifying statistical redundancy at the level of amino acid subsequences
%J IEEE Int. Conf. on Bioinformatics and Biomedicine (BIBM)
%W Houston, USA
%M DEC
%D 2021
%K conf, BIBM, c2021, c202x, c20xx, zz0122, MolBio, LAllison, AMLesk, ArunK,
   protein, information content, stats, compress, compression, library,
   fragments, sequence, subsequence, structure, indels, source code
%X "... presents a framework to characterize & identify local sequences of
   proteins that are statistically redundant under the measure of Shannon
   information content while accounting for variations in their occurrences over
   evolutionary insertions, deletions, & substitutions of amino acids. The
   identification of such local seqs. provides insights for downstream studies
   on proteins. Here, we have applied our methods to amino acid seq. data sets
   derived from a database corr.to 935,552 substructural regions of varying
   sizes, covering 113,724 proteins from the protein data bank. The results
   identify, among others, a surjective mapping between 110,598 local seqs.
   (with an avg. length of 82 AAs/seq.) & 1,493 topological shapes. ..."
   -- [<A HREF="https://doi.org/10.1109/BIBM52615.2021.9669282">doi:10.1109/BIBM52615.2021.9669282</A>]['22],
      [<A HREF="http://www.allisons.org/ll/Publications/2021BIBM">more</A>].
   Also see supplementary@[<A HREF="https://lcb.infotech.monash.edu.au/bibm2021">lcb</A>]['22].
   [Also search for: MolBio protein compression].

%A Yang Li
%A L. Allison
%A K. B. Korb
%T The difficulty of being moral
%J Theor. Comp. Sci.
%V 885
%P 77-90
%M SEP
%D 2021
%K jrnl, TCS, c2021, c202x, c20xx, zz1121, kelvin, LAllison, KBKorb,
   graph, maths, moral, complexity, Markov blanket, Bayesian network,
   BNet, Bnets, AI, NPC
%X -- [<A HREF="https://doi.org/10.1016/j.tcs.2021.06.024">doi:10.1016/j.tcs.2021.06.024</A>]['21].

%A L. Allison
%A A. S. Konagurthu
%A D. F. Schmidt
%T On universal codes for integers: Wallace Tree, Elias Omega and beyond
%J Data Compression Conference
%I IEEE
%P 313-322
%M MAR
%D 2021
%K conf, DCC, DCC21, DCC2021, c2021, c202x, c20xx, zz0321, universal code,
   ints, integer, intCodes, Elias omega, omega2, omega*, omega star, Fibonacci,
   Wallace Tree code, WTC, probability distribution, compression, entropy,
   LAllison, ArunK
%X "A universal code for the (positive) integers is a variable length code that
   can be used to store or compress a sequence of integers. It also implies a
   probability distribution on integers which can be a natural choice when the
   true distribution of a source of integers is unknown; such a code and
   distribution may be useful in statistical inference. This paper provides two
   improvements to the theory and practice of universal codes. First, it defines
   and examines a new universal code omega* (omega-star) that asymptotically
   beats the Elias omega code.  Second, it analyses the properties of a code
   proposed by Wallace based on trees, and shows it to be a universal code, to
   have desirable properties for use in inference, and to beat the Elias omega
   code on almost all integers up to the 1697-bit code-word mark. Encoding and
   decoding routines for the codes described here are implemented and available
   for interactive <A HREF="http://www.allisons.org/ll/MML/Discrete/Universal/">use[1]</A>." Also see [<A HREF="https://www.cantab.net/users/mmlist/ll/MML/Discrete/Universal/">www</A>].
   -- [<A HREF="https://www.cantab.net/users/mmlist/ll/MML/Discrete/Universal/">more1</A>],
      [<A HREF="http://www.allisons.org/ll/Publications/2021DCC">more2</A>]['21] inc. source code,
      [<A HREF="https://doi.org/10.1109/DCC50243.2021.00039">doi:10.1109/DCC50243.2021.00039</A>]['22].

%A A. S Konagurthu
%A R. Subramanian
%A L. Allison
%A D. Abramson
%A P. J. Stuckey
%A M. Garcia de la Banda
%A A. M. Lesk
%T Universal architectural concepts underlying protein folding patterns
%J Front. Mol. Biosci.,
   A Journey Through 50 Years of Structural Bioinformatics in
   Memoriam of Cyrus Chothia
%P ?-?
%M APR
%D 2021
%K jrnl, FMB, MolBio, bioinformatics, c2021, c202x, c20xx, zz0121,
   procodic, prosodic, 3D protein structure, fold, folds, tableau, motif,
   motifs, pattern, model, concept, structural, terms, fragment, supersecondary,
   local, dictionary, recurring, library, MML, II, ArunK, LAllison, AMLesk
%X "What is the architectural 'basis set' of the observed universe of protein
   structures? Using information-theoretic inference, we answer this Q. with a
   comprehensive dictionary of 1,493 substructures - called concepts - at a
   sub-domain level, based on an unbiased subset of known protein structs. ...
   An interactive site, PROCODIC, at ...[<A HREF="http://lcb.infotech.monash.edu.au/prosodic">prosodic</A>] provides access to
   & navigation of the entire dictionary of concepts, & all assoc. info.."
   -- [<A HREF="https://doi.org/10.3389/fmolb.2020.612920">doi: 10.3389/fmolb.2020.612920</A>]['21],
      [<A HREF="http://www.allisons.org/ll/Publications/2021FMB/">more</A>].

%A D. Sumanaweera
%A L. Allison
%A A. S. Konagurthu
%T Bridging the gaps in statistical models of protein alignment
%J arXiv
%M OCT
%D 2020
%K TR, MolBio, c2020, c202x, c20xx, zz1020, MML, protein alignment, sequence,
   DPA, stats, model, gap, indel, indels, substitution, scoring, matrix,
   proteins, PAM, BLOSUM, PFASUM, MMLSUM, HMM, minimum message length, MDL,
   information, Dinithi, LAllison, ArunK
%X "... demonstrates how a complete statistical model quantifying the evolution
   of pairs of aligned proteins can be constructed from a time-parameterised
   substitution matrix and a time-parameterised 3-state alignment machine. All
   parameters of such a model can be inferred from any benchmark data-set of
   aligned protein seqs.. This allows us to examine nine well-known sub.matrices
   on six benchmarks curated using various structural alignment methods; any
   matrix that does not explicitly model a 'time'-dependent Markov process is
   converted to a corr. base-matrix that does. [&] a new optimal matrix is
   inferred for each of the six benchmarks. Using Minimum Message Length (MML)
   inference, all 15 matrices are compared in terms of measuring the Shannon
   information content of each benchmark. This has resulted in a new & clear
   overall best performed time-dependent Markov matrix, MMLSUM, & its assoc.
   3-state m/c, whose properties we have analysed in this work. For std use, the
   MMLSUM series of (log-odds) scoring matrices derived from the above Markov
   matrix, are available at lcb.infotech.monash.edu.au/mmlsum "
   -- 2010.00855@[<A HREF="https://arxiv.org/abs/2010.00855">arXiv</A>]['20].

%A A. M. Lesk
%A A. S. Konagurthu
%A L. Allison
%A M. Garcia de la Banda
%A P. J. Stuckey
%A D. Abramson
%T Computer modelling of a potential agent against SARS-Cov-2 (COVID-19)
   protease
%J Proteins: Structure, Function and Bioinformatics
%V 88
%N 12
%P 1557-1558
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, SARS-CoV-2, SARSCoV2, protease,
   protein, Mpro, 3CLpro, nsp5, covid19, covalent, inSilico, ligand,
   inhibitor, Cys145, AMLesk, LAllison, ArunK
%X "We have modelled modifications of a known ligand to the SARSâCoVâ2
   (COVIDâ19) protease, that can form a covalent adduct, plus additional
   ligandâprotein hydrogen bonds."
   -- [<A HREF="https://doi.org/10.1002/prot.25980">doi:10.1002/prot.25980</A>]['20]  (online 14/7/2020).
   [Also search for: SARSCoV2 protease].

%A D. Sumanaweera
%A L. Allison
%A A. Konagurthu
%T Statistical compression of protein sequences and inference of marginal
   probability landscapes over competing alignments using finite state models
   and Dirichlet priors
%J Bioinformatics
%V 35
%N 14
%P i360-i369
%M JUL
%D 2019
%O ISMB/ECCB, Basel, .ch, July 2019
%K jrnl, conf, MolBio, c2019, c201x, c20xx, zz0719, LAllison, ArunK,
   bioinformatics, sequence, alignment, landscape, DPA, homology, protein,
   proteins, probability, probabilistic, Bayesian, information, MML, MDL,
   ISMB, ECCB
%X "The information criterion of minimum message length (MML) provides a
   powerful statistical framework for inductive reasoning from observed data. We
   apply MML to the problem of protein sequence comparison using finite state
   models with Dirichlet distributions. The resulting framework allows us to
   supersede the ad hoc cost functions commonly used in the field, by
   systematically addressing the problem of arbitrariness in alignment
   parameters, and the disconnect between substitution scores and gap costs.
   Furthermore, our framework enables the generation of marginal probability
   landscapes over all possible alignment hypotheses, with potential to
   facilitate the users to simultaneously rationalize and assess competing
   alignment relationships between protein sequences, beyond simply reporting a
   single (best) alignment. We demonstrate the performance of our program on
   benchmarks containing distantly related protein sequences."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btz368">doi:10.1093/bioinformatics/btz368</A>]['19].
   Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Protein/">protein</A>].

%A L. Allison
%A A. Konagurthu
%A D. Schmidt
%T On universal codes for integers: Wallace Tree, Elias Omega and variations
%J arXiv
%M JUN
%D 2019
%K TR, c2019, c201x, c20xx, zz0619, LAllison, ArunK, integer, universal code,
   codes, intCodes, compression, Elias, omega, omega2, omega*, omegastar, WTC,
   II, MML, Rissanen, logstar, log*, Fibonacci, asymptotic, optimality, MDL,
   robustness
%X "A universal code for the (positive) integers can be used to store or
   compress a sequence of integers. Every universal code implies a probability
   distribution on integers. This implied distribution may be a reasonable
   choice when the true distribution of a source of integers is unknown.
   Wallace Tree Code (WTC) is a universal code for integers based on binary
   trees. We give the encoding and decoding routines for WTC and analyse the
   properties of the code in comparison to two well-known codes, the Fibonacci
   and Elias omega codes. Some improvements on the Elias omega code are also
   described and examined."
   -- 1906.05004@[<A HREF="https://arxiv.org/abs/1906.05004">arXiv</A>]['19].
   Also see DCC21,
   [<A HREF="https://www.cantab.net/users/mmlist/ll/MML/Discrete/Universal/">more1</A>] and
   [<A HREF="http://www.allisons.org/ll/MML/Discrete/Universal/">more2</A>].

%A A. S. Konagurthu
%A R. Subramanian
%A L. Allison
%A D. Abramson
%A M. Garcia de la Banda
%A P. J. Stuckey
%A A. M. Lesk
%T Information-theoretic inference of an optimal dictionary of protein
   supersecondary structures
%B Protein Supersecondary Structures
%I Springer
%P 123-131
%M APR
%D 2019
%K chapter, c2019, c201x, c20xx, zz0519, LAllison, ArunK, AMLesk,
   bioinformatics, protein, structure, proteins, supersecondary, fold, tableau,
   dictionary, library, MML, minimum message length, mdl, AI, inference
%X "We recently developed an unsupervised Bayesian inference methodology to
   automatically infer a dictionary of protein supersecondary structures
   (Subramanian et al., IEEE data compression conference proceedings (DCC),
   340-349, 2017). Specifically, this methodology uses the information-theoretic
   framework of minimum message length (MML) criterion for hypothesis selection
   (Wallace, Statistical and inductive inference by minimum message length,
   Springer Science & Business Media, New York, 2005). The best dictionary of
   supersecondary structures is the one that yields the most (lossless)
   compression on the source collection of folding patterns represented as
   tableaux (matrix representations that capture the essence of protein folding
   patterns (Lesk, J Mol Graph. 13:159-164, 1995). This book chapter outlines
   our MML methodology for inferring the supersecondary structure dictionary.
   The inferred dictionary is available at [<A HREF="http://lcb.infotech.monash.edu.au/proteinConcepts/scop100/dictionary.html">www(click)</A>][/4/2019]."
   -- [<A HREF="https://doi.org/10.1007/978-1-4939-9161-7_6">doi:10.1007/978-1-4939-9161-7_6</A>]['19].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Protein/">protein</A>].)

%A L. Allison
%T Coding Ockham's Razor
%I Springer
%D 2018
%K book, text, c2018, c201x, c20xx, zz0618, LAllison, Occam, Ockham razor, MDL,
   minimum message length, description, MML, AIC, BIC, statistics, probability,
   model, distribution, estimate, estimation, likelihood, inductive inference,
   Bayesian, artificial intelligence, AI, kdd, decision, tree, Dtree, nml, mmld,
   clustering, snob, L4ref, mixture model, Gaussian, multistate, multinomial,
   vonMises, Fisher, vMF, Poisson, geometric, modelling, machine learning,
   discovery, algorithm, iris data, regression, stats, L5ref, II, AI, 27 club,
   27club, musician, graph, motif, pattern, graphs, graphModel, information,
   compression, compress, model, code, entropy, stats
%X "... inductive inference using the minimum message length (MML) principle and
   a computer. It is accompanied by a library of software to help an
   applications programmer, student or researcher in the fields of data analysis
   or machine learning to write computer programs of this kind. ..."
   -- [<A HREF="https://doi.org/10.1007/978-3-319-76433-7">doi:10.1007/978-3-319-76433-7</A>].
   uk us isbn:3319764322; uk us isbn13:978-3319764320.
     1 Introduction, 2 Discrete, 3 Integers, 4 Continuous, 5 Function-Models,
     6 Multivariate, 7 Mixture Models, 8 Function Model 2, 9 Vectors,
    10 Linear Regression, 11 Graphs, 12 Bits and Pieces, 13 An Implementation.
   (Also see the [<A HREF="https://www.cantab.net/users/mmlist/MML/A/">mmlist</A>] inc. doc and source code.)

%A D. Sumanaweera
%A L. Allison
%A A. S. Konagurthu
%T The bits between proteins
%J Data Compression Conference (DCC)
%I IEEE
%W Snowbird, Utah, USA
%M MAR
%D 2018
%K conf, DCC, DCC2018, MolBio, c2018, c201x, c20xx, zz0418, bioinformatics,
   LAllison, ArunK, Dinithi, DCC, DCC2018, protein, sequence, alignment, DPA,
   algorithm, evolutionary, model, minimum message length, MDL, MML, AIC,
   homology, information, similarity
%X "Comparison of protein sequences via alignment is an important routine in
   modern biological studies. Although the technologies for aligning proteins
   are mature, the current state of the art continues to be plagued by many
   shortcomings, chiefly due to the reliance on: (i) naive objective functions,
   (ii) fixed substitution scores independent of the sequences being considered,
   (iii) arbitrary choices for gap costs, and (iv) reporting, often, one
   optimal alignment without a way to recognise other competing sequence
   alignments. Here, we address these shortcomings by applying the
   compression-based Minimum Message Length (MML) inference framework to the
   protein sequence alignment problem. This grounds the problem in statistical
   learning theory, handles directly the complexity-vs-fit trade-off without
   ad hoc gap costs, allows unsupervised inference of all the statistical
   parameters, and permits the visualization and exploration of competing
   sequence alignment landscape."
   -- [<A HREF="http://www.allisons.org/ll/Publications/2018DCC/">more</A>],
      [<A HREF="https://doi.org/10.1109/DCC.2018.00026">doi:10.1109/DCC.2018.00026</A>]['18].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Protein/">protein</A>].)

%A A. M. Lesk
%A R. Subramanian
%A L. Allison
%A D. Abramson
%A P. J. Stuckey
%A M. G. de la Banda
%A K. S. Konagurthu
%T Universal architectural concepts underlying protein folding patterns
%J bioRxiv
%N 480194
%M DEC
%D 2018
%K TR, MolBio, c2018, c201x, c20xx, zz1120, AMLesk, LAllison, ArunK, protein,
   3D, structure, procodic, prosodic, fold, folding, concept, concepts,
   motif, pattern, substructure
%X "What is the architectural 'basis set' of the observed universe of protein
   structures? Using information-theoretic inference, we answer this question
   with a comprehensive dictionary of 1,493 substructural concepts. Each concept
   represents a topologically-conserved assembly of helices and strands that
   make contact. Any p.structure can be dissected into instances of concepts
   from this dictionary. We dissected the world-wide protein data bank ..."
   -- 480194@[<A HREF="https://www.biorxiv.org/content/10.1101/480194v2">bioRxiv</A>]['18].

%A R. Subramanian
%A L. Allison
%A P. J. Stuckey
%A M. Garcia de la Banda
%A D. Abramson
%A A. M. Lesk
%A A. S. Konagurthu
%T Statistical compression of protein folding patterns for inference of
   recurrent substructural themes
%J Data Compression Conf. (DCC)
%I IEEE
%W Snowbird, Utah, USA
%P 340-349
%M APR
%D 2017
%K conf, DCC, MolBio, c2017, c201x, c20xx, zz0517, protein, tertiary, 3D,
   super secondary, structure, motif, motifs, pattern, blocks, library,
   discovery, description, aic, MDL, minimum message length, MML,
   LAllison, AMLesk, ArunK
%X "Computational analyses of the growing corpus of three-dimensional (3D)
   structures of proteins have revealed a limited set of recurrent substructural
   themes, termed super-secondary structures. Knowledge of super-secondary
   structures is important for the study of protein evolution and for the
   modeling of proteins with unknown structures. Characterizing a comprehensive
   dictionary of these super-secondary structures has been an unanswered
   computational challenge in protein structural studies. This paper presents an
   unsupervised method for learning such a comprehensive dictionary using the
   statistical framework of lossless compression on a database comprised of
   concise geometric representations of protein 3D folding patterns. The best
   dictionary is defined as the one that yields the most compression of the
   database. Here we describe the inference methodology and the statistical
   models used to estimate the encoding lengths. An interactive website for this
   dictionary is available ..."
   -- [<A HREF="http://www.allisons.org/ll/Publications/2017DCC">more</A>]
   &  [<A HREF="https://doi.org/10.1109/DCC.2017.46">doi:10.1109/DCC.2017.46</A>]['17].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Protein/">protein</A>].)

%A J. H. Collier
%A L. Allison
%A A. M. Lesk
%A P. J. Stuckey
%A M. Garcia de la Banda
%A A. S. Konagurthu
%T Statistical inference of protein structural alignments using information and
   compression
%J J. Bioinformatics
%I OUP
%V 33
%N 1
%P 1005-1013
%M APR
%D 2017
%O bioRxiv, June 2016
%K jrnl, OUP, MolBio, c2017, c201x, c20xx, zz0317, protein, alignment,
   tertiary structure, 3D, information, MML, MMLigner, software,
   JHC, JHCollier, ArunK, LAllison, AMLesk, AIC, bic, mdl
%X "... present here a statistical framework for the precise inference of
   structural alignments, built on the Bayesian and information-theoretic
   principle of Minimum Message Length (MML). The quality of any alignment is
   measured by its explanatory powerâthe amount of lossless compression achieved
   to explain the protein coordinates using that alignment. ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btw757">doi:10.1093/bioinformatics/btw757</A>][2017] (online January 2017),
      [<A HREF="https://doi.org/10.1101/056598">bioRxiv</A>][6/2016],
      [<A HREF="http://www.allisons.org/ll/Publications/2017Bioinformatics/">more</A>].
   (Also see MMLigner@[<A HREF="http://lcb.infotech.monash.edu.au/mmligner">LCB</A>][2016].)

%A M. Duc Cao
%A L. Allison
%A T. I. Dix
%A M. Boden
%T Robust estimation of evolutionary distances with information theory
%J Mol. Biol. Evol.
%V 33
%N 5
%P 1349-1357
%M MAY
%D 2016
%K jrnl, MBE, MolBio, c2016, c201x, c20xx, zz0816, bioinformatics, evolutionary,
   phylogenetic, distance, trees, sequences, information, maximum, parsimony,
   DNA, likelihood, MML, MDL, AIC, Minh Duc Cao, LAllison, TIDix, MBoden
%X "Methods for measuring genetic dist. in phylogenetics are known to be
   sensitive to the evol. model assumed. However, there is a lack of established
   methodology to accommodate the trade-off between incorporating suff. biol.
   reality & avoiding model overfitting. [&] as trad. methods measure dists.
   based on the observed # of substitutions, they tend to underestimate dist.
   between diverged seqs. due to backward & parallel subsns. Various techniques
   were proposed to correct this, but they lack the robustness [v.] sequs. that
   are distantly related & of unequal base freqs.. ... we present a novel
   genetic dist. est. based on inf.theory that overcomes the above two hurdles.
   Instead of examining the obs. # of subsns, [it] ests. genetic dist. using
   Shannon's mutual information. This naturally provides an effective framework
   for balancing model complexity & goodness of fit. Our dist. est. is shown to
   be approx. linear to elapsed time & hence is less sensitive to the divergence
   of seq. data & compositional biased seqs.. Using extensive simulation data,
   we show that our method 1) consistently reconstructs more accurate phylogeny
   topologies than existing methods, 2) is robust in extreme condns such as
   diverged phylogenies, unequal base freqs. data, & heterogeneous mutation
   patterns, & 3) scales well with large phylogenies."  [online Feb 2016.]
   -- [<A HREF="https://doi.org/10.1093/molbev/msw019">doi:10.1093/molbev/msw019</A>]['16].
   [Also search for: MolBio evolutionary MML].

%A A. S. Konagurthu
%A P. Kasarapu
%A L. Allison
%A J. H. Collier
%A A. M. Arthur
%T On sufficient statistics of least-squares superposition of vector sets
%J J. Comp. Biol.
%V 22
%N 6
%P 487-497
%M MAY
%D 2015
%K jrnl, JCB, MolBio, bioinformatics, ArunK, LAllison, AMLesk, JHC, JHCollier,
   c2015, c201x, c20xx, zz0116, 3D, point set, tertiary, protein, structure,
   structural alignment, superposition, match, matching, estimation, stats
%X "The problem of superposition of two corr. vector sets by minimizing their
   sum-of-squares error under orthogonal transformation ... can be solved
   exactly using an alg. whose time complexity grows linearly with the # of
   correspondences. ... particularly in studies involving macromolecular
   structs.. ... formally derives a set of suff.stats. for the least-squares
   superposition problem. These s. are additive. This permits a highly efficient
   (const. time) computation of superpositions (& s.stats.) of vector sets that
   are composed from its constituent v.sets under addition or deletion op.,
   where the s.stats. of the constituent sets are already known (that is, [they]
   have been previously superposed). ... a drastic improvement in the run time
   of the methods that commonly superpose v.sets under addition or deletion
   ops., where previously these ops. were carried out ab initio (ignoring the
   s.stats.). ... demonstrate the improvement our work offers in the context of
   protein structural alignment programs that assemble a reliable structural
   alignment from well-fitting (substructural) fragment pairs. A C++ library for
   this task is available online under an open-source license."
   -- [<A HREF="https://doi.org/10.1089/cmb.2014.0154">doi:10.1089/cmb.2014.0154</A>]['16].
   (Based on the 2014 RECOMB paper.)

%A P. Kasarapu
%A L. Allison
%T Minimum message length estimation of mixtures of multivariate Gaussian and
   von Mises-Fisher distributions
%J Machine Learning
%V 100
%N 2
%P 333-378
%M MAR
%D 2015
%O ECML / PKDD, Porto, Portugal, 7-11 Sept. 2015
%K jrnl, c2015, c201x, c20xx, zz0415, AI, II, Parthan, LAllison, MDL, AIC,
   MML, minimum message length, mixture modelling, model, clustering, vonMises,
   multivariate, vMF, Fisher, protein, structure, description, classification,
   Bayesian, directional, probability distribution, mmld, Figuerdo
%X "Mixture modelling involves explaining some observed evidence using a
   combination of probability distributions. The crux of the problem is the
   inference of an optimal number of mixture components and their corr.
   parameters. This paper discusses unsupervised learning of mixture models
   using the Bayesian Minimum Message Length (MML) criterion. To demonstrate the
   effectiveness of search & inference of mixture parameters using the proposed
   approach, we select two key probability distributions, each handling
   fundamentally different types of data: the multivariate Gaussian distribution
   to address mixture modelling of data distributed in Euclidean space, & the
   multivariate von Mises-Fisher (vMF) distribution to address mixture modelling
   of directional data distributed on a unit hypersphere. The key contributions
   of this paper, in addition to the general search & inference methodology,
   include the derivation of MML expressions for encoding the data using
   multivariate Gaussian & von Mises-Fisher distributions, & the analytical
   derivation of the MML estimates of the parameters of the two distributions.
   Our approach is tested on simulated & real world data sets. For instance, we
   infer vMF mixtures that concisely explain experimentally determined 3D
   protein conformations, providing an effective null model description of
   protein structures that is central to many inference problems in structural
   bioinformatics. The experimental results demonstrate that the performance of
   our proposed search & inference method along with the encoding schemes
   improve on the state of the art mixture modelling techniques."
   -- [<A HREF="https://doi.org/10.1007/s10994-015-5493-0">doi:10.1007/s10994-015-5493-0</A>]['15],
      [<A HREF="http://www.allisons.org/ll/Publications/2015ML/">more</A>].

%A F. Petitjean
%A L. Allison
%A G. Webb
%T A statistically efficient and scalable method for log-linear analysis of
   high-dimensional data
%J ICDM
%I IEEE
%W Shenzhen (.cn)
%M DEC
%D 2014
%K proc, conf, ICDM, DM2018, c2014, c201x, c20xx, zz1214, data mining, models,
   graphical model, log linear, chordal graph, chordalysis, MML, AIC, mdl, chi2,
   chi squared, II, AI, maths, stats, decomposable, FPj, LAllison, GWebb, Monash
%X "Log-linear analysis is the primary statistical approach to discovering
   conditional dependencies between the variables of a dataset. A good
   log-linear analysis method requires both high precision & statistical
   efficiency. High precision means that the risk of false discoveries should be
   kept very low. Statistical efficiency means that the method should discover
   actual associations with as few samples as possible. Classical approaches to
   log-linear analysis make use of chi^2 tests to control this balance between
   quality & complexity.  We present an information-theoretic approach to
   log-linear analysis. We show that our approach 1) requires significantly
   fewer samples to discover the true associations than statistical approaches
   - statistical efficiency - 2) controls for the risk of false discoveries as
   well as statistical approaches - high precision - and 3) can perform the
   discovery on datasets with hundreds of variables on a standard desktop
   computer - computational efficiency."
   -- [<A HREF="http://www.allisons.org/ll/Publications/2014ICDM/">more</A>],
      [<A HREF="https://doi.org/10.1109/ICDM.2014.23">doi:10.1109/ICDM.2014.23</A>]['14].

%A J. Collier
%A L. Allison
%A A. Lesk
%A M. Garcia de La Banda
%A A. Konagurthu
%T A new statistical framework to assess structural alignment quality using
   information compression
%J ECCB
%W Strasbourg
%M SEP
%D 2014
%K conf, ECCB 14, MolBio, c2014, c201x, c20xx, zz0914, LAllison, ArunK, AMLesk,
   JHCollier, protein, 3D, similar, structure, alignment, match, MML, MDL, AIC,
   complexity, bioinformatics, 13th Euro, Conf, Comp, Biology, I value, Ivalue
%X "... proposes a new statistical framework to assess structural alignment
   quality and significance based on lossless information compression. This is
   a radical departure from the traditional approach of formulating scoring
   functions. It links the structural alignment problem to the general class of
   statistical inductive inference problems, solved using the
   information-theoretic criterion of minimum message length. Based on this, we
   developed an efficient and reliable measure of structural alignment quality,
   I-value. The performance of I-value is demonstrated in comparison with a
   number of popular scoring functions, on a large collection of competing
   alignments. Our analysis shows that I-value provides a rigorous and reliable
   quantification of structural alignment quality, addressing a major gap in
   the field."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btu460">doi:10.1093/bioinformatics/btu460</A>]['14],
      [<A HREF="http://www.allisons.org/ll/Publications/2014ECCB/">more</A>].

%A L. Allison
%T On the complexity of graphs (networks) by information content, and
   conditional (mutual) information given other graphs
%I Clayton School of the Faculty of Info. Tech., Monash Uni.
%R 2014/277
%P 14
%M JUN
%D 2014
%K c2014, c201x, c20xx, zz0614, LAllison, TR, complex, compress, compression,
   graph, network, model, graphModel, complexity, minimum message length, MML,
   simple, random, description, AI, information content, AIC, MDL, mutual,
   similarity, viagra, cialis, xanax, valium, structure, SMILES, organic, maths,
   chemical compound, MolBio, molecule, probability, likelihood, LAllison
%X '... concerns the information content of a graph, optionally conditional on
   one or more background, "common knowledge" graphs. It describes an algorithm
   to estimate this information content, and includes some examples based on
   chemical compounds.'
   -- [<A HREF="http://www.allisons.org/ll/Publications/2014Graph/">more</A>],
   &  2008.04744@[<A HREF="https://arxiv.org/abs/2008.04744">arXiv</A>][2020].

%A A. S. Konagurthu
%A P. Kasarapu
%A L. Allison
%A J. H. Collier
%A A. M. Lesk
%T On sufficient statistics of least-squares superposition of vector sets
%J RECOMB
%I SpringerVerlag
%S LNCS/LNBI
%V 8394
%M APR
%P 144-159
%D 2014
%K conf, RECOMB, MolBio, c2014, c201x, c20xx, zz0514, ArunK, LAllison, AMLesk,
   JHCollier, bioinformatics, RECOMB18, protein, structure, alignment,
   least squares, RMS, error, 3D, match, matching, additive, orthogonal, rigid,
   vector set, Kearsley, algorithm
%X "Superposition by orthogonal transformation of vector sets by minimizing the
   least-squares error is a fundamental task in many areas of science, notably
   in structural molecular biology. Its widespread use for structural analyses
   is facilitated by exact solns of this problem, computable in linear time.
   However, in several of these analyses it is common to invoke this
   superposition routine a very large number of times, often operating (through
   addition or deletion) on previously superposed vector sets. This paper
   derives a set of sufficient statistics for the least-squares orthogonal
   transformation problem. These sufficient statistics are additive. This
   property allows for the superposition parameters (rotation, translation, &
   root mean square deviation) to be computable as constant time updates from
   the statistics of partial solutions. We demonstrate that this results in a
   massive speed up in the computational effort, when compared to the method
   that recomputes superpositions ab initio .  Among others, protein structural
   alignment algorithms stand to benefit from our results."
   -- [<A HREF="https://doi.org/10.1007/978-3-319-05269-4_11">doi:10.1007/978-3-319-05269-4_11</A>]['14],
      [<A HREF="http://www.allisons.org/ll/Publications/2014RECOMB/">more</A>].

%A A. S. Konagurthu
%A L. Allison
%A D. Abramson
%A P. J. Stuckey
%A A. M. Lesk
%T How precise are reported protein coordinate data?
%J Acta Cryst.
%V D70
%N 3
%P 904-906
%M MAR
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0314, protein, 3D, tertiary, structure,
   precision, accuracy, PDB, ArunK, LAllison, AMLesk
%X "Atomic coordinates in the Worldwide Protein Data Bank (wwPDB) are generally
   reported to greater precision than the experimental structure determinations
   have actually achieved. By using information theory & data compression to
   study the compressibility of protein atomic coordinates, it is possible to
   quantify the amount of randomness in the coordinate data & thereby to
   determine the realistic precision of the reported coordinates. On avg., the
   value of each C_alpha coordinate in a set of selected p.structures solved at
   a variety of resolutions is good to about 0.1A."
   -- [<A HREF="https://doi.org/10.1107/S1399004713031787">doi:10.1107/S1399004713031787</A>]['14],
      [<A HREF="http://www.allisons.org/ll/Publications/2014ActaC/">more</A>].

%A A. S. Konagurthu
%A A. M. Lesk
%A D. Abramson
%A P. J. Stuckey
%A L. Allison
%T Statistical inference of protein "LEGO bricks"
%J ICDM
%M DEC
%D 2013
%K conf, ICDM, ICDM13, MolBio, c2013, c201x, c20xx, zz1213, LAllison, ArunK,
   AMLesk, protein, tertiary, 3D, MML, structure, structures, recurrent,
   structural, motifs, backbone, folds, MDL, library, dictionary, fragment,
   blocks, fragments, bioinformatics, data mining
%X "Proteins are biomolecules of life. They fold into a great variety of
   three-dimensional (3D) shapes. Underlying these folding patterns are many
   recurrent structural fragments or building blocks (analogous to "LEGO(r)
   bricks"). This paper reports an innovative statistical inference approach to
   discover a comprehensive dictionary of protein structural building blocks
   from a large corpus of experimentally determined protein structures. Our
   approach is built on the Bayesian and information-theoretic criterion of
   minimum message length [MML]. To the best of our knowledge, this work is the
   first systematic and rigorous treatment of a very important data mining
   problem that arises in the cross-disciplinary area of structural
   bioinformatics. The quality of the dictionary we find is demonstrated by its
   explanatory power - any protein within the corpus of known 3D structures can
   be dissected into successive regions assigned to fragments from this
   dictionary. This induces a novel one-dimensional representation of three-
   -dimensional protein folding patterns, suitable for application of the rich
   repertoire of character-string processing algorithms, for rapid
   identification of folding patterns of newly determined structures. This paper
   presents the details of the methodology used to infer the dictionary of
   building blocks, and is supported by illustrative examples to demonstrate its
   effectiveness and utility."
   -- [<A HREF="https://doi.org/10.1109/ICDM.2013.73">doi:10.1109/ICDM.2013.73</A>]['14],
      [<A HREF="http://www.allisons.org/ll/Publications/2013ICDM/">more</A>], and
      1310.1462@[<A HREF="http://arxiv.org/abs/1310.1462">arXiv</A>]['13].

%A A. S. Konagurthu
%A A. M. Lesk
%A L. Allison
%T Minimum message length inference of secondary structure from protein
   coordinate data
%J J. Bioinformatics
%I OUP
%V 28
%N 12
%P i97-i105
%M JUN
%D 2012
%O ISMB, Long Beach
%K conf, ISMB12, MolBio, c2012, c201x, c20xx, zz0612, LAllison, ArunK, AMLesk,
   SST, bioinformatics, protein, secondary structure, DSSP, assignment, helix,
   extended strand, sheet, coil, mmld, fold, MML, MDL, model
%X "Motivation: Secondary structure underpins the folding pattern and
   architecture of most proteins. Accurate assignment of the SS elts is
   therefore an important problem. Although many approx. solns of the SS
   assignment problem exist, the statement of the problem has resisted a
   consistent & math. rigorous defn. A variety of comparative studies have
   highlighted major disagreements in the way the available methods define &
   assign SS to coord.data.
   Results: We report a new method to infer SS based on the Bayesian method of
   Minimum Message Length (MML) inference. It treats assignments of SS as
   hypotheses that explain the given coord.data. The method seeks to maximise
   the joint probability of a hypothesis & the data. There is a natural null
   hypothesis & any assignment that cannot better it is unacceptable. We
   developed a program SST based on this approach & compared it to popular
   programs such as DSSP & STRIDE amongst others. Our evaln suggests that SST
   gives reliable assignments even on low resolution structures."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/bts223">doi:10.1093/bioinformatics/bts223</A>]['12].<!-- jrnl IF=5.468, Sept 2012 -->
   More: [<A HREF="http://www.allisons.org/ll/Publications/2012ISMB/">www</A>]['12].

%A E. Makalic
%A L. Allison
%T MMLD inference of multilayer perceptrons
%J Solomonoff 85th Memorial Conference
%W Melbourne
%I SpringerVerlag
%S LNCS / LNAI
%V 7070
%P 261-272
%M DEC
%D 2011
%K conf, Ray, c2011, c201x, c20xx, AI, II, Enes, enesm, MML, mmld, LAllison,
   perceptron, NN, ANN, neural network, information, MDL, complexity
%X "A multilayer perceptron comprising a single hidden layer of neurons with
   sigmoidal transfer fns can approx. any computable fn to arbitrary accuracy.
   The size of the hidden layer dictates the approximation capability of the
   multilayer perceptron & automatically determining a suitable network size for
   a given data set is an interesting question. ... considers the problem of
   inferring the size of multilayer perceptron networks with the MMLD model
   selection criterion which is based on the MML principle. The two main
   contributions of the paper are: (1) a new model seln criterion for inference
   of fully-connected multilayer perceptrons in regression problems, & (2) an
   efficient alg. for computing MMLD-type codelengths in mathematically
   challenging model classes. Empirical performance of the new alg. is
   demonstrated on artificially generated & real data sets."
   -- [<A HREF="https://doi.org/10.1007/978-3-642-44958-1_20">doi:10.1007/978-3-642-44958-1_20</A>]['14]; uk us isbn13:9783642449574.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A A. S. Konagurthu
%A L. Allison
%A P. J. Stuckey
%A A. M. Lesk
%T Piecewise linear approximation of protein structures using the principle of
   minimum message length
%J J. Bioinformatics
%V 27
%N 13
%P i43-i51
%M JUL
%D 2011
%K conf, MolBio, MML, c2011, c201x, c20xx, zz0711, ISMB, LAllison, ArunK,
   AMLesk, protein, fold, cartoon, description, ribbon diagram, structure,
   segmentation, minimum message length, MDL, information theoretic
%X "Simple & concise representations of protein-folding patterns provide
   powerful abstractions for visualizations, comparisons, classifications,
   searching & aligning structural data. Structures are often abstracted by
   replacing standard secondary structural features - that is, helices & strands
   of sheet - by vectors or linear segments. Relying solely on std secondary
   structure may result in a sig. loss of structural information. Further,
   traditional methods of simplification crucially depend on the consistency &
   accuracy of external methods to assign SS to protein coord.data. Although
   many methods exist automatically to identify SS, the impreciseness of
   definitions, along with errors & inconsistencies in experimental structure
   data, drastically limit their applicability to generate reliable simplified
   representations, especially for structural comparison.
   This article introduces a mathematically rigorous alg. to delineate protein
   structure using the elegant statistical & inductive inference framework of
   minimum message length (MML). Our method generates consistent & statistically
   robust piecewise linear explanations of protein coordinate data, resulting in
   a powerful & concise representation of the structure. The delineation is
   completely independent of the approaches of using hydrogen-bonding patterns
   or inspecting local substructural geometry that the current methods use.
   Indeed, as is common with applications of the MML criterion, this method is
   free of parameters & thresholds, in striking contrast to the existing
   programs which are often beset by them.
   The analysis of results over a large number of proteins suggests that the
   method produces consistent delineation of structures that encompasses, among
   others, the segments corresponding to standard secondary structure."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btr240">doi:10.1093/bioinformatics/btr240</A>]['11]<!-- jrnl IF=5.468, Sept 2012 -->.
   (Also see [<A HREF="http://www.allisons.org/ll/Publications/2011ISMB/">more</A>].)

%A M. D. Cao
%A T. I. Dix
%A L. Allison
%T A biological compression model and its applications
%B Software Tools and Algorithms for Biological Systems
%E H. R. Arabnia
%E Q.-N. Tran
%I SpringerVerlag
%S AEMB (Advances in Experimental Medicine and Biology)
%V 696
%P 657-666
%M APR
%D 2011
%K MolBio, AEMB, book chapter, c2011, c201x, zz0411, c20xx, LAllison, TIDix,
   Minh Duc Cao, bioinformatics, entropy, compression, DNA, protein, sequence,
   data, compress, MML, MDL
%X "A biological compression model, expert model, is presented which is superior
   to existing compression algorithms in both compression performance and speed.
   The model is able to compress whole eukaryotic genomes. Most importantly, the
   model provides a framework for knowledge discovery from biological data. It
   can be used for repeat element discovery, sequence alignment and phylogenetic
   analysis. We demonstrate that the model can handle statistically biased
   sequences and distantly related sequences where conventional knowledge
   discovery tools often fail."
   -- [<A HREF="http://www.allisons.org/ll/Publications/2011AEMB/">more</A>],
      chapter 67 [<A HREF="https://doi.org/10.1007/978-1-4419-7046-6_67">doi:10.1007/978-1-4419-7046-6_67</A>]['11],
      in: hb us$204; uk us isbn:1441970452; uk us isbn13:978-1441970459.

%A M. D. Cao
%A T. I. Dix
%A L. Allison
%T A genome alignment algorithm based on compression
%J BMC Bioinformatics
%V 11
%N 1
%P 599
%M DEC
%D 2010
%K jrnl, eJrnl, MolBio, c2010, c201x, c20xx, Minh Duc Cao, LAllison, TIDix,
   highly accessed paper, DNA, whole genome alignment, zz0111, local alignment,
   sequence, long, compress, compression, MML, MDL, BIC, poa, XM, expert model,
   XMAligner
%X "... Since genomic sequences carry genetic info., this article proposes that
   the info. content of each nucleotide in a posn should be considered in
   sequence alignment. An info.-theoretic approach for pairwise genome local
   alignment, namely XMAligner, is presented. Instead of comparing sequences at
   the character level, XMAligner considers a pair of nucleotides from two
   seqs. to be related if their mutual info. in context is significant. The
   info.content of nucleotides in sequences is measured by a lossless
   compression technique. ... Experiments on both simulated data & real data
   show that XMAligner is superior to conventional methods especially on
   distantly related seqs. & statistically biased data. XMAligner can align
   seqs. of eukaryote genome size with only a modest hardware requirement. ..."
   -- [<A HREF="http://www.allisons.org/ll/Publications/2010BMCbioinformatics/">more</A>],
  <!-- ISI j's IF=3.43, Dec 2010 -->    [<A HREF="https://doi.org/10.1186/1471-2105-11-599">doi:10.1186/1471-2105-11-599</A>][12/'10] (BMC 17/2/12 mail: 3372 accesses),
      21159205@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/21159205">pubmed</A>][2/'11].

%A M. B. Dale
%A L. Allison
%A P. E. R. Dale
%T Model selection using Minimal Message Length: an example using pollen data
%J Community Ecology
%V 11
%N 2
%P 187-201
%M DEC
%D 2010
%K jrnl, c2010, c201x, c20xx, LAllison, MML, mdl, pollen, data, segmentation,
   model, clustering, time series, timeSeries, plant, ecology, vegetation,
   cores, sediment
%X "... use of the minimum message length criterion [for] evaluating alternative
   models of data when the samples are serially ordered in space & implicitly
   in time. Much data from vegetation studies can be arranged in a sequence &
   in such cases the user may elect to constrain the clustering by zones, in
   preference to an unconstrained clustering. We use the MML principle to
   determine if such a choice provides an effective model of the data. Pollen
   data provide a suitably organised set of samples, but have other properties
   which make it desirable to examine several different models for the
   distribution of palynomorphs within the clusters. The results suggest that
   zonation is not a particularly preferred model since it captures only a small
   part of the patterns present. It represents a user expectation regarding the
   nature of variation in the data & results in some patterns being neglected.
   By using unconstrained clustering within zones, we can recover some of this
   overlooked pattern. We then examine other evidence for the nature of change
   in vegetation & finally discuss the usefulness of the MML as a guiding
   principle in model choice & its relationship to other possible criteria."
   -- [<A HREF="https://doi.org/10.1556/ComEc.11.2010.2.7">doi:10.1556/ComEc.11.2010.2.7</A>]['11].
   (Also see [<A HREF="http://www.allisons.org/ll/FP/IP/">IP</A>].)

%A A. Konagurthu
%A L. Allison
%A T. Conway
%A B. Beresford-Smith
%A J. Zobel
%T Design of an efficient out-of-core read alignment algorithm
%J WABI
%I SpringerVerlag
%S LNCS/LNBI
%V 6293
%P 189-201
%M SEP
%D 2010
%K wShop, MolBio, c2010, c201x, c20xx, zz1010, WABI, WABI10, nicta, LAllison,
   Syzygy, ArunK, Algorithms in Bioinformatics, short read, reads, NGS, align,
   mapping, next generation, DNA, sequencing, algorithm
%X "New genome sequencing technologies are poised to enter the sequencing
   landscape with significantly higher throughput of read data produced at
   unprecedented speeds & lower costs per run. However, current in-memory
   methods to align a set of reads to one or more reference genomes are
   ill-equipped to handle the expected growth of read-throughput from newer
   technologies.  ... reports the design of a new out-of-core read mapping alg.,
   Syzygy, which can scale to large volumes of read & genome data. The alg. is
   designed to run in a constant, user-stipulated amount of main memory -
   small enough to fit on standard desktops - irrespective of the sizes of read
   & genome data. Syzygy achieves a superior spatial locality-of-reference that
   allows all large data structures used in the alg. to be maintained on disk.
   We compare our prototype implementation with several popular read alignment
   programs.  Our results demonstrate clearly that Syzygy can scale to very
   large read volumes while using only a fraction of memory in comparison,
   without sacrificing performance."
   -- [<A HREF="http://www.allisons.org/ll/Publications/2010WABI/">more</A>],
      [<A HREF="https://doi.org/10.1007/978-3-642-15294-8_16">doi:10.1007/978-3-642-15294-8_16</A>]['10].
   (In: uk us isbn:3642152937; uk us isbn13:978-3-642-15293-1.<!-- WABI: 83 submissions ... 30 papers accepted -->)

%A M. B. Dale
%A L. Allison
%A P. E. R. Dale
%T A model for correlation within clusters and its use in pollen analysis
%J Community Ecology
%V 11
%N 1
%P 51-58
%M JUN
%D 2010
%K jrnl, c2010, c201x, c20xx, LAllison, MML, mdl, pollen, data, plants, ecology,
   model, segmentation, clustering, sediments, time
%X "... determine the # of clusters & also whether the model of any cluster is
   improved by introducing a factor. ... allows us to seek clusters which
   reflect directional changes rather than imposing a zonation constrained by
   spatial (& implicitly temporal) position. Minimal message length is a means
   of utilising Okham's Razor in inductive analysis. The "best" model is that
   which allows most compression of the data, which results in a minimal
   message length for the description. Fit to the data is not a sufficient
   criterion for choosing models because more complicated models will almost
   always fit better. MML combines fit to the data with an encoding of the model
   & provides a Bayesian probability criterion as a means of choosing between
   models (& classes of model). Applying the analysis to a pollen diagram from
   Southern Chile, we find that the introduction of factors does not improve the
   overall quality of the mixture model. The solution without axes in any
   cluster provides the most parsimonious solution. Examining the cluster with
   the best case for a factor to be incorporated in its description shows that
   the attributes highly loaded on the axis represent a contrast of herbaceous
   vegetation & dominant forests types. This contrast is also found when fitting
   the entire population, & in this case the factor solution is the preferred
   model. Overall, the cluster solution without factors is much preferred. Thus,
   in this case classification is preferred to ordination although more data are
   desirable to confirm such a conclusion."
   -- [<A HREF="https://doi.org/10.1556/ComEc.11.2010.1.8">doi:10.1556/ComEc.11.2010.1.8</A>][11].
   (Also see [<A HREF="http://www.allisons.org/ll/FP/IP/">IP</A>].)

%A M. D. Cao
%A L. Allison
%A T. I. Dix
%T A distance measure for genome phylogenetic analysis
%J AI09
%I SpringerVerlag
%S LNCS
%V 5866/2009
%P 71-80
%M DEC
%D 2009
%K conf, MolBio, c2009, c200x, c20xx, zz1209, Minh Duc Cao, TIDix, AI, II, AI09,
   LAllison, NICTA, bioinformatics, MML, MDL, phylogenetic, tree, evolutionary,
   XM, trees, distance, measure, matrix, information, maximum parsimony,
   maximum likelihood, method, methods, construction, reconstruction, inference,
   Plasmodium, Plasmodia
%X "Phylogenetic analyses of species based on single genes or parts of the
   genomes are often inconsistent because of factors such as variable rates of
   evolution & horizontal gene transfer.  ... phylogeny construction from
   complete genomes that is less sensitive to such inconsistency. For such long
   seqs., construction methods like maximum parsimony & maximum likelihood are
   often not possible due to their intensive computational requirement. Another
   class of tree construction methods, namely distance-based methods, require a
   measure of distances between any 2 genomes. ...  presents an information
   theoretic measure of genetic distances between genomes based on the
   biological compression algorithm 'expert model' [XM]. ...  tree of a number
   of Plasmodium parasites from their genomes ... successfully construct a
   plausible evolutionary tree for the gamma-Proteobacteria group whose genomes
   are known to contain many horizontally transferred genes."
   -- [<A HREF="https://doi.org/10.1007/978-3-642-10439-8_8">doi:10.1007/978-3-642-10439-8_8</A>]['09],
   &  [<A HREF="http://www.allisons.org/ll/Publications/2009AI/">phylogenetics</A>].
   (2009; uk us isbn:364210438X; uk us isbn13:978-3642104381).

%A J. Bernal
%A T. I. Dix
%A L. Allison
%A A. Bartholomeusz
%A L. Yuen
%T Modelling Hepatitis B virus antiviral therapy and drug resistant mutant
   strains
%J ACAL09
%I SpringerVerlag
%S LNCS
%V 5865
%P 159-168
%M DEC
%D 2009
%K conf, ACAL, MolBio, c2009, c200x, c20xx, zz1109, TIDix, LAllison, NICTA,
   vidrl, Hepatitis B, Hep B, HepB, HBV, bioinformatics, drug resistance, model,
   simulation
%X "... an individual-based model of HBV inside an artificial liver, &
   associated blood serum, undergoing antiviral therapy. This model aims to
   provide insights into the evolution of the HBV quasispecies & the
   individual contribution of HBV mutations in the outcome of therapy."
   -- [<A HREF="https://doi.org/10.1007/978-3-642-10427-5_16">doi:10.1007/978-3-642-10427-5_16</A>]['09].
   (2009; uk us isbn:3642104266; uk us isbn13:978-3642104268.)
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].)

%A M. D. Cao
%A T. I. Dix
%A L. Allison
%T Computing substitution matrices for genomic comparative analysis
%J Advances in Knowledge Discovery and Data Mining
%I SpringerVerlag
%S LNCS
%V 5476 / 2009
%P 647-655
%M APR
%D 2009
%K conf, PAKDD, MolBio, c2009, c200x, c20xx, zz0509, bioinformatics, PAKDD09,
   PAKDD13, DNA, genome, comparative analysis, comparison, substitution matrix,
   PAM, blosum, estimation, alignment, free, homology, MML, MDL, information,
   XM, Minh Duc Cao, TIDix, LAllison, (NICTA), malaria genome
%X "Substitution matrices ... and are important for many knowledge discovery
   tasks such as phylogenetic analysis and sequence alignment. ... present a
   novel algorithm that addresses this by computing a nucleotide substitution
   matrix specifically for the two genomes being aligned. ... uses compression
   ...  reconstructs, with high accuracy, the substitution matrix for
   synthesised data generated from a known matrix with introduced noise. ...
   successfully applied to real data for various malaria parasite genomes,
   which have differing phylogenetic distances and composition that lessens the
   effectiveness of standard statistical analysis techniques."
   pdf@[<A HREF="https://doi.org/10.1007/978-3-642-01307-2_64">doi:10.1007/978-3-642-01307-2_64</A>]['09], and
   [<A HREF="http://www.allisons.org/ll/Publications/2009PAKDD/">substitution matrices</A>].

%A M. D. Cao
%A T. I Dix
%A L. Allison
%T A genome alignment algorithm based on compression
%R 2009/233
%I Faculty of Info. Tech. (Clayton), Monash University
%M JAN
%D 2009
%K TR, TR233, MolBio, c2009, c200x, c20xx, bioinformatics, zz0109, FIT, Monash,
   Minh Duc Cao, TIDix, LAllison, data, DNA, sequence, compression, compressed,
   compress, MML, MDL, align, strings, information, content, free, XM, XMAligner
%X "Traditional genome alignment methods based on dynamic programming are often
   a. computational expensive, b. unable to compare the genomes of distant
   species, & c. unable to deal with low information regions. ... information-
   -theoretic approach for pairwise genome local alignment. ... the expert model
   aligner, the XMAligner, relies on the expert model compression alg.. To align
   2 seqs., XMAligner 1st compresses one sequence to measure the info. content
   at each posn in the seq.. Then the seq. is compressed again but this time
   with the background knowledge from the other seq. to obtain the conditional
   info. content. The info. content & the conditional info. content from the
   2 compressions are examined. Similar regions in the compressed seq. should
   have the conditional info. content lower than the individual info. content.
   ... applied to align the genomes of Plasmodium falciparum & P. knowlesi v.
   other 3 P. genomes with different levels of diversity. Despite the
   differences in nucleotide composition of the reference seqs., the conserved
   regions found by XMAligner in 3 alignments are relatively consistent. A
   strong correlation was found between the similar regions detected by the
   XMAligner & the hypothetical annotation of Plasmodium species. The alignment
   results can be integrated into the DNAPlatform for visualisation."
   -- [<A HREF="http://www.csse.monash.edu.au/publications/2009/tr-2009-233-abs.html">abs</A>]['09].
   [Also search for: Cao Dix Allison Bioinformatics c2010],
   and see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">compression</A>]['09].

%A L. Allison
%T Added distributions for use in clustering (mixture modelling), function
   models, regression trees, segmentation, and mixed Bayesian networks in
   Inductive Programming 1.2
%R 2008/224
%I Faculty of Info. Tech., Monash University, Australia 3800
%M APR
%D 2008
%K IP 1.2, IP1.2, TR 224, TR224, c2008, c200x, c20xx, zz0508, LAllison,
   machine learning, Geometric, Poisson, Gaussian, probability, stats, model,
   tree, segment, network, FP, MDL, minimum message length, MML, description,
   inductive inference, II, Student's t-Distribution, tDistribution
%X "Inductive programming is a machine learning paradigm combining functional
   programming (FP) with the information theoretic criterion, Minimum Message
   Length (MML). IP 1.2 now includes the Geometric and Poisson distributions
   over non-negative integers, and Student's t-Distribution over continuous
   values, as well as the Multinomial and Normal (Gaussian) distributions from
   before. All of these can be used with IP's model-transformation operators,
   and structure-learning algorithms including clustering (mixture-models),
   classification- (decision-) trees and other regressions, and mixed Bayesian
   networks, provided only that the types match between each corresponding
   component Model, transformation, structured model, and variable -- discrete,
   continuous, sequence, multivariate, and so on."
   -- [<A HREF="http://www.allisons.org/ll/Publications/2008_IP_1.2/">paper</A>],
      [<A HREF="http://www.allisons.org/ll/FP/IP/">Ind.Prog.(IP)</A>] inc. source code.

%A T. I. Dix
%A D. R. Powell
%A L. Allison
%A J. Bernal
%A S. Jaeger
%A L. Stern
%T Comparative analysis of long DNA sequences by per element
   information content using different contexts
%J BMC Bioinformatics
%V 8(S2):S10
%M MAY
%D 2007
%K jrnl, ejrnl, MolBio, c2007, c200x, c20xx, zz0407, TIDix, LAllison, sequence,
   analysis, data, compression, compress, low, mutual, information content,
   simple, complex, DNA, plot, II, MDL, AI, context, description, profile,
   signature, pattern discovery, genomic, minimum message length, MML,
   Cyanidioschyzon merolae, alga, algae, Plasmodium falciparum, gui, browser
%X "... The paper presents a methodology for exploring long DNA sequences, of
   the order of millions of bases, by means of their information content. ..."
  <!-- ISI j's IF=4.96, at '07 --> -- [<A HREF="http://www.allisons.org/ll/Publications/2007BMCbioinformatics/">long DNA</A>],
      [<A HREF="https://doi.org/10.1186/1471-2105-8-S2-S10">doi:10.1186/1471-2105-8-S2-S10</A>]['08],
      17493248@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/17493248">pubmed</A>]['11].

%A M. D. Cao
%A T. I. Dix
%A L. Allison
%A C. Mears
%T A simple statistical algorithm for biological sequence compression
%J Data Compression Conf.
%W Snowbird, Utah
%I IEEE
%P 43-52
%M MAR
%D 2007
%K conf, MolBio, II, DCC, DCC07, c2007, c200x, c20xx, zz0307, DNA, protein,
   minh, minhc, Minh Duc Cao, LAllison, TIDix, MML, MDL, compress, entropy,
   information theory, expert model, XM, profile, models, bioinformatics,
   dnacompress, pattern discovery, protein, compressible
%X "This paper introduces a novel algorithm for biological sequence compression
   that makes use of both statistical properties & repetition within sequences.
   A panel of experts is maintained to estimate the probability distribution of
   the next symbol in the sequence to be encoded. Expert probabilities are
   combined to obtain the final distribution. The resulting information sequence
   provides insight for further study of the biological sequence. Each symbol is
   then encoded by arithmetic coding. Experiments show that our algorithm
   outperforms existing compressors on typical DNA & protein sequence datasets
   while maintaining a practical running time."
  <!-- DCC is a tier-1 conf in CS .au --> -- [<A HREF="http://www.allisons.org/ll/Publications/2007DCC/">more</A>] inc. paper,
      [<A HREF="https://doi.org/10.1109/DCC.2007.7">doi:10.1109/DCC.2007.7</A>]['07].

%A R. T. O'Donnell
%A K. B. Korb
%A L. Allison
%T Causal KL: Evaluating causal discovery
%I Faculty of Info. Tech., Monash University, Clayton, Australia 3800
%R 2007/207
%P 26
%M FEB
%D 2007
%O arXiv, Nov., 2021, 2111.06029@[<A HREF="https://arxiv.org/abs/2111.06029">arXiv</A>][2021]
%K TR 207, TR207, c2007, c200x, c20xx, zz0522, LAllison, rodo, KBKorb, AI, II,
   causal model, stats, intervention, interventions, Bayesian network, networks,
   BN, models, cause, Causal Kullback Leibler distance, KL, CKL, C-KL,
   Bnet, Bnets
%X "The two most commonly used criteria for assessing causal model discovery
   with artificial data are edit-distance & Kullback-Leibler divergence,
   measured from the true model to the learned model. Both of these metrics
   maximally reward the true model. However, we argue that they are both
   insufficiently discriminating in judging the relative merits of false models.
   Edit distance, for example, fails to distinguish between strong & weak
   probabilistic dependencies. KL divergence, on the other hand, rewards
   equally all statistically equivalent models, regardless of their different
   causal claims. We propose an augmented KL divergence, which we call Causal
   KL (CKL), which takes into account causal relationships which distinguish
   between observationally equivalent models. Results are presented for three
   variants of CKL, showing that Causal KL works well in practice."
   -- cached@[<A HREF="https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.70.8316">c'teseer</A>]['21],
      [<A HREF="/publications/2006/tr-2007-207-full.pdf">pdf</A>]['07],
      [<A HREF="/publications/2006/tr-2007-207-abs.html">abs</A>]['07],
      [<A HREF="https://arxiv.org/abs/2111.06029">arXiv</A>]['21].
   Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A M. B. Dale
%A L. Allison
%A P. E. R. Dale
%T Segmentation and clustering as complementary sources of information
%J Acta Oecologica
%I Elsevier
%V 31
%N 2
%P 193-202
%M MAR
%D 2007
%K jrnl, ecology, LAllison, c2007, c200x, c20xx, segment, cluster, MML, MDL,
   II, minimum message length, description, classification, mixture model,
   modelling, BIC, ecological, vegetation, spatial, series, scale,  zz0307
%X <!-- ISI j's IF=1.03 at '06 --> "... examines the effects of using a
   segmentation method to identify change-points or edges in vegetation. It
   identifies coherence (spatial or temporal) in place of unconstrained
   clustering. ..."
   [<A HREF="http://www.allisons.org/ll/Publications/2007ActaOe/">segmentation</A>]
   [<A HREF="https://doi.org/10.1016/j.actao.2006.09.002">doi:10.1016/j.actao.2006.09.002</A>]['07]
   Auths 1 & 3 @ Griffith U., auth 2 @ Monash U.
   Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A R. T. O'Donnell
%A L. Allison
%A K. B. Korb
%T Learning hybrid Bayesian networks by MML
%J Advances in Artificial Intelligence
%I SpringerVerlag
%S LNCS/LNAI
%V 4304
%P 192-203
%D 2006
%O (19th ACS Australian Joint Conf. on Artificial Intelligence, AI06)
%K conf, c2006, c200x, c20xx, AI06, minimum message, MDL, rodo, description,
   LAllison, KBKorb, MML, length, AI, II, classification, CaMML,
   Markov Chain Monte Carlo, MCMC, graphical, BDE, graph, network, zz1206,
   local structure, CPT, decision tree, trees, Dtree, logit, logistic,
   stats, model, models, Bnet, Bnets, net, nets
%X "We use a Markov Chain Monte Carlo (MCMC) MML algorithm to learn hybrid
   Bayesian networks from observational data. Hybrid networks represent local
   structure, using conditional probability tables (CPT), logit models,
   decision trees or hybrid models, i.e., combinations of the three. We compare
   this method with alternative local structure learning algorithms using the
   MDL and BDe metrics. Results are presented for both real and artificial data
   sets. Hybrid models compare favourably to other local structure learners,
   allowing simple representations given limited data combined with richer
   representations given massive data". isbn:3540497870; isbn13:978-3540497875.
   -- [<A HREF="http://www.allisons.org/ll/Publications/2006AI/">Bayes nets</A>],
      [<A HREF="https://doi.org/10.1007/11941439_23">doi:10.1007/11941439_23</A>]['06].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A T. I. Dix
%A D. R. Powell
%A L. Allison
%A S. Jaeger
%A J. Bernal
%A L. Stern
%T Exploring long DNA sequences by information content
%I Probabilistic Modeling and Machine Learning in Structural and
   Systems Biology, Workshop Proc.
%W Tuusula, Finland
%P 97-102
%M JUN
%D 2006
%K MolBio, wShop, c2006, c200x, c20xx, modelling, models, sequence, MML, MDL,
   LAllison, minimum message length, bioinformatics, comparative, chromosome,
   description, 1D, TIDix, zz0806, approximate repeats, model, ARM, dotter,
   dot plot, plots, 2D
%X <!-- TID gave the poster --> ... long ... order of millions of bases, ...
   Also see Dix et al, BMC Bioinf., 8(S2):S10, May '07,
       [<A HREF="https://doi.org/10.1186/1471-2105-8-S2-S10">doi:10.1186/1471-2105-8-S2-S10</A>]['08],
   and [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].
   CR classn '98: F.2, I.2.6, G.3, J.3.; isbn:9521032774.

%A L. Allison
%T A programming paradigm for machine learning with a case study of
   Bayesian networks
%J ACSC2006
%P 103-111
%M JAN
%D 2006
%K conf, ACSC, ACSW, LAllison, Inductive Programming, IP, c2006, c200x, c20xx,
   MML FP, MMLF P, MMLFP, AI, minimum message length, description, MDL, zz0106,
   inference, network, net, nets, mixed, generalized, SAR, search and rescue,
   SARbayes, general, models, stats, model, trees, II, missing data, Bnet, Bnets
%X "... combines functional programming for writing statistical models &
   information theory to prevent overfitting. ... Inductive programming is
   illustrated by a case study of Bayesian networks. Networks are built from
   classification- (decision-) trees. Trees are built from partitioning
   functions & models on data-spaces. Trees, & hence networks, are general as a
   natural consequence of the method. Discrete & continuous variables, &
   missing values are handled by the networks. Finally the Bayesian networks
   are applied to a challenging data set on lost persons."
   -- [<A HREF="http://www.allisons.org/ll/Publications/2006ACSC/">Bayesian networks</A>] inc. paper,
      [<A HREF="https://dl.acm.org/doi/10.5555/1151699.1151712">acm</A>]['22].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].)

%A L. Allison
%T Inductive inference 1.1.2:  Inductive programming and a case study of
   Bayesian networks
%I Faculty of Info. Tech., Monash University, Clayton, Australia 3800
%R 2005/177
%P 18
%M OCT
%D 2005
%K TR 177, TR177, network, c2005, c200x, c20xx, zz1105, minimum message length,
   MML, LAllison, description, machine learning, AI, II, csse, lost person,
   FP, MMLFP, MMLF P, missing data, mixed, net, nets, tree, trees, dTree, mdl,
   generalized, missing data, TR153, search and rescue, SAR, Bnet, Bnets
%X Builds on the mixed Bayesian nets introduced in TR2004/153.
   Also see [<A HREF="http://www.allisons.org/ll/FP/IP/">Ind.Inf.</A>].

%A L. Allison
%T Models for machine learning and data mining in functional programming
%J J. Functional Programming
%I CUP
%V 15
%N 1
%P 15-32
%M JAN
%D 2005
%O online at JFP 23/7/2004
%K jrnl, JFP, LAllison, FP, inductive inference, II, AI, c2005, c200x, c20xx,
   Haskell, unsupervised, supervised, classification, mixture modelling, stats,
   decision tree, dTree, cTree, model trees, minimum message length, MML, type,
   zz0105, description, probability, probabilistic, statistical model, MDL,
   Bayesian, estimation, learning, mmld, MMLFP
%X <!-- ISI j's IF=1.4 at '06 --> "... Haskell & its type system are used to define & analyse the
   nature of some problems & tools in machine learning & data mining. Data
   types & type-classes for statistical models are developed that allow models
   to be manipulated in a precise, type-safe & flexible way. [SMs] considered
   inc. prob. distributions, mixture models, function-models, time-series, &
   classification- & function-model-trees. The aim is to improve ways of
   designing & programming with models, not only of applying them."
   -- [<A HREF="http://www.allisons.org/ll/Publications/2005JFP/">more</A>] inc. paper,
      [<A HREF="https://doi.org/10.1017/S0956796804005301">doi:10.1017/S0956796804005301</A>][23/7/2004].
   Also see [<A HREF="http://www.allisons.org/ll/FP/IP/">Ind.Prog.</A>] (IP),
            [<A HREF="http://www.allisons.org/ll/MML/">MML</A>] and
            [<A HREF="https://www.cantab.net/users/mmlist/MML/A/">book</A>].

%A L. Allison
%T Finding approximate palindromes in strings quickly and simply
%I School of Computer Science and Software Engineering, Monash University,
   Australia 3800
%R 2004/162
%M DEC
%D 2004
%K TR 162, TR162, palindrome, MolBio, bioinformatics, algorithm, string,
   LAllison, c2004, c200x, c20xx, zz1204
%X Described are two algorithms to find long approximate palindromes in
   a string, for example a DNA sequence.  A simple algorithm requires
   O(n)-space and almost always runs in O(k.n)-time where n is the
   length of the string and k is the number of ``errors'' allowed in the
   palindrome.  Its worst-case time-complexity is O(n^2) but this does
   not occur with real biological sequences.  A more complex algorithm
   guarantees O(k.n) worst-case time complexity.
   -- [<A HREF="http://arxiv.org/pdf/cs.DS/0412004">arxiv...pdf</A>][12/'04],
      [<A HREF="http://www.allisons.org/ll/Publications/2004TR162/">approx.palindromes</A>].

%A D. R. Powell
%A L. Allison
%A T. I. Dix
%T Modelling alignment for non-random sequences
%J Advances in Artificial Intelligence
%I SpringerVerlag
%S LNCS/LNAI
%V 3339
%P 203-214
%M DEC
%D 2004
%O 17th ACS Australian Joint Conf. on Artificial Intelligence (AI2004)
%K conf, AI, MolBio, dynamic programming algorithm, DPA, c2004, c200x, c20xx,
   similar, sequence, homology, Malignment, minimum message length, MML, MDL,
   PRSS, FASTA, BLAST, Smith Waterman, context, significance test, P values,
   Pvalue, biased, DNA, bias, plasmodium falciparum, low information content,
   score, dependent, pattern, repeats, repetitive, shuffling, masking, scoring,
   quality, Markov, model, models, hidden, HMM, PHMM, HMMER, description, pair,
   strings, DRPowell, LAllison, TIDix, bioinformatics, probabilistic, total,
   average
%X "Populations of biased, non-random seqs. may cause standard alignment
   algorithms to yield false-positive matches & false-negative misses. A std
   significance test based on the shuffling of sequences is a partial solutions
   applicable to pop'ns that can be described by simple models. Masking-out
   low information content intervals throws information away. ... new & general
   method, modelling alignment: Population models are incorporated into the
   alignment process, which can (& should) lead to changes in the rank-order of
   matches between a query seq. & a collection of seqs., compared to results
   from std algorithms. The new method is general & places very few conditions
   on the nature of the models that can be used with it. We apply modelling-
   alignment to local alignment, global alignment, optimal alignment & the
   relatedness problem.    Results: As expected, modelling-alignment & the
   standard PRSS program from the FASTA package have similar accuracy on
   sequence populations that can be described by simple models, e.g. 0-order
   Markov models. However, modelling-alignment has higher accuracy on popns that
   are mixed or that are described by higher-order models: It gives fewer false
   positives & false negatives as show by ROC curves & other results from tests
   on real and artificial data". isbn:3540240594.
   -- [<A HREF="https://doi.org/10.1007/978-3-540-30549-1_19">doi:10.1007/978-3-540-30549-1_19</A>]['11],
      [<A HREF="http://www.allisons.org/ll/Publications/2004AI/">mAlign</A>] inc software.
   [Also search for: Allison COMPJ c1999].

%A E. Makalic
%A L. Allison
%A A. Paplinski
%T MML inference of RBF neural networks for regression
%J Brazilian Symp. on Artificial Neural Networks (SBRN)
%I IEEE & Brazillian Computer Soc.
%W Sao Luis
%P 6
%M SEP
%D 2004
%K conf, ANN, network, c2004, c200x, c20xx, Enes, enesm, MML, zz1104, AI, MDL,
   minimum message length, radial basis function, RBFs, functions, description,
   LAllison, artificial, AIC
%X Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>],
   Conf [<A HREF="http://www.sbrn.elo.com.br/">sbrn</A>] 29/9-1/10/2004, isbn:8589029042.

%A L. Allison
%T Inductive inference 1.1
%I School of Computer Science and Software Engineering, Monash University,
   Australia 3800
%R 2004/153
%P 16
%M MAY
%D 2004
%K TR 153, TR153, TR148, 148, MML, MDL, MMLFP, MMLF, minimum message length,
   functional programming, FP, description, CSSE, zz0504, LAllison, AI, hybrid,
   Bayesian networks, network, mixture, classification, cluster, clustering,
   sequence, classification decision trees, tree, dTree, mixed, model, II,
   inductive inference, graphical, statistical model, machine learning, general,
   tree, models, net, nets, TR177, 177, c2004, c200x, c20xx, Bnet, Bnets
%X "... Case studies illustrate the [F] style of programming for [II]. ...
    Mixtures of Markov Models, Stateful Time-Series, Bayesian network ..."
   See [<A HREF="http://www.allisons.org/ll/Publications/200405TR153/">more</A>],
       [<A HREF="http://www.allisons.org/ll/FP/IP/">Ind.Prog.</A>] (IP),
   Also see TR2003/148, TR2005/177 and ACSC2006.

%A L. Allison
%T Inductive inference, Version 1
%I School of Computer Science and Software Engineering, Monash University,
   Australia 3800
%R 2003/148
%M DEC
%D 2003
%K TR148, TR 148, MML, MDL, II, MMLFP, MMLF, minimum, message, length, zz1203,
   functional programming, FP, data, type, class, description, CSSE, LAllison,
   statistical models, Bayesian, artificial intelligence, AI, machine learning
%X See [<A HREF="http://www.allisons.org/ll/Publications/200309/">more</A>],
    &  [<A HREF="http://www.allisons.org/ll/FP/IP/">Ind.Prog.</A>] (IP),
   Also see TR2004/153, JFP c2005, and TR2005/177.

%A E. Makalic
%A L. Allison
%A D. L. Dowe
%T MML inference of single-layer neural networks
%J Proc. of the 3rd IASTED Int. Conf. on Artificial Intelligence and
   Applications
%W Benalmadena, Spain
%P 636-642
%M SEP
%D 2003
%O TR 2003/142, CSSE, Monash University, Australia OCT 2003
%K conf, IASTED AIA, ANN, artificial neural network, minimum message length, II,
   LAllison, NN, MML, MDL, DLD, Enes, enesm, description, c2003, c200x, c20xx,
   Bayesian, Hessian, TR142, TR 142
%X "The architecture selection problem is of great importance when designing
   neural networks. A network that is too simple does not learn the problem
   sufficiently well. Conversely, a larger than necessary network presumably
   indicates overfitting & provides low generalisation performance. This paper
   presents a novel architecture selection criterion for single hidden layer
   feedforward networks. The optimal network size is determined using a version
   of the Minimum Message Length (MML) inference method. Performance is
   demonstrated on several problems & compared with a Minimum Description
   Length (MDL) based selection criterion." isbn:0889863903; issn:14827913.
   -- [<A HREF="https://doi.org/10.1007/978-3-642-44958-1_20">doi:10.1007/978-3-642-44958-1_20</A>].
   Also see: TR 2003/142, MML inference of single-layer neural networks,
    & [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A L. Allison
%T Longest biased interval and longest non-negative sum interval
%J J. Bioinformatics
%V 19
%N 10
%P 1294-1295
%M JUL
%D 2003
%K MolBio, jrnl, sequence analysis, DNA, RNA, zz0703, c2003, c200x, c20xx,
   bias, density, skew, constraints, low information content, substring,
   subarray, algorithm, maximum, longest, segment, intervals, region,
   AT CG rich, ATrich, CGrich, problem, CpG, LBI, LAllison,
   average, score, highest
%X <!-- ISI j's IF=6.0 at '06 -->... an algorithm to find the longest interval having at least a specified
   minimum bias in a sequence of characters (bases, amino acids),
   e.g. 'at least 0.95 (A+T)-rich'.  It is based on an algorithm to find
   the longest interval having a non-negative sum in a sequence of positive
   and negative numbers.  In practice, it runs in linear time; this can be
   guaranteed if the bias is rational. ...
   -- [<A HREF="http://www.allisons.org/ll/Publications/2003Bioinformatics/">LBI, inc' code</A>],
      [can analyse long sequences, e.g. whole chromosomes, very quickly.]
      [<A HREF="https://doi.org/10.1093/bioinformatics/btg135">doi:10.1093/bioinformatics/btg135</A>]['05].

%A L. J. Fitzgibbon
%A D. L. Dowe
%A L. Allison
%T Bayesian posterior comprehension via message from Monte Carlo
%J 2nd Hawaii Int. Conf. on Statistics and Related Fields (HICS)
%M JUN
%D 2003
%K conf, HICS, HICS2, HICS2003, statistics, Las Vegas, stochastic, MonteCarlo,
   MCMC, posterior probability distribution, LAllison, c2003, c200x, c20xx
%X [<A HREF="http://www.allisons.org/ll/Publications/2003HICS-l/">more</A>] inc. paper.

%A L. Allison
%T The types of models
%J 2nd Hawaii Int. Conf. on Statistics and Related Fields (HICS)
%M JUN
%D 2003
%K HICS, HICS2, c2003, c200x, c20xx, MML, MMLFP, MMLF P, MML F P, FP, MDL,
   conf, stats, type, model, II, AI, LAllison
%X -- [<A HREF="http://www.allisons.org/ll/Publications/2003HICS/">more</A>] inc. paper.
   Also see [<A HREF="http://www.allisons.org/ll/FP/IP/">Ind.Prog.</A>] (IP).

%A L. J. Fitzgibbon
%A L. Allison
%A J. W. Comley
%T Probability model type sufficiency
%J Intelligent Data Engineering and Automated Learning
%I Springer
%S LNCS
%V 2690
%P 530-534
%M MAR
%D 2003
%O (4th Int. Conf. on Intelligent Data Engineering and Automated Learning,
   IDEAL-2003, Hong Kong)
%K conf, IDEAL, IDEAL4, IDEAL2003, statistical model, sufficient statistics,
   stats, MML, c2003, c200x, c20xx, LAllison
%X "We investigate the role of sufficient statistics in generalized
   probabilistic data mining & machine learning software frameworks. Some issues
   involved in the specification of a statistical model type are discussed & we
   show that it is beneficial to explicitly include a sufficient statistic &
   functions for its manipulation in the model type's specification. Instances
   of such types can then be used by generalized learning algorithms while
   maintaining optimal learning time complexity. Examples are given for
   problems such as incremental learning & data partitioning problems (e.g.,
   change-point problems, decision trees & mixture models)"
   -- [<A HREF="http://www.allisons.org/ll/Publications/2003IDEAL-l/">more</A>] inc.paper,
    & [<A HREF="https://doi.org/10.1007/978-3-540-45080-1_72">doi:10.1007/978-3-540-45080-1_72</A>]['17],
   Hong Kong, 21-23 March 2003, EUR99.0; uk us isbn:354040550X.

%A J. W. Comley
%A L. Allison
%A L. J. Fitzgibbon
%T Flexible decision trees in a general data-mining environment
%J Intelligent Data Engineering and Automated Learning
%I Springer
%S LNCS
%V 2690
%P 761-767
%M MAR
%D 2003
%O (4th Int. Conf. on Intelligent Data Engineering and Automated Learning,
   IDEAL-2003, Hong Kong)
%K conf, IDEAL, IDEAL4, IDEAL2003, decision tree, DTree, c2003, c200x, c20xx,
   classification trees, CDMS, LAllison, monash, MML, MDL, AI, II
%X "We describe a new data-mining platform, CDMS, aimed at the streamlined
   development, comparison and application of machine learning tools. We discuss
   its type system, focussing on the treatment of statistical models as
   first-class values. This allows rapid construction of composite models -
   complex models built from simpler ones - such as mixture models,
   Bayesian networks and decision trees. We illustrate this with a flexible
   decision tree tool for CDMS which rather than being limited to discrete
   target attributes, can model any kind of data using arbitrary probability
   distributions."
   -- [<A HREF="http://www.allisons.org/ll/Publications/2003IDEAL-j/">more</A>],
      [<A HREF="https://doi.org/10.1007/978-3-540-45080-1_102">doi:https://doi.org/10.1007/978-3-540-45080-1_102</A>]['17],
   Hong Kong, 21-23 March 2003, EUR99.0; uk us isbn:354040550X.

%A L. Allison
%T Types and classes of machine learning and data mining
%J 26th Australasian Computer Science Conference (ACSC)
%P 207-215
%M FEB
%D 2003
%O ACS Series Conferences in Research and Practice in
   Information Technology V16;
   Australian Computer Science Communications, V25, #1, 2003.
%K conf, ACSC, ACSC26, ACSC2003, type, class, check, model, models, regression,
   time series, timeSeries, functional programming, FP, MML, MMLF P, MMLFP,
   Haskell, type, class, Haskell98, minimum message length, description,
   semantics, MDL, formal, inductive inference, stats, statistics, AI, II,
   zz0203, MDL, c2003, c200x, c20xx, LAllison
%X -- [<A HREF="http://www.allisons.org/ll/Publications/2003ACSC/">more</A>], inc. paper,
   uk us isbn:0909925941;  issn:14451336.

%A L. J. Fitzgibbon
%A D. L. Dowe
%A L. Allison
%T Message from Monte Carlo
%R 2002/107
%I School of Computer Science and Software Engineering, Monash University,
   Australia 3800
%M DEC
%D 2002
%K TR 107, TR107, minimum message length, MML, description, MDL, inference, II,
   Markov Chain Monte Carlo, MCMC, MMLD, reversible, jump, approximation,
   parameter estimation, AI, Bayesian, Montecarlo, Las Vegas, Lasvegas,
   model, modelling, c2002, c200x, c20xx, zz1202, LAllison, univariate,
   polynomial regression, importance sampling
%X "... [MML] is used to partition a sample from an importance sampling density
   of the model parameters into coding regions. The regions contain models that
   are similar & hence the method  can be loosely described as model clustering.
   ... The method is made practical by using the MML Boundary Rule & importance
   sampling.  The MML Boundary Rule is a result that applies to MML
   approximations in a common form & which states that the boundary of the
   optimal coding region will be isometric or approximately isometric.  This
   means that we need only consider regions with isometric boundaries.
   Importance sampling is used to efficiently evaluate expectations & integrals
   using Monte Carlo integration, ... The method requires a sample from a
   suitable importance sampling density & a means of approximating the
   Kullback-Leibler distance between any two models.  For general use, we
   suggest that the posterior is suitable for the importance sampling.  In this
   case the Message from Monte Carlo methodology becomes aligned with Bayesian
   posterior sampling & can be considered as a means of introspection into the
   posterior sample.
   We give an example of the method applied to univariate polynomial regression.
   [It] was chosen because it is a useful & intuitive problem for which the
   MML87 method can & already has been applied.  We use the posterior as an
   importance sampling density & the polynomial parameters are sampled using
   Reversible Jump Markov Chain Monte Carlo."
   Also see ICML2002, HICS2003 & [<A HREF="http://www.allisons.org/ll/MML/">MML</A>];
   [<A HREF="/publications/2002/tr-2002-107-abs.html">abs</A>][12/'02].

%A L. Allison
%T Model classes
%I School of Computer Science and Software Engineering, Monash University,
   Australia 3800
%R 2002/125
%M NOV
%D 2002
%K TR 125, TR125, c2002, c200x, c20xx, zz1102, FP, IP, model class, LAllison
%X -- [<A HREF="http://www.allisons.org/ll/Publications/2002TR125/">more</A>].

%A L. J. Fitzgibbon
%A D. L. Dowe
%A L. Allison
%T Change-point estimation using new minimum message length approximations
%J Seventh Pacific Rim Int. Conf. on Artificial Intel. (PRICAI-2002)
%W Tokyo
%I SpringerVerlag
%S LNAI
%V 2417
%P 244-254
%M AUG
%D 2002
%S LNAI
%K conf, PRICAI, PRICAI7, PRICAI02, PRICAI2002, AI, fairly strict, FSMML, MMLA,
   minimum message length, MML, inductive inference, II, description, MDL,
   sequence, segmentation, MMLD, LNAI, LAllison, DLDowe, Monash, csse,
   zz0902, c2002, c200x, c20xx
%X Authors at Comp. Sci. and S.W.E., Monash Uni., .au
   -- [<A HREF="http://www.allisons.org/ll/Publications/2002-PRICAI/">abstract</A>]; uk us isbn:3540440380,
      [<A HREF="https://doi.org/10.1007/3-540-45683-X_28">doi:10.1007/3-540-45683-X_28</A>]['24].

%A L. J. Fitzgibbon
%A D. L. Dowe
%A L. Allison
%T Univariate polynomial inference by Monte Carlo message length approximation
%J Int. Conf. Machine Learning 2002
%W Sydney
%I MorganKaufmann
%P 147-154
%M JUL
%D 2002
%K conf, ICML, ICML2002, ICML02, AI, inductive inference, II, LAllison, DLDowe,
   Minimum Message Length, MML, description, MDL, Las Vegas, MonteCarlo, MMC,
   Markov chain, MCMC, polynomial, fit, fitting, regression, Gibbs sampling,
   FSMML, SRM, univariate polynomial, regression, zz0702, c2002, c200x, c20xx
%X <!-- citeseer conf IF=2.12 at c2004 --> Message from Monte Carlo (MMC) algorithm ... compared with
   MML87 and structural risk minimization <!-- accepted 21/4/'02 --> (SRM).
   Authors: Comp. Sci. and S.W.E., Monash Uni., .au.  Also see TR 2002/107.
   -- [<A HREF="http://www.allisons.org/ll/Publications/2002-ICML/">more</A>], issn:10491910, and see
      [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A L. Stern
%A L. Allison
%A R. L. Coppel
%A T. I. Dix
%T Discovering patterns in Plasmodium falciparum genomic DNA
%J Molecular and Biochemical Parasitology
%V 118
%N 2
%P 175-186
%M DEC
%D 2001
%K MolBio, LAllison, jrnl, c2001, c200x, c20xx, Plasmodium falciparum,
   minimum message length, description, Markov, MDL, MBP, MML, Malaria, entropy,
   sequence analysis, HMM, PFSA, PFSM, information content, genome, DNA,
   pattern, repeat, repeats, DNA models, AED, approximate repeats model, repeat,
   pattern discovery, knowledge, hidden, GHMM, Bayesian, LStern, TIDix,
   bioinformatics
%X "A method has been developed for discovering patterns in DNA sequences.
   Loosely based on the well-known Lempel Ziv model for text compression, the
   model detects repeated seqs. in DNA. The repeats can be forward or inverted,
   and they need not be exact. The method is particularly useful for detecting
   distantly related seqs., and for finding patterns in seqs. of biased
   nucleotide composition, where spurious patterns are often observed because
   the bias leads to coincidental nucleotide matches. We show here the utility
   of the method by applying it to genomic seqs. of Plasmodium falciparum. A
   single scan of chromosomes 2 and 3 of P.falciparum, using our method and no
   other a priori information about the seqs., reveals regions of low complexity
   in both telomeric and central regions, long repeats in the subtelomeric
   regions, and shorter repeat areas in dense coding regions. Application of the
   method to a recently sequenced contig of chromosome 10 that has a
   particularly biased base composition detects a long internal repeat more
   readily than does the conventional dot matrix plot. Space requirements are
   linear, so the method can be used on large sequences. The observed repeat
   patterns may be related to large-scale chromosomal organization and control
   of gene expression. The method has general application in detecting patterns
   of potential interest in newly sequenced genomic material."
   -- <!-- ISI j's IF=2.7 at '06 -->[<A HREF="http://www.allisons.org/ll/Publications/2001MBP/">more</A>] inc. paper,
   [<A HREF="https://doi.org/10.1016/S0166-6851(01)00388-7">doi:10.1016/S0166-6851(01)00388-7</A>][6/'04].
   Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].

%A L. J. Fitzgibbon
%A L. Allison
%A D. L. Dowe
%T Minimum message length grouping of ordered data
%J Proc. 11th Int. Workshop on Algorithmic Learning Theory (ALT'2000)
%E H. Arimura
%E S. Jain
%E A. Sharma
%P 56-70
%W Sydney
%S LNCS
%V 1968
%M DEC
%D 2000
%K conf, minimum message length, MML, segment, minimum description length, MDL,
   ALT9, ALT2000, cut point, points, segmenting, time series, sequence analysis,
   complexity, measurement accuracy, model, LAllison, DLDowe, BIC, Monash, II,
   segmentation, problem, data, level, levels, c2000, c200x, c20xx
%X Given a series of multivariate data, approximate it by a piece-wise
   constant function. How many cut-points are there? What are the means
   and variances of each segment? Where should the cut points be placed?
   The simplest model is a single segment.  The most complex model has
   one segment per data point.  The best model is generally somewhere
   between these extremes.  Only by considering model complexity can
   a reasonable inference be made.
   -- [<A HREF="http://www.allisons.org/ll/Publications/2000-ALT/">more</A>],
      [<A HREF="https://doi.org/10.1007/3-540-40992-0_5">doi:10.1007/3-540-40992-0_5</A>]['11].

%A D. R. Powell
%A L. Allison
%A T. I. Dix
%T Fast, optimal alignment of three sequences using linear gap costs
%J J. Theor. Biol.
%V 207
%N 3
%P 325-336
%M DEC
%D 2000
%K jrnl, JTB, MolBio, Biology, multiple, sequence, alignments, similarity,
   affine, linear, cost, gaps, insert, delete, indel, indels, DNA, time, speed,
   fast, string, strings, iterative, phylogenetic, family tree, Ukkonen,
   edit distance, dynamic programming algorithm, DPA, DRPowell, LAllison, TIDix,
   c2000, c200x, c20xx, zz1100, J Theoretical Biology, bioinformatics
%X <!-- ISI j's IF=1.96 at '06 -->[...] The obvious dynamic programming algorithm for optimally
   aligning k sequences of length n runs in O(n^k) time. This is
   impractical if k >= 3 and n is of any reasonable length.
   [...] new algorithm [is] guaranteed to find the optimal alignment [...]
   particularly fast when the (three-way) edit distance is small. [...]
   O(n + d^3) on average.
   [<A HREF="http://www.allisons.org/ll/Publications/2000JTB/">paper</A>][11/'00] and code,
   [<A HREF="https://doi.org/10.1006/jtbi.2000.2177">doi:10.1006/jtbi.2000.2177</A>]['04]
   more on [<A HREF="http://www.allisons.org/ll/Bioinformatics/">bioinformatics</A>].

%A L. Allison
%A D. Powell
%A T. I. Dix
%T Modelling is more versatile than shuffling
%R 2000/83
%I School of Computer Science and Software Engineering, Monash University,
   Australia 3168
%D 2000
%K MolBio, pair, two, sequence, alignment, PFSA, hidden Markov model, PHMM,
   low medium information content, repeat, repetition, structure, pattern,
   model, shuffle, shuffling, randomize, DNA, permute, tuples, frequencies,
   family, PFSM, HMM, dynamic programming algorithm, DPA, homology, algorithm,
   minimum message length, MML, description, MDL, LAllison, DRPowell, TIDix,
   mAlignment, TR 83, TR83, c2000, c200x, c20xx, bioinformatics
%X It is shown how to incorporate almost any (left to right) model of a
   population of sequences into the alignment DPA.  Doing so is an alternative
   to shuffling/ randomizing (Fitsch; Altschul, Erickson ...) the sequences
   to correct for population biases.  The resulting algorithm gives
   fewer false positives, fewer false negatives, and can (and should)
   change the rank ordering of alignments.
   [also search for: modelling alignment]
   -- [<A HREF="http://www.allisons.org/ll/Publications/2000ali-cmprss/">more</A>] and see
      [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].

%A L. Allison
%A L. Stern
%A T. Edgoose
%A T. I. Dix
%T Sequence complexity for biological sequence analysis
%J Computers and Chemistry
%O (jrnl later became Computational Biology and Chemistry, c2006)
%V 24
%N 1
%P 43-55
%D 2000
%K jrnl, comp chem, MolBio, c2000, c200x, c20xx, data compression, compress,
   MML, MDL, DNA, mine, approximate repeats, repeat, AED, model, repetitive,
   complexity, high, moderate, low, information content, bioinformatics,
   LAllison, TIDix, computational biology and chemistry, LStern, description,
   minimum message length, bioinformatics, AI, inductive inference,
   data mining, time series, timeSeries
%X "A new statistical model for DNA considers a sequence to be a mixture of
   regions with little structure and regions that are approximate repeats of
   other subsequences, i.e. instances of repeats do not need to match each other
   exactly. Both forward- and reverse-complementary repeats are allowed. The
   model has a small number of parameters which are fitted to the data. In
   general there are many explanations for a given sequence and how to compute
   the total probability of the data given the model is shown. Computer
   algorithms are described for these tasks. The model can be used to compute
   the information content of a sequence, either in total or base by base. This
   amounts to looking at sequences from a data-compression point of view and it
   is argued that this is a good way to tackle intelligent sequence analysis
   in general."
   -- <!-- ISI j's IF=2.2 at '06 -->[<A HREF="http://www.allisons.org/ll/Publications/2000CC/">more</A>],
      [<A HREF="https://doi.org/10.1016/S0097-8485(00)80006-6">doi:10.1016/S0097-8485(00)80006-6</A>]['02].
   Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].

%A L. Allison
%T Generator and search objects in Java
%J J. Res. and Practice in Inf. Tech.
%V 32
%P 3-12
%N 1
%D 2000
%K jrnl, ACS, JRPIT, continuation, c2000, c200x, c20xx, LAllison, object, OOP,
   generators
%X -- [<A HREF="http://www.allisons.org/ll/Publications/2000JRPIT.pdf">paper</A>], and see
   more on [<A HREF="http://www.allisons.org/ll/ProgLang/Java/">Java</A>];
   also see TR97/317.

%A T. Edgoose
%A L. Allison
%T MML Markov classification of sequential data
%J Stats. and Comp.
%I Kluwer Academic
%V 9
%N 4
%P 269-278
%M SEP
%D 1999
%K jrnl, stats, computing, minimum message length, MML, description, MDL,
   statistical, inductive inference, clustering, classification, II, AI,
   sequence, data analysis, model, algorithm, mining, series, forwards,
   backwards, LAllison, c1999, c199x, c19xx, Snob, time series, timeSeries
%X -- [<A HREF="http://www.allisons.org/ll/Publications/1999-Stats-Comp/">more</A>] inc. paper,
      [<A HREF="https://doi.org/10.1023/A:1008907921792">doi:10.1023/A:1008907921792</A>]['24].

%A D. R. Powell
%A L. Allison
%A T. I. Dix
%T A versatile divide and conquer technique for optimal string alignment
%J IPL
%V 70
%N 3
%P 127-139
%D 1999
%K IPL, jrnl, c1999, c199x, c19xx, zz0899, dynamic programming algorithm, DPA,
   MolBio, DRPowell, LAllison, TIDix, bioinformatics, space, complexity,
   strings, Edit Distance, similarity, LCS, Fast, Hirschberg, Ukkonen, Myers,
   time, speed, Linear Space, Check Point, pointing, checkpoint, algorithms
%X <!-- ISI j's IF=0.56 at '06 --> A check-pointing (CP) technique uses O(n) space but is simpler
   than Hirschberg's O(n)-space technique;  H' ('97) attributes
   an O(N**2)-time simple edit-distance CP to Eppstein.  Here, CP
   is applied to more complex cost functions, e.g., linear gap costs, and ...
   to Ukkonen's O(n*d)-time DPA, even including linear gap costs,
   to give  O(n)-space,  O(n.log d + d**2)-average-time,
   effectively O(d**2)-time in many practical situations.
   -- [<A HREF="https://doi.org/10.1016/S0020-0190(99)00053-8">doi:10.1016/S0020-0190(99)00053-8</A>][6/'04],
   &  [<A HREF="http://www.allisons.org/ll/Publications/1999IPL/">Divide-and-C.</A>].

%A L. Allison
%A D. Powell
%A T. I. Dix
%T Compression and approximate matching
%J COMPJ
%V 42
%N 1
%P 1-10
%D 1999
%K jrnl, MolBio, COMPJ, Computer Journal, LAllison, DRPowell, TIDix, pair,
   string, strings, sequence, alignment, analysis, algorithm, homology,
   similarity, limits, HMM, MML, MDL, II, normalized, limit, significance test,
   testing, jie, med, DPA, low information content, repeats, repetitive, wei,
   non-random, nonrandom, compressible, bioinformatics, pair, probabilistic,
   information theory, features, complexity, time, fast, speed, shuffling,
   shuffle, randomize, DNA, edit distance, hidden Markov model, HMM, PHMM,
   c19xx, c1999, c199x, modelling, Malignment, context dependent, scoring
%X <!-- ISI j's IF=1.39 at '10 --> A population of sequences is called non-random if there is a statistical
   model and an associated compression algorithm that allows members of the
   population to be compressed, on average.  Any available statistical model
   of a population should be incorporated into algorithms for alignment of
   the sequences and doing so changes the rank-order of possible alignments
   in general.  The model should also be used in deciding if a resulting
   approximate match between two sequences is significant or not.  It is
   shown how to do this for two plausible interpretations involving pairs
   of sequences that might or might not be related.  Efficient alignment
   algorithms are described for quite general statistical models of sequences.
   The new alignment algorithms are more sensitive to what might be termed
   `features' of the sequences.  A natural significance test is shown to be
   rarely fooled by apparent similarities between two sequences that are merely
   typical of all or most members of the population, even unrelated members.
   -- [<A HREF="http://www.allisons.org/ll/Publications/1999COMPJ/">more</A>],
      [<A HREF="https://doi.org/10.1093/comjnl/42.1.1">doi:10.1093/comjnl/42.1.1</A>]['06].
   Also see [<A HREF="http://www.allisons.org/ll/Publications/2004AI/">Powell AI2004</A>].

%A L. Allison
%A T. Edgoose
%A T. I. Dix
%T Compression of strings with approximate repeats
%J Intell. Sys. in Mol. Biol. '98
%P 8-16
%M JUN
%D 1998
%K conf, MolBio, c1998, c199x, c19xx, LAllison, Monash, ISMB6, ISMB98, ISMB 98,
   DPA, inductive inference, II,  DNA, Chen, Behzadi, F. Le Fessant, protein,
   sequence analysis, data, text, repeat, compression, bioinformatics, Li,
   repetitive, kwong, hidden Markov models, HMM, low information content,
   lines, ALU, sines, ming, self similarity, AED, model, minimum message length,
   MML, description, MDL, compress, algorithm
%X "We describe a model for strings of characters that is loosely based on the
   Lempel Ziv model with the addition that a repeated substring can be an
   approximate match to the original substring; this is close to the situation
   of DNA, for example. ... The model has a small number of parameters and these
   can be estimated from the given string by an expectation-maximization (EM)
   algorithm. Each iteration of the EM algorithm takes O(n^2) time and a few
   iterations are typically sufficient. O(n^2) complexity is impractical for
   strings of more than a few tens of thousands of characters and a faster
   approximation algorithm is also given. The model is further extended to
   include approximate reverse complementary repeats when analyzing DNA
   strings. Tests include the recovery of parameter estimates from known
   sources and applications to real DNA strings."
   -- [<A HREF="http://www.allisons.org/ll/Publications/1998ISMB/">more</A>]  ISMB98, 28 June - 1 July 1998,
   [<A HREF="http://www.allisons.org/ll/Publications/1998ISMB/1998ISMB.pdf">.pdf</A>]   Montreal, Canada; uk us isbn:1577350537.
   Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">bioinformatics</A>].

%A L. Allison
%T Information-theoretic sequence alignment
%I School of Computer Science and Software Engineering, Monash University
%R 98/14
%M JUN
%D 1998
%K TR14, TR 14, MolBio, LAllison, string, strings, similarity, edit-distance,
   homology, approximate match, matching, DNA, DPA, hidden Markov model, HMM,
   low information content, repeats, repetitive, compressible, MML, MDL,
   data compression, content, sequences, c1998, c199x, c19xx, bioinformatics
%X [<A HREF="http://www.allisons.org/ll/Publications/1998TR98-14-align/">TR98/14</A>],
   Also see:  Allison, Powell and Dix, `Compression and Approximate Matching',
     Comp. J. 42(1) pp1-10, 1999,  for a fuller explanation and later results.
   Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">Bioinformatics</A>].

%A G. Pringle
%A L. Allison
%A D. L. Dowe
%T What is a tall poppy among web pages?
%J Proc. 7th Int. World Wide Web Conference (in Comp. Networks and ISDN Sys.)
%V 30
%N 1-7
%P 369-377
%M APR
%D 1998
%O Comp. Networks and ISDN Systems (Jrnl)
%I Elsevier
%K conf, WWW, WWW7, WWW98, WWWC, WWWC7, WWWC98, IWWWC, IWWWC7, IWWWC98,
   decision tree, DT, search engine, engines, rating, ranking, Lycos, Infoseek,
   Altavista, Alta vista, page, pages, LAllison, DLDowe, GPringle, Monash,
   c1998, c199x, c19xx, zz0598
%X "Search engines & indices were created to help people find information
   amongst the rapidly increasing # of World Wide Web (WWW) pages. ... treat
   modelling the workings of WWW search engines as an inductive inference
   problem. A training set of data is collected, being pages returned in
   response to typical queries. Decision trees are used as the model class for
   the search engines' selection criteria although ..."
   -- [<A HREF="http://www.allisons.org/ll/Publications/1998WWW7/">more</A>],
      [<A HREF="https://doi.org/10.1016/S0169-7552(98)00061-0">doi:10.1016/S0169-7552(98)00061-0</A>]['22].
   Uses inductive inference technology to infer why some web
   pages rank highly on certain Internet Search Engines.
   Conf. held 14-18 April 1998, Brisbane, Australia. uk us isbn:0169755298.

%A D. L. Dowe
%A L. Allison
%A G. Pringle
%T The hunter and the hunted - modelling the relationship between web pages
   and search engines
%J 2nd Pacific-Asia Conf. on Knowledge Discovery and Data Mining (PAKDD98)
%P 380-382
%M APR
%D 1998
%I SpringerVerlag
%S LNAI
%V 1394
%K conf, PAKDD2, PAKDD 98, internet, web page, decision tree, engine,
   Dtree, LAllison, GPringle, DLDowe, Monash, c1998, c199x, c19xx
%X uk us isbn:3540643834. Also see  Pringle et al  in  WWW7 pp.369-377 c1998.

%A T. Edgoose
%A L. Allison
%T Minimum message length hidden Markov modelling
%J Data Compression Conf.
%W Snowbird, Utah
%I IEEE
%P 169-178
%M MAR
%D 1998
%K conf, DCC, DCC98, model, MML, MDL, HMM, inductive inference, II, Rissanen,
   sequence, model, series, clustering, classification, data analysis, CSci,
   description, complexity, time series, timeSeries, CompSci, LAllison, Monash,
   Snob, c1998, c199x, c19xx, Snowbird, AI
%X "This paper describes a minimum message length (MML) approach to finding the
   most appropriate hidden Markov model (HMM) to describe a given sequence of
   observations. An MML estimate for the expected length of a two-part message
   stating a specific HMM and the observations given this model is presented
   along with an effective search strategy for finding the best number of
   states for the model. The information estimate enables two models with
   different numbers of states to be fairly compared which is necessary if the
   search of this complex model space is to avoid the worst locally optimal
   solutions. The general purpose MML classifier 'Snob' has been extended and
   the new program 'tSnob' is tested on 'synthetic' data and a large 'real
   world' dataset. The MML measure is found to be an improvement on the Bayesian
   information criteria (BIG) and the un-supervised search strategy."
   -- [<A HREF="http://www.allisons.org/ll/Publications/1998-DCC/">Markov-M.</A>],
      [<A HREF="https://doi.org/10.1109/DCC.1998.672145">doi:10.1109/DCC.1998.672145</A>]['18].

%A T. Edgoose
%A L. Allison
%T Unsupervised Markov classification of sequence data using MML
%J Proc. 21st Australian Comp. Sci. Conf.
%E C. McDonald
%W Perth
%I SpringerVerlag
%P 81-94
%M FEB
%D 1998
%K ACSC, ACSC21, ACSC98, inductive inference, II, time series, model, HMM,
   serial correlation, SNOB, AI, machine learning, hidden, data mining, MDL,
   LAllison, Monash, class, cluster, clustering, time series, timeSeries,
   c1998, c199x, c19xx, zz0198
%X also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>],
   uk us isbn:9813083905; order from...[<A HREF="http://www.springer.de/">springer</A>].

%A D. R. Powell
%A L. Allison
%A T. I. Dix
%A D. L. Dowe
%T Alignment of low information sequences
%J Australian Computer Science Theory Symposium, CATS '98
%W Perth
%P 215-230
%I NUS
%M FEB
%D 1998
%K conf, MolBio, align, HMM, DPA, DNA, ACSC, CATS, CATS98, LAllison, DLDowe,
   bioinformatics, probability, low information, simple, features,
   TIDix, Monash, c1998, c199x, c19xx, DRPowell
%X "Alignment of two random sequences over a fixed alphabet can be shown to be
   optimally done by a Dynamic Programming Algorithm (DPA). It is normally
   assumed that the sequences are random and incompressible and that one
   sequence is a mutation of the other. However, DNA and many other sequences
   are not always random and unstructured, and the issue arises as how to best
   align compressible sequences.  Assuming our sequences to be non-random and
   to emanate from mutations of a first order Markov model, we note that
   alignment of high information regions is more important than alignment of
   low information regions and arrive at a new alignment method for low
   information sequences which performs better than the standard DPA for data
   generated from mutations of a first order Markov model."
   -- [<A HREF="http://www.allisons.org/ll/Publications/1998CATS/">more</A>], uk us isbn:9813083921,
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">Bioinformatics</A>].)

%A T. Edgoose
%A L. Allison
%A D. L. Dowe
%T An MML classification of protein structure that knows about angles and
   sequence
%J Pacific Symposium on Biocomputing '98
%P 585-596
%M JAN
%D 1998
%K conf, MolBio, PSB, PSB3, PSB98, von Mises, vonMises, angle, dihedral, class,
   cluster, clustering, HMM, SNOB, time series, timeSeries, ARC A49602504,
   LAllison, MDL, directional, distribution, bioinformatics, Monash,
   c1998, c199x, c19xx
%I World Scientic
%X SNOB + vonMises circular probability distribution + 1st order Markov model.
   phi-psi pairs give 17 classes and a class seq' correlation matrix.
   [<A HREF="http://www.allisons.org/ll/Publications/1998PSB1/">paper</A>]
   [<A HREF="http://www-smi.stanford.edu/projects/helix/psb98/edgoose.pdf">paper.pdf@stanford.edu</A>]['98]; uk us isbn:9810232780.
   von Mises, probability density:
      f(x | mu, kappa) = (1/(2.pi.I0(kappa))).exp(kappa.cos(x-mu))
                 where I0(kappa) is a normalisation constant.
   [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].

%A D. R. Powell
%A D. L. Dowe
%A L. Allison
%A T. I. Dix
%T Discovering simple DNA sequences by compression
%J Pacific Symposium on Biocomputing '98
%P 597-608
%M JAN
%D 1998
%K conf, MolBio, PSB, PSB3, PSB98, repeat, repetition, data, model, random,
   ARC A49602504, bioinformatics, DRPowell, LAllison, DLDowe, TIDix, Monash,
   zz0198, simple, low information, Milosavljevic, Jurka, c1998, c199x, c19xx,
   compress
%I World Scientic
%X "An information-theoretic DNA compression scheme devised by Milosavljevic and
   Jurka(1993) has been used in many places in the literature for both the
   discovery of new genes and the compression of DNA. Their compression method
   applies an encoding of previously occurring runs. They use 5 different
   code-words: four being the DNA bases, A,C,G and T, and the other being a
   pointer to a previously occurring run. They advocate a code-word of length
   log2(5) for each of these and then encoding a run by a code-word of length
   2log2(n), where n is the length of the sequence. This scheme encodes the
   start of the sequence with a code-word of length log2(n) and likewise encodes
   the end of the sequence with a code-word of length log2(n). In this paper,
   we show the above coding scheme to be inefficient in various ways and improve
   upon it so that it can compress DNA. We discuss our implementation of various
   schemes some of which run in linear time."
   -- [<A HREF="http://www.allisons.org/ll/Publications/1998PSB2/">more</A>] inc. paper.
   uk us isbn:9810232780.
   Also see [<A HREF="http://www.allisons.org/ll/MML/">MML page</A>]
   and Milosavljevic '95.

%A K. B. Korb
%A C. Kopp
%A L. Allison
%T Higher education policy in Australia
%J Australian Rationalist
%N 45
%P 16-26
%M DEC
%D 1997
%O `A Statement on Higher Education Policy in Australia',
   TR 97/318, Department of Computer Science, Monash University, 1997
%K jrnl, TR318, TR 318, HER, West Review, University, Universities, funding,
   Government policy, trends, technology, quality, Carlo, LAllison, zz1297,
   c1997, c199x, c19xx
%X [<A HREF="/publications/1997/tr-cs97-318/policy.ps.gz">.ps.gz</A>],
   [<A HREF="/publications/1997/tr-cs97-318/policy.html">html</A>].

%A L. Allison
%T Java continues Prolog-like
%I Department of Computer Science, Monash University
%R 97/317
%M APR
%D 1997
%K TR317, TR 317, LAllison, c1997, c199x, c19xx
%X see: Allison, JRPIT, c2000.

%A T. C. Edgoose
%A L. Allison
%T Mixture modelling of sequential datasets
%R 96/285
%I Department of Computer Science, Monash University
%M NOV
%D 1996
%K TR285, TR 285, sequence, series, HMM, hidden Markov model, classification,
   clustering, Snob, minimum message length, MML, description, MDL, c1996,
   inductive inference, II, data sets, analysis, LAllison, Monash, c199x, c19xx
%X Data is a sequence of items.  Each item is a number of measurements.
   The program clusters items into classes.  Each class is described
   by distributions (currently finite state, or Normal, or von-Mises)
   on attributes.  The program determines the number and form of each class.
   The class of an item can be influenced by those of its neighbours.
   Partial assignment allows for uncertainty of class membership.
   Tested on artificial and real data including some weather data
   and dihedral angles from protein structures.
   [Also search for:  Snowbird DCC98],
   and see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A D. L. Dowe
%A L. Allison
%A T. I. Dix
%A L. Hunter
%A C. S. Wallace
%A T. Edgoose
%T Circular clustering of protein dihedral angles by minimum message length
%J Pacific Symposium on Biocomputing '96
%M JAN
%P 242-255
%D 1996
%I World Scientific
%O TR 95/237, Dept. Computer Science, Monash University, Oct 1995
%K PSB, PSB96, TR 237, TR237, Monash, DLD, CSW, CSWallace, LAllison, MolBio,
   classification, angle, von Mises, vonMises, protein structure,
   inductive inference, II, MML, MDL, conf, bioinformatics, c1996, c199x, c19xx
%X L. Hunter - NLM, NIH. PSB '96: 3-6 Jan 1996, Hawaii; uk us isbn:9810225784.
   [<A HREF="http://www.allisons.org/ll/Publications/1996PSB/">paper</A>].

%A R. A. Baxter
%A L. Allison
%A K. Korb
%T Regulation of on-line information services (a submission)
%M AUG
%D 1995
%K censor, censorship, regulation, control, internet, inter net, Monash,
   world wide web, LAllison, www, HREF, http, c1995, c199x, c19xx
%X Submission to the Dept. of Communications and the Arts  re  their
   consultation paper on the regulation of online information services
   of 7 July 1995.
   Also to the Senate Enquiry into Regulation of Computer On-Line Services
   (closing date for submissions 29 Sept 1995)
   See also TR224.

%A L. Allison
%T Towards modelling evolution = mutation modulo selection in sequence
   alignment
%R 95/225
%I Dept. Computer Science, Monash University
%M JUN
%D 1995
%K LAllison, Monash, TR225, TR 225, MolBio, evolution, pressure, selection,
   fit, fitness, family, phylogenetic, evolutionary tree, trees, sequence,
   multiple alignment, zz0795, c1995, c199x, c19xx, bioinformatics
%X [<A HREF="http://www.allisons.org/ll/Bioinformatics/">bioinformatics</A>].

%A L. Allison
%A R. A. Baxter
%T Protecting Our Innocents
%R 95/224
%I Dept. Computer Science, Monash University
%M JUN
%D 1995
%K LAllison, Monash, TR224, TR 224, internet, inter net,  world wide web,
   child, children, kids, K12, porn, pornography, violence, politics, sex,
   online, censorship, censor, ethics, ethical, CICA, PICS, surfwatch,
   www, HREF, http, zz0695, topical, c1995, c199x, c19xx
%X Argues that internet authors (www, ftp, ...) should be encouraged,
   NOT required, to describe their works using annotations that are
   objective and machine readable.  (This is not a censorship proposal and
   it cannot be (mis)used as one.)
   [<A HREF="/publications/1995/tr-cs95-224/1995.224.html">TR 95/224 here</A>]
   Also see: Regulation of on-line information services (a submission) Aug 1995.

%A L. Allison
%T Toward a Denotational Semantics for
   <A HREF="http://www.cs.monash.edu.au/~lloyd/tildeFP/LambdaLog">LFP</A>
   = Logic + Functional Programming, Coded in Lazy ML.
%R 94/204
%M SEP
%D 1994
%I Dept. Computer Science, Monash University
%K LAllison, logic, functional, programming, LP, FP, LFP, FLP, LambdaLog,
   LML, Monash, TR 204, TR204, c1994, c199x, c19xx
%X [<A HREF="http://www.allisons.org/ll/FP/">FP</A>].
   [<A HREF="/~lloyd/tildeFP/LambdaLog/">LFP</A>].

%A L. Allison
%T Using Hirschberg's algorithm to generate random alignments of strings
%J IPL
%V 51
%N 5
%P 251-255
%M SEP
%D 1994
%K c1994, c199x, c19xx, LAllison, Monash, jrnl, IPL, MolBio, bioinformatics, GS,
   DNA, methods, MML, minimum message length encoding, II, inductive inference,
   Hirschberg, string, sequence, alignment, similarity, homology, approximate,
   match, matching, LCS, LCSS, edit distance, Bayesian, Gibbs sampling, MCMC,
   random, sample, DPA, simulated annealing, SA, dynamic programming algorithm,
   divide and conquer, hidden Markov model, HMM, probability,
   posterior distribution, stochastic
%X <!-- ISI j's IF=0.56 at '06 --> Hirschberg's (CACM '75) recursive divide and conquer technique for
   the dynamic programming technique (LCS, LCSS, Edit Distance) is
   applied to the problem of sampling alignments of two strings
   at RANDOM from the alignments' posterior probability distribution.
   -- [<A HREF="http://www.allisons.org/ll/Publications/1994IPL/">more</A>] inc. paper,
      [<A HREF="https://doi.org/10.1016/0020-0190(94)90004-3">doi:10.1016/0020-0190(94)90004-3</A>]['04].
   Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].

%A L. Allison
%A C. S. Wallace
%T An information measure for the string to string correction problem with
   applications
%J 17th Australian Comp. Sci. Conf.
%W Christchurch, N.Z.
%P 659-668
%M JAN
%D 1994
%K LAllison, CSW, CSWallace, Monash, conf, MolBio, inductive inference, II,
   string, sequence, family, evolutionary, phylogenetic, tree, trees,
   variation, variance, uncertainty, estimate, estimation, parameters, DNA,
   multiple alignment, Gibbs sampling, sample, GS, simulated annealing SA,
   minimum message length MML, Bayesian, temperature, cooling, probabilistic,
   NZ, New Zealand, c1994, c199x, c19xx, ACSC 17, 94, ACSC17, ACSC94,
   bioinformatics, Monash
%O Australian Comp. Sci. Comm., Vol 16,  No 1(C), 1994, isbn:047302313X.
%X It has been shown how to calculate a probability for an alignment.
   Alignments are sampled from their posterior probability distribution.
   This is extended to multiple alignments (of several strings).  Averaging
   over many such alignments gives good estimates of how closely the strings
   are related and in what way.  In addition, sampling in an increasingly
   selective way gives a simulated annealing search for an optimal alignment.
   -- [<A HREF="http://www.allisons.org/ll/Publications/1994.ACSC-17/">more</A>]['24] and
      [<A HREF="http://www.allisons.org/ll/Bioinformatics/Multiple/">multiple||</A>],
   Also see the related paper, J.Molec.Evol. (39, pp.418-430, 1994),
   "The posterior probability distribution ...", for more results.

%A B. M. Jenkins
%A A. J. Davison
%A L. Allison
%A A. J. Maeder
%T A perimeter based technique for fusion of multi-sourced micrographic images
%J Dicta-93
%W Sydney Australia
%M DEC 8-10
%D 1993
%P 556-563
%K c1993, c199x, c19xx, LAllison, Monash, conf, image processing IP, shape,
   curve, signature, DICTA DICTA93, Monash
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A L. Allison
%A C. S. Wallace
%T The posterior probability distribution of alignments and its application
   to parameter estimation of evolutionary trees and to optimization of
   multiple alignments
%J J. Mol. Evol.
%V 39
%N 4
%P 418-430
%M OCT
%D 1994
%O An earlier version is TR 93/188, Dept. Comp. Sci., Monash U., July '93
%K jrnl, MolBio, JME, c1994, c199x, c19xx, LAllison, CSWallace, CSW, DNA,
   bioinformatics, optimisation, estimate, infer, parameters, algorithm,
   multiple, alignment, data, string, molecular, sequence, homology, Markov,
   family, phylogenetic, tree, trees, edit distance, Monte Carlo method, mcmc,
   simulated annealing, SA, inductive inference, II, sample, speed, Bayesian,
   dynamic programming algorithm, DPA, stochastic, methods, GS, Gibbs sampling,
   minimum message length encoding, MML, chain, minimum description length, MDL,
   transthyretin, chloramphenicol resistance gene, CAT, CATB, CATD, CATP, CATQ,
   CCOLI, ECOLI, algorithmic, mutual information, theory, significance,
   probabilistic, temperature, limits, TR 93/188, TR188
%X <!-- ISI j's IF=1.7 at '06 --> "It is shown how to sample alignments from their posterior probability
   distribution given two strings.  This is extended to sampling alignments of
   more than two strings.  The result is firstly applied to the estimation of
   the edges of a given evolutionary tree over several strings.  Secondly,
   when used in conjunction with simulated annealing, it gives a stochastic
   search method for an optimal multiple alignment."
   -- [<A HREF="http://www.allisons.org/ll/Publications/1994JME/">paper</A>] and source code,
      [<A HREF="https://doi.org/10.1007/BF00160274">doi:/10.1007/BF00160274</A>]['07].
   (The JME paper is a much expanded and changed version of TR 93/188, 1993.)

%A A. Finlay
%A L. Allison
%T A correction to the denotational semantics for Prolog of Nicholson and Foo
%I ACM
%J TOPLAS
%V 15
%N 1
%P 206-208
%M JAN
%D 1993
%K TOPLAS, jrnl, note, LAllison, Alan, alanf, Monash, DS, semantic, Prolog,
   logic programming, LP, c1993, c199x, c19xx, Monash
%X <!-- ISI j's IF=1.40 at '06 -->[<A HREF="https://doi.org/10.1145/151646.151652">doi:10.1145/151646.151652</A>][2/'04]
   Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Logic Programming</A>],
        and [<A HREF="http://www.allisons.org/ll/Semantics/">Denotational Semantics</A>].

%A L. Allison
%T Applications of recursively defined data structures
%J Aust. Comp. J.
%V 25
%N 1
%P 14-20
%M FEB
%D 1993
%O 26/6/2022: [<A HREF="https://arxiv.org/abs/2206.12795">arxiv:2206.12795</A>]
%K jrnl, ACJ, LAllison, Monash, functional applicative programming, FP,
   lazy, need, circular, program, recursive, recursion, corecursion, BFT,
   data structure, list, lists, search trees, tree, breadth first traversal,
   queue, memo, Fib, Fibonacci, n-queens, nqueens, n queens, irreducible, good,
   sequences, Axel Thue, c1993, c199x, c19xx, TR 88 119 TR88-119 TR119
%O an early version in TR 88/119 Dept. Computer Science, Monash University '88
%X "A circular program contains a data structure whose definition is
   self-referential or recursive.  The use of such a definition allows
   efficient functional programs to be written and can avoid the creation of
   intermediate data structures that would have to be garbage collected.
   This paper uses circular programs in various ways, to implement
   memo-structures and explicit search-trees to hold solutions to
   constraint-satisfaction problems."
   Examples: search trees, n-queens, irreducible sequences.
   -- [<A HREF="http://www.allisons.org/ll/Publications/1993ACJ/">more</A>],
      2206.12795@[<A HREF="https://arxiv.org/abs/2206.12795">arXiv</A>][6/2022].
   [Also search for: FP circular program].

%A L. Allison
%T A fast algorithm for the optimal alignment of three strings
%J J. Theor. Biol.
%V 164
%N 2
%P 261-269
%M SEP
%D 1993
%O TR 92/168  Dept. Computer Science, Monash University, Oct '92.
%K LAllison, Monash, jrnl, II, JTB, MolBio, bioinformatics, multiple alignment,
   edit distance, Ukkonen, three, string, strings, sequence, sequences,
   dynamic programming algorithm, DPA, TR 92 168 TR92-168 TR168,
   c1993, c199x, c19xx, J Theoretical Biology
%X <!-- ISI j's IF=1.96 at '06 -->Given 3 strings, length ~ n, 3-way edit-distance d,
   O(n.d^2) time algorithm worst case, O(n+d^3) typically.
   Tree costs 0/1/2.   ie.   xxx :0;    xxy, xx-, x-- :1;    xyz, xy- :2
   NB. Each internal node of an unrooted binary tree has 3 neighbours.
   -- [<A HREF="http://www.allisons.org/ll/Publications/1993JTB2/">more</A>],
      [<A HREF="https://doi.org/10.1006/jtbi.1993.1153">doi:10.1006/jtbi.1993.1153</A>]['04],
   and more on [<A HREF="http://www.allisons.org/ll/Bioinformatics/Three/">bioinformatics</A>].

%A L. Allison
%T Normalisation of affine gap costs used in optimal sequence alignment
%J J. Theor. Biol.
%M MAR
%D 1993
%V 161
%N 2
%P 263-269
%K LAllison, Monash, jrnl, MolBio, JTB, alignment, string, sequence analysis,
   edit distance, homology, gap, gaps, linear, indel, insert delete, Altschul,
   mutual information, similarity, hidden Markov model, HMM, bioinformatics,
   inductive inference, II, c1993, c199x, c19xx, DNA, J Theoretical Biology
%X "It is shown how to normalize the costs of an alignment algorithm that
   employs affine or linear gap costs. The normalized costs are interpreted as
   the -log probabilities of the instructions of a finite-state edit-machine.
   This gives an explicit model relating sequences that can be linked to
   processes of mutation and evolution."
   -- <!-- ISI j's IF=1.96 at '06 -->[<A HREF="http://www.allisons.org/ll/Publications/1993JTB1/">more</A>].

%A L. Allison
%T Lazy dynamic programming can be eager
%J IPL
%V 43
%N 4
%P 207-212
%M SEP
%D 1992
%K LAllison, Monash, jrnl, FP, lazy functional programming, Haskell, fast,
   efficient, dynamic programming algorithm, DPA, edit distance, LCS, LCSS,
   MolBio, approximate, similar, string, strings, match, matching, sequence,
   alignment, c1992, c199x, c19xx, bioinformatics
%X <!-- ISI j's IF=0.56 at '06 --> Lazy evaluation in a functional language is exploited to make the simple
   dynamic programming algorithm for the edit-distance problem run quickly
   on similar strings:  being lazy can be fast.
   Runs in O(n*d) time thanks to laziness.
   -- [<A HREF="http://www.allisons.org/ll/Publications/1992IPL/">more</A>],
      [<A HREF="https://doi.org/10.1016/0020-0190(92)90202-7">doi:10.1016/0020-0190(92)90202-7</A>]['07].

%A C. N. Yee
%A L. Allison
%T Fast string alignment with linear indel costs
%R TR 92/165
%I Computer Science, Monash University
%M JUL
%D 1992
%K LAllison, MolBio, string alignment, similarity, homology, Ukkonen,
   edit distance, linear indel gap cost, costs, Ukkonen, Monash,
   TR 165, TR92/165, TR165, II, c1992, c199x, c19xx, bioinformatics
%X two strings,  O(n*d) time.
   The constants in the cost function have to be "small" integers.
   [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Computing for Molecular Biology</A>].
   [Also search for: Ukkonen].

%A D. L. Dowe
%A J. Oliver
%A L. Allison
%A T. I. Dix
%A C. S. Wallace
%T Learning rules for protein secondary structure prediction
%J Proc. 1992 Department Research Conf.
%I Dept. Computer Science, University of Western Australia
%E C. McDonald
%E J. Rohl
%E R. Owens
%M JUL
%D 1992
%O TR 92/163, Dept. Computer Science, Monash University, JUN '92
%K LAllison, CSW, DLD, Monash, UWA, WA, conf, MolBio, decision tree, trees,
   graph, protein, amino acid, AA, secondary structure, SS, prediction,
   rule, rules, alpha helix, beta strand, extended sheet, coil, turn,
   CSWallace, inductive inference, II, MML, minimum message length, c1992,
   c199x, c19xx, bioinformatics, TR 92 163, TR92-163, TR163
%X Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>],
   and TR 92/163.

%A D. L. Dowe
%A J. Oliver
%A T. I. Dix
%A L. Allison
%A C. S. Wallace
%T A decision graph explanation of protein secondary structure prediction
%J 26th Hawaii Int. Conf. Sys. Sci.
%V 1
%P 669-678
%M JAN
%D 1993
%K LAllison, CSW, Monash, conf, MolBio, protein secondary structure prediction,
   conformation, alpha helix, ss, AA, beta sheet extended strand, turn, coil,
   II, inductive inference, decision graph tree, DTree, CSWallace, CSW,
   MML, Minimum message length encoding, description, MDL, Bayesian,
   TR163 163, c1993, c199x, c19xx, bioinformatics, HICSS, HICSS26, HICSS93
%X Oliver and Wallace (IJCAI '91) introduced `decision graphs' -
   a generalisation of decision trees - here applied to protein secondary
   structure prediction.
   [<A HREF="http://www.allisons.org/ll/Publications/1993.HICSS_26/">more</A>].
   Also see TR 92/163.

%A C. N. Yee
%A L. Allison
%T Reconstruction of strings past
%J Bioinformatics
%O (was Comp. Appl. BioSci.)
%V 9
%N 1
%P 1-7
%M FEB
%D 1993
%O TR 92/162, Dept. Computer Science, Monash University, May '92
%K LAllison, Monash, jrnl, MML, minimum message length, mdl, J. Bioinformatics,
   encoding, hidden Markov model, HMM, II, inductive inference, probabilistic,
   MolBio, string, sequence, alignment, homology, similarity, edit,
   evolutionary, distance, parameter estimation, r-theory,
   TR TR92-162 TR162 162, c1993, c199x, c19xx, CABIOS, J. Bioinformatics
%X Use of single optimal alignment gives biased estimates of the evolutionary
   "distance" between two strings but the r-theory, average all alignments,
   recovers accurate estimates over a very wide range of similarity.
   -- [<A HREF="http://www.allisons.org/ll/Publications/1993CABIOS/">more</A>],
      [<A HREF="https://doi.org/10.1093/bioinformatics/9.1.1">doi:10.1093/bioinformatics/9.1.1</A>]['11].
   Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].
   [<!-- ISI j's IF=6.0 at '06 -->now J. Bioinformatics].

%A L. Allison
%T Some algorithmic attacks on multiple alignment (abstract)
%J Boden Conf.
%W Thredbo, Australia
%M FEB
%D 1993
%K LAllison, Monash, RSBS, ANU, conf, MolBio, MML, II, string,
   sequence, approximate match, matching, three, DPA, bioinformatics
%X also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].

%A L. Allison
%T Estimating parameters and evolutionary distances in the inference of
   evolutionary trees (abstract)
%J Robertson Symposium.
%W Australian National University
%M JAN
%D 1993
%K LAllison, Monash, RSBS, ANU, conf, MolBio, MML, inductive inference,
   II, string, sequence, multiple alignment, approximate match,
   matching, phylogenetic, tree, trees, c1993, c199x, c19xx, bioinformatics
%X also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].

%A L. Allison
%A C. S. Wallace
%A C. N. Yee
%T Minimum message length encoding, evolutionary trees and multiple alignment
%J 25th Hawaii Int. Conf. on Sys. Sci.
%K LAllison, CSW, Monash, conf, MolBio, minimum message length encoding, MML,
   ML, evolutionary, family, phylogenetic, tree, trees, CSWallace, CSW, human,
   Bayesian, finite state, model, machine, FSM, hidden Markov model, primate,
   HMM, DNA, multiple alignment, inductive inference, II, bioinformatics, chimp,
   HICSS, HICSS25, HICCS92, TR 91 155, TR91-155, TR155, c1992, c199x, c19xx
%V 1
%P 663-674
%M JAN
%D 1992
%O TR 91/155, Dept. Computer Science, Monash University '91
%X "A method of Bayesian inference known as MML encoding is applied to inference
   of an evolutionary tree and to multiple alignment for K >= 2 strings.
   It allows the posterior odds-ratio of two competing hypotheses, for
   example two trees, to be calculated. A tree that is a good hypothesis forms
   the basis  of a short message describing the strings.  The mutation
   process is modelled by finite-state machine.  It is seen that tree
   inference and multiple alignment are intimately connected."
   -- [<A HREF="http://www.allisons.org/ll/Publications/1992.HICSS_25/">more</A>]'24],
   there is an example on the primate globin pseudo-genes.
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Trees/">Bioinformatics</A>].)

%A L. Allison
%A T. I. Dix
%A C. N. Yee
%T Shortest path and closure algorithms for banded matrices
%J IPL
%V 40
%P 317-322
%M DEC
%D 1991
%O TR 89/133, Computer Science, Monash University, Nov 1989
%K LAllison, Monash, jrnl, all pairs, shortest path, paths, APSP, closure,
   algorithm, band, banded, matrix, matrices, graph, -ve negative cycle problem,
   constraint, TR89/133, TR 89, 133, TR133, c1991, c199x, c19xx
%X <!-- ISI j's IF=0.56 at '06 --> All pairs shortest paths problem in banded (width b) matrices.
   O(n b^2) for entries in band and for negative cycle problem,
   O(n^2 b) for all pairs shortest paths  where b is band width.
   -- [<A HREF="http://www.allisons.org/ll/Publications/1991IPL/">more</A>],
      [<A HREF="https://doi.org/10.1016/0020-0190(91)90200-2">doi:10.1016/0020-0190(91)90200-2</A>]['07].

%A S. T. S. Ho
%A L. Allison
%A C. N. Yee
%A T. I. Dix
%T Constraint checking for restriction site mapping
%J 24th Hawaii Int. Conf. on Sys. Sci.
%V ?
%P ???-???
%M JAN
%D 1991
%O TR 89/129 Computer Science, Monash University, JUL '89
%K LAllison, Monash, conf, MolBio, HICSS, HICSS24, HICSS91, bioinformatics,
   restriction site mapping, RSM, map, constraint satisfaction problem CSP,
   separation theory, TR 89/129 89 129 TR89/129 TR129, c1991, c199x, c19xx
%X also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Mapping/">mapping</A>].

%A L. Allison
%A M. R. Garrett
%A A. J. Maeder
%T Particle shape characterization and comparison using curve signatures
%J 21st Conf. of the Fine Particle Society
%M AUG
%D 1990
%C San Diego
%K LAllison, Monash, conf, time warp, warping, shape, particle, closed, curve,
   signature, alignment, MML, edit distance, FPS, image processing, IP, c1990
   c199x, c19xx
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A S. Ho
%A L. Allison
%A C. N. Yee
%T Restriction site mapping for three or more enzymes
%J Comp. Appl. BioSci. (J. Bioinformatics)
%V 6
%N 3
%P 195-204
%M JUL
%D 1990
%O TR 88/117 Dept. Comp. Sci., Monash University Oct '88
%K LAllison, Monash, jrnl, MolBio, CABIOS, RSM, restriction site map, mapping,
   constraint satisfaction problem, programming, three, separation theory,
   TR 88 117 TR117 TR88/117, c1990, c199x, c19xx, J. Bioinformatics, enzyme
%X "Restriction site mapping requires a generator to put forward possible maps &
   a constraint checker to reject false maps. Ideally these combine to give an
   algorithm which calculates a sound & complete solution set. 3 algorithms for
   generation are presented & compared. Two decompose a multi-enzyme problem
   (3+) into subproblems. The constraint checker is based on separation theory.
   Some insights into the extent of constraint checking involved in & the
   feasibility of more checking for three or more enzymes are discussed. The
   trade-off between comp'n time & the soundness of the soln set is examined."
   [<!-- ISI j's IF=6.0 at '06 -->now J. Bioinformatics]
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/6.3.195">doi:10.1093/bioinformatics/6.3.195</A>],
      [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/6/3/195">jrnl</A>]['07].
   Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Mapping/">mapping</A>].

%A L. Allison
%A Du Xiaofeng
%T Relating three strings by minimum message length encoding (abstract)
%P 13
%J International Conference on Genes, Proteins and Computers
%W Chester
%I SERC Daresbury Laboratory
%M APR
%D 1990
%K LAllison, Monash, conf, MolBio, multiple, three, triple, alignment,
   LCS, LCSS, MML, family, evolutionary phylogenetic tree, bioinformatics,
   inductive inference, II, DNA, c1990, c199x, c19xx
%X also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Three/">Bioinformatics</A>].

%A L. Allison
%A C. S. Wallace
%A C. N. Yee
%T Finite-state models in the alignment of macro-molecules
%J J. Mol. Evol.
%V 35
%N 1
%P 77-89
%M JUL
%D 1992
%K LAllison, jrnl, MolBio, c1992, c199x, c19xx, TR 90/148, macromolecules,
   TR90/148, TR148, 148 inductive inference, II, DNA, bioinformatics, DPA,
   dynamic programming algorithm, mutual information, ML, string, sequence,
   comparison, alignment, minimum message length encoding, MML, FSM, FSA,
   finite state model, analysis, minimum description length, MDL, methods,
   Hidden Markov model, HMM, homology, similarity, LCS, LCSS, significance,
   evolutionary, edit distance, sequence, r-theory, linear, gap, indel, insert,
   delete, Algorithm, Time, Speed, JME, AAAI, Bayes, Bayesian, CSWallace, CSW
%O An extended abstract titled:
      Inductive inference over macro-molecules
      in joint sessions at AAAI Symposium, Stanford MAR 1990
      on  (i) Artificial Intelligence and Molecular Biology, p5-9,
      &  (ii) Theory and Application of Minimal-Length Encoding, p50-54,
   also an early version in Technical Report 90/148,
      Dept. Comp. Sci., Monash U., Australia 3168.
%X <!-- ISI j's IF=1.7 at '06 --> MML encoding is a technique of inductive inference with theoretical and
   practical advantages.  It allows the posterior odds-ratio of two theories
   or hypotheses to be calculated.  Here it is applied to the problem of
   aligning or relating two strings, in particular biological macro-molecules.
   We compare the r-theory, that the strings are related, with the null-theory,
   that they are not related. If they are related the probabilities of the
   various alignments can be calculated.  This is done for the one-, three-
   and five-state models of relation or mutation. These correspond to linear
   and piecewise linear cost functions on runs of indels.  We describe how
   to estimate the parameters of a model.  The validity of a model is itself
   a hypothesis and can be tested objectively.  This is done on real DNA
   and on artificial data. The tests on artificial data indicate limits on
   what can be inferred in various situations.  The tests on real DNA support
   either the three- or the five-state models over the one-state model.
   Finally, a fast, approximate minimum message length string comparison
   algorithm is described.
   -- [<A HREF="https://doi.org/10.1007/BF00160262">doi:10.1007/BF00160262</A>]['07].
      [<A HREF="http://www.allisons.org/ll/Publications/1992.JME/">reprint</A>] and software,
   See  C. S. Wallace  &  D.M Boulton
        An information measure for classification.
        CompJ 11(2) 185-194 Aug '68   (appendix)
        for the derivation of the coding scheme for multi-state data.
   See also (i) Bishop  &  Thompson
           (ii) Thorne,  Kishino  &  Felsenstein, and
   [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">Alignment</A>].

%A L. Allison
%A C. S. Wallace
%A C. N. Yee
%T When is a string like a string?
%J Int. Symposium on Artificial Intelligence and Mathematics
%W Ft. Lauderdale, Florida, USA
%M JAN
%D 1990
%K LAllison, CSW, CSWallace, Monash, conf, inductive inference, II, homology,
   alignment, LCS, edit distance, string, sequence, comparison, similarity,
   r-theory, macro-molecule, MolBio, DNA, uncertainty, pattern matching, MML,
   minimum message length encoding, AIM AIM90, Hidden Markov model, HMM,
   c1990, c199x, c19xx, bioinformatics
%X  -- [<A HREF="http://www.allisons.org/ll/Publications/1990AIM/">more</A>],
   and [<A HREF="http://www.allisons.org/ll/Publications/1990.148.TR/">TR90/148</A>]['24].

%A L. Allison
%A C. N. Yee
%T Minimum message length encoding and the comparison of macromolecules
%J Bulletin of Mathematical Biology
%V 52
%N 3
%M MAY
%D 1990
%P 431-453
%O TR 89/126 Computer Science, Monash University, MAY '89
%K LAllison, Monash, jrnl, minimum message length encoding, MML, c1990, c199x,
   c19xx, MDL, ML, inductive inference, II, minimum description length, DNA,
   approximate, alignment, similarity, homology, LCS, LCSS, pattern matching,
   string, sequence, comparison, Bayesian, Hidden Markov model, HMM,
   mutual information, MolBio, bioinformatics, BMB, TR 89/126, 89 126, TR89/126
%X "A method of inductive inference known as minimum message length encoding is
   applied to string comparison in molecular biology. The question of whether or
   not two strings are related and, if so, of how they are related and the
   problem of finding a good theory of string mutation are treated as inductive
   inference problems. The method allows the posterior odds-ratio of two string
   alignments or of two models of string mutation to be computed. The
   connection between models of mutation and existing string alignment
   algorithms is made explicit. A fast minimum message length alignment
   algorithm is also described."
   [<A HREF="http://www.allisons.org/ll/Publications/1990BMB/">more</A>],
   [<A HREF="https://doi.org/10.1007/BF02458580">doi:10.1007/BF02458580</A>]['06]<!-- ISI j's IF=1.58 at '06 -->.

%A C. McDonald
%A L. Allison
%T Denotational semantics of a command interpreter and their implementation
   in standard ML
%J COMPJ
%V 32
%N 5
%P 422-431
%M DEC
%D 1989
%O TR 88/7, Dept. Computer Science, UWA  '88
%K LAllison, Monash, COMPJ, jrnl, functional programming, FP, c1989, c198x,
   c19xx, shell script, scripting, command language, line, unix,
   operating system, OS, denotational semantics, DS, ML, SML, UWA,
   TR 88/7, TR88/7, 88 7
%X <!-- ISI j's IF=1.39 at '10 --> [<A HREF="https://doi.org/10.1093/comjnl/32.5.422">doi:10.1093/comjnl/32.5.422</A>]['11],
    [<A HREF="http://www.allisons.org/ll/Semantics/">Denotational Semantics</A>].

%A L. Allison
%T Continuations implement generators and streams
%J COMPJ
%V 33
%N 5
%P 460-465
%M OCT
%D 1990
%O TR 88/112 Dept. Computer Science, Monash University AUG '88
%K LAllison, Monash, jrnl, continuation, combinator, generator, nondeterminism,
   non-determinism, nqueens, n queens, n-queens, source, stream, sink, lazy,
   agent, sieve, TR 88/112, TR88/112, TR112, c1988, c198x, c19xx,
   functional programming, FP
%X <!-- ISI j's IF=1.39 at '10 --> Continuations are used to program non-deterministic generators
   and a variation on deterministic stream functions.
   Examples include the n-queens problem and the sieve of Eratosthenese.
   The continuation style has an imperative flavour but is
   functional and free of side effects.
   Some (recursive) programs can be executed in constant space.
   -- [<A HREF="http://www.allisons.org/ll/Publications/1990BCJ/">more</A>],
      [<A HREF="https://doi.org/10.1093/comjnl/33.5.460">doi:10.1093/comjnl/33.5.460</A>]['11].

%A L. Allison
%A C. N. Yee
%A M. McGaughey
%T Three-dimensional queens problems
%R TR 89/130
%I Dept. Computer Science, Monash University, Australia
%M AUG
%D 1989
%K LAllison, Monash, n queens, n-queens, queen, nqueens, chess, 3D,
   TR 89 130 TR130 TR89/130, c1989, c198x, c19xx
%X [<A HREF="http://www.allisons.org/ll/AlgDS/Recn/Queens3D/">TR89/130</A>].

%A L. Allison
%A C. Y. Yee
%T Restriction site mapping is in separation theory
%J Comp. Appl. BioSci. (J. Bioinformatics)
%V 4
%N 1
%P 97-101
%M JAN
%D 1988
%K LAllison, Monash, jrnl, CABIOS, plasmid, map, maps, mapping, combinatorial,
   enzyme, restriction site, DNA, phage, RSM, MolBio, separation theory,
   linear, constraint, programming, algorithm, inequality, c1988, c198x, c19xx,
   J. Bioinformatics, NAR, Nucl. Acids Res. special issue
%X Paper examines constraint checking during backtracking generation
   of solutions to the plasmid mapping problem.
   The constraints fall into Vaughn Pratt's separation theory.
   It is necessary and sufficient to check all simple cycles
   in the graph of restriction sites linked by fragments
   from the two single digests and the one double digest (can be generalized
   to more than two enzymes).
   In general, at level 'n' there are at most n new constraints to check.
      As an efficiency matter, only those cycles containing 1, 2 or 3
   indivisible cycles can be checked which allows a very few false maps to
   be generated.  This reduces total constraints/map from n*n to 3*n.
   -- [<A HREF="http://www.allisons.org/ll/Publications/1988CABIOS/">more</A>],
      [<A HREF="https://doi.org/10.1093/comjnl/33.5.460">doi:10.1093/comjnl/33.5.460</A>]['11].
   [jrnl is now <!-- ISI j's IF=6.0 at '06 --> J. Bioinformatics].

%A L. Allison
%T A Practical Introduction to Denotational Semantics
%S Cambridge Computer Science Texts
%I CUP
%K LAllison, UWA, text, book, textbook, CUP, denotational semantics, DS,
   programming language, languages, definition, L4REF, c1986, c198x, c19xx
%D 1986
%X [<A HREF="https://doi.org/10.1017/CBO9781139171892">doi:10.1017/CBO9781139171892</A>];
   pb, uk us isbn:0521314232, uk us isbn13:978-0521314237;
   hb, uk us isbn:0521306892, uk us isbn13:978-0521306898;
   reviewed in Computing Reviews, Nov '87 pp.574-5 and Jul '88 pp.349-350
   and in Software P & E 18(5) pp.493-494 May '88 [<A HREF="https://doi.org/10.2277/0521314232">www</A>]['07].
   (More on [<A HREF="http://www.allisons.org/ll/Semantics/">Denotational Semantics</A>].)

%A L. Allison
%T Direct semantics and exceptions define jumps and coroutines
%J IPL
%V 31
%N 6
%P 327-330
%M JUN
%D 1989
%O TR 87/90 Dept Computer Science, Monash University, 1987
%K LAllison, Monash, jrnl, denotational semantics, DS, direct, exception,
   SML, ML, jump, sequencer, goto, coroutine, control, raise, handle, catch,
   throw, IPL, TR 87/90 TR87/90 90 TR90, c1989, c198x, c19xx
%X Direct semantics and continuation semantics are the two main styles of
   denotational semantics. Direct semantics is the simpler style but cannot
   define the semantics of jumps and other sequencers. This paper shows that,
   with the addition of exceptions, direct semantics can define sequencers. In
   contrast to the use of continuation semantics, nothing need be added to the
   semantics of commands unconnected with sequencers. Since exceptions can be
   defined in terms of the lambda-calculus nothing need be added to the
   foundations of semantics.
   -- [<A HREF="https://doi.org/10.1016/0020-0190(89)90097-5">doi:10.1016/0020-0190(89)90097-5</A>]['06],
      [<A HREF="http://www.allisons.org/ll/Semantics/">Denotational Semantics</A>].

%A L. Allison
%T Circular programs and self-referential structures
%J SPE
%V 19
%N 2
%P 99-109
%M FEB
%D 1989
%O in TR87/91 Dept Computer Science, Monash University, Jan 87
%K jrnl, LAllison, Monash, applicative, functional programming, FP, circular,
   recursive, recursion, corecursion, lazy, evaluation, need, program, list,
   lists, queue, doubly linked, tree, trees, breadth first traversal, BFT,
   threaded, queues, nub, unique elements, primes, c1989, c198x, c19xx,
   TR 87/91 TR87/91 TR91 91
%X A circular program creates a data structure whose computation depends on
   itself or refers to itself.  The technique is used to implement the
   classic data structures circular and double-linked lists, threaded trees
   and queues in a functional programming language.
   -- [<A HREF="http://www.allisons.org/ll/Publications/1989SPE/">more_1</A>],
      [<A HREF="https://arxiv.org/abs/2403.01866">arxiv:2403.01866</A>]['24],
      [<A HREF="https://doi.org/10.1002/spe.4380190202">doi:10.1002/spe.4380190202</A>]['11].
   [Also search for: FP circular program].

%A L. Allison
%T Some applications of continuations
%J COMPJ
%V 31
%N 1
%P 9-11
%M FEB
%D 1988
%O in TR87/91 Dept Computer Science, Monash University, Jan 87
%K LAllison, Monash, jrnl, functional programming, FP, recursion, backtrack,
   COMPJ, backtracking, back track, coroutine, applicative, continuation, parse,
   parser, parsing, recursive descent, non-determinism, binary search tree,
   merge, combinators, TR 87/91 TR87/91 TR91 91, c1988, c198x, c19xx
%X -- [<A HREF="http://www.allisons.org/ll/Publications/1988BCJ/">more</A>]['24],
      [<A HREF="https://doi.org/10.1093/comjnl/31.1.9">doi:10.1093/comjnl/31.1.9</A>]['11].

%A L. Allison
%A T. I. Dix
%T A bit-string longest-common-subsequence algorithm
%J IPL
%V 23
%M DEC
%D 1986
%P 305-310
%K LAllison, TIDix, Monash, UWA, jrnl, MolBio, LCS, LCSS, c1986, c198x, c19xx,
   fast, algorithm, bits string, bit vector, DPA, dynamic programming algorithm,
   similarity, homology, bioinformatics, IPL, sequence, approximate, match,
   matching, strings, distance, comparison, alignment, practical, speedup,
   speed
%X "A longest-common-subsequence algorithm is described which operates in terms
   of bit or bit-string operations. It offers a speedup of the order of the
   word-length on a conventional computer."
  <!-- ISI j's IF=0.56 at '06 --> Speedup is ~ wordlength (eg. a factor of 32 or 64),  time is O(n^2/wordlength).
   [<A HREF="http://www.allisons.org/ll/Publications/1986IPL/">more</A>]+source code,
   [<A HREF="https://doi.org/10.1016/0020-0190(86)90091-8">doi:10.1016/0020-0190(86)90091-8</A>]['07].

%A A. Finlay
%A L. Allison
%T A prescription for Prolog control features based upon denotational semantics
   and its implementation in standard ML
%R TR 87/97
%I Dept. Computer Science, Monash University
%M NOV
%D 1987
%K LAllison, Monash, CSSE, Prolog, logic programming, LP, SML, ML, TR87/97,
   TR97 TR 97, c1987, c198x, c19xx, denotational semantics, DS
%X [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Logic Programming</A>]
   [<A HREF="http://www.allisons.org/ll/Semantics/">Denotational Semantics</A>].

%A L. Allison
%T Programming denotational semantics II
%J COMPJ
%V 28
%N 5
%P 480-486
%D 1985
%K COMPJ, jrnl, LAllison, UWA, denotational, DS, continuation semantics,
   languages, algol, A68, algol-68, algol68, c1985, c198x, c19xx
%X -- [<A HREF="http://www.allisons.org/ll/Publications/1985BCJ/">more</A>]['24],
      [<A HREF="http://www.allisons.org/ll/Semantics/">semantics</A>]['24].

%A L. Allison
%T Programming denotational semantics
%J COMPJ
%V 26
%N 2
%P 164-174
%D 1983
%K COMPJ, jrnl, LAllison, UWA, direct, language, denotational semantics,
   DS, Pascal, c1983, c198x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Publications/1983BCJ/">more</A>],
   [<A HREF="http://www.allisons.org/ll/Semantics/">Denotational Semantics</A>].

%A L. Allison
%T An executable Prolog semantics
%J Algol Bulletin
%N 50
%P 10-18
%M DEC
%D 1983
%K LAllison, UWA, jrnl, denotational semantics, DS, algol, algol-68, algol68,
   logic programming, LP, unification, interpreter, Prolog, c1983, c198x, c19xx
%X -- [<A HREF="http://www.allisons.org/ll/Publications/1983AlgolBulletin/">more</A>],
      [<A HREF="https://dl.acm.org/doi/10.5555/1061790.1061794">dl.acm.org/doi/10.5555/1061790.1061794</A>] -- AB in ACM digital archive,
      [<A HREF="http://www.allisons.org/ll/Semantics/B/p09/">program code</A>],
    & [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].

%A L. Allison
%T On syntax directed program editing
%J SPE
%V 13
%P 453-465
%D 1983
%K LAllison, UWA, jrnl, edit, editor, syntax-editor, SED, SDE,
   syntax directed, program, structure based, c1983, c198x, c19xx
%X <!-- ISI j's IF=0.41 at '06 --> .

%A L. Allison
%T Stable-marriages by coroutines
%J IPL
%V 16
%P 61-65
%M FEB
%D 1983
%K IPL, jrnl, c1983, c198x, c19xx, LAllison, UWA, jrnl, stable marriage problem,
   algorithm, match, coroutine, modula, two, modula2, modulaII, bipartite,
   graph, match, matching, preference, coroutine
%X The stable marriage problem is an appealing version of many pairing problems.
   A solution by coroutines is given, based on the recursive algorithm of
   McVitie and Wilson (1971). There are few published algorithms where
   coroutines are really useful but they solve this problem very naturally.
   -- <!-- ISI j's IF=0.56 at '06 -->[<A HREF="https://doi.org/10.1016/0020-0190(83)90025-X">doi:10.1016/0020-0190(83)90025-X</A>]['06],
   [<A HREF="http://www.allisons.org/ll/">LA home</A>].

%A L. Allison
%A P. Edmiston
%T A LOGO survey
%J Australian Computer Bulletin
%V 5
%N 9
%P 40
%M OCT
%D 1981
%K LAllison, UWA, jrnl, logo, programming language,
   children school education CAI, c1981, c198x, c19xx

%A L. Allison
%T Generating coset representatives for permutation groups
%J J. of Algorithms
%V 2
%P 227-244
%M SEP
%D 1981
%K LAllison, UWA, jrnl, coset, group, permutation, backtrack, backtracking,
   back track, isomorph rejection, subgroup, maths, generate, representative,
   algorithm, c1981, c198x, c19xx
%X <!-- ISI j's IF=1.14 at '06 --> .
   -- [<A HREF="https://doi.org/10.1016/0196-6774(81)90024-9">doi:10.1016/0196-6774(81)90024-9</A>]['10].

%A L. Allison
%T Phrase structures, non-determinism and backtracking
%J IPL
%V 7
%N 3
%P 139-143
%M APR
%D 1978
%K LAllison, MelbU, jrnl, grammar, parse, parsing, parser,  backtrack,
   backtracking, non-determinism, back track, back tracking,
   LL, LL1, LL(1), c1978, c197x, c19xx
%X <!-- ISI j's IF=0.56 at '06 --> -- [<A HREF="https://doi.org/10.1016/0020-0190(78)90077-7">doi:10.1016/0020-0190(78)90077-7</A>]['06],
   [<A HREF="http://www.allisons.org/ll/ProgLang/">Programming-Languages</A>].

%A L. Allison
%A A. Lock
%T A wordprocessor for the handicapped
%J ACSC 5
%W Perth
%M FEB
%D 1982
%K LAllison, UWA, conf, ACSC5, ACSC82, c1982, c198x, c19xx

%A L. Allison
%A D. Wilde
%T Phrase structures in Pascal
%J Programming Language Systems
%W Canberra
%P 29-37
%M FEB
%D 1977
%I ANUpress
%K LAllison, MelbU, conf, grammar,  parse, parsing, parser,  backtrack,
   backtracking, back track, c1977, c197x, c19xx, Pascal, LL LL1 LL(1), ACSC,
   ACSC0, structure, system
%X Essentially ACSC0, conf 24-25 Feb 1977,
   volume published in '78, isbn:0708104932.
   Also see [<A HREF="http://www.allisons.org/ll/ProgLang/">Programming-Languages</A>].


%A D. E. Rumelhart
%A G. E. Hinton
%A R. J. Williams
%T Learning representations by back-propagating errors
%J Nature
%V 323
%P 533-536
%D 1986
%K jrnl, c1986, c198x, c19xx, zz0822, ANN, NN, backprop, backpropagation,
   training, error
%X "... The procedure repeatedly adjusts the wts of the connections in the n/wk
   so as to minimize a measure of the difference between the actual output
   vector of the net & the desired output vector. ... result of the wt
   adjustments, internal 'hidden' units which are not part of the input or
   output come to represent important features of the task domain ..."
   -- [<A HREF="https://doi.org/10.1038/323533a0">doi:10.1038/323533a0</A>]['22].
   Also see backprop@[<A HREF="https://en.wikipedia.org/wiki/Backpropagation">wikip</A>]['22],
   and ANN@[<A HREF="https://en.wikipedia.org/wiki/Artificial_neural_network">wikip</A>]['22].

%A Wei Zhang
%T Shift-invariant pattern recognition neural network and its optical
   architecture
%J Proc. Annual Conf. of the Japan Soc. of Applied Physics
%D 1988
%K conf, c1988, c198x, c19xx, zz0822, ANN, convolutional NN, CNN, training,
   backpropagation, shift invariant, neocognitron, image processing
%X "... An improved error-back-propagation (EBP) training method is proposed &
   simulated for the training of the model. The proposed model is a simplified
   Neocognitron by combining the & and C layers (Fig. 1) to one layer & used for
   pattern recognition. The features of the structure of this model are that the
   fanout of each neuron is relatively small, & the connections between the
   planes are space invariant. Therefore, it can be realized optically. We have
   introduced an annealing process to improve the speed of the EBP training
   method and avoid local minimums. ..."
   Also see CNN@[<A HREF="https://en.wikipedia.org/wiki/Convolutional_neural_network">wikip</A>]['22].
   [Also search for: convolutional NN].

%A S. A. Billings
%A S. Chen
%A M. J. Korneberg
%T Identification of MIMO non-linear systems using a forward-regression
   orthogonal estimator
%J Int. J. of Control
%V 49
%N 6
%P 2157-2189
%D 1989
%K jrnl, c1989, c198x, c19xx, zz0807, system, orthogonal least squares, OLS,
   nonlinear
%X via DS and EM

%A F. Girosi
%A T. Poggio
%T Networks and the best approximation property
%J Biological Cybernetics
%V 63
%P 169-176
%D 1989
%K c1989, c198x, c19xx, ANN, NN, networks, RBF, approximation, regularization,
   multilayer
%X "n/ws can be considered as approx'n schemes. Multilayer n/ws of the
   backprop. type can approx. arb. well cts fns... We prove that n/ws derived
   from regularization theory and including Radial Basis fns have a similar
   property. ... the property of approximating continuous functions arbitrarily
   well is not sufficient for characterizing good approximation schemes. More
   critical is the property of best approximation. The main result of this paper
   is that multilayer networks, of the type used in backpropagation, are not
   best approximation. For regularization n/ws (in particular RBFs) we prove
   existence and uniqueness of best approximation."
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.18.5331">citese'r</A>]['10].

%A A. R. Barron
%T Complexity regularization with application to artificial neural networks
%B Nonparametric Functional Estimation and Related Topics
%E G. Roussos
%D 1991
%I Kluwer
%P 561-576
%K ANN, net, nets, NN, polynomial regression, minimum message length,
   MML, description, MDL, c1991, c199x, c19xx
%X via Rohan B'.

%A D. J. C. MacKay
%T Bayesian Methods for Adaptive Models
%I Calif. Inst. Tech.
%D 1991
%O 2nd ed '92
%K PhD thesis, c1991, c199x, c19xx, CalTech, artificial neural networks, NN,
   ANN, backprop, backpropagation, multilayer, network, training,
   regularisation, regularization, parameters
%X "The Bayesian f/wk for model comparison & regularisation is demonstrated by
   studying interpolation & class'n problems modelled with both linear &
   non-linear models. ... quantitatively embodies 'Occam's razor'. Over-complex
   & under-regularised models are automatically inferred to be less probable,
   even though their flexibility allows them to fit the data better. ..."
   -- [<A HREF="https://doi.org/10.7907/H3A1-WM07">doi:10.7907/H3A1-WM07</A>]['22],
      [<A HREF="http://www.inference.phy.cam.ac.uk/mackay/p0.html">www</A>][8/'02].
   Also see DJCM(1967-2016)@[<A HREF="https://en.wikipedia.org/wiki/David_J._C._MacKay">wikip</A>]['22].
   [Also search for: MacKay NN].

%A H. Gish
%T Maximum likelihood training of neural networks
%B Artificial Intelligence Frontiers in Statistics: AI and statistics III
%E D. J. Hand
%D 1993
%I Chapman and Hall, London
%K AI, inductive inference, II, artificial, net, NN, ANN,
   Bayes, Bayesian, Fisher information, FI, MML, MDL, c1993, c199x, c19xx
%X 9 refs
   isbn:0-412-40710-8
   via R o h a n  B a x t e r.

%E R. Sun
%E L. Bookman
%T Computational Architectures Integrating Neural and Symbolic Processes:
   A Perspective on the State of the Art
%I Kluwer
%D 1994
%K book, text, artificial, net, ANN, AI, computing
%X isbn:0-7923-9517-4.  email: rsun@cs.brandeis.edu (Ron Sun  12/'94)
   Chapter 1 An Introduction: On Symbolic Processing in Neural Networks
   Chapter 2 Complex Symbol-Processing in Conposit, A Transiently Localist
             Connectionist Architecture
   Chapter 3 A Structured Connectionist Approach to Inferencing and Retrieval
   Chapter 4 Hierarchical Architectures for Reasoning
   Chapter 5 Subsymbolic Parsing of Embedded Structures
   Chapter 6 Towards Instructable Connectionist Systems
   Chapter 7 An Internal Report for Connectionists
   Chapter 8 A Two-Level Hybrid Architecture for Structuring Knowledge for
              Commonsense Reasoning
   Chapter 9 A Framework for Integrating Relational and Associational
              Knowledge for Comprehension
   Chapter 10 Examining a Hybrid Connectionist/Symbolic System for the
              Analysis of Ballistic Signals
   Chapter 11 Symbolic Artificial Intelligence and Numeric Artificial Neural
              Networks: Towards a Resolution of the Dichotomy
   Chapter 12 Connectionist Natural Language Processing: A Status Report.

%A Xin Yao
%T A review of evolutionary artificial neural networks
%J Int. J. Intelligent Systems
%V 8
%P 539-567
%I JohnWiley
%D 1993
%K GA, NN, ANN, net, IJIS, jrnl
%X via enews

%A Yoshiaki Ichikawa
%A Yoshikazu Ishii
%T Retaining diversity of genetic algorithms for multivariable optimization
   and neural network learning
%J 1993 IEEE Int. Conf. on Neural Networks
%P 1110-1114
%D 1993
%K GA, NN, ANN, conf, net
%X via enews

%A J. R. McDonnel
%A D. Waagen
%T Evolving neural network connectivity
%J 1993 IEEE Int. Conf. on Neural Networks
%P 863-868
%D 1993
%K GA, NN, ANN, net, connection, arc, graph, c1993, c199x, c19xx, conf,
   mcdonnell
%X "... application of evolutionary programming, a stochastic search technique,
   for determining connectivity in FF NNs ..."
   -- [<A HREF="https://doi.org/10.1109/ICNN.1993.298671">doi:10.1109/ICNN.1993.298671</A>]['22] via enews.

%A D. J. C. MacKay
%T Probable networks and plausible predictions - a review of
   practical Bayesian methods for supervised neural networks
%J Network: Computation in Neural Systems
%V 6
%P 469-505
%D 1995
%K c1995, c199x, c19xx, NN, neural network, ANN, training, hyperparameters,
   hyper parameter, regularisation, regularization
%X "Bayesian probability theory provides a unifying framework ...
   [try] to find models that are well matched to the data, and to
   use these models to make optimal predictions. NN learning is interpreted
   as an inference of the most probable parameters for the model, given the
   training data. The search in model space (i.e., the space of architectures,
   noise models, preprocessings, regularizers and weight decay
   constants) can then also be treated as an inference problem ...
   ... this review describes practical techniques based on Gaussian
   approximations for implementation of these powerful methods for
   controlling, comparing and using adaptive networks."
   -- [<A HREF="https://doi.org/10.1088/0954-898X_6_3_011">doi:10.1088/0954-898X_6_3_011</A>['22],
      revised [<A HREF="http://www.inference.phy.cam.ac.uk/mackay/network.pdf">.pdf</A>][10/'04].
   Also see DJCM(1967-2016)@[<A HREF="https://en.wikipedia.org/wiki/David_J._C._MacKay">wikip</A>]['22].
   [Also search for: MacKay NN].

%A M. A. Arbib
%T Handbook of Brain Theory and Neural Networks
%I MITpress
%K book, text, artificial neural net, NN, ANN, CSci, zz0695
%D 1995
%X From <!-- hemail: illman@math.washington.edu --> Christopher Hillman [6/'95]
   blurb includes:
   113. Information Theory and Visual Plasticity, by Nathan Intrator.
   117. Kolmogorov's Theorem, by Vera Kurkova.
   214. Sensory Coding and Information Theory, by John Hertz.

%T Neural Networks for Identification, Prediction and Control
%A D. T. Pham
%A X. Liu
%I Springer
%D 1995
%K book, text, net, nets, NN, ANN
%X ? Hargreaves ?  003.363 p534n   <!-- via  deanm 5/1998 --> .

%A N. Jankowski
%T Applications of Levin's universal optimal search algorithm
%E E. Kacki
%J System Modeling Control '95
%V 3
%P 34-40
%M MAY
%D 1995
%I Polish Soc. of Medical Informatics
%K artificial neural network, ANN, net, NN, maze, Levin,
   universal, c1995, c199x, c19xx, optimum, search, algorithm
%X ...solutions are characterized by possibility of the maximal generalization.
   In the deterministic version of the Universal Optimal Search
   algorithm one can always generate the best solution.  It is shown that it
   is possible to find a solution by this method for problems in neural
   networks for which back-propagation type of methods face difficulties.
   Another application considered here is a problem of finding an exit-way
   from a maze.  There exists a probabilistic version of Levin's universal
   search. This work offers an alternative implementation of the
   Levin's Universal Optimal Search.
   [<A HREF="http://www.phys.uni.torun.pl/~norbert/publicat.htm">pub's</A>][10/'02]
   [<A HREF="http://www.phys.uni.torun.pl/publications/kmk/">pub's</A>][10/'02]
   [<A HREF="http://www.phys.uni.torun.pl/publications/kmk/LUS-zakopaneV95.pdf">pdf</A>][10/'02]

%T Self-Organizing Methods in Modeling
%E S. J. Farlow
%I Dekker
%D 1984
%K book, text, Barron, c1984, c198x, c19xx, statistics, stats, model,
   modelling, NN, ANN
%X (LaTrobe has a copy) <!-- via deanm  5/1998 --> .

%A K. Levenberg
%T A method for the solution of certain nonlinear problems in least squares
%J Qty. Appl. Math.
%V 2
%P 164-168
%D 1944
%K jrnl, c1944, c194x, c19xx, optimisation, optimization, peak fitting,
   Marquardt
%X search for  L' with M'.  Has been used in training ANNs.
   Also see [<A HREF="http://en.wikipedia.org/wiki/Levenberg-Marquardt_algorithm">LM@wikip</A>]['07].

%A D. W. Marquardt
%T An algorithm for the estimation of non-linear parameters
%J J. Soc. Ind. Appl. Math.
%V 11
%P 431-441
%D 1963
%K jrnl, c1963, c196x, c19xx, SIAM, peak fitting, trust region, optimisation,
   optimization, Levenberg
%X has been used in training artificial neural networks (ANN).
   Also see [<A HREF="http://en.wikipedia.org/wiki/Levenberg-Marquardt_algorithm">LM@wikip</A>]['07].

%A J. J. More
%T The Levenberg-Marquardt algorithm: Implementation and theory
%B Numerical Analysis
%E G. A. Watson
%I SpringerVerlag
%S Lecture Notes in Mathematics
%V 630
%P 104-116
%D 1978
%K conf, c1978, c197x, c19xx, Mor'e, optimisation, optimization, maximize,
   numerical analysis, methods, trust region, least squares, minimize,
   artificial neural networks, net, ANN
%X [<A HREF="http://citeseer.nj.nec.com/context/85046/0">citeseer</A>][6/'01]
   Given vector of observations y[], fit vector f(a,x), `a' params, x given.
   residuals  r[i] = a[i] - f(a,x[i])
   a[new] = a[old] + inv(J'J+D).J'r  where D a diagonal matrix,
   Jacobian  J = n x k matrix,  d f/d a[j].
   [<A HREF="http://www.ams.org/mathscinet-getitem?mr=58:3446">abs@AMS</A>]['07]
   [<A HREF="http://en.wikipedia.org/wiki/Levenberg-Marquardt_algorithm">LM@wikip</A>]['07].
   Also see [<A HREF="http://doi.acm.org/10.1145/355958.355966">doi:10.1145/355958.355966</A>] TOMS algorithm 573, NL2SOL.

%A N. Ampazis
%A S.J. Perantonis
%T Levenberg-Marquardt algorithm with adaptive momentum for the efficient
   training of feedforward networks
%J Proc. IEEE-INNS-ENNS Int. Joint Conf. on Neural Networks (IJCNN'00)
%P ?-?
%D 2000
%K IJCNN, IJCNN01, artificial, ANN, NN, conf
%X [<A HREF="http://www.computer.org/proceedings/ijcnn/0619/volume%201/06191126abs.htm">abs'</A>][6/'01]
   ... second order algorithm ... additional adaptive momentum term ...
   convergence properties.

%A W. Kaminski
%A P. Strumillo
%T Kernel orthonormalization in radial basis function neural networks
%J IEEE Trans. Neural Networks
%V 8
%N 5
%P 1177-1183
%M SEP
%D 1997
%K jrnl, ANN, NN, net, network, function, orthogonal, c1997, c199x, c19xx, RBF
%X make the hidden neurons orthogonal to each other (and normalised)
   Also see conf paper '01.

%A T. D. Gedeon
%T Measuring the significance and contributions of inputs in
   back-propagation neural networks for rules extraction and data mining
%J Brain-like Computing and Intelligent Information Sys.
%I SpringerVerlag
%P 417-434
%D 1997
%K conf, NN, network, c1997, c199x, c19xx, rule, contribution
%X auth @ CS ANU as of ['05].

%A S. Gutjahr
%T Improving the determination of the hyperparameters in Bayesian learning
%J Proc. of the 9th Australian Conf. on Neural Networks (ACNN98).
%E T.Downs, M.Frean, M.Gallagher
%W Brisbane, Australia
%P 114-118
%D 1998
%K conf, NN, ANN, hyper parameter
%X via enesm; auth @ u. karlsruhe (ira uka de)

%A H. K. H. Lee
%T Model Selection and Model Averaging for Neural Networks
%I Carnegie Mellon U.
%D 1998
%K PhD Thesis, network, ANN, NN, MCMC, Bayesian, BARS, BIC, c1998, c199x, c19xx
%X also see Lee 2000

%A H. K. H. Lee
%T A framework for nonparametric regression using neural networks
%J Pacific Rim International Conference on Artificial Intelligence
%D 2000
%P ?-?
%K conf, network, ANN, NN, MCMC, Bayesian, BARS, BIC,
   c2000, c200x, c20xx, zz0603
%X Neural networks are a useful statistical tool for nonparametric regression.
   In this paper, I develop a methodology for nonparametric regression within
   the Bayesian paradigm. I address the problem of model selection and model
   averaging, particularly the problem of searching the model space in terms
   of both the optimal number of hidden nodes in the network as well as the
   best subset of explanatory variables. I implement this with a method I call
   Bayesian Random Searching (BARS). ...
   [<A HREF="http://ftp.isds.duke.edu/WorkingPapers/00-32.ps">.ps @ duke</A>][6/'03]

%A W. Kaminski
%A P. Strumillo
%T Neural networks with orthogonalized transfer functions
%J European Symp. on Artificial Neural Networks (ESANN)
%P ?-?
%D 2001
%K conf, NN, ANN, ESANN9, orthogonal, orthonormal, basis function, functions
%X [<A HREF="http://www.dice.ucl.ac.be/Proceedings/esann/esannpdf/es2001-401.pdf">.pdf</A>][3/'03]
   Also see jrnl paper '97.

%A P. van der Smagt
%A G. Hirzinger
%T Why feed-forward networks are in a bad shape
%J Proc. 8th Int. Conf. on Art. Neural Networks
%E L. Niklasson
%E M. Boden
%A T. Ziemke
%I SpringerVerlag
%P 159-164
%D 1998
%K conf, ANN, vanDerSmagt, Hessian, condition, ill conditioned,
   sensitivity analysis, weights, network
%X via enesm

%A H. Lappalainen
%T Using an MDL-based cost function with neural networks
%J Proc. IJCNN'98
%W Anchorage
%P 2384-2389
%D 1998
%K IJCNN, IJCNN98, conf, net, artificial, ANN, complexity, MDL
%X [<A HREF="http://www.cis.hut.fi/harri/ijcnn98/">paper</A>][12/'01]
   ... presents how to efficiently use an MDL-based cost function with
   NNs.  ... cost function [] used to adapt the parameters in the network,
   but it can also include terms to measure the complexity of the structure
   of the network and can thus be applied to determine the optimal structure.
   ... convert a conventional neural network such that each parameter and
   each output of the neurons is assigned a mean and a variance.
   This greatly simplifies the computation of the description length and
   its gradient with respect to the parameters, which can then be adapted
   using standard gradient descent.
   [Also search for: MML]  and  [Also search for: ANN].

%A W. Duch
%A R. Adamczak
%A K. Grabczewski
%T Optimization of logical rules derived by neural procedures
%J 1999 Int. Joint Conf. on Neural Networks
%W Washington
%P ?-?
%M JUL
%D 1999
%K conf, neural net, network, NN, ANN, rule, wide margin classifiers
%X paper no. 741.  NNs used for ... linguistic vars and extraction
   of logfical rule s from data. .... different accuracy/ rejection
   tradeoffs ... gives probabilities of classification instead of
   yes/no answers and allows to opt' sets of rules using gradient
   procedures. ... e.g.s...
   [<A HREF="http://www.phys.uni.torun.pl/publications/kmk/99ijcn-r.pdf">.pdf</A>][5/'03]

%A H. Attias
%T Independent factor analysis with temporally structured factors
%J Advances in Neural Information Proc. Sys.
%V 12
%P 386-392
%D 2000
%K ann, c2000, c200x, c20xx, time series, timeSeries, model, IFA
%X "... [here] each factor has its own temporal stat. characteristics.
   ... EM alg. ..."
   [<A HREF="http://research.goldenmetallic.com/">home</A>]['06]

%A V. Tresp
%T A Bayesian committee machine
%J Neural Computation
%V 12
%N 11
%P 2719-2741
%D 2000
%K c2000, c200x, c20xx, zz1208, ANN, BCM
%X "The (BCM) is a novel approach to combining estimators that were trained on
   different data sets. ... main foci are gaussian process regression & related
   systems ... Somewhat surprisingly, we find that the performance of the BCM
   improves if several test points are queried at the same time & is optimal if
   the # of test points is >= the degrees of freedom of the est.  ..."
   [<A HREF="http://dx.doi.org/10.1162/089976600300014908">doi:10.1162/089976600300014908</A>]['08].

%A C. Andrieu
%A N. de Freitas
%A A. Doucet
%T Reversible jump MCMC simulated annealing for neural networks
%J Uncertainty in Artificial Intelligence:
   Proc. of the Sixteenth Conf. (UAI-2000)
%P 11-18
%D 2000
%O Sequential Bayesian estimation and model selection applied to
   neural networks, TR 341, Eng. Dept., Cambridge U., March '99.
%K conf, UAI, UAI16, UAI2000, AI, network, net, ANN, MDL, AIC, BIC, MCMC,
   Monte Carlo, deFreitas, TR341
%X We propose a novel reversible jump Markov chain Monte Carlo (MCMC)
   simulated annealing algorithm to optimize radial basis function
   (RBF) networks. This algorithm enables us to maximize the
   joint posterior distribution of the network parameters and the number of
   basis functions. It performs a global search in the joint space of the
   parameters and number of parameters, thereby surmounting the problem of
   local minima. We also show that by calibrating a Bayesian model, we can
   obtain the classical AIC, BIC and MDL model selection criteria within a
   penalized likelihood framework. Finally, we show theoretically and
   empirically that the algorithm converges to the modes of the
   full posterior distribution in an efficient way.
   [<A HREF="http://rome.exp.sis.pitt.edu/UAI/Abstract.asp?articleID=2&proceedingID=16">abs</A>][4/'02] - via  l e i g h f
   [<A HREF="http://www.cs.ubc.ca/~nando/software.html">TRs+S/W</A>][4/'02]

%A F. Gruau
%T Genetic synthesis of modular neural networks
%J Proc. of the 5th Int. Conf. on Genetic Alg.s, ICGA-93
%P 318-325
%D 1993
%K conf, ICGA93, ICGA5, c1993, c199x, c19xx, artificial neural networks, ANN, GA
%X see  t h e s i s  '94

%A F. Gruau
%T Neural Network Synthesis using Cellular Encoding and
   the Genetic Algorithm
%I Laboratoire de l'Informatique du Parallilisme,
   Ecole Normale Supirieure de Lyon
%D 1994
%K PhD theses, cellular encoding, Artificial neural networks, ANN,
   graph grammar, subproblem, subnetwork, genetic algorithm, GA, zz0502
%X ...Cellular encoding is presented as a machine language for
   neural networks, with a theoretical basis (it is a parallel
   graph grammar that checks a number of properties) and a
   compiler of high level language. ...
   ... an solve problems that were still unsolved with neural
   networks. It can automatically and dynamically decompose a
   problem into a hierarchy of sub-problems ...
   Also see [<A HREF="http://citeseer.nj.nec.com/383724.html">citeseer</A>][5/'02]

%A T. Plate
%T Controling the hyperparameter search in MacKay's Bayesian neural
   network framework
%B Neural Networks: Tricks of the Trade
%I SpringerVerlag
%S LNCS
%V 1524
%P 91-110
%D 1998
%K c1998, c199x, c19xx, hyper parameter, parameters, controlling, ANN, NN,
   network, training, selection, classification, overfitting,, regularisation
%X "...overfitting must be controlled. WAIeight penalty factors are one common
   method of providing this control. However, using weight penalties creates
   the additional search problem of finding the optimal penalty factors. MacKay
   proposed an approx. Bayesian framework for training [NNs] ...penalty factors
   are treated as hyperparameters & found in an iterative search. However, for
   classification networks trained with cross-entropy error, this search is
   slow & unstable, & it is not obvious how to improve it. This paper describes
   & compares several strategies for controlling this search ..."
   -- [<A HREF="https://doi.org/10.1007/978-3-642-35289-8_7">doi:10.1007/978-3-642-35289-8_7</A>]['22].
   [Also search for: MacKay NN].

%A S. Chen
%A E. S. Chng
%A K. Alkadhimi
%T Regularized orthogonal least squares algorithm for constructing
   radial basis function networks
%J Int. J. Control
%V 64
%N 5
%P 829-837
%D 1996
%K jrnl, c1996, c199x, c19xx, OLS, network, NN, ANN
%X via DS and EM

%A S. Lawrence
%A C. Giles
%A A. Tsoi
%T What size neural network gives optimal generalization?
   Convergence properties of backpropagation
%R CSTR-TR-3617
%I Dept. Elec. Comp. Eng., U. Queensland
%D 1996
%K TR, TR3617, c1996, c199x, c19xx, artificial, ANN, NN, selection, neurons,
   backprop, number, selection, regularization
%O UMIACS-TR-96-22, U. Maryland
%X "... a) the complexity of the required fn approx., b) the size of the nw in
   relation to the size required for an optimal solution, and c) the degree of
   noise in the training data. In general, for a) the soln found is worse when
   the function to be approx. is more complex, for b) oversize networks can
   result in lower training and generalization error, and for c) the use of
   committee or ensemble techniques can be more beneficial as the amount of
   noise in the training data is increased. For the experiments we performed,
   we do not obtain the optimal solution in any case. We further support the
   observation that larger networks can produce better training & gen. error
   using a face recognition example where a network with many more parameters
   than training points generalizes better than smaller networks."
   (Also see backprop@[<A HREF="https://en.wikipedia.org/wiki/Backpropagation">wikip</A>]['22].)

%A R. M. Neal
%T Bayesian Learning for Neural Networks
%I Springer
%S LNS
%V 118
%D 1996
%K book, text, PhD thesis, ANN, network, MCMC, c1996, c199x, c19xx, zz0703
%X Lect Notes in Stats LNS 118, book based on his PhD thesis
  (Comp Sci., U. Tor0nt0). ppb, isbn:0387947248.
  See [<A HREF="http://www.cs.toronto.edu/~radford/bnn.1996-08-26.doc/">cs.toronto</A>][7/'03]

%A F. Gruau
%A K. Quatramaran
%T Cellular encoding for interactive evolutionary robotics
%I School of Cogn. and Comp. Sci., Uni. of Sussex
%R 425
%P 23
%D 1996
%K TR425, TR 425, genetic algorithm, GA, walk, walking robot
%X ... goal is to evolve an Artificial Neural Network (ANN)
   to control the locomotion of an 8-legged robot. ...
   ... fitness is determined on a real robot ...
   ...decrease the required number of evaluations from
   1 million to 200. ...
   [<A HREF="http://cogslib.cogs.susx.ac.uk/csr_abs.php?csrp425">abs'</A>][5/'02]
   [<A HREF="ftp://ftp.cogs.susx.ac.uk/pub/reports/csrp/csrp425.ps.Z">paper</A>][5/'02]

%A F. Gruau
%T Modular genetic neural networks for six-legged locomotion
%B Artificial Evolution
%E J.-M. Alliot et al
%I SpringerVerlag
%S LNCS
%V 1063
%D 1996
%P 201-219
%K Artificial neural networks, ANN, genetic algorithm, GA, walk, walking robot,
   six leg, legs, robots, zz0502

%A B. R. Ripley
%T Pattern Recognition and Neural Networks
%I CUP
%D 1996
%K book, text, ann, NN, network, c1996, c199x, c19xx,
   Hammersley-Clifford theorem, Markov random field, fields
%X "... Hammersley-Clifford theorem [Rip96, page 250] relates the local Markov
   property to the global property and to the potential representation. ..."

%A H. Kitano
%T Designing neural networks by genetic algorithms using
   graph generation system
%J Complex Systems J.
%V 4
%P 461-476
%D 1990
%K jrnl, GA, Lsystems, L-systems
%X from a search: ...encoding method based on context-free and
   deterministic L-systems. ... heta 2 ma- trix. In cell space encoding,
   introduced by Nolo/ and Parisi [5], the neurons are encoded with
   coordinates in a 2D space. Axon trees are grown ...
   Ref from Jon m'C

%A A. Cangelosi
%A D. Parisi
%A S. Nolfi
%T Cell division and migration in a 'genotype' for neural networks
%J Network: Computation in Neural Systems
%V 5
%N 4
%P 497-515
%D ?
%K artificial neural network, ANN, genetic algorith, GA,
   genotype, phenotype, zz0502
%X [<A HREF="http://www.tech.plym.ac.uk/soc/staff/angelo/angelo_pubs.htm">Cangelosi</A>][5/'02]

%A D. Barrios
%A D. Manrique
%A M. R. Plaza
%A J. Rios
%T An algebraic model for generating and adapting neural networks by
   means of optimization methods
%J Annals of Math. and Artificial Intell.
%V 33
%N 1
%P 93-111
%D 2001
%K jrnl, network, ANN, AI, artificial, zz0703, c2001, c200x, c20xx
%X [via a ref' report]

%A X. Zeng
%A D. S. Yeung
%T Sensitivity analysis of multilayer perceptron to input and
   weight perturbations
%I IEEE Trans. on  Neural Networks
%V 12
%N 6
%P 1358-1366
%M NOV
%D 2001
%K jrnl, ANN, Hessian, sensitivity, Hessian
%X via enesm

%A M. Sugiyama
%A H. Ogawa
%T Subspace information criterion for model selection
%J Neural Computation
%I MITpress
%V 13
%P 1863-1889
%D 2001
%K letter, SIC, c2001, c200x, c20xx, Mallow, artificial neural networks,
   network, ANN
%X "... new criterion for model selection, the subspace information criterion
   (SIC), which is a generalization of Mallows's C[L]. ..."
   [<A HREF="http://neco.mitpress.org/cgi/content/abstract/13/8/1863">@mitpress</A>]['07]

%B Simulating the Evolution of Language
%E A. Cangelosi
%E D. Parisi
%D 2002
%I Springer (London)
%K zz0502
%X 1st ed 2002, pb us$110; uk us isbn:1852334282; uk us isbn13:978-1852334284.
   [<A HREF="http://www.tech.plym.ac.uk/soc/staff/angelo/angelo_pubs.htm">Cangelosi</A>][5/'02].

%A S. B. Fogel
%T An information criterion for optimal neural network selection
%I IEEE Trans. on N.N.
%V 2
%N 5
%P SEP
%D 1991
%K jrnl, IEEE, ANN, NN, networks, nets, criteria, AIC, binary,
   classification, c1991, c199x, c19xx, zz0802
%X ... derivative of Akaike inf' criterion ....  select best ANN for
   binary classification. .... arbitrary number of classes.
   [Also search for: ANN MML].   [25 refs].

%A W. A. Wright
%T Bayesian approach to neural-network modeling with input uncertainty
%J IEEE Trans. Neural Networks
%V 10
%N 6
%P 1261-1270
%M NOV
%D 1999
%K jrnl, NN, ANN, network, noise
%X [<A HREF="http://ieeexplore.ieee.org/iel5/72/17523/00809073.pdf?isNumber=17523&prod=JNL&arnumber=00809073">www</A>][8/'02].

%A H. Attia
%T Independent factor analysis
%J Neural Computation
%V 11
%N 4
%P 803-851
%M MAY
%D 1999
%K ann, nets, IFA, c1999, c199x, c19xx
%X [<A HREF="http://research.goldenmetallic.com/">home</A>]['06].

%A S. Carrato
%T Hybrid rule-based/neural approach for segmentation of MPEG compressed video
%J Multimedia Tools and Applications
%V 18
%P 187-212
%I KluwerAcademic
%D 2002
%K jrnl, neural net, network, MPEG, NN, ANN, c2002, c200x, c20xx, uniSydney
%X IK @ uSyd as of '02.
   [<A HREF="http://www.it.usyd.edu.au/~irena/">IK home</A>]['05].

%A M. Lazaro
%A I. Santamaria
%A C. Pantaleon
%T A new EM-based training algorithm for RBF networks
%J Neural Networks
%V 16
%N 1
%P 69-77
%M JAN
%D 2003
%K jrnl, radial bassis functions, RBF, NN, RBFs, expectation maximization, EM,
   Estep, local activation, train, network, c2003, c200x, c20xx, MESFET
%X "...new [EM] algorithm which speeds up the training of feedforward networks
   with local activation functions such as the Radial Basis Function (RBF)
   network. In previously proposed approaches, at each E-step the residual is
   decomposed equally among the units or proportionally to the weights of the
   output layer. However, these approaches tend to slow down the training of
   networks with local activation units. [here] we use a new E-step which
   applies a soft decomposition of the residual among the units. In particular,
   the decoupling variables are estimated as the posterior probability of a
   component given an input-output pattern. This adaptive decomposition takes
   into account the local nature of the activation function &, by allowing the
   RBF units to focus on different subregions of the input space, the
   convergence is improved...." issn:0893-6080.
   [<A HREF="http://dx.doi.org/10.1016/S0893-6080(02)00215-0">doi:10.1016/S0893-6080(02)00215-0 </A>][4/'04]
   [<A HREF="http://www.sciencedirect.com/science/article/B6T08-47NF53K-3/2/d392a7576c48415e90ab10eb5c188ef7">sciencedirect.com</A>][4/'04]
   [<A HREF="http://gtas.dicom.unican.es/comp/Nacho/Publicaciones/Revistas/paperNN2003_pub.pdf">unican.es</A>][4/'04].

%A M. Neal
%A J. Timmis
%T Timidity: A useful mechanism for robot control?
%J Informatica
%J 27
%N 4
%P 197-204
%D 2003
%K jrnl, artificial endocrine system, AI, c2003, c200x, c20xx, zzOSP, zOSP04,
   timid, homeostasis, emotion, emotive, neural network, ANN, uniKent, aber,
   behavior, immune, AIS, robotics
%X "Responses labelled as emotional in the higher animals are frequently
   portrayed as incidental to the generation of reasonable behavior. Clearly
   this view is incompatible with the reality of animal behavior as observed in
   nature, emotion plays a significant role in the generation of useful
   behaviour. Homeostasis is the product of the interaction of the nervous,
   endocrine and immune systems. This work views emotional responses as part of
   an integrated approach to the generation of behavior in artificial organisms
   via mechanisms inspired by homeostasis. The mechanism presented here employs
   the concept of a novel Artificial Endocrine System which interacts with an
   Artificial [NN] to generate behaviour which could be classified as emotive."
   MN@aber '04; [<A HREF="http://www.cs.kent.ac.uk/pubs/2003/1635/">abs</A>][9/'04].
   Also see [<A HREF="http://www.cs.kent.ac.uk/pubs/2003/1586/content.pdf">a TR</A>]['04].

%A Y. Liu
%A X. Yao
%A T. Higuchi
%T Designing neural network ensembles by minimizing mutual information
%J Computational Intelligence in Control
%E M. Mohammadian
%E R. A. Sarker
%E X. Yao
%P 1-21
%I IdeaGroup
%D 2003
%K ANN, AI, networks, c2003, c200x, c20xx, theory
%X [<A HREF="http://www.cs.bham.ac.uk/~xin/">xin yao @ u.bham</A>]['05] -- <!-- via r o h a n --> .

%A T. Evgeniou
%A C. Michelli
%A T. Pontil
%T Learning multiple tasks with kernel methods
%J J. of Machine Learning Research
%V 6
%P 615-637
%M DEC
%D 2005
%K jrnl, eJrnl, JMLR, c2005, c200x, c20xx, zz0210, AI, kernel method, machine,
   multiple task, tasks, regularization
%X "... many related tasks simultaneously using kernel methods & regularization.
   The std single-task kernel methods, such as SVMs & reg. n/ws, are
   extended to the case of multitask learning. [we] shows that ... estimating
   many task fns with reg. can be cast as a single task learning problem if a
   family of multi-task kernel fns we define is used. These ks. model relations
   among the tasks & are derived from a novel form of regularizers. Specific ks.
   that can be used for multi-t.learning are provided & experimentally tested on
   two real data sets. ..."
   -- pdf@[<A HREF="http://jmlr.csail.mit.edu/papers/volume6/evgeniou05a/evgeniou05a.pdf">jmlr</A>]['10],
   abs@[<A HREF="http://jmlr.csail.mit.edu/papers/v6/evgeniou05a.html">jmlr</A>]['10].

%A G. E. Hinton
%A R. R. Salakhutdinov
%T Reducing the dimensionality of data with neural networks
%J Science
%V 313
%N 5786
%P 504-507
%M JUL
%D 2006
%K jrnl, c2006, c200x, c20xx, zz1115, autoencoder, neural network, NN, ANN,
   training, auto encoder, feature, features, high dimension, deep learning,
   UToronto
%X "High-dimensional data can be converted to low-d. codes by training a
   multilayer NN with a small central layer to reconstruct high-d. input
   vectors. Gradient descent can be used for fine-tuning the weights in such
   'autoencoder' networks, but this works well only if the initial weights are
   close to a good soln. We describe an effective way of initializing the
   weights that allows deep autoencoder n/ws to learn low-d. codes that work
   much better than principal components analysis as a tool to reduce the
   dimensionality of data."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1127647">doi:10.1126/science.1127647</A>]['15],
      [<A HREF="http://www.cs.utoronto.ca/~hinton/">auth1</A>][2015].
   (Also see [<A HREF="http://ufldl.stanford.edu/wiki/index.php/UFLDL_Recommended_Readings">www</A>]['15].)
   [Also search for: training deep ANN] & [also search for: autoencoder ANN].

%A Y. Bengio
%A P. Lamblin
%A P. Popovici
%A H. Larochelle
%T Greedy layer-wise training of deep networks
%J NIPS
%D 2006
%K conf, c2006, c200x, c20xx, zz1115, autoencoder, neural network, NN, ANN,
   training, auto encoder, feature, features, high dimension, deep learning,
   UMontreal
%X "Complexity theory of circuits strongly suggests that deep architectures can
   be much more efficient (sometimes exponentially) than shallow architectures,
   in terms of computational elements required to represent some fns. Deep
   multi-layer NNs have many levels of non-linearities allowing them to
   compactly represent highly non-linear & highly-varying fns. However, until
   recently it was not clear how to train such deep n/ws, since gradient-based
   optimization starting from random initialization appears to often get stuck
   in poor solns. Hinton et al. recently introduced a greedy layer-wise
   unsupervised learning alg. for Deep Belief Networks (DBN), a generative model
   with many layers of hidden causal variables. In the context of the above
   optimization problem, we study this alg. empirically & explore variants to
   better understand its success & extend it to cases where the inputs are
   cts or where the structure of the input distn is not revealing enough about
   the variable to be predicted in a supervised task. Our experiments also
   confirm the hypothesis that the greedy layer-wise unsupervised training
   strategy mostly helps the optimization, by initializing weights in a region
   near a good local minimum, giving rise to internal distributed repns that are
   high-level abstractions of the input, bringing better generalization."
   -- @[<A HREF="https://papers.nips.cc/paper/3048-greedy-layer-wise-training-of-deep-networks">nips06</A>]['15].
   (Also see [<A HREF="http://ufldl.stanford.edu/wiki/index.php/UFLDL_Recommended_Readings">www</A>]['15].)
   [Also search for: training deep ANN].

%A D. Verstraeten
%A B. Schrauwen
%A M. D'Haene
%A D. Stroobandt
%T An experimental unification of reservoir computing methods
%J Neural Networks
%V 20
%N 3
%P 391-403
%< APR
%D 2007
%K jrnl, c2007, c200x, c20xx, zz0813, AI, ANN, RNN, recurrent, Neural Network,
   recurrentNN, reservoir computing
%X "... 3 different uses of a recurrent NN (RNN) as a reservoir that is not
   trained but instead read out by a simple external class'n layer ... : Liquid
   State Machines (LSMs), Echo State nwks (ESNs) & the Backprop. Decorrelation
   (BPDC) learning rule. ... present a series of experimental results that
   compares all three ... Next, we intro. a new measure for the reservoir
   dynamics based on Lyapunov exponents. Unlike prev. measures in the lit., [it]
   is dependent on the dynamics of the reservoir in response to the inputs, &
   in the cases we tried, it indicates an optimal value for the global scaling
   of the wt matrix, irrespective of the standard measures. [&] describe the
   R.C. Toolbox that was used ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.neunet.2007.04.003">doi:10.1016/j.neunet.2007.04.003</A>]['13].
   [Also search for: RNN reservoir computing].

%A S. Timotheou
%T The random neural network: A survey
%J COMPJ
%V 53
%N 3
%P 251-267
%M MAR
%D 2010
%K jrnl, COMPJ, intro, survey, c2010, c201x, c20xx, random, artificial,
   neural network, RNN, ANN, NN, spiking behaviour, signals, neurons
%X "The random neural network (RNN) is a recurrent NN model inspired by the
   spiking behaviour of biological neuronal n/ws. Contrary to most artificial
   NN models, neurons in the RNN interact by probabilistically exchanging
   excitatory & inhibitory spiking signals. The model is described by analytical
   equns, has a low complexity supervised learning alg. & is a universal
   approximator for bounded cts fns. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxp032">doi:10.1093/comjnl/bxp032</A>]['10].
   (In a special issue on RNNs.)

%A X. Glorot
%A A. Bordes
%A Y. Bengio
%T Deep sparse rectifier neural networks
%J Proc. of the 14th Int. Conf. on AI and Stats. (AISTATS)
%O JMLR W & CP 15
%D 2011
%K conf, c2011, c201x, c20xx, zz1122, ANN, deep, NN, ReLU, softplus,  softmax,
   activation function, sparse, sparsity
%X "... This paper shows that rectifying neurons are an even better model of
   biol. neurons & yield equal or better performance than hyperbolic tangent
   nwks in spite of the hard non-linearity & non-differentiability at zero,
   ... deep rectifier nwks can reach their best performance without requiring
   any unsupervised pre-training on purely supervised tasks ..."
   -- [<A HREF="https://proceedings.mlr.press/v15/glorot11a/glorot11a.pdf">www</A>]['22].
   [Also search for: ReLu] and [also search for: softmax].
   (Also see ReLU@[<A HREF="https://en.wikipedia.org/wiki/Rectifier_(neural_networks)">wikip</A>]['22].)

%A N. Shervashidze
%A et al
%T Weisfeiler-Lehman graph kernels
%J J. of Mach. Learning Res.
%V 12
%P 2539-2561
%M NOV
%D 2011
%K jrnl, JMLR, Leman, c2011, c201x, c20xx, zz0323, graph neural network, GNN,
   NN, kernel, Weisfeiler, Lehman, label, labelled, graph, maths, test,
   isomorphism
%X "... propose a family of efficient kernels for large graphs with discrete
   node labels. Key to our method is a rapid feature extraction scheme based on
   the W.-L. test of isomorphism on graphs. It maps the original g. to a seq. of
   gs., whose node attributes capture topological & label info.. ... A family of
   kernels ... inc. a highly efficient kernel comparing subtree-like patterns.
   Its runtime scales only linearly in the # of edges of the gs. & the length of
   the W.-L. g. seq. ..."
   -- [<A HREF="https://www.jmlr.org/papers/volume12/shervashidze11a/shervashidze11a.pdf">jmlr</A>]['23].
   (Also see Gkernels@[<A HREF="https://en.wikipedia.org/wiki/Graph_kernel">wikip</A>]['23],
   and GNN@[<A HREF="https://en.wikipedia.org/wiki/Graph_neural_network">wikip</A>]['23].)
   [Also search for: graph GNN].

%A A. Coates
%A A. Karpathy
%A Andrew Y. Ng
%T Emergence of object-selective features in unsupervised feature learning
%J NIPS
%D 2012
%K conf, c2012, c201x, c20xx, zz1115, deep learning, NN, ANN,
   image, images, feature, features, cat, cats, unsupervised, StanfordU
%X "... goal of discovering high-level features from unlabeled images. ... we
   aim to test the hypothesis that unsupervised feature learning methods,
   provided with only unlabeled data, can learn high-level, invariant features
   that are sensitive to commonly-occurring objects. Though a handful of prior
   results suggest that this is possible when each object class accounts for a
   large fraction of the data (as in many labeled datasets), it is unclear
   whether something similar can be accomplished when dealing with completely
   unlabeled data. A major obstacle to this test, however, is scale: we cannot
   expect to succeed with small datasets or with small numbers of learned
   features. Here, we propose a large-scale feature learning system that enables
   us to carry out this experiment, learning 150,000 features from tens of
   millions of unlabeled images. Based on two scalable clustering algs. (K-means
   & agglomerative clustering), we find that our simple system can discover
   features sensitive to a commonly occurring object class (human faces) & can
   also combine these into detectors invariant to significant global distortions
   like large translations & scale."
   -- @[<A HREF="http://papers.nips.cc/paper/4497-emergence-of-object-selective-features-in-unsupervised-feature-learning">nips</A>]['15].
   (Also see AN@[<A HREF="https://en.wikipedia.org/wiki/Andrew_Ng">wikip</A>]['15].)
   [Also search for: deep learning ANN].

%A D. P. Kingma
%A J. Lei Ba
%T ADAM: A method for stochastic optimization
%J arXiv
%M JAN
%D 2014
%O ICLR 2015
%K conf, c2014, c201x, c20xx, zz1122, deep, NN, ANN, ADAM, training,
   stochastic optimization, optimisation, optimizer, optimiser,
   gradient descent, AdaMax
%X "... first-order gradient-based optimization based on adaptive ests. of
   lower-order moments. ... We also analyze the theoretical convergence
   properties ... Empirical results demonstrate that Adam works well in
   practice ..."  [via DS]
   -- 1412.6980@[<A HREF="https://arxiv.org/abs/1412.6980">arXiv</A>]['22].

%A N. Tishby
%A N. Zaslavsky
%T Deep learning and the information bottleneck principle
%J arXiv
%M MAR
%D 2015
%O invited talk, IEEE Information Theory Workshop (ITW), 2015
%K TR, c2015, c201x, c20xx, zz0118, NN, ANN, DNN, layers, information,
   bottleneck, deep learning
%X "Deep Neural Networks (DNNs) are analyzed via the theoretical  of the
   information bottleneck (IB) principle. We first show that any DNN can be
   quantified by the mutual info. between the layers & the input & output
   variables. Using this repn we can calculate the optimal info.theoretic limits
   of the DNN & obtain finite sample generalization bounds. The advantage of
   getting closer to the theoretical limit is quantifiable both by the
   generalization bound & by the n/wk's simplicity. We argue that both the
   optimal architecture, # of layers & features/connections at each layer, are
   related to the bifurcation points of the info.bottleneck tradeoff, namely,
   relevant compression of the input layer with respect to the output layer. The
   hierarchical repn at the layered n/wk naturally corr.to the structural phase
   transitions along the information curve. We believe that this new insight can
   lead to new optimality bounds & deep learning algorithms."
   -- 1503.02406@[<A HREF="https://arxiv.org/abs/1503.02406">arXiv</A>]['17].
   [Also search for: Tishby ANN].

%A R. K. Srivastava
%A K. Greff
%A J. Schmidhuber
%T Training very deep networks
%J arXiv
%M JUL
%P pp.9
%D 2015
%K TR, c201, c201x, c20xx, zz0715, deep learning, ANN, ANNs, NN, NNs, network,
   training, recurrentNN, LSTM
%X "... training of v.deep n/wks remains an open problem. ... introduce a new
   architecture designed to overcome this. Our so-called highway n/wks allow
   unimpeded info. flow across many layers on info. highways. They are inspired
   by Long Short-Term Memory recurrent n/wks & use adaptive gating units to
   regulate the info. flow. Even with hundreds of layers, highway n/wks can be
   trained directly through simple gradient descent. This enables the study of
   extremely deep & efficient architectures."
   -- 1507.06228@[<A HREF="http://arxiv.org/abs/1507.06228">arXiv</A>]['15].
   [Also search for: training deep ANN].

%A D. Silver
%A et al ...
%A D. Hassabis
%T Mastering the game of Go with deep neural networks and tree search
%J Nature
%V 529,
%P 484-489
%M JAN
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0216, AI, ANN, NN, artificial neural network,
   reinforcement learning, Go, Fan Hui, game, policy, value,
   google, DeepMind, AlphaGo
%X "... introduce a new approach to computer Go that uses 'value networks' to
   to evaluate board posns & 'policy networks' to select moves. These deep NNs
   are trained by a novel combination of supervised learning from human expert
   games, & reinforcement learning from games of self-play. Without any
   lookahead search, the NNs play Go at the level of state-of-the-art Monte
   Carlo tree search programs that simulate thousands of random games of
   self-play. We also introduce a new search alg. that combines MC simulation
   with value & policy n/wks. ... our program AlphaGo achieved a 99.8% winning
   rate against other Go programs, & defeated the human European Go champion by
   5 games to 0. This is the first time that a computer program has defeated a
   human professional player in the full-sized game of Go, a feat prev. thought
   to be at least a decade away."  [62 refs.]
   -- [<A HREF="http://dx.doi.org/10.1038/nature16961">doi:10.1038/nature16961</A>]['16].
   (Also see RL@[<A HREF="https://en.wikipedia.org/wiki/Reinforcement_learning">wikip</A>]['22].)
   [Also search for: AI Go game].

%A M. Fraccaro
%A S. K. Sonderby
%A U. Paquet
%A O. Winther
%T Sequential neural models with stochastic layers
%J arXiv
%M MAY
%D 2016
%O NIPS 2016
%K TR, c2016, c201x, c20xx, zz1016, NN, ANN, deepmind, deep learning,
   Blizzard, TIMIT, speech, model, modelling, music
%X "How can we efficiently propagate uncertainty in a latent state repn with
   recurrent neural networks? ... introduces stochastic recurrent NNs which glue
   a deterministic recurrent NN & a state space model together to form a
   stochastic & sequential neural generative model. The clear separation of
   deterministic & stochastic layers allows a structured variational inference
   network to track the factorization of the model's posterior distn. By
   retaining both the nonlinear recursive structure of a recurrent NN &
   averaging over the uncertainty in a latent path, like a state space model, we
   improve the state of the art results on the Blizzard & TIMIT speech modeling
   data sets by a large margin, while achieving comparable performances to
   competing methods on polyphonic music modeling"
   -- 1605.07571@[<A HREF="https://arxiv.org/abs/1605.07571">arXiv</A>]['16].
   (Also see deepmind@[<A HREF="https://deepmind.com/">www</A>]['16].)

%A T. Kojima
%A et al
%T Large language models are zero-shot reasoners
%J arXiv
%M MAY
%D 2022
%K TR, AI, c2022, c202x, c20xx, zz1022, NN, ANN, large language model, LLM,
   LarLangM, natural, reasoner, MultiArith, GSM8K, AQUA-RAT, SVAMP, GSM8K
%X '... we show that LLMs are decent zero-shot reasoners by simply adding
   "Let's think step by step" before each answer. Experimental results demo.
   that our Zero-shot-CoT, using the same single prompt template, sig.
   outperforms zero-shot LLM performances on diverse benchmark reasoning tasks
   inc. arithmetics (MultiArith, GSM8K, AQUA-RAT, SVAMP), symbolic reasoning
   (Last Letter, Coin Flip), & other logical reasoning tasks (Date
   Understanding, Tracking Shuffled Objects), without any hand-crafted few-shot
   examples, e.g. increasing the accuracy on MultiArith from 17.7% to 78.7% &
   GSM8K from 10.4% to 40.7% with 175B parameter InstructGPT model, as well as
   similar magnitudes of improvements with another off-the-shelf large model,
   540B parameter PaLM ...'
   -- 2205.11916@[<A HREF="https://arxiv.org/abs/2205.11916">arXiv</A>]['22].
   [Also search for: large language model].
   (Does no one worry about "175B parameter[s]"?)

%A K. Gregor
%A F. Besse
%A D. Jimenez Rezende
%A I. Danihelka
%A D. Wierstra
%T Towards conceptual compression
%J NIPS
%D 2016
%K conf, NIPS, NIPS29, NN, ANN, c2016, c201x, c20xx, zz0220, image, images,
   representation, concept, abstraction, compress, compression
%X "We introduce convolutional DRAW, a homogeneous deep generative model
   [for] latent variable image modeling. The alg. naturally stratifies info.
   into higher & lower level details, creating abstract features & as such
   addressing one of the fundamentally desired properties of representation
   learning. [&] the hierarchical ordering of its latents creates the
   opportunity to selectively store global info. about an image, yielding a high
   quality 'conceptual compression' framework."
   -- [<A HREF="http://papers.nips.cc/paper/6542-towards-conceptual-compression">www</A>]['20],
      1604.08772@[<A HREF="https://arxiv.org/abs/1604.08772">arXiv</A>]['20].

%A A. Graves
%A et al ...
%A D. Hassibis
%T Hybrid computing using a neural network with dynamic external memory
%J Nature
%V 538
%P 471-476
%M OCT
%D 2016
%K jrnl, c2016, c201x, c20xx, zz1016, DeepMind, ANN, NN, hybrid computer,
   differentiable neural computer, DNC
%X "... introduce a machine learning model called a differentiable neural
   computer (DNC), which consists of a neural network that can read from & write
   to an external memory matrix, analogous to the random-access memory in a
   conventional computer. ... When trained with supervised learning, we
   demonstrate that a DNC can successfully answer synthetic questions designed
   to emulate reasoning & inference problems in natural language. We show that
   it can learn tasks such as finding the shortest path between specified
   points & inferring the missing links in randomly generated graphs, & then
   generalize these tasks to specific graphs such as transport networks & family
   trees. When trained with reinforcement learning, a DNC can complete a moving
   blocks puzzle in which changing goals are specified by sequences of
   symbols. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature20101">doi:10.1038/nature20101</A>]['16].
   [Also search for: deep learning NN].

%A D. Bahdanau
%A K. Cho
%A Y. Bengio
%T Neural machine translation by jointly learning to align and translate
%M MAY
%D 2016
%K TR, c2016, c201x, c20xx, zz0824, ANN, NN, natural language, translation,
   encoder, decoder, chatBot, transformerNN
%X "Neural machine translation is a recently proposed approach to m/c trans..
   Unlike the traditional statistical m/c translation, the neural m/c
   translation aims at building a single NN that can be jointly tuned to
   maximize the translation performance. ... we conjecture that the use of a
   fixed-length vector is a bottleneck in improving the performance of this
   basic encoder-decoder architecture ..."
   -- [<A HREF="https://arxiv.org/abs/1409.0473">arxiv:1409.0473</A>]['24].
   Also see transf@[<A HREF="https://en.wikipedia.org/wiki/Transformer_(deep_learning_architecture)">wikip</A>]['24].

%A R. Shwartz-Ziv
%A N. Tishby
%T Opening the black box of deep neural networks via information
%J arXiv
%M MAR
%D 2017
%K TR, c2017, c201x, c20xx, zz0317, deep learning, NN, ANN, DNN DNNs, layers,
   hidden, Tishby, Zaslavsky, stochastic gradient descent, SGD
%X "... still no comprehensive theoretical understanding of learning with Deep
   Neural Networks (DNNs) or their inner organization. Previous work [Tishby &
   Zaslavsky (2015)] proposed to analyze DNNs in the Information Plane; i.e.,
   the plane of the Mutual Information values that each layer preserves on the
   input & output variables. They suggested that the goal of the n/w is to
   optimize the Info. Bottleneck (IB) tradeoff between compression & prediction,
   successively, for each layer.  ... we ... demonstrate the effectiveness of
   the Information-Plane visualization of DNNs. ... show that the stochastic
   gradient descent (SGD) epochs have two distinct phases: fast empirical error
   minimization followed by slow representation compression, for each layer. ...
   argue that the DNN layers end up v.close to the IB theor. bound, & present a
   new theor. argument for the comp. benefit of the hidden layers."
   -- 1703.00810@[<A HREF="https://arxiv.org/abs/1703.00810">arXiv</A>]['17].

%A A. Vaswani
%A et al
%T Attention is all you need
%J NIPS
%D 2017
%O arXiv 6/2017 ... 12/2017
%K conf, NIPS, neurips, c2017, c201x, c20xx, zz0723, NN, ANN, AI, recurrent,
   convolutional, neural network, sequence transduction, attention, transformer,
   transformerNN, recurrentNN, encoder, decoder, translation
%X "The dominant seq. transd'n models are based on complex recurrent or
   convolutional NNs that inc. an encoder & a decoder. The best performing
   models also connect the encoder & decoder through an attention mechanism. We
   propose a new simple n/wk architecture, the Transformer, based solely on
   attention mechanisms, dispensing with recurrence & convolutions entirely.
   Experiments on two machine translation tasks show these models to be superior
   in quality while being more parallelizable & requiring sig. less time to
   train. Our model achieves 28.4 BLEU on the WMT 2014 English- to-German
   translation task, improving over the existing best results, inc. ensembles,
   by over 2 BLEU. On the WMT 2014 English-to-French translation task, our model
   establishes a new single-model state-of-the-art BLEU score of 41.0 after
   training for 3.5 days on eight GPUs, a small fraction of the training costs
   of the best models from the literature."
   -- 1706.03762@[<A HREF="https://arxiv.org/abs/1706.03762">arXiv</A>]['23],
    & [<A HREF="https://proceedings.neurips.cc/paper_files/paper/2017/file/3f5ee243547dee91fbd053c1c4a845aa-Paper.pdf">neurips</A>]['23].
   (Also see Transformer@[<A HREF="https://en.wikipedia.org/wiki/Transformer_(machine_learning_model)">wikip</A>]['23].)

%A L. Kaiser
%A A. N. Gomez
%A N. Shazeer
%A A. Vaswani
%A N. Parmar
%A L. Jones
%A J. Uszkoreit
%T One model to learn them all
%J arXiv
%M JUN
%D 2017
%K TR, c2017, c201x, c20xx, zz0118, NN, ANN, AI, II, convolutional layer,
   layers, deep learning, ImageNet, COCO, google
%X "... present a single model that yields good results on a # of problems
   spanning multiple domains. In particular, this single model is trained
   concurrently on ImageNet, multiple translation tasks, image captioning
   (COCO dataset), a speech recognition corpus, & an English parsing task. Our
   model architecture incorporates building blocks from multiple domains. It
   contains convolutional layers, an attention mechanism, & sparsely-gated
   layers. Each of these computational blocks is crucial for a subset of the
   tasks we train on. Interestingly, even if a block is not crucial for a task,
   we observe that adding it never hurts performance & in most cases improves it
   on all tasks. We also show that tasks with less data benefit largely from
   joint training with other tasks, while performance on large tasks degrades
   only slightly if at all."
   -- 1706.05137@[<A HREF="https://arxiv.org/abs/1706.05137">arXiv</A>]['18].
   (auth1@[<A HREF="https://research.google.com/pubs/LukaszKaiser.html">go'gle</A>],
    auth2@[<A HREF="https://aidangomez.ca">www</A>]['18].)

%A A. Krizhevsky
%A I. Sutskever
%T ImageNet classification with deep convolutional neural networks
%J CACM
%M JUN
%D 2017
%K jrnl, CACM, c2017, c201x, c20xx, zz0822, deep NN, ANN, Alexnet, ImageNet,
   image processing, convolutional neural network, training
%X "We trained a large, deep convolutional neural network to classify the 1.2
   million high-res. images in the ImageNet LSVRC-2010 contest into the 1000
   different classes. ..."
   -- [<A HREF="https://doi.org/10.1145/3065386">doi:10.1145/3065386</A>]['22].
   Also see, "... AlexNet competed in the ImageNet Large Scale Visual
   Recognition Challenge on Sep.30, 2012. The n/wk achieved a top-5 error of
   15.3%, more than 10.8 percentage pts lower than that of the runner up. ..."
   -- AN@[<A HREF="https://en.wikipedia.org/wiki/AlexNet">wikip</A>]['22].
   [Also search for: deep NN ANN]  and  [also search for: training NN].

%A E. Nyquist
%T New theory cracks open the black box of deep learning
%J Quanta
%M SEP
%D 2017
%K mag, news, views, c2017, c201x, c20xx, zz0118, NN, ANN, deep learning,
   information, dog
%X "A new idea called the 'information bottleneck' is helping to explain the
   puzzling success of today's artificial-intelligence algorithms - and might
   also explain how human brains learn. ..."
   -- [<A HREF="https://www.quantamagazine.org/new-theory-cracks-open-the-black-box-of-deep-learning-20170921/">www</A>]['18].
   [Also search for: information bottleneck ANN]  and, as always, be sceptical.

%A D. Silver
%A et al
%T Mastering the game of Go without human knowledge
%J Nature
%P 354-359
%N 7676
%V 550
%M OCT
%D 2017
%K jrnl, c2017, c201x, c20xx, zz1017, AI, Alpha, AlphaGo Zero, Go, NN, ANN,
   play, learning, learn, reinforcement
%X "...  Here we introduce an alg. based solely on reinforcement learning,
   without human data, guidance or domain knowledge beyond game rules. AlphaGo
   becomes its own teacher: a neural network is trained to predict AlphaGo's own
   move selections & also the winner of AlphaGo's games. This NN improves the
   strength of the tree search, resulting in higher quality move selection &
   stronger self-play in the next iteration. Starting tabula rasa, our new
   program AlphaGo Zero achieved superhuman performance, winning 100-0 against
   the previously published, champion-defeating AlphaGo."
   -- [<A HREF="https://doi.org/10.1038/nature24270">doi:10.1038/nature24270</A>]['17].
   (Also see RL@[<A HREF="https://en.wikipedia.org/wiki/Reinforcement_learning">wikip</A>]['22].)
   [Also seach for: AI Go game].

%A N. Ketkar
%T Introduction to PyTorch
%J Deep Learning with Python
%A Apress
%P 195-208
%M OCT
%D 2017
%K chapter, intro, survey, c2017, c201x, c20xx, zz1122, deep, NN, ANN, PyTorch,
   Python, Torch, Lua
%X "... we will cover PyTorch which is a more recent addition to the ecosystem
   of the deep learning fwk. PyTorch can be seen as a Python front end to the
   Torch engine (which initially only had Lua bindings) which at its heart
   provides the ability to define math. fns & compute their gradients. PyTorch
   has fairly good Graphical Processing Unit (GPU) support & is a fast-maturing
   framework."
   -- [<A HREF="https://doi.org/10.1007/978-1-4842-2766-4_12">doi:10.1007/978-1-4842-2766-4_12</A>]['22] in isbn13:978-1484227657 ...
   deep, training, feed forward, Theano, ..., Keras, TensorFlow, ...
   -- [<A HREF="https://doi.org/10.1007/978-1-4842-2766-4">doi:10.1007/978-1-4842-2766-4</A>]['22].
   Also see [<A HREF="https://pytorch.org/">pytorch</A>]['22].
   [Also search for: Python NN].

%A R. Vidal
%A J. Bruna
%A R. Giryes
%A A. Soatto
%T Mathematics of deep learning
%J arXiv
%M DEC
%D 2017
%K TR, c2017, c201x, c20xx, zz1217, tute, intro, ANN, NN, deep learning,
   neural net
%X "... dramatic increase in the performance of recognition systems due to the
   introduction of deep architectures for representation learning and
   classification. However, the mathematical reasons for this success remain
   elusive. This tutorial will review recent work that aims to provide a
   mathematical justification for several properties of deep networks, such as
   global optimality, geometric stability, and invariance of the learned
   representations."
   -- 1712.04741@[<A HREF="https://arxiv.org/abs/1712.04741">arXiv</A>]['17].

%A V. Mullachery
%A A. Khera
%A A. Husai
%T Bayesian neural networks
%J arXiv
%M JAN
%D 2018
%K TR, c2018, c201x, c20xx, zz0118, NN, ANN, network, PyMC3, Edward, Stan
%X "... BNNs are comprised of a Probabilistic Model and a Neural n/wk. ... to
   combine the strengths of Neural n/wks & Stochastic modeling. Neural n/wks
   exhibit continuous fn approximator capabilities. Stochastic models allow
   direct spec. of a model with known interaction between parameters to generate
   data. During the prediction phase, stochastic models generate a complete
   posterior distribution & produce probabilistic guarantees on the predictions.
   Thus BNNs are a unique combination of neural network & stochastic models with
   the stochastic model forming the core of this integration. BNNs can then
   produce probabilistic guarantees on it's predictions & also generate the
   distribution of parameters that it has learnt from the observations. That
   means, in the parameter space, one can deduce the nature & shape of the
   neural n/wk's learnt parameters. These two characteristics makes them highly
   attractive to theoreticians as well as practitioners. Recently there has been
   a lot of activity in this area, with the advent of numerous probabilistic
   programming libraries such as: PyMC3, Edward, Stan etc. ..."
   -- 1801.07710@[<A HREF="https://arxiv.org/abs/1801.07710">arXiv</A>]['18].
   [Also search for: Bayesian neural network].

%A S. Skansi
%T Introduction to Deep Learning: From Logical Calculus to
   Artificial Intelligence
%I SpringerVerlag
%S Undergrad. Topics in Comp. Sci.
%P 191
%M FEB
%D 2018
%K intro, book, text, c2018, c201x, c20xx, zz0418, AI, deep learning, ANN, NN,
   convolutional, LSTM, Word2vec, RBM, DBN
%X 1st ed 2018; pb us$44; uk us isbn:3319730037; uk us isbn13:978-3319730035.
   "... coverage includes convolutional networks, LSTMs, Word2vec, RBMs,
   DBNs, neural Turing machines, memory networks and autoencoders. ..."

%A D. Cer
%A et al
%T Universal sentence encoder
%J arXiv
%M MAR
%D 2018
%K TR, c2018, c201x, c20xx, zz0822, Universal Sentence Encoder, NN, ANN,
   sentences, similarity, natural language processing, NLP, text, embedding,
   vector, 512 dimensions, space, WEAT, TFhub, word2vec, word, words, embed,
   vectors, dimension, decoder, viaErikN
%X "... encoding sentences into embedding vectors that specifically target
   transfer learning to other NLP tasks. The models are efficient & result in
   accurate performance on diverse transfer tasks. ... investigate & report the
   relationship between model complexity, resource consumption, the availability
   of transfer task training data, and task performance. ..."
   -- 1803.11175@[<A HREF="https://arxiv.org/abs/1803.11175">arXiv</A>]['22], via ErikN.
   Also see USE@[<A HREF="https://www.tensorflow.org/hub/tutorials/semantic_similarity_with_tf_hub_universal_encoder">TensorFlow</A>]['22]
    & TF@[<A HREF="https://github.com/tensorflow">g'thub</A>]['22].
   [Also search for: natural language NN].

%A J. Howard
%A S. Ruder
%T Universal language model fine-tuning for text classification
%J arXiv
%M MAY
%D 2018
%O ACL 2018
%K TR, c2018, c201x, c20xx, zz1123, AI, large language model, LLM, LarLangM,
   NN, ANN, Jeremy Howard, ULMFiT, chatGPT
%X "... propose Universal Language Model Fine-tuning (ULMFiT), an effective
   transfer learning method that can be applied to any task in NLP, & introduce
   techniques that are key for fine-tuning a l.model. Our method sig.
   outperforms the state-of-the-art on six text classn tasks, reducing the error
   by 18-24% on the majority of datasets. [&], with only 100 labeled examples,
   it matches the performance of training from scratch on 100x more data. We
   open-source our pretrained models & code."
   -- [<A HREF="https://arxiv.org/abs/1801.06146">arxiv:1801.06146</A>]['23].
   (*Also see [<A HREF="https://www.abc.net.au/news/science/2023-11-15/jeremy-howard-taught-ai-to-the-world-and-helped-invent-chatgpt/103092474">ABC</A>][15/11/2023].*)
   [Also search for: LarLangM].

%A M. Alber
%A I. Bello
%A B. Zoph
%A P.-J. Kindermans
%A P. Ramachandran
%A Q. Le
%T Backprop evolution
%K arXiv
%M AUG
%D 2018
%K TR, c2018, c201x, c20xx, zz0818, AI, ANN, NN, backpropagation, backProp,
   deep learning, algorithm, intro, survey
%X "The back-propagation alg. is the cornerstone of deep learning. Despite its
   importance, few variations of [it] have been attempted. This work presents an
   approach to discover new variations of the back-propagation eqn. We use a
   domain specific language to describe update equns as a list of primitive
   fns. An evolution-based method is used to discover new propagation rules that
   maximize the generalization performance after a few epochs of training. We
   find several update equns that can train faster with short training times
   than std b.-p., & perform similar as standard b.-p. at convergence."
   -- 1808.02822@[<A HREF="https://arxiv.org/abs/1808.02822">arXiv</A>]['18].
   (Also see backprop@[<A HREF="https://en.wikipedia.org/wiki/Backpropagation">wikip</A>]['22].)

%A Fei Wang
%A et al ...
%A T. Rompf
%T Demystifying differentiable programming: Shift/reset the penultimate
   backpropagator
%J arXiv
%M MAR
%D 2018
%O Proc. of the ACM on Prog. Langs., vol.3, #96, pp.1-31, Aug. 2019
%K TR, c2018, c201x, c20xx, zz0922, NN, ANN, backprop, backpropagation,
   automatic differentiation, forward, reverse, training, tensorFlow
%X "... [DL] rests in crucial ways on gradient-descent opt'n & the ability to
   learn params. of a NN by backprop'ng observed errors. [but] NN architectures
   are growing increasingly sophisticated & diverse, which motivates an emerging
   quest for even more general forms of differentiable programming, where arb.
   parameterized computations can be trained by gradient descent. ... we take a
   fresh look at auto.differentiation (AD) techniques, & especially aim to
   demystify the reverse-mode form of AD that generalizes backprop. in NNs. We
   uncover a tight connection between reverse-mode AD & delimited continuations,
   which permits implementing reverse-mode AD purely via operator overloading &
   without any auxiliary data structs.. [&] show how this formulation of AD can
   be fruitfully combined with multi-stage programming (staging), leading to a
   highly efficient impl'n that combines the performance benefits of deep
   learning frameworks based on explicit reified computation graphs (e.g.,
   TensorFlow) with the expressiveness of pure library approaches (e.g.,
   PyTorch)."
   -- 1803.10228@[<A HREF="https://arxiv.org/abs/1803.10228">arXiv</A>]['22],
   or [<A HREF="https://doi.org/10.1145/3341700">doi:10.1145/3341700</A>]['22].
   (Also see AD@[<A HREF="https://en.wikipedia.org/wiki/Automatic_differentiation">wikip</A>]['22].)
   [Also search for: automatic differentiation].

%A Keyulu Xu
%A et al
%T How powerful are graph neural networks?
%J arXiv
$M OCT
%D 2018
%K TR, c2018, c201x, c20xx, zz1122, graph, NN, network, ANN, GNN, Weisfeiler,
   Lehman, Leman
%X "... GNNs follow a neighborhood aggregation scheme, where the rep'n vector of
   a node is computed by recursively aggregating & transforming rep'n vectors of
   its neighboring nodes. Many GNN variants have been proposed & have achieved
   state-of-the-art results on both node & graph classification tasks. ... Here,
   we present a theoretical framework for analyzing the expressive power of GNNs
   to capture different g.structures. ... Graph Convolutional Netwks & GraphSAGE
   ... cannot learn to distinguish certain simple graph structures. ... then
   develop a simple arch. that is provably the most expressive among the class
   of GNNs & is as powerful as the Weisfeiler-Lehman g.isomorphism test..."
   -- 1810.00826@[<A HREF="https://arxiv.org/abs/1810.00826">arXiv</A>]['22].
   (Also see GNN@[<A HREF="https://en.wikipedia.org/wiki/Graph_neural_network">wikip</A>]['22].)
   [Also search for: graph GNN].

%A P. G. Breen
%A C. N. Foley
%A T. Boekholt
%A S. Portegies Zwart
%T Newton vs the machine: solving the chaotic three-body problem using
   deep neural networks
%J arXiv
%M OCT
%D 2019
%K TR, c2019, c201x, c20xx, zz1220, deep, ANN, NN, three body problem, gravity
%X "... We show that an ensemble of solns obtained using an arbitrarily precise
   numerical integrator can be used to train a deep ANN that, over a bounded
   time interval, provides accurate solns at fixed computational cost & up to
   100 million times faster than a state-of-the-art solver. ... provide evidence
   that, for computationally challenging regions of phase-space, a trained ANN
   can replace existing numerical solvers ..."
   -- 1910.07291@[<A HREF="https://arxiv.org/abs/1910.07291">arXiv</A>]['20].

%A Swayambhoo Jain
%A et al
%T Low rank based end-to-end deep neural network compression
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, MolBio, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, NN, ANN, DNN,
   compress, simplify
%X "Deep neural networks (DNNs), despite their performance on a wide variety of
   tasks, are still out of reach for many applications as they require sig.
   comp'l resources. ... we present a low-rank based end-to-end deep NN
   compression frame-work with the goal of enabling DNNs performance to
   computationally constrained devices.The proposed framework includes
   techniques for low-rank based structural approx'n, quantization & lossless
   arith.coding. Many of these techniques have been accepted in the MPEG working
   draft on compressed NN Representations. We demonstrate the efficacy of the
   proposed framework via extensive experiments on a variety of DNNs for various
   tasks considered in this standardization activity. These techniques provide
   impressive performance on DNNs used in ImageNet Large-Scale Visual
   Recognition Challenge by compressing VGG16 by 61x, ResNet50 by almost 15x, &
   MobileNetV2 by almost 7x.
   -- [<A HREF="https://doi.org/10.1109/DCC50243.2021.00031">doi:10.1109/DCC50243.2021.00031</A>]['21].
   [Also search for: DCC21].

%A M. Soltani
%A et al
%T Compressing deep networks using Fisher score of feature maps
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, MolBio, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, NN, ANN, DNN,
   deep, neural network, compress, simplify, map
%K conf, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, NN, ANN,
   simplification, compress
%X "... propose a new structural technique for pruning deep neural networks with
   skip-connections. ... based on measuring the importance of feature maps in
   predicting the output of the model using their Fisher scores. These scores
   subsequently used for removing the less informative layers from the graph of
   the n/w. Extensive experiments on the classification of CIFAR-10, CIFAR-100,
   & SVHN data sets demonstrate the efficacy of our compressing method both in
   the # of parameters & operations.
   -- [<A HREF="https://doi.org/10.1109/DCC50243.2021.00083">doi:10.1109/DCC50243.2021.00083</A>]['21].
   [Also search for: DCC21].

%A Y. Idelbayev
%A M. A. Carreira-Perpinan
%T Neural network compression via additive combination of reshaped, low-rank
   matrices
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, NN, ANN,
   simplification, compress
%X "... NN compression has become an important problem due to the increasing
   necessity of running complex networks on small devices. We consider a form of
   n/wk compression that has not been explored before: an additive combination
   of reshaped low-rank matrices. That is, given the weights of a NN, we
   constrain them as a sum of differently shaped low-rank matrices to reduce the
   n/wk's size & inference demands. Computationally, this is a hard problem ...
   We formulate it as a model selection over the family of compressed models &
   give an optimization alg. that efficiently handles the inherent
   combinatorial structure. This results in a 'Learning-Compression' alg. which
   alternates between a std machine learning step & a step involving signal
   compression.  We demonstrate the effectiveness of the proposed  compression
   scheme & the corr. alg. on multiple networks and datasets."
   -- [<A HREF="https://doi.org/10.1109/DCC50243.2021.00032">doi:10.1109/DCC50243.2021.00032</A>]['21].
   [Also search for: DCC21].

%A L. V. Jospin
%A H. Laga
%A F. Boussaid
%A W. Buntine
%A M. Bennamoun
%T Hands-on Bayesian neural networks - A tutorial for deep learning users
%J IEEE Comp. Intel. Mag.
%V 17
%N 2
%P 29-48
%D 2022
%K intro, tute, c2022, c202x, c20xx, zz0822, deep, NN, ANN, training,
   prediction, regularization
%X "... since deep learning methods operate as black boxes, the uncertainty
   assoc. with their pred'ns is often challenging to quantify. B.statistics
   offer a formalism to understand & quantify the uncertainty assoc. with deep
   NN pred'ns. This tutorial provides [DL] practitioners with an overview of the
   relevant lit. & a complete toolset to design, implement, train, use &
   evaluate BNNs, i.e., stochastic ANNs trained using B.methods."
   -- 2007.06823@[<A HREF="https://arxiv.org/pdf/2007.06823">arXiv</A>]['22].

%T Keras
%D 2022
%K TR, c2022, c202x, c20xx, zz1122, Keras, Python, deep, NN, ANN, TensorFlow
%X ? Keras, 2018-ish onwards ?
   "Keras is an open-source software library that provides a Python interface
   for ANNs ... As of version 2.4, only TensorFlow is supported ..."
   -- Keras@[<A HREF="https://en.wikipedia.org/wiki/Keras">wikip</A>]['22].
   Also see [<A HREF="https://keras.io">keras.io</A>]['22].
   [Also search for: Python NN].

%A Ningyuan Huang
%A S. Villar
%T A short tutorial on the Weisfeiler-Lehman test and its variants
%J arXiv
%M JAN
%D 2022
%O IEEE Int. Conf. on Acoustics, Speech and Signal Proc. (ICASSP) 2021
%K TR, Leman, c2022, c202x, c20xx, zz0323, graph, graphs, maths, NN, GNN
%X "GNNs are designed to learn fns on graphs. Typically, the relevant target fns
   are invariant with respect to actions by permutations. ... The WL test can be
   generalized to a hierarchy of higher-order tests, known as k-WL. ... The goal
   of this short note is pedagogical & practical: We explain the differences
   between the WL & folklore-WL formulations ... literature. We illuminate the
   differences between the formulations by visualizing an example."
   -- [<A HREF="https://doi.org/10.48550/arXiv.2201.07083">arXiv</A>]['23],
   and [<A HREF="https://doi.org/10.1109/ICASSP39728.2021.9413523">conf</A>]['23].
   (Also see GNN@[<A HREF="https://en.wikipedia.org/wiki/Graph_neural_network">wikip</A>]['23].)
   [Also search for: graph GNN].

%A T. Le Scao
%A et al
%T What language model to train if you have one million GPU hours?
%J arXiv
%M OCT
%D 2022
%K TR, AI, c2022, c202x, c20xx, zz0322, chatbot, BLOOM, NN, ANN, transformer,
   transformerNN, openSource, openscience, chat gpt, chatgpt
%X "... In the process of building BLOOM - the Big Science Large Open-science
   Open-access Multilingual language model - our goal is to identify an
   architecture & training setup that makes the best use of our 1,000,000
   A100-GPU-hours budget.... billion-parameter scale ..."
   -- [<A HREF="https://doi.org/10.48550/arXiv.2210.15424">arXiv</A>]['23],
      BigScience [<A HREF="https://huggingface.co/bigscience">www</A>]['23].
   Also see BLOOM@[<A HREF="https://en.wikipedia.org/wiki/BLOOM_(language_model)">wikip</A>]['23].
   (NB. "OpenAI" isn't open source.)

%A Yujia Li
%A et al ...
%A O. Vinyals
%T Competition-level code generation with AlphaCode
%J Science
%V 378
%N 6624
%P 1092-1097
%M DEC
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1222, AlphaCode, ANN, NN, programming,
   transformer, transformerNN, Codeforces
%X "... we introduce AlphaCode, a system for code gen. that achieved an avg
   ranking in the top 54.3% in simulated eval'ns on recent programming comps. on
   the Codeforces platform. AlphaCode solves problems by generating millions of
   diverse programs using specially trained transformer-based networks & then
   filtering & clustering those programs to a max. of just 10 submissions. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abq1158">doi:10.1126/science.abq1158</A>]['22].

%A S. Damadi
%A G. Moharrer
%A M. Cham
%T The backpropagation algorithm for a math student
%J arXiv
%M JAN
%D 2023
%K TR, c2023, c202x, c20xx, zz0123, NN, ANN, deep, DNN, backpropagation,
   backprop, Jacobian
%X "... The (BP) alg. leverages the composite structure of the DNN to
   efficiently compute the gradient. [so] the # of layers in the network does
   not sig. impact the complexity of the calculation. The objective of this
   paper is to express the gradient of the loss fn in terms of a matrix
   multiplication using the Jacobian operator. This can be achieved by
   considering the total derivative of each layer wrt its parameters &
   expressing it as a J.matrix. The gradient can then be represented as the
   matrix product of these J.matrices. ..."
   -- 2301.09977@[<A HREF="https://arxiv.org/abs/2301.09977">arXiv</A>]['23].
   [Also search for: backpropagation NN].

%T GPT-4 Technical Report
%J arXiv
%M MAR
%D 2023
%K TR, c2023, c202x, c20xx, zz0323, chatGPT, chatGPT4, chat GPT 4, GPT4, NN,
   chatbot, transformer, transformerNN, ANN, OpenAI, text, words, images, Hinton
%X "... GPT-4 exhibits human-level performance on various professional &
   academic benchmarks, inc. passing a simulated bar exam with a score around
   the top 10% ... Transformer-based model pre-trained to predict the next token
   in a document. The post-training alignment process results in improved
   performance on measures of factuality & adherence to desired behavior. ...
   [can] accurately predict some aspects of GPT-4's performance based on models
   trained with no more than 1/1,000th the compute of GPT-4."  (99p.)
   -- 2303.08774@[<A HREF="https://doi.org/10.48550/arXiv.2303.08774">arXiv</A>]['23].
   (NB. GPT="generative pre-trained transformer".)
   Also see GPT4@[<A HREF="https://openai.com/research/gpt-4">OpenAI</A>]['23] (not "open")
   and OpenAI@[<A HREF="https://en.wikipedia.org/wiki/OpenAI">wikip</A>]['23]
   (2023: flurry of activity with google ('Bard') & microsoft (new Bing)),
   and "AI 'godfather' Geoffrey Hinton warns of dangers as he quits Google ..."
       -- [<A HREF="https://www.bbc.com/news/world-us-canada-65452940">BBC</A>][2/5/2023].
   [Also search for: ChatGPT]  and  [also search for: chatBot].

%A E. Frantar
%A D. Allstarh
%T SparseGPT: Massive language models can be accurately pruned in one-shot
%J arXiv
%M MAR
%D 2023
%K TR, c2023, c202x, c20xx, zz0923, sparseGPT, sparse GPT, parameters, prune,
   pruning, large language model, LLM, LarLangM, NN, ANN,
   OPT175B, BLOOM 176B, BLOOM176B
%X "... models can be pruned to at least 50% sparsity in one-shot, without any
   retraining, at minimal loss of accuracy. ... can execute SparseGPT on the
   largest available open-source models, OPT-175B & BLOOM-176B, in under 4.5
   hours ..."
   -- [<A HREF="https://arxiv.org/abs/2301.00774">arxiv:2301.00774</A>]['23].

%A J. Bernstein
%A et al
%T Automatic gradient descent: Deep learning without hyperparameters
%J arXiv
%M APR
%D 2023
%K TR, c2023, c202x, c20xx, zz0423, NN, ANN, architecture, training,
   backpropagation
%X "The architecture of a deep NN is defined explicitly in terms of the # of
   layers, the width of each layer & the general n/wk topology. Existing opt.
   frameworks neglect this info. in favour of implicit architectural info.
   (e.g. 2nd-order methods) ... This paper builds a new framework for deriving
   optimisation algs. that explicitly leverage neural architecture. The theory
   extends mirror descent to non-convex composite objective fns: the idea is to
   transform a Bregman divergence to account for the non-linear structure of
   neural architecture. ..."
   -- [<A HREF="https://doi.org/10.48550/arXiv.2304.05187">arxiv:2304.05187</A>]['23].
   [Also search for: training deep ANN].

%A Nelson F. Liu
%A Tianyi Zhang
%A Percy Liang
%T Verifiability in generative search engines
%M APR
%D 2023
%K TR, c2023, c202x, c20xx, zz0523, preprint, ANN, chatGPT, GPT, chatBot,
   citations, query, search, Bing Chat, BingChat, NeevaAI, perplexity.ai,
   YouChat
%X "... conduct human evaluation to audit 4 popular generative search engines -
   Bing Chat, NeevaAI, perplexity.ai, & YouChat ... responses from existing
   generative search engines are fluent & appear informative, but frequently
   contain unsupported statements & inaccurate[*] citations: on average, a mere
   51.5% of generated sentences are fully supported by citations & only 74.5%
   of citations support their assoc. sentence. ..."
   -- [<A HREF="https://cs.stanford.edu/~nfliu/papers/liu+zhang+liang.arxiv2023.pdf">stanf'd</A>]['23].
   [Also search for: GPT chatBot].  ([*]Consistent with my experience.)

%A I. Shumailov
%A et al
%T The curse of recursion: Training on generated data makes models forget
%J arXiv
%M MAY
%D 2023
%O Nature, 631, 755-759, 2024 [<A HREF="https://doi.org/10.1038/s41586-024-07566-y">www</A>]['24]
%K TR, c2023, c202x, c20xx, zz0623, ANN, NN, AI, model collapse, chatGPT, LLM,
   LarLangM, generative, autoencoder, training, chatbot, chatGPT, GPT4, GPT5,
   chatGPT4, chatGPT5, distribution, tail, GIGO
%X "Stable Diffusion revolutionised image creation from descriptive text. GPT-2,
   GPT-3(.5) and GPT-4 ... we consider what the future might hold. What will
   happen to GPT-{n} once LLMs contribute much of the language found online? We
   find that use of model-generated content in training causes irreversible
   defects in the resulting models, where tails of the original content distn
   disappear. We refer to this effect as Model Collapse and show that it can
   occur in Variational Autoencoders, Gaussian Mixture Models & LLMs. ..."
   -- 2305.174@[<A HREF="https://arxiv.org/abs/2305.17493">arXiv</A>]['23].
   [Also search for: LarLangM].

%A D. J. Mankowitz
%A et al
%T Faster sorting algorithms discovered using deep reinforcement learning
%J Nature
%V 618
%P 257-263
%M JUN
%D 2023
%K news, c2023, c202x, c20xx, zz0623, ANN, deep, sort, sorting, AlphaDev
%X "... we formulated the task of finding a better sorting routine as a
   single-player game. We then trained a new deep reinforcement learning agent,
   AlphaDev, to play this game. AlphaDev discovered small sorting algorithms
   from scratch that outperformed previously known human benchmarks ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-023-06004-9">doi:10.1038/s41586-023-06004-9</A>]['23].
   [Don't over-hype it.]

%A E. L. Bolager
%A I. Burak
%A C. Datar
%A Q. Sun
%A F. Dietrich
%T Sampling weights of deep neural networks
%J arXiv
%M JUN
%D 2023
%K TR, c2023, c202x, c20xx, zz0723, ANN, NN, sampling, sample, weight,
   training, optimization, learning
%X "We introduce a prob. distn, combined with an efficient sampling alg., for
   weights & biases of fully-connected [NNs]. In a supervised learning context,
   no iterative optimization or gradient computations of internal n/wk params
   are needed to obtain a trained n/wk. The sampling is based on the idea of
   random feature models. However, instead of a data-agnostic distn, e.g., a
   normal dist., we use both the input & the output training data of the
   supervised learning problem to sample both shallow & deep n/wks. We prove
   that the sampled n/wks we construct are universal approximators. We also show
   that our sampling scheme is invariant to rigid body transformations & scaling
   of the input data. ..."
   -- [<A HREF="https://arxiv.org/abs/2306.16830">arXiv</A>]['23].

%A G. Deletang
%A et al
%T Language modeling is compression
%J arXiv
%M SEP
%D 2023
%K TR, c2023, c202x, c20xx, zz1023, NN, ANN, large language model, LLM,
   LarLangM, modelling
%X "... It has long been established that predictive models can be transformed
   into lossless compressors and vice versa. ..."
   -- [<A HREF="https://browse.arxiv.org/abs/2309.10668">arXiv</A>]['23].
   [Also search for: MML book].

%A D. Modah
%A et al
%T Neural inference at the frontier of energy, space, and time
%J Science
%V 382
%N 6668
%P 329-335
%M OCT
%D 2023
%K jrnl, c2023, c202x, c20xx, zz1023, NN, ANN, IBM, NorthPole, chip, ResNet50,
   GPU, parallel, computer architecture
%X "... NorthPole is a neural inference architecture that blurs this boundary by
   eliminating off-chip memory, intertwining compute with memory on-chip, &
   appearing externally as an active memory chip. NorthPole is a low-precision,
   massively parallel, ..."
   -- [<A HREF="https://doi.org/10.1126/science.adh1174">doi:10.1126/science.adh1174</A>]['23].
   [Also search for: ANN chip].

%A B. M. Lake
%A M. Baroni
%T Human-like systematic generalization through a meta-learning neural network
%J arXiv
%M OCT
%D 2023
%K TR, c2023, c202x, c20xx, zz1023, NN, ANN, AI, large language model, LLmodel,
   generalisation, generalization, MLC, Fodor, Pylyshyn
%X "... we successfully address Fodor & Pylyshyn's challenge by providing
   evidence that [Anns] can achieve human-like systematicity when optimized for
   their compositional skills. ... we introduce the meta-learning for
   compositionality (MLC) ... Our results show how a std NN architecture,
   optimized for its compositional skills, can mimic human systematic
   generalization in a head-to-head comparison."
   -- [<A HREF="https://doi.org/10.1038/s41586-023-06668-3">doi:10.1038/s41586-023-06668-3</A>]['23].

%A A. Jentzen
%A B. Kuckuck
%A P. von Wurstemberger
%T Mathematical Introduction to Deep Learning: Methods, Implementations, and
   Theory
%J arXiv
%P 601
%M OCT
%D 2023
%K TR, book, intro, deep, ANN, NN, c2023, c202x, c20xx, zz1123, feedforward,
   convolutional, recurrent, SGD
%X "This book ... introduction to the topic of deep learning algs.. We review
   essential components of [DLAs] in full mathematical detail inc. different
   ANN architectures (such as fully-connected feedforward ANNs, convolutional
   ANNs, recurrent ANNs, residual ANNs, & ANNs with batch normalization) &
   different optimization algs. (such as the basic stochastic gradient descent
   (SGD) method, accelerated methods, & adaptive methods). ..."
   -- [<A HREF="https://arxiv.org/abs/2310.20360">arxiv:2310.20360</A>]['23].

%A A. Momeni
%A et al
%T Backpropagation-free training of deep physical neural networks
%J Science
%V ?
%M NOV
%D 2023
%K jrnl, c2023, c202x, c20xx, zz1223, ANN, NN, backprop, training, AI
%X "... we proposed a simple deep NN architecture augmented by a physical local
   learning (PhyLL) alg., enabling supervised & unsupervised training of deep
   physical NNs, without detailed knowledge of the nonlinear physical layer's
   properties. We trained diverse wave-based physical NNs in vowel & image
   class'n experiments, showcasing our approach's universality. ... shows
   advantages over other hardware-aware training schemes ..."
   -- [<A HREF="https://doi.org/10.1126/science.adi8474">doi:10.1126/science.adi8474</A>]['23].
   [Also search for: ANN training].

%A M. Hutson
%T How does ChatGPT âthinkâ? Psychology and neuroscience crack open
   AI large language models
%J Nature
%V 629
%P 986-988
%M MAY
%D 2024
%K news, views, chatGPT, c2024, c202x, c20xx, zz0624, large language model, LLM,
   LarLangM, chatBot, AI, ANN, explainable, stochastic parrot
%X "... Researchers have called LLMs 'stochastic parrots' ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-024-01314-y">doi:https://doi.org/10.1038/d41586-024-01314-y</A>]['24].

%A M. Brooks
%T Inside the maths that drives AI
%J Nature
%V 631
%P 244-246
%M JUL
%D 2024
%K news, views, c2024, c202x, c20xx, zz0724, AI, ANN, loss function, functions,
   noise, fitting, MAE, MSE, Huber loss
%X "Loss functions measure algorithmic errors in AI models, but there's more
   than one way to do that. Here's why the right fn is so important.  ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-024-02185-z">doi:10.1038/d41586-024-02185-z</A>]['24].

%A S. Dohare
%A et al
%T Loss of plasticity in deep continual learning
%J Nature
%V 632
%P 768-774
%M AUG
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0924, NN, deep, LarLangM, LLM, chatGPT,
   new learning
%X ".. It has been unclear whether or not deep learning methods work in
   continual l. settings. Here we show that they do not - that std
   [DL] methods gradually lose plasticity in continual-learning settings until
   they learn no better than a shallow n/wk. ... Plasticity is maintained
   indefinitely only by algs. that continually inject diversity into the n/wk
   such as our continual backprop. alg. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07711-7">doi:10.1038/s41586-024-07711-7</A>]['24].


%A A. Hyman
%T Charles Babbage, Pioneer of the Computer
%I Princeton Univ. Press
%D 1982
%K Babbage, Biography, difference engine, book, text
%X ref from K.Katz, SIGCSE 27(4) 43-50 dec 95.
   Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/">computers</A>].

%T Ruth Bader Ginsburg (1933-2020)
%J Nature
%V 586,
%P 355-355
%M OCT
%D 2020
%K Bader Ginsburg, Ruth, RBG, zz1020, notorious, obit, obituary, USA,
   Supreme Court, judge, law, legal, jurisprudence
%X "US Supreme Court justice, champion of equity, environment, democracy. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-020-02857-6">doi:10.1038/d41586-020-02857-6</A>]['20].

%A M. du Preez
%A J. Dronfield
%T Dr James Barry: A Woman Ahead of Her Time
%I Oneworld
%P 496
%M AUG
%D 2016
%K Barry, Bulkley, c2016, c201x, c20xx, zz0916, woman, women, medicine,
   surgeon, gender, Biography, book
%X "Dr James Barry was many things in his life: Inspector General of Hospitals,
   army surgeon, duellist, reformer, lady killer, eccentric. He performed the
   first successful Caesarean in the British Empire, outraged the military
   establishment ... But most astonishingly, long ago in Cork, Ireland, he had
   been a young girl and a mother. ... the amazing true story of Margaret
   Anne Bulkley, ..."
   hb stg12; uk us isbn:1780748310; uk us isbn13:9781780748313.

%T The Official Guide to Bunhill Fields
%I The Corporation of London
%D 1991
%K Bayes Thomas, Bayess' theorem, probability, grave, tomb, cemetery
%X -- via Tony O'Hag@n, l996; uk isbn:0852030339.
   The Printing and Stationery Department,
   The Corporation of London, Guildhall, London EC2P 2EJ.
   Also see [<A HREF="http://www.allisons.org/ll/Images/People/Bayes/">Bayes</A>].

%A Z. Merali
%T Pulsar discoverer Jocelyn Bell Burnell wins $3-million Breakthrough Prize
%J Nature
%V 561
%P 161
%M SEP
%D 2018
%K Bell, Jocelyn, news, c201, c201x, c20xx, zz0918, astronomy, physics, pulsar,
   pulsars, Hewish, Nobel(not) prize, NobelPrize, women, STEM, science
%X "Fifty years after discovering pulsars - compact rotating stars that emit
   beams of radiation - astrophysicist Jocelyn Bell Burnell has been awarded
   one of the most lucrative prizes in science: a US$3-million Breakthrough
   prize. ... In 1974, Hewish shared the Nobel Prize in Physics with fellow
   radio astronomer Martin Ryle, for pioneering research in astrophysics.
   Hewish was cited for his 'decisive role in the discovery of pulsars' - while
   Bell Burnell was overlooked. Bell Burnell herself has previously stated
   that she does not mind the oversight because she understands that
   Nobel prizes are not usually awarded to research students. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-018-06210-w">doi:10.1038/d41586-018-06210-w</A>]['18].
   [Also search for: Bell pulsar].

%T Margaret Betts (?-26/8/2023)
%D 1924
%K Betts, Margaret, biog, obit, code breaker, breaking, codebreaker, cypher,
   WW2, Bletchley Park, UK, STEM
%X "One of the last surviving female codebreakers who served during World War
   Two has died at the age of 99. Margaret Betts worked at Bletchley Park,
   Buckinghamshire, from the summer of 1943 until 1945. ..."
   -- [<A HREF="https://www.bbc.com/news/uk-england-beds-bucks-herts-66730683">bbc</A>][7/9/2023].
   [Also search for: Bletchley Park].

%T David Bohm (1917-1992)
%K Bohm, David, ideas, biog, quantum, physics, physicist, mind, philosophy,
   quote, quotable
%X See DB@[<A HREF="https://en.wikipedia.org/wiki/David_Bohm">wikip</A>]['23].
   See review of a book about DB [<A HREF="https://doi.org/10.1126/science.adi3423">doi:10.1126/science.adi3423</A>][3/8/2023].
   Quote: "even the electron is informed with a certain level of mind".

%T Ludwig Boltzmann
%K Boltzmann, biog, physics, statistical mechanics, distribution, c18xx
%X Ludwig Boltzmann (1844-1906).
   LB@[<A HREF="https://en.wikipedia.org/wiki/Ludwig_Boltzmann">wikip</A>]['24]
   "... p_i ~ exp(-energy_i/kT ) where ...
   p_i prob of being in state_i ... and e_i energy of state_i ..."
   -- B.distribution@[<A HREF="https://en.wikipedia.org/wiki/Boltzmann_distribution">wikip</A>]['24].

%T Sydney Brenner (1927-2019)
%J Science
%V 364
%N 6441
%P 638
%M MAY
%D 2019
%K Brenner, Sir Sydney, obit, obituary, c2019, c201x, c20xx, zz0519, biol,
   genetic code, MolBio, 2002 Nobel prize, NobelPrize, C.elegans,
   Caenorhabditis elegans, roundworm, worm, nematode
%X "Sydney Brenner, an icon of science, died on 5 April at age 92. Sydney
   helped decipher the genetic code, he pioneered the use of Caenorhabditis
   elegans for genetic analysis, he made us think, and he made us laugh."
   -- [<A HREF="https://doi.org/10.1126/science.aax8563">doi:10.1126/science.aax8563</A>]['19].
   Also see, "... One of the key methods for identifying important function
      genes was the screen for roundworms that had some functional defect, such
      as being uncoordinated, leading to the identification of new sets of
      proteins, such as the set of UNC proteins. For this work, he shared the
      2002 Nobel Prize in Physiology or Medicine with H. Robert Horvitz and
      John Sulston. â¦"
   -- SB@[<A HREF="https://en.wikipedia.org/wiki/Sydney_Brenner ">wikip</A>]['20].
   [Also search for: Sydney Brenner].


%K Chandrasekhar, biog, biography, Physics, c20xx, black holes, hole, limit,
   gravity, Eddington
%X -- SC@[<A HREF="https://en.wikipedia.org/wiki/Subrahmanyan_Chandrasekhar">wikip</A>]['20],
   1983 Nobel prize for physics.
   Also see The G
   [<A HREF="https://www.theguardian.com/education/2005/mar/31/research.highereducation">19/20/2017</A>]['20].

%T Noam Chomsky
%D 1928-
%K Chomsky, biog, biography, archive, linguist, linguistics, politics,
   www, HREF, http
%X [<A HREF="https://archivesspace.mit.edu/repositories/2/resources/1305">Noam Chomsky personal archives</A>]['20],
   [<A HREF="https://chomsky.info/">.info</A>]['20],
   [<A HREF="http://www.contrib.andrew.cmu.edu/usr/tp0x/chomsky.html">Chomsky archive</A>][??],
   or anonymous ftp to ftp.cs.cmu.edu and cd to user/cap/chomsky .

%T Cyrus Chothia (19/2/1942-26/11/2019)
%M NOV
%D 2019
%K Chothia, Cyrus, news, c2019, c201x, c20xx, zz1219, obit, obituary,
   LMB, MolBio, bioinformatics, protein structure, domains
%X "... Cyrus pioneered the use of computational methods to study the structure
   and function of proteins, and the evolution of genomes, which led to the
   birth of structural bioinformatics and computational genomics. ...
   [he] mentored over 21 scientists (19 PhD students and 2 postdocs) during his
   career, several of whom have gone on to become leaders in the field of
   bioinformatics. ..."
   -- mrc-lmb[<A HREF="https://www2.mrc-lmb.cam.ac.uk/cyrus-chothia-1942-2019/">www</A>][27/1//2019]. ---------------
   And,
   "Cyrus Chothia obituary.  Biochemist whose work was at the cutting edge
   of the understanding of protein structures, their function & evolution ...
   Like most LMB staff he ran a small group, with no more than one research
   student per year. He was scrupulously fair in his dealings with his
   colleagues, giving students full credit for their published papers, and was
   notably supportive of female researchers at a time when it was far
   from the norm. ..."
   -- The G [<A HREF="https://www.theguardian.com/science/2019/dec/12/cyrus-chothia-obituary">www</A>][13/12/2019].

%T Alonzo Church
%D 1903-1995
%K Church, Alonzo, lambda calculus, thesis, Turing, c1936, c193x, c19xx,
   effective computation, biog
%X Church's thesis (or Church-Turing thesis), roughly:-
   computation == lambda expression == Turing machine
   == any "mechanical" notion of computing == etc..
   (Also see [<A HREF="http://www.allisons.org/ll/FP/Lambda/">lambda</A>].)

%T 1917-2008: A Space Optimist (Arthur C. Clarke)
%J Nature
%V 452
%P 387
%M MAR
%D 2008
%K Clarke AC, Arthur C. Clarke, obit, biog, c2008, c200x, c20xx, zz0408,
   2001, Hal, SciFi, writer, Sci Fi
%X Arthur C. Clarke (1917-2008),
   ed: [<A HREF="http://dx.doi.org/10.1038/452387a">doi:10.1038/452387a</A>]['08].

%T John Horton Conway
%D 2020
%K Conway, John, c2020, c202x, c20xx, zz0420, obit, obituary, biography, biog,
   maths, mathematics, mathematician, algebra, finite groups, group theory,
   surreal numbers, free will theorem, FWT, game of life,
   Cambridge University, Princeton
%X John Horton Conway FRS (26 Dec. 1937 - 11 Apr. 2020), d. covid19.
   "... Born & raised in Liverpool, Conway spent the first half of his career
   at the U. of Cambridge before moving to the U.S. state of New Jersey, where
   he held the title of John von Neumann Professor Emeritus at Princeton U. for
   the rest of his career. ..."
   -- JC@[<A HREF="https://en.wikipedia.org/wiki/John_Horton_Conway ">wikip</A>]['20],
      JC@[<A HREF="https://www.math.princeton.edu/news/john-h-conway-1937-2020 ">Princeton</A>]['20],
      obit@[<A HREF="https://www.princeton.edu/news/2020/04/14/mathematician-john-horton-conway-magical-genius-known-inventing-game-life-dies-age">Princeton</A>]['20],
      obit@[<A HREF="https://www.nytimes.com/2020/04/15/technology/john-horton-conway-dead-coronavirus.html">NYT</A>][15/4/2020],
      obit@[<A HREF="https://doi.org/10.1038/d41586-020-01515-1">doi:10.1038/d41586-020-01515-1</A>][23/5/'20] Nature,
      obit@[<A HREF="https://doi.org/10.1098/rsbm.2021.0034">doi:10.1098/rsbm.2021.0034</A>]['24] Royal Soc..
   [Also search for: maths Conway].

%A S. Roberts
%T Genius At Play: The Curious Mind of John Horton Conway
%I BloomsburyUSA
%P 480
%D 2015
%K Conway, John Horton Conway, biog, biography, c2015, c201x, c20xx, zz0715,
   book, maths, mathematics, mathematician, Cambridge, Princeton
%X "... Born in Liverpool in 1937, Conway found fame as a barefoot Cambridge
   professor. He discovered the Conway groups in mathematical symmetry, &
   invented the aptly named surreal numbers, as well as the cult classic Game of
   Life ... Moving to Princeton in 1987, as a mathemagician he deployed cards,
   ropes, dice, coat hangers, & even the odd Slinky as props ..."
   1st ed 2015; hb us$16; uk us isbn:1620405938; uk us isbn13:978-1620405932.
   Also see S.Roberts in the Guardian [<A HREF="https://www.theguardian.com/science/2015/jul/23/john-horton-conway-the-most-charismatic-mathematician-in-the-world">www</A>][23/7/2015].
   [Also search for: maths Conway].


%A G. B. Dantzig
%T George Dantzig
%K Dantzig, zz0221, linear programming, simplex algorithm, optimisation,
   optimization, biography, biog
%X "... Dantzig is known for his development of the simplex algorithm, an
   alg. for solving linear programming problems ..."
   -- D@[<A HREF="https://en.wikipedia.org/wiki/George_Dantzig">wikip</A>]['21].

%A Daniel Dennett obituary: 'New atheism' philosopher who sparked debate on
   consciousness
%J Nature
%V 629
%P 997
%M MAY
%D 2024
%K Dennett, Daniel, c2024, c202x, c20xx, zz0624, obit, philosophy, cognitive,
   consciousness
%X 1942-2024
   -- [<A HREF="https://doi.org/10.1038/d41586-024-01478-7">doi:10.1038/d41586-024-01478-7</A>]['24].
   And Science [<A HREF="https://doi.org/10.1126/science.adq5873">doi:10.1126/science.adq5873</A>]['24].

%A G. Farmelo
%T The Strangest Man: The Hidden Life of Paul Dirac, Mystic of the Atom
%I BasicBooks
%P 560
%D 2011
%K Dirac, c2011, c201x, c20xx, zz1014, biography, biog, science, scientist,
   physics, physicist, 1933 Nobel prize, NobelPrize, laureate,
   quantum mechanics, theory, antimatter
%X 1st ed 2011; pb us$13; uk us isbn:0465022103; uk us isbn13:978-0465022106.
   "... among the greatest scientific geniuses of the modern age. One of
   Einstein's most admired colleagues, he helped discover quantum mechanics,
   and his prediction of antimatter was one of the greatest triumphs in the
   history of physics. In 1933 he became the youngest theoretician ever to win
   the Nobel Prize in Physics. ..."  (via AK)
   (Review @ The_G. [<A HREF="http://www.theguardian.com/science/2009/apr/02/paul-dirac-strangest-man-farmelo-quantum">www</A>][3/4/2009].)

%A P. Hoffman
%T The Man Who Loved Only Numbers: The Story of Paul Erdos and the Search for
   Mathematical Truth
%I 4th Estate / Hyperion
%D 1998
%K Erdos, maths, mathematician, biography, biog, zz0898
%X isbn:1 8570 28112; / isbn:0 7868 63825;
   see also  S c h e c h t e r  1998.

%A B. Schechter
%T My Brain is Open: The Mathematical Journeys of Paul Erdos
%I OUP / SimonAndSchuster
%D 1998
%K Erdos, maths, mathematician, biography, biog, zz0898
%X uk us isbn:0 1985 04713; / uk us isbn:0 6848 46357.

%T Philippa Fawcett (4 April 1868 - 10 June 1948)
%K Fawcett, biography, biog, women, www, c1890, c189x, c18xx, zz0623, STEM,
   maths, mathematics, tripos, mathematician, Cambridge University,
   senior wrangler, Scott, Hendry
%X "... In 1890, she became the first woman to obtain the top score in the
   Cambridge Mathematical Tripos exams. ... Her score was 13% higher than the
   second highest, but she did not receive the title of Senior Wrangler
   (Geoffrey T. Bennett in 1890), as only men were then ranked & women were
   listed separately. Women had been allowed to take the Tripos since 1880,
   after Charlotte Angas Scott was unofficially ranked as eighth wrangler. When
   the women's list was announced, Fawcett was described as 'above the senior
   wrangler'. No woman was officially awarded the first position until Ruth
   Hendry in 1992. ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Philippa_Fawcett">wikip</A>]['23].

%T Rosalind Franklin (1920-1958)
%K Franklin, c19xx, DNA, structure, biol, biology, virus,
   biog, biography, woman, scientist, women, STEM
%X E.g.,
   'Rosalind Franklin was so much more than the "wronged heroine" of DNA',
   ed., Nature, Vol.583, p.492, 21/7/2020
   -- [<A HREF="https://doi.org/10.1038/d41586-020-02144-4">doi:10.1038/d41586-020-02144-4</A>]['20].
   (Also see RF@[<A HREF="https://en.wikipedia.org/wiki/Rosalind_Franklin">wikip</A>]['20], and
   'What Rosalind Franklin truly contributed to the discovery of DNA's
   structure', Nature, 616, 657-660, April 2023,
   -- [<A HREF="https://doi.org/10.1038/d41586-023-01313-5">doi:10.1038/d41586-023-01313-5</A>]['23].)
   [Also search for: Rosalind Franklin].

%T Edward Fredkin (2/10/1934-13/6/2023)
%K Fredkin, obit, biography, biog, physics, physicist, cosmology,
   reversible, quantum, computing, computation, philosophy, pancomputationalism
%X See EF@[<A HREF="https://en.wikipedia.org/wiki/Edward_Fredkin">wikip</A>]['23]
   and N'ture [<A HREF="https://doi.org/10.1038/d41586-023-02646-x">doi:10.1038/d41586-023-02646-x</A>][2023].

%A D. Richards
%T Martin Gardner (1914-2010)
%J Science
%V 329
%N 5988
%P 157
%M JUL
%D 2010
%K Gardner, Martin, c2010, c201x, c20xx, zz0710, bio, biog, obit, meta magical,
   metamagical, maths, science, game, puzzle, sceptic, skeptic
%X "On 22 May, American author Martin Gardner died at the age of 95. Until his
   last days, he was active & writing for an eager audience. He is well known
   for his writing on mathematics, science, philosophy of science, theology, &
   magic. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1194002">doi:10.1126/science.1194002</A>]['10].
   [Also search for: Martin Gardner].

%A M. Gardner
%T Undiluted Hocus-Pocus: The Autobiography of Martin Gardner
%I PrincetonUP
%P 288
%M SEP
%D 2013
%K Gardner, Martin, c2013, c201x, c20xx,zz0913, bio, biog, biography,
   autobiography, autobio, maths, science, STEM, skeptic, debunk, pseudo,
   puzzles, games, column, writing
%X 1st ed 2013; hb us$19; uk us isbn:0691159912; uk us isbn13:978-0691159911.
   "Martin Gardner wrote the Mathematical Games column for Scientific American
   for 25 years & published more than seventy books on topics as diverse as
   magic, philosophy, religion, pseudoscience, & Alice in Wonderland. ..."
   [Also search for: Martin Gardner].

%A P. Wouters
%T Eugene Garfield (1925-2017)
%J Nature
%V 543
%N 492
%M MAR
%D 2017
%K biog, obit, c2017, c201x, c20xx, zz1119, Science Citation Index, SCI,
   bibliometrics, scientific, web of science, research, KPI, KPIs, Hindex,
   impact, papers, publications, citations, publish, perish, Shepard,
   c1873, c187x, c18xx
%X "... introduced Garfield to Shepard's Citations, a system for legal citations
   invented in 1873 that tracked how US court cases cited earlier ones ..."
   -- [<A HREF="https://doi.org/10.1038/543492a">doi:10.1038/543492a</A>]['19].
   [Also search for: citation SCI]  and  [also search for: publish perish].

%T I. J. Good
%K Good, IJGOOD, doog, biog, zz0623, ultraintelligence, c1965, c196x, c19xx, AI,
   artificial, machine, intelligence
%X "... Let an ultraintelligent m/c be defined as a m/c that can far surpass all
   the intellectual activities of any man however clever. Since the design of
   m/cs is one of these intellectual activities, an ultraintelligent m/c could
   design even better m/c; there would then unquestionably be an 'intelligence
   explosion,' & the intelligence of man would be left far behind... Thus the
   1st ultraintelligent m/c is the last invention that man need ever make,
   provided that the m/c is docile enough to tell us how to keep it under
   control. It is curious that this point is made so seldom outside of science
   fiction. It is sometimes worthwhile to take science fiction seriously. ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/I._J._Good">wikip</A>]['23];
   'Speculations Concerning the First Ultraintelligent Machine', J. Article;
   in 'Advances in Computers (1966)'.
      "According to his assistant, Leslie Pendleton, in 1998 Good wrote in an
      unpublished autobiographical statement that he suspected an
      ultraintelligent machine would lead to the extinction of man." -- wikip.
   [Also search for: IJGood].

%T Rudolf Halin (1934-2014)
%A R. Diestel
%D 2014
%K Halin, obit, biog, book, text, graph, Graphentheorie
%X "Halin was one of Wagner's three most eminent students. He is best known for
   his early papers on connectivity, & particularly for his seminal work on
   infinite graphs & their ends. ..."
   -- [<A HREF="http://dmatheorynet.blogspot.com/2014/12/dmanet-rudolf-halin-1934-2014.html">www</A>]['18].
   Halin's book:
      'Graphentheorie' vol.1, isbn:3-534-06767-3, 1981;
                  and  vol.2, isbn:3-534-06767-3, 1982.
   Also see RH@[<A HREF="https://en.wikipedia.org/wiki/Rudolf_Halin">www</A>]['18].

%A Godfrey Harold Hardy
%T A Mathematician's Apology
%D 1940
%K Hardy, GHHardy, essay, book, c1940, c194x, c19xx, zz0323, biog, autobiog,
   Ramanujan, 1729, Littlewood, maths, mathematician, quote, quotable, CPSnow
%X With C.P.Snow's foreword 1967; uk us isbn13:978-1107295599.
      "Sometimes one has to say difficult things but one
      ought to say them as simply as one knows how." -- GHH.
   Also see GHH@[<A HREF="https://en.wikipedia.org/wiki/G._H._Hardy">wikip</A>]['23].
   [Also search for: Hardy maths].

%A S. Hawking
%A M. Brenher
%T My Brief History
%I Bantam
%P 144
%M SEP
%D 2013
%K Hawking, Stephen, book, c2013, c201x, c20xx, zz1013, biography, bio, biog,
   autobiography, autobio, memoir, ALS, physicist, scientist
%X 1st ed 2013; hb us$13; uk us isbn:0345535286; uk us isbn13:978-0345535283.
   "... SH's improbable journey, from his postwar London boyhood to his years of
   international acclaim and celebrity. ... opens up about the challenges that
   confronted him following his diagnosis of ALS at age twenty-one. Tracing his
   development as a thinker, he explains how the prospect of an early death
   urged him onward through numerous intellectual breakthroughs ..."

%A L. Mlodinow
%T Stephen Hawking: A memoir of friendship and physics
%I AllenLane
%P 240
%M SEP
%D 2020
%K Hawking, Stephen, c2020, c202x, c20xx, zz1020, Physics, biog, biography,
   book
%X 1st ed 2020; pb us$22; isbn:0241438098; uk us isbn13:978-0241438091
   [Also search for: Stephen Hawking obit].

%A J. Preskill
%T Stephen Hawking (1942-2018)
%J Science
%V 360
%N 6385
%P 156-156
%M APR
%D 2018
%K Hawking, obit, obituary, c2018, c201x, c20xx, zz0418, physics, cosmology,
   black hole, holes
%X "Stephen William Hawking died on 14 March (Albert Einstein's birthday) at
   the age of 76 ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aat6775">doi:10.1126/science.aat6775</A>]['18].
   [Also search for: Stephen Hawking biog].

%T Peter Higgs obituary: physicist who predicted boson that explains why
   particles have mass
%J Nature
%V 628
%M APR
%D 2024
%K Higgs, Peter, obit, biog, c2024, c202x, c20xx, zz0524, quantum, physics,
   gravity, mass, boson, Nobel prize
%X Peter Ware Higgs, 19 May 1929 - 8 April 2014
   -- [<A HREF="https://doi.org/10.1038/d41586-024-01103-7">doi:10.1038/d41586-024-01103-7</A>]['24], and
      [<A HREF="https://doi.org/10.1126/science.adq3506">doi:10.1126/science.adq3506</A>][6/6/'24].
   Also see PH@[<A HREF="https://en.wikipedia.org/wiki/Peter_Higgs">wikip</A>]['24].

%A F. Close
%T Elusive: How Peter Higgs Solved the Mystery of Mass
%P BasicBooks
%P 304
%M JUN
%D 2022
%K Higgs, Peter, biog, biography, book, c2022, c202x, c20xx, zz0722, physics,
   mass, gravity, Higgs boson, field, KPI, KPIs, STEM, Nobel
%X 1st ed 2022; hb us$26; uk us isbn:1541620801; uk us isbn13:978-1541620803.
   "... the Higgs boson, the missing piece in understanding why particles have
   mass ... Why Peter Higgs? Drawing on years of conversations with Higgs &
   others, Close illuminates how an unprolific man became one of the world's
   most famous scientists. ..."
   (PH 2013 Nobel prize winner for physics, with Francois Englert.)
   Also see PH@[<A HREF="https://en.wikipedia.org/wiki/Peter_Higgs">wikip</A>]['22]
   and the [<A HREF="https://www.theguardian.com/science/2013/dec/06/peter-higgs-boson-academic-system">Grauniad</A>][7/12/2013].

%A F. Hoyle
%T Home is Where the Wind Blows: Chapters from a Cosmologist's Life
%I Mill Valley, Cal.: Univ. Sci. Books
%D 1994
%K Hoyle, Fred Hoyle, book, text, astronomer, astronomy, biography, bio, biog,
   steady state, auto, autobiography, zz1096
%X Fred Hoyle (24 June 1915 - 10 August 2001).
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Film/Andromeda/">A-for-A</A>].)

%T Clive James obituary: 'A man of substance'
%I BBC
%M NOV
%D 2019
%K James, Clive, Vivian, obit, obituary, news, c2019, c201x, c20xx, zz1219,
   short, quote, quotable, brevity, MML, MDL, Australian, Australia, poet,
   writer
%X 7/10/1939 - 24/11/2019.
   'He was sanguine about his own end, maintaining a short biography on
   his website, which he hoped would be used as the basis for any
   appreciation of his life that might be written.
   Journalists writing an obituary should "keep in mind that
   shorter is better, and that a single line is best", it said.'
   -- [<A HREF="https://www.bbc.com/news/entertainment-arts-13437293">bbc</A>][27/11/2019]. -----------------------
   (Also see,
   "... He also famously once said: 'Stop worrying, nobody gets out of this
   world alive.' ..."
   -- [<A HREF="https://www.abc.net.au/news/2019-11-28/clive-james-quotes-on-life-death-princess-diana-game-of-thrones/11744416">abc</A>][28/11/2019].)

%T Maryam Mirzakhani
%K Mirzakhani, c2017, c201x, c20xx, zz0917, mathematician, maths, math, STEM,
   Teichmuller, hyperbolic, Ergodic theory, symplectic,
   Fields medal, 2014, prize, obit, quote, quotable,
   StanfordUni, science, scientist, woman, women, www, HREF, http
%X Maryam Mirzakhani (1977 - 14/7/2017).
   Maths is "like being lost in a jungle and trying to use all the
   knowledge that you can gather to come up with some new tricks", M.M.,
   -- news@[<A HREF="http://news.stanford.edu/press-releases/2017/07/15/maryam-mirzakhanedal-winner-dies/">Stanf'd</A>][15/7/2017].
   MM@[<A HREF="https://en.wikipedia.org/wiki/Maryam_Mirzakhani">wikip</A>]['17].

%T John McCarthy (1927-2011)
%D 2011
%K McCarthy, Lisp, AI, c2011, c201x, c20xx, obit, obituary, computer science,
   comp sci, CSci
%X John McCarthy, 4 September 1927 - 24 October 24 2011.
   [<A HREF="http://techcrunch.com/2011/10/24/creator-of-lisp-john-mccarthy-dead-at-84/">obit</A>][10/2011] by J. Biggs,
   [<A HREF="http://en.wikipedia.org/wiki/John_McCarthy_(computer_scientist)">wikip</A>][2011],
   in Nature [<A HREF="http://dx.doi.org/10.1038/480040a">doi:10.1038/480040a</A>][11/2011], by V. Lifschitz.
   [Also search for: Lisp book].

%T Gordon Moore (3/1/1929-24/3/2023)
%K Moore, Moore's law, Intel, zz0423, biog, obit, obituary, Computers, computing
%X -- [<A HREF="https://www.bbc.com/news/world-us-canada-65073812">bbc</A>]['23],
   GM@[<A HREF="https://en.wikipedia.org/wiki/Gordon_Moore">wikip</A>],
   GM@[<A HREF="https://doi.org/10.1038/d41586-023-01978-y">doi:10.1038/d41586-023-01978-y</A>][23/6/'23],
    & [<A HREF="http://www.allisons.org/ll/Images/Film/Andromeda/Intel/">Intel</A>].

%T Katherine Johnson
%J Nature
%V 579
%P 341
%D 2020
%K Johnson, Katherine, obit, biog, NASA, STEM, woman, science, mathematics,
   zz0420, mathematician, Project Mercury, Apollo 11, Hidden Figures
%X Obituary, Katherine Johnson (1918-2020)
   -- [<A HREF="https://doi.org/10.1038/d41586-020-00749-3">doi:10.1038/d41586-020-00749-3</A>]['20].
   Also see Science, 368(6491), pp.591, 8/5/2020
   -- [<A HREF="https://doi.org/10.1126/science.abc1546">doi:10.1126/science.abc1546</A>]['20].

%A Katherine Johnson
%A Joylette Hylick
%A Katherine Moore
%T My Remarkable Journey: A Memoir
%I HarperLux
%P 352
%M JUN
%D 2021
%K book, c2021, c202x, c20xx, zz0621, woman, women, www, STEM, maths, math,
   mathematician, NASA, space, hidden figures, memoir, autobiography
%X 1st ed 2021; pb us$19; uk us isbn:0063090678; uk us isbn13:978-0063090675.
   "... K. shares her personal journey from child prodigy in the Allegheny
   Mtns of W.Virginia to NASA human computer. In her life after retirement,
   she served  as a beacon of light for her family and community alike. ..."
   [Also search for: Katherine Johnson].

%T Katalin Kariko
%K Kariko, biog, c2023, c202x, c20xx, zz1023, mRNA, vaccine,
   Nobel Prize, physiology, medicine, www, STEM, women, woman
%X -- [<A HREF="https://en.wikipedia.org/wiki/Katalin_Karik%C3%B3">wikip</A>]['23],
   [<A HREF="https://www.nobelprize.org/prizes/medicine/2023/summary/">nobelprize</A>][2023].

%T Jean-Louis Lassez
%K Lassez, jll, obit, CompSci, CLP-R, CLPR
%X Jean Louis Lassez, 24/12/1944 - ??/11/2021
   jll@[<A HREF="https://scholar.google.com/citations?user=HA1myxcAAAAJ">scholar</A>]['22].
   Also see [<A HREF="https://stephenbodio.com/2021/11/jean-louis-lassez-rip/">stephenbodio.com</A>]['21].
   [Also search for: CLPR LP].

%A E. Ott
%T Obituary: Edward N. Lorenz (1917-2008)
%J Nature
%V 453
%P 300
%M MAY
%D 2008
%K Lorenz, c2008, c200x, c20xx, obit, chaos theory
%X "... studies of atmospheric dynamics led to his accidental discovery of
   chaos theory ..."
   -- [<A HREF="http://dx.doi.org/10.1038/453300a">doi:10.1038/453300a</A>]['08].

%A D. Stein
%T Ada: A Life and a Legacy
%I MITpress
%D 1985
%K Lovelace, Ada, c1985, c198x, c19xx, Biography, text, book
%X Augusta Ada Byron (1815-1852) m. William King 1835.
   [Also search for: Ada Lovelace].

%A B. Toole
%T Ada, the Enchantress of Numbers
%I StrawberryPress
%P 456
%D 1998
%K Lovelace, Augusta, Ada, Byron, c1998, c199x, c19xx, Biography, woman, women,
   STEM, text, book, history, computing, Babbage
%X Augusta Ada Byron (1815-1852) m. William King 1835,
   from 1838 W and A are Earl and Countess of Lovelace.
   Shows that Ada Byron King foresaw many uses of computers
   -- [<A HREF="http://www.well.com/user/adatoole/">www</A>][ 4/1999].
   hb, isbn:0-912674-09-4;  pb, isbn:0-912674-18-3.
   [Also search for: Ada Lovelace].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Ockham/">Ockham Park</A>].)

%A F. Robinson
%T Ada's Ideas: The Story of Ada Lovelace, the World's First Computer Programmer
%I HarryNAbrams
%P 40
%M AUG
%D 2016
%K Lovelace, Augusta, Ada, Anna Isabella Milbanke, Lord Byron,
   c2016, c201x, c20xx, zz0916, Biography, kids, children, book,
   girl, girls, women, STEM, programming, computing
%X "... This *picture* book biography of Ada Lovelace is a compelling portrait
   of a woman who saw the potential for numbers to make art."  (via BA.)
   1st ed 2016; hb us$13; uk us isbn:141971872X; uk us isbn13:978-1419718724.

%A R. Holmes
%T Computer science: Enchantress of abstraction
%J Nature
%V 525
%N 7567
%P 30-32
%M SEP
%D 2015
%K Lovelace, Augusta, Ada, c2015, c201x, c20xx, zz0915, bicentenary, biog,
   history, computing, Babbage
%X "The bicentenary of Augusta Ada King, Countess of Lovelace, heralds the
   critical reassessment of a remarkable figure in the history of Victorian
   science. Ada Lovelace (as she is now known) was 27 years old & married with
   3 children when she published the first account of a prototype computer & its
   possible applications in 1843. Her 20,000-word paper was appended as seven
   Notes to a translation of a descriptive article, Sketch of the Analytical
   Engine Invented by Charles Babbage, Esq. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/525030a">doi:10.1038/525030a</A>]['15].
   [Also search for: Ada Lovelace].

%A M. Shubik
%T Retrospective: John Forbes Nash Jr. (1928-2015)
%J Science
%V 348
%N 6241
%P 1324
%M JUN
%D 2015
%K Nash, biog, obit, c2015, c201x, c20xx, zz0615, a beautiful mind, game theory,
   cooperative, equilibrium, Abel prize, AbelPrize, maths, obituary
%X "On 23 May, John Nash & his wife Alicia were killed in a car accident in New
   Jersey. ... J's contributions were in pure maths & game theory, which
   continues to influence the behavioral scis.. His achievements were
   remarkable, esp. given his constant battle with mental illness. ... I
   congratulated J after the announcement of the 2015 Norway award in maths
   (Abel Prize), which he shared with mathematician Louis Nirenberg. I heard
   from another friend that when John was asked about whether he rated it higher
   or lower than the Nobel Prize, he replied 'is 1/2 better than 1/3?'"
   -- [<A HREF="http://dx.doi.org/10.1126/science.aac7085">doi:10.1126/science.aac7085</A>]['15].

%T Jerzy Neyman 1894-1981
%A E. L. Lehmann
%B Biographical Memoirs
%P 393-420
%I Nat. Acad. Sci
%D 1994
%O Adapted from a biographical article written for the Dictionary of
   Scientific Biography, Supplement II
%K Neyman, Jerzy, biog, biography, memoir, c1981, c198x, c19xx, zz0919,
   stats, statistics, statistician, Berkeley
%X Jerzy Neyman 1894-1981.
   -- pdf@[<A HREF="http://www.nasonline.org/publications/biographical-memoirs/memoir-pdfs/neyman-jerzy.pdf">NASonline</A>]['19].
   Also see JN@[<A HREF="https://en.wikipedia.org/wiki/Jerzy_Neyman">wikip</A>]['19].

%A J. Gleick
%T Isaac Newton
%I HarperP
%P 288
%D 2003
%K Newton, Sir Isaac Newton, book, text, biography, c2003, c2004, c200x,
   Woolsthorpe, Philosophiae Naturalis Principia Mathematica, Newtonian,
   mechanics, motion, opticks, optics, history, maths, mathematics, calculus,
   fluxions, Lucasian Chair, Professor
%X Sir Isaac Newton 25/12/1642 - 20/3/1727 (NB. Julian cal.).
   pb;       HarperP 2004; uk us isbn:0007163185; uk us isbn13:978-0007163182.
   pb us$11; Vintage 2004, uk us isbn:1400032954; uk us isbn13:978-1400032952.
   [Also search for: Isaac Newton].

%T Celebrate the mathematics of Emmy Noether
%J Nature
%V 561
%N ?
%P 149-150
%M SEP
%D 2018
%K Noether, Emmy, c2018, c201x, c20xx, zz0918, maths, math, mathematician,
   mathematics, STEM, women, woman, Noetherian, ring, biog
%X Emmy Noether (23/3/1882 - 14/4/1935).
   "Emmy Noether was a force in mathematics - & knew it. She was fully
   confident in her capabilities & ideas. Yet a century on, those ideas, &
   their contribution to science, often go unnoticed. Most physicists are aware
   of her fundamental theorem, which puts symmetry at the heart of physical law.
   But how many know anything of her & her life? ..."
   -- editorial@[<A HREF="https://doi.org/10.1038/d41586-018-06658-w">doi:10.1038/d41586-018-06658-w</A>]['18].
   (*See EM@[<A HREF="https://en.wikipedia.org/wiki/Emmy_Noether">wikip</A>]['21].*)

%A Mark Oliphant
%K Oliphant, Mark, physics, physicist, Australian, atom, atomic bomb, biog,
   Manhattan Project
%X "Sir Marcus Laurence Elwin Oliphant, AC, KBE, FRS, FAA, FTSE
   (8 Oct 1901 - 14 July 2000) was an Australian physicist ... O. was
   instrumental in spreading the word of this finding in the [USA], thereby
   starting what became the Manhattan Project. ..."
   -- MO@[<A HREF="https://en.wikipedia.org/wiki/Mark_Oliphant">wikip</A>]['23].
   [Also search for: Manhattan Project bomb].

%A G. Rifkin
%A G. Harrar
%T The Ultimate Entrepreneur: The Story of Ken Olsen and
   Digital Equipment Corporation
%I Prima Pub., Rocklin CA
%P 336
%D 1990
%K Olsen, Ken Olsen, Kenneth, book, text, biography, DEC, PDP, PDP7, PDP9,
   PDP11, Vax, computer, computing, history, quote, quotable, prediction,
   zzPrediction, wrong, c1990, c199x, c19xx, zz0497
%X p.40:  Dec 1959 prototype PDP-1 4K words and a CRT
   p.104: Jan 1970 PDP-11 announced.
   p.175: Oct 1977 Vax 11/780 introduced.
   p.196: 17 May 1974 on pc's, Ahl proposes cheap 1-box computer,
          "Why would anyone need a computer of their own?" - Ken Olsen [...]
          "It's [the world is] not going small, stand-alone computers."
   Oops, [also search for: zzPrediction].

%T Julius Robert Oppenheimer (22/4/1904-18/2/1967)
%K Oppenheimer, physics, physicist, zz0723, biog, biography, atom, atomic bomb,
   Manhattan Project, Los Alomos, LosAlomos, WW2
%X See JRO@[<A HREF="https://en.wikipedia.org/wiki/J._Robert_Oppenheimer">wikip</A>]['23].
   A film in 2023; comment at [<A HREF="https://doi.org/10.1126/science.adj8107">doi:10.1126/science.adj8107</A>]['23].
   [Also search for: Manhattan Project bomb].

%T Elinor (Lin) Ostrom (1933-2012)
%A R. K. Wilson
%J Science
%V 337
%N 6095
%P 661
%M AUG
%D 2012
%K Ostrom, c2012, c201x, c20xx, zz0812, retrospective, obit, obituary,
   biography, economics, politics, social, policy, tragedy of the commons,
   cooperation, conservation, resource management, 2009 Nobel prize, NobelPrize
%X "... died on 12 June 2012 at the age of 78. Her husband & intellectual
   partner, Vincent O., died on 29 June 2012 at the age of 92. ... In 1973,
   L. & V. founded the Workshop in Political Theory & Policy Analysis, which
   welcomed students & faculty alike from all social science disciplines, as
   well as the occasional mathematician & anyone with an interest in
   theor.reasoning about policy problems. ... In the 2000s, Lin traveled
   farther afield, working with different groups on a wide variety of dilemmas,
   including farmers in Nepal & foresters in Nigeria & Kenya. The Nobel
   Prize [2009, Economics] gave her a marvelous soapbox ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1227725">doi:10.1126/science.1227725</A>]['12].
   [Also search for: tragedy commons].

%T C. R. Rao (1920-2023)
%K Rao, Calyampudi Radhakrishna Rao, CRRao, zz1023, biog, obit, obituary,
   stats, statistician
%X "C.R.Rao, statistician who transformed data analytics (1920-2023)"
   -- [<a HREF="https://doi.org/10.1038/d41586-023-03200-5">doi:10.1038/d41586-023-03200-5</A>]['2023].

%T Diana Rigg (1938-2020)
%K Rigg, Diana, Dame, actor, actress, obit, obituary, Emma Peel, Avengers,
   Danvers, Rebecca, Lady Olena Tyrell
%X 20 July 1938 - 10 September 2020
   -- [<A HREF="https://www.bbc.com/news/entertainment-arts-27986272">obit</A>]['20],
      [<A HREF="https://www.bbc.com/news/entertainment-arts-54106242">pics</A>]['20],
      [<A HREF="https://www.bbc.com/news/entertainment-arts-54106509">bbc</A>]['20],
      [<A HREF="https://en.wikipedia.org/wiki/Diana_Rigg">wikip</A>]['20].

%T Jorma J. Rissanen (20/10/1932 - 9/5/2020)
%D 1938-2020
%K Rissanen, Jorma, MDL, obit, obituary, biog, zz1020
%X -- [<A HREF="https://www.legacy.com/obituaries/mercurynews/obituary.aspx?pid=196223932">www</A>]['20].
   [Also search for: MDL].

%T Oliver Sacks (1933-2015)
%A D. Draaisma
%J Nature
%V 525
%N 7568
%P 188
%M SEP
%D 2015
%K Sacks, obit, c2015, c201x, c20xx, zz0915, neuroscience, neurologist, brain,
   the Man who mistook his Wife for a Hat, Musicophilia, The Mind's Eye,
   Hallucinations, On the Move, Uncle Tungsten
%X "The final stage of life, Dante wrote, is like a ship, gradually lowering its
   sails at the approach of the harbour. It is a serene image of destination -
   & eminently unfit to characterize the final decade of [OS]'s life. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/525188a">doi:10.1038/525188a</A>]['15].

%T Frank Shepard (1848-1902)
%K Shepard, citation, citations, law, legal, research, Science Citation Index,
   SCI, ISI, Shepardizing, Garfield, publications, c1873, c187x, c18xx
%X S's_cit'ns@[<A HREF="https://en.wikipedia.org/wiki/Shepard%27s_Citations">wikip</A>]['20],
   FS@[<A HREF="https://en.wikipedia.org/wiki/Frank_Shepard">wikip</A>]['20].
   [Also search for: Science Citation Index SCI].

%T Michelle Simmons
%K Simmons, biog, UNSW, quantum, zz1023, scientist, women, women,
   quantum computing, STEM, www, UNSW, Australia
%X MS@[<A HREF="https://en.wikipedia.org/wiki/Michelle_Simmons">wikip</A>]['23],
      [<A HREF="https://research.unsw.edu.au/people/scientia-professor-michelle-yvonne-simmons/publications">UNSW</A>]['23],
      [<A HREF="https://www.abc.net.au/news/science/2023-10-16/prime-minister-science-prize-michelle-simmons-quantum-physics/102979096">ABC</A>]['16/10/2023].

%T Christopher Strachey (1916-1975) - a biographical note
%A M. Campbell-Kelly
%J Annals of the History of Computing
%I IEEE
%V 7
%N 1
%P 19-42
%D 1985
%K Strachey, biography, c1985, c198x, c198x, Oxford, PRG, CS, CSci, CPL,
   history, www, HREF, http, zz0110
%X "Christopher Strachey was one of the most original computer scientists of
   his generation: his fields were computer design and programming, and he made
   important contributions to them both. He liked to say (not quite accurately)
   that he had changed the direction of his career every seven years. The
   different phases of his life and career are reflected in the five sections
   of this note."
   -- [<A HREF="http://dx.doi.org/10.1109/MAHC.1985.10001">doi:10.1109/MAHC.1985.10001</A>]['10].
   Also see special issue of Higher-Order & Symbolic Computation V13(1/2) '00,
   -- [<A HREF="http://dx.doi.org/10.1023/A:1010070228552">doi:10.1023/A:1010070228552</A>]['10].

%T Donna Strickland
%D 2018
%K Strickland, Donna, 2018 Nobel Prize, NobelPrize, physics,
   chirped pulse amplification, women, science, STEM
%X "... She was awarded the Nobel Prize in Physics in 2018, together with
   Gerard Mourou, for the practical implementation of chirped pulse
   amplification ..."
   -- DS@[<A HREF="https://en.wikipedia.org/wiki/Donna_Strickland">wikip</A>]['20].
   Also see,
   "Female Nobel prize winner deemed not important enough for Wikipedia entry"
   -- The G [<A HREF="https://www.theguardian.com/science/2018/oct/03/donna-strickland-nobel-physics-prize-wikipedia-denied">4/10/2018</A>]['20].

%T Alan Turing 1912-1954
%D 1955
%K Turing, AlanTuring, obit, 1954, Enigma
%X "Alan Mathison Turing, 1912-1954 ..."
   -- [<A HREF="https://doi.org/10.1098/rsbm.1955.0019">doi:10.1098/rsbm.1955.0019</A>]['24], Royal Soc..

%A A. Hodges
%T Alan Turing: The Enigma
%I SimonAndSchuster
%D 1983
%K Turing, Alan, AlanTuring, biography, biog, enigma, ultra, code, cypher,
   c1983, c198x, c19xx, zz0512, break, breaking, codes, information, ban,
   deciban, WW2, WWII, Bletchley Park
%X Alan Turing: The Enigma The Centenary,
   2012, pb us$14; uk us isbn:069115564X; isbn13:978-0691155647; 632 pages,
   Princeton University Press.
     "It is only a slight exaggeration to say that the British mathematician
      Alan Turing (1912-1954) saved the Allies from the Nazis, invented the
      computer and artificial intelligence, and anticipated gay liberation by
      decades - all before his suicide at age forty-one. This classic biography
      of the founder of computer science, reissued on the centenary of
      his birth ... ."
   1983, pb about us$20; uk us isbn:0802775802.
      ("Royal pardon for codebreaker Alan Turing ..."
      -- [<A HREF="http://www.bbc.co.uk/news/technology-25495315">bbc</A>][24/12/2013],
         [<A HREF="http://www.theguardian.com/science/2013/dec/24/enigma-codebreaker-alan-turing-royal-pardon">the_G.</A>][24/12/2013].)
   [Also search for: Turing biography]  and  [also search for: Bletchley Park].

%T Alan Turing: Life and Legacy of a Great Thinker
%E C. Teuscher
%I SpringerVerlag
%D 2004
%K Turing, AlanTuring, c2004, c200x, c20xx, Alan, book, biography
%X stg46, us$70, uk us isbn:3540200207.
   [Also search for: Turing biography].

%T The Essential Turing: Seminal Writings in Computing, Logic, Philosophy,
   Artificial Intelligence, and Artificial Life plus The Secrets of Enigma
%E B. J. Copeland
%I OUP
%P 622
%D 2004
%K Turing, book, text, OUP, c2004, c200x, c20xx, machine, AI, enigma, fish,
   cypher, decypher, codebreaker, code breaker, WW2, WWII, Bletchley Park,
   AlanTuring, biography
%X "In 1935, aged 22, he developed the mathematical theory upon which ...
   stored-program digital computers are modeled. ... joined the Goverment
   Codebreaking team at Bletchley Park, Buckinghamshire and played a crucial
   role in deciphering Engima, ... also contributed to the attack on the
   cyphers known as 'Fish,' which were used by the German High Command for the
   encryption of signals during the latter part of the war. ...
   his theoretical work led to the development of Britain's first computers at
   the National Physical Laboratory and the Royal Society Computing Machine
   Laboratory at Manchester University. ... also a founding father of modern
   cognitive science, theorizing that the cortex at birth is an 'unorganized
   machine' which through 'training' becomes organized 'into a universal machine
   or something like it.' He went on to develop the use of computers to model
   biological growth, launching the discipline now referred to as A.Life. ..."
   1st ed 2004; pb us$30; uk us isbn:0198250800; uk us isbn13:978-0198250807.
   [Also search for: Turing biography]  and  [also search for: AlanTuring].

%A A. A. Appel
%T Alan Turing's Systems of Logic: The Princeton Thesis
%I PrincetonUP
%P 160
%M MAY
%D 2012
%K book, text, c2012, c201x, c20xx, zz0512, c193x, PhD thesis, Logic,
   CSci, Systems of Logic Based on Ordinals, computer science, comp sci,
   halting problem, oracle, machine, computing, maths, theory, Princeton
%X 1st ed 2012; hb us$17; uk us isbn:0691155747; isbn13:978-0691155746.
   "Between inventing the concept of a universal computer in 1936 & breaking the
   German Enigma code during WWII, Alan Turing (1912-1954), the British founder
   of computer science & artificial intelligence, came to Princeton U. to study
   math.logic. Some of the greatest logicians in the world - including Alonzo
   Church, Kurt Godel, John von Neumann & Stephen Kleene - were at P. in the
   1930s, & they were working on ideas that would lay the groundwork for what
   would become known as computer science. Though less well known than his other
   work, T's 1938 Princeton PhD thesis, "Systems of Logic Based on Ordinals,"
   which includes his notion of an oracle machine, has had a lasting influence
   on comp.sci. & maths.. ... a facsimile of the original typescript of the
   thesis along with essays by Andrew Appel & Solomon Feferman ..."
   [Also search for: AlanTuring] etc..


%A G. Farr
%T Remembering Bill Tutte: Another brilliant codebreaker from World War II
%J The Conversation
%M MAY
%D 2017
%K Tutte, news, obit, biog, c2017, c201x, c20xx, zz0617, Bletchley Park,
   Lorenz, code, Colossus, computer, history computing, cypher, break, breaking,
   codebreaker, WW2, WWII
%X "One of the greatest mathematicians and codebreakers of the 20th century,
   William (Bill) Tutte, was born a century ago this Sunday, May 14. ..."</I>
   -- [<A HREF="https://theconversation.com/remembering-bill-tutte-another-brilliant-codebreaker-from-world-war-ii-77556">www</A>]['17].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">B.Park</A>].)
   [Also search for: Bletchley Park]  and  [also search for: colossus].

%T Wladyslaw Marek Turski (1938-2013)
%A A. Tarlecki
%J IPL
%V 114
%N 8
%P 397-398
%M AUG
%D 2014
%K Turski, Wlad, obit, obituary, c2014, c201x, c20xx, zz0514, WG2.1, Algol,
   Algol68, Poland, KLIPA, URAL2, ODRA 1204, ODRA1204, history, computing
%X "... took part in the development of KLIPA, a symbolic programming language
   for the Soviet-made URAL-2 computer, and designed SODA, an original operating
   system for the Polish ODRA-1204 computer  ...  elected a member, and a year
   later the scientific secretary of the famous 'Algol group', IFIP Working
   Group 2.1. A few years later, together with other signatories of the
   'minority report' criticising Algol 68 ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2014.03.015">doi:10.1016/j.ipl.2014.03.015</A>]['14].


%T Karen Uhlenbeck
%D 2019
%K Uhlenbeck, maths, mathematician, STEM, minimal surfaces, bubble, bubbles,
   guage theory, Abel prize, AbelPrize, UTexas, UniTexas, biog, women, www
%X Won the Abel prize in 2019 for "fundamental impact of her work on
   analysis, geometry and mathematical physics".
   KU@[<A HREF="https://en.wikipedia.org/wiki/Karen_Uhlenbeck">wikip</A>]['19].
   Also see the bbc[<A HREF="https://www.bbc.com/news/science-environment-47613929">19/3/2019</A>].


%A W. Aspray
%T John von Neumann and the Origins of Modern Computing
%I MITpress
%P 394
%D 1990
%K vonNeumann, von Neumann, book, text, c1990, c199x, c19xx, history,
   computing, computer, computers, stored program
%X John von Neumann (1903-1957);
   hb; isbn:0262011212; isbn13:978-0262011211.
   [Also search for: stored program computer].

%A A. Bhattacharya
%T The Man from the Future: The Visionary Life of John von Neumann
%I AllenLane
%P 368
%M FEB
%D 2022
%K vonNeumann, book, biog, biography, von Neumann, history, computing
%X 1st ed 2022; hb, us$43; uk us isbn:0241398851; uk us isbn:978-0241398852.


%A Franz de Waal
%J Nature
%V 628
%P 497
%M APR
%D 2024
%K de Waal, deWaal, c202, c202x, c20xx, zz0424, obit, biog, animal behaviour,
   social
%X "Frans de Waal (1948-2024), primatologist who questioned the uniqueness of
   human minds ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-024-01071-y">doi:10.1038/d41586-024-01071-y</A>]['24].
   [Also search for: deWaal animal behaviour].

%A K. S. Thorne
%T John Archibald Wheeler (1911-2008)
%J Science
%V 320
%N 5883
%P 1603
%M JUN
%D 2008
%K Wheeler, c2008, c200x, c20xx, obit, obituary, biog, quantum physics,
   physicist
%X "John Archibald Wheeler, one of the great theoretical physicists of the 20th
   century, died on 13 April, aged 96. I was his student, and I owe much of my
   scientific personality, style, and accomplishments to him, as do more than
   100 other physicists whom he personally mentored. Our love and respect for
   Johnny (as his wife, Janette, told us we could call him after we got our
   doctorates) was enormous. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1159820">doi:10.1126/science.1159820</A>][08].
   Also see J.A.W.@[<A HREF="https://en.wikipedia.org/wiki/John_Archibald_Wheeler">wikip</A>]['21].



%A I. James
%T Remarkable Mathematicians
%I CUP
%P 440
%M MAY
%D 2003
%K book, text, c2003, c200x, c20xx, CUP, biography, history, maths,
   mathematics, mathematician, STEM
%X 60 math'ns 1700-1910, pb au$60; uk us isbn:0521520940.

%A M. L. Shetterly
%T Hidden Figures: The American Dream and the Untold Story of
   the Black Women Mathematicians Who Helped Win the Space Race
%I WilliamMorrow
%P 368
%M SEP
%D 2016
%K book, text, c2016, c201x, c20xx, zz1016, NACA, NASA, Mercury, Apollo,
   black, colored, coloured, woman, women, maths, mathematician, math, science,
   scientist, engineer, STEM,  www, HREF, 1940s, 1950s, 1960s, West Computing,
   human computers, Dorothy Vaughan, Mary Jackson, Katherine Johnson,
   Christine Darden, Langley, film, movie
%X 1st ed 2016; hb us$18; uk us isbn:006236359X;; uk us isbn13:978-0062363596.
   "... true story of the black female mathematicians at NASA at the leading
   edge of the feminist and civil rights movement, whose calculations helped
   fuel some of America's greatest achievements in space ..."
   Also see
   DV@[<A HREF="https://en.wikipedia.org/wiki/Dorothy_Vaughan">wikip</A>]['17],
   KJ@[<A HREF="https://en.wikipedia.org/wiki/Katherine_Johnson">wikip</A>]['17],
   MJ@[<A HREF="https://en.wikipedia.org/wiki/Mary_Jackson_(engineer)">wikip</A>]['17], and
   [<A HREF="https://www.nasa.gov/katherine-johnson/">NASA</A>]['23] &
   [<A HREF="https://crgis.ndc.nasa.gov/historic/Human_Computers">NASA</A>]['17].
   (Also see The_G@[<A HREF="https://www.theguardian.com/lifeandstyle/2016/sep/05/forgot-black-women-nasa-female-scientists-hidden-figures">6/9/2016</A>],
      SciAm@[<A HREF="https://www.scientificamerican.com/article/the-story-of-nasas-real-ldquo-hidden-figures-rdquo/">24/1/2017</A>],
      "... Katherine Johnson ... dies aged 101 ..."
      [<A HREF="https://www.abc.net.au/news/2020-02-25/nasa-mathematician-katherine-johnson-dies-age-101/11997262">abc</A>][25/2/2020].
   And, a young (8-12) readers' edition, HarperCollins, pb us$8;
   uk us isbn:0062662376; uk us isbn13:978-0062662378.)
   (Also dramatised into a movie, 'Hidden Figures', 2016.)

%T Avi Wigderson
%K Wigderson, zz0424, CompSci, TuringAward, award, prize, computer science
%X "... [AW] as recipient of the 2023 ACM A.M. Turing Award for foundational 
   contributions to the theory of computation, inc. reshaping our understanding
   of the role of randomness in computation, & for his decades of intellectual 
   leadership in theoretical C.S.. ..."
   --- ACM@[<A HREF="https://awards.acm.org/about/2023-turing">www</A>]['24].
   AW@[<A HREF="https://en.wikipedia.org/wiki/Avi_Wigderson">wikip</A>]['24].


%A M. Baldwin
%T A new factor in evolution
%J American Naturalist
%V 30
%P 441-451, 536-553
%D 1896
%K biol, biology, c1996, c189x, c18xx, zz0317, Baldwin effect, evolution,
   Darwinism, natural selection, controversial, learning, adaption, ontogeny,
   heredity
%X "In several recent publications I have developed, from different points of
   view, some considerations which tend to bring out a certain influence at work
   in organic evolution which I venture to call 'a new factor". ... The problems
   involved in a theory of organic development may be gathered up under three
   great heads: Ontogeny, Phylogeny, Heredity. ..."
   -- 'a James Baldwin source page' [<A HREF="https://brocku.ca/MeadProject/Baldwin/Baldwin_1896_h.html">brocku</A>]['17].
   Also see BE@[<A HREF="https://en.wikipedia.org/wiki/Baldwin_effect">wikip</A>]['17].
   [Also search for: Baldwin effect].

%A W. L. Bragg
%T The specular reflection of X-rays
%J Nature
%V 90
%N 2250
%P 410-?
%M DEC
%D 1912
%K jrnl, Bragg, c1912, c191x, c19xx, x-ray, xray, crystallography, crystal,
   crystals, structure, Laue, crystallograph, diffraction
%X "In accordance with this, the spots in Laue's crystallographs can be shown to
   be due to partial reflection of the incident beam in sets of parallel planes
   in the crystal on which the atom centres may be arranged, the simplest of
   which are the actual cleavage planes of the crystal. This is merely another
   way of looking at the diffraction."  (via AK.)
   -- [<A HREF="http://dx.doi.org/10.1038/090410b0">doi:10.1038/090410b0</A>]['13].

%A G. U. Yule
%T A mathematical theory of evolution, based on the conclusions of
   Dr. J. C. Willis
%J Philos. Trans. Royal Soc. London, Ser. B
%V 213
%P 21-87
%D 1924
%O J. of the Royal Stat. Soc., vol.88, no.3, pp.433-436, May 1925
%K jrnl, JRSS, evolutionary, phylogenetic, tree, trees, c1924, c192x, c19xx,
   genera, species, frequency, distribution, shape, balance, Yule tree, Markov,
   biol, Udny Yule, power law, network, preferential attachment, Barabasi
%X "... Dr W. was led to 2 conclusions: (i) Species occupying large areas
   [range] are on the whole older ... (ii) The larger genera ... are on the
   whole those occupying larger areas ... (iii) The larger genera are on the
   whole older. ... ...  the proportional frequencies of genera of 1, 2, 3
   species may be expected to form a descending geometric series (i.e., a
   series with a common ratio less than unity). ..."
   -- 92117@[<A HREF="http://www.jstor.org/stable/92117">jstor</A>]['05],
    & [<A HREF="http://dx.doi.org/10.1098/rstb.1925.0002">doi:10.1098/rstb.1925.0002</A>]['15].
   (Also see "... The first use of a preferential attachment mechanism to
    explain power-law distributions appears to have been by Yule in 1925. ..."
    -- [<A HREF="http://en.wikipedia.org/wiki/Barab%C3%A1si%E2%80%93Albert_model">wikip</A>]['14].)

%A J. E. Lennard-Jones
%T Cohesion
%J Proc. of the Physical Soc.
%V 43
%N 5
%P 461-482
%M SEP
%D 1931
%K jrnl, MolBio, c1931, c193x, c19xx, zz1124, chemistry, 12 6, twelve six,
   potential, energy, force, attract, repel, bond, atom, molecule, leonard
%X -- [<A HREF="https://doi.org/10.1088/0959-5309/43/5/301">doi:10.1088/0959-5309/43/5/301</A>]['24].
   Sir John Edward Lennard-Jones, 1894-1954.
   Also see, "... v(r) = 4.eps.[(sigma/r)^{12} - (sigma/r)^{6}] ...
      r is distance, r_min=2^{1/6}.sigma where v_min=-eps ..."
   -- LJp@[<A HREF="https://en.wikipedia.org/wiki/Lennard-Jones_potential">wikip</A>]['24].
   [Also search for: molecule potential].

%A N. W. Timofeef-Reskovsky
%A K. G. Zimmer
%A M. Delbruck
%T Uber die Natur der Genmutation und der Genstruktur
   (On the nature of gene mutation and gene structure)
%J ?
%D 1935
%K MolBio, c1935, c193x, c19xx, zz0112, gene, genes, history, ideas, science,
   biol, molecular biology, physical, research, what is life, three man paper
%X Also see:
   Creating a Physical Biology: The Three-Man Paper and Early Molecular Biology,
       Ed. P.R.Sloan & B.Fogel, U.Chicago Press, 320pp.,
       2011, pb us$35, uk us isbn:0226767833; uk us isbn13:978-0226767833.
     "In 1935 geneticist N.T.-R., radiation physicist K.G.Z., & quantum
     physicist M.D. published ... known subsequently as the 'Three-Man Paper'
     ... advanced work on the physical exploration of the struct. of the gene
     through radiation physics & suggested ways in which physics could reveal
     definite info. about gene structure, mutation, & action. ... popularized
     for a wide audience in the 'What is Life?', lectures of physicist Erwin
     Schrodinger in 1944. ..."
   Reviewed@[<A HREF="http://dx.doi.org/10.1038/480317a">doi:10.1038/480317a</A>][12/'11].

%A C. B. Bridges
%T The BAR "gene" a duplication
%J Science
%V 83
%N 2148
%P 210-211
%M FEB
%D 1936
%K jrnl, MolBio, c1936, c193x, c19xx, gene, genetrics, structural variation,
   duplication, BAR double, BB, reverted, Drosophila
%X [<A HREF="http://dx.doi.org/10.1126/science.83.2148.210">doi:10.1126/science.83.2148.210</A>]['14].

%A A. I. Oparin
%T The Origin of Life
%I Macmillan
%D 1938
%K book, text, MolBio, c1938, c193x, c19xx, Oparin, biol, biology, evolution,
   start, beginning, beginnings, life, amino acids, Miller, Urey, experiment
%X Translated by Sergius Morgulis, Macmillan, 1938.
   "[The book] roughly based on a pamphlet he published in 1924 ..."
   -- about@[<A HREF="http://dx.doi.org/10.1038/491524a">doi:10.1038/491524a</A>]['12].
   (Original 1938 Nature review [<A HREF="http://dx.doi.org/10.1038/142412a0">doi:10.1038/142412a0</A>]['12], costs!)
   Dover, pb 1953, pp.270; uk us isbn:0486602133; uk us isbn13:978-0486602134.
   Acad.Press, 3rd ed 1959 pp.495; uk us asin:B0007FAZUS.

%A C. E. Shannon
%T An algebra for theoretical genetics
%I MIT
%D 1940
%K Phd thesis, c1940, c194x, c19xx, zz1113, MolBio, maths, mathematics,
   Claude Elwood Shannon, population genetics
%X 1721.1/11174@[<A HREF="http://hdl.handle.net/1721.1/11174">mit</A>]['13].
   (via T.S.)

%A K. Drew
%T Conchocelis-phase in the life-history of Porphyra umbilicalis (L.) Kutz
%J Nature
%V 164
%P 748-751
%D 1949
%K jrnl, biol, biology, laver, sea-weed, seaweed, alga Conchocelis, Porphyra,
   life cycle, edible, nori, zoospores,
   Kathleen Drew, c1949, c194x, c19xx, zz0404
%X Showed the filamentous shell boring alga Conchocelis is an
   alternate phase in the life cycle of Porphyra. -- a Manchester scientist.

%A R. Corey
%A J. Donahue
%T Interatomic distances and bond angles in the polypeptide chain of proteins
%J PNAS
%V 72
%P 2899-2900
%D 1950
%K MolBio, PNAS, jrnl, c1950, c195x, c19xx, protein structure, 3D
%X [Also search for: MolBio protein 3D structure c195x].

%A L. Pauling
%A R. B. Corey
%A H. R. Branson
%T The structure of proteins: Two hydrogen-bonded helical configurations of the
   polypeptide chain
%J PNAS
%B 37
%P 205-211
%D 1951
%K jrnl, PNAS, MolBio, c1951, c195x, c19xx, protein, secondary, structure, 3D,
   chains, helix, helices, gamma, alpha
%X (gamma not been seen -- H, B and K, '09.)

%A L. Pauling
%A R. B. Corey
%T The pleated sheet, a new layer configuration of polypeptide chains
%V PNAS
%V 37
%P 251-256
%D 1951
%K jrnl, PNAS, MolBio, c1951, c195x, c19xx, protein, secondary, structure, 3D,
   beta, sheet, strand, extended, chain

%A K. U. Linderstrom-Lang
%T Proteins and Enzymes
%I StanfordUP
%S Lane Medical Lectures, Medical Sciences, Volume VI, 115 pages
%D 1952
%K c1952, c195x, c19xx, zz0717, MolBio, protein, primary, secondary, tertiary,
   structure, origin, terminology
%X 1st ed 1952; pb, asin:B009NI2YAY.
   Kister (2013) attributes the coining of the terms primary-, secondary-,
   and tertiary-structure to L-L (1952).
   [Also search for: MolBio super secondary],  R and R (1973).

%A A. M. Turing
%T The chemical basis of morphogenesis
%J Phil. Trans. of the Royal Soc. (B)
%V 237
%N 641
%P 37-72
%M AUG
%D 1952
%O Reprinted in Bull. Math. Biol, Vol.52, No.1-2, pp.153-197, 1990
%K jrnl, BMB, c1953, c195x, c19xx, Alan Turing, AlanTuring, chemical basis,
   morphogenesis, pattern, patterning, formation, development, skin pattern,
   stripes, spots, reaction diffusion, RD, model
%X "It is suggested that a system of chemical substances, called morphogens,
   reacting together & diffusing through a tissue, is adequate to account for
   the main phenomena of morphogenesis. ... The investigation is chiefly
   concerned with the onset of instability. It is found that there are six
   essentially different forms which this may take. In the most interesting
   form stationary waves appear on the ring. It is suggested that this might
   account, for instance, for the tentacle patterns on Hydra & for whorled
   leaves. ..."
   -- [<A HREF="http://dx.doi.org/10.1098/rstb.1952.0012">doi:10.1098/rstb.1952.0012</A>]['14],
    & [<A HREF="http://www.turingarchive.org/browse.php/B/22">turingarchive</A>]['14],
    & [<A HREF="http://www.jstor.org/stable/92463">Jstor</A>]['14].
   [Also search for: morphogenesis]  and  [also search for: reaction diffusion].

%A P. J. Flory
%T Principles of Polymer Chemistry
%I CornellUP
%P 688
%D 1953
%K book, text, chemistry, chem, c1953, c195x, c19xx, zz0118, polymer chemistry,
   chain, chains
%X 1st ed 1953; hb us$99; uk us isbn:0801401348; uk us isbn13:978-0801401343.
   txt (1.5M), pdf (19.3M), ...
   -- [<A HREF="https://archive.org/details/FloryF.1953PrinciplesOfPolymerChemistry">archive.org</A>]['18].
   Go'gleBo'ks[<A HREF="https://books.google.com.au/books/about/Principles_of_Polymer_Chemistry.html?id=CQ0EbEkT5R0C">www</A>]['18].
   Buy:[<A HREF="http://www.cornellpress.cornell.edu/book/?GCOI=80140100145700">CorUP</A>]['18].

%A J. D. Watson
%A F. H. C. Crick
%T A structure for deoxyribose nucleic acid
%J Nature
%V 171
%P 737-738
%D 1953
%K jrnl, crystallography, DNA, MolBio, c1953, c195x, c19xx, Nobel prize,
   NobelPrize
%X pdf@[<A HREF="http://www.nature.com/nature/dna50/watsoncrick.pdf">www</A>]['14], and
   50th@[<A HREF="http://www.nature.com/nature/dna50/archive.html">www</A>]['14].
   (Also see,
    "... Watson has suggested that ideally Franklin would have been
     awarded the Nobel Prize in Chemistry, along with Maurice Wilkins. ..."
    -- [<A HREF="http://en.wikipedia.org/wiki/Rosalind_Franklin">wikip</A>]['14].)
   [Also search for: Rosalind Franklin DNA].

%A M. H. F. Wilkins
%A A. R. Stokes
%A H. R. Wilson
%T Molecular structure of deoxypentose nucleic acids
%J Nature
%P 738-740
%D 1953
%K jrnl, crystallography, DNA, c1953, c195x, c19xx
%X 50th@[<A HREF="http://www.nature.com/nature/dna50/archive.html">www</A>]['14], and
   [<A HREF="http://en.wikipedia.org/wiki/Rosalind_Franklin">wikip</A>]['14].

%A R. E. Franklin
%A R. G. Gosling
%T Molecular configuration of Sodium Thymonucleate
%J Nature
%P 740-741
%D 1953
%K jrnl, Rosalind Franklin, crystallography, MolBio, c1953, c195x, c19xx, DNA,
   structure
%X 50th@[<A HREF="http://www.nature.com/nature/dna50/archive.html">www</A>]['14], and
   [<A HREF="http://en.wikipedia.org/wiki/Rosalind_Franklin">wikip</A>]['14].

%A F. Crick
%T On protein synthesis (seminar)
%I UCL
%M SEP
%D 1957
%K seminar, c1957, c195x, c19xx, zz1017, MolBio, DNA, RNA, protein synthesis,
   central dogma, lecture, seminar, genes,
   double helix, biol, molecular biology, UCL, Watson
%X "Sixty years ago this week ... Francis Crick, gave a lecture in
   London in which he accurately predicted how genes work ..."
   -- [<A HREF="http://www.bbc.com/news/science-environment-41311087">www</A>]['17].

%A R. Carson
%T Silent Spring
%I Mifflin
%D 1962
%K book, text, c1962, c196x, c19xx, Rachel Carson, environment, environmental,
   birds, pollution, pesticide, insecticide, DDT, chemicals, ecology,
   ecological
%X uk us isbn:0618249060.
   "Silent Spring initially appeared serialized in three parts in the
   June 16, June 23, & June 30, 1962 issues of The New Yorker magazine."
   -- SS@[<A HREF="http://en.wikipedia.org/wiki/Silent_spring">wikip</A>]['13].

%A M. G. Rossmann
%A D. M. Blow
%T The detection of sub-units within the crystallographic asymmetric unit
%J Acta Crystallography
%V 15
%P 24-31
%D 1962
%K jrnl, MolBio, c1962, c196x, c19xx, X-ray, Xray, crystallography, protein,
   structure, molecular replacement, molecularReplacement, phase, phases,
   rotation
%X "The # of structurally identical units within one unit cell often exceeds the
   # of general pos'ns. The angular relationships between any two units, not
   related by space-group symmetry, can be found by rotating the Patterson fn
   until the rotated & original Patterson fns are brought into maximum
   coincidence. For such a rotation, the rotation fn
     R = Sum/h [|Fh|^2 {Sum/p |Fp|^2 G}]
   has a maximum value. G is an interference fn which has large values only when
   the pt p in reciprocal space is brought close to h by the rotation.
   Application of the R fn to horse haemoglobin gives a dominant peak that
   corr. accurately to the relative orientation of the alpha & beta chains."
   -- pdf@[<A HREF="http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/publications/1960.php">lab</A>]['11].
   [Also search for: MolBio Xray crystallography].

%A A. C. Traub
%A J. Orbach
%T Psychophysical studies of body-image. I. The adjustable body-distorting
   mirror
%J Arch. Gen. Psychiatry
%V 11
%P 53-66
%D 1964
%K jrnl, c1964, c196x, c19xx, body image, distorted, psychology

%A H. J. Muller
%T The relation of recombination to mutational advance
%J Mutation Research/ Fundamental and Molecular Mechanisms of Mutagenesis
%V 1
%N 1
%P 2-9
%M MAY
%D 1964
%K MolBio, Muller's ratchet, Mullers, c1964, c196x, c19xx, biol, mutation,
   error rate, mutant, fitness, selection, zz1205
%X "... a formula has been derived that approximately the ratio of the rate of
   accumulation of advantageous mutant genes in a population that undergoes
   recombination to the rate in an otherwise non-recombining one. ...  a
   irreversible ratchet mechanism exists in the non-recombining species (unlike
   the recombining ones) that prevents selection, even if intensified, from
   reducing the mutational loads below the lightest that were in existence when
   the intensified selection started, whereas, contrariwise, "drift", & what
   might be called "selective noise" must allow occasional slips of the
   lightest loads in the direction of increased weight."
   -- [<A HREF="http://dx.doi.org/10.1016/0027-5107(64)90047-8">doi:10.1016/0027-5107(64)90047-8</A>]['05].

%A D. A. Brant
%A P. J. Flory
%T The configuration of random polypeptide chains. I. Experimental Results
%J J. Amer. Chem. Soc.
%V 87
%N 13
%P 2788-2791
%MD 1965
%K jrnl, JACS, c2965, c196x, c19xx, zz0118, chemical, polymer, chain, chains,
   protein, 3D, structure, folding, random, amino acids, AA,
   theory, experimental results
%X Part 1, experimental results, 87(13), pp.2788-2791, July 1965
   -- [<A HREF="https://doi.org/10.1021/ja01091a002">doi:10.1021/ja01091a002</A>]['18].
   Part 2, theory, 87(13), pp.2791-2800, July 1965
   -- [<A HREF="https://doi.org/10.1021/ja01091a003">doi:10.1021/ja01091a003</A>]['18].
   [Also search for: Flory book].

%A R. T. Paine
%T Food web complexity and species diversity
%J Amer. Naturalist
%V 100
%N 910
%P 65-75
%M JAN-FEB
%D 1966
%K jrnl, c1966, c196x, c19xx, zz0410, food web, webs, niche, ecology,
   complexity, species diversity, predator, prey
%X '... hypothesis ... "local species diversity is directly related to the
   efficiency with which predators prevent the monopolization of the major
   requisites by one species." ...'   [35 refs].
   -- @[<A HREF="http://www.jstor.org/stable/2459379">Jstor</A>]['10],
   or @[<A HREF="http://biology.unm.edu/jhbrown/Documents/511Readings/Paine%201966.pdf">umn.edu</A>]['10].

%A A. G. Cairns-Smith
%T The origin of life and the nature of the primitive gene
%J JTB
%V 10
%N 1
%P 53-88
%M JAN
%D 1966
%K jrnl, JTB, MolBio, c1966, c196x, c19xx, zz0916, origin, origins, life,
   CairnsSmith, mineral, crystal, crystals, gene, genes, Miller, controversial
%X "It is proposed that life on earth evolved through natural selection from
   inorganic crystals. During the formation of a crystal, certain kinds of
   lattice imperfections usually replicate as a necessary part of the
   crystallization process. In so far as those imperfections that replicate are
   thus self-selecting ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0022-5193(66)90178-0">doi:10.1016/0022-5193(66)90178-0</A>][9/'16].
   [Also search for: CairnsSmith].
   (Also see the bbc[<A HREF="http://www.bbc.com/earth/story/20160823-the-idea-that-life-began-as-clay-crystals-is-50-years-old">24/8/2016</A>].)

%A W. Hennig
%T Phylogenetic Systematics
%I U. IllinoisPress
%D 1966
%K book, text, c1966, c196x, c19xx, zz0413, cladistics, taxonomy, phylogenetic,
   evolutionary, trees, tree, clade
%X (Also see [<A HREF="http://dx.doi.org/10.1038/496295a">doi:10.1038/496295a</A>]['13].)
   [Also search for: phylogenetic].

%A C. Levinthal
%T How to fold graciously
%J Mossbauer Spectroscopy in Biol. Sys.
%W Proc. of a mtg at Allerton House, Monticello, Illinois
%V 67
%N 41
%P 22-24
%D 1969
%K conf, MolBio, c2020, c202x, c20xx, zz0920, protein fold, folding, structure,
   Levinthal's paradox, energy, proteins, 3D
%X "... If we consider a protein containing 2,000 atoms with no structural
   restrictions, such a macromolecule would possess 6,000 degrees of freedom.
   ... is the final conformation necessarily the one of lowest free energy? We
   do not feel that it has to be. It obviously must be a metastable state which
   is in a sufficiently deep energy well to survive possible perturbations in a
   biological system. If it is the lowest energy state, we feel it must be the
   result of biological evolution; i.e., the first deep metastable trough
   reached during evolution happened to be the lowest energy state. You may then
   ask the question, 'Is a unique folding necessary for any random 150-amino
   acid sequence?' & I would answer, 'Probably not.' Some experimental support
   for this statement comes from the difficulty many of us are all too aware of
   in attempting to crystallize peptides. ..."
   -- [<A HREF="https://web.archive.org/web/20110523080407/http://www-miller.ch.cam.ac.uk/levinthal/levinthal.html">web.archive</A>]['20],
      [<A HREF="https://www.cc.gatech.edu/~turk/bio_sim/articles/proteins_levinthal_1969.pdf">gatech</A>]['20].
   Also see Lparadox@[<A HREF="https://en.wikipedia.org/wiki/Levinthal%27s_paradox">wikip</A>]['20].
   [Also search for: MolBio Anfinsen dogma].

%A A. M. Lesk
%T Pictorial pattern recognition and the phase problem of X-ray crystallography
%J CACM
%V 15
%N 1
%P 3-6
%M JAN
%D 1972
%K jrnl, CACM, MolBio, c1972, c197x, c19xx, X-ray, Xray, crystal, 3D, protein,
   AMLesk, structure, determination, phase problem, Patterson function, Okl, 0kl
%X "... 3D graphics systems coupled to powerful digital computers encourages the
   development of algs. adapted to this environment. ... make possible a number
   of approaches to X-ray structure determination based on molecular model
   building, i.e. the use of chemical information to frame "structural
   hypotheses" which can computationally be tested and refined by reference to
   the experimental data.  Application of std pattern recognition algs. is
   hindered by the fact that the cross-correlation between a model and the
   correct structure cannot be computed because of a fundamental incompleteness
   in the measured data. However, it is possible to compute an UPB to such a
   cross-correlation. A simple example demonstrates that this info. can be the
   basis of a technique for structure determination that can make effective use
   of an interactive graphics system. Model building by cross-correlations has
   intrinsic advantages over usual crystallographic techniques based on the
   autocorrelation or Patterson function, especially for large structures. This
   is significant, for crystallography of biological macromolecules has been and
   will continue to be a field of intense interest."  (via arunK.)
   -- [<A HREF="http://dx.doi.org/10.1145/361237.361239">doi:10.1145/361237.361239</A>]['11].

%A T. Dobzhansky
%T Nothing in biology makes sense except in the light of evolution
%J The American Biology Teacher
%V 35
%P 125-129
%M MAR
%D 1973
%K c1973, c197x, c19xx, zz0309, evolution, creationism, intelligent design,
   essay, biology, origins, life, religion, theory, science, scientific,
   Darwinian, debate, essay
%X Theodosius Dobzhansky (1900-1975)
   -- TD@[<A HREF="https://en.wikipedia.org/wiki/Theodosius_Dobzhansky">wikip</A>]['22],
      [<A HREF="http://people.delphiforums.com/lordorman/light.htm">www</A>]['09].
   Also see
     'Biology, molecular and organismic', Am. Zool., 4(4), pp.443-452, 1964,
      -- [<A HREF="http://dx.doi.org/10.1093/icb/4.4.443">doi:10.1093/icb/4.4.443</A>]['09],
     the Soc. for Integrative and Comparative Biol..

%A L. Van Valen
%T A new evolutionary law
%J Evol. Theor.
%V 1
%P 1-30
%D 1973
%K jrnl, evolution, c1973, c197x, c19xx, vanValen, sex, why,
   sexual reproduction, Red Queen hypothesis, biology, biol, origin, parasite,
   parasites, coevolution, host, hosts, species, law of extinction, death,
   demise, decline, competition
%X "All groups for which data exist go extinct at a rate that is constant for a
   given group. When this is recast in ecological form (the effective
   environment of any homogeneous group of organisms deteriorates at a
   stochastically constant rate), no definite exceptions exist although a few
   are possible. ..."
   -- [<A HREF="https://www.mn.uio.no/cees/english/services/van-valen/evolutionary-theory/volume-1/vol-1-no-1-pages-1-30-l-van-valen-a-new-evolutionary-law.pdf">uio.no</A>]['19],
      [<A HREF="https://marine.rutgers.edu/pubs/private/VanValen%201973%20Evol.%20Theor..pdf">rutg'rs</A>]['19].
   "... geometric distribution of life spans of species, genera, and families
   ... defied  any simple notion of how accumulating effects of some kind ...
   could lead to the ultimate death of a species. ... more convincingly
   explained by assuming an ongoing coevolutionary arms race between a species
   and its competitors and enemies." -- Schmid-Hempel '01.
   (*Also see V-V@[<A HREF="https://en.wikipedia.org/wiki/Leigh_Van_Valen">wikip</A>]['19],
     and [<A HREF="http://leighvanvalen.com/evolutionary-theory/">Evol.Th.</A>]['19] vols.1-12.*)
   [Also search for: sexual reproduction why].

%A W. Kabsch
%T A solution for the best rotation to relate two sets of vectors
%J Acta Crystallographica Sec.A
%V 32
%N 5
%P 922-923
%D 1976
%K jrnl, c1976, c197x, c19xx, zz1122, vector, point set, sets, points,
   superposition, rotation, 3D
%X "A simple procedure is derived which determines a best rotn of a given vector
   set into a 2nd vector set by minimizing the wtd sum of squared deviations.
   ... generalized for any given metric constraint on the transformation."
   -- [<A HREF="https://doi.org/10.1107/S0567739476001873">doi:10.1107/S0567739476001873</A>]['22].
   (Also see KA@[<A HREF="https://en.wikipedia.org/wiki/Kabsch_algorithm">wikip</A>]['22].)
   [Also search for: Kearsley c1990],  for a quat'n approach.

%A M. Levitt
%A C. Chothia
%T Structural patterns in globular proteins
%J Nature
%V 261
%N 5561
%P 552-558
%M JUN
%D 1976
%K jrnl, MolBio, c1976, c197x, c19xx, zz0916, pattern, protein, structure, fold,
   polypeptide chain, conformation, secondary, contact, domains, viaAK
%X "A simple diagrammatic representation has been used to show the arrangement
   of alpha helices and beta sheets in 31 globular proteins, which are
   classified into four clearly separated classes. The observed arrangements
   are sig. non-random in that pieces of secondary structure adjacent in seq.
   along the polypeptide chain are also often in contact in three dimensions."
   -- [<A HREF="http://dx.doi.org/10.1038/261552a0">doi:10.1038/261552a0</A>]['16].

%A G. Bell
%T The Masterpiece of Nature: The Evolution and Genetics of Sexuality
%I UCBpress
%P 635
%D 1982
%K book, text, c1982, c198x, c19xx, sex, sexual reproduction, biology, biol,
   evolution, origin, species
%X us isbn:0520045831; us isbn13:978-0520045835.

%A W. D. Hamilton
%T Pathogens as causes of genetic diversity in their host populations
%B Population biology of infectious diseases
%E R. D. Anderson
%E R. M. May
%I Springer
%P 269-296
%D 1982
%K MolBio, c1982, c198x, c19xx, why, sexual reproduction, population biology,
   evolution, origin, sex, pathogen, parastite, parasites, host, coevolution
%X [Also search for: sexual reproduction why].

%A R. Anderson
%A R. May
%T The logic of vaccination
%J New Sci.
%V 96
%N 1332
%P 410-415
%M NOV
%D 1982
%K MolBio, c1982, c198x, c19xx, zz0820, BobMay, vaccine, vaccination, infection,
   disease, epidemic, pandemic, measles, smallpox, polio, herd immunity
%X -- ref@[<A HREF="https://pubmed.ncbi.nlm.nih.gov/11655494/">ncbi</A>]['20].
   [Also search for: vaccination].

%A A. T. Brint
%A P. Willett
%T Algorithms for the identification of three-dimensional maximal common
   substructures
%J J. Chem. Inf. Comput. Sci. (? J. Chem. Info. and Modeling ?)
%V 27
%N 4
%P 152-158
%D 1987
%K jrnl, JCICS, c1987, c198x, c19xx, 3D, maximal, maximum, common, structure,
   substructure, MCS, subgraph, algorithm, Crandell, Smith, crystallography,
   chemical compound
%X "... set of atoms and assoc. interatomic dists., ..."
   (Also see [<A HREF="http://dx.doi.org/10.1021/ci00056a002">doi:10.1021/ci00056a002</A>]['08].)
   ([Also search for: geometric hashing].)

%A A. Goldsworthy
%T Why did nature select green plants?
%J Nature
%V 328
%P 207-208
%M JUL
%D 1987
%K jrnl, MolBio, c1987, c198x, c19xx, green plant, origins, origin,
   photosynthesis, why are plants green, chlorophyll, halobacterium halobium,
   bacteriorhodospin, pigment, alga, algae, light, CO2
%X Green becuse they do not absorb green light, but why not?
   Perhaps because Halobacterium halobium *does*,
   perhaps as *did* other early life forms.
   -- [<A HREF="http://dx.doi.org/10.1038/328207b0">doi:10.1038/328207b0</A>]['10].

%A F. Sanger
%A S. Nicklen
%A A. R. Coulson
%T DNA sequencing with chain-terminating inhibitors
%J PNAS
%V 74
%N 12
%P 5463-5467
%M DEC
%D 1977
%K jrnl, PNAS, MolBio, c1977, c197x, c19xx, DNA, sequencing technology, Sanger,
   sequence, nucleotide, nucleotides, dideoxy, arabinonucleoside analogues,
   chain-terminating inhibitors, varphiX174, bacteriophage, chemistry, chem,
   method, Nobel prize, NobelPrize
%X "A new method for determining nucleotide sequences in DNA is described. It
   is similar to the "plus and minus" method [Sanger, F. & Coulson, A. R. ('75)
   J. Mol. Biol. 94, 441-448] but makes use of the 2',3'-dideoxy &
   arabinonucleoside analogues of the normal deoxynucleoside triphosphates,
   which act as specific chain-terminating inhibitors of DNA polymerase. The
   technique has been applied to the DNA of bacteriophage varphiX174 and is
   more rapid and more accurate than either the plus or the minus method."
   -- [<A HREF="http://www.pnas.org/content/74/12/5463.short">pnas</A>]['09],
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/271968">pubmed</A>]['09] (free),
   full[<A HREF="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC431765/">ncbi</A>]['09].
   "FS ... awarded two Nobel Prizes. ... S's first triumph was to determine the
   complete AA seq. of the 2 polypeptide chains of insulin in '55. ... developed
   the 'dideoxy' method for seq. DNA molecules ... the Sanger method ..."
   -- FS@[<A HREF="http://en.wikipedia.org/wiki/Frederick_Sanger">wikip</A>]['09].
   [Also search for: DNA sequencing technology MolBio].

%A D. J. Abraham
%A A. J. Leo
%T Extension of the fragment method to calculate amino acid zwitterion
   and side chain partition coefficients
%J Proteins: Structure, Function and Genetics
%V 2
%P 130-152
%D 1987
%K DNA, NA, MolBio

%A P. Argos
%T Analysis of sequence-similar pentapeptides in unrelated protein tertiary
   structures: Strategies for protein folding and a guide for site-directed
   mutagenesis
%J J. Mol. Biol.
%V 197
%P 331-348
%D 1987
%K jrnl, DNA, AA, MolBio, JMB

%A R. J. T. Corbett
%A R. S. Roche
%T The identification of large peptide fragments produced from proteins of known
   sequences: a computerized approach using amino acid composition indexes and
   its application to thermolysin
%J Analytical Biochem.
%V 162
%P 546-552
%D 1987
%K DNA, AA, MolBio

%A A. Danckaert
%A C. Mugnier
%A P. Dessen
%A M. Cohen-Solal
%T A computer program for the design of optimal synthetic oligonucleotides
   probes for protein coding genes
%J Comp. Appl. BioSci.
%V 3
%P 303-307
%D 1987
%K CABIOIS, Bioinformatics, MolBio, protein, algorithm, MolBio

%A G. Deleage
%A B. Roux
%T An algorithm for protein secondary structure prediction based on class
   prediction
%J Protein Engineering
%V 1
%P 289-294
%D 1987
%K MolBio, secondary structure, SS, protein, MolBio

%A G. Deleage
%A B. Tinland
%A B. Roux
%T A computerized version of the Chou and Fasman method for predicting the
   secondary structure of proteins
%J Analytical Biochem.
%V 165
%P 200-207
%D 1987
%K MolBio, protein, AA, secondary structure

%A D. G. George
%A H. W. Mewes
%A H. Kihara
%T A standardized format for sequence data exchange
%J Protein Seq. Data Anal.
%V 1
%P 27-39
%D 1987
%K DNA, database, data base, MolBio

%A J. -F. Gibrat
%A J. Garnier
%A B. Robson
%T Further developments of protein secondary structure prediction using
   information theory. New parameters and consideration of residue pairs
%J J. Mol. Biol.
%V 198
%P 425-443
%D 1987
%K JMB, secondary structure, information theory, entropy, SS,
   alpha helix, beta sheet, extended, coil, turn, pair, pairs, GOR, MolBio
%X Garnier Osguthorpe Robson method revised for current protein data base.
   Second level approx involving pairs of residues provides a better model
   but database still not big enough to get good parameter estimates.
   Attempt to overcome this problem.
   New alg 7% better,  63% accurate for 3 states  alpha helix,
   beta sheet, coil.  (69.7% if predicted protein kept in database.)

%A O. Gotoh
%T Pattern matching of biological sequences with limited storage
%J Comp. Appl. BioSci.
%V 3
%P 17-20
%D 1987
%K CABIOS, Bioinformatics, DNA, pattern matching, similarity,
   LCS, algorithm, space, MolBio

%A B. Keil
%T Proteolysis data bank: specificity of alpha-chymotrypsin from computation of
   protein cleavage
%J Protein Seq. Data Anal.
%V 1
%P 13-20
%D 1987
%K MolBio

%A V. Krchnak
%A O. Mach
%A A. Maly
%T Computer prediction of potential immunogenic determinants from protein amino
   acid sequence
%J Analytical Biochem.
%V 165
%P 200-207
%D 1987
%K MolBio

%A A. M. Lesk
%T The Biocomputing program at EMBL
%V Trends in Biotechnology
%V 5
%P 317-318
%D 1987
%K AMLesk, EMBL, MolBio, computing, molecular biology

%A K. Nishikawa
%A H. Nakashima
%A M. Kanehisa
%A T. Ooi
%T Detection of weak sequence homology of proteins for tertiary structure
   prediction
%J Protein Seq. Data Anal.
%V 1
%P 107-116
%D 1987
%K homology, similarity, LCS, protein, tertiary structure, MolBio

%A S. Pascarella
%A F. Bossa
%T PROTEUS: a suite of programs for prediction of structural features of
   proteins using an Apple IIe
%J Comp. Appl. BioSci.
%V 3
%P 325-331
%D 1987
%K CABIOS, Bioinformatics, structure, protein, MolBio

%A W. W. Ralph
%A T. Webster
%A T. F. Smith
%T A modified Chou and Fasman protein structure algorithm
%J Comp. Appl. BioSci.
%V 3
%P 211-216
%D 1987
%K CABIOS, Bioinformatics, structure secondary, SS, tertiary, protein, MolBio

%A J. K. M. Rao
%T New scoring matrix for amino acid residue exchanges based on residue
   characteristic physical parameters
%J Int. J. Pept. Prot. Res.
%V 29
%P 276-281
%D 1987
%K LCS, similarity, distance matrix, amino acid, MolBio

%A A. H. Reisner
%A C. A. Bucholtz
%T Two-dimensional abstract representations (signatures) of proteins
%J Comp. Appl. BioSci.
%V 3
%P 171-175
%D 1987
%K CABIOS, Bioinformatics, MolBio

%A G. Von Heijne
%T SIGPEP: a sequence database for secretory signal peptides
%J Protein Seq. Data Anal.
%V 1
%P 41-42
%D 1987
%K database, data base, MolBio

%A R. Swanson
%T A unifying concept for the amino acid code
%J Bull. Math. Biol.
%V 46
%N 2
%P 187-203
%M MAR
%D 1984
%K jrnl, BMB, c1984, c198x, c19xx, DNA, genetic, amino acids, protein, Grey,
   Gray code, codon, MolBio, genetic code, similarity, hydropathic, hydrophilic,
   hydrophobic, cloisteredness, cloistered, small, large, internal, external,
   alphabet, origin
%X "The struct. of the genetic code is related to a Gray code, which is a
   plausible theor. model for an amino acid code. The proposed model implies
   that the most important factor in shaping the code was the effects of
   mistakes in translation, not effects of mutations. Another possible
   implication is that the preservation of stiffness & flexibility at
   appropriate places in a protein chain is as important in protein structure as
   the appropriate placement of hydrophilic (external) & hydrophobic (internal)
   residues. Other results are a simple conceptualization of the relationships
   among the 20 AAs & their relations to their codons. The detailed relns. are
   summarized in the following `similarity alphabet': ala, thr, gly, pro, ser;
   asp, asn, glu, gln, lys;  his, arg, trp, tyr, phe;  leu, met, ile, val, cys;
   (ATGPS DNEQK HRWYF LMIVC in the one-letter code). This alphabet falls into
   4 groups of AAs: small, external, large, internal. The approx. reln of the
   groups to their codons is expressed as: the 1st base of a codon controls size
   - a purine means a small amino acid, a pyrimidine means large; the middle
   base controls cloisterednes - purine means external, pyrimidine means
   internal. These relationships express the min. change principle upon which
   the code appears to be founded."
   -- [<A HREF="http://dx.doi.org/10.1007/BF02460068">doi:10.1007/BF02460068</A>]['07].

%A M. Zuker
%A D. Sankoff
%T RNA secondary structures and their prediction
%J Bull. Math. Biol.
%V 46
%N 4
%P 591-621
%D 1984
%K jrnl, secondary structure, SS, RNA, DPA, BMB, MolBio
%X dynamic programming algorithm to minimise free energy.

%A M. A. Jimenez-Montano
%T On the syntactic structure of protein sequences and the concept of
   grammar complexity
%J Bull. Math. Biol.
%V 46
%N 4
%D 1984
%K jrnl, MolBio, x1984, c198x, c19xx, syntax, grammar, sequence, string,
   structure, amino acid, classification of amino acids
%X grammar complexity gives a measure of aperiodicity of a sequence.
   and also an optimization criterion for evaluating categorization
   of amino acids.
   paper derives an optimum categorization of the 20 amino acids.

%A R. White
%A J-M. Lalouel
%T Chromosome mapping with DNA markers
%J Scientific American
%M FEB
%D 1988
%V 258
%N 2
%P 20-28
%K gene, chromosome, map, DNA finger print, printing, fingerprint, MolBio
%X variable sequences in the DNA of human chromosomes act as genetic
   landmarks. Individual markers serve for tracing defective genes;
   collectively the markers provide the elements of a chromosome map.
   100,000 genes on 23 pairs of chromosomes; each gene ~10,000 base pairs.
   Article about technique of finding markers or distinctive sequences
   in human genes.
   Some more general introductory material too.

%A H. M. Martinez
%T A flexible multiple sequence alignment program
%J NAR
%V 16
%N 5A
%M MAR
%D 1988
%P 1683-1692
%K NAR, DNA, LCS, alignment, multiple string, homology, similarity, MolBio

%A W. Ebeling
%A M. A. Jimenez-Montano
%T On grammars, complexity and information measures of biological
   macromolecules
%J Mathematical Biosciences
%V 52
%P 53-71
%D 1980
%K gene, RNA, protein, information theory, grammar, MolBio

%A K. L. Klatsky
%A G. D. Friedman
%A A. B. Seigelaub
%T Alcohol consumption before myocardial infarction. Results from
   the Kaiser-Permanente epidemiologic study of myocardial infarction
%J Ann. Intern. Med.
%V 81
%P 294-301
%D 1974
%K jrnl, c1974, c197x, c19xx, beer, wine, red, white, spirits, disease,
   heart, attack, attacks, cardiovascular, CHD, coronary, zz1003

%A M. Levitt
%A A. Warshel
%T Computer simulation of protein folding
%J Nature
%V 253
%P 694-698
%M FEB
%D 1975
%K jrnl, MolBio, c1975, c97x, c19xx, zz1122, protein folding, fold, simulation,
   conformation, simulate, simulation
%X "A new & very simple rep'n of protein conformations has been used together
   with energy minimisation & thermalisation to simulate protein folding. Under
   certain condns, the method succeeds in 'renaturing' bovine pancreatic
   trypsin inhibitor from an open-chain conformation into a folded conformation
   close to that of the native molecule."
   -- [<A HREF="https://doi.org/10.1038/253694a0">doi:10.1038/253694a0</A>]['22], (13 refs).
   [Also search for: protein folding simulation].

%A M. Hasegawa
%A T.-A. Yano
%T The genetic code and the entropy of protein
%J Mathematical Biosciences
%V 24
%P 169-182
%D 1975
%K jrnl, protein, c1975, c197x, c19xx, RNA, mRNA, entropy, information theory,
   MolBio
%X The entropy of amino acid sequences coded in DNA or mRNA
   is taken as a measure of diversity of proteins.
   It is considered that the higher the value of entropy, the
   greater the potential information variety coded by the nucleic acid.
   The mRNA chain is considered as a stationary second order Markov
   chain composed of the four bases. As a consequence, the biased
   DNA base composition and the rarity of the base doublet CpG of
   the higher animals are explained.
      Because code to amino acids not uniform, a uniform distribution
   of ACG and T would give a nonuniform distribution of amino acids.
   They calculate the distrib of ACG/T triples that would maximise entropy of
   protein (amino acid string) and it is close to that of higher mammals
   => get max diversity of protein for given message lengths.

%A L. L. Gatlin
%T Conservation of Shannon's redundancy for proteins
%J J. Mol. Evol.
%V 3
%P 189-208
%D 1974
%K redundancy, shannon, information theory, randomness, DNA, protein, MolBio
   JME
%X information parameters for random protein strings are derived using
   Monte Carlo methods. Real sequences are compared with random
   standards for specific lengths.
     Non-periodic proteins as a whole have random Shannon redundancies R
   except for constraints imposed by their short lengths and the genetic
   code. This random R value is conserved within the basic informational
   unit of proteins throughout the evolutionary process but not the
   components of R, D1 and D2.  Highly periodic proteins are
   identifiable from their high R value and their high D1  low D2
   pattern.  A parameter for calculating the degree of periodicity
   is defined. There is an unexpected suggestion of generalized, residual
   periodicity in proteins as a whole.

%A A. Cornish-Brown
%A A. Marson
%T Evaluation of non-randomness of protein compositions
%J J. Mol. Evol.
%V 10
%P 231-240
%D 1977
%K randomness, protein, amino acid, covarions, MolBio, JME
%X A method described for assessing non-randomness of protein compositions,
   based on the chi-squared statistic fore the differences between
   the observed numbers of residues of each type and the number
   expected for a random distribution of codons. The analysis indicates that
   changes of at least 30% of the residues in natural proteins are selected
   against.

%A F. Jacob
%T Evolution and tinkering
%J Science
%V 196
%N 4295
%P 1161-1166
%M JUN
%D 1977
%K essay, MolBio, c1977, c197x, c19xx, zz1220, protein, structure, evolution,
   bricolage, tinkering
%X -- 1744610@[<A HREF="https://www.jstor.org/stable/1744610">Jstor</A>]['20],
      [<A HREF="https://doi.org/10.1126/science.860134">doi:10.1126/science.860134</A>]['20].
   [Also search for: MolBio bricolage].

%A R. Doolittle
%T Of Urfs and Orfs: A Primer on How to Analyze Derived Amino Acid Sequences
%I UnivSciBooks
%P 103
%D 1986
%K book, text, MolBio, c1986, c1998x, c19xx, zz0920, ORF, DNA, genetics
%X 2nd edn 1991; pb us$47; uk us isbn: 0935702547; uk us isbn13:978-0935702545.
   "... seq. is 'open' when read in an appropriate frame, which is to say that
   there is a long run of AA codons before the appearance of a terminator codon.
   How can we find out if this 'unidentified reading frame' (URF) really codes
   for a genuine protein, and how can we identify it if it exists? ..."

%A A. M. Lesk
%T Molecular speleology: the exploration of crevices in proteins for
   prediction of binding sites, design of drugs and analysis of
   surface recognition
%J Acta Cryst.
%V A42
%P 83-85
%D 1986
%K jrnl, MolBio, AMLesk, c1986, c198x, c19xx, zz0420, protein 3D structure,
   surface, active site, binding site, pocket, ligand, inhibitor, drug design
%X "A method is described for analyzing molecular-surface complementarity,
   inc. the binding of ligands to proteins or the interaction of elts of
   secondary struct. in protein interiors. A computer program can identify &
   model molecules that satisfy general criteria for good binding affinity.
   Computational tests are presented. This approach is likely to have useful
   application in the analysis of surface recognition in proteins, inc. the
   identification of binding sites, & in the design of drugs for specific
   targets, by (i) suggesting potential pharmacophores to the medicinal chemist
   for further computational analysis or laboratory testing, (ii) suggestion of
   derivatives of a known ligand to enhance its affinity, or (iii) searching a
   data base of known drugs for a match to the predicted ligand."
   -- [<A HREF="https://doi.org/10.1107/S010876738609983X">doi:10.1107/S010876738609983X</A>]['20].
   [Also search for: MolBio protein surface] and [also search: for AMLesk].

%A W. R. Taylor
%T The classification of amino acid conservation
%J J. Theor. Biol.
%V 119
%P 205-218
%D 1986
%K AA, amino acid, class, classification, MolBio
%X uses Venn diagrams to represent classifications of amino acids -
   into overlapping classes.
   Aim to indicate similarity (of some attribute) in multiple alignments.

%A S. M. Stigler
%T Laplace's 1774 memoir on inverse probability
%J Statistical Science
%V 1
%N 3
%P 359-363
%D 1986
%K jrnl, stats, c1986, c198x, c19xx, zz1017, Laplace, Bayes, Bayess, theorem,
   stats, statistics, history, posterior, inverse probability,
   Memoire sur la probabilite des causes par les evenemens, c1774, c177x, c17xx
%X "Laplace's first major article on mathematical statistics was published in
   1774. It is arguably the most influential article in this field to appear
   before 1800, being the first widely read presentation of inverse probability
   and its application to both binomial and location parameter estimation. After
   a brief intro., and English translation of this epochal memoir is given."
   -- [<A HREF="https://projecteuclid.org/download/pdf_1/euclid.ss/1177013620">www</A>]['17].
   Introduction to S's translation (pp.364-378 same issue) of ...
   P.S.Laplace, Memoire sur la Probabilite des Causes par les Evenemens, 1774,
   (Memoir on the Probability of the Causes of Events),
   -- [<A HREF="https://projecteuclid.org/download/pdf_1/euclid.ss/1177013621">www</A>]['17].
   [Also search for: Bayes c17xx].

%A B. D. Silverman
%A R. Linsker
%T A measure of DNA periodicity
%J J. Theor. Biol.
%V 118
%P 295-300
%D 1986
%K DNA, base, fourier transform, FFT, MolBio
%X A fourier transform of a sequence of the 4 bases ACGT in a stretch
   of DNA is defined. Transform is invariant to labelling of bases and
   gives a measure of periodicity.
   Represents each base as a vector from the centre of a tetrahedron
   to one of the vertices.
   Resolve vectors in 3-D axes. Get fourier series of components
   in each axis. Sum the absolute values squared in the 3 directions.
   This is a scalar measure of the spectral content,
   invariant in axis choic, in permutations of bases and
   it is the FT of the inner product autocorrelation function of
   the vector-series.

%A J. Graham White
%A E. Southgate
%A J. N. Thomson
%A S. Brenner
%T The structure of the nervous system of the nematode Caenorhabditis elegans
%J Phil. Trans. Royal Soc. B
%V 314
%N 1165
%M NOV
%D 1986
%K jrnl, MolBio, c1986, c198x, c19xx, zz0324, animal, worm, nematode,
   Caenorhabditis elegans, Celegans, neurons, synapses, connectome,
   connections, network
%X "The structure & connectivity of the nervous system of the nematode
   Caenorhabditis elegans has been deduced from reconstructions of electron
   micrographs of serial sections. The hermaphrodite nervous system has a total
   complement of 302 neurons, which are arranged in an essentially invariant
   structure. Neurons with similar morphologies & connectivities have been
   grouped together into classes; there are 118 such classes. Neurons have
   simple morphologies with few, if any, branches ..."
   -- [<A HREF="https://doi.org/10.1098/rstb.1986.0056">doi:10.1098/rstb.1986.0056</A>]['23].
   [Also search for: MolBio connectome]  and  [also search for: Celegans].

%A W. H. E. Day
%A D. Sankoff
%T Computational complexity of inferring phylogenies from
   chromosome inversion data
%J J. Theor. Biol.
%V 124
%P 213-218
%D 1987
%K phylogeny, evolutionary tree, chromosome, DNA, gene, family tree, MolBio
%X problem is NP complete NPC

%A P. Tuffery
%A P. Dessen
%A C. Mugnier
%A S. Hazout
%T Restriction map construction using a complete sentences compatibility
   algorithm
%J Comp. Appl. BioSci.
%V 4
%N 1
%M JAN
%D 1988
%P 103-110
%K CABIOS, Bioinformatics, restriction site mapping, RSM, enzyme,
   plasmid, plasmap, DNA, MolBio

%A B. Bellon
%T Construction of restriction maps
%J Comp. Appl. BioSci.
%V 4
%N 1
%M JAN
%D 1988
%P 111-115
%K CABIOS, Bioinformatics, restriction site mapping, RSM, map, enzyme,
   plasmid, plasmap, DNA, MolBio
%X written in Prolog II

%A J. C. W. Shepherd
%T Method to determine the reading frame of a protein from the purine/pyrimidine
   genome sequence and its possible evolutionary justification
%J Proc. Natl. Acad. Sci. (USA)
%V 78
%N 3
%P 1596-1600
%M MAR
%D 1981
%K DNA, purine, pyrimidine, MolBio, genetic code, coding, PNAS
%X periodic variations correlate positions of p and p and of the 4 bases
   A C G T.  May be remnant of early comma free code,  suggest code
   was RNY  where   R=purine={A,G}, Y=pyrimidine={C,T}, N=any

%A R. Staden
%T Measurements of the effects that coding for a protein has on a DNA
   and their use for finding genes
%J NAR
%V 12
%N 1
%D 1984
%P 551-567
%K NAR, DNA, MolBio
%X protein genes can be found either by looking at effects
   that coding for protein has on the coding sequence.
   1. uneven use of amino acids
   2. uneven redundancy of code
   3. codon preference

%A R. Staden
%T Graphic methods to determine the function of nucleic acid sequences
%J NAR
%V 12
%N 1
%D 1984
%P 521-538
%K NAR, DNA, MolBio, function, gene, coding sequence, cdna, cds,
%X package with various plot routines to determine function of some DNA

%A A. D. McLachlen
%A R. Staden
%A D. Ross Boswell
%T A method for measuring non-random bias of a codon usage table
%J NAR
%V 12
%N 24
%D 1984
%P 9567-9575
%K NAR, DNA, MolBio

%A J. W. Fickett
%T Recognition of protein coding regions in DNA sequences
%J NAR
%V 10
%N 17
%D 1982
%P 5303-5318
%K NAR, DNA, MolBio, auto correlation, autocorrelation

%A R. Staden
%A A. D. McLachlan
%T Codon preference and its use in identifying protein coding regions in long
   DNA sequences
%J NAR
%V 10
%N 1
%P 141-156
%D 1982
%K DNA, NAR, MolBio

%A J. C. W. Shepherd
%T From primeval message to present day gene
%J Cold Spring Harbor Symp. on Quantitative Biology
%V 47
%N 2
%D 1982
%P 1099-1108
%K DNA, genetic code, RNY, purine, pyrimidine, comma free code, MolBio

%A R. Dawkins
%T The Selfish Gene
%D 1976
%I OUP
%K book, text, MolBio, pressure, selection, evolution, c1976, c197x, c19xx, OUP,
   genetics, genes, survival machines, meme, memes
%X 3rd ed 2006, uk us isbn:0199291152; uk us isbn13:978-0199291151; 30th ann..
   -- [<A HREF="http://www.simonyi.ox.ac.uk/dawkins/WorldOfDawkins-archive/Dawkins/Work/Books/selfish.shtml">blurb</A>]['06],
   -- [<A HREF="http://www.abc.net.au/rn/science/ss/stories/s1624685.htm">ABC radio</A>][29/4/'06].
   2nd ed 1989, uk us isbn:0192860925; uk us isbn13:978-0192860927.
   1st ed 1976.

%A F. H. C. Crick
%A S. Brenner
%A A. Klug
%A G. Pieczenik
%T A speculation on the origin of protein synthesis
%J Origins of Life
%V 7
%P 389-397
%D 1976
%K DNA, evolution, genetic code, RNA, tRNA, mRNA, MolBio
%X suggests protein synthesis may have begun with just a primitive tRNA
   if it could take on 2 configurations and bind to mRNA with 5 base pairs
   instead of present 3.
   Would restrict messages and early amino acids to glycine, serine,
   aspartic acid and aspargine.

%A M. Eigen
%A R. Winkler-Oswatitsch
%T Transfer-RNA: The early adaptor
%J Naturwissenschaften
%V 68
%P 217-228
%M MAY
%D 1981
%K DNA, RNA, tRNA, genetic code, MolBio, c1981, c198x, c19xx
%X evolutionary tree of tRNA calculated.
   conclude tRNA represent ancient molecules that existed in the form
   of a mutant distribution prior to their integration into genomes.

%A M. Eigen
%A R. Winkler-Oswatitsch
%T Transfer-RNA, an early gene?
%J Naturwissenschaften
%V 68
%P 282-292
%D 1981
%K DNA, RNA, tRNA, genetic code, MolBio
%X reconstruct ancient tRNA, remnant of  GNC pattern (=> 4 amino acids, N=any)
   suggests tRNA was both messenger and adaptor.

%A C. Willard
%A H. T. Nguyen
%A C. W. Schmidt
%T Existence of at least three distinct Alu subfamilies
%J J. Mol. Evol.
%V 26
%P 180-186
%D 1987
%K DNA, ALU, family, MolBio, JME, data string, strings
%X DNA data strings 89 Alu

%A M. Kreitman
%T Nucleotide polymorphism at the alcohol dehydrogenase locus
   of Drosophila melanogaster
%J Nature
%V 304
%M AUG
%D 1983
%P 412-417
%K DNA, ACGT, allele, allel, gene, MolBio
%X sequenced 11 cloned ... Adh genes from 5 natural populations.
   Of the 43 points of variation only one results in an amino acid change and
   that is responsible for the 2 variants Adh-f fast  and Adh-s slow
   found in nearly all natural populations.
   Presume that most amino acid changes to Adh would be selectively
   deleterious.

%A V. Slagel
%A E. Flemington
%A V. Traina-Dorge
%A H. Bradshaw
%A P. Deininger
%T Clustering and subfamily relationships of the Alu family in the human genome
%J J. of Molecular and Biological Evolution
%V 4
%N 1
%P 19-29
%D 1987
%K JMBE, Alu, DNA, family, cluster, consensus, concensus (!), MolBio,
   data string, strings
%X DNA data strings tkA to tkM, tubA to tubJ
   give a phylogenetic tree

%A W. Bains
%T The multiple origins of the human Alu sequences
%J J. Mol. Evol.
%V 23
%P 189-199
%D 1986
%K Alu, DNA, Phylogenetic tree, MolBio, JME, data string, strings
%X uses 62 Alus
   DNA data strings  Blur 1 2 6 7 8 10 11 13 14 19
   Tublin gene beta-5 A to J
   alpha and delta globin locus loci

%A W. Bains
%A G. C. Smith
%T A novel method for nucleic acid sequence determination
%J J. Theor. Biol.
%V 135
%P 303-307
%D 1988
%K jrnl, JTB, MolBio, sequencing by hybridization, hybridisation, SBH,
   k-mer, kmer, kmers, DNA, sequence, microarrays, micro arrays

%A P. H. Seeburg
%T The human growth hormone gene family:
   nucleotide sequences show recent divergence and predict a new
   polypeptide hormone
%J DNA
%V 1
%N 3
%D 1982
%P 239-249
%K DNA, gene, MolBio
%X uses three nonallelic human genomic DNA fragments
   which each contain one member of the growth hormone gene family

%A M. Sjostrom
%A S. Wold
%T A multivariate study of the relationship between the genetic code and
   the physical-chemical properties of amino acids
%J J. Mol. Evol.
%V 22
%P 272-277
%D 1985
%K DNA, JME, genetic code, amino acid, MolBio

%A T. Miyake
%A K. Migita
%A Y. Sakaki
%T Some KpnI family members are associated with the Alu family in the human
   genome
%J NAR
%V 11
%N 19
%D 1983
%P 6837-6446
%K DNA, KpnI, Alu, MolBio

%A I. Sawada
%A C. W. Schmid
%T Primate evolution of the alpha-globin gene cluster and its Alu-like repeats
%J J. Mol. Biol.
%V 192
%D 1986
%P 693-709
%K c1986, c198x, c19xx, ALU, JMB, alpha, globin, DNA, repeat, MolBio
%X [Also search for: MolBio ALU].

%A M. O. Dayhoff
%T Atlas of Protein Sequence and Structure, Vol. 5, supplement 3
%D 1978
%I National Biomedical Research Foundation
%K book, NBRF, protein, family, survey,  MolBio, Bioinformatics
%X was "the" database before it got too big for a book

%A B. F. Koop
%A D. Siemieniak
%A J. L. Slightoms
%A M. Goodman
%A J. Dunbar
%A P. Wright
%A E. L. Simons
%T Tarsius delta and beta globin genes: conversions, evolution and
   systematic implications
%J J. of Biological Chemistry
%V 264
%N 1
%M JAN
%D 1989
%P 68-79
%K DNA, gene, family, homology, theory, evolution, mutation, conversion,
   beta, delta, gamma, MolBio
%X has a theory of gene duplication and subsequent mutation and conversion.
   Conversions frequent after duplication, less as differences accumulate.
   Differences accumulate in non-coding regions especially.
   Also discusses relatedness or family tree
   of primates, anthropoids and the lower primate tarsius syrichta
   (Includes an alignment of genes from several animals.)

%A D. Penny
%T What, if anything, is Prochloron
%J Nature
%V 337
%M JAN
%D 1989
%P 304-305
%K DNA, gene, evolution, family, phylogenetic tree, MolBio, data string strings
   16S RNA
%X discusses reliability or otherwise of p tree calculations
   see Turner, Burger-Wiersma et al  and Morden and Golden
   DNA data strings used 16S-RNA

%A S. Turner
%A T. Burger-Wiersma
%A S. J. Giovannoni
%A L. R. Mur
%A N. R. Pace
%T The relationship of a prochlorophyte Prochlorothrix hollandacia
   to green chloroplasts
%J Nature
%M JAN
%D 1989
%V 337
%P 380-382
%K DNA, gene, evolution, family, phylogenetic tree, RNA, rRNA, MolBio,
   data string, strings, 16S rRNA, evolution, c1989, c198x, c19xx
%X claims P. hollandacia falls in cyanobacterial line of descent
   DNA data strings used 16S rRNA   from Prochlorothrix hollandica,
   cyanobacteria, green chloroplasts,
   cyanelle, and others (about 24).

%A C. W. Morden
%A S. S. Golden
%T psbA genes indicate common ancestry of prochlorophytes and chloroplasts
%J Nature
%M JAN
%D 1989
%P 382-385
%K DNA, gene, evolution, family, phylogenetic tree, MolBio, data string,
   strings, psbA, origin
%X claims P. hollandacia part of a lineage that led to chloroplasts after
   a divergence from cyanobacteria.
   DNA data strings used psbA genes which encode the photosystem II
   thylakoid protein D1, P. Hollandica, cyanobacteria, green alga,
   liverwort, several higher plants.

%A K. G. Field
%A G. J. Olsen
%A D. J. Lane
%A S. J. Giovannoni
%A M. T. Ghiselin
%A E. C. Raff
%A N. R. pace
%A R. A. Raff
%T Molecular phylogeny of the animal kingdom
%J Science
%V 239
%D 1988
%K jrnl, c1988, c198x, c19xx, DNA, phylogenetic tree, life, trees, phyla,
   classification, MolBio, data string, strings, 18s rRNA
%X DNA data strings used were 18S ribosomal RNA (have copy of data)
   everything from flatworm to human lengths from 330 to 1800 b.p.
   [Also search for: MolBio tree life]  and  [also search for: MolBio 18s rRNA].

%A W. M. Fitch
%T Towards defining the course of evolution: Minimum change for a specific
   tree topology
%J Systematic Zoology
%V 20
%P 406- 416
%D 1971
%K jrnl, MolBio, c1971, c197x, c19xx, phylogenetic, evolutionary, tree, trees,
   topology, parsimony
%X [Also search for: phylogenetic tree MolBio].

%A T. A. Reichert
%A A. K. C. Wong
%T Towards a molecular taxonomy
%J J. Mol. Evol.
%V 1
%P 97-111
%D 1971
%K JME, taxonomy, classification, cytochrome-c, information theory,
   entropy, DNA, hemoglobin, MolBio

%A J. L. Schroeder
%A F. R. Blattner
%T Least-squares method for restriction mapping
%J Gene
%V 4
%P 167-174
%D 1978
%K plasmid, restriction site map, RSM, mapping, DNA, least squares, MolBio

%A M. S. Waterman
%T Mathematical Methods for DNA Sequences
%I C.R.C. Press
%D 1989
%K DNA, alignment, comparison, book, MolBio, bioinformatics
%X about $158;   Biomed 574.87322 W328M
   [Also search for: MolBio book].

%A D. E. Ruffner
%A C. N. Sprung
%A P. P. Minghetti
%A P. E. M. Gibbs
%A A. Dugaiczyk
%T Invasion of the human albumin-alpha-fetoprotein gene family
   by Alu, Kpn and two novel repetitive DNA elements
%J Mol. Biol. Evol.
%V 4
%N 1
%P 1-9
%D 1987
%K MolBio, MBE, ALU, Blur, DNA data string strings
%X DNA data strings Alb-1 2 3 and 4, AFP-1 and 2  and Alu consensus
   suggest average time of Alu insertion in this gene family about
   15-30 million years ago.

%A A. M. Lesk
%A C. Chothia
%T How different amino acid sequences determine similar protein structures:
   The structure and evolutionary dynamics of the globins
%J J. Mol. Biol.
%V 136
%N 3
%P 225-270
%M JAN
%D 1980
%K jrnl, MolBio, JMB, c1980, c198x, c19xx, protein structure, fold, folding,
   AMLesk, sequence, globin, globins
%X via AK.

%A C. M. Rubin
%A C. M. Houck
%A P. L. Deininger
%A T. Friedmann
%A C. W. Schmid
%T Partial nucleotide sequence of the 300-nucleotide interspersed
   repeated human DNA sequences
%J Nature
%V 284
%M MAR
%P 372-374
%D 1980
%K jrnl, MolBio, c1980, c198x, c19xx, Alu, repeat, sequence, DNA
%X early paper on Alu strings.

%A C. Cantor
%A P. Schimmel
%T Biophysical Chemistry part III
%I W. H. Freeman
%C San Francisco
%D 1980
%K book, molecular biology, DNA, RNA, secondary structure, SS, MolBio
%X includes free energies of helix doublets relative to their corresponding
   single strands at 25 degrees C in neutral buffer of moderate or
   high ionic strength.
   10 doublets: AA AC AG AU CC CG CU GG GT TT.

%A M. J. E. Sternberg
%T The analysis and prediction of protein structure
%B Computing in Biological Science
%E Geisow
%E Barrett
%I Elsevier Biomedical Press
%P 143-177
%D 1983
%K protein, structure, sheet, helix, fold, MolBio

%A F. Galibert
%A F. Mandart
%A P. Tiollais
%A P. Chamay
%T Nucleotide sequence of the hepatitis B virus genome (subtype ayw) cloned in
   E. coli
%J Nature
%V 281
%P 646-650
%M OCT
%D 1979
%K jrnl hepatitis B, hepatitisB, hep, hepB, viral, c1979, c197x, c19xx, genome,
   HBV,Hepadnaviridae, MolBio, medicine, liver disease, retrovirus,
   retro-virus, viral
%X "... 3,182 nucleotides long. Location of the nonsense codons shows that the
   coding capacity of the L chain is larger than the coding capacity of the
   Schain. Eight open regions, able to code for polypeptide chains larger than
   100 amino acids, have been located. Region 6, which is the largest, covers
   more than 80% of the genome. The gene S which codes for polypeptide I of the
   Hbs Ag & was previously located between coordinates 95.1 and 73.6 is
   contained in region 7."
   [A< HREF="http://dx.doi.org/10.1038/281646a0">doi:10.1038/281646a0</A>]['05] ?pay?
   Also see: [<A HREF="http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/00.030.0.01.001.htm">ICTVdb</A>]['05] Virus Code. 30.0.1.0.001. Virus Accession number 30010001
   ... Nucleic Acid circular (but neither strand is a covalently closed circle)
   Total genome length is 3020-3320 nt, or 1700-2800 nt (for the full and short
   length strand, respectively). Nucleotide sequence deposited at EMBL/GenBank
   under the following accession number M12906; J02202; J02203; J02205; X01587;
   X02763; X65257. ...

%A G.E. Schulz
%A R.H. Schirmer
%T Principles of Protein Structure
%I SpringerVerlag
%D 1979
%K MolBio, c1979, c197x, c19xx, protein, amino acid, secondary, SS, tertiary,
   3D, structure, prediction, fold, folding, energy, bond, atomic, force,
   forces, electrostatic, van der Waals, attraction, repulsion, good book, text
%X Hargrave 547.75 S388P
   1 amino acids
   2 structural implications of polypeptide bond
   3 noncovalent forces determine protein structure  (neg powers 12:6 + coeffs)
      3.1 Dispersion forces and electron shell repulsion
      3.2 Electrostatic interactions  (neg 1 power of distance)
      3.3 Van der Waals potential
          conventional name for 3.1 and 3.2 combined:  negative 12:6:1
      3.4 Hydrogen bonds
      3.5 Entropic forces
          solvent, hydrophylic, hydrophobic, entropy
      3.6 Molecular packing
          as good as in a crystal
   4 covalent structure of proteins
   5 patterns of folding and association of polypeptide chains
   6 prediction of secondary structure of Amino Acid sequence
   7 models, display and documentation of protein structures
   8 thermodynamics and kinetics of polypeptide chain folding
          fast folders ~0.1 sec, slow folders 10 to 100 sec
          folding pathway can involve temporary structures (eg BPTI)
   9 protein evolution
  10 protein - ligand interaction
  11 structural basis of protein mechanism action and function

%A H. Okamoto
%A et al
%T Nucleotide sequence of a cloned hepatitis B virus genome, subtype ayr:
   Comparison with genomes of the other three subtypes
%J J. Gen. Virol.
%V 67
%N 11
%P 2305-2314
%M NOV
%D 1986
%K jrnl, MolBio, hepatitis B, hepatitisB, HBV, hep, hepB, c1986, c198x, c19xx,
   subtype, ayr, adw, ayw, genome, virus, viral
%X "... subtype ayr, which had been derived from the blood of a Japanese
   asymptomatic carrier. The genome was 3215 nucleotides long, and differed in
   DNA sequence by 10% from that of subtypes adw or ayw, but by only 2% from
   that of subtype adr. ..."
   Accession # [<A HREF="http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=genome&gi=16449">NC_003977</A>]['05].

%A G. N. Reeke jr
%T Protein folding: computational approaches to an exponential-time problem
%B Annual Review of Computer Science
%V 3
%D 1988
%E J. F. Traub
%P 59-84
%K protein, amino acid, polypeptide, secondary, SS, tertiary, structure,
   sheet, helix, fold, folding, MolBio

%A M. S. Waterman
%A M. Eggert
%T Letter to the editor:
   A new algorithm for best subsequence alignments with application
   to tRNA-rRNA comparison
%J J. Mol. Biol.
%V 197
%P 723-728
%D 1987
%K RNA, JMB, rrna, trna, MolBio, data string, strings, 16S Ecoli, E. coli
%X alg for finding all maximally similar subseqeunces
   extended to allow all non-intersecting similar subsequences
   with score above some preset level.
   data strings are 16S sequences from E. coli

%A T. F. Smith
%T The genetic code, information density and evolution
%J Mathematical Biosciences
%V 4
%P 179-187
%D 1969
%K DNA, genetic code, information theory, entropy, MolBio
%X information density v. nearest neighbours
   related to evolutionary rank

%A M. S. Waterman
%T Sequence alignment in the neighbourhood of the optimum with
   general application to dynamic programming
%J PNAS
%V 80
%P 3123-3124
%M MAY
%D 1983
%K PNAS, MolBio, c1983, c198x, c19xx, Proc Natl Acad Sci, DNA, DPA, approximate,
   suboptimal, sub optimal alignment, chicken hemoglobin, alpha, beta, mRNA
%X alignments within specified distance of optimum alignment
   On alpha and beta chicken hemoglobin mRNA
   uses  mismatch cost = 1,  indel(k) = 2.5+k
   Says `14 [optimal alignments], 14 with 1%, 35 within 2%, 157 within 3%,
         579 within 4% and 1317 within 5% [of optimal]'.  [?cumulative?]
   when uses 2.5+0.5k
         it is necessary to go to the list of 31 alignments within 4% of
         optimal to get the true alignment.
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">alignment prob. density</A>].)

%E M. J. Bishop
%E C. J. Rawlings
%T Nucleic Acid and Protein Sequence Analysis, a Practical Approach
%I IRL Press
%D 1987
%K MolBio, book, DNA, SS, bioinformatics, computing, algorithms
%X several contributors   many areas   introductory, book
   1. intro      2. dna sequence analysis   3. pcs
   4. databases  5. online services         6. restriction site mapping
   7. gel gels   8. sequencing projects     9. gels
   10. coding sequences    11. secondary structure RNA
   12. protein structure   13. alignment   14. inference evolutionary rel'
   [See also similar title, same ed's, '97]
   [Also search for: MolBio book].

%E M. J. Bishop
%E C. J. Rawlings
%T DNA and Protein Sequence Analysis, a Practical Approach
%I IRL Press at OUP
%D 1997
%K book, text, MolBio, c1997, c199x, c19xx, DNA, nucleic acid, bioinformatics
%X pb; uk us isbn:0199634637.
   [See also the book of 1987 with a similar title, same ed's.]
   [Also search for: MolBio book].

%A W. R. Taylor
%T Protein structure prediction
%B Nucleic Acid and Protein Sequence Analysis, a Practical Approach
%E M. J. Bishop
%E C. J. Rawlings
%I IRL Press
%D 1987
%P 285-323
%K globular, protein folding, secondary, SS, tertiary structure, domain, MolBio

%A M. J. Bishop
%A A. E. Friday
%A E. A. Thompson
%T Inference of evolutionary relationships
%B Nucleic Acid and Protein Sequence Analysis, a Practical Approach
%E M. J. Bishop
%E C. J. Rawlings
%I IRL Press
%D 1987
%P 359-385
%K inductive inference, II, maximum likelihood method, phylogenetic trees,
   DNA data string strings tRNA mDNA, alignment, homology, MolBio
%X M. J. Bishop   Uni of Cambridge Computer Lab,  Corn Exchange St, UK.
   A. E. Friday   Dept Zoology, Uni of Camb', Downing St, Camb' UK
   E. A. Thompson Dept. Stats GN22, Uni of Washington, Seattle, WA 98195, USA
 dna data strings:
    1. tRNA genes for aspartic acid from mitochondrial genome of
       man, mouse and ox
    2. mitochondrial DNA of human, chimp, gorilla, orang-utan, gibbon

%A W. M. Brown
%A E. M. Prager
%A A. Wang
%A A. C. Wilson
%T Mitochondrial DNA sequences of primates: tempo and mode of evolution
%J J. Mol. Evol.
%V 18
%D 1982
%P 225-239
%K DNA, JME, phylogenetic tree, trees, mitochondria, primate, MolBio,
   data string, strings, mDNA
%X DNA data strings  mitochondrial DNA for human, chimp, gorilla, orang-utan,
   gibbon  - primates.
   actual 896-bp sequences given     NOTE only one indel needed

%A M. J. Bishop
%A A. E. Friday
%T Molecular sequences and hominoid phylogeny
%P 150-156
%B Major Topics in Primate and Human Evolution
%E B. Wood
%E L. Martin
%E P. Andrews
%I CUP
%D 1986
%K phylogenetic tree, trees, primates, man, homo, maximum likelihood,
   inductive inference, MolBio, quote
%X various phylogenetic trees for primates
   and their likelihoods.  isbn:0521307007.
   quote:
     There is as yet no formally developed method for assessing the
     significance of the difference in likelihoods of different trees. (p.152)

%A L. H. Holley
%A M. Karplus
%T Protein secondary structure prediction with a neural network
%J Proc. Natl. Acad. Sci. (USA)
%V 86
%P 152-156
%M JAN
%D 1989
%K PNAS, protein, secondary, SS, folding, structure, neural network, MolBio,
   NN, ANN
%X 63% accurate for 3 state, alpha helix, beta sheet / strand and coil.
   Output includes indication of strength of prediction.
   When 31% strongest predictions kept then 79% accurate.
   Input layer, hidden layer, output layer.
   context -8 to +8.

%A R. Unger
%A D. Harel
%A S. Wherland
%A J. L. Sussman
%T A 3D building blocks approach to analyzing and predicting structure of
   proteins
%J Proteins: Structure, function and genetics
%V 5
%P 355-373
%D 1989
%K c1989, c198x, c19xx, MolBio, protein, secondary, SS, tertiary, structure,
   predication
%X take 82 protein structures
   Examine all 6-mers, hexamers, hexmers of 6 amino-acids
   Use cluster analysis
   Get about 100 classes of shape can replace 76% of hexamers.
   use these to reconstruct structures by sliding window
   -- [<A HREF="http://dx.doi.org/10.1002/prot.340050410">doi:10.1002/prot.340050410</A>]['11], and
   2798411@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/2798411">pubmed</A>]['11].

%A M. Eigen
%A R Winkler-Oswatitsch
%A A. Dress
%T Statistical geometry in sequence space:
   a method of quantitative comparative sequence analysis
%A Proc. Natl. Acad. Sci. (USA).
%V 85
%P 5913-5917
%M AUG
%D 1988
%K DNA strings, 5S rRNA, string comparison, family, MolBio
%X DNA data strings 5S rRNAs

%A M. Eigen
%A B. F. Lindemann
%A M. Tietze
%A R. Winkler-Oswatitsch
%A A. Dress
%A A. von Haeseler
%T How old is the genetic code? Geometry of tRNA provides an answer
%J Science
%V 244
%M MAY
%D 1989
%P 673-679
%K statistical geometry, RNA, tRNA, DNA, genetic code, MolBio, data string
   strings, vonHaeseler
%X comparative seq analysis of transfer RNA ... in sequence space
   suggests about one third  ... divergence present at the
   urkingdom level ... when archaebacteria separated from
   eubacteria.
   ... genetic code almost as old as planet.
   DNA data strings: tRNAs for various codons.

%A J. M. Thornton
%A S. P. Gardner
%T Protein motifs and data-base searching
%J TIBS
%P 300-309
%V 14
%M JUL
%D 1989
%K protein, secondary, SS, 3D, tertiary, structure, structural, motif, MolBio,
   motifs, pattern, c1989, c198x, c19xx
%X TIBS = trends in bio sciences.
   "Protein structure & sequence motifs are now recognized for many different
   p.families & topologies. To aid identification & use of these motifs in
   modelling & prediction, it has become nec. to establish consistent DBs of
   p.structure, including not only coordinates, but also derived data such as
   secondary structure location & solvent accessibilities. ... describes first
   attempts to construct such data bases & explains how they can be used."
   -- 2672454@[<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/2672454">pubmed</A>]['17].

%A J. S. Jones
%T The origin of homo sapiens: the genetic evidence
%B Major Topics in Primate and Human Evolution
%E B. Wood
%E L. Martin
%E P. Andrews
%P C.U.P.
%D 1986
%P 317-330
%K homo sapiens, primate, human, globin, hemoglobin, haemoglobin, MolBio,
   DNA data string, strings
%X includes refs to DNA data strings
   haemoglobins,  man: two alpha chains (141 AA's), two beta chains (146 AA's)
   same protein seqs in chimps
   some racial/ population studies
   mitochondrial DNA

%A B. Robson
%A E. Suzuki
%T Conformational properties of amino acid residues in globular proteins
%J J. Mol. Biol.
%V 107
%P 327-356
%D 1976
%K protein, JMB,  secondary, SS, structure, folding,
   helix, alpha, beta sheet, coil, turn,
   information theory, MolBio

%A E. Suzuki
%A B. Robson
%T Relationship between helix-coil transition parameters for
   synthetic polypeptides and helix conformation parameters for
   globular proteins. A simple model
%J J. Mol. Biol.
%V 107
%P 357-367
%D 1976
%K protein, secondary, structure, folding, alpha helix, beta sheet, turn, coil,
   JMB, information theory, SS, MolBio

%A M. K. Gilson
%A K. A. Sharp
%A B. H. Honig
%T Calculating the electrostatic potential of molecules in solution: Method and
   error assessment
%J J. of Computational Chemistry
%V 9
%N 4
%P 327-335
%D 1988
%K MolBio, jrnl, c1988, c198x, c19xx, Delphi, electrostatic field, force,
   protein, proteins, Van der Waals radius, QCPE, attraction, atomic forces
%X "... numerical method for calculating the electrostatic potential of
   molecules in soln, using the linearized Poisson-Boltzmann equn. ...
   applications to biological macromolecules. The accuracy of the method is
   assessed by comparisons with analytic solns for the case of a single charge
   in a dielectric sphere (Tanford-Kirkwood theory), which serves as a model for
   a macromolecule. ... solutions are generally accurate to within 5%. Larger
   errors occur close to the charge & the dielectric boundary, but the max error
   found at ion-bonding distance (3A) from a charge close to the boundary (1A
   deep) is only 15%. Several algorithmic improvements, described here, contrib
   to the accuracy of the method. ... s/w package, called Del Phi, ...
   PDB file to calculated electrostatic fields."
   -- [<A HREF="http://dx.doi.org/10.1002/jcc.540090407">doi:10.1002/jcc.540090407</A>]['10].

%A S. Tanaka
%A H. A. Scheraga
%T Model of protein folding: inclusion of short, medium and long range
   interactions
%J Proc. Natl. Acad. Sci. (USA).
%V 72
%N 10
%P 3802-3806
%M OCT
%D 1975
%K Protein, structure, folding, alpha helix, beta sheet, extended, turn,
   secondary, SS, tertiary, PNAS, MolBio
%X 3 steps:
   1: formation of ordered backbone structure   [? ~ secondary structure ?]
   2: formation of small contact regions by medium range interactions
   3: association of the small contact regions into the native structure
      by long range interactions.
   Empirical parameters estimated from frequencies of contact.
   A Monte Carlo simulation of protein folding developed.
   protein data string: bovine pancreatic trypsin inhibitor.

%A A. Kolinski
%A J. Skolnick
%A R. Yaris
%T Monte Carlo simulations on an equilibrium globular protein folding model
%J Proc. Natl. Acad. Sci. (USA)
%V 83
%P 7267-7271
%M OCT
%D 1986
%K PNAS, protein, secondary, SS, tertiary, structure, fold, folding,
   simulated annealing, alpha helix, beta, extended, sheet , MolBio
%X [Also search for: protein folding simulation].

%T Computer-Aided Molecular Design
%E W. Graham Richards
%I IBC Technical Services
%D 1989
%K book, c1989, c198x, c19xx, Protein, structure, folding, prediction,
   MolBio, bioinformatics
%X isbn:1852710543;  (CSci has).

%A Z. Li
%A H. A. Scheraga
%T Monte Carlo minimization approach to the multiple-minima problem
   in protein folding
%J Proc. Natl. Acad. Sci. (USA)
%V 84
%P 6611-6615
%M OCT
%D 1987
%K simulated annealing, protein tertiary structure, prediction,
   ECEPP, ECEPP/2, QCPE, MolBio
%X  few details

%A E. O. Purisima
%A H. A. Scheraga
%T An approach to the multiple-minima problem by relaxing dimensionality
%J Proc. Natl. Acad. Sci. (USA)
%V 83
%P 2782-2786
%M MAY
%D 1986
%K protein, structure, tertiary, prediction, MolBio
%X find min energy conformation in high D space then reduce dimensions
   to 3-D while satisfying constraints.

%A F. A. Momany
%A R. F. McGuire
%A A. W. Burgess
%A H. A. Scheraga
%T Energy parameters in polypeptides.  VII Geometric parameters,
   partial atomic charges, nonbonded interactions,
   hydrogen bond interactions and intrinsic torsional potentials
   for the naturally occuring amino acids
%J J. Phys. Chem.
%V 79
%N 22
%D 1975
%P 2361-2381
%K energy, protein, amino acid, acids, CNDO/2, MolBio
%X ... Procedures are described for carrying out conformational
   energy calculations on polypeptides and proteins, using these
   empirical potentials. Programs available.

%A G. Nemethy
%A M. S. Pottle
%A H. A. Scheraga
%T Energy parameters in polypeptides. 9. Updating of geometrical parameters,
   nonbonded interactions and hydrogen bond interactions for
   the naturally occuring amino acids
%J J. Phys. Chem.
%V 87
%N 11
%D 1983
%P 1883-1887
%K energy, protein, amino acid, acids, AA, ECEPP, ECEPP/2, QCPE, MolBio
%X program ECEPP/2 in the quantum chemistry program exchange
                          Chem Dept, indiana Uni, Bloomington, IN 47401
   program number QCPE454.

%A M. J. Sippl
%A G. Nemethy
%A H. A. Scheraga
%T Intermolecular potentials from crystal data. 6. Determination of
   empirical potentials for O-H...O=C hydrogen bonds from packing
   configurations
%J J. Phys. Chem.
%V 88
%N 25
%D 1984
%P 6231-6233
%K ECEPP, MolBio
   protein, amino acid, acids, conformational energy
%X calculations from small molecules.

%A Y. K. Kang
%A G. Nemethy
%A H. A. Scheraga
%T Free energies of hydration of solute molecules.  1. Improvement of
      the Hydration shell model by exact computations of overlapping volumes,
   2. Application of the hydration shell model to nonionic organic molecules,
   3. Application of the hydration shell model to charged organic molecules
%J J. Phys. Chem.
%V 91
%N 15
%P 4105-4120
%D 1987
%K MolBio, c1987, c198x, c19xx, hydration, water, H2O, energy, hydrophylic,
   hydrophobic, protein, amino acid, acids, conformational energy,
   atomic forces
%X uses volume between van der Waals radius and radius of hydration.
   Additivity of group contributions assumed.
   Tested on 130 organic molecules comparing calculated and experimental
   energies. Average absolute difference 0.46 kcal/mol and standard
   deviation 0.07 kcal/mol
   See also K. D. Gibson and H. A. Scheraga
            Volume of intersection of three spheres of unequal size.
            A simplified formula.
            J. Phys. Chem. 91 15 4121-4122 1987
   -- [<A HREF="https://doi.org/https://doi.org/10.1021/j100299a032">doi:10.1021/j100299a032</A>]['22].

%A H. A. Scheraga
%T Conformational analysis of polypeptides and proteins for the study
   of protein folding, molecular recognition and molecular design
%J J. Protein Chemistry
%V 6
%N 1
%P 61-80
%D 1987
%O Int. Conf Macromolecular Structure and Function, Japan 85
   and also Israel J Chem V27 86
%K MolBio, c1987, c198x, c19xx, protein, structure, fold, folding, alpha helix,
   beta sheet, energy, minimisation, simulation, ECEPP, ECEPP/2
%X Claims . multiple minima problem solved for small molecules.
          . energy calculations "good enough"
          . build up from small parts to whole of large molecule
            use simulated annealing or
            relax dimensionality or
            look for homologous molecule
   something of a review of Scheraga's work
   lots of stereo wire frame plots also space filling pictures
   -- [<A HREF="https://doi.org/10.1007/BF00248828">doi:10.1007/BF00248828</A>]['22].
   [Also search for: protein folding simulation].

%A H. A. Scheraga
%T Protein structure and function, from a colloidal to a molecular view
%J Carlsberg Res. Commun.
%V 49
%P 1-55
%D 1984
%K protein, structure, folding, conformation, MolBio
%X 417 refs, quite a number by S!
   a survey    some good history

%A N. Iwabe
%A K. Kuma
%A T. Miyata
%T Sequence similarity of bacteriophage SPO2 DNA polymerase with
   E.coli DNA polymerase I
%J NAR
%D 1989
%M NOV
%V 17
%N 21
%P 8866-8866
%K NAR, DNA, MolBio, Ecoli E. coli, SPO2
%X may contain DNA or protein data strings
   enews

%A H. A. Gold
%A J. N. Topper
%A D. A. Clayton
%A J. Craft
%T The RNA processing enzyme RNase MRP is identical to the Th RNP and related
   to RNase P
%J Science
%V 245
%P 1377-1380
%M SEP
%D 1989
%K MolBio, DNA, RNA, data string, strings, MRP
%X 3 RNA DNA data strings included, about 270 bases each
      Th RNA
      RNase MRP RNA (Human)
      RNase MRP RNA (Mouse)
   first 2 essentially identical
   third very similar, 2 block inserts, one or two single indels,
   a few changes.

%A O. Gotoh
%T Alignment of three biological sequences with an efficient traceback
   procedure
%J J. Theor. Biol.
%V 121
%D 1986
%P 327-337
%K JTB, homology, edit distance, three, string, strings, sequence, MolBio,
   multiple, alignment, similarity, homology, comparison
%X O(n^3) time.

%A M. Zuker
%T RNA folding
%J Meth. Enzymology
%V 180
%D 1989
%P 262-288
%K DPA RNA, secondary structure, SS, folding fold
%X via enews

%A W. Kabsch
%A C. Sander
%T Dictionary of protein secondary structure:
   pattern recognition of hydrogen-bonded and geometrical features
%J Biopolymers
%V 22
%P 2577-2637
%D 1983
%K jrnl, MolBio, c1983, c198x, c19xx, DSSP, protein, amino acid, secondary, SS,
   tertiary, structure, alpha helix, beta sheet, turn, chirality, exposure,
   bond, feature
%X Compilation for 62 globular proteins and 10,925 residues.
      Program DSSP (Define Secondary Structure of Proteins) Pascal avail. from
      Protein Data Bank, Chem Dept, Bookhaven Nat' Lab', Upton NY 11973 USA
   "For a successful analysis of the relation between amino acid seqs. & protein
   structure, an unambiguous & physically meaningful defn of sec.structure is
   essential. We have developed a set of simple & physically motivated criteria
   for sec.structure, programmed as a pattern-recognition process of hydrogen-
   -bonded & geometrical features extracted from x-ray coords.. Cooperative
   secondary structure is recognized as repeats of the elementary hydrogen-
   -bonding patterns 'turn' & 'bridge.' Repeating turns are 'helices,' repeating
   bridges are 'ladders,' connected ladders are 'sheets.' Geometric structure is
   defined in terms of the concepts torsion & curvature of differential
   geometry. Local chain 'chirality' is the torsional handedness of four
   consec. Calpha posns & is +ve for right-handed h. & -ve for ideal twisted
   beta-sheets. Curved pieces are defined as 'bends.' Solvent 'exposure' is
   given as the # of water molecules in possible contact with a residue. The end
   result is a compilation of the primary struct., inc. SS bonds, secondary
   struct., & solvent exposure of 62 different globular proteins. The
   presentation is in linear form: strip graphs for an overall view & strip
   tables for the details of each of 10.925 residues. The dictionary is also
   available in computer-readable form for protein structure prediction work."
   -- [<A HREF="http://dx.doi.org/10.1002/bip.360221211">doi:10.1002/bip.360221211</A>]['11].

%A K. Nakai
%A A. Kidera
%A M. Kanehisa
%T Cluster analysis of amino acid indices for prediction of protein structure
   and function
%J Protein Engineering
%V 2
%N 2
%P 93-100
%D 1988
%K protein structure, secondary, SS, tertiary, prediction,
   meta classification, class, MolBio
%X clusters 222 (!) published attributes of amino acids (not the AA's)
   Use a minimum spanning tree.
   get 4 regions:
      alpha a turn propensity,
      beta propensity,
      hydrophobicity,
      "other" physio-chemical properties, size etc.

%A J. M. Levin
%A J. Garnier
%T Improvements in a secondary structure prediction method based on a search
   for local sequence homologies and its use as a model building tool
%J Biochemica et Biophysica Acta
%V 955
%P 283-295
%D 1988
%K protein secondary structure, SS, prediction, local homology, GOR, MolBio
%X based on local homology
   63% correct for 3 states when predicted protein not in D base
   Using % identity with protein to be predicted to weight
   relative importance of each protein, for all proteins
   with % id > 30%, mean correct prediction is 87%.

%A J. Moult
%A M. N. G. James
%T An algorithm for determining the conformation of polypeptide segments
    in proteins by a systematic search
%J Proteins: Structure, Function and Genetics
%V 1
%P 146-163
%D 1986
%K protein, secondary SS, tertiary, structure , prediction, MolBio
%X segments <=6 residues
   Set of filters, simple rules, reduces # of conformations.
   Most important: chain integrity, avoidance too short van der Waals contacts
   of rest of protein and rest of segment.

%A J. W. Ponder
%A F. M. Richards
%T Tertiary templates for proteins.  Use of packing criteria in the
   enumeration of allowed sequences for different structural classes
%J J. Mol. Biol.
%V 193
%P 775-791
%D 1987
%K JMB, c1987, c198x, c19xx, protein, secondary SS, tertiary, structure,
   prediction, folding, MolBio, rotamers, sideChain
%X 17 of the 20 amino acids can be represented by 67 side-chain rotamers.
   Rotamer sequences by main chain plus beta carbon atoms of test structure.
   Other restrictions ...
   Likely that templates prepared from known core structures ...

%A C. M. Wilmot
%A J. M. Thornton
%T Analysis and prediction of the different types of beta-turn in proteins
%J J. Mol. Biol.
%V 203
%P 221-232
%D 1988
%K JMB, protein, secondary structure, SS, prediction, beta turn, MolBio

%A J. M. Levin
%A B. Robson
%A J. Garnier
%T An algorithm for secondary structure determination in proteins based
   on sequence similarity
%J FEBS Letters
%V 205
%N 2
%P 303-308
%M SEP
%D 1986
%K protein secondary structure, SS, prediction, MolBio
%X based on similar short homologous seqs have similar structure.
   Empirically derive a matrix which assigns similarity score
   to 2 seqs of length 7.
   Matrix scores:  identical AA's 2, common properties 1, dissimilar -1, other
   pairs 0.
   Sliding window, find hologues, get consensus prediction.
   Claim window = 7 optimal, 6 not bad, tried up to 15.

%A M. Karplus
%A J. A. McCammon
%T Dynamics of proteins: elements and function
%J Ann. Rev. Biochem.
%D 1983
%V 53
%P 263-300
%K protein, primary, secondary SS, tertiary, structure,
   folding, prediction, MolBio

%A R. Anderson
%A R. May
%T Vaccination and herd immunity to infectious diseases
%J Nature
%V 318
%P 323-329
%M NOV
%D 1985
%K jrnl, c1985, c198x, c19xx, zz0820, BobMay, vaccination, vaccine, infection,
   disease, epidemic, pandemic, measles, smallpox, polio, herd immunity,
   human health, medicine, spread, Robert Bob May
%X "An understanding of the relationship between the transmission dynamics of
   infectious agents & herd immunity provides a template for the design of
   effective control programmes based on mass immunization. Math. models of the
   spread & persistence of infection provide important insights into the problem
   of how best to protect the community against disease."
   -- [<A HREF="https://doi.org/10.1038/318323a0">doi:10.1038/318323a0</A>]['20].

%A P. Tiollais
%A C.Pourcel
%A A. Dejean
%T The hepatitis B virus
%J Nature
%V 317
%P 489-495
%M ?
%D 1985
%K jrnl, MolBio, c1985, c198x, c19xx, viral, hepatitis B, hepatitisB, hep, hepB,
   HBV
%X Also see [<A HREF="http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/00.030.0.01.001.htm">ICTVdb</A>]['05].

%A W. F. Hehre
%A L. Radom
%A et al
%T Ab Initio Molecular Orbital Theory
%I Wiley N.Y.
%D 1986
%K protein, primary, secondary SS, tertiary, structure, folding, prediction
   book, MolBio
%X Hargrave 541.28 H464A

%A T. Clark
%T A Handbook of Computational Chemistry:
   a Practical Guide to Chemical Structures and Energy
%I Wiley N.Y.
%D 1985
%K protein, primary, secondary SS, tertiary, structure, folding, prediction
   book, energy, Gaussian, MolBio
%X Hargrave 541.22 C595H
   1 chemical calculations
   2 molecular mechanics
   3 molecular orbital theory
   4 semiempirical methods
   5 ab initio methods

%A J. Garnier
%A B. Robson
%T The GOR method of predicting secondary structures in proteins
%B Prediction of Protein Structure and the Principles of Protein Conformation.
%E G. D. Fasman
%I Plenum
%D 1989
%P 417-465
%K protein secondary, SS, structure prediction, information theory, GOR, MolBio

%A B. Robson
%T Theory and application of expected information
%J Biochem. J.
%V 141
%P 853-867
%D 1974
%K GOR, protein secondary structure, SS, prediction, fold, folding,
   information theory, MolBio

%A B. Robson
%T The prediction of peptide and protein structure
%B Practical Protein Chemistry - a Handbook.
%E A. Dabre
%I Wiley
%D 1986
%P 567-607
%K protein, secondary SS, tertiary, structure, fold, folding, prediction,
   energy minimisation, simulation, survey, MolBio, c1986, c198x, c19xx,
   Hagler Huler Lifson, van der Waals
%X quantum mechanical methods,  molecular dynamics,  monte carlo techniques,
   statistical mechanics,       minimization,        rigid geometry,
   periodic sampling,           heuristics
 gives some simple energy formula:
    Eij = Aij/rij^a - Bij/rij^b + Cij/rij^c
       where a > b > c  (eg. a:b:c = 12:6:1  or  9:6:1)
    i,j range over pairs of atoms
    Aij, Bij, Cij depend on pair of atoms
    The following are Hagler Huler Lifson parameters.
    -------------------------------------------------  a:b:c 9:6:1
          Aii             Bii              Ci
    Kcal/mole A^9    Kcal/mole A^6   electron units (1eu=charge/electron)
    -------------------------------------------------
   H     445               15            0.11                        aliphatic
   C   38900             1230          (chose to neutralize CHn)     aliphatic
   C'  12500              335            0.46                        carbonyl
   O'  45800             1410           -0.46                        carbonyl
   N   36900             2020           -0.26                        amide
   H       0                0            0.26                        amide
    -----
   Aij = sqrt(Aii Ajj) etc.
     Makes the point that atom to effect of water and also vibrational energy
     are same order of magnitude as atom to atom energy.
   [Also search for: protein folding simulation].

%A A. Friday
%T Quantitative aspects of the estimation of evolutionary trees
%J Folia Primatologica
%P 221-234
%V 53
%D 1989
%K phylogenetic, family, tree, trees, model, MolBio

%A T. F. Smith
%A A. Srinivasan
%A G. Schochetman
%A M. Marcus
%A G. Myers
%T The phylogenetic history of the immunodeficiency virus
%J Nature
%V 333
%N 6173
%P 573-575
%M JUN
%D 1988
%K tree, trees, evolutionary, phylogenetic, AIDS, HIV, MolBio

%E G. D. Fasman
%T Prediction of Protein Structure and the Principles of Protein Conformation
%I Plenum
%D 1989
%K Protein secondary tertiary structure, fold, folding, energy minimization,
   book SS, MolBio
%X Biomed 574.19296011 F248P

%A B. Robson
%A J. Garnier
%T Introduction to Proteins and Protein Engineering
%I Elsevier
%D 1986
%K Protein structure, secondary SS, tertiary, fold, folding, energy,
   book, MolBio
%X isbn:0444806814.

%E M. J. Geisow
%E A. N. Barrett
%T Computing in Biological Science
%I Elsevier Biomedical Press
%D 1983
%K book, protein, MolBio, bioinformatics
%X Biomed 574.02854 G313C
   a collection of diverse papers
   1 interactive computer models of biological systems
   2 computational embryology
   3 computer analysis of bacterial cell walls
   4 calculation of biomolecular conformation (Platt and Robson) 91-142
   5 the analysis and prediction of protein structure (Sternberg)
   6 database techniquesfor 2-D gels
   7 nucleic acid morphology
   8 2D and 3D reconstruction in electron microscopy
   9 computer analysis of transient kinetic data
  10 the numerical geometry of biological structures
  11 microprocessing
   [Also search for: MolBio book].

%A A. J. Hopfinger
%T Conformational Properties of Macromolecules
%I AcademicPress
%D 1973
%K book, protein, structure, fold, folding, MolBio
%X Biomed 539.6 H792C
   1 macromolecular geometry
   2 conformational energies and potential functions
   3 accuracy and refinement of the potential functions
   4 conformational transitions in macromolecules
   5 applications of conformational potential energy calculations

%A A. M. Lesk
%A C. Chothia
%T Evolution of proteins formed by beta-sheets. I. Plastocyanin and azurin
%J J. Mol. Biol.
%V 160
%N 2
%P 309-323
%M SEP
%D 1982
%K jrnl, JMB, MolBio, c1982, c198x, c19xx, protein structure, 3D, beta sheet,
   AMLesk, immunoglobulin, domain, evolution, fold, folds
%X (NB. part I, and also a part II)
   "Plastocyanin and azurin form a family of small copper-containing proteins,
   active in the electron transport systems of plants and bacteria, resp.. ...
   we have aligned the sequences, identified homologous positions, and studied
   how the structures have changed as a result of mutations. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0022-2836(82)90178-4">doi:10.1016/0022-2836(82)90178-4</A>]['09].

%A A. M. Lesk
%A C. Chothia
%T Evolution of proteins formed by beta-sheets. II. The core of the
   immunoglobulin domains
%J J. Mol. Biol.
%V 160
%N 2
%P 325-342
%M SEP
%D 1982
%K jrnl, JMB, MolBio, c1982, c198x, c19xx, protein structure, 3D, beta sheet,
   AMLesk, immunoglobulin, domain, evolution, fold, folds
%X "... structures of 11 immunoglobulin domains available from high-res.crystal-
   -structure determinations. These include examples of the domain classes
   V[k], V[lambda], V[gamma], C[lambda], C[gamma]1, C[gamma]2 & C[gamma]3. ...
   examined how the interface between the beta-sheets accommodates these
   mutations. We describe examples of the following mechanisms.
   1. (1) Displacements & rotations of the beta-sheets rel.to each other by up
   to 2A & 20degr..  2. (2)Lateral insertion of side-chains from external loops
   into the interface region, to compensate for reductions in the volume of
   beta-sheet residues.  3. (3) Insertion of a residue into a strand to form a
   beta-bulge.  4. (4) Local changes in conformation.  5. (5) Only rarely,
   complementarity in adjacent mutations. ..."     (NB. also a part I.)
   -- [<A HREF="http://dx.doi.org/10.1016/0022-2836(82)90179-6">doi:10.1016/0022-2836(82)90179-6</A>]['09].

%A U. Burkert
%A N. L. Allinger
%T Molecular Mechanics
%I Amer. Chem. Soc.
%V Monograph 177
%D 1982
%K Protein, moecular dynamics, energy, book, MolBio

%A D. W. Nebert
%A et al
%T The P450 gene superfamily: recommended nomenclature
%J DNA
%V 6
%N 1
%D 1987
%P 1-11
%K Cytochromes P450, MolBio

%A D. K. Hawley
%A W. R. McClure
%T Compilation and analysis of Escheria Coli promoter sequences
%J NAR
%V 11
%N 8
%D 1983
%K EColi, E coli, promoter, DNA, data string, strings, NAR, MolBio
%X 168 promoter regions (-50 to +10)
   a consensus seq of 112 was determined
   DNA data sequences (rather short but lots of them)

%A B. Neveln
%T Comma-free and synchronizable codes
%J J. Theor. Biol.
%V 144
%P 209-212
%M MAY
%D 1990
%K DNA, RNA, comma free, early genetic code, early, evolution, MolBio
%X comma free code => can't get one out-of-reading-frame word in a string.
   comma free is == stagger limit of 3.
   stagger bound of 5 => can't get two adjacent out-of-frame words.
   Synchronisable <=> stagger bound of n for some finite n.
   There are 408 comma free codes having 20 words for alphabet of 4
   and word length of 3.
   There are 12,964,440 synchronisable codes having 20 words.
   The RNY code suggested as a primeval genetic code is not maximal
   in the set of codes with a S. B. of 5.
 Paper suggests synchronizability is the appropriate requirement on an early
 genetic code, not comma free ness

%A C. W. Schmid
%A Che-Kun James Shen
%T The evolution of interspersed repetitive DNA sequences in mammals and
   other vertebrates
%J Molecular Evolutionary Genetics
%E R. J. MacIntyre
%I Plenum
%D 1985
%P 323-358
%K DNA, c1985, c198x, c19xx, data string, strings, repeat, Alu, Blur, Blurs,
   MolBio
%X evolution of Alu sequences and flanking repeats
   DNA data strings, some human, includes Blurs, rodent, others

%A P. L. Deininger
%A D. J. Jolly
%A C. M. Rubin
%A T. Friedmann
%A C. W. Schmid
%T Base sequence studies of 300 nucleotide renatured repeated human DNA clones
%J J. Mol. Biol.
%D 1981
%V 151
%P 17-33
%K JMB, DNA, ALU, family, Blu, Blurs, Alus, Blur14, MolBio, data string strings
%X DNA data strings ALUs Blurs

%A J. Simms
%A D. Capon
%A D. Dressler
%T dnaG (Primase) dependent origins of DNA replication
%J J. Biological Chemistry.
%V 254
%N 24
%M DEC
%D 1979
%P 12615-12628
%K DNA, data string, strings, replication, bacteriophage, MolBio
%X nucleotide sequences of the negative strand initiation sites of
   bacteriphages St-1, phiK and alpha3
   DNA data strings and alignment p.12622, p.12623.
   Folding to hairpin loops also (secondary structures)

%A C. Chothia
%A A. M. Lesk
%A A. Tramontano
%A M. Levitt
%A et al ...
%A R. J. Poljak
%T Conformations of immunoglobulin hypervariable regions
%J Nature
%V 342
%P 877-883
%M DEC
%D 1989
%K biol, jrnl, c1989, c198x, c19xx, zz0518, AMLesk, antibody, antibodies,
   structure
%X "On the basis of comparative studies of known antibody structures and
   seqs. it has been argued that there is a small repertoire of main-chain
   conformations for at least five of the six hypervariable regions of
   antibodies, and that the particular conformation adopted is determined by a
   few key conserved residues. These hypotheses are now supported by reasonably
   successful predictions of the structures of most hypervariable regions of
   various antibodies, as revealed by comparison with their subsequently
   determined structures."
   -- [<A HREF="https://doi.org/10.1038/342877a0">doi:10.1038/342877a0</A>]['18].

%A P. Cheeseman
%A B. Kanefsky
%T Evolutionary tree reconstruction
%J AAAI Symp. Theory and Application of Minimum Length Encoding.
%M MAR
%D 1990
%P 35-39
%K MML, Minimum Message Length, MDL, phylogenetic, family, tree, trees,
   DNA, MolBio
%X alignment ~ tree
   heuristics, bottom up

%A A. Milosavljevic
%A D. Haussler
%A J. Jurka
%T Clustering of macromolecular sequences by minimal length encoding
%J AAAI Symp. Theory and Application of Minimum Length Encoding.
%M MAR
%D 1990
%P 45-49
%K MML, MDL, Minimum message length, phlogenetic tree, trees, forest, family,
   DNA, ALU, MolBio
%X says has been applied to Cytochromes P450 and the Alu sequences
   Clustering - says a nice binary tree is not always possible.
   Local search : allocate m sequences to k classes at random,
   move 1 seq accept if message length decreases - finds local minimum.
   Repeat several times.
   "Experiments suggest this is often sufficient."

%A A. V. Grigorjev
%A A. A. Mironov
%A Mapping DNA by stochastic relaxation: a new approach to fragment sizes.
%J Comp. Appl. BioSci.
%V 6
%N 2
%P 107-111
%D 1990
%K CABIOS, Bioinformatics, restriction site mapping, RSM, enzyme, map,
   simulated annealing, MolBio
%X 1: allocate sites at random,
   2: get predicted fragment lengths
   3: fit to measured lengths
   4: error is the energy
   5: move sites
   6: repeat 2 according to simulated annealing
   Shirley Ho found it

%A R. F. Mott
%A T. B. L. Kirkwood
%A R. N. Curnow
%T A test for the statistical significance of DNA sequence similarities for
   application in databank searches.
%J Comp. Appl. BioSci.
%V 5
%N 2
%P 123-131
%D 1989
%K CABIOS, Bioinformatics, DNA, alignment, homology, FASTA, FASTP, MolBio
%X  analysis of W i l b u r  L i p m a n  P e a r s o n heuristics

%A J. F. Collins
%A A. F. W. Coulson
%A A. Lyall
%T The significance of protein sequence similarities
%J Comp. Appl. BioSci.
%V 4
%N 1
%P 67-71
%D 1988
%K CABIOS, Bioinformatics, protein, alignment, homology, search,
   statistical, PAM score, MolBio

%E R. F. Doolittle
%T Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences
%J Methods in Enzymology
%I AcademicPress
%D 1990
%V 183
%K DNA, RNA, protein, NA, nucleic acid, amino acid,
   multiple, alignment, homology, consensus, sequence, pattern,
   family, phylogenetic, evolutionary, tree, trees, MolBio, MENZ
%X 1. data-bases                   2. searching dbs
   3. patterns in nucleic acid seqs
   4. predicting RNA secondary structure
   5. Aligning protein and n. a. seqs
   6. estimating sequence divergence
   7. phylogenetic trees

%A J. C. W. Shepherd
%T Ancient patterns in nucleic acid sequences
%J Methods in Enzymology
%V 183
%D 1990
%K DNA, RNY, coding region, genetic code, codon usage,
   purine, pyrimidine, MolBio, MENZ
%X see his papers on RNY purine-any-pyrimidine possible ancient code

%A D. Sankoff
%A R. Cedergren
%A Y. Abel
%T Genomic divergence through gene rearrangement
%J Methods in Enzymology
%P ??-??
%V 183
%D 1990
%K gene, genome, genomic, chromosome, mutate, diverge, change, shuffle,
   rearrange, permute, perm, permutation, rotation, duplication,
   inversion, transposition, MolBio, LAS LASS, MENZ
%X consider linear and circular genomes
   there are not enough complete DNA seq genomes yet so they use marker maps
   of EColi (Escherichia coli), Salmonella typhimurium,
      Bacillus subtilis,     Caulobacter crescentus,
      Pseudomonas aeruginosa.
   use 1. number of crossings  [LA: ~transpositions]
       2. largest subset of fragments in same order
          [LA: related to longest ascending subsequence problem, see Pritchard]
   as measures of amount of mutation
   compare pairs of genomes, get measure, compare to expected for unrelated
   strings,
   Conclusion: EColi and Salmonella closely related (~115 my),
               Caulobacter and Pseudomonas fairly closely related,
               these pairs more closely related than they are to B.s.

%A D. Sankoff
%T Inference of evolution at the level of entire genomes
%J AAAI Spring Symp. on Artificial Intelligence and Molecular Biology.
%P ??-??
%D 1990
%K mutation, gene, chromosome, genome, rearrangement, duplication, inversion,
   perm, permute, permutation, transposition, translocation, AIMB, MolBio
%X see paper with C e d e r g r e n  &  A b e l  in Methods in Enzymology '90.

%E A. Dress
%E A. von Haeseler
%T Trees and hierarchical structures
%I SpringerVerlag
%S Lect. Notes in Biomathematics
%V 84
%D 1987
%K book, c1987, c198x, c19xx, phylogenetic, evolutionary, family, tree, trees,
   ultrametric, additive, cluster, classify, parsimony, minimal change,
   MolBio, bioinformatics
%X Proc Conf at Bielefeld Oct 5-9 '87; isbn:3540524533;  or isbn:0387524533;
   Monash Comp Sci has a copy

%A G. A. Watterson
%A W. J. Ewens
%A T. E. Hall
%A A. Morgan
%T The chromosome inversion problem
%J J. Theor. Biol.
%V 99
%P 1-7
%D 1982
%K DNA, gene, genome, chromosome, MolBio, inversion, perm, permute,
   permutation, duplication, ratchet algorithm
%X circular chromosome, genes moved by inversions.
   First 3 authors in Maths Dept, last in Genetics at Monash Uni in '90

%A A. T. Brunger
%A G. M. Clore
%A A. M. Gronenborn
%A M. Karplus
%T Three-dimensional structure of proteins determined by molecular dynamics
   with interproton distance constraints: Application to crambin
%J Proc. Natl. Acad. Sci. (USA)
%V 83
%P 3801-3805
%M JUN
%D 1986
%K MolBio, PNAS, protein, tertiary, structure, fold, folding,
   energy minimisation, constrained, molecular dynamics,
   CHARMM, Explore, Explor, Xplor
%X folds subject to inter-proton constraints as gathered by NMR
   [Also search for: MolBio CHARMM].

%A G. M. Clore
%A M. Nilges
%A A. T. Brunger
%A M. Karplus
%A A. M. Gronenborn
%T A comparison of the restrained molecular dynamics and distance geometry
   methods for determining three-dimensional structures of proteins on the
   basis of interproton distances
%J FEBS Letters
%V 213
%N 2
%P 269-277
%M MAR
%D 1987
%K MolBio, protein, tertiary, structure, fold, folding, energy minimisation,
   constrained, molecular dynamics,
   CHARMM, Explore, Explor, Xplor
%X [Also search for: MolBio CHARMM].

%A M. J. Bishop
%A E. A. Thompson
%T Maximum likelihood alignment of DNA sequences
%J J. Mol. Biol.
%V 190
%P 159-165
%D 1986
%K JMB, MML, evolution, MolBio, DNA, DPA, alignment, homology, string, strings
%X adds probabilities rather than max them in dynamic programming algorithm
   "A first step might be
    to allow insertion and deletion of several bases.
    Rather than the deletion of three bases (the vertical route
    from (n,m) to (n+3,m)) having probability of order p**3
    it could be assigned a probability of order p."
    [Also search for: FSM alignment MolBio].

%A J. Felsenstein
%T Cases in which parsimony or compatibility methods will be positively
   misleading
%J Syst. Zool.
%V 27
%P 401-409
%D 1978
%K MolBio, family, phylogenetic, evolutionary tree, trees, parsimony

%A J. Felsenstein
%T Phylogenies from molecular sequences: inference and reliability
%J Ann. Review of Genetics
%V 22
%P 521-565
%D 1988
%K MolBio, phylogenetic, family, evolutionary, tree, trees, survey
%X parsimony and compatibility, distance matrix, likelihood methods
   statistics and justification of methods,
   statistical tests
   bootstrap, jackknife, other resampling methods

%A A. E. Romero-Herrera
%A H. Lehmann
%A K. A. Joysey
%A A. E. Friday
%T On the evolution of myoglobin
%J Philosophical Transactions (B)
%I Royal Society of London.
%V 283
%D 1978
%P 61-163
%K MolBio, Protein, Amino Acid, myoglobin, globin
%X myoglobin is a short term oxygen store in muscle.
   family trees based on myoglobin.

%A E. C. Holmes
%A G. Pesole
%A C. Saccone
%T Stochastic models of molecular evolution and the estimation of
   phylogeny and rates of nucleotide substitution in the hominoid primates
%J J. of Human Evolution
%V 18
%P 775-794
%D 1989
%K JHE, MolBio, phylogenetic, family, tree, trees, primate, man, human,
   psi eta globin, haemoglobin, haemoglobin
%X ((human chimp) gorilla) marginally best
   psi eta globin data found to be most consistent
   see Holmes PhD thesis L.A. has copy.

%A E. C. Holmes
%T Pattern and process in the evolution of the primates
%M NOV
%D 1989
%I Univ. of Cambridge.
%K MolBio, DNA, protein, phylogenetic, family, tree, trees, data string
   strings, globin
%X L.A. has a copy
   An appendix gives identifiers of DNA data strings used

%A M. Hasegawa
%A H. Kishino
%A Taka-aki Yano
%T Man's place in Hominoidea as inferred from molecular clocks of DNA
%J J. Mol. Evol.
%V 26
%P 132-147
%D 1987
%K JME, MolBio, DNA, primate, homo, man, family, phylogenetic, tree, trees
%X use eta globin pseudogene and mitochondrial DNA (896-bp)
   Give transition / transversion data.

%A B. E. Blaisdell
%T Markov chain analysis finds a significant influence of neighbouring bases
   in the occurrence of a base in eucaryotic nuclear DNA sequences both
   protein-coding and noncoding
%J J. Mol. Evol.
%V 21
%P 278-288
%D 1985
%K JME, MolBio, DNA, Markov process
%X 64 nuclear DNA sequences half coding half noncoding   (sources given)
   Most require at least 2nd order process, some need 3rd order.

%A B. R. Brooks
%A R. E. Bruccoleri
%A B. D. Olafson
%A D. J. States
%A S. Swaminathan
%A M. Karplus
%T CHARMM: a program for macromolecular energy minimization and dynamics
   calculations
%J J. Comput. Chem.
%V 4
%N 2
%P 187-217
%D 1983
%K MolBio, jrnl, c1983, c198x, c19xx, CHARMM, charm, protein, macro molecule,
   prediction, structure, energy minimization, molecular dynamics simulation,
   tertiary, folding, conformation, CHARMM22, CHARMM36, CMAP
%X "CHARMM (Chemistry at HARvard Macromolecular Mechanics) ... computer program
   which uses empirical energy fns to model macromolecular systems. [It] can
   read or model build structures, energy minimize them by 1st- or
   2nd-derivative techniques, perform a normal mode or molecular dynamics
   simulation ..."
   -- [<A HREF="https://doi.org/10.1002/jcc.540040211">doi:10.1002/jcc.540040211</A>][22].
   Also see [<A HREF="https://www.charmm.org/">charmm.org</A>]['22], [<A HREF="https://academiccharmm.org/">academiccharmm.org</A>]['22] & CHARMM@[<A HREF="https://en.wikipedia.org/wiki/CHARMM">wikip</A>]['22].
   [Also search for: MolBio CHARMM].

%A N. C. Cohen
%A J. M. Blaney
%A C. Humblet
%A P Gund
%A D. C. Barry
%T Molecular modeling software and methods for medicinal chemistry
%J J. of Medicinal Chemistry
%V 33
%P 883-894
%D 1990
%K Molecular modelling, MolBio, Protein folding, display
%X via enews

%A W. R. Taylor
%T A flexible method to align large numbers of biological sequences
%J J. Mol. Evol.
%V 28
%P 161-169
%D 1988
%K JME, MolBio, align, homology, lcs, multiple alignment, string, sequence,
   protein data strings cytochrome MULTAL
%X shows progressive clustering of 111 sequence cytochrome c superfamily.

%A R. N. Curnow
%A T. B. L. Kirkwood
%T Statistical analysis of deoxyribonucleic acid sequence data - a review
%J J. Royal Statistical Society, series A
%V 152
%P 199-220
%D 1989
%K JRSS, MolBio, DNA, information content, align, homology, string, sequence

%A W. R. Taylor
%T A hierarchical method to align large numbers of biological sequences
%J Methods in Enzymology
%V 183
%P 456-474
%E R. Doolittle
%D 1990
%K MolBio, MENZ, multiple alignment, align, string, sequence

%A S. Brunak
%A J. Engelbrecht
%A S. Knudsen
%T Neural network detects errors in the assignment of mRNA splice sites
%J NAR
%V 18
%N 16
%P 4797-4801
%D 1990
%K MolBio, NAR, neural network net, mRNA, genetics, gene, NN, ANN
%X trained to recognise pre-mRNA splicing signals in human genes.
   33 genes from EMBL.
   7 disturbed learning; 3 had discrepancies with original papers
   and 4 wrongly assigned splicing frames of introns.
   Training on 241 new Genbank sequences gave 9 new errors.
   input layer:  19 bases*4bits=76 units
   hidden layer: 20 units
   output layer:  2 units donor/non donor

%A H. Andreasen
%A H. Bohr
%A J. Bohr
%A S. Brunak
%A T. Bugge
%A R. M. J. Cotterill
%A C. Jacobsen
%A P. Kusk
%A B. Lautrap
%A S. B. Petersen
%A T. Saermark
%A K. Ulrich
%T Analysis of the secondary structure of the human immunodeficiency
   virus (HIV) proteins p17, gp120 and gp14 by computer modeling
   based on neural network methods
%J J. of Acquired Immune Deficiency Syndromes
%V 3
%P 615-622
%D 1990
%K MolBio, HIV, Aids, secondary structure SS, protein, folding, alpha helix,
   beta sheet, turn, ANN, NN, neural network, net
%X Multi-layer perceptron with back-propagation
   Trained on 56 proteins from brookhaven DB coordinates better than 2A.
   65% correct on 3 category: alpha, beta or turn
   Large window of 51 residues => input layer 51*20 units.
   Hidden layer 20 units.
   Used as follows: (i) NN does secondary structure.
                   (ii) tertiary structure constructed from various rules.
                  (iii) energy minimised by CHARMM

%A H. Bohr
%A J. Bohr
%A S. Brunak
%A R. M. J. Cotterill
%A H. Fredholm
%A B. Lautrap
%A S. B. Petersen
%T A novel approach to prediction of the 3-dimensional structures of protein
   backbones by neural networks
%J FEBS Letters
%V 261
%N 1
%P 43-46
%M FEB
%D 1990
%K MolBio, neural network net, NN, protein, tertiary, structure, folding, fold
%X feed forward NN.
   Trained on functionally similar but not structurally hmologous proteins
   using back propagation learning.
   Network generates tertiary structure info in distances of Calpha atoms
   in backbone: 0 if < threshold, 1 otherwise.
   Distance constraints then used to get a folded
   conformation using steepest descent minimization.
      input layer:  window of 61 AA's => 61*20 units
      hidden layer: 300 units
      output layer: 30 units 0/1 pairwise distance
                    and 3 units for alpha/beta/turn

%A H. Bohr
%A J. Bohr
%A S. Brunak
%A R. M. J. Cotterill
%A B. Lautrap
%A L. Norskov
%A O. H. Olsen
%A S. B. Petersen
%T Protein secondary structure and homology by neural networks,
   the alpha-helices in rhodopsin
%J FEBS Letters
%V 241
%N 1,2
%P 223-228
%M DEC
%D 1988
%K MolBio, Neural network net, NN, protein secondary structure SS, fold, folding
%X feed forward NN
   input layer: 51 AA => 51*20 units
   hidden layer:40 units
   output layer: 2 units alpha/other  or 3 alpha/beta/turn

%A G. L. Wilcox
%A M. Poliac
%A M. Liebman
%T Protein tertiary structure prediction using a large backpropagation network
%J Int. Neural Network Conf.
%D 1990
%P 365-369
%K conf, MolBio, c1990, c199x, c19xx, NN, INNC, Neural network net,
   protein structure, tertiary, fold, folding
%X Based on distance matrices on alpha carbon atoms.
   0, 1 and 2 hidden layers
   14 small proteins < 100 iterations to train to 95%
   not much on results OUTSIDE training set!
   [Also search for: backpropagation NN]  and  [also search for: alphafold].

%A E. Granum
%A M. G. Thomason
%A J. Gregor
%T On the use of automatically inferred Markov networks for chromosome analysis
%J Automation of Cytogenetics
%E C. Lundsteen
%E J. Piper
%I SpringerVerlag
%D 1990
%P 233-251
%K MolBio, Markov, network, infer, inference, chromosome, band, classification
%X a structural pattern recognition approach to analysis and classification
   of chromosome *** band *** patterns is presented.

%A P. E. Hardin
%A J. C. Hall
%A M. Rosbash
%T Feedback of the Drosophila period gene product on circadian cycling of its
   messenger RNA levels
%J Nature
%V 343
%P 536-540
%M FEB
%D 1990
%K jrnl, MolBio, c1990, c199x, c19xx, zz1017, body clock, circadian rhythm,
   cycle, RNA, period, per, gene, Drosophila, 2017 Nobel prize, NobelPrize,
   Physiology Medicine, publish, perish, grants, NIH, ARC, research, funding,
   quote, quotable, "luminaries"
%X "Mutations in the period (per) gene of Drosophila melanogaster affect both
   circadian and ultradian rhythms. Levels of per gene product undergo circadian
   oscillation, and it is now shown that there is an underlying oscillation in
   the level of per RNA. The observations indicate that the cycling of
   per-encoded protein could result from per RNA cycling, and that there is a
   feedback loop through which the activity of per-encoded protein causes
   cycling of its own RNA."
   -- [<A HREF="https://doi.org/10.1038/343536a0">doi:10.1038/343536a0</A>]['17].
   (*Also see,
     "... Hall not only faced hurdles when attempting to establish his
      own work, but also found the politics of research funding frustrating.
      ... funding should not be a limiting factor on the scientist, but instead
      give them the flexibility to pursue new interests and hypotheses. ..."
     -- JCH@[<A HREF="https://en.wikipedia.org/wiki/Jeffrey_C._Hall">wikip</A>]['17].
   And,
     Current Biology, V.18, No.3, 12/2/2008, pp.R101-R103,
        "... What props up biological research, at least in the vaunted US of A,
        involves a situation so deeply imbued with entitlement mentality that
        it has sunk into institutional corruption. ..."
     -- [<A HREF="https://doi.org/10.1016/j.cub.2007.12.016">doi:10.1016/j.cub.2007.12.016</A>]['17].
     [Also search for: publish perish].
   And,
     "The Nobel Prize in Physiology or Medicine 2017 was awarded jointly to
     Jeffrey C. Hall, Michael Rosbash and Michael W. Young,
     'for their discoveries of molecular mechanisms controlling the
     circadian rhythm.'"
     -- [<A HREF="https://www.nobelprize.org/nobel_prizes/medicine/laureates/2017/">nobelprize</A>]['17].*)

%A F. M. Richards
%T The protein folding problem
%J Scientific American
%M JAN
%D 1991
%P 34-41
%K MolBio, Protein folding, fold, secondary, tertiary, structure, introduction
   conformation SS

%A Wada et al.
%T ?
%J NAR
%V 18(suppl):
%P 2367-2411
%D 1990
%K MolBio, codon, frequency, usage, table, tables, NAR
%X via enews; codon frequency tables
   by others:
   There is a tabulation in NAR 14:r151-r197, 1986.
   To refresh our network memory, Mike Cherry has a more recent set of codon
   tables for 50 species available in useable, electronic form.  Try anonymous
   ftp to:
   frodo.mgh.harvard.edu              Codon usage tables for all major species
   132.183.190.10                     (GCG format)
   ( [.codon] )
   Contact: Mike Cherry*,   email: cherry@frodo.mgh.harvard.edu
   from:
   Don Gilbert              email: gilbert@bio.indiana.edu
   biocomputing office, biology dept., indiana univ., bloomington, in 47405

%A J. L. Spouge
%T Fast optimal alignment
%J Comp. Appl. BioSci.
%D 1991
%M JAN
%V 7
%N 1
%P 1-7
%K MolBio, CABIOS, Bioinformatics, fast, alignment, homology, edit distance
%X refers to Ukkonen

%A P. L.  Miller
%A P. M. Nadkarni
%A N. M. Carriero
%T Parallel computation and FASTA:  confronting the problem of
   parallel database search for a fast sequence comparison algorithm
%J Comp. Appl. BioSci.
%D 1991
%M JAN
%V 7
%N 1
%P 71-78
%K MolBio, CABIOS, Bioinformatics, alignment, homology, FASTA,
   edit distance, search, data base, database

%A J. Garnier
%A J. M. Levin
%T The protein structure code:  what is its present status?
%J Comp. Appl. BioSci.
%D 1991
%M APR
%V 7
%N 2
%P 133-142
%K MolBio, CABIOS, Bioinformatics, protein, secondary SS, tertiary,
   structure, code, prediction, fold, folding

%A A. Bairoch
%T SEQANALREF:  a sequence analysis bibliographic reference databank
%J Comp. Appl. BioSci.
%M APR
%D 1991
%V 7
%N 2
%P 268
%K MolBio, CABIOS, Bioinformatics, alignment, homology, edit distance,
   algorithm, survey, bib, bibliography

%A S. Barron
%A M. Witten
%A R. Harkness
%A J. Driver
%T A bibliography on computational algorithms in molecular biology and
   genetics
%J Comp. Appl. BioSci.
%D 1991
%M APR
%V 7
%N 2
%P 269
%K MolBio, CABIOS, Bioinformatics, algorithm, molecular, biology, bib,
   bibliography, survey

%A G. H. Gonnet
%A S. A. Benner
%T Computational biochemistry research at ETH
%M JAN
%D 1991
%K ETH, MolBio
%X c1991, c199x, c19xx, programmable interactive interface, alignment and
   tree package.
   Survey, no refs

%A M. Wolpoff
%A A. Thorne
%T The case against Eve
%J New Scientist
%M JUN
%D 1991
%P 33-37
%K c1991, c199x, c19xx, Eve, mitochondria, MolBio, DNA, evolutionary, evolution,
   family tree, human, hominid
%X 22 June '91.
   [Also search for: MolBio Eve human evolution] and the like.

%A A. Latorre
%A A. Moya
%A F. J. Ayala
%T Evolution of mitochondrial DNA in Drosophila subobscura
%J PNAS
%V 83
%P 8649-8653
%M NOV
%D 1986
%K PNAS, jrnl, c1986, c198x, c19xx, evolutionary, evolution, family, tree, DNA,
   MolBio, Eve, human, hominid, mitochondria
%X in 200,000 years we will all be called `smith' or `Li' but
   many males exist today, and will still have descendants.
   [Also search for: MolBio Eve human evolution] and the like.

%A J. S. Wainscooat
%A A. V. S. Hill
%A A. L. Boyce
%A J. Flint
%A M. Hernandez
%A S. L. Thein
%A J. M. Old
%A J. R. Lynch
%A A. G. Falusi
%A D. J. Weatherall
%A J. B. Clegg
%T Evolutionary relationships of human populations from an analysis of
   nuclear DNA polymorphism
%J Nature
%V 319
%M FEB
%D 1986
%P 491-493
%K MolBio, DNA, family, evolutionary, tree, trees, human, hominid, Eve
%X 6 feb 91
   major division of human populations into an African and a Eurasian group.

%A E. Charnov
%T The Theory of Sex Allocation
%I PrincetonUP
%V MPB-18
%P 355
%D 1982
%K book, text, MolBio, c1982, c198x, c19xx, population biology, biol, sex ratio,
   gender, male, female, birth rate, rates, birthrate
%X 1st ed 1982; pb us$78; uk us isbn:0691083126, uk us isbn13:978-0691083124.
   via enews
   >Does anyone have any figures on human male/female birthrates in
   >the U.S. and /or abroad?
    If you mean births of male vs female children, look at WORLD POPULATION
    GROWTH AND AGING, by Nathan Keyfitz and Wilhelm Flieger.  On the other hand,
    if you want age specific rates at which males and females produce offspring,
    that is a harder problem.  Female age-specific rates are everywhere, but
    male rates are rare.  One source is "Differential paternity in Libya", by
    El-Faedy and Bean (J. of Biosocial Science, 19: 395-403, 1987).
   >Also what are predominant explanations
   >as to why male/female birthrates > 1?
    The standard answer, which is due to R.A.Fisher, is that males births cost
    the mother less than female births do.  Look at pp.28-29 of THE THEORY OF
    SEX ALLOCATION, by Eric Charnov (Princeton Univ. Press, 1982).
 [L.A. has looked at this section:
 ratio of 1 at *adulthood* is favoured,
 more males die in childhood ~ males "cheaper" to mother (odd way to put it)]
    Alan R. Rogers
     USMAIL : Dept. of Anthropology, Univ. of Utah, S.L.C., UT 84112
     <!-- email: rogers@anthro.utah.edu --> .
   [Also search for: sex ratio biology].

%A J. F. C. Kingman
%T On the genealogy of large populations
%J J. of Applied Probability
%V 19, Essays in Statistical Science
%P 27-43
%D 1982
%K jrnl, MolBio, c1982, c198x, c19xx, population, gene, genes, haploid,
   evolution, phylogeny, phylogenetic, coalescent, tree, trees
%X "A new Markov chain is introduced which can be used to describe the family
   relationships among n individuals drawn from a particular generation of a
   large haploid population. The properties of this process can be studied,
   simultaneously for all n, by coupling techniques. Recent results in neutral
   mut'n theory are seen as consequences of the genealogy desc. by the chain."
   -- [<A HREF="http://links.jstor.org/sici?sici=0021-9002%281982%2919%3C27%3AOTGOLP%3E2.0.CO%3B2-0">@Jstor</A>]['08].

%A J. C. Avise
%A J. E. Neigel
%A J. Arnold
%T Demographic influences on mitochondrial DNA lineage survivorship in
   animal populations
%J J. Mol. Evol.
%D 1984
%V 20
%P 99-105
%K JME, jrnl, c1984, c198x, c19xx, human evolution, Eve, DNA, mitochondria,
   population
%X debunks the "strong" Eve hypothesis.

%A S. J. Gould
%T Hen's Teeth and Horse's Toes
%I Penguin
%D 1983
%K book, c1983, c198x, c19xx, genetics, evolution, Darwin, Darwinism,
   pressure of selection, quote, quotable, quotation, taxonomy
%X book of essays
   p72: Taxonomy is often regarded as the dullest of subjects,
        fit only for mindless ordering and sometimes denigrated within
        science as mere "stamp collecting" (a designation this
        philatelist deeply resents). ...
        But classifications both reflect and direct the way we think.
        The way we order represents the way we think.
   p278 (Protestant theologian Martin Niemoller:)
        First the Nazis went after the Jews, but I wasn't a Jew, so I did
        not react. Then they went after the Catholics but I wasn't a
        Catholic so I didn't object. Then they went after the workers,
        so I didn't stand up. Then they went after the Protestant clergy
        and by then it was too late for anybody to stand up.
   p357: On What if anything is a zebra?
        Cladistics has generated a fearful jargon, and many of its leading
        exponents in America are among the most contentious scientists
        I have ever encountered. ...
        Cladists attempt to construct hierarchies of sister groups in order to
        specify temporal order of branching in evolutionary history.
   pb; isbn:0393311031; isbn13:978-0393311037.

%A N. Mercier
%A H. Valladas
%A J-L. Joron
%A J-L. Reyss
%A F. Leveque
%A B. Vandermeersch
%T Thermoluminescence dating of the late Neanderthal remains from Saint-Cesaire
%J Nature
%V 351
%P 737-739
%M JUN
%D 1991
%K jrnl, c1991, c199x, c19xx, Neanderthal, Neandertal, homo, human, ancient
%X neanderthals around at (only) 36,000 years ago.

%A V. I. Lim
%T Structural properties of the globular organization of protein
   chains.  A stereochemical theory of globular protein secondary structure
%J J. Mol. Bio.
%V 88
%P 857-872
%D 1974
%K MolBio, protein, secondary structure, prediction, helix, sheet, beta, turn,
   JMB, alpha, SS conformation

%A T. J. Richmond
%A F. M. Richards
%T Packing of alpha-helices: geometrical constraints and contact areas
%J J. Mol. Bio.
%D 1978
%V 119
%P 537-555
%K JMB, MolBio, protein secondary structure, helix, sheet, alpha, beta, turn,
   conformation SS

%A F. E. Cohen
%A R. M. Abarbanel
%A I. D. Kuntz
%A R. J. Fletterick
%T Secondary structure assignment for alpha/beta proteins by a combinatorial
   approach.
%J Biochemistry
%D 1983
%V 22
%P 4894-4904
%K MolBio, protein secondary structure, alpha helix, beta sheet, turn, extended,
   conformation SS, algorithm, prediction

%A P. Y. Chou
%A G. D. Fasman
%T Beta-turns in Proteins
%J J. Mol. Biol.
%D 1977
%V 115
%P 135-175
%K MolBio, protein secondary structure, alpha helix, beta sheet, turn, turns,
   JMB, conformation

%A J. Novotny
%A R. Bruccoleri
%A M. Karplus
%T An analysis of incorrectly folded protein models.  Implications for
   structure predictions
%J J. Mol. Bio.
%D 1984
%P 787-818
%K MolBio, protein tertiary structure, conformation, alpha helix, helices,
   JMB, beta, strand, sheet, CHARMM, energy minimisation
%X take 2 known proteins,
   substitute some AA's, do constrained energy min' from old starting point,
   get predicted structure,
   compare with real structure of modified protein:
   they are different ...
   The predicted and real structures have comparable calculated energy!
   But there are characteristic differences in packing, solvent accessibility
   and electrostatic energy w.r.t. solvent, etc.
   [Also search for: MolBio CHARMM].

%A K. Nishikawa
%T Assessment of secondary structure prediction of proteins
   comparison of computerized Chou-Fasman method with others.
%J Biochimica et Biophysica
%V 748
%D 1983
%P 285-299
%K MolBio, protein secondary structure prediction, conformation, alpha helix,
   beta sheet, extended, turn, coil, Chou Fasman, method, test, comparison SS
%X claims methods not very accurate: 55% on alpha, beta, coil

%A N. Rawlings
%A K. Ashman
%A B. Wittman-Liebold
%T Computerised version of the Chou and Fasman protein secondary structure
   predictive method.
%J J. Peptide Protein Res.
%V 22
%D 1983
%P 515-524
%K MolBio, protein secondary structure prediction, conformation, alpha helix,
   beta sheet, extended, turn, coil, Chou Fasman, program SS
%X written in Fortran; flow chart given; uses C and F's parameters (not given)

%A A. Thorne
%A M. Wolpoff
%T Conflict over modern human origins
%J Search
%V 22
%N 5
%M JUL/AUG
%D 1991
%P 175-177
%K MolBio, mitochondria, Eve, human, homo, evolution
%X Argues against the "strong" Eve hypothesis.
   I thought Avise et al settled this ages ago.
   Includes argument from fossil evidence that there is
   no rapid change to modern man, no rapid displacement.
   [Also search for: MolBio Eve human evolution]  etc..

%A M. Kimura
%D 1957
%T Some problems of stochastic processes in genetics
%J Annals of Mathematical Statistics
%V 28
%P 882-901
%K DNA, MolBio, population genetics, diffusion, c1957, c195x, c19xx,
   mutation, fixation

%A M. Kimura
%T On the probability of fixation of mutant genes in a population population
%J Genetics
%V 47
%P 713-719
%D 1962
%K DNA, MolBio, population genetics, diffusion, c1962, c196x, c19xx,
   mutation, fixation

%A W. D. Hamilton
%T The evolution of altruistic behavior
%J The American Naturalist
%V 97
%N 896
%P 354-356
%M SEP-OCT
%D 1963
%K jrnl, c1963, c196x, c19xx, zz1013, altruism, cooperation, animal behaviour,
   human, tribe, tribes, tribal, tribalism, family, relatives, kin selection,
   Haldane
%X "... [Haldane] concluded altruism could show some advance in populations
   split into 'tribes' ..."
   -- [<A HREF="http://www.jstor.org/stable/2458473">Jstor</A>]['13].
   (Also see kin-selection@[<A HREF="http://en.wikipedia.org/wiki/Kin_selection">wikip</A>]['13].)

%A W. D. Hamilton
%T Extraordinary sex ratios
%J Science
%V 156
%N 3774
%P 477-488
%M APR
%D 1967
%K jrnl, MolBio, c1967, c196x, c19xx, population biology, sex ratio, ratios,
   biol, gender, male, female
%X [<A HREF="http://dx.doi.org/10.1126/science.156.3774.477">doi:10.1126/science.156.3774.477</A>]['13] (subscrn.$$$).
   [Also search for: sex ratio biology].

%A W. M. Fitch
%T Locating gaps in amino acid sequences to optimize the homology between
   two proteins.
%J Biochem. Genet.
%V 3
%P 99-108
%D 1969
%K jrnl, MolBio, protein, dot plot, plots, alignment algorithm, DPA
%X Biochemical Genetics H@rgrave 575.105 B615, ref in Dotter paper '96.
   Early alignment alg', idea attrib' Needleman '9/'65 (p103),
   M[i,j] = # of base mut'n to change a codon for seq1[i] to one for seq2[j],
   if possible, empty otherwise.  The summation matrix (minimise...)
   S[i,j] = S[i-1,k] + M[i,j], where k < j and M[i,j] is not empty
   {appears to be O(n**3)-time}  ... revised
   S[i,j] = S[i-1,k]+M[i,j]+G where G=0 if no gap (k=j-1), G=1 if gap (k < j-1).

%A A. J. Gibbs
%A G. A. McIntyre
%T The diagram: A method for comparing sequences. Its uses with amino
   acids and nucleotide sequences.
%J Eur. J. Biochem.
%V 16
%P 1-11
%D 1970
%K jrnl, EJB, MolBio, European journal of biochemistry, protein, dot plot,
   plots, match, matching, significance, zz0902
%X h@rgrave 574.19205 E89, '67..., ref in Dotter paper '96.
   "Similarities of the two sequences are then clearly indicated by diagonal
   rows of matches..."
   Significance: "(a) The freq's of lengths of all unbroken diag runs of
   matches are recorded and are compared [...] expected by chance and
   calculated directly (app' 1).  (b) The total # of matches ... in every
   diagonal is recorded, and again ..."

%A J. F. Crow
%A M. Kimura
%D 1970
%T An Introduction to Population Genetics Theory
%I Harper and Row
%C New York (reprinted by Burgess, Minneapolis).
%K DNA, MolBio, population genetics, diffusion, mutation, fixation
%X The assumptions are the standard ones of population genetics: a constant
   sized population with discrete generations reproducing according to a
   "Wright-Fisher" model.  The parents reproduce an offspring generation of
   infinite size by random mating, these offspring undergo a round of
   natural selection, then N adults are chosen from the survivors to live to
   adulthood.
   The diffusion approximation is obtained formally by taking a limit as
   N --> infinity and s --> 0 such that Ns = constant.  But whenever checked
   numerically these approximations have been found accurate to a quite
   amazing degree.  P.A.P. Moran showed in 1960 (I think in two papers in
   J. Australian Math Society) that the true fixation probability for
   finite N lies between the values of the above formula obtained by using
   N and N+1 in the formula.  This means the approximation is VERY accurate.
   An earlier approximation by J.B.S. Haldane in 1922 treated the case where
   4Ns is large, in which case Prob(fixation) ~= 2s when p = 1/(2N).
   (from enews by Joe Fel'n.)

%A A. D. McLachlan
%T Tests for comparing related amino-acid sequences.  Cytochrome c and
   cytochrome c551.
%J J. Mol. Bio.
%B 61
%P 409-424
%D 1971
%K JMB, jrnl, MolBio, diagonals, significance test, confidence interval, limit

%A C. B. Anfinsen
%T Principles that govern the folding of protein chains
%J Science
%V 181
%N 4096
%P 223-230
%D 1973
%K jrnl, MolBio, c1973, c197x, c19xx, zz0313, protein, fold, folding, structure,
   energy, 3D, ribonuclease A, ribonucleaseA, principle, dogma,
   1972 Nobel prize, NobelPrize
%X "The native structure [of most proteins] is determined only by the
   protein's amino acid sequence."
   -- [<A HREF="http://dx.doi.org/10.1126/science.181.4096.223">doi:10.1126/science.181.4096.223</A>]['13].
   Also see Adogma@[<A HREF="https://en.wikipedia.org/wiki/Anfinsen%27s_dogma">wikip</A>]['20].
   [Also search for: MolBio Levinthal paradox].

%A S. T. Rao
%A M. G. Rossmann
%T Comparison of super-secondary structures in proteins
%J J. Mol. Biol.
%V 76
%N 2
%P 241-256
%M MAY
%D 1973
%K jrnl, JMB, MolBio, c1973, c197x, c19xx, zz0916, protein,
   super secondary structure, superSecondary, terminology
%X "A method of comparing the conformations of different, but structurally
   related proteins is described. Local variations, such as the systematic
   translation of a helix, or the posn of deletions & insertions can be detected
   and the correspondence of only marginally similar structures can be measured.
   The occurrence of larger continuous folds ('super-secondary structures') has
   been detected in the comparison of lactate dehydrogenase with itself & with
   other protein structures."
   -- [<A HREF="http://dx.doi.org/10.1016/0022-2836(73)90388-4">doi:10.1016/0022-2836(73)90388-4</A>]['16].
   [Also search for: MolBio super secondary structure].

%A M. Kimura
%T Estimation of evolutionary sequences between homologous nucleotide
   sequences.
%J Proc. Natl. Acad. Sci. USA
%V 78
%P 454-458
%D 1981
%K PNAS, MolBio, transition, transversion, DNA, mutation, evolution, substitution

%A W. J. Ewens
%D 1979
%T Mathematical Population Genetics
%J Biomathematics
%V 9
%I SpringerVerlag
%K DNA, MolBio, population genetics, diffusion, mutation, fixation

%A R. M. Sweet
%A D. Eisenberg
%T Correlation of sequence hydrophobicities measures similarities in
   three-dimensional protein structure.
%J J. Mol. Biol.
%D 1983
%V 171
%P 479-488
%K MolBio, protein, secondary, structure, prediction, conformation,
   JMB, hydrophobic, hydrophilic, amino acid, AA, OMH
%X optimal matching hydrophobicity

%A G. D. Rose
%A A. R. Geselowitz
%A G. J. Lesser
%A R. H. Lee
%A M. H. Zehfus
%T Hydrophobicity of amino acid residues in globular proteins
%J Science
%V 229
%P 834-838
%D 1985
%K MolBio, protein, secondary, structure, conformation, hydrophobic,
   hydrophilic, amino acid, AA
%X mean area buried scale for the amino acids.

%A L. Kelly
%A L. A. Holladay
%T Comparison of scales of amino acid side chain properties by conservation
   during evolution of four proteins
%J Protein Engineering
%V 1
%N 2
%P 137-140
%D 1987
%K MolBio, protein, secondary, structure, conformation, prediction,
   hydrophobic, hydrophilic, amino acid, AA SS
%X compares 18 scales of AA properties
   on 20,627 residues in 4 families of proteins
   for correlation with secondary structure,
   apparently in alpha, beta and turn classes.
   The mean-area-buried scale of Rose et al and
   the optimised matching hydrophobicity scale of Sweet et al are best.
   (NB. reports Chou-Fasman < 55% accurate on test set.)


%A H. Suzuki
%A A.S. Kolaskar
%A S.L. Samuel
%A J. Otsuka
%A A. Tsugita
%T A protein secondary structure database (PSS)
%J Prot. Seq. Data Anal.
%V 4
%P 97-104
%D 1991
%K MolBio, protein secondary structurr, PSS, PIR, database, data base
%X via enews

%A C. E. Lawrence
%A A. A. Reilly
%T An expectation maximization (EM) algorithm for the identification and
   characterization of common sites in unaligned biopolymer sequences
%J Proteins
%V 7
%P 41-51
%D 1990
%K MolBio, c1990, c199x, c19xx, DNA, protein, site, sites, pattern,
   inductive inference, EM, likelihood
%X Proteins: structure, function and genetics
   A pattern is a sequence of "fuzzy" probabilistic chars - no indels.
   Its position, length, composition are unknown and inferred from
   given sequences.
   [Also search for: EM algorithm c196x].

%A D. Haig
%A L. D. Hurst
%T A quantitative measure of error minimization in the genetic code
%J J. Mol. Evol.
%V 33
%P 412-417
%D 1991
%K MolBio, genetic code, evolution, hydrophilic, hydrophobic, hydropathy,
   JME, polar moment, isoelectric point, amino acid, AA
%X 1 at Dept Plant Sci, Uni of Oxford
   2 at Dept Zool, Uni of Oxford
   Includes table of numerical values of Amino Acid attributes:
     polar requirement, hydropathy, molecular volume, iso-electric point.
   Generate "random" genetic codes by assigning the blocks of
   the real code to different AA's.
   For each code, calculate effect of single base substitutions,
   in each position and also overall,
   on each of the four attributes.
   Real code is very conservative esp' on hydropathy.

%A S. Henikoff
%A J. G. Henikoff
%T Automated assembly of protein blocks for database searching
%J NAR
%V 19
%N 23
%P 6565-6572
%D 1991
%K MolBio, protein, NAR, c1991, c199x, c19xx, prosite, sequence motif, motifs,
   block, blocks, pattern, family
%X Get families from prosite
   For each family, get common (fuzzy) blocks using MOTIF
   Get graph of blocks: block A precedes block B in > 50%
   Find a path through blocks: this describes the family
   Search for new instances
   Get distant relations.
   protein data strings - blocks from NCBI, cd repository/blocks
   -- [<A HREF="https://doi.org/10.1093/nar/19.23.6565">doi:10.1093/nar/19.23.6565</A>]['17].
   [Also search for: MolBio Henikoff].

%A S. Henikoff
%T Playing with blocks: some pitfalls of forcing multiple alignments
%J The New Biologist
%V 3
%N 12
%P 1148-1154
%M DEC
%D 1991
%K MolBio, c1991, c199x, c19xx, protein, block, blocks,
   multiple alignment, pattern
%X "Block alignments of multiple AA seqs. ...  Often the block alignments are
   motivated by the expectation that a protein of interest is similar in fn to
   members of a family of proteins. However, when alignments are forced by using
   ad hoc methods, it is often difficult to decide whether the proposed
   relationship is valid. ...  To illustrate some of the problems that can arise
   a few examples from the literature are analyzed. ..."
   -- [<A HREF="http://europepmc.org/article/med/1669287">www</A>]['20].
   [Also search for: MolBio Henikoff].

%A J. L. Thorne
%A H. Kishino
%A J. Felsenstein
%T An evolutionary model for maximum likelihood alignment of DNA
%J J. Mol. Evol.
%D 1991
%V 33
%P 114-124
%K JME, evolution, mutation, substitution, change, rate, rates, time, model,
   MolBio, alignment, maximum likelihood, ML
%X After Felsenstein 1981:
         s = rate of substitution,
         pi[A] = P(replace with A | subs'); pi[C], pi[G], pi[T] similarly
         f[ij](t) = transition prob' of nucleotide i->j after time t,
         then f[ij](t) = exp(-st) + pi[j](1-exp(-st))   i=j
                       = pi[j](1-exp(-st))              i~=j    (page 116)
   (See also (i) B i s h o p  &  T h o m p s o n
    and     (ii) A l l i s o n,  W a l l a c e  &  Y e e.)

%A A. K. Debnath
%A R. L. Lopez de Compadre
%A G. Debnath
%A A. J. Shusterman
%A C. Hansch
%T The structure-activity relationship of mutagenic aromatic nitro
   compounds.  Correlation with molecular orbital energies and hydrophobicity
%J J. of Medicinal Chemistry
%V 34
%N 2
%P 786-797
%M FEB
%D 1991
%K jrnl, MolBio, c1991, c199x, c19xx, SAR, chemical compound, energy,
   drug design, QSAR, Ames, TA98, mutagenicity, logP, AM1, aromatic rings
%X "A review of the lit. yielded data on over 200 aromatic & heteroaromatic
   nitro compounds tested for mutagenicity in the Ames test using S.
   typhimurium TA98. ... a quantitative structure-activity relationship (QSAR)
   has been derived for 188 congeners. The main determinants of mutagenicity are
   the hydrophobicity (modeled by octanol/water partition coefs) & the energies
   of the lowest unoccupied molecular orbitals calculated using the AM1 method.
   ... chemicals possessing 3 or more fused rings possess much greater mutagenic
   potency than compounds with 1 or 2 fused rings. Since the QSAR is based on a
   v.wide range in structural variation, aromatic rings from benzene to
   coronene are included as well as many different types of heterocycles, ..."
   -- [<A HREF="http://dx.doi.org/10.1021/jm00106a046">doi:10.1021/jm00106a046</A>]['08],
      [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/1995902">@pub med</A>]['08],
      [<A HREF="http://academic.reed.edu/chemistry/alan/">auth4</A>]['08].
   [Also search for: chemical compound SAR].

%A J. L. Thorne
%A H. Kishino
%A J. Felsenstein
%T Inching towards reality: an improved likelihood model of sequence evolution
%J J. Mol. Evol.
%D 1992
%V 34
%P 3-16
%K MolBio, DNA, alignment, model, indel, maximum likelihood ML, evolution,
   JME, rate, rates, slow, fast, substitution, edit distance,
   parameter estimation
%X new: (i) approx to multiple base indels.
       (ii) regions of fast or slow substitution
   (see also (i) B i s h o p  and T h o m p s o n
    and     (ii) A l l i s o n,  W a l l a c e & Y e e.)

%A J. Felsenstein
%T Phylogenies from restriction sites: A maximum-likelihood approach
%J Evolution
%V 46
%N 1
%P 159-173
%M FEB
%D 1992
%K jrnl, c1992, c199x, c19xx, MolBio, phylogeny, family, evolutionary tree,
   restriction site
%X "... The likelihood methods of Smouse and Li, who were able to compute
   likelihoods for up to 4 species under a simplified model of base change,
   can be extended numerically ..."
   -- @[<A HREF="http://www.jstor.org/stable/2409811">Jstor</A>]['10].

%A J. Felsenstein
%T Counting phylogenetic invariants in some simple cases
%J J. Theor. Biol.
%V 152
%P 357-376
%D 1991
%K JTB, MolBio, invariant, phylogenetic, evolutionary, family tree, trees
%X degrees of freedom/ numbers of parameters/ model fitting.

%A J. Felsenstein
%T Estimating effective population size from samples of sequences: Inefficiency
   of pairwise and segregating sites as compared to phylogenetic estimates
%J Genet. Res.
%V 59
%N 2
%P 139-147
%M APR
%M APR
%D 1991
%K MolBio,  phylogenetic, evolutionary, family tree, trees
%X abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/1628818">pubm'd</A>]['10].

%A J. Felsenstein
%T Allan Charles Wilson (1934-1991)
%J Nature
%V 353
%P 19
%K MolBio, Wilson, obituary, mitochondrial DNA, Eve

%A H. O. Smith
%A T. M. Annau
%A S. Chandrasegaran
%T Finding sequence motifs in groups of functionally related proteins
%J PNAS
%V 87
%N 2
%P 826-830
%D 1990
%K PNAS, MolBio, c1990, c199x, c19xx, protein, sequence MOTIF
%X program to find motifs in proteins.
   A motif is at least 3 amino acids separated by two gaps
   of specified max and min size.

%A A. Bairoch
%T PROSITE: A dictionary of sites and patterns in proteins
%J NAR
%V 19
%P 2241-2245
%M APR
%D 1991
%K NAR, c1991, c199x, c19xx, MolBio, protein, sites, PROSITE, site, data base,
   database, block, pattern
%X data base of sites found in several (or more) proteins.
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/2041810">pubm'd</A>]['10].

%A L. Hunter
%A D. J. States
%T Applying Bayesian classification to protein structure
%J 7th IEEE Conf on Artificial Intelligence Applications.
%M FEB
%D 1991
%P 10-16
%K MolBio, protein structure, class, classification, LHunter,
   c1991, c199x, c19xx
%X Used Cheeseman Autoclass in (x,y,z) coordinates of backbone atoms
   in proteins, window sizes 5, 6.
   This work was expanded in  Hunter & States IEEE Expert 7(4) 67-75 '92.

%A S. Henikoff
%A J. G. Henikoff
%T Amino acid substitution matrices from protein blocks
%J Proc. Natl. Acad. Sci., USA
%V 89
%N 22
%P 10915-10919
%M NOV
%D 1992
%K MolBio, PNAS, jrnl, block, Blosum, substitution matrix, c1992, c199x, c19xx,
   protein, blossum, BLOSUM62, PAM, amino acids, change, changes
%X "Methods for alignment of protein sequences typically measure similarity by
   using a substitution matrix with scores for all possible exchanges of one
   amino acid with another. The most widely used matrices are based on the
   Dayhoff model of evolutionary rates. Using a different approach, we have
   derived substitution matrices from about 2000 blocks of aligned sequence
   segments characterizing more than 500 groups of related proteins. This led
   to marked improvements in alignments and in searches using queries from each
   of the groups."
   -- [<A HREF="https://doi.org/10.1073/pnas.89.22.10915">doi:10.1073/pnas.89.22.10915</A>]['20].
   (Also see BLOSUM@[<A HREF="https://en.wikipedia.org/wiki/BLOSUM">wikip</A>]['20].)
   [Also search for: MolBio Henikoff] and
   [also search for: MolBio substitution matrix].

%A B. J. Whipp
%A S. Ward
%T Will women soon outrun men?
%J Nature
%P 25
%V 355
%N 6355
%M JAN
%D 1992
%K jrnl, sport, running, sprint, c1992, c199x, c19xx, gender, male, female,
   performance gap, improvement, stats, caseStudy, statistics, prediction,
   Tatem, marathon, times
%X "... In men the progression of V appears to be a linear function of t, with
   slopes for the different events being remarkably similar ...
   For women ... also no sig differences in the slopes ... up to the 1500m ...
   The slope, however was approx double that for men ...  Unless [something
   changes] The projecected intersection [m & f] for the marathon is 1998. ..."
   [c2004: Well that didn't come close!] [<A HREF="http://dx.doi.org/10.1038/355025a0">doi:10.1038/355025a0</A>]['04].
   Also see  S e i l e r & S a i l e r c1997,  and  T a t e m, Nature c2004

%A J. W. Fickett
%A C. S. Tung
%T Assessment of protein coding measures (review)
%J NAR
%V 20
%N 24
%P 6441-6450
%M DEC
%D 1992
%K jrnl, NAR, MolBio, gene prediction, benchmark, exon, DNA
%X ... review and synthesize the underlying coding measures from published
   algorithms. A standardized benchmark is described, and each of the measures
   is evaluated according to this benchmark. Our main conclusion is that a
   very simple and obvious measure - counting oligomers - is more effective
   than any of the more sophisticated measures.  Different measures contain
   different information. However there is a great deal of redundancy in the
   current suite of measures. We show that in future development of gene
   recognition algorithms, attention can probably be limited to six of the
   twenty or so measures proposed to date.

%A L. Hunter
%A D. J. States
%T Bayesian classification of protein structure
%J IEEE Expert
%V 7
%N 4
%P 67-75
%D 1992
%K MolBio, jrnl, protein structure, class, classification, helix,
   beta sheet, strand, turn, LHunter, c1992, c199x, c19xx
%X Extended version of paper in IEEE Conf of Applic of AI Feb 91.
   Used Cheeseman's AutoClass on (x,y,z) coordinates of backbone atoms in
   proteins, window sizes 5, 6. [High degree of correlation in attributes.]
   Found 27 classes for 5-mers.
   NB. autoclass later let run for a very long time and got ~ 100 classes.
       TID and LA tried SNOB Feb 92 and got 100+ classes (much quicker).
   -----
   Also see E d g o o s e,  A l l i s o n,  D o w e,  PSB '98 - who used
   dihedral angles and von Mises circular probability distribution.
   Angles: fewer attributes, less correlation, orientation independent,
   -- [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>],
   -- [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A L. Hunter
%T Artificial intelligence in molecular biology
%J AI Magazine
%V 11
%N 5
%D 1991
%P 27-36
%K MolBio, AI, survey, LHunter
%X general survey, covers the AAAI symposium at Stanford.

%A D. Lipman
%A W. J. Wilbur
%T Interaction of silent and replacement changes in eukaryotic coding sequences
%J J. Mol. Evol.
%V 21
%P 161-167
%D 1985
%K JME, MolBio, eukaryote, DNA, codon, reading frame, mutation, evolution,
   substitution, change, 3rd third base

%A D. J. Lipman
%A W. J. Wilbur
%T Modelling neutral and selective evolution of protein folding
%J Proc. R. Soc. Lond. B.
%D 1991
%V 245
%P 7-11
%K MolBio, fold, folding, folder, evolution, artificial model world, lattice,
   2D 2-D, pressure selection, fitness, viable, protein, mutation,
   PRS PRSB royal society
%X Studies a model evolutionary space of 2-D folders.
   2 types of residue, eg. hydrophilic and hydrophobic.
   Sequence folds on a square grid.
   2 residues are neighbours if neighbours on the grid but are not adjacent
   in the sequence.
   Energy = (sum phylic/phobic neighbours) * eps  where eps < 0.
   A seq is a functional sequence (a folder) if it has a unique min'
   energy configuration.

%A K. E. Rudd
%A W. Miller
%A C. Werner
%A J. Ostell
%A C. Tolstoshev
%T Mapping sequenced E.coli genes by computer: software, strategies and
   examples.
%J NAR.
%V 19
%N 3
%P 637-647
%D 1991
%K NAR, MolBio, gene, genes, RSM, map, maps, mapping, restriction site,
   Ecoli, E coli, assembly, align, alignment, DPA, NCBI, NIH, NLM, genome

%A K. E. Rudd
%A W. Miller
%A J. Ostell
%A D. A. Benson
%T Alignment of Escheria coli K12 DNA sequences to a genomic restriction map
%J NAR
%V 18
%N 2
%P 313-321
%D 1990
%K NAR, MolBio, gene, genes, map, maps, mapping, restriction site, RSM,
   Ecoli, E coli, assembly, align, alignment, DPA, NCBI, NIH, NLM

%A W. Miller
%A J. Barr
%A K. E. Rudd
%T Improved algorithms for searching restriction site maps
%J Comp. Appl. BioSci.
%V 7
%N 4
%D 1991
%P 447-456
%K CABIOS, Bioinformatics, MolBio, restriction site, RSM, map, maps,
   mapping, search, align, alignment, DPA, NCBI, NIH, NLM

%A W. Miller
%A J. Ostell
%A K. E. Rudd
%T An algorithm for searching restriction maps
%J Comp. Appl. BioSci.
%V 6
%N 3
%P 247-252
%D 1990
%K CABIOS, Bioinformatics, MolBio, restriction site map, maps, mapping,
   search, DPA, RSM align, alignment, DPA, NCBI, NIH NLM

%A R. F. Smith
%A T. F. Smith
%T Automatic generation of primary sequence patterns from sets of related
   protein sequences
%J PNAS
%V 87
%P 118-122
%M JAN
%D 1990
%K MolBio, c1990, c199x, c19xx, protein, pattern, patterns,
   sequence, motif, motifs, block

%A R. H. Lathrop
%A T. F. Smith
%A T. A. Webster
%A P. H. Winston
%T ARIEL: a massively parallel symbolic learning assistant for protein structure
   and function
%J Artificial Intelligence
%I MITpress
%E P. H. Winston
%E S. Shellard
%P 70-103
%D 1991
%K MolBio, AI, protein structure, function, ARIEL
%X item@[<A HREF="http://portal.acm.org/citation.cfm?id=106632">acm</A>]['10].
   uk us isbn:0262231506.

%A T. D. Schneider
%T Theory of molecular machines. I. Channel capacity of molecular machines
%J J. Theor. Biol.
%V 148
%P 83-123
%D 1991
%K JTB, MolBio, information theory, channel capacity, thermodynamics

%A T. D. Schneider
%T Theory of molecular machines. II Energy dissipation from molecular machines
%J J. Theor. Biol.
%V 148
%P 125-137
%D 1991
%K JTB, MolBio, information theory, energy, thermodynamics, noise, stability

%A T. D. Schneider
%T Information theory primer
%M DEC
%D 1990
%K information theory, MolBio

%A T. D. Schneider
%T Information and entropy of patterns in genetic switches
%B Maximum Entropy and Bayesian Methods in Science and Engineering.
%V 2
%P 147-154
%I Kluwer
%D 1988
%E G. J. Erickson
%E C. R. Smith
%K conf, information theory, entropy, thermodynamics, MolBio

%A T. D. Schneider
%A G. D. Stormo
%A L. Gold
%T Information content of binding sites on nucleotide sequences
%J J. Mol. Biol.
%V 188
%P 415-431
%D 1986
%K MolBio, binding site, sites, DNA, nucleotide, sequence, promoters
   JMB, information content theory

%A T. D. Schneider
%A G. D. Stormo
%T Excess information at bacteriophage T7 genomic promoters detected
   by random cloning technique
%J NAR
%V 17
%N 2
%P 659-674
%D 1989
%K NAR, MolBio, binding site, sites, promoter, T7, information content, theory

%A G. Z. Hertz
%A G. D. Stormo
%T Identifying DNA and protein patterns with statistically
   significant alignments of multiple sequences
%J J. Bioinformatics
%V 15
%P 563-577
%M JUL-AUG
%D 1999
%K MolBio, jrnl, pattern, sequence, motif, alignment, c1999, c199x, c19xx
%X from a ref'

%A T. D. Schneider
%A R. M. Stephens
%T Sequence logos: a new way to display consensus sequences
%J NAR
%V 18
%N 20
%P 6097- 6100
%D 1990 ?
%K NAR, MolBio, consensus, sequence, c1990, c199x, c19xx
%X uses exaggerated letter sizes in proportion to abundance.

%A A. B. Jacobson
%A H. Kumar
%A M. Zuker
%D 1985
%T Effect of spermidine on the conformation of bacteriophage MS2 RNA. Electron
   microscopy and computer modeling
%J J. Mol. Biol.
%V 181
%P 517-531
%K JMB, MolBio, RNA secondary structure prediction, conformation, folding, MS2

%A J. A. Jaeger
%A D. H. Turner
%A Zuker
%D 1989
%T Improved predictions of secondary structures for RNA
%B Methods in Enzymology
   Neuroendocrine Peptide Methodology
%P ??-??
%C San Diego, CA
%O Proc. Natl. Acad. Sci. 86 7706-7710 1989   (seen in a ref' list)
%K MolBio, MENZ, RNA secondary structure, SS, prediction, conformation,
   folding, DPA

%A M. Zuker
%A P. Stiegler
%T Optimal computer folding of large RNA sequences using thermodynamics
   and auxiliary information.
%J Nucl. Acids. Res.
%V 9
%P 133-148
%D 1981
%K jrnl, MolBio, NAR, c1981, c198x, c19xx, RNA secondary structure, SS,
   prediction, conformation, fold, folding, c1981, c198x, c19xx, NAR,
   thermodynamics, immunoglobulin gamma, dynamic programming algorithm, DPA
%X O(n^3)-time
   "... new computer method for folding an RNA molecule that finds a
   conformation of minimum free energy using published values of stacking and
   destabilizing energies. It is based on a dynamic programming algorithm from
   applied mathematics, and is much more efficient, faster, and can fold larger
   molecules than procedures which have appeared up to now [...]. Its power is
   demonstrated in the folding of a 459 nucleotide immunoglobulin gamma 1 heavy
   chain messenger RNA fragment. We go beyond the basic method to show how to
   incorporate additional information into the algorithm. This includes data on
   chemical reactivity and enzyme susceptibility. We illustrate this with the
   folding of two large fragments from the 16S ribosomal RNA of [e-coli]."
   -- [<A HREF="https://doi.org/10.1093/nar/9.1.133">doi:10.1093/nar/9.1.133</A>]['22],
      [<A HREF="http://www.bioinfo.rpi.edu/~zukerm/ref/ZUKM81.html">@rpi.edu</A>][7/'04].

%A M. Zuker
%T The use of dynamic programming algorithms in RNA secondary structure SS
   prediction.
%B Mathematical Methods for DNA Sequences
%E M. Waterman
%I CRC Press, Boca Raton.
%D 1989
%K MolBio, RNA secondary structure SS prediction, conformation, folding
   DPA

%A M. Zuker
%A R. L. Somorjai
%D 1989
%T The alignment of protein structures in 3 dimensions
%J Bull. Math. Biol.
%V 51
%N 1
%P 55-78
%K BMB, MolBio, protein, 3D, structure, alignment, match, matching, RMS,
   conformation, c1989, c198x, c19xx
%X [Also search for: MolBio protein structure alignment].

%A T. R. Cech
%A N. K. Tanner
%A I. Tinoco jnr
%A B. W. Weir
%A M. Zuker
%A P. S. Perlman
%T Secondary structure of the Tetrahymena ribosomal RNA intervening
   sequence: structural homology with fungal mitochondrial intervening
   sequences
%J Proc. Natl. Acad. Sci. USA
%V 80
%P 3903-3907
%D 1983
%K PNAS, MolBio, RNA secondary structure, SS, prediction, conformation, folding

%A S. Brunak
%A J. Engelbrecht
%A S. Knudsen
%T Prediction of human mRNA donor and acceptor sites from the DNA sequence
%J J. Mol. Biol.
%V 220
%P 49-65
%D 1991
%K MolBio, DNA, RNA, mRNA, donor, acceptor, site, sites, pattern, patterns,
   JMB, neural net, nets, intron, exon, splice, splicing, data string, strings
%X DNA data strings    33 base-pair long  segments around splice sites.
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/2067018">pubm'd</A>]['10].

%A J. A. Hunt
%A T. J. Hall
%A R. J. Britten
%T Evolutionary distances in Hawaiian Drosophila measured by DNA reassociation
%J J. Mol. Evol.
%D 1981
%V 17
%P 361-367
%K JME, MolBio, evolutionary distance

%A W. J. Wilbur
%T Codon equilibrium I: testing for homogeneous equilibrium
%J J. Mol. Evol.
%D 1985
%V 21
%P 169-181
%K JME, MolBio, codon usage, equilibrium, genetic code

%A I. Cosic
%A V. Vojisavljevic
%A M. Pavlovic
%T The relationship of the resonant recognition model to effects of
   low-intensity light on cell growth.
%J Int. J. Radiat. Biol.
%D 1989
%V 56
%N 2
%P 179-191
%K MolBio, DNA, protein

%A I. Cosic
%T Protein design by methods of digital signal analysis
%J IEEE 8th Annual Conf. of the Engineering in Medicine & Biology Society.
%P 901-905
%D 1986
%K MolBio, protein, design, function, DFT

%A Y. Takefuji
%A C. W. Lin
%A K. C. Lee
%T A parallel algorithm for estimating the secondary structure in
   ribonucleic acid
%R TR 91-118
%I Case Western Reserve Univ.,
   Centre for Automation and Intelligent Systems Research.
%D 1991
%M APR
%K MolBio, fold, folding, secondary structure, SS, prediction RNA,
   parallel algorithm

%A S. H. Bryant
%A C. E. Lawrence
%T The frequency of ion-pair substructures in proteins is quantitatively
   related to electrostatic potential: a statistical model for
   nonbonded interactions
%J Proteins: Structure, Function and Genetics
%V 9
%P 108-119
%D 1991
%K MolBio, Protein structure, AA, Amino Acid, Acids, ML, Maximum Likelihood,
   entropy, electrostatic potential, energy, ion ion-pair

%A A. R. Templeton
%A S. Blair Hedges
%A S. Kumar
%A K. Tamura
%A M. Stoneking
%T Human origins and analysis of mitochondrial DNA sequences
%J Science
%V 255
%N 5045
%P 737-739
%M FEB
%D 1992
%K MolBio, jrnl, c1992, c199x, c19xx, evolutionary, family tree, trees, Eve,
   mitochondria, parsimony, PAUP, DNA, mtDNA, origins, ancient, humans, human,
   phylogenetic, out of Africa hypothesis
%X [<A HREF="http://dx.doi.org/10.1126/science.1738849">doi:10.1126/science.1738849</A>]['09].
   Technical comments in two parts, (i) by author 1 and (ii) by the others
   the original Eve tree out of Africa;  the particular tree looks shaky
   *on the evidence used*.
   (Also see
     Nei, Kumar & Takahashi "... suggest that more attention should be given
     to testing the stat. reliability of an estimated tree rather than to
     finding the optimal tree with excessive efforts. ..."
     -- [<A HREF="http://www.pnas.org/content/95/21/12390.long">www</A>]['09].)
   [Also search for: Stoneking Eve 1987 MolBio], and more generally
   [also search for: MolBio Eve human evolution]  etc..

%A Edgar Wingender
%A T. Heinemeyer
%A D. Lincoln
%T Regulatory DNA sequences: Predictability of their function
%J Adv. Mol. Gen.
%V 4
%P 95-108
%M JAN
%D 1991
%K chapter, MolBio, c1991, c199x, c19xx, DNA, transcription factor database,
   data base, TF, TFD, site, sites, gene expression
%X "... database for transcription regulating seqs. & proteins has been
   established. Due to the high degree of degeneracy of transcription factor
   recognition seqs., an appropriate score system has been developed ..."
   -- @[<A HREF="https://www.researchgate.net/publication/230651286_Regulatory_DNA_sequences_Predictability_of_their_function">res.g'te</A>]['20].
   email: ewi of venus.gbf-braunschweig.dbp.de
   [Also search for: MolBio transcription factor].

%A M. D. Adams
%A M. Dubnick
%A A. R. Kerlavage
%A R. Moreno
%A J. M. Kelley
%A T. R. Utterback
%A J. W. Nagle
%A C. Fields
%A J. C. Venter
%T Sequence identification of 2375 human brain genes
%J Nature
%P 632-634
%M FEB
%D 1992
%V 355
%K NCBI, NLM, NIH, MolBio, brain, gene, genes, DNA, cDNA, data base,
   database, EST, pattern matching
%X Partial DNA sequencing to generate ` expressed sequence tags '.
   217 EST's putatively identified by data base search.
   Claim an approx doubling of human genes identified by sequencing
   and may be 5% of the genes in the human genome.

%A J. A. Goodrich
%A M. L. Schwartz
%A W. R. McClure
%T Searching for and predicting the activity of sites for DNA binding proteins:
   compilation and analysis of the binding sites for Escheria coli integration
   host factor (IHF).
%J NAR
%V 18
%N 17
%D 1990
%P 4993-5000
%K MolBio, DNA, bind, binding site sites, IHF, NAR, data string, strings, IHF
%X DNA data strings:
   27 IHF sites (50 bases each) aligned

%A D. Sankoff
%A C. Morel
%A R. J. Cedergren
%T Evolution of 5S RNA and the non-randomness of base replacement
%J Nature New Biology
%V 245
%M OCT
%D 1973
%P 232-234
%K MolBio, 5S, RNA, DNA, multiple alignment, family, evolutionary, phylogenetic
   tree, trees
%X iterate 3-way alignments, maybe by hand
   Table of substitution frequencies

%A A. C. Wilson
%A M. Stoneking
%A R. L. Cann
%T Ancestral geographic states and the peril of parsimony
%J Syst. Zool.
%V 40
%P 363-365
%M SEP
%D 1991
%K MolBio, c1991, c199x, c19xx, human evolution, Eve, mtDNA, parsimony,
   evolutionary tree, trees, man
%X [<A HREF="http://www.jstor.org/stable/2992328">Jstor</A>]['10].
   [Also search for: MolBio Eve human evolution].

%A W. P. Maddison
%T Squared-change parsimony reconstructions of ancestral states for
   continuous-valued characters on a phylogenetic tree
%J Syst. Zool.
%V 40
%P 304-314
%M SEP
%D 1991
%K MolBio, c1991, c199x, c19xx, evolution, Eve, mtDNA, parsimony,
   evolutionary tree, trees, man
%X [<A HREF="http://www.jstor.org/stable/2992324">Jstor</A>]['10].
   auth@[<A HREF="http://mesquiteproject.org/wpm/wayne/index.html">mesquiteproject.org</A>]['10].

%A L. Vigilant
%A M. Stoneking
%A H. Harpending
%A K. Hawkes
%A A. C. Wilson
%T African populations and the evolution of human mitochondrial DNA
%J Science
%V 253,
%P 1503-1507
%D 1991
%K MolBio, mitochondria, mtDNA, Eve, evolution, human
%X [Also search for: MolBio Eve human evolution].

%T Mobile DNA
%E D. E. Berg
%E M. M. Howe
%I Amer. Soc. for Microbiology
%D 1989
%K MolBio, DNA, repeat, repeats, ALU,ALUs, LINES, SINES, interspersed sequence,
   book, text, c1989, c198x, c19xx, repeated, repetitive, short,
   long interspersed nuclear element
%X via Darren Platt
   reviews LINES (long interspersed nuclear elements,  sequences)
   and     SINES (short ... - Alus basically)

%A D. Sankoff
%A R. J. Cedergren
%A G. Lapalme
%T Frequency of insertion-deletion, transversion, and transition
   in evolution of 5S ribosomal RNA.
%J J. Mol. Evol.
%V 7
%P 133-149
%D 1976
%K MolBio, DNA, 5S, RNA, insertion, deletion, indel, transition, transversion,
   evolution, multiple alignment, phylogenetic, family, tree cost, trees, costs,
   JME, estimation, three, data string strings
%X includes decomposing multiple seq' alignment into 3 way alignment
   at internal nodes and iterate.
  DNA (RNA) data strings: 9 sequences of length about 140 bases
                          and also a tree (figs 8 and 9).

%A J. C. Stephens
%T Statistical methods of DNA sequence analysis
   detection of intragenic recombination or gene conversion
%J Mol. Biol. Evol.
%D 1985
%V 2
%P 539-556
%K MBE, MolBio, DNA, gene conversion, recombination, model

%A S. Sawyer
%T Statistical tests for detecting gene conversion
%J Mol. Biol. Evol.
%V 6
%N 5
%P 526-538
%D 1989
%K MBE, MolBio, DNA, gene conversion, recombination, model

%A J-P. Dautricourt
%A D. Brutlag
%A B. Moxon
%A J. Fier
%T Similarity searching algorithm comparisons using massively parallel
   computing hardware.
%J Genome Sequencing Conf. III
%M SEP
%D 1991
%K MolBio, sequencing, comparison, alignment, homology, analysis
   FastA, Blast, FastDB FDB
   parallel concurrent
   Intelligenetics DEC MasPar MP-1
%X programmed smith-waterman algorithm on MasPar and use to validate
   or compare with several fast or heuristic algorithms:
   FastA, Blast, FastDB
   (notes: ~1 hour of FDB on sparcstation == 27 seconds on maspar MP-1)

%A M. C. Lawrence
%A P. C. Davis
%T CLIX: a search algorithm for finding novel ligands capable of
   binding proteins of known three-dimensional structure.
%J Proteins: structure, function and genetics
%V 12
%P 31-41
%D 1992
%K MolBio, protein structure, shape, fit, fitting, dock, docking, CSIRO, BRI
%X data base of small candidate molecules
   find ones that might fit and bind to a protein of known 3 D structure

%A S. Muggleton
%A R. D. King
%A M. J. E. Sternberg
%T Protein secondary structure prediction using logic based machine learning
%J Protein Engineering
%V 5
%N 7
%P 647-657
%D 1992
%K protein secondary structure, SS, logic, prolog, Golem,
   inductive inference, ILP, LP, MolBio, machine learning, ML, RDKing
%X see also their HICCS-25 paper.

%A R. D. King
%A S. Muggleton
%A R. A. Lewis
%A M. J. E. Sternberg
%T Drug design by machine learning:
   the use of inductive logic programming to model the structure-activity
   relationships of trimethoprim analogues binding to dihydrofolate
   reductase.
%J PNAS
%V 89
%P 11322-11326
%M DEC
%D 1992
%K jrnl, c1992, c199x, c19xx, inductive logic programming, ILP, prolog, Golem,
   machine learning, ML, MolBio, drug design, inSilico, activity, RDKing
%X "...drug design problem of modeling structure-activity relationships. The
   training data for the program were 44 trimethoprim analogues & their observed
   inhibition of E.coli dihydrofolate reductase. ..."
   -- [<A HREF="http://www.pnas.org/cgi/content/abstract/89/23/11322">pdf@pnas</A>]['08].
   (Also at Jstor.)

%A G. E. Schulz
%T A critical evaluation of methods for prediction of protein secondary
   structure.
%J Ann. Rev. Biophys. Biophys. Chem.
%D 1988
%V 17
%P 1-21
%K MolBio, protein, peptide, amino acid, AA, secondary structure, SS, prediction,
   alpha, beta, helix, sheet, turn

%A W. Kabsch
%A C. Sander
%T How good are predictions of protein structure?
%J FEBS letters
%V 155
%N 2
%M MAY
%D 1983
%P 179-182
%K MolBio, protein, peptide, amino acid, AA, secondary structure, SS, prediction,
   alpha, beta, helix, sheet, turn, data string, strings
%X protein data string strings
   list of 62 proteins of known structure
   Pessimistic: best methods (GOR + Lim) only ~ 56% for 3 helix/ sheet/ turn

%A M. A. Savageau
%T Proteins of E.coli come in sizes that are multiples of 14 kDa:
   Domain concepts and evolutionary implications.
%J PNAS
%D 1986
%P 1198-1202
%V 88
%K MolBio, protein organization, size, sizes, Ecoli, domain, evolution
%X The paper looked at about 1000 E.coli proteins and found that 46% have
   molecular masses of n x 14000 +/- 2500 where n=1,2...
   The author suggests that this indicates that this indicates a fundamental
   structural unit and that little sequence homology is seen in the units of
   similar size.
   via enews

%A F. R. Rysavy
%A M. J. Bishop
%A et al.,
%T The UK Human Genome Mapping Project online computing service
%J Comp. Appl. BioSci.
%V 8
%N 2
%D 1992
%P 149-154
%K CABIOS, Bioinformatics, MolBio, database, data base, gene, genetic,
   HUGO, Human Genome, England, UK, Europe
%X via enews

%A E. J. Demchuk
%A N. G. Esipova
%A V. G. Tymanyan
%D 1991
%T Length regularities of  genetic texts
%J Proc. of the 1st Int. Conf. on
   Electrophoresis, Supercomputing and the Human Genome.
%M APR
%P 10-13
%D 1990
%W Florida
%E C. R. Cantor
%E H. A. Lim
%I World Scientific, Singapore
%P 279-285
%K MolBio, protein, length, multiple, five
%X via enews, ref a bit garbled
   lengths of proteins tend to be multiple of 5

%A I. T. Paulsen
%A R. A. Skurray
%T Topology, structure and evolution of two families of antibiotic and
   antiseptic resistance proteins.
%I School of Biological Sciences, Univ. of Sydney
%D 1992
%K MolBio, AA, amino acid, protein, ATP, transmembrane, hydropathy
%X jono got a draft paper off author 1 ?

%A Gaston H. Gonnet
%A Mark A. Cohen
%A Steven A. Benner
%T Exhaustive matching of the entire protein sequence database
%J Science
%V 256
%N 5062
%P 1443-1445
%M JUN
%D 1992
%K MolBio, c1992, c199x, c19xx, alignment, similarity, homology, edit distance,
   PAM, PAM250, protein, gap, gaps, insert, delete, indel, indels,
   probability distribution, statistics
%X new PAM250 matrix. also discuss gap scores.
   Compared all pairs of close proteins, ie. 6.5*10^6 pairs, (in MIPS ver64)
   Analysis of 1.7*10^6 pairs showed
   1. P(gap) proportional to PAM distance,
   2. P(gap length = k) ~ k^-1.5
      in fact est'   log(P(len=k)) = -3.631 + 0.744log(PAM dist) - 1.493log(k)
      argue indel would have to fit with folded protein,
      prob 2 ends lie close in space for randomly coiled polymer
      is inversely proportional to mean volume, ie. inverse length^1.5,
      ref P. Flory, Principles of Protein Chemistry, Cornell U.P. 1953
          D.A.Brant & P.Flory J.Am.Chem.Soc. 87 p2788 1965
   Inst. for Sci. Comp. & Inst. for Organic. Chem,
   Swiss Fed' Inst' Tech', Universitatstr 16, 8092 Zurich, Switzerland.
   Paper: [<A HREF="https://doi.org/10.1126/science.1604319">doi:10.1126/science.1604319</A>],
   2876949@[<A HREF="http://www.jstor.org/stable/2876949">Jstor</A>]['18],
   pdf@[<A HREF="http://gonnet.com/papers/Science1992.pdf">gonnet.com</A>].
   [Also search for: Flory c1953]  and  [also search for: Gonnet protein].

%A D. T. Jones
%A W. R. Taylor
%A J. M. Thornton
%T The rapid generation of mutation data matrices from protein sequences
%J Comp. Appl. BioSci.
%V 8
%N 3
%P 275-282
%M JUN
%D 1992
%K MolBio, protein, amino acid, edit distance, homology, substitution matrix,
   c1992, c199x, c19xx, CABIOS, Bioinformatics, PAM, PAM250, Blosum
%X A recalculated PAM matrix.
   Proteins clustered at 85% identity [?] level.
   New PAM matrices calculated for clusters.
   Takes 20 hours on a sparc.
   [Also search for: MolBio substitution matrix].

%A Kaplan
%A S. Tavare
%A ???
%T Discussion on: sampling strategies for distances between DNA sequences
%J Biometrics
%V 46
%N 3
%P 572-582
%D 1990
%M MolBio, DNA, string, sequences, similarity, homolgy, statistics, model,
   mutation, evolution, human genome, HUGO

%A S. Tavare
%A B. Song
%T Codon preference and primary sequence structure in protein coding regions
%J Bull. Math. Biol.
%V 51
%N 1
%P 95-115
%D 1989
%K MolBio, DNA, codon, protein coding region, string, sequence, pattern, BMB

%A C. Gaboriaud
%A V. Bissery
%A T. Benchetrit
%A J. P. Mornon
%T Hydrophobic cluster analysis: an efficient new way to compare and analyse
   amino acid sequences.
%J FEBS Letters
%V 224
%N 1
%P 149-155
%D 1987
%K MolBio, protein, amino acid, AA, hydrophobic
%X His address is:   email: MORNON@FRLMCP61.BITNET  (as of '92)
   via enews

%A R. D. King
%A M. J. E. Sternberg
%T Machine learning approach for the prediction of protein secondary structure
%J J. Mol. Biol.
%V 216
%P 441-457
%D 1990
%K JMB, MolBio, protein secondary structure, SS, prediction, amino acid,
   AA, PROMIS, RDKing
%X 3 states, accuracy: 60% all proteins, 73% alpha type, 59% alpha/beta type

%A M. S. Waterman
%A J. Joyce
%A M. Eggert
%T Computer alignment of sequences
%B Phylogenetic Analysis of DNA Sequences.
%E Miyamoto
%E Cracraft
%I Oxford U. P.
%D 1991
%P 59-72
%K MolBio, DNA, multiple, alignment, string, sequence, edit distance,
   phylogenetic, family, tree, trees

%A W. D. Hamilton
%T Haploid dynamic polymorphism in a host with matching parasites - effects of
   mutation subdivision, linkage, and patterns of selection
%J J. Heredity
%I OUP
%V 84
%N 5
%P 328-338
%M SEP
%D 1993
%K jrnl, sex, why, sexual reproduction, simulation, parasite, hosts,
   coevolution
%X "... simulation of the coevolution of a sexual haploid host species with an
   asexual parasite is described in which parasites gain by matching and hosts
   by unmatching alleles at three linked and corresponding loci.  ...
   demonstrates that, via a linkage-control locus, the dynamic states described
   may provide slow (frequently reversing) selection for high or low
   recombination. An instance of intermediate confinement of linkage under the
   selection is illustrated." -- abs, only, at web of sci ['05].
   [Also search for: sexual reproduction why].

%A F. Antequera
%A A. Bird
%T Number of CpG islands and genes in human and mouse
%J PNAS
%V 90
%N 24
%P 11995-11999
%M DEC
%D 1993
%K jrnl, PNAS, c1993, c199x, c19xx, MolBio, CpG island, methylation, gene,
   human, mouse, mammal
%X "Est. of gene # in mammals is difficult due to the high proportion of
   noncoding DNA... . ...we provide a direct measurement of the # of genes in
   human & mouse. ...taken advantage of the fact that many mammalian genes are
   assoc. with CpG islands whose distinctive properties allow their physical
   sep'n from bulk DNA. Our results suggest that there are approximately 45,000
   CpG islands per haploid genome in humans & 37,000 in the mouse. Seq. comp.
   confirms that about 20% of the human CpG islands are absent from the
   homologous mouse genes. Analysis of a selection of genes suggests that both
   human & mouse are losing CpG islands over evolutionary time due to de novo
   methylation in the germ line followed by CpG loss through mutation. This
   process appears to be more rapid in rodents. Combining the number of CpG
   islands with the proportion of island-associated genes, we est. that the
   total # of genes per haploid genome is approx. 80,000 in both organisms."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.90.24.11995">doi:10.1073/pnas.90.24.11995</A>]['06].

%A A. L. Klatsky
%A M. A. Armstrong
%T Alcoholic beverage choice and risk of coronary artery disease mortality:
   do red wine drinkers do best?
%J Am. J. Cardiol.
%V 17
%P 467-469
%D 1993
%K jrnl, alcohol, beer, wine, red, white, spirits, health, heart, attack,
   attacks, disease, coronary, CHD, zz1003

%A T. MacKenzie
%A D. Platt
%A T. Dix
%T Modelling errors in restriction mapping
%J Hawaii Int. Conf. Sys. Sci. 26
%V ?
%P ???-???
%M JAN
%D 1993
%K Monash, TIDix, DMPlatt, conf, HICSS, HICSS-26, HICSS-93, 26, MolBio, RSM,
   restriction site map maps, mapping, error, errors, MML, MDL, model, RSM
%X Model errors in measuring fragment lengths with a log normal distribution
   (~ normal but maths easier).
   The "true" solution may not seem to be the "best" one,
   but tests on artificial data show it is generally in the top 5 or 10
   proposed solutions.

%A J. L. Thorne
%A H. Kishino
%T Freeing phylogenies from artifacts of alignment
%J Molec. Biol. & Evol.
%V 9
%N 6
%P 1148-1162
%M NOV
%D 1992
%K MolBio, multiple, alignment, DNA, RNA, phylogenetic, family, tree, trees
   MBE, RNA polymerase, maximum likelihood, distance matrix, data string
   strings
%X For each pair of seq's estimate a pair-wise evolutionary distance.
   The distance matrix and the standard deviations are used to infer
   a phylogenetic tree.
   DNA data strings: applied to 10 widely diverged sequences of the 2nd
   largest RNA polymerase subunit.

%A W. M. Fitch
%T Unresolved problems in DNA sequence analysis
%B Some Mathematical Questions in Biology: DNA Sequence Analysis
%S Mathematics in the Life Sciences
%V 17
%I Am. Math. Soc.
%D 1986
%E R. Miura
%P 1-18
%K MolBio, survey, DNA, AMS
%X isbn:0 8218 1167 3

%A P. H. Sellers
%T Pattern recognition in DNA
%B Some Mathematical Questions in Biology: DNA Sequence Analysis
%S Mathematics in the Life Sciences
%V 17
%I Am. Math. Soc.
%D 1986
%E R. Miura
%P 19-28
%K MolBio, DNA, RNA, string, sequence, analysis, AMS
%X isbn:0 8218 1167 3

%A M. S. Waterman
%T Probability distribution for DNA sequence comparisons
%B Some Mathematical Questions in Biology: DNA Sequence Analysis
%S Mathematics in the Life Sciences
%V 17
%I Am. Math. Soc.
%D 1986
%E R. Miura
%P 29-56
%K MolBio, DNA, RNA, string, sequence, analysis, long match, matching, segment,
   AMS
%X isbn:0 8218 1167 3

%A S. Tavare
%T Some probabilistic and statistical problems in the analysis of DNA
   sequences
%B Some Mathematical Questions in Biology: DNA Sequence Analysis
%S Mathematics in the Life Sciences
%V 17
%I Am. Math. Soc.
%D 1986
%E R. Miura
%P 57-86
%K MolBio, DNA, RNA, string, sequence, analysis, substitution, rate, rates,
   AMS, evolution, divergence
%X isbn:0 8218 1167 3

%A M. Zuker
%T RNA folding prediction: the continued need for interaction between
   biologists and mathematicians
%B Some Mathematical Questions in Biology: DNA Sequence Analysis
%S Mathematics in the Life Sciences
%V 17
%I Am. Math. Soc.
%D 1986
%E R. Miura
%P 87-124
%K MolBio, RNA, string, sequence, secondary structure, SS, fold, folding,
   AMS
%X isbn:0 8218 1167 3

%A D. G. Higgins
%A A. J. Bleasby
%A R. Fuchs
%T CLUSTAL V: improved software for multiple sequence alignment
%J Comp. Appl. BioSci.
%V 8
%N 2
%P 189-191
%D 1992
%K MolBio, multiple alignment, clustal, clustalV, similarity, homology,
   string, strings, sequence, CABIOS, Bioinformatics, jrnl
%X email: Higgins@EMBL-Heidelberg.DE

%A D. G. Higgins
%A R. Fuchs
%A P. J. Stoehr
%A G. N. Cameron
%T The EMBL data library
%J NAR
%V 20
%P 2071-2074
%D 1992
%K NAR, jrnl, MolBio, database data base, DNA, EMBL, genome
%X from a ref'

%A R. C. Griffiths
%T Genealogical-tree probabilities in the infinitely many site model
%J J. Math. Biol.
%V 27
%P 667-680
%D 1989
%K MolBio, JMB, population genetics, Monash, genealogical tree, allele

%A G. A. Watterson
%T Estimating species divergence times using multi-locus data
%B Population Genetics and Molecular Evolution
%E T. Ohia
%E K. Aoki
%P 163-183
%D 1985
%K population genetics, evolution, allele, species

%A C. Soderlund
%A D. Torney
%A C. Burks
%T Calculating shared fragments for the single digest problem
%J Hawaii Int. Conf. Sys. Sci. 26
%P ???-???
%M JAN
%D 1993
%K MolBio, digest, map, mapping, sequencing, clone, restriction fragment,
   HICSS 26, HICSS26, HICSS93, RSM

%A N. Goldman
%T Statistical tests of models of DNA substitution
%J J. Mol. Evol
%V 36
%N 2
%P 182
%M ???
%D 1993
%K MolBio, alignment, substitution, model, models, family evolutionary
   JME, phylogenetic tree trees, transition, transversion, rate, rates
%X Lots of refs.  N.G. was Adrian Friday's PhD student to '91
   via:  enews  bionet.journals.contents:
      AU Goldman-N.
      TI Statistical Tests of Models of DNA Substitution.
      SO J-Mol-Evol.  1993 36(2)  P 182.
      AB 30360182.239

%A M. I. Kanehisi
%A W. B. Goad
%T Pattern recognition in nucleic acid sequences II: an efficient method for
   finding locally stable secondary structures
%J Nuc. Acid. Res.
%V 10
%N 1
%P 265-277
%D 1982
%K MolBio, RNA, secondary structure, SS, NAR
%X O(n^2) time ???.

%A M. S. Waterman
%A T. F. Smith
%T Rapid dynamic programming algorithms for RNA secondary structure
%J Adv. Appl. Math.
%V 7
%P 455-464
%D 1986
%K MolBio, AAM, DPA, RNA secondary structure SS, fold, folding

%A D. Sankoff
%A J. B. Kruskal
%A S. Mainville
%A R. J. Cedergreen
%T Fast algorithms to determine RNA secondary structures containing multiple
   loops
%B Time Warps, String Edits and Macromolecules: The Theory and Practice of
   Sequence Comparison.
%E D. Sankoff
%E J. B. Kruskal
%I Addison-Wesley
%D 1983
%P 93-120
%K MolBio, DPA, RNA secondary structure SS, fold, folding

%A Xiaoqiu Huang
%A M. S. Waterman
%T Dynamic programming algorithms for restriction site map comparison
%J Comp. Appl. BioSci.
%V 8
%N 5
%P 511-520
%M OCT
%D 1992
%K MolBio, CABIOS, Bioinformatics, RSM, DPA, map, mapping,
   RSM, compare, match, matching

%A J. A. Lake
%T The order of sequence alignment can bias the selection of tree topology
%J Mol. Biol. Evol.
%V 8
%N 3
%P 378-385
%M MAY
%D 1991
%K family, evolutionary, phylogenetic tree, trees, multiple alignment, protein
   MolBio, MBE, jrnl, c1991, c199x, c19xx, sequence

%A D. Joseph
%A J. Meidanis
%A P. Tiwari
%T Determining DNA sequence similarity using maximum independent set
   algorithms for interval graphs
%B Algorithm Theory - SWAT '92
%E O. Nurmi
%E E. Ukkonen
%I SpringerVerlag
%S LNCS
%V 621
%P 326-337
%M JUL
%D 1992
%O 3rd Scandinavian Workshop on Algorithm Theory, Helsinki, July 1992.
%K DNA, MolBio, string, sequence, comparison, alignment, similarity,
   subsequence, maximum weight, match, independent set, double interval graph
   SWAT SWAT92 SWAT3
%X O(n log n) time, where n is # of nodes in graph. [not # chars in seqs !!!]
   Given a number of local matches between seq' A and B - possibly
   overlapping and out of order local matches -
   find a sequence of matches that are in order and non-overlapping.
   Monash, Hargrave, Mos 517.59 S283/3

%A S. A. Benner
%A M. A. Cohen
%A G. H. Gonnet
%T Empirical and structural models for insertions and deletions in the
   divergent evolution of proteins
%J J. Molec. Biol.
%V 229
%N 4
%P 1065-1082
%M FEB
%D 1993
%K MolBio, JMB, jrnl, c1993, c199x, c19zz, zz0218, protein, AA, sequence,
   alignment, gap, gaps, cost, costs, not linear, lengths,
   insertion, deletion, indel, indels
%X "... In this study, the probability of a gap in an alignment of a pair of
   homologous protein seqs. was found to increase with the evolutionary distance
   measured in PAM units (# of accepted point mutations per 100 [AA] residues).
   A relationship between the avg # of AA residues between indels & evolutionary
   distance suggests that a unit 30 to 40 amino acid residues in length remains,
   on average, undisrupted by indels during divergent evolution. Further, the
   probability of a gap was found to be inversely proportional to gap length
   raised to the 1.7 power. This empirical law fits closely over the entire
   range of gap lengths examined. Gap length distribution is largely indep. of
   evolutionary distance. These results rule out the widely used linear gap
   penalty as a satisfactory formula for scoring gaps when constructing
   alignments. Further, the observed gap length distribution can be explained by
   a simple model of selective pressures governing the acceptance of indels
   during divergent evolution. Finally, this model provides theoretical support
   for using indels as part of 'parsing algorithms', important in the de novo
   prediction of the folded structure of proteins from the sequence data."
   -- pdf@[<A HREF="http://gonnet.com/papers/InsertionsDeletions1993.pdf">gonnet.com</A>]['18],
      [<A HREF="https://doi.org/10.1006/jmbi.1993.1105">doi:10.1006/jmbi.1993.1105</A>],
      8445636@[<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/8445636">pubm'd</A>]['18].
   [Also search for: Gonnet protein]  and  [also search for: protein indels].

%A S. Tiwari
%A S. Ramachandran
%A A. Bhattacharya
%A S. Bhattacharya
%A R. Ramaswamy
%T Prediction of probable genes by Fourier analysis of genomic sequences
%J CABIOS
%V 13
%N 3
%P 263-270
%M JUN
%D 1997
%K jrnl, MolBio, CABIOS, Bioinformatics, transform, periodic, gene,
   coding, exon, GeneScan
%X major signal in coding [DNA] is a 3-base periodicity. ...use Fourier
   ... to develop a tool to recognize coding regions ...DNA.
   The 3-base period... a sharp peak at frequency f=1/3 in the Fourier...
   spectrum is a good discriminator of coding potential. [used] to detect
   probable coding regions in DNA sequences, by examining the local
   signal-to-noise ratio of the peak within a sliding window. ... overall
   accuracy is comparable to that of other techniques [but] the measure...
   is independent of training sets or existing database information, and can
   thus find general application. A computer program GeneScan which locates
   coding open reading frames and exonic regions in genomic sequences has
   been developed, and is available on request.

%A M. S. Waterman
%A J. R. Griggs
%T Interval graphs and maps of DNA
%J Bull. Math. Biol.
%V 48
%N 2
%P 189-195
%D 1986
%K MolBio, BMB, map, maps, mapping, DNA, interval graph graphs

%A Da-Fei Feng
%A R. F. Doolittle
%T Progressive sequence alignment as a prerequisite to correct phylogenetic
   trees
%J J. Mol. Evol.
%V 25
%P 351-360
%D 1987
%K MolBio, multiple alignment, string, strings, sequence, evolutionary, family,
   JME, phylogenetic, tree, trees
%X Examples given on protein sequences.

%A Zhang
%A Mesirov
%A Waltz
%T Hybrid systems for protein secondary structure prediction
%J J. Mol. Bio.
%P 1049-1063
%V 225
%N ??
%M ???
%D 1992
%K MolBio, JMB, protein, amino acid, AA, secondary structure prediction, SS
%X the training and test sets that they used, which were quite carefully
   selected.
   via enews (L a r r y  H u n t e r).

%A R. Holmquist
%T The method of parsimony: an experimental test and theoretical analysis of
   the adequacy of molecular restoration studies
%J J. Mol. Biol.
%V 135
%P 939-958
%D 1979
%K MolBio, family evolutionary phylogenetic tree trees, error errors,
   estimation, parsimony method, evolution, mutation, pressure selection,
   ancestral sequence, DNA, JMB
%X seems to be examining iterative multiple alignment cum tree inference
   based on rooted trees and 2-way cumulative alignment ? hard to tell ?
   1. Topological errors occur under specified conditions.
   2. Even given no topological errors,
      ancestral sequences inferred err significantly and
      magnitude of error increases with distance from the present day
      and can be large.
      These errors are irreducible as an inherent consequence of any
      evolutionary process in which chance processes operate within the
      constraints imposed by Darwinian selection.
      Formulae are derived which predict the errors in the ancestral seq's
      from a knowledge of only the internodal distances. The parsimony
      solution is not a reliably good solution.

%A R. Holmquist
%A T. H. Jukes
%T The current status of the REH theory
%J J. Mol. Evol.
%V 18
%P 47-59
%D 1981
%K MolBio, JME, jrnl, c1981, c198x, c19xx, random evolutionary hits REH,
   nucleotide, base, DNA, gene, mutation, evolution, fix, fixed, protein,
   amino acid, AA, substitution, replacement, change, rate, rates, model,
   estimate, time, distance, silent, codon, parsimony, Fitch
%X Bitter reply to an attack by Fitch!
   Gives parsimony methods a "big serve".
   (p.52) ... the ratio between amino acid replacement and nucleotide
          substitutions is NOT strictly time dependent, nor even approximately
          so, but also strongly depends upon the extent to which amino acid
          sequences are conserved in evolution.
   -- pdf@[<A HREF="http://www.springerlink.com/content/j66j864520p1h262/">spr'nger</A>]['09].

%A T. H. Jukes
%A S. Osawa
%T Recent evidence for evolution of the genetic code
%B Evolution of Life. Fossils, Molecules and Cultures
%E S. Osawa
%E T. Honjo
%I SpringerVerlag
%D 1991
%P 79-95
%K MolBio, nucleotide, base, genetic code, codon, amino acid
%X (chapter 2.3) Hargrave, Monash  H 575 081E.

%A D. Penny
%A M. Hendy
%T Estimating the reliability of evolutionary trees
%J Mol. Biol. Evol.
%V 3
%N 5
%P 403-417
%D 1986
%K MolBio, MBE, family, evolutionary, phylogenetic tree, trees, evolution,
%X A tree comparison metric used to
   measure increase in similarity of minimal trees
   as larger, randomly selected subsets of nucleotide [character]
   positions were taken.

%A G. J. Barton
%T Protein multiple sequence alignment and flexible pattern matching
%J Methods in Enzymology
%V 183
%P 403-428
%D 1990
%K MolBio, MENZ, multiple alignment, string, strings, sequence, protein,
   amino acid, AA, 3D, structure
%X ... alignments obtained from comparison of the protein 3-D structure
   are used as a standard against which to test an automatic method for the
   pairwise alignment of protein sequences. The accuracy of the alignments is
   shown to improve when additional nonsequence information is incorporated
   into the alignment.

%A G. J. Barton
%A M. J. E. Sternberg
%T LOPAL and SCAMP: techniques for the comparison and display of protein
   structures
%J J. Mol. Graphics
%V 6
%P 190-201
%M DEC
%D 1988
%K JMG, MolBio, protein, amino acid, AA, structure, tertiary, 3D,
   PS300 program

%A R. B. Russell
%A G. J. Barton
%T Multiple protein sequence alignment from tertiary structure comparison:
   assignment of global and residue confidence levels
%J Proteins: Structure Function and Genetics.
%V 14
%P 309-323
%D 1992
%K MolBio, protein, amino acid, AA, multiple alignment, 3D structure


%A John Tooby
%T Pathogens, polymorphism, and the evolution of sex
%J J. Theor. Biol.
%V 97
%P 557-576
%D 1992 ???
%K JTB, MolBio, evolution, origin, maintenance sex, why, sexual reproduction,
   parasite, Red Queen Theory, biol
%X via enews
   <!-- email: lfiddick@nyx.cs.du.edu --> (larry fiddick)
   Organization: University of Denver, Dept. of Math & Comp. Sci.

%A K. Yoshida
%A C. Smith
%A T. Kazic
%A G. Michaels
%A R. Taylor
%A D. Zawada
%A R. Hagstrom
%A R. Overbeek
%T Towards a human genome encyclopedia
%J Proc. Int. Conf. on 5th Generation Computer Systems
%D 1992
%P 307-320
%I ICOT
%K MolBio, data base, database, DB, human genome project, HUGO, Lucy,
   DNA, map, maps, mapping, logic programming, LP, Prolog
%X chromosome 21 as a test bed
   more than 40 maps of different kinds extracted from publications
   and integrated.
   Prolog used.

%A W. R. Taylor
%A D. T. Jones
%T Deriving an Amino Acid Distance Matrix
%J J. Theor. Biol.
%D 1993 in press
%K MolBio, amino acid, acids, AA, distance, similarity, relation, Gray code,
   JTB
%X Various methods were investigated to convert an amino acid similarity matrix
  into a low-dimensional, metric distance matrix.  Using projection techniques,
  no  unique  transformation  was   found  and  of  the  many  inversion  forms
  investigated, simple negation normalised by the diagonal  elements produced a
  good fit to the original data. An  inter-row distance also gave a  comparable
  fit and  when evaluated by weighted  least-squares minimisation  was found to
  be  preferable. A  rank-ordered form  of  the matrices  was also  derived  by
  constraining  neighbours to  be  equidistant in  (3)  space. This  produced a
  network configuration  not unlike  that produced  in a  previous analysis  of
  amino  acid  physico-chemical  properties.  The  derived   forms  might  find
  applications in  sequence alignment,  including pattern matching  algorithms,
  and the construction of phylogenetic trees.
   via enews:
      email: jones@bsmsol1.ucl.ac.uk (David Jones) Organization:
             University College London Biochemistry Department

%A W. R. Taylor
%T A template based method of pattern matching in protein sequences
%J Prog. Biophys. Mol. Biol.
%V 54
%P 159-252
%D 1991
%K MolBio, amino acid, acids, AA, protein similarity, match, genetic, Gray code,
   I Ching, I-Ching
%X This paper contains possibly the oldest  reference in  any molecular biology
  paper: Wan,  "The I  Ching", privately published  (1142 BC).  If you want  to
  know  what Gray codes,  the I  Ching, and  the genetic  code have to  do with
  representing amino acid similarities, then this is the paper for you!
   via enews:
      David Jones
      Biomolecular Structure and Modelling Unit
      University College London
   email: jones@bsmsol1.ucl.ac.uk (David Jones) Organization:
          University College London Biochemistry Department

%A J. Jurka
%A A. Milosavljevic
%T Reconstruction and analysis of human Alu genes
%J J. Mol. Evol.
%V 32
%P 105-121
%D 1991
%K JME, MolBio, ALU, DNA, repetitive, junk, evolution
%X LA has copy

%A A. K. Konopka
%T Theory of degenerate coding and informational parameters of protein
   coding genes.
%J Biochimie
%V 67
%P 455-468
%D 1985
%K MolBio, genetic code, codon, coding region, DNA, protein

%A W. R. Taylor
%A C. A. Orengo
%T Protein structure alignment
%J J. Mol. Bio.
%V 208
%N 1
%P 1-22
%M JUL
%D 1989
%K jrnl, JMB, c1989, c198x, c19xx, MolBio, protein, tertiary, structure, 3D,
   align, alignment, match, matching, fit, fitting, distance matrix, plot,
   geometry, shape, shapes
%X "A new method of comparing protein structures is described, based on distance
   plot analysis. It is relatively insensitive to insertions & deletions in
   sequence & is tolerant of the displacement of equivalent substructures
   between the 2 molecules being compared. When presented with the co-ordinate
   sets of 2 structures, the method will produce automatically an alignment of
   their sequences based on structural criteria. The method uses the dynamic
   programming optimization technique, which is widely used in the comparison of
   protein sequences & thus unifies the techniques of protein structure and
   sequence comparison. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0022-2836(89)90084-3">doi:10.1016/0022-2836(89)90084-3</A>]['07].  Also see O+T c1990.
   [Also search for: MolBio protein structure alignment].

%A W. R. Taylor
%A C. A. Orengo
%T A holistic approach to protein structure alignment
%J Protein Engineering
%V 2
%N 7
%P 505-519
%D 1989
%K MolBio, protein structure, 3D, align, alignment, match, matching,
   fit, fitting, hydrogen, bond, bonding, hypropathy, shape, shapes
%X LA has copy; see also O + T 1990

%A C. A. Orengo
%A W. R. Taylor
%T A rapid method of protein structure alignment
%J J. Theor. Biol.
%V 147
%P 517-551
%D 1990
%K MolBio, protein, structure, 3D, align, alignment, match, matching,
   fit, fitting, fast, JTB, shape, shapes
%X "A reduction in the time required to compare 2 protein structures has been
   achieved for a previously developed structure alignment method, by reducing
   the # of residue pair comparisons which must be performed between the 2
   structures. Subsets of residue pairs are selected by an iterative procedure.
   Initially, selection is based on similarities in solvent accessible surface
   areas or torsional angles or a combination of both properties, giving
   subsets containing approximately 2% of the total number of residue pairs.
   Using these subsets, a rough comparison of the two structures is generated
   by the structural alignment program. The information returned from this can
   be used to identify more accurately topologically equivalent residues in the
   2 proteins, thus enabling a new & much smaller subset (less than 0.2% of the
   total # of residue pairs) to be selected. The process of iterative refinement
   of the residue pair subsets is repeated once more, when in 95% of the
   structure comparisons tested, the correct alignment of the proteins was
   obtained. ..." See also T + O 1989 (two).
   [Also search for: MolBio protein structure alignment].

%A E. Szathmary
%T Four letters in the genetic alphabet: a frozen evolutionary optimum?
%J Proc. R. Soc. Lond. B
%V 245
%P 91-99
%D 1991
%K MolBio, gene, genetic code, codon, protein, origin, evolution
%X LA has copy

%A T. L. Bannam
%A J. I. Rood
%T Relationship between the clostridium perfringens catQ gene product
   and chloramphenicol acetyltranferases from other bacteria.
%J Antimicrobial Agents and Chemotherapy
%M MAR
%D 1991
%V 35
%N 3
%P 471-476
%K MolBio, ecoli, coli, cat, catQ, DNA, protein, data strings
%X from microbiology Monash

%A A. S. Huggins
%A T. L. Bannam
%A J. I. Rood
%T Comparative sequence analysis of the catB gene from clostridium butyricum
%J Antimicrobial Agents and Chemotherapy
%M NOV
%D 1992
%V 36
%N 11
%P 2548-2551
%K MolBio, ecoli, coli, cat, catQ, catB, DNA, protein, data strings
%X from microbiology Monash

%A S. F. Altschul
%T Amino acid substitution matrices from an information theoretic perspective
%J J. Mol. Biol.
%V 219
%P 555-565
%D 1991
%K c1991, c199x, c19xx, MolBio, JMB, amino acid, AA, protein, align alignment,
   replacement, substitution, change, matrix, score, probability, letter, PAM,
   theory, PAM-1, 1-PAM, PAM-120, 120-PAM, PAM-250, 250-PAM
%X [Also search for: MolBio substitution matrix].

%A D. J. States
%A W. Gish
%A S. F. Altschul
%T Improved sensitivity of nucleic acid database similarity searches
   using application specific scoring matrices
%J Methods: A companion to Methods in Enzymology
%V 3
%P 66-70
%D 1991
%K MolBio, DNA, align, alignment, score, change, probability,
   substitution matrix
%X [Also search for: MolBio substitution matrix].

%A J-M. Claverie
%A D. J. States
%T Information enhancement methods for large scale sequence analysis
%J Comp. Chem
%V 17
%N 2
%P 191-201
%D 1993
%O 2nd Int. Wksp. Open Prob's in Comp. Mol. Biol. '92
%K MolBio, jrnl, xnu, xblast, blast, sequence similarity, masking out
%X ... two masking methods, xnu and xblast, capable of
   eliminating most of the [false positive matches] ...

%A S. F. Altschul
%T A protein alignment scoring system sensitive at all evolutionary
   distances
%J J. Mol. Evol.
%V ??
%N ??
%P ???-???
%D in press 1992 ?
%K MolBio, JME, protein, amino acid, align,
   alignment, score, change, replacement,
   substitution, probability, matrix, PAM

%A P. A. Pevzner
%T L-tuple DNA sequencing: Computer analysis
%J J. Biomol. Struct. Dyn.
%V 7
%P 63-73
%D 1989
%K jrnl, JBSD, MolBio, hybridization, SBH, Eulerian circuit, path, SCSS

%A P. A. Pevzner
%A M. Y. Borodovsky
%A A. A. Mironov
%T Linguistics of nucleotide sequences I: The significance of deviations from
   mean statistical characteristics and prediction of the frequency of
   occurrence of words.
%J J. Biomolecular Structure and Dynamics
%V 6
%P 1013-1026
%D 1989
%K jrnl, JBSD, JBMSD, MolBio, DNA, string, sequence, word, words, tuple

%A P. A. Pevzner
%T Nucleotide sequences versus Markov models
%J Computers Chem.
%V 16
%N 2
%P 103-106
%D 1992
%K MolBio, DNA, word, frequency, frequencies, count, tuple, l-tuple, sequence,
   statistics
%X Can't describe all DNA stat's by small order Markov models.
   The dinucleotide distributions for all "long" seq's from genbank
   were analysed.
   Non-stationary dinucleotides are associated with poly-W and poly-S
   where W={A,T} and S={G,C}
   This study establishes link twixt non-stationary l-tuples and DNA
   strand symmetry.

%A P. A. Pevzner
%T Multiple alignment, communicating cost and graph matching
%J SIAM J. Appl. Math.
%V 52
%N 6
%P 1763-1779
%M DEC
%D 1992
%K SJAM, MolBio, multiple sequence, string, match, matching, align, alignment,
   approximation, maximum weighted
%X computationally efficient approximation with
   guaranteed error bounds for k sequences.
   Derived from maximum weighted matching problem for a k-vertx graph.

%A P. A. Pevzner
%T Statistical distance between texts and filtration methods in sequence
   comparison.
%J Comp. Appl. BioSci.
%V 8
%N 2
%P 121-127
%D 1992
%K CABIOS, Bioinformatics, MolBio, sequence match, matching, filter

%A P. A. Pevzner
%A M. S. Waterman
%T Multiple filtration methods and approximate pattern matching
%J sub to Algorithmica
%V ???
%P ??-??
%D 1992 ???
%K MolBio, sequence match, matching, filter

%A P. A. Pevzner
%A M. S. Waterman
%T Generalized sequence alignment and duality
%J Adv. Appl. Math.
%V 14
%N 2
%P 139-171
%D 1993
%K MolBio, c1993, c199x, c19xx, string, sequence, align, alignment, dual,
   duality problem, DPA, minimal Hilbert basis, LCS, LCSS,
   longest common subsequence
%X the Jeroslav - Schrijver characterization of the minimal Hilbert bases
   gives an O(n) estimation of the number of elementary edit operations for
   generalized LCS.
   -- [<A HREF="http://dx.doi.org/10.1006/aama.1993.1008">doi:10.1006/aama.1993.1008</A>]['10].

%A P. A. Pevzner
%T Overlapping words paradox and Conway equation
%J Supercomputing, Bioinformatics and Complex Genome Analysis
%I World Scientific
%P 71-78
%D 1993
%K MolBio, DNA, c1993, c199x, c19xx, string, sequence, word, words, tuple,
   tuples, count, counts, frequency, frequencies, significant, significance,
   Conway's, Conways, equation, variance, best bet for simpletons
%X In P's c2000 book:
   p.136: "Player 1 selects a word, A, of length l in a 0-1 alphabet.
   Player 2 (knowing A) selects a word B of length l.  The winner is whoever's
   word comes up 1st. ... If l >= 3, P2 can choose a word that beats P1 more
   often than not. ...
   Given two l-letter words, A and B, the correlation of A and B,
   AB=(c[0]...c[l-1]), is an l-letter Boolean word. The ith bit of AB is 1
   if the (n-i)-prefix (the 1st n-1 letters) of B coincides with the
   (n-i)-suffix (last n-1 letters) of A. Otherwise the
   i-th bit is 0. The correlation polynomial (Guibas & Odlyzko '81) of A and B,
   K[AB](t)=c[0]+c[1].t+...+c[l-1].t^(l-1).  Also denote K[AB]=K[AB](1/2).
   Conway eqn: The odds that B will beat A are  (K[AA]-K[BB])/(K[BB]-K[BA])."
   p.142: "variance of freq. of occurrences varies sig, between words even for
   Benoulli texts. e.g., for equi-probable {A,C,G,T} Var(AA)/Var(AT)=21/13 and
   Var(AAA)/Var(ATG)=99/59. ..."   (small alphabet, big effect).
   -- [<A HREF="http://www.cse.ucsd.edu/~ppevzner/">auth@ucsd</A>]['08].
   [Also search for: Guibas Odlyzko 1981],  [also search for: Penney game].

%A S. L. Baldauf
%A J. D. Palmer
%T Animals and fungi are each other's closest relatives: Congruent evidence
   from multiple proteins
%J PNAS
%V 90
%N 24
%P 11558-11562
%M DEC
%D 1993
%K jrnl, MolBio, PNAS, c1993, c199x, c19xx, animal, animals, fungus, fungi,
   plant, plants, evolution, protein
%X "Phylogenetic relationships among plants, animals, & fungi were examined by
   using seqs. from 25 proteins.  4 insertions/deletions were found that are
   shared by 2 of the 3 taxonomic groups in question, & all 4 are uniquely
   shared by animals & fungi relative to plants, protists, & bacteria. ... "
   -- [<A HREF="http://www.pnas.org/content/90/24/11558">PNAS</A>]['01].

%A M. Vinigron
%A P. A. Pevzner
%T Multiple sequence comparison and n-dimensional image reconstruction
%J sub to Algorithmica
%V ??
%P ??-??
%D 1992 ???
%K MolBio, multiple sequence align, alignment, noise, filter, filtration

%A P. A. Pevzner
%T DNA physical mapping and alternating Eulerian cycles in coloured graphs
%J sub to Algorithmica
%V ??
%P ??-??
%D 1992 ???
%K MolBio, restriction site map, maps,  mapping, RSM,
   order, equivalent solution, solutions

%A M. A. Ragan
%A C. J. Bird
%A E. L. Rice, R. R. Gutell, C. A. Murphy
%T A molecular phylogeny of the marine red algae (Rodophyta) based on the
   nuclear small-subunit rRNA gene
%J PNAS
%V 91
%P 7276-7280
%M JUL
%D 1994
%K jrnl, PNAS, plant biology, alga, algal, phylogenetic, tree, trees, MolBio,
   biol, bangiophytes, Porphyridiales, Florideophycidae, Hildenbrandiales,
   florideophyte, family, evolutionary, ssu rRNA, diversity
%X "...nuclear genes encoding small subunit rRNA from 39 species in 15 orders.
   Sequence divergences are relatively large, especially among bangiophytes and
   even among congeners in this group. Subclass Bangiophycidae appears
   polyphyletic, encompassing at least three lineages, with Porphyridiales
   distributed between two of these. Subclass Florideophycidae is monophyletic,
   with Hildenbrandiales, Corallinales, Ahnfeltiales, and a close association
   of Nemaliales, Acrochaetiales, and Palmariales forming the four deepest
   branches. Cermiales may represent a convergence of vegetative and
   reproductive morphologies, as family Ceramiaceae is at best weakly related
   to the rest of the order, and one of its members appears to be allied to
   Gelidiales. Except for Gigartinales, for which more data are required, the
   other florideophyte orders appear distinct and taxonomically justified. A
   good correlation was observed with taxonomy based on pit-plug
   ultrastructure. Tests under maximum-likelihood and parsimony of alternative
   phylogenies based on structure and chemistry refuted suggestions that
   Acrochaetiales is the most primitive florideophyte order and that Gelidiales
   and Hildenbrandiales are sister groups."
   -- [<A HREF="http://www.pnas.org/cgi/content/abstract/91/15/7276">pnas</A>][5/'04].

%A B. R. Levin
%A J. J. Bull
%T Short-sighted evolution and the virulence of pathogenic microorganisms
%J Trends Microbiol.
%V 2
%N 3
%P 76-81
%M MAR
%D 1994
%K jrnl, MolBio, host, parasite, coevolution, c1994, c199x, c19xx, coevolution,
   HIV
%X "... virulence may be an inadvertent consequence of mutation & selection in
   the parasite population, occurring within a host during the course of an
   infection. This type of virulence is short-sighted, in that it engenders no
   advantage to the pathogen beyond the afflicted host. Bacterial meningitis,
   poliomyelitis & AIDS are 3 candidates for this model of the evol. of v.."
   Also: [<A HREF="http://www.biology.emory.edu/research/Levin/pubs/index.html">levin lab</A>]['05].

%A P. A. Pevzner
%A R. J. Lipschutz
%T Towards DNA sequencing chips
%J Symp. Math. Found'ns of Comp. Sci.
%P 143-158
%I SpringerVerlag
%S LNCS
%V 841
%D 1994
%K conf, MFCS, SMFCS, LNCS, LNCS841, MolBio, hybridization,
   SBH, microarrays, micro array, arrays

%A S. Sze
%A P. Pevzner
%T Las Vegas algorithms for gene recognition: Suboptimal and error
   tolerant spliced alignment
%J J. Comp. Biol.
%V 4
%P 297-330?
%D 1997
%K jrnl, MolBio, c1997, c199x, c19xx, JCB, transcription, start, initiation,
   ORF, find, finding, site, sites, TIS, Monte Carlo, genes
%X from a ref'
   [Also search for: spliced alignment].

%A D.A. Steinhauer
%A E. Domingo
%A J.J. Holland
%T Lack of evidence for proofreading mechanisms associated with an RNA virus
   polymerase.
%J GENE
%V 122
%P 281-288
%D 1992
%K MolBio, RNA, virus, mutation, transition, transversion, proof reading
%X via enews

%A M. C. Milinkovitch
%A G. Orti
%A A. Meyer
%T Revised phylogeny of whales suggested by motochondrial ribosomal DNA
   sequences.
%J Nature
%V 361
%M JAN
%D 1993
%P 346-348
%K MolBio, whale, cetacea, family, evolutionary, phylogenetic tree, trees, DNA,
   data sequence, sequences, 12S, 16S, myoglobin

%A F. Tajima
%D 1992
%T Statistical method for estimating the standard errors of branch lengths in
   a phylogenetic tree reconstructed without assuming equal rates of nucleotide
   substitution among different lineages.
%J Mol. Biol. Evol.
%V 9
%P 168-181
%K MolBio, MBE, evolutionary, family, phylogenetic tree, trees
%X via enews

%A A. Rzhetsky
%A M. Nei
%D 1992
%T A simple method for estimating and testing minimum-evolution trees
%J Mol. Biol. Evol.
%V 9
%P 945-967
%K MolBio, MBE, evolutionary, family, phylogenetic tree, trees
%X via enews

%A M. Bulmer
%D 1989
%T Estimating the variability of substitution rates
%J Genetics
%V 123
%P 615-619
%K MolBio, evolutionary, family, phylogenetic tree, trees
%X via enews

%A W-H Li
%D 1993
%T Unbiased estimation of the rates of synonymous and nonsynonymous
   substitutions.
%J J. Mol. Evol.
%V 36
%P 96-99
%K MolBio, JME, evolutionary, family, phylogenetic tree, trees
%X via enews

%A W. R. Taylor
%A C. A. Orengo
%A L. H. Pearl
%T Comparison of predicted and x-ray crystal structures of retroviral
   proteases
%J Proc. 2nd Int. Conf. Protein Engineering
%E M. Ikehara
%E T. Oshima
%E K. Titani
%W Kobe, Japan
%D 1989
%P 21-27
%I SpringerVerlag
%K MolBio, protein, fold, folding, tertiary, structure, prediction, comparison,
   structure alignment, HIV protease, retrovirus, retro virus, viral
%X It had been suggested that the protease which is encoded in all retroviral
   genomes is related to the aspartyl protease family. This suggestion was
   developed by Pearl and Taylor into a detailed structural model of the
   retroviral protease of HIV which has now been confirmed in surprising detail
   from X-ray crystallography data.
   Uses the Taylor Orengo method of aligning Tertiary Structures.


%A J. W. Fickett
%A D. C. Torney
%A D. R. Wolf
%T Base compositional structure of genomes
%J Genomics
%V 13
%P 1056-1064
%D 1992
%K MolBio, long range pattern, base composition, G+C, GC content, Isochore
%X via enews

%A Pearson
%T Searching protein sequence libraries: comparison of the sensitivity and
   selectivity of the Smith-Waterman and FASTA algorithms.
%J Genomics
%V 11
%P 635-650
%D 1991
%K MolBio, sequence, string, alignment, approximate, similarity, match,
   matching, homology, FASTA, FASTP, parallel, multiprocessor, MasPar, Blast
%X email: wrp@cyclops.micr.Virginia.EDU (Bill Pearson) '93
   (Apparently he is ('93) working on a follow up paper.)

%A Despande
%A Richards
%A Pearson
%T A platform for biological sequence comparison on parallel computers
%J Comp. Appl. BioSci.
%V 7
%P 237-247
%D 1991
%K CABIOS, Bioinformatics, MolBio, sequence, string, alignment,
   approximate match, matching, similarity, homology, parallel,
   multiprocessor, FASTA, FASTP, Blast
%X email: wrp@cyclops.micr.Virginia.EDU (Bill Pearson)  '93
      Now running on networks of workstations using PVM (parallel
   virtual machine), a freely available package for almost any machine.
   If you are doing lots of sequence comparisons, I can provide you with
   PVM versions for FASTA and Smith-Waterman, with BLAST to be available
   in about a month.
        Here are some typical timings on a network of 12 Sparc IPC's
   using PVM2.4 (PVM3.0 is a little slower)
   pvm2.4, 20 protein sequences vs   annotated PIR34 (approx 10K sequences)
      nodes      11      7       3
           --------------------
      k2         78     105     207         (times in seconds)
                 76     128     206
                (73.9)
      k1        310     466     1070
                312     471     1083
                (94.6)
      ok1       559     836     1995
                532     811     1898
                (97.3)
   Smith-Waterman times are about 5X the ok1 times.  The values in parentheses
   indicate the relative efficiency of 11 nodes compared to 3 nodes. Thus
   k2 on 11 nodes is 11/3*.739 times faster; ok1 is 11/3*.973 times faster.
   Bill Pearson

%A L. Varetto
%T Typogenetics: an artificial genetic system
%J J. Theor. Biol.
%V 160
%P 185-205
%M JAN
%D 1993
%K MolBio, JTB, gene, genetics, artificial life, evolution, self replication

%A U. Arnason
%A S. Gretarsdottir
%A B. Widegren
%T Mysticete (baleen whale) relationships based upon the sequence of the
   common cetacean satellite.
%J Mol. Biol. Evol.
%V 9
%N 6
%P 1018-1028
%D 1992
%K MolBio, MBE, mysticetes, whale, whales, highly repetitive DNA,
   satellite DNA, phylogenetic, family, evolutionary tree, trees,
   data sequence
%X gives an alignment for fin, blue, gray, humpback, pygmy r., right, bowhead
   (about 1760-bp)

%E Renaud Fortuner
%T Advances in Computer Methods for Systematic Biology
   Artificial Intelligence, Databases, Computer Vision
%D 1993
%I John Hopkins
%O '90 NSF-ARTISYST conference
%K MolBio, book, text, ARTISYST, JH, JHU
%X isbn:0801844924.
      A complete listing of Hopkins books and journals is available on the
      Internet via anonymous ftp or gopher at: jhunix.jhu.hcf.edu; select the
      University Press/JHU_Press directory.
   via enews
   [Also search for: MolBio book].

%T Genetic and Physical Mapping
%E Kay E. Davies
%E Shirley M. Tilghman
%I Cold Spring Harbor Laboratory Press.
%V 1
%D 1990
%K MolBio, map, mapping, RSM, gene, genome, HUGO
%X via roland yap  '93:
   The library has vol 1, 1990.
   It appears to be an ongoing of volumes and the one I was looking for was,
   Strategies for Physical Mapping, Vol. 4, 1992.
   I don't know what's in the rest of the volume but there is a Miller paper
   in this one.
   Roland

%A R. Langridge
%A D. M. Saccocio
%T Mapping and interpreting biological information
%J CACM
%V 34
%N 11
%M NOV
%D 1991
%P 32-39
%K MolBio, map, mapping, survey, sequence analysis, biology, BI

%A S. Rao
%A Qing-Lin Zhu
%A S. Vajda
%A T. F. Smith
%T The local information content of the protein structural database
%I BioMolecular Engineering Research Centre, Boston Univ.
%D 1992
%K MolBio, BMERC, protein, SS, secondary, structure
%X a simple study of the information available within the proteins of
   known structure reveals both the limits of structure predictions based
   on overall statistical correlations between sequence and structure,
   and the areas where there is still possibility for further structural
   database exploitation.
   -- claims to explain the 60%-70% limit on SSprediction

%A S. M. Weiss
%A D. M. Cohen
%A N. Indurkhya
%T Transmembrane segment prediction from protein sequence data
%J Proc. 1st Int. Conf. Intelligent Systems for Mol. Bio.
%P ???-???
%D 1993
%K MolBio, trans, membrane, protein
%X training set: 324 proteins, 1585 segments
   NB. Nitin Indurkhya works at Telecom Blackburn Rd ('93)

%A N. Goldman
%T Nucleotide, dinucleotide and trinucleotide frequencies explain patterns
   observed in chaos game representation of DNA sequences
%J NAR
%V 21
%P 2487-2491
%D 1993
%K MolBio, c1993, c199x, c19xx, NAR, frequency, DNA, Jeffrey
%X rejects a paper by Jeffrey that proposed a way of revealing patterns in DNA.

%A B. D. James
%A G. J. Olsen
%A N. R. Pace
%T Phylogenetic comparative analysis of RNA secondary structure
%J Methods in Enzymology
%V 180
%P 227-239
%D 1989
%K MolBio, MENZ, RNA, secondary structure, SS, fold, folding, phylogeny,
   evolutionary, tree, trees

%A E. Orito
%A M. Mizokami
%A Y.Ina, E.N.Moriyama, N.Kameshima, M.Yamamoto, T.Gojobori
%T Host-independent evolution and a genetic classification of the Hepadnavirus
   family based on nucleotide sequences
%J PNAS
%V 86
%N 18
%P 7059-7062
%M SEP
%D 1989
%K jrnl, PNAS, MolBio, HBV, c1989, c198x, c19xx, sequence, genotype, genotypes,
   strain, strains, hepatitis, evolution, evolutionary tree, phylogenetic,
   phylogeny
%X "... phylogeny was undertaken to examine whether the evolution of the
   hepadnavirus family is host-dependent. Using the nucl. seqs. of 18 strains,
   we constructed phylogenetic trees. ... show that all 12 strains of [HBV] can
   be classified into 4 subgroups that are not compatible with conventional
   subtypes. We est. the rate of synonymous (silent) subs. for [HBV] to be
   4.57 x 10**-5 /site /year. ... est. that duck [HBV] diverged from a common
   ancestor about 30,000 y. ago at the earliest, that woodchuck hep. v. &
   ground squirrel hep. v. diverged about 10,000 y. ago, & that [HBV] diverged
   within the last 3000 y.. [these times] are much more recent than those of the
   host species, it suggests that the hepadnavirus family evolved independently
   of host-species divergence."
   -- [<A HREF="http://www.pnas.org/cgi/content/abstract/86/18/7059">paper@pnas</A>]['07].
   [Also search for: HBV evolution]

%A R. Girones
%A R. H. Miller
%T Mutation rate of the hepadnavirus genome
%J Virology
%V 170
%N 2
%P 595-597
%M JUN
%D 1989
%K jrnl, MolBio, c1989, c198x, c19xx, woodchuck, hepatitis, WHV, HBV,
   mutations, virus, viral, rates
%X "... we transfected 10 neonatal woodchucks with an infectious molecular clone
   of woodchuck...(WHV). ... Although the consensus nucleotide seq. remained
   unchanged, we found three differences in individual progeny genomes when
   compared to the parental genome sequence. Thus, we est. the mutation rate of
   the WHV genome to be less than or equal to 2 X 10(-4) base subs./site/year.
   This figure is one to two orders of magnitude lower than the mutation rates
   previously calculated for the positive- and negative-strand RNA viruses, but
   is similar to the mutation rate of the gag gene which is the most slowly
   evolving gene of retroviruses. ... hepadnavirus g. is relatively stable...
   when compared to other viruses that lack polymerase-assoc. proofreading..."

%A J. A. Jaeger
%A D. H. Turner
%A M. Zuker
%T Predicting optimal and suboptimal secondary structure for RNA
%J Methods in Enzymology.
%V 183
%P 281-306
%D 1990
%K MolBio, MENZ, ME, RNA, secondary structure, SS, prediction, fold, folding,
   free energy minimization
%X it is possible that ref' should be: Meth' Enz' 180 227-239 1989

%A B. A. Shapiro
%A K. Zhang
%T Comparing multiple RNA secondary structures
%J Comp. Appl. BioSci.
%V 6
%N 4
%P 309-318
%D 1990
%K MolBio, RNA secondary structure, SS, labelled, tree, trees, comparison,
   CABIOS, Bioinformatics, edit distance, similarity

%A D. Sankoff
%T Simultaneous solution of the RNA folding, alignment and protosequence
   problems.
%J SIAM J. Appl. Math.
%V 45
%P 810-825
%D 1985
%K MolBio, SJAM, RNA, secondary structure SS, fold, folding, conformation,
   string, sequence, similarity, homology, alignment, edit distance

%A R. Pachter
%A R. B. Altman
%A O. Jardetzky
%T The dependence of a protein solution structure on the quality of the
   input NMR data. Application of the double-iterated Kalman filter
   technique to oxytocin
%J J. Magnetic Resonance
%V 89
%P 578-584
%D 1990
%K JMR, MolBio, nuclear magnetic resonance, 3D, distance geometry, uncertainty,
   variance, double iterated, DIKF
%X [Also search for: oxytocin hormone].

%A D. G. Higgins
%A P. Stoehr
%T EMBLSCAN: fast approximate DNA database searches on compact disc
%J Comp. Appl. BioSci.
%V 8
%N 2
%P 137-139
%D 1992
%K MolBio, CABIOS, Bioinformatics, EMBL, scan, data base, CD

%A D. G. Higgins
%T Sequence ordinations: a multivariate analaysis approach to analysing large
   sequence data sets
%J Comp. Appl. BioSci.
%V 8
%N 1
%P 15-22
%D 1992
%K MolBio, CABIOS, Bioinformatics, string, sequence, cluster, clustering,
   principal component, coordinate analysis, PCA
%X finds all pairwise distances of n sequences,
   (tries to use a Euclidean distance)
   can embed in an (n-1)-D space
   try to embed in a reduced dimension (esp. 2 or 3-D) space.

%A J. Devereux
%A P. Haeberli
%A O. Smithies
%T A comprehensive set of sequence analysis programs for the Vax
%J Nucl. Acids. Res.
%V 12
%P 387-395
%D 1984
%K MolBio, protein, amino acid, AA, secondary structure, fold, folding,
   conformation, NAR, SS
%X via a ref

%A M. Gribskov
%A Burgess
%A J. Devereux
%T PEPPLOT, a protein secondary structure analysis program for the UWGCG
   sequence analysis software package.
%J NAR
%V 14
%N 1
%P 327-334
%K MolBio, protein, amino acid, AA, secondary structure, fold, folding,
   conformation, NAR, SS
%X via a ref

%A H. Wolf
%A S. Modrow
%A Motz
%A Jameson
%A Hermann
%A G. Fortsch
%T An integrated family of amino acid sequence analysis programs
%J Comp. Appl. BioSci.
%V 4
%N 1
%P 187-191
%D 1988
%K MolBio, protein, amino acid, AA, secondary structure, fold, folding,
   conformation, CABIOS, Bioinformatics, SS
%X via a ref

%A D. Weininger
%T SMILES, a chemical language and information system. 1. Introduction to
   methodology and encoding rules
%J J. Chem. Inf. Comput. Sci.
%V 28
%P 31-36
%D 1988
%K jrnl, JCICS, MolBio, c1988, c198x, c19xx, chemical compound, compounds,
   chemicals, molecule, language, organic, cyclic, aromatic, structural formula,
   representation, SMILES 1, .smi file format, Daylight, examples
%X 1. ATOMS: organic subset B, C, N, O, P, S, F, Cl, Br, I; hydrogens implicit;
     carbon normal 'C', aromatic 'c', similarly N/n.
     Attached H and charges always in brackets e.g. [OH-], [Fe+3] or [Fe+++].
     Non organic atoms in [].
   2. BONDS: single, double, triple, aromatic {-, =, #, :} (can omit - & :),
     e.g. CC (ethane CH_3CH_3),  C=C (ethylene CH_2=CH_2), C#N (cyanide HCN)
   3. BRANCHES: e.g. CCN(CC)CC, () can nest.
   4. Cyclic: break a "single or aromatic bond", int-labels ends
     e.g. C1CCCCC1 (cyclohexane C_6H_12), C12C3C4C1C5C4C3C25 (cubane!),
     digits may be reused (when 1st ring closed)
   5. DISCONNECTION:  struct1.struct2
   6. AROMATICITY:  c1ccccc1C(=O)O (Benzoic acid, c.f. cyclohexane),
     NB an equiv non-aromatic form (eg C1=CC=CC=C1) is
     auto-converted to aromatic form.
   Normal valences        B 3, C 4, N 3, O 2, Cl 1, Br 1, I 1.
   Lowest normal valences P 3 or 5, aliphatic S 2 or 4 or 6;
     e.g. OS(=O)(=O)O (ie, H_2SO_4).
   Also see SMILES 2, '89.
   -- [<A HREF="http://dx.doi.org/10.1021/ci00057a005">doi:10.1021/ci00057a005</A>]['08],
      [<A HREF="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">SMILES@daylight.com</A>]['08],
      [<A HREF="http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification">@wikip</A>]['08].
   [Also search for: structural formula]
   e.g. Viagra:   CCc1nn(C)c2c(=O)[nH]c(nc12)c3cc(ccc3OCC)S(=O)(=O)N4CCN(C)CC4
        Valium:   CN1C(=O)CN=C(c2ccccc2)c3cc(Cl)ccc13
        Caffeine: Cn1cnc2n(C)c(=O)n(C)c(=O)c12
        Morphine: CN1CC[C@]23[C@H]4Oc5c3c(C[C@@H]1[C@@H]2C=C[C@@H]4O)ccc5O
   Heroin: CN1CC[C@]23[C@H]4Oc5c3c(C[C@@H]1[C@@H]2C=C[C@@H]4OC(=O)C)ccc5OC(=O)C
   -- [<A HREF="http://www.daylight.com/dayhtml_tutorials/languages/smiles/smiles_examples.html">www</A>]['08].

%A B. Robson
%A J. Garnier
%T Protein structure prediction
%J Nature
%V 361
%P 506
%D 1993
%K MolBio, c1993, c199x, c19xx, protein, amino acid, AA, fold, folding,
   conformation, GOR
%X via a ref.

%A E. Maier
%A J. Hoheissel
%A L. McCarthy
%A R. Mott
%A A. Grigoriev
%A A. Monaco
%A Z. Larin
%A H. Lehrach
%T Yeast artificial chromosome clones spanning the genome of
   Schizosaccharomyces pombe
%J Nature Genetics
%V 1
%P 273-277
%D 1992
%K MolBio, YAC, clone, clones, probe, physical map mapping
%X via enews.

%A R. Mott
%A A. Grigoriev
%A E. Maier
%A J. Hoheissel
%A H. Lehrach
%T Algorithms and software tools for ordering clone libraries:
   application to the mapping of the genome of Schizosaccharomyces pombe
%J NAR
%V 21
%P 1965-1974
%D 1993
%K NAR, MolBio, YAC, clone, clones, probe, physical map, maps, mapping
%X via enews

%A H. Kishino
%A T. Miyata
%A M. Hasegawa
%T Maximum likelihood inference of protein phylogeny and the origin of
   chloroplasts
%J J. Mol. Evol.
%V 31
%P 151-160
%D 1990
%K jrnl, MolBio, JME, phylogenetic, family, evolutionary tree, trees, PAM,
   evolution, Markov model, bootstrap, psbA, c1990, c199x, c19xx

%A W. J. Wilbur
%T On the PAM matrix model of protein evolution
%J Mol. Biol. Evol.
%V 2
%N 5
%P 434-447
%D 1985
%K MolBiol, MBE, PAM1, 1PAM, PAM250, 250PAM, evolutionary distance,
   c1985, c198x, c19xx, substitution change, amino acid AA
%X [Also search for: MolBio substitution matrix].

%A Morris
%A MacArthur
%A Hutchinson
%A Thornton
%T Stereochemical Quality of protein structure coordinates
%J Proteins: Structure, Function and Genetics
%V 12
%P 345-364
%D 1992
%K MolBio, protein, amino acid acids, AA
%X via ref

%A B. W. Holloway
%A S. Dharmsthiti
%A V. Krishnapillai
%A A. F. Morgan
%A E. Ratnaningsih
%A M. I. Sinclair
%A R. Saffery
%T Chromosome organization in Pseudomonas aeruginosa
%J ???
%W Tokyo
%P ???-???
%M AUG
%D 1990
%K MolBio, map, mapping, Monash

%A B. W. Holloway
%A A. F. Morgan
%T Genome organization in pseudomonas
%J Ann. Rev. Microbiol.
%V 40
%P 79-105
%D 1986
%K MolBio, map, mapping, Monash

%A J. S. Tuttleman
%A c. Pourcel
%A J. Summers
%T Formation of the pool of covalently closed circular viral DNA in
   Hepadnavirus-infected cells
%J Cell
%V 47
%P 451-460
%M NOV
%D 1986
%K jrnl, c1986, c198x, c19xx, HBV, CCC, DHBV, duck, avian, cell nucleus, liver

%A M. W. J. Crosland
%A R. H. Crozier
%T Myrmecia pilosula, an ant with only one pair of chromosomes
%J Science
%V 231
%N 4743
%P 1278
%M MAR
%D 1986
%K jrnl, MolBio, c1986, c198x, c19xx, zz0510, one, single chromosome, pair,
   jack jumper, bull ant, ants, Myrmecia pilosula, Hymenoptera, workers,
   haploid male, Australian
%X "A new sibling species of the primitive Australian ant Myrmecia pilosula has
   a chromosome number of n=1.  C-banding techniques confirm that the 2 chrs. of
   workers are homologous. Males are haploid, as in other Hymenoptera, & their
   somatic cells contain only a single chr.. This new species is potentially of
   great importance in both laboratory & field studies on gene organization."
   -- [<A HREF="http://dx.doi.org/10.1126/science.231.4743.1278">doi:10.1126/science.231.4743.1278</A>]['10].
   ([Also search for: Parascaris equorum var. univalens] for which 2n=2.)

%A P. A. Pevzner
%A A. A. Mironov
%T Effective method for physical mapping of DNA molecule
%J ???
%P 662-670
%D 1987
%K MolBio, map, mapping
%X there is the following at foot of page:
      Translated from Molekulyarnaya Biologiya 21(3), 788-796, 1987
      0026-8933/87/2103-0662 $12.50 1987 Plenum

%A C. R. Marshall
%T Estimation of taxonomic ranges from the fossil record
%B Analytical Paleobiology
%E N. Gilinsky
%E P. W. Signor
%S Short Courses in Paleontology
%N 4
%P 19-38
%K MolBio, fossil, fossils, extinction, extinctions, paleontology

%A C. R. Marshall
%T Stratigraphy, the true order of species' originations and extinctions,
   and testing ancestor-descendant hypotheses among Caribbean Neogene
   bryozoans.
%I Dept. Earth and Space Sciences, Molecular Biology Institute,
   Univ. of California, Los Angeles
%D 1993 ?
%K MolBio, fossil, fossils, paleontology, extinction, paleontology

%A C. R. Marshall
%T Confidence intervals on stratigraphic ranges
%J Paleobiology
%V 16
%N 1
%P 1-10
%D 1990
%K MolBio, fossil, fossils, time interval range, extinction extinctions,
   paleontology

%A C. R. Marshall
%T The fossil record and estimating divergence times between lineages:
   maximum divergence times and the importance of reliable phylogenies.
%J J. Mol. Evol.
%V 30
%P 400-408
%D 1990
%K MolBio, JME, fossil, fossils, time interval, range,
   family, evolutionary tree, trees, extinction, extinctions, paleontology

%A T. Toya
%A M. Ishikawa
%A M. Hoshida
%T Parallel simulated annealing and its application to protein sequence
   matching.
%J Australian A.I.
%P ???-???
%D 1992
%K MolBio, multiple alignment

%A S. Letovsky
%A M. B. Berlyn
%T Constraint propagation techniques for genetic mapping
%B A.I. and Molecular Biology.
%E L. Hunter
%I MITpress
%D 1991
%P ???-???
%K MolBio, AIMB, map, mapping, RSM

%A M. Eigen
%T Viral quasispecies
%J Scientific American
%V 269
%N 1
%M JUL
%D 1993
%P 42-49
%K MolBio, statistical geometry, string, sequence space, virus, viral, cold,
   evolution, evolutionary tree, trees, similarity, flu, polio, HIV, AIDS,
   influenza, mutation, recombination, replication, review, introduction,
   survey
%X tension between variability: to outflank immune response
               and stability:   to preserve viral information
   (typically about 1 mutation per replication)
   HIV:   single strand 10,000 nucleotides.
   polio: highly stable, effective vaccine
   flu:   variable, vaccines to "current" strain
   HIV:   highly variable, ?exhausts immune system?, no vaccine (yet)

%A M. Eigen
%A R. Winkler-Oswatitsch
%T Statistical geometry on sequence space
%J Methods in Enzymology
%V 183
%P 505-530
%D 1990
%K MolBio, MENZ, string, sequence, evolution
%X via  T o n i   K a z i c

%A Bruce S. Weir
%T Genetic Data Analysis
%I Sinauer Assocs. Inc., Sunderland, Mass.
%D 1990
%K MolBio, text, book, c1990, c199x, c19xx, gene, string, sequence,
   evolutionary tree, trees, RSM
%X [Also search for: MolBio book].

%A M. Borodovsky
%A J. McIninch
%T GENEMARK: Parallel gene recognition for both DNA strands
%J Comp. and Chem.
%V 17
%N 2
%P 123-133
%D 1993
%K MolBio, jrnl, Gene Mark, find, finding, genes
%X [<A HREF="http://genemark.biology.gatech.edu/GeneMark/gm_info.html">info</A>][8/'00],
      [<A HREF="http://genemark.biology.gatech.edu/GeneMark/">home</A>][8/'00].
   [Also search for: gene find].

%A M. Borodovsky
%A J. McIninch
%T Prediction of gene locations using DNA Markov chain models
%J Proc. of the 2nd Int. Conf. on  Supercomputing,
   Bioinformatics and Complex Genome Analysis.
%W St. Petersburg, FL
%I World Scientific
%P 231-248
%D 1993
%K MolBio, conf, 2nd, HUGO, find, finding
%X via enews
   [Also search for: genemark].

%A R. Nussinov
%A H. J. Wolfson
%T Efficient detection of three-dimensional structural motifs in biological
   macromolecules by computer vision techniques
%J PNAS
%V 88
%P 10495-10499
%M DEC
%D 1991
%K jrnl, PNAS, MolBio, c1991, c199x, c19xx, protein, structure, motif, pattern,
   3D, shape, comparison, PNAS, image processing IP, geometric hashing, hash,
   GH, rigid motion, rotation, translation, match, matching, vector, point set
%X Note, any 3 non-colinear points define a plane and a coordinate system.
   1. preprocessing library shapes or models:
         For each "model" or library shape M,
            for each set R of 3 ref' pts, giving a coord' system
               for each other point P in M
                  calculate the coord's of P in the coordinate system
                  store an entry for < M, R > in a hash table
                  (must quantize or "round" distances)
   2. matching new shape S against the library:
         repeat choose a set R' of 3 ref' pts, compute coord' system
                for each other point P' in S
                   calculate coord of P' in the coord' system
                   increment a "vote counter" for every corresponding
                   pair of model M and ref' set R, < M, R >, in hash table.
                   [LA: ? do you require R' congruent to R ?]
         until one or more pairs < M, R > score "high enough"
         Examine models with big counts for consistency with S.
   Preprocessing step 1: time is O(n**4) per model shape.
   Space complexity of hash table is O(N * n**4), for N models.
   Matching      step 2: worst case time is O(n**4) where S has n points
   but it is usually much faster.
   Can use "clever" ways of picking R' in step 2.
   "Reduced" information eg. a ref' set of just 2 points, 2-D coords,
   can be used to speed alg' up; worst case time and space become O(n**3).
   -- [<A HREF="http://www.pnas.org/content/88/23/10495.full.pdf">www</A>]['17].
   [LA: a ref' set of just 1 pt. would come down to pair-wise distances.]
   NB. treats shape as set of pts, ignores sequential nature.

%A Fetrow
%A Bryant
%T New programs for protein tertiary structure prediction
%J Bio/Technology
%V 11
%P 479-484
%D 1993
%K MolBio, protein structure, fold, match, matching, threading
%X via enews

%A Blundell
%A Johnson
%J Catching a common fold.
%J Protein Science
%V 2
%P 877-883
%D 1993
%K MolBio, protein structure, fold, match, matching, threading
%X via enews

%A D. Eisenberg
%A J. U. Bowie
%A R. Luthy
%A S. Choe
%T 3-Dimensional Profiles For Analyzing Protein-Sequence Structure
   Relationships.
%J Faraday Discussions Of The Chemical Society
%V 93
%P 25-34
%D 1992
%K MolBio, 3-D protein structure, fold, match, matching, threading
%X via enews

%A J. U. Bowie
%A R. Luthy
%A M. Wilmanns
%A L. Wesson
%A Z. Kam
%A D. Eisenberg
%T 3-d Profiles - Principles And Applications
%J Protein Engineering
%V 6 S: 123
%D 1993
%K MolBio, protein structure, fold, match, matching, threading
%X via enews

%A R. Luthy
%A A. D. Mclachlan
%A D. Eisenberg
%T Secondary Structure-Based Profiles - Use Of Structure-Conserving Scoring
   Tables In Searching Protein-Sequence Databases For Structural Similarities.
%J Proteins-Structure Function And Genetics
%V 10
%N 3
%P 229-239
%D 1991
%K MolBio, protein structure, fold, match, matching, threading
%X via enews

%A R. Luthy
%A J. U. Bowie
%A D. Eisenberg
%T Assessment Of Protein Models With 3-Dimensional Profiles
%J Nature
%V 356:6364
%P 83-85
%D 1992
%K MolBio, protein structure, fold, match, matching, threading
%X via enews

%A J. U. Bowie
%A R. Luthy
%A D. Eisenberg
%T A Method To Identify Protein Sequences That Fold Into A Known 3-Dimensional
   Structure
%J Science
%V 253:5016
%P 164-170
%D 1991
%K MolBio, protein structure, fold, match, matching, threading
%X via enews

%A D. T. Jones
%A W. R. Taylor
%A J. M. Thornton
%T A New Approach To Protein Fold Recognition
%J Nature
%V 358:6381
%P 86-89
%D 1992
%K MolBio, protein structure, fold, match, matching, threading
%X via enews

%A C. M. Topham
%A A. Mcleod
%A F. Eisenmenger
%A J. P. Overington
%A M. S. Johnson
%A T. L. Blundell
%T Fragment ranking In modeling of protein-structure - conformationally
   constrained environmental amino-acid substitution tables
%J J. Mol. Biol.
%V 229
%N 1
%P 194-220
%D 1993
%K JMB, MolBio, protein structure, fold, match, matching, threading, PAM,
   c1993, c199x, c19xx, substitution, change, matrix
%X via enews
   [Also search for: MolBio substitution matrix].

%A A. Sali
%A J. P. Overington
%A M. S. Johnson
%A T. L. Blundell
%T From Comparisons Of Protein Sequences And Structures To Protein Modeling
   And Design.
%J Trends In Biochemical Sciences
%V 15
%N 6
%P 235-240
%D 1990
%K MolBio, 3-D, protein structure, fold, match, matching, threading
%X via enews

%A M. S. Johnson
%A J. P. Overington
%A T. L. Blundell
%T Alignment And Searching For Common Protein Folds Using A Data-Bank Of
   Structural Templates.
%J J. Mol. Biol.
%V 231
%N 3
%P 735-752
%D 1993
%K JMB, MolBio, protein structure, fold, folding, match, matching, threading
%X via enews

%A J. Overington
%A M. S. Johnson
%A A. Sali
%A T. L. Blundell
%T Tertiary Structural Constraints On Protein Evolutionary Diversity
   - Templates, Key Residues And Structure Prediction.
%J Proc. of the Royal Society of London Series B-Biological
%S 241
%N 1
%V 301
%P 132-145
%D 1990
%K MolBio, PRSS, 3-D, protein structure, fold, folding, match, matching, threading
%X via enews

%A M. Wilmanns
%A D. Eisenberg
%T 3-Dimensional Profiles From Residue-Pair Preferences - Identification
   Of Sequences With Beta/Alpha-Barrel Fold.
%J Proc. Natl. Acad. Sci. USA
%V 90
%N 4
%P 1379-1383
%D 1993
%K PNAS, MolBio, 3-D, protein structure, fold, folding, match, matching, threading,
   alpha helix, beta sheet, barrel
%X via enews

%A G. Vriend
%A C. Sander
%T Detection of common three-dimensional substructures in proteins
%J Proteins
%V 11
%P 52-58
%D 1991
%K MolBio, protein structure, 3D 3-D, match, matching
%X via email

%A A. Milosavljevic
%A J. Jurka
%T Discovery by minimal length encoding: a case study in molecular evolution
%J Machine Learning
%V 12
%P 69-87
%D 1993
%K MolBio, Alu, sequence, MML, MDL, repetitive element, junk, DNA

%A A. Milosavljevic
%A J. Jurka
%T Discovering simple DNA sequences by the algorithmic significance method
%J CABIOS
%V 9
%N 4
%P 407-411
%D 1993
%K MolBio, MML MDL, repetitive, repetition, repeat, low information content,
   c1993, c199x, c19xx, string, sequence, junk, DNA data strings,
   plasminogen activator
%X ... a seq is defined to be simple if it can be encoded
   concisely by replacing occurrences of some words by pointers to
   the previous occurrences of the same words within the same seq'.
   eg. AGTCAGTTTT  --> AGTC(1,3)(7,3)
   Tested on DNA seq of Human Tissue Plasminogen Activator Gene
   Genbank Accession # K03021 36,594 bases.
   One window at a time, window length 128, overlap 64, 4 simple subseqs found:
      1.  7170- 7225  (RY)*N run        (took 215 bits, < 256 null)
      2. 16897-17024  (AC)*N;(TC)*N
      3. 17089-17216  poly-A
      4. 23888-24458  (TGATAGA)*N run
   [Also search for: repetitive DNA].

%A A. Milosavljevic
%T Discovering sequence similarity by the algorithmic significance method
%J Proc. 1st Int. Conf. on Intelligent Systems for Molecular Biology
%E L. Hunter
%E D. Searls
%E J. Shavlik
%I AAAI Press, Menlo Park, CA
%D 1993
%P 284-291
%K Molbio, ISMB, ISMB1, ISMB93, MML, MDL, subword, subwords
%X a sequence is defined to be similar to another sequence if
   it can be encoded in a small number of bits by taking advantage of
   common subwords.

%A R. Nussinov
%A A. Jacobson
%T Fast algorithm for predicting the secondary structure of single stranded RNA
%J Proc. Natl. Acad. Sci. (USA)
%V 77
%P 6309-6313
%D 1980
%K MolBio, PNAS, c1980, c198x, c19xx, RNA, fold, folding, prediction, SS, DPA

%A B. Rost
%A C. Sander
%T Prediction of protein secondary structure at better than 70% accuracy
%I European Mol. Biol. Lab., Heidelberg
%D 1993
%O sub' J. Mol. Biol.
%K MolBio, EMBL, SS, artificial neural net, NN, ANN
%X include protein family information
   3 levels -> 70.8% on 3-state, globular proteins

%A D. B. Searls
%T The linguistics of DNA
%J American Scientist
%V 80
%N 6
%P 579-591
%M Nov-Dec
%D 1992
%K MolBio, DNA, RNA secondary structure SS, grammar, grammars, CFG, FSA, FSM,
   language, logic

%A L. Holm
%A C. Sander
%T Protein structure comparison by alignment of distance matrices
%J J. Mol. Biol.
%V 233
%N 1
%P 123-138
%M SEP
%D 1993
%K MolBio, jrnl, JMB, 3D, match, matching, pairwise, distance geometry, DALI,
   protein, EMBL superposition, shape, c1993, c199x, c19xx, matrix, partially,
   partial, order preserving
%X Calculate residue-residue (C-alpha) pairwise distance matrix for a protein.
   Use these matrices to compare 2 proteins.
   1. decompose into elementary contact patterns eg. hexapaptide-hexapeptide
      submatrices.
   2. Similar patterns in 2 matrices then paired and combined into larger
      consistent sets of pairs.
   Monte-Carlo procedure used to optimize.
   Allows gaps, reversal of chain direction and free topological connectivity
   of aligned segments.
   Did an all against all alignment of 200 structures.
   -- [<A HREF="http://dx.doi.org/10.1006/jmbi.1993.1489">doi:10.1006/jmbi.1993.1489</A>]['11],
   &  [<A HREF="http://iubio.bio.indiana.edu/soft/iubionew/molbio/protein/analysis/Dali/dali_jmb.html">indi'na</A>]['11].
   [Also search for: MolBio protein structure alignment].

%A C. E. Lawrence
%A S. F. Altschul
%A M. S. Boguski
%A J. S. Liu
%A A. F. Neuwald
%A J. C. Wootton
%T Detecting subtle sequence signals: a Gibbs sampling strategy for multiple
   alignment
%J Science
%V 262
%N 5131
%P 208-214
%M OCT
%D 1993
%K jrnl, c1993, c199x, c19xx, GS, MolBio, Monte Carlo, Monte-Carlo, string,
   strings, match, homology, motif, discovery, motifs, signal, block, blocks,
   sequence, gap, gaps, indels
%X "... difficulty of detecting subtle local residue patterns common to multiple
   seqs..  Such patterns frequently reflect similar molecular structures &
   biol. properties.  A math. definition of this "local multiple alignment"
   problem suitable for full computer automation has been used to develop a new
   & sensitive alg., based on the statistical method of iterative sampling. ...
   ...finds an optimized local alignment model for N seqs. in N-linear time,
   requiring only seconds on current workstations, & allows the simultaneous
   detection & optimization of multiple patterns & pattern repeats. ...
   illustrated [on] helix-turn-helix proteins, lipocalins & prenyltransferases."
   -- [<A HREF="http://dx.doi.org/10.1126/science.8211139">doi:10.1126/science.8211139</A>]['08].

%A S. J. Wodak
%A M. J. Rooman
%T Generation and testing protein folds
%J Curr. Opinion Struct. Biol.
%V 3
%P 247-259
%D 1993
%K MolBio, protein, structure, fold, folding, match, matching, thread,
   threading, survey
%X via enews

%A M. Hasegawa
%A A. Di-Rienzo
%A T. D. Kocher
%A A. C. Wilson
%T Toward a more accurate time scale for the human mitochondrial DNA tree
%J J. Mol. Evol.
%D 1993
%V 37
%N 4
%P 347
%K JME, MolBio, c1993, c199x, c19xx, phylogenetic, evolutionary, family tree,
   trees, rate, Di Rienzo, Eve, mtDNA, molecular clock
%X via bionet.journals.contents  AB 30370347.239.
   [Also search for: MolBio eve evolution rate].

%A Y. Kumazawa
%A M. Nishida
%T Sequence Evolution of Mitochondrial tRNA Genes and Deep-Branch Animal
   Phylogenetics
%J J. Mol. Evol.
%D 1993
%V 37
%N 4
%P 380
%K JME, MolBio, phylogenetic, evolutionary, family tree, trees, rate
%X via bionet.journals.contents  AB 30370380.239

%A U. Arnason
%A A. Gullberg
%A E. Johnsson
%A C. Ledje
%T The nucleotide sequence of the mitochondrial DNA molecule of the
   grey seal, halichoerus grypus, and a comparison with mitochondrial
   sequences of other true seals.
%J J. Mol. Evol.
%D 1993
%V 37
%N 4
%P 323-330
%K JME, MolBio, mitochondria, seals, family, evolutionary, phylogenetic,
   mGenome, tree, trees
%X via bionet.journals.contents   AB 30370323.239

%A J. Jurka
%T Approaches to identification and analysis of interspersed repetitive DNA
   sequences.
%B Automated DNA Sequencing and Analysis Techniques.
%E J. C. Venter
%P ??-??
%D 1993 submitted
%K MolBio, tandem, repeat, junk, simple, low information content,
   ALU, SINE, LINE, satellite, LOCAL
%X [Also search for: DNA ALU].

%A J. Jurka
%T Human repetitive elements
%J The Encyclopedia of Molecular Biology and Biotechnology.
%P ??-??
%D 1993 (in press)
%K MolBio, tandem, repeat, junk, DNA, simple, low information content,
   ALU, SINE, LINE, MER, THE1, satellite
%X [Also search for: DNA ALU].

%A Clark
%A Jones
%A Willett
%A Glen
%A Kenny
%T Pharmacophoric Pattern Matching In Files Of Three-Dimensional Chemical
   Structures: Comparison Of Conformational-Searching Algorithms For Flexible
   Searching
%J J. of Chemical Information and Computer Sciences
%D 1993, in press
%O 3rd Int. conference on Chemical Structures
%K JCICS, genetic algorithm GA, MolBio, structure shape, match matching, 3D,
   prediction
%X via email

%A Thomas Dandekar
%A Patrick Argos
%T Potential of genetic algorithms in protein folding and protein engineering
   simulations.
%J Protein Engineering
%V 5
%N 7
%P 637-645
%D 1992
%K algorithm, GA, MolBio, PE, fold, conformation, structure, tertiary,
   prediction
%X via email

%A David Eisenberg
%T Determining Protein Folds by Inverted and Evolutionary Protein Folding
   Algorithms
%J Proc. of the North Caroline Symp. on Molecular Modeling:
   Integration of Theory and Experiment,
%W Research Triangle Park, North Carolina
%P 21-23
%D 1993
%K GA, MolBio, fold, folding, conformation, tertiary structure, prediction
%X via email

%A D. B. McGarrah
%A R. S. Judson
%T An analysis of the genetic algorithm method of molecular conformation
   determination
%J J. Comp. Chem.
%D 1993, in press
%K JCC, GA, MolBio, fold, folding, protein, tertiary structure, prediction
%X via email

%A Steffen Schulze-Kremer
%T Genetic Algorithms in Biochemistry (GALB): Learning Protein Folding
   Pathways
%B Parallel Genetic Algorithms
%E Joachim Stender (Ed.),
%I IOS Press, Amsterdam.
%D 1992
%K c1992, c199x, c19xx, schulze kremer, GALB, GA, algorithm, MolBio, fold,
   folding trajectory, pathway, tertiary structure, prediction
%X via email

%A S. Schulze-Kremer
%T Genetic algorithms for protein tertiary structure prediction
%B Parallel Problem Solving from Nature
%N 2
%E R. Manner
%E B. Manderick
%P 391-400
%I North Holland, Amsterdam
%D 1992
%K schulze kremer, algorithm, GA, MolBio, fold, folding, conformation,
   prediction
%X via email

%A S. Schulze-Kremer
%A U. Tiedemann
%T Genetic Algorithms for Protein Tertiary Structure Prediction
%E J.-G. Ganascia
%J Int. Joint Conf. on Artificial Intelligence,
   Artificial Intelligence and Genome Workshop 26
%W Institut Blaise Pascal, Paris
%P 119-141
%D 1993
%K wShop, schulze kremer, algorithm, GA, MolBio, fold, folding, IJCAI IJCAI93,
   prediction
%X via email

%A R. Unger
%A J. Moult
%T A genetic algorithm for 3D Protein Folding Simulations
%J Proc. of the Fifth Int. Conf. on Genetic Algorithms,
%E S. Forrest
%P 581-588
%I MorganKaufmann, San Mateo, CA.
%D 1993
%K GA, MolBio, fold, conformation, tertiary structure, prediction
%X via email
   [Also search for: protein folding simulation].

%A Ron Unger
%A John Moult
%T Genetic Algorithms for Protein Folding Simulations
%J J. Mol. Biol.
%V 231
%P 75-81
%D 1993
%K JMB, GA, MolBio, fold, conformation, tertiary structure, prediction
%X via email
   [Also search for: protein folding simulation].

%A L. A. Newberg
%T A lower bound on the number of solutions to the probed partial digest
   problem.
%J Adv. Appl. Math.
%V 14
%N 2
%P 172-183
%D 1993
%K MolBio, AAM, probe, restriction sit, map, maps, mapping, RSM

%A D. Cohen
%A I. Chumakov
%A J. Weissenbach
%T A first-generation physical map of the human genome
%J Nature
%V ?
%N ?
%P ??-??
%M DEC ???
%D 1993
%K MolBio, DNA, gene, genome, genetic, map, mapping, clone
%X The data of the ceph-genethon-map (Nature paper) :
   can be accessed by :
        ftp anonymous : ceph-genethon-map.genethon.fr
                        dir  pub/ceph-genethon-map
         email: ceph-genethon-map@genethon.fr
        gopher: gopher.genethon.fr
                 -> Genethon Data
                        -> Pmap
        <A HREF="http://www.genethon.fr/genethon_en.html">Genethon www</A>
 Bruce A. Roe             Professor of Chemistry and Biochemistry
 University of Oklahoma   INTERNET: BROE@aardvark.ucs.uoknor.edu   ('94)

%A J. Hein
%T Reconstructing evolution of sequences subject to recombination using
   parsimony
%J JMB
%V 98
%N 2
%P 185-200
%M MAR
%D 1990
%K MolBio, JMB, c1990, c199x, c19xx, phylogenetic, evolutionary, tree, trees,
   graph, recombination, horizontal gene transfer, HGT
%X See [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/2134501">pubmed</A>]['09].
   via Toni Kazic
   "Allows for recombination and horizontal transfer; the
   appropriate structure is a family of trees, each node describing a segment of
   the sequence.  Two trees for neighboring subsequences differ by that
   particular subtree; so a metric of relatedness is the minimum number of
   operations to convert one tree to another.  Algorithm calculates this metric,
   then the metric is used in a dynamic programming algorithm to find the most
   parsimonious history that fits a set of sequences.  Get a family of
   phylogenies.  Not exactly what I was thinking of but not far off; main
   differences are in notation of tree families and use of parsimony.  Only
   works
   with (globally I think) prealigned sequences, which is not surprising when
   you
   think about it, but this prevents checking the hypothesis that recombination
   is a significant factor in the phylogeny of a set of sequences -- and also
   assumes rather close relationship among sequences, I suspect.  Limited to 7-8
   sequences (many trees of equivalent structure); he tried to find
   a quickie version
   cutting the search space, but it blew up as the number of recombinations
   allowed was increased.  Again, this is not surprising; this may be a more
   appropriate place to apply parsimony principles, provided recombinational
   hotspots can be excluded . . . seems a natural for Gibbs methods."

%E L. Hunter
%T Artificial Intelligence and Molecular Biology
%I MITpress
%D 1991 ?
%P 470
%K MolBio, AIMB, text, book, survey, bioinformatics, AI, LHunter,
   c1991, c199x, c19xx
%X on order for Hargrave as of Jan 94; isbn:0262581159.
   -- [<A HREF="http://www.aaai.org/Library/Books/Hunter/hunter.html">@aaai</A>]['04].
   [Also search for: MolBio book].

%A Da-Fei Feng
%A R. F. Doolittle
%T Progressive alignment and phylogenetic tree construction of protein
   sequences
%J Methods in Enzymology
%V 183
%P 375-402
%D 1990
%K MolBio, MENZ, family, evolutionary tree, trees, multiple alignment
%X via   T o n i  K a z i c.

%A J. Hein
%T Unified approach to alignment and phylogenies
%J Methods in Enzymology
%V 183
%P 626-645
%D 1990
%K MolBio, MENZ, family, evolutionary, phylogenetic tree, trees,
   multiple alignment
%X via T o n i   K a z i c.

%A H.-J. Bandelt
%A A. Dress
%T A canonical decomposition theory for metrics on a finite set
%J Adv. Math.
%V 92
%N 1
%P 47-105
%D 1992
%K MolBio, family, evolutionary, phylogenetic tree, trees

%A M. D. Hendy
%T The relationship between between simple evolutionary tree models and
   observable sequence data
%J Syst. Zool.
%V 38
%P 310-321
%D 1989
%K MolBio, family, evolutionary, phylogenetic tree, trees

%A M. Karplus
%A E. Shakhnovich
%T Protein folding: theoretical studies of thermodynamics and dynamics
%P ??-??
%B Protein Folding
%E Tom Creighton
%I W. H. Freeman, New York
%D 1992
%K MolBio, fold, chapter, text, book
%X via: Shaun D. Black, PhD   <!-- email: shaun%jason.decnet@relay.the.net --> .

%A G. J. Olsen
%A H. Matsuda
%A R. Hagstrom
%A R. Overbeek
%T fastDNAml: a tool for construction of phylogenetic trees of DNA sequences
   using maximum likelihood
%J Comp. Appl. BioSci.
%M JAN
%D 1994
%V 10
%N 1
%P 41-48
%K MolBio, CABIOS, Bioinformatics, DNAml, family, evolutionary tree, trees
%X [Also search for: probability evolutionary tree MolBio].

%A J. Skolnick
%A A. Kolinski
%T Dynamic Monte Carlo simulations of globular protein folding/unfolding
   pathways. I. Six-member, Greek key beta-barrel proteins
%J J. Mol. Biol.
%M APR
%D 1990
%V 212
%N 4
%P 787-817
%K JMB, MolBio, c1990, c199x, c19xx, Physical Models, Molecular Structure,
   Monte-Carlo Method, Plastocyanin Protein, fold, folding, Conformation,
   Proteins, diamond lattice model, pathway, trajectory, simulation
%X "In the context of a simplified diamond lattice model of a
   six-member, Greek key beta-barrel protein that is closely related in
   topology to plastocyanin, the nature of the folding and unfolding
   pathways have been investigated using dynamic Monte Carlo techniques. ..."
   -- [<A HREF="https://doi.org/10.1016/0022-2836(90)90237-g">doi:10.1016/0022-2836(90)90237-g</A>]['22] &
   see 2329583@[<A HREF="https://pubmed.ncbi.nlm.nih.gov/2329583/">pubm'd</A>]['22] for others.
   [Also search for: protein folding simulation].

%A K. A. Dill
%T Theory for the folding and stability of globular proteins
%J Biochemistry
%M MAR
%D 1985
%V 24
%N 6
%P 1501-9
%K Chemical, Polymers, Protein fold, folding, Conformation, lattice model,
   models, c1985, c198x, c19xx
%X Using lattice statistical mechanics, we develop theory to account
   for the folding of a heteropolymer molecule such as a protein to the
   globular and soluble state.
   Folding is assumed to be driven by the
   association of solvophobic monomers to avoid solvent and opposed by
   the chain configurational entropy. Theory predicts a phase
   transition as a function of temperature or solvent character.
   Molecules that are too short or too long or that have too few
   solvophobic residues are predicted not to fold. Globular molecules
   should have a largely solvophobic core, but there is an entropic
   tendency for some residues to be "out of place", particularly in
   small molecules. For long chains, molecules comprised of globular
   domains are predicted to be thermodynamically more stable than
   spherical molecules. The number of accessible conformations in the
   globular state is calculated to be an exceedingly small fraction of
   the number available to the random coil. Previous estimates of this
   number, which have motivated kinetic theories of folding, err by
   many tens of orders of magnitude.

%A D. M. Hillis
%A J. J. Bull
%A M. E. White
%A M. R. Badgett
%A I. J. Molineux
%T Experimental phylogenetics: generation of a known phylogeny
%D 1992
%J Science
%V 255
%P 589-592
%K MolBio, family, evolutionary, phylogenetic, tree, trees, T7 bacteriophage,
   data, string, sequence analysis
%X Instead of using computers to generate sequence data, he used real
   organisms (T7 bacteriophage) and let them evolve for a while in the lab
   so that he knew the "true" phylogeny.  Then he tested different tree-making
   procedures to see which ones came closest to the truth.
   enews via: Kathie Hodge <!-- email: kh11@cornell.edu --> .
   Great idea!

%A D. M. Hillis
%A J. J. Bull
%T An empirical test of bootstrapping as a method for assessing confidence in
   phylogenetic analysis
%J Syst. Biol.
%V 42
%N 2
%D 1993
%P 182-192
%K MolBio, family, evolutionary, phylogenetic, tree trees, T7 bacteriophage,
   data string, sequence analysis
%X Instead of using computers to generate sequence data, he used real
   organisms (T7 bacteriophage) and let them evolve for a while in the lab
   so that he knew the "true" phylogeny.  Then he tested different tree-making
   procedures to see which ones came closest to the truth.
   enews via: Kathie Hodge <!-- email: kh11@cornell.edu --> .
   [Also search for: probability evolutionary tree MolBio].

%A N. Goldman
%A Z. Yang
%T A codon-based model of nucleotide substitution for protein-coding DNA
   sequences
%J Mol. Biol. Evol.
%P ??-??
%M ??
%D 1994 submitted
%K MBE, codon, alignment, evolution, substitution, model, protein, amino acid,
   NIMR, MRC, AA, DNA, coding region
%X email: n_goldma OF nimr.mrc.ac.uk     ('94).

%A A. Pomiankowski
%T Swordplay and sensory bias
%J Nature
%V 368
%M APR
%D 1994
%P 494-495
%K feature, beauty, natural selection, sex, sexual, female preference,
   sword tail swordtail fish, family phylogenetic evolutionary, tree trees,
   Xiphophorous
%X News and views -  see Meyer et al in the same issue.

%A A. Meyer
%A J. M. Morrissey
%A M. Schartl
%T Recurrent origin of a sexually selected trait in Xiphophorus fishes
   inferred from a molecular phylogeny
%J Nature
%V 368
%M APR
%D 1994
%P 539-542
%K feature, beauty, natural selection, sex, sexual, female preference,
   sword tail, swordtail, fish, family, phylogenetic, evolutionary, tree, trees

%A Marcel J. J. Blommers
%A Carlos B. Lucasius
%A Gerrit Kateman
%A Robert Kaptein
%T Conformational Analysis of a Dinucleotide Photodimer with the Aid of the
   Genetic Algorithm
%J Biopolymers
%V 32
%P 45-52
%D 1992
%K genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A D. Bouzida
%A S. Jumar
%A R. H. Swendsen
%T A Simulated Annealing Appproach for Probing Biomolecular Structures
%T 26th Hawaii Int. Conf. on System Sciences
%V I
%I IEEE
%D 1993
%K HICSS, HICSS26, 26, SA, MolBio, protein, fold, folding, probe
%X via enews '94

%A J. W. Fickett
%A M. J. Cinkosky
%T A genetic algorithm for assembling chromosome physical maps
%I Unpublished draft
%D 1993
%K genetic algorithms, GA, MolBio, map, maps, mapping, RSM
%X via enews '94

%A E. Fontain
%T Application of Genetic Algorithms in the Field of Constitutional Similarity
%J J. Chem. Inf, Comput Sci.
%V 32
%P 748-752
%D 1992
%K JCICS, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A M. S. Freidrichs
%A P. G. Wolynes
%T Genetic algorithms for model biomolecular optimization problems
%I Unpublished manuscript. Noyes Lab., Uni. of Illinois, Urbana, Il, 61801.
%D '93 ???
%K genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A S. Handley
%T Automated learning of a detector for helices in protein sequences via
   genetic programming
%J Proc. of the Fifth Int. Conf. on Genetic Algorithms.
%E S. Forrest
%I MorganKaufmann, San Mateo, CA.
%P ??-??
%D 1993
%K genetic algorithms, GA, MolBio, protein, fold, folding, helix, alpha
%X via enews '94

%A Jones
%A Brown
%A Clark
%A Willett
%A Glen
%T Searching Databases of Two-Dimensional and Three-Dimensional Chemical
   Structures Using Genetic Algorithms
%J Proc. of the Fifth Int. Conf. on Genetic Algorithms
%E S. Forest
%I MorganKaufmann Publishers, San Mateo, CA
%P ??-??
%D 1993
%K genetic algorithms, GA, MolBio, protein, fold, folding, 2D, 2-D, 3D, 3-D
%X via enews '94

%A Richard S. Judson
%T Teaching Polymers to fold
%J The J. of Physical Chemistry
%V 96
%N 25
%P 10102 ???
%D 1992
%K JPC, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A R. S. Judson
%A M. E. Colvin
%A J. C. Meza
%A A. Huffer
%A D. Gutierrez
%T Do intelligent configuration search techniques outperform random search
   for large molecules?
%J Int. J. of Quantum Chemistry
%V 44
%P 277-290
%D 1992
%K IJQC, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A R. S. Judson
%A E. Jaeger
%A A. Treasurywala
%T Conformation searching methods for small molecules II: A Genetic algorithm
   approach
%J J. Comp. Chem.
%V ??
%P ??-??
%D 1993, in press
%K JCC, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A P. E. Leopold
%A E. I. Shakhnovich
%T Protein Folding Kinetics in the Dense Phase
%J 26th Hawaii Int. Conf. on System Sciences
%V I
%I IEEE
%P ??-??
%D 1993
%K HICSS, HICSS26, 26, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A Wolfgang Linert
%A Peter Margl
%A Istvan Lukovits
%T Numerical Minimization Procedures in molecular mechanics:
   structural modelling of the solvation of beta-cyclodextrin.
%J Computers & Chem.
%V 16
%N 1
%P 61-69
%D 1992
%K CC, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A C. B. Lucasius
%A G. Kateman
%T Application of genetic algorithms in chemometrics
%J Proc. of the third international conference on genetic algorithms
%E J. D. Schaffer
%I MorganKaufmann, San Mateo, CA.
%P ??-??
%D 1989
%K genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A D. Weininger
%A A. Weininger
%A J. L. Weininger
%T SMILES 2. Algorithm for generation of unique SMILES notation
%J J. Chem. Inf. Comput. Sci.
%V 29
%N 2
%P 97-101
%D 1989
%K jrnl, JCICS, MolBio, c1989, c198x, c19xx, canonical, SMILES 2,
   chemical compound, representation, molecule, structural formula,
   .smi file format, CANGEN
%X [<A HREF="http://dx.doi.org/10.1021/ci00062a008">doi:10.1021/ci00062a008</A>]['08].
   Also see SMILES 1, '98.
   -- [<A HREF="http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification">@wikip</A>]['08],
      [<A HREF="http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html">SMILES@daylight.com</A>]['08].
   [Also search for: structural formula].

%A W. Rychlik
%A R. E. Rhoads
%T A computer program for choosing optimal oligonucleotides for filter
   hybridization, sequencing and in vitro amplification of DNA
%J NAR
%V 17
%N 21
%P 8543-8551
%M NOV
%D 1989
%K jrnl, NAR, MolBio, c1989, c198x, c19xx, PCR, primer, design, selection
%X "... for choosing optimal oligodeoxyribonucleotides as probes for filter
   hybridization, primers for sequencing, or primers for DNA amplification.
   3 main factors that determine the quality of a probe are considered:
   stability of the duplex formed between the probe & target [NA], specificity
   of the probe for the intended target sequence, & self-complementarity.
   DNA duplex stability calculations are based on the nearest-neighbor
   thermodynamic values determined by Breslauer et al. [Proc. Natl. Acad. Sci.
   U.S.A. (1986), 83: 3746]. Temperatures of duplex dissociation predicted by
   the method described here were within 0.4 deg.C of the values obtained
   experimentally for 10 oligonucleotides. Calculations for specificity of the
   probe and its self-complementarity are based on a simple dynamic algorithm."
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/2587212">pub med</A>]['09].
   [Also search for: MolBio PCR primer],
   primers@[<A HREF="http://en.wikipedia.org/wiki/Primer_(molecular_biology)">wikip</A>]['09].

%A W. Rychlik
%A W. J. Spencer
%A R. E. Rhoads
%T Optimization of the annealing temperature for DNA amplification in vitro
%J NAR
%V 18
%N 21
%P 6409-6412
%D 1990
%K jrnl, NAR, MolBio, c1990, c199x, c19xx, PCR, primer, design,
   annealing temperature, TaOPT
%X "... experimentally determine the optimal annealing temp. (TaOPT) values for
   several primer-template pairs & develop a method for its calc..  The TaOPT is
   found to be a fn of the melting temps. of the less stable primer-template
   pair & of the product. The fact that experimental & calculated TaOPT values
   agree to within 0.7 deg.C eliminates the need for determining TaOPT
   experimentally. Synthesis of DNA fragments < 1 kb is more efficient if a
   variable Ta is used, s.t. the Ta is higher in each consec. cycle."
   paper@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/2243783">pub med</A>]['09].
   [Also search for: MolBio PCR primer].

%A D. M. Platt
%A T. I. Dix
%T Construction of Restriction Maps Using a Genetic Algorithm
%J 26th Hawaii Int. Conf. on System Sciences
%V I
%I IEEE
%P ??-??
%D 1993
%K HICSS 26, HICSS26, genetic algorithms, GA, MolBio, Monash, TIDix, DMPlatt,
   conf, map, maps, mapping
%X via enews '94

%A S. Schulze-Kremer
%A U. Tiedemann
%T Parameterizing Genetic Algorithms for Protein Folding Simulation
%J Proc. of the 27th Hawaii Int. Conf. on System Sciences
%P ??-??
%D 1994
%K HICSS 27, HICSS27, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94
   [Also search for: protein folding simulation].

%A R. W. Smith
%T Energy minimization in binary alloy models via genetic algorithms
%J Comput. Phys. Comm.
%V 71
%P 134-146
%D 1992
%K CPC, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A Shaojian Sun
%T Reduced representation model of protein structure prediction:
   Statistical potential and genetic algorithms
%J Protein Science
%V 2
%P 762-785
%D 1993
%K PS, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A Joachim Stender
%A Tom Addis
%T Using the Genetic Algorithm to Adapt Intelligent Systems
%B Symbols versus Neurons ?
%I IOS Press,
%C Amsterdam
%D 1990
%K genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A P. Tuffery
%A C. Etchebest
%A S. Hazout
%A R. Lavery
%T A New Approach to the Rapid Determination of Protein Side Chain Conformations
%J J. of Biomolecular Structure & Dynamics
%V 8
%N 6
%P 1267 ?
%D 1991
%K JBSD, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A P. Tuffery
%A C. Etchebest
%A S. Hazout
%A R. Lavery
%T A Critical Comparison of Search Algorithms Applied to the Optimization
   of Protein Side-Chain Conformations
%J J. Comp. Chem.
%V 14
%P 790-798
%D 1993
%K JCC, genetic algorithms, GA, MolBio, protein, fold, folding, sideChain
%X via enews '94

%A R. Unger
%A J. Moult
%T On the applicability of genetic algorithms to protein folding
%J 26th Hawaii Int. Conf. on System Sciences
%V I
%I IEEE
%P ??-??
%D 1993
%K HICSS 26, HICSS26, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A Jukka Vanhala
%A Kimmo Kaski
%T Protein folding simulation by genetic algorithms
%J 7th Nordic Symp. on Computer Simulation
%E Risto Nieminen
%E Olle Teleman
%W Espoo, Finland
%P ??-??
%D 1993
%K genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94
   [Also search for: protein folding simulation].

%A R. Wehrens
%A C. Lucasius
%A L. Buydens
%A G. Kateman
%T Sequential Assignment of 2D-NMR Spectra of Proteins Using Genetic Algorithms
%J J. Chem. Info.  Comput. Sci.
%V 33
%P 245-251
%D 1993
%K JCICS, 2D, 2-D, NMR, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A Y. L. Xiao
%A D. E. Williams
%T Genetic algorithm: a new approach to the prediction of the structure of
   molecular clusters
%J Chem. Phys. Lett.
%V ??
%P ??-??
%D 1993, in press
%K CPL, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A Y. L. Xiao
%A D. E. Williams
%T GAME: Genetic algorithm for minimization of energy, an interactive program
   for three-dimensional intermolecular interactions
%J Comput. & Chem
%D '93 ?? (submitted)
%K CC, 3D, 3-D, genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A D. C. Youvan
%A A. P. Arkin
%A M. M. Yan
%T Recursive ensemble mutagenesis - A combinatorial optimization technique
   for protein engineering
%B Parallel Problem Solving from Nature
%E R. Manner
%A B. Manderick
%V 2
%P ??-??
%I North Holland, Amsterdam
%D 1992
%K genetic algorithms, GA, MolBio, protein, fold, folding
%X via enews '94

%A E. W. Myers
%A X. Huang
%T An O(N^2 logN) restriction map comparison and search algorithm
%J Bull. Math. Biol.
%V 54
%N 4
%P 599-618
%D 1992
%K BMB, MolBio, site, map maps mapping, RSM, sparse DPA, search, searching,
   match, distance, candidate list, lists
%X O(R log P) time, O(M+P^2) space
   searching of a map with M sites for the best matches to a shorter map
   of P sites, where R is the # of matching site pairs (note R <= MP).
   ... can compute the distance between 2 RSMs with M and N sites respectively
   in O(MN(logM + logN)) time.

%A S. L. Miller
%T A production of amino acids under possible primitive earth conditions
%J Science
%V 117
%P 528-529
%D 1953
%K MolBio, origin, origins of life, amino acid, AA, c1953, c195x, c19xx,
   Oparin, experiment
%X "The idea that the organic compounds that serve as the basis of life were
   formed when the earth had an atmosphere of methane, ammonia, water and
   hydrogen instead of carbon dioxide, nitrogen, oxygen and water was suggested
   by Oparin ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.117.3046.528">doi:10.1126/science.117.3046.528</A>]['16].
   (Also see the bbc[<A HREF="http://www.bbc.com/earth/story/20160823-the-idea-that-life-began-as-clay-crystals-is-50-years-old">24/8/2016</A>].)

%A S. L. Miller
%T Production of some organic compounds under possible primitive earth
   conditions
%J J. Am. Chem. Soc.
%V 77
%P 2351-2361
%D 1955
%K JACS, MolBio, origin, origins of life, amino acid, AA
%X via: P a u l    L e p p    email: lepppaul@studentL.msu.edu  ('94)

%A G. Wachterhauser
%T Before enzymes and templates: theory of surface metabolism
%J Micro. Rev.
%V 52
%P 452-484
%D 1988
%K MR, MolBio, origin, origins of life, amino acid, AA
%X via: P a u l    L e p p    email: lepppaul@studentL.msu.edu  ('94)

%A A. G. Cairns-Smith
%T Genetic takeover and the mineral origins of life
%D 1982
%I CUP
%K MolBio, book, CUP, c1982, c198x, c19xx, CairnsSmith, origin, origins of life,
   amino acid, AA, controversial
%X via: P a u l    L e p p    email: lepppaul at studentL.msu.edu  ('94).
   [Also search for: CairnsSmith].

%A G. von Heijne
%T Sequence Analysis in Molecular Biology, Treasure Trove or Trivial Pursuit
%I AcademicPress
%D 1987
%K vonHeijne, MolBio, text, book, string, gene, DNA, protein, alignment,
   homology, similarity, map, maps
%X isbn:0127251308.

%A M. S. Babcock
%A E. P. D. Pednault
%A W. K. Olson
%T Nucleic Acid Structure Analysis: A Users Guide to a Collection of New
   Analysis Programs
%A J. of Biomolecular Structure and Dynamics
%V 11
%N 3
%P 597-628
%D 1993
%K MolBio, JBSD, DNA, structure, fold, folding

%A M. S. Babcock
%A W. K. Olson
%T A New Program for the Analysis of Nucleic Acid Structure Interpretation
%B Computation of Biomolecular Structures: Achievements, Problems and
   Perspectives
%E D. M. Soumpasis
%E T. M. Jovin
%I SpringerVerlag
%P 65-85
%D 1993
%K MolBio, DNA, structure, fold, folding

%A M. S. Babcock
%A E. P. D. Pednault
%A W. K. Olson
%T Nucleic Acid Structure Analysis: Mathematics for Local Cartesian and
   Helical Structure Parameters That are Truly Comparable Between Structures
%J J. of Molecular Biology
%V 237
%P 125-156
%D 1994
%K MolBio, JMB, DNA, structure, fold, folding

%A M. S. Babcock
%A W. K. Olson
%T The Effect of Mathematics and Coordinate System on Comparability and
   'Dependencies' of Nucleic Acid Structure Parameters
%J J. of Molecular Biology
%V 237
%P 98-125
%D 1994
%K MolBio, JMB, DNA, structure, fold, folding

%A B. Dujon
%A et al!
%T Complete DNA sequence of yeast chromosome XI
%J Nature
%V 369
%P 371-378
%M JUN
%D 1994
%K MolBio, XI, 11, eleven, gene, genetic, map, maps, mapping
%X 666,448-bp
   There are significant discrepancies with previous genetic maps.
   Trying for the largest number of authors award.

%A T. K. Attwood
%A M. E. Beck
%T PRINTS - A protein motif fingerprint database
%J Protein Engineering
%V 7
%N 7
%P ??-??
%D 1994 in press
%K PE, MolBio, protein, fingerprint, finger print, sequence, motif, alignment
%X via enews

%A A. J. Bleasby
%A J. C. Wootton
%T Constructing validated, non-redundant composite protein sequence databases
%J Protein Engineering
%V 3
%N 3
%P 153-159
%D 1990
%K PE, MolBio, c1990, c199x, c19xx, protein, fingerprint, motif, alignment,
   database, nonredundant, non redundant, COMPO, DB, PDB
%X "A strategy has been developed for the construction of a validated,
   comprehensive composite protein sequence database. Entries are amalgamated
   from primary source data bases by a largely automated set of processes in
   which redundant and trivially different entries are eliminated.  ... The
   advantages of a robust composite database for sequence similarity searching
   and information retrieval are discussed."
   -- [<A HREF="https://doi.org/10.1093/protein/3.3.153">doi:10.1093/protein/3.3.153</A>]['17].

%A C. W. Harper jr.
%T A Bayesian probability view of phylogenetic systematics
%J Syst. Zool.
%V 28
%P 547-553
%D 1979
%K MolBio, SZ, Harper-jr jnr, Bayes, family, evolutionary, tree, trees
%X via: Dr. Thomas M. Boyce, Entomology, CSIRO, GPO Box 1700, Canberra ACT 2601
   <!-- email: thomasb@ento.csiro.au   ('94) --> .

%A M. Kuhner
%A J. Felsenstein
%T A simulation comparison of phylogeny algorithms under equal and
   unequal evolutionary rates
%J Molecular Biology and Evolution
%V 11
%N 3
%P 459-468
%M MAY
%D 1994
%K MBE, c1994, c199x, c19xx, evolutionary, phylogenetic, family, tree, trees,
   metric, distance, edit, change, Robinson Foulds dT, branch score
%X we describe two metric distances between trees, the Robinson and Foulds dT
   measure and our own concoction, the Branch Score, which is the square of a
   metric distance.  The former depends only on the topology, the latter also
   on branch lengths.
   -- [<A HREF="https://doi.org/10.1093/oxfordjournals.molbev.a040126">doi:10.1093/oxfordjournals.molbev.a040126</A>]['24].
   Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
   joe OF genetics.washington.edu (IP No. 128.95.12.41) ('94).
   (Also see RFmetric@[<A HREF="https://en.wikipedia.org/wiki/Robinson%E2%80%93Foulds_metric">wikip</A>]['24].)

%E R. Altman
%E D. Brutlag
%E P. Karp
%E R. Lathrop
%E D. Searls
%T Proc. 2nd Int. Conf. on Intelligent Systems for Molecular Biology
%M AUG
%D 1994
%I AAAI Press
%K MolBio, second, ISMB, ISMB2, ISMB94
%X isbn:0-929280-68-7
   held at Stanford 14-17 August '94

%A P. Agarwal
%A D. J. States
%T The repeat pattern toolkit (RPT): analyzing the structure and evolution
   of the C. elegans genome
%J Proc. 2nd Conf. on Int. Sys. in Mol. Biol.
%P 1-9
%M AUG
%D 1994
%K MolBio, ISMB, ISMB2, ISMB94, conf, c1994, c199x, c19xx, repeat, repetitive,
   low information content, worm, nematode, Celegans, DNA, string, sequence
%X Applied to 3.6 MBases. Build a min' spanning tree of repeats.
   email: agarwal@ibc.wustl.edu     email: states@ibc.wustl.edu
   -- [<A HREF="http://ibc.wustl.edu/rpt/elegans/paper.ps">paper</A>]['94], 600K.

%A D. A. Clark
%A C. J. Rawlings
%A S. Doursenot
%T Genetic map construction with constraints
%J Proc. 2nd Conf. on Int. Sys. in Mol. Biol.
%P 78-86
%M AUG
%D 1994
%K MolBio, ISMB, ISMB2, ISMB94, map, maps, mapping,
   fingerprint, clone, probe, logic programming, LP, ElipSys
%X Use a parallel constraint LP system - Elipsys.  Authors at ICRF.
   email: dac@biu.icnet.uk      email: cjr@biu.icnet.uk    ('94)
   (see Dix and Yee, same conf)

%A T. I. Dix
%A C. N. Yee
%T A restriction mapping engine using constraint logic programming
%J Proc. 2nd Conf. on Int. Sys. in Mol. Biol.
%P 112-120
%M AUG
%D 1994
%K MolBio, Monash, TIDix, CNYee, conf, ISMB, ISMB2, ISMB94,
   logic programming, LP, CLP, CLPR, CLP(R), map, maps, mapping, RSM
%X Authors at Monash
   <A HREF="http://www.cs.monash.edu.au/">Comp Sci Monash home</A>
   (see Clark, Rawlings and Doursenot same conf)

%A L. Grate
%A M. Herbster
%A R. Hughey
%A D. Haussler
%A I. S. Mian
%A H. Noller
%T RNA modeling using Gibbs sampling and stochastic context-free grammar
%J Proc. 2nd Conf. on Int. Sys. in Mol. Biol.
%P 138-146
%M AUG
%D 1994
%K MolBio, ISMB, ISMB2, ISMB94,
   SCFG, RNA, tRNA, snRNA, secondary structure, HMM
%X authors at ucsc

%A J. L. Holloway
%A P. Cull
%T Aligning genomes with inversions and swaps
%J Proc. 2nd Conf. on Int. Sys. in Mol. Biol.
%P 195-202
%M AUG
%D 1994
%K MolBio, alignment, genome, inversion, swap, heuristic, ISMB, ISMB2, ISMB94
%X Refers to Tichy, Block Moves, '84.  Authors at Oregon State University
   email: holloway@bcc.orst.edu     email: pc@cs.orst.edu   ('94)

%A A. Milosavljevic
%T Sequence comparisons via algorithmic mutual information
%J Proc. 2nd Conf. on Int. Sys. in Mol. Biol.
%P 303-309
%M AUG
%D 1994
%K MolBio, algorithmic mutual information, tandem repeats,
   ISMB, ISMB2, ISMB94
%X Author at Argonne     email: milosav@anl.gov  ('94).
   [Also search for: MolBio alignment information].

%A D. M. Platt
%T A stochastic method for contig map assembly
%J Proc. 2nd Conf. on Int. Sys. in Mol. Biol.
%P ?-?
%M AUG
%D 1994
%K DMPlatt, daz, Monash, conf, c1994, c199x, c19xx, MolBio, ISMB, ISMB2, ISMB94,
   map, maps, genetic mapping, simulated annealing, SA
%X (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].)

%A I. Simon
%A L. Glasser
%A H. A. Scheraga
%T Calculation of protein conformation as an assembly of stable overlapping
   segments: application to bovine pancreatic trypsin inhibitor
%J PNAS
%V 88
%N 9
%P 3661-3665
%M MAY
%D 1991
%K jrnl, PNAS, MolBio, c1991, c199x, c19xx, protein, structure, overlapping,
   fragment, library
%X "... assuming that the final structure as well as properly chosen overlapping
   segments thereof are simultaneously in low-energy ... chain can be built up
   from building blocks whose conformations are determined primarily by
   short-range interactions. ... Results of this statistical analysis were used
   to determine the variable sizes of the overlapping oligopeptide building
   blocks used in the calculations; these varied from tripeptides to
   octapeptides, depending on the AA-seq.. Successive stages of approximations
   were used to combine the low-energy conformations of these building blocks
   in order to keep the # of variables in the compn to a manageable size. ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.88.9.3661">doi:10.1073/pnas.88.9.3661</A>]['13].
   [Also search for: protein structure fragment library].

%A M. R. Shen
%A M. A. Batzer
%A P. L. Deininger
%T Evolution of the master Alu gene(s)
%J J. Mol. Evol.
%V 33
%N 4
%P 311-320
%M OCT
%D 1991
%K MolBio, c1991, c199x, c19xx, JME, ALU, DNA, repeat, repetitive
%X Abstract
  A comparison of Alu sequences that comprise more recently amplified Alu
  subfamilies was made. There are 18 individual diagnostic mutations
  associated with the different subfamilies. This analysis confirmed that
  the formation of each subfamily can be explained by the sequential
  accumulation of mutations relative to the previous subfamily. Polymerase
  chain reaction amplification of orthologous loci in several primate
  species allowed us to determine the time of insertion of Alu sequences in
  individual loci. These data suggest that the vast majority of Alu elements
  amplified at any given time comprised a single Alu subfamily. We find
  that, although the individual divergence relative to a consensus sequence
  correlate reasonably well with sequence age, the diagnostic mutations are
  a more accurate measure of the age of any individual Alu family member.
  Our data are consistent with a model in which all Alu family members have
  been made from a single master gene or from a series of sequential master
  genes. This master gene(s) accumulated diagnostic base changes, resulting
  in the amplification of different subfamilies from the master gene at
  different times in primate evolution. The changes in the master gene(s)
  probably occurred individually, but their appearance is clearly
  punctuated. Ten of them have occurred within an approximately
  15-million-year time span, 40-25 million years ago, and 8 changes have
  occurred within the last 5 million years. Surprisingly, no changes
  appeared in the 20 million years separating these periods.
 Hugh Ross 78 Craig Avenue Madison, Wisconsin 53705
 608-231-6828 fax 608-231-6769,
   [Also search for; DNA ALU].

%A P. P. Minghetti
%A A. Dugaiczyk
%T The emergence of new DNA repeats and the divergence of primates
%J Proc. Nat. Acad. Sci. (USA)
%V 90
%N 5
%P 1872-1876
%M MAR 1
%D 1993
%K MolBio, PNAS, ALU, DNA, repeat, repetitive
%X Abstract
  We have identified four genetic novelties that are fixed in specific
  primate lineages and hence can serve as phylogenetic time markers. One Alu
  DNA repeat is present in the human lineage but is absent from the great
  apes. Another Alu DNA repeat is present in the gorilla lineage but is
  absent from the human, chimpanzee, and orangutan. A progenitor Xba1
  element is present in the human, chimpanzee, gorilla, and orangutan, but
  only in the human lineage did it give rise to a transposed progeny, Xba2.
  The saltatory appearance of Xba2 is an example of a one-time event in the
  evolutionary history of a species. The enolase pseudogene, known to be
  present as a single copy in the human, was found to be present in four
  other primates, including the baboon, an Old World monkey. Using the
  accepted value of 5 x 10(-9) nucleotide substitutions per site per year as
  the evolutionary rate for pseudogenes, we calculated that the enolase
  pseudogene arose approximately 14 million years ago. The calculated age
  for this pseudogene and its presence in the baboon are incongruent with
  each other, since Old World monkeys are considered to have diverged from
  the hominid lineage some 30 million years ago. Thus the rate of evolution
  in the enolase pseudogene is only about 2.5 x 10(-9) substitutions per
  site per year, or half the rate in other pseudogenes. It is concluded that
  rates of substitution vary between species, even for similar DNA elements
  such as pseudogenes. We submit that new DNA repeats arise in the genomes
  of species in irreversible and punctuated events and hence can be used as
  molecular time markers to decipher phylogenies.
 Hugh Ross 78 Craig Avenue Madison, Wisconsin 53705
 608-231-6828 fax 608-231-6769

%A Per J. Kraulis
%T MOLSCRIPT: a program to produce both detailed and schematic plots of protein
   structures
%J J. of Applied Crystallography
%D 1991
%V 24
%P 946-950
%K JAC, MolScript, MolBio, molecular graphics, protein, display,
   postscript, ps
%X MolScript is a program for creating molecular graphics in the form of
   PostScript plot files. Possible representations are simple wire models,
   CPK spheres, ball-and-stick models, text labels and Jane Richardson-type
   schematic drawings of proteins, based on atomic coordinates in various
   formats. Colour, greyscale, shading and depth cueing can be applied to the
   various graphical objects."
 via: edvard@atf1.fagmed.uit.no (Oyvind Edvardsen)              (7/'94)
 Dept. of Pharmacology, IMB, University of Tromsoe, MH, Breivika,
 N-9037 TROMSOE, NORWAY,
 email: edvard@fagmed.uit.no
 tel: +47 77 64 53 42     fax: +47 77 64 53 10
 <A HREF="http://atf1.fagmed.uit.no/mgl.html">U. Tromsoe</A>

%E M. J. Bishop
%T Guide to Human Genome Computing
%I AcademicPress
%D 1994
%K text, book, MolBio, c1994, c199x, c19xx, human genome project, HUGO
%X reviewed in Nature, 9 June 1994, No. 6480, 369:454.
   via: <!-- tim@megasun.BCH.UMontreal.CA --> (Tim Littlejohn)  (7/94)
   [Also search for: MolBio book].

%A F. Lisacek
%A Y. Diaz
%A F. Michel
%T Automatic identification of group I intron cores in genomic DNA sequences
%J J. Mol. Biol.
%V 235
%P 1206-1217
%D 1994
%K JMB, MolBio, c1994, c199x, c19xx, CNRS, Frederique van Bockstaelle, group1,
   group-1, intron, introns, CITRON, RNA folding, recognition, genome,
   sequence analysis, pseudoknot, pseudo knot, knot theory, zz1297
%X method ... successfully identified 132 out of 143 currently reported
   group I cores with a false positive rate of 10^-6 per nucleotide.
   [Also seach for: MolBio knot DNA].

%A N. El-Mabrouk
%A F. Lisacek
%T Very fast identification of RNA motifs in genomic DNA. Application to tRNA
   search in the yeast genome
%J J. Mol. Bio.
%V 264
%P 46-55
%D 1996
%K JMB, MolBio, jrnl, Frederique, van Boackstaelle, ElMabrouk,
   tRNA, tRNAscan, FAStRNA, zz1297

%A C. Darwin
%T On the Origin of Species by Means of Natural Selection
%I Murray, London
%D 1859
%K c1859, c185x, c18xx, natural selection, pressure of, evolution, Darwinism,
   book, text
%O 6th (final) ed'n 1872 ?
%X via: Warren C. Lathe III, Biology Dept.  University of Rochester  (7/'94)
        email: trey@thelab.biology.rochester.edu
   and: Charley O'Kelly               (8/'94)
        email: okelly@bch.umontreal.ca
   and: The Harvard facsimile edition (with an introduction by Ernst Mayr) is
        out in paperback (I picked up a copy at the Harvard Square Book Store
        when I was in Boston last month). The isbn:0-674-63752-6.
        Robert (BJ) Allan, University of Manitoba     (8/'94)
        email: BJ_Allan@UManitoba.ca
   <IMG SRC="/~lloyd/tildeImages/People/Darwin.small.gif">

%A C. Darwin
%T The Structure and Distribution of Coral Reefs
%I London: Smith, Elder
%D 1842
%K c1842, c184x, c18xx, book, text,  natural selection, pressure of,
   evolution, Darwinism
%X via: Warren C. Lathe III, Biology Dept.  University of Rochester  (7/'94)
   <!-- email: trey@thelab.biology.rochester.edu --> .

%A C. Darwin
%T Journal of Researches into the Geology and Natural History of the Countries
   visited During the Voyage of H.M.S. Beagle Round the World (2nd ed.)
%I London: Murray
%D 1845
%K natural selection, pressure of, evolution, Darwinism
%X via: Warren C. Lathe III, Biology Dept.  University of Rochester  (7/'94)
   <!-- email: trey@thelab.biology.rochester.edu --> .

%A C. Darwin
%T On the tendency of Species to form varieties; and on the perpetuation of
   varieties and species by natural means of selection.
%J J. Proc. Linn. Soc. (Zoll.)
%V 3
%P 45-62
%D 1858
%K c1858, c185x, c18xx, book, text,  natural selection, pressure of,
   evolution, Darwinism
%X via: Warren C. Lathe III, Biology Dept.  University of Rochester  (7/'94)
   <!-- email: trey@thelab.biology.rochester.edu --> .

%A C. Darwin
%T The Variation of Animals and Plants under Domestication
%I London: Murray
%D 1868
%K c1868, c186x, c18xx, book, text,  natural selection, pressure of,
   evolution, Darwinism
%X via: Warren C. Lathe III, Biology Dept.  University of Rochester  (7/'94)
   <!-- email: trey@thelab.biology.rochester.edu --> .

%A C. Darwin
%T The Descent of Man, and selection in Relation to Sex
%I London: Murray
%D 1874
%K c1874, c197x, c18xx, book, text, natural selection, pressure of, evolution,
   Darwinism
%X via: Warren C. Lathe III, Biology Dept.  University of Rochester  (7/'94)
   <!-- email: trey@thelab.biology.rochester.edu --> .

%A C. Darwin
%T The Different Forms of Flowers on Plants of the Same Species
%I London: Murray
%D 1877
%K c1877, c187x, c18xx, book, text, natural selection, pressure of, evolution,
   Darwinism
%X via: Warren C. Lathe III, Biology Dept.  University of Rochester  (7/'94)
   <!-- email: trey@thelab.biology.rochester.edu --> .

%A G. Schreiber
%A A. R. Aldred
%A Wei Duan
%T Choroid plexus, brain protein homeostasis and evolution
%J Today's Life Science
%M SEP
%D 1992
%P 22-28
%K MolBio, transthyretin, c1992, c199x, c19xx
%X auths, esp GS, at MelbU

%A S. J. Richardson
%A A. J. Bradley
%A Wei Duan
%A B. R. Southwell
%A L. Selwood
%A G. Schreiber
%T The expression of the transthyretin gene in liver evolved during the
   radiation of diprotodont marsupials in Australia
%J General and Comparative Endocrinology
%V 90
%N 2
%P 177-182
%M MAY
%D 1993
%K MolBio, c1993, c199x, c19xx, evolution, marsupial, mammal, protein,
   transthyretin
%X [<A HREF="http://dx.doi.org/10.1006/gcen.1993.1072">doi:10.1006/gcen.1993.1072</A>]['10].
   [Also search for: marsupial MolBio].

%A R. D. Fleischmann
%A M. D. Adams
%A O.White, R.A.Clayton, E.F.Kirkness, A.R.Kerlavage, ... et al
%T Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
%J Science
%V 269
%N 5223
%P 496-512
%M JUL
%D 1995
%K jrnl, MolBio, genome, bacterium, bacteria, c1995, c199x, c19xx, biol, first,
   shotgun sequencing, WGS, sequence assembly, L42023, genome, genomes,
   nGenome, complete
%X "An approach for genome analysis based on sequencing & assembly of
   unselected pieces of DNA from the whole chromosome has been applied to
   obtain the complete nucleotide sequence (1,830,137 bp) of the genome from
   the bacterium Haemophilus influenzae Rd. ... eliminates the need for initial
   mapping efforts & is therefore applicable to the vast array of microbial
   species for which genome maps are unavailable. The H. influenzae Rd genome
   sequence (Genome Sequence DataBase accession number L42023) represents the
   only complete genome sequence from a free-living organism. ..."
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05.]
   [Also search for: MolBio sequence assembly].

%A A. Aszodi
%A W. R. Taylor
%T Estimating polypeptide alpha-carbon distances from
   multiple sequence alignments
%J J. Math. Chem
%V 17
%N 2
%P 167-184
%M JUN
%D 1995
%K jrnl, MolBio, c1995, c199x, c19xx, zz0220, protein structure, prediction,
   MSA, alignment, CA, carbona, Amino Acid, distance
%X "The hydrophobic amino acids that make up the core of a protein can be
   expected to be closer together than the rest of the residues in the molecule
   & are likely to remain conserved during evolution due to their important
   role. ... a general theoretical framework is provided for estimating
   interresidue distances from residue hydrophobicity & conservation deduced
   from multiple alignments. While the accurate prediction of individual
   distances by statistical procedures is theoretically impossible, the method
   is able to match the distn of pred. dists. to a prescribed distn with good
   accuracy."
   -- [<A HREF="https://doi.org/10.1007/BF01164846">doi:10.1007/BF01164846</A>]['20].

%A J. C. Roach
%A C. Boysen
%A K. Wang
%A L. Hood
%T Pairwise end sequencing: A unified approach to genomic mapping and
   sequencing
%J Genomics
%V 26
%P 345-353
%D 1995
%K MolBio, jrnl, genome, assembly, genomic, DNA, ends, sequence, map, maps
%X Ref in  T a y l o r  and  S e m p l e  '02.

%A W. Duan
%A S. Richardson
%A J. J. Babon
%A R. J. Heyes
%A B. R. Southwell
%A P. J. Harms
%A R. E. H. Wettenhall
%A K. M. Dziegielewska
%A L. Selwood
%A A. J. Bradley
%A C. M. Brack
%A G. Schreiber
%T Evolution of transthyretin in marsupials
%J Eur. J. Biochem.
%V 227
%P 396-406
%D 1995
%K FEBS, jrnl, MolBio, marsupial, gene, brain, plasma protein,
   polyprotodonta, diprotodonta, dunnart, opossum, evolutionary tree,
   phylogenetic
%X (lizard (chicken ((opposum (dunnart (wallaby s.glider)))
                     ((pig sheep) ((rat mouse) (rabbit human))))))
   max parsimony tree on the primary translation product of
   transthyretin mRNA with lizard as an outgroup.
   [G.S. - Biochem, MelbU].
   [Also search for: marsupial MolBio].

%A C. M. Brack
%A W. Duan
%A A. J. Hulbert
%A G. Schreiber
%T Wallaby transthyretin
%J Comp. Biochem. Physiol.
%V 110B
%N 3
%P 523-529
%D 1995
%K jrnl, MolBio, gene, brain, plasma, protein, marsupial

%A W. Duan
%A S. J. Richardson
%A J. Kohrle
%A L. Chang
%A B. R. Southwell
%A P. J. Harms
%A C. M. Brack
%A T. M. Pettersson
%A G. S. Schreiber
%T Binding of thyroxine to pig transthyretin, its cDNA structure and other
   properties
%J Eur. J. Biochem
%V 230
%P 977-986
%D 1995
%K FEBS, jrnl, MolBio, DNA, gene, brain, plasma, protein

%A D. Kandel
%A Y. Matias
%A R. Unger
%A P. Winkler
%T Shuffling biological sequences
%J Discrete Applied Math.
%I Elsevier
%P 171-185
%V 71
%N 1-3
%M DEC
%D 1996
%K jrnl, DAM, MolBio, shuffle, sequence, permute, Eulerian tour, tours, paths,
   klets, kmer, kmers, DNA, tuples, frequency, frequencies, randomise,
   randomize, significance test, c1996, c199x, c19xx, zz0503
%X ... generate a random instance among all permutations of [sequence] s
   that exhibit the *same* frequencies of k-lets (e.g. dinucleotides,
   doublets..., triplets..a etc.)  ...  two shuffling algorithms:
   [1] a simple swapping-based alg ...; [and 2] a generation algorithm based
   on Euler tours is proven to produce precisely uniform instance, ..., time
   not much more than linear in the seq' length.
   issn:0166-218X,  [<A HREF="http://dx.doi.org/10.1016/S0166-218X(97)81456-4">doi:10.1016/S0166-218X(97)81456-4</A>][5/'03],
      [<A HREF="http://cm.bell-labs.com/cm/ms/who/pw/papers/genome.ps">preprint.ps</A>][5/'03].
   [Also search for: MolBio shuffling].

%A A. R. Aldred
%A P. Prapunpoj
%A G. Schreiber
%T Evolution of shorter and more hydrophilic transthyretin n-termini
   by stepwise conversion of exon 2 into intron 1 sequences
   (shifting the 3' splice site of intron 1)
%J Eur. J. Biochem.
%V 246
%P 401-409
%D 1997
%K FEBS, jrnl, MolBio, evolutionary, brain, plasma, protein, DNA, cDNA,
   marsupial, kangaroo, zz1297
%X 20 vertebrate species including eastern grey kangaroo.

%A K. T. Simons
%A C. Kooperberg
%A E. Huang
%A D. Baker
%T Assembly of protein tertiary structures from fragments with similar
   local sequences using simulated annealing and Bayesian scoring functions
%J J. Molec. Biol.
%V 268
%N 1
%P 209-225
%M APR
%D 1997
%K jrnl, JMB, MolBio, c1997, c199x, c19xx, zz0220, protein structure prediction,
   fragment library
%X "...  simple simulated annealing procedure to assemble native-like structures
   from fragments of unrelated protein structures with similar local seqs. using
   Bayesian scoring fns. ... investigate the effects of multiple seq. info. &
   different types of conformational constraints on the overall performance of
   the method, & the ability of a variety of recently developed scoring fns to
   recognize the native-like conformations in the ensembles of simulated
   structures."
   -- [<A HREF="https://doi.org/10.1006/jmbi.1997.0959">doi:10.1006/jmbi.1997.0959</A>]['20].
   [Also search for: MolBio protein structure library] (and/or Rosetta).

%A F. Alizadeh
%A R. M. Karp
%A L. A. Newberg
%A D. K. Weisser
%T Physical mapping of chromosomes: A combinatorial problem in molecular
   biology
%J ACM 4th Annual Symp. on Discrete Algorithms
%D 1993
%P 371-381
%K MolBio, map, maps, mapping, probe, hybridization, clone, contig,
   algorithm, maximum likelihood
%X 4 refs;  see also: Karp STOC 93,

%A R. M. Karp
%T Mapping the genome: some combinatorial problems arising in molecular
   biology
%J 25th ACM Symp. Theory of Comp.
%P 278-285
%D 1993
%I ACM Press
%K STOC, STOC25, 25, STOC93, 93, MolBio, genome hugo,
   algorithm, problem, survey, fingerprint, finger-print, finger print,
   probe probes probed, map, maps, mapping, RSM,
   sequence assembly, hybridisation, hybridization
%X 3. Lander-Waterman model
   4. Fingerprints; double digest problem, partial digest, probed
   5. Physical Mapping; unique probes, nonunique probes
   6. Mapping Using Interval Graphs
   7. Sequencing Problems; assembly, hybridization
   49 refs
   [good keywords to search bib:  MolBio map mapping RSM interval graph].

%A J. D. Kececioglu
%T Exact and approximation algorithms for DNA sequence reconstruction
%I U. Arizona
%D 1991
%K PhD thesis, MolBio, c1991, c199x, c19xx, genome, map, mapping,
   string, sequence, assembly, algorithm
%X ref' from Karp, Mapping the genome... STOC '93

%A P. Zhang
%A E. A. Schon
%A S. G. Fischer
%A E. Cayanis
%A J. Weiss
%A S. Kistler
%A P. E. Bourne
%T An algorithm based on graph theory for the assembly of contigs
   in physical mapping of DNA
%J Comp. Appl. BioSci.
%V 10
%N 3
%P 309-317
%D 1994
%K MolBio, CABIOS, bioinformatics, c1994, c199x, c19xx, map, maps, mapping,
   contig, DNA fingerprint, spanning path
%X input - set of binary overlapping relations among finite intervals
   along a real line.
   authors at Depts & Insts of Columbia University, NY;    [13 refs]
   [Also search for: Karp MolBio],  [also search for: MolBio mapping].

%A M. Rustici
%A A. M. Lesk
%T Three-dimensional searching for recurrent structural motifs in data
   bases of protein structures
%J J. Comp. Biol.
%V 1
%N 2
%D 1994
%P 121-132
%K JCB, MolBio, AMLesk, 3D, 3-D, three dimensional, pattern, motif, motifs,
   structure, structural, protein, fold, folds, c1994, c199x, c19xx
%X "... three-dimensional analog of the one-dimensional case of pattern matching
   in strings, procedures for which are widely used in molecular biology to
   search DBs of gene seqs.. Typical applications of substructure searching are:
   (i) Determining whether structural features observed in one protein structure
   are unique or recurrent, & (ii) in predictions of protein structures, to
   bridge gaps in an incomplete structural model, by searching the DB for
   peptides that link the given starting & ending points. We describe our
   analysis of the problem and our experience in developing software."
   -- [<A HREF="https://doi.org/10.1089/cmb.1994.1.121">doi:10.1089/cmb.1994.1.121</A>]['17].

%A M. A. Charleston
%A M. D. Hendy
%A D. Penny
%T The effects of sequence length, tree topology, and number of taxa
   on the performance of phylogenetic methods
%J J. COMP. BIOL.
%V 1
%N 2
%D 1994
%P 133-152
%K JCB, MolBio, phylogenetic, family, evolutionary, tree, trees,
   c1994, c199x, c19xx
%X You can find this and other information about JCB on
   <A HREF="gopher://hto-e.usc.edu">JCB gopher</A>  (9/'94)
   via: Roger Kou, USC Depts. of Mathematics and Molecular Biology  (8/'94)
   <!-- email: rkou@hto-b.usc.edu (Roger Kou) -->auth_1 @ U.Syd ['05].

%A M. A. Steel
%A L. A. Szekely
%A M. D. Hendy
%T Reconstructing Trees When Sequence Sites Evolve at Variable Rates
%J J. COMP. BIOL.
%V 1
%N 2
%D 1994
%P 153-?
%K JCB, MolBio, phylogenetic, family, evolutionary, tree, trees, rate
%X You can find this and other information about JCB on
   <A HREF="gopher://hto-e.usc.edu">JCB gopher</A>  (9/'94)
   via: Roger Kou, USC Depts. of Mathematics and Molecular Biology  (8/'94)
   <!-- email: rkou@hto-b.usc.edu (Roger Kou) --> .

%A M. Steel
%A L. Szekely
%A P. Erdos
%T The number of nucleotide sites needed to accurately reconstruct large
   evolutionary trees
%I DIMACS
%R 96-19
%D 1996
%K TR19, TR 96 19, family, phylogenetic, evolutionary, tree, trees, MolBio,
   convergence, DNA, base, bases, site, zz0200
%X <A HREF="http://dimacs.rutgers.edu/TechnicalReports/1996.html" TARGET="external">[www]</A>['00].
   ref in  F a r a c h  '98

%A P. Erdos
%A M. Steel
%A L. Szekely
%A T. Warnow
%T A few logs suffice to build (almost) all trees: part II
%J Theor. Comp. Sci.
%V 221
%P 77-118
%D 1999
%K jrnl, TCS, family, evolutionary, phylogenetic, tree, MolBio, zz0200
%X ref in  F a r a c h and K' '99.   Part I ???
   Worth it just for the title, gives even  W a d l e r  a run for the money.

%A Robert Cook-Deegan,
%T The Gene Wars, Science, Politics and the Human Genome
%I Norton, New York
%D 1994
%K MolBio, popular, book, genome, HUGO, Cook Deegan
%X It's reviewed in the July 29 '94 issue of Science.  from enews
   via: Lisa Ruthig             (8/'94)
        The Wistar Institute <!-- email: ruthig@wista.wistar.upenn.edu --> .

%A J. Hein
%A J. Stovlbaek
%T Genomic alignment
%J J. Mol. Evol.
%V 38
%P 310-316
%D 1994
%K JME, MolBio, genome, alignment, GenAl,
   coding, non-coding, reading frame, DNA

%A P. Salamon
%A J. C. Wootton
%A A. K. Konopka
%A L. K. Hansen
%T On the robustness of maximum entropy relationships for complexity
   distributions of nucleotide sequences
%J Computers Chem.
%V 17
%N 2
%P 135-148
%D 1993
%K MolBio, DNA, maximum entropy, max ent

%A J. C. Wootton
%A S. Federhen
%T Statistics of local complexity in amino acid sequences and sequence
   databases
%J Computers Chem.
%V 17
%N 2
%P 149-163
%D 1993
%K MolBio, c1993, c199x, c19xx, protein, low information content,
   repeat, repetitive
%X authors at NCBI
   [Also search for: MolBio protein information].

%A J. C. Wootton
%T Simple sequences of protein and DNA
%J DNA and Protein Sequence Analysis
%E M. J. Bishop
%E C. J. Rawlings
%I IRL Press
%D 1997
%P 169-183
%K MolBio, low information content, repeat, composition, multi state,
   multistate, distribution, low, high, complexity, zz0398
%X Defines complexity as compositional complexity,  which seems
     to be = multi-state distribution [see  B o u l t o n  &  W a l l a c e,
     J. Theor. Biol. Vol.23 pp.269-278 1969] on windows of fixed length.
   Defines patterns as usually analyzed by their content and spacing
     of residues and k-grams... .
   Defines periodicity as repetition of residue types or k-grams (p.171).
   [Also search for: information DNA MolBio].

%A J. C. Wootton
%A S. Federhen
%T Taxonomy of simple amino acid sequences
%J J. Bioinformatics and Genome Research
%C Singapore
%E H. A. Lim
%E C. R. Cantor
%I World Scientific pub.
%P 159-172
%D 1995
%K MolBio, conf, low information content, protein, repeat, repetitive
%X also see W+F '93
   [Also search for: information DNA MolBio].

%A S. Bergh
%A S. T. Cole
%T MycDB: an integrated mycobacterial database
%J Mol. Microbiol.
%P 517-534
%V 5
%D 1994
%K MolBio, MM, MycDB, tuberculosis, TB, data base,
   mycobacteria, mycobacterial, myco bacteria, AceDB
%X <A HREF="http://kiev.physchem.kth.se/MycDB.html">MycDB</A>  (9/'94)
   <A HREF="http://probe.nalusda.gov:8000/acedocs/acedbfaq.html">ACEDB</A>

%A D. A. Benson
%A M. Boguski
%A D. J. Lipman
%A J. Ostell
%T Genbank
%J NAR
%V 22
%N 17
%P 3441-3444
%M SEP
%D 1994
%K NAR, MolBio, DNA, Genbank, gene, genetic, database, data base
%X [<A HREF="http://www.ncbi.nlm.nih.gov/">NCBI home</A>][9/'94].

%A D. B. Emmert
%A P. J. Stoehr
%A G. Stoesser
%A G. N. Cameron
%T The European Bioinformatics Institute (EBI) databases
%J NAR
%V 22
%N 17
%P 3445-3449
%M SEP
%D 1994
%K NAR, MolBio, EBI, Bio Informatics, DNA, gene, database, data base
%X <A HREF="http://www.ebi.ac.uk/">EBI home</A>  (Sept '94 ?)

%A D. G. George
%A W. C. Barker
%A H. W. Mewes
%A F. Pfeiffer
%T The PIR-international protein sequence database
%J NAR
%V 22
%N 17
%P 3569-3573
%M SEP
%D 1994
%K NAR, MolBio, PIR, protein, database, data base

%A A. J. Bleasby
%A D. Akrigg
%A T. K. Attwood
%T OWL - a non-redundant composite protein sequence database
%J NAR
%V 22
%N 17
%M SEP
%D 1994
%P 3574-3577
%K NAR, MolBio, OWL, protein, data base

%A A. Bairoch
%A B. Boeckmann
%T The SWISS-PROT protein sequence data bank: current status
%J NAR
%V 22
%N 17
%P 3578-3580
%M SEP
%D 1994
%K NAR, MolBio, Swiss Prot, protein, database, data base

%A A. Bairoch
%A P. Bucher
%T PROSITE: recent developments
%J NAR
%V 22
%N 17
%P 3583-3589
%M SEP
%D 1994
%K NAR, MolBio, database, data base, protein site

%A Z. Yang
%T Maximum likelihood phylogenetic estimation from DNA sequences with
   variable rates over sites: approximate methods.
%J J. Mol. Evol.
%P 306-314
%V 39
%N 3
%D 1994
%K JME, MolBio, phylogenetic, family, evolutionary, tree, trees, rate, site
%X via enews

%A A. Zharkikh
%T Estimation of evolutionary distances between nucleotide sequences
%J J. Mol. Evol.
%V 39
%N 3
%P 315-?
%D 1994
%K JME, MolBio, phylogenetic, family, evolutionary, tree, trees, DNA
%X via enews

%A S. K. Kannan
%A T. J. Warnow
%T Inferring evolutionary history from DNA sequences
%J SIAM J. Comput.
%V 23
%N 4
%P 713-737
%M AUG
%D 1994
%K MolBio, SJC, sequence, string, family evolutionary phylogenetic, tree, trees

%A K. P. Steele
%A K. E. Holsinger
%A R. K. Jansen
%A D. W. Taylor
%T Assessing the reliability of 5S rRNA sequence data for phylogenetic
   analysis in green plants
%J Mol. Biol. Evol.
%V 8
%P 240-248
%D 1991
%K MolBio, MBE, evolutionary, family, tree, trees, DNA, RNA, rRNA, 5S
%X via <!-- email: Holsinge@UConnVM.UConn.Edu --> Kent Holsinger (10/'94)

%A S. Grumbach
%A F. Tahi
%T A new challenge for compression algorithms: genetic sequences
%J Inf. Proc. and Management
%V 30
%N 6
%P 875-886
%M ?
%D 1994
%K IPM, MolBio, DNA, RNA, string, sequence, information content, compress,
   biocompress biocompress2
%X authors@inria <!--email: stephane.grumbach inria.fr,   fariza.tahi inria.fr (11/94) --> .
   [Also search for: compress MolBio].

%A R. S. Thorpe
%A D. P. McGregor
%A A. M. Cumming
%A W. C. Jordan
%T DNA Evolution and Colonization Sequence of Island Lizards in Relation to
   Geological History: mtDNA RFLP, Cytochrome B, Cytochrome Oxidase, 12S rRNA
   Sequence, and Nuclear RAPD Analysis
%J Evolution
%V 48
%N 2
%P 230-240
%M APR
%D 1994
%K MolBio, RNA

%A R. T. Chesser
%A R. M. Zink
%T Modes of Speciation in Birds: A Test of Lynch's Method
%J Evolution
%V 48
%N 2
%P 490-497
%D 1994
%P APR
%K MolBio, species, bird, birds, Lynch

%A B. J. Bachmann
%T Linkage map of Escherichia coli K-12, edition 8
%J Microbiol Rev
%P 130-197
%V 54
%N 2
%M JUN
%D 1990
%K MolBio, microbiology review, reviews, EColi, mapping, 1991
%X [published erratum appears in Microbiol Rev 1991 Mar;55(1):191]
   <!-- email: heath@mbcf.stjude.org (Richard  11/'94) --> .

%A J. Terwilliger
%A J. Ott
%T Handbook of Human Genetic Linkage
%I Johns Hopkins Univ. Press
%D 1994
%K MolBio, book, text, map, analysis
%X <!-- email: schaffer@lcmp4.cs.rice.edu --> (Alex Schaffer  11/'94)

%A A. J. Cuticchia
%A J. Arnold
%A W. E. Timberlake
%D 1992
%T The use of simulated annealing in chromosome reconstruction experiments
   based on binary scoring
%J Genetics
%V 132
%P 591-601
%K MolBio, SA, map, maps, mapping, contig
%X email: arnold@GENOME.GENETICS.UGA.EDU  (11/'94)
   This program for ordering cloned DNA fragments into 'contig map' does so by
   permuting the rows of the clone/probe hybridization matrix so that clones
   with similar call numbers appear next to each other.
        The algorithm has been used to map the fourth chromosome of
   Aspergillus nidulans, the whole genome of Schizosaccharomyces
   pombe genome, and a region of human chromosome 9.

%A Y. Wang
%A R. A. Prade
%A J. Griffith
%A W. E. Timberlake
%A J. Arnold
%T A fast random cost algorithm for physical mapping
%J PNAS
%D 1994
%V 91
%P 11094-11098
%K MolBio, map, maps, mapping, simulated annealing, SA
%X email: arnold@GENOME.GENETICS.UGA.EDU  (11/'94)

%A R. J. Cano
%A et al
%T Amplification and sequencing of DNA from a 12-135 million year old weevil
%J Nature
%V 363
%P 536-538
%D 1993
%K MolBio, jrnl, beetle, fossil DNA, amber, preserved
%X BUT see Austin, Smith and Thomas in Trends in Ecol' and Evol' Aug '97
   ([Also search for: MolBio fossil DNA].-)

%A A. Gibbons
%T Possible dino DNA find is greeted with skepticism
%J Nature
%V 266
%P 1159
%M NOV
%D 1994
%K MolBio, jrnl, DNA, dinosaur, bone, paleontology, fossil DNA
%X comments on article by Woodard et al, 1229-1232, same issue.
   ([Also search for: MolBio fossil DNA].-)

%A S. R. Woodward
%A N. J. Weyand
%A M. Bunnell
%T DNA sequence from cretaceous period bone fragments
%J Nature
%V 266
%P 1229-1232
%M NOV
%D 1994
%K MolBio, jrnl, dinosaur, DNA, cytochrome B, cyt, cytB, paleontology,
   fossil DNA
%X [Controversial: see A. Gibbon's comments, p1159, same issue]
   DNA was extracted from 80,000,000 year old bone fragments found in strata
   of the upper cretaceous blackhawk formation in the roof of an underground
   coal mine in E. Utah.  ... PCR... sequenced a portion of the gene
   encoding mitochondrial cytochrome b.  ... differ from all other
   cytochrome b sequences in Genbank and EMBL databases. ...
   (Authors 1 and 2 at BYU, Utah, USA)
  BUT
  see Austin, Smith, Thomas in Trends in Eco' and Evol' Aug '97
  ... survival of DNA to 10,000 to 100,000 years in special conditions
  possibly, longer questionable and unproven ...
   ([Also search for: MolBio fossil DNA].-)

%A L. M. Adleman
%T Molecular computation of solutions to combinatorial problems
%J Science
%V 266
%N ?
%P 1021-1024
%M NOV
%D 1994
%K graph, algorithm, NP, NPC, Hamiltonian circuit, path, MolBio, DNA, genetic,
   molecular computation, MC, computing, problem, DNAcomputation,
   DNAcomputing, bioComputer, bioComputation, computing, c1994, c199x, c19xx
%X The tools of molecular biology were used to solve an instance of the
   directed Hamiltonian path problem. A small graph was encoded in molecules
   of DNA, and the "operations" of the computation were performed with standard
   protocols and enzymes. This experiment demonstrates the feasibility of
   carrying out computations at the molecular level.
   -- [<A HREF="http://links.jstor.org/sici?sici=0036-8075%2819941111%293%3A266%3A5187%3C1021%3AMCOSTC%3E2.0.CO%3B2-%23">paper@Jstor</A>]['05].
   [LA: Hamiltonian circuit problem: traverse (some) edges of the
           graph from a given start vertex to a given finish vertex
           such that you visit each vertex exactly once.
           (The edges are directed.)
        Only a 7 node problem, it's a start, but will it scale up? ]
   [Also search for: bioComputer].

%A H. Blincoe
%T Significant hand types in women according to relative lengths of fingers
%J Am. J. Phys. Anthrop.
%V 20
%P 45-48
%D 1962
%K bio, biol, biology, human, inheritance, hand, finger length, trait, man,
   c1962, c196x, c19xx, jrnl
%X see Kloepfer '46, Phelps '52.   Information from
   <A HREF="http://gdbwww.gdb.org/">Online Mendelian Inheritance in Man</A>.
   Chris Porter  <!-- email: cporter@gdb.org --> (12/'94)

%A H. W. Kloepfer
%T An investigation of 171 possible linkage relationships in man
%J Ann. Eugen.
%V 13
%P 35-71
%D 1946
%K bio, biol, biology, MolBio, human, inheritance, hand, finger length, trait,
   man, c1946, c194x, c19xx
%X Kloepfer (1946) studied the relative length of the index and middle fingers.
   Short index fingers (i.e., the index finger is shorter than the ring finger)
   is said to be dominant in men, recessive in women. Three phenotypes were
   noted--second longer than fourth, second equal to fourth, and second shorter
   than fourth (see Phelps '52, Blincoe '62).
   Information from <A HREF="http://gdbwww.gdb.org/">Online Mendelian Inheritance in Man</A>.
   Chris Porter  <!-- email: cporter@gdb.org --> (12/'94)

%A V. R. Phelps
%T Relative index finger length as a sex-influenced trait in man
%J Am. J. Hum.  Genet.
%V 4
%P 72-89
%D 1952
%K bio, biol, biology, human, inheritance, hand, finger length, trait, man,
   c1952, c195x, c19xx
%X see Kloepfer '46, Blincoe '62.   Information from
   <A HREF="http://gdbwww.gdb.org/">Online Mendelian Inheritance in Man</A>.
   Chris Porter  <!-- email: cporter@gdb.org --> (12/'94).

%A V. Luzzati
%T Traitement statistique des erreurs dans la determination des
   structures cristallines
%J Acta Cryst.
%V 5
%P 802-810
%D 1952
%K jrnl, Xray, crystallography, MolBio, c1952, c195x, c19xx, zz1113,
   atomic coordinates, protein structure, determination, 3D, plot, plots,
   errors, precision, estimates
%X "... method of Wilson has been .... the laws of stat. distribution of
   errors del F in the structure factors ..."
   -- [<A HREF="http://dx.doi.org/10.1107/S0365110X52002161">doi:10.1107/S0365110X52002161</A>]['13].
   Also see Murshudov and Dodson,
   [<A HREF="http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html">ccp4</A>][2013].
   [Also search for: MolBio protein structure precision].

%A E. Margoliash
%T Primary structure and evolution of cytochrome C
%J PNAS
%V 50
%N 4
^P 672-679
%M OCT
%D 1963
%K jrnl, MolBio, cytochrome C, cytochromeC, c1963, c196x, c19xx, zz0123,
   protein, human, horse, pig, rabbit, chicken, tuna, yeast, molecular clock
%X -- [<A HREF="https://doi.org/10.1073/pnas.50.4.672">doi:10.1073/pnas.50.4.672</A>]['23].
   Also see molecular clock@[<A HREF="https://en.wikipedia.org/wiki/Molecular_clock">wikip</A>]['23].

%A D. G. Arques
%A C. J. Michel
%T Periodicities in coding and noncoding regions in genes
%J J. Theor. Biol.
%V 143
%N ?
%P 307-318
%M ?
%D 1990
%K JTB, MolBio, gene, repetitive, low information content, coding, DNAs

%A S. G. Oliver
%A et al (!)
%T The complete DNA sequence of yeast chromosome III
%J Nature
%V 357
%P 38-46
%M ?
%D 1992
%K MolBio, chromosome, genome, yeast, DNA, sequencing
%X about 300K base pairs

%A J. J. Holland
%A J. C. De La Torre
%A D. A Steinhauer
%T RNA virus populations as quasispecies
%J Curr. Top. Microbiol. Immunol.
%V 176
%P 1-20
%D 1992
%K jrnl, MolBio, viral, population, c1992, c199x, c19xx, mutation, sequence,
   strain
%X "RNA virus mutation freqs. generally approach max. tolerable levels & create
   complex indeterminate quasispecies populations in infected hosts. This
   usually favors extreme rates of evolution, although periods of relative
   stasis or equilibrium, punctuated by rapid change may also occur (as for
   other life forms). Because complex quasispecies populations of RNA viruses
   arise probabilistically & differentially in every host, their compositions
   & exact roles in disease pathogenesis are indeterminate & their dirns. of
   evolution & the nature & timing of "new" virus outbreaks are unpredictable."

%A A. Gleizes
%A A. Henaut
%T A global approach for contig construction
%J Comp. Appl. BioSci.
%V 10
%N ?
%P 401-408
%M ?
%D 1994
%K CABIOS, Bioinformatics, MolBio, map, maps, mapping, contig, sequencing

%A O. Riess
%A B. Winkelmann
%A J. T. Epplen
%T Toward the complete genomic map and molecular pathology of human
   chromosome 4
%J Human Genetics
%V 94
%N 1
%M JUL
%D 1994
%P 1-?
%K MolBio, bio, biol, biology, science, human, genetics, genome, hugo,
   map, chromosome, chromosome4, chr4, four

%A V. Kukharenko
%A S. Sheleg
%A M. Freudine
%A E. Pichugina
%A A. Delvig
%T Down's syndrome, Edwards' syndrome, Patau's syndrome - synthesis of
   glycosaminoglycans.
%J Human Genetics
%V 94
%N 1
%M JUL
%D 1994
%P 80-82
%K MolBio, bio, biol, biology, science, human, genetics,
   syndrome, Down's, Edward's, Patau's

%A F. Galvagni
%A F. A. Saad
%A G. A. Danieli
%A M. Miorin
%A L. Vitiello
%A M. L. Mostacciuolo
%A C. Angelini
%T A study on duplications of the dystrophin gene: evidence of a geographical
   difference in the distribution of breakpoints by intron.
%J Human Genetics
%V 94
%N 1
%M JUL
%D 1994
%P 83-?
%K MolBio, bio, biol, biology, science, human, genetics, dystrophin, gene

%A O. Gotoh
%T Optimal alignment between groups of sequences and its application to
   multiple sequence alignment.
%J Comp. Appl. BioSci.
%V 9
%N 3
%P 361-370
%M ?
%D 1993
%K MolBio, CABIOS, Bioinformatics, string, sequence, multiple, alignment

%A O. Gotoh
%T Further improvement in methods of group-to-group sequence alignment with
   generalized profile operations.
%J Comp. Appl. BioSci.
%V 10
%N 4
%P 379-387
%M ?
%D 1994
%K MolBio, CABIOS, Bioinformatics, string, sequence, multiple, alignment

%A H. P. Yockey
%T Information Theory and Molecular Biology
%I CUP
%D 1992
%K book, text, CUP, c1992, c199x, c19xx, information theory, IT, coding,
   MolBio, bioinformatics, genetics, biol, biology, science, encoding
%X <!-- email: hpyockey@aol.com --> (HPYockey  1/'95).
   [Also search for: MolBio information theory].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A P. W. Ewald
%T Evolution of Infectious Disease
%I OUP
%D 1994
%K book, text, MolBio, c1994, c199x, c19xx, OUP, disease, medicine, virus,
   biology, science, coevolution
%X From: <!-- email: haross@students.wisc.edu --> (hugh ross   1/'95)
   [Also search for: coevolution MolBio].

%A R. R. Gutell
%A M. W. Gray
%A M. N. Schnare
%T A compilation of large subunit (23S and 23S-like) ribosomal RNA
   structures
%J Nucl. Acid. Res.
%V 21
%N 13
%P 3055-3074
%M ?
%D 1993
%K MolBio, RNA secondary structure, 23S, NAR, jrnl
%X via enews  <!-- email: samuel@selway.umt.edu -->  (2/95)

%A R. R. Gutell
%A C. R. Woese
%T Higher order structural elements in ribosomal RNAs: pseudo-konots and
   the use of noncanonical pairs
%J Proc. Natl. Acad. Sci. (USA)
%V 87
%N ?
%P 663-667
%M ?
%D 1990
%K MolBio, RNA, secondary structure, PNAS, non-canonical
%X via enews  <!-- email: samuel@selway.umt.edu -->  (2/95)

%A D. M. Platt
%A T. I. Dix
%T A model for comparing genomic restriction maps
%J 28th Hawaii Int. Conf. Sys. Sci.
%M JAN
%D 1995
%V 5
%P 24-31
%K MolBio, genome, map, maps, mapping, restriction, RSM, error. noise,
   MML, HICSS, Monash, TIDix, DMPlatt, conf, HICSS28, HICSS95

%A V. Di Francesco
%A P. J. Munson
%A J. Garnier
%T Use of multiple alignments in proteins secondary structure prediction
%J 28th Hawaii Int. Conf. Sys. Sci.
%V 5
%P 285-291
%M JAN
%D 1995
%K alignment, secondary structure, SS, protein, conformation, fold, folding,
   MolBio, HICSS, HICSS28, HICSS95, conf. DiFrancesco

%A M. Gribskov
%A R. Luthy
%A D. Eisenberg
%T Profile analysis
%J Methods in Enzymology
%I Academic Press
%V 183
%D 1991
%K MolBio, profile, profilesearch, protein, block, alignment

%A M. Hirosawa
%A Y. Totoki
%A M. Hoshida
%A M. Ishikawa
%T Comprehensive study of iterative algorithms of multiple sequence alignment
%J Comp. Appl. BioSci.
%V 11
%N 1
%P 13-18
%M FEB
%D 1995
%K MolBio, c1995, c199x, c19xx, jrnl, CABIOS, Bioinformatics,
   multiple alignment, protein
%X [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/11/1/13">jrnl</A>]['10].
   (See [<A HREF="http://www.allisons.org/ll/Bioinformatics/Multiple/">multiple</A>].)
   [Also search for: MolBio multiple alignment].

%A M. Ishikawa
%A T. Toya
%A Y. Totoki
%T Parallel application systems in genetic information processing
%J Proc. Future Gen. Comp. Sys.
%P 129-138
%I ICOT
%M DEC
%D 1994
%K MolBio, FGCS, ICOT, alignment

%A J. W. M. Hornos
%A Y. M. M. Hornos
%T Algebraic model for the evolution of the genetic code
%J Phys. Rev. Lett.
%V 71
%P 4401-4404
%M ?
%D 1993
%K MolBio, PRL, jrnl, genetic code, coding, DNA, biology
%X from Koichiro Matsuno <!-- email: kmatsuno@VOSCC.NAGAOKAUT.AC.JP --> [3/95].

%A D. Wu
%A J. Roberge
%A D. J. Cork
%A B. G. Nguyen
%A T. Grace
%T Computer visualization of long genomic sequences
%J Proc. Visualization '93
%I IEEE
%M OCT
%D 1993
%P 308-315
%K conf, MolBio, DNA, Wcurve

%A V. A. Fischetti
%A G. M. Landau
%A P. H. Sellers
%A J. P. Schmidt
%T Identifying periodic occurences of a template with applications to protein
   structure
%J IPL
%V 45
%N 1
%P 11-18
%M JAN
%D 1993
%K jrnl, IPL, MolBio, c1993, c199x, c19xx, tandem repeat, repeats, repetition,
   sequence, DNA, wraparound, wrap around dynamic programming, WDP
%X "Consider a template P of size m in which each char. matches many different
   chars. with various degrees of perfection. Given a text T of size n, we
   present a simple & practical alg. that finds the substring of T, which best
   matches some substring of Pn (Pn is the concatenation of an arbitrary # of
   copies of P). ...alg. produces the matched pair & alignment in O(mn)-time."
   -- [<A HREF="http://dx.doi.org/10.1016/0020-0190(93)90245-5">doi:10.1016/0020-0190(93)90245-5</A>]['08].
   [Also search for: MolBio tandem repeat].

%A N. Colloc'h
%A C. Etchebest
%A E. Thoreau
%A B. Henrissat
%A J. P. Mornon
%T Comparison of three algorithms for the assignment of secondary structure in
   proteins: the advantages of a consensus assignment
%J Protein Eng.
%V 6
%N 4
%P 377-382
%D 1993
%K jrnl, MolBio, c1993, c199x, c19xx, Colloch, protein, secondary structure,
   assignment, DSSP, Pcurve, Define, length distribution, helix, strand
%X "... assignments of secondary structures ... DSSP, P-Curve & Define. Their
   results have been compared for a non-redundant database of 154 proteins. On a
   residue per residue basis, the % match score is only 63% between the 3
   methods. ... differ on the number of helices or strands, thus implying a wide
   discrepancy in the length of assigned structural elts. Moreover, the length
   distribution of helices & strands points to the existence of artefacts
   inherent to each assignment alg..  [So] a consensus assignment is proposed
   where each residue is assigned to the state determined by at least 2 of the
   3 methods. ..."  [via ArunK].
   -- [<A HREF="http://dx.doi.org/10.1093/protein/6.4.377">doi:10.1093/protein/6.4.377</A>]['11],
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/8332595">pubmed</A>]['11].

%A R. Wilson
%A et al
%T 2.2Mb of contiguous nucleotide sequence from chromosome III if C. Elegans
%J Nature
%V 368
%P 32-38
%M ?
%D 1994
%K MolBio, biology, DNA, chromosome, three, III, cElegans, c elegans, nematode,
   big, long sequence

%A D. Beaver
%T Factoring: The DNA solution
%J Advances in Cryptology - Asiacrypt '94
%I SpringerVerlag
%P ?-?
%D 1994
%K conf, c1994, c199x, c19xx, MolBio, molecular computation, computing, MC,
   factor, prime, primality, bioComputer, bioComputation
%X "We consider molecular models for computing and derive a DNA-based mechanism
   for solving intractable problems through massive parallelism. ..."
   -- [<A HREF="https://doi.org/10.1007/BFb0000453">doi:10.1007/BFb0000453</A>]['22].
    Don Beaver @ [<A HREF="http://www.cse.psu.edu/~beaver/research/molec.html">psu</A>][4/95].
   [Also search for: primality]  and  [also search for: bioComputer]..

%A D. Gifford
%T On the path to computation with DNA
%J Science
%V 266
%P 993-994
%M NOV
%D 1994
%K MolBio, molecular computation, MC, c1994, c199x, c19xx, DNAcomputation,
   DNAcomputing, bioComputer, bioComputing, computing
%X [<A HREF="http://links.jstor.org/sici?sici=0036-8075%2819941111%293%3A266%3A5187%3C993%3AOTPTCW%3E2.0.CO%3B2-%23">@Jstor</A>]['05].
   Don Beaver's [<A HREF="http://www.cse.psu.edu/~beaver/research/molec.html">www page</A>][4/95].
   [Also search for: bioComputer].

%A J. Hartmanis
%T On the weight of computations
%J Bull. of the European Assoc. for Theoretical Comp. Sci.
%N 55
%M FEB
%D 1995
%P 136-138
%K ETACS, TCS, MolBio, molecular computation, MC, computing, DNA, NP, NPC,
   DNAcomputation, bioComputation, computation, bioComputer, DNAcomputing,
   computing, c1995, c199x, c19xx
%X in the Structural Complexity Column
   J.H. argued that the real problem in these kind of computations would be
   the weight. He calculated that extracting a Hamiltonian path in a graph
   with 200 nodes using DNA computers would make necessary an encoding
   in DNA sequences that would have a weight which is more than the weight
   of the earth.  -- Claus Rick <!-- email: rick@cs.uni-bonn.de  --> [4/'95]
   -- [<A HREF="http://www.cs.cornell.edu/Info/Department/Annual95/Faculty/Hartmanis.html">H@cornell</A>]['05],
      pdf@[<A HREF="www.uni-ulm.de/fileadmin/website_uni_ulm/iui.inst.../column55.pdf">U-Ulm</A>]['14].
   (LA: know the 'power' of exponentials.)
   [Also search for: bioComputer].

%A C. C. Martin
%A R. Gordon
%T Differentiation trees, a junk DNA molecular clock, and the evolution of
   neoteny in salamanders
%J J. Evol. Biol.
%V 8
%N ?
%P ?-?
%M ?
%D 1995 in press
%K MolBio, evolution, jrnl, biology, JEB
%X via D.Gordon  email: gordonr@cc.UManitoba.CA  [4/95].

%A V. Strumpen
%T Coupling hundreds of workstations for parallel molecular sequence analysis
%J SPE
%V 25
%N 3
%P 291-304
%M MAR
%D 1995
%K ssearch, parallel, farm, workstation, MolBio, string, computing
%X application was ssearch over 800 workstations,
   perform local alignment of a sequence with all members of a genetic DB.

%A K. M. Chao
%A J. Zhang
%A J. Ostell
%A W. Miller
%T A local alignment tool for very long DNA sequences
%J Comp. Appl. BioSci.
%V 11
%N 2
%P 147-153
%M APR
%D 1995
%K MolBio, CABIOS, Bioinformatics, jrnl, alignment, string, sequence, zz0595
%X [Also search for:  alignment]

%A J. D.  Thompson
%T Introducing variable gap penalties to sequence alignment in linear space
%J Comp. Appl. BioSci.
%V 11
%N 2
%M APR
%D 1995
%P 181-186
%K MolBio, CABIOS, Bioinformatics, jrnl, string, sequence, zz0595
%X [Also search for:  alignment]

%A R. Doelz
%A F. Eggenberger
%T A compression mechanism for sequence databases to improve the
   efficiency of conventional tools.
%J Comp. Appl. BioSci.
%V 11
%N 2
%P 219-223
%M APR
%D 1995
%K MolBio, CABIOS, Bioinformatics, jrnl, DNA, data, compress, zz0595

%A R. Lipton
%T Speeding up computations via molecular biology
%J ?
%D ? 1995 ?
%K molecular computation, MC, MolBio, zz0595
%X you can get Lipton's paper from:
   <A HREF="ftp://ftp.cs.princeton.edu:pub/people/rjl/bio.ps">FTP</A>
   - Marcel Turcotte  <!-- email: turcotte@IRO.UMontreal.CA --> [5/'95].

%A R. R. Birge
%T Protein based computers
%J Scientific American
%V 272
%N 3
%P 66-71
%M MAR
%D 1995
%K MolBio, jrnl, protein, molecule, computation, hybrid, 3D memory, zz0595
%X devices fabricated frpm biological molecules promise compact size and
   faster data storage ...
   ... three dimensional memories and neural networks ...

%A A. Monge
%A E. J. P. Lathrop
%A J. R. Gunn
%A P. S. Shenkin
%A R. A. Friesner
%T Computer modeling of protein folding: Conformational and energetic analysis
   of reduced and detailed protein models
%J J. Mol. Biol.
%V 247
%N 5
%P 995-1012
%M APR
%D 1995
%K MolBio, JMB, jrnl, fold, conformation, zz0595

%A M. C. R. Shastry
%A J. B. Udgaonkar
%T The folding mechanism of barstar: Evidence for multiple pathways
   and multiple intermediates
%J J. Mol. Biol.
%V 247
%N 5
%P 1013-1027
%M APR
%D 1995
%K MolBio, JMB, jrnl, c1995, c199x, c19xx, fold, protein, folding, conformation,
   pathway, trajectory, zz0595
%X "The mechanism of folding of the small protein barstar ... where US & UF are
   the slow-refolding and fast-refolding unfolded forms ..."
   -- 7723034@[<A HREF="https://pubmed.ncbi.nlm.nih.gov/7723034/">pubm'd</A>]['22].

%A Y. X. Fu
%T Linear invariants under Jukes and Cantors one-parameter model
%J J. Theor. Biol.
%V 173
%N 4
%P 339-?
%M APR
%D 1995
%K MolBio, JTB, jrnl, Cantor, evolution, mutation, DNA, zz0595

%A P. Grim
%T The greater generosity of the spatialized prisoner's dilemma
%J J. Theor. Biol.
%V 173
%N 4
%P 353-?
%M APR
%D 1995
%K JTB, c1995, c199x, c19xx, jrnl, prisoner, prisoners, PD, IPD, altruism,
   space, spatial, world, zz0595
%X (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A P. R. Sibbald
%T Deducing protein structures using logic programming: Exploiting
   minimum data of diverse types
%J J. Theor. Biol.
%V 173
%N 4
%P 361-?
%M APR
%D 1995
%K JTB, jrnl, MolBio, LP, fold, folding, prediction, zz0595

%A S. A. Kauffman
%A W. Macready
%T Search strategies for applied molecular evolution
%J J. Theor. Biol.
%V 173
%N 4
%P 427-?
%M APR
%D 1995
%K MolBio, JTB, jrnl, strategy, zz0595

%A H. Wako
%A T. Blundell
%T Use of amino acid environment-dependent substitution tables and
   conformational propensities in structure prediction from aligned
   sequences of homologous proteins I: solvent accessibility classes
%J J. Mol. Biol.
%V 238
%N ?
%P 682-692
%D 1994
%K JMB, MolBio, jrnl, protein, structure prediction, zz0695

%A H. Wako
%A T. Blundell
%T Use of amino acid environment-dependent substitution tables and
   conformational propensities in structure prediction from aligned
   sequences of homologous proteins II: secondary structures
%J J. Mol. Biol.
%V 238
%N ?
%P 693-708 ?
%D 1994
%K JMB, MolBio, jrnl, protein, secondary structure, SS, prediction, zz0695

%A R. M. Karp
%A L. A. Newberg
%T An algorithm for analysing probed partial digestion experiments
%J Comp. Appl. BioSci.
%V 11
%N 3
%P 229-235
%M JUN
%D 1995
%K MolBio, CABIOS, Bioinformatics, jrnl, partial digest problem, probe, probed,
   map, mapping, zz0895

%A M. Kamimura
%A Y. Takahashi
%T Phi-psi conformational pattern clustering of protein amino acid residues
   using the potential function method
%J Comp. Appl. BioSci.
%V 10
%N 2
%P 163-169
%M APR
%D 1994
%K MolBio, CABIOS, Bioinformatics, jrnl, structure, class, classification,
   AA, dihedral angle, zz0895
%X 19 refs

%A J. Adachi
%A M. Hasegawa
%T Improved dating of the human/chimpanzee separation in the
   mitochondrial DNA tree: heterogeneity among amino acid sites
%J J. Mol. Evol.
%M ?
%D 1995
%V 40
%N 6
%P 622-?
%K MolBio, JME, jrnl, chimp, primate, evolution, evolutionary tree

%A Z. Yang
%T Evaluation of several methods for estimating phylogenetic trees
   when substitution rates differ over nucleotide sites
%J J. Mol. Evol.
%M ?
%D 1995
%V 40
%N 6
%P 689-?
%K MolBio, JME, jrnl, evolutionary tree, family, zz0895

%A M. Q. Zhang
%A T. G. Marr
%T Alignment of molecular sequences seen as random path analysis
%J J. Theor. Biol.
%M MAY
%D 1995
%V 174
%N 2
%P 119-130
%K JTB, jrnl, MolBio, DNA, zz0895

%A L. Luo
%A G. Bai
%T The maximum information principle and the evolution of nucleotide
   sequences
%J J. Theor. Biol.
%V 174
%N 2
%M MAY
%D 1995
%P 131-136
%K JTB, jrnl, MolBio, DNA, information theory, IT, zz0895

%A D. K. Gehlhaar
%A G. M. Verkhivker
%A P. A. Rejto
%A C. J. Sherman
%A D. B. Fogel
%A L. J. Fogel
%A S. T. Freer
%T Molecular recognition of the inhibitor AG-1343 by HIV-1 protease:
   conformationally flexible docking by evolutionary programming
%J Chem. and Biol.
%V 2
%N 5
%P 317-324
%D 1995
%K evolutionary programming, EP, MolBio, protein, jrnl, zz0995
%X - Fogel   email: fogel@sunshine.ucsd.edu    [9/95].

%A L. W. Wright
%A et al
%T Computer assisted restriction site mapping - an integrated approach to
   handling experimental uncertainty
%J Comp. Appl. BioSci.
%V 10
%N 4
%P 435-442
%D 1994
%K MolBio, CABIOS, Bioinformatics, jrnl, map, RSM, zz0995
%X from Sci' Cit' index 1994

%A D. Archambaud
%A I. Saraiva Silva
%A J. Penne
%T Systolic implementation of Smith and Waterman algorithm on a SIMD
   coprocessor
%B Algorithms and Parallel VLSI III
%E M. Moonen
%E F. Catthoor
%I Elsevier
%D 1995
%K book, text, MolBio, computer architecture, parallel, SIMD, sequence,
   string alignment, similarity, homology, approximate string matching, zz1095
%X in Hargrave

%A P. Baldi
%A S. Brunak
%A Y. Chauvin
%A J. Engelbrecht
%A A. Krogh
%T Periodic sequence patterns in human exons
%J Proc. Third Int. Symp. on Int. Sys. for Molec. Biol.
%D 1995
%P 30-38
%K zz1095, ISMB, ISMB3, ISMB95, conf, MolBio, pattern, DNA, HMM, exon
%X non-T(A/T)G  x about 10 nucleotides.

%A S. R. Eddy
%T Multiple alignment using hidden Markov models
%J Proc. Third Int. Symp. on Int. Sys. for Molec. Biol.
%D 1995
%P 114-120
%K zz1095, ISMB, ISMB3, ISMB95, conf, MolBio, HMM

%A R. Parsons
%A M. E. Johnson
%T DNA sequence assembly and genetic algorithms - new results and puzzling
   insights
%J Proc. Third Int. Symp. on Int. Sys. for Molec. Biol.
%D 1995
%P 277-284
%K zz1095, ISMB, ISMB3, ISMB95, conf, MolBio, GA

%A D. B. Searls
%A K. P. Murphy
%T Automata theoretic models of mutation and alignment
%J Proc. Third Int. Symp. on Int. Sys. for Molec. Biol.
%D 1995
%P 341-349
%K zz1095, ISMB, ISMB3, ISMB95, conf, MolBio, alignment, similarity, DPA
%X Also look up  'alignment DPA'  and similar keywords in bibliography, or
   see alignment@[<A HREF="http://www.allisons.org/ll/Bioinformatics/">MolBio page</A>].

%A R. Thiele
%A R. Zimmer
%A T. Lengauer
%T Recursive dynamic programming for adaptive sequence and structure alignment
%J Proc. Third Int. Symp. on Int. Sys. for Molec. Biol.
%D 1995
%P 384-393
%K zz1095, ISMB, ISMB3, ISMB95, conf, MolBio, DPA, 3D, protein, structure, 3D
%X [Also search for: MolBio protein structure alignment].

%A M. J. Wise
%T Neweyes: a system for comparing biological sequences
%J Proc. Third Int. Symp. on Int. Sys. for Molec. Biol.
%D 1995
%P 393-401
%K zz1095, conf, ISMB, ISMB3, ISMB95, MolBio

%A A. Grigoriev
%A R. Mott
%A H. Lehrach
%T An algorithm to detect chimeric clones and random noise in genomic mapping
%J Genomics
%V 22
%P 482-486
%D 1994
%K jrnl, MolBio, chimera, clone, clones, map, maps, mapping, hybridization,
   zz1195

%A F. Alizadeh
%A R. M. Karp
%A D. K. Weisser
%A G. Zweig
%T Physical mapping of chromosomes using unique probes
%J J. Comp. Biol.
%V 2
%N 2
%DP 159-184
%D 1995
%K MolBio, computational, jrnl, JCB, physical, map, mapping, probe, DNA, zz1295

%A W. Gillett
%A J. Daues
%A L. Hanks
%A R. Capra
%T Fragment collapsing and splitting while assembling high-resolution
   restriction maps
%J J. Comp. Biol.
%V 2
%N 2
%P 185-205
%D 1995
%K MolBio, computational, jrnl, JCB, map, mapping, RSM, fragment collapse
%X fragment collapse: when 2 different genomic fragments of approximately the
   same length and occuring in the digestion of two different overlapping
   clones are incorectly identified as representative of a single genomic
   fragment.  ... techniques for detecting and correcting such anomalies.

%A M. Dyer
%A A. Frieze
%A S. Suen
%T Ordering clone libraries in computational biology
%J J. Comp. Biol.
%V 2
%N 2
%P 207-218
%D 1995
%K MolBio, computational, jrnl, JCB, clones, order, clone library, tiling
%X ...  probabilistic model ...
   give the minimum number of probes required to reconstruct the entire
   ordering of a given clone library with high probability.

%A D. S. Greenberg
%A S. Istrail
%T Physical mapping by STS hybridization: algorithmic stratgies and the
   challenge of software evaluation
%J J. Comp. Biol.
%V 2
%N 2
%P 219-273
%D 1995
%K MolBio, computational, jrnl, JCB, STS, sequence tag sites, hybridise,
   hybridize, map, mapping
%X [30 refs]

%A R. M. Idury
%A M. S. Waterman
%T A new algorithm for DNA sequence assembly
%J J. Comp. Biol.
%V 2
%N 2
%P 291-306
%D 1995
%K MolBio, computational, jrnl, JCB
%X [Also search for: MolBio sequence assembly].

%A C. Armen
%A C. Stein
%T Short superstrings and the structure of overlapping strings
%J J. Comp. Biol
%V 2
%N 2
%P 307-332
%D 1995
%K MolBio, computational, jrnl, JCB, shortest common superstring,
   super string, SCSS, zz1295

%A S. S. Skiena
%A G. Sundram
%T Reconstructing strings from substrings
%J J. Comp. Biol.
%V 2
%N 2
%P 333-354
%D 1995
%K MolBio, computational, jrnl, JCB, shortest common superstring,
   super string, SCSS, sequencing, hybridization, SBH

%A A. Milosavljevic
%T DNA sequence recognition by hybridization to short oligomers
%V 2
%N 2
%P 355-370
%D 1995
%K MolBio, computational, jrnl, JCB

%A A. R. Rubinov
%A M. S. Gelfand
%T Reconstruction of a string from substring precedence data
%V 2
%N 2
%P 371-382
%D 1995
%K MolBio, computational, jrnl, JCB, super string

%A O. Razagulyaev
%A A. Rubinov
%A M. Gelfand
%A A. Chetverin
%T Sequencing potential of nested strand hybridization
%J J. Comp. Biol.
%V 2
%N 2
%P 383-
%D 1995
%K MolBio, computational, jrnl, JCB

%A P. R. R. Courtois
%A M. L. J. Mancany
%T A probabilistic algorithm for interactive huge genome comparison
%J Comp. Appl. BioSci
%V 11
%N 6
%P 657-666
%M DEC
%D 1995
%K MolBio, CABIOS, Bioinformatics, jrnl, genome, compare, alignment, zz0196

%A C. Wills
%T When did Eve live? An evolutionary detective story
%J Evolution
%V 49
%N 4
%P 593-607
%M AUG
%D 1995
%K MolBio, jrnl, Eve, zz0296, human evolution, rate, c1995, c199x, c19xx
%X [Also search for: MolBio Eve human evolution].

%E Hillis
%E Morritz
%E Mabel
%T Molecular Systematics
%I Sinauer
%D 1996
%K MolBio, book, text, evolution, computing, Bio, Biol, zz0196
%X - Doug Eernisse <!-- DEernisse@fullerton.edu --> [1/'96].

%A F. J. Ayala
%T The myth of Eve: molecular biology and human origins
%J Science
%V 270
%P 1930-1936
%M DEC
%D 1995
%K MolBio, Eve, origin, evolution, human, hominid, DRB1 gene, zz0296,
   population size
%X ... the DRB1 genes are extremeley polymorphic ...
   coalesce into a single individual ~ 60 million years ago
   (predates ape / old world monkey split) ...  Suggests that for
   the last 60 m.y. human population size has been at least 100,000.  44 refs.
   [Also search for: MolBio Eve human evolution].

%A M. S. Springer
%T Molecular clocks and the incompleteness of the fossil record
%J J. Mol. Evol.
%V 41
%N 5
%P 531-538
%D 1995
%K MolBio, jrnl, JME, evolution, molecular clock, paeleontlogy, fossil, zz0296,
   mutation rate

%A A. Jimenez-Sanchez
%T On the origin and evolution of the genetic code
%J J. Mol. Evol.
%V 41
%N 6
%P 712-716
%D 1995
%K MolBio, JME, jrnl, DNA, translation, genetic code, zz0396
%X AB 50410712.239

%A R. O. Morgan
%A M. P. Fernandez
%T A BC200-derived element and Z-DNA as structural markers in annexin
   I genes: Relevance to Alu evolution and annexin tetrad formation
%J J. Mol. Evol.
%V 41
%N 6
%P 979-985
%D 1995
%K MolBio, JME, jrnl, gene, DNA, ALU sequence
%X AB 50410979.239

%A G. Mitchison
%A R. Durbin
%T Tree-based maximal likelihood substitution matrices and hidden
   Markov models
%J J. Mol. Evol.
%V 41
%N 6
%P 1139-1151
%D 1995
%K MolBio, JME, jrnl, c1995, c199x, c19xx, change, matrix, model, HMM, zz0396
%X AB 50411139.239
   [Also search for: MolBio substitution matrix].

%A R. Hughey
%A A. Krogh
%T Hidden Markov models for sequence analysis: extension and analysis
   of basic method
%J Comp. Appl. BioSci
%V 12
%N 2
%P 95-108
%M APR
%D 1996
%K CABIOS, Bioinformatics, jrnl, MolBio, Markov model, HMM, zz0596

%A V. Bafna
%A P. A. Pevzner
%T Genome rearrangements and sorting by reversals
%J SIAM J. Comput.
%V 25
%N 2
%P 272-289
%D 1996
%O Proc. 34th IEEE Symp. on Foundations of Comp. Sci. (FOCS93), pp148-157, 1993
%K SJC, jrnl, MolBio, complexity, time, evolution, order, rearrange, genes,
   reverse, reversal diameter, permutation, symmetric group, transposition,
   signed, unsigned, approximation algorithm, generator, Gollan, alignment,
   c1996, c199x, c19xx, zz0696
%X ... sorting by reversals, i.e., [...] reversals of arbitrary fragments.
   ... open problems ... One of these [was] Gollan's conjecture on the
   reversal diameter of the symmetric group. This paper proves the conjecture.
   ...  problem of expected reversal distance between two random permutations
   is investigated.  [it] is shown to be very close to the reversal diameter,
   [] indicating that reversal distance provides a good separation between
   related and nonrelated sequences [...] The gene rearrangement problem forces
   us to consider reversals of *signed* permutations, as the genes in DNA could
   be positively or negatively oriented. An approx' alg' for
   *signed* permutations is presented, ... performance guarantee of 3/2.
   [...] using the *signed* permutations approach, an approx' alg' for
   sorting by reversals [of *unsigned* perms] described ... perf' guar' 7/4.
   Also see   K e c e c i o g l u,   S a n k o f f,   and generators
   -- [<A HREF="http://locus.siam.org/SICOMP/volume-25/art_0225012.html">abs' SIAM</A>]['06],
   -- [<A HREF="http://epubs.siam.org/sam-bin/dbq/article/25062">abs' SIAM</A>][10/'02]
      [<A HREF="http://dimacs.rutgers.edu/People/Postdocs/Bafna.html">bafna</A>][10/'02],
      [<A HREF="http://www.cs.ucsd.edu/users/ppevzner/">ppevzner</A>][10/'02]  [Also search for: sorting reversals].

%A J. Kececioglu
%A R. Ravi
%T Of mice and men: Algorithms for evolutionary distances between genomes with
   translocation
%J Proc. of the 6th ACM-SIAM Symp. on Discrete Algorithms
%P 604-613
%D 1995
%K MolBio, conf, mouse, man, distance, inversion, reversal, reversals,
   translocation, translocations, gene order, permutation, sorting
%X ...genome rearrangement. ...
   inversion, transposition, duplication, and translocation,
   [the min' number] is called the rearrangement distance
   [here] study of genome rearrangement by translocation [which] exchanges
   material at the end of two chromosomes within a genome.
   ...present a 2-approximation algorithm...  also examine ...
   two types of rearrangements in concert [inversion and translocation]
   ...simple 2-approximation algorithm [when] the orientation of markers is
   unknown (*unsigned*), and a 3/2-approximation algorithm when orientation
   is known (*signed*).
   -- [<A HREF="http://www.cs.arizona.edu/people/kece/Research/papers/KR95.ps">paper</A>][10/'02].
   [Also search for: sorting reversals].

%A S. Hannenhalli
%A P. Pevzner
%T Transforming men into mice (polynomial algorithm for genomic distance
   problem)
%J 36th Annual IEEE Symp. on Foundations of Comp. Sci.
%P 581-592
%D 1995
%K conf, FOCS, FOCS36, FOCS95, MolBio, sort, sorting, reversals, genome,
   rearrangement, order, distance, signed, permutation, reversal,
   complexity, time, perm, mouse, man, c1995, c199x, c19xx, alignment, zz0899
%X [<A HREF="http://www-hto.usc.edu/people/hannenhalli/focs95.ps">paper</A>][10/'02]
   Polynomial-time algorithm for sorting *signed* permutations by reversals.
   [[Situation is different for unsigned perms, NP-H, see C a p r a r a '97.]]
   ... human -- mouse ~ 131 reversal/ translocation/ fusion/ fission events.
   Also see H' and P' '99.    [Also search for: sorting reversals].

%A P. Berman
%A S. Hannenhalli
%T Fast sorting by reversal
%J Combinatorial Pattern Matching, (CPM'96).
%P ?-?
%D 1996
%K conf, CPM, CMP96, sorting, reversals, signed permutations, rearrangement,
   MolBio, 1996, c199x, c19xx
%X [<A HREF="http://www-hto.usc.edu/people/Hannenhalli.html">paper</A>][10/'02]
   ...sorting *signed* perms by revs O(n**4) ... use cycle graph and propose a
   O((n**2).ack_inv(n)) algorithm where ack_inv() is inverse Ackerm@n fn.
   [i.e. to all intents and purposes O(n**2).]
   Also see  H' and P' '99.   [Also search for: sorting reversals]

%A S. Hannenhalli
%A P. A. Pevzner
%T Transforming cabbage into turnip: Polynomial algorithm for sorting signed
   permutations by reversals
%J JACM
%V 46
%N 1
%P 1-27
%M JAN
%D 1999
%O 36th Annual IEEE Symp. on Foundations of Comp. Sci., pp581-592, 1995
%K JACM, ACM jrnl, MolBio, sort, reversal, genome, rearrangement, alignment,
   zz0899, c1999, c199x, c19xx, order, distance, signed, permutation, time,
   perm
%X e.g. B. oleracea (cabbage) =  1,-5,4,-3,2  to 1,-5,4,-3,-2
   to 1,-5,-4,-3,-2  to 1,2,3,4,5  = B. campestris (turnip)!
   Reversal distance is min # of reversals to turn one *signed* permutation
   into another; d(cabbage,turnip)=3 from the above.
   -- [<A HREF="http://doi.acm.org/10.1145/300515.300516">doi:/10.1145/300515.300516</A>]['06]
   -- [<A HREF="http://www-hto.usc.edu/people/hannenhalli/stoc95.ps">stoc95</A>][10/'02].
   See Bafna and Pevzner 1996.    [Also search for: sorting reversals].

%A J. W. Fickett,
%T Finding genes by computer: the state of the art
%J Trends in Genetics
%V 12
%N 8
%P 316-320
%M AUG
%D 1996
%K MolBio, jrnl, gene, find, sequence analysis, zz0896
%X monash_lib' - B 575.105T794;  ? see also F' in Comp+Chem 20(1) p103 '96 ?

%A J. Fickett
%T The gene identification problem - an overview for developers
%J Comp. and Chem.
%V 20
%N 1
%P 103-118
%D 1996
%K jrnl, MolBio, genes, find, finding, zz0300
%X ? see also F', in Trends in Gen'ics, 12(8) p316 '96 ?

%A L. Holm
%A C. Sander
%T Mapping the protein universe
%J Science
%P 595-602
%V 273
%M AUG
%D 1996
%K jrnl, MolBio, 3D, protein, structure, shape, shapes, alignment,
   match, matching, zz0896
%X 2 Aug 1996,  37 refs.
   [Also search for: MolBio protein structure alignment].

%A R. H. Lathrop
%A T. F. Smith
%T Global optimum protein threading with gapped alignment and empirical
   pair score functions
%J J. Mol. Biol.
%V 255
%P 641-665
%D 1996
%K JMB, jrnl, MolBio, branch and bound, gap, sequence structure threading,
   protein folding, amino acid pair potential, contact potentials, zz0896
%X The problem is to thread a protein primary sequence (its amino acids)
   through the known structure of another protein (probably related to the 1st)
   so as to optimise some score  (e.g. sum of contact potentials).
   Result can be used to predict the structure of the 1st protein.
   The possibility of gaps in this threading cum alignment makes it a
   hard problem.

%A L. Wang
%A T. Jiang
%A E. L. Lawler
%T Approximation algorithms for tree alignment with a given phylogeny
%J Algorithmica
%V 16
%P 302-315
%M SEP
%D 1996
%K Molbio, jrnl, c1996, c199x, c19xx, evolutionary tree, phylogenetic trees,
   alignment, cost, zz0996
%X [Also search for:  multiple alignment].

%A O. Gotoh
%T Significant improvement in accuracy of multiple protein sequence
   alignments by iterative refinement as assessed by reference to
   structural alignments
%J J. Mol. Biol.
%V 264
%P 823-838
%D 1996
%K JMB, jrnl, MolBio, sum pairs, zz0197
%X ... four strategies for aligning large numbers of protein seq's were
   assessed ...
   The two best performing strategies ... pursue an optimal weighted
   sum-of-pairs score, where the pair weights were introduced to
   correct for uneven rep'n of subgroups ...
   ... The effects of [different] substitution matrices were found
   to be minor ...
   [Also search for: MolBio protein structure alignment].

%A A. Milosavljevic
%T Discovering dependencies via algorithmic mutual information:
   a case study in DNA sequence comparison
%J Machine Learning
%V 21
%P 35-50
%D 1995
%K MolBio, jrnl, low information content, repetitive, similarity, zz0397,
   gene, TPA, K03021, C-FMS, CFMS, PO, X14720
%X Section 2:
      source string: ATTACATGAGCATAAT
      target string: GATTACCGATGAGCTAAT
                   = G (1,4) CCG (6,6) (13,4)
      which is ~ W.F.Tichy's (ACM TOCS '84) "block moves" edit model.
   Experiment 1:
      human tissue plasminogen activator (TPA) gene 22,001-26,00 id K03021
   Experiment 2:
      TPA and human C-FMS proto-oncogene for CSF-1 receptor (PO) gene id X14720
   ([Also search for: alignment MML]).

%A F. R. Blattner
%A G. Plunkett 3rd
%A C.A.Bloch, N.T.Perna, V.Burland, M.Riley, J.Collado-Vides, et al
%T The complete genome sequence of Escherichia coli K-12
%J Science
%V 277
%N 5331
%P 1453-1462
%M SEP
%D 1997
%K jrnl, Escherichia coli, K12, E coli, Ecoli, bacterium, bacteria, prokaryote,
   genome, complete, c1997, c199x, c19xx, biol, NC_000913, NC000913, U00096,
   MolBio, whole, microbial genomes
%X 4,639,221 bp, 4,403 genes. Wisconsin team.
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=genome&gi=115">k12@genbank</A>]['05]
   -- [<A HREF="http://dx.doi.org/10.1126/science.277.5331.1453">doi:10.1126/science.277.5331.145</A>]['05]
   -- [<A HREF="http://www.sciencemag.org/cgi/content/abstract/277/5331/1453">@science</A>]['05]
   (Also see: AE005174 genome c2001)

%A S. Seiler
%A S. Sailer
%T The gender gap: Elite women are running further behind
%J Sportscience News
%P ?-?
%D 1997
%K sport, gender, male, female, men, c1997, c199x, c19xx, stats, statistics,
   caseStudy, prediction, sprint, marathon, running, times, anabolic steroids,
   drugs, Whipp, Ward, Tatem, Nature, Olympic games, olympics, performance,
   improvement
%X May-Jun 1997: "The world's fastest women are now getting slower, while the
   men keep getting faster. That's the outcome of our analysis of top running
   performances of the last 40 years. Reduced use of anabolic steroids may be
   the reason women runners are no longer becoming like men."
   "... The marathon is still showing a narrowing of the performance gap in the
   90s, owing to slower performance by males ... If the marathon is excluded,
   the mean performance gap for the six other running events has increased from
   11% in the mid 80s to 12% in the mid 90s...."
   -- [<A HREF="http://www.sportsci.org/news/news9705/gengap.html">paper</A>]['04]
   Also see [<A HREF="http://home.hia.no/~stephens/">Seiler</A>]['04],
   and [<A HREF="http://www.isteve.com/sep04.htm#dumbgap">isteve.com</A>]['04] -- pretty wild.
   For the opp' view see: W h i p p & W a r d c1992, and T a t e m c2004.

%A S. L. Miller
%A J. W. Schopf
%A A. Lazcano
%T Oparin's Origin of Life: Sixty Years Later
%J J. Mol. Evol.
%D 1997
%V 44
%N 4
%P 351-353 ?
%K JME, jrnl, Oparin, origins, zz0497
%X [Also search for: Oparin MolBio].

%A G. Schreiber
%A S. J. Richardson
%T The evolution of gene expression, structure and function of transthyretin
%J Comp. Biochem. Physiol.
%V 116B
%N 2
%P 137-160
%D 1997
%K jrnl, MolBio, bird, avian, reptile, brain, hormone, zz0697
%X authors at Dept. Biochem, Uni of Melbourne, Vic 3052

%A E. Rivals
%A O. Delgrange
%A J.-P. Delahaye
%A M. Dauchet
%A M.-O. Delorme
%A A. Henaut
%A E. Ollivier
%T Detection of significant patterns by compression algorithms: The case of
   approximate tandem repeats in DNA sequences.
%J Comp. Appl. BioSci
%V 13
%N 2
%P 131-136
%D 1997
%K MolBio, jrnl, CABIOS, Bioinformatics, low information content, sequence,
   string, pattern, repeat
%X [Also search for: MolBio compression DNA].

%A E. Rivals
%A M. Dauchet
%T Fast discerning repeats in DNA sequences with a compression algorithm
%J Proc. Genome Informatics Workshop
%W Tokyo
%I Universal Academy Press, Tokyo
%D 1997
%P 215-226
%K wShop, MolBio, genomics, repeat, repetitive, low information content, DNA,
   overlap, compress, GIW, GIW8, GIW97, c1997, c199x, c19xx
%X long direct repeats ... retrotransposition, copy, exon shuffling ...
   The repeats chosen for compression must not overlap each other as do the
   repeats which result from molecular duplications.  ... heuristic ...
   Search_Repeats ... guided by ...  length of repeat and absence of overlap.
   ... approximate repeats as clusters [LA: in the sense of near in seq']
   of exact sub-repeats.
   3 sec' for genome of Haemophilus influenza [1.8Mbp] on a Sun Ultrasparc ws.
   [Also search for: MolBio compression DNA].

%T Theoretical and Computational Methods in Genome Research
%E S. Suhai
%O Proc Int. Symp., Heidelberg, 25-27 May 1996
%I Plenum
%M MAY
%D 1997
%P 327
%K MolBio, book, conf, computing, bio, biol, gene, genes, zz0697
%X isbn:0 306 45503 X;    $123.50 Aus

%A Z. Yang
%A B. Rannala
%T Bayesian phylogenetic inference using DNA sequences: a Markov chain
   Monte Carlo method
%J Mol. Biol. Evol.
%V 14
%N 7
%P 717-724
%D 1997
%K MBE, jrnl, c1997, c199x, c19xx, MolBio, Bayes, family tree, trees,
   birth and death process, Markov model, MM, mcmc, inductive inference, zz0797
%X seq's assumed aligned, ignore gaps,
   applied to 9 species of primates.
   Sampling tree topologies.
   [Also search for: Bayesian phylogenetic tree MolBio].

%A C. Zeyl
%A G. Bell
%T The advantage of sex in evolving yeast populations
%J Nature
%V 388
%N 6641
%M JUL
%D 1997
%P 465-468
%K jrnl, origin, sex, why, sexual reproduction, mutations, evolution,
   yeast, c1997, c199x, c19xx, zz0897
%X .. sex increases the mean fitness in an environment in which
   the populations were well adapted, but not in an environment
   in which new adaptions occurred, supporting the hypothesis
   that the advantage of sexuality lay in the removal of deleterious
   mutations. ...
   [LA: for yeast].
   [Also search for: sexual reproduction why].

%A D. M. Loewenstern
%A H. Hirsh
%A P. Yianilos
%A M. Noordewier
%T DNA sequence classification using compression-based induction
%R 95-04
%I DIMACS
%M APR
%D 1995
%K DIMACS, TR 95 04, TR9504, MolBio, DNA, compress, II, pattern,
   low information content, promoter, splice junction, site
%X intuition ... given a training set S of sequences,
   concatenate and compress to get  I(S).
   Take test sequence t,  add and compress, get  I(t,S),
   now take I(t|S)=I(t,S)-I(S).
   This can be seen to follow from Bayes P(H&D)=P(D).P(H|D)=P(H).P(D|H),
   where D=t and H is the hypothesis that t "belongs to" S.
   See also `Minimum Message Length' (MML) inductive inference where
   one imagines sending a message with header H and body D|H.
  <A HREF="http://www.cs.rutgers.edu/~loewenst/index.html">[loewenst]</A>[9/97]
   (DIMACS ~ Rutgers + Princeton + AT & T Bell + Bellcore )

%A D. M. Loewenstern
%A P. N. Yianilos
%T Significantly lower entropy estimates for natural DNA sequences
%R 96-51
%I DIMACS
%M DEC
%D 1996
%O IEEE Data Compression Conf., DCC '97, (shorter version) p151-160
%K DIMACS, TR 96 51, TR9651, MolBio, DNA, compress, compression,
   pattern, low information content, pattern
%X Claims conventional compression techniques get ~ 1.9 bits/base for DNA,
   L' can sometimes get 1.66 bits/base by using inexact match info'.  And for
   *coding regions* claims 1.84 to 1.87 bits/base (compared to 1.92 before)
   when (i) predict next AA based on inexact polypeptide matches
   and (ii) predict the particular codon.
  <A HREF="http://www.cs.rutgers.edu/~loewenst/index.html">[loewenst]</A>[9/97]
   Extended abs' in IEEE Proc Data Comp Conf 1997
   (DIMACS ~ Rutgers + Princeton + AT & T Bell + Bellcore )
   DCC@IEEE: [<A HREF="http://doi.ieeecomputersociety.org/10.1109/DCC.1997.581998">doi:10.1109/DCC.1997.581998</A>]['07].
   [Also search for: DNA compress]

%A C. Cosmi
%A V. Cuomo
%A M. Ragosta
%A M. Macchiato
%T Characterization of nucleotidic sequences using maximum entropy techniques
%J J. Theor. Biol.
%P 423-432
%D 1990
%K MolBio, jrnl, JTB, nucleotide, DNA, string, compress, compression,
   codon usage, frequencies, frequency, codons, intron, exon
%X [... uses only codon usage tables and takes into account
   the length of sequences, and preserves the information
   contained in each codon by a punctual index. ...]
   Thing = DNA sequence.
   Attributes = codon usage frequencies, ie. 61 attributes.
   Class = mean codon usage frequencies.
   By simulation they get prob' of a `thing' being drawn from a `class'.
   Can get confidence measure that a seq' is `compatible' with a class.
   Use this to judge if seq' compatible with class 1 or class 2 in ...
   e.g. Eukaryote  coding v. intron; globin  coding v. intron;
        alpha-globin  coding v. intron;  ...
   ref in  L o e w e n s t e r n  TR96-51 '96

%A S. K. Kearsley
%T An algorithm for the simultaneous superposition of a structural series
%J J. Comput. Chem.
%V 11
%N 10
%P 1187-1192
%D 1990
%K jrnl, JCC, c1990, c199x, c19xx, MolBio, vector, vectors, point, set, points,
   superposition, geometric pattern matching, match, rotation, translation,
   Gerber, Muller, quaternion, quaternions, rational function optimization,
   structure, 3D
%X "A procedure [for] finding the optimal superposition of a series of chemical
   structures. Quaternions are used to represent the absolute orientation of the
   structures-rotations of the structures need never be carried out explicitly.
   The Rational Function Optimization method is used to minimize a simultaneous
   superposition residual similar to the one given by Gerber and Muller. The
   robustness of the method is illustr. by comparing a series of conformations
   of a polyene carotenoid."
   -- [<A HREF="http://dx.doi.org/10.1002/jcc.540111011">doi:10.1002/jcc.540111011</A>]['08].
   (2 sets, *each* of n pts, different frames of ref, minimise squared error;
    also see [<A HREF="http://www.allisons.org/ll/AlgDS/Numerical/Superposition/">demo</A>].)
   [Also search for: Kabsch c1976] (NB quat'ns *are* better than lat. & long).

%A A. G. Cairns-Smith
%T Seven Clues to the Origin of Life. A Scientific Detective Story
%I CUP
%P 144
%M NOV
%D 1990
%K book, c1990, c199x, c19xx, zz0916, origin, origins, life, cystals, genes,
   CairnsSmith, controversial
%X pb, uk us isbn13:9780521398282.
   "This book addresses the question of how life may have arisen on earth, in
   the spirit of an intriguing detective story. It relies on the methods of
   Sherlock Holmes, in particular his principle that one should use the most
   paradoxical features of a case to crack it. ..."
   -- CUP[<A HREF="http://www.cambridge.org/us/academic/subjects/life-sciences/evolutionary-biology/seven-clues-origin-life-scientific-detective-story">www</A>]['8/'16].
   [Also search for: CairnsSmith].
   (Also see the bbc[<A HREF="http://www.bbc.com/earth/story/20160823-the-idea-that-life-began-as-clay-crystals-is-50-years-old">24/8/2016</A>].)

%A J. M. Hall
%A M. K. Lee
%A B. Newman
%A J. E. Morrow
%A L. A. Anderson
%A B. Huey
%A M. C. King
%T Linkage of early-onset familial breast cancer to chromosome 17q21
%J Science
%V 250
%N 4988
%P 1684-1689
%M DEC
%D 1990
%K jrnl, MolBio, c1990, c199x, c19xx, zz0414, medicine, health, breast cancer,
   chr17, chr 17, 17q21, BRCA1, BRCA2
%X "Human breast cancer is usually caused by genetic alterations of somatic
   cells of the breast, but occasionally, susceptibility to the disease is
   inherited. Mapping the genes responsible for inherited breast cancer may also
   allow the identification of early lesions that are critical for the
   development of breast cancer in the general population. Chr.17q21 appears to
   be the locale of a gene for inherited susceptibility to breast cancer in
   families with early-onset disease. Genetic analysis yields a lod score
   (log of the likelihood ratio for linkage) of 5.98 for linkage of breast
   cancer susceptibility to D17S74 in early-onset families and negative lod
   scores in families with late-onset disease. Likelihood ratios in favor of
   linkage heterogeneity among families ranged between 2000:1 & greater than
   10(6):1 on the basis of multipoint analysis of four loci in the region."
   -- [<A HREF="http://dx.doi.org/10.1126/science.2270482">doi:10.1126/science.2270482</A>]['14], provided 1st evidence against BRCA1.
      Also see
   "... Researchers have identified hundreds of mutations in the BRCA1 gene,
   many of which assoc. with an increased risk of cancer. Women with an
   abnormal BRCA1 or BRCA2 gene have up to an 80% risk of developing
   breast cancer by age 90 ..."
   -- Brca1@[<A HREF="http://en.wikipedia.org/wiki/Brca1">wikip</A>]['14].

%A H. Herzel
%T Complexity of symbol sequences
%J Syst. Anal. Modl. Simul.
%P 435-444
%V 5
%D 1988
%K MolBio, jrnl, DNA, repeats, repeat, near, compress, compression,
   string, sequence
%X ref in  L o e w e n s t e r n  TR96-51 '96

%A H. Herzel
%A W. Ebeling
%A A. Schmitt
%T Entropies of biosequences: the role of repeats
%J Physical reviews E
%V 50
%D 1994
%P 5061-5071
%K MolBio, jrnl, PR, string, sequence, repeat, DNA, compress, compression, Alu
%X ref in  L o e w e n s t e r n  TR96-51 '96
   Reports that Watson et al, Recombinant DNA, '92,
   estimate that the 300bp Alu seq's, so-called because they can be cut
   with the restriction enzyme AluI, occur 900,000 times in the human genome,
   i.e. form about 9% of the genome.
   [Also search for; DNA ALU].

%A R. Mantegna
%A S. Buldyrev
%A A. Goldberger
%A S. Havlin
%A C.-K Peng
%A M. Simmons
%A H. Stanley
%T Linguistic features of noncoding DNA sequences
%J Physical Review Letters
%V 73
%D 1993
%P 3169-3172
%K MolBio, jrnl, PRL, string, sequence, structure, compress, compression,
   pattern
%X ref in  L o e w e n s t e r n  TR96-51 '96

%A J. J. Austin
%A A. B. Smith
%A R. H. Thomas
%T Palaeontology in a molecular world: the search for authentic ancient DNA
%J Trends in Ecology and Evolution
%P 303-306
%V 12
%N 8
%M AUG
%D 1997
%K jrnl, ecol, evol, MolBio, fossil DNA, ancient, dinosaur bone, Woodward, Cano,
   insect, weevil, beetle, amber, preserved, Jurassic Park
%X survival of DNA to 10,000 to 100,000 years may be possible in favourable
   conditions but longer ... questionable and unproven.  Reviews e.g.
    . Woodward et al, Nature '94 ... possible dinosaur mitochondrial DNA -
      but found in coal seam, 3km down had experienced 90 to 90 deg C
      and turned out to be mammalian contamination.
    . Cano et al, Nature 1993 ... 120-135 million y.o. weevil DNA in amber -
      but "not reproduced, serious doubts".
   [Also search for: MolBio ancient DNA].

%A K. Rice
%A T. Warnow
%T Parsimony is hard to beat
%J Computing and Combinatorics, 3rd Ann. Int. Conf. COCOON 97
%I SpringerVerlag
%S LNCS
%V 1276
%P 124-133
%D 1997
%K conf, MolBio, COCOON97, COCOON3, phylogenetic, family,
   evolutionary, tree, trees, method, zz1297
%X isbn:3-540-63357-X
   claims that the parsimony method is less affected by diameter
   increasing than distance methods of infering family trees.
   [Also search for: phylogenetic tree], [also search for: evolutionary trees].

%A D. Sankoff
%A M. Blancette
%T The median problem for breakpoints in comparative genomics
%J Computing and Combinatorics, 3rd Ann. Int. Conf. COCOON 97
%I SpringerVerlag
%S LNCS
%V 1276
%P 251-263
%D 1997
%K conf, MolBio, genome, matching, translocation, transposition, inversion,
   comparison, genes, sorting by reversals, c1997, c199x, c19xx, zz1297
%X isbn:354063357X.

%A A. O. Schmitt
%A H. Herzel
%T Estimating the entropy of DNA sequences
%J J. Theor. Biol.
%V 1888
%P 369-377
%D 1997
%K MolBio, jrnl, JTB, compress, repeat, repeats
%X see also Herzel '94.
   [Also search for: MolBio DNA entropy].

%A Wen-Lian Hsu
%T On physical mapping algorithms: an error tolerant test for the consecutive
   ones property.
%J 3rd Int. Conf. Computing and Combinatorics
%I SpringerVerlag
%M AUG
%D 1997
%K conf, c1997, c199x, c19xx, MolBio, COCOON, COCOON97, COCOON3, map, mapping,
   C1P, genetic, matrix, clone, STS, YAC, error, errors
%X also look for:   consecutive ones
                    PQ trees

%A D. K. Agrafiotis
%T A new method for analyzing protein sequence relationships based on
   Sammon maps
%J Protein Sci.
%V 6
%P 287-293
%D 1997
%K MolBio, kinase, jrnl
%X get pairwise "distance" between proteins.  Here "based onindividual
   residue similarities".  Project proetins onto 2-D plane
   s.t. pairwise distances are preserved "as closely as possible".

%A N. Goldman
%A J. L. Thorne
%A D. T. Jones
%T Using evolutionary trees in protein secondary structure prediction and
   other comparative sequence analyses.
%J J. Mol. Biol.
%V 263
%P 196-208
%D 1996
%K JMB, MolBio, phylogenetic, protein, tree, HMM

%A P. W. Goldberg
%A M. C. Golumbic
%A H. Kaplan
%A R. Shamir
%T Four strikes against physical DNA mapping
%J J. Comp. Biol.
%V 2
%P 139-152
%D 1995
%K jrnl, JCB, map, maps, genome, NP, NPC, complexity, c1995, c199x, c19xx
%X 4 simplified models of mapping are NP-complete :-(

%A A. G. Murzin
%A S. E. Brenner
%A T. Hubbard
%A C. Chothia
%T SCOP: A structural classification of proteins database for the
   investigation of sequences and structures
%J J. Mol. Biol.
%V 247
%P 536-540
%D 1995
%K JMB, MolBio, jrnl, protein, structure, sequence, c1995, c199x, c19xx,
   secondary, tertiary, family, superfamily, folds, fold, folding,
   SCOP, data base, DB
%X [<A HREF="http://scop.mrc-lmb.cam.ac.uk/scop/ref/1995-jmb-scop.pdf">pdf</A>]['04].
   Also see [<A HREF="http://scop.mrc-lmb.cam.ac.uk/scop/">mrc</A>]['04],
   ... provides a broad survey of all known protein folds, detailed
   information about the close relatives of any particular protein ...
   -- [<A HREF="http://pdb.wehi.edu.au/scop/">wehi mirror</A>[12/1997].

%A R. A. Abagyan
%A S. Batalor
%T Do aligned sequences share the same fold?
%J J. Mol. Biol.
%V 273
%P 355-368
%D 1997
%K JMB, MolBiol, c1997, c199x, c19xx, jrnl, protein, structure, folding,
   similar, homologous, primary, tertiary, prediction, family, zz1297
%X ... sometimes.  Some similar (in seq') proteins have different
   folds and some distant proteins have similar folds!
   -- [<A HREF="https://doi.org/10.1006/jmbi.1997.1287">doi:10.1006/jmbi.1997.1287</A>]['22].

%A B. Maddox
%T Rosalind Franklin: The Dark Lady of DNA
%I HarperCollins
%P 380
%M OCT
%D 2002
%K book, MolBio, DNA, Rosy, structure, double helix, 1953, c1953, Watson, Crick,
   Wilkins, Nobel prize, NobelPrize (not), biology, biol, MolBio, X-ray,
   crystallography, Xray,
   zz0103, c2002, c200x, c20xx, www, woman, women, STEM, scientist, science
%X Rosalind Elsie Franklin (25 July 1920 - 16 April 1958).
   Was she cheated of fair recognition in solving the problem?
   hb about us$30; uk us isbn:0060184078; uk us isbn13:978-0060184070.
   (Also see
   RF@[<A HREF="http://en.wikipedia.org/wiki/Rosalind_Franklin">wikip</A>]['14], and
   50th@[<A HREF="https://doi.org/10.1038/418725a">www</A>]['14].)

%A J. D. Watson
%A M. Gilman
%A J. Witkowski
%A H. Zoller
%T Recombinant DNA
%I Freeman NY
%D 1992
%K book, text, MolBio, bio, biol, molecular biology, gene, genetics
%X H e r z el '94 reports an estimate from this book that the 300bp Alu seq's
   occur 900,000 times in the human genome i.e. for 9% of it.

%A B. Lewin
%T Genes V
%I OUP
%D 1994
%K book, text, OUP, MolBio, GenesV, Genes5, GenesVI, Genes6,
   1994, 1997, bio, biol, molecular biology, gene, genetics, DNA
%X H e r z e l '94 reports from this book that the Alu
      seq's exhibit 87% homolgy to a consensus sequence.
   NB. Genes VI, Feb 1997, 1280pp, stg65, A$147 ('97), uk us isbn:0198577788.

%A P. Green
%T Against a whole-genome shotgun
%J Genome Res.
%V 7
%N 5
%P 410-417
%M MAY
%D 1997
%K perspective, MolBio, c1997, c199x, c19xx, DNA, shotgun sequencing, assembly
%X ['against' as in not supporting.]
   "... any such approach must have as high a probability of success as the
   current one and offer significant advantages (such as decreased cost).
   I argue here that the whole-genome shotgun proposed by Weber and Myers
   satisfies neither condition."
   -- [<A HREF="http://genome.cshlp.org/cgi/content/full/7/5/410">www</A>]['08].

%A C. Woese
%T The universal ancestor
%J Proc. Natl. Acad. Sci. (USA)
%V 95
%N 12
%P 6854-6859
%M JUN
%D 1998
%K PNAS, MolBio, carl, origin, origins, life, evolution,
   c1998, c199x, c19xx, zz0204
%X "A genetic annealing model for the universal ancestor of ... life ...; ...
   ... starts when "genetic temperatures" were very high, cellular entities
   (progenotes) were very simple, and information processing systems were
   inaccurate.  ... As increasingly complex and precise biological structures
   and processes evolved, both the mutation rate and the scope and level of
   lateral gene transfer, i.e., evolutionary temperature, dropped, and the
   evolutionary dynamic gradually became that characteristic of modern cells.
   ... lineages, and so organisms as we know them, did not exist at these early
   stages. The universal phylogenetic tree, therefore, is not an organismal
   tree at its base but gradually becomes one as its peripheral branchings
   emerge. The universal ancestor is not a discrete entity. It is, rather, a
   diverse community of cells that survives and evolves as a biological unit.
   This communal ancestor has a physical history but not a genealogical one.
   Over time, this ancestor refined into a smaller number of increasingly
   complex cell types with the ancestors of the three primary groupings of
   organisms arising as a result."
   -- [<A HREF="http://www.pnas.org/cgi/content/abstract/95/12/6854">pnas</A>][1/'04]

%A D. M. Loewenstern
%A H. M. Berman
%A H. Hirsch
%T Maximum a posteriori classification of DNA structure from sequence
   information.
%J Pacific Symp. Biotech.
%M JAN
%D 1998
%P ?-?
%K conf, MolBio, PSB, Lllama
%X NB. DNA structure
   <A HREF="mailto:loewenst@paul.rutgers.edu">[D.M.L. email]</A> [1/1998]

%A G. S. Michaels
%A D. B. Carr
%A M. Askenazi
%A S. Fuhrman
%A X. Wen
%A R. Somogyi
%T Cluster analysis and data visualization of large-scale gene expression data
%I Pacific Symp. on Biocomputing
%V 3
%P 42-53
%D 1998
%K MolBio, Conf, PSB98, clustering, microarray, micro arrays, zz0401
%X [<A HREF="http://www-smi.stanford.edu/projects/helix/psb98/">proc'</A>]['01]

%T Bioinformatics
%E R. Hofestadt
%E T. Lengauer
%E M. Loffler
%E D. Schomburg
%I SpringerVerlag
%S LNCS
%V 1278
%P 222
%D 1997
%O German Conf. on Bioinformatics, GCB '96, Leipzig, Sept-Oct 1996
%K conf, MolBio, c1997, c199x, c19xx, GCB96
%X 18 papers; us us isbn:3540633707; uk us isbn13:978-3540633709.

%A D. Ertas
%T Lateral separation of macromolecules and polyelectrolytes in
   microlithographic arrays.
%J Phys. Rev. Lett.
%P ?-?
%V ?
%M Feb 16
%D 1998
%K jrnl, separate, DNA, molecular, sorting, fragment, digest, digestion,
   MolBio, zz0298
%X Proposes an etched array of tiny lozenges each about four micrometers long.
   Mixture would be poured into left hand column, light molecules drift right
   more, tend to hit edge of a lozenge and fall down next column where process
   can repeat.  Lightest molecules drift farthest across most columns.
   Paper is theoretical.  Sorted molecules collected from wells at the bottom.
   Reminds one of the little games with ball-bearings and arrays of pins.
   <A HREF="http://cmtw.harvard.edu/~deniz/publications.html">[Ertaz]</A>[1998]

%A J. Lyons-Weiler
%A G. A. Hoelzer
%T Escaping from the Felsenstein zone by detecting long branches in
   phylogenetic data.
%J Molecular Phylogenetics and Evolution
%V 8
%P 375-384
%D 1997
%K MolBio, jrnl, RASA, family, evolutionary, tree, trees, zz0298
%X <A HREF="mailto:weiler@equinox.unr.edu">[email]</A>[1998]
   <A HREF="http://loco.biology.unr.edu/archives/rasa/rasa.html">[www]</A>

%A J. Lyons-Weiler
%A G. A. Hoelzer
%A R. J. Tausch
%T Optimal outgroup analysis
%J Biol. J. of the Linnean Society
%V ?
%P ?-?
%D 1998 (in press)
%K outgroup, rooted tree, family trees, phylogenetic, evolutionary, zz0298
%X <A HREF="mailto:weiler@equinox.unr.edu">[email]</A>[1998]
   <A HREF="http://loco.biology.unr.edu/archives/rasa/rasa.html">[www]</A>

%A E. C. Uberbacher
%A R. J. Mural
%T Locating protein-coding regions in human DNA sequences by a
   multiple sensor neural network approach
%J PNAS
%V 88
%P 11261-11265
%D 1991
%K jrnl, PNAS, MolBio, GRAIL, gene, genes, region,
   find, finding, NN, ANN, zz0300

%A X. Guan
%A E. C. Uberbacher
%T A fast look-up algorithm for detecting repetitive DNA sequences (Abstract)
%J Pacific Symp. Biocomputing
%P 718-719
%M JAN
%D 1996
%K conf, PSB 1, PSB1, PSB96, tandem repeats, microsatellites
%X linear time algorithm, scan DNA, looking for short words repeated
   many times ... uses technique from FLASH
   [~ geometric hashing,  see  C a l i f a n o  &  R i g o u t s o s  '93]
   Purpose seems to be to find such repeats to annotate seq'
   e.g. Human Tissue Plasminogen Activator Gene  K03021 GenBank rel 89
   (RY)* 7170-7225 and (TGATAGA)* 23888-24458,
   (AC)*(TC)* 16910-16961, A* 17107-17132.
   [Also search for: MolBio repetitive DNA].

%A S. F. Altschul
%A T. L. Madden
%A A. A. Schaffer
%A J. Zhang
%A Z. Zhang
%A W. Miller
%A D. J. Lipman
%T Gapped Blast and Psi-Blast: a new generation of protein database search
   programs
%J NAR
%V 25
%P 3389-3402
%D 1997
%K MolBio, jrnl, MolBio, NAR, c1997, c199x, c19xx, zz0498, Psi Blast, PSIBLAST,
   position specific iterated, iterative, sequence, gap, gaps, NIH, NCBI
%X Blast - fast heuristic, looked for words with a hamming distance as
   first cut to define regions of interest.
   New variation allows a small number of blocks, i.e. with gaps
   between them.  New one is faster because (i) they can raise the
   threshhold for an individual block hit and (ii) it requires two hits
   on the same diagonal before looking for an ungapped extension
   so they have been able to tinker with the threshholds.
   PSI - Position Specific Iterated (-Blast).
   See NCBI News Feb '98.
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/BLAST/blast_program.html">at nih</A>][2/'98],
      [<A HREF="http://nar.oupjournals.org/">NAR</A>][12/'01].

%A A. Muller
%A R. M. MacCallum
%A M. J. E. Sternberg
%T Benchmarking PSI-BLAST in genome annotation
%J J. of Molec. Biol.
%V 293
%P 1257-1271
%D 1999
%K jrnl, JMB, MolBio, c1999, c199x, c19xx, PSIBLAST, blast, protein,
   gene finding, find, zz1101
%X -- [<A HREF="http://www.icnet.uk/research/scirep2000/pdf/lif_ster.pdf">pdf</A>[12/'01],
      [<A HREF="http://www.bmm.icnet.uk">bmm icnet</A>][12/'01]
   [Also search for: MolBio PSIBLAST].

%T Biochemical Nomenclature and Related Documents
%E C. Liebecq
%I Portland_Press, London
%P 122-126
%D 1992
%K MolBio, DNA, c1992, c199x, c19xx, IUPAC, ISBMB, terminology, base, bases,
   characters, code, codes, representation, symbol, symbols, purine, pyrimidine,
   RNY, wildcard, wild card, cards, biol, book, Nucleotide, zz0598, alphabet
%X 2nd edn 1992
   n = a,c,g,t;
   h = a,c,t;   v = a,c,g;   d = a,g,t;   b = c,g,t;
   m = a,c;     r = a,g;     w = a,t;     s = c,g;   y = c,t;   k = g,t;
                | R | Y   |
     small 2xH: | A | T/U |   R=puRine={a,g}, Y=pYrimidine={c,t}, N=aNy
     large 3xH: | G | C   |
   The nucleotide wildcard n (any), which represents any base, is used for 3
   purposes: first, it is used to represent that a base is unknown; second, it
   is repeated 10 to 20 times to represent an arbitrarily long gap in a
   sequence between two known segments; third, it is used, as the other
   wildcards typically are, to represent a character that can be substituted
   validly as any base.
   It is likely that, in the future, the n wildcard may be designated as
   representing any valid substitution and a new wildcard `-'
   introduced to indicate an unknown base.
   Additionally, the symbols `+' or `?' may be used to show uncertainty.
   Finally, the symbol `=' is likely to be used in conjunction with an
   integer for a fixed-length space of unknown or uninteresting bases,
   e.g. `=300=' <!-- hugh at cs rmit edu au Hugh Williams 1998 --> .
   Base (bbb): Adenine, Guanine, Cytosine, Thymine, (Uracil).
   Nucleotide: bbb-monophosphate.

%A D. Greenberg
%A S. Istrail
%T The chimeric mapping problem: algorithmic strategies and
   performance evaluation on synthetic genomic data
%J Comp. and Chem.
%V 18
%N 3
%P 207-220
%D 1994
%K MolBio, jrnl, CandC, map, chimera, DNA, sequence assembly problem,
   clone, clones, hybridization
%X authors at Sandia Nat' Labs, Alg's & Discrete Maths Dept., Albuquerque, NM.
   Two optimisation criteria:
   1. minimise the number of chimeric fragments in a solution
   2. minimise the maximum number of fragments per clone in a solution.
   NP-complete of course, but claim `good' solutions in reasonable time
   on artificial test data.

%A A. Krogh
%A M. Brown
%A I. Siara Mian
%A K. Sjolander
%A D. Haussler
%T Hidden Markov models in computational biology: applications to protein
   modelling
%J J. Mol. Biol.
%V 235
%P 1501-1531
%D 1994
%K jrnl, MolBio, JMB, HMM, model, modeling, SiaraMian
%X e.g.  globin family, protein kinase catalytic domain and
   the EF-hand calcium binding motif.
   See also UCSC-CRL-92-23, Haussler et al '92
   [Also search for: MolBio HMM].

%A Y. Sakakibara
%A M. Brown
%A R. Hughey
%A I. S. Mian
%A K. Sjolander
%A R. C. Underwood
%A D. Haussler
%T Stochastic context-free grammars for tRNA modeling
%J NAR
%V 22
%P 5112-5120
%D 1994
%K MolBio, jrnl, NAR, CFG, SCFG, RNA, modelling, model
%X from a ref'; see also JMB '94;  [Also search for: HMM]

%A M. Hammer
%A et al
%T Out of Africa and back again: Nested cladistic analysis of
   human Y chromosome variation
%J Mol. Biol. and Evol.
%V 15
%P 427-???
%D 1998
%K jrnl, MolBio, MBE, c1998, c199x, c19xx, Eve, Adam, Y chromosome,
   Ychromosome, chromosomeY, chr Y, Ychr, chrY, male, Human evolution,
   tree, trees, origins, Africa, zz0798
%X "We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544
   individuals from Africa, Asia, Europe, Oceania, & the New World. Phylogenetic
   analyses of these 9 sites resulted in a tree for 10 distinct Y haplotypes
   with a coalescence time of ~150,000 years. The 10 haplotypes were unevenly
   distributed among human populations: 5 were restricted to a particular
   continent, 2 were shared between Africa & Europe, 1 was present only in the
   Old World, & 2 were found in all geographic regions surveyed. ...  Thus, the
   previously observed high levels of Y chromosomal genetic diversity in Africa
   may be due in part to bidirectional population movements. Finally, a
   comparison of our results with those from nested cladistic analyses of human
   mtDNA & beta-globin data revealed different patterns of inferences for males
   & females concerning the relative roles of population history (range
   expansions) & population structure (recurrent gene flow), thereby adding a
   new sex-specific component to models of human evolution. "
   -- [<A HREF="http://mbe.oxfordjournals.org/cgi/content/short/15/4/427">MBE</A>]['09].
   [Also search for: MolBio Eve human evolution] and
   [also search for: MolBio Adam chrY].

%A P. Underhill
%A et al
%T Detection of numerous Y chromosome biallelic polymorphisms by DHPLC
%J Genome Res.
%V 7
%P 996-???
%D 1997
%K jrnl, MolBio, GR, Eve, Adam, Y chromosome, Ychromosome, chrY, yChr male,
   Human evolution, zz0798
%X ref in New Scientist 11 July 1998, p39.
   [Also search for: MolBio Adam chrY].

%A M. Hammer
%A S. Zegura
%T The role of the Y chromosome in human evolutionary studies
%I Evol. Anthropology
%V 5
%P 116-???
%D 1996
%K jrnl, MolBio, EA, Eve, Adam, Y chromosome, Ychromosome, chrY, yChr male,
   Human evolution, zz0798
%X ref in New Scientist 11 July 1998, p39.
   [Also search for: MolBio Adam chrY] and
   [also search for: MolBio Eve human evolution].

%A J. Kleffe
%A M. Borodovsky
%T First and second moment of counts of words in random texts generated by
   Markov chains
%J Comp. Applic. Biosci.
%V 8
%P 433-441
%D 1992
%K CABIOS, Bioinformatics, MolBio, jrnl, word, string, strings, pattern,
   motif, test, model, models, count, frequency, c1992, c199x, c19xx, zz0101
%X 1st order MMs. (Instances of repetitive words can overlap self.)
   Also see Atteson '98.   (CABIOS became J. B i o i n f o r m a t i c s)

%A K. Atteson
%T Calculating the exact probability of a language-like patterns in
   biomolecular sequences
%J Intell. Sys. Mol. Biol. ISMB98
%W Montreal
%M JUL
%D 1998
%P 17-24
%K Conf, ISMB, ISMB6, ISMB98, MolBio, PROSITE, regular expression, regexp,
   pattern, motif, Markov Model, HMM, string, zz0798
%X ...probability that a random string of a certain length matches a
   regular expression.  ... improves on Kleffe and Langebacker ('90),
   and Sewell and Durbin ('95).
   Takes PROSITE patterns and calc's probabilities in strings to length 2000
   for random seq' iid and also under a first order Markov chain.
   Also see  Kleffe & Borodovsky '92.
   Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].

%A D. P. Yee
%A D. Conklin
%T Automated clustering and assembly of large EST collections
%I Intell. Sys. Mol. Biol. ISMB98
%W Montreal
%M JUL
%D 1998
%P 203-211
%K Conf, ISMB, ISMB6, ISMB98, MolBio, Expressed Sequence Tag, tags, EST,
   REX, cDNA, zz0798
%X ... REX - Recursive Est eXtender - cluster on overlapping bases,
   and assemble contigs into a concensus seq'.
   REX is a fast greedy algorithm.
   ESTs about 300bp. High error rate esp' near 3' end.
   Several EST's can tag same gene.

%A M-F. Sagot
%A E. W. Myers
%T Identifying satellites and periodic repetitions in biological sequences
%J Recomb98
%W New York
%P ??-??
%M MAR
%D 1998
%K conf, recomb2, recomb98, recomb 98, MolBio, repeat, repetitive,
   repetition, DNA, tandem, satellite, finding, Marie-France Sagot, zz0898
%X ... identifying sat's in DNA seq's.
   ... repeats in numbers between 30 and 1,000,000 copies whose
   lengths vary from 2 to hundreds of bases and appear,
   with some mutations, in TANDEM along the seq'.
   Here concentrate on short (up to 40-bp) approx' tandem repeats.
   1) filter eliminates region that do not contain a sat' with prob
      l.t. 1 in 10000.   O(n) time.
   2) exhaustive explor'n of space of all models for the
      repeating units present in the remaining regions.
      O(n.N(e,k)) time, k is len' of rep' unit, e=floor(epsilon.k)
        where N(e,k) is max num of words that have no
        more than e differences from another word of length k  (e.g. e=k/5).
      In practice usually faster than worst case.
   Author1: service d'Informatique, Institut Pasteur. ['98]
   Recomb[<A HREF="http://www.mssm.edu/biomath/recomb98/recomb98.html">1998</A>].
   [Also search for: repetitive DNA].

%A M-F. Sagot
%T Spelling approximate repeated or common motifs using a suffix tree
%J LATIN98
%P ??-??
%M ???
%D 1998
%K conf, LATIN 98, LATIN98, Marie-France Sagot, repeats, repetitive, motif,
   trees, zz0898
%X alg1: extract repeated motifs from a seq'.  Motif must occur
     a min of q times with at most e mismatches each time.
   alg2: N distinct seq's. Find motifs common to the seq's.
   In both cases, build suffix tree of the seq'(s),
   use tree to ``spell'' the valid models.
   Time O(n N^2 V(e,k))   space O(n N^2 / w)
    where n is (avg) seq' length, k is length of longest possible models,
    w is the size of a word machine, V(e,k) is num of words within Hamming
    distance k of another word of length k.
   Improves an algorithm of Waterman et al ('84).
   Author: Service d'Informatique, Institut Pasteur ['98]

%A S. F. Altschul
%A B. W. Erickson
%T Significance of nucleotide sequence alignments: a method for random
   sequence permutation that preserves dinucleotide and codon usage
%J Mol. Biol. Evol.
%V 2
%N 6
%P 526-538
%D 1985
%K MBE, MolBiolEvol, jrnl, c1985, c198x, c19xx, MolBiol, shuffle, randomise,
   randomize, shuffling, DNA, codon bias
%X choose random dinu' and codon preserving permutations ... graph theory ...
   ... generating random Eulerian walks in a directed multigraph
   after F i t c h, JMB, '83..
   -- [<A HREF="http://www.molbiolevol.org/cgi/content/abstract/2/6/526">pdf</A>][9/'01]
   (Also see  A l l i s o n  et al, [<A HREF="http://dx.doi.org/10.1093/comjnl/42.1.1">doi:10.1093/comjnl/42.1.1</A>], and
   -- [<A HREF="http://allisons.org/ll/Publications/2004AI/">LNCS 3339</A>], for a more general method.)

%A D. J. Lipman
%A W. J. Wilbur
%A T. F. Smith
%A M. S. Waterman
%T On the statistical significance of nucleic acid similarities
%J Nucl. Acids. Res.
%V 12
%N 1
%P 215-226
%M JAN
%D 1984
%K NAR, jrnl, c1984, c198x, c19xx,  MolBio, DNA, sequence alignment, codon bias

%A E. H. Blackburn
%T Telomeres: do the ends justify the means?
%J Cell
%V 37
%N 1
%P 7-8
%M MAY
%D 1984
%K jrnl, MolBio, c1984, c198x, c19xx, zz0923, chromosomes, telomere, telomerase,
   length, aging, ageing, woman, women, STEM, www, Nobel prize, Physiology,
   Medicine, Australian, scientist
%X -- [<A HREF="https://doi.org/10.1016/0092-8674(84)90295-2">doi:10.1016/0092-8674(84)90295-2</A>]['23].
   EB@[<A HREF="https://en.wikipedia.org/wiki/Elizabeth_Blackburn">wikip</A>]['23].
   EB@[<A HREF="https://orcid.org/0000-0002-4885-0544">orcid:0000-0002-4885-0544</A>]['23].
   Note, EB was awarded the 2009 Nobel Prize for Physiology or Medicine,
   shared with Carol W. Greider & Jack W. Szostak.
   Also see EB@[<A HREF="https://profiles.ucsf.edu/elizabeth.blackburn">ucsf</A>]['23].

%A W. M. Fitch
%T Random sequences
%J J. Molec. Biol.
%V 163
%P 171-176
%D 1983
%K JMB, jrnl, c1983, c198x, c19xx, MolBio, string, sequence, generate, 0order,
   1order, order0, order1, Markov model, shuffle, shuffling, DNA
%X points out (attributed to R. Brualdi) that a seq can be shuffled
   while preserving the 1st-order Markov Model (M.M.) stat's
   by generating  E u l e r i a n - C y c l e s  of a simple multi-graph.
   (Unfortunately the paper refers to the 1st-order M.M. stat's of the seq
    by the phrase ``nearest neigh'r stat's'' which clashes with
    current terminology in clustering.)
   Extended by Altschul and Erickson MBE v2 '85.
   [Pity F' didn't know about  B o u l t o n  and  W a l l a c e  in
    J. Theor. Biol. V23 pp269-278 '69 on the discrete distribution
    w.r.t. 0-order M.M. stat's].
   [Also search for: MolBio shuffling] and [also search for: Malign MML MolBio].

%T Yeast Gene Analysis
%E A. J. P. Brown
%E M. F. Tuite
%I AcademicPress
%S Methods in Microbiology
%V 26
%P 544
%D 1998
%K MolBio, book, text, Yeast, genes, genome, YAC, DNA, PEG,
   saccharomyces cerevisiae, zz0998
%X au$100; uk us isbn:0121366553; uk us isbn13:978-0121366551.

%A E. Birney
%A R. Durbin
%T Dynamite: a flexible code generating language for dynamic programming
   methods used in sequence comparison.
%J ISMB '97
%P 56-64
%D 1997
%K conf, MolBio, ISMB97, DPA, alignment
%X Given a FSM, generates code for an instance of the DPA.
   (More on FSMs [<A HREF="http://www.allisons.org/ll/Bioinformatics/">here</A>].)

%A I. Holmes
%A R. Durbin
%T Dynamic programming alignment accuracy
%J J. Comput. Biol.
%V 5
%N 3
%P 493-504
%D 1998
%K jrnl, JCB, DPA, MolBio, c1998, c199x, c19xx
%X (See also: Y e e  and  A l l i s o n,  'Reconstructionn of Strings Past',
              CABIOS (Bioinformatics) 9(1) pp.1-7, '93,
   for a look at the accuracy with which the parameters of a model
   of mutation (e.g. pr(mismatch), gap penalty etc.) can be estimated
   without systematic statistical bias over a very wide range of similarity,
   -- [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">alignment</A>].)

%A J. V. Braun
%A H-G. Muller
%T Statistical methods for DNA sequence segmentation
%J Stat. Sci.
%V 13
%N 2
%P 142-162
%D ?
%K jrnl, segment, region, regions, analysis,
   change point, banding, hidden Markov chain, model, HMM, zz1198
%X ... suitable version of the multiple change-point probelm, and ...
   ... application of split local polynomial fitting. ...
   examples use bacteriophage Lambda.  <!-- via Dean McK --> .

%A J-M. Claverie
%T Identifying coding exons by similarity search: Alu-derived and
   other potentially misleading protein sequences.
%J Genomics
%V 12
%P 838-841
%D 1992
%K MolBio, jrnl, sequence, exon, recognition, cDNA, Alu, false, match, zz0199
%X ... report a set of protein sequences exhibiting high local similarity
   to Alu repeat or vector sequences. These entries can lead to misleading
   interpretations of similarity searches.
   10 refs,  author (then) at NCBI, NLM, NIH

%A J-M. Claverie
%T A streamlined random sequencing strategy for finding exons
%J Genomics
%V 23
%P 575-581
%D 1994
%K MolBio, jrnl, shotgun, sequence assembly problem, DNA, genome, project,
   large scale, sequencing, overlap, overlaps, overlapping, M13, exon,
   vertebrate exons, contig, zz0199
%X ... [usually] candidate gene region partitioned onto 15K-20Kb pieces ...
   themselves randomly subcloned into M13 prior to sequencing with
   6 to 8-fold redundancy.  ...   Given the small average size of vertebrate
   exons, I show here that they can be detected from the computer analysis of
   the individual runs, much before completion of contiguity.
   ... [depends on] new sequence masking techniques.  ...
   [new] streamlined technique requires only 2 to 2.5-fold redundancy,
   can dispense with subcloning ...
   p578: ... [can identify exons while being] able to dispense with contig
         assembly ...
   Author (then) at NCBI, NLM, NIH

%A R. B. Altman
%T A curriculum for bioinformatics: The time is ripe (editorial)
%J J. Bioinformatics
%V 14
%N 7
%P 549-550
%D 1998
%K jrnl, MolBio, computational biology, CABIOS, zz0199, c1998, c199x, c19xx,
   curriculum, course, courses, teaching, bioinformatics, syllabus
%X NB. jrnl was called Comp Appl in BioSci's (CABIOS) until 1998.
   <A HREF="mailto:altman@smi.stanford.edu">[email]</A>

%A D. Gusfield
%T Algorithms on Strings, Trees and Sequences: Computer Science and
   Computational Biology
%I CUP
%P 554
%M MAY
%D 1997
%K MolBio, bioinformatics, book, text, c1997, c199x, c19xx, string, tree,
   sequence, CS, CSci, CUP, computing, algorithm, algorithms, bioinformatics
%X 1st ed 1997, hb us$66; uk us isbn:0521585198; uk us isbn13:978-0521585194.
   [Also search for: MolBio book].

%A J. Setubal
%A J. Mendianis
%T Introduction to Computational Molecular Biology
%I PWS Pub. Co.
%D 1997
%K MolBio, book, c1997, c199x, c19xx, bioinformatics, text, algorithms
%X ref in  A l t m a n,  Bioin'tics p550 '98
   [Also search for: MolBio book].

%A P. Baldi
%A S. Brunak
%T Bioinformatics: The Machine Learning Approach
%I MITpress
%S Adaptive Computation and Machine Learning
%P 400
%D 1998
%K book, text, c1998, c199x, c19xx, MolBio, AI, ML
%X ref in  A l t m a n,  Bioin'tics p550 '98
   2nd edn. c2001; uk us isbn:026202506X; uk us isbn13:978-0262025065.
   7x9, 400pp., 72 illus.;

%A R. Durbin
%A S. Eddy
%A A. Krogh
%A G. Mitchison
%T Biological Sequence Analysis: Probabilistic Models of Proteins and
   Nucleic Acids
%I CUP
%P 350
%D 1998
%K MolBio, book, CUP, c1998, c199x, c19xx, text, bioinformatics, DNA, protein,
   sequence, analysis, model
%X ref in  A l t m a n,  Bioin'tics p550 '98.
   1st ed 1998, hb us$80; uk us isbn:0521620414; uk us isbn13:978-0521620413;
   pb us$45; uk us isbn:0521629713; uk us isbn13:978-0521629713;
   -- [<A HREF="mailto:eddy OF genetics.wustl.edu">eddy@</A>]['00].
   [Also search for: MolBio book].

%A S. Salzberg
%A et al
%T Computational Methods in Molecular Biology
%I Elsevier Sci. N.Y.
%D 1998
%K MolBio, book, bioinformatics, text
%X ref in  A l t m a n,  Bioin'tics p550 '98

%A P. Baldi
%A S. Brunak
%A Y. Chauvin
%A A. Krogh
%T Naturally occurring nucleosome positioning signals in human exons and introns
%J J. Mol. Biol.
%V 263
%P 503-510
%D 1996
%K MolBio, JMB, jrnl, exon, intron

%A Xiao-Li Meng
%T The EM algorithm and medical studies: a historical link
%J Stat. Methods in Medical Res.
%V 6
%P 3-23
%D 1997
%K jrnl, c199c, c199x, c19xx, statistics, EM
%X [Also search for: EM algorithm].

%A F. d'Errico
%A et al
%T Neanderthal acculturation in western Europe?
%J Current Anthropology
%V 39S (?)
%P S1 (?)
%D 1998
%K jrnl, c1998, c199x, c19xx, Neanderthal, Neandertal, early man, cro-magnon,
   cromagnon, ancient, dErrico
%X ref in New Sci' #2191 p46 19 Jun '98;  says v39S pS1 could it be v395 p51?

%A G. Clark
%T Modern human origin
%J Science
%V 283
%P 2029
%D 1999
%K jrnl, c1999, c199x, c19xx, early man, cro-magnon, cromagnon,
   Neanderthal, Neandertal, ancient
%X ref in New Sci' #2191 p46 19 Jun '98

%A M. Wolpoff
%T Concocting a divisive theory
%J Evol. Anthropology
%V 7
%P 1
%D 1998
%K jrnl, c1998, c199x, c19xx, early man, cro-magnon, cromagnon, Neanderthal,
   Neandertal, ancient
%X ref in New Sci' #2191 p46 19 Jun '98

%E G. Clark
%E C. Willermet
%T Conceptual Issues in Modern Human Origins Research
%I Aldine_de_Gruyter NY
%D 1997
%K book, c1997, c199x, c19xx, early man, cro-magnon, cromagnon, Neanderthal,
   Neandertal, ancient
%X ref in New Sci' #2191 p46 19 Jun '98

%A B. Rost
%T Twilight zone of protein sequence alignments
%J Protein Eng., Design and Seln
%V 12
%N 2
%P 85-94
%M FEB
%D 1999
%K jrnl, MolBio, c1999, c199x, c19xx, zz0521, protein, sequence, alignment,
   twilight zone
%X "Seq. al. unambiguously distinguish between protein pairs of similar and
   non-similar structure when the pairwise seq. identity is high (> 40% for long
   alignments). The signal gets blurred in the twilight zone of 20-35% seq.
   identity. Here, more than a million seq. al. were analysed ..."
   -- [<A HREF="https://doi.org/10.1093/protein/12.2.85">doi:10.1093/protein/12.2.85</A>]['21].
   (NB. sequence *identity*.)
   [Also search for: MolBio protein alignment].

%T Pattern Discovery in Biomolecular Data: Tools, Techniques and Applications
%E J. T. L. Wang
%E B. A. Shapiro
%E D. Shasha
%I OUP
%D 1999
%K MolBio, bioinformatics, book, text, c1999, c199x, c19xx, OUP, zz0999
%X part 1: sequences;   part 2: 3D structure;   part 3: System components.
   hb; uk us isbn:0195119401; uk us isbn13:978-0195119404.
   -- [<A HREF="http://www.cis.njit.edu/~jason/publications/biopat.html" TARGET="WSSbook">www</A>]['99].

%A A. Abbott
%T A post-genomic challenge: learning to read patterns of protein synthesis
%J Nature
%V 402
%P 715-720
%M DEC
%D 1999
%K MolBio, proteomics, proteome, introduction, bioinformatics, genome
%X a Nature "news briefing".

%A R. Agarawala
%A V. Bafna
%A M. Farach
%A B. Narayanan
%A M. Paterson
%A M. Thorup
%T On the approximability of numerical taxonomy:
   Fitting distances by tree metrics.
%J Proc. 7th ACM-SIAM Symp. on Discrete ALg's.
%P 365-372
%I ACM
%D 1996
%K conf, family, phylogenetic, evolutionary, tree, trees, zz0200
%X ref in  F a r a c h  and K'  '98

%A M. Farach
%A S. Kannan
%T Efficient algorithms for inverting evolution
%J JACM
%V 46
%N 4
%P 437-449
%D 1999
%K jrnl, JACM, ACM, family, evolutionary, phylogenetic, tree, trees,
   distance, metric, MolBio, zz0200
%X Aim is to find a tree, labelled with mutation probabilities, which
   gives a probability distribution over (leaf) character vectors
   that is close to the observed distribution (given a mult'ple al'gnment
   of the sequences).   Papers uses 2-state {0,1} alphabet, with
   the promise of multi (i.e. 4 or 20) states to come.
   -- [<A HREF="http://doi.acm.org/10.1145/320211.320212">doi:10.1145/320211.320212</A>]['09].

%A M. Kanehisa
%T Post-Genomic Informatics
%I OUP
%M JAN
%D 1999
%P 176
%K book, text, bioinformatics, MolBio, Bio, Biol, genome, genomics, OUP, zz0300
%X pb; uk us isbn:0198503261; uk us isbn13:978-0198503262; stg20 ppb, au$51.

%A W. Feldman
%A P. A. Pevzner
%T Gray code masks for sequencing by hybridization
%J Genomics
%V 23
%P 233-235
%D 1994
%K jrnl, MolBio, mask, SBH, DNA, sequence, uniform map, maps,
   micro array, arrays, microarrays

%A S. Fodor
%A J. L. Read
%A M. C. Pirrung
%A L. Stryer
%A A. Tsai Lu
%A D. Solas
%T Light-directed spatially addressable parallel chemical synthesis
%J Science
%V 251
%P 767-773
%D 1991
%K jrnl, MolBio, mask, masks, microarray, microarrays, micro array, arrays,
   VLSIPS, very large scale immobilized polymer synthesis

%A S. Singh-Gasson
%A R. D. Green
%A Y. Yue
%A C. Nelson
%A F. Blattner
%A M. R. Sussman
%A F. Cerrina
%T Maskless fabrication of light-directed oligonucleotide microarrays using
   a digital micromirror array.
%J NatureBiotech.
%V 17
%P 974-978
%D 1999
%K jrnl, MolBio, mask, DNA, micro mirror, mirrors

%A E. M. Southern
%T DNA Chips: analysing sequence by hybridization to oligonucleotides on a
   large scale.
%J Trends in Genetics
%V 12
%P 110-115
%K jrnl, MolBio, microarray, microarrays, micro array, arrays,
   sequencing, SBH, Eulerian path, paths
%X [Also search for: microarray].

%A F. Preparata
%A A. Frieze
%A E. Upfal
%T Optimal reconstruction of a sequence from its probes
%J J. Comput'l Biology
%V 6
%N 3-4
%P 361-368
%D 1999
%K jrnl, JCB, SCSS, probe, sequencing by hybridization, SBH

%A M. Kozak
%T The scanning model for translation: an update
%J J. Cell. Biol.
%V 108
%P 229-241
%D 1989
%K jrnl, MolBio, ORF, TIS, transcription, transcribe, start, initiate, site,
   sites, scan, DNA, cDNA
%X from a ref'

%A J. Setubal
%A J. Meidanis
%T Introduction to Computational Molecular Biology
%I Brooks-Cole
%P 320
%M JAN
%D 1997
%K MolBio, book, Bioinformatics, computing, algorithms, text,
   c1997, c199x, c19xx, zz0800
%X from basic concepts to assembly, mapping, to structure predn
   hb; uk us isbn:0534952623; uk us isbn13:978-0534952624.
   [Also search for: MolBio book].

%T DNA Microarrays
%E M. Schena
%I OUP
%S Practical Approach Series
%P 232
%M JUN
%D 1999
%K book, text, OUP, c1999, c199x, c19xx, PAS, MolBio, bioinformatics, bio,
   biol, molecular biology, micro array, arrays, microarray, zz0008
%X 1999, pb; uk us isbn:0199637768; uk us isbn13:978-0199637768.

%A R. Guigo
%A S. Knudsen
%A N. Drake
%A T. Smith
%T Prediction of gene structure
%J J. Molec. Biol.
%V 26
%D 1992
%P 141-157
%K MolBio, jrnl, JMB, find, finding, GeneID, GenID
%X a ref in  S a l z b e r g  et al '96.

%A A. Dalby
%A J. G. Nourse
%A W. D. Hounshell
%A A. K. I. Gushurst
%A D. L. Grier
%A B. A. Leland
%A J. Laufer
%T Description of several chemical file formats used by computer programs
   developed at Molecular Design Limited
%J J. of Chemical Information and Computer Sciences
%P ?
%D 1992
%K jrnl, JCICS, c1992, c199x, c19xx, format, chemical, chemistry, chem, science

%A C. Chothia
%T One thousand families for the molecular biologist
%J Nature
%V 357
%P 543-544
%M JUN
%D 1992
%K news, MolBio, c1992, c199x, c19xx, protein, family, families, fold, folds,
   structure, tertiary, 3D, how many
%X "... [from] papers published over the past few months ... estimate ...
   suggest that the large majority of proteins come from no more than
   one thousand [protein] families. ...
   Assuming there is no strong bias in the databanks[!], and that the
   seq.comparisons give an accurate picture of family membership [then]
   1500 different protein families. ...  If we assume that the seq.comps.
   find 80% of related proteins [then #] familes drops to 1000. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/357543a0">doi:10.1038/357543a0</A>]['11].
   [Also search for: MolBio protein family].

%A A. G. Murzin
%A A. M. Lesk
%A C. Chothia
%T Beta-Trefoil fold. Patterns of structure and sequence in the Kunitz
   inhibitors interleukins-1 beta and 1 alpha and fibroblast growth factors
%J JMB
%V 223
%P 531-543
%D 1992
%K JMB, MolBio, jrnl, AMLesk, c1992, c199x, c19xx, beta trefoil, barrel,
   protein, secondary, structure, 3D
%X "... Erythrina caffra and wheat, the interleukins-1 beta and 1 alpha and the
   acidic and basic fibroblast growth factors have shown that they contain a
   most unusual fold. It is formed by six two-stranded hairpins. Three of these
   form a barrel structure and the other three are in a triangular array that
   caps the barrel. The arrangement of the secondary structures gives the
   molecules a pseudo 3-fold axis. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0022-2836(92)90668-A">doi:10.1016/0022-2836(92)90668-A</A>]['11],
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/1738162">ncbi</A>]['11].

%A S. J. Prestrelski
%A D. M. Byler
%A M. N. Liebman
%T Generation of a substructure library for the description and classification
   of protein secondary structure.  II. Application to spectra-structure
   correlations in Fourier transform infrared spectroscopy
%J Proteins
%V 14
%N 4
%P 440-450
%M DEC
%D 1992
%K jrnl, MolBio, c1992, c199x, c19xx, protein tertiary structure, spectra,
   spectrum, secondary
%X "Fourier transform infrared spectroscopy has become well known as a sensitive
   and informative tool for studying secondary structure in proteins. Present
   analysis of the conformation-sensitive amide I region in protein infrared
   spectra, when combined with band narrowing techniques, provides more
   information concerning protein secondary structure than can be meaningfully
   interpreted. This is due in part to limited models for secondary structure.
   Using the algorithm described in the previous paper of this series, we have
   generated a library of substructures for several trypsin-like serine
   proteases. This library was used as a basis for spectra-structure
   correlations with infrared spectra in the amide I' region, for five
   homologous proteins for which spectra were collected. Use of the substructure
   library has allowed correlations not previously possible with template-based
   methods of protein conformational analysis."
   -- [<A HREF="http://dx.doi.org/10.1002/prot.340140405">doi:10.1002/prot.340140405</A>]['11].

%A M. Burset
%A R. Guigo
%T Evaluation of gene structure prediction programs
%J Genomics
%V 34
%N 3
%P 353-367
%D 1996
%K MolBio, jrnl, c1996, c199x, c19xx, find, finding, survey
%X a ref in  S a l z b e r g  et al '96.
   (Beware defn of 'specificity' v. usual ROC;  [also search for: ROC defn].)

%A J. Henderson
%A S. Salzberg
%A K. Fasman
%T Finding genes in human DNA with a hidden Markov model
%J J. Comput. Biol
%V 4
%N 2
%P 127-141
%D 1997
%K jrnl, MolBio, VEIL, gene, find, finding
   -- [<A HREF="http://www.tigr.org/~salzberg/veil.ps.gz">www</A>][8/'00]
   See also   G l i m m e r   and   M O R G A N   in the context of MolBio.

%A G. Hutchinson
%A M. Hayden
%T The prediction of exons through an analysis of spliceable open
   reading frames
%J NAR
%V 20
%P 3453-3462
%D 1987
%K MolBio, jrnl, NAR, SORFIND, ORF, ORFs, gene, find, finding

%A D. Kulp
%A D. Haussler
%A M. G. Reese
%A F. H. Eeckman
%T A generalized hidden Markov model for the recognition of human genes in DNA
%J ISMB-96
%P 134-141
%I AAAI Press
%D 1996
%K conf, MolBio, ISMB 96, ISMB96, ISMB4, HMM,  Genie, gene find, finding
%X [<A HREF="http://linkage.rockefeller.edu/wli/gene/g-ismb96-k.html">abs'</A>][8/'00].

%A V. Solovyev
%A A. Salamov
%A C. Lawrence
%T Predicting internal exons by oligonucleotide composition and discriminant
   analysis of spliceable open reading frames
%J NAR
%V 22
%P 5156-5163
%D 1994
%K jrnl, NAR, MolBio, FGENEH, exon, intron, ORF, gene, find, finding
%X ref in  S a l z b e r g '98

%A Y. Xu
%A R. Mural
%A E. Uberbacher
%T Constructing gene models from accurately predicted exons: an application of
   dynamic programming.
%J Comput. Appl. in the Biosci.
%V 10
%N 6
%P 613-623
%D 1994
%P 613-623
%K MolBio, jrnl, BioInf, CABIOS, find, finding, Gap III, Gap3, GRAIL
%X also see Xu, Uberbacher, '91, ..., '97, ...

%A E. L. Hartland
%A S. Green
%A W. Phillips
%A R. Robins-Browne
%T Essential role of YopD in inhibition of the respiratory burst of macrophages
   by Yersinia enterocolitica
%J Infect. Immun.
%V 62
%P 4445-4453
%D 1994
%K jrnl, MolBio, c1994, c199x, c19xx, YopD, macrophage, Yersinia enterocolitica,
   microbiol, uniMelb
%X [<A HREF="http://www.microbiol.unimelb.edu.au/people/hartland/pub.html">auth1</A>]['09].

%A D. V. Laurents
%A S. Subbiah
%A M. Levitt
%T Different protein sequences can give rise to highly similar folds through
   different stabilizing interactions
%J Potein Sci.
%V 3
%N 11
%P 1938-1944
%M NOV
%D 1994
%K jrnl, MolBio, c1994, c199x, c19xx, protein, structure, alignment, CTF, L7,
   ovomucoid
%X "... interesting case of struct.similarity between 2 small, nonhomologous
   proteins, the third domain of ovomucoid ... & the C-terminal fragment of
   ribosomal L7/L12 protein (CTF). The region of sim. consists of a 3-stranded
   beta-sheet & an alpha-helix. ... the corr. elements of secondary struct.
   share a common topology, & the RMS difference for 'equivalent' Ca atoms is
   1.6A. Surprisingly, this common struct. arises from completely different
   seqs.. For the common core, the seq.identity is < 3%, & there is neither
   sig. seq.similarity nor similarity in the posn or orientation of conserved
   hydrophobic residues. This superposition raises the question of how 2
   entirely different seqs. can produce an identical structure. Analyzing this
   common region in ovomucoid revealed that it is stabilized by disulfide bonds.
   In contrast, the corresponding structure in CTF is stabilized in the
   alpha-helix by a composn of residues with high helix-forming propensities.
   ... suggests that different seqs. & different stabilizing interactions can
   produce an identical structure."
   -- [<A HREF="http://dx.doi.org/10.1002/pro.5560031105">doi:10.1002/pro.5560031105</A>]['13].
   [Also see: MolBio protein structure alignment].

%A P. H. Williams
%A K. J. Gaston
%A C. J. Humphries
%T Do conservationists and molecular biologists value differences between
   organisms in the same way?
%J Biodiversity Letters
%V 3
%P 67-78
%M MAY
%D 1994
%K jrnl, biol, diversity, c1994, c199x, c19xx, MolBio, ecology,  biodiversity,
   measure, currency, morphology, ecosystem, evolutionary, tree, trees
%X "...proponents of the idea of including weightings for species
   `distinctiveness' in biodiversity measures for conservation priorities have
   been quick to adopt genetic attribute richness as the `currency' of value to
   be maximized. However depending on how this is measured, the consequences of
   this choice may be at odds with the aims of biodiversity conservation,
   bringing into question whether choice of another currency might be more
   appropriate.  Among the candidates, morphological attributes most strongly
   influence the popular perception of diversity (because they are amenable to
   the senses) & may be most directly useful to the people. On the other hand,
   functional, ecological attributes may be more relevant to the goal of
   maintaining ecosystem services. In practice, the direct use of these
   currencies is usually prevented by the enormous sampling effort required for
   adequate direct measurement. Instead, the challenge is to improve on
   unweighted species richness as a measure of diversity, but using the best
   information on differences among organisms that is actually available in any
   particular case. Thus, using only the near-universal taxonomic class'n for
   multicellular organisms, useful indirect measures of genetic or morphological
   attribute richness can be identified, although the precise choice of measure
   depends on whether or not users are prepared to assume `clock'-like patterns
   of attribute change."
   -- [<A HREF="http://links.jstor.org/sici?sici=0967-9952%28199405%292%3A3%3C67%3ADCAMBV%3E2.0.CO%3B2-T">jStor</A>]['05]
   -- [<A HREF="http://www.nhm.ac.uk/entomology/staffpages/pwilliams.html">~williams</A>]['05]

%A Y. Xu
%A R. Mural
%A J. Einstein
%A S. Shah
%A E. Uberbacher
%T Grail: A multi-agent neural network system for gene identification
%J Proc. IEEE
%V 84
%N 10
%D ? 1997 ? (v4 = '77)
%P 1544-1552
%K jrnl, IEEE, gene, find, finding, MolBio, NN, ANN, GRAIL

%A Y. Xu
%A E. Uberbacher
%T Automated gene identification in large scale genomic sequences
%J J. Comput. Biol.
%V 4
%P 325-338
%D 1997
%K jrnl, JCB, MolBio, find, finding, zz1000
%X ref in  C a i, et al '00

%A E. E. Snyder
%A G. D. Stormo
%T Identifying of coding regions in genomic DNA
%J J. Molec. Biol.
%V 248
%P 1-18
%D 1995
%K jrnl, MolBio, JMB, GeneParser, Gene Parser, genes, find, finding

%A E. W. Myers
%T Toward simplifying and accurately formulating fragment assembly
%J J. of Computational Biology
%V 2
%P 275-290
%D 1995
%K jrnl, MolBio, JCB, c1995, c199x, c19xx, shotgun, sequence, assembly,
   assembler, assembling, string graph, stringGraph
%X "...reconstr. a DNA seq. from a collection of randomly sampled frags.. Trad.
   the objective of this problem has been to produce the shortest string that
   contains all the fragments as substrings, but in the case of repetitive
   target seqs. this objective produces answers that are overcompressed. [Here]
   reformulated as finding a max.-LH reconstruction with respect to the 2-sided
   Kolmogorov-Smirnov stat. ... argued that this is a better formulation of the
   problem. Next the frag.ass.problem is recast in graph-theoretic terms as
   ...finding a non-cyclic subgraph with certain properties .... . Finally, a
   series of graph redn trans. are given that dramatically reduce the size of
   the graph to be explored in practical inst. of the problem. ... v.important
   as the underlying problems are NP-hard. In practice, the trans.problems are
   so small that simple branch-and-bound algs. successfully solve them, thus
   permitting aux. experimental info. to be taken into a/c in the form of
   overlap, orientation, & distance constraints."
   [Also search for: MolBio stringGraph] and
   [also search for: MolBio sequence assembly].

%A E. Lander
%A L. Kruglyak
%T Genetic dissection of complex traits: guidelines for interpreting and
   reporting linkage results
%J Nature Genetics
%V 11
%P 241-247
%D 1995
%K jrnl, MolBio, c1995, c199x, c19xx, zz0514, gene, genes, genetic linkage,
   trait, stats, significance, errors, false, intro
%X "Genetic studies are under way for many complex traits, spurred by the recent
   feasibility of whole genome scans. Clear guidelines for the interpretation of
   linkage results are needed to avoid a flood of false positive claims. At the
   same time, an overly cautious approach runs the risk of causing true hints of
   linkage to be missed. We address this problem by proposing specific standards
   designed to maintain rigor while also promoting communication." [38 refs.]
   -- [<A HREF="http://dx.doi.org/10.1038/ng1195-241">doi:10.1038/ng1195-241</A>]['14].

%A M. J. Gardner
%A H. Tettelin
%A D. J. Carucci
%A et al
%T Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum
%J Science
%V 282
%N 5391
%P 1126-1132
%M NOV
%D 1998
%K MolBio, c1998, c199x, c19xx, chromosome two, chr2, chr II 2, chrII, DNA
%X [<A HREF="http://www.sciencemag.org/cgi/content/full/282/5391/1126">www</A>][1/01]
   ... Approximately 300 million to 500 million people are infected annually,
   and 1.5 million to 2.5 million lives are lost to malaria each year, ...
   ... Of the four species ... [p.f.] is the greatest cause of
   morbidity and mortality. ...
   [Also search for: Plasmodium falciparum].

%T World malaria situation in 1994 - Part I 269
%J Weekly Epidemiological Record
%I World Health Organization (WHO)
%V 72
%N 36
%P 269-274
%M 5 SEP
%D 1997
%K malaria, disease, WHO, WER, wkly, rec, MolBio, quote, quotable,
   statistics, cases, numbers, death rate, rates, infection, infected, zz0901
%X 300 to 500 million clinical cases and
   1.5 to 2.7 million deaths annually.
   ... tropical Africa est' to account for 90% of "incidence and
   the great majority of deaths."
   -- [<A HREF="http://www.who.int/wer/pdf/1997/wer7236.pdf">72(36) pdf</A>][9/'01]
   -- [<A HREF="http://www.who.int/wer/72_27_52.html">72(27-52)</A>][9/'01]
   -- [<A HREF="http://www.who.int/wer/">wer</A>][9/'01]

%A S. Salzberg
%A A. Delcher
%A S. Kasif
%A O. White
%T Microbial gene identification using interpolated Markov models
%J NAR
%V 26
%N 2
%P 544-548
%D 1998
%K Glimmer, MolBio, jrnl, NAR, microbe, gene, genes, find, finder, finding,
   model, HMM, c1998, c199x, c19xx, zz0800
%X .ps :- <A HREF="http://www.tigr.org/~salzberg/glimmer.html">[www]</A>[8/'00]
   See also   M O R G A N  1 9 9 8.

%A S. Salzberg
%A A. Delcher
%A K. Fasman
%A J. Henderson
%T A decision tree system for finding genes in DNA
%J J. Comput. Biol.
%V 5
%N 4
%P 667-680
%D 1998
%K jrnl, JCB, MolBio, MORGAN, trees, classification, gene, find, finder, zz0900
%X d' tree uses new method  to id' start codons, donor sites, acceptor sites,
   ... frame sensitive dyn' prog' alg' for finding exons/ introns, ... .
   ... optimal segmentation depends on scoring function ...  ~prob' is an exon
   ... The scoring functions are sets of d' trees.
   .ps :- <A HREF="http://www.tigr.org/~salzberg/morgan.html">[www]</A>[8/'00]
   See also  G l i m m e r  1 9 9 8.

%A H. E. Helson
%T Structure diagram generation
%J Rev. Comput. Chem.
%E Lipkowitz, K. B. and Boyd, D. B.
%I Wiley-VCH
%P 313-398
%D 1999
%K c1999, c199x, c19xx, MolBio, chemical compound, structural formula, SMILES,
   .smi file format
%X Also see
   "SMILES is a string obtained by printing the symbol nodes encountered in a
   depth-first tree traversal of a chemical graph. The chemical graph is first
   trimmed to remove hydrogen atoms and cycles are broken to turn it into a
   spanning tree."
   -- [<A HREF="http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification">@wikip</A>]['08]
   and [<A HREF="http://www.opensmiles.org/">opensmiles.org</A>]['08].
   [Also search for: structural formula].

%A M. Pertea
%A S. L. Salzberg
%A M. J. Gardner
%T Finding genes in plasmodium falciparum
%J Nature (brief comm'n)
%V 404
%M MAR
%D 2000
%K MolBio, malaria, parasite, chromosome three, chr III, chr3, chrIII
   gene, find, finding, Glimmer, GlimmerM, c2000, c200x, c20xx, zz0900
%X and a bit of a spat from Lawson et al following pp34-35.
   GlimmerM [<A HREF="http://www.tigr.org/softlab/glimmerm_htm/glimmerm.html">at tigr</A>][8/'00]
   [Also search for: MolBio Glimmer].

%A M. A. Andrade
%A N. P. Brown
%A C. Leroy
%A S. Hoersch
%A A. de Daruvar
%A C. Reich
%A A. Franchini
%A J. Tamames
%A A. Valencia
%A C. Ouzounis
%A C. Sander
%T Automated genome sequence analysis and annotation
%J J. Bioinf.
%V 15
%P 391-412
%D 1999
%I OUP
%K jrnl, MolBio, GeneQuiz, zz0900
%X ... an automatic system for preliminary functional annotation of protein
   sequences. ...
   The GeneQuiz system is publicly available for analysis of protein sequences
   -- [<A HREF="http://www.sander.ebi.ac.uk/gqsrv/submit">at ebi</A>]['99].

%A R. L. Tatusov
%A M. Y. Galperin
%A D. A. Natale
%A E. V. Koonina
%T The COG database: a tool for genome-scale analysis of protein functions and
   evolution
%J NAR
%V 28
%N 1
%P 33-36
%M JAN
%D 2000
%K jrnl, NAR, MolBio, c2000, c200x, c20xx, zz0220, COG, database, protein,
   evolution, Orthologous, COGs, KOGs, POGs
%X "... The database of Clusters of Orthologous Groups of proteins (COGs) is an
   attempt on a phylogenetic classn of the proteins encoded in 21 complete
   genomes of bacteria, archaea & eukaryotes (www.ncbi.nlm.nih.gov/COG). The
   COGs were constructed by applying the criterion of consistency of
   genome-specific best hits to the results of an exhaustive comparison of all
   protein sequences from these genomes. The DB comprises 2091 COGs that include
   56-83% of the gene products from each of the complete bacterial & archaeal
   genomes and ~35% of those from the yeast Saccharomyces cerevisiae genome. The
   COG DB is accompanied by the COGNITOR program that is used to fit new
   proteins into the COGs  ..."
   -- [<A HREF="https://dx.doi.org/10.1093%2Fnar%2F28.1.33">doi:10.1093/nar/28.1.33</A>]['20].
   Also see [<A HREF="https://www.ncbi.nlm.nih.gov/COG">COG</A>][2O2O].

%A D. Cai
%A A. Delcher
%A B. Kao
%A S. Kasif
%T Modelling splice sites with Bayes networks
%J J. Bioinf.
%I OUP
%V 16
%N 2
%P 152-158
%D 2000
%K jrnl, OUP, site, junction, MolBio, model, Bayes tree network,
   trees, networks
%X Bayes tree networks over [X0, X1, ..., Xn-1] (generalise 1st order MMs
   as used in  S a l z b e r g '97 and  R e e s e et al '97).
   ... simple 1st order MM chains are surprisingly effective at
   modelling splice sites. (p155)
   -- [<A HREF="http://bioinformatics.oupjournals.org/">bioinf...oupj...org</A>][10/'00],
      [<A HREF="http://bioinformatics.oupjournals.org/content/vol16/issue2/">16(2)</A>][10/'00],
      [<A HREF="http://www.oup.co.uk/bioinformatics/">oup/bioinformatics</A>][00].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">BioInformatics</A>].)

%A S. J. Wheelan
%A A. Marchler-Bauer
%A S. H. Bryant
%T Domain size distributions can predict domain boundaries
%J Bioinformatics
%V 16
%N 7
%P 613-618
%M JUL
%D 2000
%K jrnl, MolBio, c2000, c200x, c20xx, zz0220, protein, domain, domains, size,
   chain, length, boundary
%X " The sizes of protein domains observed in the 3D-structure database follow a
   surprisingly narrow distn. Structural domains are furthermore formed from a
   single-chain continuous segment in over 80% of instances. These observations
   imply that some choices of domain boundaries on an otherwise uncharacterized
   sequence are more likely than others, based solely on the size & segment
   number of predicted domains. ... We find that domain boundary predictions are
   surprisingly successful for sequences up to 400 residues long & that guessing
   domain boundaries in this way can improve the sensitivity of threading
   analysis."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/16.7.613">doi:10.1093/bioinformatics/16.7.613</A>]['20].

%A A. M. Lesk
%T A picture is worth 1000 words: The BLT in teaching crystal structure
%J J. Chem. Educ.
%V 77
%N 11
%P 1423
%M NOV
%D 2000
%K c2000, c200x, c20xx, AMLesk, x-ray, xRay, ha ha, crystallography, intro,
   crystal, lattice, 3D, structure, BLT, lettuce, unit, cell, primitive
%X "In explaining descriptions of crystals, many authors have emphasized the
   idea that Nature makes crystals, but human beings draw unit cell boundaries.
   The accompanying figure contains a useful classroom demonstration to drive
   this point home."
   -- [<A HREF="http://dx.doi.org/10.1021/ed077p1423">doi:10.1021/ed077p1423</A>]['11].

%A I. P. Ioshikhes
%A M. Q. Zhang
%T Large-scale human promoter mapping using CpG islands
%J Nature Genetics
%V 26
%P 61-63
%D 2000
%K jrnl, MolBio, biol, island, c2000, c200x, c20xx, CG, CpG, methylation
%X "Vertebrate genomic DNA is generally CpG depleted possibly because
   methylation of cytosines at 80% of CpG dinucleotides results in their
   frequent mutation to thymine, and thus CpG to TpG dinucleotides. [But]
   genomic regions of high G+C content (CpG islands), ...
   ... CpG islands are longer than 200bp and have over 50% of G+C content &
   CpG freq. at least 0.6 of that statistically expected. Approx. 50% of m.
   gene promoters are associated with one or more CpG islands. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/79189">doi:10.1038/79189</A>]['06].

%A M. S. Pereira
%A L. Andrade
%A S. Difrawy
%A B. L. Karger
%A E. S. Manolakos
%T Statistical learning formulation of the DNA base-calling problem and
   its solution in a Bayesian EM framework
%J Discrete Applied Mathematics
%V 104
%N 1-3
%P ?-?
%M AUG
%D 2000
%K jrnl, MolBio, zz0900
%X special issue: Combinatorial Molecular Biology H 510.5 D611.1 .
   Via Peter T'.

%A J. A. Bedell
%A I. Korf
%A W. Gish
%T MaskerAid: A performance enhancement to RepeatMasker
%J J. Bioinformatics
%V 16
%N 11
%P 1040-1041
%D 2000
%K MolBio, c2000, c200x, c20xx, repetitive element, DNA, repeat, repeats,
   repetitive, low information content, elements
%X "... software enhancement to RepeatMasker that increased the speed of
   masking more than 30-fold at the most sensitive setting."
   "... estimates suggest at least 40% of the human genome is repetitive ..."
   -- [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/reprint/16/11/1040">pdf</A>]['06] (no alg. description)
   [Also search for: RepBase] and
   [also search for: MolBio repetitive DNA].

%A M. S. Gelfand
%A A. Mironov
%A P. Pevzner
%T Gene recognition via spliced alignment
%J Proc. Natl. Acad. Sci.
%V 93
%P 9061-9066
%D 1996
%K MolBio, PNAS, jrnl, c1996, c199x, c19xx, find, finding, Procrustes, zz1000
%X ref in  B a f n a  and  H u s o n  '00.   Homology based.
   "... describes a spliced alignment alg. & s/w tool that explores all possible
   exon assemblies in polynomial time & finds the multiexon structure with the
   best fit to a related protein ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.93.17.9061">doi:10.1073/pnas.93.17.9061</A>]['22],
      [<A HREF="http://www-hto.usc.edu/software/procrustes/">usc.edu/</A>][10/'00],
      [<A HREF="/~lloyd/tildeMisc/Local/1997procrustes.html">local only</A>].
   [Also search for: Procrustes].

%A A. Goffeau
%A et al
%T Life with 6000 genes
%J Science
%V 274
%N 5287
%P 546-567
%M OCT
%D 1996
%K jrnl, MolBio, yeast, Saccharomyces cerevisiae, eukaryote, fungi, fungal,
   nGenome, c1996, c199x, c19xx, DNA, gene
%X "... seq. of 12,068 kilobases defines 5885 potential protein-encoding genes,
   approx. 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA
   molecules, & 275 transfer RNA genes. In addition, the complete seq. provides
   information about the higher order org. of yeast's 16 chrs. & allows some
   insight into their evolutionary history. The genome shows a considerable
   amount of apparent genetic redundancy, & one of the major problems to be
   tackled during the next stage of the yeast genome project is to elucidate the
   biological functions of all of these genes."
   -- [<A HREF="http://dx.doi.org/10.1126/science.274.5287.546">doi:10.1126/science.274.5287.546</A>]['07]
   Also see [<A HREF="http://www.yeastgenome.org">yeastgenome.org</A>]['07]
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=4932">s.c.@genbank</A>]['07], 12MB, 16 chrs.
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05].

%A L. Arvestad
%T Aligning coding DNA in the presence of frame-shift errors
%J Combinatorial Pattern Matching
%I SpringerVerlag
%S LNCS
%V 1264
%P 180-190
%D 1997
%K conf, CPM, CPM97, MolBio, c1997, c199x, c19xx, align, alignment, coding DNA,
   frame shift, frames, fshift, frameshift
%X "The problem of aligning two DNA seqs. wrt the fact that they are coding for
   proteins is discussed. Criteria for a good alignment of coding DNA, together
   with an alg. that satisfies them, are presented. The alg. is robust against
   frame-shifts & forgiving towards silent substitutions. The important choice
   of objective function is examined and several variants are proposed."
   "... Since gaps of a length that is not 0 mod 3 change the reading-frame,
   they are v.unlikely to occur. If the algs. do not take this into account,
   unsatisfactory alignments are computed. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-63220-4_59">doi:10.1007/3-540-63220-4_59</A>][12/'08].

%A C. Burge
%A S. Karlin
%T Prediction of complete gene structures in human genomic DNA
%I J. Mol. Biol.
%V 268
%P 78-94
%D 1997
%K jrnl, MolBio, GenScan, JMB, gene, find, finding
%X ref in  B a f n a  and  H u s o n  '00.

%A B. Olaisen
%A M. Stenersen
%A B. Mevag
%T Identification by DNA analysis of the victims of the
   August 1996 Spitsbergen civil aircraft disaster
%J Nature Genetics
%P 402-405
%V 15
%M APR
%D 1997
%K jrnl, stats, forensic pathology, body, crash
%X also see [<A HREF="http://www.math.chalmers.se/~mostad/familias/">familias</A>]['05].

%A D. C. Rapaport
%T The Art of Molecular Dynamics Simulation
%I CUP
%P 414
%D 1997
%K book, text, CUP, MolBio, c1997, c199x, c19xx, bioinformatics, protein,
   proteins, molecular dynamics, simulate, simulation, force, forces, energy,
   vibration, motion, L5Ref
%X "... describes molecular dynamics simulation, an extremely powerful technique
   that involves solving the classical many-body problem in contexts relevant
   to the study of matter at the atomic level. The method allows the prediction
   of the static and dynamic properties of substances directly from the
   underlying interactions between the molecules. ..."
   1st ed 1997; pb us$80; uk us isbn:0521599423; uk us isbn13:978-0521599429.

%A J. S. Fetrow
%A M. J. Palumbo
%A G. Berg
%T Patterns, structures, and amino acid frequencies in structural building
   blocks, a protein secondary structure classification scheme
%J Proteins
%V 27
%N 2
%P 249-271
%M FEB
%D 1997
%K jrnl, MolBio, c1997, c199x, c19xx, ANN, protein, structure, pattern,
   library, building block
%X "... autoassociative artificial neural network (autoANN) and clustering tool
   to discover intrinsic features of macromolecular structures. The hidden unit
   activations computed by the trained autoANN are a convenient low-dimensional
   encoding of the local protein backbone structure. Clustering these activation
   vectors results in a unique classification of protein local structural
   features called Structural Building Blocks (SBBs). ... describe application
   of this method to a larger database of proteins, verification of the
   applicability of this method to structure classification, and subsequent
   analysis of amino acid frequencies and several commonly occurring patterns
   of SBBs. The SBB classification method has several interesting properties:
   1) it identifies the regular secondary structures, alpha helix and
   beta strand; 2) it consistently identifies other local structure
   features (e.g., helix caps and strand caps); 3) strong amino acid preferences
   are revealed at some positions in some SBBs; and 4) distinct patterns of
   SBBs occur in the "random coil" regions of proteins. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/(SICI)1097-0134(199702)27:2<249::AID-PROT11>3.0.CO;2-M">doi:10.1002/(SICI)1097-0134(199702)27:2<249::AID-PROT11>3.0.CO;2-M</A>]['11],
      9061789@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/9061789">pubmed</A>]['11].

%A S. Kohler
%A C. F. Delwiche
%A et al
%T A plastid of probable green algal origin in Apicomplexan parasites
%J Science
%V 7
%P 1485-1489
%M MAR
%D 1997
%K jrnl, parasite, c1997, c199x, c19xx, Plasmodium falciparum, parasite,
   Apicomplexa, plastid, alga, tufA, cyanobacteria
%X "... Phylogenetic analysis of the tufA gene encoded by the 35-kb genomes of
   coccidians T. gondii and Eimeria tenella and the malaria parasite Plasmodium
   falciparum grouped this organellar genome with cyanobacteria and plastids,
   showing consistent clustering with green algal plastids. Taken together,
   these observations indicate that the Apicomplexa acquired a plastid by
   secondary endosymbiosis, probably from a green alga."
   -- [<A HREF="http://dx.doi.org/10.1126/science.275.5305.1485">doi:10.1126/science.275.5305.1485</A>]['05].

%A D. Haussler
%T Computational genefinding
%J Trends Guide to Bioinf.
%P 12-15
%D 1998
%K MolBio, gene find, survey
%X ref in  B a f n a  and  H u s o n  '00.

%A E. Rivas
%A S. R. Eddy
%T The language of RNA: a formal grammar that includes pseudoknots
%J J. Bioinformatics
%V 16
%N 4
%P 334-340
%D 2000
%K jrnl, pseudo knots, knot theory, structure, stochastic, context free grammar,
   MolBio, transformational, probabilistic, SCFG, c2000, c200x, c20xx
%X [previously] presented a polynomial time DPA for predicting
   optimal RNA secondary structure including pseudoknots. [But]
   a formal grammatical representation for RNA secondary structure with
   pseudoknots was still lacking.  ...show a 1-to-1 corr' between that
   algorithm and a formal transformational grammar. This grammar class
   encompasses the context-free grammars and goes beyond to generate
   pseudoknotted structures. The pseudoknot grammar avoids the use of
   general context-sensitive rules by introducing a small number of auxiliary
   symbols used to reorder the strings generated by an otherwise context-
   -free grammar. This formal representation of the residue correlations in
   RNA structure is important because it means we can build full probabilistic
   models of RNA secondary structure, including pseudoknots, and
   use them to optimally parse sequences in polynomial time.
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/16/4/334">paper</A>][4/'03].
   [Also search for: MolBio knot].

%A V. Bafna
%A D. H. Huson
%T The conserved exon method for gene finding
%I Proc. 8th Int. Conf. on Intell. Sys. for Mol. Biol.
%M AUG
%D 2000
%P 3-12
%K MolBio, Conf, ISMB, ISMB8, ISMB2000, gene, find, finding,
   CEM, human, mouse, zz1000
%X ... look for conserved prot' seq's by compairing pairs of DNA seq's. ...
   putative exons ... conserved regions ... splice junctions ... chain.
   It simultaneously predicts gene structures in both human and mouse
   genomic seq's (or other pairs at the appropriate evol' dist'). ...
   auth:[<A HREF="mailto:Vineet.Bafna@celera.com">mail</A>]['00].

%A P. A. Pevzner
%A Sing-Hoi Sze
%T Combinatorial approaches to finding subtle signals in DNA sequences
%I Proc. 8th Int. Conf. on Intell. Sys. for Mol. Biol.
%M AUG
%D 2000
%P 269-278
%K MolBio, Conf, ISMB, ISMB8, ISMB2000, signal, pattern, motif,
   Winnower, SPstar, find, discover, discovery, challenge problem, zz1000
%X Challenge problem: find a signal in a sample of seq's, each 600 bases long,
      and each containing an unknown signal of length 15 with 4 mismatches.
   [LA: the "each containing" is a bit of a clue, what about "most"?]
   Also see  T o m p a  '01.

%A E. Yeramian
%T Genes and the physics of the DNA double helix
%J GENE
%V 255
%P 139-150
%D 2000
%K jrnl, MolBio, gene, find, finding, zz1100
%X [via RH]
   see 151-168 same author same issue (on  p l a s' f a l c i p').

%A E. Yeramian
%T The physics of DNA and the annotation of the plasmodium falciparum genome
%J Gene
%V 255
%P 151-168
%D 2000
%K jrnl, MolBio, gene, genes, find, finding, pfalciparum, parasite,
   malaria, c2000, c200x, c20xx, zz1100
%X came up with a new way of predicting coding regions [via RH]
   see p139-150 same author same issue.

%A M. B. Eisen
%A P. T. Spellman
%A P. O. Brown
%A D. Botstein
%T Cluster analysis and display of genome-wide expression patterns
%J Proc. Nat. Acad. Sci.
%V 95
%N 25
%P 14863-14868
%M DEC
%D 1998
%K PNAS, jrnl, MolBio, c1998, c199x, c19xx, cluster, clustering,
   gene expression, micro array, arrays, microarray, zz1200
%X cluster ... genome-wide expression data ... microarray hybridization ...
   graphical output ... groups together genes of known similar function ...
   -- [<A HREF="http://www.pnas.org/cgi/content/full/95/25/14863">www</A>][12/'00].

%A P. T. Spellman
%A G. Sherlock
%A M. Q. Zhang
%A V. R. Iyer
%A K. Anders
%A M. B. Eisen
%A P. O. Brown
%A D. Botstein
%A B. Futcher
%T Comprehensive identification of cell cycle-regulated genes of the
   yeast Saccharomyces cerevisiae by microarray hybridization
%J Molec. Biol. Cell
%V 9
%N 12
%P 3273-3297
%M DEC
%D 1998
%K jrnl, MBC, MolBio, c1998, c199x, c19xx, yeast cell cycle, life cycle,
   micro array, gene, expression level, levels, regulation, G1 cyclin Cln3p,
   B-type cyclin Clb2p, YCL012W, YCL063W, YGL217C,YNL043C, YDR130C, YOL030W
%X "... create a comprehensive catalog of yeast genes whose transcript levels
   vary periodically within the cell cycle. To this end, we used DNA
   microarrays and samples from yeast cultures synchronized by three
   independent methods:  factor arrest, elutriation, and arrest of a cdc15
   temperature-sensitive mutant. Using periodicity and correlation algorithms,
   we identified 800 genes that meet an objective minimum criterion for cell
   cycle regulation. In separate experiments, designed to examine the effects
   of inducing either the G1 cyclin Cln3p or the B-type cyclin Clb2p, we found
   that the mRNA levels of more than half of these 800 genes respond to one or
   both of these cyclins. Furthermore, we analyzed our set of cell
   cycle-regulated genes for known and new promoter elements and show that
   several known elements (or variations thereof) contain information
   predictive of cell cycle regulation."  [82 refs.]
   -- [<A HREF="http://www.molbiolcell.org/cgi/content/abstract/9/12/3273">paper</A>][2/'02].
   (Also see Spellman in  P N A S '98.)
   [Also search for: yeast life cycle].

%A A. Ben-Dor
%A Z. Yakhini
%T Clustering gene expression patterns
%J Jrnl Computational Biology
%V 6
%N 3-4
%P 281-298
%D 1999
%K MolBio, genes, expression, pattern, level, levels, cluster
%X [Also search for: gene expression]
   See [<A HREF="http://www.cs.huji.ac.il/labs/compbio/publications.html">www</A>][2/'02].

%A A. Ben-Dor
%A L. Bruhn
%A N. Friedman
%A I. Nachman
%A M. Schummer
%A Z. Yakhini
%T Tissue classification with gene expression profiles
%J Proc. 4th Int. Cong. on Comp. Molec. Biol. (RECOMB 2000)
%D 2000
%K conf, MolBio, RECOMB, RECOMB4, RECOMB2000, type, types,
   level, levels, cancer, supervised classification
%X also see Ben-Dor J. Comp. Biol. '99
   ... colon ... ovarian ... bone marrow ...
   leave one out cross-validation ...
   (a) nearest neighbour, (b) S V M, (c) Ada Boost, (d) a clustering method.
   ... demonstrate success rate of at least 90% in tumor v. normal class'n
   using sets of selected genes ...
   (Also see Nachman c2004.)

%E R. Paoletti
%E A. L. Klatsky
%E A. Poli
%E S. Zakhari
%T Moderate Alcohol Consumption and Cardiovascular Disease
%I Kluwer
%D 2000
%K book, text, heart, healty, beer, wine, red, white, spirits, liquor,
   CHD, coronary, atherosclerosis, zz1003

%A V. R. Iyer
%A C. E. Horak
%A C. S. Scafe
%A D. Botstein
%A M. Snyder
%A P. O. Brown
%T Genomic binding sites of the yeast cell-cycle transcription factors SBF and
   MBF
%J Nature
%M JAN
%D 2001
%V 409
%N 6819
%P 533-538
%K jrnl, MolBio, c2001, c200x, c20xx, zz0820, Chiponchip, Chipchip, defn, chip,
   seq, yeast, cell cycle, Swi4, Swi6, Mbp1, mitotic, binding site
%X "Proteins interact with genomic DNA ... SBF & MBF are seq.-specific
   transcription factors that activate gene expression during the G1/S
   transition of the cell cycle in yeast. ... we define the genomic binding
   sites of the SBF & MBF transc.factors in vivo, by using DNA microarrays. ..."
   -- [<A HREF="https://doi.org/10.1038/35054095">doi:10.1038/35054095</A>]['20].
   [*Also see ChIP-on-chip@[<A HREF="https://en.wikipedia.org/wiki/ChIP-on-chip">wikip</A>]['20].*]

%A B. R. Green
%T Was 'molecular opportunism' a factor in the evolution of different
   photosynthetic light-harvesting pigment systems?
%J PNAS
%P 2119-2121
%N 5
%V 98
%M FEB
%D 2001
%K jrnl, PNAS, MolBio, biol, biology, photosynthesis, evolution, light, zz0504,
   red algal, chloroplasts, alga, algae, origin, origins, plant, plants,
   c2001, c200x, c20xx, chloroplast
%X [<A HREF="http://dx.doi.org/10.1073/pnas.061023198">doi:10.1073/pnas.061023198</A>][5/'04].

%A J. Shi
%A T. L. Blundell
%A K. Mizuguchi
%T FUGUE: sequence-structure homology recognition using environment-specific
   substitution tables and structure-dependent gap penalties
%J J. Mol. Biol.
%V 310
%N 1
%P 243-257
%M JUN
%D 2001
%K jrnl, JMB, MolBio, c2001, c200x, c20xx, zz0218, FUGUE, protein structure,
   sequence, alignment, gap, gaps, indel, indels, substitutions, matrix
%X "FUGUE, a program for recognizing distant homologues by seq.-struct.
   comp'son ([<A HREF="http://www-cryst.bioc.cam.ac.uk/fugue/">fugue</A>]['01]),
   has three key features. (1) Improved environment-specific substitution
   tables. Substitutions of an amino acid in a p.struct. are constrained by its
   local structural environment, which can be defined in terms of ... .
   tables have been derived from structural alignments in the HOMSTRAD database
   ([<A HREF="http://www-cryst.bioc.cam.ac.uk/homstrad/">homstrad</A>]['01]).
   (2) Automatic selection of alignment alg. with detailed structure-dependent
   gap penalties. FUGUE uses the global-local alg. to align a seq.-struct. pair
   when they greatly differ in length & uses the global alg. in other cases. The
   gap penalty at each posn of the struct. is determined according to its
   solvent accessibility [etc.], ... . (3) Combined info. from both multiple
   seqs. & multiple structures. FUGUE is designed to align multiple seqs.
   against multiple structs. to enrich the conservation/variation info.. ..."
   -- [<A HREF="https://doi.org/10.1006/jmbi.2001.4762">doi:10.1006/jmbi.2001.4762</A>]['18].
   [Also search for: protein structure sequence alignment].

%A L. J. Pitkow
%A C. A. Sharer
%A X. Ren
%A T. R. Insel
%A E. F. Terwilliger
%A L. J. Young
%T Facilitation of affiliation and pair-bond formation by vasopressin
   receptor gene transfer into the ventral forebrain of a monogamous vole
%J J. Neuroscience
%P 7392-7396
%V 21
%N 18
%M SEP
%D 2001
%K jrnl, neuro, neurosci, monogamy, polygamy, pair bonding, V1a, V1aR, male,
   neuropeptide vasopressin, oxytocin, hormone, brain, love, behaviour,
   prairie vole, social attachment
%X ... monogamy, including pair-bond formation, are facilitated by the
   neuropeptide vasopressin and are prevented by a vasopressin receptor
   [V1a receptor (V1aR)] antagonist in the male prairie vole.
   The neuroanatomical distribution of V1aR dramatically differs between
   monogamous and nonmonogamous species. V1aR binding is denser in the
   ventral pallidal region of several unrelated monogamous species compared
   with nonmonogamous species. Because the ventral pallidum is involved in
   reinforcement and addiction, we hypothesize that V1aR activation in this
   region promotes pair-bond formation via a mechanism similar to conditioning.
   ... we increased the density of V1aR binding in the ventral pallial region
   of male prairie voles. ... increased levels of both anxiety and affiliative
   behavior ... males overexpressing the V1aR in the ventral pallidal region,
   ... formed strong partner preferences after an overnight cohabitation,
   without mating, with a female. ...
   -- [<A HREF="http://www.jneurosci.org/cgi/content/abstract/21/18/7392">abs</A>][5/'03].
   [Also search for: vasopressin]  and  [also search for: oxytocin hormone].

%A W. Dubitzky
%A M. Granzow
%A D. Berrar
%T Comparing symbolic and subsymbolic machine learning approaches to
   classification of cancer and gene identification
%J Methods of Microarray Data Analysis: Papers from CAMDA'00
%E S. M.  Lin
%E K. F. Johnson
%P 151-166
%D 2001
%I Kluwer
%K conf, CAMDA, CAMDA00, MolBio, micro arrays, microarrays, Clementine
%X Uses DTree and NN from  S P S S's  Clementine s/w.
   -- [<A HREF="http://www.infj.ulst.ac.uk/~cbbg23/papers/camda00_02.pdf">.pdf</A>][4/'03],
      [<A HREF="http://www.camda.duke.edu/CAMDA00/book/">CAMDA</A>][4/'03]. isbn:0792375645.

%A R. J. Read
%T Pushing the boundaries of molecular replacement with maximum likelihood
%J Acta Crystallographia (D)
%V D57
%P 1373-1382
%D 2001
%K jrnl, MolBio, c2001, c200x, c20xx, X-ray, Xray, crystallography, protein,
   structure, determination, Beast, molecular replacement, molecularReplacement,
   Phaser software, phasing
%X "The molecular-replacement method works well with good models & simple unit
   cells, but often fails with more difficult problems. Experience with
   likelihood in other areas of crystallography suggests that it would improve
   performance significantly. For [MR], the form of the required likelihood fn
   depends on whether there is ambiguity in the rel.phases of the contributions
   from symmetry-related molecules (e.g. rotation v. translation searches).
   Likelihood fns used in structure refinement are appropriate only for
   translation (or 6-D) searches, where the correct translation will place all
   of the atoms in the model approximately correctly. A new likelihood fn that
   allows for unknown relative phases is suitable for rotation searches. It is
   shown that correlations between sequence identity & coordinate error can be
   used to calibrate params. for model quality in the likelihood fns. Multiple
   models of a molecule can be combined in a statistically valid way by setting
   up the joint prob.distribution of the true & model structure factors as a
   multivariate complex normal distribution, from which the conditional
   distribution of the true structure factor given the models can be derived.
   Tests in a new molecular-replacement program, Beast, show that the likelihood
   -based targets are more sensitive & more accurate than previous targets. The
   new multiple-model likelihood fn has a dramatic impact on success."
   -- [<A HREF="http://dx.doi.org/10.1107/S0907444901012471">doi:10.1107/S0907444901012471</A>]['11].
   (Also see Phaser@[<A HREF="http://www.phaser.cimr.cam.ac.uk/">cam</A>]['11].)
   [Also search for: MolBio Xray crystallography].

%A K. Y. Yeung
%A C. Fraley
%A A. Murua
%A A. E. Raftery
%A W. L. Ruzzo
%T Model-based clustering and data transformations for gene expression data
%J J. Bioinformatics
%V 17
%N 10
%P 977-987
%D 2001
%K MolBio, jrnl, genes, level, levels, cluster, zz0202
%X ... On real ... data, model-based approach produced clusters of quality
   comparable to a leading heuristic clustering algorithm, but with the key
   advantage of suggesting the # of clusters and an appropriate model. We also
   explored the validity of the Gaussian mixture assumption on different
   transformations of real data.  We also assessed the degree to which these
   real gene expression data sets fit multivariate Gaussian distributions both
   before and after [common] data transformations.  Suitably chosen
   transformations seem to result in reasonable fits.
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/17/10/977">pdf</A>][2/'02].
   [Also search for: gene expression]  and  [also search for: clustering].

%A A. L. Delcher
%A S. Kasif
%A R. D. Fleischmann
%A J. Peterson
%A O. White
%A S. L. Salzberg
%T Alignment of whole genomes
%J Nucl. Acids. Res.
%V 27
%N 11
%P 2369-2376
%D 1999
%K MolBio, jrnl, NAR, MUMmer, align, aligning, genome, DNA, tigr,
   suffix tree, zz1200
%X MUMmer ... suffix tree, the system is able rapidly to align sequences
   containing millions of nucleotides.
   -- [<A HREF="http://www.tigr.org/softlab/" TARGET="external">tigr/ softlab/</A>][12/'00].

%A S. M. Arfin
%A A. D. Long
%A E. T. Ito
%A L. Tolleri
%A M. M. Riehle
%A E. S. Paegle
%A G. W. Hatfield
%T Global gene expression profiling in Escherichia coli K12 - the effects of
   integration host factor
%J J. Biol. Chem.
%V 275
%N 38
%P 29672-29684
%M SEP
%D 2000
%K MolBio, jrnl, JBC, genes, express, eColi, microarray example,
   micro array, c2000, c200x, c20xx, zz1200
%X ... used nylon membranes spotted in duplicate with full-length PCR-generated
   products of each of the 4,290 predicted eColi K12 open reading frames (ORFs)
   to measure the gene expression profiles in otherwise isogenic integration
   host factor IHF+ and IHF strains. ...
   4290 ORFs, IHF+ and IHF- strains, 4 experiments. ...  Linear analysis of
   variance model. ...  The t test evaluates the difference between the means
   of two groups employing the variance within groups as an error term. ...
   ... test statistics [scaled] the difference in gene expression levels
   between genotypes relative to the obs' variance within genotypes. ...
   -- [<A HREF="http://www.jbc.org/cgi/content/full/275/38/29672">paper</A>],
      [<A HREF="http://www.jbc.org/cgi/content/full/275/38/29672/DC1">data</A>],
      [<A HREF="http://www.jbc.org/content/vol275/issue38/">V275(38)</A>][00].

%A C. Rick
%T Simple and fast linear space computation of longest common subsequence
%J Inf. Proc. Lett.
%V 75
%N 6
%P 275-282
%M NOV
%D 2000
%K IPL, c2000, c200x, c20xx, jrnl, LCS, LCSS, sequence, alignment, zz1200
%X via p.e.t. (H 10.7805 I43.6)
   [Also search for: alignment]  also see H i r s c h b e r g,
   also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">alignment</A>].
   -- [<A HREF="http://www.elsevier.nl/gej-ng/10/23/20/64/31/show/toc.htt">IPL 75(6) Nov '00</A>].

%A S. Bowman
%A et al
%T The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum
%J Nature
%V 400
%N 6744
%P 532-538
%M AUG
%D 1999
%K jrnl, MolBio, malaria, plasmodium falciparum, pf, chr III 3, chr3, chrIII,
   parasite, DNA sequence, annotations, gene predictions,
   c1999, c199x, c19xx, zz0101
%X -- [<A HREF="http://www.nature.com/nature/">nature.com/</A>][1/'01].

%A T. S. Furey
%A N. Christianini
%A N. Duffy
%A D. W. Bednarski
%A M. Schummer
%A D. Hauessler
%T Support vector machine classification and validation of cancer tissue
   samples using microarray expression data
%J J. Bioinformatics
%V 16
%N 10
%M OCT
%D 2000
%P 906-914
%K MolBio, SVM, micro arrays, zz0101
%X H 570.5 C738  [via p.e.t]

%A R. Herwig
%A A. O. Schmitt
%A M. Steinfath
%A J. O'Brien
%A H. Seidel
%A S. Meyer-Ewert
%A H. Lehrach
%A U. Radelof
%T Information theoretical probe selection for hybridisation experiments
%J J. Bioinformatics
%V 16
%N 10
%P 890-898
%M OCT
%D 2000
%K MolBio, c2000, c200x, c20xx, probes, zz0101
%X "Our cluster analysis is performed with a sequential k-means algorithm
    using mutual information as a pairwise similarity measure for the binary
    fingerprints".
   Their cluster analysis seems to be similar to median-cut.
   H 570.5 C738 [via p.e.t.]

%A Xin Chen
%A S. Kwong
%A Ming Li
%T A compression algorithm for DNA sequences and its applications in genome
   comparison
%J Genome Informatics
%V 10
%P 51-61
%D 1999
%O Genome Informatics Workshop, Tokyo, 1999
%K MolBio, wShop, GIW, GIW99
%X (also see  A l l i s o n  et al in Intel. Sys. in Mol. Biol., I.S.M.B.'98,
   -- [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">compression</A>].)
   <!-- doi.acm.org/10.1145/332306.332352  www.jsbi.org/journal/GI10.html --> .

%A E. Pizzi
%A C. Frontali
%T Low-complexity regions in plasmodium falciparum proteins
%J Genome Res.
%V 11
%N 2
%P 218-229
%M FEB
%D 2001
%K MolBio, jrnl, malaria, plasmodium falciparum, parasite, protein, repeats,
   information content, gene, genes, zz0201, c2001, c200x, c20xx
%X ... 90+% of all proteins in c2 and c3 feature low complexity regions up to
   1.8kbp and 50% of all proteins are 60+% composed of low complexity regions.
   Laboratorio di Biologia Cellulare, Istituto Superiore di Sanita, 00161 Rome
   -- [<A HREF="http://www.genome.org/cgi/content/full/11/2/218">pdf</A>][2/01].
   [Also search for: MolBio plasmodium information].

%A P. Onyango
%A et al
%A A. P. Feinberg
%T Sequence and comparative analysis of the mouse 1-megabase region orthologous
   to the human 11p15 imprinted domain
%J Genome Res.
%V 10
%N 11
%P 1697-1710
%M NOV
%D 2000
%K MolBio, jrnl, mouse, Mus, human, 11p15, DNA, imprinting, gene, genes, chr7,
   interspecies comparison, AF313042, CpG islands, zz0201
%X ... the nonexonic segments that make up 97% of the genome.
   Interspecies sequence comparison offers ...
   ... comparing a ~1-Mb imprinted genomic domain on mouse chromosome 7
   to its orthologous region on human 11p15.5 ...
   [sequence data submitted GenBank accession nos. AF313042 to AF313150.]
   -- [<A HREF="http://www.genome.org/cgi/content/full/10/11/1697">www</A>][2/'01].

%A J. C. Venter
%A et al
%T The sequence of the human genome
%J Science
%V 291
%N 5507
%P 1304-?
%M FEB
%D 2001
%K MolBio,  Science, jrnl, c2001, c200x, c20xx, Human genome, Celera, DNA, gene,
   genes, Craig, zz0201
%X A highly controversial one this, because of the commercial v. public-
   -interest implications.
   Also see  Nature, also FEB 2001.
   -- [<A HREF="http://www.sciencemag.org/cgi/content/full/291/5507/1304">inc' pdf</A>][2/01],
      [<A HREF="http://www.sciencemag.org/">Science Mag'</A>][2/'01].
   [Also search for: human nuclear genome].

%T Initial sequencing and analysis of the human genome
%Q International Human Genome Sequencing Consortium
%J Nature
%V 409
%P 860-921
%M FEB
%D 2001
%K jrnl, MolBio, c2001, c200x, c20xx, human genome, HUGO, IHGSC,
   repeat, repeats, tandem, palindromic, duplicated segment, segments,
   transposable
%X "... By contrast [to fly] the human genome is filled (> 50%) with repeated
   seqs., inc. interspersed repeats derived from transposable elts., & long
   genomic regions that have been duplicated in tandem, palindromic or dispersed
   fashion ... include large duplicated segments (50-500kb) with high seq.
   identity (98-99.9%), ..."
   -- [<A HREF="http://www.nature.com/nature/journal/v409/n6822/full/409860a0.html">@nature</A>]['08].
   [Also search for: human nuclear genome].

%T A physical map of the human genome
%Q International Human Genome Mapping Consortium (IHGSC)
%J Nature
%V 409
%N 813
%P 934-941
%M FEB
%D 2001
%K Nature, jrnl, human genome project, HUGO, Craig Venter, Science, MolBio,
   IHGSC, sequence, map, mapping, DNA, gene, genes, www, HREF, http, zz0201,
   2001, c200x, c20xx, nGenome, nuclear
%X [<A HREF="http://dx.doi.org/10.1038/35057157">doi:10.1038/35057157</A>]['08].
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05]
   Also see the (commercial and) contentious  Venter et al, Science, same date.
   [Also search for: human nuclear genome].

%A Z. Ning
%A A. J. Cox
%A J. C. Mullikin
%T SSAHA: A fast search method for large DNA databases
%J Genome Res.
%V 11
%N 10
%P 1725-1729
%M OCT
%D 2001
%K jrnl, MolBio, SNP, genome, sequence, assembly, hash, hashing, database,
   search, searching, indexing
%X ... SSAHA (Sequence Search and Alignment by Hashing Algorithm) ...
   k-tuples .. hash table ... can be three to four orders of
   magnitude faster than BLAST or FASTA, while requiring less memory
   than suffix tree methods. ... (SNP) detection and very large scale sequence
   assembly.  [authors @ S@nger]
   -- [<A HREF="http://www.genome.org/cgi/content/full/11/10/1725">paper</A>][11/'02].

%A M. S. Waterman
%T Introduction to Computational Biology: Maps, Sequences and Genomes
%I ChapmanHall
%P 448
%D 1995
%K book, text, MolBio, c1995, c199x, c19xx, bioinformatics, sequence, gene, map
%X 1st ed 1995; hb us$71; uk us isbn:0412993910; uk us isbn13:978-0412993916.
   [Also search for: MolBio book].

%A K. Quandt
%A K. Frech
%A H. Karas
%A E. Wingender
%A T. Werner
%T MatInd and MatInspector - new fast and versatile tools for
   detection of consensus matches in nucleotide sequence data
%J NAR
%V 23
%P 4878-4884
%D 1995
%K MolBio, NAR, jrnl, c1995, c199x, c19xx, pattern discovery, consensus,
   profile, DNA, TRANSFAC, IUPAC, zz0301
%X MatInd is a simple but powerful method to derive a matrix description
   of a consensus from a number of short sequences on which the definition
   of a IUPAC code would be based.  A large library (~280 entries) of
   predefined matrix descriptions for protein binding sites exists and
   has been tested for accuracy and suitability. Information about the
   transcription factors connected to these matrices can be retrieved
   from the TRANSFAC database.  MatInspector is a second software tool
   that utilizes this library of matrix descriptions to locate matches
   in sequences of unlimited length. MatInspector is almost as fast as
   a IUPAC search but has been shown to produce superior results. It assigns
   a quality rating to matches and thus allows quality-based filtering and
   selection of matches. MatInspector is able to compare one, several, or
   all sequences in a sequence file against all or selected subsets of
   matrices from the library in a single program run. It scans both
   strands of the sequence simultaneously.
   -- [<A HREF="http://www.gsf.de/biodv/matinspector.html">www</A>][3/'01].

%A B. Sinervo
%A C. M. Lively
%T The rock-paper-scissors game and the evolution of alternative male strategies
%J Nature
%V 380
%P 240-243
%D 1996
%K jrnl, c1996, c199x, c19xx, zz0120, biology, biol, game theory,
   side blotched lizard, animal, mate selection, strategy, mating, sex, morphs,
   harem minder, cheater, monogamy, polygamy
%X "... report here the application of an evolutionary stable strategy model to
   a three-morph mating system in the side-blotched lizard. Using parameter
   estimates from field data, the model predicted oscillations in morph frequs.
   & the freqs. of the three male morphs were found to oscillate over a six-year
   period in the field. The fitnesses of each morph relative to other morphs
   were non-transitive in that each morph could invade another morph when rare,
   but was itself invadable by another morph when common. Concordance between
   frequency-dependent selection and the among-year changes in morph fitnesses
   suggest that male interactions drive a dynamic 'rock-paper-scissors' game."
   -- [<A HREF="https://doi.org/10.1038/380240a0">doi:10.1038/380240a0</A>]['19].
   (Also see 'How game theory can help improve your luck at dating',
   M. Dal Borgo [<A HREF="https://www.bbc.com/future/article/20191217-how-game-theory-can-help-improve-your-luck-at-dating">bbc</A>][19/12/2019].)

%A T. Jaakkola
%A M. Diekhaus
%A D. Haussler
%T Using the Fisher kernel method to detect remote protein homologies
%J 7th Intell. Sys. Mol. Biol.
%P 149-158
%D 1999
%K ISMB 99, ISMB7, ISMB99, c1999, c199x, c19xx, MolBio, SVM, similarity,
   discriminate
%X ... Fisher score is a vector  Ux = DEL[theta] log P(X|H1,theta),  each
   component being a derivative of log likelihood for a query sequence x
   w.r.t. a particular parameter.  For 2 seq's x and x',
   K(x,x') = exp( (-1/(2 sigma**2)) (Ux-Ux')'(Ux-Ux') ),
   scaling factor sigma = median Eucl' dist between gradient vec's corr' to
   the training seq's in the family and closest gradient vec from a protein
   belonging to another protein fold. ...
   ... discriminant function
   L(x) = SUM[i:xi in H1] Li K(x,xi) - similar for H0,
   the Li are est' from +ve and -ve training examples xi.
   -- [<A HREF="http://www.ai.mit.edu/people/tommi/papers.html">www</A>][3/'01],
      [<A HREF="http://www.aaai.org/Press/Proceedings/ISMB/1999/ismb99.html">proc</A>][3/'01].

%A S. Sinha
%A M. Tompa
%T A statistical method for finding transcription factor binding sites
%J 8th Intell. Sys. Molec. Biol. (ISMB)
%P 344-354
%D 2000
%K conf, MolBio, ISMB 8, 2000, ISMB8, ISMB2000, site, transcribe, DNA, gene,
   genes, factors, promoter, pattern, motif, zz0101
%X ... enumerative statistical method for identifying good candidates for []
   transc' factor binding sites.

%A G. Bejerano
%A G. Yona
%D 2001
%T Variations on probabilistic suffix trees: statistical modeling and
   the prediction of protein families
%J J. Bioinformatics
%V 17
%N 1
%P 23-43
%M JAN
%D 2001
%K jrnl, MolBio, tree, prefix, model, family, zz0301
%X via p.e.t.;  H 570.5 C738.

%A M. Li
%A J. H. Badger
%A X. Chen
%A S. Kwong
%A P. Kearney
%A H. Zhang
%T An information-based sequence distance and its application to
   whole mitochondrial genome phylogeny
%J J. Bioinformatics
%V 17
%N 2
%P 149-154
%M FEB
%D 2001
%K MolBio, jrnl, mitochondria
%X via p.e.t.:-  Li of V' and Li, takes algorithmic information theory approach
   H 570.5 C738
   (Also see  A l l i s o n, et al, 1 9 9 8  and [<A HREF="/~lloyd/tildeStrings/">www</A>].)

%A M. Eisen
%T ScanAlyze
%D 1998
%I Stanford University
%K microarray, micro array
%X scanning software.   [Also search for: microarray].

%A W. F. van Gunsteren
%A R. Bürgi
%A C. Peter
%A X. Daura
%T The key to solving the protein-folding problem lies in an accurate
   description of the denatured state
%J Angew. Chemie Intl. Ed.
%V 40
%P 351-355
%D 2001
%K MolBio, jrnl, molecular dynamics, MD, fold, tertiary structure, zz0501
%X [<A HREF="http://igc.ethz.ch/">igc.ethz.ch</A>][5/'01].

%A H. Schafer
%A X. Daura
%A A. E. Mark
%A W. F. van Gunsteren
%T Entropy calculations on a reversibly folding peptide: Changes in
   solute free energy cannot explain folding behaviour
%J Proteins
%V 43
%P 45-56
%D 2001
%K jrnl, MolBio, molecular dynamics, MD, fold,
   protein, tertiary structure, zz0501, c2001, c200x, c20xx
%X [<A HREF="http://igc.ethz.ch/">igc.ethz.ch</A>][5/'01]

%A J. Knight
%D 2001
%T When the chips are down
%J Nature
%V 410
%N 6831
%M APR
%D 2001
%P 860-861
%K MolBio, jrnl, micro arrays, microarrays
%X [<A HREF="http://www.nature.com/ng/web_specials">www</A>]
   click on "the chipping forecast", get 60 page supplement,   H 505 N285.

%A K. Y. Yeung
%A D. R. Haynor
%A W. L. Ruzzo
%T Validating clustering for gene expression data
%J J. Bioinformatics
%V 17
%N 4
%P 309-318
%M APR
%D 2001
%K MolBio, jrnl, micro arrays, microarrays, cluster, algorithms
%X Many clustering algorithms ... proposed for
   analysis of gene expression data, but little guidance is available
   to help choose among them.  We provide a systematic framework for
   assessing the results of clustering algorithms.  Clustering algorithms
   attempt to partition the genes into groups exhibiting similar patterns
   of variation in expression level.  Our methodology is to apply a
   clustering algorithm to the data from all but one experimental
   condition.  The remaining condition is used to assess the predictive
   powers of the resulting clusters - meaningful clusters should exhibit
   less variation in the remaining conditions than clusters formed by chance.
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/17/4/309">paper</A>][2/'02]
      ---
   (pt's comment, 'should exhibit less variation' - you might not be
   lucky and the attribute you are trying to predict is actually random
   with respect to the clustering).     H 570.5 C738
   [Also search for: classification].

%A O. Weiss
%A M. A. Jimenez-Montano
%A H. Herzel
%T Information content of protein sequences
%J J. Theor. Biol.
%V 206
%N 3
%P 379-386
%M OCT
%D 2000
%K jrnl, c2000, c200x, c20xx, JTB, complexity, entropy, MolBio, zz0801,
   c2000, c200x, c20xx, sequence
%X "... proteins are fairly close to random sequences ...
   entropy reduction due to correlations is only about 1%. ...
   ...protein sequences can be regarded as slightly edited random strings. ..."
   -- [<A HREF="http://openurl.ingenta.com/content?genre=article&issn=0022-5193&volume=206&issue=3&spage=379&epage=386">open-url</A>]['07].

%A B. Ewing
%A L. Hillier
%A M. Wendl
%A P. Green
%T Base-calling of automated sequencer traces using Phred. I. Accuracy
   assessment
%J Genome Res
%V 8
%N 3
%P 175-185
%M MAR
%D 1998
%K jrnl, MolBio, c1998, c199x, c19xx, DNA, Phil, Phill, zz0801
%X [<A HREF="http://www.genome.org/cgi/content/full/8/3/175">paper</A>][8/'01].
   [see 2nd paper pp.186-194].

%A B. Ewing
%A P. Green
%T Base-calling of automated sequencer traces using Phred. II. Error
   probabilities
%J Genome Res.
%V 8
%N 3
%P 186-194
%M MAR
%D 1998
%K jrnl, MolBio, c1998, c199x, c19xx, DNA, Phil, Phill, trace, PHRED, PHRAP,
   zz0801
%X [<A HREF="http://www.genome.org/cgi/content/full/8/3/186">paper</A>][8/'01].
   See 1st paper pp.175-185.
   [Also search for: phrap],  [also search for: consed].

%A D. Gordon
%A C. Abajian
%A P. Green
%T Consed: A graphical tool for sequence finishing
%J Genome Res.
%V 8
%P 195-202
%M MAR
%D 1998
%K jrnl, MolBio, c1998, c199x, c19xx, DNA, Phil, Phill, assembly, zz0801
%X [<A HREF="http://www.genome.org/cgi/content/full/8/3/195">paper</A>][8/'01];
   [also search for: MolBio sequence assembly].

%A T. Attwood
%A D. Parry-Smith
%T Introduction to Bioinformatics
%I PrenticeHall
%D 1999
%P 240
%K book, text, c1999, c199x, c19xx, bioinformatics, computing, programming,
   molecular biology, MolBio, intro, zz0801
%X 1. Introduction                         2. Information Networks
   3. Protein Information Resources        4. Genome Information Resources
   5. DNA Sequence Analysis                6. Pairwise Alignment Techniques
   7. Multiple Sequence Analysis           8. Secondary Database Searching
   9. Building a Sequence Search Protocol 10. Analysis Packages
   pb; uk us isbn:0582327881;  uk us isbn13:978-0582327887.
   Companion site: [<A HREF="http://www.bioinf.man.ac.uk/dbbrowser/bioactivity/">www</A>][8/'01].
   [Also search for: MolBio book].

%T Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology
%E J. Glasgow
%E T. Littlejohn
%E F. Major
%E R. Lathrop
%E D. Sankoff
%E C. Sensen
%I AAAI Press
%P 234
%M JUN
%D 1998
%K MolBio, conf, ISMB, ISMB6, ISMB98
%X isbn:1-57735-053-7;  US$60 ppb;   [Also search for: MolBio]
   -- [<A HREF="http://www.aaai.org/Press/Proceedings/ISMB/1998/ismb98.html">AAAI</A>][9/'01].

%A M. H. Meisler
%T Insight/ Outlook: Evolutionarily conserved noncoding DNA in the
   human genome: How much and what for?
%J Genome Research
%V 11 ?
%P 1617-1618
%D 2001
%K jrnl, Frazer, non-coding DNA, homologous, mouse, human, zz1001
%X [<A HREF="http://www.genome.org/">genome.org</A>][10/'01]
   ... Frazer et al, mouse ~ human chr21 using oligonucleotide arrays:
      The amount of conserved non-coding sequence was
      approximately equal to the coding seq' in this region.
      Half the shared non-coding seq' was also conserved in dog. ...
   -- [<A HREF="http://mouse.ensembl.org/">mouse.ensembl.org</A>] and
      [<A HREF="http://genome.cse.ucsc.edu/">genome.cse.ucsc</A>][10/'01].

%A J. Holmes
%A W. J. Bruno
%T Evolutionary HMMs: A Bayesian appraoch to multiple alignment
%J J. Bioinformatics
%V 17
%N 9
%P 803-820
%M SEP
%D 2001
%K MolBio, jrnl, c2001, c200x, c20xx, HMM, sequence alignment, Handel
%X via  p.e.t. 10/'01.   H 570.5 C738
   [Also search for: multiple alignment],
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/17/9/803">paper pdf</A>][10/'01].
   See more on [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].

%A A. Apostolico
%A S. Lonardi
%T Compression of biological sequences by greedy off-line textual substitution
%J Data Compression Conf.
%I IEEE
%E J.A.Storer,  M.Cohn
%P 143-152
%M MAR
%D 2000
%O TR-99-037, Dept. of Comp. Sci., Purdue Uni.
%K conf, TR 37, TR37, MolBio, offline, strings, compress, information, DNA,
   sequence, Snowbird, DCC, DCC00, c2000, c200x, c20xx
%X "...one of the simplest possible steepest descent paradigms. ...performing
   repeated stages in each ... identify a sub-string of the current version of
   the text yielding the maximum compression, and then replace all those
   occurrences except one with a pair of ptrs to the untouched occurrence.
   ...somewhat dual w.r.t. the bottom up vocabulary buildup scheme considered by
   Rubin. This simple scheme already poses some interesting algorithmic problems
   In terms of performance, the method does outperform current LZ
   implementations in most of the cases. Here we show that, on bio. seqs., it
   beats all other generic compression methods & approaches the performance of
   methods specifically built around some peculiar regularities of DNA seqs.,
   such as tandem repeats & palindromes, that are neither distinguished nor
   treated selectively here. The most interesting performances, however, are
   obtained in the compression of [seq. families].  ... On such inputs, ...
   scores that are not only better than those of any other method, but also
   improve increasingly with increasing input size. ...attrib. to ... ability
   to capture distant relationships ...in a family, ..."
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/DCC.2000.838154">paper</A>]['06]
   More on bio-inf' and [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">compression</A>],
   [Also search for: low information MolBio],
   -- [<A HREF="http://www.cs.purdue.edu/homes/stelo/papers/dcc00.ps.gz">postscript</A>][10/'01],
      [<A HREF="/~lloyd/tildeMisc/Local/2000apostolico.pdf">local only</A>]['06].
   [Also search for: MolBio sequence compression].

%A I. Pe'er
%A R. Shamir
%T Spectrum alignment: Efficient resequencing by hybridization
%J Proc. of ISMB
%I AAAI Press
%P 260-268
%D 2000
%K conf, ISMB, MolBio, c2000, c200x, c20xx, spectrum, spectral, alignment,
   resequencing, hybridization, Peer
%X "... a polynomial alg. that reconstructs the seq., given the spectrum & a
   homologous seq.. This situation occurs, for example, in the identification of
   single nucleotide polymorphisms (SNPs), & whenever a homologue of the target
   seq. is known. The alg. is robust, can handle errors in the spectrum &
   assumes no knowledge of the k-mer multiplicities. ..."
   -- [<A HREF="http://acgt.cs.tau.ac.il/papers/specalign.ps">ps@tau</A>]['08],
   -- [<A HREF="http://www.aaai.org/Papers/ISMB/2000/ISMB00-027.pdf">pdf@aaai</A>].
   [Also search for: resequencing MolBio].

%A J. Buhler
%A M. Tompa
%T Finding motifs using random projections
%J RECOMB01: Proc. 5th Annual Int.  Conf. on Comp. Mol. Biol.
%W Montreal, Canada
%P 67-74
%M APR
%D 2001
%K MolBio, RECOMB, RECOMB01, conf, signal, motif, pattern, discovery,
   discover, find, zz1101
%X [<A HREF="http://www.cs.washington.edu/homes/tompa/papers/">www</A>][10/'01]
   Pevzner and Sze ('00) considered a precise version of the
   motif discovery problem and simultaneously issued an algorithmic challenge:
      Find an unknown motif M of length 15, in N strings of 600-bp
      where each planted instance differs from M in 4 positions.
   ... previous algorithms all failed on the (15,4) problem,
   P. and S. ... succeeded but failed ... harder (14,4)-, (16,5)-, and
   (18,6)-motif problems.
   We ... use random projections of the input's substrings.
   Experiments on simulated data ... this algorithm performs better ...
   Projection: Choose k of l positions of l-mer, x, as a hash function h(x),
   ... buckets ... count, ...
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].)

%A S. Hannenhalli
%A S. Levy
%T Promoter prediction in the human genome
%J Intell. Sys. in Mol. Bio.
%O Bioinformatics V17 (Supplement_1)
%P S90-S96
%M JUL
%D 2001
%K conf, ISMB, ISMB9, ISMB2001, promoters, gene, TSS, zz1101
%X authors at celera.

%A M. J. Wise
%T Oj.py: A software tool for low complexity proteins and protein domains
%J Intell. Sys. in Mol. Bio.
%O Bioinformatics V17 (Supplement_1)
%P S288-S295
%M JUL
%D 2001
%K conf, MolBio, ISMB, ISMB9, ISMB2001, Ojpy, protein, zz1101
%X Low complexity proteins and protein domains have sequences which
   appear highly non-random. Over the years, these sequences have been
   routinely filtered out during sequence similarity searches because
   interest has been focused on globular proteins, and inclusion of these
   domains can severely skew search results. However, early work on these
   proteins and more recent studies of the related area of repeated protein
   sequences suggests that low complexity protein domains have function and
   therefore are in need of further investigation. 0j.py is a new tool for
   demarcating low complexity protein domains more accurately than has been
   possible to date. The paper describes 0j.py and its use in revealing
   proteins with repeated and poly-amino-acid peptides. Statistical methods
   are then employed to to examine the distribution of these proteins across
   species, while keyword clustering is used to suggest roles performed by
   proteins through the use of low complexity domains.
   -- [<A HREF="http://www.bio.cam.ac.uk/~mw263/ftp/doc/0j.pdf">paper</A>][10/'02]
   [Also search for: compression MolBio].

%A P. A. Pevzner
%A H. Tang
%A M. S. Waterman
%T An Eulerian path approach to DNA fragment assembly
%J PNAS
%V 98
%N 17
%P 9748-9753
%M AUG
%D 2001
%K jrnl, PNAS, MolBio, c2001, c200x, c20xx, sequence assembly, assembler,
   shotgun, DNA, Eulerian, de Bruijn graph, deBruijn, superpath, readpath
%X "For the last 20 years, frag. assembly in DNA sequencing followed the
   overlap-layout-consensus [OLC] paradigm that is used in all curr. available
   assembly tools. ... proved useful in assembling clones  [but] it faces
   difficulties in genomic shotgun assembly. We abandon the classical [OLC]
   approach in favor of a new Euler alg. that, for the 1st time, resolves the
   20-year-old repeat problem in frag. assembly. Our main result is the
   reduction of the frag. assembly to a variation of the classical Eulerian
   path problem that allows one to generate accurate solutions of large-scale
   seq. problems. Euler, in contrast to the celera assembler, does not mask
   such repeats but uses them instead as a powerful fragment assembly tool."
   pdf@[<A HREF="http://www.pnas.org/content/98/17/9748.full">pnas</A>]['08],
   or @[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/11504945">pub med</A>]['08].
   [Also search for: Myers c2005] and
   [also search for: MolBio sequence assembly].

%A B. S Weinstein
%A D. Ciszek
%T The reserve-capacity hypothesis: evolutionary origins and modern implications
   of the trade-off between tumor-suppression and tissue-repair
%J Exp. Gerontology
%V 37
%N 5
%P 615-627
%M MAY
%D 2002
%K jrnl, MolBio, c2002, c200x, c20xx, zz1020, reserve capacity hypothesis,
   telomere, telomeres, telomerase, Greider, mice, mouse, lab, laboratory, long,
   risk, risks, age, ageing, PMID11909679, antagonistic pleiotropy
%X "Antagonistic pleiotropy, the evol. theory of senescence, posits that age
   related somatic decline is the inevitable late-life by-product of adaptations
   that increase fitness in early life. That concept, coupled with recent
   findings in oncology & gerontology, provides the foundation for an
   integrative theory of vertebrate senescence that reconciles aspects of the
   'accumulated damage', 'metabolic rate', and 'oxidative stress' models. We
   hypothesize that (1) in vertebrates, a telomeric fail-safe inhibits tumor
   formation by limiting cellular proliferation. (2) The same system results in
   the progressive degradation of tissue function with age. ...  We observe that
   captive-rodent breeding protocols, designed to increase reproductive output,
   simultaneously exert strong sel'n against reproductive senescence & virtually
   eliminate sel'n that would otherwise favor tumor suppression. This appears to
   have greatly elongated the telomeres of lab.mice. With their telomeric
   failsafe effectively disabled, these animals are unreliable models of normal
   senescence & tumor formation. Safety tests employing these animals likely
   overestimate cancer risks & underestimate tissue damage & consequent
   accelerated senescence."
   -- [<A HREF="https://doi.org/10.1016/s0531-5565(02)00012-8 ">doi:10.1016/s0531-5565(02)00012-8 </A>]['20].
   Also see T@[<A HREF="https://en.wikipedia.org/wiki/Telomere">wikip</A>]['20].

%A A. Caspi
%A et al
%T Role of genotype in the cycle of violence in maltreated children
%J Science
%P 851-854
%V 297
%D 2002
%K jrnl, genome, expressed, expression level, environment, nature v nurture,
   behaviour, child, children, development, monoamine oxidase, MAOA,
   maltreatment, mistreatment, gene, polymorphism, zz0503
%X "... A functional polymorphism in the gene encoding the
   neurotransmitter-metabolizing enzyme monoamine oxidase A (MAOA) was found
   to moderate the effect of maltreatment. Maltreated children with a genotype
   conferring high levels of MAOA expression were less likely to develop
   antisocial problems. These findings may partly explain why not all victims
   of maltreatment grow up to victimize others, and they provide
   epidemiological evidence that genotypes can moderate children's sensitivity
   to environmental insults."
   -- [<A HREF="http://www.sciencemag.org/cgi/content/abstract/297/5582/851">abs</A>][5/'03].
   [Also search for: MAOA gene].

%A Y. C. Martin
%A J. L. Kofron
%A L. M. Traphagen
%T Do structurally similar molecules have similar biological activity?
%J J. Medicinal Chem.
%V 45
%N 19
%M AUG
%d 2002
%K jrnl, MolBio, c2002, c200x, c20xx, zz1024, chemical compound, molecule,
   structure, similarity, activity, actives, Daylight, Tanimoto
%X "... similar compounds do not necessarily interact with the target
   macromolecule in similar ways. ..."
   -- [<A HREF="https://doi.org/10.1021/jm020155c">doi:10.1021/jm020155c</A>]['24].
   (Also see ChemSim@[<A HREF="https://en.wikipedia.org/wiki/Chemical_similarity">wikip</A>]['24].)

%A M. J. Wise
%T The POPPS: Clustering and searching using peptide probability profiles
%J 10th Int. Conf. Intell. Sys. Molec. Biol. (ISMB)
%P ?-?
%M AUG
%D 2002
%O Bioinformatics V1 N1 pp1-8 2002
%P 2002
%K conf, MolBio, ISMB, ISMB10, ISMB02, protein, proteins, unusual composition,
   families, Pfam, LEA, zz1002
%X [<A HREF="http://www.bio.cam.ac.uk/~mw263/ftp/doc/POPP.pdf">paper</A>][10/'02]
   POPPs, a suite of inter-related software tools ...to discover what is
   statistically "unusual" in the composition of an unknown protein, or to
   automatically cluster proteins into families based on peptide composition.
   ...can search for related proteins based on peptide composition. Techniques
   based on peptide composition are effective because protein sequences are far
   from random, particularly in portions of the proteins such as catalytic
   domains that are under strong conservation pressure. The POPPs refines such
   comparisons by basing them peptide probabilities rather than raw counts,
   thus removing biases due to the inherent likelihood of certain peptides over
   others. Statistically based peptide composition also provides a view of
   proteins that is, to some extent, orthogonal to that provided by sequence.
   In a proof-of-concept study, The POPP suite is able to regroup into their
   families sets of approximately 100 randomised Pfam protein domains, and is
   used to explore a set of late embryogenesis abundant (LEA) proteins.

%A E. P. Xing
%A R. M. Karp
%T Cliff: Clustering of high dimensional microarray data via
   iterative feature filtering using normalized cuts.
%J Intell. Sys. in Mol. Bio.
%O Bioinformatics V17 (Supplement_1)
%P S306-S315
%M JUL
%D 2001
%K conf, ISMB, ISMB9, ISMB2001, MolBio, cluster, cut, zz1101
%X [Also search for: classification].

%A W. J. Murphy
%A E. Eizirik
%A S. J. O'Brien
%A O. Madsen, M. Scally, C. J. Douady, E. Teeling, O. A. Ryder,
   M. J. Stanhope, W. W. de Jong, M. S. Springer
%T Resolution of the early placental mammal radiation using Bayesian
   phylogenetics
%J Science
%P 2348-???
%V 294
%N 5550
%M ???
%D 2001
%K Science, MolBio, jrnl, mammals, phylogenetic, evolutionary tree, evolution,
   family trees, Bayes, Afrotheria, Eutheria, zz1201
%X via  K e v i n  K'  [<A HREF="http://www.sciencemag.org/cgi/content/abstract/294/5550/2348">www</A>][12/'01]
   [Also search for: Bayes Molbio],  [<A HREF="http://www.sciencemag.org/">mag'</A>][12/'01],
   ... The basal split is between Afrotheria and other placentals, at about
   103m.y., and may be accounted for by the separation of South America and
   Africa in the Cretaceous.  Crown-group Eutheria may have their most recent
   common ancestry in the Southern Hemisphere (Gondwana).
   [Also search for: mammal evolutionary tree].

%A M. Kschischo
%A M. Lassig
%T Finite-temperature sequence alignment
%J Pacific Symp. Biocomp.
%V 5
%P 621-632
%D 2000
%K MolBio, conf, PSB, PSB5, stats, significance
%X [Also search for: Gibbs sampling alignment],
   [also search for: probability alignment]
   -- [<A HREF="http://www.thp.uni-koeln.de/~lassig/lass_6.html">www</A>][12/'01].

%A G. J. McLachlan
%A R. W. Bean
%A D. Peel
%T A mixture model-based approach to the clustering of
   microarray expression data.
%J J. Bioinformatics
%V 18
%N 3
%P 413-422
%M MAR
%D 2002
%K micro array, arrays, gene jrnl, MolBio, zz0402
%X via p.e.t.

%A D. C. Hoyle
%A M. Rattray
%A R. Jupp
%A A. Brass
%T Making sense of micro-array data distributions
%J J. Bioinformatics
%V 18
%N 4
%P 576-584
%D 2002
%K jrnl, MolBio, microarrays, arrays, probability, Zipf, Zipfs law, zz0602
%X ... show that mRNA transcription data from a wide range of organisms and
   measured with a range of experimental platforms show close agreement
   with Benford's law (Benford, Proc. Am. Phil. Soc. , 78, 551-572, 1938) and
   Zipf's law (Zipf, The Psycho-biology of Language: an Introduction to Dynamic
   Philology , 1936 and Human Behaviour and the Principle of Least Effort ,
   1949). The distribution of the bulk of microarray spot intensities is
   well approximated by a log-normal with the tail of the distribution
   being closer to power law. The variance, sigma**2, of log spot intensity
   shows a positive correlation with genome size (in terms of number of
   genes) and is therefore relatively fixed within some range for a given
   organism. The measured value of sigma**2 can be significantly smaller than
   the expected value if the mRNA is extracted from a sample of mixed cell
   types. Our research demonstrates that useful biological findings may result
   from analyzing microarray data at the level of entire intensity
   distributions.
   via P.E.T.   H 570.5 C738 - on display 23/5/02
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/18/4/576">paper</A>][6/2'02]
   corr: david.c.hoyle@man.ac.uk.

%A T. D. Moloshok
%A R. R. Klevecz
%A J. D. Grant
%A F. J. Manion
%A W. F. Speier
%A M. F. Ochs
%T Application of Bayesian decomposition for analysing micro-array data
%J J. Bioinformatics
%V 18
%N 4
%P 566-575
%D 2002
%K jrnl, MolBio, BD, microarrays, arrays, zz0602
%X ... Bayesian Decomposition (BD) includes two features which make it useful
   for microarray data analysis: the ability to assign genes to multiple
   coexpression groups and the ability to encode biological knowledge into
   the system. Here we demonstrate the ability of the algorithm to provide
   insight into the yeast cell cycle, including identification of five temporal
   patterns tied to cell cycle phases as well as the identification of a
   pattern tied to an ~ 40 min cell cycle oscillator. The genes are
   simultaneously assigned to the patterns, including partial assignment to
   multiple patterns when this is required to explain the expression profile.
   via P.E.T.  H 570.5 C738 - on display 23/5/02
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/18/4/566">paper</A>][6/2'02].

%A J. Felsenstein
%A M. K. Kuhner
%A J. Yamato
%A P. Beerli
%T Likelihoods on coalescents: A Monte Carlo sampling approach to
   inferring parameters from population samples of molecular data.
%B Statistics in Molecular Biology and Genetics
%E F. Seillier-Moiseiwitsch
%I Inst. of Math. Stat. and American Math. Soc.
%S IMS Lecture Notes-Monograph Series
%V 33
%P 163-185
%D 1999
%K MolBio, LAMARC, phylogenetic, evolutionary, family, tree, trees, MCMC,
   likelihood, IMS, zz0702
%X [<A HREF="ftp://evolution.genetics.washington.edu/pub/papers/ims/ims.pdf">preprint (pdf)</A>][6/'02]
   J.F., Dept. Gen'me Res., U. W@shington

%A E. Birney
%T Hidden Markov models in biological sequence analysis
%J IBM J. of Res. and Dev.
%V 45
%N 3/4
%M MAY/JUL
%D 2001
%P 449-454
%K MolBio, jrnl, IBM, HMM, model
%X via p.e.t.  H 510.7805 I61.01
   [Also search for: MolBio]

%A R. J. Cho
%A M. J. Campbell
%A E. A. Winzeler, L. Steinmetz, A. Conway, L. Wodicka, T. G. Wolfsberg,
   A. E. Gabrielian, D. Landsman, D. J. Lockhart
%A R. W. Davis
%T A genome-wide transcriptional analysis of the mitotic cell cycle
%J Mol. Cell
%V 2
%P 65-73
%D 1998
%K jrnl, MolBio, c1998, c199x, c19xx, yeast, cell, life cycle, microarray,
   micro arrays, time series, timeSeries, expression profiles, levels, analysis,
   Saccharomyces cerevisiae, mRNA, RNA, budding yeast, cells, Davis Lab
%X "... report here the genome-wide characterization of mRNA transcript levels
   during the cell cycle of the budding yeast S.cerevisiae. Cell cycle-dependent
   periodicity was found for 416 of the 6220 monitored transcripts. >25% of the
   416 genes were found directly adjacent to other genes in the genome that
   displayed induction in the same cell cycle phase, suggesting a mechanism for
   local chromosomal organization in global mRNA regulation. >60% of the
   characterized genes that displayed mRNA fluctuation have already been
   implicated in cell cycle period-specific biological roles. Because more than
   20% of human proteins display sig. homology to y. proteins ... also link a
   range of human genes to cell cycle period-specific biological functions."
   -- [<A HREF="http://dx.doi.org/10.1016/S1097-2765(00)80114-8">doi:10.1016/S1097-2765(00)80114-8</A>]['14],
      9702192@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/9702192">p'bmed</A>]['14],
   at [<A HREF="http://genome-www.stanford.edu/cellcycle/">cellcycle</A>]['14],
      [<A HREF="http://171.65.26.52/yeast_cell_cycle/cellcycle.html">cellcycle</A>][7/'02],
   at [<A HREF="http://genomics.stanford.edu/">www</A>][7/'02].
   [Also search for: yeast life cycle].

%A A. V. Lukashin
%A R. Fuchs
%T Analysis of temporal gene expression profiles: clustering by
   simulated annealing and determining the optimal number of clusters
%J J. Bioinformatics
%V 17
%N 5
%P 405-414
%D 2001
%K MolBio, jrnl, micro array, arrays, clustering, SA, zz0802
%X ... the algorithm has been tested on real gene expression data
   (expression changes during yeast cell cycle) for which the fundamental
   patterns of gene expression and the assignment of genes to clusters
   are well understood from numerous previous studies.
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/17/5/405">paper</A>][7/'02]
   lex_lukashin at biogen com;         Data see: Cho 1998.

%A S. T. Sherry et al
%T dbSNP: the NCBI database of genetic variation
%J NAR
%V 29
%P 308-311
%D 2001
%K MolBio, jrnl, NAR, c2001, c200x, c20xx, data base, SNP, SNPs, SNiP, dbSNP,
   variation, single nucleotide polymorphisms, introduction, intro
%X Also see this [<A HREF="http://www.ncbi.nlm.nih.gov/About/primer/snps.html">intro</A>][8/'02]
   e.g. AAGGTTA,
        ATGGTTA,
         ^
   [Also search for: variation illness database].

%A F. Abascal
%A A. Valencia
%T Clustering of proximal sequence space for the
   identification of protein families.
%J J. Bioinformatics
%V 18
%N 7
%P 908-921
%M JUL
%D 2002
%K jrnl, MolBio, classification, clusters, family, zz0802
%X H 570.5 C738, via P.T.

%A A. B. Olshen
%A A. N. Jain
%T Deriving quantitative conclusions from microarray expression data
%J J. Bioinformatics
%V 18
%N 7
%M JUL
%D 2002
%P 961-970
%K jrnl, MolBio, micro arrays, microarrays, levels, nearest neighbour,
   pattern classification, zz0802
%X an augmentation of k-nearest neighbour pattern classification
   H 570.5 C738, via P.T.

%A The Plasmodium Genome Database Collaborative
%T PlasmoDB: An integrative database of the P. falciparum genome
   Tools for accessing and analyzing finished and unfinished sequence data.
%J NAR
%V 29
%N 1
%P 66-69
%D 2001
%K NAR, jrnl, MolBio, plasmodium, parasite, malaria, data base,
   c2001, c200x, c20xx, www, HREF, http
%X [<A HREF="http://plasmodb.org/">plasmodb.org</A>][8/'02]
   -- [<A HREF="http://plasmodb.org/PDF/NAR2001.pdf">paper</A>][8/'02].

%A M. A. Lane
%A G. S. Roth
%A D. K. Ingram
%T 2-deoxy-d-glucose feeding in rats mimics physiological effects of
   caloric restriction
%J J. Anti-Aging Medicine
%V 1
%N 4
%P 327-337
%D 1998
%K jrnl, 2DG, 2DDG, biol, biology, age, anti aging, ageing, old, youth, diet,
   lifespan, c1998, c199x, c19xx
%X ref in Sci Am, Aug '02 p.29.
   Also see [<A HREF="http://www.sciam.com/explorations/2002/051302aging/">www</A>][8/'02].

%A G. S. Roth
%A D. K. Ingram
%A M. A. Lane
%T Caloric restriction in primates and relevance to humans
%J Annals New York Acad. Sci.
%V 928
%P 305-315
%D 2001
%K jrnl, biol, biology, age, anti aging, ageing, lifespan, old, youth, diet,
   c2001, c200x, c20xx
%X ref in Sci Am, Aug '02 p29
   Also see [<A HREF="http://www.sciam.com/explorations/2002/051302aging/">www</A>][8/'02].

%A M. Gribskov
%A N. L. Robinson
%T Use of receiver operating characteristics (ROC) analysis to evaluate
   sequence matching
%J Computers Chem.
%V 20
%N 1
%P 25-33
%D 1996
%K jrnl, MolBio, ROC, alignment, match, quality, false positive,
   negative, sensitivity, specificity, PAM, PAM200, quote
%X "... the optimal conditions for alignments and database searches are not,
   and should not be expected to be, the same." ...
   "... [unexpectedly] the optimal PAM distance for these seq' groups appears
   to be roughly 200 PAM rather than 100-120 suggested by theoretical
   considerations (Altschul '91). 2ndly while the gap initiation penalty
   is very important [...], the ROC50 plot  [...] shows a rather broad peak.
   Reasonably values [are] 20-24. [...] gap extension penalty is of
   relatively little importance." [i.e. insensitive] [...]
   "fundamental difference between the searching and alignment operations."
   [also search for: ROC]

%A O. N. Temkin
%A A. V. Zeigarnik
%A D. Bonchev
%T Chemical Reaction Networks: A Graph-Theoretical Approach
%I Bocal Raton, FL: CRC Press
%D 1996
%K book, text, network, pathway, pathways, graphs, substrate, reactions,
   metabolic, chemistry, chem, c1996, c199x, c19xx

%A M. A. Nowak
%A S. Bonhoeffer
%A A. M. Hill
%A R. Boehme
%A H. C. Thomas
%A H. McDade
%T Viral dynamics in hepatitis B virus infection
%J PNAS
%V 93
%N 9
%P 4398-4402
%M APR
%D 1996
%K lamivudine, antiviral treatment, liver, viral turnover, mathematical model,
   jrnl, PNAS, HBV, simulation, virus, zzVDRL
%X "... find that in persistently infected patients, HBV particles are cleared
   from the plasma with a half-life of approx 1.0 day, ... viral release into
   the periphery is approx 10**11 virus particles per day. we find a wide
   distribution of half-lives for virus-producing cells, ranging from 10 to 100
   days in different patients, which may ..."
   -- [<A HREF="http://www.pnas.org/cgi/content/abstract/93/9/4398">www</A>]['05].

%A A. V. Herz
%A S. Bonhoeffer
%A R. M. Anderson
%A R. M. May
%A M. A. Nowak
%T Viral dynamics in vivo: Limitations on estimates of intracellular delay and
   virus decay
%J PNAS
%V 93
%N 14
%P 7247-7251
%M JUL
%D 1996
%K jrnl, c1996, c199x, c19xx, HIV, HIV1, HBV, viral
%X "Anti-viral drug treatment ... Viral decline occurs in several phases and
   provides information on important kinetic constants of virus replication in
   vivo & pharmacodynamical properties. ... We derive analytic solutions for the
   dynamics following treatment with reverse transcriptase inhibitors, protease
   inhibitors, or a combination of both. For HIV-1, our results show that the
   phase of rapid decay in plasma virus (days 2-7) allows precise estimates for
   the turnover rate of productively infected cells. The initial quasi-
   stationary phase (days 0-1) & the transition phase (days 1-2) are explained
   by the combined effects of pharmacological & intracellular delays, the
   clearance of free virus particles, & the decay of infected cells. Reliable
   estimates of the first three quantities are not possible from data on virus
   load only; such estimates require additional measurements.
   In contrast with HIV-1, for HBV our model predicts that frequent early
   sampling of plasma virus will lead to reliable estimates of the free virus
   half-life & the pharmacological properties of the administered drug. On the
   other hand, for HBV the half-life of infected cells cannot be estimated from
   plasma virus decay."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.93.14.7247">doi:10.1073/pnas.93.14.7247</A>]['06].

%A H. Norder
%A J. W. Ebert
%A H. A. Fields
%A I. K. Mushahwar
%A K. O. Magnius
%T Complete sequencing of a gibbon hepatitis B virus genome reveals a
   unique genotype distantly related to the chimpanzee hepatitis B virus
%J Virology
%V 218
%N 1
%P 214-223
%M APR
%D 1996
%K jrnl, MolBio, c1996, c199x, c19xx, HBV, virus, viral
%X "... (HBV) strain that was transmitted from a gibbon with chronic hepatitis B
   to a chimp. that subsequently developed acute hepatitis B. ... 3,182 n. long
   ... the four open reading frames (ORFs) of this virus were all maintained,
   although there were AA subs. affecting all the ORFs. ...
   ... most similar to the chimpanzee HBV strain with which it shared 90.3%
   nucleic acid homology at the level of the complete genome and 96.3% homology
   at the level of the S-gene region corresponding to HBsAg, ...
   ...  99+% bootstrap support for the gibbon and the chimpanzee HBV to be
   grouped within the human HBV strains & that they represented later offshoots
   than the HBV strains of genotype F. However, in most of the dendrograms both
   the gibbon and the chimpanzee strains represented early lineages, indicating
   that these viruses are indigenous to their respective hosts and not recent
   acquisitions from man."

%A R. D. King
%A S. H. Muggleton
%A A. Srinivasan
%A M. J. E. Sternberg
%T Structure activity relationships derived by machine learning: The use of
   atoms and their bond connectivities to predict mutagenicity using
   inductive logic programming
%J PNAS
%V 93
%N 1
%P 438-442
%M JAN
%D 1996
%K jrnl, PNAS, MolBio, c1996, c199x, c19xx, atom, bonds, chemical compound,
   connectivity, mutagen, ILP, LP, SAR, drug design,
   rdk, RDKing, Ashwin Srinivasan
%X "... representing chemical structure by atoms and their bond connectivities
   in combination with [ILP] ... use a relational description, where the
   internal const'n of the description maps that of the object described. Our
   atom & bond connectivities rep. is a rel'l description. ILP algs. can form
   SARs with rel'l descriptions. We have tested the relational approach by
   investigating the SARs of 230 aromatic & heteroaromatic nitro compounds.
   These cmpds had been split previously into 2 subsets, 188 c. that were
   amenable to regression & 42 that were not. For the 188 c., a SAR was found
   that was as accurate as the best stat. or NN-generated SARs. The PROGOL SAR
   has the advantages that it did not need the use of any indicator vars.
   handcrafted by an expert, & the generated rules were easily comprehensible.
   For the 42 c., PROGOL formed a SAR that was significantly (P < 0.025) more
   accurate than linear reg., quadratic reg., and back-prop.. This SAR is based
   on an automatically generated structural alert for mutagenicity."
   -- [<A HREF="http://www.pnas.org/cgi/content/abstract/93/1/438">pdf@pnas</A>]['08].
   [Also search for: chemical compound SAR].

%A A. Godzik
%T The structural alignment between two proteins: Is there a unique answer?
%J Protein Sci.
%V 5
%N 7
%P 1325-1338
%M JUL
%D 1996
%K jrnl, MolBio, c1996, c199x, c19xx, evolution, protein, structure, fold,
   folds, structural, alignment, 3D, optimal, suboptimal, true, quality
%X "... For several pairs of such proteins, existing structural alignments
   obtained from the literature, as well as alignments prepared using several
   different similarity criteria, are compared with each other. It is shown that
   in general, they differ from each other, with differences increasing with
   diminishing seq. similarity. Differences are particularly strong between
   alignments optimizing global similarity measures, such as RMS deviation
   between C alpha atoms, & alignments focusing on more local features, such as
   packing or interaction pattern similarity. Simply speaking, by putting
   emphasis on different aspects of structure, different structural alignments
   show the unquestionable similarity in a different way. ..."   (via AK).
   -- [<A HREF="http://dx.doi.org/10.1002/pro.5560050711">doi:10.1002/pro.5560050711</A>]['09].
   [Also search for: MolBio protein structure alignment].

%A P. Bernaola-Galvan
%A R. Roman-Roldan
%A J. L. Oliver
%T Compositional segmentation and long-range fractal correlations in
   DNA sequences
%J Physical Review E
%V 53
%N 5
%M MAY
%D 1996
%P 5181-5189
%K MolBio, sequence, segment, c1996, c199x, c19xx, correlation, scaling
%X "...algorithm ... Jensen-Shannon entropic divergence ...decompose long-range
   correlated DNA sequences into ... compositionally homogeneous patches. By
   ...setting the significance level ... the underlying power-law distribution
   of patch lengths can be revealed. Some of the identified DNA domains were
   uncorrelated, but most of them continued to display long-range correlations
   even after several steps of recursive segmentation, thus indicating a
   complex multi-length-scaled structure for the sequence. On the other hand,
   by separately shuffling each segment, or by randomly rearranging the order
   in which the different segments occur in the sequence, shuffled sequences
   preserving the original statistical distribution of patch lengths were
   generated. Both types of random sequences displayed the same correlation
   scaling exponents as the original DNA sequence, thus demonstrating that
   neither the internal structure of patches nor the order in which these are
   arranged in the sequence is critical; therefore, long-range correlations
   ... seem to rely only on the power-law distribution of patch lengths."
   -- [<A HREF="http://www.nslij-genetics.org/dnacorr/bernaola96.pdf">pdf@nslij-genetics.org</A>][8/'03].

%A R. Dawkins
%T Climbing Mount Improbable
%I WWNorton
%D 1996
%K book, text, c1996, c199x, c19xx, zz0310, biol, biology, life, evolution,
   complexity, phenotype
%X 1st ed 1996; hb us$18; uk us isbn:0393039307; uk us isbn13:978-0393039306.

%A S. J. Gould
%T Full House: The Spread of Excellence from Plato to Darwin
%I ThreeRivers
%P 244
%D 1996
%K book, text, c1996, c199x, c19xx, zz0310, evolution, biol, biology,
   complexity, Dawkins, Human Chauvinism
%X 1st ed 1996; pb us$11; uk us isbn:0609801406; uk us isbn13:978-0609801406.
   'The human mind has a trusty device for simplifying a complex world: reduce
   to averages and identify trends. Although valuable, the risk is that we
   ignore variations and end up with a skewed view of reality. In evolutionary
   terms, the result is a view in which humans are the inevitable pinnacle of
   evolutionary progress, instead of, as SJG patiently argues, "a cosmic
   accident that would never arise again if the tree of life could be
   replanted." The implications of Gould's argument may threaten certain of our
   philosophical and religious foundations but will in the end provide us with a
   clearer view of & a greater appreciation for the complexities of our world.'
  Also see a review:
     R. Dawkins, 'Human Chauvinism', Evolution, 51(3), pp.1015-1020, 1997
     @[<A HREF="http://www.jstor.org/stable/2411179">Jstor</A>]['10].

%A G. P. Wagner
%A L. Altenberg
%T Perspective: Complex adaptations and the evolution of evolvability
%J Evolution
%V 50
%N 3
%P 967-976
%M JUN
%D 1996
%K jrnl, c1996, c199x, c19xx, zz0317, evolution, adaption, learning,
   evolvability, modularity, genotype-phenotype, pleiotropic, variability,
   natural selection, Baldwin effect
%X "... propose that the genotype-phenotype map can evolve by two main routes:
   epistatic mutns, or the creation of new genes. A common result for
   organismic design is modularity.  By modularity we mean a genotype-phenotype
   map in which there are few pleiotropic effects among characters serving
   different fns, with pleiotropic effects falling mainly among characters
   that are part of a single functional complex.  Such a design is expected to
   improve evolvability by limiting the interference between the adaptation of
   different fns. Several popn genetic models are reviewed that are
   intended to explain the evolutionary origin of a modular design. While our
   current knowledge is insufficient to assess the plausibility of these models,
   they form the beginning of a framework for understanding the evolution of the
   genotype-phenotype map."
   -- 2410639@[<A HREF="http://www.jstor.org/stable/2410639">jstor</A>]['17],
      [<A HREF="http://dx.doi.org/10.2307/2410639">doi:10.2307/2410639</A>]['17].
   [Also search for: Wagner Altenberg] and [also search for: Baldwin effect].

%A B. J. Strait
%A T. G. Dewey
%T The Shannon information entropy of protein sequences
%J Biophys. J.
%V 71
%P 148-155
%M JUL
%D 1996
%K jrnl, MolBio, c1996, c199x, c19xx, zz0920, protein sequence, entropy,
   compress, compression, bits
%X "... info. ent. is est. by three methods: a k-tuplet analysis, a generalized
   Zipf analysis, and a 'Chou-Fasman gambler.' ... The Zipf analysis & k-tuplet
   analysis give Shannon entropies of ~2.5 bits/amino acid. This entropy is much
   smaller than the value of 4.18 bits/amino acid obtained from the nonuniform
   composition of amino acids in proteins. ..."
   -- [<A HREF="https://www.cell.com/biophysj/pdf/S0006-3495(96)79210-X.pdf">www</A>]['20].
   [Also search for: MolBio protein compressible].

%A J. J. Kasianowicz
%A E. Brandin
%A D. Branton
%A D. W. Deamer
%T Characterization of individual polynucleotide molecules using a membrane
   channel
%J PNAS
%V 93
%N 24
%P 13770-13773
%M NOV
%D 1996
%K jrnl, PNAS, MolBio, c1996, c199x, c19xx, zz0714, single molecule, SMRT,
   sequencing, nanopore, Oxford, DNA, RNA
%X "... an electric field can drive single-stranded RNA & DNA molecules through
   a 2.6-nm diameter ion channel in a lipid bilayer membrane. Because the
   channel dia. can accommodate only a single strand of RNA or DNA, each polymer
   traverses the membrane as an extended chain that partially blocks the
   channel. The passage of each m. is detected as a transient decrease of ionic
   current whose duration is proportional to polymer length. Channel blockades
   can therefore be used to measure polynucleotide length. With further
   improvements, the method could in principle provide direct, high-speed
   detection of the sequence of bases in single molecules of DNA or RNA."
   -- [<A HREF="http://www.pnas.org/content/93/24/13770">pnas</A>]['14].
   [Also search for: MolBio single molecule sequencing]  and
   [also search for: MolBio nanopore].

%A S. E. Brenner
%A C. Chothia
%A T. J. P. Hubbard
%T Assessing sequence comparison methods with reliable structurally identified
   distant evolutionary relationships
%J PNAS
%V 95
%N 11
%P 6073-6078
%M MAY
%D 1998
%K jrnl, MolBio, PNAS, alignment, quality, false positive, negative, ROC,
   sensitivity, specificity, BLAST, FASTA, SSEARCH, Pvalues, Pvalue, Evalues,
   Evalue, protein, proteins, SCOP,  Wu-Blast2, c1998, c199x, c19xx
%X "Pairwise sequence comparison methods have been assessed using proteins
   whose relationships are known reliably from their structures & functions,
   as described in the SCOP database   ...   error rate of all algorithms is
   greatly reduced by using statistical scores to evaluate matches rather than
   percentage identity or raw scores. The E-value statistical scores of SSEARCH
   and FASTA are reliable: the number of false positives found in our tests
   agrees well with the scores reported. However, the P-values reported by
   BLAST and WU-BLAST2 exaggerate significance by orders of magnitude. ..."
   -- [<A HREF="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9600919">pubmedcentral</A>]['05].
   (Also see  G r i b s k o v  and R' '96.)

%A S. B. Eaton
%A M. Konner
%T Paleolithic nutrition - A consideration of its nature and current
   implications
%J NEJM
%V 312
%P 283-289
%M JAN
%D 1985
%K jrnl, NEJM, c1985, c198x, c19xx, human, health, diet, ancient, Paleolithic,
   dietary, nutrition, agriculture, hominid, homo, hunter gatherer, caveman,
   cavemen, evolutionary discordance hypothesis
%X "Humanity has existed as a genus for about 2 million years, and our prehuman
   hominid ancestors, the australopithecines, appeared at least 4 million years
   ago. ... Natural selection has provided us with nutritional adaptability;
   however, human beings today are confronted with diet-related health problems
   that were previously of minor importance and for which prior genetic
   adaptation has poorly prepared us. ... The diet of our remote ancestors may
   be a reference standard for modern human nutrition and a model for defense
   against certain 'diseases of civilization.'"
   -- [<A HREF="http://dx.doi.org/10.1056/NEJM198501313120505">doi:10.1056/NEJM198501313120505</A>]['13].
   (NB. It is just a hypothesis.)
   [Also search for: paleolithic diet].

%A A. D. McLachlan
%A D. Ross Boswell
%T Confidence limits for homology in protein or gene sequences.  The c-myc
   oncogene and adenovirus E1a protein
%J J. Mol. Biol.
%P 39-49
%V 185
%D 1985
%K JMB, jrnl, MolBio, significance test, confidence interval

%A C. Chothia
%A A. M. Lesk
%T The relation between the divergence of sequence and structure in proteins
%J EMBO J.
%V 5
%N 4
%P 823-826
%M APR
%D 1986
%K CL86, jrnl, EMBO, MolBio, c1986, c198x, c19xx, zz0416, AMLesk, protein,
   homology, homologous, 3D, structure, fold, folds, RMS
%X "Homologous proteins have regions which retain the same general fold &
   regions where the folds differ. For pairs of distantly related ps. (residue
   identity ~20%), the regions with the same fold may comprise less than half of
   each molecule. The regions with the same general fold differ in struct. by
   amounts that increase as the [AA] seqs. diverge. The [RMS] deviation in the
   posns of the main chain atoms, delta, is related to the fraction of mutated
   residu es, H, by the expression: delta(A) = 0.40 e^(1.87 H)."
   -- PMC1166865@[<A HREF="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1166865/">ncbi</A>]['16].

%A M. P. Wells
%A I. Douglas-Hamilton
%T Analysis of tusks from the Central African Republic
%J Pachyderm
%N 6
%P 16-18
%D 1986
%K c1986, c198x, c19xx, elephant, elephants, tusk, tusks, size, decrease,
   smaller, poaching, poacher, natural selection, evolution, Darwinism,
   intelligent design
%X In [<A HREF="http://www.african-elephant.org/pachy/pdfs/pachy06.pdf">pdf</A>]['13],
   I.D.-H.@[<A HREF="http://users.ox.ac.uk/~abrg/tracking/team/idhamilton.html">ox</A>]['13].
      The above does not say that elephant tusk sizes have been decreasing
      due to natural selection & poaching, but that is I.D-H's belief:
   Various newspaper articles ~2008 quoted a decrease of a half since 19C,
   e.g., [<A HREF="http://www.telegraph.co.uk/science/science-news/3322455/Why-elephants-are-not-so-long-in-the-tusk.html">D.T.</A>][20/1/2008].

%A J. G. Reich
%A W. Meiske
%T A simple statistical significance test of window scores in large dot
   matrices obtained from protein or nucleic acid sequences
%J CABIOS
%V 3
%N 1
%P 25-30
%D 1987
%K Bioinformatics, jrnl, MolBio, dot plot, plots, dotplot, McLachlan, Boswell,
   confidence interval, limits, runs, blocks, dot plot, plots
%X ... takes the correlation between overlapping windows into account.
   [Now the J. Bioinf.]   [Also see Gibbs '70.]

%A J. W. Schopf
%A B. M. Packer
%T Early Archean (3.3-billion to 3.5-billion-year-old) microfossils from
   Warrawoona Group, Australia
%J Science
%V 237
%P 70-73
%M JUL
%D 1987
%K jrnl, c1987, c198x, c19xx, stromatolite, cyanobacteria, origin, origins,
   early, ancient, life, photosynthesis, WA, fossil, microfossil
%X "Cellularly preserved filamentous & colonial fossil microorganisms have
   been discovered in bedded carbonaceous cherts from the Early Archean Apex
   Basalt & Towers Formation of NW WA. The cell types detected suggest that
   cyanobacteria, & therefore oxygen-producing photosynthesis, may have been
   extant as early as 3.3 billion to 3.5 billion years ago. These fossils are
   among the oldest now known from the geologic record; their discovery
   substantiates previous reports of Early Archean microfossils in Warrawoona
   Group strata."
   -- @[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/11539686">ncib</A>]['12].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Origin_of_life">wikip</A>]['12].)

%A C. Chothia
%A A. M.Lesk
%T Canonical structures for the hypervariable regions of immunoglobulins
%J J. Molec. Biol.
%V 196
%N 4
%P 901-917
%M AUG
%D 1987
%K biol, JMB, jrnl, MolBio, c1989, c198x, c19xx, zz0518, AMLesk, antibody,
   antibodies, structure, Fab, VL, immunoglobulin
%X "... Examination of the seqs. of immunoglobulins of unknown structure shows
   that many have hypervariable regions that are similar in size to one of the
   known structures and contain identical residues at the sites responsible for
   the observed conformation. This implies that these hypervariable regions have
   conformations close to those in the known structures. For five of the
   hypervariable regions, the repertoire of conformations appears to be limited
   to a relatively small number of discrete structural classes. We call the
   commonly occurring main-chain conformations of the hypervariable regions
   'canonical structures'. ..."
   -- [<A HREF="https://doi.org/10.1016/0022-2836(87)90412-8">doi:10.1016/0022-2836(87)90412-8</A>]['18].

%A F. M. Richards
%A C. E. Kundrot
%T Identification of structural motifs from protein coordinate data:
   Secondary structure and first-level supersecondary structure
%J Proteins: Structure, Function and Genetics
%V 3
%N 2
%P 71-84
%D 1988
%K MolBio, DDM, c1988, c198x, c19xx, proteins, super secondary structure, 3D,
   superSecondary, structure, structural, tertiary, 3D, pattern, motif,
   helix, extended, turns
%X "A computer program [to] produces a description of the SS & supersecondary
   structure of a polypeptide chain using the list of alpha carbon coords. as
   input. ... determines the initial & final residues in helices, extended
   strands, sharp turns, & omega loops. ... accomplished through the use of
   difference distance matrices. The dists. in idealized models of the segments
   are compared with the actual struct., & the diffs. are eval'd for agreement
   within preset limits. The program assigns 90-95% of the residues in most
   proteins to at least one type of secondary elt. In a 2nd step the now-defined
   helices & strands are idealized as straight line segs., & the axial dirns &
   locations are compiled from the input C alpha coordinate list. These data are
   used to check for moderate curvature ... allows a quite accurate 2D display
   of the 3D structure ..."
   -- [<A HREF="http://dx.doi.org/10.1002/prot.340030202">doi:10.1002/prot.340030202</A>]['10].
   [Also search for: MolBio super secondary structure].

%A S. J. Freeland
%A L. D. Hurst
%T The genetic code is one in a million
%J J. Mol. Evol.
%P 238-248
%M SEP
%D 1998
%K MolBio, jrnl, JME, DNA, protein, codes, origin, origins, evolution, bases,
   codon, codons, amino acids, translation, c1998, c199x, c19xx
%X ... 2nd base less efficient [error minimizing], by about 3 orders of
   magnitude, than he first and third bases. ...
   -- [<A HREF="http://www.evolvingcode.net/documents/Doc8.pdf">evolvingcode.net</A>][3/'04].

%A S. T. Cole
%T Comparative mycobacterial genomics
%J Curr. Opin. Microbiol.
%I ElsevierScience
%V 1
%N 5
%P 567-571
%M OCT
%D 1998
%K Mycobacterium tuberculosis, leprae, tuberculosis, TB, leprosy, medical,
   biol, biology, bacteria, MolBio, genome, c1998, c199x, c19xx
%X "Genomics is providing us with a mass of information about the biochemistry,
   physiology and pathogenesis of Mycobacterium tuberculosis and Mycobacterium
   leprae. Comparison of the two genome sequences is mutually enriching and
   indicates that the M. leprae genome appears to have undergone shrinkage and
   large-scale gene inactivation, which may account for the exceptionally slow
   growth of this organism."   Auth: stcole at pasteur dot fr
   Also see [<A HREF="http://www.pasteur.fr/recherche/RAR/RAR2000/Lgmb-en.html">www</A>]['04]
   and Cole c2000.

%A C. Gale
%A C. Martyn
%T Larks and owls and health, wealth, and wisdom
%J BMJ
%V 317
%P 1675-1677
%M DEC
%D 1998
%K jrnl, MBJ, c1998, c199x, c19xx, sleep pattern, patterns, zz1105, success,
   early, bed, rise, healthy, wealthy, wise, sleeping, stats
%X "To test the validity of Benjamin Franklin's maxim "early to bed and early
   to rise makes a man healthy, wealthy, and wise."
   Design: Cross sectional analysis of sleeping patterns in a nationally
   representative group of elderly people, & longitudinal investigation of
   mortality. ... 1229 men & women aged 65 & over who in 1973-4 had taken part
   in a survey funded by [DHSS] ... 356 people (29%) were defined as larks (to
   bed before 11 pm & up before 8 am) & 318 (26%) were defined as owls (to bed
   at or after 11 pm & up at or after 8 am). There was no indication that larks
   were richer than those with other sleeping patterns. On the contrary, owls
   had the largest mean income & were more likely to have access to a car. ...
   The lowest risk occurred in people who spent 8 hours in bed (adjusted
   relative risk 0.8; 0.7 to 1.0). ..."
   -- [<A HREF="http://bmj.bmjjournals.com/cgi/content/abstract/317/7174/1675">bmj</A>]['05].

%A N. Ohta
%A N, Sato
%A T. Kuroiwa
%T Structure and organization of the mitochondrial genome of the unicellular red
   alga Cyanidioschyzon merolae deduced from the complete nucleotide sequence
%J NAR
%P 5190-5298
%V 26
%N 22
%M NOV
%D 1998
%K jrnl, NAR, MolBio, red alga, algal, algae, mitochondria origin, DNA, genome,
   mGenome, c1998, c199x, c19xx, bio, biol, ATrich, D89861, NC000887
%X [ DDBJ/EMBL/GenBank accession no. D89861 ][ 7/7/'00 genbank: NC 000887].
   "... contains 34 genes for proteins including unidentified [ORFs)](3 subunits
   of cytochrome c oxidase, apocytochrome b protein, 3 subunits of F1F0-ATPase,
   7 subunits of NADH ubiquinone oxidoreductase, three 3 of succinate
   dehydrogenase, 4 proteins implicated in c-type cytochrome biogenesis, 11
   ribosomal subunits & two 2 [ORFs]), 3 genes for rRNAs & 25 genes for tRNAs.
   The G+C content of this mitochondrial genome is 27.2%. The genes are encoded
   on both strands. The genome size is comparatively small for a plant
   mitochondrial genome (32,211-bp). ... ...suggest that plant mitochondria
   originate from the same ancestor as other mitochondria and ..."
   -- [<A HREF="http://nar.oupjournals.org/cgi/content/full/26/22/5190">paper@oup</A>][7/'04],
   -- [<A HREF="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9801318">paper@pub med</A>][7/'04],
   (see 2OO4 for nuclear genome).

%A W. Northcutt
%T The Darwin Awards: Evolution in Action
%D 2000
%P 327
%K book, text, funny, fun, funn, haha, ha ha, award, c2000, c200x, c20xx
%X a favourite; uk us isbn:0525945725; uk us isbn13:978-0525945727.
   Also `Darwin Awards II: Unnatural Selection',
        2001; uk us isbn:0525946233; uk us isbn13:978-0525946236.

%A W. Northcutt
%T The Darwin Awards II: Unnatural Selection
%D 2001
%K book, award, unnatural selection, gene pool, removal from, 2001, zz1202
%X hb; uk us isbn:0525946233; uk us isbn13:978-0525946236.
   (Also vol 1; uk us isbn:0525945725; uk us isbn13:978-0525945727.)

%A P. Simmonds
%T Reconstructing the origins of human Hepatitis viruses
%J Philosophical Trans.: Biological Sci.,
   Population Biology of Emerging and Re-emerging Pathogens
%V 356
%N 1411
%P 1013-1026
%M JUL
%D 2001
%K jrnl, MolBio, c2001, c200x, c20xx, virus, viral, HBV, hepB, HCV, hepC,
   evolution, HGV, GBV
%X "... using knowledge of their rates of seq. change. While info. on the latter
   is limited to short obs. periods & ...subject to considerable error &
   uncertainty, the relatively recent times of origin for genotype of each virus
   predicted by this method (HCV, 500-2000 years; HBV, 3000 years; HGV/GBV-C,
   200 years) are quite incompatible with their epidemiological distributions
   in human populations. They also cannot easily be reconciled with the recent
   evidence for species-associated variants of HBV & HGV/GBV-C in a range of
   non-human primates. The apparent conservatism of viruses over long periods
   implied by their epidemiological distributions instead suggests that
   nucleotide sequence change may be subject to constraints peculiar to viruses
   with single-stranded genomes, or with overlapping reading frames that defy
   attempts to reconstruct evolution according to the principles of the
   'molecular clock'. Large population sizes & intense selection pressures that
   optimize fitness may be additional factors that set virus evolution apart
   from that of their hosts."
   -- [<A HREF="http://links.jstor.org/sici?sici=0962-8436(20010729)356%3A1411%3C1013%3ARTOOHH%3E2.0.CO%3B2-9">@jstor</A>]['07].

%A A. Caprara
%T Sorting by reversals is difficult
%J Proc. 1st Annual Int. Conf. on Computational Molec. Biol.
%E S. Istrail
%E P. Pevzner
%E M. Waterman
%I ACM
%D 1997
%P 75-83
%K conf, MolBio, RECOMB97, RECOMB1, permutations, sort, c1997, c199x, c19xx,
   unsigned, complexity, time, NP-hard
%X [<A HREF="http://www.or.deis.unibo.it/caprara.html">home</A>][10/'02].
   (Finding the optimal solution to) sorting *unsigned* permutations by
   reversals is NP-hard.
   [[But for signed perms - Polynomial! see H a n n e n h a l l i '95,'96,'99]]
   See C's later papers.  [Also search for: sorting reversals].

%A R. Zardoya
%A A. Meyer
%T The complete DNA sequence of the mitochondrial genome of a "living fossil"
   the Coelacanth (Latimeria chalumnae)
%J Genetic
%V 146
%N 3
%P 995-1010
%M JUL
%D 1997
%K jrnl, MolBio, c1997, c199x, c19xx, vertebrate, fish, lobe finned, Coelacanth,
   mitochondria
%X "... 16407 bp ... Max parsim. ... lungfish/c. or lungfish/tetrapod
   sistergroup ..."
   -- [<A HREF="http://www.genetics.org/content/146/3/995">www</A>]['13].
   [Also search for: Coelacanth].

%A L. Shandley
%A D. Alcorn
%A E. M. Wintour
%T Ovine amniotic and allantoic epithelia across gestation
%J The Anatomical Record
%V 248
%N 4
%P 542-553
%M AUG
%D 1997
%K jrnl, c1997, c199x, c19xx, biol, biology, sheep, lamb, ovine, gestation,
   reproduction, Lynne
%X "... With increasing gestational age, the cell ht of epithelium of the
   membranes incr., as did the # of apical microvilli & the length of zonulae
   occludentes. Epithelial cell cytoplasm incr. in complexity, & cell shape
   changed from flattened to cuboidal. Proliferation of cells occurred until
   close to term. Immunoreactivity to Ca++-ATPase was present in the basolateral
   membranes at all stages of gestation examined, but hybridization with the
   alpha & beta subunits of Na,K-ATPase was present only at or after 100 days of
   gestation.  The epithelia of the sheep amnion & allantois display
   characteristics typical of transporting epithelia. As the e. mature, changes
   related to incr. capacity for solute & fluid transport regulation occur."
   -- [<A HREF="http://dx.doi.org/10.1002/(SICI)1097-0185(199708)248:4<542::AID-AR6>3.0.CO;2-N">doi:10.1002/(SICI)1097-0185(199708)248:4<542::AID-AR6>3.0.CO;2-N</A>]['13],
      auth1@[<A HREF="http://www.linkedin.com/pub/lynne-shandley/9/614/985/">l.in</A>]['13].


%A R. L. Dunbrack jnr
%A F. E. Cohen
%T Bayesian statistical analysis of protein side-chain rotamer preferences
%J Protein Sci.
%V 6
%N 8
%P 1661-1681
%M AUG
%D 1997
%K jrnl, MolBio, c1997, c199x, c19xx, zz1122, side chain, protein, structure,
   sideChain, library, angles, bbdep, bbdep2010, phi, psi, chi1, chi2, chi3
%X "... stat. analysis of the conformations of side chains in proteins from
   [PDB]. This is an extension of the backbone-dependent rotamer library, &
   includes rotamer pop'ns & avg chi angles for a full range of phi, psi
   values. ..."
   -- [<A HREF="https://doi.org/10.1002/pro.5560060807">doi:10.1002/pro.5560060807</A>]['22],
      [<A HREF="https://pubmed.ncbi.nlm.nih.gov/9260279/">PDB</A>]['22].
   Also see DunbrackLab@[<A HREF="http://dunbrack.fccc.edu/lab/">fccc</A>]['22]
   & bbdep2010 (updated 2010).  [Also search for: Dunbrack c2011].

%A R. Plomin
%A et al ...
%A J. C. DeFries
%T Nature, nurture, and cognitive development from 1 to 16 years:
   A parent-offspring adoption study
%J Psychological Sci.
%V 8
%N 6
%P 442-447
%M NOV
%D 1997
%K jrnl, c1997, c199x, c19xx, zz0718, intelligence, IQ, nature, nurture,
   genetic, cognition, genes, parents, children, human development
%X "Children increasingly resemble their parents in cognitive abilities from
   infancy through adolescence Results obtained from a 20-year longitudinal
   adoption study of 245 adopted children and their biological and adoptive
   parents, as well as 245 matched nonadoptive (control) parents and offspring,
   show that this increasing resemblance is due to genetic factors ...
   Although these results were strongest for general cognitive ability & verbal
   ability similar results were found for other specific cognitive abilities -
   spatial ability, speed of processing, and recognition memory. ... indicate
   that within this population, genes that stably affect cognitive abilities in
   adulthood do not all come into play until adolescence & that environmental
   factors that contribute to cognitive development are not correlated with
   parents' cognitive ability."
   -- [<A HREF="https://doi.org/10.1111/j.1467-9280.1997.tb00458.x">doi:10.1111/j.1467-9280.1997.tb00458.x</A>]['18].

%A C. Bystroff
%A D. Baker
%T Blind predictions of local protein structure in CASP2 targets using the
   I-sites library
%J Proteins
%V Suppl. 1
%P 167-171
%D 1997
%K jrnl, MolBio, c1997, c199x, c19xx, I-sites, Isites, protein, library,
   dictionary, structure, motif, pattern, fragment, sequence, local structure,
   tertiary, 3D
%X "Blind predns of the local struct. of nine CASP2 targets were made using
   the I-sites library of short seq.-struct. motifs, revealing strengths &
   weaknesses in this new knowledge-based method. Many turns between secondary
   structural elements were accurately predicted. Estimates of the confidence of
   prediction correl. well with the accuracy over the whole set. Bias toward
   structs. used to develop the library was minimal, probably because of the
   extensive use of cross-validation. However, helix posns were better predicted
   by the PHD program. The method is likely to be sensitive to the quality of
   the seq. alignment. A general measure for evaluating local struct. predns is
   suggested."
   -- pdf@[<A HREF="http://www.bioinfo.rpi.edu/bystrc/pdf/Bystroff_97_proteins.pdf">rpi</A>]['13],
      Bys@[<A HREF="http://www.bioinfo.rpi.edu/bystrc/">rpi</A>]['13].
   [Also search for: protein structure fragment library].

%A D. S.Latchman
%T Transcription factors: An overview
%J Int. J. Biochem. and Cell Biol.
%V 29
%N 12
%P 1305-1312
%M DEC
%D 1997
%K MolBio, c1997, c199x, c19xx, zz0820, Transcription factor, defn, TF, TFs,
   intro, survey, transcriptionFactor, gene expression, regulation
%X -- [<A HREF="https://doi.org/10.1016/S1357-2725(97)00085-X">doi:10.1016/S1357-2725(97)00085-X</A>]['20].
   [*Also see,  "a transcription factor (TF) (or seq.-specific DNA-binding
   factor) is a protein that controls the rate of transcription of genetic
   info. from DNA to mRNA, by binding to a specific DNA seq."
   -- TFs@[<A HREF="https://en.wikipedia.org/wiki/Transcription_factor">wikip</A>]['20].*]

%A A. U. Neumann
%A N. P. Lam
%A H.Dahari, D.R.Gretch, T.E.Wiley, T.J.Layden, A.S.Perelson
%T Hepatitis C viral dynamics in vivo and the antiviral efficacy of
   interferon-alpha therapy
%J Science
%V 282
%N 5386
%P 103-107
%M OCT
%D 1998
%K jrnl, HCV, c1998, c199x, c19xx, virus, model, simulation
%X "...23 patients ... analyzed with a math. model. ... major initial effect of
   IFN is to block virion production or release, with blocking efficacies of 81,
   95, & 96% for daily doses of 5, 10, and 15 m. int. units, resp..  est.
   virion half-life (t1/2) was, on average, 2.7 hrs, with pretreatment prod'n
   and clearance of 10(12) virions/day. est. infected cell death rate exhibited
   large interpatient variation (corr. t1/2 = 1.7 to 70 days), was inversely
   correlated with baseline viral load, & was +ve correlated with alanine
   aminotransferase levels. Fast death rates were predictive of virus
   being undetectable by PCR at 3 months. ...show that infection with HCV is
   highly dynamic & that early monitoring of viral load can help guide therapy."
   -- [<A HREF="http://dx.doi.org/10.1126/science.282.5386.103">doi:10.1126/science.282.5386.103</A>]['05].

%A K. Karplus
%A C. Barrett
%A R. Hughey
%T Hidden Markov models for detecting remote protein homologies
%J J. Bioinformatics
%V 14
%N 10
%P 846-856
%D 1998 ?
%K jrnl, MolBio, HMM, model, c1998, c199x, c19xx, homology, distant,
   proteins, sequence, SAM-T98, SAMT98
%X "... method begins with a single target sequence and iteratively builds a
   HMM from the seq. and homologs found using the HMM for database search.
   SAM-T98 is also used to construct model libraries automatically from
   sequences in structural databases...."
   -- [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/reprint/14/10/846">pdf</A>]['05].

%A E. Domingo
%A E. Baranowski
%A C.M.Ruiz-Jarabo, A.M.Martin-Hernandez, J.C.Saiz, C.Escarmis
%T Quasispecies structure and persistence of RNA viruses
%J Emerging Infectious Diseases
%V 4
%N 4
%P ?-?
%M OCT-DEC
%D 1998
%K virus, viral, c1998, c199x, c19xx, zzVDRL, chronic, disease, infection,
   persist, population dynamics
%X "... in a genome distribution with an average of 5 mutations per genome, the
   expected number of genomes with 20 mutations is 26 when the population size
   is 1x10**8 viral particles but reaches 2,600 when the population size is
   2x10**11 particles, as calculated from the Poisson distribution. Fitness
   variations of the individual mutants modify the actual number of genomes in
   each mutation class. ..."
   -- [<A HREF="http://www.cdc.gov/ncidod/eid/vol4no4/domingo.htm">www</A>]['05].

%A O. Handt
%A S. Meyer
%A A. von Haeseler
%T Compilation of human mtDNA control region sequences
%J NAR
%V 26
%N 1
%P 126-12
%D 1998
%K jrnl, NAR, MolBio, c1998, c199x, c19xx, sequence, primate, mitochondrial DNA,
   HvrBase, hypervariable region, regions, zz1205
%X [<A HREF="http://www.hvrbase.de/">hvrbase.de</A>]['05].
   link @ [<A HREF="http://www.bi.uni-duesseldorf.de/research/">uni-duesseldorf</A>]['05].

%A K. Mizuguchi
%A C. M. Deane
%A T. L. Blundell
%A J. P. Overington
%T HOMSTRAD: A database of protein structure alignments for homologous families
%J Protein Sci.
%V 7
%N 11
%P 2469-2471
%D 1998
%K jrnl, MolBio, c1998, c199x, c19xx, HOMSTRAD, alignment, quality, benchmark,
   benchmarks, family, comparer
%X "... database of protein structure alignments for homologous families. The
   [DB] HOMSTRAD presently contains 130 protein families & 590 aligned
   structures, which have been selected on the basis of quality of the X-ray
   analysis & accuracy of the structure. For each family, the [DB] provides a
   structure-based alignment derived using COMPARER & annotated with JOY in a
   special format that represents the local structural environment of each amino
   acid residue. HOMSTRAD also provides a set of superposed atomic coordinates
   obtained using MNYFIT ..."
   -- [<A HREF="http://www.proteinscience.org/cgi/content/abstract/7/11/2469">paper</A>]['07],
      [<A HREF="http://www-cryst.bioc.cam.ac.uk/~homstrad/">HOMSTRAD</A>]['07].
   [Also search for: MolBio protein structure alignment].

%A C. Bystroff
%A D. Baker
%D 1998
%T Prediction of local structure in proteins using a library of
   sequence-structure motifs
%J J. Mol. Biol.
%V 281
%P 565-577
%D 1998
%K jrnl, MolBio, c1998, c199x, c19xx, protein, structure, library, dictionary,
   fragment, structure, motif, pattern, I-sites, Isites
%X "... method for local protein struct. predn based on a library of short
   seq. pattern that correlate strongly with protein 3D structural elts. The
   library was generated using an automated method for finding correlations
   between protein seq. & local struct., & contains most prev. described local
   seq.-struct. correlations as well as new relationships, including a diverging
   type-II beta-turn, a frayed helix, & a proline-terminated helix. The query
   seq. is scanned for segments 7 to 19 residues in length that strongly match
   one of the 82 patterns in the library. Matching segs. are assigned the 3D
   struct. characteristic of the corr. seq. pattern, & backbone torsion angles
   for the entire query seq. are then predicted by piecing together mutually
   compatible seg. predns. In predns of local struct. in a test set of 55
   proteins, about 50% of all residues, & 76% of residues covered by high-
   -confidence predns, were found in eight-residue segs. within 1.4A of their
   true structs.. The predns are complementary to trad. secondary struct. predns
   because they are considerably more specific in turn regions, & may
   contribute to ab initio tertiary struct. predn & fold recognition."
   -- pdf@[<A HREF="http://www.bioinfo.rpi.edu/bystrc/pdf/Bystroff_98_jmb.pdf">rpi</A>]['13],
      Bys@[<A HREF="http://www.bioinfo.rpi.edu/bystrc/">rpi</A>]['13].
   [Also search for: protein structure fragment library].

%A M. Levitt
%A M. Gerstein
%T A unified statistical framework for sequence comparison and structure
   comparison
%J PNAS
%V 95
%N 11
%P 5913-5920
%M MAY
%D 1998
%O colloquium on 'Computational Biomolecular Science,' Sept. '97
%K conf, MolBio, c1998, c199x, c19xx, stats, sequence, protein, structure,
   comparison, alignment, rmsd, P value, Pvalue
%X "... approach for assessing the sig. of seq. & struct. comparisons by using
   nearly identical stat.formalisms for both seq. & struct.. ... involves an
   all-v-all comparison of protein domains [taken ... (scop) DB] & then
   fitting a simple distn fn to the observed scores. ... attach a stat.sig. to
   each comparison score in the form of a P value, the probability that a better
   score would occur by chance. ... find that the scores for seq.matching follow
   an extreme-value distn.  The agreement, more over, between the P values that
   we derive from this distn & those reported by std programs ... validates our
   approach. Structure comparison scores also follow an extreme-value distn when
   the stats. are expressed in terms of a struct.alignment score (essentially
   the sum of reciprocated distances between aligned atoms minus gap penalties).
   We find that the traditional metric of struct.similarity, the rms deviation
   in atom posns after fitting aligned atoms, follows a different distn of
   scores & does not perform as well as the struct.alignment score. Comparison
   of the seq. & struct. stats. for pairs of proteins known to be related
   distantly shows that structural comparison is able to detect approx. twice
   as many distant relationships as seq.comparison at the same error rate. ...
   [&] are v.few pairs with sig.similarity in terms of seq. but not struct.
   whereas many pairs have sig. similarity ... of struct. but not seq.."
   -- [<A HREF="http://www.pnas.org/content/95/11/5913">pnas</A>]['13].
   [Also search for: MolBio protein structure alignment].

%A J. SantaLucia, Jr
%T A unified view of polymer, dumbbell, and oligonucleotide DNA
   nearest-neighbor thermodynamics
%J PNAS
%V 95
%N 4
%P 1460-1465
%M FEB
%D 1998
%K PNAS, jrnl, MolBio, c1998, c199x, c19xx, primer, primers, DNA,
   oligonucleotide nearest-neighbor thermodynamics, annealing, melting,
   temperature, temperatures, Santa Lucia
%X "... DNA NN Delta G^a[37] params. from seven labs. ... so that careful
   comparisons can be made. ... used data from natural polymers, synthetic
   polymers, oligonucleotide dumbbells, & oligonucleotide duplexes to derive NN
   parameters; used different methods of data analysis; ...  used different
   salt ... show that six of the studies are actually in remarkable agreement
   with one another ...  Further, a single set of parameters, derived from 108
   oligonucleotide duplexes, adequately describes polymer & oligomer
   thermodynamics. ..."
   -- [<A HREF="http://www.pnas.org/content/95/4/1460">pnas</A>]['09].
  ***[[NB. Here NN is NOT the Comp. Sci. meaning of nearest neighbour; it is
       the interactions of pairs of adjoining bases along the DNA chain
       which influence the temp. at which double stranded DNA separates.]]
   Also see [<A HREF="http://en.wikipedia.org/wiki/DNA_melting">wikip</A>].

%A D. Duboule
%A A. S. Wilkins
%T The evolution of 'bricolage'
%J Trends in Genetics
%V 14
%N 2
%P 54-59
%D 1998
%K jrnl, MolBio, c1998, c199x, c19xx, zz1220, protein, function, evolution,
   bricolage, tinkering
%X "... have revealed that most of our genes are shared by other species
   throughout the animal kingdom. Consequently, animal diversity might largely
   rely on the differential use of the same components, either at the individual
   level through divergent functional recruitment, or at a more integrated
   level, through their participation in various genetic networks. Here, we
   argue that this inevitably leads to an increase in the interdependency
   between fns that, in turn, influences the degree to which novel variations
   can be tolerated. In this 'transitionist' scheme, evolution is neither
   inherently gradualist nor punctuated but, instead, progresses from one
   extreme to the other, together with the increased complexity of organisms."
   -- [<A HREF="https://doi.org/10.1016/S0168-9525(97)01358-9">doi:10.1016/S0168-9525(97)01358-9</A>]['20].
   [Also search for: MolBio bricolage].

%A L. Dehaspe
%A H. Toivonen
%A R. D. King
%T Finding frequent substructures in chemical compounds
%J KDD
%P 30-36
%D 1998
%K conf, KDD, KDD98, c1998, c199x, c19xx, zz1114, RDKing, chemical compound,
   graph, frequent substructure, pattern, motif, DATALOG, WARMR
%X "... apply data mining to the problem of predicting chemical carcinogenicity.
   This toxicology applicn was launched at IJCAI'97 as a research challenge for
   [AI]. Our approach ... is descriptive rather than based on classification;
   the goal being to find common substructures & properties in chemical cmpds,
   ... to contribute to sci. insight. [It] contrasts with prev. m/c learning
   res. on this problem, which has mainly concentrated on predicting the
   toxicity of unknown chemicals. Our contribution to the field of data mining
   is the ability to discover useful frequent patterns that are beyond the
   complexity of assoc. rules or their known variants. This is vital to the
   problem, which requires the discovery of patterns that are out of the reach
   of simple transformations."
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.26.1344">c'teseer</A>]['14],
      pdf@[<A HREF="http://www.aaai.org/Papers/KDD/1998/KDD98-005.pdf">AAAI</A>]['18].

%A A. Caprara
%T Formulations and hardness of multiple sorting by reversals
%J Proc. 3rd Annual Int. Conf. on Comp. Molec. Biol. (RECOMB'99)
%E S. Istrail
%E P. Pevzner
%E M. Waterman
%I ACM Press
%P 84-93
%D 1999
%K conf, MolBio, RECOMB99, RECOMB3, reversal, c1999, c199x, c19xx, sort
%X [<A HREF="http://www.or.deis.unibo.it/caprara.html">home</A>][10/'02].
   [Also search for: sorting reversals].

%A A. Caprara
%T On the tightness of the alternating-cycle lower bound for
   sorting by reversals
%J J. of Combinatorial Optimization
%V 3
%P 149-182
%D 1999
%K jrnl, sort, reversal, permutation, unsigned, signed, c1999, c199x, c19xx
%X ... alternating cycle lower bound is equal to the optimal solution
   value in almost all cases, [so] algorithms effective in practice.
   ... est prob' that, for a random [unsigned] perm, the bound is not tight.
   Show this prob' is low even for small n, asymptotically O(1/n**5).
   [Shows that] "the problem of sorting by reversals and its
   alternating cycle relaxation are essentially the same problem".  Also
   consider signed permutations ... prob alt-cycle lwb not tight is O(1/n**2).
   -- [<A HREF="http://dx.doi.org/10.1023/A:1009838309166">doi:10.1023/A:1009838309166</A>]['06],
      [<A HREF="http://www.or.deis.unibo.it/caprara.html">home</A>][10/'02],
      [<A HREF="http://www.or.deis.unibo.it/alberto/sbr_coun.ps">paper</A>][10/'02].
   [Also search for: sorting reversals].

%A A. Caprara
%T Sorting permutations by reversals and Eulerian cycle decompositions
%J SIAM J. on Discrete Math.
%V 12
%P 91-110
%D 1999
%K MolBio, jrnl, SIAM, permutation, reversal, sort, sorting, NP hard,
   decomposition, alternating cycles, breakpoint graph, partitioning,
   Eulerian graphs, MinSBR, MaxACD, MaxECD, c1999, c199x, c19xx, zz1002
%X ... sorting a permutation by the minimum number of reversals (MIN-SBR),
   the problem of finding the maximum number of edge-disjoint alternating
   cycles in a breakpoint graph associated with a given permutation (MAX-ACD),
   and the problem of partitioning the edge set of an Eulerian graph into the
   maximum number of cycles (MAX-ECD). ... MAX-ECD and MAX-ACD are equivalent,
   showing the latter to be NP-hard. ... transformation from MAX-ACD to MIN-SBR,
   which is therefore shown to be NP-hard. ... approximation algorithms
   for MIN-SBR.
   [Also search for: sorting reversals],
   -- [<A HREF="http://www.or.deis.unibo.it/caprara.html">home</A>][10/'02],
      [<A HREF="http://www.or.deis.unibo.it/alberto/sbr_comp.ps">paper</A>][10/'02],
      [<A HREF="http://epubs.siam.org/SIDMA/volume-12/art_31994.html">SIAM</A>]['06],
      [<A HREF="http://epubs.siam.org/sam-bin/dbq/article/31994">SIAM</A>][10/'02].
   [Also search for: sorting reversals].

%A G. Burger
%A D. Saint-Louis
%A M. W. Gray
%A B. F. Lang
%T Complete sequence of the mitochondrial DNA of the red alga
   Porphyra purpurea: Cyanobacterial introns and shared ancestry of red and
   green algae
%J Plant Cell
%P 1675-1694
%V 11
%N 9
%M SEP
%D 1999
%K jrnl, red algae, algal, plant, plants,  phylogenetic, ancestry, origin,
   mGenome, origins, mtDNA, c1999, c199x, c19xx, biol, biology, MolBio
%X "... (mtDNA)... circular-mapping genome of 36,753-bp ... A total of 57
   densely packed genes has been identified, including the basic set typically
   found in animals & fungi, as well as 7 genes characteristic of protist &
   plant mtDNAs & specifying ribosomal proteins & subunits of
   succinate:ubiquinone oxidoreductase. ... phylogenetic analyses provide
   strong evidence that [RA] share a common ancestry with gr'n algae & plants."
   -- [<A HREF="http://www.plantcell.org/cgi/content/abstract/11/9/1675">paper</A>]['03].

%A B. Larder
%A V. De Vroey
%A Dhertogh P, Kemp S, Bloor S, Hertogs K.
%T Predicting HIV-1 phenotypic resistance from genotype using a large
   phenotype-genotype relational database
%J Antiviral Therapy
%V 4 (Supplement 1) 41
%D 1999
%O abstract 59 at the 3rd Int. Workshop on HIV Drug Resistance & Treatment
   Strategies. SanDiego, Ca.; June 23-26, 1999
%K drug resistance, c1999, c199x, c19xx, HIV, HIV1, aids, medical, MolBio

%A A. R. Zolopa
%A R. W. Shafer
%A Warford A, Montoya JG, Hsu P, Katzenstein D, Merigan TC, Efron B.
%T HIV-1 genotypic resistance patterns predict response to
   saquinavir-ritonavir therapy in patients in whom previous protease
   inhibitor therapy had failed.
%J Ann. Intern. Med.
%V 131
%P 813-821
%D 1999
%K jrnl, MolBio, medical, health, HIV, aids, genotype, pattern, drug, drugs,
   drug resistance, c1999, c199x, c19xx, HIV1, phenotype, phenotypic
%X "In patients in whom protease inhibitor-containing antiretroviral therapy
   fails, HIV-1 genotype is predictive of virologic response to subsequent
   therapy. This predictive capacity adds to that of st'd clinical evaluation."
   full [<A HREF="http://www.annals.org/cgi/content/full/131/11/813">annals</A>]['05].

%A G. Tononi
%A O. Sporns
%A G. M. Edelman
%T Measures of degeneracy and redundancy in biological networks
%J PNAS
%V 96
%N 6
%P 3257-3262
%D 1999
%K MolBio, jrnl, PNAS, c1999, c199x, c19xx, TSE, network, networks,
   degenerate, redundant, information
%X "Degeneracy, the ability of elts that are structurally different to perform
   the same fns, is a prominent property of many biol. sys. ranging from genes
   to [NNs] to evolution itself. Because structurally different elts may produce
   different outputs in different contexts, degeneracy should be distinguished
   from redundancy, which occurs when the same fn is performed by identical
   elts. However, because of ambiguities in the distinction between structure &
   fn & because of the lack of a theoretical treatment, these 2 notions often
   are conflated. By using info.theoretical concepts, we develop here functional
   measures of the d. & r. of a sys. with respect to a set of outputs. ..."
   -- @[<A HREF="http://www.pnas.org/content/96/6/3257.full">pnas</A>]['10] (13 refs).

%A C. G. Nevill-Manning
%A I. H. Witten
%T Protein is incompressible
%J Proc. Conf. on Data Compression
%P 257-266
%M MAR
%D 1999
%K conf, DCC, DCC99, MolBio, proteins, amino acid, acids, c1999, c199x, c19xx,
   compress, compression, compressible, NevillManning, Haemophilus influenzae,
   Saccharomyces cerevisiae, Methanococcus jannaschii, proteome
%X "...bio. seqs. have a fundamentally different struct. from linguistic ones,
   & standard compression schemes exhibit disappointing performance on them.
   We describe a new approach to compression that takes account of the
   underlying biochemical principles. This gives rise to a generalization of
   blending for statistical compressors where every context is used, weighted
   by its similarity to the current context. Results support what research in
   bioinformatics has shown-that there is little Markov dependency in protein.
   This cripples data compression schemes & reduces them to order zero models."
   -- [<A HREF="http://craig.nevill-manning.com/99CN-IHW-Proteincompressibl.pdf">pdf</A>]['04],
      [<A HREF="http://www.data-compression.info/Corpora/ProteinCorpus/">pdf + data</A>]['04],
      [<A HREF="http://dx.doi.org/10.1109/DCC.1999.755675">doi:10.1109/DCC.1999.755675</A>]['07].
   uk us isbn:076950096X.
   [Also search for: protein compress]

%A R. H. Lathrop
%A M. J. Pazzani
%T Combinatorial optimization in rapidly mutating drug-resistant viruses
%J J. Combinatorial Optimization
%V 3
%N 2-3
%P 301-320
%M JUL
%D 1999
%K jrnl, virus, viral, c1999, c199x, c19xx, treatment, therapy, resistance,
   drug, drugs, MolBio, HIV, AIDS, multiple
%X "... branch-and-bound algorithm ..."
   -- [<A HREF="http://www.ics.uci.edu/~pazzani/Publications/j-comb-opt.pdf">pdf@uci</A>]['05],
      [<A HREF="http://www.ics.uci.edu/~rickl/publications/1999-j-comb-opt.pdf">pdf@uci</A>]['05].

%A R. H. Lathrop
%A et al
%T Knowledge-based avoidance of drug-resistant HIV mutants
%J AI Magazine
%V 20
%N 1
%P 13-25
%D 1999
%O invited article from IAAI Conf., paper of same title
%K unref, MolBio, drugs, treatment, therapy, HIV, AIDS, pazzani
%X [<A HREF="http://www.ics.uci.edu/~rickl/publications/1999-ai-mag.pdf">pdf@uci</A>]['05].

%A J. Thompson
%A F. Plewniak
%A O. Poch
%T A comprehensive comparison of multiple sequence alignment programs
%J NAR
%V 27
%N 13
%P 2682-2690
%M JUL
%D 1999
%K jrnl, NAR, MolBio, c1999, c199x, c19xx, quality, benchmark, benchmarks,
   BAliBASE, balibase, database, examples, survey, review, accuracy, protein
%X "... using BAliBASE benchmark alignments as test cases. Even below the
   'twilight zone' at 10-20% residue identity, the best programs were capable of
   correctly aligning on average 47% of the residues. We show that iterative
   algorithms often offer improved alignment accuracy though at the expense of
   computation time. A notable exception was the effect of introducing a single
   divergent sequence into a set of closely related sequences, causing the
   iteration to diverge away from the best alignment. Global alignment programs
   generally performed better than local methods, except in the presence of
   large N/C-terminal extensions & internal insertions. ..."
   -- [<A HREF="http://nar.oxfordjournals.org/cgi/content/full/27/13/2682">paper</A>]['07],
      [<A HREF="http://www-bio3d-igbmc.u-strasbg.fr/balibase/">balibase3</A>]['07].

%A M. Tomita
%A K. Hashimoto
%A K.Takahashi, T.S.Shimizu, Y.Matsuzaki, F.Miyoshi, K.Saito, S.Tanida, K.Yugi,
   J.C.Venter, C.Hutchison
%T E-CELL: Software environment for whole-cell simulation
%J J. Bioinformatics
%V 15
%N 1
%P 72-84
%D 1999
%K jrnl, MolBio, e-cell, Ecell, c1999, c199x, c19xx, simulate, cells, cellular,
   model, modelling
%X "... allows a user to define functions of proteins, protein-protein
   interactions, protein-DNA interactions, regulation of gene expression and
   other features of cellular metabolism, as a set of reaction rules. E-CELL
   simulates cell behavior by numerically integrating the differential equations
   described implicitly in these reaction rules. The user can observe, through
   a computer display, dynamic changes in concentrations of proteins, protein
   complexes and other chemical compounds in the cell. Using this software, we
   constructed a model of a hypothetical cell with only 127 genes sufficient for
   transcription, translation, energy production and phospholipid synthesis.
   Most of the genes are taken from Mycoplasma genitalium, the organism having
   the smallest known chromosome, whose complete 580kb genome sequence was
   determined at TIGR in '95. ..."
   -- [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/15/1/72">paper</A>]['07],
      [<A HREF="http://www.e-cell.org/">e-cell.org</A>]['07].
   [Also search for: cellDesigner],  [also search for: visible cell].

%A K. Hennighausen
%A H. Remschmidt
%T The computer body image test: A procedure for the assessment of body image
   perception
%J Int. J. Methods in Psychiatric Res.
%V 8
%N 2
%P 123-128
%D 1999
%K jrnl, c1999, c199x, c19xx, psychiatry, psychology, distorted,
   eating disorder, graphics
%X "...Distorted computerized images of the subjects are presented on a computer
   monitor. The whole body & body parts can be manipulated interactively.
   Reliability, stability & validity of the perceived & ideal body image were
   obtained in a sample of 36 inpatients suffering from anorexia nervosa. The
   procedure yielded a very high reliability. Perceived & ideal body images are
   stable after a mean time interval of 60 days. Significant correlations with
   the Body Shape Questionnaire & subscales of the Eating Disorder Inventory
   indicate the validity of the procedure.. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/mpr.62">doi:10.1002/mpr.62</A>]['07].

%A P. J. Benson
%A J. L. Emery
%A E. M. Cohen-Tovee
%A M. J. Tovee
%T A computer-graphic technique for the study of body size perception and
   body types
%J Behavior Research Methods, Instruments, & Computers
%V 31
%N 3
%P 446-454
%D 1999
%K jrnl, c1999, c199x, c19xx, graphics, body image, type
%X "... approach for measuring body size estimation in normal & eating-
   -disordered women & men. Clinical categories of body types were used as
   prototypes. By comparing the subjective appearance of a person's body with
   prototypes, we can understand how different attributes of his or her body
   shape contribute to perception of body size. After lifelike random
   distortions have been applied to parts of their body image, individuals
   adjust their body shapes until they converge on their perceived veridical
   appearance. Exaggeration & minimization of particular body areas measured
   with respect to their true shape & with different prototypes can be expressed
   as numerical devia- tions. ..."
   -- [<A HREF="http://www.staff.ncl.ac.uk/m.j.tovee/technique-1999.pdf">pdf@ncl.ac.uk</A>]['07].

%A M. Tsiang
%A J. E. Rooney
%A J. J. Toole
%A C. S. Gibbs
%T Biphasic clearance kinetics of hepatitis B virus from patients during
   adefovir dipivoxil therapy
%J Hepatology
%P 1863-1869
%M JUN
%D 1999
%K jrnl, c1999, c199x, c19xx, HBV, drug, therapy, rate, rates
%X "... half life 1.1 +/- 0.3 days ..."

%A G. Benson
%T Tandem repeats finder: a program to analyze DNA sequences
%J NAR
%V 27
%N 2
%P 573-580
%M JAN
%D 1999
%K jrnl, NAR, MolBio, c1999, c199x, c19xx, zz0808, tandem repeat, TRF, sequence
%X "A tandem repeat in DNA is two or more adjacent, approximate copies of a
   pattern of nucleotides. Tandem Repeats Finder is a program to locate and
   display tandem repeats in DNA sequences. ..."
   -- [<A HREF="http://www.ingentaconnect.com/content/oup/nar/1999/00000027/00000002/art00573">www</A>]['08].
   (Also see [<A HREF="http://tandem.bu.edu/trf/trf.html">www</A>]['08].)
   [Also search for: MolBio tandem repeat].

%A G. Schneider
%A M.-L. Lee
%A M. Stahl
%A P. Schneider
%T De novo design of molecular architectures by evolutionary assembly of
   drug-derived building blocks
%J J. Comp.-Aided Drug Design
%V 14
%P 487-494
%M JUL
%D 2000
%K jrnl, c2000, c200x, c20xx, zz0620, chemical compound, library, chemistry,
   combinatorial, building block, fragment library, TOPAS, pharmacophore,
   intelligent drug design, biologically active compounds, Chembridge, Enamine
%X "An evolutionary alg. was developed for fragment-based de novo design of
   molecules (TOPAS, TOPology-Assigning System). This stochastic method ...
   generating a novel molecular structure mimicking a template structure. A set
   of ~25,000 fragment structures serves as the building block supply, ...
   obtained by a straightforward fragmentation procedure applied to 36,000 known
   drugs. Eleven reaction schemes were implemented ... In a cyclic optimization
   process, molecular architectures were generated [by] virtual synthesis, &
   the best structure of a generation was selected as the parent for the
   subsequent TOPAS cycle. Similarity measures were used to define 'fitness',
   based on 2D-structural similarity or topological pharmacophore dist. between
   the template molecule & the variants. The concept of varying library
   'diversity' during a design process was consequently implemented by using
   adaptive variant distributions. ... demonstrated for the de novo construction
   of potential thrombin inhibitors ..."
   -- [<A HREF="https://doi.org/10.1023/A:1008184403558">doi:10.1023/A:1008184403558</A>]['20].
   (Also see BldgBlockChem@[<A HREF="https://en.wikipedia.org/wiki/Building_block_(chemistry)">wikip</A>]['20].)
   [Also search for: chemical library].

%A G. H. Gonnet
%A C. Korostensky
%T Optimal scoring matrices for estimating distances between aligned sequences
%I ETH Zurich
%M JUL
%D 1999
%K TR, MolBio, c1999, c199x, c19xx, zz0717, scoring, matrix, matrices, PAM,
   DNA alignment, distance, Dayhoff, phylogenetric trees
%X "Seq. alignment is typically the 1st step in many research areas of
   bioinformatics, where some form of score or distance is derived. ... Since
   those scores and distances are the basis for further studies, it is important
   that they can be estimated as well as possible. ... we prove that the scores
   obtained from Dayhoff matrices (or from any other matrix) are not consistent
   for tree construction. Then we show how this can be corrected and how to
   create an optimal scoring matrix to estimate distances. This scoring matrix
   is optimal within a large class of estimators. ..."
   -- ps@[<A HREF="https://www.inf.ethz.ch/personal/gonnet/papers/Distance.ps">ethz</A>]['17].
   And a later 2004 version
   -- pdf@[<A HREF="http://gonnet.com/papers/Distance.pdf">gonnet.com</A>]['17].

%A N. Kannan
%A S. Vishveshwara
%T Identification of side-chain clusters in protein structures by a graph
   spectral method
%J J. Mol. Biol.
%V 292
%N 2
%P 441-464
%M SEP
%D 1999
%K jrnl, JMB, MolBio, c1999, c199x, c19xx, protein, structure, side chain,
   sideChain, spectral, graph, spectrum, analysis, Saraswati Vishveshwara
%X "... side-chain interactions are rep. by a labeled graph ... nodes represent
   the C-b atoms & edges rep. the distance between the C-b atoms. The distance
   info. & the non-bonded connectivity of the residues are rep. in ...
   Laplacian matrix. ... diagonalized & clustering info. is obtained from the
   vector components assoc. with the 2nd lowest eigenvalue & cluster centers
   are obtained from the vector components assoc. with the top eigenvalues. ...
   uses global info. for clustering & a single numeric computation is required
   to detect clusters of interest. The approach has been adopted here to detect
   a variety of side-chain clusters & identify the residue which makes the
   largest # of interactions among the residues forming the cluster (cluster
   centers). ..."     (via AL, via AK.)
   -- [<A HREF="http://dx.doi.org/10.1006/jmbi.1999.3058">doi:10.1006/jmbi.1999.3058</A>]['08].
   [Also search for: graph spectrum].

%A W. F. Doolittle
%T Phylogenetic classification and the universal tree
%J Science
%V 284
%N 5423
%P 2124-2128
%D 1999
%K jrnl, MolBio, c1999, c199x, c19xx, phylogenetic, evolutionary, tree, trees,
   life, origins, archaea, bacteria, horizontal gene transfer, HGT, lateral
%X "... phylogeneticists have constructed a "universal tree of life," taking it
   as the basis for a "natural" hierarchical classification of all living
   things. ... More challenging is evidence that most archaeal & bacterial
   genomes (& the inferred ancestral eukaryotic nuclear g.) contain genes from
   multiple sources. If "chimerism" or "lateral gene transfer" cannot be
   dismissed as trivial in extent or limited to special categories of genes,
   then no hierarchical universal classification can be taken as natural. ...
   [not] ... chosen the wrong genes, but because the history of life cannot
   properly be represented as a tree. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.284.5423.2124">doi:10.1126/science.284.5423.2124</A>]['09].
   [Also search for: MolBio tree life].

%A L. Stern
%A D. Lightfoot
%T Automated outbreak detection: A quantitative retrospective analysis
%J Epidemiology and Infection
%V 122
%P 103-110
%D 1999
%K jrnl, c1999, c199x, c19xx, public health, disease, outbreak,
   salmonella infection
%X "An automated early warning system has been developed & used for detection
   clusters of human infection with enteric pathogens. ... requires no specific
   disease modelling, & has the potential for extension to other epidemiological
   applications. A compound smoothing technique is used to determine baseline
   `normal' incidence of disease from past data, & a warning threshold for
   current data is produced by combining a statistically determined increment
   from the baseline with a fixed minimum threshold. A retrospective study of
   salmonella infections over 3 years has been conducted. ... the automated
   system achieved > 90% sensitivity, with a +ve predictive value consistently
   > 50%, demonstrating the effectiveness of the combination of statistical &
   heuristic methods for cluster detection. We suggest that quantitative
   measurements are of considerable utility in evaluating the performance of
   such systems."    auth@unimelb.

%A L. H. Hartwell
%A J. J. Hopfield
%A S. Leibler
%A A. W. Murray
%T From molecular to modular cell biology
%J Nature
%V 402
%N 6761 supplement
%M DEC
%P C47-C52
%D 1999
%K news, views, c1999, c199x, c19xx, systems biology, biol, modular, modularity,
   module, motif, scale
%X "Cellular fns, such as signal transmission, are carried out by 'modules' made
   up of many species of interacting molecules. Understanding how modules work
   has depended on combining phenomenological analysis with molecular studies.
   ... To describe biological fns, we need a vocab. that contains concepts such
   as amplification, adaptation, robustness, insulation, error correction &
   coincidence detection. ... Is cell biology modular? A functional module is,
   by defn, a discrete entity whose fn is separable from those of other modules.
   This separation depends on chemical isolation, which can originate from
   spatial localization or from chemical specificity. ..."  [34 refs].
   -- [<A HREF="http://www.nature.com/nature/journal/v402/n6761supp/full/402c47a0.html">nature</A>]['12].

%A D. W. Cruickshank
%T Remarks about protein structure precision
%J Acta Crystallogr., D, Biol. Crystallogr.
%V 55 (Pt.3)
%P 583-601
%M MAR
%D 1999
%K jrnl, Acta Cryst, MolBio, c1999, c199x, c19xx, protein structure,
   determination, 3D, atomic coordinates, precision, Xray, cystallography,
   least squares, restrained, constrained, unrestrained, precision
%X "Full-matrix least squares is taken as the basis for an examination of
   protein structure precision. A two-atom protein model is used to compare the
   precisions of unrestrained & restrained refinements. ... sigma(l) for bond
   lengths.  sigma(r) is as small as 0.01A for atoms with low Debye B values
   but incr. strongly with B. The results emphasize the distinction between
   unrestrained & restrained refinements & between sigma(r) & sigma(l). ... The
   effect of restraints as resolution varies is examined. More regular use of
   full-matrix inversion is urged to establish positional precision & hence the
   precision of non-dictionary distances in both high- & low-res. structures.
   Failing this, parameter blocks for representative residues & their neighbours
   should be inverted to gain a general idea of sigma(r) as a function of B. The
   whole discussion is subject to some caveats about the effects of disordered
   regions in the crystal."
   -- [<A HREF="http://dx.doi.org/10.1107/S0907444998012645">doi:10.1107/S0907444998012645</A>]['13],
      10089455@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/10089455">pubm'd</A>]['13].
   [Also search for: MolBio protein structure precision].

%A R. Brosch
%A S. V. Gordon
%A A. Pym,  K. Eiglmeier,  T. Garnier,  S. T. Cole
%T Comparative genomics of the mycobacteria
%J Int. J. Med. Microbiol
%V 290
%P 143-152
%D 2000
%K jrnl, IJMM, biol, biology, Mycobacterium lepra, leprae, leprosy, bacteria,
   Mycobacterium tuberculosis, TB, bacteria, c2000, c200x, c20xx, genome,
   GC rich, GCrich, content, medical
%X [<A HREF="http://www.pasteur.fr/recherche/unites/Lgmb/IJMM.pdf">IJMM.pdf@pasteur.fr</A>]['04].
   ... M.tuberculosis the overall GC content is 65.6% ...
   ... M.leprae genome (size 3,268kb), is almost 1.2Mb smaller than that of
   M. tuberculosis (4,411kb) and its GC content of ~58% ...  low amount of
   repetitive DNA in M.leprae. ...

%A S. L. Baldauf
%A A. J. Roger
%A I. Wenk-Siefert
%A W. F. Doolittle
%T A kingdom level phylogeny of eukayotes based on combined protein data
%J Science
%V 290
%P 972-977
%D 2000
%K jrnl, c2000, c200x, c20xx, SLBaldauf, eukaryote, phylogenetic tree, trees,
   evolutionary, MolBio
%X lab@[<A HREF="http://www-users.york.ac.uk/~slb14/labpage.html">york</A>]['09],
   -- [<A HREF="http://www.york.ac.uk/depts/biol/staff/slb.htm">home page</A>]['04].

%A N. Friedman
%A M. Linial
%A I. Nachman
%A D. Pe'er
%T Using Bayesian networks to analyze expression data
%J Proc. 4th Int. Conf. on Computational Molec. Biol.
%W Tokyo
%P 127-135
%D 2000
%K conf, MolBio, c2000, c200x, c20xx, micro-array, microarrays, levels, gene,
   genes, interaction, yeast, Bnet, network, net, Peer
%X "...start by showing how BNs can describe interactions between genes. ...
   present an efficient alg. capable of learning such networks & stat. method
   to assess our confidence in their features. ... apply this method to the
   S. cerevisiae cell-cycle measurements of Spellman et al. ..."
   -- [<A HREF="http://doi.acm.org/10.1145/332306.332355">doi:10.1145/332306.332355</A>]['04], isbn:1581131860.
   [Also search for: Bayesian network].

%A I Nikaido
%A E. Asamizu
%A M.Nakajima, Y.Nakamura, N.Saga, S.Tabata
%T Generation of 10,154 expressed sequence tags from a leafy gametophyte of a
   marine red alga, Porphyra yezoensis
%J DNA Res.
%V 7
%N 3
%P 223-227
%M JUN
%D 2000
%K jrnl, MolBio, EST, ESTs, cDNA, red alga, algae, algal, c2000, c200x, c20xx,
   Porphyra yezoensis, rhodophyta, tag, codon usage, bias
%X "... 10,154 5'-end ...(EST) were established from the normalized & size-
   selected cDNA libraries of a marine red alga, Porphyra yezoensis. Among the
   ESTs, 2140 were unique species, & the remaining 8014 were grouped into 1127
   species. Database search of the 3267 non-redundant ESTs by BLAST ...  showed
   that the seqs. of 1080 species (33.1%) have similarity to those of registered
   genes from various organisms including higher plants, mammals, yeasts, &
   cyanobacteria, while 2187 (66.9%) are novel. Codon usage analysis in the
   coding regions of 101 non-redundant EST groups showing significant similarity
   to known genes indicated the higher GC contents at the 3rd posn of codons
   (79.4%) than the 1st (62.2%) & the 2nd posn (45.0%), suggesting that the
   genome has been exposed to high GC pressure during evolution. ..."
   -- [<A HREF="http://www.dna-res.kazusa.or.jp/7/3/10/PDF/7_223.pdf">pdf</A>]['05],
      [<A HREF="http://www.kazusa.or.jp/en/plant/porphyra/EST/">kazusa.or.jp</A>]['05].
   Porphyra genus, 133 species reported, dimorphic life cycle,
   genome 2.7 to 5.3x10**8 bp, 2 to 7 chromosomes.
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=2788">ncbi</A>]['05].

%T Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
%A The Arabidopsis genome initiative
%J Nature
%P 796-815
%V 408
%M DEC
%D 2000
%K jrnl, Arabidopsis thaliana, flower, flowering, plant, c2000, c200x, c20xx,
   herbaceous, plants, genome, gene, genes, plastid, eukaryote, eukaryotic,
   NC003070, NC003071, NC003074, NC003075, NC003076, NC000932, NC001284, AGI,
   thale cress, nGenome, mGenome, chromosomes, nuclear, photosynthesis
%X 125Mb genome, chr-1 29Mb, chr-2 20Mb, chr-3 23Mb, chr-4 18Mb, chr-5 26Mb,
   25,498 genes. (chloroplast 154Kb, mitochondrion 367Kb.)
   "... analysis of the genomic sequence of Arabidopsis. The sequenced regions
   cover 115.4 Mb of the 125-Mb genome & extend into centromeric regions. The
   evolution of Arabidopsis involved a whole-genome duplication, followed by
   subsequent gene loss & extensive local gene duplications, giving rise to a
   dynamic genome enriched by lateral gene transfer from a cyanobacterial-like
   ancestor of the plastid. The genome contains 25,498 genes encoding proteins
   from 11,000 families, similar to the functional diversity of Drosophila &
   Caenorhabditis elegans -- the other sequenced multicellular eukaryotes.
   Arabidopsis has many families of new proteins but also lacks several common
   protein families, indicating that the sets of common proteins have undergone
   differential expansion & contraction in the 3 multicellular eukaryotes. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/35048692">doi:10.1038/35048692</A>][7/'04].
   [ 7/'04: NC_003070 chr-1, NC_003071 chr-2, NC_003074 chr-3,
            NC_003075 chr-4, NC_003076 chr-5, complete sequences;
            NC_000932 chloroplast,   complete genome, 154478-bp, circular;
            NC_001284 mitochondrion, complete genome, 366924-bp, circular. ]
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=3702">AT</A>]['08].

%A T. Egeland
%A P. Mostad
%A B. Mevag
%A M. Stenersen
%T Beyond traditional paternity and identification cases. Selecting the
   most probable pedigree
%J Forensic Science International
%P ?-?
%V 110
%N 1
%D 2000
%K jrnl, case, DNA, familias, stats, statistics
%X [<A HREF="http://folk.uio.no/thoree/papers/selectr3.pdf"> ?? pdf@uio</A>]['05],
   [<A HREF="http://www.math.chalmers.se/~mostad/familias/">familias</A>]['05].

%A A. E. Jetzt
%A H. Yu
%A G.J.Klarmann, Y.Ron, B.D.Preston, J.P.Dougherty
%T High rate of recombination throughout the human immunodeficiency virus
   type 1 genome
%J J. Virol.
%V 74
%N 3
%P 1234-1240
%M FEB
%D 2000
%K jrnl, HIV, HIV1, AIDS, MolBio, c2002, c200x, c20xx, virus, viral, type1,
   recombination rate, replication, mutation
%X "The diploid nature of [HIV1] ... The proviral progeny of heterodimeric
   virions were analyzed after a single cycle of replication, & the sequence
   heterogeneity between the 2 strains allowed direct examination of
   recombination crossovers. ... indicate that HIV-1 undergoes approx. 2 to 3
   recombination events per genome per replication cycle. ... imply that both
   HIV-1 RNAs are typically utilized during reverse transcription & that
   recombination is an important aspect of HIV-1 replication."
   -- [<A HREF="http://jvi.asm.org/cgi/content/full/74/3/1234">paper@jvi</A>]['05].

%A C. Adami
%A C. Ofria
%A T. C. Collier
%T Evolution of biological complexity
%J PNAS
%V 97
%N 9
%P 4463-4468
%M APR
%D 2000
%K jrnl, PNAS, c2000, c200x, c20xx, zz0310, Avida, aLife, biological complexity,
   evolution, information, content, environment
%X "To make a case for or against a trend in the evolution of complexity in
   biol. evoln, complexity needs to be both rigorously defined & measurable. A
   recent info.-theor. ... defn identifies genomic complexity with the amount of
   info. a seq. stores about its environment. We investigate the evoln of
   genomic complexity in popns of digital organisms & monitor in detail the
   evolutionary transitions that increase complexity. We show that, because
   natural selection forces genomes to behave as a natural 'Maxwell Demon,'
   within a fixed environment, genomic complexity is forced to increase. ...
   ... a seq.'s info. content is conditional on the environment it is to be
   interpreted within (4). ..."
   -- [<A HREF="http://www.pnas.org/content/97/9/4463.full">www</A>]['10].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Notes/Information/">information</A>].)

%A O. Sporns
%A G. Tononi
%A G. M. Edelman
%T Connectivity and complexity: the relationship between neuroanatomy and
   brain dynamics
%J Neural Networks
%V 13
%N 8-9
%P 909-922
%M OCT-NOV
%D 2000
%K jrnl, c2000, c200x, c20xx, TSE, network, brain, cerebral cortex,
   complexity, motif, information
%X "... find that specific neuroanatomical motifs are uniquely assoc. with high
   levels of complexity & that such motifs are embedded in the pattern of
   long-range cortico-cortical pathways linking segregated areas of the
   mammalian cerebral cortex. Our theoretical findings offer new insight into
   the intricate relationship between connectivity & complexity in the nervous
   system."
   -- [<A HREF="http://dx.doi.org/10.1016/S0893-6080(00)00053-8">doi:10.1016/S0893-6080(00)00053-8</A>]['10].

%A M. Lipsitch
%A T. H. Bacon
%A J. J. Leary
%A R. Antia
%A B. R. Levin
%T Effects of antiviral usage on transmission dynamics of herpes simplex virus
   type 1 and on antiviral resistance: Predictions of mathematical models
%J Antimicrobial Agents and Chemotherapy
%V 44
%N 10
%P 2824-2835
%M OCT
%D 2000
%K jrnl, MolBio, c2000, c200x, c20xx, HSV-1, HSV1, drug, anti-viral, model,
   recurrent herpes labialis, RHL, resistant
%X [<A HREF="http://www.biology.emory.edu/research/Levin/pubs/00herpes.pdf">pdf</A>]['05].
   Models the spread of resistant HSV-1 in the human population under various
   assumptions.

%A I. Eidhammer
%A I. Jonassen
%A W. R. Taylor
%T Structure comparison and structure patterns
%J J. Computational Biology
%V 7
%N 5
%P 685-716
%M OCT
%D 2000
%K jrnl, MolBio, c2000, c200x, c20xx, tertiary, 3D structures, pattern,
   shape, shapes, match, matching
%J "... investigates aspects of pairwise & multiple structure comparison, & the
   problem of automatically discover common patterns in a set of structures.
   Descriptions & representation of structures & patterns are described, as well
   as scoring & algs. for comparison & discovery. A framework & nomenclature is
   developed for classifying different methods, & many of these are reviewed &
   placed into this framework."
   -- [<A HREF="http://www.liebertonline.com/doi/abs/10.1089/106652701446152">www</A>]['06].

%A C. Notredame
%A D. Higgins
%A J. Heringa
%T T-Coffee: A novel method for multiple sequence alignments
%J J. of Molec. Biol.
%V 302
%P 205-217
%D 2000
%K jrnl, JMB, MolBio, c2000, c200x, c20xx, T-Coffee, Tcoffee, alignment,
   protein, progressive
%X [<A HREF="http://dx.doi.org/10.1006/jmbi.2000.4042">doi:10.1006/jmbi.2000.4042</A>]['07],
      [<A HREF="http://igs-server.cnrs-mrs.fr/~cnotred/Publications/Pdf/tcoffee.pdf">pdf</A>]['07],
      [<A HREF="http://www.ebi.ac.uk/t-coffee/">@EBI</A>]['07].
   [Also search for: multiple alignment MolBio].

%A D. Hanahan
%A R. A.  Weinberg
%T The hallmarks of cancer
%J Cell
%V 100
%P 57-70
%D 2000
%K jrnl, MolBio, hallmark, c2000, c200x, c20xx
%X Also see: Abbott c2006.

%A J. F. C. Kingman
%T Origins of the coalescent: 1 9 7 4 - 1 9 8 2
%J Genetics
%V 156
%P 1461-1463
%M DEC
%D 2000
%K jrnl, MolBio, c2000, c200x, c20xx, phylogeny, phylogenetic tree, trees
%X [<A HREF="http://www.genetics.org/cgi/content/full/156/4/1461">www</A>]['08].

%A Y-Y Zhang
%A J. Summers
%T Low dynamic state of viral competition in a chronic avian
   hapadnavirus infection
%J J. Virology
%V 74
%N 11
%P 5257-5265
%M JUN
%D 2000
%K jrnl, MolBio, HBV, c2000, c200x, c20xx, growth, infection, rate, rates,
   liver, strain, strains

%A J. A. Cuff
%A G. J. Barton
%T Application of multiple sequence alignment profiles to improve protein
   secondary structure prediction
%J Proteins
%V 40
%N 3
%P 502-511
%M JUN
%D 2000
%K jrnl, MolBio, c2000, c200x, c20xx, zz1222, MSA, NN, ANN, jpred, jnet
%X "The effect of training a NN sec. struct. pred. alg. with different types of
   multiple seq. alignment profiles derived from the same seqs., is shown to
   provide a range of accuracy from 70.5% to 76.4%. ... "
   -- [<A HREF="https://doi.org/10.1002/1097-0134(20000815)40:3%3C502::AID-PROT170%3E3.0.CO;2-Q">www</A>]['22].
   [Also search for: secondary structure prediction].

%A P. A. Pevzner
%T Computational Molecular Biology: An Algorithmic Approach
%I MITpress
%P 332
%D 2000
%K book, text, MolBio, bioinformatics, c2000, c200x, c20xx, programming,
   algorithm
%X "... covers a broad range of algorithmic and combinatorial topics and shows
   how they are connected to molecular biology and to biotechnology. The book
   has a substantial "computational biology without formulas" component that
   presents the biol. & computational ideas in a relatively simple manner. ..."
   1st ed 2000, hb us$46; uk us isbn:0262161974; uk us isbn13:978-0262161978.
   [Also search for: MolBio book].

%A S. Rozen
%A H. J. Skaletsky
%T Primer3 on the WWW for general users and for biologist programmers
%J Bioinformatics Methods and Protocols: Methods in Molec. Biol.
%E S. Krawetz
%E S. Misener
%I Humana Press, Totowa
%P 365-386
%D 2000
%K MolBio, c2000, c200x, c20xx, PCR, DNA, sequencing, primer, primers, design,
   designing, Primer3
%X "Designing PCR and sequencing primers are essential activities for molecular
   biologists around the world. This chapter assumes acquaintance with the
   principles and practice of PCR, ..."
   -- [<A HREF="http://dx.doi.org/10.1385/1-59259-192-2:365">doi:10.1385/1-59259-192-2:365</A>]['09],
   pdf@[<A HREF="http://jura.wi.mit.edu/rozen/papers/rozen-and-skaletsky-2000-primer3.pdf">mit</A>]['09],
   code@[<A HREF="http://primer3.sourceforge.net/">sourcefor...</A>]['09].
   [Also search for: MolBio PCR primer],
   primers@[<A HREF="http://en.wikipedia.org/wiki/Primer_(molecular_biology)">wikip</A>]['09].

%A M. Kanehisa
%A S. Goto
%T KEGG: kyoto encyclopedia of genes and genomes
%J NAR
%V 28
%N 1
%P 27-30
%M JAN
%D 2000
%K jrnl, NAR, MolBio, c2000, c200x, c20xx, KEGG, kegg1, KEGG2, gene, function,
   database, genome, pathway, pathways, metabolic, network, networks, ligand
%X "KEGG ... is a knowledge base for systematic analysis of gene functions,
   linking genomic info. with higher order f'nal info.. ... stored in the GENES
   DB, which is a colln of gene catalogs for all the completely sequenced
   genomes & some partial genomes with up-to-date annotation of gene fns. The
   higher order fn inf. is stored in the PATHWAY DB, which contains graphical
   repn of cellular processes, such as metabolism, membrane transport, signal
   transduction & cell cycle. ...  A 3rd DB in KEGG is LIGAND for the info.
   about chemical cmpds, enzyme molecules & enzymatic reactions. ..."
   -- [<A HREF="http://nar.oxfordjournals.org/cgi/content/full/28/1/27">NAR</A>]['09],
   -- [<A HREF="http://www.genome.ad.jp/kegg/">kegg</A>]['09].
   -- [<A HREF="http://www.genome.ad.jp/kegg/kegg2.html">kegg2</A>]['09].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Metabolic_network_modelling">wikip</A>].)

%A L. J. McGuffin
%A K. Bryson
%A D. T. Jones
%T The PSIPRED protein structure prediction server
%J Bioinformatics
%V 16
%N 4
%P 404-405
%M APR
%D 2000
%K jrnl, MolBio, c2000, c200x, c20xx, zz1222, psipred, ANN, NN, memsat 2,
   memsat2, GenThreader, secondary
%X "... allows users to submit a p. seq., perform a pred'n of their choice ...
   The user may select one of three pred'n methods ...: PSIPRED ...; MEMSAT 2
   or GenTHREADER ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/16.4.404">doi:10.1093/bioinformatics/16.4.404</A>]['22].
   (Also see psipred@[<A HREF="https://en.wikipedia.org/wiki/PSIPRED ">wikip</A>]['22].)

%A A. K. Abbas
%A A. H. Lichtman
%A J. S. Pober
%T Cellular and Molecular Immunology
%I WBSaundersCo
%M MAY
%D 2000
%K book, text, MolBio, c2000, c200x, c20xx, immune system, immunology, biol,
   inate, innate, adaptive, tCell, disease, response
%X 4th ed 2000, pb; uk us isbn:0721682332.
   "Intro. textbook for immunology and medical students on the principles of
   immunology and their applic. to human disease. ... explains the experimental
   obs. forming the basis for the sci. of immunology at the molecular, cellular,
   and whole-organism levels, and the resulting conclusions."

%A T. N. Petersen
%A C. Lundegaard
%A M. Nielsen
%A H. Bohr
%A J. Bohr
%A S. Brunak
%A G. P. Gippert
%A O. Lund
%T Prediction of protein secondary structure at 80% accuracy
%J Proteins
%V 41
%N 1
%P 17-20
%M OCT
%D 2000
%K jrnl, MolBio, c2000, c200x, c20xx, zz1116, protein, secondary structure,
   prediction, CASP4
%X "[SSP by] 800 neural network predictions has been developed, by use of novel
   methods such as output expansion and a unique balloting procedure. An overall
   performance of 77.2%-80.2% (77.9%-80.6% mean per-chain) for three-state
   (helix, strand, coil) prediction was obtained when evaluated on a commonly
   used set of 126 protein chains. The method uses profiles made by
   position-specific scoring matrices as input, while at the output level it
   predicts on three consecutive residues simultaneously. The predictions arise
   from tenfold, cross validated training and testing of 1032 protein sequences,
   using a scheme with primary structure NNs followed by structure filtering
   NNs. With respect to blind prediction, this work is preliminary and awaits
   evaluation by CASP4."
   -- [<A HREF="http://dx.doi.org/10.1002/1097-0134(20001001)41:1<17::AID-PROT40>3.0.CO;2-F">doi:10.1002/1097-0134(20001001)41:1<17::AID-PROT40>3.0.CO;2-F</A>]['16].
   [Also search for: MolBio secondary structure prediction].

%A M. S. Swanson
%A B. K. Hammer
%A Legionella pneumophila pathogenesis: A fateful journey from Amoebae to
   macrophages
%J Annual Rev. of Microbiology
%V 54
%P 567-613
%M OCT
%D 2000
%K jrnl, MolBio, c2000, c200x, c20xx, Legionella pneumophila pathogenesis,
   str, Corby, Philadelphia, Paris, Lens, bacteria, bacterium, amoebae, amoeba,
   macrophage, type 2, type2, type 4, type4, secretion system, systems,
   review, intro, survey, DNA, genome
%X "... 1976, when investigators from the [CDC&P] ... gram-negative bacterium
   ... establish phagosomes which are completely isolated from the endosomal
   pathway but are surrounded by endoplasmic reticulum. ... A # of factors
   contribute to L. pneumophila virulence, inc. type II and type IV secretion
   systems, a pore-forming toxin, type IV pili, flagella, & numerous other
   factors curr. under investigation.  ... resemblance to certain aspects of
   Mycobacterium, Toxoplasma, Leishmania, and Coxiella pathogenesis, ..."
   -- [<A HREF="http://dx.doi.org/10.1146/annurev.micro.54.1.567">doi:10.1146/annurev.micro.54.1.567</A>]['09].  Also see...
   Legionella@[<A HREF="http://en.wikipedia.org/wiki/Legionella">wikip</A>]['09],
   Legionella pneumophila@[<A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=Search&TermToSearch=txid446[orgn]">txid446</A>]['09],
   Legionella pneumophila str.Corby@[<A HREF="http://www.ncbi.nlm.nih.gov/nuccore/NC_009494">refseq</A>]['09],
   or L.P.str.C@[<A HREF="http://www.ncbi.nlm.nih.gov/nuccore/CP000675">genbank</A>]['09],
   str.Corby,        NC_009494, 3.6 Mb, 3200+ genes;
   str.Philadelphia 1, NC_002942, 3.4 Mb, ~3000 genes;
   str.Paris,        NC_006368, 3.5 Mb, 3000+ genes (& 131Kb plasmid NC_006365);
   str.Lens,         NC_006369, 3.3 Mb, ~3000 genes (&  60Kb plasmid NC_006366);
   [Also search for: Legionella MolBio].

%A C. Hannoun
%A P. Horal
%A M. Lindh
%T Long-term mutation rates in the hepatitis B virus genome
%J J. General Virology
%V 81
%P 75-83
%D 2000
%K jrnl, HBV, rate, error, errors, RT, c2000, c200x, c20xx, zzVIDRL, viral
%X "... retrospective approach was used that allowed the analysis of changes in
   the viral genome from transmission to late stages of infection without the
   req. for sampling early during this period. ...viral genome was seqd from
   serum samples of 3 mothers and their 10 adult children, who presumably had
   been infected vertically. The emergence of mutns between birth & sampling
   (mean 26.5y) as assessed by comparing the individual seqs. with the seq. of
   the strain assumed to have been transmitted. The mean diff. from this seq.
   were 0.02 & 0.28% in 7 asymptomatic & 1 symptomatic hepatitis B e antigen
   (HBeAg)-pos. carriers resp., & 0.62% in 5 HBeAg-neg. carriers. ...HBV genome
   is extremely stable over long periods ... during the HBeAg-pos. phase if the
   immune response (inflammation) is weak, whereas an average of 20 mutns
   emerged after development of hepatitis and/or loss of HBeAg without
   association with clinical outcome."
   -- [<A HREF="http://vir.sgmjournals.org/cgi/content/abstract/81/1/75">paper</A>]['06].

%A T. Chen
%A M.-Y. Kao
%A M. Tepel
%A J. Rush
%A G. M. Church
%T A dynamic programming approach to de novo peptide sequencing via tandem
   mass spectrometry
%J Symp. on Discrete Algorithms
%P 389-398
%D 2000
%O J. Comp. Biol., 8(3), pp.325-337, June 2001
   -- [<A HREF="http://dx.doi.org/10.1089/10665270152530872">doi:10.1089/10665270152530872</A>]['10]
%K conf, MolBio, c2000, c200x, c20xx, de novo peptide sequencing, denovo,
   protein, tandem mass spectrometry, spectrum graph, forbidden pairs path
%X The tandem mass spectrometry fragments a large # of molecules of the same
   peptide seq. into charged prefix & suffix subseqs., & then measures
   mass/charge ratios of these ions. The de nova peptide sequencing problem is
   to reconstruct the peptide seq. from a given tandem mass spectral data of
   k ions. By implicitly transforming the spectral data into an NC-spectrum
   graph G=(V,E) where |V|=2k+2, we can solve this problem in O(|V|+|E|) time &
   O(|Y|) space using dynamic programming. ... can be further used to discover a
   modified amino acid in O(|V||E|) time & to analyze data with other types of
   noise in O(|V||E|) time. ...implemented & tested on actual exp'l data."
      "... spectrum graph, where (1) a node corr.to a mass peak, & an edge,
      labeled by some amino acids, connects 2 nodes differed by the total mass
      of the AAs in the label; (2) a mass peak is transformed into several nodes
      in the graph, & each node represents a possible prefix subsequence (ion)
      for the peak."
   "... Lemma 1 The peptide seq. problem is equiv.to the problem which, given
   G=(V,E), asks for a directed path from x0 to y0 which contains exactly one
   of xj and yj for each j > 0. ..."
   -- pdf@[<A HREF="http://portal.acm.org/citation.cfm?id=338584">acm</A>]['10].

%A N. C. Lau
%A L. P. Lim
%A E. G. Weinstein
%A D. P. Bartel
%T An abundant class of tiny RNAs with probable regulatory roles in
   Caenorhabditis elegans
%J Science
%V 294
%P 858-862
%D 2001
%K jrnl, MolBio, RNA, stRNA, miRNA, lin-4, lin4, let-7, let7, gene expression,
   regulation, regulatory, siRNA, siRNAs, sRNA, sRNAs, stRNAs, microRNAs,
   miRNAs, ncRNA, C. elegans, Celegans, small, temporal, interfering, interfere,
   micro, zz1202, c2001, c200x, c20xx
%X 2 small temporal RNAs (stRNAs), lin-4 and let-7, control developmental
   timing in Caenorhabditis elegans. ...these 2 reg' RNAs are [in] a large
   class of 21- to 24-nucleotide noncoding RNAs, called microRNAs (miRNAs).
   We report on 55 previously unknown miRNAs in C. elegans. The miRNAs have
   diverse expression patterns during development: a let-7 paralog is
   temporally coexpressed with let-7; miRNAs encoded in a single genomic
   cluster are coexpressed during embryogenesis; and still other miRNAs are
   expressed constitutively throughout development. Potential orthologs of
   several of these miRNA genes were identified in Drosophila and human
   genomes. The abundance of these tiny RNAs, their expression patterns, and
   their evolutionary conservation imply that, as a class, miRNAs have broad
   regulatory functions in animals.
   -- [<A HREF="http://www.sciencemag.org/cgi/content/abstract/294/5543/858">paper</A>][11/'02].
   NB. stRNA = small temporal RNA
       siRNA = small interfering RNA

%A D. Pe'er
%A A. Regev
%A G. Elidan
%A N. Friedman
%T Inferring subnetworks from perturbed expression profiles
%J J. Bioinformatics
%V 17 (Suppl 1)
%P S215-S224
%M JUN
%D 2001
%O Proc. 9th ISMB
%K Peer, gene, levels, bayesian networks, MolBio, microarrays, micro array
%X "...expression profiles of genetic mutants provide a wide variety of
   measurements of cellular responses to perturbations. Typical analysis of
   such data identifies genes affected by perturbation & uses clustering to
   group genes of similar function. ... we discover a finer structure of
   interactions between genes, such as causality, mediation, activation, and
   inhibition by using a Bayesian network ... extend this ... to correctly
   handle perturbations, & identify sig. subnetworks of interacting genes. ..."
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/reprint/17/suppl_1/S215">pdf@oup</A>]['04].

%A M. Lagos-Quintana
%A R. Rauhut
%A W. Lendeckel
%A T. Tuschl
%T Identification of novel genes coding for small expressed RNAs
%J Science
%V 294
%P 853-858
%D 2001
%K MolBio, jrnl, small temporal RNA, stRNA, stRNAs, lin4, let7, miRNA,
   gene expression, regulation, tiny, micro
%X ...show that many 21- and 22-nt expressed RNAs, termed microRNAs, exist in
   invertebrates and vertebrates and that some of these novel RNAs, similar to
   let-7 stRNA, are highly conserved. This suggests that sequence-specific,
   posttranscriptional regulatory mechanisms mediated by small RNAs are more
   general than previously appreciated.
  [<A HREF="http://www.sciencemag.org/cgi/content/abstract/294/5543/853">paper</A>][11/'02].

%A R. C. Lee
%A V. Ambros
%T An extensive class of small RNAs in Caenorhabditis elegans
%J Science
%V 294
%P 862-864
%D 2001
%K MolBio, jrnl, small temporal RNA, stRNA, stRNAs, lin4, let7, miRNA,
   gene expression, regulation, tiny, micro, c2001, c200x, c20xx, Celegans
%X ...antisense RNAs are temporal regulators that control the timing of
   developmental events in Caenorhabditis elegans by inhibiting translation of
   target mRNAs. ...
   -- [<A HREF="http://www.sciencemag.org/cgi/content/abstract/294/5543/862">paper</A>][11/'02].

%A M. Turmel
%A C. Otis
%A C. Lemieux
%T The complete mitochondrial DNA sequence of Mesostigma viride identifies this
   green alga as the earliest green plant divergence and predicts a highly
   compact mitochondrial genome in the ancestor of all green plants
%J Mol. Biol. Evol.
%P 24-38
%V 19
%N 1
%M JAN
%D 2002
%K jrnl, MBE, MolBio, mtDNA, green alga, algae, algal, c2002, c200x, c20xx.
   mGenome, plants, origin, origins, evolution
%X "...belongs to a morphologically heterogeneous class (Prasinophyceae) that
   includes descendants of the earliest diverging green plants. ... circular
   mitochondrial genome ... (42,424-bp) & a high gene density (86.6% coding
   sequences) ... 65 genes ... predict that the common ancestor of all green
   plants had a compact mtDNA containing a minimum of 75 genes & perhaps two
   group I introns. Considering that the mitochondrial genome is much larger in
   size in land plants than in Mesostigma, we infer that mtDNA size began to
   increase dramatically in the Streptophyta either during the evolution of
   charophyte [GA] or during the trans'n from charophytes to land plants."
   -- [<A HREF="http://mbe.oupjournals.org/cgi/content/abstract/19/1/24">paper</A>]['03].

%A A. Wildenberg
%A S. Skiena
%A P. Sumazin
%T Deconvolving sequence variation in mixed DNA populations
%J Proc. of the 6th annual int. conf. on Computational biology
%I ACM
%P 311-320
%D 2002
%K conf, MolBio, population, c2002, c200x, c20xx, sequences, mutation,
   variations
%X pdf: [<A HREF="http://doi.acm.org/10.1145/565196.565238">doi:10.1145/565196.565238</A>]['05].
   proc., isbn:1581134983.

%A R. Jordan
%A L. Gold
%A C.Cummins
%A C. Hyde
%T Systematic review and meta-analysis of evidence for increasing numbers of
   drugs in antiretroviral combination therapy
%J BMJ
%V 324
%P 757-?
%M MAR
%D 2002
%K jrnl, BMJ, MolBio, virus, therapy, drug, c2002, c200x, c20xx, number,
   retroviral, HIV, AIDS, double, triple, quadruple, treatment, combinations,
   heterogeneity, trial, trials, medical, medicine, health
%X " ... 54 randomised controlled trials, most of good quality, with 66
   comparison groups were included in the analysis. For both the clinical
   outcomes and surrogate markers, combinations with up to and including three
   (triple therapy) were progressively and significantly more effective. The
   odds ratio for disease progression or death for triple therapy compared with
   double therapy was 0.6 (95% confidence interval 0.5 to 0.8). Heterogeneity
   in effect sizes was present in many outcomes but was largely related to the
   drugs used and trial quality.
   Conclusions: Evidence from randomised controlled trials supports the use of
   triple therapy. Research is needed on the effectiveness of quadruple
   therapies and the relative effectiveness of specific combinations of drugs."
   [87 refs] [<A HREF="http://bmj.bmjjournals.com/cgi/content/full/324/7340/757">paper@bmj</A>]['05] BMJ 2002;324:757 (30 March)

%A T. Egeland
%A P. Mostad
%T Statistical genetics and genetical statistics: a forensic perspective
%J Scand. J. of Statistics
%V 29
%D 2002
%K jrnl, stats, science
%X [<A HREF="http://folk.uio.no/thoree/papers/grimstad.pdf">?? pdf@uio</A>]['05]
   also see [<A HREF="http://www.math.chalmers.se/~mostad/familias/">familias</A>]['05].

%A A. Caprara
%A R. Rizzi
%T Improved approximation for breakpoint graph decomposition and
   sorting by reversals
%J J. of Combinatorial Optimization
%V 6
%P 157-182
%D 2002
%K jrnl, c2002, c200x, c20xx, MolBio, sort, reversal, break-point, stable set,
   set packing
%X [<A HREF="http://www.or.deis.unibo.it/caprara.html">home</A>][10/'02]
   -- [<A HREF="http://www.or.deis.unibo.it/alberto/bgd_rev.ps">paper</A>][10/'02].
   ... for almost all instances, sorting by reversals is == break-point graph
   decomposition. ... show how to improve the [known
   approximation ratio from 3/2 to 33/23+eps. ... uses best known approx alg
   for stable set on graph of max deg' 4 as well as for set packing where
   max size of any set is 6.
   [Also search for: sorting reversals].

%A M. J. Gardner
%A et al
%T Genome sequence of the human malaria parasite Plasmodium falciparum
%J Nature
%V 419
%P 498-511
%M OCT
%D 2002
%K jrnl, Nature, MolBio, malaria, Plasmodium falciparum, genomics, gene, genes,
   c2002, c200x, c20xx, nGenome, nuclear, zz1002
%X 23-megabases, ... 14 chromosomes, ... 5,300 genes.   doi:10.1038/nature01097
   -- [<A HREF="http://www.nature.com/nature/journal/v419/n6906/suppinfo/nature01097.html">supp' info'</A>][10/'02],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=23613362">chr1@genbank</A>]['07] 643292 bp,
      [<A HREF="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=23593254">chr2@genbank</A>]['07] 947102 bp.

%A Y. Cai
%A C. T. J. Dodson
%A A. J. Doig
%A O. Wolkenhauer
%T Information-theoretic analysis of protein sequences shows that amino
   acids self-cluster
%J J. Theor. Biol.
%V 218
%N 4
%P 419-433
%M OCT
%D 2002
%K jrnl, JTB, MolBio, clusters, protein, yeast, Saccharomyces cerevisiae,
   amino acid, non-random, nonrandom, information content
%X analyse [the] 20 [a.a.s] X the statistics of spacings between consecutive
   occurrences of X within ... Saccharomyces cerevisiae ... occurrences of
   amino acids may exhibit near random, clustered or smoothed out behaviour,
   ... If [a.a.'s] distributed randomly within a sequence, then they follow a
   Poisson process, & a histogram of the # of obs' of gap size[s] would
   [be] ~ neg. exponential dist'n. ... use differential geometric methods to
   quantify information on sequencing of [a.a.s] & groups of [them],
   via the sequences of intervals between their occurrences.
   ... an information-theoretic distance function on the 2-D space of
   stochastic processes subordinate to gamma distributions which ... [includes]
   random process as a special case. [find] maximum-likelihood estimates of
   parametric statistics show [all] 20 [a.a.s] tend to cluster, some
   substantially. ... freq's of short gap lengths tend to be higher & the
   variance of the gap lengths is greater than expected by chance. ...  [maybe
   because this] favour 2ndry structure formation or transmembrane domains. Gap
   sizes of 1 or 2 are generally disfavoured, 1 strongly so.  The only
   exceptions to this are Gln & Ser, as a result of poly(Gln) or poly(Ser)
   sequences. There are preferences for gaps of 4 & 7 that can be attributed
   to alpha-helices. ... a favoured gap of 7 for Leu is found in coiled coils.
   -- [<A HREF="http://www.idealibrary.com/links/doi/10.1006/jtbi.2002.3088">paper</A>][10/'02],
      [<A HREF="http://www.idealibrary.com/links/toc/jtbi/218/4/0">V218(4)</A>][10/'02].

%A E. E. Vitayev
%A Y. L. Orlov
%A O. V. Vishensky,  A. S. Belenok,  and N. A. Kolchanov
%T Computer system "gene discovery" to search for patterns in
   eukaryotic regulatory nucleotide sequences.
%J Molec. Biol.
%V 35
%N 6
%P 810-817
%D 2001
%O trans. from Molekulyarnaya Biologiya 35(6), pp.952-960, 2001.
%K MolBio, jrnl, genes, pattern, sequence, DNA, TRRD, c2001, c200x, c20xx
%X ... for patterns in the mutual location of context signals in ...

%A R. D. King
%A N. Marchand-Geneste
%A B. K. Alsberg
%T A quantum mechanics based representation of molecules for machine inference
%J Electronic Transactions in Artificial Intelligence
%V 5 B
%P 127-142
%D 2001
%K etai, etaij, c2001, c200x, c20xx, StruQT, StrQT, quantum topological atoms,
   relational, LP, AI, aber, RDKing
%X "...based on Bader's quantum topological atoms in molecules (AIM)...
   critical points ... zero gradients on the electron density field ...
   extend StruQT by making it relational ... endcoded in Prolog ..."
   -- [<A HREF="http://www.ep.liu.se/ej/etai/2001/008/">.pdf@ep.liu.se</A>][8/'04],
      [<A HREF="http://www.etaij.org/">etaij.org/</A>][8/'04],
      [<A HREF="http://users.aber.ac.uk/rdk/">.ps at rdk</A>][11/'02].

%A S. C. Lovell
%A et al
%T Structure validation by C_alpha geometry: phi, psi and C_beta deviation
%J Proteins: Structure, Function, and Bioinformatics
%V 50
%N 3
%P 437-450
%M FEB
%D 2003
%K MolBio, jrnl, c2017, c201x, c20xx, zz0724, validate, Validation Task Force,
   VTF, PDB, protein 3D structure, Ca, Cb, phi, psi
%X "Geometrical validation around the C_a is described, with a new C_b measure
   & updated Ramachandran plot. Deviation of the observed C_b atom from ideal
   posn provides a single measure encapsulating the major structure-validation
   info. contained in bond angle distortions ..."
   -- [<A HREF="https://doi.org/10.1002/prot.10286">doi:10.1002/prot.10286</A>]['24]
   [Also search for: protein structure validation].

%A N. Marchand-Geneste
%A K. A. Watson
%A B. Alsberg
%A R. D. King
%T A new approach to pharmacophore mapping and QSAR analysis using inductive
   logic programming.  Application to thermolysin inhibitors and glycogen
   phosphorylase b inhibitors
%J J. Med. Chem.
%V 46
%N 4
%P 653-?
%M FEB
%D 2003
%K MolBio, jrnl, ILP, inhibitor, zz1102, c2001, c200x, c20xx, aber, RDKing,
   SAR, QSAR, CoMFA, chemical compound
%X "... We unify ILP & std regression techniques to give a QSAR method that has
   the strength of ILP at describing steric structure with the familiarity &
   power of regression methods. ..."
   -- [<A HREF="https://doi.org/10.1021/jm0155244">doi:10.1021/jm0155244</A>]['22].
   [Also search for: chemical compound SAR].

%A S. R. Eddy
%T Non-coding RNA genes and the modern RNA world
%J Nature Rev. Genetics
%P 919-929
%V 2
%N 12
%M DEC
%D 2001
%K jrnl, MolBio, ncRNA, miRNA, micro, RNA, gene, c2001, c200x, c20xx, snoRNA,
   noncoding, precursor stem, miR1, miR84
%X "... surprisingly large number of new ncRNA genes. Non-coding RNAs [...] be
   particularly abundant in roles that require highly specific nucleic acid
   recognition without complex catalysis, [e.g.] in directing post-
   transcriptional regulation of gene exp'n or in guiding RNA modifications."
   -- [<A HREF="http://dx.doi.org/10.1038/35103511">doi:10.1038/35103511</A>][7/'04].

%A J. K. Percus
%T Mathematics of Genome Analysis
%I CUP
%P 139
%D 2001
%K book, text, CUP, MolBio
%X pb stg15, uk us isbn:0521585260; uk us isbn13:978-0521585262.
   hb stg40, uk us isbn:0521585171; uk us isbn13:978-0521585170.

%A P. M. Gleiss
%A P. F. Stadler
%A A. Wagner
%A D. A. Fell
%T Relevant cycles in chemical reaction networks
%J Adv. Complex Syst.
%V 4
%N 2-3
%P 207-226
%D 2001
%K jrnl, MolBio, cycle, metabolic pathways, pathway, network, graph, graphs,
   short, cycle, c2001, c200x, c20xx, substrate, hypergraph, path, paths
%X "We characterize the distributions of short cycles in a large metabolic
   network previously shown to have small world characteristics & a power law
   degree distribution.  Compared with 3 classes of random networks, including
   Erdos-Renyi random graphs & synthetic small world networks of the same
   connectivity, both the metabolic network & models for the chemical reaction
   networks of planetary atmospheres have a particularly large number of
   triangles & a deficit in large cycles. [...] propose that long cycles in
   metabolic pathways may have been selected against [...]"   [via G.F.]
   -- [<A HREF="http://www.tbi.univie.ac.at/papers/Abstracts/01-pfs-005.pdf">pdf@univie.ac.at</A>][7/'04],
      [<A HREF="http://samba.unm.edu/~wagnera/ACS01_Gleissetal.pdf">pdf@unm.edu</A>][7/'04],
      [<A HREF="http://dx.doi.org/10.1142/S0219525901000140">doi:10.1142/S0219525901000140</A>][7/'04].
   [Also search for: graphModel].

%A L. Hunter
%A R. C. Taylor
%A S. M. Leach, & R. Simon
%T GEST: a gene expression search tool based on a novel Bayesian
   similarity metric
%J J. Bioinformatics
%V 17 (suppl 1)
%P S115-S122
%M JUN
%D 2001
%K conf, MolBio, c2001, c200x, c20xx, LHunter, uniColorado, genes, levels,
   microarrays
%X [<A HREF="http://bioinformatics.oupjournals.org/cgi/reprint/17/suppl_1/S115">pdf@oup</A>]['03],
   [<A HREF="http://compbio.uchsc.edu/Hunter_lab/Hunter/">LH</A>]['03].

%A J. Felsenstein
%T Inferring Phylogenies
%I Sinauer
%P 580
%D 2001
%K book, text, MolBio, phylogenetic, evolutionary, c2001, c200x, c20xx,
   family, tree, trees, biol, biology, uniWashington, L4Ref, L5Ref
%X 2nd ed 2003.
   1st ed 2001, us$62; uk us isbn:0878931775; uk us isbn13:978-0878931774.
   -- [<A HREF="http://evolution.gs.washington.edu/">uWash</A>]['05].
   [Also search for: MolBio book].
   [Also search for: phylogenetic tree MolBio].

%A C. H. Bryant
%A S.H.Muggleton,  S.G.Oliver, D.B.Kell, P.Reiser, R.D.King
%T Combining inductive logic programming, active learning and robotics to
   discover the function of genes
%J Electronic Trans. on Artificial Intelligence
%V 5
%N B
%P 1-36
%D 2001
%K MolBio, AI, ILP, gene, function, c2001, c200x, c20xx, RDKing,
   robot scientist
%X "...component of the reasoning carried out by an ``artificial scientist''
   this paper describes ASE-Progol, ...uses [ILP] to construct hypothesised
   1st-order theories & uses a CART-like algorithm to select trials for
   eliminating ILP derived hypotheses. In simulated yeast growth tests ASE-
   Progol was used to rediscover how genes participate in the aromatic amino
   acid pathway of Saccharomyces cerevisiae. The cost of the chemicals consumed
   in converging upon a hypothesis with an accuracy of around 88% was reduced
   by 5 orders of magnitude when trials were selected by ASE-Progol [v.] being
   sampled at random. ...naive strategy of always choosing the cheapest trial
   from the set of candidate trials led to lower cumulative costs than ASE-
   Progol, both the naive strategy & the random strategy took significantly
   longer to converge upon a final hypothesis than ASE-Progol. [Eg] to reach an
   accuracy of 80%, ASE-Progol required 4 days while random sampling required 6
   days & the naive strategy required 10 days"   CHB is at comp.rgu.ac.uk ['04],
   -- [<A HREF="https://users.monash.edu.au/~lloyd/cgi-bin/glookbib_search?search_string=ilp+c20xx&index_file=..%2FINDEX">SemSchlr</A>]['22],
      [<A HREF="http://www.ida.liu.se/ext/epa/ej/etai/2001/B1/">in MI18</A>]['04] at
      [<A HREF="http://www.ida.liu.se/ext/etaij/">etaij</A>]['04].

%A N. T. Perna
%A G. Plunkett III
%A et al
%T Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
%J Nature
%V 409
%N 6819
%P 529-533
%M JAN
%D 2001
%K jrnl, E-coli, Ecoli, O157:H7 EDL933, NC_002655, NC002655, AE005174, biol,
   MolBio, prokaryote, bacteria, bacterium, food poisoning, F.R.Blattner,
   c2001, c200x, c20xx, complete, whole, genome, genomic, DNA, medical, strain,
   hamburger bug, O157H7, microbial genomes
%X 5,528,445 bp, so called "hamburger bug".
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=genome&gi=169">@genbank</A>]['05].
   (Erratum in Nature 2001 Mar 8;410(6825):240.)
   (Also see: K12 complete genome c1997)

%A N. Beerenwinkel
%A B. Schmidt
%A H.Walter, R.Kaiser, T.Lengauer, D.Hoffman, K.Korn, J.Selbig
%T Geno2pheno: Interpreting genotypic HIV drug resistance tests
%J Intelligent Sys.
%I IEEE
%V 16
%N 6
%P 35-41
%M DEC
%D 2001
%K drug resistance, SVM, DTree, test, c2001, c200x, c20xx, predict, model,
   genotype, phenotype, phenotypic, AIDS
%X "... uses the information encoded in the viral genomic sequence to predict
   resistance or susceptibility of the virus to 13 antiretroviral agents. To
   predict phenotypic drug resistance from genotype ...applied 2 ...techniques:
   decision trees & linear support vector machines. ... Except for 3 drugs, all
   error estimates ranged between 7.25 & 15.5 percent. SVMs performed slightly
   better for most drugs, but knowledge extraction was easier for DTs."
   sub'n [<A HREF="http://doi.ieeecomputersociety.org/10.1109/5254.972080">doi:10.1109/5254.972080</A>]['05],
   -- [<A HREF="http://www.geno2pheno.org/">geno2pheno.org</A>]['05],
      [<A HREF="http://cartan.gmd.de/geno2pheno.html">geno2pheno</A>][?].

%A D. J. Aldous
%T Stochastic models and descriptive statistics for phylogenetic trees,
   from Yule to today
%J Statist. Sci.
%V 16
%N 1
%P 23-34
%D 2001
%K jrnl, MolBio, tree, evolutionary, shape, c2001, c200x, c20xx, balance,
   model, biol, biology, Udnay Yule, trees, Markov
%X "In 1924 Yule observed that distributions of number of species per
   genus were typically long-tailed, & proposed a stochastic model to fit these
   data. Modern taxonomists often prefer to represent relationships between
   species via phylogenetic trees; the counterpart to Yule's observation is
   that actual reconstructed trees look surprisingly unbalanced...."
   -- [<A HREF="http://dx.doi.org/10.1214/ss/998929474">doi:10.1214/ss/998929474</A>]['05].

%A E. Doo
%A T. J. Liang
%T Molecular anatomy and pathophysiologic implications of drug resistance in
   hepatitis B virus infection
%J Gastroenterology
%V 120
%N 4
%P 1000-1008
%M MAR
%D 2001
%K jrnl, MolBio, medicine, health, c2001, c200x, c20xx, hepatitis B, hep, hepB,
   HBV, hepatitisB, virus, viral, reverse transcriptase, RT, YMDD, zzVDRL
%X "Synthesis of the hepatitis B virus (HBV) DNA genome occurs within the viral
   nucleocapsid ... Lamivudine is a potent inhibitor of HBV and [HIV] reverse
   transcriptases, but subs. of isoleucine or valine for methionine within the
   tyrosine-methionine-aspartate-aspartate (YMDD) motif are associated with
   virologic & clinical resistance to lamivudine therapy. Under lamivudine
   selection pressure, the high viral production rate & the low fidelity viral
   polymerase contribute to frequent development of the YMDD mutants. ..."

%A R. D. King
%A A. Karwath
%A A. Clare
%A L. Dehaspe
%T The utility of different representations of protein sequence for
   predicting functional class
%J J. Bioinformatics
%V 17
%N 5
%P 445-454
%M MAY
%D 2001
%K jrnl, c2001, c200x, c20xx, zz0206, representation, function, Molbio, DMP,
   phylogeny, ORF, ORFs, predict, prediction, aber, RDKing, AClare
%X "... DMP works even in the absence of a homologous p. of known function. We
   investigate the utility of different ways of representing p. sequence in DMP
   (residue frequencies, phylogeny, predicted structure) using the E.coli genome
   as a model. RESULTS: Using the different representations DMP learnt
   prediction rules that were more accurate than default at every level of
   function using every type of representation. The most effective way to
   represent sequence was using phylogeny (75% accuracy & 13% coverage of
   unassigned ORFs at the most general level of function: 69% accuracy & 7%
   coverage at the most detailed). ..."
   -- [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/5/445">jrnl</A>]['06].

%T Alternative splicing: Increasing diversity in the proteomic world
%J Trends in Genetics
%V 17
%N 2
%P 100-107
%M FEB
%D 2001
%K jrnl, MolBio, biol, biology, gene, genes, protein, c2001, c200x, c20xx,
   proteome, genome, complexity, intron, exon, splice, alternate, mRNA, RNA
%X "How can the genome of Drosophila melanogaster contain fewer genes than the
   undoubtedly simpler organism Caenorhabditis elegans? The ans. must lie within
   their proteomes. ... alternative splicing has an extremely important role in
   expanding protein diversity & might therefore partially underlie the apparent
   discrepancy between gene number & organismal complexity. Alt. splicing can
   generate more transcripts from a single gene than the number of genes in an
   entire genome. However, for the vast majority of alternative splicing events
   the functional significance is unknown. ... "
   -- [<A HREF="http://dx.doi.org/10.1016/S0168-9525(00)02176-4">doi:10.1016/S0168-9525(00)02176-4</A>]['05],
      [<A HREF="http://grad.uchc.edu/phdfaculty/gravely.html">auth</A>]['05].
   [Also search for: alternative splicing MolBio].

%T Design Principles for the Immune System and Other Distributed
   Autonomous Systems
%E L. A. Segal
%E I. R. Cohen
%S Santa Fe Inst. Studies on the Sciences of Complexity
%P 428
%D 2001
%K MolBio, wShop, c2001, c200x, c200x, book, biol, agent based, model, agents,
   models, immunity
%X hb, us$85; uk us isbn:0195136993; uk us isbn13:978-0195136999.

%A R. Huestis
%A N. Cloonan
%A M. Tchavtchitch
%A A. Saul
%T An algorithm to predict 3' intron splice sites in Plasmodium falciparum
   genomic sequences
%J Mol. Biochem. Parasitol.
%V 112
%N 1
%P 71-77
%M JAN
%D 2001
%K jrnl, c2001, c200x, c20xx, site, MolBio, malaria, parasite, sequence,
   zz0706, PfAGSS, AG, intron, introns, exon, exons, boundary,
   boundaries, uniMonash
%X "... PfAGSS, for predicting 3' splice sites in p.f. genomic sequences is
   described. Application of this program to the published P.f. chr.2 and 3 data
   suggests that existing programs result in a high error rate in assigning 3'
   intron boundaries."
   -- [<A HREF="http://dx.doi.org/10.1016/S0166-6851(00)00347-9">doi:10.1016/S0166-6851(00)00347-9</A>]['06].

%A I. Pult
%A N. Abbott
%A Y. Y.  Zhang
%A J. Summers
%T Frequency of spontaneous mutations in an avian hepadnavirus infection
%J J. Virology
%V 75
%N 20
%P 9623-9632
%M OCT
%D 2001
%K jrnl, MolBio, c2001, c200x, c20xx, HBV, duck, DHBV, mutation rate, rates,
   hepatitis
%X "...measured the freq. of revertants of a cytopathic strain of the duck
   hepatitis B virus that bears a single nucleotide subs. in the pre-S envelope
   protein open reading frame, resulting in the amino acid substitution G133E.
   Cytopathic v. mixed with known amounts of a genetically marked wild-type v.
   was injected into ducklings.  V. outgrowth was accompanied by a coselection
   of wild-type & spontaneous revertants during recovery of the ducklings from
   the acute liver injury caused by death of the G133E-infected cells. The freq.
   of individual revertants in the selected noncytopathic virus population was
   est. by determining the ratio of each revertant to the wild-type virus.
   Spontaneous revertants were found to be present at frequencies of 1 x 10(-5)
   to 6 x 10(-5) / G133E genome inoculated. A math. model was used to est. that
   the mut. rate ~ 0.8 x 10(-5) to 4.5 x 10(-5) per nucleotide per generation."
   -- [<A HREF="http://dx.doi.org/10.1128/JVI.75.20.9623-9632.2001">doi:10.1128/JVI.75.20.9623-9632.2001</A>]['07].

%A J. Buhler
%T Efficient large-scale sequence comparison by locality-sensitive hashing
%J J. Bioinformatics
%V 17
%N 5
%P 419-426
%D 2001
%K jrnl, MolBio, c2001, c200x, c20xx, LSH, locality sensitive hashing, hash,
   filter, ungapped local alignment, neighbourhood
%X "... 'LSH-ALL-PAIRS' ... to find ungapped local alignments ...
   finding local sim's with as little as 63% identity ..."
   -- [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/5/419">Bioinf</A>]['09].
   NB. [Also search for: Flash MolBio].

%A J. Gough
%A K. Karplus
%A R. Hughey
%A C. Chothia
%T Assignment of homology to genome sequences using a Library of
   hidden Markov models that represent all proteins of known structure
%J J. Mol. Biol.
%V 313
%N 4
%P 903-919
%D 2001
%K jrnl, JMB, MolBio, c2001, c200x, c20xx, sequence, protein family, families,
   super, superfamily, superfamilies, superfam, org, database, model, HMM
%X [<A HREF="http://supfam.org/SUPERFAMILY/">superfam.org</A>]['07].

%A N. V. Grishin
%T Fold change in evolution of protein structures
%J J. Struct. Biol.
%V 134
%N 2-3
%P 167-185
%M MAY-JUN
%D 2001
%K jrnl, JSB, MolBio, c2001, c200x, c20xx, evolution, protein, 3D, structure,
   fold, folds, change, changes, beta sheets, circular, homology
%X "... accumulation of examples of homologous proteins with globally distinct
   structures. Sig. seq. conservation, local structural resemblance, &
   functional similarity strongly indicate evolutionary relationships between
   these proteins despite pronounced structural differences at the fold level.
   Several mechanisms such as insertions/deletions/substitutions, circular
   permutations, & rearrangements in beta-sheet topologies account for the
   majority of detected structural irregularities. The existence of
   evolutionarily related proteins that possess different folds brings new
   challenges to the homology modeling techniques & the structure classification
   strategies & offers new opportunities for protein design in experimental
   studies."   -- via AK.
   -- [<A HREF="http://dx.doi.org/10.1006/jsbi.2001.4335">doi:10.1006/jsbi.2001.4335</A>]['09].

%A W. R. Taylor
%T Defining linear segments in protein structure
%J J. Molec. Biol.
%V 310
%N 5
%P 1135-1150
%M JUL
%D 2001
%K JMB, jrnl, MolBio, c2001, c200x, c20xx, linear, segment, protein, structure
%X "... The std method used to define line segments is to fit an axis through
   each secondary structure elt. ... has difficulties, however, both with
   inconsistent defns of s.s. & the problem of fitting a single straight line to
   a bent structure. The proc. described here avoids these problems by finding a
   set of line segs. indep. of any external s.s. defn. This allows the segs. to
   be used as a novel basis for s.s. defn by taking the avg. rise/residue along
   each axis to characterise the seg.. ... has the advantage that s.s. are
   described by a single (cts.) value that is not restricted to the conventional
   classes of alpha-helix, 310 and beta-strand.  This latter property allows
   structures without "classic" s.s. to be encoded as line segs.  that can be
   used in comparison algs.. When compared over a large # of pairs of homologous
   proteins ... found to be slightly more consistent than a widely used method
   [?DSSP?] based on hydrogen bonds."
   -- [<A HREF="http://dx.doi.org/10.1006/jmbi.2001.4817">doi:10.1006/jmbi.2001.4817</A>]['11].

%A T. Emahazion
%A L. Feuk
%A M. Jobs
%A S. L. Sawyer
%A D. Fredman
%A D. St Clair
%A J. A. Prince
%A A. J. Brooke
%T SNP association studies in Alzheimer's disease highlight problems for
   complex disease analysis
%J Trends in Genetics
%V 17
%N 7
%P 407-413
%M JUL
%D 2001
%K jrnl, MolBio, c2001, c200x, c20xx, SNPs, intro, survey, review, linkage,
   association analysis, study, risk, false positive, weak signal, signals
%X "Genetic linkage & association analyses are 2 distinct approaches to
   understanding the genetic etiology of complex disease. Assoc. analysis has
   become particularly popular in recent times, but the true utility of the
   strategy remains uncertain. To try to gain better insight into the relevant
   issues, we have used genetic association analysis to explore the etiology of
   Alzheimer's disease. Our empirical findings supplement the theor. debate,
   illustrating the general doubtfulness of previous +ve findings & the limited
   ability of typical assoc. studies based on candidate genes to discern true
   medium-sized signals from false +ves. Improvements in genotyping technologies
   & increasing the number of SNPs tested, without sophisticated allowance for
   all other issues, could simply lead to an unmanageable overload of false +ve
   signals, themselves obscuring true disease associations."
   -- [<A HREF="http://dx.doi.org/10.1016/S0168-9525(01)02342-3">doi:10.1016/S0168-9525(01)02342-3</A>]['07].

%A D. K. Agrafiotis
%T A constant time algorithm for estimating the diversity of large chemical
   libraries
%J J. Chem. Inf. Comput. Sci.
%V 41
%N 1
%P 159-167
%D 2001
%K jrnl, c2001, c200x, c20xx, chemical compound, library, diversity, stats,
   chemistry
%X "... ests. the cumulative pr.distn of intermolecular dissimilarities in the
   colln of interest & then measures the deviation of that distn from the
   respective distn of a uniform sample using the Kolmogorov-Smirnov statistic.
   ... cumulative distribution can be easily est. using pr.sampling & does not
   require exhaustive enum. of all pairwise dists. in the data set. The fn is
   intuitive, v.fast to compute, does not depend on the size of the collection,
   & can be used to perform diversity ests. on both global & local scale. ...
   it allows meaningful comparison of data sets of different cardinality & is
   not affected by the curse of dimensionality ..."
   -- [<A HREF="http://dx.doi.org/10.1021/ci000091j">doi:10.1021/ci000091j</A>]['08].
   (Also see BldgBlockChem@[<A HREF="https://en.wikipedia.org/wiki/Building_block_(chemistry)">wikip</A>]['20].)
   [Also search for: chemical library].

%A D. Adam
%T Individual genomes targeted in sequencing revolution
%J Nature
%V 411
%P 402
%M MAY
%D 2001
%K MolBio, Nature, Solexa, single molecule arrays, www, HREF, http, zz0601,
   DNA, array, short read, reads, (Illumina)
%X News item.  Possible new technology to rapidly sequence whole genomes ...
   if it scales up well.  Cambridge (UK) start up company Solexa.  ...
   100 million immobilized DNA samples ...
   -- [<A HREF="http://dx.doi.org/10.1038/35078205">doi:10.1038/35078205</A>]['08],
   -- [<A HREF="http://www.solexa.co.uk/">Solexa</A>][5/'01].
   [Also search for: Illumina sequencing technology].

%A G. Lancia
%A R. Carr
%A B. Walenz
%A S. Istrail
%T 101 optimal PDB structure alignments: a branch-and-cut algorithm for the
   maximum contact map overlap problem
%J Proc. 5th Int. Conf. on Computational biology
%P 193-202
%D 2001
%K conf, c2001, c200x, c20xx, protein, 3D, structure, alignment,
   contact map overlap, MolBio, integer linear programming
%X "...provide the first rigorous algorithm for structure comparison. ... based
   on developing an effective integer linear programming (IP) formulation ...
   contact maps overlap (CMO), and a branch-and-cut strategy ... Our algs.
   identified a gallery of optimal & near-optimal structure als. for pairs of
   proteins ... up to 80 amino acids & about 150 contacts each ... first
   provable optimal & near-optimal algs. ... reduction of the CMO optimization
   to the max. indep. set (MIS) problem ... the first effective use of IP
   methods in protein struct ... The hybrid heuristic approach that worked well
   for providing LWBs in the b. & cut alg. was tried on large proteins in a test
   set suggested by J.Skolnick. ... 528 p/w structure alignments validated the
   clustering with a 98.7% acc. (1.3% false -ve and 0% false +ve)."     via AK.
   -- [<A HREF="http://doi.acm.org/10.1145/369133.369199">doi:10.1145/369133.36919</A>]['08].
   -- [<A HREF="http://www-cryst.bioc.cam.ac.uk/~homstrad/">HOMSTRAD</A>]['07].
   [Also search for: MolBio protein structure alignment].

%A C. Grunau
%A E. Renault
%A A. Rosenthal
%A G. Roizes
%T MethDB - a public database for DNA methylation data
%J NAR
%V 29
%N 1
%P 270-274
%M JAN
%D 2001
%K jrnl, NAR, MolBio, c2001, c200x, c20xx, MethDB, Methylation, DNA, 5mC,
   5-methylcytosines, gene silencing
%X "... Methylation of cytosine in the 5 position of the pyrimidine ring is a
   major mod'n of the DNA in most organisms. In eukaryotes, the distn & # of
   5-methylcytosines (5mC) along the DNA is heritable but can also change with
   the developmental state of the cell & as a response to mod'ns of the
   environment. ... recently focused on the gene silencing effect methylation
   ... methylation patterns & methylation profiles are shown both as a graphical
   repn & as G/A/T/C/5mC-seqs. or tables with seq. posn & methylation levels,
   respectively."
   -- pdf@[<A HREF="http://nar.oxfordjournals.org/cgi/content/full/29/1/270">nar</A>]['08].
   Also C. Amoreira, W. Hindermann, C. Grunau,
        "An improved version of the DNA methylation database (MethDB)",
        NAR 31(1), 75-77, 2003 [<A HREF="http://dx.doi.org/10.1093/nar/gkg093">doi:10.1093/nar/gkg093</A>]['08].

%A J. A. Irving
%A J. C. Whisstock
%A A. M. Lesk
%T Protein structural alignments and functional genomics
%J Proteins
%V 42
%N 3
%P 378-382
%M FEB
%D 2001
%K jrnl, MolBio, c2001, c200x, c20xx, structure, 3D, alignment, fit, RMSD,
   AMLesk, closeness, size, tradeoff, trade-off, active
%X "... Prediction of protein fn from struct. has thereby become a challenging
   problem ... The strong conservation of active site conformations in
   homologous ps. suggests a method for identifying them. This depends on the
   reln. between size & goodness-of-fit of aligned substructures in homologous
   ps.. For all pairs of ps. studied, the [RMSD] as a fn of the # of residues
   aligned varies exponentially for large common substructures & linearly for
   small common substructures. The exponent of the dependence at large common
   substructures is well correlated with the RMSD of the core as originally
   calculated by Chothia & Lesk ... affording the poss. of reconciling
   different structural alignment procs.. In the region of small common
   substructures, reduced aligned subsets define active sites & can be used to
   suggest the locations of active sites in homologous proteins."
   -- [<A HREF="http://dx.doi.org/10.1002/1097-0134(20010215)42:3<378::AID-PROT70>3.0.CO;2-3">doi:10.1002/1097-0134(20010215)42:3<378::AID-PROT70>3.0.CO;2-3</A>]['12].
   [Also search for: MolBio protein structure alignment].

%A J. Tisdall
%T Beginning Perl for Bioinformatics
%I OReilly
%P 400
%D 2001
%K book, text, MolBio, bioinformatics, c2001, c200x, c20xx, computer,
   programming, bioPerl
%X 1st ed 2001; pb us$26; uk us isbn:0596000804; uk us isbn13:978-0596000806.

%A T. R. Gregory
%T Coincidence, coevolution, or causation?  DNA content, cell size, and
   the C-value enigma
%J Biol. Rev.
%V 76
%P 65-101
%D 2001
%K jrnl, MolBio, c2001, c200x, c20xx, genome, genomes, size, sizes,
   organism, complexity, nucleotypic, C-value paradox, Cvalue
%X "... sig. genome size diversity ( > 200000-fold among eukaryotes) bears no
   relationship to organismal complexity & both the origins & reasons for the
   clearly non-random distribution of this variation remain unclear. ...
   ... this 'C-value enigma' ... [/paradox], ... junk or selfish DNA ...
   ... preponderance of the available evidence instead favours the nucleotypic
   theory which postulates a causal link between bulk DNA amount & cell volume.
   Under this view."
   -- pdf@[<A HREF="http://www.uoguelph.ca/~rgregory/Biolrev.pdf">uoguelph</A>]['08],
   or pdf@[<A HREF="http://journals.cambridge.org/production/action/cjoGetFulltext?fulltextid=68620">jrnl</A>]['08].
   NB c2008: "... although the high end of this distribution (Amoeba at 700pg)
             is probably not reliable. Genome sizes are known to range more
             than 3,300-fold in animals ..."      [[1pg, 1 picogram ~ 978 Mb]]
   from [<A HREF="http://www.genomesize.com/gregorylab/research/">www</A>]['12/'08].

%A D. Jaccoud
%A K. Peng
%A D. Feinstein
%A A. Kilian
%T Diversity Arrays: a solid state technology for sequence information
   independent genotyping
%J NAR
%V 29
%N 4
%P e25
%D 2001
%K jrnl, eJrnl, c2001, c200x, c20xx, MolBio, Diversity Arrays, array, SNP,
   DArT,  microarray,  microarrays, Kilian
%X "... application of the microarray technology platform to the analysis of DNA
   polymorphisms. ...  assaying for the presence (or amount) of a specific DNA
   fragment in a representation derived from the total genomic DNA of an
   organism or a population of organisms. Two different approaches are
   presented: the first involves contrasting two representations on a single
   array while the second involves contrasting a representation with a
   reference DNA fragment common to all elements of the array. ..."
   -- [<A HREF="http://nar.oxfordjournals.org/cgi/content/full/29/4/e25">NAR</A>]['09].
   (Also see [<A HREF="http://www.diversityarrays.com/">diversityarrays.com</A>]['09] (ACT).)

%A R. Knight
%T The Origin and Evolution of the Genetic Code
%I PrincetonU.
%D 2001
%K MolBio, PhD thesis, c2001, c200x, c20xx, evolution, origin, origins,
   genetic code, codon, codons, information
%X (198pp single spaced)
   See [<A HREF="http://bayes.colorado.edu/">Col'r'do</A>]['10].

%A R. D. Knight
%A S. J. Freeland
%A L. F. Landweber
%T A simple model based on mutation and selection explains trends in codon and
   amino-acid usage and GC composition within and across genomes
%J Genome Biol.
%V 2
%N 4
%P research0010.1-0010.13
%M MAR
%D 2001
%K jrnl, MolBio, c2001, c200x, c20xx, CG, AT, composition, codon bias
%X "Correlations between genome composition (in terms of GC content) & usage of
   particular codons & AAs have been widely reported, but poorly explained. We
   show here that a simple model of processes acting at the nucleotide level
   explains codon usage across a large sample of species (311 bacteria, 28
   archaea & 257 eukaryotes). ... predicts responses (slope & intercept of the
   regression line on genome GC content) of individual codons & AAs to genome
   composition. ... Codons respond to genome composition on the basis of their
   GC content relative to their synonyms (explaining 71-87% of the variance in
   response among the different codons, depending on measure). AA responses are
   determined by the mean GC content of their codons (71-79% of the variance).
   Similar trends hold for genes within a genome. Position-dept seln for error
   minimization explains why individual bases respond differently to directional
   mutation pressure. ... Our model suggests that GC content drives codon usage
   (rather than the converse). ..."  [76 refs].
   -- [<A HREF="http://dx.doi.org/10.1186/gb-2001-2-4-research0010">doi:10.1186/gb-2001-2-4-research0010</A>]['10],
   auth@[<A HREF="http://bayes.colorado.edu/">col'r'do</A>]['10].

%A A. Aronson
%T Effective mapping of biomedical text to the UMLS Metathesaurus:
   the MetaMap program
%J Proc. American Medical Informatics Assoc. (AMIA)
%P 17-21
%D 2001
%K conf, MolBio, c2001, c200x, c20xx, UMLS, Metathesaurus, MetaMap, word, words,
   meta thesaurus, terminology, jargon, natural language, biomedical literature
%X pdf@[<A HREF="http://skr.nlm.nih.gov/papers/references/metamap_01AMIA.pdf">nih</A>['10].
   Also see umls@[<A HREF="http://www.nlm.nih.gov/research/umls/">nih</A>]['10].

%A C. Lee
%A C. Grasso
%A M. F. Sharlow
%T Multiple sequence alignment using partial order graphs
%J J. Bioinformatics
%V 18
%N 3
%P 452-464
%D 2001
%K jrnl, MolBio, c2001, c200x, c20xx, partially ordered alignment, POA
%X "... present a graph repn of an MSA that can itself be aligned
   directly by pairwise dynamic programming, eliminating the need to reduce the
   MSA to a profile. This enables our alg. (...) to guarantee that the optimal
   alignment of each new seq. v. each seq. in the MSA will be considered.
   Moreover, this alg. introduces a new edit operator, homologous recombination,
   important for multidomain seqs.. [It] has improved speed (linear time
   complexity) over existing MSA algs., enabling construction of massive &
   complex alignments (e.g. an al. of 5000 seqs. in 4h on a P_II)."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/18.3.452">doi:10.1093/bioinformatics/18.3.452</A>]['11].

%A C. A. Lipinski
%A F. Lombardo
%A B. W. Dominy
%A P. J. Feeney
%T Experimental and computational approaches to estimate solubility and
   permeability in drug discovery and development settings
%J Adv. Drug Delivery Rev.
%V 46
%N 1-3
%P 3-26
%M MAR
%D 2001
%K jrnl, c2001, c200x, c20xx, Lipinski rule of five, rule of 5, logP, drugs,
   high throughput screening, HTS, chemical compound, library, hBond,
   absorption, distribution, metabolism, excretion, ADME
%X "Exp. & comp. approaches to est. solubility & permeability in discovery &
   development settings are described. In the disc. setting 'the rule of 5'
   predicts that poor absorption or permeation is more likely when there are
   more than 5 H-bond donors, 10 H-bond acceptors, the molecular weight (MWT) is
   >500 & the calc. Log P (CLogP) >5 (or MlogP >4.15). Comp. methodology for the
   rule-based Moriguchi Log P (MLogP) calc. is described. Turbidimetric
   solubility measurement is described & applied to known drugs. High throughput
   screening (HTS) leads tend to have higher MWT & Log P & lower turbidimetric
   solubility than leads in the pre-HTS era. In the dev. setting, solubility
   calcs. focus on exact value prediction & are difficult because of
   polymorphism. Recent work on linear free energy relationships & Log P
   approaches are critically reviewed ..."
   -- [<A HREF="http://dx.doi.org/10.1016/S0169-409X(00)00129-0 ">doi:10.1016/S0169-409X(00)00129-0</A>]['08].
   Rule: An orally active drug has no more than 1 violation of the following,
    * Not more than  5 H-bond donors    (N or O atoms with >=1 H atoms),
    * Not more than 10 H-bond acceptors (N or O atoms),
    * A molecular wt < 500 g/mol,
    * A partition coefficient log P < 5.
   NB. all #s are multiples of 5, which is the origin of the rule's name.
   -- [<A HREF="http://en.wikipedia.org/wiki/Lipinski's_Rule_of_Five">wikip</A>]['08].
   (Also see BldgBlockChem@[<A HREF="https://en.wikipedia.org/wiki/Building_block_(chemistry)">wikip</A>]['20].)
   [Also search for: chemical library].

%A A. M. Lesk
%T Introduction to Protein Architecture: The Structural Biology of Proteins
%I OUP
%P 360
%D 2001
%K MolBio, c2001, c200x, c20xx, zz0416, AMLesk, book, text, L2Ref, L3Ref,
   protein, 3D, structure, fold
%X 1st ed 2001; pb us$8; uk us isbn:0198504748; uk is isbn13:978-0198504740.
   "... Topics treated include: Pattern and form in protein structure; The
   building blocks; The relationship between amino acid sequence and protein
   structure; Secondary, supersecondary and tertiary structure; Classifications
   and hierarchies of protein folding patterns; Protein evolution; How proteins
   change conformation (and why). ..."

%A A. Ben-Dor
%A B. Chor
%A R. Karp
%A Z. Yakhini
%T Discovering local structure in gene expression data: The order-preserving
   submatrix problem
%J RECOMB 2002
%D 2002
%K MolBio, microarray, micro array, sub matrix, array, BenDor, OPSM
%X ...discovery of patterns in gene expression matrices, in which each element
   gives the expression level of a given gene in a given experiment. Most
   existing methods for pattern discovery in such matrices are based on
   clustering genes by comparing their expression levels in all experiments, or
   clustering experiments by comparing their expression levels for all genes.
   Our work goes beyond such global approaches by looking for local patterns
   that manifest themselves when we focus simultaneously on a subset G of the
   genes and a subset T of the experiments. Specifically, we look for
   order-preserving submatrices (OPSMs), in which the expression levels of all
   genes induce the same linear ordering of the experiments (we show that the
   OPSM search problem is NP-hard in the worst case). Such a pattern might
   arise, for example, if the experiments in T represent distinct stages in the
   progress of a disease or in a cellular process, and the expression levels of
   all genes in G vary across the stages in the same way.
   [not clear if submitted or accepted]
   -- [<A HREF="http://dogbert.cs.technion.ac.il/publications/abstracts.html#j">paper</A>][12/'02].

%A M. Nissim-Rafinia
%A B. Kerem
%T Splicing regulation as a potential genetic modifier (Opinion)
%J Trends in Genetics
%V 18
%N 3
%P 123-127
%M MAR
%D 2002
%K MolBio, alternative splicing, gene, genes, protein, proteome, c2002, c200x,
   c20xx, splice, mRNA, RNA
%X "Inherited diseases are assoc. with profound phenotypic variability, which
   is affected strongly by genetic modifiers. The splicing machinery could be
   one such modifying sys., through a mech. involving splicing motifs & their
   interaction with a complex repertoire of splicing factors. Mut'ns in splicing
   motifs & changes in levels of splicing factors can result in diff. splicing
   patterns. Changes in the level of normal transcripts or in the relative
   pattern of different mRNA isoforms affect disease exp'n, leading to
   phenotypic variability. Here, we discuss the splicing mc in terms of its sig.
   in disease severity & its potential role as a genetic modifier."
   -- [<A HREF="http://dx.doi.org/10.1016/S0168-9525(01)02619-1">doi:10.1016/S0168-9525(01)02619-1</A>]['05].
   [Also search for: alternative splicing MolBio].

%A A. Ben-Dor
%A R. M. karp
%A B. Schwikowski
%A R. Shamir
%T The restriction scaffold problem
%J Annual Conf. on Res. in Comp. Molec. Biol.
%P 58-66
%D 2002
%K conf, MolBio, shotgun, genome, genomic, assembly, scaffold, restriction,
   map, mapping, c2002, c200x, c20xx
%X [typically] long and costly phase of finishing, [...] partial assembly forms
   several contigs whose order, orientation and relative distance is unknown.
   [...] new technique that supplements the shotgun assembly data by cheap and
   simple complete restriction digests of the target. By computationally
   combining information from the contig sequences and the fragment sizes
   measured for several different enzymes, we seek to form a "scaffold" on
   which the contigs will be placed in their correct orientation, order and
   distance. We give a heuristic search algorithm ...
   The key to the success of the search scheme is the very rapid solution of
   its two time-critical subproblems that are solved precisely in linear time.
   Our simulations indicate that with noise levels of some 3% relative error in
   measuring fragment sizes, using five enzymes, most datasets of 20 contigs
   can be correctly ordered, and the remaining ones have most of their pairs of
   neighboring contigs correct. [...]                    isbn:1581134983.
   -- [<A HREF="http://doi.acm.org/10.1145/565196.565204">paper</A>][11/'02].

%A S. Aparicio
%A et al
%T Whole genome shotgun assembly and analysis of the genome of Fugu rubripes
%J Science
%V 297
%N 5585
%P 1301-1310
%M AUG
%D 2002
%K MolBio, jrnl, c2002, c200x, c20xx, Fugu rubripes, pufferfish, puffer, fish,
   genomic, nGenome, DNA
%X "The compact genome of Fugu rubripes has been sequenced to over 95% coverage,
   and more than 80% of the assembly is in multigene-sized scaffolds. In this
   365-megabase vertebrate genome, repetitive DNA accounts for less than
   one-sixth of the sequence, and gene loci occupy about one-third of the g...."
   -- [<A HREF="http://www.sciencemag.org/cgi/content/abstract/297/5585/1301">paper</A>][11/'02].
   Originally pub' in Science Express as 10.1126/science.1072104, 25/6/'02.

%A S. Batzoglou
%A et al
%T ARACHNE: A whole-genome shotgun assembler
%J Genome Res.
%V 12
%N 1
%P 177-189
%M JAN
%D 2002
%K MolBio, jrnl, c2002, c200x, c20xx, zz1202, genome, assembly, assembler,
   sequence, DNA, genomic, shotgun, sequencing, ARACHNE
%X [<A HREF="http://www.genome.org/cgi/content/abstract/12/1/177">paper</A>]11/'02],
   -- [<A HREF="http://www-genome.wi.mit.edu/wga/">software</A>][11/'02].
   [Also search for: sequence assembly MolBio].

%A T. Hubbard
%A et al
%T The Ensembl genome database project
%J NAR
%V 30
%N 1
%P 38-41
%D 2002
%K MolBio, jrnl, c2002, c200x, c20xx, NAR, Ensembl, data base, genome
%X The Ensembl [<A HREF="http://www.ensembl.org/">www</A>] database project
   provides a bioinformatics framework to organise biology around the sequences
   of large genomes. It is a comprehensive source of stable automatic
   annotation of the human genome sequence, with confirmed gene predictions
   that have been integrated with external data sources, and is available as
   either an interactive web site or as flat files. It is also an open source
   software engineering project to develop a portable system able to handle
   very large genomes and associated requirements from sequence analysis to
   data storage and visualisation. The Ensembl site is one of the leading
   sources of human genome sequence annotation and provided much of the
   analysis for publication by the international human genome project of the
   draft genome. The Ensembl system is being installed around the world in both
   companies and academic sites on machines ranging from supercomputers to
   laptops.

%A D. C. Krakauer
%A A. Sasaki
%T Noisy clues to the origin of life
%J Proc. Royal Society B
%V ?
%P ?-?
%D 2002
%O Santa Fe Institute, 02-05-024, 2002
%K jrnl, origins, stability, stable, replication, replicators, noise,
   mutation, drift, evolution, primordial, fixation, SFI
%X The origin of stable self-replicating molecules represents a fundamental
   obstacle to the origin of life. The low fidelity of primordial replicators
   places restrictions on the quantity of information encoded in a primitive
   nucleic acid alphabet. Further difficulties for the origin of life are the
   role of drift in small primordial populations, reducing the rate of fixation
   of superior replicators, and the hostile conditions increasing developmental
   noise. Thus mutation, noise and drift are three independent stochastic
   effects that are assumed to make the evolution of life improbable. Here we
   show to the contrary how noise present in hostile early environments, can
   increase the probability of faithful replication, by amplifying selection
   in finite populations. Noise has negative consequences in infinite
   populations, whereas in finite populations, we observe a synergistic
   interaction among noise sources. Hence two factors formerly considered
   inimical to the origin of life -- developmental noise and drift in small
   populations -- can in combination give rise to conditions favorable to
   robust replication.    DOI:10.1098/rspb.2002.2127
   -- [<A HREF="http://www.santafe.edu/sfi/publications/wpabstract/200205024">preprint</A>][11/'02].

%A L. Bromham
%A D. Penny
%T The modern molecular clock
%J NatureReview Genet.
%V 4
%N 3
%P 216-224
%M MAR
%D 2003
%K jrnl, MolBio, c2003, c200x, c20xx, zz0123, evolution, time, neutral theory,
   phylogenetics
%X "The discovery of the molecular clock - a relatively const. rate of molec.
   evolution ... The unexpected constancy of rate was explained by assuming that
   most changes to genes are effectively neutral. Theory predicts several
   sources of variation in the rate of molec. evolution. However, even an
   approximate clock allows time estimates of events in evolutionary history,
   which provides a method for testing a wide range of biological hypotheses
   ranging from the origins of the animal kingdom to the emergence of new viral
   epidemics."
   -- [<A HREF="https://doi.org/10.1038/nrg1020">doi:10.1038/nrg1020</A>]['23],
   12610526@[<A HREF="https://pubmed.ncbi.nlm.nih.gov/12610526/">pubm'd</A>]['23].
   [Also search for: MolBio molecular clock].

%A E. J. Snijder
%A et al ...
%A A. E.  Gorbalenya
%T Unique and conserved features of genome and proteome of SARS-coronavirus, an
   early split-off from the coronavirus group 2 lineage
%J J. Mol. Biol.
%V 331
%N 5
%P 991-1004
%D 2003
%K MolBio, JMB, c2003, c200x, c20xx, zz0415, SARS, SARS1, SARS-CoV 1, SARSCoV,
   SARSCoV1, genome, covid, China, coronavirus, group2, polyprotein, protein,
   proteinases, protease, replicase, corona virus, NC_004718, Guangdong, China
%X "The genome organization & expression strategy of the newly identified severe
   acute respiratory syndrome coronavirus (SARS-CoV) were predicted using
   recently published genome seqs. Fourteen putative [ORFs] ... (bringing the
   total # of SARS-CoV proteins to 28). ... SARS-CoV is most closely related to
   group 2 coronaviruses. Distant homologs of cellular RNA processing enzymes
   were identified in group 2 coronaviruses, with four of them being conserved
   in SARS-CoV. ..."
   -- [<A HREF="https://doi.org/10.1016/s0022-2836(03)00865-9">doi:10.1016/s0022-2836(03)00865-9</A>]['20],
      12927536@[<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/12927536">p'bmed</A>]['20],
      30271926@[<A HREF="https://www.ncbi.nlm.nih.gov/nuccore/30271926">ncbi</A>]['20].
   (Also see, "... On 16 Nov. 2002, an outbreak of severe acute respiratory
   syndrome (SARS) began in China's Guangdong province, bordering Hong Kong ..."
   -- SARS@[<A HREF="https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus">wikip</A>]['20].)
   [Also search for: MolBio SARS]  and  [also seach for; SARS protein].

%A W. Altermann
%A J. Kazmierczak
%T Archean microfossils: a reappraisal of early life on Earth
%J Res. in Microbiol.
%M NOV
%D 2003
%K jrnl, MolBio, c2003. c200x, c20xx, zz0523, life, origin, origins, earth,
   abiogenesis, fossil, fossils, Archea, Pilbara, WA,
   LUCA, prokaryote, eukaryote
%X "The oldest fossils found thus far on Earth are c 3.49- &
   3.46-billion-year-old filamentous & coccoidal microbial remains in rocks of
   the Pilbara craton ... Morphological, geochemical & isotopic data imply,
   however, that life was relatively widespread & advanced in the Archean,
   between 3.5 & 2.5 billion years ago, with metabolic pathways analogous to
   those of recent prokaryotic organisms, including cyanobacteria, & probably
   even eukaryotes at the terminal Archean."
   -- [<A HREF="https://doi.org/10.1016/j.resmic.2003.08.006">doi:10.1016/j.resmic.2003.08.006</A>]['23].
   (Also see Abiogenesis@[<A HREF="https://en.wikipedia.org/wiki/Abiogenesis">wikip</A>]['23].)
   [Also search for: origins life] and [also search for: MolBio LUCA].

%A S. Gallus
%A et al ...
%A C. La Vecchia
%T Does pizza protect against cancer?
%J Int. J. of Cancer
%V 107
%N 2
%P 283-284
%M NOV
%D 2003
%K jrnl, c2003, c200x, c20xx, zz1019, human, health, medicine, cancer, risk,
   risks, diet, pizza, mediteranean, IgNobel, IgNoble, 2019, c2019
%X "We analyzed the potential role of pizza on cancer risk, using data from an
   integrated network of case-control studies conducted in Italy between 1991
   and 2000. ...  Odds ratios for regular pizza consumers were 0.66 (95%
   confidence interval, CI = 0.47-0.93) for oral and pharyngeal cancer, 0.41
   (95% CI = 0.25-0.69) for oesophageal, 0.82 (95% CI = 0.56-1.19) for
   laryngeal, 0.74 (95% CI = 0.61-0.89) for colon and 0.93 (95% CI = 0.75-1.17)
   for rectal cancer. Pizza appears therefore to be a favorable indicator of
   risk for digestive tract neoplasms in this population."
   -- [<A HREF="https://doi.org/10.1002/ijc.11382">doi:10.1002/ijc.11382</A>]['19].
   SG won the IgNobel prize for medicine [<A HREF="https://www.improbable.com/2019/09/12/announcing-the-2019-ig-nobel-prize-winners/">2019</A>].

%A C. E. Ophardt
%T Virtual Chembook
%I Elmhurst Coll.
%D 2003
%K MolBio, c2003, c200x, c20xx, intro, protein, tertiary, 3D, structure,
   amino acid, acids, side chain, sideChain, chains, hydrogen, disulfide,
   disulphide, bond, bonds, salt bridge, nonPolar, hydrophobic,
   Alanine Ala, Arginine, Arg, Asparagine Asn, Aspartic-acid Asp, Cysteine Cys,
   Glutamic-acid Glu, Glutamine Gln, Glycine Gly, Histidine His, Isoleucine Ile,
   Leucine Leu, Lysine Lys, Methionine Met, Phenyl-alanine Phe, Proline Pro,
   Serine Ser, Threonine Thr, Tryptophan Trp, Tyrosine Tyr, Valine Val
%X [<A HREF="http://www.elmhurst.edu/~chm/vchembook/">chembook</A>] /
   -- [<A HREF="http://www.elmhurst.edu/~chm/vchembook/565proteins.html">proteins</A>] /
   -- [<A HREF="http://www.elmhurst.edu/~chm/vchembook/567tertprotein.html">tertiary</A>]['12].
   "There are four types of bonding interactions between 'side chains' inc.:
   . hydrogen bonding (bwn two alcohols, an alcohol and an acid,
       two acids, or an alcohol and an amine or amide),
   . salt bridges (bwn +ve ammonium group & the -ve acid group. Any
       combination of the various acidic or amine amino acid),
   . disulfide bonds
       (oxidation of the sulfhydryl groups on cysteine), and
   . non-polar hydrophobic interactions (Hydrocarbon alkyl groups on ala, val,
       leu, & ile interact in this way and benzene (aromatic) rings on phe &
       tyr can "stack" together.)
   -- [<A HREF="http://www.elmhurst.edu/~chm/vchembook/561aminostructure.html">AA</A>]
      Alanine        Ala  A;
      Arginine       Arg  R;
      Asparagine     Asn  N;
      Aspartic-acid  Asp  D;
      Cysteine       Cys  C;
      Glutamic-acid  Glu  E;
      Glutamine      Gln  Q;
      Glycine        Gly  G;
      Histidine      His  H;
      Isoleucine     Ile  I;
      Leucine        Leu  L;
      Lysine         Lys  K;
      Methionine     Met  M;
      Phenyl-alanine Phe  F;
      Proline        Pro  P;
      Serine         Ser  S;
      Threonine      Thr  T;
      Tryptophan     Trp  W;
      Tyrosine       Tyr  Y;
      Valine         Val  V."
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Notes/DNA-RNA-protein/">Bioinformatics</A>].)

%A G. P. S. Raghava
%A S. M. J. Searle
%A P. C. Audley
%A J. D. Barber
%A G. J. Barton
%T OXBench: A benchmark for evaluation of protein multiple sequence alignment
   accuracy
%J BMC Bioinformatics
%V 4
%N 47
%D 2003
%K jrnl, ejrnl, c2003, c200x, c20xx, MolBio, quality, benchmark, benchmarks,
   protein multiple alignment, OXBench, AMPS, Tcoffee, CLUSTALW
%X "... describe a suite of reference alignments derived from the comparison of
   protein 3D structures together with evaluation measures & software that allow
   automatically generated alignments to be benchmarked. ... The simple
   hierarchical multiple alignment algorithm, AMPS, performed as well as or
   better than more modern methods such as CLUSTALW once the PAM250 pair-score
   matrix was replaced by a BLOSUM series matrix. AMPS gave an accuracy in
   Structurally Conserved Regions (SCRs) of 89.9% over a set of 672 alignments.
   The T-COFFEE method on a data set of families with < 8 seqs. gave 91.4%
   accuracy, significantly better than CLUSTALW (88.9%) & all other methods
   considered here. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-4-47">doi:10.1186/1471-2105-4-47</A>]['07],
      OXBench@[<A HREF="https://bio.tools/oxbench">bio.tools</A>]['20].

%A L. F. Ten Eyck
%T Full matrix refinement as a tool to discover the quality of a refined
   structure
%J Methods in Enzymology
%V 374
%P 345-369
%D 2003
%K jrnl, MolBio, c2003, c200x, c20xx, zz1113,  protein, 3D structure,
   determination, Xray, crystallography, SHELXL, SHELX, REFMAC, freeR,
   precision, resolution, restraints, least squares, TenEyck, intro
%X "... discusses the foundations of optimization. ... applicable to both
   least-squares & maximum-likelihood refinement protocols. ...  & restraints
   v. constraints. Full-matrix opt.methods coupled with the examination of the
   eigenvalues & eigenvectors of the curvature matrices provide powerful tools
   for the auto. identification of problematic regions in a refined structure.
   ... theoretically sound means of determining the precision of parameters at
   low resoln. ... The most popular full-matrix program in crystallography is
   SHELXL, which has a conjugate gradients mode as well, esp. designed for
   macromolecular refinement."
   -- [<A HREF="http://dx.doi.org/10.1016/S0076-6879(03)74016-6">doi:10.1016/S0076-6879(03)74016-6</A>]['13],
      [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/14696381">pubm'd</A>]['13].

%A W. B. Langdon
%A B. F. Buxton
%A S. J. Barrett
%T Combining machine learning techniques to predict compounds' Cytochrome P450
   high throughput screening inhibition
%J Knowledge Discovery meets Drug Discovery (poster)
%M OCT
%D 2003
%K MolBio, Clementine
%X (not that Langdon)  Uses SPSS's Clementine tool, NNs, GAs.
   -- [<A HREF="ftp://cs.ucl.ac.uk/genetic/papers/wbl_kdmdd2002.pdf">.pdf</A>][4/'03],
      [<A HREF="http://www.kdnet.org/workshop_overview1_bioinfoLeuven02.htm">workshop</A>].

%A N. Beerenwinkel
%A T. Lengauer
%A Daumer M, Kaiser R, Walter H, Korn K, Hoffmann D, Selbig J
%T Methods for optimizing antiviral combination therapies
%J J. Bioinformatics
%V 19 (suppl. 1)
%P i16-i25
%D 2003
%K conf, ISMB, ISMB11, ISMB03, MolBio, c2003, c200x, c20xx, geno2pheno, model,
   drug resistance, medical, therapy, treatment, HIV, HIV1, AIDS, SVM, method,
   ismb2003, genotype, genotypic, phenotype, phenotypic, drugs, zzVDRL
%X 1. [learn how to] predict pheno. drug-resistance from geno.
   2. model predicted resistance to drug combo
   3. search 'mutational neighbourhood' under a given treatment
   i16: HIV's high mutation rate (est ~ 3*10-5/n/repln)
   i17: IC50 conc. to inhibit repln by 50%
   i17: resistance factor  RF = IC50(clinical sample) / IC50(wild type)
   i24: recomb rate of HIV-1 ... est about 10x > than its pt subs rate
   -- [<A HREF="http://www.iscb.org/ismb2003/paperAbstracts/btg1001.pdf">pdf</A>]['05].
   Also see [<A HREF="http://www.geno2pheno.org/">geno2pheno</A>]['05].

%A N. Beerenwinkel
%A M. Daumer
%A Oette M, Korn K, Hoffmann D, Kaiser R, Lengauer T, Selbig J, Walter H
%T Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes
%J NAR
%V 31
%N 13
%P 3850-3855
%D 2003
%K jrnl, NAR, c2003, c200x, c20xx, HIV, HIV1, aids, genotype, MolBio, medical,
   genotype, genotypic, phenotype, phenotypic
%X [<A HREF="http://nar.oupjournals.org/cgi/content/abstract/31/13/3850">nar</A>]['05],
   [<A HREF="http://www.geno2pheno.org/">Geno2pheno</A>]['05].

%A A. Clare
%A R. D. King
%T Data mining the yeast genome in a lazy functional language
%J Practical Aspects of Declarative Languages (PADL'03)
%W New Orleans
%P ?-?
%M JAN
%D 2003
%K PADL5, PADL 03, PADL03, MolBio, conf, programming, FP, Haskell, PolyFARM,
   relational data, association rule, rules, c2003, c200x, c20xx, zz0103,
   Saccharomyces cerevisiae, aber, RDKing, AClare
%X [<A HREF="http://www.aber.ac.uk/compsci/Research/bio/dss/polyfarm/">PolyFARM</A>][12/'02] University of Wales Aberystwyth
   -- [<A HREF="http://users.aber.ac.uk/afc/papers/ClareKingPADL.pdf">.pdf</A>][12/'03],
      [<A HREF="http://www.research.avayalabs.com/user/wadler/padl03/">conf</A>][12/'02] W' moved to edinb' in '03.

%A R. A. Dwyer
%T Genomic Perl: From Bioformatics Basics to Working Code
%I CUP
%D 2002
%K book, text, c2002, c200x, c20xx, CUP, bioPerl, MolBio
%X stg45, hb; uk us isbn:052180177X; uk us isbn13:978-0521801775.

%A P. Baldi
%A G. W. Hatfield
%T DNA Microarrays and Gene Expression
%I CUP
%D 2002
%K book, text, MolBio, micro array, arrays, microarray, CUP,
   c2002, c200x, c20xx
%X stg35, hb; uk us isbn:0521800226; uk us isbn13:978-0521800228.

%A G. Navarro
%A M. Raffinot
%T Flexible Pattern Matching in Strings
%I CUP
%D 2002
%K book, text, c2002, c200x, c20xx, MolBio, Bioinformatics, CUP, text, search,
   match, string, searching, patterns, sequence, programming, algorithms
%X "... focusing on the algorithms and implementations that perform best in
   practice. It covers searching for simple, multiple, and extended strings,
   as well as regular expressions, exactly and approximately. ..."
   1st ed 2002; hb us$60, stg40; uk us isbn:0521813077;
   uk us isbn13:978-0521813075.

%T The Phylogenetic Handbook
%E M. Salemi
%E A.-M. Vandamme
%I CUP
%P 448
%D 2003
%K book, text, MolBio, CUP, family, evolutionary, tree, trees
%X hb stg35, uk us isbn:052180390X; uk us isbn13:978-0521803908.

%T Initial sequencing and comparative analysis of the mouse genome
%Q Mouse Genome Sequencing Consortium
%J Nature
%V 420
%P 520-562
%M DEC
%D 2002
%K jrnl, MolBio, Biol, mouse, genome, DNA, sequence, data, c2002, c200x, c20xx,
   mus musculus, animal, rodent, nuclear, nGenome, zz1202,  J.F.Abril, JFAbril
%X "... 2.5-Gb mouse genome sequence ... about 30,000 genes ... with 99% having
   direct counterparts in humans. ... So why aren't mice more like us? The
   answer probably lies in the regulation of those genes. ..."
   -- [<A HREF="http://www.nature.com/nature/mousegenome/">@nature</A>][12/'02],
      [<A HREF="http://dx.doi.org/10.1038/nature01262">doi:10.1038/nature01262</A>]['02],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10090">taxa 10090</A>]['08].

%A J. Yu et al
%T A draft sequence of the rice genome (Oryza sativa L. ssp. indica)
%J Science
%V 296
%N 5565
%P 79-92
%M APR
%D 2002
%K jrnl, rice, Oryza sativa L. ssp. indica, genome, c2002, c200x, c20xx,
   plant, plants, angiosperm, grass, grasses, gene, genes, chromosomes,
   nGenome, nuclear
%X 12 chromosomes, 466 Mb total, 26K - 55K genes.
   "... draft sequence of the rice genome for the most widely cultivated
   subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun
   sequencing. The genome was 466 megabases in size, with an estimated 46,022
   to 55,615 genes. Functional coverage in the assembled sequences was 92.0%.
   About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, &
   most of the transposons were in the intergenic regions between genes.
   Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in
   rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The
   large proportion of rice genes with no recognizable homologs is due to a
   gradient in the GC content of rice coding sequences."
   -- [<A HREF="http://www.sciencemag.org/cgi/content/full/296/5565/79">subscr'n</A>][7/'04].
   Also comment pp.92-100.
   [Also search for: rice genome c2005].
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=4530">rice</A>]['08].

%T Evolutionary Computing in Bioinformatics
%E G. B. Fogel
%E D. W. Corne
%I MorganKaufmann
%P 393
%M SEP
%D 2002
%K book, text, c2002, c200x, c20xx, biol, programming, programs
%X H 570.285 F655E 2002; uk us isbn:1558607978; uk us isbn13:978-1558607972.

%T Microarrays for the Neurosciences - An Essential Guide
%E D. H. Geschwind
%E J. P. Gregg
%I MITpress
%P 352
%M APR
%D 2002
%K book, text, c2002, c200x, c20xx, microarray, micro array, arrays,
   MolBio, biol
%X H 612.8 G389M 2002; uk us isbn:0262072297; uk us isbn13:978-0262072298.

%A N. Colgrave
%T Sex releases the speed limit on evolution
%J Nature
%V 420
%P 664-666
%M 12 DEC
%D 2002
%K jrnl, biol, biology, sex, reason, why, sexual reproduction, evolution,
   population size, clonal interference, chlorophyte Chlamydomonas reinhardtii,
   origin, c2002, c200x, c20xx, zz1202
%X "Explaining ... sex remains a key problem in... .  ...it may allow a more
   rapid adaptive response when environmental conditions change, by increasing
   the efficiency with which selection can fix beneficial mutations.
   ...show that sex can increase the rate of adaptation in the facultatively
   sexual single-celled chlorophyte Chlamydomonas reinhardtii, but that the
   benefits of sex depend crucially on the size of the population that is
   adapting: sex has a marked effect in large populations but little effect in
   small populations. Several mechanisms have been proposed to explain the
   benefits of sex in a novel environment, including stochastic effects in small
   pop'ns, clonal interference & epistasis between beneficial alleles. These
   results indicate that clonal interference is important in this system."
   -- [<A HREF="http://www.nature.com/nlink/v420/n6916/abs/nature01191_fs.html">paper</A>][12/'02] doi:10.1038/nature01191.
   [Also search for: sexual reproduction why].

%A E. E. Vityaev
%A Y. L. Orlov
%A O. V. Vishnevsky, M. A. Pozdnyakov,  N. A. Kolchanov
%T Computer system "gene discovery" for promoter structure analysis
%J In Silico Biol.
%V 2
%N 3
%P 257-262
%D 2002
%K MolBio, DNA, genes, pattern discovery, eukaryotic, binding sites, zz0103
%X "... for searching for regularities in tables of context features of DNA
   sequences involved in regulation of transcription. ...  search patterns for
   regularities have been constructed in the first-order logic augmented by
   probabilistic estimates. ..." [<A HREF="http://www.bioinfo.de/isb/2002020024/">bioinfo.de</A>]['03].
   [Also search for: gene find].

%A X. Chen
%A M. Li
%A B. Ma
%A J. Tromp
%T DNACompress: Fast and effective DNA sequence compression
%J J. Bioinformatics
%V 18
%N 12
%P 1696-1698
%M DEC
%D 2002
%K jrnl, MolBio, DNA compression, compress, DNAcompress, sequences, zz0103,
   c2002, c200x, c20xx
%X via P.E.T.:  LZW approach;  C 570.5 C738.
   [Also search for: DNA compression] and
   [also search for: MolBio compression].

%A C. H. Lineweaver
%A T. M. Davis
%T Does the rapid appearance of life on earth suggest that life is
   common in the universe
%J Astrobiology
%P 293-304
%V 2
%N 3
%D 2002
%K jrnl, MolBio, biol, biology, astro, origin, origins life, space,
   terra, lottery model, biogenesis, planet, planets, stats, statistics,
   start, begining, c2002, c200x, c20xx, zz0703
%X Astrobiology@[<A HREF="http://www.liebertpub.com/AST/">publisher</A>][7/'03].
   Also see [<A HREF="http://xxx.adelaide.edu.au/abs/astro-ph/0209385">astro-ph/0209385</A>][7/'03].
   ... Using a lottery model for biogenesis in the Universe, we convert
   the observational constraints on the rapidity of biogenesis on Earth
   into constraints on the probability of biogenesis on other terrestrial
   planets. For example, if terrestrial biogenesis took less than 200 Myr
   (and we assume that it could have taken 1 billion years) then we find
   the probability of biogenesis on terrestrial planets older than ~ 1 Gyr,
   is > 36% at the 95% confidence level. However, there are assumptions and
   selection effects that complicate this result: although we correct the
   analysis for the fact that biogenesis is a prerequisite for our existence,
   our result depends on the plausible assumption that rapid biogenesis is
   not such a prerequisite.

%A B. Morgenstern
%A O. Rinner
%A S. Abdeddaim
%A D. Haase
%A K. F. X. Mayer
%A A. W. M. Dress
%A H.-W. Mewes
%T Exon discovery by genomic sequence alignment
%J J. Bioinformatics
%V 18
%N 6
%P 777-787
%M JUN
%D 2002
%K jrnl, MolBio, c2002, c200x, c20xx, exons, coding, DNA, discover, predict,
   genome, align, alignment, dialign, PipMaker, WABA
%X "... describe a new implementation of the seq.-alignment program DIALIGN
   that has been dev. for alignment of large genomic seqs.. We compare our
   method to the al.programs PipMaker, WABA & BLAST & we show that local
   similarities identified by these programs are highly corr. to protein-coding
   regions. ..."
   -- [<A HREF="http://bioinformatics.oxfordjournals.org/content/18/6/777">pap'r</A>]['10],
   s/w@[<A HREF="http://bibiserv.techfak.uni-bielefeld.de/dialign/">u.biel'ld</A>]['12].
   [Also search for: MolBio genome alignment].

%A C. R. Woese
%T On the evolution of cells
%J PNAS
%V 99
%N 13
%P 8742-8747
%M JUN
%D 2002
%K PNAS, MolBio, c2002, c200x, zz1104, c20xx, carl, cell, communal,
   origin, origins, horizontal gene transfer, HGT
%X "... model is based on the (data supported) conjecture that the dynamic of
   horizontal gene transfer (HGT) is primarily determined by the organization
   of the recipient cell. Aboriginal cell designs are taken to be simple &
   loosely organized enough that all cellular componentry can be altered and/or
   displaced through HGT, making HGT the principal driving force in early
   cellular evolution. Primitive cells did not carry a stable organismal
   genealogical trace. Primitive cellular evolution is basically communal. The
   high level of novelty required to evolve cell designs is a product of
   communal invention, of the universal HGT field, not intralineage variation.
   It is the community as a whole, the ecosystem, which evolves. The individual
   cell designs that evolved in this way are nevertheless fundamentally
   distinct, because the initial conditions in each case are somewhat
   different. As a cell design becomes more complex & interconnected a critical
   point is reached where a more integrated cellular organization emerges, &
   vertically generated novelty can & does assume greater importance. This
   critical point is called the "Darwinian Threshold" for the reasons given."
   published on-line June 19, 2002, doi:10.1073/pnas.132266999 <!-- carl @ phylo.life.uiuc.edu --> .
   -- [<A HREF="http://www.pnas.org/cgi/content/abstract/132266999v1">pnas</A>][1/'04].

%A Y. Moreau
%A F. de Smet
%A G. Thijs
%A K. Marchal
%A B. de Moor
%T Functional bioinformatics of microarray data: From expression to regulation
%J Proc IEEE
%V 90
%N 11
%P 1722-1743
%M NOV
%D 2002
%K jrnl, MolBio, micro array, arrays, clustering, deSmet, deMoor,  zz0103
%X ...clustering of coexpressed genes with the discovery of binding motifs. ...
   -- [<A HREF="http://ieeexplore.ieee.org/iel5/5/22437/01046952.pdf">pdf</A>][1/'03],
   doi:10.1109/JPROC.2002.804681 .  issn:0018-9219.   [via P.T.].

%A J. E. Maul
%A J. W. Lilly
%A L. Cui,  C. W. dePamphilis,  W. Miller,  E. H. Harris,  D. B. Stern
%T The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a
   sea of repeats
%J Plant Cell
%P 2659-2679
%V 14
%N 11
%M NOV
%D 2002
%K jrnl, MolBio, biol, biology, plants, alga, algae, algal, genome, cGenome,
   chromosome, c2002, c200x, c20xx, chlorophyte plastid, chloroplast,
   photosynthesis, gene, repetitive DNA, SDR, SDRs, zz0704,
   short dispersed repeat, SDR, SDRs
%X "... unicellular eukaryotic alga possessing a single chloroplast that is
   widely used as a model system for the study of photosynthetic processes.
   This report analyzes the surprising structural & evolutionary features of
   the completely sequenced 203,395-bp PLASTID chromosome. The genome is
   divided by 21.2-kb inverted repeats into two single-copy regions of approx'
   80 kb & contains only 99 genes, including a full complement of tRNAs &
   atypical genes encoding the RNA polymerase. A remarkable feature is that
   >20% of the genome is repetitive DNA: the majority of intergenic regions
   consist of numerous classes of short dispersed repeats (SDRs), which may
   have structural or evolutionary significance. Among other sequenced
   chlorophyte plastid genomes, only that of the green alga Chlorella vulgaris
   appears to share this feature. ..."
   -- [<A HREF="http://www.plantcell.org/cgi/content/full/14/11/2659">plantcell.org</A>][7/'04].

%A A. Clare
%A R. D. King
%T How well do we understand the clusters found in microarray data?
%J In Silico Biology
%P n.a.
%V 2
%D 2002
%K jrnl, MolBio, inSilico, cluster, micro array, arrays, MIPS, GeneOntology,
   GenProtEC, annotation ontologies, ORF, ORFs, c2002, c200x, c20xx,
   aber, RDKing, AClare
%X "We wished to quantify the state-of-the-art of our understanding of clusters
   in microarray data. [...] systematically compared the clusters produced on
   sets of microarray data using a representative set of clustering algorithms
   (hierarchical, k-means, and a modified version of QT_CLUST) with the
   annotation schemes MIPS, GeneOntology and GenProtEC. We assumed that if a
   cluster reflected known biology its members would share related ontological
   annotations. This assumption is the basis of "guilt-by-association" and is
   commonly used to assign the putative function of proteins. To statistically
   measure the relationship between cluster and annotation we developed a new
   predictive discriminatory measure.
      We found that the clusters found in microarray data do not in general
   agree with functional annotation classes. Although many statistically
   significant relationships can be found, the majority of clusters are not
   related to known biology (as described in annotation ontologies). This
   implies that use of guilt-by-association is not supported by annotation
   ontologies. Depending on the estimate of the amount of noise in the data,
   our results suggest that bioinformatics has only codified a small proportion
   of the biological knowledge required to understand microarray data.
   The annotated clusters can be found at
   -- [<A HREF="http://www.aber.ac.uk/compsci/Research/bio/dss/gba/">www.aber.ac.uk/compsci/Research/bio/dss/gba/</A>]"
   -- [<A HREF="http://www.bioinfo.de/isb/2002/02/0046/">bioinfo.de</A>][6/'04].

%A S. D. Bentley
%A et al
%T Complete genome sequence of the model
   actinomycete Streptomyces coelicolor A3(2)
%J Nature
%V 417
%P 141-148
%M MAY
%D 2002
%K jrnl, MolBio, biol, actinomycete Streptomyces coelicolor A3(2), whole,
   complete, genome, tetracycline, erythromycin, antibiotic, antibiotics,
   medical, bacteria, bacterium, microbial genomes, c2002, c200x, c20xx,
   prokaryote
%X 8,667,507 bp, 72.1% G+C, 7825 protein predicted.
   -- [<A HREF="http://www.sanger.ac.uk/Projects/S_coelicolor/">@sanger</A>]['05],
      [<A HREF="ftp://ftp.sanger.ac.uk/pub/S_coelicolor/whole_genome/">genome</A>]['05],
   "...largest of the bacterial genomes sequenced yet, at 8.5 mbp, & contains
   7825 predicted genes. ...Over 20 gene clusters produce an abundance of
   metabolic enzymes, which yield a plethora of antibiotics, such as
   tetracycline and erythromycin, as well as anticancer and antifungal agents
   and immunosuppressants. Information from the genome will allow for
   engineering of these secondary metabolic pathways, potentially leading to
   new therapies and more potent drug delivery ..."
   -- [<A HREF="http://www.nature.com/genomics/papers/s_coelicolor.html">nature</A>]['05].

%A K, Vandepoele
%A J. Raes
%A L.De Veylder, P.Rouze, S.Rombauts, D.Inze
%T Genome-wide analysis of core cell cycle genes in Arabidopsis
%J Plant Cell
%V 14
%P 903-916
%M APR
%D 2002
%K jrnl, Arabidopsis thalia, c2002, c200x, c20xx, plant, plants, eukaryote,
   gene, Cyclin, Cyclins, E2F
%X "... to determine the core cell cycle genes in the recently completed
   A. genome seq..  ... 61 genes were identified belonging to 7 selected
   families of cell cycle regulators, for which 30 are new or corrections of
   the existing annotation. A new class of putative cell cycle regulators was
   found that probably are competitors of E2F/DP transcription factors, which
   mediate the G1-to-S progression. ... existing nomenclature for cell cycle
   genes of A. was updated, & the physical positions of all genes were compared
   with segmentally duplicated blocks in the genome, showing that 22 core cell
   cycle genes emerged through block duplications...."
   -- [<A HREF="http://www.plantcell.org/cgi/content/abstract/14/4/903">paper</A>]['05].

%A B. Ma
%A J. Tromp
%A M. Li
%T PatternHunter: Faster and more sensitive homology search
%J J. Bioinformatics
%V 18
%N 3
%P 440-445
%M MAR
%D 2002
%K jrnl, MolBio, pattern hunter, DNACompress
%X pdf@[<A HREF="http://www.bioinformatics.uwaterloo.ca/papers/02ph.pdf">02ph.pdf</A>]['05],
   pdf@[<A HREF="http://www.bioinformaticssolutions.com/functions_db_download.php?id=159">@bioinformaticssolutions</A>]['08], also see c2004.
   PH@[<A HREF="http://www.bioinformaticssolutions.com/products/ph/">bioinformaticssolutions</A>]['08].
   [Also search for: spaced seed].

%A M. D. Brasier
%A et al ...
%A N. V. Grassineau
%T Questioning the evidence for Earth's oldest fossils
%J Nature
%V 416
%N 6876
%P 76-81
%M MAR
%D 2002
%K jrnl, C2002, c200x, c20xx, origin, origins, life, cyanobacteria,
   stromatolite, WA, Western Australia, fossil, fossils, microfossils
%X "Structures resembling remarkably preserved bacterial & cyanobacterial
   microfossils from about 3,465-million-year-old Apex cherts of the Warrawoona
   Group in Western Australia currently provide the oldest morphological
   evidence for life on Earth & have been taken to support an early beginning
   for oxygen-producing photosynthesis. ... Here we report new research on the
   type & re-collected material, involving mapping, optical & electron
   microscopy, digital image analysis, micro-Raman spectroscopy & other
   geochemical techniques. We reinterpret the purported microfossil-like
   structure as secondary artefacts formed from amorphous graphite within
   multiple generations of metalliferous hydrothermal vein chert & volcanic
   glass. ..."            [i.e., against].
   -- [<A HREF="http://dx.doi.org/10.1038/416076a">doi:10.1038/416076a</A>]['12].

%A E. Domingo
%T Quasispecies theory in virology
%J J. of Virology
%V 76
%N 1
%P 463-465
%M JAN
%D 2002
%K letter, virus, viral, c2002, c200x, c20xx, RNA, MolBio
%X [38 refs] [<A HREF="http://dx.doi.org/10.1128/JVI.76.1.463-465.2002">doi:10.1128/JVI.76.1.463-465.2002</A>]['05].

%A C. Kamp
%A C. O. Wilke
%A C. Adami
%A S. Bornholdt
%T Viral evolution under the pressure of an adaptive immune system - optimal
   mutation rates for viral escape
%J Complexity
%V 8
%N 2
%P 28-33
%D 2002
%K c2002, c200x, c20xx, zz1205, MolBio, virus, rate, selection, population,
   quasispecies, mutation, error, HIV, aLife, silico
%X "...Study the conditions under which a viral quasispecies can max. its growth
   rate. The range of m.rates that allows viruses to thrive is limited from
   above due to genomic info. deterioration, & from below by insufficient
   seq. diversity ... quick eradication of the virus by the immune sys.. The
   m.rate that optimally balances these 2 requirements depends to 1st order on
   the ratio of the inverse of the virus' growth rate & the time the immune
   sys. needs to develop a specific answer to an antigen. ...virus is most
   viable if it generates exactly 1 mutation within the time it takes for the
   immune system to adapt to a new viral epitope. Exp. viral mutation rates, in
   partic. for HIV... suggest that many v. have achieved their opt. mutn rate."
   -- [<A HREF="http://arxiv.org/abs/cond-mat/0209613">arxiv.org</A>]['05].
   Also see [<A HREF="http://dllab.caltech.edu/">dllab.caltech.edu</A>]['05].

%A Z. Agur
%A Y. Daniel
%A Y. Ginosar
%T The universal properties of stem cells as pinpointed by a
   simple discrete model
%J J. Math. Biol.
%V 44
%N 1
%P 79-86
%D 2002
%K jrnl, MolBio, JMB, c2002, c200x, c20xx, stem cell, cells, stemCell,
   biol, biology
%X [Also search for: stem cell model].

%A I. Roeder
%A M. Loeffler
%T A novel dynamic model of hematopoietic stem cell organization based on the
   concept of within-tissue plasticity
%J J. Exp. Hematol.
%V 30
%N 8
%P 853-861
%M AUG
%D 2002
%K jrnl, MolBio, c2002, c200x, c20xx, stem cells, stemCell,
   models, biol, biology, blood
%X "... cell-based stochastic model is described. It makes the novel concept of
   within-tissue plasticity operational. Within a range of potential options,
   individual cells may reversibly change their actual set of properties
   depending on the influence of the local growth environment. Stochastic
   switching between the growth environments introduces fluctuations that
   eventually generate heterogeneity. Extensive model simulations are compared
   with experimental data. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/S0301-472X(02)00832-9">doi:10.1016/S0301-472X(02)00832-9</A>]['06].
   [Also search for: stem cell model].

%A M. A. Fares
%A E. C. Holmes
%T A revised evolutionary history of hepatitis B virus (HBV)
%J J. Mol. Evol.
%V 54
%N 6
%P 807-814
%D 2002
%K jrnl, JME, MolBio, c2002, c200x, c20xx, HBV, virus, viral, tree, evolution,
   phylogenetic, phylogeny, genotypes, human, chimp, ECHolmes, zzVDRL
%X "Previous studies of the evolutionary history of [HBV] have been compromised
   by intergenotype recombination & complex patterns of nucleotide substitution,
   perhaps caused by differential selection pressures. We examined the
   phylogenetic distribution of recombination events among human HBV genotypes &
   found that genotypes A plus D, & genotypes B plus C, had distinct patterns of
   recomb. suggesting differing epidemiological relns among them. By analyzing
   the nonoverlapping regions of the viral genome we found strong bootstrap
   support for some intergenotypic groupings, with evidence of a division
   between human genotypes A-E from the viruses sampled from apes & human
   genotype F. However, the earliest events in the divergence of HBV remain
   uncertain. ... could not be explained by differential selection pressures,
   as the ratio of nonsynonymous-to-synonymous substitutions (dN/dS) did not
   vary extensively among lineages & there is no strong evidence for +ve seln
   across the whole tree. Finally, we provide a new est. of the mean subs. rate
   in HBV, 4.2 x 10**-5, which suggests that divergence of HBV in humans & apes
   has occurred only in the last 6000 years."       [LA: note "nonoverlapping"]
   -- [<A HREF="http://dx.doi.org/10.1007/s00239-001-0084-z">doi:10.1007/s00239-001-0084-z</A>]['07],
   -- [<A HREF="http://www.springerlink.com/index/94BG2YH91HNLY2BV.pdf">pdf@springerlink</A>]['07],
   -- [<A HREF="http://evolve.zoo.ox.ac.uk/data.html?id=6">data@oxford.uni</A>]['07].
   [Also search for: HBV evolution]   -- [<A HREF="http://evolve.zoo.ox.ac.uk/people.html?id=holmese">Holmes@oxf</A>], later at [<A HREF="http://www.cidd.psu.edu/people/bio_holmes.html">Penn State U</A>]['07].

%A S. S. Shen-Orr
%A R. Milo
%A S. Mangan
%A U. Alon
%T Network motifs in the transcriptional regulation network of Escherichia coli
%J Nature Genetics
%V 31
%P 64-68
%M APR
%D 2002
%K jrnl, MolBio, c2002, c200x, c20xx, networks, regulatory, Ecoli, motif,
   regulation, gene, transcribe, transcription, graph, ShenOrr, data, viaAK,
   feed forward, FF, FFL, feedforward loop, single-input module, bifan, SIM,
   dense overlapping regulons, DOR, randomised, randomisation
%X "Little is known about the design principles of trans. reg. nws. that
   control gene expression in cells. ...  we sought to break down such nws. into
   basic building blocks. We generalize the notion of motifs, widely used for
   seq. analysis, to [...] networks.  ... new algorithms for systematically
   detecting nw. motifs to one of the best-characterized regulation nws., ...
   We find that much of the nw. is composed of repeated appearances of 3 highly
   sig. motifs. Each nw. motif has a specific fn in determining gene expression,
   such as generating temporal expression programs & governing the responses to
   fluctuating external signals. ..."   (online 4/'02.)
     ["... [v. randomised] networks with precisely the same # of operons,
       interactions, transcription factors & # of incoming & outgoing edges
       for each node as in the real E.coli nw ..."]
   -- [<A HREF="http://dx.doi.org/10.1038/ng881">doi:10.1038/ng881</A>]['07],
      [<A HREF="http://www.weizmann.ac.il/mcb/UriAlon/">Alon@w...</A>][08].
   (Data@[<A HREF="http://wws.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks">weizmann.ac.il</A>][10/4/15] files:
       coli1_1Inter_st.txt, coliNodesDictionary.txt,
       e-coli-transcription-network.)
   (Also see motifs@[<A HREF="http://en.wikipedia.org/wiki/Network_motif">wikip</A>]['15].)
   [Also search for: MolBio network motif].

%A S. E. Celniker
%A et al
%Q Berkeley Drosophila Genome Project
%T Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster
   euchromatic genome sequence
%J Genome Biol.
%V 3
%N 12
%P research0079.1-79.14
%D 2002
%K jrnl, ejrnl, MolBio, c2002, c200x, c20xx, fruit fly, insect, euchromatin,
   chromatin, nGenome, WGS, WGS3, DNA, sequence, metazoan, eukaryote
%X [chrs X 2L 2R 3L 3R 4 Y,  ~ 120Mb  ver 5.2, 4/'08.]
   "The Drosophila melanogaster genome was the first metazoan genome to have
   been sequenced by the whole-genome shotgun (WGS) method. ... "
   -- [<A HREF="http://dx.doi.org/10.1186/gb-2002-3-12-research0079">doi:10.1186/gb-2002-3-12-research0079</A>]['07],
   -- [<A HREF="http://genomebiology.com/drosophila/">genomebiology.com/drosophila/</A>]['07],
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=7227">taxid=7227</A>]['08].
   ("Euchromatin is a lightly packed form of chromatin ... rich in gene conc.,
   & is often (but not always) under active transcription. ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Euchromatin">Euchromatin@wikip</A>]['07].)

%A M. Morgante
%A M. Hanafey
%A W. Powell
%T Microsatellites are preferentially associated with nonrepetitive DNA in
   plant genomes
%J Nature Genetics
%V 30
%P 194-200
%D 2002
%K jrnl, MolBio, c2002, c200x, c20xx, DNA, tandem repeat, sequence, Sputnik,
   replication slippage, microsatellite, slipage, plants
%X "Microsatellites are a ubiquitous class of simple repetitive DNA seq..
   An excess of such repetitive tracts has been described in all eukaryotes
   analyzed & is thought to result from the mutational effects of replication
   slippage. ...  most microsatellites reside in regions pre-dating the recent
   genome expansion in many plants. The m. freq. was higher in transcribed
   regions, especially in the untranslated portions, than in genomic DNA.
   Contrary to previous reports suggesting a preferential mechanism for the
   origin of m. from repetitive DNA in both animals & plants, ... show
   a sig. association with the low-copy fraction of plant genomes."
   -- [<A HREF="http://dx.doi.org/10.1038/ng822">doi:10.1038/ng822</A>]['08].
   -- They modified the 'Sputnik' repeat finder.
   [Also search for: tandem repeat].

%A W. R. Taylor
%T A 'periodic table' for protein structures
%J Nature
%V 416
%N 6881
%P 657-660
%M APR
%D 2002
%K jrnl, MolBio, c2002, c200x, c20xx, zz1217, WRTaylor, protein, structure,
   folds, 3D, tertiary, possible, secondary, links, contacts
%X "... the number & variety of protein structures that exist. In the past,
   estimates have been made on the basis of the incomplete sample of structures
   currently known. These estimates have varied greatly (between 1,000 &
   10,000 ... Here I formalize both secondary & tertiary links to allow the
   rigorous & automatic definition of protein topology."
   -- [<A HREF="https://doi.org/10.1038/416657a">doi:10.1038/416657a</A>]['17],
   11948354@[<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/11948354">nlm</A>]['17].

%A W. J. Kent
%T BLAT - the BLAST-like alignment tool
%J Genome Res.
%V 12
%N 4
%P 656-664
%M APR
%D 2002
%K jrnl, MolBio, c2002, c200x, c20xx, BLAT, BLAST, alignment, sequence,
   index, indexing, kMer, genome, database, search, searching
%X "... BLAT, is more accurate & 500 x faster than popular existing tools for
   mRNA/DNA alignments & 50 x faster for protein alignments at sensitivity
   settings typically used when comparing vertebrate seqs.. BLAT's speed stems
   from an index of all nonoverlapping K-mers in the genome. ... [use] index to
   find regions in the genome likely to be homologous to the query seq.. It
   performs an alignment between homologous regions. It stitches together these
   aligned regions (often exons) into larger alignments (typically genes). ... ,
   BLAT revisits small internal exons possibly missed at the 1st stage &
   adjusts large gap boundaries that have canonical splice sites where [poss]."
   [NON-overlapping k-mer index of DB, scan linearly thru query]
   [1.3x10**7 mouse reads (x ~600b) v. human genome 16,300CPU hrs, farm 800MHz]
   [p.658: typical k 8-16 for nucl., 3-7 for AAs]
   [p.660: default init. match, nucl. 2 perfect 11-mers, AAs 3 4-mers]
   [p.661: 1-mismatch option k*(|A|-1) slower]
   [p.662: stitch & fill in, nucl. query > 5Kbp & AA > 1500, div & conq.]
   [p.663: 4 byte/index entry, h.genome, nucl. 0.9gbyte, transl. 2.5gbyte]
   -- [<A HREF="http://genome.cshlp.org/cgi/content/full/12/4/656">pdf@gr</A>]['08], and
   -- [<A HREF="http://dx.doi.org/10.1101/gr.229202">doi:10.1101/gr.229202</A>]['08].
   [Also search for: approximate indexing].

%A J. W. Raymond
%A P. Willett
%T Maximum common subgraph isomorphism algorithms for the matching of
   chemical structures
%J J. Computer-Aided Molecular Design
%V 16
%N 7
%P 521-533
%M JUL
%D 2002
%K jrnl, c2002, c200x, c20xx, intro, survey, largest, maximum common subgraph,
   MCS, induced, MCIS, MCES, graph, 2D, 3D, isomorphism, algorithm, match,
   substructure, chemical compound
%X "The maximum common subgraph (MCS) problem has become increasingly important
   in those aspects of chemoinformatics that involve the matching of 2D or 3D
   chemical structures. This paper provides a classification & a review of the
   many MCS algs., both exact & approximate, that have been described in the
   literature, & makes recommendations regarding their applicability to typical
   chemoinformatics tasks."
   -- [<A HREF="http://dx.doi.org/10.1023/A:1021271615909">doi:10.1023/A:1021271615909</A>]['08].
   (MCS: Input: 2 graphs G1 and G2.  Q: What is the largest induced subgraph
         of G1 isomorphic to a subgraph of G2?  Dec'n problem is NPC.
         Equiv. to largest clique in 'modular product' graph.  -- wikip.)

%A A. Jung
%A R. Maier
%A et al
%T Recombination: Multiply infected spleen cells in HIV patients
%J Nature
%V 418
%P 144
%M JUL
%D 2002
%K briefComm, MolBio, multiple, cell, patient, c2002, c200x, c20xx, population,
   quasispecies, virus, viral, rate, variation, provirus, proviruses, mutation,
   crossover, crossovers, infection, AIDS, HIV, provirus, V1V2
%X "...[HIV] highly prone to recombination1, although it is not obvious whether
   recombinants arise infrequently or whether they are constantly being spawned
   but escape identification because of the massive and rapid turnover of virus
   particles ... find an average of 3 or 4 proviruses per cell and evidence for
   huge numbers of recombinants and extensive genetic variation. ...
   ... recombination rate of HIV-1 is ~3 events/genome for every round of
   replication, with a range of 1 to 7 crossovers (which is about 10x greater
   than its point-substitution rate of about 0.25 per genome per round). ...
   ... With most of the infected cells harbouring 2 or 2+ genetically different
   proviruses, the necessary conditions for rampant generation of recombinants
   are fulfilled, indicating that recombination is important in shaping the
   evolution of HIV in individual patients.  ...  price that the virus pays for
   mult. infection may be a broadening of immune recog. of the infected cell."
   -- [<A HREF="http://dx.doi.org/10.1038/418144a">doi:10.1038/418144a</A>]['05].
   [Also search for: quasispecies].

%A H. Bono
%A T. Kasukawa
%A M. Furuno
%A Y. Hayashizaki
%A Y. Okazaki
%T FANTOM DB: Database of functional annotation of RIKEN mouse cDNA clones
%J NAR
%V 30
%N 1
%P 116-118
%D 2002
%K jrnl, NAR, MolBio, c2002, c200x, c20xx, FANTOM DB, FANTOMdb, mouse, clone,
   functional annotation, annotations, cDNA, coding DNA, CAGE, GSC,
   data base, database, transcribed, transcriptome, expressed
%X "... DB of Functional Annotation of RIKEN Mouse cDNA Clones, is designed to
   store seq. info. of RIKEN full-length enriched mouse cDNA clones, graphical
   views of seq. analysis results, curated functional annotation information &
   additional descriptions, inc. Gene Ontology terms. RIKEN's Mouse Gene
   Encyclopedia Project aims to collect full-length enriched cDNA clones from
   various mouse tissues, determine the full-length nucleotide sequences, infer
   their chromosomal locns by computer & characterize gene expression patterns.
   ... [< HREF="http://fantom.gsc.riken.go.jp/db/">fantom...jp</A>]['08]."
   -- [<A HREF="http://nar.oxfordjournals.org/cgi/content/full/30/1/116">NAR</A>]['08].
   Site: [<A HREF="http://fantom3.gsc.riken.jp/">fantom3</A>]['08].

%A R. Milo
%A S. Shen-Orr
%A S. Itzkovitz
%A N. Kashtan
%A D. Chklovskii
%A U. Alon
%T Network motifs: Simple building blocks of complex networks
%J Science
%V 298
%N 5594
%P 824-827
%M OCT
%D 2002
%K jrnl, MolBio, c2002, c200x, c20xx, zz0816, network, motif, block, discovery
%X "... we defined 'network motifs,' patterns of interconnections occurring in
   complex nws at numbers that are sig. higher than those in randomized nws. We
   found such motifs in nws from biochemistry, neurobiology, ecology, &
   engineering. The motifs shared by ecological food webs were distinct from the
   motifs shared by the genetic nws of E.coli & Saccharomyces cerevisiae or from
   those found in the World Wide Web. Similar motifs were found in nws that
   perform info. processing, even though they describe elts as different as
   biomolecules within a cell & synaptic connections between neurons in
   Caenorhabditis elegans. Motifs may thus define universal classes of nws. This
   approach may uncover the basic building blocks of most nws."
     ["... Each nw was scanned for all possible n-node subgraphs (in the
      present study, n=3 & 4) ... compared the real nw to suitably randomized
      nws ... Each node in the randomized nws has the same # of incoming &
      outgoing edges as the corr. node has in the real nw. ... randomized nws
      used to calculate the sig. of n-node subgraphs were generated to preserve
      the same # of appearances of all (n-1)-node subgraphs ..."]
   -- [<A HREF="http://dx.doi.org/10.1126/science.298.5594.824">doi:10.1126/science.298.5594.824</A>]['16].
   [Also search for: MolBio network motif].

%A T. Koski
%T Hidden Markov Models of Bioinformatics
%I Springer
%P 416
%D 2002
%K book, text, c2002, c200x, c20xx, MolBio, Bioinformatics, Markov model, HMM,
   L4Ref, L5Ref, hidden, profile, sequence, profiles
%X 1st ed 2002; pb us$72; uk us isbn:1402001363; uk us isbn13:978-1402001369.

%A T.-L. Wang
%A C. Maierhofer
%A M. R. Speicher
%A C. Lengauer
%A B. Vogelstein
%A K. W. Kinzler
%A V. E. Velculescu
%T Digital karyotyping
%V 99
%N 25
%P 16156-16161
%M DEC
%D 2002
%K PNAS, jrnl, MolBio, c2002, c200x, c20xx, digital karyotyping, karyotype,
   copy number, variation, variations, changes, DNA, change, cancer
%X "Alterations in the genetic content of a cell are the underlying cause of
   many human diseases, inc. cancers. ... method, called digital karyotyping,
   that provides quantitative analysis of DNA copy # at high res.. ... involves
   the isolation & enumeration of short seq. tags from specific genomic loci.
   Analysis of human cancer cells by using this method identified gross
   chromosomal changes as well as amplifications & deletions, including regions
   not previously known to be altered. Foreign DNA seqs. not present in the
   normal human genome could also be readily identified. Digital karyotyping
   provides a broadly applicable means for systematic detection of DNA copy #
   changes on a genomic scale."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.202610899">doi:10.1073/pnas.202610899</A>]['09].
   (Also see dk@[<A HREF="http://en.wikipedia.org/wiki/Karyotype#Digital_Karyotyping">wikip</A>]['09].)

%A R. Kolodny
%A P. Koehl
%A L. Guibas
%A M. Levitt
%T Small libraries of protein fragments model native protein structures
   accurately
%J J. Mol. Biol.
%V 323
%N 2
%P 297-307
%M OCT
%D 2002
%K jrnl, JMB, MolBio, c2002, c200x, c20xx, protein, local structure,
   fragment, library
%X "... represent the polypeptide chain by a seq. of rigid fragments that are
   concatenated without any degrees of freedom. Frags. chosen from a library of
   representative frags. are fit to the native struct. using a greedy build-up
   method. This gives a 1D repn of native protein 3D struct. whose quality
   depends on the nature of the library. ... novel clustering method to
   construct libraries that differ in the frag.length (4-7 residues) & # of
   representative frags. they contain (25-300). Each library is characterized by
   the quality of fit (accuracy) & # of allowed states per residue (complexity).
   We find that the accuracy depends on the complexity & varies from 2.9A for a
   2.7-state model on the basis of fragments of length 7-0.76A for a 15-state
   model on the basis of fragments of length 5. Our goal is to find repns that
   are both accurate & economical (low complexity). The models defined here are
   substantially better in this regard: with 10 states per residue we approx.
   native p.struct. to 1A compared to over 20 states per residue needed
   previously. For the same complexity, we find that longer fragments provide
   better fits. [but] libraries of longer f. must be much larger (for 10 states
   per r., a 7-residue library is 100 times larger than a 5-r. library) ..."
   -- [<A HREF="http://dx.doi.org/10.1016/S0022-2836(02)00942-7">doi:10.1016/S0022-2836(02)00942-7</A>]['13], and
   correction@[<A HREF="http://dx.doi.org/10.1016/S0022-2836(02)01438-9">doi:10.1016/S0022-2836(02)01438-9</A>]['13].
   [Also search for: protein structure fragment library].

%A A. Casini
%A A. Scozzafava
%A C. T Supuran
%T Cysteine modifying agents: A possible approach for effective cancer and
   antiviral drugs
%J Environ. Health Perspect.
%V 110 (Suppl 5)
%P 801-806
%M OCT
%D 2002
%K jrnl, MolBio, c2002, c200x, c20xx, zz0620, drug, protein, cysteine, thiol,
   Cys, zinc finger, disulfide bond, tubulin, pharmacology, drug, antiviral,
   viaAK
%X "Modification of cysteine residues in proteins, due to a) the participation
   of the thiol moiety of this [AA] in oxido-red'n reactions, b) its ability to
   strongly coordinate transition metal ions, or c) its nucleophilic nature &
   facile reaction with electrophiles, may be critically important for the
   design of novel types of pharmacological agents. ... recently led to the
   design of novel antivirals, mainly based on the reaction of zinc finger
   proteins with disulfides ... new anticancer therapeutic approaches, mainly
   targeting tubulin, have also been reported. Thus, this unique [AA] offers
   v.interesting possibilities ..."
   -- [<A HREF="https://doi.org/10.1289/ehp.02110s5801">doi:10.1289/ehp.02110s5801</A>]['20].

%A T. I. Lee
%A et al ...
%A R. A. Young
%T Transcriptional regulatory networks in Saccharomyces cerevisiae
%J Science
%V 298
%N 5594
%P 799-804
%M OCT
%D 2002
%K jrnl, MolBio, c2002, c200x, c20xx, zz0716, yeast, Saccharomyces cerevisiae,
   transcriptional, transcription, regulation, regulatory network, data,
   gene expression, autoregulation, SIM, MIM, FFL, loops, motif,  viaAK
%X "... network of regulator-gene interactions describes potential pathways
   yeast cells can use to regulate global gene expression programs. We use this
   information to identify n/w motifs, the simplest units of n/w architecture,
   & demonstrate that an automated process can use motifs to assemble a
   transcriptional regulatory network structure. ... reveal that eukaryotic
   cellular functions are highly connected through n/ws of transcriptional
   regulators that regulate other transcriptional regulators."
     ("... All 141 transcription factors listed in the Yeast
       Proteome Database ... The promoter regions of 2343 of 6270
       yeast genes (37%) were bound by one or more of the 106
       transcriptional regulators in yeast cells grown in rich medium.
       ... identify six regulatory network motifs: autoregulation,
       multicomponent loops, feedforward loops, single-input,
       multi-input, and regulator chain ...")
   -- [<A HREF="http://dx.doi.org/10.1126/science.1075090">doi:10.1126/science.1075090</A>]['16],
   &  12399584@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/12399584">pubm'd</A>]['16].
   [Also search for: regulatory network].

%A A. Lapedes
%A B. Giraud
%A C. Jarzynski
%T Using sequence alignments to predict protein structure and stability with
   high accuracy
%I Theoretical Divn, Los Alomos (LANL)
%D 2002
%K TR, LANL, c2002, c200x, c20xx, zz0712, MolBio, protein structure prediction,
   alignment, evolution, evolutionary, contact, EVfold
%X "... a seq.-based probabilistic formalism that directly addresses cooperative
   effects in networks of interacting posns in proteins, providing sig. improved
   contact prediction, as well as accurate quantitative prediction of free
   energy changes due to non-additive effects of multiple mutations. [&] ...
   the agreement of our seq.-based calculations with experimental data for both
   structure & stability demonstrates a strong reln between the stat.distn of
   protein seqs. produced by natural evolutionary processes, & the thermodynamic
   stability of the structures to which these sequences fold."    [29 pp.]
      "The hyp. is that pairs of variable residue posns, possibly distant along
      the seq. but spatially proximate in the folded molecule, will display
      sig. covariation."
   "Written 2002" -- [<A HREF="http://arxiv.org/abs/1207.2484">arxiv</A>][2012].
   [Also search for: MolBio EVfold], on indep. work.

%A T. Duster
%T Backdoor to Eugenics
%P 264
%D 2003
%K book, text, c2003, c200x, c20xx, zz0120, genetics, DNA, eugenics, human,
   health, data, big pharma, risk, risks, society
%X 1st ed 2003; uk us isbn:0415946743; uk us isbn13:978-0415946742.
   "... pros and cons of prenatal detection of birth defects; gene therapies;
   growth hormones; and substitute genetic answers to problems linked with such
   groups as Jews, Scandanavians, Native American, Arabs & African Americans."

%A P. Rogen
%A B. Fain
%T Automatic classification of protein structure by using Gauss integrals
%J PNAS
%V 100
%N 1
%P 119-124
%M JAN
%D 2003
%K MolBio, PNAS, jrnl, c2003, c200x, c20xx, classification, protein structure,
   fold, folds, Gauss, integral, Vassiliev, knot theory, invariant
%X "... The topology of a protein is captured by 30 numbers inspired by
   Vassiliev knot invariants. ... similarity of protein shapes. Under this
   metric, protein chains naturally separate into fold clusters. ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.2636460100">doi:10.1073/pnas.2636460100</A>]['11].
   [Also seach for: MolBio knot protein].

%A S. Mangan
%A U. Alon
%T Structure and function of the feed-forward loop network motif
%J PNAS
%V 100
%P 11980-11985
%D 2003
%K jrnl, PNAS, MolBio, c2003, c2003, c20xx, networks, motifs, viaAK, FFL, FF,
   loops, feed-forward loop, feedforward, transcription factors, incoherent,
   coherent, rationalisation, controversial
%X "Engineered sys. are often built of recurring circuit modules that carry out
   key fns. Transcription n/ws that regulate the responses of living cells were
   recently found to obey similar principles: they contain several biochemical
   wiring patterns, termed n/w motifs, which recur throughout the n/w. One [is]
   the feed-forward loop (FFL) ... a 3-gene pattern, is composed of 2 input
   transcription factors, one of which regulates the other, both jointly
   regulating a target gene. The FFL has 8 possible structural types, because
   each of the 3 interactions in the FFL can be activating or repressing. ...
   theoretically analyze the fns of these 8 structural types. We find that 4
   ... termed incoherent FFLs, act as sign-sensitive accelerators: they speed
   up the response time of the target gene expression following stimulus steps
   in one direction [only]. The other 4 types, coherent FFLs, act as sign-
   -sensitive delays. We find that some FFL types appear in transcription n/w
   databases much more frequently than others. In some cases, the rare FFL types
   have reduced functionality (responding to only one of their 2 input stimuli),
   which may partially explain why they are selected against. ..."
   -- [<A HREF="http://www.pnas.org/content/100/21/11980">paper@pnas</A>]['08].
   [Also search for: network motif MolBio].

%A O. Gunturkun
%T Adult persistence of head-turning asymmetry
%J Nature
%V 421
%P 711-711
%M FEB
%D 2003
%K brief communication, jrnl, kiss, Rodin, kisses, kissing, turn, left, right,
   embrace, brain development, animal behaviour, human, asymmetrical, hand,
   handed, handedness, zz0203, c2003, c200x, c20xx
%X A preference in humans for turning the head to the right, rather than to the
   left, during the final weeks of gestation and for the first six months after
   birth constitutes one of the earliest examples of behavioural asymmetry and
   is thought to influence the subsequent development of perceptual and motor
   preferences by increasing visual orientation to the right side. Here I show
   that twice as many adults turn their heads to the right as to the left when
   kissing, indicating that this head-motor bias persists into adulthood. My
   finding may be linked to other forms of sidedness (for example, favouring
   the right foot, ear or eye) that do not become established until long after
   the newborn head-turning preference has disappeared.
   -- [<A HREF="http://www.bio.psy.ruhr-uni-bochum.de/papers/Asymmetries%20of%20Kissing.pdf">.pdf</A>][2/'03],
   -- [<A HREF="http://dx.doi.org/10.1038/421711a">doi:10.1038/421711a</A>][2/'03].
   Observed 124 kissing couples ... 80 (64.5%) turned their heads
   right, 44 (35.5%) left, i.e. 2:1 R:L [13/2: NB. St Valentine's Day = 14 Feb]
   c.f. L:R handedness is 8:1.         [author at ruhr university, bochum, .de]
   [Also search for: animal handedness].

%A J. F. Crow
%T Was there life before 1953?
%J Nature genetics
%V 33
%N 4
%P 449-450
%M APR
%D 2003
%K MolBio, nature, jrnl, biology, science, DNA, double helix, survey, history
%X [<A HREF="http://dx.doi.org/10.1038/ng0403-449">doi:10.1038/ng0403-449</A>][4/'03].

%A M. Skipper
%T RNA World: The expanding universe of tiny RNAs
%J Nature Reviews Genetics
%V 4
%N 4
%P 248
%D 2003
%K nature, jrnl, biology, biol, science, MolBio, micro RNA, microRNA,
   RNAi, miRNA, stRNA, lin4, let7, c2003, c200x, c20xx, zz0503
%X The finding that RNA can regulate gene expression is among the most
   exciting discoveries made in recent years. As well as RNAi, PTGS in
   plants and quelling in Neurospora, there are the stRNAs that regulate
   developmental timing. ...
   -- [<A HREF="http://dx.doi.org/10.1038/nrg1053">doi:10.1038/nrg1053</A>][4/'03].

%A C. A. Donnelly
%A et al.
%T Epidemiological determinants of spread of causal agent of severs acute
   respiratory syndrome in Hong Kong
%J The Lancet
%M MAY
%D 2003
%K SARS, epidemiology, biology, medicine, virus, viral, infection, SARS, SARS1,
   coronvirus, corona virus, SARS-CoV 1, Guangdong, China
%X 1425 cases reported to 28 April '03 ... incubation period 6.4 days ...
   fatality rate 13/2% (age under 60), 43% (age 60+), or ...
   Published online, [<A HREF="http://image.thelancet.com/extras/03art4453web.pdf">lancet</A>][5/'03].
   (Also see SARS@[<A HREF="https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus">wikip</A>]['20].)

%A T. D. Read
%A et al
%T The genome sequence of Bacillus anthracis Ames and
   comparison to closely related bacteria
%J Nature
%V 423
%P 81-86
%D 2003
%K jrnl, anthrax, bacterium, bacteria, genome, DNA sequence, MolBio, biology,
   pX01, pX02, gene, cereus, thuringiensis, zz0503, c2003, c200x, c20xx
%X ... The B. anthracis genome sequence has been deposited at GenBank under
   accession number [AE016879]; the microarray data have been deposited at
   Gene Expression Omnibus (GEO) under accession number GSE341.
   The B. cereus 10987 unfinished genome sequence (GenBank
   accession number [NC_003909]) is available at [<A HREF="http://www.tigr.org/tdb/ufmg/">tigr</A>][5/'03].
   ... B. anthracis Ames (about 5.23 megabases) ...
   -- [<A HREF="http://dx.doi.org/10.1038/nature01586">doi:10.1038/nature01586</A>][5/'03] (see next article)

%A N. Ivanova
%A et al
%T Genome sequence of Bacillus cereus and comparative
   analysis with Bacillus anthracis
%J Nature
%V 423
%P 87-91
%D 2003
%K jrnl, anthrax, bacterium, bacteria, genome, DNA sequence, MolBio, biology,
   Bacillus thuringiensis, ATCC14579, zz0503, c2003, c200x, c20xx
%X -- [<A HREF="http://dx.doi.org/10.1038/nature01582">doi:10.1038/nature01582</A>][5/'03] (see previous article)

%T Genetic sequence of SARS virus revealed
%J NewScientist
%M APR
%D 2003
%K SARS, corona virus, coronavirus, TOR, TOR2, AY274119, viral, genome, DNA,
   RNA sequence, bioinformatics, www, HREF, http, c2003, c200x, c20xx, zz0503,
   MolBio, coronavirus, corona virus, SARS1, SARS-CoV 1, Guangdong, China,
   zoonotic
%X ... infected over 3400 in many countries around the world. ...
   ... a loop at the 3' end of the RNA appears identical to one in the
   Avian Infectious Bronchitis virus,  ... similarities with
   Bovine Coronavirus, and with a coronavirus that causes hepatitis in mice.
   ... also sequences unlike any other known coronavirus ...
   -- [<A HREF="http://www.newscientist.com/news/news.jsp?id=ns99993623">14/4/'03</A>][5/'03],
      [<A HREF="http://www.bcgsc.ca/bioinfo/SARS">bcgsc.ca/bioinfo/SARS</A>][5/'03],
      29,751 base pairs ... The SARS-associated Coronavirus (TOR2) sequence
      has been deposited in the NCBI Genbank database under accession <B>AY274119</B>
      ... Linux-based Beowulf cluster used for data analysis and sequence
      assembly builds. ...
   -- [<A HREF="http://www.who.int/csr/sars/en/">who ... sars</A>][5/'03],
      [<A HREF="http://www.cdc.gov/ncidod/sars/">cdc ... sars</A>][5/'03].
   [Also search for: Genbank].

%A R. A. Myers
%A B. Worm
%T Rapid worldwide depletion of predatory fish communities
%J Nature
%V 423
%P 280-283
%M MAY
%D 2003
%K fish, numbers, fishing, population, ecosystem, statistics, stats, caseStudy,
   trends, conservation, zz0603
%X ... We constructed trajectories of community biomass and composition of
   large predatory fishes in four continental shelf and nine oceanic systems,
   using all available data from the beginning of exploitation.
   Industrialized fisheries typically reduced community biomass by 80%
   within 15 years of exploitation.  ... we estimate that large predatory
   fish biomass today is only about 10% of pre-industrial levels. ...
   -- [<A HREF="http://dx.doi.org/10.1038/nature01610">doi:10.1038/nature01610</A>][5/'03].

%A P. Lemey
%A O. G. Pybus, B. Wang, N. K. Saksena, M. Salemi
%A A.-M. Vandamme
%T Tracing the origin and history of the HIV-2 epidemic
%J PNAS
%P ?-?
%M MAY
%D 2003
%K jrnl, PNAS, AIDS, HIV, HIV2, 2A, HIV2A, virus, evolution, origins, MolBio,
   Guinea-Bissau, gag, pol, env, DNA sequences, spread, cause, c2003, c200x,
   c20xx, zz0603, zoonotic transfer
%X ... and estimate the epidemic history of HIV-2 subtype A in Guinea-Bissau,
   the putative geographic origin of HIV-2. ... The date of the most recent
   common ancestor of HIV-2 subtype A strains was estimated to be 1940+/-16
   and that of B strains was estimated to be 1945+/-14.  ...used coalescent
   theory to estimate the past population dynamics of HIV-2 subtype A in a
   rural population of Guinea-Bissau.  ... estimates ... HIV-2 subtype A in
   Guinea-Bissau show a transition from constant size to rapid exponential
   growth around 1955-1970. Our analysis provides evidence for a zoonotic
   transfer of HIV-2 during the first half of the 20th century and an epidemic
   initiation in Guinea-Bissau that coincides with the independence war
   (1963-1974), suggesting that war-related changes in sociocultural patterns
   had a major impact on the HIV-2 epidemic.
   -- [<A HREF="http://www.pnas.org/cgi/doi/10.1073/pnas.0936469100">doi:10.1073/pnas.0936469100</A>][5/'03].

%A D. Edwards
%T Robust cluster analysis of microarray gene expression data with the
   number of clusters determined biologically
%J J. Bioinformatics
%V 19
%N 7
%P 818-824
%M MAY
%D 2003
%K jrnl, MolBio, micro arrays, clustering
%X via p.e.t., [Also search for: clustering], [also search for: mixture model].

%A W. Li
%A M. Fan
%A M. Xiong
%T SamCluster: an integrated scheme for the automatic discovery of
   sample classes using gene expression profile
%J J. Bioinformatics
%V 19
%N 7
%P 811-817
%M MAY
%D 2003
%K jrnl, MolBio, cluster, clustering, microarray, micro arrays
%X via p.e.t., [Also search for: mixture model], [also search for: clustering].

%A C. H. Lineweaver
%A D. Schwartzman
%T Cosmic thermobiology: Thermal constraints on the origin and
   evolution of life in the universe
%J arxiv.org, astrophysics
%M MAY
%D 2003
%O in "Origins", ed. J. Seckbach, 2003, Kluwer_Academic, pp.?-?
%K preprint, temperature, origin, origins of life, bacteria, high, hot, cold,
   cool, evolution, hyperthermophilic, thermophilic, 16S rRNA, tree, trees,
   family, phylogenetic, 0305214, c2003, c200x, c20xx, zz0603, MolBio, biology
%X We review the thermal history of the Universe. We obtain a new estimate
   for the thermal history of the Earth over the past four billion years using
   a biological thermometer based on (1) a rough estimate of the absolute time
   calibration of the genetic distances in the 16S rRNA-based tree of
   terrestrial life and (2) the maximum growth temperatures of the extant
   organisms used to construct the tree.  The only other thermometer on
   comparable time scales is based on a controversial interpretation of the
   oxygen 18 abundances in chert. These two thermometers are consistent with
   each other and with the idea of a roughly linear decrease in the surface
   temperature of the Earth from ~ 90 C four billion years ago to ~ 10 C today.
   Based on the hyperthermophilic domination of the roots of the tree of
   terrestrial life, and the probably universal nature of the thermal
   constraints on terrestrial biogenesis, we speculate that hyperthermophilic
   organisms dominate the roots of life emerging on any terrestrial planet.
   auth #1 @ UNSW. [<A HREF="http://www.arxiv.org/abs/astro-ph/0305214">.pdf</A>][6/'03].

%A H. Skaletsky
%A et al
%T The male-specific region of the human Y chromosome is a mosaic of
   discrete sequence classes
%J Nature
%V 423
%P 825-837
%M JUN
%D 2003
%K jrnl, MolBio, xx, yy, chromosome, Ychromosome, chrY, yChr MSY, human, HUGO,
   sex, male, female, gene, genes, DNA, genetic, c2003, c200x, c20xx, zz0703
%X male-specific region ... Y-chromosome, ... MSY, differentiates the sexes
   and [is] 95% of the chromosome's length.  ... the MSY is a mosaic of
   heterochromatic sequences and 3 classes of euchromatic sequences:
   X-transposed, X-degenerate and ampliconic. These ... contain all 156 known
   transcription units, which include 78 protein-coding genes that collectively
   encode 27 distinct proteins. The X-transposed sequences exhibit 99% identity
   to the X-chromosome. The X-degenerate sequences are remnants of ancient
   autosomes from which the modern X- and Y-chromosomes evolved. The ampliconic
   class includes large regions (about 30% of the MSY euchromatin) where
   sequence pairs show greater than 99.9% identity, which is maintained by
   frequent gene conversion (non-reciprocal transfer). The most prominent
   features here are eight massive palindromes, at least six of which contain
   testis genes.
   (19 June 2003); [<A HREF="http://dx.doi.org/10.1038/nature01722">doi:10.1038/nature01722</A>][2/'03],
   -- [<A HREF="http://www.nature.com/nature/journal/v423/n6942/suppinfo/nature01722.html">supp' material</A>][7/'03], and  see letter same issue.

%A S. Rozen
%A H. Skaletsky
%A et al
%T Abundant gene conversion between arms of palindromes in human and
   ape Y-chromosomes
%J Nature
%V 423
%P 873-876
%M JUN
%D 2003
%K jrnl, letter, letters, MSY, XX, YY, chromosome, Ychromosome, chrY, Ychr,
   palindrome, human, HUGO, sex, male, female, primate, primates, ape, apes,
   chimpanzee, testis, gene, conversion, arm, c2003, c200x, c200xx
%X 8 palindromes comprise 1/4 of the euchromatic DNA of the male-specific
   region of the human Y chromosome, the MSY. ... could be interpreted as
   evidence that the palindromes arose through duplication events that occurred
   about 100,000 years ago. Using comparative sequencing in great apes, we
   demonstrate here that at least 6 of these MSY palindromes predate the
   divergence of the human and chimpanzee lineages, which occurred about
   5 million years ago. The arms of these palindromes must have subsequently
   engaged in gene conversion, driving the paired arms to evolve in concert.
   Indeed, analysis of MSY palindrome sequence variation in existing human
   populations provides evidence of recurrent arm-to-arm gene conversion in our
   species. We conclude that during recent evolution, an average of
   approximately 600 nucleotides per newborn male have undergone Y-Y gene
   conversion, which has had an important role in the evolution of multi-copy
   testis gene families in the MSY.  (19 June 2003);
   -- [<A HREF="http://dx.doi.org/10.1038/nature01723">doi:10.1038/nature01723</A>][2/'03],
   see article same issue.

%A E. Bailes
%A et al
%A Paul M. Sharp
%T Hybrid origin of SIV in Chimpanzees
%J Science
%V 300
%N 5626
%P 1713
%M JUN
%D 2003
%K jrnl, HIV, AIDS, human, immune, virus, viral, c2003, c200x, c20xx, zz0703,
   schweinfurthi, SIVrcm, SIVgsn, troglodytes, SIVcpz
%X ... the simplest explanation appears to be that both SIVrcm and SIVgsn have
   been acquired by chimpanzees and recombined in that host. The other
   SIV-infected subspecies, P. t. schweinfurthii, is thought to have arisen
   recently due to eastward expansion from P. t. troglodytes; whether they were
   already infected by SIVcpz, or whether the virus followed later, is unclear.
   ... [<A HREF="http://dx.doi.org/10.1126/science.1080657">10.1126/science.1080657</A>][7/'03],
      [<A HREF="http://www.sciencemag.org/cgi/content/full/300/5626/1713/DC1">supp' material</A>][7/'03]  (U. Nottingham, UK).

%A Fang-Xiang Wu
%A W. J. Zhang
%A A. J. Kusalik
%T A genetic k-means clustering algorithm applied to gene expression data
%B Advances in Artificial Intelligence
%E Yang Xiang
%E Brahim Chaib-draa
%I Springer
%S LNCS
%V 2671
%P 520-526
%D 2003
%K MolBio, AI, microarray, micro arrays, cluster, zz0703
%X via p.e.t.,   H 6.3 C212 2003

%A N. Ohta
%A M. Matsuzaki
%A O. Misumi, Miyagishima SY, Nozaki H, Tanaka K, Shin-I T, Kohara Y, Kuroiwa T.
%T Complete sequence and analysis of the plastid genome of the
   unicellular red alga Cyanidioschyzon merolae.
%J DNA Res.
%P 67-77
%V 10
%N 2
%M APR
%D 2003
%K jrnl, MolBio, red alga, algae, algal, plastid genome, chloroplast, cGenome,
   DNA, gene, genes, c2003, c200x, c20xx, NC004799
%X [ 9/5/'03 genbank: 004799 ]
   "... The genome is a circular DNA composed of 149,987-bp with no inverted
   repeats. The G+C content of this plastid genome is 37.6%. The C. merolae
   plastid genome contains 243 genes, which are distributed on both strands and
   consist of 36 RNA genes (3 rRNAs, 31 tRNAs, tmRNA, and a ribonuclease P RNA
   component) and 207 protein genes, including unidentified [ORFs]. ..."
   -- [<A HREF="http://www.dna-res.kazusa.or.jp/10/2/02/HTMLA/">paper</A>][7/'04].
   [See Nature 2OO4 for the full genome]

%A C. Galli
%A et al
%T Pregnancy: A cloned horse born to its dam twin
%J Nature
%V 424
%P 635
%M AUG
%D 2003
%K jrnl, clone, cloning, cloned, foal, horses, Haflinger, c2003, c200x, c20xx,
   mare, somatic cell, pregnancy, Prometea, zz0803
%X ...clone an adult horse and show that it is possible to establish a
   viable, full-term pregnancy in which the surrogate mother is also the
   nuclear donor. The cloned offspring is therefore genetically identical
   to the mare who carried it, challenging the idea that maternal
   immunological recognition of fetal antigens influences the well-being
   of the fetus and the outcome of the pregnancy. ...
   -- [<A HREF="http://dx.doi.org/10.1038/424635a">doi:10.1038/424635a</A>][8/'03].

%A X. Chen
%T A microRNA as a translational repressor of APETALA2 in
   Arabidopsis flower development
%J Science
%V -
%N -
%P 1088060
%M JUL
%D 2003
%K RNAi, micro RNA, mRNA, miRNA, miRNA172, c2003, c200x, c20xx, zz0803,
   plant, mRNA, MolBio
%X Plant microRNAs show a high degree of sequence complementarity to,
   and are believed to guide the cleavage of, their target mRNAs. Here I show
   that miRNA172, which can base pair with the mRNA of a floral homeotic gene
   APETALA2, regulates APETALA2 expression primarily through translational
   inhibition. Elevated miRNA172 accumulation results in floral organ identity
   defects similar to those in loss-of-function apetala2 mutants. Elevated
   levels of mutant APETALA2 RNA with disrupted miRNA172 base pairing, but not
   wild type APETALA2 RNA, result in elevated levels of APETALA2 protein and in
   severe floral patterning defects. Therefore, miRNA172 likely acts in cell
   fate specification as a translational repressor of APETALA2 in
   Arabidopsis flower development.
   -- [<A HREF="http://dx.doi.org/10.1126/science.1088060">doi:10.1126/science.1088060</A>][8/'03]  auth@Rutgers-U.New-Jers'

%A J. F. Palatnik
%A E. Allen, X. Wu, C. Schommer, R. Schwab, J. C. Carrington
%A D. Weigel
%T Control of leaf morphogenesis by microRNAs
%J Nature AOP
%V ?
%N ?
%P ?
%M AUG
%D 2003
%K microRNA, miRNA, RNAi, plant, TCP, TCP4, mRNA, c2003, c200x, c20xx, zz0803,
   plants, leaf morphogenesis, leaves, MolBio
%X Plants with altered microRNA metabolism have pleiotropic developmental
   defects, but direct evidence for microRNAs regulating specific aspects
   of plant morphogenesis has been lacking. In a genetic screen, we identified
   the JAW locus, which produces a microRNA that can guide messenger RNA
   cleavage of several TCP genes controlling leaf development. MicroRNA-guided
   cleavage of TCP4 mRNA is necessary to prevent aberrant activity of the TCP4
   gene expressed from its native promoter. In addition, overexpression of
   wild-type and microRNA-resistant TCP variants demonstrates that mRNA
   cleavage is largely sufficient to restrict TCP function to its normal domain
   of activity. TCP genes with microRNA target sequences are found in a wide
   range of species, indicating that microRNA-mediated control of leaf
   morphogenesis is conserved in plants with very different leaf forms.
   -- [<A HREF="http://dx.doi.org/10.1038/nature01958">doi:10.1038/nature01958</A>][8/'03] carr'ton@Oregon-St@te.uni;
   also see [<A HREF="http://oregonstate.edu/dept/ncs/newsarch/2003/Aug03/plant.htm">OSU news</A>][8/'03].
   [Also search for: morphogenesis].

%A P. L. Antonelli
%A L. Bevilacqua
%A S. F. Rutz
%T Theories and models in symbiogenesis
%J Nonlinear Analysis: Real World Applications
%V 4
%N 5
%M DEC
%D 2003
%P 743-753
%K jrnl, MolBio, origin, origins, life, evolution, woese, margulis, biol,
   biology, cell, cells, stability, zz0204, c2003, c200x, c20xx
%X "2 modern theories of biological evolution, one by Carl Woese, & the other
   by Lynn Margulis, are modelled with Volterra-Hamilton systems. Their
   predictions are evaluated & compared within this modelling framework. For
   example, Woese's theory turns out to suffer from instability in its chemical
   exchanges processes, whereas Margulis' does not. An introduction to the
   mathematical & biological ideas is included."
   -- [<A HREF="http://dx.doi.org/10.1016/S1468-1218(02)00085-8">doi:10.1016/S1468-1218(02)00085-8</A>][1/'04],
      [<A HREF="http://www.sciencedirect.com/science/article/B6W7S-486G1PJ-1/2/b73618185567a3ca884d700d997135e3">sciencedirect</A>][1/'04].

%A J. K. Allen
%A H. M. Davey
%A D. Broadhurst,  J. K. Heald,  J. J. Rowland,  S. G. Oliver, D. B. Kell
%T High-throughput characterisation of yeast mutants for functional genomics
   using metabolic footprinting.
%J NatureBiotech.
%V 21
%P 692-696
%D 2003
%K jrnl, MolBio, mutant, footprint, biol, biology, zzOSP, zOSP04, c2003, c200x,
   c20xx, metabolomics, metabolome, aber
%X [<A HREF="http://users.aber.ac.uk/jjr/selrefs.html">jjr@aber</A>][8/'04].

%A S. M. Reader
%A K. N. Laland
%T Animal Innovation
%I OUP
%S Ecology and Evolution
%P 300
%M NOV
%D 2003
%K book, text, brain, size, behaviour, intelligence, c2003, c200x, c20xx, AI,
   dominant, inventiveness, novelty, novel, new, adaption, adjust, OUP, zz1004
%X pb, us$34, uk us isbn:0198526229; uk us isbn13:978-0198526223.
   hb, us$94, uk us isbn:0198526210; uk us isbn13:978-0198526216.

%A A. R. Parker
%T In the Blink of an Eye
%I SimonAndSchuster
%C Lond.
%P 352
%D 2003
%K book, evolution, eye, eyes, vision, sight, precambrian, cambrian explosion,
   light switch theory, hypothesis, life, animal, species, biol, biology,
   c2003, c200x, c20xx, predator, prey
%X ... active predation became possible with the advent of vision, and
   prey species found themselves under extreme pressure to adapt ...
   cambrian explosion 540My ago.  Auth in zoology@Oxf.Uni.;
   hb, Perseus, uk us isbn:0738206075; uk us isbn13:978-0738206073.

%A A. Myrick
%A A. Munasinghe
%A S. Patankar
%A D. F. Wirth
%T Mapping of the Plasmodium falciparum multidrug resistance gene 5'-upstream
   region, and evidence of induction of transcript levels by antimalarial drugs
   in chloroquine sensitive parasites
%J Molec. Microb.
%V 49
%N 3
%P 671
%M AUG
%D 2003
%K jrnl, c2003, c200x, c20xx, malaria, biol, biology, MolBio, drug resistance,
   pfmdr1, gene, genes, level, parasite, resistant
%X "...multidrug resistance gene, pfmdr1, has been shown to be involved in
   the mediation of the parasite's response to various antimalarial drugs. ...
   first evidence of induction of pfmdr1 expression in sensitive cells; and
   suggests a novel method of transcriptional control for this gene."
   -- [<A HREF="http://dx.doi.org/10.1046/j.1365-2958.2003.03597.x":doi:10.1046/j.1365-2958.2003.03597.x</A>][11/'04].

%A S. L. Baldauf
%T The deep roots of eukaryotes
%J Science
%V 300
%N 5626
%P 1703-1706
%M JUN
%D 2003
%K jrnl, uniYork, sandie, SLBaldauf, eukaryote, phylogenetic tree, trees, root,
   evolutionary, taxonomy, c2003, c200x, c20xx, MolBio, biol, biology
%X "Most ... eukaryotes can be confidently assigned to one of 8 major groups.
   After a few false starts, we are beginning to resolve relationships among
   these major groups as well. However, recent developments are radically
   revising this picture again, particularly (i) the discovery of the likely
   antiquity & taxonomic diversity of ultrasmall eukaryotes & (ii)a fundamental
   rethinking of the position of the root. Together these data suggest major
   gaps in our understanding simply of what eukaryotes are or, when it comes to
   the tree, even which end is up."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1085544">doi:10.1126/science.1085544</A>]['04],
   slb [<A HREF="http://www-users.york.ac.uk/~slb14/labpage.html">lab</A>]['09],
   -- [<A HREF="http://www.york.ac.uk/depts/biol/staff/slb.htm">U. York</A>]['04].

%A E. Pennisi
%T Modernising the tree of life
%J Science
%V 300
%N 5626
%P 1692-1697
%M JUN
%D 2003
%K news, views, evolutionary, phylogenetic, eukaryote, MolBio, biol, biology,
   c2003, c200x, c20xx, special issue
%X And on p.1694 a tree drawn for the special issue.
   -- [<A HREF="https://doi.org/10.1126/science.300.5626.1692">doi:10.1126/science.300.5626.1692</A>]['22] &
   tree@[<A HREF="https://doi.org/10.1126/science.300.5626.1694">doi:10.1126/science.300.5626.1694</A>]['22].
   [Also search for: MolBio tree life].

%A T. D. Wu
%A C. A. Schiffer
%A M. J. Gonzales
%A J.Taylor, R.Kantor, S.Chou, S.Israelski, A.Z.Zolopa, W.J.Fessel, R.W.Shafer
%T Mutation patterns and structural correlates in human immunodeficiency virus
   type 1 protease following different protease inhibitor treatements
%J J. Virology
%V ?
%P 4836-4847
%M APR
%D 2003
%K jrnl, medical, HIV, HIV1, aids, c2003, c200x, c20xx, drug resistance,
   resistant, protease, genotype, genotypic, phenotype, phenotypic
%X "... The median number of protease mutations per isolate increased from 4 in
   untreated persons to 12 in persons who had received four or more protease
   inhibitors. Mutations at 45 of the 99 amino acid positions in the protease-
   including 22 not previously associated with drug resistance-were sig.
   associated with protease inhibitor treatment. Mutations at 17 of the
   remaining 99 positions were polymorphic but not associated with drug
   treatment. Pairs & clusters of correlated (covarying) mutations were
   significantly more likely to occur in treated than in untreated persons ..."
   -- [<A HREF="http://hivdb.stanford.edu/pages/pdf/jVirology2003.pdf">stanf'd</A>]['05],
      [<A HREF="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12663790">pub med</A>]['05],
      [<A HREF="http://jvi.asm.org/cgi/content/full/77/8/4836">asm</A>]['05].

%A E. A. Gaucher
%A J. M. Thomson
%A M. F. Burgan
%A S. A. Benner
%T Inferring the palaeoenvironment of ancient bacteria on the basis of
   resurrected proteins.
%J Nature
%V 425
%N 6955
%P 285-288
%M SEP
%D 2003
%K jrnl, biol, MolBio, protein, gene, genes, evolution, c2003, c200x, c20xx,
   temperature, thermopile, CG, zz0505, Tu family, EFTu, bacteria
%X "Features of the physical environment surrounding an ancestral organism can
   be inferred by reconstructing sequences of ancient proteins made by those
   organisms, resurrecting these proteins in the laboratory, and measuring
   their properties. Here, we resurrect candidate sequences for elongation
   factors of the Tu family (EF-Tu) found at ancient nodes in the bacterial
   evol. tree, and measure their activities as a function of temperature...."
   -- [<A HREF="http://dx.doi.org/10.1038/nature01977">doi:10.1038/nature01977</A>]['05].

%A C. Chothia
%A J. Gough
%A C. Vogel
%A S. A. Teichmann
%T Evolution of the protein repertoire
%J Science
%V 300
%P 1701-1703
%D 2003
%K jrnl, MolBio, proteins, c2003, c200x, c20xx, zz0905, family, families,
   domain, domains, SCOP
%X domain ... evolutionary unit whose coding seq....
   domain family contains small p.s, &/or parts of larger ... common ancestor
   close to 50% of the seqs homologous to p. f known structure
   vertebrates, these domains belong to one of ~750 different families &
   average number of domains in a family is close to 50
   invertebrates come from one of ~670 families / genome &
   average family size is close to 20
   Domains in yeast & [large] bacteria come from ~ 550 families
   small parasitic bacteria come from ~ 220 families
   seq. id. of 40% usually => same fn; 25 to 40% identity => similar fn
   429 families whose members occur in all of the 14 known eukaryote gen.s
   form between about 80% of the domains in animals ... 90% fungi & plants
   2/3 prokaryote proteins have >= 2 domains; eukaryotes => 4/5
   -- [<A HREF="http://www.sciencemag.org/cgi/content/abstract/300/5626/1701">abs</A>]['05].

%T The Evolution of Parasitism - A Phylogenetic Perspective
%E D. T. J. Littlewood
%I AcademicPress
%S Advances in Parasitology
%V 54
%P 416
%M DEC
%D 2003
%K book, text, MolBio, biology, coevolution, cophylogeny, c2003, c200x, c20xx,
   host, parasite, cospeciation, design
%X us$160; uk us isbn:0120317540; uk us isbn13:978-0120317547.
   [Also search for: MolBio book].

%A M. A. Charleston
%T Recent advances in cophylogeny mapping
%B The evolution of parasitism: A phylogenetic perspective
%I Elsevier
%S Advances in Parasitology
%V 54
%E D. T. J. Littlewood
%P ?-?
%D 2003
%K MolBio, cophylogenetic, map, maps, parasite, host, c2003, c200x, c20xx,
   cospeciation, uniSydney, bioinformatics
%X auth @ u.syd. '05.
   [Also search for: MolBio book].

%A D. L. Chao
%A M. P. Davenport
%A S. Forrest
%A A. S. Perelson
%T Stochastic stage-structured modeling of the adaptive immune system
%J IEEE Comp. Soc. Bioinformatics Conf.
%P 124-131
%D 2003
%K conf, c2003, c200x, c20xx, MolBio, agent based, model, agents, models, CTL,
   cell, cells, Tcell, Tcells, biol
%X I'd say it is semi-agent based.
   "... model ... cytotoxic T lymphocyte (CTL) response to antigen & the
   maintenance of immunological memory. ... responses often begin with small
   no.s of cells & there is great variation among individual immune systems,
   ... implement a stochastic model that captures the life cycle of T cells
   more faithfully than det. models. Past models of the immune response have
   been differential eqn based, which do not capture stochastic effects, or
   agent-based, which are computationally expensive. We use a stochastic
   stage-structured approach that has many of the advantages of agent-based
   modeling but is much more efficient. ..."  [46 refs]
   -- [<A HREF="http://www.cs.unm.edu/~dlchao/papers/csb03/">www</A>]['06],
   "CTL population alone may have as many as 10**12 cells in a human"
   "balance between the unrealistically small # of populations used by
    analytical approaches & the unwieldy 1-agent-per-cell ...of agent-based"
   "The actual [T-cell] model has hundreds of states"

%A J. Carlton
%T The Plasmodium vivax genome sequencing project
%J Trends in Parasitology
%V 19
%N 5
%P 227-231
%M MAY
%D 2003
%K jrnl, c2003, c200x, c20xx, malaria, MolBio, Plasmodium vivax,
   parasite, health, review, intro, introduction
%X "With the successful completion of the project to sequence the [pf] genome,
   researchers are now turning their att'n to other malaria parasite species.
   Here, an update on the P. vivax genome sequencing project is presented, as
   part of the Trends in Parasitology series of reviews expanding on various
   aspects of P. vivax research."
   -- [<A HREF="http://dx.doi.org/10.1016/S1471-4922(03)00066-7">doi:10.1016/S1471-4922(03)00066-7</A>]['06].
   Also see [<A HREF="http://geneplot.plasmodb.org/">plasmodb</A>]['06],
   and [<A HREF="http://www.tigr.org/conf/vivax/">conf@tigr</A>]['06].
   [Also search for: Plasmodium vivax].

%A C. Buchen-Osmond
%T Taxonomy and classification of viruses
%B Manual of Clinical Microbiology, 8th ed
%I ASMpress
%V 2
%P 1217-1226
%D 2003
%K MolBio, data base, database, virus, viral, c2003, c200x, c20xx, genomes,
   medicine, disease, retrovirus, retro, RT
%X [<A HREF="http://www.ncbi.nlm.nih.gov/ICTVdb/">ICTVdb</A>]['05].

%A G. Getz
%A H. Gal
%A I.Kela, D.A.Notterman, E.Domany
%T Coupled two-way clustering analysis of breast cancer and
   colon cancer gene expression data
%J J. Bioinformatics
%V 19
%N 9
%P 1079-1089
%D 2003
%K jrnl, MolBio, c2003, c200x, c20xx, two way, 2D, 2way, biclustering,
   coclustering, genes, cluster
%X "... coupled 2-way clustering, a method designed to mine gene expression
   data. The method identifies submatrices of the total expression matrix,
   whose clustering analysis reveals partitions of samples (and genes) into
   biologically relevant classes. We demonstrate, on data from colon & breast
   cancer, that we are able to identify partitions that elude standard
   clustering analysis"
   -- [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/9/1079">www</A>]['06].
   (Also see bicl@[<A HREF="https://en.wikipedia.org/wiki/Biclustering">wikip</A>]['20].)
   [Also search for: biclustering] and [also search for: coclustering].

%A D. Mitchell
%A A. Bell
%T PEST sequences in the malaria parasite Plasmodium falciparum:
   a genomic study
%J Malaria J.
%V 2
%N 16
%P ?-?
%D 2003
%K MolBio, sequence, c2003, c200x, c20xx, sequence, protease calpain
%X "Inhibitors of the protease calpain are known to have selectively toxic
   effects on Plasmodium falciparum. ... The enzyme has a natural inhibitor
   calpastatin & in eukaryotes is responsible for turnover of proteins
   containing short sequences enriched in certain amino acids (PEST sequences).
   The genome of P. falciparum was searched for this protease, its natural
   inhibitor and putative substrates. ... found in 13% of the proteins on c2 ...
   potential drug target."
   -- [<A HREF="http://dx.doi.org/10.1186/1475-2875-2-16">doi:10.1186/1475-2875-2-16</A>]['06].
   Auths @ Dept Microb., Moyne Inst., Trinity Coll., Dublin 2, Rep. of Ireland

%A A. Funahashi
%A N. Tanimura
%A M. Morohashi
%A H. Kitano
%T CellDesigner: A process diagram editor for gene-regulatory and
   biochemical networks.
%J BIOSILICO
%I Elsevier
%V 1
%N 5
%P 159-162
%M NOV
%D 2003
%K MolBio, c2003, c200x, c20xx,  cell simulation, CellDesigner, cell designer,
   network
%X [<A HREF="http://www.symbio.jst.go.jp/symbio/paper/BioSilicoNov2003Funahashi.pdf">pdf</A>]['07],
   [<A HREF="http://www.celldesigner.org/">celldesigner.org</A>]['07].
   [Also search for: eCell] and [also search for: COPASI].

%A M. Hucka
%A A.Finney, H.M.Sauro, H.Bolouri, J.C.Doyle, H.Kitano, et al
%T The systems biology markup language (SBML): A medium for representation and
   exchange of biochemical network models
%J J. Bioinformatics
%V 19
%P 524-531
%D 2003
%K jrnl, MolBio, c2003, c200x, c20xx, SBML, reaction network, metabolic network,
   cell simulation
%X "... compartment; species (of chemical); reaction;
   parameter; unit_definition; rule ..."
   -- [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/reprint/19/4/524">pdf</A>]['07],
      [<A HREF="http://www.sbml.org/">sbml.org</A>]['07].
   [Also search for: cellDesigner].

%A R. Kolpakov
%A G. Kucherov
%T Finding approximate repetitions under Hamming distance
%J Theor. Comp. Sci.
%V 303
%N 1
%P 135-156
%M JUN
%D 2003
%K jrnl, MolBio, c2003, c200x, c20xx, Mreps, tandem repeat, repeats, repetition,
   repetitive, DNA, sequence
%X "... computing periodicities with K possible mismatches is studied.  2 main
   defns are considered, & for both of them an O(n K logK + S) alg. is proposed
   (n the word length, & S the size of the output). ... improves ... bound
   obtained by G. Landan & J. Schmidt in '93 (Proc. 4th Annual Symp. on
   CPM, LNCS Vol.684, pp.120-133). ..."
   -- [<A HREF="http://dx.doi.org/10.1016/S0304-3975(02)00448-6">doi:10.1016/S0304-3975(02)00448-6</A>]['08].
   [Also search for: tandem repeat] and [also search for: repetitive DNA].

%A S. Brunner
%T Fur seals and sea lions (Otariidae): identification of species and
   taxonomic review
%J Systematics and Biodiversity
%I CUP
%V 1
%N 3
%P 339-439
%M SEP
%D 2003
%K jrnl, c2003, c200x, c20xx, seal, sea lion, Biol, taxonomy, Otariidae,
   Arctocephalus, species, morphology
%X "The std anatomical descs. given to identify species of the family Otariidae
   (fur seals & sea lions), particularly those for the genus Arctocephalus, have
   been largely inconclusive. .... Recent re-examination of the genetic basis of
   taxonomic diversity within otariids required matching by comprehensive new
   studies of skull morphometry based on large sample sizes, to provide a sound
   basis for re-appraisal of species limits in the family. The typical skull
   morphology of otariids fall into 2 general characteristics: a short,
   mesocephalic skull observed primarily in the fur seals & a more
   dolichocephalic skull common in most sea lions. ... in no family of mammals,
   probably, have more diversities of opinion been expressed by zoologists, both
   with respect to the number of species in the family & their arrangement in
   genera & subfamilies, than in the Otariidae."
   -- [<A HREF="http://dx.doi.org/10.1017/S147720000300121X">doi:10.1017/S147720000300121X</A>]['07].

%A S. Schwartz
%A W. J. Kent
%A A. Smit
%A Z. Zhang
%A R. Baertsch
%A R. C. Hardison
%A D. Haussler
%A W. Miller
%T Human-mouse alignments with BLASTZ
%J Genome Res.
%V 13
%N 1
%P 103-107
%M JAN
%D 2003
%K jrnl, MolBio, c2003, c200x, c20xx, BLASTZ, gapped, human, mouse, genome,
   genomes, genomic, alignment, DNA, axt, axtBest
%X "The Mouse Genome Analysis Consortium aligned the h. & m. genome seqs. for a
   variety of purposes, using al.programs that suited the various needs. For
   investigating issues regarding genome evoln, a particularly sensitive
   method was needed to permit al. of a large % of the neutrally evolving
   regions. We selected a program called BLASTZ, an indep. implementation of the
   Gapped BLAST algorithm specifically designed for aligning 2 long genomic
   seqs.. BLASTZ was subsequently modified, both to attain efficiency adequate
   for al. entire mammalian gs. & to increase its sensitivity. ... describes
   BLASTZ, its mods., the h/w env. ..."
   p.104, alg. in a nutshell: "remove lineage specific rpts,
          for all pairs of space 12-mers (h:m), extend, ..."
   p.105: "To align 2.8Gb of human seq. v. 2.5Gb of mouse seq. took 481 days
          of CPU time & a half day [elapsed] on cluster of 1024 833Mhz PIIIs"
   -- [<A HREF="http://dx.doi.org/10.1101/gr.809403">doi:10.1101/gr.809403</A>]['08], or
   -- [<A HREF="http://genome.cshlp.org/content/13/1/103.abstract">alt</A>], or
   -- [<A HREF="http://www.psc.edu/general/software/packages/blastz/blastz.pdf">psc.edu</A>]['08].
   S/w, BLASTZ@[<A HREF="http://bio.cse.psu.edu/">psu.edu</A>]['06], and
   -- [<A HREF="http://www.psc.edu/general/software/packages/blastz/">'08</A>].
   "... the fee for initiating a gapped alignment is steep (e.g., 3000) ..."
   (Erratum (URL) in: Genome Res., 2004 Apr, 14(4), p.786.)

%A M. Wagner
%A M. Horny
%A H. Daimsz
%T Fluorescence in situ hybridisation for the identification and
   characterisation of prokaryotes
%J Current Opinion in Microbiology
%V 6
%P 302-309
%D 2003
%K MolBio, c2003, c200x, c20xx, FISH, fluorescence in situ hybridisation,
   insitu, analysis, prokaryote, rRNA
%X "... with rRNA-targeted n.acid probes ... directly identify microorganisms
   within complex samples in a few hours & therefore has widespread application
   in environmental & medical microbiology. ... sig. methodological improvements
   in FISH, [&] in the combination of this method with other techniques for
   inferring functional traits of microorganisms within their environment."
   -- [<A HREF="http://dx.doi.org/10.1016/S1369-5274(03)00054-7">doi:10.1016/S1369-5274(03)00054-7</A>]['03].

%A T. Gardner
%A D. di Bernardo
%A D. Lorenz
%A J. Collins
%T Inferring genetic networks and identifying compound mode of action via
   expression profiling
%J Science
%V 301
%N 5629
%P 102-105
%M JUL
%D 2003
%K jrnl, MolBio, NIR, c2003, c200x, c20xx, infer gene regulatory network,
   profile
%X "... used systematic transcriptional perturbations to construct a 1st-order
   model of regulatory interactions in a 9-gene subnetwork of the SOS pathway
   in E.coli.  ... correctly identified the major regulatory genes & the
   transcriptional targets of mitomycin C activity in the subnetwork.  ...
   experimentally & computationally scalable, provides a framework for
   elucidating the f'nal properties of genetic networks & identifying molecular
   targets of pharmacological compounds."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1081900">doi:10.1126/science.1081900</A>]['08].
   -- [<A HREF="https://www.bu.edu/dbin/bme/people/primary/gardner.php">TG@bu.edu</A>]['08].
   [Also search for: infer gene regulatory network].

%A B. Kelley
%A R. Sharan
%A R. M. Karp
%A T. Sittler
%A D. E. Root
%A B. R. Stockwell
%A T. Ideker
%T Conserved pathways within bacteria and yeast as revealed by global protein
   network alignment
%J PNAS
%V 100
%P 11394-11399
%D 2003
%K jrnl, PNAS, MolBio, c2003, c200x, c20xx, protein interaction, PPI, networks,
   pathBlast, graphAlignment
%X "... strategy for aligning 2 protein-protein interaction n/ws that combines
   interaction topology & protein seq. similarity to identify conserved
   interaction pathways & complexes. ... show that the p-p interaction n/ws of
   2 distantly related species, Saccharomyces cerevisiae & Helicobacter pylori,
   harbor a large complement of evolutionarily conserved pathways, & that a
   large number of pathways appears to have duplicated & specialized within
   yeast. Analysis of these findings reveals many well characterized interaction
   pathways as well as many unanticipated pathways, the sig. of which is
   reinforced by their presence in the n/ws of both species."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1534710100">doi:10.1073/pnas.1534710100</A>]['08].
   [Also search for: protein interaction network] and
   [also search for: graphAlignment].

%A K. Anand
%A et al ...
%A R. Hilgenfeld
%T Coronavirus main proteinase (3CLpro) structure: Basis for design of
   anti-SARS drugs
%J Science
%V 300
%N 5626
%P 1763-1767
%M JUN
%D 2003
%K jrnl, MolBio, c2003, c200x, c20xx, zz0520, virus, SARS-CoV-1, SARSCoV1,
   SARS, SARS1, protease, proteinase, protein, Mpro, nsp5, 3CL, 3CLpro, 3cPro,
   inhibitor, drug, UniLuebeck, Germany
%X "... The viral main proteinase (MPro, also called 3CLPro), which controls the
   activities of the coronavirus replication complex, is an attractive target
   for therapy. We determined crystal structures for human c. (strain 229E) MPro
   & for an inhibitor complex of porcine coronavirus [transmissible
   gastroenteritis virus (TGEV)] MPro, and & constructed a homology model for
   SARS c. (SARS-CoV) MPro. The structures reveal a remarkable degree of
   conservation of the substrate-binding sites, which is further supported by
   recombinant SARS-CoV MPro-mediated cleavage of a TGEV MPro substrate.
   Molec. modeling suggests that available rhinovirus 3cPro inhibitors may be
   modified to make them useful for treating SARS."
   -- 3834597@[<A HREF="https://www.jstor.org/stable/3834597">jstor</A>]['20].
   [Also search for: Coronavirus protein]  and  [also search for: MolBio SARS].

%A S. L. Baldauf
%T Phylogeny for the faint of heart: a tutorial
%J TRENDS in Genetics
%V 19
%N 6
%P 345
%M JUN
%D 2003
%K MolBio, c2003, c200x, c20xx, phylogenetic, evolutionary, tree, trees, life,
   origins, tute, tutorial, intro, methods, uniYork
%X "Phylogenetic trees seem to be finding ever broader applications, and
   researchers from very different backgrounds are becoming interested in what
   they might have to say. This tutorial aims to introduce the basics of
   building and interpreting phylogenetic trees. It is intended for those
   wanting to understand better what they are looking at when they look at
   someone else's trees or to begin learning how to build their own.  Topics
   covered include: how to read a tree, assembling a dataset, multiple sequence
   alignment (how it works and when it does not), phylogenetic methods,
   bootstrap analysis and long-branch artefacts, and software and resources."
   -- [<A HREF="http://dx.doi.org/10.1016/S0168-9525(03)00112-4">doi:10.1016/S0168-9525(03)00112-4</A>]['09],
   lab@[<A HREF="http://www-users.york.ac.uk/~slb14/labpage.html">y0rk</A>]['09].
   [Also search for: phylogenetic tree Molbio] and
   [also search for: multiple alignment MolBio].

%A A. J. S. Klar
%T Human handedness and scalp hair-whorl direction develop from a common
   genetic mechanism
%J Genetics
%V 165
%N 1
%P 269-276
%M SEP
%D 2003
%K jrnl, c2003, c200x, c20xx, zz0412, animal, human, handedness, left, right,
   handed, hand, RH, NRH, LH, lefty, lefties, ambidextrous, hair whorl, whorls,
   clockwise, counter, counterclockwise, gene, brain, hemispheres, development
%X "... The cause of handedness & its reln to the biol. specified scalp hair-
   -whorl rotation is determined here. The general public, consisting of mostly
   right-handers (RH), shows counterclockwise whorl rotn infrequently in 8.4% of
   individuals. Interestingly, non-right-handers (NRH, i.e., left-handers &
   ambidextrous) display a random mixture of clockwise & counterclockwise
   swirling patterns. Confirming this finding, in another indep. sample ...
   chosen because of their c.c.rotn, 1/2 of them are NRH. These findings of
   coupling in RH & uncoupling in NRH unequivocally establish that these traits
   develop from a common genetic mechanism. [and] handedness of the progeny of
   discordant monozygotic twins suggests that lefties are one gene apart from
   righties. Together, these results suggest (1) that a single gene controls
   handedness, whorl orientation, & twin concordance & discordance & (2) that
   neuronal & visceral (internal organs) forms of bilateral asymmetry are coded
   by separate sets of genetic pathways. The sociological impact of the study is
   discussed. "
   -- [<A HREF="http://www.genetics.org/content/165/1/269.full">www</A>]['12].
   (Also see [<A HREF="http://www.abc.net.au/catalyst/stories/3465535.htm">abc</A>][29/3/'12].)
   [Also search for: animal handedness].

%A S. B. Nabuurs
%A C. A. Spronk
%A E. Krieger
%A H. Maassen
%A G. Vriend
%A G. W. Vuister
%T Quantitative evaluation of experimental NMR restraints
%J J. Am. Chem. Soc.
%V 125
%N 39
%P 12026-12034
%M OCT
%D 2003
%K jrnl, JACS, MolBio, c2003, c200x, c20xx, NMR, protein, 3D, structure, NOE,
   NMR, determination, experimental restraint, restraints, information, RMS,
   distance space, QUEEN
%X "Nuclear Overhauser effect (NOE) data are an indispensable source of
   structural info. in biomolecular struct. determination by NMR spectroscopy.
   The number & type of experimental restraints used in the structure calc. &
   the RMS deviation of the restraints are usually reported. ... a new method
   for quantifying the info. contained in the experimental NMR restraints. ...
   based on a description of the struct. in distance space & concepts derived
   from info.theory. It allows for an objective description of the amount of
   available experimental information, which we show to be related to the
   positional uncertainty of the NMR ensemble. The measure of info. presented
   is not affected by redundancy in the experimental restraints. Using various
   examples ... successfully identifies the crucial restraints in a structure
   determination: those restraints that are both important & unique. Finally,
   we demonstrate that the method can detect a wider range of redundancy in
   experimental datasets when compared to currently available methods. Because
   our method describes the quantitative evaluation of experimental NMR
   restraints, we propose the acronym QUEEN."    (via A.L.)
   -- [<A HREF="http://dx.doi.org/10.1021/ja035440f">doi:10.1021/ja035440f</A>]['13],
      [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/14505424">pubm'd</A>]['13].

%T Computational Medicinal Chemistry for Drug Discovery
%E P. Bultinck
%E J. P. Tollenaere
%E W. Langenaeker
%E H. De Winte
%I CRC
%P 1169
%M DEC
%D 2003
%K book, text, c2003, c200x, c20xx, drugs, drug design, discovery, deWinte,
   ligand, molecular mechanics, small, chemical, 3D structure, docking,
   density functional theory
%X "... surveys molecular structure computation, intermolecular behavior,
   ligand-receptor interaction, and modeling responding to market demands in its
   selection and authoritative treatment of topics. The book examines molecular
   mechanics, semi-empirical methods, wave function-based quantum chemistry,
   density functional theory, 3-D structure generation, and hybrid methods."
   1st ed 2003, hb, stg105; uk us isbn:0824747747; uk us isbn13:978-0824747749.

%A W. C. Wheeler
%T Implied alignment: a synapomorphy-based multiple-sequence alignment method
   and its use in cladogram search
%J Cladistics
%V 19
%P 261-268
%D 2003
%K jrnl, MolBio, POY, c2003, c200x, c20xx, multiple alignment, synapomorphy,
   implied alignment, IA, phylogenetic tree, evolutionary trees,
   direct optimization, DO
%X "A method to align seq. data based on parsimonious synapomorphy schemes
   generated by direct optimization (DO; earlier termed optimization alignment)
   ... without an intervening multiple-alignment step, thereby creating topology
   -specific, dynamic homology statements. ... no multiple-alignment is required
   ... linking the unaligned sequence positions in the terminal taxa via DO
   transformation series. These "lines of correspondence" link anc.-desc. states
   &, when displayed as linearly arrayed cols. without hypothetical ancestors,
   are largely indistinguishable from std multiple alignment. ..."
   -- [<A HREF="http://dx.doi.org/10.1111/j.1096-0031.2003.tb00369.x">doi:10.1111/j.1096-0031.2003.tb00369.x</A>]['09],
   POY@[<A HREF="http://research.amnh.org/scicomp/research/projects/invertebrate-zoology/poy?q=projects/poy.php">amnh.org</A>]['09].
   [Also search for: phylogenetic tree MolBio].

%A S. Semple
%A M. Steel
%T Phylogenetics
%I OUP
%S Lecture Series in Mathematics and its Applications
%V 24
%P 256
%D 2003
%K book, text, MolBio, c2003, c200x, c20xx, bioinformatics, phylogenetic, tree,
   OUP, evolutionary, trees, L5Ref
%X 1st ed 2003; hb us$115; uk us isbn:0198509421; uk us isbn13:978-0198509424.

%A Y.-K. Yu
%A J. C. Wootton
%A S. F. Altschul
%T The compositional adjustment of amino acid substitution matrices
%V 100
%N 26
%P 15688-15693
%M DEC
%D 2003
%K jrnl, MolBio, PNAS, c2003, c200x, c20xx, zz0419, protein, amino acid,
   substitution matrix, PAM, BLOSUM, biased, composition
%X "... shows that if one demands consistency between target & back-ground
   freqs., then a log-odds substitution matrix implies a unique set of target &
   b/g freqs. as well as a unique scale. Std substitution matrices therefore are
   truly appropriate only for the comparison of proteins with standard AA
   composition. [So] present & evaluate a rationale for transforming the target
   freqs. implicit in a std matrix to freqs. appropriate for a non std context.
   ... yields asymmetric matrices for the comparison of proteins with divergent
   compositions. Earlier approaches are unable to deal with this case in a fully
   consistent manner. Composition-specific subs. matrix adjustment is shown
   to be of utility for comparing compositionally biased proteins, inc. those of
   organisms with nucleotide-biased, & therefore codon-biased, genomes or
   isochores."  [23 refs.]
   -- [<A HREF="https://doi.org/10.1073/pnas.2533904100">doi:10.1073/pnas.2533904100</A>]['19].
   [Also search for: MolBio substitution matrix].

%A J. M. Chandonia
%A G. Hon
%A N. S. Walker
%A L. Lo Conte
%A P. Koehl
%A M. Levitt
%A S. E. Brenne
%T The ASTRAL Compendium in 2004
%J NAR
%V 32
%N (Database issue)
%P D189-D192
%M JAN
%D 2004
%K jrnl, eJrnl, NAR, MolBio, c2004, c200x, c20xx, Astral, Scop, scopE, protein,
   folds, fold, folding, domain, domains
%X "... several databases & tools to aid in the analysis of protein structs,
   particularly through the use of their seqs.. Partially derived from the SCOP
   DB of protein struct.domains, it includes seqs. for each domain & other
   resources useful for studying these seqs. & domain structs.. The current
   release of ASTRAL contains 54,745 domains, >three times as many as the
   initial rel. 4 years ago. ASTRAL has undergone major transformations in the
   past 2 years. ... [astral.stanford.edu/ dead as of 3/'11]."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gkh034">doi:10.1093/nar/gkh034</A>]['11],
      astral@[<A HREF="http://astral.berkeley.edu/">berk-ley</A>]['11].
   [Also search for: MolBio SCOP].

%A R. Breitling
%A P. Armengaud
%A A. Amtmann
%A P. Herzyk
%T Rank products: A simple, yet powerful, new method to detect differentially
   regulated genes in replicated microarray experiments
%J FEBS Letters
%V 573
%N 1-3
%P 83-92
%M AUG
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, zz0413, microarray, rank product,
   probability, permutation, permutations, orderings, rankings, repeated,
   agreement, Tusher
%X "... present a novel technique for identifying differentially expressed genes
   that does not originate from a sophisticated stat.model but rather from an
   analysis of biological reasoning. ... rank products (RP) from replicate
   experiments, is fast & simple. At the same time, it provides a straightfwd &
   statistically stringent way to determine the sig. level for each gene &
   allows for the flexible control of the false-detection rate & familywise
   error rate in the multiple testing sitn of a microarray exp.. We use the RP
   technique on 3 biological data sets & show that in each case it performs more
   reliably & consistently than the non-parametric t-test variant implemented
   in Tusher et al.'s significance analysis of microarrays (SAM). ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.febslet.2004.07.055">doi:10.1016/j.febslet.2004.07.055</A>]['13],
      pdf@[<A HREF="http://www.dcs.gla.ac.uk/~rb106x/publications/RankProducts_FEBS.pdf">gla</A>]['13],
      [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/15327980">p'bmed</A>]['13].
   (Also see rnkPrd@[<A HREF="http://en.wikipedia.org/wiki/Rank_product">wikip</A>]['13].)

%A C. Bystroff
%A Y. Shao
%A X. Yuan
%T Five hierarchical levels of sequence-structure correlation in proteins
%J Applied Bioinf.
%V 3
%N 2
%P 97-104
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, I-sites, Isites, protein, structure,
   sequence, fragment, library, HMMSTR, SCALIhmm, HMMSTRcm
%X "A review ... modeling the protein folding pathway ... Stat.models ...
   for seq.-struct. correlns in proteins at 5 levels of structural complexity:
   (1) short motifs, (2) extended motifs, (3) non-local pairs of motifs,
   (4) 3D arrangements of multiple motifs, & (5) global structural homology.
   ... review ... inc. seq.profiles, HMMs & interaction potentials, for the
   first 4 levels of structural detail. The I-sites Library (folding Initiation
   sites) models local structure motifs. HMMSTR (Hidden Markov Model for
   STRucture) is a HMM for extended motifs. ...  Global seq. models ... reviewed
   elsewhere & are not discussed here. The parallels between the stat.models
   & the theor.models for folding pathways are discussed."
   -- pdf@[<A HREF="http://www.bioinfo.rpi.edu/bystrc/pdf/fivelevels.4.pdf">rpi</A>]['13],
      Bys@[<A HREF="http://www.bioinfo.rpi.edu/bystrc/">rpi</A>]['13].
   [Also search for: protein structure fragment library].

%A E. Wit
%A J. McLure
%T Statistics for Microarrays: Design, Analysis and Inference
%I Wiley
%P 278
%D 2004
%K book, text, MolBio, c2004, c200x, c20xx, bioinformatics, stats, L4Ref, L5Ref,
   microarray, microarrays
%X "... aimed at statistically-minded biologists, bioinformaticians,
   biostatisticians, and computer scientists working with microarray data ..."
   1st ed 2004; hb us$86; uk us isbn:0470849932; uk us isbn13:978-0470849934.

%A I. Eidhammer
%A I. Jonassen
%A W. R. Taylor
%T Protein Bioinformatics: An Algorithmic Approach to Sequence and
   Structure Analysis
%I Wiley
%P 376
%D 2004
%K book, text, MolBio, c2004, c200x, c20xx, bioinformatics, protein, proteins,
   structure, function, threading, algorithm, programming
%X "... Suitable both for developers and users of bioinformatics tools. ..."
   1st ed 2004; us$68; uk us isbn:0470848391; uk us isbn13:978-0470848395.

%A P. A. Pevzner
%A H. Tang
%A G. Tesler
%T De novo repeat classification and fragment assembly
%J Proc. 8th Conf. on Res. in Computational Molec. Biol.
%P 213-222
%D 2004
%O Genome Res., 14(9), pp.1786-1789, 2004
%K conf, MolBio, RECOMB, c2004, c200x, c20xx, deNovo, DNA, repeat, repeats,
   repeatgluer, gluer, repeated, mobile element, A-Bruijn, ABruijn, deBruijn,
   graph, stringGraph, sequence, assembly, assembler, tangle, tangles, UCSD
%X (BTW P.A.P. was incorrectly given as Paul..., should be Pavel.)
   "... Our new repeat classification alg. is based on the observation
   that the alignment-induced quotient space of a DNA seqs.. compactly
   represents all seq. repeats. ... leads to a simple & efficient soln of the
   repeat classification problem as well as new approaches to fragment assembly
   & multiple alignment."
   "... A-Bruijn graphs are equiv. to the de Bruijn graphs [when] A is
   the coll'n of all perfect similarities of length l (l-mers). ...
   S a seq. of length n, & A=(a[i,j]) a binary n x n "similarity matrix"
   representing the set A* of all sig. local pairwise alignments b/w regions
   from S.  A is defined as a[i,j]=1 iff posns i & j are aligned [i:j] in >=1
   p/w alignments & =0 o/w.  A represents an "adjacency matrix" of a graph
   on n vertices. Let V be the set of connected components of this g. & let v[i]
   be the connected component containing vertex i.
 **The A-BRUIJN GRAPH, G(V,E), is def. as the multi-graph on the vertex set V
   with (n-1) dir.edges (v[i],v[i+1]) i=1..n-1. ...  view the A-Bruijn graph as
   the Eulerian path obtained from the path (1,...,n) after contracting each
   conn.component into a vertex.  v[1] source, v[n] sink. ...
   Our key contribution is the A-Bruijn graph construction that deals with
   fragment assembly at the level of single-nucleotide resolution."
   pdf: [<A HREF="http://doi.acm.org/10.1145/974614.974643">doi:10.1145/974614.974643</A>]['08], and
   jrnl [<A HREF="http://genome.cshlp.org/cgi/content/full/14/9/1786">GR@cshlp</A>['08].
   software@[<A HREF="http://nbcr.sdsc.edu/euler/">sdsc</A>]['04].
   -- [<A HREF="http://www.cse.ucsd.edu/~gptesler/">auth3@ucsd</A>]['08].
   [Also search for: MolBio repeat DNA],  [also search for: MolBio stringGraph].

%A G. Ast
%T How did alternative splicing evolve?
%J Nature Reviews Genetics
%V 5
%P 773-782
%M OCT
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, splice, gene, genes, mRNA, RNA, protein,
   proteome, complexity, evolution, multicellular eukaryote, coding, intron,
   exon, Gil Ast
%X "A.S. creates transcriptome diversification, possibly leading to speciation.
   A large fraction of the protein-coding genes of multicellular organisms are
   A.S., although no regulated S. has been detected in unicellular eukaryotes
   such as yeasts. A comparative analysis of unicellular and multicellular
   eukaryotic 5' splice sites has revealed important differences - the
   plasticity of the 5' splice sites of multicellular eukaryotes means that
   these sites can be used in both constitutive and alternative splicing, & for
   the reg. of the inclusion/skipping ratio in A.S.. So, A.S. might have
   originated as a result of relaxation of the 5' splice site recognition in
   organisms that originally could support only constitutive splicing."
   -- [<A HREF="http://dx.doi.org/10.1038/nrg1451">doi:10.1038/nrg1451</A>]['05] ?subscrn?
   -- [<A HREF="http://www.tau.ac.il/~gilast/nrg1451.pdf">pdf</A>]['05],
   [Also search for: alternative splicing MolBio].

%A I. Nachman
%A A. Regev
%A N. Friedman
%T Inferring quantitative models of regulatory networks from expression data
%J J. Bioinformatics
%V 20
%N Suppl. 1
%P I248-I256
%D 2004
%K jrnl, MolBio, c2004, c200x, c200x, infer gene regulatory network, profile,
   model, genes, Michaelis Menten kinetics
%X "... present fine-grained dynamical models of gene transcription & develop
   methods for reconstructing them from gene expression data within the
   framework of a generative probabilistic model. ... employ quantitative
   transcription rates, & simultaneously est. both the kinetic parameters that
   govern these rates, & the activity levels of unobserved regulators that
   control them. We apply ... to expression datasets from yeast & show that we
   can learn the unknown regulator activity profiles, as well as the binding
   affinity params. We also introduce a novel structure learning alg. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bth941">doi:10.1093/bioinformatics/bth941</A>]['08].
   [Also search for: infer gene regulatory network].

%A S. C. Madeira
%A A. L. Oliveira
%T Biclustering algorithms for biological data analysis: A survey
%J IEEE/ACM Trans. on Comp. Biol. and Bioinformatics (TCBB)
%V 1
%N 1
%P 24-45
%M JAN-MAR
%D 2004
%K MolBio, c2004, c200x, c20xx, zz1205, survey, intro, 2way, 2D, biclustering,
   coclustering, cluster, clustering, matrix, algorithm
%X "... The goal is to find submatrices, that is, subgroups of genes &
   subgroups of conditions, where the genes exhibit highly correlated activities
   for every condition. In this paper, we refer to this class of algs. as
   biclustering. Biclustering is also referred in the literature as
   coclustering & direct clustering, among others names, & has also been used
   in fields such as information retrieval & data mining. In this comprehensive
   survey, we analyze a large number of existing approaches to biclustering, &
   classify them in accordance with the type of biclusters they can find, the
   patterns of biclusters that are discovered, the methods used to perform the
   search, the approaches used to eval. the soln, & the target applications."
      (Table 2, p.41, 19 algs (NP-hard problem).  via Robyn M.)
   -- [<A HREF="http://dx.doi.org/10.1109/TCBB.2004.2">doi:10.1109/TCBB.2004.2</A>]['06],
      [<A HREF="http://doi.ieeecomputersociety.org/10.1109/TCBB.2004.2">10.1109/TCBB.2004.2</A>]['06],
      [<A HREF="http://www.cs.princeton.edu/courses/archive/spring05/cos598E/bib/bicluster.pdf">prnctn</A>]['05].
   (Also see bicl@[<A HREF="http://en.wikipedia.org/wiki/Biclustering">wikip</A>]['15].)
   [Also search for: biclustering]  and  [also search for: coclustering].

%A G. A. McConkey
%A J. W. Pinney
%A D. R. Westhead, K.Plueckhahn, T.B.Fitzpatrick, P.Macheroux, B.Kappes
%T Annotating the Plasmodium genome and the enigma of the shikimate pathway
%J Trends in Parasitology
%P 60-65
%V 20
%N 2
%M FEB
%D 2004
%K jrnl, biol, biology, Plasmodium falciparum genome, c2004, c200x, c20xx,
   parasite, MolBio, bioinformatics, metabolic, uniLeeds, UK
%X "The completion of the [pf] genome seq. heralds a new era in the effort to
   identify all the parasite's genes along with their cellular functions. A
   combination of bioinformatics and experimental proof will facilitate this
   process. Many enzymes in metabolic processes have been identified, but
   several examples exist of incomplete pathways, such as the shikimate
   pathway. This review uses the example of the shikimate pathway to examine
   the application of bioinformatics to lead experimental design in
   post-genomic biology."
   -- [<A HREF="http://dx.doi.org/10.1016/j.pt.2003.11.001">doi:10.1016/j.pt.2003.11.001</A>][10/'04],
   DRW@[<A HREF="http://www.bioinformatics.leeds.ac.uk/publications_westhead.html">U Leeds</A>]['04].

%A A. Brakoulias
%A R. M. Jackson
%T Towards a structural classification of phosphate binding sites in
   protein-nucleotide complexes: An automated all-against-all structural
   comparison using geometric matching
%J Proteins
%V 56
%N 2
%P 250-60
%M AUG
%D 2004
%K jrnl, match, proteins, DNA, c2004, c200x, c20xx, 3D, MolBio, bioinformatics,
   site, bind, complex, cluster, clustering, uniLeeds, UK
%X "...rapid comparison of protein binding sites using geometric matching to
   detect similar three-dimensional structure. ... use the method to produce an
   all-against-all comparison of phosphate binding sites in a number of
   different nucleotide phosphate -binding proteins. The similarity search is
   combined with clustering of similar sites to allow a preliminary structural
   classification. Clustering by site similarity produces a classification of
   binding sites for the 476 representative local environments producing ten
   main clusters representing half of the representative environments. The
   similarities make sense in terms of both structural & functional
   classification schemes. The ten main clusters represent a very limited
   number of unique structural binding motifs for phosphate. These are the
   structural P-loop, di-nucleotide binding motif [FAD/NAD(P)-binding &
   Rossman-like fold] & FAD-binding motif. Similar classification schemes for
   nucleotide binding proteins have also been arrived at independently by
   others using different methods."  PMID:15211509.
   RMJ at [<A HREF="http://www.bioinformatics.leeds.ac.uk/publications_jackson.html">U Leeds</A>]['04].
   [Also search for: geometric matching].

%A C. A. Rohl
%A C. E. M. Strauss
%A K. M. S. Misura
%A D. Baker
%T Protein structure prediction using Rosetta
%J Methods in Enzymol.
%V 383
%P 66-93
%D 2004
%K MolBio, c2004, c200x, c20xx, Rosetta, ab initio, protein, tertiary, 3D,
   structure, prediction, folding, energy, PES, search, fragments, local,
   global
%X "... guiding principle of the Rosetta alg. is to attempt to mimic the
   interplay of local & global interactions in determining protein struct.. ...
   final native conformation is obtained when these fluctuating local structs.
   come together to yield a compact conformation with favorable nonlocal
   interactions ... by randomly combining these fragments, using a Monte Carlo
   sim.ann.search. The fitness of [a] conformation wrt nonlocal interactions is
   evaluated on the basis of a scoring fn [PES] derived from conformational
   stats. of known p.structs.. ..."   online 4/'04.
   -- [<A HREF="http://dx.doi.org/10.1016/S0076-6879(04)83004-0">doi:10.1016/S0076-6879(04)83004-0</A>]['12].
   [Also search for: Rosetta protein MolBio].

%A K. Lu
%A R. Asano
%A J. Davies
%T Antimicrobial resistance gene delivery in animal feeds
%J Emerging Infectious Diseases [online]
%P ?-?
%V 10
%N 4
%M APR
%D 2004
%K jrnl, genes, biol, MolBio, biology, antibiotic, Avoparcin, glycopeptide,
   genes, antimicrobial, vancomycin, vanH, vanA, vanX, disease, feed, Roche
%X "Avoparcin, a glycopeptide antimicrobial agent related to vancomycin, has
   been used extensively as a growth promoter in animal feeds for more than 2
   decades, & evidence has shown that such use contributed to the development
   of vancomycin-resistant enterococci. A cluster that includes three genes,
   vanH, vanA, & vanX, is required for high-level resistance to glycopeptides.
   In the vancomycin producer Amycolatopsis orientalis C329.2, homologs of
   these genes are present, suggesting an origin for the cluster. We found
   substantial bacterial DNA contamination in animal feed-grade avoparcin.
   Furthermore, nucleotide sequences related to the cluster vanHAX are present
   in this DNA, suggesting that the prolonged use of avoparcin in agriculture
   led to the uptake of glycopeptide resistance genes by animal commensal
   bacteria, which were subsequently transferred to humans."
   -- [<A HREF="http://www.cdc.gov/ncidod/EID/vol10no4/03-0506.htm">online</A>][4/'04].

%A R. Stindl
%T Is telomere erosion a mechanism of species extinction?
%J J. Experimental Zoology, Part B: Molecular and Developmental Evolution
%P 111-120
%V 302B
%N 2
%D 2004
%K jrnl, telomeres, DNA, extinct, extinction, loss, long, short, mass, event,
   c2004, c200x, c20xx, zz0404, species clock hypothesis, evolution
%X "According to the fossil record, 99.9% of all species that have ever lived
   on Earth have disappeared. However, only about 4% died out during the 5 mass
   extinction events ... The species clock hypothesis, as presented here, is
   based on the idea of a tiny loss of mean telomere length per generation.
   This mechanism would not rapidly endanger the survival of a particular
   species. Yet, after many thousands of generations, critically short
   telomeres could lead to the weakening & even the extinction of old species &
   would simultaneously create the unstable chromosomal environment that might
   result in the origination of new species."
   -- [<A HREF="http://dx.doi.org/10.1002/jez.b.20006">doi:10.1002/jez.b.20006</A>][4/'04].

%A I. Hornsey
%T The History of Beer and Brewing
%I Royal Society of Chemistry
%P 742
%M FEB
%D 2004
%K book, text, beer, beers, ale, ales, brew, brewer, brewers, fermentation,
   alcohol, yeast, c2004, c200x, c20xx, zz0404
%X stg40; ppb; uk us isbn:0854046305; uk us isbn13:978-0854046300.

%A J. Siemens
%A C. Lillo
%A R. A. Dumont, A. Reynolds, D. S. Williams, P. G. Gillespie
%A U. Muller
%T Cadherin 23 is a component of the tip link in hair-cell stereocilia
%J Nature
%V 428
%P 950-955
%M APR
%D 2004
%K jrnl, MolBio, Cadherin23, electrochemical signals, sense, touch, hearing,
   hair cell, cells, CDH23, biol, biology, c2004, c200x, c20xx
%X "Mechanoelectrical transduction, the conversion of mechanical force into
   electrochemical signals, underlies a range of sensory phenomena, including
   touch, hearing ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature02483">doi:10.1038/nature02483</A>][4/'04].

%A J. L. Bigelow
%A D. B. Dunson
%A J. B. Stanford;  R. Ecochard;  C. Gnoth; and B. Colombo
%T Mucus observations in the fertile window: a better predictor of
   conception than timing of intercourse
%J Human Reproduction
%I OUP
%V 19
%N 4
%P 889-892
%M APR
%D 2004
%K jrnl, biol, biology, stats, pregnancy, pregnant, vaginal,
   fertility, ovulation, conception, conceive
%X -- acting on observations can double the pregnancy rate
   -- [<A HREF="http://www.ingenta.com/journals/browse/oup/humrep">ingenta.com</A>][5/'04].

%A A. M. Nedelcu
%A O. Marcu
%A R. E. Michod
%T Sex as a response to oxidative stress: A two-fold increase in
   cellular reactive oxygen species activates sex genes
%J Proc. Royal Soc. B
%P ?-?
%V ?
%D 2004 in press
%K jrnl, origin, origins, sex, alga, algae, algal, biology, biol, zz0704, gene,
   rspb, c2004, c200x, c20xx, Volvocales, V. carteri, antimycin, MolBio, DNA,
   reproduction, why
%X "Organisms are constantly subjected to factors that can alter the cellular
   redox balance & result in the formation of a series of highly reactive
   molecules known as reactive oxygen species (ROS).  As ROS can be damaging to
   biological structures, cells evolved a series of mechanisms (e.g.,
   cell-cycle arrest, programmed cell death) to respond to high levels of ROS
   (i.e., oxidative stress).  Recently, we presented evidence that in a
   facultatively sexual lineage - the multicellular green alga Volvox carteri
   -  sex is an additional response to increased levels of stress, & likely ROS
   & DNA damage. Here, we show that in V. carteri (i) sex is triggered by a ca.
   2-fold increase in the level of cellular ROS (induced either by the natural
   sex-inducing stress, namely heat, or by blocking the mitochondrial electron
   transport chain with antimycin A), & (ii) ROS are responsible for the
   activation of sex genes. As most types of stress result in the
   overproduction of ROS, we believe that our findings will prove to extend to
   other facultatively sexual lineages, which could be indicative of the
   ancestral role of sex as an adaptive response to stress & ROS-induced DNA
   damage."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2004.2747">doi:10.1098/rspb.2004.2747</A>]?[6/'04],
   -- [<A HREF="http://eebweb.arizona.edu/Michod/Downloads/SexROS.pdf">pdf@arizona.edu</A>][6/'04],
   -- [<A HREF="http://www.unbf.ca/vip/database/volvox/Volvox2004.htm">abs@unbf.ca</A>][6/'04].

%A J.-F. Pombert
%A C. Otis
%A C. Lemieux
%A M. Turmel
%T The complete mitochondrial DNA sequence of the green alga Pseudendoclonium
   akinetum (Ulvophyceae) highlights distinctive evolutionary trends in the
   chlorophyta and suggests a sister-group relationship between the Ulvophyceae
   and Chlorophyceae
%J Molec. Biol. and Evolution
%P 922-935
%V 21
%N 5
%D 2004
%K jrnl, MBE, green alga, algae, algal, mitochondrial genome, mtDNA, bio,
   mGenome, MolBio, c2004, c200x, c20xx
%X "... At 95,880-bp, Pseudendoclonium mtDNA is the largest green-algal
   mitochondrial genome sequenced to date and has the lowest gene density.
   These derived features are reminiscent of the "expanded" pattern exhibited
   by embryophyte mtDNAs, indicating that convergent evolution towards genome
   expansion has occurred independently in the Chlorophyta and Streptophyta.
   With 57 conserved genes, the gene repertoire of Pseudendoclonium mtDNA is
   slightly smaller than those of the prasinophyte Nephroselmis olivacea and the
   trebouxiophyte Prototheca wickerhamii. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/molbev/msh099">doi:10.1093/molbev/msh099</A>][7/'04].

%A Z. Zhang
%A et al
%T Moderate mutation rate in the SARS coronavirus genome and its implications
%J BMC Evol. Biol.
%V 4
%M JUN
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, zz0521, SARS CoV, SARSCoV, SARS1,
   coronavirus, mutation, mutations, rate, diversity
%X "... Sixteen complete genomic seqs. with available clinical histories during
   the SARS outbreak were analyzed. ... The mutation rate in the SARS-CoV genome
   was est. to be 0.80-2.38x10^{-3} nucleotide subs. per site per year which is
   in the same order of magnitude as other RNA viruses. The non-synonymous &
   synonymous subs. rates were est. to be 1.16-3.30x10^{-3} & 1.67-4.67x10^{-3}
   per site per year, resp.. The most recent common ancestor of the 16 seqs was
   inferred to be present as early as the spring of 2002. The est. mutation
   rates in the SARS-CoV using multiple strategies were not unusual among
   coronaviruses & moderate compared to those in other RNA viruses. ..."
   -- [<A HREF="https://doi.org/10.1186/1471-2148-4-21">doi:10.1186/1471-2148-4-21</A>]['21].
   [Also search for: SARS mutation].

%A B. L. Gutman
%A K. K. Niyogi
%T Chlamydomonas and Arabidopsis. A dynamic duo
%J Plant Physiology
%P 607-610
%V 135
%M JUN
%D 2004
%K jrnl, green, alga, plant, plants, bio, biol, c2004, c200x, c20xx,
   photosynthesis, algae, algal
%X "... In this brief essay, we make a case for the pairing of Chlamydomonas &
   Arabidopsis as model organisms that bracket a major subset of photosynthetic
   eukaryotes, the green plants ... . By analogy with the yeast-
   mouse dyad, this green pair has tremendous potential as we enter an era of
   renewed interest in comparative biology."
   -- [<A HREF="http://www.plantphysiol.org/cgi/content/abstract/135/2/607">plantphysiol.org</A>][7/'04].

%A S. Robbens
%A S. Rombauts
%A S. Degroeve,  P. Rouze  and  Y. Van de Peer:
%T Annotation of the green alga Ostreococcus tauri (abstract)
%J Belgian Bionf. Conf
%M APR
%D 2004
%O also a poster at ISMB 31/7 - 4/7/2004
   "Annotation of the smallest Eukaryotic genome: Ostreococcus tauri"
%K conf, GREEN alga, biol, bio, bioinformatics, MolBio, algae, algal, genome,
   Ostreococcus tauri, eukaryote, c2004, c200x, c20xx, chromosome, nuclear,
   nGenome, nuclear, DNA, gene, genes, Chlorophyta, chromosomes
%X 11.5Mb, 19 chromosomes (or 18?), 0.12 to 1.5 Mb each, ~4000 predicted genes
   "... with the Laboratoire Arago, Banyuls, France, ...performing the full
   genome annotation of the unicellular green algae Ostreococcus tauri. ...the
   smallest eukaryotic organism described until now (... comparable to that of
   a bacterium) & has a nuclear genome of about 11.5 Mb, divided over 19
   chromosomes ranging in size from 120 to 1500 Kb.
   ...a relatively large nucleus with only 1 nuclear pore, 1 chloroplast,
   1 mitochondrion, 1 Golgi body & a very reduced cytoplasmic compartment.
   ... an early branch of the Chlorophyta (green algae). ..."
   -- [<A HREF="http://blizzard.ulb.ac.be/BBC04/Workshop.php?menu=abstract&id=51">abs@ulb.ac.be</A>][7/'04],
   -- [<A HREF="http://www.iscb.org/ismb2004/posters/stromATpsb.ugent.be_844.html">abs@iscb.org</A>][7/'04],
   [Also search for: Cyanidioschyzon merolae 2004],
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05].

%A M. Matsuzaki
%A et al
%T Genome sequence of the ultrasmall unicellular red alga
   Cyanidioschyzon merolae 10D
%J Nature
%P 653-657
%V 428
%N 6983
%M APR
%D 2004
%K jrnl, RED alga, algae, algal, genome, gene, genes, c2004, c200x, c20xx,
   chromosomes, chromosome, dynamin, photosynthesis, eukaryote, DDBJ, AP006483,
   nGenome, nuclear, zz0504
%X "... report the 16,520,305-base-pair sequence of the 20 chromosomes of the
   unicellular red alga Cyanidioschyzon merolae 10D as the first complete algal
   genome. We identified 5,331 genes in total, of which at least 86.3% were
   expressed. ... a lack of introns in all but 26 genes; only three copies of
   ribosomal DNA units that maintain the nucleolus; and two dynamin genes that
   are involved only in the division of mitochondria and plastids. ..."
   -- [<A HREF="http://merolae.biol.s.u-tokyo.ac.jp/publication/nature02398.pdf">pdf@merolae.biol...</A>][7/'04],
   -- [<A HREF="http://dx.doi.org/10.1038/nature02398">doi:10.1038/nature02398</A>][7/'04],
      [<A HREF="http://www.nature.com/nature/journal/v428/n6983/suppinfo/nature02398.html">supp.info.</A>]['04].
   C.M., 2%mu;m dia., unicellular, sulphate-rich hot springs, one nucleus,
   one mitochondrion, one plastid.  20 chromosomes, 0.42 to 1.62Mb, G+C 55%.
   DATA: [<A HREF="http://merolae.biol.s.u-tokyo.ac.jp/">merolae.biol.s.u-tokyo.ac.jp/</A>][7/'04],
   -- [<A HREF="http://dolphin.lab.nig.ac.jp/publish/">dolphin.lab.nig.ac.jp/publish/</A>][7/'04]
   Chrms 1-20 sub to [<A HREF="http://www.ddbj.nig.ac.jp/">DDBJ</A>] [<A HREF="http://getentry.ddbj.nig.ac.jp/getstart-e.html">get-entry</A>] with acc' #s AP006483-AP006502,
   and unassigned contigs AP006600-AP006614.
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=46309268">chr1@genbank</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=46309287">chr20@genbank</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05].
   [Also search for: Ostreococcus tauri 2004].

%A P. G. Falkowski
%A M. E. Katz
%A A. H. Knoll,  A. Quigg,  J. Raven,  O. Schofield
%A F. J. R. Taylor
%T The evolution of modern eukaryotic phytoplankton
%J Science
%V 305
%P 354-360
%D 2004
%K jrnl, phytoplankton, red, plankton, photsynthesis, green, plastid, alga,
   algal, algae, origin, origins, biol, biology, cause, causes, eukaryotes,
   c2004, c200x, c20xx
%X [<A HREF="http://www.sciencemag.org/cgi/content/full/305/5682/354">sciencemag.org</A>][7/'04],
   (Need a $ub$c'n for science.)

%A S. Ferre
%A R. D. King
%T BLID: An application of logical information systems
%J 2nd Int. Conf. on Formal Concept Analysis
%I Springer
%S LNAI
%V 2961
%P 47-54
%M FEB
%D 2004
%K conf, bio-logical intelligent database, zzOSP, zOSP04, c2004, c200x, c20xx,
   MolBio, data-base, logic, LP, macromolecule, browsing, Sebastian Ferre,
   ICFCA, ICFCA2, aber, RDKing
%X "... & analysis. We describe BLID's novel data browsing system which is
   based on the idea of Logical Information Systems. ...combined querying &
   navigation of data in BLID (extracted from public bioinf' repositories). The
   browsing language is a logic especially designed or bioinformatics. It
   currently includes sequence motifs, taxonomies, & macromolecule structures,
   and it is designed to be easily extensible, ..."; in isbn:3540210431.
   R.D.K. at U. Wales Aberystwyth;  S.F. at U. Rennes from late 2004.
   -- [<A HREF="http://users.aber.ac.uk/sbf/wit2002.ps.gz">preprint.ps@aber</A>][8/'04],
      [<A HREF="http://www.springerlink.com/link.asp?id=y296xuurted4db7t">met@link</A>][8/'04],
      [<A HREF="http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=2961&spage=47">openurl</A>][8/'04].

%A T. Cavalier-Smith
%T Only six kingdoms of life
%J Proc. Royal Soc. B
%V 271
%N 1545
%P 1251-1262
%M JUN
%D 2004
%K biol, biology, evolution, species, c2004, c200x, c20xx tree of life, trees,
   family, evolutionary, phylogenetic, phyla, kingdom, class, phylum, division,
   order, lineage, phyla, eukaryote, MolBio
%X "Sequencing genes from environmental DNA is a powerful way of exploring our
   ignorance of major microbial groups. 2 recent claims using such methods for
   numerous novel early 'kingdom-level' lineages among anaerobic eukaryotes are
   mistaken. More thorough phylogenetic analysis shows that all 8-10
   'mysterious' lineages belong in already recognized phyla within the basal
   kingdom Protozoa, mostly in known classes, sometimes known orders, families
   or genera. Our overall picture of microbial biodiversity at phylum/division
   level is already rather good & comprehensive; there are no uncharacterized
   kingdoms of life. The first eukaryotes had mitochondria & aerobic
   respiration; all anaerobic eukaryotes are secondarily derived."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2004.2705">doi:10.1098/rspb.2004.2705</A>]['04].
   [Also search for: MolBio tree life].

%A M. Edwards
%A A. J. Richardson
%T Impact of climate change on marine pelagic phenology and trophic mismatch
%J Nature
%V 430
%P 881-884
%M AUG
%D 2004
%K jrnl, Phenology, climate change, north-sea ecosystem, plankton, biol,
   ecological, c2004, c200x, c20xx, zz0804, global warming, diatoms, bloom,
   dinoflagellates, plankton
%X "...long-term data of 66 plankton taxa during the period from 1958 to 2002,
   we investigated whether climate warming signals are emergent across all
   trophic levels and functional groups ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature02808">doi:10.1038/nature02808</A>][8/'04].

%A X. She et al
%T The structure and evolution of centromeric transition regions within
   the human genome
%J Nature
%P 857-864
%V 430
%M AUG
%D 2004
%K jrnl, hugo, centromere, region, chromosome, c2004, c200x, c20xx, arms, arm,
   MolBio, pericentromeric, origin, zz0804
%X "...analysis of the structure & assembly of all human pericentromeric
   regions (5 megabases). Most chromosome arms (35 out of 43) show a gradient
   of dwindling transcriptional diversity accompanied by an increasing number
   of interchromosomal duplications in proximity to the centromere. At least
   30% of the centromeric transition region structure originates from
   euchromatic gene-containing segments of DNA that were duplicatively
   transposed towards pericentromeric regions at a rate of six-seven events per
   million years during primate evolution. This process has led to the
   formation of a minimum of 28 new transcripts by exon exaptation & exon
   shuffling, many of which are primarily expressed in the testis. The
   distribution of these duplicated segments is nonrandom among pericentromeric
   regions, suggesting that some regions have served as preferential acceptors
   of euchromatic DNA...."
   -- [<A HREF="http://dx.doi.org/10.1038/nature02806">doi:10.1038/nature02806</A>][8/'04].

%A C. Holden
%T An everlasting gender gap?
%J Science
%P 639-640
%V 305
%N 5684
%D 2004
%K gender, sport, sports, running, sprint, Olympic, male, female, stats, c2004,
   caseStudy, statistics, men, women, performance, gap, improvement,
   prediction, zz1004, Sailor,Seiler, Tatem,Guerra,Atkinson,Hay, Whipp,Ward,
   ScienceMag
%X `For a while, female runners were closing in on their male counterparts.
   Now they're barely keeping the guys' taillights in sight ...
   ... Absent unforeseen genetic or hormonal interventions, men, it seems, will
   maintain an advantage. That's due largely to their steady supply of a
   performance drug that will never be banned: endogenous testosterone, which
   boosts muscle power and oxygen capacity. The typical young man has a maximum
   oxygen use capacity, or VO2 max, of about 3.5 L/min, compared with 2 L for a
   woman, says physiologist Stephen Seiler...  Recent records support the
   gender-gap plateau, Seiler says. A few years ago, he and writer Steve Sailor
   ... Seiler recently updated these numbers for Science. He reports that from
   the world records in the 8 main running events from 100m to the marathon
   [Olympic event for w from 84], 7 suggest an increasing gender gap. The m. is
   the exception: The gap has narrowed from 11.9% to 8.4% thanks to Radcliffe's
   new record. Seiler says the current average gap is now 11.01%, up from 10.4%
   in 1989. In short, he says, "at the highest levels of perf'ce, the gender
   gap in running perf'ce has actually widened over the last 20 y..'
   -- [<A HREF="http://dx.doi.org/10.1126/science.305.5684.639">doi:10.1126/science.305.5684.639</A>][10/'04],
      [<A HREF="http://www.sciencemag.org/cgi/content/summary/305/5684/639">sciencemag</A>][10/'04].
   But [also search for: Tatem Guerra Atkinson Hay, Nature 2004].

%A A. J. Tatem
%A C. A. Guerra
%A P. M. Atkinson
%A S. I. Hay
%T Athletics: Momentous sprint at the 2156 Olympics?
%J Nature
%P 525
%V 431
%M SEP
%D 2004
%K jrnl, sport, running, sprint, Olympic, gender, male, female, stats, c2004,
   caseStudy, statistics, women, men, performance, gap, improvement,
   prediction c21xx
%X "The 2004 Olympic women's 100-metre sprint champion, Yuliya Nesterenko, is
   assured of fame and fortune. But we show here that - if current trends
   continue - it is the winner of the event in the 2156 Olympics whose name
   will be etched in sporting history forever, because this may be the 1st
   occasion on which the race is won in a faster time than the men's event...."
   -- [<A HREF="http://dx.doi.org/10.1038/431525a">doi:10.1038/431525a</A>]['04].
   But also see  * S e i l e r and S a i l e r c1997 *,
   H o l d e n, Sci'ce, 2004 [<A HREF="http://dx.doi.org/10.1126/science.305.5684.639">doi:10.1126/science.305.5684.639</A>]['04],
   H.Pe@rson [<A HREF="http://www.nature.com/news/2004/040927/full/040927-9.html">29Sept2004</A>]~[<A HREF="http://dx.doi.org/10.1038/news040927-9">doi:10.1038/news040927-9</A>]['04], and
   W h i p p & W a r d, Nature v.355, pp.25, 2 Jan c1992 [<A HREF="http://dx.doi.org/10.1038/355025a0">doi:10.1038/355025a0</A>]['04].

%A N. Pike
%A T. Tully
%T The effect of autocorrelation in environmental variability on the
   persistence of populations: an experimental test
%J Proc. Royal Soc.: Biological Sci.
%P 2143-2148
%V 271
%N 1553
%M OCT
%D 2004
%K biol, biology, evolution, ecology, c2004, c200x, c20xx, correlation,
   autocorrelation,  extinction, red noise, environment, Folsomia candida
%X "Despite its significance regarding the conservation & management of bio'
   resources, the body of theory predicting that the correlation between
   successive environmental states can profoundly influence extinction has not
   been empirically validated. Identical clonal populations from a model
   experimental system based on the collembolan Folsomia candida were used in
   ... investigate the effect of environmental autocorrelation on time to
   extinction. Environmental variation was imposed by variable implementation
   (present/absent) of a culling procedure according to treatments that
   represented 6 patterns of environmental autocorrelation.  ... While no
   difference was found among the survival functions for the various treatments,
   the time taken for 50% of the component populations to become extinct
   decreased significantly with increasing environmental autocorrelation. ...
   time to extinction was shortened as environmental autocorrelation increased."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2004.2834">doi:10.1098/rspb.2004.2834</A>]['04].

%A F. Corna
%A A. Camperio-Ciani
%A C. Capiluppi
%T Evidence for maternally inherited factors favouring male homosexuality and
   promoting female fecundity
%J Proc. Royal Soc. B
%V 271
%N 1554
%P 2217-2221
%M NOV
%D 2004
%K biol, c2004, c200x, c20xx, human, biology, gene, genes, homosexual, genetic,
   male, mother, maternal, Darwinian paradox, X chromosome, Xchromosome,
   chrX, Xchr, evolution
%X "The Darwinian paradox of male homosexuality in humans is examined, i.e. if
   male homosexuality has a genetic component & homosexuals reproduce less than
   heterosexuals, then why is this trait maintained in the population? ...
   98 homosexual & 100 heterosexual men & their relatives (a total of over 4600
   individuals), we found that female maternal relatives of homosexuals have
   higher fecundity than female maternal relatives of heterosexuals & that this
   difference is not found in female paternal relatives. The study confirms
   previous reports ... that homosexuals have more maternal than paternal male
   homosexual relatives, that homosexual males are more often later-born than
   1st-born & that they have more older brothers than older sisters. ..."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2004.2872">doi:10.1098/rspb.2004.2872</A>]['10],
   -- [<A HREF="http://www.pubs.royalsoc.ac.uk/proc_bio/proc_bio.html">RS pubns</A>][10/'04].
   Also see CAMPERIO CIANI A., CORNA F., GHIRLANDA S.
     Evidence for the influence of a genetic factor on both the likelihood of
     male homosexuality and the female fecundity.
     J. of Endocrinological Investigation, 26(3), pp.151, 2003.

%A M. A. Nobrega
%A Y. Zhu
%A I. Plajzer-Frick
%A V. Afzal
%A E. M. Rubin
%T Megabase deletions of gene deserts result in viable mice
%J Nature
%V 431
%P 988-993
%M OCT
%D 2004
%K jrnl, junk DNA, genome, c2004, c200x, c20xx, mouse, mus, gene desert,
   MolBio, biol, biology, deletion, non-coding, noncoding
%X "... show that some large-scale deletions of the non-coding DNA referred to
   as gene deserts can be well tolerated by an organism. We deleted 2 large non
   -coding intervals, 1,511 kb & 845 kb ..., from the mouse genome. Viable mice
   homozygous for the deletions were generated & were indistinguishable from
   wild-type litter mates with regard to morphology... deleted segments harbour
   1,243 non-coding sequences conserved between humans & rodents (more than
   100 bp, 70% identity)...."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03022">doi:10.1038/nature03022</A>]['04].
   [Also search for: MolBio junk DNA].

%T Finishing the euchromatic sequence of the human genome
%Q Int. Human Genome Sequencing Consortium
%J Nature
%V 431
%P 931-945
%M OCT
%D 2004
%K jrnl, HUGO, sequencing, chromosomes, map, maps, gene, genes, DNA, build35,
   nuclear, nGenome, man, homo sapiens, primate, MolBio, biol, biology,
   c2004, c200x, c20xx
%X "... (Build 35) contains 2.85 billion nucleotides interrupted by only 341
   gaps. It covers 99% of the euchromatic genome and is accurate to an error
   rate of 1 event per 100,000 bases. Many [remaining] gaps are associated with
   segmental duplications and will require focused work with new methods. The
   near-complete sequence, the 1st for a vertebrate, greatly improves the
   precision of biological analyses of the human genome including studies of
   gene number, birth and death. Notably, the human enome seems to encode
   only 20,000-25,000 protein-coding genes. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03001">doi:10.1038/nature03001</A>]['04].
   ("24 human chromosomes having accession numbers NC000001 to NC000024")
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05].

%A X. She
%A et al
%T Shotgun sequence assembly and recent segmental duplications within the
   human genome
%J Nature
%V 431
%P 927-930
%M OCT
%D 2004
%K jrnl, HUGO, DNA, genomes, whole shotgun, WGS, repeats, duplication,
   repetitive, sequencing, clone, clones, MolBio
%X "...genomes are now being sequenced at an accelerated pace primarily using
   whole-genome shotgun (WGS) sequence assembly approaches. WGS assembly was
   initially criticized because of its perceived inability to resolve repeat
   structures within genomes. Here, we quantify the effect of WGS sequence
   assembly on large, highly similar repeats by comparison of the segmental
   duplication content of two different human genome assemblies. Our analysis
   shows that large ( > 15 kb) and highly identical ( > 97%) duplications are
   not adequately resolved by WGS assembly. This leads to significant reduction
   in genome length and the loss of genes embedded within duplications.
   Comparable analyses of mouse genome assemblies confirm that strict WGS
   sequence assembly will oversimplify our understanding of mammalian genome
   structure and evolution; a hybrid strategy using a targeted clone-by-clone
   approach to resolve duplications is proposed."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03062">doi:10.1038/nature03062</A>]['04].

%A J. A. M. Graves
%A J. M. Watson
%A F. Grutzner
%T Mitotic chromosomes of the platypus (Ornithorhynchus anatinus,
   order Monotremata of Mammalian subclass Prototheria)
%B Mammalian Chromosome Atlas
%E S.J. O'Brien
%D 2004 in press
%K biol, MolBio, biology, chromosome, genome, genomes, mammal, mammals,
   monotreme, monotremes, marsupial, marsupials, Australia
%X from HGM2004 Poster 308
   "...monotreme chromosomes remain deeply puzzling. Karyotypes of both sexes
   were claimed to contain a set of chrs for which no homologues could
   be identified. At m. meiosis these presumably translocated chrs
   assemble in a multivalent chain involving the X chr. Such a system of
   translocation heterozygosity is unprecedented in vertebrates, although
   similar systems are found naturally in some plants & a few social insects.
   ... we have generated chr paints for 20 platypus chrs &
   hybridised these paints on m. & f. metaphase chrs as well as meiotic
   cells & sperm. Five paints show a different hybridisation pattern on m. & f.
   chrs. Four chrs (including the X) were identified that are
   present in one copy in m. & in two copies in f.. Additionally, four m.-
   specific chrs have been identified that detect no homologues in f.,
   but share sequences with other unpaired chrs. One of these has
   complete homology to the short arm of the X. BAC clones from one of the m.
   specific chrs contain m.-specific sequences. Position of these
   chrs at different meiotic stages revealed a consistent order of
   chrs within the meiotic chain. Co-localisation of these elements on
   mature sperm provides the first direct evidence that two different sperm
   types are produced as a result of alternate segregation in platypus."
   -- [<A HREF="http://hgm2004.hgu.mrc.ac.uk/Abstracts/Publish/WorkshopPosters/WorkshopPosters12/hgm308.html">hgm2004</A>][10/'04],
   -- [<A HREF="http://www.rsbs.anu.edu.au/Publications/index.asp">rsbs.anu.edu.au/Publications</A>]['04],
   -- [<A HREF="http://www.rsbs.anu.edu.au/profiles/jenny_graves/">profiles/jenny_graves</A>]['04],
   Also see [<A HREF="http://www.newscientist.com/news/news.jsp?id=ns99996568">NewSci</A>][10/'04].
   [Also search for: marsupial MolBio].

%A F. Grutzner
%A W.Rens, E.Tsend-Ayushi, N.El-Mogharbel,
   P.C.M. O'Brien, R.C.Jones, M.Ferguson-Smith
%A J. A. M. Graves
%T In the platypus a meiotic chain of ten sex chromosomes shares genes with
   the bird Z and mammal X chromosomes
%J Nature
%V 432
%N 7019
%P 913-916
%M DEC
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, mammal, marsupial, monotreme, platypus,
   X chromosome, genome, female, male, sex, X, Y, Z, xxxxx, yyyyy, meiosis,
   meiotic chains, sperm, bird, birds, avian, biol, biology, evolution,
   Australia, chrX, Xchr, chrZ, Zchr
%X "...Karyotypes of males, or of both sexes, were claimed to contain several
   unpaired chromosomes (including the X chr) that form a multi-chromosomal
   chain at meiosis. Such meiotic chains exist in plants & insects but are rare
   in vertebrates. How the platypus chr system works to determine sex & produce
   balanced gametes has been controversial for decades. ...demonstrate that
   platypus have five male-specific chrs (Y chrs) & five chrs present in one
   copy in males & two copies in females (X chrs). These ten chrs form a
   multivalent chain at male meiosis, adopting an alternating pattern to
   segregate into XXXXX-bearing & YYYYY-bearing sperm. Which, if any, of
   these sex chrs bears one or more sex-determining genes remains unknown. The
   largest X chr, with homology to the human X chr, lies at one end of the
   chain, & a chr with homology to the bird Z chr lies near the other end.
   This suggests an evolutionary link between mammal & bird sex chr systems,
   which were previously thought to have evolved independently."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03021">doi:10.1038/nature03021</A>][24/10/'04 online].
   [Also search for: marsupial MolBio].

%A D. C. Walker
%A J. Southgate
%A G.Hill, M.Holcombe, D.R.Hose, S.M.Wood, S.MacNeil, R.H.Smallwood
%T The Epitheliome: modelling the social behaviour of cells
%J Biosystems
%V 76
%N 1-3
%P 89-100
%D 2004
%K uniSheffield, UK, biol, biology, emergent, cell, behaviour, bioinformatics,
   agent based modelling, agents, modeling, model, models, c2004, c200x, c20xx,
   skin cell, simulation
%X [<A HREF="http://www.dcs.shef.ac.uk/~dawn/research/agent4.pdf">pp.pdf@dcs.shef.ac.uk</A>][11/'04],
      [<A HREF="http://epi1.shef.ac.uk/">epi1.shef.ac.uk</A>]['06].

%A D. C. Walker
%A S. M. Wood
%A R. H. Smallwood,  J. Southgate
%T Agent-based computational modeling of epithelial cell monolayers: Predicting
   the effect of exogenous calcium concentration on the rate of wound closure
%J IEEE Trans. in NanoBioscience
%V 3
%N 3
%P 153-163
%D 2004
%K uniSheffield, jrnl, MolBio, biol, biology, bioinformatics, cells, behaviour,
   agents, model, agent, modelling, wounds, c2004, c200x, c20xx, skin,
   epitheliome, monoloayer, mono layer, urothelial, simulation
%X [<A HREF="http://www.dcs.shef.ac.uk/~dawn/research/walker_southgate.pdf">pp.pdf@.dcs.shef.ac.uk</A>][11/'04].
   "...and compared the results to experimental observations made on real
   urothelial monlayers carried out @ Jack Birch Unit, U. York, U.K..."
   -- [<A HREF="http://epi1.shef.ac.uk/">epi1.shef.ac.uk</A>]['06].

%A A. M. Denli
%A B. B. J. Tops
%A R. H. A. Plasterk,  R. F. Ketting,  G. J. Hannon
%T Processing of primary microRNAs by the Microprocessor complex
%J Nature
%V ?
%N ?
%P ?-?
%M ?
%D 2004
%K jrnl, biol, biology, micro RNA, miRNA, Drosha, pash1, let7, dcr-1, drsh1
%X online 7 Nov 2004; [<A HREF="http://dx.doi.org/10.1038/nature03049">doi:10.1038/nature03049</A>][11/'04].
  "Mature microRNAs (miRNAs) are generated via a two-step processing pathway to
  yield 22-nucleotide small RNAs that regulate gene expression at the post-
  transcriptional level.  ..."

%A H. Pearson
%T Mouse sequencing plan aims to boost models (news)
%J Nature
%V 432
%N 5
%P 5
%M NOV
%D 2004
%K mouse, genome, genomes, disease, gene, genes
%X "Efforts to find genes involved in human disease are set to benefit from a
   plan to sequence the genetic code of 15 different mouse strains. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/432005a">doi:10.1038/432005a</A>][11/'04].

%A M. Stomp
%A J. Huisman et al
%T Adaptive divergence in pigment composition promotes phytoplankton
   biodiversity
%J Nature
%V 432
%P 104
%M NOV
%D 2004
%K jrnl, phyto-plankton, diversity, biol, biology, evolution, competition,
   picocyanobacteria
%X "...diversity of the phytoplankton has puzzled biologists for decades. ...
   enlarged rather than solved by the progressive discovery of new phototrophic
   microorganisms in the oceans, including picocyanobacteria, pico-eukaryotes,
   and bacteriochlorophyll-based and rhodopsin-based phototrophic bacteria.
   ... analysed competition for light between 2 closely related
   picocyanobacteria ...  Here we report theory & competition experiments that
   reveal stable coexistence of the two picocyanobacteria owing to partitioning
   of the light spectrum. Further competition experiments with a 3rd marine
   cyanobacterium, ... this species persists by investing in the pigment that
   absorbs the colour not used by its competitors. ... demonstrate the adaptive
   significance of divergence in pigment composition of phototrophic
   microorganisms, which allows an efficient utilization of light energy and
   favours species coexistence."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03044">doi:10.1038/nature03044</A>][11/'04].

%A G. Manzini
%A M. Rastero
%T A simple and fast DNA compressor
%J SPE
%V 34
%N 11
%P 1397-1411
%D 2004
%K jrnl, SPE, MolBio, compress, compression, c2004, c200x, c20xx, approximate,
   encoding, exact repeat, repeats
%X "...DNA sequences ... contain substrings which are duplicated except for a
   few random mutations. For this reason most DNA compressors work by searching
   & encoding approx. repeats. We depart from this strategy by searching &
   encoding only exact repeats. However, we use an encoding designed to take
   advantage of the possible presence of approximate repeats. ... leads to an
   alg. which is an order of magnitude faster than any other alg. & achieves a
   compression ratio v. close to the best DNA compressors. Another important
   feature of our algorithm is its small space occupancy which makes it
   possible to compress sequences hundreds of megabytes long, well beyond the
   range of any previous DNA compressor."   [online Aug 2004].
   -- [<A HREF="http://dx.doi.org/10.1002/spe.619">doi:10.1002/spe.619</A>]['04],
      [<A HREF="http://www.mfn.unipmn.it/~manzini/dnacorpus/SF_DNA_Comp.pdf">pp.pdf@mfn.unipmn.it</A>]['04].
   Claim good compression @ 2 micro-sec/byte(?) 1GHz P3.  Block B=20, hash,
   greedy, left to right, mutated copies ~ close blocks.
   [Also search for: compress MolBio].

%A A. Hategan
%A I. Tabus
%T Protein is compressible
%J Proc. 6th Nordic Signal Processing Symp. (NORSIG)
%W Espoo, Finland
%P 192-195
%M JUN
%D 2004
%K NORSIG, NORSIG6, MolBio, compression, compress, proteins, incompressible,
   ProtComp, amino acid, acids, c2004, c200x, c20xx, BW, Adjeroh, Nan
%X "... alg. is adaptive, such that it can become efficient for compressing
   a proteome, i.e. the ensemble of all protein seqs. of a certain organism.
   ... prot. seqs. possess stat. relevant regularities ..."
   2-pass.  Quotes a ratio of 1.3:1 for certain data-set.
   [Also see: protein is incompressible c1999],<!-- email cpy mid Dec 2004 -->
   -- [<A HREF="https://www.researchgate.net/profile/Ioan-Tabus/publication/4095934_Protein_Is_Compressible/links/56d9866808aebabdb">res'gate</A>]['22],
      [<A HREF="/~lloyd/tildeMisc/Local/2004-norsig.pdf">local only</A>][12/'04],
   isbn:9512270315. [<A HREF="http://sigwww.cs.tut.fi/~tabus/">~tabus</A>]['04].
   (*NB. Some of these numbers are rather "surprising"...
         "Note that an incorrect protein corpus that was more compressible
         somehow got into circulation at some point, resulting in sig. lower
         compression figures being reported by ProtComp (Hategan & Tabus, 2004)
         & BW (Adjeroh & Nan, 2006). The compression results of ProtComp on the
         correct protein corpus were obtained from the author's website. The
         authors of BW have 'moved to new projects' (Nan, 2006) so proper
         compression results for BW are not available." -- MDC *)
   [Also search for: MolBio protein compression].

%A S. A. Russell
%A W. Old
%A K. A. Resing
%A L. Hunter
%T Proteomic informatics
%J Int. Review of Neurobiology
%I Elsevier
%P 127-157
%V 61
%D 2004
%K MolBio, bioinformatics, proteins, protein, c2004, c200x, c20xx, chapter,
   LHunter, uniColorado, proteomics
%X [<A HREF="http://dx.doi.org/10.1016/S0074-7742(04)61006-3">doi:10.1016/S0074-7742(04)61006-3</A>]['04]. isbn:0123668638.

%A J. Parkinson
%A A. Anthony
%A J.Wasmuth,  R.Schmid,  A.Hedley,  M.Blaxter
%T PartiGene - constructing partial genomes
%J J. Bioinformatics
%V 20
%N 9
%P 1398-1404
%M JUN
%D 2004
%K jrnl, MolBio, EST, ESTs, uniEdinburgh
%X "... (ESTs) offer a low-cost ... The challenge lies in processing &
   organizing this data within a genomic context [for] large scale analyses.
   ... (1) process raw trace chromatograms into seq. objects suitable for
   submission to dbEST; (2) place these sequences within a genomic context;
   (3) perform customizable 1st-pass annotation of the data; & (4) present the
   data as HTML tables and an SQL database resource. ..." [Bio, Edinb, UK]
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/20/9/1398">abs</A>]['04].

%A J. Martin
%A et al
%T The sequence and analysis of duplication-rich human chromosome 16
%J Nature
%V 432
%P 988-994
%M DEC
%D 2004
%K jrnl, chr 16, chr16, duplicate, repeat, repeats, HUGO, c2004, c200x, c20xx,
   chromosomes, metallothionein, cadherin, iroquois, family, families, genome
%X "Human chr. 16 features one of the highest levels of segmentally duplicated
   sequence among the human autosomes. We report here the 78,884,754 base pairs
   of finished chr. 16 seq., representing over 99.9% of its euchromatin. Manual
   annotation revealed 880 protein-coding genes confirmed by 1,670 aligned
   transcripts, 19 transfer RNA genes, 341 pseudogenes & three RNA pseudogenes.
   These genes include metallothionein, cadherin & iroquois gene families, as
   well as the disease genes for polycystic kidney disease & acute
   myelomonocytic leukaemia. Several large-scale structural polymorphisms
   spanning hundreds of kilobase pairs were identified & result in gene content
   differences among humans. Whereas the segmental duplications of chr. 16 are
   enriched in the relatively gene-poor pericentromere of the p arm, some are
   involved in recent gene duplication & conversion events that are likely to
   ... impact on the evolution of primates & human disease susceptibility."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03187">doi:10.1038/nature03187</A>]['04].

%A G. Jasienska
%A A. Ziomkiewicz
%A P.T.Ellison
%A S. F. Lipson
%A I. Thune
%T Large breasts and narrow waists indicate high reproductive potential in women
%J Proc. Biological Sci.
%I Royal Soc.
%V 271
%N 1545
%P 1213-1217
%M JUN
%D 2004
%K biol, fertility, c2004, c200x, c20xx, attractiveness, beauty, waist, hip,
   hips, ratio, WHR, breast, 17 beta oestradiol, E2, oestrogen, selection, mate
%X "Physical characteristics, such as breast size & waist-to-hip ratio (WHR),
   function as important features used by human males to assess female
   attractiveness. Males supposedly pay attention to these features because they
   serve as cues to fecundity & health. Here, we document that women with higher
   breast-to-underbreast ratio (large breasts) & women with relatively low WHR
   (narrow waists) have higher fecundity as assessed by precise measurements of
   daily levels of 17-beta-oestradiol (E2) & progesterone. Furthermore, women
   who are characterized by both narrow waists & large breasts have 26% higher
   mean E2 & 37% higher mean mid-cycle E2 levels than women from three groups
   with other combinations of body-shape variables, i.e. low WHR with small
   breasts & high WHR with either large or small breasts. Such gains in hormone
   levels among the preferred mates may lead to a substantial rise in the
   probability of conception, thus providing a significant fitness benefit."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2004.2712">doi:10.1098/rspb.2004.2712</A>]['04].

%A E. M. Weston
%A A. E. Friday
%A R. A. Johnstone
%A F. Schrenk
%T Wide faces or large canines? The attractive versus the aggressive primate
%J Biology Letters
%I Royal Soc. Publ.
%V 271
%N S6
%P S416 - S419
%M DEC
%D 2004
%K jrnl, biol, beauty, homonid, dimorphism, c2004, c200x, c20xx, statistics,
   stats, shape, face, facial, width, broad, sex, sexual, selection, evolution,
   canine teeth, primates, human, anthropoid, attractiveness, mate, zz0105
%X "Hominids display marked body size dimorphism, suggestive of strong sexual
   selection, yet they lack significant sex differences in canine size that are
   commonly associated with intrasexual competition in primates. We resolve
   this paradox by examining sex differences in hominoid facial morphology. We
   show that chimpanzees, but not gorillas, exhibit clear sexual dimorphism in
   face width over & above that expected based on sex differences in body size.
   We show that this facial dimorphism, expressed as an index, is negatively
   correlated with canine dimorphism among anthropoid primates. Our findings
   suggest that a lack of canine dimorphism in anthropoids is not owing to weak
   sexual selection, but rather is associated with strong sexual selection for
   broader face width. Enlarged cheekbones are linked with attractiveness in
   humans, & we propose that the evolution of a broad face & loss of large
   canines in hominid males results from mate choice."
   -- [<A HREF="http://dx.doi.org/10.1098/rsbl.2004.0203">doi:10.1098/rsbl.2004.0203</A>]['04].

%A M. A. Harris
%A et al (!)
%Q The Gene Ontology Consortium.
%T The Gene Ontology (GO) database and informatics resource
%D 2004
%J NAR
%V 32
%P D258-D261
%M JAN
%D 2004
%K MolBio, NAR, data base, geneOntology, c2004, c200x, c20xx, genes,
   molecular function, biological process,  cellular component, protein,
   proteins, family, families, terms, biology, biol
%X "... provides structured, controlled vocabularies & classifications that
   cover several domains of molecular & cellular biology & are freely available
   for community use in the annotation of genes, gene products & sequences..."
   -- [<A HREF="http://www.geneontology.org/">www</A>]['05],
      [<A HREF="http://www.geneontology.org/GO.biblio.html">bib</A>]['05].

%A M. Li
%A B. Ma
%A D. Kisman
%A J. Tromp
%T PatternHunter II: Highly sensitive and fast homology search
%J J. Bioinformatics and Comp. Biol.
%V 2
%N 3
%P 417-439
%M SEP
%D 2004
%X jrnl, MolBio, c2004, c200x, c20xx, DNACompress, pattern hunter, patterns
%X [<A HREF="http://www.bioinformaticssolutions.com/literatures/04ph2.pdf">04ph2.pdf</A>]['05] also see 2OO2.
   [Also search for: spaced seed].

%A U. Keich
%A M. Li
%A B. Ma
%A J. Tromp
%T On spaced seeds for similarity search
%J Discrete Applied Math.
%V 138
%N 3
%P 253-263
%D 2004
%K jrnl, PatternHunter, MolBio, seed, heuristic, approximate, matching,
   c2004, c200x, c20xx, spaced, gapped, seeds
%X [<A HREF="http://www.bioinformatics.uwaterloo.ca/papers/04seeds.pdf">04seeds.pdf</A>]['05].
   -- [<A HREF="http://www.cs.cornell.edu/~keich/">keich@cs.corne11</A>]['05].
   [Also search for: PatternHunter],  [also search for: spaced seed].

%A T. J. Harlow
%A J. P. Gogarten
%A M. A. Ragan
%T A hybrid clustering approach to recognition of protein families in
   114 microbial genomes
%J BMC Bioinformatics
%V 5
%N 45
%M APR
%D 2004
%K eJrnl, MolBio, family, c2004, c200x, c20xx, microbe, bacteria, sequence,
   family, Markov cluster, link, MCL, uniQld
%X "...Standard clustering methods such as single-linkage clustering capture a
   history of cluster topologies as a function of threshold, but in practice
   their usefulness is limited because unrelated sequences join clusters before
   biologically meaningful families are fully constituted, e.g. as the result
   of matches to so-called promiscuous domains. Use of the Markov Cluster alg.
   avoids this non-specificity, but does not preserve topological or threshold
   information about protein families...."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-5-45">doi:10.1186/1471-2105-5-45</A>]['05],
      [<A HREF="http://www.biomedcentral.com/1471-2105/5/45">txt</A>]['05].
   M.A.R. @ UQ, '05.
   [Also search for: single link].

%A J. Ravela
%A R. Raina
%A S.Y.Rhee, J.M.Schapiro, R.W.Shafer
%T Probabilistic graphical models for prediction of HIV-1 drug resistance
   mutations based on antiretroviral treatment history.
%J 13th Int. HIV Drug Resistance Workshop
%W Tenerife
%M JUN
%D 2004
%K wShop, HIV, HIV1, RT, aids, c2004, c200x, c20xx, model, mutation, medical,
   MolBio, HIVdb, genotype, genotypic, phenotype, phenotypic,
   antiretrovirus, anti-retroviral, zzVDRL
%X "...A simple probabilistic graphical model predicts the presence of drug-
   resistance mutations with an accuracy of approximately 75%. Models that
   contain interactions among drugs and among mutations are under development.
   Algs. based on these models may be used to supplement drug susceptibility
   results in persons with complicated treatment histories for whom
   susceptibility testing often underestimates the extent of resistance. ..."
   -- [<A HREF="http://www.aegis.com/conferences/hivdrw/2004/110.html">abs 110</A>]['06],
      [<A HREF="http://www.informedhorizons.com/resistance2004/Posters/POSTERS/Shafer_RavelaPoster.pdf">poster</A>]['06],
      [<A HREF="http://www.aegis.com/conferences/13thHIVDrugResWkshop/110.html">abs</A>]['05], and
      [<A HREF="http://hivdb.stanford.edu/">hivdb</A>]['05].

%A A. P. Jackson
%A M. A. Charleston
%T Cophylogenetic perspective of RNA - virus evolution
%J Molec. Biol. and Evol.
%V 21
%N 1
%P 45-57
%D 2004
%K jrnl, MBE, MolBio, c2004, c200x, c20xx, cophylogeny, coevolution,
   TreeMap, congruence, cospeciation, switching, parasite, host, Hantavirus,
   Spumavirus, avian sarcoma leukosis, Lyssavirus, Arenavirus, uniSydney
%X "The extent to which viruses & their hosts codiverge remains an open Q., ...
   DNA viruses that form persistent infections are thought to be the most
   likely candidates for phylogenetic congruence. Phylogenetic reconciliation
   analysis was used to compare established phylogenies for 4 RNA viruses &
   their hosts. ... TreeMap v2.0, to find the most parsimonious combinations
   of evolutionary events able to reconcile any incongruence. ... guaranteed
   to recover all potentially optimal solutions to the reconciled tree & ...
   Phylogenies for Hantavirus, Spumavirus, & avian sarcoma leukosis virus were
   found to be significantly similar to their host trees, whereas Lyssavirus &
   Arenavirus displayed no significant congruence. ... RNA viruses are able to
   form stable associations with their hosts ..."    M.C. @ uniSydney ['05]
   -- [<A HREF="http://dx.doi.org/10.1093/molbev/msg232">doi:10.1093/molbev/msg232</A>]['05].

%A F. Tacke
%A C. Gehrke
%A T.Luedde, A.Heim, M.P.Manns, C.Trautwein
%T Basal core promoter and precore mutations in the hepatitis B virus genome
   enhance replication efficacy of Lamivudine-resistant mutants.
%J J. Virol
%V 78
%N 16
%P 8524-8535
%M AUG
%D 2004
%K jrnl, mutation, hepatitis B, hepatitisB, hep, hepB, c2004, c200x, c20xx,
   MolBio, medicine, viral, HBV, HBeAg, chronic, Lamivudine, Adefovir,
   drug resistance
%X "During chronic hepatitis B virus (HBV) infection, mutations in the
   precore (PC) or basal core promoter (BCP) region affecting HBV e antigen
   (HBeAg) expression occur commonly & represent the predominant virus species
   in patients with HBeAg-negative chronic hepatitis B. The PC mutation
   (G1896A+C1858T) creates a translational stop codon ... Adefovir may be an
   effective treatment when combinations of core & polymerase mutations occur."
   -- [<A HREF="http://dx.doi.org/10.1128/JVI.78.16.8524-8535.2004">doi:10.1128/JVI.78.16.8524-8535.2004</A>]['05],
      [<A HREF="http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15280461">pub med</A>]['05].

%A A. Ayres
%A S. Locarnini
%A A. Bartholomeusz
%T HBV genotyping and analysis for unique mutations
%B Methods Mol. Med.
%I Humanapress
%S Methods in Molecular Medicine
%V 95(1)
%P 125-149
%M JAN
%D 2004
%K eBook, c2004, c200x, c20xx, hepatitis, HBV, retro-virus, viral, zzVDRL,
   reverse transcriptase, polymerase gene, HBeAg, drug resistance, mutation,
   genotype, antiviral
%X "... mutations selected during antiviral therapy. ... reverse transcriptase
   region of the polymerase gene, in particular the catalytic domains A-E. ..."
  [<A HREF="http://biomed.humanapress.com/ChapterDetail.pasp?isbn=1-59259-669-X&ccode=1-59259-669-X:125">@humanapress</A>]['05] ?buy?, isbn:159259669X.
  auths @ vidrl / melb h

%A F. Wightman
%A T. Walters
%A A.Ayres,  S.Bowden,  A.Bartholomeusz,  D.Lau,  S.Locarnini,  S.R.Lewin
%T Comparison of sequence analysis and a novel discriminatory real-time
   PCR assay for detection and quantification of Lamivudine-resistant
   hepatitis B virus strains.
%J J. Clin. Microbiol.
%V 42
%N 8
%P 3809-3812
%M AUG
%D 2004
%K jrnl, HBV, c2004, c200x, c20xx, viral, strain, primer, drug, test
%X "... PCR-based method to quantify wild-type & lamivudine-resistant [HBV] by
   using a common forward primer paired with different reverse primers. ..."
   -- [<A HREF="http://dx.doi.org/10.1128/JCM.42.8.3809-3812.2004">doi:10.1128/JCM.42.8.3809-3812.2004</A>]['05];  TW,AA,SB,AB,SL @ vidrl/melb-h

%A M. S. S. Chang
%A S. A. Benner
%T Empirical analysis of protein insertions and deletions determining
   parameters for the correct placement of gaps in protein sequence alignments
%J J. Molec. Biol
%V 341
%N 2
%P 617-631
%M AUG
%D 2004
%K jrnl, JMB, MolBio, c2004, c200x, c20xx, protein, insertion, deletion, indel,
   indels, gap, length, lengths, gaps, sequence, alignment
%X "To understand how protein segments are inserted & deleted during divergent
   evolution, a set of pairwise alignments contained exactly one gap, &
   therefore arising from the first ins.-delins. (indel) event in the time
   separating the homologs, was examined. [they] showed that 'structure
   breaking' AAs (PGDNS) were preferred within & flanking gapped regions, as are
   two residues with hydrophilic side-chains (QE) that freq. occur at the
   surface of p.folds. Conversely, hydrophobic residues (FMILYVW) occur infreq.
   within & flanking the gapped region. These preferences are modestly different
   in p.pairs sep. by an episode of adaptive evoln, than in pairs diverging
   under strong functional constraints. Surprisingly, regions near an indel have
   not evolved more rapidly than the seq. pair overall, showing no evidence that
   an indel event must be compensated by local AA replacement. The gap-lengths
   are best approx'd by a Zipfian distn, with the prob. of a gap of length L
   decreasing as a function of L^(-1.8). These features are largely indep. of
   the length of the gap & the extent of divergence (measured by both silent &
   non-silent sequence changes) separating the two proteins. Surprisingly, AA
   repeats were discovered in more than a third of the polypeptide segments in &
   around the gap. These corr. to repeats in the DNA seq.. This suggests that a
   signature of the mechanism by which indels occur in the DNA seq. remains in
   the encoded p. seqs.. These data suggest specific tools to score gap
   placement in an alignment. They also suggest tools that distinguish true
   indels from gaps created by mistaken gene finding, inc. under-predicted &
   over-predicted introns. By providing mechanisms to identify errors, the tools
   will enhance the value of genome seq. DBs in support of integrated
   paleogenomics strategies used to extract functional information in a
   post-genomic environment."
   -- [<A HREF="https://doi.org/10.1016/j.jmb.2004.05.045">doi:10.1016/j.jmb.2004.05.045</A>]['18],
   abs@[<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/15276848">p'bm'd</A>]['18].
   [Note, "exactly one gap", "L^(-1.8)".]
   [Also search for: MolBio protein indels].

%A S. Locarnini
%T Relevance of HBV mutations in severity and progression of chronic
   hepatitis B.
%J J. Gastroenterology and Hepatology
%V 19
%P S108-S112
%D 2004
%K c2004, c200x, c20xx, HBV, quasispecies, biol, medical, mutation, virus, viral
%X "... lack of proof-reading capability, mutant viral genomes or quasispecies,
   emerge frequently. ... selection pressures, both endogenous (host immune
   clearance) & exogenous (vaccines & antiviral drugs) readily select out ..."
   -- [<A HREF="http://www.apaslindia2004.com/pdf/proceeding/JGH3655.pdf">pdf</A>]['05] auth@vidrl

%A Y. L. Orlov
%A V. N. Potapov
%T Complexity: An internet resource for analysis of DNA sequence complexity
%J NAR
%V 32
%P ?-?
%M JUL
%D 2004
%K MolBio, NAR, c2004, c200x, c20xx
%X "...low complexity may be preconditioned by strong inequality in nucleotide
   content (biased composition), by tandem or dispersed repeats or by
   palindrome-hairpin structures, [&] a combination of all these factors. ..."
   [Also search for: DNA complexity] and [also search for: MolBio compression].

%A D. Ganem
%A A. M. Prince
%T Hepatitis B virus infection - natural history and clinical consequences
%J New England J. Med.
%V 350
%N 11
%P 1118-1129
%M MAR
%D 2004
%K jrnl, NEJM, c2004, c200x, c20xx, MolBio, HBV, health, zzVDRL, health,
   medical, medicine, disease, guide, intro, life cycle
%X "In the past 10 y., remarkable strides have been made in the understanding
   of the natural history & pathogenesis of [HBV] infection. ... review these
   adv., with particular reference to the implications for antiviral therapy."
   -- [<A HREF="http://content.nejm.org/cgi/content/full/350/11/1118">nejm</A>]['06].

%A R. J. Boys
%A D. A. Henderson
%T A Bayesian approach to DNA sequence segmentation
%J Biometrics
%V 60
%N 3
%P 573-581
%M SEP
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, DNA, segment, bacteriophage lambda
%X "... compositional heterogeneity in the form of segments of similar
   structure. ... describes a Bayesian method that identifies such segments by
   using a Markov chain governed by a hidden Markov model. Markov chain Monte
   Carlo (MCMC) techniques are employed to compute all posterior quantities of
   interest & in particular, allow inferences to be made regarding the # of
   segment types & the order of Markov dependence in the DNA seq.. ... applied
   to the segmentation of the bacteriophage lambda genome, a common benchmark
   sequence used for the comparison of statistical segmentation algorithms."
   -- [<A HREF="http://dx.doi.org/10.1111/j.0006-341X.2004.00206.x">doi:10.1111/j.0006-341X.2004.00206.x</A>]['05].
   [Also search for: segmentation]

%A J-Y. Lee
%A S. Locarnini
%T Hepatitis B virus: pathogenesis, viral intermediates and viral replication
%J Clinics in Liver Disease
%I Elsevier
%V 8
%P 301-320
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, zzVDRL, HBV, intermediate, life cycle
%X "... potential to generate an almost limitless spectrum of quasispecies
   during chronic infection, the viability of the majority of these
   quasispecies is almost certainly impaired due to constraints imposed by the
   remarkably compact organization of the HBV genome. On the other hand, single
   mutations may affect more than one gene & result in complex & unpredictable
   effects on viral phenotype. ..."      issn:1089-3261.
   auths @ vidrl.

%A A. Bartholomeusz
%A B. G. Tehan
%A D. K. Chalmers
%T Comparisons of the HBV and HIV polymerase, and antiviral resistance
   mutations.
%J Antivir. Ther.
%P 9
%N 2
%P 149-160
%M APR
%D 2004
%K jrnl, c2004, c200x, c20xx, virus, viral, HBV, MolBio

%A A. Bartholomeusz
%A S. Schaefer
%T Hepatitis B virus genotypes: comparison of genotyping methods
%J Rev. Med. Virol.
%V 14
%N 1
%P 3-16
%M JAN
%D 2004
%K jrnl, c2004, c200x, c20xx, MolBio, HBV, genotype, genotypes, method, viral,
   hepadnaviruses, hepadnavirus
%X "...eight genotypes of HBV designated A to H based on greater than 8%
   nucleotide variation over the entire genome. Hepadnaviruses infecting
   primates like the chimpanzee, orangutan and gibbon are very similar and
   can be regarded as genotypes of HBV. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/rmv.400">doi:10.1002/rmv.400</A>]['06].
   auth1 @ vidrl.

%A S. Locarnini
%T Molecular virology of hepatitis B virus
%J Seminars in Liver Disease
%V 24 (Suppl 1)
%P 3-10
%D 2004
%K c2004, c200x, c20xx, HBV, MolBio, zzVDRL, viral, biol, biology, host,
   parasite
%X "... evolved a unique life cycle that results in the production of enormous
   viral loads during active replication without actually killing the infected
   cell directly. Because HBV uses reverse transcription to copy its DNA genome,
   mutant viral genomes emerge frequently. Particular selection pressures, both
   endogenous (host immune clearance) and exogenous (vaccines and antiviral
   drugs), readily select out these escape mutants. Which particular viral
   mutations or combination of mutations directly affect the clinical outcome
   of infection are not known. ..."
   -- [<A HREF="http://dx.doi.org/10.1055/s-2004-828672">doi:10.1055/s-2004-828672</A>]['06].

%A X. Lu
%A T. Block
%T Study of the early steps of the Hepatitis B Virus life cycle
%J Int. J. Med. Sci.
%V 1
%N 1
%P 21-33
%D 2004
%K jrnl, HBV, c2004, c200x, c20xx, DHBV, WHBV, SPIK, HepG2, biol, medical,
   viral
%X "... most of the early steps in the virus life cycle remain unclear. ..."
   -- [<A HREF="http://www.medsci.org/v01p0021">paper</A>]['05],
      [<A HREF="http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1074507">pubmedc.</A>]['05].

%A J. M. Keith
%A P. Adams
%A D.Bryant, D.A.E.Cochran, G.H.Lala, K.R.Mitchelson
%T Algorithms for sequence analysis via mutagenesis
%J J. Bioinformatics
%V 20
%N 15
%P 2401-2410
%D 2004
%K jrnl, algorithm, SAM, MolBio, c2004, c200x, c20xx, uniQld
%X "... The essential idea of SAM is to infer the target seq. using the seqs.
   of mutants derived from the target. ... 3 algs. used in this process. The
   1st alg. predicts the number of mutants that will be required to infer the
   target seq. with a desired level of accuracy. The 2nd alg. infers the target
   sequence itself, using the mutant sequences. The 3rd alg. assigns quality
   values to each inferred base. ..."
   "...mutation alters the DNA in such a way that the characteristics causing
   sequencing difficulties are not present in (some of) the mutants. ..." p2402
  [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bth258">doi:10.1093/bioinformatics/bth258</A>]['05].

%A A. Siepel
%A D. Haussler
%T Computational identification of evolutionarily conserved exons
%J Proc. 8th Annual Int. Conf. on Res. in Computational Molecular Biology
%P 177-186
%D 2004
%K conf, MolBio, c2004, c200x, c20xx, phylo-HMM, phyloHMM, exon, gene, genes,
   prediction, DNA
%X "... (phylo-HMMs) have recently been proposed as a means for addressing a
   multi-species version of the ab initio gene prediction problem. These models
   allow sequence divergence, a phylogeny, patterns of substitution, & base
   composition all to be considered simultaneously, in a single unified
   probabilistic model. Here, we apply phylo-HMMs to a restricted version of
   the gene prediction problem in which individual exons are sought that are
   evolutionarily conserved across a diverse set of species. We discuss 2 new
   methods for improving prediction performance: (1) the use of context-
   -dependent phylo. models, which capture phenomena such as a strong CpG
   effect in noncoding regions & a preference for synonymous rather than
   nonsynonymous substitutions in coding regions; & (2) a novel strategy for
   incorporating insertions & deletion (indels) into the state-transition
   structure of the model, ..."
   -- [<A HREF="http://doi.acm.org/10.1145/974614.974638">doi:10.1145/974614.974638</A>]['06].

%A V. V. Kapitonov
%A A. Pavlicek
%A J. Jurka
%T Anthology of human repetitive DNA
%J Encyclopedia of Molecular Cell Biology and Molecular Medicine
%V 1
%P 251-305
%I Wiley
%D 2004
%K MolBio, c2004, c200x, c20xx, repeat, repeats, low information content, DNA,
   repetitive element, elements
%X [Also search for: RepBase MolBio],
   -- [<A HREF="http://www.girinst.org/repbase/">repbase</A>]['06].
   [Also search for: repetitive DNA].

%A K. Takahashi
%A K. Kaizu
%A B. Hu
%A M. Tomita
%T A multi-algorithm, multi-timescale method for cell simulation
%J J. Bioinformatics
%V 20
%N 4
%P 538-546
%D 2004
%K jrnl, MolBio, Ecell, e-cell, c2004, c200x, c20xx, cells, simulate,
   sub-cellular, model, modelling
%X "... important problems in cell biology require the dense nonlinear
   interactions between functional modules to be considered.  ...  The utility
   of this simulation framework is demonstrated further with a 'composite'
   heat-shock response model that combines the Gillespie-Gibson stochastic
   algorithm and deterministic differential equations. Dramatic improvements in
   performance were obtained without significant accuracy drawbacks. A
   multi-timescale demonstration of coupled harmonic oscillators is also shown."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btg442">doi:0.1093/bioinformatics/btg442</A>]['07],
      [<A HREF="http://www.e-cell.org/">e-cell.org</A>]['07].

%A K. Jabbari
%A G. Bernardi
%T Cytosine methylation and CpG, TpG (CpA) and TpA frequencies
%J Gene
%V 26
%N 333
%P 143-149
%M MAY
%D 2004
%K jrnl, MolBio, CpG, TpG, DNA, c2004, c200x, c20xx, genomes, isochores,
   C-value, body temperature, methylation, zz0407
%X "... dinucleotide freq. ... DNAs from insects & mammals, [&] large DNA seqs.
   from ... Drosophila melanogaster, Anopheles gambiae, puffer fish (Takifugu
   rubripes), zebra fish (Danio rerio) & human.  ... chosen because Drosophila &
   Anopheles DNAs have an extremely low level of methylation, human DNA a high
   level & fish DNA a 2-fold higher level compared to human. ...
   (i) CpG deficiency & the corr. TpG (CpA) excess show no correlation with the
   level of DNA methylation; indeed, genomes endowed with strikingly different
   levels of DNA methylation (such as those of Drosophila & human) exhibited
   similar TpG (CpA) levels;  (ii) the correlation between GC levels of large
   (50 kb) DNA seqs. & TpA or CpG shortage levels do not appear to be due to CpG
   methylation followed by deamination;  (iii) CpG dinucleotides are more
   frequent in fishes than in mammals; interestingly, the monotreme
   Ornitorhinchus anatinus shows an intermediate CpG freq ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.gene.2004.02.043">doi:10.1016/j.gene.2004.02.043</A>]['07].

%A S. Kurtz
%A A. Phillippy
%A A. L. Delcher
%A M. Smoot
%A M. Shumway
%A C. Antonescu
%A S. L. Salzberg
%T Versatile and open software for comparing large genomes
%J Genome Biol.
%N 5:R12.
%D 2004
%K MolBio, c2004, c200x, c20xx, zz0408, genome, alignment, comparison,
   MUMmer 3, MUMmer3
%X "The newest version of MUMmer easily handles comparisons of large eukaryotic
   genomes at varying evolutionary distances, as demo. by applic. to multiple
   genomes. 2 new graphical viewing tools provide alt. ways to analyze genome
   alignments. The new system is the 1st version of MUMmer to be released as
   open-source s/w. This allows other developers to contribute to the code base
   & freely redistribute the code. The MUMmer sources are available at..."
   mummer@[<A HREF="http://mummer.sourceforge.net/">sourcefor...</A>]['08].
   [Also search for: MolBio genomic distance].

%A D. W. Mount
%T Bioinformatics: Sequence and Genome Analysis
%I Cold Spring Laboratory Press
%P 692
%D 2004
%K book, text, MolBio, c2004, c200x, c20xx, gene, strings, sequences, L5Ref,
   DNA
%X pb us$95; us isbn:0879697121; us isbn13:978-0879697129.
   [Also search for: MolBio book].

%A O. Delgrange
%A E. Rivals
%T STAR: an algorithm to search for tandem approximate repeats
%J J. Bioinformatics
%V 20
%N 16
%P 2812-2820
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, DNA, tandem repeat, TR, ATR,
   low information, sequence, information
%X "... an exact algorithm to locate approximate tandem repeats (ATR) of a motif
   in a DNA sequence. Given a motif and a DNA sequence, our method named STAR,
   identifies all segments of the sequence that correspond to significant
   approximate tandem repetitions of the motif ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bth335">doi:10.1093/bioinformatics/bth335</A>]['08].
   [Also search for: tandem repeat].

%A E. Rivals
%T A survey on algorithmic aspects of tandem repeats evolution
%J Int. J. of Foundations of Comp. Sci.
%V 15
%N 2
%P 225-257
%D 2004
%K jrnl, IJFCS, MolBio, c2004, c200x, c20xx, DNA, tandem repeat
%X [<A HREF="http://www.lirmm.fr/~rivals/ALGOSEQ/DOC/TREvolSurvey.pdf">pdf</A>]['08].
   [Also search for: tandem repeat].

%A E. Almaas
%A B. Kovacs
%A T. Vicsek
%A Z. N. Oltvai
%A A.-L. Barabasi
%T Global organization of metabolic fluxes in the bacterium Escherichia coli
%J Nature
%V 427
%P 839-843
%M FEB
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, flux, metabolic pathway, pathways,
   network, Ecoli, bacterium, bacterial, graph, graphs
%X "... activity of the metabolism is dominated by several reactions with very
   high flux.  E.coli responds to change in growth condns by reorg. the rates of
   selected fluxes predominantly within the high flx backbone.  ... probably...
   a universal feature of met. act. in all cells ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature02289">doi:10.1038/nature02289</A>]['08].
   -- [<A HREF="http://www.nd.edu/%7Ealb/Publication06/111%20Global%20organization%20of%20metabolic%20fluxes%20in%20the%20bacterium%20Escherichia%20coli/Escherichia_Nature%20427,%20839-843%20(2004).pdf">pdf@nd</A>]['08].
   -- [<A HREF="http://www.nd.edu/~alb/">A-L.B@nd</A>]['08].
   [Also search for: Barabasi graph].

%A R. C. Edgar
%T MUSCLE: multiple sequence alignment with high accuracy and high throughput
%J NAR
%V 32
%N 5
%P 1792-1797
%D 2004
%K jrnl, NAR, MolBio, c2004, c200x, c20xx, protein, clustal, clustalw,
   PREFAB, MAFFT, alignment, quality, benchmark, benchmarks
%X "... multiple alignments of protein seqs.. Elements of the alg. inc. fast
   distance estimation using kmer counting, progressive alignment using a new
   profile function we call the log-expectation score, & refinement using tree-
   -dependent restricted partitioning. The speed & accuracy of MUSCLE are
   compared with T-Coffee, MAFFT & CLUSTALW on 4 test sets of ref, alignments:
   BAliBASE, SABmark, SMART & a new benchmark, PREFAB. MUSCLE achieves the
   highest, or joint highest, rank in accuracy on each of these sets. Without
   refinement, MUSCLE achieves average accuracy statistically indistinguishable
   from T-Coffee & MAFFT, & is the fastest of the tested methods for large
   # of seqs., aligning 5000 seqs. of avg, length 350 in 7min on a [desktop]."
   -- [<A HREF="http://nar.oxfordjournals.org/cgi/content/full/32/5/1792?ijkey=48Nmt1tta0fMg&keytype=ref">paper</A>]['07],
      [<A HREF="http://www.drive5.com/muscle/">muscle</A>]['07],
      [<A HREF="http://www.drive5.com/muscle/prefab.htm">PREFAB</A>]['07].

%A M. J. Buck
%A J. D. Lieb
%T ChIP-chip: Considerations for the design, analysis, and application of
   genome-wide chromatin immunoprecipitation experiments
%J Genomics
%V 83
%N 3
%P 349-360
%M MAR
%D 2004
%K jrnl, MolBio, c2004, c200x, c200x, ChIP-chip, ChIPchip, protein, DNA,
   binding site, sites, ChIP, microarray, microarrays, review, intro, survey
%X "Chromatin immunoprecipitation (ChIP) is a well-established procedure used to
   investigate interactions between proteins and DNA. Coupled with whole-genome
   DNA microarrays, ChIPs allow one to determine the entire spectrum of in vivo
   DNA binding sites for any given protein. The design and analysis of
   ChIP-microarray (also called ChIP-chip) experiments differ significantly from
   the conventions used for more traditional microarray experiments that measure
   relative transcript levels. Furthermore, fundamental differences exist
   between single-locus ChIP approaches and ChIP-chip experiments, and these
   differences require new methods of analysis. In this light, we review the
   design of DNA microarrays, the selection of controls, the level of repetition
   required, and other critical parameters for success in the design and
   analysis of ChIP-chip experiments, especially those conducted in the context
   of mammalian or other relatively large genomes."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ygeno.2003.11.004">doi:10.1016/j.ygeno.2003.11.004</A>]['08].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/ChIP-on-chip">wikip</A>]['08].)

%A N. M. Luscombe
%A M. M. Babu
%A H. Yu
%A M. Snyder
%A S. A. Teichmann
%A M. Gerstein
%T Genomic analysis of regulatory network dynamics reveals large topological
   changes
%J Nature
%V 431
%P 308-312
%M SEP
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, networks, change, gene, transcription,
   factor, factors, hub, hubs, SIM, yeast, Saccharomyces cerevisiae,
   cell life cycle, sporulation, diauxic shift, DNA damage, stress response,
   transcription, network, data, regulation, regulatory, network, data,
   SANDY, viaAK
%X "... present the dynamics of a biol. n/w on a genomic scale, by integrating
   transcriptional regulatory information & gene-expression data for multiple
   conditions in Saccharomyces cerevisiae. ... uncover large changes in
   underlying n/w architecture that are unexpected given current viewpoints &
   random simulations. In response to diverse stimuli, transcription factors
   alter their interactions to varying degrees, thereby rewiring the n/w. A few
   TFs serve as permanent hubs, but most act transiently only during certain
   conditions. By studying sub-n/w structures, we show that environmental
   responses facilitate fast signal propagation (for example, with short
   regulatory cascades), whereas the cell cycle & sporulation direct temporal
   progression through multiple stages (for example, with highly
   inter-connected transcription factors). ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature02782">doi:10.1038/nature02782</A>]['08],
   abs@[<A HREF="http://www.nature.com/nature/journal/v431/n7006/abs/nature02782.html">jrnl</A>]['14].
   (Includes cell cycle, ..., stress response networks.)
   Also see [<A HREF="http://sandy.topnet.gersteinlab.org/index2.html">gersteinlab</A>]['15].
   [Also search for: MolBio network].

%A D. Raoult
%A S. Audic
%A C. Robert
%A C. Abergel
%A P. Renesto
%A H. Ogata
%A B. La Scola
%A M. Suzan
%A J.-M. Claverie
%T The 1.2-megabase genome sequence of mimivirus
%J Science
%V 306
%N 5700
%P 1344-1350
%M NOV
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, mimivirus, big, large, giant, mega, virus,
   mimi, Acanthamoeba polyphaga mimivirus, APMV, nucleocytoplasmic, NCLDVs,
   megavirus, viruses, viral, genome, genes, mRNA
%X "... 1,181,404-bp genome seq., consisting of 1262 putative ORFs, 10% of which
   exhibit a similarity to proteins of known fns. ... [and] Mimivirus exhibits
   many features that distinguish it from other nucleocytoplasmic large DNA
   viruses. The most unexpected is the presence of numerous genes encoding
   central protein-translation components, inc. 4 amino-acyl transfer RNA
   synthetases, peptide release factor 1, translation elongation factor EF-TU,
   & translation initiation factor 1. The genome also exhibits six tRNAs. ..."
   [maybe 900+ genes]
   -- [<A HREF="http://dx.doi.org/10.1126/science.1101485">doi:10.1126/science.1101485</A>]['08].
   (Also see news@[<A HREF="http://dx.doi.org/10.1126/science.335.6072.1035">doi:10.1126/science.335.6072.1035</A>]['12].)
   [Also search for: mimivirus].

%A B. Raphael
%A D. Zhi
%A H. Tang
%A P. Pevzner
%T A novel method for multiple alignment of sequences with repeated and
   shuffled elements
%J Genome Res.
%V 14
%N 11
%P 2336-2346
%M NOV
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, multiple, sequence, shuffled, reordered,
   POA, partial, partially ordered alignment
%X "We describe ABA (aBruijn alignment), a new method for multiple alignment
   of biological seqs.. ... ABA represents an alignment as a directed graph,
   possibly containing cycles. ... provides more flexibility than does a
   traditional alignment matrix or the recently introduced partial order
   alignment (POA) graph by allowing a larger class of evol.relationships
   between the aligned seqs.. Our graph representation is particularly well-
   -suited to the alignment of protein seqs. with shuffled &/or repeated domain
   structure, & allows one to construct multiple alignments of proteins
   containing (1) domains that are not present in all proteins, (2) domains that
   are present in different orders in different proteins, & (3) domains that are
   present in multiple copies in some proteins. [And] ABA is useful in the
   alignment of genomic seqs. that contain duplications & inversions. ..."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.2657504">doi:10.1101/gr.2657504</A>]['11].

%A J. S. Mattick
%T Opinion: RNA regulation: a new genetics?
%J Nature Reviews Genetics
%V 5
%P 316-323
%M APR
%D 2004
%K opinion, MolBio, c2004, c200x, c20xx, non coding DNA, RNA, RNAs, ncRNA,
   ncRNAs, miRNA, siRNA, gene, control, regulation, signalling, gene, genes,
   organism complexity, C-value paradox
%X "Do non-coding RNAs that are derived from the introns & exons of protein-
   -coding & non-protein-coding genes represent a fundamental advance in the
   genetic operating system of higher organisms? Recent evidence from
   comparative genomics & molecular genetics indicates that this might be the
   case. If so, there will be profound consequences for our understanding of the
   genetics of these organisms, & in particular how the trajectories of
   differentiation & development & the differences among individuals & species
   are genomically programmed. But how might this hypothesis be tested?"
   "... Prokaryotes have < 25% non-coding DNA, simple eukaryotes have between
   25 & 50% non-coding DNA & more complex fungi, plants & animals have > 50%,
   rising to ~ 98.5% ... in humans ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nrg1321">doi:10.1038/nrg1321</A>]['08].
   (Also see A.Poole, corr., [<A HREF="http://dx.doi.org/10.1038/nrg1321-c1">doi:10.1038/nrg1321-c1</A>]['08],
   which has a graph with extra genomes added, two having ~ 60K genes.)

%A A. Sandelin
%A W. Wasserman
%T Constrained binding site diversity within families of transcription factors
   enhances pattern discovery bioinformatics
%J J. Mol. Biol.
%V 338
%N 2
%P 207-215
%M APR
%D 2004
%K jrnl, JMB, MolBio, c2004, c200x, c20xx, transcription factor, binding site,
   sites, factors, TFBS, TFBSs, family, families, JASPAR, database
%X "... introduce a new direction ... based on the constraints imposed by the
   structures of DNA-binding proteins. For most structurally related families of
   transcription factors, there are clear similarities in the seqs. of the sites
   to which they bind. ... construct familial binding profiles for well-
   -characterized transcription factor families. The profiles are shown to
   classify correctly the structural class of mediating TFs for novel motifs in
   88% of cases. By incorporating the familial profiles into pattern discovery
   procedures ... functional binding sites can be found in genomic sequences of
   dramatically greater length than is possible otherwise. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jmb.2004.02.048">doi:10.1016/j.jmb.2004.02.048</A>]['09].
   Also see [<A HREF="http://jaspar.cgb.ki.se/">JASPAR</A>]['09].

%A P. M. K. Gordon
%A C. W. Sensen
%T Osprey: A comprehensive tool employing novel methods for the design of
   oligonucleotides for DNA sequencing and microarrays
%J NAR
%V 32
%N 17
%P e133
%D 2004
%K NAR, jrnl, MolBio, c2004, c200x, c20xx, DNA, PCR, primer, primers,
   design, designing, inSilico
%X "... s/w package called Osprey for the calc. of optimal oligonucleotides
   for DNA sequencing & the creation of microarrays based on either PCR-products
   or directly spotted oligomers. ... position-specific scoring matrices, for
   the sensitive & specific identification of 2ndry binding sites anywhere in
   the target seq..  ... reflects current DNA thermodynamics models, improves
   specificity & reduces the user's data preprocessing & parameterization
   requirements. Using a TimeLogic h/w accelerator ... up to 50-fold [faster]
   v. a linear search ..."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gnh127">10.1093/nar/gnh127</A>]['09],
   osprey@[<A HREF="http://osprey.ucalgary.ca/">uCalgary</A>].
   [Also search for: MolBio PCR primer],
   primers@[<A HREF="http://en.wikipedia.org/wiki/Primer_(molecular_biology)">wikip</A>]['09].

%A C. Hertz-Fowler
%A et al
%T GeneDB: A resource for prokaryotic and eukaryotic organisms
%J NAR
%V 32
%P D339-D343
%D 2004
%K NAR, jrnl, MolBio, c2004, c200x, c20xx, GeneDB, gene, database, genes, DB,
   organism
%X "... a genome DB for prokaryotic & eukaryotic organisms. ... provides a
   portal through which data generated by the Pathogen Sequencing Unit at the
   Wellcome Trust Sanger Institute & other ...  available. It combines data from
   finished & ongoing genome & expressed sequence tag (EST) projects with
   curated annotation, that can be searched, ..."       [in DataBase issue].
   -- [<A HREF="http://www.genedb.org/">genedb</A>]['09].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Metabolic_network_modelling">wikip</A>].)

%A S. Bennett
%T Solexa Ltd
%J Pharmacogenomics
%V 5
%N 4
%P 433-438
%M JUN
%D 2004
%K MolBio, c2004, c200x, c20xx, Solexa, Illumina, DNA, sequencing technology,
   short read, reads, sequence
%X "Solexa Ltd is developing an integrated sys., based on a breakthrough single
   molecule seq. tech., ... The sys., s/ware & consumables will initially be
   sold to research orgs., pharmaceutical co.s & diagnostic co.s that will
   sequence large regions of genomic DNA, inc. whole genomes, at costs several
   orders of magnitude < current levels. Solexa expects to launch its 1st
   product in '06, & as it continues to make time & cost efficiencies,
   additional products will be launched into the expanding markets that will
   have broad applic'ns in basic research through to healthcare mngmt."
   -- [<A HREF="http://dx.doi.org/10.1517/14622416.5.4.433">doi:10.1517/14622416.5.4.433</A>]['09],
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/15165179">ncbi</A>]['09].
   "Effective January 26, '07, Solexa is now part of Illumina."
   -- [<A HREF="http://www.illumina.com/pagesnrn.ilmn?ID=222">illumina.com</A>]['09],
    &  [<A HREF="http://en.wikipedia.org/wiki/Illumina_(company)">wikip</A>]['09].
   [Also search for: short read MolBio].

%A S. L. Salzberg
%A D. Church
%A M. DiCuccio,  E. Yaschenko,  J. Ostell
%T The genome assembly archive: A new public resource
%J PLoS Biol.
%V 2
%N 9
%P e285
%M SEP
%D 2004
%K MolBio, bioinformatics, data base, database, c2004, c200x, c20xx, zz1104,
   jrnl, sequence assembly, shotgun sequencing, consensus, archives, alignment,
   Trace Archive, Assembly Archive, information
%X "... genomes of an ever-growing list of species, ranging from small viruses,
   ... a few thousand nucleotides in length, to large mammalian genomes,
   3 billion nucleotides & larger. ... but decoded genomes could be even more
   valuable if important information about the genome sequence, currently being
   lost, were preserved. Occasionally questions arise about a specific position
   in the sequence or a variant in the sequence is observed in a new sample ...
   Without really being aware of it, the bioinformaticians who assemble genomes
   have for years been discarding the valuable information on how all of the
   individual sequence fragments align to the assembled chromosomes. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pbio.0020285">doi:10.1371/journal.pbio.0020285</A>][11/'04].
   [PLoS -- Pub1ic Lib of Sci, open-access, peer review].

%A R. C. Gentleman
%A et al ...
%A J. Zhang
%T Bioconductor: open software development for computational biology and
   bioinformatics
%J Gen. Biol.
%V 5
%P #R80
%M SEP
%D 2004
%K jrnl, eJrnl, MolBio, c2004, c200x, c20xx, zz0121, Bioconductor, software
%X "... an initiative for the collaborative creation of extensible software for
   computational biology and bioinformatics. ..."
   -- [<A HREF="https://doi.org/10.1186/gb-2004-5-10-r80">doi:10.1186/gb-2004-5-10-r80</A>]['21].
   Also see BC@[<A HREF="https://en.wikipedia.org/wiki/Bioconductor">wikip</A>]['21].

%A M. Chaisson
%A P. Pevzner
%A H. Tang
%T Fragment assembly with short reads
%J J. Bioinformatics
%V 20
%N 13
%P 2067-2074
%M SEP
%D 2004
%K jrnl, c2004, c200x, c20xx, MolBio, short read, reads, sequence assembly,
   assembler, DNA
%X "Current DNA seq. tech. ... reads ~ 500-750 bp, with typical coverage < 10x.
   New s.t. are emerging that produce shorter reads (len. 80-200bp) but ...
   sig. higher coverage (30x +) at low cost. Modern assembly programs & error
   correction routines have been tuned to work well with current read tech. but
   were not designed for assembly of short reads. ... analyze the limitations of
   assembling reads generated by these new technologies & present a routine for
   base-calling in reads prior to their assembly. ... while it is feasible to
   assemble such short reads, the resulting contigs will require sig. (if not
   prohibitive) finishing efforts. ..."
   pdf@[<A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/13/2067">bioin</A>]['09],
   s/w@[<A HREF="http://www.cse.ucsd.edu/groups/bioinformatics/software.htm">ucsd</A>]['04],
   and [<A HREF="http://euler-assembler.ucsd.edu/portal/">ucsd</A>]['09].
   [Also search for: short read MolBio] and
   [also search for: sequence assembly MolBio].

%A N. Kashtan
%A S. Itzkovitz
%A R. Milo
%A U. Alon
%T Efficient sampling algorithm for estimating subgraph concentrations and
   detecting network motifs
%J J. Bioinformatics
%V 20
%N 11
%P 1746-1758
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, viaAK, sample, sampling, Mfinder,
   subgraph, subgraphs, graphs, networks, motif
%X "... present a novel alg. that allows estimation of subgraph concentrations
   & detection of network motifs at a runtime that is asymptotically independent
   of the n/w size. This alg. is based on random sampling of subgraphs. Network
   motifs are detected with a surprisingly small number of samples in a wide
   variety of n/ws. ... can be applied to est. the concentrations of larger
   subgraphs in larger n/ws than was previously possible with exhaustive
   enumeration algs.. We present results for high-order motifs in several
   biological networks & discuss their possible functions."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bth163">doi:10.1093/bioinformatics/bth163</A>].
   (Also see motifs@[<A HREF="http://en.wikipedia.org/wiki/Network_motif">wikip</A>]['15].)
   [Also search for: subgraph sampling].

%A C. Bachmann-Waldmann
%A S. Jentsch
%A H. Tobler
%A F. Muller
%T Chromatin diminution leads to rapid evolutionary changes in the organization
   of the germ line genomes of the parasitic nematodes A. suum and P. univalens
%J Molec. and Biochem. Parasitol.
%V 134
%N 1
%P 53-64
%M MAR
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, parasite, nematode, worm, Ascaris suum,
   Parascaris equorum var. univalens, parasitic roundworm, DNA breakage,
   Chromatin diminution, single chromosome, pair
%X "Chromatin diminution in the parasitic nematodes Ascaris suum & Parascaris
   univalens represents a rather complex molecular phenomenon that includes
   chromosomal breakage, DNA degradation & new telomere formation. At a given
   elimination site, DNA breakage & new telomere addition does not take place at
   a single chromosomal locus but at many different places within a several
   kilobase long chromosomal region, referred to as chromosomal breakage region
   (CBR). ... present a hypothesis stating that the elimination process ensures
   the maintenance of a functional somatic genome & concomitantly allows
   extremely rapid & profound changes in the germ line genome, thereby allowing
   the development of new germ line specific functions & thus providing a
   selective advantage for the chromatin eliminating nematodes during further
   evolution."
   -- [<A HREF="http://dx.doi.org/10.1016/j.molbiopara.2003.11.001">doi:10.1016/j.molbiopara.2003.11.001</A>]['10],
   & [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/14747143">pub med</A>]['10].
   ([Also search for: Myrmecia pilosula] for which 2n=2.)

%A K. Ohara
%A T. Yoshida
%A W. Geamsakul
%A H. Motoda
%A T. Washio
%A H. Yokoi
%A Katsuhiko Takabayashi
%T Analysis of hepatitis dataset by decision tree graph-based induction
%J Discovery Challenge Workshop
%P 173-184
%D 2004
%K wShop, c2004, c200x, c20xx, hepatitis, MolBio, Dtree
%X Revised version:
   "A machine learning technique called Graph-Based Induction (GBI) efficiently
   extracts typical patterns from graph-structured data by stepwise pair
   expansion (pairwise chunking). ... greedy search. ... graph-structured data.
   ... classification tasks of a real world hepatitis data. ...  decision trees
   to classify 1) cirrhosis & non-cirrhosis (Exp.1 & 2), 2) type C & type B
   (Exp.3), & 3) +ve & -ve responses of interferon (Exp. 4).  ... (Exp.5) ...
   extract descriptive patterns for interferon therapy. ..."  [via MikeD].
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-71009-7_2">doi:10.1007/978-3-540-71009-7_2</A>]['09].

%A Qi-Shi Du
%A et al ...
%A Kuo-Chen Chou
%T Polyprotein cleavage mechanism of SARS CoV Mpro and chemical modification of
   the octapeptide
%J Peptides
%V 25
%N 11
%P 1857-1864
%M NOV
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, zz0720, KuoChenChou, SARS CoV 1, SARSCoV,
   SARSCoV1, SARS1, Mpro, protease, protein, mechanism, cleave, cleaves,
   cleaving, polyprotein, octaprotein, octapeptide, AVLQSGFR,
   3CLpro, His41, Cys, Cys145, active site, sites, distorted key, working, works
%X "The cleavage mechanism of severe acute respiratory syndrome (SARS)
   coronavirus main proteinase (Mpro or 3CLpro) for the octapeptide AVLQSGFR ...
   The catalytic dyad His-41 & Cys-145 in the active pocket between domain I
   & II seem to polarize the pi-electron density of the peptide bond between
   Gln & Ser ..."    [cleaves after the 'Q'}.
   -- [<A HREF="https://doi.org/10.1016/j.peptides.2004.06.018">doi:10.1016/j.peptides.2004.06.018</A>]['20].
   [Also search for: KuoChenChou] & [also search for: MolBio SARS Mpro cleaves].

%T Sequence and comparative analysis of the chicken genome provide unique
   perspectives on vertebrate evolution
%Q Int. Chicken Genome Seq. Consortium
%J Nature
%V 432
%P 695-716
%M DEC
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, chicken, genome, nGenome, Gallus gallus,
   bird, birds, avian, amniote, red jungle fowl,
   macrochromosome, microchromosome
%X "... draft genome seq. of the red jungle fowl, Gallus gallus. ...
   modern descendant of the dinosaurs & the first non-mammalian amniote to have
   its genome sequenced, ... approximately one billion [bp] of seq. & an est.
   20,000-23,000 genes ...
   sizes of c.chromosomes, which span a range of nearly 2 orders of magnitude
   ... chicken karyotype (2n=78) ... 38 autosomes & 1 pair of sex chrs., with
   the female as the heterogametic sex (ZW female, ZZ male ...
   project accession # AADN00000000. ... the 1st version AADN01000000."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03154">doi:10.1038/nature03154</A>]['09],
   also see chicken@[<A HREF="http://www.ncbi.nlm.nih.gov/genome/guide/chicken/">ncbi</A>]['09].

%A F. Dupuis
%A J.-F. Sadoc
%A J.-P. Mornon
%T Protein secondary structure assignment through Voronoi tesselation
%J Proteins: Struct., Function and Bioinf.
%V 55
%P 519-528
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, protein, VoTAP, polyhedron, polyhedra,
   3D Voronoi tesselation, contacts, contact matrices, DSSP, STRIDE
%X "... new automatic alg., named VoTAP ... which assigns secondary structures
   of a polypeptide chain using the list of alpha-carbon coords.. ... uses
   3D Voronoi tessellation. This geometrical tool associates with each a.a. a
   V. polyhedron, the faces of which unambiguously define contacts b/ween
   residues. Thanks to the face area, for the contacts close together along the
   primary structure (low-order contacts) a distinction is made b/ween strong &
   normal ones. This new defn yields new contact matrices, which are analyzed &
   used to assign sec.structs.. ... is performed in 2 stages. The first one uses
   contacts between residues close together along the primary struct. & is based
   on data collected on a bank of 282 well-refined nonredundant structs.. ...
   associations were made between the prints defined by these low-order contacts
   & the assignments performed by different automatic methods. The 2nd step
   focuses on the strand assignment & uses contacts b/ween distant residues.
   Comparison with several other automatic assignment methods are presented, &
   the influence of resolution on the assignment is investigated."
   -- [<A HREF="http://dx.doi.org/10.1002/prot.10566">doi:10.1002/prot.10566</A>]['11].

%A J. W. Fondon III
%A H. R. Garner
%T Molecular origins of rapid and continuous morphological evolution
%J PNAS
%V 101
%N 52
%P 18058-18063
%M DEC
%D 2004
%K PNAS, jrnl, c2004, c200x, c20xx, cis regulatory, dog breed, dogs, breeds,
   skull, measurements, skulls, ALX4, Runx2, Dlx2, genotype, phenotype
%X "Mutations in cis-regulatory seqs. ... implicated as being the predominant
   source of var'n in morphological evolution. We offer a hypothesis that
   gene-assoc. tandem repeat expansions & contractions are a major source of
   phenotypic variation in evolution. ... comparative genomic study of
   repetitive elts in dev.genes of 92 breeds of dogs. We find evidence
   for sel'n for divergence at coding repeat loci in the form of both elevated
   purity & extensive length polymorphism among different breeds. ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0408118101">doi:10.1073/pnas.0408118101</A>]['09].

%A B. Libet
%T Mind Time: The Temporal Factor in Consciousness
%I HarvardUP
%P 272
%D 2004
%K book, text, c2004, c200x, c20xx, free will, consciousness, mind, brain, self,
   awareness, unconsciousness
%X 1st ed 2004; hb us$20; isbn:0674013204; uk us isbn13:978-0674013209.
       pb 2005, pb us$20; uk us isbn:067401846X; uk us isbn13:978-0674018464.
   "Our subjective inner life is what really matters to us as human beings - &
   yet we know relatively little about how it arises. ... experiments that have
   helped us see, in clear & concrete ways, how the brain produces conscious
   awareness. ... Most notably, L's experiments reveal a substantial delay -
   the 'mind time' of the title - before any awareness affects how we view our
   mental activities. If all conscious awarenesses are preceded by unconscious
   processes, as L observes, we are forced to conclude that unconscious
   processes initiate our conscious experiences. Freely voluntary acts are found
   to be initiated unconsciously before an awareness of wanting to act - a
   discovery with profound ramifications for our understanding of free will..."

%A S. E. Boyd
%A M. Garcia de la Banda
%A R. N. Pike
%A J. C. Whisstock
%A G. B. Rudy
%T PoPS: A computational tool for modeling and predicting protease specificity
%J Proc. IEEE Comput. Syst. Bioinf. Conf.
%P 372-381
%D 2004
%K Boyd, MonashUni, conf, MolBio, c2004, c200x, c20xx, zz0820, PoPS, protease,
   proteinase, peptidase, substrate, specificity, cleave
%X "... we present PoPS, a publicly accessible bio'nf. tool
   [pops.csse.monash.edu.au] which provides a novel method for building
   comp. models of protease specificity that, while still being based on these
   amino acid seqs., can be built from any experimental data or expert knowledge
   available to the user ..."
   -- [<A HREF="http://dx.doi.org/10.1109/csb.2004.1332450">doi:10.1109/csb.2004.1332450</A>]['20].
   (Also see [<A HREF="https://doi.org/10.1142/s021972000500117x">JBCB_'05</A>]['20].)

%T The Cancer Genome Atlas
%D 2005
%K TCGA, NCI, MolBio, c2005, c200x, c20xx, zz0820, cancer, cell, cells, data,
   stats, genomic, epigenomic, transcriptomic, proteomic, dataBase
%X [<A HREF="https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga">TCGA</A>]['20],
   TCGA@[<A HREF="https://en.wikipedia.org/wiki/The_Cancer_Genome_Atlas">wikip</A>]['20].

%A C. Kosiol
%A N. Goldman
%T Different versions of the Dayhoff rate matrix
%J Mol. Biol. Evol.
%V 22
%N 2
%P 193-199
%M FEB
%D 2005
%K jrnl, MBE, MolBio, c2005, c200x, c20xx, zz0519, protein, PAM, rate, matrix,
   evolution, substitution
%X "Many phylogenetic inference methods are based on Markov models of seq.
   evolution. ... usually expressed in terms of a matrix (Q) of instantaneous
   rates of change but some models of AA replacement, most notably the PAM model
   of Dayhoff & c., were originally published only in terms of time-dependent
   prob.matrices (P(t)). Prev. published methods for deriving Q have used
   eigen-decomposition of an approximation to P(t). We show that the commonly
   used value of t is too large to ensure convergence of the ests. of elts of Q.
   We describe two simpler alternative methods for deriving Q from information
   such as that published by D. & c.. Neither of these methods requires
   approximation or e.-decomp.. We identify the methods used to derive various
   different versions of the D.model in current s/w, perform a comparison of
   existing & new implementations, &, to facilitate agreement among scientists
   using supposedly identical models, recommend that one of the new methods be
   used as a standard."
   -- [<A HREF="https://doi.org/10.1093/molbev/msi005">doi:10.1093/molbev/msi005</A>]['19].
   [Also search for: MolBio substitution matrix].

%A Y.-K. Yu
%A S. F. Altschul
%T The construction of amino acid substitution matrices for the comparison of
   proteins with non-standard compositions
%J Bioinformatics
%V 21
%N 7
%P 902-911
%M APR
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, zz0419, protein, substitution matrix,
   bias, PAM, BLOSUM
%X "... It has been argued elsewhere that standard matrices are not ideal for
   such comparisons &, furthermore, a rationale has been presented for
   transforming a std matrix for use in a non-std compositional context. ...
   presents the mathematical details underlying the compositional adjustment of
   amino acid or DNA substitution matrices. ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/bti070">doi:10.1093/bioinformatics/bti070</A>]['19].
   [Also search for: MolBio substitution matrix].

%A J. Soding
%T Protein homology detection by HMM-HMM comparison
%J Bioinformatics
%V 21
%N 7
%P 951-960
%M APR
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, zz0618, protein, sequence, similarity,
   alignment, HHSearch, HMM, profile, PSIBLAST, HMMER, PROF_SIM, COMPASS
%X "... generalized the alignment of protein seqs. with a profile hidden
   Markov model (HMM) to the case of pairwise alignment of profile HMMs. We
   present a method for detecting distant homologous relationships between
   proteins based on this approach. The method (HHsearch) is benchmarked
   together with BLAST, PSI-BLAST, HMMER and the profile-profile comparison
   tools PROF_SIM and COMPASS, in an all-against-all comparison of a DB of 3691
   p.domains from SCOP 1.63 with pairwise sequence identities below 20%. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti125">doi:10.1093/bioinformatics/bti125</A>]['18].

%A I. Van Walle
%A I. Lasters
%A L. Wyns
%T SABmark - a benchmark for sequence alignment that covers the entire known
   fold space
%J J. Bioinformatics
%V 21
%N 7
%P 1267-1269
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, protein, folds, structure, 3D, alignment,
   quality, multiple, pairwise, benchmark, benchmarks, SCOP, twilight
%X "... sets of multiple alignment problems derived from the SCOP
   classification. These sets, Twilight Zone and Superfamilies, both both cover
   the entire known fold space using sequences with very low to low, and low to
   intermediate similarity, respectively. ..."
   -- [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/full/21/7/1267">paper</A>]['07].
   "SABmark is designed to assess the performance of both multiple and
   pairwise (protein) sequence alignment algorithms ..."
   -- [<A HREF="http://bioinformatics.vub.ac.be/databases/databases.html">SABmark</A>]['07].

%A J. Jurka
%A V. V. Kapitonov
%A A. Pavlicek
%A P. Klonowski
%A O. Kohany
%A J. Walichiewicz
%T Repbase Update, a database of eukaryotic repetitive elements
%J Cytogenetic and Genome Research
%V 110
%P 462-467
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, element, repeat, repeats, repetitive, DNA,
   low information content, region, regions, RepBase, RU, interspersed,
   transposable, zz0506
%X "Repbase Update (RU) is a database of prototypic sequences representing
   repetitive DNA from different eukaryotic species...."
   Server: [<A HREF="http://www.girinst.org/repbase/update/">www</A>]['06].
   Paper:  [<A HREF="http://dx.doi.org/10.1159/000084979">doi:10.1159/000084979</A>]['06].
   via D.P.
   [Also search for: repetitive DNA] and [also search for: tandem repeat].

%A J. D. Szustakowski
%A S. Kasif
%A Z. Weng
%T Less is more: Towards an optimal universal description of protein folds
%J ECCB
%D 2005
%O J. Bioinf., 21 (suppl. 2), ii66-ii77, 2005
%K conf, MolBio, c2005, c200x, c20xx, protein, structure, fold, fragment, motif,
   library, dictionary, superSecondary, super secondary
%X "... focus on an intermediate level of regularity. ... developed automated
   methods to systematically construct a dictionary of supersec. structs. that
   can be used as 'protein parts' to describe fold-sized structs..
   ... constructed by aligning representative structs. of all known folds,
   clustering similar substructures & selecting the most descriptive substrs. in
   a MDL fashion. We show d. is compact & descriptive, capable of describing a
   substantial fraction of all known protein folds. We performed simul'ns using
   indep. sets of training & testing folds. Dicts. generated using the training
   set had high coverage over the folds in the testing set, suggesting that
   d.entries reflect general features of protein structs. & should be capable of
   describing novel protein folds."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti1111">doi:10.1093/bioinformatics/bti1111</A>]['13].
   [Also search for: protein structure fragment library] and
   [also search for: MolBio super secondary structure].

%A S. Robbens
%A B. Khadaroo
%A A.Camasses, E.Derelle, C.Ferraz, D.Inze, Y.Van de Peer, H.Moreau
%T Genome-wide analysis of core cell cycle genes in the unicellular green alga
   Ostreococcus tauri.
%J Mol. Biol. and Evol.
%P 589-597
%V 22
%N 3
%D 2005
%K jrnl, MBE, gene, green alga,  Ostreococcus tauri, algae, algal,
   evolution, c2005, c200x, c20xx, CDK gene family, cyclin, E2F
%X "...Comparing the cell cycle across species shows that its regulation is
   evolutionarily conserved; ... describe the core cell cycle genes of O.t.,
   ... marine green alga, which has diverged at the base of the green lineage,
   shows the minimal yet complete set of core cell cycle genes described to
   date. It has only one homolog of CDKA, CDKB, CDKD, cyclin A, cyclin B,
   cyclin D, cyclin H, Cks, Rb, E2F, DP, DEL, Cdc25, & Wee1. ...also added the
   APC & SCF E3 ligases to the core cell cycle gene set. ... potential of
   genome-wide analysis in the identification of divergent orthologs of cell
   cycle genes in different lineages by mining the genomes of evolutionarily."
   -- [<A HREF="http://mbe.oxfordjournals.org/cgi/content/full/22/3/589">paper</A>]['05].

%T Artificial Intelligence Methods and Tools for Systems Biology
%I SpringerVerlag
%S Computational Biology
%N 5
%E W. Dubitzky
%E F. Azuaje
%P 221
%D 2005
%K book, bioinformatics, AI, c2005, c200x, c20xx
%X us$99; uk us isbn:1402028598; uk is isbn13:978-1402028595.

%T Bioinformatics Using Computational Intelligence Paradigms
%I SpringerVerlag
%E U. Seiffert; L. C. Jain; P.Schweizer
%S Studies in Fuzziness and Soft Computing
%V 176
%P 216
%D 2005
%K book, MolBio, c2005, c200x, c20xx
%X us$90; uk us isbn:3540229019; uk us isbn13:978-3540229018.

%A O. Misumi
%A M.Matsuzaki, H.Nozaki, S.Miyagishima, T.Mori, K.Nishida, F.Yagisawa
%A Y.Yoshida, H.Kuroiwa, T. Kuroiwa
%T Cyanidioschyzon merolae genome. A tool for facilitating comparable studies
   on organelle biogenesis in photosynthetic eukaryotes.
%J Plant Physiology
%P 567-585
%V 137
%M FEB
%D 2005
%K jrnl, MolBio, red alga, Cyanidioschyzon merolae, c2005, c200x, c20xx,
   green, Chlamydomonas reinhardtii, zz0205, algae, algal, 10D, eurkaryote,
   biol, biology, phototrophs, comparative, comparison
%X "...showed that C. merolae has a mixed gene repertoire of plants & animals,
   also implying a relationship with prokaryotes, although its photosynthetic
   components were comparable to other phototrophs. The unicellular green alga
   Chlamydomonas reinhardtii has been used as a model system for molecular
   biology research on, for example, photosynthesis, motility, & sexual
   reproduction. Though both algae are unicellular, the genome size, number of
   organelles, & surface structures are remarkably different. Here, we report
   the characteristics of double membrane- & single membrane-bound organelles &
   their related genes in C. merolae & conduct comparative analyses of
   predicted protein sequences encoded by the genomes of C. merolae & C.
   reinhardtii. We examine the predicted proteins of both algae by reciprocal
   BLASTP analysis, KOG assignment, & gene annotation. The results suggest that
   most core biological functions are carried out by orthologous proteins that
   occur in comparable numbers. Although the fundamental gene organizations
   resembled each other, the genes for organization of chromatin, cytoskeletal
   components, & flagellar movement remarkably increased in C. reinhardtii.
   Molecular phylogenetic analyses suggested that the tubulin is close to plant
   tubulin rather than that of animals & fungi. ... reflect the increase in
   genome size, the acquisition of complicated cellular structures, & kinematic
   devices in C. reinhardtii."
   -- [<A HREF="http://www.plantphysiol.org/cgi/content/abstract/137/2/567">abs</A>]['05].

%A I. K. Jordan
%A et al
%T A universal trend of amino acid gain and loss in protein evolution
%J Nature
%V 433
%N 7026
%P 633-638
%M FEB
%D 2005
%K jrnl, MolBio, proteins, acids, c2005, c200x, c20xx, zz0305, biol, biology,
   GC, AT, rich, frequency, frequencies
%X "[AA] composition of proteins varies substantially between taxa &, thus, can
   evolve. ... proteins from organisms with (G+C)-rich (or (A+T)-rich) genomes
   contain more (or fewer) AAs encoded by (G+C)-rich codons. ...no universal
   trends in ... amino acid freqs. have been reported. We compared sets of
   orthologous proteins encoded by triplets of closely related genomes from 15
   taxa representing all 3 domains of life (Bacteria, Archaea & Eukaryota), &
   used phylogenies to polarize AA subs..  Cys, Met, His, Ser & Phe accrue in
   at least 14 taxa, whereas Pro, Ala, Glu & Gly are consistently lost. The
   same nine AAs are currently accrued or lost in human proteins, as shown by
   analysis of non-synonymous single-nucleotide polymorphisms. All AAs with
   declining frequencies are thought to be among the first incorporated into
   the genetic code; conversely, all AAs with increasing freqs., except Ser,
   were probably recruited late. Thus, expansion of initially under-represented
   AAs, which began over 3,400 million years ago, apparently continues..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03306">doi:10.1038/nature03306</A>]['05].

%A K. Bisova
%A D. M. Krylov
%A J. G. Umen
%T Genome-wide annotation and expression profiling of cell cycle
   regulatory genes in Chlamydomonas reinhardtii
%J Plant Physiology
%V 137
%P 475-491
%M FEB
%D 2005
%K jrnl, gene, green alga, algae, algal, c2005, c200x, c20xx, eukaryote,
   plant, plants, RDP1, RDP2, RDP3, unicellular
%X "E. cell cycles are driven by a set of regulators that have undergone
   lineage-specific gene loss, duplication, or divergence in different taxa.
   It is not known to what extent these genomic processes contribute to
   differences in cell cycle regulatory programs & cell division mechanisms
   among different taxonomic groups. We have undertaken a genome-wide
   characterization of the cell cycle genes encoded by Chlamydomonas
   reinhardtii, a unicellular e. ... of the green algal/land plant clade. ..."
   -- [<A HREF="http://www.plantphysiol.org/cgi/content/full/137/2/475">paper</A>]['05],
      [<A HREF="http://genome.jgi-psf.org/Chlre3/Chlre3.home.html">C.reinhardtii web</A>]['07].

%A C. Gilham
%A J. Peto
%A J.Simpson, E.Roman, T.O.B.Eden, M.F.Greaves, F.E.Alexander,
%T Day care in infancy and risk of childhood acute lymphoblastic leukaemia:
   findings from UK case-control study
%J BMJ ?
%P ?-?
%D 2005
%K jrnl, BMJ, medical, acute lymphoblastic leukaemia, day care, child,
   children, childhood, disease, risk, risks, social interaction, health
%X "...Increasing levels of social activity were associated with consistent
   reductions in risk of [acute lymphoblastic leukaemia (ALL)]; a dose-response
   trend was seen. ...  Although not as striking, results for non-ALL
   malignancies showed a similar pattern (P value for trend <0.001). ...
   results support the hypothesis that reduced exposure to infection in the
   first few months of life increases the risk of developing [ALL]."
   -- online April 2005
   -- [<A HREF="http://dx.doi.org/10.1136/bmj.38428.521042.8F">doi:10.1136/bmj.38428.521042.8F</A>]['05].

%A D. W. Zaidel
%A S. M. Aarde
%A K. Baig
%T Appearance of symmetry, beauty, and health in human faces
%J Brain and Cognition
%V 57
%N 3
%P 261-263
%D 2005
%K jrnl, face, faces, beauty, c2005, c200x, c20xx, attractiveness,
   appearance, asymmetry, asymmetric
%X "Sym. is an important concept in biol., being related to mate selection
   strategies, health, & survival of species. In human faces, the relevance of
   left-right sym. to attractiveness & health is not well understood.We compared
   the appearance of facial attractiveness, health, & sym. in 3 separate
   experiments. Participants inspected front views of faces on the computer
   screen & judged them on a 5-point scale according to their attractiveness in
   Exp.1, health in Exp.2, & symmetry in Exp.3. ... that sym. & attractiveness
   were not strongly related in faces of women or men while health & sym.  were
   related. There was a significant difference between attractiveness & sym.
   judgments but not between health & sym. judgments. ...a significant diff.
   between attractiveness & health. Facial symm. may be critical for the
   appearance of health but it does not seem to be critical for the appearance
   of attractiveness, not surprisingly perhaps because human faces together
   with the h. brain have been shaped by adaptive evol. to be naturally asym."
   -- [<A HREF="http://cogprints.org/4349/">cogprints</A>]['05] 5 refs, via Ch@rles.T.

%A L. Eichinger
%A et al
%T The genome of the social amoeba Dictyostelium discoideum
%J Nature
%V 435
%P 43-57
%M MAY
%D 2005
%K jrnl, MolBio, DNA, nuclear, genome, nGenome, c2005, c200x, c20xx, zz0505,
   amoebae, unicellular, multicellular, eukaryote, repeats, AT-rich, ATrich,
   slime mold, mould
%X "The social amoebae are exceptional in their ability to alternate between
   unicellular & multicellular forms. ... approximately 12,500 pred. proteins,
   [many] of which have long, repetitive AA tracts.  ... The genome is rich
   in complex repeats, 1 class of which is clustered ... A proteome-based
   phylogeny shows that the amoebozoa diverged from the animal-fungal
   lineage after the plant-animal split, but Dictyostelium seems to have
   retained more of the diversity of the ancestral genome than have plants,
   animals or fungi."  ...
   "... total genome size is estimated at 34,042,810 bp ..."
   "... genome is (A+T)-rich (77.57%) ..."
   "Seq. data for the g. ... in GenBank [DB] ... project acc. no. AAFI00000000.
   6 chr. assemblies have acc. nos. CM000150-CM000155, & their component seq.
   contigs have acc. nos. AAFI01000001-AAFI01000336."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03481">doi:10.1038/nature03481</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05].
   [Also search for: slime mold].

%A M. Monot
%A et al
%T On the origin of Leprosy
%J Science
%V 308
%N 5724
%P 1040-1042
%M MAY
%D 2005
%K jrnl, MolBio, pseudogenes, Mycobacterium leprae, bacterium, bacteria,
   c2005, c200x, c20xx, zz0505, comparative genomics, evolution, human,
   health, disease, origins, leper, lepers
%X "Leprosy, a chronic human disease with potentially debilitating neurological
   consequences, results from infection with Mycobacterium leprae. This
   unculturable pathogen has undergone extensive reductive evolution, with half
   of its genome now occupied by pseudogenes. Using comparative genomics, we
   demonstrated that all extant cases of leprosy are attributable to a single
   clone whose dissemination worldwide can be retraced from analysis of very
   rare single-nucleotide polymorphisms. The disease seems to have originated
   in E. Africa or the Near E. & spread with successive human migrations.
   Europeans or N. Africans introduced leprosy into W. Africa and the Americas
   within the past 500y.."
   -- [<A HREF="http://dx.doi.org/10.1126/science/1109759">doi:10.1126/science/1109759</A>]['05].

%A V. Macaulay
%A C. Hill
%A et al
%T Single, rapid coastal settlement of Asia revealed by analysis of
   complete mitochondrial genomes
%J Science
%V 308
%N 5724
%P 1034-1036
%M MAY
%D 2005
%K jrnl, MolBio, mGenome, c2005, c200x, c20xx, Eve, tree, mtDNA, zz0505,
   human, origin, origins, Africa
%X "...dispersal of modern humans out of Africa... routes taken across Eurasia
   are still disputed. We show that mitochondrial DNA variation in isolated
   "relict" populations in SE Asia supports the view that there was only a
   single dispersal from Africa, most likely via a S coastal route, through
   India & onward into SE Asia & .au. There was an early offshoot, leading
   ...to the settlement of the Near E. & Europe, but the main dispersal from
   India to .au ~65,000y. ago was rapid, ...likely taking only a few 000 y.."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1109792">doi:10.1126/science.1109792</A>]['05].
   [Also search for: MolBio Eve human evolution] and the like.

%A M. J. Brauer
%A A. J. Saldanha
%A K. Dolinski
%A D. Botstein
%T Homeostatic adjustment and metabolic remodeling in glucose-limited yeast
   cultures
%J Mol. Biol. Cell
%P 2503-2517
%N 5
%V 16
%M MAY
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, zz0816, yeast, network, diauxic shift,
   glucose, sugar, culture
%X "... response to glucose limitation in batch & steady-state (chemostat) ...
   following global patterns of gene expression. ... We conclude that despite
   the theoretical possibility of a switch to fully aerobic metabolism of
   glucose in the chemostat under condns of glucose scarcity, homeostatic
   mechanisms are able to carry out metabolic adjustment as if fermentation of
   the glucose is the preferred option until the glucose is entirely depleted.
   These results suggest that some aspect of actual starvation, possibly a
   component of the stress response, may be required for triggering the
   metabolic remodeling associated with the diauxic shift."
   -- [<A HREF="http://dx.doi.org/10.1091/mbc.E04-11-0968">doi:10.1091/mbc.E04-11-0968</A>]['16].

%A W. Mair1
%A M. D. W. Piper
%A L. Partridge
%T Calories do not explain extension of life span by dietary restriction in
   drosophila
%J PLoS Biology
%V 3
%N 7
%M JUL
%D 2005
%K jrnl, life expectancy, diet, dietary, food, c2005, c200x, c20xx, fruit fly,
   sugar, yeast, restrict, restriction, biol, biology, age, ageing, lifespan,
   caloric
%X "Dietary restriction (DR) extends life span in diverse organisms, inc.
   mammals, & common mechanisms may be at work. DR is often known as calorie
   restriction, because it has been suggested that reduction of calories,
   rather than of particular nutrients in the diet, mediates extension of life
   span in rodents. We here demonstrate that extension of life span by DR in
   Drosophila is not attributable to the reduction in calorie intake. Reduction
   of either dietary yeast or sugar can reduce mortality & extend life span, but
   by an amount that is unrelated to the calorie content of the food, & with
   yeast having a much greater effect per calorie than does sugar. Calorie
   intake is therefore not the key factor in the reduction of mortality rate by
   DR in this species."   55 refs.
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pbio.0030223">doi:10.1371/journal.pbio.0030223</A>]['05].

%T Bioinformatics Technologies
%E Y-P. P. Chen
%I SpringerVelag
%P 396
%D 2005
%K book, text, technology, MolBio, c2005, c200x, c20xx
%X ... describes the application of well-established concepts & techniques from
   areas like data mining, machine learning, database technologies, &
   visualization techniques to problems like protein data analysis, genome
   analysis & sequence databases. ...   (Ed.@deakin '05)
   eur70; uk us isbn:3540208739; uk us isbn13:978-3540208730.

%A A. R. Sikder
%A A. Y. Zomaya
%T An overview of protein-folding techniques: issues and perspectives
%J Int. J. Bioinformatics Res. and Applications (IJBRA)
%V 1
%N 1
%P 121-143
%D 2005
%K survey, intro, introduction, fold, structure prediction, MolBio,
   c2005, c200x, c20xx, uniSydney
%X "... This survey presents the state-of-the-art in protein structure
   prediction methods from a computer scientist perspective."

%A B. A. Larder
%A D. Wang
%A A.Revell, R.Harrigan, J.Montaner, S.Wegner, C.Lane
%T Treatment history and adherence information significantly improves
   prediction of virological response by neural networks
%J 14th Int. HIV Drug Resistance Workshop
%W Quebec
%M JUN
%D 2005
%K poster, wShop, c2005, c200x, c20xx, NN, drug, HIV, AIDS
%X "...ANN models trained using data from highly adherent patients were
   sig. more accurate than those trained with data from less adherent patients.
   Initial combined reatment history/adherent models achieved an intermediate
   level of performance, possibly due to the relatively small training set and
   large number of input variables. Combined models trained using a reduced
   mutation set showed improved performance."
   -- [<A HREF="http://www.hivrdi.org/treatment-history-and-adherence-information-quebec-abstract.htm">abs</A>]['05],
      [<A HREF="http://www.hivrdi.org/pdf/Quebec-2005-Poster-BL-FINAL.pdf">poster</A>]['05].
   auths@HIV Resistance Response Database Initiative (RDI), London,
         BC Centre for Excellence in HIV/AIDS Vancouver,
         US Military HIV Research Program, Rockville,
         Nat. Inst. of Allergy and Infectious Diseases (NIAID)

%A D. A. Drachman
%T Do we have brain to spare?
%J Neurology
%V 64
%N 12
%P 2004-2005
%M JUN
%D 2005
%K editorial, views, c2005, c200x, c20xx, zz1212, human, brain, size, estimate,
   sizes, capacity, neurons, synapses, complexity
%X "Within the liter and a half of human brain, stereologic studies estimate
   that there are ~ 20 billion neocortical neurons, with an average of 7,000
   synaptic connections each. The cerebral cortex has about 0.15 quadrillion
   synapses - or about a trillion synapses per cubic centimeter of cortex. The
   white matter of the brain contains approximately 150,000 to 180,000 km of
   myelinated nerve fibers at age 20, connecting all these neuronal elements.
   Despite the monumental number of components in the brain, Szentagothai
   estimated that each neuron is able to contact any other neuron with no more
   than six interneuronal connectionsâ - 'six degrees of separation.' ..."
   -- [<A HREF="http://dx.doi.org/10.1212/01.WNL.0000166914.38327.BB">doi:10.1212/01.WNL.0000166914.38327.BB</A>]['12].
   (About  2*10^10 neurons,  1.4*10^14 synapses.)
   [Also search for: brain size estimate].

%A N. M. El-Sayed
%A et al
%T The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease
%J Science
%V 309
%N 5733
%P 409-415
%M JUL
%D 2005
%K MolBio, jrnl, c2005, c200x, c20xx, nGenome, biology, parasite, eukaryote,
   Tritryps
%X "...revealed that the diploid genome contains a predicted 22,570 proteins
   encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the
   genome consists of repeated sequences, such as retrotransposons & genes for
   large families of surface molecules, which include trans-sialidases, mucins,
   gp63s, & a large novel family ( > 1300 copies) of mucin-associated surface
   protein (MASP) genes. Analyses of the T. cruzi, T. brucei, & Leishmania
   major (Tritryp) genomes imply differences from other eukaryotes in DNA repair
   & initiation of replication & reflect their unusual mitochondrial DNA.
   Although the Tritryp lack several classes of signaling molecules, their
   kinomes contain a large & diverse set of protein kinases & phosphatases;
   their size & diversity imply previously unknown interactions & regulatory
   processes, which may be targets for intervention"
   -- [<A HREF="http://dx.doi.org/10.1126/science.1112631">doi:10.1126/science.1112631</A>]['05],
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05].

%A Matthew Berriman
%A et al
%T The genome of the African Trypanosome Trypanosoma brucei
%J Science
%V 309
%N 5733
%P 416-422
%M JUL
%D 2005
%K MolBio, jrnl, c2005, c200x, c20xx, nGenome, biology, parasite, eukaryote,
   Tritryps, sleeping sickness
%X "African trypanosomes cause human sleeping sickness & livestock
   trypanosomiasis .... present the seq. & analysis of the 11 megabase-sized
   chromosomes of Trypanosoma brucei. The 26-mb genome contains 9068 predicted
   genes, including ~900 pseudogenes & ~1700 T. brucei specific genes. Large
   subtelomeric arrays contain an archive of 806 variant surface glycoprotein
   (VSG) genes used by the parasite to evade the mammalian immune system. Most
   VSG genes are pseudogenes, which may be used to generate expressed mosaic
   genes by ectopic recombination. Comparisons of the cytoskeleton & endocytic
   trafficking systems with those of humans & other eukaryotic organisms reveal
   major differences. A comparison of metabolic pathways encoded by the genomes
   of T. brucei, T. cruzi, & Leishmania major reveals the least overall
   metabolic capability in T. brucei & the greatest in L. major. Horizontal
   transfer of genes of bacterial origin has contributed to some of the
   metabolic differences in these parasites, & a number of novel potential drug
   targets have been identified."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1112642">doi:10.1126/science.1112642</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05].

%A Alasdair C. Ivens
%A et al
%T The genome of the kinetoplastid parasite, Leishmania major
%J Science
%V 309
%N 5733
%P 436-442
%M JUL
%D 2005
%K MolBio, jrnl, c2005, c200x, c20xx, nGenome, biology, eukaryote, Tritryps
%X Leishmania species cause a spectrum of human diseases in tropical &
   subtropical regions .... sequenced the 36 chrs. of the 32.8-mb haploid genome
   of Leishmania major (Friedlin strain) & predict 911 RNA genes, 39 pseudogenes
   & 8272 protein-coding genes, of which 36% can be ascribed a putative
   function. These include genes involved in host-pathogen interactions, such
   as proteolytic enzymes, & extensive machinery for synthesis of complex
   surface glycoconjugates. The organization of protein-coding genes into long,
   strand-specific, polycistronic clusters & lack of general transcription
   factors in the L. major, Trypanosoma brucei, & cruzi (Tritryp) genomes
   suggest that the mechanisms regulating RNA polymerase II-directed
   transcription are distinct from those operating in other eukaryotes,
   although the trypanosomatids appear capable of chromatin remodeling. Abundant
   RNA-binding proteins are encoded in the Tritryp genomes, consistent with
   active posttranscriptional regulation of gene expression."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1112680">doi:10.1126/science.1112680</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05].

%A S. Kumar
%T Molecular clocks: four decades of evolution
%J Nat. Rev. Genet.
%V 6
%P 654-662
%M AUG
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, zz0123, survey, intro, molecular clock,
   evolution, phylogenetics
%X -- [<A HREF="https://doi.org/10.1038/nrg1659">doi:10.1038/nrg1659</A>]['23].
   also see: "... Mutation rates differ between species and even between
   different regions of the genome of a single species..."
   -- clock@[<A HREF="https://en.wikipedia.org/wiki/Molecular_clock">wikip</A>]['23].

%T The map-based sequence of the rice genome
%A Int. Rice Genome Sequencing Project
%J Nature
%V 436
%P 793-800
%M AUG
%D 2005
%K jrnl, rice, c2005, c200x, c20xx, plant, Oryza sativa L. ssp. indica, genome,
   plants, angiosperm, grass, grasses, gene, genes, chromosomes,
   biol, biology
%X "... a map-based, finished quality sequence that covers 95% of the 389 Mb
   genome, including virtually all of the euchromatin and 2 complete
   centromeres. A total of 37,544 non-transposable-element-related
   protein-coding genes were identified, of which 71% had a putative homologue
   in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins
   had a putative homologue in the predicted rice proteome. 29 per cent of the
   37,544 predicted genes appear in clustered gene families. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03895">doi:10.1038/nature03895</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">genomes@ncbi</A>]['07].
   [Also search for: rice nGenome]

%A H.-L. Wu
%A S. Bagby
%A J. M. H. den van Elsen
%T Evolution of the genetic triplet code via two types of doublet codons
%J J. Molec. Evol.
%V 61
%N 1
%P 54-64
%M JUL
%D 2005
%K jrnl, JME, genetic code, evolution, c2005, c200x, c20xx, denVanElsen,
   codon, MolBio, codon, DNA, amino acid, acids, translation, origin, zz0905
%X "... propose a simple new hypothesis for code evolution involving a
   progression from singlet to doublet to triplet codons with a reading
   mechanism that moves 3 bases each step. ... triplet codons gradually evolved
   from 2 types of ambiguous doublet codons, those in which the first 2 bases
   of each 3-base window were read (prefix codons). ... explains multiple
   features of the genetic code such as the origin of the pattern of 4-fold
   degenerate & 2-fold degenerate triplet codons, the origin of its error
   minimising properties, & why there are only 20 amino acids."
   -- [<A HREF="http://dx.doi.org/10.1007/s00239-004-0224-3">doi:10.1007/s00239-004-0224-3</A>]['05].

%A S. J. Giovannoni
%A et al
%T Genome streamlining in a cosmopolitan oceanic bacterium
%J Science
%V 309
%N 5738
%P 1242-1245
%M AUG
%D 2005
%K jrnl, MolBio, Pelagibacter ubique, c2005, c200x, c20xx, SAR11 clade, biol,
   marine alpha-proteobacteria, bacteria, HTCC1062, genome, CP000084, zz0905,
   ocean, free living, microorganism
%X "The SAR11 clade consists of v. small, heterotrophic marine
   {alpha}-proteobacteria ... oceans, where they account for about 25% of all
   microbial cells. Pelagibacter ubique, the 1st cultured member of this clade,
   has the smallest genome & encodes the smallest number of predicted open
   reading frames known for a free-living microorganism.  [cf] parasitic
   bacteria & archaea with small genomes, P. ubique has complete biosynthetic
   pathways for all 20 amino acids & all but a few cofactors. P.  ubique has no
   pseudogenes, introns, transposons, extrachromosomal elements, or inteins;
   few paralogs; & the shortest intergenic spacers yet observed for any cell."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1114057">doi:10.1126/science.1114057</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=71061822">CP000084</A>]['05] 1,308,759 bp, circular.

%A P. D. Evans
%A et al
%T Microcephalin, a gene regulating brain size, continues to evolve adaptively
   in human
%J Science
%V 309
%V 5741
%P 1717-1720
%M SEP
%D 2005
%K jrnl, c2005, c200x, c20xx, evolution, gene, protein, MolBio, biol, brains,
   size, MCPH1
%X "... show that 1 genetic variant of M. in modern h., which arose ~37,000 y.
   ago, increased in freq. too rapidly to be compatible with neutral drift.
   This indicates that it has spread under strong +ve selection, ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1113722">doi:10.1126/science.1113722</A>]['05].

%A N. Mekel-Bobrov
%A et al
%T Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens
%J Science
%V 309
%V 5741
%P 1720-1722
%M SEP
%D 2005
%K jrnl, c2005, c200x, c20xx, evolution, gene, protein, MolBio, biol, brains,
   size, ASPM, abnormal spindle-like microcephaly
%X "... ASPM (abnormal spindle-like microcephaly associated) is a specific
   regulator of brain size ... 1 genetic variant of ASPM in h. arose merely
   about 5800 y. ago & ... high frequency under strong +ve selection. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1116815">doi:10.1126/science.1116815</A>]['05].

%T Initial sequence of the chimpanzee genome and comparison with the
   human genome
%Q The Chimpanzee Sequencing and Analysis Consortium
%J Nature
%V 437
%P 69-87
%M SEP
%D 2005
%K jrnl, chimp, nGenome, c2005, c200x, c20xx, zz0905, Pan troglodytes, mammal,
   MolBio, primate
%X "... draft genome seq. of the common chimpanzee (Pan troglodytes). Through
   comparison with the human genome, we have generated a largely complete
   catalogue of the genetic differences that have accumulated since the human &
   chimpanzee species diverged from our common ancestor, constituting
   approx. 35 million single-nucleotide changes, 5 million insertion/deletion
   events, & various chromosomal rearrangements...."
   -- [<A HREF="http://dx.doi.org/10.1038/nature04072">doi:10.1038/nature04072</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05].
   The Pan troglodytes diploid genome is organized in 23 pairs of
   autosomes and two sex chromosomes.

%A E. V. Linardopoulou
%A E. M. Williams
%A Y. Fan
%A C. Friedman
%A J. M. Young
%A B. J. Trask
%T Human subtelomeres are hot spots of interchromosomal recombination and
   segmental duplication
%J Nature
%V 437
%P 94-100
%M SEP
%D 2005
%K jrnl, c2005, c200x, c20xx, subtelomere, chromosome, evolution, telomere,
   MolBio, telomeres, spot
%X "... subtelomeres are polymorphic patchworks of interchromosomal segmental
   duplications at the ends of chrs.. ... evidence that these patchworks arose
   recently through repeated translocations between chr. ends. We assess the
   relative contribution of the principal mechanisms of ectopic DNA repair to
   the formation of subtelomeric duplications & find that non-homologous end-
   joining predominates. Once subtelomeric duplications arise, they are prone
   to homology-based sequence transfers as shown by the incongruent
   phylogenetic relationships of neighbouring sections. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature04029">doi:10.1038/nature04029</A>]['05].

%A A. Gillet
%A M. Sanner
%A D. Stoffler
%A A. Olson
%T Tangible interfaces for structural molecular biology
%J Structure
%V 13
%N 3
%P 483-491
%M MAR
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, protein, proteins, 3D, structure,
   interactive, modeling, models, augmented reality, tactile, touch, docking
%X "... extended our molecular modeling environment, PMV, to support the
   fabrication of a wide variety of physical molecular models, and have adapted
   an augmented reality system to allow virtual 3D representations to be
   overlaid onto the tangible molecular models. Users can easily change the
   overlaid information, switching between different representations of the
   molecule, displays of molecular properties, or dynamic information ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.str.2005.01.009">doi:10.1016/j.str.2005.01.009</A>]['13],
   Olson@[<A HREF="http://mgl.scripps.edu/projects/tangible_models/">scr'pps</A>]['13].
   [Also search for: MolBio Olson protein].

%A M. T. Ross
%A et al
%T The DNA sequence of the human X chromosome
%J Nature
%V 434
%N 7031
%P 325-337
%M MAR
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, human genome, X chromosome, Xchromosome,
   chrX, Xchr, chromosomeX, sex
%X "... X chr. has a unique biology that was shaped by its evol. as the sex chr.
   shared by males & females. We have determined 99.3% of the euchromatic seq.
   of the X chr.. Our analysis illustrates the autosomal origin of the mammalian
   sex chrs., the stepwise process that led to the progressive loss of
   recombination between X & Y, & the extent of subsequent degradation of the Y
   chr.. LINE1 repeat elts cover 1/3 of the X chr., with a distribution that is
   consistent with their proposed role as way stations in the process of X-chr.
   inactivation. We found 1,098 genes in the seq., of which 99 encode proteins
   expressed in testis & in various tumour types. A disproportionately high
   number of mendelian diseases are documented for the X chr.. Of this #, 168
   have been explained by mutations in 113 X-linked genes, which in many cases
   were characterized with the aid of the DNA seq.. ..."
   "... fig.4 ... human X v. mouse and rat X ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03440">doi:10.1038/nature03440</A>]['08].

%A M. Margulies
%A et al
%T Genome sequencing in microfabricated high-density picolitre reactors
%J Nature
%V 437
%P 376-380
%M SEP
%D 2005
%K jrnl, c2005, c200x, c20xx, zz0905, reactor, MolBio, assembly, sequence, DNA,
   sequencing technology, 454 Life Sciences, pyrosequencing
%X "... novel fibre-optic slide of individual wells & is able to sequence 25
   million bases, at 99% or better accuracy, in one four-hour run. To achieve
   an approximately 100-fold increase in throughput over current Sanger
   sequencing technology, we have developed an emulsion method for DNA
   amplification & an instrument for sequencing by synthesis using a
   pyrosequencing protocol optimized for solid support & picolitre-scale vols..
   ... [e.g.] sequencing & de novo assembly of the Mycoplasma genitalium genome
   with 96% coverage at 99.96% accuracy in one run of the machine."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03959">doi:10.1038/nature03959</A>]['05].
   -- [<A HREF="http://www.454.com/">454.com</A>]['09],
   -- [<A HREF="http://en.wikipedia.org/wiki/Pyrosequencing">wikip</A>]['09].

%A H. Kurosu
%A et al
%T Suppression of aging in mice by the hormone klotho
%J Science
%V 309
%N 5742
%P 1829-1833
%M SEP
%D 2005
%K jrnl, c2005, c200x, c20xx, age, ageing, mice, mouse, mus, insulin, IGF1,
   life span, lifespan, old, older, antiaging, antiageing, anti-aging, ageing
%X "A defect in Klotho gene expression in mice accelerates the degeneration of
   multiple age-sensitive traits. ... overexpression of Klotho in mice extends
   life span. ... circulating hormone that binds to a cell-surface receptor &
   represses intracellular signals of insulin & insulin-like growth factor 1
   (IGF1), an evolutionarily conserved mechanism for extending life span.
   Alleviation of aging-like phenotypes in Klotho-deficient mice was observed
   by perturbing insulin & IGF1 signaling, suggesting that Klotho-mediated
   inhibition of insulin & IGF1 signaling contributes to its anti-aging
   properties. Klotho protein may function as an anti-aging hormone."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1112766">doi:10.1126/science.1112766</A>]['05].
   [Also search for: aging klotho].

%A P. Bradley
%A K. M. S. Misura
%A D. Baker
%T Toward high-resolution de novo structure prediction for small proteins
%J Science
%V 309
%N 5742
%P 1868-1871
%M SEP
%D 2005
%K jrnl, c2005, c200x, c20xx, protein, tertiary structure, prediction, MolBio,
   fold, folding, Rosetta
%X "... using a combination of improved low- & high-resolution conformational
   sampling methods, improved atomically detailed potential functions that
   capture the jigsaw puzzle-like packing of protein cores, & high-performance
   computing, high-resolution structure prediction ( < 1.5 a.) can be achieved
   for small protein domains ( < 85 residues). The primary bottleneck to
   consistent high-resolution pred'n appears to be conformational sampling."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1113801">doi:10.1126/science.1113801</A>]['05].

%A P. C. Crawford
%A et al
%T Transmission of equine influenza virus to dogs
%J Science
%V ?
%P ?-?
%M ?
%D 2005
%K jrnl, horizontal, jump, c2005, c200x, c20xx, flu, dog, horse, horses,
   canine, transfer, zoonosis
%X "...  the canine influenza virus genomes form a monophyletic group,
   consistent with a single interspecies virus transfer. Molecular changes in
   the hemagglutinin suggested adaptive evolution in the new host. ..."
  [<A HREF="http://dx.doi.org/10.1126/science.1117950">doi:10.1126/science.1117950</A>]['05] online 10/'05.

%A R. Kantor
%A et al
%T Impact of HIV-1 subtype and antiretroviral therapy on protease and
   reverse transcriptase genotype: Results of a global collaboration
%J PLoS Med.
%V 2
%N 4
%P e112
%M Apr
%D 2005
%K medical, health, HIV, AIDS, c2005, c200x, c20xx, drug, drugs, treatment,
   genotypic, phenotype, phenotypic, HIV1, hivdb, resistance, resistant,
   mutations
%X "The genetic differences among HIV-1 subtypes may be critical to clinical
   management and drug resistance surveillance as antiretroviral treatment is
   expanded to regions of the world where diverse non-subtype-B viruses
   predominate. ... Non-subtype-B sequences from 3,686 persons ... Each of the
   55 known subtype B drug-resistance mutations occurred in at least one non-B
   isolate ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pmed.0020112">doi:10.1371/journal.pmed.0020112</A>]['05]
   and [<A HREF="http://hivdb.stanford.edu/">hivdb</A>]['05].

%A E. C. Holmes
%A et al
%T Whole-genome analysis of human influenza A virus reveals multiple
   persistent lineages and reassortment among recent H3N2 viruses
%J PLoS Biology
%V 3
%N 9
%P e300
%M SEP
%D 2005
%K ejrnl, flu, viral, MolBio, c2005, c200x, c20xx, H3N2, influenzaA,
   phylogenetic, strain, strains, lineage
%X "... phylogenetic analysis of 156 complete genomes of human H3N2 influenza A
   viruses collected between 1999 and 2004 ... "
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pbio.0030300">doi:10.1371/journal.pbio.0030300</A>]['05],
      [<A HREF="http://www.tigr.org/msc/infl_a_virus/publications.shtml">@tigr</A>]['05],
      [<A HREF="http://www.ncbi.nlm.nih.gov/genomes/taxg.cgi?tax=11320">A_genome@ncbi</A>]['05] x n.
   "Influenza A viral genome consists of 8, single -ve strand RNAs that can
   range between 890 and 2340 n. long. Each RNA seg. encodes 1 to 2 proteins"
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html">FLU@ncbi</A>]['05].

%A E. Ghedin
%A et al
%T Large-scale sequencing of human influenza reveals the dynamic nature of
   viral genome evolution
%J Nature
%V 437
%P 1162-1166
%M OCT
%D 2005
%K jrnl MolBio, flu, DNA, genome, c2005, c200x, c20xx, H1N1, virus, viral,
   H3N2, genome, data
%X online 5/10/'05 "... report the results of sequencing 209 complete genomes
   of the human influenza A virus, encompassing a total of 2,821,103 n.. ...
   increasing markedly the number of publicly available, complete influenza
   virus genomes, we have discovered several anomalies in these 1st 209 genomes
   that demonstrate the dynamic nature of influenza transmission & evolution.
   This new, large-scale sequencing effort promises to provide a more
   comprehensive picture of the evolution of influenza viruses & of their
   pattern of transmission through human & animal populations. All data from
   this project are being deposited, without delay, in public archives."
   -- [<A HREF="http://dx.doi.org/10.1038/nature04239">doi:10.1038/nature04239</A>]['05].
   [supp. info includes "genome sequences for all 209 samples"]
   -- [<A HREF="http://www.tigr.org/msc/infl_a_virus/publications.shtml">@tigr</A>]['05].
   Also see: PloS Biology Sep 2005.

%A J. K. Taubenberger
%A A. H. Reid
%A R.M.Lourens, R.Wang, G.Jin, T.G.Fanning
%T Characterization of the 1918 influenza virus polymerase genes
%J Nature
%V 437
%P 889-893
%M OCT
%D 2005
%K jrnl, MolBio, gene, c2005, c200x, c20xx, zz1005, Spanish flu, viral, avian,
   bird, PA, PB1, PB2
%X "... heterotrimeric polymerase complex (PA, PB1, PB2) ... differ from avian
   consensus sequences at only a small number of amino acids ... nucleotide
   sequences of the 1918 polymerase genes have more synonymous differences than
   expected, suggesting evolutionary distance from known avian strains. ...
   propose that the 1918 virus was not a reassortant virus (like those of the
   1957 and 1968 pandemics), but more likely an entirely avian-like virus that
   adapted to humans. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature04230">doi:10.1038/nature04230</A>]['05].
   [Also see: Science characterization spanish flu 2005].

%A T. M. Tumpey
%A et al
%T Characterization of the reconstructed 1918 Spanish influenza pandemic virus
%J Science
%V 310
%N 5745
%P 77-80
%M OCT
%D 2005
%K jrnl, MolBio, Spanish flu, DNA, genome, c2005, c200x, c20xx, zz1005, H1N1,
   virus, viral, genome, HA, NA, gene, genes
%X "The pandemic ... of 1918-1919 killed an est. 20 to 50 million people
   worldwide. With the recent availability of the complete 1918 influenza virus
   coding sequence, we used reverse genetics to generate an influenza virus
   bearing all 8 gene segments of the pandemic virus to study the properties
   associated with its extraordinary virulence. In stark contrast to
   contemporary human influenza H1N1 viruses, the 1918 pandemic virus had the
   ability to replicate in the absence of trypsin, caused death in mice &
   embryonated chicken eggs, & displayed a high-growth phenotype in human
   bronchial epithelial cells. Moreover, the coordinated expression of the 1918
   virus genes most certainly confers the unique high-virulence phenotype
   observed with this pandemic virus."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1119392">doi:10.1126/science.1119392</A>]['05].
   [Also see: Nature characterization spanish flu 2005].
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/genomes/influenza/list.cgi/">flu@ncbi</A>]['05].

%A S. Myers
%A L. Bottolo
%A C. Freeman,  G. McVean,  P. Donnelly
%T A fine-scale map of recombination rates and hotspots across the human genome
%J Science
%V 310
%N 5746
%P 321-324
%M OCT
%D 2005
%K jrnl, MolBio, rate, hot spot, spots, hotspot, c2005, c200x, c20xx, mutation,
   change, recombination, evolution
%X "... identify more than 25,000 recombination hotspots, together with motifs
   and sequence contexts that play a role in hotspot activity. Differences
   between the behavior of recombination rates over large (megabase) & small
   (kilobase) scales lead us to suggest a 2-stage model for recombination in
   which hotspots are stochastic features, within a framework in which
   large-scale rates are constrained."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1117196">doi:10.1126/science.1117196</A>]['05].

%A Q. Mai Le
%A et al
%T Avian flu: Isolation of drug-resistant H5N1 virus
%J Nature
%V 437
%P 1108
%M OCT
%D 2005
%K Brief Comm, jrnl, MolBio, c2005, c200x, c20xx, H5N1 strain, bird, viral,
   resistance, oseltamivir, zanamivir, Hanoi, H274Y
%X "...An H5N1 influenza virus, A/Hanoi/30408/2005, was isolated on 27 Feb.2005
   from a 14-y.-old Vietnamese girl (patient 1) who had received a prophylactic
   dose (75 mg once a day) of oseltamivir..."
   -- [<A HREF="http://dx.doi.org/10.1038/4371108a">doi:10.1038/4371108a</A>]['05].

%A P. Andolfatto
%T Adaptive evolution of non-coding DNA in Drosophila
%J Nature
%V 437
%P 1149-1152
%M OCT
%D 2005
%K jrnl, MolBio, junk DNA, fruit fly, c2005, c200x, c20xx, D. melanogaster,
   noncoding, mutation, pressure selection, constraint, intergenic regions
%X "A large fraction of eukaryotic genomes consists of DNA that is not trans.
   into protein seq., & little is known about its functional significance. ...
   show that several classes of non-coding DNA in D. are evolving considerably
   slower than synonymous sites, & yet show an excess of between-species
   divergence relative to polymorphism when compared with synonymous sites. The
   former is a hallmark of selective constraint, but the latter is a signature
   of adaptive evol., resembling general patterns of protein evol. in D.. I
   est. that about 40-70% of n. in intergenic regions ... are evolutionarily
   constrained ... results imply that, although +ve sel'n is clearly an
   important facet of protein evol., adaptive changes to non-coding DNA might
   have been considerably more common in the evolution of D. melanogaster."
   -- [<A HREF="http://dx.doi.org/10.1038/nature04107">doi:10.1038/nature04107</A>]['05].
   NB. a synonymous site is one where a mutation does not result in AA subs.

%A E. Check
%T Human genome: Patchwork people
%J Nature
%V 437
%P 1084-1086
%M OCT
%D 2005
%K news, survey, human, structural variation, evolution, c2005, c200x, c20xx,
   MolBio, biology, variation, HapMap Project, copy-number changes,
   polymorphisms, SNPs, inversions, deletions, duplications, CCL3L1, haplotype
%X "For years it was assumed that tiny differences in our genetic make-up gave
   us our individual traits. Now it seems that those characteristics are caused
   by rearrangements of large chunks of our DNA ..."  [12 refs]
   -- [<A HREF="http://dx.doi.org/10.1038/4371084a">doi:10.1038/4371084a</A>]['05];
   also see [<A HREF="http://www.hapmap.org/">hapmap.org</A>].

%A Y. Ye
%A A. Godzik
%T Multiple flexible structure alignment using partial order graphs
%J J. Bioinformatics
%V 21
%N 10
%P 2362-2369
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, multiple, alignments, 3D, structure,
   POSA, partial order, preserving, rearrange, rearrangement, POG, graph,
   protein
%X "... using a partial order graph representation of multiple alignments. POSA
   has two unique features: (1) identifies and classifies regions that are
   conserved only in a subset of input structures and (2) allows internal
   rearrangements in protein structures. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti353">doi:10.1093/bioinformatics/bti353</A>]['11].
   [Also search for: MolBio protein structure alignment].

%A K. Nordfjall
%A A. Larefalk
%A P. Lindgren
%A D. Holmberg
%A G. Roos
%T Telomere length and heredity: Indications of paternal inheritance
%J Proc. Natl. Acad. Sci.  USA
%V ?
%P ?-?
%D 2005
%K jrnl, PNAS, MolBio, health, age, aging, c2005, c200x, c200x, zz1105,
   telomeres, father, child, offspring, inherit, inheritance, inherited,
   life span, lifespan, parent, stats, caseStudy
%X "Cellular telomere length is linked to replicative life span. T. repeats are
   lost in peripheral blood cells in vivo by age & women show less t. attrition
   than men. Previous reports have indicated that t. length & chr.- specific
   t.-length patterns partly are inherited. ... link to the X chr. was
   recently suggested. ... A stat. sig. assoc. between t. lengths comparing
   father-son (P=0.011, n=20) & father-daughter (P=0.005, n=22) pairs was found.
   However, no correlation was observed between mother-daughter (P=0.463, n=23)
   or mother-son (P=0.577, n=18). The father-offspring correlation was
   highly significant (P < 0.0001), in contrast to mother-offspring (P=0.361).
   ... T. length is inherited, & evidence for a father-to-offspring heritage of
   this trait was obtained, whereas in vitro t. length maintenance was found to
   be dependent on the initial t. length."    [online 10/2005].
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0501724102">doi:10.1073/pnas.0501724102</A>]['05].

%A D. A. Steane
%T Complete nucleotide sequence of the chloroplast genome from the
   Tasmanian blue gum, Eucalyptus globulus (Myrtaceae)
%J DNA Research
%V 12
%N 3
%P 215-220
%D 2005
%K jrnl, eucalypt, c2005, c200x, c20xx, zz0106, tree, trees, angiosperms,
   angiosperm, pseudogene, angiosperm, gymnosperm, DNA, cGenome, plastid,
   uniTasmania
%X "... and compared with chloroplast genomes of tree and non-tree angiosperms
   and two softwood tree species. The 160,286 bp genome is similar in gene
   order to that of Nicotiana, with an inverted repeat (IR) (26,393 bp)
   separated by a large single copy (LSC) region of 89,012 bp and a small
   single copy region of 18,488 bp. There are 128 genes (112 individual gene
   species and 16 genes duplicated in the inverted repeat) coding for 30
   transfer RNAs, 4 ribosomal RNAs and 78 proteins. ..."
   -- [<A HREF="http://dnaresearch.oxfordjournals.org/cgi/content/abstract/12/3/215">dnares</A>]['06],
   ???[<A HREF="http://dx.doi.org/10.1093/dnares/dsi006">doi:10.1093/dnares/dsi006</A>]['06],
   "GC-content 36.9% ... comparable with that of other vascular plant plastids"
   "GenBank accession no. AY780259" [<A HREF="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=60460788">AY780259</A>]['06] [circular, 160286bp].

%A K. Florquin
%A Y. Saeys
%A S.Degroeve, P.Rouze, Y. Van de Peer
%T Large-scale structural analysis of the core promoter in mammalian and
   plant genomes
%J NAR
%V 33
%N 13
%P 4255-4264
%D 2005
%K NAR, jrnl, c2005, c200x, c20xx, MolBio, promoters, eukaryote, regions, site,
   region, structure, DNA, binding, transcription, anisotropic flexibility,
   core, IUPAC, TATA, YYANWYY, zz0106
%X "DNA encodes at least 2 independent levels of functional information. [1]for
   encoding proteins & sequence targets for DNA-binding factors, while the 2nd
   one is contained in the physical & structural properties of the DNA molecule
   itself. ...  [here] we focus on these structural properties, [v.] different
   organisms & assessing their ability to describe the core promoter. ...
   distinct types of core promoters, based on a clustering of their structural
   profiles. ... indicate that the structural profiles are much conserved within
   plants... & animals..., but differ considerably between p. & a..  [And] we
   demonstrate that these structural profiles can be an alternative way of
   describing the core promoter, in addition to more classical motif or IUPAC-
   based approaches. Using the structural profiles as discriminatory elements
   to separate p. regions from non-p. regions, reliable models can be built to
   identify core-promoter regions using a strictly computational approach."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gki737">doi:10.1093/nar/gki737</A>]['05], [76 refs].

%A C. K. Biebricher
%A M. Eigen
%T The error threshold
%J Virus Res.
%V 107
%N 2
%P 117-127
%M FEB
%D 2005
%K jrnl, MolBio, biol, viral, c2005, c200x, c20xx, quasispecies, diversity,
   population landscape, errors, sequence space
%X "... A "wild-type" virus is no longer viewed as the fittest type, but as the
   center of gravity of a population landscape. A consequence of quasispecies
   is the existence of an error threshold for selective competence. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.virusres.2004.11.002">doi:10.1016/j.virusres.2004.11.002</A>]['05].

%A B. Behzadi
%A F. Le Fessant
%T DNA compression challenge revisited
%J Symp. on Combinatorial Pattern Matching
%W Korea
%P ?-?
%M JUN
%D 2005
%K conf, CPM, CPM05, compress, MolBio, c2005, c200x, c20xx, zz0106, LeFessant,
   DNApack
%X e.g. CHNTXX(155844): 1.6103;
        HUMHBB (73308): 1.7771 bits/base, from DNApack webpage.
   -- [<A HREF="http://pauillac.inria.fr/~lefessan/papers/cpm2005.pdf">pdf@inria.fr</A>]['06].
   ([Also search for: Allison Edgoose Dix c1998], CHNTXX 1.614, HUMHBB 1.728,
   and see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">Compression</A>].)

%A J. D. Bashford
%A P. D. Jarvis
%T A base-pairing model of duplex formation. I. Watson-Crick pairing geometries
%J Biopolymers
%V 78
%N 6
%P 287-297
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, oligonucleotide duplex formation, zz0206,
   DNA, RNA, oligomers, hybrids, uniTasmania
%X "... base-pairing model of oligonucleotide duplex formation & show ...equiv.
   to the nearest-neighbor dimer methods from fits to free energy of duplex
   formation data for short DNA-DNA & DNA-RNA hybrids containing only W.-C.
   pairs. ... corr. RNA-RNA params are included. ... the connection between
   rank-deficient polymer & rank-determinant oligonucleotide parameter sets for
   DNA duplexes is transparent. ... generalized to include RNA-DNA hybrids where
   the rank-deficient model with 11 dimer params in fact provides slightly
   improved predictions relative to the standard method with 16 indep. dimer
   parameters (delta G mean errs of 4.5 & 5.4% resp.)."
   -- [<A HREF="http://dx.doi.org/10.1002/bip.20282">doi:10.1002/bip.20282</A>]['06].

%A S. Das
%A A. S. McGough
%A J. Cohen
%A J. Darlington
%T Lightweight solution for protein annotation
%J UK eScience All Hands Meeting
%W Nottingham UK
%P 396-402
%M SEP
%D 2005
%K wShop, MolBio, c2005, c200x, c20xx, annotations, ICENI, ICENI2, grid, grids,
   ImperialCollege
%X [<A HREF="http://www.allhands.org.uk/2005/proceedings/papers/512.pdf">pdf</A>]['06],
   -- [<A HREF="http://www.allhands.org.uk/2005/proceedings/">proceedings</A>]['06].

%A M. d'Inverno
%A R. Saunders
%T Agent-based modelling of stem cell self-organisation in a niche
%J Engineering Self-Organising Systems: Methodologies and Applications
%I SpringerVerlag
%S LNAI
%N 3464
%P 52-68
%D 2005
%K conf, c2005, c200x, c20xx, zz0406, agents, model, cells, MolBio, biology,
   biol, dInverno, uniWestminster
%X "...used an agent-based approach as opposed to a cellular automata approach.
   A formalisation of the non-agent and agent-based approach is given, & from
   the results of this investigation, we aim to demonstrate the advantages of
   the agent-based approach for developing biologically plausible models with
   emergent self-organising dynamics. ..."  [22 refs]
   -- [<A HREF="http://dx.doi.org/10.1007/11494676_4">doi:10.1007/11494676_4</A>]['06],
   -- [<A HREF="http://www2.wmin.ac.uk/~dinverm/cell/">auth1</A>]['06],
   -- [<A HREF="http://www.arch.usyd.edu.au/~rob/">auth2</A>]['06],
   [Also search for: stem cell model].

%A F. P. Preparata
%A L. Zhang
%A K. W. Choi
%T Quick, practical selection of effective seeds for homology search
%J J. Computational Biology
%V 12
%N 9
%P 1137-1152
%M NOV
%D 2005
%K jrnl, c2005, c200x, c20xx, MolBio, gapped seed, spaced seeds
%X [<A HREF="http://www.liebertonline.com/doi/abs/10.1089/cmb.2005.12.1137">www</A>]['06].

%A G. M. Landau
%A L. Parida
%A O. Weimann
%T Gene proximity analysis across whole genomes via PQ trees
%J J. Computational Biology
%V 12
%N 10
%P 1289-1306
%M DEC
%S 2005
%K jrnl, c2005, c200x, c20xx, MolBio, PQ tree, PQtree, gene clusters
%X "... maximal permutation pattern ... We identify a minimal consensus PQ tree
   & prove that it is equivalent to a maximal pi pattern (Eres et al., 2003) &
   each subgraph of the PQ tree corr. to a nonmaximal permutation pattern.
   ... human & rat, we found about 1.5 million common gene clusters but only
   about 500 minimal consensus PQ trees, with E. Coli K-12 & B. Subtilis
   genomes, we found only about 450 minimal consensus PQ trees out of about
   15,000 gene clusters, & when comparing eight different Chloroplast genomes,
   we found only 77 minimal consensus PQ trees out of about 6700 gene clusters.
   ..." [<A HREF="http://www.liebertonline.com/doi/abs/10.1089/cmb.2005.12.1289">www</A>]['06].

%A T. Emonet
%A C. M. Macal
%A M. J. North
%A C. E. Wickersham
%A P. Cluzel
%T AgentCell: A digital single cell assay for chemotaxis
%J J. Bioinformatics
%V 21
%N 11
%P 2714-2721
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, biol, biology, agent cell, agents, cells,
   model, AgentCell, biol, biology, Ecoli, simulation
%X "... AgentCell, a model using agent-based technology to study the
   relationship between stochastic intracellular processes & behavior of
   individual cells. ... bacterial chemotaxis, one of the best characterized
   biological systems. ... each bacterium is an agent equipped with its own
   chemotaxis network, motors & flagella. Swimming cells are free to move in a
   3D environment. Digital chemotaxis assays reproduce experimental data
   obtained from both single cells & bacterial populations."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti391">doi:10.1093/bioinformatics/bti391</A>]['06].
   Also see [<A HREF="http://flash.uchicago.edu/~emonet/biology/agentcell/">more</A>]['06].

%A W. S. Mason
%A A. R. Jilbert
%A J. Summers
%T Clonal expansion of hepatocytes during chronic woodchuck hepatitis virus
   infection
%J PNAS
%V 102
%P 1139-1144
%D 2005
%K jrnl, PNAS, c2005, c200x, c20xx, MolBio, clone, hepatocyte, liver,
   viral, WHV
%X [<A HREF="http://www.med.upenn.edu/camb/faculty/mv/mason.html">auth1</A>]['06] med upenn and...
   -- [<A HREF="http://www.fccc.edu/research/pid/mason">auth1</A>]['06] Fox Chase C. C.,
   auth2, A. J. @ IMVS Adel.

%A Z. Guo
%A H. K. Han
%A J. C. Tay
%T Sufficiency verification of HIV-1 pathogenesis based on multi-agent
   simulation
%J Proc. of the 2005 conf. on Genetic and evolutionary computation
%P 305-312
%D 2005
%K conf, MolBio, HIV, HIV1, c2005, c200x, c20xx, CD4, mutation, synctium, AIDS,
   virus, viral, based, agent, simulation, model
%X "... methods which rely on differential calculus to describe pop. dynamics,
   can be inconvenient for predicting nonuniform interactions on a spatial
   dimension. Multi-Agent (or MA) modeling ... views the immune system as a
   hierarchical structure of cooperating & competing agents, operating with
   highly coupled behaviours to exhibit emergent complexity. We adopt the
   latter approach to simulate the pathogenesis of HIV-1. We show the model
   design & the emergent results for 4 well-known hypotheses: Direct Effect on
   CD4+ cells, Rapid Viral Mutation, Syncytium Formation, & Filling of CD4+
   Receptor sites under the influence of a null model for an adaptive response
   to HIV-1. ... results indicate that AIDS is more likely to be caused by
   either Rapid Viral Mutation or Syncytium Formation."
   -- [<A HREF="http://doi.acm.org/10.1145/1068009.1068059">doi:10.1145/1068009.1068059</A>]['06].

%A S. Litwin
%A E. Toll
%A A. R. Jilbert
%A W. S. Mason
%T The competing roles of virus replication and hepatocyte death rates in the
   emergence of drug-resistant mutants: Theoretical considerations
%J J. Clinical Virology
%V 34 (S1)
%P S96-S107
%M DEC
%D 2005
%K jrnl, c2005, c200x, c20xx, MolBio, zzVDRL, viral, hepatocytes, hepatitis,
   HBV, Lamivudine, mutant, resistance, kinetics, cccDNA, computer model, rate,
   simulation, clearance
%X "Lamivudine therapy of individuals chronically infected with [HBV] may
   eventually fail due to the emergence of drug-resistant mutants. Nonetheless,
   the durability of the response generally exceeds 6-12months. This durability
   appeared surprising in view of published evidence that the replication rate
   of drug-resistant mutants might be at least 10% of the replication rate of
   uninhibited wild-type virus. ... computational model of the infected liver
   to account for the rates of replication of wild-type and drug-resistant
   mutant ... either drug-resistant mutants have much lower replication rates
   than suspected, or that spread of v. to uninfected hepatocytes that arise in
   the chronically infected l. is much slower than during de novo infections."
   -- [<A HREF="http://dx.doi.org/10.1016/S1386-6532(05)80018-6">doi:10.1016/S1386-6532(05)80018-6</A>]['06].
   parameters
   lambda_w: rate replic. (prodn & export) wild-type v. (fn of i, j, ps, r's);
   lambda_m: ditto (mutant);
   n:  max # cccDNA per cell;
   r1: rate intercell. amplif. of wild-type / cccDNA @ statup;
   r2: rate intercell. amplif. of mutant / cccDNA;
   r3: ditto for wild-type during drug treatment;
   ps: fraction of pregenoms avail. for transcompl'n by pol.
   i:  # copies of wild-type cccDNA in a cell (determined by simulation);
   j:  # copies of mutant cccDNA in a cell;
   Ku: death rate of uninfected cells (e.g. 0.0005);
   Kd: death rate of infected cells   (e.g. 0.02);
   ? : mutation-rate, wild -> mutant;
   s: fraction of exported v. that are infectious;
   p_ret: fraction retained of cccDNA on cell replic'n.

%A E. Berezikov
%A et al...
%A E. Cuppen
%T Phylogenetic shadowing and computational identification of human microRNA
   genes
%J Cell
%V 120
%N 1
%P 21-24
%M JAN
%D 2005
%K MolBio, jrnl, miRNA, microRNA, micro RNA, c2005, c200x, c20xx
%X "We sequenced 122 miRNAs in 10 primate species to reveal conservation
   characteristics of miRNA genes. Strong c. is observed in stems of miRNA
   hairpins & increased var. in loop seqs. ... striking drop in conservation
   was found for seqs immediately flanking the miRNA hairpins. This
   characteristic profile was employed to predict novel miRNAs using
   cross-species comparisons. 976 candidate miRNAs were identified by scanning
   whole-genome human/mouse & human/rat alignments. Most of the novel candidates
   are conserved also in other vertebrates (dog, cow, chicken, opossum,
   zebrafish). Northern blot analysis confirmed the expression of mature miRNAs
   for 16 out of 69 representative candidates. Additional support for the
   expression of 179 novel candidates can be found in public DBs, their
   presence in gene clusters, & literature that appeared after these predictions
   were made. Taken together ... suggest the presence of significantly higher
   numbers of miRNAs in the human genome than previously estimated."
   -- [<A HREF="http://cat.inist.fr/?aModele=afficheN&cpsidt=16445665">cat.inist.fr</A>]['06].

%A I. Bentwich
%A et al
%T Identification of hundreds of conserved and nonconserved human microRNAs
%J Nature Genetics
%V 37
%P 766-770
%D 2005
%K jrnl, MolBio, microRNA, micro RNA, miRNA, ncRNA, c2005, c200x, c20xx,
   finding, prediction, predicting, hairpin loop
%X "... noncoding RNAs of ~ 22 n. that suppress translation of target genes by
   binding to their mRNA and thus have a central role in gene regulation in
   health and disease. To date, 222 human microRNAs have been identified, 86 by
   random cloning & sequencing, 43 by computational approaches & the rest as
   putative microRNAs homologous to microRNAs in other species. To prove our
   hypothesis that the total number of microRNAs may be much larger & that
   several have emerged only in primates, we developed an integrative approach
   combining bioinformatic predictions with microarray analysis & sequence-dir.
   cloning. Here we report the use of this approach to clone & sequence 89 new
   human microRNAs ...  53 of which are not conserved beyond primates. ...
   suggest that the total number of human microRNAs is at least 800."
   -- [<A HREF="http://dx.doi.org/10.1038/ng1590">doi:10.1038/ng1590</A>]['06].

%A D. Burstein
%A I. Ulitsky
%A T. Tuller
%A B. Chor
%T Information theoretic approaches to whole genome phylogenies
%I 9th RECOMB
%P 283-295
%I SpringerVerlag
%S LNCS
%V 3500
%D 2005
%K conf, MolBio, RECOMB, RECOMB9, RECOMB05, c2005, c200x, c20xx, phylogenetic,
   evolutionary, tree, trees, average common substring, ACS, substrings,
   information theory
%X "... core of our method is a new measure of pairwise distances between seqs.,
   whose lengths may greatly vary. This measure is based on info. theoretic
   tools (KL, relative entropy). We present an alg. for ... these distances.
   The alg. uses suffix arrays to compute the distance of 2 L long sequences in
   O(L) time. It is fast enough to enable the construction of the phylogenomic
   tree for hundreds of species, & the phylogenomic forest for almost two
   thousand viruses. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/11415770_22">doi:10.1007/11415770_22</A>]['07].
   NxN pairwise dists from mutual information, ... neighbour joining, ...tree.

%A S. F. Wieland
%A F. V. Chisari
%T Stealth and cunning: Hepatitis B and Hepatitis C viruses
%J J. of Virology
%V 79
%N 15
%P 9369-9380
%M AUG
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, hepatitis, HBV, HCV, human, virus, viral,
   HBeAg, HBx, Xprotein, HBsAg, HBcAg, immune system response, suppress
%X "... HBeAg ... cross the placenta and induce neonatal tolerance. ...
   HBeAg has been shown to suppress the antibody and T-cell response to HBcAg in
   adult T-cell receptor transgenic mice, functioning either to delete or
   anergize HBcAg/HBeAg cross-reactive T cells, depending on their functional
   avidity for the tolerogenic epitope. ... (HBsAg) might also suppress immune
   elimination of infected cells by functioning as a high-dose tolerogen, ...
   HBx protein has the potential to inhibit antigen processing ..."
   And: "as many as 10**11 hepatocytes can be infected."
   "HBV behaves as a "stealth" virus in that it does not induce an innate
   response in the cells it infects."
   -- [<A HREF="http://dx.doi.org/10.1128/JVI.79.15.9369-9380.2005">doi:10.1128/JVI.79.15.9369-9380.2005</A>]['07] [180 refs]

%A N. Nitta
%T Retrovirus-based computer
%J Natural Computing
%V 4
%N 2
%P 127-139
%M JUN
%D 2005
%K jrnl, retro virus, MolBio, Biol, c2005, c200x, c20xx, computing, zz1206
%X "A practical intra-cellular biomolecular computer should work inside living
   cells without damaging them. The retrovirus-based biomolecular computer has
   been designed, by mimicking the natural processes of living cells, to enable
   the creation of a practical intra-cellular computer. Here, I review the idea
   of retrovirus-based computing, & examine its feasibility. This idea might
   lead to the development of new technologies not only for biological research,
   but also for medical purposes. In future, through the development of the in
   vivo retrovirus-based computer, gene diagnosis & gene therapy is expected to
   cooperatively work inside living cells, enabling intelligent gene therapy
   technology that uses biomolecular computing."                 [via aland]
   -- [<A HREF="http://dx.doi.org/10.1007/s11047-004-4008-x">doi:10.1007/s11047-004-4008-x</A>]['06].

%A S. G. Ball
%T Eukaryotic microalgae genomics. The essence of being a plant
%J Plant Physiology
%V 137
%P 397-398
%D 2005
%K editorial, jrnl, special issue, MolBio, c2005, c200x, c20xx, alga, algal,
   algae, micro, genomes, plants, origins, evolution
%X "... More than 1.5 billion y. ago, a flagellated eukaryote entered into
   symbiosis with a photosynthetic bacterium that was clearly related to
   present-day cyanobacteria ... subsequently diversified into 3 primary
   endosymbiotic lineages: the glaucophytes (a group of freshwater algae
   carrying primitive plastids), the rhodophytes (the red algae), & the
   viridiplantae (the true plants consisting of green algae & land plants)...."
   -- [<A HREF="http://www.plantphysiol.org/cgi/content/full/137/2/397">@jrnl</A>]['07].

%A J. M. Murray
%A S. F. Wieland
%A R. H. Purcell
%A F. V. Chisari
%T Dynamics of hepatitis B virus clearance in chimpanzees
%J PNAS
%V 102
%N 49
%P 17780-17785
%M DEC
%D 2005
%K jrnl, PNAS, MolBio, c2005, c200x, c20xx, HBV, chimp, chimpanzee,
   computer simulation, virus, viral, load, chmp, T cells, Tcell, immune system,
   cytopathic, noncytopathic, Tcells
%X "... test the extent to which cytopathic & noncytopathic T cell effector fns
   contribute to resolution of [HBV] infection in 2 acutely infected chimp's.
   Simulations based exclusively on cytopathic fns show a poor fit to the data &
   would require the destruction & regeneration of ~ 11 livers for clearance to
   occur. In contrast, a simulation based on a combination of cytopathic &
   noncytopathic fns provided a sig. better fit to the data (P < 0.001) &
   required as much as 5x less destn to clear the virus from the liver. ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0508913102">doi:10.1073/pnas.0508913102</A>]['07].

%A A. Kramvis
%A M. C. Kew
%T Relationship of genotypes of Hepatitis B virus to mutations, disease
   progression and response to antiviral therapy
%J J. of Viral Hepatitis
%I BlackwellPublishing
%V 12
%N 5
%P 456-464
%M SEP
%D 2005
%K jrnl, MolBio, HBV, c2005, c200x, c20xx, virus, viral, drug resistance,
   mutation, genotype
%X "Phylogenetic analysis has led to the classn of [HBV] into 8 genotypes,
   designated A to H. The genotypes have differences in biol. properties & show
   heterogeneity in their global distn. These attributes of the genotypes may
   account not only for differences in the prevalence of [HBV] mutants in
   various geog. regions, but also be responsible for diffs. in the clinical
   outcome & response to antiviral treatment in different population groups."
   -- [<A HREF="http://dx.doi.org/10.1111/j.1365-2893.2005.00624.x">doi:10.1111/j.1365-2893.2005.00624.x</A>]['07].

%A M. J. Aranzana
%A et al
%T Genome-wide association mapping in Arabidopsis identifies previously known
   flowering time and pathogen resistance genes
%J PLoS Genetics
%V 1
%N 5
%P e60
%D 2005
%K jrnl, ejrnl, MolBio, c2005, c200x, c20xx, plant, plants, flower, gene, GWA,
   disease, resistant
%X "... associations with flowering time & pathogen resistance in a sample of
   95 accessions for which genome-wide polymorphism data were available. In
   spite of an extremely high rate of false +ves due to population structure, we
   were able to identify known major genes for all phenotypes tested, thus
   demonstrating the potential of genome-wide association mapping in A.thaliana
   & other species with similar patterns of variation. The rate of false +ves
   differed strongly between traits, with more clinal traits showing the highest
   rate. However, the false +ve rates were always substantial regardless of the
   trait, highlighting the necessity of an appropriate genomic control in
   association studies."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pgen.0010060">doi:10.1371/journal.pgen.0010060</A>]['07].

%A V. Alexandrov
%A U. Lehnert
%A N. Echols
%A D. Milburn
%A D. Engelman
%A M. Gerstein
%T Normal modes for predicting protein motions: a comprehensive database
   assessment and associated Web tool
%J Protein Sci.
%V 14
%P 633-643
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, MolMovDB, DB, motion, proteins, mode,
   vibration, movement, movements, molecular, molecule, molecules
%X "...stat. study of the applicability of normal modes to the prediction of
   mobile regions in proteins. ... assess the degree to which the obs. motions
   found in a comprehensive data set of 377 nonredundant motions can be modeled
   by a single normal-mode vibration. We describe each motion in our data set by
   vectors connecting corresponding atoms in 2 crystallographically known
   conformations. We then measure the geometric overlap of these motion vectors
   with the displacement vectors of the lowest-freq. mode, for 1 of the
   conformations. Our study suggests that the lowest mode contains useful info.
   about the parts of a protein that move most (i.e. have the largest
   amplitudes) & about the direction of this movement. ... developed a Web tool
   for motion prediction ... apply it here to 4 representative motions - from
   bacteriorhodopsin, calmodulin, insulin, & T7 RNA polymerase."
   -- [<A HREF="http://molmovdb.org/">molmovdb.org</A>]['06],
      [<A HREF="http://molmovdb.mbb.yale.edu/">molmovdb@yale</A>]['06].

%A B. Adler
%A D. Bulach
%A P. Cullen
%A J. Davies
%A J. Rood
%A R. Coppel
%A T. Seemann
%A R. Zuerner
%A D. Alt
%A A. McGrath
%A P. Wilson
%A E. Kuczek
%T What can we learn from comparative genomics of Leptospira? (abstract)
%J 4th Int. Leptospirosis Soc. Meeting, Abstracts and Proc.
%P 130
%M NOV
%D 2005
%K conf, abstract, abs, MolBio, c2005, c200x, c20xx, VBC, bioinformatics,
   genome, genomic, analysis, Biol

%A S. H. Schneider
%A J. Lane
%T The Patient from Hell: How I Worked with My Doctors to Get the Best of
   Modern Medicine and How You Can Too
%I Da Capo Lifelong Books
%P 300
%D 2005
%K book, c2005, c200x, c20xx, medicine, medical, cancer, treatment, therapy,
   health system
%X hb, us$18; uk us isbn:0738210250; uk us isbn13:978-0738210254;
   -- [<A HREF="http://www.patientfromhell.org/">www</A>]['07].

%A Y. Zhan
%A D. Kulp
%T Model-P: Basecalling for resequencing microarrays of diploid samples
%J J. Bioinformatics
%V 21 (Suppl. 2)
%P ii182-ii189
%D 2005
%K MolBio, c2005, c200x, c20xx, base calling, ModelP, resequencing, sample
%X [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti1129">doi:10.1093/bioinformatics/bti1129</A>]['08].

%A R. M. Casey
%T Designing chemical compound libraries for drug discovery
%J Business Intelligence Network
%M DEC
%D 2005
%K online article, c2005, c200x, c20xx, chemical compounds, library,
   high throughput screening, HTS, eHTS, virtual HTS, vHTS, diversity
%X [<A HREF="http://www.b-eye-network.com/view/2039">www</A>]['08].
   (Also see BldgBlockChem@[<A HREF="https://en.wikipedia.org/wiki/Building_block_(chemistry)">wikip</A>]['20].)
   [Also search for: chemical library].

%A L. F. A. Wessels
%A M. J. T. Reinders
%A A. A. M. Hart
%A C. J. Veenman
%A H. Dai
%A Y. D. He
%A L. J. van't Veer
%T A protocol for building and evaluating predictors of disease state based on
   microarray data
%J J. Bioinformatics
%V 21
%P 3755-3762
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, cancer, microarray, feature, gene,
   genes, marker, markers, predictor, select, selection, vant Veer,  vantVeer
%X "Microarray gene expression data is increasingly employed to identify sets of
   marker genes that accurately predict disease development and outcome in
   cancer. Many computational approaches have been proposed to construct such
   predictors. ... description of a principled training and validation protocol,
   which allows objective evaluation of the complete methodology for
   constructing a predictor. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti429">doi:10.1093/bioinformatics/bti429</A>]['08].

%A M. Deshpande
%A M. Kuramochi
%A N. Wale
%A G. Karypis
%T Frequent substructure-based approaches for classifying chemical compounds
%J IEEE Trans. on Knowledge and Data Engineering
%V 17
%N 8
%P 1036-1050
%M AUG
%D 2005
%K jrnl, c2005, c200x, c20xx, chemical compound, classification, subgraph,
   frequent
%X "... presents a substructure-based classification alg. that decouples the
   substructure discovery process from the classification model construction
   & uses frequent subgraph discovery algs. to find all topological & geometric
   substructures present in the data set. The advantage of this approach is that
   during classification model construction, all relevant substructures are
   available allowing the classifier to intelligently select the most
   discriminating ones. ... scalability is ensured by the use of highly
   efficient frequent subgraph discovery algs. [&] aggressive feature seln ..."
   -- [<A HREF="http://dx.doi.org/10.1109/TKDE.2005.127">doi:10.1109/TKDE.2005.127</A>]['08].

%A A. Maayan
%A et al ...
%A R. Iyengar
%T Formation of regulatory patterns during signal propagation in a mammalian
   cellular network
%J Science
%V 309
%N 5737
%P 1078-1083
%M AUG
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, zz0716, mammalian cellular network, data,
   regulatory, FFL, FFL4, BIFAN, pattern, motif, Ma'ayan,
   signaling pathways, signalling, hippocampus, hippocampal CA1, viaAK
%X "We developed a model of 545 components (nodes) & 1259 interactions
   representing signaling pathways & cellular machines in the hippocampal CA1
   neuron. Using g.theory methods, we analyzed ligand-induced signal flow
   through the system. Specification of input & output nodes allowed us to
   identify functional modules. Networking resulted in the emergence of
   regulatory motifs, such as +ve & -ve feedback & feedforward loops, that
   process information. Key regulators of plasticity were highly connected nodes
   required for the formation of regulatory motifs, indicating the potential
   importance of such motifs in determining cellular choices between
   homeostasis & plasticity."    [|V|=545, |E|=1259, viaAK.]
   -- [<A HREF="http://dx.doi.org/10.1126/science.1108876">doi:10.1126/science.1108876</A>]['16].
   [Also search for: MolBio regulatory network].

%A R.-L. Hsiao
%A D. Stott Parker
%A H.-C. Yang
%T Support for bioindexing in BLASTgres
%J Data Integration in the Life Sciences
%I SpringerVerlag
%S LNCS
%V 3615
%P 284-287
%D 2005
%K BLASTgres, conf, DILS, MolBio, c2005, c200x, c20xx, postgres sql,
   postgreSQL, postgressql, Blast, data base, database, databases, indexing,
   DNA, sequence
%X "... Essential biodatatypes (biological datatypes such as seq.locations) &
   tools (such as the popular BLAST seq.alignment tools) are not supported in
   traditional DB systems, which has forced researchers to represent biological
   knowledge counter intuitively, & implement codes for data operations. ...
   introduces BLASTgres, an extension of the PostgresSQL DB system, that
   provides indexable biodatatypes & joinable BLAST alignment."   auths@ucla.
   -- [<A HREF="http://dx.doi.org/10.1007/11530084_23">doi:10.1007/11530084_23</A>]['08], or
   -- [<A HREF="http://www.cs.ucla.edu/~stott/bioinf/BLASTgres.pdf">pdf@ucla</A>]['08].
   -- [<A HREF="http://sourceforge.net/projects/blastgres">blastgres@sourcefor...</A>]['08].
   -- [<A HREF="http://www.postgresql.org/">postgresql.org</A>]['08].

%A J. Hu
%A B. Li
%A D. Kihara
%T Limitations and potentials of current motif discovery algorithms
%J NAR
%V 33
%P 4899-4913
%D 2005
%K jrnl, NAR, MolBio, c2995, c200x, c20xx, motif, discovery, motifs, limits,
   limitation, algorithm, intro, survey
%X "... designed a comprehensive set of performance measures & benchmarked five
   modern seq.-based motif discovery algs ... It is revealed that the nucleotide
   & the binding site level accuracy are very low, while the motif level
   accuracy is relatively high, which indicates that the algs. can usually
   capture at least one correct motif in an input sequence. ... a consensus
   ensemble algorithm has been developed ..."   [49 refs].
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gki791">doi:10.1093/nar/gki791</A>]['08].

%A R. Sharan
%A S. Suthram
%A R. M. Kelley
%A T. Kuhn
%A S. McCuine
%A P. Uetz
%A T. Sittler
%A R. M. Karp
%A T. Ideker
%T Conserved patterns of protein interaction in multiple species
%J PNAS
%V 102
%N 6
%P 1974-1979
%M FEB
%D 2005
%K jrnl, PNAS, MolBio, c2005, c200x, c20xx, protein interaction, PPI, network,
   networks, yeast, c.elegans, Celegans, fly, graphAlignment
%X "... multiple comp'n of the recently available protein-protein interaction
   n/ws of C.elegans, D.melanogaster, & S.cerevisiae. ... integrated
   p.interaction & seq. info. to reveal 71 n/w regions that were cons. across
   all 3 species & many exclusive to the metazoans.  ... found stat.sig. support
   for 4,645 previously undescribed protein fns & 2,609 [new] p.interactions. We
   tested 60 interaction predictions for yeast by 2-hybrid analysis, confirming
   ~ half of these.  Significantly, many of the predicted fns & interactions
   would not have been identified from seq.similarity alone, demonstrating that
   n/w comparisons provide essential biol. information beyond what is gleaned
   from the genome."
  "Each node in the [network alignment] graph consists of a group of seq.similar
  proteins, 1 from each species; each link between a pair of nodes represents
  conserved protein interactions between the corr. protein groups. A search
  over the n/w alignment ... to identify 2 types of conserved subn/w structures:
  short linear paths of interacting ps. which model signal transduction p/ws, &
  dense clusters of interactions which model p.complexes."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0409522102">doi:10.1073/pnas.0409522102</A>]['08].
   [Also search for: graphAlignment].

%A A. Choon Tan
%A D. Q. Naiman
%A L. Xu
%A R. L. Winslow
%A D. Geman
%T Simple decision rules for classifying human cancers from gene expression
   profiles
%J J. Bioinformatics
%V 21
%N 20
%P 3896-3904
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, top scoring pair, pairs, k TSP, kTSP,
   supervised classification, rule, cancer, profile
%X "... compared our [k-TSP] to other m/c learning techniques for class
   prediction in 19 binary & multi-class gene expression datasets involving
   human cancers. The k-TSP classifier performs as efficiently as Prediction
   Analysis of Microarray & SVM, & outperforms other learning methods (d.trees,
   k-NN & naive Bayes). ... easy to interpret as the classifier involves only a
   small # of informative genes. ... we consider the k-TSP method to be a useful
   tool for cancer classification from microarray gene expression data."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti631">doi:10.1093/bioinformatics/bti631</A>]['08].

%A G. B. Fogel
%A D. G. Weekes
%A G. Varga
%A E. R. Dow
%A A. M. Craven
%A H. B. Harlow
%A E. W. Su
%A E. Onyia
%A C. Su
%T A statistical analysis of the TRANSFAC database
%J Bio Systems
%V 81
%N 2
%P 137-54
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, TRANSFAC, transcription factor, factors,
   binding site, sites, TFBS, TFBSs
%X "Transcription factors are key regulatory elts that control gene expression.
   The TRANSFAC [DB] represents the largest repository for experimentally
   derived ... (TFBS). ... present a stat. analysis of all TFBS in the TRANSFAC
   DB. ... suggests that current defn of TFBS core regions in TRANSFAC should be
   re-examined so as to capture a more precise notion of cores. We offer insight
   into more appropriate defns of TFBS consensus seqs. & core regions. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.biosystems.2005.03.003">doi:/10.1016/j.biosystems.2005.03.003</A>]['09].

%A Y. Jung Kim
%A A. Boyd
%A B. D. Athey
%A J. M. Patel
%T miBLAST: scalable evaluation of a batch of nucleotide sequence queries with
   BLAST
%J NAR
%V 33
%N 13
%P 4335-4344
%D 2005
%K jrnl, NAR, MolBio, c2005, c200x, c20xx, query, miBlast, Blast, qGram, kMer
%X "... miBLAST, that evaluates such batch workloads efficiently. At the core,
   miBLAST employs a q-gram filtering & an index join for efficiently detecting
   similarity between the query seqs. & database seqs.. This set-oriented
   technique, which indexes both the query & the database sets, results in
   substantial performance improvements ... results show that miBLAST is sig.
   faster than BLAST in many cases. [eg] miBLAST aligned 247,965 oligonucleotide
   seqs. in the Affymetrix probe set against the Human UniGene in 1.26 days,
   compared with 27.27 days with BLAST (an improvement by a factor of 22). ..."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gki739">doi:10.1093/nar/gki739</A>]['09],
   [Also search for: megaBlast].

%A C. Francke
%A R. J. Siezen
%A B. Teusink
%T Reconstructing the metabolic network of a bacterium from its genome
%J Trends in Microbiology
%V 13
%N 11
%P 550-558
%M NOV
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, metabolic, network, networks, pathway,
   pathways, bacterium, bacterial, gene
%X "... understanding the reln between the genome & the physiology of an
   organism is an important incentive to reconstruct metabolic n/ws. The 1st
   steps in the process can be automated & it does not take much effort to
   obtain an initial metabolic reconstruction from a genome seq.. However, such
   a reconstruction is certainly not flawless & correction of the many
   imperfections is laborious. It requires the combined analysis of the
   available info. on protein seq., phylogeny, gene-context & co-occurrence but
   is also aided by high-throughput experimental data. Simultaneously, the
   reconstructed network provides the opportunity to visualize the "omics" data
   within a relevant biological functional context & thus aids the
   interpretation of those data."
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/16169729">n c b i</A>]['09],
   -- [<A HREF="http://dx.doi.org/10.1016/j.tim.2005.09.001">doi:/10.1016/j.tim.2005.09.001</A>]['09].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Metabolic_network_modelling">wikip</A>].)

%T Handbook of Computational Molecular Biology
%E S. Alurua
%I ChapmanHall
%P 1104
%M DEC
%D 2005
%K book, text, MolBio, c2005, c200x, c20xx, bioinformatics, algorithms, DNA,
   bio, biol, biological, computational biology
%X 1st ed 2005, hb us$124; uk us isbn:1584884061; uk us isbn13:978-1584884064.
   Reviewed in [<A HREF="http://dx.doi.org/10.1093/bib/bbm002">doi:10.1093/bib/bbm002</A>]['09],
   ... 38 chapters organized into eight disjoint sections/parts.
   [Also search for: MolBio book].

%A N. Beerenwinkel
%A M. Dumer
%A T. Sing
%A J. Rahnenfuhrer
%A T. Lengauer
%A J. Selbig
%A D. Hoffmann
%A R. Kaiser
%T Estimating HIV evolutionary pathways and the genetic barrier to
   drug resistance
%J J. Infectious Diseases
%V 191
%N 11
%P 1953-1960
%M JUN
%D 2005
%K jrnl, MolBio, c2005, c200x, c200x, zz0709, AIDS, HIV, virus, drug, drugs,
   resistance, zidovudine, stavudine, lamivudine, didanosine
%X "... defined the genetic barrier, a quantity that summarizes the difficulty
   for the v. to escape from the selective pressure of the drug by developing
   escape mutations. ... evol.models for zidovudine, zidovudine plus lamivudine,
   & zidovudine plus didanosine. The genetic barriers to resistance to
   zidovudine, stavudine, lamivudine, and didanosine, for the above 3 regimens,
   were computed and analyzed. ... heterogeneous. The genetic barrier to
   zidovudine resistance was increased if lamivudine was added to zidovudine
   but was decreased for didanosine. ..."
   pdf@[<A HREF="http://dx.doi.org/10.1086/430005">doi:10.1086/430005</A>]['09],
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/15871130">n c b i</A>]['09].

%A A. A. Escalante
%A O. E. Cornejo
%A D. E. Freeland
%A A. C. Poe
%A E. Durrego
%A W. E. Collins
%A A. A. Lal
%T A monkey's tale: The origin of Plasmodium vivax as a human malaria parasite
%J PNAS
%V 102
%P 1980-1985
%D 2005
%K jrnl, PNAS, MolBio, c2005, c200x, c20xx, malaria, Plasmodium vivax, parasite,
   population, evolution, human, macaque, macaques
%X "... investigate the phylogenetic relationships among 10 species of P. that
   infect primates by 3 three genes, 2 nuclear (beta-tubulin & cell division
   cycle 2) & a gene from the plastid genome (the elongation factor Tu). We find
   compelling evidence that P.vivax is derived from a species that inhabited
   macaques in Southeast Asia.  ... est. the time to the most recent common
   ancestor at 4 neutral gene loci from Asian & South American isolates (a min.
   sample of 7 isolates per locus). Our analysis estimates that the extant
   pop'n of P. vivax originated between 45,680 & 81,607 years ago. ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0409652102">doi:10.1073/pnas.0409652102</A>]['09],
   auth1@[<A HREF="http://sols.asu.edu/people/faculty/aescalante.php">ASU</A>]['09].

%A D. H. Huson
%A D. Bryant
%T Application of phylogenetic networks in evolutionary studies
%J Molec. Biol. and Evol.
%V 23
%N 2
%P 254-267
%M FEB
%D 2005
%K jrnl, MBE, SplitsTree4, MolBio, c2005, c200x, c20xx, evolutionary,
   phylogenetic, tree, trees, recombination, splitstree, splits tree, networks,
   horizontal transfer
%X "... analysis of the data may not be best served by using methods that
   enforce a tree structure but rather by a richer visualization of the data to
   evaluate its properties, at least as an essential first step. ... show how
   split networks can represent confidence sets of trees & introduce a
   conservative statistical test for whether the conflicting signal in a n/w is
   treelike. Finally, this article describes a new program, SplitsTree4, an
   interactive & comprehensive tool for inferring different types of
   phylogenetic networks from sequences, distances, & trees."
   -- pdf@[<A HREF="http://dx.doi.org/10.1093/molbev/msj030">doi:10.1093/molbev/msj030</A>]['09], free?
   SplitsTree4@[<A HREF="http://www-ab.informatik.uni-tuebingen.de/software/splitstree4">uni-tuebingen.de</A>]['09].
   [Also search for: evolutionary tree MolBio].

%A W. J. Ewens
%A G. Grant
%T Statistical Methods in Bioinformatics: An Introduction
%I Springer
%P 588
%D 2005
%K book, text, MolBio, bioinformatics, stats, c2005, c200x, c20xx, course,
   courses, learning, teaching, statistics
%X "... based on the content of a two-semester course in bioinformatics and
   computational biology; is one of the most important books in this area from
   the perspective of teaching final year undergraduates and post-graduates in
   a range of disciplines ..."
   2nd ed 2005; hb us$60; uk us isbn:0387400826; uk us isbn13:978-0387400822.
   [Also search for: MolBio book].

%A P. Davan
%A L. F. Abbott
%T Theoretical Neuroscience: Computational and Mathematical Modeling of
   Neural Systems
%I MITpress
%P 480
%M SEP
%D 2005
%K book, text, c2005, c200x, c20xx, neural, brain, systems, neurons, neuron,
   synapse, synaptic, model, modelling, biol, bio, science
%X "Part I discusses the relationship between sensory stimuli and neural
   responses, focusing on the representation of information by the spiking
   activity of neurons. Part II discusses the modeling of neurons and neural
   circuits on the basis of cellular and synaptic biophysics.
   Part III analyzes the role of plasticity in development and learning."
   1st ed 2005, pb us$23; uk us isbn:0262541858; uk us isbn13:978-0262541855.

%A C. Hamlin
%T The Hospital by the River: A Story of Hope
%I KregelPubl.
%D 2005
%K book, text, c2005, c200x, c20xx, zz0110, medicine, fistula, Africa, Ethiopia,
   Addis Ababa, Abeba, hospital, women, womens, health, gynaecology, operation,
   surgery, repair, childbirth, midwifery, obstetric, obstetrics, doctors,
   Hamlin, charity, donate, donations, good news
%X "... the life and mission of Dr. Catherine Hamlin who, with her husband Reg,
   established what has been heralded as one the most incredible medical
   programs in the modern world. ... dedicated their lives to women suffering
   the catastrophic effects of obstructed labor. ... Catherine and Reg, with
   their team of dedicated fistula surgeons, have successfully operated on over
   25,000 women, and the Addis Ababa Fistula Hospital has become a major
   teaching institutions for gynaecologists from all over Ethiopia and the
   developing world. Set against the backdrop of Ethiopia, this is a moving and
   utterly compelling account of an extraordinary life."
   1st ed 2005; pb us$10; uk us isbn:0825460719; uk us isbn13:978-0825460715.
   (Also see [<A HREF="http://www.hamlin.org.au/">.au</A>]['15],
          or [<A HREF="http://www.hamlinfistulausa.org/">usa</A>]['15],
          or [<A HREF="http://www.hamlinfistulauk.org/" >uk</A>]['15],
          or [<A HREF="http://www.hamlinfistula.org/">others</A>]['15].)
   ([<A HREF="http://maps.google.com.au/maps?f=q&source=s_q&hl=en&geocode=&q=fistula+hospital+addis+abeba+ethiopia&sll=9.004992,38.716207&sspn=0.007969,0.007532&ie=UTF8&hq=fistula+hospital&hnear=Addis+Abeba,+Ethiopia&t=h&z=13&iwloc=A">g-maps</A>].)

%A S. Itzkovitz
%A R. Levitt
%A N. Kashtan
%A R. Milo
%A M. Itzkovitz
%A U. Alon
%T Coarse-graining and self-dissimilarity of complex networks
%J Phys. Rev. E, Stat. Nonlin. Soft Matter Phys.
%V 71
%P 016127
%M JAN
%D 2005
%K eJrnl, MolBio, c2005, c200x, c20xx, self dissimilar, network, scale, grained,
   coarse graining, grain, mammalian protein signal-transduction, motif, motifs,
   simplicity
%X "Can ... n/ws ... coarse-grained into smaller & more understandable versions
   in which each node represents an entire pattern in the original n/w? ...
   electronic circuit ... mammalian protein signal-transduction n/w ...
   MAP-kinase ... We find that both bio and elec n/ws are "self dissimilar"
   with different n/w motifs at each level. ..."   [58 refs].
   'CGUs are patterns [that] serve as nodes in a CG network ...  To
   define simplicity we describe each occurrence of the subgraph, G,
   as a "black box." ... The lower the # of ports [i.e., visible nodes
   of G] the simpler ...'
   -- pdf@auth@[<A HREF="http://www.weizmann.ac.il/mcb/UriAlon/">weism...</A>]['10];
   see @[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/15697678">pubm'd</A>]['10].

%A T. R. Gregory
%T The C-value enigma in plants and animals: A review of parallels and
   an appeal for partnership
%J Annals of Botany
%V 95
%P 133-146
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, c value, Cvalue, genome size, amount, DNA
%X [<A HREF="http://dx.doi.org/10.1093/aob/mci009">doi:10.1093/aob/mci009</A>][1'0].
   [Also search for: Cvalue MolBio].

%A S. H. Bokhari
%A J. R. Sauer
%T A parallel graph decomposition algorithm for DNA sequencing with nanopores
%J J. Bioinformatics
%V 21
%N 7
%P 889-896
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, DNA, sequence, assembly, sequencing,
   nanopore
%X "... [an] extreme variation of the well-known Eul.path approach. It searches
   over a space of de Bruijn graphs until it finds one in which (a) the impact
   of errors is eliminated & (b) both possible orientations of the two ssDNA
   sequences can be identified separately & unambiguously. ...  is able to
   correctly reconstruct real DNA seqs. of the order of 10**6 bases (e.g., the
   bacterium M.pneumoniae) from simulated erroneous reads on a modest workstn in
   ~1h. [And] a parallel implementation ... on the Cray Multithreaded (MTA-2)
   supercomputer ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti129">doi:10.1093/bioinformatics/bti129</A>]['10].
   [Also search for: MolBio sequence assembly] and
   [also search for: MolBio nanopore].

%A M. Socolich
%A S. W. Lockless
%A W. P. Russ
%A H. Lee
%A K. H. Gardner
%A R. Ranganathan
%T Evolutionary information for specifying a protein fold
%J Nature
%V 437
%P 512-518
%M SEP
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, proteins, structure, fold, folding,
   problem, 3D, information
%X "Classical studies show that for many ps., the info. required for specifying
   the tertiary struct. is contained in the amino acid seq.. ... attempt to
   define the seq. rules for specifying a protein fold by computationally
   creating artificial p.seqs. using only stat. info. encoded in a multiple
   seq. alignment & no tertiary struct. info.. Experimental testing of libraries
   of artificial WW domain seqs. shows that a simple statistical energy fn
   capturing coevolution between a.a.residues is nec. & suff. to specify seqs.
   that fold into native structs..  The artificial ps. show thermodynamic
   stabilities similar to natural WW domains, & struct.determination of one
   artificial p. shows excellent agreement with the WW fold at atomic res'n. The
   relative simplicity of the info. used for creating seqs. suggests a marked
   red'n to the potential complexity of the protein-folding problem."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03991">doi:10.1038/nature03991</A>]['12].

%A U. Stelzl
%A et al ...
%A E. E. Wanker
%T A human protein-protein interaction network: A resource for annotating the
   proteome
%J Cell
%V 122
%N 6
%P 957-968
%M SEP
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, zz0415, human, protein, interaction,
   network, PPI, regulatory, data, Y2H, Axin-1, ANP32A, CRMP1, Wnt
%X "... a protein matrix of 4456 baits & 5632 preys was screened by automated
   yeast two-hybrid (Y2H) interaction mating. We identified 3186 mostly novel
   interactions among 1705 proteins, resulting in a large, highly connected
   n/w. Indep. pull-down & coimmunoprecipitation assays validated the overall
   quality of the Y2H interactions. Using topological & GO criteria, a scoring
   system was developed to define 911 high-confidence interactions among 401
   proteins. Furthermore, the n/w was searched for interactions linking
   uncharacterized gene products & human disease proteins to regulatory
   cellular pathways. Two novel Axin-1 interactions were validated
   experimentally, characterizing ANP32A & CRMP1 as modulators of Wnt
   signaling. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cell.2005.08.029">doi:10.1016/j.cell.2005.08.029</A>]['15].
      "degree distribution ... closely following a power-law"
      "24 hubs-proteins with more than 30 partners"
      *** "Table S3: ... Protein-Protein Interactions ... for 3,269 pairs of
      baits and preys (3,186 unique PPIs) [<A HREF="http://www.sciencedirect.com/science/MiamiMultiMediaURL/1-s2.0-S0092867405008664/1-s2.0-S0092867405008664-mmc3.pdf/272196/html/S0092867405008664/7f0a176f8132220f4a1b849b8633f108/mmc3.pdf">pdf</A>]['15]." ***
   [Also search for: human protein interaction network].

%A J.-F. Rual
%A et al ...
%A M. Vidal
%T Towards a proteome-scale map of the human protein-protein interaction
   network
%J Nature
%V 437
%N 7062
%P 1173-1178
%M OCT
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, human, protein interaction, network, PPI,
   data, Y2H, regulatory
%X "... describe an initial version of a proteome-scale map of human binary
   protein-protein interactions. Using a stringent, high-throughput yeast
   two-hybrid system, we tested pairwise interactions among the products of
   ~8,100 currently available Gateway-cloned open reading frames & detected
   ~2,800 interactions. This data set, called CCSB-HI1, has a verification rate
   of ~78% as revealed by an indep. co-affinity purification assay, & correlates
   sig. with other biological attributes. The CCSB-HI1 data set increases by
   ~70% the set of available binary interactions within the tested space &
   reveals > 300 new connections to over 100 disease-associated proteins. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature04209">doi:10.1038/nature04209</A>]['15].
      (Very hard to find "the" network.)
   [Also search for: human protein interaction network].

%A I. Chanda
%A A. Pan
%A C. Dutta
%T Proteome composition in Plasmodium falciparum: Higher usage of GC-rich
   nonsynonymous codons in highly expressed genes
%J JME
%V 61
%N 4
%P 513-523
%M OCT
%D 2005
%K jrnl, JMW, MolBio, c2005, c200x, c20xx, zz0518, malaria parasite,
   Plasmodium falciparum, 3D7, amino acid, composition, bias
%X "... extremely AT-rich genomes ... study analyzes the amino acid usage
   pattern in 5038 annotated protein-coding seqs. in P.falciparum clone 3D7. The
   AA composition of individual proteins, though dominated by the directional
   mutational pressure, exhibits wide variation across the proteome. ...
   frequencies of residues encoded by GC-rich codons such as Gly, Ala, Arg, &
   Pro increase significantly in the products of the highly expressed genes. ...
   Negative correlation of the expression level of proteins with respective
   molecular weights supports the notion that P.falciparum, in spite of its
   intracellular parasitic lifestyle, follows the principle of cost
   minimization."  [online 7/2005.]
   -- [<A HREF="https://doi.org/10.1007/s00239-005-0023-5">doi:10.1007/s00239-005-0023-5</A>]['18].

%A E. W. Myers
%T The fragment assembly string graph
%J J. Bioinformatics
%V 21
%N 2
%P ii79-ii85
%D 2005
%K conf, MolBio, c2005, c200x, c20xx, string graph, stringGraph, DNA, sequence,
   shotgun assembly, assembler, unitig, BOA
%X "pres. a concept & formalism, the string graph, which represents all that
   is inferable about a DNA seq. from a collection of shotgun sequencing reads
   collected from it. We give time & space efficient algs. for constructing a
   string graph given the collection of overlaps between the reads &, in
   particular, present a novel linear expected time alg. for transitive
   reduction in this context. ... demonstrates that the decomposition of reads
   into k-mers employed in the de Bruijn graph approach described earlier is not
   essential [[oo!]], & exposes its close connection to the unitig approach we
   developed @Celera. ... g.assembler called BOA (Berkeley Open Assembler) ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti1114">doi:10.1093/bioinformatics/bti1114</A>]['08],
   -- [<A HREF="http://research.janelia.org/myers/Papers/string.graph.pdf">ECCB pdf</A>]['08].
   [Also search for: MolBio ABruijn graph], and
   [also search for: sequence assembly MolBio].

%A K. Linblad-Toh
%A et al ...
%A E. S. Lander
%T Genome sequence, comparative analysis and haplotype structure of the
   domestic dog
%J Nature
%V 438
%N 7069
%P 803-819
%M DEC
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, zz0411, animal, mammal, canine, dog, dogs,
   genome, nGenome, Canis familiaris, breed, SNPs
%X "... draft genome seq. of the domestic dog (Canis familiaris), together with
   a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog
   is of particular interest because it provides important evol.info. & because
   existing breeds show great phenotypic diversity for morphological,
   physiological & behavioural traits. We use seq.comparison with the primate &
   rodent lineages to shed light on the structure & evoln of genomes & genes.
   [Most] of the most highly conserved non-coding seqs. in mammalian genomes are
   clustered near a small subset of genes with important roles in development.
   Analysis of SNPs reveals long-range haplotypes across the entire dog genome,
   & defines the nature of genetic diversity within & across breeds. The current
   SNP map now makes it possible for genome-wide assoc.studies to identify genes
   responsible for diseases & traits, with important consequences for human &
   companion animal health."
   -- [<A HREF="http://dx.doi.org/10.1038/nature04338">doi:10.1038/nature04338</A>]['11].
   (Also see the dog-g-proj@[<A HREF="http://www.broadinstitute.org/mammals/dog-genome-project">broadInst</A>]['11].)

%A B. H.  Lerner
%T Remembering Berton Roueche - master of medical mysteries
%J J. Medicine
%V 353
%P 2428-2431
%M DEC
%D 2005
%K obit, c2005, c200x, c20xx, zz0312, Berton, Roueche, Burton, medicine,
   medical detectives,  mystery, mysteries, writer, House, doctor, death
%X "'"He was never going to sleep again. Sleep was a waste of time. Then he got
   the idea I was trying to poison him. He didn't trust me, he said, & if I
   didn't leave him alone, he would tear off his clothes & run out in the street
   naked.'  Fifty years ago, these words taught the public about a horrifying
   side effect of the new 'wonder drug' cortisone: mania. The speaker was the
   wife of a man who had been treated with cortisone for his previously
   incurable periarteritis nodosa & the author q. her was BR [1910-1994] ..."
   -- [<A HREF="http://dx.doi.org/10.1056/NEJMp058147">doi:10.1056/NEJMp058147</A>]['12].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Berton_Rouech%C3%A9">wikip</A>].)

%A J. Westbrook
%A et al
%T Appendix 3.6.2 The Protein Data Bank exchange dictionary
%B Int. Tables for Crystallography, Vol. G. Definition and exchange of
   crystallographic data
%I Springer
%P 195-198
%D 2005
%K chapter, MolBio, c2005, c200x, c20xx, zz0521, protein, data, mmCIF, CIF,
   PDBx, PDBML
%X "... A key strength of the mmCIF technology is the extensibility afforded by
   a framework based on a s/w-accessible data dictionary. ..."
   -- [<A HREF="https://mmcif.wwpdb.org/docs/pubs/appendix3.6.3_pdbx.pdf">app3.6.3</A>]['21].
   Also see [<A HREF="https://mmcif.wwpdb.org/docs/pubs/pdbx-mmcif-references.html">wwpdb</A>]['21],
   at [<A HREF="https://mmcif.wwpdb.org/">wwpdb</A>]['21].

%A P. M. D. Fitzgerald
%A et al
%T Chapter 4.5. The Macromolecular dictionary (mmCIF)
%B Int. Tables for Crystallography, Vol. G. Definition and exchange of
   crystallographic data
%I Springer
%P 295-443
%D 2005
%K chapter, MolBio, c2005, c200x, c20xx, zz0521, protein, data, mmCIF, CIF,
   PDB, PDBx, PDBML
%X "Volume G describes the std data exchange & archival file format (CIF) used
   throughout crystallography. It provides in-depth information vital for
   small-molecule, inorganic and macromolecularcrystallographer ..."
   -- [<A HREF="https://mmcif.wwpdb.org/docs/pubs/AUTHOR_ch4o5.pdf">wwpdb</A>]['21].
   Also see [<A HREF="https://mmcif.wwpdb.org/docs/pubs/pdbx-mmcif-references.html">wwpdb</A>]['21],
   at [<A HREF="https://mmcif.wwpdb.org/">wwpdb</A>]['21].

%A C. B. Do
%A M. S. P. Mahabhashyam
%A M. Brudno
%A S. Batzoglou
%T ProbCons: Probabilistic consistency-based multiple sequence alignment
%J Gen. Res.
%V 15
%P 330-340
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, zz0820, protein alignment, gap, gaps,
   indel, costs
%X "... alignments, however, is a difficult comp. problem because of not only
   the high computational cost but also the lack of proper objective fns for
   measuring alignment quality. ... we introduce probabilistic consistency, a
   novel scoring fn for multiple seq. comparisons. We present ProbCons, a
   practical tool for progressive protein multiple seq. al. based on prob.
   consistency, & evaluate its performance on several std al.benchmark
   d.sets. ..."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.2821705">doi:10.1101/gr.2821705</A>]['20].
   [Also search for: MolBio protein alignment].

%A J. I. Glass
%A N. Assad-Garcia
%A N. Alperovich
%A S. Yooseph
%A M. R. Lewis
%A M. Maruf
%A C. A. Hutchison III
%A H. O. Smith
%A J. C. Venter
%T Essential genes of a minimal bacterium
%J PNAS
%V 103
%N 2
%P 425-430
%M JAN
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, minimal bacterium, artificial, life,
   Mycoplasma genitalium, laboratorium, bacteria, bacterium, gene, genes,
   essential, genome
%X "M.g. has the smallest genome of any organism that can be grown in
   pure culture. It has a minimal metabolism & little genomic redundancy. ...
   its genome is expected to be a close approx. to the minimal set of genes
   needed to sustain bacterial life. ... we identify 382 of the 482 M.g.
   protein-coding genes as essential, plus five sets of disrupted genes ...
   Genes encoding proteins of unknown function constitute 28% ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0510013103">doi:10.1073/pnas.0510013103</A>]['09],  also see...
   M.laboratorium@[<A HREF="http://en.wikipedia.org/wiki/Minimal_Genome_Project">wikip</A>]['09].

%A D. N. Cooper
%A P. D. Stenson
%A N. A. Chuzhanova
%T The Human Gene Mutation Database (HGMD) and its exploitation in the study of
   mutational mechanisms
%J Curr. Protoc. Bioinformatics
%M JAN
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, zz0514, HGMD, DB, human, mutations,
   variation, SNP, SNPs, disease, illness, health, genetic, genes, database,
   Cardiff
%X "... (HGMD) ... core collection of data on germ-line mutations in nuclear
   genes underlying or assoc. with human inherited disease
   [<A HREF="http://www.hgmd.org">www</A>]. ... include single base-pair
   substitutions in coding, regulatory, ..., as well as gross gene deletions,
   insertions, ... Each mutation is entered into HGMD only once ... By June
   2005, the database contained in excess of 53,000 different lesions detected
   in 2029 different nuclear genes ..."
   -- [<A HREF="http://dx.doi.org/10.1002/0471250953.bi0113s12">doi:10.1002/0471250953.bi0113s12</A>]['14],
      [<A HREF="http://www.hgmd.org">HGMD</A>]['14].
   [Also search for: variation illness database].

%A K. R. Rasmussen
%A J. Stoye
%A E. W. Myers
%T Efficient q-gram filters for finding all epsilon-matches over a given length
%J J. Comput. Biol.
%V 13
%N 2
%P 296-308
%M MAR
%D 2006
%O 9th RECOMB, LNCS, Vol.3678, pp.189-203, 2005
%K jrnl, JCB, MolBio, c2006, c200x, c20xx, q-gram, qGram, kmer, k-mer, match,
   filter, e-error, eError, kError
%X "Fast & exact comparison of large genomic seqs. [is hard] ... consider the
   problem of finding all epsilon-matches between 2 seqs., i.e., all local
   alignments over a given length with an error rate <= epsilon. We study this
   problem theoretically, giving an efficient q-gram filter for solving it.
   2 applications of the filter are also discussed, in particular genomic seq.
   assembly & BLAST-like seq. comparison. ... show that the method is 25 x
   faster than BLAST, while not being heuristic."
   -- [<A HREF="http://research.janelia.org/myers/Papers/qgram.filter.pdf">conf.pdf@janelia.org</A>]['08].
   [Also search for: Myers assembly c2005].

%A C. Fan
%A D. S. Oh
%A L. Wessels
%A B. Weigelt
%A D. S.A. Nuyten
%A A. B. Nobel
%A L. J. van't Veer
%A C. M. Perou
%T Concordance among gene-expression-based predictors for breast cancer
%J NEJM
%V 355
%N 6
%P 560-569
%M AUG
%D 2006
%K jrnl, NEJM, MolBio, c2006, c200x, c20xx, gene, genes, marker, markers,
   predict, predictor, set, select, selection, expression profiling,
   vant Veer,  vantVeer
%X "... To compare the predictions derived from these gene sets for individual
   samples, we obtained a single data set of 295 samples & applied 5 gene-
   -expression-based models: intrinsic subtypes, 70-gene profile, wound
   response, recurrence score, & the two-gene ratio (for patients who had been
   treated with tamoxifen).
   Results ... most models had high rates of concordance in their outcome
   predictions for the individual samples. In particular, almost all tumors
   identified as having an intrinsic subtype of basal-like, HER2-positive &
   estrogen-receptor-negative, or luminal B (assoc. with a poor prognosis) were
   also classified as having a poor 70-gene profile, activated wound response,
   & high recurrence score. The 70-gene & recurrence-score models, which are
   beginning to be used in the clinical setting, showed 77 to 81% agreement in
   outcome classification. ..."
   -- [<A HREF="http://content.nejm.org/cgi/content/abstract/355/6/560">nejm</A>]['08].

%T Systems Biology and Regulatory Genomics.  RECOMB 2005 Satellite
   Workshops on Systems Biology & Regulatory Genomics Revised Selected Papers
%E E.Eskin, T.Ideker, B.Raphael, C.Workman
%I SpringerVerlag
%S LNCS
%V 4023
%P 259
%D 2006
%O RECOMB '05
%K conf, MolBio, c2006, c200x, c20xx, genomics, metabolomics, comparative,
   gen, regulatory networks, protein interaction
%X pb; uk us isbn13:978-3540482932.

%A M. Vignuzzi
%A J. K. Stone
%A J.J.Arnold, C.E.Cameron, R.Andino
%T Quasispecies diversity determines pathogenesis through cooperative
   interactions in a viral population
%J Nature
%V 439
%P 344-348
%M FEB
%D 2006
%K letter, virus, c2006, c200x, c20xx, MolBio, biol, zz1205, error, rate,
   poliovirus, polio, polymerase, ribavirin, drug resistance, phenotype,
   genotype, G64S
%X "...population does not consist of a single genotype; rather, it is an
   ensemble of related seqs., termed quasispecies. ... been hypothesized
   that high mutation rates create a 'cloud' of potentially beneficial m. at
   the pop. level, [give] the viral q. a greater prob. to evolve & adapt ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature04388">doi:10.1038/nature04388</A>]['05].

%A V. Malaiyand
%A et al
%T Impact of CYP2A6 genotype on pretreatment smoking behaviour and nicotine
   levels from and usage of nicotine replacement therapy
%J Molecular Psychiatry
%V ?
%N ?
%P ?-?
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0206, smoking, tobacco, cigarettes, gene,
   health, therapy, level, patch, stats
%X "... CYP2A6 genotype influences smoking behaviour in a Caucasian treatment-
   seeking population & that CYP2A6 genotype affects plasma levels obtained
   from, & usage of, NRT."
   -- [<A HREF="http://dx.doi.org/10.1038/sj.mp.4001794">doi:10.1038/sj.mp.4001794</A>]['06] online Jan..

%A A. Kocsor
%A A. Kertesz-Farkas
%A L. Kajan
%A S. Pongor
%T Application of compression-based distance measures to protein sequence
   classification: a methodological study
%J J. Bioinformatics
%V 22
%N 4
%P 407-412
%MD 2006
%K jrnl, MolBio, c2006, c200x, c20xx, compress, protein, family, CBM
%X "... compression-based distance measures (CBMs) using the [LZ] and the PPMZ
   compression algs. & compared their performance with that of the Smith
   Waterman algorithm & BLAST, using nearest neighbour or [SVM] classification
   schemes. ... low & high-complexity sequence segments of the human proteome,
   CBMs values show a dependence on the length & the complexity of the seqs.
   compared. ... CBMs performed especially well on distantly related proteins
   where the perf. of a combined measure, constructed from a CBM & a BLAST
   score, approached or even slightly exceeded that of the S-W alg. & 2 HMM
   based algorithms."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti806">doi:10.1093/bioinformatics/bti806</A>]['06].

%A W. Zhong
%A P. W. Sternberg
%T Genome-wide prediction of C. elegans genetic interactions
%J Science
%V 311
%N 5766
%P 1481-1484
%M MAR
%D 2006
%K jrnl, c2006, c200x, c20xx, MolBio, interaction, gene, genes, protein,
   Saccharomyces cerevisiae, Caenorhabditis elegans, Celegans,
   Drosophila melanogaster, yeast, worm, fruit fly, function, functional,
   interaction network, zz0306
%X "To obtain a global view of functional interactions among genes in a
   metazoan genome, we computationally integrated interactome data, gene
   expression data, phenotype data, and functional annotation data from 3 model
   organisms ... and predicted genome-wide genetic interactions in C. elegans.
   The resulting genetic interaction network (consisting of 18,183 interactions)
   provides a framework for system-level understanding of gene functions. We
   experimentally tested the predicted interactions for two human disease-
   related genes and identified 14 new modifiers."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1123287">doi:10.1126/science.1123287</A>]['06].

%A J. M. Echevarria
%A A. Avellon
%T Hepatitis B virus genetic diversity
%J J. Med Virol.
%V 78
%N Suppl.1
%P s36-s42
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, HBV, viral, genomes, genotype, genotypes,
   varieties, strain, strains, variants, HBsAg, RT
%X "... replicates through an RNA intermediate because of the reverse-
   -transcriptase (RT) activity of its DNA polymerase. [So] the mutation rate
   for HBV is higher than the rate observed for most DNA viruses. HBVs are
   classified into genotypes based on genomic sequencing, & antigenic subtypes
   based on the antigenic properties of its major surface glycoprotein, the HBV
   surface antigen (HBsAg). ... Since the RT region of the genome overlaps the
   sequence encoding the HBsAg molecule, selection of drug resistant variants
   involves, in some cases, the indirect selection of HBsAg variants. Viral
   variants displaying changes in HBsAg seem to be very common among chronic
   HBV carriers; & some of these variants may emerge under the pressure of the
   neutralizing antibody response, leading to vaccine resistance & resistance
   to immunotherapy. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/jmv.20605">wiley</A>]['06].

%A A. S. Hinrichs
%A et al
%T The UCSC Genome Browser Database: update 2006
%J NAR
%V 34 (Database Issue)
%P D590-D598
%D 2006
%K NAR, MolBio, c2006, c200x, c20xx, GBD, PhastCons, Siepel
%X "... contains sequence & annotation data for the genomes of about a dozen
   vertebrate species & several major model organisms. Genome annotations
   typically include assembly data, sequence composition, genes & gene
   predictions, mRNA & expressed sequence tag evidence, comparative genomics,
   regulation, expression & variation data. The database is optimized to
   support fast interactive performance with web tools that provide powerful
   visualization & querying capabilities for mining the data. The Genome
   Browser displays a wide variety of annotations at all scales from single
   nucleotide level up to a full chromosome. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gkj144">doi:10.1093/nar/gkj144</A>]['06],
   Also see [<A HREF="http://www.bscb.cornell.edu/~siepel/pubs.html">Siepel</A>]['06].

%A G. Hamilton
%T Virology: The gene weavers
%J Nature
%V 441
%P 683-685
%M JUN
%D 2006
%K news, intro, MolBio, virus, viruses, phage, phages, c2006, c200x, c20xx,
   viral, zz0606
%X "... now thought to be some 10**31 viral particles on the planet ...
   ... Retroviruses are a type of virus that specialize in attacking animal
   cells. And roughly 8% of our genome consists of DNA copies of [them] ..."
   [14 refs] [<A HREF="http://dx.doi.org/10.1038/441683a">doi:10.1038/441683a</A>]['06].

%A J. R. S. Newman
%A S. Ghaemmaghami
%A J.Ihmels,  D.K.Breslow,  M.Noble,  J.L.DeRisi,  J.S.Weissman
%T Single-cell proteomic analysis of S. cerevisiae reveals the
   architecture of biological noise
%J Nature
%V 441
%P 840-846
%M JUN
%D 2006
%K jrnl, MolBio, gene expression, level, levels, micro arrays, microarrays,
   yeast, variation, Biol
%X "... abundance measurements of > 2500 proteins in rich & minimal media
   provide a detailed view of the cellular response to these conditions, ...
   ... argue that noise in protein expression is dominated by the stochastic
   production/destruction of [m]RNAs. Beyond this global trend, there are
   dramatic p.-specific differences in noise that are strongly corr. with a
   p.'s mode of transcription & its fn. ... proteins that respond to env.
   changes are noisy whereas those involved in p. synthesis are quiet. Thus,
   these studies reveal a remarkable structure to biological noise & suggest
   that p. noise levels have been sel. reflect the costs & potential benefits
   of this variation."
   -- [<A HREF="http://dx.doi.org/10.1038/nature04785">doi:10.1038/nature04785</A>]['06].

%A Y. V. R. Reddy
%A E. J. Perkins
%A D. A. Ramsden
%T Genomic instability due to V(D)J recombination-associated transposition
%J Genes and Development
%V 20
%P 1575-1582
%D 2006
%K MolBio, jrnl, gene, c2006, c200x, c20xx, immune system, V(D)J, VDJ, zz0606,
   T cell, Tcell, receptor, receptors, Bcell, B cells, adaptive, adaption, biol
%X "The 1st step in assembling immunoglobulin & T-cell receptors by V(D)J
   recomb. has similarities to transposon excision. The excised transposon-like
   elt then integrates into DNA targets at random in vitro, but whether this
   activity sig. threatens the genomic integrity of its host has been unclear.
   ... recover examples where the putative transposon associated with V(D)J
   recomb. integrated into the genome of a pre-B-cell line. Transposition
   accounted for a surprisingly high proportion (1/3) of integrations, while
   most of the remaining events had parallels to other aberrant V(D)J recomb.
   pathways linked to oncogenic translocation. In total, transposition occurred
   approx. once every 50,000 V(D)J recombs.. Transposition may thus contribute
   significantly to genomic instability."
   -- [<A HREF="http://www.genesdev.org/cgi/doi/10.1101/gad.1432706">doi:/10.1101/gad.1432706</A>]['06].

%A G. D. Rose
%A P. J. Fleming
%A J. R. Banavar
%A A. Maritan
%T A backbone-based theory of protein folding
%J PNAS
%V 103
%N 45
%P 16623-16633
%M NOV
%D 2006
%K jrnl, PNAS, MolBio, c2006, c200x, c20xx, zz1122, protein, structure, folding,
   back bode, backBone, side chain, sideChain
%X "... partly review, partly proposal. First, we summarize key ideas regarding
   p.folding developed over the past half-century & culminating in the current
   mindset. In this view, the energetics of side-chain interactions dominate the
   folding process, driving the chain to self-organize under folding conditions.
   Next, having taken stock, we propose an alternative model that inverts the
   prevailing side-chain/backbone paradigm. Here, the energetics of backbone
   hydrogen bonds dominate the folding process, with preorganization in the
   unfolded state. ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.0606843103">doi:10.1073/pnas.0606843103</A>]['22].
   [Also search for: sideChain backBone MolBio].

%A E. Sodergren
%A et al
%T The Genome of the Sea Urchin Strongylocentrotus purpuratus
%J Science
%V 314
%N 5801
%P 941-952
%M NOV
%D 2006
%K MolBio, jrnl, c2006, c200x, c20xx, nGenome, DNA, biol, biology,
   echinoderm, deuterostome, zz1106
%X "... 814-megabase genome of the sea urchin S.p., a model for developmental
   & systems biology. ... high heterozygosity of the genome. The genome encodes
   about 23,300 genes, including many previously thought to be vertebrate
   innovations or known only outside the deuterostomes. This echinoderm genome
   provides an evolutionary outgroup for the chordates & yields insights into
   the evolution of deuterostomes."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1133609">doi:10.1126/science.1133609</A>]['06],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">genomes@ncbi</A>]['07].

%A E. Berezikov
%A F.Thuemmler, L.W. van Laake, I.Kondova, R.Bontrop, E.Cuppen
%A R. H. A. Plasterk
%T Diversity of microRNAs in human and chimpanzee brain
%J Nature Genetics
%V ?
%P ?-?
%D 2006
%K brief comm, MolBio, c2006, c200x, c20xx, microRNA, miRNA, micro RNA,
   human, chimpanzee, brain, zz1106
%X "... massively parallel sequencing to compare the microRNA (miRNA) content of
   human & chimpanzee brains, & we identified 447 new miRNA genes. Many of the
   new miRNAs are not conserved beyond primates, indicating their recent origin,
   & some miRNAs seem species specific, whereas others are expanded in 1 species
   through duplication events. ... suggest that evolution of miRNAs is an
   ongoing process & that along with ancient, highly conserved miRNAs, there
   are a number of emerging miRNAs."  online Oct 2006
   -- but that's all! [<A HREF="http://dx.doi.org/10.1038/ng1914">doi:10.1038/ng1914</A>]['06],
      [<A HREF="http://www.biomedicalgenetics.nl/Members/Plasterk/plasterk.html">Plasterk</A>]['06].

%A R. Khaja
%A et al
%T Genome assembly comparison identifies structural variants in the
   human genome
%J Nature Genetics
%V ?
%M ?
%P ?-?
%D 2006
%K MolBio, jrnl, biol, c2006, c200x, c20xx, variant, variation, copy, copies,
   number, human, SNP, SNPs, CNV, CNVs, DNA, zz1106
%X "Numerous types of DNA variation exist, ranging from SNPs to larger
   structural alterations such as copy number variants (CNVs) and inversions.
   Alignment of DNA sequence from different sources has been used to identify
   SNPs1, 2 and intermediate-sized variants (ISVs)3. However, only a small
   proportion of total heterogeneity is characterized, and little is known of
   the characteristics of most smaller-sized (< 50 kb) variants. Here we show
   that genome assembly comparison is a robust approach for identification of
   all classes of genetic variation. Through comparison of two human assemblies
   ... identified megabases of sequence (in the form of 13,534 putative non-SNP
   events) that were absent, inverted or polymorphic in one assembly. Database
   comparison and laboratory experimentation further demonstrated overlap or
   validation for 240 variable regions and confirmed >1.5 million SNPs. Some
   differences were simple insertions and deletions, but in regions containing
   CNVs, segmental duplication and repetitive DNA, they were more complex. Our
   results uncover substantial undescribed variation in humans, highlighting the
   need for comprehensive annotation strategies to fully interpret genome
   scanning and personalized sequencing projects."   [online Nov '06].
   -- [<A HREF="http://dx.doi.org/10.1038/ng1921">doi:10.1038/ng1921</A>]['06].

%A B. Haubold
%A T. Wiehe
%T How repetitive are genomes?
%J BMC Bioinformatics
%V 7
%P 541
%D 2006
%K jrnl, genome, MolBio, c2006, c200x, c20xx, repeat, repeats, DNA, IR, string,
   short, shortest unique substring
%X "...measure of genome repetitiveness, the index of repetitiveness, Ir, which
   can be computed in time proportional to the length of the seqs. analyzed. We
   apply it to 336 genomes from all three domains of life.
   Results: The expected value of Ir is zero for random sequences of any G/C
   content and greater than zero for sequences with excess repeats. We find that
   the Ir of archaea is significantly smaller than that of eubacteria, which in
   turn is smaller than that of eukaryotes. Mouse chromosomes have a sig. higher
   Ir than human [chrs] & within each genome the Y [chr] is most repetitive. A
   sliding window analysis reveals that the human HOXA cluster & two surrounding
   genes are characterized by local minima in Ir."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-7-541">doi:10.1186/1471-2105-7-541</A>]['06].
   in [<A HREF="http://www.biomedcentral.com/bmcbioinformatics/">jrnl</A>]['06].
   [Also search for: unique substring]  and  [also search for: repeat DNA].

%A K. Deforche
%A T. Silander
%A et al
%T Analysis of HIV-1 pol sequences using Bayesian Networks: implications for
   drug resistance
%J J. Bioinformatics
%V 22
%N 24
%P 2975-2979
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, HIV1, protease inhibitor, nelfinavir,
   network
%X "...analyze direct influences between protein residues & exposure to
   treatment in clinical HIV-1 protease seqs. from diverse subtypes. We can
   determine the specific role of many resistance mutations against the
   protease inhibitor nelfinavir, & determine relationships between resistance
   mutations & polymorphisms. ... e.g., that in addition to the well-known
   major mutations 90M & 30N for nelfinavir resistance, 88S should not be
   treated as 88D but instead considered as a major mutation & explain the
   subtype-dependent prevalence of the 30N resistance pathway."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl508">doi:10.1093/bioinformatics/btl508</A>]['07].
   [Also search for: Bayesian network].

%A S. Hoops
%A S. Sahle
%A et al
%T COPASI - a COmplex PAthway SImulator
%J J. Bioinformatics
%V 22
%P 3067-3074
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, cell simulation, systems biology
%X "...biochemical simulator that offers several unique features. We discuss
   numerical issues with these features; in particular, the criteria to switch
   between stochastic & deterministic simulation methods, hybrid deterministic-
   stochastic methods, & the importance of random number generator numerical
   resolution in stochastic simulation."
   -- [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/short/22/24/3067">www</A>]['07],
      [<A HREF="http://www.copasi.org">copasi.org</A>]['07].
   [Also search for: cellDesigner]

%T Insights into the social insects from the genmome of the honeybee Apis
   mellifera
%Q The Honeybee Genome Sequencing Consortium
%J Nature
%V 443
%N 7114
%P 931-949
%M OCT
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, honey bee, bees, insect, nGenome, ATrich,
   AT-rich, CpG, hymoneptra, Apis mellifera
%X "... A. mellifera genome has high A+T & CpG contents, lacks major transposon
   families, evolves more slowly, & is more similar to vertebrates for
   circadian rhythm, RNA interference & DNA methylation genes, among others.
   ... has fewer genes for innate immunity, detoxification enzymes, cuticle-
   forming proteins & gustatory receptors, more genes for odorant receptors, &
   novel genes for nectar & pollen utilization, consistent with its ecology &
   social organization. Compared to Drosophila, genes in early developmental
   pathways differ in Apis, whereas similarities exist for functions that differ
   markedly, such as sex determination, brain function & behaviour. Population
   genetics suggests a novel African origin for the species A. mellifera &
   insights into whether Africanized bees spread throughout the New World via
   hybridization or displacement"
   "The individual accessions at the NCBI are: version 4.0
   (scaffolds CM000054-CM000069, CH876891-CH878241);..."
   --  [<A HREF="http://dx.doi.org/10.1038/nature05260"> doi:10.1038/nature05260</A>]['07]
   and [<A HREF="http://www.hgsc.bcm.tmc.edu/projects/honeybee/">Honey Bee Genome Project</A>]['07], 200 Mbp.
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">genomes@ncbi</A>]['07].

%A D. A. Bader
%A U. Roshan
%A A. Stamatakis
%T Computational grand challenges in assembling the tree of life:
   Problems and solutions
%P ?-? (Ch.4)
%B Computational Biology and Bioinformatics
%I AcademicPress
%S Advances in Computers
%V 68
%D 2006
%K MolBio, c2006, c200x, c20xx, evolutionary, phylogenetic, tree, trees,
   challenge, DNA, protein, comparing, zz0107
%X us$140, isbn:0120121689.   Also:
   Ch.1. Exposing Phylogenetic Relationships by Genome Rearrangement
         (Ying Chih Lin and Chuan Yi Tang)
   Ch.2. Models and Methods in Comparative Genomics
         (Guillaume Bourque and LouXin Zhang)
   Ch.3. Translocation Distance: Algorithms and Commplexity
         (Lusheng Wang)
   Ch.4. [this]
   Ch.5. Local Structure Comparison of Proteins
         (Jun Huan, Jan Prins, Wei Wang)
   Ch.6. Peptide Identification via Tandem Mass Spectrometry
         (Xue Wu, Nathan Edwards, Chau-Wen Tseng)
   [Also search for: MolBio tree life].

%A B. R. Holland
%A L. S. Jermiin
%A V. Moulton
%T Improved consensus network techniques for genome-scale phylogeny
%J Molec. Biol. and Evol.
%V 23
%N 5
%P 848-855
%D 2006
%O Proc. SMBE Tri-National Young Investigators' Workshop '05
%K jrnl, MolBio, MBE, c2006, c200x, c20xx, phylogenetic, evolutionary, tree,
   trees, uniEA
%X "... inclusive, approach for analyzing collections of trees arising from
   multiple genes. ..."    auth3, VM @ UEA
   -- [<A HREF="http://dx.doi.org/10.1093/molbev/msj061">doi:10.1093/molbev/msj061</A>]['07].

%A S.-Y. Rhee
%A J. Taylor
%A G.Wadhera, A.Ben-Hur, D.L.Brutlag, R.W.Shafer
%T Genotypic predictors of human immunodeficiency virus type 1 drug resistance
%J PNAS
%V 14
%N 46
%P 17355-17360
%D 2006
%K jrnl, PNAS, MolBio, c2006, c200x, c20xx, HIV 1, HIV1, predictor,
   protease, reverse transcriptase
%X "... used 5 statistical learning methods (decision trees, neural networks,
   support vector regression, least-squares regression, & least angle
   regression) to relate HIV-1 protease & reverse transcriptase mutations to in
   vitro susceptibility to 16 antiretroviral drugs. ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0607274103">doi:10.1073/pnas.0607274103</A>]['07].

%A J. W. Ho
%A C.E.Adams, J.B.Lew, T.J.Matthews, C.C.Ng, A.Shahabi-Sirjani
%A L.H.Tan, Y.Zhao, S.Easteal, S.R.Wilson, L.S. Jermiin
%T SeqVis: visualization of compositional heterogeneity in large alignments of
   nucleotides
%J J. Bioinformatics
%V 22
%N 17
%P 2162-2163
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, DNA, alignment, composition, evolution
%X "Most phylogenetic methods assume that the seqs. evolved under homogeneous,
   stationary & reversible conditions. Compositional heterogeneity in data
   intended for studies of phylogeny suggests that the data did not evolve
   under these conditions. SeqVis [Java] analysis of nucleotide content, reads
   seq. alignments in several formats & plots the nucleotide content in a
   tetrahedron. Once plotted, outliers can be identified, thus allowing for
   decisions on the applicability of the data for phylogenetic analysis."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl283">doi:10.1093/bioinformatics/btl283</A>]['07].

%A T. L. Bailey
%A N. Williams
%A C. Misleh
%A W. W. Li
%T MEME: Discovering and analyzing DNA and protein sequence motifs
%J NAR
%V 34
%P W369-W373
%D 2006
%K jrnl, NAR, MolBio, motif, c2006, c200x, c20xx, discovery, pattern, uniQld,
   UQ
%X "... works by searching for repeated, ungapped sequence patterns that
   occur in the DNA or protein sequences provided by the user. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gkl198">doi:10.1093/nar/gkl198</A>]['07].

%A K. Burrage
%A L. Hood
%A M. A. Ragan
%T Advanced computing for systems biology
%J Briefings in Bioinformatics
%V 7
%N 4
%P 390-398
%D 2006
%K c2006, c200x, c20xx, MolBio, visible cell, systems biology, IMB, uniQld, UQ
%X "... illustrate some of the range of computational and data requirements in
   systems biology with three case studies: one requiring large computation but
   small data (orthologue mapping in comparative genomics), a second involving
   complex terabyte data (the Visible Cell project) and a third that is both
   computationally and data-intensive (simulations at multiple temporal and
   spatial scales).  ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bib/bbl033">doi:10.1093/bib/bbl033</A>]['07].
   "...in silico studies of cell & molecular org'n [of] mammalian cell..."
   -- [<A HREF="http://www.visiblecell.com/">visiblecell.com</A>]['07].
   [Also search for: Ecell]

%A G. J. McLachlan
%A R. W. Bean
%A L. Ben-Tovim Jones
%T A simple implementation of a normal mixture approach to differential gene
   expression in multiclass microarrays
%J J. Bioinformatics
%V 22
%N 13
%P 1608-1615
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, micro array, microarray, arrays, UQ,
   uniQld
%X "... By converting to a z-score the value of the test statistic used to test
   the sig. of each gene, we propose a simple 2-component normal mixture that
   models adequately the distribution of this score. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl148">doi:10.1093/bioinformatics/btl148</A>]['07].

%A G. V. Matthews
%A A. Bartholomeusz
%A S. Locarnini
%A A.Ayres, J.Sasaduesz, E.Seaberg, D.A.Cooper, S.Lewin, G.J.Dore, C.L.Thio
%T Characteristics of drug resistant HBV in an international collaborative
   study of HIV-HBV-infected individuals on extended lamivudine therapy.
%J AIDS
%V 20
%N 6
%P 863-870
%D 2006
%K jrnl, MolBio, HBV, HIV, c2006, c200x, c20xx, drug resistance, hepatitis,
   drugs
%X [<A HREF="http://research.hopkinsglobalhealth.org/GlobalFacultyPage.cfm?global_faculty_id=8">thio@JohnHopkins</A>]['07].

%A J. M. Murray
%A R. H. Purcell
%A S. F. Wieland
%T The half-life of hepatitis B virions
%J Hepatology
%V 44
%N 5
%P 1117-1121
%M NOV
%D 2006
%K jrnl, c2006, c200x, c20xx, HBV, virus, viral, dynamics, virion, particle,
   MolBio
%X "... virion half-life of ...(HBV) is currently est. at ~ 1 day. This est.
   has been obtained from drug perturbation experiments with reverse
   transcriptase inhibitors. However, the analyses of those experiments have not
   considered the export of virions produced from preformed mature DNA-
   -containing HBV capsids in infected cells. Data from 3 acutely infected
   chimpanzees indicates that there is approximately 10-fold more total
   intracellular HBV DNA than HBV DNA in blood, and therefore the half-life of
   virions for chimpanzees during acute infection is 10-fold shorter at 3.8
   hours than the half-life associated with export of total intracellular HBV
   DNA. Math. model simulations duplicating the viral dynamics observed in drug
   perturbation experiments suggest a half-life of at most 4.4 hours for HBV v.
   in chronically infected humans, significantly shorter than current ests., but
   consistent with the half-lives of v. for HCV virus and HIV. This faster
   turnover of HBV in blood indicates a correspondingly higher replication rate
   & risk of mutation against hepatitis B antiviral therapy. ... find the
   half-life of HBV v. is ~ 4 hours, significantly shorter than current ests. of
   1 day. ...consistent with v. half-life ests. for HIV & [HCV]."
   -- [<A HREF="http://dx.doi.org/10.1002/hep.21364">doi:10.1002/hep.21364</A>]['07].

%A A. Wilm
%A I. Mainz
%A G. Steger
%T An enhanced RNA alignment benchmark for sequence alignment programs
%J Algorithms for Molecular Biology
%V 1
%N 19
%D 2006
%K AMB, jrnl, ejrnl, c2006, c200x, c20xx, MolBio, RNA, benchmarks, quality
%X "... traditionally tested on sets of protein sequences, of which a reference
   alignment is known. Conclusions drawn from such protein benchmarks do not
   necessarily hold for the RNA alignment problem, as was demonstrated in the
   first RNA alignment benchmark published so far. ..."  [52 refs]
   -- [<A HREF="http://dx.doi.org/10.1186/1748-7188-1-19">doi:10.1186/1748-7188-1-19</A>]['07].

%A A. Bertoletti
%A A. J. Gehring
%T The immune response during hepatitis B virus infection
%J J. Gen. Virol.
%V 87
%P 1439-1449
%D 2006
%K jrnl, MolBio, HBV, c2006, c200x, c20xx, viral, immune system
%X "...this review, how the early virological and immunological events might
   influence the development of a coordinate activation of adaptive immunity
   necessary to control HBV infection is analysed. The mechanism(s) by which
   high levels of viral antigens, liver immunological features, regulatory cells
   and dendritic cell defects might maintain the HBV-specific immunological
   collapse, typical of chronic hepatitis B patients, is also examined."
   -- [<A HREF="http://dx.doi.org/10.1099/vir.0.81920-0">doi:10.1099/vir.0.81920-0</A>]['07].

%A R. G. Abbott
%A S. Forrest
%A K. J. Pienta
%T Simulating the hallmarks of cancer
%J Artificial Life, Fall 2006
%V 12
%N 4
%P 617-634
%D 2006
%K MolBio, c2006, c200x, c20xx, simulate, simulation, biol, Alife, CancerSim,
   model, models, agent based, agents, Hanahan, Weinberg, pathway
%X "... viewed as the loss of coop. cell behaviors that normally facilitate
   multicellularity, including the formation of tissues & organs. ...
   ... CancerSim implements the hallmarks in an agent-based simulation which can
   help test the hypotheses [of] Hanahan & Weinberg ('00).  Experiments ...
   study the interactions of cell phenotype alterations, & in particular, the
   likely sequences of precancerous mutations, known as pathways. ... show that
   sequencing is an important factor in tumorigenesis, as some mutations have
   preconditions - they are selectively advantageous only in combination with
   other mutations. CancerSim enables a modeler to study the dynamics of a
   developing tumor & simulate how progression can be altered by tuning model
   parameters."
   -- [<A HREF="http://dx.doi.org/10.1162/artl.2006.12.4.617">doi:10.1162/artl.2006.12.4.617</A>]['07] via aland
   -- [<A HREF="http://www.cs.unm.edu/~forrest/cas-class/readings-2006/abbott.pdf">pdf@unm.edu</A>]['07].

%A B. Adamcsek
%A G. Palla
%A I. J. Farkas
%A I. Derenyi
%A T. Vicsek
%T CFinder: locating cliques and overlapping modules in biological networks
%J J. Bioinformatics
%V 22
%N 8
%P 1021-1023
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, module, network, clique, cliques,
   protein, cluster, clique percolation, graph, cFinder
%X "... Most cellular tasks are performed not by individual proteins, but by
   groups of functionally associated proteins, often referred to as modules.
   ... CFinder, a fast program locating & visualizing overlapping, densely
   interconnected groups of nodes in undirected graphs, & allowing the user to
   easily navigate between the original graph & the web of these groups. We show
   that in gene (protein) association networks CFinder can be used to predict
   the function(s) of a single protein & to discover novel modules. CFinder is
   also very efficient for locating the cliques of large sparse graphs."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl039">doi:10.1093/bioinformatics/btl039</A>]['07],
      [<A HREF="http://www.cfinder.org/">cfinder.org</A>]['07].

%A R. Axelrod
%A D. E. Axelrod
%A K. J. Pienta
%T Evolution of cooperation among tumor cells
%J PNAS
%V 103
%N 36
%P 13474-13479
%M SEP
%D 2006
%K jrnl, PNAS, cell, MolBio, c2006, c200x, c20xx, iterated prisoners dilemma,
   IPD, prisoner's, cancer, cooperate
%X "... Existing cancer theory suggests that individual clones of cancer cells
   evolve independently from one another, acquiring all of the genetic traits
   or hallmarks necessary to form a malignant tumor. It is also now recognized
   that tumors are heterotypic, with cancer cells interacting with normal
   stromal cells within the tissue microenvironment, including endothelial,
   stromal, and nerve cells. This tumor cell-stromal cell interaction in itself
   is a form of commensalism, because it has been demonstrated that these
   nonmalignant cells support and even enable tumor growth. Here, we add to this
   theory by regarding tumor cells as game players whose interactions help to
   determine their Darwinian fitness. ... We marshal evidence that tumor cells
   overcome certain host defenses by means of diffusible products. Our original
   contribution is to raise the possibility that two nearby cells can protect
   each other from a set of host defenses that neither could survive alone. .."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0606053103">doi:10.1073/pnas.0606053103</A>]['07], NB "possibility",
   RA@[<A HREF="http://www-personal.umich.edu/~axe/">umich</A>]['07].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A M. Boden
%A T. L. Bailey
%T Identifying sequence regions undergoing conformational change via predicted
   continuum secondary structure
%J J. Bioinformatics
%V 22
%N 15
%P 1809-1814
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, uniQld, SSPRED, prediction,
   protein, region
%X "...develop a computational method for identifying regions that are prone to
   conformational change directly from the amino acid seq.. ...uses the entropy
   of the probabilistic output of an 8-class continuum 2ndry struct. predictor.
   Results for 171 unique AA seqs. with well-characterized variable structure
   (identified in the Macromolecular movements database) indicate that the
   method is highly sensitive at identifying flexible protein regions, but false
   +ves remain a problem. ...can be used to explore conformational flexibility
   of proteins (including hypothetical or synthetic ones) whose structure is yet
   to be determined experimentally."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl198">doi:10.1093/bioinformatics/btl198</A>]['06],
      [<A HREF="http://pprowler.itee.uq.edu.au/sspred/">sspred@uq</A>]['06].
    * 3-class (H E C) or * 8-class (G H I E B T S C) [Also search for: MolMovDB]
   [Also see BMC-Bioinf. 7:68 <A HREF="http://dx.doi.org/10.1186/1471-2105-7-68">doi:10.1186/1471-2105-7-68</A> 2006].

%A D. J. Smyth
%A et al
%T A genome-wide association study of nonsynonymous SNPs identifies a type 1
   diabetes locus in the interferon-induced helicase (IFIH1) region
%J Nature Genetics
%V 38
%N 6
%P 617-619
%M JUN
%D 2006
%K jrnl, c2006, c200x, c20xx, MolBio, GWA, SNP, diabetes, diabetic, health,
   type1, nsSNP, nsSNPs, rs1990760,  T1D, IFIH1, mda-5, mda5, Helicard
%X ... stat. support for a 6th type1 diabetes (T1D) locus in the innate
   immunity viral RNA receptor gene region IFIH1 (also known as mda-5 or
   Helicard) on chromosome 2q24.3. ... association in an interim analysis of a
   genome-wide nonsynonymous SNP (nsSNP) scan, & we validated it in a case-
   -control collection & replicated it in an indep. family collection. In 4,253
   cases, 5,842 controls & 2,134 parent-child trio genotypes, the risk ratio for
   the minor allele of the nsSNP rs1990760 A -> G (A946T) was 0.86 (95% conf.
   int. = 0.82-0.90) at P = 1.42 x 10(-10).
   -- [<A HREF="http://dx.doi.org/10.1038/ng1800">doi:10.1038/ng1800</A>]['07].

%A U. Alon
%T An Introduction to Systems Biology: Design Principles of Biological Circuits
%I CRCpress
%P 320
%D 2006
%K book, MolBio, c2006, c200x, c20xx, biol, biology, network motif, motifs,
   regulatory, regulation, networks
%X us$40, uk us isbn:1584886420; uk us isbn13:9781584886426.
   Also see [<A HREF="http://www.nature.com/nature/journal/v446/n7135/full/446497a.html">essay</A>]['07].
   ... Why are gene-regulation NWs built out of only a handful of NW motifs? The
   small # of motifs seems to result from the strict constraints that biological
   circuits must meet. [E.g.] circuits must operate despite random fluctuations
   in the concentrations of the component parts, because such fluctuations seem
   to be an inherent feature of cells. This demand for robustness ...
   -- [<A HREF="http://www.weizmann.ac.il/mcb/UriAlon/">Alon@w...</A>][08].
   [Also search for: network motif MolBio].

%A E. Segal
%A et al
%T A genomic code for nucleosome positioning
%J Nature
%V 442
%P 772-778
%M AUG
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, zz1207, position, chromosome, DNA,
   chromatin, helical repeat, histone
%X "... nucleosome particles that occlude the DNA from interacting with most DNA
   binding proteins. N. have higher affinity for particular DNA seqs. reflecting
   the ability of the seq. to bend sharply, as req. by the nucleosome structure.
   ...not known whether these seq. prefs. have a sig. influence on nucleosome
   position in vivo, & thus regulate the access of other proteins to DNA.
   ... isolated n.-bound seqs. at high res. from yeast & used these seqs. in a
   new computational approach to construct & validate experimentally a n.-DNA
   interaction model, & to predict the genome-wide org. of nucleosomes.
   ... demonstrate that genomes encode an intrinsic n. org. & [this] org. can
   explain ~50% of the in vivo n. positions. This n. positioning code may
   facilitate specific chr. fns inc. transcription factor binding, transcription
   initiation & even remodelling of the n. themselves."
   -- [<A HREF="http://dx.doi.org/10.1038/nature04979">doi:10.1038/nature04979</A>]['07],
      [<A HREF="http://www.nature.com/nature/journal/v442/n7104/suppinfo/nature04979.html">supp.mat.</A>]['07].

%A C. Christiansen
%A T. Mailund
%A C. N. S. Pedersen
%A M. Randers
%A M. Stig Stissing
%T Fast calculation of the quartet distance between trees of arbitrary degrees
%J Algorithms for Molecular Biology
%V 1
%N 16
%D 2006
%K jrnl, ejrnl, c2006, c200x, c20xx, MolBio, evolutionary tree, trees, degree
%X "... The quartet distance is the number of quartets - sub-trees induced by
   4 leaves - that differs between the trees. Mostly, these algs. are restricted
   to work on binary trees, but recently we have developed algs. that work on
   trees of arbitrary degree. ... time O(n + |V|.|V'| min{id, id'}) & space
   O(n + |V|.|V'|), where n is the number of leaves in the 2 trees, V & V are
   the non-leaf nodes in T & T', respectively, & id & id' are the maximal # of
   non-leaf nodes adjacent to a non-leaf node in T & T', resp ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1748-7188-1-16">doi:10.1186/1748-7188-1-16</A>]['07].

%A W. E. Barlow
%A E. White
%A R. Ballard-Barbash
%A P. M. Vacek
%A L. Titus-Ernstoff
%A P. A. Carney
%A J. A. Tice
%A D. S. Buist
%A B. M. Geller
%A R. Rosenberg
%A B. C. Yankaskas
%A K. Kerlikowske
%T Prospective breast cancer risk prediction model for women undergoing
   screening mammography
%J J. Natl. Cancer Inst.
%V 98
%N 17
%P 1204-1214
%D 2006
%K jrnl, c2006, c200x, c20xx, breast cancer, data base, database, DB, medicine,
   risks, risk, predict, screen, mammograph, Xray, stats, data set, dataset,
   human health
%X "... Stat. sig. risk factors for breast cancer diagnosis among premenopausal
   women included age, breast density, family history of breast cancer, & a
   prior breast procedure. For postmenopausal women, the stat.sig. factors
   inc. age, breast density, race, ethnicity, family history of breast cancer,
   a prior breast procedure, body mass index, natural menopause, hormone therapy
   & a prior false-positive mammogram. The model may identify high-risk women
   better than the Gail model, although predictive accuracy was only moderate.
   The c stats. were 0.631 (95% [CI] = 0.618 to 0.644) for premenopausal women
   & 0.624 (95% CI = 0.619 to 0.630) for postmenopausal women. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/jnci/djj331">doi:10.1093/jnci/djj331</A>]['08].
   data@[<A HREF="http://www.breastscreening.cancer.gov/">www</A>]['08].

%A J.-F. Truchon
%A C. I. Bayly
%T GLARE: A new approach for filtering large reagent lists in combinatorial
   library design using product properties
%J J. Chem. Inf. Model
%V 46
%N 4
%P 1536-1548
%D 2006
%K jrnl, c2006, c200x, c20xx, GLARE, chemical compound, library, list,
   logP, polar surface area, h-bond acceptor, donor
%X "...GLARE (Global Library Assessment of REagents) ... optimal reagent
   selection in combinatorial library design. ... reduces or eliminates the time
   a medicinal chemist spends examining reagents which a priori cannot be part
   of a "good" library. ... takes the large reagent sets returned by standard
   chemical DB queries & produces often considerably reduced reagent sets that
   are well-behaved with respect to a specific template. The pruning enforces
   "goodness" constraints such as the Lipinski rule of five on the product
   properties such that any reagent selection from the resulting sets produces
   only "good" products. The alg. ... 3 important features: (i) ... GLARE uses
   a deterministic greedy procedure ... (ii) The pruning method can be biased to
   produce reagent sets with a balanced size, ... . (iii) For v.large comb. lib.
   a partitioning scheme allows libs. as large as 1012 to be eval. in 0.25s on
   an IBM AMD Opteron processor. ... validated on ... 12 libs.. ..."
   -- [<A HREF="http://dx.doi.org/10.1021/ci0504871">doi:10.1021/ci0504871</A>]['08],
      [<A HREF="http://glare.sourceforge.net/">glare.sourcefor...</A>]['08].
   (Also see BldgBlockChem@[<A HREF="https://en.wikipedia.org/wiki/Building_block_(chemistry)">wikip</A>]['20].)
   [Also search for: chemical library].

%A A. Karwath
%A L. De Raedt
%T SMIREP: predicting chemical activity from SMILES
%J J. of Chemical Information and Modeling
%V 46
%N 6
%P 2432-2444
%D 2006
%K jrnl, JCIM, c2006, c200x, c20xx, SMIREP, deRaedt, structure, activity,
   SAR, chemistry, chemical compound, deRaedt
%X "Most approaches to ... (SAR) prediction proceed in 2 steps. [1] a typically
   large set of fingerprints, or fragments of interest, is constructed (either
   by hand or by some recent data mining techniques). [2] machine learning
   techniques are applied to obtain a predictive model. The result is often not
   only a highly accurate but also hard to interpret model. ... we demonstrate
   the capabilities of a novel SAR algorithm, SMIREP, which tightly integrates
   the fragment & model generation steps & which yields simple models in the
   form of a small set of IF-THEN rules. These rules contain SMILES fragments,
   which are easy to understand to the computational chemist. SMIREP combines
   ideas from the well-known IREP rule learner with a novel fragmentation alg
   for SMILES strings. SMIREP has been evaluated on 3 problems: the prediction
   of binding activities for the estrogen receptor ...,  prediction of
   mutagenicity using the carcinogenic potency database (CPDB), & the prediction
   of biodegradability on a subset of (EFDB). ..."
   -- [<A HREF="http://dx.doi.org/10.1021/ci060159g">doi:10.1021/ci060159g</A>]['08],
      [<A HREF="http://www.cs.kuleuven.be/~lucdr/">auth2</A>]['08].
   [Also search for: chemical compound SAR].

%A A. M. Clark
%A P. Labute
%A M. Santavy
%T 2D Structure Depiction
%J J. Chem. Inf. Model.
%V 46
%N 3
%P 1107-1123
%D 2006
%K JCIM, jrnl, c2006, c200x, c20xx, chemical compound, structural formula
%X "... alg. for the depiction of 2D coordinates of chemical structures is
   described. The methods used represent a significant improvement to the state
   of the art with regard to molecular connection graphs which pose particular
   difficulty to most layout efforts. ..."
   -- [<A HREF="http://dx.doi.org/10.1021/ci050550m">doi:10.1021/ci050550m</A>]['08].
   [Also search for: structural formula].

%A B. Buttingsrud
%A E. Ryeng
%A R. King
%A B. Alsberg
%T Representation of molecular structure using quantum topology with
   inductive logic programming in structure activity relationships
%J J. of Computer-Aided Molecular Design
%V 20
%P 361-373
%V 20
%M JUN
%D 2006
%K jrnl, JCAMD, c2006, c200x, c20xx, structure activity relationship, SAR, QSAR,
   electronic structure, Bader, quantum topological atoms in molecules,
   chemical compound, compounds
%X "... previous molecular ILP repns have not been effective in describing the
   electronic structure of molecules. ... more unified & comprehensive repn
   based on Richard Bader's quantum topological atoms in molecules (AIM) theory
   where critical points in the electron density are connected through a n/w.
   AIM theory provides a wealth of chemical information about individual atoms
   & their bond connections enabling a more flexible & chemically relevant
   repn. To obtain even more relevant rules with higher coverage, we apply
   manual postprocessing and interpretation of ILP rules. ..."  [39 refs].
   pdf: [<A HREF="http://dx.doi.org/10.1007/s10822-006-9058-y">doi:10.1007/s10822-006-9058-y</A>]['08].
   [Also search for: chemical compound SAR].

%A A. V. Werhli
%A M. Grzegorczyk
%A D. Husmeier
%T Comparative evaluation of reverse engineering gene regulatory networks with
   relevance networks, graphical Gaussian models and Bayesian networks
%J J. Bioinformatics
%V 22
%N 20
%P 2523-2531
%M OCT
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, network, infer, inference, II, model, BN,
   gene, expression
%X "... (1) Relevance networks (RNs): pairwise association scores independent of
   the remaining network; (2) graphical Gaussian models (GGMs): undirected
   graphical models with constraint-based inference, and (3) Bayesian networks
   (BNs) ... On Gaussian observational data, BNs and GGMs were found to
   outperform RNs. The difference in performance was not significant for the
   non-linear simulated data and the cytoflow data ... active interventions in
   the form of gene knockouts and over-expressions are required to exploit the
   full potential of BNs."
   -- [<A HREF="http://www.bioss.sari.ac.uk/staff/adriano/research.html">auth1</A>]['06].
   [Also search for: Bayesian network].

%A M. Bansal
%A G. Della Gatta
%A D. di Bernardo
%T Inference of gene regulatory networks and compound mode of action from time
   course gene expression profiles
%J J. Bioinformatics
%V 22
%N 7
%P 815-822
%M SEP
%D 2006
%K MolBio, c2006, c200x, c20xx, TSNI, network, profile, time series, timeSeries,
   E coli, Ecoli, gene expression, infer gene regulatory network
%X "... show that it is possible to recover the gene regulatory network from a
   time series data of gene expression following a perturbation to the cell. We
   show this both on simulated data and on a nine gene subnetwork part of the
   DNA-damage response pathway (SOS pathway) in the bacteria E. coli."
   pdf: [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl003">doi:10.1093/bioinformatics/btl003</A>]['08].
   Also see [<A HREF="http://dibernardo.tigem.it/wiki/index.php/Time_Series_Network_Identification_TSNI">www</A>]['08].
   [Also search for: infer gene regulatory network].

%A A. Clare
%A A. Karwath
%A H. Ougham
%A R. D. King
%T Functional bioinformatics for Arabidopsis thaliana
%J J. Bioinformatics
%V 22
%N 9
%P 1130-1136
%D 2006
%K jrnl, MolBio, aber, RDKing, AClare, c2006, c200x, c20xx, plant, plants, gene,
   genes, function, prediction, Arabidopsis thaliana
%X "... predicted the functional class of a high percentage of the Arabidopsis
   genes with currently unknown function. These predictions are interpretable
   and have good test accuracies. We describe in detail seven of the rules
   produced."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl051">doi:10.1093/bioinformatics/btl051</A>]['08].

%A A. A. Margolin
%T ARACNE: An Algorithm for the reconstruction of gene regulatory networks in
   a mammalian cellular context.
%J BMC Bioinformatics
%V 7
%N Suppl.1 : S7
%D 2006
%O NIPS Workshop on New Problems and Methods in Comp. Biol., Dec., 2004
%K wShop, MolBio, ARACNE, c2006, c200x, c20xx, genes, network, mammal, cell,
   cMYC, micro array, expression profile, infer gene regulatory network
%X "... prove that ARACNE reconstructs the n/w exactly (asymptotically) if the
   effect of loops in the n/w topology is negligible, & we show that the alg.
   works well in practice, even in the presence of numerous loops & complex
   topologies. We assess ARACNE's ability to reconstruct transcriptional
   regulatory n/ws using both a realistic synthetic dataset & a microarray
   dataset from human B cells. On synthetic datasets ARACNE achieves very low
   error rates & outperforms established methods, such as Relevance n/ws &
   Bayesian n/ws. Application to the deconvolution of genetic n/ws in human B
   cells demonstrates ARACNE's ability to infer validated transcriptional
   targets of the cMYC proto-oncogene. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-7-S1-S7">doi:10.1186/1471-2105-7-S1-S7</A>]['08].
   [Also search for: infer gene regulatory network].

%A A. S. Konagurthu
%A P. J. Stuckey
%A J. C. Whisstock
%A A. M. Lesk
%T MUSTANG: A MUltiple STructural AligNment alGorithm
%J Proteins: Structure, Function and Bioinformatics
%V 64
%N 3
%P 559-574
%M AUG
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, ArunK, AMLesk, MUSTANG, multiple, protein,
   structure, structural, alignment, maximal fragment pairs, 3D,
   DALI, POSA, MALECON, MultiProt
%X "... program constructs a multiple alignment using the spatial info. of the
   C(alpha) atoms in the set. Broadly based on the progressive pairwise
   heuristic, this alg. gains accuracy through novel & effective refinement
   phases. MUSTANG reports the multiple sequence alignment & the corr.
   superposition of structures. Alignments generated by MUSTANG are compared
   with several handcurated alignments in the literature [and] the benchmark
   alignments of 1033 alignment families from the HOMSTRAD DB. The performance
   of MUSTANG was compared with DALI at a pairwise level, & with other multiple
   structural alignment tools such as POSA, CE-MC, MALECON, & MultiProt. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/prot.20921">doi:10.1002/prot.20921</A>]['08].
   NB. auth1 @monash from 2011.
   [Also search for: MolBio protein structure alignment].

%A U. Roehm
%A T.-M. Die
%T How to BLAST your database - a study of stored procedures for BLAST searches
%J Database Systems for Advanced Applications
%I SpringerVerlag
%S LNCS
%V 3882
%P 807-816
%D 2006
%K conf, MolBio, c2006, c200x, c20xx, dbBLAST, db Blast, search, DNA, DBMS,
   stored procedure, database, data base, sequence, uniSydney
%X "Stored procs. are an important feature of all major DB systems that allows
   to exec. application logic within DB servers. ... [report] experiences to
   implement a popular sci. alg. [BLAST] as stored procs. within a relational
   DB. We implemented the ungapped, nucleotide version of the BLAST alg. with
   4 different relational DB engines, both commercial & open source. In an
   experimental evaluation, we compared our dbBLAST implementations with a
   std file-based BLAST impl. from NCBI with regard to the impl. effort, runtime
   perf., & scalability. ... although our dbBLAST runs faster than the file-
   -based BLAST program for short query seqs., all implementations lack
   scalability. However, the results also indicate that stored procs. require
   sig. less development effort - both in time & space - than trad. programming
   approaches."  auths@U.Sydney.
   -- [<A HREF="http://dx.doi.org/10.1007/11733836_58">doi:10.1007/11733836_58</A>]['08].
   -- [<A HREF="http://www.cs.su.oz.au/~roehm">auth1</A>]['08].

%A P. J. Uren
%A R. M. Cameron-Jones
%A A. H. J. Sale
%T Promoter prediction using physico-chemical properties of DNA
%J Computational Life Sciences II: Proc. of the 2nd Int. Symp.
%P 21-31
%M SEP
%D 2006
%K conf, CompLife, c2006, c200x, c20xx, uniTas, MolBio, promoters, DNA, property
%X "The ability to locate promoters within a section of DNA is known to be a
   very difficult & very important task in DNA analysis. ... an approach that
   incorporates the concept of DNA as a complex molecule using several models of
   its physico-chemical properties. A SVM is trained to recognise promoters by
   their distinctive physical & chemical properties. ... by combining models, we
   can improve upon the classification accuracy obtained with a single model. We
   also show that by examining how the predictive accuracy of these properties
   varies over the promoter, we can reduce the # of attributes needed. ... apply
   this method to a real-world problem. ... demonstrate that such an approach
   has significant merit in its own right. ... suggest better results from a
   planned combined approach to promoter prediction using both physicochemical
   and sequence based techniques."   (In: uk us isbn:3540457674.)
   -- [<A HREF="http://eprints.utas.edu.au/00000284/">pdf@uniTas</A>]['08].

%A N. C. Jones
%A D. Zhi
%A B. J. Raphael
%T AliWABA: Alignment on the web through an A-Bruijn approach
%J NAR
%V 34
%P W613-W616
%M JUL
%D 2006
%K jrnl, NAR, eJrnl, MolBio, c2006, c200x, c20xx, ABruijn, graph, multiple,
   alignment, ABA, algorithm
%X "Multiple sequence alignment ... A-Bruijn Alignment (ABA) is a method for
   multiple sequence alignment ... AliWABA is a web server that provides tools
   to generate alignments with ABA, visualize the resulting ABA graphs and
   extract subsequences from ABA graphs. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gkl288">doi:10.1093/nar/gkl288</A>]['08].

%A M. Koyuturk
%A Y. Kim
%A U. Topkara
%A S. Subramaniam
%A W. Szpankowski
%A A. Grama
%T Pairwise local alignment of protein interaction networks guided by models of
   evolution
%J J. Computational Biology
%V 13
%N 2
%P 182-199
%M MAR
%D 2006
%O see Recomb 2005
%K jrnl, MolBio, c2006, c200x, c20xx, protein interaction, network, model,
   graphAlignment, mawish, PPI
%X "... focus here on discovering protein sets that induce subnets that are
   highly conserved in the interactome of a pair of species. ... framework that
   formally defines the pairwise local alignment problem for PPI networks,
   models the problem as a graph opt. problem, & presents fast algs. ... .
   ... base our framework on duplication/divergence models that focus on
   understanding the evolution of PPI networks. ..."
   pdf@[<A HREF="http://www.cs.purdue.edu/homes/spa/papers/jcb.pdf">purdue</A>]['08].
   Also recomb 05 [<A HREF="http://dx.doi.org/10.1007/11415770_4">pdf</A>]['08].
   -- [<A HREF="http://www.cs.purdue.edu/homes/koyuturk/mawish/">s/w</A>]['06].
   [Also search for: protein interaction network] and
   [also search for: graphAlignment].

%A J. Flannick
%A A. Novak
%A B. Srinivasan
%A H. McAdams
%A S. Batzoglou
%T Graemlin: General and robust alignment of multiple large interaction networks
%J Genome Res.
%V 16
%P 1169-1181
%D 2006
%K jrnl, MolBio, Graemlin, c2006, c200x, c20xx, protein interaction, network,
   PPI, graphAlignment
%X "... Graemlin's probabilistic formulation of the topology-matching problem
   eliminates earlier restrictions on the possible architecture of conserved
   modules. Most important, G. is the first prog. capable of multiple alignment
   of an arbitrary number of n/ws. ...  performed the 1st quantitative
   comparison of n/w aligners. Using data sets containing known biol. modules as
   a benchmark ... find that G. achieves substantial gains in sensitivity over
   previous methods while offering fast & scalable searches of multiple, large
   n/ws. [and] present detailed analyses of several alignments that suggest
   interesting hypotheses about protein function."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.5235706">doi:10.1101/gr.5235706</A>]['08].
   Web-interface@[<A HREF="http://graemlin.stanford.edu">Stanf.</A>]['06].
   [Also search for: protein interaction network] and
   [also search for: graphAlignment].

%A V. Svicher
%A T. Sing
%A M. M. Santoro
%A F. Forbici
%A F. Rodriguez-Barrios
%A A. Bertoli
%A N. Beerenwinkel
%A M. C. Bellocchi
%A F. Gago
%A A. d'Arminio Monforte
%A et al
%T Involvement of novel human immunodeficiency virus type 1 reverse
   transcriptase mutations in the regulation of resistance to nucleoside
   inhibitors
%J J.  Virol.
%V 80
%N 14
%P 7186-7198
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, HIV, Aids, virus, viral, drug resistance,
   reverse transcriptase, RT, mutation, nucleoside, inhibitor, treatment, model,
   mutations, HIV1, lamivudine, geno2pheno
%X "We characterized 16 addnl mutns in HIV type 1 (HIV-1) reverse transcriptase
   (RT) whose role in drug resistance is still unknown by analyzing 1,906
   plasma-derived HIV-1 subtype B pol seqs. from 551 drug-naive patients & 1,355
   nucleoside RT inhibitor (NRTI)-treated patients. 12 mutns +vely assoc. with
   NRTI treatment strongly correlated both in pairs & in clusters with known
   NRTI resistance mutns on divergent evol. pathways. ... T39A, K43E/Q, K122E,
   E203K, & H208Y clustered with the nucleoside analogue mut. 1 cluster (NAM1;
   M41L+L210W+T215Y). ... treatment failure in the presence of K43E, K122E, or
   H208Y was sig. assoc. with higher viremia & lower CD4 cell count.
   ... Our study provides evidence of novel RT mutational patterns that
   regulate +vely and/or -vely NRTI resistance & strongly suggests that other
   mutns beyond those currently known to confer resistance should be considered
   for improved prediction of clinical response to antiretroviral drugs."
   pdf@[<A HREF="http://dx.doi.org/10.1128/JVI.02084-05">doi:10.1128/JVI.02084-05</A>]['08],
   -- [<A HREF="http://www.geno2pheno.org/">geno2pheno.org</A>]['08].

%A P. J. Ingram
%A M. P. H. Stumpf
%A J. Stark
%T Network motifs: Structure does not determine function
%J BMC Genomics
%V 7
%N 108
%M MAY
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, zz0816, biological networks, motif,
   FFL, bifan, bi-fan, systems biology, controversial
%X "... develop an ordinary differential equn model of the bi-fan motif &
   analyse variants of the motif corr. to its behaviour under various condns.
   ... We find that there is no characteristic behaviour for the motif, & with
   the correct choice of parameters & of internal structure, v. different,
   indeed even opposite behaviours may be obtained. Even with this relatively
   simple model, the bi-fan motif can exhibit a wide range of dynamical
   responses. This suggests that it is difficult to gain sig. insights into
   biological fns simply by considering the connection architecture of a gene
   n/wk, or its decomposition into simple structural motifs. It is necessary to
   supplement such structural info. by kinetic parameters, or dynamic time
   series experimental data, both of which are currently difficult to obtain."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2164-7-108">doi:10.1186/1471-2164-7-108<A>]['16].
   (Also see motifs@[<A HREF="https://en.wikipedia.org/wiki/Network_motif">wikip</A>]['16].)

%A L. Franke
%A H. van Bakel
%A L. Fokkens
%A E. D. de Jong
%A M. Egmont-Petersen
%A C. Wijmenga
%T Reconstruction of a functional human gene network, with an application for
   prioritizing positional candidate genes
%J Am. J. Human Genetics
%V 78
%N 6
%P 1011-1025
%M JUN
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, human, gene, genes, regulatory, network,
   networks, genenetwork
%X "... developed a functional human gene n/w that integrates info. on genes &
   the functional relationships between genes, based on data from [KEGG]
   the Biomolecular Interaction Network Database, Reactome,
   the Human Protein Reference Database, the Gene Ontology database,
   predicted protein-protein interactions, human yeast 2-hybrid interactions, &
   microarray co-expressions. We applied this network to interrelate positional
   candidate genes from different disease loci & then tested 96 heritable
   disorders for which the Online Mendelian Inheritance in Man database
   reported at least three disease genes. Artificial susceptibility loci, each
   containing 100 genes, were constructed around each disease gene, & we used
   the n/w to rank these genes on the basis of their functional interactions.
   By following up the top 5 genes / artificial locus, we were able to detect
   at least one known disease gene in 54% of the loci studied, representing a
   2.8-fold increase over random selection. ..."
   paper@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/16685651">pub med</A>]['09].
   -- [<A HREF="http://humgen.med.uu.nl/~lude/genenetwork/">genenetwork</A>]['09] ?broken?.
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Gene_regulatory_network">wikip</A>].)
   [Also search for: Molbio network].

%A J. S. Hallinan
%A D. R. Bradley
%A J. S. Mattick
%A J. H. Wiles
%T Effects of an RNA control layer on the state space of boolean models of
   genetic regulatory networks
%J IEEE Congress on Evolutionary Computation
%P 2551-2555
%M JUL
%D 2006
%K conf, c2006, c200x, c20xx, MolBio, model, miRNA, ncRNA, ncRNA, uniQld,
   network, regulation, genes, attractor, attractors
%X "... now evident that much of the genome of humans & other complex organisms
   is transcribed into non-protein-coding RNAs. Some of these RNAs are
   processed into small regulatory RNAs, such as microRNAs, that control many
   aspects of animal & plant development. It has been suggested that regulatory
   RNAs represent an additional control layer that was critical to the
   emergence of complex organisms. We examine this poss. using a model of cell
   differentiation based on attractors in boolean n/ws. ... show that an
   additional layer of RNA control modeled as fast temporal links can sig.
   increase the # of attractors in boolean models of genetic reg. n/ws
   (analogous to the number of cell types in a complex organism). [but] also
   has the power to simplify the state space structure. We explore the condns
   under which these different outcomes occur."
   -- [<A HREF="http://dx.doi.org/10.1109/CEC.2006.1688626">doi:10.1109/CEC.2006.1688626</A>]['08].

%A R. E. Mills
%A C. T. Luttig
%A C. E. Larkins
%A A. Beauchamp
%A C. Tsui
%A W. S. Pittard
%A S. E. Devine
%T An initial map of insertion and deletion (INDEL) variation in the
   human genome
%J Genome Res.
%V 16
%P 1182-1190
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, indel, indels, insertions, deletions,
   insertion, deletion, variation, polymorphism, variations, human genome, dbSNP
%X "... an initial map of human INDEL variation ... 415,436 unique INDEL
   polymorphisms. ... identified with a computational approach using DNA
   re-sequencing traces that originally were generated for SNP discovery
   projects. They range from 1bp to 9989bp ... split almost equally between
   ins. & dels., relative to the chimpanzee seq.. ... hotspots ... with up to
   48-fold regional increases in INDEL and/or SNP variation compared with the
   chromosomal averages for the same chromosomes. ..."
   Free: [<A HREF="http://dx.doi.org/10.1101/gr.4565806">doi:10.1101/gr.4565806</A>]['08].

%A G. A. Turkan
%A et al
%T The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
%J Science
%V 313
%N 5793
%P 1596-1604
%M SEP
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, black cottonwood, Populus trichocarpa,
   tree, trees, wood, woody, plant, plants, genome, nGenome
%X [[485 Mb, 19 chrs, 45,555 genes est.]]
   "... draft genome of the black cottonwood tree, Populus trichocarpa.
   ... More than 45,000 putative protein-coding genes were identified. ...
   a whole-genome duplication event; about 8000 pairs of duplicated genes from
   that event survived in the Populus genome. A 2nd, older dupl. event is
   indistinguishably coincident with the divergence of the Populus & Arabidopsis
   lineages. ... "
   -- [<A HREF="http://dx.doi.org/10.1126/science.1128691">doi:10.1126/science.1128691</A>]['08].
   -- [<A HREF="http://www.populus.db.umu.se/">populus.db.umu.se</A>]['08],
   -- [<A HREF="http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html">jgi-psf.org/</A>]['08],
   -- [<A HREF="http://en.wikipedia.org/wiki/Populus_trichocarpa">wikip</A>]['08].

%A R. Akada
%A et al
%T PCR-mediated seamless gene deletion and marker recycling in
   Saccharomyces cerevisiae
%J Yeast
%V 23
%N 5
%P 399-405
%M APR
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, PCR, gene, genes, delete, deletion,
   knockout, hisG, loxP, HIS3, URA3, Saccharomyces cerevisiae, yeast, scarless
%X "Repeated gene manipulations can be performed in yeast by excision of an
   introduced marker. Cassette modules containing a marker flanked by 2 direct
   repeat seqs. of hisG or loxP have often been used for marker recycling, but
   these leave 1 copy of the repeats in the chr. after excision. Genomic copies
   of a repeat can cause increased mistargeting of constructs containing the
   same repeats or unexpected chromosomal rearrangements via intra- or
   interchromosomal recombinations. Here, we describe a novel marker recycling
   procedure that leaves no scar in the genome, which we have designated
   seamless gene deletion. A 40 base seq. derived from an adjacent region to the
   targeted locus was placed in an integrating construct to generate direct
   repeats after integration. Seamless HIS3 deletion was achieved via a PCR
   fragment that consisted of a URA3 marker attached to a 40 base repeat-
   -generating seq. flanked by HIS3 targeting seqs. at both ends.
   Transformation of the designed construct resulted in his3 disruption & the
   generation of 40 base direct repeats on both sides of URA3 in the targeted
   locus. The resulting his3::URA3 disruptants were plated on 5-fluoroorotic
   acid medium to select for URA3 loss. All the selected colonies had lost URA3
   precisely by recombination between the repeats, resulting in his3 deletion
   without any extraneous seqs. left behind in the chromosome."
   -- [<A HREF="http://dx.doi.org/10.1002/yea.1365">doi:10.1002/yea.1365</A>]['09],
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/16598691">pub med</A>]['09].

%A M. Hu
%A J. Yao
%A K. Polyak
%T Methylation-specific digital karyotyping
%J Nature Protocols
%V 1
%P 1621-1636
%D 2006
%K MolBio, c2006, c200x, c20xx, methylation specific digital karyotyping, MSDK,
   methylation analysis, DNA, AscI,  NlaIII
%X "... describe a recently developed method - methylation-specific digital
   karyotyping (MSDK) - that enables comprehensive & unbiased genome-wide DNA
   methylation analysis. Using a combination of a methylation-sensitive mapping
   enzyme (for example, AscI) & a fragmenting enzyme (for example, NlaIII),
   short seq. tags can be obtained & uniquely mapped to genome location. The #
   of tags in an MSDK library reflects the methylation status of the mapping
   enzyme sites. Generation of MSDK libraries can be completed in 7-10 days,
   whereas seq. & data analysis requires an additional 3-4 weeks."
   -- [<A HREF="http://dx.doi.org/10.1038/nprot.2006.278">doi:10.1038/nprot.2006.278</A>]['09],
   auth3@[<A HREF="http://www.hms.harvard.edu/dms/bbs/fac/polyak.html">harv@rd</A>]['09].

%A F. D. Ciccarelli
%A T. Doerks
%A C. von Mering
%A C. J. Creevey
%A B. Snel
%A P. Bork
%T Toward automatic reconstruction of a highly resolved tree of life
%J Science
%V 311
%N 5765
%P 1283-1287
%M MAR
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, phylogenetic, evolutionary, tree of life,
   trees, universal, horizontal gene transfer, HGT, Acidobacteria,
   Proteobacteria, bacteria
%X "... automatable procedure for reconstructing the tree of life with branch
   lengths comparable across all 3 domains. The tree has its basis in a
   concatenation of 31 orthologs occurring in 191 species with sequenced
   genomes. It revealed interdomain discrepancies in taxonomic classification.
   Systematic detection and subsequent exclusion of products of horizontal gene
   transfer increased phylogenetic resolution, allowing us to confirm accepted
   relationships and resolve disputed and preliminary classifications. [eg] we
   place the phylum Acidobacteria as a sister group of {delta}-Proteobacteria,
   support a Gram-positive origin of Bacteria, and suggest a thermophilic last
   universal common ancestor."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1123061">doi:10.1126/science.1123061</A>]['09].
   [Also search for: MolBio tree life].

%A H. J. Newton
%A F. M. Sansom
%A V. Bennett-Wood
%A E. L. Hartland
%T Identification of Legionella pneumophila-specific genes by genomic
   subtractive hybridization with Legionella micdadei and identification of
   lpnE, a gene required for efficient host cell entry
%J Infection & Immunity
%V 74
%N 3
%P 1683-1691
%M MAR
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, Legionella pneumophila, genes, lpnE, gene,
   longbeachae, micdadei, gormanii, jordanis, lpg2222, THP-1, THP1, A549, lpnE,
   bacteria, bacterium
%X "... identify genes that may contribute to the virulence of L. pneumophila,
   we performed genomic subtractive hybridization b/w L. pneumophila serogroup 1
   strain 02/41 & L. micdadei strain 02/42. ... Southern hybridization [to]
   determine the dist'n of 41 seqs., rep. 40 ORFs with a range of putative fns
   among L. pneumophila isolates of various serogroups [&] strains of Legionella
   longbeachae, L. micdadei, Legionella gormanii, & Legionella jordanis. ...
   Disruption of an L. pneumophila-specific gene (lpg2222 locus tag) encoding a
   putative protein with 8 tetratricopeptide repeats [=>] reduced entry into the
   macrophage-like cell line, THP-1, & the type II alveolar epithelial cell
   line, A549. The gene was subs. renamed lpnE, for "L. pneumophila entry." ...
   revealed important genetic diffs. b/w L. pneumophila & other L. species ..."
   -- [<A HREF="http://dx.doi.org/10.1128/IAI.74.3.1683-1691.2006">doi:10.1128/IAI.74.3.1683-1691.2006</A>]['09],
   Legionella@[<A HREF="http://en.wikipedia.org/wiki/Legionella">wikip</A>]['09],
   Legionella pneumophila str. Corby@[<A HREF="http://www.ncbi.nlm.nih.gov/nuccore/NC_009494">refseq</A>]['09],
   -- [<A HREF="http://www.microbiol.unimelb.edu.au/people/hartland/pub.html">Hartland</A>]['09].

%A E. T. Steenkamp
%A J. Wright
%A S. L. Baldauf
%T The protistan origins of animals and fungi
%J Molec. Biol. and Evolution
%V 23
%N 1
%P 93-106
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, phylogenetic, evolution, tree, holozoa,
   animal, fungus, eukaryotes, Protozoa, opisthokont, Opisthokonta, protist
%X "Recent molecular studies suggest that Opisthokonta, the eukaryotic
   supergroup including animals & fungi, should be expanded to include a
   diverse collection of primitively single-celled eukaryotes previously
   classified as Protozoa. ... Our results show that members of all opisthokont
   protist groups encode a ~12-amino acid insertion in EF-1{alpha}, previously
   found exclusively in animals & fungi. Phylogenetic analyses of combined
   multigene data sets including a diverse set of opisthokont & nonopisthokont
   taxa place all of the proposed opisthokont protists unequivocally in an
   exclusive clade with animals & fungi. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/molbev/msj011">doi:10.1093/molbev/msj011</A>]['09],
   lab@[<A HREF="http://www-users.york.ac.uk/~slb14/labpage.html">york</A>]['09].

%A G. S. Vernikos
%A J. Parkhill
%T Interpolated variable order motifs for identification of horizontally
   acquired DNA: Revisiting the Salmonella pathogenicity islands
%J J. Bioinformatics
%V 22
%N 18
%P 2196-2203
%M SEP
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, motif, alien hunter, DNA, foreign,
   horizontal transfer, gene, HGT, genes, detection, SPI, HGT,
   interpolated variable order motifs, IVOM
%X "... Interpolated Variable Order Motifs (IVOMs), which exploits compositional
   biases using variable order motif distributions & captures more reliably the
   local composition of a seq. compared with fixed-order methods. ...
   2nd-order, 2-state [HMM] is implemented in a change-point detection
   framework. We applied the IVOM approach to the genome of Salmonella enterica
   serovar Typhi CT18, a well-studied prokaryote in terms of HGT events ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl369">doi:10.1093/bioinformatics/btl369</A>]['09] (free?),
   program@[<A HREF="http://www.sanger.ac.uk/Software/analysis/alien_hunter/">sanger</A>]['09].

%A S. K. Volkman
%A et al
%T A genome-wide map of diversity in Plasmodium falciparum
%J Nature Genetics
%V 39
%P 113-119
%D 2006
%K MolBio, jrnl, c2006, c200x, c20xx, Plasmodium falciparum, parasite, genomes,
   variability, diversity, population, SNP, SNPs
%X "... extensive sequencing of 16 geographically diverse parasites & identified
   46,937 SNPs, demonstrating rich diversity among P.falciparum parasites
   (pi=1.16E-3) & strong correlation with gene fn. We identified multiple
   regions with signatures of selective sweeps in drug-resistant parasites, inc.
   a previously unidentified 160-kb region with extremely low polymorphism in
   pyrimethamine-resistant parasites. We further characterized 54 worldwide
   isolates by genotyping SNPs across 20 genomic regions. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/ng1930">doi:10.1038/ng1930</A>]['09],
   malaria@[<A HREF="http://www.broadinstitute.org/compbio/pub/malaria/">broad inst.</A>]['09].

%A Y. Astier
%A O. Braha
%A H. Bayley
%T Toward single molecule DNA sequencing: Direct identification of
   ribonucleoside and deoxyribonucleoside 5'-monophosphates by using an
   engineered protein nanopore equipped with a molecular adapter
%J J. Am. Chem. Soc.
%V 128
%N 5
%P 1705-1710
%M FEB
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, DNA sequencing, technology, adaptor,
   Oxford Nanopore Technologies, single molecule, SMRT, nanoporetech
%X "... show that single molecule detection with a modified protein nanopore can
   be used to identify ribonucleoside & 2'-deoxyribonucleoside 5'-monophosphates
   ... Distinct levels of current block are observed for each of the 4 members
   of a set of nucleoside 5'-monophosphates when the molecules bind within a
   mutant alpha-hemolysin pore, (M113R)(7), equipped with the molecular adapter
   heptakis-(6-deoxy-6-amino)-beta-cyclodextrin. While our results compare
   favorably with alternative approaches, further work will be required to
   improve the accuracy of identification of the ...bases, to feed each released
   nucleotide into the pore, & to ensure that every nucleotide is captured by
   the adapter."
   -- [<A HREF="http://dx.doi.org/10.1021/ja057123+">doi:10.1021/ja057123+</A>]['09],
   and [<A HREF="http://www.nanoporetech.com/">nanoporetech.com</A>]
     / [<A HREF="http://www.nanoporetech.com/sequences">sequences</A>]['09].
   [Also search for: MolBio single molecule sequencing]  and
   [also search for: MolBio nanopore].

%A R. Konecny
%A et al ...
%A J. A. McCammon
%T Electrostatic properties of cowpea chlorotic mottle virus and
   cucumber mosaic virus capsids
%J Biopolymers
%V 82
%N 2
%P 106-120
%M JUN
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, cowpea chlorotic mottle virus, viral,
   cucumber mosaic, CCMV, CMV, capsid, Brownian dynamics
%X "... investigated using numerical solutions to the Poisson-Boltzmann equn.
   Experimentally ... shown that CCMV particles swell in the absence of
   divalent cations when the pH is raised from 5 to 7. CMV, although
   structurally homologous, does not undergo this transition. An analysis of the
   calculated electrostatic potential confirms that a strong electrostatic
   repulsion at the calcium-binding sites in the CCMV capsid is most likely the
   driving force for the capsid swelling process during the release of Ca. The
   binding interaction between the encapsulated genome material (RNA) inside of
   the capsid and the inner capsid shell is weakened during the swelling
   transition. This probably aids in the RNA release process, ..."
   -- [<A HREF="http://dx.doi.org/10.1002/bip.20409">doi:10.1002/bip.20409</A>],
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/16278831">pub-med</A>].
   (auth1@[<A HREF="http://ctbp.ucsd.edu/affiliates/showperson.php?id=129">ucsd</A>]['10].)

%A B. Hochner
%A T. Shomrat
%A G. Fiorito
%T The octopus: A model for a comparative analysis of the evolution of learning
   and memory mechanisms
%J Biol. Bull.
%V 210
%N 3
%P 308-317
%M JUN
%D 2006
%K jrnl, biol, biology, c2006, c200x, c20xx, zz0615, octopus, brain, VL, MSF,
   nervous system, marine invertebrate, Coleoidea, Cephalopoda, cephalopod,
   common, O. vulgaris, learning, memory, behaviour, convergent, evolution,
   neural, synapse
%X "... adaptation of modern neurophysiological methods to the study of the
   central nervous system of the octopus ... The emerging results suggest that
   a convergent evolutionary process has led to the selection of vertebrate-like
   neural organization & activity-dependent long-term synaptic plasticity. As
   octopuses & vertebrates are very remote phylogenetically, this convergence
   suggests the importance of the shared properties for the mediation of
   learning & memory."
   -- [<A HREF="http://www.biolbull.org/content/210/3/308.full">www</A>]['15].

%A M. Borodovsky
%A S. Ekisheva
%T Problems and Solutions in Biological Sequence Analysis
%I CUP
%P 360
%D 2006
%K book, text, CUP, c2006, c200x, c20xx, bioinformatics, MolBio, sequence,
   course, exercises, programming, examples
%X "Companion to the highly successful textbook, Biological Sequence Analysis
   by Durbin et al. provides fully worked solutions to the original problems,
   as well as new, fully worked problems."
   1st ed 2006; pb us$35; uk us isbn:0521612306; uk us isbn13:978-0521612302.
   [Also search for: MolBio book].

%A C. D. Murray
%A E. Patchick
%A S. Pettifer
%A T. Howard
%A J. Kalkarni
%A C. Bamford
%T Investigating the efficacy of a virtual mirror box in treating phantom limb
   pain in a sample of chronic sufferers
%J Int. J. of Disability and Human Development
%V 5
%P 227-234
%D 2006
%K jrnl, body image, amputee, amputation, c2006, c200x, c20xx
%X [<A HREF="http://aig.cs.man.ac.uk/research/phantomlimb/">project@U.Manchester</A>]['07].

%A T. Dagan
%A W. Martin
%T The tree of one percent
%J Genome Biology
%V 7
%D 2006
%K jrnl, eJrnl, c2006, c200x, c20xx, zz0409, evolutionary, phylogenetic, tree,
   trees, universal, lateral, horizontal gene transfer, HGT
%X "2 sig. evolutionary processes are fundamentally not tree-like in nature -
   lateral gene transfer among prokaryotes & endosymbiotic gene transfer (from
   organelles) among eukaryotes. To incorporate such processes into the bigger
   picture of early evolution, biologists need to depart from the preconceived
   notion that all genomes are related by a single bifurcating tree."
   -- [<A HREF="http://dx.doi.org/10.1186/gb-2006-7-10-118">10.1186/gb-2006-7-10-118</A>]['09].
   (Also see [<A HREF="http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html?full=true">New Sci</A>]['09].)

%E P. Muller
%T Crystal Structure Refinement: A Crystallographer's Guide to SHELXL
%I IUCr/Oxford
%D 2006
%K book, text, c2006, c200x, c20xx, ShelX, ShelXL, X ray, Xray, crystallography,
   protein structure determination
%X [Also search for: ShelX].

%A J. Chen
%A W. Hsu
%A M. L. Lee
%A S.-K. Ng
%T NeMoFinder: Dissecting genome-wide protein-protein interactions with
   meso-scale network motifs
%J KDD '06
%P 106-115
%D 2006
%K conf, KDD, MolBio, c2006, c200x, c20xx, zz0415, NeMofinder, network, motif,
   pattern, discovery, yeast, PPI
%X "... describe an efficient network motif discovery alg., NeMoFinder, that can
   mine meso-scale n/w motifs that are repeated & unique in large PPI networks.
   Using [it] successfully discovered, for the first time, up to size-12 n/w
   motifs in a large whole-genome S.cerevisiae (Yeast) PPI network. ..."
   -- [<A HREF="http://dx.doi.org/10.1145/1150402.1150418">doi:10.1145/1150402.1150418</A>]['15],
      pdf@[<A HREF="https://www.msu.edu/~jinchen/KDD06.pdf">msu</A>]['15].
   (Also see, "... extract frequent trees & after that expands them
              into non-isomorphic graphs ..."
              -- motifs@[<A HREF="http://en.wikipedia.org/wiki/Network_motif">wikip</A>]['15].)
   [Also search for: network motif discovery].

%A T. Hamelryck
%A J. T. Kent
%A A. Krogh
%T Sampling realistic protein conformations using local structural bias
%J PLoS Comput. Biol.
%V 2
%N 9
%P e131
%D 2006
%K jrnl, eJrnl, MolBio, 2006, c200x, c20xx, zz0413, protein, structure,
   conformation, prediction, sampling, fragment, Rosetta, FB5, FwBt
%X "... use of a divide-and-conquer strategy ... a conformational sampling
   method generates plausible candidate structures, which are subsequently
   accepted or rejected using an energy fn. ... often corr. to separating local
   structural bias from the long-range interactions that stabilize the compact,
   native state. However, sampling p.conformations that are compatible with the
   local structural bias encoded in a given protein seq. is a long-standing open
   problem, esp. in cts space. We describe an elegant & math. rigorous method
   ... show that it readily generates native-like protein confs. simply by
   enforcing compactness. ... have far-reaching implications for protein
   struct. predn, determination, simulation, & design."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pcbi.0020131">doi:10.1371/journal.pcbi.0020131</A>]['13].
   [Also search for: FB5 probability distribution].

%A D. Adjeroh
%A Fei Nan
%T On compressibility of protein sequences
%J Proc. the Data Comp. Conf.
%M MAR
%D 2006
%K conf, DCC, MolBio, c2006, c200x, c20xx, zz0122, protein, compress, BW,
   compression, ProtComp, Hategan, Tabus
%X "... Based on an observed genome-scale long-range correlation in concatenated
   protein seqs. from different organisms, we propose a method to exploit this
   unusual redundancy in compressing the p.seqs.. The result is a sig. reduction
   in the # of bits required for representing the seqs.. We report results in
   bits per symbol (bps) of 2.27, 2.55, 3.11 & 3.44 for p.seqs. from
   M.jannaschii, H.influenzae, S.cerevisiae, & H.sapiens ..."
   -- [<A HREF="https://doi.org/10.1109/DCC.2006.56">doi:10.1109/DCC.2006.56</A>]['22].
   (*NB. Some of these numbers are rather "surprising"...
         "Note that an incorrect protein corpus that was more compressible
         somehow got into circulation at some point, resulting in sig. lower
         compression figures being reported by ProtComp (Hategan & Tabus, 2004)
         & BW (Adjeroh & Nan, 2006). The compression results of ProtComp on the
         correct protein corpus were obtained from the author's website. The
         authors of BW have 'moved to new projects' (Nan, 2006) so proper
         compression results for BW are not available." -- MDC *)
   [Also search for: MolBio protein compression].

%A G. Hampikian
%A T. Andersen
%T Absent Sequences: Nullomers and primes
%J Pacific Symp. on Biocomputing
%P 355-366
%M JAN
%D 2007
%K PSB12, PSB07, conf, MolBio, c2007, c200x, c20xx, DNA of doom, nullomer,
   prime, protein, peptoprime, forbidden, fatal, lethal, absent, rare, missing,
   infrequent, unusual, sequence, substring, word, minimal, short, MAW, words,
   antiMotif, unMotif
%X nullomer: a seq. absent from a selected species or groups of species.
   prime:    a seq. absent from all GenBank.
   "... we have found 43 seqs. & their compliments which are not found in the
   2 published human genomes. Of these seqs., 4 11-mers & their complements
   currently have no seq. match in any reported human sequence in GenBank ...
   ... length 15 is the shortest length at which primes (absent seqs.) are
   found. At this length there are 60370 primes that are not found in any of
   the DNA sequence data.  ...also processed all available protein seqs., &
   identified 1799 primes of length 5."
   -- [<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb07/hampikian.pdf">pdf</A>]['06],
      [<A HREF="http://biology.boisestate.edu/hampikian/">auth1@boisestate</A>]['06].
   [Also search for: missing substring]  and  [also search for: nullomer].

%A A. Chatr-aryamontri
%A A. Ceol
%A L. M. Palazzi
%A G. Nardelli
%A M. V. Schneider
%A L. Castagnol
%A G. Cesareni
%T MINT: the Molecular INTeraction database
%J NAR
%V 35
%M JAN
%D 2007
%K jrnl, NAR, MolBio, c2007, c200x, c20xx, zz1016, network, gene, proetin,
   interation, PPI, MINT, HomoMINT
%X "... aims at storing, in a structured format, information about molecular
   interactions (MIs) by extracting experimental details from work published in
   peer-reviewed journals. ..."
   -- [<A HREF="https://dx.doi.org/10.1093/nar/gkl950">doi:10.1093/nar/gkl950</A>]['16].
   (MINT@[<A HREF="http://mint.bio.uniroma2.it/">uniroma2</A>]['16],
    MINT@[<A HREF="http://mint.bio.uniroma2.it/mint/">uniroma2</A>]['07].)

%A R. L. Warren
%A G. G. Sutton
%A S. J. M.Jones
%A R. A. Holt
%A Assembling millions of short DNA sequences using SSAKE
%J J. Bioinformatics
%V 23
%N 4
%P 500-501
%D 2007
%K jrnl, MolBio, SSAKE, c2007, c200x, c20xx, zz0207, de novo, denovo, assembly,
   sequence, DNA, Solexa, short read, reads, sequencing
%X "... produces millions of short DNA sequences of 25nt each. ... repeats in
   large genomes & the inability of short sequences to uniquely & unambiguously
   characterize them, the short read length limits applicability for de novo
   sequencing. However, given the sequencing depth & the throughput of this
   instrument, stringent assembly of highly identical sequences can be achieved.
   ... SSAKE, a tool for aggressively assembling millions of short nucleotide
   sequences by progressively searching through a prefix tree for the longest
   possible overlap between any two sequences. SSAKE is designed to help
   leverage the information from short sequence reads by stringently assembling
   them into contiguous sequences."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl629">doi:10.1093/bioinformatics/btl629</A>]['07],
   [Also search for: short read MolBio].

%A Z. Zhu
%A Y.-S. Ong
%T Memetic algorithms for feature selection on microarray data
%J Proc. 4th Int. Symp. on Neural Networks
%W Nanjing, China
%P 1327-1335
%M JUN
%D 2007
%O LNCS vol.4491
%K conf, ISSN, ISSN4, MolBio, c2007, c200x, c20xx, zz0816, microarrays,
   features, Markov blanket
%X "... two novel memetic algorithms ... the first MA is a Wrapper-Filter
   Feature Selection Algorithm (WFFSA) fine-tunes the populn of [GA] solns by
   adding or deleting features based on univariate feature filter ranking
   method. The second MA approach, Markov Blanket-Embedded [GA] (MBEGA),
   fine-tunes the populn of solns by adding relevant features, removing
   redundant and/or irrelevant features using Markov blanket. Our empirical
   studies on synthetic & real world microarray dataset suggest that both
   memetic approaches select more suitable gene subset than the basic GA & at
   the same time outperforms GA in terms of classification predictions.  ..."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-72383-7_155">doi:10.1007/978-3-540-72383-7_155</A>]['16], isbn13:9783540723820.

%A A. Ferro
%A R. Giugno
%A G. Pigola
%A A. Pulvirenti
%A C. Di Pietro
%A M. Purrello
%A M. Ragusa
%T Sequence similarity is more relevant than species specificity in
   probabilistic backtranslation
%J BMC Bioinformatics
%V 8:58
%M FEB
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, protein, DNA, coding, cDNA, prediction,
   predict, back translate, translation, backtranslate, backtranslation
%X "Backtranslation is the process of decoding a sequence of amino acids into
   the corresponding codons. All synthetic gene design sys. include a b.t.
   module. The degeneracy of the genetic code makes b.t. potentially ambiguous.
   ... EasyBack ... trained with a set of proteins with known cDNA coding seqs.,
   constructed from the input protein by querying the NCBI databases with BLAST.
   Unlike existing software, the proposed method allows the quality of
   prediction to be estimated. When tested on a group of proteins that show
   different degrees of sequence conservation, EasyBack outperforms other
   published methods in terms of precision. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-8-58">doi:10.1186/1471-2105-8-58</A>]['07].
   [Also search for: 3D matching].

%A J. Krumsiek
%A R. Arnold
%A T. Rattei
%T Gepard: a rapid and sensitive tool for creating dotplots on genome scale
%J J. Bioinformatics
%V 23
%N 8
%P 1026-1028
%M ?
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, dot plot, dotplot
%X "... quick creation of dotplots. It utilizes suffix arrays to reduce the
   time complexity of dotplot calculation to Theta(m*log n). A client-server
   mode, which is a novel feature for dotplot creation s/w, allows the user to
   calc. dotplots & color them by functional annotation without any prior
   downloading of seq. or annotation data."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btm039">doi:10.1093/bioinformatics/btm039</A>]['10],
   gep@[<A HREF="http://mips.gsf.de/services/analysis/gepard">gsf.de</A>]['07].
   [Also search for: MolBio genome alignment].

%A V. Z. Spassov
%A L. Yan
%A P. K. Flook
%T The dominant role of side-chain backbone interactions in structural
   realization of amino acid code. ChiRotor: A side-chain prediction
   algorithm based on side-chain backbone interactions
%J Protein Sci.
%V 16
%N 3
%P 494-506
%M MAR
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, zz1122, ChiRotor, protein structure,
   folding, dynamics, trajectory, side chain, sideChain angles, backbone,
   conformation
%X "... our results suggest that side-chain-backbone interactions play the
   major role in side-chain packing, in stabilizing the folded structs., & in
   differentiating the folded structs. from the unfolded or misfolded structs.,
   while the interactions between side chains have a secondary effect. ..."
   -- [<A HREF="https://doi.org/10.1110/ps.062447107">doi:10.1110/ps.062447107</A>]['22].
   [Also search for: sideChain backBone MolBio].

%A R. J. Taft
%A M. Pheasant
%A J. S. Mattick
%T The relationship between non-protein-coding DNA and eukaryotic complexity
%J Bioessays
%V 29
%N 3
%P 288-299
%M MAR
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, eukaryotic, biological, complexity, DNA,
   C G value paradox, Cvalue, Gvalue, genes, proteins, intron, introns,
   cis-acting, trans, regulatory, non coding, noncoding, RNA, miRNA, siRNA
%X "... 2 intriguing paradoxes in mol.biol.  - the inconsistent relationship
   between organismal complexity & (1) cellular DNA content & (2) the # of
   protein-coding genes - ref. to as the C-value & G-value paradoxes, resp..
   The C-value paradox may be largely explained by varying ploidy. The G-value
   paradox is more problematic, as the extent of protein coding seq. remains
   relatively static over a wide range of developmental complexity. We show by
   analysis of sequenced genomes that the relative amount of non-protein-coding
   seq. increases consistently with complexity. We also show that the distn of
   introns in complex organisms is non-random. Genes composed of large amounts
   of intronic sequence are sig. overrepresented amongst genes that are highly
   expressed in the nervous system, & amongst genes downregulated in embryonic
   stem cells & cancers. We suggest that the informational paradox in complex
   organisms may be explained by the expansion of cis-acting regulatory elts &
   genes specifying trans-acting non-protein-coding RNAs."
   -- [<A HREF="http://dx.doi.org/10.1002/bies.20544">doi:10.1002/bies.20544</A>]['10],
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/17295292">ncbi</A>]['10].

%A E. Krissinel
%T On the relationship between sequence and structure similarities in proteomics
%J J. Bioinformatics
%V 23
%N 6
%P 717-723
%D 2007
%K jrnl, c2007, c200x, c20xx, MolBio, similar, similarity, protein, SCOP,
   fold, folds, hydropathic profile, alignment, primary, tertiary, families
%X "... Statistical analysis of multiple & pairwise structural alignments of
   protein structures within SCOP folds is performed. The results indicate that
   multiple conservation of residue identity is not common & that relationship
   between sequence & structure may be explained by a model based on the
   assumption that protein structure is tolerant to residue substitutions
   preserving hydropathic profile of the sequence. This model also explains the
   origin & specific value of the sequence similarity threshold, noticed in many
   previous studies, below which structural resemblance is not stat. expected."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btm006">doi:10.1093/bioinformatics/btm006</A>]['07].

%A M. A. Apostol
%A et al ...
%A D. Eisenberg
%T Atomic structures of amyloid cross-beta spines reveal varied steric zippers
%J Nature
%V 447
%P 454-457
%M APR
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, zz0820, amyloid fibril, prion, disease,
   2OL9, GNNQQNY, protein, prions, alpha, beta spine, tau, Sup35, folded,
   misfolded, Alzheimer's, Alzheimers
%X "Amyloid fibrils formed from different proteins, each assoc. with a
   particular disease, contain a common cross-beta spine. ... the fibril-forming
   segment GNNQQNY of the yeast prion protein Sup35, was recently revealed ...
   ... It is a pair of beta-sheets, with the facing side chains of the two
   sheets interdigitated in a dry 'steric zipper'. ... report some 30 other
   segments from fibril-forming proteins ... include segs from the Alzheimer's
   amyloid-beta & tau proteins, the PrP prion protein, insulin, islet amyloid
   polypeptide (IAPP), lysozyme, myoglobin, alpha-synuclein & beta-microglobulin
   suggesting that common structural features are shared by amyloid diseases ...
   13 of these microcrystals all reveal steric zippers, but with variations ..."
   -- [<A HREF="https://doi.org/10.1038/nature05695">doi:10.1038/nature05695</A>]['20] (online 29/4/2007).
   Also see 2OL9@[<A HREF="http://doi.org/10.2210/pdb2OL9/pdb">PDB</A>]['20].
   [Also search for: prion disease].

%A J. M. Asara
%A M. H. Schweitzer
%A L. M. Freimark
%A M. Phillips
%A L. C. Cantley
%T Protein sequences from Mastodon and Tyrannosaurus rex revealed by mass
   spectrometry
%J Science
%V 316
%N 5822
%P 280-285
%M APR
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, fossil, proteins, Tyrannosaurus rex, Trex,
   DNA, Mammut americanum, mastodon, collagen peptide, sequence, zz0407, zz0908,
   controversial
%X "... used mass spectrometry to obtain protein seqs. from bones of a 160,000
   to 600,000-year-old extinct mastodon (Mammut americanum) & a 68-million-y.-
   -old dinosaur (Tyrannosaurus rex). The presence of T.rex seqs. indicates that
   their peptide bonds were remarkably stable. Mass spectrometry can thus be
   used to determine unique seqs. from ancient organisms from peptide
   fragmentation patterns, ...
   If the unknown peptide is identical in seq. to a protein region from an
   organism whose genes or proteins have previously been seq'd, then the frag.
   pattern (the mass/charge ratios & relative intensities of peaks) will match a
   theor. frag. pattern from a seq. in publicly available protein [DB] or from
   the frag. pattern of a synthetically derived peptide, to confirm its id.."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1137614">doi:10.1126/science.1137614</A>]['07],
      [<A HREF="http://www.sciencemag.org/cgi/content/full/316/5822/280/DC1">supplement</A>]['07].
   But also see [<A HREF="http://dx.doi.org/10.1126/science.1155006">doi:10.1126/science.1155006</A>][8/'08],
   and [<A HREF="http://dx.doi.org/10.1126/science.1157829">doi:10.1126/science.1157829</A>][8/'08],
   and "Fresh doubts over T. rex chicken link," Nature, v.454, Aug 2008
   -- [<A HREF="http://dx.doi.org/10.1038/4541035a">doi:10.1038/4541035a</A>]['08].
   [Also search for: MolBio fossil protein].

%T Evolutionary and biomedical insights from the Rhesus Macaque genome
%Q Rhesus Macaque Genome Sequencing and Analysis Consortium.
%J Science
%V 316
%N 5822
%P 222-234
%M APR
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, primate, genome, rheMac, rheMac2,
   nGenome, macaques, monkey, Macaca mulatta
%X "... highly accurate human genome sequence and a draft of the chimpanzee
   genome have been generated & compared. The chimpanzee shared a common
   ancestor with h. approx. 6 Mya ... By contrast, the genome of the rhesus
   macaque has diverged farther from our own, with an average human-macaque
   seq. identity of ~93%. Fig.1 shows the inferred common ancestor for all 3
   species, as well as a common ancestor that predated the human-chimpanzee
   divergence. A characteristic that is found in humans but not in the chimp.
   can be recognized as a loss in the chimpanzee if it is present in the macaque
   or it can be recognized as a gain in the human if it is absent in macaque.
   In principle, this 3-way comparison should make it possible to pinpoint many
   changes & identify specific underlying mutational mechanisms, which could
   have been critically important during the past 25 m.y. in shaping the biology
   of the 3 primate species. ..."             [other rel. papers in same issue]
   -- [<A HREF="http://dx.doi.org/10.1126/science.1139247">doi:10.1126/science.1139247</A>]['07],
      [<A HREF="http://http://www.sciencemag.org/cgi/content/full/316/5822/222/DC1">supporting material</A>]['07],
      [<A HREF="http://www.hgsc.bcm.tmc.edu/projects/rmacaque/">rmacaque@baylor</A>]['07],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">genomes@ncbi</A>]['07] taxid=9544, chromosomes: 20+X+Y.

%A R. D. Hernandez
%A M. J. Hubisz
%A et al
%T Demographic histories and patterns of linkage disequilibrium in Chinese and
   Indian Rhesus Macaques
%J Science
%V 316
%N 5822
%P 240-243
%M APR
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, Macaca mulatta, primate, evolution,
   macaque, species, history, India, China, zz0407
%X "... Population genetic analyses of the 1467 single-nucleotide polymorphisms
   discovered suggest that the 2 pop'ns separated about 162,000 years ago ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1140462">doi:10.1126/science.1140462</A>]['07],
      [<A HREF="http://www.hgsc.bcm.tmc.edu/projects/rmacaque/">rmacaque@baylor</A>]['07].

%A P. M. Ravdin
%A et al
%T The decrease in breast-cancer incidence in 2003 in the United States
%J The New England J. of Medicine
%V 356
%P 1670-1674
%M APR
%D 2007
%K jrnl, c2007, c200x, c20xx, HRT, estrogen, oestrogen, stats, medical,
   hormone replacement therapy, medicine, risk, risks, human, women,
   USA, health
%X "... age-adjusted incidence rate of breast cancer in women in the [USA] fell
   sharply (by 6.7%) in 2003, as compared with the rate in 2002. Data from 2004
   showed a leveling off relative to the 2003 rate, with little additional
   decrease. ... seems to be temporally related to the first report of the
   Women's Health Initiative and the ensuing drop in the use of
   hormone-replacement therapy among postmenopausal women in the [USA]. ..."
   -- [<A HREF="http://content.nejm.org/cgi/content/full/356/16/1670">paper@NEJM</A>]['07].
   Also see The Lancet
   -- [<A HREF="http://dx.doi.org/10.1016/S0140-6736(07)60534-0">doi:10.1016/S0140-6736(07)60534-0</A>]['07].

%A J. Doyle
%A M. Csete
%T Rules of engagement
%J Nature
%V 446
%N 7138
%P 860
%M APR
%D 2007
%K jrnl, essay, MolBio c2007, c200x, c20xx, zz0507, metablic network, networks,
   pathways, architecture, evolution, perturbations, perturbation
%X Complex engineered and biological systems share protocol-based architectures
   that make them robust and evolvable, but with hidden fragilities to rare
   perturbations.
   -- [<A HREF="http://dx.doi.org/10.1038/446860a">doi:10.1038/446860a</A>]['07],
      [<A HREF="http://www.nature.com/nature/focus/arts/essays/">essays@nature</A>]['07],
      [<A HREF="http://userwww.service.emory.edu/~mcsete/index.html">Csete@emory</A>]['07].

%A H. Rottenberg
%T Coevolution of exceptional longevity, exceptionally high metabolic rates,
   and mitochondrial DNA-coded proteins in mammals
%J Experimental Gerontology
%V 42
%N 4
%P 364-373
%M APR
%D 2007
%K jrnl, c2007, c200x, c20xx, MolBio, evolution, aging, longevity, mitochondria,
   mitochondrial DNA, basal metabolic rate, mammal, reactive oxygen species,
   lie span, lifespan, age aging, ageing, metabolism
%X "Mammals' longevity is inversely related to mass-specific basal metabolic
   rate because the generation of reactive oxygen species constrains lifespan.
   Longevity increases with body mass ...  In placental mammals the longevity
   residuals from the power laws that describe longevity as a function of mass-
   -specific basal metabolic rates, or body mass, are + corr. with the relative
   rates of evolution of cytochrome b, a generator of reactive oxygen species.
   ...  compatible with the hypothesis that, in placental mammals, the
   accelerated evolution of mtDNA-coded proteins, allowed the extension of
   lifespan by selecting mutations that reduce the generation of reactive oxygen
   species, mostly by increasing internal proton leak, that accelerates
   mitochondrial electron transport."
   -- [<A HREF="http://dx.doi.org/10.1016/j.exger.2006.10.016">doi:10.1016/j.exger.2006.10.016</A>]['07].

%A K. C. Pang
%A S. Stephen
%A M. E. Dinger
%A P. G. Engstrom
%A B. Lenhard
%A J. S. Mattick
%T RNAdb 2.0 - an expanded database of mammalian non-coding RNAs
%J NAR
%V 35
%P D178-D182
%D 2007
%K jrnl, NAR, MolBio, RNA, DBMS, c2007, c200x, c20xx, uniQld, miRNA, miRNAs,
   ncRNA, ncRNAs, PIWI
%X "...nucleotide seqs. & annotations for tens of thousands of non-housekeeping
   ncRNAs, inc. a wide range of mammalian microRNAs, small nucleolar RNAs &
   larger mRNA-like ncRNAs. Some of these have documented functions &/or
   expression patterns, but the majority remain of unclear significance, &
   include PIWI-interacting RNAs, ncRNAs identified from the latest rounds of
   large-scale cDNA seq. projects, putative antisense transcripts, as well as
   ncRNAs predicted on the basis of structural features & alignments.
   Improvements to the database comprise not only new & updated ncRNA datasets,
   but also provision of microarray-based expression data & closer interface
   with more specialized ncRNA resources such as miRBase & snoRNA-LBME-db."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gkl926">doi:10.1093/nar/gkl926</A>]['07],
   &  [<A HREF="http://research.imb.uq.edu.au/RNAdb">RNAdb</A>]['07].

%Q Opossum Genome Sequencing Consortium
%A T. S. Mikkelsen
%A at al
%T Genome of the marsupial Monodelphis domestica reveals innovation in
   non-coding sequences
%J Nature
%V 447
%P 167
%D 2007
%K jrnl, MolBio, opossum, marsupial, nGenome, c2007, c200x, c20xx, zz0507,
   short tailed opossum, tail, Monodelphis domestica, DNA, sequence
%X "... high-quality draft of the genome sequence of the grey, short-tailed
   opossum (Monodelphis domestica). ... strong influence of biased gene
   conversion on nucleotide sequence composition, & a relationship between
   chromosomal characteristics & X chromosome inactivation. Comparison of o. &
   eutherian genomes also reveals a sharp difference in evolutionary innovation
   between protein-coding & non-coding functional elements. ...  transposons as
   a major creative force in the evolution of mammalian gene regulation."
   -- [<A HREF="http://dx.doi.org/10.1038/nature05805">doi:10.1038/nature05805</A>]['07].
   "All analysed data sets can be obtained from
   -- [<A HREF="http://www.broad.mit.edu/mammals/opossum/">www.broad.mit.edu/mammals/opossum/</A>]['07].
   This Monodelphis domestica whole-genome shotgun project has been deposited at
   DDBJ/EMBL/GenBank under NCBI accession code AAFR00000000.
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/Genomes/">ncbi.../Genomes/</A>]['05].
   [split from the placental mammal lineage about 180m.y. ago].
   [Also search for: marsupial MolBio].

%A S. de Groot
%A T. Mailund
%A J. Hein
%T Comparative annotation of viral genomes with non-conserved gene structure
%J J. Bioinformatics
%V 23
%N 9
%P 1080-1089
%M MAY
%D 2007
%K jrnl, c2007, c200x, c20xx, MolBio, virus, gene, genome, annotate, HIV, HBV,
   overlapping
%X "... Conventional ... HMM-based gene-finding algs. may typically find it
   difficult to identify multiple coding regions, since in general their
   topologies do not allow for the presence of overlapping or nested genes. ...
   present an HMM based gene-finding program, which allows for coding in
   unidirectional nested & overlapping reading frames, to annotate 2 homologous
   aligned viral genomes. Our method does not insist on conserved gene structure
   between the 2 seqs., thus making it applicable for the pairwise comparison of
   more distantly related sequences. ... 15 pairwise alignments of 6 different
   HIV2 genomes. Given sufficient evolutionary distance between the 2 sequences,
   we achieve sensitivity of ~84-89% & specificity of ~97-99.9%. We additionally
   annotate 3 pairwise alignments of the more distantly related HIV1 & HIV2, as
   well as of 2 different hepatitis viruses, attaining results of ~87%
   sensitivity & ~98.5% specificity. We subsequently incorporate prior knowledge
   by "knowing" the gene structure of 1 sequence & annotating the other
   conditional on it. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btm078">doi:10.1093/bioinformatics/btm078</A>]['07].

%A A. Molnar
%A F. Schwach
%A D. J. Studholme
%A E. C. Thuenemann
%A D. C. Baulcombe
%T miRNAs control gene expression in the single-cell alga
   Chlamydomonas reinhardtii.
%J Nature
%V ?
%P ?-?
%M ?
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, miRNA, siRNA, alga, algae, algal, dicer,
   argonaute, evolution, unicellular, eukaryotic, eukaryote, zz0607
%X "...[miRNAs] released by a Dicer nuclease as a 22-24-nucleotide RNA duplex
   from a precursor in which an imperfectly matched inverted repeat forms a
   partly double-stranded region. 1 of the 2 strands is then recruited by an
   Argonaute nuclease that is the effector protein of the silencing mechanism.
   Short interfering RNAs (siRNAs), which are similar to miRNAs, are also
   produced by Dicer ... we show that the unicellular alga Chlamydomonas
   reinhardtii contains miRNAs, putative evolutionary precursors of miRNAs &
   species of siRNAs resembling those in higher plants. The common features of
   miRNAs and siRNAs in an alga and in higher plants indicate that complex
   RNA-silencing systems evolved before multicellularity & were a feature of
   primitive eukaryotic cells."   (Online May 2007)
   -- [<A HREF="http://dx.doi.org/10.1038/nature05903">doi:10.1038/nature05903</A>]['07].

%A E. H. Margulies
%A et al ...
%A A. Sidow
%T Analyses of deep mammalian sequence alignments and constraint predictions for
   1% of the human genome
%J Gen. Res.
%V 17
%N 6
%P 760-774
%M JUN
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, Encode, zzEncode, project, DNA,
   alignment, genome
%X "... present orthologous sequence generation, alignment, and evolutionary
   constraint analyses of 23 mammalian species for all ENCODE targets.
   Alignments were generated using four different methods; comparisons
   of these methods reveal large-scale consistency but substantial
   differences in terms of small genomic rearrangements,
   sensitivity (sequence coverage), and
   specificity (alignment accuracy). ..."
   [Also search for: MolBio genome alignment].
      (NB. terminology for 'sensitivity' & 'specificity' (?precision?) is
      somewhat at odds with ROC; [also search for: ROC defn].)

%T Genome-wide association study of 14,000 cases of seven common diseases and
   3,000 shared controls
%Q The Wellcome Trust Case Control Consortium
%J Nature
%V 447
%P 661-678
%M JUN
%D 2007
%K jrnl, c2007, c200x, c20xx, MolBio, genomics, stats, disease, gene, genes,
   associated, linked, GWA, bipolar disorder, coronary artery disease, Crohn's,
   rheumatoid arthritis, diabetes, zz0607
%X "... 24 indep. assoc. signals at P < 5 times 10**-7:
   1 in bipolar disorder,  1 in coronary artery disease,  9 in Crohn's disease,
   3 in rheumatoid arthritis, 7 in type 1 diabetes, & 3 in type 2 diabetes....
   ... identified a large number of further signals (including 58 loci with
   single-point P values between 10**-5 & 5 times 10**-7) likely to yield
   additional susceptibility loci. The importance of appropriately large samples
   was confirmed by the modest effect sizes obs. at most loci identified. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature05911">doi:10.1038/nature05911</A>]['07].

%A P. Kapranov
%A et al
%T RNA maps reveal new RNA classes and a possible function for pervasive
   transcription
%J Science
%V 316
%N 5830
%P 1484-1488
%M JUN
%D 2007
%K jrnl, c2007, c200x, c20xx, MolBio, class, map, sRNA, sRNAs, lRNA, lRNAs
%X "...The genomic origins & the associations of human nuclear & cytosolic
   polyadenylated RNAs longer than 200 (nt) & whole-cell RNAs less than 200 nt
   were investigated in this genome-wide study. Subcellular addresses for
   nucleotides present in detected RNAs were assigned, & their potential
   processing into short RNAs was investigated. Taken together, these obs.
   suggest a novel role for some unannotated RNAs as primary transcripts for the
   production of short RNAs. 3 potentially functional classes of RNAs have been
   identified, 2 of which are syntenically conserved & correlate with the
   expression state of protein-coding genes.  ... support a highly interleaved
   organization of the human transcriptome."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1138341">doi:10.1126/science.1138341</A>]['07].

%T Identification and analysis of functional elements in 1% of the human genome
   by the ENCODE pilot project
%Q The ENCODE Project Consortium
%J Nature
%V 447
%P 799-816
%M JUN
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, zz0607, Encyclopedia of DNA Elements,
   ENCODE, zzEncode, project, functional element, transcription, regulation,
   cCRE, cCREs, junk DNA, mRNA, non-coding, noncoding, regulation
%X "... the genome is pervasively transcribed, such that the majority of its
   bases can be found in primary transcripts, inc. non-protein-coding
   transcripts, & those that extensively overlap one another. Second, systematic
   examination of transcriptional regulation has yielded new understanding about
   transcription start sites, including their relationship to specific
   regulatory seqs. & features of chromatin accessibility & histone
   modification. Third, a more sophisticated view of chromatin structure has
   emerged, including its inter-relationship with DNA replication &
   transcriptional regulation. Finally, integration of these new sources of
   information, in particular with respect to mammalian evolution based on
   inter- & intra-species sequence comparisons, has yielded new mechanistic &
   evolutionary insights ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature05874">10.1038/nature05874</A>]['07],
      [<A HREF="http://www.genome.gov/10506161">genome.gov/10506161</A>]['07],
      [<A HREF="http://www.genome.gov/ENCODE/">genome.gov/ENCODE</A>['08],
      encode@[<A HREF="http://genome.ucsc.edu/ENCODE/">ucsc</A>]['08].
   (Also see Nature, vol.583, pp.693-698, 29/7/20
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2449-8">doi:10.1038/s41586-020-2449-8</A>]['20].)
   [Also search for: MolBio Encode project].

%A G. Pollastri
%A A. J. M. Martin
%A C. Mooney
%A A. Vullo
%T Accurate prediction of protein secondary structure and solvent accessibility
   by consensus combiners of sequence and structure information
%J BMC Bioinformatics
%D 2007
%V 8:201
%K jrnl, ejrnl, MolBio, c2007, c200x, c20xx
%X "... high-throughput machine learning systems for the prediction of protein
   secondary structure & solvent accessibility that exploit homology to proteins
   of known structure, where available  ...  [if] seq. similarity exceeding 30%,
   secondary structure prediction quality is approx. 90%, close to its
   theoretical max., & 2-class solvent accessibility roughly 85%. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-8-201">doi:10.1186/1471-2105-8-201</A>]['07],
      [<A HREF="http://distill.ucd.ie/">distill.ucd.ie</A>]['07].

%A J. R. Wible
%A G. W. Rougier
%A M. J. Novacek
%A R. J. Asher
%T Cretaceous eutherians and Laurasian origin for placental mammals near the
   K/T boundary
%J Nature
%V 447
%P 1003-1006
%M JUN
%D 2007
%K jrnl, c2007, c200x, c20xx, marsupial, marsupials, placental, mammal,
   fossil, fossils, Placentalia, Cretaceous, phylogenetic analysis, evolution,
   eutherian, afrotherians, xenarthrans
%X "... we report the discovery of a new well-preserved mammal from the Late
   Cretaceous of Mongolia & a broad-scale phylogenetic analysis. Our results
   exclude Cretaceous fossils from Placentalia, place the origin of Placentalia
   near the Cretaceous/Tertiary (K/T) boundary in Laurasia rather than much
   earlier within the Cretaceous in the S. Hemisphere, & place afrotherians &
   xenarthrans in a nested rather than a basal position, within Placentalia."
   "... We reconstructed the phylogenetic relationships of Maelestes by
   parsimony analysis of 408 morphological characters (127 dental, 212
   craniomandibular & 69 postcranial) across 69 taxa ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature05854">doi:10.1038/nature05854</A>]['07].
   [i.e., placental / marsupial split just *after* the end of the dinosaurs].
   [differs from genetic inferences].
   [Also search for: marsupial MolBio].

%A R. A. Hoskins
%A et al
%T Sequence finishing and mapping of Drosophila melanogaster Heterochromatin
%J Science
%V 316
%N 5831
%P 1625-1628
%M JUN
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, fruit fly, heterochromatin, WGS, WGS3,
   pericentromeric, centromere, telomere, telomeric
%X "... heterochromatic regions of Drosophila melanogaster contain 20 million
   bases (Mb) of sequence amenable to mapping, sequence assembly, and finishing.
   We describe the generation of 15 Mb of finished or improved heterochromatic
   seq. with the use of available clone resources and assembly methods. ..."
   "... The whole-genome shotgun sequence (WGS3) was the foundation ..."
   -- [<A HREF="10.1126/science.1139816">doi:10.1126/science.1139816</A>]['07].
   "Heterochromatin is a genetically inactive region of chromosomes that either
   lacks genes or contains genes that are repressed. ... Both centromeres and
   telomeres are heterochromatic ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Heterochromatin">Heterochromatin@wikip</A>]['07].

%A K. Foerster
%A T. Coulson
%A B. C. Sheldon
%A J. M. Pemberton
%A T. H. Clutton-Brock
%A L. E. B. Kruuk
%T Sexually antagonistic genetic variation for fitness in red deer
%J Nature
%V 447
%P 1107-1110
%M JUN
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, gene, genes, male, female, father,
   daughter, gender, sex, selection, selective pressure, males, females,
   antagonostic, battle, sexes, evolution, dimorphism, polygynous mating,
   strategy, zz0707
%X "... theoretical predictions of equilibrium genetic variance under mutation-
   -selection balance are usually lower than the observed values, & the reason
   for this is unknown. The potential role of sexually antagonistic selection in
   maintaining genetic variation has received little attention in this debate,
   surprisingly given its potential ubiquity in dioecious organisms. At fitness-
   -related loci, a given genotype may be selected in opposite directions in the
   2 sexes. Such sexually antagonistic selection will reduce the otherwise-
   -expected positive genetic correlation between male & female fitness. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature05912">doi:10.1038/nature05912</A>]['07] [31 refs]

%A A. A. Ptitsyn
%A S. Zvonic
%A J. M. Gimble
%T Digital signal processing reveals circadian baseline oscillation in majority
   of mammalian genes
%J PLoS Computational Biology
%V 3
%N 6
%P e120
%M JUN
%D 2007
%K jrnl, eJrnl, MolBio, c2007, c200x, c20xx, PLoS, day, night, clock,
   gene, genes, expression, level, levels, daily, variation, cycle, rhythm,
   cycle, cyclic, mammal, mammals
%X "... identifies circadian baseline oscillation in almost 100% of all
   expressed genes. Consequently, circadian oscillation in gene expression
   should be evaluated in any study related to biological pathways. Changes in
   gene expression caused by mutations or regulation of environmental factors
   (such as photic stimuli or feeding) should be considered in the context of
   changes in the amplitude and phase of genetic oscillations."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pcbi.0030120">doi:10.1371/journal.pcbi.0030120</A>]['07].


%A F. Warneken
%A B. Hare
%A A. P. Melis
%A D. Hanus
%A M. Tomasello
%T Spontaneous altruism by chimpanzees and young children
%J PLoS Biology
%V 5
%N 7
%P e184
%M JUN
%D 2007
%K jrnl, eJrnl, c2007, c200x, c20xx, chimp, chimps, human, child, cooperate,
   cooperation, help, prisoners dilemma, animal, behaviour, food, experiment
%X "... report experimental evidence that chimpanzees perform basic forms of
   helping in the absence of rewards spontaneously & repeatedly toward humans &
   conspecifics. In 2 comparative studies, semi-free ranging chimps. helped an
   unfamiliar h. to the same degree as did h. infants, irrespective of being
   rewarded (exp.1) or whether the helping was costly (exp.2). In a 3rd study,
   cs. helped an unrelated conspecific gain access to food in a novel situation
   that req. subjects to use a newly acquired skill on behalf of another..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pbio.0050184">doi:10.1371/journal.pbio.0050184</A>]['07], [30 refs].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A Z. L. Brumme
%T Evidence of differential HLA class I-mediated viral evolution in functional
   and accessory/regulatory genes of HIV-1
%J PLoS Pathogens
%V 3
%N 7
%P e94
%M JUL
%D 2007
%K jrnl, eJrnl, c2007, c200x, c20xx, MolBio, zz0707, HIV, HIV1, HIVI, HLA, CTL,
   mutation, mutations, drug resistance, protease, reverse transcriptase, RT,
   ELISpot,linkage disequilibrium
%X "Despite the formidable mutational capacity & sequence diversity of HIV-1,
   evidence suggests that v. evolution in response to specific selective
   pressures follows generally predictable mutational pathways. Population-
   -based analyses of clinically derived HIV seqs. may be used to identify
   immune escape mutations in viral genes; ... We applied a viral lineage-
   -corrected analytical method to investigate HLA class I-associated seq.
   imprinting in HIV protease, reverse transcriptase (RT), Vpr, & Nef in a large
   cohort of chronically infected, antiretrovirally naive individuals. A total
   of 478 unique HLA-associated polymorphisms were observed & organized into a
   series of "escape maps," which identify known & putative cytotoxic T
   lymphocyte (CTL) epitopes under selection pressure in vivo. ... The design
   of preventative & therapeutic CTL-based vaccine approaches could incorporate
   information on predictable escape pathways." [43 refs]
   -- [<A HREF="http://dx.doi.org/10.1371/journal.ppat.0030094">doi:10.1371/journal.ppat.0030094</A>][7/'07].

%A N. H. Putnam
%A et al
%T Sea anemone genome reveals ancestral Eumetazoan gene repertoire and genomic
   organization.
%J Science
%V 317
%N 5834
%P 86-94
%M JUL
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, Nematostella vectensis, Cnidaria,
   Cnidarian, animal, animals, analysis, evolution
%X "... along with corals, jellyfish, & hydras, constitute the oldest eumetazoan
   phylum, the Cnidaria.  ... Nematostella vectensis. The sea anemone genome is
   complex, with a gene repertoire, exon-intron structure, & large-scale gene
   linkage more similar to vertebrates than to flies or nematodes, implying that
   the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth
   of the inferred genes of the ancestor are eumetazoan novelties, which are
   enriched for animal functions like cell signaling, adhesion, & synaptic
   transmission. Analysis of diverse pathways suggests that these
   gene "inventions" along the lineage leading to animals were likely already
   well integrated with preexisting eukaryotic genes in the eumetazoan
   progenitor."
   "... assembly ~ 357 megabases (Mb) ... Currently [] no map ...
   a total genome size of ~ 450 Mb. ...  est. ~18,000 [] genes ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1139158">doi:10.1126/science.1139158</A>]['07].

%A N. A. Christakis
%A J. H. Fowler
%T The spread of obesity in a large social network over 32 years
%V 357
%N 4
%P 370-379
%M JUL
%D 2007
%K jrnl, c2007, c200x, c20xx, zz0707, health, biol, medicine, obese, weight,
   risk, risks, stats, human, Framingham heart study, USA
%X "... We evaluated a densely interconnected social network of 12,067 people
   assessed repeatedly from '71 to '03 as part of the Framingham Heart Study.
   ... discernible clusters of obese persons (body-mass index ...], >=30) were
   present in the network at all time pts, & the clusters extended to 3 degrees
   of separation. These clusters did not appear to be solely attributable to the
   selective formation of social ties among obese persons. ..."
   -- [<A HREF="http://content.nejm.org/cgi/content/full/357/4/370">papare</A>]['07].
   (Also see [<A HREF="http://www.framinghamheartstudy.org/">F.H.study</A>]['12].

%A R. M. Clark
%A et al
%T Common sequence polymorphisms shaping genetic diversity in Arabidopsis
   thaliana
%J Science
%V 317
%N 5836
%P 338-342
%M JUL
%D 2007
%K jrnl, c2007, c200x, c20xx, MolBio, polymorphism, DNA, gene, genes, plant,
   plants, SNP
%X "... 20 diverse strains (accessions). More than 1 million nonredundant single
   -nucleotide polymorphisms (SNPs) were identified at moderate false discovery
   rates (FDRs), and ~4% of the genome was identified as being highly dissimilar
   or deleted relative to the reference genome seq.. Patterns of polymorphism
   are highly nonrandom among gene families, with genes mediating interaction
   with the biotic environment having exceptional polymorphism levels. At the
   chromosomal scale, regional variation in p. was readily apparent. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1138632">doi:10.1126/science.1138632</A>]['07].

%A M. Kruspe
%A P. F Stadler
%T Progressive multiple sequence alignments from triplets
%J BMC Bioinformatics
%V 8
%P 254
%M JUL
%D 2007
%K jrnl, eJrnl, c2007, c200x, c20xx, zz0707, MolBio, alignment, three, triplet,
   aln3nn, clustal, clustalw, DNA, protein
%X "... The 3-way Neighbor-Net based al.-program aln3nn is shown to compare
   favorably on both protein sequences & nucleic acids sequences. In the latter
   case one easily can include scoring terms that consider secondary structure
   features. Overall, the quality of resulting alignments in general exceeds
   that of CLUSTALW or other..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-8-254">doi:10.1186/1471-2105-8-254</A>]['07].
   [Also search for: multiple alignment]

%A P. Ferragina
%A R. Giancarlo
%A V. Greco
%A G. Manzini
%A G. Valiente
%T Compression-based classification of biological sequences and structures via
   the Universal Similarity Metric: experimental assessment.
%J BMC Bioinformatics
%V 8
%P 252
%M JUL
%D 2007
%K jrnl, eJrnl, MolBio, c2007, c200x, c20xx, compress, zz0807, sequence,
   structure, USM, cluster, clustering
%X "... test the USM methodology by using 25 compressors ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-8-252">doi:10.1186/1471-2105-8-252</A>]['07].
   [Also search for: MolBio compress]

%A B. Bengoudifa
%A R. Mieusset
%T Thermal asymmetry of the human scrotum
%J Human Reproduction
%V 22
%N 8
%P 2178-2182
%M AUG
%D 2007
%K jrnl, c2007, c200x, c20xx, zz0919, human, anatomy, male, body, health,
   reproduction, scrotum, testicle, sperm, fertility, temperature, postman,
   postmen, symmetry, asymmetry, Ig, funny, ha ha, hahah, IgNobel prize, ignoble
%X "... Lack of thermal symmetry was seen in the right and left scrotum, whether
   naked or clothed, and this applied regardless of position or activity when
   clothed. This thermal difference between right and left scrotum could
   contribute to the asymmetry in the male external genital organs."
   -- [<A HREF="https://doi.org/10.1093/humrep/dem133">doi:10.1093/humrep/dem133</A>]['19].
   And it won an IgNobel prize for anatomy in 2019
   [<A HREF="https://www.bbc.com/news/world-us-canada-49687538">bbc</A>][13/9/2019],
   [<A HREF="https://www.improbable.com/2019/09/12/announcing-the-2019-ig-nobel-prize-winners/">2019</A>].

%A V. Sangar
%A D. J Blankenberg
%A N. Altman
%A A. M. Lesk
%T Quantitative sequence-function relationships in proteins based on
   gene ontology
%J BMC Bioinformatics
%V 8
%P 294
%M AUG
%D 2007
%K jrnl, eJrnl, MolBio, AMLesk, c2007, c200x, c20xx, zz0807, protein,
   similarity, sequence, homology, function, family, families, PFAM, DB
%X "...present a quantitative study of seq. & function divergence, based on the
   Gene Ontology classification of fn. ... relationship between seq. divergence
   & fn divergence in 6828 protein families from the PFAM database.  ...
   correlated the divergence in seqs. determined from pairwise alignments & the
   divergence in fn determined by path lengths in the Gene Ontology graph,
   taking into account the fact that many proteins have multiple fns. ...
   show that, among homologous proteins, the proportion of divergent functions
   decreases dramatically above a threshold of seq. similarity at about 50%
   residue identity. For proteins with more than 50% residue identity, transfer
   of annotation between homologs will lead to an erroneous attribution with a
   totally dissimilar function in fewer than 6% of cases. This means that for
   very similar proteins (about 50% identical residues) the chance of completely
   incorrect annotation is low; however, because of the phenomenon of
   recruitment, it is still non-zero."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-8-294">doi:10.1186/1471-2105-8-294</A>]['07].

%A L. Martinez
%A R. Andreani
%A J. Mario Martinez
%T Convergent algorithms for protein structural alignment
%J BMC Bioinformatics
%V 8
%P 306
%M AUG
%D 2007
%K jrnl, eJrnl, MolBio, c2007, c200x, c20xx, zz0807, algorithm, tertiary,
   structure, protein, LOVO, STRUCTAL score
%X "... the maximization of scoring fns in protein al. is interpreted as a Low
   Order Value Optimization (LOVO) problem. The new interp. provides a f/w for
   the development of algs. based on well established methods of cts optn. The
   resulting algs are convergent & increase the scoring fs at every iteration.
   The solns obtained are critical pts of the scoring fns. 2 algs are
   introduced : One is based on the maximization of the scoring fn with DPA
   followed by the cts maximization of the same score, with respect to the
   protein position, using a smooth Newtonian. ... The 2nd alg. replaces the
   DPA step by a fast proc. for computing the corr. between atoms. The algs. are
   shown to be very effective for the maximization of the STRUCTAL score."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-8-306">doi:10.1186/1471-2105-8-306</A>]['07].

%A A.-M. Neutel
%A et al
%A P. C. de Ruiter
%T Reconciling complexity with stability in naturally assembling food webs
%J Nature
%V 449
%P 599-602
%M OCT
%D 2007
%K jrnl, c2007, c200x, c20xx, food web, webs, ecology, niche, stable, stability,
   complexity, diversity, three link, feedback loop, loops, network,
   predator, prey
%X "... because in random-pattern models complexity leads to instability. ...
   nonrandom patterns in the strengths of the interactions between predators &
   prey strongly enhance system stability ... The stability of the food webs was
   captured by measuring the weight of feedback loops of 3 interacting 'species'
   locked in omnivory. Low predator-prey biomass ratios in these omnivorous
   loops were shown to have a crucial role in preserving stability as
   productivity & complexity increased during succession. ... show the build-up
   of food-web complexity in natural productivity gradients & pin down the
   feedback loops that govern the stability of whole webs. They show that it is
   the heaviest 3-link feedback loop in a network of predator-prey effects that
   limits its stability. Because the weight of these feedback loops is kept
   relatively low by the biomass build-up in the successional process,
   complexity does not lead to instability."
   -- [<A HREF="http://dx.doi.org/10.1038/nature06154">doi:10.1038/nature06154</A>]['10].

%A S. S. Merchant
%A et al
%T The Chlamydomonas genome reveals the evolution of key animal and plant
   functions
%J Science
%V 318
%N 5848
%P 245-250
%M OCT
%D 2007
%K jrnl, c2007, c200x, c20xx, MolBio, unicellular, green, alga, algae, algal,
   genome, nGenome, eukaryote, chloroplasts, chloroplast, flagella, flagellum,
   zz1007
%X "Chlamydomonas reinhardtii is a unicellular green alga ...
   ... We seq. the ~120-MB nuclear genome of Chlamydomonas & performed
   comparative phylogenomic analyses identifying genes encoding uncharacterized
   proteins that are likely assoc. with the function & biogenesis of
   chloroplasts or eukaryotic flagella. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1143609">doi:10.1126/science.1143609</A>]['07].
   "... DDBJ/EMBL/GenBank under the  project accession ABCN00000000."
   "... most recent set, ...sub. as the first version, ABCN01000000."

%A B. Qian
%A et al
%T High-resolution structure prediction and the crystallographic phase problem
%J Nature
%V 450
%N 7167
%P 259-264
%M NOV
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, proteins, protein, tertiary, structure,
   prediction, determination, X-ray, Xray, crystallography, MolProbity,
   phase problem, Rosetta, RosettaAtHome, Rosetta@home
%X "The energy-based refinement of low-resolution protein structure models to
   atomic-level accuracy is a major challenge ... new approach to refining
   protein structure models that focuses sampling in regions most likely to
   contain errors while allowing the whole structure to relax in a physically
   realistic all-atom force field. ... show that all-atom refinement can
   produce de novo protein structure predictions that reach the high accuracy
   required for molecular replacement without any experimental phase information
   & in the absence of templates suitable for molecular replacement from the
   Protein Data Bank. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature06249">doi:10.1038/nature06249</A>]['07],
   -- [<A HREF="http://www.rosettacommons.org/software/">rosettacommons</A>]['07].
   Also see [<A HREF="http://www.nature.com/news/2007/071016/full/449765a.html">news</A>]['07]:
      "...Rosetta breaks a p's seq. into short stretches that can be matched to
      identical stretches from proteins with known structures. These shapes
      offer many ways to sew the protein under study back together, and the
      program chooses those that minimize the free energy..."
   [Also search for: MolBio Xray crystallography].

%A W-B. Jin
%A F-L. Wu
%A D. Kong
%A A-G. Guo
%T HBV-encoded microRNA candidate and its target
%J Computational Biology and Chemistry
%V 31
%N 2
%P 124-126
%M APR
%D 2007
%K MolBio, c2007, c200x, c20xx, miRNA, vmiRNA, virus, viral, hepatits B, HBV
%X "... Several viruses (e.g. ... ) has been reported to encode miRNAs. Here,
   we extend the analysis of miRNA-encoding potential to [HBV]. Using comp.
   approaches, we found that HBV putatively encodes only 1 candidate pre-miRNA.
   We then matched deduced mature miRNA sequence from this pre-miRNA against a
   [DB] of 3' [UTR] from the human genome. Surprisingly, none of cellular
   transcripts could potentially be targeted by the viral miRNA (vmiRNA) seq..
   However, 1 viral mRNA was found to be targeted by the vmiRNA when we searched
   the target from viral mRNAs. We propose that HBV has evolved to use vmiRNAs
   as a means to regulate its own gene expression for its benefit."
   -- [<A HREF="http://dx.doi.org/10.1016/j.compbiolchem.2007.01.005">doi:10.1016/j.compbiolchem.2007.01.005</A>]['08].
   "miRNA seq CAUGUCCUACUGUUCAAGCCUC, loc on HBV 1850-1871, ...,
   potential target location 1886-1907, 2549-2570 3081-3012."

%A W. Hoffmann
%A C. Terschueren
%A D. B. Richardson
%T Childhood leukemia in the vicinity of the Geesthacht Nuclear Establishments
   near Hamburg, Germany
%J Environ. Health Perspect.
%V 115
%N 6
%P 947-952
%M JUN
%D 2007
%K jrnl, c2007, c200x, c20xx, leukemia, leukaemia, child, health, cancer,
   nuclear power, station, stations, atomic energy, stats
%X "... 14 cases were ascertained in the study area, whereas 4.0 were expected
   based on national referent rates ['90-'05: SIR=3.5; 95% (CI), 1.9-5.9].
   The excess was not confined to the early 1990s; for the more recent time
   period '99-'05, the SIR is still elevated (SIR=2.7; 95% CI, 0.9-6.2).
   SIRs of greatest magnitude were observed for children 0-4 years of age
   (SIR=4.9; 95% CI, 2.4-9.0) & for residents south of the Elbe (SIR=7.5;
   95% CI, 2.8-16.4). ..."
   -- [<A HREF="http://dx.doi.org/10.1289/ehp.9861">doi:10.1289/ehp.9861</A>]['08].

%A J. Boekhorst
%A B. Snel
%T Identification of homologs in insignificant BLAST hits by exploiting
   extrinsic gene properties.
%J BMC Bioinformatics
%V 8
%P 356
%D 2007
%K jrnl, c2007, c200x, c20xx, MolBio, homolog, local alignment, property,
   gene properties
%X "Homology is a key concept in both evol. biology & genomics. Detection of h.
   is crucial in fields like the functional annotation of protein seqs. & the
   id. of taxon specific genes. Basic h. searches are still freq. performed
   by pairwise search methods such as BLAST. Vast improvements have been made
   in the id. of homologous proteins by using more advanced methods that use
   seq. profiles. However additional improvement could be made by exploiting
   sources of genomic info. other than primary seq. or tertiary struct.."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-8-356">doi:10.1186/1471-2105-8-356</A>]['07].
   -- Using basic gene properties like gene length & gene order dramatically
   improves the division of results in the BLAST 'gray zone' into spurious
   matches & genuine hits.

%A D. Benedetto
%A E. Caglioti
%A C. Chica
%T Compressing proteomes: The relevance of medium range correlations
%J URASIP J. on Bioinformatics and Systems Biology
%V 2007
%P 60723
%D 2007
%K jrnl, eJrnl, MolBio, c2007, c200x, c20xx, zz1107, proteome, protein,
   sequences, compress
%X "... nonrandomness of proteome seqs. by analysing the correlations that
   arise between AAs at short & medium range, ... between AAs located 10 or 100
   residues apart; respectively. We show that stat. models that consider these
   2 types of correlation are more likely to seize the info. contained in
   protein seqs. & thus achieve good compression rates. ...[propose] cause for
   this redundancy is related to the evol. origin of proteomes & protein seqs."
   -- [<A HREF="http://dx.doi.org/10.1155/2007/60723">doi:10.1155/2007/60723</A>]['07].
   [Also search for: compress protein]

%A J. C. Biro
%T The proteomic code: a molecular recognition code for proteins
%J Theor. Biol. and medical Modelling
%V 4
%P 45
%M NOV
%D 2007
%K jrnl, eJrnl, MolBio, review, c2007, c200x, c20xx, zz1107, protein,
   amino acids, SeqPlot, SeqForm, SeqX, SHARP, Mekler, Blalock, codons, codon
%X "The Proteomic Code is a set of rules by which info. in genetic material is
   transferred into the physico-chemical properties of AAs. ... how individual
   AAs interact with each other during folding & in specific protein-protein
   interactions. The PC is part of the redundant Genetic Code. Review The 25y.-
   -old history of this concept is reviewed from the 1st indep. suggestions by
   Biro & Mekler, through the works of Blalock, Root-Bernstein, Siemion, Miller
   & others, followed by the discovery of a Common Periodic Table of Codons &
   Nucleic Acids in '03 & culminating in the recent conceptualization of
   partial complementary coding of interacting AAs as well as the theory of the
   nucleic acid-assisted protein folding. Methods & concs. A novel cloning
   method for the design & production of specific, high-affinity-reacting
   proteins (SHARP) is presented. ... based on the concept of proteomic codes &
   is suitable for large-scale industrial prodn of spec. interacting peptides."
   -- [<A HREF="http://dx.doi.org/10.1186/1742-4682-4-45">doi:10.1186/1742-4682-4-45</A>]['07] [103 refs],
   -- [<A HREF="http://www.janbiro.com">janbiro.com</A>]['07].

%A M. E. Huntley
%A D. G. Redalje
%T CO2 mitigation and renewable oil from photosynthetic microbes: A new
   appraisal.
%J Mitigation and Adaptation Strategies for Global Change
%I SpringerVerlag
%V 12
%N 4
%P ?-?
%M MAY
%D 2007
%K c2007, c200x, c20xx, alga, algal, algae, biofuel, biofuels, bio fuel,
   biodiesel,  photosynthesis, microbe, greenshouse gas, gases,
   renewable energy
%X "... present evidence to demonstrate that a rate of 3200 GJ/ha/yr is
   feasible using species with known performance characteristics under
   conditions that prevail in the existing production system. At this rate, it
   is possible to replace reliance on current fossil fuel usage equivalent to
   ~300 EJ/yr - & eliminate fossil fuel emissions of CO2 of ~6.5 GtC/yr - using
   only 7.3% of the surplus arable land projected to be available by 2050. By
   comparison, most projections of biofuels production from terrestrial energy
   crops would require in excess of 80% of surplus arable land. Oil production
   cost is estimated at $84/bbl, assuming no improvements in current technology.
   We suggest enhancements that could reduce cost to $50/bbl or less."
   -- [<A HREF="http://dx.doi.org/10.1007/s11027-006-7304-1">doi:10.1007/s11027-006-7304-1</A>]['07].

%A M. Fieder
%A S. Huber
%T Parental age difference and offspring count in humans
%J Biology Letters
%I Royal Soc. Publ.
%V 3
%N 6
%P 689-691
%M DEC
%D 2007
%K jrnl, c2007, c200x, c20xx, parent, parents, age, old man, young woman,
   child, children
%X "... investigated the association among age differences between partners &
   offspring count. ... sample of approx. 10000 post-reproductive Swedish men &
   women who did not change their partner between the birth of their first &
   last child, we find max. offspring count in men if their partner is approx.
   6 years younger, & in women if their partner is approximately 4 years older.
   [and] that after separation, on avg., both men & women shift to a partner
   younger than the 1st, albeit in women the new partner is still older than the
   female herself. We conclude that the age pref. for the partner yields fitness
   benefits for both men & women & may thus be an evol. acquired trait."
   -- [<A HREF="http://dx.doi.org/10.1098/rsbl.2007.0324">doi:rsbl.2007.0324</A>]['08].

%T Quantities, Units and Symbols in Physical Chemistry
%I IUPAC, RSC Publ.
%D 2007
%K book, text, c2007, c200x, c20xx, unit, symbol, quantity, chemical, green,
   IUPAC, Int. Union of Pure and Applied Chemistry
%X "... compilation of widely used terms and symbols from many sources together
   with brief understandable definitions. The style of the manual is not simply
   a book of rules, but more a manual of assistance and advice to meet the
   everyday needs of the practicing scientist."
   3rd ed, uk us isbn:0854044337; uk us isbn13:978-0854044337.
   -- [<A HREF="http://www.iupac.org/">iupac.org</A>]['08].

%T RasMol 2.7.4.2 Manual
%D 2007
%K manual, TR, c2007, c200x, c20xx, Molecular Graphics Visualisation Tool,
   openRasMol, open Ras Mol, visualise, visualize, protein, molecule
%X [<A HREF="http://www.rasmol.org/">rasmol.org</A>]['08].

%T The IUPAC International Chemical Identifier (InChI)
%I IUPAC
%D 2007
%K c2007, c200x, c20xx, chemical compound, structural formula, InChIKey,
   IUPAC, format
%X [<A HREF="http://old.iupac.org/inchi/release102.html">iupac</A>][5/'08].
   "e.g. ethanol, CH3 CH2 OH, InChI=1/C2H6O/c1-2-3/h3H,2H2,1H3."
   -- [<A HREF="http://en.wikipedia.org/wiki/InChI">@wikip</A>]['08].
   [Also search for: structural formula]

%A S. Leclercq
%A E. Rivals
%A P. Jarne
%T Detecting microsatellites within genomes: significant variation among
   algorithms
%J BMC Bioinformatics
%V 8
%P 125
%D 2007
%K jrnl, eJrnl, MolBio, c2007, c200x, c20xx, zz0808, microsatellite,
   tandem repeat, DNA, repeats, genome, algorithm, survey,  TRF, Mreps,
   Sputnik, STAR, RepeatMasker
%X "Microsatellites are short, tandemly-repeated DNA sequences ... compared
   the detection efficiency of 5 of them (TRF, Mreps, Sputnik, STAR, &
   RepeatMasker) ...",  via JZ.
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-8-125">doi:10.1186/1471-2105-8-125</A>]['08].
   [Also search for: repetitive DNA].

%A A. Leigh
%T Algae bloom again
%J Nature
%V 447
%P 520-521
%M MAY
%D 2007
%K news, c2007, c200x, c20xx, algae, alga, algal, bio diesel, biodiesel,
   NREL, LiveFuels, Solix, GreenFuel, renewable, solar, fuel, fuels, energy
%X "... According to figures compiled by the Global Petroleum Club, a business
   community for leaders in the oil, gas and energy industries, soya typically
   produces 450 litres of biodiesel per hectare per year; canola 1,200 litres;
   and oil palm 6,000 litres. Researchers predict that a hectare of algae could
   produce 90,000 litres of biodiesel ... Doing all this on a commercial scale
   isn't straightforward, however. ... "
   -- [<A HREF="http://dx.doi.org/10.1038/447520a">doi:10.1038/447520a</A>]['08].
   Also see [<A HREF="http://en.wikipedia.org/wiki/Algae_fuel">wikip</A>]['08].

%E G. Stolovitzky
%T Reverse Engineering Biological Networks: Opportunities and Challenges in
   Computational Methods for Pathway Inference.
%I New York Acad. Sci.
%V 1115
%P 287
%M NOV
%D 2007
%K MolBio, conf, c2007, c200x, c20xx, proc, DREAM, DREAM2, network, gene,
   systematics
%X "... The DREAM project brings together a diverse group of researchers to
   clarify potentials and limitations of the enterprise of reverse engineering
   cellular networks. ...",  19 papers.  Proc., us isbn:157331689X.
   (Also see [<A HREF="http://wiki.c2b2.columbia.edu/dream/index.php/">DREAM</A>]['08].)
   [Also search for: TSNI].
   [Also search for: infer gene regulatory network].

%A P. J. Uren
%A R. M. Cameron-Jones
%A A. H. J. Sale
%T MAUSA: Using simulated annealing for guide tree construction in
   multiple sequence alignment.
%S LNAI
%P 599-608
%D 2007
%K conf, c2007, c200x, c20xx, uniTas, MolBio
%X In: uk us isbn:3540769269.

%A C. Acquisti
%A G. Poste
%A D. Curtiss
%A S. Kumar
%T Nullomers: Really a matter of natural selection?
%J PLoS ONE
%V 2
%N 10
%M OCT
%D 2007
%K eJrnl, MolBio, c2007, c200x, c20xx, nullomer, nullomers, DNA, CpG, CpGs,
   minimal, short, absent, missing, substring, word, MAW, forbidden, lethal,
   antimotif, Hampikian, Andersen
%X "... we show that the hypermutability of CpG dinucleotides, rather than the
   natural selection against the nullomer seqs., is likely the reason for the
   phenomenal event of short seq. motifs becoming nullomers. Furthermore, many
   reported human nullomers differ by only 1 nucleotide, which reinforces the
   role of mutation in the evol. of the constellation of nullomers in pops. &
   species. The known nullomers in chimp., cow, dog, & mouse genomes show
   patterns that are consistent with those seen in humans."  [9 refs].
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0001022">doi:10.1371/journal.pone.0001022</A>]['08].
   [Also search for: missing substring]  and  [also search for: nullomer].

%A Z. Jiang
%A H. Tang
%A M. Ventura
%A M. F. Cardone
%A T. Marques-Bonet
%A X. She
%A P. A Pevzner
%A E. E Eichler
%T Ancestral reconstruction of segmental duplications reveals punctuated cores
   of human genome evolution
%J Nature Genetics
%V 39
%N 11
%P 1361-1368
%M NOV
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, segment, segmental, duplication, core,
   duplicons, duplicon, copy number polymorphism, evolution,
   ABruijn, deBruijn, de Bruijn, WGAC, RepeatGluer
%X "Human segmental dupls. are hotspots for nonallelic homologous recombination
   leading to genomic disorders, copy-number polymorphisms & gene & transcript
   innovations. The complex structure & history of these regions have precluded
   a global evolutionary analysis. Combining a modified de-Bruijn graph alg.
   with comparative genome seq. data, we identify the origin of 4,692 ancestral
   dupl. loci & use these to cluster 437 complex duplication blocks into 24
   distinct groups. The seq.-divergence data between ancestral-derivative pairs
   & a comparison with the chimpanzee & macaque genome support a 'punctuated'
   model of evoln. ... human segmental duplications are freq. organized around
   'core' duplicons, which are enriched for transcripts &, in some cases,
   encode primate-specific genes undergoing +ve selection. We hypothesize that
   the rapid expansion & fixation of some intrachromosomal segmental duplns
   during great-ape evolution has been due to the selective advantage conferred
   by these genes & transcripts embedded within these core duplications."
   pdf: [<A HREF="http://dx.doi.org/10.1038/ng.2007.9">doi:10.1038/ng.2007.9</A>]['08] (online Oct 2007), or
   -- [<A HREF="http://proteomics.bioprojects.org/pavel/papers/ancestral_reconstruction.pdf">bioprojects.org</A>],
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/17922013">pub med</A>]['08].

%A S. Levy
%A et al
%T The diploid genome sequence of an individual human
%J PLoS Biology
%V 5
%N 10
%P e254
%M SEP
%D 2007
%K jrnl, eJrnl, MolBio, c2007, c200x, c20xx, mammal, human genome, nGenome,
   genomes, nuclear
%X "... [cf ref genome] more than 4.1 million DNA variants, encompassing 12.3Mb.
   These variants (of which 1,288,319 were novel) included 3,213,401 single
   nucleotide polymorphisms (SNPs), 53,823 block substitutions (2-206 bp),
   292,102 heterozygous insertion/deletion events (indels)(1-571 bp),
   559,473 homozygous indels (1-82,711 bp), 90 inversions, as well as numerous
   segmental duplications and copy number variation regions. ..."
   ([<A HREF="http://www.ncbi.nlm.nih.gov/Genbank">genbank</A>]) accession
   number are: AADD00000000 (WGSA) and ABBA01000000.
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pbio.0050254">doi:10.1371/journal.pbio.0050254</A>]['08].
   [Also search for: human nuclear genome].

%A M. C. Riley
%A A. Clare
%A R. D. King
%T Locational distribution of gene functional classes in Arabidopsis thaliana
%J BMC Bioinformatics
%V 8
%N 112
%D 2007
%K jrnl, eJrnl, MolBio, aber, c2007, c200x, c20xx, Arabidopsis thaliana, plant,
   plants, location, position, class, GO, RDKing, AClare
%X "... developed a novel b. method based on Monte Carlo methods & Greenwood's
   spacing stat. for the computational analysis of the distribution of
   individual functional classes of genes (from GO). We used this to make the
   first comprehensive stat. analysis of the relationship between gene fn class
   & location on a genome. Analysis of the distribution of all genes except
   tandem duplicates on the 5 chrs. of A. thaliana reveals that the distribution
   on chrs. I, II, IV & V is clustered at P=0.001. Many fn classes are clustered
   with the degree of clustering within an individual class generally consistent
   across all 5 chrs. A novel & surprising result was that the locational
   distribution of some fn classes were sig. more evenly spaced than would be
   expected by chance. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-8-112">doi:10.1186/1471-2105-8-112</A>]['08].

%T A second generation human haplotype map of over 3.1 million SNPs
%Q The International HapMap Consortium
%J Nature
%V 449
%P 851-861
%M OCT
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, HapMap, hapmap2, haplotypes, SNPs, human,
   variation, variability
%X "... Phase II HapMap ... characterizes > 3.1 million human SNPs in 270
   individuals from 4 geographically diverse popns & inc. 25-35% of common SNP
   variation in the popns surveyed. The map is est. to capture untyped
   common variation with an average maximum r**2 of between 0.9 & 0.96 depending
   on popn. We demonstrate that the current gen. of commercial genome-wide
   genotyping products captures common Phase II SNPs with an avg max. r**2 of
   up to 0.8 in African & up to 0.95 in non-African popns ... also reveal novel
   aspects of the structure of linkage disequilibrium. ... 10-30% of pairs of
   individuals within a population share >= 1 region of extended genetic
   identity arising from recent ancestry & that up to 1% of all common variants
   are untaggable, primarily because they lie within recombination hotspots. ...
   ... recombination rates vary systematically around genes & between genes of
   different fn.  Finally, we demo. increased differentiation at non-synonymous,
   [v.] synonymous, SNPs, resulting from systematic differences in the strength
   or efficacy of natural selection between populations."
   -- [<A HREF="http://dx.doi.org/10.1038/nature06258">doi:10.1038/nature06258</A>]['08],
   @[<A HREF="http://www.hapmap.org/downloads/presentations/nature_hapmap3.pdf">hapmap</A>],
   -- [<A HREF="http://www.hapmap.org/">hapmap.org</A>]['08].

%A J. C. Dohm
%A C. Lottaz
%A T. Borodina
%A H. Himmelbauer
%T SHARCGS, a fast and highly accurate short-read assembly algorithm for
   de novo genomic sequencing
%J Genome Res.
%V 17
%P 1697-1706
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, short read, reads, sequence, assembler,
   denovo
%X "... developed the SHARCGS algorithm to assemble short-read (25-40-mer) data
   with high accuracy & speed. The efficiency of SHARCGS was tested on BAC
   inserts from 3 eukaryotic species, on 2 yeast chromosomes, & on 2 bacterial
   genomes ... . We show that 30-mer-based BAC assemblies have N50 sizes >20kbp
   for Drosophila & Arabidopsis & >4kbp for human in simulations taking missing
   reads & wrong base calls into account. We assembled 949,974 contigs with
   length >50 bp, & only one single contig could not be aligned error-free
   [v.] the ref. seqs.. ..."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.6435207">doi:10.1101/gr.6435207</A>]['07].
   [Also search for: short read MolBio].

%A H. Huang
%A B. M. Jedynak
%A J. S. Bader
%T Where have all the interactions gone? Estimating the coverage of two-hybrid
   protein interaction maps
%J PLoS Computational Biol.
%V 3
%N 11
%P e214
%M NOV
%D 2007
%K jrnl, eJrnl, MolBio, c2007, c200x, c20xx, protein, proteins, interaction,
   PPI, map, false, positive, negative, overlap, consistency, errors, false,
   error rates, controversial, reproducible,  reproducibility,
   yeast, Saccharomyces cerevisiae, fly, worm, networks, network, data,
   systems biology, Y2H
%X "Yeast 2-hybrid screens ... mapping pairwise physical interactions b/w
   proteins. The fraction of interactions detected in indep. screens can be
   v.small [why?] ... from either a high false-discovery rate ... or a high
   false -ve rate ... extend capture-recapture theory to provide the 1st unified
   model for false +ve & false -ve rates for 2-hybrid screens. Analysis of
   yeast, worm & fly data indicates that 25% to 45% of the reported interactions
   are likely false +ve. Membrane proteins have higher false-discovery rates on
   avg., & signal transduction proteins have lower rates. The overall false -ve
   rate ranges from 75% for worm to 90% for fly, ... & a 55% to 85% false -ve
   rate due to proteins that appear to be systematically lost from the assays.
   Finally, statistical model selection conclusively rejects the Erdos-Renyi
   n/w model in favor of the power law model for yeast & the truncated power
   law for worm & fly degree distributions.  ...
   from our web site [<A HREF="http://www.baderzone.org">@baderzone.org</A>]."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pcbi.0030214">doi:10.1371/journal.pcbi.0030214</A>]['08].
   [Also search for: protein interaction network] and
   [also search for: MolBio network reproducibility].

%A J. Fredslund
%A M. Lange
%T Primique: automatic design of specific PCR primers for each sequence in a
   family
%J BMC Bioinformatics
%V 8
%N 369
%D 2007
%K jrnl, eJrnl, MolBio, c2007, c200x, c20xx, PCR, primer, primers, design,
   designing, Primique
%X "... primique, a new graphical, user-friendly, fast, web-based tool ...
   designs specific primers for each sequence in an uploaded set. Further, a
   secondary set of sequences not to be amplified by any primer pair may be
   uploaded. Primers with high sequence similarity to non-target sequences are
   selected against. Lastly, the suggested primers may be checked against the
   NCBI databases for possible mis-priming. ..."
   -- [<A HREF="http://www.biomedcentral.com/1471-2105/8/369">doi:/1471-2105/8/369</A>]['09].
   [Also search for: MolBio PCR primer],
   primers@[<A HREF="http://en.wikipedia.org/wiki/Primer_(molecular_biology)">wikip</A>]['09].

%A W. Liu
%A B. Schmidt
%A G. Voss
%A W. Mueller-Wittig
%T Streaming algorithms for biological sequence alignment on GPUs
%J IEEE Trans. on Parallel and Distributed Sys.
%V 18
%N 9
%P 1270-1281
%D 2007
%O related in misc confs
%K jrnl, MolBio, c2007, c200x, c20xx, algorithm, graphics processor, unit,
   GPU, GPUs, streaming, scanning, grid, gpu meme
%X "... approach to high performance biological seq. alignment based on
   commodity PC graphics hardware. Using modern graphics processing units (GPUs)
   for high performance computing is facilitated by their enhanced
   programmability & motivated by their attractive price/performance ratio &
   incredible growth in speed. To derive an efficient mapping onto this type of
   architecture, we have reformulated [DP] based alignment algs. as streaming
   algs. in terms of computer graphics primitives. ... GPU-based approach
   allows speedups of > 1 order of magnitude [wrt] optimized CPU impls."
   -- [<A HREF="http://dx.doi.org/10.1109/TPDS.2007.1069">doi:10.1109/TPDS.2007.1069</A>]['09],
   auth2@[<A HREF="http://www3.ntu.edu.sg/home/ASBSchmidt/">ntu.sg</A>]['09].

%A D. S. Johnson
%A A. Mortazavi
%A R. M. Myers
%A B. Wold
%T Genome-wide mapping of in vivo protein-DNA interactions
%J Science
%V 316
%N 5830
%P 1497-1502
%M JUN
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, ChIP, seq, ChIPseq, peak, peaks, find,
   finding
%X "... seq.census method was then used to map in vivo binding of the neuron-
   -restrictive silencer factor (NRSF; also known as REST, for repressor
   element-1 silencing transcription factor) to 1946 locns in the human g.. The
   data display sharp resolution of binding position [+/-50 base pairs (bp)],
   which facilitated our finding motifs and allowed us to identify noncanonical
   NRSF-binding motifs. These ChIPSeq data also have high sens. & spec.
   [ROC area >/= 0.96] & stat.confidence (P < 10**(-4)), properties that were
   important for inferring new candidate interactions. These include key [TF]
   in the gene n/w that regulates pancreatic islet cell dev.."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1141319">doi:10.1126/science.1141319</A>]['09].
   [Also search for: ChIP seq peak MolBio].

%A T. Owen-Hughes
%A M. Engeholm
%T Pyrosequencing positions nucleosomes precisely
%J Genome Biol.
%V 8
%N 6
%P 217
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, 454 sequencing, pyrosequencing,
   Roche, H2A.Z, H2AZ, DNA, short read, reads
%X "New parallel-sequencing technology has recently been used to map with
   unprecedented accuracy the posns of nucleosomes enriched for the histone
   variant H2A.Z throughout the yeast genome. ... "
   -- [<A HREF="http://dx.doi.org/10.1186/gb-2007-8-6-217">doi:10.1186/gb-2007-8-6-217</A>]['09].
   Also see [<A HREF="http://www.454.com/">454.com</A>]['09].
   [Also search for: short read MolBio].

%A P. L. Brennan
%A et al ...
%A T. R. Birkhead
%T Coevolution of male and female genital morphology in waterfowl
%J PLoS ONE
%V 2
%N 5
%P e418
%D 2007
%K jrnl, eJrnl, c2007, c200x, c20xx, biol, bird, birds, genitalia, genitals,
   shape, conflict, rape, forced, copulation, duck, ducks, sex, sexes, spiral
%X "Most birds have simple genitalia; males lack external genitalia & females
   have simple vaginas. However, male waterfowl have a phallus whose length
   (1.5-40cm) & morphological elaborations vary among species & are +vely
   correlated with the freq. of forced extra-pair copulations among waterfowl
   species. ... morphological complexity in female genital morphology in
   waterfowl & describe variation vaginal morphology that is unprecedented in
   birds. ... comprises 2 anatomical novelties: (i) dead end sacs, &
   (ii) clockwise coils. ... appear to function to exclude the intromission of
   the counter-clockwise spiralling male phallus without female cooperation.
   ... vaginal elaboration is +vely correlated with phallus length, demo. that
   f.morphological complexity has co-evolved with male phallus length. ...
   results suggest that females have evolved a cryptic anatomical mechanism of
   choice in response to forced extra-pair copulations."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0000418">doi:10.1371/journal.pone.0000418</A>]['09].

%A G. Robertson
%A et al
%T Genome-wide profiles of STAT1 DNA association using chromatin
   immunoprecipitation and massively parallel sequencing
%J NatureMethods
%D 2007
%V 4
%N 8
%P 651-657
%M JUN
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, STAT 1, STAT1, ChIP seq, ChIPseq, peak,
   find, finding, findPeaks
%X "... map STAT1 targets in interferon-gamma (IFN-gamma)-stimulated &
   unstimulated human HeLa S3 cells, & compared the method's performance to
   ChIP-PCR & to ChIP-chip for 4 chrs.. By ChIP-seq, using 15.1 & 12.9 million
   uniquely mapped seq. reads, & an est. false discovery rate of less than
   0.001, we identified 41,582 & 11,004 putative STAT1-binding regions in
   stimulated & unstimulated cells, respectively. Of the 34 loci known to
   contain STAT1 interferon-responsive binding sites, ChIP-seq found 24 (71%).
   ChIP-seq targets were enriched in seqs. similar to known STAT1 binding
   motifs. Comparisons with 2 ChIP-PCR data sets suggested that ChIP-seq
   sensitivity was between 70% & 92% & specificity was at least 95%"
   -- [<A HREF="http://dx.doi.org/10.1038/nmeth1068">doi:10.1038/nmeth1068</A>]['09],
   s/w @[<A HREF="http://www.bcgsc.ca/platform/bioinfo/software/findpeaks">bcgsc.ca</A>]['09],
   and [<A HREF="http://vancouvershortr.sourceforge.net/">srcFrg</A>]['09].
   [Also search for: ChIP seq peak MolBio].

%A P. Baldi
%A R. W. Benz
%A D. S. Hirschberg
%A S. J. Swamidass
%T Lossless compression of chemical fingerprints using integer entropy codes
   improves storage and retrieval
%J J. Chem. Inf. Model.
%V 47
%N 6
%P 2098-2109
%D 2007
%K jrnl, c2007, c200x, c20xx, fingerprint, signature, code, compress,
   chemical, compounds, molecules
%X "... we combine stat.models of fingerprints with integer entropy codes, such
   as Golomb & Elias codes, to encode the indices or the run lengths of the
   fingerprints. After reordering the fingerprint components by decreasing
   freq. order, the indices are monotone-inc. & the run lengths are quasi-
   -monotone-inc., & both exhibit power-law distribution trends. ... derive new
   efficient, lossless, compression algs. for monotone integer seqs.: monotone
   value (MOV) coding & monotone length (MOL) coding. [v.] lossy systems that
   use 1024 or more bits / molecule, we can achieve lossless compression of
   long chemical fingerprints based on circular substructures in slightly over
   300 bits / molec., close to the Shannon entropy limit ..."
   -- [<A HREF="http://dx.doi.org/10.1021/ci700200n">doi:10.1021/ci700200n</A>]['12].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A M. W. Coolen
%A A. L. Statham
%A M. Gardiner-Garden
%A S. J. Clark
%T Genomic profiling of CpG methylation and allelic specificity using
   quantitative high-throughput mass spectrometry: critical evaluation and
   improvements
%J NAR
%V 35
%N 18
%P e119
%D 2007
%K jrnl, eJrnl, c2007, c200x, c20xx, MolBio, NAR, methylation, Garvan Inst, NSW,
   au, DNA, CpG, allele, epigenetic, epigenetics
%X "... associated with changes in gene expression without a change to the DNA
   sequence.  ... for a detailed, high-throughput & quantitative method of
   analysis to discover & validate normal & aberrant DNA methylation profiles
   in large sample cohorts. ... present an improved protocol using base-specific
   fragmentation & MALDI-TOF mass spectrometry that enables a sensitive &
   high-throughput method of DNA methylation analysis, ..."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gkm662">doi:10.1093/nar/gkm662</A>]['09] (free '09).
   auth4@[<A HREF="http://www.garvan.org.au/about-us/our-people/associate-professor-susan-clark">garvan</A>]['09].

%A P. Medvedev
%A K. Georgiou
%A G. Myers
%A M. Brudno
%T Computability of models for sequence assembly
%J Algorithms in Bioinformatics
%I SpringerVerlag
%S LNCS
%V 4645
%P 289-301
%D 2007
%K conf, MolBio, c2007, c200x, c20xx, sequence assembly, short read, reads, DNA,
   string graph, deBruijn, aBruijn, computational complexity, NP-hard, NPhard,
   Chinese postman problem
%X "Graph-theoretic models ... for seq. assembly. [and] hardness of the
   underlying graph algs. has remained open.  ... present 2 theoretical results
   about the complexity of these models for seq. assembly. [1] show seq.
   assembly to be NP-hard under 2 different models: string graphs & de Bruijn
   graphs. Together with an earlier result on the NP-hardness of overlap graphs,
   this demonstrates that all of the popular graph-theoretic seq. assembly
   paradigms are NP-hard. [2] give the 1st, to our knowledge, optimal polynomial
   time alg. for genome assembly that explicitly models the double-strandedness
   of DNA. We solve the Chinese Postman Problem on bidirected graphs using
   bidirected flow techniques & show to how to use it to find the shortest
   double stranded DNA seq. which contains a given set of k-long words. ...
   applications to seq. by hybridization & short read assembly"
   pdf@[<A HREF="http://www.cs.toronto.edu/~brudno/medvedev_etal_wabi07.pdf">toronto</A>][09],
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-74126-8_27">doi:/10.1007/978-3-540-74126-8_27</A>]['09],
   [Also search for: sequence assembly MolBio].

%A R. S. Lasken
%T Single-cell genomic sequencing using multiple displacement amplification
%J Current Opinion in Microbiology
%V 10
%N 5
%P 510-516
%M OCT
%D 2007
%K jrnl, c2007, c200x, c20xx, MolBio, 454 Life Sciences, pyrosequencing,
   DNA, short read, reads
%X "Single microbial cells can now be seq. using DNA amplified by the Multiple
   Displacement Amplification (MDA) reaction. The few femtograms of DNA in a
   bacterium are amplified into micrograms of high molecular weight DNA suitable
   for DNA library construction & Sanger seq.. The MDA-generated DNA also
   performs well when used directly as template for pyrosequencing by the
   454 Life Sciences method. While MDA from single cells loses some of the
   genomic seq., this approach will greatly accelerate the pace of seq. from
   uncultured microbes. The genetically linked seqs. from single cells are also
   a powerful tool to be used in guiding genomic assembly of shotgun sequences
   of multiple organisms from environmental DNA extracts (metagenomics)."
   -- [<A HREF="http://dx.doi.org/10.1016/j.mib.2007.08.005">doi:10.1016/j.mib.2007.08.005</A>]['09].
   [Also search for: short read MolBio].

%A J. O. Korbel
%A et al
%A M. Snyder
%T Paired-end mapping reveals extensive structural variation in the human genome
%J Science
%V 318
%N 5849
%P 420-426
%M OCT
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, Paired-end mapping, ends, map, read,
   reads, human genome, variation, variations, inversion, inversions, african,
   european,  structural variants, SVs, PEM
%X "... intro. high-throughput & massive paired-end mapping (PEM), a large-scale
   genome-seq. method to identify structural variants (SVs) ~3kb or larger that
   combines the rescue & capture of paired ends of 3-kb fragments, massive 454
   seq., & a comp. approach to map DNA reads onto a ref.g..  ... African & in a
   putatively Euro. individual & identified shared & divergent SVs rel. to the
   ref.g.. ... fine-mapped > 1000 SVs & documented that the # of SVs among
   humans is >> than initially hypothesized; ...  The breakpoint junction seqs.
   of > 200 SVs were determined with a novel pooling strategy & comp. analysis.
   ... provided insights into the mechanisms of SV formation in humans."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1149504">doi:10.1126/science.1149504</A>]['09].
   (Also see snyder@[<A HREF="http://www.yale.edu/snyder/">yale</A>['09].)
   [Also search for: MolBio human genome variation].

%A X. Hu
%A Y. Pan
%T Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications
%I Wiley
%S Series in Bioinformatics
%P 363
%D 2007
%K MolBio, book, text, c2007, c200x, c20xx, bioinformatics, AI
%X "... The purpose of this edited book is to bring together the ideas &
   findings of data mining researchers & bioinformaticians by discussing
   cutting-edge research topics such as, gene expressions, protein/RNA structure
   prediction, phylogenetics, sequence & structural motifs, genomics &
   proteomics, gene findings, drug design, RNAi & microRNA analysis, text mining
   in bioinformatics, modelling of biochemical pathways, biomedical ontologies,
   system biology & pathways, & biological database management."
   1st ed 2007, hb us$105; uk us isbn:047177796X; uk us isbn13:978-0471777960.
   [Also search for: MolBio book].

%A E. R. Mardis
%T ChIP-seq: Welcome to the new frontier
%J NatureMethods
%V 4
%N 8
%P 613-614
%M AUG
%D 2007
%K news, views, MolBio, c2007, c200x, c20xx, Chromatin immunoprecipitation,
   intro, ChIP seq, ChipSeq, DNA, protein, interaction, binding site, sites,
   transcription factors, peak, peaks, find, finder, finding
%X [<A HREF="http://dx.doi.org/10.1038/nmeth0807-613">doi:10.1038/nmeth0807-613</A>]['09],
   and @[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/17664943">pubmed</A>]['09].
   [Also search for: ChIP seq peak MolBio].

%A M. D. Robinson
%A G. K. Smyth
%T Moderated statistical tests for assessing differences in tag abundance
%J J. Bioinformatics
%V 23
%N 21
%P 2881-2887
%M SEP
%D 2007
%K jrnl, MolBio, WEHI, c2007, c200x, c20xx, test, digital gene expression, DGE,
   zz1109, tag, tags, differential expression, counting, negative binomial
%X "... Various tests of differential expression have been proposed for
   replicated DGE data using binomial, Poisson, neg.binomial or pseudo-
   -likelihood (PL) models for the counts [not] usable when the # of replicates
   is v.small. ... [we] develop tests using the neg.binomial distn to model
   overdispersion relative to the Poisson, & use conditional weighted likelihood
   to moderate the level of overdispersion across genes. ... applicable even
   with the smallest # of libraries, but it also proves to be more powerful
   than previous strategies when more libraries are available. ... is equally
   applic. to other counting technologies, such as proteomic spectral counts.
   An R package ... [<A HREF="http://bioinf.wehi.edu.au/resources/">wehi</A>]['07]."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btm453">doi:10.1093/bioinformatics/btm453</A>]['09].

%A D. DeCaprio
%A et al ...
%A J. E. Galagan
%T Conrad: Gene prediction using conditional random fields
%J Genome Res.
%V 17
%N 9
%P 1389-1398
%M SEP
%D 2007
%X jrnl, c2007, c200x, c20xx, conditional random field, CRF, SMCRF, GHMM, gene,
   predict, prediction, calling
%X "... Conrad, ... gene predictor based on semi-Markov conditional random
   fields (SMCRFs) ...[not] based on generalized hidden Markov models (GHMMs) &
   trained by maximum likelihood, Conrad is discriminatively trained to max
   annotation accuracy. ...  On Cryptococcus neoformans, configuring Conrad to
   reproduce the predictions of a 2-species phylo-GHMM closely matches the
   performance of Twinscan. ...  SMCRFs are a promising framework for gene
   pred'n because of their highly modular nature, simplifying the process of
   designing & testing potential indicators of gene structure. ..."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.6558107">doi:10.1101/gr.6558107</A>]['10],
   s/w@[<A HREF="http://www.broadinstitute.org/annotation/conrad/">BroadInst</A>]['10].

%A Z. Annan
%A P. Durand
%A F. J. Ayala
%A C. Arnathau
%A P. Awono-Ambene
%A F. Simard
%A F. G. Razakandrainibe
%A J. C. Koella
%A D. Fontenille
%A F. Renaud
%T Population genetic structure of Plasmodium falciparum in the two main
   African vectors, Anopheles gambiae and Anopheles funestus
%J PNAS
%V 104
%P 7987-7992
%D 2007
%K jrnl, PNAS, MolBio, c2007, c200x, c20xx, malaria, Plasmodium falciparum,
   population, genetic, diversity, variability, variation, genomes, evolution,
   parasite, mosquito
%X "... assayed 7 microsatellite loci in 746 oocysts from 183 infected mosquito
   guts. Genetic polymorphism was v.high in parasites isolated from both vector
   species. The expected heterozygosity (H E) was 0.79 in both species; the
   observed heterozygosities (H O) were 0.32 in A. funestus & 0.42 in A. gambiae
   indicating considerable inbreeding within both vector species. Mean selfing
   (s) between genetically identical gametes was s=0.33. Differences in the rate
   of inbreeding were stat.insig. among sites & between the 2 vector species.
   ...because of the high rate of inbreeding, linkage disequilibrium was v.high;
   it was significant for all 21 loci pairs in A. gambiae & for 15 of 21 pairs
   in A. funestus, ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0702715104">doi:10.1073/pnas.0702715104</A>]['09],
   auth3@[<A HREF="http://www.faculty.uci.edu/profile.cfm?faculty_id=2134">UCI</A>]['09].

%A F. Yue
%A J. Tang
%T A divide-and-conquer implementation of three sequence alignment and
   ancestor inference
%J Proc. 1st IEEE Int. Conf. on Bioinformatics and Biomedicine
%P 143-150
%D 2007
%K conf, MolBio, c2007, c200x, c20xx, three, alignment, BIBM, MSAM
%X "... alg. to simultaneously align 3 biol. seqs. with affine gap model &
   infer their common ancestral sequence. [it] can be further extended to
   perform tree alignment for more sequences, & eventually unify the 2
   procs. of phylogenetic reconstruction & seq.alignment. The novelty ... is:
   it applies the d.-&-c. strategy so that the memory usage is
   reduced from O (n**3) to O (n**2), while at the same time, it is based on
   DP & optimal a. is guaranteed. Traditionally, 3 seq. alignment is ltd
   by the huge demand of memory space & can only handle seqs. < than 200 chars.
   long. With the new improved alg., we can produce the optimal alignment of
   sequences of several thousand characters long. ..."
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/BIBM.2007.40">doi:10.1109/BIBM.2007.40</A>]['09].
   [Also search for: MolBio alignment three],
   [also search for: alignment divide conquer].

%A T. H. Ogden
%A M. S. Rosenberg
%T Alignment and topological accuracy of the direct optimization approach via
   POY and traditional phylogenetics via ClustalW + PAUP
%J Systematic Biology
%V 56
%N 2
%P 182-193
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, phylogenetic tree, evolutionary trees,
   POY, treelength, direct optimization, multiple alignment, sequence, Heath
%X "... Direct optimization frameworks for simultaneously est. alignments &
   phylogenies ... One such method, implemented in the program POY ...
   Simulation of seqs. containing ins. & del. events was performed in order to
   directly compare a widely used method of [MSA] (ClustalW) & subsequent
   parsimony analysis in PAUP with direct optimization via POY. ... In almost
   all cases (99.95%), ClustalW produced more accurate alignments than POY-
   -implied alignments, judged by the proportion of correctly identified
   homologous sites. Topological accuracy ... for POY topologies & topologies
   generated under parsimony in PAUP from the ClustalW alignments were also
   compared. In 44.94% of the cases, Clustal [+] PAUP were more accurate than
   POY, whereas in 16.71% of the cases POY [was] more topologically accurate
   (38.38% of the time they were equally accurate). Comparisons between POY
   hypothesized alignments & the true alignments indicated that, on average, as
   alignment error increased, topological accuracy decreased."
   -- [<A HREF="http://dx.doi.org/10.1080/10635150701281102">doi:10.1080/10635150701281102</A>]['09].
   [Also search for: phylogenetic tree MolBio].

%T Genetic Variation: A Laboratory Manual
%E M. P. Weiner
%A S. B. Gabriel
%A J. C. Stephens
%I CSH Lab. Press
%P 172
%D 2007
%K book, text, manual, MolBio, c2007, c200x, c20xx, L5Ref, genes,
   variations, SNPs
%X 1st ed 2007; pb us$165; uk us isbn:0879697806; uk us isbn13:978-0879697808.
   "A Laboratory Manual is the first compendium of protocols specifically geared
   towards genetic variation studies, and includes thorough discussions on their
   applications for human and model organism studies. Intended for graduate
   students and professional scientists in clinical and research settings, it
   covers the complete spectrum of genetic variation-from SNPs & microsatellites
   to more complex DNA alterations, including copy number variation ..."
   [Also search for: manual MolBio].

%A W. Miller
%A et al
%T 28-way vertebrate alignment and conservation track in the UCSC genome browser
%J Genome Res.
%V 17
%N 12
%P 1797-1808
%M DEC
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, zz1208, vertebrate, vertebrates,
   alignment, genome, genomes, browse, UCSC browser
%X "... describes a set of alignments of 28 vertebrate genome seqs. that is
   provided by the UCSC Genome Browser. The alignments can be viewed on the
   Browser at [<A HREF="http://genome.ucsc.edu">www</A>], downloaded in bulk by
   anonymous FTP from [<A HREF="http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way">www</A>],
   or analyzed with the Galaxy server at [<A HREF="http://g2.bx.psu.edu">www</A>]['07].
   ... study the extent to which start codons & stop codons in the human seq.
   are conserved in other species, showing that start codons are in general more
   poorly conserved than stop codons. Finally, an investigation of the
   phylogenetic depth of conservation for several classes of fn elts in the h.g.
   reveals striking diffs. in the rates & modes of decay in alignability. ..."
   Free pdf@[<A HREF="http://dx.doi.org/10.1101/gr.6761107">doi:10.1101/gr.6761107</A>]['08].

%A J. A. Grochow
%A M. Kellis
%T Network motif discovery using subgraph enumeration and symmetry-breaking
%J RECOMB
%E T. Speed
%E H. Huang
%O Res. in Comp. Molec. Biol., LNCS 4453
%I SpringerVerlag
%P 92-106
%M APR
%D 2007
%K conf, MolBio, RECOMB, c2007, c200x, c20xx, zz0214, maths, graph, motif,
   networks, cliques, protein, interaction, transcription regulatory network,
   Pachter, nonsense, controversial, system, science,
   Barabasi, publish, papers, PPI
%X "... present a novel alg. for discovering large network motifs that achieves
   these goals, based on a novel symmetry-breaking technique, which eliminates
   repeated isomorphism testing, leading to an exponential speed-up over prev.
   methods. ... is made possible by reversing the trad. network-based search at
   the heart of the alg. to a motif-based search, which also eliminates the need
   to store all motifs of a given size & enables parallelization & scaling.
   [&] enables us to study the clustering properties of discovered motifs,
   revealing even larger network elements.  We apply this alg. to the protein-
   -protein interaction network & transcription regulatory network of
   S.cerevisiae, & discover several large network motifs, which were prev.
   inaccessible to existing methods, including a 29-node cluster of 15-node
   motifs corresponding to the key transcription machinery of S. cerevisiae."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-71681-5_7">doi:10.1007/978-3-540-71681-5_7</A>]['14]; isbn13:978-3540716808.
   (* BUT also see  "... When I saw the number 27,720 I had a hunch that
       somehow some canonical combinatorial set had been enumerated. ...
       27,720 = 220*126 = (12 choose 3) * (9 choose 4). ...
       first, a clique or a stable set can hardly be considered an interesting
       'network motif.' ...  Second, there is a large literature on finding
       cliques in graphs, none of which Grochow-Kellis cited or seemed to
       be familiar with. ..."
    -- Lior Pachter [<A HREF="http://liorpachter.wordpress.com/2014/02/12/why-i-read-the-network-nonsense-papers/">w'press</A>]['14]. *)
   [Also search for: protein interaction network].

%A G. S. Enge
%A et al
%T Evidence for wavelike energy transfer through quantum coherence in
   photosynthetic systems
%J Nature
%V 446
%P 782-786
%M APR
%D 2007
%K jrnl, c2007, c200x, c20xx, zz1016, biology, plant, photosynthesis,
   quantum physics, FMO bacteriochlorophyll, Chlorobium tepidum, 77K
%X "... The energy transfer mechanism is often described by semiclassical models
   that invoke 'hopping' of excited-state populations along discrete energy
   levels ... Here we extend previous 2D electronic spectroscopy investigations
   of the FMO bacteriochlorophyll complex, and obtain direct evidence for
   remarkably long-lived electronic quantum coherence playing an important part
   in energy transfer processes within this system. The q.coherence manifests
   itself in characteristic, directly observable q. beating signals among the
   excitons within the Chlorobium tepidum FMO complex at 77K. This wavelike
   characteristic of the energy transfer within the photosynthetic complex can
   explain its extreme efficiency, in that it allows the complexes to sample
   vast areas of phase space to find the most efficient path."
   -- [<A HREF="http://dx.doi.org/10.1038/nature05678">doi:10.1038/nature05678</A>]['16].

%A G. Evangelista
%A G. Minervini
%A P. L. Luisi
%A F. Polticelli
%T RandomBlast a tool to generate random "never born protein" sequences
%J Bio-algorithms and Med-systems
%V 3
%P 27-31
%D 2007
%K MolBio, c2007, c200x, c20xx, protein, artificial, random, never born, NBPs,
   generating, randomBlast
%X "In an accompanying paper by Minervini et al., we deal with the sci.problem
   of studying the seq. to structure relns in 'never born proteins' (NBPs), ie
   p.seqs. which have never been observed in nature. The study of the structural
   & functional properties of NBPs requires the gen. of a large library of
   protein seqs. characterized by the absence of any sig.similarity with all the
   known p.seqs. ... describe the implementation of a simple ..."
   auth2@[<A HREF="http://scholar.google.com/citations?user=54aGRawAAAAJ&hl=en">sclr</A>]['13].
   [Also search for: randomBlast].

%A A. Wlodawer
%A W. Minor
%A Z. Dauter
%A M. Jaskolski
%T Protein crystallography for non-crystallographers, or how to get the best
   (but not more) from published macromolecular structures
%J FEBS J.
%V 275
%N 1
%P 1-21
%M JAN
%D 2008
%K jrnl, FEBS, MolBio, c2008, c200x, c20xx, protein, 3D, crystallography,
   structure, determination, introduction, intro, outline
%X "... attempts to provide a brief outline of technical aspects of c. & to
   explain the meaning of some params. that should be evaluated by users of
   macromolecular structs. in order to interpret, but not over-interpret, the
   info. present in the coordinate files & in their description. A discussion
   of the extent of the info. that can be gleaned from the coord. of structs.
   solved at different resolution, as well as problems & pitfalls encountered
   in structure determination and interpretation are also covered."
   -- [<A HREF="http://dx.doi.org/10.1111/j.1742-4658.2007.06178.x">doi:10.1111/j.1742-4658.2007.06178.x</A>]['13] (online 11/'07).

%A G. M. Sheldrick
%T A short history of SHELX
%J Acta Crystallography
%V A64 (Pt 1)
%P 112-122
%M JAN
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz0710, X-ray, Xray, crystallography,
   ShelX, ShelXS, ShelXD, protein, structure refinement, determination, 3D,
   citation, citations, publication, metrics, journal, impact factor, IF, JIF
%X "An account is given of the development of the SHELX system of computer
   programs from SHELX-76 to the present day. ... SHELXL is the most widely used
   program for small-molecule refinement and SHELXS and SHELXD are often
   employed for structure solution despite the availability of objectively
   superior programs. ..."
   -- [<A HREF="http://dx.doi.org/10.1107/S0108767307043930">doi:10.1107/S0108767307043930</A>]['10],
   ShelX@[<A HREF="http://shelx.uni-ac.gwdg.de/SHELX/">gwdg</A>]['10].
 (Apparently cited a huge(!) number of times in '09, e.g., see
 [<A HREF="http://dx.doi.org/10.1038/466179b">doi:10.1038/466179b</A>]['10].)

%A D. G. Gibson
%A G. A. Benders
%A C. Andrews-Pfannkoch
%A E. A. Denisova
%A H. Baden-Tillson
%A J. Zaveri
%A T. B. Stockwell
%A A. Brownley
%A D. W. Thomas
%A M. A. Algire
%A C. Merryman
%A L. Young
%A V. N. Noskov
%A J. I. Glass
%A J. Craig Venter
%A C. A. Hutchison III
%A H. O. Smith
%T Complete chemical synthesis, assembly, and cloning of a Mycoplasma
   genitalium genome
%J Science
%V 319
%N 5867
%P 1215-1220
%M FEB
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, Mycoplasma genitalium, genome, artificial,
   minimal bacterium, bacteria, life, essential, gene, genes, laboratorium,
   JCVI 1, JCVI1 G37
%X "... synthesized a 582,970 bp Mycoplasma genitalium genome. ...
   M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium
   G37 except MG408, which was disrupted by an antibiotic marker to block
   pathogenicity & to allow for selection. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1151721">doi:10.1126/science.1151721</A>]['09], also see...
   M.laboratorium@[<A HREF="http://en.wikipedia.org/wiki/Minimal_Genome_Project">wikip</A>]['09],
   381 genes.

%A A. D. Smith
%A Z. Xuan
%A M. Q. Zhang
%T Using quality scores and longer reads improves accuracy of
   Solexa read mapping
%J BMC Bioinformatics
%V 9
%N 128
%M FEB
%D 2008
%K jrnl, eJrnl, MolBio, c2008, c200x, c20xx, RMAP, software, cshl, resequencing,
   map, score, short, read, reads, millions, ChIP seq, ChIPseq, Illumina
%X "2nd gen sequencing ...  (e.g. ChIP-sequencing). ... The Solexa/Illumina 1G
   sequencer can produce 10s of millions of reads... from 25-50nt, in a single
   experiment. Accurately mapping the reads back to a reference genome is a
   critical task in almost all applications. Two sources of info. that are often
   ignored when mapping reads from the S.technology are the 3' ends of longer
   reads, which contain a much higher freq. of seq. errors, & the base-call
   quality scores. ... we developed the RMAP tool, which can map reads having
   a wide range of lengths & allows base-call quality scores to determine
   which posns in each read are more important when mapping. We applied RMAP to
   analyze data re-seq. from 2 human BAC regions for varying read lengths ..."
   s/w: [<A HREF="http://rulai.cshl.edu/rmap/">@cshl</A>]['08].
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-9-128">doi:10.1186/1471-2105-9-128</A>]['08].
   [Also search for: resequencing MolBio],
   [also search for: short read MolBio].

%A C. Fan
%A N. Pu
%A X. Wang
%A Y. Wang
%A L. Fang
%A W. Xu
%A J. Zhang
%T Agrobacterium-mediated genetic transformation of grapevine
   (Vitis vinifera L.) with a novel stilbene synthase gene from
   Chinese wild Vitis pseudoreticulata
%J Plant Cell, Tissue and Organ Culture
%I Springer
%V 92
%N 2
%P 197-206
%M FEB
%D 2008
%K jrnl, c2008, c200x, c20xx, phytoalexin resveratrol, vines, red wine, health
%X "... resveratrol concentration in the transgenic plants was 5.5 times higher
   than that in non-transformed control plants."
   -- [<A HREF="http://dx,doi.org/10.1007/s11240-007-9324-2">doi:10.1007/s11240-007-9324-2</A>]['08].
   (Resveratrol <I>may</I> be assoc with longevity and reduced heart disease,
   or not.-)

%A D. Hernandez
%A P. Francois
%A L. Farinelli
%A M. Osteras
%A J. Schrenzel
%T De novo bacterial genome sequencing: Millions of very short reads assembled
   on a desktop computer
%J Genome Res.
%V 18
%N 5
%P 802-809
%M MAY
%D 2008
%K jrnl, MolBio, Edena, EDENA, c2008, c200x, c20xx, bacteria, DNA, de novo,
   denovo, sequencing, assembly, short read, reads, overlap graph, overlaps,
   short dead end, deadend, p-bubble fixing
%X "... propose a de novo assembler s/w that is dedicated to process [short
   reads]. Based on a classical overlap graph repn & on the detection of
   potentially spurious reads, our s/w generates a set of accurate contigs of
   several kilobases that cover most of the bacterial genome. ... validated by
   comparing data sets that were obtained experimentally for Staphylococcus
   aureus strain MW2 & Helicobacter acinonychis strain Sheeba with that of their
   published genomes acquired by conventional sequencing of 1.5- to 3.0-kb
   fragments. We also provide indications that the broad coverage achieved by
   high-throughput sequencing might allow for the detection of clonal
   polymorphisms in the set of DNA molecules being sequenced."
   1. short reads data processed to remove redundant info.
   2. overlaps of a minimum size are computed & an overlap graph constructed
      (read ~ vertex,  overlap ~ (bidirected-)edge (weighted))
   3. graph cleaned by removing transitive & spurious edges & resolving bubbles
   4. min. size contigs that are unambig. rep. in the g. output.
   -- [<A HREF="http://dx.doi.org/10.1101/gr.072033.107">doi:10.1101/gr.072033.107</A>]['08].
   Edena@[<A HREF="http://www.genomic.ch/edena.php">genomic.ch</A>]['08].
   [Also search for: short read MolBio].

%A A. S. Konagurthu
%A A. M. Lesk
%T On the origin of distribution patterns of motifs in biological networks
%J BMC Systems Biology
%D 2008
%V 2
%N 73
%M AUG
%D 2008
%K jrnl, eJrnl, MolBio, c2008, c200x, c20xx, network, pattern, motif, model,
   graphModel, Alon, AMLesk, ArunK, biological, transcription, regulatory,
   subgraph, subgraphs, frequent, feedforward, bi fan, bifan, FFL, SIM, MIM,
   regulon, NICTA
%X "Inventories of small subgraphs in bio.n/ws have identified
   commonly-recurring patterns, called motifs. The inference that these ms. have
   been selected for fn rests on the idea that their occurrences are sig. more
   freq. than random. ... [we find] in contrast, that the freqs. of appearance
   of common subgraphs are similar in natural & corr. random n/ws. ... Indeed,
   certain topological features of biol. n/ws give rise naturally to the common
   appearance of the motifs. ...  question whether freqs of occurrences are
   reasonable evidence that the structures of motifs have been selected for
   their f'nal contribution to the operation of n/ws."
   -- [<A HREF="http://dx.doi.org/10.1186/1752-0509-2-73">doi:10.1186/1752-0509-2-73</A>]['08].  [auth1 @ nicta '08].
   [Also search for: network motif MolBio].

%A A. C. Belden
%A N. R. Thomson
%A J. L. Luby
%T Temper tantrums in healthy versus depressed and disruptive preschoolers:
   Defining tantrum behaviors associated with clinical problem
%J J. of Pediatrics
%V 152
%N 1
%P 117-122
%M JAN
%D 2008
%K jrnl, psychiatry, c2008, c200x, c20xx, preschool, pre school, behavior,
   behaviour
%X "... Disruptive preschoolers displayed violence during tantrums sig. more
   often than the depressed and healthy grps. The disruptive grp had sig. more
   tantrums at school/daycare than the depressed & healthy grps. The disruptive
   grp had a more difficult time recovering from tantrums than healthy
   preschoolers. In addition, depressed preschoolers were more aggressive toward
   objects & other people than healthy children. Finally, depressed preschoolers
   displayed significantly more self-harmful tantrum behav. than preschoolers in
   the healthy & disruptive grps."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jpeds.2007.06.030">doi:10.1016/j.jpeds.2007.06.030</A>]['08].
   auth1@Dept Psych., Washington U., Med., St.Louis

%A M. Nowacki
%A et al
%T RNA-mediated epigenetic programming of a genome-rearrangement pathway
%J Nature
%V 451
%P 153-158
%M JAN
%D 2008
%K jrnl, c2008, c200x, c20xx, MolBio, RNA, RNAi, zz0108, Oxytricha trifallax,
   unicellular eukaryote
%X "Genome-wide DNA rearrangements occur in many eukaryotes but are most
   exaggerated in ciliates, making them ideal model systems for epigenetic
   phenomena. During development of the somatic macronucleus, Oxytricha
   trifallax destroys 95% of its germ line, severely fragmenting its chromosomes
   & then unscrambles hundreds of thousands of remaining fragments by
   permutation or inversion. Here we demonstrate that DNA or RNA templates can
   orchestrate these genome rearrangements in Oxytricha, supporting an
   epigenetic model for seq.-dependent comparison between germline & somatic
   genomes. A complete RNA cache of the maternal somatic genome may be available
   at a specific stage during development to provide a template for correct &
   precise DNA rearrangement. We show the existence of maternal RNA templates
   that could guide DNA assembly, & that disruption of specific RNA molecules
   disables rearrangement of the corresponding gene. Injection of artificial
   templates reprogrammes the DNA rearrangement pathway, suggesting that RNA
   molecules guide genome rearrangement."
   -- [<A HREF="http://dx.doi.org/10.1038/nature06452">doi:10.1038/nature06452</A>]['08].

%A D. M. Kristensen
%A et al
%T Prediction of enzyme function based on 3D templates of evolutionarily
   important amino acids.
%J BMC Bioinformatics
%V 9
%N 17
%D 2008
%K jrnl, eJrnl, MolBio, c2008, c200x, c20xx, acid, template, protein,
   Evolutionary Trace Annotation, ETA
%X "... many new structs. but often these have no known molecular fn.. One
   approach to recover this info. is to use 3D templates - structure-fn motifs
   that consist of a few functionally critical AAs & may suggest fn similarity
   when geom. matched to other structures. ... Based on evol. info. & heuristics
   an Evolutionary Trace Annotation (ETA) pipeline built templates for 98
   enzymes, half taken from the PSI, & sought matches in a non-redundant
   structure database. On avg. each template matched 2.7 distinct proteins, of
   which 2.0 share the first 3 Enzyme Commission digits as the template's enzyme
   of origin. In many cases (61%) a single most likely fn could be predicted as
   the annotation with the most matches, & in these cases such a plurality vote
   identified the correct fn with 87% acc.. ETA ... complementary to seq.
   homology-based annotations. When matches are required to both geometrically
   match the 3D template & to be seq. homologs found by BLAST or PSI-BLAST, the
   annotation accuracy is greater than either method alone, especially in the
   region of lower seq. id. where homology-based annot. are least reliable."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-9-17">doi:10.1186/1471-2105-9-17</A>]['08].

%A S. Christley
%A N. F. Lobo
%A G. Madey
%T Multiple organism algorithm for finding ultraconserved elements
%J BMC Bioinformatics
%V 9
%N 15
%D 2008
%K jrnl, eJrnl, c2008, c200x, c20xx, zz0108, MolBio, element, miRNA,
   exact, pattern, discovery, Pediculus humanus humanus, louse
%X "Ultraconserved elts. are nucleotide or protein seqs. with 100% identity (no
   mismatches, insertions, or deletions) in the same organism or between 2 or
   more organisms. ... these conserved regions are assoc. with micro RNAs, mRNA
   processing, development & transcription regulation. ... alg. & provide freely
   available s/w which can find all of the ultraconserved seqs. between genomes
   of multiple organisms. Our alg. takes a combinatorial approach that finds all
   seqs. without requiring the genomes to be aligned. The alg. is sig. faster
   than BLAST & is designed to handle very large genomes efficiently. We ran our
   alg. on several large comparative analyses to evaluate its effectiveness; one
   compared 17 vertebrate genomes where we find 123 ultraconserved elts. longer
   than 40bps shared by all of the organisms, & another compared the human body
   louse, Pediculus humanus humanus, against itself & select insects to find
   thousands of non-coding, potentially functional seqs.."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-9-15">doi:10.1186/1471-2105-9-15</A>]['08].

%A T. W. Lam
%A W. K. Sung
%A S. L. Tam
%A C. K. Wong
%A S. M. Yiu
%T Compressed indexing and local alignment of DNA
%J J. Bioinformatics
%V 24
%N 6
%P 791-797
%D 2008
%K jrnl, c2008, c200x, c20xx, MolBio, index, search, BWT SW, BWTSW, strings,
   approximate, indexing, align, search, substring, match
%X "... indexes are designed for exact pattern matching, which is too stringent
   for biol. appl.. ...  In practice, biologists use heuristic-based s/w such as
   BLAST, which is very efficient but does not guarantee to find all local
   alignments.  ... show how to build s/w called BWT-SW that exploits a BWT
   index of a text T to speed up the [DPA] for finding all local alignments.
   ... BWT-SW is very efficient (e.g. aligning a pattern of length 3,000 with
   the human genome takes less than a minute). ..."
   [-- <A HREF="http://dx.doi.org/10.1093/bioinformatics/btn032">doi:10.1093/bioinformatics/btn032</A>]['08],
   --BWTSW@[<A HREF="http://i.cs.hku.hk/~ckwong3/bwtsw/">hku.hk</A>]['08].
   [Also search for: approximate indexing],
   [also search for: compressed index].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/BWT/">BWT</A>].)

%A O. Jaillon
%A et al
%T Translational control of intron splicing in eukaryotes
%J Nature
%V 451
%P 359-362
%M JAN
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, splice, eukaryote, gene, genes, splice,
   mRNA, alternative, Paramecium tetraurelia, introns, nonsense, NMD, UPF1
%X "... Splicing is guided locally by short conserved seqs., but genes typically
   contain many potential splice sites, & the mechanisms spec. the correct sites
   remain poorly understood. In most organisms, short introns recognized by the
   intron definition mechanism cannot be efficiently predicted solely on the
   basis of seq. motifs. In multicellular e., long introns are recognized
   through exon definition & most genes produce multiple mRNA variants through
   alternative splicing. The nonsense-mediated mRNA decay (NMD) pathway may
   further shape the observed sets of variants by selectively degrading those
   containing premature termination codons ... show that the tiny introns of the
   ciliate Paramecium tetraurelia are under strong selective pressure to cause
   premature termination of mRNA translation in the event of intron retention, &
   that the same bias is observed among the short introns of plants, fungi &
   animals. By knocking down the two P. tetraurelia genes encoding UPF1, a
   protein that is crucial in NMD, we show that the intrinsic efficiency of
   splicing varies widely among introns & that NMD activity can significantly
   reduce the fraction of unspliced mRNAs. The results suggest that, indep. of
   alternative splicing, species with large intron numbers universally rely on
   NMD to compensate for suboptimal splicing efficiency & accuracy."
   -- [<A HREF="http://dx.doi.org/10.1038/nature06495">doi:10.1038/nature06495</A>]['08].

%A K. E. Jones
%A et al
%T Global trends in emerging infectious diseases
%J Nature
%V 451
%P 990-993
%M FEB
%D 2008
%K jrnl, c2008, c200x, c20xx, disease, public health, epidemic, origin, origins,
   emerge, zz0208
%X "... confirm that EID origins are significantly correlated with
   socio-economic, environmental and ecological factors, ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature06536">doi:10.1038/nature06536</A>]['08].

%A A. Tanay
%A E. D. Siggia
%T Sequence context affects the rate of short insertions and deletions in
   flies and primates
%J Genome Biology
%V 9
%N R37
%D 2008
%K jrnl, eJrnl, c2008, c200x, c20xx, zz0308, MolBio, insertion, deletion,
   indel, indels, rates, DNA, fly, primate
%X "... extensive correlations between sequence contexts & indel rates &
   building principled models for predicting these rates from the seq..
   According to our results, the rate of insertions or deletions of specific
   lengths can vary by more than 100 fold, depending on the surrounding seq..
   ... exemplify this by showing how degenerate loci in human exons are
   selected to reduce their frame shifting indel propensity. ..."
   -- [<A HREF="http://dx.doi.org/9:R37doi:10.1186/gb-2008-9-2-r37">doi:10.1186/gb-2008-9-2-r37</A>]['08].

%A E. Lindqvist
%A D. Cesarini
%A B. Wallace
%T Does parental age difference affect offspring count in humans?
   Comment on Fieder and Huber.
%J Biology Letters
%I Royal Soc. Publ.
%V 4
%N 1
%P 78-79
%M FEB
%D 2008
%K jrnl, c2008, c200x, c20xx, parent, parents, old, husband, wife, age,
   difference, young woman, old man, behaviour, mate selection,
   children, zz0308
%X [<A HREF="http://dx.doi.org/10.1098/rsbl.2007.0514">doi:10.1098/rsbl.2007.0514</A>]['08].
   [Also search for: Fieder Huber]

%A J. Hert
%A M. J. Keiser
%A J. J. Irwin
%A T. I. Oprea
%A B. K. Shoichet
%T Quantifying the relationships among drug classes
%J J. Chem. Inf. Model
%V 48
%N 4
%P 755-765
%M APR
%D 2008
%K jrnl, c2008, c200x, c20xx, zz1213, drug, drugs, classes, class, similarity,
   Similarity Ensemble Approach, SEA, bioinformatics, chemoinformatics, ligands,
   ECFP4, FCFP4, FEPOPS
%X "The similarity of drug targets is typically measured using seq. or struct.
   info..  ... consider chemo-centric approaches that measure target similarity
   on the basis of their ligands ... We calculated the similarities between
   hundreds of drug targets and their ligands & mapped the relationship between
   them in a formal network. Bioinformatics networks were based on the BLAST
   similarity between sequences, while chemoinformatics networks were based on
   the ligand-set similarities calculated with either the Similarity Ensemble
   Approach (SEA) or a method derived from Bayesian statistics. By multiple
   criteria, bioinformatics & chemoinformatics networks differed substantially,
   & only occasionally did a high seq. sim. corr. to a high ligand-set
   similarity. [v.] the chemoinformatics networks were stable to the method used
   to calculate the ligand-set similarities & to the chemical repn of the
   ligands. Also, the chemoinformatics networks were more natural & more
   organized, by network theory, than their bioinformatics counterparts:
   ligand-based networks were found to be small-world & broad-scale."
   -- [<A HREF="http://dx.doi.org/10.1021/ci8000259">doi:10.1021/ci8000259</A>]['13].

%A J. Elmen
%A et al
%T LNA-mediated microRNA silencing in non-human primates
%J Nature
%V 452
%N 7189
%P 896-899
%M APR
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0408, MolBio, miRNA, primate, liver,
   hepatitis C, HCV, cholesterol, miR-122, miR122, LNA-antimiR
%X "... we show that the simple systemic delivery of a unconjugated,
   PBS-formulated locked-nucleic-acid-modified oligonucleotide (LNA-antimiR)
   effectively antagonizes the liver-expressed miR-122 ..."
   "... miR-122 is a liver-expressed miRNA implicated in cholesterol &
   lipid metabolism & in hepatitis C virus (HCV) replication..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature06783">doi:10.1038/nature06783</A>]['08], online 26/3/'08.

%A D. A. Wheeler
%A et al
%T The complete genome of an individual by massively parallel DNA sequencing
%J Nature
%V 452
%N 7189
%P 872-876
%M APR
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz0408, DNA, sequencing, sequencer,
   sequence, J.D.Watson, JDWatson, 454 sequencing, SNP, SNPs, ABKV01000000
%X "... report the DNA seq. of a diploid genome of [an] individual, James D.
   Watson, sequenced to 7.4-fold redundancy in 2 months using massively parallel
   sequencing in picolitre-size reaction vessels. ... completed in 2 months at
   approx. 1/100 of the cost of traditional capillary electrophoresis methods.
   Comp. of the sequ. to the ref. genome led to the id. of 3.3 million single
   nucleotide polymorphisms, of which 10,654 cause [AA] substitution within the
   coding seq.. [and] identified small-scale (2-40,000 [bp]) ins. & del.
   polymorphism as well as copy # variation resulting in the large-scale gain &
   loss of chromosomal segs. ranging from 26,000 to 1.5 million [bp]. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature06884">doi:10.1038/nature06884</A>]['08],
   "... contigs from the assembly of 454-reads not matching the
   ref.genome are deposited in Genbank under accession number
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=ABKV01000000">ABKV01000000</A>]. ..."

%T Genetics bill cruises through Senate.  Unanimous vote welcomed by
   personal genomics companies
%J Nature
%V 453
%N 7191
%P 9
%M MAY
%D 2008
%K news, c2008, c200x, c20xx, genes, genetic, discrimination, health insurance,
   cover, law, legal, rights, society, test, testing
%X "The unanimous vote last week by the US Senate to outlaw discrimination
   against people on the basis of their genetic information is being celebrated
   by civil-rights groups, which have long campaigned for the safeguards.
   Personal-genomics companies are also cracking open the champagne - they have
   a lot to gain from the bill becoming law.
      Once enacted, the Genetic Information Nondiscrimination Act (GINA) will
   forbid employers & health insurers from using people's genetic info. against
   them in decisions on hiring, firing, promotion & insurance coverage &
   pricing. The House of Representatives should pass the legislation this week,
   after which it is expected to be signed into law by Pres. George W. Bush..."
   -- [<A HREF="http://dx.doi.org/10.1038/453009a">doi:10.1038/453009a</A>]['08] online 30/4/'08

%A M. Bauer
%A S. M. Schuster
%A K. Sayood
%T The average mutual information profile as a genomic signature
%J BMC Bioinformatics
%V 9
%N 48
%M JAN
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, signatures
%X "Occult organizational structures in DNA seqs. may hold the key to
   understanding functional & evolutionary aspects of the DNA molecule. Such
   structures can also provide the means for identifying & discriminating
   organisms using genomic data. Species specific genomic signatures are useful
   in a variety of contexts such as evolutionary analysis, assembly &
   classification of genomic seqs. from large uncultivated microbial communities
   & a rapid identification system in health hazard situations. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-9-48">doi:10.1186/1471-2105-9-48</A>]['08],
   [Also search for: MolBio sequence information].

%A N. Cannata
%A M. Schroder
%A R. Marangoni
%A P. Romano
%T A semantic web for bioinformatics: Goals, tools, systems, applications
%J BMC Bioinformatics
%V 9 (Suppl 4) : S1
%M APR
%D 2008
%O Seventh NETTAB workshop, 12-15 June, '07.
%K MolBio, c2008, c200x, c20xx, zz0508, www, system, NETTAB
%X [<A HREF="http://dx.doi.org/10.1186/1471-2105-9-S4-S1">doi:10.1186/1471-2105-9-S4-S1</A>]['08].

%A W. C. Warren
%A et al
%T Genome analysis of the platypus reveals unique signatures of evolution
%J Science
%V 453
%P 175-183
%M MAY
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz0508, mammal, Prototheria, marsupial,
   Monotremata, monotreme, Platypus, Ornithorhynchus anatinus, nGenome
%X "... Monotremata are considered to belong to the mammalian subclass
   Prototheria, which diverged from the therapsid line that led to the Theria
   & subsequently split into the marsupials (Marsupialia) & eutherians
   (Placentalia). The divergence of monotremes & therians falls into the large
   gap in the amniote phylogeny between the eutherian radiation about 90 (Myr)
   ago & the divergence of mammals from the sauropsid lineage around 315 Myr
   ... Of the 1.84 (Gb) of assembled seq., 437 (Mb) were ordered & oriented
   along 20 of the platypus chromosomes. ...
   ... the 52 platypus chromosomes show no correlation between the position of
   orthologous genes on the small platypus chrs. & chicken microchromosomes;
   for the unique 5X chr. of platypus we reveal considerable seq. alignment
   similarity to chicken Z & no orthologous gene alignments to human X, ...
   18,527 protein-coding genes predicted ...
   DDBJ/EMBL/[<A HREF="http://www.ncbi.nlm.nih.gov/">GenBank</A>]
   under the project accession AAPN00000000"
   -- [<A HREF="http://dx.doi.org/10.1038/nature06936">doi:10.1038/nature06936</A>][5/'08].
   [2.2 billion bp; 52 chromosomes; 10 sex chrs (5X & 5Y); ~18.5K genes].
   [Also search for: marsupial MolBio].

%A K. Baerenfaller
%A et al
%T Genome-scale proteomics reveals Arabidopsis thaliana gene models and
   proteome dynamics
%J Science
%V 320
%N 5878
%P 938-941
%M MAY
%D 2008
%K jrnl, c2008, c200x, c20xx, plant, plants, gene expression, TAIR7, PepSplice
%X "...proteome map ... organ-specific proteome catalogs that we generated for
   different organs, developmental stages, & undifferentiated cultured cells. We
   matched 86,456 unique peptides to 13,029 proteins & provide expression
   evidence for 57 gene models that are not represented in the TAIR7 protein
   database. ...
   PepSplice was specifically designed for operating in large search spaces
   which allowed us to identify peptides containing post-translational
   modifications ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1157956">doi:10.1126/science.1157956</A>]['08].

%A W. Ritchie
%A F.-X. Theodule
%A D. Gautheret
%T Mireval: A web tool for simple microRNA prediction in genome sequences
%J J. Bioinformatics
%V 24
%N 11
%P 1394-1396
%D 2008
%K jrnl, MolBio, c2008,c200x,c20xx, zz0608, miRNA, microRNA, Mireval, sequence
%X "... four criteria that we labeled secondary structure analysis,
   conservation analysis, cluster analysis, and miRBase BLAST.
   Users decide which ... analyses ... carried on & receive a full report ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn137">doi:10.1093/bioinformatics/btn137</A>]['08].

%A R. Sasidharan
%A M. Gerstein
%T Genomics: Protein fossils live on as RNA
%J Nature
%V 453
%P 729-731
%M JUN
%D 2008
%K MolBio, news, c2008, c200x, c20xx, zz0608, pseudo gene,
   pseudogene, pseudogenes, noncoding DNA, RNA, RNAi, endo siRNA
%X "Pseudogenes constitute many of the non-coding DNA sequences that make up
   large parts of genomes. Once considered merely protein fossils, it now
   emerges that some of them have active regulatory roles. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/453729a">doi:10.1038/453729a</A>]['08].

%A S.-D. Zhang
%A T. W. Gant
%T A simple and robust method for connecting small-molecule drugs using
   gene-expression signatures
%J BMC Bioinformatics
%V 9
%P 258
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, drug design, signature, gene-expression,
   profile, connectivity map, similar properties, pharmacology
%X "Interaction of a drug or chemical with a biological system can result in a
   gene-expression profile or signature characteristic of the event. Using a
   suitably robust alg. these sigs. can potentially be used to connect molecules
   with similar pharmacological or toxicological properties ... have built on
   the principles of the Connectivity Map to present a simpler & more robust
   method for the construction of reference gene-expression profiles & for the
   connection scoring scheme, ... potential use in the drug development pipeline
   for the early recognition of pharmacological & toxicological properties in
   chemicals & new drug candidates & also ... in other 'omics sciences."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-9-258">doi:10.1186/1471-2105-9-258</A>]['08].

%A S. Bethard
%A Z. Lu
%A J. H. Martin
%A L. Hunter
%T Semantic role labeling for protein transport predicates
%J BMC Bioinformatics
%V 9
%P 277
%M JUN
%D 2008
%K MolBio, SRL, c2008, c200x, c20xx, zz0608, predicate, semantics, function
%X "Automatic semantic role labeling (SRL) is a natural language processing
   (NLP) technique that maps sentences to semantic representations. ...
   biomedical predicates describing protein transport in GeneRIFs - manually
   curated sentences focusing on gene functions. ... We collected 837 GeneRIFs
   describing movements of proteins between cellular components, ... Our models
   were able to label protein transport semantic roles with 87.6% precision &
   79.0% recall when using manually annotated protein boundaries, & 87.0%
   precision & 74.5% recall when using automatically identified ones. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-9-277">doi:10.1186/1471-2105-9-277</A>]['08].

%A E. Lopez-Garcia
%A R. M. van Dam
%A T. Y. Li
%A F. Rodriguez-Artalejo
%A F. B. Hu
%T The relationship of coffee consumption with mortality
%J Annals of Internal Medicine
%V 148
%N 12
%P 904-914
%M JUN
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0608, drinking, coffee, caffeine, health,
   zzCoffee, neutral or positive, risk, risks, human, life expectancy
%X "... After adjustment for age, smoking, & other CVD & cancer risk factors,
   the relative risks for all-cause mortality in men across categories of coffee
   consumption (< 1 cup per month, 1 cup per month to 4 cups per week, 5 to 7
   cups per week, 2 to 3 cups per day, 4 to 5 cups per day, & >6 cups per day)
   were 1.0, 1.07 (95% CI, 0.99 to 1.16), 1.02 (CI, 0.95 to 1.11), 0.97 (CI,
   0.89 to 1.05), 0.93 (CI, 0.81 to 1.07), & 0.80 (CI, 0.62 to 1.04),
   respectively (P for trend = 0.008). For women, the relative risks were 1.0,
   0.98 (CI, 0.91 to 1.05), 0.93 (CI, 0.87 to 0.98), 0.82 (CI, 0.77 to 0.87),
   0.74 (CI, 0.68 to 0.81), & 0.83 (CI, 0.73 to 0.95), respectively (P for
   trend < 0.001). This inverse association was mainly due to a moderately
   reduced risk for CVD mortality & was independent of caffeine intake. By
   contrast, coffee consumption was not statistically significantly assoc.
   with risk for cancer death after adjustment for potential confounders.
   Decaffeinated coffee consumption was assoc. with a small reduction in
   all-cause & CVD mortality. ...  Regular coffee consumption was not assoc.
   with an increased mortality rate in either men or women. The possibility of a
   modest benefit of coffee consumption on all-cause & CVD mortality needs to be
   further investigated."   [49 refs].
   -- [<A HREF="http://www.annals.org/cgi/content/full/148/12/904">www</A>]['08].
   [Also search for: zzCoffee].

%A J. Allali
%A M.-F. Sagot
%T A multiple layer model to compare RNA secondary structures
%J SPE
%V 38
%N 8
%P 775-792
%M JUL
%D 2008
%K jrnl, SPE, MolBio, c2008, c200x, c20xx, RNA, secondary, structure, MiGaL
%X "...new data structure, called MiGaL for Multiple Graph Layer, composed of
   various graphs linked together by relations of abstraction/refinement. ...
   useful for representing info. ... described at different levels of
   abstraction, each level corresponding to a graph. We then propose an alg. for
   comparing 2 MiGaLs. ...  step-by-step comparison starting with the most
   abstract level.  ... [a] natural model for comparing RNA secondary structs
   that may be seen at different levels of detail, going from the seq. of
   nucleotides, single or paired with another to participate in a helix, to the
   n/w of multiple loops that is believed to represent the most conserved part
   of RNAs having similar function. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.846">doi:10.1002/spe.846</A>]['08].

%A N. H. Putnam
%A et al
%T The amphioxus genome and the evolution of the chordate karyotype
%J Nature
%V 453
%P 1064-1071
%M JUN
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, Branchiostoma floridae, Florida lancelet,
   Lancelets, Branchiostomidae, Chordata, amphioxus, chordate
%X "Lancelets ('amphioxus') are the modern survivors of an ancient chordate
   lineage, with a fossil record dating back to the Cambrian period. Here we
   describe the structure and gene content of the highly polymorphic ~520
   megabase genome of the Florida lancelet Branchiostoma floridae..." [80 refs]
   -- [<A HREF="http://dx.doi.org/10.1038/nature06967">doi:10.1038/nature06967</A>]['08],
      [<A HREF="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7739">tax id=7739</A>]['08].

%A J. A. Tennessen
%T Positive selection drives a correlation between non-synonymous/synonymous
   divergence and functional divergence.
%J J. Bioinformatics
%V 24
%N 12
%P 1421-1425
%M JUN
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz0608, protein, evolution, mutation,
   selection, pressure, functional divergence, dN, dS, synonymous, non,
   nonsynonymous, bacteria
%X "Functional divergence among proteins is often assumed to be strongly
   influenced by natural selection, as inferred from the ratio of non-
   -synonymous nucleotide divergence (dN) to synonymous n.d. (dS). That is, the
   more a mutation changes protein fn, the more likely it is to be either
   selected against or selectively favored, & because the dN/dS ratio is a
   measure of natural selection, this ratio can be used to predict the degree of
   fn divergence (dF). However, these hypotheses have rarely been experimentally
   tested. ... novel method to address this issue, & demonstrate that divergence
   in bacteria-killing activity among animal antimicrobial peptides is
   positively correlated with the log of the dN/dS ratio. The primary cause of
   this pattern appears to be that +ve selected substitutions change protein fn
   more than neutral subs. do. Thus, the dN/dS ratio is an accurate estimator of
   adaptive functional divergence."  [auth @ Oregon State U.]
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn205">doi:10.1093/bioinformatics/btn205</A>]['08].

%A F. De Rango
%A et al
%T Cognitive Functioning and Survival in the Elderly: The SSADH C538T
   Polymorphism
%J Ann. Hum. Genet.
%P ?-?
%M MAY
%D 2008
%K MolBio, c2008, c200x, c20xx, age, ageing, cognitive ability, elderly,
   lifespan, SSADH, ALDH5A1, GABA, gene, longevity, IQ
%X "The variability of the Succinic Semialdehyde Dehydrogenase (SSADH, or
   ALDH5A1) gene affects both pathological & normal phenotypes correlated to
   cognitive function. We tested the association between the C538T polymorphism
   of the SSADH gene & preservation of cognitive function in the elderly, & its
   possible effects on survival. A sample from southern Italy (514 subjects; 18-
   -107 years) was screened for C538T variability. We found that, within the
   65-85 years age range, the T/T genotype is overrepresented in subjects with
   impaired cognitive function (23 >= MMSE) compared to those with conserved
   cognitive function (MMSE > 23). Furthermore, we found that the T/T genotype
   affects survival after 65 y.of age. In fact, after this age, the survival
   function of T/T homozygous subjects is lower than that of the others. Given
   that the enzymatic activity of the protein encoded by allele T is 82.5% of
   the activity of the protein encoded by allele C, our results suggest that the
   efficiency of the SSADH enzyme is important for the preservation of cognitive
   function & survival in the elderly."
   Department of Cell Biology, University of Calabria, 87036 Rende, Italy.
   -- [<A HREF="http://dx.doi.org/10.1111/j.1469-1809.2008.00450.x">doi:10.1111/j.1469-1809.2008.00450.x</A>]['08].

%A M. J. Sanderson
%T Phylogenetic signal in the eukaryotic tree of life
%J Science
%V 321
%N 5885
%P 121-123
%M JUL
%D 2008
%X jrnl, MolBio, c2008, c200x, c20xx, zz0708, trees, evolutionary, evolution,
   eukaryote, phylogeny
%X "Mol. seq. data have been sampled from 10% of all species known to science.
   Although it is not yet feasible to assemble these data into a single [tree]
   it is possible to quantify how much phylogenetic signal is present. Analysis
   of 14,289 phylogenies built from 2.6 million seqs. in GenBank suggests that
   signal is strong in vertebrates & specific groups of nonvertebrate model
   organisms. Across eukaryotes, however, although phylogenetic evidence is very
   broadly distributed, for the average species in the DB it is equivalent to
   less than 1 well-supported gene tree. This analysis shows that a stronger
   sampling effort aimed at genomic depth, in addition to taxonomic breadth,
   will be required to build high-resolution phylogenetic trees at this scale."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1154449">doi:10.1126/science.1154449</A>]['08].

%A C. Lemaitre
%A E. Tannier
%A C. Gautier
%A M.-F. Sagot
%T Precise detection of rearrangement breakpoints in mammalian chromosomes
%J BMC Bioinformatics
%V 9
%N 286
%M JUL
%D 2008
%K jrnl, eJrnl, c2008, c200x, c20xx, zz0708, MolBio, chromosome, mammal,
   breakpoint, break point, segment, segmentation, genome organisation, synteny
%X "Genomes undergo large structural changes that alter their organisation. The
   chromosomal regions affected by these rearrangements are called breakpoints,
   while those which have not been rearranged are called synteny blocks. We
   developed a method to precisely delimit rearrangement breakpoints on a genome
   by comparison with the genome of a related species. Contrary to current
   methods which search for synteny blocks & simply return what remains in the
   genome as breakpoints, we propose to go further & to investigate the
   breakpoints themselves in order to refine them."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-9-286">doi:10.1186/1471-2105-9-286</A>]['08].

%A M. Campillos
%A M. Kuhn
%A A.-C. Gavin
%A L. J. Jensen
%A P. Bork
%T Drug target identification using side-effect similarity
%J Science
%V 321
%N 5886
%P 263-266
%M JUL
%D 2008
%K jrnl, c2008, c200x, c20xx, drug design, discovery, drugs, side effects,
   similar
%X "Targets for drugs have so far been predicted on the basis of molecular or
   cellular features, e.g., by exploiting similarity in chemical structure or in
   activity across cell lines. We used phenotypic side-effect similarities to
   infer whether 2 drugs share a target. Applied to 746 marketed drugs, a n/w of
   1018 side effect-driven drug-drug relations became apparent, 261 of which are
   formed by chemically dissimilar drugs from different therapeutic indications.
   ... tested 20 of these unexpected drug-drug relations & validated 13 implied
   drug-target relations by in vitro binding assays, of which 11 reveal
   inhibition constants equal to less than 10 micromolar. 9 of these were tested
   & confirmed in cell assays, ... feasibility of using phenotypic information
   to infer molecular interactions & hinting at new uses of marketed drugs."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1158140">doi:10.1126/science.1158140</A>]['08] [29 refs].

%A Y. Cao
%A A. Charsti
%A L.-C. Cheng
%A T. Jiang
%A T. Girke
%T ChemmineR: a compound mining framework for R
%J J. Bioinformatics
%V 24
%N 15
%P 1733-1734
%M AUG
%D 2008
%K jrnl, c2008, c200x, c20xx, MolBio, small molecules, data, drug discovery,
   ChemmineR, ChemMine, R
%X "Software applications for structural similarity searching and clustering of
   small molecules play an important role in drug discovery & chemical genomics.
   ... integrated with the online ChemMine environment & allows bidirectional
   communications between the two services."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn307">doi:10.1093/bioinformatics/btn307</A>]['08].

%A S. Guang
%A A. F. Bochner
%A D. M. Pavelec
%A K. B. Burkhart
%A S. Harding
%A J. Lachowiec
%A S. Kennedy
%T An Argonaute transports siRNAs from the cytoplasm to the nucleus
%J Science
%V 321
%N 5888
%P 537-541
%M JUL
%D 2008
%K jrnl, c2008, c200x, c20xx, MolBio, siRNA, si RNA, RNAi, DNA, nucleus, cell,
   Argonaute protein, NRDE-3, NRDE3, gene expression, regulate
%X "...conducted a genetic screen to identify factors essential for RNA
   interference (RNAi) in nuclei of Caenorhabditis elegans & identified the
   Argonaute protein NRDE-3. In the absence of small interfering RNAs (siRNAs),
   NRDE-3 resides in the cytoplasm. NRDE-3 binds siRNAs generated by RNA-
   -dependent RNA polymerases acting on [mRNA] templates in the cytoplasm
   & redistributes to the nucleus. Nuclear redistribution of NRDE-3 requires a
   functional nuclear localization signal, is required for nuclear RNAi, &
   results in NRDE-3 association with nuclear-localized nascent transcripts.
   Thus, specific Argonaute proteins can transport specific classes of small
   reg. RNAs to distinct cellular compartments to regulate gene expression."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1157647">doi:10.1126/science.1157647</A>]['08].

%A A. Statnikov
%A L. Wang
%A C. F. Aliferis
%T A comprehensive comparison of random forests and support vector machines
   for microarray-based cancer classification.
%J BMC Bioinformatics
%D 2008
%V 9
%N 1
%P 319
%M JUL
%D 2008
%K jrnl, eJrnl, c2008, c200x, c20xx, zz0808, MolBio, microarray, micro array,
   arrays, microarrays, random forest, SVM, machine
%X "... identify methodological biases of prior work comparing random forests
   & SVMs & conduct a new rigorous evaluation of the 2 algs. that corrects
   these limitations. ... use 22 diagnostic & prognostic datasets  ...
   ... on avg & in the majority of microarray datasets, random forests are
   outperformed by SVMs both in the settings when no gene selection is
   performed & when several popular gene selection methods are used."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-9-319">doi:10.1186/1471-2105-9-319</A>]['08].

%A I. Neamatullah
%A et al
%T Automated de-identification of free-text medical records
%J BMC Medical Informatics and Decision Making
%V 24
%N 8:32
%M JUL
%D 2008
%K jrnl, eJrnl, c2008, c200x, c20xx, zz0808, data base, privacy, de identity,
   remove, removal, deindentify, record, DBMS, data sharing, HIPAA,
   protected health information, PHI
%X "... out-performs a single human de-identifier (0.81) and performs at
   least as well as a consensus of two human de-identifiers (0.94). ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1472-6947-8-32">doi:10.1186/1472-6947-8-32</A>]['08].

%A H. Pearson
%T 'Virophage' suggests viruses are alive
%J Nature
%V 454
%P 677
%M AUG
%D 2008
%K news, MolBio, c2008, c200x, c20xx, zz0808, Sputnik, virus, mamavirus,
   mimivirus, Acanthamoeba polyphaga, viruses, viral, alive, life, live
%X "... huge virus with, as later work revealed, a genome harbouring more than
   900 protein-coding genes -- at least 3 x more than that of the biggest
   previously known v. ..."      [mimivirus ~ 1.2-Mb genome, ?900+ genes]
   -- [<A HREF="http://www.nature.com/news/2008/080807/full/454677a.html">www</A>]['08],
   -- [<A HREF="http://dx.doi.org/10.1038/454677a">doi:10.1038/454677a</A>]['08].
   (Also see "... small virus Sputnik, 50 nm in size, found assoc. with a new
   strain of APMV ..." [<A HREF="http://dx.doi.org/10.1038/nature07218">doi:10.1038/nature07218</A>][08].)
   [Also search for: mimivirus].

%A R. F. Service
%T Problem Solved (sort of)
%J Science
%V 321
%N 5890
%P 784-786
%M AUG
%D 2008
%K news, MolBio, c2008, c200x, c20xx, zz0808, proteins, protein, folding, fold,
   tertiary, 3D, structure, prediction, intro
%X "... brought them to the verge of being able to make predictions about
   proteins they haven't even discovered ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.321.5890.784">doi:10.1126/science.321.5890.784</A>]['08].

%A R. E. Green
%A et al
%T A complete Neandertal Mitochondrial genome sequence determined by
   high-throughput sequencing
%J Cell
%V 134
%N 3
%P 416-426
%M AUG
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0808, DNA, mGenome, early human, ancient,
   evolution, hominid, homo, Neandertal, Neanderthal,  mitochondria
%X "A complete mitochondrial (mt) genome seq. was reconstructed from a 38,000y
   Neandertal individual with 8341 mtDNA seqs. identified among 4.8Gb of DNA
   generated from ~ 0.3g of bone. Analysis of the assembled seq. unequivocally
   establishes that the Neandertal mtDNA falls outside the variation of extant
   human mtDNAs, & allows an estimate of the divergence date between the 2 mtDNA
   lineages of 660,000-140,000y. Of the 13 proteins encoded in the mtDNA,
   subunit 2 of cytochrome c oxidase of the mitochondrial electron transport
   chain has experienced the largest number of AA substitutions in human
   ancestors since the separation from Neandertals. There is evidence that
   purifying selection in the Neandertal mtDNA was reduced compared with other
   primate lineages, suggesting that the effective pop.size of N. was small."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cell.2008.06.021">doi:10.1016/j.cell.2008.06.021</A>]['08].
   [EMBL accession number AM948965.]  (Also see draft nuclear genome FEB c2009.)

%A M. Srivastava
%A et al
%T The Trichoplax genome and the nature of placozoans
%J Nature
%V 454
%P 955-960
%M AUG
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz0808, Trichoplax adhaerens, nGenome,
   DNA, placozoan, flat animals, metazoan, placozoans, eumetazoan
%X "As arguably the simplest free-living animals, placozoans may represent a
   primitive metazoan form, yet their biology is poorly understood. ... report
   the sequencing & analysis of the ~98 million bp nuclear genome of the
   placozoan Trichoplax adhaerens. ..."
   DDBJ/EMBL/GenBank accession number ABGP00000000
   -- [<A HREF="http://dx.doi.org/10.1038/nature07191">doi:10.1038/nature07191</A>]['08].
   (Also see [<A HREF="http://www.jgi.doe.gov/trichoplax">www.jgi.doe.gov/trichoplax</A>].)

%A P. C. Ng
%A Q. Zhao
%A S. Levy
%A R. L. Strausberg
%A J. C. Venter
%T Individual genomes instead of race for personalized medicine
%J Clinical Pharmacology & Therapeutics
%V 84
%N 3
%P 306-309
%D 2008
%K c2008, c200x, c20xx, zz0908, MolBio,  human genome, medicine, medical,
   Venter, Watson, personalized, genomics, race, drug, reactions, drugs
%X "The cost of seq. & genotyping is aggressively decreasing, enabling pervasive
   personalized genomic screening for drug reactions. Drug-metabolizing genes
   have been characterized sufficiently to enable practitioners to go beyond
   simplistic ethnic characterization & into the precisely targeted world of
   personal genomics. We examine six drug-metabolizing genes in V. & W., 2
   Caucasian men whose genomes were recently seq.. Their genetic differences
   underscore the importance of personalized genomics over a race-based approach
   to medicine. To attain truly personalized medicine, the sci. community must
   aim to elucidate the genetic & env. factors that contribute to drug reactions
   & not be satisfied with a simple race-based approach."
   -- [<A HREF="http://dx.doi.org/10.1038/clpt.2008.114">doi:10.1038/clpt.2008.114</A>]['08].

%A A. Rao
%A A. O. Hero III
%A D. J. States
%A J. D. Engel
%T Using directed information to build biologically relevant influence networks
%J J. Bioinformatics and Comp. Biol.
%V 6
%N 3
%P 493-519
%M JUN
%D 2008
%K jrnl, JBCB, MolBio, c2008, c200x, c20xx, network, BN, DTI,
   gene, regulation, regulatory, expression
%X "... propose a network inference methodology, based on the directed
   information (DTI) criterion, that incorporates the biology of transcription
   within the framework so as to enable experimentally verifiable inference. We
   use publicly available embryonic kidney and T-cell microarray datasets to
   demonstrate our results. We present two variants of network inference via
   DTI - supervised and unsupervised - and the inferred networks relevant to
   mammalian nephrogenesis and T-cell activation. ..."
   -- [<A HREF="http://dx.doi.org/10.1142/S0219720008003515">doi:10.1142/S0219720008003515</A>]['08].
   [Also search for: influence network].

%A H. Ben Hassen
%A A. Masmoudi
%A A. Rebai
%T Causal inference in biomolecular pathways using a Bayesian network approach
   and an implicit method.
%J J Theor. Biol.
%V ?
%P ?-?
%M MAY
%D 2008
%K jrnl, JTB, MolBio, c2008, c200x, c20xx, infer, II, pathway, gene expression,
   regulation, network, networks
%X "introduce... Implicit networks [IN] which provide, like BNs, a graphical
   modelling f/w that encodes the joint pr. dist. for a set of random vars.
   within a DAG. We show that INs, when used ...with appropriate
   stat. techniques, are very attractive for their ability to understand &
   analyze biol. data. ... consider the use of Implicit networks for causal
   inference in biomolecular pathways. ... an IN encodes dependencies among
   vars. (proteins, genes), can be trained to learn causal relationships
   (regulation, interaction) between them & then used to predict the biol.
   response given the status of some key proteins or genes in the n/w. We show
   that INs offer efficient methodologies for learning from obs. without prior
   knowledge & thus provide a good alternative to classical inference in
   BNs when priors are missing. ... application to simulated data for a
   simplified signal transduction pathway of the epidermal growth factor
   receptor (EGFR) protein."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jtbi.2008.04.030">doi:10.1016/j.jtbi.2008.04.030</A>]['08].
   [Also search for: Bayesian network].

%A S. Sharma
%A F. Ding
%A N. V. Dokholyan
%T iFoldRNA: Three-dimensional RNA structure prediction and folding
%J J. Bioinformatics
%V 24
%N 17
%P 1951-1952
%M SEP
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz0808, iFoldRNA, 3D, RNA, fold, folding
%X "... rapidly explores RNA conformations using discrete molecular dynamics
   simulations of input RNA sequences. Starting from simplified linear-chain
   conformations, RNA molecules (< 50 nt) fold to native-like structures within
   half an hour of simulation, facilitating rapid RNA structure prediction.
   All-atom reconstruction of energetically stable conformations generates
   iFoldRNA predicted RNA structures. The pred. RNA structs. are within 2-5 A
   RMS deviations (RMSDs) from corr. experimentally derived structs.. RNA
   folding params. inc. specific heat, contact maps, simulation trajectories,
   gyration radii, RMSDs from native state, fraction of native-like contacts
   are accessible ..."   (online June '08).
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn328">doi:10.1093/bioinformatics/btn328</A>]['08].
   (Also see [<A HREF="http://iFoldRNA.dokhlab.org">s/w@dokhlab.org</A>].)

%A T. Hayakawa
%A R. Culleton
%A H. Otani
%A T. Horii
%A K. Tanabe
%T Big bang in the evolution of extant malaria parasites
%J Molecular Biology and Evolution
%V ?
%N ?
%P ?-?
%D 2008
%K jrnl,MBE, MolBio, c2008, c200x, c20xx, zz0908, parasite, malaria, Plasmodium,
   host, hosts, mammal, tree, trees, diversification, coevolution
%X "...propose a novel scenario of m. parasite-host co-evolution. A phylogenetic
   tree constructed using the m. parasite mitochondrial genome reveals that the
   extant primate, rodent, bird & reptile parasite lineages rapidly diverged
   from a common ancestor during an evolutionary short time period. This rapid
   diversification occurred long after the establishment of the primate, rodent,
   bird & reptile host lineages, which implies that host-switch events
   contributed to the rapid diversification of extant m. parasite lineages.
   ... rapid diversification coincides with the radiation of the mammalian
   genera, suggesting that adaptive radiation to new mammalian hosts triggered
   the rapid diversification of extant malaria parasite lineages."
   (On line Aug. 2008.) [<A HREF="http://dx.doi.org/10.1093/molbev/msn171">doi:10.1093/molbev/msn171</A>]['08].

%A O. Lao
%A et al
%T Correlation between genetic and geographic structure in Europe
%J Current Biology
%V 18
%N 16
%P 1241-1248
%M AUG
%D 2008
%K jrnl, MolBio, Biol, c2008, c200x, c20xx, gene, genes, genetic, Europe, study,
   European, region, regions, regional, diversity, variation, distance,
   SNP genotype data, autosomal
%X "... investigated Affymetrix GeneChip 500K genotype data from 2,514
   individuals belonging to 23 different subpops., widely spread over Europe.
   ...found only a low level of genetic differentiation between subpops., the
   existing diffs. were characterized by a strong continent-wide correlation
   between geographic & genetic dist.. [&] mean heterozygosity was larger, &
   mean linkage disequilibrium smaller, in S. [v.] N. Europe. Both parameters
   clearly showed a clinal distribution that provided evidence for a spatial
   continuity of genetic diversity in Europe. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cub.2008.07.049">doi:10.1016/j.cub.2008.07.049</A>]['08].

%A H. Walum
%A et al
%T Genetic variation in the vasopressin receptor 1a gene (AVPR1A) associates
   with pair-bonding behavior in humans.
%J PNAS
%V ?
%P ?-?
%D 2008
%K jrnl, PNAS, MolBio, c2008, c200x, c20xx, zz0908, AVPR1A, RS3, V1aR, AVP,
   marriage, divorce, vasopressin receptor 1a, gene, love, pair bond, human,
   vole, voles, male, men, man, marital problems, fidelity, faithful
%X "Pair-bonding has been suggested to be a critical factor in the evol. dev. of
   the social brain. The brain neuropeptide arginine vasopressin (AVP) exerts an
   important influence on pair-bonding behavior in voles. There is a strong
   assoc. between a polymorphic repeat seq. in the 5' flanking region of the
   gene (avpr1a) encoding 1 of the AVP receptor subtypes (V1aR), & proneness for
   monogamous behavior in males of this species. It is not yet known whether
   similar mechanisms are important also for human pair-bonding. Here, we report
   an assoc. between 1 of the human AVPR1A repeat polymorphisms (RS3) & traits
   reflecting pair-bonding behavior in men, including partner bonding, perceived
   marital problems, & marital status, & show that the RS3 genotype of the males
   also affects marital quality as perceived by their spouses. ... suggest an
   assoc. between a single gene & pair-bonding behavior in humans, & indicate
   that the well characterized influence of AVP on pair-bonding in voles may be
   of relevance also for humans."  (online Sept 2008),
   pdf@[<A HREF="http://dx.doi.org/10.1073/pnas.0803081105">doi:10.1073/pnas.0803081105</A>][9/'08].
   [Also search for: vasopressin].

%A G. Della Gatta
%A M. Bansal
%A A. Ambesi-Impiombato
%A D. Antonini
%A C. Missero
%A D. di Bernardo
%T Direct targets of the TRP63 transcription factor revealed by a combination of
   gene expression profiling and reverse engineering
%J Genome Res.
%V 18
%P 939-948
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, TSNI, target, TRP63, factors, regulation,
   gene expression, infer gene regulatory network
%X "... measuring time-course (dynamic) gene expression profiles upon
   perturbation of the transcription factor under study, & in applying a novel
   "reverse-engineering" alg. (TSNI) to rank genes according to their prob. of
   being direct targets. Using primary keratinocytes as a model system, we
   identified novel transcriptional target genes of TRP63, a crucial regulator
   of skin development. TSNI-predicted TRP63 target genes were validated by
   Trp63 knockdown & by ChIP-chip to identify TRP63-bound regions in vivo. ...
   revealed that short sampling times, in the order of minutes, are needed to
   capture the dynamics of gene expression in mammalian cells. ... TRP63
   transiently regulates a subset of its direct targets, ... importance of
   considering temporal dynamics when identifying transcriptional targets. ...
   uncovered a previously unsuspected transient regulation of the AP-1 complex
   by TRP63 through direct regulation of a subset of AP-1 components. ..."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.073601.107">doi:10.1101/gr.073601.107</A>]['08] (online Apr 08).
   Also see [<A HREF="http://dibernardo.tigem.it/wiki/index.php/Time_Series_Network_Identification_TSNI">www</A>]['08].
   [Also search for: infer gene regulatory network].

%A M. Selbach
%A et al
%T Widespread changes in protein synthesis induced by microRNAs
%J Nature
%V 455
%P 58-63
%M SEP
%D 2008
%K jrnl, c2008, c200x, c20xx, MolBio, miRNA, microRNA, gene expression
%X "... new proteomic approach to measure changes in synthesis of several
   thousand proteins in response to miRNA transfection or endogenous miRNA
   knockdown. In ||, we quantified mRNA levels using microarrays. ... show that
   a single miRNA can repress the production of hundreds of proteins, but that
   this repression is typically relatively mild. A # of known features of the
   miRNA-binding site such as the seed seq. also govern repression of human
   protein synthesis, & we report additional target seq. characteristics. We
   demonstrate that, in addition to downregulating mRNA levels, miRNAs also
   directly repress translation of hundreds of genes. ... suggest that a miRNA
   can, by direct or indirect effects, tune protein synthesis from thousands of
   genes.
   -- [<A HREF="http://dx.doi.org/10.1038/nature07228">doi:10.1038/nature07228</A>]['08].
   (Also search for: miRNA).

%A D. Baek
%A et al
%T The impact of microRNAs on protein output
%J Nature
%V 455
%P 64-71
%M SEP
%D 2008
%K jrnl, c2008, c200x, c20xx, MolBio, miRNA, microRNA, gene expression
%X "MicroRNAs are endogenous ~23-nucleotide RNAs that can pair to sites in the
   mRNAs of protein-coding genes to downregulate the expression ...
   use quantitative mass spectrometry to measure the response of thousands of
   proteins after introducing microRNAs into cultured cells & after deleting
   mir-223 in mouse neutrophils. The identities of the responsive proteins
   indicate that targeting is primarily through seed-matched sites located
   within favourable predicted contexts in 3' UTRs. Hundreds of genes were
   directly repressed, albeit each to a modest degree, by individual microRNAs.
   Although some targets were repressed without detectable changes in mRNA
   levels, those translationally repressed by more than 1/3 also displayed
   detectable mRNA destabilization, & for the more highly repressed targets,
   mRNA destabilization usually comprised the major component of repression.
   The impact of microRNAs on the proteome indicated that for most interactions
   microRNAs act as rheostats to make fine-scale adjustments to protein output."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07242">doi:10.1038/nature07242</A>]['08].
   (Also search for: miRNA).

%A R. C. G. Holland
%A et al
%T BioJava: an open-source framework for bioinformatics
%J J. Bioinformatics
%V 24
%N 18
%P 2096-2097
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, bio java
%X online Aug 2008 [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn397">doi:10.1093/bioinformatics/btn397</A>]['08].
   Also see [<A HREF="http://www.biojava.org">www</A>]['08].
   [Also search for: BioJava].

%A T. Bereczkei
%A G. Hegedus
%A G. Hajnal
%T Facialmetric similarities mediate mate choice: sexual imprinting on
   opposite-sex parents
%J Proc. Royal Soc. B
%V ?
%P ?-?
%M ?
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0908, face, facial, similar, parent, spouse,
   mate, selection, partner, Oedipus, imprint, wife, husband, mother, father
%X "... direct evidence for assessing facial resemblance between subjects'
   partner & subjects' parents. 14 facial proportions were measured on 312
   adults belonging to 52 families, & the correlns between family members were
   compared with those of pairs randomly sel. from the popn. Spouses proved to
   be assortatively mated in the majority of measured facial proportions.
   Sig.correlns have been found between the young men & their partner's father
   (but not his mother), esp. on facial proportions belonging to the central
   area of the face. Women also showed resemblance to their partner's mother
   (but not to their father) in the facial characteristics of their lower face.
   Replicating our previous studies, facial photos. of participants were also
   matched by indep. judges who ascribed higher resemblance between partners, &
   subjects & their partners' opposite-sex parents, compared with controls. ...
   ...support the sexual imprinting hypothesis which states that children shape
   a mental template of their opposite-sex parents & search for a partner who
   resembles that perceptual schema. The fact that only the facial metrics of
   opposite-sex parents showed resemblance to the partner's face tends to rule
   out the role of familiarity in shaping mating preferences. Our findings also
   reject several other rival hypos.. The adaptive value of imprinting-related
   human mating is discussed, & a hypo. is made of why different facial areas
   are involved in males' & females' search for resemblance."  online Sep 2008.
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2008.1021">doi:10.1098/rspb.2008.1021</A>]['08].

%A S. E. Forde
%A R. E. Beardmore
%A I. Gudelj
%A S. S. Arkin
%A J. N. Thompson
%A L. D. Hurst
%T Understanding the limits to generalizability of experimental evolutionary
   models.
%J Nature
%V 455
%P 220-223
%M SEP
%D 2008
%K jrnl, c2008, c200x, c20xx, Ecoli, T7, Escherichia coli, lambda bacteriophage,
   MolBio, model, aLife, simulation, limit, diversity
%X "... using the relationship between phenotypic diversity & resource input in
   the T7-E.coli co-evolving sys. as a case history. We establish a math. model
   ... framed as 1 instance of a super-class of host-parasite co-evolutionary
   models, & show that it captures experimental results. ...
   ... A combination of in vitro systems & appropriately config'd math. models
   is an effective means to isolate results particular to the in vitro system,
   to characterize systems likely to behave differently & to understand the
   biology underpinning those alternatives."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07152">doi:10.1038/nature07152</A>]['08].

%A M. A. Nowak
%A H. Ohtsuki
%T Prevolutionary dynamics and the origin of evolution
%J PNAS
%V ?
%P ?-?
%D 2008
%K PNAS, jrnl, c2008, c200x, c20xx, zz0908, MolBio, evolution, pre, life,
   prelife, prebiotic, natural selection, live, living, origin, origins
%X "Life is that which replicates & evolves. The origin of life is also the
   origin of evolution. A fundamental Q. is when do chemical kinetics become
   evolutionary dynamics? ... formulate a general math. theory for the origin
   of evol.. All known life on earth is based on biol. polymers, which act as
   info. carriers & catalysts. ...any theory for the origin of life must address
   the emergence of such a system. We describe prelife as an alphabet of active
   monomers that form random polymers. Prelife is a generative sys. that can
   produce info.. Prevolutionary dynamics have selection & mutation, but no
   replication. Life marches in with the ability of replication: Polymers act
   as templates for their own reproduction. Prelife is a scaffold that builds
   life. Yet, there is competition between life & prelife. There is a phase
   transition: If the effective replication rate exceeds a critical value, then
   life outcompetes prelife. Replication is not a prereq. for seln, but instead,
   there can be seln for replication. Mutation leads to an error threshold
   between life & prelife."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0806714105">doi:10.1073/pnas.0806714105</A>]['08].

%A K. N. Houk
%A P. Ha-Yeon Cheong
%T Computational prediction of small-molecule catalysts
%J Nature
%V 455
%P 309-313
%M SEP
%D 2008
%X comment, note, intro, c2008, c200x, c20xx, catalyst, MolBio, computer,
   chemical reaction, chemistry, simulation, Gaussian 70, Gaussian70
%X "Most organic and organometallic catalysts have been discovered through
   serendipity or trial and error ... Gaussian 70 ..." [37 refs]
   -- [<A HREF="http://dx.doi.org/10.1038/nature07368">doi:10.1038/nature07368</A>]['08].

%A R. A. Holt
%A S. J.M. Jones
%T The new paradigm of flow cell sequencing
%J Genome Res.
%V 18
%P 839-846
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz1008, DNA, flow cells, flowCell,
   capillary, sequencing, review, survey, intro
%X "... A new gen. of instruments that utilize primed synthesis in flow
   cells to obtain, simultaneously, the seq. of millions of different DNA
   templates has changed the field. We compare & contrast these new seq.
   platforms ... While these platforms outperform capillary instruments in terms
   of bases per day & cost/base, the short length of seq. reads obtained from
   most instruments & the limited # of samples that can be run simultaneously
   imposes some practical constraints on seq.  applications. However, recently
   developed methods for paired-end seq. & for array-based direct seln of
   desired templates from complex mixtures extend the utility of these platforms
   for genome analysis. Given the ever increasing demand for DNA seq. info., we
   can expect cts improvement of this new gen. of instruments & their eventual
   replacement by even more powerful technology."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.073262.107">doi:10.1101/gr.073262.107</A>]['08].
   [Also search for: MolBio flowCell].

%A R. Li
%A Y. Li
%A K. Kristiansen
%A J. Wang
%T SOAP: Short oligonucleotide alignment program
%J J. Bioinformatics
%V 24
%N 5
%P 713-714
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, SOAP, soap2, software, DNA, re sequencing,
   resequencing, resequence, Illumina, Solexa, short read, reads
%X "... developed a program SOAP for efficient gapped & ungapped alignment of
   short oligonucleotides onto ref. seqs.. ... is designed to handle the huge
   amounts of short reads generated by parallel seq. using the new generation
   Illumina-Solexa seq. technology. SOAP is compatible with numerous
   applications, including single-read or pair-end resequencing, small RNA
   discovery & mRNA tag sequence mapping. SOAP is a command-driven program,
   which supports multi-threaded parallel computing, & has a batch module for
   multiple query sets."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn025">doi:10.1093/bioinformatics/btn025</A>]['08].
   Also see [<A HREF="http://soap.genomics.org.cn/">soap@.cn</A>]['08], and
   -- [<A HREF="http://soap.genomics.org.cn/soapaligner.html#down2">soap2</A>]['09].
      "2 min. [for] one million single-end reads onto the human ref. genome.
      on 64-bit CPU with SSE, 8GB mem."
   [Also search for: resequencing MolBio],
   [also search for: short read MolBio].

%A L. Zullo
%A G. Sumbre
%A C. Agnisola
%A T. Flash
%A B. Hochner
%T Nonsomatotopic organization of the higher motor centers in octopus
%J Curr. Biol.
%V 19
%N 19
%P 1632-1636
%M OCT
%D 2009
%K jrnl, biol, c2019, c200x, c20xx, zz0615, biology, octopus, brain,
   nervous system, neuromuscular, arms, movement
%X "Hyperredundant limbs with a virtually unlimited # of degrees of freedom
   (DOFs) pose a challenge for both biol. & comp'l systems of motor control. In
   the flexible arms of the octopus, simplification strategies have evolved to
   reduce the number of controlled DOFs. ... nervous system is hierarchically
   organized. A relatively small central brain integrates a huge amount of
   visual & tactile information ... issues commands to lower motor centers
   controlling the elaborated neuromuscular system of the arms. ... raises new
   questions on the organization of the octopus brain & whether & how it
   represents the rich movement repertoire. ... brain microstimulation in freely
   behaving animals & stimulated the higher motor centers - the basal lobes -
   thus inducing discrete & complex sets of movements. ... found no stimulation
   site where movements of a single arm or body part could be elicited. Discrete
   & complex components have no central topographical organization but are
   distributed over wide regions."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cub.2009.07.067">doi:10.1016/j.cub.2009.07.067</A>]['15].

%A S. A. Smith
%A M. J. Donoghue
%T Rates of molecular evolution are linked to life history in flowering plants
%J Science
%V 322
%N 5898
%P 86-89
%M OCT
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, flowering, plant, plants, asterids,
   rosids, monocotyledons, rate, molecular clock, tree of life, trees
%X "Variable rates of molec. evol. have been documented across the tree of life,
   but the cause of this observed variation within & among clades remains
   uncertain. ... it has been suggested that life history traits are correlated
   with the rate of molec. evol., but previous studies have yielded conflicting
   results. Exceptionally large phylogenies of 5 major angiosperm clades
   demonstrate that rates of m.e. are consistently low in trees & shrubs, with
   relatively long generation times, as compared with related herbaceous plants,
   which generally have shorter generation times. Herbs show much higher rates
   of m. change but also much higher variance in rates. Correlates of life
   history attributes have long been of interest to biologists, & our results
   demonstrate how changes in the rate of m.m. that are linked to life history
   traits can affect measurements of the tempo of evolution as well as our
   ability to identify & conserve biodiversity."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1163197">doi:10.1126/science.1163197</A>]['08].
   [Also search for: MolBio tree life].

%A M. D. Prokosch
%A R. G. Cossa
%A J. E. Scheib
%A S. A. Blozis
%T Intelligence and mate choice: Intelligent men are always appealing
%J Evolution and Human Behavior
%V ?
%N ?
%P ?-?
%D 2008 ?
%K jrnl, c2008, c200x, c20xx, zz1008, human behaviour, mate selection, choice,
   WAIS, intelligence, male, man, female, woman, brains, intelligence, IQ,
   creativity
%X "... participants (204 women) assessed the long- & short-term mate appeal
   of videos of 15 men with known measures of intelligence performing verbal
   & physical tasks. Findings indicate that both intelligence & creativity
   independently predicted mate appeal across mating contexts, but no
   conception-risk effects were detected. We discuss implications of these
   findings for the role of intelligence & creativity in women's mate choices."
   -- [<A HREF="http://dx.doi.org/10.1016/j.evolhumbehav.2008.07.004">doi:10.1016/j.evolhumbehav.2008.07.004</A>]['08] online Sept 2008.

%A J. M. Carlton
%A et al
%T Comparative genomics of the neglected human malaria parasite
   Plasmodium vivax
%J Nature
%V 455
%P 757-763
%M OCT
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz1008, malaria, Plasmodium vivax, Pvivax,
   nGenome, AAKM00000000
%X "... vivax is responsible for 25-40% of the ~515 million annual cases of
   m. worldwide. Although seldom fatal, the parasite elicits severe &
   incapacitating  ...  describe the synteny & isochore structure of P.vivax
   chrs., & show that the parasite resembles other m. parasites in gene
   content & metabolic potential, but possesses novel gene families & potential
   alternative invasion pathways not recognized previously. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07327">doi:10.1038/nature07327</A>]['08].
   Seq. & annotation data ... deposited in [<A HREF="http://www.ncbi.nlm.nih.gov/">GenBank</A>]
   under the project accession [<A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=search&term=AAKM00000000">AAKM00000000</A>]
   and are also available @ [<A HREF="http://plasmodb.org">PlasmoDB</A>]
   A minimal tiling path of clones covering each chr. is available through the
   m. repository [<A HREF="http://www.mr4.org">MR4</A>], & a long-oligo array
   through the Pathogen Fn. Gen. Resource [<A HREF="http://pfgrc.jcvi.org">center</A>].
   [Also search for: Plasmodium vivax].

%A A. Pain
%A et al
%T The genome of the simian and human malaria parasite Plasmodium knowlesi
%J Nature
%V 455
%P 799-803
%M OCT
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, Plasmodium knowlesi, Pknowlesi, nGenome,
   AM910983, AM910996, malaria, Macaca fascicularis, kra monkey
%X "... natural vertebrate host is Macaca fascicularis (the 'kra' monkey) [but]
   now increasingly recognized as a sig. cause of human m., particularly in SE
   Asia ...  close phylogenetic relationship to P.vivax, the 2nd most important
   species of human m. parasite. Despite their relatedness, there are important
   phenotypic differences between them, such as host blood cell preference,
   absence of a dormant liver stage or 'hypnozoite' in P. knowlesi, & length of
   the asexual cycle ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07306">doi:10.1038/nature07306</A>]['08].
   "... 14 chrs. of the H strain of P.knowlesi sub. to EMBL with accession #s
   AM910983 - AM910996. The annotation & seq. data are also available @
   -- [<A HREF="http://www.genedb.org">genedb</A>] & [<A HREF="http://www.plasmodb.org">plasmodb</A>]."

%A C. M. Holman
%T Trends in human gene patent litigation
%J Science
%V 322
%N 5899
%P 198-199
%M OCT
%D 2008
%K policy, c2008, c200x, c20xx, human, gene, genes, patent, patents, law, legal,
   litigation, court case, society, social, factors, impact, progress
%X "Critics have long warned that patents claiming human genes pose a
   substantial threat to public health and the progress of science ... Congress
   is considering legislation that would prospectively ban the patenting of not
   only human genes, but any "nucleotide sequence, or its functions or
   correlations, or the naturally occurring products it specifies". ... In 2004,
   Jensen & Murray identified 4270 U.S. patents claiming at least 1 human gene
   & concluded that 1/5 of known human genes were claimed in a patent. ... I
   identified 31 human gene patent litigations, dating back to 1987. ...
   seems a relatively small number. ..."  [25 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1160687">doi:10.1126/science.1160687</A>]['08].

%A I. Ionita-Laza
%A N. M. Laird
%A B. A. Raby
%A S. T. Weiss
%A C. Lange
%T On the frequency of copy number variants
%J J. Bioinformatics
%V 24
%N 20
%P 2350-2355
%M OCT
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, CNV, CNVs, copy number variant
%X "Est. the freq. distribution of copy number variants (CNVs) ... results
   suggest that the current skew toward low-frequency CNVs may not be
   representative of the true freq.d., but may be due, among other reasons, to
   the non-negligible false -ve rates that characterize CNV detection methods.
   Moreover, false +ves are also likely, as low-freq. CNVs are hard to detect
   with small sample sizes & technologies that are not ideally suited for their
   detection. Without appropriate validation methods, such as incorporation of
   biologically relevant information (eg, in our case, the transmission of
   heritable CNVs from parents to offspring), it is difficult to assess the
   validity of specific CNVs, & even harder to obtain reliable freq. ests.."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn421 ">doi:10.1093/bioinformatics/btn421">]['08].

%A H. Jiang
%A W. Hung Wong
%T SeqMap: mapping massive amount of oligonucleotides to the genome
%J J. Bioinformatics
%V 24
%N 20
%P 2395-2396
%M OCT
%D 2008
%K jrnl, MolBio, seqmap, c2008, c200x, c20xx, zz1008, SeqMap, software, align,
   resequencing, sequence, reference genome, short read, reads, millions,
   high throughput sequencing machines
%X "SeqMap is a tool for mapping large amount of short seqs. to the genome. ...
   designed for finding all the places in a ref. genome where each seq. may come
   from. ... ultra high-throughput seq'ing m/cs. ... can map 10s of millions of
   short seqs. to a genome of several billions of n..  Multiple substitutions &
   [indels] of the nucleotide bases in the seqs. can be tolerated & therefore
   detected ... typical mapping ... done in a few hrs on a ... PC.  [7 refs].
   Parallel use of SeqMap on a cluster is also very straightforward."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn429">doi:10.1093/bioinformatics/btn429</A>]['08];  (auth2@stats,Stanf.U.).
   s/w: [<A HREF="http://biogibbs.stanford.edu/~jiangh/SeqMap/">www</A>]['08].
   (Test data came from Mortazavi c2008).
   [Also search for: resequencing MolBio],
   [also search for: short read MolBio].

%A A. Novak
%A I. Miklos
%A R. Lyngso
%A J. Hein
%T StatAlign: An extendable software package for joint Bayesian estimation of
   alignments and evolutionary trees
%J J. Bioinformatics
%V 24
%N 20
%P 2403-2404
%M OCT
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, alignment, evolutionary, phylogenetic,
   tree, trees, MCMC, multiple, alignment, sequence, strings
%X "... extendable s/w package in the Java prog.lang. that samples from the
   joint posterior distribution of phylogenies, alignments & evolutionary
   params. by applying the Markov chain Monte Carlo method. ...
   1 million MCMC steps on 13 seqs. of papain family cystein proteinases with
   avg. length 223 ... performed in < 20hrs [and] the convergence of the
   Markov chain is relatively fast: based on the log-likelihood trace, 10,000
   steps were sufficient for convergence on this dataset."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn457">doi:10.1093/bioinformatics/btn457</A>]['08];  (auths@stats,Ocf'd.U.).
   [Also search for: Bayesian phylogenetic tree MolBio].

%A A. Mortazavi
%A B. A. Williams
%A K. McCue
%A L. Schaeffer
%A B. Wold
%T Mapping and quantifying mammalian transcriptomes by RNA-Seq
%J NatureMethods
%V 5
%N 7
%P 621-628
%M JUL
%D 2008
%K eJrnl, MolBio, c2008, c200x, c20xx, mammal, transcriptome, short read, reads,
   data, RNA-Seq, RNAseq, sequence, ChIPseq, ERANGE, woldlab
%X "... mouse transcriptomes by deeply seq. them & recording how freq. each gene
   is rep. in the seq. sample (RNA-Seq). [gives] digital measure of the presence
   & prevalence of transcripts from known & previously unknown genes. We report
   ref. measurements composed of 41-52 m. mapped 25bp reads for poly(A)-selected
   RNA from adult mouse brain, liver & skeletal muscle tissues. ...
   Although > 90% of uniquely mapped reads fell within known exons, the
   remaining data suggest new & revised gene models, inc. changed or additional
   promoters, exons & 3' untranscribed regions, as well as new candidate miRNA
   precursors. RNA splice events ... were detected directly by mapping
   splice-crossing sequence reads. We observed 1.45 x 10(5) distinct splices, &
   alt. splices were prominent, with 3,500 different genes expressing >= 1 ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nmeth.1226">doi:10.1038/nmeth.1226</A>]['08].
   Auths in Biol @ Caltech;  corr: woldb at caltech edu.
   Code+data: [<A HREF="http://woldlab.caltech.edu/rnaseq/">rnaseq@caltech</A>].

%A J. C. Dohm
%A C. Lottaz
%A T. Borodina
%A H. Himmelbauer
%T Substantial biases in ultra-short read data sets from high-throughput
   DNA sequencing
%J NAR
%V 36
%N 16
%P e105
%D 2008
%K eJrnl, MolBio, NAR, c2008, c200x, c20xx, short read, reads, bias,
   errors, ELAND, Illumina, Solexa
%X "... generated & analyzed 2 Illumina 1G ultra-short read data sets, i.e.
   2.8 million 27mer reads from a Beta vulgaris genomic clone & 12.3 million
   36mers from the Helicobacter acinonychis genome. We found that error rates
   range from 0.3% at the beginning of reads to 3.8% at the end of reads. Wrong
   base calls are frequently preceded by base G. Base substitution error freqs.
   vary by 10 to 11 x, with A > C transversion being among the most freq. &
   C > G transversions among the least freq. subs. errors. [Indels] of single
   bases occur at very low rates. When simulating re-sequencing we found a
   20 x sequencing coverage to be sufficient to compensate errors by correct
   reads. The read coverage of the sequenced regions is biased; the highest read
   density was found in intervals with elevated GC content. High Solexa quality
   scores are over-optimistic & low scores underestimate the data quality. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gkn425">doi:10.1093/nar/gkn425</A>]['08].
   [Also search for: short read MolBio],
   [also search for: SHARCGS MolBio].

%A L. Schietgat
%A J. Ramon
%A M. Bruynooghe
%A H. Blockeel
%T An efficiently computable graph-based metric for the classification of small
   molecules
%J Int. Conf. on Discovery Science
%P ?-?
%S LNCS
%V ???
%M OCT
%D 2008
%K conf, c2008, c200x, c20xx, graph, graphs, metric, distance, molecule,
   chemical compound, compounds
%X "... focus on is drug discovery. Although graphs have become very popular for
   the representation of molecules, a lot of ops. on graphs are NP-complete.
   Representing the molecules as outerplanar graphs ... & using the
   block-and-bridge preserving subgraph isomorphism, we define a metric & we
   present an alg. for computing it in polynomial time. We evaluate this metric
   & more generally also the block-and-bridge preserving matching operator on a
   large dataset of molecules, obtaining favorable results."
   -- [<A HREF="https://lirias.kuleuven.be/bitstream/123456789/186720/1/schietgat_ds08.pdf">pdf@kuleuven</A>]['08].

%A D. R. Zerbino
%A E. Birney
%T Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
%J Genome Res.
%V 18
%N 5
%P 821-829
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, short read, reads, sequence, Solexa,
   de Bruijn, deBruijn, graph, de novo, denovo, genomic, assembly, assembler,
   TourBus, Breadcrumb
%X "... [Velvet] to manipulate de Bruijn graphs for genomic seq. assembly. A
   deB. graph is a compact rep'n based on short words (k-mers) that is ideal for
   high coverage, very short read (25-50bp) data sets. Applying Velvet to very
   short reads & paired-ends information only, one can produce contigs of
   sig. length, up to 50kb N50 length in simulations of prokaryotic data &
   3kb N50 on simulated mammalian BACs. When applied to real Solexa data sets
   without read pairs, Velvet generated contigs of ~8kb in a prokaryote & 2kb in
   a mammalian BAC, in close agreement with our simulated results without
   read-pair info.. Velvet represents a new approach to assembly that can
   leverage v.short reads ... with read pairs to produce useful assemblies."
   p.826: 1. hash reads -> k-mers (p.822)
          2. construct the graph  (p.822)
          3. correct errors       (p.822, p.823 Tour-Bus, p.824)
          4. resolve repeats      (p.825 Breadcrumb)
   pdf: [<A HREF="http://dx.doi.org/10.1101/gr.074492.107">doi:10.1101/gr.074492.107</A>]['08].
   [Also search for: short read MolBio].

%A H. Li
%A J. Ruan
%A R. Durbin
%T Mapping short DNA sequencing reads and calling variants using mapping
   quality scores
%J Genome Res.
%V 18
%N 11
%P 1851-1858
%D 2008
%K MAQ, jrnl, MolBio, DNA, HengLi, JueRuan, c2008, c200x, c20xx, variant,
   mapping quality score, shotgun short read, reads, assembly, mate pair,
   sequence, resequencing
%X "... major issue in efficiently aligning short reads to a ref.genome &
   handling ambiguity or lack of accuracy in this alignment. ... introduce the
   concept of mapping quality, a measure of the confidence that a read actually
   comes from the position it is aligned to by the mapping alg.. We describe
   the s/w MAQ that can build assemblies by mapping shotgun short reads to a
   ref.genome, using quality scores to derive genotype calls of the consensus
   seq. of a diploid genome, e.g., from a human sample. MAQ makes full use of
   mate-pair info. & ests. the error probability of each read alignment. ..."
   "MAQ stands for Mapping and Assembly with Quality."
   "... MAQ 1st indexes read seqs. & scans the ref.genome seq. ...
   6 hash tables ... Given 8-bp reads, e.g., the 6 templates are
   11110000, 00001111, 11000011, 00111100, 11001100, and 00110011, ...
   all reads into memory ... 24-bit hash ..."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.078212.108">doi:10.1101/gr.078212.108</A>]['08] open access,
   s/w@[<A HREF="http://maq.sourceforge.net">http://maq.sourcefor...</A>]['08].
   [Also search for: resequencing MolBio],
   [also search for: short read MolBio].

%A M. L. Kern
%A H. S.Friedman
%T Do conscientious individuals live longer? A quantitative review
%J Health Psychology
%V 27
%N 5
%P ?-?
%M SEP
%D 2008
%K jrnl, c2008, c200x, c20xx, ageing, age, long, life, span, human, lifespan,
   conscientious, conscientiousness, persistent, industrious, organized,
   disciplined
%X "... Higher levels of conscientiousness were significantly and positively
   related to longevity (r = .11, 95% CI = .05-.17). Associations were strongest
   for the achievement (persistent, industrious) & order (organized,
   disciplined) facets of c.. ... Results strongly support the importance of
   conscientiousness-related traits to health across the life span. ..."
   -- [<A HREF="http://dx.doi.org/10.1037/0278-6133.27.5.505">doi:10.1037/0278-6133.27.5.505</A>]['08].

%T Alemtuzumab vs. interferon beta-1a in early multiple sclerosis
%Q The CAMMS223 Trial Investigators
%J NEJM
%V 359
%N 17
%P 1786-1801
%M OCT
%D 2008
%K jrnl, NEJM, c2008, c200x, c20xx, early multiple sclerosis, MS, schlerosis,
   Alemtuzumab,  interferon beta-1a, CD52, trial, health, medical, medicine
%X "... Alemtuzumab, a humanized monoclonal antibody that targets CD52 on
   lymphocytes & monocytes, may be an effective treatment for early MS. ...
   ... sig. reduced the rate of sustained accumulation of disability, [v.]
   interferon beta-1a (9.0% vs. 26.2%; hazard ratio, 0.29; 95% [CI], 0.16 to
   0.54; P < 0.001) & the annualized rate of relapse (0.10 vs. 0.36; hazard
   ratio, 0.26; 95% CI, 0.16 to 0.41; P < 0.001). The mean disability score on a
   10-pt scale improved by 0.39 pt in the alemtuzumab group & worsened by 0.38pt
   in the interferon beta-1a group (P < 0.001). In the a. group, the lesion
   burden ... was reduced, as compared with that in the interferon beta-1a group
   (P=0.005). From month 12 to 36, brain vol. ... increased in the alemtuzumab
   group but decreased in the interferon beta-1a group (P=0.02). ..."
   -- [<A HREF="http://content.nejm.org/cgi/content/short/359/17/1786">nejm</A>]['08].

%A A. Grimson
%A et al
%T Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals
%J Nature
%V 455
%P 1193-1197
%M OCT
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, miRNA, microRNA, PIWI, piRNA, piRNAs,
   evolution, bilaterian, bilateria, animal, bilateral symmetry, miRNAs,
   starlet sea anemone, cnidarian Nematostella vectensis, sponge,
   poriferan Amphimedon queenslandica
%X "In bilaterian animals, such as humans, flies & worms, hundreds of miRNAs,
   some conserved throughout bilaterian evoln, collectively regulate a
   substantial % of the transcriptome. [and] miRNAs, other bilaterian small
   RNAs, known as Piwi-interacting RNAs (piRNAs), protect the g. from
   transposons. ... identify small RNAs from animal phyla that diverged before
   the emergence of the Bilateria. The cnidarian Nematostella vectensis (starlet
   sea anemone), a close rel. to the Bilateria, possesses an extensive
   repertoire of miRNA genes, 2 classes of piRNAs & a complement of proteins
   specific to small-RNA biol. comp. to that of humans. The poriferan Amphimedon
   queenslandica (sponge), one of the simplest animals & a distant relative of
   the Bilateria, also possesses miRNAs, both classes of piRNAs & a full
   complement of the small-RNA machinery. Animal miRNA evoln seems to have been
   relatively dynamic, with precursor sizes & mature miRNA seqs. differing
   greatly between poriferans, cnidarians & bilaterians. Nonetheless, miRNAs &
   piRNAs have been available as classes of riboregulators to shape gene
   expression throughout the evolution & radiation of animal phyla."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07415">doi:10.1038/nature07415</A>]['08].

%A C. L. Kahn
%A B. J. Raphael
%T Analysis of segmental duplications via duplication distance
%J J. Bioinformatics
%V 24
%N 16
%P i133-i138
%D 2008
%K conf, MolBio, c2008, c200x, c20xx, DNA, segment, segmental duplication,
   duplicated
%X "...difficulty in analyzing seg. duplications is that many duplications are
   complex mosaics of fragments of numerous other segmental duplications. ...
   ... novel measure called duplication dist. ... min. # of duplications
   necessary to create a target string by repeated insertions of fragments of a
   source string. We derive an efficient alg. to compute duplication distance,
   & we use the alg. to analyze segmental duplications in the human genome. Our
   analysis reveals possible ancestral relationships between segmental
   duplications including numerous examples of duplications that contain
   multiple, nested insertions of fragments from one or more other duplications.
   ... also identify a small # of segmental duplications that appear to have
   seeded many other duplications in the genome, lending support to a 2-step
   model of segmental duplication in the genome."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn292">doi:10.1093/bioinformatics/btn292</A>['08], or
   -- [<A HREF="http://www.cs.brown.edu/courses/csci2950-c/Papers/Kahn_Raphael_Bioinformatics.pdf">pdf@brown</A>]['08].
   ([Also search for: Tichy block moves].)

%A F. De Bona
%A S. Ossowski
%A K. Schneeberger
%A G. Ratsch
%T Optimal spliced alignments of short sequence reads
%J J. Bioinformatics
%V 24
%N 16
%P i174-i180
%M AUG
%D 2008
%K conf, MolBio, c2008, c200x, c20xx, spliced, splice, alignment, short read,
   reads, QPALMA, deBona, raetsch, site, sites
%X "... QPALMA, for computing accurate spliced alignments which takes advantage
   of the read's quality info. [&] computational splice site predictions. ...
   uses a training set of spliced reads with quality info. & known alignments.
   It uses a large margin approach similar to SVMs to est. its parameters to
   maximize alignment accuracy. In computational experiments, we illustrate that
   the quality information as well as the splice site predictions help to
   improve the alignment quality. [for] mapping of massive amounts of sequencing
   data typically generated by the new technologies, we have combined our method
   with a fast mapping pipeline based on enhanced suffix arrays. Our algs. were
   optimized & tested using reads produced with the Illumina Genome Analyzer for
   the model plant Arabidopsis thaliana. ..."
   -- [<A HREF="http://www.fml.mpg.de/raetsch/projects/qpalma">s/w</A>]['08];
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn300">doi:10.1093/bioinformatics/btn300</A>]['08], or
   -- [<A HREF="http://www.iscb.org/uploaded/css/24/2840.pdf">pdf@iscb</A>].
   [Also search for: short read MolBio] & [also search for: spliced alignment].

%A A. N. Papadopoulos
%A A. Lyritsis
%A Y. Manolopoulos
%T SkyGraph: an algorithm for important subgraph discovery in relational graphs
%J Data Mining and Knowledge Discovery
%V 17
%N 1
%P 57-76
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, sky graph, skygraph, subgraph, skyline,
   microarray application
%X "... propose a methodology to support such preferences by applying subgraph
   discovery in relational graphs towards retrieving important connected
   subgraphs. The importance of a subgraph is determined by: (i) the order of
   the subgraph (the # of vertices) & (ii) the subgraph edge connectivity
   [as in the size of the min-cut set].  The performance of the proposed
   technique is evaluated by using real-life [&] synth. gen. data sets."
   -- [<A HREF="http://dx.doi.org/10.1007/s10618-008-0109-y">doi:10.1007/s10618-008-0109-y</A>]['08].

%A E. C. Hayden
%T How to get the most from a gene test.  New tools squeeze more
   research out of personal genomics
%J Nature
%V 456
%P 11
%D 2008
%K news, MolBio, c2008, c200x, c20xx, zz1108, 23andMe, deCODEme, Promethease,
   Omicia, startup, startups, tool, genetic, test, tests
%X "... much more enlightening than these results, which cost Gall more than
   $1,400, was a free online program called Promethease that he used to further
   analyse the data. ..."
   "... Omicia ... is designing s/w to make sense of entire genome seqs. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/456011a">doi:10.1038/456011a</A>]['08].

%A B. Maher
%T Personal genomes: The case of the missing heritability
%J Nature
%V 456
%P 18-21
%D 2008
%K news, MolBio, c2008, c200x, c20xx, genetic, genetics, genome, disease, trait,
   traits, heredity, heritability, risks, GWAS, CBV, CNVs
%X "When scientists opened up the human genome, they expected to find the
   genetic components of common traits and diseases. But they were nowhere to
   be seen. Brendan Maher shines a light on six places where the missing loot
   could be stashed away. ..."  [12 refs], online 5 Nov 2008.
   -- [<A HREF="http://dx.doi.org/10.1038/456018a">doi:10.1038/456018a</A>]['08].
   (Also see GWAS@[<A HREF="https://en.wikipedia.org/wiki/Genome-wide_association_study">wikip</A>]['20].)

%A J. M.  Rothberg
%A J. H. Leamon
%T The development and impact of 454 sequencing
%J NatureBiotech.
%V 26
%N 10
%P 1117-1124
%M OCT
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, DNA sequencing, technology,
   454 Life Sciences, Roche, pyrosequencing, short read, reads,
   homopolymer repeats, homo polymer, review, intro
%X "... Key breakthroughs in the development of the 454 sequencing platform
   inc. higher throughput, simplified all in vitro sample preparation & the
   miniaturization of sequencing chemistries, enabling massively parallel
   sequencing reactions to be carried out at a scale & cost not previously
   possible. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nbt1485">doi:10.1038/nbt1485</A>]['09],
   -- [<A HREF="http://www.454.com/">454.com</A>]['09],
   "454 GS FLX Titanium series reagents sequence 400-600 million b. / 10hr run
    ... 99% accuracy at the 400th base ... erroneous base calls can be a
    problem with homopolymers ... US patent 7,211,390 (patft.uspto.gov) 1/5/07"
   -- [<A HREF="http://en.wikipedia.org/wiki/454_Life_Sciences">wikip</A>]['09].
   [Also search for: short read MolBio].

%A D. R. Bentley
%A et al
%T Accurate whole human genome sequencing using reversible terminator chemistry
%J Nature
%V 456
%P 53-59
%M NOV
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz1108, human genome, high through put,
   throughput, re sequencing, resequencing, short read, Illumina,
   Yoruba, Nigeria, Nigerian, Africa, African
%X "... an approach that generates several billion bases of accurate nucleotide
   seq. per experiment at low cost. Single molecules of DNA are attached to a
   flat surface, amplified in situ & used as templates for synthetic sequencing
   with fluorescent reversible terminator deoxyribonucleotides. Images ...
   We demonstrate application of this approach to human g. sequencing on
   flow-sorted X chrs. & then scale the approach to determine the genome seq. of
   a male Yoruba from Ibadan, Nigeria. We build an accurate consensus seq. from
   >30 x avg. depth of paired 35-base reads. We characterize 4 million [SNPs] &
   4 hundred thousand structural variants, many of which were prev. unknown.
   ...effective for accurate, rapid & econ. whole-g. re-seq. ..." online Nov 08.
   -- [<A HREF="http://dx.doi.org/10.1038/nature07517">doi:10.1038/nature07517</A>]['08].
   [Also search for: short read MolBio] and
   [also search for: resequencing MolBio].

%A J. Wang
%A et al
%T The diploid genome sequence of an Asian individual
%J Nature
%V 456
%P 60-65
%M NOV
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, human, nuclear, genome, nGenome, genomes,
   asian, Asia
%X "... 1st diploid genome seq. of an Asian individual. ... sequenced to
   36-fold avg. coverage using massively parallel sequencing tech.. We aligned
   the short reads onto the NCBI human reference genome to 99.97% coverage, &
   guided by the ref. g., we used uniquely mapped reads to assemble a
   high-quality consensus sequence for 92% of the Asian individual's genome. We
   identified approximately 3 million single-nucleotide polymorphisms (SNPs)
   inside this region, of which 13.6% were not in the dbSNP database. ..."
   ... data in deposited EBI/NCBI short read archive (accession # ERA000005).
   see http://yh.genomics.org.cn   SNPs & indels have been submitted to NCBI
   dbSNP and will be available in ver. 130.
   -- [<A HREF="http://dx.doi.org/10.1038/nature07484">doi:10.1038/nature07484</A>][08].
   [Also search for: human nuclear genome].

%A C. Comins
%A L. Heinemann
%A K. Harrington
%A A. Melcher
%A J. De Bono
%A H. Pandha
%T Reovirus: Viral therapy for cancer 'as nature intended'
%J Clinical Oncology
%V 20
%N 7
%P 548-554
%D 2008
%K jrnl, c2008, c200x, c20xx, health, medicine, reovirus, cancer, tumor, tumour,
   oncolytic, cell, cytotoxic, cytotoxicity, therapy, deBono
%X "Oncolytic viruses are tumour selective & able to lyse cancer cells after
   infection. Reovirus is an example of a wild-type oncolytic virus & is
   currently being investigated as a potential novel therapy for cancer. This
   overview gives a brief description of what is known about reovirus biology &
   summarises the preclinical data related to its oncolytic ability. The
   completed & ongoing clinical trials involving reovirus, both as a single
   agent & in combination with chemotherapy & radiotherapy, ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.clon.2008.04.01">doi:10.1016/j.clon.2008.04.01</A>]['08].

%A C. B. Do
%A C.-S. Foo
%A S. Batzoglou
%T A max-margin model for efficient simultaneous alignment and folding of
   RNA sequences
%J Proc. 16th ISMB
%P i68-i76
%D 2008
%O Proc. is a supplement to J. Bioinformatics, 24(13), i68-i76, 2008
%K conf, ISMB, MolBio, c2008, c200x, c20xx, RNA, secondary structure, consensus,
   fold, folding, sequence, maximum, max margin, RAF, CONTRAfold, CONTRAlign
%X "... RAF (RNA Alignment & Folding), an efficient alg. for simultaneous
   alignment & consensus folding of unaligned RNA seqs.. ... RAF exploits
   sparsity in the set of likely pairing & alignment candidates for each
   nucleotide (as identified by the CONTRAfold or CONTRAlign programs) to
   achieve an effectively quadratic running time for simultaneous pairwise
   alignment & folding. RAF's fast sparse dynamic programming, in turn, serves
   as the inference engine within a discriminative machine learning alg. for
   parameter estimation. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn177">doi:10.1093/bioinformatics/btn177</A>]['08].

%A M. Kalaev
%A V. Bafna
%A R. Sharan
%T Fast and accurate alignment of multiple protein networks
%J RECOMB
%P 246-256
%D 2008
%K conf, RECOMB, RECOMB08, MolBio, c2008, c200x, c20xx, network, networks,
   protein, interaction, alignment, layered, graph, graphAlignment
%X "... efficient multiple n/w alignment alg.. ... present a novel framework
   for the problem. ...a novel representation of multiple n/ws that is only
   linear in their size as opposed to current exponential representations.
   ...alg. is v.efficient, being capable of aligning 10 n/ws with tens of
   thousands of proteins each in minutes. ... alg. outperforms a previous
   strategy for the problem that is based on progressive alignment, & produces
   results that are more in line with current biological knowledge."
 * Network ~ layer.  Inter-layer edge (prot[i], prot[j]) if seq simlar *
   pdf@[<A HREF="http://www.cs.tau.ac.il/~roded/nbm.pdf">tau.ac.il</A>]['08],
   or [<A HREF="http://dx.doi.org/10.1007/978-3-540-78839-3_21">doi:10.1007/978-3-540-78839-3_21</A>]['08].
   Also see [<A HREF="http://www.cs.tau.ac.il/~roded/">auth3</A>].
   [Also search for: networkBlast]  and  [also search for: graphAlignment].

%A M. Kalaev
%A M. Smoot
%A T. Ideker
%A R. Sharan
%T NetworkBLAST: Comparative analysis of protein networks
%J J. Bioinformatics
%V 24
%N 4
%P 594-596
%D 2008
%X jrnl, MolBio, c2008, c200x, c20xx, protein, interaction, network,
   networkBlast, graphAlignment, motif
%X "The identification of protein complexes is a fundamental challenge in
   interpreting protein-protein interaction data. Cross-species analysis allows
   coping with the high levels of noise that are typical to these data. The
   NetworkBLAST web-server provides a platform for identifying protein complexes
   in p.-p. interaction n/ws. It can analyze a single n/w or two n/ws from
   different species. In the latter case, NetworkBLAST outputs a set of
   putative complexes that are evol. conserved across the two n/ws."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btm630">doi:10.1093/bioinformatics/btm630</A>]['08].
   Server@[<A HREF="http://www.cs.tau.ac.il/~roded/networkblast.htm">tau.ac.il</A>]['08].
   Also see [<A HREF="http://www.cs.tau.ac.il/~roded/">auth4</A>].
   [Also search for: graphAlignment].

%A A. McCann
%A J. A. Cotton
%A J. O. McInerney
%T The tree of genomes: An empirical comparison of genome phylogeny
   reconstruction methods.
%J BMC Evolutionary Biology
%V 8
%P 312
%M NOV
%D 2008
%K jrnl, eJrnl, MolBio, c2008, c200x, c20xx, evolutionary, phylogenetic, tree,
   trees, method, intro, survey, conditioned reconstruction,
   horizontal gene transfer, HGT
%X "... reconstructing species phylogenies has moved from the analysis of a
   single gene to the analysis of multiple g. & even completed genomes. The
   simplest method of scaling up is to use familiar analysis methods on a larger
   scale & this is the most popular approach. However, duplications & losses of
   genes along with horizontal gene transfer (HGT) can lead to a situation where
   there is only an indirect relationship between gene & genome phylogenies. ...
   examine 5 widely-used approaches & their variants to see if indeed they are
   more-or-less saying the same thing. ... focus on Conditioned Reconstruction
   as it is a method that is designed to work well even if HGT is present. ...
   ...confirm ... method has a sys. bias. We show that no 2 methods produce the
   same results & most current methods of inferring genome phylogenies produce
   results that are sig. different to other methods. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2148-8-312">doi:10.1186/1471-2148-8-312</A>]['08].

%A W. Miller
%A et al
%T Sequencing the nuclear genome of the extinct woolly mammoth
%J Nature
%V 456
%P 387-390
%M NOV
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz1208, woolly mammoth, wooly, mamoth,
   Mammuthus primigenius, nuclear, genome, nGenome, Pleistocene, old, fossil,
   ancient, mammoths, elephantid, DNA
%X "... '94, 2 indep. groups extracted DNA from several Pleistocene epoch
   mammoths & noted differences among individual specimens ... ancient DNA is
   often fragmented & damaged, & studies to date have typically focused on short
   mitochondrial seqs., ... we describe 4.17 billion bases (Gb) of seq. from
   several mammoth specimens, 3.3 b. (80%) of which are from the woolly mammoth
   (Mammuthus primigenius) genome & thus comprise an extensive set of genome-
   -wide seq. ... support earlier reports that elephantid genomes exceed 4Gb.
   The est. divergence rate between mammoth & African elephant is half of that
   b/w human & chimp.. The obs. # of nucleotide diffs. between 2 particular
   mammoths was ~ 1/8 of that b/w one of them & the African elephant, corr. to
   a sepn between the mammoths of 1.5-2.0 Myr. The est. prob. that orthologous
   e. & m. amino acids differ is 0.002, corr. to about 1 residue/protein. ..."
   "Seq.@NCBI trace arch. accession # [<A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=search&term=SRA001810">SRA001810</A>]"
   -- [<A HREF="http://dx.doi.org/10.1038/nature07446">doi:10.1038/nature07446</A>]['08],
   mammoth@[<A HREF="http://mammoth.psu.edu/">psu</A>].
   [Also search for: MolBio ancient DNA].

%A Xin
%A Stone
%T Tainted milk scandal: Chinese Probe Unmasks High-Tech Adulteration with
   Melamine
%J Science
%P 1310-1311
%M NOV
%D 2008
%K news, c2008, c200x, c20xx, China, food adulteration, law, illegal, baby,
   milk
%X "A weeks-long investigation into China's tainted milk scandal has left
   scientists astonished by the technical sophistication of those who used
   melamine to adulterate food products."
   -- [<A HREF="http://dx.doi.org/10.1126/science.322.5906.1310">doi:10.1126/science.322.5906.1310</A>]['08].

%A C. G. Mullighan
%A L. A. Phillips
%A X. Su
%A J. Ma
%A C. B. Miller
%A S. A. Shurtleff
%A J. R. Downin
%T Genomic analysis of the clonal origins of relapsed acute lymphoblastic
   leukemia
%J Science
%V 322
%N 5906
%P 1377-1380
%M NOV
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, origin, cancer, relapse, abnormality,
   abnormalities, copy number variation, CNA, lymphoblastic leukemia,
   childhood, child, clonal, variation
%X "Most children with [ALL] can be cured, but the prognosis is dismal for the
   minority of patients who relapse ... performed genome-wide DNA copy #
   analyses on matched diagnosis & relapse samples from 61 pediatric patients
   with ALL. The diagnosis & relapse samples typically showed different patterns
   of genomic copy # abnormalities (CNAs), with the CNAs acquired at relapse
   preferentially affecting genes implicated in cell cycle regulation & B cell
   development. Most relapse samples lacked some of the CNAs present at
   diagnosis, which suggests that the cells responsible for relapse are
   ancestral to the primary leukemia cells. Backtracking studies revealed that
   cells corresponding to the relapse clone were often present as minor subpopns
   at diagnosis. ... suggest that genomic abnormalities contrib. to ALL relapse
   are sel. for during treatment & they pt to new targets for therap... "
   -- [<A HREF="http://dx.doi.org/10.1126/science.1164266">doi:10.1126/science.1164266</A>]['08].
   [Also search for: MolBio cancer clonal].

%A B. Calcott
%A D. Balcan
%A P. A. Hohenlohe
%T A publish-subscribe model of genetic networks
%J PLoS One
%V 3
%N 9
%P e3245
%D 2008
%K jrnl, eJrnl, MolBio, c2008, c200x, c20xx, zz1208, PLoS, gene, regulatory,
   regulation, network, networks, Boolean NK model, attractor, attractors,
   state space, degree distribution, miRNA, ncRNA, ncRNAs
%X "... simple model of genetic regulatory n/ws in which reg. connections among
   genes are mediated by a limited # of signaling molecules. Each gene in our
   model produces (publishes) a single gene product, which regulates the
   expression of other genes by binding to regulatory regions that corr.
   (subscribe) to that product. We explore the consequences ... for the
   properties of single n/ws & for the evolution of populations of n/ws. Degree
   distributions of randomly constructed n/ws, particularly multimodal in-degree
   distributions, which depend on the length of the reg.seqs. & the # of poss.
   gene products, differed from simpler Boolean NK models. In simulated evoln of
   populations of n/ws, single mutations in regulatory or coding regions
   resulted in multiple changes in regulatory connections among genes, or
   alternatively in neutral change that had no effect on phenotype. This
   resulted in remarkable evolvability in both # & length of attractors, leading
   to evolved n/ws far beyond the expectation of these measures based on random
   distributions. Surprisingly, this rapid evolution was not accompanied by
   changes in degree distribution; degree distribution in the evolved n/ws was
   not substantially different from that of randomly generated n/ws. The  ,,,
   model also allows exogenous gene products to create an environment, which may
   be noisy or stable, in which dynamic behavior occurs. In simulations, n/ws
   were able to evolve moderate levels of both mutational & env'l robustness."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0003245">doi:10.1371/journal.pone.0003245</A>]['08].

%A C. Pichon
%A B. Felden
%T Small RNA gene identification and mRNA target predictions in bacteria
%J J. Bioinformatics
%V 24
%N 24
%P 2807-2813
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz1208, sRNA, sRNAs, miRNA, RNA, predict,
   prediction, bacteria, bacterial, bacterium, gene regulation, virulence
%X "Bacterial small ribonucleic acids (sRNAs) that are not ribosomal & transfer
   or messenger RNAs were initially identified in the 60s, ... [but] fns are
   still under active investigation today. ... play central roles in gene
   expression regulation ... some are also implicated in bacterial virulence.
   ... large subset of these sRNAs act by an antisense mechanism thanks to
   pairing interactions with dedicated mRNA targets, usually around their
   translation start sites, to modulate gene expression at the
   posttranscriptional level.  ... computational analyses of the bacterial
   genomes ... have predicted the existence of a plethora of sRNAs, some ...
   confirmed to be expressed in vivo. ... review ... "     (yes V.24, No.24).
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn560">doi:10.1093/bioinformatics/btn560</A>]['08].

%A J. R. Miller
%A A. L. Delcher
%A S. Koren
%A E. Venter
%A B. P. Walenz
%A A. Brownley
%A J. Johnson
%A K. Li
%A C. Mobarry
%A G. Sutton
%T Aggressive assembly of pyrosequencing reads with mates
%J J. Bioinformatics
%V 24
%D 24
%P 2818-2824
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, short read, reads, Celera, CABOG, ABI,
   FLX, sequence assembly, assembler, mate pair, best overlap graph, greedy,
   tangles
%X "... Celera Assembler was modified for combinations of ABI 3730 & '454' FLX
   reads. The revised pipeline called CABOG (Celera Assembler with the Best
   Overlap Graph) is robust to homopolymer run length uncertainty, high read
   coverage & heterogeneous read lengths. In tests on 4 genomes, it generated
   the longest contigs among all assemblers tested. It exploited the mate
   constraints provided by paired-end reads from either platform to build larger
   contigs & scaffolds, which were validated by comparison to a finished
   reference sequence. A low rate of contig mis-assembly was detected in some
   CABOG assemblies, ... reduced in the presence of sufficient mate pair data."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn548">doi:10.1093/bioinformatics/btn548</A>]['08].
   "open-source s/w@[<A HREF="http://wgs-assembler.sf.net">sf.net</A>]".
   "discards '454' reads that include at least one 'N'"
   "recognizes mated reads as those [containing] '454' linker seqs."
   "read-trimming step"    "overlaps ... seed is a k-mer ... k=22"
   "cycles eliminated by deletion of one [arb.] edge"
   [Also search for: short read MolBio].

%A M. A. Wozniak
%A A. P. Mee
%A R. F. Itzhak
%T Herpes simplex virus type 1 DNA is located within Alzheimer's disease
   amyloid plaques
%J J. Pathology
%V 217
%N 1
%P 131-138
%M SEP
%D 2008
%K jrnl, c2008, c200x, c20xx, zz1208, medical, medicine, Alzheimer's disease,
   Alzheimers, herpes, HSV, HSV1, cold sores, sore, beta amyloid plaque, Abeta
%X "... used in situ [PCR] to detect herpes simplex virus type 1 DNA, &
   immunohistochemistry or thioflavin S staining to detect amyloid plaques.
   ... striking localization of [HSV1] DNA within plaques: in A's disease brains
   90% of the plaques contained the viral DNA & 72% of the DNA was assoc. with
   plaques; in aged normal brains, which contain amyloid ps. at a lower freq.,
   80% of plaques contained herpes simplex virus type 1 DNA but only 24% of the
   viral DNA was plaque-associated (p < 0.001). We suggest ... because in aged
   normal individuals, there is a lesser production &/or greater removal of
   beta-amyloid (Abeta), so that less of the viral DNA is seen to be assoc. with
   Abeta in the brain.  ... suggest that this virus is a major cause of amyloid
   ps. & hence probably a sig. aetiological factor in A's disease ... pt to
   [use] of antiv. agents to treat the disease & possibly of vaccination to
   prevent it."
   -- [<A HREF="10.1002/path.2449">doi:10.1002/path.2449</A>]['08].

%A G. J. Faulkner
%A A. R. Forrest
%A A. M. Chalk
%A K. Schroder
%A Y. Hayashizaki
%A P. Carninci
%A D. A. Hume
%A S. M. Grimmond
%T A rescue strategy for multimapping short sequence tags refines surveys of
   transcriptional activity by CAGE
%J Genomics
%V 91
%N 3
%P 281-288
%M MAR
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, uniQld, CAGE, multimap, multimapping,
   multi mapping, short, tag, read, reads, survey, transcriptome, fantom,
   multiple locations, mouse
%X "... (CAGE) is a high-throughput, tag-based method designed to survey the 5'
   end of capped full-length cDNAs. ...  A drawback of the CAGE approach ... has
   been the removal of as many as 40% of CAGE seq. tags due to their mapping to
   multiple genomic locations. ... a novel strategy to assign CAGE tags to their
   most likely source promoter region. ... the % of protein-coding mouse ...
   detected ... improved from 42.9 to 57.8% ... with no red'n in CAGE to
   microarray correlation. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ygeno.2007.11.003">doi:10.1016/j.ygeno.2007.11.003</A>]['08].
   -- [<A HREF="http://grimmond.imb.uq.edu.au/sean.html">Grimmond</A>]['08].

%A J. Bedo
%T Microarray design using Hilbert-Schmidt independence criterion
%J 3rd IAPR Int. Conf., PRIB
%P 288-298
%I SpringerVerlag
%S LNBI
%V 5265
%M OCT
%D 2008
%K conf, MolBio, PRIB, c2008, c200x, c20xx, microarray, feature selection,
   subset, HSIC, Hilbert Schmidt independence criterion, NICTA
%X "... selecting a small subset of clones from a large pool for creation of a
   microarray plate. A new kernel based ... experiments indicate that subsets
   sel. by the HSIC resulted in equiv. or better perf. than supervised feature
   seln [and] the subsets are not target specific."

%A A. Morgulis
%A G. Coulouris
%A Y. Raytselis
%A T. L. Madden
%A R. Agarwala
%A A. A. Schaffer
%T Database indexing for production MegaBLAST searches
%J J. Bioinformatics
%V 24
%N 16
%P 1757-1764
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, search, query, megaBlast, blast, miBlast,
   makembindex, seed, seeds
%X "... developed a new version of the MegaBLAST module of BLAST that does the
   initial phase of finding short seeds for matches by searching a DB index.
   ... developed a program makembindex that preprocesses the DB into a data
   struct. for rapid seed searching. We show that the new 'indexed MegaBLAST'
   is faster than the 'non-indexed' version for most practical uses.  ...
   indexed MegaBLAST is faster than miBLAST, another implementation of BLAST
   nucleotide searching with a preprocessed DB for most of the 200 queries
   we tested. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn322">doi:10.1093/bioinformatics/btn322 </A>]['09].
   s/w@[<A HREF="http://www.eecs.umich.edu/miblast/download.html">umich</A>]['09].
   [Also search for: miBlast].

%A T. D. Harris
%A et al
%A Z. Xie
%T Single-molecule DNA sequencing of a viral genome
%J Science
%V 320
%N 5872
%P 106-109
%M APR
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, single molecule sequencing, DNA,
   technology, viral, virus, Helicos, S. R. Quake
%X "... report an amplification-free method for determining the n.sequence of
   > 280,000 individual DNA molecules simultaneously. A DNA polymerase adds
   labeled nucleotides to surface-immobilized primer-template duplexes in
   stepwise fashion, & the asynchronous growth of individual DNA molecules was
   monitored by fluorescence imaging. Read lengths of > 25 bases & equivalent
   phred software program quality scores approaching 30 were achieved. We used
   this method to sequence the M13 virus to an average depth of > 150x & with
   100% coverage; thus, we resequenced the M13 genome with high-sensitivity
   mutation detection. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1150427">doi:10.1126/science.1150427</A>]['09].
   (Also see [<A HREF="http://www.helicosbio.com/">helicosbio.com</A>]['09].)
   [Also search for: MolBio single molecule sequencing].

%T RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity
%E K. V. Morris
%I CaisterAcademicPress
%P 228
%M MAR
%D 2008
%K book, text, MolBio, c2008, c200x, c20xx, RNA, DNA, gene, genes, regulation,
   activation, silencing, miRNA, siRNA, RNAi, saRNA, RNAa epigenetics
%X "... Topics include: gene silencing and gene activation, the hammerhead
   ribozyme, epigenetic regulation, RNAi, microRNA, and pyknons. ... intended
   for readers with teaching or research interests in RNA, the regulation of
   gene expression, genetics, genomics or molecular biology. ..."
   1st ed, hb, stg150, uk us isbn:1904455255; uk us isbn13:978-1904455257.

%A A. S. Konagurthu
%A P. J. Stuckey
%A A. M. Lesk
%T Structural search and retrieval using a tableau representation of
   protein folding patterns
%J J. Bioinformatics
%V 24
%N 5
%P 645-651
%D 2008
%K jrnl, MolBio, ArunK, c2008, c200x, c20xx, TableauSearch, tableau search,
   TabSearch, protein structure, similar, score, fold, folds, search, MUSTANG,
   AMLesk, maximally, max, similar subtableau, integer, quadratic, programming
%X "... provide several methods to search for similar folding patterns using
   a concise tableau rep'n of proteins that encodes the relative geometry
   of secondary structural elts. ... [1.] allows the extraction of identical &
   v.closely-related p. folding patterns in const.-time (per hit). Next, we
   address the hard computational problem of extraction of maximally-similar
   subtableaux, when comparing 2 tableaux. We solve the problem using
  [QAP] Quadratic & Linear int. prog. formulations & demo. their power to
   identify subtle structural similarities, esp. when protein structs.
   sig. diverge. Finally, we describe a rapid & accurate method for
   comparing a query structure against a database of protein domains,
   TableauSearch. TableauSearch is rapid enough to search the entire structural
   [DB] in secs. on a std desktop computer. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btm641">doi:10.1093/bioinformatics/btm641</A>]['09] (free?),
   TabSearch@[<A HREF="http://hollywood.bx.psu.edu/TabSearch/">psu</A>]['10].
   [Also search for: MolBio Mustang].

%A M. J. Chaisson
%A P. A. Pevzner
%T Short read fragment assembly of bacterial genomes
%J Genome Res.
%V 18
%P 324-330
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, short read, reads, sequence assembly,
   Eulerian, EulerSR, Euler SR, USR, EulerUSR, A-Bruijn, aBruijn,
   graphs, assembler
%X "... Current fragment assembly algs. have been implemented & optimized for
   mate-paired Sanger-based [long] reads, & thus do not perform well on short
   reads produced by short read technologies. ... new Eulerian assembler that
   generates nearly optimal short read assemblies of bacterial genomes & ...
   assemble reads in the case of the popular hybrid protocol when short & long
   Sanger-based reads are combined."  (online Dec '07.)
      "... Pevzner et al. ('04) proposed a new Eulerian assembler based on
   the notion of A-Bruijn graphs. ... deals with errors in reads by inducing
   vertices with ungapped alignments that allow mismatches ...
   graph-simplification techniques that remove erroneous edges. ... A similar
   approach was recently described by Myers('05) & Medvedev et al.('07). ..."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.7088808">doi:10.1101/gr.7088808</A>]['09],
   eulerSR@[<A HREF="http://euler-assembler.ucsd.edu/portal/">ucsd</A>]['09].
   [Also search for: short read MolBio],
   [also search for: sequence assembly MolBio].

%A B. Paten
%A J. Herrero
%A K. Beal
%A S. Fitzgerald
%A E. Birney
%T Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment
   with paralogs
%J Genome Res.
%V 18
%N 11
%P 1814-1828
%M NOV
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, Enredo, Pecan, paralog, whole, genomes,
   alignment
%X "Pairwise whole-genome alignment involves the creation of a homology map,
   capable of performing a near complete transformation of 1 g. into another.
   For multiple gs. this problem is generalized to finding a set of consistent
   homology maps for converting each genome ..."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.076554.108">doi:10.1101/gr.076554.108</A>]['09].

%A G. Ciriello
%A C. Guerra
%T A review on models and algorithms for motif discovery in
   protein-protein interaction networks
%J Briefings in Functional Genomics
%V 7
%N 2
%P 147-156
%M MAR
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, graph, model, motif, protein, PPI,
   discovery, pattern, interaction network, random, intro, review, introduction,
   survey, NeMoFINDER, MFINDER
%X "... The approaches proposed in the literature often differ in the defn of a
   motif, the way the occurrences of a motif are counted & the way their stat.
   significance is assessed. This has strong implications on the computational
   complexity of the discovery process & on the type of results that can be
   expected. This review presents in a systematic way the different comp'l
   settings outlining their main features and limitations."  [70 refs].
   -- [<A HREF="http://dx.doi.org/10.1093/bfgp/eln015">doi:10.1093/bfgp/eln015</A>]['10].
   [Also search for: network motif discovery].

%A M. P. Styczynski
%A K. L. Jensen
%T I. Rigoutsos
%A G. Stephanopoulos
%T BLOSUM62 miscalculations improve search performance
%J NatureBiotech.
%V 26
%N 3
%P 274-275
%M MAR
%D 2008
%K note, errata, c2008, c200x, c20xx, zz0411, MolBio, BLOSUM, Henikoff, blocks,
   blosum62, blosum50, error, software, miscalculation, mistake,
   protein, amino acid, substitution matrix, matrices
%X "... we noticed errors in the s/w source code used to create the initial
   BLOSUM family of matrices
   (@ ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blosum/blosum.tar.Z).
   The result of these errors is that the BLOSUM matrices - BLOSUM62, BLOSUM50,
   etc. - are quite different from the m. that should have been calc. using the
   alg. described by Henikoff & H.. Obviously, minor errors in research, &
   particularly in s/w src.code, are quite common. This case is noteworthy
   for three reasons: 1st, the BLOSUM m. are ubiquitous in comp.biol.;
   2nd, these errors have gone unnoticed for 15 years; & 3rd, the
   'incorrect' matrices perform better than the 'intended' matrices. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nbt0308-274">doi:10.1038/nbt0308-274</A>]['11].
   [Also search for: MolBio substitution matrix] and
   [also search for: MolBio BLOSUM].

%A D. Hambrook
%A et al
%T Empathy, systemizing, and autistic traits in anorexia nervosa: A pilot study
%J British J. of Clinical Psychology
%J British Psychological Soc.
%V 47
%N 3
%P 335-339
%M SEP
%D 2008
%K jrnl, c2008, c200x, c20xx, anorexia nervosa, anorexic, autism, autistic,
   spectrum, mental health, trait, empathy, social
%X "... examined whether patients with AN would display an empathizing-
   -systemizing psychometric profile similar to that found in autism spectrum
   disorders (ASD), & whether people with AN would score highly on a measure of
   autistic traits. ...  healthy controls (HC) ... AN patients & HCs did not
   differ significantly in their self-reported empathy & systemizing. AN
   patients scored sig. higher than HCs on the autism-spectrum quotient. ..."
   -- [<A HREF="http://dx.doi.org/10.1348/014466507X272475">doi:10.1348/014466507X272475</A>]['09].
   (Also see [<A HREF="http://www.newscientist.com/article/mg20227054.900-anorexia-linked-to-autistic-thinking.html">New Sci.</A>]['09].)

%A V. Pandey
%A R. C. Nutter
%A E. Prediger
%T Applied Biosystems SOLiD system: Ligation-based sequencing
%B Next-Generation Genome Sequencing: Towards Personalized Medicine
%E M. Janitz
%I Wiley
%P 29-41
%M SEP
%D 2008
%K MolBio, c2008, c200x, c20xx, SOLiD System, Solid, sequencing, technology,
   Applied Biosystems, DNA, data, diBase, colour, color, space,
   AppliedBiosystems, Life Technologies, short read, reads
%X In, 1st ed 2008, us$160; uk us isbn:3527320903; uk us isbn13:978-3527320905,
   -- [<A HREF="http://www3.appliedbiosystems.com/">AB</A>]['09].
   Colour      A   C   G   T  -2nd base
   Space   |A|blu grn yel red|
       1st |C|grn blu red yel|
       base|G|yel red blu grn|
           |T|red yel grn blu| -[<A HREF="http://www.iscb.org/uploaded/css/36/12104.pdf">iscb</A>]['09],
   "2008 merger Applied Biosystems & Invitrogen ... new co. Life Technologies"
   -- [<A HREF="http://en.wikipedia.org/wiki/Applied_Biosystems">wikip</A>]['09].
   [Also search for: short read MolBio].

%A S. J. Pidot
%A H. Hong
%A T. Seemann
%A J. L. Porter
%A M. J. Yip
%A A. Men
%A M. Johnson
%A P. Wilson
%A J. K. Davies
%A P. F. Leadlay
%A T. P. Stinear
%T Deciphering the genetic basis for polyketide variation among mycobacteria
   producing mycolactones
%J BMC Genomics
%V 9
%P 462
%D 2008
%K jrnl, eJrnl, MolBio, c2008, c200x, c20xx, mycobacteria, mycobacterium,
   Tim Stinear, microbiol, unimelb, Torsten, VBC
%X "... The mycolactone PKS locus on pMUM002 revealed the same large, 3-gene
   structure and extraordinary pattern of near-identical PKS domain seq.
   repetition as observed in pMUM001 with greater than 98.5% nucleotide identity
   among domains of the same fn. Intra- & inter-strain comparisons suggest that
   the extreme seq. homogeneity seen among the mls PKS genes is caused by freq.
   recombination-mediated domain replacement. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2164-9-462">doi:10.1186/1471-2164-9-462</A>]['09].
   (Last auth @[<A HREF="http://www.microbiol.unimelb.edu.au/research/groups/stinear.html">microbiol.unimelb</A>] as of ['09].)

%A V. Yanovsky
%A S. R. Rumble
%A M. Brudno
%T Read mapping algorithms for single molecule sequencing data
%J Proc. of Workshop on Algorithms in Bioinformatics (WABI)
%P ?-?
%D 2008
%K wShop, c2008, c200x, c20xx, MolBio, single molecule, Heliscope, SMS,
   SHRiMP, short read, reads, mapping, weighted sequence graph, WSG
%X "... Heliscope ... higher error rate ... weighted sequence graph (WSG) ...
   fast impl. of Smith Waterman ... vectorized instructions ...
   part of the SHort Read Mapping Package (SHRiMP) ..."  [13 refs].
   pdf@[<A HREF="http://www.cs.toronto.edu/~brudno/yanovsky_wabi08.pdf">toron'o</A>],
   -- [<A HREF="http://www.cs.toronto.edu/~brudno/">auth3</A>]['09],
   -- [<A HREF="http://compbio.cs.toronto.edu/shrimp">shrimp</A>]['09].
   [Also search for: short read MolBio].

%A A. Clements
%A F. Gabouriaud
%A J. F. Duval
%A J. L. Farn
%A A. W. Jenney
%A O. Wijburg
%A E. L. Hartland
%A R. A. Strugnell
%T The major surface-associated saccharides of Klebsiella pneumoniae contribute
   to host cell association
%J PloS ONE
%V 3
%P e3817
%D 2008
%K jrnl, eJrnl, MolBio, c2008, c200x, c20xx, Hartland, microbiol, uniMelb,
   bacterium, bacteria, bacterial, immune system, Klebsiella pneumoniae
%X "... bacterial surface provides the 1st barrier against innate immune
   mechanisms as well as mediating attachment to cells/surfaces to resist
   clearance.  ... the 2 major polysaccharide layers, capsule &
   lipopolysaccharide (LPS), were absent or truncated, to investigate the
   ability of these layers to protect against innate immune mechanisms ...
   The capsule alone was found to be essential for resistance to complement
   mediated killing while both capsule & LPS were involved in cell-assoc.,
   albeit through different mechanisms. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0003817">doi:10.1371/journal.pone.0003817</A>]['09].
   -- [<A HREF="http://www.microbiol.unimelb.edu.au/people/hartland/pub.html">auth7</A>]['09].

%A J. Novembre
%A et al
%A C. D. Bustamante
%T Genes mirror geography within Europe
%J Nature
%V 456
%P 98-101
%M NOV
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz0609, population genetics, Europe, map,
   European, human, race, races, racial, genetic, differentiation, variation
%X "... Advances in high-throughput genotyping technology have markedly improved
   our understanding of global patterns of human genetic var'n & suggest the
   potential to use large samples to uncover var'n among closely spaced popns..
   ... characterize genetic v. in a sample of 3,000 Euro. individuals genotyped
   at over half a million var. DNA sites in the human genome. Despite low avg.
   levels of genetic differentiation among Europeans ... close corr. btwn
   genetic & geog. dists.; ... geographical map of Europe arises naturally as
   an efficient 2-dimensional summary of genetic variation in Europeans. ...
   ... DNA can ... infer their geog. origin often to within a few hundred km."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07331">doi:10.1038/nature07331</A>]['09].
   There is an Addendum (13 November 2008) associated with this document.
   (Also see [<A HREF="http://www.eeb.ucla.edu/Faculty/Novembre/">Novembre lab</A>]['09],
   and [<A HREF="http://alice.berkeley.edu/">Bustamante lab</A>]['09].)

%A M. P. Cox
%A et al
%A M. F. Hammer
%T Testing for archaic Hominin admixture on the X-chromosome: Model likelihoods
   for the modern human RRM2P4 region from summaries of genealogical topology
   under the structured coalescent
%J Genetics
%V 178
%P 427-437
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz0609, human, evolution, migration,
   x chromosome, Hominin, RRM2P4, Xchromosome, Xchr, chrX, Adam, Hammer lab,
   population genetics, stats
%X pdf@[<A HREF="http://hammerlab.biosci.arizona.edu/publications/Cox_2008_Genetics_v178_p427.pdf">.arizona.edu</A>]['09],
   -- [<A HREF="http://hammerlab.biosci.arizona.edu/publications/supplementary_data/Cox_2008_Genetics_Supplemental_Materials.pdf">Supplemental_Mat.</A>]['09].
   (Also see [<A HREF="http://hammerlab.biosci.arizona.edu">hammerlab@ariz.</A>]['09].)

%A B. H. Junker
%A F. Schreiber
%T Analysis of Biological Networks
%I Wiley
%P 368
%D 2008
%K book, text, MolBio, c2008, c200x, c20xx, zz0609, biological networks,
   network, biol, motifs
%X "... intro. to the structural analysis of bio. n/ws at the interface of
   bio.  & computer sci..  ... overview of biological n/ws & graph theory/graph
   algs. & goes on to explore: global n/w properties, n/w centralities, n/w
   motifs, n/w clustering, Petri nets, signal transduction & gene reg'n n/ws,
   protein interaction n/ws, metabolic n/ws, phylogenetic n/ws, ecological n/ws,
   and correlation n/ws."
   1st ed 2008, hb us$72; uk us isbn:0470041447; uk us isbn13:978-0470041444.
   [Also search for: MolBio network motif].

%A H. Lin
%A Z. Zhang
%A M. Q. Zhang
%A M. Li
%T ZOOM! Zillions of oligos mapped
%J J. Bioinformatics
%V 24
%N 21
%P 2431-2437
%M NOV
%D 2008
%K jrnl, MolBio, HaoLin, c2008, c200x, c20xx, zoom, map, align, short reads
%X "... framework for how full sensitivity mapping can be done in the most
   efficient way, via spaced seeds. Using the framework, we have developed ...
   ZOOM, which is able to map the Illumina/Solexa reads of 15x coverage of a
   human genome to the ref. h.genome in 1 CPU-day, allowing 2 mismatches, at
   full sensitivity. ..."
   -- [<A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn416">www</A>]['09],
   zoom@[<A HREF="http://www.bioinformaticssolutions.com/products/zoom/index.php">bioinformaticssolutions</A>][6/'09],
   [Also search for: short read MolBio].

%A F. M. Sansom
%A P. Riedmaier
%A H. J. Newton
%A M. A. Dunstone
%A C. E. Muller
%A H. Stephan
%A E. Byres
%A T. Beddoe
%A J. Rossjohn
%A P. J. Cowan
%A A. J. F. d'Apice
%A S. C. Robson
%A E. L. Hartland
%T Enzymatic properties of an ecto-nucleoside triphosphate diphosphohydrolasa
   from Legionella pneumophila
%J J. Biol. Chem.
%V 283
%N 19
%P 12909-12918
%M MAY
%D 2008
%K jrnl, JBC, MolBio, c2008, c200x, c20xx, Triphosphate Diphosphohydrolase,
   Legionella pneumophila, bacteria, bacterium, Lpg1905, ATP, ADP, NTPDase
%X "... Recently, we id. an ecto-nucleoside triphosphate diphosphohydrolase
   (NTPDase) from L. pneumophila, termed Lpg1905, ... the 1st prokaryotic
   member of the CD39/NTPDase1 family of enzymes, ... Here we ex. the substrate
   specificity of Lpg1905 & showed that apart from ATP & ADP, the enzyme
   catalyzed the hydrolysis of GTP & GDP but had limited activity against CTP,
   CDP, UTP, & UDP. Based on [AA] residues conserved in the apyrase conserved
   regions of eukaryotic NTPDases, we generated 5 site-directed mutants,
   Lpg1905E159A, R122A, N168A, Q193A, & W384A. Although the mutations E159A,
   R122A, Q193A, & W384A abrogated activity completely, N168A resulted in
   decreased activity caused by reduced affinity for nucleotides. ...
   ... thereby demonstrating the importance of NTPDase activity to L.pneumophila
   infection. ... demonstrated important diffs. to mammalian NTPDases &
   different sensitivities to NTPDase inhibitors that may reflect underlying
   structural variations."
   -- [<A HREF="http://dx.doi.org/10.1074/jbc.M801006200 ">doi:10.1074/jbc.M801006200 </A>]['09],
   Legionella@[<A HREF="http://en.wikipedia.org/wiki/Legionella">wikip</A>]['09],
   Legionella pneumophila str. Corby@[<A HREF="http://www.ncbi.nlm.nih.gov/nuccore/NC_009494">refseq</A>]['09],
   [Also search for: Hartland].

%A A. J. Pask
%A R. R. Behringer
%A M. B. Renfree
%T Resurrection of DNA function in vivo from an extinct genome
%J PLoS One
%V 3
%N 5
%P e2240
%M MAY
%D 2008
%K jrnl, eJrnl, MolBio, c2008, c200x, c20xx, zz0715, mammal, marsupial,
   thylacine, Thylacinus cynocephalus, Tasmanian tiger, Australia,
   Col2A1, DNA, ancient
%X "... Using a transgenic approach, it was possible to resurrect DNA fn in
   transgenic mice. ... demonstrate that the thylacine Col2A1 enhancer directed
   chondrocyte-specific expression in this extinct mammalian species in the
   same way as its orthologue does in mice. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0002240">doi:10.1371/journal.pone.0002240</A>]['15], auths@UniMelb.
   (Also see abc [<A HREF="http://www.abc.net.au/science/articles/2008/05/20/2249769.htm">20/5/2008</A>].)

%A A. Loytynoja
%A N. Goldman
%T Phylogeny-aware gap placement prevents errors in sequence alignment and
   evolutionary analysis
%J Science
%V 320
%N 5883
%P 1632-1635
%M JUN
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, phylogenetic tree, multiple alignment,
   trees
%X "... Traditional multiple sequence alignment methods disregard the
   phylogenetic implications of gap patterns that they create & infer
   systematically biased alignments with excess deletions & substitutions, too
   few insertions, & implausible insertion-deletion-event histories. We present
   a method that prevents these systematic errors by recognizing insertions &
   deletions as distinct evolutionary events. We show theoretically &
   practically that this improves the quality of sequence alignments &
   downstream analyses over a wide range of realistic alignment problems. These
   results suggest that insertions & sequence turnover are more common than is
   currently thought & challenge the conventional picture of sequence evolution
   & mechanisms of functional & structural changes."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1158395">doi:10.1126/science.1158395</A>].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Multiple/">multiple-alignment</A>].)

%A H. Ji
%A H. Jiang
%A W. Ma
%A D. S. Johnson
%A R. M. Myers
%A W. H. Wong
%T An integrated software system for analyzing ChIP-chip and ChIP-seq data
%J NatureBiotech.
%V 26
%N 11
%P 1293-1300
%M NOV
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, CisGenome, browser, ChIP, seq,
   peak finding, peaks, transcription factor binding site, sites, NRSF, REST,
   Nanog, Sox2, negative control sample
%X "... CisGenome, a s/w sys. for analyzing genome-wide chromatin
   immunoprecipitation (ChIP) data. ... A built-in browser allows visualization
   of array images, signals, gene structure, conservation, & DNA seq. & motif
   info.. ... We demonstrate [on] data for the transcription factor NRSF/REST,
   a study of ChIP-seq analysis with or without a negative control sample, & an
   analysis of a new motif in Nanog- and Sox2-binding regions."  [49 refs].
   -- [<A HREF="http://dx.doi.org/10.1038/nbt.1505">doi:10.1038/nbt.1505</A>]['09],
   free@[<A HREF="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596672/">ncbi</A>]['09],
   sw@[<A HREF="http://www.biostat.jhsph.edu/~hji/cisgenome/">jhsph</A>]['09],
   sw@[<A HREF="http://biogibbs.stanford.edu/~jihk/CisGenome/index.htm">stnf'</A>]['09].
   p.7 ... when a negative control sample is available ...
     Divide genome into non-overlapping windows w[0], w[1], ... .
     Counts: ChIP sample k[1,i] & control k[2,i] for w[i];  n[i]=k[1,i]+k[2,i].
     Conditional dist'n for k[1,i] is binomial(n[i],p[0]) where
     p[0] is est. from "windows with small total counts".
   [Also search for: ChIP seq peak MolBio].

%A D. V. Zurawski
%A K. M. Mumy
%A J. A. Prentice
%A L. Badea
%A E. L. Hartland
%A B. A. McCormick
%A A. T. Maurelli
%T NleE/OspZ family of effector proteins is required for PMN transepithelial
   migration, a characteristic shared by enteropathogenic Escherichia coli and
   Shigella flexneri infections
%J Infect. Immun.
%V 76
%P 369-379
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, NleE, OspZ, protein, PMN, T3SS, secretion,
    enteropathogenic Escherichia coli, Shigella flexneri, bacteria, bacterium
%X "Enteropathogenic Escherichia coli (EPEC) and Shigella flexneri are human
   host-specific pathogens that infect intestinal epithelial cells. ...
   conclude that OspZ and NleE have similar roles in the upstream induction of
   host signaling pathways required for PMN transepithelial migration in
   Shigella and EPEC infections."
   pdf@[<A HREF="http://dx.doi.org/10.1128/IAI.00684-07">doi:10.1128/IAI.00684-07</A>]['09],
   pdf@[<A HREF="http://www.ncbi.nlm.nih.gov/entrez/utils/fref.fcgi?PrId=3494&itool=AbstractPlus-nondef&uid=17984206&db=pubmed&url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17984206">pubmed</A>]['09],
   -- [<A HREF="http://www.microbiol.unimelb.edu.au/people/hartland/pub.html">auth1</A>]['09].

%A A. Valouev
%A et al
%T Genome-wide analysis of transcription factor binding sites based on
   ChIP-Seq data
%J NatureMethods
%V 5
%P 829-834
%D 2008
%K jrnl, MolBio, Sidow, c2008, c200x, c20xx, ChIP seq, ChIPseq, peak, find,
   QuEST, site
%X "... quantitative enrichment of sequence tags (QuEST) ... stat. f/work based
   on the kernel density est. approach, which uses ChIP-Seq data to determine
   positions where protein complexes contact DNA. Using QuEST, we discovered
   several thousand binding sites for the human transcription factors SRF, GABP
   & NRSF at an average resolution of about 20bp. MEME motif-discovery tool
   -based analyses of the QuEST-identified seqs. revealed DNA binding by
   cofactors of SRF, providing evidence that cofactor binding specificity can be
   obtained from ChIP-Seq data. By combining QuEST analyses with Gene Ontology
   (GO) annotations & expression data, we illustrate how general fns of
   transcription factors can be inferred."  (online Aug 2008).
   -- [<A HREF="http://dx.doi.org/10.1038/nmeth.1246">doi:10.1038/nmeth.1246</A>]['09],
   s/w@[<A HREF="http://mendel.stanford.edu/SidowLab/downloads/quest/">stanf'd</A>]['09].
   [Also search for: ChIP seq peak MolBio].

%A W. Gu
%A T. Castoe
%A D. J. Hedges
%A M. A. Batzer
%A D. D. Pollock
%T Identification of repeat structure in large genomes using repeat probability
   clouds
%J Analytical Biochemistry
%V 380
%N 1
%P 77-83
%D 2008
%K c2008, c200x, c20xx, MolBio, repeat, repeats, DNA, p cloud, clouds, Pcloud,
   dark matter, LINEs, SINEs, transposable, retrotransposon, ucshc
%X "... Algorithms were implemented to efficiently calculate exact counts for
   any length oligonucleotide in large genomes. Based on these oligonucleotide
   counts, oligonucleotide excess probability clouds, or "P-clouds," were
   constructed. P-clouds are composed of clusters of related oligonucleotides
   that occur, as a group, more often than expected by chance. After
   construction, P-clouds were mapped back onto the genome, and regions of high
   P-cloud density were identified as repetitive regions based on a sliding
   window approach. ..."
   last[<A HREF="http://pmb.uchsc.edu/faculty/pollock/">auth</A>]['09],
   lab-[<A HREF="http://www.evolutionarygenomics.com/Welcome2.html">page</A>]['09].
   [Also search for: DNA information content] and
   [also search for: repetitive DNA].

%A S. Hober
%A M. Uhlen
%T Human protein atlas and the use of microarray technologies
%J Current Opinion in Biotechnology
%V 19
%N 1
%P 30-35
%M FEB
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, Human protein atlas, HPR, HPA, proteins,
   proteome, interaction, systems biology
%X "... Recently, novel strategies to focus *directly* on protein levels have
   been developed. To assess global protein expression in a systematic & high-
   -throughput manner, methods based on design of specific affinity ligands to
   recognize the proteins have been presented. By subsequently using these
   affinity molecules for detection of the corresponding proteins in a wide
   range of platforms, important information can be gained. This article focuses
   on strategies to profile protein levels & in particular the human protein
   atlas initiative & the use of microarray technologies."  [29 refs].
   -- [<A HREF="http://dx.doi.org/10.1016/j.copbio.2007.11.006">doi:10.1016/j.copbio.2007.11.006</A>]['09].
   Also see [<A HREF="http://proteinatlas.org/">proteinatlas.org</A>]['09].

%A K. E. Whelan
%A R. D. King
%T Using a logical model to predict the growth of yeast
%J BMC Bioinformatics
%V 9
%P e97
%M FEB
%D 2008
%K jrnl, eJrnl, MolBio, c2008, c200x, c20xx, zz1114, aber, RDKing, iFF708,
   iND750, yeast, Saccharomyces cerevisiae, metabolic, network, pathways
%X "A logical model of the known metabolic processes in S.cerevisiae was
   constructed from iFF708, an existing Flux Balance Analysis (FBA) model, &
   augmented with information from the KEGG online pathway database ... Compared
   to the FBA model, the logical model has information on an additional 263
   putative genes & 247 additional reactions. The correctness of this model
   was evaluated by comparison with iND750 ... ROC analysis & other stat.
   studies revealed that use of the simpler logical form & larger coverage
   results in no sig. degradation of performance compared to iND750."
   (rdk@[<A HREF="http://www.cs.manchester.ac.uk/about-us/staff/profile/?ea=ross.king">Man.U.</A>]['14].)

%A F. J. Burkowski
%T Structural Bioinformatics: An Algorithmic Approach
%I ChapmanHall
%P 429
%D 2008
%K book, text, MolBio, c2008, c200x, c20xx, zz0809, bioinformatics,
   protein structure, RNA, programming, algorithm
%X 1st ed 2008, hb us$80; uk us isbn:1584886838; uk us isbn13:978-1584886839.
   "... key algorithms to solve problems related to macromolecular structure.
   ... protein structure can produce symmetry & beauty as well as biological
   function. ... gives many eg.s of dynamic programming applications, inc.
   RNA secondary structure prediction & protein sequence alignment. ..."
   [Also search for: MolBio book].

%A S. R. Eddy
%T A probabilistic model of local sequence alignment that simplifies statistical
   significance estimation
%J PLoS Computational Biol.
%M MAY
%D 2008
%K jrnl, eJrnl, MolBio, c2008, c200x, c20xx, zz0918, HMMER, HMM, HMMER2,
   protein, alignment, profile
%X "... Optimal local seq. alignment scores follow Gumbel distributions, but
   determining an important param. of the distribution (L) requires
   time-consuming computational simulation. Moreover, optimal alignment scores
   are less powerful than probabilistic scores that integrate over alignment
   uncertainty ('Forward' scores), but the expected distribution of Forward
   scores remains unknown. Here, I conjecture that both expected score distns
   have simple, predictable forms when full probabilistic modeling methods are
   used. For a probabilistic model of local seq. alignment, optimal alignment
   bit scores ('Viterbi' scores) are Gumbel-distributed with constant L = log 2,
   & the high scoring tail of Forward scores is exponential with the same
   constant L. Simulation studies support these conjectures over a wide range of
   profile/seq. comparisons, using 9,318 profile-hidden Markov models from the
   Pfam database. This enables efficient & accurate determination of
   expectation values (E-values) for both Viterbi & Forward scores for
   probabilistic local alignments."
   -- [<A HREF="https://doi.org/10.1371/journal.pcbi.1000069">doi:10.1371/journal.pcbi.1000069</A>]['18], [<A HREF="http://hmmer.org/">hmmer.org</A>]['18].
   [Also search for: HMMER].

%A J. F. Knabe
%A C. L. Nehaniva
%A M. J. Schilstra
%T Do motifs reflect evolved function? - No convergent evolution of genetic
   regulatory network subgraph topologies
%J Biosystems
%V 94
%N 1-2
%P 68-74
%M OCT-NOV
%D 2008
%O 7th Int. Workshop on Info. Processing in Cells and Tissues - IPCAT '07
%K jrnl, MolBio, c2008, c200x, c20xx, regulatory, biological networks, motif,
   pattern, randomized, frequent, subgraph, subgraphs, controversial
%X "... Whether motifs (subgraph patterns that occur more often than in
   randomized n/ws) have specific functions as elementary computational circuits
   has been cause for debate. ... approach the issue using n/ws that abstractly
   model natural genetic regulatory networks (GRNs) which are evolved to show
   dynamical behaviors. ... Only when drastically restricting n/w size, so that
   one motif corr. to a whole functionally evolved n/w, was preference for
   particular connection patterns found. This suggests that in non-restricted,
   bigger n/ws, entanglement with the rest of the n/w hinders topological
   subgraph analysis."   (i.e., a sceptic.)
   -- [<A HREF="http://dx.doi.org/10.1016/j.biosystems.2008.05.012">doi:10.1016/j.biosystems.2008.05.012</A>]['10]$$.
   (Also see motifs@[<A HREF="https://en.wikipedia.org/wiki/Network_motif">wikip</A>]['16].)
   [Also search for: network motif MolBio].

%A B. D. Ondov
%A A. Varadarajan
%A K. D. Passalacqua
%A N. H. Bergma
%T Efficient mapping of Applied Biosystems SOLiD sequence data to a
   reference genome for functional genomic applications
%J J. Bioinformatics
%V 24
%N 23
%P 2776-2777
%M DEC
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, SOCS, short read, reads, hashing,
   color space, colour
%X "... SOLiD data ... 'color space' ... describe SOCS (short oligonucleotide
   color space), a program for efficient mapping of SOLiD sequence data to a
   ref.genome within color space. SOCS is built on an iterative var'n of the
   Rabin-Karp string alg. ... Our hash fn enumerates a subset of the seq. being
   hashed using 2 bits/color (the size of the subset is constrained by memory
   limitations on the hash table). ...  mapped a 32 million read data set to
   the complete human genome (v.36.3) [at h=4] in ~17 h on an 8 node (64 core)
   cluster."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn512">doi:10.1093/bioinformatics/btn512</A>][11/'09],
   sw@[<A HREF="http://socs.biology.gatech.edu/">g. tech</A>]['09].
   [Also search for: short read MolBio].

%A A. S. Konagurthu
%A A. M. Lesk
%T Single and multiple input modules in regulatory networks
%J Proteins
%V 73
%N 2
%P 320-324
%M NOV
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, motif, motifs, gene regulatory network,
   model, graphModel, ArunK, AMLesk, feed forward loop, feedforward, FFL,
   single, multiple, input, SIM, MIM, Luscombe
%X "Interactions between transcription factors & target genes form regulatory
   n/ws that control target gene expression. ... contain canonical motifs, inc.
   the feed forward loop (FFL), ...  published defns of the SIM & MIM are
   unclear & often used inconsistently. Here, we provide, for the first time, a
   complete & consistent definition of SIM & MIM, & algs. for enumerating SIMs &
   MIMs in any n/w. From the alg. point of view, enumeration of SIMs & MIMs is
   substantially harder than enumerating FFLs. We compare the distributions of
   motifs in the Yeast regulatory n/w under different physiological condns,
   reported earlier by the landmark paper of Luscombe et al."
   -- [<A HREF="http://dx.doi.org/10.1002/prot.22053">doi:10.1002/prot.22053</A>]['10].

%A J. Whitney
%A A. Easter
%A K. Tchanturia
%T Service users' feedback on cognitive training in the treatment of anorexia
   nervosa: A qualitative study
%J Int. J. of Eating Disorders
%V 41
%N 6
%P 542-550
%D 2008
%K jrnl, IJED, c2008, c200x, c20xx, anorexia, anorexic, eating disorder,
   disordersm, mental health, autism, autistic, Cognitive Remediation Therapy,
   CRT
%X "... There is little evidence to guide the treatment of anorexia nervosa.
   Cognitive Remediation Therapy (CRT) may be helpful in reducing perfectionism
   and rigidity and preparing patients for involvement in later psychological
   interventions ... Written feedback, following 10 CRT sessions, from 19 AN
   patients was analyzed using grounded theory approach ... Patients' feedback
   was generally positive. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/eat.20536">doi:10.1002/eat.20536</A>]['09].
   (Also see [<A HREF="http://www.newscientist.com/article/mg20227054.900-anorexia-linked-to-autistic-thinking.html">New Sci.</A>]['09].)

%A O. Martinez
%A M. H. Reyes-Valdes
%T Defining diversity, specialization, and gene specificity in transcriptomes
   through information theory
%J PNAS
%V 105
%N 28
%P 9709-9714
%M JUL
%D 2008
%K PNAS, jrnl, MolBio, c2008, c200x, c20xx, zz1210, diversity, genes,
   information, transcriptome
%X "... define transcriptome diversity as the Shannon entropy of its frequency
   distribution. Gene specificity is defined as the mutual information between
   the tissues and the corresponding transcript, allowing detection of either
   housekeeping or highly specific genes and clarifying the meaning of these
   concepts in the literature. ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0803479105">doi:10.1073/pnas.0803479105</A>]['10], [26 refs].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">compression</A>].)

%A S. C. Li
%A D. Bu
%A X. Gao
%A M. Li
%T Designing succinct structural alphabets
%J J. Bioinformatics
%V 24
%N 13
%P i182-i89
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, protein, local structure, fragment,
   library
%X "The 3D struct. ... can be assembled from the substructures corresponding to
   small segments of this seq.. For each small seq. seg., there are only a few
   more likely substructures. We call them the 'structural alphabet' for this
   seg.. Classical approaches such as ROSETTA used sequence profile ...
   In contrast, we utilize more structural information, such as solvent
   accessibility and contact capacity, for finding structural fragments.
   ... Int. linear prog. technique ... derive the best combination of these
   seq. & structural information items. ... 50% improvement over the previous
   accuracies. ... construct more accurate protein structures than the
   state-of-art ab initio p.struct.predn programs such as ROSETTA. [&] able to
   reduce the Kolodny's library size by a factor of 8, at the same accuracy."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn165">doi:10.1093/bioinformatics/btn165</A>]['13].
   [Also search for: protein structure fragment library].

%A M. Ouali
%A R. D. King
%T Cascaded multiple classifiers for secondary structure prediction
%J Protein Sci.
%V 9
%N 6
%P 1162-1176
%D DEC
%D 2008
%K jrnl, MolBio, c2008, c200x, c20xx, zz1221, RDKing, protein,
   secondary structure, prediction, long range, interaction
%X "We describe a new classifier for protein S.S. pred'n that is formed by
   cascading together different types of classifiers using neural n/wks & linear
   discrimination. ... achieves an accuracy of 76.7% (... Jack-knife proc.) on a
   new nonredundant dataset of 496 nonhomologous seqs. (...). This database was
   esp. designed to train & test protein PSS methods, & it uses a more stringent
   defn of homologous seq. than in prev. studies. We show that it is possible to
   design classifiers that can highly discriminate the three classes (H,E,C)
   with an accuracy of up to 78% for beta-strands, using only a local window &
   resampling techniques. This indicates that the importance of long-range
   interactions for the pred'n of beta-... has been probably prev. overest'd."
   -- [<A HREF="https://doi.org/10.1110/ps.9.6.1162">doi:10.1110/ps.9.6.1162</A>].
   [Also search for: protein secondary structure prediction].

%A A. H. Paterson
%A et al
%T The Sorghum bicolor genome and the diversification of grasses
%J Nature
%V 457
%N 7229
%P 551-556
%M JAN
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, Sorghum bicolor genome, broomcorn,
   nGenome, plant, grass, crop, grain
%X "Sorghum, an African grass related to sugar cane & maize ... initial analysis
   of the ~ 730-megabase Sorghum bicolor (L.) Moench genome, placing ~ 98% of
   genes in their chromosomal context using whole-genome shotgun seq. validated
   by genetic, physical & syntenic information. Genetic recombination is largely
   confined to about 1/3 of the sorghum genome with gene order & density similar
   to those of rice. Retrotransposon accumulation in recombinationally
   recalcitrant heterochromatin explains the approximately 75% larger genome
   size of sorghum compared with rice. Although gene & repetitive DNA
   distributions have been preserved since palaeopolyploidization ~ 70 m.years
   ago, most duplicated gene sets lost 1 member before the sorghum-rice
   divergence. Concerted evolution makes 1 duplicated chromosomal segment appear
   to be only a few m.y. old. ~ 24% of genes are grass-specific & 7% are
   sorghum-specific. Recent gene & microRNA duplications may contribute to
   sorghum's drought tolerance."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07723">doi:10.1038/nature07723</A>]['09],
   &  [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/19189423?dopt=Abstract">pub med</A>][09],
   760 Mbase with 2*n = 2*10 = 20 chr, [<A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=txid4557[orgn]">txid4557[orgn]</A>]['09].

%A S. C. Madeira
%A A. L. Oliveira
%T A polynomial time biclustering algorithm for finding approximate expression
   patterns in gene expression time series
%J Algs. for Molec. Biol.
%V 4
%N #8
%M JUN
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0720, gene ecpression, time series, timeSeries,
   biclustering, coclustering
%X "... propose e-CCC-Biclustering, a biclustering alg. that finds & reports all
   maximal contiguous column coherent biclusters with approx. expression
   patterns in time polynomial in the size of the time series gene expression
   matrix. This polynomial time complexity ..."
   -- [<A HREF="https://doi.org/10.1186/1748-7188-4-8">doi:10.1186/1748-7188-4-8</A>]['20].
   (Also see bicl@[<A HREF="https://en.wikipedia.org/wiki/Biclustering">wikip</A>]['20].)

%A B. L. Magnanti
%A M. T. Dorak
%A L. Parker
%A A. W. Craft
%A P. W. James
%A R. J. Q. McNally
%T Geographical analysis of thyroid cancer in young people from northern
   England: Evidence for a sustained excess in females in Cumbria
%J European J. of Cancer
%V 45
%N 9
%P 1624-1629
%M JUN
%D 2009
%K jrnl, c2009, c200x, c20xx, thyroid cancer, gender, Chernobyl explosion,
   nuclear reactor, accident,
   Secret Diary of a Call Girl, London, du, Belle de Jour
%X "A previous study found a thyroid cancer excess in Cumbria following the
   Chernobyl explosion, but did not analyse sex-specific effects. ... examines
   sex differences in the incidence of thyroid cancer. 95 primary thyroid
   carcinomas (69 f., 26 m.) diagnosed in those aged 0-24 during 1968-2005 were
   identified from the Northern Region Young Persons' Malignant Disease Reg'ry.
   Age-standardised incidence rates (ASRs), rate ratios (RRs) & 95% [CIs] were
   calculated.  For males, the ASR was 0.6 per million person-y. during the
   pre-Chernobyl period (1968-1986), and was 1.8 per m. person-y. during the
   post-Chernobyl period (1987-2005). For females ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ejca.2008.12.024">doi:10.1016/j.ejca.2008.12.024</A>]['09], accepted 12/'08, online Jan./'09.
  (11/'09: It seems that auth1 also wrote, Secret Diary of a Call Girl, 2008,
           uk us isbn:044654082X; uk us isbn13:978-0446540827.)
  [Chernobyl: 26 April 1986; see [<A HREF="http://www.bbc.co.uk/search/news/chernobyl">bbc</A>][4/'11].]

%A N. Stokes
%A Y. Li
%A L. Cavedon
%A J. Zobel
%T Exploring criteria for successful query expansion in the genomic domain
%J Information Retrieval
%V 12
%N 1
%P 17-50
%M FEB
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, BioTALA, NICTA, TREC, query expansion,
   document retrieval
%X "... we compare & contrast the effectiveness of [some] biomed. knowledge
   sources used by TREC 2006 Genom'cs Track participants for expansion. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/s10791-008-9073-9">doi:10.1007/s10791-008-9073-9</A>]['09],
   -- [<A HREF="http://www.nicta.com.au/research/projects/BioTALA">BioTALA</A>]['09].

%A R. Swanson
%A M. Vannucci
%A J. W. Tsai
%T Information theory provides a comprehensive framework for the evaluation of
   protein structure predictions
%J Proteins
%V 74
%N 3
%P 701-711
%M FEB
%D 2009
%K jrnl, MolBio, c2009, c201x, c20xx, protein, 3D, structure, information,
   similarity, match, matching
%X "Protein structure prediction has a # of important ad hoc similarity measures
   for evaluating predictions, but would benefit from a measure that is able to
   provide a common framework for a broad range of comparisons. Here ... a
   mutual information-like measure can provide a comprehensive framework for
   evaluating protein structure prediction of all types. We discuss the concept
   of information, its application to secondary struct., & the obstacle to
   applying it to 3D struct.. Based on insights from the secondary struct. case,
   we present an approach to work around the 3D difficulties, & develop a method
   to measure the mutual information provided by a 3D struct. prediction. We
   integrate the evaluation of all types of protein struct. prediction into a
   single frame work, & compare the amount of information provided by various
   prediction methods, including secondary struct. prediction. Within this
   broadened framework, the idea that struct. is better preserved than sequence
   during evolution is evaluated quantitatively for the globin family. A nearly
   perfect sequence match in the globin family corresponds to about 300 bits of
   information, whereas a nearly perfect structural match for the same two
   proteins corresponds to about 2500 bits of information, where bits of
   information describes the probability of obtaining a match of similar
   closeness by chance. Mutual information provides both a theoretical basis for
   evaluating struct. similarity & an explanatory surround for existing
   similarity measures."
   -- @[<A HREF="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629808/">ncbi</A>]['11],
   -- [<A HREF="http://dx.doi.org/10.1002/prot.22186">doi:10.1002/prot.22186</A>]['11].
   [Also search for: MolBio information theory].

%A M. J. Chaisson
%A D. Brinza
%A P. A. Pevzner
%T De novo fragment assembly with short mate-paired reads: Does the
   read length matter?
%J Genome Res.
%V 19
%N 2
%P 336-346
%M FEB
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, short read, reads, DNA, assembly,
   mate pair, pairs, paired, gaplength, denovo, length, EulerSR, EulerUSR, USR
%X "Increasing read length is currently viewed as the crucial condition for
   fragment assembly with next-generation seq. tech.. However, introducing mate-
   -paired reads ... raises the question as to whether the read length (as
   opposed to GapLength) even matters. We describe a new tool, EULER-USR, for
   assembling mate-paired short reads and use it to analyze the question of
   whether the read length matters. ... we present an approach that substitutes
   [error] trimming with error correction using repeat graphs.  ... one may
   extend seq. reactions that degrade with length "past their prime" to where
   the error rate grows > what is normally acceptable for fragment assembly."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.079053.108">doi:10.1101/gr.079053.108</A>]['09].
   pdf@[<A HREF="http://www-cse.ucsd.edu/~dbrinza/cv/pub/preprint.gr.079053.108.pdf">ucsd</A>]['09],
   s/w@[<A HREF="http://euler-assembler.ucsd.edu/portal/">ucsd</A>]['09].
   [Also search for: short read MolBio],
   [also search for: sequence assembly MolBio].

%A T. Marques-Bonet
%A et al ...
%A E. E. Eichler
%T A burst of segmental duplications in the genome of the African great ape
   ancestor
%J Nature
%V 457
%P 877-881
%M FEB
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, primate, macaque, monkey, orang-utan,
   orangutan, chimpanzee, human, evolution, origins, segment, duplication,
   ancestral
%X "... we perform a systematic analysis of duplication content of 4 primate
   genomes (macaque, orang-utan, chimpanzee & human) ... to understand the
   pattern & rates of genomic dupl'n during hominid evolution. [find] the
   ancestral branch leading to human & African great apes shows the most sig.
   increase in duplication activity both in terms of base pairs & ... of events.
   ... discover striking examples of recurrent & indep. gene-containing
   duplications within the gorilla & chimp. [not] in the human lineage. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07744">doi:10.1038/nature07744</A>]['09].

%A K. L. Klump
%A et al
%T Academy for eating disorders position paper: Eating disorders are serious
   mental illnesses
%J Int. J. of Eating Disorders
%V 42
%N 2
%P 97-103
%D 2009
%K jrnl, IJED, c2009, c200x, c20xx, anorexia nervose, anorexic, autism,
   autistic, spectrum, mental health, disorder, psychology, psychological
%X [<A HREF="http://dx.doi.org/10.1002/eat.20589">doi:10.1002/eat.20589</A>]['09].
   (Also see [<A HREF="http://www.newscientist.com/article/mg20227054.900-anorexia-linked-to-autistic-thinking.html">New Sci.</A>]['09].)

%A A. V. Badyaev
%T Evolutionary significance of phenotypic accommodation in novel
   environments: an empirical test of the Baldwin effect
%J Phil. Trans. of the Royal Soc. B
%V 364
%N 1520
%P 1125-1141
%M APR
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0317, Baldwin effect, evolution,
   natural selection
%X "... I show that this process is consistent with the origin of novel
   adaptations during colonization of North America by the house finch. The
   induction of developmental variation by novel environments of this species's
   expanding range was followed by homeostatic channelling, phenotypic
   accommodation & directional cross-generational transfer of a subset of
   induced developmental outcomes favoured by natural seln. These results
   emphasize three principal points. First, contemporary novel adaptations
   result mostly from reorganization of existing structures that shape newly
   expressed variation, giving natural selection an appearance of a creative
   force. Second, evolutionary innovations & maintenance of adaptations are
   different processes. Third, both the Baldwin & parental effects are probably
   a transient state in an evolutionary cycle connecting initial phenotypic
   retention of adaptive changes & their eventual genetic determination &, thus,
   the origin of adaptation and evolutionary change."
   -- [<A HREF="http://dx.doi.org/10.1098/rstb.2008.0285">doi:10.1098/rstb.2008.0285</A>]['17].
   [Also search for: Baldwin effect].

%A M. Brazil
%A D. A. Thomas
%A B. K. Nielsen
%A P. Winter
%A C. Wulff-Nilsen
%A M. Zachariasen
%T A novel approach to phylogenetic trees: d-Dimensional geometric Steiner trees
%J Networks
%V 53
%N 2
%P 104-111
%M MAR
%D 2009
%K jrnl, c2009, c200x, c20xx, phylogenetic trees, evolutionary tree, Steiner,
    multidimensional scaling
%X "... novel distance-based method for the determination of phylogenetic trees.
   ... based on multidimensional scaling & Euclidean Steiner trees in
   high-dimensional spaces. Preliminary computational experience shows that the
   use of Euclidean Steiner trees for finding phylogenetic trees is a viable
   approach. Experiments also indicate that the new method is comparable with
   results produced by neighbor joining (Saitou & Nei, Mol Biol Evol 4 ('87),
   406-425)."  (online Oct '08).
   -- [<A HREF="http://dx.doi.org/10.1002/net.20279">doi:10.1002/net.20279</A>]['09],
   a1@[<A HREF="http://www.ee.unimelb.edu.au/staff/brazil/">ee.unimelb</A>]['09],
   a2@[<A HREF="http://people.eng.unimelb.edu.au/dathomas/">eng.unimelb</A>]['09].

%A J. Rozowsky
%A et al
%T PeakSeq enables systematic scoring of ChIP-seq experiments relative to
   controls
%J NatureBiotech.
%V 27
%P 66-75
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz1009, ChIP seq, ChIPseq, peak, find,
   gerstein, PeakSeq, control, mappability, open chromatin, STAT 1, STAT1,
   Pol II 2, PolII, Pol2
%X "... 2 deeply seq'd data sets for human RNA polymerase II & STAT1, each with
   matching input-DNA controls, we describe a general scoring approach to
   address unique challenges in ChIP-seq data analysis. ... based on the obs.
   that sites of potential binding are strongly correlated with signal peaks in
   the control, likely revealing features of open chromatin. We develop a 2-pass
   strategy called PeakSeq to compensate for this. ... compensates for signal
   caused by open chromatin, as revealed by inclusion of the controls. The 1st
   pass identifies putative binding sites & compensates for genomic variation
   in the 'mappability' of sequences. The 2nd pass filters out sites not
   sig. enriched compared to the normalized control ... enables us to optimize
   experimental design by estimating the depth of sequencing required for a
   desired level of coverage & demonstrating that more than 2 replicates
   provides only a marginal gain in information."  [via JohnM].
   -- [<A HREF="http://dx.doi.org/10.1038/nbt.1518">doi:10.1038/nbt.1518</A>]['09],
   and [<A HREF="http://www.gersteinlab.org/proj/PeakSeq/">g'lab.org</A>]['09].
   [Also search for: ChIP seq peak MolBio].

%A J. Eid
%A et al
%T Real-time DNA sequencing from single polymerase molecules
%J Science
%V 323
%N 5910
%P 133-138
%M JAN
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz0109, single molecule, DNA, sequencing,
   experimental, high throughput, dNTP, dNTPs, Pacific Biosciences
%X "present single-molecule, real-time sequencing data obtained from a DNA
   polymerase performing uninterrupted template-directed synthesis using 4
   distinguishable fluorescently labeled ... (dNTPs). We detected the temporal
   order of their enzymatic incorporation into a growing DNA strand with
   zero-mode waveguide nanostructure arrays, which provide optical observation
   volume confinement & enable parallel, simultaneous detection of thousands of
   single-molecule sequencing reactions. Conjugation of fluorophores to the
   terminal phosphate moiety of the dNTPs allows continuous observation of DNA
   synthesis over 000s of bases without steric hindrance. The data report
   directly on polymerase dynamics, revealing distinct polymerization states &
   pause sites corresponding to DNA secondary structure. Seq. data were aligned
   with the known reference sequence to assay biophysical parameters of
   polymerization for each template position. Consensus seqs. were generated
   from the single-molecule reads at 15-fold coverage, showing a median accuracy
   of 99.3%, with no systematic error beyond fluorophore-dependent error rates."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1162986">doi:10.1126/science.1162986</A>]['09]; auths@Pacific Biosciences.
   (Also see PacBiosci@[<A HREF="http://en.wikipedia.org/wiki/Pacific_Biosciences">wikip</A>]['14].)
   [Also search for: MolBio single molecule sequencing].

%A T. V. Pollet
%A D. Nettle
%T Partner wealth predicts self-reported orgasm frequency in a sample of
   Chinese women
%J Evolution and Human Behavior
%V ?
%N ?
%P ?-?
%D 2009
%K jrnl, human behaviour, c2009, c200x, c20xx, zz0209, men, women, man, woman,
   male, female, sex, orgasm, income, wealth, rich, mate selection, choice
%X "There has been considerable speculation about the adaptive significance of
   the human female orgasm, with 1 hypothesis being that it promotes
   differential affiliation or conception with high-quality males. ... sample
   from the Chinese Health and Family Life Survey. We found that women report
   more frequent orgasms the higher their partner's income is. This result
   cannot be explained by possible confounds such as women's age, health,
   happiness, educational attainment, relationship duration, wealth difference
   between the partners, difference between the partners in educational
   attainment, & regional location. It appears consistent with the view that
   female orgasm has an evolved adaptive function."  (online Jan '09.)
   -- [<A HREF="http://dx.doi.org/10.1016/j.evolhumbehav.2008.11.002">doi:10.1016/j.evolhumbehav.2008.11.002</A>][1/'09],
      [<A HREF="http://www.staff.ncl.ac.uk/daniel.nettle/">auth2</A>['09].

%A S. Christley
%A Y. Lu
%A C. Li
%A X. Xie
%T Human genomes as email attachments
%J J. Bioinformatics
%V 25
%N 2
%P 274-275
%D 2009
%K MolBio, c2009, c200x, c20xx, zz0209, genome, DNA, compress, compression,
   conditional
%X "... any two human genomes are more than 99% identical, so it is much more
   efficient to store genomes as variations from a common reference genome ..."
   [The achieve 4MB for a human g. given a reference genome.]
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn582">doi:10.1093/bioinformatics/btn582</A>]['09].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">compression</A>].)

%A B. Langmead
%A C. Trapnell
%A M. Pop
%A S. L. Salzberg
%T Ultrafast and memory-efficient alignment of short DNA sequences to the
   human genome
%J Genome Biology
%V 10
%N R25
%M MAR
%D 2009
%K MolBio, eJrnl, jrnl, BowTie, c2009, c200x, c20xx, DNA, sequence, short read,
   reads, BW, BWT, string, Maq, Soap
%X "... Bowtie is an ultrafast, memory-efficient short read aligner geared
   toward quickly aligning large sets of short DNA sequences (reads) to
   mammalian genomes. It aligns 35-bp reads to the human g. at a rate of 25
   million reads/hr on a typical workstation with 2 gigabytes of memory. Bowtie
   indexes the genome with a Burrows-Wheeler index to keep its memory footprint
   small: as small as 1.1 GB for the human g. (using -z). ... about 35x faster
   than Maq & over 250x faster than SOAP when aligning to the human g.. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/gb-2009-10-3-r25">doi:10.1186/gb-2009-10-3-r25</A>]['10],
   code@[<A HREF="http://bowtie-bio.sourceforge.net/">sourcefor...</A>]['09].
   auth2@[<A HREF="http://www.cs.umd.edu/~cole/">umd</A>]['09].
   [Also search for: short read MolBio].

%A M. J. Benton
%T The Red Queen and the Court Jester: Species diversity and the role of biotic
   and abiotic factors through time
%J Science
%V 323
%N 5915
%P 728-732
%M FEB
%D 2009
%K review, MolBio, c2009, c200x, c20xx, zz0209, Darwin, evolution, spcies,
   origin, biotic, abiotic, red queen, biol, competition
%X "Evolution may be dominated by biotic factors, as in the Red Queen model, or
   abiotic factors, as in the Court Jester model, or a mixture of both. The two
   models appear to operate predominantly over different geographic and temporal
   scales: Competition, predation, and other biotic factors shape ecosystems
   locally and over short time spans, but extrinsic factors such as climate and
   oceanographic and tectonic events shape larger-scale patterns regionally and
   globally, and through thousands and millions of years. Paleobiological
   studies suggest that species diversity is driven largely by abiotic factors
   such as climate, landscape, or food supply, and comparative phylogenetic
   approaches offer new insights into clade dynamics. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1157719">doi:10.1126/science.1157719</A>]['09].
   (In a special issue on Darwin [<A HREF="http://www.sciencemag.org/darwin/">www</A>][09].)

%A N. Shubin
%A C. Tabin
%A S. Carroll
%T Deep homology and the origins of evolutionary novelty
%J Nature
%V 457
%P 818-823
%M FEB
%D 2009
%K review, MolBio, c2009, c200x, c20xx, zz0209, biology, evolution, origin, eye,
   eyes, limb, limbs, fin, fins, Hox, species, intelligent design, Darwin
%X "Do new anatomical structures arise de novo, or do they evolve from pre-
   -existing structures? Advances in developmental genetics, palaeontology and
   evolutionary developmental biology have recently shed light on the origins of
   some of the structures that most intrigued Charles Darwin, including animal
   eyes, tetrapod limbs and giant beetle horns. In each case, structures arose
   by the modification of pre-existing genetic regulatory circuits established
   in early metazoans. The deep homology of generative processes and cell-type
   specification mechanisms in animal development has provided the foundation
   for the independent evolution of a great variety of structures."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07891">doi:10.1038/nature07891</A>]['09].
   (In a special issue on Darwin [<A HREF="http://www.nature.com/nature/journal/v457/n7231/">v457/7231</A>].)

%A D. Y.F. Mak
%A G. Benson
%T All hits all the time: parameter-free calculation of spaced seed sensitivity
%J J. Bioinformatics
%V 25
%N 3
%P 302-308
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, spaced seed, seeds, PatternHunter
%X "... how how to eliminate the need for prior param. spec. by exploiting a
   simple obs.: given a homology model, the alignments hit by a particular seed
   remain the same regardless of the prob.params.. Only the weights assigned to
   those alignments change. [so] if we know all the hits, we can easily (&
   quickly) find optimal seeds. ... efficient preprocessing step, which is
   computed once/seed. Then we show several increasingly efficient methods to
   find the optimal seed when given specific prob.params.. ... how to determine
   exactly which seeds can never be optimal under any set of prob.params.. ...
   leads to the startling observation that out of thousands of seeds, only a
   handful have any chance of being optimal. We then show how to identify
   optimal seeds & the boundaries within prob. space where they are optimal."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn643">doi:10.1093/bioinformatics/btn643 </A>]['09].
   "... pr=0.7, L=64, ... PatternHunter seed (111*1**1*1**11*111) ..."
   [Also search for: spaced seed MolBio].

%A J. Chiquet
%A A. Smith
%A G. Grasseau
%A C. Matias
%A C. Ambroise
%T SIMoNe: Statistical Inference for MOdular NEtworks
%J J. Bioinformatics
%V 25
%N 3
%P 417-418
%D 2009
%K SIMoNe, MolBio, c2009, c200x, c20xx, Gaussian graphical model, models,
    gene-regulatory network, regulation, networks, microarrays, inference
%X "... R package SIMoNe ... enables inference of gene-regulatory networks based
   on partial correlation coeffs. from microarray experiments. Modelling gene
   expn data with a Gaussian graphical model (hereafter GGM), the alg. ests.
   non-zero entries of the concentration matrix, in a sparse & possibly high-
   -dimensional setting. ... searches for a latent modular structure to drive
   the inference proc. through adaptive penalization of the conc.matrix."
   s/w@[<A HREF="http://cran.r-project.org/web/packages/simone/">cran</A>]['09].
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn637">doi:10.1093/bioinformatics/btn637</A>]['09].
   [Also search for: gene regulatory network]  [can also try adding: inference].

%A M. H. Schwitzer
%A et al ...
%A J. M. Asara
%T Biomolecular characterization and protein sequences of the Campanian
   Hadrosaur B. canadensis
%J Science
%V 324
%N 5927
%P 626-631
%M MAY
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, fossil, protein, Hadrosaur,
   Brachylophosaurus canadensis, Tyrannosaurus rex, MOR 1125, MOR1125, Trex,
   controversial
%X "Molecular preservation in non-avian dinosaurs is controversial. We present
   multiple lines of evidence that endogenous proteinaceous material is
   preserved in bone fragments and soft tissues from an 80-million-year-old
   Campanian hadrosaur, Brachylophosaurus canadensis [... MOR 2598].
   Microstructural and immunological data are consistent with preservation of
   multiple bone matrix and vessel proteins, and phylogenetic analyses of
   B. collagen seq. by mass spectrometry robustly support the bird-dinosaur
   clade, consistent with an endogenous source for these collagen peptides.
   These data complement earlier results from T.rex (MOR 1125) and confirm that
   molecular preservation in Cretaceous dinosaurs is not a unique event."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1165069">doi:10.1126/science.1165069</A>]['12].
   [Also search for: MolBio fossil protein].

%A V. Makinen
%A G. Navarro
%A J. Siren
%A N. Valimaki
%T Storage and retrieval of individual genomes
%J RECOMB
%P 121-137
%M MAY
%D 2009
%K conf, RECOMB, Recomb09, MolBio, c2009, c200x, c20xx, genome, many, genomes,
   self index, compressed, indexing, string, strings
%X A repetitive seq. coll'n is one where portions of a base seq. of length n are
   repeated many times with small variations, forming a coll'n of total
   length N. ... Flexible & efficient data analysis on a such typically huge
   coll'n is plausible using suffix trees. However, s.t. occupies O(N logN) bits
   which very soon inhibits in-memory analyses. Recent advances in full-text
   self-indexing reduce the space of suffix tree to O(N log sigma) bits, where
   sigma is the alphabet size. ...  develop a new family of self-indexes suited
   for the rep.seq.coll'n setting. Their expected space requirement depends only
   on the length n of the base seq. & the number s of variations in its repeated
   copies. That is, the space reduction factor is no longer constant, but
   depends on N/n ..."
   --[<A HREF="http://dx.doi.org/10.1007/978-3-642-02008-7_9">doi:10.1007/978-3-642-02008-7_9</A>]['10].
   Also see tech rep:
     Run-Length Compressed Indexes for Repetitive Sequence Collections,
     TR C-2008-42@[<A HREF="http://www.cs.helsinki.fi/group/suds/papers/mnsv08.pdf">helsink'</A>]['09].
   auth1@[<A HREF="http://www.cs.helsinki.fi/u/vmakinen/">helsink'</A>]['09].
   [Also search for: compressed genome MolBio].

%A N. Malhis
%A Y. S. N. Butterfield
%A M. Ester
%A S. J. M. Jones
%T Slider - maximum use of probability information for alignment of short
   sequence reads and SNP detection
%J J. Bioinformatics
%V 25
%N 1
%P 6-13
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, short read, reads, DNA, Slider
%X "... reduces the alignment problem space by utilizing each read base's
   probabilities given in the prb files. ... given that Slider matches bases
   with probs. other than the most probable, it sig. reduces the % of base
   mismatches. The result is that its SNP predictions are more accurate than
   other SNP prediction approaches used today that start from the most probable
   sequence, including those using base quality. ...
   ... aligned a set of 12 flowcell lanes, 82.6 million reads ... to the human
   ref.genome using Eland, RMAP & Slider.  S. aligned the reads for all lanes
   in 28h 30m with < 2GB of memory (using the -Xmx2G [Java] option) about 2/3
   of the time that Eland took ... RMAP by far took a lot longer ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btn565">doi:10.1093/bioinformatics/btn565</A>]['09],
   slider@[<A HREF="http://www.bcgsc.ca/platform/bioinfo/software/slider">bcgsc.ca</A>]['09].
   [Also search for: short read MolBio].

%S S. Paabo
%T A Neanderthal perspective on human origins
%J American Assoc. Adv. Sci., Annual Meeting
%M FEB
%D 2009
%K AAAS, conf, MolBio, c2009, c200x, c20xx, zz0309, Neandertal, Neanderthal,
   genome, ancient, human, origin, fossil, DNA
%X pdf@[<A HREF="http://www.aaas.org/meetings/2009/program/lectures/media/paabo_presentation.pdf">aaas</A>]['09],
   "... sequenced more than one billion DNA fragments extracted from 3 Croatian
   Neandertal fossils, using novel methods dev. for this project. ... closest
   relatives of currently living humans. They lived in Europe & parts of Asia
   until they became extinct about 30,000y. ago. ...",
   press-kits@[<A HREF="http://www.eva.mpg.de/english/press-kit-neandertal.htm">eva.mpg.de</A>]['09],
   neandertal@[<A HREF="http://www.eva.mpg.de/neandertal/">eva.mpg.de</A>] project.
   (Also see the mitochondr'al genome in '08.)
   [Also search for: MolBio ancient DNA].

%A Yuan-Ping Pang
%A et al ...
%A S. Brimijoin
%T Selective and irreversible inhibitors of Aphid acetylcholinesterases: steps
   toward human-safe insecticides
%J PLoS One
%V 4
%N 2
%P e4349
%D 2009
%K jrnl, eJrnl, MolBio, c2009, c200x, c20xx, zz0409, protein, binding, site,
   Aphid, Schizaphis graminum, insect, insecticide, pesticide, AChE, Cys,
   inhibitor, methanethiosulfonate, acetylcholinesterase
%X "... We prev. reported that a cysteine residue (Cys), found at the AChE
   active site in aphids & other insects but not mammals, might serve as a
   target for insect-selective pesticides. However, aphids have two different
   AChEs (termed AP & AO), & only AP-AChE carries the unique Cys. The absence of
   the active-site Cys in AO-AChE might raise concerns about the utility of
   targeting that residue. Herein we report the development of a
   methanethiosulfonate-containing small molecule that, at 6.0muM, irreversibly
   inhibits 99% of all AChE activity extracted from the greenbug
   aphid (Schizaphis graminum) without any measurable inhibition of the
   human AChE. ..."
   -- [<A HREF="https://dx.doi.org/10.1371%2Fjournal.pone.0004349">doi:10.1371%2Fjournal.pone.0004349</A>]['09].
   [Also search for: MolBio Cys inhibitor].
   (Also see Acet...@[<A HREF="https://en.wikipedia.org/wiki/Acetylcholinesterase">wikip</A>]['20].)

%A Yuan-Ping Pang
%A et al ...
%A S. Brimijoin
%T Selective and irreversible inhibitors of mosquito Acetylcholinesterases for
   controlling malaria and other mosquito-borne diseases
%J PLoS One
%V 4
%N 8
%P e6851
%M AUG
%D 2009
%K jrnl, MolBio, c2020, c202x, c20xx, zz0920, AMTS 17, AMTS17, BPA 11, BPA11,
   methanethiosulfonate, insect, insecticide, mosquito, aphid,
   acetylcholinesterase, AChE, inhibitor, cysteine, Cys
%X "... a free [Cys] residue at the entrance of the active site of
   acetylcholinesterase (AChE) in some insects but not in mammals, birds, &
   fish. These insects have two AChE genes (AP & AO), & only AP-AChE carries the
   Cys residue. ... Recently we reported a Cys-targeting small molecule that
   irreversibly inhibited all AChE activity extracted from aphids while an
   identical exposure caused no effect on the human AChE. Full inhibition of
   AChE in aphids indicates that AP-AChE contributes most of the enzymatic
   activity & suggests that the Cys residue might serve as a target for
   developing better aphicides. ..."
   -- [<A HREF="https://dx.doi.org/10.1371/journal.pone.0006851">doi:10.1371/journal.pone.0006851</A>]['20].
   [Also search for: MolBio Cys inhibitor].

%A Y. Bar-Yam
%A D. Harmon
%A B. de Bivort
%T Attractors and democratic dynamics
%J Science
%V 323
%N 5917
%P 1016-1017
%M FEB
%D 2009
%K news, c2009, c200x, c20xx, zz0309, MolBio, attractor, transcription, cell,
   cellular, differentiation, gene, regulation regulatory, transcription,
   systems, attractor
%X "... study how embryonic cells navigate a series of intermediate
   transcriptional states before settling into a final adult state;
   microbiologists identify the mechanisms by which transcription is altered by
   environmental perturbation; & oncologists seek to identify how cells switch
   from benign to cancerous. Consider two concepts of transcriptional reg'n.
   In a "molecular autocracy," master genes respond to environmental or
   developmental stimuli by regulating 000s of genes, either directly or through
   other transcription factors. In a "molecular democracy," all genes exert a
   regulatory influence on all other genes, & phenotypic change ..."  [14 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1163225">doi:10.1126/science.1163225</A>]['09].

%A J. Schacherer
%A J. A. Shapiro
%A D. M. Ruderfer
%A L. Kruglyak
%T Comprehensive polymorphism survey elucidates population structure of
   Saccharomyces cerevisiae
%J Nature
%V 458
%P 342-345
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0309, MolBio, yeast, polymorphism, diversity,
   species, Saccharomyces cerevisiae, genome, variability, variation, SNP, SNPs
%X "... polymorphisms among individuals within a species is essential both for
   studying the genetic basis of phenotypic differences & for elucidating the
   evolutionary history of the species. Large-scale polymorphism surveys have
   recently been reported for human, mouse & Arabidopsis thaliana. ...  [We]
   detected 1.89 million [SNPs] ... grouped into 101,343 distinct segregating
   sites. We also identified 3,985 deletion events of length > 200bp among the
   surveyed strains. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07670">doi:10.1038/nature07670</A>]['09].
   (The y.genome is ~12,068 k bp, so auths would avg a "site" every 120bp.)
   [Also search for: yeast nGenome].

%A S. Kimura
%A S. Nakayama
%A M. Hatakeyama
%T Genetic network inference as a series of discrimination tasks
%J J. Bioinformatics
%V 25
%N 7
%P 918-925
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, genetic network, networks, task, learn,
   infer
%X "... method infers genetic n/ws by obtaining classifiers capable of
   predicting the signs of the derivatives of the gene expression levels. ...
   we defined a genetic n/w inference problem as a series of discrimination
   tasks, then solved the ... tasks with a linear programming m/c. ... results
   demonstrated that the proposed method is capable of correctly inferring
   genetic n/ws, & doing so more than 500 x faster than the other inf.methods
   based on sets of differential equns. ... applied our method to actual
   expression data of the bacterial SOS DNA repair system. ... our approach
   relates to the inference method based on the S-system model. Though our
   method provides no est. of the kinetic parameters, it should be useful for
   researchers interested only in the n/w structure of a target system."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btp072">doi:10.1093/bioinformatics/btp072</A>]['09].

%A A. Z. Worden
%A et al
%T Green evolution and dynamic adaptations revealed by genomes of the marine
   Picoeukaryotes Micromonas
%J Science
%V 324
%N 5924
%P 268-272
%M APR
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz0409, Picoeukaryotes Micromonas, tiny,
   marine, photosynthesis, alga, algae, plant, plants, evolution
%X "Picoeukaryotes ... organisms less than 2 micrometers in dia.. Photosynthetic
   marine picoeukaryotes in the genus Micromonas ...  belong to an anciently
   diverged sister clade to land plants. Although Micromonas isolates have high
   18S ribosomal RNA gene identity, we found that genomes from 2 isolates shared
   only 90% of their predicted genes. ..."
   "... Genome assemblies together with predicted gene models and annotations
   were deposited at DNA Data Bank of Japan/EMBL/GenBank under the project
   accession #s ACCO00000000 and ACCP00000000 for RCC299 & CCMP1545, resp.."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1167222">doi:10.1126/science.1167222</A>]['09].

%A I. Zhidkov
%A E. A. Livneh
%A E. Rubin
%A D. Mishmar
%T mtDNA mutation pattern in tumors and human evolution are shaped by
   similar selective constraints
%J Genome Res.
%V 19
%P 576-580
%M APR
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, tumor, cancer, cancers, mitochondria,
   DNA, genome, tumors, mtDNAs, selective, selection
%X "Multiple human mutational landscapes of normal & cancer condns are currently
   available. However, while the unique mutational patterns of tumors have been
   extensively studied, little attention has been paid to similarities b/w
   malignant & normal condns. Here ... pattern of mutations in the mitochondrial
   genomes (mtDNAs) of cancer (98 seqs.) & natural pop'ns (2400 seqs.). De novo
   mtDNA mutations in cancer preferentially colocalized with ancient variants in
   human phylogeny. A sig. portion of the cancer mutations was organized in
   recurrent combinations (COMs), reaching a length of 7 mutations, which also
   colocalized with ancient variants. Thus, by analyzing similarities rather
   than differences in patterns of mtDNA mutations in tumor & human evolution,
   we discovered evidence for similar selective constraints, suggesting a
   functional potential for these mutations."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.083477.108">doi:10.1101/gr.083477.108</A>]['09].

%A Y. M. D. Lo
%A R. W. K. Chiu
%T Next-generation sequencing of plasma/serum DNA: an emerging research and
   molecular diagnostic tool
%J Clinical Chem.
%V 55
%N 4
%P 730-738
%M APR
%D 2009
%K news, views, c2009, c200x, c20xx, MolBio, new, next, NGS, blood, serum,
   DNA, RNA
%X "... cell-free DNA and RNA molecules present in plasma and serum ... Three
   groups have reported the use of massively parallel sequencing technologies in
   the analysis of plasma/serum DNA ... Beck et al. obtained a total of 450,000
   sequences from 50 apparently healthy individuals. ..."   [15 refs].
   -- [<A HREF="http://dx.doi.org/10.1373/clinchem.2009.123661">doi:10.1373/clinchem.2009.123661</A>]['09].

%A R. D. King
%A J. Rowland
%A S. G. Oliver
%A M. Young
%A W. Aubrey
%A E. Byrne
%A M. Liakata
%A M. Markham
%A P. Pir
%A L. N. Soldatova
%A A. Sparkes
%A K. E. Whelan
%A A. Clare
%T The automation of science
%J Science
%V 324
%N 5923
%P 85-89
%M APR
%D 2009
%K jrnl, c2009, c200x, c20xx, biology, RDKing, AClare, robot, scientist, Adam
%X "... report the development of Robot Scientist 'Adam,' which advances the
   automation of both. Adam has autonomously generated functional genomics
   hypotheses about the yeast Saccharomyces cerevisiae & experimentally tested
   these hypotheses by using laboratory automation. We have confirmed Adam's
   conclusions through manual experiments. To describe Adam's research, we have
   developed an ontology & logical language. The resulting formalization
   involves over 10,000 different research units in a nested treelike structure,
   10 levels deep, that relates the 6.6 million biomass measurements to their
   logical description. This formalization describes how a machine contributed
   to scientific knowledge."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1165620">doi:10.1126/science.1165620</A>]['14].
   RK@[<A HREF="http://www.cs.manchester.ac.uk/about-us/staff/profile/?ea=ross.king">CS</A>]['14],
   or [<A HREF="http://www.mib.ac.uk/people/staffprofile/kingr.aspx">mib</A>]['14],
   AC@[<A HREF="http://users.aber.ac.uk/afc/">Aber</A>]['14].

%A D. Charles
%T Biofuels: Corn-based ethanol flunks key test
%J Science
%V 324
%N 5927
%P 587
%M MAY
%D 2009
%K news, c2009, c200x, c20xx, zz0509, ethanol, greenhouse gas, gases, CO2, fuel,
   bio fuels, biofuel, biofuels, land use, gasoline, petrol, hydrocarbon,
   Searchinger
%X "... the California Air Resources Board (CARB) adopted a low-carbon fuel
   standard that requires greater use of fuels that cause lower greenhouse
   emissions, compared with gasoline ... Corn-based ethanol doesn't meet that
   test and won't benefit from the new standard, CARB says, because diverting
   corn into ethanol production increases deforestation and the clearing of
   grasslands. ... Timothy] Searchinger has found that corn ethanol produces
   twice the greenhouse gas emissions of gasoline, for every mile driven, once
   emissions from land conversion are counted (Sci., 29 Feb. '08, p.1238). ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.324_587">doi:10.1126/science.324_587</A>]['09].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.1151861">doi:10.1126/science.1151861</A>]['08].)

%A E. Tannier
%A C. Zheng
%A D. Sankoff
%T Multichromosomal median and halving problems under different genomic
   distances
%J BMC Bioinformatics
%V 10
%P 120
%D 2009
%K jrnl, eJrnl, MolBio, c2009, c200x, c20xx, problem, distance, algorithm, DCJ,
   complexity, unichromosomal, multichromosomal, genomes, chromosomes, circular,
   breakpoint distance, reversal distance, double, rearrangement, evolution
%X "Genome median & genome halving are combinatorial optimization problems
   that aim at reconstructing ancestral genomes as well as the evol. events
   leading from the ancestor to extant species. ...  The complexity ...
   unichromosomal genomes (perms.) has been settled for both the breakpoint
   dist. & the reversal dist.. Although the multichromosomal case has often
   been assumed to be a simple generalization ..., it is also a relaxation so
   that complexity in this context does not follow from existing results, & is
   open for all dists.. ...
   ... a surprising polynomial result for the breakpoint median & guided
   halving problems in g. with circular & linear chrs., ... the multichr.
   problem is actually easier than the unichr. problem. Still other
   variants of these problems are NPC, inc. the DCJ double dist. problem,
   previously mentioned as an open question. ..."  [PubMedID=19386099].
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-10-120">doi:10.1186/1471-2105-10-120</A>]['09].

%A J. T. Glessner
%A et al
%T Autism genome-wide copy number variation reveals ubiquitin and
   neuronal genes
%J Nature
%V 459
%P 569-573
%M MAY
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz0609, gene, genetic, autism, autistic,
   mental health, ASD, Autism spectrum disorder, Aspergers, NRXN1, CNTN4, NLGN1,
   ASTN2UBE3A, PARK2, RFWD2, FBXO40, AK123120, CNV, CNVs
%X "... cohort of 859 ASD cases & 1,409 healthy ... were genotyped with
   ~550,000 SNP markers, ... to comprehensively identify CNVs conferring
   susceptibility to ASDs. +ve findings were eval. in an indep. cohort of 1,336
   ASD cases & 1,110 controls .... several new susceptibility genes encoding
   neuronal cell-adhesion molecules, inc. NLGN1 & ASTN2, were enriched with CNVs
   in ASD [v.] controls (P=9.5 * 10**-3). ... CNVs within or surrounding genes
   involved in the ubiquitin pathways, inc. UBE3A, PARK2, RFWD2 & FBXO40, were
   affected by CNVs not observed in controls (P=3.3 * 10**-3). [and]
   duplications 55kbases upstream of compl'y DNA AK123120 (P=3.6 * 10**-6).
   ... rare [but] they target genes involved in neuronal cell-adhesion or
   ubiquitin degradation, indicating that these 2 important gene n/ws expressed
   within the central nervous sys. may contrib. to ... susceptibility of ASD."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07953">doi:10.1038/nature07953</A>]['09].

%A H. Li
%A R. Durbin
%T Fast and accurate short read alignment with Burrows-Wheeler transform
%J J. Bioinformatics
%V 25
%N 14
%P 1754-1760
%M MAY
%D 2009
%K jrnl, MolBio, HengLi, c2009, c200x, c20xx, short read, reads, alignment,
   align, BWT, Burrows Wheeler index, BWT, string, compressed index,
   BWA, MAQ, SAM, SAMtools
%X "... implemented Burrows-Wheeler Alignment tool (BWA), a new read al.package
   ... based on backward search with [BWT], to efficiently align short seq.reads
   against a large ref. seq. such as the h.genome, allowing mismatches & gaps.
   BWA supports both base space reads, e.g. from Illumina seq. m/cs, & color
   space reads from AB SOLiD machines. Evaluations on both simulated & real
   data suggest that BWA is ~10-20x faster than MAQ, while achieving similar
   accuracy. In addition, BWA outputs alignment in the new standard SAM
   (Sequence Alignment/Map) format. Variant calling & other downstream analyses
   after the al. can be achieved with the open source SAMtools s/w package."
   "... Because exact repeats are collapsed on 1 path ... main reason [fast]."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btp324">doi:10.1093/bioinformatics/btp324 </A>]['09],
  "... within edit distance 2 ...  2 million high-quality 35bp reads v.
  human g. in 20 mins, 2.3GB ..."
   -- [<A HREF="http://maq.sourceforge.net/bwa-man.shtml">bwa-man</A>]@[<A HREF="http://maq.sourceforge.net/">maq</A>][7/'09].
   [Also search for: short read MolBio].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/BWT/">BWT</A>].)

%T The Biology of Genomes, 5-9 May 2009, Cold Spring Harbor, New York:
   Water flea boasts whopper gene count
%J Science
%V 324
%N 5932
%P 1252
%M JUN
%D 2009
%K news, views, c2009, c200x, c20xx, MolBio, genome, water flea, pea aphid,
   fleas, aphids, Daphnia pulex, arthropods, arthropod, genes
%X "... Daphnia pulex, a crustacean common in lakes and ponds around the world.
   Since '04, the Department of Energy Joint Genome Institute in Walnut Creek,
   Ca., and a consortium that now numbers 350 investigators from 17 countries
   have been sequencing and analyzing the 200-million-base genome from a
   Daphnia that lived in a pond along the Pacific coast of Oregon. It is one of
   just two noninsect arthropods to be deciphered to date. ...
   ... seemed to have about 25,000 genes - a lot, but no record-breaker.
   Eventually, however, gene-finding programs found 31,000, ...  experiments
   have revealed as many as 8000 more genes that gene-finding annotation
   programs missed ... tops the gene count of the newly seq. genome of another
   tiny creature: the pea aphid, which sports 34,600 genes ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.324_1252a">doi:10.1126/science.324_1252a</A>]['09].

%A C. Zimmer
%T On the origin of sexual reproduction
%J Science
%V 324
%N 5932
%P 1254-1256
%M JUN
%D 2009
%K news, essay, MolBio, c2009, c200x, c20xx, zz0609, origin, origins, sex,
   sexual, reproduction, why, reason, Darwin, evolution
%X 'Why sex? In the sixth essay in Science's series in honor of the Year of
   Darwin, Carl Zimmer explores why so many species take such a labyrinthine
   path to reproduction, when straightforward routes are available.
   For Darwin, sex was a big question mark. "We do not even in the least know
   the final cause of sexuality; why new beings should be produced by the union
   of the two sexual elements," he wrote in 1862. "The whole subject is as yet
   hidden in darkness." ...'
   -- [<A HREF="http://dx.doi.org/10.1126/science.324_1254">doi:10.1126/science.324_1254</A>]['09].

%A D. Monroe
%T Genomic clues to DNA treasure sometimes lead nowhere
%J Science
%V 325
%N 5937
%P 142-143
%M JUL
%D 2009
%K news, MolBio, Rubin, c2009, c200x, c20xx, zz0709, genome, gene, regions,
   sequence conservation, DNA, genes, conserved region, function, evolution,
   mutation, ultraconserved, enhancer, enhancers
%X "... researchers looked at "ultraconserved" 200-base-long seqs. previously
   found to be identical in rats, mice, & humans and at others that were similar
   even in fish. The strategy worked- or so they thought. When they inserted
   those seqs. into mice, more than half turned on an accompanying reporter
   gene in particular tissues at a specific developmental stage.
   But when the LBNL team looked deeper at 4 promising candidates, they were
   surprised that none of them caused any obvious problem when deleted from the
   mouse genome. "There are a lot of [seqs.] that we thought if we knocked [one]
   out, it would kill the animal," Rubin recalls- but that didn't happen. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.325_142">doi:10.1126/science.325_142</A>]['09].

%A J. R. Banavar
%A A. Maritan
%T Ecology: Towards a theory of biodiversity
%J Nature
%V 460
%P 334-335
%M JUL
%D 2009
%K news, MolBio, c2009, c200x, c20xx, zz0709, bio diversity, biodiversity,
   ecology, ecological, Aguiar
%X "... First, some context. Life is a non-equilibrium phenomenon involving a
   'dual-diffusion' process. ... The environment is itself shaped by the
   individuals that make up the community, leading to a dynamic feedback
   mechanism. de Aguiar et al. present computer sim'ns of a specific neutral
   model of dual diffusion along with the process of sexual reproduction. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/460334a">doi:10.1038/460334a</A>]['09].
   [Also search for: Aguiar c2009].

%A M. A. M. de Aguiar
%A M. Baranger
%A E. M. Baptestini
%A L. Kaufman
%A Y. Bar-Yam
%T Global patterns of speciation and diversity
%J Nature
%V 460
%P 384-387
%M JUL
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, biological, bio, biol, diversity,
   ecology, ecological, evolution, speciation, model, computer simulation,
   Alife
%X "... report the simulation of pop'ns with sexual rep'n, mutation & dispersal.
   ... simulated time dependence of speciation rates, species-area relationships
   & species abundance dist'ns consistent with the behaviours found in nature.
   ... predict steady speciation rates, more species in 1-D environments than
   2-D env's, 3 scaling regimes of species-area relationships & log-normal
   distributions of species abundance with an excess of rare species & a tail
   that may be approx. by Fisher's logarithmic series. These are consistent with
   dependences reported [inc.] global birds & flowering plants, ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08168">doi:10.1038/nature08168</A>]['09].

%A Gu-Gang Chang
%T Quaternary structure of the SARS Coronavirus main protease
%J Molec. Biol. of the SARS-Coronavirus
%P 115-128
%M JUL
%D 2009
%K MolBiol, c2009, c200x, c20xx, zz0620, SARS CoV 1, SARSCoV, coronavirus,
   SARS1, corona virus, protein, protease, Mpro, 3CLpro, inhibitor, Cys145,
   C145, mechanism, works, working, operation, cleave, cleaves, cleaving,
   Michaelis complex, PLpro
%X "... The functional unit of the main protease is a dimer in which each
   subunit has a Cys145-His41 catalytic dyad, with His41 acting as a general
   base. There is also a close correlation between dimer formation and the
   enzyme catalytic activity. A flip-flop mechanism is proposed for the main
   protease, in which the two subunits are used alternately in acylation and
   deacylation. ..."
   "... Mpro cleaves [polyprotein] pp1a at 11 sites containing the canonical
   Leu-Gln-?-(Ala/Ser) seq. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-03683-5_8">doi: 10.1007/978-3-642-03683-5_8</A>]['20].
   [Also search for: MolBio SARS Mpro cleaves].

%A M. Berriman
%A et al
%T The genome of the blood fluke Schistosoma mansoni
%J Nature
%V 460
%P 352-358
%M JUL
%D 2009
%K jrnl, c2009, c200x, c20xx, MolBio, genome, nGenome, blood fluke, parasite,
   Schistosoma mansoni, tropical disease, schistosomiasis, micro-exon,
   microexon, alternative splicing, Smansoni, Lophotrochozoa, flatworm
%X "S.mansoni is responsible for the neglected tropical disease schistosomiasis
   that affects 210 million people in 76 countries. ... analysis of the 363
   megabase nuclear g. of the blood fluke. It encodes at least 11,809 genes,
   with an unusual intron size distribution, and new families of micro-exon
   genes that undergo frequent alternative splicing. As the first seq. flatworm,
   & a representative of the Lophotrochozoa, ..."
   "annotated g.seq. ... sub. EMBL with the accession #s FN357292-FN376313.
   All data @ [<A HREF="http://www.genedb.org/genedb/smansoni/">genedb.org</A>]['09]."
   (363 mega-bases, seven autosomal chrs, + ZW sex-determination pairs,
   40% of the g. repetitive.)
   -- [<A HREF="http://dx.doi.org/10.1038/nature08160">doi:10.1038/nature08160</A>]['09].

%A B. Schmidt
%A R. Sinha
%A B. Beresford-Smith
%A S. J. Puglisi
%T A fast hybrid short read fragment assembly algorithm
%J J. Bioinformatics
%V 25
%N 17
%P 2279-2280
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, Taipan, RMIT, sequence assembly, graph,
   fragment, fragments,  Greedy Extension,  Edena, DNA
%X "... sequencing tech. ... massive numbers of reads in reasonable time.
   Existing ... tools can be classified into 2 categories: greedy ext'n-based &
   graph-based. ... graph-based approaches are generally superior in terms of
   assembly quality, [resources] very high. ... present Taipan, an assembly
   alg. which can be viewed as a hybrid of these 2 approaches ... uses greedy
   ext'n for contig const'n but at each step realizes enough of the corr. read
   graph to make better decisions as to how assembly should continue. We show
   that this approach can achieve an assembly quality at least as good as the
   graph-based approaches used in the popular Edena & Velvet assembly tools
   using a moderate amount of computing resources. ... available at
   sw@[<A HREF="http://taipan.sourceforge.net">src frg</A>]['09]."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btp374">doi:10.1093/bioinformatics/btp374 </A>]['09].
   [Also search for: sequence assembly MolBio].

%A R. Li
%A C. Yu
%A Y. Li
%A T.-W. Lam
%A S.-M. Yiu
%A K. Kristiansen
%A J. Wang
%T SOAP2: an improved ultrafast tool for short read alignment
%J J. Bioinformatics
%V 25
%N 15
%P 1966-1967
%M AUG
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, SOAP 2, SOAP2, short read, reads,
   BW, BWT, string
%X "SOAP2 is a sig. improved version of ... SOAP.  ... We used a Burrows Wheeler
   Transformation (BWT) compression index to substitute the seed strategy for
   indexing the ref. seq. in the main memory. ... [Only] 5.4 GB & improved
   alignment speed by 20-30 times. ... compatible with both single- & paired-end
   reads. ..."  [6 refs].
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btp336">doi:10.1093/bioinformatics/btp336</A>['09],
   soap@[<A HREF="http://soap.genomics.org.cn/">genomics.org.cn/</A>]['09].
   [Also search for: resequencing MolBio],
   [also search for: short read MolBio].

%A J. J. W. Wiltzius
%A et al ...
%A D. Eisenberg
%T Molecular mechanisms for protein-encoded inheritance
%J Nat. Struct. & Molec. Biol.
%V 16
%P 973-978
%M AUG
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz0820, protein, fibril, folded,
   elk prion, disease, prions, beta sheet, mechanism, misfolded, 3FVA, NNQNTF
%X "... phenotypic variants encoded by protein 'conformations'. However, it is
   unclear how a protein conformation can be stable enough to endure
   transmission between cells or organisms. ... describe new polymorphic crystal
   structures of segments of prion & other amyloid proteins, which offer two
   structural mechanisms for the encoding of prion strains. ... prion strains
   are encoded by alternative packing arrangements (polymorphs) of beta-sheets
   formed by the same segment of a protein; in segmental polymorphism, prion
   strains are encoded by distinct beta-sheets built from different segments of
   a protein. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nsmb.1643">doi:10.1038/nsmb.1643</A>]['20].
   Also see 3FVA@[<A HREF="http://doi.org/10.2210/pdb3FVA/pdb">PDB</A>]['20].
   [Also search for: prion disease].

%A C. Hodges
%A L. Bintu
%A L. Lubkowska
%A M. Kashlev
%A C. Bustamante
%T Nucleosomal fluctuations govern the transcription dynamics of
   RNA polymerase II
%J Science
%V 325
%N 5940
%P 626-628
%M AUG
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, RNA, polymerase II, pol 2, pol2, polII,
   nucleosomal, nucleosome, histones, histone, DNA, transcription, transcribed
%X "RNA polymerase II (Pol II) must overcome the barriers imposed by nucleosomes
   during transcription elongation. ... follow individual Pol II complexes as
   they transcribe nucleosomal DNA. ... indicate that the n. behaves as a
   fluctuating barrier that locally increases pause density, slows pause
   recovery, & reduces the apparent pause-free velocity of Pol II. The pol.,
   rather than actively separating DNA from histones, functions instead as a
   ratchet that rectifies nucleosomal fluctuations. [and] transcription through
   a nucleosome involves transfer of the core histones behind the transcribing
   polymerase via a transient DNA loop.  ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1172926">doi:10.1126/science.1172926</A>].
   (Also see [<A HREF="http://www.sciencemag.org/cgi/content/full/325/5940/547">persp.</A>].)

%A R. Giancarlo
%A D. Scaturro
%A F. Utro
%T Textual data compression in computational biology: a synopsis
%J J. Bioinformatics
%V 25
%N 13
%P 1575-1586
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz0809, compress, compression,
   survey, intro
%X [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btp117"> doi:10.1093/bioinformatics/btp117</A>]['09].

%A D. Pushkarev
%A N. F. Neff
%A S. R. Quake
%T Single-molecule sequencing of an individual human genome
%J NatureBiotech.
%P ?-?
%V ?-?
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz0809, single molecule sequencing, DNA,
   short read, reads
%X "... report the use of single-molecule methods to seq. [a] human genome.
   We aligned billions of 24-70 bp reads (32bp avg.) to ~90% of the [NCBI]
   ref.genome, with 28x avg. coverage. ... on 1 sequencing instrument by a
   single operator with 4 data collection runs. Single-molecule sequencing
   enabled analysis of human genomic information without the need for cloning,
   amplification or ligation. We determined ~2.8 million [SNPs] with a
   false +ve rate of less than 1% as validated by Sanger sequencing & 99.8%
   concordance with SNP genotyping arrays. We identified 752 regions of copy #
   variation by analyzing coverage depth alone & validated 27 of these ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nbt.1561">doi:10.1038/nbt.1561</A>]['09],  online Aug '09;
   auth3@[<A HREF="http://thebigone.stanford.edu/">stanf.u</A>]['09].
   [Also search for: short read MolBio].

%A D. Normile
%T Stem cell research: Recipe for induced pluripotent stem cells just got
   clearer
%J Science
%V 325
%N 5942
%P 803
%M AUG
%D 2009
%K news, views, c2009, c200x, c20xx, MolBio, pluripotent, stem cell, cells,
   stemCell, iPS, p53, gene
%X "... 5 letters publ. online in Nature on 9 Aug. ...  showing that p53, a gene
   noted for its role in suppressing tumors, hinders the gen'n of iPS cells. ...
   suggests ways to control the formation of iPS cells, [but must] be used
   judiciously because p53 helps ensure the fitness of generated cells ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.325_803a">doi:10.1126/science.325_803a</A>]['09].
   [Also search for: MolBio stem cell].

%A I. McCalman
%T Darwin's Armada: Four Voyages and the Battle for the Theory of Evolution
%I Norton
%P 432
%M AUG
%D 2009
%K book, text, c2009, c200x, c20xx, zz1109, Charles Darwin, evolution, origin,
   origins, theory, natural selection, species, biol, biology
%X "... of five parts. The first four recount the exploration expedition
   experiences of Darwin, Joseph Hooker, Thomas Huxley, and Alfred Wallace.
   The fifth describes the events surrounding the publication of Darwin's and
   Wallace's papers on evolution and the subsequent battles to win support for
   their theory. ..."
   1st ed 2009, hd us$20; uk us isbn:0393068145; uk us isbn13:978-0393068146.

%A J.-I. Kim
%A et al
%T A highly annotated whole-genome sequence of a Korean individual
%J Nature
%V 460
%P 1011-1015
%M AUG
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz0809, human genome, Korean, Korea, asia,
   asian
%X "... To date, h.genome seqs. have been reported ... 3 distinct geographical
   regions: a Yoruba African, 2 individuals of NW Euro. origin, and ... China.
   Here ... Korean individual, known as AK1. ...  Alignment to the NCBI ref.,
   a composite of several ethnic clades, disclosed nearly 3.45 million
   [SNPs], inc. 10,162 non-synonymous SNPs, & 170,202 [indels] ..."
   "Data ... deposited ... NCBI short read archive under accession #SRA008370.
   ...also available freely from [<A HREF="http://gmi.ac.kr">.kr</A>]. SNPs &
   indels are deposited in the dbSNP database under handle GMI. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08211">doi:10.1038/nature08211</A>]['09].

%A N. Le Novere
%A et al
%A H. Kitano
%T The systems biology graphical notation
%J Nature
%V 27
%P 735-741
%M AUG
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, S.Boyd, SBGN, diagram, activity,
   systems biology, biol
%X corrected Sept. 2009
   "... present the Systems Biology Graphical Notation (SBGN), a visual language
   dev. by a community of biochemists, modelers & computer scis.. SBGN consists
   of 3 complementary languages: process diagram, entity relationship diagram
   & activity flow diagram. ... enable scientists to represent n/works of
   biochemical interactions in a standard, unambiguous way. We believe that SBGN
   will foster efficient & accurate representation, visualization, storage,
   exchange & reuse of information on all kinds of biological knowledge, from
   gene regulation, to metabolism, to cellular signaling."
   -- [<A HREF="http://dx.doi.org/10.1038/nbt.1558">doi:10.1038/nbt.1558</A>]['11] (via arun2).

%A F. Luciania
%A S. A. Sisson
%A H. Jiang
%A A. R. Francis
%A M. M. Tanaka
%T The epidemiological fitness cost of drug resistance in Mycobacterium
   tuberculosis
%J PNAS
%V 106
%N 4
%P 14711-14715
%M AUG
%D 2009
%K jrnl, PNAS, MolBio, c2009, c200x, c20xx, zz0113, TB, bacteria, mycobacteria,
   drug resistance, disease, risks, UWS, uniWS
%X "... acquisition of resistance to antibs. results in a longer duration of
   infection in a host ... may come at a cost through a decreased transmission
   rate. ... whether the overall fitness of drug-r. strains is higher than that
   of sensitive strains - essential info. for predicting the spread of the
   disease. ... directly est. the transmission cost of drug resistance, the rate
   at which r. evolves, & the relative fitness of r.strains. These ests. are
   made by using explicit models of the transmission & evoln of sensitive &
   r. strains of M.tuberculosis, using approx. Bayesian compn, & molec.
   epidemiology data from Cuba, Estonia, & Venezuela. We find that the
   transmission cost of drug r. relative to sensitivity can be as low as 10%,
   that r. evolves at rates of ~ 0.0025-0.02/case/year, & that the overall
   fitness of r.strains is comparable with that of sensitive strains.
   Furthermore, the contribution of transmission to the spread of drug r. is
   v.high compared with acquired r. due to treatment failure (up to 99%). ...
   suggest that the prevalence of tuberculosis may decline with successful
   treatment, but the proportion of cases assoc. with r. is likely to increase."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0902437106">doi:10.1073/pnas.0902437106</A>]['13],
   auth4@[<A HREF="http://www.uws.edu.au/staff_profiles/uws_profiles/professor_andrew_francis">UWS</A>]['13].

%A J. Schroder
%A H. Schroder
%A S. J. Puglisi
%A R. Sinha
%A B. Schmidt
%T SHREC: A short-read error correction method
%J J. Bioinformatics
%V 25
%N 17
%P 2157-2163
%M SEP
%D 2009
%K SHREC, jrnl, MolBio, c2009, c200x, c20xx, zz0809, shrek, short read, reads,
   sequencing, base calling, errors, error correction
%X "... new alg. for correcting errors in short-read data that uses a
   generalized suffix trie on the read data as the underlying data structure.
   ... show that the method can identify erroneous reads with sensitivity &
   specificity of over 99% & 96% for simulated data with error rates of up to
   3% as well as for real data. [and] achieves an error correction accuracy of
   over 80% for simulated data and over 88% for real data. ..."
   -- pdf@[<A HREF="http://dx.doi.org/10.1093/bioinformatics/btp379">doi:10.1093/bioinformatics/btp379</A>]['09],
   shrec@[<A HREF="http://www.informatik.uni-kiel.de/~jasc/Shrec/">uni-kiel.de</A>][6/'10].
   [Also search for: short read MolBio] and
   [also search for: MolBio base calling error correction].

%A J. A. Marshall Graves
%T Sex determination: Birds do it with a Z gene
%J Nature
%V 461
%P 177-178
%M SEP
%D 2009
%K news, views, c2009, c200x, c20xx, Z chromosome, chr Z, chrZ, Zchr, sex,
   gender, determining, bird, birds, Z, Zchr, chrZ, Wchr, chrW, W, ZW, ZZ,
   DMRT1 gene
%X "... this all-important locus is revealed as a gene on the Z chr known for
   its proclivity for determining sex in all kinds of animals. ... males having
   two Z chrs & females a single Z & a W chr. The sex-chr pairs of most mammals
   & birds share none of their suites of genes, but the gene-rich bird Z chr &
   the condensed & gene-poor W chr show uncanny parallels with the mammalian X
   & Y chrs. The ZW & XY sex-chr pairs evidently evolved from different non-sex
   chr (autosome) pairs as one of the two partners acquired a sex-determining
   locus & then degenerated. ... Smith et al.1 provide direct evidence that the
   DMRT1 gene is the long sought bird sex-determining gene. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/461177a">doi:10.1038/461177a</A>]['09];
   Also see [<A HREF="http://dx.doi.org/10.1038/nature08298">doi:10.1038/nature08298</A>]['09].

%A C. A. Smith
%A K. N. Roeszler
%A T. Ohnesorg
%A D. M. Cummins
%A P. G. Farlie
%A T. J. Doran
%A A. H. Sinclair
%T The avian Z-linked gene DMRT1 is required for male sex determination in the
   chicken
%J Nature
%V 461
%P 267-271
%M SEP
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, xx0909, Z chromosome, chr Z, chrZ, Zchr,
   sex, gender, determining, bird, birds, Z, Zchr, chrZ, W, Wchr, chrW, ZW, ZZ,
   DMRT1 gene, dosage, SOX9, chicken, chickens, fowl
%X "Sex in birds is chromosomally based ... In the chicken & all other birds,
   the homogametic sex is male (ZZ) & the heterogametic sex is female (ZW). ...
   Here we used RNA interference (RNAi) to knock down DMRT1 in early chicken
   embryos. Reduction of DMRT1 protein expression in ovo leads to feminization
   of the embryonic gonads in genetically male (ZZ) embryos. ... results
   indicate that DMRT1 is required for testis determination in the chicken. Our
   data support the Z dosage hypothesis for avian sex determination."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08298">doi:10.1038/nature08298</A>]['09].

%A D. N. Ciccone
%A et al
%T KDM1B is a histone H3K4 demethylase required to establish maternal genomic
   imprints
%J Nature
%V 461
%P 415-418
%M SEP
%D 2009
%K jrnl, c2009, c200x, c200x, MolBio, DNA, methylation, AOF1, amine oxidase,
   LSD1, lysine demethylase, KDM1, KDM1B, LSD1, H3K4, demethylase,
   imprinted genes, imprinting, gene, oogenesis
%X "Differential DNA methylation of the paternal & maternal alleles regulates
   the parental origin-specific expression of imprinted genes in mammals. The
   methylation imprints are established in male & female germ cells during
   gametogenesis ... Here we show that amine oxidase (flavin-containing) domain1
   (AOF1), a protein related to the lysine demethylase KDM1 (also known as
   LSD1), functions as a histone H3 lysine 4 (H3K4) demethylase & is required
   for de novo DNA methylation of some imprinted genes in oocytes. AOF1, now
   renamed lysine demethylase 1B (KDM1B) ... Our results suggest that
   demethylation of H3K4 is critical for establishing the DNA methylation
   imprints during oogenesis."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08315">doi:10.1038/nature08315</A>]['09].
   (Also see news & views [<A HREF="http://dx.doi.org/10.1038/461359a">doi:10.1038/461359a</A>]['09].)

%A J. T. Bridgham
%A E. A. Ortlund
%A J. W. Thornton
%T An epistatic ratchet constrains the direction of glucocorticoid receptor
   evolution
%J Nature
%V 461
%P 515-519
%M SEP
%D 2009
%K jrnl, MolBio, c2009, c200x, c200x, zz0909, protein, proteins, evolution,
   reversibility, reverse, restrictive mutations, glucocorticoid receptor
%X "The extent to which evolution is reversible has long fascinated ... By
   studying the reversibility of evol'y changes in protein struct. & fn, these
   limitations can be overcome. ... show, using the evolution of hormone
   specificity in the vertebrate glucocorticoid receptor as a case-study, that
   the evol. path by which this protein acquired its new fn soon became
   inaccessible to reverse exploration. ... demonstrate that 5 subsequent
   'restrictive' mutations, which optimized the new specificity of the
   g.receptor, also destabilized elts of the protein structure that were
   required to support the ancestral conformation. Unless these ratchet-like
   epistatic substitutions are restored to their ancestral states, reversing the
   key function-switching mutations yields a non-functional protein. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08249">doi:10.1038/nature08249</A>]['09].

%A K. Kimura
%A Y. Suzuki
%A Y. Sugano
%A A. Koike
%T Computation of rank and select functions on hierarchical binary string and
   its application to genome mapping problems for short-read DNA sequences
%J J. Comput. Biol.
%P ?-?
%M ?
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, short read, reads, compressed index, BWT,
   rank, select
%X "... efficient in-practice algs. for computing rank & select fns. on a binary
   string, based on a novel data structure, a hierarchical binary string with
   hierarchical accumulatives.  ... required space overhead ratio is only about
   3.5% irrespective of the string length. Values of rank & select fns. are
   computed hierarchically in ceil((log2 n)/8) iterations, where n is the string
   length. ... large-scale short-read DNA sequence data, especially produced by
   ultra-high-throughput new-generation DNA sequencers. The algs. are applied to
   the binarization of the BWT of the human genome DNA seq.. For the sake of
   high-speed performance, we adopted a somewhat stringent mapping condition
   that allows at most a single-base mismatch (either a subs'n, [indel] of a
   single base) per query sequence. ..."   [Online Sept '09].
   -- [<A HREF="http://dx.doi.org/10.1089/cmb.2008.0146">doi:10.1089/cmb.2008.0146</A>]['09] via TS.
   * [Also search for: short read MolBio],  [also search for: rank select].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/BWT/">BWT</A>].)

%A C. Spyrou
%A R. Stark
%A A. G. Lynch
%A S. Tavare
%T BayesPeak: Bayesian analysis of ChIP-seq data
%J BMC Bioinformatics
%V 10
%P 299
%D 2009
%K jrnl, eJrnl, BayesPeak, c2009, c200x, c20xx, MolBio, ChIP seq, DNA, protein,
   binding sites, site, transcription factor, HMM, MCMC algorithm, stochastic,
   peak, peaks, find, finding, finder, Chromatin immunoprecipitation,
   mapability, mappability
%X "... BayesPeak, uses a fully Bayesian hidden Markov m. to detect enriched
   locns in the genome. ... accommodates the nat.features of Solexa/Illumina
   sequencing data & allows for overdispersion in the abundance of reads in
   different regions. [&] a control sample can be incorporated in the analysis
   to account for experimental & sequence biases.  MCMC algs. ... to est. the
   posterior dist'n of the model params., & posterior probs. are used to detect
   the sites of interest. ..."   [36 refs].
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-10-299">doi:10.1186/1471-2105-10-299</A>]['09].
   [Also search for: ChIP seq peak MolBio].

%A T.-K. Yeha
%A C.-Y. Changa
%A C.-Y. Hud
%A T.-C. Yehe
%A M.-Y. Lin
%T Association of catechol-O-methyltransferase (COMT) polymorphism and academic
   achievement in a Chinese cohort
%J Brain and Cognition
%V ?
%N ?
%P ?-?
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, biol, biology, gene, genes, brain, memory,
   cognition, stress, anxiety, Met, 158Met, catechol-O-methyltransferase, COMT,
   academic, achievement, exam, examination, performance
%X "Catechol-O-methyltransferase (COMT) is a methylation enzyme that catalyzes
   the degradation pathway & inactivation of dopamine. It is accepted widely as
   being involved in the modulation of dopaminergic physiology & prefrontal
   cortex (PFC) function. ... COMT 158Met allele may be advantageous for PFC-
   -related cognitive abilities; however, it is also assoc. with increased
   anxiety, depression, & emotional vulnerability in response to stress ...
   ... 779 Taiwanese 10th-grade volunteers ... Scores from the Basic Competency
   Test (BCT), an annual national competitive entrance examination, ... results
   indicated that students bearing homozygous for the Met allele tended to
   perform more poorly in all BCT subtests as compared to the other groups. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.bandc.2009.07.011">doi:10.1016/j.bandc.2009.07.011</A>]['09].

%A J. C. Wang
%T Untangling the Double Helix DNA Entanglement and the Action of the DNA
   Topoisomerases
%I Cold Spring Harbor Laboratory Press
%P 245
%D 2009
%K book, text, c2009, c200x, c20xx, zz1009, MolBio, biol, biology, DNA,
   double helix, super coil, supercoil, helical, superhelical, scissile strand,
   replication, chromosome, topoisomerase
%X 1st ed 2009; pb us$45, us isbn:0879698799, us isbn13:9780879698799 (?);
                hb us$79; us isbn:0879698632, us isbn13:9780879698638.
   Reviewed [<A HREF="http://dx.doi.org/10.1126/science.1177945">doi:10.1126/science.1177945</A>]['09].
   Also see J.C.Wang, JMB, 55(3), pp.523-533, Feb. 1971,
   -- [<A HREF="http://dx.doi.org/10.1016/0022-2836(71)90334-2">doi:/10.1016/0022-2836(71)90334-2</A>].

%A C. K. Yoon
%T Naming Nature: The Clash Between Instinct and Science
%I W.W.Norton
%P 352
%D 2009
%K book, text, c2009, c200x, c20xx, zz1009, taxonomy, taxonomic, biology, biol,
   biological, botany, botanical, classification, taxa, species, families,
   natural history
%X 1st ed 2009, hb us$19; uk isbn:0393061973; uk isbn13:978-0393061970.
   Reviewed in [<A HREF="http://dx.doi.org/10.1038/461597a">doi:10.1038/461597a</A>]['09].

%A J. A. L. Armour
%T Human genetics: Sharp focus on the variable genome
%J Nature
%V 461
%P 735-736
%M OCT
%D 2009
%K news, views, MolBio, c2009, c200x, c20xx, zz1009, human genome, genetic,
   variability, variation, diversity, SNP, SNPs, survey, summary, intro,
   copy number variation, CNV, CNVs
%X "Copy-number variation - deleted or duplicated regions of DNA - is widespread
   in the human genome. A systematic population survey of the common variants
   provides an invaluable resource for further studies. ..." [9 refs].
   -- [<A HREF="http://dx.doi.org/10.1038/461735a">doi:10.1038/461735a</A>]['09].

%A T. A. Manolio
%A et al
%T Finding the missing heritability of complex diseases
%J Nature
%V 461
%P 747-753
%M OCT
%D 2009
%K review, survey, intro, MolBio, c2009, c200x, c20xx, medicine, disease,
   heredity, association study, studies, genetic, risk, risks, CNV, CNVs,
   human health
%X "Genome-wide assoc.studies have identified hundreds of genetic variants
   assoc. with complex human diseases and traits ... Most variants identified so
   far confer relatively small increments in risk, [how] 'missing' heritability
   can be explained. Here we examine potential sources of missing h. and propose
   research strategies ..."  [84 refs].
   -- [<A HREF="http://dx.doi.org/10.1038/nature08494">doi:10.1038/nature08494</A>]['09].

%A F. Ozsolak
%A A. R. Platt
%A D. R. Jones
%A J. G. Reifenberger
%A L. E. Sass
%A P. McInerney
%A J. F. Thompson
%A J. Bowers
%A M. Jarosz
%A P. M. Milos
%T Direct RNA sequencing
%J Nature
%V 461
%P 814-818
%M OCT
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, Helicos, DNA, RNA, sequencing,
   RNA seq, RNAseq
%X "... report direct single molecule RNA sequencing without prior conversion of
   RNA to cDNA. We applied this technology to seq. femtomole quantities of
   poly(A)+ Saccharomyces cerevisiae RNA using a surface coated with poly(dT)
   oligonucleotides to capture the RNAs at their natural poly(A) tails &
   initiate seq. by synthesis. We observed transcript 3' end heterogeneity &
   polyadenylated small nucleolar RNAs. This study provides a path to
   high-throughput & low-cost direct RNA sequencing ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08390"> doi:10.1038/nature08390</A>]['09],
   (Also see [<A HREF="http://www.helicosbio.com/">helicosbio.com</A>]['09].)

%A E. Lieberman-Aiden
%A et al
%T Comprehensive mapping of long-range interactions reveals folding principles
   of the human genome
%J Science
%V 326
%N 5950
%P 289-293
%M OCT
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, Lander, Dekker, genome, 3D, fold, folding,
   folded, DNA, chromosome, chromosomes, open, closed, chromatin, conformation,
   Hi-C, HiC
%X "... Hi-C ... 3D architecture of whole genomes by coupling proximity-based
   ligation with massively parallel sequencing. We constructed spatial proximity
   maps of the human g. ... at a resolution of 1 megabase. ... confirm the
   presence of chromosome territories & the spatial proximity of small,
   gene-rich chr's. ... additional level of genome organization ... spatial
   segregation of open & closed chromatin to form 2 genome-wide compartments.
   At the megabase scale, the chromatin conformation is consistent with a
   fractal globule, a knot-free, polymer conformation that enables maximally
   dense packing while preserving the ability to easily fold & unfold any
   genomic locus. The fractal globule is distinct from the more commonly used
   globular equilibrium model. ..."  [37 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1181369">doi:10.1126/science.1181369</A>]['09].

%A C. Micheletti
%A H. Orland
%T MISTRAL: a tool for energy-based multiple structural alignment of proteins
%J J. Bioinformatics
%V 25
%N 20
%P 2663-2669
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz1009, protein structure, structures,
   alignment, matching, rotation, translation, MISTRAL
%X "... multiple protein alignment based on the minimization of an energy fn
   over the low-dimensional space of the relative rotations & translations of
   the molecules. The energy min'n avoids combinatorial searches & returns
   p/wise al.scores for which a reliable a priori statistical sig. ..."
      "... The optimal superposn of a given set of proteins is obt. by min. a
   suitable protein-p. interaction energy. The min. of the energy fn is carried
   out in the low-D space corr. to the orientations (translations & rotations)
   of the molecules in a given Cartesian ref.frame. Once the molecules are
   optimally oriented, the residue-residue correspondences are established by
   using simple criteria based on spatial proximity. Such corr. are therefore
   not sought by assuming any a priori seq. directionality among or within
   blocks of aligned residues in the two proteins ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btp506">doi:10.1093/bioinformatics/btp506</A>]['09],
   and [<A HREF="http://ipht.cea.fr/protein.php">server</A>]['09].

%A R. Lister
%A et al
%T Human DNA methylomes at base resolution show widespread epigenomic
   differences
%J Nature
%V 482
%N 7271
%P 315-322
%M NOV
%D 2009
%K jrnl, c2009, c200x, c20xx, MolBio, DNA, genome, methylation, epigenetic,
   epigenomic, methylome, nonCG, human embryonic stem cells, cell,
   foetal, fetal fibroblast, fibroblasts, map, cytosines
%X "... present the 1st genome-wide, single-base-resolution maps of methylated
   cytosines in a mammalian genome, from both human embryonic stem cells & fetal
   fibroblasts, along with comparative analysis of mRNA & small RNA components
   of the transcriptome, several histone modifications, & sites of DNA-protein
   interaction for several key regulatory factors. Widespread differences ... in
   the composition & patterning of cytosine methylation between the 2 genomes.
   Nearly 1/4 of all m. identified in embryonic stem cells was in a non-CG
   context ... embryonic stem cells may use different m. mechanisms to affect
   gene regulation. M. in non-CG contexts showed enrichment in gene bodies &
   depletion in protein binding sites & enhancers. Non-CG m. disappeared upon
   induced differentiation of the embryonic stem cells, & was restored in
   induced pluripotent stem cells. ... hundreds of differentially m. regions
   proximal to genes involved in pluripotency & differentiation, & widespread
   reduced m. levels in fibroblasts assoc. with lower transc. activity. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08514">doi:10.1038/nature08514</A>]['09], online Oct 2009,
   also see h-methylome@[<A HREF="http://neomorph.salk.edu/human_methylome/">salk</A>]['09].

%A N. J. Fast
%T S. Chen
%T When the boss feels inadequate: Power, incompetence, and aggression
%J Psychological Sci.
%V ?
%P ?-?
%M online Oct '09
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1009, human behaviour, boss, bosses, bully,
   psychology, bullying, the office, ego, competence, competent, incompetence,
   incompetent, power, aggression, aggressive
%X "... 4 studies demo. that individuals with power become aggressive when they
   feel incompetent in the domain of power. Regardless of whether power was
   measured in the workplace (1 & 4), manipulated via role recall (2), or
   assigned in the lab. (3), it was associated with heightened aggression
   when paired with a lack of self-perceived competence. As hypothesized, this
   aggression appeared to be driven by ego threat: A. was eliminated among
   participants whose sense of self-worth was boosted (3 & 4). ... findings
   suggest that (a) power paired with self-perceived incompetence leads to
   aggression, & (b) this aggressive response is driven by feelings of ego
   defensiveness. ..."  (online Oct '09).
   -- [<A HREF="http://dx.doi.org/10.1111/j.1467-9280.2009.02452.x">doi:10.1111/j.1467-9280.2009.02452.x</A>][online 10/'09].

%A J. M. Coffin
%A J. P. Stoye
%T A new virus for old diseases?
%J Science
%V 326
%N 5952
%P 530-531
%M OCT
%D 2009
%K perspective, c2009, c200x, c20xx, MolBio, xenotropic murine leukemia virus,
   views, XMRV, MRV, prostate cancer, chronic fatigue, endogenous viruses, viral
%X "... xenotropic murine leukemia virus-related virus (XMRV) in about 2/3 of
   patients diagnosed with chronic fatigue syndrome. ... The virus 1st was
   described about 3 years ago in a few prostate cancer patients, & recently
   detected in nearly 1/4 of all prostate cancer biopsies. ... been isolated
   from both prostate cancer & CFS patients ... Endogenous viruses, such as
   xenotropic MLV, arise when retroviruses infect germline cells. The integrated
   viral DNA, or provirus, is passed on to offspring as part of the host genome.
   Endogenous proviruses form a large part of the genetic complement of modern
   mammals - about 8% of the human genome, ..."  [11 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1181349">doi:10.1126/science.1181349</A>]['09].

%A I. Krajbich
%A C. Camerer
%A J. Ledyard
%A A. Range
%T Using neural measures of economic value to solve the public goods free-rider
   problem
%J Science
%V 326
%N 5952
%P 596-599
%M OCT
%D 2009
%K jrnl, c2009, c200x, c20xx, public good, game, human behaviour, benefit,
   group, free rider, freerider, cheat, individual, cost, goods, benefits
%X "Every social group needs to decide when to provide public goods & how to
   allocate the costs among its members. Ideally, this decision would maximize
   the group's net benefits while also ensuring that every individual's benefit
   is greater than the cost he or she has to pay. Unfortunately, the economic
   theory of mechanism design has shown that this ideal soln is not feasible
   when the group leadership does not know the values of the individual group
   members for the public good. We show that this impossibility result can be
   overcome in lab.settings by combining technologies for obtaining neural
   measures of value (functional magnetic resonance imaging-based pattern
   class'n) with carefully designed institutions that allocate costs based on
   both reported & neurally measured values."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1177302">doi:10.1126/science.1177302</A>]['09].

%A P. E. McGovern
%T Uncorking the Past: The Quest for Wine, Beer, and Other Alcoholic Beverages
%I U. California Press
%P 348
%M OCT
%D 2009
%K book, text, c2009, c200x, c20xx, zz1109, wine, beer, alchohol, beverage,
   booze, history, origin, origins, alchoholic drinks, fermentation, fermented,
   beers, wines, mead, viniculture
%X "... trail of archaeological, chemical, artistic, & textual clues, ...  how
   humans created & enjoyed fermented beverages across cultures. ... explores a
   provocative hypothesis about the integral role such libations have played in
   human evolution. We discover, for example, that the cereal staples of the
   modern world were probably domesticated for their potential in making
   quantities of alcoholic beverages. These include the delectable rice wines of
   China & Japan, the corn beers of the Americas, & the millet & sorghum drinks
   of Africa. Humans also learned how to make mead from honey & wine from
   exotic fruits of all kinds-even from the sweet pulp of the cacao (chocolate)
   fruit in the New World. ..."
   1st ed 2009, hb us$20; uk us isbn:0520253795; uk us isbn13:978-0520253797.

%A R. Rohs
%A S. M. West
%A A. Sosinsky
%A P. Liu
%A R. S. Mann
%A B. Honig
%T The role of DNA shape in protein-DNA recognition
%J Nature
%V 461
%P 1248-1253
%M OCT
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz1109, protein, DNA, recognition,
   recognize, recognise, interaction, shape, major, minor groove, grooves,
   AT rich, atRich, TpA, polyA
%X "The recognition of specific DNA seqs. by proteins is thought to depend on
   2 types of mechanism: one that involves the formation of hydrogen bonds with
   specific bases, primarily in the major groove, & one involving sequence-
   -dependent deformations of the DNA helix. ... analysing the [3D] structures
   of protein-DNA complexes, here we show that the binding of arginine residues
   to narrow minor grooves is a widely used mode for protein-DNA recognition.
   ... Minor-groove narrowing is often associated with the presence of A-tracts,
   AT-rich sequences that exclude the flexible TpA step. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08473">doi:10.1038/nature08473</A>]['09].

%E A. A. Komar
%T Single Nucleotide Polymorphisms: Methods and Protocols
%I Humana
%S Methods in Molecular Biology
%P 466
%M OCT
%D 2009
%K book, text, MolBio, c2009, c200x, c20xx, single nucleotide polymorphism,
   SNP, SNPs
%X 2nd ed 2009; hb us$88;  uk us isbn:1603274103; uk us isbn13:978-1603274104.
   1st ed 2002; hb us$115; uk us isbn:0896039684; uk us isbn13:978-0896039681.

%A L. E. Zanno
%A D. D. Gillette
%A L. B. Albright
%A A. L. Titus
%T A new North American therizinosaurid and the role of herbivory in 'predatory'
   dinosaur evolution
%J Proc. Royal Soc. B
%B 276
%N 1672
%P 3505-3511
%M OCT
%D 2009
%K jrnl, PRS, PRSB, c2009, c200x, c20xx, paleontology, dinosaur, fossil,
   Nothronychus graffami, Merle H Graffam, therizinosauria, hypercarnivory,
   carnivore, predator, evolution
%X "... Max. parsimony optimizations of character evoln within our study
   indicate an ancestral origin for dietary plasticity & facultative herbivory
   (omnivory) within the clade. ... suggest that hypercarnivory in paravian
   dinosaurs is a secondarily derived dietary specialization & provide a
   potential mechanism for the invasion of novel morpho- & ecospace early in
   coelurosaurian evolution - the loss of obligate carnivory & origin of
   dietary opportunism."  [online July 2009.]
   Named in honour of M.Graffam who discovered the holotype, 2 miles N. of
   Big Water, Utah, in tropic shale layers 93my old. (LA met MG in 2012.)

%A Z. R. M. Kashani
%A H. Ahrabian
%A E. Elahi
%A A. Nowzari-Dalini
%A E. S. Ansari
%A S. Asadi
%A S. Mohammadi
%A F. Schreiber
%A A. Masoudi-Nejad
%T Kavosh: A new algorithm for finding network motifs
%J BMC Bioinformatics
%V 10
%P ?
%M OCT
%D 2009
%K jrnl, eJrnl, c2009, c200x, c20xx, zz0914, Kavosh, biol, network, motif,
   FANMOD, MAVisto, Mfinder
%X "... new alg. (Kavosh), for finding k-size n/w motifs with less memory & CPU
   time in comparison to other existing algorithms. Our alg. is based on
   counting all k-size sub-graphs of a given graph (directed or undirected). We
   eval. our alg. on biol. n/ws of E.coli & S.cereviciae, & also on non-biol.
   n/ws: a social & an electronic n/w. ... comparing the obtained results with
   three well-known motif finding tools. For comparison, the CPU time, memory
   usage & the similarities of obtained motifs are considered. Besides, Kavosh
   can be employed for finding motifs of size greater than eight ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-10-318">doi:10.1186/1471-2105-10-318</A>]['14].  (F.Schreiber @mon'sh c2013.)
   *** [Also search for: enumerate subgraph graph].

%A H. Hasegawa
%A L. Holm
%T Advances and pitfalls of protein structural alignment
%J Curr. Opin. Struct. Biol.
%V 19
%N 3
%P 341-348
%M JUN
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, protein, structure, alignment, 3D,
   survey, intro, methods, scoring, tmScore, rmsd
%X "... A variety of methods use different repns, scoring fns, & optimization
   algs., & they generate contradictory results even for moderately distant
   structures.  Seq.mutations, insertions, & deletions are accommodated by
   plastic deformations of the common core, retaining the precise geometry
   of the active site, & peripheral regions may refold completely. Therefore
   struct.comparison methods that allow for flexibility & plasticity generate
   the most biologically meaningful alignments. Active research dirns inc. both
   the search for fold invariant features & the modeling of structural
   transitions in evolution. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.sbi.2009.04.003">doi:10.1016/j.sbi.2009.04.003</A>]['09],
      [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/19481444">p'bmed</A>]['09].

%A S. A. Hollingsworth
%A D. S. Berkholz
%A P. A. Karplus
%T On the occurrence of linear groups in proteins
%J Protein Sci.
%V 18
%N 6
%M JUN
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz0212, linear groups, protein, structure,
   repeating, 3D, alpha, beta, 310, 2.27, pi, Pii, helices
%X "Linear groups - polypeptide conformations based on a single repeating
   phi-psi pair are a foundational concept ... . Now, ultra-high resolution
   protein structures provide a resource for an accurate empirical and
   systematic assessment of the linear groups that truly exist in proteins.
   Here, a purely conformation-based survey of linear groups shows that only
   three distinct phi-psi-regions occur: a diverse set of extended conformations
   mostly present as beta-strands, a broad population of polyproline-II-like
   spirals, and a tight cluster that includes the highly populated alpha-helix
   and the conformationally-similar but much less populated 310-helix. Rare,
   short left-handed alpha-/310-helical turns with repeating phi-psi-angles
   occur, but none are longer than three residues. Misperceptions dispelled by
   this study are the existence of 2.27- and pi-helices as linear groups, the
   existence of specific ideal phi-psi-angles for each linear group, and the
   existence of a substantive difference in the phi-psi-preferences for parallel
   v. antiparallel beta-strands. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/pro.133">doi:10.1002/pro.133</A>]['12],
    & [<A HREF="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774442/">nc'i</A>]['12].
   [Also search for: Hollingsworth MolBio].

%A N. Martin-Orozco
%A et al ...
%A C. Dong
%T T Helper 17 cells promote cytotoxic T cell activation in tumor immunity
%J J. Immunity
%V ?
%P ?-?
%M ?
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, T cells, TH1, T helper cell 17, TH, TH17,
   interleukin 17, IL-17, IL17, autoimmune disease, cancer, CD8, mice
%X "Although [Th17] cells have been found in tumor tissues, their fn in cancer
   immunity is unclear. We found that interleukin-17A (IL-17A)-deficient mice
   were more susceptible to developing lung melanoma. Conversely, adoptive T
   cell therapy with tumor-specific Th17 cells prevented tumor development.
   Importantly, the Th17 cells retained their cytokine signature & exhibited
   stronger therapeutic efficacy than Th1 cells. Unexpectedly, therapy using
   Th17 cells elicited a remarkable activation of tumor-specific CD8+ T cells,
   which were necessary for the antitumor effect. ..."  [online Oct 2009].
   -- [<A HREF="http://dx.doi.org/10.1016/j.immuni.2009.09.014">doi:10.1016/j.immuni.2009.09.014</A>]['09]?,
   & news@[<A HREF="http://www.mdanderson.org/newsroom/news-releases/2009/th17-cells-summon-an-immune-system-strike-against-cancer.html">mdanderson</A>]['09] C. Center.

%T A proposal to obtain whole-genome sequence for 10,000 vertebrate species
%Q Genome 10K Community of Scientists
%J J. Hered.
%V ?
%P ?-?
%M NOV
%D 2009
%K news, c2009, c200x, c20xx, zz1109, MolBio, 10K, genomes, genome10k, proposal,
   sequencing
%X [<A HREF="http://genome10k.org/">genome10k.org</A>]['09],
   -- [<A HREF="http://jhered.oxfordjournals.org/">J. of H.</A>]['09].

%A H. J. E. Beaumont
%A J. Gallie
%A C. Kost
%A G. C. Ferguson
%A P. B. Rainey
%T Experimental evolution of bet hedging
%J Nature
%V 462
%P 90-93
%M NOV
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, bet hedging, hedge, multiple phenotypes,
   environmental change, changes, conditions, bets
%X "Bet hedging - stochastic switching between phenotypic states - is a
   canonical example of an evolutionary adaptation that facilitates persistence
   in the face of fluctuating environmental conditions. Although bet hedging is
   found in organisms ranging from bacteria to humans direct evidence for an
   adaptive origin of this behaviour is lacking. Here we report the de novo
   evolution of bet hedging in experimental bacterial populations. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08504">doi:10.1038/nature08504</A>]['09].

%A C. M. Wade
%A et al
%T Genome sequence, comparative analysis, and population genetics of the
   domestic horse
%J Science
%V 326
%N 5954
%P 865-867
%M NOV
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz1109, horse, Equus caballus, genome,
   nGenome, breed, breeds, horses, ECA, ECA11
%X "... genome of the horse (Equus caballus [ECA]). The g. is rel. repetitive
   but has little segmental duplication. Chrs. appear to have undergone few
   historical rearrangements: 53% of equine chromosomes show conserved synteny
   to a single human chr..  Equine chr. 11 is shown to have an evolutionary new
   centromere devoid of centromeric satellite DNA, suggesting that centromeric
   fn may arise before satellite repeat accumulation. Linkage disequilibrium,
   showing the influences of early domestication of large herds of female h., is
   intermediate in length between dog & human, & there is long-range haplotype
   sharing among breeds."
   "64 (2N) equine chromosomes. ... 2.5- to 2.7-Gb genome size"  [18 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1178158">doi:10.1126/science.1178158</A>]['09].
   "Seqs have [<A HREF="http://www.ncbi.nlm.nih.gov/Genbank/">GenBank</A>]
   accession #s AAWR02000001 - AAWR02055316.  1,163,466 discovery SNPs have
   accession #s rs6844103 - rs69617090 in dbSNP 130".

%A T. de Lange
%T How telomeres solve the end-protection problem
%J Science
%V 326
%N 5955
%P 948-952
%M NOV
%D 2009
%K views, MolBio, c2009, c200x, c20xx, telomere, telomeres, damage, DNA,
   degredation, chromosomes
%X "The ends of eukaryotic chromosomes have the potential to be mistaken for
   damaged or broken DNA & must therefore be protected from cellular DNA damage
   response pathways. Otherwise, cells might permanently arrest in the cell
   cycle, & attempts to "repair" the chr. ends would have devastating
   consequences for genome integrity. This end-protection problem is solved by
   protein-DNA complexes called telomeres. Studies of mammalian cells have
   recently uncovered the mechanism by which telomeres disguise the chr. ends.
   Comparison to unicellular eukaryotes reveals key diffs. in ... response
   systems that inadvertently threaten chr. ends. Telomeres appear to be
   tailored to these var'ns, explaining their var. structure & composition."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1170633">doi:10.1126/science.1170633</A>]['09].

%A P. S. Schnable
%A et al ...
%A R. K. Wilson
%T The B73 maize genome: complexity, diversity, and dynamics
%J Science
%V 326
%N 5956
%P 1112-1115
%M NOV
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, maize, B73, grain, crop, plant, plants,
   Zea mays, grass, genome, nGenome, genes
%X "... an improved draft nucleotide sequence of the  2.3-gigabase genome  of
   maize ...  Over 32,000 genes were predicted, of which 99.8% were placed on
   ref.chromosomes. Nearly 85% of the genome is composed of hundreds of families
   of transposable elts., dispersed nonuniformly across the genome. These were
   responsible for the capture & amplification of numerous gene fragments &
   affect the composition, sizes, & positions of centromeres. We also report on
   the correlation of methylation-poor regions with Mu transposon insertions &
   recombination, & copy number variants with insertions &/or deletions, as well
   as how uneven gene losses between duplicated regions were involved in
   returning an ancient allotetraploid to a genetically diploid state ..."
      "... The 10 chromosomes of the maize genome ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1178534">doi:10.1126/science.1178534</A>]['10].

%A A. Stivala
%A A. Wirth
%A P. J. Stuckey
%T Tableau-based protein substructure search using quadratic programming
%J BMC Bioinformatics
%V 10
%P 153
%M MAY
%D 2009
%K jrnl, eJrnl, MolBio, c2009, c200x, c20xx, protein, structure, tableau,
   integer, quadratic, programming, maximal, max, similar, subtableau
%X "... detecting substructural similarities in proteins using tableaux.
   Tableaux are compared efficiently by solving the quadratic program (QP)
   corresponding to the quadratic integer program (QIP) formulation of the
   extraction of maximally-similar tableaux. ..."
   -- <A HREF="http://dx.crossref.org/10.1186/1471-2105-10-153">doi:10.1186/1471-2105-10-153</A>]['11].
   [Also search for: MolBio Mustang].

%A C. Trapnell
%A L. Pachter
%A S. L. Salzberg
%T TopHat: Discovering splice junctions with RNA-Seq
%J Bioinformatics
%V 25
%N 9
%N 1
%P 1105-1111
%M MAY
%D 2009
%K MolBio, cjrnl, c2009, c200x, c20xx, zz0820, TopHat, mRNA, RNAseq, RNAseq,
   splice junction, splicing, isoForm
%X "... millions of short seq. fragments ...  We mapped the RNA-Seq reads from a
   recent mammalian RNA-Seq experiment & recovered more than 72% of the splice
   junctions reported by the annotation-based s/w from that study, along with
   nearly 20,000 prev. unreported junctions. The TopHat pipeline is much faster
   than prev. systems, mapping nearly 2.2 million reads per CPU hour ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btp120">doi:10.1093/bioinformatics/btp120</A>]['20] (online March 2009).
   (Also see TopHat2@[<A HREF="https://doi.org/10.1186/gb-2013-14-4-r36">doi:10.1186/gb-2013-14-4-r36</A>][25/4/2013].)
   [Also search for: MolBio RNAseq].

%A A. Powell
%A S. Shennan
%A M. G. Thomas
%T Late Pleistocene demography and the appearance of modern human behavior
%J Science
%V 324
%N 5932
%P 1298-1301
%M JUN
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz1213, human, evolution, Homo sapiens,
   behavior, behaviour, culture, demography, population size, Paleolithic
%X "The origins of modern h.behavior are marked by increased symbolic &
   technological complexity in the archaeological record. In W.Eurasia this
   transition, the Upper Paleolithic, occurred about 45,000 y. ago, but many of
   its features appear transiently in S.Africa about 45,000 y. earlier. We show
   that demography is a major determinant in the maintenance of cultural
   complexity & that variation in regional subpopn density &/or migratory
   activity results in spatial structuring of cultural skill accumulation.
   Genetic ests. of regional popn size over time show that densities in early
   Upper Paleolithic Europe were similar to those in sub-Saharan Africa when
   modern behavior first appeared. Demographic factors can thus explain
   geographic variation in the timing of the first appearance of modern behavior
   without invoking increased cognitive capacity."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1170165">doi:10.1126/science.1170165</A>]['13].

%A B. Rupp
%T Biomolecular Crystallography. Principles, Practice, and Application to
   Structural Biology
%I Garland Sci., NY
%P 829
%D 2009
%K book, text, MolBio, c2009, c200x, c20xx, crystallography, X ray, Xray,
   protein, crystal, 3D, molecular, structure, determination, structures,
%X "fundamentals, practices, and applications of protein crystallography."
   1st ed 2009, hb us$141; uk us isbn:0815340818; uk us isbn13:9780815340812.
   [Also search for: MolBio Xray crystallography].

%T Sequence Alignment: Methods, Models, Concepts, and Strategies
%E M. S. Rosenberg
%I U. Calif. Press
%P 337
%D 2009
%K book, text MolBio, c2009, c200x, c20xx, method
%X us isbn:0520256972; us isbn13:978-0520256972.
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">alignment</A>].)

%A W. C. Wheeler
%A G. Giribet
%T Phylogenetic hypotheses and the utility of multiple alignment
%B Sequence alignment: methods, models, concepts, and strategies
%E M. S. Rosenberg
%I U. Calif. Press
%P 95-150
%D 2009
%K MolBio, UCP, c2009, c200x, c20xx, phylogenetic tree, evolutionary trees,
   multiple alignment, sequence
%X auth1@[<A HREF="http://research.amnh.org/scicomp/ward_wheeler.html">amnh.org</A>]['09].
   [Also search for: phylogenetic tree MolBio],
   [also search for: multiple alignment MolBio].

%A K. Liu
%A S. Nelesen
%A S. Raghavan
%A C. R. Linder
%A T. Warnow
%T Barking up the wrong treelength: The impact of gap penalty on alignment and
   tree accuracy
%J IEEE/ACM Trans. Comput. Biol. Bioinform.
%V 6
%N 1
%P 7-21
%M JAN-MAR
%D 2009
%K MolBio, c2009, c200x, c20xx, POY, phylogenetic tree, multiple alignment,
   Ogden, Rosenberg
%X "... POY ... Ogden & Rosenberg reported on a simulation study in which they
   compared POY [v.] alignment using ClustalW & then analyzing the resultant
   alignment using maximum parsimony. ... Our study suggests that optimizing
   under an affine gap penalty might produce alignments that are better than
   ClustalW alignments, & competitive with those produced by the best current
   alignment methods. We also show that optimizing under this affine gap penalty
   produces trees whose topological accuracy is better than ClustalW + MP, &
   competitive with the current best two-phase methods."
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/19179695">pubmed</A>]['09],
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.63">doi:10.1109/TCBB.2008.63</A>]['09] $ieee$.

%A L. Fisher
%T The Perfect Swarm: The Science of Complexity in Everyday Life
%I BasicBooks
%P 288
%M DEC
%D 2009
%K book, text, c2009, c200x, c20xx, zz0310, swarm, swarms, swarming, flock,
   flocking, animal behaviour, aLife, social networking, crowd dynamics
%X "... follow the crowd 60% of the time [only!] ..."
   1st ed 2009; hb us$16; uk us isbn:046501884X; uk us isbn13:978-0465018840.

%A Z. Weinberg
%A J. Perreault
%A M. M. Meyer
%A R. R. Breaker
%T Exceptional structured noncoding RNAs revealed by bacterial metagenome
   analysis
%J Nature
%V 462
%P 656-659
%M DEC
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz1209,noncoding RNA, ncRNA, bacteria,
   bacterium, bacterial metagenome, ribozymes, ribozyme
%X "Estimates of the total # of bacterial species indicate that [DBs] carry only
   a tiny fraction of the total amount of DNA seq. space represented by this
   division of life. ... Given that large structured RNAs are known to carry out
   complex biochemical functions such as protein synthesis & RNA processing
   reactions, identifying more RNAs of great size & intricate structure is
   likely to reveal additional biochemical functions ... We applied an updated
   computational pipeline to discover ncRNAs that rival the known large
   ribozymes in size & structural complexity or that are among the most abundant
   RNAs in bacteria that encode them. ..."  [62 refs].
   -- [<A HREF="http://dx.doi.org/10.1038/nature08586">doi:10.1038/nature08586</A>]['09].

%A R. Huxley
%A C. M. Y. Lee
%A F. Barzi
%A L. Timmermeister
%A S. Czernichow
%A V. Perkovic
%A D. E. Grobbee
%A D. Batty
%A M. Woodward
%T Coffee, decaffeinated coffee, and tea consumption in relation to incident
   type 2 diabetes mellitus. A systematic review with meta-analysis
%J Arch. Intern. Med.
%V 169
%N 22
%P 2053-2063
%M DEC
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1209, type2 diabetes, medicine, health, lower,
   zzCoffee, positive, less, risk, risks, human, life expectancy,
   coffee, decaffeinated, tea
%X "Coffee consumption has been reported to be inversely assoc. with risk of
   type 2 diabetes mellitus. Similar ... reported for decaffeinated coffee &
   tea. ... meta-analyses for the assoc. between coffee, decaffeinated coffee,
   & tea consumption with risk of diabetes. ... found an inverse log-linear
   relationship between coffee consumption & subsequent risk of diabetes s.t.
   every additional cup of coffee consumed in a day was assoc. with a 7%
   reduction in the excess risk of diabetes relative risk, 0.93 [95% CI,
   0.91-0.95]) after adjustment for potential confounders. ..."
   -- [<A HREF="http://archinte.ama-assn.org/cgi/content/short/169/22/2053">www</A>]['09].
   (Caf. and decaf., both.)   [Also search for: zzCoffee].

%T Mapping human genetic diversity in Asia
%Q The HUGO Pan-Asian SNP Consortium
%J Science
%V 326
%N 5959
%P 1541-1545
%M DEC
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, human, origins, evolution, migration,
   Asian, population movement, language, race, racial
%X "... report a large-scale survey of autosomal variation from a broad
   geographic sample of Asian human populations. ... show that genetic ancestry
   is strongly corr. with linguistic affiliations [&] geography. Most pop'ns
   show relatedness within ethnic/linguistic groups, despite prevalent gene flow
   among pop'ns. > 90% of East Asian (EA) haplotypes could be found in either
   S.E. Asian (SEA) or Central-South Asian (CSA) pop'ns & show clinal structure
   with haplotype diversity decreasing from south to north. [&] 50% of EA
   haplotypes were found in SEA only & 5% were found in CSA only, indicating
   that SEA was a major geographic source of EA populations."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1177074">doi:10.1126/science.1177074</A>]['09].

%A A. Kong
%A et al ...
%A K. Stefansson
%T Parental origin of sequence variants associated with complex diseases
%J Nature
%V 462
%P 868-874
%M DEC
%D 2009
%K jrnl, MolBio, deCODE, c2009, c200x, c20xx, Iceland, mother, father, parent,
   SNP, SNPs, rs2334499, 11p15, type 2, type2, diabetes, methylation, gene,
   inherit, inherited, child, disease, human health, risk, risks
%X "Effects of susceptibility variants may depend on from which parent they are
   inherited. ... the impact of parental origin has largely been ignored. Here
   we show that for 38,167 Icelanders genotyped using [SNP] chips, the parental
   origin of most alleles can be determined. ... used a combination of genealogy
   & long-range phasing. ... focused on SNPs that assoc. with diseases & are
   within 500 kilobases of known imprinted genes. Seven indep. SNP assocs. were
   examined. Five - one with breast cancer, one with basal-cell carcinoma &
   three with type-2 diabetes - have parental-origin-specific associations. ...
   [&] observed a novel association between the SNP rs2334499 at 11p15 & type-2
   diabetes. Here the allele that confers risk when paternally inherited is
   protective when maternally transmitted. We identified a differentially
   methylated CTCF-binding site at 11p15 & demonstrated correlation of
   rs2334499 with decreased methylation of that site."
   -- [<A  HREF="http://dx.doi.org/10.1038/nature08625">doi:10.1038/nature08625</A>]['09].

%A G. Sander van Doorn
%A P. Edelaar
%A F. J. Weissing
%T On the origin of species by natural and sexual selection
%J Science
%V 326
%N 5960
%P 1704-1707
%M DEC
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1209, origin, new, species, speciation,
   model, divergence, split, sexual preference, mating
%X  "... a simple model, we demo. that disruptive ecological selection favors
   the evoln of sexual prefs. for ornaments that signal local adaptation. Such
   prefs. induce assortative mating wrt ecological characters & enhance the
   strength of disruptive sel'n. Natural & sexual sel'n thus work in concert to
   achieve local adaptation & reproductive isolation, even in the presence of
   substantial gene flow. The resulting speciation process ensues without the
   divergence of mating prefs., avoiding problems that have plagued previous
   models of speciation by sexual selection."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1181661">doi:10.1126/science.1181661</A>]['09].

%A P. J. Stephens
%A D. J. McBride
%A et al ...
%A M. R. Stratton
%T Complex landscapes of somatic rearrangement in human breast cancer genomes
%J Nature
%V 462
%P 1005-1010
%M DEC
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, cancer, genome, DNA, rearrangement
%X "Multiple somatic rearrangements are often found in cancer genomes, but the
   underlying processes of rearrangement and the effects of this are unclear.
   A paired-end sequencing strategy is now used to map somatic rearrangements
   in human breast cancer genomes. More rearrangements in some breast cancers
   are found than previously recognized, including frequent tandem duplications
   that may reflect a specific defect in DNA maintenance. Short overlapping
   sequences at most rearrangement junctions indicate that these have been
   mediated by non-homologous end-joining DNA repair, although varying sequence
   patterns indicate that multiple processes of this type are operative. Several
   expressed in-frame fusion genes were identified but none was recurrent. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08645">doi:10.1038/nature08645</A>]['09].

%A D. Wu
%A P. Hugenholtz
%A et al ...
%A J. A. Eisen
%T A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
%J Nature
%V 462
%P 1056-1060
%M DEC
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, zz0110, phylogenetic, tree, evolutionary,
   evolution, microbe, microbial, bacteria, bacterium, Archaea
%X "... now nearly 1,000 completed bacterial and archaeal genomes available
   most of which were chosen for sequencing on the basis of their physiology.
   [so] the perspective provided by the currently available genomes is limited
   by a highly biased phylogenetic distribution. To explore the value added by
   choosing m.genomes for seq. on the basis of their evol. relationships, we
   have seq. and analysed the genomes of 56 culturable species of Bacteria and
   Archaea selected to maximize phylogenetic coverage. ... demonstrated
   pronounced benefits ([v.] an equiv. set of genomes randomly selected from the
   existing [DB]) ... results strongly support the need for systematic
   'phylogenomic' efforts to compile a phylogeny-driven 'Genomic Encyclopedia of
   Bacteria and Archaea' ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08656">doi:10.1038/nature08656</A>]['09].
   [Also search for: phylogenetic tree MolBio].

%A E. K. Costello
%A C. L. Lauber
%A M. Hamady
%A N. Fierer
%A J. I. Gordon
%A R. Knight
%T Bacterial community variation in human body habitats across space and time
%J Science
%V 326
%N 5960
%P 1694-1697
%M DEC
%D 2009
%K jrnl, MolBio, c2009, c200x, c20xx, bacteria, bacterium, human body,
   community, skin
%X "... surveyed bacteria from up to 27 sites in seven to nine healthy adults
   on four occasions. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1177486">doi:10.1126/science.1177486</A>]['10],
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/19892944">n c b i</A>]['10].
   (last auth@[<A HREF="http://chem.colorado.edu/index.php?option=com_content&view=article&id=263:rob-knight&catid=41:faculty&Itemid=93">col'rado</A>]['10].)

%A E. Grafahrend-Belau
%A B. H. Junker
%A C. Klukas
%A D. Koschuzki
%A F. Schreiber
%A H. Schwobermeyer
%T Topology of plant metabolic networks
%B Plant Metablic Networks
%E J. Schwender
%I SpringerVerlag
%P 173-209
%D 2009
%K MolBio, chapter, intro, survey, c2009, c200x, c20xx,
   plant, metabolic, network
%X "Metabolic networks can be modeled as graphs, i.e., math. structures
   consisting of vertices (rep. objects such as metabolites) & edges/hyper-edges
   (rep. the connection between objects such as reactions). An example of a very
   simple metabolic network is shown in Fig.7.1. Often the term network refers
   to an informal concept describing a structure composed of objects &
   connections, whereas the term graph refers to an abstract math. structure
   formed by a set of Vs. & a set of Es.. ... "  [122 refs]
   -- [<A HREF="http://dx.doi.org/10.1007/978-0-387-78745-9_7">doi:10.1007/978-0-387-78745-9_7</A>]['10].
   [in: us$143; uk us isbn:0387787445; uk us isbn13:978-0387787442.]

%A G. Minervini
%A et al ...
%A F. Polticelli
%T Massive non-natural proteins structure prediction using grid technologies
%J BMC Bioinformatics
%V 10 (suppl.6):S22
%D 2009
%K conf, MolBio, c2009, c200x, c20xx, random, protein, artificial, NBP, NBPs,
   RandomBlast, structure, folds
%X "... A large random protein seq. library (2*10^4 seqs.) was generated
   ... structs. were predicted using Rosetta. ... [most] NBPs, according to
   Rosetta, are characterized by a compact 3D struct. with a high secondary
   structure content. Structure compactness & surface polarity are comparable
   to those of natural proteins, suggesting similar stability & solubility.
   Deviations are observed in a helix-beta strands relative content & in
   hydrophobic core composition, as NBPs appear to be richer in helical
   struct. & aromatic AAs wrt natural proteins. ... suggest that the ability
   to form a compact, ordered & water-soluble struct. is an intrinsic property
   of polypeptides. The tendency of random seqs. to adopt alpha helical folds
   indicate that all-alpha ps. may have emerged early in pre-biotic evoln. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-10-S6-S22">doi:10.1186/1471-2105-10-S6-S22</A>]['13].
      (Describes RandomBlast and the use of Rosetta. Arguments might be
      somewhat circular because of the way that Rosetta was derived.)
   [Also search for: randomBlast].

%A J. T. Bonner
%T The Social Amoebae: The Biology of Cellular Slime Molds
%I PrincetonUP
%P 156
%D 2009
%K book, text, biol, biology, c2009, c200x, c20xx, zz0813, slime mold, mould,
   molds, moilds, myxomycetes, amoeba, amoebae, multicellular
%X 1st ed 2009; pb us$24; uk us isbn13:978-0691139395.
   "... Slime molds are very different from other organisms; they feed as
   individual amoebae before coming together to form a multicellular organism
   that has a remarkable ability to move and orient itself in its environment.
   Furthermore, these social amoebae display a sophisticated division of labor;
   within each organism, some cells form the stalk and others become the spores
   that will seed the next generation. ... examines all these parts together,
   giving a balanced, concise, and clear overview of slime mold biology, from
   molecules to cells to multicells, as he advances some unconventional and
   unexpected insights. ..."
   -- [<A HREF="http://press.princeton.edu/titles/8952.html">PP</A>].
   [Also search for: slime mold].

%A B. Borrell
%T Fraud rocks protein community
%J Nature
%V 462
%D 2009
%K jrnl, academic, university, scientific, research, fraud, fake, faked,
   misconduct, ethics, protein crystallography, Krishna Murthy, UAlabama,
   USA, science, grant, grants, NIH
%X "University finds that researcher falsified data supporting 11 protein
   structures. ... The finding by a university misconduct investigation that a
   crystallographer 'more likely than not' faked almost a dozen protein
   structures has left the field in shock. The fraud is the largest ever in
   protein crystallography. ... the University of Alabama at Birmingham
   concluded that H.M.Krishna Murthy acted alone in fabricating & falsifying
   results that appeared in ten papers published during the past decade. ..."
   -- [<A HREF="https://doi.org/10.1038/462970a">doi:10.1038/462970a</A>]['18].
   4/2018: "... received a ten-year government funding ban in the United States.
      ... The fraudulent research was supported by six grants from the US
      National Institutes of Health. ...  a judge has now rejected his
      appeal. ..." Nature, 556, 278-279, 2018
      -- [<A HREF="https://doi.org/10.1038/d41586-018-04599-y">doi:10.1038/d41586-018-04599-y</A>][18/4/'18] (mid article).

%A P. Emsley
%A et al
%T Features and development of Coot
%J Acta Crystallogr. D Biol. Crystallogr.
%V 66
%N 4
%P 486-501
%M APR
%D 2010
%K MolBio, jrnl, c2010, c201x, c20xx, zz0923, Coot, protein, crystallography,
   structure, validation, X-ray, Xray, UniOxford, OxfordU
%X "Coot is a molecular-graphics application for model building and validation
   of biological macromolecules ... tools are provided for model validation as
   well as interfaces to external programs for refinement ..."
   -- [<A HREF="https://doi.org/10.1107/S0907444910007493">doi:10.1107/S0907444910007493</A>]['23].
   Also see Coot@[<A HREF="https://en.wikipedia.org/wiki/Coot_(software)">wikip</A>]['23].

%A P. Horvath
%A R. Barrangou
%T CRISPR/Cas, the immune system of bacteria and archaea
%J Science
%V 327
%N 5962
%P 167-170
%M JAN
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0516, CRISPR, CAS, gene editing
%X "... In many Bacteria & most Archaea, clustered regularly interspaced short
   palindromic repeats (CRISPR) form peculiar genetic loci, which provide
   acquired immunity against viruses & plasmids by targeting nucleic acid in a
   sequence-specific manner. These hypervariable loci take up genetic material
   from invasive elts & build up inheritable DNA-encoded immunity over time.
   Conversely, viruses have devised mutational escape strategies that allow them
   to circumvent the CRISPR/Cas system, albeit at a cost. CRISPR features may be
   exploited for typing purposes, epidemiological studies, host-virus ecological
   surveys, building specific immunity against undesirable genetic elements, &
   enhancing viral resistance in domesticated microbes."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1179555">doi:10.1126/science.1179555</A>]['16].
   Also see CRISPR@[<A HREF="https://en.wikipedia.org/wiki/CRISPR">wikip</A>]['16].
   [Also search for: MolBio CRISPR].

%A K. S. Raines
%A et al ...
%A J. Miao
%T Three-dimensional structure determination from a single view
%J Nature
%V 463
%P 214-217
%P ?-?
%M JAN
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, ankylography, protein, tertiary structure,
   3D, molecule, image, imaging, laser, Ewald sphere
%X "...present a 3D imaging modality, termed ankylography (... Greek ankylos
   curved & graphein writing) which under certain circumstances enables complete
   3D structure determination from a single exposure using a monochromatic
   incident beam. We demonstrate that when the diffraction pattern of a finite
   object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D
   structure of the object is in principle determined by the 2D spherical
   pattern. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08705">doi:10.1038/nature08705</A>]['11].
   [Also search for: MolBio ankylography].

%A M. Hamady
%A C. Lozupone
%A R. Knight
%T Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial
   communities including analysis of pyrosequencing and PhyloChip data
%J ISME J.
%V 4
%P 17-27
%M JAN
%D 2010
%K jrnl, ISME, MolBio, c2010, c201x, c20xx, UniFrac, phylogenetic, evolutionary,
   microbe, bacteria
%X "... new array-based implementation offers orders of magnitude improvements
   over the original version. New 3D visualization of PCA results, with the
   option to view multiple coordinate axes simultaneously, provides a powerful
   way to quickly identify patterns that relate vast numbers of microbial
   communities.  ...  show that a Fast UniFrac analysis using a reference tree
   recaptures patterns that could not ..."  (online 27 Aug '09)
   -- [<A HREF="http://dx.doi.org/10.1038/ismej.2009.97">doi:10.1038/ismej.2009.97</A>]['10],
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/19710709">n c b i</A>]['10].
   (last auth@[<A HREF="http://chem.colorado.edu/index.php?option=com_content&view=article&id=263:rob-knight&catid=41:faculty&Itemid=93">col'rado</A>]['10].)

%A J. Schmutz
%A S. B. Cannon
%A ...
%A S. A. Jackson
%T Genome sequence of the palaeopolyploid soybean
%J Nature
%V 463
%P 178-183
%M JAN
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0110, soy, soya, soybean, Glycine max,
   Gmax, edamame, bean, beans, oilseed, legume, legumes, plant, plants,
   nGenome, genome
%X "... 1.1-gigabase genome by a whole-genome shotgun approach and integrated
   it with physical and high-density genetic maps to create a chromosome-scale
   draft sequence assembly. We predict 46,430 protein-coding genes, 70% more
   than Arabidopsis and similar to the poplar genome which, like soybean, is an
   ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur
   in chromosome ends, which comprise less than one-half of the genome but
   account for nearly all of the genetic recombination. Genome duplications
   occurred at approximately 59 and 13 million years ago, resulting in a highly
   duplicated genome with nearly 75% of the genes present in mult. copies. ..."
   ... 950Mb, ~ 85% sequenced ... 20 chrs ...
   ... DDBJ/EMBL/GenBank accession # ACUP00000000 ...
   -- [<A HREF="http://dx.doi.org/10.1038/nature08670">doi:10.1038/nature08670</A>]['10],
   (minor) correction [<A HREF="http://dx.doi.org/10.1038/nature08957">doi:10.1038/nature08957</A>]['10].

%A E. D. Pleasance
%A R. K. Cheetham
%A ...
%A M. R. Stratton
%T A comprehensive catalogue of somatic mutations from a human cancer genome
%J Nature
%V 463
%P 191-196
%M JAN
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, cancer, melanoma, genome, mutation,
   change, changes, damage, repair, malignant, lymphoblastoid cell
%X "... sequenced the genomes of a malignant melanoma and a lymphoblastoid cell
   line from the same person, providing the first comprehensive catalogue of
   somatic mutations from an individual cancer. ..."
   ... [in] www.ebi.ac.uk/ega/ under accession #[<A HREF="http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&id=EGAS00000000052">EGAS00000000052</A>]['10],
   -- [<A HREF="http://dx.doi.org/10.1038/nature08658">doi:10.1038/nature08658</A>]['10].

%A J. F. Hughes
%A H. Skaletsk
%A ...
%A D. C. Page
%T Chimpanzee and human Y chromosomes are remarkably divergent in structure and
   gene content
%J Nature
%V 463
%P 536-539
%M JAN
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0210, human, chimp, primate, evolution,
   Y chromosome, chrY, Ychr, male specific Y, MSY
%X "... The human Y chr. began to evolve from an autosome hundreds of millions
   of years ago, acquiring a sex-determining fn & undergoing a series of
   inversions that suppressed crossing over with the X ...
   ... The chimpanzee MSY contains twice as many massive palindromes as the
   human MSY, yet it has lost large fractions of the MSY protein-coding genes &
   gene families present in the last common ancestor. We suggest that the
   extraordinary divergence of the chimpanzee & human MSYs was driven by 4
   synergistic factors: the prominent role of the MSY in sperm production,
   genetic hitchhiking effects in the absence of meiotic crossing over, freq.
   ectopic recombination within the MSY, & species differences in mating
   behaviour. Although genetic decay may be the principal dynamic in the evoln
   of newly emergent Y chrs., wholesale renovation is the paramount theme in the
   continuing evolution of chimpanzee, human & perhaps other older MSYs."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08700">doi:10.1038/nature08700</A>]['10] online 13/1/'10.
      cDNA seqs. of chimp. ampliconic genes ... [<A HREF="http://www.ncbi.nlm.nih.gov">genbank</A>]
      accession #s AY958084 (BPY2), AY958081 (CDY), AY958083 (DAZ),
      AY995201/2 (RBMY), AY958082 (TSPY) and AY995203 (XKRY).
      Chimp. testis cDNA seqs. ... accession #s EX654441-EX654483.

%A M. Pacholec
%A et al
%T SRT1720, SRT2183, SRT1460, and resveratrol are not direct activators of SIRT
%J J. Biol. Chem.
%M JAN
%D 2010
%K jrnl, JBC, c2010, c201x, c20xx, zz0110, SRT1720, resveratrol, SIRT, SIRT1,
   ageing, lifespan
%X "Sirtuins catalyze NAD+-dependent protein deacetylation and are critical
   regulators of transcription, apoptosis, metabolism and aging. There are seven
   human sirtuins (SIRT1-7) and SIRT1 has been implicated as a key mediator of
   the pathways downstream of calorie restriction that have been shown to delay
   the onset and reduce the incidence of age-related diseases ...
   we have assessed purported SIRT1 activators by employing biochemical assays
   utilizing native substrates, including a p53-derived peptide substrate
   lacking a fluorophore as well as the purified native full length protein
   substrates p53 and acetyl-CoA synthetase1. SRT1720, its structurally related
   compounds SRT2183 and SRT1460, and resveratrol do not lead to apparent
   activation of SIRT1 with native peptide or full length protein substrates,
   while they do activate SIRT1 with peptide substrate containing a covalently
   attached fluorophore. ..."
   -- [<A HREF="http://dx.doi.org/10.1074/jbc.M109.088682">doi:10.1074/jbc.M109.088682</A>]['10].
   (Also see [<A HREF="http://dx.doi.org/10.1111/j.1747-0285.2009.00901.x">doi:10.1111/j.1747-0285.2009.00901.x</A>]['10].)
   [Also search for: resveratrol].

%A R. Li
%A W. Fan
%A ...
%A J. Wan
%T The sequence and de novo assembly of the giant panda genome
%J Nature
%V 463
%P 311-317
%M JAN
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, giant panda, nGenome, genome,
   Ailuropoda melanoleuca, ( Ailuropoda melanoleura inError )
%X "... draft sequence of the giant panda genome. The assembled contigs
   (2.25-gigabases (Gb)) cover approximately 94% of the whole genome, and the
   remaining gaps (0.05-Gb) seem to contain carnivore-specific repeats and
   tandem repeats. Comparisons with the dog and human showed that the panda
   genome has a lower divergence rate. ..."
   "... 20-pairs of autosomes and one pair of sex chromosomes (2n=42) ..."
   "... accession ACTA00000000 ... version ACTA01000000 ... "
   -- [<A HREF="http://dx.doi.org/10.1038/nature08696">doi:10.1038/nature08696</A>]['10].
   (Also see [<A HREF="http://panda.genomics.org.cn/">www</A>]['10].)

%A C. Venditti
%A A. Meade
%A M. Pagel
%T Phylogenies reveal new interpretation of speciation and the Red Queen
%J Nature
%V 463
%P 349-352
%M JAN
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0110, red queen hypothesis, evolution,
   biol, origin, species, speciation, reproductive isolation
%X "The Red Queen describes a view of nature in which species continually evolve
   but do not become better adapted. ... but no test of its claim that
   speciation occurs at a constant rate has ever been made against competing
   models that can predict virtually identical outcomes, ... Here we use
   101 phylogenies of animal, plant & fungal taxa to test the constant-rate
   claim against four competing models. ...  We find that the hypotheses that
   speciation follows the accumulation of many small events that act either
   multiplicatively or additively found support in 8% & none of the trees, resp.
   A further 8% of trees hinted that the probability of speciation changes
   according to the amount of divergence from the ancestral species, &
   6% suggested speciation rates vary among taxa. By comparison, 78% of the
   trees fit the simplest model in which new species emerge from single events,
   each rare but individually sufficient to cause speciation. This model
   predicts a constant rate of speciation, & provides a new interpretation of
   the Red Queen: the metaphor of species losing a race against a deteriorating
   environment is replaced by a view linking speciation to rare stochastic
   events that cause reproductive isolation. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08630">doi:10.1038/nature08630</A>]['10],
   also see [<A HREF="http://dx.doi.org/10.1038/463306a">views</A>]['10].

%A L. E Palmer
%A M. Dejori
%A R. Bolanos
%A D. Fasulo
%T Improving sequence assembly using machine learning and comparative genomics
   for overlap correction
%J BMC Bioinformatics
%V 11
%N 33
%M JAN
%D 2010
%K jrnl, eJrnl, MolBio, c2010, c201x, c20xx, sequence assembly, contig, contigs
%X "... an approach that extends the Minimus assembler by a data driven step to
   classify overlaps as true or false prior to contig construction. We trained
   several different classification models ... using various statistics derived
   from overlaps of reads available from prior seq.projects. ... included
   %-mismatch & k-mer freqs. within the overlaps as well as a comparative
   genomics score derived from mapping reads to multiple ref.genomes. We show
   that in real whole-genome sequencing data from the E.coli & S.aureus genomes,
   by providing a curated set of overlaps to the contigging phase of the a., we
   nearly doubled the median contig length (N50) without sacrificing coverage of
   the genome or increasing the number of mis-assemblies. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-11-33">doi:10.1186/1471-2105-11-33</A>]['10].
   [Also search for: MolBio sequence assembly].

%A E. J. Steen
%A et al
%T Microbial production of fatty-acid-derived fuels and chemicals from
   plant biomass
%J Nature
%V 463
%P 559-562
%M JAN
%D 2010
%K jrnl, LS9, c2010, c201x, c20xx, zz0210, bio fuel, fuels, biofuel, diesel,
   biodiesel, eColi, renewable, resources, plant, fibre, biomass
%X "... Fatty acids are composed of long alkyl chains & represent nature's
   "petroleum", being a primary metabolite used by cells for both chemical &
   energy storage fns. These energy-rich molecules are today isolated from plant
   & animal oils for a diverse set of products ranging from fuels to
   oleochemicals. A more scalable, controllable & economic route to this
   important class of chemicals would be through the microbial conversion of
   renewable feedstocks, such as biomass-derived carbohydrates. Here we
   demonstrate the engineering of Escherichia coli to produce structurally
   tailored fatty esters (biodiesel), fatty alcohols, & waxes directly from
   simple sugars. Furthermore, we show engineering of the biodiesel-producing
   cells to express hemicellulases, a step towards producing these compounds
   directly from hemicellulose, a major component of plant-derived biomass."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08721">doi:10.1038/nature08721</A>]['10]. (Company 'LS9'.)
   (Also see [<A HREF="http://dx.doi.org/10.1038/463409a">news</A>].)

%A O. U. Nalbantoglu
%A D. J. Russell
%A K. Sayood
%T Data compression concepts and algorithms and their applications to
   bioinformatics
%J Entropy
%V 12
%N 1
%P 34-52
%D 2010
%K jrnl, survey, MolBio, c2010, c201x, c20xx, zz0310, compression, compress
%X "[D.C.] at its base is concerned with how information is organized in data.
   ... review the ways in which ideas & approaches fundamental to the theory &
   practice of D.C. have been used in the area of bioinf.. ... basic theor.
   ideas from D.C., [e.g.,] entropy, mutual info., & complexity have been used
   for analyzing biol. seqs. ... to discover hidden patterns, infer phylo.
   relationships b/w organisms & study viral pop'ns. ... how inferred grammars
   for biol.seqs. have been used to uncover structure in biol.seqs.."
   -- [<A HREF="http://dx.doi.org/10.3390/e12010034">doi:10.3390/e12010034</A>]['10], free.
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">compression</A>].)

%A D. P. Lane
%A C. Fang Cheok
%A C. Brown
%A A. Madhumalar
%A F. J. Ghadessy
%A C. Verma
%T Mdm2 and p53 are highly conserved from placozoans to man
%J Cell Cycle
%V 9
%N 3
%P 540-547
%M FEB
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, Mdm2, p53, protein, proteins, evolution,
   Nematostella vectensis, placazoa, eumetazoa
%X "The p53 protein is the most commonly mutated tumor suppressor gene in man.
   ... recent discovery of p53 family genes in the sea anemone Nematostella
   vectensis.  ... like their human counterparts, are responsible for DNA
   damage-induced cellular apoptosis, albeit restricted to the germ cell
   compartment in model organisms such as the nematode & fruit fly. In
   vertebrates from zebrafish to man the function of p53 is tightly & absolutely
   constrained by a negative regulator Mdm2. However the Mdm2 gene has not been
   detected in the genome of the model nematode (C.elegans) & insect
   (D.melanogaster) species. We have found that the p53 gene & the Mdm2 gene are
   present in Placozoans, one of the simplest of all free living multi-cellular
   organisms, implying that both proteins arose much earlier in evolution than
   previously thought. Detailed seq. analysis shows the exceptional retention of
   key features of both proteins from man to placazoan implying that the
   p53-Mdm2 interaction & its regulation have been conserved from a basal
   eumetazoan since the pre-cambrian era over one billion y. ago."
   -- [<A HREF="http://www.landesbioscience.com/journals/cc/article/10516/">www</A>]1/'10] -- open access.

%A I. Ilinkin
%A J. Ye
%A R. Janardan
%T Multiple structure alignment and consensus identification for proteins
%J BMC Bioinformatics
%V 11
%N 1
%P 71
%M FEB
%D 2010
%K jrnl, eJrnl, MolBio, MAPSCI, c2010, c201x, c20xx, protein, structure,
   multiple, match, matching, 3D, mammoth, matt
%X "An algorithm is presented to compute a multiple structure alignment for a
   set of proteins and to generate a consensus (pseudo) protein which captures
   common substructures ...  heuristic in that it computes an approximation to
   the optimal alignment that minimizes the sum of the pairwise distances
   between the consensus and the transformed proteins. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-11-71">doi:10.1186/1471-2105-11-71</A>]['10].
   [Also search for: MolBio protein structure alignment].

%T Genome sequencing and analysis of the model grass Brachypodium distachyon
%Q Int. Brachypodium Initiative
%J Nature
%V 463
%P 763-768
%M FEB
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0210, genome, nGenome, grass, grasses,
   grain, crop, plant, Pooideae, brachybase, Brachypodium distachyon, wild
%X "Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae,
   provide the bulk of human nutrition and are poised to become major sources of
   renewable energy. Here we describe the genome sequence of the wild grass
   Brachypodium distachyon (Brachypodium), which is, to our knowledge, the
   first member of the Pooideae subfamily to be sequenced. ..."
   "... diploid inbred line Bd21 was seq. ..."
   "... The five Brachypodium chromosomes ..." (about 300Mbp)
   -- [<A HREF="http://dx.doi.org/10.1038/nature08747">doi:10.1038/nature08747</A>]['10],
   and [<A HREF="http://www.brachypodium.org/">b...org</A>].
   "... shotgun seq ... DDBJ/EMBL/GenB@nk under the accession # ADDN00000000"
   {"...bread wheat g. ~ 17,000 megabases ... three independent genomes ..."}

%A F. S. Collins
%T The Language of Life: DNA and the Revolution in Personalized Medicine
%I Harper
%P 368
%D 2010
%K book, text, MolBio, c2010, c201x, c20xx, zz0210, DNA, HUGO, risk, risks,
   medical, medicine, human health, genes, testing
%X "... Human Genome Project, headed by C., and which mapped the entire
   human genome.  C. is also not shy about taking on large political issues.
   He points out problems with our current health-care system, discusses stem-
   -cell research, and in a cogent commentary, recommends - with caveats -
   direct-to-consumer DNA testing. By using case studies throughout ..."
   1st ed 2010; hb us$18; uk us isbn:0061733172; uk us isbn13:978-0061733178.

%A J. Ni
%A A. Waldman
%A L. M. Khachigian
%T c-Jun regulates shear- and injury-inducible Egr-1 expression, vein graft
   stenosis after autologous end-to-side transplantation in rabbits, and
   intimal hyperplasia in human saphenous veins
%J J. Biol. Chem.
%V 285
%P 4038-4048
%M NOV
%D 2010
%K jrnl, JBC, MolBio, c2010, c201x, c20xx, zz1113, DZ13, skin cancer, drug,
   cJun, Egr1, MMP2, ERK1, p38, research, possible misconduct, fraud,
   Australia, UNSW
%X "Coronary artery bypass graft failure represents an unsolved problem ...
   Our objective here was to evaluate the effect of targeted inhibition of the
   bZIP transcription factor c-Jun on intimal hyperplasia in human saphenous
   veins and vein graft stenosis after autologous end-to-side transplantation.
   ... These data demonstrate that strategies targeting c-Jun may be useful for
   the prevention of vein graft stenosis. Control of one important shear-
   -responsive transcription factor by another indicates the existence of
   transcriptional amplification mechanisms that magnify the vascular response
   to cell injury or stress through inducible transcriptional networks."
   -- [<A HREF="http://dx.doi.org/10.1074/jbc.M109.078345">doi:10.1074/jbc.M109.078345</A>]['13].
   (Also see [<A HREF="http://www.abc.net.au/news/2013-08-12/trials-of-skin-cancer-drug-dz13-suspended-amid-misconduct-claims/4881622">abc</A>][13/8/2013].
   And, "Journal issues correction on paper..."
   -- [<A HREF="http://www.abc.net.au/news/2013-11-05/journal-corrects-paper-co-authored-by-levon-khachigian/5070582">abc</A>][5/11/2013].
   And [<A HREF="http://www.abc.net.au/news/2014-04-17/research-investigations-mounting-for-embattled-professor/5397516">abc</A>][16/4/2014].)
   [Also search for: UNSW Khachigian].

%A S. Myers
%A et al ...
%A P. Donnelly
%T Drive against hotspot motifs in primates implicates the PRDM9 gene in
   meiotic recombination
%J Science
%V 327
%N 5967
%P 876-879
%M FEB
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, hotspot, motif, DNA, PRDM9,
   trimethylation, recombination, meiotic crossover
%X "Although present in both humans & chimpanzees, recombination hotspots, at
   which meiotic crossover events cluster, differ markedly in their genomic
   locns between the species. ... a 13-base pair seq. motif previously assoc.
   with the activity of 40% of human hotspots does not function in chimp. & is
   being removed by self-destructive drive in the human lineage. Multiple lines
   of evidence suggest that the rapidly evolving zinc-finger protein PRDM9 binds
   to this motif & that seq. changes in the protein may be responsible for
   hotspot diffs. b/w species. The involvement of PRDM9, which causes histone
   H3 lysine 4 trimethylation, implies that there is a common mechanism for
   recombination hotspots in eukaryotes but raises questions about what forces
   have driven such rapid change."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1182363">doi:10.1126/science.1182363</A>]['10].

%A J. Xu
%A Y. Zhang
%T How significant is a protein structure similarity with TM-score = 0.5?
%J J. Bioinformatics
%V 26
%N 7
%P 889-995
%M APR
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, TM sore, TMscore, protein, structure,
   significance, fold, match
%X "... all-to-all gapless structural match on 6684 non-homologous single-domain
   proteins in the PDB ... the TM-scores follow an extreme value distribution.
   The data allow us to assign each TM-score a P-value that measures the chance
   of 2 randomly selected p. obtaining a >= TMscore. With a TMs at 0.5 ... its
   Pvalue is 5.5*10^-7 ... Second, we examine the posterior prob. of the same
   fold proteins from three datasets SCOP, CATH & the consensus of SCOP & CATH.
   ... the posterior prob. from different datasets has a similar rapid phase
   transition around TM-score=0.5. [So] TM-score can be used as an approx. but
   quantitative criterion for protein topology classn, i.e. p.pairs with a
   TM-score >0.5 are mostly in the same fold while those with a TM-score < 0.5
   are mainly not in the same fold."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btq066">doi:10.1093/bioinformatics/btq066</A>]['13].
   [Also search for: MolBio protein structure alignment].

%A K. Sayood
%T Computational Genomic Signatures
%I Morgan & Claypool
%M APR
%D 2010
%K book, text, MolBio, c2010, c201x, c20xx, bioinformatics, genome, signature,
   zz0510
%X 1st ed 2010; pb us$40; uk us isbn:1608451453; uk us isbn13:978-1608451456.

%A M. D. Robinson
%A A. Oshlack
%T A scaling normalization method for differential expression analysis of
   RNA-seq data
%J Geno. Biol.
%V 11
%N R25
%M MAR
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0820, RNA-seq, RNAseq, normalization,
   normalisation, stats
%X "... we show that normalization continues to be an essential step in the
   analysis. We outline a simple and effective method for performing n. & show
   dramatically improved results for inferring differential expression in
   simulated & publicly available data sets."
   -- [<A HREF="https://doi.org/10.1186/gb-2010-11-3-r25">doi:10.1186/gb-2010-11-3-r25</A>]['20].
   [Also search for: RNAseq normalization].

%A A. S. Konagurthu
%A A. M. Lesk
%T Cataloging topologies of protein folding patterns
%J J. Molec. Recognit.
%V 23
%N 2
%P 253-257
%M MAR-APR
%D 2010
%K invited, festschrift, MolBio, c2010, c201x, c20xx, topology, protein, fold,
   AMLesk, folds, folding, pattern, structure, tableau, tableaux, search, ArunK
%X "Comparing & classifying protein folding patterns allows organizing the known
   structs., structure search & retrieval, & investigation of general principles
   of protein architecture. We have been developing a concise tableau rep'n of
   protein folding patterns, based on the order & contact patterns of elts of
   secondary struct.: helices & strands of sheet (...). The tableaux provide a
   database, derived from the world-wide protein data bank, mineable in studies
   of protein architecture, including: (i) determination of stat.properties of
   s.s. contacts in an unbiased set of protein domains, (ii) investigations of
   the range of, & relationships among, protein topologies, (iii) investigation
   of the relationship between local structure of proteins & the complete
   folding topology, (iv) potential for fold identification from amino acid
   seq., & (v) the basis for a complete enumeration of possible protein folding
   patterns, which can be compared with the corpus of known structures."
   -- [<A HREF="http://dx.doi.org/10.1002/jmr.1006">doi:10.1002/jmr.1006</A>]['11].
   And "... Underlying the tableau rep'n is the idea that the essence of a
       prot. folding pattern is the order, along the chain, of the helices &
       strands of a sheet & the geometry of interaction of the pairs of
       s.struct. elts. that are in contact. ..."
   [Also search for: MolBio protein tableau].

%A E. Pennisi
%T On rarity and richness
%J Science
%V 327
%N 5971
%P 1318-1319
%M MAR
%D 2010
%K news, c2010, c201x, c20xx, Grosberg, Vermeij, ecology, evolution, diversity,
   rare, life, species, speciation, land, terrestrial, tropics, ocean, marine
%X "2 researchers have taken a stab at explaining why oceans have far fewer
   species than terrestrial habitats. ... Back in the Devonian period,
   400 million y. ago, the seas were home to an abundance of species, perhaps
   even more than on land. But about 110 m.y. ago, land plants went
   through a burst of speciation ... The trigger for this terrestrial explosion,
   Grosberg and Vermeij say, was the evolution of a more efficient way in which
   land plants use water. ... The development of dispersed communities "is the
   key to the current extraordinary diversity of species on land," Grosberg
   says: High-density populations are at increased risk of being eaten or wiped
   out by disease, while dispersed communities face reduced competition and
   predation. ... About 110 m.y. ago, higher leaf-vein densities - and
   increases in the number of leaves - resulted in greater biomass production.
   All this added energy set in motion a positive feedback loop that encouraged
   more specialization. Speciation took off, particularly in the tropics. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.327.5971.1318">doi:10.1126/science.327.5971.1318</A>]['10].

%A S. Roch
%T Toward extracting all phylogenetic information from matrices of evolutionary
   distances
%J Science
%V 327
%N 5971
%P 1376-1379
%M MAR
%D 2010
%K report, MolBio, c2010, c201x, c20xx, zz0310, phylogenetic, evolutionary,
   tree, trees, reconstruction, distance matrix, matrices, molecular clock,
   UPGMA, WPGMA, MRCA, agglomerative, bottom up, maximum likelihood
%X "...  because of their intrinsic reliance on summary statistics,
   distance-matrix methods are assumed to be less accurate than likelihood-based
   approaches. [here] pairwise seq. comparisons are shown to be more powerful
   than previously hypothesized. A statistical analysis of certain
   dist.-based techniques indicates that their data requirement for large
   evolutionary trees essentially matches the conjectured performance of
   max.likelihood methods - challenging the idea that summary statistics lead
   to suboptimal analyses. On the basis of a connection between ancestral state
   reconstruction and dist. averaging, the critical role played by the
   covariances of the dist.matrix is identified."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1182300">doi:10.1126/science.1182300</A>]['10],
   &  [<A HREF="http://dx.doi.org/10.1126/science.1187797">doi:10.1126/science.1187797</A>]['10].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Trees/">trees</A>].)

%A A. Ratan
%A Y. Zhang
%A V. M. Hayes
%A S. C. Schuster
%A W. Miller
%T Calling SNPs without a reference sequence
%J BMC Bioinformatics
%V 11
%P e130
%M MAR
%D 2010
%K jrnl, eJrnl, c2010, c201x, c20xx, SNP, SNPs, sequence, DIAL, allele, alleles
%X "... describe a computational pipeline, called DIAL (De novo Identification
   of Alleles), for identifying single-base substitutions between two closely
   related genomes without the help of a reference genome. The method works even
   when the depth of coverage is insufficient for de novo assembly, and it can
   be extended to determine small insertions/deletions. ... [test on] genome of
   Dr. James Watson (to detect heterozygous positions) and recent Illumina data
   from orangutan ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-11-130">doi:10.1186/1471-2105-11-130</A>]['10].

%A A. Nemeth
%A et al
%A G. Langst
%T Initial genomics of the human nucleolus
%J PLoS Genetics
%V 6
%N 3
%P e1000889
%M MAR
%D 2010
%K jrnl, eJrnl, MolBio, c2010, c201x, c20xx, zz0410, human, cell, nucleus, DNA,
   packing, packaging, chromatin domains, NAD, nucleolus, nucleoli, eukaryotic,
   eukaryote
%X "... genomics of a nuclear compartment of the eukaryotic cell. 454 sequencing
   & microarray analysis revealed the pattern of nucleolus-assoc. chromatin
   domains (NADs) ... & certain satellite repeats as the major building blocks
   of NADs, which constitute about 4% of the genome. ... our findings describe
   the nature of DNA seqs. assoc. with the human nucleolus & provide insights
   into the fn of the nucleolus in genome organization & establishment of
   nuclear architecture."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pgen.1000889">doi:10.1371/journal.pgen.1000889</A>]['10].
   ("97 regions, constituting about 4% of the ge., assoc. with nucleoli")

%A J. F. Conrad
%A et al
%A M. E. Hurles
%T Origins and functional impact of copy number variation in the human genome
%J Nature
%V 464
%N 7289
%P 707-712
%M APR
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, DNA, human, copy number variation, CNV,
   CNVs, disease, health
%X "Structural variations of DNA greater than 1 kb in size account for most
   bases that vary among human genomes, but are still relatively under-
   -ascertained. ... generate a comprehensive map of 11,700 CNVs greater than
   443 bp, of which most (8,599) have been validated independently ...
   ... identified 30 loci with CNVs that are candidates for influencing disease
   susceptibility. Despite this, having assessed the completeness of our map &
   the patterns of linkage disequilibrium between CNVs & SNPs, we conclude
   that, for complex traits, the heritability void left by genome-wide
   association studies will not be accounted for by common CNVs."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08516">doi:10.1038/nature08516</A>]['10].

%A L. Ding
%A et al ...
%A E. R. Mardis
%T Genome remodelling in a basal-like breast cancer metastasis and xenograft
%J Nature
%V 464
%P 999-1005
%M APR
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, breast cancer, genome, genomes, mutation,
   mutations, CTNNA1, basal, metastasis, xenograft
%X "Massively parallel DNA sequencing technologies ... genetic changes assoc.
   with tumour progression. ... describe the genomic analyses of 4 DNA samples
   from an African-American patient with basal-like breast cancer: peripheral
   blood, the primary tumour, a brain metastasis and a xenograft derived from
   the primary tumour. ... The differential mutation frequencies and structural
   variation patterns in metastasis and xenograft compared with the primary
   tumour indicate that secondary tumours may arise from a minority of cells
   within the primary tumour."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08989">doi:10.1038/nature08989</A>]['10].

%A H. Ledford
%T Big science: The cancer genome challenge
%J Nature
%V 464
%P 972-974
%M APR
%D 2010
%K news, views, survey, MolBio, c2010, c201x, c20xx, cancer, genome, genomes,
   gene, genes, IDH1, CTNNA1, sequences, disease, database, search, mining,
   cause, problem, challenge
%X "Databases could soon be flooded with genome sequences from 25,000 tumours.
   H.L. looks at the obstacles researchers face as they search for meaning in
   the data. ... "
   -- [<A HREF="http://dx.doi.org/10.1038/464972a">doi:10.1038/464972a</A>]['10].

%A E. Marshall
%T Cancer gene patents ruled invalid
%J Science
%V 328
%N 5975
%P 153
%M APR
%D 2010
%K news, MolBio, c2010, c201x, c20xx, gene, genes, patent, patents, law, court,
   BRAC, BRAC1, BRAC2, Myriad, Judge Robert Sweet
%X '... last week: A federal judge in New York City used sweeping language to
   invalidate a handful of human gene patents, casting doubt on hundreds more.
   The decision applies only in NY state and is sure to be appealed - a process
   that could take years. Still, it undercuts the idea that DNA seq. can be
   owned. ... ruled that key discoveries from the mid-1990s, the BRCA1 & BRCA2
   genes assoc. with breast & ovarian cancers, are not truly inventions. They
   are "products of nature," he writes in a blunt 29 March opinion. ...'
   --  [<A HREF="http://dx.doi.org/10.1126/science.328.5975.153">doi:10.1126/science.328.5975.153</A>]['10].

%A A. M. Labin
%A E. N. Ribak
%T Retinal glial cells enhance human vision acuity
%J Phys. Rev. Lett.
%V 104
%N 15
%P 158102 (4 pages)
%M APR
%D 2010
%K jrnl, eJrnl, c2010, c201x, c20xx, zz0510, eye, vision, evolution, acuity,
   (not) mistake, optimal, optimise, glial, Muller, cells, retina,
   photoreceptor, rods, cones
%X "We construct a light-guiding model of the retina outside the fovea, in which
   an array of glial (Muller) cells permeates the depth of the retina down to
   the photoreceptors. Based on measured refractive indices, we propagate light
   to obtain a sig. increase of the intensity at the photoreceptors. For pupils
   up to 6mm width, the coupling between neighboring cells is only a few %. Low
   cross talk over the whole visible spectrum also explains the insensitivity to
   chromatic aberrations of the eye. The retina is revealed as an optimal
   structure designed for improving the sharpness of images."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.104.158102">doi:10.1103/PhysRevLett.104.158102</A>]['10].

%A M. Doebeli
%A I. Ispolatov
%T Complexity and diversity
%J Science
%V 328
%N 5977
%P 494-497
%M APR
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0509, complexity, diversity, biol, bio,
   phenotype, space, high, dimensionality
%X "The mechanisms for the origin & maintenance of biol.diversity are not fully
   understood. It is known that frequency-dependent seln, generating advantages
   for rare types, can maintain genetic variation & lead to speciation, but in
   models with simple phenotypes (that is, low-dimensional phenotype spaces),
   freq.dependence needs to be strong to generate diversity. However, we show
   that if the ecological properties of an organism are determined by multiple
   traits with complex interactions, the condns needed for freq.-dependent seln
   to generate diversity are relaxed to the point where they are easily
   satisfied in high-[D] phenotype spaces. ... reflected in properties of
   Eigenvalues of quadratic forms. Because all living organisms have at least
   hundreds of phenotypes, this casts the potential importance of freq.dep. for
   the origin & maintenance of diversity in a new light."   [37 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1187468">doi:10.1126/science.1187468</A>]['10].

%A P. Freddolino
%A et al
%T Challenges in protein-folding simulations
%J NaturePhysics
%V 6
%P 751-758
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz1122, protein folding, simulation,
   pathway, trajectory
%X "... at present, such simulations are limited in several respects, inc. the
   inability of mol.dynamics force fields to completely reproduce the true
   potential energy surfaces of proteins, the need for sim'ns to extend to the
   millisecond timescale for the folding of many proteins & the difficulty
   inherent in obtaining sufficient sampling to properly characterize the
   extremely heterogeneous folding processes & then analysing those data
   efficiently. We review recent progress in the sim'n of three common model
   systems ..."
   -- [<A HREF="https://doi.org/10.1038/nphys1713">doi:10.1038/nphys1713</A>]['22], also
   see 21297873@[<A HREF="https://pubmed.ncbi.nlm.nih.gov/21297873/">pubm'd</A>]['22].
   (And folding@[<A HREF="https://www.ks.uiuc.edu/Research/folding/">uiuc</A>]['22].)
   [Also search for: protein folding simulation].

%A C. Trapnell
%A et al ...
%A L. Pachter
%T Transcript assembly and quantification by RNA-Seq reveals unannotated
   transcripts and isoform switching during cell differentiation
%J Nature Biotech.
%V 28
%P 511-515
%M MAY
%D 2010
%K MolBio, jrnl, c2010, c201x, c20xx, zz0820, Cufflinks, mRNA, RNAseq, RNA seq,
   isoform, gene expression
%X "... we intro. such algs. in an open-source s/w program called Cufflinks. To
   test Cufflinks, we sequenced & analyzed > 430 million paired 75-bp RNA-Seq
   reads from a mouse myoblast cell line over a differentiation time series. We
   detected 13,692 known transcripts & 3,724 prev. unannotated ones ... Over the
   time series, 330 genes showed complete switches in the dominant transcription
   start site (TSS) or splice isoform, and we observed more subtle shifts in
   1,304 other genes. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nbt.1621">doi:10.1038/nbt.1621</A>]['20].

%A Y. Barash
%A et al...
%A B. J. Frey
%T Deciphering the splicing code
%J Nature
%V 465,
%P 53-59
%M MAY
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0510, spice, alternative splicing, RNA,
   mRNA, multiple, messenger, gene, intron, introns, exon, exons,
   regulatory, regulation
%X "Alternative splicing has a crucial role in the generation of biological
   complexity, & its misregulation is often involved in human disease. Here we
   describe the assembly of a 'splicing code', which uses combinations of
   hundreds of RNA features to predict tissue-dependent changes in alternative
   splicing for thousands of exons. The code determines new classes of splicing
   patterns, ... "  [50 refs]
   -- [<A HREF="http://dx.doi.org/10.1038/nature09000">doi:10.1038/nature09000</A>]['10];
   also see news@[<A HREF="http://dx.doi.org/10.1038/465045a">doi:10.1038/465045a</A>]['10].

%A Z. Gao
%A et al ...
%A J-K. Zhu
%T An RNA polymerase II- and AGO4-associated protein acts in RNA-directed
   DNA methylation
%J Nature
%V 465
%P 106-109
%M MAY
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, RNA polymerase, AGO4, DNA, methylation,
   siRNA, Argonaute, Argonaute4, AGO4, DRM2, RdDM, RDM1, Arabidopsis
%X "... In plants, 24-nucleotide small interfering RNAs (siRNAs) bound to the
   effector protein, Argonaute 4 (AGO4), can direct de novo DNA methylation by
   the methyltransferase DRM2. Here we report a new regulator of RNA-directed
   DNA methylation (RdDM) in Arabidopsis: RDM1. Loss-of-function mutations in
   the RDM1 gene impair the accumulation of 24-nucleotide siRNAs, reduce DNA m.,
   & release transcriptional gene silencing at RdDM target loci. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09025">doi:10.1038/nature09025</A>]['10].

%A R. E. Green
%A et al ...
%A S. Paabo
%T A draft sequence of the Neandertal genome
%J Science
%V 328
%N 5979
%P 710-722
%M MAY
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0510, neandertal genome, nGenone,
   DNA, human, humans, hominins, ancient, old, evolution, neanderthal,
   Nobel prize 2022
%X "... disappearing 30,000 years ago. We present a draft seq. of the N.genome
   composed of more than 4 billion nucleotides from 3 individuals. Comparisons
   of the N.genome to the genomes of 5 present-day humans from different parts
   of the world identify a number of genomic regions that may have been affected
   by +ve seln in ancestral modern humans, including genes involved in
   metabolism & in cognitive & skeletal development. We show that Neandertals
   shared more genetic variants with present-day humans in Eurasia than with
   present-day humans in sub-Saharan Africa, suggesting that gene flow from N.
   into the ancestors of non-Africans occurred before the divergence of
   Eurasian groups from each other."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1188021">doi:10.1126/science.1188021</A>]['10].
   (Paabo was awarded the 2022 Nobel prize for Physiology or Medicine;
   see [<A HREF="https://doi.org/10.1126/science.adf1103">doi:10.1126/science.adf1103</A>][3/10/2022].)
   [Also search for: ancient human DNA].

%A S. Volinia
%A et al ...
%A C. M. Croce
%T Reprogramming of miRNA networks in cancer and leukemia
%J Genome Res.
%V 20
%P 589-599
%M MAY
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, network, networks, hub, hibs, miRNA,
   cancer, leukemia, hsa-miR-103/106, oncogenesis
%X "We studied miRNA profiles in 4419 human samples (3312 neoplastic,
   1107 nonmalignant), corr.to 50 normal tissues & 51 cancer types. ...
   inferred genetic networks from miRNA expression in normal tissues & cancer.
   ... Nonmalignant tissues & cancer n/ws displayed a change in hubs, the most
   connected miRNAs. hsa-miR-103/106 were downgraded in cancer, whereas
   hsa-miR-30 became most prominent. Cancer n/ws appeared as built from
   disjointed subn/ws, ...  identify key miRNA cliques in cancer. We also
   investigated miRNA copy number alterations in 744 cancer samples, at a
   res'n of 150kb ..."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.098046.109">doi:10.1101/gr.098046.109</A>]['10].
   * But [also search for: Croce c2022].

%A T. Makino
%A A. McLysaght
%T Ohnologs in the human genome are dosage balanced and frequently associated
   with disease
%J PNAS
%V 107
%N ?
%P ?-?
%M MAY ?
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0510, disease, medical, risks, ohnolog,
   gene, copy number, variation, chromosome, whole genome duplication,
   dosage balance, WGD, SSD CNV, down, downs syndrome, chr21
%X "About 30% of protein-coding genes in the human g. are related through two
   whole genome duplication (WGD) events. ... [a] popular hypothesis is that
   dosage balance constraints are a major determinant of duplicate gene
   retention. We test this hypothesis & show that WGD-duplicated genes
   (ohnologs) have rarely experienced subsequent small-scale duplication (SSD) &
   are also refractory to copy number variation (CNV) ... show that ohnologs
   have a strong assoc. with human disease. ... Down Syndrome (DS) caused by
   trisomy 21 is widely assumed to be caused by dosage effects, & 75% of prev.
   reported candidate genes for this syndrome are ohnologs that experienced no
   other CN changes. We propose the remaining dosage-balanced ohnologs on chr21
   as candidate DS genes. ... clearly show a persistent resistance to dose
   changes in genes duplicated by WGD. Dosage balance constraints simultaneously
   explain duplicate gene retention & essentiality after WGD."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0914697107">doi:10.1073/pnas.0914697107</A>]['10].

%A A. Benjamin
%A et al ...
%A S. W. Turner
%T Direct detection of DNA methylation during single-molecule, real-time
   sequencing
%J NatureMethods
%M MAY
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0510, DNA, sequencing, SMRT, bisulfite,
   conversion methylation, epigenome, epigenetics, PacBio, Pacific Biosciences
%X "... direct detection of DNA methylation, without bisulfite conversion,
   through single-molecule, real-time (SMRT) sequencing. In SMRT sequencing,
   DNA polymerases catalyze the incorporation of fluorescently labeled
   nucleotides into complementary nucleic acid strands. ... "
   -- [<A HREF="http://dx.doi.org/10.1038/nmeth.1459">doi:10.1038/nmeth.1459</A>]['10].
   (Also see [<A HREF="http://dx.doi.org/10.1038/465145a">doi:10.1038/465145a</A>]['10].)
   [Also search for: MolBio single molecule sequencing].

%A D. L. Theobald
%T A formal test of the theory of universal common ancestry
%J Nature
%V 465
%N 7295
%P 219-222
%M MAY
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0510, origin, origins, evolution, early,
   life, monophyly, last universal common ancestor, ancestry, UCA, LUCA, LUA,
   stats, test
%X "... provide the first, to my knowledge, formal, fundamental test of UCA,
   without assuming that seq.similarity implies genetic kinship. I test UCA by
   applying model selection theory to molecular phylogenies, focusing on a set
   of ubiquitously conserved proteins that are proposed to be orthologous.
   Among a wide range of biol.models involving the indep. ancestry of major
   taxonomic groups, the model seln tests are found to overwhelmingly support
   UCA irrespective of the presence of horizontal gene transfer & symbiotic
   fusion events. ... provide powerful stat. evidence corroborating the
   monophyly of all known life."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09014">doi:10.1038/nature09014</A>]['10],
      [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/20463738">p'bmed</A>]['14],
      LUCA@[<A HREF="http://en.wikipedia.org/wiki/Last_universal_ancestor">wikip</A>]['14],
      Theob.@[<A HREF="http://www.bio.brandeis.edu/faculty/theobald.html">br@ndeis</A>]['14].
   (Also see [<A HREF="http://dx.doi.org/10.1038/465168a">doi:10.1038/465168a</A>]['10].)
   [Also search for: MolBio LUCA].

%A T-K. Kim
%A et al ...
%A M. E. Greenberg
%T Widespread transcription at neuronal activity-regulated enhancers
%J Nature
%V 465
%N 7295
%P 182-187
%M MAY
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, enhancer, gene regulation, transcription,
   CBP, RNAPII, RNA, miRNA, eRNA
%X "... identified ~12,000 neuronal activity-regulated enhancers that are bound
   by the general transcriptional co-activator CBP ... Notably, RNAPII at
   enhancers transcribes bi-directionally a novel class of enhancer RNAs (eRNAs)
   within enhancer domains defined by the presence of histone H3 monomethylated
   at lysine 4. The level of eRNA expression at neuronal enhancers +ve
   correlates with the level of messenger RNA synthesis at nearby genes, ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09033">doi:10.1038/nature09033</A>]['10].
   (Also see [<A HREF="http://dx.doi.org/10.1038/465173a">doi:10.1038/465173a</A>]['10].)

%A A. Zemach
%A I. E. McDaniel
%A P. Silva
%A D. Zilberman
%T Genome-wide evolutionary analysis of eukaryotic DNA methylation
%J Science
%V 328
%N 5980
%P 916-919
%M MAY
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, methylation, methylome, DNA, conservation,
   eukaryote, plant, methyltransferase, Dnmt1, Dnmt3, CMT, DRM,
   transposable element, phylogenetic, evolutionary, tree
%X "Eukaryotic cytosine methylation represses transcription but also occurs in
   the bodies of active genes, & the extent of methylation biology conservation
   is unclear. We quantified DNA m. in 17 e.genomes & found that gene body m. is
   conserved between plants & animals, whereas selective m. of transposons is
   not. We show that m. of plant transposons in the CHG context extends to green
   algae & that exclusion of histone H2A.Z from m. DNA is conserved between
   plants & animals, & we present evidence for RNA-directed DNA m. of fungal
   genes. Our data demonstrate that extant DNA m. systems are mosaics of
   conserved & derived features, & indicate that gene body m. is an ancient
   property of eukaryotic genomes."  [18 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1186366">doi:10.1126/science.1186366</A>]['10].
   Extras@[<A HREF="http://www.sciencemag.org/cgi/content/full/science.1186366/DC1">scimag</A>]['10],
     "... The catalytic domains of the indicated DNA methyltransferase proteins
     were aligned ... To improve the al. between Dnmt3 & DRM, we moved
     the C-terminal seqs. containing cons. motifs I-IV of the DRM catalytic
     domain to the N terminus, for a final aligned set of 555 chars. ..."
   (Also see perspective@[<A HREF="http://dx.doi.org/10.1126/science.1190738">doi:10.1126/science.1190738</A>]['10].)

%A Z. Duan
%A et al ...
%A S. Noble
%T A three-dimensional model of the yeast genome
%J Nature
%V 465
%P 363-367
%M MAY
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0510, yeast, eukaryote, 3D, structure,
   genome, DNA, Saccharomyces cerevisiae, nucleolus, chrXII, chr12, rDNA,
   centromere, breakpoint
%X "Layered on top of info. conveyed by DNA seq. & chromatin are higher order
   structures that encompass portions of chrs., entire chrs., & even whole
   genomes ... Here we developed a method to globally capture intra- & inter-
   -chromosomal interactions, & applied it to generate a map at kilobase
   resolution of the haploid genome of S.cerevisiae. ... Extensive regional &
   higher order folding of individual chrs. is observed. Chr.XII exhibits a
   striking conformation that implicates the nucleolus as a formidable barrier
   to interaction between DNA seqs. at either end. Inter-chromosomal contacts
   are anchored by centromeres & include interactions among transfer RNA genes,
   among origins of early DNA replication & among sites where chromosomal
   breakpoints occur. Finally, we constructed a three-dimensional model ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08973">doi:10.1038/nature08973</A>]['10].

%T A catalog of reference genomes from the human microbiome
%Q The Human Microbiome Jumpstart Reference Strains Consortium
%J Science
%V 328
%N 5981
%P 994-999
%M MAY
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, human, microbiome, microbes,
   microorganisms
%X "The human microbiome refers to the community of microorganisms, inc.
   prokaryotes, viruses, and microbial eukaryotes, that populate the human body.
   ... sequencing of hundreds of microbial reference genomes, coupled to
   metagenomic sequencing from multiple body sites. ... present results from an
   initial reference genome sequencing of 178 microbial genomes. ... This
   analysis resulted in a set of 30,867 polypeptides, of which 29,987 (~97%)
   were unique. In addition, this set of microbial genomes allows for ~40% of
   random seqs. from the microbiome of the gastrointestinal tract to be assoc.
   with organisms based on the match criteria used. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1183605">doi:10.1126/science.1183605</A>]['10].

%A D. Sankoff
%A C. Zheng
%A Q. Zhu
%T The collapse of gene complement following whole genome duplication
%J BMB Bioinformatics
%V 11
%P 313
%M MAY ?
%D 2010
%K jrnl, eJrnl, MolBio, c2010, c201x, c20xx, zz0510, paralog,
   whole genome duplication, event, WGD
%X "... compare 15 genomes descending from 6 eukaryotic WGD events 20-450 Mya.
   We characterize the collapse over time through the distribution of runs of
   reduced paralog pairs in duplicated segments. Descendant genomes of the same
   WGD event behave as replicates. ... Both the contiguous regions of reduction-
   -resistant pairs & the concentration of runs of single copy genes on a single
   chromosome are evidence of transcriptional co-regulation, dosage sensitivity
   or other functional interaction constraining the reduction process. These
   constraints & their evolution over time show a consistent pattern across
   evolutionary domains & a highly reproducible pattern, as replicates, for the
   several descendants of a single WGD."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2164-11-313">doi:10.1186/1471-2164-11-313</A>]['10].

%A D. T. Barken
%A et al
%T Prediction of protease substrates using sequence and structure features
%J Bioinformatics
%V 26
%N 14
%P 1714-1722
%M JUL
%D 2010
%K MolBio, c2010, c201x, c20xx, zz0820, salilab, protease, proteinase, cleave,
   substrate, specificity, Granzyme B, GranzymeB, GrB, caspases, GrBah
%X "... we present a BioI. method based on support vector machine (SVM)
   learning that identifies seq. & structural features important for protease
   recognition of substrate peptides & then uses these features to predict
   novel substrates. ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btq267">doi:/10.1093/bioinformatics/btq267</A>]['20].

%A D. G. Gibson
%A et al ...
%A J. C. Venter
%T Creation of a bacterial cell controlled by a chemically synthesized genome
%J Science
%V JUL
%P 52-56
%M JUL
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, life, artificial, bacteria, bacterium,
   cell, synthesized genome, DNA, synthetic, Mycoplasma, mycoides JCVI-syn1.0,
   zz0510, capricolum
%X "We report the design, synthesis, & assembly of the 1.08-Mbp Mycoplasma
   mycoides JCVI-syn1.0 genome starting from digitized genome seq. info. & its
   transplantation into a Mycoplasma capricolum recipient cell to create new
   M.mycoides cells that are controlled only by the synthetic chr.. The only DNA
   in the cells is the designed synthetic DNA seq., inc. "watermark" seqs. &
   other designed gene deletions & polymorphisms, & mutns acquired during the
   building process. The new cells have expected phenotypic properties & are
   capable of continuous self-replication."  [online May 2010].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1190719">doi:10.1126/science.1190719</A>]['10].

%A J. M. Cock
%A et al ...
%A P. Wincker
%T The Ectocarpus genome and the independent evolution of multicellularity in
   brown algae
%J Nature
%V 465
%P 617-621
%M JUN
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0610, brown algae, alga, algal, genome,
   seaweed, sea weed, nGenome, Ectocarpus siliculosus, Dillwyn, Lyngbe,
   eukaryotes, Stramenopiles, Phaeophyceae, evolution, multicellular,
   multi cellular
%X "... seaweeds ... We report the 214-million base pair (Mbp) genome sequence
   of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model
   organism for brown algae, closely related to the kelps ...
   16,256 protein coding genes  ...  EMBL acc. #s CABU01000001-CABU01013533,
   (FN647682-FN649242, FN649726-FN649760) ..."
   ??? 25 chrs ???
   -- [<A HREF="http://dx.doi.org/10.1038/nature09016">doi:10.1038/nature09016</A>]['10],
   project@[<A HREF="http://www.genoscope.cns.fr/spip/Ectocarpus-siliculosus,740.html">cns.fr</A>]['10].
   [Also search for: alga nGenome].

%A J. M. Gomez
%A M. Verdu
%A F. Perfectti
%T Ecological interactions are evolutionarily conserved across the entire
   tree of life
%J Nature
%V 465
%P 918-921
%M JUN
%D 2010
%K jrnl, c2010, c201x, c20xx, ecology, role, roles, niche, niches, interaction,
   conservation, evolution
%X "... phenotypic traits regulating species interactions are largely a legacy
   of their ancestors, ... assumed that ecological interactions are phylo.
   conserved, with closely related species interacting with similar partners.
   However, the existing empirical evidence is inadequate to appropriately
   evaluate ... In fact, most studies on the evolution of ecol'l interactions
   have focused on specialized organisms, such as some parasites or insect
   herbivores belonging to a limited subset of the overall tree of life. Here
   we study the evol'n of host use in a large & diverse group ... both
   specialist & generalist acellular, unicellular & multicellular organisms. We
   show that, as previously found for specialized interactions, generalized
   interactions can be evolutionarily conserved. Significant phylogenetic
   conservatism of interaction patterns was equally likely to occur in symbiotic
   & non-sy. interactions, [&] in mutualistic & antagonistic interactions.
   Host-use differentiation among species was higher in phylo.conserved clades,
   irrespective of their generalization degree & taxonomic position within the
   tree of life. ... strongly suggest a shared pattern in the org'n of biol.sys.
   through evolutionary time, mediated by marked conservatism of ecological
   interactions among taxa."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09113">doi:10.1038/nature09113</A>][1'0].

%A I. S. Povolotskaya
%A F. A. Kondrashov
%T Sequence space and the ongoing expansion of the protein universe
%J Nature
%V 465,
%P 922-926
%M JUN
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0610, protein, proteins, evolution,
   mutation, change, sequence space, constraints, constrained
%X "The need to maintain the structural & fn'l integrity of an evolving protein
   severely restricts the repertoire of acceptable amino-acid substitutions.
   However, it is not known whether these restrictions impose a global limit on
   how far homologous protein seqs. can diverge from each other. Here we explore
   the limits of protein evolution using seq. divergence data. ... ...& measure
   this rate for ancient proteins, those that were present in the last universal
   common ancestor. We show that ancient proteins are still diverging from each
   other, indicating an ongoing expansion of the protein seq. universe. The slow
   rate of this divergence is imposed by the sparseness of functional protein
   seqs. ... & the ruggedness of the p.fitness landscape: ~98% of sites cannot
   accept an AA subst'n [now] but a vast majority of all sites may eventually be
   permitted to evolve when other, compensatory, changes occur. Thus ~3.5x10**9
   yr has not been enough to reach the limit of divergent evoln of ps., & for
   most ps. the limit of seq. similarity imposed by common fn may not exceed
   that of random seqs.."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09105">doi:10.1038/nature09105</A>]['10].

%A J. T. Simpson
%A R. Durbin
%T Efficient construction of an assembly string graph using the FM-index
%J J. Bioinformatics
%V 26
%N 12
%P i367-373
%M JUN
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz1111, SGA, denovo, sequence assembly,
   assembler, stringGraph, Jared Simpson
%X "... Standard overlap assembly methods have time complexity O(N^2), where N
   is the sum of the lengths of the reads. We use the Ferragina-Manzini index
   (FM-index) derived from the Burrows-Wheeler transform to find overlaps of
   length at least tau among a set of reads. As well as an approach that finds
   all overlaps then implements transitive reduction to produce a string graph,
   we show how to output directly only the irreducible overlaps, sig.shrinking
   memory req. & reducing compute time to O(N), indep. of depth. Overlap-based
   assembly methods naturally handle mixed length read sets, inc. capillary
   reads or long reads promised by the 3rd gen. seq. technologies. ...  pave[s]
   the way for overlap-based assembly approaches to be developed that scale to
   whole vertebrate genome de novo assembly."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btq217">doi:10.1093/bioinformatics/btq217</A>]['11],
   auth1@[<A HREF="http://people.pwf.cam.ac.uk/js779/">cam</A>]['11],
   (Also see a JS talk@[<A HREF="http://www.youtube.com/watch?v=9h3mYjWK4SQ">uTube</A>]['11].)
   [Also search for: MolBio stringGraph].

%A S. Gavrilets
%T Rapid transition towards the division of labor via evolution of
   developmental plasticity
%J PLoS Comput. Biol.
%V 6
%N 6
%P e1000805
%M JUN
%D 2010
%K jrnl, eJrnl, c2010, c201x, c20xx, zz0610, cell, cells, multi cellular,
   multicellular, differentiation, organism, selfish, cooperation, evolution,
   organs, model, division of labor, labour
%X "... major evolutionary transitions is the division of labor between
   components of the emerging higher-level evolutionary unit. E.g.s include the
   separation of germ & soma in simple multicellular organisms, appearance of
   multiple cell types & organs in more complex organisms, ...  How the divn of
   labor was achieved in the face of selfishness of lower-level units is
   controversial. I present a simple math. model describing the evol.emergence
   of the divn of labor via developmental plasticity starting with a colony of
   undifferentiated cells & ending with completely differentiated multicellular
   organisms. I explore how the plausibility & the dynamics ... depend on its
   fitness advantage, mutation rate, costs of developmental plasticity, & the
   colony size. ... shows that the transition to differentiated multicellularity
   which has happened many times in the history of life, can be achieved
   relatively easily. My approach is expandable in a number of dirns inc. the
   emergence of mult. cell types, complex organs, or casts of eusocial insects."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pcbi.1000805">doi:10.1371/journal.pcbi.1000805</A>]['10], [62 refs].
   (Suggests that given >= 2 "tasks" in order to prosper, the "trick" is the
   evol'n of genes that can suppress the activity of one trait or another.

%A A. El Albani
%A et al ...
%A A. Meunier
%T Large colonial organisms with coordinated growth in oxygenated environments
   2.1-Gyr ago
%J Nature
%V 466
%N 7032
%P 100-104
%M JUL
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, colony, multicellular, life, origins,
   evolution, organism, Palaeoproterozoic Francevillian, Gabon
%X "... report the discovery of centimetre-sized structures from the 2.1-Gyr-old
   black shales of the Palaeoproterozoic Francevillian B Formation in Gabon,
   which we interpret as highly organized & spatially discrete populations of
   colonial organisms. The structures are up to 12cm in size & have
   characteristic shapes, with a simple but distinct ground pattern of flexible
   sheets &, usually, a permeating radial fabric. Geochemical analyses suggest
   that the sediments were deposited under an oxygenated water column ...
   suggest that the organisms showed cell-to-cell signalling & coordinated
   responses, as is commonly associated with multicellular organization. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09166">doi:10.1038/nature09166</A>]['10].

%A A. K. Maunakea
%A et al ...
%A J. F. Costello
%T Conserved role of intragenic DNA methylation in regulating alternative
   promoters
%J Nature
%V 466
%P 253-257
%M JUL
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0710, DNA, methylation, methylated,
   gene, CpG, alternative, promoter, promoters, H3K4, SHANK3, differentiation,
   tissue, cell type
%X "... known that the methylation of DNA in 5' promoters suppresses gene
   expression, the role of DNA m. in gene bodies is unclear. ... generated a
   map of DNA m. from the human brain encompassing 24.7 million of the 28
   million CpG sites. From the dense, high-resolution coverage of CpG islands,
   the majority of m. CpG islands were shown to be in intragenic & intergenic
   regions, whereas less than 3% of CpG islands in 5' promoters were m.. The
   CpG islands in all 3 locations overlapped with RNA markers of transcription
   initiation, & unm. CpG islands also overlapped significantly with
   trimethylation of H3K4, a histone modification enriched at promoters. The
   general & CpG-island-specific patterns of m. are conserved in mouse tissues.
   An in-depth investigation of the human SHANK3 locus & its mouse homologue
   demonstrated that this tissue-specific DNA m.  regulates intragenic promoter
   activity in vitro & in vivo. These m.-regulated alternative transcripts are
   expressed in a tissue- & cell type-specific manner, & are expressed
   differentially within a single cell type from distinct brain regions. These
   results support a major role for intragenic m. in regulating cell context-
   -specific alternative promoters in gene bodies."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09165">doi:10.1038/nature09165</A>]['10].

%A S. E. Prochnik
%A eta l ...
%A D. F. Rokhsar
%T Genomic analysis of organismal complexity in the multicellular green alga
   Volvox carteri
%J Science
%V 329
%N 5988
%P 223-226
%M JUL
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, genome, green alga, algae, algal,
   evolution, Volvox carteri, Chlamydomonas reinhardtii, organism, complexity,
   protein
%X "The multicellular green alga Volvox carteri & its morphologically diverse
   close relatives (the volvocine algae) ... We sequenced the 138-mega bp genome
   of V. carteri & compared its ~14,500 predicted proteins to those of its
   unicellular relative Chlamydomonas reinhardtii. Despite fundamental
   differences in organismal complexity & life history, the 2 species have
   similar protein-coding potentials & few species-specific protein-coding gene
   predictions. Volvox is enriched in volvocine-algal-specific proteins, inc.
   those assoc. with an expanded & highly compartmentalized extracellular
   matrix. ... shows that increases in organismal complexity can be assoc. with
   mods. of lineage-specific proteins rather than large-scale invention of
   protein-coding capacity."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1188800">doi:10.1126/science.1188800</A>]['10].

%A R. E. Ricklefs
%A D. C. Outlaw
%T A molecular clock for malaria parasites
%J Science
%V 329
%N 5988
%P 226-229
%M JUL
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, plasmodium, malaria, parasite, falciparum,
   human, avian, bird, cytochrome b, origin, evolution
%X "The evolutionary origins of new lineages of pathogens are fundamental to
   understanding emerging diseases. Phylogenetic reconstruction based on DNA
   seqs. has revealed the sister taxa of human pathogens, but the timing of host
   -switching events, including the human malaria pathogen P.falciparum, remains
   controversial. Here, we establish a rate for cytochrome b evolution in avian
   malaria parasites relative to its rate in birds. We found that the parasite
   cytochrome b gene evolves about 60% as rapidly as that of host cytochrome b,
   corr.to ~1.2% sequence divergence per m.years. ... puts the origin of P.
   falciparum at 2.5 m.years ago, the initial radiation of mammalian P. at
   12.8 Ma, & the contemporary global diversity of the Haemosporida across
   terrestrial vertebrates at 16.2 Ma."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1188954">doi:10.1126/science.1188954</A>]['10].

%A C. L. Oskam
%A et al ...
%A M. Bunce
%T Fossil avian eggshell preserves ancient DNA
%J Proc. Royal Soc. B
%V 277
%N 1690
%P 1991-2000
%M JUL
%D 2010
%K jrnl, PRSB, MolBio, c2010, c201x, c20xx, zz1012, fossil, old, ancient, DNA,
   bird, bids, eggs, NZ, moa, Dinornithiformes, Aepyornis, Mullerornis,
   Genyornis, Allentoft
%X "... show, to our knowledge, for the first time that fossil eggshell is a
   previously unrecognized source of ancient DNA (aDNA). We describe the
   successful isolation & amplification of DNA from fossil eggshell up to 19ka
   old. aDNA was successfully characterized from eggshell obtained from N.Z.
   (extinct moa & ducks), Madagascar (extinct elephant birds) & Australia (emu
   & owl). Our data demonstrate excellent preservation of the nucleic acids,
   evidenced by retrieval of both mitochondrial & nuclear DNA from many of the
   samples. ... the preservation of DNA in Pleistocene eggshell from .au &
   Holocene deposits from Madagascar indicates that eggshell is an excellent
   substrate for the long-term preservation of DNA in warmer climates. ..."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2009.2019">doi:10.1098/rspb.2009.2019</A>]['12].
   [Also search for: MolBio ancient DNA] and
   [also search for: MolBio fossil DNA].

%A A. E Teschendorff
%A S. Severini
%T Increased entropy of signal transduction in the cancer metastasis phenotype
%J BMC Sys. Biol.
%V 4
%P e104
%M JUL
%D 2010
%K jrnl, eJrnl, MolBio, c2010, c201x, c20xx, zz0715, local, network entropy,
   information, signal, signaling, signalling, protein interaction, PPI,
   breast cancer, metastatic
%X "... Based on the observation that frequent genomic alterations underlie a
   more aggressive cancer phenotype, we asked if such an effect could be
   detectable as an increase in the randomness of local gene expn patterns.
   Using a breast cancer gene expression data set & a model n/w of protein
   interactions we derive constrained weighted n/ws defined by a stochastic
   information flux matrix reflecting expression correlations between
   interacting proteins. ... propose & compute an entropy measure that
   quantifies the degree of randomness in the local pattern of info. flux around
   single genes. By comparing the local entropies in the non-metastatic v.
   metastatic breast cancer n/ws, we here show that breast cancers that
   metastasize are characterised by a small yet sig. increase in the degree of
   randomness of local expn patterns. We validate this result in three
   additional breast cancer expn data sets & demo. that local entropy better
   characterises the metastatic phenotype than other non-entropy based measures.
   We show that increases in entropy can be used to identify genes & signalling
   pathways implicated in breast cancer metastasis ..."
      "*weights* to the edges in the PIN-mRNA network. ...
       propose the following entropy measure ... similar to the
       local disparity/heterogeneity index of weighted networks ...
       local entropy of node is
       S_i = -(1/log k_i) SUM_[j in N(i)] (p_ij log p_ij)"
   -- [<A HREF="http://dx.doi.org/10.1186/1752-0509-4-104">doi:10.1186/1752-0509-4-104</A>]['15].

%A D. W. McShea
%A R. N. Brandon
%T Biology's First Law: The Tendency for Diversity and Complexity to
   Increase in Evolutionary Systems
%I U. of Chicago Press
%P 184
%D 2010
%K book, text, MolBio, c2010, c201x, c20xx, zz0710, ZFEL, biol, biology,
   science, zero force evolutionary law, complexity, diversity, ecology,
   evolution, life
%X "... shows how the ZFEL can be applied to the study of diversity & complexity
   & examines its wider implications for biol.. Intended for evolutionary
   biologists, paleontologists, & other scientists studying complex systems ..."
   1st ed 2010; hb us$44; us isbn:0226562255; us isbn13:978-0226562254;
                pb us$14; us isbn:0226562263; us isbn13:978-0226562261.
   (ZFEL = zero-force evolutionary law.)

%T Networks in Cell Biology
%E M. Buchanan
%E G. Caldarelli
%E P. De Los Rios
%E F. Rao
%E M. Vendruscolo
%I CUP
%P 280
%D 2010
%K book, text, MolBio, CUP, c2010, c201x, c20xx, zz0710, L5Ref, network, cells,
   systems, biol, gene regulatory networks, metabolic
%X "... introduction to complex n/w science & its biological applications. ...
   for grad.students & researchers in physics, biology & biochemistry, &
   presents ideas & techniques from fields outside the reader's own area of
   specialization."
   1st ed 2010; hb us$75; uk us isbn:0521882737; uk us isbn13:978-0521882736.

%A K. Mahmood
%A A. S. Konagurthu
%A J. Song
%A A. M. Buckle
%A G. I. Webb
%A J. C. Whisstock
%T EGM: Encapsulated gene-by-gene matching to identify gene orthologs and
   homologous segments in genomes
%J J. Bioinformatics
%V ?
%N ?
%P ?-?
%M ?
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, ArunK, gene, family, bipartite matching,
   EGM
%X "Identification of functionally equivalent genes in different species ...
   ... (EGM) approach, a method that employs a graph matching strategy to
   identify gene orthologs & conserved gene segments. Given a pair of genomes,
   EGM constructs a global gene match for all genes taking into account gene
   context & family info.. The Hungarian method for identifying the maximum
   weight matching in bipartite graphs is employed, where the resulting matching
   reveals one-to-one corr. between nodes (genes) in a manner that maximizes the
   gene similarity & context. ..."  [online Jun 2010], via ArunK.
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btq339">doi:10.1093/bioinformatics/btq339</A>]['10].

%A M. Soskine
%A D. S. Tawfik
%T Mutational effects and the evolution of new protein functions
%J NatureReview Genet.
%V 11
%N 8
%P 572-582
%M AUG
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0123, protein, mutation, evolution,
   function, pleiotropic, fitness, selection
%X "The divergence of new genes & proteins occurs through mutations that
   modulate protein fn. ... can have different effects on organismal fitness
   depending on the environment, as well as opposite effects on protein fn &
   dosage. We review the pleiotropic effects of mutations. We discuss how they
   affect the evolution of gene & protein fn, & ... propose several factors that
   can affect the divergence of new protein fns, inc. mutational trade-offs &
   hidden, or apparently neutral, variation."
   -- [<A HREF="https://doi.org/10.1038/nrg2808">doi:10.1038/nrg2808</A>]['23],
   20634811@[<A HREF="https://pubmed.ncbi.nlm.nih.gov/20634811/">pubm'd</A>]['23].

%A M. Srivastava
%A et al ...
%A D. J. Jackson
%T The Amphimedon queenslandica genome and the evolution of animal complexity
%J Nature
%V 466
%P 720-726
%M AUG
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, Amphimedon queenslandica genome, nGenome,
   multicellular, animal, animals, metazoa, metazoans, metazoan, demosponge,
   sponge, evolution
%X "... analysis enabled by the sequencing of the sponge genome reveals genomic
   events linked to the origin & early evolution of animals, including the
   appearance, expansion & diversification of pan-metazoan transcription factor,
   signalling pathway & structural genes. ... Notably, many of the genes assoc.
   with the emergence of animals are also implicated in cancer, which arises
   from defects in basic processes assoc. with metazoan multicellularity."
   ... 167-megabase-pair assembly ... captures ~97% of the protein-coding
   ... ~30,000 predicted protein-coding loci ... 18,693 (63%) have identifiable
   homologues in other organisms ...
   ... DDBJ/EMBL/GenBank project accession ACUQ00000000.
   -- [<A HREF="http://dx.doi.org/10.1038/nature09201">doi:10.1038/nature09201</A>]['10].

%A S. Cooper
%A et al ...
%A Z. Popovi & Foldit players
%T Predicting protein structures with a multiplayer online game
%J Nature
%V 466
%P 756-760
%M AUG
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0810, protein, structure, folding, 3D,
   Rosetta, foldit, game
%X "... describe Foldit, a multiplayer online game that engages non-scientists
   in solving hard prediction problems. Foldit players interact with protein
   structures using direct manipulation tools and user-friendly versions of
   algorithms from the Rosetta structure prediction methodology4, while they
   compete and collaborate to optimize the computed energy. We show that top-
   -ranked Foldit players excel at solving challenging structure refinement
   problems in which substantial backbone rearrangements are necessary to
   achieve the burial of hydrophobic residues. Players working collaboratively
   develop a rich assortment of new strategies and algorithms ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09304">doi:10.1038/nature09304</A>]['10].

%A Y.-Y. Ahn
%A J. P. Bagrow
%A S. Lehmann
%T Link communities reveal multiscale complexity in networks
%J Nature
%V 466
%P 761-764
%M AUG
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, link, dendrogram, community, network
%X "... Communities in n/ws often overlap such that nodes simultaneously belong
   to several groups. Meanwhile, many n/ws are known to possess hierarchical
   organization, where communities are recursively grouped into a hierarchical
   structure1. However, the fact that many real n/ws have communities with
   pervasive overlap, where each & every node belongs to more than one group,
   has the consequence that a global hierarchy of nodes cannot capture the
   relationships between overlapping groups. Here we reinvent communities as
   groups of links rather than nodes & show that this unorthodox approach
   successfully reconciles the antagonistic organizing principles of overlapping
   communities & hierarchy. In contrast to the existing literature, which has
   entirely focused on grouping nodes, link communities naturally incorporate
   overlap while revealing hierarchical organization. We find relevant link
   communities in many n/ws ..."
   "... we consider a community to be a set of closely interrelated links.
   ... We use hierarchical clustering with a similarity between *links* ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09182">doi:10.1038/nature09182</A>]['10].
   [Also search for: network community].

%A Y. Bhattacharjee
%T Defining select agents by DNA sequence
%J Science
%V 329
%N 5992
%P 615
%M AUG
%D 2010
%K news, MolBio, c2010, c201x, c20xx, zz0810, DNA, select agent, bio security,
   bioSecurity, germ war, warfare, anthrax
%X "To work with dangerous pathogens such as anthrax, U.S. researchers must
   follow strict rules governing so-called select agents, or potential
   bioweapons. But what about a DNA seq. ordered from a company that contains
   some of the genes that make anthrax deadly? Currently, such an entity - or
   an artificial organism designed with such DNA - would not be subject to the
   same regulations ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.329.5992.615">doi:10.1126/science.329.5992.615</A>]['10].

%A J. Bascompte
%T Structure and dynamics of ecological networks
%J Science
%V 329
%N 5993
%P 765-766
%M AUG
%D 2010
%K views, c2010, c201x, c20xx, ecology, network, web, ecological, antagonistic,
   mutually beneficial, interaction, trophic, mutualistic, ecology, diversity
%X "... Antagonistic interactions tend to be arranged in compartments, whereas
   mutualistic interactions tend to be nested ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1194255">doi:10.1126/science.1194255</A>]['10].
   (Also see [<A HREF="http://dx.doi.org/10.1038/nature12380">comment</A>]['13].)

%A V. K. McElheny
%T Drawing the Map of Life: Inside the Human Genome Project
%I BasicBooks
%P 384
%D 2010
%K book, text, MolBio, c2010, c201x, c20xx, zz0810, human genome project, HUGO,
   DNA
%X 1st ed 2010; hb us$18; uk us isbn:046504333X; uk us isbn13:978-0465043330.

%A C. K. Cornwallis
%A S. A. West
%A K. E. Davis
%A A. S. Griffin
%T Promiscuity and the evolutionary transition to complex societies
%J Nature
%V 466
%P 969-972
%M AUG
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0810, cooperation, breeding, sex,
   evolution, family, monogamy, polygamy, relatedness, bird, birds, society,
   animal behaviour
%X "Theory predicts that the evoln of cooperative behaviour is favoured by low
   levels of promiscuity leading to high within-group relatedness. However, in
   vertebrates, cooperation often occurs between non-relatives & promiscuity
   rates are among the highest recorded. Here we resolve this apparent
   inconsistency with a phylogenetic analysis of 267 bird species, demo. that
   coop.breeding is assoc. with low promiscuity; that in coop.species, helping
   is more common when p. is low; & that intermediate levels of p. favour kin
   discrimination. ...  suggest that p. is a unifying feature across taxa in
   explaining transitions to and from cooperative societies."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09335">doi:10.1038/nature09335</A>]['10].
   [Also search for: polygamy] and/or [also search for: monogamy].

%E P. Mukkany
%E A. P. Roberts
%T Clostridium difficile: Methods and Protocols
%S Methods in Molecular Biology
%I Humana
%P 216
%D 2010
%K book, text, MolBio, c2010 c201x, c20xx, biol, biology, microbiology,
   bacterium, bacteria, Clostridium difficile, antibiotic, drug, resistance
%X 1st ed 2010; hb us$95; uk us isbn:1603273646; uk us isbn13:978-1603273640.
   "Clostridium difficile, a major nosocomial pathogen shown to be a primary
   cause of antibiotic-associated disease, has emerged as a highly transmissible
   and frequently antibiotic-resistant organism, causing a considerable burden
   on health care systems worldwide.  ... lists of the necessary materials and
   reagents, step-by-step, readily reproducible laboratory protocols, and notes
   highlighting tips on troubleshooting and avoiding known pitfalls."

%A I. L. Berg
%A R. Neumann
%A K.-W. G. Lam
%A S. Sarbajna
%A L. Odenthal-Hesse
%A C. A. May
%A A. J. Jeffreys
%T PRDM9 variation strongly influences recombination hot-spot activity and
   meiotic instability in humans
%J Nature Genetics
%V ?
%N ?
%P ?-?
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0910, PRDM 9, PRDM9, hot spot, spots,
   DNA, recombination, rearrangement, meiotic instability, human, gene, genes,
   CCNCCNTNNCCNC, CMT1A, HNPP
%X "PRDM9 ...identified as a likely trans regulator of meiotic recombination
   hot spots in humans & mice. PRDM9 contains a zinc finger array that, in h.,
   can recognize a short seq. motif assoc. with hot spots ... possibly
   triggering hot-spot activity via chromatin remodeling. ... report that h.
   genetic var'n at the PRDM9 locus has a strong effect on sperm hot-spot
   activity, even at hot spots lacking the seq.motif. ... even trigger the
   appearance of a new hot spot, suggesting that PRDM9 is a major global
   regulator of hot spots in h.. Variation at the PRDM9 locus also influences
   aspects of genome instability - specifically, a megabase-scale rearrangement
   underlying 2 genomic disorders [&] minisatellite instability - implicating
   PRDM9 as a risk factor for some pathological genome rearrangements."
   -- [<A HREF="http://dx.doi.org/10.1038/ng.658">doi:10.1038/ng.658</A>]['10].
   (online Sept 2010.)

%A H. Ji
%A et al ...
%A A. P. Feinberg
%T Comprehensive methylome map of lineage commitment from haematopoietic
   progenitors
%J Nature
%V 467
%P 338-342
%M SEP
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz1010, Epigenetic modification, DNA,
   epigenome, methylation, CpG, cell, differentiation, tissue, Haematopoiesis,
   MPP, MPPs, CLPs, haematopoietic progenitors
%X "Epigenetic modifications must underlie lineage-specific differentiation as
   terminally differentiated cells express tissue-specific genes, but their DNA
   sequence is unchanged. Haematopoiesis provides a well-defined model to study
   epigenetic modifications during cell-fate decisions, as multipotent
   progenitors (MPPs) differentiate into progressively restricted myeloid or
   lymphoid progenitors. Although DNA methylation is critical for myeloid
   versus lymphoid differentiation, as demonstrated by the myeloerythroid bias
   in Dnmt hypomorphs, a comprehensive DNA methylation map of haematopoietic
   progenitors, or of any multipotent/oligopotent lineage, does not exist. Here
   we examined 4.6 million CpG sites throughout the genome for MPPs, common
   lymphoid progenitors (CLPs) ... "
   -- [<A HREF="http://dx.doi.org/10.1038/nature09367">doi:10.1038/nature09367</A>]['10].

%A W. Liu
%A et al
%A B. H. Hahn
%T Origin of the human malaria parasite Plasmodium falciparum in gorillas
%J Nature
%V 467
%P 420-425
%M SEP
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0910, malaria, Plasmodium falciparum,
   human, gorilla, origin, Africa
%X "... develop a single-genome amplification strategy to identify &
   characterize Plasmodium  spp. DNA seqs. in faecal samples from wild-living
   apes. Among nearly 3,000 specimens collected from field sites [in] central
   Africa, we found Plasmodium infection in chimpanzees (Pan troglodytes) &
   western gorillas (Gorilla gorilla), but not in eastern gs. (Gorilla beringei)
   or bonobos (Pan paniscus). ... phylogenetic analyses of full-length
   mitochondrial seqs., human P. falciparum formed a monophyletic lineage within
   the gorilla parasite radiation. ... indicate that P.falciparum is of gorilla
   origin & not of chimpanzee, bonobo or ancient human origin."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09442">doi:10.1038/nature09442</A>]['10].

%A G. Miller
%T Scientific misconduct: Misconduct by postdocs leads to retraction of papers
%J Science
%V 329
%N 5999
%P 1583
%M SEP
%D 2010
%K news, c2010, c201x, c20xx, zz1010, scandal, misconduct, postdoc, postdocs,
   scientific, papers, paper, PNAS, JNCI, research, retraction, retracted,
   retract, gene therapy, cancer, phiBT1, Clostridium perfringens,
   bacteriophage, enzyme, Savio L C Woo, Li Chen, Zhiy Li
%X "... two postdoctoral fellows working in the lab of noted gene-therapy
   researcher Savio Woo had been fired for research misconduct. ... Woo had been
   cleared of any wrong-doing in an internal investigation & had voluntarily
   retracted four research ps.. ... process of elimination suggests they are
   Li Chen & Zhiyu Li, each the first author on 2 retracted ps. & the only ones
   not currently listed in the Mount Sinai directory as faculty members. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.329.5999.1583">doi:10.1126/science.329.5999.1583</A>]['10]
   and [<A HREF="http://news.sciencemag.org/scienceinsider/2010/09/mount-sinai-says-misconduct-by-p.html">www</A>]['10].
   [Also search for: misconduct].

%E D. Fenyo
%T Computational Biology
%S Methods in Molecular Biology
%I HumanaPress
%P 327
%M SEP
%D 2010
%K book, text, MolBio, c2010, c201x, c20xx, zz0111, bioinformatics, survey
%X 1st ed 2010; hb us$110; uk us isbn:1607618419; uk us isbn13:978-1607618416.
   "... a broad survey of computational biology methods by focusing on their
   applications, including primary sequence analysis, protein structure
   elucidation, transcriptomics and proteomics data analysis, and exploration
   of protein interaction networks. ..."

%A S. Kondo
%A T. Miura
%T Reaction-diffusion model as a framework for understanding biological
   pattern formation
%J Science
%V 329
%N 5999
%P 1616-1620
%M SEP
%D 2010
%K review, survey, intro, c2010, c201x, c20xx, zz1010, Turing, gradient,
   reaction diffusion, RD, model, self regulated, regulating, spatial,
   pattern formation, animal development, morphology, biol, biology, graphics,
   morphogenesis
%X "The Turing, or reaction-diffusion (RD), model is one of the best-known
   theoretical models used to explain self-regulated pattern formation in the
   developing animal embryo. Although its real-world relevance was long debated,
   a # of compelling e.g.s have gradually alleviated much of the skepticism
   surrounding the model. ... can generate a wide variety of spatial patterns,
   & math.studies have revealed the kinds of interactions required for each,
   giving this model the potential for application as an experimental working
   hypothesis in a wide variety of morphological phenomena. ... we describe the
   essence of this theory for experimental biologists unfamiliar with the model,
   using e.g.s from exp.studies ... "
   -- [<A HREF="http://dx.doi.org/10.1126/science.1179047">doi:10.1126/science.1179047</A>]['10].
   [Also search for: morphogenesis]  and  [also search for: reaction diffusion].

%A D. Zhi
%A M. Shatsky
%A S. E. Brenner
%T Alignment-free local structural search by writhe decomposition
%J J. Bioinformatics
%V 26
%N 9
%P 1176-1184
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, protein, structure, search, matching,
   knot theory, writhe decomposition
%X "... Projection methods map a structure to a point in a high-dimensional
   space and compare two structures by measuring distance between their
   projected points.  ... [new] approach that can rapidly detect global as well
   as local structural similarities.  Local structural search is enabled by a
   topology-inspired writhe decomposition protocol that produces a small number
   of fragments while ensuring that similar structures are cut in a similar
   manner. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btq127">doi:10.1093/bioinformatics/btq127</A>]['11].
   [Also seach for: MolBio knot protein].

%A S. Potter
%T Designer Genes: A New Era in the Evolution of Man
%I RandomHouse
%P 208
%D 2010
%K book, text, MolBio, c2010, c201x, c20xx, bioinformatics, designer, gene,
   genes, ethics, risks, science, biol, medicine, human health, society
%X 1st ed 2010; hb us$17; uk us isbn:140006905X; uk us isbn13:978-1400069057.
   '... Potter, professor of pediatrics at Children's Hospital Medical Center
   in Cincinnati, ... we are quickly reaching the point where our ability to
   manipulate genes "could well mean the end of the human race as we know it,
   but perhaps the beginning of something better." ... '

%A P. Arensburger
%A et al, ...
%A P. W. Atkinson
%T Sequencing of Culex quinquefasciatus establishes a platform for mosquito
   comparative genomics
%J Science
%V 330
%N 6000
%P 86-88
%M OCT
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, Culex quinquefasciatus, genome, nGenome,
   insect, mosquito, mosquitoes, vector, virus, viral, pathogens,
   West Nile virus, Culex pipiens
%X "C. q. (the southern house mosquito) is an important mosquito vector of
   viruses such as West Nile virus & St. Louis encephalitis virus, as well as of
   nematodes that cause lymphatic filariasis. C.q. is one species within the
   Culex pipiens species complex & can be found throughout tropical & temperate
   climates of the world. The ability of C.q. to take blood meals from birds,
   livestock, & humans contributes to its ability to vector pathogens between
   species. ... describe the genomic seq. of C.q.: Its repertoire of 18,883
   protein-coding genes is 22% larger than that of Aedes aegypti & 52% larger
   than that of Anopheles gambiae with multiple gene-family expansions, inc.
   olfactory & gustatory receptors, salivary gland genes, & genes assoc.with
   xenobiotic detoxification."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1191864">doi:10.1126/science.1191864</A>]['10].
   "The assembled g. [in] GenBank ... accession # AAWU00000000."

%A J. Cohen
%T Painful failure of promising genital herpes vaccine
%J Science
%V 330
%N 6002
%P 304
%M OCT
%D 2010
%K news, c2010, c201x, c20xx, biol, medicine, medical, Herpes simplex virus 2,
   HSV-2, HSV2, vaccine, trial, genital
%X "A vaccine designed to ward off genital herpes has failed in a large clinical
   trial, abruptly ending the product's seemingly promising future. After 8
   years of study in more than 8000 women in the [US] & Canada, there was not
   even a hint of a +ve result against the [STD] caused by herpes simplex
   virus-2 ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.330.6002.304">doi:10.1126/science.330.6002.304</A>]['10].

%A D. E. Shaw
%A et al
%A W. Wriggers
%T Atomic-level characterization of the structural dynamics of proteins
%J Science
%V 330
%N 6002
%P 341-346
%M OCT
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz1010, protein folding, structure,
   prediction, molecular dynamics, BPTI, fold, conformation, simulation
%X "... examined 2 fundamental processes in protein dynamics - p.folding &
   conformational change within the folded state - by means of extremely long
   all-atom MD simulations conducted on a special-purpose m/c. Equilibrium
   simulations of a WW protein domain captured multiple folding & unfolding
   events that consistently follow a well-defined folding pathway; separate
   simulations of the protein's constituent substructures shed light on possible
   determinants of this pathway. A 1-millisec. simulation of the folded p. BPTI
   reveals a small # of structurally distinct conformational states whose
   reversible interconversion is slower than local relax'ns within those
   states by a factor of more than 1000."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1187409">doi:10.1126/science.1187409</A>]['10].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.330.6002.308-a">news</A>],
    and [<A HREF="http://www.allisons.org/ll/Bioinformatics/">bioinformatics</A>].)
   [Also search for: protein folding simulation].

%A K. Daily
%A P. Rigor
%A S. Christley
%A X. Xie
%A P. Baldi
%T Data structures and compression algorithms for high-throughput sequencing
   technologies
%J BMC Bioinformatics
%V 11
%N 1
%P 514
%D 2010
%K MolBio, jrnl, eJrnl, c2010, c201x, c20xx, data compression, compress,
   HTS, NGS
%X "... rapid parallel sequencing of v.large #s of relatively short nucleotide
   sequences, in applications ranging from genome sequencing & resequencing to
   digital microarrays & ChIP-Seq experiments. ..." (online Oct 2010)
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-11-514">doi:10.1186/1471-2105-11-514</A>]['10].
   [Also search for: short read MolBio].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">bioinformatics</A>].)

%A N. Lane
%A W. Martin
%T The energetics of genome complexity
%J Nature
%V 467
%P 929-934
%M OCT
%D 2010
%K MolBio, c2010, c201x, c20xx, cell, cellular, prokaryote, eukaryote,
   mitochondria, evolution, complex, complexity, innovation, life, genetics,
   genome size, genomes, energy
%X "All complex life is composed of eukaryotic (nucleated) cells. The eukaryotic
   cell arose from prokaryotes just once in four billion y., & otherwise
   prokaryotes show no tendency to evolve greater complexity. Why not?
   Prokaryotic genome size is constrained by bioenergetics. The endosymbiosis
   that gave rise to mitochondria restructured the distribution of DNA in
   relation to bioenergetic membranes, permitting a remarkable 200,000-fold
   expansion in the # of genes expressed. This vast leap in genomic capacity was
   strictly dependent on mitochondrial power, & prerequisite to eukaryote
   complexity: the key innovation en route to multicellular life."
   "... The cost of DNA replication itself accounts for just 2% of the energy
   budget of microbial cells during growth ... protein synthesis accounts for
   a remarkable ~75% ..."  [74 refs].
   -- [<A HREF="http://dx.doi.org/10.1038/nature09486">doi:10.1038/nature09486</A>]['10].

%A E. E. Goldberg
%A J. R. Kohn
%A R. Lande
%A K. A. Robertson
%A S. A. Smith
%A B. Igic
%T Species selection maintains self-incompatibility
%J Science
%V 330
%N 6003
%P 493-495
%M OCT
%D 2010
%K jrnl, biol, MolBio, c2010, c201x, c20xx, plant, plants, self fertilization,
   outcrossing, Solanaceae, species diversity
%X "... Self-incompatibility, the ability of hermaphrodites to enforce
   outcrossing, is freq. lost in flowering plants, enabling self-fertilization.
   We show, however, that in the nightshade plant family (Solanaceae), species
   with functional self-incomp. diversify at a sig. higher rate than those
   without it. The apparent short-term advantages of potentially self-
   -fertilizing individuals are therefore offset by strong species selection,
   which favors obligate outcrossing."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1194513">doi:10.1126/science.1194513</A>]['10].

%T A map of human genome variation from population-scale sequencing
%Q The 1000 Genomes Project Consortium
%J Nature
%V 467
%P 1061-11073
%M OCT
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz1110, 1000, thousand, human, genomes,
   project, variation, variability, humans
%X "... undertook 3 projects: low-coverage whole-genome sequencing of
   179 individuals 4 four populations; high-coverage sequencing of
   2 mother-father-child trios; & exon-targeted sequencing of 697 individuals
   from 7 pop'ns. ... On avg., each person is found to carry ~ 250 to 300
   loss-of-fn variants in annotated genes & 50 to 100 variants previously
   implicated in inherited disorders. ... From the 2 trios we directly est. the
   rate of de novo germline base subst. mutns to be ~10**-8/bp/generation. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09534">doi:10.1038/nature09534</A>]['10].

%A P. H. Sudmant
%A et al ...
%A E. E. Eichler
%T Diversity of human copy number variation and multicopy genes
%J Science
%V 330
%N 6004
%P 641-646
%M OCT
%D 2010
%K MolBio, jrnl, c2010, c201x, c20xx, zz1110, copy number variation, CNV,
   copies, multicopy genes, disease association, human
%X "... analyzing short-read mapping depth for 159 human genomes, we demo.
   accurate est. of absolute copy # for duplications as small as 1.9 kbp,
   ranging from 0 to 48 copies. We identified 4.1 million "singly unique
   nucleotide" posns informative in distinguishing specific copies & used them
   to genotype the copy & content of specific paralogs within highly duplicated
   gene families. These data identify human-specific expansions in genes assoc.
   with brain development, reveal extensive population genetic diversity, &
   detect signatures consistent with gene conversion in the human species. Our
   approach makes ~1000 genes accessible to g.studies of disease assoc.."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1197005">doi:10.1126/science.1197005</A>]['10].

%A K. Eitner
%A U. Koch
%A T. Gaweda
%A J. Marciniak
%T Statistical distribution of amino acid sequences: a proof of
   Darwinian evolution
%J J. Bioinformatics
%V 26
%N 23
%P 2933-2935
%M OCT
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, amino acids, frequency, frequencies,
   stats, probability distribution
%X "... the quantity of amino acids, dipeptides & tripeptides for all proteins
   available in the UNIPROT-TREMBL database & the listing for sel. species &
   enzymes. UNIPROT-TREMBL contains p.seqs. assoc. with computationally
   generated annotations & large-scale functional characterization. Due to the
   distinct metabolic pathways of AA & their physicochemical properties, the
   quantities of subpeptides in proteins vary. We have proved that the distn of
   AAs, dip. & trip. is statistical which confirms that the evol.biodiversity
   development model is subject to the theory of indep. events. It seems
   interesting that certain short peptide combinations occur relatively rarely
   or even not at all. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btq571">doi:10.1093/bioinformatics/btq571</A>]['12].
   [Graphs, but no numbers as such.-(]

%A S. A. Hollingsworth
%A P. A. Karplus
%T A fresh look at the Ramachandran plot and the occurrence of standard
   structures in proteins
%J Biomol. Concepts
%V 1
%N 3-4
%P 271-283
%M OCT
%D 2010
%K MolBio, c2010, c201x, c20xx, protein, 3D, tertiary, structure, folds,
   local, Ramachandran plot, phi, psi, linear groups, alpha, 310, pi, Pii,
   helices
%X "The R.plot is among the most central ... . However, with the increasing
   numbers of known protein-structs. & greater accuracy of ultra-high resolution
   protein s., we are still learning more about the basic principles of protein
   s.. Here we use high fidelity conformational information to explore novel
   ways, such a geo-style & wrapped R.plots, to convey some of the basic aspects
   of the R.plot & of protein conformation. We point out the pressing need for a
   standard nomenclature for peptide conformation & propose [one]. Finally, we
   summarize some recent conceptual advances related to the building blocks of
   protein structure. The results for linear groups imply the need for
   substantive revisions in how the basics of protein structure are handled."
   -- [<A HREF="http://dx.doi.org/10.1515/BMC.2010.022">doi:10.1515/BMC.2010.022</A>]['12],
    & [<A HREF="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061398/">nc'i</A>]['12].
   [Also search for: Hollingsworth MolBio].

%A M. Yarus
%T Life from an RNA World: The Ancestor Within
%I HarvardUP
%P 208
%D 2010
%K MolBio, book, text, c2010, c201x, c20xx, zz1110, Biol, RNA, evolution,
   origin, origins, life, ribonucleic acid
%X 1st ed 2010; hb us$23, stg19;
   us isbn:0674050754; uk us isbn13:978-0674050754.
   "A majority of evolutionary biologists believe that we now can envision our
   biological predecessors - not the first, but nearly the first, living beings
   on Earth. Life from an RNA World is about these vanished forebears, sketching
   them in the distant past just as their workings first began to resemble our
   own. ..."

%A Q. M. Mitrovich
%A et al ...
%A A. D. Johnson
%T Evolution of yeast noncoding RNAs reveals an alternative mechanism for
   widespread intron loss
%J Science
%V 330
%N 6005
%P 838-841
%M NOV
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, intron, loss, snoRNA, small nucleolar RNA,
   RNA seq, RNAseq
%X "The evolutionary forces responsible for intron loss are unresolved. Whereas
   res. has focused on protein-coding genes, here we analyze noncoding small
   nucleolar RNA (snoRNA) genes in which introns, rather than exons, are
   typically the functional elts. Within the yeast lineage exemplified by the
   human pathogen Candida albicans, we find - through deep RNA sequencing &
   genome-wide annotation of splice junctions - extreme compaction & loss of
   assoc. exons, but retention of snoRNAs within introns. In the S.yeast lineage
   however, we find it is the introns that have been lost through widespread
   degeneration of splicing signals. This intron loss, perhaps facilitated by
   innovations in snoRNA processing, is distinct from that observed in
   protein-coding genes wrt both mechanism & evolutionary timing."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1194554">doi:10.1126/science.1194554</A>]['10].

%T Beyond Cladistics: The Branching of a Paradigm
%E D. M. Williams
%E S. Knapp
%I U. California Press
%D 2010
%K book, text, MolBio, Biol, c2010, c201x, c20xx, zz1210, evolution, inference,
   phylogeny, phylogenetic, systematics, sepcies, methods, clades, cladistic
%X "Cladistics, or phylogenetic systematics - an approach to discovering,
   unraveling, & testing hypotheses of evolutionary history - took hold during
   a turbulent & acrimonious time in the history of systematics. During this
   period - the 1960s & 1970s - much of the foundation of modern systematic
   methodology was established as cladistic approaches became widely accepted.
   Virtually complete by the end of the 1980s, the wide perception has been that
   little has changed. This vol. vividly illustrates that cladistic
   methodologies have continued to be developed, improved upon, & effectively
   used in ever widening analytically imaginative ways.  ..."
   2010; hb us$65; uk us isbn:0520267729; uk us isbn13:978-0520267725.
   [Also search for: phylogentic book MolBio].

%A M. P. Muehlenbein
%T Human Evolutionary Biology
%I CUP
%P 634
%D 2010
%K book, text, MolBio, CUP, c2010, c201x, c20xx, zz1210, human evolution,
   anthropology, phenotype, genetic, variation
%X "... topics in human evolution, variation and adaptability for professionals
   and students in biological anthropology, evolutionary biology, medical
   sciences and psychology. The chapters are organized around four broad themes,
   with sections devoted to phenotypic and genetic variation within and between
   human populations, reproductive physiology and behavior, growth & development
   & human health from evolutionary and ecological perspectives. ..."
   1st ed 2010; pb us$65; uk us isbn:052170510X; uk us isbn13:978-0521705103.

%A S. Haddock
%A C. Dunn
%T Practical Computing for Biologists
%I SinauerAssocs.
%P 538
%K book, text, MolBio, c2010, c201x, c20xx, zz0111, bioinformatics, computing,
   computer programming, biol, biology, analysis
%X "To help with the increasingly large data sets that many scientists deal with
   ... illustrates how to use many freely available computing tools to work
   more powerfully and effectively. The book was born out of the authors'
   experiences developing tools for their research and to fix other biologist's
   computational problems."
   1st ed 2010; pb us$60; uk us isbn:0878933913; uk us isbn13:978-0878933914.
   [Also search for: MolBio book programming].

%A H. Ledford
%T Drug giants turn their backs on RNA interference.  A once much-touted
   technique faces a difficult transition to the clinic
%J Nature
%V 468
%P 487
%M NOV
%D 2010
%K news, views, MolBio, c2010, c201x, c20xx, zz1210, RNA, interference, RNAi,
   drug, drugs, Roche
%X "Not long ago ... RNA interference (RNAi) seemed to be on the fast track to
   commercial success. Its discovery in 1998 revealed a new way to halt the
   production of specific proteins ... Yet all that seemed like ancient history
   last week when drugs and diagnostics corporation Roche in Basel .. - a major
   investor in RNAi-based drug research - announced it was killing its
   programme after spending 3 years & > $500 million on the technique. ...
   companies confront the challenge of delivering RNA molecules, which are
   notoriously fragile, to target cells in the human body, and then coaxing
   those cells to take up the RNA. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/468487a">doi:10.1038/468487a</A>]['10].

%A A. Ben-Shem
%A L. Jenner
%A G. Yusupova
%A M. Yusupov
%T Crystal structure of the eukaryotic ribosome
%J Science
%V 330
%N 6008
%P 1203-1209
%M NOV
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz1210, biol, ribosome, structure, 80S,
   subunit, cell, protein synthesis, eukaryote, mRNA, tRNA, ratcheted, crystal
%X "... The crystal structure of the yeast 80S ribosome determined at 4.15A
   resolution reveals the higher complexity of eukaryotic r., which are 40%
   larger than their bacterial counterparts. Our model shows how eukaryote-
   -specific elts considerably expand the n/w of interactions within the r. &
   provides insights into eukaryote-specific features of protein synthesis. Our
   crystals capture the r. in the ratcheted state, which is essential for
   translocation of mRNA & transfer RNA (tRNA), & in which the small r.subunit
   has rotated wrt the large subunit. We describe the conformational changes in
   both r.subunits that are involved in ratcheting & their implications in
   coordination b/ween the 2 assoc. subunits & in mRNA & tRNA translocation."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1194294">doi:10.1126/science.1194294</A>]['10].

%A G. Nyamundanda
%A L. Brennan
%A I. C. Gormley
%T Probabilistic principal component analysis for metabolomic data
%J BMC Bioinformatics
%V 11
%P 571
%M NOV
%D 2010
%K jrnl, eJrnl, MolBio, c2010, c201x, c20xx, zz1210, components, stats,
   probabilistic principal component analysis, PPCA, PPCCA, MetabolAnalyze
%X "... probabilistic principal component analysis (PPCA) which addresses some
   of the limitations of PCA, is reviewed & extended [to] probabilistic
   principal component & covariates analysis (PPCCA) ... provides a flexible
   approach to jointly model metabolomic data & additional covariate info.. The
   use of a mixture of PPCA models for discovering the # of inherent groups in
   metabolomic data is demonstrated. The jackknife technique is employed to
   construct confidence intervals for estimated model params. throughout. The
   optimal # of principal components is det. through the use of the [BIC]
   model selection tool ... modified to address the high-dim. of the data. ...
   A software package called MetabolAnalyze, freely available ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-11-571">doi:10.1186/1471-2105-11-571</A>]['10].
   [Also search for: principal components stats],  and
   [also search for: factor analysis stats].

%T Bioinformatics for Comparative Proteomics
%S Methods in Molecular Biology
%E C. H. Wu
%E C. Chen
%I HumanaPress
%P 387
%M NOV
%D 2010
%K book, text, MolBio, c2010, c201x, c20xx, zz0211, proteomics
%X 1st ed 2010; hb us$110; uk us isbn:1607619768; uk us isbn13:978-1607619765.
   "... Structured in three major sections, this detailed volume covers basic
   bioinformatics frameworks relating to comparative proteomics, bioinformatics
   databases and tools for proteomics data analysis, and integrated
   bioinformatics systems and approaches for studying comparative proteomics
   in the systems biology context. ..."

%A R. B. Cooley
%A D. J. Arp
%A P. A. Karplus
%T Evolutionary origin of a secondary structure: pi-helices as cryptic but
   widespread insertional variations of alpha-helices that enhance protein
   functionality
%J J. Mol. Biol.
%V 404
%N 2
%P 232-246
%M NOV
%D 2010
%K jrnl, JMB, MolBio, c2010, c201x, c20xx, protein structures, 3D, alpha, pi,
   Pii, helix, helices, bulge, bulges, looping out
%X "... pi-helices are rare in protein structures but have been correlated with
   functional sites. ... show that pi-helices are the same as structures known
   as alpha-bulges, alpha-aneurisms, pi-bulges, & looping outs, & are evol.
   derived by the insertion of a single residue into an alpha-helix. ...
   explains both why pi-helices are cryptic, being rarely annotated despite
   occurring in 15% of known ps., & why they tend to be assoc. with fn.
   An analysis of pi-helices in the diverse ferritin-like superfamily
   illustrates their tendency to be conserved in protein families & identifies
   a putative pi-helix-containing primordial precursor, a 'missing link'
   intermediary form of the ribonucleotide reductase family, vestigial
   pi-helices, & a novel function for pi-helices that we term a 'peristaltic-
   -like shift.' This new understanding of pi-helices paves the way for this
   generally overlooked motif to become a noteworthy feature that will aid in
   tracing the evolution of many protein families, guide investigations of
   protein & pi-helix functionality ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jmb.2010.09.034">doi:10.1016/j.jmb.2010.09.034</A>]['12],
    & [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/20888342">nc'i</A>]['12].

%A M. Jaskelioff
%A et al ...
%A R. A. DePinho
%T Telomerase reactivation reverses tissue degeneration in aged
   telomerase-deficient mice
%J Nature
%V ?
%P ?-?
%M DEC ?
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz1210, mice, mouse, age, ageing, DNA,
   telomere, telomeres, telomerase, knockout, TERT, 4OHT, reversal, reverse,
   effects, lifespan
%X "... engineered a knock-in allele encoding a 4-hydroxytamoxifen (4-OHT)-
   -inducible telomerase reverse transcriptase-oestrogen receptor (TERT-ER)
   under transcriptional control of the endogenous TERT promoter. Homozygous
   TERT-ER mice have short dysfunctional telomeres & sustain increased DNA
   damage signalling and classical degenerative phenotypes upon successive
   generational matings and advancing age. Telomerase reactivation in such late
   generation TERT-ER mice extends telomeres, reduces DNA damage signalling and
   associated cellular checkpoint responses, allows resumption of proliferation
   in quiescent cultures, and eliminates degenerative phenotypes across
   multiple organs including testes, spleens and intestines. Notably, somatic
   telomerase reactivation reversed neurodegeneration ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09603">doi:10.1038/nature09603</A>]['10].

%A F. Wolfe-Simon
%A et al ...
%A R. S. Oremland
%T A bacterium that can grow by using arsenic instead of phosphorus
%J Science
%V ?
%N ?
%P ?-?
%M DEC
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz1210, biol, biology, life, evolution,
   Arsenic, Phosphorus, bacteria, GFAJ-1, GFAJ1, Halomonadaceae, Mono Lake,
   DNA, protein
%X "Life is mostly composed of the elts carbon, hydrogen, nitrogen, oxygen,
   sulfur, & phosphorus. Although these 6 elts make up nucleic acids, proteins
   & lipids & thus the bulk of living matter, it is theor. possible that some
   other elts in the periodic table could serve the same fns. Here, we describe
   a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake,
   California, which substitutes arsenic for phosphorus to sustain its growth.
   Our data show evidence for arsenate in macromolecules that normally contain
   phosphate, most notably nucleic acids & proteins. Exchange of one of the
   major bioelts may have profound evolutionary & geochemical significance."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1197258">doi:10.1126/science.1197258</A>]['10] online Dec 2010.

%T Genetic Variation: Methods and Protocols
%E M. R. Barnes
%E G. Breen
%I HumanaPress
%S Methods in Molecular Biology
%P 388
%D 2010
%K book, text, manual, MolBio, c2010, c201x, c20xx, zz0111, variations,
   SNPs, CNV, VNTRs
%X 1st ed 2010; hb us$139; uk us isbn:1603273662; uk us isbn13:978-1603273664.
   "... address the rising importance of genome variation, both at the level of
   the individual and in population-based studies of disease, with a collection
   of detailed protocols reflecting the nature and impact of genetic variation
   on human phenotypes. The contributions cover a majority of the most
   important forms of genetic variation studied today, including single
   nucleotide polymorphisms (SNPs), insertions/deletion (indels), copy number
   variation (CNVs), variable number tandem repeats (VNTRs), mitochondrial
   variation, mobile elements, and epigenetic variation. ..."
   [Also search for: manual MolBio],  or [also search for: book MolBio].

%A Z. A. Shah
%A R. C. Li
%A A. S. Ahmad
%A T. W. Kensler
%A M. Yamamoto
%A S. Biswal
%A S. Dore
%T The flavanol (-)-epicatechin prevents stroke damage through the Nrf2/HO1
   pathway
%J J. Cereb. Blood Flow Metab.
%V 30
%N 12
%P 1951-1961
%M DEC
%D 2010
%K jrnl, c2010, c201x, c20xx, medicine, health, chocolate, stroke, good news,
   flavanols, epicatechin
%X "Epidemiologic studies have shown that foods rich in polyphenols, such as
   flavanols, can lower the risk of ischemic heart disease; however, the
   mechanism of protection has not been clearly established. ... investigated
   whether epicatechin (EC), a flavanol in cocoa and tea, is protective against
   brain ischemic damage in mice. ...  Cell viability assays with neuronal
   cultures further confirmed that EC could protect neurons against oxidative
   insults. ..."
   -- @[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/20442725">nlm</A>]['11].
   [Also search for: epicatechin].

%A C. de Duve
%A N. Patterson
%T Genetics of Original Sin: The Impact of Natural Selection on the Future of
   Humanity
%I YaleUP
%P 256
%M DEC
%D 2010
%K book, text, c2010, c201x, c20xx, deDuve, human behaviour, biology, society,
   tribal, tribe, group, rivalry, competition, cooperation
%X 1st ed 2010, hb us$23; us isbn:0300165072; us isbn13:978-0300165074.
   "... explores the inordinate and now dangerous rise of humankind.  His
   explanation for this self-defeating success lies in the process of natural
   selection, which favors traits that are immediately useful, regardless of
   later consequences. Thus, the human genome determines such properties as
   tribal and group cohesion and collaboration and often fierce and irrational
   competition with and hostility toward other groups' attributes that were
   once useful but now often ruinously dysfunctional."

%A C. Frydman
%A C. Camerer
%A P. Bossaerts
%A A. Rangel
%T MAOA-L carriers are better at making optimal financial decisions under risk
%J Proc. R. Soc. B
%V ?
%P ?-?
%D 2010 (online)
%K jrnl, c2010, c201x, c20xx, MolBio, warrior gene, Monoamine oxidase A,
   MAO-A, MAOA L, MAOAL, gene, risk, 5-HTT, 5HTT, DRD4, polymorphisms
%X "... Consistent with previous literature, we found that carriers of the
   MAOA-L polymorphism were more likely to take financial risks. Our
   computational choice model, rooted in established decision theory, showed
   that MAOA-L carriers exhibited such behaviour because they are able to make
   better financial decisions under risk, and not because they are more
   impulsive. In contrast, we found no behavioural or computational differences
   among the 5-HTT and DRD4 polymorphisms."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2010.2304">doi:10.1098/rspb.2010.2304</A>]['10].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Monoamine_oxidase_A">wikip</A>]['10],
     "... A version of the primate monoamine oxidase-A g. has been ref. to as
     the warrior g.. Several different versions of the g. are found in different
     individuals, although a functional gene is present in most h. ...)
   [Also search for: MAOA gene].

%T CurlySMILES: a chemical language to customize and annotate encodings of
   molecular and nanodevice structures
%J J. Cheminform.
%V 3
%N 1
%M JAN
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0720, CurlySMILES, SMILES, chemical compound
%X "CurlySMILES is a chemical line notation which extends SMILES with
   annotations for storage, retrieval & modeling of interlinked, coordinated,
   assembled & adsorbed molecules in supramolecular structures & nanodevices.
   Annotations are enclosed in curly braces & anchored to an atomic node or at
   the end of the molecular graph depending on the annotation type. ..."
   -- [<A HREF="https://doi.org/10.1186/1758-2946-3-1">doi:10.1186/1758-2946-3-1</A>]['20].
   [Also search for: SMILES chemical].

%A D. H. Huson
%A R. Rupp
%A C. Scornavacca
%T Phylogenetic Networks: Concepts, Algorithms and Applications
%I CUP
%P 374
%M JAN
%D 2011
%K book, text, MolBio, c2011, c201x, c20xx, CUP, phylogenetic, network,
   phylogeny, evolution
%X 1st ed 2011; hb us$52; uk us isbn:0521755964; uk us isbn13:978-0521755962.
   "... when reticulate events such as hybridization, horizontal gene transfer
   or recombination are believed to be involved, phylogenetic n/ws that can
   accommodate non-treelike evolution have an important role to play. ...
   provides the 1st interdisciplinary overview of phylo. n/ws. Beginning
   with a concise intro. to both phylo. trees and phylog. n/ws, the fundamental
   concepts and results are then presented for both rooted and unrooted phylo.
   n/ws. Current approaches and algorithms available for computing phylo. n/ws
   from different types of datasets are then discussed [with] examples of their
   application to real biological datasets. ..."
   [Also search for: MolBio phylogenetic].

%A N. J. Croucher
%A et al...
%A S. D. Bentley
%T Rapid Pneumococcal evolution in response to clinical interventions
%J Science
%V 331
%N 6016
%P 430-434
%M JAN
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0211, Pneumococcal, mulitdrug,
   drug resistance, drugs, Streptococcus pneumoniae, bacterium, bacterial,
   recombination, resistant, antigens, PMEN1, Spain23F, 19A
%X "Epidemiological studies of the naturally transformable bacterial pathogen
   Streptococcus pneumoniae have previously been confounded by high rates of
   recombination. Sequencing 240 isolates of the PMEN1 (Spain23F-1)
   multidrug-resistant lineage enabled base substitutions to be distinguished
   from polymorphisms arising through horizontal sequence transfer. More than
   700 recombinations were detected, with genes encoding major antigens
   frequently affected. Among these were 10 capsule-switching events, one of
   which accompanied a population shift as vaccine-escape serotype 19A isolates
   emerged in the USA after the introduction of the conjugate polysaccharide
   vaccine. The evolution of resistance to fluoroquinolones, rifampicin, and
   macrolides was observed to occur on multiple occasions. This study details
   how genomic plasticity within lineages of recombinogenic bacteria can permit
   adaptation to clinical interventions over remarkably short time scales."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1198545">doi:10.1126/science.1198545</A>]['11].

%A R. Lister
%A et al ...
%A J. R. Ecker
%T Hotspots of aberrant epigenomic reprogramming in human induced pluripotent
   stem cells
%J Nature
%V 471
%P 68-73
%M FEB
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0720, cell, cellular differentiation,
   cells, tissue types, kinds, epigenetic, induced pluripotent stem cells,
   iPSCs, histone, regulation
%X "... Somatic cell reprogramming involves epigenomic reconfig., conferring
   iPSCs with characteristics similar to embryonic stem (ES) cells. However, it
   remains unknown how complete the reestablishment of ES-cell-like DNA
   methylation patterns is throughout the genome. Here we report the first
   whole-genome profiles of DNA methylation at single-base resolution in five
   human iPSC lines, along with methylomes of ES cells, SCs, & differentiated
   iPSCs & ES cells. iPSCs show sig. reprogramming variability ... iPSCs share
   megabase-scale differentially methylated regions proximal to centromeres &
   telomeres that display incomplete reprogramming of non-CG m., & differences
   in CG m. & histone modifications. Lastly, differentiation of iPSCs into
   trophoblast cells revealed that errors in reprogramming CG m. are transmitted
   at a high freq., providing an iPSC reprogramming signature that is maintained
   after differentiation."
   -- [<A HREF="https://doi.org/10.1038/nature09798">doi:10.1038/nature09798</A>]['20].
   (Also see cellDiff@[<A HREF="https://en.wikipedia.org/wiki/Cellular_differentiation">wikip</A>]['20].)

%A R. E. Mills
%A et al
%T Mapping copy number variation by population-scale genome sequencing
%J Nature
%V 470
%P 59-65
%M FEB
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0211, copy number variation, CNV, CNVs,
   SV, SVs, structural variants, variation, human, humans, 1000 genomes project
%X "... constructed a map of unbalanced SVs (that is, copy # variants) based on
   whole genome DNA sequencing data from 185 human genomes, integrating evidence
   from complementary SV discovery approaches with extensive experimental
   validations. Our map encompassed 22,025 deletions & 6,000 additional SVs,
   including insertions & tandem duplications. Most SVs (53%) were mapped to
   nucleotide resolution, which facilitated analysing their origin & functional
   impact. We examined numerous whole & partial gene deletions with a genotyping
   approach & observed a depletion of gene disruptions amongst high frequency
   deletions. Furthermore, we observed differences in the size spectra of SVs
   originating from distinct formation mechanisms, & constructed a map of SV
   hotspots formed by common mechanisms. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09708">doi:10.1038/nature09708</A>]['11].

%A H. Ledford
%T Gene reading steps up a gear
%J Nature
%V 470
%P 155
%M FEB
%D 2011
%K news, views, MolBio, c2011, c201x, c20xx, zz0211, gene, sequencing,
   third generation, single molecule, Turner, Pacific Biosciences
%X "... Pacific Biosciences set a high bar for its own success in 2008, when
   chief technology officer Stephen Turner boasted that the instruments would
   be able to sequence a human genome in just 15 minutes by 2013, ... After
   several delays, customers have now been told to expect their machines in the
   second quarter of this year. ... cost of its machines (US$700,000 ...
   Turner did not reiterate his pledge for a 15-minute human genome. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/470155a">doi:10.1038/470155a</A>].
   (Also see [<A HREF="http://dx.doi.org/10.1056/NEJMoa1012928">doi:10.1056/NEJMoa1012928</A>].)
   [Also search for: MolBio single molecule sequencing].

%A M. Baker
%T Genomics: Genomes in three dimensions
%J Nature
%V 470
%P 289-294
%M FEB
%D 2011
%K views, MolBio, c2011, c201x, c20xx, genome, 3D, structure, genomic, nucleus,
   pack, packed, gene expression, genes, regulation, histones
%X "... the three-dimensional structures of chromosomes coiled in the nucleus.
   Far from being the random result of packing 2 metres of DNA into a sphere
   perhaps 10 micrometres across, the structures vary across cell types and
   exert an as-yet-mysterious influence on gene expression. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/470289a">doi:10.1038/470289a</A>]['11].

%A K. S. Drlica
%A D. S. Perlin
%T Antibiotic Resistance: Understanding and Responding to an Emerging Crisis
%I FTpress
%P 288
%M FEB
%D 2011
%K book, text, MolBio, c2011, c201x, c20xx, zz0311, medical, drug resistance,
   human health, risks, infectious disease, bacteria, infection, drugs,
   antibiotics
%X 1st ed 2011; hb us$35; uk us isbn:0131387731; uk us isbn13:978-0131387737.

%A R. Cook-Deegan
%T Gene Patents: The Shadow of Uncertainty
%J Science
%V 331
%N 6019
%P 873-874
%M FEB
%D 2011
%K views, c2001, c201x, c20xx, MolBio, gene, genes, patent, patents, law,
   law, business, risks, human
%X "... The year 2010 was tumultuous in the world of gene patents. In February,
   the Secretary's Advisory Committee on Genetics, Health, and Society approved
   a report that recommended exemptions from patent infringement liability for
   research and for diagnostic use. On 29 March, Judge Robert Sweet of the
   federal district court for southern New York turned gene patents on their
   heads by ruling that contested claims over BRCA1 and BRCA2 genes were
   invalid. Most of the ruling argued that DNA molecules cannot be patented
   because they are embodiments of information and products of nature, and
   another section argued that the methods claims did not pass muster. That
   ruling is being appealed, and the final resolution may not be for several
   more years. In December, the Court of Appeals for the Federal Circuit
   reaffirmed the patentability of a diagnostic method.  ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1203458">doi:10.1126/science.1203458</A>]['10].

%A R. D. Hernandez
%A et al ...
%A M. Przeworski
%T Classic Selective Sweeps Were Rare in Recent Human Evolution
%J Science
%V 331
%N 6019
%P 920-924
%M FEB
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, human, evolution, selection, mutations,
   variation, diversity, genomes, natural selection
%X "Efforts to identify the genetic basis of human adaptations from polymorphism
   data have sought footprints of 'classic selective sweeps' (in which a
   beneficial mutation arises & rapidly fixes in the population).Yet it
   remains unknown whether this form of natural seln was common in our
   evolution. We examined the evidence for classic sweeps in resequencing data
   from 179 human genomes. As expected under a recurrent-sweep model, we found
   that diversity levels decrease near exons & conserved noncoding regions. In
   contrast to expectation, however, the trough in diversity around human-
   -specific amino acid substitutions is no more pronounced than around
   synonymous substitutions. Moreover, relative to the genome background, amino
   acid & putative regulatory sites are not sig. enriched in alleles that are
   highly differentiated between populations. These findings indicate that
   classic sweeps were not a dominant mode of human adaptation over the
   past ~250,000 years. "
   -- [<A HREF="http://dx.doi.org/10.1126/science.1198878 ">doi:10.1126/science.1198878 </A>]['11].

%A A. E. Cust
%A M. Harland
%A E. Makalic
%A D. Schmidt
%A et al ...
%A M. A. Jenkins
%T Melanoma risk for CDKN2A mutation carriers who are relatives of
   population-based case carriers in Australia and the UK
%J J. Med. Genet.
%V ?
%N ?
%P ?-?
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, enesm, melanoma, skin cancer, CDKN2A,
   risk, risks, human health
%X "Background CDKN2A mutations confer a substantial risk of cutaneous melanoma;
   however, the magnitude of risk is uncertain. Methods The study estimated the
   hazard ratio (HR) & the average age specific cumulative risk (ie, penetrance)
   of reported melanoma for CDKN2A mutation carriers in case families using a
   modified segregation analysis of the first & higher degree relatives of
   35 population-based cases.  ...  It is est. that 16% (95% CI 10% to 27%) of
   UK & 20% (95% CI 13% to 30%) of Australian CDKN2A mutation carriers would be
   diagnosed with melanoma by age 50 years, & 45% (95% CI 29% to 65%) &
   52% (95% CI 37% to 69%), resp., by age 80 y.. Conclusions Contrary to
   the strong assoc. between UV radiation exposure & melanoma risk for the
   general popn, CDKN2A mutation carriers appear to have the same cumulative
   risk of melanoma irrespective of the ambient UV irradiance of the region in
   which they live."  (online Feb 2011.)
   -- abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/21325014">pubmed</A>]['11].

%A K. Shimizu
%A K. Tsuda
%T SlideSort: All pairs similarity search for short reads
%J J. Bioinformatics
%V 27
%N 4
%P 464-470
%M FEB
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0511, slidesort, sort, short read,
   reads
%X "... an exact alg. SlideSort that finds all similar pairs from a string pool
   in terms of edit distance. Using an efficient pattern growth alg., SlideSort
   discovers chains of common k-mers to narrow down the search. Compared to
   existing methods based on single k-mers, our method is more effective in
   reducing the number of [ED] calculations. In comparison to backtracking
   methods such as BWA, our method is much faster in finding remote matches,
   scaling easily to tens of millions of seqs.. Our s/w has an additional fn of
   single link [linkage] clustering, which is useful in summarizing short reads
   for further processing. ...
   s/w@[<A HREF="http://www.cbrc.jp/~shimizu/slidesort/">www</A>]['11]."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btq677">doi:10.1093/bioinformatics/btq677</A>]['11].
   [Also search for: short read MolBio].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/BWT/">BWT</A>].)

%A T. Conway
%A A. J. Bromage
%T Succinct data structures for assembling large genomes
%J J. Bioinformatics
%V 27
%N 4
%P 479-486
%M FEB
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0511, nicta, compact, sequence assembly,
   succinct data structure, de Bruijn, deBruijn, aBruijn, graph
%X "... use entropy compressed or succinct data structures to create a practical
   rep'n of the de Bruijn assembly graph, which requires at least a factor of
   10 less storage than the kinds of structures used by deployed methods.
   Moreover, because our representation is entropy compressed, in the presence
   of sequencing errors it has better scaling behaviour asymptotically than
   conventional approaches. We present results of a proof-of-concept assembly
   of a human genome performed on a modest commodity server."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btq697">doi:10.1093/bioinformatics/btq697</A>]['11].
   [Also search for: Conway MolBio nicta].

%A D. B. Wake
%A M. H. Wake
%A C. D. Specht
%T Homoplasy: From detecting pattern to determining process and mechanism of
   evolution
%J Science
%V 331
%N 6020
%P 1032-1035
%M FEB
%D 2011
%K review, MolBio, c2011, c201x, c20xx, zz0311, homoplasy, evolution, DNA,
   convergence, phylogenetic
%X 'Understanding the diversification of phenotypes through time -  "descent
   with modificationâ - has been the focus of evol. biol. for 150 y.. If,
   contrary to expectations, similarity evolves in unrelated taxa, researchers
   are guided to uncover the genetic & developmental mechanisms responsible.
   Similar phenotypes may be retained from common ancestry (homology), but a
   phylogenetic context may instead reveal that they are indep.derived, due to
   convergence or parallel evolution, or less likely, that they experienced
   reversal. Such examples of homoplasy present opportunities to discover the
   foundations of morphological traits. A common underlying mechanism may exist,
   & components may have been redeployed in a way that produces the "same"
   phenotype. New, robust phylogenetic hypotheses & molec., genomic, &
   developmental techniques enable integrated exploration of the mechanisms by
   which similarity arises.'  [53 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1188545">doi:10.1126/science.1188545</A>]['11].

%A X. Gao
%A H. Chen
%A M. A. Schwarzschild
%A A. Ascherio
%T Use of ibuprofen and risk of Parkinson's disease
%J Neurology
%V ?
%N ?
%P ?-?
%M MAR
%D 2011
%K jrnl, c2001, c201x, c20xx, Parkinson's, Parkinsons, disease, risk, risks,
   reduced, medical, ibuprofen,  drug, drugs, NSAID, NSAIDs, pain killers,
   protect, protection, aspirin, asprin, human health
%X "... We identified 291 incident PD cases during 6 years of follow-up. Users
   of ibuprofen had a significantly lower PD risk than nonusers (relative risk
   [RR], adjusted for age, smoking, caffeine, & other covariates =0.62; 95%
   confidence interval [CI] 0.42-0.93; p=0.02). There was a dose-response
   relationship between tablets of ibuprofen taken per week & PD risk (p trend
   =0.01). In contrast, PD risk was not sig. related to use of aspirin (RR=0.99;
   95% CI 0.78-1.26), other NSAIDs (RR=1.26; 95% CI 0.86-1.84), or acetaminophen
   (RR=0.86; 95% CI 0.62-1.18). Similar results were obtained in the
   meta-analyses: the pooled RR was 0.73 (95% CI 0.63-0.85; p< 0.0001) for
   ibuprofen use, whereas use of other types of analgesics was not assoc. with
   lower PD risk.  ..." online March 2, 2011.
   -- [<A HREF="http://dx.doi.org/10.1212/WNL.0b013e31820f2d79">doi:10.1212/WNL.0b013e31820f2d79</A>]['11].
   (men and women who used ibuprofen two+ times per week were about 38%
   less likely to develop P.'s disease than those who regularly used aspirin,
   acetaminophen, or other NSAIDs (non-steroidal anti-inflammatory drug).
   auths@Harvard School of Public Health (HSPH).. NB. Ibu. has side effects.)

%A A. Fornito
%A et al ...
%A E. T. Bullmore
%T Genetic influences on cost-efficient organization of human cortical
   functional networks
%J J. of Neuroscience
%V 31
%N 9
%P 3261-3270
%M MAR
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0311, biol, biology, genetics, human, inherited,
   brain, cortical network, parents, organization
%X "... report evidence that one such principle for functional cortical networks
   involves finding a balance between maximizing communication efficiency and
   minimizing connection cost, referred to as optimization of network cost-
   -efficiency. We measured spontaneous fluctuations of the blood oxygenation
   level-dependent signal using functional magnetic resonance imaging in healthy
   monozygotic (16 pairs) & dizygotic (13 pairs) twins & characterized cost-
   -efficient properties of brain network functional connectivity between 1041
   distinct cortical regions. At the global network level, 60% of the
   interindividual variance in cost-efficiency of cortical functional networks
   was attributable to additive genetic effects. ..."
   -- [<A HREF="http://dx.doi.org/10.1523/JNEUROSCI.4858-10.2011">doi:10.1523/JNEUROSCI.4858-10.2011 </A>]['11].
      (Some of the strongest [genetic] effects we found were in the prefrontal
      cortex.  This part of the brain plays an important role in things like
      thinking, planning, and memory.)

%A H. Nowotny
%A G. Testa
%T Naked Genes: Reinventing the Human in the Molecular Age
%I MITpress
%P 192
%M MAR
%D 2011
%K book, text, MolBio, c2011, c201x, c20xx, zz0411, science, genetics,
   human, society, law, politics, personalized medicine, sport
%X 1st ed 2011; hb us$25; uk us isbn:0262014939; uk us isbn13:978-0262014939.
   "... examine the interaction between these dramatic advances in the life
   sciences & equally dramatic political reconfigurations of our societies. They
   bring wit & freshness of perspective to ongoing debates over topics ranging
   from assisted reproduction & personalized medicine to genetic sports doping,
   revealing both surprising continuities & radical discontinuities between the
   latest advances in the life sciences & long-standing human traditions. The
   task of institutions in the molecular age, they argue, is to make a
   pluralistic society possible by carving a legitimate free space that allows
   experimentation with new forms of biological life as well as with new forms
   of social life."

%T Bioinformatics for Omics Data: Methods and Protocols
%E B. Mayer
%I Humana
%S Methods in Molecular Biology
%P 596
%M MAR
%D 2011
%K book, text, MolBio, c2011, c201x, c20xx, bioinformatics, systems biology
%X hb us$126; 1st ed 2011; uk us isbn:1617790265; uk us isbn13:978-1617790263.

%T High-Throughput Next Generation Sequencing
%E Y. M. Kwon
%E S. R. Ricke
%I SpringerVerlag
%S Methods in Molecular Biology
%V 733
%P 319
%M MAR
%D 2011
%K book, text, MolBio, c2011, c201x, c20xx, zz0511, DNA, sequencing
%X 1st ed 2011; hb us$94; uk us isbn:1617790885; uk us isbn13:978-1617790881.
   "... the next generation sequencing methods allow scientists to grasp
   system-wide landscapes of the complex molecular events taking place in
   various biological systems, including microorganisms and microbial
   communities. ..."

%A J. Qian
%A A. Hintze
%A C. Adami
%T Colored motifs reveal computational building blocks in the C. elegans brain
%J PLoS ONE
%V 6
%N 3
%P e17013
%M MAR
%D 2011
%K jrnl, c2011, c201x, c20xx, biology, biol, C.elegans, brain, network, graph,
   cells,  vertex labelled, patterns, subnetwork, motif, motifs, feed forward,
   bi fan, bifan, Celegans
%X "Complex n/works can often be decomposed into less complex sub-n/works ...
   In real n/works, 2 motifs that are topol.identical but whose nodes perform
   very different fns will play very diff. roles in the n/work. ... [combining]
   info. about the biol.fn of these nodes, thus coloring nodes by fn. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0017013">doi:10.1371/journal.pone.0017013</A>]['12].
   [Also search for: network motif].

%A G. T. Johnson
%A L. Autin
%A D. S. Goodsell
%A M. F. Sanner
%A A. J. Olson
%T ePMV embeds molecular modeling into professional animation software
   environments
%J Structure
%V 19
%N 3
%P 293-303
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0512, ePMV, protein, structure, 3D,
   interactive, merchandise, proteins, modelling, models
%X "... developed an open-source plug-in, embedded Python Molecular Viewer
   (ePMV), that runs molecular modeling s/w directly inside of professional 3D
   animation applications (hosts) to provide simultaneous access to the
   capabilities of these newly connected systems. Uniting host & scientific
   algs. into a single interface allows users from varied b/g to assemble
   professional quality visuals & to perform comp. experiments with relative
   ease. By enabling easy exchange of algs., ePMV can facilitate
   interdisciplinary research, smooth commn between broadly diverse specialties,
   & provide a common platform to frame & visualize the increasingly detailed
   intersection(s) of cellular & molecular biology."
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/21397181">nih</A>]['13],
   Olsen@[<A HREF="http://mgl.scripps.edu/projects/tangible_models/">scr'pps</A>]['13].
   [Also search for: MolBio Olson protein].

%A M. Wolhsen
%T Biopunk: DIY Scientists Hack the Software of Life
%I ???
%M APR
%D 2011
%K book, text, MolBio, c2011, c201x, c20xx, zz0411, bioinformatics, biopunk,
   DIY, home, science, DNA, computing, IP, open source, creative commons
%X hb us$16; 1st ed 2011; uk us isbn:1617230022; uk us isbn13:978-1617230028.

%A A. Wochner
%A J. Attwater
%A A. Coulson
%A P. Holliger
%T Ribozyme-catalyzed transcription of an active ribozyme
%J Science
%V 332
%N 6026
%P 209-212
%M APR
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0411, origin, origins, life, evolution,
   ribozyme, self replication, RNA polymerase
%X "A critical event in the origin of life is thought to have been the emergence
   of an RNA molecule capable of replicating a primordial RNA 'genome.' ...
   describe the evoln & engineering of an RNA polymerase ribozyme capable of
   synthesizing RNAs of up to 95 nucleotides in length. To overcome its seq.
   dependence, we recombined traits evolved separately in different ribozyme
   lineages. This yielded a more general polymerase ribozyme that was able to
   synthesize a wider spectrum of RNA seqs., as we demo. by the accurate
   synthesis of an enzymatically active RNA, a hammerhead endonuclease ribozyme.
   This recapitulates a central aspect of an RNA-based genetic system: the
   RNA-catalyzed synthesis of an active ribozyme from an RNA template."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1200752">doi:10.1126/science.1200752 </A>]['11].
   (Also see persp.@[<A HREF="http://dx.doi.org/10.1126/science.1205379">doi:10.1126/science.1205379</A>].)

%A F. Smagulova
%A et al ...
%A G. V. Petukhova
%T Genome-wide analysis reveals novel molecular features of mouse recombination
   hotspots
%J Nature
%V 472
%P 375-378
%M APR
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0411, mouse, genome, recombination,
   meiotic, hotspot, trimethylation, histone, H3
%X "... Hotspot centres are mapped with ~ 200-nucleotide precision, which allows
   analysis of the fine structural details of the preferred recombination sites.
   We determine that hotspots share a centrally distributed consensus motif,
   possess a nucleotide skew that changes polarity at the centres of hotspots &
   have an intrinsic preference to be occupied by a nucleosome. Furthermore, we
   find that the vast majority of recombination initiation sites in mouse males
   are assoc. with testis-specific trimethylation of lysine 4 on histone H3 that
   is distinct from histone H3 lysine 4 trimethylation marks associated with
   transcription. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09869">doi:10.1038/nature09869</A>]['11].

%A I. Kifer
%A R. Nussinov
%A H. J. Wolfson
%T GOSSIP: a method for fast and accurate global alignment of
   protein structures
%J J. Bioinformatics
%V 27
%N 7
%P 925-932
%M APR
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, 3D, protein structure, global alignment,
   GOSSIP, alignment, algorithm
%X "... GOSSIP ... for a global all-against-all alignment of any set of protein
   structures. ... detects similarities between structures down to a certain
   cutoff (a param. of the program), hence allowing it to detect similar
   structures at a much higher speed than local structure alignment methods.
   GOSSIP compares many structures in times which are several orders of mag.
   faster than well-known available structure alignment servers, & it is also
   faster than a database scanning method. We evaluate GOSSIP both on a dataset
   of short structural fragments & on 2 large seq.-diverse struct. benchmarks.
   ... for a threshold of 0.6 & above, the speed of GOSSIP is obtained with no
   compromise of the accuracy of the alignments or of the # of detected global
   similarities. ... s/w@[<A HREF="http://bioinfo3d.cs.tau.ac.il/gossip/">www</A>]."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btr044">doi:10.1093/bioinformatics/btr044</A>]['11].
   [Also search for: MolBio protein structure alignment].

%A D. Koslicki
%T Topological entropy of DNA sequences
%J J. Bioinformatics
%V 27
%N 8
%P 1061-1067
%M APR
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, topological entropy, sequence
%X "... define a new approx. to topological entropy free ... We compute its
   expected value & apply this defn to the intron & exon regions of the human
   genome to observe that as expected, the entropy of introns are sig. higher
   than that of exons. We also find that introns are less random than expected:
   their entropy is lower than the computed expected value. [and] the perplexing
   phenomena that introns on chr.Y have atypically low & bimodal entropy,
   possibly corr.to random seqs. (high entropy) & seqs. that posses hidden
   structure or function (low entropy)."
     "... p[w](n) = |{u : |u|=n & n appears as a subword of w}|.
          That is, p[w](n) represents the # of different n-length subwords
          (overlaps allowed) that appear in w. ...
      ... Defn 3 (topological entropy)
      Let w be a finite seq. of len. |w|, let n be a unique int s.t.
      4^n+n-1 <= |w| < 4^(n+1)+(n+1)-1
      then for w[1]^(4^n+n-1), the first 4^n_n-1 letters of w,
      H[top](w) = log4(p[w[1]]^(4^n+n-1)(n)) / n. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btr077">doi:10.1093/bioinformatics/btr077</A>]['11].
   (Also see top.ent@[<A HREF="http://en.wikipedia.org/wiki/Topological_entropy">wikip</A>]['11],
    and  see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">compression</A>].)

%A J. Jiao
%A et al ...
%A C. W. dePamphilis
%T Ancestral polyploidy in seed plants and angiosperms
%J Nature
%V 473
%P 97-100
%M MAY
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0511, plant, angiosperm, genomes,
   polyploidy, evolution, monocot, eudicot, seed, flowering, plants
%X "Whole-genome duplication (WGD), or polyploidy, followed by gene loss &
   diploidization has long been recognized as an important evol.force in animals
   fungi & other organisms esp. plants. The success of angiosperms has been
   attrib., in part, to innovations assoc. with gene or whole-genome
   duplications but evidence for proposed ancient genome duplications pre-dating
   the divergence of monocots & eudicots remains equivocal in analyses of
   conserved gene order. Here we use comprehensive phylogenomic analyses of
   sequenced plant genomes & more than 12.6 million new expressed-seq.-tag seqs.
   from phylogenetically pivotal lineages to elucidate two groups of ancient
   gene duplications - one in the common ancestor of extant seed plants & the
   other in the common ancestor of extant angiosperms. Gene duplication events
   were intensely conc. ~ 319 & 192 m.y. ago, implicating 2 WGDs in ancestral
   lineages shortly before the diversification of extant seed plants & extant
   angiosperms, resp.. Significantly, these ancestral WGDs resulted in the
   diversification of regulatory genes important to seed & flower development,
   suggesting that they were involved in major innovations that ultimately
   contributed to the rise & eventual dominance of seed plants & angiosperms."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09916">doi:10.1038/nature09916</A>]['11].

%A J. Sun
%A V. Singh
%A R. Kajino-Sakamoto
%A A. Aballay
%T Neuronal GPCR controls innate immunity by regulating noncanonical unfolded
   protein response genes
%J Science
%V 332
%N 6030
%P 729-732
%M MAY
%D 2011
%K jrnl, c2011, c021x, c20xx, innate, immune, system, inate, OCTR 1, OCTR1,
   GPCR, ASH, ASI, unfolded protein response, UPR, Caenorhabditis elegans,
   inflammatory, neurone, nervous system, neuronal
%X "The unfolded protein response (UPR), which is activated when unfolded or
   misfolded p. accumulate in the endoplasmic reticulum, has been implicated in
   the normal physiology of immune defense & in several human diseases, inc.
   diabetes, cancer, neurodegenerative disease, & inflammatory disease. ... we
   found that the nervous system controlled the activity of a noncanonical UPR
   pathway required for innate immunity in C.elegans. OCTR-1, a putative
   octopamine G protein-coupled catecholamine receptor (GPCR, G protein-coupled
   receptor), functioned in sensory neurons designated ASH & ASI to actively
   suppress innate immune responses by down-regulating the exp'n of noncanonical
   UPR genes pqn/abu in nonneuronal tissues. ... suggest a molecular mechanism
   by which the nervous sys. may sense inflammatory responses & respond by
   controlling stress-response pathways at the organismal level."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1203411">doi:10.1126/science.1203411</A>]['11].

%A M. Li
%A et al ...
%A V. G. Cheung
%T Widespread RNA and DNA sequence differences in the human transcriptome
%J Science
%V ?
%P ?-?
%M MAY
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0511, human, transcriptome, DNA, RNA,
   editing, transcription, controversial, science, central dogma
%X "The transmission of information from DNA to RNA is a critical process. We
   compared RNA sequences from human B cells of 27 individuals to the corr. DNA
   seqs. from the same individuals & uncovered more than 10,000 exonic sites
   where the RNA seqs. do not match that of the DNA. All 12 possible categories
   of discordances were observed. These differences were nonrandom, as many
   sites were found in multiple individuals & in different cell types, inc.
   primary skin cells & brain tissues. Using mass spectrometry, we detected
   peptides that are translated from the discordant RNA seqs. & thus do not
   corr. exactly to the DNA seqs.. These widespread RNA-DNA differences in the
   human transcriptome provide a yet-unexplored aspect of genome variation."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1207018">doi:10.1126/science.1207018</A>][11].
   (Sceptics@[<A HREF="http://dx.doi.org/10.1038/473432a">doi:10.1038/473432a</A>]['11] 'Evidence of altered RNA stirs debate'.)
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Notes/DNA-RNA-protein/">dogma</A>].)

%A K. Rhrissorrakrai
%A K. C. Gunsalus
%T MINE: Module Identification in Networks
%J BMC Bioinformatics
%V 12
%P 192
%M MAY
%D 2011
%K jrnl, eJrnl, MolBio, c2011, c201x, c20xx, zz0611, protein, interaction,
   network, mining, gene modules, MINE, MCODE, CFinder, NEMO, SPICi, MCL
%X "Graphical models of network associations are useful for both visualizing
   and integrating multiple types of association data. Identifying modules, or
   groups of functionally related gene products ... developed an agglomerative
   clustering method that is able to identify highly modular sets of gene
   products within highly interconnected molecular interaction n/wks. MINE
   outperforms MCODE, CFinder, NEMO, SPICi, & MCL in identifying non-exclusive,
   high modularity clusters when applied to the C.elegans protein-protein
   interaction network. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-12-192">doi:10.1186/1471-2105-12-192</A>]['11].
   (And, 'Erratum to: MINE: Module Identification in Networks,'
         R & G, BMC Bioi. 17:80, Feb. '16,
         [<A HREF="http://dx.doi.org/10.1186/s12859-016-0929-5">doi:10.1186/s12859-016-0929-5</A>]['16].)
   [Also search for: MolBio network motif].

%A J. Koperwas
%A K. Walczak
%T Tree edit distance for Leal-labelled trees on free leafset and its comparison
   with frequent subsplit dissimilarity and popular distance measures
%J BMC Bioinformatics
%V 12
%P 204
%M MAY
%D 2011
%K jrnl, eJrnl, MolBio, c2011, c201x, c20xx, zz0611, tree, trees, edit distance,
   consensus, leaf labelled, free leafset, metric, RF, MAST, frequent subsplit,
   contraction, pruning, E31, NFC, NFC21
%X "... used in bioinformatics for modelling of evolution history of genes &
   species & also in linguistics ... we introduce the tree e.d. designed for
   leaf labelled trees on free leafset, which occurs to be a metric. It is
   presented together with tree edit consensus tree notion. We provide
   statistical evaluation of provided measure with respect to R-F, MAST &
   frequent subsplit based dissimilarity measures as the reference measures. ...
   proven to be a metric & has the advantage of using different costs for
   contraction & pruning, therefore their properties can be tuned depending on
   the needs of the user. Two of the presented methods carry the most
   interesting properties. E(3,1) is very discriminative (having a wide range of
   values) & has a very regular distance distribution which is similar to a
   normal distribution in its shape & is good both for similar & non-similar
   trees. NFC(2,1) on the other hand is proportional or nearly proportional to
   the # of mutation ops. used, irrespective of their type."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-12-204">doi:10.1186/1471-2105-12-204</A>]['11].

%A B. G. Hall
%T Phylogenetic Trees Made Easy: A How-to Manual
%I SinauerAssoc.
%P 255
%M MAY
%D 2011
%K book, text, MolBio, c2011, c201x, c20xx, zz0611, intro, L4Ref, L5Ref, tree,
   evolutionary
%X 4th ed 2011; pb us$45; uk us isbn:0878936068; uk us isbn13:978-0878936069.
   [Also search for: MolBio phylogenetic tree].

%A M. H.-Y. Fritz
%A R. Leinonen
%A G. Cochrane
%A E. Birney
%T Efficient storage of high throughput DNA sequencing data using
   reference-based compression
%J Genome Res.
%V 21
%N 5
%P 734-740
%M MAY
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0611, DNA, sequence, short reads,
   storage, disc, resequencing, genomes
%X "... Our approach works for resequencing experiments that target well-studied
   genomes. We align new seqs. to a reference genome & then encode the diffs.
   between the new seq. & the reference genome for storage. Our compression
   method is most efficient when we allow controlled loss of data in the saving
   of quality information & unaligned seqs.. With this new compression method we
   observe exponential efficiency gains as read lengths increase, & the
   magnitude of this efficiency gain can be controlled by changing the amount of
   quality information stored. Our compression method is tunable: The storage
   of quality scores & unaligned seqs. may be adjusted for different experiments
   to conserve information or to minimize storage costs, & provides one
   opportunity to address the threat that increasing DNA seq. volumes will
   overcome our ability to store the seqs.."  (online Jan 2011.)
   -- [<A HREF="http://dx.doi.org/10.1101/gr.114819.110">doi:10.1101/gr.114819.110</A>]['11].

%A I. F. Fokkema
%A P. E. Taschner
%A G. C. Schaafsma
%A J. Celli
%A J. F. Laros
%A J. T. den Dunnen
%T LOVD v.2.0: The next generation in gene variant databases
%J Hum. Mutat.
%V 32
%N 5
%P 557-563
%M MAY
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0514, LOVD, human, genetic, gene,
   variation, mutation, health, illness, disease, database, Leiden
%X "... store information on gene sequence variation assoc. with human
   phenotypes & are frequently used as a reference by researchers & clinicians.
   ... To reduce redundancy, patient & sequence variant data are stored in
   separate tables. Tables are linked to generate connections between sequence
   variant data for each gene & every patient. ... Currently, the LOVD Website
   [<A HREF="http://www.LOVD.nl/">www</A>] lists 71 public LOVD installations
   hosting 3,294 gene variant DBs with 199,000 variants in 84,000 patients. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/humu.21438">doi:10.1002/humu.21438</A>]['14],
      [<A HREF="http://www.LOVD.nl/">LOVD</A>].
   [Also search for: variation illness database].

%A F. DiMaio
%A et al ...
%A D. Baker
%T Improved molecular replacement by density- and energy-guided protein
   structure optimization
%J Nature
%V 473
%P 540-543
%M MAY
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, 3D, protein structure, determination,
   x ray, Xray, crystallography, molecular replacement, unit cell, Autobuild,
   chain tracing, solving, Rosetta
%X "Molecular replacement procedures, which search for placements of a starting
   model within the crystallographic unit cell that best account for the
   measured diffraction amplitudes, followed by automatic chain tracing methods,
   have allowed the rapid solution of large numbers of protein crystal structs..
   Despite extensive work, molecular replacement or the subsequent rebuilding
   usually fail with more divergent starting models based on remote homologues
   with < 30% seq.identity. ... this limitation can be subs. reduced by
   combining algs. for protein struct. modelling with those developed for
   crystallographic struct. determination. ... integrating Rosetta struct.
   modelling with Autobuild chain tracing yielded high-res'n structures for 8 of
   13 X-ray diffraction data sets that could not be solved in the labs. of
   expert crystallographers & that remained unsolved after applic'n of an
   extensive array of alt.approaches. We est. that the new method should allow
   rapid struct.detn without experimental phase info. for over half the cases
   where current methods fail, given diffraction data sets of better than 3.2A
   res'n, four or fewer copies in the asymmetric unit, & the availability of
   structs. of homologous proteins with > 20% seq.identity."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09964">doi:10.1038/nature09964</A>]['11], and
   pdf@[<A HREF="http://depts.washington.edu/bakerpg/drupal/node/389">wash.</A>]['11].
   [Also search for: MolBio molecular replacement].

%A M. V. Shapovalov
%A R. L. Dunbrack jnr
%T A smoothed backbone-dependent rotamer library for proteins derived from
   adaptive kernel density estimates and regressions
%J Structure
%V 19
%N 6
%P P844-858
%M JUN
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz1122, protein, structure, side chain,
   sideChain, bbdep, bbdep2010, angles, phi, psi, chi, ch1, ch2, chi3
%X "... A new version of the backbone-dependent rotamer library has been
   developed using adaptive kernel density ests. for the rotamer freqs. &
   adaptive kernel reg'n for the mean dihedral angles & variances. ... allows
   for evaluation of the rotamer probabilities, mean angles, & variances as a
   smooth & cts fn of phi & psi."
   -- [<A HREF="https://doi.org/10.1016/j.str.2011.03.019">doi:10.1016/j.str.2011.03.019</A>]['22].
   Also see DunbrackLab@[<A HREF="http://dunbrack.fccc.edu/lab/">fccc</A>]['22]
   & bbdep2010.  [Also search for: Dunbrack c1997].

%A R. Dunn
%T The Wild Life of Our Bodies: Predators, Parasites, and Partners That Shape
   Who We Are Today
%I HarperCollins
%P 304
%M JUN
%D 2011
%K book, text, c2011, c201x, c20xx, zz0611, biology, biol, human, body,
   parasite, bugs, bacteria, pathogens
%X 1st ed 2011; hb us$16; uk us isbn:006180648X; uk us isbn13:978-0061806483.
   "... while "clean living" has benefited us in some ways, it has also made us
   sicker in others. We are trapped in bodies that evolved to deal with the
   dependable presence of hundreds of other species. As D. reveals, our modern
   disconnect from the web of life has resulted in unprecedented effects that
   immunologists, evolutionary biologists, psychologists, and other scientists
   are only beginning to understand. Diabetes, autism, allergies, many anxiety
   disorders, autoimmune diseases, and even tooth, jaw, and vision problems are
   increasingly plaguing bodies that have been removed from the ecological
   context in which they existed for millennia.  ..."

%A A. Fontdevila
%T The Dynamic Genome: A Darwinian Approach
%I OUP
%P 248
%M JUL
%D 2011
%K book, text, MolBio, c2011, c201x, c20xx, zz0811, OUP, genome, DNA, adaptive,
   adaption, evolution, junk, transposable elements, transposon
%X 1st ed 2011; hb us$84; uk us isbn:019954137X; uk us isbn13:978-0199541379.
   '... The predominance of non-coding DNA in the human genome, the long-term
   adaptive role of so called "junk DNA" in the evolution of new functions, and
   the key evolutionary differences that define our humanity are just some of
   the controversial issues that this book examines in the context of Darwinian
   evolution. The author's principle intention is to show that whilst genomics
   is revealing new and previously unanticipated mechanisms and sources of
   variability ...'
   [Also search for: MolBio junk DNA].

%A M. J. Sanderson
%A M. M. McMahon
%A M. Steel
%T Terraces in phylogenetic tree space
%J Science
%V 333
%N 6041
%P 448-450
%M JUL
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0811, evolutionary, tree, trees,
   terrace
%X "... the tree of life is the construction of species-rich phylogenies from
   multilocus - but often incomplete - sequence data sets. We describe
   previously unknown structure in the landscape of solns to the tree
   reconstruction problem, comprising sometimes vast "terraces" of trees with
   identical quality, arranged on islands of phylogenetically similar trees.
   Phylogenetic ambiguity within a terrace can be characterized efficiently &
   then ameliorated by new algs. for obtaining a terrace's maximum-agreement
   subtree or by identifying the smallest set of new targets for additional
   sequencing. Algs. to find optimal trees or estimate Bayesian posterior tree
   distributions may need to navigate strategically in the neighborhood of
   large terraces in tree space."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1206357">doi:10.1126/science.1206357</A>]['11].
   [Also search for: MolBio phylogenetic tree].

%A C. Ryan
%A C. Jetha
%T Sex at Dawn: How We Mate, Why We Stray, and What It Means for
   Modern Relationships
%I HarperPerennial
%P 432
%M JUL
%D 2011
%K book, text, c2011, c201x, c20xx, zz1212, human, primate, animal, chimp,
   bonobo, behaviour, society, love, sex, sexuality, fidelity, infidelity,
   cheating, unfaithful, monogamy, promiscuity, marriage, pair bond, bonding,
   conflict, cooperation, relationship
%X 1st ed 2100; pb us$8; uk us isbn:0061707813; uk us isbn13:978-0061707810.
   "... debunks almost everything we 'know' about sex, weaving together
   convergent, frequently overlooked evidence from anthropology, archaeology,
   primatology, anatomy, and psychosexuality to show how far from human nature
   monogamy really is. In Sex at Dawn, the authors expose the ancient roots of
   human sexuality while pointing toward a more optimistic future illuminated
   by our innate capacities for love, cooperation, and generosity."
   (Also see the 'Science Show', ABC radio, 18/2/2012
   [<A HREF="http://www.abc.net.au/radionational/programs/scienceshow/is-monogamy-unnatural3f/3818274">www</A>]['12].)

%A E. Arunan
%A et al ...
%A D. J. Nesbitt
%T Definition of the hydrogen bond (IUPAC Recommendations 2011)
%J Pure and Applied Chemistry
%V 83
%N 8
%P 1637-1641
%M ?
%D 2011
%K jrnl, c2011, c201x, c20xx, IUPAC, chem, chemistry, hydrogen bond, Hbond,
   bonds, defn, definition, criteria, criterion
%X "A novel defn for the H.bond is recommended here. It takes into account the
   theor. & experimental knowledge acquired over the past century. [It] insists
   on some evidence. Six criteria are listed that could be used as evidence for
   the presence of a H.bond."  [Online 7/2011.]
   Consider X-H...Y-Z
      1. ... electrostatic ... charge transfer ...
      2. ... X-H covalent and polarized, ...
      3. ... X-H...Y usually linear ...
      4. ... X-H usually lengthens as H...Y forms ...
      5. characteristic NMR signature ...
      6. ... Gibbs energy ... > thermal energy of the sys ...
   -- [<A HREF="http://dx.doi.org/10.1351/PAC-REC-10-01-02">doi:10.1351/PAC-REC-10-01-02</A>]['11].

%A Y. Li
%A et al ...
%A H.-W. Deng
%T Comparative studies of de novo assembly tools for next-generation
   sequencing technologies
%J J. Bioinformatics
%V 27
%N 15
%P 2031-2037
%M AUG
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0811, sequence assembly, de novo,
   deNovo, tool, sequencing, SSAKE, VCAKE, Euler-sr, Edena, Velvet, ABySS,
   SOAP, SOAPdenovo, short reads
%X "... compared the performance of commonly used de novo assembly tools
   specifically designed for next-generation sequencing data, including SSAKE,
   VCAKE, Euler-sr, Edena, Velvet, ABySS and SOAPdenovo. ... using several
   perf.criteria, inc. N50 length, seq.coverage & assembly accuracy. Various
   properties of read data, inc. single-end/paired-end, seq. GC content, depth
   of coverage & base calling error rates, were investigated for their effects
   on the perf. of different assembly tools. [And] the computation time &
   memory usage ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btr319">doi:10.1093/bioinformatics/btr319</A>]['11].
   [Also search for: MolBio sequence assembly].

%A W. J. Urba,
%A D. L. Longo
%T Redirecting T cells
%J New Engl. J. Med.
%V 365
%P 754-757
%M AUG
%D 2011
%K editorial, news, views, c2011, c201x, c20xx, zz0911, NEJM, MolBio, T cell,
   Tcell, cells, cancer, health, medicine, medical, melanoma, lymphocytes,
   gene transfer, therapy, June, tumor, tumour, Lymphocytic Leukemia, CLL, CD19
%X "The pursuit of tumor-reactive T cells as a cancer therapy has continued
   unabated since the discovery of the graft-versus-leukemia effect in patients
   undergoing allogeneic hematopoietic stem-cell transplantation. Some successes
   have been noted: the adoptive transfer of Epstein-Barr virus (EBV)-specific
   T cells can prevent and treat post-transplantation lymphomas, and the
   adoptive transfer of in vitro activated and expanded autologous tumor-
   -infiltrating lymphocytes after systemic depletion of lymphocytes induces
   durable complete remissions in some heavily pretreated patients with
   metastatic melanoma. Therapy with tumor-infiltrating lymphocytes is difficult
   and expensive, and it has benefited only patients with melanoma. Redirecting
   T cells by gene transfer of ..."
   -- [<A HREF="http://www.nejm.org/doi/full/10.1056/NEJMe1106965">doi:10.1056/NEJMe1106965</A>]['11].  (NB. 3 patients.)
   Also see study@[<A HREF="http://penncancer.org/penn_news.cfm?ID=1610">ACC</A>]['11].

%A C. Rowe
%A S. D. Healy
%T Is bigger always better?
%J Science
%V 333
%N 6043
%P 708-709
%M AUG
%D 2011
%K views, c2011, c201x, c20xx, zz0811, biology, evolution, mate selection,
   sexual, trait, traits, male, female, peacock, tungara,
   Physalaemus pustulosus, frog, calls, beauty, attractive
%X "Darwin was famously puzzled by the length of a peacock's train - what made
   it so big and so elaborate? The theory of sexual seln provided us with the
   answer: Females choose males with more exaggerated traits ...
   [.e.g.] although female frogs prefer male frogs with longer calls, the
   females are less able to discriminate between males as their calls become
   longer, perhaps constraining the evoln of call length. ...  consistent with
   Weber's law, which holds that as the magnitude of 2 stimuli increases,
   a greater difference is required to distinguish between them. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1210723">doi:10.1126/science.1210723</A>]['11],  [9 refs].

%A O. Penner
%A P. Grassberger
%A M. Paczuski
%T Sequence alignment, mutual information, and dissimilarity measures for
   constructing phylogenies
%J PLoS One
%V 6
%N 1
%P e14373
%M JAN
%D 2011
%K jrnl, eJrnl, MolBio, c2011, c201x, c20xx, zz0811, alignment, evolutionary,
   phylogenetic, phylogeny, tree, trees, measure, entropy,
   animal mitochondrial DNA
%X "... a simple approach to get robust estimates of MI from global pairwise
   alignments. Our main result uses algorithmic (Kolmogorov) info.theory, but
   we show that similar results can also be obtained from Shannon theory. For
   animal mitochondrial DNA our approach uses the alignments made by popular
   global alignment algs. to produce MI estimates that are strikingly close to
   estimates obtained from the alignment free methods mentioned above ...
   Several versions of MI based distances outperform conventional distances in
   distance-based phylogeny. Even a simplified version based on single letter
   Shannon entropies, which can be easily incorporated in existing s/w packages,
   gave superior results throughout the entire animal kingdom. But we see the
   main virtue of our approach in a more general way. [eg] it can also help to
   judge the relative merits of different alignment algs., by estimating the
   significance of specific alignments. It strongly suggests that information
   theory concepts can be exploited further in sequence analysis."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0014373">doi:10.1371/journal.pone.0014373</A>]['11],
      21245917@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/21245917">pubmed</A>]['11].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">compression</A>].)

%A S. G. Trevino
%A N. Zhang
%A M. P. Elenko
%A A. Luptak
%A J. W. Szostak
%T Evolution of functional nucleic acids in the presence of nonheritable
   backbone heterogeneity
%J PNAS
%P 13492-13497
%N 33
%V 108
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0112, evolution, life, RNA, origin, origins,
   replication, nucleic acid, DNA, TNA, T7
%X "... RNA, which can both transfer information from generation to gen. through
   replication directed by base-pairing, & carry out biochemical activities ...
   suggest that homogeneous monomers might not have been nec. if populations of
   heterogeneous nucleic acid molecules could evolve reproducible fn. For such
   evolution to be possible, fn would have to be maintained despite the repeated
   scrambling of backbone chemistry from gen. to gen.. ... tested this
   possibility in a simplified model system, by using a T7 RNA polymerase
   variant capable of transcribing NAs that contain an ~ 1:1 mixture of deoxy-
   & ribonucleotides. We readily isolated nucleotide-binding aptamers by
   utilizing an in vitro seln process that shuffles the order of deoxy- &
   ribonucleotides in each round. We describe two such RNA/DNA mosaic NA
   aptamers that specifically bind ATP & GTP, resp.. We conclude that
   nonheritable variations in NA backbone struct. may not have posed an
   insurmountable barrier to the emergence of functionality in early NAs."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1107113108">doi:10.1073/pnas.1107113108</A>]['12].

%A D. Gront
%A D. W. Kulp
%A R. M. Vernon
%A C. E. M. Strauss
%A D. Baker
%T Generalized fragment picking in Rosetta: Design, protocols and applications
%J PLoS One
%V 6
%N 8
%P e23294
%M AUG
%D 2011
%K jrnl, eJrnl, MolBio, c2011, c201x, c20xx, PLoS, Rosetta, pick, fragment,
   library, ab initio, protein, tertiary, structure, prediction, nnmake
%X "Rosetta ... begin with coarse grained Monte Carlo searches in which the
   moves are based on short frags. extracted from a DB of known structs.. ...
   describe a new OO program for picking frags. that greatly extends the
   functionality of the prev.program (nnmake) ... demonstrate that the program
   provides at least as good building blocks for ab-initio struct.prediction as
   the prev.program, & provide e.g.s of the wide range of applic'ns ..."
      "... f.libraries seeks to accurately rep. not the most prob.conformation
      for a given seq.seg., but the entire dist'n of conformation ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0023294">doi:10.1371/journal.pone.0023294</A>]['12].
   [Also search for: Rosetta protein MolBio].
   [Also search for: protein structure fragment library].

%A Y. Liu
%A B. Schmidt
%A D. L Maskel
%T Parallelized short read assembly of large genomes using de Bruijn graphs
%J BMC Bioinformatics
%V 12
%N 1
%P 354
%M AUG
%D 2011
%K jrnl, eJrnl, MolBio, c2011, c201x, c20xx, zz0911, short read, reads,
   de Bruijn, deBrujn, sequence, assembly, parallel, Velvet, ABySS, SOAPdenovo,
   SOAP denovo, de novo
%X "... PASHA, a parallelized short read assembler using deB. graphs, which
   takes advantage of hybrid computing architectures consisting of both
   shared-memory multi-core CPUs & distributed-memory compute clusters to gain
   efficiency & scalability.  ... able to produce more contiguous high-quality
   assemblies in shorter time compared to 3 leading assemblers: Velvet, ABySS
   & SOAPdenovo. ... scalability for large genome datasets is demonstrated with
   human genome assembly. ... achieves competitive assembly quality with faster
   exec.speed on the same compute resources, yielding an NG50 contig size of
   503 with the longest correct contig size of 18,252, & an NG50 scaffold size
   of 2,294. [And] human assembly is completed in about 21 hours with only
   modest compute resources. ..."   (online Aug 2011)
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-12-354">doi:10.1186/1471-2105-12-354</A>]['11].
   [Also search for: short read Molbio] and [also search for: deBruijn MolBio].

%A A. W. Barclay
%A J. Brand-Miller
%T The Australian paradox: A substantial decline in sugars intake over the same
   timeframe that overweight and obesity have increased
%J Nutrients
%V 3
%N 4
%P 491-504
%M APR
%D 2011
%K jrnl, eJrnl, c2011, c201x, c20xx, zz0214, health, diet, sugar, intake,
   sweet drinks, fructose, corn syrup, consumption, weight, obesity, Australia,
   University, Sydney, UniSydney, USyd, conduct, scientific research, errors,
   mistakes, scandal
%X "... prevalence of obesity has increased 3 fold in Australians since 1980. In
   Au., the UK & USA, per capita consumption of refined sucrose decreased by
   23%, 10% & 20% respectively from 1980 to 2003. When all sources of nutritive
   sweeteners, including high fructose corn syrups, were considered, per capita
   consumption decreased in Au. (-16%) & the UK (-5%), but increased in the USA
   (+23%). In Au., there was a reduction in sales of nutritively sweetened
   beverages by 64 million liters from 2002 to 2006 & a reduction in % of
   children consuming sugar-sweetened beverages between 1995 & 2007. The
   findings confirm an 'Australian Paradox' - a substantial decline in refined
   sugars intake over the same timeframe that obesity has increased. The
   implication is that efforts to reduce sugar intake may reduce consumption but
   may not reduce the prevalence of obesity."
   -- [<A HEF="http://dx.doi.org/10.3390/nu3040491">doi:10.3390/nu3040491</A>]['14].
   (And, 'Trends in added sugar supply and consumption in Australia: there
          is an Australian Paradox,' BMC Public Health, 2013 Sep 30; 13:898
   -- [<A HEF="http://dx.doi.org/10.1186/1471-2458-13-898">doi:10.1186/1471-2458-13-898</A>]['14].)
   auth2@[<A HREF="http://sydney.edu.au/medicine/people/academics/publications/jennieb.php">Syd.U.</A>].
   BUT see, "Sugar research paper contained 'inadvertent errors';
            Professor Jennie Brand-Miller defends findings,"
   [<A HREF="http://www.abc.net.au/news/2014-02-13/errors-force-nutritionists-to-correct-controversial-sugar-paper/5258024">13/2/2014</A>], and
   Background Briefing
   [<A HREF="http://www.abc.net.au/radionational/programs/backgroundbriefing/2014-02-09/5239418#transcript">9/2/2014</A>].

%A B. P. Zietsch
%A P. Santtila
%T Genetic analysis of orgasmic function in twins and siblings does not support
   the by-product theory of female orgasm
%J Animal Behaviour
%V ?
%P ?-?
%M SEP
%D 2011
%K jrnl, c2011, c201x, c20xx, animal, human, behaviour, orgasm, sex, male,
   female, twin, heritable, genetic, evolution, mate selection, choice,
   pair bonding, by product
%X "The evolutionary basis of human female orgasm has been subject to furious
   scientific debate, which has recently intensified. Many adaptive explanations
   have been proposed, invoking functions from pair bonding & mate selection
   to sucking up sperm .... The popular alternative theory is that female orgasm
   is not adaptive & is only evolutionarily maintained as a by-product of
   ongoing selection on the male orgasm - ejaculation system. This theory has
   not been adequately tested. We tested one of its central tenets: that seln
   pressure on the male orgasm is partially transmitted to the female via a
   positive cross-sex correlation in orgasmic fn ... questionnaire data from
   over 10,000 Finnish twins & siblings, we found sig. genetic variation in
   both male & female orgasmic fn, but no sig. correlation between opposite-
   -sex twins & siblings. This suggests that different genetic factors
   underlie male & female orgasmic fn & that seln pressures on male orgasmic
   function do not act substantively on female orgasmic function.  These results
   challenge the by-product theory of female orgasm."   [online Sept 2011].
   -- [<A HREF="http://dx.doi.org/10.1016/j.anbehav.2011.08.002">doi:10.1016/j.anbehav.2011.08.002</A>]['11].

%A L. Nogueira
%A I. Ramirez-Sanchez
%A G. A. Perkins
%A A. Murphy
%A P. R. Taub
%A G. Ceballos
%A F. J. Villarreal
%A M. C. Hogan
%A M. H. Malek
%T (-)-epicatechin enhances fatigue resistance and oxidative capacity in mouse
   muscle
%J J. of Physiology
%V 589
%N 18
%P 4615-4631
%M SEP
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0911, medical, health, benefit, dark chocolate,
   good news, exercise, fatigue, fitness, mice, flavanol, cacao, cocoa,
   epicatechin, ent catechin, entcatachin, antioxidant, WayneState
%X "... show here that mice fed for 15 days with (-)-epicatechin (present in
   dark chocolate) had improved exercise performance accompanied by: (1) an
   increased # of capillaries in the hindlimb muscle; and (2) an increased
   amount of muscle mitochondria as well as signalling for mitochondrial
   biogenesis. These results suggest that (-)-epicatechin increases the capacity
   for muscle aerobic metabolism, thereby delaying the onset of fatigue. ..."
   -- [<A HREF="http://dx.doi.org/10.1113/jphysiol.2011.209924">doi:10.1113/jphysiol.2011.209924</A>]['11],
   last auth@[<A HREF="http://cphs.wayne.edu/bio.php?id=75656">wayne</A>]['11].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Catechin">wikip</A>].)
   [Also search for: epicatechin].

%A F. Khatib
%A F. DiMaio
%A S. Cooper
%A M. Kazmierczyk
%A M. Gilski
%A S. Krzywda
%A H. Zabranska
%A I. Pichova
%A J. Thompson
%A Z. Popovic
%A M. Jaskolski
%A D. Baker
%T Crystal structure of a monomeric retroviral protease solved by protein
   folding game players
%J Nature Structural & Molecular Biology
%V ?
%P ?-?
%M SEP
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0911, Foldit, protein structure, fold,
   folding, game, M-PMV retroviral protease, enzyme, monomeric, MPMV,
   retrovirus
%X "Following the failure of a wide range of attempts to solve the crystal
   structure of M-PMV retroviral protease by molecular replacement, we
   challenged players of the protein folding game Foldit to produce accurate
   models of the protein. Remarkably, Foldit players were able to generate
   models of sufficient quality for successful molecular replacement & subs.
   structure detn. The refined structure provides new insights for the design
   of antiretroviral drugs."  (online Sept 2011).
   -- [<A HREF="http://dx.doi.org/10.1038/nsmb.2119">doi:10.1038/nsmb.2119</A>]['11].

%A D. L. Katz
%A K. Doughty
%A A. Ali
%T Cocoa and chocolate in human health and disease
%J Antioxidants and Redox Signaling
%V 15
%N 10
%M OCT
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0822, dark chocolate, consumption, positive,
   cocoa, catechin, epicatechin, flavonoids, antioxidants, human health
%X " ... The epicatechin content of cocoa is primarily responsible for its
   favorable impact on vascular endothelium via its effect on both acute &
   chronic upregulation of nitric oxide production. Other cardiovascular effects
   are mediated through anti-inflammatory effects of cocoa polyphenols, &
   modulated through the activity of NF-kB. Antioxidant effects of cocoa may
   directly influence insulin resistance &, in turn, reduce risk for diabetes.
   Further ..."
   -- [<A HREF="https://doi.org/10.1089/ars.2010.3697">doi:10.1089/ars.2010.3697</A>]['22] and
      [<A HREF="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696435/">ncbi</A>]['22].
   [Also search for: chocolate].

%A M. Rasmussen
%A et al ...
%A E. Willerslev
%T An Aboriginal Australian genome reveals separate human dispersals into Asia
%J Science
%V 334
%N 6052
%P 94-98
%M OCT
%D 2011
%K MolBio, jrnl, c2011, c201x, c20xx, zz0911, human genome, aborigine,
   aboriginal, native, Australia, au, origins, populations, migration,
   dispersal
%X "... genomic seq. obtained from a 100-year-old lock of hair donated by an
  Aboriginal man from SW Australia in the early 20th C. We detect no evidence of
  European admixture & estimate contamination levels to be below 0.5%. We show
  that Aboriginal Australians are descendants of an early human dispersal into
  eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate
  from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We
  also find evidence of gene flow between populations of the two dispersal waves
  prior to the divergence of Native Americans from modern Asian ancestors. Our
  findings support the hypothesis that present-day Aboriginal Australians
  descend from the earliest humans to occupy Australia, likely representing one
  of the oldest continuous populations outside Africa."  (online Sept 2011.)
  -- [<A HREF="http://dx.doi.org/10.1126/science.1211177">doi:10.1126/science.1211177</A>]['11].

%A R. C. Francis
%T Epigenetics: The Ultimate Mystery of Inheritance
%I WWNorton
%P 234
%M JUN
%D 2011
%K book, text, c2011, c201x, c20xx, zz1011, MolBio, genetics, epigenetics,
   epigenetic effects, inheritance, gene, modification, environment, risks,
   human health, medical
%X 1st ed 2011; hb us$16; uk us isbn:0393070050; uk us isbn13:978-0393070057.
   "... refers to the recent discovery that stress in the environment can impact
   an individual's physiology so deeply that those biological scars are actually
   inherited by the next several generations. For instance, a recent study has
   shown that men who started smoking before puberty caused their sons to have
   significantly higher rates of obesity. And obesity is just the tip of the
   iceberg - many researchers believe that epigenetics holds the key to
   understanding cancer, Alzheimer's, schizophrenia, autism, and diabetes. ..."

%A R. Brooks
%T Sex, Genes and Rock 'n' Roll: How Evolution Has Shaped the Modern World
%I UNSWpress
%P 320
%M JUN
%D 2011
%K book, c2011, c201x, c200x, zz0212, UNSW, sex, genes, rock and roll,
   human behaviour, society, culture, social
%X 1st ed 2011; pb us$17; isbn:1742231608; isbn13:978-1742231600;
     and  2012; hb us%50; isbn:1611682363; isbn13:978-1611682366.
   "... argues that the origins of [various] 21st century problems can be
   found where the ancient forces of evolution collide with modern culture and
   economics. ..."

%A C. Kosiol
%A N. Goldman
%T Markovian and non-Markovian protein sequence evolution: Aggregated Markov
   process models
%J JMB
%V 411
%N 4
%M AUG
%D 2011
%K jrnl, MolBio, JMB, c2011, c201x, c20xx, zz0616, DNA, protein, codon,
   amino acid, substitution, matrix, process, evolution
%X "...  We show that the observed time-dependent behavior can be explained
   qualitatively by modeling protein sequence evolution as an aggregated Markov
   process (AMP): a time-homogeneous Markovian substitution model observed only
   at the level of the amino acids encoded by the protein-coding DNA sequence.
   The study of AMPs sheds new light on the relationship between amino
   acid-level & codon-level models of sequence evolution, & our results suggest
   that protein evolution should be modeled at the codon level rather than using
   amino acid substitution models."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jmb.2011.06.005">doi:10.1016/j.jmb.2011.06.005</A>]['16].
   [Also search for: MolBio substitution matrix].

%A E. L. Dempster
%A et al ...
%A J. Mill
%T Disease-associated epigenetic changes in monozygotic twins discordant for
   schizophrenia and bipolar disorder
%J Human Molec. Genetics
%V 20
%P ?-?
%M OCT
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz1011, epigenetics, gene, human, twins,
   twin, schizophrenia, SZ, bipolar disorders, BD, mental health, ST6GALNAC1,
   GPR24, ZNF659, methylated, methylation, psychosis, psychiatric
%X "... performed a genome-wide analysis of DNA methylation on peripheral blood
   DNA samples obtained from a unique sample of MZ twin pairs discordant for
   major psychosis. ... Pathway analysis of our top loci highlighted a sig.
   enrichment of epigenetic changes in biological networks & pathways directly
   relevant to psychiatric disorder & neurodevelopment. The top psychosis-assoc.
   differentially methylated region, significantly hypomethylated in affected
   twins, was located in the promoter of ST6GALNAC1 overlapping a previously
   reported rare genomic duplication observed in SZ. The mean DNA methylation
   diff. at this locus was 6%, but there was considerable heterogeneity between
   families, with some twin pairs showing a 20% difference in methylation. We
   subsequently assessed this region in an independent sample of postmortem
   brain tissue from affected individuals & controls, finding marked
   hypomethylation (>25%) in a subset of psychosis patients. Overall, our data
   provide further evidence [of] a role for DNA methylation diffs. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/hmg/ddr416">doi:10.1093/hmg/ddr416</A>]['11].
   [Also search for: methylation epigenetics MolBio].

%A V. Gewin
%T Education: Inspiration for informatics
%J Nature
%V 478
%P 143-145
%M OCT
%D 2011
%K news, views, c2011, c201x, c20xx, zz1011, MolBio, bioinformatics, education,
   course, courses, degree, degrees, training
%X "... Picking a programme with comprehensive training modules in statistics,
   computer science and/or biology can be an effective strategy. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nj7367-143a">doi:10.1038/nj7367-143a</A>]['11].

%A R. Cheong
%A A. Rhee
%A C. J. Wang
%A I. Nemenman
%A A. Levchenko
%T Information transduction capacity of noisy biochemical signaling networks
%J Science
%V 334
%N 6054
%P 354-358
%M OCT
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz1011, biol, information theory,
   network, signal, signals, cell, network, TNF
%X "Molecular noise restricts the ability of an individual cell to resolve input
   signals of different strengths & gather info. about the external environment.
   Transmitting info. through complex signaling n/ws with redundancies can
   overcome this limitation. We developed an integrative theoretical &
   experimental framework, based on the formalism of info. theory, to
   quantitatively predict & measure the amount of info. transduced by molecular
   & cellular n/ws. Analyzing tumor necrosis factor (TNF) signaling revealed
   that individual TNF signaling pathways transduce info. sufficient for
   accurate binary decisions, & an upstream bottleneck limits the info. gained
   via multiple integrated pathways. Negative feedback to this bottleneck could
   both alleviate & enhance its limiting effect, despite decreasing noise.
   Bottlenecks likewise constrain info. attained by n/ws signaling through
   multiple genes or cells."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1204553">doi:10.1126/science.1204553</A>]['11].

%A K. I. Bos
%A et al ...
%A J. Krause
%T A draft genome of Yersinia pestis from victims of the Black Death
%J Nature
%V 478
%P 506-510
%M OCT
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz1111, black death, 14C, plague, genome,
   Yersinia pestis, Ypestis, nGenome, bacterium, bacteria
%X "... report a reconstructed ancient genome of Yersinia pestis at 30-x avg.
   coverage from Black Death victims securely dated to episodes of pestilence-
   -assoc. mortality in London, England, 1348-1350. Genetic architecture &
   phylogenetic analysis indicate that the ancient organism is ancestral to most
   extant strains & sits v.close to the ancestral node of all Y.pestis commonly
   assoc. with human infection. Temporal ests. suggest that the Black Death of
   1347-1351 was the main historical event responsible for the introduction &
   widespread dissemination of the anc. to all currently circulating Y.pestis
   strains pathogenic to humans, & further indicates that contemporary Y.pestis
   epidemics have their origins in the medieval era. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature10549">doi:10.1038/nature10549</A>]['11].

%A R. W. Meredith
%A et al ...
%A W. J. Murphy
%T Impacts of the Cretaceous terrestrial revolution and KPg extinction on mammal
   diversification
%J Science
%V 344
%N 6055
%P 521-524
%M OCT
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz1111, mammal, mammals, family,
   phylogenetic, evolutionary, tree, evolution, KPg, Eocene, cretaceous
%X "... constructed a molecular supermatrix for mammalian families and analyzed
   these data with likelihood-based methods & relaxed molecular clocks.
   Phylogenetic analyses resulted in a robust phylogeny with better resolution
   than phylogenies from supertree methods. Relaxed clock analyses support the
   long-fuse model of diversification & highlight the importance of including
   multiple fossil calibrations that are spread across the tree. Molecular time
   trees & diversification analyses suggest important roles for the Cretaceous
   Terrestrial Revolution & Cretaceous-Paleogene (KPg) mass extinction in
   opening up ecospace that promoted interordinal & intraordinal diversification
   respectively. By contrast, diversification analyses provide no support for
   the hypothesis concerning the delayed rise of present-day mammals during the
   Eocene Period."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1211028">doi:10.1126/science.1211028</A>]['11].
   [Also search for: MolBio mammal evolutionary tree].

%A K. Lindorff-Larsen
%A S. Piana1
%A R. O. Dror
%A D. E. Shaw
%T How fast-folding proteins fold
%J Science
%V 334
%N 6055
%P 517-520
%M OCT
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, protein, fold, folding, simulation,
   molecular dynamics
%X "... report the results of atomic-level molec.dynamics simns, over periods
   ... between 100micro-secs & 1ms, that reveal a set of common principles
   [for] folding of 12 structurally diverse proteins. In simulations conducted
   with a single physics-based energy fn, the proteins, representing all 3 major
   structural classes, spontaneously & repeatedly fold to their experimentally
   determined native structures. Early in the folding process, the protein
   backbone adopts a nativelike topology while certain secondary structure elts
   & a small # of nonlocal contacts form. In most cases, folding follows a
   single dominant route in which elts of the native struct. appear in an order
   highly correlated with their propensity to form in the unfolded state."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1208351">doi:10.1126/science.1208351</A>]['11].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.1214018">persp.</A>]['11].)
   [Also search for: protein folding simulation].

%A A. R. Jex
%A et al ...
%A R. B. Gasserr
%T Ascaris suum draft genome
%J Nature
%V 479
%P 529-533
%M NOV
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz1111, genome, nGenome, parasite, worm,
   nematode, Ascaris suum, common roundworm, nematodiases, disease
%X 272,782,664 bp, GC 38%.
   "... In humans, the diseases caused by these parasites result in ~135,000
   deaths annually, with a global burden comparable with that of malaria or
   tuberculosis in disability-adjusted life years. Ascaris alone infects
   ~1.2 billion people ...report the 273-megabase draft genome of Ascaris suum
   & compare [to] other nematode genomes. This genome has low repeat content
   (4.4%) & encodes about 18,500 protein-coding genes. Notably, the A.suum
   secretome (about 750 molecules) is rich in peptidases linked to the
   penetration & degradation of host tissues, & an assemblage of molecules
   likely to modulate or evade host immune responses. ..." (online Oct 2011).
   -- [<A HREF="http://dx.doi.org/10.1038/nature10553">doi:10.1038/nature10553</A>]['11].

%A P. Pevzner
%A R. Shamir
%T Bioinformatics for Biologists
%I CUP
%P 392
%M NOV
%D 2011
%K book, text, MolBio, c2011, c201x, c20xx, zz0112, biology
%X 1st ed 2011; pb us$60; uk us isbn:1107648874; uk us isbn13:978-1107648876.
   "... computational procedures are developed and applied to central topics in
   bioinformatics and genomics, such as the genetic basis of disease, genome
   evolution or the tree of life concept. ..."

%A K. N. Harper
%A M. K. Zuckerman
%A M. L. Harper
%A J. D. Kingston
%A G. J. Armelagos
%T The origin and antiquity of syphilis revisited: An Appraisal of
   Old World pre-Columbian evidence for treponemal infection
%J Am. J. Physical Anthropology
%V 146
%N Suppl. 53
%P 99-133
%M NOV
%D 2011
%K jrnl, c2011, c201x, c20xx, STD, syphilis, syphillis, medicine, venereal,
   disease, Treponema pallidum, bacterium, bacteria, chancre,
   Columbus, 1493, 1490s, c1490, c149x, old world, new world, origin
%X "For nearly 500 years, scholars have argued about the origin & antiquity of
   syphilis. Did Columbus bring the disease from the New World to the Old World?
   Or did syphilis exist in the Old World before 1493? ... evaluate all 54 publ.
   reports of pre-Columbian, Old World treponemal disease using a standardized,
   systematic approach. The certainty of diagnosis & dating of each case is
   considered, & novel information pertinent to the dating of these cases, inc.
   radiocarbon dates, is presented. Among the reports, we did not find a single
   case of Old World treponemal disease that has both a certain diagnosis & a
   secure pre-Columbian date. We also demonstrate that many of the reports use
   nonspecific indicators to diagnose treponemal disease, do not provide
   adequate info. about the methods used to date specimens, & do not include
   high-quality photographs of the lesions of interest. Thus, despite an
   increasing # of publ. reports of pre-Columbian treponemal infection, it
   appears that solid evidence supporting an Old World origin for the disease
   remains absent."
   -- [<A HREF="http://dx.doi.org/10.1002/ajpa.21613">doi:10.1002/ajpa.21613</A>]['13].
   (Also see The G. [<A HREF="http://www.theguardian.com/science/2013/oct/27/wellcome-prize-katherine-wright-syphilis-columbus">www</A>]['13].)

%A I. R. Schwab
%T Evolution's Witness: How Eyes Evolved
%I OUP
%P 328
%M NOV
%D 2011
%K book, OUP, text, c2011, c201x, c20xx, zz1211, evolution, eye, eyes,
   trilobite, Cambrian, Euglena, biology, biol, intelligent design
%X 1st ed 2011; hb us$51; uk us isbn:0195369742 ; uk us isbn13:978-0195369748 .
   "... the 1st known eye appeared in a trilobite during the Cambrian
   explosion ~543 million years ago. ... a crucible of evoln & teemed with
   anatomic creativity although the journey to formed vision actually began
   billions of years before that. The Cambrian period, however, spawned nearly
   all morphologic forms of the eye, followed by descent over hundreds of
   m.years providing an unimaginable variety of eyes with at least ten
   different designs. Some eyes display spectacular creativity with mirror,
   scanning or telephoto optics. Some of these ocular designs are merely
   curiosities, while others offer the finest visual potential packed into a
   small space ltd only by the laws of diffraction or physiological optics. ..."

%A E. S. Reich
%T Three-dimensional technique on trial. Critics take a hard look at
   ankylography, a proposed method for revealing molecular structures from
   single pictures
%J Nature
%V 480
%N 7377
%P ?-?
%M DEC
%D 2011
%K news, views, MolBio, c2011, c201x, c20xx, zz1211, ankylography, protein,
   tertiary, structure, reconstruction, 3D, image, imaging, picture, laser, Miao
%X "Imagine developing a detailed and accurate three-dimensional model from a
   single two-dimensional photograph. That is the promise of ankylography ...
   subjects such as complex proteins that can be glimpsed only once before they
   are destroyed by the high-powered lasers used to image them. ... developed by
   John Miao, a physicist at [UCLA] ..."
   -- [<A HREF="http://dx.doi.org/10.1038/480303a">doi:10.1038/480303a</A>]['11].
   [Also search for: MolBio ankylography].

%A R. J. Read
%A et al
%T A new generation of crystallographic validation tools for the
   Protein Data Bank
%J Structure
%V 19
%D 10
%P 1395-1412
%M OCT
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0724, MolProbity, PDB,
   protein 3D structure, validation, validate, VTF, Richardson
%X "... The Task Force recommends that a small set of validation data be
   presented in an easily understood format, relative to both the full PDB & the
   applicable resolution class, with greater detail available to interested
   users. ... recommend that referees & editors judging the quality of
   structural experiments have access to a concise summary of well-established
   quality indicators. ..."
   -- [<A HREF="https://doi.org/10.1016%2Fj.str.2011.08.006">doi:10.1016%2Fj.str.2011.08.006</A>]['24].
   [Also search for: protein structure validation].

%A D. Sasseta
%A et al ...
%A C. Bandi
%T Phylogenomic evidence for the presence of a flagellum and cbb3 oxidase in the
   free-living mitochondrial ancestor
%J J. Mol. Biol. Evol.
%V 28
%N 12
%P 3285-3296
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, zz0112, evolution, eukaryote, prokaryote,
   origins, mitochondria, Candidatus Midichloria mitochondrii, genome,
   Rickettsiales, FMA, flagellum, eukaryogenesis, eukaryotes, biol, biology
%X "... two broad and competing [hypotheses]: [b] that the host was a
   phagocytotic proto-eukaryote that preyed upon the free-living mitochondrial
   ancestor (hereafter FMA), & [b] the host was an archaebacterium that
   engaged in syntrophy with the FMA. ... Reconstructions of the FMA based on
   genome content of Rickettsiales representatives - generally considered to be
   the closest living relatives of mitochondria - indicate that it was
   nonmotile & aerobic. We have sequenced the genome of Candidatus Midichloria
   mitochondrii, ... it possesses unique gene sets found in no other R., inc.
   26 genes assoc. with flagellar assembly, & a cbb3-type cytochrome oxidase.
   ... & indicate that the FMA possessed a flagellum, & could undergo oxidative
   phosphorylation under both aerobic & microoxic conditions. ... indicate that
   the FMA played a more active & potentially parasitic role in eukaryogenesis
   than currently appreciated & provide an explanation for how the symbiosis
   could have evolved under low levels of oxygen."  [online Jun 2011].
   -- [<A HREF="http://dx.doi.org/10.1093/molbev/msr159">doi:10.1093/molbev/msr159</A>]['11].

%A P. Machanick
%A T. L. Bailey
%T MEME-ChIP: Motif analysis of large DNA datasets
%J J. Bioinformatics
%V 27
%N 12
%P 1696-1697
%D 2011
%K jrnl, MolBio, c2011, c201x, c20xx, meme chip, ChIP seq, ChIPseq, motifs,
   AME, DREME, binding, peaks, ChIPed TF, RhodesUni, ZA, viaAJM
%X "... MEME-ChIP web service is designed to analyze ChIP-seq 'peak region' -
   short genomic regions surrounding declared ChIP-seq 'peaks'. ...
   performs (i) ab initio motif discovery, (ii) motif enrichment analysis,
   (iii) motif visualization, (iv) binding affinity analysis & (v) motif
   identification. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btr189">doi:10.1093/bioinformatics/btr189</A>]['13],
   auth1@[<A HREF="http://homes.cs.ru.ac.za/philip/">ru.ac.za</A>], via ajm.

%A D. S. Marks
%A L. J. Colwell
%A R. Sheridan
%A T. A. Hopf
%A A. Pagnani
%A R. Zecchina
%A C. Sander
%T Protein 3D structure computed from evolutionary sequence variation
%J PLoS One
%V 6
%N 12
%P e28766
%M DEC
%D 2011
%K jrnl, eJrnl, MolBio, PLoSone, c2011, c201x, c20xx, zz0112, protein, 3D,
   structure, prediction, EVfold, ev fold, evolution, sequence space,
   evolutionary couplings
%X "The evolutionary trajectory of a protein through seq. space is constrained
   by its fn. Coll'ns of seq.homologs record the outcomes of millions of evol.
   experiments ... ask whether we can infer evol.constraints from a set of
   seq.homologs of a protein. The challenge is to distinguish true co-evolution
   couplings from the noisy set of observed correlations. We address this
   challenge using a max.ent.model of the protein seq., constrained by the
   stats. of the multiple seq.alignment, to infer residue pair couplings.
   Surprisingly, we find that the strength of these inferred couplings is an
   excellent predictor of residue-residue proximity in folded structs.. [&] the
   top-scoring residue couplings are sufficiently accurate & well-distributed to
   define the 3D protein fold with remarkable accuracy. We quantify ... by
   computing, from seq. alone, all-atom 3D structures of fifteen test proteins
   from different fold classes ... inc. a G-protein coupled receptor. ...
   [the] signals provide sufficient info. to determine accurate 3D protein
   structure to 2.7-4.8A C(a)-RMSD error ... over at least 2/3 of the p. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0028766">doi:10.1371/journal.pone.0028766</A>]['12],
   & @[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/22163331">pubm'd</A>]['12].
   Also see [<A HREF="http://evfold.org/">evfold.org</A>]['12], and
   [also search for: MolBio EVfold].


%A Z. Zhang
%A C. Xing
%A L. Wang
%A B. Gong
%A H. Liu
%T IndelFR: A database of indels in protein structures and their
   flanking regions
%J NAR
%V 40
%N D1
%P D512-D518
%M JAN
%D 2012
%K NAR, MolBio, c2012, c201x, c20xx, zz0618, protein, gap, gaps, indel, indels
%X "Recent studies showed that indels could affect their flanking regions and
   they are important for protein function and evolution. ... The IndelFR DB
   contains 2,925,017 indels with flanking regions extracted from 373,402
   structural alignment pairs of 12,573 non-redundant domains from 1053
   superfamilies. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gkr1107">doi:10.1093/nar/gkr1107</A>]['18].
   [Also search for: MolBio protein indels].

%A D. T. Jones
%A D. W. Buchan
%A D. Cozzetto
%A M. Pontil
%T PSICOV: Precise structural contact prediction using sparse inverse
   covariance estimation on large multiple sequence alignments
%J J. Bioinformatics
%V 28
%N 2
%P 184-190
%M JAN
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz1014, Psicov, structure, contact map,
   protein, residue, contacts, predict, predicting, prediction
%X "... present a novel method, PSICOV, which intro. the use of sparse inverse
   covariance estn to the problem of protein contact predn. ... builds on work
   which had prev. demo. corrections for phylogenetic & entropic correlation
   noise & allows accurate discrimination of direct from indirectly coupled
   mutation correlns in the MSA. ... displays a mean precision substantially
   better than the best performing normalized mutual info. approach & Bayesian
   n/ws. For 118 out of 150 targets, the L/5 (i.e. top-L/5 predns for a protein
   of length L) precision for long-range contacts (seq. separation > 23) was
   >= 0.5, which represents an improvement sufficient to be of sig. benefit in
   p.struct. predn or model quality assessment."   [via AK.]
     "... 21x21 sample covariance matrix
         S_ij^ab = (1/n)SUM_k=1..n (x_i^ak - x~_i^a)(x_j^bk - x~_j^b) where
      x_i^ak is a binary variable (x in {0,1}) indicating the
      presence or absence of AA type a at col i in row k and
      x_j^bk ... type b at column j in row k. ..."
      [i.e., for each position pair (i,j) get a 21x21 cov. mat.]
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btr638">doi:10.1093/bioinformatics/btr638</A>]['14] (open).
      psicov@[<A HREF="http://bioinf.cs.ucl.ac.uk/downloads">ucl.ac</A>]['12].

%A R. Giancarlo
%A D. Scaturro
%A F. Utro
%T Textual data compression in computational biology: Algorithmic techniques
%J Comp. Sci. Review
%V 6
%N 1
%P 1-25
%M JAN
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0314, bioinformatics, compress,
   model, compression, information, encoding, DNA, protein
%X "... Rather surprisingly, the use of data compression is pervasive in
   computational biology. Starting from that one, the focus of this companion
   review is on the computational methods involved in the use of data compn in
   comp.biol.. Indeed, although one would expect ad hoc adaptation of
   compression techniques to work on biological data, unifying & homogeneous
   algorithmic approaches are emerging. Moreover, given that experiments based
   on parallel sequencing are the future for biological research, data
   compression techniques are among a handful of candidates that seem able,
   successfully, to deal with the deluge of sequence data they produce;
   although, until now, only in terms of storage & indexing, with the analysis
   still being a challenge ..."  [225 refs.]
   -- [<A HREF="http://dx.doi.org/10.1016/j.cosrev.2011.11.001">doi:10.1016/j.cosrev.2011.11.001</A>]['14].
   [Also search for: MolBio compression].

%A L.-M. Chen
%A et al ...
%A R. O. Donis
%T In vitro evolution of H5N1 avian influenza virus toward human-type receptor
   specificity
%J Virology
%V 422
%N 1
%P 105-113
%M JAN
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, flu, H5N1, H5, HA, virus, viral, human,
   transmission, transmissible, infection, illness, disease, pandemic, alpha23,
   alpha2-3, sialosides, S227N, D187G, E190G, Q196R, Q226L, G228S
%X "Acquisition of alpha2-6 sialoside receptor specificity by alpha2-3 specific
   highly-pathogenic avian influenza viruses (H5N1) is thought to be a prereq.
   for efficient transmission in h.. By in vitro selection for binding alpha2-6
   sialosides, we identified 4 variant viruses with a.acid subst. in the
   hemagglutinin (S227N, D187G, E190G, & Q196R) that revealed modestly increased
   alpha2-6 & minimally decreased alpha2-3 binding by glycan array analysis.
   However, a mutant virus combining Q196R with mutations from prev.pandemic
   viruses (Q226L & G228S) revealed predominantly alpha2-6 binding. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.virol.2011.10.006">doi:10.1016/j.virol.2011.10.006</A>]['12].

%A W. E. Collins
%T Plasmodium knowlesi: A Malaria parasite of monkeys and humans
%J Annual Rev. of Entomology
%V 57
%P 107-121
%M JAN
%D 2012
%K MolBio, c2012, c201x, c20xx, zz1114, Asia, medicine, health, malaria,
   Plasmodium knowlesi, malariae, Anopheles leucosphyrus, mosquito,
   monkey, human, transmission, risks
%X "P.knowlesi is a malaria parasite of monkeys of SE Asia that is transmitted
   by mosquitoes of the Anopheles leucosphyrus group. Humans are frequently
   infected with this parasite & misdiagnosed as being infected with P.malariae.
   The parasite was a major monkey animal model for developing antimalarial
   vaccines & investigations of the biology of parasite invasion. P.knowlesi
   is the first monkey malaria parasite genome to be sequenced and annotated."
   -- [<A HREF="http://dx.doi.org/10.1146/annurev-ento-121510-133540">doi:10.1146/annurev-ento-121510-133540</A>]['14].
   [Also search for: Plasmodium knowlesi].

%A A. J. Wargacki
%A et al ...
%A Y. Yoshikuni
%T An engineered microbial platform for direct biofuel production from brown
   macroalgae
%J Science
%V 335
%N 6066
%P 308-313
%M JAN
%D 2012
%K jrnl, c2012, c201x, c20xx, alga, algae, algal, macroalgae,
   macroalga, seaweed, Ecoli, E coli, Vibrio splendidus, alginate,
   ethanol synthesis, bioethanol, biofuel, BAL, renewable, sustainable
%X "Prospecting macroalgae (seaweeds) as feedstocks for bioconversion into
   biofuels & commodity chem.compounds is limited primarily by the availability
   of tractable microorganisms that can metabolize alginate polysaccharides.
   ... present the discovery of a 36-kbp DNA fragment from Vibrio splendidus
   encoding enzymes for alginate transport & metabolism. The genomic integration
   of this ensemble, together with an engineered system for extracellular
   alginate depolymerization, generated a microbial platform that can
   simultaneously degrade, uptake, & metabolize alginate. When further
   engineered for ethanol synthesis, this platform enables bioethanol production
   directly from macroalgae via a consolidated process, achieving a titer of
   4.7% vol/vol & a yield of 0.281 weight ethanol/weight dry macroalgae
   (equiv. to ~80% of the max theoretical yield from the sugar composition in
   macroalgae)."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1214547">doi:10.1126/science.1214547</A>]['12].
    & [<A HREF="http://dx.doi.org/10.1126/science.335.6066.273">news</A>]['12].

%A H. S. Greig
%A P. Kratina
%A P. L. Thompson
%A W. J. Palen
%A J. S. Richardson
%A J. B. Shurin
%T Warming, eutrophication, and predator loss amplify subsidies between
   aquatic and terrestrial ecosystems
%J Global Change Biol.
%V 18
%N 2
%P 504-514
%M FEB
%D 2012
%K jrnl, c2012, c201x, c20xx, ecosystem, ecosystems, top predator loss,
   global warming, CO2, climate change, carbon balance
%X "... demonstrated that predatory fish decoupled aquatic & terrestrial
   ecosystems by reducing the emergence of aquatic organisms & suppressing the
   decomposition of terrestrial plant detritus. [V.] warming & nutrients
   enhanced cross-ecosystem exchanges by increasing emergence & decomposition,
   & these effects were strongest in the absence of predators. Furthermore, we
   found that warming advanced while predators delayed the phenology of insect
   emergence. ... demonstrate that anthropogenic perturbations may extend well
   beyond ecosystem boundaries by influencing cross-ecosystem subsidies. We
   find that these changes are sufficient to substantially impact recipient
   communities & potentially alter the carbon balance between aquatic &
   terrestrial ecosystems & the atmosphere."  [online Oct '11].
   -- [<A HREF="http://dx.doi.org/10.1111/j.1365-2486.2011.02540.x">doi:10.1111/j.1365-2486.2011.02540.x</A>]['13],
   lab@[<A HREF="http://faculty.forestry.ubc.ca/richardson/">ubc</A>]['13].

%A B. E. Murdoch
%A M. L. Ng
%A C. H. Barwood
%T Treatment of articulatory dysfunction in Parkinson's disease using repetitive
   transcranial magnetic stimulation
%J Euro. J. Neurol.
%V 19
%N 2
%M FEB
%D 2012
%P 340-347
%K jrnl, c2012, c201x, c20xx, zz0913, human health, magnet, stimulate,
   UQ, uniQld, controversial, University, Queensland, withdrawl, retraction,
   scandal, ethics, integrity, fraud, authorship,
   academic, misconduct, scientific, research
%X "... High-frequency (5Hz) rTMS was applied to 10 active stimulation & 10
   sham placebo patients for 10 min/day (3000 pulses), for 10 days & speech
   outcome measures & lingual kinematic params. recorded at baseline & 1 week,
   2 & 12 months post-stimulation. The findings demonstrated +ve treatment-
   -related changes observed in the active rTMS group when compared to the sham
   placebo control group at 2 & 12 months post-stimulation in speech
   intelligibility, communication efficiency ratio, maximum velocity of tongue
   movements & distance of tongue movements. ..."  [online Oct 2011.]
   -- [<A HREF="http://dx.doi.org/10.1111/j.1468-1331.2011.03524.x">doi:10.1111/j.1468-1331.2011.03524.x </A>]['13].
      ALSO SEE, "... The University released a statement today saying that
      'no primary data can be located, & no evidence has been found that
      the study described in the article was conducted.'"
      -- [<A HREF="http://www.abc.net.au/news/2013-09-03/uq-investigates-study-that-might-never-have-happened/4932648">abc</A>][3/9/2013].
      And, "... Queensland's Crime and Misconduct Commission (CMC) has now
      accepted that finding. ..."
      -- [<A HREF="http://www.abc.net.au/news/2013-11-07/uq-investigates-fresh-claims-of-research-misconduct/5077276">abc</A>][8/11/2013].
      Later, "... issues involve 'attribution of authorship' in a small number
      of papers and the "statistical approach" taken in one. ..."
      -- [<A HREF="http://www.abc.net.au/news/2014-01-21/more-concerns-over-uq-academics-accused-of-fabricating-study/5210838">abc</A>][21/1/2014].
   [Also search for: misconduct] & [also search for: transcranial stimulation].

%A M. Hajiaghayi
%A A. Condon
%A H. H. Hoos
%T Analysis of energy-based algorithms for RNA secondary structure prediction
%J BMC Bioinformatics
%V 12
%P 22
%M FEB
%D 2012
%K jrnl, eJrnl, MolBio, c2012, c201x, c20xx, zz0212, algorithm, RNA,
   secondary structure, prediction, free energy, MFE, MEA, accuracy
%X "... Minimum free energy (MFE) predictions are widely used ... three main
   findings. First, using the bootstrap percentile method, we show that the
   avg F-measure accuracy of the MFE & (pseudo-)MEA-based algs, as measured on
   our largest datasets with over 2000 RNAs from diverse families, is a reliable
   est (within a 2% range with high confidence) of the accuracy of a popn of RNA
   molecules represented by this set. However, average accuracy on smaller
   classes of RNAs such as a class of 89 Group I introns used previously in
   benchmarking alg accuracy is not reliable enough to draw meaningful
   conclusions about the relative merits of the MFE & MEA-based algs. Second, on
   our large datasets, the alg with best overall accuracy is a pseudo MEA-based
   alg of Hamada et al. that uses a generalized centroid estimator of base
   pairs. However, between MFE & other MEA-based methods, there is no clear
   winner in the sense that the relative accuracy of the MFE versus MEA-based
   algs changes depending on the underlying energy parameters. Third, of the
   four param.sets we considered, the best accuracy for the MFE-, MEA-based, &
   pseudo-MEA-based methods is 0.686, 0.680, & 0.711, resp (on a scale from 0
   to 1 ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-13-22">doi:10.1186/1471-2105-13-22</A>]['12].

%A A. Y. Mulkidjaniana
%A A. Yu Bychkovc
%A D. V. Dibrova
%A M. Y. Galperine
%A E. V. Koonin
%T Origin of first cells at terrestrial, anoxic geothermal fields
%J PNAS
%V ?
%P ?-?
%M FEB
%D 2012
%K PNAS, jrnl, c2012, c201x, c20xx, origins, life, cell, cells, protocell,
   geothermal, pool, pools, earth
%X "All cells contain much more potassium, phosphate, & transition metals than
   modern (or reconstructed primeval) oceans, lakes, or rivers. Cells maintain
   ion gradients by using sophisticated, energy-dependent membrane enzymes
   (membrane pumps) that are embedded in elaborate ion-tight membranes. The 1st
   cells could possess neither ion-tight membranes nor membrane pumps, so the
   concentrations of small inorganic molecules & ions within protocells & in
   their environment would equilibrate. Hence, the ion composition of modern
   cells might reflect the inorganic ion composition of the habitats of
   protocells. We attempted to reconstruct the 'hatcheries' of the 1st cells ...
   ... inference primordial, proteins & functional systems show affinity to &
   functional requirement for K+, Zn2+, Mn2+, & phosphate. ... must have evolved
   in habitats with a high K+/Na+ ratio & relatively high concentrations of Zn,
   Mn, & phosphorous ... compatible with emissions of vapor-dominated zones of
   inland geothermal systems. ... shallow ponds of condensed & cooled
   geothermal vapor that were lined with porous silicate minerals mixed with
   metal sulfides and enriched in K+, Zn2+, and phosphorous compounds."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1117774109">doi:10.1073/pnas.1117774109</A>]['12], online Feb 2012.

%A D. C. Price
%A et al ...
%A D. Bhattacharya1
%T Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and
   plants
%J Science
%V 335
%N 6070
%P 843-847
%M FEB
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0212, genome, nGenome, alga, algae,
   Cyanophora paradoxa, algal, plant, plants, photosynthesis, photosynthetic,
   plastid, organelle, eukaryote, Plantae, evolution, Chlamydiae, Chlamydia,
   cytosol, glaucophyte, CCMP329
%X "The primary endosymbiotic origin of the plastid in eukaryotes more than
   1 billion years ago led to the evolution of algae & plants. We analyzed
   draft genome & transcriptome data from the basally diverging alga Cyanophora
   paradoxa & provide evidence for a single origin of the primary plastid in
   the eukaryote supergroup Plantae.  C.paradoxa retains ancestral features of
   starch biosynthesis, fermentation, & plastid protein translocation common
   to plants & algae but lacks typical eukaryotic light-harvesting complex
   proteins. Traces of an ancient link to parasites such as Chlamydiae were
   found in the genomes of C.paradoxa & other Plantae. Apparently, Chlamydia-
   -like bacteria donated genes that allow export of photosynthate from the
   plastid & its polymerization into storage polysaccharide in the cytosol."
      "... 70 Mbp nuclear genome from the glaucophyte C.paradoxa
      CCMP329 (Pringsheim strain)  ... 27,921 C. paradoxa proteins ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1213561">doi:10.1126/science.1213561</A>]['12].

%A R. Secord
%A et al ...
%A J. Krigbaum
%T Evolution of the earliest horses driven by climate change in the
   paleocene-eocene thermal maximum
%J Science
%V 335
%N 6071
%P 959-962
%M FEB
%D 2012
%K jrnl, biology, c2012, c201x, c20xx, horse, mammal, body, size, temperature,
   CO2, global warming, equine, equid, Paleocene-Eocene Thermal Maximum, PETM,
   small, little, Bergmann's rule, Sifrhippus
%X "... many mammals became smaller during the Paleocene-Eocene Thermal Maximum
   (PETM), but the timing and magnitude of that change relative to climate
   change have been unclear. A high-resolution record of continental climate &
   equid body size change shows a directional size decrease of ~30% over the
   first ~130,000 y. of the PETM, followed by a ~76% increase in the recovery
   phase of the PETM. These size changes are -ve correl. with temp. inferred
   from oxygen isotopes in mammal teeth & were probably driven by shifts in
   temp. & possibly high atmospheric CO2 concentrations. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1213859">doi:10.1126/science.1213859</A>]['12],
   and [<A HREF="http://dx.doi.org/10.1126/science.1219233">comment</A>]['12].

%A B. P. Blackburne
%A S. Whelan
%T Measuring the distance between multiple sequence alignments
%J Bioinformatics
%V 28
%N 4
%P 495-502
%M FEB
%D 2012
%K MolBio, c2012, c201x, c20xx, zz0321, distance between sequence alignments,
   difference, multiple alignment, MSA, sum pairs, total column count, score
%X "... By measuring the differences between inferred alignments, we may be able
   to develop an understanding of how these differences (i) relate to the
   objective fns & heuristics used in MSA methods, & (ii) affect downstream
   analyses. Results: We introduce four metrics to compare MSAs, which include
   the posn in a seq. where a gap occurs or the location on a phylogenetic tree
   where an insertion or deletion (indel) event occurs. ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btr701">doi:10.1093/bioinformatics/btr701</A>]['21].

%A B. Winney
%A et al ...
%A W. Bodmer
%T People of the British Isles: Preliminary analysis of genotypes and
   surnames in a UK-control population
%J Euro. J. Human Genetics
%V 20
%N 2
%P 203-210
%M FEB
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0314, Leslie, human, genetics, Europe,
   UK, Britain, POBI, PoBI, project, population, structure, genotype, HLA-A,
   HLAA, DRB1, SNP, SNPs, haplotypes, regions, regional, surname, peoples,
   Anglo Saxon, Viking, Norman
%X "...  describe the collection of a cohort of rural UK samples (The People of
   the British Isles), aimed at providing a well-characterised UK-control
   popn that can be used as a resource by the research community, as well as
   providing a fine-scale genetic information on the British popn. ... some 4000
   samples have been collected, the majority of which fit the criteria of
   coming from a rural area & having all four grandparents from ~ the same area.
   Analysis of the first 3865 samples that have been geocoded indicates that 75%
   have a mean distance between grandparental places of birth of 37.3km, & that
   about 70% of grandparental places of birth can be classed as rural. Prelim.
   genotyping of 1057 samples demonstrates the value of these samples for
   investigating a fine-scale popn struct. within the UK, & shows how this can
   be enhanced by the use of surnames."
      "... genotyped as replication controls for WTCCC2 on both the
   Illumina 1.2M and Affymetrix v6.0 whole-genome SNP platforms ..."
   -- [<A HREF="http://dx.doi.org/10.1038/ejhg.2011.127">doi:10.1038/ejhg.2011.127</A>]['14],
      pdf@[<A HREF="http://www.peopleofthebritishisles.org/pobipaper.pdf">pobi</A>]['14],
      [<A HREF="http://www.peopleofthebritishisles.org/">PoBI</A>]['14].
   [auth_8, Stephen Leslie, @mcri Melb 2013.]

%A A. Scally
%A et al ...
%A R. Durbin
%T Insights into hominid evolution from the gorilla genome sequence
%J Nature
%V 483
%P 169-175
%M MAR
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0312, gorilla, nGenome, genome, genes,
   primates, great apes, evolution, chimpanzee
%X "... propose a synthesis of genetic & fossil evidence consistent with placing
   the human-chimpanzee & human-chimp.-gorilla speciation events at ~ 6 & 10
   million years ago. In 30% of the genome, gorilla is closer to human or
   chimp. than the latter are to each other; this is rarer around coding genes,
   indicating pervasive seln throughout great ape evolution, & has functional
   consequences in gene expression. A comparison of protein coding genes reveals
   ~ 500 genes showing accelerated evolution on each of the gorilla, human &
   chimpanzee lineages, & evidence for parallel acceleration, particularly of
   genes involved in hearing. We also compare the western & eastern gorilla
   species, est. an avg. seq. divergence time 1.75 million years ago ..."
   "... EMBL accession numbers FR853080 to FR853106 ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature10842">doi:10.1038/nature10842</A>]['12].

%A Y. Kanfi
%A et al ...
%A H. Y. Cohen
%T The sirtuin SIRT6 regulates lifespan in male mice
%J Nature
%V 438
%P 218-221
%M MAR
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, age, ageing, process, gene, SIRT 6, SIRT6,
   lifespan, mouse, sirtuins, sirtuin
%X "... the role of the seven mammalian sirtuins, SIRT1 to SIRT7 (homologues of
   the yeast sirtuin Sir2), in regulating lifespan is unclear. ...show that male
   but not female transgenic mice overexpressing Sirt6 have a sig.longer
   lifespan than wild-type mice. Gene expression analysis revealed sig.diffs.
   between male Sirt6-transgenic mice & male wild-type mice: transgenic males
   displayed lower serum levels of insulin-like growth factor 1 (IGF1), higher
   levels of IGF-binding protein 1 & altered phosphorylation levels of major
   components of IGF1 signalling, a key pathway in the regulation of lifespan.
   ... shows the reg'n of mammalian lifespan by a sirtuin family member & has
   important therapeutic implications for age-related diseases." [online Feb].
   -- [<A HREF="http://dx.doi.org/10.1038/nature10815">doi:10.1038/nature10815</A>]['12].
   [Also search for: lifespan ageing].

%A J. R. Stewart
%A C. B. Stringer
%T Human evolution Out of Africa: The role of refugia and climate change
%J Science
%V 335
%N 6074
%P 1317-1321
%M MAR
%D 2012
%K jrnl, c2012, c201x, c20xx, human, evolution, origins, Africa, migration,
   Neandertal, neanderthal, Denisovan, speciation, refuge, refugium
%X "Although an African origin of the modern human species is generally accepted
   the evol.processes involved in the speciation, geog.spread, & eventual
   extinction of archaic h. outside of A. are much debated. An additional
   complexity has been the recent evidence of limited interbreeding between
   modern h. & the Neandertals & Denisovans. Modern h. migrations & interactions
   began during the buildup to the Last Glacial Maximum, starting ~100,000y ago.
   By examining the history of other organisms through glacial cycles, valuable
   models for evol. biogeography can be formulated. According to one such model,
   the adoption of a new refugium by a subgroup of a species may lead to
   important evolutionary changes."  [128 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1215627">doi:10.1126/science.1215627</A>]['12].

%A A. Adamatzky
%A et al ...
%A X.-S. Yang
%T Are motorways rational from slime mould's point of view?
%J arXiv
%M MAR
%D 2012
%K TR, c2012, c201x, c20xx, zz0312, slime mould, mold, motorway, freeway, road,
   system, Physarum polycephalum, optimization, optimisation, Randic index
%X "We analyse ... experimental lab. approxn of motorways n/works with slime
   mould Physarum polycephalum ... For each geog.entity we repd major urban
   areas by oat flakes & inoculated the slime mould in a capital. After SM
   spanned all urban areas with a n/wk of its protoplasmic tubes we extracted a
   generalised Physarum graph from the n/w & compared the graphs with an
   abstract motorway graph using most common measures.  ... found that the SM
   approx. best of all the motorway graphs of Belgium, Canada & China, & that
   for all entities studied the best match between Physarum & motorway g. is
   detected by the Randic index (molecular branching index)."  [56 refs].
   -- arxiv.[<A HREF="http://arxiv.org/abs/1203.2851">1203.2851</A>]['12],
      auth1@[<A HREF="http://uncomp.uwe.ac.uk/adamatzky/">uwe</A>]['12].
   [Also search for: slime mold].

%A D. B. Stouffer
%A M. Sales-Pardo
%A M. I. Sirer
%A J. Bascompte
%T Evolutionary conservation of species' roles in food webs
%J Science
%V 335
%N 6075
%P 1489-1492
%M MAR
%D 2012
%K jrnl, c2012, c201x, c20xx, ecology, ecological, food web, webs, network,
   species, role, roles, community, stability, nestedness
%X "... It remains unclear ... how much a community's persistence depends on the
   identities of the species present, or how much the role played by each
   species varies as a fn of the community in which it is found. We measured
   species' roles by studying how s. are embedded within the overall n/wk & the
   subs. dynamic implications. Using data from 32 empirical food webs, we find
   that species' roles & dynamic importance are inherent species attributes &
   can be extrap. ... on the basis of taxonomic class'n alone. ..." [65 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1216556">doi:10.1126/science.1216556</A>]['12].
   (Also see [<A HREF="http://dx.doi.org/10.1038/nature12380">comment</A>]['13].)

%A J. J. Smith
%A K. Sumiyama
%A C. T. Amemiya
%T A living fossil in the genome of a giving fossil: Harbinger transposons in
   the Coelacanth genome
%J Mol. Biol. Evol.
%V 29
%N 3
%P 985-993
%M MAR
%D 2012
%K jrnl, MBE, MolBio, c2012, c201x, c20xx, repeats, LatiHarb, LatiHarb1,
   harbi harbi1, naif, naif1, tsnare, tsnare1, transposon,
   fish, Coelacanth, Latimeria chalumnae
%X "... repetitive complement. This analysis uncovered a class of interspersed
   elts (Latimeria Harbinger 1-LatiHarb1) that is a major contributor to
   coelacanth genome structure & gene content (~1% to 4% or the g.).  Seq.
   analyses indicate that 1) each ~8.7 kb LatiHarb1 elt contains two coding
   regions, a transposase gene & a gene whose fn is as yet unknown (MYB-like)
   & 2) copies of LatiHarb1 retain biological activity in the coelacanth genome.
   Functional analyses verify transcriptional & enhancer activities of LatiHarb1
   in vivo & reveal transcriptional decoupling that could permit MYB-like genes
   to play functional roles not directly linked to transposition. Thus,
   LatiHarb1 represents the first known instance of a harbinger-superfamily
   transposon with contemporary activity in a vertebrate genome. ... corroborate
   the notion that exaptation of anciently active harbinger elements gave rise
   to at least two vertebrate genes (harbi1 & naif1) & indicate that the
   vertebrate gene tsnare1 also traces its ancestry to this transposon
   superfamily. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/molbev/msr267">doi:10.1093/molbev/msr267</A>]['13].
   [Also search for: Coelacanth].
  (Also see assembly@[<A HREF="http://asia.ensembl.org/Latimeria_chalumnae/">ens'mble</A>]['13],
   2gbp, 19,569 coding genes.)

%A Y. Qi
%A M. Oja
%A J. Weston
%A W. S. Noble
%T A unified multitask architecture for predicting local protein properties
%J PLoS One
%V 7
%N 3
%P e32235
%M MAR
%D 2012
%K jrnl, eJrnl, MolBio, c2012, c201x, c20xx, zz0114, protein, local, prediction,
   secondary structure, property, properties
%X "... we propose to use multitask learning to train a single, joint model that
   exploits the dependencies among these various [protein] labeling tasks. We
   describe a deep neural network architecture that, given a p.seq., outputs a
   host of predicted local properties, including secondary structure, solvent
   accessibility, transmembrane topology, signal peptides & DNA-binding
   residues. The n/w is trained jointly on all these tasks in a supervised
   fashion, augmented with a novel form of semi-supervised learning in which the
   model is trained to distinguish between local patterns from natural &
   synthetic p.seqs.. The task-independent architecture of the n/w obviates the
   need for task-specific feature engineering. We demo. that, for all of the
   tasks that we considered, our approach leads to stat.sig. improvements in
   performance, relative to a single task neural n/w approach, & that the
   resulting model achieves state-of-the-art performance."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0032235">doi:10.1371/journal.pone.0032235</A>]['14],
    & [<A HREF="http://noble.gs.washington.edu/papers/qi2012unified.html">u.wash</A>]['14].

%A J. Haidt
%T The Righteous Mind: Why Good People Are Divided by Politics and Religion
%I Pantheon
%P 448
%M MAR
%D 2012
%K book, text, c2012, c20x, c20xx, right, wrong, morality, religion, moral,
   ethics, culture, politics, left, right, liberal, conservative, group, tribe,
   tribal, groupishness, human behaviour
%X 1st ed 2012; hb us$18; uk us isbn:0307377903; isbn13:978-0307377906.
   "... starting point is moral intuition - the nearly instantaneous perceptions
   we all have ... . These intuitions feel like self-evident truths, making us
   righteously certain that those who see things differently are wrong. H. shows
   us how these intuitions differ across cultures, inc. the cultures of the
   political left and right. ... to draw a map of the moral domain, & he
   explains why conservatives can navigate that map more skillfully than can
   liberals. He then examines the origins of morality, overturning the view that
   evolution made us fundamentally selfish creatures. But rather than arguing
   that we are innately altruistic, he makes a more subtle claim - that we are
   fundamentally groupish. It is our groupishness, he explains, that leads to
   our greatest joys, our religious divisions, & our political affiliations.
   ... shows what each side is right about, & why we need the insights of
   liberals, conservatives, and libertarians to flourish as a nation."
   [Also search for: left right politics].

%A J. T. Simpson
%A R. Durbin
%T Efficient de novo assembly of large genomes using compressed data structures
%J Genome Res.
%V 22
%N 3
%P 549-556
%M MAR
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz1114, DNA, SGA, sequence assembly,
   string graph, stringGraph, denovo
%X "... present memory efficient data structures & algs. for assembly using the
   FM-index derived from the compressed Burrows-Wheeler transform, & a new
   assembler based on these called SGA (String Graph Assembler). ...  algs. to
   error-correct, assemble, & scaffold large sets of seq.data. SGA uses the
   overlap-based string graph model of assembly, unlike most de novo assemblers
   that rely on de Bruijn graphs, & is simply parallelizable. We demonstrate the
   error correction & assembly performance of SGA on 1.2 billion seq.reads from
   a human genome, which we are able to assemble using 54GB of memory. The
   resulting contigs are highly accurate & contiguous, while covering 95% of the
   ref.genome (exc. contigs < 200bp in length). Because of the low memory
   requirements & parallelization without requiring inter-process communication,
   SGA provides the first practical assembler to our knowledge for a
   mammalian-sized genome on a low-end computing cluster."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.126953">doi:10.1101/gr.126953</A>]['14].
   [Also search for: MolBio sequence assembly] and
   [also search for: MolBio stringGraph].

%A H. A. David
%T First (?) occurrence of common terms in mathematical statistics
%J The American Statistician
%V 49
%N 2
%P 121-133
%M MAY
%D 1995
%K jrnl, c1995, c199x, c19xx, zz1017, stats, statistics, terms, term,
   terminology, jargon, probability, II, first, use, origins
%X "A list of over 300 terms commonly used in math. stat. is presented with
   their apparent first occurrence in print. Some of the more interesting
   problems encountered in preparing the list are described."
   -- [<A HREF="https://www.jstor.org/stable/2684625">Jstor</A>]['17]
   or [<A HREF="https://doi.org/10.2307/2684625">doi:10.2307/2684625</A>]['17],
      [<A HREF="https://doi.org/10.1080/00031305.1995.10476129">doi:10.1080/00031305.1995.10476129</A>]['17].
   And in 1998,
   'First ... - A Second List, with Corrections',
   The Amer. Stat'n, 52(1), 36-40, 1998
   -- [<A HREF="https://doi.org/10.1080/00031305.1998.10480535">doi:10.1080/00031305.1998.10480535</A>]['19].

%A J. Hopper
%A E. Makalic
%A D. Schmidt
%A M. Bui
%A J. Stone
%A M. Kapuscinski
%A D. Park
%A M. Jenkins
%A M. Southey
%T 'Next-generation' genome wide association studies
%J Hered. Cancer in Clin. Pract.
%V 10
%P #A48
%M APR
%D 2012
%K jrnl, MolBio, GWAS, c2012, c201x, c20xx, zz0720, stats, Illumina 5M SNP,
   SNPs, breast cancer
%X "The 1st wave of cancer ... (GWAS) have revealed tens of indep. loci marked
   by common variants of unknown or likely no functional significance that
   explain about 5-10% of familial risk for the particular disease. The approach
   taken to date has been conservative ... the Bonferroni procedure for
   selecting candidate phase II SNPs ignores many SNPs that happen to fail an
   extremely low p-value threshold. While ... does guarantee control of false
   ^ves, it seems counterintuitive to the purpose of phase I, which is to gen.
   hypotheses based on promising candidates. ... It is plausible that more info.
   should be extracted if: (i) higher order interactions are fitted, (ii) highly
   selected cases and controls are used in phase I, (iii) large replication
   studies are used, esp. if involving existing GWAS data, (iv) the non-indep.
   of SNPs is taken into account using, e.g. BEAGLE CALL or haplotype analyses,
   (v) focus is on candidate gene pathways, and/or functional SNPs, and
   (vi) rarer and more SNPs, such as is available from the Illumina 5M SNP chip,
   are used. ... also discuss the design of a large int. breast cancer GWAS
   using the Illumina 5M SNP chip, phase I cases enriched for family history,
   pop'n-based phase II cases and controls, pop'n-based family study of
   candidate SNPs, and GxG analyses using 'massively parallel' super computing."
   -- [<A HREF="https://doi.org/10.1186/1897-4287-10-S2-A48">doi:10.1186/1897-4287-10-S2-A48</A>]['20].
   [Also search for: GWAS].

%A M. Baker
%T Proteomics: The interaction map
%J Nature
%V 484
%P 271-275
%M APR
%D 2012
%K news, views, c2012, c201x, c20xx, zz0512, MolBio, protein interaction, PPI,
   network, map, yeast two-hybrid, luminescence-based mammalian interactome,
   Y2H, LUMIER, fragment complementation, PCA, mammalian interaction trap,
   MAPPIT
%X "... Although the two research groups had explored the full colln of proteins
   in the same organism using the same yeast two-hybrid (Y2H) assay, the two
   papers found fewer than 150 interactions in common - only 10% of the findings
   that either team dubbed high quality. Most scientists regarded the results as
   so riddled with artefacts that they were useless. ... Besides Y2H, lower-
   -throughput tests in mammalian cells can be used to screen interactions;
   these tests include luminescence-based mammalian interactome (LUMIER),
   mammalian protein-protein interaction trap (MAPPIT), protein arrays &
   protein-fragment complementation assay (PCA). Although these are orders of
   magnitude slower than Y2H, they can probe interactions in a more relevant
   context. ..." [12 refs].
   -- [<A HREF="http://dx.doi.org/10.1038/484271a">doi:10.1038/484271a</A>]['12].

%A A. Q. Zhou
%A C. S. O'Hern
%A L. Regan
%T The power of hard-sphere models: Explaining side-chain dihedral angle
   distributions of Thr and Val
%J Biophys J.
%V 102
%N 10
%P 2345-2352
%M MAY
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0523, protein structure, dihedral angle,
   angles, local, side chain, sideChain, Thr, Val, probability distribution
%X "...  we investigate to what extent simple hard-sphere models can be used to
   predict side-chain conformations. The dist'n of the side-chain d.angle x1 of
   Val & Thr in proteins of known structure show distinctive features ... can be
   explained using only local steric interactions in a dipeptide mimetic. Our
   results emphasize the power of simple physical approaches & their importance
   for future advances in protein engineering and design."
   -- [<A HREF="https://doi.org/10.1016/j.bpj.2012.01.061">doi:10.1016/j.bpj.2012.01.061</A>]['23].
   [Also search for: MolBio protein side chain].

%A P. Pringle
%A S. P. Smiley
%T Experiment Eleven: Dark Secrets Behind the Discovery of a Wonder Drug
%I WalkerAndCo
%P 288
%M MAY
%D 2012
%K book, text, c2012, c201x, c20xx, zz0512, biol, biology, medical, medicine,
   ethics, law, case, scientific, science, scandal, research, academic,
   microbiology, Selman Waksman, Albert Schatz, streptomycin, drug, MTB, TB,
   Mycobacterium tuberculosis, big pharma, bacterium, antibiotic, patent,
   Nobel prize, NobelPrize, academic misconduct
%X 1st ed 2012; hb us$18; uk us isbn:0802717748; uk us isbn13:978-0802717740.
   "In 1943, Albert Schatz, a young Rutgers College Ph.D. student, worked on a
   wartime project in microbiol. Prof. Selman Waksman's lab, searching for an
   antibiotic to fight infections on the front lines & at home. In his 11th
   experiment on a common bacterium found in farmyard soil, AS discovered
   streptomycin, the first effective cure for tuberculosis, one of the world's
   deadliest diseases. As director of AS's research, SW took credit for the
   discovery, belittled AS's work, & secretly enriched himself with royalties
   from the s.patent filed by the pharmaceutical company Merck. In an
   unprecedented lawsuit, young AS sued SW, & was awarded the title of
   'co-discoverer' & a share of the royalties. But two years later Prof.SW alone
   was awarded the Nobel Prize. AS disappeared into academic obscurity..."

%A J. L. Stein
%A et al ...
%A P. M. Thompson
%T Identification of common variants associated with human hippocampal and
   intracranial volumes
%J Nature Genetics
%V ?
%P ?-?
%M APR
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0412, brain, size, volume, IQ, hippocampus,
   hippocampal, gene, association, rs7294919, rs10784502, TESC, HMGA2, DDR2
%X "... volume of the hippocampus is a biomarker of incipient Alzheimer's
   disease & is reduced in schizophrenia, major depression ... report genome-
   -wide assoc. meta-analyses & replication for mean bilateral hippocampal,
   total brain & intracranial vols. from a large multinational consortium. The
   intergenic variant rs7294919 was assoc. with hippocampal vol. (12q24.22;
   N=21,151; P=6.70 * 10^-16) & the expression levels of the positional
   candidate gene TESC in brain tissue. [&] rs10784502, located within HMGA2,
   was assoc. with intracranial vol. (12q14.3; N=15,782; P=1.12 * 10^-12).
   We also identified a suggestive assoc. with total brain volume at rs10494373
   within DDR2 (1q23.3; N=6,500; P=5.81 * 10^-7)."  [online Apr 2012].
   -- [<A HREF="http://dx.doi.org/10.1038/ng.2250">doi:10.1038/ng.2250</A>]['12].
   (IQ difference depends on a change of a C to a T;
   HMGA2 previously linked with height.)

%A V. B. Pinheiro
%A et al ...
%A P. Holliger
%T Synthetic genetic polymers capable of heredity and evolution
%J Science
%V 336
%N 6079
%P 341-344
%M APR
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0412, enzyme, artificial DNA, polymer,
   life, six, XNA, XNAs, base, bases
%X "... show that genetic information can be stored in & recovered from six
   alternative genetic polymers based on simple nucleic acid architectures not
   found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers,
   which bind their targets with high affinity & specificity, demonstrating that
   beyond heredity, specific XNAs have the capacity for Darwinian evolution &
   folding into defined structures. Thus, heredity & evolution, two hallmarks of
   life, are not limited to DNA & RNA but are likely to be emergent properties
   of polymers capable of information storage."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1217622">doi:10.1126/science.1217622</A>]['12].
   [Also search for: XNA MolBio].

%A J. Glynn
%T My Sister Rosalind Franklin: A Family Memoir
%I OUP
%P 160
%M APR
%D 2012
%K book, text, OUP, MolBio, history, DNA, structure, double helix,
   c2012, c201x, c20xx, zz0912, woman, women, science, scientist, Watson, Crick
%X 1st ed 2012; hb us$28; uk us isbn:0199699623; uk us isbn13:978-0199699629.
   "Rosalind Franklin is famous in the history of sci. for her contribution to
   the discovery of the structure of DNA, ... about how her work was affected
   by her position as a woman scientist. Above all she was a distinguished
   scientist, not only in her work on DNA, but also in her earlier work on
   coals & carbons & in her later work on viruses.
   ... her sister, the writer & historian JG, paints a full picture of R.'s
   life. ... her early education, her time as a science student at Cambridge,
   & her relations with her family, to her life as an adult & her time in
   Paris & at King's, G. shows how much her sister achieved & how she was
   influenced by the social & intellectual climate of the period she worked in."
   [Also search for: Rosalind Franklin DNA].

%T Nanopore-Based Technology
%I Humana
%S Methods in Molecular Biology
%P 278
%M APR
%D 2012
%K book, text, MolBio, Biol, c2012, c201x, c20xx, zz0512, Oxford, nanpore,
   nano pore, high throughput, DNA, single molecule, SMRT, sequencing
%X 1st ed 2012; hb us$120; uk us isbn:1617797723; uk us isbn13:978-1617797729.
   "Nanopores ... tiny holes in cellular membranes used for recognition &
   transport of ions and molecules between compartments within the cell, ...
   ... leads toward the promise of ultra-fast sequencing of DNA molecules ...
   volume covers single molecule characterization techniques utilizing
   biological pores, ... artificial membranes, computational studies ..."
   [Also search for: MolBio nanopore]  and
   [also search for: MolBio single molecule sequencing].

%A B. Chern
%A I. Ochoa
%A A. Manolakos
%A A. No
%A K. Venkat
%A T. Weissman
%T Reference based genome compression
%J arXiv
%M APR
%D 2012
%K TR, MolBio, c2012, c201x, c20xx, zz0814, resequencing, DNA, differences,
   reference based genome compression, hg18
%X "... propose an alg. to compress a target genome given a known reference
   genome. The proposed alg. first generates a mapping from the ref. to the
   target g., & then compresses this mapping with an entropy coder. As an
   illustration of the performance: applying our alg. to James Watson's g. with
   hg18 as a ref., we are able to reduce the 2991 megabyte (MB) genome down to
   6.99 MB, while Gzip compresses it to 834.8 MB."
   -- 1204.1912@[<A HREF="http://arxiv.org/abs/1204.1912">arXiv</A>]['14].

%A Yuan-Ping Pang
%A S. Brimijoin
%A D. W  Ragsdale
%A Kun Yan Zhu
%A R. Suranyi
%T Novel and viable acetylcholinesterase target site for developing effective
   and environmentally safe insecticides
%J Curr. Drug Targets
%A. 2012 Apr;
%V 13
%N 4
%P 471-482
%M APR
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0820, pest, insect, aphid, insecticide,
   acetylcholinesterase, AChE, anticholinesterase, cysteine, cys, Cys289, 2AZG,
   inhibitor, AMTS13, anti-malaria, mosquito
%X "... This review summarizes the lit. data that support the hypothesis that an
   insect-specific cysteine residue located at the opening of the
   acetylcholinesterase active site is a promising target site for developing
   new insecticides with reduced off-target toxicity & low propensity for insect
   resistance. ... discuss the differences between targeting the insect-specific
   cysteine residue & targeting the ubiquitous catalytic serine residue of
   acet... ... Also discussed is the prospect of developing cysteine-targeting
   antichol... as effective & environmentally safe insecticides for control of
   disease vectors, crop damage, & residential insect pests within the financial
   confines of the present insecticide market."
   -- [<A HREF="https://doi.org/10.2174/138945012799499703">doi:10.2174/138945012799499703</A>]['20].
   [Also search for: MolBio insecticide].

%A E. Pennisi
%T Genome sequencing: Search for pore-fection
%J Science
%V 336
%N 6081
%M MAY
%D 2012
%K news, MolBio, c2012, c201x, c20xx, zz0512, DNA, single molecule, SMRT,
   sequence, sequencing, nano pore, Oxford Nanopore Technologies, Brown,
   next generation, solid state, Kawai
%X "At long last, nanopore sequencing seems poised to leave the lab, promising a
   new & better way to decode DNA. In a packed Florida conf.center 3 months ago,
   Clive Brown ... Oxford Nanopore has promised to sell its new protein-pore
   sequencers by the end of the year ... Brown reported decoding a 48,000-base
   genome of a bacteriophage, a virus that infects bacteria, by first linking
   the ends of the two strands of its DNA, then threading the entire genome,
   first one strand & then the other, through a pore in one pass. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.336.6081.534">doi:10.1126/science.336.6081.534</A>]['12].
      Also see 'Going Solid-State', E. Pennisi,
   "... many in the field envision replacing these biological channels with
   solid-state ones. ...Since 2005, Tomoji Kawai, a physical chemist at Osaka U.
   [&] colleagues have experimented with a pore in a silicon wafer ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.336.6081.536">doi:10.1126/science.336.6081.536</A>]['12].
   [Also search for: MolBio nanopore] and
   [also search for: MolBio single molecule sequencing].

%A M. Y. Dennis
%A et al ...
%A E. E. Eichler
%T Evolution of human-specific neural SRGAP2 genes by incomplete segmental
   duplication
%J Cell
%V ?
%N ?
%P ?-?
%M MAY
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0512, human evolution, brain, homo,
   Australopithecus, man, gene, development, duplication, SRGAP 2, SRGAP2,
   SRGAP2B, SRGAP2C, SRGAP2D, Slit-Robo Rho GTPase-activating protein,
   duplicate
%X "... show that the promoter & first nine exons of SRGAP2 duplicated from
   1q32.1 (SRGAP2A) to 1q21.1 (SRGAP2B) ~3.4 m.years ago (mya). Two larger
   duplications later copied SRGAP2B to chr. 1p12 (SRGAP2C) & to proximal
   1q21.1 (SRGAP2D) ~2.4 & ~1 mya, resp.. Seq. & expression analyses show
   that SRGAP2C is the most likely duplicate to encode a functional protein &
   is among the most fixed human-specific duplicate genes. Our data suggest a
   mechanism where incomplete duplication created a novel gene function -
   antagonizing parental SRGAP2 function - immediately 'at birth' 2-3 mya, which
   is a time corr.to the transition from Australopithecus to Homo & the
   beginning of neocortex expansion." [online May 2012].
   -- [<A HREF="http://dx.doi.org/10.1016/j.cell.2012.03.033">doi:10.1016/j.cell.2012.03.033</A>]['12].

%A D. Sarewitz
%T Beware the creeping cracks of bias
%J Nature
%V 485
%N 7397
%P 149
%M MAY
%D 2012
%K views, c2012, c201x, c20xx, zz0512, science, scientific research, stats,
   bias, biases, drug trial, trials, study, studies, findings, replication,
   positive, false, results
%X "... Bias is an inescapable elt of research, esp. in fields such as
   biomedicine that strive to isolate cause-effect relations in complex systems
   in which relevant vars. & phenomena can never be fully identified or
   characterized. Yet if biases were random, then multiple studies ought to
   converge on truth. Evidence is mounting that biases are not random. A Comment
   in Nature in March reported that researchers at Amgen were able to confirm
   the results of only six of 53 'landmark studies' in preclinical cancer
   res. (C. G. Begley & L. M. Ellis Nature 483, 531-533; 2012). For more than a
   decade, & with increasing freq., scientists & journalists have pointed out
   similar problems. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/485149a">doi:10.1038/485149a</A>]['12].
   [Also search for: Ioannidis Research].

%A J. de Silva
%T BRCA1/2 mutations, fertility and the grandmother effect
%J Proc. Royal Soc. B
%V ?
%P ?-?
%M MAY
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0512, breast cancer, BRCA1, BRCA2,
   carrier, tolomere, telomeres, female, fertility, mutation, ageing,
   grandmothers, human health, stats, antagonistic pleiotropy theory
%X "Various mutations in the 'breast cancer genes' BRCA1 and BRCA2 increase the
   lifetime risks of developing breast & ovarian cancers to high levels ...
   a recent study showing that BRCA1/2 mutations increase female fertility
   (# of children born) by nearly 50% demands a reanalysis of the seln operating
   on these alleles. ... One answer may be the grandmother effect. ..."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2012.0542">doi:10.1098/rspb.2012.0542</A>]['12] (online May 2012).

%A M. F. Berger
%A et al ...
%A L. A. Garraway
%T Melanoma genome sequencing reveals frequent PREX2 mutations
%J Nature
%V 485
%P 502-506
%M MAY
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0612, melanoma, genome, skin cancer,
   sun exposure, burn, gene, genes, PREX2, PTEN, Rac, mutation
%X "... sequenced the genomes of 25 metastatic melanomas & matched germline DNA.
   A wide range of point mutn rates was observed: lowest in m. whose primaries
   arose on non-UV-exposed hairless skin of the extremities (3 & 14 / Mb ...),
   intermediate in those originating from hair-bearing skin of the trunk
   (5-55/Mb), & highest in a patient with a doc.history of chronic sun exposure
   (111/Mb). Analysis of whole-g. seq. data identified PREX2
   (phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2) -
   a PTEN-interacting protein & -ve regulator of PTEN in breast cancer - as a
   sig. mutated gene with a mutn freq. of ~ 14% ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11071">doi:10.1038/nature11071</A>]['12].

%A T. Conway
%A J. Wazny
%A A. Bromage
%A J. Zobel
%A B. Beresford-Smith
%T Gossamer - a resource efficient de novo assembler
%J J. Bioinformatics
%V ?
%P ?-?
%M MAY
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0512, sequence, assembly, DNA,
   Gossamer, space, short read, de novo, deNovo, deBruijn
%X "... have developed Gossamer, an implementation of the de Bruijn approach to
   assembly that requires close to the theoretical minimum of memory, but still
   allows efficient processing. Our results show that it is space efficient,
   and produces high quality assemblies."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bts297">doi:10.1093/bioinformatics/bts297</A>]['12].
   [Also search for: sequence assembly MolBio].

%A P. A. Karplus
%A K. Diederichs
%T Linking crystallographic model and data quality
%J Science
%V 336
%N 6084
%P 1030-1033
%M MAY
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0512, protein, Xray, X-ray, crystallography,
   quality, data, precision, accuracy, structure, determination, resolution,
   Rmerge, CC*, CCstar
%X "... refinement R values measure the agreement b/ween obs. & calc.data.
   Analogously, R_merge values reporting on the agreement between multiple
   measurements of a given reflection are used to assess data quality. Here, we
   show that despite their widespread use, R_merge values are poorly suited for
   determining the high-res. limit & that current std protocols discard much
   useful data. We introduce a statistic that ests. the correlation of an obs.
   data set with the underlying (not measurable) true signal; this quantity,
   CC*, provides a single statistically valid guide for deciding which data are
   useful. CC* also can be used to assess model & data quality on the same
   scale, & this reveals when data quality is limiting model improvement."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1218231">doi:10.1126/science.1218231</A>]['12].
   (Also see persp.@[<A HREF="http://dx.doi.org/10.1126/science.1222162">www</A>].)

%A A. Bankevich
%A et al ...
%A P. A. Pevzner
%T SPAdes: a new genome assembly algorithm and its applications to
   single-cell sequencing
%J J. Comput. Biol.
%V 19
%N 5
%P 455-457
%M MAY
%D 2012
%K jrnl, JCB, MolBio, c2012, c201x, c20xx, zz1012, SPAdes, sequence assembly,
   DNA, sequencing, EVSC, de novo, deNovo
%X "... Assembly of single-cell data is challenging because of highly
   non-uniform read coverage as well as elevated levels of sequencing errors &
   chimeric reads. ... SPAdes, a new assembler for both single-cell & std
   (multicell) assembly, & demo. that it improves on the recently released
   E+V-SC assembler (specialized for single-cell data) & on popular assemblers
   Velvet & SoapDeNovo (for multicell data). SPAdes generates single-cell
   assemblies, providing info. about genomes of uncultivatable bacteria that
   vastly exceeds what may be obtained via trad. metagenomics studies. ...
   available@[<A HREF="http://bioinf.spbau.ru/spades">www</A>]['12] ..."
   -- [<A HREF="http://dx.doi.org/10.1089/cmb.2012.0021">doi:10.1089/cmb.2012.0021</A>]['12],
      @[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/22506599">pubmed</A>]['12].
   [Also search for: MolBio sequence assembly].

%A W. Timp
%A J. Comer
%A A. Aksimentiev
%T DNA base-calling from a nanopore Using a Viterbi algorithm
%J Biophysical J.
%V 102
%N 10
%P pL37-L39
%M MAY
%D 2012
%K jrnl, eJrnl, MolBio, c2014, c201x, c20xx, zz0714, single molecule, SMRT,
   sequencing, sequence, base calling, error, errors
%X "... demonstrate a method to decode 3-bp-resolution nanopore electrical
   measurements into a DNA seq. using a Hidden Markov model. ... shows
   tremendous potential for accuracy (~98%), even with a poor [SNR]."
   -- [<A HREF="http://dx.doi.org/10.1016/j.bpj.2012.04.009">doi:10.1016/j.bpj.2012.04.009</A>]['14].
   [Also search for: MolBio nanopore] and
   [also search for: MolBio SMRT errors].

%A Q. Liu
%A et al ...
%A W. A. Hendrickson
%T Structures from anomalous diffraction of native biological macromolecules
%J Science
%V 336
%N 6084
%P 1033-1037
%M MAY
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0512, protein, Xray, X-ray, crystallography,
   multi single wavelength anomalous diffraction, SAD, MAD
%X "... Typical de novo phase evalns depend on incorporating heavier atoms than
   those found natively; most commonly, multi- or single-wavelength anomalous
   diffraction (MAD or SAD) experiments exploit selenomethionyl proteins. Here,
   we realize routine structure determination using intrinsic anomalous
   scattering from native macromolecules. We devised robust procedures for
   enhancing the signal-to-noise ratio in the slight anomalous scattering from
   generic native structures by combining data measured from multiple crystals
   at lower-than-usual x-ray energy. Using this multicrystal SAD method (5-13
   equiv. crystals), we determined structures at modest resolution (2.8 to 2.3A)
   for native proteins varying in size (127-1148 unique residues) & # of sulfur
   sites (3 to 28). With no requirement for heavy-atom incorporation, such
   exps. provide an attractive alternative to selenomethionyl SAD exps.."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1218753">doi:10.1126/science.1218753</A>]['12].
   (Also see persp.@[<A HREF="http://dx.doi.org/10.1126/science.1222162">www</A>].)

%A B.-A. S. Bhullar
%A et al ...
%A A. Abzhanov
%T Birds have paedomorphic dinosaur skulls
%J Nature
%V 487
%P 223-226
%M JUL
%D 2012
%K jrnl, c2012, c201x, c20xx, neoteny, evolution, bird, birds, dinosaur, skull,
   brain, size, shape, infant, juvenile, adult, paedomorphic, peramorphosis,
   pedomorphism, avian, morphometric, morph, morphing
%X "... analysed the variability of a series of landmarks on all known theropod
   dinosaur skull ontogenies as well as outgroups & birds. The 1st dimn of
   variability captured ontogeny, indicating a conserved ontogenetic trajectory.
   The 2nd dimn accounted for phylogenetic change towards more bird-like
   dinosaurs. Basally branching eumaniraptorans & avialans clustered with
   embryos of other archosaurs, indicating paedomorphosis. Our results reveal at
   least four paedomorphic episodes in the history of birds combined with
   localized peramorphosis (development beyond the adult state of anc.) in the
   beak. Paedomorphic enlargement of the eyes & assoc. brain regions parallels
   the enlargement of the nasal cavity & olfactory brain in mammals. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11146">doi:10.1038/nature11146</A>]['12], online May 2012.
   (Also recommended: 'After Many a Summer', by Aldous Huxley;
    uk us isbn:1566630185; uk us isbn13:978-1566630184.)

%A S. K. Pham
%A A. Sirotkin
%A G. Tesler
%A P. A. Pevzner
%A M. A. Alekseyev
%J Pathset graphs: A novel approach for comprehensive utilization of paired
   reads in genome assembly
%J J. Comput. Biol.
%V ?
%P ?-?
%M JUL
%D 2012
%K jrnl, JCB, MolBio, c2012, c201x, c20xx, zz1012, sequence assembly,
   mate pairs, pair, reads, PDBG, pathset, graph, pathsets
%X "... the recently proposed Paired de Bruijn Graph (PDBG) approach
   incorporates the mate-pair information directly in the assembly g. structure.
   However, the PDBG approach faces difficulties when the variation in the
   insert sizes is high. [So] we first transform mate-pairs into edge-pair
   histograms that allow one to better est. the dist. between edges in the
   assembly g. that represent regions linked by multiple mate-pairs. [&] we
   combine the ideas of mate-pair transformation & PDBGs to construct new data
   structs for g.assembly: pathsets & pathset graphs."
   -- [<A HREF="http://dx.doi.org/10.1089/cmb.2012.0098">doi:10.1089/cmb.2012.0098</A>]['12].
   [Also search for: MolBio sequence assembly].

%A T. A. Hopf
%A L. J. Colwell
%A R. Sheridan
%A B. Rost
%A C. Sander
%A D. S. Marks
%T Three-dimensional structures of membrane proteins from genomic sequencing
%J Cell
%V 149
%P 1-5
%M JUN
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0712, 3D, protein, structure,
   prediction, EVfold, evolutionary couplings, contacts, transmembrane
%X "... amino acid covariation in proteins, extracted from the evolutionary
   seq. record, can be used to fold transmembrane ps.. ... predict previously
   unknown 3D structures for 11 transmembrane ps. (with up to 14 helices) from
   their seqs. alone. The prediction method (EVfold_membrane) applies a maximum
   entropy approach to infer evolutionary covariation in pairs of seq. posns
   within a protein family & then generates all-atom models with the derived
   pairwise distance constraints. We benchmark ... with blinded de novo computn
   of known transmembrane p.structures from 23 families, demonstrating
   unprecedented accuracy of the method for large transmembrane ps.. We show how
   the method can predict oligomerization, functional sites, & conformational
   changes in transmembrane proteins. ..."
      "Our hypothesis is that evolution conserves interactions between residues
      that are important to maintaining structure & fn by constraining the sets
      of mutations that are accepted at interacting sites. To find these ...
      build a multiple sequence alignment..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cell.2012.04.012">doi:10.1016/j.cell.2012.04.012</A>]['12].
   [Also search for: MolBio EVfold].

%A E. Lounkine
%A et al ...
%A L. Urban
%T Large-scale prediction and testing of drug activity on side-effect targets
%J Nature
%V 486
%N 7403
%P 361-367
%M JUN
%D 2012
%K jrnl, c2012, c201x, c20xx, zz1113, MolBio, drug, drugs, interactions,
   side effects, offTargets, off targets, sideEffects, association metric,
   chemical structure, similarity
%X "... use a comp.strategy to predict the activity of 656 marketed drugs on 73
   unintended 'side-effect' targets. ~half of the predictions were confirmed,
   either from proprietary DBs unknown to the method or by new experimental
   assays. Affinities for these new off-targets ranged from 1nM to 30Î¼M. To
   explore relevance, we developed an assoc.metric to prioritize those new
   off-targets that explained side effects better than any known target of a
   given drug, creating a drug-target-adverse drug reaction network. Among these
   new associations was the prediction that the abdominal pain side effect of
   the synthetic oestrogen chlorotrianisene was mediated through its newly
   discovered inhibition of the enzyme cyclooxygenase-1. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11159">doi:10.1038/nature11159</A>]['13].
   (Also see [<A HREF="http://www.nature.com/news/project-ranks-billions-of-drug-interactions-1.14245">news</A>][26/11/2013].)

%A J. I. Sulkowska
%A et al ...
%A A. Stasiak
%T Conservation of complex knotting and slipknotting patterns in proteins
%J PNAS
%V ?
%P ?
%M JUN
%D 2012
%K jrnl, PNAS, MolBio, c2012, c201x, c20xx, zz0612, knot, knots, slip,
   slipknot, slipknots, S31, S3131, K31, K3131, protein, 3D structure,
   conserved, folding, pathway, trajectory
%X "While analyzing all available protein structures for the presence of knots
   & slipknots, we detected a strict conservation of complex k.patterns within
   & between several p.families despite their large seq.divergence. Because
   p.folding pathways leading to knotted native p.structures are slower & less
   efficient than those leading to unknotted ps. with similar size & seq., the
   strict conservation of the k.patterns indicates an important physiological
   role of knots & slipknots in these ps.. Although little is known about the
   functional role of knots, recent studies have demonstrated a protein-
   -stabilizing ability of ks. & slipks.. Some of the conserved k.patterns occur
   in ps. forming transmembrane channels where the slipknot loop seems to strap
   together the transmembrane helices forming the channel." online Jun..
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1205918109">doi:10.1073/pnas.1205918109</A>]['12]($), & auth1@[<A HREF="https://ctbp.ucsd.edu/~jsulkow/">ucsd</A>]['12].
   [Also seach for: MolBio knot protein].

%A F. Hufsky
%A K. Durhrkop
%A F. Rasche
%A M. Chimani
%A S. Bocker
%T Fast alignment of fragmentation trees
%J J. Bioinformatics
%V 28
%N 12
%P i265-i273
%M JUL
%D 2012
%K conf, MolBio, c2012, c201x, c20xx, zz0712, ISMB, mass spectography, tree,
   algorithm
%X "... Aligning fragmentation trees is computationally hard. [But] we present
   three exact algorithms for the problem: a dynamic programming (DP) algorithm,
   a sparse variant of the DP, and an Integer Linear Program (ILP). ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bts207">doi:10.1093/bioinformatics/bts207</A>]['12].

%A M. S. Bansal
%A E. J. Alm
%A M. Kellis
%T Efficient algorithms for the reconciliation problem with gene duplication,
   horizontal transfer and loss
%J J. Bioinformatics
%V 28
%N 12
%P i283-i291
%M JUL
%D 2012
%K conf, MolBio, c2012, c201x, c20xx, ISMB, gene, organism, species, tree,
   trees, duplication transfer loss, reconcile, DTL, algorithm
%X "... input consists of a gene family phylogeny & the corr. species phylogeny,
   & the goal is to reconcile the two by postulating speciation, gene
   duplication, horizontal gene transfer & gene loss events. ... referred to as
   duplication-transfer-loss (DTL) reconciliation ... present two new algs. for
   the ... problem that are dramatically faster than existing algs., both
   asymptotically & in practice. We also extend the standard ... model by
   considering distance-dependent transfer costs, which allow for more accurate
   reconciliation & give an efficient alg. for DTL reconciliation under this
   extended model. We implemented our new algs. & demonstrated up to
   100 000-fold speed-up over existing methods ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bts225">doi:10.1093/bioinformatics/bts225</A>]['12].

%A Q. Zhou
%A D. Bachtrog
%T Sex-specific adaptation drives early sex chromosome evolution in Drosophila
%J Science
%V 337
%N 6092
%P 341-345
%M JUL
%D 2012
%K jrnl, MolBio, biol, c2012, c201x, c20xx, zz0712, sex, chromosomes, evolution,
   neo, X, Y, male, female, Drosophila miranda
%X "Most species' sex chromosomes are derived from ancient autosomes and show
   few signatures of their origins. We studied the sex chromosomes of Drosophila
   miranda, where a neo-Y chr. originated only ~1 million years ago. Whole-
   -genome and transcriptome analysis reveals massive degeneration of the neo-Y,
   that male-beneficial genes on the neo-Y are more likely to undergo
   accelerated protein evolution, and that neo-Y genes evolve biased expression
   toward male-specific tissues - the shrinking gene content of the neo-Y
   becomes masculinized. In contrast, although older X chrs. show a paucity of
   genes expressed in male tissues, neo-X genes highly expressed in male-
   -specific tissues undergo increased rates of protein evolution if haploid in
   males. Thus, the response to sex-specific selection can shift at different
   stages of X differentiation, resulting in masculinization or
   demasculinization of the X-chromosomal gene content."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1225385">doi:10.1126/science.1225385</A>]['12].

%A D. Simoncini
%A F. Berenger
%A R. Shrestha
%A K. Y. J. Zhang
%T A probabilistic fragment-based protein structure prediction algorithm
%J PLoS ONE
%V 7
%N 7
%P e38799
%M JUL
%D 2012
%K jrnl, eJrnl, MolBio, c2012, c201x, c20xx, zz0712, EdaFold, protein,
   structure
%X "... present EdaFold, a new method for fragment-based protein structure
   prediction based on an Estimation of Distribution Algorithm. Fragment-based
   approaches build protein models by assembling short fragments from known
   protein structures. Whereas the probability mass functions over the fragment
   libraries are uniform in the usual case, we propose an algorithm that learns
   from previously generated decoys & steers the search toward native-like
   regions. A comparison with Rosetta AbInitio protocol shows that EdaFold is
   able to generate models with lower energies & to enhance the percentage of
   near-native coarse-grained decoys on a benchmark of proteins. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0038799">doi:10.1371/journal.pone.0038799 </A>]['12].
   [Also search for: Rosetta MolBio], a refinement of the Rosetta est. step.

%A A. James
%A J. W. Pitchford
%A M. J. Plank
%T Disentangling nestedness from models of ecological complexity
%J Naure
%V 487
%P 227-230
%M JUL
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0813, ecology, nestedness, network, networks,
   web, biol, biology, biological, diversity, species, interactions,
   model, stats
%X "... ecological communities, in which large #s of species exhibit -ve (eg,
   competition or predation) & +ve (eg, mutualism) inter'ns with one another.
   Nestedness in mutualistic ecological n/wks is the tendency for ecological
   specialists to interact with a subset of species that also interact with more
   generalist species. Recent math. & comp. analysis has suggested that such
   nestedness increases species richness. By examining prev. results & applying
   comp. approaches to 59 empirical data sets representing mutualistic plant-
   -pollinator n/wks, we show that this statement is incorrect. A simpler
   metric - the # of mutualistic partners a species has - is a much better
   predictor of individual species survival & hence, community persistence.
   Nestedness is, at best, a secondary covariate rather than a causative factor
   for biodiversity in mutualistic communities. Analysis of complex n/wks should
   be accompanied by analysis of simpler, underpinning mechanisms that drive
   multiple higher-order network properties."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11214">doi:10.1038/nature11214</A>]['13].
   (Also see [<A HREF="http://dx.doi.org/10.1038/nature12380">comment</A>]['13].)

%A E. Sanchez-Guerrero
%A E. Chen
%A M. Kockx
%A S.-W. An
%A B. H. Chong
%A L. M. Khachigian
%T IL-1beta signals through the EGF receptor and activates Egr-1 through
   MMP-ADAM
%J PLoS ONE
%V 7
%N 7
%P e39811
%M JUL
%D 2012
%K jrnl, eJrnl, MolBio, c2012, c201x, c20xx, zz1013, MMP, siRNA, Egr1, EGFR,
   scientific research, Australia, UNSW, University of New South Wales,
   Professor Levon Khachigian, NHMRC, grants, scandal, fraud,
   possible misconduct
%X "The immediate-early gene Egr-1 controls the inducible expression of many
   genes implicated in the pathogenesis of a range of vascular disorders ...
   we show that Egr-1 expression induced by IL-1beta is dependent on
   metalloproteinases (MMP) & a disintegrin & a metalloproteinase (ADAM).
   Pharmacologic MMP/ADAM inhibitors & siRNA knockdown prevent IL-1beta
   induction of Egr-1. ... Finally, we show that IL-1beta-inducible wound repair
   after mechanical injury requires both EGFR & MMP/ADAM. This study reports
   for the first time that Egr-1 induction by IL-1beta involves EGFR &
   MMP/ADAM-dependent EGFR phosphorylation."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0039811">doi:10.1371/journal.pone.0039811</A>]['13].
   [Also search for: UNSW Khachigian].
   (Also see [<A HREF="http://www.abc.net.au/news/2013-10-22/fresh-concerns-over-prof-levon-khacigian-research/5038644">abc</A>][22/10/2013].
   And [<A HREF="http://www.abc.net.au/news/2014-04-17/research-investigations-mounting-for-embattled-professor/5397516">abc</A>][16/4/2014].)

%A J. Das
%A H. Yu
%T HINT: High-quality protein interactomes and their applications in
   understanding human disease
%J BMC Sys. Biol.
%V 6
%P e92
%M JUL
%D 2012
%K jrnl, eJrnl, MolBio, c2012, c201x, c20xx, zz0415, HINT, protein, interaction,
   PPI, network, data, hub, hubs, PPI, interactome, data, human, yeast,
   Saccharomyces cerevisiae, Schizosaccharomyces pombe, Oryza sativa
%X "... a DB of high-quality protein-protein interactomes for human,
   Saccharomyces cerevisiae, Schizosaccharomyces pombe, & Oryza sativa. These
   were collected from several DBs & filtered both systematically & manually to
   remove low-quality/erroneous interactions. The resulting datasets are
   classified by type (binary physical interactions vs. co-complex assocns) &
   data source (high-throughput systematic setups vs. literature-curated
   small-scale experiments). We find strong sociological sampling biases in
   literature-curated datasets of small-scale interactions. An interactome
   without such sampling biases was used to understand n/w properties of human
   disease-genes - hubs are unlikely to cause disease, but if they do, they
   usually cause multiple disorders.  ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1752-0509-6-92">doi:10.1186/1752-0509-6-92</A>]['15].

%A M. Balter
%T Ice age tools hint at 40,000 years of bushman culture
%J Science
%V 337
%N 6094
%P 512
%M Aug
%D 2012
%K news, c2012, c201x, c20xx, human, evolution, origins, archaeology, Africa,
   prehistory, bushmen
%X "Archaeologists studying a South African cave say they have found
   44,000-year-old artifacts - including bone tools and poisoned arrowheads -
   nearly identical to those still in use by hunter-gatherers. ... calls the
   finds the oldest known examples of 'modern culture,' the adaptations that
   enabled Homo sapiens to make it through the last Ice Age and survive to the
   present day. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.337.6094.512">doi:10.1126/science.337.6094.512</A>]['12].

%A C. Koch
%T Modular biological complexity
%J Science
%V 337
%N 6094
%P 531-532
%M Aug
%D 2012
%K news, MolBio, c2012, c201x, c20xx, zz0812, biology, system, systems,
   interaction, modularity, components
%X "It has been argued that the tech. capability to fully simulate the human
   brain on digital computers will exist within a decade. This is taken to imply
   that we will comprehend its functioning, eliminate all diseases, & 'upload'
   ourselves to computers. Although such predictions excite the imagination,
   they are not based on a sound assessment of the complexity of living systems.
   ... characterized by large #s of highly heterogeneous components, be they
   genes, proteins, or cells. ... interact causally in myriad ways across a very
   large spectrum of space-time, from nanometers to meters & from mi.sec. to
   years. A complete understanding of these systems demands that a large
   fraction of these interactions be experimentally or comp.probed. This is
   very difficult. ...
   ... The discovery of modular, hierarchical structures that capture the
   behavior of complex systems in a causal manner is essential to speed up
   solving these challenging problems. This emphasizes the need to develop
   heuristic methods to discover modules. For if appropriate modules cannot be
   found, understanding of life will escape us."  [10 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1218616">doi:10.1126/science.1218616</A>]['12].

%A S. Shultz
%A E. Nelson
%A R. I. M. Dunbar
%T Hominin cognitive evolution: Identifying patterns and processes in the
   fossil and archaeological record
%J Royal Soc. Phil. Trans. B
%V 367
%P 2130-2140
%M AUG
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0719, human, intelligence, IQ, hominins,
   brain size, hominin encephalization, aeolian deposition, palaeoclimate,
   cognition, evolution, Homo erectus, Homo sapiens
%X "... Using both absolute & residual brain size estimates, we show that
   hominin brain evolution was likely to be the result of a mix of processes;
   punctuated changes at approximately 100 kya, 1 Mya & 1.8 Mya are supplemented
   by gradual within-lineage changes in Homo erectus & Homo sapiens sensu lato.
   While brain size increase in Homo in Africa is a gradual process, migration
   of hominins into Eurasia is associated with step changes at ~400 kya &
   ~100 kya. We then demonstrate that periods of rapid change in hominin brain
   size are not temporally associated with changes in environmental
   unpredictability or with long-term palaeoclimate trends. Thus, we argue that
   commonly used global sea level or Indian Ocean dust palaeoclimate records
   provide little evidence for either the variability selection or aridity
   hypotheses explaining changes in hominin brain size. Brain size change at
   approximately 100 kya is coincident with demographic change & the appearance
   of fully modern language. However, gaps remain in our understanding of the
   external pressures driving encephalization, which will only be filled by
   novel applications of the fossil, palaeoclimatic & archaeological records."
   -- [<A HREF="https://dx.doi.org/10.1098/rstb.2012.0115">doi:10.1098/rstb.2012.0115</A>]['19].
   (Also see the bbc[<A HREF="http://www.bbc.com/future/story/20190709-has-humanity-reached-peak-intelligence">10/4/2019</A>].)

%A A. Prlic
%A et al
%A S. Willis
%T BioJava: an open-source framework for bioinformatics in 2012
%J J. Bioinformatics
%V 28
%N 20
%P 2693-2695
%M AUG
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0717, biology, platform, BioJava, Java,
   openSource, protein structure, sequence alignment
%X "BioJava is an open-source project for processing of biological data in the
   Java programming language. We have recently released a new version (3.0.5),
   which is a major update to the code base that greatly extends its
   functionality. ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/bts494">doi:10.1093/bioinformatics/bts494</A>]['17].
   Also see [<A HREF="http://www.biojava.org/">www</A>]['17].
   [Also search for: BioJava].

%A A. Schurger
%A J. D. Sitt
%A S. Dehaene
%T An accumulator model for spontaneous neural activity prior to self-initiated
   movement
%J PNAS
%V ?
%N ?
%P ?-?
%M AUG
%D 2012
%K jrnl, PNAS, c2012, c201x, c20xx, zz0812, brain, free will, mind, intention,
   consciousness, self, awareness, move, readiness, Libet,
   electroencephalography, signal, human
%X "A gradual buildup of neuronal activity known as the 'readiness potential'
   reliably precedes voluntary self-initiated movements, in the avg time locked
   to movement onset. ... presumed to reflect the final stages of planning &
   preparation for movement. Here we present a different interpretation of the
   premovement buildup. We used a leaky stochastic accumulator to model the
   neural decision of 'when' to move in a task where there is no specific
   temporal cue, but only a general imperative to produce a movement after an
   unspec. delay on the order of several secs.. ...  accounts for the behavioral
   & electroencephalography data recorded from human subjects performing the
   task & also makes a specific predn that we confirmed in a 2nd
   electroencephalography experiment: Fast responses to temporally unpredictable
   interruptions should be preceded by a slow -ve-going voltage deflection
   beginning well before the interruption itself, even when the subject was not
   preparing to move at that particular moment."
   -- [<A HREF="http://www.pnas.org/content/early/2012/08/03/1210467109">pnas</A>]['12],
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1210467109">doi:10.1073/pnas.1210467109</A>]['12].
   [Also search for: Libet free will].

%A A. Kong
%A et al ...
%A K. Stefansson
%T Rate of de novo mutations and the importance of father's age to
   disease risk
%J Nature
%V 488
%N 7412
%P 471-475
%M AUG
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz1212, parent, father, age, genetic,
   mutation, rate, SNP, DNA, molecular clock, human, humans, evolution, Eve
%X "Mutations generate sequence diversity & provide a substrate for selection.
    ... a study of genome-wide mutn rates by seq. the entire genomes of 78
    Icelandic parent-offspring trios at high coverage. We show that in our
    samples, with an average father's age of 29.7, the avg de novo mutn rate is
    1.20x10^-8 per nucleotide per generation. ... the diversity in mutn rate of
    [SNPs] is dominated by the age of the father at conception of the child. The
    effect is an increase of ~two mutns/year. An exponential model ests.
    paternal mutns doubling every 16.5 y.. After accounting for random Poisson
    variation, father's age is est. to explain nearly all of the remaining
    variation in the de novo mutn counts. ... shed light on the importance of
    the f's age on the risk of diseases such as schizophrenia & autism."
    -- [<A HREF="http://dx.doi.org/10.1038/nature11396">doi:10.1038/nature11396</A>]['12].
    (NB. 1.2x10^-8 is the de novo rate; add in the mother's contribution.
    So, |genome| x 2 x rate = 6x10^9 x 10^-8 = 60/gen., if father is ~30y.o.)

%A K. E. Langergraber
%A et al ...
%A L. Vigilant
%T Generation times in wild chimpanzees and gorillas suggest earlier
   divergence times in great ape and human evolution
%J PNAS
%V 109
%N 39
%P 15716-15721
%M AUG
%D 2012
%K jrnl, PNAS, MolBio, c2012, c201x, c20xx, zz1212, primate, human, chimp,
   gorilla, Neanderthal, modern, evolution, DNA, mutation rate,
   molecular clock, Eve
%X "Fossils & molec. data are two indep. sources of info. that should in
   principle provide consistent inferences of when evolutionary lineages
   diverged. Here we use an alt. approach to genetic inference of species split
   times in recent human & ape evoln that is indep. of the fossil record. We
   first use genetic parentage info. on a large # of wild chimpanzees & mountain
   gorillas to directly infer their avg. generation times. ... compare these
   gen.time ests. with those of humans & apply recent ests. of the human
   mutn rate per gen. to derive ests. of split times of great apes & humans that
   are indep. of fossil calibration. We date the human-chimp. split to at least
   7-8 million years & the popn split between Neanderthals & modern h. to
   400,000-800,000y ago. This suggests that molec. divergence dates may not be
   in conflict with the attribution of 6- to 7-million-y-old fossils to the
   human lineage & 400,000-y-old fossils to the Neanderthal lineage. "
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1211740109">doi:10.1073/pnas.1211740109</A>]['12].
   [Also search for: MolBio Eve human evolution]  etc..

%A A. D'Hont
%A et al ...
%A P. Wincker
%T The banana (Musa acuminata) genome and the evolution of monocotyledonous
   plants
%J Nature
%V 488
%P 213-217
%M AUG
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0812, eukaryote, plant, plants, banana,
   Musa acuminata, genome, nGenome, monocotyledon, Zingiberales, commelinid,
   Poaceae, eudicotyledon, bananas, triploid, food, foods, risks
%X "Bananas (Musa spp.), inc. dessert & cooking types, are giant perennial
   monocotyledonous herbs of the order Zingiberales, a sister group to the well-
   -studied Poales, which include cereals. ... Musa domestication process
   started some 7,000 years ago in SE Asia. ... Half of the current prodn
   relies on somaclones derived from a single triploid genotype (Cavendish).
   ... draft seq. of the 523-megabase genome of a M.acuminata doubled-haploid
   genotype ... detected three rounds of whole-genome duplications ..."
   "... GenBank CAIC01000001-CAIC01024424, HE806462-HE813974, HE813975-HE813985"
   -- [<A HREF="http://dx.doi.org/10.1038/nature11241">doi:10.1038/nature11241</A>]['12] (open).
   And, "... Regardless of ploidy or genome type, b. have a haploid complement
   of 11 chromosomes:
   -- M.a@[<A HREF="http://www.ncbi.nlm.nih.gov/genome/10976">nih</A>]['12].

%A J. A. Baron
%T Aspirin and cancer: Trials and observational studies
%J J. Natl. Cancer Inst.
%V ?
%N ?
%M ?
%D 2012
%K editorial, JNCI, c2012, c201x, c20xx, health, cancer reduction, aspirin,
   asprin
%X "Aspirin recently celebrated its commercial centenary, but the exciting news
   has been a series of articles by Rothwell et al. that report on the follow-up
   of cardiovascular trials begun in the late 1970s & afterward. ... suggest
   striking efficacy of a. in reducing cancer mortality. One of the recent
   reports analyzed short-term, in-trial incidence & mortality data from 51
   trials. ... a. conferred a 31% redn in c.mortality 5-10 y. after subjects
   were randomized to study treatment, though there was essentially no redn
   during the first 5 years.  ..."  online 10 Aug..
   -- [<A HREF="http://dx.doi.org/10.1093/jnci/djs338">doi:10.1093/jnci/djs338</A>]['12].

%A E. J. Jacobs
%A C. C. Newton
%A S. M. Gapstur
%A M. J. Thun
%T Daily aspirin use and cancer mortality in a large US cohort
%J J. Natl. Cancer Inst.
%V ?
%N ?
%M ?
%D 2012
%K jrnl, JNCI, c2012, c201x, c20xx, health, cancer reduction, medication,
   daily, aspirin, asprin
%X "... trials of daily aspirin for prevention of vascular events found a
   substantial redn (rel.risk [RR] = 0.63, 95% [CI] = 0.49 to 0.82) in overall
   cancer mortality during follow-up occurring after 5 y. on aspirin. However
   the magnitude of the effect of daily a. use, particularly long-term use, on
   cancer mortality is uncertain. ..."   online 10 Aug., 10pp.
   -- [<A HREF="http://dx.doi.org/10.1093/jnci/djs318">doi:10.1093/jnci/djs318</A>]['12].

%A J. Zeng
%A G. Konopka
%A B. G. Hunt
%A T. M. Preuss
%A D. Geschwind
%A S. V. Yi
%T Divergent whole-genome methylation maps of human and chimpanzee brains
   reveal epigenetic basis of human regulatory evolution
%J Amer. J. Human Genetics
%V ?
%N ?
%P ?-?
%M AUG
%D 2012
%K MolBio, jrnl, c2012, c201x, c20xx, zz0812, DNA, methylation, epigenetics,
   brain, human, chimp, prefrontal cortex, gene expression, regulation, cancer,
   neurological, psychological, disorders
%X "... generated nucleotide-resolution whole-genome methylation maps of the
   prefrontal cortex of multiple humans & chimpanzees. Levels & patterns of DNA
   m. vary across individuals within species according to the age & the sex of
   the individuals. [&] found extensive species-level divergence in patterns of
   DNA m. & that hundreds of genes exhibit sig. lower levels of promoter m. in
   the human brain than in the chimpanzee brain. [&] investigated the functional
   consequences of m. differences in h. & c. by integrating data on gene
   expn generated with next-gen. seq. methods, & we found a strong reln between
   differential m. & gene expn. Finally ... differentially m. genes are
   strikingly enriched with loci assoc. with neurological disorders,
   psychological disorders, & cancers. ... demonstrate that differential DNA
   m. might be an important molecular mechanism driving gene-expn divergence
   between human & chimp. brains & might potentially contribute to the
   evolution of disease vulnerabilities. ..."  (online Aug 2012).
   -- [<A HREF="http://dx.doi.org/10.1016/j.ajhg.2012.07.024">doi:10.1016/j.ajhg.2012.07.024</A>]['12].

%A A. Maxmen
%T Calorie restriction falters in the long run. Genetics and healthy
   diets matter more for longevity
%J Nature
%V 488
%N 7413
%P 569
%M AUG
%D 2012
%K news, c2012, c201x, c20xx, zz0912, ageing, NIA, lifespan, old, health,
   calories, caloric, diet, dietary, intake, diet, dietary, food, eating,
   restrict, restriction
%X "... The verdict, from a 25-year study in rhesus monkeys fed 30% less than
   control animals, represents another setback for the notion that a simple,
   diet-triggered switch can slow ageing. Instead, the findings, published this
   week in Nature, suggest that genetics and dietary composition matter more
   for longevity than a simple calorie count. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/488569a">doi:10.1038/488569a</A>]['12].
   (See Mattison et al [<A HREF="http://dx.doi.org/10.1038/nature11432">doi:10.1038/nature11432</A>][9/2012].)

%A P. C. Trimmer
%A J. A.R. Marshall
%A L. Fromhage
%A J. M. McNamara
%A A. I. Houston
%T Understanding the placebo effect from an evolutionary perspective
%J Evolution and Human Behaviour
%V ?
%P ?-?
%M AUG
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0912, placebo, medicine, medication, effect,
   immune system, response, mind, psychology, model,
   Humphrey, The mind made flesh, OUP
%X "... it is initially puzzling why, if people are capable of recovering, they
   need a placebo to do so. Based on an argument put forward by Humphrey [Great
   expectations: the evol. psyc. of faith-healing & the p.effect. ... 2002 ...]
   we present simple math.models of the p.effect that involve a trade-off
   between the costs & benefits of allocating resources to a current problem.
   ... show why the effect occurs & how its magnitude & timing can depend on
   different factors. We identify a particular aspect of belief which may
   govern the effect & conclude that a deeper understanding of why the p.effect
   exists may allow it to be invoked more easily in the future." online Aug '12.
   -- [<A HREF="http://dx.doi.org/10.1016/j.evolhumbehav.2012.07.004">doi:10.1016/j.evolhumbehav.2012.07.004</A>]['12].

%A A. Perdomo-Ortiz
%A N. Dickson
%A M. Drew-Brook
%A G. Rose
%A A. Aspuru-Guzik
%T Finding low-energy conformations of lattice protein models by
   quantum annealing
%J Scientific Reports
%V 2
%P #571
%M AUG
%D 2012
%K jrnl, eJrnl, c2012, c201x, c20xx, zz1213, Dwave, quantum computing,
   lattice model of protein folding problem
%X "Lattice protein folding models are a cornerstone of comp. biophysics.
   Although these models are a coarse grained repn, they provide useful insight
   into the energy landscape of natural ps.. Finding low-energy 3D structures
   is an intractable problem even in the simplest model, the Hydrophobic-Polar
   (HP) model. Description of protein-like properties are more accurately
   described by generalized models, such as the one proposed by Miyazawa &
   Jernigan (MJ), which explicitly take into a/c the unique interactions among
   all 20 AAs. There is theor. & exp. evidence of the advantage of solving
   classical opt.problems using quantum annealing over its classical analogue
   (sim.annealing). ... present a benchmark implementation of quantum annealing
   for lattice protein folding problems (six different experiments up to 81
   superconducting quantum bits). This 1st implementation of a biophysical
   problem paves the way towards studying opt.problems in biophys. & stat.
   mechanics using quantum devices."  [50 refs]
     ("In lattice folding, the seq. of AAs defining the p. is viewed as a seq.
      of beads connected by strings (peptide bonds). This bead chain occupies
      pts on a two- or three-dimensional lattice [grid].")
   -- [<A HREF="http://dx.doi.org/10.1038/srep00571">doi:10.1038/srep00571</A>]['13].

%A F. Liu
%A et al
%T A genome-wide association study identifies five loci influencing facial
   morphology in Europeans
%J PLoS Genet.
%V 8
%N 9
%P e1002932
%D 2012
%K eJrnl, MolBio, c2012, c201x, c20xx, zz0613, DNA, genetics, genes, human,
   appearance, face, nose, PRDM16, PAX3, TP63, C5orf50, COL17A1,
   policing, police, clues, GWAS
%X "... identified five indep. genetic loci assoc. with different facial
   phenotypes, suggesting ... five candidate genes - PRDM16, PAX3, TP63,
   C5orf50, & COL17A1 - in the determination of the human face. Three of them
   have been implicated prev. in vertebrate craniofacial development & disease,
   & the remaining two genes potentially represent novel players in the molec.
   n/wks governing facial development. ... PAX3 influencing the posn of the
   nasion replicates a recent GWAS of facial features. [&] to the reported GWA
   findings, we established links between common DNA variants prev. assoc. with
   NSCL/P at 2p21, 8q24, 13q31, and 17q22 ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pgen.1002932">doi:10.1371/journal.pgen.1002932</A>]['13].

%A M. Remmert
%A A. Biegert
%A A. Hauser
%A J. Soding
%T HHblits: lightning-fast iterative protein sequence searching by
   HMM-HMM alignment
%J Nature Methods
%V 9
%P 173-175
%D 2012
%K jrnl, MolBio, HHblits, HH blits, c2012, c201x, c20xx, zz0220, protein,
   profile HMM, amino acid, multiple sequence alignment, MSA, hhblitz, blitz,
   HHsearch, HHsuite, MSA, PSIBLAST
%X "... We present an open-source, general-purpose tool that represents both
   query & database seqs. by profile hidden Markov models (HMMs): 'HMM-HMM-based
   lightning-fast iterative seq. search' (HHblits). Compared to the seq.-search
   tool PSI-BLAST, HHblits is faster owing to its discretized-profile prefilter,
   has 50-100% higher sensitivity & generates more accurate alignments."
   -- [<A HREF="https://doi.org/10.1038/nmeth.1818">doi:10.1038/nmeth.1818</A>]['20],
    & HH@[<A HREF="https://github.com/soedinglab/hh-suite">g'thub</A>]['22],
      HH@[<A HREF="https://en.wikipedia.org/wiki/HH-suite">wikip</A>]['22],
      hhblits@[<A HREF="http://toolkit.genzentrum.lmu.de/hhblits/">lmu.de</A>]['20] dead?
   [Also search for: MolBio protein alignment].

%A J. R. Ecker
%A W. A. Bickmore
%A I. Barroso
%A J. K. Pritchard
%A Y. Gilad
%A E. Segal
%T Genomics: ENCODE explained
%J Nature
%V 489
%P 52-55
%M SEP
%D 2012
%K MolBio, news, intro, c2012, c201x, c20xx, zz0912, ENCODE project, zzEncode,
   human genome, gene, genes, transcription, regulation, promoter, cell type,
   differentiation, junk, DNA
%X "The Encyclopedia of DNA Elements (ENCODE) project dishes up a hearty banquet
   of data that illuminate the roles of the functional elements of the human
   genome. Here, six scientists describe the project and discuss how the data
   are influencing research directions across many fields."
   -- [<A HREF="http://dx.doi.org/10.1038/489052a">doi:10.1038/489052a</A>]['12].
   The issue of the journal had several papers on Encode and findings.
   [Also search for: MolBio encode project] and
   [also search for: MolBio Encode c2013].

%A G. M. Weinstock
%T Genomic approaches to studying the human microbiota
%J Nature
%V 489
%N 7415
%P 250-256
%M SEP
%D 2012
%K review, MolBio, c2012, c201x, c20xx, zz0912, human, gut, microbes, bacteria
%X "The human body is colonized by a vast array of microbes, which form
   communities of bacteria, viruses & microbial eukaryotes that are specific
   to each anatomical environment. Every community must be studied as a whole
   because many organisms have never been cultured independently, & this poses
   formidable challenges. The advent of next-gen. DNA sequencing has allowed
   more sophisticated analysis & sampling of these complex sys. by culture-
   -indep. methods. ... revealing differences in community struct. between
   anatomical sites, between individuals, & between healthy & diseased states,
   & are transforming our view of human biology."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11553">doi:10.1038/nature11553</A>]['12].

%A D. J. Selkoe
%T Preventing Alzheimer's disease
%J Science
%V 337
%N 6101
%P 1488-1492
%M SEP
%D 2012
%K news, c2012, c201x, c20xx, medicine, risks, Alzheimer's, Alzheimers,
   beta amyloid, APP, PSEN1, PSEN2, exercise, preventing, prevention,
   human health
%X "... Recent clinical trial failures suggest that we must treat the disease
   earlier than in its mild to moderate stages, & major progress in validating
   presymptomatic biomarkers now makes secondary prevention trials possible.
   We will learn more about the natural history of the disease & any partial
   therapeutic responses from detailed analyses of recent trial ..."  [44 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1228541">doi:10.1126/science.1228541</A>]['12].

%A C. M. Schelbusch
%A et al ...
%A M. Jakobsson
%T Genomic variation in seven Khoe-San groups reveals adaptation and complex
   African history
%J Science
%V ?
%P ?-?
%M SEP
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, human, origins, SNPs, SNP, Khoe San, Khwe,
   Nama, evolution, out of Africa, African, populations, chromosome6, chr6,
   chromosome10, chr10
%X "The history of click-speaking Khoe-San, & African poplns in general, remains
   poorly understood. We genotyped ~2.3 million SNPs in 220 southern Africans &
   found that the K.-S. diverged from other poplns ~100,000 y.ago, but structure
   within the K.-S. dated back to about 35,000 y.ago. Genetic variation in
   various sub-Saharan poplns did not localize the origin of modern humans to a
   single geog.region within A.; instead, it indicated a history of admixture &
   stratification. ... evidence of adaptation targeting muscle fn & immune
   response, potential adaptive introgression of UV-light protection, & seln
   predating modern h. diversification involving skeletal & neurological
   development. These new findings illustrate the importance of African genomic
   diversity in understanding human evolutionary history." (online Sep 2012).
   -- [<A HREF="http://dx.doi.org/10.1126/science.1227721">doi:10.1126/science.1227721</A>]['12].

%A M. Babu
%A et al ...
%A J. F. Greenblatt
%T Interaction landscape of membrane-protein complexes in Saccharomyces
   cerevisiae
%J Nature
%V 489
%N 7417
%P 585-589
%M SEP
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0912, membrane proteins, complex,
   interaction, network, interact, eukaryote, Saccharomyces cerevisiae, yeast,
   interactome
%X "... no global characterization of MP-complex membership has been described
   so far. Here we report a complete survey of 1,590 putative integral,
   peripheral & lipid-anchored MPs from S.cerevisiae, which were affinity
   purified in the presence of non-denaturing detergents. The identities of the
   co-purifying proteins were det. by tandem mass spectrometry & subs. used to
   derive a high-confidence physical interaction map encompassing 1,726 membrane
   protein-protein interactions & 501 putative heteromeric complexes assoc. with
   the various cellular membrane sys.. ... reveals unexpected physical assoc.
   underlying the membrane biology of eukaryotes ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11354">doi:10.1038/nature11354</A>]['12].

%A G.-E. Seralini
%A et al ...
%A J. S. de Vendomois
%T Long term toxicity of a Roundup herbicide and a Roundup-tolerant genetically
   modified maize
%J Food and Chemical Toxicology
%V ?
%P ?-?
%M SEP
%D 2012
%K health, medicine, risks, c2012, c201x, c20xx, zz1012, genetically modified,
   GM, GMO, crops, crop, maize, roundup tolerant, monsanto, cancer, rat, rats,
   transgene, trial, stats, controversial
%X "The health effects of a Roundup-tolerant genetically modified maize (from
   11% in the diet), cultivated with or without Roundup, & Roundup alone (from
   0.1 ppb in water), were studied 2 years in rats. In females, all treated
   groups died 2-3 times more than controls, & more rapidly. This difference was
   visible in 3 male groups fed GMOs. ... Females developed large mammary tumors
   almost always more often than & before controls, ... males, liver congestions
   & necrosis were 2.5-5.5 times higher. ...  These results can be explained by
   the non linear endocrine-disrupting effects of Roundup, but also by the
   overexpression of the transgene in the GMO & its metabolic consequences."
   -- [<A HREF="http://dx.doi.org/10.1016/j.fct.2012.08.005">doi:10.1016/j.fct.2012.08.005</A>]['12].  Note, controversial!

%A J. Romiguier
%A V. Ranwez
%A E.J.P. Douzery
%A N. Galtier
%T Genomic evidence for large, long-lived ancestors to placental mammals
%J Mol. Biol. and Evol.
%V ?
%P ?-?
%M SEP
%D 2012
%K jrnl, MBE, MolBio, c2012, c201x, c20xx, zz1012, GC, animal, mammal,
   evolution, ancestor, size, age, life span, lifespan,
   Cretaceous, Mesozoic, Paleocene, Tertiary, early
%X "It is widely assumed that our mammalian ancestors, which lived in the
   Cretaceous era, were tiny animals that survived massive asteroid impacts ...
   modern forms after dinosaurs went extinct, 65 Mya. ... Here we use
   full-genome data to est. the longevity & body mass of early p.mammals.
   Analysing 36 fully-seq. m. genomes, we reconstruct 2 aspects of the ancestral
   genome dynamics, namely GC-content evoln & non-synonymous over synonymous
   rate ratio. ...  est. that early p.ms. had a life-span > 25y., & a body mass
   > one kg. ... similar to current primates ..." [online 4 Sept. 2012].
   -- [<A HREF="http://dx.doi.org/10.1093/molbev/mss211">doi:10.1093/molbev/mss211</A>]['12].
   (Apparently, today, GC and the ratio corr. with size and lifespan.)

%A G. Arora
%A R. Mezencev
%A J. F. McDonald
%T Human cells display reduced apoptotic function relative to chimpanzee cells
%J PLoS ONE
%V 7
%N 9
%P e46182
%M SEP
%D 2012
%K jrnl, eJrnl, MolBio, c2012, c201x, c20xx, zz1012, brain size,
   gene expression, cell death, cancer, human, chimp, fibroblastic, fibroblast
%X "Prev. published gene expression analyses suggested that apoptotic fn may be
   reduced in humans rel. to chimpanzees & led to the hypothesis that this
   difference may contribute to the relatively larger size of the human brain
   & the increased propensity of h. to develop cancer. ... we sought to further
   test the hyp. that humans maintain a reduced apoptotic fn rel. to ch. by
   conducting a series of apoptotic fn assays on h., ch. & macaque primary
   fibroblastic cells. Human cells consistently displayed sig. reduced apoptotic
   fn rel. to the ch. & macaque cells. ... consistent with earlier findings
   indicating that apoptotic fn is reduced in h. rel. to ch.."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0046182">doi:10.1371/journal.pone.0046182</A>]['12].

%A R. Fortey
%T Horseshoe Crabs and Velvet Worms: The Story of the Animals and Plants that
   Time has Left Behind
%I Knopf
%P 374
%D 2012
%O Survivors: The Animals and Plants That Time Has Left Behind
   (HarperCollins 2011)
%K book, text, c2012, c201x, c20xx, zz1012, biol, evolution, crab, arthropod,
   worm, animal, plant, old, ancient, natural history, features, survivor
%X 1st ed 2012. us$29. uk us isbn:0307263614; uk us isbn13:978-0307263612.
   Survivors..., 2011; stg25. uk us isbn13:978-0007209866.
   (Review@[<A HREF="http://dx.doi.org/10.1126/science.1228913">doi:10.1126/science.1228913</A>]['12].)

%A N. M. Daniels
%A S. Nadimpalli
%A L. J. Cowen
%T Formatt: Correcting protein multiple structural alignments by incorporating
   sequence alignment
%J BMC Bioinformatics
%V 13
%P 259
%M OCT
%D 2012
%K jrnl, eJrnl, MolBio, c2012, c201x, c20xx, zz1012, Formatt, Matt,
   protein, structure, 3D, alignment, Homstrad, SABmark, benchmark
%X "... Formatt, a multiple structure al. based on the Matt purely geometric
   multiple structure al. program, that also takes into account seq.similarity
   when constructing als.. ... F. outperforms Matt & other popular struct.
   al. programs on the popular Homstrad benchmark. For the SABmark twilight zone
   benchmark set that captures more remote homology, F. & Matt outperform other
   programs; depending on choice of embedded seq.aligner, F. produces either
   better seq. & structural als. with a smaller core size than M., or similarly
   sized als. with better seq.sim., for a small cost in average RMSD. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-13-259">doi:10.1186/1471-2105-13-259</A>]['12].

%A M. E. Allentoft
%A et al ...
%A M. Bunce
%T The half-life of DNA in bone: Measuring decay kinetics in 158 dated fossils
%J Proc. Royal Soc. B
%V ?
%P ?-?
%M OCT
%D 2012
%K jrnl, PRSB, MolBio, c2012, c201x, c20xx, zz1012, DNA, mtDNA, half life,
   decay, fossil, ancient, NZ, Moa, bone
%X "... analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of
   the extinct NZ moa, we confirm empirically a long-hypothesized exponential
   decay relationship. The avg. DNA half-life [here] was est. to be 521 years
   for a 242bp mtDNA seq., corr. to a per nucleotide fragmentation rate (k) of
   5.5*10^6 per year. ... temp. of 13.1C ... almost 400 times slower than
   predicted from publ. kinetic data of in vitro DNA depurination at pH5.
   Although best described by an exponential model (R2=0.39), considerable
   sample-to-sample variance in DNA preservation could not be accounted for by
   geologic age. This variation likely derives from differences in taphonomy &
   bone diagenesis, which have confounded previous, less spatially constrained
   attempts to study DNA decay kinetics. Lastly, by calculating DNA fragn rates
   on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice
   as fast as mtDNA. ..."   (online 10 Oct. 2012)
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2012.1745">doi:10.1098/rspb.2012.1745</A>]['12].
   ([Also search for: MolBio fossil DNA].-)

%A N. Vaidya
%A M. L. Manapat
%A I. A. Chen
%A R. Xulvi-Brunet
%A E. J. Hayden
%A N. Lehman
%T Spontaneous network formation among cooperative RNA replicators
%J Nature
%V 491
%P 72-77
%M NOV
%D 2012
%K jrnl, MolBio, RNA, c2012, c201x, c20xx, zz1012, replicator, networks,
   early, nascent, origin, evolution, life, world, Azoarcus ribozyme,
   cooperation
%X "... Here we show that mixtures of RNA fragments that self-assemble into
   self-replicating ribozymes spontaneously form cooperative catalytic cycles
   & networks. We find that a specific three-membered nw. has highly cooperative
   growth dynamics. When such cooperative nws. are competed directly against
   selfish autocatalytic cycles, the former grow faster, indicating an
   intrinsic ability of RNA pop'ns to evolve greater complexity through
   cooperation. We can observe the evolvability of nws. through in vitro
   selection. Our experiments highlight the advantages of cooperative behaviour
   even at the molecular stages of nascent life."     (online 18/10/'12.)
      "... To create a coop.nw., we fragmented the Azoarcus ribozyme into two
      pieces in three different ways with the intent of observing how they could
      spontaneously reassemble via intermolecular cooperation ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11549">doi:10.1038/nature11549</A>]['12].

%A M. S. Breen
%A C. Kemena
%A P. K. Vlasov
%A C. Notredame
%A F. A. Kondrashov
%T Epistasis as the primary factor in molecular evolution
%J Nature
%V 490
%P 535-538
%M OCT
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz1012, amino acid, substitution,
   protein, evolution, epistasis, defn, fitness, stats
%X "... unclear to what degree long-term protein evoln is constrained by
   epistasis, that is, instances when substitutions that are accepted in one
   genotype are deleterious in another. ... est. of the prevalence of e. in
   long-term protein evoln by relating data on AA usage in 14 organelle proteins
   & 2 nuclear-encoded proteins to their rates of short-term evoln. ... multiple
   alignments of at least 1,000 orthologues for each of these 16 proteins from
   species from a diverse phylogenetic b/g & ... avg. site contained ~ eight
   different AAs. ... without epistasis an avg. site should accept two-fifths of
   all possible AAs, & the avg. rate of AA subs. should ... be ~ three-fifths
   lower than the rate of neutral evoln. [But] the measured rate of AA subs. in
   recent evoln is 20x lower than the rate of neutral evoln & an order of
   magnitude lower than that expected in the absence of epistasis. ... indicate
   that e. is pervasive throughout protein evoln: about 90% of all AA subs. have
   a neutral or beneficial impact only in the genetic b/g in which they occur, &
   must therefore be deleterious in a different b/g of other species. ... show
   that most AA subs. have different fitness effects in different species &
   that e. provides the primary conceptual framework to describe the tempo &
   mode of long-term protein evoln."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11510">doi:10.1038/nature11510</A>]['12].

%A A. Alileche
%A J. Goswami
%A W. Bourland
%A M. Davis
%A G. Hampikian
%T Nullomer derived anticancer peptides (NulloPs): Differential lethal effects
   on normal and cancer cells in vitro
%J Peptides
%V ?
%P ?-?
%M SEP
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz1112, DNA, protein, nullomer, cancer,
   IC50, cell, death, kill, cells, PolyArgNulloPs, 9R, RRRRRNWMWC,
   9S1R, RRRRRWCMNW, 124R, effect, missing, absent, word, MAW, substring
%X "We demo. the 1st use of the nullomer (absent seqs.) approach to drug
   discovery & development. Nullomers are the shortest absent seqs. determined
   in a species, or group of species. By identifying the shortest absent peptide
   seqs. from the NCBI DBs, we screened several potential anti-cancer peptides.
   In order to improve cell penetration & solubility we added short poly
   arginine tails (5Rs), & initially solubilized the peptides in 1M trehalose.
   The results for one of the absent seqs. 9R (RRRRRNWMWC), & its scrambled
   version 9S1R (RRRRRWCMNW) are reported here. We refer to these peptides
   derived from nullomers as PolyArgNulloPs. A control PolyArgNulloP, 124R
   (RRRRRWFMHW), was also inc.. The lethal effects of 9R & 9S1R are mediated by
   mitochondrial impairment as demo. by increased ROS prodn, ATP depletion, cell
   growth inhibition, & ultimately cell death. These effects increase over time
   for cancer cells with a concomitant drop in IC-50 for breast & prostate
   cancer cells. This is in sharp contrast to the effects in normal cells, which
   show a decreased sensitivity to the NulloPs over time." (online Sept.)
   -- [<A HREF="http://dx.doi.org/10.1016/j.peptides.2012.09.015">doi:10.1016/j.peptides.2012.09.015</A>]['12].
   [Also search for: missing substring]  and [also search for: nullomer].

%A L. D. Ward
%A M. Kellis
%T Evidence of abundant purifying selection in humans for recently acquired
   regulatory functions
%J Science
%V 337
%N 6102
%P 1675-1678
%M SEP
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0815, regulatory, ENCODE,
   controversial
%X "Although only 5% of the human genome is conserved across mammals, a
   substantially larger portion is biochemically active, raising the q. of
   whether the additional elts evolve neutrally or confer a lineage-specific
   fitness advantage. ... integrate human variation info. from the 1000 Genomes
   Project & activity data from the ENCODE Project. A broad range of transcribed
   & regulatory nonconserved elts show decreased human diversity, suggesting
   lineage-specific purifying seln. Conversely, conserved elts lacking activity
   show increased human diversity, suggesting that some recently became
   nonfunctional. Regulatory elts under human constraint in nonconserved regions
   were found near color vision & nerve-growth genes, consistent with purifying
   seln for recently evolved fns. Our results suggest continued turnover in
   regulatory regions, with at least an additional 4% of the human genome
   subject to lineage-specific cons"
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22956687/">pubm'd</A>]['15] (free),
      [<A HREF="http://dx.doi.org/10.1126/science.1225057">doi:10.1126/science.1225057</A>]['15].
   (* BUT, "We find on closer inspection of their data that the polymorphism
         trends are primarily attributable to mutational variation & technical
         artifacts rather than seln." -- Green & Ewing,
         [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/23661742">Sci.2013</A>].
    And, [also search for: Bray Pachter c2012]. *)

%A M. Yamaguchi
%A Y. Mori
%A Y. Kozuka
%A H. Okada
%A K. Uematsu
%A A. Tame
%A H. Furukawa
%A T. Maruyama
%A C. O. Worman
%A K. Yokoyama
%T Prokaryote or eukaryote? A unique microorganism from the deep sea
%J J. Electron Microsc.
%D 2012
%V 61
%N 6
%P 423-431
%M SEP
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0915, Parakaryon myojinensis, biol,
   prokaryote, eukaryote, endosymbionts, life, organism, origins, evolution,
   cell nucleus
%X "... eukaryotes are considered to have evolved from prokaryotes, there were
   no previously known intermediate forms between them. The differences in their
   cellular structures are so vast that the problem of how es. could have
   evolved from ps. is one of the greatest enigmas in biology. Here, we report a
   unique organism with cellular structures appearing to have intermediate
   features between ps. & es., which was discovered in the deep sea off the
   coast of Japan using electron microscopy & structome analysis. The organism
   was 10 mu-m long & 3 mu-m in dia., having > 100 times the volume of E.coli.
   It had a large 'nucleoid', consisting of naked DNA fibers, with a single
   nucleoid membrane & endosymbionts that resemble bacteria, but no
   mitochondria. Because this organism appears to be a life form distinct from
   both ps. & es. but similar to es., we named this unique microorganism the
   'Myojin parakaryote' with the scientific name of Parakaryon myojinensis
   ('next to (eu)karyote from Myojin') after the discovery locn & its
   intermediate morphology. The existence of this organism is an indication of
   a potential evolutionary path between prokaryotes & eukaryotes."
   -- [<A HREF="http://dx.doi.org/10.1093/jmicro/dfs062">doi:10.1093/jmicro/dfs062</A>]['15],
      23024290@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/23024290">p'bmed</A>]['15].
   (Also see abc[<A HREF="http://www.abc.net.au/science/articles/2015/08/31/4292949.htm">4/9/2015</A>].)

%T An integrated map of genetic variation from 1,092 human genomes
%Q The 1000 Genomes Project Consortium
%J Nature
%V 491
%P 56-65
%M NOV
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz1112, genome, variations, SNP, SNPs,
   polymorphisms, insertions, deletions, thousand, humans
%X "... describe the genomes of 1,092 individuals from 14 populations,
   constructed using a combination of low-coverage whole-genome and exome
   sequencing. ... provide a validated haplotype map of 38million single
   nucleotide polymorphisms, 1.4million short insertions and deletions, and more
   than 14,000 larger deletions. We show that individuals from different
   populations carry different profiles of rare and common variants ... captures
   up to 98% of accessible single nucleotide polymorphisms at a frequency of
   1% in related populations ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11632">doi:10.1038/nature11632</A>]['12] (open),
      [<A HREF="http://www.nature.com/nature/journal/v491/n7422/full/nature11632.html">www</A>]['12].

%A N. Koga
%A R. Tatsumi-Koga
%A G. Liu
%A R. Xiao
%A T. B. Acton
%A G. T. Montelione
%A D. Baker
%T Principles for designing ideal protein structures
%J Nature
%V 491
%P 222-227
%M NOV
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz1112, protein, 3D, tertiary, structure,
   fold, folding, energy, rules, inSilico, principle, secondary, design, designs
%X "... natural proteins fold into unique ordered structs.. [How] encoded in
   AA seqs. is complicated by energetically unfavourable non-ideal features -
   for example kinked alpha-helices, bulged beta-strands, strained loops &
   buried polar groups - that arise in ps. from evol. seln for biol. fn or from
   neutral drift. ... an approach to designing ideal p.structs. stabilized by
   completely consistent local & non-local interactions. ... based on a set of
   rules relating sec.struct. patterns to protein tertiary motifs, which make
   possible the design of funnel-shaped p.folding energy landscapes leading into
   the target folded state. Guided by these rules, we designed seqs. predicted
   to fold into ideal p.structs. consisting of alpha-helices, beta-strands &
   minimal loops. Designs for five different topologies were found to be
   monomeric & very stable & to adopt structs. in soln nearly identical to the
   comp.models. ... illuminate how the folding funnels of natural ps. arise &
   provide the foundation for engineering a new gen'n of functional proteins
   free from natural evoln."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11600">doi:10.1038/nature11600</A>]['12].

%A D. Scheele
%A N. Striepens
%A O. Gunturkn
%A S. Deutschlande
%A W. Maier
%A K. M. Kendrick
%A R. Hurlemann
%T Oxytocin modulates social distance between males and females
%J J. of Neuroscience
%V 32
%N 46
%P 16074-16079
%M NOV
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz1112, oxytocin, OXT, hormone, love,
   fidelity, attachment, attraction, human, behaviour,
   man, men, male, women, female
%X "... randomized placebo-controlled trial, we provide the first behavioral
   evidence that the intranasal administration of OXT stimulates men in a
   monogamous relationship, but not single ones, to keep a much greater distance
   (~10-15cm) between themselves & an attractive woman during a 1st encounter.
   This avoidance of close personal proximity occurred in the physical presence
   of female but not male experimenters & was indep. of gaze dirn & whether the
   female experimenter or the subject was moving. We further confirmed this
   unexpected finding using a photograph-based approach/avoidance task that
   showed again that OXT only stimulated men in a monogamous reln to approach
   pictures of attractive women more slowly. ... cannot be attributed to OXT
   altering the attitude of monogamous men toward attractive w. or their
   judgments of & arousal by pictures of them. ... results suggest that where
   OXT release is stimulated during a monogamous rel'p, it may additionally
   promote its maintenance by making men avoid signaling romantic interest to
   other w. through close-approach behavior during social encounters. ... may
   help to promote fidelity within monogamous human relationships."
   -- [<A HREF="http://dx.doi.org/10.1523/JNEUROSCI.2755-12.2012">doi:10.1523/JNEUROSCI.2755-12.2012</A>]['12].
   [Also search for: oxytocin hormone].

%A S. R. Harris
%A et al ...
%A S. J. Peacock
%T Whole-genome sequencing for analysis of an outbreak of
   meticillin-resistant Staphylococcus aureus: a descriptive study
%J The Lancet
%V ?
%P ?
%M NOV
%D 2012
%K jrnl, c2012, c201x, c20xx, zz1112, golden staph, antibiotic, resistance,
   meticillin resistant Staphylococcus aureus, MRSA, superbug, bacteria,
   bacterium, medicine, medical, health, risks, infection control, hospital,
   human health
%X "... The hospital infection-control team identified 12 infants colonised with
   MRSA in a 6 month period in 2011, who were suspected of being linked, but a
   persistent outbreak could not be confirmed with conventional methods. With
   whole-genome sequencing, we identified 26 related cases of MRSA carriage ...
   ... & confirm that MRSA carriage by a staff member had allowed the outbreak
   to persist during periods without known infection on the SCBU & after a
   deep clean. ..." (online Nov 2012).
   -- [<A HREF="http://dx.doi.org/10.1016/S1473-3099(12)70268-2">doi:10.1016/S1473-3099(12)70268-2</A>]['12].

%A J. K. Wegner
%A et al ...
%A E. Willighagen
%T Cheminformatics
%J CACM
%V 55
%N 11
%P 65-75
%M NOV
%D 2012
%K jrnl, CACM, news, intro, c2012, c201x, c20xx, zz1112, chemistry, molecule,
   small, ligand, informatics, chemical compound, physical, properties, SMILES,
   PubChem, database, repository, collection, software, NIH
%X "... in 2004 a large public small-molecule structure repository
   ([<A HREF="http://pubchem.ncbi.nlm.nih.gov">PubChem</A>]) was made freely
   available by the National Library of Medicine (part of the U.S. National
   Institutes of Health) and soon followed by other databases. Likewise, while
   many of the foundational algorithms of cheminformatics have been described
   since the 1950s, open-source software implementing many of them have become
   accessible only since the mid-1990s. ..." [40 refs], via LS.
   -- [<A HREF="http://dx.doi.org/10.1145/2366316.2366334">doi:10.1145/2366316.2366334</A>]['12].

%A K. A. Dill
%A J. L. MacCallum
%T The protein-folding problem, 50 years on
%J Science
%V 338
%N 6110
%P 1042-1046
%M NOV
%D 2012
%K review, survey, intro, MolBio, c2012, c201x, c20xx, zz1112, protein fold,
   folding, 3D, tertiary structure, prediction, energy, force, forces
%X "... The term refers to three broad questions: (i) What is the physical code
   by which an amino acid seq. dictates a protein's native structure? (ii) How
   can proteins fold so fast? (iii) Can we devise a computer alg. to predict
   protein structures from their seqs.? We review progress ... In a few cases,
   computer simulations of the physical forces in chemically detailed models
   have now achieved the accurate folding of small ps.. We have learned that
   ps. fold rapidly because random thermal motions cause conformational changes
   leading energetically downhill toward the native struct., a principle that is
   captured in funnel-shaped energy landscapes. & thanks in part to the large
   PDB of known structs., predicting p.struct. is now far more successful than
   was thought poss. in the early days. What began as three Qs of basic sci.
   one half-century ago has now grown into the full-fledged res.field of
   protein physical science."  [72 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1219021">doi:10.1126/science.1219021</A>]['12].
   (Also see Pfolding@[<A HREF="https://en.wikipedia.org/wiki/Protein_folding">wikip</A>]['22].)

%A R. Brenchley
%A et al ...
%A N. Hall
%T Analysis of the bread wheat genome using whole-genome shotgun sequencing
%J Nature
%V 491
%P 705-710
%M NOV
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz1212, bread, wheat, genome, nGenome,
   Triticum aestivum, plant, hexaploid, polyploid, ploidy,
   food, crop, crops, farmed
%X "Bread wheat (Triticum aestivum) ... report the sequencing of its large,
   17-gigabase-pair, hexaploid genome using 454-pyrosequencing, & comparison of
   this with the seqs. of diploid ancestral & progenitor genomes. We identified
   between 94,000 & 96,000 genes, & assigned two-thirds to the three component
   genomes (A, B & D) of hexaploid wheat. High-resolution synteny maps
   identified many small disruptions to conserved gene order. We show that the
   hexaploid genome is highly dynamic, with sig. loss of gene family members
   on polyploidization & domestication, & an abundance of gene fragments. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11650">doi:10.1038/nature11650</A>]['12] (open).

%A A. M. Zaki
%A et al ...
%A R. A. M. Fouchier
%T Isolation of a novel Coronavirus from a man with pneumonia in Saudi Arabia
%J NEJM
%V 367
%P 1814-1820
%M NOV
%D 2012
%K jrnl, NEJM, MolBio, c2012, c201x, c20xx, zz0520, MERS, HCoV-EMC, HCoVEMC,
   MERSr, genome, SARS, middle east, camels, bats, zoonotic, virus,
   betacoronavirus, MERS1, coronavirus, corona virus, HKU4, HKU5
%X "... The virus represents a novel betacoronavirus species. The closest known
   relatives are bat coronaviruses HKU4 and HKU5. Here, the clinical data, virus
   isolation, and molecular identification are presented. The clinical picture
   was remarkably similar to that of the severe acute respiratory syndrome
   (SARS) outbreak in 2003 and reminds us that animal coronaviruses can cause
   severe disease in humans."
   -- [<A HREF="https://doi.org/10.1056/NEJMoa1211721">doi:10.1056/NEJMoa1211721</A>]['20].
    (Also see, "... virus isolated from sputum samples from a person who
    fell ill in a 2012 outbreak ..."
    -- MERS@[<A HREF="https://en.wikipedia.org/wiki/Middle_East_respiratory_syndrome-related_coronavirus">wikip</A>]['20].)
    [Also search for: coronavirus] and [also search for: MolBio SARS].

%A P. Feijao
%A J. Meidanis
%T Extending the algebraic formalism for genome rearrangements to include linear
   chromosomes
%J Advances in Bioinf. and Comp. Biol.
%I SpringerVerlag
%S LNCS
%V 7409
%P 13-24
%D 2012
%K MolBio, c2012, c201x, c20xx, zz0415, rearrangement, DNA, genome, chromosome,
   similarity, genomic distance, cut, join, DCJ, 2break,
   Kbreak, k break, distance
%X "... the order in which genes appear in chrs., & applies to circular chrs.
   only. By shifting our attention to genome adjacencies, we are able to extend
   this theory to linear chrs. in a v.natural way, & extend the dist. formula to
   the general multichromosomal case, with both linear & circular chrs.. The
   resulting distance, which we call algebraic dist. here, is v.similiar to, but
   not quite the same as, DCJ distance. We present linear time algs. to compute
   it & to sort genomes. We also show how to compute the algebraic dist. from
   the adjacency graph. Some results on more general k-break distances are given
   with algebraic dist. being 2-break dist. under our interpretation."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-31927-3_2">doi:10.1007/978-3-642-31927-3_2</A>]['15].
   [Also search for: MolBio Pevzner permutation] and
   [also search for: MolBio genomic distance].

%A B. A. Curtis
%A et al ...
%A J. M. Archibald
%T Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
%J Nature
%V 492
%P 59-65
%M DEC
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz1212, alga, algae, algal, nGenome,
   genome, genomes, photosynthesis, cryptophyte Guillardia, Bigelowiella natans,
   plastid, nucleomorph, eukaryote, endosymbiosis, evolution, transfer, genes
%X "Cryptophyte & chlorarachniophyte algae are transitional forms in the
   widespread secondary endosymbiotic acquisition of photosynthesis by
   engulfment of eukaryotic algae. ... sequenced the nuclear genomes of the
   cryptophyte Guillardia theta & the chlorarachniophyte Bigelowiella natans.
   Both genomes have >21,000 protein genes & are intron rich, & B.natans
   exhibits unprecedented alt.splicing for a single-celled organism. ...
   reveal extensive genetic & biochemical mosaicism with both host- &
   endosymbiont-derived genes servicing the mitochondrion, the host cell
   cytosol, the plastid & the remnant endosymbiont cytosol of both algae.
   Mitochondrion-to-nucleus gene transfer still occurs in both organisms but
   plastid-to-n. & nucleomorph-to-n. transfers do not, which explains why a
   small residue of essential genes remains locked in each nucleomorph."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11681">doi:10.1038/nature11681</A>]['12], open.
   [Also search for: MolBio alga], etc..

%A R. Seth
%A et al ...
%A M. A. Ros
%T Hox genes regulate digit patterning by controlling the wavelength of a
   Turing-type mechanism
%J Science
%V 338
%N 6113
%P 1476-1480
%M DEC
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, biol, Hox gene, digits, fingers, toes,
   toe, patterning, growth, repetitive, Turing, reaction diffusion, RD,
   polydactyly, polydactyl, pentadactyl, Hoxa13, Hoxd11, Hoxd12, Hoxd13,
   morphogenesis, formation, pattern
%X "The formation of repetitive structures (such as stripes) in nature is often
   consistent with a reaction-diffusion mechanism, or Turing model, of self-
   -organizing systems. We used mouse genetics to analyze how digit p. (an
   iterative digit/nondigit pattern) is generated. ... progressive redn in
   Hoxa13 & Hoxd11-Hoxd13 genes (... distal Hox genes) from the Gli3-null b/g
   results in progressively more severe polydactyly, displaying thinner &
   densely packed digits. Combined with computer modeling, ... argue for a
   Turing-type mechanism underlying digit p., in which the dose of distal Hox
   genes modulates the digit period or wavelength. The phenotypic similarity
   with fish-fin endoskeleton patterns suggests that the pentadactyl state has
   been achieved through modification of an ancestral Turing-type mechanism."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1226804">doi:10.1126/science.1226804</A>]['12].
   [Also search for: reaction diffusion].

%A N. Bray
%A L. Pachter
%T Comment on "Evidence of Abundant and Purifying Selection in Humans for
   Recently Acquired Regulatory Functions"
%J arXiv
%M DEC
%D 2012
%K TR, arXiv, c2012, c201x, c20xx, zz0214, Ward, Manolis Kellis, Barzel,
   Albert Laszlo Barabasi, network, networks, motif, discovery,
   nonsense, MolBio, controversial, scientific, research, publish, papers
%X "Ward and Kellis (Reports, Sept. 5 2012) identify regulatory regions in
   the human genome exhibiting lineage-specific constraint and estimate the
   extent of purifying selection. There is no statistical rationale for the
   examples they highlight, and their estimates of the fraction of the genome
   under constraint are biased by arbitrary designations of completely
   constrained regions."
   -- 1212.3076@[<A HREF="http://arxiv.org/abs/1212.3076">arXiv</A>]['14].
   [Also search for: Ward Kellis c2012].
   (* Also see LP@[<A HREF="http://liorpachter.wordpress.com/2014/02/12/why-i-read-the-network-nonsense-papers/">w'rdpress</A>][12/2/2014] ...
   [<A HREF="http://liorpachter.wordpress.com/2014/02/10/the-network-nonsense-of-albert-laszlo-barabasi/">w'rdpress</A>][10/2/2014]. *)

%A G. Zhang
%A et al ...
%A J. Wang
%T Comparative analysis of bat genomes provides insight into the evolution of
   flight and immunity
%J Science
%V ?
%P ?-?
%M DEC
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0113, bat, bats, DNA, genome, nGenome,
   immune system, flight, flying, animal, mammal, fruit bat, bats,
   Pteropus alecto, Myotis davidii, virus, Nipha, Hendra, Ebola, SARS, SARS1,
   virus, factor kB, factorKB
%X "... notorious reservoir hosts for some of the world's most highly pathogenic
   viruses, including Nipah, Hendra, Ebola, & severe acute respiratory
   syndrome (SARS). To identify genetic changes associated with the development
   of bat-specific traits, we performed whole-genome sequencing & comparative
   analyses of two distantly related bat species, fruit bat Pteropus alecto &
   insectivorous Myotis davidii. We discovered an unexpected concentration of
   positively selected genes in the DNA damage checkpoint & nuclear factor-kB
   pathways that may be related to the origin of flight, as well as expansion
   & contraction of important gene families.  ..."   (online Dec.'12).
   -- [<A HREF="http://dx.doi.org/10.1126/science.1230835">doi:10.1126/science.1230835</A>]['12].

%A P.V. Afonine
%A et al
%T Towards automated crystallographic structure refinement with phenix.refine
%J Acta Crystallogr. D Biol. Crystallogr.
%V 68
%P 352-367
%D 2012
%K MolBio, c2012, c201x, c20xx, zz0923, LBNL, PHENIX, protein, 3D, structure,
   refinement, x ray, Xray crystallography
%X "phenix.refine is a program within the PHENIX package that supports
   crystallographic structure refinement against experimental data with a wide
   range of upper resolution limits using a large repertoire of model
   parameterizations ..."
   -- [<A RFE="https://doi.org/10.1107/S0907444912001308">doi:10.1107/S0907444912001308</A>]['23]/
   (Also see phenix@[<A HREF="https://phenix-online.org">www</A>]['23].)

%A Soojin Yi
%T Neutrality and molecular clocks
%J Nat. Ed. Knowledge
%V 4
%N 2
%D 2013
%K intro, survey, tutorial, c213, c201x, c20xx, zz0123, MolBio, molecular clock,
   evolution, fibrinopeptide, hemoglobin, haemoglobin, cytochrome c, rate,
   neutral theory
%X "... one of the most tantalizing findings was the observation that protein
   sequence change seemed to occur at a rate proportional to the time since the
   evolutionary divergence of species. The term 'molecular clock' was coined to
   describe the phenomenon ..."
   -- [<A HREF="https://www.nature.com/scitable/knowledge/library/neutrality-and-molecular-clocks-100492542/">www</A>]['23].
   also see clock@[<A HREF="https://en.wikipedia.org/wiki/Molecular_clock">wikip</A>]['23].

%A B. De Martino
%A S. M. Fleming
%A N. Garrett
%A R. J. Dolan
%T Confidence in value-based choice
%J Nature Neuroscience
%V 16
%P 105110
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0715, decisions, human behaviour, brain,
   ventromedial prefrontal cortex, vmPFC, rostrolateral, confidence,
   decision making, choice, deMartino
%X "... How subjective confidence & valuation of choice options interact at the
   level of brain & behavior is unknown. Using a dynamic model of the decn
   process, we show that confidence reflects the evolution of a decn variable
   over time, explaining the observed reln between confidence, value, accuracy &
   reaction time. As predicted by our dynamic model, we show that a functional
   magnetic resonance imaging signal in human ventromedial prefrontal cortex
   (vmPFC) reflects both value comparison & confidence in the value comparison
   process. Crucially, individuals varied in how they related confidence to
   accuracy, allowing us to show that this introspective ability is predicted by
   a measure of functional connectivity between vmPFC & rostrolateral prefrontal
   cortex. Our findings provide a mechanistic link between noise in value
   comparison & metacognitive awareness of choice, enabling us both to want &
   to express knowledge of what we want."
   -- [<A HREF="http://dx.doi.org/10.1038/nn.3279">doi:10.1038/nn.3279</A>]['15].

%A L. Redecke
%A et al ...
%A H. N. Chapman
%T Natively inhibited Trypanosoma brucei Cathepsin B structure determined by
   using an X-ray laser
%J Science
%V 339
%N 6116
%P 227-230
%M JAN
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0113, TbCatB, X ray, Xray, crystallography,
   protein, 3D structure, determination, room temperature
%X "... combining two recent innovations, in vivo crystallization & serial
   femtosecond crystallography, we obtained the room-temperature 2.1 A resoln
   struct. of the fully glycosylated precursor complex of TbCatB. The structure
   reveals the mechanism of native TbCatB inhibition & demonstrates that new
   biomolecular info. can be obtained by the 'diffraction-before-destruction'
   approach of x-ray free-electron lasers from hundreds of thousands of
   individual microcrystals."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1229663">doi:10.1126/science.1229663</A>]['13].

%A E. E. Schadt
%A S. Woo
%A K. Hao
%T Bayesian method to predict individual SNP genotypes from
   gene expression data
%J Nature Genetics
%V 44
%P 603-608
%M JAN
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0113, genetic, privacy, person,
   personal, genome, SNP, SNPs, identify, identification, identifying, people,
   information, profiling, RNA, eQTL, eQTLs, data, anonymous
%X "... Employing published putative cis eQTLs, we developed a B.approach to
   predict SNP genotypes that is based only on RNA expn data. We show that
   predicted gs. can accurately & uniquely identify individuals in large
   popns. When inferring gs. from an expn data set using eQTLs of the same
   tissue type (but from an indep.cohort), ... able to resolve 99% of the
   identities of individuals in the cohort at P_adjusted <= 10^-5. When eQTLs
   derived from one tissue were used to predict genotypes using expn data from
   a different tissue, the identities of 90% of the study subjects could be
   resolved at P_adjusted <= 10^-5. We discuss the implications of deriving
   genotypic information from RNA data deposited in the public domain."
   -- [<A HREF="http://dx.doi.org/10.1038/ng.2248">doi:10.1038/ng.2248</A>]['13].

%A G. R. Crabtree
%T Our fragile intellect. Part I and Part II
%J Trends in Genetics
%V 29
%N 1
%P 1-3 and 3-5
%M JAN
%D 2013
%K views, opinion, c2013, c201x, c20xx, zz0413, human, intelligence, clever,
   intellect, intellectual, development, IQ, brain, genes, XLID, evolution,
   Flynn effect
%X "New developments in genetics, anthropology, & neurobiology predict that a
   very large # of genes underlie our intellectual & emotional abilities, making
   these abilities genetically surprisingly fragile.  I would wager that if an
   average citizen from Athens of 1000BC were to appear suddenly among us, he or
   she would be among the brightest & most intellectually alive of our
   colleagues & companions, with a good memory, a broad range of ideas, & a
   clear-sighted view of important issues. Furthermore, I would guess that he
   or she would be among the most emotionally stable of our friends &
   colleagues. ...
   studies indicate that mutn of ~215 intellectual deficiency (ID)
   genes on the X chr. give rise to XLID and/or emotional disability ... about
   25% of the genes on the X.. Of these, 86 have been characterized & do not
   seem to be neomorphs (a gain of inappropriate fn). ... conservative est. that
   ~10% of all human genes are implicated in intellectual fn. Because mutn of
   any one of these g. can give rise to intellectual disability ... they do not
   operate as a robust network, but rather as links in a chain, failure of any
   one of which leads to intellectual disability. The X chr. does not appear to
   be enriched for genes required for intellectual development, [so] we can
   extrapolate that between 2000 & 5000 genes are needed for intellectual &
   emotional fn."
   -- [<A HREF="http://dx.doi.org/10.1016/j.tig.2012.10.002">doi:10.1016/j.tig.2012.10.002</A>]['13], and
   pt2[<A HREF="http://dx.doi.org/10.1016/j.tig.2012.10.003">doi:10.1016/j.tig.2012.10.003</A>]['13].

%A J. Zhow
%A D. S. Wishart
%T An improved method to detect correct protein folds using partial clustering
%J BMC Bioinformatics
%V 14
%N 11
%P ?
%M JAN
%D 2013
%K eJrnl, jrnl, MolBio, c2013, c201x, c20xx, zz0713, protein structure, 3D,
   clustering, identifying, folds, decoy set, sets, HS Forest HSforest,
   RMSD, GDT-TS, GDTts, scoring, quality
%X "... hypothesized that a more efficient 'partial' clustering approach in
   combination with an improved scoring scheme could sig. improve both the speed
   & performance of existing candidate selection methods. ... propose a new
   scheme that performs rapid but incomplete clustering on protein decoys. ...
   detects structurally similar decoys (measured using either C_alpha RMSD or
   GDT-TS score) & extracts representatives from them without assigning every
   decoy to a cluster. We integrated our new clustering strategy with several
   different scoring fns to assess both the performance & speed in identifying
   correct or near-correct folds. Experimental results on 35 Rosetta decoy sets
   & 40 I-TASSER decoy sets show that our method can improve the correct fold
   detection rate as assessed by two different quality criteria. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-14-11">doi:10.1186/1471-2105-14-11</A>]['13].

%A L. L. Moroz
%A et al ...
%A E. Rogaev
%T The genome of the Ctenophore Pleurobrachia bachei: Molecular insights into
   independent origins of nervous systems
%J Annual Mtg, Soc. for Integrative and Comparative Biol.
%M JAN
%D 2013
%K MolBio, c2013, c2013, c20xx, zz0213, brain, nervous system, evolution,
   independent, independently, twice, Ctenophora, comb jelly, jellies,
   sea gooseberry, Pleurobrachia, Ctenophore, HOX gene
%X '... The phylum Ctenophora (comb jellies) is one of the earliest animal
   lineages with well-recognized nervous & "true" mesoderm-derived muscular
   systems. The sea gooseberry (Pleurobrachia), has one of the most compact
   genomes within this group. ... phylogenomic analysis is consistent with the
   most basal phylogenetic position of Ctenophores within the animal tree. This
   hypothesis is further supported by comparative analysis of selected gene
   families (inc. the apparent absence of HOX genes in Pleurobrachia). 2nd, our
   experimental data indicate that the nervous system in ctenophores is one of
   the most distinct in its morphological & molecular organization. Many
   "classical bilaterian neuron-specific" genes either are not present or, if
   present, they are not expressed in neurons. Finally, we identified novel
   markers for ctenophores neurons. Combined, these data suggest that at least
   some of the ctenophore neural populations were evolved independently from
   those in other animals."
   -- [<A HREF="http://sicb.org/meetings/2012/schedule/abstractdetails.php?id=527">sicb</A>]['13],
      M@[<A HREF="http://www.whitney.ufl.edu/research_programs/moroz-lab.htm">ufl</A>]['13].

%A S. C. Madeira
%A M. C. Teixeira
%A I. Sa-Correia
%A A. L. Oliveira
%T Identification of regulatory modules in time series gene expression data
   using a linear time biclustering algorithm
%J IEEE/ACM Trans. on Comp. Biol. and Bioinf.
%V 7
%N 1
%M JAN-MAR
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, zz0720, CCC biclustering, coclustering,
   contiguous, consecutive, columns, time series, timeSeries, gene expression
%X "... most biclustering formulations are NP-hard [but] restrict the problem to
   the identification of maximal biclusters with contiguous columns, which
   corr.to coherent exp'n patterns shared by a group of genes in consec. time
   pts. This restriction leads to a tractable problem. ... linear time
   complexity of CCC-Biclustering relies on the use of a discretized matrix &
   efficient string proc. techniques based on suff'x trees. ... Results obtained
   using the transcriptomic expression patterns occurring in Saccharomyces
   cerevisiae in response to heat stress ..."
   -- [<A HREF="https://doi.org/10.1109/TCBB.2008.34">doi:10.1109/TCBB.2008.34</A>]['20],
    & [<A HREF="https://www.inesc-id.pt/ficheiros/publicacoes/4706.pdf">.pt</A>]['20].
   (Also see bicl@[<A HREF="https://en.wikipedia.org/wiki/Biclustering">wikip</A>]['20].)

%A Le Cong
%A et al ...
%A F. Zhang
%T Multiplex genome engineering using CRISPR/Cas systems
%J Science
%V 339
%N 6121
%P 819-823
%M FEB
%D 2010
%K jrnl, MolBio, c2013, c201x, c20xx, zz0416, gene editing, therapy,
   CRISPR, Cas
%X "... type II prokaryotic CRISPR ... /Cas adaptive immune sys. has been shown
   to facilitate RNA-guided site-specific DNA cleavage. We engineered two
   different type II CRISPR/Cas systems & demonstrate that Cas9 nucleases can be
   directed by short RNAs to induce precise cleavage at endogenous genomic loci
   in human & mouse cells. Cas9 can also be converted into a nicking enzyme to
   facilitate homology-directed repair with minimal mutagenic activity. Lastly,
   multiple guide seqs. can be encoded into a single CRISPR array to enable
   simultaneous editing of several sites within the mammalian genome,
   demonstrating easy programmability & wide applicability of the RNA-guided
   nuclease technology."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1231143">doi:10.1126/science.1231143</A>]['16].
   Also see CRISPR@[<A HREF="https://en.wikipedia.org/wiki/CRISPR">wikip</A>]['16].
   [Also search for: MolBio CRISPR].

%A M. A. O'Leary
%A et al ...
%A A. L. Cirranello
%T The placental mammal ancestor and the post-K-Pg radiation of placentals
%J Science
%V 339
%N 6120
%P 662-667
%M FEB
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0213, biology, evolution, K-Pg, KPg,
   Cretaceous Paleogene, boundary, Chicxulub impact, asteroid, extinction,
   phylogenetic, evolutionary, fossil, Xenarthra, Epitheria, Sundatheria,
   Dermoptera, Scandentia, Placentalia, mammal, mammals
%X "To discover interordinal relationships of living & fossil placental mammals
   & the time of origin of placentals relative to the Cretaceous-Paleogene
   (K-Pg) boundary, we scored 4541 phenomic characters de novo for 86 fossil &
   living species. Combining these data with molecular sequences, we obtained a
   phylogenetic tree that, when calibrated with fossils, shows that crown clade
   Placentalia & placental orders originated after the K-Pg bdry. Many nodes
   discovered using molec.data are upheld, but phenomic signals overturn
   molecular signals to show Sundatheria (Dermoptera + Scandentia) as the sister
   taxon of Primates, a close link between Proboscidea (elephants) & Sirenia
   (sea cows), & the monophyly of echolocating Chiroptera (bats). Our tree
   suggests that Placentalia first split into Xenarthra & Epitheria; extinct
   New World species are the oldest members of Afrotheria."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1229237">doi:10.1126/science.1229237</A>]['13].
   (Other articles about Chicxulub in the jrnl issue.)

%A M. J. Telford
%T The animal tree of life
%J Science
%V 339
%P 6121
%P 764-766
%M FEB
%D 2013
%K views, c2013, c201x, c20xx, zz0312, MolBio, tree, evolutionary,
   phylogenetic, family, animal evolution, species
%X "... Field et al.'s landmark publication 25 years ago of an analysis
   of animal relationships based on ribosomal RNA (rRNA) sequences ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1234378">doi:10.1126/science.1234378</A>]['13].
   [Also search for: MolBio tree life].

%A D. Graur
%A Y. Zheng
%A N. Price
%A R. B. R. Azevedo
%A R. A. Zufall
%A E. Elhaik
%T On the immortality of television sets: "function" in the human genome
   according to the evolution-free gospel of ENCODE
%J Genome Biol. and Evolution
%V ?
%P ?-?
%M FEB
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0313, Encode, project, zzEncode,
   junk DNA, functional, Science, bioinformatics, biol, biology,
   controversial, stoush, fuss
%X "A recent slew of ENCODE Consortium publications ... idea that more than 80%
   of the human genome is functional. ... flies in the face of current ests.
   according to which the fraction of the genome that is evolutionarily
   conserved through purifying selection is under 10%. Thus, according to the
   ENCODE C., a biol. fn can be maintained indefinitely without seln, which
   implies that at least 80-10=70% of the g. is perfectly invulnerable to
   deleterious mutations, either because no mutns can ever occur in these
   'functional' regions, or because no mutation in these regions can ever be
   deleterious. This absurd conclusion was reached through various means,
   chiefly (1) by employing the seldom used 'causal role' defn of biol. fn &
   then applying it inconsistently to different biochem. properties, (2) by
   committing a logical fallacy known as 'affirming the consequent,' (3) by
   failing to appreciate the crucial difference between 'junk DNA' & 'garbage
   DNA,' (4) by using analytical methods that yield biased errors & inflate
   ests. of functionality, (5) by favoring stat. sensitivity over specificity, &
   (6) by emphasizing stat.sig. rather than the magnitude of the effect. Here,
   we detail the many logical & methodological transgressions involved in
   assigning functionality to almost every nucleotide in the human genome. The
   ENCODE results were predicted by one of its authors to necessitate the
   rewriting of textbooks. We agree, many textbooks dealing with marketing,
   mass-media hype, & public relns may well have to be rewritten."  Online 20/2.
   -- [<A HREF="http://dx.doi.org/10.1093/gbe/evt028">doi:10.1093/gbe/evt028</A>]['13].
   [Also search for: MolBio Encode project] and
   [also search for: MolBio junk DNA].
   Also see [<A HREF="http://www.guardian.co.uk/science/2013/feb/24/scientists-attacked-over-junk-dna-claim">the_G.</A>][24/2/'13].
   [Controversial. You have to love a good stoush.]

%A A. A. Ahimastos
%A P. J. Walker
%A C. Askew
%A A. Leicht
%A E. Pappas
%A E. Blombery
%A C. M. Reid
%A J. Golledge
%A B. A. Kingwell
%T Effect of ramipril on walking times and quality of life among patients with
   peripheral artery disease and intermittent claudication: a randomized
   controlled trial
%J JAMA
%V 309
%N 5
%P 453-460
%M FEB
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0915, drug, trial, ramipril, Altace,
   human health, Baker IDI Melbourne, scandal, science, scientific research,
   fraud, misconduct, fabrication, ethics, retraction, paper
%X "... Among patients with intermittent claudication, 24-week treatment with
   ramipril resulted in significant increases in pain-free and maximum treadmill
   walking times compared with placebo. This was associated with a significant
   increase in the physical functioning component of the SF-36 score."
   -- [<A HREF="http://dx.doi.org/10.1001/jama.2012.216237">doi:10.1001/jama.2012.216237</A>]['15].
   BUT see abc@[<A HREF="http://www.abc.net.au/news/2015-09-17/high-profile-researcher-admits-to-fabricating-scientific-results/6781958">17/9/2015</A>],
      [<A HREF="http://retractionwatch.com/2015/09/14/fabricated-results-retract-jama-clinical-trial-plus-a-sub-analysis-of-the-data/">retractionwatch</A>]['15].

%A S. Luca
%A T. Mihaescu
%T History of BCG vaccine
%J Maedica (Bucur)
%V 8
%N 1
%P 53-58
%M MAR
%D 2013
%K jrnl, MolBio, tuberculosis, TB, c2013, c201x, c20xx, zz0422, human health,
   disease, BCG, vaccine, vaccination, tubercle bacillus,
   Bacille Calmette Guerin
%X "... (TB) is still responsible for 2 million deaths every year despite being
   a treatable airborne infectious disease. 'Consumption' and 'Phthisis' were
   terms historically used to describe TB, which was responsible for one in four
   deaths in the 19th C.. ... the emergence of multi-drug resistant TB & the
   current TB-HIV epidemic ... Bacille Calmette-Guerin (BCG) is the only vaccine
   available today and has been used for more than 90 years with astonishing
   safety records. However, its efficacy remains controversial. ..."
   -- [<A HREF="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3749764/">www</A>]['22].
   [Also search for: BCG vaccine].

%A B. P. Hubbard
%A et al ...
%A D. A. Sinclair
%T Evidence for a common mechanism of SIRT1 regulation by allosteric activators
%J Science
%V 339
%N 6124
%P 1216-1219
%M MAR
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0313, SIRT1 deacetylase, STACs, FOXO3a,
   activator, sirtuin, ageing, lifespan, resveratrol, red wine
%X "A molecule that treats multiple age-related diseases would have a major
   impact on global health ... The SIRT1 deacetylase has drawn attention in this
   regard as a target for drug design. Yet controversy exists around the
   mechanism of sirtuin-activating compounds (STACs). We found that specific
   hydrophobic motifs found in SIRT1 substrates such as PGC-1alpha & FOXO3a
   facilitate SIRT1 activation by STACs. A single amino acid in SIRT1, Glu230,
   located in a structured N-terminal domain, was critical for activation by all
   prev. reported STAC scaffolds & a new class of chemically distinct
   activators. In primary cells reconstituted with activation-defective SIRT1,
   the metabolic effects of STACs were blocked. Thus, SIRT1 can be directly
   activated through an allosteric mechanism common to chem.diverse STACs."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1231097">doi:10.1126/science.1231097</A>]['13].
   [Also search for: resveratrol].

%A M. B. Ahrens
%A M. B. Orger
%A D. N. Robson
%A J. M. Li
%A P. J. Keller
%T Whole-brain functional imaging at cellular resolution using
   light-sheet microscopy
%J NatureMethods
%V 10
%N ?
%P 413-420
%M MAR
%D 2013
%K jrnl, c2013, c201x, c20xx, biology, brain, cell, cells, neurons, connections,
   activity, zebrafish, GCaMP5G, hindbrain, neuropil, inferior olive, images,
   time series, connectomics, chalearn, challenge
%X "... use light-sheet microscopy to record activity, reported through the
   genetically encoded calcium indicator GCaMP5G, from the entire volume of the
   brain of the larval zebrafish in vivo at 0.8Hz, capturing more than 80% of
   all neurons at single-cell resolution. Demonstrating how this technique can
   be used to reveal functionally defined circuits across the brain, we identify
   two populations of neurons with correlated activity patterns. One circuit
   consists of hindbrain neurons functionally coupled to spinal cord neuropil.
   The other consists of an anatomically symmetric population in the anterior
   hindbrain, with activity in the left & right halves oscillating in antiphase,
   on a timescale of 20s, & coupled to equally slow oscillations in the
   inferior olive."  [via KK].
   -- [<A HREF="http://dx.doi.org/10.1038/nmeth.2434">doi:10.1038/nmeth.2434</A>]['14].
   (Also see challenge@[<A HREF="http://connectomics.chalearn.org/">chalearn</A>]['14].)
   [Also search for: MolBio connectome].

%A F. L. Mendez
%A et al ...
%A M. F. Hammer
%T An African American paternal lineage adds an extremely ancient root to the
   human Y chromosome phylogenetic tree
%J Amer. J. Human Genetics
%V 92
%N 3
%P 454-459
%M MAR
%D 2013
%K jrnl, AJHG, MolBio, c2013, c201x, c20xx, zz0313, Y chromosome, chr Y, chrY,
   Ychr,chromosomeY, Ychromosome, DNA, human, evolution, origins, male, father,
   Adam, Eve, MRCA, TMRCA, phylogenetic tree, homo sapiens
%X "... discovery of an African American Y chr. that carries the ancestral state
   of all SNPs that defined the basal portion of the Y chr. phylogenetic tree.
   We sequenced ~240kb of this chr. to identify private, derived mutns on this
   lineage, which we named A00. ... estimated the time to the most recent common
   ancestor (TMRCA) for the Y tree as 338 thousand y. ago (kya) (95% CI=237-581
   kya). Remarkably, this exceeds current ests. of the mtDNA TMRCA, as well as
   those of the age of the oldest anatomically modern human fossils. The
   extremely ancient age [&] rarity of the A00 lineage ... point to the
   importance of considering more complex models for the origin of Y chr.
   diversity. These models inc. ancient popln structure & the possibility of
   archaic introgression of Y chrs. into anatomically modern humans. The A00
   lineage was discovered in a large DB of consumer samples of African Americans
   & has not been identified in trad. hunter-gatherer poplns from sub-SaharanA..
   This underscores how the stochastic nature of the genealogical process can
   affect inference from a single locus & warrants caution during the
   interpretation of the geographic location of divergent branches of the Y chr.
   phylogenetic tree for the elucidation of human origins."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ajhg.2013.02.002">doi:10.1016/j.ajhg.2013.02.002</A>]['13].
   (338 thousand y. ago)
   [Also search for: MolBio human evolution Adam]  and
   [also search for: MolBio human evolution Eve].

%A E. M. Leffler
%A et al ...
%A M. Przeworski
%T Multiple instances of ancient balancing selection shared between humans and
   chimpanzees
%J Science
%V 339
%N 6127
%P 1578-1582
%M MAR
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0413, chimp, human, evolution, primate,
   SNPs, MHC, immune system, host, pathogen
%X "... genome-wide scan for long-lived balancing selection by looking for
   combinations of SNPs shared between h. & c.. [&] to the major
   histocompatibility complex, we identified 125 regions in which the same
   haplotypes are segregating in the two species, all but two of which are
   noncoding. In six cases, there is evidence for an ancestral polymorphism that
   persisted to the present in h. & c.. Regions with shared haplotypes are sig.
   enriched for membrane glycoproteins, & a similar trend is seen among shared
   coding polymorphisms. These findings indicate that ancient balancing seln has
   shaped human variation & point to genes involved in host-pathogen
   interactions as common targets."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1234070">doi:10.1126/science.1234070</A>]['13].

%A D. Sharon
%A H. Tilgner
%A F. Grubert
%A M. Snyder
%T A single-molecule long-read survey of the human transcriptome
%J NatureBiotech
%V 31
%N 11
%P 1009-1014
%M MAR
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0714, human, DNA, RNA, transcriptome,
   Pacific Biosciences, single molecule, sequencing
%X "... use single-molecule long-read seq. tech. from Pacific Biosciences to
   sequence the polyadenylated RNA complement of a pooled set of 20 human organs
   & tissues without the need for fragmentation or amplification. ... full-
   -length RNA molecules of up to 1.5kb can readily be monitored with little
   seq. loss at the 5' ends. For longer RNA molecules more 5' nucleotides are
   missing, but complete intron structures are often preserved. In total, we
   identify ~14,000 spliced GENCODE genes. High-confidence mappings are
   consistent with GENCODE annotations, but > 10% of the alignments represent
   intron structures that were not previously annotated. As a group, transcripts
   mapping to unannotated regions have features of long, noncoding RNAs. Our
   results show the feasibility of deep sequencing full-length RNA from complex
   eukaryotic transcriptomes on a single-molecule level."
   -- [<A HREF="http://dx.doi.org/10.1038/nbt.2705">doi:10.1038/nbt.2705</A>]['14].
   (Also see PacBiosci@[<A HREF="http://en.wikipedia.org/wiki/Pacific_Biosciences">wikip</A>]['14].)
   [Also search for: MolBio single molecule sequencing].

%A M. Broom
%A J. Rychtar
%T Game-Theoretical Models in Biology
%I ChapmanAndHall
%P 520
%M MAR
%D 2013
%K book, text, c2013, c201x, c20xx, zz0813, game theory, biol, biology,
   prisoners dilemma, IPD, hawk dove, war of attrition, replicator,
   ESS, stable, strategy, animal behaviour
%X 1st ed 2013; hb us$58; uk us isbn:1439853215; uk us isbn13:978-1439853214.
   "... wide range of topics in evolutionary games, including matrix games,
   replicator dynamics, the hawk-dove game, & the prisoners' dilemma. It
   covers the evolutionarily stable strategy, a key concept in biological games,
   and offers in-depth details of the mathematical models. ..."

%A H.-Q. Ling
%A et al ...
%A J. Wang
%T Draft genome of the wheat A-genome progenitor Triticum urartu
%J Nature
%V 496
%P 87-90
%M APR
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0413, plant, grass, wheat, bread,
   plants, Triticum urartu, AABBDD, einkorn, nGenome, genome, diploid
%X "... The A-genome, as a basic genome of bread wheat & other polyploid
   wheats, e.g., T.turgidum (AABB), T.timopheevii (AAGG) & T.zhukovskyi
   (AAGGAmAm), is central to wheat evoln, domestication & genetic improvement.
   The progenitor species of the A-genome is the diploid wild einkorn wheat
   T.urartu, which resembles cultivated wheat more extensively than do Aegilops
   speltoides (the ancestor of the B genome) & Ae.tauschii (the donor of the D
   genome), esp. in the morphology & development of spike & seed. ...
   ... est. the genome size to be 4.9Gb ... seven hypothetical chromosomes ...
   DDBJ/EMBL/GenBank under accession number AOTI00000000 ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11997">doi:10.1038/nature11997</A>]['13],
   & @[<A HREF="http://dx.doi.org/10.5524/100050">CLiMB</A>]['13].

%A J. Jia
%A et al ...
%A J. Wang
%T Aegilops tauschii draft genome sequence reveals a gene repertoire for
   wheat adaptation
%J Nature
%V 496
%P 91-95
%M APR
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0413, plant, grass, wheat, bread,
   plants, Ae, Aegilops tauschii, Triticum turgidum, nGenome, genome, diploid,
   tetraploid, hexaploid wheat, aestivum, AABBDD
%X "About 8,000 years ago ... a spontaneous hybridization of the wild diploid
   grass Aegilops tauschii (2n=14; DD) with the cultivated tetraploid wheat
   Triticum turgidum (2n=4x=28; AABB) resulted in hexaploid wheat
   (T. aestivum; 2n=6x=42; AABBDD) ... describe sequencing the Ae.tauschii
   genome  ... 43,150 protein-coding genes ... 4.36-Gb genome ...
   DDBJ/EMBL/GenBank under accession number AOCO000000000 ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12028">doi:10.1038/nature12028</A>]['13],
   & @[<A HREF="http://dx.doi.org/10.5524/100054">CLiMB</A>]['13].

%A C. T. Amemiya
%A et al ...
%A K. Lindblad-Toh
%T The African coelacanth genome provides insights into tetrapod evolution
%J Nature
%V 496
%P 311-316
%M APR
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0413, coelacanth, genome, nGenome,
   fish, Latimeria chalumnae, fin, fins, lobe finned, limb, limbs, tetrapods
%X "... report the genome sequence of the African c., Latimeria chalumnae.
   ... phylogenomic analysis, we conclude that the lungfish, & not the c., is
   the closest living relative of tetrapods. C. protein-coding genes are sig.
   more slowly evolving than those of tetrapods, unlike other genomic features.
   Analyses of changes in genes & regulatory elts during the vertebrate
   adaptation to land highlight genes involved in immunity, nitrogen excretion &
   the development of fins, tail, ear, eye, brain & olfaction. Functional assays
   of enhancers involved in the fin-to-limb transition & in the emergence of
   extra-embryonic tissues show the importance of the c. genome as a blueprint
   for understanding tetrapod evolution."
   "... 48 chrs.  Draft is 2.86Gb composed of 2.18Gb of seq. plus gaps ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12027">doi:10.1038/nature12027</A>]['13].
   [Also search for: Coelacanth].

%A K. Howe
%A et al ...
%A D. L. Stemple
%T The zebrafish reference genome sequence and its relationship to
   the human genome
%J Nature
%V 496
%P 498-503
%M APR
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0413, zebrafish, fish, genome, nGenome
%X "... generated a high-quality sequence assembly of the zebrafish genome, made
   up of an overlapping set of completely sequenced large-insert clones that
   were ordered and oriented using a high-resolution high-density meiotic map.
   Detailed automatic and manual annotation provides evidence of more than
   26,000 protein-coding genes, the largest gene set of any vertebrate so far
   sequenced. Comparison to the human reference genome shows that approximately
   70% of human genes have at least one obvious zebrafish orthologue. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12111">doi:10.1038/nature12111</A>]['13].

%A K. Michailidou
%A et al ...
%A D. F. Easton
%T Large-scale genotyping identifies 41 new loci associated with breast cancer
   risk
%J Nature Genetics
%V 45
%N 4
%P 353-361
%M APR
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0414, breast cancer, GWAS, SNP, SNPs,
   enesm, Makalic, Schmidt, risk, risks, human, women, health
%X "... We report here a meta-analysis of 9 genome-wide assoc. studies, inc.
   10,052 breast cancer cases & 12,575 controls of European ancestry, from which
   we selected 29,807 SNPs for further genotyping. These SNPs were genotyped in
   45,290 cases & 41,880 controls of European ancestry from 41 studies in the
   Breast Cancer Association Consortium (BCAC). The SNPs were genotyped as part
   of a collaborative genotyping experiment involving four consortia
   (Collaborative Oncological Gene-environment Study, COGS) & used a custom
   Illumina iSelect genotyping array, iCOGS, comprising more than 200,000 SNPs.
   We identified SNPs at 41 new breast cancer susceptibility loci at genome-wide
   significance (P < 5 x 10^-8). Further analyses suggest that more than 1,000
   additional loci are involved in breast cancer susceptibility."
   -- [<A HREF="http://dx.doi.org/10.1038/ng.2563">doi:10.1038/ng.2563</A>]['14].
   (Also see [<A HREF="http://dx.doi.org/10.1038/bjc.2013.747">doi:10.1038/bjc.2013.747</A>][1/2014].)
   (Also see GWAS@[<A HREF="https://en.wikipedia.org/wiki/Genome-wide_association_study">wikip</A>]['20].)

%A J. O'Muircheartaigh
%A et al ...
%A S. C. L. Deoni
%T Typical patterns of Myelin neurodevelopment and cognitive abilities in
   babies and toddlers
%J ISMRM 21
%M APR
%D 2013
%K conf, c2013, c201x, c20xx, zz1013, myelin, human, brain, plasticity,
   learning, language, languages, child, children, speech, development,
   disorder, multilingual, OMuircheartaigh
%X "The trajectory of myelination in the developing brain is coupled with
   progressive optimisation of cognitively relevant brain networks. Here we use
   a multivariate technique, independent component analysis, to parcellate
   quantitative myelin maps (mcDESPOT) from 200 children between 3 months &
   5 y., into clusters with consistent developmental trajectories. We demo.
   distributed, functionally relevant, systems that myelinate concurrently."
   (Also see [<A HREF="http://www.bbc.co.uk/news/health-24446292">bbc</A>][9/10/2013]
   and [<A HREF="http://scholar.google.com.au/citations?user=nV3kJD4AAAAJ">gs</A>]['13].)

%A F. J. Ruhli
%A M. Henneberg
%T New perspectives on evolutionary medicine: the relevance of microevolution
   for human health and disease
%J BMC Medicine
%V 11
%P 115
%M APR
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0813, human, diet, health, ancient, pathogen
%X "Evolutionary medicine (EM) ... to explain the present-day state of human
   health. Here, we propose a different approach by addressing more empirical &
   health-oriented research concerning past, current & future microevolutionary
   changes of human structure, functions & pathologies. Studying generation-to-
   -generation changes of human morphology that occurred in historical times, &
   still occur in present-day popns under the forces of evolution, helps to
   explain medical condns & warns clinicians that their current practices may
   influence future humans. Also, analyzing historic tissue specimens such as
   mummies is crucial in order to address the molec.evoln of pathogens, of the
   human genome, & their coadaptations."
   -- [<A HREF="http://dx.doi.org/10.1186/1741-7015-11-115">doi:10.1186/1741-7015-11-115</A>]['13].

%A G. Szoniec
%A M. J. Ogorzalek
%T Entropy of never born protein sequences
%J Springerplus
%V 2
%N 1
%P 200
%M DEC
%D 2013
%O DEC 2013, but online APR 2013
%K eJrnl, MolBio, c2013, c201x, c20xx, zz0713, protein structure, folds,
   entropy, information theory, random, real, artificial, synthetic, NBP, NBPs,
   proteins, RandomBlast
%X (NB. Ent. of NBp *sequences*.)
   "A Never Born protein [NBp] is a theoretical protein which does not occur in
   nature. ... why some proteins were selected & some were not during evolution
   is not known ... Both block & relative entropies are similar what means that
   both protein kinds contain strongly random seqs..  An artificially gen. NBp
   seq. is closely as random as a natural one. ... suggests that protein seln
   during evoln was rather random/non-deterministic.  Natural proteins have no
   noticeable unique features in information theory sense."
   "... 20% of [NBPs] fold ... in lab. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/2193-1801-2-200">doi:10.1186/2193-1801-2-200</A>]['13] (via TS).
   [Also search for: randomBlast].

%A G. Zhang
%A et al ...
%A D. Cai
%T Hypothalamic programming of systemic ageing involving IKK-beta, NF-kB and
   GnRH
%T Nature
%V ?
%P ?-?
%M MAY
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0513, age, ageing, longevity, lifespan, mouse,
   mice, IKK beta, IKKb, IkB, I kappa B, NFkB, NfkB, GnRH, hypothalmus,
   neurogenesis, medical, health
%X "... it is unknown whether an individual tissue primarily works to mediate
   the ageing progress & control lifespan. ... show that the hypothalamus is
   important for the development of whole-body ageing in mice, & that the
   underlying basis involves hypothalamic immunity mediated by IkºB kinase-beta
   (IKK-beta), nuclear factor kB (NF-kB) & related microglia-neuron immune
   crosstalk. Several interventional models were developed showing that ageing
   retardation & lifespan extn are achieved in m. by preventing ageing-related
   hypothalamic or brain IKK-b & NF-kB activn. ... revealed that IKK-b & NF-bB
   inhibit gonadotropin-releasing hormone (GnRH) to mediate ageing-related
   hypothalamic GnRH decline, & GnRH treatment amends ageing-impaired
   neurogenesis & decelerates ageing. ... the hypothalamus has a programmatic
   role in ageing development via immune-neuroendocrine integration, & immune
   inhibition or GnRH restoration in the hypothalamus/brain represent two
   potential strategies for optimizing lifespan & combating ageing-related
   health problems."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12143">doi:10.1038/nature12143</A>]['13].

%A L. Salichos
%A A. Rokas
%T Inferring ancient divergences requires genes with strong phylogenetic signals
%J Nature
%V 497
%P 327-331
%M MAY
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0513, DNA, evolutionary, family,
   phylogenetic, tree, trees, divergence, multiple genes, incongruence
%X "To tackle incongruence, the topological conflict between different gene
   trees, phylogenomic studies couple concatenation with practices such as rogue
   taxon removal or the use of slowly evolving genes. P.analysis of 1,070
   orthologues from 23 yeast genomes identified 1,070 distinct gene trees, which
   were all incongruent with the phylogeny inferred from concatenation.
   Incongruence severity increased for shorter internodes located deeper in the
   phylogeny. Notably, whereas most practices had little or -ve impact on the
   yeast phylogeny, the use of genes or internodes with high avg. internode
   support sig. improved the robustness of inference. We obtained similar
   results in analyses of vertebrate & metazoan phylogenomic data sets. These
   results question the exclusive reliance on concatenation & assoc. practices,
   & argue that selecting genes with strong phylogenetic signals & demonstrating
   the absence of sig. incongruence are essential for accurately reconstructing
   ancient divergences."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12130">doi:10.1038/nature12130</A>]['13].

%A R. Dallai
%A M. Gottardo
%A D. Mercati
%A R. Machida
%A Y. Mashimo
%A Y. Matsumura
%A R. G. Beutel
%T Divergent mating patterns and a unique mode of external sperm transfer in
   Zoraptera: an enigmatic group of pterygote insects
%J Naturwissenschaften
%P
%M MAY
%D 2013
%K jrnl, Biol, c2013, c201x, c20xx, sex, reproduction, evolution, origins,
   winged insect, Pterygota, Zoraptera, Zorotypus impolitus, magnicaudell,
   ground lice, louse, angel, Hexapoda, copula, copulation, spermatophore,
   spermatozoon, sperm
%X "A remarkable external sperm transfer is described for the 1st time in a
   species of a group of winged insects (Pterygota), the enigmatic Zoraptera.
   Mating & sperm transfer of two species of the order were examined in detail,
   documented, & compared with each other & with patterns described for other
   species belonging to the order. The behavior differs strikingly in Zorotypus
   impolitus & Zorotypus magnicaudelli. A copula is performed by males & females
   of the latter, as it is also the case in other z. species & generally in
   pterygote insects. [v.] males of Z.impolitus do not copulate but deposit
   small (100mu_m in dia.) spermatophores externally on the abdomen of the f..
   Each spermatophore contains only 1 giant spermatozoon (3mm long & 3mu_m wide)
   a unique feature in the entire Hexapoda. External s. transfer in Pterygota is
   a highly unusual case of evolutionary reversal. The v.small relict group
   Z. displays a uniform general morphology but exhibits very different
   reproductive structures & patterns of mating behavior. This may be an extreme
   form of a more general sitn in insects, with a specific form of seln
   resulting in an accelerated rate of evolution in the reproductive system."
   -- [<A HREF="http://dx.doi.org/10.1007/s00114-013-1055-0">doi:10.1007/s00114-013-1055-0</A>]['13].
   [Also search for: sex origin].

%A B. Nystedt
%A et al ...
%A S. Jansson
%T The Norway spruce genome sequence and conifer genome evolution
%J Nature
%V 497
%P 579-584
%M MAY
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0613, plant, plants, tree, conifer,
   spruce, nGenome, genome, DNA, Picea abies, gymnosperm, conifers, Norwegian
%X "... draft assembly of the 20-gigabase g. of Norway spruce (Picea abies), the
   first available for any gymnosperm. The # of well-supported genes (28,354) is
   similar to the > 100 times smaller genome of Arabidopsis thaliana, & there is
   no evidence of a recent whole-g. duplication in the gymnosperm lineage.
   Instead, the large g. size seems to result from the slow & steady acc'n of a
   diverse set of long-terminal repeat transposable elts, poss. owing to the
   lack of an efficient elimination mechanism. Comparative sequencing of Pinus
   sylvestris, Abies sibirica, Juniperus communis, Taxus baccata & Gnetum gnemon
   reveals that the transposable elt diversity is shared among extant conifers.
   Expression of 24-nucleotide small RNAs, previously implicated in transposable
   elt silencing, is tissue-specific & much lower than in other plants. [&]
   identify numerous long ( > 10,000-bp) introns, gene-like fragments,
   uncharacterized long non-coding RNAs and short RNAs. ..." [50 refs].
   "Most conifers have 12 (2n = 24) chromosomes"
   -- [<A HREF="http://dx.doi.org/10.1038/nature12211">doi:10.1038/nature12211</A>]['13].

%Q Social Science Genetic Association Consortium
%A C. A. Rietveld
%A et al ...
%A P. D. Koellinger
%T GWAS of 126,559 individuals identifies genetic variants associated with
   educational attainment
%J Science
%V 340
%N 6139
%P 1467-1471
%M MAY
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0613, gene, genes, brain, education,
   schooling, tertiary, GWAS, rs9320913, rs11584700, rs4851266, SNPs, brain, IQ,
   intelligence, genetics, achievement, anterior caudate nucleus
%X "... study of educational attainment ... in a discovery sample of 101,069
   individuals & a replication sample of 25,490. Three indep. SNPs are genome-
   -wide sig. (rs9320913, rs11584700, rs4851266), & all 3 replicate. Est.effects
   sizes are small (R^2 ~ 0.02%), approx. 1 month of schooling per allele. A
   linear polygenic score from all measured SNPs accounts for ~2% of the
   variance in both educational attainment & cognitive fn. Genes in the region
   of the loci have previously been assoc. with health, cognitive, & central
   nervous system phenotypes, & bioinformatics analyses suggest the involvement
   of the anterior caudate nucleus. ... provide promising candidate SNPs for
   follow-up work, & our effect size estimates can anchor power analyses in
   social-science genetics."  [Science Express 30 May '13].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1235488">doi:10.1126/science.1235488</A>]['13].
   (Also see GWAS@[<A HREF="https://en.wikipedia.org/wiki/Genome-wide_association_study">wikip</A>]['20].)

%A J. D. Wolchok
%A et al ...
%A M. Sznol
%T Nivolumab plus ipilimumab in advanced melanoma
%J NEJM
%V ?
%P ?-?
%M JUN
%D 2013
%K jrnl, NEJM, medicine, c2013, c201x, c20xx, zz0613, skin cancer, melanoma,
   drug, drugs, ipilimumab, CTLA 4, CTLA4, nivolumab, PD 1, PD1, cytotoxic,
   antibody,, antibodies, treatment, immune system
%X "... ipilimumab (an antibody against cytotoxic T-lymphocyte-assoc. antigen 4
   [CTLA-4]) prolongs overall survival, & nivolumab (an AB v. the programmed
   death 1 [PD-1] receptor) produced durable tumor regression in a phase 1
   trial. On the basis of their distinct immunologic mechanisms of action &
   supportive preclinical data, we conducted a phase 1 trial of nivolumab
   combined with ipilimumab in patients with advanced melanoma."
   -- [<A HREF="http://www.nejm.org/doi/full/10.1056/NEJMoa1302369">doi:10.1056/NEJMoa1302369</A>]['13].

%A G. Zhao
%A et al ...
%A P. Zhang
%T Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom
   molecular dynamics
%J Nature
%V 497
%P 643-646
%M MAY
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0613, HIV, HIV1, Aids, virus, capsid,
   proteins, 3D structure, units
%X "... capsid is best described by a 'fullerene cone' model in which hexamers
   of the capsid protein are linked to form a hexagonal surface lattice that is
   closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein
   contains an amino-terminal domain (NTD) comprising seven alpha-helices & a
   beta-hairpin, a carboxy-terminal domain (CTD) comprising four a.-helices, &
   a flexible linker with a 310-helix connecting the two structural domains.
   Structures ... have been det. by X-ray crystallography; however, structural
   info. regarding the assembled capsid & the contacts between the assembly
   units is incomplete. ... report the cryo-electron microscopy structure of a
   tubular HIV-1 capsid-protein assembly at 8A resolution ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12162">doi:10.1038/nature12162</A>]['13].

%A C.-Shan Chin
%A D. H Alexander
%A P. Marks
%A A. A Klammer
%A J. Drake
%A C. Heiner
%A A. Clum
%A A. Copeland
%A J. Huddleston
%A E. E Eichler
%A S. W Turner
%A J. Korlach
%T Nonhybrid, finished microbial genome assemblies from long-read SMRT
   sequencing data
%J NatureMethods
%V 10
%N 6
%P 563-569
%M MAY
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0714, DNA, sequencing, single molecule,
   SMRT, Pacific Biosciences, HGAP
%X "... hierarchical genome-assembly process (HGAP) for high-quality de novo
   microbial genome assemblies using only a single, long-insert shotgun DNA
   library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing.
   ... uses the longest reads as seeds to recruit all other reads for
   construction of highly accurate preassembled reads through a directed acyclic
   graph-based consensus procedure, which we follow with assembly using off-the-
   -shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not
   require highly accurate raw reads for error corr'n. We demo. efficient genome
   assembly for several microorganisms using as few as three SMRT Cell zero-mode
   waveguide arrays of sequencing & for BACs using just one SMRT Cell. Long
   repeat regions can be successfully resolved with this workflow. [&] describe
   a consensus alg. that incorporates SMRT sequencing primary quality values to
   produce de novo genome sequence exceeding 99.999% accuracy."
   -- [<A HREF="http://dx.doi.org/10.1038/nmeth.2474">doi:10.1038/nmeth.2474</A>]['14].
   [Also search for: MolBio single molecule sequencing].

%A L. Cheng
%A et al ...
%A J. Corander
%T Hierarchical and spatially explicit clustering of DNA sequences with BAPS
   software
%J Mol. Biol. Evol.
%V 30
%N 5
%P 1224-1228
%M MAY
%D 2013
%K jrnl, MBE, MolBio, c2013, c201x, c20xx, zz0418, BAPS, DNA, sequence, nested,
   genetic population structure, phylogeographics, evolutionary epidemiology,
   Borrelia burgdorferi, spatialepidemiology, epidemiology, rhierbaps
%X "... introduce two upgrades to the Bayesian Analysis of Population Structure
   (BAPS) s/w, which enable 1) spatially explicit modeling of variation in DNA
   sequences & 2) hierarchical clustering of DNA seq. data to reveal nested
   genetic popn structures. We provide a direct interface to map the results
   from spatial clustering with Google Maps using the portal
   www.spatialepidemiology.net & illustrate this approach using seq. data from
   Borrelia burgdorferi. The usefulness of hierarchical clustering is demo.
   through an analysis of the metapopulation structure within a bacterial
   popn experiencing a high level of local horizontal gene transfer. The tools
   that are introduced are freely available at [<A HREF="http://www.helsinki.fi/bsg/software/BAPS/">www</A>]."
   -- [<A HREF="http://dx.doi.org/10.1093/molbev/mst028">doi:10.1093/molbev/mst028</A>]['18].
   (Also see rhierbaps@[<A HREF="https://github.com/gtonkinhill/rhierbaps">github</A>]['18].)

%A G. G. Graham
%A M. J. Davies
%A R. O. Day
%A A. Mohamudally
%A K. F. Scott
%T The modern pharmacology of paracetamol: therapeutic actions, mechanism of
   action, metabolism, toxicity and recent pharmacological findings
%J Inflammopharmacology
%V 21
%N 3
%P 201-232
%M JUN
%D 2013
%K jrnl, c2013, c20x, c20xx, zz0615, uws, biology, medicine, pharmacology,
   health, human, paracetamol, drug, inflammation, COX, COX1, COX2, NSAID,
   NSAIDs
%X "...  [paracetamol] has a spectrum of action similar to that of NSAIDs &
   resembles particularly the COX-2 selective inhibitors. ... mode of action of
   paracetamol has been uncertain, but it is now generally accepted that it
   inhibits COX-1 & COX-2 through metabolism by the peroxidase fn of these
   isoenzymes. ... p. does not suppress the severe inflammation of rheumatoid
   arthritis & acute gout but does inhibit the lesser inflammation resulting
   from extraction of teeth & is also active in a variety of inflammatory tests
   in experimental animals. ... multiple inflammatory pathologies including
   atherosclerosis & rheumatic diseases. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/s10787-013-0172-x">doi:10.1007/s10787-013-0172-x</A>]['15].
   (auth5@uws 2015.)

%A E. Ibarra-Laclette
%A et al ...
%A L. Herrera-Estrella
%T Architecture and evolution of a minute plant genome
%J Nature
%V 498
%P 94-98
%K JUN
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0613, plant, plants, genome, WGD,
   small, tiny, nGenome, carnivorous bladderwort, Utricularia gibba
%X "It has been argued that the evolution of plant genome size is principally
   unidirectional & increasing owing to the varied action of whole-g. dupl'ns
   (WGDs) & mobile elt proliferation. However, extreme genome size redns have
   been reported in the angiosperm family tree. Here we report the seq. of the
   82-megabase genome of the carnivorous bladderwort plant Utricularia gibba.
   Despite its tiny size, the U.gibba genome accommodates a typical # of genes
   for a plant, with the main difference from other plant genomes arising from
   a drastic redn in non-genic DNA. Unexpectedly, we identified at least three
   rounds of WGD in U.gibba since common ancestry with tomato (Solanum) & grape
   (Vitis). The compressed architecture of the U.gibba genome indicates that a
   small fraction of intergenic DNA, with few or no active retrotransposons, is
   sufficient to regulate & integrate all the processes required for the
   development & reproduction of a complex organism."
   "... [82mb] (G+C)-rich U.gibba genome accommodates about 28,500 genes ..."
   [c.f., the spruce genome is 20G.]
   -- [<A HREF="http://dx.doi.org/10.1038/nature12132">doi:10.1038/nature12132</A>]['13].

%A N. J. Noh
%A et al ...
%A C. Webber
%T Network topologies and convergent aetiologies arising from deletions and
   duplications observed in individuals with autism
%J PLoS Genet
%V 9
%N 6
%P e1003523
%D 2013
%K eJrnl, MolBio, c2013, c201x, c20xx, zz0613, autism spectrum disorder, ASD,
   autistic, gene, genes, CNV, CNVs, deletion, duplication, gene, genes, brain,
   mental health, copy number variation, CNV, CNVs
%X "... Considering four sets of de novo copy # variants (CNVs) identified in
   181 individuals with autism & exploiting mouse functional genomics & known
   protein-protein interactions, we identified a large & sig. interconnected
   interaction n/wk. It contains 187 genes affected by CNVs drawn from 45% of
   the patients we considered & 22 genes prev. implicated in ASD, of which 192
   form a single interconnected cluster. On avg., those patients with copy #
   changed genes from this n/w possess changes in 3 n/w genes, suggesting that
   epistasis mediated through the n/w is extensive. ... genes that are highly
   connected within the n/w, & thus whose copy # change is predicted by the
   n/w to be more phenotypically consequential, are sig. enriched among patients
   that possess only a single ASD-associated n/w copy # changed gene (p=0.002).
   Strikingly, deleted or disrupted genes from the n/w are sig. enriched in
   GO-annotated positive regulators ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pgen.1003523">doi:10.1371/journal.pgen.1003523</A>]['13].

%A A. Snowball
%A et al ...
%A R. C. Kadosh
%T Long-term enhancement of brain function and cognition using cognitive
   training and brain stimulation
%J Curr. Biol.
%V 23
%N 11
%P 987-992
%M JUN
%D 2013
%K c2013, c201x, c20xx, zz0814, brain, electrical, stimulation, cognition,
    thinking, improvement, smarter, quicker, performance, arithmetic, recall,
    human, transcranial, magnetic, TRNS, TDCS, TMS,
    risks, side effects, controversial
%X "Noninvasive brain stimulation has shown considerable promise for enhancing
   cognitive fns ...  we investigate whether transcranial random noise
   stimulation (TRNS) can improve learning & subsequent performance on complex
   arithmetic tasks. ...  Five consec. days of TRNS-accompanied cognitive
   training enhanced the speed of both calculation- & memory-recall-based
   arithmetic learning. ...  Testing 6 months after training revealed long-
   -lasting behavioral & physiological modifications in the stimulated group
   [v.] sham controls for trained & nontrained calculation material. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cub.2013.04.045">doi:10.1016/j.cub.2013.04.045</A>]['14].
   (Also see [<A HREF="http://www.bbc.com/news/health-22556735">bbc</A>][17/5/2013],
      [<A HREF="http://dx.doi.org/10.1016/10.3389/fnhum.2014.00600">opinion</A>][5/8/2014] at [<A HREF="http://journal.frontiersin.org/Journal/10.3389/fnhum.2014.00600/full">FHN</A>][5/8/2014], and
      [<A HREF="http://www.bbc.com/news/health-27343047">bbc</A>][23/8/2014</A>].)
   [Also search for: transcranial stimulation].

%A H. Ledford
%T Myriad ruling causes confusion; change to gene patents leaves US biotech in
   a lather
%J Nature
%V 498
%N 7454
%P ?
%M JUN
%D 2013
%K news, c2013, c201x, c20xx, zz0613, MolBio, gene, genes, patent, patents, law,
   patentable, business, US, supreme court, courts, Myriad, BRAC1, BRAC2,
   natural, modified, DNA, cDNA
%X "... On 13 June, the US Supreme Court ended the 30-year-old practice of
   awarding patents on human genes ... naturally occurring human genes cannot
   be patented [but] patents can be claimed on modified DNA [and] gave explicit
   patent protection to a modified form of DNA called complementary DNA (cDNA),
   which is made in the lab with an enzyme that creates DNA using an RNA
   template.  ..."
   -- [<A HREF="http://dx.doi.org/10.1038/498281a">doi:10.1038/498281a</A>]['13].
   (Also see E. Marshall, Science, vol.340, no.6139, pp.1387-1388, 21 June 2013
   -- [<A HREF="http://dx.doi.org/10.1126/science.340.6139.1387">doi:10.1126/science.340.6139.1387</A>]['13].)

%A G. Bresler
%A M. Bresler
%T D. Tse
%T Optimal assembly for high throughput shotgun sequencing
%J Proc. Third Annual RECOMB Satellite Workshop on (RECOMB-seq 2013)
%D 2013
%K wShop, MolBio, c2013, c201x, c20xx, zz0314, sequence, assembly, algorithm,
   DEBRUIJN, MultiBridging, short read, reads, length
%X "... framework for the design of optimal assembly algs. for shotgun seq.
   under the criterion of complete reconstruction. We derive a lower bound on
   the read length & the coverage depth required for reconstruction in terms of
   the repeat statistics of the genome. ... design a de Brujin graph based
   assembly alg. which can achieve very close to the LWB for repeat statistics
   of a wide range of sequenced genomes, inc. the GAGE datasets. The results are
   based on a set of nec. & suff. conditions on the DNA seq. & the reads for
   reconstruction. The conditions can be viewed as the shotgun sequ. analogue of
   Ukkonen-Pevzner's nec. & suff. conditions for Sequencing by Hybridization."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-14-S5-S18">doi:10.1186/1471-2105-14-S5-S18</A>]['14], [27 refs].

%A Y. M. Shtarkman
%A Z. A. Kocer
%A R. Edga
%A R. S. Veerapaneni
%A T. D'Elia
%A P. F. Morris
%A S. O. Rogers
%T Subglacial Lake Vostok (Antarctica) accretion ice contains a diverse set of
   sequences from aquatic, marine and sediment-inhabiting bacteria and eukarya
%J PLoS ONE
%V 8
%N 7
%P e67221
%M JUL
%D 2013
%K jrnl, eJrnl, MolBio, c2013, c201x, c20xx, zz0713, Antarctica, lake, Vostok,
   subglacial, DNA, sequences, life
%X "... obtained 3,507 unique gene seqs from concentrates of 500 ml of
   0.22 mu_m filtered accretion ice meltwater. Taxonomic classifications (to
   genus and/or species) were possible for 1,623 of the seqs. Species
   determinations in combination with mRNA gene seq results allowed deduction of
   the metabolic pathways represented in the accretion ice &, by extension, in
   the lake. ~ 94% of the seqences were from Bacteria & 6% were from Eukarya.
   Only two sequences were from Archaea. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0067221">doi:10.1371/journal.pone.0067221</A>]['13].
   (Caution: *might* be past contamination.)

%A T. B. Quental
%A C. R. Marshall
%T How the Red Queen drives terrestrial mammals to extinction
%J Science
%V 341
%N 6143
%P 290-292
%M JUL
%D 2013
%K jrnl, biol, c2013, c201x, c20xx, zz0713, red queen, evolution, extinction,
   extinct, species, mammal, gamblers ruin, gambler, diversity
%X "Most species disappear by the processes of background extinction, yet those
   processes are poorly understood. We analyzed the evolutionary dynamics of 19
   Cenozoic terrestrial mammalian clades with rich fossil records that are now
   fully extinct or in diversity decline. We find their diversity loss was not
   just a consequence of 'gamblers ruin' but resulted from the evol.loss to the
   Red Queen, a failure to keep pace with a deteriorating environment. Diversity
   loss is driven equally by both depressed origination rates & elevated
   extinction rates. Although we find diversity-dependent origination &
   extinction rates, the diversity of each clade only transiently equaled the
   implied equilibrium diversity. Thus, the processes that drove diversity loss
   in terrestrial mammal clades were fundamentally nonequilibrial & overwhelmed
   diversity-dependent processes."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1239431">doi:10.1126/science.1239431</A>][13].
   [Also search for: Red Queen biol].

%A P. S. Churchland
%T Touching a Nerve: The Self as Brain
%I WWNorton
%P 304
%M JUL
%D 2013
%K book, text, c2013, c201x, c20xx, zz0713, brain, mind, self, consciousness,
   free will, soul, philosophy
%X 1st ed 2013; hb us$18; uk us isbn:0393058328; uk us isbn13:978-0393058321.
   "What happens when we accept that everything we feel and think stems not from
   an immaterial spirit but from electrical and chemical activity in our brains?
   ... how the latest research into consciousness, memory, and free will can
   help us reexamine enduring philosophical, ethical, and spiritual questions:
   What shapes our personalities? How do we account for near-death experiences?
   How do we make decisions? And why do we feel empathy for others? ..."
   [Also search for: free will].

%A K. Matija
%A S. Mile
%T SW# - GPU enabled exact alignments on genome scale
%J J. Bioinformatics
%V ?
%P ?-?
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0713, GPU, alignment, DPA
%X "... SW#, a new CUDA GPU enabled & memory efficient implementation of dynamic
   programming algs. for local alignment. It can be use as either a standalone
   appln or a library. Although there are other GPU implns of the Smith-Waterman
   alg., SW# is the only one publicly available that can produce seq.als. on
   genome-wide scale. For long seqs., it is at least a few hundred times faster
   than a CPU version of the same alg.." (online July 2013).
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btt410">doi:10.1093/bioinformatics/btt410</A>]['13],
      SW#@[<A HREF="http://complex.zesoi.fer.hr/SW.html">fer.hr</A>]['13].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">Alignment</A>].)

%A Y. Li
%A et al ...
%A S. ye
%T FtsZ protofilaments use a hinge-opening mechanism for constrictive force
   generation
%J Science
%V 341
%N 6144
%P 392-395
%K M JUL
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0713, protein, structure, hinge, FtsZ,
   guanosine triphosphatase, Zring, T3 loop, cytokinesis, bacterial
%X "The essential bacterial p. FtsZ is a guanosine triphosphatase that self-
   -assembles into a struct. at the divn site termed the 'Z ring'. During
   cytokinesis, the Zring exerts a constrictive force on the membrane by using
   the chemical energy of guanosine triphosphate hydrolysis. However, the
   structural basis of this constn remains unresolved. Here, we present the
   crystal structure of a guanosine diphosphate-bound Mycobacterium tuberculosis
   FtsZ protofilament, which exhibits a curved conformational state. The s.
   reveals a longitudinal interface that is important for fn. The protof.
   curvature highlights a hydrolysis-dept conformational switch at the T3 loop
   that leads to longitudinal bending between subunits, which could generate
   sufficient force to drive cytokinesis."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1239248">doi:10.1126/science.1239248</A>]['13].

%A A. Mashaghi
%A G. Kramer
%A P. Bechtluft
%A B. Zachmann-Brand
%A A. J. M. Driessen
%A B. Bukau
%A S. J. Tans
%T Reshaping of the conformational search of a protein by the chaperone trigger
   factor
%J Nature
%V 500
%P 98-101
%M JUL
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0813, protein folding, chaperone,
   chaperones, trigger factor, TF, chaperonin, MBP, misfold, state
%X "... chaperones are known to improve folding yields by suppressing
   aggregation between polypeptides before this conformational search starts ...
   ... experimental evidence has been scarce so far. ... To investigate the
   effect of TF from E.coli on the conf.search of polyps. to their native state,
   we investigated individual maltose binding protein (MBP) molecules using
   optical tweezers. Here we show that TF binds folded structs. smaller than one
   domain, which are then stable for seconds & ultimately convert to the native
   state. Moreover, TF stimulates native folding in constructs of repeated MBP
   domains. ... indicate that TF promotes correct folding by protecting
   partially folded states from distant interactions that produce stable
   misfolded states. As TF interacts with most newly synthesized proteins in
   E.coli, we expect these findings to be of general importance ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12293">doi:10.1038/nature12293</A>]['13].

%A C. Opiea
%A Q. D. Atkinson
%A R. I. M. Dunbar
%A S. Shultz
%T Male infanticide leads to social monogamy in primates
%J PNAS
%V ?
%P ?-?
%M JUL
%D 2013
%K jrnl, biol, c2013, c201x, c20xx, zz0813, mammal, primate, social, human,
   animal behaviour, pair bond, bonding, monogamy, male infanticide,
   altriciality, biparental, parenting
%X "Although common in birds, social monogamy, or pair-living, is rare among
   mammals ... A number of hypotheses have been proposed ...  Primates are
   unusual among m. because monogamy has evolved indep'ly in all of the major
   clades. ... combine trait data across 230 primate species with a Bayesian
   likelihood framework to test for correl. evoln between monogamy & a range of
   traits to evaluate the competing hypotheses. We find evidence of correlated
   evoln between social monogamy & both female ranging patterns & biparental
   care, but the most compelling explanation for the appearance of monogamy is
   male infanticide. ... reliably increases the probability of a shift to social
   monogamy, whereas monogamy allows the secondary adoption of paternal care &
   is assoc. with a shift to discrete ranges. The origin of social monogamy in
   primates is best explained by long lactation periods caused by altriciality,
   making primate infants particularly vulnerable to infanticidal males. We show
   that biparental care shortens relative lactation length, thereby reducing
   infanticide risk & increasing reproductive rates. These phylogenetic analyses
   support a key role for infanticide in the social evolution of primates, &
   potentially, humans."  [online 29 July 2013].
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1307903110">doi:10.1073/pnas.1307903110</A>]['13].
   [Also search for: monogamy].

%A X. Tian
%A et al ...
%A A. Seluanov
%T High-molecular-mass hyaluronan mediates the cancer resistance of the
   naked mole rat
%J Nature
%V 499
%N 7458
%P ?-?
%M JUL
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, cancer, resistance, ageing, rodent, rats,
   naked mole rat, Heterocephalus glaber, hyaluronan, HA, HAase, HAS2, HYAL2
%X "The naked mole rat (Heterocephalus glaber) displays exceptional longevity,
   with a max. lifespan exceeding 30 years. ... unusual resistance to cancer.
   ... found that NMR fibroblasts secrete extremely high-molecular-mass
   hyaluronan (HA), which is over five times larger than human or mouse HA. This
   ... HA accumulates abundantly in naked mole-rat tissues owing to the
   decreased activity of HA-degrading enzymes & a unique seq. of hyaluronan
   synthase 2 (HAS2). [&], the NMR cells are more sensitive to HA signalling, as
   they have a higher affinity to HA compared with mouse or human cells.
   Perturbation of the signalling pathways sufficient for malignant
   transformation of mouse fibroblasts fails to transform naked mole-rat cells.
   However, once high-molecular-mass HA is removed by either knocking down HAS2
   or overexpressing the HA-degrading enzyme, HYAL2, naked mole-rat cells
   become susceptible to malignant transformation ..."  [21 refs]
   -- [<A HREF="http://dx.doi.org/10.1038/nature12234">doi:10.1038/nature12234</A>]['15].
   [Also search for: cancer mole rat].

%A B. Barzel
%A A.-L. Barabasi
%T Network link prediction by global silencing of indirect correlations
%J Nature Biotech.
%V 31
%P 720-725
%M JUL
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0816, networks, controversial, Ecoli,
   silencing, correlation, systems biology, biological, II
%X "Predictions of physical & functional links between cellular components are
   often based on correlations between experimental measurements, such as gene
   expression. However, correlations are affected by both direct & indirect
   paths, confounding our ability to identify true pairwise interactions. Here
   we exploit the fundamental properties of dynamical correlations in nwks to
   develop a method to silence indirect effects. The method receives as input
   the observed correlations between node pairs & uses a matrix transformation
   to turn the correlation matrix into a highly discriminative silenced matrix,
   which enhances only the terms assoc. with direct causal links. Against
   empirical data for Ecoli regulatory interactions, the method enhanced the
   discriminative power of the correlations by twofold, yielding >50% predictive
   improvement over trad. correlation measures & 6% over mutual info..  ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nbt.2601">doi:10.1038/nbt.2601</A>]['16].
   (* BUT, "... Nature Biotechnology cited two of its studies that were
      called into question by scientists who could not replicate the
      conclusions ..."
      -- [<A HREF="http://dx.doi.org/10.1038/520276a">doi:10.1038/520276a</A>]['16]. *)
   [Also search for: Barabasi networks] and
   [also search for: Hayden rule c2015].

%A P. Doherty
%T Pandemics: What Everyone Needs to Know
%I OUP
%P 272
%M AUG
%D 2013
%K book, text, c2013, c201x, c20xx, zz0820, PCDoherty, infection, disease,
   epidemic, pandemic, vaccine, vaccination, spread, resistance, pathogen,
   virus, viruses, Spanish flu, influenza, SARS, Wuhan, human, public health
%X 1st ed 2013; hb us$82; uk us isbn:0199898103; uk us isbn13:978-0199898107.
  "... an essential guide to one of the truly life-or-death issues of our age.
   In concise, question-and-answer format, he explains the causes of pandemics,
   how they can be counteracted with vaccines and drugs, and how we can better
   prepare for them in the future. ..."

%A D. Lukas
%A T. H. Clutton-Brock
%T The evolution of social monogamy in mammals
%J Science
%V 342
%N 6145
%P 526-530
%M AUG
%D 2013
%K jrnl, Biol, c2013, c201x, c20xx, zz0813, mammal, primate, human, monogamy,
   animal behaviour, parenting
%X "... show that the ancestral condition for all mammalian groups is of
   solitary individuals & that social monogamy is derived almost exclusively
   from this social system. The evolution of social monogamy does not appear to
   have been associated with a high risk of male infanticide, & paternal care
   is a consequence rather than a cause of social monogamy. Social monogamy has
   evolved in nonhuman mammals where breeding females are intolerant of each
   other & female density is low, suggesting that it represents a mating
   strategy that has developed where males are unable to defend access to
   multiple females."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1238677">doi:10.1126/science.1238677</A>]['13].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.1242001">views</A>]['13].)
   [Also search for: monogamy].

%A G. D. Poznik
%A et al ...
%A C. D. Bustamante
%T Sequencing Y chromosomes resolves discrepancy in time to common ancestor of
   males versus females
%J Science
%V 341
%N 6145
%P 562-565
%M AUG
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0813, DNA, Ychr, y chromosome, chrY,
   chr Y, origin, modern human, Adam, Eve, evolution, hypothesis, MRCA, TMRCA
%X "The Y chromosome and the mitochondrial genome have been used to est. when
   the common patrilineal & matrilineal ancestors of humans lived. We seq. the
   genomes of 69 males from nine popns, inc. two in which we find basal branches
   of the Y-chr. tree. We identify ancient phylogenetic structure within African
   haplogroups & resolve a long-standing ambiguity deep within the tree.
   Applying equivalent methodologies to the Y chr. & the mitochondrial genome,
   we est. the time to the most recent common ancestor (TMRCA) of the Y chr. to
   be 120 to 156 thousand years & the mitochondrial genome TMRCA to be 99 to 148
   thousand years. ... suggest that, contrary to previous claims, male lineages
   do not coalesce significantly more recently than female lineages."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1237619">doi:10.1126/science.1237619</A>]['13].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.1242899">views</A>].)
   (Note, it is not necessary that the male & female MRCAs knew each other.-)
   [Also search for: MolBio Adam]  and  [also search for: MolBio Eve].

%A P. Francalacci
%A et al ...
%A F. Cucca
%T Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome
   phylogeny
%J Science
%V 341
%N 6145
%P 565-569
%M AUG
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0813, DNA, Ychr, y chromosome, chrY,
   chr Y, origin, modern human, Adam, Eve, MRCA, TMRCA
%X "Genetic variation within the male-specific portion of the Y chr. (MSY) can
   clarify the origins of contemporary popns, but prev. studies were hampered by
   partial genetic info.. Population sequencing of 1204 Sardinian males
   identified 11,763 MSY single-nucleotide polymorphisms, 6751 of which have
   not previously been observed. We constructed a MSY phylogenetic tree
   containing all main haplogroups found in Europe, along with many Sardinian-
   -specific lineage clusters within each haplogroup. ... calibrated with
   archaeological data from the initial expansion of the Sardinian popn ~7700
   years ago. The ages of nodes highlight different genetic strata in Sardinia &
   reveal the presumptive timing of coalescence with other human popns. We
   calculate a putative age for coalescence of ~180,000 to 200,000 y.ago,
   which is consistent with prev. mitochondrial DNA-based ests.."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1237947">doi:10.1126/science.1237947</A>]['13].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.1242899">views</A>].)

%A G. Stoll
%A et al ...
%A A. Palotie
%T Deletion of TOP3B a component of FMRP-containing mRNPs, contributes to
   neurodevelopmental disorders
%J Nature Neuroscience
%V ?
%P ?-?
%M AUG
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0813, TOP3B, TOP 3B, TOP3beta, beta,
   FMRP, mRNP, mRNPs, autism, schizophrenia, fragile X, fragileX, X chromosome,
   Xchr, chrX, 22q11.22, Finland, brain, development, disorder, Finland
%X "... rarity of most high-impact genetic variants typically precludes the
   poss. of accruing stat. evidence that they are assoc. with a given trait. We
   found that the enrichment of a rare chr. 22q11.22 deln in a recently expanded
   N.Finnish sub-isolate enabled the detection of assoc. between TOP3B & both
   schizophrenia & cognitive impairment. Biochem. analysis of TOP3B revealed
   that this topoisomerase was a component of cytosolic messenger
   ribonucleoproteins (mRNPs) & was catalytically active on RNA. The recruitment
   of TOP3B to mRNPs was indep. of RNA cis-elements & was coupled to the co-
   -recruitment of FMRP, the disease gene product in fragile X mental
   retardation syndrome. Our results indicate a prev. unknown role for TOP3B in
   mRNA metabolism & suggest that it is involved in neurodev. disorders."
   -- [<A HREF="http://dx.doi.org/10.1038/nn.3484">doi:10.1038/nn.3484</A>]['13].

%A V. Roukos
%A T. C. Voss
%A C. K. Schmidt
%A S. Lee
%A D. Wangsa
%A T. Misteli
%T Spatial dynamics of chromosome translocations in living cells
%J Science
%V 341
%N 6146
%P 660-664
%M AUG
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0813, cancer, cell, medical, health,
   DNA, chromosomes, double strand break, DSB, DSBs, translocation, error,
   errors
%X "... demonstrate that translocations form within hours of the occurrence of
   double-strand breaks (DSBs) & that their formation is cell cycle-indep..
   Translns form preferentially between prepositioned genome elts, &
   perturbation of key factors of the DNA repair machinery uncouples DSB pairing
   from transln formation. These observations generate a spatiotemporal [!]
   framework for the formation of translocations in living cells."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1237150">doi:10.1126/science.1237150</A>]['13].

%A L. B. Alexandrov
%A et al ...
%A M. R. Stratton
%T Signatures of mutational processes in human cancer
%J Nature
%V 500
%N ?
%P 415-421
%M AUG
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0813, medicine, health, cancer, cell,
   DNA, mutation, kataegis, signature, signs, repair,
   APOBEC, BRCA1, BRCA2, stats
%X "... analysed 4,938,362 mutns from 7,042 cancers & extracted more than 20
   distinct mutational signatures. Some are present in many c. types, notably a
   sig. attributed to the APOBEC family of cytidine deaminases, whereas others
   are confined to a single cancer class. Certain sigs. are assoc. with age of
   the patient at c. diagnosis, known mutagenic exposures or defects in DNA
   maintenance, but many are of cryptic origin. [&] to these genome-wide
   mutational sigs., hypermutation localized to small genomic regions 'kataegis'
   is found in many c. types. ... reveal the diversity of mutational processes
   underlying the development of c., with potential implications for
   understanding of cancer aetiology, prevention & therapy." [online Aug 2013.]
   -- [<A HREF="http://dx.doi.org/10.1038/nature12477">doi:10.1038/nature12477</A>]['13].

%A D. van Ditmarsch
%A et al ...
%A J. B. Xavier
%T Convergent evolution of hyperswarming leads to impaired biofilm formation in
   pathogenic bacteria
%J Cell Reports
%V ?
%P ?-?
%M AUG
%D 2013
%K jrnl, biol, c2013, c201x, c20xx, zz0813, bacterium, hyper swarming, swarm,
   Pseudomonas aeruginosa, FleN, mutation, selection, motility
%X "Most bacteria in nature live in surface-assoc. communities rather than
   planktonic popns. ... show that subjecting Pseudomonas aeruginosa to repeated
   rounds of swarming, a collective form of surface migration, drives
   remarkable parallel evoln toward a hyperswarmer phenotype. In all indep.
   evolved hyperswarmers, the reproducible [hs] phenotype is caused by parallel
   pt mutations in a flagellar synthesis regulator, FleN, which locks the
   naturally monoflagellated bacteria in a multiflagellated state & confers a
   growth rate-indep. advantage in swarming. Although hyperswarmers outcompete
   the ancestral strain in swarming competitions, they are strongly outcompeted
   in biofilm formation, which is an essential trait for P.aeruginosa in
   environmental & clinical settings. The finding that evoln in swarming
   colonies reliably produces evoln of poor biofilm formers supports the
   existence of an evol. trade-off between motility & biofilm formation."
   -- [<A HREF="http://dx.doi.org/10.1016/j.celrep.2013.07.026">doi:10.1016/j.celrep.2013.07.026</A>]['13].

%A I. Manov
%A et al ...
%A I. Shams
%T Pronounced cancer resistance in a subterranean rodent, the blind mole-rat,
   Spalax: in vivo and in vitro evidence
%J BMC Biology
%V 11
%P e91
%M AUG
%D 2013
%K jrnl, eJrnl, biol, c2013, c201x, c20xx, Asian blind mole rat, rats,
   anti, cancer, resistance, spalacid, Spalax, Nrf2, HO1, rodent, carcinogen
%X "... Treating animals with 3-Methylcholantrene (3MCA) and
   7,12-Dimethylbenz(a) anthracene/12-O-tetradecanoylphorbol-13-acetate
   (DMBA/TPA), two potent carcinogens, confirmed Spalax high resistance to
   chemically induced cancers. While all mice and rats developed the expected
   tumors following treatment with both carcinogens, among Spalax no tumors were
   observed after DMBA/TPA treatment, while 3MCA induced benign fibroblastic
   proliferation in 2 Spalax individuals out of12, and only a single animal from
   the advanced age group developed malignancy 18 months post-treatment. The
   remaining animals are still healthy 30 months post-treatment. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1741-7007-11-91">doi:10.1186/1741-7007-11-91</A>]['13].
   [Also search for: cancer mole rat].

%A T.-T. Lin
%T Statin use and the incidence of dementia in the elderley: a nation-wide
   data survey
%J Euro. Soc. Cardiology (ESC) Congress
%M AUG
%D 2013
%K conf, c2013, c201x, c20xx, zz0913, dementia, statins, human health, ageing
%X "High dose statins prevent dementia. Conclusion - Risk of new-onset dementia
   was decreased in elderly subjects who received statins in either high daily
   dosage or total dosage. ..."
   -- slides@[<A HREF="http://www.escardio.org/about/press/esc-congress-2013/press-conferences/Documents/slides/lin.pdf">esc</A>]['13].
   "... The study of nearly 58,000 patients found that high potency statins had
   the strongest protective effects against dementia. ... BUT recent reports of
   statin-associated cognitive impairment have led the US [FDA] to list
   statin-induced cognitive changes, especially for the older population,
   in its safety communications. ..."
   -- p.r.@[<A HREF="http://www.escardio.org/about/press/press-releases/esc13-amsterdam/Pages/statins-dementia-elderly.aspx">esc</A>]['13].

%A M. Fox
%A L. A. Knapp
%A P. W. Andrews
%A C. L. Fincher
%T Hygiene and the world distribution of Alzheimer's disease
%J Evol., Medicine and Public Health
%V ?
%P eot015
%M AUG
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0913, hygiene hypothesis, hygene, health,
   medicine, Alzheimer's disease, dementia
%X "... it appears that hygiene is positively associated with AD risk. Countries
   with greater degree of sanitation and lower degree of pathogen prevalence
   have higher age-adjusted AD DALY rates. Countries with greater degree of
   urbanization and wealth exhibit higher age-adjusted AD DALY rates. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/emph/eot015">doi:10.1093/emph/eot015</A>]['13].

%A C. R. O'Donnell
%A H. Wang
%A W. B. Dunbar
%T Error analysis of idealized nanopore sequencing
%J Electrophoresis
%I WileyVCH
%V 34
%N 15
%P 2137-2144
%M AUG
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0714, nanopore, single molecule, SMRT,
   read, reads, base calling, error, errors, analysis
%X "... error analysis of an idealized nanopore seq. method in which ionic
   current measurements are used to seq. intact single-stranded DNA in the pore
   ... Examples of systematic channel errors when more than one nucleotide
   affects the current amplitude are detailed, which if present will persist
   regardless of coverage. Absent such errors, random errors assoc. with
   tracking through homopolymer regions are shown to necessitate reading known
   seqs. (Ecoli K-12) at least 140 times to achieve 99.99% accuracy (Q40). By
   exploiting the ability to reread each strand at each pore in an array,
   arbitrary positioning on an error rate versus throughput tradeoff curve is
   possible if systematic errors are absent, with throughput governed by the
   number of pores in the array & the enzyme turnover rate."   [via M.]
   -- [<A HREF="http://dx.doi.org/10.1002/elps.201300174">doi:10.1002/elps.201300174</A>]['14], $ub$cription.
   [Also search for: MolBio single molecule sequencing]  and
   [also search for: MolBio SMRT errors].

%A J. A. Anguera
%A J. Boccanfuso
%A J. L. Rintoul
%A O. Al-Hashimi
%A F. Faraji
%A J. Janowich
%A E. Kong
%A Y. Larraburo
%A C. Rolle
%A E. Johnston
%A A. Gazzale
%T Video game training enhances cognitive control in older adults
%J Nature
%V 501
%P 97-101
%M SEP
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0913, age, ageing, brain, video game, gaming,
   NeuroRacer, multitasking, gain, gains, benefit, human, aged, old, adult
%X "Cognitive control is defined by a set of neural processes that allow us to
   interact with our complex environment in a goal-directed manner. ... show
   that multitasking performance, as assessed with a custom-designed 3D video
   game (NeuroRacer), exhibits a linear age-related decline from 20 to 79 years
   of age. By playing an adaptive version of NeuroRacer in multitasking training
   mode, older adults (60 to 85 y.) reduced multitasking costs compared to both
   an active control group & a no-contact control group, attaining levels beyond
   those achieved by untrained 20-year-old participants, with gains persisting
   for 6 months. ... resulted in performance benefits that extended to untrained
   cognitive control abilities (enhanced sustained attention & working memory),
   with an increase in midline frontal theta power predicting the training-
   -induced boost in sustained attention & preservation of multitasking
   improvement 6 months later. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12486">doi:10.1038/nature12486</A>]['13].

%A D. Ornish
%A et al ...
%A E. H. Blackburn
%T Effect of comprehensive lifestyle changes on telomerase activity and telomere
   length in men with biopsy-proven low-risk prostate cancer: 5-year follow-up
   of a descriptive pilot study
%J Lancet Oncology
%V ?
%P ?-?
%M SEP
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0913, exercise, diet, lifestyle, eating, stress,
   activity, exercise, telomeres, length, five years, prostate, cancer,
   human health, ageing
%X "... Men in the intervention group followed a programme of comprehensive
   lifestyle changes (diet, activity, stress management, & social support) ...
   Relative telomere len. increased from baseline by a median of 0.06 telomere
   to single-copy gene ratio (T/S)units (IQR-0.05 to 0.11) in the lifestyle
   intervention group, but decreased in the control group (-0.03 T/S units,
   -0.05 to 0.03, diff p=0.03).  When data from the two groups were combined,
   adherence to lifestyle changes was sig. assoc. with rel. telomere length
   after adjustment for age & the length of follow-up (for each % pt increase
   in lifestyle adherence score, T/S units increased by 0.07, 95% CI 0.02-0.12,
   p=0.005). At 5 years, telomerase activity had decreased from baseline by 0.25
   (-2.25 to 2.23) units in the lifestyle intervention group, & by
   1.08 (-3.25 to 1.86) units in the control group (p=0.64) & was not assoc.
   with adher. to lifestyle changes (rel. risk 0.93, 95% CI 0.72-1.20, p=0.57)."
   -- [<A HREF="http://dx.doi.org/10.1016/S1470-2045(13)70366-8">doi:10.1016/S1470-2045(13)70366-8</A>]['13], online Sept.2013,
   and [<A HREF="http://www.bbc.co.uk/news/health-24111357">bbc</A>][17/9/2013].
   (NB. small study, tentative.)
   [Also search for: telomere aging].

%A R. A. Dunlop
%A P. A. Cox
%A S. A. Banack
%A K. J. Rodgers
%T The non-protein amino acid BMAA is misincorporated into human proteins in
   place of l-serine causing protein misfolding and aggregation
%J PLoS One
%V 8
%N 9
%P e75376
%M SEP
%D 2013
%K jrnl, eJrnl, MolBio, c2013, c201x, c20xx, zz1013, motor neurone disease, ALS,
   Amyotrophic Lateral Sclerosis, beta-N-methylamino-L-alanine, BMAA,
   l-serine, amino acid, protein misfold, misfolding, cyanobacteria,
   blue green alga, algae, toxin, contamination, diet, Guam
%X "Mechanisms of protein misfolding ... Amyotrophic Lateral Sclerosis (ALS),
   Alzheimer's disease (AD), Parkinson's disease (PD), Lewy Body Dementia (LBD),
   & Progressive Supranuclear Palsy (PSP). ... We here report that a non-protein
   amino acid, beta-N-methylamino-L-alanine (BMAA), can be misincorporated in
   place of l-serine into human proteins. We also report that this
   misincorporation can be inhibited by l-serine. Misincorporation of BMAA into
   human neuroproteins may shed light on putative associations between human
   exposure to BMAA produced by cyanobacteria & an increased incidence of ALS."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0028090">doi:10.1371/journal.pone.0028090</A>]['13].  [auth1 @ UTS.]
   (Also see [<A HREF="http://www.abc.net.au/news/2013-09-26/scientists-discover-potential-cause-of-motor-neurone-disease/4981598">abc</A>][26/9/2013].)

%A P. Tabakow
%A et al ...
%A G. Rasman
%T Transplantation of autologous olfactory ensheathing cells in complete human
   spinal cord injury
%J Cell Transplant.
%V 22
%N 9
%D 2013
%K jrnl, c2013, c201x, c20xx, zz1014, medicine, spinal cord, injury, spine,
   column, nerve, nerves, transplant, cell, treatment, human
%X "Numerous studies in animals have shown the unique property of olfactory
   ensheathing cells to stimulate regeneration of lesioned axons in the spinal
   cord. In a Phase I clinical trial, weassessed the safety & feasibility of
   transplantation of autologous mucosal olfactoryensheathing cells &
   olfactory nerve fibroblasts in patients with complete spinal cord injury. ...
   ... Observations at 1 year indicate that the obtaining, culture &
   intraspinal transplantation ofautologous olfactory ensheathing cells was
   safe & feasible. The significance of the neurological improvement in the
   transplant recipients & the extent to which the cell transplants contributed
   to it will require larger numbers of patients."
   -- ?[<A HREF="http://dx.doi.org/10.3727/096368913X663532">doi:10.3727/096368913X663532</A>]['14]?
   at [<A HREF="https://www.cognizantcommunication.com/journal-titles/cell-transplantation">cognizant</A>]['14],
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/23561833">p'bmed</A>]['14],
   last_auth@[<A HREF="https://iris.ucl.ac.uk/iris/browse/profile?upi=GRAIS26">ucl.ac</A>]['14].
   NB. still very experimental.
   (Also see [<A HREF="http://www.bbc.com/news/health-29645760">bbc</A>][21/10/'14].)

%A N. E. Potter
%A L. Ermini
%A E. Papaemmanuil
%A G. Cazzaniga
%A G. Vijayaraghavan
%A I. Titley
%A A. Ford
%A P. Campbell
%A L. Kearney
%A M. Greaves
%T Single-cell mutational profiling and clonal phylogeny in cancer
%J Genome Res.
%V 23
%P 2115-2125
%M NOV
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz1113, cancer, cell, diversity, genetic,
   clonal, mutations, variation, variants
%X "... cancer is a dynamic evolutionary process in which intraclonal, genetic
   diversity provides a substrate for clonal selection & a source of therapeutic
   escape. The complexity & topography of intraclonal genetic architectures
   have implications for biopsy-based prognosis & for targeted therapy.
   High-depth, next-generation sequencing (NGS) ... a microfluidic platform
   unbiased single-cell selection ... chimeric gene fusions, copy # alterations,
   & single-nucleotide variants. We show, in this proof-of-principle study,
   that the method has a low error rate & can provide detailed subclonal
   genetic architectures & phylogenies."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.159913.113">doi:10.1101/gr.159913.113</A>]['13],
      [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/24056532">pubm'd</A>]['13].
   (Also see [<A HREF="http://www.bbc.co.uk/news/health-24957089">bbc</A>][16/11/2013].)
   [Also search for: MolBio cancer clonal].

%Q The Genographic Consortium
%A G. Brandt
%A et al ...
%A K. W. Alt
%T Ancient DNA reveals key stages in the formation of central European
   mitochondrial genetic diversity
%J Science
%V 342
%N 6155
%P 257-261
%M OCT
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz1013, human, history, prehistory,
   Europe, races, mitochondria, mtDNA, Neolithic, Mesolithic, Bronze Age,
   origins
%X "...  generated mtDNA profiles of 364 individuals from prehistoric cultures
   in Central Europe to perform a chronological study, spanning the Early
   Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the
   common era). We used this transect through time to identify four marked
   shifts in genetic composition during the Neolithic period, revealing a key
   role for Late Neolithic cultures in shaping modern Central European genetic
   diversity."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1241844">doi:10.1126/science.1241844</A>]['13].
   [Also search for: MolBio ancient DNA].

%A P. J. Yang
%A J. C. Pham
%A J. Choo
%A D. L. Hu
%T Law of urination: All mammals empty their bladders over the same duration
%J arXiv
%M OCT
%D 2013
%O American Physical Soc. Divn of Fluid Dynamics, Nov. 2013
%K arXiv, c2013, c201x, c20xx, zz1013, zz0915, pee, peeing, urine, bladder,
   mammal, Law of Urination, urinating, duration, time, urethra, IgNobel
%X "The urinary system evolved to eject fluids from the body quickly &
   efficiently. ... we elucidate the hydrodynamics of urination across five
   orders of magnitude in animal mass, from mice to elephants. Using high-speed
   fluid dynamics videos & flow-rate measurement at Zoo Atlanta, we discover the
   "Law of Urination", which states animals empty their bladders over nearly
   constant duration of average 21 seconds (s.d. 13s.), despite a difference in
   bladder volume from 100mL to 100L. ... made possible by the increasing
   urethra length of large animals which amplifies gravitational force & flow
   rate. ... demo. the challenges faced by the urinary system for rodents &
   other small mammals for which urine flow is limited to single drops. ...
   reveal the urethra evolved as a flow-enhancing device, enabling the urinary
   system to be scaled up without compromising its fn. ... may help in the
   diagnosis of urinary problems in animals & in inspiring the design of
   scalable hydrodynamic systems based on those in nature."
   -- 1310.3737@[<A HREF="http://arxiv.org/abs/1310.3737">arXiv</A>]['13].
   (???igNobel 2014 anyone?-)
   (Yes! But in 2015 - see bbc@[<A HREF="http://www.bbc.com/news/science-environment-34278595">18/9/2015</A>]!)
   [Also search for: defecation poo].

%A J. C. Venter
%T Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life
%I VikingAdult
%P 240
%M OCT
%D 2013
%K book, MolBio, c2013, c201x, c20xx, zz1013, synthetic, life, nature, DNA
%X 1st ed 2013; hb us$17; uk us isbn:0670025402; uk us isbn13:978-0670025404.
   "In 2010, scientists led by JCV became the 1st to successfully create
   'synthetic life' ... most important and exciting phase of biological research
   one that will enable us to actually write the genetic code for designing new
   species to help us adapt and evolve for long-term survival. The science of
   synthetic genomics will have a profound impact on human existence, inc.
   chemical and energy generation, health, clean water and food production,
   environmental control, and possibly even our evolution. ..."

%A M. Balter
%T Ancient DNA links native Americans with Europe
%J Science
%V 342
%N 6157
%P 409-410
%M OCT
%D 2013
%K news, c2013, c201x, c20xx, zz1013, MolBio, human, American, native,
   Europeean, Asian, migration, origins, history, DNA, Willerslev
%X "... the complete nuclear genome of a Siberian boy who died 24,000 y. ago -
   the oldest complete genome of a modern human sequenced to date. ...
   apparently descended not from East Asians, but from people who had lived in
   Europe or W.Asia. The finding suggests that about a third of the ancestry of
   today's Native Americans can be traced to 'western Eurasia,' with the other
   two-thirds coming from eastern Asia, ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.342.6157.409">doi:10.1126/science.342.6157.409</A>]['13].
   [Also search for: MolBio ancient DNA].

%A E. A. Rodland
%T Compact representation of k-mer de Bruijn graphs for genome read assembly
%J BMC Bioinformatics
%V 14
%N 10
%P ?-?
%M OCT
%D 2013
%K jrnl, eJrnl, MolBio, c2013, c201x, c20xx, zz1113, sequence assembly,
   genome, deBruijn, graph,, FM index, k mer, kMer, kFM index, succinct, space,
   short read, reads
%X "... The FM-index, which is based on the BW transform ... the memory required
   to store [index] is in the same order of magnitude as the strings themselves.
   However, reads from high throughput seqs. mostly have high coverage & so
   contain the same substrings multiple times from different reads. ... present
   a mod. of the FM-index, which I call the kFM-index, for indexing the set of
   k-mers from the reads. For DNA seqs, this requires 5 bit of info. [per]
   vertex of the corr. de Bruijn subgraph, i.e. for each different (k-1)-mer,
   plus some additional o'head, typically 0.5 to 1 bit/vertex, for storing the
   equiv. of the FM-index for walking the underlying de B. graph & reproducing
   the actual k-mers efficiently. The kFM-index could replace more memory
   demanding data structs. for storing the de B. k-mer graph repn of seq. reads.
   A Java implementation ... provided ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-14-313">doi:10.1186/1471-2105-14-313</A>]['13].
   [Also search for: short read MolBio].

%A M. J. Wiser
%A N. Ribeck
%A R. E. Lenski
%T Long-term dynamics of adaptation in asexual populations
%J Science
%V 342
%P 1364-1367
%M DEC
%D 2013
%K jrnl, Biol, c2013, c201x, c20xx, zz1113, bacteria, bacterial, Ecoli,
   Escherichia coli, population, mutation, evolution, selection, fitness
%X "... examine fitness trajectories for 12 Escherichia coli populations
   during 50,000 generations. Mean fitness appears to increase without bound,
   consistent with a power law. We also derive this power-law relation
   theoretically by incorporating clonal interference & diminishing-returns
   epistasis into a dynamical model of changes in mean fitness over time."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1243357">doi:10.1126/science.1243357</A>]['13], online 14/11/13, 40 refs.
   (Also see news@[<A HREF="http://dx.doi.org/10.1126/science.342.6160.790">www</A>][15/11/13].)

%A S. Jin
%A Y. Li
%A R. Pan
%A X. Zou
%T Characterizing and controlling the inflammatory network during influenza A
   virus infection
%J Scientific Reports
%V 4
%P e3799
%M JAN
%D 2014
%K eJrnl, MolBio, c2014, c201x, c20xx, zz0614, health, medicine, biology,
   inflammatory network, entropy, inflammation, flu, fluA, H5N1, H1N1,
   influenza A, virus, TLR2, IL1beta, IL10, NFkappaB, TNFSF10, HDAC4, HDAC5,
   protein interaction, PPI, signaling, signalling, DMGBDE
%X "... characterizing the inflammatory n/w & identifying key proteins by
   combining high-throughput data & computational techniques. We constructed the
   cell-specific normal & inflammatory networks for H5N1 & H1N1 infections ...
   demonstrated that better discrimination between normal & inflammatory n/ws by
   n/w entropy than by other topological metrics. ..."
    * "... First, the rough PPI n/w containing 90 nodes & 412 edges
      [supp. fig. S18] was constructed using PPI databases ... Pearson correln
      coeffs. ... filter ...  obtained the refined normal & inflammatory n/ws
      induced by H5N1 & H1N1. ... built the ordinary differential equation (ODE)
      models for the refined n/ws & used an improved conjugate gradient method
      (ICG) to identify the params. in the models. Finally, Akaike Info.
      Criterion (AIC) was employed to determine whether the interactions between
      two proteins were sig. or just false positives ..."
    * "... we proposed a definition of network entropy ..."
    * "local n/w entropy of node i,
      S_i = -(1/log k_i) SUM_(j in N(i)) (p_ij log p_ij)
         where k_i is degree(i) [ref 21, Teschendorff 2010]. ...
      global network entropy, S = SUM_i=1..n (C_i S_i)
         where degree centrality C_i = k_i/(n-1)."
   -- [<A HREF="http://dx.doi.org/10.1038/srep03799">doi:10.1038/srep03799</A>]['15].
   (supp. fig. S18 is not m/c readable.)

%A K. Prufer
%A et al ...
%A S. Paabo
%T The complete genome sequence of a Neanderthal from the Altai Mountains
%J Nature
%V 505
%N 7481
%P 43-49
%M JAN
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0114, Neanderthal, genome, nGenome, DNA,
   human, ancestor, ancient, old, Denisovan, modern humans
%X "... a high-quality genome sequence of a Neanderthal woman from Siberia. We
   show that her parents were related at the level of half-siblings & that
   mating among close relatives was common among her recent ancestors. [&]
   sequenced the genome of a Neanderthal from the Caucasus to low coverage. An
   analysis of the relationships & popln history of available archaic genomes &
   25 present-day human genomes shows that several gene flow events occurred
   among Neanderthals, Denisovans & early modern humans, possibly inc. gene flow
   into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of
   low magnitude, occurred among many hominin grps in the Late Pleistocene. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12886">doi:10.1038/nature12886</A>]['13] online 19/12/2013.
   [Also search for: ancient human DNA].

%A Shuai Cheng Li
%T The difficulty of protein structure alignment under the RMSD
%J Algorithms for Molec. Biol.
%V 8
%N 1
%M JAN
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz1214, protein, structure, alignment, 3D,
   RMSD, LCP
%X "P.structure alignment is often modeled as the largest common point set (LCP)
   problem based on the ... (RMSD) ... To study why the LCP problem is difficult
   we define a natural variant of the problem, called the minimum aligned
   distance (MAD) [where] the length of the subseq. to obtain is specified in
   the input; & instead of fulfilling a threshold, the RMSD between the pts of
   the two subsequs. is to be minimized. ... By placing a limit on the distance
   between consecutive pts, & assuming that the pts are specified as integral
   values, we show that both problems are equally difficult, in the sense that
   they are reducible to each other. In this case, both problems can be exactly
   solved in polynomial time, although the time complexity remains high. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1748-7188-8-1">doi:10.1186/1748-7188-8-1</A>]['14].
   [Also search for: MolBio protein structure alignment] and
   [also search for: Kearsley vector sets].

%A M. G. Rossmann
%T Super-secondary structure: A historical perspective
%P 1-4
%B Protein Supersecondary Structures
%S Methods in Molec. Biol.
%I Springer
%V 932
%M JAN
%D 2013
%K chapter, MMB, MolBio, c2013, c201x, c20xx, zz0916, protein, superSecondary,
   super secondary structure, fold, folds, function, Rossmann, rossman,
   historical, history, origin
%X "The history of the concept of protein folds is discussed, starting with
   the original concept of super-secondary structure. This has led to the
   recognition of a fairly small number of distinct folds defining individual
   domains within larger proteins. Each fold can usually be associated with a
   specific fn. Thus the active site of an enzyme is likely to be at the
   boundary between domains, each contributing a simple fn to a more complex
   process."
   -- [<A HREF="http://dx.doi.org/10.1007/978-1-62703-065-6_1">doi:10.1007/978-1-62703-065-6_1</A>]['16].
   [Also search for: MolBio super secondary structure].

%A C. H. S. Barwood
%A B. E. Murdoch
%T Cognitive linguistic deficits in relapsing-remitting multiple sclerosis
%J Aphasiology
%V 27
%N 12
%P 1459-1471
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0414, deficit, human health, language, MS,
   UQ, uniQld, controversial, University, Queensland, withdrawl, retraction,
   scandal, ethics, integrity, academic, scientific, research
%X "... findings suggestive of both expressive language and
   higher-level language dysfunction in RR subtype MS ..."
   RETRACTED 4/2014; see [<A HREF="http://www.abc.net.au/news/2014-04-04/uq-research-retraction-barwood-murdoch/5368800">abc</A>][5/4/2014].
   [Also search for: Barwood Murdoch].

%A A. Dobin
%A et al ...
%A T. R. Gingeras
%T STAR: ultrafast universal RNA-seq aligner
%J Bioinformatics
%V 29
%N 1
%P 15-21
%M OCT
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0820, RNA seq, RNAseq, mapping,
   reference, reads, splice junction, splicing
%X "... align our large (> 80 billon reads) ENCODE Transcriptome RNA-seq dataset
   we developed the Spliced Transcripts Alignment to a Reference (STAR) s/w ...
   550 million 2x76bp paired-end reads per hour on a modest 12-core server ...
   can discover non-canonical splices and chimeric (fusion) transcripts ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/bts635">doi:10.1093/bioinformatics/bts635</A>]['20].
   [Also search for: MolBio RNAseq].

%A Y. Okada
%A et al ...
%A R. M. Plenge
%T Genetics of rheumatoid arthritis contributes to biology and drug discovery
%J Nature
%V ?
%N ?
%P ?-?
%M DEC
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz1213, rheumatoid arthritis, RA, GWAS,
   association study, SNP, SNPs, gene, genes
%X "... a genome-wide assoc. study meta-analysis in a total of > 100,000
   subjects of European & Asian ancestries (29,880 RA cases & 73,758 controls),
   by evaluating ~10 million SNPs. We discovered 42 novel RA risk loci at a
   genome-wide level of sig., bringing the total to 101 (refs 2, 3, 4). We
   devised an in silico pipeline using established bioinformatics methods based
   on functional annotation, cis-acting expression quantitative trait loci &
   pathway analyses - as well as novel methods based on genetic overlap with
   human primary immunodeficiency, haematological cancer somatic mutations &
   knockout mouse phenotypes - to identify 98 biological candidate genes at
   these 101 risk loci. We demonstrate that these genes are the targets of
   approved therapies for RA ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12873">doi:10.1038/nature12873</A>]['13], online 25/12/2013.

%A F. F. Ryan
%A et al ...
%A A. D. Baxevanis
%T The genome of the Ctenophore Mnemiopsis leidyi and its implications for cell
   type evolution
%J Science
%V 342
%N 6164
%M DEC
%D 2013
%K jrnl, MolBio, c2013, c201x, c20xx, zz0415, Ctenophore Mnemiopsis leidyi,
   ctenophore, animal, animals, comb jellyfish, jelly fish, genome, nGenome,
   evolution, sponges, cell types
%X "... sequenced, assembled, & annotated the genome of the ctenophore M.leidyi.
   Our phylogenomic analyses of both AA posns & gene content suggest that
   ctenophores rather than sponges are the sister lineage to all other animals.
   M. lacks many of the genes found in bilaterian mesodermal cell types,
   suggesting that these cell types evolved indep.. The set of neural genes in
   M. is similar to that of sponges, indicating that sponges may have lost a
   nervous sys.. ... present a newly supported view of early animal evoln ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1242592">doi:10.1126/science.1242592</A>]['15].

%A A. S. Konagurthu
%A A. M. Lesk
%T Structure description and identification using the tableau representation of
   protein folding patterns
%P 51-59
%B Protein Supersecondary Structures
%E A. E. Kister
%S Methods in Molec. Biol.
%I Springer
%D 2013
%K chapter, MolBio, c2013, c201x, c20xx, zz0717, protein, structure, 3D, fold,
   folding, tableau, motif, pattern, super secondary structure, superSecondary,
   AMLesk, ArunK, MMB
%X "... a concise tableau representation of protein folding patterns, based on
   the order & contact patterns of elts of secondary struct.: helices & strands
   of sheet. The tableaux provide a DB, derived from the protein data bank,
   minable for studies on the general principles of protein architecture, inc.
   investigation of the relationship between local supersecondary structure of
   proteins & the complete folding topology. This chapter outlines the tableaux
   representation of protein folding patterns & methods to use them to identify
   structural & substructural similarities."  [online July 2012.]
   -- [<A HREF="https://doi.org/10.1007/978-1-62703-065-6_4">doi:10.1007/978-1-62703-065-6_4</A>]['17].
   [Also search for: MolBio protein tableau].

%A Y. Yamauchi
%A J. M. Riel
%A Z. Stoytcheva
%A M. A. Ward
%T Two Y genes can replace the entire Y chromosome for assisted reproduction in
   the mouse
%J Science
%V 343
%N 6166
%P 69-62
%M JAN
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0114, yChromosome, Y chromosome, yChr,
   chrY, male, sex, gender, mammal, mammalian, rodent, mouse, mice, genes,
   Sry, testis, Eif2s3y, spermatogenesis
%X "... have prev. shown that, with the use of assisted reproduction, live
   offspring can be obtained from mice lacking the entire Y chr. long arm. Here,
   we demonstrate that live mouse progeny can also be generated by using germ
   cells from males with the Y chr. contribution limited to only two genes, the
   testis determinant factor Sry and the spermatogonial proliferation factor
   Eif2s3y. Sry is believed to function primarily in sex determination during
   fetal life. Eif2s3y may be the only Y chr. gene required to drive mouse
   spermatogenesis, allowing formation of haploid germ cells that are functional
   in assisted reproduction. Our findings are relevant, but not directly
   translatable, to human male infertility cases."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1242544">doi:10.1126/science.1242544</A>]['14], online 21/11/13.
   [Also search for: MolBio chrY].

%A B. Venkatesh
%A et al ...
%A W. C. Warren
%T Elephant shark genome provides unique insights into gnathostome evolution
%J Nature
%V 505
%N 7482
%M JAN
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0114, genome, nGenome, animal, fish,
   shark, tetrapod, gnathostome, cartilaginous, Chondrichthyes,
   Callorhinchus milii, CD4, adaptive immune system
%X "... whole-genome analysis of a cartilaginous fish, the elephant shark
   (Callorhinchus milii). ... the C.milii genome is the slowest evolving of all
   known vertebrates, inc. the 'living fossil' coelacanth, & features extensive
   synteny conservation with tetrapod genomes, making it a good model for
   comparative analyses of gnathostome genomes. Our functional studies suggest
   that the lack of genes encoding secreted calcium-binding phosphoproteins in
   cartilaginous fishes explains the absence of bone in their endoskeleton.
   Furthermore, the adaptive immune system of cartilaginous fishes is unusual:
   it lacks the canonical CD4 co-receptor & most transcription factors,
   cytokines & cytokine receptors related to the CD4 lineage, despite the
   presence of polymorphic major histocompatibility complex class-II molecules.
   It thus presents a new model for understanding the origin of adaptive
   immunity."
   "... 0.937 gigabases ... predicted ... 18,872 protein-coding genes ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12826">doi:10.1038/nature12826</A>]['14].

%A D. Borota
%A E. Murray
%A G. Keceli
%A A. Chang
%A J. M Watabe
%A M. Ly
%A J. P Toscano
%A M. A Yassa
%T Post-study caffeine administration enhances memory consolidation in humans
%J Nature Neuroscience
%V ?
%P ?-?
%D 2014
%K jrnl, eJrnl, c2014, c201x, c20xx, zz0114, brain, learning, study, memory,
   zzCoffee, positive, coffee, caffeine, human
%X "... used post-study caffeine administration to test its effect on memory
   consolidation using a behavioral discrimination task. Caffeine enhanced
   performance 24 h after administration according to an inverted U-shaped
   dose-response curve; this effect was specific to consolidation and not
   retrieval. We conclude that caffeine enhanced consolidation of long-term
   memories in humans."   (online Jan 2014.)
   -- [<A HREF="http://dx.doi.org/10.1038/nn.3623">doi:10.1038/nn.3623</A>]['14].
   [200 milligrams / day ~ two espressos *seems* optimal.]
   [Also search for: zzCoffee].

%A C. J. Burden
%A P. Leopardi
%A S. Foret
%T The distribution of word matches between markovian sequences with periodic
   boundary conditions
%J J. Comput. Biol.
%V 21
%N 1
%P 41-63
%M JAN
%D 2014
%K jrnl, JCB, MolBio, c2014, c201x, c20xx, zz0114, words, counts, sequence,
   D2 statistic, stats
%X "Abstract Word match counts have trad. been proposed as an alignment-free
   measure of similarity for biol.seqs.. The D2 statistic, which simply counts
   the # of exact word matches between two sequences, is a useful test bed for
   developing rigorous mathematical results ... Here we derive exact formulas
   for the mean & variance of the D2 statistic for Markovian seqs. of any order,
   & demo. through Monte Carlo simulations that the entire distribution is
   accurately characterized by a Polya-Aeppli distribution for seq.lengths of
   biological interest. ... novel in that Markovian dependency is defined for
   seqs. with periodic boundary conditions, & this enables exact analytic
   formulas ... [&] a preliminary comparison between the approx. D2 distn
   computed with the theor. mean & variance under a M.hypothesis & an empirical
   D2 distn from the human genome."
   -- [<A HREF="http://dx.doi.org/10.1089/cmb.2012.0277">doi:10.1089/cmb.2012.0277</A>]['14],
      [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/24160839">pubm'd</A>]['14] via TS.

%A J. Gollihar
%A M. Levy
%A A. D. Ellington
%T Many paths to the origin of life
%J Science
%V 343
%N 6168
%P 259-260
%M JAN
%D 2014
%K views, news, MolBio, c2014, c201x, c20xx, zz0114, life, start, beginning,
   origin, origins, self replication, replicating, chemistry, biol, biology,
   prebiotic
%X "... Initial insights that biological compounds could be generated by
   prebiotic means quickly ran up against a gap in our understanding of how
   unguided syntheses could result in defined templates for replication. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1246704">doi:10.1126/science.1246704</A>]['14].

%A M. J. Landrum
%A J. M. lee
%A G. R. Riley
%A W. Jang
%A W. S. Rubenstein
%A D. M Church
%A D. R. maglott
%T ClinVar: Public archive of relationships among sequence variation and
   human phenotype
%J NAR
%V 42
%N 1
%P D980-5
%M JAN
%D 2014
%K jrnl, eJrnl, NAR, MolBio, c2014, c201x, c20xx, zz0514, ClinVar, genetic,
   gene, variation, sequence, human, health, clinical, association studies,
   disease, mutation, illness, database
%X "ClinVar [<A HREF="http://www.ncbi.nlm.nih.gov/clinvar/">www</A>] provides a
   freely available archive of reports of relationships among medically
   important variants & phenotypes. ...  relationship of that variation to human
   health & the evidence supporting each interpretation. ...  ClinVar is also
   based on the phenotypic descriptions maintained in MedGen
   [<A HREF="http://www.ncbi.nlm.nih.gov/medgen">www</A>]. Each ClinVar record
   represents the submitter, the variation & the phenotype ..."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gkt1113">doi:10.1093/nar/gkt1113</A>]['14],
      ClinVar@[<A HREF="https://www.ncbi.nlm.nih.gov/clinvar/">NIH</A>]['14].
   [Also search for: variation illness database].

%A H. Obokata
%A T. Wakayama
%A Y. Sasai
%A K. Kojima
%A M. P. Vacanti
%A H. Niwa
%A M. Yamato
%A C. A. Vacanti
%T Stimulus-triggered fate conversion of somatic cells into pluripotency
%J Nature
%V 505
%N 7485
%P 641-647
%M JAN
%D 2014
%K jrnl, biology, c2014, c201x, c20xx, zz0714, stem cell, cells, STAP, low pH,
   acid, errors, retraction, scandal, misconduct, peer review, referees,
   refereeing, scientific research, controversial,
   Japan, Kobe, RIKEN, Kadota, Andrabi, Takata, Tokoro, Terashita, Yonemura
%X "... report a unique cellular reprogramming phenomenon, called stimulus-
   -triggered acquisition of pluripotency (STAP), which requires neither nuclear
   transfer nor the intro. of transcription factors. ... strong external
   stimuli such as a transient low-pH stressor reprogrammed mammalian somatic
   cells, resulting in the generation of pluripotent cells. ... ...
   also demonstrate the derivation of robustly expandable pluripotent cell lines
   from STAP cells. Thus, our findings indicate that epigenetic fate
   determination of mammalian cells can be markedly converted in a
   context-dependent manner by strong environmental cues."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12968">doi:10.1038/nature12968</A>]['14].
   (And a 2nd paper, pp.676-680, same issue.)
   * But see,
       "Nature today retracted two controversial papers on stem cells
       that it published in January ... Questions remain over what exactly
       was the basis for claims ..."
       -- [<A HREF="http://dx.doi.org/10.1038/nature.2014.15501">doi:10.1038/nature.2014.15501</A>][2/7/2014].
   And
       "A Japanese stem cell scientist at the heart of a scandal over
       false claims and fabricated research has resigned ..."
       -- [<A HREF="http://www.bbc.com/news/health-30534674">bbc</A>][19/12/2014].

%A S. Sankararaman
%A S. Mallick
%A M. Dannemann
%A K. Prufer
%A J. Kelso
%A S. Paabo
%A N. Patterson
%A D. Reich
%T The genomic landscape of Neanderthal ancestry in present-day humans
%J Nature
%V ?
%N ?
%P ?-?
%M FEB
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0214, DNA, genome, genes, human,
   Neanderthal, ancient, old, evolution, keratin
%X "... The antiquity of Neanderthal gene flow into modern humans means that
   genomic regions that derive from Neanderthals in any one human today are
   usually < than a hundred kb in size. ... We systematically infer Neanderthal
   haplotypes in the genomes of 1,004 present-day humans. Regions that harbour a
   high freq. of Neanderthal alleles are enriched for genes affecting keratin
   filaments, suggesting that N.alleles may have helped modern humans to adapt
   to non-African environments. We identify multiple N.-derived alleles that
   confer risk for disease, suggesting that N.alleles continue to shape human
   biology. An unexpected finding is that regions with reduced N. ancestry are
   enriched in genes, implying seln to remove genetic material derived from
   Neanderthals. Genes that are more highly expressed in testes than in any
   other tissue are especially reduced in N.ancestry, & there is an ~fivefold
   redn of N.ancestry on the X chr., which is known from studies of diverse
   species to be esp. dense in male hybrid sterility genes. ... suggest that
   part of the explanation for genomic regions of reduced N.ancestry is
   N.alleles that caused decreased fertility in males when moved to a modern
   human genetic background." (online 29 Jan 2014.)
   -- [<A HREF="http://dx.doi.org/10.1038/nature12961">doi:10.1038/nature12961</A>]['14].
   [Also search for: Vernot Akey zz0214].

%A B. Vernot
%A J. M. Akey
%T Resurrecting surviving Neandertal lineages from modern human genomes
%J Science
%V ?
%N ?
%P ?-?
%M FEB
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0214, DNA, genome, genes, humans,
   Neanderthal, evolution, skin
%X "Anatomically modern humans overlapped & mated with Neandertals s.t. non-
   -African humans inherit ~1-3% of their genomes from N. ancestors. We
   identified N. lineages that persist in the DNA of modern humans, in whole-
   -genome seqs. from 379 European & 286 East Asian individuals, recovering over
   15Gb of introgressed seq. that spans ~20% of the N. genome (FDR=5%). Analyses
   of surviving archaic lineages suggests that there were fitness costs to
   hybridization, admixture occurred both before & subsequent to divergence of
   non-African modern humans, & N. were a source of adaptive var'n for loci
   involved in skin phenotypes. ... provide a new avenue for paleogenomics
   studies, allowing substantial amounts of pop'n-level DNA seq. info. to be
   obtained from extinct groups even in the absence of fossilized remains."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1245938">doi:10.1126/science.1245938</A>]['14]. (online 29/1/2014.)
   [Also search for: Sankararaman Mallick zz0214].

%A G. J. Milinovich
%A G. M. Williams
%A A. C. A. Clements
%A W. Hu
%T Internet-based surveillance systems for monitoring emerging infectious
   diseases
%J The Lancet Infectious Diseases
%V 14
%N 2
%P 160-168
%M FEB
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0214, internet, disease, epidemic, internet,
   google, flu, flutrends, GFT, big data, bigData, search, terms, searches,
   warning, health, query, queries
%X "... We review studies that have exploited internet use & search trends to
   monitor two such diseases: influenza & dengue. Internet-based surveillance
   systems have good congruence with trad. surveillance approaches. [&] internet
   -based approaches are logistically & economically appealing. However, they do
   not have the capacity to replace trad. ss.; they should not be viewed as an
   alternative, but rather an extension. Future research should focus on using
   data generated through internet-based surveillance & response systems to
   bolster the capacity of trad. ss. for emerging infectious diseases."
   -- [<A HREF="http://dx.doi.org/10.1016/S1473-3099(13)70244-5">doi:10.1016/S1473-3099(13)70244-5</A>]['14].
   (Also see [<A HREF="http://www.abc.net.au/news/2014-02-03/qld-scientists-to-develop-system-to-track-disease-outbreaks-onli/5235266">abc</A>][21'2'2014], and
   fluTrends@[<A HREF="https://www.google.org/flutrends/about/how.html">g'gle</A>]['14].
   But also see [<A HREF="http://dx.doi.org/10.1126/science.1248506">doi:10.1126/science.1248506</A>]['14].)

%A K. Avlund
%A et al ...
%A R. Lund
%T Copenhagen Aging and Midlife Biobank (CAMB) An introduction
%J J. Aging and Health
%V 26
%N 1
%P 5-20
%M FEB
%D 2014
%K jrnl, health, c2014, c201x, c20xx, zz0514, CAMB, database, stats,
   aging, ageing, health, mortality, study, longitudinal, cohort, men, women,
   risk, risks, Denmark, Danish, stress, stressful, relations, marriage, work,
   employment, unemployment
%X "... it has become increasingly evident that the initial signs of
   age-associated changes in health appear well before older age, and often
   develop in earlier stages of adulthood. ..."
   -- [<A HREF="http://dx.doi.org/10.1177/0898264313509277">doi:10.1177/0898264313509277</A>]['14],
      Lund@[<A HREF="http://publichealth.ku.dk/staff/?id=155127&vis=medarbejder">ku.dk</A>]['14].
  (Also see
   'Stressful social relations and mortality: a prospective cohort study,'
   J. Epidem. & Comm. Health, May 2014,
      "... Frequent worries/demands from partner or children were assoc. with
      50-100% increased mortality risk. Frequent conflicts with any type of
      social reln were assoc. with 2-3 times increased mortality risk. ..."
   -- [<A HREF="http://dx.doi.org/10.1136/jech-2013-203675">doi:10.1136/jech-2013-203675</A>]['14], and
      [<A HREF="http://www.abc.net.au/news/2014-05-10/study-finds-stressful-marriage-more-likely-to-kill-men/5444260">abc</A>][10/5/2014].)

%A E. C. Hayden
%T Data from pocket-sized genome sequencer unveiled. Results from Oxford
   Nanopore's MinION are promising, but fall short of high expectations
%J Nature
%V 2014
%P ?-?
%M FEB
%D 2014
%K news, MolBio, c2014, c201x, c20xx, zz0714, Oxford Nanopore, MinION, GridION,
   single molecule, SMRT, sequencing, genome, sequencer, launch, DNA
%X 14 Feb: "A good first shot, but not a game-changer - yet. That seems to be
     the consensus among scientists after today's first public release of data
     produced by the MinION, an advanced & highly anticipated DNA-sequencing
     device developed by UK company Oxford Nanopore Technologies. ...
     avg. length of the seqs. generated on the MinION is 5.4kb, with some as
     long as 10kb. Jaffe also found that the MinION seemed to have difficulty
     seq.  particular parts of the bacterial genomes that he studied. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature.2014.14724">doi:10.1038/nature.2014.14724</A>]['14].  And,
   17 Feb: "ONTech, based in Oxf. UK, revealed the initial results from its
     GridION system at the Advances in Genome Biology & Technology meeting in
     Marco Is., Fl. ... expects to start selling its new m/c in the 2nd half
     of this year [&] plans to launch the world's 1st miniaturized, disposable
     sequencer - the MinION - which will retail for less than US$900. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature.2012.10051">doi:10.1038/nature.2012.10051</A>]['14].
   (Also see Oxf_Nano@[<A HREF="https://www.nanoporetech.com/">www</A>]['14].)
   [Also search for: Oxford Nanopore]  and
   [also search for: MolBio single molecule sequencing].

%A E. Postma
%T A relationship between attractiveness and performance in professional
   cyclists
%J Biol. Lett.
%I Royal Soc.
%V 10
%N 2
%P ?-?
%M FEB
%D 2014
%K jrnl, biology, c2014, c201x, c20xx, zz0214, attractiveness, mate selection,
   athlete, cyclist, fitness, male, face, faces, facial, human, attractive,
   beauty, Tour de France
%X "Females often prefer to mate with high quality males, & one aspect of
   quality is physical performance. Although a preference for physically fitter
   males is therefore predicted, the relationship between attractiveness &
   performance has rarely been quantified. ... ask whether variation in
   (endurance) performance is assoc. with variation in facial attractiveness
   within elite prof.cyclists that finished the 2012 Tour de France. ...
   riders that performed better were more attractive, & that this preference was
   strongest in women not using a hormonal contraceptive. ... within this
   preselected but rel. homogeneous sample of the male popn, facial
   attractiveness signals endurance performance. Provided that there is a reln
   between performance-mediated attractiveness & reproductive success, this
   suggests that human endurance capacity has been subject to sexual seln in our
   evolutionary past."
   -- [<A HREF="http://rsbl.royalsocietypublishing.org/lookup/doi/10.1098/rsbl.2013.0966">doi:10.1098/rsbl.2013.0966</A>]['14],
   EP@[<A HREF="http://www.erikpostma.net/publications.html">www</A>]['14].
   (Also see [<A HREF="http://www.bbc.co.uk/news/science-environment-26034659">bbc</A>]['5/1/2014].)

%A S. V. Rajagopala
%A et al
%A P. Uetz
%T The binary protein-protein interaction landscape of Escherichia coli
%J Nature Biotech.
%V 32
%N 3
%P 285-290
%M FEB
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0415, protein interaction, network,
   PPI, data, Escherichia coli, bacterium, bacteria, E coli, Ecoli, Y2H
%X "... performed yeast two-hybrid screens of 3,305 baits against 3,606 preys
   (~70% of the E.coli proteome) in duplicate to generate a map of 2,234
   interactions, which approx. doubles the # of known binary PPIs in E.coli.
   Integration of binary PPI & genetic-interaction data revealed functional
   dependencies among components involved in cellular processes, inc. envelope
   integrity, flagellum assembly & protein quality control.  ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nbt.2831">doi:10.1038/nbt.2831</A>]['15].
   (The supplementary material [<A HREF="http://www.nature.com/nbt/journal/v32/n3/full/nbt.2831.html#supplementary-information">www</A>] contains
   PPIs derived by various methods.
   "We sampled the entire search space twice independently, which resulted
   in 2,234 high-quality PPIs among 1,269 proteins (Supplementary Table-2)."
   *** "To obtain a more comprehensive ... data set, named 'combined-binary'
   data set, contains 3,946 binary interactions among 2,048 proteins
   (Fig.3 and Supplementary <A HREF="http://www.nature.com/nbt/journal/v32/n3/extref/nbt.2831-S4.xls">Table-5</A>.xls)." ***
   "estimated ... total size of the interactome is ~10,000 PPIs".)

%A M. D. Cao
%A S. Balasubramanian
%A M. Boden
%T Sequencing technologies and tools for short tandem repeat variation detection
%J Briefings in Bioinformatics
%I OUP
%V ?
%P ?-?
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, UniQld, short tandem repeats, STR, STRs,
   repetitive, length, variant, DNA, Minh Duc Cao
%X "... present here a comprehensive survey & empirical evaluation of current
   sequencing technologies & bioinformatics tools in all stages of an analysis
   pipeline. While there is not one optimal pipeline to suit all circumstances,
   we find that the choice of alignment & repeat genotyping tools greatly
   impacts the accuracy & efficiency by which short tandem repeat variation can
   be detected. We further note that to detect variation relevant to many
   repeat diseases, it is essential to choose technologies that offer either
   long read-lengths or paired-end sequencing, coupled with specific genotyping
   tools."  [Online Feb 2014.]
   -- [<A HREF="http://dx.doi.org/10.1093/bib/bbu001">doi:10.1093/bib/bbu001</A>]['14].
   [Also search for: repetitive DNA].

%A M. Luksza
%A M. Lassig
%T A predictive fitness model for influenza
%J Nature
%V 507
%N 7490
%P 57-61
%M MAR
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0314, virus, flu, evolution, human,
   A/H3N2, AH3N2, strains, model, haemagglutinin, fitness, prediction
%X "The seasonal human influenza A/H3N2 virus undergoes rapid evolution, which
   produces sig. year-to-year seq. turnover in the popn of circulating strains.
   ... develop a fitness model for haemagglutinin that predicts the evolution of
   the viral popn ... Two factors are shown to determine the fitness of a
   strain: adaptive epitope changes & deleterious mutations outside the
   epitopes. We infer both fitness components for the strains circulating in a
   given year, using population-genetic data of all previous strains. From
   fitness & freq. of each strain, we predict the freq. of its descendent
   strains in the following year. ... suggests a principled method for vaccine
   selection. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13087">doi:10.1038/nature13087</A>]['14].

%A M. Duc Cao
%A E. Tasker
%A K. Willadsen
%A M. Imelfort
%A S. Vishwanathan
%A S. Sureshkumar
%A S. Balasubramanian
%A M. Boden
%T Inferring short tandem repeat variation from paired-end short reads
%J NAR
%V 42
%N 3
%P e16
%D 2014
%K jrnl, NAR, MolBio, c2014, c201x, c20xx, zz0314, nioinformatics,
   tandem repeats, STR, STRs, microsatellites, paired end, read, reads,
   STRviper, Minh Duc Cao
%X "... present a Bayesian method to estimate repeat-length variation from
   paired-end seq. read data. ... makes variant calls based on deviations in
   seq. frag. sizes, allowing the analysis of repeats at lengths of relevance to
   a range of phenotypes. We demonstrate the method's ability to detect &
   quantify changes in repeat lengths from short read genomic seq. data across
   genotypes. We use the method to estimate repeat variation among 12 strains of
   Arabidopsis thaliana & demonstrate experimentally that our method compares
   favourably against existing methods. Using this method, we have identified
   all repeats across the genome, which are likely to be polymorphic. [&] our
   predicted polymorphic repeats also included the only known repeat expansion
   in A.thaliana, suggesting an ability to discover potential unstable repeats."
      "... (STRs), or 'microsatellites', are repeat seqs. that have units
      between 2 & 6bp. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gkt1313">doi:10.1093/nar/gkt1313</A>]['14].

%A C. M. Rufo
%A Y. S. Moroz
%A O. V. Moroz
%A J. Stohr
%A T. A. Smith
%A X. Hu
%A W. F. DeGrado
%A I. V. Korendovych
%T Short peptides self-assemble to produce catalytic amyloids
%J Nature Chemistry
%V ?
%P ?-?
%M MAR
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0314, peptide, 3D structure,
   self assembling, amyloid, fibrils, fibril, self organizing, origins,
   Zn, zinc, enzyme, enzymes, catalysts
%X "Enzymes fold into unique 3D structures ... However, much shorter peptides
   can achieve well-defined conformations through the formation of amyloid
   fibrils. To test whether short a.-forming peptides might ... be capable of
   enzyme-like catalysis, we designed a series of seven-residue peptides that
   act as Zn2+-dependent esterases. Zn2+ helps stabilize the fibril formation,
   while also acting as a cofactor to catalyse acyl ester hydrolysis. These
   results indicate that prion-like fibrils are able to not only catalyse their
   own formation, but they can also catalyse chemical reactions. Thus, they
   might have served as intermediates in the evolution of modern-day enzymes.
   These results also have implications for the design of self-assembling
   nanostructured catalysts including ones containing a variety of biological
   and non-biological metal ions."  [online Mar 2014.]
   -- [<A HREF="http://dx.doi.org/10.1038/nchem.1894">doi:10.1038/nchem.1894</A>]['14].

%A O. Oyebode
%A V. Gordon-Dseagu
%A A. Walker
%A J. S. Mindell
%T Fruit and vegetable consumption and all-cause, cancer and CVD mortality:
   analysis of health survey for England data
%J J. Epidemiol Community Health
%V ?
%N ?
%P ?-?
%M MAR
%D 2014
%K jrnl, eJrnl, c2014, c201x, c20xx, zz0414, health, human, diet, fruit,
   vegetables, eating, lifespan, survey, epidemiology, epidemiological,
   cardio, cancer, risks, UK, England, stats
%X "... Fruit & vegetable consumption was assoc. with decreased all-cause
   mortality (adjusted HR for 7+ portions 0.67 (95% CI 0.58 - 0.78), reference
   category < 1 portion). This assoc. was more pronounced when excluding deaths
   within a year of baseline (0.58 (0.46 - 0.71)). Fruit & veg. consumption was
   assoc. with reduced cancer (0.75 (0.59 - 0.96)) & cardiovascular mortality
   (0.69 (0.53 - 0.88)). Vegs. may have a stronger assoc. with mortality than
   fr. (HR for 2 to 3 portions 0.81 (0.73 - 0.89) & 0.90 (0.82 - 0.98), resp.).
   Consumption of vegetables (0.85 (0.81 - 0.89) per portion) or salad
   (0.87 (0.82 - 0.92) per portion) were most protective, while frozen/canned
   fruit consumption was apparently assoc. with increased mortality
   (1.17 (1.07 - 1.28) per portion). ...
   benefits seen in up to 7+ portions daily. ..."  [Online 31 March 2014.]
   -- [<A HREF="http://dx.doi.org/10.1136/jech-2013-203500">doi:10.1136/jech-2013-203500</A>]['14].

%A C. Mellberg
%A S. Sandberg
%A M. Ryberg
%A M. Eriksson
%A S. Brage
%A C. Larsson
%A T. Olsson
%A B. Lindahl
%T Long-term effects of a Palaeolithic-type diet in obese postmenopausal women:
   a 2-year randomized trial
%J Euro. J. of Clinical Nutrition
%V 68
%P 350-357
%M MAR
%D 2014
%K jrnl, Biol, c2014, c201x, c20xx, zz0614, human, diet, health, weight, stats,
   caveman, Stone Age, ancient, Palaeolithic diet, eating,
   Nordic Nutrition Recommendations, NNR
%X "... Palaeolithic-type diet (PD) [v.] Nordic Nutrition Recommendations (NNR).
   ... Both groups sig. decreased total fat mass at 6 months (-6.5 & -2.6kg) &
   24 m. (-4.6 & -2.9kg), with a more pronounced fat loss in the PD group at
   6 m. (P < 0.001) but not at 24 m. (P=0.095). Waist circumference &
   sagittal dia. also decreased in both the groups, with a more pronounced
   decrease in the PD group at 6 m. (-11.1 vs -5.8cm, P=0.001 & -3.7 vs -2.0cm,
   P < 0.001, resp.). Triglyceride levels decreased sig. more at 6 & 24 m. in
   the PD group than in the NNR group (P < 0.001 & P=0.004). Nitrogen excretion
   did not differ between the groups. A PD has greater beneficial effects vs an
   NNR diet regarding fat mass, abdominal obesity & triglyceride levels in obese
   postmenopausal women; effects not sustained for anthropometric measurements
   at 24 m.. Adherence to protein intake was poor in the PD group. The long-term
   consequences of these changes remain to be studied."
   -- [<A HREF="http://dx.doi.org/10.1038/ejcn.2013.290">doi:10.1038/ejcn.2013.290</A>]['14].
   (Also see bbc [<A HREF="http://www.bbc.com/future/story/20140617-should-we-all-eat-like-cavemen">17/6/2014</A>].)
   [Also search for: paleolithic diet].

%A R. Chowdry
%A et al
%T Association of dietary, circulating, and supplement fatty acids with coronary
   risk: A systematic review and meta-analysis
%J Annals of Internal Medicine
%V 160
%N 6
%P 398-406
%M MAR
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0814, medicine, human, health, diet, risk,
   risks, fatty acid, coronary, heart, disease, attack, metaanalysis, medical,
   monounsaturated, saturated, fat, fats
%X "... There were 32 observational studies (512,420 participants) of fatty
   acids from dietary intake; 17 obs. studies (25,721 participants) of fatty
   acid biomarkers; and 27 randomized, controlled trials (105,085 participants)
   of fatty acid supplementation. ... Current evidence does not clearly support
   cardiovascular guidelines that encourage high consumption of polyunsaturated
   fatty acids and low consumption of total saturated fats. ..."
   -- [<A HREF="http://dx.doi.org/10.7326/M13-1788">doi:10.7326/M13-1788</A>]['14].

%A A. Roth
%A et al ...
%A S. P. Shah
%T PyClone: Statistical inference of clonal population structure in cancer
%J Nature Methods
%V 11
%P 396-398
%M MAR
%D 2014
%K MolBio, c2014, c201x, c20xx, zz1214, PyClone, cancer, genome, clonal, cell,
   clustering, variation, diversity, mutation, CNV, Canada, UBC
%X "... statistical model for inference of clonal popln structures in cancers.
   PyClone is a Bayesian clustering method for grouping sets of deeply sequenced
   somatic mutns into putative c.clusters while estimating their cellular
   prevalences & accounting for allelic imbalances intro. by segmental
   copy-number changes & normal-cell contamination. Single-cell sequencing
   validation demonstrates PyClone's accuracy."
   -- [<A HREF="http://dx.doi.org/10.1038/nmeth.2883">doi:10.1038/nmeth.2883</A>]['14].
   [Also search for: cancer genome diversity],
   [also search for: MolBio cancer clonal] and
   [also search for: cancer genome].

%A Jianzhu Ma
%A Sheng Wang
%A Zhiyong Wang
%A Jinbo Xu
%T MRFalign: Protein homology detection through alignment of Markov random
   fields
%J PLoS Comp. Biol.
%V ?
%M MAR
%D 2014
%K jrnl, eJrnl, MolBio, c2014, c201x, c20xx, zz1015, protein, alignment,
   MRFalign, MRF, field, structure prediction
%X "... new homology detection method MRFalign, consisting of three key
   components: 1) a Markov Random Fields (MRF) repn of a protein family; 2) a
   scoring fn measuring similarity of two MRFs; & 3) an efficient ADMM
   (Alternating Direction Method of Multipliers) alg. aligning two MRFs.
   Compared to HMM that can only model very short-range residue correlation,
   MRFs can model long-range residue interaction pattern and thus, encode
   information for the global 3D structure of a protein family. [So] MRF-MRF
   comparison for remote homology detection shall be much more sensitive than
   HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign
   outperforms several popular HMM or PSSM-based methods in terms of both
   alignment accuracy & remote homology detection & that MRFalign works
   particularly well for mainly beta proteins. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pcbi.1003500">doi:10.1371/journal.pcbi.1003500</A>]['15].
  (Also see: J. Ma, 'Protein Structure Prediction by ...' --
  1510.05682@[<A HREF="http://arxiv.org/abs/1510.05682">arXiv</A>][19/10/2015].)

%A R. Chowdury
%A et al ...
%A E. Di Angelantonio
%T Association of dietary, circulating, and supplement fatty acids with
   coronary risk: A systematic review and meta-analysis
%J Ann. Intern. Med.
%V 160
%N 6
%P 398-406
%M MAR
%D 2014
%K medicine, c2014, c201x, c20xx, zz0716, human, health, risk, disease, fat,
   heart, coronary, food, diet, dietary, butter, saturated, trans, unsaturated,
   monounsaturated, polyunsaturated, fatty, acid, acids, omega 3 6, omega3,
   omega6, meta study, analysis, metastudy, metaanalysis, controversial
%X "Guidelines advocate changes in fatty acid consumption to promote
   cardiovascular health. ... There were 32 observational studies (512,420
   participants) of fatty acids from dietary intake; 17 obs. studies (25,721
   participants) of fatty acid biomarkers; & 27 randomized, controlled trials
   (105,085 participants) of fatty acid supplementation. In obs. studies,
   relative risks for coronary disease were 1.03 (95% CI, 0.98 to 1.07) for
   saturated, 1.00 (CI, 0.91 to 1.10) for monounsaturated, 0.87 (CI, 0.78 to
   0.97) for ... Current evidence does not clearly support cardiovascular
   guidelines that encourage high consumption of polyunsaturated fatty acids &
   low consumption of total saturated fats."
   -- [<A HREF="http://dx.doi.org/10.7326/M13-1788">doi:10.7326/M13-1788</A>]['16].
   (Also see [<A HREF="http://www.nhs.uk/news/2014/03March/Pages/Saturated-fats-and-heart-disease-link-unproven.aspx">nhs.uk</A>]['16].
   Also see contrary@[<A HREF="https://phcuk.org/wp-content/uploads/2016/05/Eat-Fat-Cut-The-Carbs-and-Avoid-Snacking-To-Reverse-Obesity-and-Type-2-Diabetes-National-Obesity-Forum-Public-Health-Collaboration.pdf">phcuk.org</A>]['16] (unknown).)

%A A. Rzhetsky
%A S. C. Bagley
%A K. Wang
%A C. S. Lyttle
%A E. H. Cook Jr
%A R. B. Altman
%A R. D. Gibbons
%T Environmental and state-level regulatory factors affect the incidence of
   autism and intellectual disability
%A PLoS Comp. Biol.
%V 10
%N 3
%P e1003518
%M MAR
%D 2014
%K Biol, jrnl, eJrnl, c2014, c201x, c20xx, zz0314, risks, autism, ASD, ID,
   human, mental health, intellectual disability, pollution, environment,
   epidemiologic, toxin, toxins, congenital malformations, maladies, disease,
   US, USA
%X "... compare environmental, phenotypic, socioeconomic & state-policy factors
   in a unified geospatial framework, we analyzed the spatial incidence patterns
   of ASD & ID using an insurance claims dataset covering nearly 1/3 of the US
   popn. .. used the rate of congenital malformations of the reproductive system
   as a surrogate for env.exposure of parents to unmeasured developmental risk
   factors, inc. toxins. Adjusted for gender, ethnic, socioeconomic, &
   geopolitical factors, the ASD incidence rates were strongly linked to pop.-
   -normalized rates of congenital malformations of the reproductive system in
   males (an inc. in ASD incidence by 283% for every percent inc. in incidence
   of malformations, 95% CI: [91%, 576%], p < 6x10^-5). Such congenital
   malformations were barely sig. for ID (94% increase, 95% CI: [1%, 250%],
   p=0.0384). Other congenital malformations in males (exc. those affecting the
   repro.sys.) appeared to sig. affect both phenotypes: 31.8% ASD rate inc.
   (CI: [12%, 52%], p < 6x10^-5), & 43% ID rate ... [&] the state-mandated rigor
   of diagnosis of ASD by a pediatrician or clinician for consideration in the
   special ed.system was predictive of a considerable decrease in ASD & ID
   incidence rates (98.6% ... p = 0.02475 ...). Thus, the observed spatial
   variability of both ID & ASD rates is assoc. with env. & state-level
   regulatory factors; the magnitude of influence of compound environmental
   predictors was ~3 x greater than that of state-level incentives. The est.
   county-level random effects exhibited marked spatial clustering, strongly
   indicating existence of as yet unidentified localized factors driving
   apparent disease incidence. Finally, we found that the rates of ASD & ID at
   the county level were weakly but sig. correlated ..., while for females the
   correlation was much stronger (0.197, p < 2.26x10^-16)."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pcbi.1003518">doi:10.1371/journal.pcbi.1003518</A>]['14].

%A D. H. Crawford
%A I. Johannessen
%A A. B. Rickinson
%T Cancer Virus: The discovery of the Epstein-Barr Virus
%I OUP
%M APR
%D 2014
%K MolBio, book, text, c2014, c201x, c20xx, zz0414, Epstein Barr, virus, EBV,
   medicine, human health, risks,
   Burkitt's Lymphoma, cancer, glandular fever, Hodgkin's Disease
%X 1st ed 2014; hb us$21; uk us isbn:0199653119; uk us isbn13:978-0199653119.
   "... discovered in 1964. At the time, the very idea of a virus underlying a
   cancer was revolutionary. Cancer is, after all, not catching. Even now, the
   idea of a v. causing c. surprises many people. But EBV, named after its
   discoverers, Sir Anthony E. & Dr Yvonne B. ...  Almost everyone carries it,
   yet it is only under certain circumstances that it produces disease. It has
   been assoc. with different, apparently unrel., diseases in different popns:
   Burkitt's Lymphoma, producing tumors in the jaw, in African children; a nasal
   tumor in China; glandular fever in Europe & the USA; & the majority of cases
   of Hodgkin's Disease everywhere.  ..."

%A D. Cortez
%A R. Marin
%A D. Toledo-Flores
%A L. Froidevaux
%A A. Liechti
%A P. D. Waters
%A F. Grutzner
%A H. Kaessmann
%T Origins and functional evolution of Y chromosomes across mammals
%J Nature
%V 508
%N 7497
%P 488-493
%M APR
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0414, mammal, mammalian, evolution,
   Y chromosome, Ychromosome, Ychr, chrY, size, gender, sex, birds, avian,
   monotreme, marsupial, placental, AMH, SRY, therian, gene, genes, origin,
   repeat, rich
%X "Y chromosomes underlie sex determination in mammals, but their repeat-rich
   nature has hampered sequencing & assoc. evolutionary studies. Here we trace
   Y evolution across 15 representative mammals ... uncover three indep. sex
   chr. originations in mammals & birds (the outgroup). The original placental
   & marsupial (therian) Y, containing the sex-determining gene SRY, emerged in
   the therian ancestor approximately 180-million years ago, in parallel with
   the 1st of five monotreme Y chrs., carrying the probable sex-determining gene
   AMH. The avian W chr. arose ~140-million years ago in the bird ancestor. The
   small Y/W gene repertoires, enriched in regulatory fns, were rapidly defined
   following stratification (recombination arrest) & erosion events & have
   remained considerably stable. Despite expression decreases in therians, Y/W
   genes show notable conservation of proto-sex chr. expression patterns,
   although various Y genes evolved testis-specificities through differential
   regulatory decay. Thus, although some genes evolved novel fns through spatial
   /temporal expression shifts, most Y genes probably endured, at least
   initially, because of dosage constraints."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13151">doi:10.1038/nature13151</A>]['14].
   (Also see [<A HREF="http://dx.doi.org/10.1038/nature.2014.15103">comment</A>]['14].)

%A D. W. Bellot
%A et al ...
%A D. C. Page
%T Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators
%J Nature
%V 508
%N 7497
%P 494-499
%M APR
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0414, mammal, mammalian, evolution,
   Y chromosome, Ychromosome, Ychr, chrY, size, gender, male, sex, function,
   selection, gene, genes, fate, future, placental, marsupial
%X "The human X & Y chrs evolved from an ordinary pair of autosomes, but
   millions of y. ago genetic decay ravaged the Y chr, & only 3% of its
   ancestral genes survived. We reconstructed the evol. of the Y chr across
   eight mammals to identify biases in gene content & the selective pressures
   that preserved the surviving ancestral genes. ... indicate that survival was
   nonrandom, & in two cases, convergent across placental & marsupial mammals.
   We conclude that the gene content of the Y chr became specialized through
   seln to maintain the ancestral dosage of homologous X-Y gene pairs that fn
   as broadly expressed regulators of transcription, translation & protein
   stability. We propose that beyond its roles in testis determination &
   spermatogenesis, the Y chr is essential for male viability, & has
   unappreciated roles in Turner's syndrome & in phenotypic differences b/w
   the sexes in health & disease."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13206">doi:10.1038/nature13206</A>]['14].
   (Also see [<A HREF="http://dx.doi.org/10.1038/nature.2014.15103">comment</A>]['14].)

%A H. Holstege
%A et al ...
%A E. A. Sistermans
%T Somatic mutations found in the healthy blood compartment of a 115-year
   old woman demonstrates oligoclonal hematopoiesis
%J Genome Res.
%V ?
%P ?-?
%M APR
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0414, human, health, ageing, aging,
   W115, woman, Hendrikje van Andel-Schipper, old, centarian, stem cell,
   white, cells, blood, HSC, WBC, DNA, telomere, length
%X "The somatic mutation burden in healthy white blood cells (WBCs) is not well
   known. Based on deep whole-genome sequencing, we est. that ~450 somatic
   mutations accumulated in the nonrepetitive genome within the healthy blood
   compartment of a 115-yr-old woman. The detected mutations appear to have been
   harmless passenger mutations: They were enriched in noncoding, AT-rich
   regions that are not evolutionarily conserved, & they were depleted for
   genomic elements where mutations might have favorable or adverse effects on
   cellular fitness, such as regions with actively transcribed genes. The
   distribution of variant allele frequencies of these mutations suggests that
   the majority of the peripheral white blood cells were offspring of two
   related hematopoietic stem cell (HSC) clones. Moreover, telomere lengths of
   the WBCs were significantly shorter than telomere lengths from other tissues.
   Together, this suggests that the finite lifespan of HSCs, rather than
   somatic mutation effects, may lead to hematopoietic clonal evolution at
   extreme ages."
   -- [<A HREF="http://dx.doi.org/10.1101/gr.162131.113">doi:10.1101/gr.162131.113</A>]['14].

%A R. J. Colman
%A et al ...
%A R. M. Anderson
%T Caloric restriction reduces age-related and all-cause mortality in
   rhesus monkeys
%J NatureComms
%V 5
%P e3557
%M APR
%D 2014
%K jrnl, eJrnl, c2014, c201x, c20xx, zz0514, primate, aging, ageing, delay,
   longevity, lefespan, health, caloric restriction, calories, CR,
   restricted diet, benefits, primate, monkey, NIA
%X "... we show that CR sig. improves age-related & all-cause survival in
   monkeys on a long-term ~30% restricted diet since young adulthood. These
   data contrast with observations in the 2012 NIA intramural study report,
   where a difference in survival was not detected between control-fed & CR
   monkeys. A comparison of body weight of control animals from both studies
   with each other, & against data collected in a multi-centred relational
   database of primate ageing, suggests that the NIA control monkeys were
   effectively undergoing CR. Our data indicate that the benefits of CR on
   ageing are conserved in primates."
   -- [<A HREF="http://dx.doi.org/10.1038/ncomms4557">doi:10.1038/ncomms4557</A>]['14].
   (Also see [<A HREF="http://www.bbc.com/news/health-26837211">bbc</A>][2/4/2014].)

%A M. A. Keller
%A A. V. Turchin
%A M. Ralser
%T Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a
   plausible Archean ocean
%J Molec. Sys. Biol.
%V 10
%N 4
%P ?-?
%M APR
%D 2014
%K MSB, eJrnl, MolBio, c2014, c201x, c20xx, zz0514, origin, life, evolution,
   RNA, pre DNA, metabolism, glycolysis, glucose, pentose phosphate pathway
%X "... reconstructed potential scenarios for oceans of the prebiotic Archean
   based on the composition of early sediments. We report that the resultant
   reaction milieu catalyses the interconversion of metabolites that in modern
   organisms constitute glycolysis & the pentose phosphate pathway. The 29
   observed reactions inc. the formation &/or interconversion of glucose,
   pyruvate, the nucleic acid precursor ribose-5-phosphate & the amino acid
   precursor erythrose-4-phosphate, antedating reactions sequences similar to
   that used by the metabolic pathways. [&] the Archean ocean mimetic increased
   the stability of the phosphorylated intermediates & accelerated the rate of
   intermediate reactions & pyruvate production. The catalytic capacity of the
   reconstructed ocean milieu was attributable to its metal content. The
   reactions were particularly sensitive to ferrous iron Fe(II), which is
   understood to have had high concentrations in the Archean oceans. These
   obs. reveal that reaction seqs. that constitute central carbon metabolism
   could have been constrained by the iron-rich oceanic environment of the early
   Archean. ... metabolism could thus date back to the prebiotic world."
   -- [<A HREF="http://dx.doi.org/10.1002/msb.20145228">doi:10.1002/msb.20145228</A>]['14],
   or [<A HREF="http://msb.embopress.org/content/10/4/725">embopress</A>]['14].

%A D. Gokhman
%A et al ...
%A L. Carmel
%T Reconstructing the DNA methylation maps of the Neandertal and the Denisovan
%J Science
%V 344
%N 6183
%P 523-527
%K MolBio, jrnl, c2014, c201x, c20xx, zz0514, DNA, genome, methylation, DMRs,
   archaic, human, Neandertal, Denisovan, epigenome, HOXD,
%X "... reconstructed the full DNA methylation maps of the Neandertal & the
   Denisovan by harnessing the natural degradation processes of m. & unm.
   cytosines. Comparing these ancient m.maps to those of present-day humans, we
   identified ~2000 differentially m. regions (DMRs). ... found substantial
   m. changes in the HOXD cluster that may explain anatomical diffs. between
   archaic & present-day humans. [&] found that DMRs are sig. more likely to be
   assoc. with diseases. ... provides insight into the epigenetic landscape of
   our closest evolutionary relatives & opens a window to explore the
   epigenomes of extinct species. "
   -- [<A HREF="http://dx.doi.org/10.1126/science.1250368">doi:10.1126/science.1250368</A>]['14].

%A H. Reyes-Centeno
%A S. Ghirotto
%A F. Detroit
%A D Grimaud-Herve
%A G. Barbujani
%A K. Harvati
%T Genomic and cranial phenotype data support multiple modern human dispersals
   from Africa and a southern route into Asia
%J PNAS
%V 111
%N 20
%P 7248-7253
%M MAY
%D 2014
%K jrnl, PNAS, c2014, c201x, c20xx, zz0814, modern, human, Homo sapiens,
   out of Africa, early humans, prehistory, origins, ancient, migration,
   Australia, Asia, Melanesia, archaeology, Pleistocene
%X "Despite broad consensus on Africa as the main place of origin for
   anatomically modern humans, their dispersal pattern ... continues to be
   intensely debated. ... recent genetic studies, as well as accumulating
   archaeological & paleoanthropological evidence, challenge this parsimonious
   model. They suggest instead a 'southern route' dispersal into Asia as early
   as the late Middle Pleistocene [~130ky], followed by a separate dispersal
   [~50ky] into N Eurasia. ... test these competing out-of-A. scenarios by
   modeling hyp.geographical migration routes & assessing their correln with
   neutral populn differentiation, as measured by genetic polymorphisms &
   cranial shape variables of modern human populns from Africa & Asia. We show
   that both lines of evidence support a multiple-dispersals model in which
   Australo-Melanesian populations are relatively isolated descendants of an
   early dispersal, whereas other Asian populations are descended from, or
   highly admixed with, members of a subsequent migration event. "
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1323666111">doi:10.1073/pnas.1323666111</A>]['14].

%A S. A. Villeda
%A et al ...
%A T. Wyss-Coray
%T Young blood reverses age-related impairments in cognitive function and
   synaptic plasticity in mice
%J Nature Medicine
%V ?
%P ?-?
%M MAY
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0514, health, ageing, aging, animal, mouse,
   mice, aged, old, blood, rejuvenation, brain, mental, cognitive, AMP, Creb,
   GDF11, antiageing, antiaging
%X "... report that exposure of an aged animal to young blood can counteract &
   reverse pre-existing effects of brain aging at the molec., structural,
   functional & cognitive level. Genome-wide microarray analysis of
   heterochronic parabionts - in which circulatory systems of young & aged
   animals are connected - identified synaptic plasticity - related
   transcriptional changes in the hippocampus of aged mice. ... At the cognitive
   level, systemic admin. of young blood plasma into aged mice improved age-
   -related cognitive impairments in both contextual fear conditioning & spatial
   learning & memory. ...  mediated, in part, by activation of the cyclic AMP
   response elt binding protein (Creb) in the aged hippocampus. Our data
   indicate that exposure of aged mice to young blood late in life is capable of
   rejuvenating synaptic plasticity & improving cognitive fn."  [online 4/2014.]
   -- [<A HREF="http://dx.doi.org/10.1038/nm.3569">doi:10.1038/nm.3569</A>]['14].
   (Also see more@[<A HREF="http://dx.doi.org/10.1126/science.344.6184.570">9/May</A>], GDF11.)
   [Recommended: Aldous Huxley's novel, 'After Many a Summer,'
    uk us isbn:1566630185; uk us isbn13:978-1566630184.]

%T ENCODE debate revived online
%J Nature
%V 509,
%N 7499
%P 137
%M MAY
%D 2014
%K news, views, c2014, c201x, c20xx, zz0514, MolBio, controversial, stoush,
   fuss, ENCODE, zzEncode, Encyclopedia of DNA Elements, database,
   scientific research
%X "In the social-media age, scientific disagreements can quickly become public
   -  & vitriolic. A report from the ENCODE (Encyclopedia of DNA Elements)
   Project consortium proposes a framework for quantifying the functional parts
   of the human genome. It follows a controversial 2012 Nature paper by the same
   group that concluded that 80%..."
   -- [<A HREF="http://dx.doi.org/10.1038/509137e">doi:10.1038/509137e</A>]['14].
   [Also search for: zzEncode MolBio].

%A D. A. Malyshev
%A K. Dhami
%A T. Lavergne
%A T. Chen
%A N. Dai
%A J. M. Foster
%A I. R. Correa
%A F. E. Romesberg
%T A semi-synthetic organism with an expanded genetic alphabet
%J Nature
%V 509
%P 385-388
%M MAY
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0514, biology, biol, artificial,
   bacterium, Ecoli, DNA, extended, expanded, UBPs, d5SICS, dNaM
%X "... developed a class of UBPs formed between nucleotides bearing hydrophobic
   nucleobases, exemplified by the pair formed between d5SICS and dNaM
   (d5SICS-dNaM) ... show that an exogenously expressed algal nucleotide
   triphosphate transporter efficiently imports the triphosphates of both d5SICS
   & dNaM (d5SICSTP & dNaMTP) into E.coli, and that the endogenous replication
   machinery uses them to accurately replicate a plasmid containing d5SICS-dNaM.
   ...  the resulting bacterium is the first organism to propagate stably an
   expanded genetic alphabet."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13314">doi:10.1038/nature13314</A>]['14].

%A R. L. Charles
%A et al ...
%A P. Eaton
%T Protection from hypertension in mice by the Mediterranean diet is
   mediated by nitro fatty acid inhibition of soluble epoxide hydrolase
%J PNAS
%V ?
%P ?-?
%M MAY
%D 2014
%K jrnl, biol, c2014, c201x, c20xx, zz0514, health, disease, traditional,
   mediterranean diet, nitrite, nitrate, blood pressure, heart,
   nitro fatty acids, hypertension, blood pressure, medicine
%X "[MD] characterized by consumption of unsaturated fats with vegetables rich
   in nitrite & nitrate, resulting in endogenous formation of nitro fatty acids.
   These reactive lipids adduct to soluble epoxide hydrolase, inhibiting it to
   lower blood pressure. Mice genetically engineered to be resistant to this
   adductive inhibition had high blood pressure basally & their hydrolase
   activity was fully resistant to inhibition by nitro fatty acid supplied
   directly or generated via the [MD]. Similarly nitro fatty acid lowered blood
   pressure & abrogated cardiac hypertrophy in a hypertension model in wild-type
   mice, but was ineffective in mutant mice. Thus, protection from hypertension
   afforded by the [MD] is mediated by nitro-fatty acid-dependent inhibition of
   soluble epoxide hydrolase."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1402965111">doi:10.1073/pnas.1402965111</A>]['14].

%A N. N. Ivanova
%A et al ...
%A E. M. Rubin
%T Stop codon reassignments in the wild
%J Science
%V 344
%N 6186
%P 909-913
%M MAY
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0514, genetic code, stop, codon, codons,
   opal, amber, change, reassignment, bacteria, bacterium, bacteriophage
%X "... scanning 5.6 trillion bp of metagenomic data for stop codon reassignment
   events, we detected recoding in a substantial fraction of the > 1700
   environmental samples examined. We observed extensive opal & amber stop codon
   reassignments in bacteriophages & of opal in bacteria. ... indicate that
   bacteriophages can infect hosts with a different genetic code & demonstrate
   phage-host antagonism based on code differences. The abundance & diversity of
   genetic codes present in environmental organisms should be considered in the
   design of engineered organisms with altered genetic codes in order to
   preclude the exchange of genetic info. with naturally occurring species."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1250691">doi:10.1126/science.1250691</A>]['14].

%A M.-S. Kim
%A et al
%A A. Pandey
%T A draft map of the human proteome
%J Nature
%V 509
%N 7502
%P 575-581
%M MAY
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0614, human, protein, proteins,
   proteome, map, database, humanproteomemap, .in, tissue, genes
%X "... present a draft map of the human proteome using high-resolution
   Fourier-transform mass spectrometry. In-depth proteomic profiling of 30
   histologically normal human samples, including 17 adult tissues, 7 fetal
   tissues & 6 purified primary haematopoietic cells, resulted in identification
   of proteins encoded by 17,294 genes accounting for ~ 84% of the total
   annotated protein-coding genes in humans. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13302">doi:10.1038/nature13302</A>]['14].
   See [<A HREF="http://www.humanproteomemap.org">humanproteomemap</A>]['14].
   (Also see [<A HREF="http://www.bbc.com/news/science-environment-27592655">bbc</A>][28/5/2014].)
   [Also search for: ProteomicsDB map c2014] same issue.

%A D. J. Dunstan
%A D. J. Hodgson
%T Snails home
%J Physica Scripta
%V 89
%N 6
%P ?-?
%M MAY
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0714, biology, snail, snails, home, homing,
   instinct, gardening, garden, slug, slugs, pest, control, stats, model
%X "... has freq. been reported that snails that are marked & removed from
   a garden are later found in the g. again. ... often cited as evidence for a
   homing instinct. We report a systematic study of the snail popn in a small
   suburban g., in which large #s of snails were marked & removed over a
   period of about 6 months. While many returned, inferring a homing instinct
   from this evidence requires statistical modelling. Monte Carlo techniques
   demonstrate that movements of snails are better explained by drift under the
   influence of a homing instinct than by random diffusion. Max.likelihood
   techniques infer the existence of two groups of snails in the g.: members
   of a larger popn that show little affinity to the g. itself, & core
   members of a local g. population that regularly return to their home if
   removed. The data are strongly suggestive of a homing instinct, but also
   reveal that snail-throwing can work as a pest management strategy."
   -- [<A HREF="http://dx.doi.org/10.1088/0031-8949/89/06/068002">doi:10.1088/0031-8949/89/06/068002</A>]['14].

%A M. Wilhelm
%A et al
%A B. Kuster
%T Mass-spectrometry-based draft of the human proteome
%J Nature
%V 509
%N 7502
%P 582-587
%M MAY
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0614, human, protein, proteins,
   proteome, map, database, ProteomicsDB, .de, tissue, genes, lincRNA, lincRNAs
%X "... present a mass-spectrometry-based draft of the human proteome & a
   public, high-perf., in-memory DB for real-time analysis of terabytes of big
   data, called ProteomicsDB. The information assembled from human tissues,
   cell lines & body fluids enabled estimation of the size of the protein-coding
   genome, & identified organ-specific & a large # of translated lincRNAs
   (long intergenic non-coding RNAs) ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13319">doi:10.1038/nature13319</A>]['14].
   See [<A HREF="https://www.proteomicsdb.org/">ProteomicsDB</A>]['14].
   (Also see [<A HREF="http://www.bbc.com/news/science-environment-27592655">bbc</A>][28/5/2014].)
   [Also search for: humanproteomemap map c2014] same issue.

%A A. H. Laszlo
%A et al ...
%A J. H. Grundlach
%T Decoding long nanopore sequencing reads of natural DNA
%J NatureBiotech.
%V ?
%P ?-?
%M JUN
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0714, single molecule, sequencing, SMRT,
   nanopore, MspA, 4mer, sequence, read, base calling, error, errors, DNA
%X "... interpret the procession of ion current levels observed during the
   translocation of DNA through the pore MspA. As ~ four nucleotides affect the
   ion current of each level, we measured the ion current corr. to all 256 four-
   -nucleotide combinations (quadromers). This q.map is highly predictive of ion
   current levels of prev. unmeasured seqs. derived from the bacteriophage phi
   X 174 genome. [&] show nanopore seq. reads of phi X 174 up to 4,500 bases in
   length, which can be unambiguously aligned to the phi X 174 ref. genome, &
   demonstrate proof-of-concept utility with respect to hybrid genome assembly
   & polymorphism detection. ..."  [via M.]
   -- [<A HREF="http://dx.doi.org/10.1038/nbt.2950">doi:10.1038/nbt.2950</A>]['14].
   [Also search for: MolBio nanopore].

%A X. Fang
%A et al ...
%A J. Wang
%T Genome-wide adaptive complexes to underground stresses in blind mole rats
   Spalax
%J NatureComms
%V 5
%P e3966
%M JUN
%D 2014
%K jrnl, eJrnl, MolBio, c2014, c201x, c20xx, zz0614, mammal, blind mole rat,
   BMR, Spalax galili, genome, nGenome, DNA, SINEs, hypoxia, cancer, p53
%X "... sequence & analyse the BMR genome & transcriptome, highlighting the
   poss. genomic adaptive responses to the underground stressors. ... show high
   rates of RNA/DNA editing, reduced chr. rearrangements, an over-repn of short
   interspersed elements (SINEs) probably linked to hypoxia tolerance,
   degeneration of vision & progression of photoperiodic perception, tolerance
   to hypercapnia & hypoxia & resistance to cancer. The remarkable traits of the
   BMR, together with its genomic & transcriptomic information, enhance our
   understanding of adaptation to extreme environments & will enable the
   utilization of BMR models for biomedical research in the fight against
   cancer, stroke & cardiovascular diseases."  [70 refs.]
   -- [<A HREF="http://dx.doi.org/10.1038/ncomms4966">doi:10.1038/ncomms4966</A>]['14].
   (Also see [<A HREF="http://www.bbc.com/news/science-environment-27684001">bbc</A>][4/6/2014].)
   [Also search for: mole rat].

%A T. Watanabe
%A et al ...
%A Y. Kawaoka
%T Circulating avian influenza viruses closely related to the 1918 virus have
   pandemic potential
%J Cell Host and Microbe
%V 15
%N 6
%P 692-705
%M JUN
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0614, human, health, disease, 1918,
   flu, virus, influenza, Spanish, pandemic, risk, risks, airborne transmission,
   bird, avian
%X "... phylogenetic & geographic analyses revealed the global prevalence of
   avian influenza virus genes whose proteins differ only a few AAs from the
   1918 pandemic influenza virus, suggesting that 1918-like pandemic v. may
   emerge in the future. ... generated & characterized a v. composed of avian
   influenza viral segments with high homology to the 1918 v.. This v. exhibited
   pathogenicity in mice & ferrets higher than that in an authentic avian
   influenza v.. [&] acquisition of seven AA substitutions in the viral
   polymerases & the hemagglutinin surface glycoprotein conferred respiratory
   droplet transmission to the 1918-like avian virus in ferrets, demonstrating
   that contemporary avian influenza vs. with 1918 virus-like proteins may have
   pandemic potential."
   -- [<A HREF="http://dx.doi.org/10.1016/j.chom.2014.05.006">doi:10.1016/j.chom.2014.05.006</A>]['14].
   (Controversial, dangerous.  Also see
    the_G@[<A HREF="http://www.theguardian.com/science/2014/jun/11/crazy-dangerous-creation-deadly-airborne-flu-virus">www</A>]['14].)

%A A. Rudiny
%A M. Song
%A J. Geller
%T Mapping biological entities using the longest approximately common prefix
   method
%J BMC Bioinformatics
%V 15
%P e187
%M JUN
%D 2014
%K jrnl, eJrnl, MolBio, c2014, c201x, c20xx, zz0614, sequence, strings, string,
   map, mapping, longest approximately common prefix, match, approximate,
   matching, similarity, duplicate detection, spelling correction
%X "... introduces the (LACP) method as an alg. for approx. string matching that
   runs in linear time. We compare the LACP method for performance, precision
   & speed to nine other well-known string matching algs.. ... use two
   multiple-source samples from the Unified Medical Language System (UMLS) &
   two SNOMED Clinical Terms-based samples. [&] we present a spell checker based
   on the LACP method.  Conclusions: [LCAP] method completes its string
   similarity evalns in less time than all 9 string similarity methods used for
   comparison. [It] outperforms these 9 approx. string matching methods in its
   Maximum F1 measure when evaluated on three out of the four datasets, & in its
   avg. precision on two of the four datasets."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-15-187">doi:10.1186/1471-2105-15-187</A>]['14].
   [Also search for: approximate string matching].

%A W. A. Akanni
%A C. J. Creevey
%A M. Wilkinson
%A D. Pisani
%T L.U.St: a tool for approximated maximum likelihood supertree reconstruction
%J BMC Bioinformatics
%V 15
%P e183
%D 2014
%K jrnl, eJrnl, MolBio, c2014, c201x, c20xx, zz0614, LUST, phylogenetic, family,
   tree, trees, supertree, approximate
%X "... present the L.U.St package, a python tool for approx. max. LH supertree
   inference & illustrate its applicn using a genomic data set for the placental
   mammals. ... allows the calcn of the approx. LH of a supertree, given a set
   of input trees, performs heuristic searches to look for the supertree of
   highest LH, & performs statistical tests of two or more supertrees. [It]
   implements a winning sites test allowing ranking of a collecn of apriori
   selected hypotheses, given as a collecn of input supertree topologies. [&]
   outputs a file of input-tree-wise LH scores that can be used as input to
   CONSEL for calculn of std tests of two trees ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-15-183">doi:10.1186/1471-2105-15-183</A>]['14].

%A N. Natarajan
%A I. S. Dhillon
%T Inductive matrix completion for predicting gene-disease associations
%J J. Bioinformatics
%V 30
%N 12
%P i60-i68
%M JUN
%D 2014
%K jrnl, eJrnl, MolBio, c2014, c201x, c20xx, zz0614, gene, disease, association,
   studies, GWAS, matrix completion, Online Mendelian Inheritance in Man, OMIM,
   IMC, rank, Catapult method, Nomad, uTexas, uniTexas
%X "... novel matrix-completion method called Inductive Matrix Completion to the
   problem of predicting gene-disease assoc.; it combines multiple types of
   evidence (features) for diseases & g. to learn latent factors that explain
   the observed g.-d. assocns. We construct features from different biol.
   sources such as microarray expn data & disease-related textual data. A
   crucial advantage of the method is that it is inductive; it can be applied to
   diseases not seen at training time, unlike trad. matrix-completion approaches
   & n/w-based inference methods that are transductive. ... Comparison with
   state-of-the-art methods on diseases from the Online Mendelian Inheritance in
   Man (OMIM) database shows that the proposed approach is substantially better
   - it has close to one-in-four chance of recovering a true assocn in the top
   100 predns, [v] the recently proposed Catapult method (2nd best) that has
   < 15% chance. We demo. that the inductive method is particularly effective
   for a query disease with no previously known gene assocns, & for predicting
   novel genes, i.e. genes that are previously not linked to diseases. ..."
   "Completion: P ~ W x H^t, where W is n x k, H is m x k, and k << m, n."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btu269">doi:10.1093/bioinformatics/btu269</A>]['14],
      bigdata.ices@[<A HREF="http://bigdata.ices.utexas.edu/project/gene-disease">utex</A>]['14].

%A R. Krishnan
%A et al ...
%A R. A. Fisher
%T A bacteriophage capsid protein provides a general amyloid interaction
   motif (GAIM) that binds and remodels misfolded protein assemblies
%J J. Mol. Biol.
%V 426
%N 13
%M JUN
%D 2014
%K jrnl, JMB, MolBio, c2014, c201x, c20xx, zz0715, brain, disease, alzheimers,
   M13, phage, g3p, protein, amyloid, fold, misfold, misfolded, misfolding,
   aBeta, GAIM, AAIC, NPT088, NeuroPhage
%X "... show that the gene 3 protein (g3p) of filamentous bacteriophage mediates
   potent generic binding to the amyloid fold. We have characterized the amyloid
   binding & conformational remodeling activities using an array of techniques,
   inc. X-ray fiber diffraction & NMR. The mechanism for g3p binding with
   amyloid appears to reflect its physiological role during infection of
   E.coli, which is dependent on temp.-sensitive interdomain unfolding &
   cis-trans prolyl isomerization of g3p. [&] a natural receptor for g3p,
   TolA-C, competitively interferes with A_beta binding to g3p. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jmb.2014.04.015">doi:10.1016/j.jmb.2014.04.015</A>]['15].
   Also see, "... At AAIC 2015, Richard Fisher, PhD, of NeuroPhage Pharma. ...
      & colleagues shared the results of tests with NPT088, a new type of
      therapeutic that includes the [GAIM] Motif ..."
   -- pr@[<A HREF="https://www.alz.org/aaic/releases_2015/Sun-930amET.asp">alz.org</A>][7/2015].

%A E. J. Radford
%A et al ...
%A A. C. Ferguson-Smith
%T In utero undernourishment perturbs the adult sperm methylome and
   intergenerational metabolism
%J Science
%V ?
%M ?
%P ?-?
%M JUL
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0714, DNA, methylation, epigenetic,
   inheritance, starvation, starved, underfed, famine, F1, F2, fetal, embryo,
   development, child, offspring, generation, health, diabetes
%X "... demonstrate that the in utero nutritional environment of F1 embryos
   alters the germline DNA methylome of F1 adult males in a locus-specific
   manner. Differentially methylated regions are hypomethylated & enriched in
   nucleosome-retaining regions. A substantial fraction is resistant to early
   embryo methylation reprogramming, potentially impacting F2 development.
   Differential methylation is not maintained in F2 tissues, yet locus-specific
   expression is perturbed. Thus, in utero nutritional exposures during critical
   windows of germ cell development can impact the male germline methylome,
   associated with metabolic disease in offspring."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1255903">doi:10.1126/science.1255903</A>]['14].

%A C. Gilissen
%A et al ...
%A J. A. Veltman
%T Genome sequencing identifies major causes of severe intellectual disability
%J Nature
%V 511
%N 7509
%P 344-347
%M JUL
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0714, cause, intellectual disability,
   severe, impairment, identify, CNV, CNVs, SNV, SNP
%X "... Microarray studies &, more recently, exome seq. have demo. the
   importance of de novo copy number variations (CNVs) & single-nucleotide
   variations (SNVs) in ID, but [most] cases remain undiagnosed ... applied
   whole-genome seq. to 50 patients with severe ID & their unaffected parents.
   ... 84 de novo SNVs affecting the coding region were identified, which showed
   a stat.sig. enrichment of loss-of-fn mutations [&] an enrichment for genes
   previously implicated in ID-related disorders. [&] we identified eight de
   novo CNVs, including single-exon & intra-exonic deletions, [&]
   interchromosomal duplications. These CNVs affected known ID genes more
   frequently than expected. On the basis of diagnostic interpretation of all
   de novo variants, a conclusive genetic diagnosis was reached in 20 patients.
   Together with one compound heterozygous CNV causing disease in a recessive
   mode, this results in a diagnostic yield of 42% in this extensively studied
   cohort, & 62% as a cumulative estimate in an unselected cohort. ... suggest
   that de novo SNVs & CNVs affecting the coding region are a major cause of
   severe ID. Genome seq. can be applied as a single genetic test to reliably
   identify & characterize the comprehensive spectrum of genetic var'n,
   providing a genetic diagnosis in the majority of patients with severe ID."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13394">doi:10.1038/nature13394</A>]['14].

%A V. Bhatia
%A S. I. Barroso
%A M. L. Garcia-Rubio
%A E. Tumini
%A E.  Herrera-Moyano
%A A. Aguilera
%T BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export
   factor PCID2
%J Nature
%V 511
%N 7509
%P 362-365
%M JUL
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0714, human, cancer, gene, mRNP, BRCA2,
   BRCA 2, R loops, Rloops, TREX 2, TREX2, mRNP, Ser139, gamma H2AX, 53BP1,
   PCID2, GANP, DSS1, repair, instability
%X "... instability is freq. mediated by R-loops formed by DNA-RNA hybrids & a
   displaced single-stranded DNA. ... show that the human TREX-2 complex, which
   is involved in mRNP biogenesis & export, prevents genome instability as
   determined by the accumulation of gamma-H2AX (Ser-139 phosphorylated histone
   H2AX) & 53BP1 foci & single-cell electrophoresis in cells depleted of the
   TREX-2 subunits PCID2, GANP & DSS1. We show that the BRCA2 repair factor,
   which binds to DSS1, also assoc. with PCID2 in the cell. ... results indicate
   that R-loops are frequently formed in cells & that BRCA2 is req. for their
   processing. This link between BRCA2 & RNA-mediated genome instability
   indicates that R-loops may be a chief source of replication stress &
   cancer-assoc. instability."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13374">doi:10.1038/nature13374</A>]['14].
   [Also search for: MolBio BRCA2].

%A T. Hackl
%A R. Hedrich
%A J. Schultz
%A F. Forster
%T Proovread: large-scale high-accuracy PacBio correction through iterative
   short read consensus
%J J. Bioinformatics
%V 7
%P ?-?
%M JUL
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0714, Pacific Biosciences, sequencing,
   short read, single molecule, SMRT, base calling, errors, error correction,
   rate
%X "... proovread, a hybrid correction pipeline for SMRT reads, which can be
   flexibly adapted on existing hardware & infrastructure from a laptop to a
   high-performance computing cluster. On genomic & transcriptomic test cases
   covering Escherichia coli, Arabidopsis thaliana & human, proovread achieved
   accuracies up to 99.9% & outperformed the existing hybrid corr'n programs.
   [&] proovread-corrected seqs. were longer & the throughput was higher. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btu392">doi:10.1093/bioinformatics/btu392</A>]['14].
   [Also search for: MolBio SMRT errors] and
   [also search for: MolBio base calling error correction].

%T Biological insights from 108 schizophrenia-associated genetic loci
%Q Schizophrenia Working Group of the Psychiatric Genomics Consortium
%J Nature
%V 511
%N 7510
%P 421-427
%M JUL
%D 2014
%K jrnl, MolBio, GWAS, c2014, c201x, c20xx, zz0714, human, schizophrenia,
   brain, mental health, gene, genes, DRD2, immune system
%X "Schizophrenia is a highly heritable disorder. ... report a multi-stage
   schizo. [GWAS] of up to 36,989 cases & 113,075 controls. We identify
   128 indep. assoc. spanning 108 conservatively defined loci that meet genome-
   -wide sig., 83 of which have not been prev. reported. Assocns were enriched
   among genes expressed in brain, providing biol. plausibility ... Many
   findings have the potential to provide entirely new insights into aetiology,
   but assocns at DRD2 & several genes involved in glutamatergic
   neurotransmission highlight molecules of known & potential therapeutic
   relevance to s. ... assocns were enriched among genes expressed in tissues
   that have important roles in immunity, providing support for the speculated
   link between the immune system & s.."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13595">doi:10.1038/nature13595</A>]['14].
   [Also search for: MolBio brain GWAS].

%A A. Cadeddu
%A E. K. Wylie
%A J. Jurczak
%A M. Wampler-Doty
%A B. A. Grzybowski
%T Organic chemistry as a language and the implications of chemical linguistics
   for structural and retrosynthetic analyses
%J Angewandte Chemie
%V 126
%N 31
%P 8246-8250
%M JUL
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0814, chemistry, organic, chemical, words,
   molecules, information
%X "Methods of comp.linguistics are used to demo. that a nat.language such as
   English & organic chemistry have the same structure in terms of the freq. of,
   resp., text fragments & molecular fragments. This quantitative corr. suggests
   that it is possible to extend the methods of computational corpus linguistics
   to the analysis of organic molecules. It is shown that within organic
   molecules bonds that have highest info. content are the ones that 1) define
   repeat/symmetry subunits & 2) in asymmetric molecules, define the loci of
   potential retrosynthetic disconnections. L.-based analysis appears
   well-suited to the analysis of complex structural & reactivity patterns
   within organic molecules."
   -- [<A HREF="http://dx.doi.org/10.1002/ange.201403708">doi:10.1002/ange.201403708</A>]['14].

%A M. A. Lancaster
%A J. A. Knoblich
%T Organogenesis in a dish: Modeling development and disease using
   organoid technologies
%J ScienceMag
%V 345
%N 6194
%P ?-?
%M JUL
%D 2014
%K jrnl, Biol, MolBio, c2014, c201x, c20xx, zz0820, organoid, organelle, organs,
   tissue types
%X "... Organoids are derived from pluripotent stem cells or isolated organ
   progenitors that differentiate to form an organlike tissue exhibiting
   multiple cell types that self-organize to form a structure not unlike the
   organ in vivo ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1247125">doi:10.1126/science.1247125</A>]['20].
   [Also search for: organelle].

%A C. M. Rands
%A S. Meader
%A C. P. Ponting
%A G. Lunter
%T 8.2% of the human genome is constrained: Variation in rates of turnover
   across functional element classes in the human lineage
%J PLoS Genetics
%V 10
%N 7
%P e1004525
%M JUL
%D 2014
%K jrnl, eJrnl, MolBio, c2014, c201x, c20xx, zz0714, human, genome, junk DNA,
   non-coding, noncoding, functional, constrained, pressure of selection,
   evolution
%X "... it remains unclear what fraction of the human genome confers fn, where
   this seq. resides, & how much is shared with other mammalian species. ...
   address these issues by identifying & characterising seq. that has been
   constrained wrt insertions & deletions for pairs of eutherian genomes over a
   range of divergences. Within noncoding seq., we find increasing amounts of
   mutually constrained seq. as species pairs become more closely related,
   indicating that noncoding constrained seq. turns over rapidly. We est. that
   half of present-day noncoding constrained seq. has been gained or lost in ~
   the last 130 million years (half-life in units of divergence time,
   d_1/2 = 0.25-0.31). While enriched with ENCODE biochem. annotations, much of
   the short-lived constrained seqs. we identify are not detected by models
   optimized for wider pan-mammalian conservation. ... By contrast, protein
   coding seq. has been highly stable, with an est. half-life of over a billion
   years (d_1/2 = 2.1-5.0). ... est. that 8.2% (7.1-9.2%) of the human g. is
   presently subject to -ve seln & thus is likely to be functional, while only
   2.2% has maintained constraint in both human & mouse since these species
   diverged. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pgen.1004525">doi:10.1371/journal.pgen.1004525</A>]['14].
   (Also read The_G.@[<A HREF="http://www.theguardian.com/science/2014/jul/24/10-percent-human-dna-functional-genome-biological-baggage">24/7/2014</A>].)
   [Also search for: MolBio junk DNA].

%A T. J. Littlejohns
%A et al ...
&A D. J. Llewellyn
%T Vitamin D and the risk of dementia and Alzheimer disease
%J Neurology
%V ?
%P ?-?
%M AUG
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0814, human health, medicine, Alzheimers,
   disease, dementia, risk, risks, stats, vitamin D, vitaminD
%X "... One thousand six hundred fifty-eight elderly ambulatory adults free from
   dementia, cardiovascular disease, & stroke who participated in the US popn-
   -based Cardiovascular Health Study between 1992-1993 & 1999 were included.
   ... During a mean follow-up of 5.6y., 171 participants developed all-cause
   dementia, inc. 102 cases of A.disease. ... results confirm that vitamin D
   deficiency is assoc. with a subst. increased risk [ > x 2] of all-cause
   dementia & A.disease. This adds to the ongoing debate about the role of
   vitamin D in nonskeletal conditions."  [online 8/2014.]
   -- [<A HREF="http://dx.doi.org/10.1212/WNL.0000000000000755">doi:10.1212/WNL.0000000000000755</A>]['14],
      D.J.L.@[<A HREF="https://medicine.exeter.ac.uk/about/profiles/index.php?web_id=David_Llewellyn">ex't'r</A>]['14].

%A N. J. Roberts
%A et al ...
%A S. Shou
%T Intratumoral injection of Clostridium novyi-NT spores induces antitumor
   responses
%J Sci. Transl. Med.
%V 6
%N 249
%P 249ra111
%M AUG
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0814, medicine, cancer, bacterium, bacteria,
   Clostridium novyi-NT, novyiNT, spore, rat, dog, trial, tumor, tumour
%X "Species of Clostridium bacteria are notable for their ability to lyse tumor
   cells growing in hypoxic environments. We show that an attenuated strain of
   Clostridium novyi (C. novyi-NT) induces a microscopically precise, tumor-
   -localized response in a rat orthotopic brain tumor model after intratumoral
   injection. ... found that intratumoral injection of C. novyi-NT spores was
   well tolerated in companion dogs bearing spontaneous solid tumors, with the
   most common toxicities being the expected symptoms associated with bacterial
   infections. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/scitranslmed.3008982">doi:10.1126/scitranslmed.3008982</A>]['14].

%A C. Clark
%A J. Kalita
%T A comparison of algorithms for the pairwise alignment of biological networks
%J J. Bioinformatics
%V 30
%N 16
%P 2351-2359
%M AUG
%D 2014
%K jrnl, survey, MolBio, c2014, c201x, c20xx, zz0814, network, graph, align,
   match, matching, PPI, algorithm, heuristic, pairwise, GRAAL, C-GRAAL,
   MI-GRAAL, GHOST, IsoRank, NATALIE 2.0, NETAL, PINALOG, SPINAL,
   NAPAbench, IsoBase, benchmark, bench mark
%X "... many algs. have been proposed for the purpose of p/wise n/w alignment -
   finding a mapping from the nodes of one n/w to the nodes of another [s.t.]
   the mapped nodes can be considered to corr. [wrt] both their place in the
   n/w topology & their biol.attributes. ...  finding dramatic differences
   between existing algs. in the quality of the alignments they produce. ...
   ... protein-protein interaction (PPI) n/w ...
   ... Most aligners ... [(i)] local ... [& (ii)] maximum-weight bipartite
   matching problem ..."     [Online 5/2014.]
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btu307">doi:10.1093/bioinformatics/btu307</A>]['14].

%A S. K. Gire
%A et al ...
%A P. C. Sabeti
%T Genomic surveillance elucidates Ebola virus origin and transmission during
   the 2014 outbreak
%J Science
%V ?
%P ?-?
%M AUG
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0914, Ebola, virus, EBOV, genome, variation,
   Africa, Liberia, Guinea, Sierra Leone, outbreak, epidemic, Contagion,
   human health, disease, Zmapp
%X "... Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone,
   & Nigeria. We sequenced 99 Ebola v.genomes from 78 patients in S.L. to
   ~2,000x coverage. We observed a rapid accumulation of interhost & intrahost
   genetic var'n ... This W.African variant likely diverged from Middle African
   lineages ~2004, crossed from Guinea to Sierra Leone in May 2014, & has
   exhibited sustained human-to-human transmission subsequently, with no
   evidence of additional zoonotic sources. Since many of the mutns alter
   protein seqs. & other biol. meaningful targets, they should be monitored for
   impact on diagnostics, vaccines, & therapies critical to outbreak response."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1259657">doi:10.1126/science.1259657</A>]['14] (online Aug 2014).
   (Also comment [<A HREF="http://dx.doi.org/10.1126/science.345.6200.989">www</A>]['14],
    and progress [<A HREF="http://dx.doi.org/10.1038/514284a">16/10/14</A>].)
   [Also search for: Ebola virus].

%A J.-B. Petit
%A et al ...
%A J. Marioni
%T Identifying cell types from spatially referenced single-cell expression
   datasets
%J PLoS Comp. Biol.
%V ?
%M SEP
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0720, scRNAseq, cell expression profile,
   tissue, 3D, spatial, HMRF, MRF, Markov random field, clustering,
   Wholemount, WiSH
%X "...  experimental technology, such as Wholemount in Situ Hybridizations
   (WiSH) & single-cell RNA-sequencing. ... now possible to study gene expn
   levels in thousands of cells from the same tissue type. After generating such
   data one of the key goals is to cluster the cells into groups that correspond
   to both known & putatively novel cell types. Whilst many clustering algs.
   exist, they are typically unable to incorporate information about the spatial
   dependence between cells within the tissue under study. When such info.
   exists it provides important insights that should be directly inc. in the
   clustering scheme. To this end we have developed a clustering method that
   uses a Hidden Markov Random Field (HMRF) model to exploit both quantitative
   measures of expression & spatial information. ..."
   -- [<A HREF="https://doi.org/10.1371/journal.pcbi.1003824">doi:10.1371/journal.pcbi.1003824M</A>]['20].
   [Also search for: Markov random field]  and  [also search for: scRNAseq].

%A F. Deboeud
%A et al ...
%A P. Lashermes
%T The coffee genome provides insight into the convergent evolution of
   caffeine biosynthesis
%J Science
%V 345
%N 6201
%P 1181-1184
%M SEP
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0914, coffee, Coffea canephora,
   genome, nGenome, caffeine, plant, asterid angiosperm, eudicot,
   N-methyltransferase
%X "... displays a conserved chromosomal gene order among asterid angiosperms.
   Although it shows no sign of the whole-genome triplication identified in
   Solanaceae species such as tomato, the genome includes several species-
   -specific gene family expansions, among them N-methyltransferases (NMTs)
   involved in caffeine production, defense-related genes, & alkaloid &
   flavonoid enzymes involved in secondary compound synthesis. Comparative
   analyses of caffeine NMTs demonstrate that these genes expanded through
   seq. tandem duplns indep. of genes from cacao & tea, suggesting that c. in
   eudicots is of polyphyletic origin."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1255274">doi:10.1126/science.1255274</A>]['14].

%A C. A. Rietveld
%A et al ...
%A P. D. Koellinger
%T Common genetic variants associated with cognitive performance identified
   using the proxy-phenotype method
%J PNAS
%V ?
%P ?-?
%M SEP
%D 2014
%K jrnl, PNAS, MolBio, c2014, c201x, c20xx, zz0914, human, gene, genes,
   intelligence, KNCMA1, NRXN1, POU2F3, SCRT, rs1487441, rs7923609, rs2721173,
   GWAS, cognition, memory, learning, brain, synaptic plasticity
%X "We identify common genetic variants assoc. with cog. perf. using a two-stage
   approach, which we call the proxy-phenotype method. First, we conduct a
   [GWAS] of ed.attainment in a large sample (n=106,736), which produces a set
   of 69 ed.-assoc. SNPs. Second, using indep. samples (n=24,189), we measure
   the assoc. of these ed.-associated SNPs with cog.performance. Three SNPs
   (rs1487441, rs7923609, & rs2721173) are sig. assoc. with cog. perf. after
   correction for multiple hypothesis testing. In an indep. sample of older
   Americans (n=8,652), we also show that a polygenic score derived from the
   ed.-assoc. SNPs is assoc. with memory & absence of dementia. Convergent
   evidence from a set of bioinfo analyses implicates four specific genes
   (KNCMA1, NRXN1, POU2F3, & SCRT). All of these genes are assoc. with a
   particular neurotransmitter pathway involved in synaptic plasticity, the main
   cellular mechanism for learning & memory."  [online 9/2014.]
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1404623111">doi:10.1073/pnas.1404623111</A>]['14].
   [Also search for: Social Science Genetic Association Consortium].

%A Y. Takashima
%A et al ...
%A A. Smith
%T Resetting transcription factor control circuitry toward ground-state
   pluripotency in human
%J Cell
%V 158
%N 6
%P 1254-1269
%M SEP
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0914, human, biol, biology, stem cell,
   cells, naive, embryonic, pluripotent, ESC, NANOG, KLF2, ERK, TFCP2L1, KLF4
%X "... Current h. pluripotent stem cells lack the transcription factor
   circuitry that governs the ground state of mouse embryonic stem cells (ESC).
   ... report that short-term expression of two components, NANOG & KLF2, is
   suff. to ignite other elts of the n/w & reset the h. pluripotent state.
   Inhibition of ERK & protein kinase C sustains a transgene-indep. rewired
   state. Reset cells self-renew continuously without ERK signaling, are
   phenotypically stable, & are karyotypically intact. They differentiate in
   vitro & form teratomas in vivo. Metabolism is reprogrammed with activation of
   mitochondrial respiration as in ESC. DNA methylation is dramatically reduced
   & transcriptome state is globally realigned across multiple cell lines.
   Depletion of ground-state transcription factors, TFCP2L1 or KLF4, has
   marginal impact on conventional h. pluripotent stem cells but collapses the
   reset state. These findings demo. feasibility of installing & propagating
   functional control circuitry for ground-state pluripotency in human cells."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cell.2014.08.029">doi:10.1016/j.cell.2014.08.029</A>]['14].
   [Also search for: stem cell].

%A I. Lazaridis
%A et al ...
%A J. Krause
%T Ancient human genomes suggest three ancestral populations for present-day
   Europeans
%J Nature
%V 513
%N 7518
%P 409-413
%M SEP
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0914, human, evolution, origins,
   Europe, ancient, Palaeolithic, lineage, genome, population
%X "We seq. the genomes of a ~7,000-year-old farmer from Germany & eight
   ~8,000-year-old hunter-gatherers from Luxembourg & Sweden. We analysed these
   & other ancient genomes with 2,345 contemporary humans to show that most
   present-day Europeans derive from >= three highly differentiated popns:
   W.European hunter-gatherers, who contributed ancestry to all Europeans but
   not to near Easterners; ancient N.Eurasians related to Upper Palaeolithic
   Siberians, who contributed to both Europeans & near Easterners; & early
   European farmers, who were mainly of near Eastern origin but also harboured
   W.European hunter-gatherer related ancestry. We model these popns' deep
   relationships & show that early European farmers had ~44% ancestry from a
   'basal Eurasian' popn that split before the diversification of other
   non-African lineages."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13673">doi:10.1038/nature13673</A>]['14].
   [Also search for: human origins MolBio].

%A D. Fisman
%A E. Khoo
%A A. Tuite
%T Early epidemic dynamics of the West African 2014 Ebola outbreak: Estimates
   derived with a simple two-parameter model
%J PLoS Current Outbreaks
%M SEP
%D 2014
%K c2014, c201x, c20xx, zz1014, Ebola, virus, outbreak, epidemic, stats, math,
   model, Africa, Liberia, prediction, zoonotic filovirus
%X "... utilized a simple, two param. math. model of epidemic growth & control,
   to characterize epidemic growth patterns in West Africa, to evaluate the
   degree to which the epidemic is being controlled, & to assess the potential
   implications of growth patterns for epidemic size. Models demonstrated good
   fits to data. Overall basic reproductive number (R0) for the epidemic was
   est. to be between 1.6 & 2.0, consistent with prior outbreaks. However, we
   identified only weak evidence for the occurrence of epidemic control in
   W.Africa as a whole, & essentially no evidence for control in Liberia
   (though slowing of growth was seen in Guinea & Sierra Leone). It is projected
   that small redns in transmission would prevent tens of thousands of future
   infections. These findings suggest that there is an extraordinary need for
   improved control measures for the 2014 Ebola epidemic, especially in L.,
   if catastrophe is to be averted."  [14 refs.]
   -- [<A HREF="http://currents.plos.org/outbreaks/article/obk-14-0036-early-epidemic-dynamics-of-the-west-african-2014-ebola-outbreak-estimates-derived-with-a-simple-two-parameter-model/">plos.org</A>][8/9/2014].
   [Also search for: Ebola virus].

%A E. M. Standen
%A T. Y. Du
%A H. C. E. Larsson
%T Developmental plasticity and the origin of tetrapods
%J Nature
%V 513
%N 7516
%P 54-58
%M SEP
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0115, biol, biology, evolution, fish, fishes,
   bichir, Polypterus, actinopterygians, elpistostegid, evolution, tetrapod,
   limb, limbs, land, leg, legs, walking, Tiktaalik
%X "The origin of tetrapods from their fish antecedents, ~400 million years ago,
   was coupled with the origin of terrestrial locomotion & the evolution of
   supporting limbs. Polypterus is a member of the basal-most group of
   ray-finned fish (actinopterygians) & has many plesiomorphic morphologies that
   are comparable to elpistostegid fishes, which are stem tetrapods. Polypterus
   therefore serves as an extant analogue of stem tetrapods, allowing us to
   examine how developmental plasticity affects the 'terrestrialization' of
   fish. We measured the developmental plasticity of anatomical & biomechanical
   responses in P. reared on land. Here we show the remarkable corr. between the
   environmentally induced phenotypes of terrestrialized P. & the ancient
   anatomical changes in stem tetrapods, & we provide insight into stem tetrapod
   behavioural evolution. Our results raise the possibility that environmentally
   induced developmental plasticity facilitated the origin of the terrestrial
   traits that led to tetrapods."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13708">doi:10.1038/nature13708</A>]['15],
      standenlab@[<A HREF="http://www.standenlab.com/">www</A>]['15] (U.Ottawa).

%A F. M. Harold
%T In Search of Cell History: The Evolution of Life's Building Blocks
%I UChicago
%P 304
%M OCT
%D 2014
%K book, text, MolBio, c2014, c201x, c20xx, zz1014, cells, cells, beginning,
   start, origin, biology, biol
%X 1st ed 2014; pb  us$36; us isbn:022617428X; us isbn13:978-0226174280.
                hb us$105; us isbn:022617414X; us isbn13:978-0226174143.
   "... investigates the full scope of cellular history. Assuming only a basic
   knowledge of cell biology, H. examines such pivotal subjects as the
   relationship between cells and genes; the central role of bioenergetics in
   the origin of life; the status of the universal tree of life with its three
   stems and viral outliers; and the controversies surrounding the last
   universal common ancestor. ..."

%A M. Gnanavel
%A P. Mehrotra
%A R. Rakshambikai
%A J. Martin
%A N. Srinivasan
%A R. M. Bhaskara
%T CLAP: A web-server for automatic classification of proteins with special
   reference to multi-domain proteins
%J BMC Bioinformatics
%V 15
%P 343
%M OCT
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz1114, CLAP, protein, domain, domains
%X "... in the case of multi-domain proteins, the alignment quality might be
   poor due to varied lengths of the proteins, domain shuffling or circular
   permutations. Multi-domain proteins are ubiquitous in nature, hence
   alignment-free tools, which overcome the shortcomings of a.-based protein
   comparison methods, are required. Further, existing tools classify proteins
   using only domain-level information & hence miss out on the info. encoded in
   the tethered regions or accessory domains. [We] takes into account the
   full-length seq. of a protein, consolidating the complete seq. info. to
   understand a given protein better. ... Our web-server, CLAP (Classification
   of Proteins), is one such a.-free s/w for automatic classification of protein
   seqs.. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-15-343">doi:10.1186/1471-2105-15-343</A>]['14],
      25282152@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/25282152">p'bmed</A>]['14].

%A Q. Fu
%A et al ...
%A S. Paabo
%T Genome sequence of a 45,000-year-old modern human from western Siberia
%J Nature
%V 514
%N 7523
%P 445-449
%M OCT
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz1014, modern, human, genome, ancient,
   old, DNA, Homo sapiens, Ust'-Ishim, lineage, Neanderthal, Asia
%X "... high-quality g. seq. of a ~45,000-year-old modern human male from
   Siberia. [He] derives from a populn that lived before - or simultaneously
   with - the separation of the populns in W and E Eurasia & carries a similar
   amount of Neanderthal ancestry as present-day Eurasians. However, the genomic
   segments of N.ancestry are substantially longer than those observed in
   present-day individuals, indicating that N. gene flow into the ancestors of
   [him] occurred 7,000-13,000 years before he lived. We est. an autosomal
   mutn rate of 0.4*10^-9 to 0.6*10^-9 per site per year, a Y chr. mutn rate of
   0.7*10^-9 to 0.9*10^-9 per site per year based on the additional substn that
   have occurred in present-day non-Africans compared to this genome, & a
   mitochondrial mutn rate of 1.8*10^-8 to 3.2*10^-8 per site per year based on
   the age of the bone."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13810">doi:10.1038/nature13810</A>]['14].
   (And comment [<A HREF="http://dx.doi.org/10.1038/514413a">www</A>]['14].)
   [Also search for: ancient human DNA].

%A J. A. Lewnard
%A et al ...
%A A. P. Galvani
%T Dynamics and control of Ebola virus transmission in Montserrado, Liberia:
   a mathematical modelling analysis
%J The Lancet
%V ?
%P ?-?
%M OCT
%D 2014
%K jrnl, c2014, c201x, c20xx, zz1014, medicine, Ebola, virus, outbreak,
   epidemic, Africa, Liberia, stats, model, prediction
%X "... developed a transmission model of Ebola virus that we fitted to reported
   EVD cases & deaths in Montserrado County, Liberia. We used this model to
   assess the effectiveness of expanding EVD treatment centres, increasing case
   ascertainment, & alloc. protective kits for controlling the outbreak in M..
   We varied the efficacy of protective kits from 10% to 50%. ...
   ... We estimated the basic reproductive # for EVD in Montserrado to be 2Â·49
   (95% CI 2Â·3-82Â·60). We expect that allocating 4800 additional beds at EVD
   t.centres & increasing case ascertainment five-fold in Nov., 2014, can avert
   77,312 (95% CI 68,400-85,870) cases of EVD rel. to the status quo by Dec 15,
   2014. Complementing these measures with protective kit alloc. raises the
   expectation as high as 97,940 (90,096-105,606) EVD cases. If deployed by Oct
   15, 2014, equiv. interventions would have been expected to avert 137,432
   (129,736-145,874) cases of EVD. If delayed to Nov 15, 2014, we expect the
   interventions will at best avert 53,957 (46,963-60,490) EVD cases. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/S1473-3099(14)70995-8">doi:10.1016/S1473-3099(14)70995-8</A>]['14], online Oct 2014.
   Also see [<A HREF="http://dx.doi.org/10.1016/S1473-3099(14)70851-5">comment</A>]['14].
   [Also search for: Ebola virus].

%A J. Tiihonen
%A et al ...
%A T. Paunio
%T Genetic background of extreme violent behavior
%J Molec. Psych.
%V ?
%P ?-?
%M OCT
%D 2014
%K jrnl, c2014, c201x, c20xx, zz1114, human behaviour, gene, genes, violent,
   violence, association, law, crime, criminal, prison, murder, homicide,
   MAOA, CDH13, genotype
%X "... results, from two indep. cohorts of Finnish prisoners, revealed that a
   monoamine oxidase A (MAOA) low-activity genotype (contrib. to low dopamine
   turnover rate) as well as the CDH13 gene (coding for neuronal membrane
   adhesion protein) are assoc. with extremely violent behavior (at least 10
   committed homicides, attempted homicides or batteries). No substantial signal
   was observed for either MAOA or CDH13 among non-violent offenders, indicating
   that findings were specific for violent offending ... imply that at least
   about 5-10% of all severe violent crime in Finland is attrib. to the
   aforementioned MAOA & CDH13 genotypes."  [online 10/2014.]
   -- [<A HREF="http://dx.doi.org/10.1038/mp.2014.130">doi:10.1038/mp.2014.130</A>]['14].
   [Also search for: MAOA gene].

%A A. Wagner
%T Arrival of the Fittest: Solving evolution's greatest puzzle
%I OneWorld Publ.
%P 301
%M OCT
%D 2014
%K book, text, MolBio, c2014, c201x, c20xx, zz1214, protein, evolution,
   variation, innovation, fitness, spaces, possible, Darwinism
%X 1st ed 2014; hb us$21; uk us isbn:1591846463; uk us isbn13:978-1591846468.
   "... [W] has found that adaptations are not just driven by chance, but by a
   set of laws that allow nature to discover new molecules and mechanisms in a
   fraction of the time that random variation would take. ..."
   Auth: AW@[<A HREF="http://www.ieu.uzh.ch/wagner/">U.Zurich</A>]['14].
   (Also see, Andreas Wagner and William Rosen,
      'Spaces of the possible: universal Darwinism and the wall between
      technological and biological innovation,'
      J.R.Soc. Interface, 11, 20131190, 21 May 2014  [127 refs]
      -- [<A HREF="http://dx.doi.org/10.1098/rsif.2013.1190">doi:10.1098/rsif.2013.1190</A>]['14].)

%A D. A. Baum
%A B. Baum
%T An inside-out origin for the eukaryotic cell
%J BMC Biology
%V 12
%P e76
%M OCT
%D 2014
%K jrnl, eJrnl, MolBio, c2014, c201x, c20xx, zz0215, biol, evolution, cell,
   complex, cells, prokaryote, eukaryote, nucleues, bleb, blebs, mitochondria
%X "Drawing on diverse aspects of cell biology & phylogenetic data, we invert
   the trad. interpretation of eukaryotic cell evolution. We propose that an
   ancestral prokaryotic cell, homologous to the modern-day nucleus, extruded
   membrane-bound blebs beyond its cell wall. These blebs functioned to
   facilitate material exchange with ectosymbiotic proto-mitochondria. The
   cytoplasm was then formed through the expansion of blebs around
   proto-mitochondria, with cts spaces between the blebs giving rise to the
   endoplasmic reticulum, which later evolved into the eukaryotic secretory
   system. Further bleb-fusion steps yielded a cts plasma membrane, which
   served to isolate the endoplasmic reticulum from the environment. ...
   consistent with diverse kinds of data & provides an alt. framework by which
   to explore & understand the dynamic organization of modern eukaryotic cells.
   It also helps to explain a # of prev. enigmatic features of cell biology,
   inc. the autonomy of nuclei in syncytia & the subcellular localization of
   protein N-glycosylation, & makes many predictions, including a novel
   mechanism of interphase nuclear pore insertion."
   -- [<A HREF="http://dx.doi.org/10.1186/s12915-014-0076-2">doi:10.1186/s12915-014-0076-2</A>]['15].

%A K. M. Steinberg
%A et al ...
%A R. K. Wilson
%T Single haplotype assembly of the human genome from a hydatidiform mole
%J Genome Res.
%V ?
%M NOV
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz1114, human genome, nGenome, reference,
   complete, sequence, DNA, quality, gaps, GRCh37, CHM1,
   Genome Reference Consortium
%X "... While the current human reference genome sequence is of very high
   quality, gaps & misassemblies remain due to biological & technical
   complexities. Large repetitive sequences & complex allelic diversity are
   the two main drivers of assembly error. ... several resources from this DNA
   including a set of end-sequenced & indexed BAC clones & 100 x Illumina
   whole-genome shotgun (WGS) sequence coverage.  ... to generate a draft
   assembly, CHM1_1.1 (NCBI AssemblyDB GCA_000306695.2). ..."  [online 11/2014.]
   -- [<A HREF="http://dx.doi.org/10.1101/gr.180893.114">doi:10.1101/gr.180893.114</A>]['14].
   (Also see comment@[<A HREF="http://dx.doi.org/10.1038/515323a">www</A>]['14].)

%A Y. Je
%A E. Giovannucci
%T Coffee consumption and total mortality: a meta-analysis of twenty
   prospective cohort studies
%J J. Nutrition
%V
%P 1162-1173
%M NOV
%D 2014
%K jrnl, c2014, c201x, c20xx, zz1117, human health, coffee, risk, risks,
   zzCoffee, positive, death, life expectancy
%X "... Pooled relative risks (RR) with 95% CI were calculated using a
   random-effects model. We identified twenty studies of coffee consumption &
   total mortality, including 129,538 cases of deaths among the 973,904
   participants. The RR of total mortality for the high v. low category of
   coffee consumption was 0.86 (95% CI 0.80, 0.92). The pooled RR for studies
   using >= 2-4 cups/d as a cut-off for the high category was similar to that
   for studies using >= 5-9 cups/d as the cut-off. By geographical region, the
   inverse association tended to be stronger for the eight studies conducted
   in Europe (RR 0.78, 95% CI 0.70, 0.88) and three studies carried out in
   Japan (RR 0.82, 95% CI 0.73, 0.92) than for the nine studies conducted in
   the USA (RR 0.92, 95% CI 0.84, 1.00). The inverse assoc. was similar for
   men (RR 0.81, 95% CI 0.73, 0.90) and women (RR 0.84, 95% CI 0.79, 0.89).
   A weak, but significant, inverse association was found with moderate
   coffee consumption (1-2 cups/d; RR 0.92, 95% CI 0.87, 0.98). High
   decaffeinated coffee consumption was also found to be associated with a
   lower risk of death, but the data are limited. Our findings indicate that
   coffee consumption is associated with a reduced risk of total mortality."
   -- 24279995@[<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/24279995">pubm'd</A>]['17].
   [Also search for: zzCoffee].
   (Also see abc[<A HREF="http://www.abc.net.au/news/2017-11-21/coffee-does-it-reduce-heart-attack-risk-the-conversation/9175064">21/11/</A>]['17].)

%A J. C. Horvath
%A J. D. Forte
%A O. Carter
%T Evidence that transcranial direct current stimulation (tDCS) generates
   little-to-no reliable neurophysiologic effect beyond MEP amplitude modulation
   in healthy human subjects: A systematic review
%J Neuropsychologia
%V 66
%P 213-236
%M JAN
%D 2015
%K jrnl, c2015, c201x, c20xx, zz1214, brain, psychology, mental, controversial,
   transcranial direct current stimulation, tDCS, electrical, magnetic, TMS, MEP
%X "... Of the 30 neurophysiological outcome measures reported by at least two
   different research groups, tDCS was found to have a reliable effect on only
   one: MEP amplitude. Interestingly, the magnitude of this effect has been
   sig. decreasing over the last 14 years. ..." [proofs online Nov 2014]
   -- [<A HREF="http://dx.doi.org/10.1016/j.neuropsychologia.2014.11.021">doi:10.1016/j.neuropsychologia.2014.11.021</A>]['14] (online 11/'14).
   (Also see tDCS@[<A HREF="https://en.wikipedia.org/wiki/Transcranial_direct-current_stimulation">wikip</A>]['16].)
   [Also search for: transcranial stimulation].

%A H. J. Gierman
%A et al ...
%A S. K. Kim
%T Whole-genome sequencing of the world's oldest people
%J PLoS One
%V 9
%N 11
%P e112430
%M NOV
%D 2014
%K jrnl, eJrnl, MolBio, c2014, c201x, c20xx, zz1114, genome, human, age, aging,
   ageing, aged, longevity, lifespan, old, oldest, centarian, supercentarian,
   genetics, genes, TSHZ3, DSC2
%X "Supercentenarians (110 y.+) are the world's oldest people. Seventy four are
   alive worldwide, with twenty two in the US. We performed whole-g. seq. on
   17 supercentenarians to explore the genetic basis underlying extreme human
   longevity. We found no sig. evidence of enrichment for a single rare protein-
   -altering variant or for a gene harboring different rare protein altering
   variants in SC [v.] control genomes. We followed up on the gene most enriched
   for rare protein-altering variants in our cohort of SCs, TSHZ3, by seq. it in
   a second cohort of 99 long-lived individuals but did not find a sig.
   enrichment. The genome of one SC had a pathogenic mutation in DSC2, known to
   predispose to arrhythmogenic right ventricular cardiomyopathy, which is
   recommended to be reported to this individual as an incidental finding
   according to a recent posn statement by the American College of Med. Genetics
   & Genomics. Even with this pathogenic mutation, the proband lived to over
   110y. The entire list of rare protein-altering variants & DNA seq. of all 17
   supercentenarian genomes is available as a resource to assist the discovery
   of the genetic basis of extreme longevity in future studies."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0112430">doi:10.1371/journal.pone.0112430</A>]['14].
   (So, nothing obvious.)

%A B. Misof
%A et al ...
%A X. Zhou
%T Phylogenomics resolves the timing and pattern of insect evolution
%J Science
%V 346
%N 6210
%P 763-767
%M NOV
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0815, phylogenetic, tree, trees,
   controversial, evolution, evolutionary, animals, animal, insects, insect,
   holometabolous
%X "... inferred the phylogeny of insects from 1478 protein-coding genes.
   Phylogenomic analyses of nucleotide & AA seqs., with site-specific nucleotide
   or domain-specific AA substn models, produced stat. robust & congruent
   results resolving previously controversial phylogenetic relns. We dated the
   origin of insects to the Early Ordovician [~479 million years ago (Ma)], of
   insect flight to the Early Devonian (~406 Ma), of major extant lineages to
   the Mississippian (~345 Ma), & the major diversification of holometabolous
   insects to the Early Cretaceous. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1257570">doi:10.1126/science.1257570</A>]['15].
   (* But also see Comment by Tong et al, 2015
    -- [<A HREF="http://dx.doi.org/10.1126/science.aaa5460">doi:10.1126/science.aaa5460</A>]['15]. *)

%A K. Aoshima
%A et al ...
%A Y. Oda
%T A simple peak detection and label-free quantitation algorithm for
   chromatography-mass spectrometry
%J BMC Bioinformatics
%V 15
%P 376
%M NOV
%D 2014
%K jrnl, c2014, c201x, c20xx, zz1214, peak, peaks, picking, find, finding,
   histogram, AB3D, MZmine, MSight, SuperHirn, OpenMS
%X "...  there are still issues to be improved for recent label-free methods,
   such as how to reduce false +ve/-ves of the candidate peaks, how to expand
   scalability & how to enhance & automate data processing. AB3D (A simple
   label-free quantitation alg. for Biomarker Discovery in Diagnostics & Drug
   discovery using LC-MS) has addressed these issues & has the capability to
   perform label-free quantitation using MS1 for proteomics study. ...
   Comparisons were then carried out between widely used s/w tools such as
   MZmine, MSight, SuperHirn, OpenMS & our algorithm AB3D, using the same
   LC-MS datasets. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/s12859-014-0376-0">doi:10.1186/s12859-014-0376-0</A>]['14].
   [Also search for: peak finding].

%A F. V. Martinez
%A P. Feijao
%A M. D. V. Braga
%A J. Stoye
%T On the family-free DCJ distance
%J Algorithms in Bioinformatics
%I SpringerVerlag
%S LNCS
%V 8701
%D 2014
%P pp 174-186
%K MolBio, c2014, c201x, c20xx, zz0415, distance, genome, chromosome,
   similarity, double cut and join, DCJ, genes, genomic distance, rearrangement
%X "... Rearrangement ops., such as the so called double-cut-and-join (DCJ) ...
   In a family-based setting, genes are grouped into gene families & efficient
   algs. were already proposed to compute the DCJ dist. between two given
   genomes. ... we propose the problem of computing the DCJ dist. of two given
   genomes without prior gene family assignment, directly using the pairwise
   similarity between genes. ... new family-free DCJ dist., prove that the
   family-free DCJ dist. problem is APX-hard, & provide an integer linear
   program to its soln."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-662-44753-6_14">doi:10.1007/978-3-662-44753-6_14</A>]['15].
   [Also search for: MolBio genomic distance].

%A R. Payne
%A et al ...
%A P. J. R. Goulder
%T Impact of HLA-driven HIV adaptation on virulence in populations of high
   HIV seroprevalence
%J PNAS
%V ?
%P ?-?
%M DEC
%D 2014
%K jrnl, PNAS, MolBio, c2014, c201x, c20xx, zz1214, AIDS, HIV, virus, viral,
    HLA, host, adaption, evolution
%X "... investigate the impact on HIV virulence of HIV adaptation to HLA
   molecules that protect against disease progression, such as HLA-B*57 &
   HLA-B*58:01. We analyzed cohorts in Botswana & S.Africa, two countries
   severely affected by the HIV epidemic. In B., where the epidemic started
   earlier & adult seroprevalence has been higher, HIV adaptation to HLA inc.
   HLA-B*57/58:01 is greater compared with S.A. (P=7*10^-82), the protective
   effect of HLA-B*57/58:01 is absent (P=0.0002), & popn viral replicative
   capacity is lower (P=0.03). ... suggest that viral evoln is occurring
   relatively rapidly, & that adaptn of HIV to the most protective HLA alleles
   may contribute to a lowering of viral replication capacity at the popn level,
   & a consequent redn in HIV virulence over time. ..."  [online Dec 2014.]
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1413339111">doi:10.1073/pnas.1413339111</A>]['14].

%A A. I. Taylor
%A et al ...
%A P. Holliger
%T Catalysts from synthetic genetic polymers
%J Nature
%V ?
%P ?-?
%M DEC
%D 2014
%K jrnl, MolBio, c2014, c201x, c200x, zz1214, XNA, XNAs, RNA, polymer, enzyme,
   catalyst, XNAzymes, FANA, HNA, CeNA, metalloenzyme, FANAzyme, synthetic,
   artificial, life, origins
%X "... The ability of synthetic genetic polymers (XNAs) with alt. backbone
   chemistries not found in nature to fold into defined structs. & bind ligands
   raises the possibility that these too might be capable of forming catalysts
   (XNAzymes). ... report the discovery of such XNAzymes, elaborated in four
   different chemistries (arabino nucleic acids, ANA; 2'-fluoroarabino nucleic
   acids, FANA; hexitol nucleic acids, HNA; & cyclohexene nucleic acids, CeNA)
   directly from random XNA oligomer pools, exhibiting in trans RNA endonuclease
   & ligase activities. [&] an XNA-XNA ligase metalloenzyme in the FANA f/work,
   establishing catalysis in an entirely synthetic sys. & enabling the synthesis
   of FANA oligomers & an active RNA endonuclease FANAzyme from its constituent
   parts. These results extend catalysis beyond biopolymers & establish
   technologies for the discovery of catalysts in a wide range of polymer
   scaffolds not found in nature. ..."  [online 1/12/2014.]
   -- [<A HREF="http://dx.doi.org/10.1038/nature13982">doi:10.1038/nature13982</A>]['14].
   [Also search for: XNA MolBio].

%A J. C. A. Joordens
%A et al ...
%A W. Roebroeks
%T Homo erectus at Trinil on Java used shells for tool production and engraving
%J Nature
%V ?
%P ?-?
%M DEC
%D 2014
%K jrnl, c2014, c201x, c20xx, zz1214, ancient art, shell, cave, Homo erectus,
   human, hominin, hominims, evolution,
   Asia, Java, Indonesia, Trinil, Dubois, Hauptknochenschicht
%X "... report on a fossil freshwater shell assemblage from the
   Hauptknochenschicht (main bone layer) of Trinil (Java, Indonesia), the type
   locality of Homo erectus discovered by E.Dubois in 1891 (refs 2, 3). In the
   Dubois collection (in the Naturalis museum, Leiden, The Netherlands) we found
   evidence for freshwater shellfish consumption by hominins, one unambiguous
   shell tool, & a shell with a geometric engraving. We dated sediment contained
   in the shells with 40Ar/39Ar & luminescence dating methods, obtaining a
   max.age of 0.54+/-0.10 million years & a min.age of 0.43+/-0.05 m.years.
   This implies that the Trinil Hauptknochenschicht is younger than previously
   estimated. Together, our data indicate that the engraving was made by Homo
   erectus, & that it is considerably older than the oldest geometric engravings
   described so far ..."  [online 3/12/2014.]
   -- [<A HREF="http://dx.doi.org/10.1038/nature13962">doi:10.1038/nature13962</A>]['14].

%A T. Gagie
%A S. J. Puglisi
%T Searching and indexing genomic databases via kernelization
%J arXiv
%M DEC
%D 2014
%K arXiv, TR, MolBio, c2014, c201x, c20xx, zz1214, DNA, search, database,
   compressed, LZ, reference
%X "... Several authors have recently suggested searching or indexing only one
   ref. genome & the parts of the other genomes where they differ. ... we survey
   the twenty-year history of this idea & discuss its relation to kernelization
   in parameterized complexity."   [via TS.]
   -- 1412.1591@[<A HREF="http://arxiv.org/abs/1412.1591">arXiv</A>]['14].

%A E. D. Jarvis
%A et al ...
%A G. Zhang
%T Whole-genome analyses resolve early branches in the tree of life of modern
   birds
%J Science
%V 346
%N 6215
%P 1320-1331
%M DEC
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz1214, evolutionary, phylogenetic, tree,
   bird, birds, Passerea, Columbea, landbird, avian, evolution,
   Cretaceous, Paleogene
%X "...  genome-scale phylogenetic analysis of 48 species representing all
   orders of Neoaves using phylogenomic methods created to handle genome-scale
   data. We recovered a highly resolved tree that confirms prev. controversial
   sister or close relationships. We identified the first divergence in Neoaves,
   two groups we named Passerea & Columbea, representing indep. lineages of
   diverse & convergently evolved land & water bird species. Among Passerea, we
   infer the common ancestor of core landbirds to have been an apex predator &
   confirm indep. gains of vocal learning. Among Columbea, we identify pigeons &
   flamingoes as belonging to sister clades. Even with whole genomes, some of
   the earliest branches in Neoaves proved challenging to resolve, which was
   best explained by massive protein-coding seq. convergence & high levels of
   incomplete lineage sorting that occurred during a rapid radiation after the
   Cretaceous-Paleogene mass extinction event about 66 million years ago. "
   -- [<A HREF="http://dx.doi.org/10.1126/science.1253451">doi:10.1126/science.1253451</A>]['14].
   [Also search for: birds MolBio]  and  [also search for: MolBio tree life].

%A M. Yano
%A H. Mori
%A Y. Akiyama
%A T. Yamada
%A K. Kurokawa
%T CLAST: CUDA implemented large-scale alignment search tool
%J BMC Bioinformatics
%V 15
%P e406
%M DEC
%D 2014
%K jrnl, eJrnl, MolBio, c2014, c201x, c20xx, zz1214, CLAST, CUDA, metagenomics,
   GPU
%X "Background Metagenomics is a powerful methodology to study microbial
   communities, but it is highly dependent on nucleotide seq. similarity
   searching against seq. DBs. ... developed a tool, which we named CLAST (CUDA
   implemented large-scale alignment search tool), that enables analyses of
   millions of reads & thousands of ref. genome seqs., & runs on NVIDIA Fermi
   architecture graphics processing units. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/s12859-014-0406-y">doi:10.1186/s12859-014-0406-y</A>]['14].

%A C. Tomasetti
%A B. Vogelstein
%T Variation in cancer risk among tissues can be explained by the number of
   stem cell divisions
%J Science
%V 347
%N 6217
%P 78-81
%M JAN
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz0115, human health, cancer, risk, risks,
   tissue type, DNA, mutation
%X "Some tissue types give rise to human cancers millions of times more often
   than other tissue types. Although this has been recognized for more than a
   century, it has never been explained. Here, we show that the lifetime risk of
   cancers of many different types is strongly correlated (0.81) with the total
   # of divisions of the normal self-renewing cells maintaining that tissue's
   homeostasis. These results suggest that only a third of the variation in
   cancer risk among tissues is attributable to environmental factors or
   inherited predispositions. The majority is due to 'bad luck,' that is, random
   mutations arising during DNA replication in normal, noncancerous stem cells.
   This is important not only for understanding the disease but also for
   designing strategies to limit the mortality it causes."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1260825">doi:10.1126/science.1260825</A>]['15].
   (Also see: "... bad luck explained two-thirds of the *variation*
               in cancer rates in different tissues ..."
    -- [<A HREF="[<A HREF="http://dx.doi.org/10.1126/science.347.6219.224">discussion</A>]['15].)

%A H. Y. Xiong
%A et al ...
%A B. J. Frey
%T The human splicing code reveals new insights into the genetic determinants of
   disease
%J Science
%V 347
%N 6218
%M JAN
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0115, gene, genes, splice, mutation,
   DNA, RNA, splicing, mRNA, human, health, disease, autism
%X "... Analysis of more than 650,000 intronic & exonic variants revealed
   widespread patterns of mutation-driven aberrant splicing. Intronic disease
   mutations that are > 30 n. from any splice site alter splicing nine times as
   often as common variants, & missense exonic disease mutations that
   have the least impact on protein function are five times as likely as others
   to alter splicing. We detected tens of thousands of disease-causing mutations
   including those involved in cancers & spinal muscular atrophy. Examination of
   intronic & exonic variants found using whole-genome seq. of individuals with
   autism revealed misspliced genes with neurodevelopmental phenotypes. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1254806">doi:10.1126/science.1254806</A>]['15].

%A I. Sillitoe
%A et al ...
%A C. A. Orengo
%T CATH: comprehensive structural and functional annotations for
   genome sequences
%J NAR
%M JAN
%D 2015
%K jrnl, NAR, MolBio, c2015, c201x, c20xx, zz0717, CATH, protein, structure, 3D,
   domain, domains, CATH40
%X "The latest version of the CATH-Gene3D protein structure classification
   database (4.0, [<A HREF="http://www.cathdb.info">www</A>]) provides
   annotations for over 235,000 protein domain structs. & inc. 25 million domain
   predictions. This article provides an update on the major developments in the
   2 years since the last publn in this j. including: sig. improvements to the
   predictive power of our functional families (FunFams); the release of our
   'current' putative domain assignments (CATH-B); a new, strictly non-redundant
   data set of CATH domains suitable for homology benchmarking experiments
   (CATH-40) and a number of improvements to the web pages."
   -- [<A HREF="http://dx.doi.org/10.1093/nar/gku947">doi:10.1093/nar/gku947</A>]['17].

%T Integrative analysis of 111 reference human epigenomes
%Q Roadmap Epigenomics Consortium
%A A. Kundaje
%A et al
%J Nature
%V 518
%N 7539
%P 317-330
%M FEB
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0215, epigenetics, DNA, human,
   epigenome, epigenomics, chromatin, methylation, health, disease,
   gene expression, regulation, regulatory networks, ChromHMM
%X "... generated the largest collection so far of h. epigenomes for primary
   cells & tissues. Here we describe the integrative analysis of 111 ref. h.
   epigenomes generated as part of the programme, profiled for histone
   modification patterns, DNA accessibility, DNA methylation & RNA expression.
   We establish global maps of regulatory elts, define regulatory modules of
   coordinated activity, & their likely activators & repressors. We show that
   disease- & trait-assoc. genetic variants are enriched in tissue-specific
   epigenomic marks, revealing biologically relevant cell types for diverse
   human traits, & providing a resource for interpreting the molecular basis of
   human disease. Our results demonstrate the central role of epigenomic
   information for understanding gene regulation, cellular differentiation &
   human disease."
   -- [<A HREF="http://dx.doi.org/10.1038/nature14248">doi:10.1038/nature14248</A>]['15].
   (Article is part of a special issue on epigenomics
    [<A HREF="http://dx.doi.org/10.1038/518314a">10.1038/518314a</A>].)

%A M. Balter
%A A. Gibbons
%T Indo-European languages tied to herders
%J Science
%V 347
%N 6224
%P 814-815
%M FEB
%D 2015
%K news, views, MolBio, c2015, c201x, c20xx, zz0215, ancient DNA, human,
   evolution, phylogenetic, tree, tree, trees, language, bioRxiv, herder,
   proto, Yamnaya
%X "... A new study uses ancient DNA to suggest that a massive migration of
   herders from the east shaped the genomes of most living Europeans - and that
   these immigrants may have been the source of Proto-Indo-European (PIE), the
   mysterious ancestral tongue from which the more than 400 Indo-European
   languages sprang. Based on DNA gathered from dozens of ancient skeletons, the
   study, described last week in a preprint posted on the bioRxiv server ... One
   surprise is that a migration of herders from the steppes of today's Russia &
   Ukraine about 4500 years ago significantly shifted the genetic makeup of
   today's Europeans. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.347.6224.814">doi:10.1126/science.347.6224.814</A>]['15],
   or [<A HREF="http://www.sciencemag.org/content/347/6224/814.summary">p.814</A>]['15].
   [Also search for: ancient human DNA].

%A E. T. Cirulli
%A et al ...
%A D. B. Goldstein
%T Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and
   pathways
%J Science
%V 347
%N 1436
%P 1436-1441
%M MAR
%D 2015
%K MolBio, jrnl, c2015, c201x, c20xx, zz0315, amyotrophic lateral sclerosis,
   human health, disease, gene, genes, ALS, TBK1, OPTN, p62, SQSTM1
%X "Amyotrophic lateral sclerosis (ALS) is a devastating neurological disease
   with no effective treatment. We report the results of a moderate-scale
   sequencing study aimed at increasing the # of genes known to contribute to
   predisposition for ALS. ... whole-exome sequencing of 2869 ALS patients &
   6405 controls. Several known ALS genes were found to be assoc., & TBK1 (the
   gene encoding TANK-binding kinase 1) was identified as an ALS gene. TBK1 is
   known to bind to & phosphorylate a number of proteins involved in innate
   immunity & autophagy, inc. optineurin (OPTN) & p62 (SQSTM1/sequestosome),
   both of which have also been implicated in ALS. These observations reveal a
   key role of the autophagic pathway in ALS & suggest specific targets for
   therapeutic intervention."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaa3650">doi:10.1126/science.aaa3650</A>]['15].

%A S. Hecht Orzack
%A J. W. Stubblefield
%A V. R. Akmaev
%A P. Colls
%A S. Munne
%A T. Scholl
%A D. Steinsaltz
%A J. E. Zuckerman
%T The human sex ratio from conception to birth
%J PNAS
%V ?
%P ?
%M MAR
%D 2015
%K jrnl, PNAS, c2015, c201x, c20xx, zz0415, biology, biol, human, sex ratio,
   male, female, embryo, fetus, foetus, fetal, foetal, mortality, numbers
%X "We describe the trajectory of the human sex ratio from conception to birth
   by analyzing data from (i) 3- to 6-d-old embryos, (ii) induced abortions,
   (iii) chorionic villus sampling, (iv) amniocentesis, & (v) fetal deaths &
   live births. ... Our est. of the sex ratio at conception is 0.5 (proportion
   male), which contradicts the common claim that the sex ratio at conception is
   male-biased. The sex ratio among abnormal embryos is male-biased, & the sex
   ratio among normal embryos is female-biased. These biases are assoc. with the
   abnormal/normal state of the sex chrs & of chrs 15 & 17. The sex ratio may
   decrease in the first week or so after conception (due to excess male
   mortality); it then increases for at least 10-15 wk (due to excess female
   mortality), levels off after ~20 wk, & declines slowly from 28 to 35 wk (due
   to excess male mortality). Total female mortality during pregnancy exceeds
   total male mortality. ..."  [online 30/3/'15.]
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1416546112">doi:10.1073/pnas.1416546112</A>]['15].
   (Also see The G. [<A HREF="http://www.theguardian.com/science/2015/mar/30/female-embryos-more-likely-to-die-in-pregnancy-than-males-study-claims">30/3/'15</A>].)
   [Also search for: sex ratio biology].

%A S. Khuri
%A S. Wuchty
%T Essentiality and centrality in protein interaction networks revisited
%J BMC Bioinformatics
%V 16
%P e109
%M APR
%D 2015
%K jrnl, eJrnl, MolBio, c2015, c201x, c20xx, zz0415, interaction, network,
   protein, PPI, MDSet, essential, eMDset
%X "Background minimum dominating sets (MDSet) [[an NPC problem]] of protein
   interaction n/wks allow the control of underlying protein interaction n/wk
   through their topological placement. While essential proteins are enriched
   in MDSets, we hypothesize that the stat. properties of biol. fns of essential
   genes are enhanced when we focus on essential MDSet proteins (e-MDSet). ...
   networks of E.coli, S.cerevisiae & H.sapiens, defined as subsets of proteins
   whereby each remaining p. can be reached by a single interaction. ...
   observed that their topological placement allowed e-MDSet proteins to provide
   a +ve correlation between degree & lethality, connect more protein complexes,
   & have a stronger impact on n/wk resilience than essential proteins alone.
   [and] found that interactions between e-MDSet ps. appeared more frequently
   within complexes, while interactions of e-MDSet ps between complexes were
   depleted. Finally, these e-MDSet proteins classified into functional
   groupings that play a central role in survival & adaptability. ... we surmise
   that e-MDSets may provide a new method of eval. the core ps of an organism."
   -- [<A HREF="http://dx.doi.org/10.1186/s12859-015-0536-x">doi:10.1186/s12859-015-0536-x</A>]['15].
   [Also search for: protein interaction network].

%A P. Thomas
%A et al ...
%A U. Leser
%T Computer-assisted curation of a human regulatory core network from the
   biological literature
%J J. Bioinformatics
%V 31
%N 8
%P 1258-1266
%K APR
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0515, human, regulatory network,
   transcription factors, text mining
%X "... developed a text-mining-assisted workflow to systematically extract
   knowledge about regulatory interactions between human TFs from the biol.
   literature. We applied this workflow to the entire Medline ... The top-2500
   sentences contained ~900 sentences that encompass relations already known in
   databases. By manually curating the remaining 1625 top-ranking sentences, we
   obtained more than 300 validated regulatory relationships that were not
   present in a regulatory DB ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btu795">doi:10.1093/bioinformatics/btu795</A>]['15].

%A E. Palkopoulou
%A et al ...
%A L. Dalen
%T Complete genomes reveal signatures of demographic and genetic declines in the
   Woolly Mammoth
%J Current Biol.
%V ?
%P ?-?
%M APR
%D 2015
%K MolBio, c2015, c201x, c20xx, zz0515, woolly mammoth, wooly, mamoth,
   Mammuthus primigenius, genome, nGenome, inbreeding, extinction,
   decline, ancient, DNA
%X "... present high-quality complete genome seqs. from two woolly mammoths
   (Mammuthus primigenius). The 1st m. was sequenced at 17.1-fold coverage &
   dates to ~4,300 y. before present, representing one of the last surviving
   individuals on Wrangel Island. The 2nd m., seq. at 11.2-x cvg., was obtained
   from an ~44,800-y.-o. specimen from the Late Pleistocene popn in NE Siberia.
   ... reveal a popn bottleneck during the Middle or Early Pleistocene, & a more
   recent severe decline in the ancestors of the Wrangel m. at the end of the
   last glaciation. A comparison of the two genomes shows that the Wrangel m.
   has a 20% redn in heterozygosity as well as a 28-x increase in the fraction
   of the genome that comprises runs of homozygosity. We conclude that the
   popn on Wrangel Is., which was the last surviving WM popn, was subject to
   reduced genetic diversity shortly before it became extinct."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cub.2015.04.007">doi:10.1016/j.cub.2015.04.007</A>]['15].
   [Also search for: MolBio ancient DNA].

%A K. Achim
%A et al ...
%A J. C. Marioni
%T High-throughput spatial mapping of single-cell RNA-seq data to tissue of
   origin
%J Nat. Biotechnol.
%V 33
%N 5
%P 503-509
%M MAY
%D 2015
%K jrnl, eJrnl, MolBio, c2015, c201x, c20xx, zz0720, scRNAseq, scRNA-seq, RNA,
   mRNA, cell expression profile, tissue
%X "... cell type identity ... we present a high-throughput method to identify
   the spatial origin of cells assayed by single-cell RNA-sequencing within a
   tissue of interest. ... mRNA profiles ..."
   -- [<A HREF="https://doi.org/10.1038/nbt.3209">doi:10.1038/nbt.3209</A>]['20].
   [Also search for: scRNAseq].

%A A. J. Lumley
%A et al ...
%A M. J. G. Gage
%T Sexual selection protects against extinction
%J Nature
%V 522
%N 7557
%P 470-473
%M JUN
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0515, biology, origins, sex, costs, evolution,
   mutation, inbred, inbreeding, mate selection, competition, genetic capture,
   male, female, sexual reproduction, flour beetle, Tribolium castaneum
%X "Reproduction through sex carries substantial costs, mainly because only half
   of sexual adults produce offspring. It has been theorized that these costs
   could be countered if sex allows sexual seln to clear the universal fitness
   constraint of mutation load. Under sexual seln, competition between (usually)
   males & mate choice by (usually) females create important intraspecific
   filters for reproductive success, so that only a subset of males gains
   paternity. If reproductive success under sexual seln is dependent on
   individual condn, which is contingent to mutn load, then sexually sel.
   filtering through 'genic capture' could offset the costs of sex because it
   provides genetic benefits to popns. Here we test this theory experimentally
   by comparing whether popns with histories of strong v. weak sexual seln purge
   mutn load & resist extinction differently. After evolving replicate
   popns of the flour beetle Tribolium castaneum for 6 to 7 years under
   conditions that differed solely in the strengths of sexual seln, we revealed
   mutn load using inbreeding. Lineages from popns that had prev.
   experienced strong sexual seln were resilient to extinction & maintained
   fitness under inbreeding, with some families continuing to survive after 20
   generations of sib x sib mating. [v.] lineages derived from popns that
   experienced weak or non-existent sexual seln showed rapid fitness declines
   under inbreeding, & all were extinct after generation 10. Multiple mutns
   across the genome with individually small effects can be difficult to clear,
   yet sum to a sig. fitness load; our findings reveal that sexual seln reduces
   this load, improving popn viability in the face of genetic stress."
   -- [<A HREF="http://dx.doi.org/10.1038/nature14419">doi:10.1038/nature14419</A>]['15]. (online 18/5/15; auths  UEA.)
   (Also see [<A HREF="http://www.abc.net.au/news/2015-05-19/why-do-men-exist-scientific-study-offers-an-explanation/6480198">abc</A>][18/5/2015].)

%A S. Harmand
%A et al ...
%A H. Roche
%T 3.3-million-year-old stone tools from Lomekwi 3, West Turkana, Kenya
%J Nature
%V 521
%N 7552
%P 310-315
%M MAY
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0515, human, evolution, stone tool, origins,
   knapping, Homo, Pliocene, hominim, fossil, fossils, Oldowan, archaeology
%X "... long supposed that the earliest stone tools were made by the genus Homo
   & that this technological development was directly linked to climate change &
   the spread of savannah grasslands. New fieldwork in West Turkana, Kenya, has
   identified evidence of much earlier hominin technological behaviour. We
   report the discovery of Lomekwi 3, a 3.3-million-year-old archaeological site
   where in situ stone artefacts ... The Lomekwi 3 knappers, with a developing
   understanding of stone's fracture properties, combined core redn with
   battering activities. Given the implications of the L.3 assemblage for models
   aiming to converge environmental change, hominin evoln & techn origins, we
   propose for it the name 'Lomekwian', which predates the Oldowan by 700,000 y.
   & marks a new beginning to the known archaeological record."
   -- [<A HREF="http://dx.doi.org/10.1038/nature14464">doi:10.1038/nature14464</A>]['15].

%A G. Lima-Mendez
%A et al ...
%A J. Raes
%T Determinants of community structure in the global plankton interactome
%J Science
%V 348
%N 6237
%P ?-?
%M MAY
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0515, biology, biological, plankton, ocean,
   interaction network, Tara Oceans project
%X "Species interaction n/wks are shaped by abiotic & biotic factors. ...  we
   studied the photic zone interactome using environmental factors & organismal
   abundance profiles & found that env. factors are incomplete predictors of
   community structure. We found assocns across plankton functional types &
   phylogenetic groups to be nonrandomly distrib. on the n/wk & driven by both
   local & global patterns. We identified interactions among grazers, primary
   producers, viruses, & (mainly parasitic) symbionts & validated n/wk-generated
   hypotheses using microscopy to confirm symbiotic relns. We have thus provided
   a resource to support further research on ocean food webs & integrating
   biological components into ocean models."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1262073">doi:10.1126/science.1262073</A>]['15].

%A W. W. C. Tang
%A et al ...
%A M. A. Surani
%T A unique gene regulatory network resets the human germline epigenome for
   development
%J Cell
%V 161
%N 6
%P 1453-1467
%M JUN
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0615, epigenetics, DNA, methylation,
   germ cells, PGCs, parent, child, epigenetic, influence
%X "The epigenome is extensively reprogrammed in the mammalian germline & in
   preimplantation embryos. E.reprogramming during preimplantation development
   resets the gametic epigenome for naive pluripotency ... whereas reprogramming
   in primordial germ cells (PGCs), which includes erasure of genomic imprints
   & potentially epimutations, restores full germline potency for the
   transmission of genetic & epigenetic info. ... Recent studies on
   preimplantation embryos have provided some insights on this process in
   humans, but our knowledge of the human germline remains imprecise."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cell.2015.04.053">doi:10.1016/j.cell.2015.04.053</A>]['15].

%A S. Malikic
%A A. W. McPherson
%A N. Donmez
%A C. S. Sahinalp
%T Clonality inference in multiple tumor samples using phylogeny
%J J. Bioinformatics
%V 31
%N 9
%P 1349-1356
%M MAY
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0615, tumor, tumour, cancer,
   phylogenetic, clonal, tree, trees, CITUP
%X "... in silico determination of the clonal subpopns remains a challenge. We
   address this [by] a novel combinatorial method, named clonality inference in
   tumors using phylogeny (CITUP), that infers clonal popns & their freqs. while
   satisfying phylog. constraints & [can] exploit data from multiple samples.
   Using simulated datasets & deep seq. data from two cancer studies, we show
   that CITUP predicts clonal freqs. & the underlying phylogeny with high
   accuracy."  [auths@SimonFraser. via RH.]
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btv003">doi:10.1093/bioinformatics/btv003</A>]['15],
      25568283@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/25568283?dopt=Abstract">pubm'd</A>]['15].
   (Also see citup@[<A HREF="http://sourceforge.net/projects/citup/">srcf'rge</A>]['15].)
   [Also search for: MolBio cancer clonal].

%A F. Jeanquartier
%A C. Jean-Quartier
%A A. Holzinger
%T Integrated web visualizations for protein-protein interaction databases
%J BMC Bioinformatics
%V 16
%M JUN
%D 2015
%K jrnl, eJrnl, MolBio, c2015, c201x, c20xx, zz0615, PPI, protein interaction,
   APID, Biogrid, CPDB, IntAct, I2D, Mentha, HomoMINT, PINV, StringDB, UniHI,
   biological, network, DB, DBMS, database, tools
%X "... selected M=10 out of N=53 resources supporting visualization, & we
   tested against the following set of criteria: interoperability, data
   integration, quantity of possible interactions, data visualization quality &
   data coverage. The study reveals differences in usability, visualization
   features & quality as well as the quantity of interactions. StringDB is the
   recommended first choice. CPDB presents a comprehensive dataset & IntAct lets
   the user change the network layout. A comprehensive comparison table is
   available via web. ..."   [67 refs.]
    * "Interoperatibility ... Summarizes a tool's network export
      options (e.g. textual, graphics, individual format) ..."
    * "Agile Protein Interaction DataAnalyzer (APID), BioGrid, ConsensusPathDB
      (CPDB), IntAct - Molecular Interaction Database, Interologous Interaction
      Database (I2D), Mentha - The Interactome Browser, Molecular INTeraction
      database (MINT), or more specific its separate annotation of human PPIs
      called HomoMINT, Protein Interaction Network Visualizer (PINV), StringDB
      - Search Tool for the Retrieval of Interacting Genes/Proteins, & Unified
      Human Interactome (UniHI)]"
   -- [<A HREF="http://dx.doi.org/10.1186/s12859-015-0615-z">doi:10.1186/s12859-015-0615-z</A>]['15].

%A E. Zorita
%A P. Cusco
%A J. Filion
%T Starcode: sequence clustering based on all-pairs search
%J J. Bioinformatics
%V 31
%N 12
%P 1913-1919
%M JUN
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0615, Starcode, sequence, strings,
   poucet search, trie
%X "... describe an exact alg. to determine which pairs of seqs. lie within a
   given Levenshtein dist.. For error correction or redundancy redn purposes,
   matched pairs are then merged into clusters of similar seqs.. The efficiency
   of starcode is attributable to the poucet search, a novel implementation of
   the Needleman-Wunsch alg. performed on the nodes of a trie. On the task of
   matching random barcodes, starcode outperforms seq. clustering algs. in both
   speed & precision."  [online Jan 2015.]
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btv053">doi:10.1093/bioinformatics/btv053</A>]['15].

%A G. S. Forrester
%A A. Rodriguez
%T Slip of the tongue: Implications for evolution and language development
%J Cognition
%V 141
%P 103-111
%M AUG
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0322, human behaviour, thought, concentration,
   tongue, mouth, handedness, speech, manual
%X "A prevailing theory regarding the evolution of language implicates a
   gestural stage prior to the emergence of speech. In support of a transition
   of human language from a gestural to a vocal system, articulation of the
   hands and the tongue are underpinned by overlapping left hemisphere dominant
   neural regions. Behavioral studies demonstrate that human adults perform
   sympathetic mouth actions in imitative synchrony with manual actions.
   Additionally, right-handedness for precision manual actions in children has
   been correlated with the typical development of language, while a lack of
   hand bias has been associated with psychopathology. ... The rate of tongue
   protrusions was influenced by the motor requirements of the task and tongue
   protrusions were significantly right-biased for only precision manual motor
   action ..."
   -- [<A HREF="https://doi.org/10.1016/j.cognition.2015.04.012">doi:10.1016/j.cognition.2015.04.012</A>]['22].

%A Q. Fu
%A et al ...
%A S. Paabo
%T An early modern human from Romania with a recent Neanderthal ancestor
%J Nature
%V 524
%N 7564
%P 216-219
%M AUG
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0615, human, evolution, ancestor, DNA,
   ancient, homo sapiens, European, Neanderthal
%X "... analyse DNA from a 37,000-42,000-year-old modern human from Pestera cu
   Oase, Romania. ... we use an enrichment strategy to isolate [DNA] sites that
   are informative about its relationship to Neanderthals & present-day humans.
   We find that on the order of 6-9% of the genome of the Oase individual is
   derived from N., more than any other modern human seq. to date. Three
   chromosomal segments of N. ancestry are over 50 centimorgans in size,
   indicating that this individual had a N. ancestor as recently as four to six
   generations back. [But] does not share more alleles with later Europeans than
   with E.Asians, suggesting that the Oase popn did not contribute substantially
   to later humans in Europe."   [online 22/6/15.]
   -- [<A HREF="http://dx.doi.org/10.1038/nature14558">doi:10.1038/nature14558</A>]['15].
   [Also search for: MolBio ancient human DNA].

%A C. W. Carter jr
%A R. Wolfenden
%T tRNA acceptor stem and anticodon bases form independent codes related to
   protein folding
%J PNAS
%V 112
%N 24
%P 7489-7494
%M JUN
%D 2015
%K MolBio, PNAS, jrnl, c2015, c201x, c20xx, zz0715, DNA, RNA world, protein,
   side chains, tRNA, genetic code, evolution, origin, origins, life, LUCA
%X "Aminoacyl-tRNA synthetases recognize tRNA anticodon & 3' acceptor stem
   bases. Synthetase Urzymes acylate cognate tRNAs even without
   anticodon-binding domains, in keeping with the possibility that acceptor stem
   recognition preceded anticodon recognition. Representing tRNA identity elts
   with two bits/base, we show that the anticodon encodes the hydrophobicity of
   each AA side-chain as rep. by its water-to-cyclohexane distn coeff., & this
   relationship holds true over the entire temp. range of liquid water. The
   acceptor stem codes preferentially for the surface area or size of each
   side-chain, as represented by its vapor-to-cyclohexane distn coeff.. These
   orthogonal experimental properties are both nec. to account satisfactorily
   for the exposed surface area of AAs in folded proteins. [&] the acceptor stem
   codes correctly for beta-branched & carboxylic acid side-chains, whereas the
   anticodon codes for a wider range of such properties, but not for size or
   beta-branching. ... suggest that genetic coding of 3D protein structs evolved
   in distinct stages, based initially on the size of the AA & later on its
   compatibility with globular folding in water."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1507569112">doi:10.1073/pnas.1507569112</A>]['15].
   [Also search for: origin genetic code].

%A M. El-Kebir
%A L. Oesper
%A H. Acheson-Field
%A B. J. Raphael
%T Reconstruction of clonal trees and tumor composition from multi-sample
   sequencing data
%J J. Bioinformatics
%V 31
%N 12
%P i62-i170
%M JUN
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0715, AncesTree, clone, clonal tree,
   trees, cancer, variant, variation, mutation, tumor, tumour
%X "... formalize the problem of reconstructing the clonal evolution of a tumor
   using single-nucleotide mutations as the variant allele frequency (VAF)
   factorization problem. We derive a combinatorial characterization of the
   solns to this problem & show that the problem is NP-complete. We derive an
   integer linear programming soln to the VAF factorization problem in the case
   of error-free data & extend this soln to real data with a probabilistic model
   for errors. The resulting AncesTree algorithm ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btv261">doi:10.1093/bioinformatics/btv261</A>]['15]. (auths@brownU.edu.)
   [Also search for: MolBio cancer clonal].

%A Cheng Liang
%A Yue Li
%A Jiawei Luo
%A Zhaolei Zhang
%T A novel motif-discovery algorithm to identify co-regulatory motifs in large
   transcription factor and microRNA co-regulatory networks in human
%J J. Bioinformatics
%V 31
%N 14
%P 2348-2355
%M JUL
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0715, regulatory network, transcription,
   gene, glioblastoma multiforme (GBM), Alzheimer disease (AD), coregulatory,
   ENCODE, data, dataset, motif, pattern, bi-fan, bifan,  TF-miRNA, CoMoFinder
%X "... alg. CoMoFinder to accurately & efficiently identify composite n/wk
   motifs in genome-scale co-regulatory n/wks. We define composite n/wk motifs
   as n/wk patterns involving at least one TF, one miRNA & one target gene that
   are statistically sig. than expected. Using two published disease-related
   co-regulatory n/wks, we show that CoMoFinder outperforms existing methods in
   both accuracy & robustness. We then applied CoMoFinder to human TF-miRNA
   co-regulatory n/wk derived from The Encyclopedia of DNA Elements project &
   identified 44 recurring composite n/wk motifs of size 4. The functional
   analysis revealed that genes involved in the 44 motifs are enriched for
   sig. higher number of biological processes or pathways comparing with
   non-motifs. We further analyzed the identified composite bi-fan motif &
   showed that gene pairs involved in this motif structure tend to physically
   interact & are functionally more similar to each other than expected."
     {"(i) composite subg. enum.; (ii) grouping composite subgs. into
      isomorphic classes & recording their # of occurrences & (iii) generating
      a random network ensemble ... stat. sig. ..."};  {"the size k of the
      composite n/wk motifs in our study is moderate (i.e. 3 & 4), making
      exhaustive enum. feasible"}
     {bifan: v1 -> v3, v1 -> v4, v2 -> v3, & v2 -> v4}
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btv159">doi:10.1093/bioinformatics/btv159</A>]['15].
   [Also search for: MolBio regulatory network].

%A J. Shin
%A et al ...
%A H. Song
%T Single-cell RNA-seq with Waterfall reveals molecular cascades underlying
   adult neurogenesis
%J Cell Stem Cell
%V 17
%N 3
%P 360-372
%M SEP
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0720, Waterfall, single cell RNA seq,
   RNAseq, scRNAseq, expression, trajectory
%X "... single-cell transcriptomes of adult hippocampal quiescent neural stem
   cells (qNSCs) and their immediate progeny. We further developed Waterfall, a
   bioinformatic pipeline ... reconstructed cts developmental trajectory. ..."
   -- [<A HREF="https://doi.org/10.1016/j.stem.2015.07.013">doi:10.1016/j.stem.2015.07.013</A>]['20].
   (Also see RNAseq@[<A HREF="https://en.wikipedia.org/wiki/RNA-Seq">wikip</A>]['20].)
   [Also search for: scRNAseq].

%A U. Schmidt
%T Secret Science: A Century of Poison Warfare and Human Experiments
%I OUP
%P 320
%M SEP
%D 2015
%K book, OUP, c2015, c201x, c20xx, zz0715, biol, biological, chemical, weapons,
   warfare, ethics, Ronald Maddison, CS gas, sarin, Bacillus globigii,
   Porton Down, UK, Australia, Innisfail, Queensland
%X "There have long been allegations that many servicemen had been duped into
   taking part in trials with toxic agents at top-secret Allied research
   facilities. In Britain, a whole army of over 21,000 soldiers had participated
   in secret experiments between 1939 & 1989. ... a comprehensive history of
   chemical & biol. weapons research by former Allied powers ... the cover-up of
   the death of a British serviceman in 1953. ...
   1st ed 2015; hb us$32; uk us isbn:019929979X; uk us isbn13:978-0199299799.

%A E. Benson
%A A. Mohammed
%A J. Gardell
%A S. Masich
%A E. Czeizler
%A P. Orponen
%A B. Hogberg
%T DNA rendering of polyhedral meshes at the nanoscale
%J Nature
%V 523
%P 441-444
%M JUL
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0715, DNA, origami, structure, mesh, shape,
   self assembly, nanostructure, routeing, Eulerian, A-trails, Atrails
%X "... present a general method of folding arbitrary polygonal digital meshes
   in DNA that readily produces structs. that would be very difficult to realize
   using prev. approaches. [It] is highly automated, using a routeing alg. based
   on graph theory & a relaxation simulation that traces scaffold strands
   through the target structs.. [&] unlike conventional origami designs built
   from close-packed helices, our structs. have a more open conformation with
   one helix/edge & are therefore stable under the ionic condns usually used in
   biological assays."
   -- [<A HREF="http://dx.doi.org/10.1038/nature14586">doi:10.1038/nature14586</A>]['15].

%A S. Yang
%A et al ...
%A Dacheng Tian
%T Parent-progeny sequencing indicates higher mutation rates in heterozygotes
%J Nature
%V 523
%P 463-467
%M JUL
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0715, DNA, mutation, rate, rates,
   mutations, heterozygote, homozygote, evolution
%X "... we call mutation events directly using a parent-offspring sequencing
   strategy focusing on Arabidopsis & using rice & honey bee for replication.
   ... show that mutn rates are higher in heterozygotes & in proximity to
   crossover events. A correln between recombination rate & intraspecific
   diversity is in part owing to a higher mutn rate in domains of high
   recombination/diversity. Implicating diversity per se as a cause, we find an
   ~3.5-fold higher mutn rate in heterozygotes than in homozygotes, with mutns
   occurring in closer proximity to heterozygous sites than expected by chance.
   ... If segregating mutns predispose to a higher local mutn rate, clusters of
   genes dominantly under purifying seln (more commonly homozygous) & under
   balancing seln (more commonly heterozygous), might have low & high mutn
   rates, resp.. Our results are consistent with this, there being a ten times
   higher mutn rate in pathogen resistance genes, expected to be under +ve or
   balancing seln. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature14649">doi:10.1038/nature14649</A>]['15].

%A P. Skoglund
%A et al ...
%A D. Reich
%T Genetic evidence for two founding populations of the Americas
%J Nature
%V ?
%P ?-?
%M JUL
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0715, human, origins, ancient DNA,
   Surui, Karitiana, Amazonian, American, Indians, Australian, aborigines,
   New Guinea, Andaman Islands
%X "... analyse genome-wide data to show that some Amazonian Native Americans
   descend partly from a Native American founding popn that carried ancestry
   more closely related to indigenous Australians, New Guineans & Andaman
   Islanders than to any present-day Eurasians or Native Americans. This
   signature is not present to the same extent, or at all, in present-day
   N. & Central Americans or in a ~12,600-year-old Clovis-assoc. genome,
   suggesting a more diverse set of founding popns of the Americas than
   previously accepted."  [Online July 2015.]
   -- [<A HREF="http://dx.doi.org/10.1038/nature14895">doi:10.1038/nature14895</A>]['15].

%A G. De Palma
%A et al ...
%A P. Bercik
%T Microbiota and host determinants of behavioural phenotype in maternally
   separated mice
%J NatureComms
%V 6
%P e7735
%M JUL
%D 2015
%K jrnl, eJrnl, c2015, c201x, c20xx, zz0815, biol, biology, microbiology,
   anxiety, stress, gut, bacteria, brain, behaviour, flora, faecal transplants,
   shy, daring, mice
%X "...  investigate the role of the intestinal microbiota in the development of
   impaired gut fn & altered behaviour later in life. Using germ-free & specific
   pathogen-free mice, we demo. that MS alters the
   hypothalamic-pituitary-adrenal axis & colonic cholinergic neural regulation
   in a microbiota-indep. fashion. However, microbiota is required for the
   induction of anxiety-like behaviour & behavioural despair. Colonization of
   adult germ-free MS & control mice with the same microbiota produces distinct
   microbial profiles, which are assoc. with altered behaviour in MS, but not
   in control mice. ... indicate that MS-induced changes in host physiology lead
   to intestinal dysbiosis, which is a critical determinant of the abnormal
   behaviour that characterizes this model of early-life stress."
   -- [<A HREF="http://dx.doi.org/10.1038/ncomms8735">doi:10.1038/ncomms8735</A>]['15].
   (i.e., stress -> gut bacteria -> behaviour / mental_health --
    Also see abc@[<A HREF="http://www.abc.net.au/science/articles/2015/07/29/4282292.htm">29/7/2015</A>].)

%A N. Kasthuri
%A et al ...
%A J. W. Lichtman
%T Saturated reconstruction of a volume of neocortex
%J Cell
%V 162
%N 3
%P 648-661
%M JUL
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0815, brain, cell, cells, neuron, neurons,
   synapse, synapses, dendrite, axon, glia, mouse, database, connections
%X "... Annotated database of 1,700 synapses from a
    saturated reconstruction of cortex ..."
   "... structure of neural tissue at nanometer resolution and use them to
   generate a saturated reconstruction of a sub-volume of mouse neocortex in
   which all cellular objects (axons, dendrites, and glia) and many sub-cellular
   components (synapses, synaptic vesicles, spines, spine apparati,
   postsynaptic densities, & mitochondria) are rendered and itemized in a
   database. We explore these data to study physical properties of brain
   tissue. ... refute the idea that physical proximity is sufficient to predict
   synaptic connectivity (the so-called Peters' rule). ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cell.2015.06.054">doi:10.1016/j.cell.2015.06.054</A>]['15].
   (Also see news@[<A HREF="http://dx.doi.org/10.1038/nature.2015.18105">www</A>][30/7/2015].)

%A Jun Lv
%A et al ...
%A Zhengming Chen
%T Consumption of spicy foods and total and cause specific mortality: population
   based cohort study
%J BMJ
%V 351
%P ?-?
%M AUG
%D 2015
%K jrnl, BMJ, c2015, c201x, c20xx, zz0815, human, health, medicine, risk, age,
   ageing, longevity, lifespan, old, food, spice, spices, diet, spicy food,
   chilli pepper, capsaicin, antioxidant, anti oxidant, alcohol, zzAlcohol,
   China, stats
%X "... During 3,500,004 person years of follow-up between 2004 & 2013 (median
   7.2 y.), a total of 11,820 men & 8,404 women died. Abs. mortality rates
   according to spicy food consumption categories were 6.1, 4.4, 4.3, & 5.8
   deaths / 1000 person y. for participants who ate spicy foods less than once
   a week, 1 or 2, 3 to 5, & 6 or 7 days a week, respectively. Spicy f. cons'n
   showed highly consistent inverse assoc. with total mortality among both men &
   women after adjustment for other known or potential risk factors. In the
   whole cohort, [v.] with those who ate spicy foods < once a week, the adjusted
   hazard ratios for death were 0.90 (95% CI 0.84-0.96), 0.86 (0.80-0.92),
   & 0.86 (0.82-0.90) for those who ate spicy food 1 or 2, 3 to 5, & 6 or 7 days
   a week, resp.. Compared with those who ate spicy foods < once a week, those
   who consumed spicy foods 6 or 7 days a week showed a 14% relative risk
   reduction in total mortality. The inverse assoc. between spicy f. consumption
   & total mortality was stronger in those who did not consume alcohol than
   those who did (P=0.033 for interaction). Inverse assoc. were also observed
   for deaths due to cancer, ischemic heart diseases, & respiratory d.. ..."
   -- [<A HREF="http://dx.doi.org/10.1136/bmj.h3942">doi:10.1136/bmj.h3942</A>]['15].
   (Also see The G. [<A HREF="http://www.theguardian.com/world/2015/aug/05/frequent-spicy-meals-linked-to-human-longevity">www</A>][15/8/2015].)
   [Also search for: longevity diet].

%A C. Hammond
%T The Basics of Crystallography and Diffraction
%I OUP
%P 537pp
%D 2015
%K book, text, c2015, c201x, c20xx, zz0815, Xray, X-ray, crystallography,
   reciprocal lattice, electron, diffraction, charge, Penrose,
   quasiperiodic, aperiodic
%X "... shows how an understanding of crystal structures, both inorganic &
   organic may be built up from simple ideas of atomic & molecular packing.
   Beginning with (2D) e.g.s of patterns & tilings, the concepts of lattices,
   symmetry pt & space groups are developed. 'Penrose' tilings & quasiperiodic
   structures are also included. The reciprocal lattice & its importance in
   understanding the geometry of light, X-ray & electron diffraction patterns is
   explained in simple terms, leading to Fourier analysis in diffraction,
   c.structure determination, image formation & the diffraction-ltd resolution
   in these techniques. ... The 4th edn has been revised throughout, & includes
   new sections on Fourier analysis, Patterson maps, direct methods, charge
   flipping, group theory in crystallography, & a new chapter on the description
   of physical properties of crystals by tensors ..."
   4th ed 2015; pb us$59.95; uk us isbn:0198738684; uk is isbn13:978-019873868.

%A C. B. Albertin
%A et al ...
%A D. S. Rokhsar
%T The octopus genome and the evolution of cephalopod neural and morphological
   novelties
%J Nature
%V 524
%N 7564
%P 220-224
%M AUG
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0815, Coleoid cephalopod, animal,
   marine invertebrate, bilaterian, Octopus bimaculoides, genome, nGenome,
   evolution, protocadherin, C2H2, neural, nervous system, brain
%X "... sequenced the genome & multiple transcriptomes of the California
   two-spot octopus, Octopus bimaculoides. We found no evidence for hypothesized
   whole-genome dupln in the o. lineage. The core developmental & neuronal gene
   repertoire of the o. is ~ to that found across invertebrate bilaterians,
   except for massive expansions in two gene families prev. thought to be
   uniquely enlarged in vertebrates: the protocadherins, which regulate neuronal
   development, & the C2H2 superfamily of zinc-finger transcription factors.
   Extensive messenger RNA editing generates transcript & protein diversity in
   genes involved in neural excitability, as prev. described, [&] in genes
   participating in a broad range of other cellular fns. We identified hundreds
   of cephalopod-specific genes, many of which showed elevated expression levels
   in such specialized structures as the skin, the suckers & the nervous system.
   ... evidence for large-scale genomic rearrangements that are closely assoc.
   with transposable elt expansions. Our analysis suggests that substantial
   expansion of a handful of gene families, along with extensive remodelling of
   genome linkage & repetitive content, played a critical role in the evoln of
   cephalopod morphological innovations inc. their large & complex nervous sys."
   -- [<A HREF="http://dx.doi.org/10.1038/nature14668">doi:10.1038/nature14668</A>]['15] (open).

%A S. Khor
%T The short-cut network within protein residue networks
%J arXiv
%M AUG
%D 2015
%K TR, MolBio, c2015, c201x, c20xx, zz0815, protein, structure,
   short cut, network, PRN, folding, 2EZN
%X "A protein residue network (PRN) is a network of interacting AAs within a
   protein. We describe characteristics of a sparser, highly central & more
   volatile sub-n/wk of a PRN called the short-cut n/wk (SCN), as a p. folds
   under molecular dynamics (MD) simuln with the goal of understanding how
   ps form navigable small-world n/wks within themselves. The edges of an SCN
   are found via a local greedy search on a PRN. SCNs grow in size &
   transitivity strength as a p. folds, & SCNs from successful MD trajectories
   are better formed in these terms. Findings from an investigation on how to
   model the formation of SCNs using dynamic graph theory, & suggestions to move
   fwd are presented. A SCN is enriched with short-range contacts & its
   formation correlates positively with secondary struct. formation. Thus our
   approach to modeling PRN formation, in essence p. folding from a graph
   theoretic view point, is more in tune with the notion of increasing order to
   a random graph than the other way around, & this increase in order coincides
   with improved navigability of PRNs."
   -- 1508.02798@[<A HREF="http://arxiv.org/abs/1508.02798">arXiv</A>]['15].

%A K. D. Lafferty
%A et al ...
%A A. M. Kuris
%T A general consumer-resource population model
%J Science
%V 349
%N 6250
%P 854-857
%M AUG
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0815, food web, webs, model, predator, prey,
   parasite, host, micropredator, food
%X "Food-web dynamics arise from predator-prey, parasite-host, & herbivore-plant
   interactions. Models for such interactions include up to three consumer
   activity states (questing, attacking, consuming) & up to four resource
   response states (susceptible, exposed, ingested, resistant). Articulating
   these states into a general model allows for dissecting, comparing, &
   deriving consumer-resource models. We specify this general model for 11
   generic consumer strategies that group mathematically into predators,
   parasites, & micropredators & then derive conditions for consumer success,
   including a universal saturating functional response. We further show how to
   use this framework to create simple models with a common math. lineage &
   transparent assumptions. Underlying assumptions, missing elts, & composite
   params. are revealed when classic consumer-resource models are derived from
   the general model."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaa6224">doi:10.1126/science.aaa6224</A>]['15].

%A S. Leivers
%A L. W. Simmons
%A G. Rhodes
%T Men's sexual faithfulness judgments may contain a kernel of truth
%J PLoS One
%V 10
%N 8
%P e0134007
%M AUG
%D 2015
%K jrnl, eJrnl, c2015, c201x, c20xx, zz0915, human behaviour, men, women, sex,
   faithful, fidelity, man, woman, judgement, picture, photograph, face,
   appearance
%X "...  extra-pair copulations (EPCs) ...  men were asked to select the more
   faithful of two women &/or ii) providing men with full person images. In
   Experiment 1, men rated 34 women, for whom we had self-reported EPC behavior,
   on faithfulness, trustworthiness or attractiveness from either face or full
   person photographs. They then completed a forced choice task, selecting the
   more faithful of two woman from 17 pairs of images, each containing one woman
   who had reported no EPCs & one who had reported two or more EPCs. Men were
   unable to rate faithfulness with any accuracy, replicating previous findings.
   However, when asked to choose the more faithful of two women, they performed
   significantly above chance, although the ability to judge faithfulness at
   above-chance levels did not generalize to all pairs of women ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0134007">doi:10.1371/journal.pone.0134007</A>]['15].
   (NB. "Previously, accuracy in faithfulness judgments has only been found for
         women judging men's faces [11].)

%A I. A. Hatton
%A et al ...
%A M. Loreau
%T The predator-prey power law: Biomass scaling across terrestrial and aquatic
   biomes
%J Science
%V 349
%N 6252
%P ?-?
%M SEP
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0915, ecology, biomass, predator, prey, food web
%X "... assembled a global data set for 2260 communities of large mammals,
   invertebrates, plants, & plankton. We find that predator & prey biomass
   follow a general scaling law with exponents consistently near 3/4. ...
   implies that the structure of the biomass pyramid becomes increasingly
   bottom-heavy at higher biomass. Similar exponents are obtained for community
   production-biomass relations, suggesting conserved links between ecosystem
   structure & fn. These exponents are similar to many body mass allometries, &
   yet ecosystem scaling emerges indep. from individual-level scaling, which is
   not fully understood. ... suggest a greater degree of ecosystem-level
   organization than prev. recognized & a more predictive approach to e.theory."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aac6284">doi:10.1126/science.aac6284</A>]['15].

%A S. S. Hall
%T A trial for the ages
%J Science
%V 349
%N 6254
%P 1274-1278
%M SEP
%D 2015
%K news, Barzilai, c2015, c201x, c20xx, zz0915, human, health, aging, ageing,
   mortality, metformin, drug trial, FDA
%X 'Scientists are seeking the [FDA]'s blessing for an unprecedented clinical
   trial - the first test of a drug to specifically target the process of human
   aging. In some 3000 elderly people ... plan to conduct a trial in which half
   the subjects would get a placebo & half would get an old (indeed, ancient)
   drug for type 2 diabetes called metformin, which has been shown to modify
   aging in some animal studies. Because there is still no accepted biomarker
   for aging, the drug's success would be judged by whether it can delay the
   development of several diseases whose incidence increases dramatically with
   age: cardiovascular disease, cancer, & cognitive decline, along with
   mortality. When it comes to these diseases, Barzilai says, "Aging is a bigger
   risk factor than all of the other factors combined."'
   -- [<A HREF="http://dx.doi.org/10.1126/science.349.6254.1274">doi:10.1126/science.349.6254.1274</A>]['15].

%T A global reference for human genetic variation
%Q The 1000 Genomes Project Consortium
%J Nature
%V 526
%N 7571
%P 68-74
%M OCT
%D 2015
%K jrnl, c2015, c201x, c20xx, zz1015, thousand, genome, human, variation
%X "... report completion of the project, having reconstructed the genomes of
   2,504 individuals from 26 populations using a combination of low-coverage
   whole-genome sequencing, deep exome sequencing, and dense microarray
   genotyping. ..."
      -- [<A HREF="http://dx.doi.org/10.1038/nature15393">doi:10.1038/nature15393</A>]['15].

%A R. O. Prum
%A J. S. Berv
%A A. Dornburg
%A D. J. Field
%A J. P. Townsend
%A E. M. Lemmon
%A A. R. Lemmon
%T A comprehensive phylogeny of birds (Aves) using targeted next-generation
   DNA sequencing
%J Nature
%V 526
%N 7574
%P 569-573
%M OCT
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz1015, bird, birds, Aves, evolutionary,
   phylogenetic tree, Neoave, caprimulgiform, mesite, waterbird, landbird,
   Opisthocomus hoazin, Cretaceous Palaeogene, extinction, evolution, avian
%X "... investigate avian phylogeny with an unprecedented scale of data:
   > 390,000 bases of genomic seq. data from each of 198 species of living
   birds, representing all major avian lineages, & two crocodilian outgroups ...
   Bayesian & max. likelihood analyses yielded highly supported & nearly
   identical phylogenetic trees for all major avian lineages. Five major clades
   form successive sister groups to the rest of Neoaves: (1) a clade inc.
   nightjars, other caprimulgiforms, swifts, & hummingbirds; (2) a clade uniting
   cuckoos, bustards, & turacos with pigeons, mesites, & sandgrouse; (3) cranes
   & their relatives; (4) a comprehensive waterbird clade, inc. all diving,
   wading, & shorebirds; & (5) a comprehensive landbird clade with the enigmatic
   hoatzin (Opisthocomus hoazin) as the sister group to the rest ... our
   divergence time analyses are congruent with the palaeontological record,
   supporting a major radiation of crown birds in the wake of the
   Cretaceous-Palaeogene (K-Pg) mass extinction."
   -- [<A HREF="http://dx.doi.org/10.1038/nature15697">doi:10.1038/nature15697</A>]['15].

%A S. Saha
%A S. Rajasekaran
%T ERGC: an efficient referential genome compression algorithm
%J J. Bioinformatics
%V 31
%N 21
%P 3468-3475
%M OCT
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz1115, ERGC, DNA, compress, compression
%X "... Five different next-gen. seq. data compression problems have been
   identified & studied in the literature. ... a novel alg. for one of these
   problems known as reference-based genome compression. ... compression ratios
   that are better than those of the currently best performing algs.. The time
   to compress & decompress the whole genome is also very promising."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btv399">doi:10.1093/bioinformatics/btv399</A>]['15].

%A Jianzhu Ma
%A Sheng Wang
%A Zhiyong Wang
%A Jinbo Xu
%T Protein contact prediction by integrating joint evolutionary
   coupling analysis and supervised learning
%J J. Bioinformatics
%V 31
%N 21
%P 3506-3513
%M OCT
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz1115, CoinDCA, protein, family,
   contact, fold, folding, multiple alignment
%X "... presents a group graphical lasso (GGL) method for contact predn that
   integrates joint multi-family EC analysis & supervised learning to improve
   accuracy on proteins without many sequence homologs. Different from existing
   single-family EC analysis that uses residue coevolution info. in only the
   target protein family, our joint EC analysis uses residue coevolution in both
   the target family & its related families, which may have divergent seqs. but
   similar folds. To implement this, we model a set of related protein families
   using Gaussian graphical models & then coestimate their parameters by
   max.-likelihood, subject to the constraint that these parameters shall be
   similar to some degree. ..."
      "... new method CoinDCA (coestimation of inverse matrices for
      direct-coupling analysis) for contact prediction ... We use Random
      Forests, a popular supervised learning method, to predict the prob. of
      two residues forming a contact from a variety of protein features. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btv472">doi:10.1093/bioinformatics/btv472</A>]['15].

%A V. D. Menachery
%A et al ...
%A Zhengli-Li Shi
%A R. S. Baric
%T A SARS-like cluster of circulating bat coronaviruses shows potential for
   human emergence
%J NatureMedicine
%V 21
%P 1508-1513
%M NOV
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0521, risk, risks, SARSCoV, SARS CoV,
   MERS, corona virus, coronavirus, SHC014, Zhengli-Li Shi, bat lady, batwoman,
   Wuhan Institute of Virology, WIV, laboratory, China, bats, spike protein,
   ACE2
%X "... we examine the disease potential of a SARS-like virus, SHC014-CoV, which
   is currently circulating in Chinese horseshoe bat popns. Using the SARS-CoV
   reverse genetics system, we generated & characterized a chimeric virus
   expressing the spike of bat coronavirus SHC014 in a mouse-adapted SARS-CoV
   backbone. The results indicate that group 2b viruses encoding the SHC014
   spike in a wild-type backbone can efficiently use multiple orthologs of the
   SARS receptor human angiotensin converting enzyme II (ACE2), replicate
   efficiently in primary human airway cells & achieve in vitro titers
   equivalent to epidemic strains of SARS-CoV. Additionally, in vivo experiments
   demonstrate replication of the chimeric virus in mouse lung with notable
   pathogenesis. Evaluation of available SARS-based immune-therapeutic &
   prophylactic modalities revealed poor efficacy; both monoclonal antibody &
   vaccine approaches failed to neutralize & protect from infection with CoVs
   using the novel spike protein. On the basis of these findings, we
   synthetically re-derived an infectious full-length SHC014 recombinant virus
   & demonstrate robust viral replication both in vitro & in vivo. Our work
   suggests a potential risk of SARS-CoV re-emergence from viruses currently
   circulating in bat popns."
   -- [<A HREF="https://doi.org/10.1038/nm.3985">doi:10.1038/nm.3985</A>]['21].

%A I. Pipoly
%A V. Bokony
%A M. Kirkpatrick
%A P. F. Donald
%A T. Szekely
%A A. Liker
%T The sex-determination system predicts adult sex ratios in tetrapods
%J Nature
%V 527
%N 7576
%P 91-94
%M NOV
%D 2015
%K biol, c2015, c201x, c20xx, zz1115, adult sex ratio, ASR, gender, male,
   female, animal, tetrapod, amphibian, reptile, heterogamety, biology
%X "... we assess whether the type of genetic sex determination influences the
   ASR using data from 344 species in 117 families of tetrapods. ... taxa with
   female heterogamety have a sig. more male-biased ASR (proportion of males:
   0.55 +/-0.01 (mean +/-s.e.m.)) than taxa with male heterogamety
   (0.43 +/-0.01). The genetic sex-determination system explains 24% of
   interspecific variation in ASRs in amphibians & 36% in reptiles. We consider
   several genetic factors that could contribute to this pattern, inc. meiotic
   drive & sex-linked deleterious mutations, but further work is needed to
   quantify their effects. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature15380">doi:10.1038/nature15380</A>]['15].
   [Also search for: sex ratio biology].

%A E. Pennisi
%T Fossils, cells point to early appearance of the brain
%J Science
%V 350
%N 6262
%P 729-730
%M NOV
%D 2015
%K news, c2015, c201x, c20xx, zz1115, brain, nervous system, origin, fossil,
   animal, vertebrate, arthropod, evolution, origins, Strausfeld, Arendt
%X "Hundreds of millions of years ago, animals reached a major milestone: They
   acquired a brain. But just when & how that happened has been elusive, not
   least because paleontologists thought that the soft, fragile tissues of the
   central nervous system would leave few traces in the fossil record. Now,
   researchers have shown that such soft tissue can fossilize in the right
   conditions & described a complex brain from multiple 520-million-year-old
   fossils. That brain has the same three-part structure as modern arthropods &
   vertebrates. The work helps establish that brains evolved earlier than
   previously thought. A separate group has proposed just how that might have
   happened. They suggest a change in feeding strategies & the development of a
   protomouth were key to kicking off nervous system development. ..."
      "... Nicholas Strausfeld, a neuro scientist at the U. Arizona, Tuscon, &
      his colleagues ...16 November issue of Current Biology ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.350.6262.729">doi:10.1126/science.350.6262.729</A>]['15].

%A G. D. Edgecombe
%A Xiaoya Ma
%A N. J. Strausfeld
%T Unlocking the early fossil record of the arthropod central nervous system
%J Philosophical Trans. B
%I The Royal Soc.
%V 370
%N 1684
%P ?-?
%M NOV
%D 2015
%K jrnl, c2015, c201x, c20xx, zz1115, brain, central nervous system, CNS,
   origin, fossil, animal, vertebrate, arthropod, panarthropod, euarthropod,
   onychophoran, tardigrade, evolution, ancient, origins,
   Cambrian, Burgess Shale
%X "Extant panarthropods (euarthropods, onychophorans & tardigrades) are
   hallmarked by stunning morphological & taxonomic diversity, but their
   central nervous systems (CNS) are relatively conserved. The timing of
   divergences of the ground pattern CNS organization of the major panarthropod
   clades has been poorly constrained because of a scarcity of data from their
   early fossil record. Although the CNS has been documented in 3D detail in
   insects from Cenozoic ambers, it is widely assumed that these tissues are
   too prone to decay to withstand other styles of fossilization or
   geologically older preservation. However, Cambrian Burgess Shale-type
   compressions have emerged as sources of fossilized brains & nerve cords.
   CNS in these Cambrian fossils are preserved as carbon films or as iron
   oxides/hydroxides after pyrite in assoc. with carbon. Experiments with
   carcasses compacted in fine-grained sediment depict preservation of neural
   tissue for a more prolonged temporal window than anticipated by decay
   experiments in other media. CNS & compound eye characters in exceptionally
   preserved Cambrian fossils predict divergences of the mandibulate &
   chelicerate ground patterns by Cambrian Stage 3 (ca 518 Ma), a dating that
   is compatible with molecular estimates for these splits."
   -- [<A HREF="http://dx.doi.org/10.1098/rstb.2015.0038 ">doi:10.1098/rstb.2015.0038 </A>]['15].

%A Y. Ma
%A M. Wang
%A K. Su
%A M. D. Li
%T The significant association of Taq1A genotypes in DRD2/ANKK1 with smoking
   cessation in a large-scale meta-analysis of Caucasian populations
%J Translational Psychiatry
%V 5
%N 12
%P e686
%M DEC
%D 2015
%K jrnl, c2015, c201x, c20xx, zz1215, cigarette, tobacco,  smoking, smoker,
   gene, Taq1A, addiction, addictive, human, health, caucasian, white,
   behaviour, stopping, quitting, DRD2, ANKK1
%X "... The A1-dominant model that considers A1/* (*=A1 or A2) & A2/A2 as two
   genotypes & compares their freqs. in current & former smokers was applied. A
   total of 22 studies with 11,075 subjects were included in the meta-analyses.
   Considering the potential influence of between-study heterogeneity, we
   conducted stratified meta-analyses with the Comprehensive Meta-Analysis
   statistical s/w (ver.2.0). Results based on either cross-sectional or
   longitudinal studies consistently showed a stat. sig. assoc. between Taq1A
   A1/* genotypes & smoking cessation. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/tp.2015.176">doi:10.1038/tp.2015.176</A>]['15].
   [Also search for: tobacco smoking].

%A E. Rivas
%A S. R. Eddy
%T Parameterizing sequence alignment with an explicit evolutionary model
%J BMC Bioinf.
%V 16
%N 406
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0322, sequence, alignment, model
%X "... identify & implement several probabilistic evolutionary models
   compatible with the affine-cost insertion/deletion model used in std pairwise
   seq. alignment. Assuming an affine gap cost imposes important restrictions[!]
   on the realism of the evolutionary models ..."
   -- [<A HREF="https://doi.org/10.1186/s12859-015-0832-5">doi:10.1186/s12859-015-0832-5</A>]['22].
   [Also search for: MolBio alignment evolutionary model].

%A A. Hammond
%A et al ...
%A T. Nolan
%T A CRISPR-Cas9 gene drive system targeting female reproduction in tha
   malaria mosquito vector Anopheles gambiae
%J Nature Biotech.
%V 34
%P 78-83
%D 2016
%K jrnl, MolBio, c2015, c201x, c20xx, zz0718, gene drive, geneDrive, CRISPR Cas9
%X "Gene drive systems that enable super-Mendelian inheritance of a transgene
   have the potential to modify insect populations over a timeframe of a few
   years. ... identified three genes (AGAP005958, AGAP011377 and AGAP007280)
   that confer a recessive female-sterility phenotype upon disruption, and
   inserted into each locus CRISPR-Cas9 gene drive constructs designed to target
   and edit each gene.  ... transmission rates to progeny of 91.4 to 99.6% ..."
   -- [<A HREF="https://doi.org/10.1038/nbt.3439">doi:10.1038/nbt.3439</A>]['18]  (online 12/2015).
   (Also see news@[<A HREF="https://doi.org/10.1038/nature.2015.18974">doi:10.1038/nature.2015.18974</A>][2015],
   but mice more difficult [<A HREF="https://doi.org/10.1038/d41586-018-05665-1">doi:10.1038/d41586-018-05665-1</A>][6/7/2018].
   [Also search for: MolBio gene drive].

%A S. E. Ahnert
%A J. A. Marsh
%A H. Hernandez
%A C. V. Robinson
%A S. A. Teichmann
%T Principles of assembly reveal a periodic table of protein complexes
%J Science
%V 350
%N 6266
%M DEC
%D 2015
%K jrnl, MolBio, protein, c2015, c201x, c20xx, zz1215, quaternary, complex,
   structure, 3D
%X "...  we sought a comprehensive understanding of the general principles
   underlying quaternary structure organization in p.complexes. We first
   examined the fundamental steps by which [pcs] can assemble, using exp. &
   structure-based characterization of assembly pathways. Most assembly
   transitions can be classified into three basic types, which can then be used
   to exhaustively enumerate a large set of possible quaternary structure
   topologies. These topologies, which include the vast majority of observed
   protein complex structures, enable a natural organization of p.complexes into
   a periodic table. On the basis of this table, we can accurately predict the
   expected frequencies of quaternary structure topologies, inc. those not yet
   observed. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaa2245">doi:10.1126/science.aaa2245</A>]['15].

%A V. Alva
%A J. Soding
%A A. N. Lupas
%T A vocabulary of ancient peptides at the origin of folded proteins
%J eLife
%M DEC
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz1220, protein structure, fold, motif,
   pattern, ancient, peptide, origin, RNA, fragment
%X "... only a few thousand domain prototypes, but the origin of these
   themselves has remained unclear. We are pursuing the hypothesis that they
   arose by fusion & accretion from an ancestral set of peptides active as
   co-factors in RNA-dep't replication & catalysis. Should this be true,
   contemporary domains may still contain vestiges of such peptides, which could
   be reconstructed by a comparative approach in the same way in which ancient
   vocabularies have been reconstructed by the comparative study of modern
   languages. To test this, we compared domains representative of known folds &
   identified 40 fragments whose similarity is indicative of common descent ...
   We propose that they represent the observable remnants of a primordial
   RNA-peptide world."
   -- [<A HREF="https://doi.org/10.7554/elife.09410">doi:10.7554/elife.09410</A>]['20],
      [<A HREF="https://pubmed.ncbi.nlm.nih.gov/26653858/">p'bmed</A>]['20].

%A Xing-Yi Ge
%A et al
%A Zheng-Li Shi
%T Coexistence of multiple coronaviruses in several bat colonies in an
   abandoned mineshaft
%J Virologica Sinica
%V 31
%P 41-44
%M FEB
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz1220, coronavirus, virus, SARS, origin,
   origins, Wuhan, WIV, lab, laboratory, Tongguan, Yunnan, China, bat, bats,
   RdRp, RaTG13, horseshoe bat, Rhinolophus affinis, Shi Zhengli, bat lady,
   batwoman, SARS1
%X "Since the 2002-2003 severe acute respiratory syndrome (SARS) outbreak ... We
   conducted a surveillance of coronaviruses in bats in an abandoned mineshaft
   in Mojiang County, Yunnan Province, China, from 2012-2013. Six bat species
   were frequently detected in the cave: Rhinolophus sinicus, Rhinolophus
   affinis, Hipposideros pomona, Miniopterus schreibersii, Miniopterus
   fuliginosus, & Miniopterus fuscus. By sequencing PCR products of the
   coronavirus RNA-dependent RNA polymerase gene (RdRp), we found a high freq.
   of infection by a diverse group of coronaviruses in different bat species in
   the mineshaft. Sequenced partial RdRp fragments had 80%-99% nucleic acid
   sequence identity with well-characterized Alphacoronavirus species, inc.
   BtCoV HKU2, BtCoV HKU8, & BtCoV1, and unassigned species BtCoV HKU7 & BtCoV
   HKU10. ..."
   -- [<A HREF="https://doi.org/10.1007/s12250-016-3713-9">doi:10.1007/s12250-016-3713-9</A>]['20].
   Also see bat lady [<A HREF="https://www.bbc.com/news/world-asia-china-55364445">bbc</A>][22/12/2020].
   [Also search for: MolBio SARS origin].

%A V. F. Scalfani
%A et al ...
%A J. E. Bara
%T Programmatic conversion of crystal structures into 3D printable files
   using Jmol
%J J. of Cheminformatics
%V 8
%N 66
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0620, Jmol, JSmol, protein, structure,
   3D, interactive, visualisation, computer graphics, modelling, molecule,
   SMILES, SMARTS, CIF
%X "... A collection of over 30,000 crystal structures in crystallographic
   info. file (CIF) format from the Crystallography Open Database (COD) were
   programmatically converted into 3D printable files (VRML format) using
   Jmol scripting. ..."
   -- [<A HREF="https://doi.org/10.1186/s13321-016-0181-z">doi:10.1186/s13321-016-0181-z</A>] openaccess.
   Also see
      [<A HREF="https://doi.org/10.1186/s13321-016-0160-4">doi:10.1186/s13321-016-0160-4</A>]['20] openaccess,
    & Jmol@[<A HREF="http://jmol.sourceforge.net">s'rceforge</A>]['20].

%A Olmos-Alonso
%A et al
%T Pharmacological targeting of CSF1R inhibits microglial proliferation and
   prevents the progression of Alzheimer's-like pathology
%J Brain
%V ?
%P ?-?
%M ?
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0116, human, brain, dementia, Alzheimers,
   health, risks, disease, CSF1R, inflammation,
   Diego Gomez-Nicola, USouthampton
%X GN@[<A HREF="https://scholar.google.co.uk/citations?user=Xe6rGMcAAAAJ&hl=en">scholar</A>]['16].
   Also see news@[<A HREF="http://www.mrc.ac.uk/news/browse/study-shows-beneficial-effects-of-blocking-brain-inflammation-in-an-experimental-model-of-alzheimer-s/">mrc</A>][1/2016] and
   bbc[<A HREF="http://www.bbc.com/news/health-35254649">8/1/2016</A>].

%A A. I. Tomescu
%A P. Medvedev
%T Safe and complete contig assembly via omnitigs
%J arXiv
%M JAN
%D 2016
%O ? RECOMB 2016 ?
%K TR, conf, MolBio, c2016, c201x, c20xx, zz0116, DNA, sequence assembly,
   algorithm, reads, unitigs, omnitigs, contigs, contig
%X "... output consists of contigs - a set of strings that are promised to
   appear in any genome that could have generated the reads. From the intro. of
   contigs 20 y. ago, assemblers have tried to obtain longer & longer contigs,
   but the following Q was never solved: given a genome graph G (e.g. a
   de Bruijn, or a string graph), what are all the strings that can be safely
   reported from G as contigs?  ... we finally answer this Q, & also give a
   polynomial time alg. to find them. Our experiments show that these strings,
   which we call omnitigs, are 66% to 82% longer on avg. than the popular
   unitigs, & 29% of dbSNP locns have more neighbors in omnitigs than
   in unitigs."
   -- 1601.02932@[<A HREF="http://arxiv.org/abs/1601.02932">arXiv</A>]['16].
   [Also search for: MolBio sequence assembly].

%A S. Berard
%A A. Chateau
%A N. Pompidor
%A P. Guertin
%A A. Bergeron
%A K. M. Swenson
%T Aligning the unalignable: bacteriophage whole genome alignments
%J BMC Bioinformatics
%M JAN
%D 2016
%K jrnl, eJrnl, MolBio, c2016, c201x, c20xx, zz0116, DNA, alignment, alpha,
   partial order, graph
%X "... propose a multiple alignment strategy that exploits functional
   collinearity shared by related strains of bacteriophages, & uses partial
   orders to capture mosaicism of sets of genomes. As classical alignments do,
   the computed alignments can be used to predict that genes have the same
   biological fn, even in the absence of detectable similarity. The Alpha
   aligner implements these ideas in visual interactive displays, & is used to
   compute several examples of alignments of Staphylococcus aureus &
   Mycobacterium bacteriophages, involving up to 29 genomes. Using these
   datasets, we prove that Alpha alignments are at least as good as those
   computed by standard aligners. ..." [13/1/2016].
   -- [<A HREF="http://dx.doi.org/10.1186/s12859-015-0869-5">doi:10.1186/s12859-015-0869-5</A>]['16].

%A A. Sekar
%A et al ...
%A S. A. McCarroll
%T Schizophrenia risk from complex variation of complement component 4
%J Nature
%V ?
%N ?
%P ?-?
%M JAN
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0216, human, mental health, illness,
   schizophrenia, brain, development, gene, major histocompatibility complex,
   MHC SNP, C4, C4A, C4B,
%X "... Schizophrenia's strongest genetic assoc. at a popln level involves
   variation in the major histocompatibility complex (MHC) locus, but the genes
   & molecular mechanisms accounting for this have been challenging to identify.
   Here we show that this assocn arises in part from many structurally diverse
   alleles of the complement component 4 (C4) genes. We found that these alleles
   generated widely varying levels of C4A & C4B expression in the brain, with
   each common C4 allele associating with s. in proportion to its tendency to
   generate greater expression of C4A. Human C4 protein localized to neuronal
   synapses, dendrites, axons, & cell bodies. In mice, C4 mediated synapse
   elimination during postnatal development. These results implicate excessive
   complement activity in the development of s. & may help explain the reduced
   #s of synapses in the brains of individuals with schizophrenia."
   -- [<A HREF="http://dx.doi.org/10.1038/nature16549">doi:10.1038/nature16549</A>]['16]  (online 1/2016).

%A Sheng Wan
%A Jian Peng
%A Jianzhu Ma
%A Jinbo Xu
%T Protein secondary structure prediction using deep convolutional neural
   fields
%J NatureSciReports
%V 6
%N #18962
%M JAN
%D 2016
%K jrnl, eJrnl, MolBio, c2016, c201x, c20xx, zz1122, deepCNF, deepSSP,
   protein secondary structure, NN, ANN, Random Field, CRF
%X "... we present DeepCNF (...) for protein SS pred'n. ... a Deep Learning
   extension of Conditional Neural Fields (CNF), which is an integration of
   Cond.Random Fields (CRF) & shallow NNs. DeepCNF can model not only complex
   seq.-structure relationship by a deep hierarchical architecture, but also
   interdependency between adjacent SS labels, so it is much more powerful than
   CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy,
   ~85% SOV score & ~72% Q8 accuracy, resp., on the CASP & CAMEO test proteins,
   greatly outperforming currently popular predictors ..."   (via SR)
   -- [<A HREF="https://doi.org/10.1038/srep18962">doi:10.1038/srep18962</A>]['22],
     1512.00843@[<A HREF="https://arxiv.org/abs/1512.00843">arXiv</A>]['22],
     DeepCNF_AUC@[<A HREF="https://github.com/realbigws/DeepCNF_AUC">github</A>]['22].
   [Also search for: MolBio secondary structure prediction].

%A V. Afreixo
%A J. M. O. S. Rodrigues
%A C. A. C. Bastos
%A R. M. Silva
%T The exceptional genomic word symmetry along DNA sequences
%J BMC Bioinformatics
%M FEB
%D 2016
%K MolBio, c2016, c201x, c20xx, zz0216, DNA, sequence, Chargaff, parity rule,
   single strand, reverse, complement
%X "...parity of the frequencies of reverse complementary oligonucleotides could
   be a mere consequence of the single nucleotide parity rule, if nucleotide
   independence is assumed. Exceptional symmetry (symmetry beyond that expected
   under an indep. nucleotide assumption) was proposed prev. as a meaningful
   measure of the extension of the second parity rule to oligonucleotides. The
   global exceptional symmetry was detected in long and short genomes. ...
   conclude that the exceptional symmetry is a local phenomenon in genome seqs.
   with distinct characteristics along the sequence of each chr.. The local
   exceptional symmetry along the genomic seqs. shows outlying segments, & those
   segments have high biological annotation density."
     ["The single strand symmetry states that, in each DNA strand, the
      proportion of an oligonucleotide should be similar to that of its
      reverse complement. There is no knowledge about why the parity is
      needed and there is no consensual explanation for the occurrence of
      the single strand phenomenon."]
   -- [<A HREF="http://dx.doi.org/10.1186/s12859-016-0905-0">doi:10.1186/s12859-016-0905-0</A>]['16].

%A R. A. Watson
%A E. Szathmary
%T How can evolution learn?
%J Trends in Ecology and Evolution
%V 31
%N 2
%P 147-157
%M FEB
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0317, MolBio, evolution, learning, evolvability,
   adaption, ecology, individuality, Baldwin effect, Wagner, Altenberg
%X "The theory of evolution links random variation & seln to incremental
   adaptation. In a different intellectual domain, learning theory links
   incremental adaptation (e.g., from +ve &/or -ve reinforcement) to intelligent
   behaviour. Specifically, learning theory explains how incr. adaptation can
   acquire knowledge from past experience & use it to direct future behaviours
   toward favourable outcomes. Until recently such cognitive learning seemed
   irrelevant to the 'uninformed' process of evoln. In our opinion, however,
   new results formally linking evolutionary processes to the principles of
   learning might provide solutions to several evolutionary puzzles - the
   evoln of evolvability, the evoln of ecological organisation, & evolutionary
   transitions in individuality. If so, the ability for evoln to learn might
   explain how it produces such apparently intelligent designs."
   -- [<A HREF="http://dx.doi.org/10.1016/j.tree.2015.11.009">doi:10.1016/j.tree.2015.11.009</A>]['17].
   (Also see the bbc[<A HREF="http://www.bbc.com/earth/story/20170301-life-may-actually-be-getting-better-at-evolving">2/3/17</A>].)
   [Also search for: Wagner Altenberg] and [also search for: Baldwin effect].

%A S. Bastkowski
%A V. Moulton
%A A. Spillner
%A T. Wu
%T The minimum evolution problem is hard: a link between tree inference and
   graph clustering problems
%J J. Bioinformatics
%V 32
%N 4
%P 518-522
%M FEB
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0216, evolutionary, phylogenetic, tree,
   trees, distance method, DNA, NPC, problem
%X "... show that Rzhetsky and Nei's ME problem is NP-complete, & so probably
   computationally intractable. ... by linking the ME problem to a graph
   clustering problem called the quasi-clique decomposition problem, which has
   recently also been shown to be NP-complete. We also discuss how this link
   could potentially open up some useful new connections between phylogenetics
   & g. clustering."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btv623">doi:10.1093/bioinformatics/btv623</A>]['16].

%A N. A. Kovacs
%A A. S. Petrov
%A K. A. Lanier
%A L. D. Williams
%T Frozen in time: The history of proteins
%J Mol. Biol. Evol.
%V 34
%N 5
%P 1252-1260
%M MAY
%D 2017
%K jrnl, MBE, c2017, c201x, c20xx, zz1117, MolBio, protein, ribosome,
   origin of life, origins, evolution, folding, ribosomal, rprotein,
   beta hairpin
%X "The ribosome is imprinted with a detailed molecular chronology of the
   origins and early evolution of proteins. ... show that when arranged by
   evolutionary phase of ribosomal evolution, ribosomal protein (rProtein)
   segments reveal an atomic  level history  of  protein  folding ... RNA
   stabilized polypeptide assemblies, which evolved in a stepwise process into
   globular domains, bypassing the immense space of random unproductive seqs..
   Coded proteins originated as oligomers and polymers created by the ribosome,
   on the ribosome and for the ribosome.  Synthesis of increasingly longer
   products was iteratively coupled with lengthening and maturation of the
   ribosomal exit tunnel. Protein catalysis appears to be a late byproduct of
   selection for sophisticated and finely controlled assembly."
   -- [<A HREF="https://doi.org/10.1093/molbev/msx086">doi:10.1093/molbev/msx086</A>]['17] (online 15/2/2017),
   or pdf@[<A HREF="http://ww2.chemistry.gatech.edu/~williams/publications/LDW_115.pdf">gaTech</A>]['17],
   at wLab@[<A HREF="http://ww2.chemistry.gatech.edu/~williams/">gaTech</A>]['17].

%A Jie Yang
%A et al
%A J. Ortega-Hernandez
%T The fuxianhuiid ventral nerve cord and early nervous system evolution in
   Panarthropoda
%J PNAS
%V ?
%N ?
%P ?-?
%M MAR
%D 2016
%K jrnl, PNAS, c2016, c201x, c20xx, zz0316, fossil, brain, nervous system,
   nerve cord, evolution, Cambrian, fuxianhuiid, Panarthropoda, arthropod,
   euarthropod, Onychophora, Ecdysozoa, Tardigrada,
   Chengjiangocaris kunmingensis
%X "... describe the neurological architecture of the ventral nerve cord (VNC)
   in the upper-stem group euarthropod Chengjiangocaris kunmingensis from the
   early Cambrian Xiaoshiba Lagerstatte (S.China). The VNC of C.k. comprises a
   homonymous series of condensed ganglia that extend throughout the body, each
   assoc. with a pair of biramous limbs. Submillimetric preservation reveals
   numerous segmental & intersegmental nerve roots emerging from both sides of
   the VNC ... The fuxianhuiid VNC indicates that ancestral neurological
   features of Ecdysozoa persisted into derived members of stem-group
   Euarthropoda but were later lost in crown-group reps.. ... illuminate the VNC
   ground pattern in Panarthropoda & suggest the indep. secondary loss of
   cycloneuralian-like neurological characters in Tardigrada & Euarthropoda."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1522434113">doi:10.1073/pnas.1522434113</A>]['16], (online 3/2016).
   (Also see [<A HREF="http://www.cam.ac.uk/research/news/520-million-year-old-fossilised-nervous-system-is-most-detailed-example-yet-found">www</A>][1/3/2016].)

%A M. J. McDonald
%A D. P. Rice
%A M. M. Desai
%T Sex speeds adaptation by altering the dynamics of molecular evolution
%J Nature
%V 531
%N 7593
%P 233-236
%M MAR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0316, sex, evolution, mutation, adaption,
   advantage, clonal interference
%X "... One longstanding hypothesis argues that sex is beneficial because
   recombination speeds adaptation4. Theory has proposed several distinct
   population genetic mechanisms that could underlie this advantage. [E.g.], sex
   can promote the fixation of beneficial mutations either by alleviating
   interference competition (the Fisher-Muller effect) or b separating them
   from deleterious load (the ruby in the rubbish effect). Previous experiments
   confirm that sex can increase the rate of adaptation ... we present the
   first, to our knowledge, comparison between the seq.-level dynamics of
   adaptation in experimental sexual & asexual Saccharomyces cerevisiae popns,
   which allows us to identify the specific mechanisms by which sex speeds
   adaptation. We find that sex alters the molecular signatures of evolution by
   changing the spectrum of mutations that fix, & confirm theor. predictions
   that it does so by alleviating clonal interference. We also show that
   substantially deleterious mutations hitchhike to fixation in adapting asexual
   populations. In contrast, recombination prevents such mutations from fixing.
   Our results demonstrate that sex both speeds adaptation & alters its
   molecular signature by allowing natural selection to more efficiently sort
   beneficial from deleterious mutations."
   -- [<A HREF="http://dx.doi.org/10.1038/nature17143">doi:10.1038/nature17143</A>]['16].

%A M. D. Cao
%A D. Ganesamoorthy
%A M. A. Cooper
%A L. J. M. Coin
%T Realtime analysis and visualization of MinION sequencing data with npReader
%J J. Bioinformatics
%V 32
%N 5
%P 764-766
%M MAR
%D 2016
%K jrnl MolBio, c2016, c201x, c20xx, zz0316, Minh Duc Cao, MinION, npReader,
   single molecule, nanopore, SMRT, sequencing, genome, sequencer
%X "... npReader, an open-source s/w package to facilitate real-time analysis
   of MinION sequencing data. [It] can simultaneously extract seq. reads &
   stream them to downstream analysis pipelines while the samples are being
   sequenced on the MinION device. It provides a cmd line interface for easy
   integration into a bioinformatics work flow, [&] a graphical user interface
   which concurrently displays the statistics of the run. It also provides an
   application programming interface for development of streaming algs. in order
   to fully utilize the extent of nanopore sequencing potential.
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btv658">doi:10.1093/bioinformatics/btv658</A>]['16].
   [Also search for: MolBio single molecule sequencing].

%A M. Meyer
%A et al ...
%A S. Paabo
%T Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins
%J Nature
%V ?
%N ?
%P ?-?
%M MAR
%A 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0316, fossil, ancient, DNA, genome,
   mitochondria, mtDNA, Neanderthal, Denisovan, hominim, human, humans, Spain
%X "... While the Sima de los Huesos hominins share some derived morphological
   features with Neanderthals, the mitochondrial genome retrieved from one
   individual from Sima de los Huesos is more closely related to the
   mitochondrial DNA of Denisovans than to that of Ns.. However, since the
   mtDNA does not reveal the full picture of relationships among popns, we have
   investigated DNA preservation in several individuals found at Sima de los
   Huesos. Here we recover nuclear DNA seqs. from two specimens, which show that
   the Sima de los Huesos hominins were related to Ns. rather than to Ds.,
   indicating that the popn divergence between Ns. & Ds. predates 430,000 years
   ago. A mtDNA recovered from one of the specimens shares the prev. described
   relationship to D. mtDNAs, suggesting, among other possibilities, that the
   mtDNA gene pool of Ns. turned over later in their history." (online /2016.)
   -- [<A HREF="http://dx.doi.org/10.1038/nature17405">doi:10.1038/nature17405</A>]['16].
   (Also see [<A HREF="http://www.bbc.com/news/science-environment-35806992">bbc</A>][15/3/2016].)
   [Also search for: MolBio ancient DNA].

%A C. A. Hutchison III
%A et al ...
%A C. Venter
%T Design and synthesis of a minimal bacterial genome
%J Science
%V 351
%N 6280
%P ?-?
%M MAR
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0416, bacterium, bacteria, small,
   minimal, genome, life, biology, essential, genes
%X "... In 2010, a 1079-kb genome based on the genome of Mycoplasma mycoides
   (JCV-syn1.0) was chemically synthesized & supported cell growth when
   transplanted into cytoplasm. Hutchison III et al. used a design, build, &
   test cycle to reduce this genome to 531_kb (473 genes). The resulting
   JCV-syn3.0 retains genes involved in key processes such as transcription &
   translation, but also contains 149 genes of unknown function."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aad6253">doi:10.1126/science.aad6253</A>]['16].

%A N. Luhmann
%A A. Thevenin
%A A. Ouangraoua
%A R. Wittler
%A C. Chauve
%T The SCJ small parsimony problem for weighted gene adjacencies (extended
   version)
%J arXiv
%M MAR
%D 2016
%K TR, MolBio, c2016, c201x, c20xx, zz0416, gene, genes, adjacent, linkage,
   Single-Cut-or-Join, SCJ problem,  Sankoff Rousseau
%X "Reconstructing ancestral gene orders in a given phylogeny ... Most existing
   methods compare conserved features in extant genomes in the phylogeny to
   define potential ancestral gene adjacencies, & either try to reconstruct all
   ancestral genomes under a global evolutionary parsimony criterion, or,
   focusing on a single ancestral genome, use a scaffolding approach to select
   a subset of ancestral gene adjacencies. ... describe an exact alg. for the
   small parsimony problem that combines both approaches. We consider that gene
   adjacencies at internal nodes of the species phylogeny are weighted, & we
   introduce an objective fn defined as a convex combination of these weights &
   the evolutionary cost under the Single-Cut-or-Join (SCJ) model. We propose a
   Fixed-Parameter Tractable alg. based on the Sankoff-Rousseau [DPA], that also
   allows to sample co-optimal solutions."
   -- 1603.08819@[<A HREF="http://arxiv.org/abs/1603.08819">arXiv</A>]['16].

%A B. J. Hintze
%A et al
%T Molprobity's ultimate rotamer-library distributions for model validation
%J Proteins: Structure, Function, and Bioinformatics
%V 84
%N 9
%P 1177-1189
%M MAR
%D 2016
%K jrnl, MolBio, c2016, c20x, c20xx, zz0724, MolProbity, protein 3D structure,
   validation, validate, backbone
%X "... updated MolProbity rotamer-library distributions derived from an
   order-of-magnitude larger and more stringently quality-filtered dataset of
   about 8000 (vs. 500) protein chains ..."
   -- [<A HREF="https://doi.org/10.1002/prot.25039">doi:10.1002/prot.25039</A>]['24] and
      [<A HREF="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4983197/">PMC4983197</A>]['24].
   [Also search for: PDB structure validation].

%A D. Gordon
%A et al ...
%A E. E. Eichler
%T Long-read sequence assembly of the gorilla genome
%J Science
%V 352
%N 6281
%P ?-?
%M APR
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0416, animal, primate, gorilla,
   genome, Ngenome, gene, genes, gorillas
%X "... Sequencing from a single individual decreased assembly fragmentation &
   recovered previously missed genes & noncoding loci. Mapping short-read seqs.
   from additional gs. helped reconstruct a 'pan' gorilla seq. documenting
   genetic variation. Comparison with human genomes revealed species-specific
   differences ranging in size from one to thousands of bases in length, inc.
   some that are likely to affect gene regulation."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aae0344">doi:10.1126/science.aae0344</A>]['16].

%A K. Neupane
%A D. A. N. Foster
%A D. R. Dee
%A H. Yu
%A F. Wang
%A M. T. Woodside
%T Direct observation of transition paths during the folding of proteins and
   nucleic acids
%J Science
%V 352
%N 6282
%P 239-242
%M APR
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0416, protein, DNA, fold, folding, path,
   pathway, trajectory, molecule, macromolecule, dynamics
%X "... We measured transition paths for both nucleic acid & protein folding,
   using optical tweezers to observe the microscopic diffusive motion of single
   molecules traversing energy barriers. The avg. transit times & the shapes of
   the transit-time distributions agreed well with theoretical expectations for
   motion over the [1D] energy landscapes reconstructed for the same molecules,
   validating the physical theory of folding reactions. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aad0637">doi:10.1126/science.aad0637</A>]['16].
   (Also see Pfolding@[<A HREF="https://en.wikipedia.org/wiki/Protein_folding">wikip</A>]['22].)

%A F. L. Mendez
%A G. David Poznik
%A S. Castellano
%A C. D. Bustamante
%T The divergence of Neandertal and modern human Y chromosomes
%J AJHG
%V 98
%N 4
%P 728-734
%M APR
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0416, human, ancient, DNA, genome,
   chr Y, Ychr, Ychromosome, chrY, chromosomeY, evolution, evolutionary,
   ancestry, modern human, Neandertal, Neanderthal, El Sidron, ElSidron,
   PCDH11Y, TMSB4Y, USP9Y, KDM5D
%X "... we analyze ~120 kb of exome-captured Y-chr. DNA from a Neandertal
   individual from El Sidron, Spain. We investigate its divergence from
   orthologous chimpanzee & modern human seqs. & find strong support for a model
   that places the N. lineage as an outgroup to modern human Y chrs. - inc. A00,
   the highly divergent basal haplogroup. We est. that the time to the most
   recent common ancestor (TMRCA) of N. & modern human Y chrs. is ~588 thousand
   years ago (kya) (95% [CI]: 447-806 kya). This is ~2.1 (95% CI: 1.7-2.9) times
   longer than the TMRCA of A00 & other extant modern human Y-chr. lineages.
   ... suggests that the Y-chr. divergence mirrors the popn divergence of N. &
   modern human ancestors, & it refutes alternative scenarios of a relatively
   recent or super-archaic origin of N. Y chr.. The fact that the N. 'Y' we
   describe has never been observed in modern humans suggests that the lineage
   is most likely extinct. We identify protein-coding differences between N. &
   modern human Y chr., including potentially damaging changes to PCDH11Y,
   TMSB4Y, USP9Y, & KDM5D. Three of these changes are missense mutations in
   genes that produce male-specific minor histocompatibility (H-Y) antigens.
   Antigens derived from KDM5D, e.g., are thought to elicit a maternal immune
   response during gestation. ... possible that incompatibilities at >= 1 of
   these genes played a role in the reproductive isolation of the two groups."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ajhg.2016.02.023">doi:10.1016/j.ajhg.2016.02.023</A>]['16].
   (Also see the [<A HREF="http://www.abc.net.au/news/2016-04-08/neanderthal-y-chromosome-disappeared-from-modern-men/7308982?section=science">abc</A>][8/4/2016].)
   [Also search for: ancient human DNA].

%A P. Bonizzoni
%A G. Della Vedova
%A Y. Pirola
%A M. Previtali
%A R. Rizzi
%T FSG: Fast string graph construction for de novo assembly of reads data
%J arXiv
%M APR
%D 2016
%K TR, MolBio, c2016, c201x, c20xx, zz0416, DNA, sequence assembly, FM index,
   FMindex, SGA, stringGraph, deNovo
%X "The string graph for a collection of next-generation reads is ...
   we explore a novel approach to compute the string graph, based on the
   FM-index & Burrows-Wheeler Transform. We describe a simple alg. that uses
   only the FM-i. repn of the collection of reads to construct the string graph,
   without accessing the input reads. [It] has been integrated into the SGA
   assembler as a standalone module to construct the string g.. ... has been
   assessed on a std benchmark, showing that FSG is sig. faster than SGA while
   maintaining a moderate use of main memory, & showing practical advantages in
   running FSG on multiple threads.
   -- 1604.03587@[<A HREF="http://arxiv.org/abs/1604.03587">arXiv</A>]['16].
   [Also search for: MolBio sequence assembly] and [also search for: FMindex].

%A S. Verma
%A R. Dixit
%A K. C. Pandey
%T Cysteine proteases: Modes of activation and future prospects as
   Pharmacological targets
%J Front. Pharmacol.
%M APR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0820, MolBio, cysteine, protease, Cys, cystine,
   target, drug design, proteinase
%X "... Proteases are classified according to their catalytic site, &
   distributed into four major classes: cysteine p., serine p., aspartic p., &
   metalloproteases. ... involved in multiple fns such as extracellular matrix
   turnover, antigen presentation, processing events, digestion, immune
   invasion, hemoglobin hydrolysis, parasite invasion, parasite egress, &
   processing surface proteins. ..."
   -- 1604.03587@[<A HREF="https://doi.org/10.3389/fphar.2016.00107">doi:10.3389/fphar.2016.00107</A>]['20].
   [Also search for: cysteine protease].

%A C. T. Bauch
%A R. McElreath
%T Disease dynamics and costly punishment can foster socially imposed monogamy
%J NatureComms
%V 7
%P 11219
%M APR
%D 2016
%K eJrnl, c2016, c201x, c20xx, zz0416, human, behaviour, society, family,
   marriage, polygamy, monogamy, polygyny, sexually transmitted infection,
   disease, sex, health, STD, STI, STDs, STIs
%X "Socially imposed monogamy in humans is an evolutionary puzzle because it
   requires costly punishment by those who impose the norm. Moreover, most
   societies were - and are - polygynous; yet many larger human societies
   transitioned from p. to socially imposed m. beginning with the advent of
   agriculture & larger residential groups. We use a simulation model to explore
   how interactions between group size, sexually transmitted infection (STI)
   dynamics & social norms can explain the timing & emergence of socially
   imposed monogamy. Polygyny dominates when groups are too small to sustain
   STIs. However, in larger groups, STIs become endemic (esp. in concurrent
   polygynist n/wks) & have an impact on fertility, thereby mediating multilevel
   seln. Punishment of polygynists improves monogamist fitness within groups by
   reducing their STI exposure, & between groups by enabling punishing
   monogamist groups to outcompete polygynists. This suggests pathways for the
   emergence of socially imposed m., & enriches our understanding of costly
   punishment evolution."
   -- [<A HREF="http://dx.doi.org/10.1038/ncomms11219">doi:10.1038/ncomms11219</A>]['16].
   [Also search for: monogamy].
   (Also see bbc [<A HREF="http://www.bbc.com/earth/story/20160412-sexually-transmitted-infections-may-have-reshaped-our-lives">12/4/2016</A>].)

%A R. Boisseau
%A D. Vogel
%A A. Dussutour
%T Habituation in non-neural organisms: Evidence from slime moulds
%J Proc. Royal Soc. London B
%D 2016
%K jrnl, PRSB, biol, c2016, c201x, c20xx, zz0516, Physarum polycephalum,
   slime mould, mold, organization, adaption, habituation, learning, behaviour
%X "Learning, defined as a change in behaviour evoked by experience ... Here we
   demonstrate habituation, an unmistakable form of learning, in the non-neural
   organism Physarum polycephalum. In our experiment, using chemotaxis as the
   behavioural output & quinine or caffeine as the stimulus, we showed that
   P.polycephalum learnt to ignore q. or c. when the stimuli were repeated, but
   responded again when the stimulus was withheld for a certain time. ..."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2016.0446">doi:10.1098/rspb.2016.0446</A>]['16],
   auth3@[<A HREF="http://dussutou.free.fr/publication_audrey_dussutour.html">.fr</A>]['16].
   [Also search for: slime mold].
   (Also see the ABC[<A HREF="http://www.abc.net.au/news/2016-04-27/slime-mould-can-learn-even-without-brain/7363176">27/4/2016</A>].)

%A D. Grun
%A et al ...
%A A. van Oudenaarden
%T De novo prediction of stem cell identity using single-cell transcriptome data
%J Cell Stem Cell
%V 19
%N 2
%P 266-277
%M AUG
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0720, single cell RNA seq, RNAseq,
   scRNAseq, scRNA seq, trajectory, expression, stemCell
%X "... StemID, an alg. for id. stem cells among all detectable cell types
   within a popn. We demonstrate that StemID recovers two known adult stem cell
   popns, Lgr5+ cells in the small intestine & hematopoietic stem cells in the
   bone marrow. We apply StemID to predict candidate multipotent cell ..."
      "... reduce the dimensionality ... single inter-cluster link [linkage]
       ... medoid ..."
   -- [<A HREF="https://doi.org/10.1016/j.stem.2016.05.010">doi:10.1016/j.stem.2016.05.010</A>]['20].
   [Also search for: scRNAseq]  and  [also search for: single link].

%A R. Rabatin
%A B. Brejova
%A T. Vinar
%T Using sequence ensembles for seeding alignments of MinION sequencing data
%J arXiv
%M JUN
%D 2016
%K TR, c2016, c201x, c20xx, zz0716, MolBio, DNA, sequencing, nanopore, MinION,
   read, short reads, sequence assembly
%X "... prone to high sequencing error rates of up to 30%. Since most of these
   errors are insertions or deletions, it is v.difficult to adapt popular
   seed-based algs. designed for aligning data sets with much lower error
   rates. Base calling of MinION reads is typically done using HMMs. ... we
   propose to represent each sequencing read by an ensemble of seqs. sampled
   from such a probabilistic model. ... can improve the sensitivity & false +ve
   rate of seeding an alignment compared to using a single representative base
   call seq. for each read."
   -- 1606.08719@[<A HREF="http://arxiv.org/abs/1606.08719">arXiv</A>]['16].

%A E. H. Wilson
%A et al ...
%A D. Platt
%T Genotype specification language
%J ACS Synthetic Biology
%V 5
%N 6
%P 471-478
%M JUN
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0118, genetic engineering, DPlatt, daz,
   Amyris, DNA, GSL
%X "... Genotype Specification Language (GSL), a language that facilitates the
   rapid design of large & complex DNA constructs used to engineer genomes. The
   GSL compiler implements a high-level language based on traditional genetic
   notation, as well as a set of low-level DNA manipulation primitives. The
   language allows facile incorporation of parts from a library of cloned DNA
   constructs & from the 'natural' library of parts in fully sequenced &
   annotated genomes. GSL was designed to engage genetic engineers in their
   native language while providing a framework for higher level abstract
   tooling. To this end we define four language levels, Level 0 (literal DNA
   sequence) through Level 3, with increasing abstraction of part selection &
   construction paths. GSL targets an intermediate language based on DNA slices
   that translates efficiently into a wide range of final output formats, such
   as FASTA & GenBank, & includes formats that specify instructions & materials
   such as oligonucleotide primers to allow the physical construction of the GSL
   designs by individual strain engineers or an automated DNA assembly core
   facility."
   -- [<A HREF="https://doi.org/10.1021/acssynbio.5b00194">doi:10.1021/acssynbio.5b00194</A>]['18].

%A V. Vinciotti
%A E. C. Wit
%A R. Jansen
%A E. J. C. N. de Geus
%A B. W. J. H. Penninx
%A D. I. Boomsma
%A P. A. C. 't Hoen
%T Consistency of biological networks inferred from microarray and sequencing
   data
%J BMC Bioinformatics
%M JUN
%D 2016
%K jrnl, eJrnl, MolBio, c2016, c201x, c20xx, zz0716, biol, network, data,
   regulatory, gene regulation, microarray, controversial, reproducibility,
   reproducible, consistency, systems biology, tHoen
%X "... Our analysis shows that individual node variances can have a remarkable
   effect on the connectivity of the resulting n/w. Their inconsistency across
   platforms & the fact that the variability level of a node may not be linked
   to its regulatory role mean that, failing to scale the data prior to the
   network analysis, leads to networks that are not reproducible across
   different platforms & that may be misleading. Moreover, we show how the
   reproducibility of networks across different platforms is sig. higher if
   networks are summarised in terms of enrichment amongst functional groups of
   interest, such as pathways, rather than at the level of individual
   edges. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/s12859-016-1136-0">doi:10.1186/s12859-016-1136-0</A>]['16].
   [Also search for: MolBio regulatory network] and
   [also search for: MolBio network reproducibility].

%A H. Davtya
%A et al ...
%A A. Ghochikyan
%T Alzheimer's disease Advax^CpG- adjuvanted MultiTEP-based dual and single
   vaccines induce high-titer antibodies against various forms of tau and
   A-beta pathological molecules
%J Scientific Reports
%V 6
%R 28912
%D 2016
%K MolBio, c2016, c201x, c20xx, zz0716, Alzheimer's disease, dementia,
   human health, vaccine, trial, mice, AdvaxCpG, A-beta, aBeta, beta amyloid,
   plaque, plaques, tau, AV-1980R, AV1980R
%X "... decided to generate vaccines, targeting Abeta (AV-1959R), Tau (AV-1980R)
   or Abeta/tau (AV-1953R) B cell epitopes, based on immunogenic MultiTEP
   platform & evaluate the immunogenicity of these vaccines ...  In sum,
   AV-1959R & AV-1980R formulated with AdvaxCpG adjuvant were identified as
   promising immunogenic vaccines for ongoing pre-clinical assessment & future
   human clinical trials."
   -- [<A HREF="http://dx.doi.org/10.1038/srep28912">doi:10.1038/srep28912</A>]['16].

%A J. P. Beauchamp
%T Genetic evidence for natural selection in humans in the contemporary
   United States
%J PNAS
%V 113
%N 28
%P 7774-7779
%M JUL
%D 2016
%K jrnl, PNAS, MolBio, c2016, c201x, c20xx, zz0716, human, evolution, GWAS,
   natural selection, educational attainment, level, education, menopause,
   reproductive success, children, USA
%X "... construct polygenic scores that use individuals' genotypes to predict
   their body mass index, educational attainment (EA), glucose concentration,
   height, schizophrenia, total cholesterol, & (in females) age at menarche. I
   then examine associations between these scores & fitness to test whether
   natural seln has been occurring. My study sample includes individuals of
   European ancestry born between 1931 and 1953 who participated in the Health
   and Retirement Study, a representative study of the US population. My results
   imply that natural selection has been slowly favoring lower EA in both
   females & males, and are suggestive that natural selection may have favored
   a higher age at menarche in females. For EA, my estimates imply a rate of
   selection of about -1.5 mo of education per generation (which pales in
   comparison with the increases in EA observed in contemporary times). Although
   they cannot be projected over more than one generation, my results provide
   additional evidence that humans are still evolving - albeit slowly, esp.
   compared with the rapid changes that have occurred over the past few
   generations due to cultural & environmental factors."
      "... Both females and males who had no children have a sig. higher mean
      score of EA than those who had one or more children ... my est. of a
      directional seln differential of EA of about -1.5 mo of education per
      generation pales in comparison with the increase of 6.2y in the mean
      level of EA ... for native-born Americans born between 1876 & 1951 ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1600398113">doi:10.1073/pnas.1600398113</A>]['16],
      [<A HREF="http://www.pnas.org/content/113/28/7774">pnas</A>]['16].

%A M. C. Weiss
%A F. L. Sousa
%A N. Mrnjavac
%A S. Neukirchen
%A M. Roettger
%A S. Nelson-Sathi
%A W. F. Martin
%T The physiology and habitat of the last universal common ancestor
%J Nature Microbiol.
%V 1
%P #16116
%M JUL
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0816, biol, evolution, LUCA, origins,
   life, progenote, genes, archaea, bacteria, prokaryote, microbe
%X "... investigated all clusters & phylogenetic trees for 6.1 million protein
   coding genes from sequenced prokaryotic genomes in order to reconstruct the
   microbial ecology of LUCA. Among 286,514 protein clusters, we identified 355
   protein families (~0.1%) that trace to LUCA by phylogenetic criteria. Because
   these proteins are not universally distributed, they can shed light on LUCA's
   physiology. Their fns, properties & prosthetic groups depict LUCA as
   anaerobic, CO2-fixing, H2-dependent with a Wood-Ljungdahl path-way, N2-fixing
   & thermophilic. LUCA's biochemistry was replete with FeS clusters & radical
   reaction mechanisms. Its cofactors reveal dependence upon transition metals,
   flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin,
   corrins & selenium. Its genetic code required nucleoside modifications &
   S-adenosyl methionine-dependent methylations. The 355 phylogenies identify
   clostridia & methanogens, whose modern lifestyles resemble that of LUCA, as
   basal among their respective domains. LUCA inhabited a geochemically active
   environment rich in H2, CO2 & iron. The data support the theory of an
   autotrophic origin of life involving the W.-L. path-way in a hydrothermal
   setting."    [i.e., 355 genes.]
   -- [<A HREF="http://dx.doi.org/10.1038/nmicrobiol.2016.116">doi:10.1038/nmicrobiol.2016.116</A>]['16],
   &  WFM@[<A HREF="http://www.molevol.hhu.de/en/prof-dr-w-f-martin.html">hhu.de</A>]['16].
   [Also search for: MolBio LUCA].

%A Zhicheng Ji
%A Hongkai Ji
%T TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq
   analysis
%J NAR
%V 44
%N 13
%P e117
%M JUL
%D 2016
%K jrnl, eJrnl, MolBio, c2016, c201x, c20xx, zz0720, single cell RNA seq,
   RNAseq, scRNAseq, expression, time series, timeSeries, trajectory alignment
%X "... Tools for Single Cell Analysis (TSCAN) is a s/w tool [for] in silico
   pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis. ... uses a
   cluster-based min.span.tr. (MST) approach to order cells. Cells are
   1st grouped into clusters & an MST is then constructed to connect cluster
   centers. Pseudo-time is obtained by projecting each cell onto the tree, & the
   ordered seq. of cells can be used to study dynamic changes of gene expression
   along the pseudo-time. Clustering cells before MST construction reduces the
   complexity of the tree space. ... often leads to improved cell ordering. ..."
   -- [<A HREF="https://doi.org/10.1093/nar/gkw430">doi:10.1093/nar/gkw430</A>]['20].
   Also see TSCAN@[<A HREF="https://github.com/zji90/TSCAN">g'thub</A>]['20].
   (Also see RNAseq@[<A HREF="https://en.wikipedia.org/wiki/RNA-Seq">wikip</A>]['20].)
   [Also search for: scRNAseq].

%A R. F. Service
%T This protein designer aims to revolutionize medicines and materials
%J Science
%M JUL
%D 2016
%K news, views, MolBio, c2016, c201x, c20xx, zz1016, Baker, UWashington,
   protein, proteins, 3D, structure, prediction, fold, folding,
   ab initio modeling, design, abInitio, Rosetta
%X "...an ab initio folding program called Rosetta, which broke new ground by
   scanning a target protein for short amino acid stretches that typically fold
   in known patterns and using that information to help pin down the molecule's
   overall 3D configuration. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaf5862">doi:10.1126/science.aaf5862</A>]['16].

%A O. Tenaillon
%A et al ...
%A R. E. Lenski
%T Tempo and mode of genome evolution in a 50,000-generation experiment
%J Nature
%V 536
%N 7615
%P 165-170
%M AUG
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0816, evolution, Ecoli, genome,
   mutation, mutations, selection, bottleneck
%X "... analysed 264 complete genomes from 12 E.coli populations to characterize
   their dynamics over 50,000 generations. The popns that retained the ancestral
   mutation rate support a model in which most fixed mutns are beneficial, the
   fraction of beneficial mutns declines as fitness rises, & neutral mutns
   accumulate at a constant rate. We also compared these popns to
   mutn-accumulation lines evolved under a bottlenecking regime that minimizes
   selection. Nonsynonymous mutns, intergenic mutns, insertions & deletions are
   overrepresented in the long-term popns, further supporting the inference that
   most mutns that reached high frequency were favoured by selection. These
   results illuminate the shifting balance of forces that govern genome
   evolution in populations adapting to a new environment."
   -- [<A HREF="http://dx.doi.org/10.1038/nature18959">doi:10.1038/nature18959</A>]['16].

%A P. L. Lockwood
%A M. A. J. Apps
%A V. Valton
%A E. Viding
%A J. P. Roiser
%T Neurocomputational mechanisms of prosocial learning and links to empathy
%J PNAS
%V ?
%P ?-?
%M AUG
%D 2016
%K jrnl, PNAS, c2016, c201x, c20xx, zz0816, human behaviour, empathy, kindness,
   generosity, generous, reward, brain, social, prosocial,
   subgenual anterior cingulate cortex, sgACC
%X "... To behave prosocially we must learn the consequences of our actions for
   other people. Empathy, the ability to vicariously experience & understand the
   affect of others, is hypothesized to be a critical facilitator of prosocial
   behaviors, but the link between empathy & prosocial behavior is still
   unclear. During functional magnetic resonance imaging (fMRI) participants
   chose between different stimuli that were probabilistically associated with
   rewards for themselves (self), another person (prosocial), or no one
   (control). Using computational modeling, we show that people can learn to
   obtain rewards for others but do so more slowly than when learning to obtain
   rewards for themselves. fMRI revealed that activity in a posterior portion of
   the subgenual anterior cingulate cortex/basal forebrain (sgACC) drives
   learning only when we are acting in a prosocial context & signals a
   prosocial prediction error conforming to classical principles of
   reinforcement learning theory. ..."  [online Aug 2016.]
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1603198113">doi:10.1073/pnas.1603198113</A>]['16].
   [Also search for: IPD dilemma].

%A M. Lek
%A et al ...
%A D. G. MacArthur
%Q Exome Aggregation Consortium
%T Analysis of protein-coding genetic variation in 60,706 humans
%J Nature
%V 536
%V 7616
%P 285-291
%M AUG
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0816, exome, database, DB, human, DNA,
   protein, health, variations, mutations, genes, risk, risks, disease
%X "... describe the aggregation & analysis of high-quality exome
   (protein-coding region) DNA seq. data for 60,706 individuals of diverse
   ancestries generated as part of the Exome Aggregation Consortium (ExAC). ...
   contains an avg of one variant every eight bases of the exome, & provides
   direct evidence for the presence of widespread mutational recurrence. ...
   used this catalogue to calculate objective metrics of pathogenicity for
   seq. variants, & to identify genes subject to strong selection against
   various classes of mutation; identifying 3,230 genes with near-complete
   depletion of predicted protein-truncating variants, with 72% of these genes
   having no currently established human disease phenotype. Finally, we demo.
   that these data can be used for the efficient filtering of candidate
   disease-causing variants, & for the discovery of human 'knockout' variants
   in protein-coding genes."
   -- [<A HREF="http://dx.doi.org/10.1038/nature19057">doi:10.1038/nature19057</A>]['16].

%A N. Ostrov
%A et al
%A G. M. Church
%T Design, synthesis, and testing toward a 57-codon genome
%J Science
%V 353
%N 6301
%P 819-822
%M AUG
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0816, codons, genetic code, life, Ecoli
%X "... report computational design, synthesis, & progress toward assembly of a
   3.97-megabase, 57-codon Escherichia coli genome in which all 62,214 instances
   of seven codons were replaced with synonymous alternatives across all
   protein-coding genes. We have validated 63% of recoded genes by individually
   testing 55 segments of 50 kilobases each. ... 91% of tested essential genes
   retained functionality with limited fitness effect. We demonstrate
   identification & correction of lethal design exceptions, only 13 of which
   were found in 2229 genes. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaf3639">doi:10.1126/science.aaf3639</A>]['16].

%A M. Ziemann
%A Y. Eren
%A A. El-Osta
%T Gene name errors are widespread in the scientific literature
%J Genome Biology
%V 17
%P 177
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0916, microsoft, excel, xls, xlsx, tsv,
   spreadsheet, file, software, genes, error, scientific research, papers
%X "The spreadsheet software Microsoft Excel, when used with default settings,
   is known to convert gene names to dates and floating-point numbers. A
   programmatic scan of leading genomics journals reveals that ~ one-fifth of
   papers with supplementary Excel gene lists contain erroneous gene name
   conversions."
   -- [<A HREF="http://dx.doi.org/10.1186/s13059-016-1044-7">doi:10.1186/s13059-016-1044-7</A>]['16].

%A J. Sevigny
%A et a ...
%A A. Sandrock
%T The antibody aducanumab reduces ABeta plaques in Alzheimer's disease
%J Nature
%V 537
%N 7618
%P 50-56
%M SEP
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0916, Alzheimers disease, ABeta, Amyloid beta,
   plaque, dementia, human, health, aducanumab, drug, phase2, memory
%X "... deposition of amyloid-beta (Abeta) plaques & neurofibrillary tangles in
   the brain ... Antibody-based immunotherapy against Abeta to trigger its
   clearance or mitigate its neurotoxicity has so far been unsuccessful. Here we
   report the generation of aducanumab, a human monoclonal antibody that
   selectively targets aggregated Abeta. In a transgenic mouse model of AD,
   aducanumab is shown to enter the brain, bind parenchymal Abeta, & reduce
   soluble & insoluble Abeta in a dose-dependent manner. In patients with
   prodromal or mild AD, one year of monthly intravenous infusions of aducanumab
   reduces brain Abeta in a dose- & time-dependent manner. This is accompanied
   by a slowing of clinical decline measured by Clinical Dementia Rating - Sum
   of Boxes & Mini Mental State Examination scores. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature19323">doi:10.1038/nature19323</A>]['16].
   (Also see the bbc[<A HREF="http://www.bbc.com/news/health-37222863">31/8/2016</A>].)

%A L. Pagani
%A et al ...
%A M. Metspalu
%T Genomic analyses inform on migration events during the peopling of Eurasia
%J Nature
%V ?
%N ?
%P ?-?
%M SEP
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0916, human evolution, out of Africa,
   population, early, origins, spread, migration, Papuan, EGDP
%X "... present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a
   dataset of 483 high-coverage human genomes from 148 popns worldwide, inc.
   379 new genomes from 125 popns, which we group into diversity & seln sets. We
   analyse this dataset to refine estimates of continent-wide patterns of
   heterozygosity, long- & short-distance gene flow, archaic admixture, &
   changes in effective popn size through time as well as for signals of +ve or
   balancing selection. We find a genetic signature in present-day Papuans that
   suggests that at least 2% of their genome originates from an early & largely
   extinct expansion of anatomically modern humans (AMHs) out of Africa. ...
   with evidence from the western Asian fossil record, & admixture between AMHs
   & Neanderthals predating the main Eurasian expansion, our results contribute
   to the mounting evidence for the presence of AMHs out of Africa earlier than
   75,000 years ago."  [online 9/2016.]
   -- [<A HREF="http://dx.doi.org/10.1038/nature19792">doi:10.1038/nature19792</A>]['16].

%A P.-S. Huang
%A S. E. Boyken
%A D. Baker
%T The coming of age of de novo protein design
%J Nature
%V 537
%P 320-327
%M SEP
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz1016, protein, 3D, structure,
   ab initio, prediction, de novo, inSilico, design, Rosetta
%X "There are 20^200 possible amino-acid seqs. for a 200-residue protein, of
   which the natural evolutionary process has sampled only an infinitesimal
   subset. De novo p.design explores the full seq. space, guided by the physical
   principles that underlie p.folding. Computational methodology has advanced to
   the point that a wide range of structures can be designed from scratch with
   atomic-level accuracy. Almost all p.engineering so far has involved the
   modification of naturally occurring proteins; it should now be possible to
   design new functional proteins from the ground up to tackle current
   challenges in biomedicine & nanotechnology."
   -- [<A HREF="http://dx.doi.org/10.1038/nature19946">doi:10.1038/nature19946</A>]['16].

%A J. M. Dybas
%A A. Fiser
%T Development of a motif-based topology-independent structure comparison method
   to identify evolutionarily related folds
%J Proteins: Structure, Function, and Bioinformatics
%I Wiley
%V 84
%N 12
%P ?-?
%M SEP
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0418, SmotifCOMP, protein, structure,
   fold, super-secondary-structure, motif, library
%X "... describe a novel, super-secondary-structure motif-based,
   topology-independent structure comparison method (SmotifCOMP) that is able to
   quantitatively identify structural relationships between disparate
   topologies. The basis of SmotifCOMP is a systematically defined SSS motif
   library whose representative geometries are shown to be saturated in the
   PDB & exhibit a unique distn within the known folds. SmotifCOMP offers a
   robust & quantitative technique to compare domains that adopt different
   topologies since [it] does not rely on a global superposition.  SmotifCOMP is
   used to perform an exhaustive comparison of the known folds & the identified
   relationships are used to produce a nonhierarchical repn of the fold space
   that reflects the notion of a cts & connected fold universe. ..."
   -- [<A HREF="https://doi.org/10.1002/prot.25169">doi:10.1002/prot.25169</A>]['18],
   &  PMC5118133@[<A HREF="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118133/">ncbi</A>]['18].
   [Also search for: MolBio protein structure motif].

%A E. C. Hayden
%T A radical revision of human genetics. Why many 'deadly' gene mutations are
   turning out to be harmless
%J Nature
%V 538
%N 762
%P 154-157
%M OCT
%D 2016
%K news, views, MolBio, c2016, c201x, c20xx, zz1016, gene, genes, genetic,
   mutation, human health, risk, disease, diseases, D178N, prion,
   Exome Aggregation Consortium, ExAC
%X "Lurking in the genes of the average person are about 54 mutations that look
   as if they should sicken or even kill their bearer. But they don't. Sonia
   Vallabh hoped that D178N was one such mutation. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/538154a">doi:10.1038/538154a</A>]['16].
   [Also search for: prion disease].

%A A.-S. Malaspinas
%A et al ...
%A E. Willerslev
%T A genomic history of Aboriginal Australia
%J Nature
%V 538
%N 762
%P 207-214
%M OCT
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz1016, Australia, Aborigine, Koori,
   Papua New Gionea, PNG, Papuan, Pama Nyungan, history, human, evolution,
   origins
%X "... generate high-coverage genomes for 83 Aboriginal Australians (speakers
   of Pama-Nyungan languages) & 25 Papuans from the New Guinea Highlands. We
   find that Papuan & A.Australian ancestors diversified 25-40 thousand years
   ago (kya), suggesting pre-Holocene popn structure in the ancient continent of
   Sahul (Au., New Guinea & Tasmania). However, all of the studied A.Australians
   descend from a single founding popn that differentiated ~10-32 kya. We infer
   a popn expansion in NE Australia during the Holocene epoch (past 10,000
   years) assoc. with limited gene flow from this region to the rest of
   Australia, consistent with the spread of the Pama-Nyungan languages. We
   estimate that A.Australians & Papuans diverged from Eurasians 51-72 kya,
   following a single out-of-Africa dispersal, & subsequently admixed with
   archaic popns. Finally, we report evidence of selection in A.Australians
   potentially assoc. with living in the desert."
   -- [<A HREF="http://dx.doi.org/10.1038/nature18299">doi:10.1038/nature18299</A>]['16].

%A R. Elhesha
%A T. Kahveci
%T Identification of large disjoint motifs in biological networks
%J BMC Bioinformatics
%V ?
%M OCT
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz1016, network, motif, SUBDUE, FSG,
   discovery
%X "... Often, different copies of a given motif topology in a n/w share nodes
   or edges. ... develop a scalable alg. for finding n/w motifs. Unlike most of
   the existing studies, [it] counts independent copies of each motif topology.
   We introduce a set of small patterns & prove that we can construct any larger
   pattern by joining those patterns iteratively. By iteratively joining already
   identified motifs with those patterns, our alg. avoids (i) constructing
   topologies which do not exist in the target network (ii) repeatedly counting
   the freq. of the motifs generated in subsequent iterations. Our experiments
   on real & synthetic n/ws demonstrate that our method is sig. faster & more
   accurate than the existing methods including SUBDUE & FSG."
   -- [<A HREF="http://dx.doi.org/10.1186/s12859-016-1271-7">doi:10.1186/s12859-016-1271-7</A>]['16].
   [Also search for: network motif].

%A N. L Bray
%A H. Pimentel
%A P. Melsted
%A L. Pachter
%T Near-optimal probabilistic RNA-seq quantification
%J Nat. Biotech.
%V 34
%P 525-527
%M APR
%D 2016
%K MolBio, jrnl, c2016, c201x, c20xx, zz0820, kallisto, RNAseq, PseudoAlignment,
   pseudo, mRNA, mapping, reference
%X "... kallisto, an RNA-seq quantification program that is two orders of
   magnitude faster than prev. approaches & achieves similar accuracy. Kallisto
   pseudoaligns reads to a reference, producing a list of transcripts that are
   compatible with each read while avoiding alignment of individual bases. We
   use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in
   < 10 min on a standard laptop computer. This removes a major computational
   bottleneck in RNA-seq analysis."
   -- [<A HREF="http://dx.doi.org/10.1038/nbt.3519">doi:10.1038/nbt.3519</A>]['20].
   [Also search for: PseudoAlignment].

%A D. van Dijk
%A et al ...
%A D. Pe'er
%T MAGIC: A diffusion-based imputation method reveals gene-gene interactions in
   single-cell RNA-sequencing data
%J bioRxiv
%M FEB
%D 2017
%O Cell 174(3), pp.716-729, 26/7/2018 [<A HREF="http://dx.doi.org/10.1016/j.cell.2018.05.061">doi:10.1016/j.cell.2018.05.061</A>]['20].
%K MAGIC, MolBio, c2017, c201x, c20xx, zz0820, Dana Peer, scRNAseq, scRNA seq,
   impute, imputation, abundance, zero, dropout, colinearity, manifold,
   nearest neighbour, trajectory, diffusion, graph, cell, cells, gene expression
%X "... scRNA-seq technologies suffer from many sources of sig. technical noise,
   the most prominent of which is 'dropout' due to inefficient mRNA capture. ...
   MAGIC (Mark'v Affinity-based Graph Imputation of Cells), a method for
   imputing missing values, & restoring the structure of the data. After MAGIC,
   we find that two- & three-D gene interactions are restored & that MAGIC is
   able to impute complex & non-linear shapes of interactions ..."
   -- [<A HREF="http://dx.doi.org/10.1101/111591">doi:10.1101/111591</A>]['20].
   (A seminar@[<A HREF="https://www.youtube.com/watch?v=8KpIDpPEGV4&feature=emb_rel_err">ubend</A>]['20].)
   [Also search for: scRNAseq].

%A R. Patro
%A et al ...
%A C. Kingsford
%T Salmon: Fast and bias-aware quantification of transcript expression using
   dual-phase inference
%J Nat. Methods
%V 14
%P 417-419
%M MAR
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0820, scRNAseq, scRNA seq, RNAseq,
   Salmon, pseudo, PseudoAlignment, map mRNA reference, gene expression profile
%X "... Salmon, a lightweight method for quantifying transcript abundance from
   RNA-seq reads. Salmon combines a new dual-phase parallel inference alg. &
   feature-rich bias models with an ultra-fast read mapping procedure. ... the
   1st transcriptome-wide quantifier to correct for fragment GC-content bias,
   which, as we demo. here, substantially improves the accuracy of abundance
   estimates & the sensitivity of subsequent differential expression analysis."
   -- [<A HREF="http://dx.doi.org/10.1038/nmeth.4197">doi:10.1038/nmeth.4197</A>]['20].
   [Also search for: PseudoAlignment].

%T 80th Anniversary of the Harvard study of adult development (HSAD)
%M APR
%D 2017
%K TR, news, c2017, c201x, c20xx, zz0123, HSAD, human, development, behaviour,
   happiness, health, stats
%X Anniversary [<A HREF="https://news.harvard.edu/gazette/story/2017/04/over-nearly-80-years-harvard-study-has-been-showing-how-to-live-a-healthy-and-happy-life/">www</A>]['23].
   *HSAD [<A HREF="https://www.adultdevelopmentstudy.org/">www</A>]['23].

%T O. Rozenblatt-Rosen
%A M. J. T. Stubbington
%A A. Regev
%A S. A. Teichmann
%T The Human Cell Atlas: from vision to reality
%J Nature
%V 550
%P 451-453
%M OCT
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz1117, human, cell, cells, www, HREF,
   cellAtlas
%X "Our knowledge of the cells that make up the human body, and how they vary
   from person to person, or throughout development and in health or disease,
   is still very limited. This week, a year after project planning began ..."
   -- [<A HREF="https://doi.org/10.1038/550451a">doi:10.1038/550451a</A>]['17].
   Home page: [<A HREF="https://www.humancellatlas.org/">humancellatlas</A>]['17].

%A E. Qi
%A D. Wang
%A B. Gao
%A Y. Li
%A G. Li
%T Block-based characterization of protease specificity from substrate sequence
   profile
%J BMC Bioinformatics
%V 18
%N #438
%M OCT
%D 2017
%K MolBio, jrnl, c2017, c201x, c20xx, zz0820, protease, distance, cleave, pops,
   cleaves, cleaving, cleavage, site, profile, sites, substrate, specificity,
   octopeptide, prosper, MEROPS
%X "... propose a novel block-based approach to reveal the potential combns of
   [AAs] which may regulate the action of proteases. Using the entropies of
   eight blocks centered at a cleavage bond, we created a distance matrix for
   61 proteases to compare their specificities. After quantitative analysis, we
   discovered a # of prominent blocks, each of which consists of successive
   [AAs] near a cleavage bond, intuitively characterizing the site cooperation
   of the substrate sequences.  ..."
   -- [<A HREF="https://doi.org/10.1186/s12859-017-1851-1">doi:10.1186/s12859-017-1851-1</A>]['20].
   [Also search for: protease specificity].
   (Also see [<A HREF="https://www.ebi.ac.uk/merops/">MEROPS</A>]['20].)

%A G. La Manno
%A et al ...
%A S. Linnarsson
%T Molecular diversity of midbrain development in mouse, human, and stem cells
%J Cell
%V 167
%N 2
%P 566-580.e19
%M OCT
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0720, LaManno, human, mouse, brain,
   glia, stem cells, stemCell, scRNA-seq, scRNAseq
%X "... We performed single-cell RNA seq. to examine ventral midbrain
   development in human & mouse. We found 25 molecularly defined human cell
   types, inc. five subtypes of radial glia-like cells & four progenitors. In
   the mouse, two mature fetal dopaminergic neuron subtypes diversified into
   five adult classes during postnatal development. Cell types & gene expression
   were generally conserved across species, but with clear differences in cell
   proliferation, developmental timing, & dopaminergic neuron development. ..."
   -- [<A HREF="https://doi.org/10.1016/j.cell.2016.09.027">doi:10.1016/j.cell.2016.09.027</A>].
   [Also search for: MolBio stem cell].

%A A. R. Hoelzel
%T The road to speciation runs both ways
%J Science
%V 354
%N 6311
%P 414-415
%M OCT
%D 2016
%K news, c2016, c201x, c20xx, zz1016, genes, gene exchange, animal, species,
   evolution, bonobo, Pan paniscus, chimpanzee, Pan troglodytes, chimp
%X "Some species, such as the giraffe or bottlenose dolphin, are immediately
   recognizable & might seem immutable. In fact, their evolutionary stories are
   often more complicated. Regional populations of giraffe with distinct pelage
   patterns have only recently been recognized as four different species. ...
   de Manuel et al.[<A HREF="http://dx.doi.org/10.1126/science.aag2602">www</A>] describe the relationship between two other iconic species
   in unprecedented detail, comparing whole genomes from populations of bonobo
   (Pan paniscus) & chimpanzee (Pan troglodytes). They report evidence for gene
   flow between these species, contributing to our increasing appreciation for
   the complexities of the process of speciation. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaj2007">doi:10.1126/science.aaj2007</A>]['16].

%A T. Muramatsu
%A et al ...
%A S. Yokoyama
%T SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel
   subsite cooperativity
%J PNAS
%V 113
%N 46
%P 12997-13002
%M NOV
%D 2016
%K jrnl, PNAS, MolBio, c2016, c201x, c20xx, zz0720, SARS CoV 1, SARS1, 3CLpro,
   Mpro, protease, cleave, cleaves, cleaving, polyprotein, pp1a, pp1b, works,
   working, specificity, Cys, Cys145, site, sites, concensus, profile
%X "The 3C-like protease (3CLpro) of severe acute respiratory syndrome
   coronavirus (SARS-CoV) cleaves 11 sites in the polyproteins, inc. its own
   N- and C-terminal autoprocessing sites, by recognizing P4-P1 and P1'. In this
   study, we determined the crystal structure of 3CLpro with the C-terminal
   prosequence & the catalytic-site C145A mutation, in which the enzyme binds
   the C-terminal prosequence of another molecule. ..."
    [cleaves RQCSGVTFQGKFKKIVKG,
             TSITSAVLQSGFRKMAFP,
             PCIKVATVQSKMSDVKCT,
             MLDNRATLQAIASEFSSL,
             RANSAVKLQNNELSPVAL,
             SLAATVRLQAGNATEVPA,
             DQLREPLMQSADASTFLN,
             MYTPHTVLQAVGACVLCN,
             PRRNVATLQAENVTGLFK,
             LWNTFTRLQSLENVAYNV,
             VETFYPKLQASQAWQPGV, after the Q I think. & concensus logo profile]
   -- [<A HREF="https://doi.org/10.1073/pnas.1601327113">doi:10.1073/pnas.1601327113</A>]['20].
   [Also search for: MolBio SARS Mpro cleaves].

%A M. Worobey
%A et al ...
%A H. W. Jaffe
%T 1970s and 'Patient 0' HIV-1 genomes illuminate early HIV/AIDS history in
   North America
%J Nature
%V 539
%N 7627
%P 98-101
%M NOV
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz1116, virus, viral, HIV 1, HIV1,
   genomes, DNA, AIDS, evolution, phologeny, phylogenetic, patient0
%X "... We serologically screened > 2,000 1970s serum samples & developed a
   highly sensitive approach for recovering viral RNA from degraded archival
   samples. ... report eight coding-complete genomes from US serum samples from
   1978-1979 - eight of the nine oldest HIV-1 group M genomes to date. This
   early, full-genome 'snapshot' reveals that the US HIV-1 epidemic exhibited
   extensive genetic diversity in the 1970s but also provides strong evidence
   for its emergence from a pre-existing Caribbean epidemic. Bayesian
   phylogenetic analyses estimate the jump to the US at ~1970 & place the
   ancestral US virus in New York City with 0.99 posterior prob. support,
   strongly suggesting this was the crucial hub of early US HIV/AIDS
   diversification. ... We also recovered the HIV-1 genome from the individual
   known as 'Patient 0' (ref. 5) & found neither biol. nor historical evidence
   that he was the primary case in the US or for subtype B as a whole ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature19827">doi:10.1038/nature19827</A>]['16].

%A R. Rizzi
%A M. Cairo
%A V. Makinen
%A D. Valenzuela
%T Diploid alignment is NP-hard
%J arXiv
%M NOV
%D 2016
%K TR, MolBio, c2016, c201x, c20xx, zz1116, diploid, genome, alignment,
   sequence, labelled DAG
%X "... Sequence analysis literature is, however, almost solely built under the
   model of a single haplotype seq. representing a species. ... we show that not
   only raising the abstraction level creates conceptual difficulties, but also
   the computational complexity will change for a natural non-trivial extension
   of optimal alignment to diploids. ... can also be seen as an extension of
   seq.alignment to labelled directed acyclic graphs (labeled DAGs). Namely, we
   show that a covering alignment of two labeled DAGs is NP-hard. A covering
   al. is to find two paths P1(A) & P2(A) in DAG A & two paths P1(B) & P2(B) in
   DAG B that cover the nodes of the graphs & maximize sum of the global al.
   scores: S(L(P1(A)),L(P1(B)))+S(L(P2(A)),L(P2(B))), where L(P) is the
   concatenation of labels on the path P. Pair-wise al. of haplotype seqs.
   forming a diploid chromosome can be converted to a two-path coverable
   labelled DAG, & then the covering al. models the similarity of two diploids
   over arbitrary recombination."
   -- 1611.05086@[<A HREF="https://arxiv.org/abs/1611.05086">arXiv</A>]['16].

%A C. O. Mackenzie
%A J. Zhou
%A G. Grigoryan
%T Tertiary alphabet for the observable protein structural universe
%J PNAS
%D 2016
%M NOV
%V 113
%N (47)
%P E7438-E7447
%K jrnl, PNAS, MolBio, c2016, c201x, c20xx, zz0218, protein, tertiary,
   structure, fold, folding, building blocks, motifs, patterns, TERMs
%X "... we decompose the set of known protein structures into standard reusable
   building blocks, which we call ter.struct. motifs (TERMs). Strikingly,
   we find that only ~600 TERMs describe 50% of the known protein structural
   universe at sub-Angstrom resolution. Furthermore, we find the natural
   utilization of TERMs gives us a means of uncovering sequence-structure
   relationships. ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.1607178113">doi:10.1073/pnas.1607178113</A>]['18].
   [Also search for: MolBio protein structure pattern].

%A P. Mitteroeckera
%A S. M. Huttegger
%A B. Fischer
%A M. Pavlicev
%T Cliff-edge model of obstetric selection in humans
%J PNAS
%V ?
%M DEC
%D 2016
%K jrnl, PNAS, c2016, c201x, c20xx, zz1216, human evolution, pelvis, fetus,
   Caesarean section, birth canal, fitness, head, size, fetopelvic, medicine,
   baby, mother, maternal
%X "Compared with other primates, human childbirth is difficult because the
   fetus is large relative to the maternal pelvic canal. It is a long-standing
   evolutionary puzzle why the pelvis has not evolved to be wider ...  present
   a math. model that explains the high rates of fetopelvic disproportion by
   the discrepancy between a wide symmetric phenotype distribution & an
   asymmetric, 'cliff-edged' fitness fn. Only weak seln for a large newborn, a
   narrow pelvis, or both is necessary to account for the high incidence of
   fetopelvic disproportion. Because the regular use of Caesarean sections has
   reduced maternal mortality, the model predicts an evol. response of fetal or
   maternal dimensions, increasing the rates of fetopelvic disproportion."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1612410113">doi:10.1073/pnas.1612410113</A>]['16], [online 5/12/2016].
   (Also see, "... Over the past 50 or 60 years, this rate has increased
    to about 3.3-3.6%, so up to 36 in 1,000 births. ..."
    -- [<A HREF="http://www.bbc.com/news/science-environment-38210837">bbc</A>][6/12/2016].)

%A M. Florio
%A T. Namba
%A S. Paabo
%A M. Hiller
%A W. B. Huttner
%T A single splice site mutation in human-specific ARHGAP11B causes
   basal progenitor amplification
%J Sci. Adv.
%V 2
%N 12
%P e1601941
%M DEC
%D 2016
%K eJrnl, MolBio, c2016, c201x, c20xx, zz1216, human, brain, homo sapiens,
   DNA, gene, mutation, size, evolution, RhoGAP, neocortex, ARHGAP11B
%X "The gene ARHGAP11B promotes basal progenitor amplification and is
   implicated in neocortex expansion. It arose on the human evolutionary lineage
   by partial duplication of ARHGAP11A, which encodes a Rho guanosine
   triphosphatase activating protein (RhoGAP). However, a lack of 55 nucleotides
   in ARHGAP11B mRNA leads to loss of RhoGAP activity by GAP domain truncation
   and addition of a human-specific carboxy-terminal amino acid sequence. We
   show that these 55 nucleotides are deleted by mRNA splicing due to a single
   C->G substn that creates a novel splice donor site. We reconstructed an
   ancestral ARHGAP11B complementary DNA without this substitution. Ancestral
   ARHGAP11B exhibits RhoGAP activity but has no ability to increase basal
   progenitors during neocortex development. Hence, a single nucleotide
   substitution underlies the specific properties of ARHGAP11B that likely
   contributed to the evolutionary expansion of the human neocortex."
   -- [<A HREF="http://dx.doi.org/10.1126/sciadv.1601941">doi:10.1126/sciadv.1601941</A>]['16], open.

%A A. Caspi
%A et al ...
%A T. E. Moffitt
%T Childhood forecasting of a small segment of the population with
   large economic burden
%J Nature Human Behaviour
%V 1
%N 0005
%M DEC
%D 2016
%K jrnl, c2016, c201x, c20xx, zz1216, human, health, brain, development,
   Dunedin longitudinal study, NZ, stats, correlation
%X "The Dunedin Study research team reports that a small segment of the
   population accounts for a disproportionate share of costly service use in a
   society's health-care, criminal-justice, and social welfare systems, and that
   these adults can be identified as young as age 3 years by paediatric tests of
   brain health. ... cohort of 1,000 children born in one city, from birth to
   midlife. The strong connection between early-childhood development and costly
   adult outcomes underscores the need for preventive health and education
   programs for children and families."
   -- [<A HREF="http://dunedinstudy.otago.ac.nz/news-and-events/article/53">www</A>]['16].
   Paper@[<A HREF="http://dx.doi.org/10.1038/s41562-016-0005">doi:10.1038/s41562-016-0005</A>]['16].
   Also see the [<A HREF="http://www.bbc.com/news/health-38281663">bbc</A>][13/12/2016].
   (?Eugenics not.?)

%A S. Shukla
%A et al
%T The Onion Genomic Resource: A genomics and bioinformatics driven resource for
   onion breeding
%J Plant Gene
%V 8
%P 9-15
%M DEC
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0717, plant, onion, Allium cepa L.,
   onions, crop, genome, nGenome, OGR
%X "... one of the most challenging plant species to be worked on ... houses
   information of assembly of 20,204 publicly available onion expressed sequence
   tags (ESTs), available 20,755 assembled transcripts and 249,987 unigenes from
   Allium cepa transcriptome shotgun assembly (TSA) along with their annotations
   and functional significance. ..."
   -- [<A HREF="https://doi.org/10.1016/j.plgene.2016.09.003">doi:10.1016/j.plgene.2016.09.003</A>]['17].
   Also see oniongenome.[<A HREF="http://www.oniongenome.net/">net</A>]['17].
   (NB. about 15GB! human 3GB.)

%A S. Ovchinnikov
%A et al ...
%A D. Baker
%T Protein structure determination using metagenome sequence data
%J Science
%V 355
%N 6322
%P 294-298
%M JAN
%D 2017
%K MolBio, jrnl, c2017, c201x, c20xx, zz0117, Rosetta, protein structure,
   prediction, fold, folds, folding, 3D, contacts, families
%X "... there are still ~5200 protein families with unknown structure outside
   the range of comparative modeling. We show that Rosetta structure prediction
   guided by residue-residue contacts inferred from evol. info. can accurately
   model proteins that belong to large families & that metagenome seq. data
   more than triple the # of protein families with sufficient seqs. for
   accurate modeling. We then integrate metagenome data, contact-based
   structure matching, & Rosetta structure calculations to generate models for
   614 protein families with currently unknown structures; 206 are membrane
   proteins & 137 have folds not represented in the Protein Data Bank. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aah4043">doi:10.1126/science.aah4043</A>]['17].

%A L. M. Zahn
%A G. Riddihough
%T Building on nature's design
%J Science
%V 355
%N 6329
%P 1038-1039
%M MAR
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0317, MolBio, Saccharomyces cerevisiae, yeast,
   genome, Sc2.0, synthetic, chromosomes, eukaryotic, eukaryote
%X intro. to special issue on Synthetic Yeast Genome Project (Sc2.0)
-- [<A HREF="http://dx.doi.org/10.1126/science.355.6329.1038">doi:10.1126/science.355.6329.1038</A>]['17].

%A F. Markowetz
%T All biology is computational biology
%J PLoS Biology
%M MAR
%D 2017
%K eJrnl, jrnl, MolBio, Biol, c2017, c201x, c20xx, zz0317, bioinformatics,
   views, opinion, scientific research
%X "Here, I argue that computational thinking & techniques are so central to the
   quest of understanding life that today all biol. is comp. biol..
   Computational biol. brings order into our understanding of life, it makes
   biological concepts rigorous & testable, & it provides a reference map that
   holds together individual insights. The next modern synthesis in biol. will
   be driven by math., stat., & comp. methods being absorbed into mainstream
   biological training, turning biology into a quantitative science."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pbio.2002050">doi:10.1371/journal.pbio.2002050</A>]['17].

%A T. Koeman
%A et al ...
%A R. Vermeulen
%T Occupational exposure and amyotrophic lateral sclerosis in a
   prospective cohort
%J BMJ
%V ?
%P ?-?
%M MAR
%D 2017
%K jrnl, BMJ, c2017, c201x, c20xx, zz0417, amyotrophic lateral sclerosis, ALS,
   motor neurone disease, human health, risk, risks, electrical, magnetic,
   field, fields, ELF-MFs, ELFMFs, brain
%X "... within the prospective Netherlands Cohort Study, 58,279 men and 62,573
   women aged 55-69 years at enrolment in 1986 were followed up for 17.3 years
   on ALS mortality. ... Occupational exposure to solvents, pesticides, metals,
   extremely low frequency magnetic fields (ELF-MFs) & electrical shocks was
   estimated by means of job exposure matrices (JEMs). ... Occupational exposure
   to ELF-MF showed a possible assocn with ALS mortality among men: HR for ever
   holding a job with high exposure v. background 2.19 (95% (CI): 1.02 to 4.73)
   & HR for the highest tertile of cumulative exposure v. background 1.93
   (95% CI 1.05 to 3.55). ... strengthen the evidence suggesting a +ve
   association between ELF-MF exposure and ALS. ..."
   -- [<A HREF="http://dx.doi.org/10.1136/oemed-2016-103780">doi:10.1136/oemed-2016-103780</A>]['17].

%A J. A. Byrne
%A C. Labbe
%T Striking similarities between publications from China describing single
   gene knockdown experiments in human cancer cell lines
%J Scientometrics
%V 110
%N 3
%P 1471-1493
%M MAR
%D 2017
%K jrnl, c2017, c201x, c20xx, zz1117, MolBio, stats, China, TPD52L2, gene,
   genes, cancer, scientific research, misconduct, papers,
   science, academic, ethics, fraud, laziness, errors, retraction
%X "Comparing 5 publications from China that described knockdowns of the human
   TPD52L2 gene in human cancer cell lines identified unexpected similarities
   between these publns, flaws in experimental design, & mis-matches between
   some described experiments & the reported results. ... two of these TPD52L2
   publns have been retracted. One retraction notice stated that while the
   authors claimed that the data were original, the experiments had been
   out-sourced to a biotech. company. Using search engine queries, automatic
   text-analysis, different similarity measures, & further visual inspection,
   we identified 48 examples of highly similar papers describing single gene
   knockdowns in 1-2 human cancer cell lines that were all published by
   investigators from China. The incorrect use of a particular TPD52L2 shRNA
   sequence as a negative or non-targeting control was identified in 30/48 (63%)
   of these publns, using a combination of Google Scholar searches & visual
   inspection. Overall, these results suggest that some publns describing the
   effects of single gene knockdowns in human cancer cell lines may include the
   results of experiments that were not performed by the authors. This has
   serious implications for the validity of such results, & for their
   application in future research."
   -- [<A HREF="https://doi.org/10.1007/s11192-016-2209-6">doi:10.1007/s11192-016-2209-6</A>]['17].

%A R. Rostom
%A V. Svensson
%A S. A. Teichmann
%A G. Kar
%T Computational approaches for interpreting scRNA-seq data
%M MAY
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0720, single cell RNA seq, RNAseq,
   scRNAseq, analysis, cell types, gene expression levels
%X "... new modes of data analysis, building on high-dimensional data mining
   techniques. Here, we consider biological questions for which scRNA-seq data
   is used, both at a cell & gene level, & describe tools available for these
   types of analyses. This is an exciting & rapidly evolving field, where
   clustering, pseudotime inference, branching inference & gene-level analyses
   are particularly informative areas of computational analysis."
   -- [<A HREF="https://doi.org/10.1002/1873-3468.12684">doi:10.1002/1873-3468.12684</A>]['20].
   [Also search for: scRNAseq].

%A S. Gore
%A et al
%T Validation of structures in the Protein Data Bank
%J Structure
%V 25
%N 12
%P 1916-1927
%M DEC
%D 2017
%K MolBio, jrnl, c2017, c201x, c20xx, zz0724, validate, Validation Task Force,
   VTF, PDB, protein 3D structure, OneDep, MolProbity
%X "... OneDep data processing, validation reports for 3D structures of
   biological macromolecules are produced. ..."
   -- [<A HREF="https://doi.org/10.1016/j.str.2017.10.009">doi:10.1016/j.str.2017.10.009</A>]['24].

%A H. A. Lewin
%A et al ...
%A G. Zhang
%T Earth BioGenome Project: Sequencing life for the future of life
%J PNAS
%V 115
%N 17
%P 4325-4333
%M APR
%D 2018
%K jrnl, PNAS, MolBio, c2018, c201x, c20xx, zz1118, Earth BioGenome Project,
   EBP, DNA
%X "... present a perspective on the Earth BioGenome Project (EBP), a moonshot
   for biology that aims to sequence, catalog, and characterize the genomes of
   all of Earth's eukaryotic biodiversity over a period of 10 years. ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.1720115115">doi:10.1073/pnas.1720115115</A>]['18].
   Also see [<A HREF="https://www.earthbiogenome.org">EBP</A>]['18].

%A P. J. Yang
%A M. LaMarca
%A C. Kaminski
%A D. I. Chu
%A D. L. Hu
%T Hydrodynamics of defecation
%J Soft Matter
%V ?
%M APR
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0517, biol, biology, poo, NASA challenge
%X "... we investigate the defecation of mammals from cats to elephants using
   the dimensions of large intestines & feces, videography at Zoo Atlanta,
   cone-on-plate rheological measurements of feces & mucus, & a math. model of
   defecation. The diameter of feces is comparable to that of the rectum, but
   the length is double that of the rectum, indicating that not only the r. but
   also the colon is a storage facility for feces. Despite the length of r.
   ranging from 4 to 40cm, mammals from cats to elephants defecate within a
   nearly constant duration of 12+/-7 sec. (N=23). We rationalize this
   surprising trend by the model, which shows that feces slide along the large
   intestine by a layer of mucus, similar to a sled sliding through a chute.
   Larger animals have not only more feces but also thicker mucus layers, which
   facilitate their ejection. Our model accounts for the shorter & longer
   d.times assoc. with diarrhea & constipation, respectively. ..."
   -- [<A HREF="http://dx.doi.org/10.1039/C6SM02795D">doi:10.1039/C6SM02795D</A>]['17].
   (Runner up in the NASA poo challenge [<A HREF="https://herox.com/SpacePoop/update/1277?kme=challenge_post_email&km_challenge_post_email=1277">www</A>]['17].
   And also see [<A HREF="http://www.bbc.com/earth/story/20170427-why-do">bbc</A>][1/5/2017].)
   [Also search for: urination ignobel]. Is this a bid for another prize?

%A D. I. Bolnick
%A W. E. Stutz
%T Frequency dependence limits divergent evolution by favouring rare immigrants
   over residents
%J Nature
%V 546
%N 7657
%P 285-288
%M MAY
%D 2017
%K jrnl, biology, biol, c2017, c201x, c20xx, zz0617, evolution, parasites,
   frequency-dependent, divergent, selection, diversity, histocompatibility,
   speciation, ecology
%X "Two distinct forms of natural selection promote adaptive biological
   diversity. Divergent seln occurs when different environments favour different
   phenotypes, leading to increased differences between popns. Negative
   frequency-dependent seln occurs when rare variants within a popn are favoured
   over common ones, increasing diversity within popns. ... found -ve
   freq.-dependence: survival was highest for the locally rare ecotype, rather
   than natives. Also, individuals with locally rare major histocompatibility
   complex (MHC) class IIb genotypes were infected by fewer parasites. This
   negative freq.-dependent seln will tend to favour rare immigrants over common
   residents, amplifying the effect of migration & undermining the efficacy of
   divergent natural seln to drive popn differences. The only signal of
   divergent seln was a tendency for foreign fish to have higher parasite loads
   than residents, after controlling for MHC genotype rarity. Freq.-dependent
   ecological interactions have long been thought to promote speciation. Our
   results suggest a more nuanced view in which -ve freq. dependence alters the
   fate of migrants to promote or constrain evol. divergence between popns."
   -- [<A HREF="http://dx.doi.org/10.1038/nature22351">doi:10.1038/nature22351</A>]['17] (online 5/2017).

%A K. Street
%A et al ...
%A S. Dudoit
%T Slingshot: cell lineage and pseudotime inference for single-cell
   transcriptomics
%J BMC Genomics
%V 19
%N 477
%M JUN
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0720, single cell RNA seq, RNAseq,
   scRNAseq, expression, cell type, lineage, TSCAN, Monocle, DPT
%X "... Slingshot, a novel method for inferring cell lineages and pseudotimes
   from single-cell gene expression data. In prev. published datasets, Slingshot
   correctly identifies the biological signal for one to three branching
   trajectories. ..."
      "... first stage uses a cluster-based MST ... second stage, we propose a
      novel method called simultaneous principal curves, to fit smooth branching
      curves to these lineages ..."
   -- [<A HREF="https://doi.org/10.1186/s12864-018-4772-0">doi:10.1186/s12864-018-4772-0</A>]['20].
   (Also see RNAseq@[<A HREF="https://en.wikipedia.org/wiki/RNA-Seq">wikip</A>]['20].)
   [Also search for: scRNAseq].

%A E. Pennisi
%T Mysterious unchanging DNA finds a purpose in life
%J Science
%V 356
%N 6341
%P 892
%M JUN
%D 2017
%K news, views, c2017, c201x, c20xx, zz0617, MolBio, ultra conserved elements,
   UCE, UCEs,  DNA, ultraconserved, ARX gene, brain, development, hippocampus,
   Dickel
%X "... at the Biology of Genomes meeting here, Dickel had presented what may be
   the first compelling evidence of what these much-discussed stretches of DNA
   do. ... researchers found 481 genome segments, 200 to more than 700 bases
   long, that were 100% identical in humans, rats, and mice. These same segments
   were at least 95% identical in chickens and dogs ... At first, knocking out
   these elements, whether singly or in pairs, seemed to leave the mice
   unaffected. But when Dickel and a developmental neuroscientist took a close
   look at the brains of the mice, they detected abnormal numbers of neurons or
   a shrunken hippocampus ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.356.6341.892">doi:10.1126/science.356.6341.892</A>]['17],
      [<A HREF="http://science.sciencemag.org/content/356/6341/892.full">www</A>]['17].

%A A. M. Calvin
%A et al
%T Childhood intelligence in relation to major causes of death in
   68 year follow-up: prospective population study
%J BMJ
%V 357
%P j2708
%M JUN
%D 2017
%K jrnl, BMJ, c2017, c201x, c20xx, zz0717, human, health, medicine, IQ, ageing,
   lifespan, longevity, risks
%X "... Childhood intelligence was inversely associated with all major causes of
   death. The age and sex adjusted hazard ratios (& 95% c.i.) per 1 SD (about
   15 points) advantage in intelligence test score were strongest for
   respiratory disease (0.72, 0.70 to 0.74), coronary heart disease (0.75,
   0.73 to 0.77), and stroke (0.76, 0.73 to 0.79). Other notable associations
   (all P < 0.001) were observed for deaths from injury (0.81, 0.75 to 0.86),
   smoking related cancers (0.82, 0.80 to 0.84), digestive disease (0.82,
   0.79 to 0.86), and dementia (0.84, 0.78 to 0.90). ..."
   -- [<A HREF="https://doi.org/10.1136/bmj.j2708">doi:10.1136/bmj.j2708</A>]['17].

%A Y.-J. Feng
%A et al ...
%A P. Zhang
%T Phylogenomics reveals rapid, simultaneous diversification of three major
   clades of Gondwanan frogs at the Cretaceous-Paleogene boundary
%J PNAS
%V ?
%P ?-?
%M JUL
%D 2017
%K jrnl, PNAS, MolBio, c2017, c201x, c20xx, zz0717, animal, amphibian, Anura,
   frog, Hyloidea, Microhylidae, Natatanura, evolution, phylogenetic, tree,
   Cretaceous Paleogene bounday, K-Pg, KPg, KPB
%X "... using a molecular dataset of unprecedented size, inc. 88-kb characters
   from 95 nuclear genes of 156 frog species, [+] 20 fossil-based calibrations,
   our analyses result in the most strongly supported phylogeny of all major
   f.lineages and provide a timescale of f.evolution that suggests much younger
   divergence times than suggested by earlier studies. Unexpectedly, our
   divergence-time analyses show that three species-rich clades (Hyloidea,
   Microhylidae, & Natatanura), which together comprise ~ 88% of extant anuran
   species, simultaneously underwent rapid diversification at the
   Cretaceous-Paleogene (K-Pg) boundary (KPB) [66Mya]. [&] anuran families &
   subfamilies containing arboreal species originated near or after the KPB. ...
   suggest that the K-Pg mass extinction may have triggered explosive radiations
   of frogs by creating new ecological opportunities. ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.1704632114">doi:10.1073/pnas.1704632114</A>]['17].
   (Also see the [<A HREF="http://www.bbc.com/news/science-environment-40482039">bbc</A>][3/7/2017].)

%A K. Kupferschmidt
%T Labmade smallpox is possible, study shows
%V Science
%V 357
%N 6347
%P 115-116
%M JUL
%D 2017
%K news, views, c2017, c201x, c20xx, zz0717, MolBio, smallpox, virux, variola,
   horsepox, poliovirus, disease, risk, risks, danger, security,
   mail order, GeneArt
%X "... Ever since virologists stitched together DNA seqs to make a poliovirus
   from scratch 15 years ago - a feat that triggered an intense debate about the
   risks of synthetic biology - researchers have said the same might be possible
   for a much more complex virus that causes the most feared infectious disease
   in human history: smallpox. ... In 2016, David Evans, a virologist at the U.
   of Alberta in Edmonton, Canada, led a team that quietly synthesized horsepox,
   a virus believed to have gone extinct decades ago, from DNA fragments ordered
   online and delivered in the mail. ..."
-- [<A HREF="https://doi.org/10.1126/science.357.6347.115">doi:10.1126/science.357.6347.115</A>]['17].

%A S. Kelk
%A F. Pardi
%A C. Scornavacca
%A L. van Iersel
%T Finding the most parsimonious or likely tree in a network with respect to an
   alignment
%J arXiv
%M JUL
%D 2017
%K TR, MolBio, c2017, c201x, c20xx, zz0717, multiple sequence alignment,
   parsimony, evolutionary, phylogenetic, tree, network
%X "Phylogenetic networks are often constructed by merging multiple conflicting
   phylogenetic signals into a directed acyclic graph. It is interesting to
   explore whether a n/wk constructed in this way induces biol.-relevant
   phylogenetic signals that were not present in the input. Here we show that,
   given a multiple alignment A for a set of taxa X & a rooted phylogenetic n/wk
   N whose leaves are labelled by X, it is NP-hard to locate the most
   parsimonious ph.tree displayed by N (wrt A) even when the level of N - the
   max. # of reticulation nodes within a biconnected component - is 1 & A
   contains only 2 distinct states. (If, additionally, gaps are allowed the
   problem becomes APX-hard.) We also show that under the same condns, &
   assuming a simple binary symmetric model of character evolution, finding the
   most likely tree displayed by the n/wk is NP-hard. These -ve results contrast
   with earlier work on parsimony in which it is shown that if A consists of a
   single column the problem is fixed parameter tractable in the level. We
   conclude with a discussion of why, despite the NP-hardness, both the
   parsimony & likelihood problem can likely be well-solved in practice."
   -- 1707.03648@[<A HREF="https://arxiv.org/abs/1707.03648">arXiv</A>]['17].
   [Also search for: MolBio phylogenetic].

%A G. Rocklin
%A et al ...
%A D. Baker
%T Global analysis of protein folding using massively parallel design,
   synthesis, and testing
%J Nature
%V 357
%N 6347
%P 168-175
%M JUL
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0717, protein, fold, folds, folding,
   structure, 3D, design, Rosetta
%X "... We combined computational protein design, next-gen. gene synthesis, & a
   high-throughput protease susceptibility assay to measure folding & stability
   for > 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000
   point mutants, & 30,000 -ve control seqs.. ... identified > 2500 stable
   designed proteins in four basic folds - a # sufficient to enable us to
   systematically examine how seq. determines folding & stability in uncharted
   protein space. Iteration between design & experiment increased the design
   success rate from 6% to 47%, produced stable proteins unlike those found in
   nature for topologies where design was initially unsuccessful, & revealed
   subtle contributions to stability as designs became increasingly optimized.
   Our approach achieves the long-standing goal of a tight feedback cycle
   between computation & experiment & has the potential to transform
   computational protein design into a data-driven science."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aan0693">doi:10.1126/science.aan0693</A>]['17].

%A J. D. Welch
%A A. J. Hartemink
%A J. F. Prins
%T MATCHER: Manifold alignment reveals correspondence between single cell
   transcriptome and epigenome dynamics
%J Genome Biol
%V 18
%N 138
%M JUL
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0820, manifold alignment, scRNA-seq,
   scRNAseq, matcher, gene expression, epigenetic, scM&T-seq, scMTseq,
   sc-GEM, scGEM, ATACseq, cell types, pseudoTime
%X "... an approach for integrating multiple types of single cell measurements.
   MATCHER uses manifold alignment [Ham03] to infer single cell multiomic
   profiles from transcriptomic & epigenetic measurements performed on different
   cells of the same type. Using scM&T-seq & sc-GEM data ... predicts true
   s.cell correlations between DNA methylation & gene expression ..."
      ["... [assume] variation among cells can be explained mainly by a single
       latent variable ('pseudotime') ... cells in each experiment are sampled
       from the same population, process, and cell type ..."]
   -- [<A HREF="https://doi.org/10.1186/s13059-017-1269-0">doi:10.1186/s13059-017-1269-0</A>]['20].
   Also see MA@[<A HREF="https://en.wikipedia.org/wiki/Manifold_alignment">wikip</A>]['20].
   [Also search for: MolBio scRNAseq].

%A D. Graur
%T An upper limit on the functional fraction of the human genome
%J Genome Biol. Evol.
%V ?
%P evx121
%M JUL
%D 2017
%K jrnl, eJrnl, MolBio, c2017, c201x, c20xx, zz0717, human genome, junk DNA,
   useless, functional, purpose
%X "For the human pop'n to maintain a const. size from generation to generation,
   an increase in fertility must compensate for the reduction in the mean
   fitness of the pop'n caused, among others, by deleterious mutations. The
   required increase in fertility due to this mutational load depends on the
   # of sites in the genome that are functional, the mutation rate, & the
   fraction of deleterious mutations among all mutations in functional regions.
   These dependencies & the fact that there exists a max. tolerable replacement
   level fertility can be used to put an upper limit on the fraction of the
   h.genome that can be functional. Mutational load considerations lead to the
   conclusion that the functional fraction within the human genome cannot exceed
   25%, and is probably considerably lower."
   -- [<A HREF="https://doi.org/10.1093/gbe/evx121">doi:10.1093/gbe/evx121</A>]['17].
   [Also search for: MolBio junk DNA].

%A J. B. Losos
%T Improbable Destinies: Fate, Chance, and the Future of Evolution
%I RiverheadBooks
%D 2017
%K book, text, c2017, c201x, c20xx, zz0717, biology, origins, life,
   convergent, divergent, chance, contingency
%X 1st ed 2017; hb us$18; uk us isbn:0399184929; uk us isbn13:978-0399184925.
   "Earth's natural history is full of fascinating instances of convergence:
   phenomena like eyes and wings and tree-climbing lizards that have evolved
   independently, multiple times. But evolutionary biologists also point out
   many examples of contingency, cases where the tiniest change - a random
   mutation or an ancient butterfly sneeze - caused evolution to take a
   completely different course. ..."
   (Also see [<A HREF="https://doi.org/10.1126/science.aan8380">www</A>]['17].)

%A H. Sauquet
%A et al ...
%A J. Schonenberger
%T The ancestral flower of angiosperms and its early diversification
%J NatureComms
%N 16047
%M AUG
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0817, biol, plant, plants, angiosperm,
   flora, floral, flower, perianth, tepal, stamen, carpel, phylogeny, evolution
%X "... report model-based reconstructions for ancestral flowers at the deepest
   nodes in the phylogeny of angiosperms, using the largest data set of floral
   traits ever assembled. We reconstruct the ancestral angiosperm flower as
   bisexual and radially symmetric, with more than two whorls of three separate
   perianth organs each (undifferentiated tepals), more than two whorls of three
   separate stamens each, and more than five spirally arranged separate carpels.
   Although uncertainty remains for some of the characters, our reconstruction
   allows us to propose a new plausible scenario for the early diversification
   of flowers, leading to new testable hypotheses for future research on
   angiosperms."
   -- [<A HREF="https://doi.org/10.1038/ncomms16047">doi:10.1038/ncomms16047</A>]['17].

%A H. Ma
%A et al ...
%A S. Mitalipov
%T Correction of a pathogenic gene mutation in human embryos
%J Nature
%V ?
%P ?-?
%M AUG
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0817, human, embryo, genetic, edit, CRISPR Cas9,
   disease, medicine, MYBPC3
%X "... describe the correction of the heterozygous MYBPC3 mutation in human
   preimplantation embryos with precise CRISPR-Cas9-based targeting accuracy and
   high homology-directed repair efficiency by activating an endogenous,
   germline-specific DNA repair response. Induced double-strand breaks (DSBs) at
   the mutant paternal allele were predominantly repaired using the homologous
   wild-type maternal gene instead of a synthetic DNA template. By modulating
   the cell cycle stage at which the DSB was induced, we were able to avoid
   mosaicism in cleaving embryos and achieve a high yield of homozygous embryos
   carrying the wild-type MYBPC3 gene w/o evidence of off-target mutations ..."
   -- [<A HREF="https://doi.org/10.1038/nature23305">doi:10.1038/nature23305</A>]['17].

%A L. Cimmino
%A et al ...
%A I. Aifantis
%T Restoration of TET2 function blocks aberrant self-renewal and
   leukemia progression
%J Cell
%V ?
%M AUG
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0817, health, cancer, leukemia, MDS,
   AML, vitamin C, vitaminC, TET2, Tet2, TET, gene
%X "... generated a reversible transgenic RNAi mouse to model restoration of
   endogenous Tet2 expression. Tet2 restoration reverses aberrant hematopoietic
   stem & progenitor cell (HSPC) self-renewal in vitro & in vivo. Treatment with
   vitamin C, a co-factor of Fe2+ & alpha-KG-dependent dioxygenases, mimics TET2
   restoration by enhancing 5-hydroxymethylcytosine formation in Tet2-deficient
   mouse HSPCs & suppresses human leukemic colony formation & leukemia
   progression of primary human leukemia PDXs. Vitamin C also drives DNA
   hypomethylation & expression of a TET2-dependent gene signature in human
   leukemia cell lines. Furthermore, TET-mediated DNA oxidation induced by
   vitamin C treatment in leukemia cells enhances their sensitivity to PARP
   inhibition & could provide a safe & effective combination strategy to
   selectively target TET deficiency in cancer."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cell.2017.07.032">doi:10.1016/j.cell.2017.07.032</A>]['17].

%A J. J. Brocks
%A et al ...
%A T. Liyanage
%T The rise of algae in Cryogenian oceans and the emergence of animals
%J Nature
%V 548
%N 7669
%P 578-581
%M AUG
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0817, earth, origins, life, alga, algae,
   animal, oxygen, cyanobacteria, Cryogenian, Archaeplastida, Sturtian,
   Marinoan, rhizarian, eumetazoan, Ediacaran, palaeontology
%X "The transition from dominant bacterial to eukaryotic marine primary
   productivity was one of the most profound ecological revolutions in the
   Earth's history ... present a molecular fossil record of eukaryotic steroids
   demonstrating that bacteria were the only notable primary producers in the
   oceans before the Cryogenian period (720-635 million y. ago). Increasing
   steroid diversity & abundance marks the rapid rise of marine planktonic
   algae (Archaeplastida) in the narrow time interval between the Sturtian &
   Marinoan 'snowball Earth' glaciations, 659-645 m.y. ago. We propose that the
   incumbency of cyanobacteria was broken by a surge of nutrients supplied by
   the Sturtian deglaciation. The 'Rise of Algae' created food webs with more
   efficient nutrient & energy transfers, driving ecosystems towards larger &
   increasingly complex organisms. ..."  [online 16/8/2017.]
   -- [<A HREF="http://dx.doi.org/10.1038/nature23457">doi:10.1038/nature23457</A>]['17].

%A B. Adhikari
%A J. Cheng
%T Improved protein structure reconstruction using secondary structures,
   contacts at higher distance thresholds, and non-contacts
%J BMC Bioinformatics
%V ?
%M AUG
%D 2017
%K jrnl, eJrnl, MolBio, c2017, c201x, c20xx, zz0917, CONFOLD, protein structure,
   CASP, de novo structure prediction, secondary structure, contacts
%X "... Using a data set consisting of 496 structural domains released in recent
   CASP experiments & a dataset of 150 representative p.structures, ... discuss
   three techniques to improve the reconstruction accuracy using true contacts -
   adding sec.structs, increasing contact distance thresholds, & adding
   non-contacts. We find that reconstruction using sec.structures & contacts can
   deliver accuracy higher than using full contact maps. Similarly, we
   demonstrate that non-contacts can improve reconstruction accuracy not only
   when the used non-contacts are true but also when they are predicted. On the
   dataset consisting of 150 proteins, we find that by simply using low ranked
   predicted contacts as non-contacts & adding them as additional restraints,
   can increase the reconstruction accuracy by 5% when the reconstructed models
   are evaluated using TM-score. ..."
   -- [<A HREF="https://doi.org/10.1186/s12859-017-1807-5">doi:10.1186/s12859-017-1807-5</A>]['17].

%A M. Reimann
%A et al ...
%A H. Markram
%T Cliques of neurons bound into cavities provide a missing link between
   structure and function
%J Frontiers in Comput. Neurosci.
%M JUN
%D 2017
%K jrnl, brain, mind, c2017, c201x, c20xx, zz1017, bluebrain, Blue Brain,
   neocortex, clique, cavity, network, neuron, Hess, Markram
%X "... taking the direction of synaptic transmission into account, constructing
   graphs of a network that reflect the direction of information flow, &
   analyzing these directed gs. using algebraic topology. Applying this approach
   to a local n/wk of neurons in the neocortex revealed a remarkably intricate &
   prev. unseen topology of synaptic connectivity. The synaptic n/wk contains an
   abundance of cliques of neurons bound into cavities that guide the emergence
   of correlated activity. In response to stimuli, correlated activity binds
   synaptically connected neurons into functional cliques & cavities that evolve
   in a stereotypical seq. toward peak complexity. We propose that the brain
   processes stimuli by forming increasingly complex functional cliques &
   cavities."
  -- [<A HREF="https://doi.org/10.3389/fncom.2017.00048">doi:10.3389/fncom.2017.00048</A>]['17].
  (Also see bluebrain@[<A HREF="http://bluebrain.epfl.ch/">www</A>]['17].)

%A J. T. Vogelstein
%A et al
%T A community-developed open-source computational ecosystem for big neuro data
%J NatureMethods
%V 15
%N 11
%P 846-847
%M OCT
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0323, brain, neurons, synapses,
   network
%X "Big imaging data is becoming more prominent in brain sciences across
   spatiotemporal scales & phylogenies. We have developed ... storage,
   visualization, & analysis of these data in the cloud, thusfar spanning 20+
   publ'ns & 100+ terabytes inc. nanoscale ultrastructure, microscale
   synaptogenetic diversity, & mesoscale whole brain connectivity, making
   NeuroData the largest and most diverse open repository of brain data."
   -- [<A HREF="https://doi.org/10.48550/arXiv.1804.02835">arXiv</A>]['23],
      [<A HREF="https://doi.org/10.1038/s41592-018-0181-1">doi:10.1038/s41592-018-0181-1</A>]['23].


%A A. Verma
%A B. E. Engelhardt
%T A robust nonlinear low-dimensional manifold for single cell RNA-seq data
%J bioRxiv
%M OCT
%D 2018
%O BMC Bioinformatics vol.21, #324, 2020
%K TR, MolBio, c2018, c201x, c20xx, zz1220, scRNAseq, nonlinear, manifold,
   GPLVM
%X "... Analysis of these [scRNA-seq] sparse, high-dimensional experimental
   results requires dimension reduction. Several methods have been developed to
   est. low-dimensional embeddings for filtered & normalized single cell data.
   However, methods have yet to be developed for unfiltered & unnormalized count
   data. We present a nonlinear latent variable model with robust, heavy-tailed
   error & adaptive kernel learning to estimate low-dimensional nonlinear
   structure in scRNA-seq data. Gene expression in a single cell is modeled as a
   noisy draw from a Gaussian process in high dimensions from low-dim. latent
   positions. This model is called the Gaussian process latent variable model
   (GPLVM). We model residual errors with a heavy-tailed Student's t-distn ..."
   -- [<A HREF="https://doi.org/10.1101/443044">bioRxiv</A>]['18] or
   BMC[<A HREF="https://doi.org/10.1186/s12859-020-03625-z">doi:10.1186/s12859-020-03625-z</A>]['20].
   [Also search for: scRNAseq manifold].

%A H. J. Noh
%A et al
%T Integrating evolutionary and regulatory information with a multispecies
   approach implicates genes and pathways in obsessive-compulsive disorder
%J NatureComms
%V 8
%P e774
%M OCT
%D 2017
%K MolBio, jrnl, eJrnl, c2017, c201x, c20xx, zz1017, human, health, gene,
   genetics, risk, risks, medicine, psychology, behaviour,
   obsessive compulsive disorder, OCD, SSRI, antidepressants,
   brain, NRXN1, HTR2A, CTTNBP2, REEP3
%X " ... sequenced coding and regulatory elements for 608 genes potentially
   involved in obsessive-compulsive disorder in human, dog, and mouse. Using a
   new method that prioritizes likely functional variants, we compared 592 cases
   to 560 controls and found four strongly associated genes, validated in a
   larger cohort. suggest synaptic adhesion as a key component in compulsive
   behaviors ..."
   -- [<A HREF="https://doi.org/10.1038/s41467-017-00831-x">doi:10.1038/s41467-017-00831-x</A>]['17].

%A E. Latorre
%A et al ...
%A L. W. Harries
%T Small molecule modulation of splicing factor expression is associated with
   rescue from cellular senescence
%J BMC Cell Biol.
%V 18
%N 31
%M OCT
%D 2017
%K jrnl, eJrnl, MolBio, c2017, c201x, c20xx, zz0118, biology, cell, aging,
   ageing, senescence, ERK, resveralogue, resveratrol, mRNA, splicing,
   UniEssex, UEssex
%X "... Treatment with resveralogues was assoc. with altered splicing factor
   expression & rescue of multiple features of senescence. This rescue was
   indep. of cell cycle traverse & also indep. of SIRT1, SASP modulation or
   senolysis. Under growth permissive conditions, cells demonstrating restored
   splicing factor expression also demonstrated increased telomere length,
   re-entered cell cycle & resumed proliferation. These phenomena were also
   influenced by ERK antagonists & agonists. This is the first demo. that
   moderation of splicing factor levels is assoc. with reversal of cellular
   senescence in human primary fibroblasts. Small molecule modulators of such
   targets may therefore represent promising novel anti-degenerative therapies."
   -- [<A HREF="https://doi.org/10.1186/s12860-017-0147-7">doi:10.1186/s12860-017-0147-7</A>]['17].
   [Also search for: resveratrol].

%A S. Nmepomnyachiy
%A N. Ben-Tal
%A R. Kolodny
%T Complex evolutionary footprints revealed in an analysis of reused protein
   segments of diverse lengths
%J PNAS
%V 114
%N 44
%P ?
%M OCT
%D 2017
%K jrnl, PNAS, MolBio, c2017, c201x, c20xx, zz0618, BenTal, theme, themes,
   protein, structure, pattern, evolution, recurring, reuse, segment, fragment,
   library, ECOD, HHSearch
%X "... To systematically explore the evolutionary traces of segment 'reuse'
   across proteins, we developed an automated methodology that identifies reused
   segments from protein alignments. We search for 'themes' - segs. of >=35
   residues of similar seq. & structure - reused within representative sets of
   15,016 domains [Evolutionary Classification of Protein Domains (ECOD)
   database] or 20,398 chains [Protein Data Bank (PDB)]. We observe that theme
   reuse is highly prevalent & that reuse is more extensive when the length
   threshold for identifying a theme is lower. Structural domains, the best
   characterized form of reuse in proteins, are just one of many complex &
   intertwined evolutionary traces. Others include long themes shared among a
   few proteins, which encompass & overlap with shorter themes that recur in
   numerous proteins. ..."
   -- [<A HREF="https://dx.doi.org/10.1073/pnas.1707642114">doi:10.1073/pnas.1707642114</A>]['18].
    & supp@[<A HREF="http://www.pnas.org/content/suppl/2017/10/19/1707642114.DCSupplemental">www</A>]['18].
   ["... 'themes' - segs. of >=35 residues of similar seq. & structure ...
    present an automated pipeline to identify segs. of various lengths [35-200]
    of reused seqs. [themes] that also have similar structs. ...
    align all-vs.-all ... calc. for each sig. alignment the % of similarity of
    aligned residues and the rmsd of the C_a atoms of the aligned residues. ...
    similarity n/wks [where sim > 40% & rmsd < 3.5A] ... connected cmpts ..."]
   [Also search for: MolBio protein structure pattern].

%A L. F. Wilson
%A et al ...
%A D. C. Whiteman
%T How many cancer cases and deaths are potentially preventable? Estimates for
   Australia in 2013
%J Int. J. Cancer
%V ?
%P ?-?
%M OCT
%D 2017
%K jrnl, c2017, c201x, c20xx, zz1217, human, health, medicine, cancer, death,
   stats, risks, alcohol, zzAlcohol, smoking, tobacco, diet, exercise
%X "... aimed to quantify the proportions & numbers of cancer deaths & cases in
   Australia in 2013 attributable to 20 modifiable factors in eight broad
   groupings that are established causes of cancer, namely: tobacco smoke
   (smoking & second-hand), dietary factors (low intake of fruit, non-starchy
   vegetables & dietary fibre; & high intake of red & processed meat),
   overweight/obesity, alcohol, physical inactivity, solar ultraviolet
   radiation, infections (seven agents), & reproductive factors (lack of
   breastfeeding, menopausal hormone therapy use, combined oral contraceptive
   use). ...  Of all cancer deaths in Australia in 2013, ~ 38% overall (males
   41%, females 34%) could be attributed to the factors assessed; the corr. PAF
   for cancer cases was 33% (males 34%, females 32%). Tobacco smoke was the
   leading cause of cancer deaths & cases, with PAFs of 23 & 13%, resp.,
   followed by dietary factors (5% deaths/5% cases), overweight/obesity (5%/4%)
   & infections (5%/3%). Cancer sites with the highest #s of potentially
   preventable deaths/cases were lung (n=6,776/9,272), colorectum
   (n=1,974/7,380) & cutaneous melanoma (n=1,390/7,918). We estimate that
   ~ 16,700 cancer deaths & 41,200 cancer cases could be prevented in Australia
   each year if people's exposures to 20 causal factors were aligned with levels
   recommended to minimise cancer risk."
   -- [<A HREF="https://doi.org/10.1002/ijc.31088">doi:10.1002/ijc.31088</A>]['17].

%A K. Michailidou
%A et al (!)
%T Association analysis identifies 65 new breast cancer risk loci
%J Nature
%V 551
%N 7678
%P 92-94
%M OCT
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0720, breast cancer, GWAS, Schmidt, Makalic,
   SNPs
%X "... report the results of a genome-wide association study of breast cancer
   in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases
   and 13,104 controls of East Asian ancestry1. We identified 65 new loci that
   are associated with overall breast cancer risk at P < 5x10^{-8}. The majority
   of credible risk single-nucleotide polymorphisms in these loci fall in
   distal regulatory elements ..."
   -- [<A HREF="https://doi.org/10.1038/nature24284">doi:10.1038/nature24284</A>]['20].
   (Also see GWAS@[<A HREF="https://en.wikipedia.org/wiki/Genome-wide_association_study">wikip</A>]['20].)

%A F. McNally
%T Competing chromosomes explain junk DNA
%J Science
%V 358
%N 6363
%P 594-595
%M NOV
%D 2017
%K news, views, MolBio, c2017, c201x, c20xx, zz1117, chromosome, eukaryote,
   sexual reproduction, genes, meiosis, meiotic, cell, egg, female, centromere,
   spindle, selfish DNA, CDC42
%X "The vast majority of eukaryotes have two copies of each chromosome and
   reproduce sexually. Meiosis is a vital process that produces gametes (eggs
   and sperm) by reducing the number of chromosome copies to one ... It is a
   fundamental tenet of genetics that there is a random, 50% chance for any
   particular chromosome to be segregated into the egg versus the polar body.
   However, cases in which one copy of a chromosome is inherited with greater
   than 50% frequency have been reported in many species ... Thus, the essential
   DNA sequences that mediate accurate chromosome segregation are actually
   'selfish' (or parasitic) genetic elements that have invaded our genome."
   -- [<A HREF="https://doi.org/10.1126/science.aaq0200">doi:10.1126/science.aaq0200</A>]['17].
   Points to
      [<A HREF="https://doi.org/10.1126/science.aan0092">doi:10.1126/science.aan0092</A>]['17].

%A S. S. Khan
%A et al
%A D. E. Vaughan
%T A null mutation in SERPINE1 protects against biological aging in humans
%J Sci. Adv.
%V 3
%N 11
%P eaao1617
%M NOV
%D 2017
%K jrnl, eJrnl, c2017, c201x, c20xx, zz1117, MolBio, gene, human, ageing,
   aging, longevity, lifespan, mutation, Plasminogen activator inhibitor-1,
   PAI-1, PAI1, senescence, SERPINE1, SERPINE, Amish
%X "Plasminogen activator inhibitor-1 (PAI-1) has been shown to be a key
   component of the senescence-related secretome and a direct mediator of
   cellular senescence. ... the role of PAI-1 in human longevity remains
   unclear. We hypothesized that a rare loss-of-function mutation in SERPINE1
   (c.699_700dupTA), which encodes PAI-1, could play a role in longevity and
   metabolism in humans. We studied 177 members of the Berne Amish community,
   which included 43 carriers of the null SERPINE1 mutation. Heterozygosity was
   assoc. with sig. longer leukocyte telomere length, lower fasting insulin
   levels, and lower prevalence of diabetes mellitus. In the extended Amish
   kindred, carriers of the null SERPINE1 allele had a longer life span. Our
   study indicates a causal effect of PAI-1 on human longevity, which may be
   mediated by alterations in metabolism. Our findings demonstrate the utility
   of studying loss-of-function mutations in populations with geographic and
   genetic isolation and shed light on a novel therapeutic target for aging."
   -- [<A HREF="https://doi.org/10.1126/sciadv.aao1617">doi:10.1126/sciadv.aao1617</A>]['17].

%A M.-C. Luo
%A et al ...
%A J. Dvorak
%T Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
%J Nature
%V 551
%P 498-502
%M NOV
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz1117, plant, wheat, genome, nGenome,
   Aegilops tauschii, food crop, grass, grasses, chromosomes,
   PRJNA341983, PRJEB23317
%X "Aegilops tauschii is the diploid progenitor of the D genome of hexaploid
   wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource
   for wheat. ... reveal that the Ae. tauschii genome has a greater number of
   dispersed duplicated genes than other sequenced genomes and its chromosomes
   have been structurally evolving an order of magnitude faster than those of
   other grass genomes. The decay of colinearity with other grass genomes
   correlates with recombination rates along chromosomes. We propose that the
   vast amounts of very similar repeated sequences cause frequent errors in
   recombination and lead to gene duplications and structural chromosome
   changes that drive fast genome evolution."
      "... The wheat and Aegilops genomes have seven chromosomes, which
      evolved by dysploid reductions from twelve ancestral chromosomes. ..."
   -- [<A HREF="https://doi.org/10.1038/nature24486">doi:10.1038/nature24486</A>]['17].
   PRJNA341983@[<A HREF="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA341983">ncbi</A>]['17],
   PRJEB23317@[<A HREF="https://www.ebi.ac.uk/ena/data/view/PRJEB23317">ebi</A>]['17].

%A P. M. Harrison
%T fLPS: Fast discovery of compositional biases for the protein universe
%J BMC Bioinformatics
%V 18
%N 476
%M NOV
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz1117, fLPS, protein,
   amino acid, sequence, bias, biased, composition
%X "... a process of probability minimization. First, contigs are constructed
   for each amino-acid type out of seq. windows with a low degree of bias;
   second, these contigs are searched exhaustively for low-probability subseqs.
   (LPSs); third, such LPSs are iteratively assessed for merger into possible
   multiple-residue biases. At each of these stages, efficiency measures are
   taken to avoid or delay probability calculations unless/until they are
   necessary. On a current desktop workstation, the fLPS algorithm can annotate
   the biased regions of the yeast proteome (>5700 sequences) in <1 ..."
   -- [<A HREF="https://doi.org/10.1186/s12859-017-1906-3">doi:10.1186/s12859-017-1906-3</A>]['17].
   [Also search for: biased sequence].

%A R. Poole
%A P. Roderick
%A J. A. Fallowfield
%A P. C. Hayes
%T Coffee consumption and health: Umbrella review of meta-analyses of
   multiple health outcomes
%J BMJ
%V 359
%M NOV
%D 2017
%K jrnl, BMJ, c2017, c201x, c20xx, zz1117, coffee, zzCoffee, positive,
   human health, caffeine consumption, longevity, mortality, cardiovascular
%X "... meta-analyses of observational and interventional studies of coffee
   consumption & any health outcome. ... largest relative risk reduction at
   intakes of three to four cups a day versus none, inc. all cause mortality
   (relative risk 0.83, 95% CI 0.83 to 0.88), cardiovascular mortality
   (0.81, 0.72 to 0.90), and cardiovascular disease (0.85, 0.80 to 0.90).
   High v. low consumption was assoc. with an 18% lower risk of incident cancer
   (0.82, 0.74 to 0.89).  ...  Coffee consumption seems generally
   safe within usual levels of intake, with summary estimates indicating largest
   risk reduction for various health outcomes at three to four cups a day, &
   more likely to benefit health than harm. Robust randomised controlled trials
   are needed to understand whether the observed associations are causal.
   Importantly, outside of pregnancy, existing evidence suggests that coffee
   could be tested as an intervention without significant risk of causing harm.
   Women at increased risk of fracture should possibly be excluded."
   -- [<A HREF="https://doi.org/10.1136/bmj.j5024">doi:10.1136/bmj.j5024</A>]['17].
   [Also search for: zzCoffee].

%A Y. Zhang
%A et al ...
%A F. E. Romesberg
%T A semi-synthetic organism that stores and retrieves increased
   genetic information
%J Nature
%V 551
%N ?
%P 644-647
%M NOV
%D 2017
%K jrnl, c2017, c201x, c20xx, zz1217, MolBio, DNA, DNA6, DNAplus, artificial,
   semi-synthetic, dNaM, dTPT3, unnatural codons, tRNAs
%X "... semi-synthetic organisms whose DNA harbours two additional letters that
   form a third, unnatural base pair. Previous efforts to generate such
   semi-synthetic organisms2 culminated in the creation of a strain of E.coli
   that, by virtue of a nucleoside triphosphate transporter from Phaeodactylum
   tricornutum, imports the requisite unnatural triphosphates from its medium
   and then uses them to replicate a plasmid containing the unnatural base pair
   dNaM-dTPT3. ... Here we report the in vivo transcription of DNA containing
   dNaM and dTPT3 into mRNAs with two different unnatural codons and tRNAs with
   cognate unnatural anticodons, and their efficient decoding at the ribosome to
   direct the site-specific incorporation of natural or non-canonical amino
   acids into superfolder green fluorescent protein. The results demonstrate
   that interactions other than hydrogen bonding can contribute to every step
   of information storage and retrieval ..."
   -- [<A HREF="https://doi.org/10.1038/nature24659">doi:10.1038/nature24659</A>]['17].

%A C. Zhao
%A S. Sahni
%T Cache and energy efficient algorithms for Nussinov's RNA folding
%J BMC Bioinformatics (Suppl. 15, ICCABS)
%V 18
%M DEC
%D 2017
%K conf, c2017, c20x, c20xx, zz1217, MolBio, RNA, fold, folding, Nussinov,
   algorithm, ByRow, ByBox, Transpose, speed
%X "... Three cache-efficient algorithms, ByRow, ByRowSegment & ByBox, for
   Nussinov's RNA folding are developed.  ... depending on the computational
   platform & programming language, either ByRow or ByBox give best run time &
   energy performance. The C version of these algs. reduce run time by as much
   as 97.2% & energy consumption by as much as 88.8% relative to Classical & by
   as much as 56.3% & 57.8% relative to Transpose. The Java versions reduce run
   time by as much as 98.3% relative to Classical & by as much as 75.2% relative
   to Transpose. Transpose achieves run time & energy efficiency at the expense
   of memory as it takes twice the memory required by Classical. ..."
   -- [<A HREF="https://doi.org/10.1186/s12859-017-1917-0">doi:10.1186/s12859-017-1917-0</A>]['17].
   [Also search for: RNA folding].

%A C. Y. Feigin
%A et al ...
%A A. J. Pask
%T Genome of the Tasmanian tiger provides insights into the evolution and
   demography of an extinct marsupial carnivore
%J Nature Ecol. and Evol.
%V ?
%P ?-?
%M DEC
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz1217, Australia, animal, marsupial,
   Tasmanian Tiger, thylacine, Thylacinus cynocephalus, genome, nGenome
%X "... Despite last sharing a common ancestor with the eutherian canids
   ~160 million years ago, their phenotypic resemblance is considered the most
   striking example of convergent evolution in mammals. The last known thylacine
   died in captivity in 1936 ... sequenced the genome of a preserved thylacine
   pouch young specimen to clarify the phylogenetic position of the thylacine
   within the carnivorous marsupials ... a long-term decline in genetic
   diversity starting well before the arrival of humans in Australia. ...
   amino acid homoplasies between the thylacine and canids are largely
   consistent with neutral evolution. ..."
   -- [<A HREF="https://doi.org/10.1038/s41559-017-0417-y">doi:10.1038/s41559-017-0417-y</A>]['17].
   "Genome sequence reads have been deposited in the Sequence Read Archive
   as BioProject PRJNA354646, BioSample SAMN06049672."
   (Also see the ABC[<A HREF="http://www.abc.net.au/news/science/2017-12-12/thylacine-tasmanian-tiger-genetics-evolution/9246832">12/12/2017</A>].)
   [Also search for: marsupial nGenome].


%A N. D. Rawlings
%A et al ...
%A R. D Finn
%T The MEROPS database of proteolytic enzymes, their substrates and inhibitors
   in 2017 and a comparison with peptidases in the PANTHER database
%J NAR
%V 46
%N D1
%P D624-D632
%M JAN
%D 2018
%K NRA, jrnl, MolBio, c2018, c201x, c20xx, zz0820, MEROPS, protease, proteinase,
   peptidase, enzyme, inhibitor, substrate, cleave, cleavage, specificity, pops,
   database, collection, DB,
%X "... an integrated source of info. about peptidases, their substrates
   & inhibitors. The hier.class'n is: protein-species, family, clan,
   with an id. at each level. ..."
   -- [<A HREF="https://doi.org/10.1093/nar/gkx1134">doi:10.1093/nar/gkx1134</A>]['20].
   Also see MEROPS@[<A HREF="http://www.ebi.ac.uk/merops/">www</A>]['20].

%A T. Nawy
%T Spatial transcriptomics
%J Nat. Methods
%V 15
%M JAN
%D 2018
%K news, views, MolBio, c2018, c201x, c20xx, zz0820, spatial, transcriptome,
   RNA, mRNA, cells, gene expression levels, tissue
%X -- [<A HREF="https://doi.org/10.1038/nmeth.4542">doi:10.1038/nmeth.4542</A>]['20].

%A A. N. Cowell
%A et al
%T Mapping the malaria parasite druggable genome by using in vitro evolution
   and chemogenomics
%J Science
%V 359
%N 6372
%P 191-199
%M JAN
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0118, malaria, Plasmodium falciparum,
   drug resistance, adaption, mutation, thymidylate, benzoquinazolinone,
   farnesyltransferase, pyrimidinedione, dipeptidylpeptidase, arylurea
%X "... performed a genome analysis of 262 Plasmodium falciparum parasites
   resistant to 37 diverse compounds. We found 159 gene amplifications & 148
   nonsynonymous changes in 83 genes associated with drug-resistance
   acquisition, where gene amplifications contributed to one-third of
   resistance acquisition events. Beyond confirming previously identified
   multidrug-resistance mechanisms, we discovered hitherto unrecognized drug
   target-inhibitor pairs, including thymidylate synthase & a
   benzoquinazolinone, farnesyltransferase & a pyrimidinedione, & a
   dipeptidylpeptidase & an arylurea. ..."
   -- [<A HREF="https://doi.org/10.1126/science.aan4472">doi:10.1126/science.aan4472</A>]['18].
  [Also search for: Plasmodium falciparum].

%A M. J. Ryan
%T A Taste for the Beautiful: The Evolution of Attraction
%I PrincetonUP
%P 208
%M JAN
%D 2018
%K book, text, c2018, c20x, c20xx, zz0118, biol, biology, attractiveness,
   sexual, mate selection, beauty, human, animal behaviour, evolution, peacock
%X 1st ed 2018; hb us$24; uk us isbn:0691167265; uk us isbn13:978-0691167268.
   "... [how] scientists have taken up where Darwin left off and transformed
   our understanding of sexual selection, shedding new light on human behavior
   in the process. ..."

%A Z. Liu
%A et al
%T Cloning of Macaque monkeys by somatic cell nuclear transfer
%J Cell
%V ?
%M JAN
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0118, clone, cloning, cloned, Macaque monkey,
   Macaca fascicularis, mammal, Dolly
%X "... successfully cloned cynomolgus monkeys (Macaca fascicularis) by somatic
   cell nuclear transfer (SCNT). ... For SCNT using fetal monkey fibroblasts,
   6 pregnancies were confirmed in 21 surrogates and yielded 2 healthy babies.
   For SCNT using adult monkey cumulus cells, 22 pregnancies were confirmed in
   42 surrogates and yielded 2 babies that were short-lived. In both cases,
   genetic analyses confirmed that the nuclear DNA and mitochondria DNA of the
   monkey offspring originated from the nucleus donor cell and the oocyte
   donor monkey, respectively. Thus, cloning macaque monkeys by SCNT is feasible
   using fetal fibroblasts."
   -- [<A HREF="https://doi.org/10.1016/j.cell.2018.01.020">doi:10.1016/j.cell.2018.01.020</A>]['18],
   or [<A HREF="http://www.cell.com/cell/abstract/S0092-8674(18)30057-6">www</A>]['18].

%A M. Jain
%A et al ...
%A M. Loose
%T Nanopore sequencing and assembly of a human genome with ultra-long reads
%J Nature Biotech.
%V ?
%M JAN
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0218, Oxford Nanopore, MinION, DNA,
   sequencing, NG50, N50, GRCh38
%X "... sequencing & assembly of a reference genome for the human GM12878
   Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore
   sequencer. 91.2 Gb of seq. data, representing ~30x theoretical coverage, were
   produced. Reference-based alignment enabled detection of large structural
   variants & epigenetic modifications. De novo assembly of nanopore reads alone
   yielded a contiguous assembly (NG50 ~3Mb). We developed a protocol to
   generate ultra-long reads (N50 > 100 kb, read lengths up to 882 kb).
   Incorporating an additional 5x coverage of these ultra-long reads more than
   doubled the assembly contiguity (NG50 ~6.4Mb). The final assembled genome
   was 2,867 million bases in size, covering 85.8% of the reference. Assembly
   accuracy, after incorporating complementary short-read sequencing data,
   exceeded 99.8%. Ultra-long reads enabled assembly & phasing of the 4-Mb major
   histocompatibility complex (MHC) locus in its entirety, measurement of
   telomere repeat length, & closure of gaps in the reference human genome
   assembly GRCh38."  (online 29/1/2018.)
   -- [<A HREF="https://doi.org/10.1038/nbt.4060">doi:10.1038/nbt.4060</A>]['18].

%A J. L. Morris
%A et al ...
%A P. C. J. Donaghue
%T The timescale of early land plant evolution
%J PNAS
%V ?
%P ?-?
%M JAN
%D 2018
%K jrnl, PNAS, MolBio, c2018, c201x, c20xx, zz0218, biol, biology, land plants,
   origin, origins, evolution, fossil, fossils, bryophyte, tracheophyte,
   Cambrian, Ordovocian, Embryophyta, Viridiplantae, phylogenetic, phylogenomic
%X "... establish a timescale for early land plant evolution that integrates
   over competing hypotheses on bryophyte-tracheophyte relationships. We
   estimate land plants to have emerged in a middle Cambrian - early Ordovocian
   interval, & vascular plants to have emerged in the Late Ordovician-Silurian.
   This timescale implies an early establishment of terrestrial ecosystems by
   land plants that is in close accord with recent estimates for the origin of
   terrestrial animal lineages. ... Here, we establish a timescale for early
   land plant evolution that integrates over topological uncertainty by
   exploring the impact of competing hypotheses on bryophyte-tracheophyte
   relationships, among other variables, on divergence time estimation.
   We codify 37 fossil calibrations for Viridiplantae following best practice.
   We apply these calibrations in a Bayesian relaxed molecular clock analysis of
   a phylogenomic dataset encompassing the diversity of Embryophyta & their
   relatives within Viridiplantae. ... For all analyses, a Cambrian origin of
   Embryophyta is recovered with highest probability. The estimated ages for
   crown tracheophytes range from Late Ordovician to late Silurian. ... implies
   an early establishment of terrestrial ecosystems by land plants that is in
   close accord with recent estimates for the origin of terrestrial animal
   lineages. ..."  [online Feb 2018.]
   -- [<A HREF="https://doi.org/10.1073/pnas.1719588115">doi:10.1073/pnas.1719588115</A>]['18].
   [Also search for: origin plants].
   (Also see, "... Land plants evolved from 'pond scum' about
    500 million years ago, according to new research. ..."
    -- bbc[<A HREF="http://www.bbc.com/news/science-environment-43116836">20/2/2018</A>].)

%A S. Lamarre
%A et al ...
%A E. Maza
%T Optimization of an RNA-Seq differential gene expression analysis depending
   on biological replicate number and library size
%J Front. Plant Sci.
%V ?
%P ?-?
%M FEB
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0820, gene expression levels, RNAseq,
   stats, RNA-seq, replicate number, library size, DESeq, DESeq2, edgeR,
   normalization, normalisation
%X "... we conducted both an analysis of a two-condition experiment (with eight
   biol. replicates per condition) to compare the results with prev. benchmark
   studies, & a meta-analysis of 17 experiments with up to 18 biol. conditions
   eight biological replicates & 100 million (M) reads per sample. ..."
   -- [<A HREF="https://doi.org/10.3389/fpls.2018.00108">doi:10.3389/fpls.2018.00108</A>]['20].
  [Also search for: RNAseq MolBio].

%A M. Amodio
%A S. Krishnaswamy
%T MAGAN: Aligning biological manifolds
%J arXiv
%M FEB
%D 2018
%O 35th ICML
%K Conf, ICML, MolBio, c2018, c201x, c20xx, zz0820, MAGAN, scRNAseq,
   mass cytometry, manifold alignment
%X "... many types of natural and physical systems ... different types of
   measurements ... important to align the manifolds arising from each
   measurement in order to integrate such data and gain an improved picture of
   the system. We tackle this problem using generative adversarial networks
   (GANs). ... present a new GAN called the Manifold-Aligning GAN (MAGAN) that
   aligns two manifolds s.t. related points in each measurement space are
   aligned together. ... [e.g.] single-cell biology ... scRNAseq and proteomic
   (mass cytometry) ..."
   -- 1803.00385@[<A HREF="https://arxiv.org/abs/1803.00385">arXiv</A>]['20],
      [<A HREF="http://proceedings.mlr.press/v80/amodio18a/amodio18a.pdf">mlrPress</A>]['20].
   Also see MA@[<A HREF="https://en.wikipedia.org/wiki/Manifold_alignment">wikip</A>]['20].
   [Also search for: scRNAseq]  and  [also search for: Ham03].

%A K. R. Moon
%A J. S. Stanley
%A D. Burkhardt
%A D. van Dijk
%A G. Wolf
%A S. Krishnaswamy
%T Manifold learning-based methods for analyzing single-cell RNA-sequencing data
%J Current Opinion in Sys. Biol.
%V 7
%P 36-46
%M FEB
%D 2018
%K MolBio, jrnl, survey, intro, c2020, c202x, c20xx, zz1220, manifold alignment,
   single cell RNA seq, scRNAseq
%X "... Manifold learning provides a powerful structure for alg. approaches to
   process the data, extract its dynamics, & infer patterns in it. ... we cover
   manifold learning-based methods for denoising the data, revealing gene
   interactions, extracting pseudotime progressions with model fitting,
   visualizing the cellular state space via dimensionality reduction, &
   clustering the data."
   -- [<A HREF="https://doi.org/10.1016/j.coisb.2017.12.008">doi:10.1016/j.coisb.2017.12.008</A>]['20].
   [Also search for: scRNAseq].

%A S. Nowoshilow
%A et al ...
%A E. M. Myers
%T The axolotl genome and the evolution of key tissue formation regulators
%J Nature
%V 554
%P 50-55
%M FEB
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0218, animal, tetrapod, amphibian,
   salamander, Mexican axolotl, Ambystoma mexicanum, genome, nGenome, tissue,
   regulator, regeneration, Pax3, Pax7, HoxA, DNA sequencing, MARVEL
%X "... report the sequencing & assembly of the 32-gigabase-pair axolotl genome
   using an approach that combined long-read sequencing, optical mapping &
   development of a new g.assembler (MARVEL). We observed a size expansion of
   introns & intergenic regions, largely attributable to multiplication of long
   terminal repeat retroelements. We provide evidence that intron size in
   developmental genes is under constraint & that species-restricted genes may
   contribute to limb regeneration. The axolotl g. assembly does not contain the
   essential developmental gene Pax3. However, mutation of the axolotl Pax3
   paralogue Pax7 resulted in an axolotl phenotype that was similar to those
   seen in Pax3-/- & Pax7-/- mutant mice. The axolotl genome provides a rich
   biological resource for developmental & evolutionary studies."
   -- [<A HREF="https://doi.org/10.1038/nature25458">doi:10.1038/nature25458</A>]['18].
   (Note, 32GB, 10x human.)

%A C. O'Donovan
%A A. Meade
%A C. Venditti
%T Dinosaurs reveal the geographical signature of an evolutionary radiation
%J Nature Ecology and Evolution
%V ?
%M FEB
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0218, biology, dinosaur, evolution, spread,
   Cretaceous, speciation, diversity, extinction, model, simulation, ODonovan
%X "Dinosaurs dominated terrestrial ecosystems across the globe for over
   100 million years ... use a biogeographical model to reconstruct the
   dinosaurs' ancestral locations, revealing the spatial mechanisms that
   underpinned this 170-million-year-long radiation. We find that dinosaurs
   spread rapidly initially, followed by a sig. continuous & gradual reduction
   in their speed of movement towards the Cretaceous/Tertiary boundary (66
   million years ago). This suggests that the predominant mode of dinosaur
   speciation changed through time with speciation originally largely driven by
   geographical isolation - when dinosaurs speciated more, they moved further.
   This was gradually replaced by increasing levels of sympatric speciation
   (species taking advantage of ecological opportunities within their existing
   environment) as terrestrial space became a limiting factor. Our results
   uncover the geographical signature of an evolutionary radiation."
   -- [<A HREF="https://doi.org/10.1038/s41559-017-0454-6">doi:10.1038/s41559-017-0454-6</A>][18].

%A M. J. Gandal
%A et al ...
%A D. H. Geschwind
%T Shared molecular neuropathology across major psychiatric disorders parallels
   polygenic overlap
%J Science
%V 359
%N 6376
%P 693-697
%M FEB
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0218, medicine, human, mental health, disorders,
   illness, autism, schizophrenia, bipolar disorder, depression, alcoholism,
   psychiatric, genes, genetic, SNPs
%X "... used transcriptomic profiling as a quantitative readout of molecular
   brain-based phenotypes across five major psychiatric disorders - autism,
   schizophrenia, bipolar disorder, depression, and alcoholism - compared with
   matched controls. We identified patterns of shared and distinct
   gene-expression perturbations across these conditions. The degree of sharing
   of transcriptional dysregulation is related to polygenic (single-nucleotide
   polymorphism-based) overlap across disorders, suggesting a substantial
   causal genetic component ..."
   -- [<A HREF="https://doi.org/10.1126/science.aad6469">doi:10.1126/science.aad6469</A>]['18],
      [<A HREF="http://science.sciencemag.org/content/359/6376/693">www</A>]['18].

%A K. H. Eng
%A et al ...
%A K. O. Odunsi
%T Paternal lineage early onset hereditary ovarian cancers: A familial ovarian
   cancer registry study
%J PLoS Genetics
%V ?
%M FEB
%D 2018
%K jrnl, eJrnl, MolBio, c2018, c201x, c20xx, zz0218, human health, breast,
   ovarian, prostate, cancer, genes, mutation, x chromosome, Xchromosome,
   Xchr, chrX, chr-X, father, grandmother, grand mother, sister
%X "Given prior evidence that an affected woman conveys a higher risk of ovarian
   cancer to her sister than to her mother, we hypothesized that there exists an
   X-linked variant evidenced by transmission to a woman from her paternal
   grandmother via her father. ... We performed germline X-chr. exome sequencing
   on 186 women with ovarian cancer from the registry. The rate of cancers was
   28.4% in paternal grandmother/ granddaughter pairs & 13.9% in maternal pairs
   consistent with an X-linked dominant model ... observed an association
   between prostate cancer in men and ovarian cancer in his mother and daughters
   (odds ratio, OR=2.34, p=0.034).  Unaffected mothers with affected
   daughters produced sig. more daughters than sons (ratio=1.96, p < 0.005).
   We performed exome sequencing in reported BRCA negative cases from the
   registry.  Considering age-of-onset , one missense variant (rs176026 in
   MAGEC3) reached chr.-wide significance (Hazard ratio HR=2.85, 95%CI:
   1.75-4.65) advancing the age of onset by 6.7 years.  In addition to the
   well-known contribution of BRCA, we demonstrate that a genetic locus on the
   X-chromosome contributes to ovarian cancer risk.  An X-linked pattern of
   inheritance has implications for genetic risk stratification.  Women with an
   affected paternal grandmother and sisters of affected women are at increased
   risk for ovarian cancer.  Further work is required to validate this variant
   and to characterize carrier families."
   -- [<A HREF="https://doi.org/10.1371/journal.pgen.1007194">doi:10.1371/journal.pgen.1007194</A>]['18].

%A J. Xie
%A et al
%A P. Zhow
%T Dampened STING-dependent interferon activation in bats
%J Cell Host and Microbe
%V ?
%N ?
%M FEB
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0218, bat, bats, virus, immune system,
   viral, host, parasite, zoonotic, reservoir,
   interferon, S358, STING, TLR9, IFI16, AIM2
%X "... whether bats have an altered DNA sensing/defense system to balance high
   cytosolic DNA levels remains an open question. We demonstrate that bats have
   a dampened interferon response due to the replacement of the highly conserved
   serine residue (S358) in STING, an essential adaptor protein in multiple DNA
   sensing pathways. Reversing this mutation by introducing S358 restored STING
   functionality, resulting in interferon activation & virus inhibition.
   Combined with previous reports on bat-specific changes of other DNA sensors
   such as TLR9, IFI16, & AIM2, our findings shed light on bat adaptation to
   flight, their long lifespan, & their unique capacity to serve as a virus
   reservoir."
   -- [<A HREF="https://doi.org/10.1016/j.chom.2018.01.006">doi:10.1016/j.chom.2018.01.006</A>]['18].

%A Y. Li
%A et al ...
%A V. Y. Bolshakov
%Y Maternal and early postnatal immune activation produce dissociable effects on
   neurotransmission in mPFC-Amygdala circuits
%J J. Neurosci.
%M FEB
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0318, human health, immune system, pregnancy,
   mother, flu, prenatal, postnatal, child, allergy, anxiety, autism,
   schizophrenia, ASD, psychiatric disorder
%X "Inflammatory processes may be involved in the pathophysiology of
   neuropsychiatric illnesses including Autism Spectrum Disorder (ASD). Evidence
   from studies in rodents indicates that immune activation during early
   development can produce core features of ASD (social interaction deficits,
   dysregulation of communication, increases in stereotyped behaviors and
   anxiety), although the neural mechanisms of these effects are not thoroughly
   understood. We treated timed-pregnant mice ... Our findings raise the
   possibility that prenatal and postnatal immune activation may affect
   different cellular targets within brain circuits that regulate some of the
   core behavioral signs of conditions such as ASD. ..."
   -- [<A HREF="https://doi.org/10.1523/JNEUROSCI.3642-17.2018">doi:10.1523/JNEUROSCI.3642-17.2018</A>]['18].
   (Also see the abc[<A HREF="http://www.abc.net.au/news/2018-02-27/allergies-flu-in-pregnancy-could-lead-to-autism-adhd/9488532">27/2/2018</A>].)

%A D. Garrido-Martin
%A F. Pazos
%T Effect of the sequence data deluge on the performance of methods for
   detecting protein functional residues
%J BMC Bioinformatics
%V 19
%P e67
%M FEB
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0318, multiple sequence alignment,
   protein function, database, family
%X "... we evaluate how the growth and change with time in the content of seq.
   DBs affect 5 seq.-based approaches for detecting functional sites &
   subfamilies. We do that by recreating historical versions of the multiple
   seq.alignments that would have been obtained in the past based on the DB
   contents at different time points, covering a period of 20 years. ...  Our
   results show that the number of families to which these methods can be
   applied sharply increases with time, [But] while their ability to detect
   potentially functional residues remains almost constant."
   -- [<A HREF="https://doi.org/10.1186/s12859-018-2084-7">doi:10.1186/s12859-018-2084-7</A>]['18].

%A P. Dabrowski-Tumanski
%A et al ...
%A J. I Sulkowska
%T KnotProt 2.0: a database of proteins with knots and other entangled
   structures
%J NAR
%V 47
%N (D1)
%P D367-D375
%D 2019
%K jrnl, NAR, MolBio, c2019, c201x, c20xx, zz0223, knot, knotted, protein,
   3D structure, knotoid, entanglement, KnotProt, KnotProt2
%X "... collects info. about proteins which form knots & other entangled
   structures. New features in KnotProt 2.0 include the characterization of both
   probabilistic & deterministic entanglements which can be formed by disulfide
   bonds & interactions via ions, a refined characterization of entanglement in
   terms of knotoids, the identification of the so-called cysteine knots, ...
   [now] contains >2000 entangled structures ..."
   -- [<A HREF="https://doi.org/10.1093/nar/gky1140">doi:10.1093/nar/gky1140</A>]['23].
   [Also seach for: MolBio knot protein].

%A A. G. Allegrini
%A S. Selzam
%A K. Rimfeld
%A S. von Stumm
%A J. B. Pingault
%A R. Plomin
%T Genomic prediction of cognitive traits in childhood and adolescence
%J Molec. Psychiatry
%V 24
%P 819-827
%M FEB
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0519, human behaviour, personality,
   nature, nurture, children, parents, education, predict, prediction, genes,
   genetic, cognition
%X "...  build prediction models of general cognitive ability & educational
   achievement. ... compared the performances of multi-trait genomic & polygenic
   scoring methods. In a representative UK sample of 7,026 children at ages 12 &
   16, we show that we can now predict up to 11% of the variance in intelligence
   & 16% in educational achievement. We also show that predictive power
   increases from age 12 to age 16 & genomic predictions do not differ for girls
   & boys. We found that multi-trait genomic methods were effective in boosting
   predictive power. Prediction accuracy varied across polygenic score
   approaches, however results were similar for different multi-trait &
   polygenic score methods. We discuss general caveats of multi-trait methods &
   polygenic score prediction, & conclude that polygenic scores for educational
   attainment & intelligence are currently the most powerful predictors in the
   behavioural sciences."
   -- [<A HREF="https://doi.org/10.1038/s41380-019-0394-4">doi:10.1038/s41380-019-0394-4</A>]['19].

%A F. A. Wolf
%A et al ...
%A F. J. Theis
%T PAGA: graph abstraction reconciles clustering with trajectory inference
   through a topology preserving map of single cells
%J Genome Biol.
%V 20
%P #59
%M MAR
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz0720, single cell RNA seq, RNAseq,
   trajectory, scRNAseq
%X "... Partition-based graph abstraction (PAGA) provides an interpretable
   graph-like map of the arising data manifold, based on est. connectivity of
   manifold partns [<A HREF="https://github.com/theislab/paga">g'thub</A>]."
   -- [<A HREF="https://doi.org/10.1186/s13059-019-1663-x">doi:10.1186/s13059-019-1663-x</A>]['20].
   [Also search for: scRNAseq].

%A M. Hajdinjak
%A et al ...
%A J. Kelso
%T Reconstructing the genetic history of late Neanderthals
%J Nature
%V ?
%M MAR
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0318, Neanderthal, ancient DNA,
   genetics, human
%X "... use hypochlorite treatment of as little as 9mg of bone or tooth powder
   to generate between 1- and 2.7-fold genomic coverage of five Neanderthals
   who lived around 39,000 to 47,000 years ago (that is, late Neanderthals),
   thereby doubling the number of Neanderthals for which genome sequences are
   available. Genetic similarity among late Neanderthals is well predicted by
   their geographical location, and comparison to the genome of an older
   Neanderthal from the Caucasus indicates that a population turnover is
   likely to have occurred, either in the Caucasus or throughout Europe, towards
   the end of Neanderthal history. ..."
   -- [<A HREF="https://doi.org/10.1038/nature26151">doi:10.1038/nature26151</A>]['18].

%A V. M. Narasimhan
%A et al ...
%A D. Reich
%T The genomic formation of South and Central Asia
%J bioRxiv
%M MAR
%D 2018
%K TR, c2018, c201x, c20xx, zz0418, MolBio, human evolution, South, Asia,
   Europe, Eurasia, Steppe, Indo-European, India, Indus, Iran, genetics,
   BMAC, Bactria Margiana, ancient DNA, spread, language
%X "... generated genome-wide data from 362 ancient individuals, inc. the first
   from eastern Iran, Turan (Uzbekistan, Turkmenistan, & Tajikistan), Bronze Age
   Kazakhstan, & South Asia. ... document a southward spread of genetic ancestry
   from the Eurasian Steppe, correlating with the archaeologically known
   expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze
   Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples
   of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered
   in Turan ... but there is no evidence that the main BMAC population
   contributed genetically to later S.Asians. Instead, Steppe communities
   integrated farther south throughout the 2nd millennium BCE, & we show that
   they mixed with a more S.population ... By co-analyzing ancient DNA & genomic
   data from diverse present-day S.Asians, we show that Indus Periphery-related
   people are the single most important source of ancestry in S.Asia ...
   Our results show how ancestry from the Steppe genetically linked Europe &
   S.Asia in the Bronze Age, & identifies the popns that almost certainly were
   responsible for spreading Indo-European languages across much of Eurasia."
   -- [<A HREF="https://doi.org/10.1101/292581">doi:10.1101/292581</A>]['18].
   (Also see ReichLab@[<A HREF="https://reich.hms.harvard.edu/">harv'rd</A>]['18].)

%A T. D. Otta
%A et al ...
%A F. Prugnolle
%T Genomes of all known members of a Plasmodium subgenus reveal paths to
   virulent human malaria
%J Nature Microbiology
%V ?
%M MAY
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0518, malaria, plasmodium falciparum,
   praefalciparum, Laverania, stevor, human, parasite, genome, genomes
%X "Plasmodium falciparum, the most virulent agent of human malaria, shares a
   recent common ancestor with the gorilla parasite Plasmodium praefalciparum.
   ... generated multiple genomes from all known Laverania species. ... The
   complete genome sequence of the closest ancestor of P. falciparum enables us
   to estimate the timing of the beginning of speciation to be 40,000-60,000
   years ago followed by a population bottleneck around 4,000-6,000 years ago.
   Our data allow us also to search in detail for the features of P.falciparum
   that made it the only member of the Laverania able to infect and spread in
   humans."
   -- [<A HREF="https://doi.org/10.1038/s41564-018-0162-2">doi:10.1038/s41564-018-0162-2</A>]['18].
   (Also see the bbc[<A HREF="http://www.bbc.com/news/science-environment-44146321">22/5/2018]</A>].)
   [Also search for: plasmodium falciparum].

%A T. R. Simoes
%A et al ...
%A R. L. Nydam
%T The origin of squamates revealed by a Middle Triassic lizard from the
   Italian Alps
%J Nature
%V 557
%P 706-709
%M MAY
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0518, animal, tetrapod, squamate,
   lizard, lizards, reptile, dinosaur, extinction, evolution, Middle Triassic,
   Jurassic, Megachirella wachtler, fossil
%X "Modern squamates (lizards, snakes and amphisbaenians) are the world's most
   diverse group of tetrapods along with birds ... oldest known fossils dating
   from the Middle Jurassic period - 168 m.y. ago. The evolutionary origin of
   squamates is contentious because of several issues: (1) a fossil gap of
   ~70 million years exists between the oldest known fossils and their estimated
   origin ... we shed light on these problems ... articulated fossil reptile
   Megachirella wachtleri (Middle Triassic period, Italian Alps). We also
   present a phylogenetic dataset, combining fossils and extant taxa, and
   morphological and molecular data. ... present evidence that M.wachtleri is
   the oldest known stem squamate. Megachirella is 75 million years older than
   the previously known oldest squamate fossils ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-018-0093-3">doi:10.1038/s41586-018-0093-3</A>]['18].

%A I. K. Suzuki
%A et al ...
%A P. Vanderhaeghen
%T Human-specific NOTCH2NL genes expand cortical neurogenesis through
   Delta/Notch regulation
%J Cell
%V 173
%N 6
%P 1370-1384
%M MAY
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0618, animal, human, brain, size,
   gene, genes, NOTCH2NLA, NOTCH2NL, NOTCH2, NOTCH, chr1, chromosome1, Delta,
   neocortex, cortex, development, evolution, RNA seq, RNAseq
%X "The cerebral cortex underwent rapid expansion & increased complexity during
   recent hominid evolution. Gene duplications constitute a major evolutionary
   force, but their impact on human brain development remains unclear. Using
   tailored RNA sequencing (RNA-seq), we profiled the spatial & temporal
   expression of hominid-specific duplicated (HS) genes in the human fetal
   cortex & identified a repertoire of 35 HS genes displaying robust & dynamic
   patterns during cortical neurogenesis. Among them NOTCH2NL, human-specific
   paralogs of the NOTCH2 receptor, stood out for their ability to promote
   cortical progenitor maintenance. NOTCH2NL promote the clonal expansion of
   human cortical progenitors, ultimately leading to higher neuronal output. At
   the molecular level, NOTCH2NL function by activating the Notch pathway
   through inhibition of cis Delta/Notch interactions. Our study uncovers a
   large repertoire of recently evolved genes active during human corticogenesis
   & reveals how human-specific NOTCH paralogs may have contributed to the
   expansion of the human cortex."
   -- [<A HREF="https://doi.org/10.1016/j.cell.2018.03.067">doi:10.1016/j.cell.2018.03.067</A>]['18].
   [Also search for: human NOTCH2NL].

%A I. T. Fiddes
%A et al ...
%A D. Haussler
%T Human-specific NOTCH2NL genes affect Notch signaling and cortical
   neurogenesis
%J Cell
%V 173
%N 6
%P 1356-1369
%M MAY
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0618, animal, human, brain, size,
   gene, genes, NOTCH2NLA, NOTCH2NL,NOTCH2, NOTCH, chr1, chromosome1, 1q21.1,
   macrocephaly, autism, schizophrenia, neocortex
%X "... find that three paralogs of human-specific NOTCH2NL are highly expressed
   in radial glia. Functional analysis reveals that different alleles of
   NOTCH2NL have varying potencies to enhance Notch signaling by interacting
   directly with NOTCH receptors. Consistent with a role in Notch signaling,
   NOTCH2NL ectopic expression delays differentiation of neuronal progenitors,
   while deletion accelerates differentiation into cortical neurons. [&]
   NOTCH2NL genes provide the breakpoints in 1q21.1 distal deletion/duplication
   syndrome, where duplications are associated with macrocephaly & autism &
   deletions with microcephaly & schizophrenia. Thus, the emergence of
   human-specific NOTCH2NL genes may have contributed to the rapid evolution of
   the larger human neocortex, accompanied by loss of genomic stability at the
   1q21.1 locus & resulting recurrent neurodevelopmental disorders."
   -- [<A HREF="https://doi.org/10.1016/j.cell.2018.03.051">doi:10.1016/j.cell.2018.03.051</A>]['18].
   [Also search for: human NOTCH2NL].

%A D. J. Pereira Gray
%A et al ...
%A P. H. Evans
%T Continuity of care with doctors - a matter of life and death? A systematic
   review of continuity of care and mortality
%J BMJ Open
%V 8
%N 6
%M JUN
%D 2018
%K jrnl, eJrnl, BMJopen, c2018, c201x, c20xx, zz0718, human, health, risk,
   risks, healthcare, doctor, doctors, GPs, NHS, medicare, mortality
%X "... Systematic review without meta-analysis. ... Of the 726 articles
   identified in searches, 22 fulfilled the eligibility criteria. The studies
   were all cohort or cross-sectional & most adjusted for multiple potential
   confounding factors. These studies came from nine countries with very
   different cultures & health systems. We found such heterogeneity of
   continuity & mortality measurement methods & time frames that it was not
   possible to combine the results of studies. However, 18 (81.8%) high-quality
   studies reported statistically significant reductions in mortality, with
   increased continuity of care. 16 of these were with all-cause mortality.
   Three others showed no association & one demonstrated mixed results. These
   significant protective effects occurred with both generalist & specialist
   doctors. ..."
   -- [<A HREF="http://dx.doi.org/10.1136/bmjopen-2017-021161">doi:10.1136/bmjopen-2017-021161</A>]['18].
   So, try to stick with one doctor.

%A A. Scaiewicz
%A M. Levitt
%T Unique function words characterize genomic proteins
%J PNAS
%V ?
%P ?-?
%M JUN
%D 2018
%K jrnl, PNAS, MolBio, c2018, c201x, c20xx, zz0718, protein, domain, domains,
   architecture, MDA, unique function words, UFW, profile, profiles,
   conserved, CDART
%X "... Using clustering to collapse redundant profiles into unique function
   words (UFWs), we find that over the years 2009-2016, the # of UFWs saturates
   while the # of seqs. matched by a combination of two or more UFWs grows
   exponentially. Between 2009 & 2016 the # of protein seqs. from known species
   increased 10-fold from 8 million to 85 million. About 80% of these seqs.
   contain at least one region recognized by the conserved domain architecture
   retrieval tool (CDART) as a seq. motif. Motifs provide clues to biol. fn but
   CDART often matches the same region of a protein by two or more profiles.
   Such synonyms complicate ests. of functional complexity. We do full-linkage
   clustering of redundant profiles by finding maximum disjoint cliques: Each
   cluster is replaced by a single representative profile to give what we term a
   unique fn word (UFW). From 2009 to 2016, the # of seq. profiles used by CDART
   increased by 80%; the # of UFWs increased more slowly by 30%, indicating that
   the # of UFWs may be saturating. The # of seqs. matched by a single UFW
   (seqs. with single domain architectures) increased as slowly as the # of
   different words, whereas the # of seqs. matched by a combination of two or
   more UFWs in seqs. with multiple domain architectures (MDAs) increased at the
   same rate as the total # of seqs.. This combinatorial arrangement of a ltd #
   of UFWs in MDAs accounts for the genomic diversity of protein seqs.. Although
   eukaryotes & prokaryotes use very similar sets of 'words' or UFWs (57%
   shared), the 'sentences' (MDAs) are different (1.3% shared)."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1801182115">doi:10.1073/pnas.1801182115</A>]['18] (online 6/2018).

%A M. Griesmann
%A et al ...
%A S. Cheng
%T Phylogenomics reveals multiple losses of nitrogen-fixing
   root nodule symbiosis
%J Science
%V 361
%N 6398
%P eaat1743
%M JUL
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0718, angiosperm, NFN symbiosis,
   convergent, evolution, plant
%X "... Molecular phylogenies show that NFN symbiosis is restricted to four
   angiosperm orders - Fabales, Fagales, Cucurbitales, and Rosales - that
   together form the monophyletic NFN clade. However, only 10 of the 28 plant
   families within this clade contain species engaged in the NFN symbiosis. Even
   within these 10 families, most genera do not form this symbiosis. ...
   sequenced the genomes of seven nodulating species belonging to the Fagales,
   Rosales, and Cucurbitales orders and the legume subfamily Caesalpinioideae.
   We complemented this dataset by sequencing three genomes of nonnodulating
   species from the Cucurbitales and from the legume subfamilies Cercidoideae
   and Papilionoideae. ... We found that multiple independent losses of
   NFN symbiosis occurred in the four orders of the NFN clade. These results
   suggest that NFN symbiosis has previously been more common than currently
   evident and that this symbiosis is subject to an underestimated adverse
   selection pressure."
   -- -- [<A HREF="http://dx.doi.org/10.1126/science.aat1743">doi:10.1126/science.aat1743</A>]['18].
   (Also see [<A HREF="http://science.sciencemag.org/content/361/6398/125">news</A>]['18].)

%A A. Medlar
%A L. Holm
%T TOPAZ: asymmetric suffix array neighbourhood search for massive
   protein databases
%J BMC Bioinformatics
%V 19
%P 278
%M AUG
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0818, proteins, homolgy, Blast,
   SANS, SANSparallel, UniProtK, TOPAZ, seeds
%X "... many methods have been proposed as alternatives to BLAST that make an
   explicit trade-off between sensitivity & speed. One such method,
   SANSparallel, uses a parallel implementation of the suffix array
   neighbourhood search (SANS) technique to achieve high speed & provides
   several modes to allow for greater sensitivity at the expense of performance.
   ... present a new approach called asymmetric SANS together with scored seeds
   & an alternative suffix array ordering scheme called optimal substitution
   ordering. ... In our benchmark, searching UniProtKB for homologous proteins
   to the Dickeya solani proteome, TOPAZ took less than 3 minutes to achieve a
   sensitivity of 0.84 compared to BLAST."
   -- [<A HREF="https://doi.org/10.1186/s12859-018-2290-3">doi:10.1186/s12859-018-2290-3</A>]['18].

%A V. Slon
%A et al ...
%A S. Paabo
%T The genome of the offspring of a Neanderthal mother and a Denisovan father
%J Nature
%V ?
%P ?-?
%M AUG
%D 2018
%K jrnl, MolBio, c2018, c201x, c20xx, zz0818, ancient, human, fossil, DNA,
   Neanderthal, Denisovan, evolution, Denisova 11, Denisova11, interbreeding,
   Pleistocene, hominin
%X "Neanderthals & Denisovans are extinct groups of hominins that separated from
   each other more than 390,000 years ago. ... present the genome of
   'Denisova 11', a bone fragment from Denisova Cave (Russia) & show that it
   comes from an individual who had a N. mother & a D. father. The father, whose
   genome bears traces of N. ancestry, came from a popn related to a later D.
   found in the cave. The mother came from a population more closely related to
   Neanderthals who lived later in Europe than to an earlier N. found in D.
   Cave, suggesting that migrations of Ns. between eastern & western Eurasia
   occurred sometime after 120,000 years ago. The finding of a first-generation
   N.-D. offspring among the small # of archaic specimens sequenced to date
   suggests that mixing between Late Pleistocene hominin groups was common when
   they met."
   -- [<a HREF="https://doi.org/10.1038/s41586-018-0455-x">doi:10.1038/s41586-018-0455-x</A>]['18].
   [Also search for: ancient DNA].

%A I. Bobrovskiy
%A J. M. Hope
%A A. Ivantsov
%A B. J. Nettersheim
%A C. Hallmann
%T Ancient steroids establish the Ediacaran fossil Dickinsonia as one of the
   earliest animals
%J Science
%V 361
%N 6408
%P 1246-1249
%M SEP
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0119, ancient, life, fossil, fossils, Ediacaran,
   Ediacara, Dickinsonia, cholesteroids, steroid, cholesterol, animal,
   Brachina Gorge, Flinders Ranges, Reg Sprigg
%X "The first complex organisms emerged during the Ediacaran period, around 600
   million years ago. ... show that lipid biomarkers extracted from organically
   preserved Ediacaran macrofossils unambiguously clarify their phylogeny.
   Dickinsonia and its relatives solely produced cholesteroids, a hallmark of
   animals. Our results make these iconic members of the Ediacara biota the
   oldest confirmed macroscopic animals in the rock record, indicating that the
   appearance of the Ediacara biota was indeed a prelude to the Cambrian
   explosion of animal life."
   -- [<A HREF="https://doi.org/10.1126/science.aat7228">doi:10.1126/science.aat7228</A>]['18].
   (Ediacaran Period ... from the end of the Cryogenian 635 Mya, to the
   beginning of the Cambrian 541 Mya. ... name from the Ediacara Hills where
   geologist Reg Sprigg first discovered fossils of the eponymous Ediacara
   biota in 1946 ... Brachina Gorge in the Flinders Ranges ... E.biota include
   the oldest definite multicellular organisms (with specialized tissues) ..."
   -- Ediacaran@[<A HREF="https://en.wikipedia.org/wiki/Ediacaran">wikip</A>]['19].)

%A J. G. Greener
%A S. M. Kandathil
%A D. T. Jones
%T Deep learning extends de novo protein modelling coverage of genomes using
   iteratively predicted structural constraints
%J NatureComms
%V 10
%N #3977
%M SEP
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz0220, protein structure prediction, NN,
   ANN, DMPfold, CASP, CASP12
%X "The inapplicability of AA covariation methods to small protein families ...
   Recently, deep learning has shown promise in allowing accurate
   residue-residue contact prediction even for shallow sequence alignments. ...
   introduce DMPfold ... predict inter-atomic distance bounds, the main chain
   hydrogen bond n/wk, & torsion angles ... Applied to all Pfam domains without
   known structures, confident models for 25% of these so-called dark families
   were produced in under a week on a small 200 core cluster. DMPfold provides
   models for 16% of human proteome UniProt entries without structures,
   generates accurate models with fewer than 100 seqs. in some cases, & is
   freely available."
   -- [<A HREF="https://doi.org/10.1038/s41467-019-11994-0">doi:10.1038/s41467-019-11994-0</A>]['20],
      1811.12355@[<A HREF="https://arxiv.org/abs/1811.12355">arXiv</A>]['20].
   [Also search for: MolBio protein deep learning].

%A J. J. Walsh
%A et al ...
%A M. S. Tremblay
%T Associations between 24 hour movement behaviours and global cognition in
   US children: a cross-sectional observational study
%X The Lancet
%V ?
%M SEP
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0918, health, human, child, early childhood,
   children, development, health, electronic devices, internet, www, web,
   device, TV, tablet, screen, screens, time, cognition, exercise
%X "... Complete movement behaviour data were available for 4520 participants.
   The mean # of guideline recommendations met was 1.1 (SD 0.9). Overall, 2303
   (51%) participants met the sleep recommendation, 1655 (37%) met screen time,
   & 793 (18%) met the physical activity r.. 3190 (71%) participants met at
   least one r., whereas 216 (5%) of participants met all three recommendations.
   Global cognition was + assoc. with each additional recommendation met
   (b=1.44, 95% CI 0.82-2.07, p < 0.0001). Compared with meeting none of the
   recommendations, associations with superior global cognition were found in
   participants who met all three recommendations (b=3.89, 95% CI 1.43 to 6.34,
   p=0.0019), the screen time recommendation only (b=4.25, 2.50-6.01,
   p < 0.0001), & both the screen time and the sleep recommendations (b=5.15,
   3.56-6.74, p < 0.0001).  ..."
   -- [<A HREF="https://doi.org/10.1016/S2352-4642(18)30278-5">doi:10.1016/S2352-4642(18)30278-5</A>]['18].
   (Also see the [<A HREF="https://www.bbc.com/news/health-45651725">bbc</A>][27/9/2018].)

%A Y. Erlich
%A T. Shor
%A I. Peer
%A S. Carmi
%T Identity inference of genomic data using long-range familial searches
%J Science
%V ?
%P ?
%M OCT
%D 2018
%K jrnl, MolBio, eaau4832, c2018, c201x, c20xx, zz1018, human, DNA, ancestry,
   relatives, relations, genealogy, familial, genetic, privacy, security,
   law, policing, forensic, DNAland, GEDmatch, GATACCA
%X "Consumer genomics databases have reached the scale of millions of
   individuals. Recently, law enforcement authorities have exploited some of
   these databases to identify suspects via distant familial relatives. ...
   We project that about 60% of the searches for individuals of European-descent
   will result in a third cousin or closer match, which can allow their
   identification using demographic identifiers. [&] could implicate nearly any
   US-individual of European-descent in the near future. We demonstrate that the
   technique can also identify research participants of a public sequencing
   project. Based on these results, we propose a potential mitigation strategy
   & policy implications to human subject research."
   -- [<A HREF="https://doi.org/10.1126/science.aau4832">doi:10.1126/science.aau4832</A>]['18].  (44 refs.)
   (?Here comes 'GATACCA'?)

%A A. Husby
%A J. Wohlfahrt
%A N. Oyen
%A M. Melbye
%T Pregnancy duration and breast cancer risk
%J NatureComms
%V 9
%P e4255
%M OCT
%D 2018
%K jrnl, eJrnl, c2018, c201x, c20xx, zz1018, human, health, breast cancer,
   pregnancy, women, female, risks
%X "Full-term pregnancies reduce a woman's long-term breast cancer risk, while
   abortions have been shown to have no effect. ... found the reduction in
   b.cancer risk was not observed for pregnancies lasting 33 weeks or less,
   but restricted to those pregnancies lasting 34 weeks or longer. ... suggest
   that a distinct biological effect introduced around week 34 of pregnancy
   holds the key to understand pregnancy-assoc. b.cancer protection."
   -- [<A HREF="https://doi.org/10.1038/s41467-018-06748-3">doi:10.1038/s41467-018-06748-3</A>]['18].

%A L. Nunney
%T Size matters: height, cell number and a person's risk of cancer
%J Proc. Royal Soc. B
%V 285
%N 1889
%P ?-?
%M OCT
%D 2018
%K jrnl, PRSB, c2018, c201x, c20xx, zz1018, human health, risk, risks, height,
   cancer, Peto's paradox, IGF-1, IGF1
%X "The multistage model of carcinogenesis predicts cancer risk will increase
   with tissue size, since more cells provide more targets for oncogenic somatic
   mutation. However, this increase is not seen among mammal species of
   different sizes (Peto's paradox), ... the hazard ratio for overall cancer
   risk per 10cm increase in human height (HR10) is ~ 1.1, indicating a 10%
   increase in c.risk per 10cm; however, an alternative explanation invokes an
   indirect effect of height, with factors that increase c.risk indep.
   increasing adult height. ... For overall c.risk the HR10 predicted v.
   observed was 1.13 versus 1.12 for women % 1.11 versus 1.09 for men,
   suggesting that cell # variation provides a null hypothesis for assessing
   height effects. ..."
   -- [<A HREF="https://doi.org/10.1098/rspb.2018.1743">doi: 10.1098/rspb.2018.1743</A>]['18].
   (Also see the [<A HREF="https://www.abc.net.au/news/science/2018-10-24/height-cancer-risk-tall-genetic-cells-carcinogensis/10404910">abc</A>][10/2018].)

%A P. J. Yang
%A et al ...
%A D. Hu
%T How do wombats make cubed poo?
%J 71st Annual Meeting of the APS Division of Fluid Dynamics
%M NOV
%D 2018
%K conf, c2018, c201x, c20xx, zz1118, biol, biology, wombat, Australia,
   marsupial, animal, poo, scat, scats, feces, faeces, cube, cubic, E19.00001,
   IgNobel prize, Ig, funny, ha ha haha
%X "Wombats are fossorial herbivorous Australian marsupials with the distinctive
   feature of producing cubic feces, which is unique in the animal kingdom. In
   the built world, cubic structures are created by extrusion or injection
   molding, but there are few examples of this feat in nature. We investigate
   how wombats produce cubic feces, through investigation of the structure and
   mechanics of two dissected alimentary systems of wombats - derived from
   veterinary euthanized individuals following motor vehicle collisions in
   Tasmania, Australia. In the final 8% of the intestine, feces changed from a
   liquid-like state into a solid state composed of separated cubes of length
   2cm. This shape change was due to the azimuthally varying elastic properties
   of the intestinal wall. By emptying the intestine and inflating it with a
   long balloon, we found that the local strain varies from 20 percent at the
   cube's corners to 75 percent at its edges. Thus, the intestine stretches
   preferentially at the walls to facilitate cube formation. This study
   addresses the long-standing mystery of cubic scat formation and provides
   insight into new manufacturing techniques for non-axisymmetric structures
   using soft tissues."
   -- [<A HREF="http://meetings.aps.org/Meeting/DFD18/Session/E19.1">www</A>]['18].
   (Also see the [<A HREF="https://www.bbc.com/news/world-australia-46258616">bbc</A>][20/11/2018].)
   ?IgNobel possibility? You betcha: physics [<A HREF="https://www.improbable.com/2019/09/12/announcing-the-2019-ig-nobel-prize-winners/">2019</A>].
   [Also search for: wombat poo] and [also search for: Yang urination].

%A C. M. Werner
%A et al ...
%A U. Laufs
%T Differential effects of endurance, interval, and resistance training on
   telomerase activity and telomere length in a randomized, controlled study
%J Euro. Heart J.
%P ehy585
%M NOV
%D 2018
%K jrnl, eJrnl, c2018, c201x, c20xx, zz0119, human health, aging, ageing,
   aerobic, endurance, resistance, exercise, training, telomere, length,
   telomerase, cellular, CD14, CD34
%X "... This randomized controlled trial shows that endurance training, IT, and
   RT protocols induce specific cellular pathways in circulating leucocytes.
   Endurance training and IT, but not RT, increased telomerase activity and TL
   which are important for cellular senescence, regenerative capacity, and thus,
   healthy aging."  [44 refs.]
   -- [<A HREF="https://doi.org/10.1093/eurheartj/ehy585">doi:10.1093/eurheartj/ehy585</A>]['18].

%A S. Luo
%A et al ...
%A T. Huang
%T Biparental inheritance of mitochondrial DNA in humans
%J PNAS
%V ?
%P ?-?
%M NOV
%D 2018
%K jrnl, PNAS, MolBio, c2018, c201x, c20xx, zz1118, mitochondria, DNA, mtDNA,
   human, mother, father, paternal, parent, heteroplasmy
%X "... we identified three unrelated multigeneration families with a high level
   of mtDNA heteroplasmy (ranging from 24 to 76%) in a total of 17 individuals.
   Heteroplasmy of mtDNA was independently examined by high-depth whole mtDNA
   sequencing analysis in our research laboratory and in two Clinical Laboratory
   Improvement Amendments and College of American Pathologists-accredited
   laboratories using multiple approaches. A comprehensive exploration of mtDNA
   segregation in these families shows biparental mtDNA transmission with an
   autosomal dominant like inheritance mode. Our results suggest that, although
   the central dogma of maternal inheritance of mtDNA remains valid, there are
   some exceptional cases where paternal mtDNA could be passed to the
   offspring. ..."  (online 28/11/2018)
   -- [<A HREF="https://doi.org/10.1073/pnas.1810946115">doi:10.1073/pnas.1810946115</A>]['18].
   [Also search for: MolBio mtDNA].

%A M. AlQuraishi
%T Some thoughts on a mysterious universe
%J wordpress
%M DEC
%D 2018
%K news, views, MolBio, c2018, c201x, c20xx, zz1218, MolBio, protein, folding,
  structure, prediction, CASP, CASP13, AlphaFold, DeepMind, google
%X "... you may have heard that DeepMind's debut went rather well. So well in
   fact that not only did they take first place, but put a comfortable distance
   between them and the second place predictor ..."
   -- [<A HREF="https://moalquraishi.wordpress.com/">www</A>]['18].
   (*See [<A HREF="http://predictioncenter.org/casp13/index.cgi">casp13</A>]['18].*)
   [Also search for: MolBio alphafold].

%A S. A. Purro
%A et al ...
%A J. Collinge
%T Transmission of amyloid-beta protein pathology from cadaveric pituitary
   growth hormone
%J Nature
%V ?
%N ?
%P ?-?
%M DEC
%D 2018
%K jrnl, c2018, c201x, c20xx, zz1218, human health, risk, risks,
   Creutzfeldt-Jakob disease, CJD, Alzheimers, transmission, prion
%X "We previously reported the presence of amyloid-beta protein (Abeta) deposits
   in individuals with Creutzfeldt-Jakob disease (CJD) who had been treated
   during childhood with human cadaveric pituitary-derived growth hormone
   (c-hGH) contaminated with prions. ..."
      -- [<A HREF="https://doi.org/10.1038/s41586-018-0790-y">doi:10.1038/s41586-018-0790-y</A>]['18].
   [Also search for: prion disease].

%A Haoji Wu
%A et al ...
%A B. D. Humphries
%T Comparative analysis and refinement of human PSC-derived kidney organoid
   differentiation with single-cell transcriptomics
%J Cell Stem Cell
%V 23
%N 6
%P 869-881.e8
%M DEC
%D 2018
%K jrnl, MolBio, organoid, c2018, c201x, c20xx, zz0720, kidney, transcriptome,
   PSC, BDNF, Dropseq, scRNAseq. scRNA-seq
%X "...We compared two directed differentiation protocols by single-cell
   transcriptomics of 83,130 cells from 65 organoids with single-cell
   transcriptomes of fetal and adult kidney cells. Both protocols generate a
   diverse range of kidney cells with differing ratios, but organoid-derived
   cell types are immature, and 10%-20% of cells are non-renal. Reconstructing
   lineage relationships by pseudotemporal ordering identified ligands,
   receptors, & transcr'n factor networks associated with fate decisions. ..."
   -- [<A HREF="https://doi.org/10.1016/j.stem.2018.10.010">doi:10.1016/j.stem.2018.10.010</A>]['20].
   [Also search for: scRNAseq MolBio].

%A H. Naci
%A et al
%T How does exercise treatment compare with antihypertensive medications?
   A network meta-analysis of 391 randomised controlled trials assessing
   exercise and medication effects on systolic blood pressure
%J British J. Sports Med.
%V ?
%P ?-?
%M DEC
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0119, human health, blood pressure, SBP,
   hypertension, exercise
%X "... Assuming equally reliable estimates, the SBP-lowering effect of exercise
   among hypertensive populations appears similar to that of commonly used
   antihypertensive medications. Generalisability of these findings to
   real-world clinical settings should be further evaluated."
   -- [<A HREF="https://doi.org/10.1136/bjsports-2018-099921">doi:10.1136/bjsports-2018-099921</A>]['18], online 18/12/2018.

%A M. Gehringer
%A S. A. Laufer
%T Emerging and re-emerging warheads for targeted covalent inhibitors:
   Applications in Medicinal Chemistry and Chemical Biology
%J J. Med. Chem.
%V 62
%N 12
%P 5673-5724
%M DEC
%D 2018
%K MolBio, jrnl, c2018, c201x, c20xx, zz0820, drug design, warhead, ligand,
   inhibitor, Cys, TCI, TCIs, reactivity, anions
%X "... Currently, targeting noncatalytic cysteine residues with acrylamides &
   other alpha,beta-unsaturated carbonyl compounds is the predominant strategy
   in TCI development. ... provides an overview of warheads - beyond
   a,b-unsaturated amides - recently used in the design of targeted covalent
   ligands. Promising reactive groups that have not yet demonstrated their
   utility in TCI development are also highlighted. ..."
   -- [<A HREF="https://doi.org/10.1021/acs.jmedchem.8b01153">doi:10.1021/acs.jmedchem.8b01153</A>]['20],
      [<A HREF="https://europepmc.org/article/MED/30565923">www</A>]['20].

%A R. Molania
%T Identification and removal of unwanted variation in large gene expression
   data
%I Uni. Melb.
%D 2018
%K PhD thesis, MolBio, stats, c2018, c201x, c20xx, zz0820, RNAseq, RNA-seq,
   mRNA, Nanostring, nCounter, gene expression levels, microarray, purity,
   batch effects, normalisation, normalization, screening,
   The Cancer Genome Atlas, TCGA
%X "Gene expression experiments ...  include: identifying & classifying disease
   types, assessing the transcriptional differences between the state of a
   disease & normal cells, & identifying biomarkers to predict clinical outcome
   of diseases such as cancer, ..."
   -- [<A HREF="http://hdl.handle.net/11343/226888">www</A>]['20].
   [WEHIseminar 4/8/'20].
   [Also search for: MolBio RNAseq].

%A S. C. Potter
%A A. Luciani
%A S. R. Eddy
%A Y. Park
%A R. Lopez
%A R. D. Finn
%T HMMER web server: 2018 update
%J NAR
%V 46
%N W1
%P W200-W204
%M JUL
%D 2018
%K MolBio, c2018, c201x, c20xx, zz0121, profile, alignment, HMM, HMMER,
   JackHMMER
%X "... provides fast searches against widely used seq. DBs & profile hidden
   Markov model (HMM) libraries ... The jackhmmer search alg. allows iterative
   searches against a seq. DB, where subsequent queries are profile HMMs built
   from the aligned hit sequences of a preceding search. ..."
   -- [<A HREF="https://doi.org/10.1093/nar/gky448">doi:10.1093/nar/gky448</A>]['21].
   [Also search for: MolBio HMMER].

%A J. M. Jumper
%A N. F. Faruk
%A K. F. Freed
%A T. R. Sosnick
%T Trajectory-based training enables protein simulations with accurate folding
   and Boltzmann ensembles in cpu-hours
%J PLoS Comp. Biol.
%M DEC
%D 2018
%K jrnl, eJrnl, MolBio, c2018, c201x, c20xx, zz1222, Upside, protein folding,
   simulation, trajectory
%X "... we use the contrastive divergence technique from mach.l. to train from
   simulations of 450 proteins. ... the computational efficiency of the model
   enables high accuracy through the precise tuning of the Boltzmann ensemble.
   ... applied to our recently developed Upside model, where the free energy for
   side chains is rapidly calculated at every time-step, allowing for a smooth
   energy landscape without steric rattling of the side chains. After this
   contrastive divergence training, the model is able to de novo fold proteins
   up to 100 residues on a single core in days. ..."
   -- [<A HREF="https://doi.org/10.1371/journal.pcbi.1006578">doi:10.1371/journal.pcbi.1006578</A>]['22].  (JJ involved with AlphaFold).
   [Also search for: protein folding simulation].

%A H. A. Grunwald
%A et al ...
%A K. L. Cooper
%T Super-Mendelian inheritance mediated by CRISPR-Cas9 in the
   female mouse germline
%J Nature
%V ?
%N ?
%P ?-?
%N JAN
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz0119, gene drive, mammal, mouse,
   CRISPR Cas9, biology, risks
%X "A gene drive biases the transmission of one of the two copies of a gene such
   that it is inherited more frequently than by random segregation. Highly
   efficient gene drive systems have recently been developed in insects ... we
   use an active genetic elt that encodes a guide RNA, which is embedded in the
   mouse tyrosinase (Tyr) gene, to evaluate whether targeted gene conversion can
   occur when CRISPR-Cas9 is active in the early embryo or in the developing
   germline. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-0875-2">doi:10.1038/s41586-019-0875-2</A>]['19].
   [Also search for: MolBio gene drive].

%A S. S. Dominy
%A et al ...
%A J. Potema
%T Porphyromonas gingivalis in Alzheimer's disease brains: Evidence for disease
   causation and treatment with small-molecule inhibitors
%J Sci. Adv.
%V 5
%M 1
%P ?-?
%M JAN
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0119, human, brain, Alzheimers disease,
   Porphyromonas gingivalis, gingival, gingipains, bacterium, Cortexyme,
   periodontitis, plaques, Tau, ubiquitin, dementia
%X "Porphyromonas gingivalis, the keystone pathogen in chronic periodontitis,
   was identified in the brain of Alzheimer's disease patients. Toxic proteases
   from the bacterium called gingipains were also identified in the brain of
   Alzheimer's patients, and levels correlated with tau and ubiquitin
   pathology. ... we designed and synthesized small-molecule inhibitors
   targeting gingipains. ..."
   -- [<A HREF="https://doi.org/10.1126/sciadv.aau3333">doi:10.1126/sciadv.aau3333</A>]['19].

%A S. Mayer
%A et al ...
%A A. R. Kriegstein
%T Multimodal single-cell analysis reveals physiological maturation in the
   developing human neocortex
%J Neuron
%V 102
%N 1
%P 143-158.e7
%M APR
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz0720, cell, human, brain, neocortex,
   neurons, glia, HTR2A, neurotransmitter, differentiation
%X "... While single-cell RNA sequencing has revealed cellular diversity,
   physiological heterogeneity has yet to be mapped onto these developing &
   diverse cell types. By combining measurements of intracellular Ca2+
   elevations in response to neurotransmitter receptor agonists & RNA sequencing
   of the same single cells, we show that Ca2+ responses are cell-type-specific
   & change dynamically with lineage progression. Physiological response
   properties predict molecular cell identity & additionally reveal diversity
   not captured by single-cell transcriptomics. ..."
   -- [<A HREF="https://doi.org/10.1016/j.neuron.2019.01.027">doi:10.1016/j.neuron.2019.01.027</A>]['20].
   [Also search for: MolBio cell differentiation].

%A F. Chao
%A P. Gerland
%A A. R. Cook
%A L. Alkema
%T Systematic assessment of the sex ratio at birth for all countries and
   estimation of national imbalances and regional reference levels
%J PNAS
%M APR
%D 2019
%K jrnl, PNAS, c2019, c201x, c20xx, zz0419, population, selective abortion,
   birth, births, son, boys, daughter, girls, babies, sex ratio, stats, balance,
   imbalance, SRB, China, India, human, biology, biol
%X "The sex ratio at birth (SRB; ratio of male to female live births) imbalance
   in parts of the world over the past few decades is a direct consequence of
   sex-selective abortion, driven by the coexistence of son preference ...
   develop Bayesian methods for SRB estimation for all countries from 1950 to
   2017. We model the SRB regional & national reference levels, the fluctuation
   around national reference levels, & the inflation. The estimated regional
   reference levels range from 1.031 (95% uncertainty interval [1.027; 1.036])
   in sub-Saharan Africa to 1.063 [1.055; 1.072] in southeastern Asia, 1.063
   [1.054; 1.072] in eastern Asia, & 1.067 [1.058; 1.077] in Oceania. We
   identify 12 countries with strong statistical evidence of SRB imbalance
   during 1970-2017, resulting in 23.1 [19.0; 28.3] million missing f.births
   globally. The majority of those missing f.births are in China, with
   11.9 [8.5; 15.8] million, & in India, with 10.6 [8.0; 13.6] million."
      ("... Under normal circumstances, SRB varies in a narrow range around 1.05
      ... maximum SRB since the start of [SRB-] inflation are in China (1.179
      [1.141; 1.221] in 2005), Armenia (1.176 [1.150; 1.203] in 2000), ...")
   -- [<A HREF="https://doi.org/10.1073/pnas.1812593116">doi:10.1073/pnas.1812593116</A>]['19].
   [Also search for: sex ratio biology].

%A M. AlQuraishi
%T AlphaFold at CASP13
%J Bioinformatics
%V ?
%M MAY
%D 2019
%K news, views, MolBio, c2019, c201x, c20xx, zz0819, protein, fold, folding,
   de novo, deNovo, structure prediction, distance, angle, NN, ANN,
   Al Quraishi, google, deepmind, alphafold, alphafold1, alfafold,
   conf, CASP 13, CASP13
%X "... DeepMind's [CASP13] entry, AlphaFold, placed first in the Free
   Modeling (FM) category, which assesses methods on their ability to predict
   novel protein folds (the Zhang group placed first in the Template-Based
   Modeling (TBM) category, which assess methods on predicting proteins whose
   folds are related to ones already in the Protein Data Bank.) DeepMind's
   success generated significant public interest. Their approach builds on two
   ideas developed in the academic community during the preceding decade:
   (i) the use of co-evolutionary analysis to map residue co-variation in
   protein sequence to physical contact in protein structure, and (ii) the
   application of deep neural networks to robustly identify patterns in protein
   sequence and co-evolutionary couplings & convert them into contact maps ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btz422">doi:10.1093/bioinformatics/btz422</A>]['19] (corrected proof).
   (*Also see alphafold@[<A HREF="https://deepmind.com/blog/alphafold/">deepmind</A>][2019].*)
   [Also search for: MolBio alphafold].

%A R. Salomon
%A et al
%T Droplet-based single cell RNAseq tools: a practical guide
%J Lab. Chip
%V 19
%N 10
%P 1706-1727
%M MAY
%D 2019
%K MolBio, c2019, c201x, c20xx, zz0820, droplet, flow cell, flowCell, intro,
   survey, guide, scRNA seq, scRNAseq, RNAseq, DropSeq, inDrop, 10X
%X "Droplet based scRNA-seq sys. such as Drop-seq, inDrop & Chromium 10X ...
   scRNA-seq technologies in the res.lab.. ...  we provide a practical guide
   through all the steps involved in a typical scRNA-seq experiment. ..."
   -- [<A HREF="https://doi.org/10.1039/c8lc01239c">doi:10.1039/c8lc01239c</A>]['20],
      abs@[<A HREF="https://pubmed.ncbi.nlm.nih.gov/30997473/">p'bmed</A>]['20].
   [Also search for: scRNAseq]  and  [also search for: MolBio flowCell].

%A E. R. Gamazon
%A A. H. Zwinderman
%A N. J. Cox
%A D. Denys
%A E. M. Derks
%T Multi-tissue transcriptome analyses identify genetic mechanisms underlying
   neuropsychiatric traits
%J Nature Genetics
%V ?
%P ?-?
%M MAY
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0519, MolBio, genes, gene, human,
   mental illness, health, psychiatric disorder, schizophrenia, bipolar, ADHD,
   depression, PrediXcan, GWAS, brain
%X "... provide comprehensive analyses using transcriptome data from an
   unprecedented collection of tissues to gain pathophysiological insights into
   the role of the brain, neuroendocrine factors (adrenal gland) &
   gastrointestinal systems (colon) in psychiatric disorders. In each tissue, we
   perform PrediXcan analysis & identify trait-assoc. genes for schizophrenia
   (n associations=499; n unique genes=275), bipolar disorder (n assoc.=17;
   n unique genes=13), attention deficit hyperactivity disorder (n assoc.=19;
   n unique genes=12) & broad depression (n assoc.=41; n unique genes=31).
   Importantly, both PrediXcan & summary-data-based Mendelian
   randomization/heterogeneity in dependent instruments analyses suggest
   potentially causal genes in non-brain tissues, showing the utility of these
   tissues for mapping psychiatric disease genetic predisposition. Our analyses
   further highlight the importance of joint tissue approaches as 76% of the
   genes were detected only in difficult-to-acquire tissues."
   -- [<A HREF="https://doi.org/10.1038/s41588-019-0409-8">doi:10.1038/s41588-019-0409-8</A>]['19].

%A M. Krenn
%A et al
%T Self-referencing embedded strings (SELFIES): A 100% robust molecular string
   representation
%J arXiv
%M MAY
%D 2019
%O Mach. Learn., Sci. Technol. (MLST), 1, 045024, Oct., 2020
%K TR, c2019, c201x, c20xx, zz1221, SELFIES, SMILES, molecule, representation,
   chemical compound, molecule, string
%X "... the std strings molecular rep'n SMILES shows substantial weaknesses
   in that task because large fractions of strings do not corr. to valid
   molecules. ... we solve this problem at a fundamental level & introduce
   SELFIES (SELF-referencIng Embedded Strings), a string-based rep'n of
   molecules which is 100% robust. Every SELFIES string corresponds to a valid
   molecule, & SELFIES can represent every molecule. SELFIES can be directly
   applied in arb. m/c learning models without the adaptation of the models;
   each of the generated molecule candidates is valid. In our experiments, the
   model's internal memory stores two orders of magnitude more diverse molecules
   than a similar test with SMILES. [&] as all molecules are valid, it allows
   for explanation & interp'n of the internal working of the generative models."
   -- 1905.13741@[<A HREF="https://arxiv.org/abs/1905.13741">arXiv</A>]['21].
   [Also search for: chemical SMILES].

%A B. Nikolay
%A et al
%J NEJM
%T Transmission of Nipah virus - 14 years of investigations in Bangladesh
%M MAY
%D 2019
%K MolBio, jrnl, NEJM, c2019, c201x, c20xx, zz0121, nipah, virus, NiV, RNAvirus,
   henipavirus, fruit bats, fruitBat, bat, pig, pigs
%X "... Of 248 Nipah virus cases identified, 82 were caused by person-to-person
   transmission, corr. to a reproduction number (i.e., the avg # of secondary
   cases per case patient) of 0.33 (95% [CI], 0.19 to 0.59) ..."
   -- [<A HREF="https://www.nejm.org/doi/10.1056/NEJMoa1805376">doi:10.1056/NEJMoa1805376</A>]['21].
   Also see, "... ~50 to 75% risk of death ..."
   -- nipah@[<A HREF="https://en.wikipedia.org/wiki/Nipah_virus_infection">wikip</A>]['21].

%A K. J. Gan
%A T. C. Sudhof
%T Specific factors in blood from young but not old mice directly promote
   synapse formation and NMDA-receptor recruitment
%J PNAS
%V ?
%P ?-?
%M JUN
%D 2019
%K jrnl, PNAS, c2019, c201x, c20xx, zz0619, human health, age, ageing, aging,
   brain, young blood, mouse, mice, THBS 4, THBS4, SPARCL 1, SPARCL1, NMDA,
   proteins
%X "... we show that serum extracted from the blood of young but not old mice,
   when applied to neurons transdifferentiated from human embryonic stem cells,
   directly increased dendritic arborization, augmented synapse numbers, doubled
   dendritic spine-like structures, and elevated synaptic N-methyl-d-aspartate
   (NMDA) receptors, thereby increasing synaptic connectivity. Mass spectrometry
   revealed that thrombospondin-4 (THBS4) and SPARC-like protein 1 (SPARCL1)
   were enriched in serum from young mice. Strikingly, recombinant THBS4 and
   SPARCL1 both increased dendritic arborization and doubled synapse numbers in
   cultured neurons. In addition, SPARCL1 but not THBS4 tripled NMDA
   receptor-mediated synaptic responses. Thus, at least two proteins enriched in
   young blood, THBS4 and SPARCL1, directly act on neurons as synaptogenic
   factors. ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.1902672116">doi:10.1073/pnas.1902672116</A>]['19].

%A P. Muralidhar
%T Mating preferences of selfish sex chromosomes
%J Nature
%V 570
%P 376-379
%M JUN
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0619, sexual, sex, mate selection, preference,
   male, female, trait, traits, Fisher runaway, Zahavi handicap, birds, animals,
   DNA, fitness, ornamentation, chromosome X W, Wchr, chrW, Xchr, chrX
%X "The evolution of female mating preferences for harmful male traits is a
   central paradox of sexual selection. Two dominant explanations for this
   paradox are Fisher's runaway process, which is based on genetic correlations
   between preference and trait and Zahavi's handicap principle, in which the
   trait is an honest costly signal of male quality. ...  present a mechanism
   for the evolution of female mating preferences for harmful male traits that
   is based on the selfish evolutionary interests of sex chrs. ... female-biased
   genetic elements - such as the W and X sex chromosomes - will evolve mating
   preferences for males who display traits that reduce their fitness and/or
   that of their male offspring, but increase fitness in female offspring. In
   particular, W-linked preferences can cause nearly lethal male traits to
   sweep to fixation. Sex-linked preferences can drive the evolution of traits
   such as ornamental handicaps and male parental care, and can explain
   variation in ornamentation and behaviour across taxa with divergent
   sex-determining mechanisms."
   [Also search for: sex chromosome].

%A F. Thomas
%A T. Madsen
%A M. Giraudeau
%A D. Misse
%A R. Hamede
%A O. Vincze
%A F. Renaud
%A B. Roche
%A B. Ujvari
%T Transmissible cancer and the evolution of sex
%J PLoS Biology
%V 17
%N 6
%P e3000275
%M JUN
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz0619, biology, biol, sex, sexual,
   asexual, reproduction, transmissible cancer, evolution, reasons, origins,
   Tasmanian devil
%X "The origin & subsequent maintenance of sex & recombination are among the
   most elusive & controversial problems in evolutionary biology. ... propose a
   novel hypothesis, suggesting that sexual reproduction not only evolved to
   reduce the -ve effects of the accumulation of deleterious mutations &
   processes assoc. with pathogen &/or parasite resistance but also to prevent
   invasion by transmissible selfish neoplastic cheater cells, henceforth
   referred to as transmissible cancer cells. Sexual repro. permits systematic
   change of the multicellular organism's genotype & hence an enhanced detection
   of trans. c.cells by immune system. Given the omnipresence of oncogenic
   processes in multicellular organisms, together with the fact that
   transmissible c.cells can have dramatic effects on their host fitness, our
   scenario suggests that the benefits of sex & concomitant recombination will
   be large & permanent, explaining why sexual reproduction is, despite its
   costs, the dominant mode of reproduction among eukaryotes."
   -- [<A HREF="https://doi.org/10.1371/journal.pbio.3000275">doi:10.1371/journal.pbio.3000275</A>]['19].
   (Also see the abc[<A HREF="https://www.abc.net.au/news/science/2019-06-08/transmissible-cancer-tasmanian-devils-evolution-of-sex/11183112">8/6/2019</A>].)

%A G. Musser
%A D. Ksepka
%A D. J. Field
%T New material of Paleocene-Eocene Pellornis (Aves: Gruiformes) clarifies the
   pattern and timing of the extant Gruiform radiation
%J Diversity
%V 11
%N 7
%P 102
%M JUN
%D 2019
%K c2019, c201x, c20xx, zz0719, biology, evolution, phylogeny, bird, birds,
   survived, ground dwelling, arboreal, dinosaur, Cretaceous mass extinction,
   Pellornis mikkelseni, Ralloidea, Gruiforme, Neoaves
%X "Pellornis mikkelseni is an early gruiform from the latest Paleocene-earliest
   Eocene Fur Formation of Denmark. At ~54 million years old, it is among the
   earliest clear records of the Gruiformes. The holotype specimen, & only
   material thus far recognised, was originally considered to comprise a partial
   postcranial skeleton. ...
   Phylogenetic analyses recover a clade containing P.mikkelseni, Messelornis,
   Songzia and crown Ralloidea, supporting P.mikkelseni as a crown gruiform.
   The phylogenetic position of P.mikkelseni illustrates that some recent
   divergence time analyses have underestimated the age of crown Gruiformes.
   Our results suggest a Paleocene origin for this important clade, bolstering
   evidence for a rapid early radiation of Neoaves following the end-Cretaceous
   mass extinction."
   -- [<A HREF="https://doi.org/10.3390/d11070102 ">doi:10.3390/d11070102 </A>]['19].
   (Also see NatGeo[<A HREF="https://news.nationalgeographic.com/2018/05/dinosaurs-asteroid-birds-forests-fires-paleontology-science/">24/5/2018</A>].

%A S. J. Cook
%A et al ...
%A S. W. Emmons
%T Whole-animal connectomes of both Caenorhabditis elegans sexes
%J Nature
%V 571
%P 63-71
%M JUL
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz0323, animal, insect, fly, brain,
   Drosophila, male, female, neurons, synapses, network, connectivity,
   connectome, flyconnectome
%X "... We present quantitative connectivity matrices that encompass all
   connections from sensory input to end-organ output across the entire animal,
   information that is necessary to model behaviour. ... differs between sexes
   at multiple levels. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-1352-7">doi:10.1038/s41586-019-1352-7</A>]['23].
   (Also see [<A HREF="https://flyconnecto.me/">flyconnectome</A>]['23] and
   connectome@[<A HREF="https://en.wikipedia.org/wiki/Connectome">wikip</A>].)
   [Also search for: MolBio connectome].

%A R. Molania
%A J. A. Gagnon-Bartsch
%A A. Dobrovic
%A T. P. Speed
%T A new normalization for Nanostring nCounter gene expression data
%J NAR
%V 47
%N 12
%P 6073-6083
%M JUL
%D 2019
%K jrnl, NAR, MolBio, c2019, c201x, c20xx, zz0820, stats, normalisation,
   amount, batch effects, RUV-III, RUVIII, RUV3, technical replicate,
   pseudoreplicate, expression levels, RNA-seq, RNAseq
%X "The Nanostring nCounter gene expression assay uses molecular barcodes &
   single molecule imaging to detect & count hundreds of unique transcripts in a
   single reaction. These counts need to be normalized to adjust for the amount
   of sample, variations in assay efficiency & other factors. ... we present a
   new n.method, Removing Unwanted Variation-III (RUV-III), which makes vital
   use of technical replicates & suitable control genes. We also propose an
   approach using pseudo-replicates when tech.replicates are not available. ..."
   -- [<A HREF="https://doi.org/10.1093/nar/gkz433">doi:10.1093/nar/gkz433</A>]['20].

%A V. Kiselev
%A et al ...
%A M. Hemberg
%T Analysis of single cell RNA-seq data
%I Sanger Inst.
%M JUL
%D 2019
%K intro, course, MolBio, c2019, c20x, c20xx, zz0820, scRNA-seq, scRNAseq,
   Sanger, uk, cells, transcriptome data, mRNA, RNA, gene expression
%X "Today it is possible to obtain genome-wide transcriptome data from single
   cells using high-throughput sequencing (scRNA-seq). ..."
   -- [<A HREF="https://scrnaseq-course.cog.sanger.ac.uk/website/index.html">www</A>]['20].
   [Also search for: scRNAseq].

%A D. Kim
%A et al ...
%A S. L. Salzberg
%T Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
%J Nat. Biotechnology
%V 37
%P 907-915
%M AUG
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz0820, HISAT, HISAT2, DNA, RNA, mRNA,
   mapping, reference, scRNAseq, scRNA seq, BWT, FMindex, GFM
%X "... HISAT2 (hierarchical indexing for spliced alignment of transcripts 2)
   that can align both DNA & RNA seqs. using a graph Ferragina Manzini index. We
   use HISAT2 to represent & search an expanded model of the human reference
   genome in which over 14.5 million genomic variants in combination with
   haplotypes  ... outperforms other computational methods & matches or exceeds
   the performance of laboratory-based assays."
   -- [<A HREF="https://doi.org/10.1038/s41587-019-0201-4">doi:10.1038/s41587-019-0201-4</A>]['20],
    & s/w@[<A HREF="http://daehwankimlab.github.io/hisat2/">gith'b</A>]['20].
   [Also search for: scRNAseq].

%A M. Steinegger
%A et al ...
%A J. Soding
%T HH-suite3 for fast remote homology detection and deep protein annotation
%J BMC Bioinformatics
%V 20
%N 1
%P 473
%M SEP
%D 2019
%K jrnl, eJrnl, MolBio, c2019, c201x, c20xx, zz0121, HMM, profile, HH, HHblits,
   HHsuite, HH suite, HHsearch, HMMER, alignment
%X "... developed a single-instruction multiple-data (SIMD) vectorized
   implementation of the Vit.alg. for profile HMM alignment & introduced
   various other speed-ups. ..."
   -- [<A HREF="https://doi.org/10.1186/s12859-019-3019-7">doi:10.1186/s12859-019-3019-7</A>]['21].
   [Also search for: HHsuite]  and  [also search for: MolBio HMM].

%A M. S. Johnson
%A A. Martsu
%A S. Kryazhimskiy
%A M. M. Desai
%T Higher-fitness yeast genotypes are less robust to deleterious mutations
%J Science
%V 366
%N 6464
%P 490-493
%M OCT
%D 2019
%K jrnl, c2019, c201x, c20xx, zz1019, biology, evolution, fitness, robustness,
   robust, selection, fitest, fittest, mutation, yeast
%X "... In many microbial systems, diminishing-returns epistasis contributes to
   a tendency for more-fit genotypes to be less adaptable, but no analogous
   patterns for robustness are known. To understand how rob. varies across
   genotypes, we measure the fitness effects of hundreds of individual insertion
   mutations in a panel of yeast strains. We find that more-fit strains are less
   robust: They have distributions of fitness effects with lower mean & higher
   variance. These differences arise because many mutations have more strongly
   deleterious effects in faster-growing strains. This -ve correlation between
   fitness & robustness implies that second-order seln for robustness will tend
   to conflict with first-order selection for fitness."
   -- [<A HREF="https://doi.org/10.1126/science.aay4199">doi:10.1126/science.aay4199</A>]['19].

%A L. E. Crawford
%A et al ...
%A K. G. Lambert
%T Enriched environment exposure accelerates rodent driving skills
%J J. Behavioural Brain Research
%V ?
%M OCT
%D 2019
%K jrnl, c2019, c201xx, c20xx, zz1019, animal, rodent, rat, rats, car, vehicle,
   ROV, drive, driving, skill, ratmobile, Dehydroepiandrosterone,
   corticosterone, neurochemistry, DHEA, interest, stress, CORT, funny, haha
%X "... preliminary research establishing that rats could be taught to drive a
   rodent operated vehicle (ROV) in a fwd dirnction, as well as steer in more
   complex navigational patterns, male rats housed in an enriched environment
   were exposed to the rodent driving regime. Compared to std-housed rats,
   enriched-housed rats demonstrated more robust learning ... suggesting that
   driving training, regardless of housing group, enhanced markers of emotional
   resilience. ... confirm the importance of enriched environments in preparing
   animals to engage in complex behavioral tasks. ..."  [online 16/10/2019]
   -- [<A HREF="https://doi.org/10.1016/j.bbr.2019.112309">doi:10.1016/j.bbr.2019.112309</A>]['19].
   Also see the [<A HREF="https://www.bbc.com/news/world-us-canada-50167812">bbc</A>][24/10/2019].
   (I can see an IgNobel prize in the making.)

%A A. V. Anzalone
%A et al ...
%A D. R. Liu
%T Search-and-replace genome editing without double-strand breaks or donor DNA
%J Nature
%V ?
%N ?
%P ?-?
%M OCT
%D 2019
%K jrnl, c2019, c201x, c20xx, MolBio, zz1119, medical, DNA, Cas9, crispr,
   editing, editting, pegRNA, primeEditing,  prime editing,
   sickle cell disease, Tay-Sachs, HEXA, PRNP
%X "Most genetic variants that contribute to disease1 are challenging to correct
   efficiently & without excess byproducts. Here we describe primeediting,
   a versatile & precise genome editing method that directly writes new
   genetic information into a specified DNA site using a catalytically impaired
   Cas9 fused to an engineered reverse transcriptase, programmed with a prime
   ed. guide RNA (pegRNA) ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-1711-4">doi:10.1038/s41586-019-1711-4</A>]['19].
   See the [<A HREF="https://www.bbc.com/news/health-50125843">bbc</A>][21/10/2019].

%A A. W. Senior
%A R. Evans
%A J. Jumper
%A et al ...
%A D. Hassibis
%T Protein structure prediction using multiple deep neural networks in the
   13th Critical Assessment of Protein Structure Prediction (CASP13)
%J Proteins: Structure, Function, and Bioinformatics
%V 87
%N 12
%P 1141-1148
%M OCT
%D 2019
%K jrnl, MolBio, CASP, CASP13, c2019, c201x, c20xx, zz1219, AlphaFold, ANN, NN,
   alphafold1, A7D, DeepMind, tertiary, 3D, protein structure prediction,
   MSA, pairwise distance, Zscores, GDT_TS, GDTTS, GDTnet, google
%X "We describe AlphaFold, the protein structure prediction system that was
   entered by the group A7D in CASP13. Submissions were made by three
   free-modeling (FM) methods which combine the predictions of three neural
   networks. All three systems were guided by predictions of distances between
   pairs of residues produced by a NN. Two systems assembled fragments produced
   by a generative NN, one using scores from a n/wk trained to regress GDT_TS.
   The third system shows that simple gradient descent on a properly constructed
   potential is able to perform on par with more expensive traditional search
   techniques & without requiring domain segmentation. In the CASP13 FM
   assessors' ranking by summed z-scores, this system scored highest with 68.3
   vs 48.2 for the next closest group (an average GDT_TS of 61.4). The system
   produced high-accuracy structures (with GDT_TS scores of 70 or higher) for
   11 out of 43 FM domains. Despite not explicitly using template information,
   the results in the template category were comparable to the best performing
   template-based methods."  [36 refs.]
   -- [<A HREF="https://doi.org/10.1002/prot.25834">doi:10.1002/prot.25834</A>]['19].
   "... NN trained to predict the dists. d_ij between the beta-carbon atoms of
   pairs of residues. ... predict distances between two 64-residue fragments of
   a chain ... 220 2D residual blocks with 128 channels & dilated 3x3 convol'ns,
   elu nonlinearity with dropout & batch normalization. [uh?] ..."
      -- sec 2.1
   [Also search for: AlphaFold MolBio].
   (*Also see alphafold@[<A HREF="https://deepmind.com/blog/article/alphafold">deepmind</A>]['19].*)
   [Also search for: 3D protein structure prediction ANN].

%A A. Stefanie Reinhold
%A J. Ignacio Sanguinetti-Scheck
%A K. Hartmann
%A M. Brecht
%T Behavioral and neural correlates of hide-and-seek in rats
%J Science
%V 365
%N 6458
%P 1180-1183
%M SEP
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0421, animal behaviour, rat, rats,
   hide and seek, play, fun, game, games
%X "... We played hide-and-seek, an elaborate role-play game, with rats. We did
   not offer food rewards but engaged in playful interactions after finding or
   being found. Rats quickly learned the game & learned to alternate between
   hiding v. seeking roles. They guided seeking by vision & memories of past
   hiding locations & emitted game event-specific vocalizations. When hiding,
   rats vocalized infrequently & they preferred opaque over transparent hiding
   enclosures, a preference not observed during seeking. Neuronal recordings
   revealed intense prefrontal cortex activity that varied with game events &
   trial types ('hide' versus 'seek') & might instruct role play. The elaborate
   cognitive capacities for hide-and-seek in rats suggest that this game might
   be evolutionarily old."
   -- [<A HREF="https://doi.org/10.1126/science.aax4705">doi:10.1126/science.aax4705</A>]['21].
   (Surely an IgNobel prize contender?)

%A J. Ding
%A A. Regev
%T Deep generative model embedding of single-cell RNA-Seq profiles on
   hyperspheres and hyperbolic spaces
%J bioRxiv
%M NOV
%D 2019
%K TR, c2019, c201x, c20xx, MolBio, scRNA seq, scRNAseq, ScPhere, hypersphere,
   stats, dimension, dimensionality reduction, pseudotemporal, pseudotime
%X "Single-cell RNA-Seq ... While dimensionality reduction is a crucial step ...
   Here, we introduced scPhere, a scalable deep generative model to embed cells
   into low-dimensional hyperspherical or hyperbolic spaces, as a more accurate
   rep. of the data. ... resolves cell crowding, corrects multiple, complex
   batch factors, facilitates interactive visualization of large datasets, &
   gracefully uncovers pseudotemporal trajectories. ..."
   -- [<A HREF="https://www.biorxiv.org/content/10.1101/853457v1">bioRxiv</A>]['20].
   [Also search for: MolBio scRNAseq].

%A T. N. Tran
%A G. D. Bader
%T Tempora: cell trajectory inference using time-series single-cell RNA
   sequencing data
%J bioRxiv
%M NOV
%D 2019
%K TR, MolBio, c2019, c201x, c20xx, zz0720, cell, RNA seq, RNAseq, scRNAseq,
   trajectory, alignment, time series, timeSeries, Monocle, TSCAN, Slingshot,
   PAGA, StemID
%X "Single-cell RNA sequencing (scRNAseq) can map cell types, states &
   transitions during dynamic biol. processes such as development & regen.. Many
   trajectory inference methods have been developed ... Tempora, a novel cell
   trajectory inference method that orders cells using time info. from
   time-series scRNAseq data. ... Tempora accurately inferred developmental
   lineages in human skeletal myoblast differentiation & murine cerebral cortex
   development ..."
   -- [<A HREF="https://doi.org/10.1101/846907">doi:10.1101/846907 </A>]['20].
   (Also see RNAseq@[<A HREF="https://en.wikipedia.org/wiki/RNA-Seq">wikip</A>]['20].)
   [Also search for: scRNAseq].

%A B. Mayne
%A O. Berry
%A C. Davies
%A J. Farley
%A S. Jarman
%T A genomic predictor of lifespan in vertebrates
%J Sci. Reports
%V 121
%N #17866
%M DEC
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz1219, MolBio, DNA, age, lifespan, animal,
   species, vertebrate, mammal, extinct, methylation, CpG sites, gene promoters,
   DNAm, longevity, stats, AnAge
%X "... Ageing involves the decline of diverse biological functions and places a
   limit on a species' max. lifespan. Ageing is assoc. with epigenetic changes
   involving DNA methylation. [&] an analysis of mammals showed that the density
   of CpG sites in gene promoters, which are targets for DNA methylation, is
   corr. with lifespan. Using 252 whole genomes & DBs of animal age & promotor
   seqs., we show a pattern across vertebrates. ... The lifespan clock
   accurately predicts max. lifespan in vertebrates (R2=0.76) from the density
   of CpG sites within only 42 selected promoters. ..."
   -- [<A HREF="https://doi.org/10.1038/s41598-019-54447-w">doi:10.1038/s41598-019-54447-w</A>]['19].

%A T. Z. T. Jensen
%A et al ...
%A H. Schroeder
%T A 5700 year-old human genome and oral microbiome from chewed birch pitch
%J NatureComms
%V ?
%M DEC
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz1219, human, ancient DNA, genome,
   stone age, Denmark, Scandinavia, Europe
%X "... complete ancient human genome & oral microbiome sequenced from a 5700
   year-old piece of chewed birch pitch from Denmark. We sequence the human
   genome to an average depth of 2.3x & find that the individual who chewed the
   pitch was female & that she was genetically more closely related to western
   hunter-gatherers from mainland Europe than hunter-gatherers from central
   Scandinavia. We also find that she likely had dark skin, dark brown hair &
   blue eyes. In addition, we identify DNA fragments from several bacterial &
   viral taxa, inc. Epstein-Barr virus, as well as animal & plant DNA, which may
   have derived from a recent meal. ..."
   -- [<A HREF="https://doi.org/10.1038/s41467-019-13549-9">doi:10.1038/s41467-019-13549-9</A>]['19].
   [Also search for: MolBio ancient DNA].

%A L. Bohnenkamper
%A M. D. V. Braga
%A D. Doerr
%A J. Stoye
%T Computing the rearrangement distance of natural genomes
%J arXiv
%M JAN
%D 2020
%K TR, MolBio, c2020, c202x, c20xx, zz0120, genome, sorting, rearrangement,
   genomic distance, homology, genes, double cut and join, DCJ
%X "... genomic distance ...  Substantial results include the polynomial-time
   computability of the inversion dist. by Hannenhalli & Pevzner in 1995 & the
   intr. of the double-cut & join (DCJ) dist. by Yancopoulos et al. in 2005. ...
   we present an alg. solving the genomic dist. problem for natural genomes, in
   which any marker may occur an arbitrary # of times. ... based on a new graph
   data structure, the multi-relational diagram, that allows an elegant
   extension of the ILP by Shao, Lin & Moret to count runs of markers that are
   under- or over-represented in one genome with respect to the other & need to
   be inserted or deleted, resp.. With this extension, previous restrictions on
   the genome configurations are lifted, for the first time enabling an
   uncompromising rearrangement analysis. Any marker seq. can directly be used
   for the distance calculation. The evaluation of our approach shows that it
   can be used to analyze genomes with up to a few ten thousand markers, which
   we demonstrate on simulated & real data."
   -- 2001.02139@[<A HREF="https://arxiv.org/abs/2001.02139">arXiv</A>]['20].
   [Also search for: MolBio genomic distance].

%A A. W. Senior
%A et al ...
%A D. Hassabis
%T Improved protein structure prediction using potentials from deep learning
%J Nature
%V 577
%P 706-710
%M JAN
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0220, protein structure prediction,
   AlphaFold, google, deep, ANN, NN, CNN, CASP, CASP13, free modelling, FM,
   contacts, HHblits, details
%X "... we show that we can train a neural network to make accurate predictions
   of the distances between pairs of residues, which convey more info. about the
   struct. than contact predictions. Using this info., we construct a potential
   of mean force that can accurately describe the shape of a protein. We find
   that the resulting potential can be optimized by a simple gradient descent
   alg. to generate structs. without complex sampling procedures. The resulting
   system, named AlphaFold, achieves high accuracy, even for seqs. with fewer
   homologous seqs.. In the recent Critical Assessment of Protein Structure
   Prediction (CASP13) - a blind assessment of the state of the field -
   AlphaFold created high-accuracy structs. (with template modelling (TM)
   scores of 0.7 or higher) for 24 out of 43 free modelling domains, whereas
   the next best method, which used sampling & contact info., achieved such
   accuracy for only 14 out of 43 domains. ..."
      "... a CNN trained on PDB structures ... predicts a discrete prob. distn
      P(dij|S, MSA(S)) for every ij pair in any 64x64 region of the LxL
      distance matrix ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-1923-7">doi:/10.1038/s41586-019-1923-7</A>]['20],
   &  preprint@[<A HREF="https://discovery.ucl.ac.uk/id/eprint/10089234/1/343019_3_art_0_py4t4l_convrt.pdf">UCL</A>]['22].
   [Also search for: CASP MolBio] and see AF@[<A HREF="https://en.wikipedia.org/wiki/AlphaFold">wikip</A>]['22].

%A H. Imachi
%A et al ...
%A K. Takai
%T Isolation of an archaeon at the prokaryote-eukaryote interface
%J Nature
%V 577
%P 519-525
%M JAN
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0220, evolution, origins, tree of life,
   E3, phylogenetic, prokaryote, eukaryote, archae, Asgard loki, Lokiarchaeota,
   Candidatus Prometheoarchaeum syntrophicum, organelle, coccus
%X "... Current data suggest that eukaryotes may have emerged from an archaeal
   lineage known as 'Asgard' archaea. Despite the eukaryote-like genomic
   features that are found in these a., the evolutionary transition from archaea
   to e. remains unclear ... Here we report the decade-long isolation of an
   Asgard archaeon related to Lokiarchaeota from deep marine sediment. The
   archaeon - 'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1 - is an
   anaerobic, extremely slow-growing, small coccus (around 550nm dia.) that
   degrades amino acids through syntrophy. Although eukaryote-like intracellular
   complexes have been proposed for A.archaea, the isolate has no visible
   organelle-like structure. Instead, Ca. P. syntrophicum is morphologically
   complex & has unique protrusions that are long & often branching. On the
   basis of the available data obtained from cultivation & genomics, & reasoned
   interpretations of the existing literature, we propose a hypothetical model
   for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E3)
   model."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-1916-6">doi:10.1038/s41586-019-1916-6</A>]['20].
   (Also see Lokiarchaeota@[<A HREF="https://en.wikipedia.org/wiki/Lokiarchaeota">wikip</A>]['20].)
   [Also search for: MolBio tree life].

%A A. B. Barron
%A B. Hare
%T Prosociality and a sociosexual hypothesis for the evolution of same-sex
   attraction in humans
%J Frontiers in Psychol.
%V 10
%N 2955
%M JAN
%D 2019
%K jrnl, c2020, c202x, c20xx, zz0220, human, evolution, same, sex, SSSA,
   attraction, sexuality, society, behaviour
%X "... develop a novel argument for the evolution of SSSA that focuses on the
   likely adaptive social consequences of SSSA. We argue that SSAT evolved as
   just one of a suite of traits responding to strong seln for ease of social
   integration or prosocial behavior. A strong driver of recent human behavioral
   evolution has been seln for reduced reactive aggression, increased social
   affiliation, social communication, & ease of social integration. In many
   prosocial mammals sex has adopted new social fns in contexts of social
   bonding, social reinforcement, appeasement, & play. We argue that for humans
   the social fns & benefits of sex apply to same-sex sexual behavior as well as
   heterosexual behavior. [so] we propose a degree of SSSA, was selected for in
   recent human evolution for its non-conceptive social benefits. ..."
    -- [<A HREF="https://doi.org/10.3389/fpsyg.2019.02955">doi:10.3389/fpsyg.2019.02955</A>]['20].

%A A. K. Wesselink
%A et al ...
%A K. J. Rothman
%T Seasonal patterns in fecundability in North America and Denmark: a
   preconception cohort study
%J Hum. Reprod.
%M JAN
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0220, human, reproduction, birth, conception,
   pregnancy, fecund, fecundity, baby, babies, stats, periodic, season,
   seasonal, cyclic, model, USA, Denmark
%X "... Initiation of pregnancy attempts peaked in September, with stronger
   seasonality in N.America than in Denmark (48 vs. 16% higher prob. initiating
   attempts in Sept. compared with March). After accounting for seasonal
   variation in initiation of pregnancy attempts, we observed modest seasonal
   variation in fecundability, with a peak in the late fall & early winter in
   both cohorts, but stronger peak/low ratios in N.A. (1.16; 95% [CI]: 1.05,
   1.28) than in D. (1.08; 95% CI: 1.00, 1.16). When we stratified the NA data
   by latitude, we observed the strongest seasonal variation in the southern USA
   (peak/low ratio of 1.45 [95% CI: 1.14, 1.84]), with peak fecundability in
   late November. ..."
   -- [<A HREF="https://doi.org/10.1093/humrep/dez265">doi:10.1093/humrep/dez265</A>]['20].
   (auth1@[<A HREF="https://www.bu.edu/sph/profile/amelia-wesselink/">bu</A>]['20].)

%A R. Wu
%A et al
%T A new coronavirus associated with human respiratory disease in China
%J Nature
%V 579
%P 265-269
%M FEB
%D 2020
%K jrnl, MN908947.3, c2020, c202x, c20xx, zz0220, 2019-nCoV, 2019nCoV, covid 19,
   covid19, WH-Human-1, SARS2, SARS-CoV-2, SARSCoV2, genome, WHHuman1, MolBio,
   coronavirus, corona virus, Wuhan, China, RNA, virus, viral, Coronaviridae,
   Betacoronavirus, Sarbecovirus, zoonotic disease, infection, bat, bats
%X "... a novel RNA virus from the family Coronaviridae, designed here as
   WH-Human-1 coronavirus. Phylogenetic analysis of the complete viral genome
   (29,903 nucleotides) revealed that the virus was most closely related
   (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus
   Betacoronavirus, subgenus Sarbecovirus) previously sampled from bats in
   China. This outbreak highlights the ongoing capacity of viral spill-over from
   animals to cause severe disease in humans."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2008-3">doi:10.1038/s41586-020-2008-3</A>][2/2020]  (online Feb 2020)..
   "GenBank: MN908947.3 ...
   Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome.
   Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ..." (~30Kb)
   -- [<A HREF="https://www.ncbi.nlm.nih.gov/nuccore/MN908947.3">ncbi</A>][12/2/2020].
   (Also see [<A HREF="https://en.wikipedia.org/wiki/2019_novel_coronavirus">wikip</A>]['20].)
   [Also search for: MolBio SARS].

%A Qing Tang
%A Ke Pang
%A Xunlai Yuan
%A Shuhai Xiao
%T A one-billion-year-old multicellular chlorophyte
%J Nature Ecology & Evoln
%M FEB
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0320, biol, biology, green plant, plants,
   seaweed, alga, algae, Viridiplantae, Chlorophyte, Proterocladus antiquus,
   fossil, ancient, origin, origins, evolution, multicellular, photosynthesis
%X "... we report abundant millimetre-sized, multicellular & morphologically
   differentiated macrofossils from rocks ~ 1,000 million y. ago. These fossils
   are described as Proterocladus antiquus new species & are interpreted as
   benthic siphonocladalean chlorophytes, suggesting that chlorophytes acquired
   macroscopic size, multicellularity & cellular differentiation nearly a
   billion y. ago, much earlier than prev. thought."
   -- [<A HREF="https://doi.org/10.1038/s41559-020-1122-9">doi:10.1038/s41559-020-1122-9</A>]['20].
   Also see [<A HREF="https://www.abc.net.au/news/2020-02-25/billion-year-old-chinese-seaweed-discovered-by-scientists/11998720">abc</A>][25/2/2020].

%A M. W. McGeoch
%A S. Dikler
%A J. E. M. McGeoch
%T Hemolithin: a meteoritic protein containing iron and lithium
%X arXiv
%M MAR
%D 2020
%K TR, MolBio, c2020, c202x, c20xx, zz0320, protein, meteorite, Acfer 086,
   meteorites, space, CV3, extraterrestrial
%X "...  characterizes the first protein to be discovered in a meteorite. Amino
   acid polymers prev. observed in Acfer 086 & Allende meteorites have been
   further characterized in Acfer 086 via high precision MALDI mass spectrometry
   to reveal a principal unified structure of molec. wt 2320 Daltons that
   involves chains of glycine & hydroxy-glycine residues terminated by iron
   atoms, with additional oxygen & lithium atoms. Signal-to-noise ratios up to
   135 have allowed the quantification of iron & lithium in the various MALDI
   fragments via the isotope satellites due to their respective minority
   isotopic masses 54Fe & 6Li. Analysis of the complete spectrum of isotopes
   assoc. with each molec. fragment shows 2H enhancements above terrestrial
   avg 25,700 parts per thousand (sigma=3,500, n=15), confirming
   extra-terrestrial origin & hence the existence of this molecule within the
   asteroid parent body of the CV3 meteorite class. The molecule is tipped by
   an iron-oxygen-iron grouping that in other terrestrial contexts has been
   proposed to be capable of absorbing photons & splitting water into hydroxyl
   & hydrogen moieties."
   -- [<A HREF="https://arxiv.org/abs/2002.11688">arXiv</A>]['20].

%A B. Liu
%A et al ...
%A S. Otto
%T Spontaneous emergence of self-replicating molecules containing nucleobases
   and amino acids
%J J. Amer. Chem. Soc.
%V 142
%N 9
%P 4184-4192
%M FEB
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0320, biol, biology, chemstry, origins, start,
   beginnings, life, DNA, RNA, peptide, self replication, replicating
%X "...  recent hypothesis of 'RNA-peptide coevolution' suggests that the
   current close relationship between amino acids & nucleobases may well have
   extended to the origin of life. ... show how the interplay between these
   compound classes can give rise to new self-replicating molecules using a
   dynamic combinatorial approach. We report two strategies for the fabrication
   of chimeric AA/nucleobase self-replicating macrocycles capable of exponential
   growth. The 1st relies on mixing nucleobase- & peptide-based building blocks,
   where the ligation of these two gives rise to highly spec. chimeric ring
   structures. The 2nd starts from peptide nucleic acid (PNA) building blocks in
   which nucleobases are already linked to AAs from the start. While prev.
   reported nucleic acid-based self-replicating systems rely on pre-synthesis of
   (short) oligonucleotide seqs., self-replication in the present systems start
   from units containing only a single nucleobase. Self-repl'n is accompanied by
   self-assembly, spontaneously giving rise to an ordered 1D arrangement of
   nucleobase nanostructures."
   -- [<A HREF="https://doi.org/10.1021/jacs.9b10796">doi:10.1021/jacs.9b10796</A>]['20].

%A T. Shimomura
%A et al ...
%A K. Irie
%T A native prokaryotic voltage-dependent calcium channel with a novel
   selectivity filter sequence
%J eLife
%V ?
%M FEB
%D 2020
%K jrnl, ejrnl, MolBio, c2020, c202x, c20xx, zz0320, protein, calcium channel,
   evolution, Ca, Ca2, Na, Cavs, CavMr, Navs, prokaryote, eukaryote
%X "... The struct. of Cavs is similar to that of voltage-dep. Na+ channels
   (Navs). It is known that prokaryotic Navs can obtain Ca2+ selectivity by
   -ve charge mutns of the selectivity filter, but native prokaryotic Cavs had
   not yet been identified. We report the first id. of a native prokaryotic Cav,
   CavMr, whose selectivity filter contains a smaller # of -ve charged residues
   than that of artificial prokaryotic Cavs. A relative mutant whose selectivity
   filter was replaced with that of CavMr exhibits high Ca2+ selectivity.
   Mutational analyses revealed that the glycine residue of the CavMr
   selectivity filter is a determinant for Ca2+ sel.. This glycine residue is
   well conserved among subdomains I and III of eukaryotic Cavs. ... provide new
   insight into the Ca2+ sel. mechanism that is conserved from prokaryotes to
   eukaryotes."
   -- [<A HREF="https://doi.org/10.7554/eLife.52828">doi:10.7554/eLife.52828</A>]['20].

%A L. Zhang
%A et al ...
%A R. Hilgenfeld
%T Alpha-Ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus
   replication: Structure-based design, synthesis, and activity assessment
%J J. Med. Chem.
%V ?
%M FEB
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0620, coronavirus, enterovirus, 3Cpro,
   SARS-CoV, SARSCoV, 3CLpro, Mpro, protease, ketoamide, rupintrivir
%X "... to obtain near-equipotent, broad-spectrum antivirals against
   alphacoronaviruses, betacoronaviruses, and enteroviruses, we pursued a
   structure-based design of peptidomimetic alpha-ketoamides as inhibitors of
   main and 3C proteases. Six crystal structures of protease-inhibitor complexes
   were determined as part of this study. Compounds synthesized were tested
   against the recombinant proteases as well as in viral replicons and
   virus-infected cell cultures; most of them were not cell-toxic. ..."
   -- [<A HREF="https://doi.org/10.1021/acs.jmedchem.9b01828">doi:10.1021/acs.jmedchem.9b01828</A>]['20].
   [Also search for: SARSCoV2 protease].

%T The BCG World Atlas
%D ?
%K zz0420, BCG, tuberculosis, TB, vaccine, vaccination, trained immunity,
   human health, data, medical, medicine, public health policy, policies
%X Au: 1950s-mid 1980s @ school age.
   UK: 1953-2005 @ age 12-13y.        ... etc.
   -- [<A HREF="http://www.bcgatlas.org/">www</A>]['20].
   [Also search for: BCG vaccine].

%A N. van Doremalen
%A et al
%T Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV-1
%J NEJM
%M MAR
%D 2020
%K jrnl, NEJM, c2020, c202x, c20xx, zz0420, Wuhan, China, covid19, covid 19,
   SARS-CoV-2, SARSCoV2, SARS2, coronavirus, pandemic, corona virus, survival,
   human health, risks
%X "... SARS-CoV-2 remained viable in aerosols throughout the duration of our
   experiment (3 hours), with a redn in infectious titer from 103.5 to 102.7
   TCID_50 per liter of air. ... SARS-CoV-2 was more stable on plastic &
   stainless steel than on copper & cardboard, & viable virus was detected up to
   72h after application to these surfaces (Figure 1A), although the virus
   titer was greatly reduced (from 103.7 to 100.6 TCID_50 per milliliter of
   medium after 72h on plastic & from 103.7 to 100.6 TCID_50 per milliliter
   after 48 hours on stainless steel). ..."
    -- [<A HREF="https://doi.org/10.1056/NEJMc2004973">doi:10.1056/NEJMc2004973</A>]['20].
   [Also search for: covid19].

%A S. D. Evans
%A I. V. Hughes
%A J. G. Gehling
%A M. L. Droser
%T Discovery of the oldest bilaterian from the Ediacaran of South Australia
%J PNAS
%V ?
%M MAR
%D 2020
%K jrnl, PNAS, c2020, c202x, c20xx, zz0420, early animal, bilaterian,
   Ediacara Biota, Ikaria wariootia, origins, fossil, South Australia
%X "The transition from simple, microscopic forms to the abundance of complex
   animal life that exists today is recorded within soft-bodied fossils of the
   Ediacara Biota (571 to 539Ma). Perhaps most critically is the 1st appearance
   of bilaterians - animals with two openings & a through-gut-during this
   interval. ... Here, we describe the fossil Ikaria wariootia, one of the
   oldest bilaterians identified from South Australia. This organism is
   consistent with predictions based on modern animal phylogenetics that the
   last ancestor of all bilaterians was simple & small & represents a rare
   link between the Ediacaran & the subsequent record of animal life."
   -- [<A HREF="https://doi.org/10.1073/pnas.2001045117">doi:10.1073/pnas.2001045117</A>]['20].
   Also see the [<A HREF="https://www.bbc.com/news/science-environment-52019468">bbc</A>][24/3/2020].

%A S. R. Hackett
%A et al
%A R. S. McIsaac
%A Learning causal networks using inducible transcription factors and
   transcriptome-wide time series
%J Mol. Syst. Biol.
%N 16
%P e9174
%M MAR
%D 2020
%K jrnl, eJrnl, MolBio, c2020, c202x, c20xx, zz0820, IDEA, Bnet, network,
   model, transcription factor, TF, TFs, gene expression, budding yeast, Aft1
%X "... IDEA (the Induction Dynamics gene Expression Atlas), a dataset
   constructed by indep. inducing hundreds of transcription factors (TFs) &
   measuring time-courses of the resulting gene exp'n responses in budding
   yeast. Each experiment captures a regulatory cascade connecting a single
   induced regulator to the genes it causally regulates. ... IDEA contains
   >200 TF induction experiments with 20 million individual observations &
   100,000 signal-containing dynamic responses. As an application of IDEA, we
   integrate all timecourses into a whole-cell transcriptional model ..."
   -- [<A HREF="https://doi.org/10.15252/msb.20199174">doi:10.15252/msb.20199174</A>]['20].
   (some auths @Calico Life Sci.)

%A K. G. Andersen
%A A. Rambaut
%A W. Ian Lipkin
%A E. C. Holmes
%A R. F. Garry
%T The proximal origin of SARS-CoV-2
%J NatureMedicine
%V 26
%P 450-452
%M MAR
%D 2020
%K news, views, MolBio, c2020, c202x, c20xx, zz1220, coronavirus, zoonotic,
   virus, SARS, origin, origins, SARS1, SARS-CoV-2, SARSCoV2, SARS2, covid19,
   origin, spike protein, RBD, ACE2, furin, polybasic cleavage, RaTG13,
   Rhinolophus affinis, bat, pangolin
%X "... It is improbable that SARS-CoV-2 emerged through laboratory manipulation
   ... It is possible that a progenitor of SARS-CoV-2 jumped into humans,
   acquiring the genomic features described above through adaptation during
   undetected human-to-human transmission. ..."
   -- [<A HREF="https://doi.org/10.1038/s41591-020-0820-9">doi:10.1038/s41591-020-0820-9</A>]['20].
   Also see [<A HREF="https://www.bbc.com/news/world-asia-china-55364445">bbc</A>][22/12/2020].
   [Also search for: MolBio SARS origin].

%A Ming Wang
%A et al ...
%A Tiangang Liu
%T Nanopore target sequencing for accurate and comprehensive detection of
   SARS-CoV-2 and other respiratory viruses
%J bioRxiv
%M MAR
%D 2020
%O Small, 16(32), 2002169, June 2020
%K TR, MolBio, c2020, c202x, c20xx, zz0621, SARS-CoV-2, SARSCoV2, SARS2,
   covid19, coronavirus, virus, pandemic, Wuhan, China, origin, origins,
   C24034T, G28077C, sequence, SRA, Bloom, controversial, deleted
%X "... we developed nanopore target sequencing (NTS) to detect SARS-CoV-2 &
   other respiratory viruses simultaneously within 6-10h. ...  NTS is thus
   suitable for contemporary COVID-19 diagnosis; moreover, this platform can be
   further extended for diagnosing other viruses or pathogens."
   -- bioRxiv [<A HREF="https://doi.org/10.1101/2020.03.04.20029538">doi:10.1101/2020.03.04.20029538</A>]['21] and in
      Small [<A HREF="https://doi.org/10.1002/smll.202002169">doi:10.1002/smll.202002169</A>]['21].
   (Also see, 'Recovery of deleted deep sequencing data sheds more light on
    the early Wuhan SARS-CoV-2 epidemic'
    -- J.D.Bloom, BioRxiv [<A HREF="https://doi.org/10.1101/2021.06.18.449051">doi:/10.1101/2021.06.18.449051</A>][6/2021], and
   'Deleted coronavirus genome seqs trigger scientific intrigue',
   -- Nature 6/2021 [<A HREF="https://doi.org/10.1038/d41586-021-01731-3">doi:10.1038/d41586-021-01731-3</A>]['21] and
   "Did a Chinese team 'obscure' early coronavirus sequences?"
   -- J.D.Cohen, Sci., 2/7/2021 [<A HREF="https://doi.org/10.1126/science.373.6550.15">doi:10.1126/science.373.6550.15</A>]['21].)
   [Also search for: SARSCoV2 origins].

%A L. Zhang
%A D. Lin
%A X. Sun
%A U. Curth
%A C. Drosten
%A L. Sauerhering
%A S. Becker
%A K. Rox
%A R. Hilgenfeld
%T Crystal structure of SARS-CoV-2 main protease provides a basis for
   design of improved alpha-ketoamide inhibitors
%J Science
%V 368
%N 6489
%P 409-412
%O eabb3405
%M APR
%D 2020
%K MolBio, jrnl, c2020, c202x, c20xx, zz0410, SARS, SARS2, SARS-CoV-2, SARSCoV2,
   SARSr, covid 19, covid19, virus, coronavirus, Wuhan, China, protein,
   protease, Mpro, nsp5, 3CL, 3CLpro, inhibitor, structure, alpha ketoamide,
   human, lung, lungs, Germany, DZIF
%X "... An attractive drug target among coronaviruses is the main protease
   (M^{pro},3CL^{pro}), due to its essential role in processing the polyproteins
   that are translated from the viral RNA. We report the X-ray structures of the
   unliganded SARS-CoV-2 Mpro & its complex with an alpha-ketoamide inhibitor.
   This was derived from a previously designed inhibitor but with the P3-P2
   amide bond incorporated into a pyridone ring to enhance the half-life of the
   compound in plasma. Based on the structure, we developed the lead compound
   into a potent inhibitor of the SARS-CoV-2 M^{pro}. The pharmacokinetic
   characterization of the optimized inhibitor reveals a pronounced lung
   tropism & suitability for administration by the inhalative route."
   -- [<A HREF="https://doi.org/10.1126/science.abb3405">doi:10.1126/science.abb3405</A>]['20].
   (Also see SARS-CoV-2@[<A HREF="https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2">wikip</A>]['20].)
   [Also search for: MolBio covid]  and  [also search for: MolBio SARS]

%A A. C. Walls
%A et al ...
%A D. Veesler
%T Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein
%J Cell
%V 181
%N 2
%P 281-292
%M APR
%D 2020
%K jrnl, Cell, MolBio, c2020, c202x, c20xx, zz0520, SARS-CoV-2, SARSCoV2, SARS2,
   virus, covid-19, covid19, spike glycoprotein, structure, protein, ACE2,
   furin, S1, S2, S1S2
%X "... show that SARS-CoV-2 S uses ACE2 to enter cells & that the
   receptor-binding domains of SARS-CoV-2 S & SARS-CoV S bind with similar
   affinities to human ACE2, correlating with the efficient spread of SARS-CoV-2
   among humans. We found that the SARS-CoV-2 S glycoprotein harbors a furin
   cleavage site at the boundary between the S1/S2 subunits ..."
   -- [<A HREF="https://doi.org/10.1016/j.cell.2020.02.058">doi:10.1016/j.cell.2020.02.058</A>]['20].
   [Also search for: MolBio covid] and  [also search for: MolBio SARS].

%A D. E. Gordon
%A et al ...
%A N. J. Krogan
%T A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
%J Nature
%V 583
%P 459-468
%M APR
%D 2020
%K MolBio, jrn, c2020, c202x, c20xx, zz0602, SARS-CoV-2, coronavirus, SARS2,
   SARSCoV2, covid-19, covid19, interactome, target, interaction network,
   nsp, protein, proteins, sigma1, sigma2, drug, reuse
%X "... we cloned, tagged & expressed 26 of the 29 SARS-CoV-2 proteins in human
   cells & identified the human proteins physically assoc. with each using
   affinity-purification mass spectrometry (AP-MS), identifying 332
   high-confidence SARS-CoV-2-human p.-p. interactions (PPIs). Among these, we
   identify 66 druggable human ps. or host factors targeted by 69 compounds
   (29 FDA-approved drugs, 12 drugs in clinical trials, & 28 preclinical
   compounds). Screening a subset of these in multiple viral assays identified
   two sets of pharmacological agents that displayed antiviral activity:
   inhibitors of mRNA translation & predicted regulators of the Sigma1 &
   Sigma2 receptors. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2286-9">doi:10.1038/s41586-020-2286-9</A>][30/4/2020],
      [<A HREF="https://www.biorxiv.org/content/10.1101/2020.03.22.002386v1">biorx'v</A>]['20].
   (Also see [<A HREF="https://zoiclabs.com">zoiclabs.com</A>][6/2020].)
   [Also search for: SARSCoV2 protein].

%A Chengxin Zhang
%A Wei Zheng
%A S. M. Mortuza
%A Yang Li
%A Yang Zhang
%X "DeepMSA: constructing deep multiple sequence alignment to improve contact
   prediction and fold-recognition for distant-homology proteins
%J Bioinformatics
%V 36
%N 7
%P 2105-2112
%M APR
%D 2020
%K MolBio, c2020, c292x, c20xx, zz0121, protein, deep MSA, deepMSA,
   multiple sequence alignment
%X "... DeepMSA was utilized to generate MSAs for residue-level contact
   prediction by six coevolution & deep learning-based programs, which resulted
   in an accuracy increase in long-range contacts by up to 24.4% compared to the
   default programs. Next, multiple threading programs are performed for
   homologous structure identification, where the average TM-score of the
   template alignments has over 7.5% increases with the use of the new DeepMSA
   profiles. Finally, DeepMSA was used for secondary structure prediction ..."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btz863">doi:10.1093/bioinformatics/btz863</A>]['21].
  [Also search for: MolBio multiple alignment protein].

%A J. Li
%A et al ...
%A Q. Liang
%T Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients
   reveal potential virulence factors influencing SARS-CoV-2 pathogenesis
%J bioRxiv
%M APR
%D 2020
%K TR, MolBio, c2020, c202x, c20xx, zz0520, SARS-CoV-2, SARSCoV2,  SARS2,virus,
   proteins, protein, interaction network, nsp9, nsp10, NKRF, covid-19, covid19,
   human health, disease
%X "... We exploited an integrated proteomics approach to systematically
   investigate intra-viral & virus-host interactomes for the identification of
   unrealized SARS-CoV-2 host targets & participation of cellular proteins in
   the response to viral infection using peripheral blood mononuclear cells
   (PBMCs) isolated from COVID-19 patients. ... elucidated 251 host proteins
   targeted by SARS-CoV-2 & more than 200 host proteins that are sig. perturbed
   in COVID-19 derived PBMCs. From the interactome, we further identified that
   non-structural protein nsp9 % nsp10 interact with NKRF, a NF-KB repressor, &
   may precipitate the strong IL-8/IL-6 mediated chemotaxis of neutrophils &
   overexuberant host inflammatory response ..."
   -- preprint@[<A HREF="https://www.biorxiv.org/content/10.1101/2020.03.31.019216v1">bioRxiv</A>]['20].
   [Also search for: SARSCoV2 protein] and [also search for: SARS interaction].

%A I. Astuti
%A Ysrafil
%T Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of
   viral structure and host response
%J Diabetes Metab. Syndr.
%V 14
%N 4
%P 407-412
%M JUL-AUG
%D 2020
%K MolBio, survey, intro, review, c2020, c202x, c20xx, zz0820, SARSCoV2,
   SARS-CoV-2, virus, covd-19, covid19, ACE2, nsp, nsp3, nsp5, Wuhan, China,
   protein, immune response, system
%X "... provide a complete review related to structure, origin, & how the body
   responds to this virus infection & explain the possibility of an immune
   system over-reaction or cytokine storm. We also inc. an explanation of how
   this virus creates modes of avoidance to evade immune system attacks. ..."
   -- [<A HREF="https://doi.org/10.1016/j.dsx.2020.04.020">doi:10.1016/j.dsx.2020.04.020</A>]['20] (online 18/4/2020) (45 refs),
      PMC7165108@[<A HREF="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165108/">ncbi</A>]['20].
   [Also search for: MolBio SARSCoV2],  maybe add Intro.

%A A. Montagne
%A et al ...
%A B. V. Zlokovic
%T APOE4 leads to blood-brain barrier dysfunction predicting cognitive decline
%J Nature
%V 581
%P 71-76
%M MAY
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0520, medicine, human, biology, risks,
   Alzheimer's disease, BBB, APOE4, apolipoprotein E, protein, amyloid, tau
%X -- [<A HREF="https://doi.org/10.1038/s41586-020-2247-3">doi:10.1038/s41586-020-2247-3</A>]['20].

%A S. Horvath
%A et al
%T Reversing age: Dual species measurement of epigenetic age with a single clock
%J bioRxiv
%M MAY
%D 2020
%K TR, c2020, c202x, c20xx, zz0522, MolBio, age, reverse, aging, ageing,
   lifespan, rejuvenation, senescence, young, blood plasma, epigenetic
%X "Young blood plasma is known to confer beneficial effects on various organs
   in mice. However, it was not known whether young plasma rejuvenates cells &
   tissues at the epigenetic level; whether it alters the epigenetic clock,
   which is a highly-accurate molecular biomarker of aging. ... we developed &
   validated six different epigenetic clocks for rat tissues ... We employed
   these six clocks to investigate the rejuvenation effects of a plasma fraction
   treatment in different rat tissues. The treatment more than halved the
   epigenetic ages of blood, heart, & liver tissue. A less pronounced, but stat.
   sig., rejuvenation effect could be observed in the hypothalamus. ... was
   accompanied by progressive improvement in the fn of these organs ... Cellular
   senescence, which is not assoc. with epigenetic aging, was also considerably
   reduced in vital organs. ... demonstrates that a plasma-derived treatment
   markedly reverses aging according to epigenetic clocks & benchmark biomarkers
   of aging."
   -- [<A HREF="https://doi.org/10.1101/2020.05.07.082917">doi:10.1101/2020.05.07.082917</A>]['22],
    & [<A HREF="https://www.biorxiv.org/content/10.1101/2020.05.07.082917v1">bioRxiv</A>][5/'20].
   (?'After Many a Summer' (1939), Aldous Huxley?)

%A Jun Lan
%A et al
%T Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2
   receptor
%J Nature
%V 581
%P 215-220
%M MAY
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0520, MolBio, SARS-CoV-2, spike protein,
   structure, receptor, SARSCoV2, SARS2, ACE2, covid19
%X "...  crystal structure of the receptor-binding domain (RBD) of the spike
   protein of SARS-CoV-2 bound to the cell receptor ACE2 ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2180-5">doi:10.1038/s41586-020-2180-5</A>]['20].
   [Also search for: SARS ACE2].

%A J. Shang
%A et al...
%A Fang Li
%T Structural basis of receptor recognition by SARS-CoV-2
%J Nature
%V 581
%P 221-224
%M MAY
%K jrnl, c2020, c202x, c20xx, zz0520, MolBio, SARS-CoV-2, spike protein,
   structure, receptor, SARSCoV2, SARS2, angiotensin converting enzyme 2, ACE2
%X "... SARS-CoV-2 and SARS-CoV recognize the same receptor-angiotensin-
   -converting enzyme 2 (ACE2) ... we determined the crystal structure of the
   receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 (engineered
   to facilitate crystallization) in complex with ACE2. In comparison with the
   SARS-CoV RBD, an ACE2-binding ridge in SARS-CoV-2 RBD has a more compact
   conformation; moreover, several residue changes in the SARS-CoV-2 RBD
   stabilize two virus-binding hotspots at the RBD-ACE2 interface.  ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2179-y">doi:10.1038/s41586-020-2179-y</A>]['20].
   [Also search for: SARS ACE2].

%A Yan Gao
%A et al
%T Structure of the RNA-dependent RNA polymerase from COVID-19 virus
%J Science
%V 368
%N 6492
%P 779-782
%M MAY
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, SARS-CoV-2, SARSCoV2, SARS2, RNA,
   polymerase, protein, structure, covid19, covid 19, nsp12, nsp 12, RdRp
%X "...  cryo-electron microscopy structure of COVID19 virus full-length nsp12
   in complex with cofactors nsp7 and nsp8 at 2.9-A resolution. [&] to the
   conserved architecture of the polymerase core of the viral polymerase family,
   nsp12 possesses a newly identified B-hairpin domain at its N terminus. A
   comparative analysis model shows how remdesivir binds to this polymerase. The
   structure provides a basis for the design of new antiviral therapeutics that
   target viral RdRp."
   -- [<A HREF="https://doi.org/10.1126/science.abb7498">doi:10.1126/science.abb7498</A>]['20].
   [Also search for: SARS polymerase].

%A K. J. Karczewski
%A et al ...
%A G. Tiao
%T The mutational constraint spectrum quantified from variation in
   141,456 humans
%J Nature
%V 581
%P 434-443
%M MAY
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0520, human, genome, genomes, genes,
   variant, inactivate, loss, Genome Aggregation Database, gnomAD
%X "Genetic variants that inactivate protein-coding genes are a powerful source
   of info. about the phenotypic consequences of gene disruption: genes that are
   crucial for the fn of an organism will be depleted of such variants in
   natural pop'ns ... However, predicted loss-of-fn variants are enriched for
   annotation errors, & tend to be found at extremely low freqs. ... Here we
   describe the aggregation of 125,748 exomes & 15,708 genomes from human seq.
   studies into the Genome Aggregation Database (gnomAD). We identify 443,769
   high-confidence predicted loss-of-fn variants ... we classify human
   protein-coding genes along a spectrum that represents tolerance to
   inactivation, validate this ...  and show that it can be used to improve the
   power of gene discovery for both common and rare diseases."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2308-7">doi:10.1038/s41586-020-2308-7</A>]['20].

%A A. S. Pillai
%A et al ...
%A J. W. Thornton
%T Origin of complexity in haemoglobin evolution
%J Nature
%J Nature
%V 581
%P 480-485
%M MAY
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0520, haemoglobin, multimeric complex,
   oxygen transport, tetramer, origin
%X "... we use ancestral protein reconstruction & biophysical assays to
   elucidate the origins of vertebrate haemoglobin, a heterotetramer of
   paralogous alpha- & beta-subunits that mediates respiratory oxygen transport
   & exchange by cooperatively binding [O] with moderate affinity. We show that
   modern h. evolved from an ancient monomer & characterize the historical
   'missing link' through which the modern tetramer evolved - a noncooperative
   homodimer with high [O] affinity that existed before the gene duplication
   that generated distinct alpha- & beta-subunits. Reintroducing just two
   post-duplication historical substns into the ancestral p. is sufficient to
   cause strong tetramerization by creating favourable contacts with more
   ancient residues on the opposing subunit. These surface substns markedly
   reduce oxygen affinity & even confer cooperativity ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2292-y">doi:10.1038/s41586-020-2292-y</A>]['20].

%A A. Douangamath
%A et al ...
%A M. A. Walsh
%T Crystallographic and electrophilic fragment screening of the SARS-CoV-2
   main protease
%J bioRxiv
%M MAY
%D 2020
%O Nat. Comms., 11, #5047, Oct. 2020
%K TR, MolBio, c2020, c202x, c20xx, zz0620, SARS-CoV-2, SARSCoV2, covid-19,
   covid19, 3CLpro, Mpro, Cys, protease, inhibitor, DSI-poised, DSIpoised,
   Enamine, MiniFrags, FragLites, York3D, SpotFinder, chemical fragment library,
   Z31792168, Z1220452176, Z18197050, Z1367324110, 5R84
%X "... we performed a large-scale screen of electrophile & non-covalent
   fragments through a combined mass spectrometry & X-ray approach against the
   SARS-CoV-2 main protease ... Our crystallographic screen identified 71 hits
   that span the entire active site, [&] 3 hits at the dimer interface. ..."
   -- [<A HREF="https://doi.org/10.1101/2020.05.27.118117">doi:10.1101/2020.05.27.118117</A>]['20],
      [<A HREF="https://www.nature.com/articles/s41467-020-18709-w">www</A>]['20].
      "... Fragments were soaked into crystals ..."
   (Also see 5R84@[<A HREF="https://www.rcsb.org/structure/5R84">www</A>]['20].)
   [Also search for: MolBio SARS Mpro].

%A J. Liang
%A et al ...
%A T. C. Karagiannis
%T Interaction of the prototypical alpha-ketoamide inhibitor with the SARS-CoV-2
   main protease active site in silico: Molecular dynamic simulations highlight
   the stability of the ligand-protein complex
%J Comput. Biol. Chem.
%V 87
%P 107292
%M MAY
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, SARS-CoV-2, SARSCoV2, protease,
   Mpro, alpha-ketoamide, MonashUni
%X "... An important target is the SARS-CoV-2 main protease (Mpro), involved in
   processing translated viral proteins. Peptidomimetic A-ketoamides represent
   prototypical inhibitors of Mpro. A recent attempt at designing a compound
   with enhanced pharmacokinetic properties has resulted in the synthesis &
   evaln of the A-ketoamide 13b analogue. Here, we performed molecular docking &
   molec.dynamics simulations to further characterize the interaction of
   A-ketoamide 13b with the active site of the SARS-CoV-2 Mpro. ..."
   -- [<A HREF="https://doi.org/10.1016/j.compbiolchem.2020.107292">doi:10.1016/j.compbiolchem.2020.107292</A>]['20] (online May 2020),
      32485652@[<A HREF="https://pubmed.ncbi.nlm.nih.gov/32485652/">pubm'd</A>]['20].
   [Also search for: SARSCoV2 Mpro].

%A F. K. Yoshimoto
%T The proteins of Severe Acute Respiratory Syndrome Coronavirus-2
   (SARS CoV-2 or n-COV19), the cause of COVID-19
%J The Protein J.
%V 39
%P 198-216
%M MAY
%D 2020
%K jrnl. MolBio, c2020, c202x, c20xx, zz0620, SARS2, SARS-CoV-2, SARSCoV2,
   SARS2, covid-19, covid19, nsp, spike, coat, protein, proteins, protease,
   proteinase, review, virus, survey, intro, introduction, nsp1, nsp5
%X "... recent global pandemic (termed COVID-19 for 'coronavirus disease 2019')
   caused by the severe acute respiratory syndrome cor...-2 (SARS CoV-2) ...
 * NSP1  YP_009725297.1 180 AAs Induce host mRNA (leader protein) cleavage;
 * NSP2  YP_009725298.1 638 AAs Binds to PHBs 1, 2;
 * NSP3  YP_009725299.1 1945 AAs Release NSPs 1, 2, 3 (Papain like proteinase);
 * NSP4  YP_009725300.1 500 AAs Membrane rearrangement;
 * NSP5  YP_009725301.1 306 AAs Cleaves 11 sites (3C-like proteinase [3CLpro])
                                NSP polyprotein;
 * NSP6  YP_009725302.1 290 AAs Generates autophagosomes;
 * NSP7  YP_009725303.1  83 AAs Dimerizes with NSP8;
 * NSP8  YP_009725304.1 198 AAs Stimulates NSP12;
 * NSP9  YP_009725305.1 113 AAs Binds to helicase(?);
 * NSP10 YP_009725306.1 139 AAs Stimulates NSP16(?);
 * NSP11 YP_009725312.1  13 AAs Unknown;
 * NSP12 YP_009725307.1 932 AAs Copies viral RNA (RNA polymerase)
                                methylation (guanine);
 * NSP13 YP_009725308.1 601 AAs Unwinds duplex RNA (Helicase);
 * NSP14 YP_009725309.1 527 AAs 5'-cap RNA (3'to 5'exonuclease,
                                guanine N7-methyltransferase);
 * NSP15 YP_009725310.1 346 AAs Degrade RNA to (endoRNAse/endoribonuclease)
                                evade host defense;
 * NSP16 YP_009725311.1 298 AAs 5'-cap RNA ...  methylation (adenine); ..."
   -- [<A HREF="https://link.springer.com/article/10.1007/s10930-020-09901-4">spr'nger</A>]['20],
      [<A HREF="https://doi.org/10.1007/s10930-020-09901-4">doi:s10930-020-09901-4</A>]['20], online 23/5/2020,
      [<A HREF="https://pubmed.ncbi.nlm.nih.gov/32447571/">pubm'd</A>]['20].

%A J. Lee
%A et al ...
%A K. R. Koehler
%T Hair-bearing human skin generated entirely from pluripotent stem cells
%J Nature
%V 582
%P 399-404
%M JUN
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, human, stem cells, stemCell, hair,
   skin, organoid, scRNA-seq, scRNAseq
%X "The skin is a multilayered organ, equipped with appendages (that is,
   follicles and glands), that is critical for regulating body temperature and
   the retention of bodily fluids, guarding against external stresses and
   mediating the sensation of touch and pain. ... report an organoid culture
   system that generates complex skin from human pluripotent stem cells. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2352-3">doi:10.1038/s41586-020-2352-3</A>]['20].
   [Also search for: organoid] and [also search for: scRNAseq].

%A J. Xu
%A et al ...
%A J. D. Sutherland
%T Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides
%J Nature
%V 582
%P 60-66
%M JUN
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0602, DNA, RNA, genetic code, origin,
   origins, life, evolution, deoxyribonucleosides, prebiotic, urine
%X "... Here we demonstrate a high-yielding, completely stereo-, regio- &
   furanosyl-selective prebiotic synthesis of the purine deoxyribonucleosides:
   deoxyadenosine & deoxyinosine. Our synthesis uses key intermediates in the
   prebiotic synthesis of the canonical pyrimidine ribonucleosides (cytidine &
   uridine), & we show that, once generated, the pyrimidines persist throughout
   the synthesis of the purine deoxyribonucleosides, leading to a mixture of
   deoxyadenosine, deoxyinosine, cytidine & uridine. These results support the
   notion that purine deoxyribonucleosides & pyrimidine ribonucleosides may have
   coexisted before the emergence of life."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2330-9">doi:10.1038/s41586-020-2330-9</A>]['20].

%A E. J. Emanuel
%T Which Country Has the World's Best Health Care?
%I PublicAffairs
%P 464
%M JUN
%D 2020
%K book, text, c2020, c202x, c20xx, zz0620, human health, medicine, medical,
   healthcare system, hospital, affordable care, politics, policy, best, worst,
   USA, NHS, covid 19, covid19
%X 1st ed 2020; hb us$24; uk us isbn:1541797736; uk us isbn13:978-1541797734.
   "The US spends more than any other nation, nearly $4 trillion, on healthcare.
   Yet, for all that expense, the US is not ranked #1-not even close. ..."
   And, "... the [US] ranked just above China, the worst performer. The [US]
     came in dead last in terms of systems ranked 'notably poor' for each
     dimension. No system is crowned outright winner. Four emerge as very strong
     contenders: those of Germany, the Netherlands, Norway & Taiwan, each with
     laudable features such as broad choice, excellent coordination of long-term
     care and affordability ..."
     -- [<A HREF="https://doi.org/10.1038/d41586-020-01748-0">doi:10.1038/d41586-020-01748-0</A>]['20].
   [Also search for: healthcare].

%A L. M. Cassidy
%A et al ...
%A D. G. Bradley
%T A dynastic elite in monumental Neolithic society
%J Nature
%V 582
%P 384-388
%M JUN
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0620, ancient DNA, Newgrange,
   passage tomb, tombs, Ireland, Eire, incest, Neolithic, megalithic, elite
%X "... present evidence that a social stratum of this type was established
   during the Neolithic period in Ireland. We sampled 44 whole genomes, among
   which we identify the adult son of a 1st-degree incestuous union from remains
   that were discovered within the most elaborate recess of the Newgrange
   passage tomb. Socially sanctioned matings of this nature are very rare, & are
   documented almost exclusively among politico-religious elites-specifically
   within polygynous & patrilineal royal families that are headed by god-kings.
   We identify relatives of this individual within two other major complexes of
   passage tombs 150km to the west of Newgrange, as well as dietary differences
   & fine-scale haplotypic structure ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2378-6">doi:10.1038/s41586-020-2378-6</A>]['20].
   (Also see the [<A HREF="https://www.bbc.com/news/science-environment-53059527">bbc</A>][17/6/2020].)
   [Also search for: megalithic].

%A R. Horton
%T The COVID-19 Catastrophe: What's Gone Wrong and How to Stop It Happening
   Again
%I Polity
%P 140
%M JUN
%D 2020
%K book, c2020, c202x, c20xx, zz0620, public health, covid 19, covid19, Wuhan,
   China, healthcare, WHO, NHS, human health, policy, politics, pandemic
%X 1st ed 2020; hb us$67; uk us isbn:1509546456; uk us isbn13:978-1509546459.
   "...  Richard Horton, editor of the medical j. The Lanc't, scrutinizes the
   actions that governments around the world took - and failed to take - as the
   virus spread from its origins in Wuhan to the global pandemic that it is
   today. He shows that many Western governments & their sci.advisors made
   assumptions about the virus & its lethality that turned out to be mistaken.
   Valuable time was lost while the v. spread unchecked, leaving health systems
   unprepared for the avalanche of infections that followed. ..."

%A J. Beumer
%A et al ...
%A H. Clevers
%T High-resolution mRNA and secretome atlas of human enteroendocrine cells
%J Cell
%V 181
%P 1291-1306
%M JUN
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0620, human, enteroendocrine cell,
   endocrine, EEC, EECs, mRNA, hormone, secreted, intestine, gut, obesity,
   diabetes, cell atlas, GLP-1, GLP1, insulin, Lgr5+, genes, Teichmann,
   cellAtlas, single cell RNA seq, RNAseq, scRNAseq
%X "Enteroendocrine cells (EECs) sense intestinal content & release hormones to
   regulate gastrointestinal activity, systemic metabolism, ... Here, we
   describe an organoid-based platform for functional studies of human EECs.
   EEC formation is induced in vitro by transient expression of NEUROG3. A set
   of gut organoids was engineered in which the major hormones are fluorescently
   tagged. A single-cell mRNA atlas was generated for the different EEC subtypes
   & their secreted products were recorded by mass-spectrometry. We note key
   differences to murine EECs, inc. hormones, sensory receptors, & transcription
   factors. Notably, several hormone-like molecules were identified. Inter-EEC
   communication is exemplified by secretin-induced GLP-1 secretion. ..."
   -- [<A HREF="https://doi.org/10.1016/j.cell.2020.04.036">doi:10.1016/j.cell.2020.04.036</A>]['20].
   (Also see EEC@[<A HREF="https://en.wikipedia.org/wiki/Enteroendocrine_cell">wikip</A>]['20].)
   [Also search for: scRNAseq].

%A W. Dai
%A et al ...
%A H. Liu
%T Structure-based design of antiviral drug candidates targeting the SARS-CoV-2
   main protease
%J Science
%V 368
%N 6497
%P 1331-1335
%M JUN
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0620, SARS-CoV-2, SARSCoV2, 3CLpro,
   Mpro, protease, inhibitor, thiol, covid-19, covid19, 6LZE, 6M0K, 11a, 11b,
   cys145, inSilico, inVitro
%X "... We designed & synthesized two lead compounds (11a & 11b) targeting Mpro.
   Both exhibited excellent inhibitory activity & potent anti-SARS-CoV-2
   infection activity. The x-ray crystal structures of SARS-CoV-2 Mpro in
   complex with 11a or 11b, both determined at a resolution of 1.5A, showed that
   the aldehyde groups of 11a & 11b are covalently bound to cysteine 145 of
   Mpro. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abb4489">doi:10.1126/science.abb4489</A>]['20].
      "...toxicity ... rats ... dogs ..."
   [Also search for: SARSCoV2 protease].

%A R. Singh
%A et al
%T Unsupervised manifold alignment for single-cell multi-omics data
%J bioRxiv
%M JUN
%D 2020
%K TR, MolBio, c2020, c202x, c20xx, zz0321, MMD-MA, MMDMA, scRNAseq, scRNA,
   manifold alignment, learning
%X "Integrating single-cell measurements that capture different properties of
   the genome is vital to extending our understanding of genome biology. This
   task is challenging due to the lack of a shared axis across datasets obtained
   from different types of single-cell experiments. ... unsupervised algs. that
   are capable of aligning single-cell experiments are critical to learning an
   in silico co-assay that can help draw corr. among the cells. Maximum mean
   discrepancy-based manifold alignment (MMD-MA) is such an unsupervised alg.
   ... we apply MMD-MA to two recent datasets that measure transcriptome &
   chromatin accessibility in ~2000 single cells ..."
   -- [<A HREF="https://doi.org/10.1101/2020.06.13.149195">doi:10.1101/2020.06.13.149195</A>]['21],
      [<A HREF="https://www.biorxiv.org/content/10.1101/2020.06.13.149195v1">bioRxiv</A>]['21].
   Talk: [<A HREF="https://drive.google.com/file/d/174tK5uIOtD-mZc0LRhomqNd5O6ZfPGkO/view">www</A>]['20].
   [Also search for: scRNAseq].

%A D. J. McGiver
%A et al
%T Coronavirus surveillance of wildlife in the Lao People's
   Democratic Republic detects viral RNA in rodents
%J Archives of Virology
%M JUN
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0620, corona virus, viruses, coronavirus, covid,
   SE, Asia, China, Vietnam, Laos, wet, wildlife market, zoonotic,
   betacoronavirus, OC43, HKU1
%X "... hunting, sale, & consumption of wild animals in SE Asia increases the
   risk for such [zoonotic] incidents. We sampled & tested rodents (851) & other
   mammals & found betacoronavirus RNA in 12 rodents. The seqs. belong to two
   separate genetic clusters & are closely related to those of known rodent
   coronaviruses detected in the region & distantly related to those of human
   coronaviruses OC43 & HKU1. ..."
   -- [<A HREF="https://doi.org/10.1007/s00705-020-04683-7">doi:10.1007/s00705-020-04683-7</A>]['20].
   [Also search for: zoonotic].

%A K. M. Sakamoto
%A et al ...
%A R. J.Deshaies
%T Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box
   complex for ubiquitination and degradation
%J PNAS
%V 98
%N 15
%P 8554-8559
%M JUL
%D 2020
%K jrnl, PNAS, MolBio, c2020, c202x, c20xx, zz0620, Protacs, drug, drugs,
   design, protein, Skp1-Cullin-F,  SCF, MetAP-2, MetAP2, Protac 1, Protac1
%X "... many proteins are regulated by ubiquitin-dependent proteolysis. ...
   ubiquitin ligase complex, Skp1-Cullin-F box complex containing Hrt1 (SCF).
   We sought to artificially target a protein to the SCF complex for
   ubiquitination & degradation. To this end, we tested methionine
   aminopeptidase-2 (MetAP-2) ... Protac-1 mediates the ubiquitination &
   degradation of a foreign substrate by SCF provides a basis to begin testing
   Protacs in vivo in addition to other targets known to promote disease."
  -- [<A HREF="https://doi.org/10.1073/pnas.141230798">doi:10.1073/pnas.141230798</A>]['20].
   (Also see [<A HREF="https://en.wikipedia.org/wiki/Proteolysis_targeting_chimera">wikip</A>]['20].)

%A H. J. Abel
%A et al ...
%A I. M. Hall
%T Mapping and characterization of structural variation in 17,795 human genomes
%J Nature
%V 583
%P 83-89
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, human genomes, DNA,
   structural variations
%X "... used a scalable pipeline to map & characterize structural variants in
   17,795 deeply sequenced human genomes. ... release site-freq. data to create
   the largest, to our knowledge, whole-genome-seq.-based struct.variant
   resource so far. On average, individuals carry 2.9 rare s.variants that
   alter coding regions; these variants affect the dosage or struct. of 4.2
   genes & account for 4.0-11.2% of rare high-impact coding alleles. Using a
   comp'l model, we est. that s.variants account for 17.2% of rare alleles
   genome-wide, with predicted deleterious effects that are equiv. to
   loss-of-fn coding alleles; ~90% of such s.variants are noncoding deletions
   (mean 19.1 per genome). We report 158,991 ultra-rare s.variants & show that
   2% of individuals carry ultra-rare megabase-scale s.variants, nearly half of
   which are balanced or complex rearrangements. Finally, we infer the dosage
   sensitivity of genes & noncoding elts, & reveal trends that relate to elt
   class & conservation. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2371-0">doi:10.1038/s41586-020-2371-0</A>]['20],  pub. 27/5/2020.

%A J. C. Wheat
%A et al
%A U. Steidl
%T Single-molecule imaging of transcription dynamics in somatic stem cells
%J Nature
%V 583
%P 431-436
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, smFISH, single molecule RNA,
   fluorescent insitu hybridization, PU1, Spi1, Gata1, Gata2, stemCell,
   somatic, adult
%X "... we use single-molec. RNA fluorescent in situ hybridization (smFISH) on
   mouse stem cells derived from haematopoietic tissue to measure the
   transcription dynamics of three key genes that encode transcription factors:
   PU.1 ([AKA] Spi1), Gata1 & Gata2. ... infrequent, stochastic bursts of
   transcription result in the co-expression of these antagonistic transcription
   factors in the majority of haematopoietic stem & progenitor cells. Moreover,
   by pairing smFISH with time-lapse microscopy & the analysis of pedigrees, we
   find that although individual stem-cell clones produce descendants that are
   in transcriptionally related states - akin to a trans.priming phenomenon -
   the underlying transition dynamics between states are best captured by
   stochastic & reversible models. As such, a stoch. process can produce
   cellular behaviours that may be incorrectly inferred to have arisen from
   deterministic dynamics. We propose a model whereby the intrinsic stoch'y of
   gene expn facilitates, rather than impedes, the concomitant maintenance of
   transcriptional plasticity & stem cell robustness."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2432-4">doi:10.1038/s41586-020-2432-4</A>]['20].
   (Also see StemC@[<A HREF="https://en.wikipedia.org/wiki/Stem_cell">wikip</A>]['20].)

%A J. A. Jaimes
%A et al
%T Phylogenetic analysis and structural modeling of SARS-CoV-2 spike protein
   reveals an evolutionary distinct & proteolytically sensitive activation loop
%J J. Mol. Biol.
%V 432
%N 10
%P 3309-3325
%M MAY
%D 2020
%K jrnl, JMB, MolBio, c2020, c202x, c20xx, zz0920, SARS-CoV-2, SARSCoV2, SARS2,
   spike protein, phylogeny, tree, betacoronavirus
%X "... we perform structural modeling of the SARS-CoV-2 spike glycoprotein. Our
   data provide support for the similar receptor utilization between SARS-CoV-2
   and SARS-CoV, despite a relatively low amino acid similarity in the receptor
   binding module. ..."
   -- [<A HREF="https://doi.org/10.1016/j.jmb.2020.04.009">doi:10.1016/j.jmb.2020.04.009</A>]['20]

%A G. Andreatta
%A K. Tessmar-Raible
%T The still dark side of the Moon: Molecular mechanisms of lunar-controlled
   rhythms and clocks
%J JMB
%V 432
%N 12
%P 3525-3546
%M MAY
%D 2020
%K jrnl, JMB, MolBio, c2020, c202x, c20xx, zz0920, biology, biol, clock, cycle,
   cyclic, rythm, moon, lunar, circatidal, circalunar, circadian, transcriptome,
   effects
%X "... many marine species exhibit lunar rhythms, and also the number of
   documented 'lunar-rhythmic' terrestrial species is increasing. ..."
   -- [<A HREF="https://doi.org/10.1016/j.jmb.2020.03.009">doi:10.1016/j.jmb.2020.03.009</A>]['20].
   [Also search for: moon lunar].

%A D. Bojkova
%A et al ...
%A C. Munch
%T Proteomics of SARS-CoV-2-infected host cells reveals therapy targets
%J Nature
%V 583
%P 469-472
%M MAY
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0710, SARS-CoV-2, SARSCoV2, covid-19,
   protein, coronavirus, cell pathways, inhibitor, Caco2, cycloheximide,
   emetine
%X "... we identify the host cell pathways that are modulated by SARS-CoV-2 &
   show that inhibition of these pathways prevents viral replication in h.cells.
   We established a human cell-culture model for infection with a clinical
   isolate of SARS-CoV-2. Using this cell-culture system, we determined the
   infection profile of SARS-CoV-2 by translatome & proteome proteomics at
   different times after infection. ... revealed that SARS-CoV-2 reshapes
   central cellular pathways such as translation, splicing, carbon metabolism,
   protein homeostasis (proteostasis) & nucleic acid metabolism. Small-molecule
   inhibitors that target these pathways prevented viral replication in cells.
   Our results reveal the cellular infection profile of SARS-CoV-2 & have
   enabled the identification of drugs that inhibit viral replication. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2332-7">doi:10.1038/s41586-020-2332-7</A>]['20].
   [Also search for: SARSCoV2 protein].

%A A. M. Andrianov
%A Y. V. Kornoushenko
%A A. D. Karpenko
%A I. P. Bosko
%A A. V. Tuzikov
%T Computational discovery of small drug-like compounds as potential inhibitors
   of SARS-CoV-2 main protease
%J J. Biomolec. Structs. and Dynamics
%V ?
%P ?-?
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, SARS-CoV-2, SARSCoV2, Mpro,
   3CLpro, protease, protein, inhibitor, ligand, X77, Pharmit, His41, Met49,
   Cys145, Met165, Gln189, inSilico
%X "... mimicry of the high affinity ligand X77, potent non-covalent inhibitor
   of SARS-COV-2 main protease (MPro). In doing so, the X77-mimetic candidates
   were predicted based on the crystal X77-MPro structure by a public
   web-oriented virtual screening platform Pharmit. ... Calculation revealed
   5 top-ranking compounds that exhibited a high affinity to the active site of
   SARS-CoV-2 MPro. ... van der Waals interactions with the functionally
   important residues of the enzyme, such as His-41, Met-49, Cys-145, Met-165, &
   Gln-189 ..."
   -- [<A HREF="https://doi.org/10.1080/07391102.2020.1792989">doi:10.1080/07391102.2020.1792989</A>]['20]  (online 7/2020),
      12275390/1@[<A HREF="https://chemrxiv.org/articles/preprint/Computational_Discovery_of_Small_Drug-like_Compounds_as_Potential_Inhibitors_of_SARS-CoV-2_Main_Protease/12275390/1">chemRxiv</A>]['20].
   [Also search for: SARSCoV2 protease].

%A P. M. Folegatti
%A et al ...
%A A. J. Pollard
%T Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2:
   a preliminary report of a phase 1/2, single-blind, randomised controlled
   trial
%J The Lancet
%V 396
%N 10249
%P P467-478
%M AUG
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0720, SARS-CoV-2, SARSCoV2, covid19, covid-19,
   ChAdOx1, vaccine, Oxford, UniOxford, clinical trial
 %X "... We did a phase 1/2, single-blind, randomised controlled trial in five
   trial sites in the UK of a chimpanzee adenovirus-vectored vaccine
   (ChAdOx1 nCoV-19) expressing the SARS-CoV-2 spike protein compared with a
   meningococcal conjugate vaccine (MenACWY) as control. ... ChAdOx1 nCoV-19
   showed an acceptable safety profile, and homologous boosting increased
   antibody responses. ..."
   -- [<A HREF="https://doi.org/10.1016/S0140-6736(20)31604-4">doi:10.1016/S0140-6736(20)31604-4</A>]['20]  (online JUL 2020).
   [Also search for: SARSCoV2].

%A M. Di Antonio
%A et al ...
%A S. Balasubramanian
%T Single-molecule visualization of DNA G-quadruplex formation in live cell
%J Nat. Chem.
%V 12
%P 832-837
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0720, DiAntonio, DNA, quadruplex, G4s,
   four stranded, gene expression, cell cycle, SiR-PyPDS
%X "Substantial evidence now exists to support that formation of DNA
   G-quadruplexes (G4s) is coupled to altered gene expression. ..."
      ("G-quadruplexes (G4s) are non-canonical structures that can form within
       guanine-rich nucleic-acid sequences ... over 700,000 distinct sites that
       can form G4s ...")
   -- [<A HREF="https://doi.org/10.1038/s41557-020-0506-4">doi:10.1038/s41557-020-0506-4</A>]['20]  (18 refs, online 20/7/2020).
  (4 guanines can form a square.)

%A D. Jebb
%A et al ...
%A E. C. Teeling
%T Six reference-quality genomes reveal evolution of bat adaptations
%J Nature
%V 583
%P 578-584
%M JUL
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0720, MolBio, bat, bats, Chiroptera, Ngenome,
   genome, genomes, evolution, Scrotifera, echolocation, immunity,
   immune system, APOBEC3, LRRC70, IL36G, viral, viruses
%X "... the first reference-quality genomes of six bat species (Rhinolophus
   ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis,
   Pipistrellus kuhlii & Molossus molossus). ... identified a basal origin for
   bats within Scrotifera. ... found selection & loss of immunity-related genes
   (including pro-inflammatory NF-kB regulators) & expansions of anti-viral
   APOBEC3 genes, which highlights molecular mechanisms that may contribute to
   the exceptional immunity of bats...."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2486-3">doi:10.1038/s41586-020-2486-3</A>]['20].
   [Also search for: MolBio bat genome].

%A Peng He
%A et al ...
%A B. J. Wold
%T The changing mouse embryo transcriptome at whole tissue and
   single-cell resolution
%J Nature
%V 583
%P 760-767
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0820, scRNAseq, scRNA-seq, mouse,
   embryo, development, cell, tissue, type, embryogenesis, gene expression,
   animal, mammal
%X "During mammalian embryogenesis, differential gene expression gradually
   builds the identity & complexity of each tissue & organ system. Here we
   systematically quantified mouse polyA-RNA from day 10.5 of embryonic
   development to birth, sampling 17 tissues & organs. The resulting
   developmental transcriptome ... Focusing on the developing limb, single-cell
   RNA data identified 25 candidate cell types ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2536-x">doi:10.1038/s41586-020-2536-x</A>]['20].
   [Also search for: scRNAseq].

%A Jingyun Yang
%A et al ...
%A Xiawei Wei
%T A vaccine targeting the RBD of the S protein of SARS-CoV-2 induces
   protective immunity
%J Nature
%V ?
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0820, SARS-CoV-2, SARSCoV2, vaccine,
   SARS2, S-RBD, SRBD, spike protein
%X "... Here we showed that a recombinant vaccine comprising residues 319-545
   of the S-RBD could induce a potent functional antibody response in the
   immunized mice, rabbits & non-human primates (Macaca mulatta) as early as
   7 or 14 days after a single dose injection ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2599-8">doi:10.1038/s41586-020-2599-8</A>]['20]  (online 29/7/2020).
   (Apparently over 100 *potential* vacs. are in the works.)
   [Also search for: SARSCoV2 vaccine].

%A A. G. Wrobel
%A et al ...
%T SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on
   virus evolution and furin-cleavage effects
%J NatureStructAndMolBio
%V 27
%P 763-767
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0521, SARS-CoV-2, SARS2, covid-19,
   covid19, RaTG13, virus, horseshoe bats, Wuhan, China, pandemic, origin,
   spike protein, ACE2, furin cleavage, glycoprotein
%X "SARS-CoV-2 is thought to have emerged from bats, possibly via a secondary
   host. Here, we investigate the relationship of spike (S) glycoprotein from
   SARS-CoV-2 with the S protein of a closely related bat virus, RaTG13. ...
   there are key differences in their properties, inc. a more stable precleavage
   form of human S & about 1,000-fold tighter binding of SARS-CoV-2 to human
   receptor. ... suggest that cleavage at the furin-cleavage site decreases the
   overall stability of SARS-CoV-2 S & facilitates the adoption of the open
   conformation that is required for S to bind to the ACE2 receptor."
   -- [<A HREF="https://doi.org/10.1038/s41594-020-0468-7">doi:10.1038/s41594-020-0468-7</A>]['21].
   [Also search for: MolBio RATG13] and [also search for: SARS origin].

%A K. H. Miga
%A et al ...
%A A. M. Phillippy
%T Telomere-to-telomere assembly of a complete human X chromosome
%J Nature
%V 585
%P 79-84
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0920, human, genome, X chromosome,
   Xchromosome, chromosomeX, Xchr, chrX, GRCh38, CHM13
%X "... we present a human genome assembly that surpasses the continuity of
   GRCh382, along with a gapless, telomere-to-telomere assembly of a human
   chromosome. This was enabled by high-coverage, ultra-long-read nanopore
   seq. of the complete hydatidiform mole CHM13 genome, combined with
   complementary technologies for quality improvement & validation. Focusing our
   efforts on the human X chromosome3, we reconstructed the centromeric
   satellite DNA array (~3.1 Mb) & closed the 29 remaining gaps ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2547-7">doi:10.1038/s41586-020-2547-7</A>]['20].

%A M. Minguez-Toral
%A B. Cuevas-Zuviria
%A M. Garrido-Arandia
%A L. F. Pacios
%T A computational structural study on the DNA-protecting role of the
   tardigrade-unique Dsup protein
%J Sci. Reports
%V 10
%N #13424
%M AUG
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0820, MolBio, biol, tardigrade, invertebrate,
   animal, DNA, damage suppression, protection, Dsup, disordered protein
%X "The remarkable ability of t. to withstand a wide range of physical & chem.
   extremes ... By means of molec. mod., calculations of electrostatic
   potentials & electric fields, & all-atom molec. dynamics sim'ns, we obtained
   a dynamic picture of the Dsup-DNA interaction. ... suggest that the protein
   is intrinsically disordered, which enables Dsup to adjust its structure to
   fit DNA shape. Strong electrostatic attractions & high protein flexibility
   drive the formation of a molecular aggregate in which Dsup shields DNA. While
   the precise mechanism of DNA protection conferred by Dsup remains to be
   elucidated, our study provides some molec. clues of their assoc. that could
   be of interest for further investigation in this line."
   -- [<A HREF="https://doi.org/10.1038/s41598-020-70431-1">doi:10.1038/s41598-020-70431-1</A>]['20].

%A A. D. Rathnayake
%A et al ...
%A Kyeong-Ok Chang
%T 3C-like protease inhibitors block coronavirus replication in vitro and
   improve survival in MERS-CoV-infected mice
%J Sci. Trans. Med.
%V 12
%N 557
%P #eabc5332
%M AUG
%D 2020
%K jrnl, eJrnl, MolBio, c2020, c202x, c20xx, zz0920, MERS, protease inhibitor,
   3CLpro, Mpro, mouse, SARS, SARS1, MERSCov, MERS, SARS2,
   Huh-7, Huh7, Vero E6, VeroE6
%X "... We describe herein the struct.-guided optimization of a series of
   inhibitors of the coronavirus 3C-like protease (3CLpro), an enzyme essential
   for viral replication. The optimized compounds were effective against several
   human coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2 in an enzyme
   assay & in cell-based assays using Huh-7 and Vero E6 cell lines. ... [mouse]
   survival [went] from 0 to 100% ..."
   -- [<A HREF="https://doi.org/10.1126/scitranslmed.abc5332">doi:10.1126/scitranslmed.abc5332</A>]['20].
   [Also search for: MolBio 3CLpro inhibitor].

%A W. Vuong
%A et al ...
%A M. J. Lemieux
%T Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and
   blocks virus replication
%J Nat. Comms.
%V 11
%P #4282
%M AUG
%D 2020
%K jrnl, eJrnl, MolBio, c2020, c202x, c20xx, zz0920, SARS, SARS2, SARSCoV2,
   protease, 3CLpro, inhibitor, drug, cat, cats, feline, GC373, GC376, Cys145
%X "... prodrug GC376, a dipeptide-based p.inhibitor. Here, we show the prodrug
   & its parent GC373, are effective inhibitors of the Mpro from both SARS-CoV
   & SARS-CoV-2 with IC50 values in the nanomolar range. Crystal structures of
   SARS-CoV-2 Mpro with these inhibitors have a covalent modification of the
   nucleophilic Cys145. NMR analysis reveals that inhibition proceeds via
   reversible formation of a hemithioacetal. GC373 & GC376 are potent inhibitors
   of SARS-CoV-2 replic'n in cell culture. They are strong drug candidates ..."
   -- [<A HREF="https://doi.org/10.1038/s41467-020-18096-2">doi:10.1038/s41467-020-18096-2</A>]['20],
      GC376@[<A HREF="https://en.wikipedia.org/wiki/GC376">wikip</A>]['20].
   [Also search for: SARSCoV2 inhibitor].

%A M. Thoms
%A et al ...
%A R. Beckmann
%T Structural basis for translational shutdown and immune evasion by the Nsp1
   protein of SARS-CoV-2
%J Science
%V 369
%N 6508
%P 1249-1255
%M SEP
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0920,  SARSCoV2, nsp1, protein,
   structure
%X "... virulence factor nonstructural protein 1 (Nsp1) also shuts down
   translation of host messenger RNA. Thoms et al. determined a 2.6A resolution
   cryo-electron microscopy structure of a reconstituted complex of Nsp1 bound
   to the human 40S ribosomal subunit and showed that Nsp1 blocks the mRNA
   entry tunnel. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abc8665">doi:10.1126/science.abc8665</A>]['20].
   [Also search for: SARSCoV2 Nsp1].

%A B. Boras
%A et al ...
%A C. Allerton
%T Discovery of a novel inhibitor of Coronavirus 3CL protease as a
   clinical candidate for the potential treatment of COVID-19
%J bioRxiv
%M SEP
%D 2020
%K TR, MolBio, c2020, c202x, c20xx, zz1020, PF-07304814, PF07304814,
   PF-00835231, PF00835231, Mpro, 3CLpro, Pfizer, protease, inhibitor,
   phosphate, covid19, SARS-CoV-2, SARSCov2, therapy
%X "...  The designed phosphate prodrug PF-07304814 is metabolized to
   PF-00835321 which is a potent inhibitor in vitro of the coronavirus family
   3CLpro, with selectivity over human host protease targets. Furthermore,
   PF-00835231 exhibits potent in vitro antiviral activity against SARS-CoV-2
   as a single agent and it is additive/synergistic in combination with
   remdesivir. We present the ADME, safety, and in vitro antiviral activity
   data to warrant clinical evaluation."
   -- [<A HREF="https://doi.org/10.1101/2020.09.12.293498">bioRxiv</A>]['20].
   [Also search for: MolBio 3CLpro inhibitor].

%A D. Zaidman
%E at al ...
%A F. von Delft
%A N. London
%T An automatic pipeline for the design of irreversible derivatives identifies a
   potent SARS-CoV-2 Mpro inhibitor
%J bioRxiv
%M SEP
%D 2020
%K TR, c2020, c202x, c20xx, zz1120, MolBio, covalentizer, covalent, inhibitor,
   3CLpro, Mpro, Cys, cysteine, protease, covid19, SARS-CoV-2, SARSCoV2, ligand,
   von Delft, vonDelft
%X "... covalentizer, a computational pipeline for creating irreversible
   inhibitors based on complex structures of targets with known reversible
   binders. ... We found ~11,000 cysteines in close proximity to a ligand across
   8,386 protein-ligand complexes in the PDB. Of these, the protocol identified
   1,553 structures with covalent predictions. In prospective eval'n against a
   panel of kinases, five out of nine predicted cov.inhibitors showed IC50 ..."
   -- 2020.09.21.299776v1@[<A HREF="https://www.biorxiv.org/content/10.1101/2020.09.21.299776v1">biorxiv</A>]['20]  (77 refs).
   [Also search for: MolBio 3CLpro inhibitor].

%A J. Kaiser
%T Found: genes that sway the course of the coronavirus
%J Science
%V 370
%N 6514
%P 275-276
%M OCT
%D 2020
%K news, views, MolBio, c2020, c202x, c20xx, zz1020, covid-19, covid19, SARS2,
   genes, severity, IFNAR2, OAS, DPP9, TYK2, baricitinib, CCR2, SLC6Z20, FOXP4,
   chr3
%X "... a UK group studying more than 2200 COVID-19 patients has pinned down
   common gene variants that are linked to the most severe cases of the disease,
   and that point to existing drugs that could be repurposed to help ..."
   -- [<A HREF="https://doi.org/10.1126/science.370.6514.275">doi:10.1126/science.370.6514.275</A>]['20],
      [<A HREF="https://science.sciencemag.org/content/370/6514/275">www</A>]['20].

%A J. W. Rausch
%A et al ...
%A M. F. Kearney
%T Low genetic diversity may be an Achilles heel of SARS-CoV-2
%J PNAS
%M OCT
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0521, SARS CoV 2, Nsp14, SARSCoV2,
   Ebola, H1N1, HBV, HIV, HIV1, flu, HCV, RNA virus, coronavirus,
   diversity, APD, ACE2
%K "... SARS-CoV-2 genetic diversity is remarkably low, almost entirely the
   product of genetic drift, and should not be expected to impede development
   of a broadly protective vaccine. ... coronaviruses evolved nonstructural
   protein 14 (nsp14), which ... excises misincorporated ribonucleotides from
   nascent strands ... This error-correcting capacity was unknown among RNA
   viruses prior to its discovery in SARS-CoV-1 ... error rate more than
   10-fold lower than that of other RNA viruses ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.2017726117">doi:10.1073/pnas.2017726117</A>]['21].
   Paper includes the diversity (avg pairwise dist.) of several viruses.
   (* Also see [<A HREF="https://doi.org/10.1073/pnas.2008281117">doi:10.1073/pnas.2008281117</A>][8/'21]. *)
   [Also search for: SARS mutation].

%A S. Keretsu
%A S. P. Bhujbal
%A S. Joo Cho
%T Rational approach toward COVID-19 main protease inhibitors via molecular
   docking, molecular dynamics simulation and free energy calculation
%J Sci. Reps.
%V 10
%N #17716
%M OCT
%D 2020
%K MolBio, jrnl, ejrnl, c2020, c202x, c20xx, zz0221, 3CL pro, 3CLpro, protease,
   MEROPS, SARS-CoV-2, SARS2, SARSCov2, inhibitor, saquinavir, aclarubicin,
   TMC-310911, TMC310911, faldaprevir
%X "... A combination of modeling studies was performed to identify potential
   3CLpro inhibitors from the protease inhibitor database MEROPS
   [<A HREF="https://www.ebi.ac.uk/merops/index.shtml">www</A>]. Binding energy
   evaluation identified key residues for inhibitor design. We found 15
   potential 3CLpro inhibitors with higher binding affinity than that of an
   alpha-ketoamide inhibitor determined via X-ray structure. Among them,
   saquinavir and three other investigational drugs aclarubicin, TMC-310911, &
   faldaprevir could be suggested as potential 3CLpro inhibitors. We recommend
   further experimental investigation of these compounds."
   -- [<A HREF="https://doi.org/10.1038/s41598-020-74468-0">doi:10.1038/s41598-020-74468-0</A>]['21].
   [Also search for: MolBio 3CLpro inhibitor].

%A L. Shenhav
%A D. Zeevi
%T Resource conservation manifests in the genetic code
%J Science
%V 370
%N 6517
%P 683-687
%M NOV
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz1120, DNA, genetic code, proteins,
   codon, codons, amino acids, origins, mutations
%X "... we study this 'resource-driven selection' by using metagenomic &
   single-cell data of marine microbes, alongside environmental measurements.
   We show that a sig. portion of the selection exerted on microbes is explained
   by the environment & is assoc. with nitrogen availability. Notably, this
   resource conservation optimization is encoded in the structure of the std
   genetic code, providing robustness against mutations that increase carbon &
   nitrogen incorporation into protein seqs. This robustness generalizes to
   codon choices from multiple taxa across all domains of life, inc. the human
   genome."
   -- [<A HREF="https://doi.org/10.1126/science.aaz9642">doi:10.1126/science.aaz9642</A>]['20].

%A M. Mart-Solarne
%A et al ...
%A M. Babu
%T Combinatorial expression of GPCR isoforms affects signalling and
   drug responses
%J Nature
%V 587
%P 650-656
%M NOV
%D 2020
%K MolBio, jrnl, c2020, c202x, c20xx, zz1120, GPCR protein, isoform, response,
   gpcrdb, GPCRs
%X "... GPCR-mediated signalling can differ because of changes in the sequence
   or expression of the receptors, leading to signalling bias when comparing
   diverse physiological systems. An underexplored source of such bias is the
   generation of functionally diverse GPCR isoforms with different patterns of
   expression across different tissues. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2888-2">doi:10.1038/s41586-020-2888-2</A>]['20].
   Also see [<A HREF="https://gpcrdb.org">gpcrdb.org</A>]['20].
   [Also search for: MolBio GPCR].

%A B. Halford
%T Covalent drugs go from fringe: Designing molecules that make bonds with
   their biological targets is in vogue
%J Chem. and Eng. News
%V 98
%N 43
%P 28-33
%M NOV
%D 2020
%K MolBio, intro, TR, covalent bond, protein, drug, inhibitor, asprin,
   Bortezomib, Ibrutinib, MRTX849, acrylamide, Rilzabrutinib
%X "Although drugs that make covalent bonds with their biol. targets are as old
   as the pharmaceutical industry, intentionally designing molecules that make
   such bonds is relatively new. ... successful drugs like ibrutinib & new tools
   ..."
   -- [<A HREF="https://cen.acs.org/pharmaceuticals/drug-discovery/Covalent-drugs-fringe-field-fashionable/98/i43">www</A>]['20].
   [Also search for: MolBio covalent inhibitor].

%A B. Qin
%A et al
%T Acrylamide fragment inhibitors that induce unprecedented conformational
   distortions in enterovirus 71 3C and SARS-CoV-2 main protease
%J bioRxiv
%M NOV
%D 2020
%K MolBio, TR, c2020, c202x, c20xx, zz1120, covalent, inhibitor, 3Cpro, 3CLpro,
   Mpro, protease, Enterovirus, Enterovirus71, SARSCoV2, SARS-CoV-2
%X "... describe the successful application of quantitative irreversible
   tethering (qIT) to identify acrylamide fragments that selectively target the
   active site cysteine of the 3C protease (3Cpro) of Enterovirus 71 ...
   re-purpose these hits towards the main protease (Mpro) of SARS-CoV-2 ..."
   -- 10.1101/2020.11.06.370916v1@[<A HREF="https://www.biorxiv.org/content/10.1101/2020.11.06.370916v1">bioRxiv</A>]['20].
   [Also search for: MolBio 3CLpro inhibitor].

%A R. F. Service
%T 'The game has changed.' AI triumphs at protein folding
%J Science
%V 370
%N 6521
%P 1144-1145
%M DEC
%D 2020
%K MolBio, news, views, c2020, c202x, c20xx, zz1220, CASP, CASP14,
   protein, fold, folding, structure, prediction, AlphaFold, DeepMind, ANN, NN
%X "[AI] has solved one of biology's grand challenges: predicting how proteins
   curl up from a linear chain of AAs into 3D shapes that allow them to carry
   out life's tasks. ... the DeepMind method will have far-reaching effects,
   among them helping researchers identify protein-based targets for novel
   medications. Because contest rules require competitors to reveal enough of
   their methods for others to make use of them, organizers say it's only a
   matter of months before other groups match DeepMind's success."
   -- [<A HREF="https://doi.org/10.1126/science.370.6521.1144">doi:10.1126/science.370.6521.1144</A>]['20].
   (Also see Pfolding@[<A HREF="https://en.wikipedia.org/wiki/Protein_folding">wikip</A>]['22].)
   [Also search for: MolBio AlphaFold].

%A B. Dereka
%A et al
%T Crossover from hydrogen to chemical bonding
%J Science
%V 371
%N 6525
%P 160-164
%M JAN
%D 2021
%K c2021, c202x, c20xx, zz0121, chemistry, chemical bonding, hydrogen bond, FHF
%X "Hydrogen bonds (H-bonds) can be interpreted as a classical electrostatic
   interaction or as a covalent chemical bond if the interaction is strong
   enough. [so] short strong H-bonds exist at an intersection between
   qualitatively different bonding descriptions, with few experimental methods
   to understand this dichotomy. ... demonstrate a distinct crossover in
   spectroscopic properties from conventional to short strong H-bonds, which
   identify where hydrogen bonding ends and chemical bonding begins."
   -- [<A HREF="https://doi.org/10.1126/science.abe1951">doi:10.1126/science.abe1951</A>]['21].

%A K. Sahlin
%T Strobemers: an alternative to k-mers for sequence comparison
%J BioRxiv
%M JAN
%D 2021
%K MolBio, TR, c2021, c202x, c20xx, zz0221, Strobemer, Kmers, gapped, seeds
%X "... a single mutation will mutate k consec. k-mers & makes most k-mer based
   applications for seq. comparison sensitive to variable mutation rates. Many
   techniques have been studied to overcome this sensitivity, e.g., spaced
   k-mers & k-mer permutation techniques, but these techniques do not handle
   indels well. ...propose strobemers as an alternative to k-mers for seq.
   comparison. Intuitively, strobemers consists of linked minimizers. We show
   that under a certain minimizer selection technique, strobemers provide more
   evenly distributed sequence matches than k-mers & are less sensitive to
   different mutation rates & distributions. ..."  [via AK]
   -- at[<A HREF="https://doi.org/10.1101/2021.01.28.428549">bioRxiv</A>]['21].

%A T. van der Valk
%A et al
%T Million-year-old DNA sheds light on the genomic history of mammoths
%J Nature
%M FEB
%D 2021
%K MolBio, c2021, c202x, c20xx, zz0321, ancient DNA, fossil, woolly mammoth,
   M. primigenius, mamoth, Pleistocene
%X "... report the recovery of genome-wide data from three mammoth specimens
   dating to the Early and Middle Pleistocene subepochs, two of which are more
   than one million years old. We find that two distinct mammoth lineages were
   present in eastern Siberia during the Early Pleistocene. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-03224-9">doi:10.1038/s41586-021-03224-9</A>]['21].
   [Also search for: MolBio ancient DNA].

%A F. Ronquist
%A et al
%T Universal probabilistic programming offers a powerful approach to
   statistical phylogenetics
%J CommunicationsBiology
%V 4
%P #244
%K FEB
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0823, phylogenetic, tree, PPL,
   Senderov, Broman
%X "Stat. phylogenetic analysis currently relies on complex, dedicated s/w
   packages, making it difficult for evolutionary biologists to explore new
   models & inference strategies. ... we show that universal probabilistic
   programming languages (PPLs) solve the expressivity problem, while still
   supporting automated generation of efficient inference algs.. To prove the
   latter point, we develop automated generation of sequential Monte Carlo (SMC)
   algs. for PPL descriptions of arbitrary biol. diversification (birth-death)
   models. ..."
   -- [<A HREF="https://doi.org/10.1038/s42003-021-01753-7">doi:10.1038/s42003-021-01753-7</A>]['23].
   Correction: missing figs [<A HREF="https://doi.org/10.1038/s42003-021-01922-8">www</A>][3/2021].
   [Also search for: probabilistic programming].

%T WHO-convened Global Study of Origins of SARS-CoV-2: China Part,
   Joint WHO-China Study 14 January - 10 February 2021, Joint Report
%I WHO
%D 2021
%K report, WHO, MolBio, c2021, c202x, c20xx, zz0621, SARS CoV 2, SARSCoV2,
   SARS2, covid 19, covid19, virus, Wuhan, WIV, Huanan wet market, China,
   origin, origins, investigation, pandemic, transmission,
   hypotheses, theories, RaTG13, bat, bats, laboratory, lab, leak
%X "... The joint international team comprised 17 Chinese & 17 international
   experts from other countries, the World Health Organization (WHO), the
   Global Outbreak Alert and Response Network (GOARN), and the World
   Organisation for Animal Health (OIE) (Annex B). ...
   [p.119-120 on a possible 'lab incident':] ... a laboratory origin of the
   pandemic was considered to be extremely unlikely ..."
   -- pdf@[<A HREF="https://www.who.int/docs/default-source/coronaviruse/who-convened-global-study-of-origins-of-sars-cov-2-china-part-joint-report.pdf">www</A>]['21].
   (Also see, e.g., [<A HREF="https://www.bbc.com/news/world-asia-china-57268111">bbc</A>][28/5/2021].)
   [Also search for: MolBio SARS2 origin].

%A D. Diaz-Dominguez
%A G. Navarro
%T A grammar compressor for collections of reads with applications to the
   construction of the BWT
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, MolBio, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021,
   DNA sequencing, grammar compressor, compression
%X "We describe a grammar for DNA sequencing reads from which we can compute the
   BWT directly. Our motivation is to perform in succinct space genomic analyses
   that require complex string queries not yet supported by repetition-based
   self-indexes. Our approach is to store the set of reads as a grammar, but
   when required, compute its BWT to carry out the analysis by using
   self-indexes. Our experiments in real data showed that the space red'n we
   achieve with our compressor is competitive with LZ-based methods & better
   than entropy-based approaches. Compared to other popular grammars, in this
   kind of data, we achieve, on avg., 12% extra compression & require less
   working space and time."
   -- [<A HREF="https://doi.org/10.1109/DCC50243.2021.00016">doi:10.1109/DCC50243.2021.00016</A>]['21].
   [Also search for: DCC21].

%A M. Roberts
%A et al ...
%A C.-B. Schonlieb
%T Common pitfalls and recommendations for using machine learning to detect and
   prognosticate for COVID-19 using chest radiographs and CT scans
%J NatureMachineIntell.
%M MAR
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0621, hype, AI, deep learning, NN, ANN,
   human health, covid19, diagnosis, stats, biases, errors, mistakes,
   weaknesses, validation, flaws, CLAIM, methodology, scientific research
%X "Machine learning methods offer great promise for fast & accurate detection &
   prognostication of coronavirus disease 2019 (COVID-19) from std-of-care chest
   radiographs (CXR) & chest computed tomography (CT) images. ... [BUT] Our
   review finds that *none* of the models identified are of potential clinical
   use due to methodological flaws &/or underlying biases. This is a major
   weakness, given the urgency with which validated COVID-19 models are needed.
   To address this, we give many recommendations which, if followed, will solve
   these issues & lead to higher-quality model development & well-documented
   manuscripts."
   -- [<A HREF="https://doi.org/10.1038/s42256-021-00307-0">doi:10.1038/s42256-021-00307-0</A>]['21].

%A B. Vernot
%A et al
%T Unearthing Neanderthal population history using nuclear and mitochondrial
   DNA from cave sediments
%J Science
%M APR
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0421, ancient DNA, Neanderthal, human,
   history, cave, sediment, Spain
%X "... developed methods for the enrichment & analysis of nuclear DNA from
   sediments, & applied them to cave deposits in W.Europe & S.Siberia dated to
   between ~ 200,000 & 50,000 y. ago. We detect a population replacement in
   N.Spain ~100,000 y. ago, accompanied by a turnover of mitochondrial DNA. We
   also identify two radiation events in Neanderthal history during the early
   part of the Late Pleistocene. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abf1667">doi:10.1126/science.abf1667</A>]['21].

%A Yang Zhou
%A et al
%T Platypus and echidna genomes reveal mammalian biology and evolution
%J Nature
%V 592
%P 756-762
%M APR
%D 2021
%K jrnl, MolBio, biol, c2021, c202x, c20xx, zz0521, mammal, therian, monotreme,
   platypus, Ornithorhynchus anatinus, echidna, Tachyglossus aculeatus,
   Australia, genome, nGenome, chromosome, sex, multiX, multiY
%X "... generate and analyse reference genomes of the platypus (Ornithorhynchus
   anatinus) & echidna (Tachyglossus aculeatus), which represent the only two
   extant monotreme lineages ... We provide evidence that the monotreme sex
   chromosome complex originated from an ancestral chromosome ring
   configuration ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-03039-0">doi:10.1038/s41586-020-03039-0</A>]['21].

%A B. Halford
%T Pfizer unveils its oral SARS-CoV-2 inhibitor
%J Chem. & Eng. News (ISSN 0009-2347)
%V 99
%N 13
%M APR
%D 2021
%K MolBio, c2021, c202x, c20xx, zz0521, PF-07321332, PF07321332, SARS2,
   SARS-CoV-2, SARSCoV2, Mpro, 3CLpro, protease, inhibitor, drug, coronavirus
%X "... The compound, which is currently in Phase 1 clinical trials, is the
   first orally administered compound in the clinic that targets the main
   protease ..."
   -- [<A HREF="https://cen.acs.org/acs-news/acs-meeting-news/Pfizer-unveils-oral-SARS-CoV/99/i13">www</A>]['21].
   [Also search for: MolBio 3CLpro inhibitor].

%A C. P. Roca
%A et al ...
%A A. Listn
%T AutoSpill is a principled framework that simplifies the analysis of
   multichromatic flow cytometry data
%J NatureComms.
%V 12
%M MAY
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0223, AutoSpill, JHC, Collier, VIB,
   flow cytometry, spectral, fluorescence, autofluorescence, stats
%X "... we present AutoSpill, an alternative method for calculating spillover
   coefficients. The approach combines automated gating of cells, calculation of
   an initial spillover matrix based on robust linear regression, & iterative
   refinement to reduce error. ..."
   -- [<A HREF="https://doi.org/10.1038/s41467-021-23126-8">doi:10.1038/s41467-021-23126-8</A>]['23] jrnl MAY 2021, and
      [<A HREF="https://doi.org/10.1101/2020.06.29.177196">doi:10.1101/2020.06.29.177196</A>]['23] bioRxiv JUN 2020.
   [Also search for: flow cytometry].

%A M. C. Wibowo
%A et al
%T Reconstruction of ancient microbial genomes from the human gut
%J Nature
%M MAY
%D 2021
%K MolBio, jrnl, c2021, c202x, c20xx, zz0521, human, gut, microbiome,
   microbiota, health, diet, ancient, modern, Methanobrevibacter smithii,
   genome, microbe, faeces, faecal
%X "... we performed a large-scale de novo assembly of microbial genomes from
   palaeofaeces. From eight authenticated human palaeofaeces samples
   (1,000-2,000 years old) with well-preserved DNA from southwestern USA &
   Mexico, we reconstructed 498 medium- & high-quality microbial genomes. Among
   the 181 genomes with the strongest evidence of being ancient & of human gut
   origin, 39% represent previously undescribed species-level genome bins. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-03532-0">doi:10.1038/s41586-021-03532-0</A>]['21].

%A J. D. Bloom
%A et al ...
%T Investigate the origins of COVID-19
%J Science
%V 372
%N 6543
%P 694
%M MAY
%D 2021
%K letter, MolBio, c2021, c202x, c20xx, zz0521, covid-19, covid19, WHO,
   investigation, SARS2, SARSCoV2, SARS-CoV-2, bat, virus, origin, origins,
   theories, Wuhan laboratory, lab, accident, China, controversial
%X "... In May 2020, the World Health Assembly requested that the WHO
   director-general work closely with partners to determine the origins of
   SARS-CoV-2. ... Although there were no findings in clear support of either a
   natural spillover or a lab accident, the team assessed a zoonotic spillover
   from an intermediate host as 'likely to very likely,' & a lab. incident as
   'extremely unlikely'. Furthermore, the two theories were not given balanced
   consideration. Only 4 of the 313 pages of the report & its annexes addressed
   the possibility of a laboratory accident. ... As [18]scientists with relevant
   expertise, we agree with the WHO director-general, the United States & 13
   other countries, & the European Union that greater clarity about the origins
   of this pandemic is necessary & feasible to achieve. We must take hypotheses
   about both natural & lab.  spillovers seriously until we have suff.data. A
   proper investigation should be transparent, objective, data-driven, inclusive
   of broad expertise, subject to independent oversight, & responsibly managed
   to minimize the impact of conflicts of interest. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abj0016">doi:10.1126/science.abj0016</A>]['21].
   [Also search for: SARS2 origin] and [also search for: Wuhan laboratory].
   (Also see SciMag[<A HREF="https://doi.org/10.1126/science.acx9371">18/10/21</A>]['21].)

%A A. Idris
%A et al ...
%A K. V. Morris
%T A SARS-CoV-2 targeted siRNA-nanoparticle therapy for COVID-19
%J Molecular Therapy
%M MAY
%D 2021
%K jrnl, MolBio, c2021 c202x, c20xx, zz0621, SARSCoV2, SARS CoV2, SARS2,
   covid 19, covid19, therapy, mouse, siRNA, GriffithUni, Qld
%X "... we present a highly effective small interfering RNA (siRNA) therapeutic
   against SARS-CoV-2 infection using a novel lipid nanoparticle (LNP) delivery
   system. Multiple siRNAs targeting highly conserved regions of the ...
   virus were screened, & three candidate siRNAs emerged that effectively
   inhibit the virus by greater than 90% either alone or in combination with one
   another. We simultaneously developed & screened two novel LNP formulations
   for the delivery of these candidate siRNA therapeutics to the lungs, an
   organ that incurs immense damage during ... infection. Encapsulation of
   siRNAs in these LNPs followed by in vivo injection demonstrated robust
   repression of virus in the lungs & a pronounced survival advantage to the
   treated mice. ..."
   -- [<A HREF="https://doi.org/10.1016/j.ymthe.2021.05.004">10.1016/j.ymthe.2021.05.004</A>]['21].
   [Also search for: covid19 therapy].

%A Yafei Mao
%A et al ...
%A E. E. Eicher
%T A high-quality bonobo genome refines the analysis of hominid evolution
%J Nature
%P 77-81
%M JUN
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0621, primate, great ape, chimpanzee,
   bonobo, genome, nGenome, Pan paniscus, PRJNA526933, SRP301932, hominid,
   evolution, incomplete lineage sorting, ILS
%X "... describe a fully annotated, high-quality bonobo genome assembly ... more
   than 98% of genes are completely annotated & 99% of the gaps are closed ...
   identify more than 5,569 fixed structural variants that specifically
   distinguish the b. & chimp. lineages. ... We produce a high-res. map of
   incomplete lineage sorting & est. that ~ 5.1% of the human genome is
   genetically closer to chimpanzee or bonobo & that more than 36.5% of the
   genome shows incomplete lineage sorting if we consider a deeper phylogeny
   inc. gorilla & orangutan. We also show that 26% of the segments of incomplete
   lineage sorting between hum. & chimp. or human & bonobo are non-randomly
   distributed & that genes within these clustered segments show sig. excess of
   amino acid replacement compared to the rest of the genome."
      "... The Bionano map of bonobo Mhudiblu is deposited in the NCBI under
      BioProject accession # PRJNA526933. The raw PacBio HiFi data of bonobo
      Mhudiblu & gorilla Kamilah are deposited in the NCBI under SRA acc.
      # SRP301932 under BioProject acc. # PRJNA691628. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-03519-x">doi:10.1038/s41586-021-03519-x</A>]['21].
   (Also see ILS@[<A HREF="https://en.wikipedia.org/wiki/Incomplete_lineage_sorting">wikip</A>]['21].)

%A J. P. Rogers
%A et al ...
%A A. D. Rooney
%T Neurology and neuropsychiatry of COVID-19: a systematic review and
   meta-analysis of the early literature reveals frequent CNS manifestations and
   key emerging narratives
%J J. Neurology, Neurosurgery & Psychiatry
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0621, human health, pandemic, long term,
   covid-19, longCovid, covid19, side effects, health, illness, risks
%X "... Studies reporting prevalences of neurological or neuropsychiatric
   symptoms were synthesised into meta-analyses to estimate pooled prevalence.
   ... The symptoms with the highest prevalence were anosmia (43.1% (95% CI
   35.2%-51.3%), n=15,975, 63 studies), weakness (40.0% (95% CI 27.9%-53.5%),
   n=221, 3 studies) ... depression ..."
   -- [<A HREF="https://jnnp.bmj.com/content/early/2021/06/03/jnnp-2021-326405">www</A>]['21],
      [<A HREF="http://dx.doi.org/10.1136/jnnp-2021-326405">doi:10.1136/jnnp-2021-326405</A>]['21].
   [Also search for: longCovid].

%A Y. Souilmi
%A et al ...
%A D. Enard
%T An ancient viral epidemic involving host coronavirus interacting genes more
   than 20,000 years ago in East Asia
%J Curr. Biol.
%V ?
%M JUN
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0621, coronavirus, RNA, corona virus,
   zoonotic transfer, SARS, SARS2, covid 19, covid19, CoVVIP, CoV-VIP genes
%X "... we apply evolutionary analyses to human genomic datasets to recover
   selection events involving tens of human genes that interact with
   coronaviruses, inc. SARS-CoV-2, that likely started more than 20,000 y. ago.
   These adaptive events were limited to the pop'n ancestral to E.Asian pop'n.
   Multiple lines of functional evidence support an ancient viral selective
   pressure, & E.Asia is the geographical origin of several modern coronavirus
   epidemics. An arms race with an ancient coronavirus, or with a different
   virus that happened to use similar interactions ..."
   -- [<A HREF="https://doi.org/10.1016/j.cub.2021.05.067">doi:10.1016/j.cub.2021.05.067</A>]['21].
   [Also search for: zoonotic virus].

%A O. J. Kennedy
%A et al
%T All coffee types decrease the risk of adverse clinical outcomes in
   chronic liver disease: a UK Biobank study
%J BMC Public Health
%V 21
%N #970
%M JUN
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0621, human, health, risks, liver disease, CLD,
   zzCoffee, caffeine, ground, instant, decaf, coffee, positive
%X "... The finding that all types of coffee are protective against CLD is
   sig. given the increasing incidence of CLD worldwide & the potential of
   coffee as an intervention to prevent CLD onset or progression."
   -- [<A HREF="https://doi.org/10.1186/s12889-021-10991-7">doi:10.1186/s12889-021-10991-7</A>]['21].
   [Also search for: zzCoffee].

%A M. Baek
%A et al ...
%A D. Baker
%T Accurate prediction of protein structures and interactions using a 3-track
   network
%J Science
%M JUL
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0722, protein structure prediction,
   tertiary, 3D, complexes, Rosetta, Rose TTA fold, RoseTTAFold, ANN, NN,
   opensource, open source, CASP14
%X "... obtained the best performance with a 3-track n/wk in which info. at the
   1D seq. level, the 2D distance map level, & the 3D coordinate level is
   successively transformed & integrated. The 3-track n/wk produces structure
   predictions with accuracies approaching those of DeepMind in CASP14, enables
   the rapid soln of challenging X-ray crystallography & cryo-EM structure
   modeling problems, & provides insights into the fns of proteins of currently
   unknown structure. ... also enables rapid generation of accurate
   protein-protein complex models from seq. info. alone, short circuiting
   traditional approaches which require modeling of individual subunits followed
   by docking. We make the method available to the sci. community to speed
   biological research."
   -- [<A HREF="https://doi.org/10.1126/science.abj8754">doi:10.1126/science.abj8754</A>]['22].
   Also see site@[<A HREF="https://www.ipd.uw.edu/2021/07/rosettafold-accurate-protein-structure-prediction-accessible-to-all/">uw.edu</A>]['22],
    & RoseTTAFold@[<A HREF="https://github.com/RosettaCommons/RoseTTAFold">g'thub</A>]['22],
    & core eukaryotic protein complexes@[<A HREF="https://doi.org/10.1126/science.abm4805">doi:10.1126/science.abm4805</A>]['22].
   [Also search for: 3D protein structure prediction ANN].

%A N. K. Schaefer
%A B. Shapiro
%A R. E. Green
%T An ancestral recombination graph of human, Neanderthal, and Denisovan genomes
%J Sci. Adv.
%V 16
%V 7
%N 29
%P eabc0776
%M JUL
%D 2021
%K MolBio, eJrnl, c2021, c202x, c20xx, zz0721, SARGE, ARG, DNA, human, homo,
   hominin, hominid, evolution, Neanderthal, Denisovan, ancient DNA,
   incomplete lineage sorting, ILS
%X "... We describe a new ancestral recombination graph inference alg. that
   scales to large genome-wide datasets & demo. its accuracy on real & simulated
   data. ... generate a g.-wide ancestral recomb. g. incl. human & archaic
   hominin genomes. From this, we generate a map within human genomes of archaic
   ancestry & of genomic regions not shared with archaic hominins either by
   admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the
   modern h. genome is uniquely h.. We also find evidence of multiple bursts of
   adaptive changes specific to modern hs. within the past 600,000 years
   involving genes related to brain development & function."
   -- [<A HREF="https://doi.org/10.1126/sciadv.abc0776">doi:10.1126/sciadv.abc0776</A>]['21].

%A J. Jumper
%A et al ...
%A D. Hassabis
%T Highly accurate protein structure prediction with AlphaFold
%J Nature
%V 596
%P 583-589
%M JUL
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0721, protein structure prediction,
   AlphaFold, ANN, NN, alphafold2, tertiary, 3D, CASP 14, CASP14
%X "... We validated an entirely redesigned version of our NN-based model,
   AlphaFold, in the challenging 14th Critical Assessment of protein Structure
   Prediction (CASP14), demonstrating accuracy competitive with experimental
   structures in a majority of cases & greatly outperforming other methods. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-03819-2">doi:10.1038/s41586-021-03819-2</A>]['21].
   (Also see next paper in this vol. & a video talk about alphafold 1 and 2
   -- [<A HREF="https://www.youtube.com/watch?v=nGVFbPKrRWQ">www</A>]['22].)
   [Also search for: 3D protein structure prediction ANN].

%A K. Tunyasuvunakool
%A et al ...
%A D. Hassabis
%T Highly accurate protein structure prediction for the human proteome
%J Nature
%V 596
%P 590-596
%M JUL
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0721, protein structure prediction,
   AlphaFold, alphafold2, human
%X "... we dramatically expand structural coverage by applying the
   state-of-the-art machine learning method, AlphaFold, at scale to almost the
   entire human proteome (98.5% of h. proteins). The resulting dataset covers
   58% of residues with a confident pred'n, of which a subset (36% of all r.)
   have very high confidence. We introduce several metrics developed by building
   on the AlphaFold model, & use them to interpret the dataset, identifying
   strong multi-domain pred'ns as well as regions likely to be disordered.
   Finally, we provide some case studies illustrating how high-quality pred'ns
   may be used to generate biol.hypotheses. ... we are making our pred'ns freely
   available to the community via a public DB (hosted by EBI at [<A HREF="https://alphafold.ebi.ac.uk/">www</A>]). ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-03828-1">doi:10.1038/s41586-021-03828-1</A>]['21].
   (Also see prev. paper in this vol. & the [<A HREF="https://www.bbc.com/news/science-environment-57929095">bbc</A>][23/7/2021].)

%A T. A. Tummino
%A et al
%T Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2
%J Science
%V 373
%N 6554
%P 488-489
%M JUL
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0821, covid-19, covid19, SARS-CoV-2,
   SARSCoV2, antiviral, drug, drugs, inhibitor, phospholipidosis,
   hydroxychloroquine, azithromycin, amiodarone
%X "... we became concerned that phospholipidosis was a shared mechanism
   underlying the antiviral activity of many repurposed drugs. For all of the
   23 cationic amphiphilic drugs we tested, inc. hydroxychloroquine,
   azithromycin, amiodarone, & four others already in clinical trials,
   phospholipidosis was monotonically correlated with antiv. efficacy.
   Conversely, drugs active against the same targets that did not induce
   phospholipidosis were not antiv. Phospholipidosis depends on the physicochem.
   properties of drugs & does not reflect specific target-based activities -
   rather, it may be considered a toxic confound ..."
   -- [<A HREF="https://doi.org/10.1126/science.abi4708">doi:10.1126/science.abi4708</A>]['21].
   [Also search for: MolBio SARSCoV2 drug].

%A A. Madani
%A et al ...
%A N. Naik
%T Deep neural language modeling enables functional protein generation across
   families
%J BioRxiv
%M JUL
%D 2021
%K TR, MolBio, c2021, c202x, c20xx, zz0821, ProGen, artificial, new, protein,
   ANN, model, proteins, generate
%X "... Viewing amino acid seqs as a language, we demo. that a deep
   learning-based language model can generate functional artificial protein
   seqs across families, ... Artificial ps. show similar activities & catalytic
   efficiencies as representative natural lysozymes, inc. hen egg white
   lysozyme, while reaching as low as 44% identity to any known
   naturally-evolved p.. The X-ray crystal structure of an enzymatically active
   artificial p. recapitulates the conserved fold & positioning of active site
   residues found in natural ps. ... ProGen is a 1.2 billion- [approx 20^7]
   -parameter NN trained using a publicly available dataset of 280 million
   protein seqs. ..."   (via daz.)
   -- [<A HREF="https://doi.org/10.1101/2021.07.18.452833">doi:10.1101/2021.07.18.452833</A>]['21].

%A S. Joel
%A G. MacDonald
%T We're not that choosy: Emerging evidence of a progression bias in romantic
   relationships
%J Personality and Social Psych. Rev.
%V 25
%N 4
%P 317-343
%M JUL
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0222, human behaviour, mate selection,
   psychology, romance, love, relationship, commitment, dating, marriage,
   partner
%X "... we argue that humans are biased toward pro-relationship decisions -
   decisions that favor the initiation, advancement, & maintenance of romantic
   relationships. We first review evidence for a progression bias in the
   context of relationship initiation, investment, & breakup decisions. We next
   consider possible theoretical underpinnings - both evolutionary & cultural -
   that may explain why getting into a relationship is often easier than getting
   out of one, & why being in a less desirable relationship is often preferred
   over being in no relationship at all. We discuss potential boundary condns
   that the phenomenon may have, as well as its implications for existing
   theoretical models of mate selection & relationship development."
   -- [<A HREF="https://doi.org/10.1177/10888683211025860">doi:10.1177/10888683211025860</A>]['22].
   [Also search for: mate selection].
   (Also look for Tim Minchin's song "If I Didn't Have You" and see
   www.bbc.com/worklife/article/
   20220124-why-people-arent-as-picky-in-love-as-they-think
   at the bbc[28/1/2022].)

%A R. L. Townshend
%A et al ...
%A R. O. Dror
%T Geometric deep learning of RNA structure
%J Science
%V 373
%N 6558
%P 1047-1051
%M AUG
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0921, RNA structure, prediction,
   ARES, geometric, geometry, NN, ANN
%X "... introduce a m/c learning approach that enables identification of
   accurate structural models without assumptions about their defining
   characteristics, despite being trained with only 18 known RNA struct.. The
   resulting scoring fn, the Atomic Rotationally Equivariant Scorer (ARES),
   substantially outperforms previous methods ... By learning effectively even
   from a small amount of data, our approach overcomes a major limitation of
   std deep NNs. Because it uses only atomic coordinates as inputs &
   incorporates no RNA-specific information ..."
   -- [<A HREF="https://doi.org/10.1126/science.abe5650">doi:10.1126/science.abe5650</A>]['21].
   [Also search for: MolBio RNA structure prediction].

%A E. Callaway
%T The mutation that helps Delta spread like wildfire
%J Nature
%V 596
%P 472-473
%M AUG
%D 2021
%K news, views, c2021, c202x, c20xx, zz0821, SARS-CoV-2, SARS2, virus, covid-19,
   covid19, alpha, delta, variant, strain, mutation, P681R, infection
%X "... Delta is at least 40% more transmissible than is the Alpha ...
   epidemiological studies suggest. ... groups have zeroed in on a mut'n that
   alters a single [AA] in the SARS-CoV-2 spike protein ... The change,
   which is called P681R ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-02275-2">doi:10.1038/d41586-021-02275-2</A>['21].
   [[Really for the links to 5 preprints.]]

%A J. Hippisley-Cox
%A et al
%T Risk of thrombocytopenia and thromboembolism after covid-19 vaccination and
   SARS-CoV-2 positive testing: self-controlled case series study
%J BMJ
%V 374
%M AUG
%D 2021
%K jrnl, MolBio, BMJ, c2021, c202x, c20xx, zz0921, medicine, SARS-CoV-2, SARS2,
   virus, covid-19, vaccine, vaccination, risk, risks, Oxford-AstraZeneca, AZ,
   covid19, ChAdOx1-S, Pfizer-BioNTech, BNT162b2, complications, blood clot,
   clots
%X "... Participants 29,121,633 people were vaccinated with first doses
   (19,608,008 with Oxford-AstraZeneca (ChAdOx1 nCoV-19) & 9,513,625 with
   Pfizer-BioNTech (BNT162b2 mRNA)) & 1,758,095 people had a +ve SARS-CoV-2
   test. People aged >=16 years who had first doses of the ChAdOx1 nCoV-19 or
   BNT162b2 mRNA vaccines & any outcome of interest were included in the study.
   ... The study found increased risk of thrombocytopenia after ChAdOx1 nCoV-19
   vaccination (incidence rate ratio 1.33, 95% c.i. 1.19 to 1.47 at 8-14 days)
   & after a +ve SARS-CoV-2 test (5.27, 4.34 to 6.40 at 8-14 days) ... The risks
   of most of these events were substantially higher & more prolonged after
   SARS-CoV-2 infection than after vaccination in the same population."
   -- [<A HREF="https://doi.org/10.1136/bmj.n1931">doi:10.1136/bmj.n1931</A>]['21].
   (Also see "Covid: Vaccine complications dwarfed by virus risks"
   -- [<A HREF="https://www.bbc.com/news/health-58347434">bbc</A>][27/8/2021].)

%A S. Gazit
%A et al
%T Comparing SARS-CoV-2 natural immunity to vaccine-induced immunity:
   reinfections versus breakthrough infections
%J medRxiv
%M AUG
%D 2021
%K TR, c2021, c202x, c20xx, zz0921, SARS-CoV-2, SARS2, virus, covid-19, covid19,
   infection, Pfizer BNT162b2, vaccine, immunity
%X "... vaccinees had a 13.06-fold (95% CI, 8.08 to 21.11) increased risk for
   breakthrough infection with the Delta variant [v] those previously infected,
   when the 1st event (infection or vaccination) occurred during Jan - Feb of
   2021. ... evidence of waning natural immunity was demonstrated, though ...
   vaccinees had a 5.96-fold ... increased risk for b.infection & a 7.13-fold
   ... increased risk for symptomatic disease. ... vaccinees were also at a
   greater risk for COVID-19-related-hospitalizations compared [v] those that
   were previously infected. ..."
   -- [<A HREF="https://doi.org/10.1101/2021.08.24.21262415">doi:10.1101/2021.08.24.21262415</A>]['21].
   [NB. a preprint.]

%A C. Bayly-Jones
%A J. Whisstock
%T Mining folded proteomes in the era of accurate structure prediction
%J bioRxiv
%M AUG
%D 2021
%K TR, c2021, c202x, c20xx, zz0222, MolBio, fold, protein, proteome, alphaFold
%X "... In the era of accurate struct. pred'n owing to advances in Mc/L
   techniques, prev. curated seq. databases have become a rich source of biol.
   info.. Here, we use bioinf. fold recognition algs. to scan the entire
   AlphaFold structure database to identify novel protein family members,
   infer fn & group predicted protein structures. ..."
   -- [<A HREF="https://doi.org/10.1101/2021.08.24.457439">doi:10.1101/2021.08.24.457439</A>]['22].

%A Yu Liu
%A et al ...
%A L. Cronin
%T Exploring and mapping chemical space with molecular assembly trees
%J Sci. Adv.
%V 7
%N 39
%M SEP
%D 2021
%K jrnl, c2021, c202x, c20xx, zz1124, compound, molecule, graph, AssemblyTheory
%X "... Assembly theory is an approach to compare the intrinsic complexity &
   properties of molecules by the min. # of steps needed to build up the target
   graphs. Here, we apply this approach to prebiotic chemistry, gene seqs.,
   plasticizers, & opiates. ... Monte Carlo (MC) alg. ..."
   -- [<A HREF="https://doi.org/10.1126/sciadv.abj2465">doi:10.1126/sciadv.abj2465</A>]['24].

%A J. M. perkel
%T Single-cell proteomics takes centre stage
%J Nature
%V 597
%P 580-582
%M SEP
%D 2021
%K news, views, MolBio, c2021, c202x, c20xx, zz0921, single cell proteomics,
   proteoCHIP, inanoPOTS, SCoPE-MS, SCoPEMS, proteins
%X "Deducing the full protein complement of individual cells has long played
   second fiddle to transcriptomics. That's about to change. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-02530-6">doi:10.1038/d41586-021-02530-6</A>]['21].

%A M. Kozlov
%T COVID-vaccine booster shot shows promise in Israeli study
%J Nature
%M SEP
%D 2021
%K news, c2021, c202x, c20xx, zz1021, covid-19, covid19, vaccine, pandemic,
   booster dose, vaccination, infection
%X "Older Israelis who have received a third dose of a COVID-19 vaccine are much
   less likely to test positive for SARS-CoV-2 or to develop severe COVID-19
   than are those who have had only two jabs, according to a highly anticipated
   study published on 15 Sept. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-02516-4">doi:10.1038/d41586-021-02516-4</A>]['21].
  Article: 'Protection of BNT162b2 Vaccine Booster against Covid-19 in Israel',
  NEJM, SEP, 2021
  "At least 12 days after the booster dose, the rate of confirmed infection was
  lower in the booster group than in the nonbooster group by a factor of 11.3
  ... In a secondary analysis, the rate of confirmed infection at least 12 days
  after v. was lower than the rate after 4 to 6 days by a factor of 5.4 ..."
  -- [<A HREF="https://doi.org/10.1056/NEJMoa2114255">doi:10.1056/NEJMoa2114255</A>]['21].
  (Also see
  'COVID vaccine immunity is waning - how much does that matter?'
  Nature, 597, pp.606-607, SEP, 2021
  -- [<A HREF="https://doi.org/10.1038/d41586-021-02532-4">doi:10.1038/d41586-021-02532-4</A>]['21].)

%A T. Chari
%A J. Banerjee
%A L. Pachter
%T The specious art of single-cell genomics
%J bioRxiv
%M SEP
%D 2021
%K TR, MolBio, c2021, c202x, c20xx, zz1121, single cell, scRNA seq, scRNAseq,
   dimension reduction, dimensionality, t-SNE, tSNE, PCA, UMAP, 2D, 3D
%X "Dim. redn is std practice for filtering noise & identifying relevant
   dimensions in large-scale data analyses. In biology, single-cell expression
   studies almost always begin with redn to two or three D to produce
   'all-in-one' visuals of the data that are amenable to the human eye, & these
   are subs. used for qualitative & quantitative analysis of cell relationships.
   However, there is little theoretical support for this practice. ... find
   extensive distortions incurred on the global & local properties of biol.
   patterns relative to the high dimensional, ambient space. In lieu of this, we
   propose semi-supervised dim. redn to higher dimension, & show that such
   targeted redn guided by the metadata assoc. with single-cell experiments
   provides useful latent space repns for hypothesis-driven biol. discovery."
   -- [<A HREF="https://doi.org/10.1101/2021.08.25.457696">doi:10.1101/2021.08.25.457696</A>]['21].
   [Also search for: scRNAseq]  and  [also search for: dimension reduction].

%A S. C. Campbell-Staton
%T Ivory poaching and the rapid evolution of tusklessness in African elephants
%J Science
%V 374
%N 6566
%P 483-487
%M OCT
%D 2021
%K jrnl, c2021, c202x, c20xx, zz1021, elephant, tusk, tusks, loss, tuskless,
   ivory, poaching, Africa, selection
%X "... We examined the impacts of ivory poaching during the Mozambican Civil
   War (1977 to 1992) on the evolution of African savanna elephants (Loxodonta
   africana) ... Whole-genome scans implicated two candidate genes with known
   roles in mammalian tooth development (AMELX & MEP1a) ... One of these loci
   (AMELX) is assoc. with an X-linked dominant, male-lethal syndrome in humans
   that diminishes the growth of maxillary lateral incisors (homologous to
   e.tusks). ..."
   -- [<A HREF="https://doi.org/10.1126/science.abe7389">doi:10.1126/science.abe7389</A>]['21].
   (I recall 1st hearing about the increase in the % of
   tuskless elephants at a conf in the 1990s.)

%A S. R. R. Kolora
%A et al
%T Origins and evolution of extreme life span in Pacific Ocean rockfishes
%J Science
%V 374
%N 6569
%P 842-847
%M NOV
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz1121, lifespan, ageing, gene, genes,
   butyrophilin, longevity, fish, rockfish, CpG TpG, CpGTpG, insulin signaling
%X "... assembled the genomes of 88 rockfish species & from these identified
   repeated signatures of +ve seln in DNA repair pathways in long-lived taxa &
   137 longevity-assoc. genes with direct effects on life span through insulin
   signaling & with pleiotropic effects through size & environmental
   adaptations. A genome-wide screen of structural variation reveals copy #
   expansions in the immune modulatory butyrophilin gene family in long-lived
   species. The evolution of different rockfish life histories is coupled to
   genetic diversity & reshapes the mutational spectrum driving segregating
   CpG-TpG variants in long-lived species. These analyses highlight the genetic
   innovations that underlie life history trait adaptations &, in turn, how they
   shape genomic diversity."
   -- [<A HREF="https://doi.org/10.1126/science.abg5332">doi:10.1126/science.abg5332</A>]['21].
   [Also search for: MolBio ageing].

%A L. J. Harmon
%A et al
%T Causes and consequences of apparent timescaling across all estimated
   evolutionary rates
%J Annual Rev. of Ecol., Evol., and Systematics
%V 52
%P 587-609
%M NOV
%D 2021
%K MolBio, jrnl, c2021, c202x, c20xx, zz0622, evolution rate, timescale
%X "... All evolutionary rate estimates, inc. rates of molec. evol., trait evol.
   & lineage diversification, share a similar scaling pattern with time: The
   highest rates are those measured over the shortest time interval. This
   creates a disconnect between micro- & macroevolution ... We break down
   possible explanations for scaling into two categories, estimation error &
   model misspecification, & discuss how both apply to each type of rate. ..."
   -- [<A HREF="https://doi.org/10.1146/annurev-ecolsys-011921-023644">doi:10.1146/annurev-ecolsys-011921-023644</A>]['21].

%A A. G. Mainous III
%A et al
%T COVID-19 Post-acute sequelae among adults: 12 month mortality risk
%J Frontiers in Medicine
%M DEC
%D 2021
%K jrnl, c2021, c202x, c20xx, zz1221, SARS CoV 2, SARSCoV2, covid19, covid-19,
   long term, covid, longCovid, hospitalization, hospitalisation, human health,
   illness, risks, mortality, death
%X "... The 12-month adjusted all-cause mortality risk was sig. higher for
   patients with severe COVID-19 compared to both C19 -ve patients (HR 2.50;
   95% CI 2.02, 3.09) & mild C19 patients (HR 1.87; 95% CI 1.28, 2.74). ...
   Patients with a C19 hospitalization were at sig. increased risk for future
   mortality. In a time when nearly all C19 hospitalizations are preventable
   this study points to an important & under-investigated sequela of C19 & the
   corr. need for prevention."
      "... The mild/moderate C19 patients were not at increased risk of death
      compared to the C19 -ve group ..."
   -- [<A HREF="https://doi.org/10.3389/fmed.2021.778434">doi:10.3389/fmed.2021.778434</A>]['21].
   (Also see The Grauniad[<A HREF="https://www.theguardian.com/world/2021/dec/01/severe-covid-infection-doubles-chances-of-dying-in-following-year-study">www</A>][1/12/2021].)
   [So if hospitalized, >2x the risk of dying in the following 12 months.]
   [Also search for: longCovid].

%A J. Sourimant
%A et al
%T 4'-Fluorouridine is an oral antiviral that blocks respiratory syncytial
   virus and SARS-CoV-2 replication
%J Science
%V ?
%M DEC
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz1221, SARSCoV2, covid-19, covid19,
   antiviral, drug, 4'-fluorouridine, 4'-FlU, 4FLU, EIDD-2749, EIDD2749,
   EIDD-2801, molnupiravir, polymerase, RdRP, inhibitor
%X "... We describe 4'-fluorouridine (4'-FlU, EIDD-2749), a ribonucleoside
   analog that inhibits RSV, related RNA viruses, & SARS-CoV-2 with high
   selectivity index in cells & human airway epithelia organoids. Polymerase
   inhibition within in vitro RdRP assays established for RSV & SARS-CoV-2
   revealed transcriptional stalling after incorporation. Once-daily oral
   treatment was highly efficacious at 5 mg/kg in RSV-infected mice or 20 mg/kg
   in ferrets infected with different SARS-CoV-2 variants-of-concern, initiated
   24 or 12 hours after infection, respectively. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abj5508">doi:10.1126/science.abj5508</A>]['21],
      [<A HREF="https://www.science.org/doi/10.1126/science.abj5508">www</A>]['21].

%A D. R. Owen
%A et al
%T An oral SARS-CoV-2 Mpro inhibitor clinical candidate for the treatment of
   COVID-19
%J Science
%M DEC
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz1221, covid19, SARS-CoV-2, SARSCoV2,
   mPro, inhibitor, drug, PF-07321332, PF07321332
%X "... report the discovery & characterization of PF-07321332, an orally
   bioavailable SARS-CoV-2 main protease inhibitor with in vitro pan-human
   coronavirus antiviral activity & excellent off-target selectivity & in vivo
   safety profiles. PF-07321332 has demonstrated oral activity in a
   mouse-adapted SARS-CoV-2 model & has achieved oral plasma concentrations
   exceeding the in vitro antiviral cell potency in a phase 1 clinical trial in
   healthy human participants."
   -- [<A HREF="https://doi.org/10.1126/science.abl4784">doi:10.1126/science.abl4784</A>]['21].

%A C. D. Wallis
%A et al
%T Association of surgeon-patient sex concordance with postoperative outcomes
%J JAMA Surgery
%M DEC
%D 2021
%K jrnl, c2022, c202x, c20xx, zz0122, human, health, risks, hospital, surgery,
   patient, surgeon, male, female, doctor, sex, gender, operation, outcome
%X "... Sex discordance between surgeon & patient was assoc. with a sig.
   increased likelihood of composite adverse postoperative outcomes (adjusted
   odds ratio [aOR], 1.07; 95% CI, 1.04-1.09), as well as death (aOR, 1.07;
   95% CI, 1.02-1.13), & complications (aOR, 1.09; 95% CI, 1.07-1.11) but not
   readmission (aOR, 1.02; 95% CI, 0.98-1.07). While assocs. were consistent
   across most subgroups, patient sex sig. modified this assoc., with worse
   outcomes for female patients treated by male surgeons (compared with female
   patients treated by female surgeons: aOR, 1.15; 95% CI, 1.10-1.20) but not
   male patients treated by female surgeons ..."
   -- [<A HREF="https://doi.org/10.1001/jamasurg.2021.6339">doi:10.1001/jamasurg.2021.6339</A>]['22].
   (Also see The G [<A HREF="https://www.theguardian.com/society/2022/jan/04/women-more-likely-die-operation-male-surgeon-study?CMP=oth_b-aplnews_d-3">www</A>][4/1/2022].)

%A G. D. Rose
%T Reframing the protein folding problem: Entropy as organizer
%J Biochemistry
%V 60
%N 49
%P 3753-3761
%M DEC
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0722, protein folding, fold, 3D,
   tertiary, 3D, structure, entropy, energy, hydrogen bond, bonds
%X "... this Perspective introduces a different mechanism, one that emphasizes
   conformational entropy as the principal organizer in protein folding ... If
   even a single backbone polar group is satisfied by solvent when unfolded but
   buried & unsatisfied when folded, that energy penalty alone, ~ +5 kcal/mol,
   would rival almost the entire free energy of protein stabilization, typically
   between -5 & -15 kcal/mol under physiological condns. Consequently, upon
   folding, buried backbone polar groups must form hydrogen bonds, & they do so
   by assembling scaffolds of alpha-helices &/or strands of beta-sheet ...
   conformational restrictions imposed by backbone-backbone hydrogen bonding in
   the scaffold are seq.-indep., enabling mutation - & thus evolution - without
   sacrificing the structure."
   -- [<A HREF="https://doi.org/10.1021/acs.biochem.1c00687">doi:10.1021/acs.biochem.1c00687</A>]['22].
   (Also see Pfolding@[<A HREF="https://en.wikipedia.org/wiki/Protein_folding">wikip</A>]['22].)

%A C. L. Brooks
%A et al
%T Classical molecular dynamics
%J J. Chem. Phys.
%V 154
%P 100401
%M MAR
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz1222, history, survey, intro, views,
   special issue, software, CHARMM, GROMACS, LAMMPS, NAMD, protein folding,
   simulation, molecular dynamics, trajectory, pathway
%X "... highlights both developments in & applications of classical molecular
   simulation in 67 articles. ... inc. discussion of some of the major s/w
   packages for classical molecular dynamics (MD), inc. Amber, CHARMM, GROMACS,
   LAMMPS, and NAMD. ..."  (74 refs)
   -- [<A HREF="https://doi.org/10.1063/5.0045455">doi:10.1063/5.0045455</A>]['22].
   [Also search for: protein folding simulation].

%A A. Robert
%A P. Kl. Barkoutsos
%A S. Woerner
%A I. Tavernelli
%T Resource-efficient quantum algorithm for protein folding
%J NPJ Quantum Inf.
%V 7
%N #38
%D 2021
%K jrnl, MolBio, c2021, c202x, c20xx, zz0324, protein, 3D, folding, structure
%X "... we present a model Hamiltonian with O(N^4) scaling & a corr. q.
   variational alg. for the folding of a polymer chain with N monomers on a
   lattice. The model reflects many physico-chem. properties of the p., reducing
   the gap between coarse-grained rep'n & mere lattice models. [&] we use a
   robust & versatile opt'n scheme, bringing together variational q.alg.
   specifically adapted to classical cost fns & evolutionary strategies to
   simulate the folding of the 10 amino acid Angiotensin on 22 qubits. The same
   method is also successfully applied to the study of the folding of a 7 AA
   neuropeptide using 9 qubits on an IBM 20-qubit q.computer ..."
   -- [<A HREF="https://doi.org/10.1038/s41534-021-00368-4">doi:10.1038/s41534-021-00368-4</A>]['21].
   [Also search for: quantum computing algorithm].

%A J. Simon
%A et al
%T Light to moderate coffee consumption is associated with lower risk of
   death: a UK Biobank study
%M JAN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1124, coffee, zzCoffee, health, cardiovascular
%X "... Coffee consumption of up to three cups per day was assoc. with
   favourable CV outcomes. Regular c. consumption was also assoc. with a likely
   healthy pattern of CMR metrics in keeping with the reverse of age-related
   cardiac alterations."
   -- [<A HREF="https://doi.org/10.1093/eurjpc/zwac008">doi:10.1093/eurjpc/zwac008</A>]['24].
   (Also see[<A HREF=" https://www.bbc.com/future/article/20201028-the-benefits-of-coffee-is-coffee-good-for-health">bbc</A>]['2024].)
   [Also search for: zzCoffee].

%A P. Verschaffelt
%A J. H. Collier
%A et al
%T Unipept visualizations: an interactive visualization library for biological
   data
%J Bioinf.
%V 38
%N 2
%M JAN
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0223, JHC, VIB, javascript,
   software, bioinformatics, metaproteomics, D3.js
%X "... JavaScript package to generate interactive visualizations of both
   hierarchical & non-hierarchical quantitative data. It provides four different
   visualizations: a sunburst, a treemap, a treeview & a heatmap. Every
   visualization is fully configurable, supports TypeScript & uses the excellent
   D3.js library."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btab590">doi:10.1093/bioinformatics/btab590</A>]['22].

%A L. J. Underland
%T The impact of weight change and measures of physical functioning on mortality
%J J. Amer. Geriatrics Soc.
%V ?
%P ?-?
%M JAN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0122, stats, human, health, medicine, ageing,
   longevity, risk, risks, mortality, lifespan, gender, women, weight,
   grip strength
%X "Lower grip strength & measures of physical functioning are assoc. with
   all-cause mortality. Relationships among long-term weight loss, physical
   functioning, & mortality in older women are understudied. ... Weight loss of
   5% or more percent body weight was assoc. with a hazard ratio of 1.66
   (1.37-2.01) for all-cause mortality. Weight gain was not related to mortality
   or cardiovascular outcomes. Those in the highest grip strength quartile had a
   hazard ratio of 0.51 (0.39-0.66) for all-cause mortality. ..."
   -- [<A HREF="https://doi.org/10.1111/jgs.17626">doi:10.1111/jgs.17626</A>]['22] (online Jan 2022).
   [Also search for: lifespan ageing].

%A K. Bjornevik
%A et al
%T Longitudinal analysis reveals high prevalence of Epstein-Barr virus
   associated with multiple sclerosis
%J Science
%V ?
%M JAN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0122, human health, multiple sclerosis, MS,
   medicine, cause, stats, B cell, Bcell, LMP1, LMP2A, Epstein Barr virus, EBV,
   glandular fever, autoimmune, disease, risk, risks
%X "... tested the hypothesis that MS is caused by ... (EBV) in a cohort
   comprising more than 10 million young adults on active duty in the US mil.,
   955 of whom were diagnosed with MS during their period of service. Risk of
   MS increased 32-fold after infection with EBV but was not increased after
   infection with other v., inc. the similarly transmitted cytomegalovirus.
   Serum levels of neurofilament light chain, a biomarker of neuroaxonal
   degeneration, increased only after EBV seroconversion. These findings cannot
   be explained by any known risk factor for MS & suggest EBV as the leading
   cause of MS."
   -- [<A HREF="https://doi.org/10.1126/science.abj8222">doi:10.1126/science.abj8222</A>]['22] (online Jan 2022).
   (Also see persp@[<A HREF="https://doi.org/10.1126/science.abm7930">doi:10.1126/science.abm7930</A>][13/1/2022].)

%A G. G. Rosenthal
%A M. J. Ryan
%T Sexual selection and the ascent of women: Mate choice research since Darwin
%V 375
%N 6578
%M JAN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0122, mate selection, mating, sex, sexual,
   human behaviour, men, women, attraction, biology, biol
%X "Darwin's theory of sexual selection fundamentally changed how we think about
   sex & evolution. ... Contemporaries dismissed D's conjecture of a 'taste for
   the beautiful' as favoring particular mates over others, but there is now
   overwhelming evidence for a primary role of both male & female mate choice in
   sexual seln. D's misogyny precluded much analysis of the 'taste'; an
   increasing focus on mate choice mechanisms before, during, & after mating
   reveals that these often evolve in response to seln pressures that have
   little to do with sexual seln on chosen traits. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abi6308">doi:10.1126/science.abi6308</A>]['22],
      auth1[<A HREF="https://orcid.org/0000-0003-0342-9024">www</A>]['22],
      auth2[<A HREF="https://orcid.org/0000-0002-6381-9545">www</A>]['22].
   [Also search for: mate selection].

%A J. Hahn
%A et al
%T Vitamin D and marine omega 3 fatty acid supplementation and incident
   autoimmune disease: VITAL randomized controlled trial
%J BMJ
%M JAN
%D 2022
%V 376
%K jrnl, BMJ, c2022, c202x, c20xx, zz0222, human health, medicine, disease,
   stats, vitamin D, vitaminD, omega 3, omega3, fish oil, fishoil, psoriasis,
   rheumatoid arthritis, polymyalgia rheumatica, autoimmune thyroid disease
%X "... 25,871 participants, consisting of 12,786 men >=50 years & 13,085 women
   >=55 years at enrollment. ... Vitamin D (2000 IU/day) or matched placebo, &
   omega 3 fatty acids (1000 mg/day) or matched placebo. ... Vitamin D
   supplementation for five years, with or without omega 3 fatty acids, reduced
   autoimmune disease by 22%, while omega 3 fatty acid supplementation with or
   without vitamin D reduced the autoimmune disease rate by 15% (not stat.sig.).
   Both treatment arms showed larger effects than the reference arm (vitamin D
   placebo & omega 3 fatty acid placebo)."
   -- [<A HREF="https://doi.org/10.1136/bmj-2021-066452">doi:10.1136/bmj-2021-066452</A>]['22].

%A T. Bose
%A et al
%A A. Yonath
%T Origin of life: protoribosome forms peptide bonds and links RNA and protein
   dominated worlds
%J NAR
%V 50
%N 4
%P 1815-1828
%M FEB
%D 2022
%K jrnl, NAR, MolBio, c2022, c202x, c20xx, zz0323, life, origin, origins, start,
   begin, RNA, protein, proto ribosome, protoribosome,
   peptidyl transferase centre
%X "... Our earlier comparative structural studies suggested that a universal
   internal small RNA pocket-like segment called by us the protoribosome, which
   is still embedded in the contemporary ribosome, is a vestige of the
   primordial r.. Herein, after constructing such pockets, we show using the
   'fragment reaction' & its analyses by MALDI-TOF & LC-MS mass spectrometry
   techniques, that several protoribosome constructs are indeed capable of
   mediating peptide-bond formation. These findings present strong evidence
   supporting our hypothesis on origin of life & on ribosome's construction,
   thus suggesting that the protoribosome may be the missing link between the
   RNA dominated world & the contemporary nucleic acids/proteins life."
   -- [<A HREF="https://doi.org/10.1093/nar/gkac052">doi:10.1093/nar/gkac052</A>]['23].
   (Also see discussion@[<A HREF="https://doi.org/10.1038/d41586-023-00574-4">www</A>]['23].)
   [Also search for: MolBio origin life].

%A C. Wymant
%A et al
%T A highly virulent variant of HIV-1 circulating in the Netherlands
%J Science
%V 375
%N 6580
%P 540-545
%M FEB
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0222, HIV-1, HIV1, aids, virus, strain,
   variant, increased virulence, risk, risks, medicine
%X "We discovered a highly virulent variant of subtype-B HIV-1 in [.nl].
   One hundred nine individuals with this variant had a 0.54 to 0.74 log10
   increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load [v.], &
   exhibited CD4 cell decline twice as fast as, 6604 individuals with other
   subtype-B strains. ... Genetic sequence analysis suggests that this variant
   arose in the 1990s from de novo mutation ..."
   -- [<A HREF="https://doi.org/10.1126/science.abk1688">doi:10.1126/science.abk1688</A>]['22].

%A L. Spinney
%T Pandemics disable people - the history lesson that policymakers ignore
%J Nature
%V 602
%P 383-385
%M FEB
%D 2022
%K news, views, c2022, c202x, c20xx, zz0222, human health, risk, risks,
   covid 19, polio, flu, long covid19, longCovid, long term, pandemic, Wuhan,
   Spanish influenza, encephalitis lethargica, disease, virus
%X "Influenza, polio and more have shown that infections can change lives even
   decades later. Why the complacency over possible long-term effects of
   COVID-19? ... "
   -- [<A HREF="https://doi.org/10.1038/d41586-022-00414-x">doi:10.1038/d41586-022-00414-x</A>['22].

%A Yan Xie
%A et al
%T Long-term cardiovascular outcomes of COVID-19
%J Nature Medicine
%M FEB
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0222, human health, long term, covid 19,
   covid19, stats, risk, risks, heart disease
%X "... we used national healthcare databases from the US Dept of Veterans
   Affairs to build a cohort of 153,760 individuals with COVID-19, as well as
   two sets of control cohorts with 5,637,647 ... We show that, beyond the first
   30 d after infection, individuals with COVID-19 are at increased risk of
   incident cardiovascular disease spanning several categories, inc.
   cerebrovascular disorders, dysrhythmias, ischemic & non-ischemic heart
   disease, pericarditis, myocarditis, heart failure & thromboembolic disease.
   These risks & burdens were evident even among individuals who were not
   hospitalized during the acute phase ... Our results provide evidence that the
   risk & 1-year burden of c.disease in survivors of acute COVID-19 are
   substantial. ..."
   -- [<A HREF="https://doi.org/10.1038/s41591-022-01689-3">doi:10.1038/s41591-022-01689-3</A>]['22].
   (Also see [<A HREF="https://doi.org/10.1126/science.ada1117">doi:10.1126/science.ada1117</A>]['22].)
   [Also search for: covid19 long term].

%A A. Wilder Wohns
%A et al ...
%A G. McVean
%T A unified genealogy of modern and ancient genomes
%J Science
%V 375
%N 6583
%M FEB
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0222, MolBio, human, evolution, origin, genomes,
   genome, phylogeny, tree, humans, homo sapiens, ancient, origins
%X "... present a unified tree seq. of 3601 modern & eight high-coverage ancient
   human genome seqs ... We calculate the distribution of the time to most
   recent common ancestry between the 215 populations of the constituent
   datasets, revealing patterns consistent with substantial variation in
   historical popln size & evidence of archaic admixture in modern humans. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abi8264">doi:10.1126/science.abi8264</A>]['22].
   [Also search for: MolBio human evolution].

%A G. Zolotarov
%A et al
%T MicroRNAs are deeply linked to the emergence of the complex octopus brain
%J bioRxiv
%M FEB
%D 2022
%K TR, c2022, c202x, c20xx, zz0322, biol, biology, MolBio, brain, octopus,
   miRNA, microRNA, nervous system, animal, cephalopod
%X "Soft-bodied cephalopods such as the octopus are exceptionally intelligent
   invertebrates with a highly complex nervous system that evolved indep. from
   vertebrates. Because of elevated RNA editing in their nervous tissues, we
   hypothesized that RNA regulation may play a major role in the cognitive
   success of this group. ... show that the major RNA innovation of soft-bodied
   cs. is a massive expansion of the miRNA gene repertoire. ... propose that
   miRNAs are intimately linked to the evolution of complex animal brains."
   -- [<A HREF="https://doi.org/10.1101/2022.02.15.480520">doi:10.1101/2022.02.15.480520</A>]['22].
   [Also search for: brain octopus].

%A B. B. Sun
%A et al
%T Genetic associations of protein-coding variants in human disease
%J Nature
%V ?
%M FEB
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0222, human health, genetic, variations,
   disease, illness, BioBank, FinnGen, rare
%X "... Here we combined whole-exome sequencing in 392,814 UK Biobank
   participants with imputed genotypes from 260,405 FinnGen participants
   (653,219 total individuals) to conduct association meta-analyses for 744
   disease endpoints across the protein-coding allelic frequency spectrum,
   bridging the gap between common and rare variant studies. We identified 975
   associations, with more than one-third being previously unreported. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-04394-w">doi:10.1038/s41586-022-04394-w</A>]['22].

%A H. Hirai
%A Y. Iwamasa
%T Reconstructing phylogenetic trees from multipartite quartet systems
%J Algorithmica
%V 84
%P 1875-1896
%M FEB
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0722, phylogenetic tree, quartet,
   compatibility, induced, problem, algorithm
%X "... One of important problems in phylogenetic analysis is to assemble a
   global p.tree from small p.trees, particularly, quartet trees. Quartet
   Compatibility is the problem of deciding whether there is a p.tree inducing
   a given collection of quartet trees, & to construct such a p.tree if it
   exists. It is known that Quartet Compatibility is NP-hard & that there are
   only a few results known for polynomial-time solvable subclasses. ... we
   introduce two novel classes of quartet systems, called complete multipartite
   quartet system & full multipartite quartet system, & present polynomial-time
   algs. for Quartet Compatibility for these systems."
   - [<A HREF="https://doi.org/10.1007/s00453-022-00945-9">doi:10.1007/s00453-022-00945-9</A>]['22].

%A M. E. Bragina
%A et al
%T SwissSimilarity 2021 web tool: Novel chemical libraries and additional
   methods for an enhanced ligand-based virtual screening experience
%J Int. J. Mol. Sci.
%V 23
%N 2
%P 811
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz1024, Swiss Similarity, SwissSimilarity,
   SMILES, approximate, similar, chemical compound, molecule, library, search
%X "... a web tool for low-to-high-throughput virtual screening of multiple
   chemical libraries to find molecules similar to a compound of interest ..."
   -- [<A HREF="https://doi.org/10.3390/ijms23020811">doi:10.3390/ijms23020811</A>]['24].
   Also see [<A HREF="http://www.swisssimilarity.ch">swisssimilarity.ch</A>]['24].

%A L. Smirnova
%A et al
%T Organoid intelligence (OI): The new frontier in biocomputing and
   intelligence-in-a-dish
%J Front. Sci.
%M FEB
%D 2023
%K jrnl, c2023, c202x, c20xx, zz0323, AI, brain, cell, cells, biological,
   wetware, biol, computing, organoid, in vitrio, dish, frontiers
%X "Recent advances in human stem cell-derived brain organoids promise to
   replicate critical molecular & cellular aspects of learning & memory &
   possibly aspects of cognition in vitro. ... We envisage complex, networked
   interfaces whereby brain organoids are connected with real-world sensors &
   output devices, & ultimately with each other & with sensory organ organoids
   (e.g. retinal organoids), and ..."
   -- [<A HREF="https://doi.org/10.3389/fsci.2023.1017235">doi:10.3389/fsci.2023.1017235</A>]['23]
   in [<A HREF="https://www.frontiersin.org/journals/science/article-hubs/organoid-intelligence-a-new-biocomputing-frontier">www</A>]['23].
   [Also search for: computing AI brain organoid].

%A M. E. Babey
%A et al
%T Brain-derived CCN3 is an osteoanabolic hormone that sustains bone in
   lactating females
%J BioRxiv
%M FEB
%D 2024
%K MolBio, TR, c2024, c202x, c20xx, zz0724, lactation, mammal, mammals, female,
   CCN3, Ca, calcium, osteoporosis, estrogen, bone, bones
%X "... we report that brain-derived CCN3 (Cellular Communication Network
   factor3) secreted from KISS1 neurons of the arcuate nucleus (ARCKISS1) fills
   this [estrogen] void & functions as a potent osteoanabolic factor to promote
   bone mass in lactating females ..."
   -- [<A HREF="https://doi.org/10.1101/2023.08.28.554707">doi:10.1101/2023.08.28.554707</A>]['24].

%A S. Nurk
%A et al
%T The complete sequence of a human genome
%J Science
%V 376
%N 6588
%P 44-53
%M MAR
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0422, human genome, nGenome,
   chromosomes, telomere, centromere, acrocentric, reference,
   T2T-CHM13, C2TCHM13
%X "... the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055
   billion-base pair seq. of a h.genome, T2T-CHM13, that includes gapless
   assemblies for all chr. except Y, corrects errors in the prior references,
   & introduces nearly 200 million bps of seq. containing 1956 gene predictions,
   99 of which are pred. to be protein coding. The completed regions inc. all
   centromeric satellite arrays, recent segmental duplications, & the short
   arms of all five acrocentric chromosomes ..."
   -- [<A HREF="https://doi.org/10.1126/science.abj6987">doi:10.1126/science.abj6987</A>]['22].
   (in special issue on completeing the human genome.)

%A Longxing Cao
%A et al ...
%A D. Baker
%T Design of protein binding proteins from target structure alone
%J Nature
%V ?
%M MAR
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0422, protein, computer design, silico,
   antibody
%X "... The design of proteins that bind to a specific site on the surface of a
   target p. using no info. other than the 3S structure of the target remains an
   outstanding challenge. We describe a general soln to this problem which
   starts with a broad exploration of the very large space of possible binding
   modes to a selected region of a p.surface, & then intensifies the search in
   the vicinity of the most promising binding modes. We demonstrate its very
   broad applicability by de novo design of binding proteins to 12 diverse
   p.targets ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-04654-9">doi:10.1038/s41586-022-04654-9</A>]['22] (online 24/3/2022).
   [Also search for: MolBio protein design].

%A A. Kousathanas
%A et al
%T Whole-genome sequencing reveals host factors underlying critical COVID-19
%J Nature
%V 607
%P 97-103
%M MAR
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0722, covid 19, covid19, risk, risks,
   genes, GenOMICC, IL10RB, PLSCR1, BCL11A, FUT2, ATP11A, MUC1, SELE, ICAM5,
   CD209, severe illness
%X "... comparison of genomes from individuals who are critically ill with those
   of pop'n controls to find underlying disease mechanisms. Here we use
   whole-genome sequencing in 7,491 critically ill individuals compared with
   48,400 controls to discover & replicate 23 indep. variants that sig.
   predispose to critical COVID-19. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-04576-6">doi:10.1038/s41586-022-04576-6</A>]['22].

%A K. Roper
%A et al ...
%A R. D. King
%T Testing the reproducibility and robustness of the cancer biology literature
   by robot
%J J. Royal Soc., Interface
%M APR
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0422, MolBio, robot, Eve, robotic, automated,
   science, scientific research, breast cancer, MCF7, GWAS, reproducibility
%X "... From 12,260 papers, we automatically extracted statements predicted to
   describe experimental results regarding a change of gene expression in
   response to drug treatment in breast cancer, from these we selected 74
   statements of high biomedical interest. To test the reproducibility of these
   statements, two different teams used the laboratory automation system Eve &
   two breast cancer cell lines (MCF7 & MDA-MB-231). Stat. sig. evidence for
   repeatability was found for 43 statements, & sig. evidence for
   reproducibility/robustness in 22 statements. In two cases, the automation
   made serendipitous discoveries. The reproduced/robust knowledge provides
   sig. insight into cancer. We conclude that semi-automated reproducibility
   testing is currently achievable ..."
   -- [<A HREF="https://doi.org/10.1098/rsif.2021.0821">doi:10.1098/rsif.2021.0821</A>]['22].

%A E. Callaway
%T What's next for AlphaFold and the AI protein-folding revolution
%J Nature
%V 604
%P 234-238
%M APR
%D 2022
%K news, views, c2022, c202x, c20xx, zz0422, MolBio, protein, structure,
   folding, prediction, AlphaFold, applications
%X "... AlphaFold caused a sensation in December 2020, when it dominated a
   contest called the Critical Assessment of Protein Structure Prediction, or
   CASP. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-00997-5">doi:10.1038/d41586-022-00997-5</A>]['22].
   (Also see Pfolding@[<A HREF="https://en.wikipedia.org/wiki/Protein_folding">wikip</A>['22].)
   [Also search for: AlphaFold].

%A A. Cagan
%A et al
%T Somatic mutation rates scale with lifespan across mammals
%J Nature
%V ?
%M APR
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0422, DNA, genome, somatic mutation,
   mutations, rate, lifespan, age, ageing, animal, mammal, lifespan
%X "... we performed whole-genome sequencing of 208 intestinal crypts from 56
   individuals to study the landscape of somatic mutation across 16 mammalian
   species. ... Notably, the somatic mutn rate per year varied greatly across
   species & exhibited a strong inverse relationship with species lifespan, with
   no other life-history trait studied showing a comparable assoc.. Despite
   widely different life histories among the species we examined - inc.
   variation of ~ 30-fold in lifespan & ~ 40,000-fold in body mass - the
   somatic mutn burden at the end of lifespan varied only by a factor of ~3.
   These data unveil common mutational processes across mammals, & suggest that
   somatic mutn rates are evolutionarily constrained & may be a contributing
   factor in ageing."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-04618-z">doi:10.1038/s41586-022-04618-z</A>]['22].
   [Also search for: MolBio ageing].

%A M. A. Field
%A et al
%T The Australian dingo is an early offshoot of modern breed dogs
%J ScienceAdvances
%V 8
%N 16
%M APR
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0422, dog, dingo, canine, wolf, genome,
   evolution, breeding
%X "... We identified large chromosomal differences relative to the current dog
   reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as
   found in breed dogs. Phylogenetic analyses using variant pairwise matrices
   show that the dingo is distinct from five breed dogs with 100% bootstrap
   support when using Greenland wolf as the outgroup. Functionally, we observe
   differences in methylation patterns between the dingo and German shepherd dog
   genomes and differences in serum biochemistry and microbiome makeup. Our
   results suggest that distinct demographic and environmental conditions have
   shaped the dingo genome. In contrast, artificial human selection has likely
   shaped the genomes of domestic breed dogs after divergence from the dingo."
   -- [<A HREF="https://doi.org/10.1126/sciadv.abm5944">doi:10.1126/sciadv.abm5944</A>]['22].
   (Also see [<A HREF="https://www.abc.net.au/news/rural/2022-04-23/dingo-or-feral-dog-science-advances-genetic-sequence/101010896">abc</A>][23/4/2022].)

%A Y. Oba
%A et al
%T Identifying the wide diversity of extraterrestrial purine and pyrimidine
   nucleobases in carbonaceous meteorites
%J Nat. Commun.
%V 13
%N #2008
%M APR
%D 2022
%K MolBio, jrnl, c2022, c202x, c20xx, zz0522, extraterrestrial, meteorite,
   DNA, ACGT, RNA, ACGTU
%X "... report the detection of nucleobases in three carbonaceous meteorites
    ... In addition to previously detected purine nucleobases in meteorites such
    as guanine and adenine, we identify various pyrimidine nucleobases such as
    cytosine, uracil, and thymine ..."
   -- [<A HREF="https://doi.org/10.1038/s41467-022-29612-x">doi:10.1038/s41467-022-29612-x</A>]['22].
   (Also see [<A HREF="https://www.abc.net.au/news/2022-04-27/australian-meteorite-one-of-three-with-key-dna-building-blocks/101018500">ABC</A>]['27/4/2022].)

%A V. D. Longo
%A R. M. Anderson
%T Nutrition, longevity and disease: From molecular mechanisms to interventions
%J Cell
%V 185
%N 9
%P 1455-1470
%M APR
%D 2022
%K jrnl, review, c2022, c202x, c20xx, human health, aging, ageing, lifespan,
   diet, diets, nutrition, carbohydrate, fasting
%X "... we analyze aging & nutrition studies in simple organisms, rodents,
   monkeys, & humans to link longevity to conserved growth & metabolic pathways
   & outline their role in aging & age-related disease ..."
   "... a mid to high carbohydrate & low but sufficient protein intake that is
   mostly plant based but includes regular consumption of
   pesco-vegetarian-derived protein ..."
   -- [<A HREF="https://doi.org/10.1016/j.cell.2022.04.002">doi:10.1016/j.cell.2022.04.002</A>]['22].

%A C. Outeiral
%A D. A. Nissley
%A C. M. Deane
%T Current structure predictors are not learning the physics of protein folding
%J Bioinformatics
%V 38
%N 7
%P 1881-1887
%M APR
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz1222, protein folding, structure,
   pathway, trajectory, AlphaFold 2, RoseTTAFold, trRosetta, RaptorX, DMPfold,
   EVfold, SAINT2, Rosetta, uniOxford
%X "... deep learning ... unprecedented success at predicting a protein's
   crystal structure, but it is not clear if these models are learning the
   physics of how ps. dynamically fold ... find evidence that their simulated
   dynamics capture some info. about the folding pathway, but their predictive
   ability is worse than a trivial classifier using seq.-agnostic features like
   chain length. The folding trajectories produced are also uncorrelated with
   experimental observables such as intermediate structs. & the folding rate
   constant. ... suggest that recent advances in structure pred'n do not yet
   provide an enhanced understanding of protein folding."
   -- [<A HREF="https://doi.org/10.1093/bioinformatics/btab881">doi:10.1093/bioinformatics/btab881</A>]['22]  (online Jan 2022).
   [Also search for: protein folding trajectory].

%A G. Vogel
%T New versions of Omicron are masters of immune evasion
%J Science
%V ?
%M MAY
%D 2022
%K news, views, c2022, c202x, c20xx, zz0522, virus, SARS-CoV-2, covid 19,
   covid19, omicron, BA1, BA2, BA.2, BA.2.12.1, BA3, BA4, BA5, variant, variants
%X "... Epidemiologists & virologists [in S.Africa] are watching closely as
   cases there rise sharply again, just 5 months after the Omicron variant
   caused a dramatic surge. This time, the drivers are two new subvariants of
   Omicron named BA.4 and BA.5 ..."
   -- [<A HREF="https://doi.org/10.1126/science.adc9473">doi:10.1126/science.adc9473</A>]['22].
   [Also search for: covid variant].

%A J. Huang
%A et al
%T Evidence for reduced BRCA2 functional activity in Homo sapiens after
   divergence from the chimpanzee-human last common ancestor
%J Cell Reports
%V 39
%N 5
%M MAY
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0522, BRCA, BRCA2, DSS1, Homo sapiens,
   primate, evolution, fertility, cancer, DNA repair
%X "We performed a comparative analysis of human & 12 non-human primates to
   identify seq. variations in known cancer genes. We identified 395
   human-specific fixed non-silent substitutions that emerged during evolution
   of human. Using bioinformatics analyses for functional consequences, we
   identified a # of substitutions that are predicted to alter protein function;
   one of these mutations is located at the most evolutionarily conserved domain
   of human BRCA2."
   -- [<A HREF="https://doi.org/10.1016/j.celrep.2022.110771">doi:10.1016/j.celrep.2022.110771</A>]['22].

%A M. Yafia
%A et al
%T Microfluidic chain reaction of structurally programmed capillary flow events
%J Nature
%V 605
%P 464-469
%M MAY
%D 2022
%K MolBio, jrnl, c2022, c202x, c20xx, zz0522, lab on a chip, microfluidic,
   capillary flow
%X "... we introduce the microfluidic chain reaction (MCR) as the conditional,
   structurally programmed propagation of capillary flow events. Monolithic
   chips integrating a MCR are 3-dimensionally printed, & powered by the free
   energy of a paper pump, autonomously execute liquid handling algs.
   step-by-step. With MCR, we automated (1) the sequential release of 300
   aliquots across chained, interconnected chips, (2) a protocol for severe
   acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) antibodies detection in
   saliva & (3) a thrombin generation assay ... MCRs are untethered from &
   unencumbered by peripherals, encode programs structurally in situ & can form
   a frugal, versatile, bona fide lab-on-a-chip with wide-ranging applications
   in liquid handling and point-of-care diagnostics."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-04683-4">doi:10.1038/s41586-022-04683-4</A>]['22].

%A T. Bonnet
%A et al ...
%A L. E. B. Kruuk
%T Genetic variance in fitness indicates rapid contemporary adaptive evolution
   in wild animals
%J Science
%V 376
%N 6596
%P 1012-1016
%M MAY
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0622, MolBio, genetics, evolution,
   genes, fitness, trait, traits, selection, adaption, variation, Darwinism,
   population dynamics
%X "The rate of adaptive evol'n, the contribution of sel'n to genetic changes
   that increase mean fitness, is determined by the additive genetic variance
   in individual relative fitness. To date, there are few robust estimates of
   this parameter for natural populations, & ... unclear whether adaptive
   evolution can play a meaningful role in short-term pop'n dynamics. We
   developed & applied quantitative genetic methods to long-term datasets from
   19 wild bird & mammal pop'ns & found that, while estimates vary between
   pop'ns, additive genetic variance in relative fitness is often substantial &,
   on avg., twice that of previous estimates. We show that these rates of
   contemporary adaptive evolution can affect pop'n dynamics & hence that
   natural seln has the potential to partly mitigate effects of current
   environmental change."
   -- [<A HREF="https://doi.org/10.1126/science.abk0853">doi:10.1126/science.abk0853</A>]['22].
   (Also see opinion [<A HREF="https://doi.org/10.1126/science.abo4624">doi:10.1126/science.abo4624</A>]['22].)

%A D. Liu
%A et al
%T Association of sugar-sweetened, artificially sweetened, and unsweetened
   coffee consumption with all-cause and cause-specific mortality
%J Annals of Internal Medicine
%M MAY
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0622, zzCoffee, coffee consumption, caffeine,
   decaf, diet, human health
%X "... Moderate consumption of unsweetened and sugar-sweetened coffee was
   associated with lower risk for death."
   -- [<A HREF="https://doi.org/10.7326/M21-2977">doi:10.7326/M21-2977</A>]['22].
   (Also see The G@[<A HREF="https://www.theguardian.com/food/2022/may/30/coffee-drinkers-may-be-at-lower-risk-of-early-death-study-suggests">www</A>][31/5/2022].)
   [Also search for: coffee consumption].

%T Prevalence of ongoing symptoms following coronavirus (COVID-19) infection in
   the UK: 6 May 2022
%M MAY
%D 2022
%K TR, news, report, c2022, c202x, c20xx, zz0622, covid 19, covid19, long covid,
   longCovid, UK, stats
%X "... An est. 1.8 million people living in private households in the UK
   (2.8% of the population) were experiencing self-reported long COVID (symptoms
   persisting for more than four weeks after the first suspected coronavirus
   (COVID-19) infection that were not explained by something else) as of
   3 April 2022 ..."
   -- [<A HREF="https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/bulletins/prevalenceofongoingsymptomsfollowingcoronaviruscovid19infectionintheuk/6may2022#main-points">www</A>]['22].

%A A. A. Rosenberg
%A A. Marx
%A A. M. Bronstein
%T Codon-specific Ramachandran plots show amino acid backbone conformation
   depends on identity of the translated codon
%J Nat. Commun.
%V 13
%N 1
%M MAY
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0622, DNA, protein, structure, folding,
   genes, codon, codons
%X "... there is evidence to suggest that codon usage affects co-translational
   protein folding & the final structure of the expressed p.. Here we develop a
   method for computing & comparing codon-specific R.plots & demonstrate that
   the backbone dihedral angle distns of some synonymous codons are
   distinguishable with stat. sig. for some sec. structures. This shows that
   there exists a dependence between codon identity & backbone torsion of the
   translated amino acid. Although these findings cannot pinpoint the causal
   direction of this dependence, we discuss the vast biological implications
   should coding be shown to directly shape p.conformation & ..."
   -- [<A HREF="https://doi.org/10.1038/s41467-022-30390-9">doi:10.1038/s41467-022-30390-9</A>]['22].

%A M. D. Esposti
%A et al
%T On the bacterial ancestry of mitochondria: new insights with
   triangulated approaches
%J bioRxiv
%M MAY
%D 2022
%K TR, MolBio, c2022, c202x, c20xx, zz0823, origin, origins, mitochondria,
   bacteria, eukaryote, eukaryotic
%X "... The precise bacterial origin of mitochondria &, consequently, the
   metabolic ancestry of our cells remains controversial - despite the vast
   genomic information that is now available. Here we triangulate across
   multiple phylogenomic & molecular approaches to pinpoint the most likely
   living relatives of the ancestral b. from which mitochondria originated."
   -- [<A HREF="https://doi.org/10.1101/2022.05.15.491939">doi:10.1101/2022.05.15.491939</A>]['23].
    [Also search for: MolBio eukaryote mitochondria origin].

%A N. M. Mwaniki
%A E. Garrison
%A N. Pisanti
%T Fast exact string to D-texts alignments
%J arXiv
%M JUN
%D 2022
%K TR, c2022, c202x, c20xx, zz0622, MolBio, dText, dString, degenerate,
   indeterminate, uncertain, alignment, pangenome, supragenome, genes
%X "... aligning a seq. to a pangenome  ... A fast & accurate soln to this
   problem can serve as a toolkit to many crucial tasks such as read-correction,
   Multiple Seq. Al. (MSA), genome assemblies, variant calling, just to name a
   few. ... propose a new, fast & exact method to align a string to a D-string,
   the latter possibly rep. an MSA, a pan-genome or a partial assembly. ..."
   -- 2206.03242@[<A HREF="https://arxiv.org/abs/2206.03242">arXiv</A>]['22].
   ("... The D-string (or D-text) T contains some deterministic
    & some non-deterministic segments. ...")
   (See, "... a pan-genome is the entire set of genes from all strains within a
    clade. More generally, it is the union of all the genomes of a clade. ..."
    -- [<A HREF="https://en.wikipedia.org/wiki/Pan-genome">wikip</A>]['22].)
   [Also search for: indeterminate dString].

%A X. Shen
%A et al
%T Synonymous mutations in representative yeast genes are mostly strongly
   non-neutral
%J Nature
%V ?
%M JUN
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0622, codons, mutations, genes
   synonymous, silent, nonsynonymous, fitness, yeast
%X "... we constructed 8,341 yeast mutants each carrying a synonymous,
   nonsynonymous or nonsense mutn in one of 21 endogenous genes with diverse
   fns & expression levels & measured their fitness rel. to the wild type in a
   rich medium. Three-quarters of syn.mutns resulted in a sig. reduction in
   fitness ... Both syn. & nonsyn. mutns freq. disturbed the level of mRNA
   expression of the mutated gene, & the extent of the disturbance partially
   predicted the fitness effect. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-04823-w">doi:10.1038/s41586-022-04823-w</A>]['22].
   [***BUT see L.Kruglyak et al 4/2023***]

%A E. R. Arunachaleswaran
%A A. De
%A S. Kannan
%T Reconstructing ultrametric trees from noisy experiments
%J arXiv
%M JUN
%D 2022
%K TR, MolBio, c2022, c202x, c20xx, zz0622, ultrametric tree, trees, phylogeny,
   noise, noisy, experiment
%X "... Our results are the following: 1. Suppose the length of every edge in
   the unknown tree is at least ~O(1/sqrt(n)) fraction of the length of a
   root-leaf path. Then, we give an efficient alg. to reconstruct the topology
   of the tree for a broad family of dist.-based noise models. & show that if
   the edges are asymptotically shorter, then topology reconstruction is
   information-theoretically impossible.  2. [&] for a specific dist.-based
   noise model - which we refer to as the homogeneous noise model - we show that
   the edge weights can also be approximately reconstructed under the same
   quantitative lower bound on the edge lengths."
   -- 2206.07672@[<A HREF="https://arxiv.org/abs/2206.07672">arXiv</A>]['22].

%A S. Zhang
%A et al
%T Multiomic analysis reveals cell-type-specific molecular determinants of
   covid-19
%J Cell Sys.
%M JUN
%D 2022
%K jrnl. c2022, c202x, c20xx, zz0622, MolBio, jrnl, long covid 19, covid19,
   GWAS, genotype, NK cell, NKcell, Tcell, risk, risks, genes, immune
%X "... single-cell multiome profiling of human lungs ... We discover > 1,000
   risk genes across 19 cell types, which account for 77% of the SNP-based
   heritability for severe disease. Genetic risk is particularly focused within
   natural killer (NK) cells & T cells, placing the dysfunction of these cells
   upstream of severe disease. Mendelian randomization & single-cell profiling
   of human NK cells support the role of NK cells & further localize genetic
   risk to CD56bright NK cells, which are key cytokine producers during the
   innate immune response. Rare variant analysis confirms the enrichment of
   severe-disease-associated genetic variation within NK-cell risk genes. ..."
   -- [<A HREF="https://doi.org/10.1016/j.cels.2022.05.007">doi:10.1016/j.cels.2022.05.007</A>]['22].

%A M. Izutsu
%A R. E. Lenski
%T Experimental test of the contributions of initial variation and new mutations
   to adaptive evolution in a novel environment
%J bioRxiv
%M JUN
%D 2022
%K MolBio, TR, c2022, c202x, c20xx, zz0622, bacteria, Ecoli, evolution,
   mutation, fitness, genetic variation, adaption
%X "... we performed an experiment using E.coli to compare the contributions of
   initial genetic variation & new mutations to adaptation in a new environment.
   ... there were no differences in fitness among the treatments after 500 or
   2000 generations in the new environment, despite the variation in fitness
   among the founders. These results indicate that new mutations quickly
   overcame, & eventually contributed more to adaptation, than did the initial
   variation. ..."
   -- [<A HREF="https://doi.org/10.1101/2022.05.31.494207">doi:10.1101/2022.05.31.494207</A>]['22].

%A B. A. Reinke
%A et al
%T Diverse aging rates in ectothermic tetrapods provide insights for the
   evolution of aging and longevity
%J Science
%M JUN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0622, animal, herpetiles, turtle, tortoise,
   cold blooded, ectotherm, ageing, rate, aging, lifespan
%X "... study of aging rates & longevity across wild tetrapod ectotherms, using
   data from 107 pop'ns (77 species) of nonavian reptiles & amphibians. We test
   hypotheses of how thermoregulatory mode, environmental temperature,
   protective phenotypes, & pace of life history contribute to demographic
   aging. Controlling for phylogeny & body size, ectotherms display a higher
   diversity of aging rates compared with endotherms & include phylogenetically
   widespread evidence of negligible aging. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abm0151">doi:10.1126/science.abm0151</A>]['22].
   [Also search for: anuimal lifespan].

%A M. D. Bunting
%A et al
%T Generation of gene drive mice for invasive pest population suppression
%J Applications of Genome Modulation and Editing
%S Methods in Molec. Biol.
%I HumanaPress
%V 2495
%P 203-230
%M JUN
%D 2022
%K chapter, MolBio, c2022, c202x, c20xx, zz1122, Australia, mouse, mice, pest,
   gene drive, CRISPR Cas9, eradication
%X "Gene drives are genetic elts that are transmitted to greater than 50% of
   offspring & have potential for pop'n modification or suppression. While gene
   drives are known to occur naturally, the recent emergence of CRISPR-Cas9 ...
   Here, we discuss the prospects for gene drive development in mice, inc.
   synthetic 'homing drive' & X-shredder strategies ... also provide detailed
   protocols for generation of gene drive mice through incorporation of
   plasmid-based transgenes in a targeted & non-targeted manner. ..."
   -- [<A HREF="https://doi.org/10.1007/978-1-0716-2301-5_11">doi:10.1007/978-1-0716-2301-5_11</A>]['22].
   [Also search for: MolBio gene drive].

%A S. Loomba
%A et al
%T Connectomic comparison of mouse and human cortex
%J Science
%V 377
%N 6602
%P ?-?
%M JUL
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0722, biology, animal, brain, cerebral cortex,
   human, mouse, connectome, connections, neuron, neurons, synapses,
   interneuron
%X "The h.cerebral cortex houses 1000 times more neurons than that of the
   cerebral cortex of a mouse, but the possible differences in synaptic circuits
   between these species are still poorly understood. ... 3D electron microscopy
   of mouse, macaque, & human ... The 2.5-fold increase in interneurons in h.
   compared with mice was compensated by a change in axonal connection
   probabilities & therefore did not yield a commensurate increase in
   inhibitory-v.-excitatory synaptic input balance on h. pyramidal cells. Rather
   increased inhibition created an expanded interneuron-to-interneuron n/wk,
   driven by an expansion of interneuron-targeting interneuron types & an
   increase in their synaptic selectivity for interneuron innervation. These
   constitute key neuronal n/wk alterations in the human cortex."
   -- [<A HREF="https://doi.org/10.1126/science.abo0924">doi:10.1126/science.abo0924</A>]['22].
   (Also see connectome@[<A HREF="https://en.wikipedia.org/wiki/Connectome">wikip</A>].)
   [Also search for: MolBio connectome].

%A R. Van Noorden
%T Investigators found plagiarism and data falsification in work from
   prominent cancer lab
%J Nature
%V 607
%P 650-652
%M JUL
%D 2022
%K news, c2022, c202x, c20xx, zz0722, academic misconduct, plagiarism,
   falsification, university management, academia, science, Carlo Croce, OSU,
   Michela Garofalo, Flavia Pichiorri, cancer research, Ohio State University
%X "Ohio State University investigations identified misconduct by two
   scientists in lab of high-profile cancer researcher Carlo Croce. The uni.
   has cleared Croce of misconduct, but disciplined him over management
   problems. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-02002-5">doi:10.1038/d41586-022-02002-5</A>]['22].
   [Also search for: academic misconduct].

%A N. Fallach
%A et al
%T Pregnancy outcomes after SARS-CoV-2 infection by trimester: A large,
   population-based cohort study
%J PLoS One
%V ?
%M JUL
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0722, human health, risk, risks, covid 19,
   covid19, SARSCoV2, premature birth, preterm, PTB, miscarriage
%X "... While first & second trimester infections were not assoc. with PTB
   (p > 0.8), third trimester infections & in particular after 34 weeks of
   gestation had a greater risk of PTB with adjusted ORs of 2.76 (95% CI
   1.63-4.67) & 7.10 (95% CI 2.44-20.61), resp.. PTB risk was further heightened
   in symptomatic third trimester infections (OR = 4.28, 95% CI 1.94-9.25). SGA
   risk was comparable between study groups across all trimesters of infection.
   Pregnancy loss incidence was similar in both groups (adjusted OR = 1.16;
   95% CI 0.90-1.50)."
   -- [<A HREF="https://doi.org/10.1371/journal.pone.0270893">doi:10.1371/journal.pone.0270893</A>]['22].

%A Ruidong Wu
%A et al
%T High-resolution de novo structure prediction from primary sequence
%J bioRxiv
%M JUL
%D 2022
%K TR, MolBio, c2022, c202x, c20xx, zz0722, protein structure prediction,
   tertiary, 3D, ANN, NN, omegafold, RoseTTAFold, RosettaFold
%X "... we introduce OmegaFold, the first computational method to successfully
   predict high-resolution protein structure from a single primary seq. alone.
   Using a new combination of a protein language model that allows us to make
   predictions from single seqs. & a geometry-inspired transformer model
   trained on protein structures, ..."
   -- [<A HREF="https://doi.org/10.1101/2022.07.21.500999">doi:https://doi.org/10.1101/2022.07.21.500999</A>]['22], ho hum?
   [Also search for: 3D protein structure prediction ANN].

%A E. Callaway
%T 'The entire protein universe': AI predicts shape of nearly every known
   protein
%J Nature
%V ?
%N ?
%P ?-?
%M JUL
%D 2022
%X news, views, MolBio, c2022, c202x, c20xx, zz0722, Alphafold, alphaFold2,
   3D, tertiary, protein structure prediction, NN, ANN
%X "... Researchers have used AlphaFold - the revolutionary AI n/wk - to predict
   the structures of some 200 million proteins from 1 million species, covering
   nearly every known protein on the planet. The data dump will be freely
   available on a database set up by DeepMind ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-02083-2">doi:10.1038/d41586-022-02083-2</A>]['22].
   [Also search for: 3D protein structure prediction ANN].

%A Xiao-Ai Zhang
%A et al
%T A zoonotic henipavirus in febrile patients in China
%J NEJM
%V 387
%N 5
%P 470-472
$M AUG
%D 2022
%K jrnl, NEJM, c2022, c202x, c20xx, zz0822, virus, human, shrew, zoonotic,
   Shandong, Henan, China, novel Langya henipavirus, LayV, henipavirus
%X "... investigators in China identified a new henipavirus assoc. with a
   febrile human illness. This virus was also found in shrews. ..."
   -- [<A HREF="https://doi.org/10.1056/nejmc2202705">doi:10.1056/nejmc2202705</A>]['22].
   (Also see [<A HREF="https://www.bbc.com/news/world-asia-china-62489808">bbc</A>][10/8/2022.)
   [Also search for: virus china].

%A M. Worobey
%A et al
%T The Huanan seafood wholesale market in Wuhan was the early epicenter of the
   COVID-19 pandemic
%J Science
%V 377
%N 6609
%P ?-?
%M AUG
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0822, covid19, covid-19, China, Wuhan, Huanan,
   pandemic, SARS-CoV-2, SARSCoV2, SARS 2, SARS2, origin, zoonotic virus
%X "... We show here that the earliest known COVID-19 cases from Dec.2019, inc.
   those without reported direct links, were geographically centered on this
   market. We report that live SARS-CoV-2-susceptible mammals were sold at the
   market in late 2019 & that within the market, SARS-CoV-2-+ve environmental
   samples were spatially assoc. with vendors selling live mammals. Although
   there is insufficient evidence to define upstream events, & exact
   circumstances remain obscure, our analyses indicate that the emergence of
   SARS-CoV-2 occurred through the live wildlife trade in China & show that the
   Huanan market was the epicenter of the COVID-19 pandemic."
   -- [<A HREF="https://doi.org/10.1126/science.abp8715">doi:10.1126/science.abp8715</A>]['22].
   [Also search for: covid19 origin].

%A M. Pascal-Torner
%A et al
%T Comparative genomics of mortal and immortal cnidarians unveils novel keys
   behind rejuvenation
%J PNAS
%V 119
%N 36
%P e2118763119
%M AUG
%D 2022
%K jrnl, PNAS, MolBio, c2022, c202x, c20xx, zz0822, animal, Turritopsis dohrnii,
   rubra, jelly fish, jellyFish, genes, immortal, longevity, aging, ageing,
   rejuvenation, telomere, telomerepolycomb
%X "... present & compare whole-genome assemblies of T. dohrnii & the
   nonimmortal Turritopsis rubra using auto. & manual annotations, together with
   the transcriptome of life cycle reversal (LCR) process of T. dohrnii. We have
   identified variants & expansions of genes assoc. with replication, DNA
   repair, telomere maintenance, redox environment, stem cell pop'n, &
   intercellular comm'n. [&] we have found silencing of polycomb repressive
   complex 2 targets & activation of pluripotency targets during LCR, which
   points to these transc'n factors as pluripotency inducers in T. dohrnii. ...
   we propose these factors as key elts in the ability of T. dohrnii to undergo
   rejuvenation."
   -- [<A HREF="https://doi.org/10.1073/pnas.2118763119">doi:10.1073/pnas.2118763119</A>]['22].

%A Xueqiu Lin
%A et al
%T Nested epistasis enhancer networks for robust genome regulation
%J Science
%V 377
%N 6610
%P 1077-1085
%K AUG
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0922, epistasis, biological network,
   regulation, enhancer, promoter, interaction, gene expression, BRD4
%X "Mammalian genomes have multiple enhancers spanning an ultralong distance
   (> megabases) to modulate important genes ... CRISPRi screening with m/c
   learning to define quantitative enhancer-enhancer interactions. We find that
   the ultralong distance enhancer n/wk has a nested multilayer architecture
   that confers functional robustness of gene expression. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abk3512">doi:10.1126/science.abk3512</A>]['22].
   [Also search for: MolBio interaction network].

%A J. M. Perkel
%T Smart software untangles gene regulation in cells
%J Nature
%V 609
%P 428-431
%M SEP
%D 2022
%K news, views, survey, MolBio, c2022, c202x, c20xx, zz0922, gene regulatory,
   network, interaction, promoter, transcription factor, Inferelator, ATACseq,
   RNAseq, SCENIC+, single-cell, CellOracle, SINGE, BEELINE, Quackenbush,
   maxATAC, scRNAseq
%X "Working out how a cell is wired lets researchers find key regulators of
   behaviour ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-02826-1">doi:10.1038/d41586-022-02826-1</A>]['22].
   [Also search for: MolBio interaction network] & [also search for: scRNAseq].

%A R. Pearce,
%A Yang Li,
%A G. S. Omenn,
%A Yang Zhang
%T Fast and accurate ab initio protein structure prediction using deep
   learning potentials
%J PLoS Comp. Biol
%M SEP
%D 2022
%K jrnl, eJrnl, MolBio, c2022, c202x, c20xx, zz1122, DeepFold, NN, ANN,
   DeepMSA, 3D, protein structure prediction, gradient descent, simulation,
   trRosetta, DMPfold
%X "... an open-source program, DeepFold, which integrates spatial restraints
   predicted by multi-task deep residual neural-networks along with a
   knowledge-based energy fn to guide its gradient-descent folding simulations.
   ... Of particular interest is the modeling performance on the most difficult
   targets with v.few homologous seqs., where DeepFold achieved an avg TM-score
   that was 40.3% higher than trRosetta & 44.9% higher than DMPfold.  ..."
   -- [<A HREF="https://doi.org/10.1371/journal.pcbi.1010539">doi:10.1371/journal.pcbi.1010539</A>]['22].
   [Also search for: 3D protein structure prediction], maybe include ANN.

%A A. Pinson
%A et al
%T Human TKTL1 implies greater neurogenesis in frontal neocortex of modern
   humans than Neanderthals
%J Science
%V 377
%N 6611
%P ?-?
%M SEP
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz0922, gene, TKTL1, modern human,
   Neanderthal, brain, development, neurons, neuron, neurogenesis
%X "... In light of our finding that TKTL1 expression in fetal human neocortex
   is particularly high in the developing frontal lobe, our study implies that
   because of the single amino acid-based activity of hTKTL1, neocortical
   neurogenesis in modern humans was and is greater than it was in Neanderthals,
   in particular in the frontal lobe."
   -- [<A HREF="https://doi.org/10.1126/science.abl6422">doi:10.1126/science.abl6422</A>]['22].
   [Also search for: MolBio Neanderthal].

%A V. Lalchand
%A et al
%T Modelling technical and biological effects in scRNA-seq data with
   scalable GPLVMs
%J arXiv
%M SEP
%d 2022
%K TR, MolBio, c2022, c202x, c20xx, zz0624, scRNA seq, scRNAseq,
   GPLVM, Dinithi Sumanaweera
%X "... we extend a popular approach for probabilistic non-linear dimensionality
   reduction, the Gaussian process latent variable model, to scale to massive
   single-cell datasets while explicitly accounting for technical & biological
   confounders. The key idea is to use an augmented kernel which preserves the
   factorisability of the lwb allowing for fast stochastic variational
   inference. We demonstrate its ability to reconstruct latent signatures of
   innate immunity recovered in Kumasaka et al. (2021) ..."
   -- [<A HREF="https://arxiv.org/abs/2209.06716">arxiv:2209.06716</A>]['24].
   [Also search for: scRNAseq].

%A F.S. Dunn
%A et al
%T A crown-group cnidarian from the Ediacaran of Charnwood Forest, UK
%J Nature Ecol. and Evol.
%V 6
%P 1095-1104
%M AUG
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1022, biology, biol, ancient, animal, jellyfish,
   coral, corals, Ediacaran, animalia, fossil, Auroralumina attenboroughii,
   medusozoan
%X "... we describe a new fossil cnidarian - Auroralumina attenboroughii gen.
   et sp. nov. - from the Ediacaran of Charnwood Forest (557-562 million years
   ago) that shows two bifurcating polyps enclosed in a rigid, polyhedral,
   organic skeleton with evidence of simple, densely packed tentacles. ... a
   stem-group medusozoan &, therefore, the oldest crown-group cnidarian. ..."
   -- [<A HREF="https://doi.org/10.1038/s41559-022-01807-x">doi:10.1038/s41559-022-01807-x</A>]['22].
   (Also see animal@[<A HREF="https://en.wikipedia.org/wiki/Animal">wikip</A>]['22].)
   [Also search for: ancient animal].

%A D. Lagarde
%A L. Kazak
%T The timing of eating controls energy use. Synchronizing food intake with
   the body clock boosts thermogenesis and limits obesity
%J Science
%V 378
%N 6617
%M OCT
%D 2022
%K news, c2022, c202x, c20xx, zz1022, human healthm diet, fasting, eating,
   time restricted, weight, obesity
%X "... Diet-induced obesity is modeled in mice by using energy-dense, high-fat
   diets. When the time window of high-fat food intake is restricted
   [time-restricted feeding (TRF)], weight gain is attenuated, but the
   underlying mechanisms are not resolved. On page 276 of this issue, Hepler et
   al. reveal that TRF during the active period of the circadian clock (at
   night) protects mice from diet-induced obesity by enhancing adipocyte
   thermogenesis."
   -- [<A HREF="https://doi.org/10.1126/science.ade6720">doi:10.1126/science.ade672</A>]['22].

%A L. Skov
%A et al
%T Genetic insights into the social organization of Neanderthals
%J Nature
%V 610
%P 519-525
%M OCT
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz1022, ancient DNA, Neanderthal, hominin,
   Chagyrskaya, Okladnikov cave, mitochondria, Ychromosome, Ychr, chrY, chr Y
%X "... present genetic data for 13 Neanderthals from two Middle Palaeolithic
   sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave &
   2 from Okladnikov Cave ... Some Chagyrskaya individuals were closely related
   ... best explained by female migration between communities ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-05283-y">doi:10.1038/s41586-022-05283-y</A>]['22].
   [Also search for: MolBio ancient DNA]  and  [also search for: Neanderthal].

%A C. Doust
%A et al
%T Discovery of 42 genome-wide significant loci associated with dyslexia
%J NatureGenetics
%V ?
%P ?-?
%M OCT
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1022, MolBio, dyslexia, genes, GWAS
%X "... Family studies of dyslexia suggest heritability up to 70% ...
   genome-wide assoc. study of 51,800 adults self-reporting a dyslexia diagnosis
   & 1,087,070 controls & identified 42 indep. genome-wide sig. loci: 15 in
   genes linked to cognitive ability/educational attainment, & 27 new &
   potentially more specific to dyslexia. ..."
   -- [<A HREF="https://doi.org/10.1038/s41588-022-01192-y">doi:10.1038/s41588-022-01192-y</A>]['22].

%A Zeming Lin
%A et al
%T Evolutionary-scale prediction of atomic level protein structure with a
   language model
%J bioRxiv
%M OCT
%D 2022
%O Science, 379(6637), pp.1123-1130, MAR 2023
%K TR, c2022, c202x, c20xx, zz1122, MolBio, protein structure, fold, prediction,
   LLM, NN, deep, META, metaAI, esmatlas, ESMFold, metagenomic, ESM, META
%X "... Leveraging the insight that language models learn evolutionary patterns
   across millions of seqs., we train models up to 15B params., the largest
   language model of proteins to date. As the language models are scaled they
   learn information that enables prediction of the 3D structure of a protein
   at the resolution of individual atoms. ... 60x faster ..."
   -- [<A HREF="https://www.biorxiv.org/content/10.1101/2022.07.20.500902v2">bioRxiv</A>]['22].
   Also see [<A HREF="https://esmatlas.com/">esmatlas</A>]['22] and
   comments [<A HREF="https://doi.org/10.1038/d41586-022-03539-1">doi:10.1038/d41586-022-03539-1</A>]['22].
   (?is no one bothered at 15B params?)
   [Science 379(6637) MAR 2023 [<A HREF="https://doi.org/10.1126/science.ade2574">doi:10.1126/science.ade2574</A>]['23].]
   [Also search for: protein structure prediction].

%A O. E. Wilson
%A et al
%T Image-based analyses from an online repository provide rich information on
   long-term changes in morphology and human perceptions of rhinos
%J People & Nature
%N OCT
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1122, rhino, horn, length, size,
   poaching, evolution
%X "... > 4000 rhino images, including both artistic portrayals (1481-2021) &
   photographs (taken between 1862-2021) ... Finally, we found evidence for
   declining horn length over time across species, perhaps related to selective
   pressure of hunting, & indicating a utility for image-based approaches in
   understanding societal perceptions of large vertebrates and trait evolution."
   -- [<A HREF="https://doi.org/10.1002/pan3.10406">doi:10.1002/pan3.10406</A>]['22].
   (I believe a similar phenomenon is observed with elephant tusks.)

%A E. A. Albornoz
%A et al ...
%A T. M. Woodruff
%T SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through
   spike protein
%J Molecular Psychiatry (2022
%M NOV
%D 2022
%K MolBio, jrnl, c022, c2021, c202x, c20xx, zz1122, SARSCoV2, covid 19, covid19,
   Parkinson's, symptoms, human health, UQ, UniQueensland
%X "... results support a possible mechanism of microglial innate immune
   activation by SARS-CoV-2, which could explain the increased vulnerability to
   developing neurological symptoms akin to Parkinson's disease in COVID-19
   infected individuals, and a potential therapeutic avenue for intervention."
   -- [<A HREF="https://doi.org/10.1038/s41380-022-01831-0">doi:10.1038/s41380-022-01831-0</A>]['22];
   also see the [<A HREF="https://www.abc.net.au/news/2022-11-01/qld-covid-parkinsons-disease-research-brain/101596180">ABC</A>]['1/11/2022].
   [Also search for: SARSCoV2 health].

%A M. Terao
%A et al
%T Turnover of mammal sex chromosomes in the Sry-deficient Amami spiny rat is
   due to male-specific upregulation of Sox9
%J PNAS
%V 119
%N 49
%P e2211574119
%M NOV
%D 2022
%K jrnl, PNAS, MolBio, c2022, c202x, c20xx, zz1122, mammal, Amami spiny rat,
   rodent, Tokudaia osimensi, sex, determining, male, female, chromosome,
   mammalian, Xchr, XO, Ychr loss, chrX, chrY, Sox9, SRY, genes, Enh14
%X "... We here report our discovery of a male-specific duplication of an
   enhancer of Sox9 in the Amami spiny rat Tokudaia osimensis, in which males &
   females have only a single X chr. (XO/XO) & the Y chr. & Sry are completely
   lost. ... Sex-related genomic differences were limited to a male-specific
   duplication of a 17-kb unit located 430 kb upstream of Sox9 on an autosome.
   Hi-C analysis using male spiny rat cells showed the duplicated region has
   potential chromatin interaction with Sox9. ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.2211574119">doi:10.1073/pnas.2211574119</A>]['22].

%A K. H. Kjaer
%A et al
%T A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA
%J Nature
%V 612
%P 283-291
%M DEC
%D 2022
%K jrnl, MolBio, c2022, c202x, c20xx, zz1222, ancient DNA, environmental, eDNA,
   mastodon, Greenland
%X "... we report an ancient environmental DNA (eDNA) record describing the rich
   plant & animal assemblages of the Kap Kobenhavn Formation in North Greenland,
   dated to around two million years ago. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-05453-y">doi:10.1038/s41586-022-05453-y</A>]['22].
   [Also search for: MolBio ancient DNA].
   (Also see later news [<A HREF="https://doi.org/10.1038/d41586-023-02242-z">www</A>]['23].)

%A D. V. Tikhonenkov
%A et al
%T Microbial predators form a new supergroup of eukaryote
%J Nature
%M DEC
%D 2022
%K MolBio, jrnl, c2022, c202x, c20xx, zz1222, evolution, eukaryote, microbes,
   microbe, tree, life, Provora, Nebulidia, Nibbleridia, 18S rRNA
%X "... Here we report ten previously undescribed strains of microbial predators
   isolated through culture that collectively form a diverse new supergroup of
   eukaryotes, termed Provora. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-05511-5">doi:10.1038/s41586-022-05511-5</A>]['22].
   (Also see [<A HREF="https://newatlas.com/biology/tree-of-life-new-branch-unique-predator-organisms/">www</A>]['22].)
   [Also search for: MolBio tree life].

%A W. Msemburi
%A et al
%T The WHO estimates of excess mortality associated with the COVID-19 pandemic
%J Nature
%M DEC
%D 2022
%K MolBio, jrnl, c2022, c202x, c20xx, zz1222, covid19, covid 19, human health,
   pandemic, death, deaths, WHO, stats, estimate
%X "... we report a comprehensive & consistent measurement of the impact of the
   COVID-19 pandemic by estimating excess deaths, by month, for 2020 & 2021. We
   predict the pandemic period all-cause deaths in locations lacking complete
   reported data using an overdispersed Poisson count framework that applies
   Bayesian inference techniques to quantify uncertainty. We estimate 14.83
   million excess deaths globally, 2.74 times more deaths than the 5.42 million
   reported as due to COVID-19 for the period. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-05522-2">doi:10.1038/s41586-022-05522-2</A>]['22].

%A Sunghwan Kim
%A et al
%T PubChem 2023 update
%J NAR
%V 51
%N D1
%P D1373-D1380
%M JAN
%D 2023
%K jrnl, NAR, MolBio, c2023, c202x, c20xx, zz1024, PubChem, chemical compound,
   molecule, library, similarity, similar, search, SMILES
%X "... In the past two years, a number of changes were made to PubChem. Data
   from more than 120 data sources was added ..."
   -- [<A HREF="https://doi.org/10.1093/nar/gkac956">doi:10.1093/nar/gkac956</A>]['24].
   Also see [<A HREF="https://pubchem.ncbi.nlm.nih.gov/">pubchem</A>]['24].

%A R. Lipsh-Sokolik
%A et al
%T Combinatorial assembly and design of enzymes
%J Science
%V379
%N 6628
%P 195-201
%M JAN
%D 2023
%K MolBio, jrnl, c2023, c202x, c20xx, zz0123, CADENZ, enzyme, protein, folding
%X "... We introduce an atomistic & machine learning strategy for the
   combinatorial assembly & design of enzymes (CADENZ) to design fragments that
   combine with one another to generate diverse, low-energy structures with
   stable catalytic constellations. We applied CADENZ to endoxylanases ... a
   10-fold improved hit rate & more than 10,000 recovered enzymes. This
   design-test-learn loop can be applied, in principle, to any modular protein
   family ..."
   -- 36634164@[<A HREF="https://pubmed.ncbi.nlm.nih.gov/36634164/">p'bmed</A>['23],
   [<A HREF="https://doi.org/10.1126/science.ade9434">doi:10.1126/science.ade9434</A>]['23].

%A A. Madani
%A et al
%T Large language models generate functional protein sequences across diverse
   families
%J Nat. Biotech.
%V ?
%M JAN
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0123, NN, ANN, proteins, drug, design,
   ProGen, anti bacteria
%X "... we describe ProGen, a language model that can generate protein seqs.
   with a predictable fn across large protein families, akin to generating
   grammatically & semantically correct natural language sentences on diverse
   topics. ... was trained on 280 million protein seqs. from > 19,000 families &
   is augmented with control tags specifying protein properties. ... Artificial
   proteins fine-tuned to five distinct lysozyme families showed similar
   catalytic efficiencies as natural lysozymes, with seq. identity to natural
   proteins as low as 31.4%. ..."
   --- [<A HREF="https://doi.org/10.1038/s41587-022-01618-2">doi:10.1038/s41587-022-01618-2</A>]['23].
   ("identity ... 31.4%.")

%A H. Guo
%A et al
%T SGLT2 inhibitor ameliorates endothelial dysfunction associated with the
   common ALDH2 alcohol flushing variant
%J Sci. Trans. Med.
%V 15
%N 680
%M JAN
%D 2023
%K MolBio, jrnl, c2023, c202x, c20xx, zz0123, aldehyde dehydrogenase 2, ALDH2,
   ALDH2*2, alcohol, human health, heart, risks
%X "... alcohol flushing variant known as ALDH2*2 affects ~8% of the world's
   pop'n. Even in heterozygous carriers, this missense variant leads to a severe
   loss of ALDH2 enzymatic activity & has been linked to an increased risk of
   coronary artery disease (CAD). ... our results suggest that ALDH2*2 induces
   EC dysfunction & that SGLT2i may potentially be used as a preventative
   measure against CAD for ALDH2*2 carriers."
   -- [<A HREF="https://doi.org/10.1126/scitranslmed.abp9952">doi:10.1126/scitranslmed.abp9952</A>]['23].
   [Also search for: dehydrogenase].

%A B. Magondu
%A et al
%T Drying dynamics of pellet feces
%J Soft Matter
%N 4
%M JAN
%D 2023
%K jrnl, c2023, c202x, c20xx, zz0223, wombat, poo, square, shape, animal,
   fecal, feces, faeces, faecal, droppings, square, cube, cubes, cubed
%X "... Understanding the factors that lead to fecal shape may provide a better
   understanding of animal health & diet. In this combined experimental &
   theoretical study, we test the hypothesis that pellet feces are formed by
   drying processes in the intestine. ... Across 22 species of mammals, we
   report a transition from cylindrical to pellet feces if fecal water content
   drops below 0.65. ..."
   -- [<A HREF="https://pubs.rsc.org/en/content/articlelanding/2023/SM/D2SM00359G#!divRelatedContent&articles">www</A>]['23].
   (Also see the [<A HREF="https://www.abc.net.au/news/2023-02-21/wombats-square-poo-research-how-consistent-cubes-made/102000530">abc</A>][21/11/2023].)
   [Also search for: wombat poo].

%A S. C. Larsson
%A et al
%T Appraisal of the causal effect of plasma caffeine on adiposity, type 2
   diabetes, and cardiovascular disease: two sample mendelian randomisation
   study
%J BMJ
%M MAR
%D 2023
%K jrnl, BMJ, c2023, c202x, c20xx, zz0323, zzCoffee, coffee consumption,
   caffein, positive, type2, diabetes, heart, cardiac, BMI, CYP1A2, AHR,
   human health
%X "... Results Higher genetically predicted plasma caffeine concentrations were
   assoc. with lower body mass index ... Conclusions Higher plasma caffeine
   concentrations might reduce adiposity and risk of type 2 diabetes. ..."
   "... In a dose-response meta-analysis, the risk of type 2 d. decreased by 7%
   for each cup per day increase of caffeinated coffee (an avg cup contains ~
   70-150 mg c.) & by 6% for each cup per day increase of decaf. coffee. ..."
   --- [<A HREF="https://doi.org/10.1136/bmjmed-2022-000335">doi:10.1136/bmjmed-2022-000335</A>]['23].
   [Also search for: zzCoffee].

%A D. Sumanaweera
%A et al
%T Gene-level alignment of single cell trajectories informs the progression of
   in vitro T cell differentiation
%J bioRxiv
%M MAR
%D 2023
%O Nature Methods, SEP 2024,
   [<A HREF="https://doi.org/10.1038/s41592-024-02378-4">doi:10.1038/s41592-024-02378-4</A>]['24]
%K TR, MolBio, Biol, c2023, c202x, c20xx, zz0323, zz1024, Dinithi, single cell,
   trajectory, alignment, dynamic time warp, DTW, warping, Genes2Genes, G2G,
   T cell, cells, Tcell, scRNAseq, Teichmann, lab, cellAlign
%X "...  we describe Genes2Genes, a Bayesian info.-theoretic DP framework for
   aligning single-cell trajectories ... Across both real life & simulated
   datasets, Genes2Genes accurately captured different alignment patterns, &
   revealed that T cells differentiated in vitro matched to an immature in vivo
   state while lacking the final TNFalpha signaling ..."
   -- [<A HREF="https://doi.org/10.1101/2023.03.08.531713">doi:10.1101/2023.03.08.531713</A>]['23] bioRxiv.
   [Also search for: scRNAseq] & [also search for: trajectory alignment].

%A M. Winding
%A et al ...
%A M. Zlatic
%T The connectome of an insect brain
%J Science
%V 379
%N 6636
%P ?-?
%M MAR
%D 2023, MolBio, c2023, c202x, c20xx, zz0323, animal, insect, fly, Drosophila,
   larva, brain, connectome, network, connections, synapse, synapses
%X "... (Drosophila larva) with rich behavior, inc. learning, value computation,
   & action selection, comprising 3016 neurons & 548,000 synapses. ..."
   -- [<A HREF="https://pubmed.ncbi.nlm.nih.gov/36893230/">p'bm'd</A>]['23],
      [<A HREF="https://doi.org/10.1126/science.add9330">doi:10.1126/science.add9330</A>]['23].
   (Also see connectome@[<A HREF="https://en.wikipedia.org/wiki/Connectome">wikip</A>].)
   [Also search for: MolBio connectome].

%A J. R. Wold
%A et al
%T The promise and challenges of characterizing genome-wide structural
   variants: A case study in a critically endangered parrot
%J Molec. Ecol. Res.
%P ?-?
%M MAR
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0923, animal, bird, parrot, kakapo, NZ,
   Strigops habroptilus, genome, species, variant
%X "... Here, we explore a near whole-species resequence data set, & long-read
   seq. data for a subset of highly represented individuals in the critically
   endangered kakapo (Strigops habroptilus). ..."
   -- [<A HREF="https://doi.org/10.1111/1755-0998.13783">doi:10.1111/1755-0998.13783</A>]['23].

%A D. Lewis
%A et al
%T COVID-origins data from Wuhan market published: What scientists think
%J Nature
%V 616
%P 225-226
%M APR
%D 2023
%K news, views, MolBio, c2023, c202x, c20xx, zz0423, virus, covid 19, covid19,
   SARS CoV 2, SARSCoV2, SARS2, origin, pandemic, Wuhan, China, animal, host
%X "First peer-reviewed analysis of the Chinese swabs confirms animal DNA was
   present in samples that tested positive for SARS-CoV-2. ..." [3 refs].
   -- [<A HREF="https://doi.org/10.1038/d41586-023-00998-y">doi:10.1038/d41586-023-00998-y</A>]['23].
   [Also search for: SARSCoV2 origins].

%A S. Rajapaksa
%A A. S. Konagurthu
%A A. M. Lesk
%T Sequence and structure alignments in post-AlphaFold era
%J Current Opinion in Structural Biol.
%V 79
%N #102539
%M APR
%D 2023
%K MolBio, jrnl, c2023, c202x, c20xx, zz0223, protein, structure, structural,
   3D, alignment, ArunK, AMLesk
%X "... we suggest that when aligning homologous proteins, lacking experimental
   structures, better results can be obtained by a structural alignment of
   predicted structs. than by an alignment based only on amino-acid seqs.. We
   present a quantitative eval'n, based on pairwise alignments of seqs. &
   structures (both predicted & experimental) to support this hypothesis."
   -- [<A HREF="https://doi.org/10.1016/j.sbi.2023.102539">doi:10.1016/j.sbi.2023.102539</A>]['23].
   [Also search for: MolBio protein structural alignment].

%A I. D. Lutz
%A et al
%T Top-down design of protein architectures with reinforcement learning
%J Science
%V 380
%N 6642
%P 266-273
%M APR
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0423, protein design, silico
%X "... the subunits of naturally occurring protein assemblies often fit
   together with substantial shape complementarity to generate architectures
   optimal for fn in a manner not achievable by current design approaches. We
   describe a 'top-down' reinforcement learning-based design approach that
   solves this problem using Monte Carlo tree search to sample protein
   conformers in the context of an overall architecture & specified functional
   constraints. Cryo-electron microscopy structures of the designed disk-shaped
   nanopores & ultracompact icosahedra are v.close to the comp. models. ..."
   -- [<A HREF="https://doi.org/10.1126/science.adf6591">doi:10.1126/science.adf6591</A>]['23].
   [Also search for: MolBio protein design].

%A L. Kruglyak
%A et al
%T Insufficient evidence for non-neutrality of synonymous mutations
%J Nature
%V 616
%P E8-E9
%M APR
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0423, silent, mutation, codon, codons,
   Shen, yeast, non neutral, nonNeutral, doubt
%X ... arising from, Shen et al 2022, 'Synonymous mutations in
   representative yeast genes are mostly strongly non-neutral' ...
   -- [<A HREF="https://doi.org/10.1038/s41586-023-05865-4">doi:10.1038/s41586-023-05865-4</A>]['23].

%A N. Foley
%A et al
%T A genomic timescale for placental mammal evolution
%J Nature
%V 380
%N 6643
%P ?-?
%M APR
%D 2023
%M APR
%D 2023
%K jrnl, c2023, c202x, c20xx, zz0523, MolBio, phylogenetic, tree, life,
   phylogeny, animal, placental, mammal, Cretaceous K-Pg, KPg, evolution
%X "... We provide a comprehensive phylogenetic analysis of genetic variation
   across an alignment of 241 placental mammal genome assemblies ... Genomic
   time trees reveal an accumulation of cladogenic events before & immediately
   after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for
   Cretaceous continental vicariance & the K-Pg extinction in the placental
   radiation."
   -- [<A HREF="https://doi.org/10.1126/science.abl8189">doi:10.1126/science.abl818</A>]['23].
   [Also search for: MolBio tree life].

%A S. Adee
%T We Are Electric: The New Science of Our Body's Electrome
%I CanongateTrade
%M APR
%D 2023
%K book, text, c2023, c202x, c20xx, zz0723, cell, cellular, electrical,
   electrome, bioelectricity, biol, biology
%X 1st ed 2023; hb us$37; uk us isbn:1838853324; uk us isbn13:978-1838853327.
   "... discover your body's electrome. Every cell in our bodies - bones, skin,
   nerves, muscle - has a voltage, like a tiny battery. ..."

%A J. R. Xue
%A et al ...
%A S. K. Reilly
%T The functional and evolutionary impacts of human-specific deletions in
   conserved elements
%J Science
%V 380
%N 6643
%P ?-?
%M APR
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz1223, animal, ape, primate, chimp,
   human, hCONDELs, hCONDEL, PPP2CA, LOXL2, deletion, Capellini
%X "... identified & characterized 10,032 human-specific conserved deletions
   (hCONDELs). These short (avg. 2.56 bp) deletions are enriched for human brain
   functions across genetic, epigenomic, & transcriptomic datasets. Using
   massively parallel reporter assays in six cell types, we discovered 800
   hCONDELs conferring sig. differences in regulatory activity, half of which
   enhance rather than disrupt regulatory fn. We highlight several hCONDELs with
   putative human-specific effects on brain development, inc. HDAC5, CPEB4, &
   PPP2CA. Reverting an hCONDEL to the ancestral seq. alters the expression of
   LOXL2 & developmental genes involved in myelination & synaptic fn. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abn2253">doi:10.1126/science.abn2253</A>]['23].
   [Also search for: MolBio human evolution genes].
   (Also see [<A HREF="https://www.bbc.com/future/article/20231122-the-genes-that-made-us-truly-human-may-also-make-us-ill">bbc</A>][23/11/2023], and
   Capellini@[<A HREF="https://scholar.google.ca/citations?user=eWKKbKAAAAAJ&hl=en">sch'lar</A>]['23].)

%A P. Gainza
%A et al
%T De novo design of protein interactions with learned surface fingerprints
%J Nature
%V 617
%P 176-184
%M MAY
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0523, protein interaction, surface, ANN,
   proteins, binding site
%X "... we use a geometric deep-learning framework operating on protein surfaces
   that generates fingerprints to describe geometric & chem. features that are
   critical to drive protein-protein interactions ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-023-05993-x">doi:10.1038/s41586-023-05993-x</A>]['23].
   [Also search for: MolBio protein interaction].

%A Z. Zhang
%A et al
%T Increased hyaluronan by naked mole-rat HAS2 extends lifespan in mice
%J bioRxiv
%M MAY
%D 2023
%K TR, c2023, c202x, c20xx, zz0623, MolBio, naked mole rat, longevity, HAS2,
   hyaluronic acid, HMW-HA, HMWHA, lifespan, ageing, aging
%X "Abundant high molecular weight hyaluronic acid (HMW-HA) contributes to
   cancer resistance and possibly longevity of the longest-lived rodent, the
   naked mole-rat ..."
   -- [<A HREF="https://doi.org/10.1101/2023.05.04.539405">bioRxiv</A>]['23].
   [Also search for: MolBio HAS2].

%A A. P. Ragsdale
%A et al
%T A weakly structured stem for human origins in Africa
%J Nature
%V 617
%P 755-763
%M MAY
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0623, modern human, phylogenetic tree,
   Homo sapiens, origin, evolutionary, Africa
%X "... We infer a reticulated African population history in which present-day
   population structure dates back to Marine Isotope Stage 5. The earliest
   population divergence among contemporary populations occurred 120,000 to
   135,000 years ago and was preceded by links between two or more weakly
   differentiated ancestral Homo populations connected by gene flow over
   hundreds of thousands of years. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-023-06055-y">doi:10.1038/s41586-023-06055-y</A>]['23].
   [Also search for: MolBio human evolution].

%A M. Leslie
%T Can 'toxic' bilirubin treat a variety of illnesses?
%J Science
%M JUN
%D 2023
%K news,views, c2023, c202x, c20xx, zz0623, human, health, bilirubin, Bilix,
   antioxidant
%X "New view of molecule's good side has inspired South Korean company to plan
   testing a synthetic version in people ..."
   -- [<A HREF="https://doi.org/10.1126/science.adj1440">doi:10.1126/science.adj1440</A>]['23].

%A L. F. K. Kuderna
%A et al
%T A global catalog of whole-genome diversity from 233 primate species
%J Science
%V 380
%N 6648
%M JUN
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0623, evolution, primates, tree,
   phylogeny, phylogenetic, species, apes, monkeys
%X "... present high-coverage whole-genome data from 233 primate species rep.
   86% of genera & all 16 families. This dataset was used, together with fossil
   calibration, to create a nuclear DNA phylogeny & to reassess evolutionary
   divergence times among primate clades. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abn7829">doi:10.1126/science.abn7829</A>]['23].
   [Also search for: primates tree MolBio].

%A S.A. Castner
%A et al
%T Longevity factor klotho enhances cognition in aged nonhuman primates
%J NatureAging
%V ?
%M JUL
%D 2023
%K jrnl, c2023, c202x, c20xx, zz0723, anti aging, ageing, Klotho, memory loss,
   primates, trial, health, lifespan, longevity
%X "... We validated the rhesus form of the klotho protein in mice showing it
   increased synaptic plasticity and cognition. We then found that a single
   administration of low-dose, but not high-dose, klotho enhanced memory in aged
   nonhuman primates. ..."
   -- [<A HREF="https://doi.org/10.1038/s43587-023-00441-x">doi:10.1038/s43587-023-00441-x</A>]['23],
   and comment@[<A HREF="https://doi.org/10.1038/d41586-023-02214-3">doi:10.1038/d41586-023-02214-3</A>]['23].
   [Also search for: aging klotho].

%A V. Lammi
%A et al
%T Genome-wide association study of long COVID
%J medRxiv
%M JUL
%D 2023
%K TR, c2023, c202x, c20xx, zz0723, human health, long covid 19, covid19, GWAS,
   FOXP4, gene
%X "... perform a genome-wide association study for Long COVID inc. up to 6,450
   Long COVID cases & 1,093,995 population controls from 24 studies across 16
   countries. We identified the first genome-wide sig. assoc. for Long COVID at
   the FOXP4 locus. ..."
   -- medRxiv [<A HREF="https://doi.org/10.1101/2023.06.29.23292056">doi:10.1101/2023.06.29.23292056</A>]['23].

%A P. P. Madupe
%A et al
%T Enamel proteins reveal biological sex and genetic variability within
   southern African Paranthropus
%J bioRxiv
%M JUL
%D 2023
%K TR, MolBio, c2023, c202x, c20xx, zz0723, ancient, human, protein, enamel,
   hominim, Paranthropus robustus, SAfrica, AMELY
%X "... we report the mass spectrometric (MS) sequencing of enamel proteomes
   from four ca. 2 million year (Ma) old dental specimens attributed
   morphologically to P. robustus, from the site of Swartkrans ..."
   -- bioRxiv [<A HREF="https://doi.org/10.1101/2023.07.03.547326">doi:10.1101/2023.07.03.547326</A>]['23].
   (Also see comment [<A HREF="https://doi.org/10.1038/d41586-023-02242-z">www</A>]['23].)

%A Liang Liang
%A et al
%T Complementary Alu sequences mediate enhancer-promoter selectivity
%J Nature
%V 619
%P 868-875
%M JUL
%D 2023
%K MolBio, c2023, c202x, c20xx, zz0723, ALU, DNA, sequence, gene, promoter
%X "... discover that 37.9% of the enhancer-promoter RNA interaction sites are
   overlapped with Alu seqs.. ... Knockout of Alu elts compromises
   enhancer-promoter looping ... Mapping 535,404 noncoding risk variants back to
   the enhancer-promoter RNA interaction maps enabled us to construct
   variant-to-fn maps for interpreting their molecular fns, inc. 15,318
   deletions or insertions in 11,677 Alu elts that affect 6,497 protein-coding
   genes. ... demonstrate that polymorphic Alu insertion at the PTK2 enhancer
   can promote tumorigenesis. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-023-06323-x">doi:10.1038/s41586-023-06323-x</A>]['23].
   [Also search for: MolBio ALU].

%A J. J. Edwards
%A et al
%T Exercise training and resting blood pressure: a large-scale pairwise and
   network meta-analysis of randomised controlled trials
%J British J. of Sports Med.
%M JUL
%D 2023
%K jrnl, c2023, c202x, c20xx, zz0723, human health, isometric, study, stats,
   trial, aerobic, exercise, systolic, SBP, diastolic, DBP, blood pressure,
   wall squat, plank
%X "... 70 randomised controlled trials were ultimately inc. in the final
   analysis, with a pooled sample size of 15,827 participants ... sig. redns in
   resting SBP & DBP ... & isometric exercise training (-8.24/-4.00mm Hg,
   p < 0.001). ..."
   -- [<A HREF="https://doi.org/10.1136/bjsports-2022-106503">doi:10.1136/bjsports-2022-106503</A>]['23].
   Also see the [<A HREF="https://www.bbc.com/news/health-66303982">bbc</A>][26/7/2023].

%A A. Rhie
%A et al
%T The complete sequence of a human Y chromosome
%J bioRxiv
%M JUL
%D 2023
%K TR, MolBio, c2023, c202x, c20xx, zz0923, human, nGenome, genome,
   Y chromosome, Ychr, chrY
%X "... complex repeat structure including long palindromes, tandem repeats, &
   segmental duplications ... Here, the Telomere-to-Telomere (T2T) consortium
   presents the complete 62,460,029 base pair sequence of a human Y chromosome
   from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y ..."
   -- [<A HREF="https://www.biorxiv.org/content/10.1101/2022.12.01.518724v2">bioRxiv</A>]['23].
   [Also search for: MolBio human Ychr].

%A A. Haghani
%A et al
%T DNA methylation networks underlying mammalian traits
%J Science
%V 381
%N 6658
%M AUG
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0823, DNA methylation, animal, mammal,
   mammals, human, HOXL, longevity, lifespan, evolution, phylogenetic,
   phyloepigenetic tree, trait, trees
%X "Using DNA methylation profiles (n=15,456) from 348 mammalian species, we
   constructed phyloepigenetic trees ... identified 55 distinct cytosine
   modules, of which 30 are related to traits such as max. life span, adult
   weight, age, sex, & human mortality risk. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abq5693">doi:10.1126/science.abq5693</A>]['23].

%A O. Geiger
%A et al
%T Multiple approaches of cellular metabolism define the bacterial ancestry of
   mitochondria
%J SciAdv.
%M AUG
%D 2023
%K jrnl, MolBio, 2023, c202x, c20xx, zz0823, origin, origins, mitochondria,
   eukaryote, eukaryotes, sphingolipids, cardiolipin
%X "... we use multiple approaches to define the most likely living relatives of
   the ancestral bacteria from which m. originated. These bacteria live in
   marine environments & exhibit the highest frequency of aerobic traits &
   genes for the metabolism of fundamental lipids that are present in the
   membranes of eukaryotes, sphingolipids, and cardiolipin."
   -- [<A HREF="https://doi.org/10.1126/sciadv.adh0066">doi:10.1126/sciadv.adh0066</A>]['23],
   also see O.G@[<A HREF="https://www.ccg.unam.mx/en/otto-geiger/">unam.mx</A>]['23].
   [Also search for: MolBio eukaryote mitochondria origin].

%A A. B. Schroer
%A et al
%T Platelet factors attenuate inflammation and rescue cognition in ageing
%K Nature
%M AUG
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0823, mental, brain, anti ageing, aging,
   young, antiaging, antiageing, blood, platelets, cognition, hippocampus,
   PF4, CXCL4, CXCR3, mouse
%X "... we show that platelet factors transfer the benefits of young blood to
   the ageing brain. Systemic exposure of aged male mice to a fraction of blood
   plasma from young mice containing platelets decreased neuroinflammation in
   the hippocampus at the transcriptional & cellular level & ameliorated
   hippocampal-dependent cognitive impairments ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-023-06436-3">doi:10.1038/s41586-023-06436-3</A>]['23].
   [Also search for: young blood ageing].

%A Wangjie Hu
%A et al
%T Genomic inference of a severe human bottleneck during the Early to
   Middle Pleistocene transition
%J Science
%V 381
%N 6661
%P ?-?
%M AUG
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0923, human, evolution, origins,
   population, bottleneck, Pleistocene
%X "... calculated the composite likelihood for present-day human genomic
   seqs. of 3154 individuals. Results showed that human ancestors went through
   a severe pop'n bottleneck with about 1280 breeding individuals between
   around 930,000 & 813,000 y. ago. [It] lasted for about 117,000 years &
   brought human ancestors close to extinction. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abq7487">doi:10.1126/science.abq7487</A>]['23].
   [Also search for: human Pleistocene]  and  [also search for: human origins].

%A I. Barrio-Hernandez
%A et al
%T Clustering-predicted structures at the scale of the known protein universe
%J Nature
%M SEP
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0923, protein, 3D, structure,
   clustering, classification, Foldseek
%X "... over 214 million predicted structures are available in the AlphaFold
   database ... we have clustered all of the structures in the AlphaFold DB,
   identifying 2.30 million non-singleton structural clusters, of which 31% lack
   annotations representing probable previously undescribed structures. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-023-06510-w">doi:10.1038/s41586-023-06510-w</A>]['23].
   [Also search for: protein predicted structure classification].

%A J. Durairaj
%A et al
%T Uncovering new families and folds in the natural protein universe
%J Nature
%M SEP
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz0923, protein, 3D, predicted, structure,
   clustering, classification, AFDB90, AFDB90v4
%X "... we examine the extent to which the AlphaFold database DB structurally
   illuminated this 'dark matter' of the natural protein universe at high
   predicted accuracy. We further describe the protein diversity that these
   models cover as an annotated interactive seq. similarity network, accessible
   at https://uniprot3d.org/atlas/AFDB90v4. By searching for novelties from
   seq., structure, & semantic perspectives, we uncovered the beta-flower fold,
   added multiple protein families to Pfam database ..."
   [Also search for: protein predicted structure classification].

%A A. Sharma
%A et al ...
%A L. Cronin
%T Assembly theory explains and quantifies selection and evolution
%J Nature
%V 622
%N 7982
%P 321-328
%M OCT
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz1023, AssemblyTheory, AssemblyIndex,
   components, life, chemical, controversial?
%X "... assembly theory (AT) as a framework that does not alter the laws of
   physics, but redefines the concept of an 'object' on which these laws act.
   AT conceptualizes objects not as point particles, but as entities defined by
   their possible formation histories. ... discloses a new aspect of physics
   emerging at the chemical scale, whereby history & causal contingency
   influence what exists."
   -- [<A HREF="https://doi.org/10.1038/s41586-023-06600-9">doi:10.1038/s41586-023-06600-9</A>]['23].
   (Also see AT@[<A HREF="https://en.wikipedia.org/wiki/Assembly_theory">wikip</A>]['23].)
   [Also search for: AssemblyTheory] & [also search for: AssemblyIndex].

%A M. L. Boby
%A et al
%T Open science discovery of potent noncovalent SARS-CoV-2 main protease
   inhibitors
%J Nature
%V 382
%N 6671
%M NOV
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz1123, covid-19, SARS-CoV-2, SARSCoV2,
   SARS2, virus, protease inhibitor, ensitrelvir, openScience
%X "...  we report the results of the COVID Moonshot - a fully open science,
   crowdsourced, & structure-enabled drug discovery campaign ... > 18,000
   compound designs, > 2400 synthesized compounds, > 490 ligand-bound x-ray
   structures, > 22,000 alchemical free-energy calculations, and > 10,000
   biochemical measurements - all of which were made publicly available in real
   time. The recently approved antiviral ensitrelvir was identified in part
   based on crystallographic data from the COVID Moonshot Consortium. ..."
   -- [<A HREF="https://doi.org/10.1126/science.abo7201">doi:10.1126/science.abo7201</A>]['23].

%A L. Samuni
%A M. Surbeck
%T Cooperation across social borders in bonobos
%J Science
%V 382
%N 6672
%P 805-809
%M NOV
%D 2023
%K jrnl, c2023, c202x, c20xx, zz1123, animal behaviour, primate, chimpanzee,
   chimp, bonobo, Pan paniscus, social, ingroup, outgroup, cooperation
%X "... We show that, as in humans, +ve assortment supports bonobo cooperation
   across borders. B. cooperative attitudes toward in-group members informed
   their cooperative relationships with out-groups, in particular, forming
   connections with out-group individuals who also exhibited high cooperation
   tendencies. ..."
   -- [<A HREF="https://doi.org/10.1126/science.adg0844">doi:10.1126/science.adg0844</A>]['23].

%A A. Papkou
%A et al
%T A rugged yet easily navigable fitness landscape
%J Science
%V 382
%N 6673
%M NOV
%D 2023
%K jrnl, MolBio, Biol, c2023, c202x, c20xx, zz1123, dihydrofolate reductase,
   evolution, adaption, genetic algorithm, fitness, landscape
%X "Fitness landscape theory predicts that rugged landscapes with multiple peaks
   impair Darwinian evol., but experimental evidence is limited. ... we used
   genome editing to map the fitness of >260,000 genotypes of the key metabolic
   enzyme dihydrofolate reductase in the presence of the antibiotic trimethoprim
   which targets this enzyme. ... landscape is highly rugged & harbors 514
   fitness peaks. However, its highest peaks are accessible to evolving popn via
   abundant fitness-increasing paths. Different peaks share large basins of
   attraction that render the outcome of adaptive evolution highly contingent on
   chance events. Our work shows that ruggedness need not be an obstacle to D.
   evoln but can reduce its predictability. If true in general, the complexity
   of optimization problems on realistic landscapes may require reappraisal."
   -- [<A HREF="https://doi.org/10.1126/science.adh3860">doi:10.1126/science.adh3860</A>]['23].
   [Also search for: genetic algorithm landscape].

%A J. B. Ingraham
%A et al
%T Illuminating protein space with a programmable generative model
%J Science
%V 623
%P 1070-1078
%M NOV
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz1223, Chroma, protein, structure, deep,
   ANN
%X "... introduce Chroma, a generative model for proteins & protein complexes
   that can directly sample novel protein structures & seqs., & that can be
   conditioned to steer the generative process towards desired properties &
   functions. ... predicted inter-residue geometries & a general low-temp.
   sampling alg. for diffusion models. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-023-06728-8">doi:10.1038/s41586-023-06728-8</A>]['23].
   [Also search for: MolBio protein deep ANN].

%A Sandun Rajapaksa
%T Statistical and Information-Theoretic Exploration of Amino Acid Sequence
   Relationships with Higher-Order Levels of Protein Description
%I Monash University
%K PhD thesis, c2023, c202x, c20xx, zz0124, MolBio, protein structure, model,
   MML, Monash, MonashUni
%M NOV
%D 2023
%X "Understanding the relationship of amino acid seqs., their divergence in
   evolution & their patterns of conservation across varying structural levels
   (secondary, super-secondary & tertiary structures of proteins) provide useful
   clues about how protein shapes come about, how they function & how they
   evolve, with the potential to inform new directions in protein studies. This
   thesis is the culmination of a set of formal statistical & information
   theoretic explorations that aim to increase our understanding of the specific
   relationships & constraints imposed by the amino acid seq. of proteins when
   compared to their higher-order structures."
   -- [<A HREF="https://doi.org/10.26180/24549793.v1">doi:10.26180/24549793.v1</A>]['24].
   [Also search for: MolBio protein structure].

%A E. Calloway
%T World's biggest set of human genome sequences opens to scientists
%J Nature
%V 624
%P 16-17
%M NOV
%D 2023
%K news, views, MolBio, c2023, c202x, c20xx, zz1223, BioBank, human, genomics,
   many, genomes, health, data, UK
%X "The world's largest collection of full human genomes has just gone live. The
   UK Biobank - a repository of health, genomic & other biol. data - today
   released complete genome seqs. from every one of the 500,000 British
   volunteers in the DB. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-023-03763-3">doi:10.1038/d41586-023-03763-3</A>]['23].
   Also see, "Whole genome assoc. testing in 333,100 individuals across three
   biobanks identifies rare non-coding single variant & genomic aggregate
   associations with height"
   -- [<A HREF="https://doi.org/10.1101/2023.11.19.566520">doi:10.1101/2023.11.19.566520</A>][20/11/2023] at bioRxiv.

%A E. Long
%A Jianzhi Zhang
%T Evidence for the role of selection for reproductively advantageous alleles
   in human aging
%J SciAdv
%V 9
%N 49
%P ?-?
%M DEC
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz1223, human health, lifespan, ageing,
   children, PGS, UK biobank, antagonistic pleiotropy
%X "... 276,406 U.K. Biobank participants. We observe a strong, negative genetic
   correl'n between reproductive traits & life span. Individuals with higher
   polygenetic scores for reproduction (PGSR) have lower survivorships to age 76
   (SV76), & PGSR increased over birth cohorts from 1940 to 1969. Similar trends
   are seen from individual genetic variants examined. The antagonistically
   pleiotropic variants are often assoc. with cis-regulatory effects across
   multiple tissues or on multiple target genes. ..."
   -- [<A HREF="https://doi.org/10.1126/sciadv.adh4990">10.1126/sciadv.adh4990</A>]['23].
   (Ant.Pl.: 1957, Williams proposed that mutns contributing to aging could be
   +vely sel. if they are advantageous early in life, promoting earlier
   reproduction or more offspring. ...)

%A F. Wong
%A et al ...
%A J. C. Collins
%T Discovery of a structural class of antibiotics with explainable deep learning
%J Nature
%M DEC
%D 2023
%K jrnl, MolBio, c2023, c202x, c20xx, zz1223, drug, discovery, AI, antibiotic
%X "... Here we reasoned that the chemical substructures associated with
   antibiotic activity learned by NN models can be identified & used to predict
   structural classes of antibiotics. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-023-06887-8">doi:10.1038/s41586-023-06887-8</A>]['23].
   [Also search for: MolBio drug discovery].

%A M. E. Allentoft
%A et al
%T Population genomics of post-glacial western Eurasia
%J Nature
%V 625
%P 301-311
%M JAN
%D 2024
%K jrnl, MolBio, c2024, c202x, c20xx, zz0124, genomes, human, evolution,
   ancient DNA, Europe, Asia, Mesolithic, Neolithic, Holocene, Yamnaya
%X "we shotgun-sequenced 317 genomes-mainly from the Mesolithic & Neolithic
   periods - from across N & W Eurasia. These were imputed alongside published
   data to obtain diploid genotypes from more than 1,600 ancient humans. ...
   The genetic origin & fate of the Yamnaya have remained elusive, but we show
   that hunter-gatherers from the Middle Don region contributed ancestry to
   them ... "
   -- [<A HREF="https://doi.org/10.1038/s41586-023-06865-0">doi:10.1038/s41586-023-06865-0</A>]['24].
   [Also search for: ancient DNA human].

%A C.M. Hults
%A et al
%T Still little evidence sex differences in spatial navigation are evolutionary
   adaptations
%J OpenScience
%I Royal Soc.
%M JAN
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0124, navigation, sense of direction, male,
   female, men, women, differences, human, animal, behaviour
%X "A putative male advantage in wayfinding ability is the most widely
   documented sex difference in human cognition & has also been observed in
   other animals. ... Consistent with the prev. result, we found little evidence
   that sex diffs. in spatial navigation & home range size are related. We
   conclude that sex diffs. in spatial ability are more likely due to
   experiential factors &/or unselected biological side effects, rather than
   functional outcomes of natural selection."
   -- [<A HREF="https://doi.org/10.1098/rsos.231532">doi:10.1098/rsos.231532</A>]['24].

%A P. T. Mee
%A et al
%T Mosquitoes provide a transmission route between possums and humans for
   Buruli ulcer in southeastern Australia
%J NatureMicrobiology
%M JAN
%D 2024
%K jrnl, MolBio, c2024, c202x, c20xx, zz0124, human health, risk, risks,
   possum, mosquito, Mycobacterium ulcerans, Buruli ulcers, Aedes notoscriptus
%X "... Bacterial genomic analysis confirmed shared single-nucl.-polymorphism
   profiles for M.ulcerans detected in mosquitoes, possum excreta & humans.
   These findings indicate Ae. notoscriptus probably transmit M.ulcerans in
   SE Australia & highlight m. control as a Buruli ulcer prevention measure."
   -- [<A HREF="https://doi.org/10.1038/s41564-023-01553-1">doi:10.1038/s41564-023-01553-1</A>]['24].
   Also see the [<A HREF="https://www.abc.net.au/news/2024-01-24/buruli-ulcer-possum-mosquito-human-link-research/103383064">abc</A>][24/1/2024</A>].

%A Min Deng
%A Jinhan Yu
%A D. G. Blackmond
%T Symmetry breaking and chiral amplification in prebiotic ligation reactions
%J Nature
%V 626
%P 1019-1024
%M FEB
%D 2024
%K jrnl, MolBio, c2024, c202x, c20xx, zz0324, DNA, protein, chiral, chirality,
   handedness, left, levo, dextro, life, evolution
%X "... Here, in studying a new prebiotically plausible route to proteinogenic
   peptides, we discovered that the reaction favours heterochiral ligation (that
   is, the ligation of l monomers with d monomers). Although this finding seems
   problematic for the prebiotic emergence of homochiral l-peptides, we
   demo., paradoxically, that this heterochiral preference provides a mechanism
   for enantioenrichment in homochiral chains. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07059-y">doi:10.1038/s41586-024-07059-y</A>]['24].
   (Also see [<A HREF="https://doi.org/10.1126/science.z7lwj33">doi:10.1126/science.z7lwj33</A>]['24].)

%A T. Matreux
%A et al
%T Heat flows enrich prebiotic building blocks and enhance their reactivity
%J Nature
%V 628
%P 110-116
%M APR
%D 2024
%K jrnl, MolBio, c2024, c202x, c20xx, zz0424, early, life, origins, biopolymer
%X "The emergence of biopolymer building blocks is a crucial step during the
   origins of life ... Here we show that heat flows through thin, crack-like
   geo-compartments could have provided a widely available yet selective
   mechanism that separates more than 50 prebiotically relevant building blocks
   from complex mixtures of amino acids, nucleobases, nucleotides,
   polyphosphates & 2-aminoazoles. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07193-7">doi:10.1038/s41586-024-07193-7</A>]['23].

%A K. Dudnyk
%A et al
%T Sequence basis of transcription initiation in the human genome
%J Science
%V 384
%N 6694
%M APR
%D 2024
%K MolBio, jrnl, c2024, c202x, c20xx, zz0424, DNA, transcription site, promoter,
   gene
%X "...We identify key seq. patterns that contribute to human promoter activity,
   each activating transcription with distinct position-specific effects. [&]
   we explain the seq. basis of bidirectional transcription at promoters,
   identify the links between promoter seq. & gene expression variation across
   cell types, & explore the conservation of seq. determinants of transcription
   initiation across mammalian species."
   -- [<A HREF="https://doi.org/10.1126/science.adj0116">doi:10.1126/science.adj0116</A>]['24].

%A C. Borrles
%A A. Koenig
%T Female-biased birth sex ratio in a female dispersal primate suggests local
   resource competition
%J Biol. Lett.
%M MAY
%D 2024
%K biology, MolBio, jrnl,  c2024, c202x, c20xx, zz0624, biased sex ratio,
   Phayre's leaf monkey, primate, animal, dispersal, gender, female
%X "... local resource competition (LRC) which can be reduced if the birth sex
   ratio (BSR) is biased towards members of the dispersing sex ..."
   -- [<A HREF="https://doi.org/10.1098/rsbl.2024.0002">doi:10.1098/rsbl.2024.0002</A>]['24].
   [Also search for: biology sex ratio].

%A P. Fernandez
%A et al
%T A 160 Gbp fork fern genome shatters size record for eukaryotes
%J iScience
%M MAY
%D 2024
%K jrnl, eJrnl, c2024, c202x, c20xx, zz0624, MolBio, biology, eukaryote, plant,
   fern, Tmesipteris oblanceolata, huge, genome, DNA
%X "... we report the discovery of an even larger eukaryotic genome in
   Tmesipteris oblanceolata, a New Caledonian fork fern. At 160.45 Gbp/1C, this
   record-breaking genome challenges current understanding and opens new avenues
   to explore the evolutionary dynamics of genomic gigantism."
   -- [<A HREF="https://doi.org/10.1016/j.isci.2024.109889">doi:10.1016/j.isci.2024.109889</A>]['24].

%A M. Karasikov
%A et al
%T Indexing all life's known biological sequences
%J bioRxiv
%M MAY
%D 2024
%K MolBio, TR, c2024, c202x, c20xx, zz0624, index, DNA, protein, sequence,
   search
%X "... We make Petabases of DNA seqs across all clades of life, inc. viruses,
   bacteria, fungi, plants, animals, & humans, fully searchable & make the
   indexes available to the res.community. The indexes are a highly compressed
   rep'ns of the input seqs (up to 5800x) & fit on a single consumer hard drive
   (~100 USD). We present the underlying methodological f/wk, called MetaGraph,
   that allows us to scalably index very large sets of DNA or protein seqs
   using annotated De Bruijn graphs. ..."
   -- [<A HREF="https://www.biorxiv.org/content/10.1101/2020.10.01.322164v3">doi:10.1101/2020.10.01.322164v3</A>]['24].

%A S. Ocklenburg
%T Rare variants and handedness: spotlight on TUBB4B
%J Trends in Genetics
%M MAY
%D 2024
%K news, MolBio, c2024, c202x, c20xx, zz0724, animal, behaviour, handedness,
   left, TUBB4B, gene
%X "Twin studies suggest that additive genetic effects account for ~ 1/4 of the
   variance in handedness. ...  evidence for a role of rare protein-coding
   variants in handedness. These inc. the gene encoding beta-tubulin, TUBB4B,
   suggesting that microtubules are relevant for handedness ontogenesis."
   -- [<A HREF="https://doi.org/10.1016/j.tig.2024.05.001">doi:10.1016/j.tig.2024.05.001</A>]['24].
   [Also search for: animal handedness].

%AP. Sharma
%A et al
%T Contextual and combinatorial structure in sperm whale vocalisations
%J Nature Comm'n
%V 15
%N 3617
%M MAY
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0724, sperm whale, whales, animal, language,
   Physeter macrocephalus, codas
%X "... communicate using sequences of clicks called codas. While a subset of
   codas have been shown to encode information about caller identity ... we
   report prev. undescribed features of codas that are sensitive to the
   conversational context in which they occur, & systematically controlled &
   imitated across whales. ... show that codas form a combinatorial coding
   system in which rubato & ornamentation combine with two context-indep.
   features we call rhythm & tempo ..."
   -- [<A HREF="https://doi.org/10.1038/s41467-024-47221-8">doi:10.1038/s41467-024-47221-8</A>]['24] also see
   [<A HREF="https://www.bbc.com/future/article/20240709-the-sperm-whale-phonetic-alphabet-revealed-by-ai">bbc</A>]['24].

%A K. D. Makova
%A et al
%T The complete sequence and comparative analysis of ape sex chromosomes
%J Nature
%V 630
%P 401-411
%M MAY
%D 2024
%K jrnl, MolBio, animal, primate, ape, sex chromosome, chrY, Ychr, chrX, Xchr,
   bonobo, Pan paniscus, chimpanzee, Pan troglodytes, western lowland gorilla,
   Gorilla, Bornean orangutan, Pongo pygmaeus, Sumatran orangutan, Pongo abelii,
   siamang gibbon, Symphalangus syndactylus, evolution
%X "... Compared with the X chromosomes, the ape Y chrs. vary greatly in size &
   have low alignability & high levels of structural rearrangements ... Many Y
   chromosome genes expand in multi-copy families & some evolve under purifying
   selection ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07473-2">doi:10.1038/s41586-024-07473-2</A>]['24].

%A M. G. Durrant
%A et al
%T Bridge RNAs direct programmable recombination of target and donor DNA
%J Nature
%M JUN
%D 2024
%K jrnl, MolBio, c2024, c202x, c20xx, zz0624, bridge RNA, CRISPR,
   genome editing
%X "... The IS110 bridge recombination system expands the diversity of
   nucleic-acid-guided systems beyond CRISPR and RNA interference, offering a
   unified mechanism for the three fundamental DNA rearrangements - insertion,
   excision and inversion - that are required for genome design."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07552-4">doi:10.1038/s41586-024-07552-4</A>]['24];
   also see
   [<A HREF="https://doi.org/10.1038/d41586-024-01461-2">news</A>]['24].

%A E. Panciroli
%A et al
%T Jurassic fossil juvenile reveals prolonged life history in early mammals
%J Nature
%M JUL
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0724, animal, mammal, evolution, Krusatodon
%X "... We report exceptionally complete juvenile & adult specimens of the
   Middle J. docodontan Krusatodon ... Our findings suggest that early diverging
   mammaliaforms did not experience the same life histories as extant
   small-bodied mammals & the fundamental shift to faster growth over a shorter
   lifespan may not have taken place in mammaliaforms until during or after the
   Middle Jurassic."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07733-1">doi:10.1038/s41586-024-07733-1</A>]['24].

%A E. R. R. Moody
%A et al
%T The nature of the last universal common ancestor and its impact on the
   early Earth system
%K Nature Ecol. and Evol.
%M JUL
%D 2024
%K jrnl, MolBio, c2024, c202x, c20xx, zz0724, early, ancient,  life, origins,
   evolution, LUCA, last common ancestor, DNA, genes, phylogenetic
%X "... Phylogenetic reconciliation suggests that LUCA had a genome of at least
   2.5Mb (2.49-2.99Mb), encoding around 2,600 proteins, comparable to modern
   prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic
   acetogen that possessed an early immune system. ..."
   -- [<A HREF="https://doi.org/10.1038/s41559-024-02461-1">doi:10.1038/s41559-024-02461-1</A>]['24].
   [Also search for: MolBio LUCA].

%A Liming Li
%A et al
%T Recurrent gene flow between Neanderthals and modern humans over the
   past 200,000 years
%J Science
%V 385
%N 6705
%M JUL
%D 2024
%K jrnl, MolBio, c2024, c202x, c20xx, zz0724, neanderthal, ancient human,
   genome, genes, evolution, IBDmix
%X"... We show that these patterns are caused by gene flow from modern humans
   to Neanderthals & est. that the Vindija & Altai Neanderthal genomes have
   53.9Mb (2.5%) & 80.0Mb (3.7%) of human-introgressed sequences, resp.. ..."
   -- [<A HREF="https://doi.org/10.1126/science.adi1768">doi:10.1126/science.adi1768</A>]['24].

%A M. Sandoval-Velasco
%A et al
%T Three-dimensional genome architecture persists in a 52,000-year-old
   woolly mammoth skin sample
%M JUL
%D 2024
%K MolBio, jrnl, c2024, c202x, c20xx, zz0724, woolly mammoth, ancient, DNA,
   Mammuthus primigenius, chromosome, aDNA HiC
%X "... use PaleoHi-C to map chromatin contacts & assemble its genome, yielding
   28 chromosome-length scaffolds. Chromosome territories, compartments, loops,
   Barr bodies, & inactive X chromosome (Xi) superdomains persist. The active &
   inactive genome compartments in mammoth skin more closely resemble Asian
   elephant skin than other elephant tissues ..."
   -- [<A HREF="https://doi.org/10.1016/j.cell.2024.06.002">doi:10.1016/j.cell.2024.06.002</A>]['24].
   Also see [<A HREF="https://www.abc.net.au/news/science/2024-07-12/woolly-mammoth-chromosomes-resconstructed-from-skin/104059130">abc</A>]['24].

%A A. Gibbons
%T The most ancient human genome yet has been sequenced - and it's a Denisovan's
%J Science
%M JUL
%D 2024
%K news, views, MolBio, c2024, c202x, c20xx, zz0724, ancient human DNA,
   Denisovan, evolution, Neanderthal
%X "200,000-year-old DNA from Siberian cave shows our elusive, extinct cousins
   mated repeatedly with Neanderthals ..."
   -- [<A HREF="https://doi.org/10.1126/science.zi9n4zp">doi:10.1126/science.zi9n4zp</A>]['24].

%A A. A. Widjaja
%A et al
%T Inhibition of IL-11 signalling extends mammalian healthspan and lifespan
%J Nature
%M JUL
%D 2024
%K jrnl, MiolBio, c2024, c202x, c20xx, zz0724, IL-11, IL11, Il11ra1, antiIL11,
   lifespan, aging, ageing, longevity, mammal, mouse, inflammation
%X "For healthspan & lifespan, ERK, AMPK & mTORC1 represent critical pathways &
   inflammation is ... Deletion of Il11 or Il11ra1 protects against metabolic
   decline, multi-morbidity & frailty in old age. Administration of anti-IL-11
   to 75-week-old mice for 25 weeks improves metabolism & muscle function, &
   reduces ageing biomarkers and frailty across sexes. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07701-9">doi:10.1038/s41586-024-07701-9</A>]['24].

%A E. Chi Fru
%A et al
%T Hydrothermal seawater eutrophication triggered local macrobiological
   experimentation in the 2100 Ma Paleoproterozoic Francevillian sub-basin
%J Precambrian Research
%V 409
%M AUG
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0724, ChiFru, biology,biol, early, ancient,
   complex life, multicellular, animal, evolution, origins, fossil, fossils,
   phosphorus, controversial
%X "... Here we couple an episode of intense submarine hydrothermal alteration
   of a nutrient-rich seafloor reservoir to the collision of the Congo-Sao
   Francisco cratons at ~2100 Ma, to unravel a paleo-geodynamic incident of
   seawater P enrichment in the Paleoproterozoic Francevillian sub-basin. We
   propose that this previously unrecognized local pulse in dissolved seawater
   P concentration, of comparable magnitude to Ediacaran seawater levels, set
   the stage for Earth's earliest biospheric experimentation towards
   macrobiological complexity ~2100 million years ago."
   -- [<A HREF="https://doi.org/10.1016/j.precamres.2024.107453">doi:10.1016/j.precamres.2024.107453</A>][24].
   Also see [<A HREF="https://www.bbc.com/news/articles/c3geyvpxpeyo">bbc</A>][29/7/2024].


%A M. Taquet,
%T Cognitive and psychiatric symptom trajectories 2-3 years after hospital
   admission for COVID-19: a longitudinal, prospective cohort study in the UK
%T The Lancet
%M JUL
%D 2024
%K jrnl, Biol, medicine, c2024, c202x, c20xx, zz0824, covid 19, covid19, long,
   mental, cognitive, IQ, decline, effects, health, risks
%X "... Participants had worse cognitive scores than would be expected on the
   basis of their sociodemographic characteristics across all cognitive domains
   tested (avg. score 0·71 SD below the mean [IQR 0·16-1·04]; p < 0·0001) ..."
   -- [<A HREF="https://doi.org/10.1016/S2215-0366(24)00214-1">doi:10.1016/S2215-0366(24)00214-1</A>]'24].

%Q FlyWire Consortium
%J Nature
%V 634
%P 35-36
%M OCT
%D 2024
%K MolBio, insect, Drosophila melanogaster, fruit fly, brain, connectome,
   connections, wiring, neurons, synapses
%X "Neuroscientists have reconstructed the first complete wiring map of the
   fruit-fly brain, including 140,000 neurons and more than 50 million
   connections"
   -- [<A HREF="https://www.nature.com/collections/hgcfafejia">www</A>]['24],
      [<A HREF="https://doi.org/10.1038/d41586-024-03029-6">doi:10.1038/d41586-024-03029-6</A>]['24].

%A I. Seet
%A et al
%T Rapid computation of the assembly index of molecular graphs
%J arXiv
%M OCT
%D 2024
%K TR, MolBio, c2024, c202x, c20xx, zz1024, AssemblyIndex, chemical compound,
   molecule, graph, duplicate subgraph, maths, algorithm, AssemblyTheory
%X "... to find the least # of steps required to make its molecular g. by
   recursively using prev. made structures ... propose an exact alg. to
   efficiently find [Ass.Is] of large molecules inc. some natural products. ...
   start by identifying the largest possible duplicate sub-g.s during the
   sub-g. enumeration process & subsequently implement a [DP] strategy with a
   branch & bound heuristic to exploit already used duplicates & reject
   impossible states in the enumeration ..."
   -- [<A HREF="https://arxiv.org/abs/2410.09100">arxiv:2410.09100</A>]['24].
   [Also search for: AssemblyIndex] & [also search for: AssemblyTheory].

%A A. S. Labade
%A et al
%T Expansion of insitu genome sequencing links nuclear abnormalities to
   hotspots of aberrant euchromatin repression
%J bioRxiv
%M OCT
%D 2024
%K TR, MolBio, c2024, c202x, c20xx, zz1024, ExIGS, single cell, protein, DNA
%X "... describe expansion in situ genome sequencing (ExIGS), a technology that
   enables sequencing of genomic DNA & superresolution localization of nuclear
   proteins in single cells ..."
   -- [<A HREF="https://doi.org/10.1101/2024.09.24.614614">biorxiv</A>]'24].
   (Also see [<A HREF="https://doi.org/10.1038/d41586-024-03276-7">comment</A>]['24].)

%A A. J. Faure
%A et al
%T The genetic architecture of protein stability
%J Nature
%V 634
%P 995-1003
%M SEP
%D 2024
%K jrnl, MolBio, c2024, c202x, c20xx, zz1024, design, intelligible
%X "... Here, by experimentally sampling from seq. spaces larger than 10^{10},
   we show that the genetic architecture of at least some proteins is remarkably
   simple, allowing accurate genetic prediction in high-dim. seq. spaces with
   fully interpretable energy models. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07966-0">doi:10.1038/s41586-024-07966-0</A>]['24].


%A A. V. Zeigarnik
%T On hypercycles and hypercircuits in hypergraphs
%P 377-383
%B Discrete Mathematical Chemistry
%E P. Hansen
%E P. W. Fowler
%E M. Zheng
%S DIMACS Discrete Math. and Theoretical Comp. Sci.
%V 51
%D 2000
%I Amer. Math. Soc.
%K hyper-graph, cycle, cycles, hyper-circuit, path, paths, c2000, c200x, c20xx,
   reaction, reactions, substrate, chemical, AMS
%X [<A HREF="http://dimacs.rutgers.edu/Volumes/Vol51.html">order</A>][7/'04].

%A N. Lane
%T Oxygen: The Molecule That Made The World
%I OUP
%P 384
%D 2002
%K book, text, OUP, chemistry, biology, biol, life, animal, animals, size, big,
   large, earth, atmosphere, atmospheric, gas, gases, mixture, ratio, amount,
   concentration, dragonfly, c2002, c200x, c20xx, zz0103
%X Three hundred million years ago, dragonflies grew as big as seagulls, with
   wingspans nearly a yard across. Researchers claim they could have flown only
   if the air had contained more oxygen than today-probably as much as 35%.
   But oxygen is a toxic gas. Fruit flies raised at twice the normal level of
   oxygen live half as long as their siblings. If atmospheric oxygen reached
   35% in the Carboniferous, why did oxygen promote exuberant growth, instead
   of rapid aging and death? ....
   About us$35. uk us isbn:0198508034.


%A L. G. Kraft
%T ???
%I Dept. Elec. Eng., MIT
%D 1949
%K MSc, masters thesis, Kraft inequality, c1949, c194x, c19xx, prefix code,
   data compression, encoding
%X There exists a prefix code with code-words of lengths l1, l2, ..., LN
   iff SUM[i=1..N]{ 1/2^li } <= 1.
   [ref from G.F.]

%A J. G. Cleary
%A I. H. Witten
%T Data compression using adaptive coding and partial string matching
%J IEEE Trans. on Communications
%V 32
%N 4
%P 396-402
%D 1984
%O Compression Conf. IEEE Soc. Press, 52-61.
%K conf, text, data, compress, compression, PPM, c1984, c198x, c19xx,
   arithmetic coding, encoding, arithmeticCoding
%X "The recently dev. technique of arithmetic coding, in conjunction with a
   Markov model of the source, is a powerful method of DC in situations where a
   linear treatment is inappropriate. AC allows the model to be constructed
   dynamically by both encoder & decoder during the course of the transmission,
   & has been shown to incur a smaller coding overhead than explicit
   transmission of the model's statistics. But there is a basic conflict between
   the desire to use high-order Markov models & the need to have them formed
   quickly as the initial part of the msg is sent. ... describes how the
   conflict can be resolved with partial string matching, & reports experimental
   results which show that mixed-case English text can be coded in as little as
   2.2 bits/ character with no prior knowledge of the source."
   -- pdf@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.14.4305">c'teseer</A>]['16].
   [Also search for: arithmeticCoding].

%A J. Bentley
%A D. Sleator
%A R. Tarjan
%A V. Wei
%T A locally adaptive compression scheme
%J CACM
%V 29
%N 4
%P 320-330
%D 1986
%K jrnl, CACM, c1986, c198x, c19xx, data, compression, compress, adapt, local,
   adaptive, move to front encoding, MTF
%X "... based on a simple heuristic for self-organizing sequential search and
   on variable-length encodings of integers. We prove that it never performs
   much worse than Huffman coding and can perform substantially better;
   experiments on real files show that its performance is usually quite close to
   that of Huffman coding. Our scheme has many implementation advantages: it is
   simple, allows fast encoding and decoding, and requires only one pass over
   the data to be compressed (static Huffman coding takes two passes)."
   -- [<A HREF="http://doi.acm.org/10.1145/5684.5688">doi:10.1145/5684.5688</A>]['09],
   pdf@[<A HREF="http://www.cs.cmu.edu/~sleator/papers/adaptive-data-compression.pdf">cmu</A>]['09].

%A P. E. Tischer
%A R. T. Worley
%A A. J. Maeder
%A M. Goodwin
%T Context-based lossless image compression
%J COMPJ
%V 36
%N 1
%P 69-77
%M ?
%D 1993
%K COMPJ, jrnl, image processing, IP, compress, data, compression,
   Monash, Tischer, Tisher

%A T. C. Bell
%A J. G. Cleary
%A I. H. Witten
%T Text Compression
%I PrenticeHall
%P 318
%D 1990
%K data compression, book, text, c1990, c199x, c19xx, compress, computing, CSci,
   arithmetic coding, arithmeticCoding, encoding, data model, modelling
%X The source for the arithmetic coder described in Chap.5 of Bell,
   Cleary, and Witten's book `Text Compression' is available
   via anonymous ftp from ftp.cpsc.ucalgary.ca (136.159.7.18) in directory
   /pub/projects/arithmetic.coding.  It only comes with a simple order-0 model
   but it's set up so that adding your own more sophisticated one is
   straightforward.
      A low precision arithmetic coding implementation avoiding hardware
   division is available on the same site (ftp.cpsc.ucalgary.ca) in
   /pub/projects/arithmetic.coding/low.precision.version, file
   low.precision.version.shar.
      Kris Popat <!-- popat@image.mit.edu --> has worked on `Scalar
   Quantization with Arithmetic Coding.'  It describes an arithmetic coding
   technique which is quite general and computationally inexpensive.  The
   documentation and example C code are available via anonymous ftp from
   media-lab.media.mit.edu (18.85.0.2), in /pub/k-arith-code.
      The program 'urban' in ddjcompr.zip (see item 12 above) is a high order
   arithmetic coder working at the bit level. It is written by
   Urban Koistinen <!-- md85-epi@nada.kth.se -->.
   pb, uk us isbn:0139119914; uk us isbn13:978-0139119910.
   [Also search for: arithmeticCoding].

%A G. Cormack
%A N. Horspool
%T Data Compression using dynamic Markov modelling
%J COMPJ
%P 541-550
%V 30
%N 6
%M DEC
%D 1987
%K COMPJ, jrnl, c1987, c198x, c19xx, zz0395, DMC, data compression, compress,
   computing, arithmetic coding, data model, modelling, hidden Markov model,
   HMM, Guazzo
%X [<A HREF="http://www.cs.uvic.ca/~nigelh/Publications/DMC.pdf">pdf@.uvic.ca</A>]['07].
   The DMC program is available in plg.uwaterloo.ca:/pub/dmc/*.c. It
   implements the algorithm described in `Data Compression using Dynamic
   Markov Modelling', by Gordon Cormack and Nigel Horspool, Computer
   Journal 30:6 (December 1987).  This program uses Guazzo's version of
   arithmetic coding.
   - via PT <!-- email: pet@bruce.cs.monash.edu.au -->  [3/'95]

%A M. Nelson
%A J-L. Gailly
%T The Data Compression Book: featuring fast, efficient data compression
   techniques in C
%I M&T books (NY)
%P 527
%D 1992
%K book, text, c1992, c199x, c19xx, computing, CSci, zz0695
%X 2nd ed c1995, pb, uk us isbn:1558514341; uk us isbn13:978-1558514348.
   Hargrave library 005.746 N428D

%A G. Held
%A T. R. Marshall
%T Data Compression: Techniques and Applications: Hardware and
   Software Considerations
%I Chichester, UK
%D 1991
%K book, text, c1991, c199x, c19xx, computing, CSci, zz0695
%X hb, uk us isbn:0471929417; uk us isbn13:978-0471929413.
   Hargrave library 005.746 H474D3

%E Y. Fisher
%T Fractal Image Compression - Theory and Application
%I SpringerVerlag
%D 1994
%K fractal compression, data compression, compress, image processing, IP,
   text, book, c1995, c199x, c19xx, computing, zz0795
%X hb, uk us isbn:0387942114; uk us isbn13:978-0387942117. (N.Y.)
   Hargrave H 621-367.F537F.

%A I. H. Witten
%A A. Moffat
%A T. C. Bell
%T Managing Gigabytes: Compressing and Indexing Documents and Images
%I Van Nostrand Reinhold
%P 429
%M MAR
%D 1994
%K book, text, giga bytes, data compression, index, text, image, compress,
   document, ppm, c1994, c199x, c19xx
%X 2nd edn c1999, hb, uk us isbn:1558605703; uk us isbn:0442018630; US$54.95.
   [<A HREF="http://www.cs.mu.oz.au/mg/">m.g.@cs.mu</A>]['05]
   I.H.W. at Waikato NZ;  A.M. at Dept Comp Sci Melb' Uni;
   T.C.B. at Canterbury NZ

%A M. Burrows
%A D. J. Wheeler
%T A block-sorting lossless data compression algorithm
%R 124
%I SRC (Digital, DEC, Palo Alto)
%P 18
%M MAY
%D 1994
%K TR, SRC, SRC124, TR124, data compression, compress, text, string,
   reversible, block, sort, ST, move to front, MTF, c1994, c199x, c19xx,
   Burrows, Wheeler, BW, transform, BWT, BWC
%X 1. Forms a certain (reversible) permutation of the input data,
   2. use simple move-to-front compression algorithm incorporating a ...
   3. Huffman coder (or similar) to state positions in MTF list
   [<A HREF="ftp://ftp.digital.com/pub/DEC/SRC/research-reports/SRC-124.ps.Z">ftp.digital.com/...</A>][??]
   [<A HREF="http://gatekeeper.dec.com/pub/DEC/SRC/research-reports/abstracts/src-rr-124.html">TR</A>]['06]
   [<A HREF="http://www.data-compression.info/Algorithms/BWT/">d'c'.info</A>]['06]
   'The transform is done by sorting all rotations of the text, then taking the
   last column. E.g., the text "^BANANA@" is transformed into "BNN^AA@A"'  --
   BWT@[<A HREF="http://en.wikipedia.org/wiki/Burrows-Wheeler_transform">wikip</A>]['08].
   [Also search for: BWT string].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/BWT/">BWT</A>].)

%A J. G. Cleary
%A W. J. Teahan
%A I. H. Witten
%T Unbounded length contexts for PPM
%J Data Compression Conference
%D 1995
%P 52-61
%D 1995
%K conf, DCC, text, compress, PPM, c1995, c199x, c19xx, string, text,
   prediction by partial matching, PPMC, Burrows Wheeler transform
%X H 5.74605 D232D  (via P.T.)
   also relates it to the Burrows - Wheeler compression method.
   [Also search for: Burrows Wheeler BWT] <!-- [jcleary|wjt|ihw]@waikato.ac.nz --> .

%A S. Chen
%A J. H. Reif
%T Efficient lossless compression of trees and graphs
%J DCC
%I IEEE
%P 428-??
%D 1996
%K conf, DCC, c1996, c199x, c19xx, compress, tree, graph
%X "...problem of compressing a data struct. (e.g. tree, undirected & directed
   graphs) in an efficient way while keeping a similar structure in the
   compressed form. To date, there has been no proven optimal alg. for this
   problem. We use the idea of building LZW tree in LZW compression to compress
   a binary tree generated by a stationary ergodic source in an optimal
   manner.  ... extend our tree comp. alg. to compress undirected & DAGs."
   -- [<A HREF="http://www.cs.duke.edu/~chen/papers/graph.ps">.ps@duke</A>]['08].
 * ["... compressing Tree and G. into a similar but smaller form s.t. many
    properties of the original [] are kept ...".]
   [Also search for: compress graph].

%A P. M. Fenwick
%T The Burrows-Wheeler transform for block sorting text compression
%J COMPJ
%V 39
%N 9
%P 731-740
%D 1996
%K COMPJ, jrnl, text compression, compress, file, c1996, c199x, c19xx,
   string, text, Burrows, Wheeler, BW, transform, BWT, BWC, MTF, zz0897
%X "A recent development in text compression is a block sorting alg. which
   permutes the input text according to a special sort proc. & then processes
   the permuted text with Move-To-Front (MTF) & a final statistical compressor.
   ...combines good speed with excellent compression perf.. ...investigates the
   fundamental op'n of the alg. & presents some improvements based on that
   analysis. Although block sorting is clearly related to previous compression
   techniques, it appears that it is best described by techniques derived from
   work by Shannon on the prediction & entropy of English text. A simple model
   is developed which relates the compression to the proportion of zeros after
   the MTF stage."   [14 refs].
   [<A HREF="http://dx.doi.org/10.1093/comjnl/39.9.731">doi:10.1093/comjnl/39.9.731</A>].  See B and W c1994.

%A C. G. Nevill-Manning
%A I. H. Witten
%T Compression and explanation using hierarchical grammars
%J COMPJ
%P 103-116
%V 40
%N 2/3
%D 1997
%K jrnl, compj, data, text, music, SEQUITUR, grammar, c1997, c199x, c19xx,
   inference, model, rule, rules, compress, explain, NevillManning
%X "... SEQUITUR, that identifies hierarchical structure in sequences of
   discrete symbols & uses that information for compression. On many practical
   sequences it performs well at both compression & structural inference,
   producing comprehensible descriptions of sequence structure in the form of
   grammar rules. The algorithm can be stated concisely in the form of 2
   constraints on a [CFG]. Inference is performed incrementally, the structure
   faithfully representing the input at all times. It can be implemented
   efficiently & [...] approximately linear [time] in sequence length. ..."
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_40/Issue_03/Vol40_03.body.html#AbstractNevill">@oup</A>][6/'04] auths @ W@ik@to.
   [<A HREF="http://craig.nevill-manning.com/publications/97NM-IHW-Compress.pdf">auth1</A>][6/'04]

%A M. M. Reid
%A R. J. Millar
%A N. D. Black
%T Second generation image coding: an overview
%J ACM Computing Surveys
%V 29
%N 1
%M MAR
%D 1997
%P 3-29
%K jrnl, survey, compression, DCT, image processing, comp, 2nd, wavelet,
   lossy, lossless, zz0997
%X A seurvey paper, 2 pages of references.

%A J. Cleary
%A W. J. Teahan
%T Unbounded length contexts for PPM
%J COMPJ
%V 40
%N 2/3
%D 1997
%P 67-75
%K COMPJ, jrnl, text, data, compress, compression, PPM, PPM*, PPMstar, zz1297
%X PPM* uses contexts of unbounded length - using full information
   in ALL substrings does improve compression (at a computational cost).
   - in Special Issue on Lossless Compression.

%A S. Bunton
%T Semantically motivated improvements for PPM variants
%J COMPJ
%V 40
%N 2/3
%D 1997
%P 76-93
%K COMPJ, jrnl, c1997, c199x, c19xx, text, data, compress, compression, PPM
%X - in Special Issue on Lossless Compression.

%A F. M. J. Willems
%A Y. M. Shtarkov
%A Tj. J. Tjalkens
%T The context-tree weighting method: basic properties
%J IEEE Trans. Info. Theory
%P 653-664
%M MAY
%D 1995
%K jrnl, compress, data compression, tree source, weight, CTW, binary
%X ... for binary tree sources that performs the "double mixture".
   Using a context tree, this method weights in an efficient recursive
   way the coding distributions corresponding to all bounded memory
   tree sources ...
   <A HREF="http://ei0.ei.ele.tue.nl/~frans/ResearchCTW.html">[www]</A>[1/1998]

%A F. M. J. Willems
%A Y. M. Shtarkov
%A Tj. J. Tjalkens
%T Context weighting for general finite context sources
%J IEEE Trans. Info. Theory
%P 1514-1520
%M SEP
%D 1996
%K jrnl, compress, data compression, weight, CTW
%X see also authors '95 on tree-sources.
   <A HREF="http://ei0.ei.ele.tue.nl/~frans/ResearchCTW.html">[www]</A>[1/1998]

%A B. Meyer
%A P. Tischer
%T TMW - a new method for lossless image compression
%J Proc. Int. Picture Coding Symp.
%D 1997
%P 533-538
%K conf, data compression, image, compress, blend, blending, TMW, CALIC,
   PCS, PCS97, c1997, c199x, c19xx, zz0298
%X linear predictors, implicit segmentation,
   blending probability distributions, achieves
   3.92 bits per pixel on [Lena Soderberg] 'Lenna grey' v. 4.05 by CALIC.
   -- [<A HREF="http://www.cs.monash.edu.au/">[www.cs.monash.edu.au]</A>].

%A U. Gunther
%A P. Hertling
%A R. Nicolescu
%A M. Titchener
%A Representing variable-length codes in fixed-length T-depletion format for
   encoders and decoders
%J J. Universal Comp. Sci.
%P 1207-1225
%V 3
%N 11
%M NOV
%D 1997
%K jrnl, JUCS, compression, data, code, encode, decode, T-code, Tcode, Tcodes
%X "T-Codes are a class of variable-length codes. Their self-synchronisation
   properties are useful in compression & communication appl'ns where error
   recovery rather than error correction is at issue, for example, in digital
   telephony. T-Codes may be used without error correction or additional
   synchronisation mechanisms. Typically, the representation of variable-length
   codes is a problem in computers based on a fixed-length word arch..  ..."
   [<A HREF="http://www.jucs.org/jucs_3_11/representing_variable_length_codes">abs</A>]['04] (pdf restricted), auths@u.auckland.nz

%A R. Nicolaescu
%A M. Titchener
%T Uniqueness theorems for T-codes
%J Romanian J. Information Sci. and Tech.
%P 243-258
%V 1
%N 3
%D 1998
%K jrnl, Tcode, Tcodes, code, theorem, compression, compress, data, content,
   self synchronization, synchronisation, variable length
%X "... overview of some of the current work on T-codes, a class of var.-length
   codes which exhibit strong self-synchronization properties but also provide
   an effective framework for describing & computing string complexity &
   information content. Secondly we present a number of underlying mathematical
   results, specifically the core uniqueness results presented in full in[6].
   These establish the relationship between maximal-length strings & their
   resp. T-code sets, as conjectured[9] & reflected in empirical obs.. ..."
   <!-- r.nicolaescu auckland.ac.nz -->auths@cs.u.auckland.nz .

%A B. Meyer
%A P. Tisher
%T Extending TMW for near lossless compression of greyscale images
%J Data Compression Conf.
%P ?-?
%D 1998
%K conf, DCC, DCC98, TMW, CALIC, LOCO, image compression, data, compress,
   zz0298, c1998, c199x, c19xx, MonashUni
%X Outperforms CALIC by 2 to 10% in lossless mode.
   Outperforms LOCO in lossy mode.
   See also Meyer and Tisher '97
   <A HREF="http://www.csse.monash.edu.au">[csse.monash.edu.au]</A>.

%A P. A. J. Volf
%A F. M. J. Willems
%T Switching between two universal source coding algorithms
%J Proc. Data Compression Conf.
%P 491-500
%M ???
%D 1998
%K conf, DCC, compress, data, text, algorithm, c1998, c199x, c19xx, combine,
   blend, compression, weighting, weight, compressor, compressors, switching
%X "... a switching method which can be used to combine 2 sequential universal
   source coding algs.. The switching method treats these 2 algs. as black-boxes
   & can only use their ests. of the prob. distributions for the consecutive
   symbols of the source seq.. Three weighting algs. based on this switching
   method are presented. Empirical results show that all 3 weighting algs. give
   a performance better than the performance of the source coding algs. they
   combine."
   [<A HREF="http://dx.doi.org/10.1109/DCC.1998.672217">doi:10.1109/DCC.1998.672217</A>]['08].

%A C. S. Burrus
%A J. A. Barreto
%A I. W. Selesnick
%T Iterative reweighted least squares design of FIR filters
%J IEEE Trans. Signal Proc.
%V 42
%N 11
%P 2926-2936
%M NOV
%D 1994
%K jrnl, c1994, c199x, c19xx, FIR filter, parameter estimation, re weighted
%X via  B. M e y e r  and  P. T i s c h e r

%A P. Franti
%A T. Hatakka
%T Context model automata for text compression
%J COMPJ
%V 41
%N 7
%P 474-485
%D 1998
%K jrnl, COMPJ, text, data compression, compress, FSA, FSM, finite state,
   automaton, machine, machines, PPM, GDMC, zz0499
%X ... Using the CMA formalism as our tool, we study the behaviour
   of the [PPM and GDMC] models.
   [15 refs]

%A J. A. Storer
%T Data Compression: Methods and Theory
%I Comp. Sci. Press
%D 1988
%K book, text, DC, compress
%X via GF

%A D. J. A. Welsh
%T Codes and Cryptography
%D 1988
%I OUP
%K book, text, good, code, coding, cryptography, L4Ref
%X via G.F.

%A A. Moffat
%A R. M. Neal
%A I. H. Witten
%T Arithmetic coding revisited
%J ACM Trans. on Information Sys.
%V 16
%N 3
%P 256-294
%M JUL
%D 1998
%K jrnl, data compression, compress, c1998, c199x, c19xx, encoding
%X also see [<A HREF="http://www.cs.mu.oz.au/~alistair/arith_coder/">cs.mu.oz.au</A>][7/'03].
   [Also search for: arithmeticCoding].

%A N. Deo
%A B. Litow
%T A structural approach to graph compression
%J MFCS Workshop on Communications
%P 91-101
%D 1998
%K wShop, c1998, c199x, c19xx, graph, graphs, compress, compression,
   bounded, genus, arboricity
%X "We consider g. compression in terms of g. families. ... show that graphs of
   bounded genus can be compressed to O(n) bits where n is the # of vertices.
   We identify a property based on separators that makes O(n)-bit compression
   possible for some graphs of bounded arboricity." [9 refs].
   -- [<A HREF="http://www.cs.jcu.edu.au/Research/profiles/bruce/mfcs98_deo.ps">ps@jcu</A>]['08].
      ["The genus of a g. is the minimal int. n s.t. the g. can be drawn without
      crossing itself on a sphere with n handles (i.e. an oriented surface of
      genus n). Thus, a planar graph has genus 0, because it can be drawn on a
      sphere without self-crossing. -- wikip.]
   [Also search for: compress graph].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/Graph/">graphs</A>].)

%A A. Moffat
%T An improved data structure for cumulative probability tables
%J SPE
%V 29
%N 7
%P 647-659
%D 1999
%K jrnl, SPE, data, compress, compression, CPT, table, symbols, frequencies,
   arithmetic coding, c1999, c199x, c19xx
%X In '94 Peter Fenwick at the University of Auckland devised an elegant
   mechanism for tracking the cumulative symbol frequency counts that are
   required for adaptive arithmetic coding. His structure spends O(log n) time
   per update when processing the s'th symbol in an alphabet of n symbols.
   In this note we propose a small but significant alteration to this
   mechanism, and reduce the running time to O(log(1+s)) time per update.
   If a probability-sorted alphabet is maintained, so that symbol s in the
   alphabet is the s'th most frequent, the cost of processing each symbol is
   then linear in the number of bits produced by the arithmetic coder.
   Also see [<A HREF="http://www.cs.mu.oz.au/~alistair/arith_coder/">cs.mu.oz.au</A>][7/'03].

%A H. Liefke
%A D. Suciu
%T XMILL: An efficient compressor for XML data
%J ACM SIGMOD Conf 2000
%W Dallas, Texas
%I ACM
%M MAY
%D 2000
%P 153-164
%K conf, SIGMOD, XML, data compression, compress, zz0900
%X isbn:1581132182;
   Can use specific compressors for different types of text
   as suggested by tags/ content type in XML.
   -- [<A HREF="http://www.research.att.com/~suciu/strudel/external/files/_F1998686332.ps">www</A>][8/'00].

%A T. Suel
%A J. Yuan
%T Compressing the graph structure of the Web
%J Proc. of the IEEE Data Compression Conf.
%P 213-?
%D 2001
%K conf, DCC, DCC01, c2001, c200x, c20xx, www, world wide web, graph, graphs,
   hyper links, compress
%X "... graphs [of the www] involve hundreds of millions of nodes and even more
   edges, highly space-efficient data structures are needed to fit the data in
   memory. A 1st step in this direction was done by the DEC Connectivity Server,
   which stores the graph in compressed form.  ..."
   -- [<A HREF="http://cis.poly.edu/suel/papers/graph.ps">ps@poly</A>]['08],
      [<A HREF="http://doi.ieeecomputersociety.org/10.1109/DCC.2001.917152">$19@ieee</A>]['08].
   [Also search for: compress graph].

%A J. Bentley
%A D. McIlroy
%T Data compression with long repeated strings
%J Information Sciences
%V 135
%N 1-2
%P 1-11
%M ?
%D 2001
%O Data Compression Using Long Common Strings,
   Data Compression Conference (DCC '99), pp287-295, March 29-31, 1999
%K jrnl, string, text, LZ, compress, information, pattern matching,
   algorithm, Karp, Rabin, zz0503, c2001, c200x, c20xx, DCC99
%X LZ ... encoding repeated strings that occur in a small sliding window.
   We propose ... long strings ... far apart ... rare in most doc's ...
   frequent in software sys's ... and news articles ...  our scheme is
   computationally efficient ... experiments ... effectively compresses
   some classes of input.   --  B is at B e l l  L a b s,  M at Dartmouth
   (Employs the Karp and Rabin ('87) randomized pattern matching alg.)
   Inf Sci:[<A HREF="http://dx.doi.org/10.1016/S0020-0255(01)00097-4">doi:10.1016/S0020-0255(01)00097-4</A>][7/'03],
   Inf Sci:[<A HREF="http://www.sciencedirect.com/science/article/B6V0C-437XRW4-1/2/7dc298286f8e7c626d61d5f77064703c">science direct</A>][7/'03]r,
   DCC99:  [<A HREF="http://www.computer.org/proceedings/dcc/0096/00960287abs.htm">abs</A>][5/'03] IEEE, needs subsc'n.

%A A. Moffat
%A A. Turpin
%T Compression and Coding Algorithms
%I KluwerAcademic
%M MAR
%D 2002
%K book, text, data, compress, data, text, compression, algorithm, code, codes,
   PPM, c2002, c200x, c20xx
%X us$110, hb, uk us isbn:0792376684; uk us isbn13:978-0792376682.
   Also see [<A HREF="http://www.cs.mu.oz.au/~alistair/arith_coder/">cs.mu.oz.au</A>][7/'03].

%A D. Benedetto
%A E. Caglioti
%A V. Loreto
%T Language trees and zipping
%J Physical Rev. Lett.
%V 88
%N 4
%P #048702
%M JAN
%D 2002
%K Phys, letters, physics, 048702, zip, LZ77, compress, compression, c2002,
   relatedness, author identification, attribution, tree, family,c200x, c20xx,
   evolutionary tree, trees, free text, classification, semantic distance,
   similarity, categorization, email, mail, filter, filtering, spam
%X ... we present a very general method for extracting information from a
   generic string of characters, e.g., a text, a DNA sequence, or a time
   series. Based on data-compression techniques, its key point is the
   computation of a suitable measure of the remoteness of two bodies of
   knowledge. We present the implementation of the method to linguistic
   motivated problems, featuring highly accurate results for language
   recognition, authorship attribution, and language classification.
   [<A HREF="http://link.aps.org/abstract/PRL/v88/e048702">paper</A>][12/'02]  doi:10.1103/PhysRevLett.88.048702,
   [<A HREF="http://ojps.aip.org/journal_cgi/dbt?KEY=PRLTAO&Volume=88&Issue=4">issue</A>][2/'02],
   [<A HREF="http://www.aip.org/enews/physnews/2002/split/575-2.html">alert</A>][2/'02].

%A D. Shkarin
%T PPM: One step to practicality
%J Proc. Data Compression. Conf.
%P 202-211
%D 2002
%K conf, DCC, c2002, c200x, c20xx, Snowbird, order, information inheritance,
   PPM, PPMII, cPPMII, contexts, escape, symbols, length, order, data,
   compress, compression
%X ... PPM with information inheritance ...
   The main difficulty ... statistics insufficiency in [longer] contexts. ...
   ... similarity of dist'n fns in parent and child contexts...
   [<A HREF="http://datacompression.info/Miscellaneous/PPMII_DCC02.pdf">.pdf</A>][7/'03]
   [also search for: PPM].

%A Z. Arnavut
%T Inversion coding
%J COMPJ
%P 46-57
%V 47
%N 1
%M JAN
%D 2004
%K jrnl, compj, Burrows, Wheeler, BW, transform, BWC, code, coding, compress,
   compression, file, string, text, data, c2004, c200x, c20xx, zz0101
%X "The Burrows-Wheeler Compression (BWC) described by Burrows & Wheeler has
   received considerable attention. An essential part of BWC schemes is the
   Move-to-Front coder (recency ranking). In this paper we introduce a
   different coding (ranking) scheme, the inversion coder. We prove the
   information theoretic relationship between interval ranks & canonical
   sorting permutations. We also introduce a faster & more memory
   efficient-algorithm for inversion ranks. Finally, we explore the
   relationship between inversion ranks & recency ranks & show that inversion
   coding is superior to interval ranking as well as recency ranking."
   -- [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_47/Issue_01/470046.sgm.abs.html">www</A>][1/'04]

%A R. S. Bird
%A S.-C. Mu
%T Inverting the Burrows-Wheeler transform
%J JFP
%V 14
%N 6
%P 603-612
%D 2004
%K jrnl, JFP, c2004, c200x, c20xx, FP, inverse BWT, invert, BW transform,
   compress, compression, data, string, text, Schindler, Chapin, Tate
%X "The Burrows-Wheeler Transform is a string-to-string transform which, when
   used as a preprocessing phase in compression, significantly enhances the
   compression rate. However, it often puzzles people how the inverse transform
   is carried out. In this pearl we to exploit simple equational reasoning to
   derive the inverse of the [B-W] transform from its specification. We also
   outline how to derive the inverse of two more general versions of the
   transform, one proposed by Schindler and the other by Chapin and Tate."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796804005118">doi:10.1017/S0956796804005118</A>].
   [Also search for: Burrows Wheeler c1994].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/BWT/">BWT</A>].)

%A B. Litow
%A N. Deo
%T Graph compression and the zeros of polynomials
%J IPL
%V 92
%N 1
%P 39-44
%M OCT
%D 2004
%K jrnl, IPL, c2004, c200x, c20xx, graphs, compress, zero, polynomial
%X "We explore a novel quantitative relationship between the compressibility of
   directed graphs & the disposition of the zeros of polynomials with rational
   coefficients. The connection highlights the genericity of incompressible
   graphs & the genericity of polynomials all of whose zeros are simple."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2004.06.004">doi:10.1016/j.ipl.2004.06.004</A>]['07] [13 refs].
   auth1@JCU.au
   [Also search for: compress graph].

%A P. Skibiski
%A S. Grabowski
%A S. Deorowicz
%T Revisiting dictionary-based compression
%J SPE
%V 35
%N 15
%P 1455-1476
%D 2005
%K jrnl, SPE, text, c2005, c200x, c20xx, PPM, zz1105, compress, data
%X "An attractive way to increase text c. is to replace words with refs. to a
   text dictionary .... exist a few works in this area, they do not fully
   exploit the c. possibilities or consider alternative preprocessing variants
   for various compressors in the latter phase. ...discuss several aspects of
   dictionary-based c., ... present a PPM/BWCA-oriented scheme, ... ratios
   higher by 2-6% than the state-of-the-art StarNT ..., greater speed. ... an
   alternative scheme designed for LZ77 c., with the advantage over StarNT of
   reaching up to 14% in combination with gzip."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.678">doi:10.1002/spe.678</A>]['05].

%A M. Mahoney
%T Adaptive weighing of context models for lossless data compression
%I Florida Tech.
%R CS-2005-16
%D 2005
%K TR16, TR 16, c2005, c200x, c20xx, PAQ, weight, text, data, model,
   PAQ6, PAQ8, paq8hp12any, Hutter prize, competition, LPAQ, FPAQ
%X pdf@[<A HREF="http://www.cs.fit.edu/~mmahoney/compression/cs200516.pdf">fit</A>]['10], describes paq6;
   auth@[<A HREF="http://www.cs.fit.edu/~mmahoney/compression/">fit</A>]['10],
     "paq8hp12any May 20 '07, A.Ratushnyak, updated Jan. 9, '09) is a
     specialized version which has won the Hutter Prize."

%A L. Peshkin
%T Structure induction by lossless graph compression
%J Data Compression Conf.
%I IEEE
%P 53-62
%M MAR
%D 2007
%K conf, DCC, DCC07, c2007, c200x, c20xx, graph, graphs, network, networks,
   compress, GraphiTour, maximum cardinality, matching problem,
   common substructure, zz0407
%X "... automate the discovery of structure in vast & evergrowing collection of
   relational data commonly represented as graphs, for example genomic networks.
   A novel alg. ... Graphitour, for structure induction by lossless graph
   compression is presented & illustrated by a clear & broadly known case of
   nested structure in a DNA molecule. This work extends to graphs some well
   established approaches to grammatical inference previously applied only to
   strings. The bottom-up graph compression problem is related to the max.
   cardinality (non-bipartite) max. cardinality matching problem. The alg.
   accepts a variety of graph types including directed graphs & graphs with
   labeled nodes & arcs. ..."
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/DCC.2007.73">doi:10.1109/DCC.2007.73</A>]['07]
   (<A HREF="/~lloyd/tildeMisc/Local/2007-DCC-graph.pdf">local</A>).
   [Also search for: compress graph].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/Graph/">graphs</A>].)

%A L. Gueguen
%A M. Datcu
%T The model based similarity metric
%J Data Compression Conf.
%I IEEE
%P 382
%M MAR
%D 2007
%K poster, conf, DCC, DCC07, c2007, c200x, c20xx, similar
%X " ... a new info. measure based on models. 1st we make the strong assumption
   that for any obj. x there exists a model M[x] s.t. K(x)=K(x|M[x])+K(M[x]).
   So Li's similarity metric between two objects x & y is reformulated, in the
   case when K(x) <= K(y),
     d(x,y) =    a {K(x,y|M[x,y]) - K(x|M[x])) / K(y|M[y]}
            + (1-a){K(M[x,y]) - K(M[x])) / K(M[y]},
            where a = K(y|M[y])/(K(y|M[y])+K(M[y])) = K(y|M[y])/K(y).
   ...The left[!] part measures the similarity between objs. expressed in their
   models, while the 2nd [part] measures the similarity between models. ...
   when a goes to 0, the sim. metric is more based on the models' complexity.
   ... when a tends to 1, the sim. metric takes into a/c mostly the sim. between
   the randomness of objects. The object y is highly random when a~1, while it
   is highly deterministic when a~0. ... if we consider y|M[x] as a new obj. z
   with its assoc. model M[z], the sim. metric becomes:
     d'(x,y) = a{K(z|M[z]) / K(y|M[y])} + (1-a){K(M[z]) / K(M[y])}
   ... representing an object by its model enables to compare it to another
   using the proposed sim.. [And] the model constitutes a compact representation
   of objects."
   [<A HREF="http://dx.doi.org/10.1109/DCC.2007.76">doi:10.1109/DCC.2007.76</A>]['08].
   ([<A HREF="/~lloyd/tildeMisc/Local/2007-DCC-similarity.pdf">local</A>].)

%A J. Sun
%A E. M. Bollt
%A D. ben-Avraham
%T Graph compression - save information by exploiting redundancy
%J J. Statistical Mechanics: Theory and Experiment
%I IOP
%N P06001
%M JUN
%D 2008
%K eJrnl, c2008, c200x, c20xx, sparse, graphs, compress, benAvraham
%X "... introducing the idea of redundancy, we find a way to measure the overlap
   of neighbors between nodes in n/ws. We exploit symmetry & information by
   making use of the overlap in neighbors & analyzing how info. is reduced by
   shrinking the n/w &, using the specific data structure we created, we
   generalize the problem of compression as an optimization problem on the
   possible choices of orbits. To find a reasonably good solution to this
   problem ... a greedy alg. to determine the orbit of symmetry ids. ..."
   -- [<A HREF="http://dx.doi.org/10.1088/1742-5468/2008/06/P06001">doi:10.1088/1742-5468/2008/06/P06001</A>]['08].
   [Also search for: compress graph].

%A M. Crochemore
%A L. Ilie
%A W. F. Smyth
%T A simple algorithm for computing the Lempel Ziv factorization
%J Proc. of the Data Compression Conf.
%I IEEE
%P 482-488
%D 2008
%K conf, DCC, DCC08, c2008, c200x, c20xx, LZ, ZL, string, strings, compress,
   suffix array, repetitions, repeats, runs, factorization,  factorisation
%X "We give a space-efficient simple alg. for computing the Lempel-Ziv f. of a
   string. For a string of length n over an integer alphabet, it runs in O(n)
   time independently of alphabet size and uses o(n) additional space."
   "The LZ factorization of w is the decomposition w = u0 u1 ... uk, where each
   ui (except possibly uk) is the longest prefix of ui ui+1 ... uk that has
   another occ. to the left in w or a single letter [if] this prefix is empty."
   [<A HREF="http://dx.doi.org/10.1109/DCC.2008.36">doi:10.1109/DCC.2008.36</A>]['08].
   In: us isbn13:978-0-7695-3121-2.

%A M. Hayashida
%A T. Akutsu
%T Comparing biological networks via graph compression
%I Proc. 3rd Int. Symp. on Optimization and Systems Biology
%S LNOR
%V 11
%P 168-176
%M SEP
%D 2009
%O BMC Systems Biology, in press as of 2010
%K conf, MolBio, OSB, OSB09, LNOR, c2009, c200x, c20xx, biological network,
   networks, graph, compression, compress, graphitour
%X "... an original n/w struct. is comp. by iteratively contracting identical
   edges.  ... similarity ~ compression ratio of the concat. n/ws. ...
   ... modify graphitour ..."
   -- pdf@[<A HREF="http://www.aporc.org/LNOR/11/OSB2009F23.pdf">aporc.org</A>]['10].
   [Also search for: compress graph].

%A A. Farina
%A G. Navarro
%A J. R. Parama
%T Boosting text compression with word-based statistical encoding
%J COMPJ
%V 55
%N 1
%P 111-131
%M JAN
%D 2012
%K jrnl, COMPJ, c2012, c201x, c20xx, zz0112, text compression, compress,
   compressed, p7zip, natural language, English, index, indexing
%X "Semistatic word-based byte-oriented compressors ... natural language ...
   compression ratios around 30-35%, they allow fast direct searching of
   compressed text. [shpw] these compressors have even more benefits. We show
   that most of the state-of-the-art compressors benefit from compressing not
   the original text, but the compressed repn obtained by a word-based byte-
   -oriented statistical compressor. [eg] p7zip with a dense-coding
   preprocessing achieves even better compression ratios & much faster compn
   than p7zip alone. We [cr] < 17% in typical large English texts ... show that
   typical self-indexes also profit from our preprocessing step.  ... present a
   new suffix-free Dense-Code-based compressor that compresses slightly better
   [than tagged Huff.].  [and] show how some self-indexes can handle non-suffix-
   -free codes. [so] the compressed/indexed text req. ~35% of the space of the
   original text & allows indexed searches for both words & phrases."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxr096">doi:10.1093/comjnl/bxr096</A>]['12], online Sept '10.
   [Also search for: text compression] and [also search for: compressed index].


%T Manchester Baby and Mark 1
%D 1998
%K 1948, c1948, c194x, c19xx, Computer, History, historic, computing,
   conservation society, Manchester University, Mark1, first, stored program,
   memory, Kilburn, Williams, cathode ray tube, architecture, old, CRT,
   computers, 1998, www, HREF, http, zz0198
%X Experimental machine ran 11.00am Monday 21st June 1948 and calculated
   the highest factor of a number -  Computer Conservation Society.
   -- [<A HREF="http://curation.cs.manchester.ac.uk/computer50/www.computer50.org/mark1/new.baby.html">manch'er</A>][2018],
      [<A HREF="https://web.archive.org/web/20120504133240/http://www.computer50.org/">web.archive</A>]['23].
   (Also see Baby@[<A HREF="https://en.wikipedia.org/wiki/Manchester_Baby">wikip</A>]['23] and
   [<A HREF="http://news.bbc.co.uk/2/hi/technology/7465115.stm">BBC</A>]['20/6/2008].)

%A S. Gill
%T Parallel programming
%J COMPJ
%V 1
%N 1
%P 2-10
%D 1958
%K c1958, c195x, c19xx, jrnl, COMPJ, computer, computing, c1958, c195x, c19xx
%X "By parallel programming is meant the control of 2 or more operations which
   are executed virtually simultaneously, & each of which entails following a
   series of instructions. This can be brought about in a single computer
   either by equipping it with more than 1 control unit, or by allowing time-
   -sharing of 1 control unit between several activities; the latter case seems
   of greater practical interest. Some of the advantages to be gained & some of
   the programming problems to be solved in putting these ideas into practice
   are discussed."
   -- [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_01/Issue_01/010002.sgm.abs.html">paper</A>]['04].

%A G. E. Moore
%T Cramming more components onto integrated circuits
%J Electronics Magazine
%V 38
%N 8
%P 114-117
%M APR
%D 1965
%O reprinted Proc. IEEE, vol.86, no.1, Jan., 1998
%K c1965, c196x, c19xx, zz0415, Moore's law, Moores law, computing, integrated,
   Intel, electronic, circuit, semiconductor, component, density,
   chip, chips, doubling
%X "With unit cost falling as the number of components per circuit rises, by
   1975 economics may dictate squeezing as many as 65,000 components on a single
   silicon chip. ..."
   -- pdf@[<A HREF="http://www.cs.utexas.edu/~fussell/courses/cs352h/papers/moore.pdf">utex</A>]['15],
      $$$@[<A HREF="http://dx.doi.org/10.1109/JPROC.1998.658762">doi:10.1109/JPROC.1998.658762</A>]['15].
   Also see M_Law@[<A HREF="http://en.wikipedia.org/wiki/Moore%27s_law">wikip</A>]['15].

%A S. G. Younis
%A T. F. Knight jr
%T Practical implementation of charge recovering asymptotically zero power CMOS
%J Proc. of the 1993 Symp. on Research on Integrated Systems
%W Seattle
%P 234-250
%D 1993
%K conf, energy, reversible, logic, computation, c1993, c199x, c19xx, energy,
   recovery, recover, electronics, consumption, save, saving, hardware,
   circuit, circuits, gate, gates
%X "... new CMOS logic family, Charge Recovery Logic (CRL), with a power
   dissipation that falls with the square of the operating freq., as opposed
   to the linear drop of conventional CMOS ...  relies on constructing an
   explicitly reversible pipelined logic gate, where the information necc'
   to recover the energy used to compute a value is provided by computing its
   logical inverse. Info' necc' to uncompute the inverse is available from
   the subsequent inverse logic stage. ... anticipate enery savings of over
   99% per logic op'n [if] clocked sufficiently slowly."
   -- [<A HREF="http://www.ai.mit.edu/people/tk/lowpower/crl.ps">crl.ps@ai.mit.edu</A>][9/'04].

%A P. J. Bird
%T LEO: The First Business Computer
%I Hasler Pub. Ltd., Berkshire UK
%D 1994
%P 272
%K book, text, history, early, old, computer, computers, computing, LEO,
   J. Lyons and Co. Ltd., England, UK, 1951, c1951, c195x, c19xx, zz0596
%X isbn:0952165104.  Good review by P.E.Ceruzzi in Comp Rev p112-113 Feb 96
   Lyons Electronic Office, Leo, built by J. Lyons and Co (a UK catering
   company!), operational Sept 1951.
   Also see [<A HREF="http://www.leo-computers.org.uk">leo-computers.org.uk</A>][8/'03]
   [Also search for: LEO Lyons]

%A D. Caminer
%A J. Aris
%A P. Hermon
%A F. Land
%T User-Driven Innovation: The World's First Business Computer (LEO)
%I McGrawHill
%P 392
%D 1996
%O ? LEO: The Incredible Story of the World's First Business Computer ? '97 ?
%K book, text, LEO, history, early, old, computer, computers, computing, c1951,
   c195x, c19xx, zz0803 J. Lyons and Co Ltd, England, UK, tea shop, shops
%X Lyons Electronic Office, Leo. uk us isbn:0077092368. hb.
   [Also search for: LEO Lyons]. uk us isbn:0070095019.

%A G. Ferry
%T A Computer Called LEO: Lyons Teashops and the World's First Office Computer
%I FourthEstate
%P 240
%D 2003
%K book, text, history, early, old, computer, computers, computing, c1951,
   c195x, c19xx, zz0803, J. Lyons and Co Ltd, England, UK, tea shop, shops
%X about stg16.00. isbn:1841151858.
   "... LEO was, essentially, a copy of the EDSAC with a few hardware
   innovations and some limited software advances. Its main claim to
   fame is in the applications area. ... "
   [<A HREF="http://dx.doi.org/10.1038/424616a">review -- doi:10.1038/424616a</A>][8/'03]
   Aug c2004, ppb, stg8.00, isbn:1841151866.  [Also search for: LEO Lyons].

%A E. Organick
%T Computer System Organization: The B5700/B6700 Series
%I AcademicPress
%D 1973
%K book, text, Burroughs, 5700, 6700, B5700, B6700, computer architecture,
   stack, cactus, display, c1973, c197x, c19xx
%X enews: D.Sand [11/'95].

%A W. D. Hillis
%A G. L. Steele
%T The Connection Machine
%D 1986
%I MITpress
%K connection machine, CM, CM-2, CM2, massively parallel, supercomputer,
   super computer, book, text, zz0196, c1986, c198x, c19xx
%X ref hill86b in   D a v i e  `an intro to fp sys' using hask'll'.

%A W. D. Hillis
%A L. W. Tucker
%T The CM-5 Connection machine: a scalable supercomputer
%J CACM
%V 36
%N 11
%P 31-40
%M NOV
%D 1993
%K CACM, CM5, CM, super computer, parallel, MIMD, c1993, c199x, c19xx
%X reviewed in Comp. Rev. 35(10) p525 Oct '94
   See also CM2

%A M. Campbell-Kelly
%T ICL and the evolution of the British mainframe
%J COMPJ
%V 38
%N 5
%P 400-412
%D 1995
%K COMPJ, jrnl, computer, computing, history, ICL, 1900, 4-70, 2900, zz1295,
   c1995, c199x, c19xx
%X 6 photographs which are also good for nostalgia and the fashions of the day.
   [23 refs].
   [<A HREF="http://dx.doi.org/10.1093/comjnl/38.5.400">doi:10.1093/comjnl/38.5.400</A>]['10].

%A R. Jozsa
%T Entanglement and quantum computation
%J Geometric Issues in the Foundations of Sci.
%I OUP
%M JUL
%D 1997
%K conf, c1997, c199x, c19xx, quantum computing, algorithm, information, state,
   QFT, speedup, collapse, entanglement, entangled, entangle, superposition,
   physics, intro
%X "We argue that entanglement is the essential non-classical ingredient which
   provides the computational speed-up in q.algs. as compared to algs. based on
   the processes of classical physics." [24 refs]
   -- [<A HREF="https://arxiv.org/abs/quant-ph/9707034">arxiv:quant-ph/9707034</A>]['24].
   [Also search for: quantum computing].

%A G. Kane
%A J. Heinrich
%T MIPS RISC Architecture
%I PrenticeHall
%D 1992
%K book, text, computer architecture, R2000, R3000
%X reduced instruction set computer
   ref' in  J. R. L a r u s'  SPIM notes '93

%A C. Kopp
%T Code morphing - the shape of the future
%J Systems Magazine
%M AUG
%D 2000
%I AuscomPubl.
%P 20-28
%K computer architecture, VLIW, CISC, Crusoe, Intel, Transmeta, zz0800
%X Introduction to code morphing and computer architecture trends c2000.
   Publisher: [<A HREF="http://www.auscoms.com.au/">www</A>][9/'00]
   Sys' Mag': [<A HREF="http://www.auscoms.com.au/sysintro.htm">www</A>][9/'00].

%A I. E. Sutherland
%T Micropipelines (the Turing award lecture)
%J CACM
%V 32
%N 6
%P 720-738
%M JUN
%D 1989
%K jrnl, micropipeline, micro pipeline, computer architecture, Sun, MS

%A Tony Sale
%T The Colossus Computer (1943-1996) And How It Helped to Break the
   German Lorenz Cipher in WWII
%I M&M Baldwin
%M NOV
%D 1998
%K c1998, c199x, c19xx, booklet, computer history, Colossus, cypher, ciphers,
   Bletchley Park, WW2, wwII, world war two, code, codes, breaking,
   cryptography, zz1004
%X [Also search for: Bletchley Park].
   1st ed 1998; uk us isbn:0947712364; uk us isbn13:978-0947712365.
   See [<A HREF="http://www.codesandciphers.org.uk/">codesandciphers.org.uk</A>]['04].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">B.Park</A>].)

%T Principles of Asynchronous Circuit Design: A Systems Perspective
%E J. Sparso
%E S. B. Furber
%I Kluwer
%P 360
%D 2001
%K book, text, computer architecture
%X Also see async logic [<A HREF="http://www.cs.man.ac.uk/async/">www</A>][8/'02].
   uk us isbn:0792376137.  us$115.
   [<A HREF="http://www.imm.dtu.dk/~jsp/">jsp</A>][8/'02].

%T High Performance Cluster Computing: Architectures and Systems
%E R. Buyya
%I PrenticeHall
%P 881
%M JUN
%D 1999
%K book, text, parallel, cluster, clusters, computer networks, MPI, zz1002
%X uk us isbn:0130137847.   About us$68.

%A W. Gropp
%A E. Lusk
%A A. Skjellum
%T Using MPI - 2nd Edition: Portable Parallel Programming with
   the Message Passing Interface
%I MITpress
%P 350
%M NOV
%D 1999
%K book, text, MPI, messages, openMP, parallel, network, computer,
   clusters, zz1002
%X us isbn:0262571323.  About us$40.

%A R. J. Anderson
%T Security Engineering: A Guide to Building Dependable Distributed Systems
%I Wiley
%P 640
%D 2001
%K book, text, c2001, c200x, c20xx, zz0414, computer, network, security, build,
   cryptography, bank, banking, military, DRM, attack, attacks, hacking, crime,
   internet, system
%X 1st ed 2001; pb us$17; uk us isbn:0471389226; uk us isbn13:978-0471389224.
   2nd ed 2008; hb us$57; uk us isbn:0470068523; uk us isbn13:978-0470068526.
   "...  for today's programmers who need to build systems that withstand
   malice as well as error (but have no time to go do a PhD in security), this
   book illustrates basic concepts through many real-world system design
   successes and failures. Topics range from firewalls, through phone phreaking
   and copyright protection, to frauds against e-businesses. ..."
   (Also see book@[<A HREF="https://www.cl.cam.ac.uk/~rja14/book.html">cam.ac.uk</A>]['14].)

%E G. Trogemann
%E A. Y. Nitussov
%E W. Ernst
%A A. Y. Nitussov (trans.)
%T Computing in Russia : the history of computer devices and information
   technology revealed
%P 350
%I Braunschweig; Wiesbaden: Vieweg
%D 2001
%K book, text, c2001, c200x, c20xx, zz1218, ternary, computer, computers,
   history, Russia, Russian, Soviet, Setun, 1958, Brusentsov
%X -- 39089515@[<A HREF="https://trove.nla.gov.au/version/39089515">nla.gov.au</A>]['18].
   (Also see, "... The first modern, electronic ternary computer Setun was
   built in 1958 in the Soviet Union at the Moscow State University by
   Nikolay Brusentsov ..."
   -- TC@[<A HREF="https://en.wikipedia.org/wiki/Ternary_computer">wikip</A>]['18].)
   [Also search for: ternary computer].

%A W. Gropp
%A E. Lusk
%A T. Sterling
%T Beowulf Cluster Computing with Linux (2nd ed.)
%I MITpress
%P 618
%D 2003
%K book, text, OS, unix, c2003, c200x, c20xx, computer, parallel, farm,
   network, MPI, PVM, machine
%X 2nd ed 2003; stg21.50; us isbn:0262692929.

%A D. A. Patterson
%A J. L. Hennessy
%T Computer Organization and Design: The Hardware / Software Interface
%I MorganKaufmann
%P 656
%D 2004
%K book, text, c2004, c200x, c20xx, computers, architecture, hardware
%X 4th ed 2008; pb us$74; uk us isbn:0123744938; uk us isbn13:978-0123744937.
      "Covers the revolutionary change from sequential to parallel computing,
       with a new chapter on parallelism and sections in every chapter
       highlighting parallel hardware and software topics. ..."
   3rd ed 2004; pb us$65; uk us isbn:1558606041; uk us isbn13:978-1558606043.

%A M. Glusker
%A D. M. Hogan
%A P. Vass
%T The ternary calculating machine of Thomas Fowler
%J IEEE Annals of the History of Computing
%V 27
%N 3
%P 4-22
%M JUL-SEP
%D 2005
%K jrnl, c2005, c200x, c20xx, zz1218, 1840, 19C, Thomas Fowler, history,
   computing, computer, computers, balanced ternary, calculator
%X "In 1840, Thomas Fowler, a self-taught English mathematician & inventor,
   created a unique ternary calculating machine. Recently, all detail of this
   machine was lost. A research project begun in 1997, uncovered sufficient
   information to enable the recreation of a physical concept model of Fowler's
   machine. The next step is to create a historically accurate replica."
   -- [<A HREF="https://doi.org/10.1109/MAHC.2005.49">doi:10.1109/MAHC.2005.49</A>]['18].
     (Note: 'balanced ternary' has base 3 & digits for -1,0,+1, {n,z,p} say,
      0='z', 1='p', 2='pn' (i.e., 3-1), 3='pz', 4='pp', 5='pnn' (9-3-1), etc.;
      to negate a number, swap all 'p's to 'n's and all 'n's to 'p's.)
     ['Description of a calculating machine, invented by Mr. Thomas Fowler of
      Torrington in Devonshire', Archive Papers, A.DeMorgan,
      The Royal Soc., London, 1840.]
   (Also see TF@[<A HREF="https://en.wikipedia.org/wiki/Thomas_Fowler_(inventor)">wikip</A>]['18].)
   [Also search for: ternary computer].

%A F. Land
%T Leo II and the Model T Ford
%J COMPJ
%V 49
%N 6
%P 650-656
%M NOV
%D 2006
%K COMPJ, jrnl, c2006, c200x, c20xx, history of computing, computers, computer,
   Lyons Electronic Office, Leo2, LeoII, Leo
%X "The paper describes an order processing and stock control application
   implemented at the Ford Motor Company's spare parts depot at Aveley in
   the late 1950s. A major feature was the effective combination of computer
   and punched card technology, which was the key to success."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxl041">doi:10.1093/comjnl/bxl041</A>]['06].
   [Also search for: LEO Lyons].

%A S. Furber
%A S. Temple
%T Neural systems engineering
%J J. Royal Soc. Interface
%V 4
%P 193-206
%D 2007
%K jrnl, c2007, c200x, c20xx, zz1019, NN, ANN, ManchesterUni, UManchester,
   SpiNNaker
%X "...  At present, however, knowledge about the operational principles of the
   brain is far from complete, so attempts at emulation must employ a great
   deal of assumption and guesswork ... o computer engineers have something to
   contribute, alongside neuroscientists, psychologists, mathematicians and
   others, to the understanding of brain and mind, which remains as one of the
   great frontiers of science?"
   -- [<A HREF="http://dx.doi.org/10.1098/rsif.2006.0177">doi:10.1098/rsif.2006.0177</A>]['19].
   [Also search for: SpiNNaker].
   Also see SpiNNaker@[<A HREF="http://apt.cs.manchester.ac.uk/projects/SpiNNaker/">manchester</A>]['19].

%A G. Colon-Bonet
%A P. Winterrowd Jr
%T Multiplier evolution: A family of multiplier VLSI implementations
%J COMPJ
%V 51
%N 5
%P 585-594
%M SEP
%D 2008
%K jrnl, COMPJ, c2008, c200x, c20xx, implementation, multiplication,
   computer hardware, arithmetic
%X "... overview of 4 floating pt multiplier implementations spanning
   microprocessor designs from c1992 to the present. The alg. of each multiplier
   is explored in detail, & key measures of area, delay & design complexity are
   compared. The approaches span from a simple linear array to a full tree-based
   n/w, each targeted at efficient VLSI implementation. ... show a progression
   of impl. techniques encompassing a 20x increase in ... performance ..."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm123">doi:10.1093/comjnl/bxm123</A>]['08].
   [Also search for: multiplier].

%A M. Hassaballah
%A S. Omran
%A Y. B. Mahdy
%T A review of SIMD multimedia extensions and their usage in scientific and
   engineering applications
%J COMPJ
%V 51
%N 6
%P 630-649
%D 2008
%K jrnl, COMPJ, c2008, c200x, c20xx, intel, IA 32, IA32, MMX, SSE, SSE2, SSE3,
   SIMD, extension, streaming, scientific, programming, computing, hardware,
   instructions, algorithm, graphics processor, unit, GPU, GPUs, streaming,
   scanning
%X "... The SIMD computational technique was introduced in the IA-32 Intel
   arch. with MMX tech. & then further enhanced with Intel's introduction of
   streaming SIMD extensions (SSE), SSE 2 (SSE2) & SSE 3 (SSE3). Although
   programming using these SIMD extensions enables s/w to achieve higher
   performance, several exiting sci. applications are not affected. ... gives
   an overview of SIMD multimedia extensions. ... reviews recent trends to use
   multimedia extensions to accelerate many applications such as multimedia,
   scientific & engineering applications, & argues for further use in other
   significant computationally intensive applications."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm099">doi:10.1093/comjnl/bxm099</A>]['08].

%A R. Kastner
%A A. Hosangadi
%A F. Fallah
%T Arithmetic Optimization Techniques for Hardware and Software Design
%I CUP
%P 200
%D 2010
%K book, text, CUP, c2010, c201x, c20xx, zz0710, computer, hardware, arithmetic,
   technique, FIR filters
%X "Obtain better system performance, lower energy consumption, and avoid hand-
   -coding arithmetic functions with this concise guide to automated
   optimization techniques for hardware and software design. High-speed
   architectures for implementing FIR filters are also covered, whilst clearly
   explained algorithms and illustrative examples make it easy to understand
   and implement the techniques."
   1st ed 2010; hb stg70; uk us isbn:0521880998; uk us isbn13:978-0521880992.

%A J. Smiley
%T The Man Who Invented the Computer: The Biography of John Atanasoff,
   Digital Pioneer
%I Doubleday
%P 256
%D 2010
%K book, text, c2010, c201x, c20xx, zz1210, Atanasoff, history, computer,
   computers, computing
%X 1st ed 2010; hb us$17; uk us isbn:0385527136; uk us isbn13:978-0385527132.
   "... In 1936, Atanasoff & his colleague, A.E.Brandt, modified an IBM
   tabulator - which used punched cards to add or subtract values represented by
   the holes in the cards - to get it to perform in a better, faster, & more
   accurate way. One Dec. evening in '37, Atanasoff, still struggling to hit
   upon a formula that would allow a m/c to replicate the human brain, drove
   from Ames, Iowa, to Rock Island, Ill., where, over a bourbon & soda in
   a roadside tavern, he sketched his ideas for a m/c that would become the
   computer. As with many scientific discoveries or inventions, however, the
   original genius behind the innovation is often obscured by later, more
   aggressive, & savvy scientists who covet the honor for themselves. ..."
   (Reviewed in [<A HREF="http://dx.doi.org/10.1038/468760a">n@ture</A>]['10].)
   [Also search for: history computer].

%A D. Barron
%T EDSAC: A programmer remembers
%J COMPJ
%V 54
%N 1
%P 139-142
%M JAN
%D 2011
%K jrnl, COMPJ, c2011, c201x, c20xx, zz0211, EDSAC, computer, computers,
   computing, history, cambridge, uk, delay line, lines
%X "The author is one of the very few people still alive who programmed the
   electronic delay storage automatic calculator (EDSAC), and he describes what
   it was like to be involved in those pioneering days, with an account of life
   in the Mathematical Laboratory and the mechanics of using the machine. The
   paper goes on to describe the hardware and software of the Cambridge EDSAC
   computer specifically from the user's point of view."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxp115">doi:10.1093/comjnl/bxp115</A>]['11].
   [Also search for: history computer].
   (Also see other papers in the same issue.)

%A S. J. Pennycook
%A S. D. Hammond
%A G. R. Mudalige
%A S. A. Wright
%A S. A. Jarvis
%T On the acceleration of wavefront applications using distributed many-core
   architectures
%J COMPJ
%V 55
%N 2
%P 138-153
%M FEB
%D 2012
%K jrnl, COMPJ, c2012, c201x, c20xx, zz0212, parallel, computing, computer, GPU,
   k-blocking, Bluegene, NVIDIA, speedup, speed up, cluster, wavefront,
   wave front
%X "... employ a recently developed port of the LU solver (from the NAS Parallel
   Benchmark suite) to investigate the performance of [wavefront] algs. on high-
   -performance computing solns from NVIDIA (Tesla C1060 & C2050) [and] trad.
   clusters (AMD/InfiniBand & IBM BlueGene/P). ... demonstrate that while the
   theor.perfo. of GPU solns will far exceed those of many trad. technologies,
   the sustained application performance is currently comparable for sci.
   wavefront applications. Finally, a breakdown of the GPU soln is conducted,
   exposing PCIe overheads & decomposition constraints. A new k-blocking
   strategy is proposed to improve the future performance of this class of
   algorithm on GPU-based architectures."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxr073">doi:10.1093/comjnl/bxr073</A>]['12].

%T Alan Turing and His Contemporaries: Building the World's First Computers
%E S. Lavington
%I British Informatics Soc.
%P 126
%M FEB
%D 2012
%K book, text, c2012, c201x, c20xx, zz0312, Alan Turing, computer, history, WW2,
   WWII, computing, technology, uk, Ferranti, English Electric, Elliott,
   British Tabulating Machine Company
%X 1st ed 2012; pb us$23; uk isbn:1906124906; uk isbn13:978-1906124908.
   "... Turing took an early lead on the theory side, along with fellow
   mathematicians on both sides of the Atlantic. This is the story of the people
   and projects that flourished in the post-war period. By 1955 the computers
   produced by companies such as Ferranti, English Electric, Elliott Brothers &
   the British Tabulating Machine Co. ..."
   [Also search for: computer history book], optionally drop book.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">B.Park</A>].)

%A W. K. Grassmann
%T A computer built with relays and a mechanical memory, and ALGOL
%J COMPJ
%V 55
%N 11
%P 1309-1316
%M NOV
%D 2012
%K jrnl, COMPJ, c2012, c201x, c20xx, zz1112, history, computer, computing,
   Zuse, Z4, Zurich, ETH, Stiefel, Rutishauser, Speiser, programming language,
   Algol 58, Algol58, relay
%X "ALGOL was formulated in Zurich in 1958, & this paper explores some of the
   reasons why this happened in Zurich & not in the USA. One factor may have
   been that the 1st computer on the continent, the Z4, was installed in Z. in
   1950. This computer was built by Zuse during the Second World War. It used
   relays for its arith. & control units, but it had a mechanical memory.
   Though the machine had limited capabilities, it provided valuable programming
   experience to a # of researchers, in particular to Stiefel, Rutishauser &
   Speiser at the ETH Zurich. Already in 1952, Rutishauser formulated a higher
   programming construct, a counted loop, & he also indicated how to convert
   math.exps. into m/c language. We also should mention that Bauer, who
   was influenced by Rutishauser, also developed a method to implement
   math.exps., but he used computer h/ware for the task. The two started to
   collaborate, & they formulated a preliminary lang. in 1957. This l. was then
   formalized at a ACM/GAMM meeting in Z. under the name Int. Algebraic Lang.,
   or IAL, a language later renamed ALGOL 58."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxr132">doi:10.1093/comjnl/bxr132</A>]['12].
   (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/Algol60/">Algol60</A>].)

%A T. Pfeil
%A et al ...
%A K. Meier
%T Six networks on a universal neuromorphic computing substrate
%J arXiv
%M OCT
%D 2012
%K arXiv, c2012, c201x, c20xx, zz1212, computer, neural network, ANN, hardware,
   Spikey chip, brainscales, brainInets, blueBrain, neurons
%X "... present a highly configurable neuromorphic computing substrate & use it
   for emulating several types of NNs. ... a mixed-signal chip, with analog
   implementations of neurons & synapses & digital transmission of action
   potentials. ... inherent parallelism, a high speed-up factor & low power
   consumption ... Its configurability allows the realization of almost
   arbitrary network topologies & the use of widely varied neuronal & synaptic
   parameters. Fixed-pattern noise inherent to analog circuitry is reduced by
   calibration routines. ... describe the successful emulation of six different
   NNs which cover a broad spectrum of both structure & functionality."
   -- @[<A HREF="http://arxiv.org/abs/1210.7083">arXiv</A>].   (?T0 anyone?)
   (Also see [<A HREF="http://brainscales.kip.uni-heidelberg.de/">BrainScaleS</A>]@uni-heidelberg.)

%A M. M. Shulaker
%A G. Hills
%A N. Patil
%A H. Wei
%A H.-Y. Chen
%A H.-S. Philip Wong
%A S. Mitra
%T Carbon nanotube computer
%J Nature
%V 501
%N 7468
%P 526-530
%M SEP
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0913, carbon, nano tube, tubes, computing, gate,
   circuit, technology, SUBNEG, CNFET
%X "... Digital circuits based on transistors fabricated from carbon nanotubes
   (CNTs) have the potential to outperform silicon by improving the energy-delay
   product, a metric of energy efficiency, by more than an order of magnitude.
   Hence, CNTs are an exciting complement to existing semiconductor tech.. Owing
   to substantial fundamental imperfections inherent in CNTs, however, only very
   basic circuit blocks have been demonstrated. Here we show how these
   imperfections can be overcome, & demonstrate the first computer built
   entirely using CNT-based transistors. The CNT computer runs an O/S that is
   capable of multitasking: as a demonstration, we perform counting & integer-
   -sorting simultaneously. In addition, we implement 20 different instructions
   from the commercial MIPS instruction set to demonstrate the generality of
   our CNT computer. This experimental demonstration is the most complex
   carbon-based electronic system yet realized. ...
   The CNT computer is a one-instn-set computer, implementing the SUBNEG
   (subtract & branch if -ve) instn ... The CNFET computer is composed of 178
   CNFETs, with each CNFET comprising ~10-200 CNTs ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12502">doi:10.1038/nature12502</A>]['13].

%A D. Piso
%A J. D. Bruguera
%T Obtaining accurate error expressions and bounds for floating-point
   multiplicative algorithms
%J COMPJ
%V 57
%N 2
%P 319-331
%M FEB
%D 2014
%K jrnl, COMPJ, c2014, c201x, c20xx, zz0214, computer arithmetic, algorithm.
   division, reciprocal, square root, reciprocal, hardware, Goldschmidt,
   accuracy, errors
%X "Multiplicative Newton-Raphson and Goldschmidt algs. are widely used in
   current processors to implement division, reciprocal, square root & square
   root reciprocal operations. Based on an initial approxn of a given accuracy,
   several iterations are performed until ...  compare the optimal multiplier
   size obtained from our error analysis with the multipliers in the
   floating-point division & square root units of some popular processors & we
   conclude that the multiplier size & its area can be reduced by, ~ 10%."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxs170">doi:10.1093/comjnl/bxs170</A>]['14].

%A M. Ward
%T Half-century milestone for IBM mainframes
%I BBC
%M APR
%D 2014
%K news, bbc, c2014, c201x, c20xx, zz0414, computer, computers, history,
   IBM, System 360, ICL, 1900, mainframe, mainframes, SysRq, computing
%X "The first System 360 mainframe was unveiled on 7 April 1964 ..."
   -- bbc [<A HREF="http://www.bbc.com/news/technology-26886579">6/4/2014</A>].

%A P. A. Merolla
%A et al ...
%A D. S. Modha
%T A million spiking-neuron integrated circuit with a scalable communication
   network and interface
%J Science
%V 345
%N 6197
%P 668-673
%M AUG
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0814, computer, computing, architecture,
   parallel, neuron, ANN, chip, image processing, processor,
   IBM, TrueNorth, SpiNNaker, Movidius
%X "... developed an efficient, scalable, & flexible non-von Neumann arch. that
   leverages contemporary silicon tech.. ... built a 5.4-billion-transistor chip
   with 4096 neurosynaptic cores interconnected via an intrachip n/w that
   integrates 1 million programmable spiking neurons & 256 million configurable
   synapses. Chips can be tiled in 2D via an interchip commn interface,
   seamlessly scaling the architecture to a cortexlike sheet of arbitrary size.
   The arch. is well suited to many applicns that use complex neural n/ws in
   real time, for example, multiobject detection & classification. With
   400-pixel-by-240-pixel video input at 30frames/sec, the chip consumes
   63 milliwatts."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1254642">doi:10.1126/science.1254642</A>]['14].
   [Also search for: SpiNNaker]  and  [also search for: ANN chip].
   Also see SpiNNaker@[<A HREF="http://apt.cs.manchester.ac.uk/projects/SpiNNaker/">manchester</A>]['19].
   (Also see [<A HREF="http://www.bbc.com/news/science-environment-28688781">bbc</A>][8/8/2014].)

%A I. L. Markov
%T Limits on fundamental limits to computation
%J Nature
%V 512
%N 7513
%P 147-154
%M AUG
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0814, computer, computing, hardware, limit,
   electronics, technology, speed, Moore, Moore's law, Moores, densities
%X "... improvements in computer h/w have been supported by periodic doubling
   of transistor densities in ICs over the past 50y.. Such Moore scaling now
   requires ever-increasing efforts, stimulating res. in alt. h/w & stirring
   controversy. To help eval. emerging technologies & increase our understanding
   of IC scaling ... rev. fund'l limits to compn in the areas of manufacturing,
   energy, physical space, design & verification effort & algs.. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13570">doi:10.1038/nature13570</A>]['14].

%A M. Prezioso
%A et al ...
%A D. B. Strukov
%T Training and operation of an integrated neuromorphic network based on
   metal-oxide memristors
%J Nature
%V 521
%N 7550
%P 61-64
%M MAY
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0515, hardware, ANN, memristor, electronic,
   circuit, device, computer, perceptron
%X "Despite much progress in semiconductor integrated circuit technology, the
   extreme complexity of the human cerebral cortex, with its approximately
   10^14 synapses, makes the h/ware implementation of neuromorphic n/wks with a
   comparable # of devices exceptionally challenging. ... discrete memristors
   have been used as artificial synapses in neuromorphic n/wks. ... extended to
   crossbar arrays of phase-change memristive devices. ... single-layer
   perceptron ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature14441">doi:10.1038/nature14441</A>]['15].

%T Proc. 7th Int. Conf. on Reversible Computation
%W Grenoble
%I SpringerVerlag
%M JUL
%D 2015
%K conf, c2015, c201x, c20xx, zz0715, reversible, computing, machines, circuit,
   quantum
%X uk us isbn13:978-3319208602.

%A M. M. Waldrop
%T The chips are down for Moore's law
%J Nature
%V 530
%P 144-147
%M FEB
%D 2016
%K news, views, c2016, c201x, c20xx, computers, computer architecture,
   Moore, Moores, law, silicon chip, circuit density
%X "The semiconductor industry will soon abandon its pursuit of Moore's law. Now
   things could get a lot more interesting.  Next month, the worldwide
   semiconductor industry will formally acknowledge what has become increasingly
   obvious to everyone involved: Moore's law, the principle that has powered the
   information-technology revolution since the 1960s, is nearing its end. ...
   But in the early 2000s, when the features began to shrink below about
   90 nanometres, that automatic benefit began to fail. As electrons had to move
   faster and faster through silicon circuits that were smaller and smaller,
   the chips began to get too hot. ...
   -- [<A HREF="http://dx.doi.org/10.1038/530144a">doi:10.1038/530144a</A>]['16].

%A T. Jones
%A A. Brown
%A I. Bush
%A S. C. Benjamin
%T QuEST and high performance simulation of quantum computers
%J Sci. Reports
%V 9
%N #10736
%M JUL
%D 2019
%J jrnl, c2019, c201x, c20xx, zz-723, quantum computer, computing, simulation,
   simulator, QuEST, Tyson Jones, UOxford, ProjectQ, qHipster, Quantum++,
   OpenSource
%X "... QuEST, the Quantum Exact Simulation Toolkit, & compare it to ProjectQ,
   qHipster & a recent distributed implementation of Quantum++. QuEST is the
   first open source, hybrid multithreaded & distributed, GPU accelerated
   simulator ... benchmark QuESTâs sim'n of random circuits of up to 38 qubits,
   distributed over up to 2048 compute nodes, each with up to 24 cores ..."
   -- [<A HREF="https://doi.org/10.1038/s41598-019-47174-9">doi:10.1038/s41598-019-47174-9</A>]['23].
   (Also see TJ@[<A HREF="https://tysonjones.io">www</A>]['23].)

%T How a cake company pioneered the first office computer
%I BBC
%M NOV
%D 2019
%K computer history, LEO, Leo, c2019, c201x, c20xx, c195x, zz1219, computing,
   business, Lyons Electronic Office, Mary Coombs, programmer, woman, women,
   UK, cakes
%X "... [memory on] Leo1 was 2K ..."   (video 3:45)
   -- [<A HREF="https://www.bbc.com/news/av/stories-50559357/how-a-cake-company-pioneered-the-first-office-computer">bbc</A>][27/11/2019].
   Also see Leo@[<A HREF="https://en.wikipedia.org/wiki/LEO_(computer)">wikip</A>]['19] and
   the Science Museum [<A HREF="https://www.sciencemuseum.org.uk/objects-and-stories/meet-leo-worlds-first-business-computer">www</A>]['19].
   [Also search for: LEO Lyons] and [also search for: computer history].

%A B. Ainsworth
%T Trevor Pearcey and the development of CSIRAC - An Australian
   first-generation computer
%I IEEE Annals of the History of Computing
%V 45
%N 4
%P 53-63
%M OCT-DEC
%D 2023
%K jrnl, 1949, c194x, c195x, zz1124, c2023, Australia, history, computing
%X "In Nov. 1949, a team led by Trevor Pearcey & Maston Beard ran the first
   successful tests on their digital computer designated CSIR/CSIRO Mark 1,
   later to be called CSIRAC, at the CSIRO Divn of Radiophysics, Sydney ..."
   -- [<A HREF="https://doi.ieeecomputersociety.org/10.1109/MAHC.2023.3306780">doi:10.1109/MAHC.2023.3306780</A>]['24].
   (Also see TP@[<A HREF="https://www.eoas.info/biogs/P001249b.htm">EoAS</A>]['24].)
   [Also search for: history computer].

%A Hongwei Cai
%A et al ...
%A Feng Guo
%T Brain organoid reservoir computing for artificial intelligence
%J NatureElectronics
%V 6
%P 1032-1039
%M DEC
%D 2023
%K jrnl, c2023, c202x, c20xx, zz1223, brain organoid, cell, cells, Brainoware,
   wetware, biol, computing, AI, ANN
%X "... we report an [AI] hardware approach that uses adaptive reservoir
   computation of biological NNs in a brain organoid. In this approach - which
   is termed Brainoware - computation is performed by sending & receiving
   information from the brain organoid using a high-density multielectrode
   array. ..."
   -- [<A HREF="https://doi.org/10.1038/s41928-023-01069-w">doi:10.1038/s41928-023-01069-w</A>]['23].
   [Also search for: computing AI brain organoid].

%A D. Genkina
%T Brain-inspired computer approaches brain-like size; gestalt design yields
   flexibility and neuromorphic computational scale
%J IEEE Spectrum
%M MAY
%D 2024
%K news, c2024, c202x, c20xx, zz0624, SpiNNcloud SpiNNaker, SpiNNaker1,
   neuromorphic, computer, computing, chip, DresdenUT, TUDresden, UManchester,
   ANN, Loihi, NorthPole
%X "... Dresden, Germany-based startup SpiNNcloud Systems announced that its
   hybrid supercomputing platform ... SpiNNcloud ... is available for sale ..."
   -- [<A HREF="https://spectrum.ieee.org/neuromorphic-computing-spinnaker2">www</A>[8/5/24].
   Also see [<A HREF="https://spinncloud.com/">spinncloud</A>]['24]
   and  [<A HREF="https://www.bbc.com/news/articles/cx99qv2w1ddo">bbc</A>][18/6/2024</A>].
   [Also search for: neuromorphic computer].


%A P. Sugden
%T The Complete History of Jack the Ripper
%I Robinson
%D 1995
%P 544
%K book, text, reference, Philip Sugden, good, Jack the Ripper, Whitechapel,
   murder, murders, murderer, crime, c1888, c188x
%X Murders 1888-1891. Ripper's probably 5, 31 Aug - 9 Nov 1888.
   pb '02 isbn:0786709324.   pb '95 isbn:0786702761.  hb '94 isbn:0786701242.
   (See [<A HREF="http://www.met.police.uk/history/ripper.htm">police</A>][11/'02].)

%A P. Begg
%A M. Fido
%A K. Skinner
%T The Jack the Ripper A-Z
%I Headline
%P 560
%D 1996
%K book, text, good, Jack the Ripper, Whitechapel, murder, murders,
   murderer, crime, c1888, c188x
%X Murders 1888-1891. Ripper's probably 5, 31 Aug - 9 Nov 1888. isbn:0747255229.
   (See [<A HREF="http://www.met.police.uk/history/ripper.htm">police</A>][11/'02].)

%A S. P. Evans
%A K. Skinner
%T Jack the Ripper: Letters from Hell
%I SuttonPub.
%M SEP
%D 2001
%P 316
%K book, letters, documents
%X "...The authors are the first to have read, examined and
   photographed every letter. ...".  isbn:0750925493.

%A S. P. Evans
%A K. Skinner
%T The Ultimate Jack the Ripper Sourcebook
%I ConstableRobinson
%M JAN
%D 2002
%K book, letters, documents, murder
%X "...Providing an overview of the crimes and the police investigation, the
   two editors have collated all the known official records, supplemented by
   important [] information, to produce an encyclopaedia of Ripper research."
   2002, pb, isbn:1841194522.  Oct 2000, hb, isbn:1841192252.

%A P. Cornwell
%T Portrait of a Killer: Jack the Ripper -- Case Closed
%I PutnamPubl
%M NOV
%D 2002
%P 352
%K popular book, Jack the Ripper, Whitechapel, murder, murders, murderer,
   crime, Walter Sickert, c1888, c188x
%X Cornwell argues her case that the murderer was the painter
   Walter Sickert (1860-1942)  isbn:0399149325.  (UK isbn:0316861596.)
   Sickert painted a series the ``Camden Town Murders'' in 19xx.
   Is this Patricia C's instantiation of a common obsession or
   is she onto something?
   (See [<A HREF="http://www.met.police.uk/history/ripper.htm">police</A>][11/'02].)


%A M. Wallace
%T Communicating with Databases in Natural Language
%I EllisHorwood
%P 170
%D 1984
%K book, text, mgw, Mark, database, DB, c1984, c198x, c19xx
%X uk us isbn:0470201053.  Based in his Phd thesis.
   Auth' an F.I.T. Prof, Mon@sh as of Feb 2OO4 [<A HREF="http://www.bsys.monash.edu.au/people/wallace/mgw_web_page.html">home</A>][5/'04].

%A Elmasri
%A Navathe
%T Fundamentals of Database Systems, 2nd Edn
%I Benjamin Cummings
%D 1994
%K book, text, computing, computer, database, databases, data base, DBMS
%X from Jan Jongejan, Dept. Comp.Sci., Univ. of Groningen, Netherlands (12/'94)
   <!-- email: jjan@cs.rug.nl --> .

%A H. Pruyt
%A M. Lewis
%T Database Management with dBase and SQL: A Practical Introduction
%I ChapmanHall
%D 1993
%P 232
%K data base, database, book, text, DB, DBMS
%X uk us isbn:0-412-47750-5.

%E G. Gottlob
%E M. Y. Vardi
%T DataBase Theory, ICDT'95
%M JAN
%D 1995
%I SpringerVerlag
%S LNCS
%V 893
%K data base, DB, book, text, conf, ICDT, ICDT95, DBMS

%A M. R. Ault
%T Oracle 7.0 Administration and Management
%I Wiley
%D 1994
%P 516
%K book, text, data base, DB, database, relational, RDBMS, DBMS, computing

%A F. McFadden
%A J. A. Hoffer
%T Modern Database Management
%I AddisonWesley
%D 1995
%K book, text, DB, data base, DBMS
%X 4th ed 1995, pb us%53; uk us isbn:0-8053-6039-5.

%A T. Connolly
%A C. Begg
%A A. Strachan
%T Database Systems: A Practical Approach to Design, Implementation and
   Management
%P 839
%I AddisonWesley
%D 1995
%K book, text, DB, DBMS, data base
%X uk us isbn:0-201-42277-8;  ppb  $60.

%A T. Imielinski
%A H. Mannila
%T A database perspective on knowledge discovery
%J CACM
%I ACM
%P 58-64
%V 39
%N 11
%M NOV
%D 1996
%K c1996, c199x, c19xx, DB, DBMS, data mining, rule, rules, data base, bases,
   inductive
%X [<A HREF="http://doi.acm.org/10.1145/240455.240472">doi:10.1145/240455.240472</A>][7/'04]
   [Also search for: supervised classification].

%A H. Blockeel
%A L. De Raedt
%T Inductive database design
%J Proc. of the 10th Int. Symp. on Methodologies for Intelligent Systems
%P 376-385
%I SpringerVerlag
%S LNAI
%V 1079
%D 1996
%K conf, IDB, DBMS, deRaedt, inductive data-base, bases, relation, deductive,
   predicate, inductive logic programming, ILP, LP, c1996, c199x, c19xx
%X "When designing a (deductive) database, the designer has to decide for each
   predicate (or relation) whether it should be defined extensionally or
   intensionally as well as to list the integrity constraints of the domain.
   An intelligent system is presented to assist the designer in this task. It
   starts from an example database in which all predicates are defined
   extensionally. It then tries to compact the database by transforming
   extensionally defined predicates into intensionally defined ones. The
   intelligent system employs techniques from the area of inductive logic
   programming."  [auths @ cs.kuleuven.ac.be]
   -- [<A HREF="http://www.cs.kuleuven.ac.be/cgi-bin-dtai/publ_info.pl?id=17198">.ps@kuleuven.ac.be</A>][7/'04].

%A N. R. Adam
%A A. Gangopadhyay
%T Database Issues in Geographic Information Systems
%I Kluwer
%S Adv. in Database Systems
%V 6
%P 152(?)
%M JUN
%D 1997
%K book, text, DB, DBMS, GIS, cartography, computer, data-base, bases
   spatial data, query, queries
%X au$141 ('97), uk us isbn:0-7923-9924-2.

%A C. J. Date
%T An Introduction to Database Systems
%I AddisonWesley
%I 1999
%K book, text, c1999, c199x, c19xx, databases, data base, DBMS, relational,
   RDBMS, normal form, forms, theory, computing, computer
%X 7th ed c1999; uk us isbn:0201385902; uk us isbn13:978-0201385908.

%A H. T. El-Khatib
%A M. H. Williams
%A D. H. Marwick
%A L. M. Mackinnon
%T Using a distributed approach to retrieve and integrate
   information from heterogeneous distributed databases
%J COMPJ
%V 45
%N 4
%D 2002
%P 381-394
%K jrnl, Compj, data base, bases, mixed, Corba, XML, Java, ElKhatib, zz0802
%X [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_45/Issue_04/">jrnl</A>][8/'02]
   [37 refs].

%A A. Formica
%A M. Missikoff
%T Concept similarity in SymOntos: An enterprise ontology management tool
%J COMPJ
%V 45
%N 6
%P 583-594
%D 2002
%K jrnl, compj, c2002, c200x, c20xx, concept, terminology, terms, like,
   similar, zz1202
%X [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_45/Issue_06/450583.sgm.abs.html">paper</A>][12/'02]

%A M. Whitehorn
%A B. Marklyn
%T Inside Relational databases
%I Springer
%P 345
%D 2001
%K book, text, database, data base, bases
%X CJ review '03: bit narrow, an introduction, stg24.50.  isbn:1852334010.

%T Relational Data Mining
%E S. Dzeroski
%E N. Lavrac
%I Springer
%P 398
%D 2001
%K book, text
%X collection, various authors, hb, stg35.  isbn:3540422897.

%A J. Worsley
%A J. Drake
%T Practical PostgreSQL
%I OReilly
%P 636
%D 2001
%K book, text, PostgreSQL, c2002, c200x, c20xx, postgressql, postgres SQL,
   database, databases, data base, bases, DBMS, object, relational, RDBMS,
   open source, opensource
%X "Arguably the most capable of all the open source databases, PostgreSQL is an
   object-relational database management system first developed in 1977 by UCB"
   1st ed 2002, pb, uk us isbn:1565928466; uk us isbn13:978-1565928466.
   [<A HREF="http://www.postgresql.org/">.postgresql.org</A>]['08].
   [Also search for: PostgreSQL].

%E P. D. Gray
%E L. Kerschberg
%E P. J. H. King
%E A. Poulovassilis
%T The Functional Approach to Data Management - Modeling, Analyzing and
   Integrating Heterogeneous Data
%I SpringerVerlag
%P 483
%D 2004
%K book, text, FP, programming, DB, DBMS, heterogeneous, c2004, c200x, c20xx,
   mixed, data base, database, bases, paradigm, Kleisli, Tambis, Amos
%X stg54, eur70; isbn:3540003754.
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_47/Issue_04/470506.sgm.abs.html">review@oup.co.uk</A>]['04].

%A K. Douglas
%T PostgreSQL (2nd Edn), Developer's Library
%I Sams
%P 1032
%D 2005
%K book, text, PostgreSQL, c2005, c200x, c20xx, postgressql, postgres SQL,
   database, databases, data base, bases, DBMS, relational, RDBMS
%X 2nd ed 2005, pb us$31; isbn:0672327562; isbn13:978-0672327568.
   "Open source database ... developer. Whether you're developing with C, C++,
   ODBC, Embedded SQL, Java, Tcl/Tk, Perl, Python or PHP, you'll find a
   comprehensive description of the PostgreSQL API for your language of choice
   ... administrator. You will learn how to install PostgreSQL on Windows,
   Linux, and Unix systems ..."
   [<A HREF="http://www.postgresql.org/">.postgresql.org</A>]['08].

%A C. Olston
%A B. Reed
%A U. Srivastava
%A R. Kumar
%A A. Tomkins
%T Pig Latin: A not-so-foreign language for data processing
%J SIGMOD '08
%P ?-?
%M JUN
%D 2008
%K sigmod, DBMS, c2008, c200x, c20xx, zz0809, Pig Latin, PigLatin, parallel,
   Teradata, conf, SQL, map reduce, Hadoop, Yahoo, large scale, big,
   data base, database, DB
%X "... Parallel DB products, e.g., Teradata, offer a soln, but are usually
   prohibitively expensive at this scale. ... The success of the more procedural
   [v. decl. SQL] map-reduce programming model, & its assoc. scalable impln on
   commodity h/w, is evidence of the above. However, the map-reduce paradigm is
   too low-level & rigid, & leads to a great deal of custom user code that is
   hard to maintain, & reuse.  We describe a new language called Pig Latin that
   we have designed to fit in a sweet spot between the decl. style of SQL, &
   the low-level, proc. style of map-reduce.  ... compiles Pig Latin into
   physical plans that are exec. over Hadoop, an open-source, map-reduce impln.
   ... examples of how engineers at Yahoo! are using Pig to dramatically reduce
   the time req. for the development & execution ..."
   -- pdf@[<A HREF="http://www.cs.cmu.edu/~olston/publications/sigmod08.pdf">cmu.edu</A>]['09],
   and [<A HREF="http://research.yahoo.com/node/2200">yahoo</A>]['09].

%A T. Kyte
%T Oracle Database 9i, 10g, and 11g Programming Techniques and Solutions
%I Apress
%P 832
%D 2010
%K book, text, c2010, c201x, c20xx, DBMS, Oracle, database, DB, pi, 10g, 11g
%X 2nd ed 2010; pb us$43; uk us isbn:1430229462; uk us isbn13:978-1430229469.
   "... aimed at Oracle Database administrators, at PL/SQL and Java developers
   writing code to be deployed inside the database, and at developers of
   external applications who use Oracle Database as a data store. ..."

%T neo4j
%D 2007 ?
%K NEO4J, database, c200x, c20xx, zz0520, DBMS, graph, DBMS
%X "Neo4j is a graph database management system developed by Neo4j, Inc.
   Described by its developers as an ACID-compliant transactional database with
   native graph storage and processing ..."
   -- neo4j@[<A HREF="https://en.wikipedia.org/wiki/Neo4j">wikip</A>]['20].
   Also see neo4j@[<A HREF="https://neo4j.com/">www</A>]['20] (uses f'ng'rpr'nt'rs).


%A E. M. Soloway
%A B. Woolf
%A E. Rubin
%A P. Barth
%T Meno II: an intelligent tutoring system for novice programmers
%J 7th IJCAI
%D 1981
%M AUG
%V 1
%K IJCAI IJCAI81, programming, bug, debug, debugging, Meno Meno2 MenoII
%P 975-977

%J Proc. ACM Sigsoft/Sigplan Software Engineering Symposium on
   High-Level Debugging
%M AUG
%D 1983
%O Sigplan 18(8)
%K bug, debug, debugging, programming
%X M. A. Linton  Knowledge based debugging 23-24
   R. L. Sedlmeyer, W. B. Thompson & P. E. Johnson
      Knowledge based fault localization ... 25-31

%A M. L. Miller
%T A structured planning and debugging environment for elementary programming
%B Intelligent Tutoring Systems
%E D. Sleeman
%E J. S. Brown
%I Academic Press
%P 119-135
%D 19??
%K bug, debug, debugging, programming

%A M. Elsom-Cook
%A B. du Boulay
%T A Pascal program checker
%J European Conf. on Artificial Intelligence (7th)
%M JUL
%D 1986
%P 90-95
%K ECAI, syntax bug, debug

%A W. Lewis Johnson
%A E. Soloway
%T Proust: knowledge-based program understanding
%J IEEE Trans. on Software Engineering
%V SE-11
%N 3
%P 267-275
%M MAR
%D 1985
%K Proust, bug, debug, debugging, programming, novice

%A W. Lewis Johnson
%A E. SOloway
%T Proust
%J Artificial Intelligence
%P 179-190
%J Byte
%M APR
%D 1985
%K programming, bug, debug, debugging

%A J. C. Huang
%T Detection of data flow anomaly through program instrumentation
%J IEEE Trans. on Software Engineering
%V SE-5
%N 3
%M MAY
%D 1979
%P 226-236
%K bug, debug, debugging


%A W. S. Cooper
%T Probability theory as the basis of text retrieval
%J Proc. 54th Mtg of the American Soc. for Info. Sci.
%V 28
%P 366-369
%D 1991
%K conf, ASIS, information, document, retrieval, IR
%X 4 page abs;  16 refs

%A W. J. Wilbur
%T A retrieval system based on automatic relevance weighting of search terms
%J Proc. 55th Annual Meeting of the American Soc. for Information Science
%V 29
%P 216-220
%D 1992
%K ASIS, 55, document retrieval, information, retrieve, IR, search term terms,
   cosine, relevance, mutual, Bayes, Bayesian, c1992, c199x, c19xx, MedLine
%X ... our formulation departs from the usual in that it is based on
   considering pairs of documents, and terms contribute to the score
   (log odds of relevance) in a symmetric manner.
   Terms which appear in both documents in a pair contribute positively
   to the score and terms that occur in one document contribute negatively.
   This allows the length of a document to become a negative factor in the
   scoring as it is in the cosine formula commonly used in vector retrieval.
   16 refs
   [LA, hint: also look for   NCBI MedLine   in the bib']

%A W. J. Wilbur
%T An information measure of retrieval performance
%J Information Systems
%V 17
%N 4
%P 283-298
%D 1992
%K jrnl, IS, IR, information theory, c1992, c199x, c19xx, recall, precision,
   relevance, document
%X H 010.7805 I43.9           19 refs

%A D. F. Ghazfan
%A K. B. Korb
%A M. Indrawan
%A B. Srinivasan
%T A Bayesian network model for information retrieval
%J 5th Australian Conf. Info. Sys.
%C Melbourne
%M ?
%D 1994
%P 259-271
%K monash, conf, information, document, retrieval, IR, probability,
   search, relevance, net, Desra, KBKorb, Srini

%A R. Siemens
%T Practical content analysis techniques for text-retrieval in large, untagged
   text-bases
%J Systems Documentation: Proc. 11th Annual Int. Conf.
%W Waterloo, Ont., Canada
%M OCT
%D 1993
%I ACM Press, N.Y.
%P 293-299
%K information retrieval, IR

%A G. Salton
%T Developments in automatic text retrieval
%J Science
%V 253
%P 974-980
%M AUG
%D 1991
%K jrnl, text, information, retrieve, IR, large, query, search

%A G. Salton
%A C. Buckley
%T Term-weighted approaches to automatic text retrieval
%J Inf. Proc. & Mngmt.
%V 24
%N 5
%P 513-523
%M ?
%D 1988
%K IPM, jrnl, text, information, retrieve, IR, large, query, search
%X ... assignment of appropriately weighted single terms produces retrieval
   results that are superior to those obtainable with more elaborate
   text representations. ...

%A G. Salton
%T Automatic Text Processing: The Transformation, Analysis and Retrieval of
   Information by Computer
%I Addison-Wesley
%D 1989
%K book, text, information, retrieve, IR, index, indexing, large,
   query, find, search
%X isbn:0-201-12227-8.
   1. The information Environment   8. Conventional Text Retrieval Systems
   2. The Computer Environment      9. Automatic Indexing
   3. The Automated Office         10. Advanced Information Retrieval Models
   4. Text Editing and Formatting  11. Language Analysis and Understanding
   5. Text Compression             12. Automatic Text Transformations
   6. Text Encryption              13. Paperless Informations Systems
   7. File-Accessing Systems

%A N. Fuhr
%T Models for retrieval with probabilistic indexing
%J Inf. Proc. & Mngmt.
%V 25
%N 1
%P 55-72
%M ?
%D 1989
%K IPM, jrnl, text, information, retrieve, IR, large, query, search, BII, RPI
%X describes and compares 3 models:
   1. binary independent indexing (BII)
   2. retrieval with probabilistic indexing (RPI)
   3. ext'n of binary indexing retrieval
   The weights for any of the above can be provided by an application of the
   Darmstadt indexing approach (DIA) ...

%A G. Salton
%A C. Buckley
%T Improving retrieval performance by relevance feedback
%J J. Amer. Soc. for Information Sci.
%V 41
%N 4
%P 288-297
%D 1990
%K JASIS, ASIS, jrnl, text, information, retrieve, IR, query, search, feed back

%A S. E. Robertson
%A K. Sparck Jones
%T Relevance weighting of search terms
%J J. Amer. Soc. for Information Sci.
%V 27
%N ?
%P 129-146
%M MAY-JUN
%D 1976
%K JASIS, ASIS, jrnl, text, c1976, c197x, c19xx, information, retrieve, IR,
   query, search, weight

%A P. S. Jacobs
%A L. F. Rau
%T Innovations in text interpretation
%J Artificial Intelligence
%V 63
%N 1-2
%P 143-191
%M OCT
%D 1993
%K AI, jrnl, text, understanding, natural language, analysis, NL, NLA,
   TRUMP, TRUMPET, zz0595
%X reviewed in Comp' Rev' p122 Feb 1995

%A H. Turtle
%A W. B. Croft
%T Inference networks for document retrieval
%I ACM
%J ?
%D 1990
%P ?-?
%K information, document

%A H. R. Turtle
%A W. B. Croft
%T Efficient probabilistic inference for text retrieval
%I ?
%J ?
%D 1990 ?
%K information, document

%A H. Turtle
%A W. B. Croft
%T Evaluation of an inference network-based retrieval model
%J ACM Trans. Info. Sys.
%V 9
%N 3
%P 187-222
%M JUL
%D 1991
%K TOIS, IS, jrnl, text, information retrieval, IR, retrieve, text,
   search, CIIR, c1991, c199x, c19xx, zz0595
%X 45 refs;   authors at U Mass'

%A N. Fuhr
%A C. Buckley
%T Optimizing document indexing and search term weighting based on
   probabilistic models
%J Proc. 1st Text Retrieval Conf.
%P 89-99
%D 1993
%K TREC, text, information retrieval, IR, weight, search,
   relevance feedback, zz0695
%X 9 refs

%A F. Sebastiani
%T A probabilistic terminological logic for modelling information retrieval
%J 17th ACM SIGIR Int. Conf. on Res. and Dev. in Info. Retrieval
%M JUL
%D 1994
%K text, information retrieval, IR, zz0695
%X available from <A HREF="http://www.dcs.glasgow.ac.uk/">www</A> [6/'95]

%T special issue on information retrieval
%J COMPJ
%V 35
%N 3
%D 1992
%K information retrieval, IR, text, computing, zz0695

%A N. Fuhr
%T Probabilistic models of information retrieval
%J COMPJ
%V 35
%N 3
%D 1992
%P 243-255
%K information retrieval, IR, text, survey, compj, jrnl
%X 54 refs

%A H. R. Turtle
%A W. B. Croft
%T A comparison of text retrieval models
%J COMPJ
%V 35
%N 3
%D 1992
%P 279-290
%K information retrieval, IR, text, compj, jrnl
%X 38 refs

%A J. P. Callan
%A W. B. Croft
%A S. M. Harding
%T The INQUERY retrieval system
%J sub' 3rd Int. Conf. on Databases and Exp. Sys. Appli.
%D 1992
%K conf, INQUERY, document, text, information, probabilistic
%X 16 pages; "... up to 400,000 documents ..."
   email:<A HREF="mailto:croft@cs.umass.edu">croft</A>[1992]

%A C. J. van Rijsbergen
%T Probabilistic retrieval revisited
%J COMPJ
%V 35
%N 3
%D 1992
%P 291-298
%K information retrieval, model, models, IR, text, compj, jrnl, vanRijsbergen
%X 27 refs

%A P. B. Danzig
%A Shih-Hao Li
%A K. Obraczka
%T Distributed indexing of autonomous internet services
%J Computing Systems
%V 5
%N 4
%P 433-459
%D 1992
%K jrnl, internet, information retrieval, IR, agent, indie, indexing

%A M. F. Scwartz
%A A. Emtage
%A B. Kahle
%A B. C. Neuman
%T A comparison of internet resource discovery approaches
%J Computing Systems
%V 5
%N 4
%P 461-493
%D 1992
%K jrnl, internet, information retrieval, IR

%A M. Bowman
%A L. L. Peterson
%A A. Yeatts
%T Univers: an attribute-based name server
%J SPE
%V 20
%N 4
%P 403-424
%P APR
%D 1990
%K SPE, jrnl, information retrieval, IR, internet

%A D. D. Lewis
%T Learning in information retrieval
%J Proc. 8th Int. Workshop on Machine Learning
%P 235-239
%D 1991
%K ML8, ML91, conf, information retrieval, IR, zz1295
%X [42 refs]

%A J. L. Fagan
%T The effectiveness of a nonsyntactic approach to automatic phrase indexing
   for document retrieval
%J J. Amer. Soc. for Information Sci.
%V 40
%N 2
%P 115-132
%D 1989
%K JASIS, ASIS, jrnl, information retrieval, IR, zz0196
%X 43 refs

%A E. D. Liddy
%A W. Paik
%A E. S. Yu
%T Text categorization for multiple users based on semantic features from a
   machine-readable dictionary
%J ACM Trans. Inf. Syst.
%V 12
%N 3
%P 278-295
%M JUL
%D 1994
%K ACM, TIS, jrnl, information retrieval, IR, filter, zz0296
%X filters text
   text taken from Wall Street jrnl stories
   good review in Comp Rev p591-2 Nov 95

%A S. K. M. Wong
%A Y. Y. Yao
%T On modelling information retrieval with probabilistic inference
%J ACM Trans. Inf. Syst.
%V 13
%N 1
%P 38-68
%M JAN
%D 1995
%K ACM, TIS, jrnl, information retrieval, IR, probability, term weights

%A K. L. Kwok
%T A network approach to probabilistic information retrieval
%J ACM Trans. Inf. Syst.
%V 13
%N 3
%P 324-353
%M JUL
%D 1995
%K ACM, TIS, jrnl, information retrieval, IR, probability,
   neural net, ANN, NN

%A C. J. van Rijsbergen
%T Information Retrieval
%I Butterworths
%D 1979
%K book, text, good, vanRijsbergen, IR, c1979, c197x, c19xx, document
%X 2nd edn available on the wwweb at Glasgow dcs as of - [2/'96]
   1st edn 1975, 2nd edn 1979, reprinted '80;     H 029.7V274.I2

%A J. D. Cohen
%T Highlights: language- and domain-independent automatic indexing terms for
   abstracting
%J J. Am. Soc. Inf. Sci.
%V 46
%N 3
%P 162-174
%M APR
%D 1995
%K jrnl, JASIS, information retrieval, IR, abstract, term, terms, zz0496
%X review in Comp Rev p125 Feb '96
   H SER 010.6 A5125

%A H. Chen
%T Machine learning for information retrieval: neural networks,
   symbolic learning and genetic algorithms
%J J. Am. Soc. Inf. Sci.
%V 46
%N 3
%P 124-216
%M APR
%D 1995
%K jrnl, JASIS, machine learning, information retrieval, IR, ID3, ID5R, NN, ANN
%X review in Comp Rev p127 Feb '96
   H SER 010.6 A5125

%A R. M. Losee
%A W. Stephanie
%T Sublanguage terms: dictionaries, usage and automatic classification
%J J. Am. Soc. Inf. Sci.
%V 46
%N 7
%M AUG
%D 1995
%P 519-529
%K JASIS, jrnl, document, jargon, specialized terminology, c1995, c199x, c19xx,
   vocabulary, text, subject area, word frequencies, zz0996
%X see  Comp Rev 37(7) p 364 Jul 96

%A R. M. Fung
%A B. A. Del Favero
%T Applying Bayesian networks to information retrieval
%J CACM
%V 38
%N 5
%M MAR
%D 1995
%P 42-48
%K jrnl, IR, document, text, Bayes, network, probabilistic, DelFavero, zz1196

%A J. D. Bovey
%T Building a thesaurus for a collection of cartoon drawings
%J J. Inf. Sci.
%V 21
%N 2
%P 115-122
%M JUL
%D 1995
%K JIS, jrnl, information retrieval, IR, cartoon, picture, image, key word,
   keywords
%X it seems that the University of Kent has a collection of 80,000
   British newspaper cartton drawings.
   Good review by R. J. T u f t s   Comp Rev 37(11) p592 Nov 96

%A U. Manber
%A S. Wu
%T GLIMPSE: a tool to search through entire file systems
%R 93-34
%I Dept. Comp. Sci., U. of Arizona
%M OCT
%D 1993
%O 1994 Winter Usenix Tech. Conf., pp.23-32
%K conf, TR, TR9334, Glimpse, grep, agrep, webglimpse, text search,
   block addressing, address, index, indexing, find, c1993, c199x, c19xx, www
%X Inverted indexes give fast searches for AND, OR queries but
     indexes are large, typically 50% to 300% of original file size.
   Glimpse trades some time to save space;
     its indexes are typically 2% to 4% of collection size.
   Uses 2-level-searching:
     index provides pointers to *area* where info' may be found, not precise
     location.  The area is then searched sequentially.
     Uses agrep to search both the index and the local files.
     This allows approx' matching and regular expressions.
   [<A HREF="http://glimpse.cs.arizona.edu/">glimpse.cs.arizona.edu</A>][9/97].

%A R. Muth
%A U. Manber
%T Approximate multiple string search
%J 7th Annual Combinatorial Pattern Matching Symp.
%C Laguna Beach, CA
%P 75-86
%M JUN
%D 1996
%O TR 94-17, Comp. Sci, U. Ariz0na, May '93
%K conf, CPM, CPM7, CPM96, search, searching, text, string,
   hash, two level hashing, glimpse, c1996, c199x, c19xx
%X ... fast search, large text, multiple strings, allowing one error ...
   ... 1MB text, 1000 patterns, under 1 second ...
   [<A HREF="http://webglimpse.org/pubs/approx-multi.ps">.ps</A>][11/'02]

%A I. H. Witten
%A C. Nevill-Manning
%A R. McNab
%A S. Cunningham
%T A public library based on full-text retrieval
%J CACM
%V 41
%N 4
%P 71-75
%M APR
%D 1998
%K jrnl, text, retrieve, retrieval, information, search, searching, document,
   New Zealand, NZ, NZDL, library, big, gigabytes, zz0499
%X (ihw|rjmcnab|sallyjo) at cs.waikato.ac.nz and cnevill at stanford.edu
   e.g. 40,000 comp sci tech reports, one million pages, 400M words,
        from 300 sites, 2.3G of text from 34Gb of postscript/pdf source.
   Uses the algorithm of
   M o f f a t and B e l l  J. Amer. Soc. Info. Sci. 46(7) 537-550 ?'95?
   which "can invert an estimated 5Gb of raw text in only
          12 hours with only 40Mb of main memory",
   so "Collections of tens of gigabytes seem quite feasible."
   [<A HREF="http://www.nzdl.org/">www.nzdl.org</A>] and
   [<A HREF="http://www.cs.waikato.ac.nz/cs/Research/">Research</A>] in
   [<A HREF="http://www.cs.waikato.ac.nz/">www.cs.waikato.ac.nz</A>] [4/1999]

%A A. Moffat
%A T. A. H. Bell
%T In situ generation of compressed inverted files
%J J. Amer. Soc. Info. Sci.
%V 46
%N 7
%P 537-550
%D 1995
%K jrnl, c1995, c199x, c19xx, JASIS, information, text, retrieval, retrieve,
   search, searching, inverted file, index, indexing, big, gigabytes, zz0499
%X "An inverted index stores, for each term that appears in a colln of docs., a
   list of doc.numbers containing that term. ... Boolean or informal ranked
   queries are to be answered. Constn of the index is, however, a nontrivial
   task. Simple methods using in-memory data structures cannot be used for large
   collns because they require too much random access storage, & traditional
   disk-based methods require large amounts of temporary file space. ... new
   indexing alg. designed to create large compressed inverted indexes in situ.
   It makes use of simple compression codes for the +ve ints & an in-place
   external multi-way mergesort. The new tech. has been used to invert a
   two-gigabyte text colln in under 4hrs, using < 40 megabytes of temporary
   disk space, and less than 20 megabytes of main memory."
   [<A HREF="http://dx.doi.org/10.1002/(SICI)1097-4571(199508)46:7%3C537::AID-ASI7%3E3.0.CO;2-P">doi:10.1002/(SICI)1097-4571(199508)46:7%3C537::AID-ASI7%3E3.0.CO;2-P</A>]['09].
   (W i t t e n  et al c.a.c.m. 41(4) p75 '98, state that the algorithm
   "can invert an estimated 5Gb of raw text in only
    12 hours with only 40Mb of main memory."

%A F. Crestani
%A M. Lalmas
%A C. J. van Rijsbergen
%A I. Campbell
%T "Is this document relevant? ... Probably": A survey of probabilistic
    models in information retrieval
%J ACM Comp. Surveys
%V 30
%N 4
%P 528-552
%M DEC
%D 1998
%K jrnl, survey, IR, text, retrieve, search, relevant, vanRijsbergen,
   c1998, c199x, c19xx, zz0799
%X about 6 columns of refs

%A E. Frank
%A C. Chiu
%A I. H. Witten
%T Text categorization using compression models
%J Proc. Data Compression Conf. (poster)
%I IEEE Press
%P ?-?
%D 2000
%O Full version working paper 00/2, Dept. of Comp. Sci., U. of Waikato.
%K conf, DCC, category, model, c2000 c200x, c20xx,  categorisation, classify
%X [<A HREF="http://www.cs.waikato.ac.nz/~ml/publications/2000/00EF-CC-IHW-Categorization.pdf">.pdf</A>]['04]

%A T. Joachims
%T The maximum-margin approach to learning text classifiers
%I GI-Edition - Lecture Notes in Informatics (LNI)
%I Kollen Verlag, Bonn
%D 2002
%O Ausgezeichnete Informatikdissertationen 2001, D.  Wagner et al. (Hrsg.),
%K text classification, wide margin, margins, separation, .de, SVM
%X [<A HREF="http://www.cs.cornell.edu/People/tj/">author</A>][5/'03]

%A G. Nenadic
%A I. Spasic
%A S. Ananiadou
%T Terminology-driven mining of biomedical literature
%J Bioinformatics
%P 938-943
%V 19
%N 8
%D 2003
%K jrnl, text, data, MolBio, term, terms, variant recognition,
   acronym, acronyms, terminology, jargon, zz0503
%X ...framework for terminology-driven mining from biomedical literature.
   ...integrates the following components: automatic term recognition,
   term variation handling, acronym acquisition, automatic discovery of term
   similarities and term clustering. The term variant recognition is
   incorporated into terminology recognition process by taking into account
   orthographical, morphological, syntactic, lexico-semantic and pragmatic term
   variations.  ...address acronyms as a common way of introducing term
   variants in biomedical papers. Term clustering is based on the automatic
   discovery of term similarities. We use a hybrid similarity measure, where
   terms are compared by using both internal and external evidence. The measure
   combines lexical, syntactical and contextual similarity. Experiments on
   terminology recognition and clustering performed on a corpus of MEDLINE
   abstracts recorded the precision of 98% and 71% respectively.
   [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/19/8/938">www</A>][5/'03]  auth'1 at Umist UK

%A H. Shatkay
%A R. Feldman
%T Mining the biomedical literature in the genomic era: An overview
%J J. Computational Biology
%V 10
%N 6
%P 821-855
%M DEC
%D 2003
%K jrnl, JCB, data mining, c2003, c200x, c20xx, MolBio, document, text,
   bio-medical, survey, inro, introduction, Hagit Shatkay
%X modified: [<A HREF="http://www.shatkay.org/papers/JCB03.ps">.ps</A>]['05] 43pp,
   [<A HREF="http://www.shatkay.org/">auth1</A>]['05].

%A A. Rzhetsky
%A Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H,
%A Duboue P A, Weng W, Wilbur W J, Hatzivassiloglou V
%A C. Friedman
%T GeneWays: A system for extracting, analyzing, visualizing, and
   integrating molecular pathway data
%J J. Biomed. Informatics
%V 37
%N 1
%P 43-53
%M FEB
%D 2004
%K jrnl, GeneWays, geneway, c2004, c200x, c20xx, data mining, text, document,
   MolBio, pathway, article
%X "...such as automated selection of articles pertinent to MB, or ... analyzes
   interactions between molecular substances, drawing on multiple sources of
   information to infer a consensus view of molecular networks. GeneWays is
   designed as an open platform, allowing researchers to query, review, and
   critique stored information."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jbi.2003.10.001">doi:10.1016/j.jbi.2003.10.001</A>]['05].

%A M. Krauthammer
%A C. A. Kaufmann
%A T. C. Gilliam
%A A. Rzhetsky
%T Molecular triangulation: Bridging linkage and molecular-network information
   for identifying candidate genes in Alzheimer's disease
%J PNAS
%V 101
%N 42
%P 15148-15153
%M OCT
%D 2004
%K jrnl, PNAS, c2004, c200x, c20xx, data mining, text, document, MolBio,
   pathway, network, article, Alzheimers, links, graphs, graph, gene, medical
%X "... First, we perform an automated literature analysis that predicts
   physical interactions (edges) among candidate disease genes (seed nodes,
   selected on the basis of prior information) and other molecular entities. We
   derive models of molecular networks from this analysis and map the seed nodes
   to them. We then compute the graph-theoretic distance (the minimum number of
   edges that must be traversed) between the seed nodes and all other nodes in
   the network. ..."
   -- [<A HREF="http://www.pnas.org/cgi/content/abstract/101/42/15148">pnas.org</A>]['05].

%A J. Zobel
%A A. Moffat
%T Inverted files for text search engines
%J Computing Surveys
%I ACM
%V 38
%N 2
%P ?-?
%M JUL
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0808, inverted file, search engine, retrieve,
   retrieval, query, survey, introduction
%X [205 refs] [<A HREF="http://dx.doi.org/10.1145/1132956.1132959">doi:10.1145/1132956.1132959</A>]['08].
   Auths @ melb uni, c2OO8.


%A V. Donzeau-Gouge
%A G. Huet
%A G. Kahn
%A B. Lang
%T Introduction au systeme mentor at a ses applications
%I IRIA
%D 1979??
%K edit, editor, program, tree, program development
%X claimed available, they never reply

%A V. Donzeau-Gouge
%A G. Huet
%A G. Kahn
%A B. Lang
%T The mentor program manipulation system
%I IRIA
%M Oct
%D 1979
%K program, edit, editor
%X claimed available, they never reply

%A V. Donzeau-Gouge
%A G. Huet
%A G. Kahn
%A B. Lang
%A J. J. Levy
%T A structure oriented program editor:
   a first step towards computer assisted programming
%J International Computing Symposium
%D 1975
%E F. Gelenbe
%E D. Potier
%I North Holland
%P 113-120
%K program, edit, editor,  mentor
%X claimed available, they never reply

%A D. W. Embley
%A G. Nagy
%T Behavioural aspects of text editors
%J Computing Surveys
%V 13
%N 1
%P 33-70
%M Mar
%D 1981
%K edit, editor, text, behaviour, human factors

%A D. C. Engelbart
%A W. K. English
%T A research center for augmenting human intellect
%J AFIPS
%V 33
%D 1968
%P 395-410
%K text, edit, editor, construction, document, project

%A C. W. Fraser
%T A compact, portable CRT-based text editor
%J SPE
%V 9
%P 121-125
%D 1975
%M Feb
%K edit, editor, screen editor
%X built as front end to a line editor -
   reused code, compact, portable

%A K. Lock
%T Structuring programs for multiprogram time-sharing on-line applications
%J AFIPS Conf. Proceedings FJCC
%V 27 (1)
%D 1965
%K edit, editor, syntax directed
%X Atkinson et al 1981 credit this as the earliest syntax based editor system.
   incremental

%A J. Nievergelt_at_al
%T ACSES, an automated computer science education system
%J Angewandte Informatik
%P 135-142
%D 1975
%K Plato, structure, edit, editor
%X includes P. Mateti

%A T. Teitelbaum
%A T. Reps
%T The Cornell program synthesizer: a syntax-directed programming environment
%J CACM
%M Sep
%D 1981
%V 24
%N 9
%P 563-573
%K syntax directed, edit, editor

%A A. Van Dam
%A D. E. Rice
%T On-line text editing: a survey
%J Computing Surveys
%V 3
%N 3
%M Sep
%D 1971
%P 93-114
%K edit, editor

%A T. R. Wilcox
%A A. M. Davis
%A M. H. Tindall
%T The design and implementation of a table driven, interactive
   diagnostic programming system
%J CACM
%V 19
%N 11
%P 609-616
%M Nov
%D 1976
%K CAPS, debugging
%X runs under Plato, several languages

%A J. Wilander
%T An interactive programming system for Pascal
%J BIT
%V 20
%D 1980
%P 163-174
%K debugging, Pathcal

%A S. R. Wood
%T Z - the 95% program editor
%J Sigplan
%V 16
%N 6
%D 1981
%P 1-7
%K Z, editor, program, structure

%A F. C. Heeman
%T Incremental parsing of expressions
%J J. Systems Software
%V 13
%P 55-69
%D 1990
%K incremental parser, parse, expression, edit, editor
%X user edits text by appearance
   algorithm adjusts parse tree.


%A R. S. Bird
%T Using circular programs to eliminate multiple traversals of data
%J Acta Informatica
%V 21
%P 239-250
%N 3
%M OCT
%D 1984
%K FP, functional programming, recursive, recursion, lazy evaluation, need,
   jrnl, circular program, self reference, data structure, structures,
   c1984, c198x, c19xx
%X Also see [<A HREF="http://www.allisons.org/ll/FP/Lambda/Examples/">FP</A>],
   and [also search for: circular program FP].

%A R. M. Burstall
%A J. Darlington
%T A transformation system for developing recursive programs
%J JACM
%P 44-67
%V 24
%N 1
%M JAN
%D 1977
%K FP, functional programming, recursion, c1977, c197x, c19xx, transform,
   jrnl, JACM

%A M. S. Feather
%T A system for assisting program transformation
%J TOPLAS
%V 4
%N 1
%M JAN
%D 1982
%P 1-20
%K jrnl, TOPLAS

%A U. Honschopp
%A W. M. Lippe
%A F. Simon
%T Compiling functional languages for Von Neumann machines
%P 22-27
%J ACM Symp. on Programming Languages
%W San Francisco
%M JUN
%D 1983
%K FP, compiler

%A R. J. M. Hughes
%T Super combinators - a new implementation technique for
   applicative languages
%J ACM Symp. on Lisp and functional programming
%W Pittsburgh
%M AUG
%D 1982
%O see also Oxford PRG-28
%K conf, FP, SKI, functional programming, lambda lifting, combinatory logic,
   c1982, c198x, c19xx
%X [Also search for: FP combinatory logic].

%A A. Pettorossi
%T Improving memory utilization in transforming recursive programs
%J 7th Mathematical Foundations of Computer Science
%W Zakopane
%M SEP
%D 1978
%P 416-425
%O SpringerVerlag LNCS 64, MFOCS, FOCS
%K FP, functional programming,  garbage collection,  destructive operator

%A J. Schwarz
%T Verifying the safe use of destructive operations in applicative programs
%J 3rd Int. Symp. on Programming
%W Paris
%D 1978
%P 395-411
%K FP, functional,   optimisation, garbage collection

%A D. A. Turner
%T Recursion equations as a programming language
%B Functional Programming and its Applications
%I CUP
%D 1982
%K book, text, CUP, FP, functional, applicative, KRC, c1982, c198x, c19xx

%A M. J. Gordon
%A R. Milner
%A C. P. Wadsworth
%T Edinburgh LCF
%I SpringerVerlag
%S LNCS
%V 78
%D ?
%K book, text, CS, CSci, theory, logic for computable functions, FP, type,
   types, polymorphic, polymorphism, check, cgecking, ML, SML
%X also see  H i n d l e y.

%A D. A. Turner
%T A new implementation technique for applicative languages
%J SPE
%V 9
%N 1
%P 31-49
%M JAN
%D 1979
%K jrnl, SPE, c1979, c197x, c19xx, FP, applicative, functional programming,
   combinator, SKI, S K I, combinator, combinatory logic, language,
   lambda calculus, lazy, need, reduction, L4REF
%X "... shown how by using results from combinatory logic an applicative
   language, such as LISP, can be translated into a form from which all bound
   variables have been removed. A machine is described which can efficiently
   execute the resulting code. This impln is compared with a conventional
   interpreter & found to have a number of advantages. Of these the most
   important is that programs which exploit higher order fns to achieve great
   compactness of expression are executed much more efficiently."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.4380090105">doi:10.1002/spe.4380090105</A>]['13].
   Note, (S x y z) = (x z (y z)),  (K x y) = x,  (I x) = x.

%A D. P. Friedman
%A C. T. Haynes
%A E. Kohlbecker
%T Programming with continuations
%B Program Transformation and Programming Environments
%S NATO ASI Series F V8
%E P. Pepper
%I SpringerVerlag
%D 1984
%P 263-274
%K FP, c1984, c198x, c19xx, functional programming,  semantics,  Scheme,
   Scheme84, continuation
%X continuations are first class values.
   [Also search for: FP continuation].

%A P. Henderson
%T Purely functional operating systems
%B Functional Programming and its Applications: an Advanced course
%E J. Darlington
%E P. Henderson
%E D. Turner
%I CUP
%P 177-191
%D 1982
%K FP, functional programming, applicative, lazy, need, stream, streams, OS,
   CUP, c1982, c198x, c19xx
%X Also see Stirling TRs.

%A T. Johnsson
%T Efficient compilation of lazy evaluation
%J Proc. ACM 1984 Symp. on Compiler Construction
%I ACM
%P 58-69
%W Montreal
%M JUN
%D 1984
%K FP, lazy, need, functional programming, applicative, compile, compiler,
   c1984, c198x, c19xx, G-machine, Gmachine, lazy, graph reduction, evaluation,
   combinator, tag, tags, tagged, non-strict, implementation
%X "... an efficient implementation of a lazy functional language, compiling to
   code for ordinary computers. It is based on combinator-like graph reduction:
   the user defined fns are used as rewrite rules in the graph. Each function is
   compiled into an instn seq. for an abstract graph redn m/c, called the
   G-machine, the code reduces a fn application graph to its value. The G-m.
   instns are then translated into target code. Speed improvements by almost two
   orders of mag. over previous lazy evaluators have been measured ..."
   -- [<A HREF="http://dx.doi.org/10.1145/502949.502880">doi:10.1145/502949.502880</A>]['12].

%A U. Reddy
%T Narrowing as the operational semantics of functional languages
%J Proc. IEEE Logic Programming '85.
%P 138-151
%D 1985
%O Dept Computer Science, University of Utah
%K FP, conf, c1985, c198x, c19xx,  LFP, FLP, LP, LP85, prolog, logic variable,
   applicative, functional, language, unification, unify, lazy, need

%A J. Backus
%T Can programming be liberated from the von Neumann style?
   A functional style and its algebra of programs
%J CACM
%V 21
%N 8
%M AUG
%D 1978
%K jrnl, L3Ref, L4REF, c1978, c197x, c19xx, FP, FFP, functional programming,
   language, applicative, reduction, program, CACM, ACM Turing award lecture
%X "... Functional programs deal with structured data, are often nonrepetitive
   & nonrecursive, are hierarchically constructed, do not name their arguments,
   & do not require the complex machinery of procedure declarations to become
   generally applicable. Combining forms can use high level programs to build
   still higher level ones in a style not possible in conventional languages.
   Associated with the functional style of programming is an algebra of
   programs whose variables range over programs & whose operations are combining
   forms. This algebra can be used to transform programs & to solve equations
   whose "unknowns" are programs in much the same way one transforms equations
   in high school algebra. ..."    Turing award lecture
   -- [<A HREF="http://doi.acm.org/10.1145/359576.359579">doi:10.1145/359576.359579</A>]['07].

%A J. Backus
%T Function level programs as mathematical objects
%J Proc. ACM Conf. on Functional Languages and Computer Architecture
%M OCT
%D 1981
%P 1-10
%K conf, c1981, c198x, c19xx, FP, FFP, reduction, functional programming,
   applicative, theory, high-order, form, fpca, fplca, fplca81, fpca81
%X 'Most programs written today are "object-level" programs. That is, programs
   describe how to combine various "objects" (i.e., numbers, symbols, arrays,
   etc) to form other objects until the final "result objects" have been formed.
   New objects are constructed from existing ones by the application of various
   object-to-object fns such as + or matrix inversion. Conventional, von Neumann
   programs are object level; "expressions" on the right side of assignment
   statements are exclusively concerned with building an object that is then to
   be stored. Lambda calculus based languages, such as LISP & ISWIM [Landin 66],
   are also, in practice, object level languages, although they have the means
   to be more.'
   -- [<A HREF="http://dx.doi.org/10.1145/800223.806757">doi:10.1145/800223.806757</A>]['16].

%A F. Warren Burton
%T Annotations to control parallelism and reduction order in the
   distributed evaluation of functional programs
%J TOPLAS
%V 6
%N 2
%M APR
%D 1984
%P 159-174
%K jrnl, TOPLAS, FP, programming

%A D. P. Friedman
%A D. S. Wise
%T Cons should not evaluate its arguments
%B Automata, Languages and Programming
%I Edinburgh University Press
%P 257-284
%D 1976
%K FP, lazy, need, non-strict, evaluation, functional programming, Lisp, L4REF,
   c1976, c197x, c19xx

%A J. Gibert
%A J. Shepherd
%T From algebra to compiler:
   a combinator based implementation of functional programming
%I Dept Computer Science, University of Melbourne
%K TR, FP, functional, applicative, combinator, compiler
%D 1983
%X [Also search for: FP combinator].

%A M. P. Georgeff
%A G. Eddy
%T Functional Pascal: an extension of Pascal to higher order functions
%R TR 27
%I Dept Computer Science, Monash University
%M DEC
%D 1982
%K functional programming, fPascal, fPc, FP, TR 27, TR27, programming, Monash,
   c1982, c198x, c19xx

%A G. J. Eddy
%A M. Georgeff
%T The implementation of higher order functions in Pascal
%R TR 33
%D 1983
%K FP, TR33, TR 33, functional programming, Pascal, applicative,
   functional programming, fPascal, fPc

%A P. L. Wadler
%T Listlessness is better than laziness
%M AUG
%D 1984
%R CMU-CS-85-171
%I Computer Science Dept  Carnegie-Mellon University
%O see 1984 ACM Symp. on lisp and functional programming p45-52
%K TR, FP, functional programming, lazy, need, transform, transformation,
   c1984, c198x, c19xx
%X removes intermediate lists
   (LA: Wins the best title award.)

%A L. Cardelli
%T A polymorphic lambda calculus with type: type
%R 10
%I Systems Research Centre, 130 Lytton Ave., Palo Alto, California 94301
%M MAY
%D 1986
%K FP, type, data, datatype, check, checking, inference, lambda calculus,
   polymorphic, functional programming, applicative
%X (LA has.)

%A S. R. Vegdahl
%T A survey of proposed architectures for the execution of functional languages
%J IEEE Trans. on Computers
%V C-33
%N 12
%M DEC
%D 1984
%P 1050-1071
%K FP, survey, architecture, machine, multiprocessor,
   functional, applicative programming, dataflow, demand driven,
   hypertorus, hypercube

%A Manton Matthews
%A Yogeesh Kamath
%T The FP-shell
%J Proc. of the USENIX Summer Conf.
%W Salt Lake City, Utah
%M JUN
%D 1984
%P 133-140
%K FP, FPsh, functional programming, applicative, command language, shell
%X Backus FP used as command language for Unix.
   See Implementation of an FP-Shell,  IEEE SE-13, 5 May '87, pp.532-539.

%A Y. H. Kamath
%A M. M. Matthews
%T Implementation of an FP-shell
%J IEEE Trans. on Software Engineering
%V SE-13
%N 5
%M MAY
%D 1987
%P 532-539
%O see The FP-shell  Usenix Summer Conf. June 84 p133-140
%K Command language,   shell, Fpsh,  functional programming, FP, Unix
%X Backus FP used as command language in Unix.
   [Also search for: FP shell].

%T Combinators and Functional Programming Languages
%S LNCS
%V 242
%I SpringerVerlag
%D 1987
%K FP, book, c1987, c198x, c19xx, functional, applicative, combinator,
   combinatorial, logic, s k i, SKI, combinatory logic
%X [Also search for: FP combinatory logic].

%E G. Cousineau
%E P-L. Curien
%E B. Robinet
%T Combinators and functional programming languages
%W Val d'Ajol, France
%I SpringerVerlag
%S LNCS
%V 242
%M MAY
%D 1985
%K FP, combinator
%X P. Bellot, B. Robinet,    Streams are not dreams
   L. Cardelli               Amber
   L. Cardelli               The Amber machine
   T. Coquand                Sur l'analogie entre les propositions et les types
   G. Cousineau, P-L. Curien, M. Manny, A. Suarez
        Combinateurs categoriques et implementation des languages fonctionnels
   R. Hindley                Combinators and lambda calculus
   G. Huet                   Cartesian closed categories and lambda calculus
   J. Lambek              Cartesian closed categories and typed lambda calculii
   S. L. Peyton Jones        An introduction to fully lazy supercombinators

%A L. Cardelli
%T The Amber machine
%P 48-70
%B Combinators and Functional Languages
%I SpringerVerlag
%S LNCS
%V 242
%E G. Cousineau
%E P-L. Curien
%E B. Robinet
%D 1985
%K FP, functional, applicative programming, abstract machine,
   interpreter, implementation, graphics, bitmap, persistent, object, objects

%A R. Hindley
%T Combinators and lambda-calculus
%P 104-122
%B Combinators and Functional Languages
%I SpringerVerlag
%S LNCS
%V 242
%E G. Cousineau
%E P-L. Curien
%E B. Robinet
%D 1985
%K FP, functional, applicative programming, lambda calculus, combinator, logic,
   combinatory logic, SKI, S K I B, c1985, c198x, c19xx

%A S. L. Peyton Jones
%T An introduction to fully-lazy supercombinators
%P 176-208
%B Combinators and Functional Languages
%I SpringerVerlag
%S LNCS
%V 242
%E G. Cousineau
%E P-L. Curien
%E B. Robinet
%D 1985
%K FP, functional, applicative programming, lambda calculus, lazy, need,
   combinator, super, SKI, S K I, c1985, c198x, c19xx

%A R. S. Bird
%T A formal development of an efficient supercombinator compiler
%J Science of Computer Programming
%P 113-138
%V 8
%N 2
%M APR
%D 1987
%K SCP, FP, S K I, SKI, combinator, supercombinator, functional,
   applicative programming, lambda calculus, implementation, compile
%X worst case running time O(n log n)  where n is size of output.

%A C. T. Haynes
%A D. P. Friedman
%A M. Wand
%T Obtaining coroutines with continuations
%J Computer Languages
%V 11
%N 3/4
%P 143-153
%D 1986
%K FP, continuation, coroutine, control, Scheme, functional,
   applicative programming, c1986, c198x, c19xx
%X continuations when provided to the programmer [ in scheme ] provide
   a control abstraction of sequential computation.
   Power illustrated by implementing a variety of coroutine mechanisms.

%A M. Takeichi
%T Partial parameterization eliminates multiple traversals of data structures
%J Acta Informatica
%V 24
%P 57-77
%D 1987
%N 1
%M FEB
%K FP, functional, applicative programming, transformation,
   lazy, need, evaluation, circular program
%X Using partial parameterization and lazy evaluation
   a transformation can eliminate multiple traversals of a data structure.
   [Also search for: circular program FP].

%A M. S. Joy
%A V. J. Rayward-Smith
%A F. W. Burton
%T Efficient combinator code
%J Computer Languages
%V 10
%N 3/4
%P 211-224
%D 1985
%K FP, combinator, s k i, ski, functional, applicative programming, optimise,
   c1985, c198x, c19xx
%X choices of combinators s k i b c s' b' c' y
   algorithms for compiling
   for optimisation examined.
   [Also search for: FP combinator].

%E J. P. Jouannaud
%T Functional Programming Languages and Computer Architecture
%I SpringerVerlag
%S LNCS
%V 201
%M SEP
%D 1985
%W Nancy, France
%K FP, fpca, fplca, fplca85, fpca85
%X D. A. Turner Miranda: non-strict functional language with polymorphic types
   M. L. Welcome, S. K. Skedzielewski. Dataflow optimization in IF1
   C. Clack, S. L. Peyton Jones. Strictness analysis - a practical approach
   G. Cousineau, P. L. Curien, M. Mauny. The categorical abstract machine
   P. Bellot. High order programming in extended FP
   S. Abramsky, R. Sykes. Secd-m: virtual machine for applicative  programming
   M. J. Shute, P. E. Osmon, C. L. Hankin. Cobweb: combinator reduction arch'
   P. Wadler. How to replace failure by a list of success
   J. Hughes. Lazy memo functions
   D. A. Plaisted. An architecture for fast data movement in the FFP machine
   J. T. O'Donell An architecture that efficiently updates associative
      aggregates in applicative programming languages
   T. Johnsson. Lambda lifting : transforming programs to recursive equations
   S. K. Debray. Optimizing almost tail recursive prolog programs
   M. Sheeran. Designing regular array architectures using higher order functions
   M. Ercegovac, M. Schlag, D. Patel. vFP : an environment for the multi level
      specification, analysis and synthesis of hardware algorithms
   J. Hughes A distributed garbage collection algorithm
   D. R. Brownbridge  Cyclic reference counting for combinator machines
   D. S. Wise. Design for a multiprocessing heap with on-board reference counting
   M. F. Young. A functional language and modular architecture for scientific computing
   R. S. Nikhil. Practical polymorphism
   P. Dybjer  Program verification in a logical theory of constructions
   V. J. Bush, J. R. Gurd. Transforming recursive programs for execution on
     parallel machines (single and double recursive schemes, dynamic, FP)
   L. Augustsson. Compiling pattern matching
   B. Goldberg. P. Hudak. Serial combinators : optimal grains of parallelism
   R. B. Kieburtz. The G Machine : a fast graph-reduction evaluator

%A T. Johnsson
%T Lambda lifting: transforming programs to recursive equations
%P 190-203
%B Functional Programming Languages and Computer Architecture
%I SpringerVerlag
%V 201
%S LNCS
%M SEP
%D 1985
%E J. P. Jouannaud
%K FP, supercombinators, super combinator, transformation, lambda calculus,
   functional, applicative programming, optimization, fpca, fplca, fplca85,
   fpca85, c1985, c198x, c19xx
%X Transforms lambda calculus into recursive equations - supercombinators
   with no non local variables hence no environment needed to evaluate.
   Lazy ML used.

%A J. Hughes
%T Lazy memo functions
%P 129-146
%B Functional Programming Languages and Computer Architecture
%I SpringerVerlag
%V 201
%S LNCS
%M SEP
%D 1985
%E J. P. Jouannaud
%K FP, functional, applicative programming, memo function,  circular structure,
   hash cons, conf, fpca, fplca, fplca85, fpca85
%X memo function avoids recomputation of results,
   result of function applied to circular structure can be circular:
      let rec ones = 1.ones;
      let rec map f []=[] |
              map f (a::b) = (f a)::(map f b);
      map succ ones;
   [Also search for: circular program FP].

%A P. Wadler
%T How to replace failure by a list of successes
%P 113-128
%B Functional Programming Languages and Computer Architecture
%I SpringerVerlag
%S LNCS
%V 201
%M SEP
%D 1985
%E J. P. Jouannaud
%K FP, exception handling, throw, catch,  backtracking,  pattern matching,
   parse, parser, parsing, functional programming, techniques, practice,
   lazy evaluation, call by need, fpca, fplca, fplca85, fpca85, L4REF
%X (Arguably an even better title than PW's Listlessness one.)

%A G. C. Gopalakrishnan
%A M. K. Srivas
%T Implementing functional programs using mutable abstract data types
%J Information Processing Letters
%V 26
%M JAN
%D 1988
%P 277-286
%K jrnl, IPL, FP, functional, applicative programming, optimise, optimize,
   destructive operator, mutable assignment
%X gives sufficient conditions for functional program to
   be executed with destructive assignment operators,
   without copying.
   Graph used to represent dependencies.

%A R. S. Bird
%T Tabulation techniques for recursive programs
%J Computing Surveys
%V 12
%N 4
%M DEC
%D 1980
%P 403-417
%K recursive function,  redundancy,  tabulation,  transformation,
   recursion elimination,   memo, memoise, c1980, c198x, c19xx

%A J. Backus
%T Programming language semantics and closed applicative languages
%J ACM Symp. on the Principles of Programming Languages
%P 71-86
%D 1973
%K conf, POPL, POPL73, functional, applicative language, reduction,  FP, FFP,
   c1973, c197x, c19xx
%X "... proposes axioms to define a seq. of language-classes; the most general
   is that of 'programming language', the most restricted has some simple &
   attractive properties. Here 'language' is used in its traditional sense as
   referring to a set of interpreted expressions. We are concerned with the
   syntax of an expn only to the degree needed to relate its structure to its
   'meaning'. A clear distinction is drawn between a 'language' & the many
   possible 'realizations' of that language. This intro. comprises a survey &
   opinionated discussion of the contents of the paper, therefore the reader who
   wishes to get on with the technical exposition can skip to the next section."
   -- [<A HREF="http://dx.doi.org/10.1145/512927.512934">doi:10.1145/512927.512934</A>]['16].

%A R. S. Bird
%T Improving programs by the introduction of recursion
%J CACM
%V 20
%N 11
%D 1977
%P 856-863
%K tranform, transformation, program, recursion, fold, unfold

%A J. Backus
%T The algebra of functional programs: functional level reasoning
   linear equations and extended definitions
%B Formalization of Programming Concepts
%I SpringerVerlag
%S LNCS
%V 107
%P 1-43
%M APR
%D 1981
%W Peniscola, Spain
%K conf, c1981, c198x, z19zz, FP, FFP, linear equation, recursion, algebra
%X "In [B 78] we introduced a functional style of programming ..."
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-10699-5_91">doi:10.1007/3-540-10699-5_91</A>]['16].

%A J. Backus
%T Is computer science based on the wrong fundamental concept of program?
   An extended concept
%B Algorithmic Languages
%E de Bakker
%E vanVliet
%I IFIP
%D 1981
%P 133-165
%K FP, c1981, c198x, c19xx, FFP, functional programming, state

%A K. Nokel
%A R. Rehbold
%A M. M. Richter
%T Remarks on SASL and the verification of functional programming languages
%B Computation Theory and Logic
%E E. Borger
%I SpringerVerlag
%S LNCS
%V 270
%D 1987
%P 265-276
%K FP, SASL, logic, theory, verification, proof, applicative language
%X large introduction to SASL
   then logic for SASL.   Boyer Moore theorem prover adapted to
   non-strictness of SASL.
   induction over 1. natural numbers, 2. properly terminated finite lists
      3. fixed point induction,  4. lifting principle:
         (forall x (finite(x)=>P(x))) => forall x P(x)
   example verifies append function.

%A G. Cousineau
%A P.-L. Curien
%A M. Mauny
%T The categorical abstract machine
%J Science of Computer Programming
%V 8
%D 1987
%P 173-202
%K FP, combinator, SECD, CAM, S K I, SKI, ML, lazy, functional, applicative,
   call be value, call by need
%X variable names replaced by 'level number' removes name clashes.
   combinators translated into a machine code.
   a stack is the only saving mechanism.
   proved correct.
   implementation of ML as example.

%A A. Church
%T A set of postulates for the foundation of logic
%J Annals of Mathematics
%S 2
%V 33
%N 2
%P 346-366
%M APR
%D 1932
%K jrnl, Alonzo, lambda calculus, FP, c1932, c193x, c19xx, formal logic,
   postulate, postulates, free variable, variables
%X "... present a set of postulates for the foundation of formal logic,
   in which we avoid the use of the free, or real, variable, and in which
   we introduce a certain restriction on the law of the excluded middle
   as a means of avoiding the paradoxes connected with the math. of
   the transfinite ..."
   -- @[<A HREF="http://www.jstor.org/stable/1968337">Jstor</A>]['09] (via JR).
   (Also see 2nd paper of same title Oct '33
   -- @[<A HREF="http://www.jstor.org/pss/1968702">Jstor</A>]['09].)

%A A. Church
%T A set of postulates for the foundation of logic (2nd paper)
%J Annals of Mathematics
%S 2
%V 34
%N 4
%P 839-864
%M OCT
%D 1933
%K jrnl, Alonzo, lambda calculus, FP, c1933, c193x, c19xx, formal logic,
   postulate, postulates, free variable, variables
%X "... [set of postulates in paper 1] requires some modification in
   order to render it free from contradiction. ..."
   -- @[<A HREF="http://www.jstor.org/pss/1968702">Jstor</A>]['09] (via JR).
   (Also see paper 1, same title, '32,
   -- @[<A HREF="http://www.jstor.org/stable/1968337">Jstor</A>]['09].)

%A S. C. Kleene
%T Proof by cases in formal logic
%J The Annals of Mathematics
%S 2
%V 35
%N 3
%P 529-544
%M JUL
%D 1934
%K maths, theory, formal, logic, c1934, c193x, c19xx, computability,
   completeness
%X "... axioms and rules ... proposed by A.Church['32,'33]. ..."
   -- @[<A HREF="http://www.jstor.org/stable/1968749">Jstor</A>]['09] (via JR).

%A S. C. Kleene
%T A theory of positive integers in formal logic. Part I
%J American J. of Mathematics
%V 57
%N 1
%P 153-173
%M JAN
%D 1935
%K maths, theory, logic, c1935, c193x, c19xx, completeness, foundations,
   positive integer, integers
%X "... development of a system of logic based on the postulates propsed
   by A.Church['32,'33]. ... adequate for the theory of +ve integers, by
   exhibiting a construction of a sig. portion of the theory within the
   system. ..."
   -- @[<A HREF="http://www.jstor.org/stable/2372027">Jstor</A>]['09] (via JR).
   [Also search for: Church c193x].

%A S. C. Kleene
%T A theory of positive integers in formal logic. Part II
%J American J. of Mathematics
%V 57
%N 2
%P 219-244
%M APR
%D 1935
%K maths, theory, logic, c1935, c193x, c19xx, computability, completeness,
   foundations, positive integer, integers
%X -- @[<A HREF="http://www.jstor.org/stable/2371199">Jstor</A>]['09] (via JR)
   [Also search for: Church c193x].

%A S. C. Kleene
%A J. B. Rosser
%T The inconsistency of certain formal logics
%J The Annals of Mathematics
%S 2
%V 36
%N 3
%P 630-636
%M JUL
%D 1935
%K maths, theory, logic, c1935, c193x, c19xx, consistency, completeness,
   foundations, inconsistency, logics, Richard paradox
%X "We discuss some formal logics which are inconsistent in the sense that
   every formula in their notation is provable, irrespective of its meaning
   under the interpretation intended for the symbols. This results from the
   presence of a form of the Richard paradox, ..."
   -- @[<A HREF="http://www.jstor.org/stable/1968646">Jstor</A>]['09] (via JR).

%A A. Church
%T An unsolvable problem of elementary number theory
%J American J. of Mathematics
%V 58
%N 2
%P 345-363
%M APR
%D 1936
%K jrnl, Alonzo, Entscheidungsproblem, Turing, decision, halting problem,
   decidability, lambda calculus, conversion, FP, c1936, c193x, c19xx,
   completeness, logic, maths, theory, computable
%X "There is a class of problems of elementary number theory which can be stated
   in the form that is required to find an effectively calculable function f
   of n +ve integers s.t. f(x_1,...,x_n)=2 is a necc. and suff.
   condn for the truth of certain propositions of elem. num. th. ..."
   -- @[<A HREF="https://www.jstor.org/stable/2371045">Jstor:2371045</A>]['09],
   or  [<A HREF="https://doi.org/10.2307/2371045">doi:10.2307/2371045</A>]['17].
   [Also search for: Turing 1936]  and  [also search for: Kleene c193x].
   (Also see [<A HREF="http://www.allisons.org/ll/FP/Lambda/">lambda</A>].)

%A A. Church
%T A note on the Entscheidungsproblem
%J The J. of Symbolic Logic
%V 1
%N 1
%P 40-41
%M MAR
%D 1936
%K Alonzo, Entscheidungsproblem, Turing, decision, halting problem,
   c1936, c193x, c19xx, halting problem, computable, maths, logic, theory
%X -- @[<A HREF="http://www.jstor.org/stable/2269326">Jstor</A>]['09] via JR.
   And a correction in Sept. '36.
   [also search for: Church 193x],  [and for: Kleene c193x].

%A A. Church
%T Correction to a note on the Entscheidungsproblem
%J The J. of Symbolic Logic
%V 1
%N 3
%P 101-102
%M SEP
%D 1936
%K Alonzo, Entscheidungsproblem, Turing, halting problem, c1936, c193x, c19xx
%X -- [<A HREF="http://www.jstor.org/stable/2269030">Jstor</A>] via JR.
   [also search for: Church 193x],  [and for: Kleene c193x].

%A A. Church
%T The Calculi of Lambda conversion
%I PrincetonUP
%S Annals of Mathematical Studies
%N 6
%P 77
%D 1941
%K FP, book, text, lambda calculus, Alonzo Church, thesis, alpha, beta,
   reduction, functional programming, applicative, L4REF, c1941, c194x, c19xx,
   mathematics, computer science, CSci, theory
%X pb, us$35, us isbn:0691083940; us isbn13:978-0691083940;
   reprinted in 1985 from the 1941 original.
   -- book@[<A HREF="https://press.princeton.edu/titles/2390.html">pr'nceton</A>]['17].
   (Also see [<A HREF="http://www.allisons.org/ll/FP/Lambda/">lambda</A>].)

%A H. B. Curry
%A R. Feys
%T Combinatory Logic
%I NorthHolland
%D 1958
%K FP, book, text, combinator, SKI, Y S K I, book, text, mathematics, maths,
   theory, combinatorial logic, CS, CSci,  c1958, c195x, c19xx

%A D. Clement
%T The natural dynamic semantics of mini standard ML
%J Proc. Theory and Practice of Software Development, TAPSOFT 87
%I SpringerVerlag
%V 250
%M MAR
%D 1987
%E H. Ehrig
%E R. Kowalski
%E G. Levi
%E U. Montanari
%P 67-81
%K FP, ML, SML, c1987, c198x, c19xx, Typol
%X specification in Typol
   can produce type checkers, interpreters, translators.

%A P. Henderson
%A J. H. Morris
%T A lazy evaluator
%J 3rd ACM Symp. on Principles of Programming Languages
%P 95-103
%M JAN
%D 1976
%K FP, functional programming, lazy, need, call by need, name, call by name,
   non-strict, implementation, evaluation, conf, POPL,
   L4Ref, c1976, c197x, c19xx
%X "A different way to execute pure LISP programs is presented. It delays the
   evaluation of parameters and list structures without ever having to perform
   more evaluation steps than the usual method. Although the central idea can
   be found in earlier work this paper is of interest since it treats a rather
   well-known language and works out an algorithm which avoids full
   substitution. A partial correctness proof using Scott-Strachey semantics is
   sketched in a later section."
   -- [<A HREF="http://doi.acm.org/10.1145/800168.811543">doi:10.1145/800168.811543</A>][4/'04].

%A R. W. Harper
%T Standard ML input/output
%M JUN
%D 1985
%I Dept. Computer Science, University of Edinburgh
%K FP, ML, SML, input, output, basic io, I/O

%A D. MacQueen
%T Modules for standard ML
%M OCT
%D 1985
%I Dept. Computer Science, University of Edinburgh
%K FP, module, ML, SML, signature, data type, types, inheritance, sharing

%A R. Harper
%T Introduction to standard ML, preliminary draft
%I Dept. Computer Science, University of Edinburgh
%M OCT
%D 1985
%K FP, ML, SML, functional, programming, applicative language

%A J. Lambek
%A P. J. Scott
%T Introduction to Higher Order Categorical Logic
%I CUP
%S Cambridge studies in advanced mathematics
%P 304
%D 1986
%K book, text, CUP, c1986, c198x, c19xx, L5Ref, category theory, logic,
   lambda calculus, model, interpretation, intuitionistic theory, topos
%X category theory, lambda calculi and correspondence to cartesian closed
   categories,  intuitionistic higher order theories and their correspondence
   to toposes.
   pb, us$41, uk us isbn:0521246652; uk us isbn13:978-0521356534.
   Reviewed R. D. T e n n e n t  Comp. Rev. Dec '87, V28 No12 p.627.

%A R. J. Karia
%T Towards a parallel architecture for functional languages
%B Future Parallel Computers
%E P. Treleaven
%E M. Vanneschi
%D 1986
%S LNCS
%V 272
%I SpringerVerlag
%P 270-285
%K FP, parallel computer, functional, applicative programming language
%X cobweb parallel architecture
   discusses strict versus lazy  parallelism opportunities

%A P. H. Hartel
%A A. H. Veen
%T Statistics on graph reduction of SASL programs
%J SPE
%V 18
%N 3
%M MAR
%D 1988
%P 239-253
%K FP, execution statistics, SASL, functional, applicative programming,
   jrnl, SPE, graph reduction, SKI, lazy, time, space, speed, efficiency, L4REF,
   combinator, c1988, c198x, c19xx
%X 4 small and 4 medium sized (lazy) SASL programs
   using Turner's combinator reducer
   counts % of combinators used, size and growth of graph, depth
   and size of graph, sharing, reference counts, life of node.
   24 refs.

%A M. Joy
%A T. Axford
%T A standard for a graph representation for functional programs
%J Sigplan
%V 23
%N 1
%M JAN
%D 1988
%P 75-82
%K FP, functional, programming applicative, SASL, PIFL

%A Shaon-Jon Chao
%A B. R. Bryant
%T Denotational semantics for program analysis
%J Sigplan
%V 23
%N 1
%M JAN
%D 1988
%P 83-91
%K data flow analysis, symbolic evaluation, static analysis, optimise

%A Fer-Jan de Vries
%T A functional program for the fast Fourier transform
%J Sigplan
%V 23
%N 1
%M JAN
%D 1988
%P 67-74
%K FP, FFT, fast Fourier transform, Miranda, deVries, functional programming,
   c1988, c198x, c19xx
%X application of Miranda to FFT.

%A R. S. Bird
%T The promotion and accumulation strategies in transformational programming
%J TOPLAS
%V 6
%N 4
%M OCT
%D 1984
%P 487-504
%K program transformation, refinement, promote, promotion, accumulate,
   jrnl, TOPLAS
%X promotion: exploit recursive structure of the dominant term of an algorithm
   accumulation: accumulating parameter;
   examples: 1. determining if a digraph is acyclic and
             2. constructing longest subsequence of a given seq' of vertices
                that forms a connected path in a given digraph.

%A L. Cardelli
%T The Functional Abstract Machine
%I AT&T Bell Labs
%R TR-107
%D 1983
%K FP, functional programming, SML, FAM, interpreter, implementation

%A L. Cardelli
%T Compiling a Functional Language
%J ACM Lisp and Functional Programming Conf.
%W Austin Texas
%D 1984
%K FP,FAM, interpreter, implementation, functional abstract machine,
   LFPC LFPC84

%A D. W. Shipman
%T The functional data model and the data language DAPLEX
%J ACM Trans. on Data Base Systems
%V 6
%N 1
%M MAR
%D 1981
%K FP,functional programming, data model, data base, database, DAPLEX, TODS

%A D. A. Turner
%T Functional programming as executable specifications
%B Mathematical Logic and Programming Languages
%E C. A. R. Hoare
%E J. C. Shepherdson
%I PrenticeHall
%D 1986
%P 29-54
%K FP,Miranda, functional programming, polymorphic types,
   prototype
%X includes (knight) knight's tour of chess board as an example

%A B. Goldberg
%A P. Hudak
%T Alfalfa: distributed graph reduction on a hypercube multiprocessor
%J Proc. of the Los Alomos Workshop on Graph Reduction
%D 1986
%K FP,functional, applicative , programming , parallel machine

%A J. Hughes
%A P. Wadler
%T Projections for strictness analysis
%J Proc. of the Functional Languages and Computer Architecture Conf.
%D 1987
%O SpringerVerlag, LNCS vol.274
%P 385-407
%K FP,functional, applicative, lazy, need, programming ,
   strict, backward, strictness analysis fpca fplca fplca87 fpca87

%A F. Bellegarde
%T Rewriting systems on FP expressions that reduce the number of
   sequences they yield
%J Proc. ACM Symp. on Lisp and Functional Programming
%M AUG
%D 1984
%K FP, functional programming , transform, transformation,
   intermediate data structures, structure

%A F. Bellegarde
%T Convergent term rewriting systems can be used for program transformation
%J Proc. Workshop on Programs as Data Objects
%I SpringerVerlag
%S LNCS
%V 217
%E H. Ganziger
%E N. D. Jones
%D 1985
%K FP, functional, applicative , programming,
   transform, transformation, intermediate data structures

%A D. Barstow
%T Automatic programming for streams
%J Proc. of the 9th Int. Joint Conf. on Artificial Intelligence.
%M AUG
%D 1985
%K FP, stream, streams, sequences, functional, applicative, programming

%A G. Kahn
%A D. MacQueen
%T Coroutines and Networks of Parallel Processes
%J Proc. 1977 IFIP Congress
%I NorthHolland
%W Amsterdam
%D 1977
%K FP, coroutine, process, stream, streams

%A P. Wadler
%T Applicative languages, program transformation and list operators
%J Proc. ACM Conf. on Functional Programming Languages and
   Computer Architecture
%M OCT
%D 1981
%K FP, functional programming, applicative, language, list, stream, streams,
   fpca, fplca, fplca81, fpca81

%A P. Wadler
%T Listlessness is better than laziness II: composing listless functions
%J Proc. Workshop on Programs as Data Objects
%I SpringerVerlag
%S LNCS
%V 217
%E H. Ganziger
%E N. D. Jones
%D 1985
%K FP, functional programming, applicative, list, stream, streams
%X preorder listless function composition

%E H. Ganzinger
%E N. D. Jones
%T Programs as Data Objects: proceedings of a workshop
%W Copenhagen
%D 1985
%I SpringerVerlag
%S LNCS
%V 217
%K FP
%X S. Abramsky        Strictness and polymorphic invariance         1
   F. Bellegarde      Convergent term rewriting systems can
                      be use for program transformation            24
   G.L. Burn, C.L. Hankin, S. Abramsky        The theory of strictness
                analysis for higher order functions                42
   H. Christiansen    Recognition of generative languages          63
   H. Ganzinger       Modular first order specifications of
                      operational semantics                        82
   R. Giegerich       logic specification of code generation
                                                techniques         96
   J. Hughes          Strictness detection on non-flat domains    112
   D. Maurer          Strictness computation using special L exps 136
   A. Mycroft, N.D. Jones        A relational framework for
                      abstract interpretation                     156
   F. Nielson         Expected forms of data flow analyses        172
   F. Nielson, H.R. Hanna        Code generation from two-level
                      denotational meta-languages                 192
   B. Nordstrom       Multilevel functions in Martin-Lof's type theory 206
   D.A. Schmidt       An implementation from a direct semantics definition 222
   P. Sestoft         The structure of a self-applicable partial evaluator 236
   V.F. Turchin       Program transformation by supercompilation  257
   P. Wadler          Listlessness is better than laziness II:
                      composing listless functions                282
   M. Wand            From interpreter to compiler: a representational
                      derivation                                  306

%A F. Bellegarde
%T Convergent term rewriting systems can be used for program transformation
%B Programs as Data Objects
%E H. Ganzinger
%E N. D. Jones
%I SpringerVerlag
%S LNCS
%V 217
%P 24-41
%K FP, program transformation, Medee, list, sequence, stream
%X style of programming based on sequences or streams defined using
   recurrence relations. want tor remove intermediate structures.
   Use about 90 axioms from algebra of FP progams.

%A F. Nielson
%A H. R. Nielson
%T Code generation from two-level denotational meta-languages
%B Programs as Data Objects
%E H. Ganzinger
%E N. D. Jones
%I SpringerVerlag
%S LNCS
%V 217
%P 192-205
%K FP,denotational semantics, two level, compile time, run time,
   compile-time, run-time
%X TML type system:
   ct ::= A | ct1x...xctk | ct1+...+ctk | rec X.ct | X | ct1->ct2 | rt
   rt ::= _A| rt1x...xrtk | rt1+...+rtk | _rec_X.rt| _X| rt1->rt2
   compile time can talk about ct and rt but rt about rt only.

%A V. F. Turchin
%T Program transformation by supercompilation
%B Programs as Data Objects
%E H. Ganzinger
%E N. D. Jones
%I SpringerVerlag
%S LNCS
%V 217
%P 257-281
%K FP, supercompiler, partial evaluation, Refal,

%A P. Buneman
%A R. E. Frankel
%T An implementation technique for database query languages
%J ACM Trans. on Database Systems
%V 7
%N 2
%M JUN
%D 1982
%P 164-186
%K FP, FQL, lazy, functional, applicative, query language, relational,
   data base, database, coroutine

%A M. Takeichi
%T Lambda-hoisting: a transformation technique for fully lazy evaluation of
   functional programs
%J New Generation Computing
%V 5
%D 1988
%P 377-391
%K FP, fully lazy, functional programming, applicative,
   program transformation, lambda lift, lifting, hoisting
%X Closely related to lambda lifting
   and to Takeichi's Acta Informatica paper.
   Example:  el n L selects the nth element of L,
   let rec el = lambda n. lambda L. if (n=1) (hd L) (el (n-1) (tl L));
   let snd = el 2;
   Use of snd twice causes  'el 2'  to be evaluated twice,
   transform to
   let rec el = lambda n. lambda L. a (hd L) (b (tl L))
      where rec a = if (n=1),
                b = el (n-1)
   if snd is used, it is precomputed for a second use:
   snd == lambda L. a1(hd L)(b1 (tl L))
      where rec a1=if false,
                b1=(lambda L. a2(hd L)(b2 (tl L)),
                      where rec a2=if true,
                                b2=el(n2-1),
                                n2=2
                    ),
                n1=1
   [Also search for: lambda lifting FP].

%A A. Dwelly
%T Synchronizing the I/O behaviour of functional programs with feedback
%J IPL
%V 28
%P 45-51
%D 1988
%M MAY
%K FP,lazy, functional, applicative programming, interactive program,
   input, output, IO, prompt

%A A. Laville
%T Lazy pattern matching in the ML language
%J Foundations of Software Technology and Theoretical Computer Science,
   7th Conf.
%W Pune, India
%M DEC
%D 1987
%I SpringerVerlag
%S LNCS
%V 287
%E K. V. Nori
%P 400-419
%K FP, lazy, or, and, pattern matching, LML, SML, functional programming,
   applicative, by cases
%X eg. parallel or
    or(false, false) =false |
    or(true,  _    ) = true |
    or(_    , true ) = true       does not have a lazy pattern matcher
   Problem in a lazy ML (miranda ?) do not want to force unnecessary
   evaluation just for the pattern matching.

%A P. Wadler
%T Applicative style programming, program transformation and list operators
%J Proc. Conf. on Functional Programming Languages and
   Computer Architecture
%D 1981
%W Portsmouth
%I ACM
%P 25-32
%K FP,applicative, functional programming,
   list, map, gen, upto, red, reduce,  filter, fpca, fplca, fplca81, fpca81

%A M. Bellia
%A E. Dameri
%A P. Degano
%A G. Veli
%A M. Martelli
%T A formal model for lazy implementations of a Prolog-compatible functional
   language
%B Implementations of Prolog
%E J.A. Campbell
%S Ellis Horwood Series in Artificial Intelligence
%I Ellis Horwood
%C Chichester, England
%D 1984
%K FP, LFP, FLP, LP, Prolog, imp_prolog
%P 309-326

%A Bernhard Moller
%T An algebraic semantics for busy (data-driven) and lazy (demand-driven)
   evaluation and its application to a functional language
%J Proc. of the Tenth Int. Colloqium on Automata,
   Languages and Programming
%E J. Diaz
%W Barcelona, Spain
%O LNCS 154
%M JUL
%D 1983
%K FP,icalp, icalp10, ialp83
%P 513-526

%A Lennart Augustsson
%T A compiler for lazy ML
%J Conf. Record of the ACM Symp. on LISP and Functional Programming
%W Austin, Texas
%M JUL
%D 1984
%P 218-227
%K FP,slfp, slfp84, c1984, c198x, c19xx,
   ML, LML, typed functional programming, implementation
%X <A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A> ('94)

%A S. K. Debray
%T Optimizing almost-tail-recursive Prolog programs
%J Proc. of the 1985 Symp. on
   Functional Programming Languages and Computer Architecture
%W Nancy, France
%M SEP
%D 1985
%E Jean-Pierre Jouannaud
%O LNCS 201
%K fpca, fplca, fpca85, fplca85,
   FP, transformation, tail recursion
%P 204-219

%A E. Saint-James
%T Recursion is more efficient than iteration
%J Conf. Record of the ACM Symp. on LISP and Functional Programming
%W Austin, Texas
%P 228-234
%M JUL
%D 1984
%K slfp, slfp84, FP, Lisp implementation, tail recursion, optimisation

%A G. L. Steele
%T Debunking the expensive procedure call myth or,
   procedure call implementations considered harmful or,
   lambda: the ultimate goto
%J Proc. Annual Conf. of the ACM
%D 1977
%P 153-162
%K c1977, c197x, c19xx, FP, scheme, functional, applicative, implementation,
   tail recursion, tail-recursion, compile, optimise, optimisation

%A G. L. Steele
%A G. J. Sussman
%T Design of a Lisp-based microprocessor
%J CACM
%M NOV
%D 1980
%V 23
%N 11
%P 628-645
%K FP, lisp, micro, vlsi

%A A. Wikstrom
%B Functional Programming Using Standard ML
%I PrenticeHall
%D 1987
%K FP, text, book, Standard ML, SML, functional programming language
%X hb, isbn:0133319687;
   pb, isbn:0133316610;
   Hargrave, Monash  H 005.133 M685 WIK.F.
   (Also see [<A HREF="http://www.allisons.org/ll/FP/SML/">on SML</A>].)

%T ACM Symp. on Lisp and Functional Programming
%I ACM
%D 1984
%K conf, FP, slfp, lfp, Lisp
%W Austin, Texas
%X   isbn:0-89781-142-3.
     1 R. A. Brooks, R. P. Gabriel. A critique of common lisp
     9 R. H. Halstead jr. Implementation of multilisp: lisp on a multiprocessor
    18 C. T. Haynes, D. P. Friedman. Engines build process abstractions
    25 R. P. Gabriel, J. McCarthy. Queue based multi processing lisp
    45 P. Wadler. Listlessness is better than laziness: lazy evaluation and
          garbage collection at compile time
    53 A. Goldberg, R. Paige. Stream processing
    63 F. Bellegarde. Rewriting systems on FP expressions that reduce the number
          of sequences they yield
    74 J. S. Givler, R. B. Kieburtz. Schema recognition for program
          transformation.
    85 P. Conte, X. Rodel. Formes: an object and time oriented system for music
          composition and synthesis
    96 R. B. Dannenberg. Arctic: a functional language for real time control
   104 M. Sheeran. muFP a lanhuage for VLSI design
   113 J. Chailloux, M. Devin, JM. Hullot. Le lisp a portable and efficient
          lisp system
   123 G. Stefan, et al. Dialisp - a lisp machine
   129 R. L. Bates. D. Dyer, M. Feber. Recent developments in ISI interlisp
   140 H. G. Okuno et al. Tao: a fast interpreter centred lisp system on lisp
          machine elis
   150 S. Wholey, S. E. Fahlman. The design of an instruction set for common
          lisp
   159 W. R. Stoye, T. J. W. Clarke, A. C. Norman. Some practical methods
          for rapid combinator reduction
   167 P. Hudak, B. Goldberg. Experiments in diffused combinator reduction
   177 R. E. Griswold. Expression evaluation in the icon programming language
   184 R. Milner. A proposal for standard ML
   198 D. MacQueen. Modules for standard ML
   208 L. Cardelli. Compiling a functional language.
   218 L. Augustsson. A compiler for lazy ML
   228 E. Saint-James. Recursion is more efficient than iteration
   235 D. A. Moon. Garbage collection in a large lisp system.
   247 H. Lieberman. Steps towards better debugging tools for lisp
   256 R. A. Brooks. Trading data space for reduced time and code space
          in real time garbage collection on stock hardware
   263 T. Katayama. Type inference and type checking for functional programming
          languages
   273 A. Pettorossi. A powerful strategy for deriving efficient programs by
          transformations
   282 W. Dosch, B. Moller. Busy and lazy FP with infinite objects
   293 C. T. Haynes, D. P. Friedman, M. Wand. Continuations and coroutines.
   299 H. Stoyan. Early lsip history (56-59)
   311 G. Smolka. Making control and data flow in large programs explicit
   323 Y. Malachi, R. Waldinger. Tablog: the deductive tableau programming
          language
   331 J. des Rivieres, B. C. Smith. The implementation of procedurally
          reflective languages
   348 D. P. Friedman, M. Wand. Reification: reflection without metaphysics
   356 W. Clinger. The scheme 311 compiler: an exercise in denotational
       semantics

%A F. W. Burton
%T Nondeterminism with referential transparency in functional programming
   languages
%J COMPJ
%V 31
%N 3
%M JUN
%D 1988
%P 243-247
%K FP, functional, applicative, programming, nondeterminism, non determinism,
   backtrack, choice, fail
%X a program is passed an infinite tree of two valued decisions
   along with its "proper" input.
   The decisions are fixed at run time.
   Once fixed, a decision remains unchanged, so equivalent expressions
   must always have the same value.
   [Also search for: FP nondeterminism].

%A F. G. Harrison
%A H. Khoshnevisan
%T Algebraic transformation techniques for functional languages
%J COMPJ
%V 31
%N 3
%M JUN
%D 1988
%P 229-242
%K FP, functional, applicative, programming, tranform, linear, bounded,
   recursion, loop, memo, optimise

%A H. Sondergaard
%A P. Sestoft
%T Nondeterminism in functional languages
%D 1988
%M JUL
%J submitted COMPJ
%K FP, functional programming, choice, non determinism, denotational semantics

%T Graph Reduction
%E J. H. Fasel
%E R. M. Keller
%I SpringerVerlag
%S LNCS
%V 279
%M SEP
%D 1986
%O Proc. Workshop on Graph Reduction, Santa Fe, New Mexico, USA
%K FP, LNCS, 279, functional, applicative, programming,
   implementation, combinator, ski, Gmachine, G-machine
%X RMIT library has a copy
   1 H.-G. Oberhauser. On the correspondence of lambda style reduction and
      combinator style reduction.
  26 K. Berkling  Head order reduction: a graph reduction scheme for the
      operational lambda calculus
  49 J. Fairbairn  A simple abstract machine to execute supercombinators
  53 J. Goguen, C. Kirchner, J. Meseguer  Concurrent term rewriting as a
      model of computation
  94 B. Goldberg, P. Hudak  Alfalfa: distributed graph reduction on a
      hypercube multiprocessor
 114 R. Michelson at al. Prallel graph reduction on a supercomputer
 119 T. Johnsson  Target code generation from G-machine code
 160 M. Castan et al  Towards the design of a parallel graph reduction machine:
      the MaRS project
 181 P. G. Harrison, M. J. Reeve  The parallel graph reduction machine Alice
 203 R. M. Keller et al  Overview of Rediflow II development
 215 M.C.J.D. van Eekelen, M. J. Plasmeijer  Specification of reduction
      strategies in term rewriting systems
 240 F. W. Burton  Controlling reduction partial order in functional parallel
      programs
 252 A. Deb  Parallel garbage collection for graph machines
 265 I. Watson, P. Watson  Graph reduction in a parallel virtual memory
      environment
 275 R. B. Kieburtz  Performance measurement of a G-machine implementation
 297 S. Tighe et al  A flexible architectural study methodology
 312 P. Hudak  Arrays, non-determinism, side-effects and parallelism: a
      functional perspective
 328 P. Wadler  A new array operation
 336 Arvind, R. S. Nikhil, K. K. Pingali  I-structures: data structures for
      parallel computing
 370 B. Jayaraman, G. Gupta  Parallel execution of an equational language
 382 G. Lindstrom  Implementing logical variables on a graph reduction
      architecture
 401 U. S. Reddy  Functional logic languages  part 1
 426 J. Staples, P. J. Robinson  Unification of quantified terms

%A R. Michelsen
%A L. Smith
%A E. Williams
%A B. Yantis
%T Parallel graph reduction on a supercomputer: a status report
%B Graph Reduction
%S LNCS
%V 279
%D 1986
%E J. H. Fasel
%E R. M. keller
%P 114-118
%O Proc. Workshop on Graph Reduction  at Santa Fe, Oct 86
%K FP, alfalfa, Cray, cc, c, functional, applicative, implementation,
   programming, supercombinator, combinator, FPtoC, lambda lift lifting
%X cray x-mp
   translate to serial combinators and then into C

%T ACM Conf. on Lisp and Functional Programming
%I ACM
%M AUG
%D 1986
%K FP, c1986, c198x, c19xx, lfp, slfp, lfp86, slfp86
%X CSci has a copy
   1 S. Thompson.  Laws in Miranda
  13 D. Clement, et al. A simple applicative language: mini ML
  28 D. K. Gifford, J. M. Lucassen. Integrating functional and imperative
     programming
  39 C. N. Alberga et al. Experience with an uncommon lisp
  54 J. Padget. Desiderata for the standardisation of lisp
  67 R. A. Brooks et al. Design of an optimising dynamically retargetable
     compiler for common lisp
  86 D. H. Bartley, J. C., Jensen. The implementation of PC scheme
  94 J. Fairbairn, S. C. Wray. Code generation techniques for functional
     languages
 105 T. Knight. An architecture for mostly functional languages. (Symbolics)
 113 M. Lemaitre et al. Mechanisms for efficient multiprocessor combinator
    reduction.
 122 J. D. Ramsdell. The Curry chip
 132 A. Bloss, P. Hudak. Variations on strictness analysis
 143 R. Kent et al. Expansion passing style: beyond conventional macros
 151 E. Kohlbecker et al. Hygenic macro expansion
 162 H-J. Boehm et al. Exact real arithmetic: a case study in higher
     order programming
 174 J. L. White. Reconfigurable, retargetable bignums: a case study
     in efficient portable lisp system building
 192 P. Steenkiste, J. Hennessy. Lisp on a reduced instruction set processor
 202 V. Sarkar, J. Hennessey. Partitioning parallel programs for macro
     dataflow
 212 M. Scheevel. Norma: a graph reduction processor
 220 C. Clack, S.L. Peyton-Jones. The four-stroke reduction engine
 233 P. Lee, U. Pleban. On the use of Lisp in implementing denotational
     semantics
 249 H. R. Nielson, F. Nielson. Semantics directed compiling for functional
     languages
 258 A. Bawden. Connection graphs
 266 M. Mauny, A. Suarez. Implementing functional languages on the
     categorical abstract machine
 279 G. L. Steele, W. D. Hillis. Connection machine lisp: fine grained parallel
     symbolic processing
 298 M. Wand, D. P. Friedman. The mystery of the tower revealed: a
     non-reflective tower.
 308 J. C. Mitchell. A type-inference approach to reduction properties and
     semantics of polymorphic expressions.
 320 B. Jayaraman et al. Equations, sets and reduction semantics for
     functional and logic programming.
 322 S. R. Thatte. Towards a semantic theory for equational programming
     languages.
 343 C-W. Lerman, D. Maurer. A protocol for distributed  reference counting
 351 P. Hudak. A semantic model of reference counting and its abstraction
 364 M. Rudalics. Distributed copying garbage collection.

%A J. Fairbairn
%A S. C. Wray
%T Code generation techniques for functional languages
%J ACM Conf. on Lisp and Functional Programming
%M AUG
%D 1986
%P 94-104
%K FP, lfp, lfp86, Ponder, lazy, need, applicative

%A C. Clack
%A S. L. Peyton-Jones
%T The four-stroke reduction engine
%J ACM Conf. on Lisp and Functional Programming
%M AUG
%D 1986
%P 220-232
%K FP, lfp, lsp86, functional, applicative, parallel, task, process

%A H. R. Nielson
%A F. Nielson
%T Semantics directed compiling for functional languages
%J ACM Conf. on Lisp and Functional Programming
%M AUG
%D 1986
%P 249-257
%K FP, lfp, lfp86, two level denotational semantics, compile time, run time

%A A. W. Appel
%A D. B. MacQueen
%T A standard ML compiler
%J Functional Programming Languages and Computer Architecture
%O SpringerVerlag LNCS 274
%M SEP
%D 1987
%P 301-324
%K FP, ML, SML, compile. functional, applicative, implementation,
   fpca, fplca, fpca87, fplca87
%X Hargrave: H 005.1 J86F/3

%A M. P. Georgeff
%T A scheme for implementing functional values on a stack machine
%J ACM Symp. on Lisp and Functional Programming
%D 1982
%P 188-195
%K FP, partial parameterisation, recursion, programming,
   lfp, lfp82, slfp, slfp82
%X e is in simple form if:
   1. e is an atom  or
   2. e = (e1 e2 .. en) and ei in simple form   or
   3. e = lambda x1..xn.e1 and e1 in simple form and basic valued.

%A H. Barendregt
%T The Lambda Calculus: its Syntax and Semantics
%I NorthHolland
%D 1981
%K FP, functional programming, text, book, c1981, c198x, c19xx, reduction,
   normal form
%X 1st ed 1981;
   2nd ed 1985, pb, uk us isbn:0444875085, uk us isbn13:978-0444875082;
   2012, pb us$25, uk us isbn:184890066X, uk us isbn13:978-1848900660.
   "Modern encyclopedic reference work on the lambda calculus and combinatory
   logic. First 70 pages (of 611 total) are probably more than sufficient
   intro. for most needs, does not generally address comp.-sci.-related issues."
   (Also see [<A HREF="http://www.allisons.org/ll/FP/Lambda/">lambda</A>].)

%A R. Hindley
%A J. Seldin
%T Introduction to Combinators and Lambda Calculus
%S London Mathematical Society Student Texts #1
%I CUP
%P 360
%D 1986
%K FP, functional programming, SKI, text, book, combinatorial logic, Curry,
   intro, combinator, SKI, type, types, theory, models, lambda calculi,
   CUP, c1986, c198x, c19xx
%X "... new version is thoroughly revised and offers a fully up-to-date account
   of the subject, ... . The grammar and basic properties of both combinatory
   logic and lambda-calculus are discussed, followed by an introduction to
   type-theory. Typed and untyped versions of the systems, and their differences
   are covered. Lambda-calculus models, which lie behind much of the semantics
   of programming languages, are also explained in depth. ..."
   2nd ed 2008; hb stg32; uk us isbn:0521898854; uk us isbn13:978-0521898850.
   1st ed 1986.
   (Also see [<A HREF="http://www.allisons.org/ll/FP/Lambda/">lambda</A>].)

%A S. L. Peyton Jones
%T Flic - a functional language intermediate code
%P 30-48
%J Sigplan notices
%V 23
%N 8
%M AUG
%D 1988
%K functional, applicative, language, programming, FP, FLIC

%A M. Mauny
%A A. Suarez
%T Implementing functional languages in the categorical abstract machine
%J ACM Conf. on Lisp and Functional Programming
%D 1986
%M AUG
%W Cambridge, Massachusetts
%P 266-278
%K FP, functional programming, lfp, cam, combinator, inria

%A Ph. Schnoebelen
%T Refined compilation of pattern-matching for functional languages
%J Science of Computer Programming
%V 11
%D 1988
%P 133-159
%K SCP, FP, functional programming, pattern matching, functional language,
   by cases

%A L. Augustsson
%T Compiling pattern matching
%B Functional Programming Languages and Computer Architecture
%S LNCS
%V 201
%I SpringerVerlag
%D 1985
%P 368-381
%K FP, functional programming, fpca, fplca, fpca85, fplca85

%A S. Peyton Jones
%A J. Salkild
%T The spineless tagless G-machine
%J FPLCA
%A ACM
%P ?-?
%D 1989
%K conf, c1989, c198x, c19xx, fplca, fplca89, functional programming, language,
   FP, implementation, lazy, graph reduction, spineless, tagless, tag, STG,
   tail recursion, G-machine, Gmachine
%X "The Spineless Tagless G-Machine is an abstract machine designed to support
   higher-order functional languages. This presentation of the machine falls
   into three parts. Firstly we give a general discussion of the design issues
   involved in implementing non-strict functional languages. Next, we present
   the STG language ..."
   -- [<A HREF="http://dx.doi.org/10.1145/99370.99385">doi:10.1145/99370.99385</A>]['12],
   preprint@[<A HREF="http://research.microsoft.com/apps/pubs/default.aspx?id=67083">ms</A>]['12].
   [Also search for: FP Gmachine].

%A C. Runciman
%T What about the natural numbers?
%J Comput. Lang.
%V 14
%N 3
%P 181-191
%D 1989
%K jrnl, lazy number, computer arithmetic, total, functional programming, FP,
   numeric type, types, Num, closed, integers, ints, c1989, c198x, c19xx,
   numerical, system
%X auth@cs york ['04].
   [Also search for: FP number system].

%A J.Launchbury
%T Projection Factorisations in Partial Evaluation
%I Comp. Sci., Glasgow
%D 1989
%O Projection Factorisations in Partial Evaluation, CUP, pp.163, '91,
   isbn:0521414970.
%K PhD thesis, functional programming, FP, c1989, c198x, c19xx, factorisations,
   Launchbury, launchberry
%X "...propose using domain projections in binding-time analysis. This allows a
   greater level of data separation than before because values are no longer
   treated atomically. In particular, we are able to pinpoint static values
   within data structures containing both static and dynamic parts. An
   interesting consequence of using domain projections is that we are able to
   demonstrate an intimate relationship between binding-time analysis and
   strictness analysis. ..."

%A J. Hughes
%T Why functional programming matters
%J COMPJ
%P 98-107
%V 32
%N 2
%M APR
%D 1989
%K functional, applicative, lazy, by need, lambda, FP, c1989, c198x, c19xx,
   jrnl, game tree, gametree, tic tac toe, alpha beta pruning, L4REF
%X As software becomes more and more complex, it is more and more important
   to structure it well. Well-structured software is easy to write, easy to
   debug, and provides a collection of modules that can be re-used to reduce
   future programming costs.  Conventional languages place conceptual limits
   on the way problems can be modularised. Functional languages push those
   limits back. In this paper we show that two features of functional languages
   in particular, higher-order functions and lazy evaluation, can contribute
   greatly to modularity. As examples, we manipulate lists and trees, program
   several numerical algorithms, and implement the alpha-beta heuristic
   (an algorithm from Artificial Intelligence used in game-playing programs).
   Since modularity is the key to successful programming, functional languages
   are vitally important to the real world.
   -- [<A HREF="http://www.math.chalmers.se/~rjmh/Papers/whyfp.html">abs+paper</A>][5/'03].

%A R. Frost
%A J. Launchbury
%T Constructing natural language interpreters in a lazy functional language
%J COMPJ
%K functional programming, applicative, lazy, by need, interpreter,
   lambda, FP, parse, parser
%P 108-121
%V 32
%N 2
%M APR
%D 1989

%A R. S. Bird
%T Algebraic identities for program calculation
%J COMPJ
%K functional programming, applicative, lazy, by need, lambda, FP,
   algebra, proof, transformation, L4REF
%P 122-126
%V 32
%N 2
%M APR
%D 1989

%A L. Augustsson
%A T. Johnsson
%T The Chalmers lazy-ML compiler
%J COMPJ
%K functional programming, applicative, lazy, by need, language, lambda, FP,
   implementation, LML ML, L4REF
%P 127-141
%V 32
%N 2
%M APR
%D 1989
%X [<A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A>]['94].

%A S. C. Wray
%A J. Fairbairn
%T Non-strict languages - programming and implementation
%J COMPJ
%P 142-151
%V 32
%N 2
%M APR
%D 1989
%K functional, applicative, lazy, by need, lambda, FP,
   implementation, Ponder, c1989, c198x, c19xx

%A A. Bloss
%A P. Hudak
%A J. Young
%T An optimising compiler for a modern functional language
%J COMPJ
%K functional, applicative, lazy, by need, lambda, FP,
   implementation, compile, optimise optimize
%P 151-161
%V 32
%N 2
%M APR
%D 1989

%A P. Hudak
%T Conception, evolution and application of functional programming languages
%J Comp. Surveys
%V 21
%N 3
%P 359-411
%D 1989
%K functional programming, FP, survey, use, jrnl

%A S. B. Jones
%A A. F. Sinclair
%T Functional programming and operating systems
%J COMPJ
%P 162-174
%V 32
%N 2
%M APR
%D 1989
%K functional, applicative, lazy, by need, language, lambda, FP, OS,
   stream streams, IO, input output, c1989, c198x, c19xx

%A S. L. Peyton Jones
%T Parallel implementations of functional programming languages
%J COMPJ
%P 175-186
%V 32
%N 2
%M APR
%D 1989
%K functional, applicative, lazy, by need, lambda, FP,
   speculative evaluation, GRIP

%A R. Bird
%A P. Wadler
%T Introduction to Functional Programming
%I PrenticeHall
%D 1988
%K good, text, book, FP, functional programming, language, L3Ref, L4REF
%X hb, isbn:0134841891;
   pb, isbn:0134841972;
   (also see 2nd edn '98.)

%A E. Moggi
%T Computational lambda-calculus and monads
%I LFCS, Dept. Comp. Sci., Edinburgh U.
%R ECS-LFCS-88-66
%P 23
%M OCT
%D 1988
%K TR8866, TR 88 66, functional programming, c1988, c198x, c19xx, FP,
   monad, monadic, categorical semantics, category, input, output, IO,
   side effect, effects
%X [<A HREF="http://www.disi.unige.it/person/MoggiE/ftp/lc88.pdf">pdf</A>]['05].

%A F. W. Burton
%A R. L. Page
%T Distributed random number generation
%J J. of Functional Programming
%V 2
%N 2
%P 203-212
%M APR
%D 1992
%K jrnl, JFP, FP, c1992, c199x, c19xx, zz0306, generator, generators, RNG,
   PRNG, split, parallel
%X cited in [<A HREF="http://haskell.org/ghc/docs/latest/html/libraries/base/System-Random.html">System-Random</A>]['06]

%A S. E. Panitz
%A M. Schmidt-Schauss.
%T TEA: Automatically proving termination of programs in non-strict
   higher-order functional language.
%J 4th Int. Symp. on Static Analysis
%P 345-360
%I SpringerVerlag
%S LNCS
%V 1302
%D 1997
%K functional programming, non-strict, lazy, program, FP, c1997, c199x, c19xx,
   high order, function, Haskell, nonStrict, uniFrankfurt
%X [<A HREF="http://www.ki.informatik.uni-frankfurt.de/papers/panitz/sas97.ps">.ps</A>]['04].
   [<A HREF="http://www.ki.informatik.uni-frankfurt.de/tea/tea.html">TEA</A>][12/'04].

%A A. Telford
%A D. Turner
%T Ensuring streams flow
%J 6th Int. Conf. Algebraic Methodology and Software Technology (AMAST '97)
%W Sydney
%P 509-523
%I SpringerVerlag
%S LNCS
%V 1349
%M DEC
%D 1997
%K conf, total functional programming, FP, c1997, c199x, c19xx, productive,
   codata, ESFP, stream, infinite, coinductive type, calculus of constructions,
   types, abstract interpretation, AMAST, AMAST97
%X "It is our aim to produce an elementary strong FP (ESFP) system. ... ESFP
   should include structures such as streams which can be computationally
   unwound infinitely often. We describe a syntactic analysis to ensure that
   infinitely proceeding structs., which we shall term codata, are productive.
   This analysis is an extension of the check for guardedness that has been
   used with definitions over coinductive types in Martin-Lof's type theory &
   in the calculus of constructions. Our analysis is presented as a form of
   abstract interpretation that allows a wider syntactic class of corecursive
   definitions to be recognised as productive than in previous work. Thus
   programmers will have fewer restrictions on their use of infinite streams
   within a strongly normalizing functional language."
   -- [<A HREF="http://www.cs.kent.ac.uk/pubs/1997/499/">.ps</A>][12/'04].
   Also see T+T c2000.

%A L. Augusteijn
%T Sorting morphisms
%J 3rd Int. Summer School on Advanced Functional Programming
%P 1-27
%M SEP
%D 1998
%O In Advanced F.P., S.D.Swierstra et al (eds), SpringerVerlag, LNCS, vol.1608
%K conf, FP, sort, functional programming, c1998, c199x, c19xx, catamorphism,
   anamorphism, morphism, afp, afp3, afp98
%X Sorting ... can be classified in many different ways.  ...here ... by
   expressing the algorithms as functional programs and to classify them by
   means of their recursion patterns [which] can be classified as the natural
   recursion patterns that destruct or construct a given data-type, the so
   called cata- and anamorphisms respectively. ...selection of the recursion
   pattern [is] the major design decision, in most cases leaving no more room
   for more decisions in the design of the sorting algorithm. [also] the
   use of alternative data structures may lead to new sorting algorithms.
   -- [<A HREF="http://www.di.uminho.pt/afp98/PAPERS/Lex.ps">.ps</A>][8/'03].
   23 pages (in, isbn:3540662413).

%A O. Danvy
%T Online type-directed partial evaluation
%J (Fuji) Int. Symp. on Functional and Logic Programming
%P 271-295
%D 1998
%I World_Scientific
%O RS-97-53, BRICS.dk, Dec '97, 31pp.
%K FLOPS, FLOPS98, conf, FP, types, functional programming, c1998, c199x, c19xx
%X ...extend type-directed partial evaluation (a.k.a. ``reduction-free
   normalization'' and ``normalization by evaluation'') to make it online,
   by enriching it with primitive operations (delta-rules). Each call to
   a primitive operator is either unfolded or residualized, depending on
   the operands and either with a default policy or with a user-supplied
   filter. The user can also specify how to residualize an operation,
   by pattern-matching over the operands. Operators may be pure or have a
   computational effect.
      We report a complete implementation of online type-directed partial
   evaluation in Scheme, extending our earlier offline implementation.
   Our partial evaluator is native in that it runs compiled code instead
   of using the usual meta-level technique of symbolic evaluation.
   -- [<A HREF="http://www.brics.dk/RS/97/53/">RS-97-53</A>][5/'03].

%A S. L. Peyton Jones
%A E. Meijer
%A D. Leijen
%T Scripting COM components in Haskell
%J 5th Int. Conf. on Software Reuse
%M JUN
%D 1998
%K conf, ICSR, ICSR5, FP, functional programming, scripting, language,
   component object model, COM, zz0503, c1998, c199x, c19xx
%X [<A HREF="http://research.microsoft.com/Users/simonpj/Papers/com.ps.gz">.ps.gz</A>][5/'03].

%A R. Bird
%A T. E. Scruggs
%A Mastropieri
%T Introduction to Functional Programming (2nd ed)
%I PrenticeHall
%P 460
%M APR
%D 1998
%K book, text, c1998, c199x, c19xx, good, L2Ref, L3Ref, FP, Haskell
%X 2nd ed c1998, pb, uk us isbn:0134843460; uk us isbn13:978-0134843469;

%A G. Hutton
%A E. Meijer
%T Functional Pearl: Monadic parsing in Haskell
%J J. of Functional Prog.
%V 8
%N 4
%P 437-444
%M JUL
%D 1998
%K jrnl, JFP, FP, parse, parser, programming, combinators, monad
%X "...defining recursive descent parsers in Haskell. In the spirit of one-stop
   shopping, the paper combines material from three areas into a single source.
   The three areas are functional parsers, the use of monads to structure
   functional programs, and the use of special syntax for monadic programs in
   Haskell. More specifically, the paper shows how to define monadic parsers
   using do notation in Haskell. ..."
   -- [<A HREF="http://www.cs.nott.ac.uk/~gmh/pearl.pdf">.pdf</A>][5/'04].
   [<A HREF="http://www.dcs.glasgow.ac.uk/jfp/bibliography/References/huttonm1998:437.html">JFP</A>][10/'02],
   [<A HREF="http://uk.cambridge.org/journals/JFP/">CUP</A>][10/'02],
   Also a longer TR and s/w at [<A HREF="http://www.cs.nott.ac.uk/~gmh/bib.html">gmh</A>][5/'04].

%A D. I. Bevan
%A G. L. Burn
%A R. J. Karia
%A J. D. Robson
%T Principles for the design of a distributed memory architecture for
   parallel graph reduction.
%J COMPJ
%V 32
%N 5
%P 461-469
%D 1989
%K FP, applicative, functional, programming, implementation, parallel machine,
   multi processor

%A P. Kelly
%T Functional Programming for Loosely-Coupled Multiprocessors
%I MITpress
%D 266
%M JAN
%D 1989
%S Research Monograph in Parallel and Distributed Computing
%K FP, book, text, c1989, c198x, c19xx, functional, applicative, multi,
   parallel
%X US$25.95, stg23, pb, uk us isbn:0262610574; uk us isbn13:978-0262610575.

%A A. W. Appel
%T Runtime tags aren't necessary
%J Lisp and Symbolic Computing
%V 2
%N 2
%P 153-162
%M JUN
%D 1989
%K FP, functional programming, garbage collection, GC, polymorphic type, tag
%X Hargrave 005.13305 277I

%A J. Backus
%A J. H. Williams
%A E. Wimmers
%T An introduction to the programming language FL
%M JUN
%D 1990
%K FL, FP, c1991, c199x, c19xx, zz0724, computer programming language,
   definition, PLD, FP, FL, function level
%X Also see 
   FL manual [<A HREF="http://theory.stanford.edu/~aiken/publications/trs/RJ7100.pdf">stanf'd</A>]['24],
   and FL@[<A HREF="https://wikipedia.org/wiki/FL_(programming_language)">wikip</A>]['24],
   and JBackus@[<A HREF="https://en.wikipedia.org/wiki/John_Backus">wikip</A>]['24].
   [Also search for: Backus FP].

%A H. Sondergaard
%A P. Sestoft
%T Referential transparency, definiteness and unfoldability
%J Acta Informatica
%V 27
%P 505-517
%D 1990
%K FP, functional, nondeterminism, determinism
%X [Also search for: FP nondeterminism].

%A D. Ungar
%T Generation scavenging: a non-disruptive high performance storage reclamation
   algorithm
%J ACM Sigsoft/Sigplan Software Engineering Symp. on
   Practical Software Development Environments.
%M MAY
%D 1984
%P 157-167
%K FP, functional, applicative, programming, garbage collection
%X Claims uses < 2% CPU time on one smalltalk implementation.
   Variation on copying compactor collectors.
   Objects that survive  several collections assumed to remain useful
   and become `old'; not scavenged again.

%A P. Hudak
%A R. M. Keller
%T Garbage collection and task deletion in distributed applicative
   processing systems
%J ???
%D 1982
%P 168-178
%K FP, parallel, distributed, applicative, functional, programming,
   implementation, garbage, collection, task, process, spawn, spark
%X Processing elements have only local store.
   Connected by a communication network.
   Virtual addressing => a PE may ref any other node in system.

%E T. Ho
%E R. H. Halstead jr
%T Parallel Lisp: Languages and Systems
%I SpringerVerlag
%S LNCS
%V 441
%D 1989
%M JUN
%K FP, lisp, functional, applicative programming language, parallel, concurrent
%X proc US/Japan workshop on parallel lisp.
   Hargrave lib has copy

%E E. Chiricozzi
%E A. D'Amico
%T Parallel Processing and Applications
%I NorthHolland
%D 1988
%O Proc Int Conf on Parallel Processing and Applications,
   L'Aquila Italy 23-25 Sept 1987
%K FP, functional programming, concurrent, grain, DAmico
%X isbn:0 444 70412 4;      Caufield campus library has it.
   W. G. Vree.  The grain size of parallel computations in a func prog
   (LA: a real application to tide prediction)           363-370
   E. Nocker and R. Plasmeyer
   Combinator reduction on a parallel G-machine, pp.399-412.

%A G. L. Burn
%T Evaluation transformers - a model for the parallel evaluation
   of functional languages (extended abstract)
%J Third Conf. on
   Functional Programming Languages and Computer Architecture
%D 1987
%I SpringerVerlag
%S LNCS
%V 274
%P 446-470
%K FP, fpca, fpca87, fplca, fplca87,
   functional programming, lambda, parallel, speculative,
   execution, evaluation, transformer, strictness, strict, analysis,
   abstract interpretation
%X defn: safe = no exp evaluated unless eventually needed.

%A S. L. Peyton Jones
%T The Implementation of Functional Programming Languages
%I PrenticeHall
%S Int. Series in Computer Science
%D 1987
%K FP, functional programming, language, implementation, super, combinator,
   supercombinator, graph reduction, lazy, by need,
   text, book, c1987, c198x, c19xx
%X 1st ed 1987; uk us isbn:013453333X;
   and@[<A HREF="http://research.microsoft.com/en-us/um/people/simonpj/papers/slpj-book-1987/">ms</A>]['12].

%A P. H. Hartel
%T Performance of lazy combinator graph reduction
%J SPE
%V 21
%N 3
%P 299-330
%M MAR
%D 1991
%K FP, SPE, functional, programming, applicative, implementation, lambda,
   graph, reduction, speed, performance, efficiency, statistics

%A H. R. Nielson
%A F. Nielson
%T Automatic binding time analysis for a typed lambda-calculus
%J Science of Computer Programming
%V 10
%P 139-176
%D 1988
%K FP, lambda calculus, functional programming, bind, binding time,
   abstract interpretation, two-level semantics.

%A F. Warren Burton
%A Hsi-Kai Yang
%T Manipulating Multilinked Data Structures in a Pure Functional Language
%J SPE
%V 20
%N 11
%P 1167-1185
%M NOV
%D 1990
%K jrnl, SPE, FP, lazy, functional, programming, circular program,
   multi link, links, cyclic, multilink, recursive, data structure, graph
%X [Also search for: circular program FP].

%A A. W. Appel
%T Compiling with Continuations
%I CUP
%D 1991
%P 272
%K functional, applicative, programming, language, implementation, compiler,
   text, book, c1991, c199x, c19xx, compile, control, data flow, continuation,
   standard ML, SML
%X control and data flow represented using continuations.
   illustrated by compiler for standard ML.
   hb, uk us isbn:0521416957; uk us isbn13:978-0521416955. list $34.95

%A J. Launchbury
%T A strongly-typed self-applicable partial evaluator
%J Functional Programming Languages and Computer Architectures (FPCA)
%P 145-164
%M AUG
%D 1991
%K conf, FPCA, FPCA5, c1991, c199x, c19xx, FP, partial evaluation, strong,
   type, types, mix, compiler, interpreter
%X FPCA5; isbn:0387543961.
   -- [<A HREF="http://www.cse.ogi.edu/~jl/">jl</A>][2OO1].

%A K. Pingali
%A K. Ekanadham
%T Accumulators: new logic variable abstractions for functional languages
%J Theor. Comp. Sci.
%V 81
%P 201-221
%D 1991
%K TCS, FP, LFP, FLP, LP, functional programming, accumulator, logic variable

%A M. Bellia
%A G. Levi
%T The relation between logic and functional languages: a survey
%J J. Logic. Prog.
%D 1986
%V 3
%P 217-236
%K FP, LFP, FLP, LP, functional, logic, programming language, survey

%A G. Lindstrom
%T Functional programming and the logical variable
%J Proc. 12th ACM Symp. on Princ. of Prog. Lang.
%D 1985
%P 266-280
%K FP, LFP, FLP, LP, functional, logic, programming, POPL, POPL12

%A J. Darlington
%A A. J. Field
%A H. Pull
%T The unification of functional and logic languages
%B Logic Programming: Functions Relations and Equations.
%D 1985
%E D. DeGroot
%E G. Lindstrom
%I PrenticeHall
%P 37-70
%K FP, LP, LFP, FLP, logic functional programming

%A A. H. Borning
%T Constraints and functional programming
%J 6th IEEE Phoenix Conf on Computers and Communication
%I IEEE
%D 1987
%P 300-306
%K FP, CFP, IEEE, constraint, logic functional programming

%A G. L. Burn
%A C. Hankin
%A S. Abramsky
%T Strictness analysis for higher-order functions
%J Sci. of Comput. Prog.
%V 7
%P 249-278
%D 1986
%K FP, functional programming, lazy, strict, strictness analysis,
   optimisation, high order, high-order

%A G. Burn
%T Lazy Functional Languages: Abstract Interpretation and Compilation
%S Research Monographs in Parallel and Distributed Computing.
%I Pitman
%D 1991
%K FP, functional programming, lazy, abstract interpretation,
   optimisation, strict, strictness, text, book

%A C. Clack
%A S. L. Peyton-Jones
%T Strictness analysis - a practical approach
%B Functional Programming Languages and Computer Architecture.
%E J-P. Jouannaud
%P 35-49
%S LNCS
%V 201
%I SpringerVerlag
%D 1985
%K conf, FP, functional programming, lazy, strict, strictness analysis,
   FPLCA, FPLCA85

%A A. J. Field
%A P. G. Harrison
%T Functional Programming
%S Int. Computer Science Series
%I Addison-Wesley
%D 1988
%K FP, functional programming language, book, lazy

%A B. A. Sijtsma
%T Verification and derivation of infinite-list programs
%I Rijksuniversiteit, Groningen
%M OCT
%D 1988
%K FP, functional programming, lazy, circular program, recursion,
   recursive, list, lists, PhD thesis
%X (do not have.)
   [Also search for: circular program FP].

%A B. A. Sijtsma
%T On the productivity of recursive list definitions
%J TOPLAS
%V 11
%N 4
%P 633-649
%M OCT
%D 1989
%K jrnl, TOPLAS, FP, functional programming, lazy, circular program,
   termination, recursion, recursive, list, lists
%X [Also search for: circular program FP].

%A H.P. Barendregt
%A M.C.J.D. van Eekelen
%A J.R.W. Glauert
%A J.R. Kennaway
%A M.J. Plasmeijer
%A M.R. Sleep
%T Term graph rewriting
%J Proc. Parallel Architectures and Languages Europe
%I SpringerVerlag
%V LNCS 259
%P 141-158
%D 1987
%K FP, functional programming, lambda calculus, term rewriting, graphs,
   reduction, UEA, East Anglia

%A H. P. Barendregt
%A J. R. Kennaway
%A J. W. Klop
%A M. R. Sleep
%T Needed reduction and spine strategies for the lambda calculus
%J Information and Computation
%V 75
%N 3
%P 191-231
%D DEC
%D 1987
%K jrnl, c1987, c198x, c19xx, FP, functional programming, lambda calculus,
   term rewriting, spine, reduction, UEA, East Anglia, evaluation strategy,
   reduction, redex, need, neededness
%X "A redex R in a lambda-term M is called needed if in every redn of M to
   normal form (some residual of) R is contracted. Among others the following
   results are proved:  1. R is needed in M iff R is contracted in the leftmost
   reduction path of M.  2. Let View the R:M0->M1->M2->... reduce redexes
   Ri: Mi->M_i+1, and have the property that forall i, exists j>=i . Rj is
   needed in Mj. Then R is normalising, i.e., if M0 has a normal form, then
   R is finite & terminates at that normal form.  3. Neededness is an
   undecidable property, but has several efficiently decidable approxns,
   various versions of the so-called spine redexes."
   -- [<A HREF="http://dx.doi.org/10.1016/0890-5401(87)90001-0">doi:10.1016/0890-5401(87)90001-0</A>]['13].

%A J. R. W. Glauert
%A J. R. Kennaway
%A M. R. Sleep
%T Dactl: a computational model and compiler target language based on graph
   reduction
%J ICL Technical J.
%V 5
%N 3
%P 509-537
%D 1987
%K FP, functional programming, lambda calculus, term rewriting, DACTL,
   reduction, UEA, East Anglia

%A J.R. Kennaway
%T On graph rewritings
%K FP, functional programming, lambda calculus, term rewriting,
   graph
%J Th. Comp. Sci.
%V 52
%P 37-58
%D 1987

%A J.R. Kennaway
%T Implementing term rewrite languages in Dactl
%J Proc. Colloquium on Trees and Algebra in Programming
%E M. Dauchet
%E M. Nivat
%V LNCS 299
%I SpringerVerlag
%P 102-116
%D 1988
%K FP, functional programming, lambda calculus, term graph rewriting, DACTL

%A J. R. W. Glauert
%A K. Hammond
%A J. R. Kennaway
%A G. A. Papadopoulos
%T Using DACTL to implement declarative languages
%J CONPAR'88
%P 116-124
%D 1988
%K wShop, FP, functional programming, lambda calculus, term rewriting, DACTL,
   CONPAR, CONPAR88, UEA, East Anglia

%A J.R. Kennaway
%T Sequential evaluation strategies for parallel-or and related reduction
   systems.
%J Annals of Pure and Applied Logic
%V 43
%P 31-56
%D 1989
%K jrnl, FP, functional programming, lambda calculus, term rewriting, reduction

%A J. R. W. Glauert
%A J. R. Kennaway
%A M. R. Sleep
%T Dactl: an experimental graph rewriting language
%J Proc. 4th Int. Workshop on Graph Grammars and their Application
   to Computer Science
%D 1990
%V LNCS 532
%I SpringerVerlag
%P 378-395
%K wShop, FP, functional programming, lambda calculus, term rewriting, DACTL,
   graph, UEA, East Anglia

%A M.J. Plasmeijer
%A M.C.J.D. van Eekelen
%A J.E.W. Smetsers
%T Parallel graph rewriting on loosely coupled machine architectures
%P 354-371
%J Proc. 2nd Int. Workshop on Conditional and Typed Rewriting Systems
%W Montreal
%D 1990
%K wShop, FP, functional programming, lambda calculus, term rewriting, graphs,
   parallel, concurrent

%A J. R. Kennaway
%T Graph rewriting in some categories of partial morphisms
%J Proc. 4th Int. Workshop on Graph Grammars and their Application
   to Computer Science
%D 1990
%S LNCS
%V 532
%I SpringerVerlag
%P 490-504
%K wShop, graphs, category, morphism, FP, functional programming, grammar,
   lambda calculus, term rewriting, rewrite, UEA, East Anglia

%A J. R. Kennaway
%T The specificity rule for lazy pattern-matching in ambiguous term rewrite
   systems.
%J Proc. 3rd European Symp. on Programming
%V LNCS 432
%I SpringerVerlag
%P 256-270
%D 1990
%K FP, functional programming, lambda calculus, term rewriting, lazy,
   pattern matching, UEA, East Anglia

%A J. R. Kennaway
%T Implementing term rewrite languages in Dactl
%K FP, functional programming, lambda calculus, term rewritinga, DACTL,
   UEA, East Anglia
%J Th. Comp. Sci.
%V 72
%N 2-3
%P 225-250
%D 1990
%O Revised and expanded version of the paper of the same name in CAAPU88.

%A J. R. Kennaway
%A J. W. Klop
%A M. R. Sleep
%A F. J. de Vries
%T Transfinite reductions in orthogonal term rewriting systems (ext' abs')
%J Proc. 4th Int. Conf. on Rewriting Techniques & Applications
%V LNCS 488
%I SpringerVerlag
%P 1-12
%D 1991
%K conf, FP, functional programming, lambda calculus, term rewriting,
   reduction, UEA, East Anglia

%A C. L. Hankin
%T Static Analysis of Term Graph Rewriting Systems
%K FP, functional programming, lambda calculus, term rewriting,
   PARLE, PARLE91, graph
%J Proc. PARLE'91 vol 2
%V LNCS 506
%I SpringerVerlag
%P 367-384
%D 1991

%A S. Smetsers
%A E. Nocker
%A J. van Groningen
%A M.J. Plasmeijer
%T Generating efficient code for lazy functional languages
%J Proc. Conf. on Functional Languages and Computer Architecture
%P 592-617
%V LNCS 523
%I SpringerVerlag
%D 1991
%K FP, functional programming, lambda calculus, term rewriting,
   code generation, compilation, lazy, FLCA

%A P. Wadler
%T The essence of functional programming
%J 19th POPL
%W Santa Fe
%I ACM
%M JAN
%P 1-14
%D 1992
%K conf, POPL, POPL19, FP, functional programming, monad, monads, exception,
   state, continuations, type, types, c1992, c199x, c19xx

%A S. Peyton Jones
%A P. Wadler
%T Imperative functional programming
%J 20th POPL
%I ACM
%P ??-??
%M JAN
%D 1993
%K POPL, POPL20, POPL93, conf, c1993, c199x, c19xx, FP, monad, monads, state,
   side effect, array, destructive, update, assign, assignment, variable,
   change, continuation, type types

%A P. Wadler
%T Fixing some space leaks with a garbage collector
%J SPE
%V 17
%N 9
%P 595-608
%M SEP
%D 1987
%K jrnl, SPE, lazy functional programming, FP, heap, space, leak, leaks,
   memory, GC, garbage collector

%A Ian Holyer
%T Functional Programming with Miranda
%D 1992 ?
%I Pitman UK
%K text, book, FP, Miranda, functional programming language, applicative,
   lambda calculus, lazy, call by need
%X uk us isbn:0-273-03453-7.    via enews.

%A C. K. Gomard
%T A self-applicable partial evaluator for the lambda calculus:
   correctness and pragmatics
%J TOPLAS
%V 14
%N 2
%M APR
%D 1992
%P 147-172
%K FP, functional, applicative, programming, lambda calculus,
   self application, partial evaluation, compiler generator CC, mix
%X 39 refs
   from University of Copenhagen

%A P. J. Koopman
%A P. Lee
%A D. P. Siewiorek
%T Cache behaviour of combinator graph reduction
%J TOPLAS
%V 14
%N 2
%M APR
%D 1992
%P 265-297
%K FP, functional programming, implementation, combinator,
   graph reduction, SKI, performance, cache, TIGRE
%X from CMU, 39 refs
   simulated abstract machine TIGRE

%A J. Darlington
%A Yi-ke Guo
%A H. Pull
%T A new perspective on integrating functional and logic languages
%I Dept. Computing, Imperial College, London.
%M FEB
%D 1992
%K functional, logic, declarative programming , FP, LP, constraint, DCP,
   LFP, FLP

%A A. Davie
%T An Introduction to Functional Programming Systems Using Haskell
%I CUP
%D 1992
%K FP, text, book, CUP, c1992, c199x, c19xx, functional programming language,
   Haskell, lazy, call by need, lambda calculus, parallel, eager, evaluation,
   L3Ref, decidable, type checking, system, types, quote, black hole, quotable
%X hb, uk us isbn:0521258308; uk us isbn13:978-0521258302; stg42.50.
   pb, uk us isbn:0521277248; uk us isbn13:978-0521277242; stg14.95.
      Ch 4. Types: "It is becoming clear ... that type sytems can be a trap for
      the unwary, a black hole into which programming language designers can
      fall if they are not careful to stay above the event horizon. The real
      trouble is that a too powerful type system is not amenable to type
      checking, far less inference in the sense that it may not be decidable
      whether an object has a given type or not. ..."

%T Functional Programming, Glasgow 1990
%E S. L. Peyton Jones
%E G. Hutton
%E C. K. Hobt
%S Workshops in Computing
%I SpringerVerlag
%M AUG
%D 1990
%K wShop, functional programming, lazy, FP, workshop, book
%X isbn:0387196676.  in Hargrave lib..

%A L. C. Paulson
%T ML for the Working Programmer
%I CUP
%D 1991
%K text, book, CUP, c1991, c199x, c19xx, FP, standard ML, SML, functional,
   applicative language, programming
%X 2nd ed c1996, pb, uk us isbn:052156543X; uk us isbn13:978-0521565431.
   From: Larry Paulson   email: lcpcl.cam.ac.uk   [6/'95]
   <A HREF="ftp://ftp.cl.cam.ac.uk/ml/working.tar.gz">ftp.../working.tar.gz</A>
   (Also see [<A HREF="http://www.allisons.org/ll/FP/SML/">on SML</A>].)

%A Graham Hutton
%T Parsing using combinators
%B Functional Programming, Glasgow
%E Davis
%E Hughes
%I SpringerVerlag
%D 1989
%P ???-???
%K FP, functional programming, parse, parser, parsing, combinator
   c1989, c198x, c19xx
%X via enews

%A S. L. Peyton Jones
%T Implementing lazy functional languages on stock hardware: the
   Spineless Tagless G-machine
%J JFP
%V 2
%N 2
%P 127-202
%M APR
%D 1992
%K jrnl, JFP, FP, c1992, c199x, c19xx, language, Gmachine
%X "The Spineless Tagless G-machine is an abstract machine designed to support
   non-strict higher-order F. languages. [...] three parts.  Firstly, we give a
   general discussion of the design issues involved in implementing non-strict
   F.languages. Next, we present the STG language, an austere but recognizably-
   -functional language, which as well as a denotational meaning has a well-
   -defined operational semantics. The STG language is the 'abstract machine
   code' for the Spineless Tagless G-machine. Lastly, we discuss the mapping of
   the STG language onto stock hardware. The success of an abstract machine
   model depends largely on how efficient this mapping can be made, though this
   topic is often relegated to a short section. Instead, we give a detailed
   discussion of the design issues and the choices we have made. Our principal
   target is the C language, treating the C compiler as a portable assembler."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796800000319">doi:10.1017/S0956796800000319</A>]['13].
   [Also search for: FP Gmachine].

%A R. E. Jones
%T Tail recursion without space leaks
%J JFP
%V 2
%N 1
%P 73-79
%M JAN
%D 1992
%O TR 72, U. Kent, .uk, '90
%K jrnl, c1992, c199x, c19xx, JFP, FP, functional programming, FP, lazy,
   call by need, space, garbage, memory leak, JFP, management, collection,
   G-machine, Gmachine, tail recursion
%X "The G-machine (Johnsson, 1987; Peyton Jones, 1987) is a compiled graph
   redn m/c for lazy F.languages. ... compiler contains many optimisations to
   improve performance. One set of such optimisations is designed to improve the
   performance of tail rec. fns. Unfortunately [it] is subject to a space leak -
   objects are unnecessarily preserved by the garbage collector. This paper
   analyses why a particular form of space leak occurs in the G-m., & presents
   some ideas for fixing this problem. ..."
   -- pdf@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.45.5083">c'teseer</A>]['12],
   or [<A HREF="http://dx.doi.org/10.1017/S0956796800000277">doi:10.1017/S0956796800000277</A>]['12] JFP.
   [Also search for: tail recursion].

%A J. H. You
%T Outer narrowing for equational theories based on constructors
%J Proc. ICALP '88
%I SpringerVerlag
%S LNCS
%V 317
%P 727-741
%D 1988
%K FP, LP, LFP, FLP, ICALP, ICALP88, functional programming, logic variable,
   unify, unification

%A G. S. Frandsen
%A C. Sturtivant
%T What is an efficient implementation of the lambda-calculus?
%B Functional Programming Languages and Computer Architecture
%E J. Hughes
%D 1991
%I SpringerVerlag
%S LNCS
%V 523
%P 289-312
%K FP, functional programming, time complexity, efficiency, reduction,
   lambda calculus, FPLCA, FPCA, FPLCA91, FPCA91, c1991, c199x, c19xx
%X ~From: gsfrandsen OF daimi.aau.dk (Gudmund Skovbjerg Frandsen)  '92.

%A B. Bjerner
%T Time Complexity of Programs in Type Theory (Thesis)
%I Dept. of Computer Science, University of Goteborg, Sweden.
%D 1989
%K FP, functional programming, type, types, theory, efficiency, thesis
%X via enews '92
   ~From: ajt1@ukc.ac.uk (Alastair Telford)
   There is one source that you might be interested in. This  is  on
   (Martin-Lof's) type theory and is a thesis.

%A H. Schwichtenberg
%T An upper bound for reduction sequences in typed lambda-calculus
%J Arch. Math. Logic
%V 30
%D 1991
%P 405-408
%K FP, functional programming, efficiency, complexity, time, lambda calculus
   reduction
%X via enews '92

%A M. Hanus
%T Efficient Implementation of Narrowing and Rewriting
%B Proc. Int. Workshop on Processing Declarative Knowledge.
%D 1991
%I SpringerVerlag
%S LNAI
%V 567,
%P 344-365
%K wShop, ALF, functional logic programming, FP, LP, LFP, FLP
%X via enews Dec 92
   [<A HREF="http://www.informatik.uni-kiel.de/~mh/systems/ALF.html">www</A>]['07].

%A M. Hanus
%T Improving Control of Logic Programs by Using Functional Logic Languages
%B Proc. of the 4th Int. Symp. on Programming Language
   Implementation and Logic Programming.
%D 1992
%P 1-23
%I SpringerVerlag
%S LNCS
%V 631
%K ALF, functional logic programming, implementation, FP, LP, LFP, FLP
%X via enews Dec 92
   The ALF system is available for free and is implemented in
   C, Prolog and ALF. It is not a toy language since we have
   implemented larger problems with ALF (there exists approximately
   1 MByte source code for ALF). Contact me if you are interested in
   getting more information.
      Michael Hanus
      MPI Informatik            eMail: michael OF mpi-sb.mpg.de
      Im Stadtwald              Phone: +49 681 302 5436
      W-6600 Saarbruecken       Fax:   +49 681 302 5401
      Germany
   [<A HREF="http://www.informatik.uni-kiel.de/~mh/systems/ALF.html">www</A>]['07].

%A G. Cheng
%A Z. Yun-Zheng
%T A "functional + logic" programming language in interpretation-compilation
   implementation
%J Lisp & Symbolic Computing
%V 5
%N 3
%P 133-156
%M SEP
%D 1992
%K LSC, JLSC, functional logic programming language implementation, FP,
   LP, LFP, FLP, prolog, lisp, all, set, setof, any, the, solution, query,
   solve, constraint, Yun Zheng
%X Lisp + Prolog
   has (ALL X, Y    p(X,Y) & q( ... ))   all solutions
       (ANY k X, Y  p(...)...)           first k solutions
       (THE X, Y    p(...)...)           one solution
   has assert.

%A J. A. Goguen
%T Higher-order functions considered unnecessary for higher-order programming
%B Research Topics in Functional Programming
%P ???-???
%I ???
%D 1988
%K functional programming, FP, OBJ, OBJ3, KCL, logic, high order function
%X via enews
   "If you have any questions about obtaining OBJ3, please call Judith
   Burgess at (415) 859-5924 or contact us by email at
   obj3dist OF csl.sri.com.  For technical questions, please contact Mr.
   Timothy Winkler at (415) 859-3192 or by email at obj3sys OF csl.sri.com.
   OBJ runs on top of AKCL.  You need licenses for both OBJ and KCL in
   order to use it, but both of those licenses are free.  You can order a
   full tape from SRI for US$150.

%A F. Kamareddine
%T A system at the cross-roads of functional and logic programming
%J Science of Computer Programming.
%V 19
%P 239-279
%D 1992
%K jrnl, functional logic programming, FP, LP, LFP, FLP, SCP, type theory

%A C. Myers
%A C. Clack
%A E. Poon
%T Programming with Standard ML
%I PrenticeHall
%D 1993
%K text, book, c1993, c199x, c19xx, standard ML, SML,
   functional, applicative programming language, FP, Meyers
%X pb, uk us isbn:0137220758; uk us isbn13:978-0137220755. (301pp)
      Organization: University of Westminster
      Chapter 1:  Operators, Values and Types
      Chapter 2:  Functions
      Chapter 3:  Lists
      Chapter 4:  Curried and Higher Order Functions
      Chapter 5:  Managing Environments
      Chapter 6:  User-defined Types
      Chapter 7:  Modules
      Appendix A: File Handling       Appendix B: Additional Features
      Appendix C: Procedural Features Appendix D: The Initial SML Environment
      Appendix E: SML Interfaces      Appendix F: Delaying Evaluation
      From: colin at westminster.ac.uk (Colin Myers)
   (Also see [<A HREF="http://www.allisons.org/ll/FP/SML/">on SML</A>].)

%A P. G. Harrison
%T A higher-order approach to parallel algorithms
%J COMPJ
%V 35
%N 6
%P 555-566
%D 1992
%O TR DoC 92/11, Dept. of Computing, Imperial College May '92
%K FP, functional programming, high order, data parallel algorithm, MIMD,
   jrnl, COMPJ, transformation, divide and conquer
%X identify small set of high order fns that can be implemented efficiently
   on the parallel machine and which can be used to express parallel
   algorithms.
   Such H.O. fns allow generic programs to be written in which much
   parallelism may be explicit.

%A F. E. J. Kruseman Aretz
%T On a recursive ascent parser
%J IPL
%D 1988
%V 29
%P 201-206
%K jrnl, IPL, recursive ascent, parse, parser, parsing, functional programming,
   FP, c1988, c198x, c19xx

%A R. Leermakers
%A L. Augusteijn
%A F. E. J. Kruseman Aretz
%T A functional LR-parser
%J Theor. Comp. Sci.
%D 1992
%V 104
%P 313-323
%K jrnl, TCS, recursive ascent, parse, parser, parsing, FP

%A R. Leermakers
%T Recursive ascent parsing: from Earley to Marcus
%J Theor. Comp. Sci.
%V 104
%D 1992
%P 299-312
%K jrnl, TCS, FP, recursive ascent, parse, parser, parsing

%A R. Leermakers
%T The Functional Treatment of Parsing
%I Kluwer Academic Publishers
%D 1993
%K book, text, parse, parser, parsing, functional programming, recursive
   ascent, descent, FP

%A K. R. Traub
%T Sequential Implementation of Lenient Programming Languages
%R MIT/LCS/TR-417
%I Laboratory for Computer Science, MIT
%D 1988
%K PhD thesis, Id, lazy, non-strict, nonstrict, lenient, speculative,
   functional, applicative programming, FP, TR 417 TR417, parallel, concurrent,
   c1988, c198x, c19xx

%A R. S. Nikhil
%A Arvind
%T Id: A language with implicit parallelism,
   Id solutions to the four "Salishan problems"
%R Computation Structures Group Memo 305
%I Laboratory for Computer Science, MIT
%M FEB
%D 1990
%K Id, lazy, non-strict, nonstrict, lenient, speculative, functional,
   applicative, programming, FP, CSG, TR 305, parallel, concurrent,
   statistics, performance, time
%X sec'n 2 Hamming's problem
   sec'n 3 The paraffins problem
   sec'n 4 A doctor's office
   sec'n 5 Skyline matrix solver
   given f(arg) then f and arg are evaluated in parallel
   if f needs arg' then it waits until arg is ready
   but the 2 branches if an `if' (& case ...) are not evaluated speculatively
   claim this generally controls the waste possible in spec' eval'.
   There are special annotations for where laziness is needed.

%A Werner Hans
%A Rita Loogen
%A Stefan Winkler
%T On the Interaction of Lazy Evaluation and Backtracking
%D 1992
%P 355-369
%J Programming Lanugage Implementation and Logic Programming
%E M. Bruynooghe
%E M. Wirsing
%I SpringerVerlag
%S LNCS
%V 631
%W Leuven, Belgium
%K logic functional programming, LP, FP, lazy
%X via enews

%A J. J. Moreno-Navarro
%A H. Kuchen
%A R. Loogen
%A M. Rodriguez-Artalejo
%T Lazy Narrowing in a Graph Machine
%J Proc. of the 2nd Int. Conf. on Algebraic and Logic Programming
%W Nancy, France
%I SpringerVerlag
%S LNCS
%V 463
%D 1990
%P 298-317
%K logic functional programming, LP, FP, lazy, ICALP-2, ICALP-90,
   ICALP, Navarro
%X via enews

%A J. Gibbons
%T Upwards and downwards accumulations on trees
%J Mathematics of Program Construction
%E R. S. Bird
%A C. C. Morgan
%E J. C. P. Woodcock
%I SpringerVerlag
%S LNCS
%V 669
%D 1993
%P 122-138
%O Proc. of the Massey Functional Programming Workshop,
   E. Ireland and N. Perry (eds), '92
%K wShop, functional programming, FP, tree, accumulation
%X "An accumulation is a higher-order operation over structured objects of some
   type; it leaves the shape of an object unchanged, but replaces each element
   of that object with some accumulated information about the other elements.
   Upwards and downwards accumulations on trees are two instances of this
   scheme; they replace each element of a tree with some function -- in fact,
   some homomorphism -- of that element's descendants and of its ancestors,
   respectively. These two operations can be thought of as passing information
   up and down the tree."           (from the H@skell m@il list 2/'04,
   -- [<A HREF="http://web.comlab.ox.ac.uk/oucl/work/jeremy.gibbons/publications/index.html#accumulations">.ox.ac.uk</A>][2/'04].)

%A J. A. Jimenez-Martin
%A J. Marino
%A J. J. Moreno-Navarro
%T Some Techniques for the Efficient Compilation of Lazy Narrowing into Prolog
%J Proc. of LOPSTR'92
%W Manchester, UK
%I SpringerVerlag
%S Workshops in computer science
%V ???
%D 1993
%K wShop, logic functional programming, LP, FP, lazy, LOPSTR, LOPSTR-92
%X via enews

%A J. J. Moreno-Navarro
%A H. Kuchen
%A J. Marino
%A W. Hans
%A S. Winkler
%T Efficient Lazy Narrowing using Demandedness  Information
%J Proc. of the fifth Int. Symp. on Programming Language
   Implementation and Logic Programming
%W Tallinn, Estonia
%I SpringerVerlag
%S LNCS
%V 714
%D 1993
%P 167-183
%K logic functional programming, LP, FP, lazy, PLILP, PLILP-5, PLILP-93, Navarro
%X via enews

%A Julio Marino Carballo
%A Angel Herranz Nieva
%A J. J. Moreno Navarro
%T Demandedness Analysis with Dependence Information for Functional Logic
   Languages
%J Int. Logic Programming Symp.
%D 1993 to appear
%W Vancouver, Canada
%S Workshop on Global Compilation
%P ???-???
%K logic functional programming, LP, FP, lazy, ILP, ILP-93
%X via enews

%A Arvind
%A R. S. Nikhil
%A K. K. Pingali
%T I-structures: data structures for parallel computing
%J TOPLAS
%D 1989
%M OCT
%V 11
%N 4
%P 598-632
%K Id, I structure, I-structure, Istructure,
   functional, applicative programming, FP
%X via enews

%A R. Jagadeesan
%A P. Panangaden
%A K. K. Pingali
%T A fully abstract semantics for a functional language with logic variables
%J Proc. Fourth IEEE Symp. on Logic in Computer Science
%W Asilomar, CA
%P 294-303
%D 1989
%M JUN
%K Id, Cid, I structure, I-structure, Istructure,
   logic, functional, applicative, programming FP, LFP, FLP, LP, variable,
   4th, LCS-4, LCS4, LCS89, LCS-89
%X ... integrate logic variables into functional languages.
   ... present an operational semantics for the language and an
   abstract semantics that expresses meanings as closure operators
   on a Scott domain. We also show that the DS is fully abstract wrt the OS.
   12 refs;  isbn:0-8186-1954-6;  Hargrave H 005.13105 S989P.

%A J. D. Ullman
%T Elements of ML Programming
%I PrenticeHall
%D 1993
%K text, book, c1993, c199x, c19xx, functional, programming, FP, Standard, ML,
   SML, SML/NJ
%X from:    ullman OF Theory.Stanford.EDU   9/93
   Book's focus is SML/NJ, and it assumes that the student
   has experience programming in a conventional language like C.
   Here is the table of contents. ---jdu
   [see 2nd ed c1997, pb, uk us isbn:0137903871; uk us isbn13:978-0137903870.]
   (Also see [<A HREF="http://www.allisons.org/ll/FP/SML/">on SML</A>].)

%A J. D. Ullman
%T Elements of ML Programming: ML97 Edition
%I PrenticeHall
%P 383
%M DEC
%D 1997
%K book, text, functional, applicative, programming, FP
   Standard ML, 97, SML, NJ, SML97, ML97, zz0802
%X 2nd ed 1997; pb; uk us isbn:0137903871; uk us isbn13:978-0137903870.
   (Also see [<A HREF="http://www.allisons.org/ll/FP/SML/">on SML</A>].)

%A K. E. Iverson
%T Programming in J
%I Iverson Software Inc., Toronto.
%D 1992
%K APL, J, jj, applicative, operator, FP, programming language,
   c1992, c199x, c19xx
%X (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/J/">on J</A>].)

%A P. G. Harrison
%A H. Koshnevisan
%T On the synthesis of function inverses
%J Acta Informatica
%D 1992
%V 29
%P 211-239
%K jrnl, Acta Inf, functional, applicative program, FP, function, inverse,
   c1992, c199x, c19xx
%X via enews

%A R. Stansifer
%T ML Primer
%I PrenticeHall
%P 160
%D 1992
%K text, book, standard ML, SML, functional, applicative programming language,
   FP
%X us$21; uk us isbn:0-13-561721-9.
   (Also see [<A HREF="http://www.allisons.org/ll/FP/SML/">on SML</A>].)

%A G. H. Roberts
%T Another note on recursive ascent
%J IPL
%D 1989
%V 32
%N 5
%P 263-266
%K jrnl, IPL, functional, parse, parser, parsing, FP, LL, LR, LR(1)
%X via enews

%A R. Leermakers
%T A recursive ascent Earley parser
%J IPL
%V 41
%P 87-91
%D 1992
%K jrnl, IPL, parse, parser, parsing, FP, functional, LL, LR, LR(1)
%X via enews

%A L. C. Paulson
%T Logic and Computation: Interactive Proof with Cambridge LCF
%I ???
%D ???
%K ML, SML, FP, LCF, logic for computable functions, theorem prover
%X via enews '93

%E S. Abramsky
%E D. M. Gabbay
%E T. S. E. Maibaum
%T Handbook of Logic in Computer Science
%I Oxford: Clarendon Press
%D 1992
%K book, text, c1992, c199x, c19xx, theorem prover, assistant, proof, proving,
   maths, ML, SML, FP
%X via enews
   [Also search for: theorem proving].

%A P. H. Hartel
%A K. G. Langendoen
%T Benchmarking Implementations of Lazy Functional Languages
%J FPCA '93
%P 341-349
%I ACM
%D 1993
%K bench mark, functional programming, FP, lazy, call by need, FPCA FPCA93,
   conf, benchmark, language
%X via guy tremblay
   Mentions a number of programs used to benchmark various  implementations
   of  lazy  functional  languages.   (Note  that the source code for these
   programs can be obtained through ftp: they  are  available  for  various
   languages: Clearn, LML, Haskell, Intermediate).

%A J. D. Hill
%T The AIM is Laziness in a Data-Parallel Language
%B Functional Programming
%I ???
%P VI-1--14
%D 1993
%K functional programming, FP, lazy, call by need, data parallel
%X via guy tremblay
   After   discussing   the  conflict  between  laziness  and  parallelism
   discusses the POD paradigm, including desugaring and compilation and the
   derivation  of  a  parallel scan that can be applied to infinite lists."
   (Quoted from A.D. Ben-Dyke).

%A P. Wadler
%T Monads and composable continuations
%J J. Lisp & Symb. Comp.
%V 7
%N 1
%P 39-56
%M JAN
%D 1994
%K JLSC, LSC, functional programming, FP, monad, continuation, c1994, c199x,
   c19xx, jrnl

%A Y. Kashiwagi
%A D. S. Wise
%T Graph algorithms in a lazy functional programming language
%J Proc. of the 4th Int. Symp. on Lucid and Intensional Programming
%M APR
%D 1991
%P ??-??
%K FP, functional programming, lazy, graph, graphs, algorithm, David Wise
%X via enews

%A S. L. Peyton Jones
%A D. Lester
%T A modular fully-lazy lambda lifter in Haskell
%J SPE
%V 21
%N 5
%M MAY
%D 1991
%P ??-??
%K jrnl, SPE, functional programming, FP, fully, lazy, lambda, lift, lifting
%X from Mark Leone  (mleone OF cs.cmu.edu)

%A F. Nielson
%A H. Nielson
%T 2-level lambda-lifting
%J ESOP 1988
%I SpringerVerlag
%S LNCS
%V 300
%P ??-??
%D 1988
%K functional programming, FP, lambda, lift, lifting, ESOP, ESOP88, 2 two level
%X from Mark Leone  (mleone OF cs.cmu.edu)

%A A. Appel
%A T. Jim
%T Continuation-passing, closure-passing style
%J POPL 1989
%P ??-??
%D 1989
%K functional programming, FP, lambda, lift, lifting, POPL, POPL89,
   continuation, pass, passing, closure
%X from Mark Leone  (mleone OF cs.cmu.edu)
   A closely related technique is closure-conversion.

%A M. Wand
%A P. Steckler
%T Selective and Lightweight Closure Conversion
%J POPL 1994
%P ??-??
%D 1994
%K functional programming, FP, lambda, lift, lifting, POPL, POPL94, closure
%X from Mark Leone  (mleone OF cs.cmu.edu)
   A closely related technique is closure-conversion

%A P. Sestoft
%T Replacing function parameters by global variables
%J FPCA 1989
%P ??-??
%D 1989
%K functional programming, FP, lambda, lift, lifting, FPCA, FPCA89
%X from Mark Leone  (mleone OF cs.cmu.edu)
   inverse problem to lambda lifting ???

%A K. Hammond
%T The spineless tagless G-machine - NOT!
%I ?
%D 1993
%K TR, c1993, c199x, c19xx, FP, functional programming, implementation, RISC,
   lazy, graph reduction, Gmachine, G-machine, tag, tags, tagged, STG
%X "To tag or not to tag: that is the question: Whether 'tis faster in the cache
   to suffer The delays of tagless nodes, Or break the pipe no more And make a
   branch that hits the cache. To load, to jump; To jump: perchance to stall;
   Ay, there's the run.
   ... The paper on the HDG parallel machine [KLB91] contains an intruiging
   paragraph. Comparing Peyton Jones' and Salkild's [STG] [PeSa89] with the
   < nu, G >- Machine [AuJo89], Kingdon, Lester and Burn observe that
   In theory Augustsson & Johnsson are right. ... In practice, on trad. h/ware
   Peyton Jones & S. are correct.  [Now], RISC chips have become commonplace,
   and features which used to be confined to supercomputers or large mainframes,
   such as pipelined execution or multiple independent instruction units, ..."
   -- @[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.54.8854">c'teseer</A>]['12].
   (Inc. a review of tagging.)
   [Also search for: FP Gmachine].

%A R. Plasmeijer
%A M. van Eekelen
%T Functional Programming and Parallel Graph Rewriting
%I AddisonWesley
%D 1993
%K text, book, c1993, c199x, c19xx, functional programming, FP, G-machine,
   Gmachine, ABC machine, ABC-machine, implementation, compile compiler,
   rewrite, vanEekelen
%X It describes an abstract machine called the ABC-machine which has similar
   goals to the G-machine.
   via: Dr David Wakeling   david OF dcs.exeter.ac.uk   '94.

%A G. Michaelson
%T An Introduction to Functional Programming through Lambda Calculus
%I AddisonWesley
%P 335
%D 1989
%K text, book, c1989, c198x, c19xx, intro, FP, lazy, call by need,
   normal order, form
%X uk us isbn:0201178125; uk us isbn13:978-0201178128.
   (Also see [<A HREF="http://www.allisons.org/ll/FP/Lambda/">lambda</A>].)

%A J. Sargeant
%T Uniting functional and object-oriented programming
%J Int. Symp. on Object Technologies for Adv. Software
%W Kanazawa, Japan
%M NOV
%D 1993
%I SpringerVerlag
%S LNCS
%V 742
%P 1-26
%K FP, object oriented, OO, OOP, OOPS LNCS742

%A A. Poulovasslis
%A C. Small
%T A Functional Programming Approach to Deductive Databases
%J Proc. VLDB'91
%P ?-?
%M SEP
%D 1991
%K conf, VLDB, functional programming, FP, database, data base, DB, FDB, DBMS
%X I would like to point out that PFL (Persistent Functional Language) is
   already in use as the name of a functional database programming
   language developed by Alex Poulovasslis (of King's College London) and
   Carol Small (of Birkbeck College London).  Details of PFL can be found
   Alex (alex OF dcs.kcl.ac.uk), Carol (carol OF dcs.bbk.ac.uk), or myself.
   via: simonc OF dcs.kcl.ac.uk   (8/'94)

%A A. Poulovasslis
%A C. Small
%T A Domain-Theoretic Approach to Integrating Functional and Logic Database
   Languages
%J Proc. VLDB'93
%P ?-?
%D 1993
%K conf, VLDB, functional programming, FP, database, data base, DB, FDB
%X I would like to point out that PFL (Persistent Functional Language) is
   already in use as the name of a functional database programming
   language developed by Alex Poulovasslis (of King's College London) and
   Carol Small (of Birkbeck College London).  Details of PFL can be found
   Alex (alex OF dcs.kcl.ac.uk), Carol (carol OF dcs.bbk.ac.uk), or myself.
   via: simonc OF dcs.kcl.ac.uk   (8/'94)

%A A. D. Martinez
%A R. Wachenchauzer
%A R. D.  Lins
%T Cyclic reference counting with local mark-scan
%J IPL
%V 34
%M FEB
%D 1990
%P ?-?
%K jrnl, IPL, garbage collection, GC, count, functional programming, FP
%X <!-- via email: mjn OF netcom.com (The Sixth Replicant  10/'94) --> .

%A R. D. Lins
%T Cyclic reference counting with lazy mark-scan
%J IPL
%V 44
%M DEC
%D 1992
%P ?-?
%K jrnl, IPL, garbage collection, GC, count, functional programming, FP
%X <!-- via email: mjn OF netcom.com (10/'94) --> .

%A P. Hudak
%A M. P. Jones
%T Haskell vs. Ada vs. C++ vs. Awk vs. ... An experiment in
   software prototyping productivity
%I Dept of Comp. Sci., Yale Uni.
%M JUL
%D 1994
%K TR, rapid, fast, prototype, cplusplus, cc, Naval Surface Warfare Center,
   NSWC, geometric region server, software development, specification,
   functional programming, FP
%X "We describe the results of an experiment in which several conventional
   programming languages, together with the functional language Haskell, were
   used to prototype a Naval Surface Warfare Center (NSWC) requirement for a
   Geometric Region Server. The resulting programs and development metrics were
   reviewed by a committee chosen by the Navy. The results indicate that the
   Haskell prototype took significantly less time to develop and was
   considerably more concise and easier to understand than the corresponding
   prototypes written in several different imperative languages, including Ada
   and C++."
   -- [<A HREF="http://www.cs.chalmers.se/ComputingScience/Research/Functional/Fudgets/haskell-vs-ada-abstract.html">abs and .ps</A>]['04].

%A A. D. Gordon
%T Functional Programming and Input/Output
%S Distinguished Dissertations in Computer Science
%I CUP
%M SEP
%D 1994
%O PhD thesis, Camb. Uni., 1993 (and TR #285)
%K c1994, c199x, c19xx, FP, input, output, PhD thesis, book, text, CUP, CSci,CS,
   monad, monads, monadic IO, Landin stream, continuation passing, language,
   contextual equivalence, applicative bisimulation
%X stg25, uk us isbn:0521471036; hb, CUP,
   -- [<A HREF="http://research.microsoft.com/~adg/Publications/fpio.html">Summary</A>]['05].
   [<A HREF="http://www.cl.cam.ac.uk/users/adg/fpio.html">Summary</A>][11/'94].
   1. Introduction                       2. A Calculus of Recursive Types
   3. A Metalanguage for Semantics       4. Operational Precongruence
   5. Theory of the Metalanguage         6. An Operational Theory of FP
   7. Four Mechanisms for Teletype I/O   8. Monadic I/O
   9. Summary                            email: adg at cl cam ac uk (11/'94)
   "... We study simplified forms of four widely-implemented I/O mechanisms:
   (i) side-effecting,  (ii) Landin-stream,  (iii) synchronised-stream &
   (iv) continuation-passing I/O. ..."
   -- [<A HREF="http://www.cl.cam.ac.uk/users/adg/">home page (11/'94)</A>],
   pdf@[<A HREF="http://research.microsoft.com/en-us/um/people/adg/publications/fpio.pdf">ms</A>]['97].
   (And based on Ch.7, 'An operational semantics for I/O in a lazy functional
   language', FPCA, pp.136-145, 1993, pdf@[<A HREF="http://dx.doi.org/10.1145/165180.165199">doi:10.1145/165180.165199</A>]['13].)

%A C. Reade
%T Elements of Functional Programming
%I AddisonWesley
%D 1989
%K book, text, c1989, c198x, c19xx, FP, CSci, CS
%X hb, uk us isbn:0201129159; uk us isbn13:978-0201129151.

%A G. Tremblay
%T Parallel Implementation of Lazy Functional Languages Using Abstract Demand
   Propagation
%I McGill University
%M NOV
%D 1994
%K PhD thesis, functional programming, FP, lazy, lenient, strict,
   nonstrict, non-strict, evaluation, parallel, Id
%X <A HREF="ftp://ftp-acaps.cs.mcgill.ca/incoming/tremblay/">FTP 2/'95</A>
   see Tremblay's thesis...
   <!-- email: tremblay OF bluebeard.cs.mcgill.ca   (2/'95) --> .

%A A. Asperti
%A C. Giovannetti
%A A. Naletto
%T The Bologna optimal higher-order machine
%R UBLCS-95-9
%I Lab. for Comp. Sci., U. of Bologna, Italy
%D 1995
%O JFP, 6(6), pp.763-810, Nov. 1996
%K FP, c1995, c199x, c19xx, zz0719, functional programming, language, BOHM,
   graph reduction, reduction, Lamping, Gonthier, Asperti, share, lambda,
   sharing, implementation
%X "... prototype implementation of the core of a functional language based
   on (a variant of) Lamping's optimal graph reduction technique
   (Lamping, 1990; Gonthier et al., 1992a; Asperti, 1994). ..."
   -- [<A HREF="https://doi.org/10.1017/S0956796800001994">doi:10.1017/S0956796800001994</A>]['19].
   Also see
   [<A HREF="http://pauillac.inria.fr/~levy/confer-2/ppr1/node80.html">inria</A>]['19].
   [Also search for: FP BOHM].

%A S. J. Sullivan
%A B. G. Zorn
%T Numerical analysis using nonprocedural paradigms
%J ACM Trans. on Math. Software
%V 21
%N 3
%P 267-298
%M SEP
%D 1995
%K jrnl, TOMS, c1995, c199x, c19xx, paradign, FP, functional programming,
   ML, SML, Haskell, interpolation, optimization, Gaussian elimination,
   sparse matrices
%X "... survey on the innovative features of a handful of languages that offer
   new features that can be valuable in [NA], & a survey of the pros & cons of
   [them] with regards to work in [NA]. Language features such as polymorphism,
   1st-class functions, & [OO-]programming offer improved writability,
   readability, reliability, & maintenance of computer software. ...discusses
   language features & uses, & includes a comparison of current implementations.
   ... introduction to nonprocedural language features for persons working in
   [N-]math. & as an exploration of some of the language requirements of
   [N-]math. for persons working in language development. ... C++, Fortran 77,
   Fortran 90, Haskell, Lisp/CLOS, Modula-3, Sather, & SML [wrt] a variety of
   [NA] tasks: interpolation, optimization, array access & update, iteration,
   recursion, random number gen., & Gaussian elimination on sparse matrices."
   pdf: [<A HREF="http://doi.acm.org/10.1145/210089.210093">doi.acm.org/10.1145/210089.210093</A>]['06].

%A P. Roe
%T A simple implementation of divide and conquer parallelism (expressed in
   Haskell)
%J Australian Comp. Sci. Communications
%P ?-?
%V 17
%N 1
%M FEB
%D 1995
%K conf, ACSC, functional programming, FP, parallel, c1995, c199x, c19xx, QUT
%X [<A HREF="http://sky.fit.qut.edu.au/~roe/papers/acsc18.ps.gz">acsc18.ps.gz OF fit.qut.edu.au</A>]['05].
   auth @ fit.qut.edu.au ['05].

%A E. Meijer
%A J. Jeuring
%T Merging monads and folds for functional programming
%J 1st Int. Spring School on Advanced Functional Programming Techniques
%W Baastad, Sweden
%M MAY
%D 1995
%K FP, monad, foldl
%X "[...] discuss the simultaneous use of generalised fold operators and monads
   to structure functional programs. Generalised fold operators structure
   programs after the decomposition of the value they consume. Monads structure
   programs after the computation of the value they produce. Our programs
   abstract both from the recursive processing of their input as well as from
   the side-effects in computing their output. ..."
   -- [<A HREF="http://www.cs.uu.nl/~johanj/publications/mmf.ps">~johanj .ps</A>][6/'04].

%A G. Tremblay
%A G. R. Gao
%T The impact of laziness on parallelism and the limits of strictness
%J High Performance Functional Computing
%P ?
%M APR
%D 1995
%K functional programming, FP, lazy, lenient, strict, nonstrict, non-strict,
   speculative, evaluation, strictness, analysis, parallel, Id, HPFC, conf
%X ...novel approach to strictness analysis (called abstract demand
   propagation).    ...little parallelism... can be identified...
   ...even when speculative evaluation is introduced...
   When a program's result is known to be finite, then strictness analysis can
   generate almost as much parallelism as can be obtained from a lenient
   implementation.  Thus strictness analysis is not sufficient and should be
   combined with some form of termination analysis and that there is little
   hope to extract much parallelism for programs that really require laziness.
   <A HREF="ftp://ftp-acaps.cs.mcgill.ca/incoming/tremblay/">FTP 2/'95</A>
   see the HPFC-paper...     47 refs
   <!-- email: tremblay OF bluebeard.cs.mcgill.ca   (2/'95) --> .

%T Applications of Functional Programming
%E C. Runciman
%E D. Wakeling
%I UCLpress
%D 1995
%K book, text, functional programming, FP, application, program, programs,
   FLARE project, c1995, c199x, c19xx, uniYork
%X isbn:1857283775; HB.  Ed's @ York U., UK

%A C. K. Gomard
%A N. D. Jones
%T A partial evaluator for the untyped lambda-calculus
%J JFP
%V 1
%N 1
%P 21-69
%M JAN
%D 1991
%K jrnl, JFP,functional programming, FP, JFP, jrnl, mix, c1991, c199x, c19xx
%X via (email: torbenm OF diku.dk) Torben AEgidius Mogensen (2/'95)

%A C. K. Holst
%A J. Hughes
%T A loop-detecting interpreter for lazy programs
%J Draft Proc., 4th Annual Glasgow Workshop on Func. Prog.
%W Skye, Scotland
%I Glasgow University
%P 199-209
%M ?
%D 1991
%K functional programming, FP, conf, wkshp, mix
%X via (email: torbenm OF diku.dk) Torben AEgidius Mogensen (2/'95)

%A W.-N. Chin
%T Fully lazy higher-order removal
%J Workshop on Partial Evaluation and Semantics-Based Program Manipulation
%E C. Consel
%P 38-47
%I Yale Uni.
%M JUN
%D 1992
%O YALEU/DCS/RR-909
%K PEPM, PEPM92, functional programming, FP, lazy, laziness, PE,
   conf, CSci, computing, programming languages
%X This paper presents a method for removing higher-order functions from
   programs. The method encourages laziness in the resulting code by ensuring
   that no unnecessary code duplications occur. Currying is removed and
   function arguments are wrapped in a scope around the body of the code.
   This is not always possible - some curried functions return inherently
   higher-order functions which can not be isolated.
   via <!-- email: thiemann OF informatik.uni-tuebingen.de --> Peter Thiemann  [4/'95]

%A J. L. Krivine
%T Lambda-Calculus, Types and Models
%I Ellis Horwood
%D 1993
%P 180
%K book, text, c1993, c199x, c19xx, functional programming, FP, type, model,
   CSci, L4Ref, zz0595
%X hb, uk us isbn:0130624071; uk us isbn13:978-0130624079.
   reviewed in Comp' Surveys p97 Feb '95.

%A K. E. Schauser
%A S. C. Goldstein
%T How much non-strictness do lenient programs require?
%J FPCA 95
%P ?-?
%M JUN
%D 1995
%K conf, FPCA, FPCA8, FPCA95, FP, c1995, c199x, c19xx, lazy, lenient, strict,
   non-strict, strictness, zz0995, functional, conditional, data structure,
   programming, Id90, evaluation, program, programs, parallel
%X "... Lenient evaluation combines non-strict semantics with eager
   evaluation [Tra91].  ... non-strictness incurs a large overhead as it
   requires dynamic scheduling and synchronization [for parallelism]. ...
   This paper studies a large set of lenient programs and quantifies the degree
   of non-strictness they require. ... identify several forms of [n.s.] inc'
   functional, conditional, and data structure [n.s.].  ...  This paper refutes
   the myth that lenient programs require extensive non-strictness."
   -- [<A HREF="http://www-2.cs.cmu.edu/~seth/papers/fpca95.ps">fpca95.ps@cs.cmu.edu</A>][10/'04].
   s2.2. "... Lenient eval'n starts the eval'n of the fn body f in parallel
   with the eval'n of all the arg's e1 to en, evaluating each only as far as
   the data dependencies permit; ..."

%A J. F. Th. Kamperman
%A H. R. Walters
%T Lazy rewriting and eager machinery
%B Rewriting Techniques and Applications
%E J. Hsiang
%I SpringerVerlag
%S LNCS
%V 914
%P 147-162
%D 1995
%K functional programming, FP, lazy, eager, evaluation, zz0995
%X - Pum Walters   pum OF cwi.nl  [8/'95]

%A M. Beemster
%T Strictness optimization for graph reduction machines (why Id might not be
   strict)
%J TOPLAS
%V 16
%N 5
%M SEP
%D 1994
%P 1449-1466
%K TOPLAS, jrnl, Id, functional programming, FP, strict, strictness analysis,
   jrnl, lenient evaluation, non-strict, optimise, optimize, zz1195
%X review: Comp Rev, Sep 95 p481.

%A V. Poirriez
%T MLOG: a strongly typed confluent functional language with logical variables
%J Theor. Comput. Sci.
%V 122
%P 201-223
%M JAN
%D 1994
%K TCS, jrnl, MLOG, functional programming, FP, FLP, logic variable,
   suspend, suspension, zz0296
%X extends ML, implemented in CAML light.
   ... suspends evaluation of free logic variables ...
   instantiated, all suspended evaluations that can continue
   the evaluation are activated. Suspensions are first class objects ....
   Reviewed Comp Rev p582 Nov '95.

%A P. V. Murthy
%A V. Rajaraman
%T Implementation of speculative parallelism in functional languages
%J IEEE Trans. Parallel Distrib. Syst.
%V 5
%N 11
%P 1197-1205
%M NOV
%D 1994
%K jrnl, functional programming, FP, parallel, concurrent, speculative, zz0196
%X poor review by McGraw in Comp Rev p582 Nov '95

%A D. J. King
%A J. Launchbury
%T Lazy depth-first search and linear graph algorithms in Haskell
%I cs.tu-berlin.de
%D 1994
%K TR, FP, c1994, c199x, c19xx, graph, graphs, depth first search, traversal,
   algorithm, strongly connected, component, components
%X "Depth-first search is the key to a wide variety of graph algs.. ... we
   explore the implementation of depth first search in a lazy functional
   language. For the 1st time in such languages we obtain a linear-time
   implementation. But we go further. Unlike traditional imperative
   presentations, algs. are constructed from individual components, which may
   be reused to create new algs.. Furthermore, the style of program is quite
   amenable to formal proof, which we exemplify through a calculational-style
   proof of a strongly-connected components alg.."
   -- [<A HREF="http://uebb.cs.tu-berlin.de/papers/external/functional-state-guis/linear-dfs.ps.gz">.ps.gz@tu-berlin</A>]['08].
   [Also search for: Tarjan c1972].

%A H. G. Baker
%T CONS should not CONS its arguments, Part II: Cheney on the M.T.A.
%J SIGPLAN Notices
%V 30
%N 9
%P 17-20
%M SEP
%D 1995
%K SIGPLAN, c1995, c199x, c19xx, zz0916, FP, functional programming, trampoline,
   tail recursion, stack, trampolining, trampolined, jumps, thunk
%X "Previous Schemes for implementing full tail-recursion when compiling into C
   have required some form of 'trampoline' to pop the stack. We propose solving
   the tail-recn problem in the same manner as Standard ML ... by allocating all
   frames in the (garbage-collected) heap. The Scheme program is translated into
   continuation-passing style, so the target C fns never return. The C stack
   pointer then becomes the allocation pointer for a Cheney-style copying
   garbage collection scheme. Our Scheme can use C fn calls, C arguments, C
   variable-arity fns, & separate compilation without requiring complex
   block-compilation of entire programs. Our C version of the 'Boyer" benchmark
   is available at ftp://ftp.netcom.com/pub/hb/hbaker/cboyer13.c."
   --[<A HREF="http://dx.doi.org/10.1145/214448.214454">doi:10.1145/214448.214454</A>]['16].
   (Also see trampoline@[<A HREF="https://en.wikipedia.org/wiki/Trampoline_(computing)">wikip</A>]['16].)

%A W. Burton
%A E. Meijer
%A P. Sansom,  S. Thompson, and  P. Wadler
%T Views: An extension to Haskell pattern matching
%D 1996
%K proposal, proposed, extension, functional programming, FP
%X "... proposal is to support pattern matching in the context of abstract
   datatype. ..."
   -- [<A HREF="http://www.haskell.org/development/views.html">haskell.org</A>][6/'04].

%A R. Bird
%A O. de Moor
%A P. Hoogendijk
%T Generic functional programming with types and relations
%J J. of Functional Programming
%V 6
%N 1
%D 1996
%K jrnl, functional programming, FP, type, relation
%X (from the H@sekll m@il list 2/'04)
   -- [<A HREF="http://www.comlab.ox.ac.uk/oucl/work/oege.demoor/papers/gen.ps.gz">.ps.gz</A>][2/'04].

%A P. H. Hartel
%A H. Glaser
%T The resource constrained shortest path problem implemented in
   a lazy functional language
%J JFP
%V 6
%N 1
%P 29-45
%M JAN
%D 1996
%O CSTR-94-05, Dept. of Electr. and Comp. Sci, Univ. of Southampton, UK
%K jrnl, JFP, FP, paths, Haskell, dynamic programming, lazy evaluation,
   c1996, c199x, c19xx, zz0104
%X "The resource constrained shortest path problem is an NP-hard problem for
   which many ingenious algorithms have been developed. These algorithms are
   usually implemented in FORTRAN or another imperative programming language.
   We have implemented some of the simpler algorithms in a lazy functional
   language. Benefits accrue in the software engineering of the
   implementations. Our implementations have been applied to a standard
   benchmark of data files, which is available from the Operational Research
   Library of Imperial College, London. The performance of the lazy functional
   implementations, even with the comparatively simple algorithms that we have
   used, is competitive with a reference FORTRAN implementation."
   -- [<A HREF="http://www.dcs.gla.ac.uk/jfp/bibliography/References/hartelg1996%3A29.html">abs'@jfp</A>][1/'04].
   [<A HREF="http://wwwhome.cs.utwente.nl/~pieter/">~pieter</A>][1/'04].
   [<A HREF="http://www.ecs.soton.ac.uk/~hg/">~hg</A>][1/'04].

%A C. Runciman
%A N. Rojemo
%T Heap profiling for space efficiency
%J 2nd Int. School on Advanced Functional Programming
%I SpringerVerlag
%S LNCS
%V 1129
%P 159-183
%D 1996
%K FP, profile, uniYork, Hat, space, memory, profile, c1996, c199x, c19xx
%X try [<A HREF="http://www.cs.york.ac.uk/fp/">fp@york.uk</A>][5/'03].
   <!-- I used to think this was pp.34-41 --> uk us isbn:3540616284.

%A J. Hughes
%T Type specialisation of the lambda-calculus; or, a new paradigm for
   partial evalauation based on type inference
%J Dagstuhl Seminar on Partial Evaluation
%M FEB
%D 1996
%K PE1996, functional programming, FP, types, c1996, c199x, c19xx, zz0503
%X ... e.g. power n x -f n=1 then x else x * power (n-1) x
   ... if n known to be 3 ... power3 x = x*x*x ...
   -- [<A HREF="http://www.math.chalmers.se/~rjmh/TypedPE/revision.ps">revision.ps</A>][5/'03],
   [<A HREF="http://www-pu.informatik.uni-tuebingen.de/pe1996/abstracts.html#abstract27">abs</A>][5/'03].

%A U. S. Reddy
%T Global state considered unnecessary: an introduction to object-based
   semantics
%J J. Lisp and Symb. Comp.
%V 9
%N 1
%P 7-76
%M FEB
%D 1996
%K jrnl, JLSC, functional programming, FP, state, variable, L4Ref, zz0396

%A I. Stark
%T Categorical models for local names
%J J. Lisp and Symb. Comp.
%V 9
%N 1
%P 77-107
%M FEB
%D 1996
%K jrnl, JLSC, functional programming, FP, state, name, variable,
   category theory, zz0396

%A J. Springer
%A S. N. Kamin
%T Strictness analysis in the imperative lambda calculus
%J J. Lisp and Symb. Comp.
%V 9
%N 1
%P 109-143
%M FEB
%D 1996
%K jrnl, JLSC, functional programming, FP, strict, zz0396

%A P. Hudak
%A T. Makucevich
%A S. Gadde
%A B. Whong
%T Haskore music notation - an algebra of music
%J JFP
%V 6
%N 3
%P 465-483
%M MAY
%D 1996
%K FP, JFP, score, scores, music, musical, note, notes, notation, tempo, scales,
   jrnl, Haskell, c1996, c199x, c19xx, zz1102
%X ... simple algebraic approach to music description and composition called
   Haskore.  In this framework, musical objects consist of primitive notions
   such as notes and rests,  operations to transform musical objects such as
   transpose and tempo-scaling, and operations to combine musical objects to
   form more complex ones, such as concurrent and sequential composition. ...
   -- [<A HREF="http://haskell.cs.yale.edu/haskore/">haskore</A>][10/'02] inc' tutorial.

%A R. Sekar
%A I. V. Ramakrishnan
%T Fast strictness analysis based on demand propagation
%J TOPLAS
%V 17
%N 6
%P 896-937
%M NOV
%D 1996
%K ACM, Toplas, jrnl, lazy evaluation, functional programming, FP,
   optimisation, strict, strictness analysis, zz0496
%X 39 refs

%A L. Leung
%A P. Mishra
%T Reasoning about simple and exhaustive demand in higher-order lazy languages
%J Functional Programming and Computer Architecture
%I SpringerVerlag
%P ?-?
%D 1991
%K FPCA, FPCA91, conf, functional programming, FP, high order, lazy evaluation,
   strict, structness analysis, optimisation, zz0496
%X ref' in  S e k a r  and ...  '95

%A S. Kamin
%T Head-strictness is not a monotonic abstract property
%J IPL
%V 41
%N 4
%P 195-198
%M MAR
%D 1992
%K IPL, jrnl, functional programming, FP, strict, strictness analysis,
   weak head normal form, WHNF, optimisation, zz0496
%X ref' in  S e k a r  and ... '95.

%A K. Davis
%T Higher-order binding-time analysis
%B Partial Evaluation and Semantics Based Program Manipulation
%I ACM Press
%P ?-?
%D 1993
%K functional programming, FP, strict, strictness analysis, lazy evaluation,
   high order, optimisation, zz0496
%X ref in  S e k a r  and ...  '95

%A K. Dybvig
%A R. Hieb
%A C. Bruggeman
%T Syntactic abstraction in Scheme
%J Lisp and Symbolic Computation
%I SpringerVerlag, formerly KluwerAcademic
%V 5
%N 4
%P 295-326
%M DEC
%D 1993
%K functional programming, FP, c1993, c199x, c19xx, zz0106, template, meta,
   macro, hygenic macros, metaprogramming, name capture, scope, scoping
%X "... describes an efficient macro system that prevents inadvertent capturing
   while maintaining the correlation between source and object code. The macro
   system allows the programmer to define program transformations using an
   unrestricted, general-purpose language. ..."
   .. [<A HREF="http://dx.doi.org/10.1007/BF01806308">doi:10.1007/BF01806308</A>]['05].
   [Also search for: template FP].

%A P. Severi
%T Normalisation in Lambda Calculus and its Relation to Type Inference
%I Eindhoven Univ.
%D 1997 ?
%K PhD thesis, FP, functional programming, check, zz0197
%X isbn:9038602189.
   Hargrave H Mos 511.2 S498N
   not sure of the date but "new book" in Hargrave 1/97

%A N. D. Jones
%T An introduction to partial evaluation
%J Comp. Surveys
%V 28
%N 3
%M SEP
%D 1996
%P 480-503
%K comp. surveys, jrnl, PE, mix, zz0297, c1996, c199x, c19xx
%X [[p]] [in1, in2] = [[p   ]] in2
                         in1
   e.g.
   if f(n, x) = if n=0 the 1 else
                   if even(n) then sqr(f(n div 2, x)) else x*f(n-1, x)
   Knowing n=5 say, p5 = x*sqr(sqr(x))
   Knowing x is no help (unless it is -1, 0 or 1)

%A M. Hanus
%T Combining lazy narrowing and simplification
%J Proc. 6th Int. Symp. Prog. Lang. Impl. and Logic Prog.
%P 370-384
%D 1994
%I SpringerVerlag
%S LNCS
%V 844
%K conf, PLILP, PLILP94, PLILP6, laziness, functional programming,
   narrow, reduction, FP, LP, FLP
%X ... presents an important improvement of lazy narrowing
   by incorporating deterministic simplification steps into
   lazy narrowing derivations.  These [...] reduce the search
   space so that in some cases infinite search spaces are
   reduced to finite ones.  [...] completeness of lazy narrowing
   is not destroyed [...]
   14 refs<!-- michael OF mpi-sb.mpg.de --> .

%A J. Gibbons
%T Deriving tidy drawings of trees
%J J. of Functional Programming
%V 6
%N 3
%P 535-562
%M JUN
%D 1996
%K jrnl, JFP, FP, tree, draw, drawing
%X (from H@skell m@il list 2/'04)
   -- [<A HREF="http://web.comlab.ox.ac.uk/oucl/work/jeremy.gibbons/publications/index.html#deriving">ox.ac.uk</A>][2/'04].

%A A. Church
%T Introduction to Mathematical Logic
%I PrincetonUP
%S Annals of Mathematics Studies
%P 378
%D 1996
%K book, text, theory, computer science, logical calculus
%X pb, us$45, us isbn:0691029067; us isbn13:978-0691029061;
   reprinted in 1996 from the 1956 original.

%A R. Sekar
%A I. V. Ramakrishnan
%A P. Mishra
%T On the power and limitations of strictness analysis
%J JACM
%V 44
%N 3
%P 505-525
%M MAY
%D 1997
%K jrnl, JACM, strict, lazy, call by need, abstract interpretation,
   functional programming, FP, zz1297
%X see also A.Mycroft

%A M. Wallace
%A C. Runciman
%T Heap compression and binary I/O in Haskell
%D 1997
%J Proc. of the 2nd Haskell Workshop
%I ACM
%P ?-?
%M JUN
%D 1997
%K wshop, functional programming, FP, IO, memory management, storage, nhc,
   c1997, c199x, c19xx, uniYork, MWallace
%X "Two new facilities for Haskell are described: compression of data values in
   memory, & a new scheme for binary I/O. These facilities, although they can
   be used individually, can also be combined because they use the same binary
   representations for values. Heap compression in memory is valuable because
   it enables programs to run on smaller machines, or conversely allows
   programs to store more data in the same amount of memory. Binary I/O is
   valuable because it makes the file storage and retrieval of heap data
   structures smooth & painless. The combination of heap compression & binary
   I/O allows data transfer to be both fast & space-efficient.  All the
   facilities described have been implemented in a variant of Rojemo's nhc
   compiler. Example applications are demonstrated, with performance results
   for space & speed."
   -- [<A HREF="ftp://ftp.cs.york.ac.uk/pub/malcolm/hw97.html">.ps</A>][4/'04] Authors at Y0rk U, UK.

%A L. M. G. Feijs
%A M. A. Reniers
%T Lazy functional programs in a concurrent environment
%J COMPJ
%V 40
%N 9
%P 572-584
%D 1997
%K compj, jrnl, c1997, c199x, c19xx, FP, lazy, functional programming,
   behaviour, input output, IO, streams, zz0498
%X [...] Landin-style input/output stream [...] makes it possible
   to write functional programs which behave as reactive systems [...]
   [But, FP] lacks the capabilities for specification and reasoning which are
   needed to analyse the communication behaviours of the program
   and its environment. We propose to use the Algebra of Communicating
   Processes (ACP) for that purpose. [...]   24 refs.
   [Also search for: functional FP IO].

%E C. Clack
%E K. Hammond
%E T. Davie
%T Implementation of functional languages
%I Springer
%S LNCS
%V 1467
%P 375
%D 1997
%K wShop, functional programming, IFL9, IFL97, IFL, FP
%X uk us isbn:3540648496;  dm82, au$81 as of 11/98.
   7th workshop, St Andrews Sept 97, published 98.

%A J. Karczmarczuk
%T Generating power of lazy semantics
%J Theor. Computer Science
%V 187
%N 1-2
%P 203-219
%M NOV
%D 1999
%K jrnl, TCS, c1999, c199x, c19xx, lazy evaluation, infinite power series,
   functional programming, FP, algebra, algebraic manipulation
%X "We discuss the use of the lazy evaluation scheme as coding tool in some
   algebraic manipulations. We show - on several examples - how to process the
   infinite power series or other open-ended data structures with co-recurrent
   algs., which simplify enormously the coding of recurrence relns or solving
   eqns in the power series domain. The important point is not the "infinite"
   length of the data, but the fact that the algs. use open recursion, & the
   user never thinks about the truncation."
   -- [<A HREF="http://users.info.unicaen.fr/~karczma/arpap/lazysem.pdf">pdf@unicaen</A>]['07].

%A M. M. T. Chakravarty
%T On the Massively Parallel Execution of Declarative Programs
%I Technische Universitat Berlin, Fachbereich Informatik
%D 1997
%K PhD thesis, parallel, functional programming, FP, c1997, c199x, c19xx,
   MMTChakravarty, relations, agent, agents, UNSW, uniNSW
%X "... extends the typed lambda calculus by co-ordinating relations, ...called
   D, includes a basic notion of agents, which are represented by relations &
   may form parallel ensembles. Such agents communicate via equational
   constraints on unbound vars; & they can exhibit indeterminate behaviour,
   which is important for some parallel algorithms. Agents are 1st-class values
   in the sense that they support full higher-order programming. Computational
   tasks are realized within these agents as purely functional subcomputations.
   D is a declarative framework for parallel programming, which has a logic
   semantics based on an encoding into linear logic as well as a parallel
   operational semantics derived from the logic semantics.  This work also
   introduces an extension of the the Spineless Tagless G-machine, ..."
   -- [<A HREF="http://www.cse.unsw.edu.au/~chak/papers/diss.html">ps@unsw</A>]['05].

%A P. Sestoft
%T Deriving a lazy abstract machine
%J JFP
%V 7
%N 3
%P 231-264
%M MAY
%D 1997
%K jrnl, JFP, c1997, c199x, c19xx, zz1114, FP, functional programming, lambda,
   Krivine, abstract, lazy, evaluation strategy, call by name, viaJR
%X "We derive a simple abstract machine for lazy evaluation of the lambda
   calculus, starting from Launchbury's natural semantics. Lazy eval. here means
   non-strict eval. with sharing of argument evaluation, i.e. call-by-need. The
   m/c we derive is a lazy version of Krivine's abstract m/c, which was
   originally designed for call-by-name eval.. We extend it with datatype
   constructors & base values, so the final m/c implements all dynamic aspects
   of a lazy functional language."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796897002712">doi:10.1017/S0956796897002712</A>]['14],
      969887@[<A HREF="http://dl.acm.org/citation.cfm?id=969887">acm</A>]['14]..

%A M. M. T. Chakravarty
%A Y. Guo
%A M. Kohler
%A H. C. R. Lock
%T Goffin: Higher-order functions meet concurrent constraints
%J Sci. of Computer Prog.
%V 30
%N 1-2
%P 157-199
%D 1998
%K jrnl, Goffin, parallel, functional programming, FP, MMTChakravarty
%X "... higher-order constraint-based language ... "
   -- pdf@[<A HREF="http://www.cse.unsw.edu.au/~chak/papers/CGKL98.html">unsw</A>]['05].

%A J. Gibbons
%T Polytypic downwards accumulations
%J Mathematics of Program Construction
%E J. Jeuring
%W Marstrand, Sweden
%P ?-?
%M JUN
%D 1998
%S LNCS
%V 1422
%K conf, functional programming, FP, polytypical, downward, accumulation
%X (from H@skell m@il list 2/'04)
   -- [<A HREF="http://web.comlab.ox.ac.uk/oucl/work/jeremy.gibbons/publications/index.html#polyda">ox.ac.uk</A>][2/'04].

%A A. Asperti
%A S. Guerrini
%T The Optimal Implementation of Functional Programming Languages
%I CUP
%P 340
%D 1998
%K book, text, CUP, c1998, c199x, c19xx, FP, reduction, lambda calculus, lazy,
   graph, super combinator, supercombinator, optimal reduction, sharing,
   Lamping, evaluation, supercombinator, zz0498
%X [supercom. can cause] a catastrophic exponential explosion in reduction
   time.  Optimal reduction ... introduced by Lamping in '90, solves the
   sharing problem....
   stg40, Au$98.50, hb, uk us isbn:0521621127; uk us isbn13:978-0521621120.
   [Also search for: FP BOHM].

%A C. Okasaki
%T Purely Functional Data Structures
%I CUP
%P 200
%D 1998
%K book, text, CUP, programming, language, FP, lazy, c1998, c199x, c19xx,
   Haskell, SML, zz0498
%X c1998, hb, uk us isbn:0521631246; uk us isbn13:978-0521631242.
   c1999, pb, uk us isbn:0521663504; uk us isbn13:978-0521663502.

%A M. Wallace
%A C. Runciman
%T The bits between the lambdas: binary data in a lazy functional language
%J Proc. of the 1st Int. Symp. on Memory Management.
%W Vancouver
%I ACM
%P 107-117
%M OCT
%D 1998
%K symp, functional programming, FP, lambda, MWallace, Haskell, uniYork,
   B-tree, Btree, Btrees, c1998, c199x, c19xx, zzOSP, zOSP04
%X "... storage media are usually assumed to have a minimum atomic unit of
   transfer of one byte. However, sometimes it is useful to have an even finer
   storage granularity of one bit, for instance in order to compress data. ...
   describes an API in the lazy functional language Haskell for treating
   storage media as arbitrary-length streams of bits without byte-alignment
   constraints. So far as possible, storage media are treated uniformly. In
   particular, bit-stream memory & binary files share the same API -- a new &
   useful abstraction over memory management & file management. This uniformity
   of access leads to a novel technique for lazy random-access to files in a
   purely functional manner. We also describe a technique for automatically
   deriving compressed binary representations of user-defined data structures,
   whose operations provide both in-heap data compression & convenient
   high-level binary I/O. Of many possible applications, we illustrate the
   processing of Huffman-encoded image data, & a bibliographic information
   system which uses lazy B-trees for efficient storage management."
   -- [<A HREF="http://doi.acm.org/10.1145/286860.286872">doi:10.1145/286860.286872</A>][4/'04]. Also see W and R '97.

%A M. M. T. Chakravarty
%T C -> Haskell, or Yet Another Interfacing Tool
%E P. Koopman
%E C. Clack
%J Implementation of Functional Languages, 11th. Int. Workshop (IFL'99)
%D 1999
%I SpringerVerlag
%S LNCS
%V 1868
%K wShop, IFL, FP, FFI, interface, foreign function, functional programming,
   C, cc, header files, library, c1999, c199x, c19xx, marshaling, marshalling
%X This paper discusses a new method for typed functional languages to access
   libraries written in a lower-level language. More specifically, it
   introduces an interfacing tool that eases Haskell access to C libraries.
   The tool obtains information about the C data type definitions and function
   signatures by analysing the C header files of the library. It uses this
   information to compute the missing details in the template of a Haskell
   module that implements a Haskell binding to the C library. Hooks embedded
   in the binding file signal where, which, and how C objects are accessed
   from Haskell. The Haskell code in the binding file determines Haskell type
   signatures and marshaling details. The approach is lightweight and does not
   require an extra interface description language.
   -- [<A HREF="http://www.cse.unsw.edu.au/~chak/papers/Cha99b.html">inc' .ps</A>][9/'03] -- at UNSW.

%A M. Frigo
%T A fast Fourier transform compiler
%J Proc. 1999 ACM SIGPLAN Conf. on Prog. Lang. Design and Implementation.
%M MAY
%D 1999
%K conf, PLDI99, FFT, FFTW, west, objective Caml, oCaml, application,
   realworld, functional programming, FP, c1999, c199x, c19xx, C, cc, code
%X See [<A HREF="http://homepages.inf.ed.ac.uk/wadler/realworld/fftw.html">fftw</A>]['04]:-
   "FFTW is a fast C library for computing the Fast Fourier Transform (FFT) in
   one or more dimensions, including real-complex and parallel transforms. It
   is typically faster than most other public-domain FFT software, and is even
   competitive with vendor-optimized libraries for specific hardware (see the
   benchmarks on our home page).
   The performance-critical code in FFTW was automatically generated by a
   program written in Objective Caml. The generated code consists of
   specialized transforms for small sizes, dubbed "codelets," which ..."

%A J. Gibbons
%T Generic downwards accumulations
%J Sci. of Computer Programming
%V 37
%N 1-3
%P 37-65
%D 2000
%K jrnl, functional programming, FP, c2000, c200x, c20xx, accumulation,
   downward
%X (from H@skell m@il list 2/'04)
   -- [<A HREF="http://web.comlab.ox.ac.uk/oucl/work/jeremy.gibbons/publications/index.html#genda">ox.ac.uk</A>][2/'04].

%A R. Hinze
%T Generalizing generalized tries
%J JFP
%V 10
%N 4
%P 327-351
%M JUL
%D 2000
%K jrnl, JFP, FP, trie, data structures, type, types, first, second,
   1st, 2nd, order, generalised, general
%X ... define tries and operations on tries generically for arbitrary
   datatypes of first-order kind, including parameterized and
   nested datatypes. ...  requires rank-2 type signatures and second-order
   nested datatypes. ...
   -- [<A HREF="http://www.dcs.glasgow.ac.uk/jfp/bibliography/References/hinze2000:327.html">JFP</A>][9/'02].
   [<A HREF="http://uk.cambridge.org/journals/JFP/">CUP</A>][10/'02].

%A S. Antoy
%A R. Echahed
%T A needed narrowing strategy
%J JACM
%V 47
%N 4
%P 776-822
%M JUL
%D 2000
%K jrnl, JACM, functional programming, FP, logic, LP, FLP, call by need, lazy,
   narrowing, zz1100

%T Implementation of Functional Languages
%E M. Mohnen
%E P. Koopman
%I SpringerVerlag
%S LNCS
%V 2011
%P 267
%M SEP
%D 2000
%O 12th Int. Workshop IFL 2000, Aachen
%K wShop, IFL12, IFL2000, proc, FP, functional programming, interpreter,
   compiler, zz0801, c2000, c200x, c20xx
%X pb, uk us isbn:3540419195; uk us isbn13:978-3540419198, about au$75.

%A S. Thompson
%T Haskell: The Craft of Functional Programming
%S Int. Comp. Sci.
%I AddisonWesley
%D 1999
%P 528
%K book, text, functional programming, FP, Haskell, Haskell98, H98,
   c1999, c199x, c19xx, Hugs, Hugs98, zz0801
%X 2nd ed c1999, pb, uk us isbn:0201342758; uk us isbn13:978-0201342758;
    1. Intr' FP               2. Getting started with H' & Hugs
    3. Basic types & definitions    4. Designing & writing programs
    5. tuples and lists       6. Programming with lists
    7. functions over lists   8. Reasoning about programs
    9. Patterns & generalization   10. Functions as values
   11. Program development   12. Type classes
   13. Checking types        14. Algebraic types
   15. e.g.: Huffman codes   16. Abstract data types (ADT)
   17. Lazy programming      18. Programming with actions
   19. Program behaviour     20. Conclusion
   -- [<A HREF="http://www.cs.kent.ac.uk/people/staff/sjt/craft2e/">notes</A>][10/'03].
   (Also see [<A HREF="http://www.allisons.org/ll/FP/">FP</A>].)

%A M. Wallace
%A C. Runciman
%T Haskell and XML: Generic combinators or type-based translation?
%J Proc. Int. Conf. on Functional Programming
%W Paris
%P 148-159
%M SEP
%D 1999
%K conf, ACM, ICFP, ICFP4, ICFP99, Haskell, FP, functional programming, XML,
   HaXML, Haskell2Xml, Xtract, DTD, type, types, combinator, MWallace,
   uniYork, c1999, c199x, c19xx
%X isbn:1581131119;  [<A HREF="http://www.cs.york.ac.uk/fp/HaXml/icfp99.html">www</A>][11/'01].
   ... two complementary approaches to writing XML document-processing
   applications in a functional language.  ... 1: The generic tree structure
   of XML documents is used as the basis for the design of a library
   of combinators for generic processing: selection, generation, and
   transformation of XML trees.  ... 2: Use a type-translation framework
   for treating XML document type definitions (DTDs) as declarations of
   algebraic data types, and a derivation of the corresponding functions
   for reading and writing documents as typed values in Haskell.
   -- [<A HREF="http://www.cs.york.ac.uk/fp/HaXml/">HaXML</A>][11/'01].

%A P. Wadler
%T A formal model of pattern matching in XSL
%R Technical Report
%I Bell-Labs
%M JAN
%D 1999
%K TR, XSL, XML, DTD
%X [<A HREF="http://www.cs.bell-labs.com/~wadler/xsl/">at bell</A>][11/'01].

%A K. Crary
%A R. Harper
%A S. Puri
%T What is a recursive module?
%J Proc. of the ACM Conf. on Programming Language Design and Implementation
%V 34
%N 5
%O ACM SIGPLAN Notices
%P 50-63
%D 1999
%K conf, PLDI, PLDI99, functional programming, ML, SML, FP, modules, high,
   higher order, c1999, c199x, c19xx

%A A. van Deursen
%A P. Klint
%A J. Visser
%T Domain-specific languages: An annotated bibliography
%J ACM SIGPLAN Notices
%V 35
%N 6
%P 26-36
%M JUN
%D 2000
%K acm, sigplan, language, embedded, functional programming, FP, survey,
   programming, application domains, c2000, c200x, c20xx
%X "We survey the literature available on the topic of domain-specific
   languages as used for the construction and maintenance of software systems.
   We list a selection of 75 key publications in the area, and provide a
   summary for each of the papers. Moreover, we discuss terminology, risks and
   benefits, example domain-specific languages, design methodologies, and
   implementation techniques." ...
    . Subroutine libraries...
    . Object-oriented frameworks and component frameworks...
    . Domain-specific language (DSL)...
   -- [<A HREF="http://homepages.cwi.nl/~arie/papers/dslbib/">html</A>]['04].

%A P. Thiemann
%T Modeling HTML in Haskell
%B Practical Aspects of Declarative Languages
%P 263-277
%D 2000
%K PADL, c2000, c200x, c20xx, HTML, XML, DTD, FP, model, modelling
%X from  cite seer.    [Also search for: HaXML].

%A H.-W. Loidl
%A U. Klusik
%A K. Hammond
%A R. Loogen
%A P. Rinder
%T GpH and Eden: Comparing two parallel functional languages on a
   Beowulf cluster
%J 2nd Scottish Funct. Progr. Workshop, trends in Functional Programming
%V 2
%P 39-52
%D 2000
%O Intellect 2OO1
%K functional programming, FP, LinSolv, Ray Tracer, rayTracer, rays, tracing,
   wShop, programs, algorithm, ghc, par, seq, parMap, speedup, clusters
%X [<A HREF="http://www.mathematik.uni-marburg.de/~loogen/paper/ComparisonGpHEdenSFP2000.ps">.ps</A>][3/'04];
   see [<A HREF="http://cvs.haskell.org/cgi-bin/cvsweb.cgi/fptools/nofib/parallel/">cvs.haskell.org</A>][3/'04].

%A C. Okasaki
%T An overview of Edison
%J ACM SIGPLAN Haskell Workshop
%P ?-?
%M SEP
%D 2000
%O Electronic Notes in Theor. Comp. Sci. vol.41, 2001
%K wshop, Haskell, Edison, data structure, structures, functional programming,
   FP, sequence, associative collection, set, sets, priority queue, queues,
   finite map, maps, c2000, c200x, c20xx
%X ...library of d.s. in H. sequences, collections (e.g. sets, priority queues),
   associative collections (finite maps ...)...
   -- [<A HREF="http://www.cs.nott.ac.uk/~gmh/papers/5.ps">.ps</A>][2/'04],
      [<A HREF="http://www.cs.columbia.edu/~cdo/edison">edison</A>]['00].

%A S. Peyton Jones
%A J.-M. Eber
%A J. Seward
%T Composing contracts: An adventure in financial engineering
%J Proc. 5th Int. Conf. on Functional Programming
%W Montreal
%P 280-292
%M SEP
%D 2000
%K conf, ICFP5, FP, contract, insurance, mlFi, Lexifi, c2000, c200x, c20xx,
   risk, manage, financial derivatives, application, realworld, zz0404,
   Haskell, library, lazy, option, options, market, markets, automatic,
   programming
%X "Financial & insurance contracts do not sound like promising territory for
   [FP] & formal semantics, but in fact we have discovered that insights from
   programming languages bear directly on the complex subject of describing &
   valuing a large class of contracts. [...] combinator library that allows us
   to describe such contracts precisely, & a compositional denotational
   semantics that says what such contracts are worth. We sketch an
   implementation of our combinator library in Haskell. Interestingly, lazy
   evaluation plays a crucial role."
   -- [<A HREF="http://doi.acm.org/10.1145/351240.351267">doi:10.1145/351240.351267</A>][/'04],  isbn:1581132026.
   Also see [<A HREF="http://homepages.inf.ed.ac.uk/wadler/realworld/lexifi.html">Lexifi</A>]['04].
   [Also search for: automatic contract programming].

%A R. Hinze
%T A simple implementation technique for priority search queues
%J Proc. of the 6th ACM SIGPLAN Int. Conf. on Functional Programming
%W Florence
%P 110-121
%D 2001
%K conf, ICFP, ICFP6, priority queue, finite map, maps, c2001, c200x, c20xx,
   FP, ADT, data, shortest-path, paths, graph, graphs, view, views, zz0604
%X    [[Defn PSQ: seach(key) plus priority-queue operations (get min value).]]
   "... new implementation technique for priority search queues. This abstract
   data type is an amazing blend of finite maps & priority queues. Our
   implementation supports logarithmic access to a binding with a given key &
   constant access to a binding with the minimum value. Priority search queues
   can be used, for instance, to give a simple, purely functional
   implementation of Dijkstra's single-source shortest-paths algorithm. A
   non-technical concern of the paper is to foster abstract data types & views.
   Priority search queues have been largely ignored by the [FP] community & we
   believe that they deserve to be known better. Views prove their worth both
   in defining a convenient interface to the abstract data type & in providing
   a readable implementation."    isbn:1581134150.
   -- [<A HREF="http://doi.acm.org/10.1145/507635.507650">doi:10.1145/507635.507650</A>][6/'04].
   [Also search for: queue FP].

%A M. Burnett
%A J. Atwood
%A R. Walpole Djang
%A H. Gottfried
%A J. Reichwein
%A S. Yang
%T Forms/3: A first-order visual language to explore the boundaries of the
   spreadsheet paradigm
%J JFP
%V 11
%P 155-206
%M MAR
%D 2001
%K jrnl, JFP, FP, spread-sheet, zz1103, forms, forms3
%X ref in  P e y t o n J o n e s '03

%A J. Karczmarczuk
%T Functional differentiation of computer programs
%J J. High-Order and Symbolic Computation
%V 14
%P 35-57
%D 2001 ?
%K jrnl, HOSC, FP, derivative, derivatives, calculus, lazy, numeric, numerical,
   arithmetic, scientific computing, c2001, c200x, c20xx, zz0903
%X "This paper describes the lazy implementation of the (forward) automatic
   differentiation techniques, permitting - in a very concise way - to
   generate all derivatives of a numerical expression within a program."
   -- [<A HREF="http://users.info.unicaen.fr/~karczma/arpap/diffalg.pdf">.pdf</A>][9/'03]. (auth@Uni.Caen.fr)

%A M. D. McIlroy
%T The music of streams
%J IPL
%V 77
%N ?
%P 189-195
%D 2001
%K jrnl, IPL, data stream, network, processes, functional programming, FP,
   power stream composition, lists, lazy evaluation, c2001, c200x, c20xx, zz0603
%X -- [<A HREF="http://www.cs.dartmouth.edu/~doug/music.ps.gz">preprint</A>][6/'03].
   (NB. not computer generated music.)  M at Dartmouth.

%A M. Shields
%A E. Meijer
%T Type-indexed rows
%J Symp. on Principles of Prog. Lang.
%P 261-275
%M JAN
%D 2001
%K POPL, POPL28, POPL01, TIR, FP, XMLLambda, Table, row, column, record, XML,
   DTD, XSL
%X via cite seer
   Record calculi use labels to distinguish between the elements
   of products and sums. ... [but here] indexed by their type alone.
   The calculus, TIR, can express tuples, recursive datatypes, monomorphic
   records, polymorphic extensible records, and closed-world style type-based
   overloading. Our motivating application of TIR, however, is to encode the
   ``choice'' types of XML, and the ``unordered tuple'' types of SGML.  Indeed,
   TIR is the kernel of the language XMLambda, a lazy functional language
   with direct support for XML types (``DTDs'') and terms (``documents'').
      The system is built from rows, equality constraints, insertion
   constraints and constrained, or qualified, parametric polymorphism.
   The test for constraint satisfaction is complete, and for constraint
   entailment is only mildly incomplete. We present a type checking algorithm,
   and show how TIR may be implemented by a type-directed translation which
   replaces type-indexing by conventional natural-number indexing. ...
   -- [<A HREF="http://www.cse.ogi.edu/~mbs/pub/type_indexed_rows/">www</A>][11/'01].

%A S. Kahrs
%T Functional Pearl: Red-black trees with types
%J JFP
%V 11
%N 4
%P 425-432
%M JUL
%D 2001
%K jrnl, JFP, c2001, c200x, c20xx,  FP, programming, tree, type, data structure
%X [<A HREF="http://www.dcs.gla.ac.uk/jfp/bibliography/jfp01.html">JFP</A>][10/'02].
   [<A HREF="http://uk.cambridge.org/journals/JFP/">CUP</A>][10/'02].

%A M. Erwig
%T Inductive graphs and functional graph algorithms
%J JFP
%V 11
%N 5
%P 467-492
%M SEP
%D 2001
%K jrnl, JFP, c2001, c200x, c20xx, FP, graph, library, FGL, data structures,
   inductively defined, data type, types, structure, graph, graphs, algorithm,
   functional programming, Haskell, ML, SML
%X "... new style of writing graph alg's in F. lang's [..] based on an
   alternative view of graphs as inductively defined data types. We show how
   this graph model can be implemented efficiently [...] graph algorithms can
   be succinctly given by recursive function definitions based on [it] ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796801004075">doi:10.1017/S0956796801004075</A>]['05],
   pdf@[<A HREF="http://web.engr.oregonstate.edu/~erwig/papers/InductiveGraphs_JFP01.pdf">oreg'n</A>]['10],
   Func' graph library [<A HREF="http://www.cs.orst.edu/~erwig/fgl/">fgl</A>][10/'02],
   [<A HREF="http://www.cs.orst.edu/~erwig/papers/abstracts.html#JFP01">abs, paper</A>][10/'02],
   [<A HREF="http://www.cs.orst.edu/~erwig/">M.E. home</A>][10/'02].
      type Node  = Int                      -- a Node is "identified" by an Int
      type Adj b = [(b,Node)]          -- list of Edges into, or out of, a Node
      type Context a b = (Adj b, Node, a, Adj b)   -- ([into],Node,label,[out])
      data Graph a b = Empty | Context a b & Graph a b
      -- 'a' is Node label type; 'b' is edge label type.
      -- The Adjs in a Context can only link to currently defined Nodes.

%A M. Shields
%T Static Types for Dynamic Documents
%I Oregon Health and Science Univ.
%P 261
%M FEB
%D 2001
%K PhD Thesis, c2001, c200x, c20xx, document, XML, HTML, FP, Haskell,
   type-indexed rows, OGI, OHSU
%X [Also search for: FP XML];
   [<A HREF="http://www.cse.ogi.edu/~mbs/pub/thesis/">www</A>][11/'01].

%A F. Rabhi
%A G. Lapalme
%T Algorithms: A Functional Approach
%I AddisonWesley
%P 256
%M JUL
%D 1999
%K book, text, c1999, c199x, c19xx, algorithm, data structures, structure,
   functional programming, FP, Haskell, zz0602
%X pb us$59, uk us isbn:0201596040; uk us isbn13:978-0201596045.
   ... challenges more traditional methods of teaching algorithms by
   using a functional programming context, with Haskell as the
   implementation language. ...

%A Z. Hu
%A W.-N. Chin
%A M. Takeichi
%T Calculating a new data mining algorithm for market basket analysis
%J J. Functional and Logic Programming
%N 8
%M OCT
%D 2001
%P n.a.
%O Revised version of the paper presented at PADL'00, pp.169-184, 2OO0.
%K eJrnl, JFLP, functional programming, PADL, PADL00, FP, Zhenjiang Hu, zz0602,
   frequent item set, FIS, sets, items, data mining, c2001, c200x, c20xx, FP,
   shopping basket
%X "The general goal of data mining is to extract interesting correlated
   information from large collection of data. A key computationally-intensive
   subproblem of data mining involves finding frequent sets in order to help
   mine association rules for market basket analysis. Given a bag of sets and
   a probability, the frequent set problem is to determine which subsets occur
   in the bag with some minimum probability. This paper provides a convincing
   application of program calculation in the derivation of a new and fast
   algorithm for this practical problem. Beginning with a simple but
   inefficient specification expressed in a functional language, the new
   algorithm is calculated in a systematic manner from the specification by
   applying a sequence of known calculation techniques."    (on-line jrnl).
   [<A HREF="http://www.ipl.t.u-tokyo.ac.jp/~hu/pub/tech.html">papers</A>][6/'02],
   [<A HREF="http://www.cs.nmsu.edu/~complog/conferences/padl00/">PADL 00</A>][6/'02], isbn:3540669922,
   [<A HREF="http://danae.uni-muenster.de/lehre/kuchen/JFLP/articles/2001/S01-02/JFLP-A01-08.pdf">uni-muenster</A>][6/'04].

%A G. E. Moss
%A C. Runciman
%T Inductive benchmarking for purely functional data structures
%J JFP
%I CUP
%V 11
%N 5
%P 525-556
%M SEP
%D 2001
%K jrnl, FP, c2001, c200x, c20xx, data structure, speed, time, uniYork,
   benchmark, DUG, profiling, Auburn, decision, classification, tree
%X "... tool for inductive benchmarking. This tool, Auburn, can generate
   benchmarks across a wide distribution of uses. ... define 'the use of a data
   structure', upon which we build the core algorithms of Auburn: How to gen.
   a benchmark from a desc. of use, and how to extract a desc. of use from an
   application. ...apply inductive classification techniques to obtain decision
   trees for the choice between competing data structs.. We test Auburn by
   benchmarking several implementations of 3 common data structures:
   queues, random-access lists and heaps...."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796801004063">doi:10.1017/S0956796801004063"</A>][11/'04].

%A P. Thiemann
%T A typed representation for HTML and XML documents in Haskell
%J JFP
%V 12
%N 4, 5
%P 435-468
%M JUL
%D 2002
%K jrnl, JFP, FP, Haskell, HTML, XML, SGML, type, types, zz1002
%X [<A HREF="http://www.dcs.glasgow.ac.uk/jfp/bibliography/References/thiemann2002:435.html">JFP</A>][10/'02].
   ...a family of embedded domain specific languages for generating HTML and
   XML documents. Each language is implemented as a combinator library in
   Haskell. The generated HTML/XML documents are guaranteed to be well-formed.
   In addition, each library can guarantee that the generated documents are
   valid XML documents to a certain extent (for HTML only a weaker guarantee
   is possible). On top of the libraries, Haskell serves as a meta language to
   define parameterized documents, to map structured documents to HTML/XML, to
   define conditional content, or to define entire web sites.
   The combinator libraries support element-transforming style, a programming
   style that allows programs to have a visual appearance similar to HTML/XML
   documents, without modifying the syntax of Haskell.
   -- [<A HREF="http://uk.cambridge.org/journals/JFP/">CUP</A>][10/'02].

%A I. S. Diatchki
%A M. P. Jones
%A T. Hallgren
%T A formal specification of the Haskell 98 module system
%J PLI, Haskell Workshop
%D 2002
%K wShop, PLI, functional programming, FP, modules, executable, prototype,
   definition, H98
%X Many programming languages provide means to split large programs into
   smaller modules. The module system of a language specifies what
   constitutes a module and how modules interact.This paper presents a
   formal specification of the module system for the functional programming
   language Haskell. Although many aspects of Haskell have been subjected
   to formal analysis, the module system has, to date, been described only
   informally as part of the Haskell language report. As a result, some
   aspects of it are not well understood or are under-specified; this
   causes difficulties in reasoning about Haskell programs, and leads
   to practical problems such as inconsistencies between different
   implementations. One significant aspect of our work is that the
   specification is written in Haskell, which means that it can also be
   used as an executable test-bed, and as a starting point for Haskell
   implementers.  -- [<A HREF="http://doi.acm.org/10.1145/581690.581692">www</A>][2/'03].

%A P. W. Trinder
%A H. W. Loidl
%A R. F. Pointon
%T Parallel and distributed Haskells
%J JFP
%V 12
%N 4, 5
%P 469-510
%M JUL
%D 2002
%K jrnl, JFP, c2002, c200x, c20xx, FP, Haskell, network, networks, zz1002
%X [<A HREF="http://www.dcs.glasgow.ac.uk/jfp/bibliography/References/trinderlp2002:469.html">JFP</A>][10/'02],
   [<A HREF="http://uk.cambridge.org/journals/JFP/">CUP</A>][10/'02].

%A E. Meijer
%T Server side web scripting in Haskell
%J JFP
%V 10
%N 1
%P 1-18
%M JAN
%D 2000
%K jrnl, JFP, FP, HTML, CGI, cgibin, cgi-bin, Common Gateway Interface, www,
   script, HTTP, web server, c2000, c200x, c20xx, quotation, quotable,
   lesson, observation, programming style, type class, classes
%X "...(CGI) ...imposes much accidental complexity on the programmer. The...
   library documented in this paper hides all this unpleasantness by using the
   common sense `design pattern' of separating model & presentation. Low-level
   query string requests are represented by association lists, & primitive HTTP
   responses ... constructed using a set of HTML generating combinators. ...
   programmer only needs to write a worker function that maps an abstract
   request into an abstract response. A (higher-order) wrapper function then
   transmutes the worker into a real low-level CGI script that deals with the
   exact format of concrete requests & responses as required by the CGI std."
   -- [<A HREF="http://research.microsoft.com/~emeijer/Papers/CGI.pdf">paper.pdf</A>][5/'03].
   pdf:[<A HREF="http://titles.cambridge.org/journals/JFP/">JFP@CUP</A>][1/'04],
   [<A HREF="http://www.dcs.glasgow.ac.uk/jfp/bibliography/References/meijer2000:1.html">JFP</A>][10/'02].
   Observation: "Experienced H' programmers know of the duality between alg'
     data types and type classes.  ... H' style overloading is a powerful tool
     but it can be dangerous in the hands of inexperienced programmers. ...
     to make overloading really convenient we have to use a trick ..."

%A C. Elliott
%A P. Hudak
%T Functional reactive animation
%J ACM SIGPLAN Int. Conf. on Functional Programming
%P 263-273
%M JUN
%D 1997
%K conf, FP, Conal Elliott, computer graphics, interactive, FRAN, multimedia,
   multi-media, ICFP, ICFP97, zz1102
%X Fran (Functional Reactive Animation) is a collection of data types and
   functions for composing richly interactive, multimedia animations. The
   key ideas in Fran are its notions of behaviors and events. Behaviors are
   time-varying, reactive values, while events are sets of arbitrarily complex
   conditions, carrying possibly rich information. Most traditional values can
   be treated as behaviors, and when images are thus treated, they become
   animations. ...
   -- [<A HREF="http://www.research.microsoft.com/users/conal/papers/icfp97.ps">paper</A>][10/'02].

%A T. Sheard
%A S. Peyton-Jones
%T Template meta-programming for Haskell
%J Proc. of the workshop on Haskell
%I ACM
%P 1-16
%D 2002
%K wShop, templates, functional programming, FP, zz1002, compile-time,
   skeleton, program patterns, pattern, metaprogramming, type, types,
   polytypic, macro, macros, in-line, inline, expansion
%X "...extension to the purely functional programming language Haskell that
   supports compile-time meta-programming. The purpose of the system is to
   support the algorithmic construction of programs at compile-time. The
   ability to generate code at compile time allows the programmer to implement
   such features as polytypic programs, macro-like expansion, user directed
   optimization (such as inlining), and the generation of supporting data
   structures and functions from existing data structures and functions.
   Our design is being implemented in the Glasgow Haskell Compiler, ghc."
   -- [<A HREF="http://doi.acm.org/10.1145/581690.581691">TH paper</A>][10/'02]
   and [<A HREF="http://research.microsoft.com/~simonpj/tmp/notes2.ps">TH ver.2</A>]['05].
   us isbn:1581136056.  [Also see: generic Haskell (etc.)]
   [<A HREF="http://www.haskell.org/th/">haskell.org/th/</A>][2/'04].

%A C. Okasaki
%T Techniques for embedding postfix languages in Haskell
%J Proc. of the workshop on Haskell
%I ACM
%P 105-113
%D 2002
%K workshop, FP, embedded language, languages, functional programming
%X One popular use for Haskell in recent years has been as a host language
   for domain-specific embedded languages. But how can one embed a postfix
   language in Haskell, given that Haskell only supports prefix and infix
   syntax? This paper describes several such embeddings for increasingly
   complex postfix languages.
   -- [<A HREF="http://doi.acm.org/10.1145/581690.581699">paper</A>][10/'02].
   us isbn:1581136056.

%A M. P. Jones
%T Type classes with functional dependencies
%J Proc. 9th European Symp. on Prog. (ESOP 2000)
%W Berlin
%I SpringerVerlag
%S LNCS
%V 1782
%P 230-244
%M MAR
%D 2000
%K conf, ESOP, ESOP9, functional programming, types, class, dependency,
   dependencies, multi parameter, multiple parameters, FMap, OO, OOP, check,
   checking, collection types, c2000, c200x, c20xx, zz1102
%X Type classes ... allow programmers to define functions that can be used
   on a set of different types, with a potentially different implementation
   in each case. For example, type classes are used to support equality and
   numeric types, and for monadic programming. A commonly requested extension
   to support `multiple parameters' allows a more general interpretation of
   classes as relations on types, and has many potentially useful applications.
   Unfortunately, many of these e.g.s do not work well in practice...
   ambiguities and inaccuracies in inferred types ... delay detect... errors.
   ... illustrates problems... examples... .  isbn:3-540-67263-X.
   -- [<A HREF="http://cse.cse.ogi.edu/PacSoft/publications/2000/fundeps-esop2000.pdf">paper</A>][11/'02],
      [<A HREF="http://link.springer.de/link/service/series/0558/bibs/1782/17820230.htm">@springer</A>][11/'02],
      [<A HREF="http://www.cse.ogi.edu/~mpj/">mpj home</A>][11/'02].

%A E. Meijer
%A S. Finne
%T Lambada, Haskell as a better Java
%J Proc. Haskell Workshop 2000
%P ?-?
%D 2000
%K wShop, functional programming, FP, JNI, hDirect, c2001, c200x, c20xx, zz0204
%O Electronic notes in Theor. C. S. 41(1) '01.
%X ... interoperation between Haskell ... and Java.
   ... rests on Java Native interface (JNI). ...
   -- [<A HREF="http://research.microsoft.com/~emeijer/Papers/Lambada.pdf">.pdf</A>][2/'04].
   (Also see [<A HREF="http://www.allisons.org/ll/FP/Haskell/">on Haskell</A>],
    and      [<A HREF="http://www.allisons.org/ll/ProgLang/Java/">on Java</A>].)

%A J. Hughes
%T Generalising monads to arrows
%J Science of Computer Programming
%V 37
%P 67-111
%M MAY
%D 2000
%K jrnl, FP, arrow, arrows, monad, monadic, c2000, c200x, c20xx, type, types,
   combinators, monad, Haskell
%X "... I propose a generalisation of monads, which I call arrows, with sig.
   wider applicability. The paper shows how many of the techniques of monadic
   programming generalise to the new setting, ..."
   -- [<A HREF="https://doi.org/10.1016/S0167-6423(99)00023-4">doi:10.1016/S0167-6423(99)00023-4</A>]['24],
      [<A HREF="http://www.cs.chalmers.se/~rjmh/Papers/arrows.pdf">v1.pdf@chalmers.se</A>]['04] (later changed somewhat).
   [Also search for: FP arrows].

%A K. Claessen
%A P. Ljunglo
%T Typed logical variables in Haskell
%J Haskell Workshop
%V 41
%N 1
%P ?-?
%D 2000
%O Electronic Notes in Theor. Comp. Sci.
%K wShop, variable, functional, FP, c2000, c200x, c20xx, logic programming, LP,
   FLP, programming, prolog, type, types, term, predicate, unification
%X [<A HREF="http://www.cs.chalmers.se/~peb/pubs/p00-logvars-Haskell.pdf">pdf@chalmers.se</A>]['05].

%A L. Wong
%T Kleisli, a functional query system
%J JFP
%P 19-56
%V 10
%N 1
%M JAN
%D 2000
%K jrnl, JFP, FP, c2000, c200x, c20xx, Limsoon Wong, Singapore, bioinformatics,
   data integration, database, databases, heterogeneous, data bases, base
%X "Kleisli is a modern data integration system that has made a significant
   impact on bioinformatics data integration. ... brief introduction to the
   Kleisli system & an e.g. to illustrate its uses in [bioinformatics]. The
   primary query language provided ... is called CPL, which is a functional
   query language whose surface syntax is based on the comprehension syntax.
   Kleisli is itself implemented using the functional language SML. ..."
   -- [<A HREF="http://sdmc.lit.org.sg:8080/~limsoon/psZ/wls-jfp98-3.pdf">pp.pdf@sg</A>]['03],
      [<A HREF="http://dx.doi.org/10.1017/S0956796899003585">doi:10.1017/S0956796899003585</A>]['10].

%A M. Goldberg
%T An adequate and efficient left-associated binary numeral system in the
   lambda calculus
%J JFP
%V 10
%N 6
%P 607-623
%M NOV
%D 2000
%K jrnl, JFP, c2000, c200x, c20xx, FP, number, system, binary integers, integer,
   numerals, lambda calculus, ints, int, succ, pred, arithmetic
%X "introduces a sequence of l-exps modeling the binary expansion of integers...
   derive expressions computing the test for 0, the successor fn, & the
   predecessor fn, thereby showing the seq. to be an adequate numeral system,
   i.e. one in which all recursive fns are l-definable. These fns can be
   computed efficiently; To this end, we introduce a notion of complexity that
   is independent of the order of evaluation."
   z ~ zero bit, w ~ one bit,
   zero=lambda zw.z; one =lambda zw.w; two=lambda zw.zw; ...  (ie reversed)
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796800003804">doi:10.1017/S0956796800003804</A>]['08].

%A G. Tremblay
%T Lenient evaluation is neither strict nor lazy
%J Computer Languages
%V 26
%N 1
%P 43-66
%M JUN
%D 2001
%K jrnl, lenient evaluation, functional programming, FP, c2001, c200x, c20xx,
   non-strict, nonstrict
%X "... Is a non-strict language necessarily lazy? What additional
   expressiveness brings non-strictness, with or without laziness? This paper
   tries to shed some light on these questions ..."
   -- [<A HREF="http://www.info.uqam.ca/~tremblay/Tremblay01.html">abs</A>][7/'04].

%A G.-Q. Zhang
%A Leon Smith
%T A collection of functional libraries for theory of computation
%J Proc. 39th ACM-SE Conf.
%P 83-90
%M MAY
%D 2001
%K conf, c2001, c200x, c20xx, functional programming, FP, FSM, FSA, library,
   automata, machines
%X "... libraries for automata theory & Turing machines in the FP languages SML
   & Haskell. ... In Haskell, we provide an implementation of deterministic &
   non-det. FSMs, the conversion from the non-det. one to a det. one, state
   minimization, & constructions such as union, intersection, concatenation, &
   Kleene star on non-det. m/cs. Conversion from regular exps. to FSMs can be
   achieved straightforwardly in terms of these constructions. ..."
   ps@[<A HREF="http://webster.cs.uga.edu/~jam/acm-se/review/referee/gqz.ps">.uga.edu</A>]['09].

%A G. Tremblay
%A B. Malenfant
%T Lenient evaluation and parallelism
%J Computer Languages
%V 26
%N 1
%P 27-41
%M JUN
%D 2001
%K jrnl, lenient evaluation, functional programming, FP, c2001, c200x, c20xx,
   parallel, concurrent, strict, lazy, non-strict, nonstrict, evaluation,
   strategy
%X "... present a formal parallel model of three evaluation strategies (strict,
   lenient, and lazy), along with an examination of the impact of these
   evaluation strategies on the implicit parallelism that can be extracted from
   programs. This formal semantics, expressed using a parallel notation
   (pi-calculus), makes it possible to show why lenient evaluation can be seen
   as more naturally parallel."
   -- [<A HREF="http://www.info.uqam.ca/~tremblay/TremblayMal01.html">abs</A>][7/'04].

%A J. R. Dermoudy
%T Effective Runtime Management of Parallelism in a
   Functional Programming Context
%I U. of Tasmania
%D 2001 under assessment
%K PhD Thesis, functional programming, FP, Haskell, uTas, uniTas,
   c2001, c200x, c20xx, speculative evalutation
%J "... using parallel execution, load distribution, and speculative evaluation.
   This is an important challenge given the increasing complexity of sw systems,
   the decreasing cost of individual processors, and the appropriateness of the
   functional paradigm for parallelisation. ... The results of the experiments
   add evidence of the usefulness of speculative evaluation in general and
   effective speculative evaluation in particular."
   -- [<A HREF="http://www.comp.utas.edu.au/users/dermoudy/jd3.html">abs</A>]['05].

%A B. Lisper
%A J. Malmstrom
%T Haxcel: A spreadsheet interface to Haskell
%J Proc. 14th Int. Workshop on the Implementation of Functional Languages
%W Madrid
%P 206-222
%M SEP
%D 2002
%K wShop, Haxcel, cell, cells, FP, spread-sheet, sheets, c2002, c200x, c20xx,
   programming, zz0903
%X "The spreadsheet paradigm offers a fast interactive loop, where the effects
   of updates to definitions and data are immediately visible. This makes the
   paradigm attractive for program development, where redefinitions can be
   immediately tested and the results displayed. We have designed a simple,
   compilerindependent spreadsheet interface to Haskell, where cells host
   Haskell definitions."
   -- [<A HREF="http://www.mrtc.mdh.se/publications/0435.ps">.ps</A>][9/'03],
      [<A HREF="http://www.mrtc.mdh.se/publications/0435.pdf">.pdf</A>][9/'03].
   Haxcel: A... written in Java (slides)
   -- [<A HREF="http://www.mds.mdh.se/~dal98jmm/haxcel/pres.pdf">.pdf</A>][9/'03].

%A A. van Weelden
%A R. Plasmeijer
%T Towards a strongly typed functional operating system
%J Proc. 14th Int.  Workshop on the Implementation of Functional Languages
%E R. Pe?a
%I SpringerVerlag
%M SEP
%D 2002
%S LNCS
%V 2670
%P ?-?
%K wshop, IFL, OS, systems, functional programming, FP, zz0204
%X [<A HREF="ftp://ftp.cs.kun.nl/pub/Clean/papers/2003/vWeA2003-Famke.pdf">.pdf</A>][2/'04].

%A K. Claessen
%A C. Runciman
%A O. Chitil
%A J. Hughes
%A M. Wallace
%T Testing and tracing lazy functional programs using QuickCheck and Hat
%J 4th Summer School in Advanced Functional Programming
%W Oxford
%M AUG
%D 2002
%P 40 pages
%O (final version in Springer LNCS 2638, 2OO3)
%K FP, test, trace, tracing, execution, debug, debugging, space, time,
   QuickCheck, Hat, c2002, c200x, c20xx, MWallace, uniYork
%X "... misunderstand the properties of their own programs, or those of others,
   & so commit errors. ... aim to provide functional programmers with tools for
   testing & tracing programs. ... testing means 1st specifying what behaviour
   is acceptable ..., then finding out whether behaviour ... matches ..."
   -- [<A HREF="http://www.cs.york.ac.uk/fp/hat/afp2002.ps.gz">.ps.gz@york</A>][8/'04],
      [<A HREF="http://www.springerlink.com/link.asp?id=9qhce993jrecc9dx">springerlink</A>][8/'04].

%A M. M. T. Chakravarty
%A G. C. Keller
%T An Introduction to Computing with Haskell
%I PearsonEd
%P 150
%D 2002
%K book, text, FP, functional programming, c2002, c200x, c20xx, Haskell, teach,
   teaching, computer, curriculum, CSC1, CSC101, CS1, CS101, L1REF
%X au$40; pb, uk us isbn:1740094042; uk us isbn13:978-1740094047.
   The original English version has been reviewed in JFP 14(2), March 2OO4,
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796803215033">doi:10.1017/S0956796803215033</A>][7/'04].
   The approach of the book was discussed in an Educational Pearl in the
   JFP, 14(1), Jan 2OO4,
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796803004805">doi:10.1017/S0956796803004805</A>][7/'04].

%A K. Claessen
%A J. Hughes
%T Specification-based testing with QuickCheck
%B Fun of Programming
%E J. Gibbons
%E O. de Moor
%I PalgraveMacmillan
%S Cornerstones of Computing
%P 288
%M MAR
%D 2003
%K quick check, test, testing, FP, c2003, c200x, c20xx
%X The book it's in is stg42, isbn:0333992857.
   [also search for: QuickSearch]

%A A. van Weelden
%A R. Plasmeijer
%T A functional shell that dynamically combines compiled code
%J Proc. 15th Int. Workshop on the Implementation of Functional Languages
%M SEP
%D 2003
%K wshop, IFL, shell, functional programming, FP, command interpreter, zz0304
%X Submitted to Selected Papers Review of
   Proc. 15th Int. Workshop on the Implementation of Functional Languages
   -- [<A HREF="ftp://ftp.cs.kun.nl/pub/Clean/papers/2003/vWeA2003-Esther.pdf">.pdf</A>][2/'04].

%A A. Pardo
%T Generic accumulations
%E J. Gibbons
%E J. Jeuring
%J Proc. of the IFIP TC2 Working Conf. on Generic Programming
%I Kluwer Academic Publ.
%D 2003
%K conf, functional programming, FP, accumulation
%X (from H@skell m@il list 2/'04)
   [<A HREF="http://www.fing.edu.uy/~pardo/papers/wcgp02.ps.gz">fing.edu.uy</A>][2/'04],
   [<A HREF="http://web.comlab.ox.ac.uk/oucl/work/jeremy.gibbons/publications/index.html#wcgp">ox.ac.uk</A>][2/'04].

%A J. R. Dermoudy
%T A novel approach to parenting in functional program evaluation
%J 26th Australasian Computer Science Conf. (ACSC)
%P 217-226
%M FEB
%D 2003
%K conf, FP, distributed, parallel, concurrent, speculation, speculation,
   speculative, evaluation strategy, zz0203, c2003, c200x, c20xx, ACSC2003,
   thread, threads, functional programming, ACSC, Haskell
%X uni tas' [<A HREF="http://www.comp.utas.edu.au/users/dermoudy/">home</A>]['05].

%A B. Pope
%A L. Naish
%T A program transformation for debugging Haskell 98
%J 26th Australasian Computer Science Conf. (ACSC)
%P 227-236
%M FEB
%D 2003
%K conf, FP, functional programming, FP, debug, zz0203, c2003, c200x, c20xx,
   ACSC2003
%X unimelb.

%T The Fun of Programming (Cornerstones of Computing)
%E J. Gibbons
%E O. de Moor
%I Palgrave - Macmillan
%P 288
%M MAR
%D 2003
%K book, text, c2003, c200x, c20xx, functional programming, FP, CS, CSci,
   Comp Sci, zz0603
%X pb, uk us isbn:0333992857; uk us isbn13:978-0333992852;
   hb, uk us isbn:1403907722; uk us isbn13:978-1403907721.

%A R. Ennals
%A S. Peyton-Jones
%T Optimistic evaluation: An adaptive evaluation strategy for
   non-strict programs
%J Proc. 8th ACM SIGPLAN Int. Conf. on Functional Programming
%P 287-298
%D 2003
%O also ACM SIGPLAN Vol.38 No.9, pp.287-298, Sept. 2003
%K conf, ICFP, c2003, c200x, c20xx, functional programming, FP, evaluation,
   reduction, strategy, speculative, eager, lazy, optimistic, non-strict,
   zz0903
%X "... Optimistic evaluation ... evaluates a thunk speculatively but
   it has an abortion mechanism to back out if it makes a bad choice. ...
   ... many programs speed up [by] 5-25%, some improve dramatically, and
   none go more than 15% slower."
   -- pdf@[<A HREF="http://www.cl.cam.ac.uk/users/rje33/icfp2003.pdf">cam</A>][9/'03],
      [<A HREF="http://dx.doi.org/10.1145/944746.944731">doi:10.1145/944746.944731</A>]['13].
   [Also search for: speculative FP].

%A N. Nethercote
%A A. Mycroft
%T The cache behaviour of large lazy functional programs on stock hardware
%J Proc. of the workshop on Memory system performance
%I ACM
%P 44-55
%D 2003
%W Berlin
%K wshop, FP, programming, c2003, c200x, c20xx, zz0404, compiler, Intel, x86,
   implementation, execution, run, running, speed, time, optimization,
   efficiency, L2 cache, stall, stalls, branch misprediction, ghc, Haskell
%X "... hardware counters & a simple yet accurate execution cost model to
   analyse some large Haskell programs on the x86 architecture. [...] not
   interact well with modern processors -- L2 cache data miss stalls & branch
   misprediction stalls account for up to 60% & 32% of execution time resp'.
   [...] code exhibits little exploitable instruction-level parallelism.
   [...] use simulation to pinpoint cache misses at the instruction level.
   [...] apply prefetching to minimise the cost of write misses, speeding up
   [...] programs by up to 22%. We conclude with more ideas for changing [ghc]
   & its garbage collector to improve the cache performance of large programs."
   -- [<A HREF="http://doi.acm.org/10.1145/773146.773044">doi:10.1145/773146.773044</A>][4/'04].
   auth's at Cam.U.; issn:03621340.

%A S. Peyton Jones
%A A. Blackwell
%A M. Burnett
%T A user-centred approach to functions in excel
%J ICFP
%I ACM
%P 165-176
%D 2003
%K conf, ACM, ICFP8, Sigplan, FP, spreadsheet, spread-sheet, Excel, MS Office,
   function, functional programming, zz1103
%X "...extensions to the Excel ... integrate user-defined functions into the
   spreadsheet grid, rather than treating them as a "bolt-on". Our 1st
   objective was to bring the benefits of additional programming language
   features to a system that is often not recognised as a programming language.
   2nd, in a project involving the evolution of a well-established language,
   compatibility with previous versions is a major issue, and maintaining this
   compatibility was our second objective. Third and most important, the
   commercial success of spreadsheets is largely due to the fact that many
   people find them more usable than programming languages for programming-like
   tasks. ...3rd objective (...) to maintain this usability advantage. Simply
   making Excel more like a conventional programming language would not meet
   these objectives and constraints. We have therefore taken an approach to our
   design work that emphasises the cognitive requirements of the user as a
   primary design criterion. The analytic approach that we demonstrate in this
   project is based on recent developments in the study of programming
   usability, including the Cognitive Dimensions of Notations and the
   Attention Investment model of abstraction use. We believe that this approach
   is also applicable to the design and extension of other programming
   languages and environments."
   Simon Peyton Jones is @  Microsoft Research, Cambridge
   -- [<A HREF="http://doi.acm.org/10.1145/944705.944721">doi.acm.org/10.1145/944705.944721</A>][11/'03], inc' .pdf.

%A K. Hammond
%A R. Loogen
%A J. Berhold
%T Automatic skeletons in template Haskell
%J Proc. of 2003 Workshop on High Level Parallel Programming.
%P ?-?
%M JUN
%D 2003
%K wShop, template, templates, Haskell, functional programming, FP, type,
   types, skeleton, compile time, Eden, parallel, concurrent, farm, zz0204
%X -- [<A HREF="http://www.haskell.org/th/papers/hlpp.ps">.ps</A>][2/'04],
      [<A HREF="http://www.haskell.org/th/">haskell.org/th/</A>][2/'04].

%T Implementation of Functional Languages
%I SpringerVerlag
%S LNCS
%V 3145
%M SEP
%D 2003
%K wShop, FP, programming language, Int workshop, IFL 15, IFL2003, IFL15
%X 15th Int. Workshop on IFL, eur42, isbn:3540237275.

%A P. Blain
%T Call By Push Value, a Functional/Imperative Synthesis
%I Kluwer
%P 396
%M DEC
%D 2003
%K book, text, FP, functional, programming languages, semantics, value, name
%X auth at U. Birm'ham, uk. us$156.
   hb, uk us isbn:1402017308; uk us isbn13:978-1402017308.

%A M. M. T. Chakravarty
%A G. Keller
%T An approach to fast arrays in Haskell
%J 4th Summer School and Workshop on Advanced Functional Programming 2002.
%I SpringerVerlag
%S LNCS
%V 2638
%P 27-58
%D 2002
%K wShop, FP, c2002, c200x, c20xx, zz0408, array, arrays, vector, vectors,
   code vectorisation, vectorization, array fusion
%X "Many array-centric algorithms from computational science and engineering,
   especially those based on dynamic and irregular data structures, can be
   coded rather elegantly in a purely functional style. The challenge, when
   compared to imperative array languages, is performance."
   -- [<A HREF="http://www.cse.unsw.edu.au/~keller/CK03.html">@unsw</A>]['08].
   Notes, pb, 2003, us$94, uk us isbn:3540401326; uk us isbn13:978-3540401322.

%A H. Nilsson
%A J. Peterson
%A P. Hudak
%T Functional hybrid modeling
%J Proc. Int. Workshop on Practical Aspects of Declarative Languages
%I SpringerVerlag
%S LNCS
%V 2562
%P 376-390
%M JAN
%D 2003
%K wShop, PADL, FP, FP, programming, Yampa, c2003, c200x, c20xx, model,
   simulation, simulate, physical, reactive, FRP, YaleUni, zz0605
%X "...mod. & sim. of physical sys. is of key importance in many areas of sci.
   & eng., & thus can benefit from high-quality software tools. ...we have
   demonstrated how FP can form the basis of an expressive lang. for causal
   hybrid modeling & sim.. There is a growing realization, however, that a mov
   e toward non-causal modeling is nec. for coping with the ever increasing
   size & complexity of modeling problems. ... combine the strengths of FP &
   non-causal modeling to create a powerful, strongly typed fully declarative
   modeling lang. that provides mod. & sim. capabilities beyond the current
   state of the art. Although our work is still in its very early stages, we
   believe that this paper clearly articulates the need for improved modeling
   languages & shows how FP tech. can ..."
   -- [<A HREF="http://www.haskell.org/yale/papers/padl03/fhm.ps.gz">.ps.gz</A>]['05],
      [<A HREF="http://haskell.org/yampa/">yampa</A>]['05].

%A M. M. T. Chakravarty
%A G. Keller
%T The risks and benefits of teaching purely functional programming in
   first year
%J JFP
%I CUP
%P 113-123
%V 14
%D 2004
%K jrnl, JFP, education, curriculum, university, New South Wales, NSW, UNSW,
   zz0404, JFP, FP
%X "We argue that teaching purely functional programming as such in freshman
   courses is detrimental to both the curriculum as well as to promoting the
   paradigm. Instead, we need to focus on the more general aims of teaching
   elementary techniques of programming and essential concepts of computing.
   We support this viewpoint with experience gained during several semesters of
   teaching large first-year classes (up to 600 students) in Haskell. These
   classes consisted of computer science students as well as students from
   other disciplines. We have systematically gathered student feedback by
   conducting surveys after each semester. This article contributes an approach
   to the use of modern functional languages in first year courses and, based
   on this, advocates the use of functional languages in this setting."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796803004805">doi:10.1017/S0956796803004805</A>][3/'04].
   (Also see [<A HREF="http://www.allisons.org/ll/FP/">FP</A>].)

%A B. Mcnamara
%A Y. Smaragdakis
%T Functional programming with the FC++ library
%J JFP
%I CUP
%P ?-?
%V ?
%D 2004
%K jrnl, JFP, c2004, c200x, c20xx, FP, fc++, fcplusplus, cc, gcc, zz0304
%X "... library supporting functional programming in C++. Prior approaches to
   encoding higher order functions in C++ have suffered with respect to
   polymorphic functions from either lack of expressiveness or high complexity.
   In contrast, FC++ offers full & concise support for higher-order polymorphic
   functions through a novel use of C++ type inference. The FC++ library has a
   number of useful features, including a generalized mechanism to implement
   currying in C++, a lazy list class which enables the creation of infinite
   data structures, a subtype polymorphism facility, & an extensive library of
   useful fn's, including a large part of the Haskell Standard Prelude. ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796803004969">doi:10.1017/S0956796803004969</A>][3/'04].

%A M. D. McIlroy
%T Enumerating the strings of regular languages
%J JFP
%I CUP
%P ?-?
%V ?
%D 2004
%K jrnl, FP, JFP, zz0404, language, string, expression, NFA, nondeterministic,
   non-deterministic, finite state automaton, NFSA, strings, enumerate, LOS,
   length ordered, closure, generate, c2004, c200x, c20xx
%X "Haskell code is developed for two ways to list the strings of the language
   defined by a regular expression: directly by set operations & indirectly by
   converting to & simulating an equivalent automaton. The exercise illustrates
   techniques for dealing with infinite ordered domains & leads to an effective
   standard form for nondeterministic finite automata."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796803004982">doi:10.1017/S0956796803004982</A>][4/'04].
   [Defines an NFSA by mutually rec. declarations.]
   [Also search for: FP nondeterminism].

%A S. Ronchi Della Rocca
%A L. Paolini
%T The Parametric Lambda Calculus
%P 250
%I SpringerVerlag
%M FEB
%D 2004
%K book, text, L4Ref, functional programming, FP, semantics, call by name,
   value, lazy
%X 2004, eur50, au$95; hb, uk us isbn:3540200320; uk us isbn13:978-3540200321.

%A M. Felleisen
%A R. B. Findler
%A M. Flatt
%A S. Krishnamurthi
%T The structure and interpretation of the computer science curriculum
%J JFP
%V ?
%P ?-?
%D 2004
%K jrnl, JFP, c2004, c200x, c20xx, how, program design, OO, OOP, 1st year, CSC,
   programming, CSC1, L1Ref, teach, teaching, first, Abelson, Sussman, zz0704
%X "[20] ago Abelson & Sussman's Structure & Interpretation of Computer
   Programs radically changed the intellectual landscape of introductory
   computing courses. Instead of teaching some currently fashionable
   programming language, it employed Scheme & [FP] to teach important ideas.
   Introductory courses based on the book showed up around the world & made
   Scheme & [FP] popular. Unfortunately, these courses quickly disappeared
   again due to shortcomings of the book & the whimsies of Scheme. Worse, the
   experiment left people with a bad impression of Scheme & [FP] in general.
   In this pearl, we propose an alternative role for [FP] in the 1st-year
   curriculum. Specifically, we present a framework for discussing the
   1st-year curriculum &, based on it, the design rationale for our book &
   course, dubbed How to Design Programs. The approach emphasizes the
   systematic design of programs. Experience shows that it works extremely well
   as a preparation for a course on object-oriented programming."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796804005076">doi:10.1017/S0956796804005076</A>][7/'04].
   ([<A HREF="http://www.htdp.org/">the book</A>][7/'04] c2OO1 MIT press; us isbn:0262062186; 720pp, us$67.)

%A Chung-chieh (Ken) Shan
%T Higher-order modules in System F-omega and Haskell (draft)
%J n.a.
%M JUL
%D 2004
%K FP, functional programming
%K pre-print, KenShan, ML, SML, module, functors, generative, applicative,
   type, types, polymorphism, polymorphic, existential, c2004, c200x, c20xx
%X "To argue that it is practical to extend core Haskell to support higher-
   order modules, we translate Dreyer, Crary, & Harper's higher-order module
   system (2OO2, 2OO3) into System F-om. Our translation is the 1st to fully
   treat generative functors (with existential types) alongside applicative
   ones (with Skolemized types). Applicative functors correspond to higher-
   order polymorphism in idiomatic Haskell-abstract, higher-kinded type
   constructors, accompanied by term combinators. Higher-order functors
   correspond to higher-rank polymorphism in F, which is practical to add to
   Haskell & has been added (Peyton Jones & Shields 2OO4).  The difference
   between generative & applicative functors boils down to whether existential
   type variables scope under or over the typing context. Thus we can express
   functor bodies that mix generative & applicative parts, which are
   inconvenient to simulate in Dreyer et al.'s language.  Also, we exclude the
   avoidance problem (the lack of minimal supersignatures) because existential
   quantification is primitive in F-om. Although modules are 1st-class values,
   type sharing & the phase distinction are both preserved: the programmer can
   make fine-grained trade-offs between opaque & transparent types, & 2 modules
   are statically equivalent just in case they have the same type. Our work can
   guide further improvements to modularity in Haskell & ML."
   -- [<A HREF="http://www.eecs.harvard.edu/~ccshan/xlate/">harvard.edu/~ccshan</A>][8/'04].

%A A. Pang
%A D. Stewart
%A S. Seefried
%A M. M. T. Chakravarty
%T Plugging Haskell in
%J ACM SIGPLAN Haskell workshop
%W Snowbird, Utah
%P 10-21
%M SEP
%D 2004
%K wShop, plug in, plugin, plugins, FFI, dynamic loading, type, types
%X "Extension languages enable users to expand the functionality of an appl'n
   without touching its source code. Commonly, these languages are dynamically
   typed languages, such as Lisp, Python, or domain-specific languages, which
   support runtime plugins via dynamic loading of components. We show that
   Haskell can be comfortably used as a statically typed extension language,
   and that it can support type-safe dynamic loading of plugins using dynamic
   types. Moreover, we discuss how plugin support is especially useful to
   applications where Haskell is used as an embedded domain-specific language
   (EDSL). We explain how to realise type-safe plugins using dynamic types,
   runtime compilation, and dynamic linking, exploiting infrastructure provided
   by the Glasgow Haskell Compiler. We demonstrate the practicability of our
   approach with several applications that serve as running examples."
   -- [<A HREF="http://www.cse.unsw.edu.au/~dons/hs-plugins/paper/">@unsw.edu.au</A>][9/'04].

%A D. Leijen
%T wxHaskell - A portable and concise GUI library for Haskell
%J ACM SIGPLAN Haskell workshop
%W Snowbird, Utah
%P 57-68
%M SEP
%D 2004
%K wShop, computer graphics, FP, c2004, c200x, c20xx, zz1004, wxWidgets,
   wxWidget, portable, interface, C++, Cplusplus, cc
%X "wxHaskell is a graphical user interface (GUI) library for Haskell that is
   built on wxWidgets: a free industrial strength GUI library for C++ that
   provides a common interface that has been ported to all major platforms,
   including Windows, Gtk, and MacOS X. In contrast with many other libraries,
   wxWidgets retains the native look-and-feel of each particular platform. We
   show how distinctive features of Haskell, like parametric polymorphism,
   higher-order functions, and first-class computations, can be used to present
   a concise and elegant monadic interface for portable GUI programs."
   -- [<A HREF="http://www.cs.uu.nl/~daan/download/papers/wxhaskell.pdf">pdf</A>][9/'04],
      [<A HREF="http://www.cs.uu.nl/~daan/pubs.html">Daan L, cs.uu.nl</A>][9/'04],
      [<A HREF="http://wxhaskell.sourceforge.net/">@sourceforge.net/</A>][9/'04].

%A S. Seefried
%A M. Chakravarty
%A G. Keller
%T Optimising embedded DSLs using template Haskell
%J 3rd Int. Conf. on Generative Programming and Component Engineering
%P 186-205
%W Vancouver
%M OCT
%D 2004
%K conf, template Haskell, c2004, c200x, c20xx, PanTHeon, meta-programming,
   embedded language, FP
%X [<A HREF="http://www.cse.unsw.edu.au/~sseefried/papers/papers.html">sseefried@unsw</A>]['05].
   Also see [<A HREF="http://www.haskell.org/th/">haskell.org/th</A>]['05].

%A C. Hankin
%T An Introduction to Lambda Calculi for Computer Scientists
%I Kings College Publ.
%P 180
%D 2004
%K book, text, c2004, c200x, c20xx, lambda calculus, computer science, CSci,
   L3Ref, L4Ref, CSci, Maths
%X "... book emphasises the proof theory for the type-free lambda-calculus. The
   first six chapters concern this calculus and cover the basic theory,
   reduction, models, computability, and the relationship between the
   lambda-calculus and combinatory logic. Ch.7 presents a variety of typed
   calculi ..."
   pb, us$17; uk us isbn:0954300653; uk us isbn13:978-0954300654.
   (Also see [<A HREF="http://www.allisons.org/ll/FP/Lambda/">lambda</A>].)

%A M. Wallace
%T Modular architectural representation and analysis of fault propagation and
   transformation
%J Formal Foundations of Embedded Sys. & Component-Based Software Arch.
%W Edinburgh
%P ?-?
%M APR
%D 2005
%O ENTCS, pp.46-63, Elsevier
%K faults, FPTC, failure, behaviour, system, architecture, hardware, software,
   uniYork, MWallace, HIRTS, high integrity real-time systems, RTS, error,
   conf, errors, value, late, stale, early, omission, comission, compositional,
   fix, fixed, point
%X "... hardware and software components ... description of how components are
   combined ... together with an FPTC expression of each compt's failure
   behaviour, the failure prop's of the whole system..."<!-- ?TACAS 2OO5? --> .
   -- [<A HREF="http://www.cs.york.ac.uk/plasma/talkrelated/tacas05.pdf">pdf@york</A>][10/'04].
   ... for 1-input, 1-output component:  (* = normal, no failure)
      * -> late (source)                     early -> * (sink)
      omission -> omission (propagate)       late -> value (transform)
   semantics... maximal token-set... fixed-point... must terminate.

%A O. Kiselyov
%A C.-C. Shan
%A D. P. Friedman
%A A. Sabry
%T Backtracking, interleaving, and terminating monad transformers
   (Functional Pearl)
%J Int. Conf. Functional Programming
%P ?-?
%D 2005
%K conf, ICFP, FP, LP, backtrack, transform, monads, c2005, c200x, c20xx,
   nondeterminism, once, bagOfN, cut, MonadPlus, success, failure, zz0605,
   fair disjunction, conjunction, transformer, interleaving
%X [<A HREF="http://pobox.com/~oleg/ftp/papers/LogicT.pdf">pdf</A>]['05].
   [Also search for: FP nondeterminism]  and  [also search for: continuation].

%A T. Hallgren
%A M. P. Jones
%A R. Leslie
%A A. Tolmach
%T A principled approach to operating system construction in Haskell
%J Int. Conf. Functional Programming
%P ?-?
%D 2005
%K conf, ICFP, FP, Haskell, OS, systems, c2005, c200x, c20xx, House, hOp
%X [<A HREF="http://www.cse.ogi.edu/~hallgren/">auth1</A>]['05].

%A M. Erwig
%A S. Kollmansberger
%T Probabilistic functional programming in Haskell
%J J. of Functional Programming
%V 16
%N 1
%P 21-34
%D 2006
%K JFP, jrnl, FP, c2006, c200x, c20xx, simulation, event, simulations, values,
   stochastic, probability, oregonstate, MErwig, SKollmansberger
%X "... referential transparency ... seems to be violated when contemplating
   ... functions to describe probabilistic events, such as rolling a die: It is
   not clear at all what exactly the outcome will be, & neither is it
   guaranteed that the same value will be produced repeatedly. However, these
   2 seemingly incompatible notions can be reconciled if probabilistic values
   are encapsulated in a data type.
      ... demonstrate such an approach by describing a probabilistic ... (PFP)
   library for H.. We will show that the proposed approach not only facilitates
   probabilistic programming in F. languages, but in particular can lead to
   v. concise programs & simulations. ... simulations can be spec. indep. from
   their method of execution. That is, we can either fully simulate or
   randomize any simulation without altering the code which defines it. "
   -- [<A HREF="http://web.engr.oregonstate.edu/~erwig/papers/PFP_JFP05.pdf">pdf</A>]['05],
      [<A HREF="http://web.engr.oregonstate.edu/~erwig/pfp/">code</A>]['05].
   [search for: probability FP], unfortunately P.F.P. also means 'par@llel FP'!
   [<A HREF="http://dx.doi.org/10.1017/S0956796805005721">doi:10.1017/S0956796805005721</A>]['05].

%A R. Hinze
%A R. Paterson
%T Finger trees: A simple general-purpose data structure
%J JFP
%V 16
%N 2
%P 197-217
%M MAR
%D 2006
%K jrnl, JFP, FP, c2006, c200x, c20xx, tree, sequence, priority queue
%X "...introduce 2-3 finger trees, a functional representation of persistent
   sequences supporting access to the ends in amortized constant time, &
   concat. & splitting in time log. in the size of the smaller piece. ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796805005769">doi:10.1017/S0956796805005769</A>]['06].

%A M. Erwig
%A R. Abraham
%A S. Kollmansberger
%T Gencel: A program generator for correct spreadsheets
%J JFP
%V 16
%N 3
%P 293-325
%M MAY
%D 2006
%M jrnl, JFP, FP, c2006, c200x, c20xx, spreadsheet, spread sheet, sheets
%X "A huge discrepancy between theory & practice exists in 1 popular applic.
   area of FP  - spreadsheets. Although s. are the most frequently used
   (functional) programs, they fall short of the quality level that is expected
   of FPs, which is evidenced by the fact that existing s. contain
   many errors, some of which have serious impacts. We have developed a
   template spec. lang. that allows the definition of s. templates that
   describe possible s. evolutions. This lang. is based on a table
   calculus that formally captures the process of creating & modifying
   s.. We have developed a type system for this calculus that can
   prevent type, reference, & omission errors from occurring in s..
   On the basis of the table calculus we have developed Gencel, a system for
   generating reliable s.. We have implemented a prototype version of
   Gencel as an extension of Excel."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796805005794">doi:10.1017/S0956796805005794</A>]['06].

%A R. B. Findler
%A M. Flatt
%T Slideshow: Functional presentations
%J JFP
%V 16
%N 4-5
%P 583-619
%M JUL-SEP
%D 2006
%K jrnl, JFP, FP, power point, powerpoint, c2006, c200x, c20xx, slide, slides,
   show, presentation, computer graphics, PLT Scheme, zz1106
%X "Among systems for creating slide presentations, the dominant ones offer
   essentially no abstraction capability. Slideshow represents our effort over
   the last several years to build an abstraction-friendly slide system with
   PLT Scheme. We show how functional programming is well suited to the task of
   slide creation, we report on the programming contructs that we have developed
   for slides, and we describe our solutions to practical problems in rendering
   slides. We also describe experimental extensions to DrScheme that support a
   mixture of programmatic and WYSIWYG slide creation."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796806006010">doi:10.1017/S0956796806006010</A>]['06].

%T Church's Thesis After 70 Years
%E A. Olszewski
%E J. Wolenski
%E R. Janusz
%I Ontos Mathematical Logic
%P 551
%D 2006
%K book, text, c2006, c200x, c20xx, lambda calculus, calculii, FP, computable,
   computability, Alonzo, Church, Church's, Churchs, thesis, computing, CSci
%X 2006; hb us$160; uk us isbn:3938793090; uk us isbn13:978-3938793091.
   "Church's Thesis (CT) was first published by Alonzo Church in 1935. CT is a
   proposition that identifies two notions: an intuitive notion of an
   effectively computable function defined in natural numbers with the notion of
   a recursive fn. Despite the many efforts of prominent scientists, CT has
   never been disproven. There exists a vast literature concerning the thesis.
   The aim of this book is to provide a one vol. summary of the state of
   research on [it]. These include the following: different formulations of CT,
   CT & intuitionism, CT & intensional mathematics, CT & physics, the epistemic
   status of CT, CT & philosophy of mind, provability of CT & CT & [FP]."
   [Also search for: Turner Church c2006].

%A D. Turner
%T Church's Thesis and Functional Programming
%J Church's Thesis After 70 Years
%E A. Olszewski et al
%P 518-544(?)
%D 2006
%K c2006, c200x, c20xx, Church, lambda calculus, FP
%X "The earliest statement of Church's Thesis, from Church (1936) p.356 is
   We now define the notion, already discussed, of an effectively calculable
   function of positive integers by identifying it with the notion of a
   recursive function of positive integers (or of a lambda-definable
   function of positive integers). ..."
   -- pdf@[<A HREF="http://www.cs.kent.ac.uk/people/staff/dat/miranda/ctfp.pdf">kent.uk</A>]['12].
   [Also search for: Church Thesis After 70 Years].
   (Also see [<A HREF="http://www.allisons.org/ll/FP/Lambda/">lambda</A>].)

%A S. Peyton Jones
%A D. Vytiniotis
%A S. Weirich
%A M. Shields
%T Practical type inference for arbitrary-rank types
%K JFP
%V 17
%N 1
%P 1-82
%M JAN
%D 2007
%K jrnl, JFP, c2007, c200x, c20xx, types, types, higher-rank, high, polymorphism
%X "... functions with higher-rank types - that is, functions that take
   polymorphic functions as their args.. Complete type inference is known to be
   undecidable for higher-rank (impredicative) type systems, but in practice
   programmers are more than willing to add type annotations to guide the type
   inference engine, & to document their code. ... We write the type-inference
   engine using a monadic framework: it turns out to be a particularly
   compelling example of monads in action. ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796806006034">doi:10.1017/S0956796806006034</A>]['07].

%A D. Wakeling
%T Spreadsheet functional programming
%J JFP
%V 17
%N 1
%P 131-143
%M JAN
%D 2007
%K jrnl, JFP, c2007, c200x, c20xx, spreadsheets, spread sheet, FP, JFP, zz0207,
   Haskell, Excel
%X "... making a standard spreadsheet, such as Excel, work with a standard
   FP language, such as Haskell. ... show one way that this can be done. ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796806006186">doi:10.1017/S0956796806006186</A>]['07].

%A G. Rossi
%A E. Panegai
%A E. Poleo
%T JSetL: A Java library for supporting declarative programming in Java
%J SPE
%V 37
%N 2
%P 115-149
%M FEB
%D 2007
%K jrnl, SPE, c2007, c200x, c20xx, zz0207, FP, LP, functional, logic,
   logical variable, constraint solving
%X "...logical variables, list & set data structures (possibly partially
   specified), unification & constraint solving over sets, non-determinism..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.749">doi:10.1002/spe.749</A>]['07].

%A G. Hutton
%T Programming in Haskell
%I CUP
%P 184
%D 2007
%K book, text, CUP, c2007, c200x, c20xx, FP, functional programming, language,
   L3ref, zz0507
%X 1. Introduction;       2. First steps;         3. Types and classes;
   4. Defining functions; 5. List comprehensions; 6. Recursive functions;
   7. Higher-order functions; 8. Functional parsers; 9. Interactive programs;
   10. Declaring types and classes; 11. The countdown problem;
   12. Lazy evaluation;             13. Reasoning about programs;
   1st ed 2007,   stg.24; uk us isbn:0521692695; uk us isbn13:978-0521692694.
   2nd ed 2016, pb us$41; uk us isbn:1316626229; uk us isbn13:978-1316626221.

%T Trends in Functional Programming (#7)
%E H. Nilsson
%I Intellect
%D 2007
%K symposium, proc, c2007, c200x, c20xx, FP
%X pb; uk us isbn:1841501883; uk us isbn13:978-1841501888.

%A R. Lammel
%T Google's MapReduce programming model - revisited
%J Sci. of Comp. Programming
%V 68
%N 3
%P 208-237
%M OCT
%D 2007
%K jrnl, SCP, FP, c2007, c200x, c20xx, mapReduce, MR, map reduce, google,
   googles, Sawzall
%X "Google's MapReduce ... serves for processing large data sets in a massively
   parallel manner. [we] ... 1st rigorous description of the model including its
   advancement as Google's domain-specific language Sawzall. ... reverse-
   -engineer ... an executable spec.. We also identify & resolve some
   obscurities ... [use] Haskell ... 3 components: (i) the basic program
   skeleton that underlies MapReduce computations; (ii) the opportunities for
   parallelism in executing MapReduce computations; (iii) the fundamental
   characteristics of Sawzall's aggregators as an advancement of the MapReduce
   approach. Our development does not formalize the more implementational
   aspects of an actual, distributed execution of MapReduce computations."
   -- [<A HREF="http://dx.doi.org/10.1016/j.scico.2007.07.001">doi:10.1016/j.scico.2007.07.001</A>]['09], and
   src & pdf@[<A HREF="http://www.cs.vu.nl/~ralf/MapReduce/">cs.vu.nl</A>]['09].
   [Also search for: mapReduce MR].

%A B. O'Sullivan
%A J. Goerzen
%A D. Stewart
%T Real World Haskell
%I OReilly
%P 300
%M AUG
%D 2008
%K book, text, c2008, c200x, c20xx, zz0408, functional programming, FP,
   practical, programs, application, applications, languages, declarative
%X 1st ed 2008; pb, stg22, us$50;
   uk us isbn:0596514980; uk us isbn13:978-0596514983.
   [Also search for: Haskell FP].

%A R. J. Ennals
%T Adaptive evaluation of non-strict programs
%I Uni. of Cambridge, Comp. Lab.
%R UCAM-CL-TR-730
%M AUG
%D 2008
%K TR, TR 730, TR730, c2008, c200x, c20xx, functional programming, FP,
   optimistic, speculative, non-strict evaluation, lazy
%X "TR based on a dissertation submitted June 2004 ... present a new evaluation
   strategy ... Optimistic Evaluation. OE blends lazy & eager evaln under the
   guidance of an online profiler. [It] observes the running program & decides
   which expressions should be evaluated lazily, & which should be evaluated
   eagerly. We show that the worst case performance of OE relative to Lazy
   Evaluation can be bounded with an upper bound chosen by the user. Increasing
   [it] allows the profiler to take greater risks & potentially achieve better
   average performance. ..."
   -- abs@[<A HREF="http://www.cl.cam.ac.uk/techreports/UCAM-CL-TR-730.html">cam</A>]['13],
      pdf@[<A HREF="http://www.cl.cam.ac.uk/techreports/UCAM-CL-TR-730.pdf">cam</A>]['13].
   [Also search for: FP non-strict evaluation].

%A Z. M. Ariola
%A H. Herbelin
%T Control reduction theories: the benefit of structural substitution
%J JFP
%V 18
%P 373-419
%M MAY
%D 2008
&K JFP, jrnl, FP, c2008, c200x, c20xx, theory, control mechanisms, jump, jumps,
   term, terms, call by value, Parigot
%X "The historical design of the call-by-value theory of control relies on the
   reification of evaluation contexts as regular functions and on the use of
   ordinary term application for jumping to a continuation. To the contrary,
   the control calculus, developed by the authors, distinguishes between jumps
   and terms. This alternative calculus, which derives from Parigot's
   lambda[...]-calculus, works by direct structural substitution of evaluation
   contexts. ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796807006612">doi:10.1017/S0956796807006612</A>]['08].

%A Y. Minsky
%A S. Weeks
%T Caml trading - experiences with functional programming on Wall Street
%J JFP
%V 18
%N 4
%P 553-564
%M JUL
%D 2008
%K jrnl, JFP, c2008, c200x, c20xx, zz0608, FP, OCaml finance, financial,
   trade, share, shares, stocks, trading
%X "Jane Street Capital is a successful proprietary trading company that uses
   OCaml as its primary development language. We have over twenty OCaml
   programmers and hundreds of thousands of lines of OCaml code. ... "
   -- [<A HREF="http://dx.doi.org/10.1017/S095679680800676X">doi:10.1017/S095679680800676X</A>]['08].

%A K. Donnelly
%A M. Fluet
%T Transactional events
%J JFP
%V 18
%P 649-706
%D 2008
%O 11th ACM SIGPLAN Int. Conf. on FP
%K jrnl, JFP, FP, c2008, c200x, c20xx, zz1208, concurrent, transaction, event,
   sequencing combinator, rendezvous
%X "Concurrent programs require high-level abstractions ... to manage complexity
   & enable compositional reasoning. ... introduce a novel concurrency
   abstraction, dubbed transactional events [ATE], which combines 1st-class
   synchronous message passing events with all-or-nothing transactions. ...
   e.g., guarded synchronous receive can be implemented as an ATE ...
   [and] 3-way rendezvous can be impl. as an ATE, which is impossible
   using 1st-class events alone. ... a sequencing combinator whose semantics
   enforces an all-or-nothing transactional property ... This ... with a
   non-deterministic choice combinator, gives transactional events the
   compositional structure of a monad-with-plus. ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796808006916">doi:10.1017/S0956796808006916</A>]['08].

%A J. M. Spivey
%T Algebras for combinatorial search
%J JFP
%V 19
%P 469-487
%M AUG
%D 2009
%K jrnl, JFP, c2009, c200x, c20xx, zz0809, depth first, breadth, bounded,
   search, combinatorial
%X "Combinatorial search strategies including depth-first, breadth-first and
   depth-bounded search are shown to be different implementations of a common
   algebraic specification that emphasizes the compositionality of the
   strategies. This specification is placed in a categorical setting that
   combines algebraic specifications and monads." (online June '09.)
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796809007321">doi:10.1017/S0956796809007321</A>]['09].

%A R. Hinze
%T The Bird tree
%J JFP
%V 19
%N 5
%P 491-508
%M SEP
%D 2009
%K jrnl, JFP, FP, c2009, c200x, c20xx, zz1009, Bird, tree, trees, Stern, Brocot,
   Calkin, Wilf circular, program, loopless, rational numbers, rationals,
   enumerate, enumeration
%X bird :: Tree Rational
   bird = Node 1 (1 / (bird+1)) ((1 / bird) + 1)
      where / and * are 'lifted' to Tree.
   The b.tree contains each positive rational number exactly once,
   as do the Stern-Brocot (Graham et al. 1994) & Calkin-Wilf trees
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796809990116">doi:10.1017/S0956796809990116</A>]['09], [12 refs].
   [Also search for: circular program FP].

%A R. Hinze
%T Purely functional 1-2 brother trees
%J JFP
%V 19
%P 633-644
%M NOV
%D 2009
%K jrnl, JFP, FP, c2009, c200x, c20xx, zz1109, brother, tree, trees, balanced,
   data structures
%X "... balanced search trees, 1-2 brother trees (Ottmann et al. '79), which
   deserves to be better known. Brother trees lend themselves well to a
   functional implementation with deletion as straightforward as insertion
   both running in logarithmic time. Furthermore, brother trees can be
   constructed from ordered lists in linear time ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796809007333">doi:10.1017/S0956796809007333</A>]['09].

%A T. Schrijvers
%A P. Stuckey
%A P. Wadler
%T Monadic constraint programming
%J JFP
%V 19
%P 663-697
%M NOV
%D 2009
%K jrnl, JFP, FP, c2009, c200x, c20xx, constraint programming, monad, monads
%X "A constraint programming system combines 2 essential components: a
   constraint solver & a search engine. The constraint solver reasons about
   satisfiability of conjunctions of constraints, & the search engine controls
   the search for solns by iteratively exploring a disjunctive search tree
   defined by the constraint program. ... give a monadic defn of CP in which the
   solver is defined as a monad threaded through the monadic search tree. We are
   then able to define search & search strategies as 1st-class objects that can
   themselves be built or extended by composable search transformers. Search
   transformers give a powerful & unifying approach to viewing search in
   CP, & the resulting CP system is first class & extremely flexible."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796809990086">doi:10.1017/S0956796809990086</A>]['09].

%A R. Bird
%T Pearls of Functional Algorithm Design
%I CUP
%P 295
%M OCT
%D 2010
%K book, text, CUP, c2010, c201x, zz1010, c20xx, FP, functional programming
%X "... sources as diverse as games & puzzles, intriguing combinatorial tasks,
   & more familiar areas such as d@ta compr'ssion & string matching. ..."
   1st ed 2010; hb us$48; uk us isbn:0521513383; uk us isbn13:978-0521513388.
   [Also search for: FP functional book].

%A R. S. Bird
%T Building a consensus: A rectangle covering problem
%J JFP
%V 21
%P 119-128
%D 2011
%K pearl, jrnl, JFP, FP, c2011, c201x, c20xx, zz0411, rectangle, covering,
   consensus, saturation, closure, Schafer, de Moor, deMoor,
   containment checking, cube, cubes
%X "... roughly speaking one is given a finite set of rectangles RS & a r. R
   completely covered by RS. The task is to construct a single rectangle
   covering R among the elts of a larger set of rectangles associated with RS,
   called the saturation of RS. The saturation of RS is the closure of RS under
   so-called consensus operations, a term coined in (Quine, 1959), in which two
   rectangles are combined in two distinct ways to form new rectangles. The
   rectangle problem is a simplified version of containment-checking, a crucial
   component in a type inference alg. for Datalog programs (Schafer & de Moor,
   2010). In the Schafer-de Moor alg. the problem is generalised to cubes in
   n-space rather than rectangles in 2-space, the components of each cube are
   given by propositional formulae rather than by intervals on the real line, &
   certain equality & inhabitation constraints are taken into account. Oege felt
   that the central proof, Lemma 15 in (Schafer & de Moor, 2010), deserved to be
   simplified so he posed the rectangle problem as a special case. This pearl
   was composed in response to the challenge."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796810000316">doi:10.1017/S0956796810000316</A>]['11].

%A S. Fischer
%A O. Kiselyov
%A C.-C. Shan
%T Purely functional lazy nondeterministic programming
%J JFP
%V 21
%N 4-5
%P 413-465
%M SEP
%D 2011
%K jrnl, JFP, c2011, c201x, c20xx, zz1111, FP, functional programming,
   nondeterminism, nondeterministic, choice, pure
%X "Functional logic programming and probabilistic programming have demo. the
   broad benefits of combining laziness (nonstrict evaln with sharing of the
   results) with nondeterminism. Yet these benefits are seldom enjoyed in
   FP because the existing features for nonstrictness, sharing, & nondet. in
   F.languages are tricky to combine. We present a practical way to write
   purely functional lazy nondeterministic programs that are efficient &
   perspicuous. We achieve this goal by embedding the programs into existing
   languages (such as Haskell, SML, & OCaml) with high-quality implementations,
   by making choices lazily & representing data with nondet. components, by
   working with custom monadic data types & search strategies, & by providing
   equational laws for the programmer to reason about their code."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796811000189">doi:10.1017/S0956796811000189</A>]['11].
   [Also search for: FP nondeterminism].

%A D. A. Turner
%T Some history of functional programming languages (invited talk)
%J 13th Int. Symp. on Trends in Functional Programming
%I SpringerVerlag
%S LNCS
%V 7829
%P 1-20
%D 2012
%K conf, TFP, c2012, c201x, c20xx, zz0916, DATurner, FP, functional programming,
   language, history, computing, laziness,
   lambda calculus, Lisp, Algol60, ISWIM, PAL, SASL, NPL, Hope, Miranda
%X "We study a series of milestones leading to the emergence of lazy, higher
   order, polymorphically typed, purely functional programming languages.
   (An invited lecture given at TFP12, St Andrews University, 12 June 2012.)"
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-40447-4_1">doi:10.1007/978-3-642-40447-4_1</A>]['16].

%A R. Bird
%T Thinking Functionally with Haskell
%I CUP
%P 354
%M DEC
%D 2014
%K book, text, c2014, c201x, c20xx, zz0315, FP, functional, programming,
   Haskell, computer, L1Ref, L2Ref
%X "... enables students to apply calculational reasoning to their programs,
   both to understand their properties and to make them more efficient. The book
   has been designed to fit a first- or second-year undergraduate course and is
   a thorough overhaul and replacement of his earlier textbooks. It features
   case studies in Sudoku and pretty-printing, and over 100 carefully selected
   exercises with solutions. ..."
   1st ed 2014; pb us$44; uk us isbn:1107452643; uk us isbn13:978-1107452640.
       2017(?!) hb us$86; uk us isbn:1107087201; uk us isbn13:978-1107087200.
   [Also search for: FP Haskell book].

%A D. Friedman
%A C. Eastlund
%I MITpress
%P 248
%M JUL
%D 2015
%K book, text, c2015, c201x, c20xx, zz0515, computer programming, proof,
   verification, FP, schemer, L2Ref, L3Ref
%X 1st ed 2015; pb us$30; uk us isbn: 0262527952; uk us isbn13:978-0262527958.
   "... inductive proofs as a way to determine facts about computer programs.
   ... assumes only knowledge of recursive programs & lists (as presented in
   the first three chapters of The Little Schemer) ..."

%A M. Avanzini
%A U. D. Lago
%A G. Moser
%T Analysing the complexity of functional programs: Higher-order meets
   first-order
%J arXiv
%M JUN
%D 2015
%O ICFP 2015 paper, long version
%K TR, ICFP, c2015, c201x, c20xx, zz0615, FP, time
%X "... the complexity of higher-order f.programs can be analysed automatically
   by applying program transformations to a defunctionalized versions of them,
   & feeding the result to existing tools for the complexity analysis of
   1st-order term rewrite systems. This is done while carefully analysing
   complexity preservation & reflection of the employed transformations s.t. the
   complexity of the obtained term rewrite system reflects on the complexity of
   the initial program. [&] describe suitable strategies for the appln of the
   studied transns & provide ample experimental data ..."
   -- 1506.05043@[<A HREF="http://arxiv.org/abs/1506.05043">arXiv</A>]['15].

%A K. Grygiel
%A P. Lescanne
%T Counting and generating terms in the binary lambda calculus
%J JFP
%V 25
%P e24 (29pp)
%M DEC
%D 2015
%K jrnl, JFP, c2015, c201x, c20xx, zz0116, FP, binary lambda calculus,
   generate, random terms
%X "In ... 'Binary lambda calculus and combinatory logic,' John Tromp presents
   a simple way of encoding lambda calculus terms as binary seqs. ... we study
   the #s of binary strings of a given size that represent lambda terms &
   derive results from their generating fns, esp. that the # of terms of size n
   grows roughly like 1.963447954^n. [&] we use this approach to generate random
   lambda terms using Boltzmann samplers."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796815000271">10.1017/S0956796815000271</A>]['16].

%A L. Fegeras
%T An algebra for distributed big data analytics
%J JFP
%V 27
%M DEC
%D 2017
%K jrnl, JFP, c2017, c201x, c20xx, zz0118, FP, functional programming, monoid,
   big, data analysis, MRQL, join, joins, parallel, query, queries, map reduce,
   mapReduce, Hadoop, Pregel, groupBy, orderBy, coGroup, cMap, collections
%X "... an algebra for data-intensive scalable computing based on monoid
   homomorphisms that consists of a small set of operations that capture most
   features supported by current domain-specific languages for data-centric
   distributed computing. This algebra is being used as the formal basis of
   MRQL, which is a query processing & optimization system for large-scale
   distributed data analysis. The MRQL semantics is given in terms of monoid
   comprehensions, which support group-by & order-by syntax & can work on
   heterogeneous collections without requiring any extension to the monoid
   algebra. We present the syntax & semantics of monoid comprehensions & provide
   rules to translate them to the monoid algebra. We give evidence of the
   effectiveness of our algebra by presenting some important optimization rules,
   such as converting nested queries to joins."
   -- [<A HREF="https://doi.org/10.1017/S0956796817000193">doi:10.1017/S0956796817000193</A>]['18].
   (*A 'monoid' has an associative binary operation & has an identity element.*)

%A D. Darais
%A D. van Horn
%T Constructive Galois connections
%J JFP
%V 29
%P e11
%M JUL
%D 2019
%K jrnl, eJrnl, FP, JFP. c2019, c201x, c20xx, zz0719, Galois connection,
   functional programming, language, semantics, proof, proofs, theorem proving,
   maths, assistant, abstract interpretation, gradual typing
%X "Galois connections are a foundational tool for structuring abstraction in
   semantics, and their use lies at the heart of the theory of abstract
   interpretation. Yet, mechanization of Galois connections using proof
   assistants remains limited to restricted modes of use ...  presents
   constructive G.connections, a variant of G.connections that is effective both
   on paper & in proof assistants ...  identify a restricted mode of use of
   classical GCs which is both general and amenable to mechanization in
   dependently typed functional programming languages. Crucial to our metatheory
   is the addition of monadic structure to GCs to control a 'specification
   effect.' Effectful calculations may reason classically, while pure
   calculations have extractable computational content. ...  provide two case
   studies in mechanizing existing proofs from the literature: the first uses
   calculational abstract interpretation to design a static analyzer, and the
   second forms a semantic basis for gradual typing. Both mechanized proofs
   closely follow their original paper-and-pencil counterparts, employ reasoning
   principles not captured by prev. mechanization approaches, support the
   extraction of verified algs., and are novel."
   -- [<A HREF=" https://doi.org/10.1017/S0956796819000066">doi:10.1017/S0956796819000066</A>]['19].
   Also see GC@[<A HREF="https://en.wikipedia.org/wiki/Galois_connection">wikip</A>]['19].
   [Also search for: maths proof assistant] and
   [also search for: theorem proving].

%A R. S. Bird
%T An optimal, purely functional implementation of the Garsia-Wachs algorithm
%J JFP
%V 30
%N e3
%M JAN
%D 2020
%K JFP, FP, c2020, c202x, c20xx, zz0220, Garsia Wachs algorithm,
   minimum cost binary tree, code, search trees, optimum
%X "The Garsia-Wachs alg. ... for building a binary leaf tree whose cost is as
   small as possible. ... described in more detail below, but the task is
   essentially the same as that of building a Huffman coding tree with the added
   constraint that the fringe of the tree has to be exactly the given list of
   inputs (in H.coding, the fringe of the tree can be any permutation of the
   input) ..."
   -- [<A HREF="https://doi.org/10.1017/S0956796819000194">doi:10.1017/S0956796819000194</A>]['20].
   [Also search for: Garsia Wachs algorithm].

%A J. D. Stone
%T Algorithms for Functional Programming
%I Springer
%P 265
%M FEB
%D 2020
%K book, text, c2020, c20x, c20xx, zz0820, algorithm, FP, Scheme, L2Ref, L3Ref
%X 1st ed 2018; hb us$55; uk us isbn:0387955704; uk us isbn13:978-0387955704.
   [Also search for: book FP algorithm].

%A M. Bendokowski
%T How to generate random lambda terms?
%J arXiv
%M MAY
%D 2020
%K TR, c2020, c202x, c20xx, zz0520, FP, lambda calculus, term, terms, random,
   test, testing, compiler, QuickCheck, survey
%X "We survey several methods of generating large random lambda-terms, focusing
   on their closed and simply-typed variants. We discuss methods of exact- and
   approximate-size generation, as well as methods of achieving size-uniform and
   non-uniform outcome distributions."
   -- 2005.08856@[<A HREF="https://arxiv.org/abs/2005.08856">arXiv</A>]['20].

%A R. Bird
%A J. Gibbons
%T Algorithm Design with Haskell
%I CUP
%P 450
%M SEP
%D 2020
%K book, text, c2020, c202x, c20xx, zz0620, zz0920, FP, Functional Programming,
   CUP, Haskell, computer programming, algorithms
%X 1st ed 2020; hb us$65; uk us isbn:1108491618; uk us isbn13:978-1108491617.
   "...devoted to five main principles of algorithm design: divide & conquer,
   greedy algorithms, thinning, dynamic programming, & exhaustive search. ..."
   [Also search for: FP Functional Programming].

%A T. Petricek
%T Composable data visualizations (a functional pearl)
%J JFP
%V 31
%M JUN
%D 2021
%K JFP, jrnl, FP, c2021, c202x, c20xx, zz1021, data, visualisation,
   visualization, Compost, compost.js
%X "Let's say we want to create the two charts in Fig.1. The chart on the left
   is a bar chart that shows two different values for each bar. The chart on the
   right consists of two line charts that share the x axis with parts of the
   timeline highlighted using two different colors. ..."
   -- [<A HREF="https://doi.org/10.1017/S0956796821000046">doi:10.1017/S0956796821000046</A>]['21].
   "... Compost is a plain JavaScript library. You use it by writing [js] code
   that generates a chart using some 15 basic Compost primitives."
   -- Compost@[<A HREF="https://compostjs.github.io/">g'thub</A>]['21].

%A R. Hinze
%A C. Runciman
%T Super-naturals
%J JFP
%M JAN
%D 2022
%K jrnl, JFP, FP, c2022, c202x, c20xx, zz0222, functional programming, lazy,
   evaluation, numbers, number system, natural, superNatural
%X "Functional programmers who enjoy working with lazy data structures sometimes
   wish numeric comp'ns were lazy too. ... [e.g.] length xs > 0 forces evaln of
   the entire spine of the list xs - a needless expense. ..."
   -- [<A HREF="https://doi.org/10.1017/S0956796822000028">doi:10.1017/S0956796822000028</A>]['22].
   [Also search for: FP numbers].

%A M. Hanus
%T From Logic to Functional Logic Programs
%J arXiv
%M MAY
%D 2022
%K TR, FP, LP, c2022, c202x, c20xx, zz0522, program
%X "LP is a flexible programming paradigm due to the use of predicates without
   a fixed data flow. To extend logic languages with the compact not'n of FP,
   there are various proposals to map evaluable fns into predicates in order to
   stay in the LP framework. Since amalgamated F+L languages offer flexible as
   well as efficient evaluation strategies, we propose an opposite approach ...
   By mapping logic programs into functional logic programs with a trans'n
   based on inferring functional dependencies, we develop a fully automatic
   transformation which keeps the flexibility of LP but can improve computations
   by reducing infinite search spaces to finite ones."
   -- 2205.06841@[<A HREF="https://arxiv.org/abs/2205.06841">arXiv</A>]['22].

%A J. T. Kristensen
%A R. Kaarsgaard
%A M. K. Thomsen
%T Jeopardy: An invertible functional programming language
%J arXiv
%M SEP
%D 2022
%O 34th Symp. on Impl. & Appl. of Func. Lang., 31 Aug - 2 Sep, 2022
%K TR, c2022, c202x, c20xx, zz0922, FP, Jeopardy, reversible, invertible,
   inverse, algorithm, program, computing, uninvertible
%X "... we introduce Jeopardy, a functional prog. lang. that guarantees program
   invertibility without imposing local reversibility. In particular, Jeopardy
   allows the limited use of uninvertible -- & even nondeterministic! --
   operations, provided that they are used in a way that can be statically
   determined to be invertible. However, guaranteeing invertibility is not
   obvious. Thus, we furthermore outline three approaches that can give a
   partial static guarantee."
   -- 2209.02422@[<A HREF="https://arxiv.org/abs/2209.02422">arXiv</A>]['22].

%A B. Ahrens
%A K. Wullaert
%T Category theory for programming
%J arXiv
%M SEP
%D 2022
%K TR, intro, notes, c2022, c202x, c20xx, zz0922, category theory, FP, type,
   types, datatype, monad, maths, algebra
%X "... a brief intro. to some elts of category theory. The choice of topics is
   guided by applications to [FP]. Firstly, we study initial algebras, which
   provide a math. characterization of datatypes & recursive fns on them.
   Secondly, we study monads, which give a math. framework for effects in
   F.langs.. The notes include many problems & solutions."
   -- 2209.01259@[<A HREF="https://arxiv.org/abs/2209.01259">arXiv</A>]['22].
   [Also search for: category theory].

%A S. Dash
%A Y. Kaddar
%A H. Paquet
%A S. Staton
%T Affine monads and lazy structures for Bayesian programming
%J arXiv
%M DEC
%D 2022
%O accepted for POPL 2023
%K TR, c2022, c202x, c20xx, zz1222, FP, probability, LazyPPL, AI, II, monad,
   measures, laziness
%X "We show that streams & lazy data structures are a natural idiom for
   programming with infinite-dimensional Bayesian methods such as Poisson
   processes, Gaussian ps., jump ps., Dirichlet ps., & Beta ps.. ... synthetic
   probability theory, is to work with two separate monads: an affine monad of
   probability, which supports laziness, & a commutative, non-affine monad of
   measures, which does not. (Affine means that T(1)~=1.) We show that the
   separation is important from a decidability perspective, & that the recent
   model of quasi-Borel spaces supports these two monads. To perform B.inference
   with these examples, we introduce new inference methods that are specially
   adapted to laziness; they are proven correct by reference to the
   Metropolis-Hastings-Green method. Our theor. development is implemented as a
   Haskell library, LazyPPL."
   -- 2212.07250@[<A HREF="https://arxiv.org/abs/2212.07250">arXiv</A>]['22].
   [Also search for: FP probability].

%A O. Danvy
%T Folding left and right matters: Direct style, accumulators, and continuations
%J JFP
%V 33
%N #e2
%M FEB
%D 2023
%K jrnl, JFP, c2023, c202x, c20xx, zz0323, FP, foldl, foldr, accumulator,
   continuation, tail recursion, programming
%X "The equivalence of folding left & right over Peano numbers & lists makes it
   possible to minimalistically inter-derive (1) structurally recursive fns in
   direct style, (2) structurally tail-recursive fns that use an accumulator, &
   (3) structurally tail-recursive fns in delimited continuation-passing style,
   using Ohori & Sasano's lightweight fusion by fixed-point promotion. ..."
   -- [<A HREF="https://doi.org/10.1017/S0956796822000156">doi:10.1017/S0956796822000156</A>]['23].
   [Also search for: FP continuation].

%A W. Swierstra
%T A correct-by-construction conversion from lambda calculus to
   combinatory logic
%J JFP
%V 33
%N e11
%D 2023
%K jrnl, JFP, c2023, c202x, c20xx, zz1223, FP, lambda calculus,
   combinatorial, combinatory logic, combinator, SKI, S K I
%X "This pearl defines a translation from well-typed lambda terms to combinatory
   logic, where both the preservation of types & the correctness of the
   translation are enforced statically."
   -- [<A HREF="https://doi.org/10.1017/S0956796823000084">doi:10.1017/S0956796823000084</A>]['23].
   [Also search for: FP combinatory logic]

%A J.-P. Bernardy
%A P. Jansson
%T Domain-specific tensor languages
%J arXiv
%M DEC
%D 2023
%K TR, c2023, c202x, c20xx, zz1223, FP, Haskell, tensor, tensors, programming,
   language, DSL, EDSL
%X "... that are currently in use for tensor algebra are either
   1. array-oriented languages that do not enforce or take advantage of tensor
   properties & algebraic structure or 2. follow the categorical structure of
   tensors but require the programmer to manipulate tensors in an unwieldy
   point-free not'n. ... We bridge the gap by defining a DSL, embedded in H.,
   whose syntax closely captures the index not'n for tensors in wide use in the
   literature. The semantics of this EDSL is defined in terms of the algebraic
   structures which define tensors in their full generality. ..."
   -- [<A HREF="https://arxiv.org/abs/2312.02664">arXiv:2312.02664</A>]['23].

%A C.Moy
%T Knuth-Morris-Pratt illustrated
%J JFP
%V 34
%N e3
%M JAN
%D 2024
%K FP, JFP, c2024, c202x, c20xx, zz0224, string, pattern matching, search
%X "... This paper constructs KMP incrementally, using pictures to illustrate
   each step. The end result is easier to comprehend. [&] the derivation uses
   only elementary FP techniques."
   -- [<A HREF="https://doi.org/10.1017/S0956796824000017">doi:10.1017/S0956796824000017</A>]['24].
   [Also search for: Knuth Morris Pratt string].


%A M. Feeley
%A M. Turcotte
%A G. Lapalme
%T Using Multilisp for Solving Constraint Satisfaction Problems:
   an Application to Nucleic Acid 3D Structure Determination
%J J. Lisp and Symbolic Computation
%V 7
%N 2/3
%P 231-247
%M ?
%D 1994
%K JLSC, MC-Sym, MC Sym, MolBio, functional programming, FP, multi Lisp,
   3-D, three dimensional, constraint
%X This software is an optimized variant of the MC-SYM system.
   This system computes the 3D shape of a piece of nucleic acid molecule
   given the sequence of nucleotides and a set of constraints to satisfy.
   It is mostly used by molecular biologists.   (16 refs)
   FTP from ftp.merl.com:/pub/LASC/nucleic.tar.Z
   email: feeley@iro.umontreal.ca
   via email: wadler@dcs.gla.ac.uk   (8/'94)

%A F. Major
%A G. Lapalme
%A R. Cedergren
%T Domain Generating Functions for Solving Constraint Satisfaction Problems
%J J. Functional Programming
%V 1
%N 2
%P 213-227
%D 1991
%K JFP, MC-Sym, MC Sym, MolBio, functional programming, FP,
   3-D, three dimensional, constraint
%X This software is an optimized variant of the MC-SYM system.
   This system computes the 3D shape of a piece of nucleic acid molecule
   given the sequence of nucleotides and a set of constraints to satisfy.
   It is mostly used by molecular biologists.
   FTP from ftp.merl.com:/pub/LASC/nucleic.tar.Z
   email: feeley@iro.umontreal.ca
 via: wadler@dcs.gla.ac.uk   (8/'94)

%A F. Major
%A M. Turcotte
%A D. Gautheret
%A G. Lapalme
%A E. Fillion
%A R. Cedergren
%T The Combination of Symbolic and Numerical Computation for Three-Dimensional
   Modeling of RNA
%J Science
%V 253
%P 1255-1260
%M Sept
%D 1991
%K MC-Sym, MC Sym, MolBio, functional programming, FP, constraint,
   3D, 3-D, three dimensional
%X This software is an optimized variant of the MC-SYM system.
   This system computes the 3D shape of a piece of nucleic acid molecule
   given the sequence of nucleotides and a set of constraints to satisfy.
   It is mostly used by molecular biologists.
   FTP from ftp.merl.com:/pub/LASC/nucleic.tar.Z
   email: feeley@iro.umontreal.ca
 via: wadler@dcs.gla.ac.uk   (8/'94).

%A W. deHoon
%T Designing a Spreadsheet in a Pure Functional Graph Rewriting Language
%I Department-of-Informatics, University-of-Nijmegen
%D 1993
%K spreadsheet, spread-sheet, functional programming, FP, application,
   Clean, MSc thesis, de Hoon
%X In Clean. The spreadsheet includes a Clean and a Miranda parser
   and evaluator, and cell entries can be arbitrary functions.
   via enews,  [also search for: deHoon 1995].

%A M. Wallace
%A C. Runciman
%T Extending a functional programming system for embedded applications
%J SPE
%V 25
%N 1
%P 73-96
%M JAN
%D 1995
%K jrnl, SPE, FP, Gofer, IO device handler, process, uniYork, application,
   marble, marbles, sorter, real-time programming, c1995, c199x, c19xx
%X auths at cs.york.ac.uk

%A W. de Hoon
%A L. Rutten
%A M. van Eekelen
%T Implementing a functional spreadsheet in Clean
%J J. of Functional Programming
%V 5
%N 3
%P 383-414
%M JUL
%D 1995
%K jrnl, deHoon, FP, JFP, spread-sheet, c1995, c199x, c19xx, zz0903
%X "It has been claimed that recent developments in the research on the
   efficiency of code generation and on graphical input/output interfacing
   have made it possible to use a functional language to write efficient
   programs that can compete with industrial applications written in a
   traditional imperative language. As one of the early steps in verifying
   this claim, this paper describes a first attempt to implement a spreadsheet
   in a lazy, purely functional language. ..."
   -- [<A HREF="http://www.dcs.gla.ac.uk/jfp/bibliography/References/hoonre1995:383.html">abs</A>][9/'03].

%A Weichang Du
%A W. W. Wadge
%T A 3D spreadsheet based on intensional logic
%J IEEE Software
%V ?
%P ?-?
%M MAY
%D 1990
%X via enews

%A Weichang Du
%A W. W. Wadge
%T The eductive implementation of a three-dimensional spreadsheet
%J SPE
%V ?
%P ?-?
%M NOV
%D 1990
%X via enews

%A P. B. Cragg
%A M. King
%T Spreadsheet modelling abuse: An opportunity for OR?
%J J. Opl. Res. Soc.
%V 44
%N 8
%P 743-752
%M AUG
%D 1993
%K JORS
%X via enews.

%A D. Jackson
%A E. J. Rollins
%T A new model of program dependences for reverse engineering
%J Proc. SIGSOFT Conf. on Foundations of Software Engineering
%W New Orleans
%P ?
%M DEC
%D 1994
%K ChopShop, ML, SML, functional programming, FP, application, SIGSOFT, conf
%X <A HREF="/afs/cs.cmu.edu/project/chopshop/pub/papers/fse94.ps">FSE94.ps</A>
   interprocedural dataflow analysis of C programs, analyzer written in SML
   Gene Rollins   email: rollins+@cs.cmu.edu  (2/'95)

%A D. Jackson
%A E. J. Rollins
%T Abstraction mechanisms for pictorial slicing
%J Proc. Workshop on Program Comprehension
%W Washington, DC
%P ?
%M NOV
%K ChopShop, ML, SML, functional programming, FP, application, conf
%D 1994
%X <A HREF="/afs/cs.cmu.edu/project/chopshop/pub/papers/wpc94.ps">WPC94.ps</A>
   interprocedural dataflow analysis of C programs, analyzer written in SML
   Gene Rollins   email: rollins+@cs cmu edu  (2/'95).

%A K. Hanna
%T Interactive visual functional programming
%J Proc. Int. Conf. on Functional Programming
%I ACM
%P 100-112
%M OCT
%D 2002
%K conf, functional, FP, visual, interactive, edit, live, spreadsheet, zz0903,
   stylesheet, spread-sheet, sheets, Haskell, Vital, Vital1, Vital2,
   Kent, c2002, c200x, c20xx
%X "Vital is a Haskell-based visual programming environment. It is particularly
   intended for supporting the open-ended, incremental development style often
   preferred by non-specialist users (engineers, scientists, analysts, etc.) in
   which successive steps of program development are motivated and informed by
   results so far obtained. In Vital, a Haskell module may be associated with
   a worksheet on which its declarations and expressions may be located and
   their values graphically displayed. The form such displays take is
   determined by a type-indexed stylesheet. The values may be unbounded in
   extent and are lazily evaluated to the required extent as the user moves
   the viewport around the worksheet. The environment embodies the principles
   of direct manipulation. In particular, it allows declarations to be edited
   by mouse gestures on the graphical representation of their values. For
   example, a user might create a data structure (perhaps a triangular array or
   a tree) by evaluating a function and then copy-and-paste values into its
   elements. All such changes are immediately reflected in the Haskell source
   code and hence in the values of any dependent declarations."
   ... a Java application ...
   -- [<A HREF="http://www.cs.kent.ac.uk/projects/vital/">vital</A>][9/'03].
   [Also search for: FP spreadsheet].


%A R. Milner
%T Synthesis of communicating behaviours
%J MFCS 7
%D 1978
%I SpringerVerlag
%S LNCS
%V 64
%P ?-?
%K LNCS64, MFCS, MFCS78, MFCS7, conf, CS, CSci, parallel, concurrent, theory,
   communication, message based, passing, synchronization, behaviour
%X see also LNCS 92, 1 9 8 0;
   also C.A.R.Ho@re CSP in C A C M  Aug  1 9 7 8.

%A R. Milner
%T A Calculus of Communicating Systems
%I SpringerVerlag
%S LNCS
%V 92
%D 1980
%K LNCS92, CCS, CSP, parallel, process, communication, theory, equivalence,
   congruence, observation, message, passing, book, text, c1980, c198x, c19xx
%X LA has (or had!); uk us isbn:0387102353.   See also LNCS 64, 1 9 7 8.
   (Also see
    [<A HREF="http://www.allisons.org/ll/FP/LambdaCCS/">L-CCS</A>],
    CCS@[<A HREF="https://en.wikipedia.org/wiki/Calculus_of_communicating_systems">wikip</A>]['18].)

%A C. A. R. Hoare
%T Communicating sequential processes
%J CACM
%V 21
%N 8
%P 666-677
%M AUG
%D 1978
%K jrnl, CACM, CSP, CCS, parallel, concurrent, message passing
%X [Also search for: CCS],
   and C.A.R.'s book on CSP '85.

%A C. A. R. Hoare
%T Communicating Sequential Processes
%I PrenticeHall
%S Series in Computer Science
%D 1985
%K text, book, CSP, CCS, parallel, process, communication, message passing
%X [Also search for: CCS],
   and Hoare C.A.C.M. Aug '78.

%A J. Madsen
%T An experiment in formal definition of operating system facilities
%J IPL
%V 6
%N 6
%P 187-189
%M NOV
%D 1977
%K semantics, IPL,  OS, OS/360,  OS-360,  OS360

%A M. J. C. Gordon
%T The denotational semantics of sequential machines
%J IPL
%V 10
%N 1
%M FEB
%D 1980
%P 1-3
%K automata, theory

%A M. Broy
%T Denotational semantics of a communicating processes based on
   a language for applicative multiprogramming
%V 17
%N 1
%J IPL
%M JUL
%D 1983
%P 29-35
%K CSP, IPL, parallel, message communication,  CCS, applicative,
   functional programming, concurrent, PFL, PFP

%A M. Broy
%T Semantics of communicating processes
%J Information and Control
%V 61
%N 3
%P 202-246
%M JUN
%D 1984
%K semantics, parallel, message, communication, process, theory, CCS, CSP,
   trace, behaviour
%X semantics of a simple language for describing tightly coupled synchronous
   systems is defined:
      skip, abort, action, sequence, nondeterministic choice, guarded choice,
      parallel composition, hiding actions, recursion
   Operational semantics given by rewrite rules.
   Abstract denotational semantics also given by observable behaviour
   and fixed points - traces.
   Properties of language analysed and algebraic laws discussed.
   Comparisons with other methods of definition.

%A M. Hennessy
%A R. Milner
%T Algebraic laws for nondeterminism and concurrency
%J JACM
%V 23
%N 1
%P 137-161
%M JAN
%D 1985
%K jrnl, JACM, communication, CSP, CCS, theory, equivalence, congruence
%X "Since a nondeterministic and concurrent program may, in general,
   communicate repeatedly with its environment, its meaning cannot be presented
   naturally as an input/output function (as is often done in the denotational
   approach to semantics). In this paper, an alternative is put forth. First, a
   definition is given of what it is for two programs or program parts to be
   equivalent for all observers; then two program parts are said to be
   observation congruent if they are, in all program contexts, equivalent. The
   behavior of a program part, that is, its meaning, is defined to be its
   observation congruence class. The paper demonstrates, for a sequence of
   simple languages expressing finite (terminating) behaviors, that in each
   case observation congruence can be axiomatized algebraically. Moreover, with
   the addition of recursion and another simple extension, the algebraic
   language described here becomes a calculus for writing and specifying
   concurrent programs and for proving their properties." --
   -- [<A HREF="http://doi.acm.org/10.1145/2455.2460">doi.acm.org/10.1145/2455.2460</A>][1/'04].

%A D. H. Grit
%A R. L. Page
%T Deleting irrelevant tasks in an expression oriented multiprocessor system
%J TOPLAS
%V 3
%N 1
%P 49-59
%M JAN
%D 1981
%K multiprocessor, kill,garbage collection, GC, applicative, functional,
   recursive, GC, recursion,  termination

%A D. Ron
%A F. Rosemberg
%A A. Pnueli
%T A hardware implementation of the CSP primitives and its verification
%I Dept Applied Maths, Weizmann Institute
%D 1984
%K CSP, CCS, hardware

%A S. D. Brookes
%T On the relationship of CCS and CSP
%B Automata, Languages and Programming
%S LNCS
%V 154
%I SpringerVerlag
%D 1983
%P 83-96
%K CCS, CSP, parallel, concurrent, communication

%A C. A. R. Hoare
%T Notes on CSP
%R 83-4
%I Dept. Computer Science, University of Wollongong
%M MAR
%D 1983
%K CSP, CCS, communication, parallel

%A T. I. Dix
%T Exceptions and interrupts in CSP
%J Science of Computer Programming
%V 3
%P 189-204
%D 1983
%K CSP, CCS, exception, interrupt, communication, parallel

%A J. C. Raoult
%T Properties of a notation for combining functions
%J JACM
%V 30
%N 3
%M JUL
%D 1983
%P 595-611
%K pipe, parallel, communication, functional, applicative, unix, shell
%O follows paper in
   9th International Colloqium on Automata Languages and Programming
   Aarrhus Denmark 1982.

%A J. Shultis
%T A functional shell
%P 202-211
%J Proc. Sigplan 83 Symposium on Programming Language Issues in
   Software Systems
%V 18
%N 6
%W San Francisco
%I A.C.M.
%D 1983
%K unix, shell, functional, applicative, command language
%X FP Backus

%A E. Astesiano
%A E. Zucca
%T Parametric channels via label expressions in CCS
%J Theoretical Computer Science
%V 33
%P 45-63
%D 1984
%K jrnl, TCS, parallel, concurrent, CCS, CSP, channel
%X ... extend CCS by allowing (channel-) label expressions. ...
   [9 refs].

%A K. R. Apt
%T Correctness proofs of distributed termination algorithms
%B Logics and Models of Concurrent Systems
%E K. R. Apt
%I SpringerVerlag
%D 1985
%K CSP, CCS, termination, proof, correctness

%A K. R. Apt
%T Correctness proofs of distributed termination algorithms
%J TOPLAS
%V 8
%N 3
%M JUL
%D 1986
%P 388-405
%K CSP, CCS, verification, proof, distributed, parallel
%X problem of correctness of solutions to distributed termination problem
   is addressed. Proof method developed applied to a solution to
   the problem. Reason about liveness properties of temporal logic
   using new notion of weak total correctness.

%A K. R. Apt
%A N. Francez
%T Modelling the distributed termination convention of CSP
%J TOPLAS
%M JUL
%D 1984
%V 6
%N 3
%P 370-379
%K CSP, CCS, termination

%A F. Baiardi
%A N. de Francesco
%A G. Vaglini
%T Development of a debugger for a concurrent language
%J IEEE Transactions on Software Engineering
%M APR
%D 1986
%V 12
%N 4
%P 547-553
%K debug, debugging, debugger, CCS, CSP, concurrent, parallel

%A L. Bouge
%T Repeated synchronous snapshots and their implementation in CSP
%B Automata, Languages and Programming
%S LNCS
%V 194
%I SpringerVerlag
%E W. Brauer
%D 1985
%K CSP, CCS, debug, debugging, snapshot

%A G. N. Buckley
%A A. Silberschatz
%T An effective implementation of the generalised input output construct
   in CSP
%J TOPLAS
%V 5
%N 2
%P 223-235
%M APR
%D 1983
%K CCS, CSP, message passing, input-output, input, output, parallel, concurrent

%A R. Francis
%A I. Mathieson
%T Language tools for exploring concurrency
%J 9th Australian Computer Science Conference
%W Canberra
%D 1986
%M JAN
%K ACSC, ACSC9, CCS, CSP, concurrent, parallel

%A J. Gait
%T A debugger for concurrent programs
%J SPE
%V 15
%N 6
%P 539-554
%M JUN
%D 1985
%K concurrent, parallel, debug, debugging, debugger

%A J. A. Bergstra
%A J. W. Klop
%T Algebra of communicating processes with abstraction
%J Theoretical Computer Science
%V 37
%P 77-121
%D 1985
%K jrnl, TCS, CCS, CSP, parallel, concurrent, acyclic process graph, ACP

%A J. Gait
%T A probe effect in concurrent programs
%J SPE
%V 16
%N 3
%P 225-233
%M MAR
%D 1986
%K concurrent, parallel, debug, debugger, debugging

%A E. R. Olderog
%A C. A. R. Hoare
%T Specification-oriented semantics for communicating processes
%J Acta Informatica
%V 23
%P 9-66
%D 1986
%K CSP, CCS, parallel, concurrent, specification, semantics

%A T. J. Roper
%A C. J. Barter
%T A communicating sequential process language and implementation
%J SPE
%V 11
%P 1215-1234
%D 1981
%K CSP, CCS, parallel, concurrent, implementation

%A E. T. Smith
%T A debugger for message based processes
%J SPE
%V 15
%N 11
%P 1073-1086
%M NOV
%D 1985
%K CSP, parallel, concurrent, message passing, debug, debugger, debugging

%A C. J. Fidge
%T Reproducible tests in CSP
%J 10th Australian Computer Science Conference
%W Geelong
%M JAN
%D 1987
%K ACSC, ACSC10, CSP, debug, debugger, debugging, trace, snapshot, parallel,
   concurrent, message, nondeterminism
%X The difficulty of testing and debugging CSP programs is compounded by their
   inherent non-determinism. We illustrate a simple approach to recording and
   replaying traces of the control paths followed as a means of controlling
   this unpredictability. Where these traces would become unmanageably long,
   a variant of Bouge's repeated snapshot algorithm is used to put an upper
   bound on trace length. Some knowledge of CSP is assumed.
   NB. CSP simulator written in Lisp.

%A R. H. Halstead
%T Multilisp: a language for concurrent symbolic computation
%J TOPLAS
%V 7
%N 4
%M OCT
%D 1985
%P 501-538
%K concurrent, parallel, lisp, functional, applicative, multilisp,
   multiprocessor, process, scheduler, scheduling, garbage collector, GC
%X multilisp on Concert, a 32 processor computer
   8 processors running at time of paper
   delay [exp]      expression not evaluated until needed, like lazy
   future [exp]     place holder can be used while [exp] eval'd in ||allel
   touch [exp]      forces exp's evaluation to finish
   pcall f a b c    f a b c evaluated in ||allel and then f called

%A S. Abramsky
%T Reasoning about concurrent systems
%B Distributed Computing
%I Chambers-Duce, academic press
%D 1984
%P 307-319
%O A simple proof theory for non-deterministic recursive programs
   Dept of Computer Science and Statistics
   Queen Mary College 1982
%K functional, applicative, parallel, concurrent, communication,
   network, process, model, theory

%A J. W. De Bakker
%A J. I. Zucker
%T Processes and the denotational semantics of concurrency
%J Information and Control
%V 1
%N 2
%P 153-158
%D 1982
%K CCS, CSP, process, processes, communicate, communication, communicating,
   message, semantics, theory

%A S. D. Brookes
%A C. A. R. Hoare
%A W. Roscoe
%T A theory of communicating sequential processes
%J JACM
%V 31
%N 3
%P 560-599
%D 1984
%K CSP, theory, semantics, communicating, sequential, process, processes,
   message, communicate

%A R. Milner
%T Lectures on a calculus for communicating systems
%B Seminar on Concurrency
%I SpringerVerlag
%S LNCS
%V 197
%P 197-220
%D 1985
%K CCS, CSP, communicating, communication, sequential, process, processes,
   parallel, concurrent, message passing

%A A. Salomma
%T Two complete axiom systems for the algebra of regular events
%J JACM
%V 13
%N 1
%P 158-169
%D 1966
%K axiom, axioms, algebra, theory, semantics, regular, event, events,
   trace, action, actions, parallel, communicate, communicating

%A P. Hudak
%A B. Goldberg
%T Serial Combinators : optimal grains of parallelism
%P 382-399
%B Functional Programming Languages and Computer Architecture
%I SpringerVerlag
%S LNCS
%V 201
%M SEP
%D 1985
%E J. P. Jouannaud
%K functional, applicative, language,  combinator, parallel, multiprocessor
%X translates functional program into combinators suitable for execution on
   a multiprocessor with no shared memory. Argues granularity of a fixed
   set of combinators is too fine; of user defined functions is too coarse.
   serial combinator introduced, optimal granularity in some sense.
   Simulation results given.

%A V. J. Bush
%A J. R. Gurd
%T Transforming recursive programs for execution on parallel machines
%P 350-367
%B Functional Programming Languages and Computer Architecture
%I SpringerVerlag
%S LNCS
%V 201
%M SEP
%D 1985
%E J. P. Jouannaud
%K transformation, optimise, optimize,  functional, applicative, programming,
   parallel, multiprocessor,  dataflow, data flow,
   linear recursion, binary recursion,  FP
%X equivalent linear and binary recursive schema schemata
   binary one gives fan out good for many processors,    e.g.,:
      let fact n = f n 1
         where rec f n m = if n .le. m then m
                           else let mid = (n+m)div 2   -- n .gt. mid .ge. m
                                in  (f n (mid+1))*(f mid m)   -- binary rec
   suggest choice linear / binary form can be dynamic on number of
   free processors.
   There are examples with functions on lists too, and discussion
   of space time usage.
   Transformation not always applicable.
   Given in Backus FP and therefore programs hard to read.

%A R. H. Campbell
%A A. N. Habermann
%T The specification of process synchronization by path expressions
%B Operating Systems, Proc.
%W Rocquencourt, France
%M APR
%D 1974
%E E. Gelenbe
%E C. Kaiser
%I SpringerVerlag
%S LNCS
%V 16
%P 89-102
%K path expression,  synchronise, synchronize,  communication, message,
   parallel

%A M. Broy
%T Nondeterministic data flow programs: how to avoid the merge anomaly
%J Science of Computer Programming
%V 10
%D 1988
%P 65-85
%K nondeterminism, CSP, CCS, parallel, process, message, communication,
   merge anomaly,  denotational semantics
%X simple prog lang for networks of loosely coupled,
   communicating nondeterministic agents. two possible graphical
   interpretations are discussed: finite cyclic and infinite
   acyclic tree-like graphs. Operational semantics.
   Merge anomally described etc.
   Two fixed-point semantics given, one avoids merge anomaly
   other includes it.  They are proved consistent with the
   respective operational definitions.

%A N. Francez
%T Distributed termination
%J TOPLAS
%V 2
%N 1
%M JAN
%D 1980
%P 42-55
%K concurrent program, parallel, distributed process, communication,
   message passing, termination,
   CSP, CCS

%A R. Milner
%T A modal characterisation of observable machine behaviour
%B Trees and Algebra in Programming; 6th CAAP
%I SpringerVerlag
%S LNCS
%V 112
%M MAR
%D 1981
%E E. Astesiano
%E C. Bohm
%P 25-34
%K CCS, observation equivalence, modal logic
%X properties of machines that can be ascertained from a finite experiment.
   seeking machine equivalence.
   particularly interested in divergence.

%A K. R. Apt
%A C. Delporte-Gallet
%T Syntax directed analysis of liveness properties of while programs
%J Information and Control
%V 68
%N 1-3
%M Jan-May
%D 1986
%P 223-253
%K live, liveness, while program

%A K. R. Apt
%T Limits for automatic verification of finite state concurrent systems
%J IPL
%V 22
%N 6
%P 307-309
%M MAY
%D 1986
%K temporal logic, proof, liveness, safety, CCS, CSP
%X previous results on programs are not extendable to program schema

%A M. Hennessy
%T Proving systolic systems correct
%J TOPLAS
%V 8
%N 3
%M JUL
%D 1986
%P 344-387
%K CCS, verification, proof, parallel, concurrent system
%X a language for describing communicating systems is described.
   can define desired behaviours, their specifications, and implementations.
   proof techniques for    I satisfies S
   based on syntactic transformations and induction.
   examples: palindrome recogniser, and a sort machine

%A K. L. Wrench
%T CSP-i: an implementation of communicating sequential processes
%J SPE
%B 18
%N 6
%M JUN
%D 1988
%K SPE, jrnl, CSP, CSPi, communication, parallel, message passing, language,
   implementation

%A L. Lamport
%T Solved problems, unsolved problems and non-problems in concurrency
%J 3rd PODC Conference Proceedings
%I ACM
%D 1984
%P 34-44
%K synchronization, mutual exclusion, producer consumer, concurrent,
   semaphore, message
%X entertaining
   Invited address

%A L. Lamport
%T A fast mutual exclusion algorithm
%I Digital Systems Research Centre
%C Palo Alto, California
%R 7
%M NOV
%D 1985
%O ACM Trans. Comput. Sys. 15(1) p1-11 Feb 1987 has same title.
%K synchronization, mutual exclusion, critical region, lock, locks, parallel,
   concurrent
%X connecting processors with shared memory without test and set
   and without inhibiting interrupts
   just need atomic read and write.
   IF contention does not happen then 5 instructions to enter CR and 2
   to leave it, independent of number of processors.
 Algorithm for process number i:
   start: b[i]:=true;                 {was false}
          x:=i;                       {x, y shared}
          if y .ne. 0 then b[i]:=false; {contention}
                       await y=0
                       goto start fi;
          y:=i;
          if x .ne. i then b[i]:=false;   {contention}
                       for j:=1 to N do await not b[j] od; {check all out of CR}
                       if y .ne. i then await y=0;
                                      goto start fi
          fi;
          critical section;
          y:=0;
          b[i]:=false

%A R. Milner
%T Communication and Concurrency
%I PrenticeHall
%D 1989
%K CSP, CCS, communication, channel, process, parallel, message passing,
   text, book, pi calculus, piCalculus, c1989, c198x, c19xx
%X uk us isbn:0131150073.
   [Also search for: CCS], and for CSP.
   (Also see CCS@[<A HREF="https://en.wikipedia.org/wiki/Calculus_of_communicating_systems">wikip</A>]['18].)

%A K. Hammond
%T Parallel SML: a functional language and its implementation in Dactl
%I PitmanPress
%M DEC
%D 1990
%K ML, SML, DACTL, functional language, implementation, parallel, concurrent
   book, UEA
%Z Published version of PhD thesis -- much more detail on Dactl, with a
   simple introduction and several (largish) examples, including a
   parallel type-inference engine.
   K. Hammond Implementing functional languages for parallel machines
   PhD thesis University of East Anglia '88.

%E I. Guessarian
%T Semantics of Systems of Concurrent Processes
%I SpringerVerlag
%S LNCS
%V 469
%D 1990
%O Proc. LITP Spring Summer School in Theoretical Computer Science.
%K LNCS 469, LNCS469, LITP, CCS, CSP, concurrent, parallel, process,
   trace, traces

%A J. H. Reppy
%T CML: A higher concurrent language
%J PLDI
%P 293-305
%M JUN
%D 1991
%K conf, PLDI, CML, concurrent ML, parallel, FP, PFP, c1991, c199x, c19xx,
   programming, zz0904
%X [<A HREF="http://doi.acm.org/10.1145/113445.113470">pp.pdf@doi.acm.org/10.1145/113445.113470</A>]['04].

%A R. Milner
%T The Polyadic pi-Calculus: A Tutorial
%I LFCS, U. Edinb.
%D 1991
%O in 'Logic and Algebra of Specification', SpringerVerlag, 1993
%K TR, c1991, c199x, c19xx, zz0218, FP, PFP, parallel, concurrent,
   naming, replication, commitment, bisimilarity,
   pi calculus, piCalculus, polyadic
%X "The pi-calculus is a model of concurrent computation based upon the
   notion of naming. It is first presented in its simplest and original form,
   with the help of several illustrative applications. Then it is generalized
   from monadic to polyadic form. Semantics is done in terms of both a reduction
   system and a version of labelled transitions called commitment; the known
   algebraic axiomatization of strong bisimilarity is given in the new setting,
   and so also is a characterization in modal logic. Some theorems about the
   replication operator are proved. Justification for the polyadic form is
   provided by the concepts of sort and sorting which it supports. Several
   illustrations of different sortings are given. One example is the
   presentation of data structures as processes which respect a particular
   sorting; another is the sorting for a known translation of the l-calculus
   into pi-calculus. For this translation, the equational validity of
   fi-conversion is proved with the help of repli..."
   -- TR@[<A HREF="http://www.lfcs.inf.ed.ac.uk/reports/91/ECS-LFCS-91-180/">ed.ac.au</A>]['18].
   [Also search for: piCalculus].

%A G. Aharoni
%A D. G. Feitelson
%A A. Barak
%T A run-time algorithm for managing the granularity of parallel functional
   programs
%J J. of Functional Programming
%D to appear
%V ??
%N ??
%P ???-???
%K JFP, jrnl, FP, functional applicative programming language, implementation,
   concurrent, parallel, multi multiprocessor, fine, grain, granularity
%X Department of Computer Science, The Hebrew University of Jerusalem,
   Jerusalem 91904, Israel,
   contact: gadi at cs.huji.ac.il
 via enews Nov 92.

%A M. Boreale
%A R. De Nicola
%T Testing equivalences for mobile processes
%J Proc. CONCUR '92
%I SpringerVerlag
%S LNCS
%V 630
%P 2-16
%D 1992
%K parallel concurrent model theory semantics, pi calculus piCalculus,
   process, CCS CSP, deNicola
%X via Michael Baldamus  baldamus at cs.tu-berlin.de
       Technical University of Berlin, Germany.

%E H. Kuchen
%E R. Loogen
%J Proceedings of the 4th International Workshop on the Parallel
   Implementation of Functional Languages
%D 1992 ???
%I RWTH Aachen, Germany
%K parallel, concurrent, multiprocessor, functional, applicative, programming,
   language, FP, PFP, PFL, PIFL
%X From: ad at dcs.st-and.ac.uk (Tony Davie)
   Organization: St.Andrews University     Feb '93.

%A C. Lin
%A L. Snyder
%T A comparison of programming models for shared memory multiprocessors
%J Proc. Int. Conf. on Parallel Programming
%V 2
%P 163-170
%D 1990
%K functional, applicative, programming, parallel, concurrent, multi-processor,
   process, FP, PFP, PFL
%X ... preliminary evidence is presented suggesting that the non-shared
   programming memory model is actually better for shared memory machines than
   the shared memory model.

%A J. H. Reppy
%T High Order Concurrency
%I Dept. Comp. Sci. Cornell University
%M JUN
%D 1992
%K functional, applicative, programming, parallel, concurrent, multi-processor,
   process, PhD thesis, FP, PFP, PFL, CML, synchronous communication

%A J. H. Reppy
%T CML: a higher-order concurrent language
%J ACM SIGPLAN '91 Conf. on Programming Language Design and Implementation
%V 26
%N 6
%M JUN
%D 1991
%P 293-305
%K functional, applicative programming language, ML, CML, FP, PFP, PFL,
   PLDI, high order, parallel, concurrent, process, thread, threads,
   synchronous communication

%A C. D. Krumvieda
%T DML: packaging high-level distributed abstractions in SML
%J Proc. 3rd Int. Workshop on Standard ML
%E R. Harper
%P ???-???
%M SEP
%D 1991
%W Carnegie Mellon University
%K functional, applicative, programming, parallel, concurrent, multi-processor,
   process, ML, DML, SML, FP, PFP, PFL, CMU, asynchronous communication

%A R. Milner
%T Elements of interaction
%J CACM
%V 36
%N 1
%P 78-89
%M JAN
%D 1993
%K jrnl, cacm, CCS, pi calculus, piCalculus, parallel, concurrent, interact,
   process, lambda, c1993, c199x, c19xx, TuringAward
%X TuringAward lecture -- [<A HREF="http://doi.acm.org/10.1145/151233.151240">doi:doi.acm.org/10.1145/151233.151240</A>][1/'04].
   "... So in the Scott-Strachey [denotational semantics] approach, the meaning
   of an imperative program lies in the domain given by the equation
   (Program Meanings = Memories -> Memories) ...
   with nondeterminism in mind we can redefine the meanings of programs as
   (Program Meanings = Memories -> P(Memories)) ...
   But concurrency has a shock in store ..."
   [Also search for: CCS]  and  [also search for: piCalculus].

%A P. Bailey
%A M. Newey
%T An extension of ML for distributed memory multiprocessors
%J Proc. 16th Australian Computer Science Conference
%V 15
%N 1
%P 387-396
%M FEB
%D 1993
%K functional, applicative, programming, parallel, concurrent, multi-processor,
   process, paraML, ML, SML, FP, PFP, PFL, AP1000, c1993, c199x, c19xx,
   ACSC 16 ACSC16
%X channels, processes, buffered

%A R. Milner
%T Functions as processes
%B Automata, Languages and Programming (17th Int. Coll.)
%I SpringerVerlag
%S LNCS
%V 443
%P 167-180
%M JUL
%D 1990
%W Warwick Uni., UK
%O Functions as processes, Math. Structs. in Comp. Sci., 2(2),
   pp.119-141, June 1992
%K ICALP, ICALP17, ICALP90, c1992, c1990, c199x, c19xx, functional programming,
   concurrent, parallel, process, theory, PFL, CCS, CSP, pi calculus, piCalculus
%X Shows that lazy evaluation and strict evaluation
   of (ordinary) lambda calculus can be coded in the pi-calculus...
   "... exhibits accurate encodings of the lambda-calculus in the pi-calculus.
   The former is canonical for calculation with fns, while the latter is a
   recent step (Milner et al. 1989) towards a canonical treatment of concurrent
   processes. With quite simple encodings, two l-calculus reduction strategies
   are simulated very closely; each reduction in l-calculus is mimicked by a
   short seq. of redns in pi-calculus. Abramsky's precongruence of applicative
   bisimulation (Abramsky 1989) over l-calculus is compared with that induced by
   the encoding of the lazy l-calculus into pi-calculus; a similar comparison is
   made for call-by-value l-calculus."
   -- [<A HREF="https://doi.org/10.1017/S0960129500001407">doi:10.1017/S0960129500001407</A>]['18].
   [Also search for: piCalculus].
   (Also see [<A HREF="http://www.allisons.org/ll/FP/LambdaCCS/">L-CCS</A>].)

%A R. Milner
%A J. Parrow
%A D. Walker
%T A calculus of mobile processes, parts I and II
%J Information and Computation
%M SEP
%D 1992
%P 1-40 & 41-77
%O Tech' rep's LFCS-89-85 and LFCS-89-86
%K jrnl, IC, functional programming, concurrent, parallel, process, theory,
   PFL, CCS, CSP, pi calculus, piCalculus
%X also look for  CCS  and for  CSP in the bib'y
   [<A HREF="http://www.lfcs.inf.ed.ac.uk/reports/89/ECS-LFCS-89-85/">pt-1</A>]['07],
   [<A HREF="http://www.lfcs.inf.ed.ac.uk/reports/89/ECS-LFCS-89-86/">pt-2</A>]['07].

%A R. Milner
%T The polyadic pi-calculus: a tutorial
%B Logic and Algebra of Specification
%E F. L. Bauer
%E W. Brauer
%E H. Schwichtenberg
%I SpringerVerlag
%P 203-246
%D 1993
%K parallel, concurrent, process, theory, CCS, pi calculus, piCalculus,
   FP, PFL, zz0396
%X uk us isbn:3-540-55813-6.

%A F. Nielson
%T The typed lambda-calculus with first-class processes
%J PARLE '89 Parallel Architectures and Languages Europe Vol 2
%W Eindhoven
%P 357-373
%M JUN
%D 1989
%I SpringerVerlag
%S LNCS
%V 366
%K PARLE, PARLE89, LNCS366, lambda calculus, process, concurrent, parallel,
   datatype, type, types, check, checking, port, channel, CCS, CSP, PFL
%X type of a process is the set of its I/O possibilities (formalised).
   21 refs
   Hargrave lib' 004.35 C748/89 Vol2

%A R. Cooper
%A C. Krumvieda
%T Distributed Programming with Asynchronous Order Channels in Distributed ML
%J Proceedings of the ACM SIGPLAN Workshop on ML and its Applications
%W San Francisco, California
%M JUN
%P 134-148
%D 1992
%K sigplan, ML, SML, DML, FP, functional programming, parallel,
   concurrent, process, PFL, asynchronous, communication, channel, port
%X via Peter Bailey  peterb at cs.anu.edu.au  23/4/93

%A S. Leinwand
%A J. A. Goguen
%A T. Winkler
%T Cell and ensemble architecture for the rewrite rule machine
%J Proc. 5th Int. Conf. on Fifth Generation Computer Systems, Vol 3.
%I SpringerVerlag
%D 1988
%P 869-878
%K RRM, FP, functional programming, parallel, concurrent, architecture,
   term rewriting, ICOT
%X Hargrave lib' H 004. I61.7/88 Vol 3

%A J. Cupitt
%T Another New Scheme for Writing Functional Operating Systems
%W UKC Computing Laboratory, University of Kent, Canterbury,
%R 52
%D 1988
%K KAOS, OS, FP, functional programming, KRC

%A J. Cupitt
%T A Brief Walk Through KAOS
%W University of Kent at Canterbury Computing Laboratory
%R 58
%D 1989
%K KAOS, operating system OS, functional programming, FP

%A J. Cupitt
%T The Design and Implementation of an Operating System in a Functional
   Language
%W Computing Laboratory, University of Kent Canterbury, Kent
%D 1990
%K KAOS, functional programming, FP, operating system OS, PhD Thesis

%A Kent Karlsson
%T Nebula: A Functional Operating System
%R Programming Methodology Group Memo LPM11
%I Laboratory for Programming Methodology, Chalmers University of Technology,
   Goteborg
%D 1981
%K OS, functional programming, FP, PRG

%A A. D. Gordon
%T An operational semantics for I/O in a lazy functional language
%J Functional Programming and Computer Architecture 93
%P 136-145
%M JUN
%D 1993
%W Copenhagen
%K c1993, c199x, c19xx, FPCA, FPCA93, functional programming, FP, IO,
   input output
%X [Also search for: Gordon FP IO].

%A R. M. Burstall
%A R. J. Popplestone
%T The POP-2 Reference Manual
%J Machine Intelligence
%V 2
%P 205-246
%D 1968
%E E. Dale
%E D. Michie
%I Oliver and Boyd, Edinburgh, Scotland.
%K POP, POP2, POP-2

%A S. Prasad
%T Towards a Symmetric Integration of Concurrent and Functional Programming
%I Department of Computer Science, SUNY Stony Brook, NY.
%M DEC
%D 1991
%K PhD thesis, functional programming language, FP,
   ML, SML, parallel, concurrent, Facile
%X via Sanjiva Prasad  E-mail: sanjiva at ecrc.de  '93

%A S. Prasad
%A A. Giacalone
%A P. Mishra
%T Operational and algebraic semantics of Facile:
   A symmetric integration of concurrent and functional programming
%B Proceedings of the 17th International Colloquium on
   Automata, Languages and Programming (ICALP'90)
%S LNCS
%V 443
%I SpringerVerlag
%M JUL
%D 1990
%P 765-780
%K functional programming language, FP, ML, SML, parallel, concurrent,
   Facile, ICALP, ICALP90, ICALP17
%X via Sanjiva Prasad  E-mail: sanjiva at ecrc.de  '93

%A M. Hennessy
%T Algebraic Theory of Processes
%I MITpress
%D 1988
%K text, book, CCS, CSP, process, agent, algebra, parallel, concurrent,
   interaction, message, communication, equivalence

%A W. Schreiner
%T Parallel Functional Programming --- An Annotated Bibliography
%R TR 93-24
%I RISC-Linz, Johannes Kepler University, Linz, Austria
%M MAY
%D 1993
%K parallel, concurrent, multiprocessor, multi-processor, multi, strict, lazy,
   lenient, strictness analysis, functional programming, FP, PFP, PFL,
   bibliography, survey, RISC Linz, TR93-24, TR24, 93 24
%X via enews Oct 93.
   You can retrieve the paper by anonymous ftp from ftp.risc.uni-linz.ac.at
   (193.170.36.100) in pub/reports/parlab/pfpbib.dvi.Z (or pfpbib.ps.Z).
   The bibliography lists 350 publications mostly including full abstracts.
      Wolfgang Schreiner
      Research Institute for Symbolic Computation (RISC-Linz)
      Johannes Kepler University, A-4040 Linz, Austria
      From: schreine at risc.uni-linz.ac.at (Wolfgang Schreiner)
      Tel: +43 7236 3231 66  Fax: +43 7236 3231 30

%A B. K. Szymanski
%T Parallel Functional Languages and Compilers
%I ACM Press, NY
%P 414
%D 1991
%K text, book, applicative programming, language, implementation, FP,
   concurrent, Lucid, EPL, Sisal, Haskell, Id, Crystal, PTRAN
%X us$45.25; us isbn:0-201-52243-8.

%A B. C. Pierce
%A D. N. Turner
%T Pict: A programming language based on the pi-calculus
%R CSCI-476
%I Indiana U.
%M MAR
%D 1997
%O pp.?-?, Proof, Language and Interaction: Essays in Honour of Robin Milner,
   G.Plotkin, C.Stirling, M.Tofte, MITpress, 2000, isbn:0262161885.
%K TR 476, TR476, CSCI476, FP, PFP, CCS, zz0903, parallel, concurrent,
   pi calculus, piCalculus, type, data types,
   c1997, c199x, c19xx,  programming language definition, PLD
%X "The π-calculus ... concurrent programming. ... familiar type systems
   for the λ-calculus have direct counterparts in the π-calculus,
   ... strong static typing ... Pict, a strongly-typed concurrent prog' lang'
   [based on] an explicitly-type π-calculus core language."
   [<A HREF="http://www.cis.upenn.edu/~bcpierce/papers/pict-design.ps">pict-design.ps, i.e. TR476</A>]['04]
   [<A HREF="http://www.cis.upenn.edu/~bcpierce/papers/pict/Html/Pict.html">Pict page</A>]['04]
   B.C.P., at [<A HREF="http://www.cis.upenn.edu/~bcpierce/">upenn</A>]['04], was at Indiana, and at Camb'.U.

%E K. Hammond
%E G. Michaelson
%T Research Directions in Parallel Functional Programming
%I SpringerVerlag
%M NOV
%D 1999
%K book, text, FP, PFP, concurrent, ML, BSP, strict, proof, verification,
   data parallelism, dataflow, distributed, Clean, zz0802
%X ppb. uk us isbn:1852330929.
  Part I - Fundamentals
   Introduction, Foundations, Programming Language Constructs, Proof,
   Realisations for Strict Languages, Realisations for Non-Strict Languages
  Part II - Current Research Areas
   Data Parallelism, Cost Modelling, Shaping Distributions, Performance
   Monitoring, Memory Performance of Dataflow Programs, Portability of
   Performance in the BSP Model, Algorithmic Skeletons, Coordination Languages,
   Parallel and Distributed Programming in Concurrent Clean, Functional Process
   Modelling, Validating Programs in Concurrent ML, Explicit Parallelism
  Part III - Conclusions
   Large Scale Functional Applications, Summary, References, Glossary, Index

%A J. H. Reppy
%T Concurrent Programming in ML
%I CUP
%P 324
%M AUG
%D 1999
%K book, text, CML, parallel, ML, SML, c1999, c199x, c19xx, FP, PFP, CUP,
   programming language definition, PLD, zz0904
%X "Concurrent Programming ML (CML), included as part of the SML of [NJ] (SML/
   NJ) distribution, combines the best features of concurrent programming &
   [FP]. ... book focuses on the use of concurrency to implement naturally
   concurrent applications. In addition to a tutorial introduction to
   programming in CML, the book presents 3 extended examples using CML for
   practical systems programming: a parallel software build system, a simple
   concurrent window manager, & an implementation of distributed tuple spaces.
   This book also illustrates advanced SML programming techniques, & includes a
   chapter on the implementation of concurrency using features provided by the
   SML/NJ system. ...".
   hb; uk us isbn:0521480892; uk us isbn13:978-0521480895.
   [<A HREF="http://people.cs.uchicago.edu/~jhr/">auth</A>]['04].

%A J. Christiansen
%A F. Huch
%T Searching for deadlocks while debugging concurrent Haskell programs
%J ACM Int. Conf. Functional Programming
%P 28-39
%D 2004
%K conf, FP, c2004, c200x, c20xx, zz0106, program, deadlock, debug, parallel,
   forkIO, monad, thread, debugger, CHD, ICFP
%X "... approach to searching for deadlocks in Concurrent Haskell programs. The
   search is based on a redefinition of the IO monad which allows the reversal
   of Concurrent H's concurrency primitives. ... possible to implement this
   search by a backtracking alg. checking all possible schedules of the system.
   ... integrated in the Concurrent Haskell Debugger (CHD), & auto. searches for
   deadlocks in the background while debugging. ... easy to use & the small
   modifications of the source program are done by a preprocessor. In the tool
   we use iterative deepening as search strategy which quickly detects deadlocks
   close to the actual sys. configuration & utilizes idle time during debugging
   at the best."  [21 refs]
   [<A HREF="http://10.1145/1016850.1016858">doi:10.1145/1016850.1016858</A>]['06].

%A R. Loogen
%A Y. Ortega-Mallen
%A R. Pena-Mari
%T Parallel functional programming in Eden
%J J. of Functional Programming
%V 15
%N 3
%P 431-475
%M MAY
%D 2005
%K jrnl, JFP, c2005, c200x, c20xx, FP, PFP, concurrent
%X "... constructs to control parallel evaluation of processes. Although
   processes are defined explicitly, communication & synchronisation issues are
   handled in a way transparent to the programmer. ... override the inherently
   sequential demand-driven (lazy) evaluation strategy of its computation
   language Haskell. ... three case studies ..."
   [<A HREF="http://dx.doi.org/10.1017/S0956796805005526">doi:10.1017/S0956796805005526</A>]['05]
   [also search for: PFP].

%A S. J. Gay
%A M. J. Hole
%T Subtyping for session types in the Pi calculus
%J Acta Informatica
%V 42
%N 2-3
%P 191-225
%D 2005
%K jrnl, c2006, c200x, c20xx, Honda, FP, PFP, parallel, concurrent, type,
   checking, programming, subtype, sessions, communication, uniGlasgow,
   pi calculus, client-server protocol
%X "Extending the pi calculus with the session types proposed by Honda et al.
   allows high-level specifications of structured patterns of communication,
   such as client-server protocols, to be expressed as types & verified by
   static typechecking. We define a notion of subtyping for session types,
   which allows protocol specifications to be extended in order to describe
   richer behaviour; for example, an implemented server can be refined without
   invalidating type-correctness of an overall system. We formalize the syntax,
   operational semantics & typing rules of an extended pi calculus, prove that
   typability guarantees absence of run-time communication errors, & show that
   the typing rules can be transformed into a practical typechecking algorithm."
   [<A HREF="http://dx.doi.org/10.1007/s00236-005-0177-z">doi:10.1007/s00236-005-0177-z</A>]['06], "Malcolm Hole died on 28th February 2004,
   a few weeks after the original submission of this paper."
   [<A HREF="http://www.dcs.gla.ac.uk/publications/paperdetails.cfm?id=7950">abs</A>]['06], auth1 @ U. Glasgow.

%T Advanced Topics in Bisimulation and Coinduction
%E D. Sangiorgi
%E J. Rutten
%I CUP
%S Cambridge Tracts in Theor. Comp. Sci.
%P 340
%M NOV
%D 2011
%K book, text, CUP, c2011, c201x, c20xx, zz0112, L4Ref, L5Ref, pfp, process,
   processes, bisumulation, proof, verification, behaviour, theory, CSci
%X 1st ed 2011; hb us$92; uk us isbn:1107004977; uk us isbn13:978-1107004979.
   "Coinduction is a method for specifying and reasoning about infinite data
   types and automata with infinite behaviour. In recent years, it has come to
   play an ever more important role in the theory of computing. It is studied in
   many disciplines, including process theory and concurrency, modal logic and
   automata theory ..."
   [Also search for: PFP process].

%A S. Marlow
%T Parallel and Concurrent Programming in Haskell: Techniques for Multicore and
   Multithreaded Programming
%I OReillyMedia
%P 322
%M AUG
%D 2013
%K book, text, c2013, c201x, c20xx, zz0713, parallel, concurrent, programming,
   functional, FP, thread, threads, multi threaded, multicore, Haskell,
   par Monad, Repa, Accelerate, GPU
%X 1st ed 2013; pb us$33; uk us isbn:1449335942; uk us isbn13:978-1449335946.
   "... the language's many APIs and frameworks for writing both parallel and
   concurrent programs. ... learn how parallelism exploits multicore processors
   to speed up computation-heavy programs, and how concurrency enables you to
   write programs with threads for multiple interactions. ..."

%A K. C. Sivaramakrishnan
%A L. Ziarek
%A S. Jagannathan
%T MultiMLton: A multicore-aware runtime for standard ML
%J JFP
%V ?
%P 1-62
%N NOV
%D 2014
%K jrnl, JFP, c2014, c201x, c20xx, zz1214, ML, SML, MLton, MultiMLton, ACML,
   concurrent ML, threads, implementation, compiler, multi core, cores,
   parallel, concurrency, Azul Vega, SCC
%X "MultiMLton is an extension of the MLton compiler & runtime sys. that targets
   scalable, multicore architectures. It provides specific support for ACML, a
   derivative of Concurrent ML that allows for the constrn of composable
   asynchronous events. To effectively manage asynchrony, we require the runtime
   to efficiently handle potentially large #s of lightweight, short-lived
   threads, many of which are created specifically to deal with the implicit
   concurrency intro. by asynchronous events. ... & provide experimental results
   over a range of parallel benchmarks & different multicore architectures inc.
   an 864 core Azul Vega 3, & a 48 core non-coherent Intel SCC (Single-Cloud
   Computer), that justify our design decisions."  [online 12/14].
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796814000161">doi:10.1017/S0956796814000161</A>]['14].

%A J. Berthold
%A H.-W. Loidl
%A K. Hammond
%T PAEAN: Portable and scalable runtime support for parallel Haskell dialects
%J JFP
%V 26
%N ?
%P e10 (39pp)
%M JUL
%D 2016
%K jrnl, FP, PFP, c2016, c201x, c20xx, zz0716, parallel, concurrent, Haskell,
   memory, distributed, GHC, PAEAN, GpH, Eden, EdI, HdPH, DpH, ParMonad
%X "... What is needed is an easy way to abstract over the implementation &
   hardware levels, while presenting a simple parallelism model to the
   programmer. The PArallEl shAred Nothing runtime system design aims to provide
   a portable & high-level shared-nothing implementation platform for parallel
   Haskell dialects. It abstracts over major issues such as work distribution &
   data serialisation, consolidating existing, successful designs into a single
   framework. It also provides an optional virtual shared-memory programming
   abstraction for (possibly) shared-nothing parallel machines, such as modern
   multicore/manycore architectures or cluster/cloud computing systems. It
   builds on, unifies & extends, existing well-developed support for
   shared-memory parallelism that is provided by the widely used GHC Haskell
   compiler. This paper summarises the state-of-the-art in shared-nothing
   parallel Haskell implementations, introduces the PArallEl shAred Nothing
   abstractions, shows how they can be used to implement three distinct
   parallel Haskell dialects, & demonstrates that good scalability can be
   obtained on recent parallel machines."  [online 7/'16.]
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796816000010">doi:10.1017/S0956796816000010</A>]['16].

%A K. Pruiksma
%A F. Pfenning
%T Back to futures
%J JFP
%V 32
#N e6
%M FEB
%D 2022
%K jrnl, JFP, PFP, c2022, c202x, c20xx, zz0322, linear futures, adjoint logic,
   parallel, concurrent, concurrency, programming language, Seax, fork, join
%X "... starting with a concurrent language based on a Curry-Howard interp'n of
   adjoint logic, to which we add three atomic primitives that allow us to
   encode sequential composition & various forms of synchronization. ...
   allowing us to encode futures, fork/join parallelism, & monadic concurrency
   in the same framework. ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796822000016">doi:10.1017/S0956796822000016</A>]['22] (online 28/2/2022).
   [Also search for: PFP language].

%A A. R. Bendixen
%A B. B. Bojesen
%A H. Huttel
%A S. Lybech
%T A generic type system for higher-order psi-calculi
%J arXiv
%M SEP
%D 2022
%O pp.43-59, Proc. Combined 29th Int. Workshop on Expressiveness in Concurrency
   & 19th Workshop on Structural Operational Semantics (EXPRESS/SOS) 2022
   [<A HREF="https://dx.doi.org/10.4204/EPTCS.368.3">www</A>]['22]
%K TR, c2022, c202x, c20xx, zz0922, FP, PFP, pi, psi calculus, HOpsi, CHOCS,
   piCalculus, psiCalculus, type, types
%X "The Higher-Order psi-calculus framework (HOpsi) is a generalisation of many
   first- & higher-order extensions of the pi-calculus. It was proposed by
   Parrow et al. who showed that higher-order calculi such as HOpi & CHOCS can
   be expressed as HOpsi-calculi. In this paper we present a generic type system
   for HOpsi-calculi ..."
   -- 2209.02354@[<A HREF="https://arxiv.org/abs/2209.02354">arXiv</A>]['22].
   [Also search for: piCalculus] and [also search for: psiCalculus].


%A M. Dekking
%T Recurrent sets
%J Adv. in Math.
%V 44
%P 78-104
%D 1982
%K fractals, fractal, space filling curve, curves

%A M. Dekking
%A M. Mendes France
%A A. van der Poorten
%T FOLDS!
%J Math. Intell.
%P 130-138
%P 173-195
%D 1982
%K fractals, fractal, space filling curve, curves

%A S. Eilenberg
%T Automata, languages, and machines, Volume A
%I AcademicPress
%D 1974
%K fractals, fractal, space filling curve, curves

%A D. Hilbert
%T Uber die stetige Abbildung einer Linie auf ein Flachenstuck
%J Math. Annalen
%V 38
%P 459-460
%D 1891
%K jrnl, c1891, c189x, c18xx, fractals, fractal, space filling curve, curves

%A B. B. Mandelbrot
%T The Fractal Geometry of Nature
%I W. H. Freeman
%P 468
%D 1983
%K book, text, c1983, c198x, c19xx, fractals, fractal, space filling curve,
   curves, dimension, set, graphics
%X 1st ed 1983; hb us$34; uk us isbn:0716711869; uk us isbn13:978-0716711865.

%A E. H. Moore
%T On certain crinkly curves
%I Trans. Am. Math. Soc.
%P 72-90
%D 1900
%K jrnl, c1900, c190x, c19xx, fractals, fractal, space filling curve, curves

%A G. Peano
%T Sur une courbe, qui remplit toute une aire plane
%J Math. Annalen
%D 1890
%P 157-160
%K jrnl, c1890, c189x, c18xx, fractals, fractal, space filling curve, curves

%A O. Salon
%T Automates en plusieurs dimensions
%J to appear ?
%K fractals, fractal, space filling curve, curves

%A W. Sierpinski
%T Sur une courbe cantorienne qui contient
   une image biunivoque et continue de toute courbe donnee
%J Comptes Rendus Acad. Sci., Paris
%V 162
%P 629-632
%D 1916
%O ? Oeuvres Choisies, Tome II, pp.107-119 ?
%K jrnl, c1916, c191x, c19xx, carpet, fractals, fractal, space filling curve,
   curves

%A W. Sierpinski
%T Sur une nouvelle courbe continue qui remplit toute une aire plane
%J Oeuvres Choisies, Tome II
%P 52-66
%D 1916+/-
%K fractals, fractal, space filling curve, curves

%A R. Siromoney
%A K. G. Subramanian
%T Space-filling curves and infinite graphs
%B Graph-grammars and their application to computer science
%S Lecture Notes in Computer Science V153
%I SpringerVerlag
%P 380-391
%D 1983
%K LNCS 153, fractals, fractal, space filling curve, curves

%A S. M. Casey
%T Formulating fractals
%J Computer Language
%V 4
%N 4
%P 28-40
%M Apr
%D 1987
%K fractals, fractal, space filling curve, curves

%A A. J. Cole
%T A note on space filling curves
%J SPE
%V 13
%D 1983
%P 1181-1189
%K fractals, fractal, space filling curve, curves

%A A. J. Fisher
%T A new algorithm for generating Hilbert curves
%J SPE
%V 16
%P 5-12
%D 1986
%K fractals, fractal, space filling curve, curves

%A L. M. Goldschlager
%T Short algorithms for space-filling curves
%J SPE
%V 11
%P 99-100
%D 1981
%K jrnl, SPE, c1981, c198x, c19xx,fractals, fractal, space filling curve,
   curves

%A A. Null
%T Space-filling curves, or how to waste time with a plotter
%J SPE
%V 1
%P 403-410
%D 1971
%K fractals, fractal, space filling curve, curves

%A J. A. B. Palmer
%T A Fortran procedure for drawing some space-filling curves
%J SPE
%V 16
%P 559-574
%D 1986
%K fractals, fractal, space filling curve, curves

%A N. Wirth
%T Algorithms + data structures = programs
%I PrenticeHall
%D 1976
%K text, book, c1976, c197x, c19xx, good, L2Ref, Pascal, fractals, fractal,
   dataStructure, DS, space filling curve, curves
%X Good general book on important algorithms and DS.
   uk us isbn:0130224189; uk us isbn13:978-0130224187.

%A I. H. Witten
%A B. Wyvill
%T On the generation and use of space-filling curves
%J SPE
%V 13
%P 519-525
%D 1983
%K fractals, fractal, space filling curve, curves

%A A. K. Dewdney
%T Computer recreations
%J Scientific American
%M Aug
%P 8-14
%D 1985
%K fractals, fractal, Mandelbrot set, strange, attractor
%X z:=c{a complex number}; count:=0;
   while |z| <= 2 and count < 2000 do
   begin z:=z^2+c; count+:=1
   end
   if does not diverge in limit then in the set (black)
   else plot colour dependent on the size of count.

%A A. Blumer
%A A. Ehrenfeucht
%A D. Hassler
%A M. Warmuth
%T Classifying learnable geometric concepts with Vapnick-Chervonenkis dimension
%J ACM Symposium on Theory of Computing
%N 18
%P 273-282
%D 1986
%K ACM TC, inductive inference, concept, class, learn, complexity

%A L. G. Valiant
%T A theory of the learnable
%J CACM
%V 27
%N 11
%P 1134-1142
%M Nov
%D 1984
%K learn, learning, class, concept, inductive inference, complexity

%A W. Buntine
%T A critique of the Valiant model
%J IJCAI-89
%D 1989
%K ijcai, IJCAI, inductive logic, noise free

%A L. G. Valiant
%T Deductive learning
%J Phil. Trans. Royal Soc. Series A
%V 312
%P 441-446
%D 1984
%K deductive, learn, concept, boolean functions

%A Michael F. Barnsley
%A Arnaud Jacquin
%A Francois Malassenet
%A Laurie Reuter
%A Alan D. Sloan
%T Harnessing Chaos for Image Synthesis
%J Computer Graphics
%V 22
%N 4
%P 131-140
%M AUG
%D 1988
%K fractal, image, data, compression, CG, IP
%X via enews:
   The paper says "We introduce two new IFS[Iterated Function
      Systems]-based algorithms.  The first one, the Collage algorithm, is a
      geometric modeling tool for interactively finding iterated funciton
      system codes.  The second one is called the Measure Rendering
      algorithm.  It applies chaotic dynamics to the computation of the
      geometry and texture of IFS encode images."
   However, the detailed description of the Collage "algorithm" says that
   it requires human input for each image, so it isn't an algorithm, at
   least according to the way I understand the term.  I feel that the
   abstract of this paper is very misleading.

%A A. E. Jacquin
%T A Novel Fractal Block-Coding Technique for Digital images
%J IEEE ICASSP
%P 2225-2228
%D 1990
%V 4
%K IP, block code coding, fractal, data, image, processing, compression
%X via enews: madler@pooh.caltech.edu
   says details thin cos of $'s!

%A M. F. Barnsley
%A J. H. Elton
%T A new class of Markov processes for image encoding
%J J. Appl. Prob.
%D ????
%V ??
%P ???-???
%K image compression, processing, IP, Markov, process, model, fractal
%X a ref says 1985 and also `to appear' in the J

%A M. F. Barnsley
%A A. D. Sloan
%T Image Compression
%J J. Appl. & Comp. Math.
%D ????
%V ??
%P ???-???
%K image compression, processing, IP, fractal
%X as of 1991 it was to appear in the J

%E J. L. Encarnacao
%E H. -O. Peitgen
%E G. Sakas
%E G. Englert
%T Fractal Geometry and Computer Graphics
%I SpringerVerlag
%M JUL
%D 1992
%K text, book, fractal, fractals, geometry, graphics, CG,
   image processing, analysis, IP

%A M.F. Barnsley
%A A. D. Sloan
%T A better way to compress images
%J BYTE
%P 215-223
%M JAN
%D 1988
%K fractal, image processing, IP, compression
%X via enews

%A A. E. Jacquin
%T A novel fractal block-coding technique for digital images
%J IEEE Int. Conf. on Acoustics, Speech & Signal Process.
%P ???-???
%M ???
%D 1990
%K fractal, image processing, IP, compression
%X via enews

%E D. G. Green
%E T. J. Bossomaier
%T Complex Systems: From Biology to Computation
%I IOS Press, Amsterdam
%D 1993
%K c1993, c199x, c19xx, Alife, complex systems, chaos, fractal, fractals
%X uk us isbn:90 5199 117 7.
          Life: Natural and Artificial                                  ..   1
 Paulien Hogeweg
  As large as life and twice as natural: Bioinformatics
  and the artificial life paradigm                                      ..   2
 Doug Seeley and Simon Ronald
  The emergence of connectivity and fractal time in the
  evolution of random digraphs                                          ..  12
 David Green
  Emergent behaviour in biological systems                              ..  24
 John Watterson
  The wave-cluster model of water-protein interactions                  ..  36
 Paul-Michael Agapow
  Computer viruses: the inevitability of evolution?                     ..  46
 Tony Roberts and Mark Knackstedt
  Pattern formation in physical and biological growth                   ..  55
 Ann Preece and Craig Johnson
  Recovery of model coral communities: complex behaviour from
  parameters operating at different spatial scales                      ..  69
 Pedro Paulo Balbi de Oliveira
  Methodological issues within a framework to support a
  class of artificial life worlds in cellular automata                  ..  82
 Zoran Aleksic
  Computation in inhomogeneous cellular automata                        ..  97
          Fractals, Chaos and Non-linear Dynamics                       .. 105
 Neville Fletcher
  Nonlinear dynamics and chaos in musical instruments                   .. 106
 Jon McCormack
  Interactive evolution of L-system grammars for computer
  graphics modelling                                                    .. 118
 Mark Knackstedt and Muhammad Sahimi
  The effect of premeability heterogeneity on viscous fingers
  in porous media                                                       .. 131
 Jacques Blanc-Talon
  Recognition and generation of fractal patterns by using
  syntactic techniques                                                  .. 141
 Dominique Luzeaux
  From beta-expansions to chaos and fractals                            .. 153
 Keith Tognetti and Graham Winley
  The uniform emergence of points on a circle                           .. 162
 Margot Lyon
  Complexity and emergence: the seduction and reduction of
  non-linear models in the social sciences                              .. 173
 JeanPierre Paillet
  Steps to an ecology of form                                           .. 181
 Thomas Kirk and Gwidon W. Stachowiak
  Fractal computer inage analysis of particle morphology                .. 193
          Information and control                                       .. 209
 Kit Dampney, Michael S.J. Johnson and Paul Deuble
  Taming large complex information systems                              .. 210
 Clive Cooper
  Complexity in C3I systems                                             .. 223
 Andrew Finegan
  Soft systems methodology: an alternative approach to knowledge
  elicitation onm complex and poorly defined systems                    .. 232
 George M. Bryan and Wayne E. Moore
  A self-organizing load balancing system                               .. 242
 Tim Payne
  Central fusion of sensor information using reasoned feedback          .. 248
 Patrick Fu and John P. Barford
  Reduction of modelling error of complex biosystems by an AI approach  .. 260
          Emergent Computation: Natural and Artificial                  .. 271
 Geoffrey Fox
  Advances in parallel computing                                        .. 272
 Hong Xie
  Parallel algorithms for the distance embedding problem                .. 288
 Abdesselam Bouzerdoum
  Convergence of symmetric shunting competitive neural networks         .. 301
 Jonathon Baxter
  The evolution of learning algorithms for artificial neural networks   .. 313
 David Howard and William Moran
  Self-annealing when learning a markov random field image model        .. 327
 Tony Burkitt
  External inputs to attractor neural networks                          .. 341
 David Cake
  Computer simulation of plasticity in the primary motor cortex         .. 351
 Terry Bossomaier, Jevan Pipitone and Geoff Stuart
  Neural dynamics in biological visual information processing           .. 361


%A J. Horn
%A D. E. Goldberg
%A K. Deb
%T Long path problems
%P 149-158
%B Parallel Problem Solving from Nature -
   PPSN III, Int. Conf. on Evolutionary Computation, Proc.
%E Y. Davidor
%E H.-P. Schwefel
%E R. Maenner
%I SpringerVerlag
%S LNCS
%V 866
%D 1994
%K genetic algorithm, GA
%X <A HREF="ftp://GAL4.GE.UIUC.EDU:/pub/papers/Publications/Horn/LongPath.PPSN94.ps.Z">FTP (12/'94)</A>
   Jeffrey Horn,  email: jeffhorn OF uiuc.edu  (12/'94)

%A H. G. Cobb
%A J. J. Grefenstette
%T Genetic algorithms for tracking changing environments
%J Genetic Algorithms: Proc. Fifth Int. Conf.
%W San Mateo
%I MorganKaufmann
%P 523-530
%D 1993
%K ICGA93, ICGA5, ICGA, GA, computing
%X via John Grefenstette <!-- email: gref OF aic.nrl.navy.mil --> (12/'94)

%A J. J. Grefenstette
%T Genetic algorithms for changing environments
%J Proc. Parallel Problem Solving from Nature-2
%E R. Maenner
%E B. Manderick
%I North-Holland
%P 137-144
%D 1992
%K GA, computing
%X via John Grefenstette <!-- email: gref OF aic.nrl.navy.mil --> (12/'94)

%A J. M. Fitzpatrick
%A J. J. Grefenstette
%T Genetic algorithms in noisy environments
%J Machine Learning
%V 3
%N 2-3
%P 101-120
%D 1988
%K noise
%X via John Grefenstette <!-- email: gref OF aic.nrl.navy.mil --> (12/'94)

%A D. Fogel
%T Evolutionary Computation: Toward a New Philosophy of Machine Intelligence
%I IEEE
%D 1995
%K book, text, evolutionary computing, CSci, genetic algorithm GA, AI
%X the inspiration, philosophy, history, mathematics,
   actualizations, and perspectives of evolutionary computation, including
   genetic algorithms, evolution strategies, and evolutionary programming.
   isbn:0-7803-1048-0.
   email: fogel OF sunshine.ucsd.edu (Fogel  1/'95)

%A A. Colorni
%A M. Dorigo
%A V. Maniezzo
%T Genetic Algorithms and Highly Constrained Problems. The time-table case
%J Parallel Problem Solving From Nature - Proc. of the 1st Workshop, PPSN 1
%I SpringerVerlag
%S LNCS
%V ?
%P 55-59
%D 1991
%K GA, conf, time table, timetable, tabling, problem
%X via: Andrew Hawken  a.hawken OF qmw.ac.uk   [4/'95]

%A P. K. Tsang
%A T. Warwick
%T Applying Genetic Algorithms to Constraint Satisfaction Optimization Problems
%J Proc. of the 9th European Conf. on Artificial Intelligence.
%P 649-654
%I Pitman
%D 1990
%K GA, ECAI, ECAI9, ECAI90, CSP
%X via: Andrew Hawken  a.hawken OF qmw.ac.uk   [4/'95]

%A L. Davis
%A S. Coombs
%T Genetic Algorithms and Communication Link Speed Design. Constraints and
   Operators
%J Proc. of the 2nd Int. Conf. on Genetic Algorithms.
%P 256-260
%I Lawrence Erlbaum Associates
%D 1988 ?
%K GA
%X via: Andrew Hawken  a.hawken OF qmw.ac.uk   [4/'95]

%A W. Siedlecki
%A J. Sklandsky
%T Constrained Genetic Optimization via Dynamic Reward-Penalty Balancing and
   Its Use in Pattern Recognition
%J Proc. of the 3rd Int. Conf. on Genetic Algorithms
%W George Mason University
%I MorganKaufman
%D 1989
%P ?-?
%K GA, algorithm, PR, image processing IP
%X via: Andrew Hawken  a.hawken OF qmw.ac.uk   [4/'95]

%A A. Homaifar
%A C. Qi
%A S. Lai
%T Constrainted Optimization Via Genetic Algorithms
%J Simulation
%V 62
%N 4
%P 242-253
%M APR
%D 1994
%K GA, jrnl, constraint, CSP
%X via: Andrew Hawken  a.hawken OF qmw.ac.uk   [4/'95]

%A P. M. Pardalos
%A J. B. Rosen
%T Constrained Global Optimization: Algorithms and Applications
%S LNCS
%V 268
%I SpringerVerlag
%D 1987
%P ?
%X via: Andrew Hawken  a.hawken OF qmw.ac.uk   [4/'95]

%A C. A. Floudas
%A P. M. Pardalos
%T A Collection of Test Problems for Constrained Global Optimization Algorithms
%I SpringerVerlag
%S LNCS
%V 455
%D 1990
%K constraint, GA
%P ?
%X via: Andrew Hawken  a.hawken OF qmw.ac.uk   [4/'95]

%A Z. Michalewicz
%A C. Janikow
%T Handling Constraints in Genetic Algorithms
%J Proc. of the 4th Int. Conf. on Genetic Algorithms
%P 151-157
%I MorganKaufman
%D 1991
%K GA, constraint, CSP
%X via: Andrew Hawken  a.hawken OF qmw.ac.uk   [4/'95]

%A J. T. Richardson
%A M. R. Palmer
%A G. Liepina
%A M. Hilliard
%T Some Guidlines for Genetic Algorithms with Penalty Functions
%J Proc. of the 3rd Int. Conf. on Genetic Algorithms
%W George Mason University
%I MorganKaufman
%P ?-?
%D 1989
%K GA
%X via: Andrew Hawken  a.hawken OF qmw.ac.uk   [4/'95]

%A J. H. Holland
%T Adaption in Natural and Artificial Systems
%I MITpress
%D 1992
%K genetic algorithm, GA, book, text

%A J. Holland
%T Hidden Order: How Adaptation Builds Complexity
%I AddisonWesley
%D 1995
%K complex systems, computing, book, text, zz0895
%X isbn:0-201-40793-0; US$24.00, 185pp
   - Ted Belding <!-- Ted.Belding OF umich.edu --> [8/95]

%A T. Baeck
%T Evolutionary Algorithms in Theory and Practice
%I OUP
%P 327
%M SEP
%D 1995
%K book, text, AI, EA, GA, computing, zz1095
%X Part I: Comparison of Evolutionary Algorithms
      1. Organic evolution and problem solving
      2. Specific evolutionary algorithms
      3. Artificial landscapes    4. An empirical comparison
   Part II: Extending Genetic Algorithms
      5. Selection                6. Mutation
      7. An experiment in meta-evolution
   isbn:0-19-509971-0; US $48.00/$38.40 (discount until December 31st)
   - Thomas Baeck (email: baeck OF home.informatik.uni-dortmund.de) [10/95]

%E A. V. Sebald
%E L. J. Fogel
%T Proceedings of the 3rd Annual Conference on Evolutionary Programming
%I WorldScientific
%D 1994
%K Proc, conf, EP, EP3, EP95, AI, computing, zz1195
%X isbn:981-02-1810-9;   in Hargrave

%A X. Yao
%T Evolutionary stability in the n-person iterated prisoner's dilemma
%J Biosystems
%V 37
%N 3
%P 189-197
%D 1996
%K jrnl, prisoners, dilemma, PD, IPD, game, zz0296
%X From: <!-- email: fogel OF sunshine.ucsd.edu --> Fogel  [2/'96]

%A E. A. Billard
%T Adaptation in a stochastic prisoner's dilemma with delayed information
%J Biosystems
%V 37
%N 3
%P 211-227
%D 1996
%K jrnl, prisoners, PD, IPD, dilemma, game, zz0296
%X From: <!-- email: fogel OF sunshine.ucsd.edu --> Fogel  [2/'96]

%A J. Epstein
%A R. Axtell
%T Growing Artificial Societies: Social Science From The Bottom Up
%D 1996
%K book, artificial life, complex systems, swarm, sugarscape, sugar scape,
   agents, zz1097
%X Brookings Institution
   Simulation based on metabolic needs, food resources, health, ... .

%A C. Ferreira
%T Gene expression programming: A new adaptive algorithm for solving problems
%J Complex Systems
%V 13
%N 2
%P 87-129
%D 2001
%K jrnl, genetic algorithm, GA, GEP, c2001, c200x, c20xx, multiplexer, GP rule,
   expression tree
%X "GEP, a genotype/phenotype GA (linear & ramified), ... new technique for the
   creation of computer programs. GEP uses character linear chrs. composed of
   genes structurally organized in a head & a tail. The chrs. function as a
   genome & are subjected to mod. by means of mutn, trans., root trans., gene
   trans., gene recomb., & one- & two-point recomb.. The chrs. encode expn trees
   which are the object of selection. The creation of these separate entities
   (genome & expression tree) with distinct functions allows the alg. to
   perform with high efficiency that greatly surpasses existing adaptive
   techniques. ... illustrate the power & versatility of GEP includes symbolic
   regression, sequence induction with & without constant creation, block
   stacking, cellular automata rules for the density-classification problem, &
   2 problems of bool. concept learning: the 11-multiplexer & GP rule problem."
   [<A HREF="http://www.complex-systems.com/Archive/volume13/issue2/article01/abstract.html">abs</A>]['05],
   [<A HREF="http://www.gene-expression-programming.com/gep/GEPBiblio.asp">gene-expression-programming.com</A>]['05].


%A G. E. Collins
%T A method for overlapping and erasure of lists
%C CACM
%V 3
%N 12
%P 655-657
%M DEC
%D 1960
%K jrnl, CACM, c1960, c196x, c19xx, garbage collection, GC, list,
   reference counting, count, counts

%A H. Schorr
%A W. M. Waite
%T An efficient machine-independent procedure for garbage collection in
   various list structures
%J CACM
%V 10
%N 8
%P 501-506
%M AUG
%D 1967
%K garbage collection, GC, pointer reversing, traversal, list
%X uses a small fixed amount of workspace  (no stack)

%A R. W. Topor
%T The correctness of the Schorr-Waite list marking algorithm
%J Acta Inf.
%V 11
%N 3
%P 211-222
%M ?
%D 1979
%K garbage collection, GC, proof, correctness

%A M. Broy
%A P. pepper
%T Combining algebraic and algorithmic reasoning: an approach to the
   Schorr-Waite algorithm
%J TOPLAS
%V 4
%N 3
%P 362-381
%M JUL
%D 1982
%K garbage collection, GC, proof, correctness

%A D. R. Brownbridge
%T Cyclic reference counting for combinator machines
%J Proc. Conf. on Functional programming languages and computer architecture
%I SpringerVerlag
%S LNCS
%V 201
%P 273-288
%M JUN
%D 1985
%K conf, FPCA, c1985, c198x, c19xx, zz1115, garbage collection, GC,
   functional programming, FP
%X "... extending std ref count alg. cycles can be handled at little extra
   cost. Cyclic ref counting uses one extra bit/pointer & /object & one
   one extra ref count /object. ..."  (via JoelR.)
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-15975-4_42">doi:10.1007/3-540-15975-4_42</A>]['15].

%A S. Aditya
%A C. H. Flood
%A J. E. Hicks
%T Garbage collection for strongly-typed languages using run-time type
   reconstruction
%J SIGPLAN Lisp Pointers
%V 7
%D 1994
%P 12-23
%K Sigplan, jrnl, garbage collection, type, types, GC, zz1195
%X review: Comp Rev Sep 95 p481

%A D. Kafura
%A M. Mukherji
%A M. Douglas
%T Concurrent and distributed garbage collection of active objects
%J IEEE Trans. Parallel Distrib. Sys.
%V 6
%N 4
%M APR
%D 1995
%K jrnl, object, garbage collection, GC, zz0197
%X good review by C. S c h r o e d e r  in Comp Rev p529 Oct 96.

%A D. F. Bacon
%A P. Cheng
%A V. T. Rajan
%T A unified theory of garbage collection
%J OOPSLA
%P 50-68
%D 2004
%K conf, OOPSLA, OOPSLA04, c2004, c200x, c20xx, garbage collection, GC

%A R. Jones
%A A. Hosking
%A E. Moss
%T The Garbage Collection Handbook: The Art of Automatic Memory Management
%I Chapman & Hall, CRC Applied Algorithms and Data Structures
%M AUG
%D 2012
%K book, text, c2012, c201x, c20xx, garbage collection, GC, FP. OO, OOP,
   programming languages, implementation
%X [Also search for: garbage collection GC].

%A M. Elsman
%A N. Hallenberg
%T Integrating region memory management
%J JFP
%V 31
%N e4
%M FEB
%D 2021
%K jrnl, JFP, FP, c2021, c202x, c20xx, zz0521, garbage collection, GC,
   memory management, region, generation, MLton, MLkit
%X "We present a region-based memory management scheme with support for
   generational garbage collection. The scheme features a compile-time region
   inference alg., which associates values with logical regions ..."
   -- [<A HREF="https://doi.org/10.1017/S0956796821000010">doi:10.1017/S0956796821000010</A>]['21].

%A A. Mingkun Yang
%A T. Wrigstad
%T Deep dive into ZGC: A modern garbage collector in OpenJDK
%J ACM Trans. on Prog. Languages and Sys.
%V 44
%N 4
%P 1-34
%M DEC
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1022, garbage collection, GC, ZGC, Java,
   openJDK
%X "ZGC is a modern, non-generational, region-based, mostly concurrent,
   parallel, mark-evacuate collector recently added to OpenJDK. It aims at
   having GC pauses that do not grow as the heap size increases, offering low
   latency even with large heap sizes ..."
   -- [<A HREF="https://doi.org/10.1145/3538532">doi:10.1145/3538532</A>]['22] online Oct 2022.


%A Hero of Alexandria
%T Pneumatica.  Automata.  Mechanica.  etc.
%D approx 10-70 AD
%K Hero, Heron, c00xx, c0xxx, ancient Greece, Alexandria, history, science,
   pneumatics, automaton, automata, Staton, automatic, theatre, theater,
   hydraulics, aeolipile, steam engine, robot
%X [<A HREF="http://en.wikipedia.org/wiki/Hero_of_Alexandria">wikip</A>]['12].
   -- [<A HREF="http://www.mlahanas.de/Greeks/HeronAlexandria.htm">heron</A>]['12],
      [<A HREF="http://www.mlahanas.de/Greeks/HeronAlexandria2.htm">2</A>]['12],
      [<A HREF="http://www.mlahanas.de/Greeks/Technology/AncientGreekTechnology011.html">theatre</A>]['12].

%A W. F. Lloyd
%T Two Lectures on the Checks to Population
%I OUP
%D 1833
%K tragedy of the commons, c1833, c183x, c18xx, population, limit, growth,
   zzEthics, limits, ethics, sustainability, resources, human, behaviour,
   cooperation, competition
%X "Reprinted (in part) in:
      'Population, Evolution, and Birth Control',
      G. Hardin, Ed. (Freeman, San Francisco, 1964), p.37" -- Hardin (c1968).
   pdf@[<A HREF="http://socserv.mcmaster.ca/econ/ugcm/3ll3/senior/TwoLecturesPopulation.pdf">mcmaster.ca</A>]['09],
   scan@[<A HREF="http://books.google.com.au/books?id=kQt9Kg-chXAC&ots=seD7XAI8M7&dq=Two%20Lectures%20on%20the%20Checks%20to%20Population&pg=PP1#v=onepage&q=&f=false">go'gle</A>]['09].
   [Also search for: tragedy commons].

%A J. Tyndall
%T On radiation through the earth's atmosphere
%M JAN
%D 1863
%O reprinted 1872
%K lecture, c1863, 186x, c18xx, zz1213, cause, global warming, greenhouse gas,
   gases, effect, earth, atmosphere, radiant, heat, night, nighttime,
   temperature, radiative forcing
%X "... emphasized that our environment would be much colder at
   nighttime in the absence of the greenhouse effect ..."
   -- JT@[<A HREF="http://en.wikipedia.org/wiki/John_Tyndall">wikip</A>]['13].
   'Contributions to Molecular Physics in the Domain of Radiant Heat,' 1872
   -- scan@[<A HREF="http://archive.org/stream/contributionsto01tyndgoog">www</A>]['13].
   [Also search for: cause global warming].

%A S. Arrhenius
%T On the influence of carbonic acid in the air upon the temperature of
   the ground
%J The London, Edinburgh and Dublin Philosophical Mag. and J. of Sci.
%S 5
%V 41
%N 251
%P 237-276
%M APR
%D 1896
%O pres. Swedish Acad. of Sci., 11 Dec. 1895
%K jrnl, c1896, c189x, c18xx, zz1213, Svante, climate change, global warming,
   cause, greenhouse gas, gases, CO2, carbon dioxide, fossil fuel, fuels
%X First to suggest that human use of fossil fuels would lead to global warming.
   scan@[<A HREF="http://www.globalwarmingart.com/images/1/18/Arrhenius.pdf">www</A>]['13],
   dF = alpha log(C / C0),  where C is CO2 conc. in ppm,
      F is radiative forcing, energy_received-energy_radiated, in W/m^2,
      alpha est. between 5 and 7.
   dT = lambda dF, where the sensitivity, lambda ~ 0.8 K/(W/m^2),
       gives +3 K warming for doubling of CO2.
   -- SA@[<A HREF="http://en.wikipedia.org/wiki/Svante_Arrhenius">wikip</A>]['13],
   and F@[<A HREF="http://en.wikipedia.org/wiki/Radiative_forcing">wikip</A>]['13].
   [Also search for: cause global warming].

%A C. Adler
%T The international catalogue of scientific literature
%J Science
%V 6
%N 136
%P 184-201
%M AUG
%D 1897
%K jrnl, c1897, c189x, c18xx, zz0320, Catalogue of Scientific Literature,
   bibliometrics, papers, publications, Science Citation Index, SCI
%X -- [<A HREF="https://doi.org/10.1126/science.6.136.184">doi:10.1126/science.6.136.184</A>]['20].
   (Also see, "... an attempt ... to catalogue all papers published in sci.
      periodicals back to the year 1800 & produce a bibliographic index
      organised by author. ..."
      -- CofSP@[<A HREF="https://en.wikipedia.org/wiki/Catalogue_of_Scientific_Papers">wikip</A>]['20].)
   [Also search for: science index sci].

%A F. W. Lanchester
%T Mathematics in warfare
%J Aircraft in Warfare
%D 1916
%O Reprinted in, 'The World of Mathematics', Vol. 4,
                 J. R. Newman (ed), pp.2138-2159, 1956
%K c1916, c191x, c19xx, zz1214, Lanchester's laws, laws, theory, linear,
   quadratic, differential, maths, war, warfare, combat, armies, model
%X Lanchester@[<A HREF="http://en.wikipedia.org/wiki/Lanchester%27s_laws">wikip</A>]['14].
   'The World of Mathematics,' Vol.4@[<A HREF="http://www.archive.org/details/TheWorldOfMathematicsVolume4">archive.org</A>]['14],
      Vol.4@[<A HREF="https://archive.org/stream/TheWorldOfMathematicsVolume4/Newman-TheWorldOfMathematicsVolume4#page/n121/mode/2up">archive.org</A>]['14].

%A G. R. G. Mure
%T Aristotle's Posterior Analytics
%B Aristotle Organon And Other Works
%E W. D. Ross
%D 1925
%K chapter, c1925, c192x, c19xx, zz1117, Aristotle, Organon, philosophy,
   reasoning
%X [<A HREF="https://archive.org/details/AristotleOrganon">www</A>][2017].
   Also see [<A HREF="http://www.logicmuseum.com/authors/aristotle/posterioranalytics/posterioranalytics.htm">www</A>][2017].

%A E. W. H.
%T Catalogue of Scientific Papers
%V 116
%P 129-130
%M JUL
%D 1925
%K c1925, c192x, c19xx, zz0320, Catalogue of Scientific Papers, Royal Society,
   bibliometrics, publications, literature, papers, science citation index, SCI,
   research, KPI, KPIs, impact, journals
%X "With the publ'n of the vol. before us, the indexing of the sci. papers of
   the 19th century under their authors' names has been successfully brought to
   a close. It is unnecessary to reiterate the high opinion which we have
   previously expressed of the practical utility of this monumental undertaking
   & of the high standard of accuracy maintained by its successive editors &
   their staffs. The 'Catalogue Scientific Papers' is an indispensable tool for
   the research student and historian of science alike."
   -- [<A HREF="https://doi.org/10.1038/116129a0">doi:10.1038/116129a0</A>]['20].
      (Also see, "... an attempt ... to catalogue all papers published in sci.
      periodicals back to the year 1800 & produce a bibliographic index
      organised by author. ..."
      -- CofSP@[<A HREF="https://en.wikipedia.org/wiki/Catalogue_of_Scientific_Papers">wikip</A>]['20].)
   [Also search for: science index sci].

%A C. M. Case
%T Scholarship in Sociology
%J Sociology and Social Res.
%V 12
%P 323-340
%D 1928
%K c1928, c192x, c19xx, zz0820, publish or perish, quote, quotable, aphorism,
   academic, academia, university, scientific, research, management, journals,
   pressure, KPI, KPIs
%X "Publish or perish" attributed:
      "... The earliest known use of the term [P or P] in an
      academic context was in a 1928 journal article. ..."
   -- PorP@[<A HREF="https://en.wikipedia.org/wiki/Publish_or_perish">wikip</A>]['20].
   [Also search for: publish perish].

%A D. H. Lawrence
%T Lady Chatterley's Lover
%D 1928
%K book, novel, c1928, c192x, c19xx, english, gamekeeper, game keeper, adultery,
   Lady Chatterley, Zern, haha, ha ha, funny, review
%X 1st ed 1928.
   Bantam c198x; uk us isbn:0553212621; uk us isbn13:978-0553212624.
   And, off the wwweb, a memorable review of it:
     'Although written many years ago, Lady Chatterley's Lover has just been
     reissued by the Grove Press, and this pictorial account of the day-by-day
     life of an English gamekeeper is full of considerable interest to outdoor
     minded readers, as it contains many passages on pheasant raising, the
     apprehending of poachers, ways to control vermin, and other chores and
     duties of the professional gamekeeper.
     Unfortunately one is obliged to wade through many pages of extraneous
     material in order to discover and savour these sidelights on the
     management of a Midlands shooting estate, and in this reviewer's opinion
     the book cannot take the place of J.R.Miller's "Practical Gamekeeping."'
   -- Ed Zern, Field and Stream, p.142, November 1959.

%A G. Polya
%T How to Solve It
%I Doubleday
%P 253
%D 1945
%K book, text, c1945, c194x, c19xx, problem solving, plan, mathematics, maths,
   strategies
%X prnt 2004 PrUP, pb us$11; uk us isbn:069111966X, uk us isbn13:978-0691119663.
   "... reveals how the mathematical method of demonstrating a proof or
   finding an unknown can be of help in attacking any problem that can be
   'reasoned' out - from building a bridge to winning a game of anagrams. ..."

%A George Blake
%T Westering Sun
%I Collins, Lond.
%D 1946
%K book, c1946, c194x, c19xx, Garvel novels, novel, wanted
%X <!-- P.K. -->modern edn, London Century c1983; uk isbn:0712602054.
   George Blake 1893-1961.

%A G. Orwell
%T Politics and the English Language
%D 1946
%K book, essay, c1946, c194x, c19xx, zz0524, Orwell, Blair, English, language,
   newspeak, brevity, brief, good writing, style, meaning, Shooting an Elephant
%X "... 1. Never use a metaphor, simile, or other figure of speech which ...
   2. Never use a long word where a short one will do.  3. If it is possible to
   cut a word out, always cut it out.  4. Never use the passive where you can
   use the active. Never use a foreign phrase, a scientific word, or a jargon
   word if you can think of an everyday English equivalent.  6. Break any of
   these rules sooner than say anything outright barbarous. ..."
   -- PEL@[<A HREF="https://en.wikipedia.org/wiki/Politics_and_the_English_Language">wikip</A>]['24].
     (Also 'Politics and the English language' in Writers on Writing,
     R. Neale (ed) OUP pp.173-183, 1992, orig: Shooting an Elephant and
     other Essays, 1950 written about 1945 A G.O. essay in a collection.
     G.O. pen name of Eric Blair 1903-1950.)
   [Also search for: Orwell] and [also search for: newspeak].

%A J. von Neumann
%A O. Morgenstern
%T Theory of Games and Economic Behaviour
%I PrincetonUP
%D 1947
%K book, game theory, zero sum, two player, 2player, economics,
   vonNeumann, c1947, c194x, c19xx
%X And a 60th Anniversary Commemorative Edn, PrincetonUP, pp.776,
   2007, pb us$86, uk us isbn:0691130612; uk us isbn13:978-0691130613.

%A I. Asimov
%T I, Robot
%D 1950
%K sci fi, SciFi, novel, fiction, book, c1950, c195x, c19xx, robots,
   laws of robotics
%X stg.7 as of 2015; uk us isbn:000753227X, uk us isbn13:978-0007532278.

%T Dynamics of Climate: Proc. Held October 26-28, 1955
%E R. L. Pfeffer
%I Sponsored jointly by Inst. for Adv. Study, Princeton, &
   Geophys. Res. Directorate
%D 1955
%K proc, conf, c1955, c195x, c19xx, zz0721, weather, climate, prediction,
   simulation, model, modelling, CO2, greenhouse gas, global warming,
   von Neumann, vonNeumann, history, computing, computers
%X Cat. entry [<A HREF="https://catalogue.nla.gov.au/Record/836807">nla.gov.au</A>]['21].
   "For example, only about 1/100,000 of all water on earth occurs in vapor form
   in the atmosphere, yet the presence of water vapour makes a difference of
   40 deg. C in the avg. temp. of the earth. This is more than twice the diff.
   between the temp. at the time of max. glaciation and that at the time of
   total deglaciation of the earth" -- John von Neumann,
   quoted by G.Dyson on p.171 of "Turing's Cathedral" 2012.
   Attendees also discussed rising CO2 and climate effects.
   [Also search for: global warming].

%A C. N. Parkinson
%T Parkinson's law
%J The Economist
%D 1955
%K Parkinson's law, Parkinsons, c1955, c195x, c19xx, zz1119, funny laws,
   Stefan Thurner, University of Vienna, management, Faculty, bureaucratisation
%X "It is a commonplace observation that work expands so as to fill the
   time available for its completion." British naval historian & author
   Cyril Northcote Parkinson wrote that opening line for an essay in
   The Economist in 1955, but the concept known as 'Parkinson's Law' still
   lives on today. ...
   1 scholar who has taken a serious look at Parkinson's Law is Stefan Thurner,
   professor in Science of Complex Systems at the Medical University of Vienna.
   Thurner says he became interested in the concept when the faculty of med. at
   the U. of Vienna split into its own indep. university in 2004. Within a
   couple years, he says, the Med.U. of Vienna went from being run by 15 people
   to 100, while the # of scientists stayed about the same. 'I wanted to
   understand what was going on there, & why my bureaucratic burden did not
   diminish - on the contrary it increased,' he says. ..."
   -- bbc[<A HREF="https://www.bbc.com/worklife/article/20191107-the-law-that-explains-why-you-cant-get-anything-done">9/11/2019</A>]['19].
   [Also search for: funny law].
   (Also see Stefan Thurner@[<A HREF="https://en.wikipedia.org/wiki/Stefan_Thurner">wikip</A>]['19].)

%A A. Thom
%T A statistical examination of the megalithic sites in Britain
%J J. Royal Stat. Soc. (A)
%P 275-295
%V 118
%N 3
%D 1955
%K jrnl, JRSS, stone circle, circles, c1955, c195x, c19xx, zz0204, stats,
   yard, site, UK
%X -- [<A HREF="https://doi.org/10.2307/2342494">doi:10.2307/2342494</A>]['24] at Jstor.
   [Also search for: megalithic stone circle].

%A E. Garfield
%T Citation indexes for science: A new dimension in documentation through
   association of ideas
%J Science
%V 122
%N 3159
%P 108-111
%M JUL
%D 1955
%K jrnl, c1955, c195x, c19xx, zz1119, Garfield, scientific research, papers,
   publications, web, science citation index, SCI, history, citations, impact,
   KPI, KPIs, bibliometrics, publish, perish
%X -- [<A HREF="https://doi.org/10.1126/science.122.3159.108">doi:10.1126/science.122.3159.108</A>['19].
   [Also search for: citation publications].

%E B. S. Bloom
%T Taxonomy of Educational Objectives: The Classification of
   Educational Goals: Handbook I, Cognitive Domain
%D 1956
%K book, text, education, teaching, learning, c1956, c195x, c19xx, curriculum,
   goal, objective, test, testing, hierarchy, skill, mastery
%X Knowledge     - knowledge of major ideas, list, define, tell, describe...
   Comprehension - translate into new context, interpret, contrast, predict...
   Application   - new situations, solve problems, apply, solve, change, ...
   Analysis      - seeing patterns, analyze, separate, order, ...
   Synthesis     - use old ideas to create new ones, predict, combine, modify..
   Evaluation    - compare ideas, assess, reasoned argument, assess, decide...
   (After e.g. [<A HREF="http://www.coun.uvic.ca/learn/program/hndouts/bloom.html">www</A>]['04].)

%A L. S. Penrose
%A R. Penrose
%T A self-reproducing analogue
%J Nature
%V 179
%N 4571
%P 1183
%M JUN
%D 1957
%K jrnl, c1957, c195x, c19xx, self reproducing, assembling, copying, assembly,
   machine, shape, organism, Alife
%X "The most striking peculiarity of living organisms is their property of
   self-reproduction. The most elementary forms, virus or phage particles, can
   reproduce themselves in favourable circumstances only, & this principle
   applies also to the multiplication of nucleic acid complexes in chromosomes.
   It is sometimes thought that the self-reproducing properties of nucleic acid
   depend upon its highly complex structure. Consequently, any mechanical
   analogue for self-reproduction would involve very intricate mechanisms. This
   does not seem to be so, & the device described here has the critical
   reproductive property although it is of the simplest character."
   -- [<A HREF="http://dx.doi.org/10.1038/1791183a0">doi:10.1038/1791183a0</A>]['12].
   [Also search for: Penrose c195x].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">bioinformatics</A>].)

%A M. Gardner
%T Fads and Fallacies in the Name of Science
%I Dover
%D 1957
%K book, text, c1957, c195x, c19xx, zz0510, Martin Gardner, Mathemagical,
   fad, fallacy, science, pseudoscience, Dianetics, Velikovsky,
   UFO, flying saucers
%X "Fair, witty appraisal of cranks, quacks, & quackeries of science &
   pseudoscience: hollow earth, Velikovsky, orgone energy, Dianetics, flying
   saucers, Bridey Murphy, food & medical fads, etc. ..." -- New Yorker
   2nd ed 1957; pb us$10; uk us isbn:0486203948; uk us isbn13:978-0486203942.
   (M.Gardner died in May 2010, aged 95.)

%A A. Samuel
%T Some studies in machine learning using the game of checkers
%J IBM J.
%V 3
%N 3
%P 210-229
%M JUL
%D 1959
%K IBM, jrnl, c1959, c195x, c19xx, draughts, board, game playing, AI, Samuels,
   minimax, IBMjrnl, chequers, term, machine learning, coined
%X "2 machine-learning procedures have been investigated in some detail using
   the game of checkers. Enough work has been done to verify the fact that a
   computer can be programmed so that it will learn to play a better game of
   checkers than can be played by the person who wrote the program. Furthermore,
   it can learn to do this in a remarkably short period of time (8 or 10 hours
   of machine-playing time) when given only the rules of the game, a sense of
   direction, & a redundant & incomplete list of parameters which are thought
   to have something to do with the game, but whose correct signs & relative
   weights are unknown & unspecified. The principles of [ML] verified by these
   experiments are, of course, applicable to many other situations."
   -- [<A HREF="http://www.research.ibm.com/journal/rd/033/ibmrd0303B.pdf">pdf@ibmj</A>]['07].
   [Also search for: checkers].
   Must be one of the first uses of the term "machine learning".

%A G. Cocconi
%A P. Morrison
%T Searching for interstellar communications
%K Nature
%V 184
%P 844-846
%M SEP
%D 1959
%K jrnl, c1959, c195x, c19xx, zz0909, inter stellar, extra terrestrial,
   intelligence, life, interstellar, extraterrestrial, alien, aliens, universe,
   galaxy, radio, signal, signals, communication, message, SETI, Drake equation
%X "No theories yet exist which enable a reliable estimate of the probabilities
   of (1) planet formation, (2) origin of life, (3) evolution of societies
   possessing advanced scientific capabilities. ..."
   -- 19 Sept. 1959, pdf@[<A HREF="http://dx.doi.org/10.1038/184844a0">doi:10.1038/184844a0</A>].
   (Also see SETI at 50 @[<A HREF="http://dx.doi.org/10.1038/461316a">doi:10.1038/461316a</A>][9/'09],
   Kaplan opinion@[<A HREF="http://dx.doi.org/10.1038/461345a">doi:10.1038/461345a</A>][9/'09],
   and [<A HREF="http://www.allisons.org/ll/Images/Film/Andromeda/era/">A for Andromeda</A>].-)
   [Also search for: extraterrestrial life].

%A F. Hoyle
%A J. Elliot
%T A for Andromeda
%I SouvenirPress
%D 1962
%K book, Fred Hoyle, c1962, c196x, c19xx, andromeda galaxy, TV, sci fi, SciFi,
   space, alien life, extraterrestrial, computer, android, humanoid, AI,
   intelligence
%X 1962, uk isbn:0285501658.
   Reprint H.C. 1985; uk us isbn:0380233665; uk us isbn13:978-0380233663.
   Reprint 2005, pb us$11; isbn:0285635883; uk us isbn13:978-0285635883.
   Also see "the Andromeda Breakthrough" 1964.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Film/Andromeda/">A-for-A</A>].)

%A A. Thom
%T The megalithic unit of length
%J J. of the Royal Stat. Soc. (A)
%P 243-251
%V 125
%N 2
%D 1962
%K jrnl, JRSS, yard, stats, c1962, c196x, c19xx, zz0104
%X [<A HREF="http://links.jstor.org/sici?sici=0035-9238%281962%29125%3A2%3C243%3ATMUOL%3E2.0.CO%3B2-W">at Jstor</A>][1/'04].
   [Also search for: megalithic stone circle].

%A T. Rado
%T On non-computable functions
%J Bell Systems Tech. J.
%V 41
%N 3
%P 877-884
%M MAY
%D 1962
%K jrnl, c1962, c196x, c19xx, zz0406, busy beaver problem, BB, computability,
   Tibor Rado, Turing machine, UTM
%X "The construction of non-computable fns ... is based on the principle that a
   finite, non-empty set of non-neg. ints has a largest elt. Also [it] is used
   only for sets which are exceptionally well-defined by current standards. No
   enumeration of computable fns is used, & in this sense the diagonal process
   is not employed. Thus, it appears that an apparently self-evident principle,
   of constant use in every area of maths., yields non-constructive entities."
   -- pdf@[<A HREF="https://doi.org/10.1002/j.1538-7305.1962.tb00480.x">doi:10.1002/j.1538-7305.1962.tb00480.x</A>]['19], at IEEE.
     BB(n) = max # of running steps over all terminating n-state 2-symbol TMs
     1, 6, 21, 107, 47,176,870, ?...   (alternately max # of '1's written).
   (Also see BB@[<A HREF="https://en.wikipedia.org/wiki/Busy_beaver">wikip</A>['19].)
   [Also search for: Busy Beaver].

%A F. J. Vine
%A D. H. Matthews
%T Magnetic anomalies over oceanic ridges
%J Nature
%V 199
%P 947-949
%M SEP
%D 1963
%K jrnl, c1963, c196x, c19xx, zz0913, geology, earth, plate, tectonics, ridge,
   magnetic field, reversal, seafloor, spreading, continental drift, Morley
%X [<A HREF="http://dx.doi.org/10.1038/199947a0">doi:10.1038/199947a0</A>]['13].
   Also see [<A HREF="http://en.wikipedia.org/wiki/Vine-Matthews-Morley_hypothesis">wikip</A>]['13].

%A B. L. Clarke
%T Multiple authorship trends in scientific papers
%J Science
%V143
%N 3608
%P 822-824
%M FEB
%D 1964
%K jrnl, c1964, c196x, c19xx, zz1122, bibliometrics, multiple authors, trends,
   publications, papers, science, scientific research
%X "Since 1946 biomedical writers have shown no marked trend toward multiple
   authorship; the avg # of authors per paper remains steady at about 2.3. This
   is in strong contrast to the conclusion of Price from a study of Chemical
   Abstracts that the chemists' trend toward four or more authors per paper has
   been during this period, & continues to be, steeply exponential. ..."
   -- [<A HREF="https://doi.org/10.1126/science.143.3608.822">doi:10.1126/science.143.3608.822</A>]['22],
      [<A HREF="ttps://www.semanticscholar.org/paper/Multiple-Authorship-Trends-in-Scientific-Papers-Clarke/82c606aac6ce83932626595724b236b32bff149b">Sem'Sclr</A>]['22].
   [Also search for: multiple authors trends].

%A F. Hoyle
%A J. Elliot
%T The Andromeda Breakthrough
%I HarperAndRow
%D 1964
%K book, c1964, c196x, c19xx, SciFi, sci fi, TV, space, computer,
   alien life, intelligence, android, quote, quotable
%X 1964.  Also see "A for Andromeda" 1962.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Film/Andromeda/">A-for-A</A>].)
    Says Professor Madeleine Dawnay, as she stomps on a cigarette butt,
    "You know what life is? A spot of soot. Carbon, nitrogen. Add various
    bits of dirt to taste. Mix with water and stir well. And that's life."
    -- The Roman Peace (The Andromeda Breakthrough 37'30",
       02/08/62, BBC, Fred Hoyle and John Elliot).

%A I. Asimov
%T Visit to the World's Fair of 2014
%I ?
%M AUG
%D 1964
%K essay, views, c1964, c196x, c19xx, c201 c201x, zz0414, robot, robots, AI,
   Isaac Asimov, future, prediction, futurology, zzPrediction
%X "The New York World's Fair of 1964 is dedicated to 'Peace Through
   Understanding.' Its glimpses of the world of tomorrow rule out thermonuclear
   warfare. And why not? If a thermonuclear war takes place, the future will not
   be worth discussing. So let the missiles slumber eternally on their pads and
   let us observe what may come in the nonatomized world of the future. ...
   Robots will neither be common nor very good in 2014, but they will be in
   existence. ... An experimental fusion-power plant or two will already exist
   in 2014. ... Much effort will be put into the designing of vehicles with
   'Robot-brains' ... The world of A.D. 2014 will have few routine jobs that
   cannot be done better by some machine than by any human being. ..."
   -- [<A HREF="http://www.nytimes.com/books/97/03/23/lifetimes/asi-v-fair.html">NYT</A>]['14].
   Also see [<A HREF="http://www.bbc.com/news/technology-27069716">bbc</A>][21/4/2014].
   (Not too bad, as long term (50y) predictions go.)

%A W. D. Hamilton
%T The genetical evolution of social behaviour. I
%J JTB
%V 7
%N 1
%P 1-16
%M JUL
%D 1964
%K jrnl, JTB, c1964, c196x, c19xx, social, animal, behaviour, evolution,
   altruism, cooperation, self sacrifice, family, relatives, spite, greenbeard,
   prisoner's dilemma, IPD, Hamilton's rule, hamiltons
%X "... interactions between relatives on one another's fitness. Making use of
   Wright's Coefficient of Relationship as the measure of the proportion of
   replica genes in a relative, a quantity is found which incorporates the
   maximizing property of Darwinian fitness. ... named 'inclusive fitness'.
   Species following the model should tend to evolve behaviour such that each
   organism appears to be attempting to maximize its inclusive fitness. This
   implies a limited restraint on selfish competitive behaviour and possibility
   of limited self-sacrifices. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0022-5193(64)90038-4">doi:10.1016/0022-5193(64)90038-4</A>]['10].
   (Also see Sci., [<A HREF="http://dx.doi.org/10.1126/science.1178332">doi:10.1126/science.1178332</A>]['10],
   n@ture, [<A HREF="http://dx.doi.org/10.1126/science.1189675">doi:10.1126/science.1189675</A>]['10].)
   [Also search for: Hamilton rule].

%A A. Thom
%T The larger units of length of megalithic man
%J J. Royal Stat. Soc. (A)
%P 527-533
%V 127
%N 4
%D 1964
%K jrnl, c1964, c196x, c19xx, stats, JRSS, yard, unit
%X [<A HREF="http://links.jstor.org/sici?sici=0035-9238%281964%29127%3A4%3C527%3ATLUOLO%3E2.0.CO%3B2-P">at Jstor</A>][1/'04].
   [Also search for: megalithic stone circle].

%A E. Garfield
%T Can citation indexing be automated?
%J Methods for Mechanized Documentation
%I Stat. Assoc.
%P 84-90
%D 1964
%O Essay of an Information Scientist, vol.1, pp.84-90, 1962-73,
   Current Contents, #9, March 4, 1970
%K conf, c1964, c196x, c19xx, zz1122, bibliometrics, science citation index,
   SCI, ISI, scientific research
%X "The main characteristics of conventional language-oriented indexing systems
   are itemized & compared to the characteristics of citation indexes. The
   advantages & disadv. are discussed in relation to the capability of the
   computer automatically to simulate human critical processes reflected in the
   act of citation. It is shown that a considerable standardization of document
   presentations will be necessary & probably not achievable for many years if
   we are to achieve automatic referencing. On the other hand, many citations,
   now fortuitously or otherwise omitted, might be supplied by computer
   analyses of text."
   -- [<A HREF="http://garfield.library.upenn.edu/essays/V1p084y1962-73.pdf">garfield.library.upenn</A>]['22].
   [Also search for: Garfield bibliometrics].

%A S. Lin
%A R. Rado
%T Computer studies of Turing machine problems
%J JACM
%V 12
%N 2
%P 196-212
%M APR
%D 1965
%K jrnl, JACM, c1965, c196x, c19xx, zz0219, busy beaver, problem, halting
%X -- [<A HREF="https://doi.org/10.1145/321264.321270">doi:10.1145/321264.321270</A>]['19].
   (Also see,
   "The results of this paper had already appeared in part in Lin's 1963
   doctoral dissertation, under R's guidance. L & R prove that SUM(3)=6 &
   S(3)=21 by proving that all 3-state 2-symbol TMs which don't halt within 21
   steps will never halt. (Most are proven automatically by a computer program,
   however 40 are proven by human inspection." -- wikip.)
   [Also search for: Busy Beaver].

%A C. J. C. McOustra
%T Legal protection for computer programs
%J COMPJ
%V 8
%N 4
%P 289-296
%M JAN
%D 1966
%K COMPJ, jrnl, c1966, c196x, c19xx, program, law, rights, copyright,
   zzLaw, copy right
%X -- [<A HREF="https://doi.org/10.1093/comjnl/8.4.289">doi:10.1093/comjnl/8.4.289</A>]['24].

%A A. Thom
%T Megalithic Sites in Britain
%I OUP
%P 184
%M DEC
%D 1967
%K book, text, stonehenge, stone henge, megalithic circle, circles, yard,
   site, stone circle, c1967, c196x, c19xx, OUP
%X Thom (1894-1985). uk us isbn:0198131488.  Also see: Patrick.
   [Also search for: megalithic stone circle].

%A M. V. Malin
%T The Science Citation Index: A new concept in indexing
%J Library Trends
%P 374-387
%M JAN
%D 1968
%K c1968, c196x, c19xx, zz0820, bibliometrics, citation index, source index,
   corporate index, SCI, history, scientific research, literature, papers,
   bibliometrics, publications, citations, references
%X -- [<A HREF="https://www.ideals.illinois.edu/bitstream/handle/2142/6392/librarytrendsv16i3h_opt.pdf">www</A>]['20].
   [Also search for: science citation index history].

%A G. Hardin
%T The tragedy of the commons
%J Science
%V 162
%N 1243-1248
%D 1968
%K jrnl, c1968, c196x, c19xx, tragedy of the commons, behaviour, cooperation,
   sustainability, resources, population, limits, morality, ethics, Lloyd
%X "... a scenario first sketched in a little-known pamphlet in 1833 by a
   mathematical amateur named William Forster Lloyd (1794-1852). ...
   ... The only way we can preserve & nurture other & more precious freedoms is
   by relinquishing the freedom to breed, & that very soon. 'Freedom is the
   recognition of necessity'--and it is the role of education to reveal to all
   the necessity of abandoning the freedom to breed. Only so, can we put an end
   to this aspect of the tragedy of the commons."
   -- [<A HREF="http://dx.doi.org/10.1126/science.162.3859.1243">doi:10.1126/science.162.3859.1243</A>]['09].
   [Also search for: tragedy commons].

%A Philip K. Dick
%T Do Androids Dream of Electric Sheep?
%D 1968
%K book, c1968, c196x, c19xx, SciFi, science fiction, android, replicant,
   Deckard, nexus6, Rachel Rosen, Blade Runner
%X 1st ed 1968.  Later ed 1996; uk us isbn:0345404475.

%A A. C. Clarke
%T 2001: A Space Odyssey
%P 320
%D 1968
%K book, SciFi, science fiction, c1968, c196x, c19xx, Artificial Intelligence,
   AI, computer, HAL 9000, mind, consciousness, space, monolith, alien life,
   extraterrestrial
%X 2000 ed, pb us$8, uk us isbn:0451457994; uk us isbn13:978-0451457998.
   1999 ed, hb,      uk us isbn:0451198492; uk us isbn13:978-0451198495.
   25-ann ed 1993; pb us$12; uk us isbn:0451452739; uk us isbn13:978-0451452733.

%A P. R. Ehrlich
%T The Population Bomb
%I SierraClub / BallantineBooks
%P 201
%D 1968
%K book, text, c1968, c196x, c19xx, limits, growth, earth, resources,
   population explosion, control, Malthusian crisis, sustainability, food
%X 1st ed 1968; uk us isbn:1568495870.
   (Also see [<A HREF="http://en.wikipedia.org/wiki/The_Population_Bomb">wikip</A>]['13].)
   [Also search for: limits growth resources].

%A R. J. Solomonoff
%T The search for artificial intelligence
%J Electronics and Power
%P 8-11
%M JAN
%D 1968
%K c1968, c196x, c19xx, AI
%X [<A HREF="http://world.std.com/~rjs/searchforai.pdf">www</A>]['12].

%A R. K. Merton
%T The Matthew effect in science. The reward and communication systems of
   science are considered
%J Science
%V 159
%N 3810
%P 56-63
%M JAN
%D 1968
%K c1968, c196x, c19xx, zz0814, publish, perish, scientific research,
   Matthew effect, principle, law, laws, funny, mathew, ethics, credit, impact,
   precedence, priority, promotion, rich get richer, reputation, collaboration,
   recognition, exploitation
%X "... the Matthew effect was construed in terms of enhancement of the posn of
   already eminent scientists who are given disproportionate credit in cases of
   collaboration or of indep. multiple discoveries. ... we note other possible
   kinds of consequences, this time for the communication system of science.
   The Matthew effect may serve to heighten the visibility of contributions to
   sci. by scientists of ack. standing & to reduce the visibility of [the]
   less well known. ... [we] find a correlation between the redundancy fn
   of multiple discoveries & the focalizing fn of eminent men of sci.
   a fn which is reinforced by the great value these men place upon finding
   basic problems & by their self-assurance. ... partly the result of
   experiences & assocns in creative sci.environments ... encourages them to
   search out risky but important problems ... A macrosocial ver. of the
   M.principle is apparently involved in those processes of social seln that
   currently lead to the conc. of sci.resources & talent."
   -- [<A HREF="http://dx.doi.org/10.1126/science.159.3810.56">doi:10.1126/science.159.3810.56</A>]['14],
   pdf@[<A HREF="http://www.garfield.library.upenn.edu/merton/matthew1.pdf">U.Penn</A>]['14].
      ['For unto every one that hath shall be given, and he shall have
      abundance: but from him that hath not shall be taken even that
      which he hath.' -- Matthew 25:29.]
   [Also search for: publish perish]  and  [also search for: Stigler law].

%A S. Cook
%T The complexity of theorem-proving procedures
%J Proc. 3rd Annual ACM Symposium on Theory of Computing
%P 151-158
%D 1971
%K conf, c1971, c197x, c19xx, NP complete, NPC, decision problem, complexity,
   algorithm, nondeterministic, non-deterministic, Turing machine,
   polynomial time, reducible, reducibility, theorem proving, hard problems
%X "It is shown that any recognition problem solved by a polynomial time-bounded
   nondet. Turing machine can be "reduced" to the problem of determining whether
   a given propositional formula is a tautology. Here "reduced" means, roughly
   speaking, that the 1st problem can be solved deterministically in poly.time
   provided an oracle is available for solving the 2nd. From this notion of
   reducible, polynomial degrees of difficulty are defined, & it is shown that
   the problem of determining tautologyhood has the same polynomial degree as
   the problem of determining whether the 1st of 2 given graphs is isomorphic to
   a subgraph of the 2nd. Other examples are discussed. A method of measuring
   the complexity of proof procedures for the predicate calculus is introduced
   & discussed."
   -- [<A HREF="http://doi.acm.org/10.1145/800157.805047">doi:10.1145/800157.805047</A>]['07].
   [Also search for: PNPproblem].

%A V. V. Fedorov
%T Theory of Optimal Experiments
%I AcademicPress
%D 1972
%K book, text, experiment, design, optimum, c1972, c197x, c19xx, learning,
   cost
%X uk us isbn:0122507509.

%A P. G. Barker
%T Syntactic definition and parsing of molecular formulae:
   Part 1, Initial syntax definition and parser implementation
%J COMPJ
%V 18
%N 4
%P 355-359
%D 1975
%K jrnl, COMPJ, c1975, c197x, c19xx, formula, chemical compound,
   parser, parsing
%X "A first level syntax specification for chemical formulae is presented and a
   simple algorithm which enables the parsing of such formulae is described.
   The algorithm may be usefully employed in the design of interactive software
   for computer-based learning & database query systems. Particular emphases is
   given to the use of a structured approach to the implementation of the p.."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/18.4.355">doi:10.1093/comjnl/18.4.355</A>]['08].
   [Also search for: chemical compound].

%E C. Sagan
%T Communication with Extraterrestrial Intelligence
%I MITpress
%P 428
%M MAR
%D 1975
%K book, text, c1975, c197x, c19xx, extraterrestrial, life, alien, aliens,
   intelligence, communication, contact, space, universe, SETI, CETI
%X 1975; pb; uk us isbn:0262690373; uk us isbn13:978-0262690379.
   "The first int. conf. on the problem of extraterrestrial civilizations, and
   contact with them, was held in September 1971 in Soviet Armenia. [It] was a
   gathering of specialists working in a wide variety of fields - astronomy,
   physics, radiophysics, computer science and technology, chemistry, biology,
   linguistics, archaeology, anthropology, sociology, and history - and included
   many scientists whose reputations are worldwide. For example, Freeman Dyson,
   Philip Morrison, and Charles Townes were among the American participants;
   their Russian counterparts were of comparable distinction. [It] was jointly
   organized by the U.S. Natl Acad. of Sci. (with assistance from the U.S.
   Natl Sci. Foundation) and the U.S.S.R. Academy of Sciences. Scientists from
   several other countries also participated.
   Many aspects of the problem of extraterrestrial civilizations were discussed
   in detail, and these discussions are fully presented in this book. Particular
   attention is devoted to the following questions: the plurality of planetary
   systems in the universe, the origin of life on Earth, the possibility of life
   arising on cosmic bodies, the origin and evolution of intelligence, the
   origin and development of technological civilizations, problems in searching
   for intelligent signals or for evidence of astroengineering activities, and
   the problems and possible consequences of establishing contact with
   extraterrestrial civilizations."
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Film/Andromeda/">A for Andromeda</A>].)

%A A. Thom
%T The distances between stones in stone rows
%J J. Royal Stat. Soc. (A)
%P 253-257
%V 141
%N 2
%D 1978
%K jrnl, c1978, c197x, c19xx, JRSS, yard, megalithic, row, stone
%X [<A HREF="http://links.jstor.org/sici?sici=0035-9238%281978%29141%3A2%3C253%3ATDBSIS%3E2.0.CO%3B2-3">at Jstor</A>][1/'04].
   [Also search for: megalithic stone].

%A A. Thom
%T Megalithic Lunar Observatories
%I OUP
%P 128
%M JUN
%D 1978
%K book, c1978, c197x, c19xx, lunar, moon, observatory, stone circle, stats, OUP
%X uk us isbn:0198581327.
   [Also search for: megalithic stone circle].

%A D. T. Campbell
%T Assessing the impact of planned social change
%J Evaluation and Program Planning
%V 2
%N 1
%P 67-90
%D 1979
%K jrnl, c1979, c197x, c19xx, zz0319, Campbell's, Campbells, Campbell, law,
   laws, cambell, measure, impact, KPI, KPIs, JIF, Hindex, quote, quotable,
   funny, scientific research, assessment, management, university, distortion,
   corruption, corrupt, bibliometrics, game, gaming, spoof, spoofing, abuse
%X "It is a special characteristic of all modern societies that we consciously
   decide on and plan projects designed to improve our social systems. It is our
   universal predicament that our projects do not always have their intended
   effects. Very probably we all share in the experience that often we cannot
   tell whether the project had any impact at all, so complex is the flux of
   historical changes that would have been going on anyway, and so many are the
   other projects that might be expected to modify the same indicators. ..."
   -- [<A HREF="https://doi.org/10.1016/0149-7189(79)90048-X">doi:10.1016/0149-7189(79)90048-X</A>]['19].
   Campbell's law: "The more any quantitative social indicator is used for
      social decision-making, the more subject it will be to corruption
      pressures and the more apt it will be to distort and corrupt the social
      processes it is intended to monitor."
      -- CL@[<A HREF="https://en.wikipedia.org/wiki/Campbell%27s_law">wikip</A>]['19].
   (Also see 'Incentive malus ...', The Economist 24/9/2016 [<A HREF="https://www.economist.com/science-and-technology/2016/09/24/incentive-malus">www</A>]['19].)
   [Also search for: Goodhart law]  and  [also search for: publish perish].

%A A. Thom
%T Megalithic Remains in Britain and Brittany
%I OUP
%P 204
%D 1979
%K book, c1979, c197x, c19xx, stone circle, circles, OUP
%X uk us isbn:0198581564.
   [Also search for: megalithic stone circle].

%A D. R. Hofstadter
%T Godel, Escher, Bach: An Eternal Golden Braid
%I BasicBooks
%P 800
%D 1979
%K book, text, c1979, c197x, c19xx, recursion, self reference, AI, paradoxes
%X 20th ann ed 1999; us$13; uk us isbn:0465026567; uk is isbn13:978-0465026562.

%A J. Figueras
%T Chemical symbol string parser
%J J. Chem. Inf. Comput. Sci.
%V 23
%N 1
%P 48-52
%D 1983
%K jrnl, c1983, c198x, c19xx, parsing, chemical compound, formula, formulae
%X [<A HREF="http://dx.doi.org/10.1021/ci00037a009">doi:10.1021/ci00037a009</A>]['08].

%A M. O. Rabin
%D 1983
%T Transaction protection by beacons
%J J. Computer and Sys. Sci.
%V 27
%P 256-267
%D 1985
%K jrnl, JCSS, c1985, c198x, c19xx, random mumbers, number, bit, bits,
   security, encryption, cypher, cipher, beacon, signing, probabilistic,
   randomised, everlasting encryption, privacy, confidential, mail
%X "Protocols for implementing contract signing, confidential disclosures, and
   certified mail in an electronic mail system are proposed. These transactions
   are provably impossible without a trusted intermediary. However, they can be
   implemented with just a small probability of a participant cheating his
   partner, by use of a beacon emitting random integers. Applications include
   privacy protection of personal information in data banks, as well as the
   protection of business transactions."
   abs:[<A HREF="http://dx.doi.org/10.1016/0022-0000(83)90042-9">doi:10.1016/0022-0000(83)90042-9</A>]['04].
   (For random bits [also search for: CSWallace random c1990].)

%A H. Cobban
%T The Palestinian Liberation Organisation. People, Power and Politics
%I CUP
%S Cambridge Middle East Library
%N 5
%P 320
%M JAN
%D 1984
%K book, text, CUP, politics, middle east, PLO, Lebanon, Israel, Fateh,
   Helena Cobban, c1984, c198x, c19xx
%X -- [<A HREF="https://doi.org/10.1017/CBO9780511622007">CUP</A>]['24].
   <!-- Hcobban at aol com, 1/2005 -->pb, stg25; uk us isbn:0521272165; uk us isbn13:9780511622007..

%A K. Thompson
%T Reflections on trusting trust
%J CACM
%V 27
%N 8
%P 761-763
%M OCT
%D 1984
%K Turing award lecture, c1984, c198x, c19xx, zz1213, Unix, CC, Trojan horse,
   compiler
%X "To what extent should one trust a statement that a program is free of
   Trojan horses? Perhaps it is more important to trust the people who wrote
   the software. ..."
   -- [<A HREF="http://dx.doi.org/10.1145/358198.358210">doi:10.1145/358198.358210</A>]['14].

%A A. K. Dewdney
%T Computer Recreations
%J Sci. Am.
%P 16-26
%M DEC
%D 1985
%K SciAm, Golomb ruler, rules, combinatorial problem, combinatorics, puzzle,
   constraint, constraints, c1985, c198x, c19xx
%X Sci.Am. column "...and a follow up on March c1986, page 21."
   -- [<A HREF="http://4c.ucc.ie/~tw/csplib/prob/prob006/refs.html">v@nBeek</A>][10/'04].
   "A Golomb ruler is a set of integers (marks) a(1) < ... < a(n) s.t. all the
   differences a(i)-a(j) (i > j) are distinct. Clearly we may assume a(1)=0.
   Then a(n) is the length of the Golomb ruler. For a given number of marks, n,
   ... [find] the shortest Golomb rulers. Such rulers are called optimal."
   e.g. n=4, one opt ruler,  [0,1,4,6], length=6.
        n=5, two opt rulers, [0,1,4,9,11] and [0,3,4,9,11], length=11.
   -- [<A HREF="http://www.research.ibm.com/people/s/shearer/grule.html">J.She@rer</A>][10/'04],
      [<A HREF="http://members.aol.com/golomb20/">aol.com/golomb20</A>][10/'04].
   (The rulers are relevant to communications, and codes.)

%A J. C. Lagarias
%T The 3x+1 problem and its generalizations
%J The American Mathematical Monthly
%V 92
%N 1
%P 3-23
%M JAN
%D 1985
%K 3X+1 puzzle, 3Xplus1, 3N+1, 3n+1, 3nPlus1, problem,
   Collatz, Syracuse, Kakutani, Hasse, Ulam, c1985, c198x, c19xx
%X This problem is an old one (it goes back to at least the sixties), and it
   has been referred to in many different ways: the 3x+1 problem, the Collatz
   problem, the Syracuse problem, Kakutani's problem, Hasse's algorithm,
   Ulam's problem.  Please, let us not call it Hofstadter's problem also.
   None of the essential questions have been solved.  It is not even known if
   almost all +ve integers end up going to 4,2,1,4,....
   A +ve result is that
   almost all +ve integers have an iterate smaller than the starting
   value.  The conjecture that all +ve integers go to 1 has been verified
   up to 2^40, and the length of a nontrivial cycle in +ve integers is
   at least 275,000.
   [Also search for: Collatz problem].

%A L. Lamport
%T LaTeX - A Document Preparation System
%I AddisonWesley
%D 1985
%K book, text, Tex, LaTex, manual, paper, papers, macros,
   formatting, markup language, c1985, c198x, c19xx
%X uk us isbn:020115790X.

%A D. Roberts
%T From Swampland to Farmland: A History of the
   Koo-Wee-Rup Flood Protection District
%I Rural Water Commission of Victoria
%D 1985
%K book, swamp, farm, farming, land, Koowerup, Victoria, Australia, c1985
%X isbn:0724155759.  -- via Eric S', '03.

%A E. Artin
%T Theory of braids
%J Annals of Mathematics
%V 48
%P 101-126
%N 1
%M JAN
%D 1947
%K jrnl, braid, braids, plat, platt, platting, weave, weaving, knot theory,
   sennet, c1947, c194x, c19xx
%X -- [<A HREF="https://www.jstor.org/stable/1969218">jstor:1969218</A>]['24].

%A E. Artin
%T The theory of braids
%J American Scientist
%V 38
%N 1
%P 112-119
%M JAN
%D 1950
%K c1950, c195x, c19xx, braid, braids, plat, platt, platting, weave, weaving,
   knot theory, sennet
%X -- [<A HREF="https://www.jstor.org/stable/27826294">jstor:27826294</A>]['24].

%A R. Doll
%A A. B. Hill
%T Smoking and carcinoma of the lung.  Preliminary report
%J British Med. J.
%P 739-748
%D 1950
%K jrnl, BMJ, smoke, tobacco, cigarettes, cigarette, health, mortality, cancer,
   smoking, c1950, c195x, c19xx, stats, statistics
%X [Also search for: Doll c1998], and later.

%A E. L. Wynder
%A E. A. Graham
%T Tobacco smoking as a possible etiologic factor in bronchogenic carcinoma
%J J. Amer. Med. Assoc.
%V 143
%P 329-336
%D 1950
%K jrnl, JAMA, smoke, cigarettes, cigarette, cancer, lung, health, mortality,
   smoking, stats, statistics, c1950, c195x, c19xx

%A M. L. Levin
%A H. Goldstein
%A P. R. Gerhardt
%T Cancer and tobacco smoking
%J J. Amer. Med. Assoc.
%D 1950
%V 143
%P 336-338
%K jrnl, smoking, smoke, tobacco, cigarettes, cigarette, lung cancer, cause,
   health, mortality, stat, statistics, JAMA, c1950, c195x, c19xx
%X [Also search for: smoking cause cancer].

%A C. A. Mills
%A M. M. Porter
%T Tobacco smoking habits and cancer of the mouth and respiratory system
%J Cancer Res.
%D 1950
%V 10
%P 539-542
%K jrnl, smoking, smoke, tobacco, cigarettes, lung cancer, cause, health,
   mortality, cigarette, stat, statistics, c1950, c195x, c19xx, habit
%X [Also search for: smoking cause cancer].

%A R. Schrek
%A L. A. Baker
%A G. P. Ballard
%A S. Dolgoff
%T Tobacco smoking as an etiologic factor in disease
%J Cancer Res.
%D 1950
%V 10
%P 49-58
%K jrnl, smoking, smoke, tobacco, cigarettes, lung cancer, cause, health,
   mortality, cigarette, stat, statistics, c1950, c195x, c19xx
%X [Also search for: smoking cause cancer].

%A R. Doll
%A A. B. Hill
%T A study of the aetiology of carcinoma of the lung
%J British Med. J.
%D 1952
%P 1271-1286
%K jrnl, smoking, smoke, tobacco, cigarettes, lung cancer, cause, health,
   mortality, cigarette, smoking, stat, statistics, BMJ, c1952, c195x, c19xx
%X [Also search for: Doll 1950] and later, e.g.,  Doll BMJ.

%A Y. Anzai
%T Recognition of coalition by computer in a three-person game
%J Behavioural Science
%V 22
%P 403-421
%D 1977
%K game, theory, coalition, cooperation, 3-person

%A K. Appel
%A W. Haken
%T Every planar graph is four colourable
%J Bulletin of the Amer. Math. Soc.
%V 82
%N 5
%M SEP
%D 1976
%K jrnl, Koch, 4-colour, four colour map theorem, colouring, coloring, color,
   graph, maths, c1976, c197x, c19xx, computer, proof
%X ('... Part I:  Discharging',  Illinois J. Math., 21(3), pp.429-490, 1977,
    -- [<A HREF="https://doi.org/10.1090/conm/098">doi:10.1090/conm/098</A>]['24],
    pdf@[<A HREF="http://projecteuclid.org/euclid.ijm/1256049011">projecteuclid</A>]['14], and
    '... Part II: Reducibility', Illinois J. Math., 21(3), pp.491-567, 1977,
    pdf@[<A HREF="http://projecteuclid.org/euclid.ijm/1256049012">projecteuclid</A>]['14].)
   Also see 1989, uk us isbn:0821851039.
   Also see [<A HREF="http://dx.doi.org/10.1038/scientificamerican1077-108">Sci.Am</A>]['11], 1989.

%A J. Jaynes
%T The Origin of Consciousness in the Breakdown of the Bicameral Mind
%D 1976
%K book, c1976, c197x, c19xx, Bicameral, bicammeral, tricameral, consciousness,
   human, mind, body, brain, evolution, conscious, psychology, origins,
   God, Gods, voices, auditory, hallucination, controversial
%X 1st ed 1976; uk us isbn:0395207290.
   Reprinted c1990, pb us$15; uk isbn:0140174915;
      uk us isbn:0618057072; uk us isbn13:978-0618057078;
   [Also search for: Bicameral Mind].
   (Also see
   -- [<A HREF="http://en.wikipedia.org/wiki/Bicameralism_(psychology)">wikip</A>]['12],
   -- [<A HREF="http://en.wikipedia.org/wiki/Bicameral_mind">wikip</A>]['09].)

%A D. W. Barron
%T Fragments of an old testament
%J Computer Bulletin
%M SEP
%D 1976
%P 16
%K c1976, c197x, c19xx, joke, computer history, ICL, machine, numbers,
   serial numbers, funny, ha ha, haha

%A R. P. Brent
%T The parallel evaluation of general arithmetic expressions
%J JACM
%V 21
%N 2
%M APR
%D 1974
%P 201-206
%K jrnl, arithmetic expression,  compilation,  complexity,  time, parallel,
   optimise, optimize
%X n >= 1 variables and constants, +, *, /, ( )
   time  4 log2 n + 10(n-1)/p  using p >= 1 processors
   within constant factor of optimal  best possible
   Sharper result without '/'.

%A B. T. Bennett
%A R. B. Potts
%T Arrays and brooks
%J J. Australian. Math. Soc.
%D 1967
%P 23-31
%X combinatorial, problems, rooks, queens, nqueens, bishops,
   knights, chess board

%A F. P. Brooks
%T The Mythical Man-Month
%I AddisonWesley
%D 1975
%K book, text, software engineering, SWE, c1975, c197x, c19xx, crisis, deadline,
   productivity, project management
%X "The classic book on the human elements of software engineering. ..."
   2nd ed 1995; pb us$33; uk us isbn:0201835959; uk us isbn13:978-0201835953.

%A R. Baker
%T Whist tournaments
%J Proc. 6th S.E. Conf. on Combinatorics, Graph Theory and Computing
%P 89-100
%D ????
%K whist tournament, combinatorial problem

%A G. Pinski
%A F. Narin
%T Citation influence for journal aggregates of scientific publications:
   Theory, with application to the literature of physics
%J Info. Proc. & Management
%V 12
%N 5
%P 297-312
%D 1976
%K jrnl, c1976, c197x, c19xx, zz1122, bibliometrics, publication, impact,
   citations, ISI, eigenvalue, pagerank, journals, JIF, science
%X "... for determining citation based influence measures for sci. jrnls,
   subfields & fields. Starting with the cross citing matrix between js. or
   between aggregates of js., an eigenvalue problem is formulated ... influence
   weight for each j. or aggregate. Two other measures, the influence per
   publication & the total influence are then defined. ..."
   -- [<A HREF="https://sci2s.ugr.es/sites/default/files/files/TematicWebSites/hindex/PinskiNarin1976.pdf">ugr.es</A>]['22],
      [<A HREF="https://doi.org/10.1016/0306-4573(76)90048-0">doi:10.1016/0306-4573(76)90048-0</A>]['22].

%T BLAS (Basic Linear Algebra Subprograms)
%D 1979 +
%K Basic Linear Algebra Subprograms, BLAS, zz0221, OpenBLAS, software,
   numerical methods, scientific computing, netlib, vectors, matrices, matrix
%X -- [<A HREF="https://en.wikipedia.org/wiki/Basic_Linear_Algebra_Subprograms">wikip</A>]['21],
      blas@[<A HREF="http://www.netlib.org/blas/">netl'b</A>]['21].
   [Also search for: BLAS numerical].

%A C. Berge
%A C. C. Chen
%A V. Chvatal
%A C. S. Seow
%T Combinatorial properties of polyominoes
%I School of Computer Science, McGill University, Montreal
%R 80.7
%M MAY
%D 1980
%O Combinatorica, 1, pp.217-224, 1981
%K polyomino, polyominoe, pentominoe
%X -- [<A HREF="https://doi.org/10.1007/BF02579327">doi:10.1007/BF02579327</A>]['24].

%A T. E. Cheatham
%A G. H. Holloway
%A J. A. Townley
%T Symbolic evaluation and the analysis of programs
%J IEEE Transactions on Software Engineering
%V SE-5
%N 4
%M JUL
%D 1979
%P 402-417
%K symbolic execution, evaluation,  abstract interpretation,
   optimise, optimize, verification

%A I. M. Campos
%A G. Estrin
%T Sara aided design of software for concurrent systems
%J AFIPS Conf. Proc.
%V 47
%D 1978
%P 325-335
%K workbench, work bench, tool, tools, programming

%A W.-L. Chow
%T On the algebraical braid group
%J Annals of Mathematics
%P 654-658
%V 49
%N 3
%M JUL
%D 1948
%K jrnl, braid, braids, knot, knots theory, group, weave
%X [Also search for: braid].

%A J. Cohen
%A R. Sitver
%T A case study in program transformation: translation into Polish
%J IEEE Transactions on Software Engineering
%V SE-5
%N 6
%M NOV
%D 1979
%P 593-606
%K jrnl, program transformation, reverse polish, shunting algorithm

%A B. E. Carpenter
%A R. W. Doran
%A K. Hopper
%T Non-recursive recursion
%J SPE
%V 7
%P 263-269
%D 1977
%K jrnl, SPE, recursion, goto, tail, c1977, c197x, c19xx

%A B. Chandrasekaran
%T Artificial intelligence - the past decade
%B Advances in Computers
%E M. Rubinoff
%E M. C. Yovits
%V 13
%P 169-232
%D 1975
%K survey AI, Winograd, Strips, Planner, Analogy, c1975, c197x, c19xx

%A Megiddo Nimrod
%T The Weighted Euclidean 1-center Problem
%J Mathematics of Operations Research
%V 8
%N 4
%M NOV
%D 1983
%P 498-504
%K circle, points, convex hull, geometry
%X over the news:
   to find smallest circle enclosing n points in the plane.
   It *is* a well-studied problem, with a tight time bound (given
   weighted distances) of
        O (n (log n)**3 (log log n)**2).
   If the distances are unweighted, the problem can be solved in linear time.

%A Megiddo Nimrod
%T Linear-Time Algorithms for Linear Programming in R**3 and Related Problems
%J SIAM J. of Computing
%V 12
%N 4
%M NOV
%D 1983
%P 759-776
%K LinearProgramming, jrnl, circle, points, convex hull, geometry, 3D
%X from the news:
   to find smallest circle enclosing n points in the plane, ?this is R3?

%A R. J. Chevance
%T Design of high level language oriented processors
%J Sigplan
%M OCT
%D 1977
%V 12
%N 10
%P 10-32
%K high level language, architecture, machine, oriented, processor
%X good bibliography as of 1977.

%A E. F. Codd
%T A relational model of data for large shared data banks
%J CACM
%V 13
%N 6
%P 377-387
%M JUN
%D 1970
%K jrnl, CACM, data base, database, relation, relational, normalise, normalize,
   normal form, c1970, c197x, c19xx

%A B. W. Aldiss
%T Supertoys Last All Summer Long: And Other Stories of the Future
%D 1969
%P 256
%O Orbit UK, or Griffin USA, 2001
%K book, c1969, c196x, c19xx, science fiction, Brian, Super Toys, AI,
   Artificial Intelligence, movie, film, Stanley Kubrick, Spielberg, zz1101
%X uk us isbn:0312280610;
   also see [<A HREF="http://www.allisons.org/ll/Images/Film/AI/">AI</A>].

%A P. C. Poole
%A W. M. Waite
%T Machine independent software
%J Proc. ACM 2nd Symp. Operating System Principles
%W Princeton, New Jersey
%P ?-?
%D 1969
%K conf, PCPoole, c1969, c196x, c19xx, software, portability

%A L. Peter
%A R. Hull
%T The Peter Principle: Why things always go wrong
%I HarperPerennial
%P 192
%D 1969
%K book, c1969, c196x, c19xx, Peter Principle, principal, law, laws, Peter,
   peters, boss, bosses, job, jobs, promotion, productivity, management,
   level of incompetence, incompetent, funny, haha, ha ha
%X ?? ed 1998; pb us$20; uk us isbn:0688275443; uk is isbn13:978-0688275440.
   (Also see  E. P. L a z e a r,  2 0 0 4.)
   [Also search for: funny law].

%A T. C. Schelling
%T Models of segregation
%J Amer. Econ. Rev.
%V 59
%N 2
%P 488-493
%D 1971
%K jrnl, c1969, c196x, c19xx, zz0914, model, simulation, dynamic, agent based,
   game theory, human behaviour, sociology, neighbourhood, local, separation,
   tipping, micromotive, race, USA, economics, 2005 Nobel Prize, NobelPrize,
   Dr Strangelove, collateral damage
%X paper@[<A HREF="http://www.jstor.org/stable/1823701">Jstor</A>]['14].
   ("... awarded the 2005 Nobel Memorial Prize in Economic Scis. (shared with
      R.Aumann) for 'having enhanced our understanding of conflict and
      cooperation through game-theory analysis'. ... conversations between
      Kubrick, S., & George eventually led to the 1964 movie 'Dr.Strangelove
      or: How I Learned to Stop Worrying and Love the Bomb.' ... S. is also
      cited for the first known use of the phrase collateral damage in his
      May 1961 article entitled 'Dispersal, Deterrence, and Damage' ..."
      -- TS@[<A HREF="http://en.wikipedia.org/wiki/Thomas_Schelling">wikip</A>]['14].)
   (Also see,
        'Dynamic Models of Segregation,' J. of Math. Sociology, 1(2),
         pp.143-186, 1971
         -- pdf@[<A HREF="http://www.stat.berkeley.edu/~aldous/157/Papers/Schelling_Seg_Models.pdf">b'rkley</A>]['14].)

%A M. C. Newey
%A P. C. Poole
%A W. M. Waite
%T Abstract machine modelling to produce portable software - a review and
   evaluation
%J SPE
%V 2
%P 107-136
%D 1972
%K jrnl, SPE, PCPoole, jrnl, programming languages, compiler, compilers,
   portability, code

%A K. Popper
%T The Logic of Scientific Discovery
%I Hutchinson
%D 1972
%K book, text, karl, philosophy of science, inference, process, prediction,
   predict, theory, hypothesis, c1972, c197x, c19xx
%X Popper (1902-1994)  (ref #1 in  K i n g  et al 2OO4).

%A R. J. Dakin
%A P. C. Poole
%T A mixed code approach
%J COMPJ
%V 16
%N 3
%D 1973
%P 219-222
%K jrnl, mitem, PCPoole, editor, compiler, interpreter, pseudo code
%X heavily used parts of editor are compiled,
   lightly used parts are interpreted.

%A M. J. O'Donell
%T A critique of the foundations of Hoare style programming logics
%J CACM
%V 25
%N 12
%M DEC
%D 1982
%P 927-935
%K jrnl, program verification, proof, logic, soundness, correctness
%X some Hoare rules are not sound;
   clarifies definitions of correctness of a logic;
   only strongest definition is acceptable
   corrects unsound rules;
   probably need a more flexible notation than Hoare's.

%A E. W. Dijkstra
%T Guarded commands, nondeterminacy and formal derivation of programs
%J CACM
%V 18
%N 8
%P 453-457
%M AUG
%D 1975
%K jrnl, CACM, c1975, c197x, c19xx, if, do, conditional, loop, guarded command,
   nondeterminacy, nondeterministic

%A E. W. Dijkstra
%T A Discipline of Programming
%I PrenticeHall
%D 1976
%O 1997
%K text, book, structured programming, methodology, c1976, c197x, c19xx
%X uk us isbn:013215871X;

%A S. Dasgupta
%T The organization of microprogram stores
%J Computing Surveys
%V 11
%N 1
%M MAR
%D 1979
%K microprogram, microprogramming, computer, architecture, firmware, read-only,
   writeable control store, c1979, c197x, c19xx
%X survey

%A R. Davis
%A B. G. Buchanan
%T Meta-level knowledge: overview and applications
%J IJCAI-77
%P 920-927
%D 1977
%K meta level knowledge, expert system

%A D. W. Davies
%T Some regular properties of the data encryption standard algorithm
%J Advances in Cryptology, CRYPTO 82
%E D. Chaum
%E R. L. Rivest
%E A. T. Sherman
%I Plenum Press
%P 89-96
%D 1982
%K code, cryptography, DES, cypher, cipher

%A J. L. Elshoff
%T An investigation into the effects of the counting method used on
   software science measurements
%J Sigplan
%P 30-44
%M FEB
%D 1978
%K software measure, metric

%A N. Francez
%T A case for a forward predicate transformer
%J IPL
%V 6
%N 6
%P 196-198
%M DEC
%D 1977
%K predicate transformer, axiom, axiomatics, precondition

%A N. Francez
%T B. Klebansky
%A A. Pnueli
%T Backtracking in recursive computations
%J Acta Informatica
%V 8
%P 125-144
%D 1977
%K alternative operator, nondeterminism, choice, semantics
%X Denotational semantics of recursive equations with the alternative
   operator. Can use recursion and backtracking.
   Uses set valued functions in semantics.

%A W. S. Ford
%A V. C. Hamacher
%T Low level architecture features for supporting process communication
%J COMPJ
%V 20
%N 2
%P 156-162
%M MAY
%D 1977
%K jrnl, architecture, communicate, message, process, mailbox

%A R. W. Floyd
%T The paradigms of programming
%J CACM
%V 22
%N 8
%M AUG
%D 1979
%P 455-460
%K jrnl, award, paradigm, computer programming, c1979, c197x, c19xx
%X the 1978 Turing award lecture.

%A A. Fitzsimmons
%A T. Love
%T A review and evaluation of software science
%J Computing Surveys
%V 10
%N 1
%M MAR
%D 1978
%P 3-18
%K c1978, c197x, c19xx, software science, software metric
%X survey of Halstead's SS,
   attempts to predict program size, complexity, number of bugs etc.
   from statistical measurements of programs or problems.

%A N. V. Findler
%T Studies in machine cognition using the game of poker
%J CACM
%M APR
%D 1977
%V 20
%N 4
%P 230-245
%K AI, machine learning, c1977, c197x, c19xx, game playing, risk, bluff,
   poker, c1977, c197x, c19xx
%X [Also search for: poker AI].

%A F. Bohnenblust
%T The algebraical braid group
%J Annals of Mathematics
%V 48
%N 1
%M JAN
%D 1947
%P 127-136
%K jrnl, c1947, c194x, c19xx, algebraic, braid, knot, plat, platt, sennet

%A M. Blum
%A D. Kozen
%T On the power of the compass (or why mazes are easier to search than graphs)
%J 19th Annual Symposium on the Foundations of Computer Science
%P 132-142
%D 1978
%M OCT
%K conf, c1978, c197x, c19xx, maze, graph, automata
%X finite automata searching a maze, visit every reachable cell
    moves north, south, east, west
    results: there is a finite state automata with 2 pebbles that
             can search all mazes,
             there are 2 FSA which together can search all mazes,
             there is a logspace algorithm to search all mazes.

%E R. H. Austing
%E B. H. Barnes
%E D. T. Bonnette
%E G. L. Engel
%E G. Stokes
%T Curriculum 78
%J CACM
%V 22
%N 3
%M MAR
%D 1979
%P 147-165
%K CACM, jrnl, c1979, c197x, c19xx, computing, curriculum, teach, teaching,
   syllabus, courses

%A P. Benioff
%T The computer as a physical system: A microscopic quantum mechanical
   Hamiltonian model of computers as represented by Turing machines
%J J. Stat. Physics
%M MAY
%D 1980
%K jrnl, c1980, c198x, c19xx, zz0623, quantum computing, computer
%X "... a microscopic q.mechanical model of computers as represented by Turing
   m/cs is constructed. It is shown that for each number N & TM Q there exists a
   Hamiltonian H_N^Q & a class of appropriate initial states s.t. if c is such
   an initial state, then psi Q^N(t)=exp(-1H_N^Qt)psi Q^N(0) correctly describes
   at timest 3,t 6,...,t_{3N} model states that corr. to the completion of the
   first, second, ..., Nth computation step of Q. The model parameters can be
   adjusted so that for an arbitrary time interval d around t 3,t 6,...,t 3N,
   the 'machine' part of psi Q^N(t) is stationary."
   -- [<A HREF="https://doi.org/10.1007/BF01011339">doi:10.1007/BF01011339</A>]['23].
   [Also search for: quantum computer].

%A J. L. Bentley
%A J. B. Saxe
%T Generating sorted lists of random numbers
%J ACM Trans. on Math. Software
%V 6
%N 3
%P 359-364
%M SEP
%D 1980
%K jrnl, TOMS, c1980, c198x, c19xx, random number, numbers, RNG, PRNG, generate,
   uniform, ascending, descending, ordered, list, lists, incremental,
   incrementally, efficient, generate, generating, sample, sampling, different,
   distinct
%X "... linear worst-case time (if it can call a perfectly random gen. for
   a single uniform) ... If the #s are not req. to be gen. all at once
   [can do it incrementally in] constant [space]."          -- via DS, '08.
   pdf: [<A HREF="https://doi.org/10.1145/355900.355907">doi:10.1145/355900.355907</A>]['08].
   (i.e. better than:  Generate n numbers; sort; use them 1 at a time.)
   (Uses, L2: The prob. dist'n of the max of n indep. random #s from U[0,1]
   is the same as that of the nth root of a single # from U[0,1].)

%A A. Ralston
%A M. Shaw
%T Curriculum 78 - is Computer Science really that unmathematical
%J CACM
%M FEB
%D 1980
%V 23
%N 2
%P 67-70
%K CACM, jrnl, c1980, c198x, c19xx, curriculum, teach, teaching, syllabus,
   CSci, Comp Sci, maths, mathematics, education

%A E. B. Koffman
%A P. L. Miller
%A C. E. Wardle
%T Recommended curriculum for CS1, 1984
%J CACM
%V 27
%N 10
%M OCT
%D 1984
%K CACM, jrnl, c1984, c198x, c19xx, CS1, CSC1, CS101, CSC101, curriculum,
   teach, teaching, syllabus

%A A. Ralston
%T The first course in computer science needs a mathematics corequisite
%J CACM
%V 27
%N 10
%D OCT
%D 1984
%P 1002-1005
%K CACM, jrnl, c1984, c198x, c19xx, curriculum, teach, teaching, syllabus

%A A. S. Fraenkel
%A M. R. Garey
%A D. S. Johnson
%A T. Schaefer
%A Y. Yesha
%T The complexity of checkers on an N x N board - preliminary report
%J 19th Annual Symposium on Foundations of Computer Science, FOCS
%D 1978
%M OCT
%P 55-64
%K checkers, chequers, Pspace, hard, complete
%X shown Pspace hard.
   under some assumption on drawing rule shown Pspace complete

%A E. F. Gehringer
%A D. P. Siewiorek
%A Z. Segall
%T Parallel Processing: the Cm* Experience
%I Digital Press/ DEC, Bedford, MA.
%D 1986
%K c1986, c198x, c19xx, Cm*, Cm star, multiprocessor, Hydra, computer,
   architecture
%X Cm*   50 processor system, Carnegie Mellon University;  isbn:0-932376-91-6.
   Reviewed Computing Reviews Dec 1987 p.620 V.28 No.12.

%A R. Y. Kain
%A C. E. Landwehr
%T On access checking in capability-based systems
%J IEEE Trans. on Software Engineering
%V SE-13
%N 2
%M FEB
%D 1987
%P 202-207
%K capability, DoD, security, *-property
%X reviewed Computing Reviews,  Dec 1987 V28 N12 p.641.

%A S. Sokolowski
%T Soundness of Hoare's logic: an automated proof using LCF
%J TOPLAS
%V 9
%N 1
%M JAN
%D 1987
%P 100-121
%K TOPLAS, jrnl, c1987, c198x, c19xx, LCF, axiom, axiomatics, logic
%X experiment with Edinburgh LCF theorem prover.
   the application is an example.
   purpose to investigate proof organization.
   Initial proof used a contradictory axiom!
   Continuity property must be checked by hand for all axioms unless
   known consistent.
   Reviewed  Computing Reviews  Dec 1987  V28 N12  p.644.

%A L. M. Goldschlager
%T A unified approach to models of synchronous parallel machines
%P 89-94
%D ????
%K complexity, parallel machine

%A R. L. Constable
%A et al
%T Implementing mathematics with the Nuprl proof development system
%I PrenticeHall
%D 1986
%K book, text, logic, constructive mathematics, Pearl
%X Reviewed in Computing Reviews Jan 1988 p55; uk us isbn:0-13-451832-2.
   part 1 tutorial on typed lambda calc, proofs and evaluation in Nuprl,
   part 2 system ref manual,
   part 3 advanced material and extended examples.

%A S. J. Bartlett
%A P. Suber
%T Self-Reference: Reflections on Reflexivity
%I Matinus Nijhoff
%S Philosophy Library
%V 21
%D 1987
%K c1987, c198x, c19xx, self reference, reflexivity, paradox, logic, philosophy
%X [Also search for: logic paradox].

%A W. W. Rouse Ball
%T Mathematical Recreations and Essays
%I University of Toronto Press
%K RouseBall
%X edited,   1st ed about 1937, 12th ed about 1974:
   isbn:0-8020-1844-0; cloth; isbn:0-8020-6138-9; paper.

%A S. W. Golomb
%T Polyominoes
%I George Allen and Unwin
%D 1965
%K book, text, polyomino, polyominoe, pentominoe, c1965, c196x, c19xx
%X also see c1995 book.

%A D. Gries
%T An illustration of current ideas on the derivation of correctness
   proofs and correct programs
%J IEEE Transactions on Software Engineering
%V SE-2
%N 4
%M DEC
%D 1976
%P 238-244
%K SWE, verification, structured programming, proof

%A D. Gries
%T An exercise in proving parallel programs correct
%J CACM
%V 20
%N 12
%M DEC
%D 1977
%P 921-930
%K on the fly garbage collector, proof, verification, parallel, concurrent,
   program, correctness, c1977, c197x, c19xx
%X development and proof of a parallel garbage collection algorithm.

%A D. Gries
%T Is sometime ever better than always
%J TOPLAS
%V 1
%N 2
%M OCT
%D 1979
%P 258-265
%K correctness, verification, proof
%X intermittent assertion method illustrated.

%A R. Landauer
%T Irreversibility and heat generation in the computing process
%J IBM J. of Res. and Dev.
%V 5
%N 3
%P 183-191
%D 1961
%K jrnl, IBM, c1961, c196x, c19xx, zz0714, quantum, quantumComputer, computing,
   computer, logic, gate, gates, energy, entropy, time, reversible,
   logical reversibility, information, principle, irreversibility,
   thermodynamics, dissipation, heat, state
%X "It is argued that computing machines inevitably involve devices which
   perform logical functions that do not have a single-valued inverse. This
   logical irreversibility is assoc. with physical irreversibility & requires a
   minimal heat generation, per machine cycle, typically of the order of kT for
   each irreversible fn. This dissipation serves the purpose of standardizing
   signals & making them indep. of their exact logical history. Two simple, but
   representative, models of bistable devices are subjected to a more detailed
   analysis of switching kinetics to yield the relationship between speed &
   energy dissipation, & to est. the effects of errors induced by thermal
   fluctuations."
   -- copy@[<A HREF="http://www.pitt.edu/~jdnorton/lectures/Rotman_Summer_School_2013/thermo_computing_docs/Landauer_1961.pdf">pitt.edu</A>]['13].
   [Also search for: Bennett c197x] and [also search for: reversible computing].
   (Also see rev.comp@[<A HREF="http://en.wikipedia.org/wiki/Reversible_computing">wikip</A>]['14].)

%A M. Gardner
%T Mathematical Games: diversions that clarify group theory, particularly
   by the weaving of braids
%J Scientific American
%M DEC
%D 1965
%P 166-177
%K braid, group theory, sennet, weave
%X [Also search for: braid].

%A J. R. Gurd
%A C. C. Kirkham
%A I. Watson
%T The Manchester prototype dataflow computer
%J CACM
%V 28
%N 1
%M JAN
%D 1985
%P 34-52
%K jrnl, dataflow, MU, c1985, c198x, c19xx
%X instruction activated when inputs are available.  1 to 2 MIPS.

%A M. H. Halstead
%A V. Schneider
%T A self-assessment procedure dealing with software science
%J CACM
%V 23
%N 8
%M AUG
%D 1980
%P 475-480
%K software science, program metric

%A D. Deutsch
%T Quantum theory, the Church-Turing principle & the universal quantum computer
%J Proc. Royal Society, A400, 97
%D 1985
%K Church's thesis, Church, quantum computer, quantumComputer, computable,
   computing, c1985, c198x, c19xx
%X in which he discusses abstract machines more
   powerful than classical Turing devices.  (from enews.)

%A J. Maddox
%T Towards the quantum computer
%J Nature
%V 316
%P 573
%M AUG
%D 1985
%K c1985, c198x, c19xx, Church's thesis, computability, quantum, computing
%X review of D. Deutsch's article
   wherein he discusses the sad fact that ordinary Turing machines, which map
   only integers to integers, have been overtaken by models which conform
   better to quantum reality.
   -- [<A HREF="https://doi.org/10.1038/316573a0">doi:10.1038/316573a0</A>]['24].

%A La'szlo' Kalma'r
%T An Argument Against the Plausibility of Church's Thesis
%J Constructivity in Mathematics, Proc. of the Colloquium
   held at Amsterdam
%D 1957
%I NorthHolland
%K computability, effective, Church, Laszlo, Kalmar, c1957, c195x, c19xx,
   uniform, uniformity, constructive, proof
%X (from enews)
   he writes (page 73):
   "In particular, I do not suppose the calculation method to be 'uniform'.
   By the way, such an uniformity assumption seems to have no objective
   meaning. For a school-boy, the method for the solution of the diverse
   arithmetical problems he has to solve does not seem uniform until he
   learns to solve equations; and several methods in algebra, geometry and
   theory of numbers which are now regarded group-theoretic methods were not
   considered as uniform before group-theory has been discovered."
      Uniformity is the most fundamental assumption in computation theory, and
   disposing of it would require deeper arguments than the one above.

%A D. Deutsch
%T ?
%J Int. J. Theoretical Phys
%V 24
%P 1-41
%D 1985
%K IJTP, quantum computer, computing, computability, Church, Church's thesis,
   UTM, UQC, universal quantum computer
%X via enews
      apparently more detail on quantum theory, the Church-Turing principle
   and the universal quantum computer:
   Most of the claims he makes seem to me well founded.  If indeed we could
   build a universal quantum computer, I believe the test he proposes of
   Everett's 'Many Worlds' interpretation would work.  In particular, such
   a test would discriminate between Everett's interpretation and Cramer's
   'Transactional' interpretation
   [JG Cramer, Rev Mod Phys 58 (1986) pp 647-687].
      Returning momentarily to the computer science aspects - I think Deutsch
   has also made a good case that a Turing machine cannot simulate a general
   physical system but a universal quantum computer can.  If you believe the
   human brain to be an instance of a physical system, you can argue that the
   attempt to simulate it by a Turing machine is fundamentally misconceived.
   I, for one, would indeed so argue.

%A T. Erber
%A S. Putterman
%T Randomness and Quantum Mechanics - Nature's Ultimate Cryptogram?
%J Nature
%V 318
%P 41-43
%M NOV
%D 1985
%K computability, Church, Church's thesis, quantum computer, computing
%X via enews:
   inverse thinking to the line of thought of Deutsch.
   They reason: Hmm, Quantum Computers being more
   powerful than a Turing Machine seems fishy. Perhaps the simplest
   physical systems instead of being "equivalent to algorithms and
   computers of unbounded complexity" are really finite in some sense,
   and propose an experiment (very hard to do though - see below) that
   would look at a binary on-off signature of a fluorescing isolated
   ion with a cryptographic magnifying glass. The technology is now
   available to isolate small numbers and even single ions and neutral
   atoms, but the experimental setup is extremely difficult. There were
   letters to Nature on the plausibility of the experimental design after
   the paper was published. I had a poster on this at the 1986 Computers
   and Math Conf.. Does anybody know if the proceeding of that
   conference were published?
      Albert Boulanger<!-- email: aboulanger@bbn.com -->.

%A R. Hill
%T A First Course in Coding Theory
%I OUP
%S Oxford Applied Mathematics and Computing Science Series
%D 1986
%K book, text, OUP, c1986, c198x, c19xx, coding theory
%X Notation                                         xi.
   1 Introduction to error-correcting codes          1.
   2 The main coding theory problem                 11.
   3 An introduction to finite fields               31.
   4 Vector spaces over finite fields               41.
   5 Introduction to linear codes                   47.
   6 Encoding and decoding with a linear code       55.
   7 The dual code, tha parity-check matrix,
     and syndrome decoding                          67.
   8 The Hamming codes                              81.
   9 Perfect codes                                  97.
  10 Codes and Latin squares                       113.
  11 A double-error correcting decimal code and
       an introduction to BCH codes                125.
  12 Cyclic codes                                  141.
  13 Weight enumerators                            165.
  14 The main linear coding theory problem         175.
  15 MDS codes                                     191.
  16 Concluding remarks, related topics, and
     further reading                               201.

%A P. Cheeseman
%A M. Self
%A J. Stutz
%A J. Kelly
%A W. Taylor
%A D. Freeman
%T Autoclass: a Bayesian classification system
%I NASA Ames Research Centre
%D 1988
%K classification, induction, taxonomy, machine learning,
   minimum message length encoding, MML, description, MDL
%O 5th Int. Conf. on Machine Learning, c1988, c198x, c19xx
%X User assumes there is a classification of some type.
   User does not specify number of classes or values of parameters
   of classes.  The algorithm finds the most probable classification given
   these very few assumptions.  Random data yields 1 class.
   Class membership is probabilistic, but usually an object
   is strongly in just one class.  Cheeseman claims similar to
   Wallace's method [also search for: Wallace MML SNOB].
   E.g., has been used to classify spectra of infra-red stars or sources.
   [Also search for: mixture SNOB].

%A V. P. Srini
%T An architectural comparison of data flow systems
%J IEEE Computer
%M MAR
%D 1986
%P 68-87
%K dataflow, data flow, survey

%A P. C. Capon
%A D. Morris
%A J. S. Rohl
%A I. R. Wilson
%T The MU5 compiler target language and autocode
%J Computer J.
%V 15
%N 2
%P ?-?
%D 1972
%K jrnl, COMPJ, compilers, computer system, architecture,
   programming languages, MU5, UK, Manchester, c1972, c197x, c19xx
%X JSR became Prof of CS at UWA.

%A R. N. Ibett
%A P. C. Capon
%T The development of the MU5 computer system
%J CACM
%V 21
%N 1
%M JAN
%D 1978
%P 13-24
%K MU5, pipeline, Manchester, architecture, ICL, c1978, c197x, c19xx

%A D. R. Innes
%T Interval analysis, pagination and program locality
%J IPL
%V 5
%N 4
%M OCT
%D 1976
%P 91-96
%K page, paging, locality, virtual memory

%A D. R. Innes
%T Exploiting the least recently used page replacement algorithm
%J SPE
%V 7
%P 271-273
%D 1977
%M MAR
%K LRU, paging, virtual memory

%A A. J. Jammel
%A H. G. Stiegler
%T Managers versus monitors
%J Information Processing 77
%I IFIP
%E B. Gilchrist
%P 827-830
%K monitor, operating system

%A A. P. Kyne
%T Proving properties of programs that manipulate dynamic data structures
%J ACSC 1
%M FEB
%D 1978
%K ACSC, verification, array

%A S. H. Lavington
%A G. Thomas
%A D. B. G. Edwards
%T The MU5 multicomputer communication system
%J IEEE Transactions on Computers
%V C-26
%N 1
%M JAN
%D 1977
%P 19-28
%K exchange, MU5, crossbar switch, communication, network

%A N. K. Madsen
%A G. H. Rodrigue
%A J. I. Karush
%T Matrix multiplication by diagonals on a vector/ parallel machine
%J IPL
%V 5
%N 2
%M JUN
%D 1976
%P 41-45
%K matrix multiplication, parallel, vector, machine, diagonal

%A B. B. Mandelbrot
%T Fractals, Form Chance and Dimension
%I W. H. Freeman and Co.
%D 78??
%K fractal, dimension, self similar, scaling, scale, c1978, c197x, c19xx

%A R. A. De Millo
%A R. J. Lipton
%A A. J. Perlis
%T Social processes and proofs of theorems and programs
%J CACM
%V 22
%N 5
%M MAY
%D 1979
%P 271-280
%K jrnl, ACM, program proof, verification, c1979, c197x, c19xx
%X argue that verification such an effort compared to programming that
   it will never be easily and widely used and therefore
   should not dominate programming language design.

%A A. J. Perlis
%T Epigrams on programming
%J SIGPLAN
%I ACM
%V 17
%N 9
%P 7-13
%M SEP
%D 1982
%K computer programming, jrnl, epigram, quote, quotes, quotable, quip,
   aphorism, wit, funny, saying, syntactic sugar, c1982, c198x, c19xx
%X E.g., 1.One man's constant is another man's variable.
         2.Functions delay binding: data structures induce binding. Moral:
           Structure data late in the programming process.  ...
         7.It is easier to write an incorrect program than understand a
           correct one.  ...
         31.Simplicity does not precede complexity, but follows it.  ...
   local [<A HREF="/~lloyd/tildeMisc/1982/Perlis-Epigrams.html">copy</A>].

%A G. L. Miller
%T Riemann's hypothesis and tests for primality
%J JCSS
%V 13
%P 300-317
%D 1976
%O Proc. 7th annual ACM Symp. on Theory of Computing (STOC) '75
%K JCSS, jrnl, c1976, c197x, c19xx, Rabin, prime, number, primes, primality,
   test, testing, extended, Riemann, Reimann, Rieman, Riemanns, hypothesis
%X "... present new upper bounds on the complexity of algs. for testing the
   primality of a number. The 1st UPB is 0(n^(1/7)); it improves the prev. best
   known bound of 0(n^(1/4)) due to Pollard. The 2nd UPB is dependent on the
   Extended Riemann Hypothesis (ERH): assuming ERH, we produce an alg. which
   tests primality & runs in time 0((log n)^4) steps. Thus we show that
   primality is testable in time a polynomial in the length of the binary
   representation of a number. Finally, we give a partial soln to the
   relationship between the complexity of computing the prime factorization of
   a num., computing the Euler phi fn, & computing other related functions."
   -- STOC@[<A HREF="http://dx.doi.org/10.1145/800116.803773">doi:10.1145/800116.803773</A>]['11].
      (Also show a class of fns, inc. Euler phi fn are computationally
      equiv. to factoring integers.)
   [Also search for: primality]  and  [also search for: Rabin primality].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Primes/">primality</A>].)

%A D. Morris
%A P. C. Treleaven
%T A stream processing network
%J Sigplan Conf. on Programming Languages for Parallel and Vector Machines
%P 107-112
%D 1975
%K stream processing

%A A. J. Maeder
%A S. A. Wynton
%T Some parallel methods for polynomial root-finding
%J Journal of Computational and Applied Mathematics
%V 18
%P 71-81
%D 1987
%K parallel algorithm, polynomial, zero, root finding, solving

%A C. Babbage
%T On the Mathematical Powers of the Calculating Engine
%D 1837
%O in B. Randell, The Origins of Digital Computers, Springer-Verlag 1973
%K Babbage, history, mechanical, calculator, c1837, c183x, c18xx, computer,
   difference, anaytical, computers, computing, difference, architecture,
   origin
%X ref in  B r o m l e y  '82.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/">computers</A>].)
   [Also search for: history computing].

%A H. P. Babbage
%T Babbage's Calculating Engines
%I London, E and F. N. Spon
%D 1889
%O reprint, pp.342, Tomash (Los Angeles) 1982
%K Babbage, Menabrae, Ada Lovelace, analytical, difference, engine, history,
   computer, computing, calculating, mechanical, Bromley, c1889, c188x, c18xx,
   book, text, origin
%X collection edited by Henry Provost Babbage,
   new introduction by Bromley,  ref in  Bromley '82.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/">computers</A>].)
   [Also search for: history computer book], (omit 'book' if you like).

%A B. Randell
%T The Origins of Digital Computers
%I SpringerVerlag
%D 1973
%K book, c1973, c197x, c19xx, history, origin, computer, computing, Babbage
%O 3rd ed 1983
%X 3rd ed isbn:0387113193;  ref in  B r o m l e y  '82.
   [Also search for: history computer book] (omit 'book' if you like).

%A M. V. Wilkes
%T Babbage as a computer pioneer
%J Proc. Babbage Memorial Meeting
%D 1971
%O Historia Mathematica, p415-440, 1977
%K Babbage, c1971, c197x, c19xx, analytical, difference, engine, history,
   computer, computing, calculating, mechanical
%X ref in  B r o m l e y  '82.
   (Also see [<A HREF="http://http://www.allisons.org/ll/Images/Computers/">Babbage</A>].)
   [Also search for: history computing].

%A A. G. Bromley
%T Charles Babbage's Analytical Engine, 1838
%J Annals of the History of Computing
%B 4
%N 3
%P 196-217
%M JUL
%D 1982
%K jrnl, c1982, c198x, c19xx, computer, Babbage, Mill, difference, analytic,
   historical, old, mechanical, calculate, calculator
%X 9 refs;
   Annals of H of C:    621.3819509 ANN  Caulfield 1980-
                        H 510.7805 A613  H'grave '79-'91
   IEEE ann' of H of C  H 510.7805 A613  '92-
   (Also see [<A HREF="http://http://www.allisons.org/ll/Images/Computers/">Babbage</A>].)

%A A. G. Bromley
%T Difference and analytical engines
%J Computing Before Computers: The History of Computing
%E W. Asprey
%P 59-98
%I Univ. Ohio Press
%D 1989
%K book, c1989, c198x, c19xx, Charles Babbage, mechanical, history,
   computing, computer, engine, Mill, old

%A A. G. Bromley
%T Analog computing devices
%J Computers before Computing: The History of Computing
%E W. Asprey
%P 156-199
%I U. of Ohio Press
%D 1990
%K chapter, c1990, c199x, c19xx, history, computer, computers, analog, analogue,
   old, book, text, c1990, c199x, c19xx, nonStandard computing
%X (In book hb us$58; uk us isbn:0813800471; uk us isbn13:978-0813800479.)
   [Also search for: history computing] & [also search for: analogue computing].

%A A. G. Bromley
%T Analytical Engine
%J Encyclopedia of Computer Science 3rd edn
%E A. Ralston
%E E. D. Reilly
%I VanNostrandReinhold
%P 68
%D 1993
%K Charles Babbage, mechanical, history, computing, computer, Mill, old, zz1197
%X Hargrave 004.03 R164E3.
   [Also search for: history computing].

%T Metcalfe's law
%D 1993
%K Metcalfe, laws, c1993, c199x, c19xx, zz0521, laws, telecommunications,
   Gilder
%X "Metcalfe's law states that the value of a telecommunications n/wk is
   proportional to the square of the # of connected users of the system
   (n^2). First formulated in this form by George Gilder in 1993,[1] &
   attributed to Robert Metcalfe in regard to Ethernet ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Metcalfe%27s_law">wikip</A>]['21].
   [Also search for: funny law].

%A F. Glover
%A E. Taillard
%A D. De Werra
%T A user's guide to tabu search
%J Ann. Oper. Res.
%V 41
%P 3-28
%D 1993
%K tabu search, c1993, c199x, c19xx, heuristic, meta-heuristics, metaHeuristic,
   deWerra

%A A. G. Bromley
%T Difference engine
%A A. Ralston
%E E. D. Reilly
%I VanNostrand Reinhold
%P 431-432
%D 1993
%J Encyclopedia of Computer Science 3rd edn
%K Charles Babbage, c1993, c199x, c19xx, mechanical, history, origin, computing,
   computer, old, tables, calculating
%X (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/">computers</A>].)

%A G. J. Tee
%T The heritage of Charles Babbage in Australasia
%J Annals of the History of Computing
%V 5
%N 1
%M JAN
%D 1983
%P 45-60
%K jrnl, c1983, c198x, c19xx, Babbage, difference engine, analytical engine
%X "Charles Babbage's eldest son, Benjamin Herschel Babbage (1815-1878) migrated
   to South Australia in 1851, & numerous descendants now live in Australia &
   New Zealand. Many relics of Charles Babbage are now in Australasia ..."
   -- [<A HREF="https://doi.org/10.1109/MAHC.1983.10006">doi:10.1109/MAHC.1983.10006</A>]['24].

%A G. J. Tee
%T The pioneering women mathematicians
%J The Mathematical Intelligencer
%V 5
%N 4
%P 27-36
%D 1983
%K Hypatia, Agnesi, Somerville, Augusta Ada Countess of Lovelace, Babbage,
   Sophie Germain, women, science, mathematics, maths,
   STEM, c1983, c198x, c19xx
%X -- [<A HREF="https://doi.org/10.1007/BF03026507">doi:10.1007/BF03026507</A>]['19].
   [Also search for: women maths].

%A J. K. Ousterhout
%A D. A. Scelza
%A P. S. Sindhu
%T Medusa: an experiment in distributed operating system structure
%J CACM
%M FEB
%D 1980
%V 23
%N 2
%P 92-105
%K medusa, operating system, CM*, multiprocessor, multi

%A H. Noot
%T Structured text formatting
%J SPE
%V 13
%P 79-94
%D 1983
%N 1
%M JAN
%K format, formatting, text

%A D. C. Oppen
%T Prettyprinting
%J TOPLAS
%V 2
%N 4
%M OCT
%D 1980
%P 465-483
%K pretty printing, prettyprinting, formatting, text editing

%A P. Naur
%T An experiment on program development
%J BIT
%V 12
%D 1972
%P 347-365
%K programming methodology, 8-queens, nqueens
%X stepwise refinement example is 8 queens

%A R. Nevatia
%T Locating object boundaries in textured environments
%J IEEE Transactions on Computers
%M NOV
%D 1976
%P 1170-1175
%V C-25
%N 11
%K boundary, edge, detection, image processing, texture

%A R. M. Russell
%T The Cray-1 computer system
%V CACM
%V 21
%N 1
%M JAN
%D 1978
%P 63-72
%K c1978, c197x, c19xx, Cray, Cray1, array, vector machine, computer

%A J. A. H. Shepperd
%T Braids which can be plaited with their threads tied together at each end
%J Proc. Royal Soc. of London.
%V AV265
%D 1962
%P 229-244
%K braid, plait, sennet, permutation, group
%X decision procedure and calculation algorithm .
   All paits on 3 strings can be done with ends tied, not all for > 3.

%A C. D. Stamopoulos
%T Parallel image processing
%J IEEE Transactions on Computers
%V C-24
%N 4
%M APR
%D 1975
%P 424-433
%K cellular logic, pattern recognition

%A A. L. Samuel
%J IBM Journal
%T Some studies in machine learning using the game of checkers II -
   recent progress
%M NOV
%D 1967
%P 601-617
%K jrnl, c1967, c196x, c19xx, checkers, chequers, game, AI, c1967, c196x, c19xx
%X Legendary game playing program
   [Also search for: samuel c1959].

%A A. Zahavi
%T Mate selection - a selection for a handicap
%J JTB
%V 53
%P 205-214
%D 1975
%K jrnl, JTB, c1975, c197x, c19xx, handicap principle, peacock, peacocks tail,
   biol, evolution

%A A. Zahavi
%T The cost of honesty (further remarks on the handicap principle)
%J J. Theor. Biol.
%V 67
%P 603-605
%D 1977
%K jrnl, JTB, c1977, c197x, c19xx, mate selection, attraction,
   deception, deceit, honesty
%X -- [<A HREF="https://doi.org/10.1016/0022-5193(77)90061-3">doi:10.1016/0022-5193(77)90061-3</A>]['24].

%A B. A. Sheil
%T The psychological study of programming
%J Computing Surveys
%V 13
%N 1
%M MAR
%D 1981
%P 101-120
%K psychology, computer programming, human factors

%A H. A. Simon
%A S. K. Reed
%T Modelling strategy shifts in a problem-solving task
%J Cognitive Psychology
%V 8
%P 86-97
%D 1976
%K problem solving, missionaries and cannibals, hint, clue, strategy

%A S. G. Tucker
%T Microprogram control for System/360
%J IBM Systems J.
%V 6
%N 4
%D 1967
%P 222-241
%K 360, jrnl, IBM

%A R. Turner
%A B. Strecker
%T Use of the LRU stack depth distribution for simulation of paging behaviour
%J CACM
%M NOV
%D 1977
%V 20
%N 11
%P 795-798
%K page, virtual memory, least recently used, working set, fault

%A I. Watson
%A J. Gurd
%T The data flow project
%M MAY
%D 1977
%I Computer Science dept, Manchester University
%K dataflow machine

%A I. Watson
%A J. Gurd
%T A prototype data flow computer with token labelling
%J National Computer Conf.
%D 1979
%P 623-628
%K dataflow machine

%A D. J. J. van der Knijff
%T Software physics and program analysis
%J Australian Computer J.
%V 10
%N 3
%M AUG
%D 1978
%P 82-86
%K metric, jrnl, ACJ

%A J. Weizenbaum
%T Eliza - a computer program for the study of natural language
   communication between man and machine
%J CACM
%V 9
%N 1
%P 36-45
%M JAN
%D 1966
%K jrnl, CACM, c1966, c196x, c19xx, AI, natural language, Eliza, doctor, script,
   conversation, chatBot
%X "ELIZA is a program operating within the MAC time-sharing system at MIT which
   makes certain kinds of natural language conversation between man & computer
   possible. Input sentences are analyzed on ... Responses are generated by
   reassembly rules associated with selected decomposition rules. ... A
   discussion of some psychological issues relevant to the ELIZA approach as
   well as of future developments ..."
   -- [<A HREF="https://doi.org/10.1145/365153.365168">doi:10.1145/365153.365168</A>]['22].
   [Also search for: chatBot].

%A N. Wirth
%T On the composition of well-structured programs
%J Computing Surveys
%V 6
%N 4
%M DEC
%D 1974
%P 247-259

%A N. Wirth
%T Program development by stepwise refinement
%J CACM
%V 14
%N 4
%M APR
%D 1971
%P 221-227

%A D. L. Waltz
%T An English language question answering system for a large relational database
%J CACM
%V 21
%N 7
%M JUL
%D 1978
%P 526-539
%K planes, natural language, data base

%A W. Wulf
%A E. Cohen
%A W. Corwin
%A A. Jones
%A R. Levin
%A C. Pierson
%A F. Pollock
%T Hydra: the kernel of a multiprocessor operating system
%J CACM
%V 17
%N 6
%M JUN
%D 1974
%P 337-345
%K jrnl, CACM, c1974, c197x, c19xx, Hydra, CM*, CMstar, multiprocessor

%A W. M. Waite
%T The mobile programming system: stage2
%J CACM
%V 13
%N 7
%M JUL
%D 1970
%P 415-421
%K macro, bootstrap

%A M. M. Zloof
%A S. P. de Jong
%T The system for business automation (SBA): programming language
%J CACM
%V 20
%N 6
%M JUN
%D 1977
%P 385-396
%K form, forms

%A E. C. Zeeman
%T levels of structure in catastrophe theory illustrated by applications
   in the social and biological sciences
%J Proc. Int. Congress of Mathematicians
%W Vancouver
%D 1974
%P 533-546
%K catastrophe theory

%T Zilog Z80 manual
%D 1982 ?
%K microprocessor, Z80

%A V. Booth
%T Writing a Scientific Paper
%I The Biochemical Society (London)
%D 1971 (4th edn. 77)
%K style, guide

%A S. D. Supanekar
%T Computer study of knots
%J Computer Graphics and Image Processing
%V 11
%P 150-161
%D 1979
%K knot, theory, Tait
%X uses Tait representation.

%A J. M. Diamond
%T Why cats have nine lives
%J Nature
%V 332
%P 586-587
%D 1988
%K cat, fall, falling, terminal velocity, nine lives

%A R. Graham
%A D. Knuth
%A O. Patashnik
%T Concrete Mathematics
%I AddisonWesley
%P 672
%D 1988
%K book, text, maths, math, c1988, c198x, c19xx, sums, recurrence,
   discrete probability
%X 2nd ed '94, us$70 -> us$48, isbn:0201558025; isbn13:978-0201558029.
   From (Wayne Folta) <!-- email: folta@tove.umd.edu  -->.  Sat Nov  5 08:21:04 1988 from enews.

%A S. W. Golomb
%T Sphere packing, coding metrics and chess puzzles
%J Chapel Hill Conf. on Combinatorial Mathematics and its Applications
%M MAY
%D 1970
%E R. C. Rose
%P 176-189
%K n-queens, nqueens, torus, toroidal, superqueen, octagon

%A S. W. Golomb
%A L. R. Welch
%T Perfect codes in the Lee metric and the packing of polyominoes
%J SIAM Journal of Applied Mathematics
%V 18
%N 2
%P 302-317
%M JAN
%D 1970
%K code, polyominoe, polyomino, c1970, c197x, c19xx

%A J. Pearl
%T Probabilistic Reasoning in Intelligent Systems:
   Networks of Plausible Inference
%I MorganKaufmann
%C San Mateo, California
%D 1988
%K book, text, Artificial Intelligence, Bayesian inference, II
%X isbn:0934613737.

%A J. Jaffar
%T Presburger arithmetic with array segments
%J IPL
%V 12
%N 2
%P 79-82
%D 1981
%K assertion, theorem prover, inequality

%A G. Polya
%T Uber die doppelt-periodischen losungen des n-damen problems
%B Mathematische Unterhaltungen und Spiele
%I Teuber
%W Leipzig
%D 1918
%P 364-374
%E W. E. M. G. Ahrens
%K n-queens, nqueens, queen, problem, doubly periodic
%X [Also search for: N queens problem].

%A Ming Li
%A P. M. B. Vitanyi
%T Two decades of applied Kolmogorov complexity
%J Proc. Structure in Complexity Theory, Third Annual Conf.
%M JUN
%D 1988
%W Washington
%I IEEE
%P 80-101
%K Kolmogorov, complexity, MML, compression, coding, encoding
%X a survey paper, they are going to write a book.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%T The Theory of Partitions
%A G. E. Andrews
%I AddisonWesley
%C Reading, MA
%D 1976
%P 68-87
%K book, text, c1976, c197x, c19xx, partition

%A M. Fleischmann
%A S. Pons
%T Electrochemically induced nuclear fusion of deuterium
%J J. Electroanalytic Chemistry
%V 261
%M APR
%D 1989
%P 301-308
%K nuclear, fusion, cold, Paladium, Pd, PD
%X electrolysis of heavy water + lithium salts LiOD
   with platinum anode, paladium cathode
   reports fusion in paladium producing heat, neutrons and gamma rays
   [Caused quite a stir for a while, but
   no one else could convincingly repeat it.]

%A G. L. Steele jr
%T The telnet song (Control-UpArrow Q.")
%J CACM
%V 27
%N 4
%M APR
%D 1984
%P 347-348
%K control-uparrow Q, control, up arrow, binary recursive, great quux,
   recursion, c1984, c198x, c19xx, Steele
%X [<A HREF="https://doi.org/10.1145/358027.1035691">doi:10.1145/358027.1035691</A>]['05].

%A D. Hofstadter
%T Metamagical Themas
%I Penguin Books
%D 1986
%K recursion, games, recreation, cooperate, defect, prisoner's dilemma, PD, IPD

%A A. K. Dewdney
%T Computer recreations
%J Scientific American
%P 166-169
%M Oct
%D 1987
%K iterated prisoner's dilemma, c1987, c198x, c19xx, PD, IPD, cooperate, defect,
   MAD, cooperation, mutually assured destruction, game, nuclear arms race
%X variation on coop-defect,  payoff matrix changes in attempt
   to model development of nuclear arms and likely effects if used
   over past few decades.
   Refers to Professor Homer-Dixon, Centre for International Studies,
             292 Main Street, Cambridge, Mass. 02142 USA   ran a competition.
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A G. A. Hedlund
%T Remarks on the work of Axel Thue on sequences
%J Nordisk Matematisk Tidskrift
%W Oslo
%V 15
%P 148-150
%D 1967
%K c1967, c196x, c19xx, reducible, irreducible,
   good, sequence, repeat, Dijkstra, Thue
%X Axel Thue's work often independently rediscovered.
   . seq irreducible if no block repeat ....BB....
   . infinite irreducible seq over 3 letters
   . infinite seq with no triple block repeats ...BBB...  over two letters
   . related to   almost periodicity,  unending chess game,  group theory.
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/Factors/">factors</A>].)

%A A. Thue
%T Uber unendliche zeichenreihen
%J Videnskabsselskabets Skrifter, I Mat.-nat. K1.
%W Christiania
%D 1906
%K c1906, c190x, c19xx, reducible, irreducible,
   good, sequence, repeat, Dijkstra, Thue, words, factors, word
%X Also known as Dijkstra good sequences.

%A A. M. Turing
%T On computable numbers, with an application to the  entscheidungsproblem
%J Proc., London Mathematical Society
%V 2
%N 42
%P 230-265
%D 1936
%K jrnl, c1936, c193x, c19xx, AlanTuring, Alan, Turing machine, halting problem,
   UTM, computability, decision problem, decidability, completeness,
   maths, CSci, theory, Godel
%X -- [<A HREF="https://doi.org/10.1112/plms/s2-42.1.230">doi:10.1112/plms/s2-42.1.230</A>]['24].
   And also no.43, pp.544-546.
   Halting problem;
   also see [<A HREF="https://turingarchive.kings.cam.ac.uk">turingarchive</A>]['24];
   [also search for: Church c1936]  and  [also search for: AlanTuring].

%A G. S. Callendar
%T The artificial production of carbon dioxide and its influence on temperature
%J Quarterly J. of the Royal Meteorological Soc.
%V 64
%N 275
%P 223-240
%M APR
%D 1938
%K jrnl, c1938, c193x, c19xx, zz0413, climate change, cause, global warming,
   rate, anthropogenic, CO2, greenhouse gas, gases, fossil fuel, fuels,
   energy production, oil, coal
%X "By fuel combustion man has added about 150,000 million tons of CO2 to the
   air during the past half century. The author estimates from the best
   available data that approx. 3/4 of this has remained in the atmosphere. The
   radiation absorption coefficients of CO2 & water vapour are used to show the
   effect of CO2 on 'sky radiation.' From this the increase in mean temp., due
   to the artificial production of CO2, is est. to be at the rate of 0.003C.per
   year at the present time. The temp. observations at 200[?] meteorological
   stations are used to show that world temps. have actually increased at an
   average rate of 0.005C.per year during the past half century."
   -- [<A HREF="http://dx.doi.org/10.1002/qj.49706427503">doi:10.1002/qj.49706427503</A>]['13].
   (Also see [<A HREF="http://www.guardian.co.uk/environment/blog/2013/apr/22/guy-callendar-climate-fossil-fuels">the_G</A>][23/4/2013].)

%A M. Rejewski
%T An application of the theory of permutations in breaking the enigma cipher
%J Applicationes Mathematicae
%V 16
%N 4
%P ?-?
%D 1980
%K c193x, computers, cypher, cipher, ciphers, crytography, cryptology, codes,
   ww2, WWII, Poland, Polish, bombs, bomba, bombe, cyclometer, zz0803,
   permutation group, machine, Marian Rejewski, QWERTZU
%X Warsaw 1980. Received 13.5.1977. Typeset version Enrico Grigolon, 11/'02.
   -- [<A HREF="https://doi.org/10.4064/am-16-4-543-559">doi:10.4064/am-16-4-543-559</A>]['24],
      [<A HREF="http://www.impan.gov.pl/Great/Rejewski/article.html">article</A>][8/'03].
   [Also search for: enigma machine] & [also search for: Bletchley Park].

%A M. Rejewski
%T How Polish mathematicians broke the enigma cipher
%J Annals of the History of Computing
%V 3
%N 3
%P 213-234
%D 1981
%K jrnl, Marian Rejewski, c193x, c1981, c198x, c19xx, zz0803, cypher, cipher,
   ciphers, crytography, codes, ww2, WWII, Poland, bombs, bomba, bombe,
   cyclometer, permutation group, machine, QWERTZU
%X ... personal view of ... Polish Cipher Bureau '32 - '39 as mathematicians
   worked to decipher the codes of the military version of the Enigma. The
   author, who was a participant, relates details of the device & the successes
   & frustrations involved in the work. He also describes mathematical
   principles that enabled ...break[ing]...versions of the Enigma code & to
   construct technical devices (cyclometers & "bombs") that facilitated
   decipherment of Enigma-coded messages.
   -- [<A HREF="https://doi.org/10.1109/MAHC.1981.10033">doi:10.1109/MAHC.1981.10033</A>]['24].
   [Also search for: enigma machine].

%A C. A. E. Goodhart
%T Problems of Monetary Management: The U.K. Experience
%B Monetary Theory and Practice
%E A. S. Courakis
%P 91-121
%D 1984
%K Goodharts, Goodhart's law, laws, c1984, c198x, c19xx, zz0319, assessment, UK,
   measure, evaluation, funny, ranking, impact, JIF, KPI, KPIs, Hindex,
   scientific research, university, distortion, corruption, bibliometrics,
   misuse, gaming
%X "In 1971 the monetary authorities in the UK adopted a new approach to
   monetary management, a change of policy announced & described in several
   papers on competition & credit control. The subsequent experience of trying
   to operate this revised system has, however, been troublesome & at times
   unhappy. The purpose here is to examine certain aspects of recent monetary
   developments in order to illustrate a number of more general analytical
   themes which may have relevance among several countries."
   -- [<A HREF="https://doi.org/10.1007/978-1-349-17295-5_4">doi:10.1007/978-1-349-17295-5_4</A>]['19].
   in: uk us isbn:0333360591; uk us isbn13:978-1349172955;
       uk us isbn13:9780333360606 ?
   [[MonashUni library seems to have a copy, offsite. '19]]
      (Previously I thought it was in:
      'Inflation, Depression, and Economic Policy in the West',
      pp.111-146, 1981. ??Maybe also??)
   See, "... original formulation [of G's law] was:
        'Any observed statistical regularity will tend to collapse once
        pressure is placed upon it for control purposes.' ..."
   And, "... has been phrased by Marilyn Strathern as
        'When a measure becomes a target, it ceases to be a good measure.' ..."
   And, "... All metrics of scientific evaluation are bound to be abused. ...
        ... because people start to game it. ..."
   -- GL@[<A HREF="https://en.wikipedia.org/wiki/Goodhart%27s_law">wikip</A>]['19].
   [Also search for: Campbell law]  and  [also search for: publish perish].

%A M. Rejewski
%T Mathematical solution of the enigma cipher
%J Cryptologia
%V 6
%N 1
%M JAN
%P 1-37
%D 1982
%K jrnl, c193x, c1982, c198x, c19xx, zz0803, computers, cypher, cipher, ciphers,
   cryptology, crytography, codes, ww2, WWII, Poland, Polish, bombs, bomba,
   bombe, cyclometer, permutation group, machine, Marian Rejewski, QWERTZU
%X [Also search for: enigma].

%A R. Axelrod
%A W. D. Hamilton
%T The evolution of cooperation
%J Science
%V 211
%N 4489
%M MAR
%D 1981
%P 1390-1396
%K jrnl, c1981 c198x, c19xx, iterated prisoners dilemma, PD, IPD game, defect,
   cooperate, altruism, behaviour
%X "Cooperation in organisms, whether bacteria or primates, has been a
   difficulty for evolutionary theory since Darwin. On the assumption that
   interactions between pairs of individuals occur on a probabilistic basis, a
   model is developed based on the concept of an evolutionarily stable strategy
   in the context of the Prisoner's Dilemma game. Deductions from the model, &
   the results of a computer tournament show how cooperation based on
   reciprocity can get started in an asocial world, can thrive while
   interacting with a wide range of other strategies, & can resist invasion
   once fully established. Potential applications include specific aspects of
   territoriality, mating, & disease."
   -- [<A HREF="http://dx.doi.org/10.1126/science.7466396">doi:10.1126/science.7466396</A>]['07].
   -- [<A HREF="http://www-personal.umich.edu/~axe/">auth@umich</A>]['07].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A R. Axelrod
%T The evolution of cooperation
%I BasicBooks
%W New York
%D 1984
%K book, c1984, c198x, c19xx, iterated prisoners dilemma, PD, IPD game, defect,
   cooperate, cooperative, altruism
%X uk us isbn:0465021212; uk us isbn13:9780465021215.
   -- [<A HREF="http://www-personal.umich.edu/~axe/">auth@umich</A>]['07].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A R. Axelrod
%A D. Dion
%T The further evolution of cooperation
%J Science
%V 242
%N 4884
%P 1385-1390
%M DEC
%D 1988
%K jrnl, c1988, c198x, c19xx, prisoners dilemma, PD, IPD game, defect,
   cooperate, noise, shadow of future, dynamics and structure of population
%X "... There was a fixed probability (called the "shadow of the future") of the
   game ending on the next move ... Faulty transmission of strategy choices
   (noise) severely undercuts the effectiveness of reciprocating strategies. .."
   -- [<A HREF="http://dx.doi.org/10.1126/science.242.4884.1385">doi:10.1126/science.242.4884.1385</A>]['07].

%A R. Axelrod
%T The evolution of strategies in the iterated prisoner's dilemma
%J Genetic Algorithms and Simulated Annealing
%E L. Davis
%D 1987
%I Pitman, London
%P 32-41
%K c1987, c198x, c19xx, GA, genetic algorithm, tit for tat, prisoners dilemma,
   game, learn, learning PD, IPD
%X [<A HREF="http://www-personal.umich.edu/~axe/">auth@umich</A>]['07].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A Ha-yong Zhou
%A J. J. Grefenstette
%T Induction of finite state automata by genetic algorithms
%J Proc IEEE Conf. on Systems Man and Cybernetics
%M OCT
%D 1986
%P 170-174
%V 1
%K GA, genetic algorithm, FSA, inductive inference, II, learn, learning
%X breed FSA that describe given example binary strings
   Limited to at most 8 states.

%A E. A. Gold
%T Complexity of automaton identification from given data
%J Information and Control
%V 37
%P 302-320
%D 1978
%K FSA, inductive inference, II, language, machine, learn, learning, examples
%X a lack of negative evidence => cannot learn language above Finite State
   Grammar

%A D. Angluin
%T Inductive inference of formal languages from positive data
%J Information and Control
%V 45
%P 117-135
%D 1980
%K IC, language, machine learning learn ML, AI, II, example examples, grammar
   grammars rule rules (Agluin)
%X see E. A. G o l d;    via enews.

%A Y. G. Leclerc
%T Simplicity of description as the basis for visual interpretation
%J AAAI Symp on The Theory and Application of Minimal Length Encoding
%M MAR
%D 1990
%P 100-104
%K image processing, machine vision, MML, MDL

%A R. Solomonoff
%T A system for incremental learning based on algorithmic probability
%J AAAI Symp on The Theory and Application of Minimal Length Encoding
%M MAR
%D 1990
%P 140-146
%K machine learning, inductive inference, II, MML, MDL
   minimum message description length encoding, algorithmic complexity AC
   stochastic, probability

%A Hellmuth Kneser
%T Reelle analytische Loesungen der Gleichung phi(phi(x)) = e^x
   und verwandter Funktionalgleichungen
%J J. Reine Angew. Math.
%V 187
%D 1948
%P 56-67
%K c1948, c194x, c19xx, half exp, exponential, function
%X f(x) such that f(f(x))=exp(x)
   from enews: Lambert Meertens, CWI, Amsterdam<!-- email: lambert of cwi.nl -->.

%A M. Li
%A P. M. B. Vitanyi
%T Inductive reasoning and Kolmogorov complexity
%J J. Comp. and Sys. Sci.
%V 44
%P 343-384
%D 1992
%O Proc. 4th Conf on Structure in Complexity Theory, IEEE 165-185 1989.
%K JCSS, MML, MDL, SCT, information theory, inductive inference, II,
   machine learning, handwritten character recognition, SCT
%X [Also search for: MML].

%A N. Dodd
%T Optimization of Network Structure using Genetic Techniques
%J IEEE: Proc. of the Int. Joint Conf. on Neural Networks
%V 3
%P 965-968
%W San Diego, CA.
%D 1990
%K neural net, network, NN, genetic algorithm, GA

%A S. Harp
%A T. Samad
%A A. Guha
%D 1989
%T Towards the Genetic Synthesis of Neural Networks
%J Proc. of the Third Int. Conf. on Genetic Algorithms
%P 360-369
%W San Mateo, CA
%I MorganKaufmann
%K neural net, network, NN, genetic algorithm, GA

%A G. Miller
%A P. Todd
%A S. Hegde
%D 1989
%T Designing Neural Networks using Genetic Algorithms
%J Proc. of the Third Int. Conf. on Genetic Algorithms
%P 379-384
%K neural net, network, NN, genetic algorithm, GA

%A D. Whitley
%A T. Starkweather
%T Optimising small neural networks using a distributed genetic algorithm
%J Int. Joint Conf. on Neural Networks
%M JAN
%D 1990
%W Washington, D.C.
%V 1
%P 206-209
%I IEEE
%K IEEE, IJCNN, IJCNN90, NN,
   neural net, network, genetic algorithm, subpopulation
%X Subpopulations in parallel.
   Occasional swapping of individuals between populations.
   Mix competition and diversity.
   Rough guide: 10 subpopulations, population size 200-1000,
                subpopulation size X, swap after 5X recombinations.
   Used to optimise weights of a nn for 4 problems:
       exclusive or xor problem
       424 encoder
       two versions of 2 bit adder

%A Kai-Fu Lee
%T Automatic Speech Recognition
%I Kluwer
%D 1989
%K speech, recognition, sphinx, hidden Markov model, HMM
%X isbn:0-89838-296-3.
   A to D -> Fourier analysis and time slice -> sequence of vectors ->
      seq of class (0-255) (of vectors) -> hidden Markov model -> best match
   (very like string edit distance)
   discusses problems of small vocabulary v. large vocabulary
                         one speaker      v. several speakers
                         single words     v. continuous speech
   accuracy v. storage and speed;  phoneme or word level models etc.
   [See also:  edit distance]

%A L. R. Rabiner
%T A tutorial on hidden Markov models and selected applications in speech
   recognition
%J IEEE
%V 77
%N 2
%D 1989
%P 257-286
%K HMM, model, jrnl
%X [Tim E '97]  See also  L e e '89

%A R. K. Brayton
%A G. D. Hachtel
%A C. T. McCullen
%A A. L. Sangiovanni-Vincentelli
%T Logic Minimization Algorithms for VLSI Synthesis
%I Kluwer
%K logic, boolean, circuit, SOP, minimization, VLSI
%X isbn:0-89838-164-9.

%A P. K. Simpson
%T Artificial Neural Systems
%I Pergamon Press
%D 1990
%K neural net, network, nn

%A Maren
%A Harston
%A Pap
%T Handbook of Neural Computing Applications
%I AcademicPress
%D 1990
%K neural net, network, nn
%X isbn:0125460902;

%A G. Welchman
%T The Hut Six Story
%I HamishHamilton
%P 277
%D 1978
%K book, text, enigma, machine, ultra,  code, cypher, cipher, break, breaking,
   codes, cryptanalysis, WW2, WWII, Bletchley Park, Ultra, hut 6, hut6,
   Gordon Welchman
%X pb, stg8.50, uk us isbn:0947712348.
   (ref in Hodges `Alan T the Enigma' p.548.)
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">B.Park</A>].)
   [Also search for: Bletchley Park].

%A R. Harris
%T Enigma
%I IvyBooks
%D 1996
%K fiction, book, novel, Enigma, Ultra, code, cypher, cipher, cryptanalysis,
   world war two, ww2, wwII, zz1001
%X uk us isbn:0804115486;  This is a novel, but
   [also search for: AlanTuring]  or  [also search for: Enigma].

%T Meta-Heuristics: Theory and Applications
%E I. H. Osman
%E J. P. Kelly
%W Dordrecht, .nl
%I Kluwer
%D 1996
%K meta-heuristics, metaHeuristic

%A K. Piwakowski
%T Applying tabu search to determine new Ramsey graphs
%J Electronic J. of Combinatorics
%V 3
%N 1
%D 1996
%K eJrnl, graph, number, numbers, c1996, c199x, c19xx
%X "... new lower bounds for ... R(3,13) >= 59, R(4,10) >= 80, R(4,11) >= 96,
   R(4,12) >= 106, R(4,13) >= 118, R(4,14) >= 129 and R(5,8) >= 95.
   -- [<A HREF="https://doi.org/10.37236/1230">doi:10.37236/1230</A>]['24].

%A H. Sebag-Montefiore
%T Enigma: The Battle for the Code
%I Wiley
%P 432
%D 2001
%K book, c2001, c200x, c20xx, code, break, breaking, ultra, world war two,
   code, codes, cypher, cipher, ww2, wwII
%X uk us isbn:0471407380; uk us isbn13:978-0297842514.
   [Also search for: AlanTuring] and [also search for: Bletchley Park].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">B.Park</A>].)

%A T. Kohonen
%T Adaptive, Associative, and Self-Organizing Functions in Neural Computing
%J Applied Optics
%V 26
%N 23
%P 4910-4918
%D 19??
%K NN, neural net, network
%X via enews

%A R. Balzer
%T A 15 year perspective on automatic programming
%J IEEE Trans. on Software Engineering
%V SE-11
%N 11
%M NOV
%D 1985
%P 1257-1268
%K automatic programming, survey

%A H. E. Chandler
%A V. de P. Roper
%T Citation indexing: Uses and limitations
%J The Indexer
%V 17
%N 4
%M OCT
%D 1991
%K c1991, c199x, c19xx, zz0820, science citation index, history, SCI,
   scientific literature, source, citation index, corporate, permuterm,
   history, examples, use
%X "... Explanations, with examples, are given of the four parts of the C.I.
   published by the Inst. for Sci. Inf.: the Source i., Citation I., Permuterm
   I., & Corporate I.. ..."
   -- [<A HREF="https://www.theindexer.org/files/17-4/17-4_243.pdf">www</A>]['20].

%A M. Rabbani
%A P. W. Jones
%T Digital Image Compression Techniques
%S Tutorial Text Series
%V TT7
%I SPIE Press, Bellingham, WA, USA
%D 1991
%K image compression, text, book, survey
%X Part 1: Background - Digital images and image compression.
   Part 2: Information Theory Concepts - Source models and entropy, Variable-
           length codes, Entropy estimation and lossless compression, Rate-
           distortion theory and lossy compression.
   Part 3: Lossless Compression Techniques - Bit plane encoding, Lossless
           predictive coding, Lossy plus lossless residual encoding.
   Part 4: Lossy Compression Techniques - Lossy predictive coding (DPCM),
           Transform coding (includes JPEG baseline algorithm), Block truncation
           coding, Vector quantization, Subband coding, Hierarchical coding,
           Choosing a lossy compression technique.
   Appendix: Compression of color images.
   isbn:0819406481; (softbound)
   SPIE member $34/nonmember N. America $42/Nonmember overseas $48/.

%A D. Robinson
%A P. Robinson
%T Rememberance of things parsed
%J Comp. Bull.
%M FEB
%D 1991
%P 22-24
%K language, translation, dictionary, inference, II, bible, rosetta stone,
   malachi
%X from the "same" text in two different languages infer
   a dictionary translating language 1 into 2.
   British and Foreign Bible Society
   no refs.

%A K. Lindgren
%T Evolutionary Phenomena in Simple Dynamics
%J Proc. of the second Artificial Life workshop
%I AddisonWesley.
%D ?91?
%K prisoners dilemma, tit for tat, tit-for-tat, noise, noisy, genetic algorithm
   machine learning, evolution, GA   PD, IPD
%X Tit for tat but occasional unconditional cooperation,
   via enews from:
   Nicol N. Schraudolph, CSE Dept.
   Univ. of California, San Diego
   <!-- email: nici%cs@ucsd.{edu,bitnet,uucp}  -->.

%A P. W. Stephens
%A A. I. Goldman
%T The structure of quasicrystals
%J Scientific American
%M APR
%D 1991
%P 24-31
%K c1991, c199x, c19xx, quasi crystal, crystals, quasicrystal, aperiodic,
   tiling
%X [Also search for: aperiodic tiling].

%A J. Kay
%A J. Lubin
%A G. Poiner
%A M. Prosser
%T Not even well begun: Women in computing courses
%I University of Sydney
%D 1991
%K CSci, computing, course, courses, survey, women, gender, women, science,
   STEM, c1991, c199x, c19xx
%X [Also search for: women computing].

%A D. Swade
%T The construction of Charles Babbage's difference engine
%J Annals of the History of Computing
%V 13
%N 1
%D 1991
%P 82-83
%K jrnl, c1991, c199x, c19xx, history, Babbage, computing, difference engine
%X Science Museum UK is building Babbage's difference engine
   (not his analytic engine which ~ computer)
   to celebrate 200-th anniversary of Babbage's death (1771).
   4000 parts, 3 tons, 10x6x1.5 feet
   Being built in materials and with accuracy of Babbage's day.
   The D.E. calculates 7th order polynomials to 30 decimal places.
   (Also see [<A HREF="http://allisons.org/ll/Images/Computers/">comps</A>].)

%A Joan Fisher Box
%T R. A. Fisher: The Life of a Scientist
%I Wiley
%D 1978
%K book, RAFisher, biography, stats, statistics, statistician,
   genetics, eugenics, maximum likelihood
%X Ronald Aylmer Fisher 17 Feb 1890 - 29 July 1962,
   both a personal and a scientific biography.  isbn:0471093009.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Fisher.RA/">RAF</A>].)

%A J. Mercer
%T West Antarctic ice sheet and CO2 greenhouse effect: a threat of disaster
%J Nature
%V 271
%N 5643
%P 321-356
%M JAN
%D 1978
%K jrnl, c1978, c197x, c19xx, zz1215, climate change, greenhouse gas, CO2,
   global warning, ice sheet, sea level rise, Antarctica, glaciers, melt
%X -- [<A HREF="http://dx.doi.org/10.1038/271321a0">doi:10.1038/271321a0</A>]['15].

%A G. J. Chaitin
%T Towards a mathematical definition of "life"
%B The Maximum Entropy Formalism Conf.
%E R. D. Levine
%E M. Tribus
%D 1978
%P 477-498
%I MITpress
%K conf, c1978, c197x, c19xx, information theory, life, mutual information,
   algorithmic complexity, AC
%X "...[re life] "complexity," "organism, " and "information content," are
   sometimes used in ways remarkably analogous to the approach of alg. info.
   theory, ... submit that this is not a coincidence ... propose and discuss a
   measure of degree of organization & structure of geometrical patterns which
   is based on the alg. version of S.'s concept of mutual info.. ... intended
   as a contribution to vonN.'s program of formulating mathematically the
   fundamental concepts of biology in a very general setting, i.e., in highly
   simplified model universes."   (In uk us isbn:0262120801.)
   -- pdf@[<A HREF="http://www.umcs.maine.edu/~chaitin/mit.pdf">m@ine.edu</A>][' 10].
   [Also search for: life definition].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%E J. H. Bennett
%T Natural Selection, Heredity, and Eugenics.  Including selected
   correspondence of R. A. Fisher with Leonard Darwin and others
%I Clarendon Press, Oxford
%D 1983
%K book, text, c1983, c198x, c19xx, Darwinism, evolution, Fisher, RAFisher,
   natural, pressure of selection
%X uk us isbn:0198581777;
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Fisher.RA/">RAF</A>].)

%A J. Antonisse
%T A New Interpretation of Schema Notation that Overturns the Binary Encoding
   Constraint
%J Proc. of the Third Int. Conf. on Genetic Algorithms and
   their Applications
%D 1989
%P 86-91
%K GA, genetic algorithm, automatic programming, program, machine learning
%X via enews.

%A J. J. Grefenstette
%T A System for Learning Control Plans with Genetic Algorithms
%J Proc. of the Third Int. Conf. on Genetic Algorithms and their Applications
%D 1989
%P 183-190
%K GA, genetic algorithm, automatic programming, program, machine learning
%X via enews

%A D. F. Gordon
%A J. J. Grefenstette
%T Explanations of Empirically Derived Reactive Plans
%J Proc. of the Seventh Int. Conf. on Machine Learning
%P ????
%D 1990
%K GA, genetic algorithm, automatic programming, program, machine learning
%X via enews.

%A H. J. Antonisse
%A K. S. Keller
%T Genetic Operators for High-Level Knowledge Representations
%J Proc. of the Second Int. Conf. on Genetic Algorithms and Their Applications
%D 1987
%P 69-76
%K GA, genetic algorithm, automatic programming, program, machine learning
%X via enews.

%A J. R. Koza
%T Hierarchical genetic algorithms operating on populations of computer programs
%J Proc. of the Eleventh Int. Joint Conf. on Artificial Intelligence
%D 1989
%P 768-774
%K GA, c1989, c198x, c19xx, genetic algorithm, genetic programming,
   geneticProgramming, automatic programming, automaticProgramming, program,
   machine learning, AI
%X "... describes computer experiments, using the author's 4341 line LISP
   program, in five areas of AI, namely (1) seq. induction (e.g. inducing a
   computational procedure for the recursive Fibonacci seq. & inducing a
   computational proc. for a cubic polynomial seq.), (2) automatic programming
   (e.g. discovering a computational proc. for solving pairs of linear equns,
   solving quadratic equns for complex roots, & discovering trigonometric
   identities), (3) machine learning of fns (e.g.  learning a Boolean
   multiplexer fn previously studied in neural net & classifier system work &
   learning the exclusive-or & parity fn), (4) planning (e.g. developing a
   robotic action seq. that can stack an arbitrary initial configuration of
   blocks into a specified order), & (5) pattern recognition (e.g.
   translation-invariant recognition of a simple one dimensional shape in a
   linear retina)"
   -- pdf@[<A HREF="https://www.cs.bham.ac.uk/~wbl/biblio/gp-html/Koza89.html">BHam</A>]['16].
   [Also search for: geneticProgramming].

%A K. De Jong
%T On Using Genetic Algorithms to Search Program Spaces
%J Proc. of the 2nd Int. Conf. on Genetic Algorithms
%D 1987
%P 210-216
%K conf, c1987, c198x, c19xx, deJong, GA, genetic algorithm,
   automatic programming, automaticProgramming, geneticProgramming, program,
   machine learning, AI
%X via enews

%A A. S. Bickel
%A R. W. Bickel
%T Tree Structured Rules in Genetic Algorithms
%J Proc. of the Second Int. Conf. on Genetic Algorithms and Their Applications
%D 1987
%P 77-81
%K GA, genetic algorithm, automatic programming, program, machine learning
%X via enews

%A C. Fujiki
%A J. Dickinson
%T Using the genetic algorithm to generate LISP source code to solve
   the prisoner's dilemma
%J Proc. of the Second Int. Conf. on Genetic Algorithms
   and Their Applications
%D 1987
%P 236-240
%K c1987, c198x, c19xx, conf, 2nd ICGA, GA, genetic algorithm, program, AI,
   automatic programming, machine learning, learn, symbolic regression, PD, IPD
%X The usual, deterministic version of P. D.
   The Lisp programs are of a restricted form(!), basically a chain of
   if ... then ... elsif ... then ... elsif ... then ... else ... fi.
   Allowed tests apply to past history, move number (knows last round),
   actions are to cooperate or defect.
   *No recursion*.

%A S. A. Kauffman
%T Antichaos and adaption
%J Scientific American
%M AUG
%D 1991
%P 64-70
%K chaos, antichaos, order, selection, evolution,
   self organization, organisation, self-organization

%A Y. Moses
%A D. Dolev
%A J. Y. Halpern
%T Cheating husbands and other stories: a case study of knowledge, action
   and communication
%J Distributed Computing
%I SpringerVerlag
%V 1
%N 3
%P 167-176
%M SEP
%D 1986
%K c1986, c198x, c19xx, concurrency, communication, synchronous asynchronous,
   common knowledge, cheat, cheating, unfaithful, wife, wives, husband,
   husbands, cuckold, cuckolds, distributed protocols, protocol, paradox,
   infidelity, Josephine's problem, puzzle, induction, logic
%X "The relationship between knowledge & action is a fundamental one: a
   processor in a computer n/w (or a robot or a person, for that matter) should
   base its actions on the knowledge (or information) it has. One of the main
   uses of communication is passing around information that may eventually be
   required by the receiver in order to decide upon subsequent actions.
   Understanding the relationship between knowledge, action, & communication is
   fundamental to the design of computer network protocols, intelligent robots,
   etc. By looking at a number of variants of the cheating husbands puzzle, we
   illustrate the subtle relationship between knowledge, communication, & action
   in a distributed environment."
   -- [<A HREF="http://dx.doi.org/10.1007/BF01661170">doi:10.1007/BF01661170</A>]['09], or...
   pdf of [<A HREF="http://dx.doi.org/10.1145/323596.323616">85 conf version</A>]['09].
   Less pc:  N married couples live in a small village.  Each man knows of
      all other unfaithful wives (and knows this is the case) and assumes
      his own wife to be faithful.  If a man learns his w is u then he is
      bound to shoot her at dusk.  This situation continues for some years
      but it offends God who, one Sunday, announces "there is at least one
      unfaithful w."  (It so happens that there are n unfaithful w,
      N >= n > 0.)  What subsequently happens?
      (Note, before Sunday each cuckold knows of n-1,
      although if n > 1 everyone already knew n > 0:-)

%A B. N. Freeman-Benson
%A J. Maloney
%A A. Borning
%T An incremental constraint solver
%J CACM
%V 33
%N 1
%P 54-63
%M JAN
%D 1990
%K jrnl, CACM, c1990, c199x, c19xx, constraint, CLP, delta-blue, thing, thinglab
%X 46 refs

%A L. Hunter
%T Knowledge acquisition planning for inference from large databases
%J HICSS-23
%V 2
%P 35-44
%I IEEE
%D 1990
%K AI, database data base, mining, HICSS HICSS23 HICSS90

%A L. Hunter
%T Finding paradigm cases or when is a case worth remembering?
%J Proc. 1989 case-based reasoning workshop.
%D 1989
%P 57-61
%K AI case based

%A Wen-mei W. Hwu
%T An enabling compiler technology for superscalar and multiprocessor
   architectures
%J HICCS-25
%D 1992
%K compiler parallel superscalar superscalar multiprocessor,
   HICCS HICSS25 HICSS92
%X day seminar at HICCS

%A P. Cheeseman
%A M. Self
%A J. Stutz
%A W. Taylor
%T AutoClass - a summary
%I NASA Ames Research Center
%D 1991??
%K MML, MDL, Bayesian, inductive inference, II, class classification, AutoClass
%X [Also search for: Snob classification].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Notes/SNOB/">snob</A>].)

%A P. Cheeseman
%A J. Kelly
%A M. Self
%A J. Stutz
%T Automatic Bayesian induction of classes
%J Proc. 2nd Annual Artificial Intelligence Research Forum.
%I NASA AMES
%P 224-239
%D 1987
%K Bayesian, classification, inductive inference, II,
   MML MDL, information theory, minimum message length encoding,
   AutoClass, description, c1987, c198x, c19xx
%X [Also search for: Snob classification].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Notes/SNOB/">Snob</A>].)

%A R. Hanson
%A J. Stutz
%A P. Cheeseman
%T Bayesian classification with correlation and inheritance
%J IJCAI-91
%P 692-698
%M JAN
%D 1991
%K MML MDL, inductive inference, II, hierarchical, classification,
   minimum message length encoding, class, description, correlation,
   IJCAI, IJCAI12, IJCAI91, AutoClass, c1991, c199x, c19xx
%X [Also search for: Snob classification].

%A P. Cheeseman
%A B. Kanefsky
%A W. M. Taylor
%T Where the really hard problems are
%J IJCAI-91
%I MorganKauffman
%V 1
%P 331-337
%D 1991
%K conf, IJCAI, MML, MDL, NP, NPC, complete, optimization, Hamiltonian circuit,
   minimum message length, encoding, graph colouring, K-sat,  description,
   traveling, travelling salesman, c1991, c199x, c19xx
%X For some NPC problems, eg. K-sat, typical cases are easy.
   So hard instances must be rare (assuming NP != NPC).
   Paper shows NPC problems can be summarised by at least one "order parameter".
   The hard problems occur at a critical value of this parameter. ...
   ... marks the value at which the probability of a solution changes abruptly
   from near 0 to near 1. It is the high density of wellseparated almost solns
   (local minima) at this boundary that cause search algs. to "thrash". This
   boundary is a type of phase transition and we show that it is preserved under
   mappings between problems. We show that for some P problems either there is
   no phase transition or it occurs for bounded N ...
   -- [<A HREF="http://www.aaai.org/ocs/index.php/IJCAI/IJCAI-09/paper/viewFile/436/650">IJCAI</A>]['10],
   or [<A HREF="http://dli.iiit.ac.in/ijcai/IJCAI-91-VOL1/PDF/052.pdf">ac.in</A>]['10],
   or [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.32.3552&rep=rep1&type=pdf">cite...</A>]['10].
   (Also see [<A HREF="http://dx.doi.org/10.1511/2002.2.113">doi:10.1511/2002.2.113</A>].)

%A W. Kozaczuk
%T Enigma: How the German Machine Cipher Was Broken and
   How It Was Read by the Allies in World War Two
%I University Publications of America
%D 1984
%K book, text, Wladyslaw Kozaczuk, Kasparek, c1984, c198x, c19xx, c193x,
   ww2, WWII, Rejewski, cipher, cypher, cyphers, Poland, Polish, cryptography,
   cryptanalysis, code, codes, machine, Ultra
%X Translated by Christopher Kasparek.  From an online ref'.
   [also search for: enigma],  isbn:0890935475.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">BP</A>].)

%A P. Cheeseman
%T On finding the most probable model
%B Computational Models of Scientific Discovery and Theory Formation
%E J. Shrager
%E P. Langley
%P 73-95
%D 1990
%I MorganKauffman
%K Bayesian, inductive inference, II, model, MML, MDL, c1990, c199x, c19xx

%E J. Shrager
%E P. Langley
%T Computational Models of Scientific Discovery and Theory Formation
%I MorganKauffman
%D 1990
%K text, book, symposium, inductive inference, II, machine learning, AI,
   model, hypothesis
%X library of congress # 90-4907;    15 papers / chapters
   K e v i n   K o r b  has a copy.  asin / isbn:1558601317;

%A P. Cheeseman
%T Probabilistic versus fuzzy reasoning
%B Uncertainty in Artificial Intelligence
%I Elsevier Science Pub.
%D 1986
%E L. N. Kanal
%E J. F. Lemmer
%K AI, uncertain, reasoning, Bayesian, probabilistic, fuzzy,
   c1986, c198x, c19xx

%A Bell
%A Witten
%A Cleary
%T Modelling for Text Compression
%J Computing Surveys
%V 21
%V DEC
%D 1989
%P 557-592
%K survey, text compression, model, models
%X via A. Moffat

%A S. Kirkpatrick
%A C. D. Gelatt_jr.
%A M. P. Vecchi
%T Optimization by simulated annealing
%J Science
%V 220
%N 4598
%M MAY
%D 1983
%P 671-679
%K jrnl, simulated annealing, algorithm, optimize, optimization,
   circuit layout, travelling salesman, problem
%X "... briefly review the central constructs in comb. opt. & in stat. mech.
   ... show hoe the M.alg. ... provides a natural tool ... [applied to]
   component placement and wiring ..."
   -- [<A HREF="https://www.jstor.org/stable/1690046">jstor:1690046</A>]['24],
      [<A HREF="https://doi.org/10.1126/science.220.4598.671">Sci.</A>]['24].
   [Also search for: simulated annealing algorithm].

%A T. Gilovich
%A R. Vallone
%A A. Tversky
%T The hot hand in basketball: On the misperception of random sequences
%J Cognitive Psychology
%V 17
%P 295-314
%M 1985
%K jrnl, c1985, c19xx, c19xx, hot hands, basketball, stats, model, performance,
   sport, goals, scores, runs, segmentation, form, slump, run, runs, streak,
   winning, law of small numbers, Philadelphia 76ers, Boston Celtics, Cornell
%X "We investigate the origin & the validity of common beliefs regarding
   'the hot hand' & 'streak shooting' in the game of basketball. B.players &
   fans alike tend to believe that a player's chance of hitting a shot are
   greater following a hit than following a miss on the prev. shot. However,
   detailed analyses of the shooting records of the Philadelphia 76ers provided
   no evidence for a positive correlation between the outcomes of successive
   shots. The same conclusions emerged from free-throw records of the Boston
   Celtics, & from a controlled shooting experiment with the men & women of
   Cornell's varsity teams. The outcomes of previous shots influenced Cornell
   players' predictions but not their performance. The belief in the hot hand &
   the 'detection' of streaks in random seqs. is attributed to a general
   misconception of chance according to which even short random seqs. are
   thought to be highly representative of their generating process."
   -- [<A HREF="http://dx.doi.org/10.1016/0010-0285(85)90010-6">doi:10.1016/0010-0285(85)90010-6</A>]['12].
   (BUT [also search for: hot hand stats] for a different conclusion.)

%A M. Opper
%A D. Haussler
%T Generalization performance of Bayes optimal classification algorithm for
   learning a perceptron
%J Physical Review Letters
%M MAY
%D 1991
%P 2677-2680
%V 66
%N 20
%K statistics, perceptron, NN, neural net, training, learning

%A J. R. Quinlan
%T Determinate literals in inductive logic programming
%J IJCAI-91
%P 746-750
%M JAN
%D 1991
%K inductive inference, II, ILP, rule, rules, prolog, machine learning,
   FOIL, GOLEM, IJCAI, IJCAI91

%A G. E. Hinton
%A S. J. Nowlan
%T How learning can guide evolution
%J Complex Systems
%V 1
%P 495-502
%D 1987
%K machine learning, AI
%X via enews

%A J. Maynard Smith
%T When learning guides evolution
%D 1987
%J Nature
%V 329
%P 761-762
%K machine learning, AI
%X via enews

%A E. Y. Shapiro
%T An algorithm that infers theories from facts
%J IJCAI-81
%D 1981
%P 446-451
%K inductive inference, II, machine learning, AI, logic, fact rule,
   theory theories, ILP, LP, prolog, IJCAI, IJCAI81

%A E. M. Gold
%T Language identification in the limit
%J Information and Control
%V 10
%P 447-474
%D 1967
%K c1967, c196x, c19xx, inductive inference, II, ML, machine learning, language,
   AI, grammar, rule rules
%X from refs in previous entry

%A E. Garfield
%A A. Welljams-Dorof
%T Of Nobel class: A citation perspective on high impact research authors
%J Theor. Medicine
%V 13
%P 117-135
%M JUN
%D 1992
%K jrnl, c1992, c199x, c19xx, zz1222, bibliometrics, impact, productivity,
   papers, publications, citations, ISI, scientific research, Nobel prize,
   academia, quote, quotable, publish, perish
%X "... to determine if quantitative rankings of highly cited research authors
   confirm Nobel prize awards. ..."
   -- [<A HREF="https://doi.org/10.1007/BF02163625">doi:10.1007/BF02163625</A>]['22].
 * "productivity (articles per author), author impact (citations per author), &
   article impact (citations per paper)."
 * "[in 1961] the avg Nobel author received 169 citations, 30 times more than
   the avg author (5.5). [&] Nobelists were far more productive than the avg.
   They published 58.1 cited papers, 17 times more than the avg (3.37). But as a
   result, the average Nobelist-authored paper was cited 2.9 times, 'only' about
   double the average article (1.6)."
   [Also search for: publish perish].

%A S. Muggleton
%A A. Srinivasan
%A M. Bain
%T Compression, significance and accuracy
%J 9th Int. Machine Learning Conf.
%W Aberdeen
%D 1992
%I MorganKauffman
%K inductive logic programming, ILP, prolog, Golem, MML, MDL, compression,
   minimum message description length encoding, inductive inference, II, AI,
   automatic programming, automaticProgramming, machine learning ML ML9 ML92,
   c1992, c199x, c19xx
%X From section 3 Compression and Proof Encoding:
      For each example covered by the hypothesis on the input tape,
      let us define its proof complexity to be the sum of the log of
      the choice points involved in deriving the example using SLDNF
      resolution.
   From appendix A.2.2 Proof Encoding:
      hypothesis  normal(Year) :- year(Year), not(leap4(Year)).
                  leap4(Year)  :- mod(Year, 4, 0).
      To encode one example, say   normal(1581):
         Use clause 1 (no choice)
         [LA: assumes we know it's a normal(something) example].
         In the body of clause, year(Year) matches any of year(1) to year(1993)
         so this choice requires log(1993) bits, about 15 bits,
         The rest of the proof is then completely determined.
      Extensions: for non-generative clauses add substitutions
                  true +ve / false +ve
   [LA: in the above example, I don't really see that the null theory
        is any worse.  normal(1581) only involves a statement of the int.]
   [Also search for: ILP learning].

%A D. R. Hanson
%T Compact Recursive-descent Parsing of Expressions
%J SPE
%V 15
%N 12
%P 1205-1212
%M DEC
%D 1985
%K Recursive descent parsing, Expression, Precedence, Compiler,
   parse parser
%X via enews

%A G. J. Chaitin
%T Undecidability and randomness in pure mathematics
%J EUROPALIA 89 Conf. Self-Organization
%W Brussels
%P ???-???
%M SEP
%D 1989
%K omega, undecidability, decidability, random, randomness, foundations, theory,
   formal systems, halting problem, omega, number, EUROPALIA 89,
   halts, halting, probability, conf, EUROPALIA89
%O pp.307-313 in some collection
%X Omega=SUM[p halts] { 1 / ( 2**|p| ) },
   i.e. sum over programs, p, that halt, where |p| is the size of p in bits.
   A "very random" and essentially incomputable number.
   [Also search for: algorithmic information theory].

%A G. J. Chaitin
%T Algorithmic information and evolution
%J Int. Union of Biological Sciences Workshop on Biological Complexity
%M APR
%D 1988
%W Paris
%P ???-???
%K information theory, complexity, MML, MDL, halting problem
   evolution, complex systems
%O pp.314-318 in some collection.

%A C. H. Bennett
%T The thermodynamics of computation - a review
%J Int. J. of Theor. Physics
%T 21
%V 12
%P 905-940
%D 1982
%K jrnl, c1982, c198x, c19xx, zz1117, quantum computing, computing, reversible,
   energy, Fredkin, Toffoli, quote, waste heat, quotable
%X "Computers may be thought of as engines for transforming free energy into
   waste heat and mathematical work. Existing electronic computers dissipate
   energy vastly in excess of the mean thermal energy kT, for purposes such as
   maintaining volatile storage devices in a bistable condition, synchronizing
   and standardizing signals, and maximizing switching speed. On the other hand,
   recent models due to Fredkin and Toffoli show that in principle ..."
   -- [<A HREF="https://link.springer.com/article/10.1007%2FBF02084158">spr'nger</A>]['17].
   [Also search for: reversible computing].

%A G. J. Chaitin
%T Algorithmic Information Theory
%I CUP
%D 1987
%K book, CUP, information theory, complexity, halting problem, MML, MDL, AIT,
   minimum message description length encoding, algorithmic complexity, AC,
   omega, c1987, c198x, c19xx
%X uk us isbn:9971504804.
   (Reviewed in: The J. of Symbolic Logic, 54(2), Jun.,1989, pp.624-627
    @[<A HREF="http://www.jstor.org/stable/2274882">Jstor</A>].)

%A G. J. Chaitin
%T Randomness in arithmetic
%J Scientific American
%M JUL
%D 1988
%P 80-85
%K random, randomness, information theory, complexity, halting problem,
   minimum message length encoding, MML, MDL, description
%X [Also search for: algorithmic information theory].

%A G. J. Chaitin
%T The Berry paradox
%J Complexity
%V 1
%N 1
%P 26-30
%D 1995
%K Berry, Berry's paradox, Berrys, paradox, recursion, logic, maths, theory,
   zz0795, c1995, c199x, c19xx, finitely many integers, infinite
%X p9: ... the first positive integer that cannot be named in less
       than a billion words. ...
   (Also see in Complex Systems and Binary Networks, LecNotesPhys 461-461/'95,
   -- [<A HREF="http://dx.doi.org/10.1007/BFb0103569">doi:10.1007/BFb0103569</A>]['09]).
   [Also search for: Berry paradox], [and for: algorithmic information theory].

%A G. J. Chaitin
%T Randomness in arithmetic and the decline and fall of reductionism in pure
   mathematics
%B Nature's Imagination
%E J. Cornwell
%I OUP
%P 27-44
%D 1995
%K chapter, c1995, c199x, c19xx, algorithm, complete, completeness, foundations,
   algorithmic information theory, maths, logic, theory, zz0795
%X [Also search for: algorithmic information theory].

%A D. A. Pomerleau
%T Progress in neural network-based vision for autonomous robot driving
%J Proc. of the 1992 Intelligent Vehicles Symposium
%D 1992
%K neural net network, AI, artificial intelligence, NN, ANN, car drive driving,
   autonomous vehicle
%X via email

%A D. A. Pomerleau
%T ALVINN: An Autonomous Land Vehicle In a Neural Network
%J Advances in Neural Information Processing Systems
%D 1989
%V 1
%E D. S. Touretzky
%I MorganKaufmann
%K ALVINN, neural net, network, AI, artificial intelligence, NN, ANN,
   car, drive, driving
%X via email

%A D. S. Touretzky
%A D. A. Pomerleau
%T What's hidden in the hidden units?
%J BYTE
%D 1989
%V 14
%N 8
%M AUG
%P 227-233
%K neural net, network, AI, artificial intelligence, NN, ANN, car, drive, driving
%X via email

%A J. F. Shepanski
%A S. A. Macy
%T Teaching artificial neural networks to drive:
   manual training techniques for autonomous systems
%J Proc. of the 1987 Neural Information  Processing Systems Conf.
%D 1987
%P 693-700
%E D. Z. Anderson
%K neural net, network, AI, artificial intelligence, NN, ANN, car, drive, driving
%X via email

%A J. J. Shepanski
%T Fast learning in artificial neural systems: multilayer perceptron training
   using optimal estimation
%J Proc. of the Int. Conf. on Neural
   Network [?Intelligence?]
%D 19??
%P 465-472
%I IEEE Press
%W New York
%K neural net, network, AI, artificial intelligence, NN, ANN, car,
   drive, driving
%X via email
   guess dates between '87 and '92.

%A T. S. Ray
%T Landmark eigenshape analysis:  Homologous contours: Leaf shape
   in Syngonium Araceae
%J American Journal of Botany
%V 79
%N 1
%D 1992
%P 69-76
%K image processing, IP, shape analysis, leaf leaves, homology, outline,
   contour
%X via enews

%A R. M. Fujimoto
%A Hwa-chung Feng
%T A shared memory algorithm and proof for the generalized alternative
   construct in CSP
%J Int. J. Parallel Programming
%V 16
%N 3
%M JUN
%D 1987
%P 215-242
%K CSP, parallel language, communication, synchronization, synchronize

%A D. Nychka
%A S. Ellner
%A A. R. Gallant
%A D. McCaffrey
%T Finding chaos in noisy systems
%J J. Royal Statistical Society Ser. B
%V 54
%P 399-426
%D 1992
%K JRSS, time series prediction, forecasting, chaos
%X via enews

%A D. McCaffrey
%A S. Ellner
%A A. R. Gallant
%A D. Nychka
%T Estimating the Lyapunov exponent of a chaotic system with nonparametric
   regression
%J J. Amer. Stat. Assoc.
%V ?
%P ?-?
%D 1992 ?
%K jrnl, JASA, time series prediction, forecasting, chaos, c1992, c199x, c19xx
%X (in press; to appear this Fall). via enews

%A D. M. Wolpert
%A R. C. Miall
%T Detecting chaos with neural networks
%J Proc. Roy. Soc. Lond. B
%V 242
%P 82-86
%D 1990
%K c1990, c199x, c19xx, neural net, NN, ANN, chaos, time series prediction,
   forecasting
%X via enews

%A Martin Casdagli
%T Nonlinear Prediction of Chaotic Time Series
%J Physica D
%V 35
%P 335-356
%D 1989
%K time series prediction, forecasting, chaos
%X via enews

%A R. A. Earnshaw
%A N. Wiseman
%T An Introductory Guide to Scientific Visualization
%I SpringerVerlag
%M JUN
%D 1992
%P 120
%X text, book, visualization, visualization, graphics
%X isbn:3540546642;  hb

%A R. Beer
%A H. Chiel
%A L. Sterling
%T The Artificial Insect Project
%J American Scientist
%V ??
%P ???-???
%M SEP
%D 1990
%K AI, artificial intelligence, robot, insect, walk, walking
%X via email

%A R. Brooks
%T Intelligence without Representation
%J Artificial Intelligence
%V 47
%P 139-160
%M ???
%D 199?
%K AI, artificial intelligence, robot, insect, walk, walking
%X via email

%A D. Fass
%A Y. Wilks
%T Preference Semantics, Ill Formedness, and Metaphor
%D 1983
%J S Americal Journal of Computational Linguistics
%V 9
%N 3-4
%K NL, NLP, natural language processing, parsing
%X via enews

%A T. Howells
%T VITAL: A Connectionist Parser
%D 1988
%J Cognitive Science 88
%K NL, NLP, natural language processing, parsing, NN, artificial neural net
   network
%X via enews

%A J. B. Pollack
%A D. L. Waltz
%T Parallel Interpretation of Natural Language
%D 1984
%J Proc. FGCS, ICOT.
%K NL, NLP, natural language processing, parsing
%X via enews

%A R. C. Schank
%T Interestingness: Controlling Inferences
%D 1979
%J Artificial Intelligence
%V 12
%P 273-297
%K NL, NLP, natural language processing, parsing, interesting
%X via enews

%A S. Small
%A G. Cottrell
%A et al.
%T Toward Connectionist Parsing
%D 1982
%J Proc. AAAI-82, AAAI.
%K NL, NLP, natural language processing, parsing, NN, artificial neural net
   network
%X via enews

%A L. A. Zadeh
%T PRUF - a meaning representation language for natural languages
%D 1981
%B Fuzzy Reasoning and its Applications,
%E Mamdani
%E Gaines
%I AcademicPress
%K NL, NLP, natural language processing, parsing
%X via enews

%E Halbert White
%T Artificial Neural Networks - Approximation and Learning Theory
%M AUG
%D 1992
%K AI, ANN, NN, neural net network, machine learning
%X isbn:1-55786-329-6.  price: 40 pounds, 320 pages, via enews

%A Gerald Tesauro
%T Practical Issues in Temporal Difference Learning
%J Machine Learning
%V 8
%N 3/4
%M MAY
%D 1992
%K AI, NN, ANN, neural net, network, back gammon, backgammon, game
%X The basic idea is to learn a connectionist position evaluator though self
   play.  Supporting this are ideas from control theory, especially the backing
   up of lookahead using dynamic programming.
   Near expert level of play.
   via enews.
   [Also search for: backgammon].

%A A. G. Barto
%A S. J. Bradtke
%A S. P. Singh
%T Real-time learning and control using asynchronous dynamic programming
%I Dept of Comp. Sci., U. of Massachusetts, Amhurst MA.
%R 91-57
%M Aug
%D 1991
%K AI, NN, ANN, neural net, network, game, play, playing
%X Also, vol 8 of Machine Learning 1992 is a special issue on reinforcement
   learning.  via enews.
   (Also see RL@[<A HREF="https://en.wikipedia.org/wiki/Reinforcement_learning">wikip</A>]['22].)

%A G. Tesauro
%A T. Sejnowski
%T A Parallel Network that Learns to Play Backgammon
%J Artificial Intelligence
%V 39
%P 357-390
%D 1990
%K AI, NN, ANN, neural net, network, game play playing, back gammon, backgammon
%X supervised system.  via enews.
   [Also search for: backgammon].

%A A. D. Marshall
%A R. R. Martin
%T Computer Vision, Models and Inspection
%I World Scientific
%S Robotics and Automated Systems
%V 4
%D 1992
%K text, book, image processing, IP, computer machine vision, model
%X via  R o b y n  O w e n  UWA.  isbn:9810207727;

%A M. Li
%A P. Vitanyi
%T Introduction to Kolmogorov Complexity and its Applications
%I SpringerVerlag
%M AUG
%D 1993
%P 546
%K text, book, c1993, c199x, c19xx, Ming, inductive inference, AI, II, PAC,
   machine learning, compression, information, minimum length encoding,
   Kolmogorov, algorithmic, complexity
%X 3rd ed 2008; hb us$60; uk us isbn:0387339981; isbn13:978-0387339986.
   1st ed 1993; hb us$59; uk us isbn:0-387-94053-7.
      1. Preliminaries
      2. Algorithmic Complexity
      3. Algorithmic Probability
      4. Inductive Reasoning
      5. Lower Bound
      6. Resource-Bounded Complexity
      7. Algorithmic Physics
   It covers the basics of Kolmogorov complexity as well as advanced topics
   such as inductive inference, Pac-learning, lower bounds of computation,
   VLSI area-time complexity, language compression, algorithmic thermodynamics,
   algorithmic chaos, etc.  It is an interesting book.  -- Tao Li.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)
   [Also search for: MML].

%A J. R. Quinlan
%T C4.5: Programs for Machine Learning
%I MorganKaufmann
%P 302
%D 1992
%K book, decision tree, trees, C4.5, C45, C4_5, ID3, inductive inference, II,
   rule, rules
%X Book only: isbn:1-55860-238-0; isbn13:978-1558602380,
              $44.95 U.S.  $49.45 International.
   Book and Software: isbn:1-55860-240-2; $69.95 U.S.  $76.00 International.
   Software only: isbn:1-55860-239-9; $34.95 U.S. $38.45 International.
   [C4.5, extension of Q's earlier ID3 alg..]
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/Dtree/">Dtree</A>].)

%E B. G. Buchanan
%E D. C. Wilkins
%T Readings in Knowledge Acquisition and Learning: Automating the Construction
   and Improvement of Programs
%D 1992 ???
%I MorganKauffman
%K automatic program generation

%A A. M. Turing
%T Computing machinery and intelligence
%J Mind: A Quarterly Review of Psychology and Philosophy
%I OUP
%V 59
%N 236
%P 433-460
%M OCT
%D 1950
%K jrnl, c1950, c195x, c19xx, Alan, AlanTuring, Turing test, Imitation Game,
   imitate, Loebner prize, mind, artificial intelligence, AI, HAL, think,
   thought, learning, computer, machine, can machines think, intelligent
%X 'I propose to consider the question, "Can machines think?" This should begin
   with definitions of the meaning of the terms "machine" & "think." The
   definitions might be framed so as to reflect so far as possible the normal
   use of the words, but this attitude is dangerous, If the meaning of the words
   "machine" & "think" are to be found by examining how they are commonly used
   it is difficult to escape the conclusion that the meaning & the answer to
   the question, "Can machines think?" is to be sought in a statistical survey
   such as a Gallup poll. But this is absurd. Instead of attempting such a
   defn I shall replace the q. by another, which is closely related to it & is
   expressed in relatively unambiguous words.
   The new form of the problem can be described in terms of a game which we call
   the "imitation game." It is played with three people, a man (A), a woman (B),
   & an interrogator (C) who may be of either sex. The interrogator stays in a
   room apart front the other two. The object of the game for the interrogator
   is to determine which of the other two is the man & which is the woman. He
   knows them by labels X & Y, & at the end of the game he says either "X is
   A & Y is B" or "X is B & Y is A." The interrogator is allowed to put
   questions to A & B thus:
   C: Will X please tell me the length of his or her hair?
   Now suppose X is actually A, then A must answer. It is A's object in the game
   to try & cause C to make the wrong identification. His answer might therefore
   be: "My hair is shingled, & the longest strands are about nine inches long."
   In order that tones of voice may not help the interrogator the answers should
   be written, or better still, typewritten. The ideal arrangement is to have a
   teleprinter communicating between the two rooms. Alternatively the question
   & answers can be repeated by an intermediary. The object of the game for
   the third player (B) is to help the interrogator. The best strategy for her
   is probably to give truthful answers. She can add such things as "I am the
   woman, don't listen to him!" to her answers, but it will avail nothing as
   the man can make similar remarks.
   We now ask the question, "What will happen when a machine takes the part of
   A in this game?" Will the interrogator decide wrongly as often when the game
   is played like this as he does when the game is played between a man & a
   woman? These questions replace our original, "Can machines think?" '
   -- [<A HREF="http://www.jstor.org/stable/2251299">jstor:2251299</A>]['24],
    & [<A HREF="http://loebner.net/Prizef/TuringArticle.html">loebner</A>]['04].
   Also see [<A HREF="https://turingarchive.kings.cam.ac.uk/publications-lectures-and-talks-amtb/amt-b-9">Intelligent machinery</A>]['24] (1948) at
      [<A HREF="https://turingarchive.kings.cam.ac.uk">turingarchive</A>]['24].
   [Also search for: AlanTuring]  and  [also search for: Chomsky c1999].

%A Hubert L. Dreyfus
%T What Computers Can't Do: A Critique of Artificial Reason
%I Harper
%D 1972
%K computer, machine, artificial, intelligence, AI, think, thought, mind,
   consciousness, GOFAI, book, text, c1972, c197x, c19xx, HAL, robot
%X 1st ed 1972.
   2nd ed 1979; uk us isbn:0060906243; uk us isbn13:978-0060906245.
   3rd edition, see: What Computers Still can't do: A Critique of
                     Artificial Reason.
   [Also search for: computer AI HAL].

%A D. H. Meadows
%A D. L. Meadows
%A J. Randers
%T The Limits to Growth
%I UniverseBooks
%P 205
%D 1972
%K book, text, c1972, c197x, c19xx, Club of Rome, limits, growth, resources,
   earth, sustainability, population, food, minerals, energy, economics,
   prediction, zzPrediction
%X 1st ed 1972; uk us isbn:0876631650.
   (Also see [<A HREF="http://en.wikipedia.org/wiki/The_Limits_to_Growth">wikip</A>]['13].)
   [Also search for: limits growth resources].

%T Lenna Soderberg
%J Playboy
%P 138-140
%M NOV
%D 1972
%K c1972, c197x, c19xx, Lenna, Soderberg, Sjooblom, Lena, image processing,
   scan, scanned, photo, playboy, centrefold, centerfold, playmate
%X "Lena Soderberg (b 31 March 1951 Sweden) appeared as a Playmate in the
   Nov 1972 issue of Playboy magazine, under the name Lenna Sjooblom. Her
   centerfold was photographed by Dwight Hooker.  Her photo (known as Lenna) is
   often used to test algs. in digital image processing. She was a guest at the
   50th annual Conf. of the Soc. for Imaging Sci. & Tech. in 1997 where she
   gave a presentation about herself."
   -- [<A HREF="http://en.wikipedia.org/wiki/Lena_S%C3%B6derberg">wikip</A>]['12],
      [<A HREF="http://www.cs.cmu.edu/~chuck/lennapg/lenna.shtml">cmu</A>]['12].

%A H. L. Dreyfus
%T What Computers Still Can't Do: A Critique of Artificial Reason
%I MITpress
%D 1992
%K computer, machine, artificial intelligence, AI, HAL, think, thought, mind,
   human, consciousness, GOFAI, book, text, c1992, c199x, c19xx
%X 1st ed 1992; pb us$20; uk us isbn:0-262-54067-3; uk us isbn13:978-0262540674.
   DREWP   $17.50 (US).  Reviewed in Comp Rev 289-290 Jun '93.
   [Also search for: computer AI HAL].

%A H. L. Dreyfus
%A S. E. Dreyfus
%T Mind Over Machine: The Power of Human Intuition and Expertise in the
   Era of the Computer
%I The Free Press
%D 1986
%K computer, machine, artificial, intelligence, AI, HAL, think, thought, mind,
   human, consciousness, c1986, c198x, c19xx

%A R. Penrose
%T The Emperor's New Mind
%I OUP
%D 1989
%K book, text, OUP, computer, machine, artificial intelligence, chaos, physics,
   determinism, AI, HAL, think, thought, mind, quantum, brain, consciousness,
   c1989, c198x, c19xx
%X see also:- Penrose, 'The Large, the Small and the Human Mind,' CUP, '97?
   [Also search for: quantum mind brain].

%A R. Penrose
%T The Large, the Small and the Human Mind
%I CUP
%D 1997 ?
%K book, text, CUP, Roger, artificial intelligence, AI, HAL, consciousness,
   mind, brain, conscious, thought, quantum, microtubules, determinism,
   c1997, c199x, c19xx, zz0497
%X Brief review in The Age, Sat' 5 Apr 1997, suggests cost only $9.95 ?!
   Apparently it's :- microtubules in brain cells, quantum effects,
   objective reduction of wave function, consciousness,
   machines don't have microtubules so ... not conscious (ever).
   uk us isbn:0521785723;       See also "Emperor's New Mind," '89.

%A D. C. Dennett
%T Brainstorms: Philosophical Essays on Mind and Psychology
%I Bradford Books
%D 1981
%K mind, think, thought, computer, machine, artificial intelligence, AI

%A K. R. Popper
%T Indeterminism in quantum physics and classical physics
%J British J. for the Philosophy of science
%V 1
%P 179-188
%D 1951
%K determinism, quantum physics, AI

%A L. Festinger
%T A Theory of Cognitive Dissonance
%I StanfordUP
%D 1957
%K book, text, c1957, c195x, c19xx, psychology, cognitive dissonance, beliefs,
   belief, justification, human behaviour, social groups, comparison, prophecy,
   apocalyptic cult, cults, doomsday, believers
%X LF@[<A HREF="http://en.wikipedia.org/wiki/Leon_Festinger">wikip</A>]['13].

%A J. Searle
%T Minds, Brains and Science
%I HarvardUP
%D 1984
%K mind, brain, think, thought, artificial intelligence, AI, computer, machine

%A T. Forester
%T High-tech hype: Myths and realities in the IT revolution
%J 61st ANZAAS Congress
%W Brisbane
%P ???-???
%M SEP
%D 1992
%K high, tech, information, technology, IT, forecast, future, prediction,
   zzPrediction, urban, myth, legend, leisure, electronic cottage, cashless,
   society, paperless, office, ANZAAS, ANZAAS61, ANZAAS92, pollution, jargon,
   infoglut, info glut, technobabble, technobable, techno babble,
   communicaholism, privacy, information superhighway, internet, super highway,
   ISH, www, web, c1992, c199x, c19xx
%X LA has copy; read it!  Contents:
   Megatrends or Megamistakes
     . the "leisure" society   . the "workerless" factory
     . the "paperless" office  . the "electronic cottage"
     . the "cashless" society  . "teledemocracy"         . "robot teachers"
   Why Technology Predictions Go Wrong
   MegaMistakes,  New Social Problems
     . computer unreliability  . software theft
     . hacking and viruses     . invasion of privacy
   New Psychological Maladies
     . InfoGlut      . communicaholism
     . techno-babble . putting humans back in the picture.
   [Also search for: society internet].

%A S. E. Dreyfus
%A A. M. Law
%T The Art and Theory of Dynamic Programming
%I AcademicPress
%S Maths. in Sci. and Eng.
%V 130
%D 1977
%K dynamic programming, DP, DPA, text, book, travelling salesman,
   salesperson, sales, TSP, shortest path, paths
%X uk us isbn:0122218604.

%A U. Ramer
%T An iterative procedure for the polygonal approximation of plane curves
%J Computer Graphics and Image Processing
%V 1
%P 244-256
%D 1972
%K polygon, fit, fitting, shape, perimeter, outline, closed curve,
   approximation, image processing, IP

%A D. H. Douglas
%A T. K. Peuker
%T Algorithms for the reduction of the number of points required to represent
   a digitized line or its caricature
%J The Canadian Geographer
%V 10
%N 2
%M DEC
%D 1973
%P 112-122
%K polygon, fit, fitting, shape, perimeter, approximation, outline,
   closed curve, image processing, IP

%A Y. Kurozumi
%A W. A. Davis
%T Polygonal approximation by the minimax method
%J Computer Graphics and Image Processing
%V 19
%P 248-264
%D 1982
%K polygon, fit, fitting, shape, perimeter, approximation, outline,
   closed curve, image processing, IP
%X 24 refs,  a survey and a particular method.

%A G. T. Leavens
%A M. Vermeulen
%T 3x+1 Search Programs
%J Computers and Mathematics with Applications
%M DEC
%D 1992
%V 24
%N 11
%P 79-99
%K 3X+1 puzzle, problem, Collatz, Syracuse, Kakutani, Hasse, Ulam, CMA,
   c1992, c199x, c19xx
%X via enews; 11 references.
   [Also search for: Collatz problem].

%A C. H. A. Koster
%T A technique for parsing ambiguous grammars
%D 1975
%E D. Siefkes
%P 233-246
%I SpringerVerlag
%S LNCS
%V 26
%K parse, parser, affix grammar, non-deterministic, backtrack, back track
   operators

%A Balanjaninath Edupuganty
%T Two Level Grammars: An Implementable Metalanguage for
   Consistent and Complementary Language Specifications
%I Univ. of Alabama in Birmingham
%D 1987
%K PhD thesis, parse, parser, grammar, 2-level, VWG, operators

%A R. V. Book
%T Thue systems as rewriting systems
%J J. Symbolic Comp
%V 3
%N 1-2
%P 39-68
%M FEB-APR
%D 1987
%K jrnl, c1987, c198x, c19xx, zz0524, Thue systems, system, semi, semiThue,
   Post, strings, nondeterministic, rewriting, unconventional, SRS
%X "... survey of recent results on Thue systems, where the systems are viewed
   as rewriting systems on strings over a finite alphabet. The emphasis is on
   Thue systems with the Church-Rosser property, where the notion of red'n is
   based on length-decreasing rewriting rules. The main effort is expended in
   outlining the properties of such systems, paying close attention to the issue
   of the possible decidability of properties & to the issue of the comp'al
   complexity of decidable properties. Since Thue systems may also be considered
   as presentations of monoids, the language of monoids (& groups) is used to
   describe some of these properties."
   -- [<A HREF="https://doi.org/10.1016/S0747-7171(87)80021-4">doi:10.1016/S0747-7171(87)80021-4</A>],
   at [<A HREF="https://core.ac.uk/download/pdf/81946844.pdf">c're</A>]['24].
   [Also search for: Thue rewriting system].

%T Memory Management
%I SpringerVerlag
%S LNCS
%V 637
%E Y. Bekker
%E J. Cohen
%D 1992
%K memory management, garbage collection, allocation, IWMM 92, MM, GC, IWMM92

%A O. Hansson
%A A. Mayer
%A M. Valtorta
%T A new result on the complexity of heuristics for the A* algorithm
%J Artificial Intelligence
%V 55
%N 1
%M MAY
%D 1992
%P 129-143
%K AI, artificial intelligence, heuristic, combinatorial, constraint
   satisfaction problem, search, A*, Astar
%X via enews

%A R. Bahlke
%A G. Snelting
%T The PSG system: from formal language definition to interactive programming
   environments
%J TOPLAS
%M OCT
%D 1986
%V 8
%N 4
%P 547-576
%K context sensitive grammar, CSG, attribute, checking, PSG
%X via enews.

%A F.-J. Grosch
%A G. Snelting
%T Inference-Based Overloading Resolution for ADA
%B Programming Language Implementations and Logic Programming
%D 1990
%E P. Deransart
%E J. Maluszynnski
%P 30-44
%I SpringerVerlag
%S LNCS
%V 456
%K context sensitive grammar, CSG, attribute, checking, overload, over load,
   type, types, operator, Ada, inference, programming languages
%X via enews

%A G. Snelting
%T The calculus of context relations
%J Acta ?Informatica?
%D 1991
%V 28
%N 5
%P 411-445
%K context sensitive grammar, CSG, attribute, checking
%X via enews

%A G. Kahn
%A B. Lang
%A B. Melese
%A E. Morcos
%T Metal: A formalism to specify formalisms
%J Science Of Computer Programming
%D 1983
%V 3
%N 2
%P 151-188
%K context sensitive grammar, CSG, attribute, checking, metal
%X via enews

%A C. S. Wallace
%T Physically random generator
%J Computer Systems Science and Engineering
%V 5
%N 2
%P 82-88
%M APR
%D 1990
%I Butterworth and Co.
%K Monash, jrnl, c1990, c199x, c19xx, random number generation, RNG,
   CSW, CSWallace
%X (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A A. R. Jensen
%T How Much Can We Boost IQ and Scholastic Achievement?
%J Harvard Educational Review
%P 1-123
%D 1969
%K c1969, c196x, c19xx, IQ, nature, nurture, genetics, genes, race, racial,
   infamous, controversial, debate, human, behaviour, environment, education,
   Jensenism, heritability
%X "[AJ] argues that the failure of recent compensatory edn efforts to produce
   lasting effects on children's IQ & achievement suggests that ..."
   -- abs@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.138.980">c'teSe'r</A>]['14].

%A W. V. O. Quine
%T only a quote:
      Creatures inveterately wrong in their inductions have a pathetic
      but praiseworthy tendency to die before reproducing their kind
%D 1969?
%K learn, learning, evolution, intelligence, fitness, survival, igNobel,
   inductive inference, II, quote, quotable, quotation, c1969, c196x, c19xx
%X From <!-- email: andy hendrix.ece.uiuc.edu --> Tue Dec  1 03:11:10 1992
        The quote comes from a chapter by W.V.O. Quine which is titled "natural
   Kinds".  The copy I have is a xerox of the chapter which a professor
   gave me.  Unfortunately, I don't know the title of the book.  However,
   the first page has a reference suggesting this chapter is a reprint from
   "Ontological Relativity and Other Essays" by
   W.V.O. Quine (New York: Columbia Press, 1969)
   pp. 114-138.
   Hope that helps.
        If you hunt down the chapter and read it I would love to discuss it.
   I haven't read it in years, but I seem to remember it was rather tough
   going.  I very abstract view of epistemology if I remember correctly.
      Andy Bereson  <!-- email: bereson at cs.uiuc.edu (217)244-3617 --> .

%A C. Langton
%T Computation on the edge of chaos
%J Physica D
%V 42
%N 1-3
%P 12-37
%D 1990
%K chaos, order, computability, P, NP, NPC
%X via enews

%T Analogical and Inductive Inference, Int. Wksp. AII '92
%E K. P. Jantke
%I SpringerVerlag
%S LNAI
%V 642
%D 1992
%K AII, inductive inference, II, AI, analogical

%A M. Delest
%T Enumeration of polyominoes using MACSYMA
%J Theor. Comp. Sci.
%V 79
%N 1
%P 209-226
%M FEB
%D 1991
%K TCS, enumerate, combinatorics, polyomino, polyominoe, polyominoes,
   pentominoe, c1991, c199x, c19xx
%X reviewed in Comp. Rev. 33(11) p620 Nov '92

%A P. Suetens
%A P. Fua
%A A. J. Hanson
%T Computational strategies for object recognition
%J ACM Comp. Surv.
%V 24
%N 1
%P 1-62
%M MAR
%D 1992
%K object, image, recognition, processing, IP, survey, model, template
%X reviewed in Comp. Rev. 33(11) p624 '92

%A E. Grimson
%T Object Recognition by Computer
%I MITpress
%M MAY
%D 1990
%K text, book, object, image, recognition, processing, IP, survey, model,
   template
%X CR Rev. 9203-0137

%A J. Oliver
%T Decision graphs - an extension of decision trees
%J 4t Int. Conf. Artificial Intelligence and Statistics
%W Florida
%M JAN
%D 1993
%P 343-350
%O TR 92/173, '92, Dept. Computer Science, Monash University, Australia 3168
%K AIM, AIM, C1993, c199x, c19xx, conf, AI, AIS, AIS4, AIS93, decision tree,
   trees, graph, DTree, DGraph, MML, minimum message description length, MMLP,
   encoding, MDL, Monash, AIC, AI, machine learning, inductive inference, II,
   TR 92 173, TR173
%X "... Decision Graphs, a generalization of decision trees. We present an
   inference scheme to construct decision graphs using the Minimum Message
   Length Principle. Empirical tests demonstrate that this scheme compares
   favourably with other decision tree inference schemes. This work provides a
   metric for comparing the relative merit of the decision tree and decision
   graph formalisms for a particular domain."
   -- pdf@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.52.1476">citeseer</A>]['17].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/DGraph/">Dgraph</A>].)
   [Also search for: Dgraph decision].

%A W. R. Franklin
%A V. Akman
%T Adaptive grid for polyhedral visibility in object space: An implementation
%J COMPJ
%V 31
%N 1
%P 56-60
%D 1988
%K uniform grid, polygon, polyhedral, membership, intersection, overlap, CAD
%X via enews

%A P. Wyard
%T Context free grammar induction using genetic algorithms
%J Proc. 4th Int. Conf. on Genetic Algorithms
%W San Diego
%D 1991
%P 514-518
%K algorithm, GA, context-free CFG, machine learning, language matched brackets
   parentheses, GNF
%X 16 refs
   Learnt grammar for language of matching brackets.
   Target grammar in GNF (!) form:
      S -> (R   S -> (RS   R -> (RR   R -> )
   (GNF rules: LeftVar -> RightTerm ListOfVars , GNF== CNF.)
   equivalent chromosome:
      [(S,"(",[R]),(S,"(",[R,S]),(R,"(",[R,R]),(R,")",[])].
   chromosome length can change under x-over.
   Mutation/rule 1/200; population 1000; 20 to 100 test strings;
   5 runs, 2 found grammar, one in 16 generations.
   [Could not learn the grammar for `equal numbers of a's and b's
    in 40 generations by which time it had converged.]

%A W. Poundstone
%T Prisoner's Dilemma
%I OUP
%D 1993
%P 304
%O Doubleday, NY, '92
%K OUP, prisoner prisoners, tit for tat, TFT, tit-for-tat, PD, IPD, text, book,
   MAD, non zero sum game theory, chicken, von Neumann, c1993, c199x, c19xx,
   altruism, self sacrifice, cooperate, defect, behaviour
%X stg7.99 pbk.   uk us isbn:019286162X.
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A J. Horgan
%T Last words of a quantum heretic
%J New Scientist
%M 27 FEB
%D 1993
%P 38-42
%K c1993, c199x, c19xx, David Bohm, quantum mechanics theory, relativity,
   hidden variable variables, interpretation, physics, implicate order,
   nonlocality, non-locality
%X David Bohm died October 1992 aged 74.
   [Also search for: physics Bohm].
   Also see DB@[<A HREF="https://en.wikipedia.org/wiki/David_Bohm">wikip</A>]['23].

%A M. Mitchell Waldorp
%T Complexity: The Emerging Science at the Edge of Order and  Chaos
%I Simon and Shuster/Viking
%D 1992
%P 380
%K artificial, life, complexity, order, chaos, emergent behaviour
%X $23 US
   Reviewed in Nature: by Richard Dawkins 361: p507, via enews.

%A K. M. Ali
%A M. J. Pazzani
%T Hydra: a noise tolerant relational concept learning algorithm
%J sub to IJCAI
%D 1993
%I Dept. Comp. Sci., University of California, Irvine.
%K inductive inference, II, AI, machine learning, FOIL, Horn clause, ILP,
   explanation based, relation, noise, error, expert system

%A R. Beer
%A J. C. Gallagher
%T Evolving dynamic neural networks for adaptive behavior
%J Adaptive Behavior
%V 1
%N 1
%P 90-119
%D 199? ???
%K AB, AI, ANN, artificial neural net network, insect, cockroach,
   genetic algorithm, GA, behaviour
%X via enews march '93:
   <!-- email: (beer alpha.ces.cwru.edu) (johng alpha.ces.cwru.edu)  -->.
   They evolve 6-neuron chemotaxic beasties with two sensors and two wheels
   and also train a cockroach simulation to walk.  You may want to e-mail
   <!-- kv07@iastate.edu --> (Kurt von Roeschlaub) for information as well,
   he has implimented a version of the 1st experiment with more bells
   and whistles.
   from: Dan <!-- email: Danwell@IASTATE.EDU -->.

%A R. Berger
%T The undecidability of the domino problem
%J Mem. Amer. Math Soc.
%V 66
%P ???-???
%D 1966
%K MAMS, AMS, tile, tiling, plane, decidability, domino
%X via enews

%A R. M. Robinson
%T Undecidability and nonperiodicity for tilings of the plane
%J Inv. Math
%V 12
%P 117-209
%D 1971
%K tile, tiling, plane, decidability, domino
%X via enews

%A ???
%T Effective transformations on infinite trees, with applications to high
   undecidability, dominoes, and fairness
%J JACM
%V 33
%N 1
%P 224-248
%D 1986
%K ACM, tile, tiling, plane, tree, decidability, domino
%X via enews

%A M. Angell
%T Publish or perish: a proposal
%J Ann Intern Med.
%V 104
%N 2
%P 261-262
%M FEB
%D 1986
%K views, c1986, c198x, c19xx, publish, perish, science, scientific research,
   topN, publications, papers, research, productivity, promotion, impact,
   quality, gift authorship, guest author, abuse, fraud, ethics, LPU, zzEthics
%X "Because promotion & funding of physicians in academic medicine are closely
   linked to the # of their publications, investigators feel impelled to publish
   as frequently as possible. ... leads to a number of unfortunate practices in
   medical publishing, inc. undertaking trivial studies because they yield rapid
   results, needlessly reporting the same study in installments, reporting a
   study more than once, & listing as authors people only marginally involved in
   the study. It may also be a motivation for fraud. An effective way to reduce
   these offenses & affirm the supremacy of substance over volume in scientific
   research would be to place a ceiling on the # of publications that can be
   considered in evaluating a candidate for promotion or funding. Each pub'n
   would then receive commensurately more attention, both from the researcher &
   from those judging the work."
   -- [<A HREF="http://dx.doi.org/10.7326/0003-4819-104-2-261">doi:10.7326/0003-4819-104-2-261</A>]['13].
   [Also search for: publish perish].

%A H. D. Ebbinghaus
%T Domino threads and complexity
%B ???
%I SpringerVerlag
%S LNCS
%V 270
%P 131-142
%D ?
%K tile, tiling, plane, decidability, domino
%X via enews

%A Grunbaum
%A Shephard
%T Tilings and Patterns
%I W. H. Freeman
%D 1987
%K text, book, tile, tiling, plane, decidability, domino
%X via enews

%A J. Schaeffer
%A J. Culberson
%A N. Treloar
%A B. Knight
%A P. Lu
%A D. Szafron
%T A world championship caliber checkers program
%J Artif. Intell.
%V 53
%M FEB
%D 1992
%P 273-289
%K jrnl, AI, artificial intelligence, checkers, chequers, draughts, game,
   play, playing
%X reviewed in ACM Comp Rev Feb 93  p 124.
   [Also search for: checkers game].

%A J. Rissanen
%T Information Theory and Neural Nets
%B Mathematical Perspectives on Neural Networks
%D 1993
%I Lawrence Erlbaum
%E P. Smolensky
%E M. Mozer
%E D. Rumelhart
%K AI, artificial neural net, ANN, NN, MDL, IT,
   cost, inductive inference, II, text, book, minimum description length

%A W. Buntine
%A A. S. Weigend
%T Bayesian Back-Propagation
%J Complex Systems
%V 5
%N 6
%P 603-643
%D 1991
%K c1991, c199x, c19xx, artificial neural net, ANN, NN, backpropagation,
   backprop, MML, MDL, cost, inductive inference, II, AI, regularization,
   training, sparse, pruning
%X "... presents approx. Bayesian methods to stat. components of back-prop.:
   choosing a cost fn & penalty term (interpreted as a form of prior prob.),
   pruning insig. weights ... extend some heuristic techniques suggested in the
   lit., & in most cases require a small additional factor in comp'n during
   back-propagation or computation once back-prop. has finished."
   -- [<A HREF="https://www.complex-systems.com/abstracts/v05_i06_a04/">www</A>]['22],
   pdf@[<A HREF="https://wpmedia.wolfram.com/uploads/sites/13/2018/02/05-6-4.pdf">w'lfram</A>]['22].
   [Also search for: backpropagation NN].
   Also see backprop@[<A HREF="https://en.wikipedia.org/wiki/Backpropagation">wikip</A>]['22].

%A S. J. Nowlan
%A G. E. Hinton
%T Simplifying Neural Networks by Soft Weight-Sharing
%J Neural Computation
%V 4
%P 473-493
%D 1992
%K artificial neural net, ANN, NN, MML, MDL, cost, inductive inference, II,
   AI, NC

%A G. E. Hinton
%A D. van Camp
%T Keeping neural networks simple by minimizing the description length of
   the weights
%J Proc. COLT '93
%W Santa Cruz
%P 5-13
%M JUL
%D 1993
%K conf, c1993, c199x, c19xx, II, neural network, ANN, vanCamp, MDL, weight,
   bits back, complexity, borrow
%X H a r r i   V a l p o l a  ~harri at cis.hut.fi '00
   believes (thesis node 30)  H + v.C  coined the term "bits back" but
   see  W a l l a c e '86 ACSC9 for the technique's first use,
   and also W a l l a c e ICCI '90 pp.72-81.
   [Also search for: bits back II].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].)

%A J. Hesser
%A R. Manner
%A O. Stucky
%T Optimization of Steiner trees using genetic algorithms
%J Proc. of the Third Int. Conf. on Genetic Algorithms
%E J. David Schaffer
%P 231-236
%W Arlington, VA
%M JUN
%D 1989
%I MorganKaufmann Publ., Inc.
%K genetic algorithm, GA, Steiner tree, trees, Proc 3rd Int Conf
%X From: <!-- email: cpeck@uckbv1.ece.uc.edu --> Charles Peck '93
   In this paper the application of a Genetic Algorithm (GA) to the Steiner
   tree problem is described.  The performance of the GA is compared to that of
   the Simulated Annealing Algorithm (SA) and one the the best conventional
   algorithms given by Rayward-Smith and Clare (RCA).
      According to our results, all three algorithms find the optimum and
   converge equally fast,  i.e., GA and SA need not more function evaluations
   than the RCA that has even been improved by the relaxation heuristic. The GA
   reaches the optimum in a smaller number of generations which is considered
   the reason why it did not show an even better performance.

%A C. Ho-Stuart
%A H. S. M. Zedan
%A M. Fang
%T Congruent weak bisimulation with dense real time
%J IPL
%V 46
%N 2
%M MAY
%D 1993
%P 55-62
%K real-time, real time, CCS, CSP, process, temporal logic
   Ho Stuart

%A H. U. Vogel
%T The great well of China
%J Scientific American
%M JUN
%D 1993
%P 86-91
%K well-drilling, well drill, drilling, bore, boring, Sichuan, SA
%X 1000 metres deep drilled in 1835.

%A Jean-Louis Lassez
%A Tien Huynh
%A Ken McAloon
%T Simplification and elimination of redundant linear arithmetic constraints
%B Proc. of the North American Conf. on Logic Programming
%P 37-51
%D 1989
%V 13
%K constraint, CLP, CLP(R), logic programming, LP, Prolog
%X via enews

%A M. Milinski
%T Cooperation wins and stays
%J Nature
%V 364
%M 1 JUL
%D 1993
%P 12-13
%K c1993, c199x, c19xx, prisoners prisoner's dilemma, cooperate, defect,
   TFT, tit for tat, tit-for-tat, GA, PD, IPD
%X news and views short review of an article by Nowak and Sigmund
   on evolution of probabilistic algorithms for the problem.
   [Also search for: prisoners dilemma].

%A M. Nowak
%A K. Sigmund
%T A strategy of win-stay, lose-shift that outperforms tit-for-tat in
   the prisoner's dilemma game
%J Nature
%V 364
%M 1 JUL
%D 1993
%P 56-58
%K prisoners, prisoner's, dilemma, PD, IPD, cooperate, altruism, defect,
   TFT, tit for tat, tit-for-tat, GA, lose shift win stay
%X (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A D. Abramson
%A H. Dang
%T School timetables: a case study in simulated annealing
%P 103-124
%B Applied Simulated Annealing
%E R. V. V. Vidal
%I SpringerVerlag
%S Lect. Notes in Economics and Mathematical Systems.
%V 396
%D 1992 ? or 1993 ?
%K LNEMS, SA, time table, tables, tabling, scheduling, computer architecture
%X special purpose architecture for (certain) simulated annealing problems.

%A D. Abramson
%T A very high speed architecture for simulated annealing
%J Computer
%I IEEE
%M MAY
%D 1992
%P 27-36
%K SA, time, table, tables, tabling, scheduling, computer architecture

%A R. J. Collins
%A D. R. Jefferson
%T AntFarm: towards simulated evolution
%J Artificial Life II
%E J. D. Farmer
%E C. Langton
%E S. Rasmussen
%E C. Taylor
%I AddisonWesley
%D 1991
%K ant farm, genetic algorithm GA, CM, AL, ALII, AL2, AL91
%X via enews
   apparently uses a Connection Machine CM and a large chromosome 25000 bits?

%A Jon Bentley
%T Programming Pearls
%I AddisonWesley
%D 1986
%K text, book, problem solving, algorithm, algorithms, computer programming,
   programs, source, interview, problems, good, gem, gems, pearl, tricks,
   idea, ideas, ah ha, ahha, c1986, c198x, c19xx
%X 2nd ed 2000, pb us$33; uk us isbn:0201657880; uk us isbn13:978-0201657883;
      "... [after] 14 years, Bentley has substantially updated his essays to
      reflect current programming methods and environments. [And] there are
      three new essays on testing, debugging, and timing, set representations,
      string problems. All the original programs have been rewritten, and an
      equal amount of new code has been generated. ..."
      1st ed 1986; uk us isbn:0201103311.
   [Also search for: Bentley book programming].

%A Jon Bentley
%T More Programming Pearls
%I AddisonWesley
%D 1988
%K text, book, c1988, c198x, c19xx, good, problem solving, tricks, techniques,
   pearl, computer programming, algorithm, algorithms
%X 1st ed 1988, pb us$27; uk us isbn:0-201-11889-0; uk us isbn13:978-0201118896.
   [Also search for: Bentley book programming].

%A Xiolin Wu
%T Image coding by adaptive tree-structured segmentation
%J IEEE Trans. on Info. Theory
%V 38
%N 6
%M NOV
%D 1992
%P 1755-1767
%K TIT, information theory, image processing, IP, binary tree, partition,
   segment
%X Binary-tree partitioning of an image.
   Each (sub-)partition by a line of slope  0, 45, 90 or 135 degrees
   at an arbitrary position.
   (Reasonably fast way to find the best candidate line in each direction.)
   Piecewise constant approximation of image.
   Tree transmitted in breadth-first order so that image is "refined"
   as more segments arrive.
   Example images look better than the common 4-way block method.
   Lossy, but could be made loss-less.

%A J. Holland
%T Adaptation in Natural and Artificial Systems
%I MITpress
%D 2nd ed 199? ???
%K genetic algorithms, GA, text, book
%X isbn:0-262-58111-6.
   <!-- email: john-henry@ub.cc.umich.edu --> via enews -- '92.

%A S. Le Grand
%A K. Merz
%T The application of the genetic algorithm to the minimization of potential
   energy functions
%J The Journal of Global Optimization
%D 1993 ? to appear
%P ??-??
%K genetic algorithms, GA, JGO, protein fold, folding, structure prediction
%X (70 entry) bibliography.    via enews.

%A A. Kapsalis
%A V. J. Rayward-Smith
%A G. D. Smith
%T Solving the graphical Steiner tree problem using genetic algorithms
%J J. of the Operational (??) Research Society
%V 44
%N 4
%P 397-406
%D 1993
%K jrnl, c1993, c199x, c19xx, genetic algorithms, GA, JORS
%X via enews
   -- [<A HREF="http://www.cmp.uea.ac.uk/research/publications.jsp?action=startsearch&query=author:%22Rayward-Smith,%20V%22">vjrs</A>]['06].

%A Pippa Hilary Rull
%A Barry An
%T BARRY: An autonomous train-spotter
%J Image and Vision
%V ??
%N ??
%D 1993
%P 499-506
%K jrnl, c1993, c199x, c19xx, image processing, IP, train spotter spotting,
   joke, spoof, satire, funny haha ha ha
%X "We have taken a set of well-understood algorithms and combined them in a
   commercial application: trainspotting ... can indeed perform its task
   satisfactorily for many hours without the sustenance that human spotters
   require (flasks of hot tea, sandwiches etc.) ..."
   -- 24324307@[<A HREF="https://core.ac.uk/outputs/24324307/">core.ac.uk</A>['24].

%A J. R. Peck
%T Friendship and the evolution of cooperation
%J J. Theor. Biol.
%V 162
%P 195-228
%D 1993
%K c1993, c199x, c19xx, jrnl, JTB, iterated, prisoner's dilemma, PD, IPD,
   cooperate, defect, tit-for-tat, tit for tat, TFT, friend, like, world,
   movement
%X investigates "movement" and the maintenance of relationships.
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A Bryant A. Julstrom
%T A genetic algorithm for the rectilinear Steiner problem
%J Proc. of the 5th Int. Conf. on Genetic Algorithms
%P ??-??
%D 1993
%I Morgan-Kaufmann
%K ICGA, ICGA5, ICGA-5, ICGA93, ICGA-93, Steiner tree, trees, GA, fifth
%X via enews <!-- email: julstrom@eeyore.stcloud.msus.edu -->.

%A D. B. Fogel
%T Evolving behaviours in the iterated prisoner's dilemma
%J Evolutionary Computation.
%V 1
%N 1
%P 77-97
%D 1993
%K PD, IPD, cooperation, FSM, recognize, recognition
%X evolves finite state machines ( at most 8 states) for iterated P. D.
   p89: It is speculative but reasonable to presume that each population of
   FSMs evolves initial sequences of symbols which form patterns that can
   be recognized by other FSMs.
   (He played FSMs from different trials.)
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A S. L. Lima
%T Iterated prisoner's dilemma: an approach to evolutionary stable cooperation
%J American Naturalist
%V 134
%N 5
%M NOV
%D 1989
%P 828-834
%K AN, PD, IPD, ESS, TFT, cooperation, altruism, reciprocity, defect

%A R. Noe
%T A veto game played by baboons: a challenge to the use of the prisoner's
   dilemma as a paradigm for reciprocity and cooperation
%J Anim. Behav.
%V 39
%P 78-90
%D 1990
%K AB, PD, IPD, cooperation, altruism, reciprocity, defect, rank,
   animal, baboon, behaviour, veto game theory
%X a veto game:
      salesman A has a right shoe to sell
      salesmen B and C each have a left shoe to sell
      a single shoe is worth nothing
      so A plays B off against C.

%A L. A. Dugatkin
%T N-person games and the evolution of cooperation: a model based on predator
   inspection in fish
%J JTB
%V 142
%P 123-135
%D 1990
%K JTB, n person game, prisoner's dilemma, PD, IPD, cooperation, altruism,
   reciprocity, fish, inspect, predator, defect, animal bahaviour
%X a few individuals in a shoal cautiously approach a predator.
   Why take the risk?

%A J. J. Bull
%A W. R. Rice
%T Distinguishing mechanisms for the evolution of cooperation
%J JTB
%V 149
%P 63-74
%D 1991
%K JTB, prisoner's dilemma, PD, IPD, cooperation, altruism, reciprocity,
   behaviour, defect, partner choice fidelity, yucca moth fig wasp
%X under partner-choice models, individuals are associated for just
   one interaction, but an assymetry enables one member to differentially
   reward cooperation v. defection in advance of any possible exploitation.
   Possible examples ... are provided by the yucca / yucca-moth and
   the fig / fig-wasp system.

%A M. Mesterton-Gibbons
%T An escape from the prisoner's dilemma
%J J. Math. Biol.
%V 29
%P 251-269
%D 1991
%K JMB, PD, IPD, cooperation, reciprocity, altruism, defect, foraging,
   recognition, behaviour
%X ... model of foraging for egg sites. ...
   reveals equivalence of selfishness and altruism.
   The resulting game is unconditionally a PD is players have perfect
   recognition; otherwise it yields either PD or 2 e. stable strategies,
   or a unique cooperative ESS, depending on parameter values.
   Thus unrecognition can favour cooperation.

%A M. Nowak
%T Stochastic strategies in the prisoner's dilemma
%J Theor. Population Biol.
%V 38
%P 93-112
%D 1990
%K TPB, PD, IPD, cooperation, altruism, reciprocity, defect, stability, ESS,
   probabilistic
%X A complete analysis of all strategies where the probability to cooperate
   depends only on the opponent's previous move is given for the infinitely
   iterated PD. All Nash solutions are characterised. A necessary
   condition for evolutionary stability against invasion by pressure of
   selection is found. A mutation selection model is discussed which
   enables us to quantify the possibility to succeed over less cooperative
   strategies by means of reciprocity.
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A J. Farrell
%A R. Ware
%T Evolutionary stability in the repeated prisoner's dilemma
%J Theor. Population Biol.
%V 36
%P 161-166
%D 1989
%K TPB, PD, IPD, cooperation, reciprocity, altruism, defect, ESS,
   tit for tat, TFT, tit-for-tat
%X We show that
   no finite mixture of tit-for-n-tats can be evolutionarily stable.

%A R. Boyd
%T Mistakes allow evolutionary stability in the repeated prisoner's dilemma
   game
%J J. Theor. Biol.
%V 136
%P 47-56
%D 1989
%K JTB, PD, IPD, cooperation, reciprocity, altruism, defect, probabilistic,
   error, noise, misunderstanding, mistake, tit for tat, TFT, tit-for-tat,
   ESS, stochastic
%X Here I show that if there is always some prob'
   that individuals will make a mistake, then a pure trategy can be an ESS
   provided that it is "strong perfect equilibria" against iteslef.
   ie. it is the best poss' response to itself for every possible seq'
      of behaviour.
   Both unconditional-defect and a modified tit-for-tat have this property.
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A J. J. Bull
%A I. J. Molineux
%T Molecular genetics of adaption in an experimental model of cooperation
%J Evolution
%V 46
%N 4
%P 882-895
%D 1992
%K biol, cooperation, DNA bacteriophage f1, host, parasite,
   prisoner's dilemma, PD, IPD
%X ... parasitic bacteriophage (f1) and a bacterial host.

%A K. Savatsky
%A R. G. Reynolds
%T A hierarchical model of the evolution of cooperation in cultural systems
%J BioSystems
%V 23
%P 261-279
%D 1989
%K BS, prisoner's dilemma, PD, IPD, cooperation, reciprocity, altruism, defect,
   llama herd herder herders, cheat, cheating, stress, culture, human behaviour
%X Examines data documenting cooperative practices amongst llama herders
   of the Ayacucho basin of Peru:
      each herder may help another by making a donation of reproductive llamas
   to a failing herd. This is a costly donation. There is no expectation of
   reciprocal assistance from that herder to anyone in the donor's family,
   It is spontaneous gift giving.
      Simulations done with various models. Apparently without donations
   any individual herd likely to go through a bad patch and die out
   in ~ 70 years.
   With donations, most herds last indefinitely.
   What about cheating ... refuse to offer assistance or donate a dud llama ...

%A B. Borstnik
%A D. Pumpernik
%A I. L. Hofacker
%A G. L. Hofacker
%T An ESS-analysis for ensembles of prisoner's dilemma strategies
%J J. Theor. Biol.
%V 142
%P 189-200
%D 1990
%K JTB, PD, IPD, ESS, cooperation, reciprocity, altruism, defect,
   collusion, group
%X R > (T+S)/2  a set of strategies can be singled out which do not
   lose against any other strategy while cooperating with themselves.
   Such a set is uninvadable by other PD strategies if it constitutes more
   than half of the total population.

%A J. McCormack
%T Interactive evolution of L-system grammars for computer graphics modelling
%B Complex Systems
%E D. Green
%E T. Bossomaier
%P 118-130
%I IOS Press
%D 1993
%K L-systems, L-system, Lsystem, Lindenmayer, Monash, probabilistic grammar,
   rule, plant
%X 25 refs; uk us isbn:90-5199-117-7.
   L-system is probabilitic grammar to create plants (say).
   Difficult to design grammar explicitly.
   So user watches and influences evolution (selection) to get desired effect.

%A P. Prusinkiewicz
%A A. Lindenmayer
%T The Algorithmic Beauty of Plants
%I SpringerVerlag
%D 1991
%O 1996, isbn:0387946764.
%K text, book, L-systems, L-system, probabilistic grammar, rule, plant,
   self organisation, complex systems, Lsystems, Lsystem, c1991, c199x, c19xx
%X 1991, uk us isbn:3540972978;  1996, uk us isbn:0387946764.

%A P. Prusinkiewicz
%A A. Lindenmayer
%A J. Hanan
%T Developmental models of herbaceous plants for computer imagery purposes
%J Computer Graphics
%V 22
%N 4
%P 141-150
%M AUG
%D 1988
%K L-systems, L-system, probabilistic grammar, rule, plant

%A L. Ingber
%T Simulated annealing: Practice versus theory
%J Mathl. Comput. Modelling
%V ???
%N ???
%D 1993 to appear
%P ???
%O ftp.caltech.edu:pub/ingber
%K adaptive simulated annealing, quenching, SA
%X via enews (9/93) from:
   || Prof. Lester Ingber                                                ||
   || Lester Ingber Research                                             ||
   || P.O. Box 857                   EMail: ingber at alumni.caltech.edu ||
   || McLean, VA  22101             Archive: ftp.caltech.edu:/pub/ingber ||

%A A. Schrijver
%T Theory of Linear and Integer Programming
%I Wiley
%S A Wiley-Interscience publication.
%P 471
%D 1986
%O p.484, 1998
%K text, book, LinearProgramming, linear programming, integer programming
%X via enews.   uk us isbn:0471982326.
   [Also search for: linearProgramming].

%A Bauer
%A Liepins
%T Genetic algorithms and stock market timing trading rules
%J 11th Int. Symposium on Forecasting, NYC June
%P 9-12,
%D 1991
%K eleventh, algorithm, GA, exchange, trade, forecast
%X via enews

%A R. E. Marks
%T Breeding hybrid strategies: optimal behaviour for oligopolists
%J J. of Evolutionary Economics
%V 2
%P 17-38
%D 1992
%K JEE, genetic algorithm, GA, prisoner's dilemma, PD, tit-for-tat,
   tit for tat, TFT
%X via enews

%A E. Schoneburg
%T Stock Price Prediction Using Neural Networks: A Project Report
%J Neurocomputing
%I Elsevier
%D 1990
%K exchange, SE, NN, ANN, net
%X via enews, presume it's in a jrnl?

%A King Sun Fu
%T Syntactic Methods in Pattern Recognition
%I AcademicPress, NY
%D 1974
%K SPR, book, text
%X uk us isbn:0122695607.

%A D. E. Knuth
%T Structured programming with go to statements
%J ACM Computing Surveys
%I ACM
%V 6
%N 4
%P 261-301
%M DEC
%D 1974
%K jrnl, ACM, c1974, c197x, c19xx, zz0608, harmful, go to, goto, statement,
   command, programming, methodology
%X Scanned pdf [<A HREF="http://doi.acm.org/10.1145/356635.356640">doi:10.1145/356635.356640</A>]['08].

%E King Sun Fu
%T Syntactic Pattern Recognition: Applications
%I SpringerVerlag
%D 1977
%K SPR, book, text
%X isbn:038707841X;

%A King Sun Fu
%T Syntactic Pattern Recognition and Applications
%I PrenticeHall
%D 1982
%K SPR, book, text
%X isbn:038707841X;

%A P. C. Chi
%A D. S. Nau
%T Improving game board evaluator with genetic algorithms
%J Proc. - 1988 Spring Symposium Series: Computer Game Playing
%P 29-30
%W Stanford, CA
%M MAR
%D 1988
%I Americ. Assoc. Artificial Intelligence
%K genetic algorithm GA, AAAI AI
%X via enews

%A K. Steiglitz
%T Two non-standard paradigms for computation: Analog machines and
   cellular automata
%B Performance limits in communication theory and practice
%P 173-192
%D 1988
%S NATO ASI, NSSE
%V 142
%I Springer
%K chapter, c1988, c198x, c19xx, zz1117, analog, analogue, quantum,
   non standard, nonStandard, computing, complexity, NPC, strong Church thesis
%X "Serious roadblocks have been encountered in several areas of computer
   application, for example in the solution of intractable (NP-complete)
   combinatorial problems, or in the simulation of fluid flow. In this talk we
   will explore two alternatives to the usual kinds of computers, and ask if
   they provide some hope of ultimately by-passing what appear to be essential
   difficulties."               (from a ref in Shor 1995.)
   [Also search for: analogue computing].

%A N. Dachi
%A K. Matsuo
%T Ecological dynamics under different selection-rules in distributed and
   iterated prisoner dilemma game
%B Parallel Problem Solving from Nature
%E H.P.Schwefel
%E R.Manner
%I SpringerVerlag
%S LNCS
%V 496
%D 1991
%O Proc. of the 1st Workshop on Parallel Problem Solving from Nature
   (PPSN1), Dortmund, 1-3 October 1990)
%P 388-394
%K prisoner's dilemma PD, tit-for-tat, tit for tat, TFT, cooperate, defect
%X (Manner's name has an umlaut over the a.) via enews.

%E J. Doyne Farmer
%E A. Lapedes
%E Norman H. Packard
%E B. Wendroff
%T Evolution, games, and learning
%I NorthHolland, Amsterdam
%D 1986
%K prisoner's dilemma PD, game, genetic algorithm GA, text, book
%X via enews.  asin / isbn:0444870318;

%A Heinz Muhlenbein
%T Darwin's continent cycle theory and its simulation by the prisoner's
   dilemma
%J Complex Systems
%V 5
%N 5
%P 459-478
%D 1992
%K CS, prisoner's dilemma PD
%X (Muhlenbein's name has an umlaut over the u.)
   via enews

%A J. H. Nachbar
%T Evolution in the finitely repeated prisoner's dilemma
%J J. of Economic Behaviour and Organization
%V 19
%N 3
%P 307-326
%D 1992
%K prisoner's dilemma PD, tit-for-tat, tit for tat, TFT, cooperate, defect
   JEBO, genetic algorithm GA, iterated
%X via enews

%A E. Ann Stanley
%A D. Ashlock
%A L. Tesfatsion
%T Iterated prisoner's dilemma with choice and refusal of partners
%P 131-178
%E C. Langton
%B Artificial Life III
%V 16
%S Santa Fe Institute Studies in the Sciences of Complexity
%I AddisonWesley
%D 1993
%O Proc. 3rd Conf. on Artificial Life.
%K AL, AI, prisoner's, prisoners dilemma, PD, tit-for-tat, tit for tat, TFT,
   cooperate, defect, refuse, choose, friend friendship
%X via enews

%A K. Lindgren
%A M. G. Nordahl
%T Cooperation and community structure in artificial ecosystems
%J Artificial Life
%V 1
%N 1and2
%P 15-38
%D 19??
%K AL, AI, prisoner's, prisoners dilemma, PD, tit-for-tat, tit for tat TFT,
   cooperate, defect, friend, friendship
%X via enews:  <!-- email: danwell@iastate.edu -->  '94

%A Glance, Natalie S.
%A Bernado A. Huberman
%T The outbreak of cooperation
%J J. of Math. Sociology
%V 17
%D 1993
%K JMS, prisoner's dilemma, PD, cooperate, defect
%X via enews

%A J. Miller
%T The coevolution of automata in the repeated prisoner's dilemma
%R Working Paper 89-003
%I Santa Fe Institute
%D 1989
%K SFI, prisoner's dilemma, PD, tit-for-tat, tit for tat, TFT,
   cooperate, defect, genetic algorithm, GA, evolution, FSA, FSM
%X via enews

%A A. Heck
%T Introduction to Maple
%I SpringerVerlag
%D 1993
%K Maple, symbolic math, maths, mathematics, linear, algebra, text, book
%X 125 refs.  isbn:3540976620;   <!-- email: heck@can.nl  ('93) -->.
   Also see Maple 2 0 0 1.

%A J.-M. Cornil
%A P. Testud
%T An Introduction to Maple V
%I SpringerVerlag
%D 2001
%K Maple5, MapleV, Maple, book, text
%X uk us isbn:3540664424.

%A M. A. Nowak
%A R. M. May
%T Evolutionary games and spatial chaos
%J Nature
%V 359
%P 826-829
%M OCT
%D 1992
%K game, prisoner's dilemma, PD, tit-for-tat, tit for tat, cooperate, defect,
   genetic algorithm GA, space, spatial, grid, 2D 2-D, neighbour
%X Players in a 2-D grid, play neighbours (and self) each round,
   replaced by occupant or neighbour on highest score.
   "In this paper we consider only 2 kinds of players:
   those who always cooperate, C, and those who always defect, D."
          C    D
      C  R,R  S,T   T > R > P > S    N and M use R=1, T=b, S=P=0 and vary b > 1
      D  T,S  P,P
   Players play eight neighbours and also self.
   If b > 1.8 a 2x2 or larger cluster of D will continue to grow at corners
   although not necc' along edges.
   If b < 1.8 big D clusters will shrink.
   If b < 2 a 2x2 or larger cluster of C will grow.
   If b > 2 C clusters do not grow.
   Most interesting regime is  2 > b > 1.8
   Chaotic patterns emerge but the asymptotic fraction of Cs is
   fC ~ 0.318 (= 12 log2 - 8) for almost all start configurations
   and proportions.
   If players play 8 neighbours only,  5/3 > b > 8/5,  fC ~ 0.299.
   If 4 neighbours and self, 2 > b > 5/3, self excluded 3/2 > b > 4/3,
   fC ~ 0.374.
   Hexagonal arrays give complex patterns but show less of the lacy fractal
   character unless self-interaction is weighted more heavily.

%A M. R. Garey
%A D. S. Johnson
%T Computers and Intractability: A Guide to the Theory of NP-Completeness
%I FreemanPress
%P 338
%D 1979
%K text, book, c1979, c197x, c19xx, good, classic, L4Ref, L5Ref, P, NP complete,
   co-NP, coNP, NPC, complexity, nondeterministic, non deterministic,
   polynomial time, algorithm, tractable, intractable, computing
%X 1st ed 1979, pb us$57; uk us isbn:0716710455; uk us isbn13:978-0716710455.
                      hb; uk us isbn:0716710447; uk us isbn13:978-0716710448.
   (Also see CandI@[<A HREF="http://en.wikipedia.org/wiki/Computers_and_Intractability">wikip</A>]['14].)

%A L. S. Penrose
%T Self-reproducing machines
%J Scientific American
%V 200
%N 6
%P 105-113
%M JUN
%D 1959
%K SA, c1959, c195x, c19xx, self reproduction, reproduce, replication, machine,
   shape, assembly, assemble, build, DNA
%X via Chris Langton  <!-- email: cgl OF lanl.gov -->  '93.
   The most complex machine here can encode a sequence of information - LA.
   [Also search for: Penrose c195x].

%A A. N. Shirayayev
%T Selected works of A. N. Kolmogorov. Vol 3 Information Theory and Theory of
   Algorithms
%I Kluwer
%D 1993
%O Nauka, Moscow '87
%K text, book, anthology, II, inductive inference, MML, MDL
   algorithmic complexity, minimum message length encoding, description

%E Andreas S. Weigend
%E Neil A. Gershenfeld
%T Time Series Prediction: Forecasting the Future and Understanding the Past
%I AddisonWesley
%M SEP
%D 1993
%K Santa Fe, Santa-Fe, time series prediction, ANN, NN, artificial neural net,
   Bach, exchange rate rates economics, hidden Markov model HMM
   text, book
%X enews <!-- email: weigend@sabai.cs.colorado.edu --> Andreas Weigend '93
   Paperback isbn:0-201-62602-0;  US$32.25 (672 pages)
   Hardcover isbn:0-201-62601-2;  US$49.50 (672 pages)
  1  The Future of Time Series: Learning and Understanding
          Neil A. Gershenfeld and Andreas S. Weigend
 Section I.  DESCRIPTION OF THE DATA SETS__________________________________
  73  Lorenz-Like Chaos in NH3-FIR Lasers
          Udo Huebner, Carl-Otto Weiss, Neal Broadus Abraham, and Dingyuan Tang
 105  Multi-Channel Physiological Data: Description and Analysis
          David R. Rigney, Ary L. Goldberger, Wendell C. Ocasio, Yuhei Ichimaru, George B. Moody, and Roger G. Mark
 131  Foreign Currency Dealing: A Brief Introduction Jean Y. Lequarre
 139  Whole Earth Telescope Observations of the White Dwarf Star (PG1159-035)
          J. Christopher Clemens
 151  Baroque Forecasting: On Completing J.S. Bach's Last Fugue
          Matthew Dirst and Andreas S. Weigend
 Section II. TIME SERIES PREDICTION________________________________________
 175  Time Series Prediction by Using Delay Coordinate Embedding
          Tim Sauer
 195  Time Series Prediction by Using a Connectionist Network with Internal Delay Lines
          Eric A. Wan
 219  Simple Architectures on Fast Machines: Practical Issues in Nonlinear Time Series Prediction
          Xiru Zhang and Jim Hutchinson
 243  Neural Net Architectures for Temporal Sequence Processing
          Michael C. Mozer
 265  Forecasting Probability Densities by Using Hidden Markov Models with Mixed States
          Andrew M. Fraser and Alexis Dimitriadis
 283  Time Series Prediction by Using the Method of Analogues
          Eric J. Kostelich and Daniel P. Lathrop
 297  Modeling Time Series by Using Multivariate Adaptive Regression Splines (MARS)
          P.A.W. Lewis, B.K. Ray, and J.G. Stevens
 319  Visual Fitting and Extrapolation
          George G. Lendaris and Andrew M. Fraser
 323  Does a Meeting in Santa Fe Imply Chaos? Leonard A. Smith
 Section III.  TIME SERIES ANALYSIS AND CHARACTERIZATION___________________
 347  Exploring the Continuum Between Deterministic and Stochastic Modeling
          Martin C. Casdagli and Andreas S. Weigend
 367  Estimating Generalized Dimensions and Choosing Time Delays:
      A Fast Algorithm Fernando J. Pineda and John C. Sommerer
 387  Identifying and Quantifying Chaos by Using Information-Theoretic
      Functionals Milan Palus
 415  A Geometrical Statistic for Detecting Deterministic Dynamics
          Daniel T. Kaplan
 429  Detecting Nonlinearity in Data with Long Coherence Times
          James Theiler, Paul S. Linsay, and David M. Rubin
 457  Nonlinear Diagnostics and Simple Trading Rules for High-Frequency
      Foreign Exchange Rates Blake LeBaron
 475  Noise Reduction by Local Reconstruction of the Dynamics Holger Kantz
 Section IV.  PRACTICE AND PROMISE_________________________________________
 493  Large-Scale Linear Methods for Interpolation, Realization, and
      Reconstruction of Noisy, Irregularly Sampled Data
          William H. Press and George B. Rybicki
 513  Complex Dynamics in Physiology and Medicine
          Leon Glass and Daniel T. Kaplan
 529  Forecasting in Economics Clive W.J. Granger
 539  Finite-Dimensional Spatial Disorder: Description and Analysis
          V.S. Afraimovich, M.I. Rabinovich, and A.L. Zheleznyak
 557  Spatio-Temporal Patterns: Observations and Analysis Harry L. Swinney
 571  Bibliography (800 references)

%A J. L. Balcazar
%A J. Diaz
%A J. Gabarro
%T Structural Complexity I
 and Structural Complexity II
%D 1993 ?
%I SpringerVerlag
%S EATCS Monographs on Theoretical Computer Science
%K text, book, complexity, P, NP, NPC, complete, completeness
%X  table of contents of volume I (which has 191 pages):
  1 Basic notions about models of computation
  2 Time and space bounded computations
  3 Central complexity classes
  4 Time bounded Turing reductibilities
  5 Nonuniform complexity
  6 Probabilistic complexity
  7 Uniform diagonaliazion
  8 The polynomial time hierarchy
 Via enews '93.

%A Chee Keng Yap
%T Theory of Complexity Classes, Volume 1
%D 1994 ?
%I OUP
%K text, book, OUP, complexity, P, NP, NPC, complete, completeness
%X 8 first chapters have 419 pages). Here is the table of contents.
  1  Initiation to complexity theory
  2  The Turing model: Basic results
  3  Introduction to the class NP
  4  Reductibilities
  5  Complete languages
  6  Separation results
  7  Alternation choices
  8  Stochastic choices
  9  Constructive hierarchies
  10 Circuits
 via enews '93

%A ???
%T Catalog of Complexity Classes
%B Handbook on Theoretical Computer Science
%E J. Van Leeuwen
%D ???
%P ??-??
%I Elsevier
%K HTCS, TCS, complexity, P, NP, NPC, complete, completeness
%X via enews '93

%A Z. Michalewicz
%T Genetic Algorithms + Data Structures = Evolution Programs
%I SpringerVerlag
%D 1992
%K text, book, c1992, c199x, c19xx, genetic algorithm, GA, evolutionary,
   geneticProgramming, programming, EP
%X The second, extended edition of my book just appeared from   (8/'94)
   Springer-Verlag (isbn:3-540-58090-5;). It has additional 90
   pages, an index and a simple C code of a GA. The price is
   $39 (hardcover). To order, call 1-800-SPRINGE(R).
   Organization: University of NC at Charlotte
   email: root@uncc.edu (Operator)

%A J. R. Koza
%T Genetic Programming
%I MITpress
%D 1992
%K text, book, algorithm, GA, automatic, automaticProgramming, program,
   genetic programming, geneticProgramming, c1992, c199x, c19xx
%X uk us isbn:0-262-11170-5.

%A R. N. Williams
%T Adaptive Data Compression
%I Kluwer
%D 1991
%K text, book, file, information, compress, compression, image processing, IP,
   DHPC, DMC, Markov model, FSM, c1991, c199x, c19xx
%X Hargrave library:   H 005.746 W726 A.

%A Kai-Fu Lee
%A Sanjoy Mahajan
%T The development of a world class Othello program
%J AI Journal
%V 43
%N 1
%P 21-36
%M APR
%D 1990
%K jrnl, AI, c1990, c199x, c19xx, Othello, board game, games, play, playing
%X "... describe an Othello program, BILL, that has far surpassed the generation
   of O. programs represented by IAGO. Its performance is due to a combination
   of factors. ... Finally, we applied Bayesian learning to combine features in
   BILL's evaluation fn. ..."
   -- [<A HREF="https://doi.org/10.1016/0004-3702(90)90068-B">doi:10.1016/0004-3702(90)90068-B</A>]['23],
   pdf@[<A HREF="https://matthieu-zimmer.net/~matthieu/courses/python/othello.pdf">www</A>]['23].
   [Also search for: Othello game].

%E F. H. Hinsley
%E A. Stripp
%T Code Breakers - the Inside Story of Bletchley Park
%I OUP
%D 1993
%K OUP, text, book, c1993, c199x, c19xx, cypher, cipher, decode, break,breaking,
   crack, enigma, codes, world war 2, two, WW2, WWII, Ultra
%X (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">B.Park</A>].)

%A E. A. Lord
%A C. B. Wilson
%T The Mathematical Description of Shape and Form
%I Ellis Horwood
%S Mathematics and its Applications
%D 1984
%K text, book
%X uk us isbn:0-85312-722-0;
   by two architects.

%A L. L. Cavalli-Sforza
%A A. Piazza
%A P. Menozzi
%A J. Mountain
%T ??? genes and language ???
%J Proc. Natl. Acad. Sci. (USA)
%V 85
%P 6002-6006
%D 1988
%K PNAS, Cavalli Sforza, human, natural language, linguistics, linguistic,
   evolution, MolBio, gene, family, evolutionary, phylogenetic tree, trees
%X via J o e  F e l s e n s t e i n
   [Also search for: natural language evolution].

%A L. L. Cavalli-Sforza
%A E. Minch
%A J. L. Mountain
%T Coevolution of genes and languages revisited
%J Proc. Natl. Acad. Sci. (USA)
%V 89
%P 5620-5624
%M JUN
%D 1992
%K PNAS, Cavalli Sforza,
   human, natural language, linguistics, linguistic distance,
   MolBio, gene, evolution, family, evolutionary, phylogenetic tree, trees
%X In an earlier paper it was shown that linguistic families of languages
   spoken by a set of 38 populations associate rather strongly with an
   evolutionary tree of the same populations derived from genetic data. While
   the correlation was clearly high, there was no evaluation of statistical
   significance; no test was available at the time. This gap has now been
   filled by adapting to this aim a procedure based on the consistency index,
   and the level of significance is found to be much stronger than 10^-3.
   Possible reasons for coevolution of strictly genetic characters and the
   strictly cultural linguistic system are discussed briefly. Results of this
   global analysis are compared with those obtained in independent local
   analyses.
   ---
   In chapter 14 of Origin of Species, Darwin predicted that if one could
   reconstruct the tree of human evolution one would have the best
   classification of human languages.    30 refs.
   [Also search for: natural language evolution].

%A L. L. Cavalli-Sforza
%A M. W. Feldman
%T Cultural Transmission and Evolution
%I Princeton Univ. Press
%D 1981
%K Cavalli Sforza, text, book, human, natural language, linguistics, c1981,
   c198x, c19xx

%A M. Ruhlen
%T A Guide to the World's Languages, Vol 1: Classification
%I Stanford Univ. Press
%D 1987, 1991
%K text, book, human, natural language, linguistics, evolution

%A L. L. Cavalli-Sforza
%A P. Menozzi
%A A. Piazza
%T History and Geography of Human Genes
%I Princeton Univ. Press
%D 1992
%K Cavalli Sforza, text, book, human, natural language, linguistics,
   MolBio, genetics, gene, family, evolutionary tree, trees

%E A. Piazza
%E L. L. Cavalli-Sforza
%T Language Change and Biological Evolution
%I Stanford Univ. Press
%D 1992
%K Cavalli Sforza, text, book, human, natural language, linguistics,
   MolBio, genetics, gene, family, evolutionary tree, trees

%A L. L. Cavalli-Sforza
%T Genes, peoples and languages
%J Scientific American
%P 104-110
%M NOV
%D 1991
%K SA, Cavalli Sforza, human, natural language, linguistics, evolution,
   MolBio, gene, family, evolutionary, phylogenetic tree, trees
%X via Jon Patrick

%A J. D. Carroll
%A J. J. Chang
%T Analysis of Individual Differences in Multidimensional Scaling via an N-way
   Generalization of the 'Eckart-Young' Decomposition
%J Psychometrika
%V 35
%P 283-319
%D 1970
%K multi dimensional, multi-dimensional, scale scaling, data, distance matrix,
   components, basis, Eckart Young
%X via enews

%A M. L. Davison
%T Multidimensional Scaling
%I John Wiley and Sons
%C New York
%D 1983
%K multi dimensional, multi-dimensional, scale scaling, data, distance matrix,
   components, basis
%X via enews

%A D. H. Krantz
%A R. D. Luce
%A P. Suppes
%A A. Tversky
%T Foundations of Measurement
%I AcademicPress
%C New York
%D 1971
%K multi dimensional, multi-dimensional, scale scaling, data, distance matrix,
   components, basis
%X via enews

%A G. Rabinowitz
%T A Procedure for Ordering Object Pairs Consistent with the Multidimensional
   Unfolding Model
%J Psychometrika
%V 41
%P 349-373
%D 1976
%K multi dimensional, multi-dimensional, scale scaling, data, distance matrix,
   components, basis
%X via enews

%A S. S. Schiffman
%A M. L. Reynolds
%A F. W. Young
%T Introduction to Multidimensional Scaling
%I AcademicPress.
%C New York
%D 1981
%K multi dimensional, multi-dimensional, scale scaling, data, distance matrix,
   components, basis
%X via enews

%A R. A. Fisher
%T Cigarettes, cancer and statistics
%J Centennial Review
%D 1958
%V 2
%P 151-166
%K RAFisher, smoke, smoking, tobacco, cigarettes, cancer, health, mortality,
   cigaratte, smoking, stats, c1958, c195x, c19xx, cause, causality

%A R. A. Fisher
%T Smoking. The Cancer Controversy: Some Attempts to Assess the Evidence
%I OliverAndBoyd
%D 1958
%K RAFisher, smoke, tobacco, cigarettes, health, mortality, cause, causality,
   cigarette, smoking, effect, genetic, stats, statistics, controversial,
   c1958, c195x, c19xx, scientific research, zzEthics, ethics
%X A 47 page pamphlet.
   @[<A HREF="http://www.york.ac.uk/depts/maths/histstat/smoking.htm">york</A>][6/'04].
   [Also search for: RAFisher smoking] and
   [also search for: smoking cause cancer].

%A W. S. Torgerson
%T Theory and Methods of Scaling
%I John Wiley and Sons
%C New York
%D 1958
%K multi dimensional, multi-dimensional, scale scaling, data, distance matrix,
   components, basis
%X via enews

%A Henrik Esbensen
%A Pinaki Mazumder
%T A Genetic Algorithm for the Steiner Problem in a Graph
%J Proc. of the European Design and Test Conf.
%W Paris, France
%M FEB
%D 1994 (to appear)
%K GA, Steiner Tree, trees
%X [NB. In a graph.]
   You can get a copy by sending me an email.  (12 / '93)
   Henrik Esbensen, Computer Science Department, Aarhus University,
   DK-8000 Aarhuc C, Denmark.  <!-- email: hesbensen@daimi.aau.dk -->.

%A G. Janacek
%A L. Swift
%T Time Series Forecasting, Simulation, Application
%I Ellis Horwood
%D 1993
%K text, book, AR, ARMA

%A R. Hummel
%A I. Rigoutsos
%T Geometric hashing as a Bayesian maximum likelihood object recognition method
%I IBM T. J. Watson Research Center
%D 1993 in prep
%K TR, IBM, c1993, c199x, c19xx, GH, hash, hashing, shape, form,
   approximate match, matching, machine vision
%X 40 refs
   email: hummel at cs.nyu.edu and  email: rigoutso at watson.ibm.com.
   [Also search for: Rigoutsos], [and for: Flash].

%A P. D. Stolley
%T When genius errs: R. A. Fisher and the lung cancer controversy
%J Am. J. Epidemiol.
%M MAR
%D 1991
%V 133
%N 5
%P 416-425
%K jrnl, RAFisher, smoke, smoking, tobacco, cigarettes, health, mortality,
   cause, causality, effect, ethics, zzEthics, bias, stats, statistics, smoker,
   cigarette, controversial, c1991, c199x, c19xx, scientific research,
   conflict of interest
%X "R.A. Fisher's work on lung cancer and smoking is critically reviewed. The
   controversy is placed in the context of his career and personality. Although
   Fisher made invaluable contributions to the field of statistics, his
   analysis of the causal association between lung cancer and smoking was
   flawed by an unwillingness to examine the entire body of data available and
   prematurely drawn conclusions. His views may also have been influenced by
   personal and professional conflicts, by his work as a consultant to the
   tobacco industry, and by the fact that he was himself a smoker."
   At Oxf. J's online.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Fisher.RA/">R.A.F.</A>].)
   [Also search for: RAFisher smoking] and
   [also search for: smoking cause cancer].

%A I. Rigoutsos
%A R. Hummel
%T Several results on affine invariant geometric hashing
%J Proc. 8th Israeli Conf. on Artificial Intelligence and Computer Vision.
%M DEC
%D 1991
%P ??-??
%K conf, c1991, c199x, c19xx, GH, hash, hashing, shape, form, approximate match,
   matching, machine vision
%X 13 refs.

%A I. Rigoutsos
%A R. Hummel
%T Massively parallel model matching, geometric hashing on the connection
   machine
%J Computer
%I IEEE
%P 33-42
%M FEB
%D 1992
%K jrnl, c1992, c199x, c19xx, GH, hash, hashing, shape, form, approximate match,
   matching, machine vision
%X 11 refs.

%A T. S. Ray
%T An evolutionary approach to synthetic biology, Zen and the art of creating
   life
%J Artificial Life
%V 1
%N 1
%P ??-??
%I MITpress
%D 1993 in press
%K Tierra, c1993, c199x, c19xx, machine, computer, AL, Alife, brittle,
   brittleness, self reproduction, sex,, organism, eveolution
%X 96 refs   <!-- email: ray@udel.edu -->.
   [Also seach for: Alife].

%A T. S. Ray
%A J. Hart
%T Evolution of differentiated multi-threaded digital organisms
%J 6th Int. Conf. on Artificial Life
%W UCLA
%D 1998
%E C. Adami et al
%P 295-304
%K Tierra, Alife, AL, AI, organism, evolution, evolve, cell differentiation,
   tissue, organism, c1998, c199x, c19xx, zz0999
%X See other papers in `Tierra' in the bibliography.
   Also [<A HREF="http://www.hip.atr.co.jp/~ray/">~ray</A>] [9/'99].
   [Also search for: Alife]  and  [also search for: Tierra].

%A J. Grefenstette
%A R. Gopal
%A B. Rosimaita
%A D. Van Gucht
%T ???
%J ???
%P ?-?
%D well before 1993
%K genetic algorithm, GA, travelling salesman, sales man, salesperson, person,
   chromosome, permutation, cross over cross-over, vanGucht
%X Choose some arbitrary fixed order of cities  eg. a, b, c, d, e.
   For a given tour, eg. acedb, systematically remove cities from the ordered
   list, writing down the city's position in the list just before removal,
   eg. acedb == 12321
   Now it turns out that when you cross-over 2 such representations
   you get another valid tour
   eg. acedb x abced   ->  acbed and abedc
       12321   11121   ->  12121 and 11321
         ---   --
   [LA: it's a "context sensitive" representation; 14321 and 54321 are very
   different tours; crossover will tend to stuff-up what follows the cross.]

%A Becker
%A Chambers
%A Wilks
%T The New S Language
%I Wadsworth
%D 1988
%K statistics, package, stats, text, book, S, Splus, S-plus, S+
%X <A HREF="http://www.statsci.com/">www.statsci.com</A> [5/'95].
   <!-- via  S u e  C l a n c y   clance@syd.dms.csiro.au  '94 -->.
   See  V e n a b l e s and  R i p l e y  '99.
   [Also search for: RR stats].

%A Chambers
%A Hastie
%T Statistical Models in S
%I Wadsworth
%D 1992
%K statistics, package, stats, text, book, S, Splus, S-plus, S+, language
%X <A HREF="http://www.statsci.com/">www.statsci.com</A> [5/'95].
   <!-- via  S u e  C l a n c y   clance@syd.dms.csiro.au  '94 -->.
   isbn:0412052911.   See  V e n a b l e s and  R i p l e y  '99.
   [Also search for: RR stats].

%A W. N. Venables
%A B. D. Ripley
%T Modern Applied Statistics with S-PLUS. 3rd edn
%I Springer
%P 501
%D 1999
%K book, text, stats, package, S, Splus, S+, zz0200
%X 3rd ed 1999; hb us$65; uk us isbn:0-387-98825-4;
   Dr. Venables is now Statistician with CSIRO in Queensland, having
   been at the Department of Statistics, University of Adelaide for many
   years previously. Professor Ripley holds the Chair of Applied Statistics
   at the University of Oxford.
   S-PLUS is a commercial system of the Data Analysis Products Division of
   MathSoft Inc. The book is also useful with R, a freely-available
   open-source statistical system `not unlike S'. We have tried where
   possible to use code that works in all versions of S-PLUS and in R.
   [via  r o h a n  2/'00].
   [Also search for: RR stats].

%A L. Breiman
%A J. J. Friedman
%A R. A. Olshen
%A C. J. Stone
%T Classification and Regression Trees
%D 1984
%I Wadsworth
%O reprinted by ChapmanAndHall
%K CART, tree, stats, statistics, text, book, c1984, c198x, c19xx, DTree,
   one standard error rule, cross validation
%X M Mos517.23 B835C
   (Also see [<A HREF="http://www.allisons.org/ll/Publications/2005JFP/">IP</A>].)

%A J. H. Friedman
%A B. W. Silverman
%T Flexible Parsimonious Smoothing and Additive Modeling
%J Technometrics
%D 1989
%V 31
%P 3-39
%K classification, regression, tree, trees, CART, stats, statistics

%A J. H. Friedman
%T Multivariate Adaptive Regression Splines
%J Annals of Statistics
%D 1991
%V 19
%N 1
%P 1-141
%K AS, classification, regression, tree, trees, CART, stats, statistics, spline

%E T. Subba Rao
%T Developments in Time Series Analysis
%I ChapmanAndHall
%D 1993
%K text, book

%A S. Muggleton
%T Inductive logic programming: derivations, successes and shortcomings
%J SIGART Bulletin
%V 5
%N 1
%M JAN
%D 1994
%P 5-11
%K ILP, rule, rules, prolog, LP, inference, II, machine learning, survey,
   review, introduction, derivation
%X a special section on ILP

%A T. Bayes
%T An essay towards solving a problem in the doctrine of chances
%J Philosophical Trans. of the Royal Soc. of London
%V 53
%P 370-418
%D 1763
%O reprinted in Biometrika 45(3/4) 293-315 Dec 1958
%K Reverend Thomas Bayes, jrnl, Bayesian, joint, conditional, probability,
   Bayes's theorem, Bayess, Doctrine of Chances, chance,
   MML, MDL, c1763, 1763, c1764, 1764, c176x, c17xx, 18C
%X (Thomas Bayes, 1702-1761, also see [<A HREF="http://www.allisons.org/ll/Images/People/Bayes/">Bayes</A>].)
   (In particular:
      "... Prop.3: The probability that two subsequent events will both happen
       is a ratio compounded of the probability of the 1st, and the probability
       of the 2nd on supposition the 1st happens. ..." [p.290])
   Reprinted in Biometrika 45(3,4), pp.293-315, December 1958,
   -- [<A HREF="http://www.jstor.org/stable/2333180">Jstor</A>],
      [<A HREF="http://links.jstor.org/sici?sici=0006-3444%28195812%2945%3A3%2F4%3C293%3ASITHOP%3E2.0.CO%3B2-B">B@Jstor</A>][11/'02].
   (i) An Essay towards Solving a Problem in the Doctrine of Chances. By the
   Late Rev. Mr. Bayes, F. R. S. Communicated by Mr. Price, in a Letter to
   John Canton, A. M. F. R. S., pp.370-418,
   Philosophical Transactions of the Royal Society, Vol.53, pp.376-398 (1763)
   -- [<A HREF="http://www.jstor.org/stable/105741">Jstor</A>]['14],
      [<A HREF="http://links.jstor.org/sici?sici=0260-7085%281763%2953%3C370%3AAETSAP%3E2.0.CO%3B2-5">here</A>].
   (ii) A Demonstration of the Second Rule in the Essay towards the Solution
   of a Problem in the Doctrine of Chances, Published in the Philosophical
   Trans., Vol. LIII. Communicated by the Rev. Mr. Richard Price, in a
   Letter to Mr. John Canton, M. A. F. R. S.,
   Vol.54, pp.298-310 (1764)
   -- [<A HREF="http://www.jstor.org/stable/105565">Jstor</A>]['14],
      [<A HREF="http://links.jstor.org/sici?sici=0260-7085%281764%2954%3C296%3AADOTSR%3E2.0.CO%3B2-8">here</A>].
   [Also search for: Peirce c187x].
   (Also see, uk us isbn:0852030339, about Bayes.)

%A H. Bunke
%A U. Buehler
%T Applications of approximate string matching to 2D shape recognition
%J Pattern Recognition
%V 26
%N 12
%P 1797-1812
%M DEC
%D 1993
%K PR, 2D, 2-D, shape, match, matching, recognition, image processing, IP
%X via PT,  H510.7805 P316.

%A D. I. Perrett
%A K. A. May
%A S. Yoshikawa
%T Attractive characteristics of female faces: preference for non-average shape
%J Nature
%V 368
%N 6468
%P 239-242
%M 17 MAR
%D 1994
%K beauty, attractive, pretty, feminine, human, face, c1994, c199x, c19xx,
   selection
%X argues against the "average is beauty" hypothesis,
   so ... may lead to evolution of human features away from present norms:-
      The finding that photographic and digital composites (blends) of faces
   are considered to be attractive has led to the claim that attractiveness is
   averageness. This would encourage stabilizing selection, favouring
   phenotypes with an average facial structure. The 'averageness hypothesis'
   would account for the low distinctiveness of attractive faces but is
   difficult to reconcile with the finding that some facial measurements
   correlate with attractiveness. An average face shape is attractive but may
   not be optimally attractive. Human preferences may exert directional
   selection pressures, as with the phenomena of optimal outbreeding and sexual
   selection for extreme characteristics. Using composite faces, we show here
   that, contrary to the averageness hypothesis, the mean shape of a set of
   attractive faces is preferred to the mean shape of the sample from which the
   faces were selected. In addition, attractive composites can be made more
   attractive by exaggerating the shape differences from the sample mean.
   Japanese and caucasian observers showed the same direction of preferences
   for the same facial composites, suggesting that aesthetic judgements of face
   shape are similar across different cultural backgrounds. Our finding that
   highly attractive facial configurations are not average shows that
   preferences could exert a directional selection pressure on the evolution of
   human face shape.
   -- [<A HREF="http://perception.st-and.ac.uk/Attractiveness/abst_nat94.htm">abs</A>][12/'02].
   Also see Perrett '98 in Nature.

%A P. W. Shor
%T Polynomial-time algorithms for prime factorization and discrete logarithms on
   a quantum computer
%J Proc. of the 35th Annual Symp. on Foundations of Comp. Sci., Santa Fe, 1994
%M NOV
%D 1994
%O arXiv, AUG 1995
%K conf, c1994, c199x, c19xx, zz113, Shor, Shors, quantum computing, algorithm,
   reversible, factor, factors, factoring, integer, factorization,
   factorisation, composite, prime, primes, modular exponentiation, logarithm,
   complexity, NPC, BQP, strong Church thesis, precision
%X "A digital computer is generally believed to be an efficient universal
   computing device; that is, it is believed able to simulate any physical
   computing device with an increase in computation time of at most a polynomial
   factor. This may not be true when quantum mechanics is taken into
   consideration. This paper considers factoring integers & finding discrete
   logarithms, two problems which are generally thought to be hard on a
   classical computer & have been used as the basis of several proposed
   cryptosystems. Efficient randomized algorithms are given for these two
   problems on a hypothetical quantum computer. These algorithms take a number
   of steps polynomial in the input size, e.g., the number of digits of the
   integer to be factored."
   -- v2, 9508027v2@[<A HREF="http://arxiv.org/abs/quant-ph/9508027v2">arXiv</A>]['13].
   [Also search for: quantum computing factorization],
   [also search for: quantum QFT],
   [also search for: Vergis 1986], [also search for: Steiglitz 1988].
   (Also see, "... SA consists of two parts: 1. A classical red'n of the
    factoring problem to the problem of order-finding. ... 2. A q.alg. to
    solve the order-finding problem ..."
    -- S_Alg@[<A HREF="https://en.wikipedia.org/wiki/Shor%27s_algorithm">wikip</A>]['18] &
       Dlog@[<A HREF="https://en.wikipedia.org/wiki/Discrete_logarithm">wikip</A>]['20] &
       a video@[<A HREF="https://www.youtube.com/watch?v=6qD9XElTpCE">ubend</A>]['21].)

%A D. A. Rowland
%A D. I. Perrett
%T Manipulating facial appearance through shape and color
%J IEEE Computer Graphics and Applications
%V 15
%N 5
%P 70-76
%M SEP
%D 1995
%K beauty, attractive, pretty, human, face, colour, emotion, emotions
%X Human faces are perceived to differ along many dimensions.  Some dimensions
   can be defined by objectively different categories such as old/ young or
   male/ female but others reflect more subjective categories such as
   attractive/ unattractive and happy/ sad.  In this paper we explain a
   technique for determining the consistent (or ``prototypic'') visual
   characteristics (shape and color) of a category of faces.  We describe a
   method for evaluating and visualizing the extent to which prototypes differ.
   Information derived from prototypes can be used to reconstruct a plausibly
   colored image of an individual's face originally recorded in black and
   white.  Information from pairs of prototypes can also be used to define shape
   and color transformations which allow individual face images to be moved in
   appearance along quantifiable dimensions in ``face space.''  A given face
   image can thus be made to look older or younger, more or less masculine/
   feminine, etc.  Transformation performed in a given direction can be made
   either interpolating between two prototypes (e.g. making a male face less
   masculine) or as an extrapolation beyond the prototype (e.g. enhancing
   the masculinity of a male face).  Although the processing has been developed
   to analyze and manipulate face images the same principles can be applied to
   other visually homogeneous classes.
   -- [<A HREF="http://psy.st-andrews.ac.uk/people/lect/dp.shtml">DP home</A>][12/'02].
   -- [<A HREF="http://www.computer.org/cga/cg1995/g5070abs.htm">IEEE</A>][12/'02] (must pay)
   Also see Perrett '94, '98 in N@ture.

%A M. T. Cox
%A A. Ram
%T Choosing learning strategies to achieve learning goals
%J AAAI Spring Symposium: Goal-Driven Learning
%M MAR
%D 1994
%P 12-21
%K goal, goals, driven, machine learn, strategy

%A Y. G. Leclerc
%T Constructing simple stable descriptions for image partitioning
%J Int. J. Comp. Vision.
%V 3
%P 73-102
%D 1989
%K IJCV, CV, computer vision, image processing, IP, MML, MDL, chain code
%X ... construct a complete and stable description of an image -
   in terms of a specified description language - that is the simplest in
   the sense of being the shortest. We show that a descriptive language
   limited to a low-order polynomial decription of the intensity variation
   within region and a chain-code [8 connected] like description of
   the region boundaries yields intuitively satisfying partitions
   for a wide class of images.  ...  [29 refs].

%E T. Lee
%T Mathematical Computation with Maple V: Ideas and Applications
%I Birkhauser
%O Proc. Maple Summer Workshop and Symposium
%D 1993
%K Maple, MapleV, Maple5, Maple93
%X isbn:0-8176-3724-9.
   isbn:3-7643-3724-9.

%T The Oxford Advanced Learners' Dictionary
%E ?
%D 1994
%K dictionary, English, word, words, enews, ftp
%X via enews: In fact, I found the headwords from ... at
   black.ox.ac.uk /ota/dictionaries.  Although Collins'
   dictionary was referred to in the documentation files, I was unsurprised
   to discover that I couldn't find a full on-line version.
   Ian Billups, School of Computer Science, University of Birmingham,
   Birmingham, B15 2TT. UK.    tel: +44-21-414-3734  fax: 4281    ('94)
   <!-- email: I.R.Billups@cs.bham.ac.uk -->.

%A I. H. Witten
%A T. C. Bell
%A A. Moffat
%A C. G. Nevill-Manning
%A T. C. Smith
%A H. Thimbleby
%T Semantic and generative models for lossy text compression
%J COMPJ
%V 37
%N 2
%P 83-87
%M APR
%D 1994
%K COMPJ, model, compress, precis, abstract, Hemmingway, Lena, Lenna, martini,
   April1, 1April, 1 first of April, humour, satire, satirical, joke, funny,
   haha, ha-ha, ha, spoof, c1994, c199x, c19xx
%X ... sometimes the richness and literary texture of the prose improves. ...
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/37.2.83">doi:10.1093/comjnl/37.2.83</A>]['08].
   (How can we make this the most cited paper in the world?)

%A D. E. Goldberg
%T Messy genetic algorithms: Motivation, analysis, and first results
%J Complex Systems
%V 3
%P 493-530
%D 1989
%K genetic algorithm, GA, messy, permutation, perm, travelling salesman, TSP
%X <!-- email: raj.subramani@newcastle.ac.uk   5/94 -->.

%A D. E. Goldberg
%T Messy genetic algorithms revisited: Studies in mixed size and scale
%J Complex Systems
%V 4
%P 415-444
%D 1990
%K genetic algorithm, GA, messy, permutation, perm, travelling salesman, TSP
%X <!-- email: raj.subramani@newcastle.ac.uk   5/94 -->.

%A D. E. Goldberg
%A K. Deb
%A B. Korb
%T Do not worry, be messy
%J Proc. of the fourth Int. Conf. on Gen. Alg.
%P 24-30
%I Morgan-Kaufmann publ., Los Altos, CA
%D 1991
%K conf, c1991, c199x, c19xx, genetic algorithm, GA, messy, permutation, perm,
   travelling salesman, TSP, GA4
%X <!-- email: raj.subramani of newcastle.ac.uk   5/94  -->.

%A ???
%T ???
%J New Scientist
%P ??-??
%M 4th Dec
%D 1993
%K MML, MDL, inductive inference, II, prehistoric, megalithic stone circle,
   circles, yard, Stonehenge, Stone Henge, Thom, Patrick
%X via Jon Patrick.

%A Wirt Atmar
%J IEEE Transactions on neural networks
%P ??-??
%V 5
%N 1
%M JAN
%D 1994
%K TNN, ANN, NN, artificial neural net works, evolve, evolution
%X IEEE log number 9213876.
   <!-- via enews: Jeff Marcks,  MarcksJE@lfwc.lockheed.com   '94 -->.

%A J. Martin
%A C. McClure
%T Diagrammatic Techniques for Analysts and Programmers
%I PrenticeHall
%D 1985
%K text, book, graph, DAG, draw, drawing, layout

%A N. Wirth
%A J. Gutknecht
%T Project Oberon, the Design of an Operating System and Compiler
%I AddisonWesley
%D 1992
%K text, book, good, Oberon, ETH, Zurich, computer programming language,
   OS, module, software, computing, CSci, L3Ref
%X Good book. This system was designed; it did not just escape.

%A S. A. Kauffman
%T The Origins of Order: Self-Organization and Selection in Evolution
%I OUP
%D 1993
%K self organization, organisation, OUP, GA, genetic algorithm, chaos,
   text, book, emergent
%X via enews

%A A. Colorni
%A M. Dorigo
%A V. Maniezzo
%T Distributed Optimization by Ant Colonies
%J Proc. of ECAL91 - European Conf. on Artificial Life,
%A 1991
%W Paris, France,
%I Elsevier Publishing
%K ant, ants, ECAL
%X ftp iridia.ulb.ac.be (164.15.11.65) or
   ftp zucca.idsia.ch (192.132.252.1)
   set transmission to binary (just type the command BINARY)
   cd to /pub/dorigo/conferences get the papers
   IC.06-ECAL91.ps.gz
   via enews '94.

%A A. Colorni
%A M. Dorigo
%A V. Maniezzo
%D 1992
%T An Investigation of some Properties of an Ant Algorithm
%J Proc. of the Parallel Problem Solving from Nature Conf. (PPSN 92)
%W Brussels, Belgium
%I Elsevier Publishing
%K ant, ants, PPSN92
%X ftp iridia.ulb.ac.be (164.15.11.65)
   or ftp zucca.idsia.ch (192.132.252.1)
   set transmission to binary (just type the command BINARY)
   cd to /pub/dorigo/conferences get the papers
   IC.08-PPSN92.ps.gz
   via enews '94.

%A M. Dorigo
%A V. Maniezzo
%A A. Colorni
%D 1991
%T The Ant System: An Autocatalytic Optimizing Process
%R 91-016
%I Politecnico di Milano, Italy
%O (Revised version Sub' IEEE Transactions on Systems, Man, and Cybernetics)
%K ant, ants
%X ftp iridia.ulb.ac.be (164.15.11.65) or
   ftp zucca.idsia.ch (192.132.252.1)
   set transmission to binary (just type the command BINARY)
   cd to /pub/dorigo/tec.reps get the paper TR.03-IEEE-SMC.ps.gz
   via enews '94.

%A D. J. Cook
%A L. B. Holder
%T Substructure Discovery using Minimum Description Length and Background
   Knowledge
%J J. Artificial Intelligence Research
%P 231-255
%V 1
%D 1994
%K JAIR, AI, genetic algorithms, GA, message, MML, encoding, MDL
%X The ftp access to this paper is (fom the JAIR FAQ):
   2.3.3) Obtaining Articles Via FTP
   You can use anonymous FTP to obtain a file from the JAIR distribution sites
   at either Carnegie Mellon University (CMU) or the University of Genoa.
   CMU Machine:   p.gp.cs.cmu.edu        main directory: /usr/jair/pub
   Genoa Machine: ftp.mrg.dist.unige.it  main directory:  pub/jair/pub
   For example, to get the file volume1/ginsberg93a.ps from CMU, invoke
   the FTP program, then type "open p.gp.cs.cmu.edu".  At the login
   prompt, enter "anonymous", and at the password prompt, enter your net
   address.  You will then be logged in.  Typing "cd /usr/jair/pub" will put
   you into our public directory. You can then type "cd volume1" followed by
   "get ginsberg93a.ps".  Finally, type "quit".
   To get the same paper from Genoa, you use the same procedure, except
   that you type "open ftp.mrg.dist.unige.it" to get to the machine in
   Genoa, and "cd pub/jair/pub" for our public directory.
   Charlie Clelland Dept of Comp and Maths, Deakin University, Geelong,
                    Victoria, 3217.  Phone: +61 52 272880              ('94).

%A E. Lindelof
%T COBRA: The Computer-Designed Bidding System
%I Victor Gollancz Ltd, London
%D 1983
%K COBRA, text, book, computer designed, AI, bridge, card, cards,
   game, play, playing, bid, biding
%X A volume in the Master Bridge Series (series editor H.W. Kelsey);
   isbn:0-575-02987-0.
   <!-- email: ianf@aifh.ed.ac.uk (Ian Frank)   (7/94) -->.

%A D. Kraines
%A ?
%T Learning to Cooperate with Pavlov; an adaptive strategy for the iterated
   prisoner's dilemma with noise
%J Theory and Decision
%V 35
%P 107-150
%D 1993
%K TD, prisoner's dilemma, cooperate, defect
%X See our paper
   via: David Kraines, Dept of Mathematics, Duke University  (8/'94)
        <!-- email: dkrain@math.duke.edu -->.

%A Paechter
%A et al
%T Two Solutions to the General Timetable Problem Using Evolutionary Methods
%J First IEEE Conf. on Evolutionary Computation, Orlando
%P 300-305
%D 1994
%K time table, timetable, tabling, genetic algorithm, GA
%X isbn:0-7803-1899-4.
   <!-- email: rhh@matilda.vut.edu.au (Robert Hinterding)  (8/'94) -->.

%A K. Lindgren
%A M. Nordahl
%T Evolutionary dynamics of spatial games
%J Physica D
%V 75
%P 292-309
%D 1994
%K c1994, c199x, c19xx, jrnl, evolution, cooperation, defect, cooperate,
   iterated prisoner's dilemma, PD, IPD, game
%X A lattice model of coevolution of strategies for two-person 2X2 matrix
   games is introduced. The model allows evolution in an unbounded space of
   strategies. In particular we explore the region of parameter space
   corresponding to the Prisoner's dilemma, and classify the types of
   dynamical and evolutionary behavior that appear. For certain restricted
   strategy spaces we explore the complete space of lattice games." (p. 308)
   <!-- email: chandler@ux1.cso.uiuc.edu (Hugh Chandler  9/'94) -->.

%A D. L. Dowe
%T Are Maxwell's equations logically consistent?
%J American Math. Monthly
%P ?-?
%M OCT
%D 1986
%K DLD, AMM, Maxwell

%A H. Minsky
%T Stabilizing an Unstable Economy
%I McGrawHill
%P 350
%D 1986
%K book, text, c1986, c198x, c19xx, economics, stability, crash, crashes,
   recession, instability, bubble, financial, economist, crises, crisis,
   hedge, speculative, Ponzi, borrower, leverage
%X (Hyman Philip Minsky, 23/9/1919-24/10/1996.)
   1st ed 1986; uk us isbn:0071592997; uk us isbn13:978-0071592994.
   "... financial theory of investment, one that is startlingly relevant today.
   He explains why the American economy has experienced periods of debilitating
   inflation, rising unemployment, and marked slowdowns-and why the economy is
   now undergoing a credit crisis that he foresaw ..." -- 2OO8.
   (Also see HM@[<A HREF="http://en.wikipedia.org/wiki/Hyman_Minsky">wikip</A>]['14].)

%A D. Dowe
%T On the existence of sequences of co-prime pairs of integers
%J J. Australian Math. Soc.
%S A
%P 84-89
%V 47
%N 1
%M AUG
%D 1989
%K DLD, JAM, JAMS, sequence, coprime, pair

%A D. L. Dowe
%A S. B. Landy
%T The Derivatives of x to the Power x at x=1
%J Gazette of the Australian Math. Soc.
%P 95-98
%V 17
%N 4
%M AUG
%D 1990
%K DLD

%A D. L. Dowe
%T Can Black force a win
%J J. Int. Computer Chess Assoc.
%P 165-166
%V 13
%N 3
%M SEP
%D 1990
%O Gazette of the Australian Math. Soc., 1990
%K DLD

%A D. L. Dowe
%T Chess - Can Black force a win
%J Gazette of the Australian Math. Soc.
%P 158-159
%V 17
%N 5
%M OCT
%D 1990
%O J. Int. Computer Chess Assoc., 1990
%K DLD

%A R. Garigliano
%A A. Purvis
%A P. A. Giles
%A D. J. Nettleton
%T Genetic Algorithms and Shape Representation
%J Proc. of the 2nd Annual Conf. on Evolutionary Programming
%E D. B. Fogel
%E W. Atmar
%A 1993
%P 40-47
%K genetic algorithm GA, Proc
%X via: D J Nettleton    email: D.J.Nettleton@durham.ac.uk  (11/'94)

%A P. A. Giles
%T Iterated Function Systems and Shape Representation
%I University of Durham, UK.
%D 1990
%K genetic algorithm GA, PhD thesis
%X via: D J Nettleton    <!-- email: D.J.Nettleton@durham.ac.uk --> (11/'94)

%A A. K. Dewdney
%T The cellular automata programs that create Wireworld, Rugworld and
   other diversions
%J Sci. Am.
%V 262
%N 1
%P 146-149
%M JAN
%D 1990
%K magazine, automaton, program c1990, c199x, c19xx, game of life, computation,
   wire-world, programming
%X A Java animation [<A HREF="http://www.quinapalus.com/wi-java.html">quinapalus.com</A>]['05].
   -- [<A HREF="http://www.csd.uwo.ca/faculty/akd/">Dewdney</A>]['05].

%A J. R. Quinlan
%T Learning logical definitions from relations
%J Machine Learning
%V 5
%N 3
%P 239-266
%M AUG
%D 1990
%K FOIL, relation, ILP, logic, c1990, c199x, c19xx, first order rule, rules,
   clauses, relational data
%X "...describes FOIL, a system that learns Horn clauses from data expressed as
   relations. FOIL is based on ideas that have proved effective in attribute-
   -value learning systems, but extends them to a 1st-order formalism. This new
   system has been applied successfully to several tasks taken from the machine
   learning literature."
   s4, p242: "... find, for ONE target relation at a time, clauses that
   define the relation in terms of itself and the other relations. ..."
   e.g. can-reach(X1,X2):-linked-to(X1,X3),can-reach(X3,X2);  5.2 list, member,
   append, reverse;  5.3 arch, eastbound, endgame;  5.6 eleusis
   -- [<A HREF="http://dx.doi.org/10.1023/A:1022699322624">doi:10.1023/A:1022699322624</A>]['05].
   [Also search for: FFOIL].

%T A Nest of Vipers (Perspectives on contemporary legend)
%I SheffieldAcademic
%P 164
%D 1990
%K conf, urban legends, myth, rumour, c198x, c19xx, society, research, zz0904
%X "...the fifth and final volume in the Perspectives on Contemporary Legend
   series and features a selection of the papers presented at the 5th and 6th
   Int. Sem. on Contemporary Legend held in Sheffield, 1987 and 1988..."
   us$50; uk isbn:1850752567.
   -- [<A HREF="http://www.panam.edu/faculty/mglazer/isclr/isclr.htm">Int. Soc. C.L. Res.</A>][9/'04].

%A D. E. Hoskins
%A J. Vagners
%T Image Compression using Iterated Function Systems and Evolutionary
   Programming:  Image Compression without Image Metrics
%J 26th Asilomar Conf. on Signals, Systems and Computers.
%D 1992
%P ?-?
%K genetic algorithm, GA, image compression, IC, conf 26
%X via: D J Nettleton    <!-- email: D.J.Nettleton@durham.ac.uk --> (11/'94)

%A D. H. Wolpert
%T Memory systems, computation, and the second law of thermodynamics
%J Int. J. of Theor. Physics
%I SpringerVerlag
%V 31
%N 4
%P 743-785
%D 1992
%K jrnl, c1992, c199x, c19xx, zz0509, memory, memories, arrow of time,
   remember, past, future
%X "A memory is a physical sys. for transferring info. from one moment in time
   to another, where that information concerns something external to the system
   itself. ... [argue] on info. theoretic & stat. mechanical grounds that useful
   memories must be of one of two types, exemplified by memory in abstract
   computer programs & by memory in photographs. Photograph-type memories work
   by exploiting a collapse of state space flow to an attractor state. ...
   ... theory of reversible compn tells us that in any such collapsing,
   regardless of whether the collapsing proceeds from the past to the future or
   v.v., the collapsing must increase the entropy of the system. In concert with
   the 2nd law, this establishes the logical necessity of the empirical
   observation that photograph-type memories are temporally asymmetric (they
   can tell us about the past but not about the future). Under the assumption
   that human memory is a photograph-type memory, this result also explains why
   we humans can remember only our past & not our future. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/BF00670829">doi:10.1007/BF00670829</A>]['09],
   dhw@[<A HREF="http://ti.arc.nasa.gov/profile/dhw/">nasa</A>]['09].
   (Also search for: arrow time].)

%A J. Levy-Vehel
%A E. Lutton
%T Optimization of Fractal Functions using Genetic Algorithms
%I Institut National de Recherche en Informatique et an Automatique.
%C Le Chesnay Cedex, France.
%R 1941
%D 1993
%K genetic algorithm, GA, TR TR1941
%X via: D J Nettleton    <!-- email: D.J.Nettleton@durham.ac.uk --> (11/'94)

%A D. J. Nettleton
%A R. Garigliano
%T Evolutionary Algorithms and a Fractal Inverse Problem
%J Journal of Biological and Information Processing Systems (BioSystems)
%I Elsevier
%D 1994 in press
%K genetic algorithm, GA, jrnl
%X via: D J Nettleton    email: D.J.Nettleton@durham.ac.uk  (11/'94)

%A D. J. Nettleton
%A R. Garigliano
%T Evolving Fractals
%J Journal of Computers and Graphics
%I Pergamon Press
%D 1994 in press
%K JCG, jrnl, genetic algorithm, GA
%X via: D J Nettleton    email: D.J.Nettleton@durham.ac.uk  (11/'94)

%A D. J. Nettleton
%A R. Garigliano
%T Shape Representation and Evolutionary Algorithms
%J IEE Colloquium on Genetic Algorithms in Image Processing and Vision
%W Savoy Place, London
%M OCT
%D 1994
%K genetic algorithm, GA, IP
%X via: D J Nettleton    email: D.J.Nettleton@durham.ac.uk  (11/'94)

%A D. J. Nettleton
%T Evolutionary Algorithms in Artificial Intelligence: A Comparative
   Study Through Applications
%I University of Durham, UK
%D 1994
%K PhD thesis (submitted), genetic algorithm, GA
%X via: D J Nettleton    email: D.J.Nettleton@durham.ac.uk  (11/'94)

%A E. R. Vrscay
%T Iterated Function Systems: Theory, applications and the inverse problem
%B Fractals Geometry and Analysis
%E J. Belair
%E S. Dubuc
%D 1991
%P 405-468
%I Kluwer Academic Publishers
%K genetic algorithm, GA
%X via: D J Nettleton    <!-- email: D.J.Nettleton@durham.ac.uk --> (11/'94)

%A E. R. Vrscay
%T Moment and Collage Methods for the Inverse Problem of Fractal Construction
   with Iterated Function Systems
%B Fractal in the Fundamental and Applied Sciences
%E H. O. Peitgen
%E J. M. Henriques
%E L. F. Penedo
%D 1991
%P 443-461
%I Elsevier Science Publishers
%K genetic algorithm, GA
%X via: D J Nettleton    <!-- email: D.J.Nettleton@durham.ac.uk --> (11/'94)

%A D. Burton
%T History of Mathematics: An Introduction, Third Edition
%I Wm.C.Brown
%D 1995
%K book, text, history, maths
%X via enews

%T Computing Curricula 1991
%J CACM
%V 34
%N 6
%P 69-84
%M JUN
%D 1991
%K ACM IEEE, computing, CSci, curricula, curriculum, teaching, course, 1991
%X a summary of the ACM/IEEE-CS joint curriculum task force report.
   See also curriculum '68, and efforts in '79, '88.
   <!-- filed under `curricula' -->.

%A G. Bennett
%A P. Smith
%T Contemporary Legend: The First Five Years: Abstracts and Bibliographies
   from the Sheffield Conf. on Contemporary Legend, 1982-1986
%P 151
%D 1991
%I SheffieldAcademic
%K book, urban legends, rumour, myth, c198x, c19xx, conf, society, research
%X us$75; isbn:1850751919.
   -- [<A HREF="http://www.panam.edu/faculty/mglazer/isclr/isclr.htm">Int. Soc. C. L. Res.</A>][9/'04].

%A S. L. Feld
%T Why your friends have more friends than you do
%J Amer. J. Sociology
%P 1464-1477
%M MAY
%D 1991
%K jrnl, c1991, c199x, c19xx, zz0413, friendship paradox, friend, social,
   networks, probability, stats, sampling bias
%X -- 2781907@[<A HREF="http://www.jstor.org/stable/2781907">Jstor</A>]['13].
   ("People with more friends are more likely to be your friend in
    the first place; that is, they have a higher propensity to
    make friends in the first place."
    -- [<A HREF="http://en.wikipedia.org/wiki/Friendship_paradox">wikip</A>]['13].)

%A P. van Emde Boas
%T Machine models and simulations
%B Handbook of theoretical computer science
%V A: algorithms and complexity
%E J. van Leeuwen
%P 1-66
%D 1991
%K chapter, c1991, c199x, c19xx, zz1117, model, simulation, vanEmdeBoas,
   invariance thesis, Church thesis, NPC, quantum computing, complexity, NPC
%X "In complexity theory ... The invariance thesis states that reasonable
   sequential models simulate each other with polynomial overhead in time and
   constant factor overhead in space. The parallel computation thesis states
   that parallel time is the equivalent of sequential space. Rather than using
   these theses as absolute truths we use them as heuristic tools by which two
   machine classes of well-behaved devices are separated from the more
   irregular devices. ..."
   -- [<A HREF="https://www.illc.uva.nl/Research/Publications/Reports/CT-1989-02.text.pdf">uva.nl</A>]['17],
   and in isbn:0444880712, MITpress.  (From a ref in Shor 1985.)

%A A. Bundy
%A H. MacQueen
%T The new software copyright law
%J COMPJ
%V 37
%N 2
%P 79-82
%M APR
%D 1994
%K zzLaw, c1994, c199x, c19xx, copyright, compj, jrnl, law, legal, protection,
   software, program, computer
%X U.K. software copyright law.

%A F.-J. Lapointe
%A P. Legendre
%T A classification of pure malt Scotch whiskies
%J Appl. Statist.
%V 43
%N 1
%P 237-257
%M ?
%D 1994
%K class, classification, cluster, clustering, whisky, malt, single, spirits,
   distillery, Scotch, Scotland, stats, statistics, c1994, c199x, c19xx
%X email: lapoinf@ere.umontreal.ca ['94];
   data: 109 Scotches x 68 binary variables.
   Lap.@[<A HREF="http://www.dcs.ed.ac.uk/home/jhb/whisky/lapointe/text.html">dcs</A>]['13].

%A D. J. Booth
%T Foundation Discrete Mathematics for Computing
%I ChapmanAndHall
%M JAN
%D 1995
%P 272
%K maths, book, text
%X isbn:0-412-56280-4.

%A A. Pearl
%T Women in computing, introduction
%P 26-28
%J CACM
%V 38
%N 1
%P 26-28
%M JAN
%D 1995
%K women, computing, CACM, jrnl, c1995, c199x, c19xx, special issue, women,
   computer science, STEM
%X "The world is changing & the demographics of the workforce are changing with
   it. At one time there was hope that our exciting new field of computer
   science would not only revolutionize the technical world in which we live,
   but break new ground in professional access & equity for women. This
   optimism has given way to pragmatism. If we want the best & the brightest
   women to participate fully in our profession, we must take a long hard look
   at our professional practices & conventions. The goal of this special section
   is to provide computer professionals with the information to understand the
   issues that women confront in their workplace & with the resources to
   successfully diversify their workplace. I hope you will save this issue of
   Communications as a reference for many years to come. I also hope that, as
   opportunities for women in computer science expand, the need for the
   specialized resources & programs we described here diminishes."
   -- [<a HREF="https://doi.org/10.1145/204865.204873">doi:10.1145/204865.204873</A>]['19].
   [Also search for: women computing].

%A M. Klawe
%A N. Levenson
%T Women in computing: where are we now
%P 29-44
%J CACM
%V 38
%N 1
%M JAN
%D 1995
%K women, computing, special issue, WCAR, TAP, women, science, computing, STEM
%X <A HREF="http://www.cs.yale.edu/HTML/YALE/CS/HyPlans/tap/tap.html">TAP</A>
   [Also search for: women computing].

%A D. W. Gurer
%T Pioneering women in computer science
%P 45-54
%J CACM
%V 38
%N 1
%P 45-54
%M JAN
%D 1995
%K women, computing, c1995, c199x, c19xx, special issue, Ada, Hopper, Keller,
   Clapp, Estrin, women, computer science, STEM
%X -- [<A HREF="https://doi.org/10.1145/204865.204875">doi:10.1145/204865.204875</A>]['19],
    & [<A HREF="https://courses.cs.washington.edu/courses/csep590/06au/readings/p175-gurer.pdf">wash...edu</A>]['19].
   [Also search for: women computing].

%A K. Hemenway
%T Human nature and the glass ceiling in industry
%P 55-62
%J CACM
%V 38
%N 1
%M JAN
%D 1995
%K women, computing, special issue, women, science, STEM
%X [Also search for: women computing].

%A S. Lawrence Pfleeger
%A N. Mertz
%T Executive mentoring: what makes it work
%P 63-74
%J CACM
%V 38
%N 1
%M JAN
%D 1995
%K women, computing, special issue

%A V. Oechtering
%A R. Behnke
%T Situations and advancement measures in Germany
%P 75-82
%J CACM
%V 38
%N 1
%M JAN
%D 1995
%K women, computing, special issue

%A J. F. Rouet
%T Cognitive processing of hyperdocuments: when does non-linearity help?
%J Hypertext: Proc. of the ACM Conf.
%W Milano
%M NOV
%D 1992
%P 131-140
%I ACM Press, N.Y.
%K hypertext, hyper text, document, nonlinear, non-linear,
   cognitive, cognition
%X ... review of 45 studies of cognition finds:
      no consistent evidence for the advantage of hypertext over linear
      presentation formats. Instead, the efficiency of nonlinear documents
      varies according to  a) the subject's expertise,  b) interface features
      and  c) task requirements  [abs p131].
   Reviewed in Comp. Rev. 35(10) p542 Oct '94.

%E D. Grover
%T The Protection of Computer Software - Its Technology and Application
%I British Computer Society
%S Monographs in Informatics
%D 1989, 1992
%K zzLaw, BCS, book, text, law, legal, program, copyright, computing, program
%X 2nd edition, isbn:0521424623.

%A N. Wirth
%T A plea for lean software
%J Computer
%I IEEE
%V ?
%N ?
%P 64-68
%M ?
%D 1995
%K computing, programming, software engineering, SE, fatware, flabware, oberon,
   L3ref, L4ref, zz0595
%X Argues for lean, mean, well designed software, not meaningless gimmicks.
   See the books and papers on `Oberon'

%A T. Sleator
%A H. Weinfurter
%T Realizable universal quantum logic gates
%J Phys. Rev. Lett.
%V 74
%P 4087-?
%D 1995
%K c1995, c199x, c19xx, quantum, computer, PRL, jrnl
%X They give us a universal 2-bit quantum gate.
   From: <!-- email: sarfatti@ix.netcom.com --> Jack Sarfatti  [6/'95].

%A L. Shashaani
%T Gender differences in mathematics experience and attitude and
   their relation to computer attitude
%J Educational Technology
%V 35
%N 5
%M MAY / JUN
%D 1995
%P 32-38
%K gender, boy, girl, boys, girls, maths, mathematics, computing,
   education, jrnl, zz0795
%X via  ajh  [7/'95].

%A R. C. Pinkerton
%T Information theory and melody
%J Scientific American
%D 1956
%V 194
%N 2
%P 77-86
%K c1956, c195x, c19xx, arts, music, tune, melody, information theory, IT,
   beauty, art, jrnl, zz0795
%X Ian Johnston    <!-- email:  idj@physics.su.oz.au --> [7/'95].

%A I. Johnston
%T Measured Tones: the Interaction of Physics and Music
%D 1989
%I IOP Press, Bristol
%K c1989, c198x, c19xx, book, text, arts, music, tune, melody, physics, science,
   information theory, IT, zz0795
%X See  chap 9.
   Ian Johnston    <!-- email:  idj@physics.su.oz.au --> [7/'95].

%A H. Meinhardt
%T The Algorithmic Beauty of Sea Shells
%I Springer
%D 1995
%P 204
%K book, text, shape, form, pattern, zz0795
%X reviewed in Nature V375, p745-746, 29 June '95

%A A. J. Fridland
%T Human Facial Expression: an Evolutionary View
%I AcademicPress
%P 369
%D 1994
%K book, text, face, facial, expression, zz0795

%A E. A. Cavazos
%A G. Morin
%T Cyberspace and the Law: Your Rights and Duties in the Online World
%I MITpress
%D 1994
%P 215
%K book, text, law, legal, right, duty, privacy, contract, libel, crime,
   zzLaw, computing, zz0895
%X Reviewed in Computing Surveys p249-250 May '95.
   From the review, the book seems to be strongly oriented to U.S. law.
   us isbn:0-262-53123-2.

%A G. Tesauro
%T Temporal difference learning and TD-Gammon
%J CACM
%V 38
%N 3
%P 58-68
%M MAR
%D 1995
%K jrnl, CACM, c1995, c199x, c19xx, zz1218, back gammon, backgammon, TD gammon,
   TDgammon, AI, game, games, playing, reinforcement learning
%X "...  complex board games such as Go, chess, checkers, Othello, & backgammon
   has been widely regarded as an ideal testing ground for exploring a variety
   of concepts & approaches in AI & ML. Such board games offer the challenge of
   tremendous complexity & sophistication required to play at expert level. At
   the same time, the problem inputs & performance measures are clear-cut & well
   defined, & the game environment is readily automated in that it is easy to
   simulate the board, the rules of legal play, & the rules regarding when the
   game is over & determining the outcome."
   -- [<A HREF="https://doi.org/10.1145/203330.203343">doi:10.1145/203330.203343</A>]['18].
   [Also search for: backgammon].
   (Also see RL@[<A HREF="https://en.wikipedia.org/wiki/Reinforcement_learning">wikip</A>]['22].)

%A D. Spender
%T Nattering on the Net: Women, Power and Cyberspace
%I Spinifex
%P 278
%D 1995
%K book, text, c1995, c199x, c19xx, computing, internet, inter net, www,
   women, STEM, feminism, zz0995
%X rrp $24.95 (Aus), isbn:1875559094.
   [Also search for: women computing].

%E L. Shear
%T Computers and Schools
%D 1995
%I Australian Council for Ed. Res.
%K book, text, school, kids, children, learn, zz0995
%X isbn:0-86431-183-4.

%A W. Stallings
%T Protect Your Privacy: A Guide for PGP Users
%I Prenticeall
%D 1995
%P 302
%K PGP, book, text, pretty good privacy, protection, security, encryption,
   public key, CSci, computing, zz1095, c1995, c199x, c19xx
%X uk us isbn:0-13-185596-4;  review in Comp Rev Jul 95  p339-340
   [Also search for: public key encryption].

%A P. Samuelson
%T Copyright's fair use doctrine and digital data
%J CACM
%V 37
%N 1
%P 21-27
%M JAN
%D 1994
%K zzLaw, c1994, c199x, c19xx, copyright, law, legal, fair use, computing,
   InterNet, zz1095

%A C. Stoll
%T Silicon Snake Oil: Second Thoughts on the Information Highway
%I Doubleday NY
%D 1995
%P 247
%K book, text, infobahn, superhighway, web, internet, sceptic, zz1195
%X isbn:0-385-41993-7.

%A D. Shasha
%A C. Lazere
%T Out of their Minds: The Lives and Discoveries of 15 Great Computer
   Scientists
%I SpringerVerlag
%D 1995
%K book, text, biography, science, maths, mathematics, computing,
   CS, CSci, zz1195
%X in dept'l library.

%J CACM
%V 38
%N 12
%M DEC
%D 1995
%K CACM, jrnl, ethics, zzEthics, ethical, law, legal, internet, computing,
   c1995, c199x, c19xx, zz1295
%X special issue on ethics and computer use: email, privacy, accountability,
   etc.

%T Report on regulation of computer on-line services (part 2)
%I Senate Select Committee, Parliament of the Commonwealth of Australia
%M NOV
%D 1995
%P 43
%K online, internet, regulation, law, censor, censorship,
   community standards, media, government, gov, senate, enquiry, zz1295
%X Senate Select Committee on Community Standards
   Relevant to the Supply of Services
   Utilising Electronic Technologies.
   isbn:0-642-23413-2; (set);   isbn:0-642-23596-1; (pt 2)

%A I. L. Chuang
%A R. Laflamme
%A P. W. Shor
%A W. H. Zurek
%T Quantum computers, factoring and decoherence
%J Science
%V 270
%P 1633-1635
%M DEC
%D 1995
%K quantum computer, coherence, decoherence, algorithm, c1995, c199x, c19xx,
   prime number, numbers, factor, factors, factoring, algorithm, CSci,
   q-bit, bits, zz0196, computing
%X ... factors to an L-digit number in ~ L^2 time (v. exp(L^(1/3))) can be
   found by a QC that simultaneously follows all paths corr' to
   distinct classical inputs, obtaining the solution from the coherent quantum
   interference of the alternatives.  ... the decoherence process degrades the
   pattern ... an exponential decay ... is inevitable.
   However even [so] ... QC can be useful as long as a sufficiently low
   decoherence rate can be achieved to allow meaningful results to
   be extracted from the calc'n.  8 Dec 1995.
   Also see [<A HREF="http://arxiv.org/abs/quant-ph/9503007">arxiv</A>]['04].
   [Also search for: Shor algorithm quantum].

%A A. Barenco
%A et al
%A H. Weinfurter
%T Elementary gates for quantum computation
%J Phys.Rev. A52, 3457
%D 1995
%K quantum computer, q-bit, bits, qbits, gate, gates, c1995, c199x, c19xx,
   algorithm, networks, circuit, circuits, xor, universal, sufficient,
   Deutsch Toffoli, CCNOT
%X "We show that a set of gates that consists of all one-bit quantum
   gates (U(2)) & the two-bit exclusive-or gate (that maps Boolean values
   $(x,y)$ to $(x,x \oplus y)$) is universal in the sense that all unitary
   operations on arbitrarily many bits $n$ (U($2^n$)) can be expressed as
   compositions of these gates. We investigate the number of the above gates
   required to implement other gates, such as generalized Deutsch-Toffoli
   gates, that apply a specific U(2) transformation to one input bit if & only
   if the logical AND of all remaining input bits is satisfied. These gates
   play a central role in many proposed constructions of quantum computational
   networks. We derive upper & lower bounds on the exact number of elementary
   gates required to build up a variety of two-and three-bit quantum gates, the
   asymptotic number required for $n$-bit Deutsch-Toffoli gates, & make some
   obs's about the number required for arbitrary $n$-bit unitary operations."
   -- [<A HREF="http://arxiv.org/abs/quant-ph/9503016">arxiv</A>][8/'04].
   Also see q.gates@[<A HREF="https://en.wikipedia.org/wiki/Quantum_logic_gate">wikip</A>]['24].

%A N. Karunanithi
%A J. Alspector
%T Feature-based and clique-based user models for movie selection
%J 5th Int. Conf. on User Modelling
%P 29-34
%M JAN
%D 1996
%K user model, filter, filtering
%X clique - a set of users whose movie ratings are "similar"
   1548 movies,  242 internet users rated an average of 177 (0 to 456) movies
   each.  Selected 10 who rated > 350 movies as a target group.
   The clique based approach gave better results than an ANN trained up on
   features:  category (25 categories e.g. action, comedy, ...),
              MPAA rating (6 ratings e.g. PG-13, R, G, ...),
              Maltin rating (0.0 .. 1.0),
              Acad award (0.0, 0,5, 1.0 == not nom', nominated, won),
              length (minutes, normalised), origin (0/1 == non USA / USA)

%A P. Sparaco
%T Board Faults Ariane 5 Software
%J Aviation Week and Space Technology
%P 33-34
%M JUL
%D 1996
%K AWST, jrnl, Ariane5, bug, software bugs, rocket, launcher, zz0896
%X Fundamantal errors in the design and testing of the software for
   the inertial reference system (IRS) caused the failure of the
   first Ariane 5, according to the investigations board.
      ... a failure caused by a numerical overflow in an unused and
   unneeded software routine.
   ...
   29 July '96.

%A H. Lieberman
%T Intelligent graphics
%J CACM
%P 38-48
%V 39
%N 8
%M AUG
%D 1996
%K CACM, jrnl, graphical, GUI, page layout, constraint, analogy,
   introduction, survey, zz0896
%X 19 refs

%A D. Gentner
%A J. Nielson
%T The anti-Mac interface
%J CACM
%P 70-82
%V 39
%N 8
%M AUG
%D 1996
%K CACM, jrnl, graphical user interface, interfaces, GUI, Mac, Macintosh,
   motif, desk top metaphore, windoze, windows, windows95, icon, wimp,
   wysiwyg, wysiati, zz0896
%X WIMP    - windows icon menu pointer
   WYSIWYG - what you see is what you get
   WYSIATI - what you see is all there is
   22 refs.

%A A. N. Pargellis
%T The spontaneous generation of digital "life"
%J Physica D
%V 91
%P 86-96
%D 1996
%K jrnl, c1996, c199x, c19xx, physicaD, Alife, artificial life, organism, zz0896
%X "Digital cells, consisting of seqs. of computer ops which code for
   self-replication, spontaneously emerge from a primordial 'soup', initially
   composed only of random seqs.. The probability of generating a
   self-replicator increases with the # of ops in its seq.. Random mutations
   drive the self-replicators to evolve into more efficient & complex organisms
   as they compete with other species for the computer system's two main
   resources, cpu time & internal memory. The initially large replicators first
   reduce their size by eliminating useless ops. Later, their size increases
   again as they optimize their repl'n efficiency by adding more subroutines."
   -- [<A HREF="https://doi.org/10.1016/0167-2789(95)00268-5">doi:10.1016/0167-2789(95)00268-5</A>].
   [Also search for: Alife]  and  [also search for: Alife organism].

%A S. J. Gibbs
%A D. Tsichritzis
%T Multimedia Programming: Objects, Environments and Frameworks
%I ACM Press / Addison-Wesley
%D 1995
%P 323
%K Multi media, frame works, works, text, book, zz0996
%X isbn:0-201-42282-4;    $35
   see Comp Rev 37(7) p339 Jul 96

%A M. H. Brown
%T Algorithm Animation
%I MITpress
%D 1988
%K book, ACM distinguished dissertation, PhD, computer program, zz1196
%X from  B e n   T e e s e 's report '96

%A A. P. Clark
%T Adaptive Detectors for Digital Modems
%I Pentech Press, London
%D 1989
%K book, text, detector, modem, data communications, signal processing, zz0197
%P 453
%X isbn:0-7273-0112-8.

%A P. Aigrain
%T Polyomino tilings, cellular automata and codicity
%J Theor. Comput. Sci.
%V 147
%N 1-2
%P 165-180
%M AUG
%D 1995
%K TCS, jrnl, tiling, theory, polyomino, polyominoe, polyominoes,
   c1995, c199x, c19xx

%A S. W. Golomb
%T Polyominoes
%I PrincetonUP
%P 248
%D 1995
%K book, text, polyomino,  polyominoe, c1995, c199x, c19xx, tiling
%X hb, us$55, isbn:0691085730, also see his c1965 book.

%A M. Blum
%A H. Wasserman
%T Reflections on the Pentium division bug
%J IEEE Trans. Comput.
%V 45
%N 4
%P 385-393
%M APR
%D 1996
%K jrnl, Pentium, bug, bugs, divide, hardware, computer, arithmetic,
   error, Intel, c1996, c199x, c19xx

%E D. G. Stork
%T HAL's Legacy. 2001's Computer as Dream and Reality
%I MITpress
%P 352
%D 1997
%K book, c1997, c199x, c19xx, AI, Hal, 2001 space odyssey, Arthur C. Clarke,
   Kubrick, film, movie, zz0297
%X hb us$22, uk us isbn:0-262-19378-7; uk is isbn13:978-0262193788.
   "I became operational ... in Urbana, Illinois, on January 12, 1997."
   "I'm sorry Dave, I'm afraid I can't do that."
   [Also search for: AI HAL].

%E V. Lesser
%E L. Gasser
%T Proc. 1st Int. Conf. on Multiagent Systems
%I MITpress
%D 1995
%M JUN
%W San Francisco
%P 900
%K conf, agent, agents, multi, AAAI
%X isbn:0-262-62102-9;  LESPP   $70 (US)

%A E. Seymour
%A N. Hewitt
%T Talking About Leaving: Why Undergraduates Leave the Sciences
%I Westview Press
%D 1997
%K book, text, under graduates, science, students, university, tertiary,
   education, women, science, STEM, gender, minorities, zz0297
%X Mentioned in `The Australian' (Higher Ed') p39 Wed' 5 Feb 97
   Asked 460 students at 13 US Universities why they left science.
      ... many problems stemmed from science's elitism.
      Women are socialised to assess performance based on [...] feedback ...
      Sci/Math/Eng majors also seem hostile to minority students ...

%A H. Brody
%T Great expectations: why technology predictions go awry
%J Technolgy Review
%V 94
%N 5
%P 38-44
%M JUL
%D 1991
%K jrnl, c1991, c199x, c19xx, future, futurology, prediction, technobabble,
   quote, quotes, quotable, zz0497, development, market forecasts, zzPrediction,
   gallium arsenide, Josephson junction
%X some great ($) flops as of '91: video text, video disc, gallium arsenide,
      Xray lithography, Josephson junctions.
   Unpredicted hits: the computer, the pc.
   Roller-coaster: computer CD-rom predicted hit in 1980s came good in 1990s.
   Some great quotes unfortunately without precise ref's:
   The illusion of knowing what's going to happen is worse than not knowing.
      -- Utterback, MIT.
   Technology development ~ ouija board,  Everybody's got their hand on it
   but it always feels like somebody else is moving it.
      -- Lucky, Bell Labs.
   [Also search for: zzPrediction].

%A R. Martens
%A L. Claesen
%T On-line signature verification: discrimination emphasised
%J 4th Int. Conf. Document Analysis and Recognition (ICDAR '97)
%V II
%P 657-660
%M AUG
%D 1997
%K conf, signature, hand writing, handwriting, match, matching
%X "Narrowly seen, this paper presents an on-line signature verification
   system, based on 3D force patterns & pen inclination angles, as recorded
   during signing. The feature extraction mechanism is based on the well-known
   elastic matching technique. In contradiction to previous work in the same
   area however, we emphasise the importance of the final step in the process:
   the discrimination based on the extracted features. We show that by choosing
   the right discrimination approach we are able to improve the quality of the
   entire verification process drastically. The techniques we compare for
   discrimination, however, are not specific to signature verification, but
   should be considered carefully in every process, where a classification
   decision is made out of a set of parameters."
   -- [<A HREF="http://csdl.computer.org/comp/proceedings/icdar/1997/7898/00/78980657abs.htm">abs</A>][2/'04] (?subscribed?)
   [Also search for: shape match] or [also search for: curve match].

%A H. Berghel
%T Email - the good, the bad and the ugly
%J CACM
%V 40
%N 4
%M APR
%D 1997
%P 11-15
%K jrnl, CACM, internet, electronic mail, email, social consequences,
   privacy, spam, spamming
%X <A HREF="http://www.acm.org/~hlb/">[HLB]</A> [4/'97].

%A M. Williams
%T A History of Computing Technology
%I IEEE Comp. Soc.
%D 1997
%P 530
%K book, text, c1997, c199x, c19xx, computer, computers, historical, zz0797
%X 1. The beginning;   2. Early aids to calculation
   3. Mechanical...    4. Babbage Machines
   5. Analog           6. mechanical Monsters
   7. Electronic ...   8. Stored Program
   9. Later Dev'       Appendix
   isbn:0-8186-7739-2;  $A58.

%A R. Rosenberg
%T The Social Impact of Computers
%D 1997
%P 448
%I AcademicPress
%K book, text, society, computer, effect, privacy, employment, work, zz0797
%X isbn:0-12-597131-1;  $A52

%A K. L. Verco
%A M. J. Wise
%T Plagiarism a la mode: a comparison of automated systems for detecting
   suspected plagiarism
%J COMPJ
%V 39
%N 9
%P 741-750
%D 1996
%K COMPJ, jrnl, c1996, c199x, c19xx, plagiarism, cheating, cheat, detection,
   detector, detect, copy, copying, zz0897
%X 18 refs

%A R. Kalakota
%A A. Whinston
%T Frontiers of Electronic Commerce
%I AddisonWesley
%P 850
%D 1996
%K book, text, ecommerce, internet, www, buy, buying, sell, selling, zz1097
%X uk us isbn:0-201-84520-2; pb $63.
   Too big.

%A W. W. Gibbs
%T Taking computers to task
%J Scientific American
%P 64-71
%M JUL
%D 1997
%K social consequences, society, hype, hyperbole, future, prediction,
   zzPrediction, flabware, flab ware, bloat, word, microsoft, word97, HCI, HCF,
   CHI, CHI97, information technology, IT, business, productivity, 2007, zz1097
%X Discusses the lack of startling productivity gains despite
   the impressive performance gains of computer hardware.
   MS-word: 1992 version 2.0C has 311 commands,  word97 has 1033 commands.
   It will be fun to check this one in the year 2007.
   "Word 2000 (PC) and 2001 (Mac) have over 1200 built-in commands"
   -- [<A HREF="http://www.melbpc.org.au/pcupdate/2207/2207article6.htm">melbpc.org</A>][7/2002].
   [Also search for: zzPrediction].

%A T. Pearcey
%T A History of Australian Computing
%I ChisholmInstTech
%D 1988
%P 192
%K computer, computers, Australia, aus, au, oz, history, historical, old,
   c1988m, c198x, c19xx, computing, zz1197
%X Hargrave 004.0994 P359H,  Caulf' 004.0994 PEA.
   [Also search for: history computing].

%A M. Tabor
%A A. Goriely
%T ?
%J Phys. Rev. Lett.
%V ?
%N ?
%P ?-?
%M Feb
%D 1998
%K jrnl, telephone handset cables, coil, coiling, twist, plant tendril,
   tendrils, kink, fun, funn, zz0298
%X Tabor - Unic. Arizona,  Goriely - Brussels free Univ.
   See `this week', p12 New Scientist 31 Jan 1998.

%T Proc. First Int. Workshop on Information Hiding
%E R. Anderson
%W Cambridge UK
%I SpringerVerlag
%S LNCS
%V 1174
%M May
%D 1996
%K conf, 1st, steganography, information hiding, hide, water mark, watermark,
   marks, watermarking, copyright protection, www, zz0198
%X <A HREF="http://www.cl.cam.ac.uk/~fapp2/steganography/">[web]</A>[2/1998].
   uk us isbn:3-540-61996-8;   #31.50stg, 26 papers

%A R. J. Anderson
%A F. A. P. Petitcolas
%T On the limits of steganography
%J IEEE J. Selected Areas in Communications
%V ?
%P ?-?
%M ?
%D 1998 ? (to appear)
%K jrnl, IEE, J-SAC, copyright, privacy, watermark, water mark, protection,
   steganography, zz0298
%X ... formidable obstacles that lie in the way of information hiding
   systems ... However theoretical considerations lead to ideas of
   practical value, ...  Finally we show that public-key information
   hiding systems exist ...
   <A HREF="http://www.cl.cam.ac.uk/~fapp2/steganography/">[web]</A>[2/1998].

%A E. Burke
%A K. Jackson
%A J. H. Kingston
%A R. Weare
%T Automated university timetabling: the state of the art
%J COMPJ
%V 40
%N 9
%P 565-571
%D 1997
%K COMPJ, jrnl, school, time table, tabling, tables, zz0498
%X 29 refs

%A I. Fried
%T Syndrome E
%J The Lancet
%V 350
%N 9094
%P 1845-1847
%M DEC
%D 1997
%K jrnl, c1997, c199x, c19xx, zz1115, human, behaviour, evil, syndromeE,
   psychology, risk, risks, kill, killer, mass, murder, killing, massacre,
   terrorism, terrorist, nazi, nazis, genocide, Pol Pot, Rwanda, violence,
   orbitofrontal, amygdala, neocortical, prefrontal cortex, PFC, brain,
   cognitive fracture, hypothesis, prediction
%X "The transformation of groups of previously nonviolent individuals into
   repetitive killers of defenceless members of society has been a recurring
   phenomenon throughout history. ... Affected individuals show obsessive
   ideation, compulsive repetition, rapid desensitisation to violence,
   diminished affective reactivity, hyperarousal, environmental dependency,
   group contagion, & failure to adapt to changing stimulus-reinforcement
   associations. Yet memory, language, planning, & problem-solving skills remain
   intact. The main risk factors are male sex & age between 15 & 50. A
   pathophysiological model - 'cognitive fracture' - is hypothesised, where
   hyperaroused orbitofrontal & medial prefrontal cortices tonically inhibit the
   amygdala & are no longer regulated by visceral & somatic homoeostatic
   controls ordinarily supplied by subcortical systems. It is proposed that the
   syndrome is a product of neocortical development rather than the
   manifestation of a disinhibited primitive brain. Early recognition of
   symptoms & signs could lead to prevention through education & isolation of
   affected individuals. ..."  [20 refs].
   -- [<A HREF="http://dx.doi.org/10.1016/S0140-6736(97)09385-9">doi:10.1016/S0140-6736(97)09385-9</A>]['15].

%A J. Doran
%A P. Bizony
%T Starman
%I Bloomsbury
%D 1998
%K book, biography, Yuri Gagarin, space flight, USSR, Russian
%X review in New Scientist p46, 25 April 1998
   isbn:0747536880.

%A J. Hoffstein
%A J. Pipher
%A J. H. Silverman
%T NTRU: A ring based public key cryptosystem
%J Alg. Number Theory (ANTS III), Portland, OR
%M JUN
%D 1998
%S LNCS
%V 1423
%P 267-288
%K conf, c1998, c199x, c19xx, zz1020, public key encryption, cryptography,
   NTRU, NTRUEncrypt, short, shortest vector problem, SVP, lattice based,
   polynomial ring, factoring
%X "We describe NTRU ..."
   -- [<A HREF="https://web.archive.org/web/20071021011338/http://www.ntru.com/cryptolab/pdf/ANTS97.pdf">www</A>]['20].
   Also see, "... relies on the presumed difficulty of factoring certain
   polynomials in a truncated polynomial ring into a quotient of two polynomials
   having very small coefficients. ... alg. problem of lattice red'n in certain
   lattices. ..."
   -- NTRU@[<A HREF="https://en.wikipedia.org/wiki/NTRUEncrypt#cite_note-1 ">wikip</A>]['20].
   [Also search for: lattice based cryptography].

%A D. I. Perrett
%A K. Lee
%A I. Penton-Voak
%A D. M. Burt
%A D. Rowland
%A S. Yoshikawa
%A S. P. Henzi
%A D. Castles
%A S. Akamatsu
%T Sexual dimorphism and facial attractiveness
%J Nature
%V 394
%N 6696
%P 884-887
%D 1998
%K jrnl, face, appearance, beauty, c1998, c199x, c19xx, pretty, features, sex,
   sexual, perceptions, selection, attractive, faces, proportions, male,
   female, feminine, masculine, human, dimorphism, average
%X Testosterone-dependent secondary sexual characteristics in males may signal
   immunological competence and are sexually selected for in several species.
   In humans, oestrogen-dependent characteristics of the female body correlate
   with health and reproductive fitness and are found attractive. Enhancing the
   sexual dimorphism of human faces should raise attractiveness by enhancing
   sex-hormone-related cues to youth and fertility in females, and to dominance
   and immunocompetence in males. Here we report the results of asking subjects
   to choose the most attractive faces from continua that enhanced or
   diminished differences between the average shape of female and male faces.
   As predicted, subjects preferred feminized to, average shapes of a female
   face. This preference applied across UK and Japanese populations but was
   stronger for within-population judgements, which indicates that
   attractiveness cues are learned.  Subjects preferred feminized to average or
   masculinized shapes of a male face. Enhancing masculine facial
   characteristics increased both perceived dominance and negative attributions
   (for example, coldness or dishonesty) relevant to relationships and paternal
   investment. These results indicate a selection pressure that limits sexual
   dimorphism and encourages neoteny in humans.
   -- [<A HREF="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v394/n6696/abs/394884a0_fs.html">@nature</A>][12/'02].
   -- [<A HREF="http://perception.st-and.ac.uk/Attractiveness/abst_nat98.htm">abs</A>][12/'02].
   -- [<A HREF="http://psy.st-andrews.ac.uk/people/lect/dp.shtml">DP home</A>][12/'02].

%A D. Dennett
%T The Dennett Quartet
%I MITpress
%D 1998
%K book, books, Brainchildren, Brainstorms, Elbow Room, Intentional Stance,
   AI, cognition, consciousness
%X boxed set of 4 books by D.D., available in USA, individual books elsewhere.
   us isbn:026-254-0916;  $60US.

%A C. H. Bennett
%T Quantum information and computation
%J Physics Today
%V 48
%N 10
%P 24-30
%M OCT
%D 1995
%K jrnl, c1995, c199x, c19xx, physics, quantum, computer, computing, reversible
%X ref in Sci Am JUN 98 p.55.
   [Also search for: Bennett computing].
   [Also search for: Qbism].

%A N. A. Gershenfeld
%A I. L. Chuang
%T Bulk spin resonance quantum computation
%J Science
%V 275
%P 350-356
%M JAN
%D 1997
%K jrnl, quantum computer, computing
%X 17 Jan 97
   ref in Sci Am JUN 98 p.55.

%A L. K. Grover
%T Quantum mechanics helps in searching for a needle in a haystack
%J Phys. Rev. Lett.
%V 79
%N 2
%P 325-328
%M JUL
%D 1997
%K jrnl, computer, computation
%X 14 JUL 97;  ref in Sci Am JUM 98 p.55.

%E Coady
%T Why Universities Matter
%D 1999 ?
%I ???
%K University, managerialism, policy, management, education, conflict, unimelb,
   Melbourne University Press, MUP, mu, private, Australia, Australian,
   universities, academic, administration, c1999, c199x, c19xx, zz0998
%X Not yet (9/1998) published, an anthology edited by philosopher Tony Coady
   created a fuss when it was rejected by Melbourne University Press.
   The book is critical of the "new managerialism" sweeping universities.
   The press rejected the book because it promoted a `traditional'
   (and important) view of u's without giving alternative [managerial?]
   views.  Trouble is ... the chairman of MUP press is Barry Sheehan, also
   chief exec' of `Melbourne University Private'.
   Many academics see a conflict of interest and even censorship here.
   Of course UNSW Press, Allen and Unwin, Scribe and other publishers are
   now queueing up to publish and promote the now "controversial" book!
   - see The Australian p.38, 2 Sept. 1998.

%A S. Alexander
%A J. McKenzie
%A H. Geissinger
%T An evaluation of information technology projects for university learning:
   The CAUT experience
%I ?
%D 1998
%K IT, report, multi-media, multimedia, teach, teaching, CAUT, DEET,
   zz0998
%X DEET Commissioned Study 1996-98
   Analysed 104 projects.  Found students learned less via IT
   than via human teaching, on many (but not all) projects.
   Shirley Alexander's <A HREF="http://www.iim.uts.edu.au/about/sa.shtml">home page</A>[9/1998],
   (see also Australian p44, 2 September 1998),
   -- [<A HREF="http://www.canberra.edu.au/CUTSD/announce/ExSumm.html">ExSumm.html</A>][9/1999].

%T RoboCup 97: Robot Soccer World Cup 1
%E H. Kitano
%I SpringerVerlag
%S LNCS
%V 1395
%D 1998
%P 520
%K book, text, AI, robot, robots, robotics, robo-cup, soccer, football, zz0998
%X A$82 ('98);  isbn:3-540-64473-3.

%A N. Dershowitz
%A E. M. Reingold
%T Calendrical Calculations
%I CUP
%D 1997
%P 307
%K book, text, calendar, calendars, calender, Gregorian, Julian, Ethiopic,
   Islamic, Bahai, Jewish, Mayan, Hindu, Chinese, y2k, year 2000 problem,
   fixed date, dates, CUP
%X 14 calendars,
   us$22.95; uk us isbn:0-521-56474-3;  - ACM Comp Rev p251 May '98.

%A D. Curtis Schleher
%T Electronic Warfare in the Information Age
%I Artech House
%M DEC
%D 1998
%P 327
%K book, infowar, info war, ECM, ECCM, radar
%X isbn:0-89006-526-8;  au$144 as of 11/98

%A G. Stocker
%A C. Schopf
%T Infowar
%I Springer
%M OCT
%D 1998
%P 300
%K book, info war, information, hacker, hacking, security
%X uk us isbn:3-211-83191-6;  au$56.50,  dm57.00  as at 11/98.

%E E. Burke
%E M. Carter
%T Practice and theory of automated timetabling II
%I Springer
%S LNCS
%V 1408
%P 273
%D 1997
%K proc, conf, PATAT2, PATAT97, PATAT, automatic, time table, tabling, zz0199
%X 17 papers.  isbn:3-540-64979-4;  au$66, dm66 as of 11/98

%E W. Hansmann
%E W. T. Hewitt
%E W. Purgathofer
%T Visualization in Scientific Computing '98
%I Springer
%P 151
%D 1998
%K proc, conf, visualisation, visualize, data, statistics, zz0199
%X proc of the Eurographics workshop , Germany April 2-22 '98.
   uk us isbn:3-211-83209-2;  dm85, au$84 as of 11/98.

%A R. Frieden
%T Physics from Fisher Information
%I CUP
%D 1998 ?
%K book, text, law, laws, Stam, information theory, philosophy science, zz0299
%X Author at Optical Sci' Center, U. of Arizona.
   Article about his ideas in New Scientist, 30 Jan '99, p24-28.
   Cramer-Roa inequality ~  "when the error in a measurement is multiplied
   by the amount of the Fisher inf' in the measurement, the result
   is a number never less than one." (p26, New Sci article).

%A D. R. Olsen
%T Developing User Interfaces
%I MorganKaufmann
%P 442
%D 1998
%K book, text, interface, GUI, zz0399
%X isbn:1-55860-418-9;  us$50;  rev' in Comp Rev p443 Sep 98.

%A N. Kock
%T A case of academic plagiarism
%J CACM
%V 42
%N 7
%P 96-104
%M JUL
%D 1999
%K jrnl, law, legal, copyright, copy right, c1999, c199x, c19xx, zz0799,
   scientific misconduct, academic, University, plagiarism, fraud,
   The Learning Organization
%X Recounts the case of a paper (by the author) being plagiarised
   by another academic and submitted to a journal.
   -- [<A HREF="http://doi.acm.org/10.1145/306549.306594">doi:10.1145/306549.306594</A>]['10],
   was [<A HREF="http://www.acm.org/pubs/citations/journals/cacm/1999-42-7/p96-kock/">web-copy</A>][7/1999].
   [Also search for: academic misconduct].

%A S. Fowler
%T GUI design Handbook
%I McGrawHill
%D 1998
%P 318
%K book, GUI, guis, graphical user interface, interfaces, zz0799
%X uk us isbn:0-07-059274-8;  us$43.
   Favourable review  ACM Comp Rev 40(2) pp101 Feb '99.

%A G. M. Weinberg
%T The Psychology of Computer Programming (Silver Anniversary edn)
%I DorsetHouseNY
%P 296
%D 1998
%K book, text, good, 1971, c1998, c199x, c19xx
%X 1st published 1971,  isbn:0-932633-42-0.

%A Perilla Kinchin
%T Miss Cranston
%S Scots lives
%I Edinburgh, HMS publ., or Pomegranate Eur.?
%D 1998
%K Charles Rennie Mackintosh, Scottish, Scotland, Glasgow, tea rooms, design,
   designer, whitecockade, white cockade, c1998, c199x, c19xx
%P 112
%X see [<A HREF="http://www.whitecockade.co.uk/">whitecockade.co.uk</A>][8/'01];
   isbn:1901663132;  or  isbn:0764906925;  - from 2 different source.

%A Norman N. Greenwood
%T Chemistry of the Elements
%I Butterworth/Heinemann
%D 1997
%P 1341
%K chemistry, book, text, Mossbauer spectroscopy
%X 2nd edition
   -- [<A HREF="http://www.chem.leeds.ac.uk/People/Greenwood.html">www</A>][7/01].

%A T. Mark Ellison
%T Induction and inherent similarity
%J Workshop on Similarity and Categorisation
%D 1997
%K wShop, SimCat, SimCat97, c1997, c199x, c19xx, inductive inference, II
%X "...problem of induction, and then proposes a solution based on similarity
   measures and topographic mapping. The premisses of this solution are the
   following. (i) Naturally occurring data and representations are embedded in
   spaces with non-trivial similarity structures. (ii) Natural cognitive
   mappings between spaces of representation are topographic mappings. The
   uniformity presumption can be justified by these two premisses. "
   -- [<A HREF="http://www.dai.ed.ac.uk/conferences/simcat/ell.htm">abs</A>]['06],
   -- [<A HREF="http://markellison.net/">MarkE</A>]['06].

%A A. Zahavi
%A A. Zahavi
%T The Handicap Principle: A Missing Piece of Darwin's Puzzle
%P 304
%I OUP
%D 1997
%K book, text, communication, c1997, c199x, c19xx, evolution, honesty, signal,
   signals, signalling, animal behaviour, cooperation, liar, liars, deception,
   peacock, peacocks tail
%X us$21; uk us isbn:0195100352; uk us isbn13:9780195129144.
   [Also search for: prisoners dilemma].

%A J. A. Christen
%A C. D. Litton
%T A Bayesian approach to wiggle-matching
%J Jrnl of Archaeological Science
%V 22
%N 6
%P 719
%M NOV
%D 1995
%K jrnl, Archaeology, c1995, c199x, c19xx, zz0999
%X via rohan b' 9/99.

%A B. Singer
%T Modernity, hyperstimulus, and the rise of popular sensationalism
%B Cinema and the Invention of Modern Life
%I UCalPress
%P 72-102 ?
%D 1995
%K c1995, c199x, c19xx, hyperstimulus, hyper stimulus, marketing, advertising,
   exaggerated, mega, stimulate, stimulated, stimulation, hyperstimulation,
   superstimulus, super, supernormal, stimuli, sensation, sensational, pleasure,
   thrill, craving, addiction, evolution
%X "... Michael Davis coined an apt ... term ... modernity, he declared
   in 1910 was defined by 'hyperstimulus'. ..."
      (M. M. Davis, 'The exploitation of pleasure,' Russell Sage Foud'n 1911.)
   [Also earch for: hyperstimulus].

%A S. Dreyfuss
%T Underground: Tales of Hacking, Madness, and Obsession on the
   Electronic Frontier
%I MandarinAustralia
%P 324
%D 1997
%K book, text, c1997, c199x, c19xx, Suelette Dreyfus, hacker, hacking, computer,
   computers, intrusion, Australia, au, WANK, worm, 8lgm, black hat, blackhat,
   Mendax, Julian Assange, Parmaster
%X "... overview of intrustion activities focusing on the UK, Australia, and the
   United States. It covers the late 80's to the early nineties with stories on
   incidents such as the WANK Worm outbreak and 8lgm's activities. ..."
   1st ed 1997; uk us isbn:1863305955; uk us isbn13:978-1863305952;
   (auth hon'ry @ IT unimelb c2010).
   UG@[<A HREF="http://www.gutenberg.org/etext/4686">Gutenb'rg</A>]['03].
   [Also search for: wikileaks].

%T Multilingualism, Literacy and Dyslexia
%E L. Peer
%E G. Reid
%I DavidFulton
%D 2000
%K book, text, c2000, c200x, c20xx, language, languages, dyslexic, reading,
   learning difficulty
%X from New Sci', p65, 14 Jun '03.

%A B. Schneier
%T Secrets and Lies
%I JohnWiley
%D 2000
%K book, text, c2000, c200x, c20xx, code, codes, coding, cryptography,
   cypher, cipher, ciphers, encryption, secret, security, zz0900
%X uk us isbn:0471253111.

%A Chang-Shing Perng
%A Haixun Wang
%A Sylvia R. Zhang
%A D. Stott Parker
%T Landmarks: A new model for similarity-based pattern querying in
   time series databases
%J 16th Int. Conf. on Data Engineering (ICDE'2000)
%P ?-?
%W San Diego
%D 2000
%K conf, ICDE, ICDE2000, landmark
%X [<A HREF="http://citeseer.nj.nec.com/262805.html">ci te see r</A>]['00];
   -- [<A HREF="http://www.cs.ucla.edu/~hxwang/">www</A>]['00].

%A M. A. Rodruigez-Girones
%A M. Enquest
%T The evolution of female sexuality
%J Animal Behaviour
%V 61
%N 4
%P 695-704
%D 2001
%K jrnl, biol, biology, sex, strategy, female, male, mate, mating, monogamy,
   mathematical model, sexual activity, www, http, HREF, zz0701
%X Females in monogamous species tend to be more sexually active than
   ... in species with other mating systems. ...consider the possibility that
   female sexuality has evolved because more sexually active females have
   received more male assistance.  ... model ... no direct cue available to
   males indicating whether the female is fertile. Instead males might respond
   to female behaviour as an indirect cue. The latter could favour increased
   female sexuality if males tend to stay longer with more sexually active
   females. Our results show that female sexual behaviour can have a
   significant impact on social behaviour and that sexually active females and
   sexual behaviour outside fertile periods can evolve under some
   circumstances. ...
   -- [<A HREF="http://www.academicpress.com/anbehav">Animal Behaviour</A>][11/'01].
      [<A HREF="http://www.idealibrary.com/links/toc/anbe/61/4/0">V61(4) inc' pdf</A>][11/'01].
   -- [<A HREF="http://ethology.zool.su.se/~magnus/">M. E.'s home page</A>][7/'01].
      [<A HREF="http://rerumnatura.zool.su.se/refweb/rodr01/evolution.html">html</A>][7/'01].

%A A. W. Appel
%A E. W. Felten
%T Technological access control interferes with noninfringing scholarship
%J CACM
%V 43
%N 9
%P ?-?
%M SEP
%D 2000
%K CACM, jrnl, copyright, copy right, digital recording millenium, act, law,
   zzLaw, music, millenium, data, protection, secure, initiative, challenge,
   recording, social issue, issues, zz0701
%X also TR-617-00 Princeton
   -- [<A HREF="http://ncstrl.cs.princeton.edu/expand.php3?id=TR-617-00">TR-617-00</A>][7/'01] (ps and pdf)

%A N. Lin
%T Advanced Linux 3D Graphics Programming
%I Wordware Publ.
%P 650
%P 2001
%K book, text, graphics, interactive, zz0901
%X isbn:1-55622-853-8;  About US$60.00,  au$128;

%A G. Carbone
%A A. Lesniak
%A D. Stoddard
%T Open Source Enterprise Solutions
%I Wiley
%M MAR
%D 2001
%P 512
%K book, text, opensource, gnu, Microsoft, MS, proprietary, licence, copyright,
   Linux, windows, copyright, business, software, applications,
   IT, c2001, c200x, c20xx, zz0901
%X isbn:0-471-41744-0;

%A M. Srinivasan
%A J. S. Chahl
%A K. Weber
%A S. Venkatesh
%A M. G. Nagle
%A S. W. Zhang
%T Robot navigation inspired by principles of insect vision
%B Field and Service Robotics
%E A. Zelinsky
%I SpringerVerlag
%P 12-16
%D 1998
%K AI, conf, insect, eye, visual flow, motion, vision, navigate, robots, zz0901
%X ?chapter? in a book.
   Possibly also in  Robotics & Autonomous Sys. V26(2-3) pp203-216 '99 or '00

%A B. Aldiss
%T Like human, like machine
%J New Scientist
%P 40-43
%N 2308
%M SEP
%D 2001
%K magazine, opinion essay, artificial intelligence, AI, film, movie, book,
   zz1001, Supertoys last all summer long, super toy, toys, robot, robots,
   android, androids, extended consciousness, EXTC, feelings, human, love,
   emotion, self awareness, 1969, 2001, science fiction, scifi,
   Brian Aldiss, Stanley Kubrick, Steven Spielberg
%X New Scientist, pp40-43, 15 Sept 2001.
   Brian Aldiss wrote ``Supertoys last all summer long'' in 1969.
   This gives his views on that story, Stanley Kubrick's development of the
   idea, and the Steven Spielberg film ``Artificial Intelligence'' (2001).

%A S. J. Olshansky
%A B. Carnes
%A W. W. Norton
%T The Quest for Immortality
%I ?
%D 2001
%K book, age, ageing, aging, longevity, live long, old,
   antioxidants, anti-oxidants, diet, diets, c2001, c200x, c20xx, zz1001
%X isbn:0393048365. stg 20.0.

%A R. Ellis
%T Aquagenesis: The Origin of Life in the Sea
%I Viking/Penguin
%D 2001
%K book, origins, aquatic, seas, water
%X isbn:0670030236.  US$26

%A N. P. B. Bollen
%A S. F. Gray
%A R. E. Whaley
%T Regime switching in foreign exchange rates: Evidence from
   currency option prices
%J Journal of Econometrics
%V 94
%N 1-2
%M JAN
%D 2000
%P 239-276
%K jrnl, economics, currency, rate, time series, options, value, pricing, prediction, zz1201
%X [<A HREF="http://mba.vanderbilt.edu/nick.bollen/research/bgw1.htm">abs' html</A>][12/'01].
      [<A HREF="http://mba.vanderbilt.edu/nick.bollen/research/BGW.pdf">pdf</A>][12/'01].
   -- [<A HREF="http://www.elsevier.nl/homepage/sae/econbase/econom/">jrnl</A>][12/'01].
   ... A [...] model with independent shifts in mean and variance exhibits a closer fit
   and more accurate variance forecasts than a range of other models. ...

%A James Watt
%T parallel motion
%D 1784
%K link, linkage, links, rectilinear motion, straight-line mechanism,
   c1784, c178x, c17xx
%X 3 links, *nearly* straight line motion.
   Used in some cars to locate a live axle.
   [Also search for: Peaucellier].

%A Captain Charles-Nicolas Peaucellier (1832-1913)
%T Peaucellier linkage
%D 1864
%K link, linkage, links, cell, rectilinear motion, straight-line mechanism
%X ... articulated system invented in 1864; the device of Peaucellier or
   parallelepiped of Peaucellier makes it possible to transform a
   rectilinear motion into a circular motion.
   -- [<A HREF="http://www.bibliotheque.polytechnique.fr/">www</A>][12/'01].
   (Also see Panhard rod, and Watts linkage re cars).

%T Non Campus Mentis: World History According to College Students
%A A. Henriksson
%I Workman
%M SEP
%D 2001
%K book, funny, haha, ha ha, joke, exam answers, essays, Vestal Virgins,
   c2001, c200x, c20xx
%X isbn:0761122745. ... the Stoned Age, Joan of Ark, Florence of Arabia,
   Vestigal Virgins dedicated to burning the internal flame, and more!

%A K. Sigmon
%A T. A. davis
%T MATLAB Primer
%I ChapmanHall
%D 2001
%K book, text, c2001, c200x, c20xx, maths, MATLAB
%X isbn:1584882948.

%A D. C. Glass
%A C. N. Gray
%T Estimating mean exposures from censored data: Exposure to
   benzene in the Australian petroleum industry
%J Ann. Occup. Hygiene
%V 45
%N 4
%P 275-282
%D 2001
%K jrnl, c2001, c200x, c20xx, estimate, exposure, petrol, health, chemical,
   stats, censored, oil refinery, refineries, Cohen's method
%X "... Each job or task in the industry was assigned a Base Estimate (BE) of
   exposure derived from task-based personal exposure assessments carried out
   by the company occupational hygienists. The BEs corresponded to the est.
   arithmetic mean exposure to benzene for each job or task & were used in a
   deterministic alg. to estimate the exposure of subjects in the study...."
   -- [<A HREF="http://annhyg.oxfordjournals.org/cgi/content/abstract/45/4/275">pdf</A>]['06],
   -- [<A HREF="http://www.med.monash.edu.au/epidemiology/">Dept</A>][2/'02].

%A D. Glass
%A G. Adams
%A R. Manuell
%A J. Bisby
%T Retrospective exposure assessment for benzene in the Australian
   petroleum industry
%J Ann. Occup. Hygiene
%V 44
%N 4
%P 301-320
%D 2000
%K jrnl, estimate, exposure, petrol, health, chemical, c2000, c200x, c20xx
%X [<A HREF="http://www.med.monash.edu.au/epidemiology/">Dept</A>][2/'02].

%A P. Hilton
%A D. Holton
%A J. Pedersen
%T Mathematical Vistas
%I SpringerVerlag
%P 350
%M JAN
%D 2002
%K book, text, maths, introduction, four colour map theorem, color,
   Fermat's last theorem, Fermat, problem, vista, c2002, c200x, c20xx
%X A "popular" book, us$59, uk us isbn:0387950648.

%E H. Kuhn
%E S. Nasar
%T The Essential John Nash
%I PrincetonUP
%P 244
%M DEC
%D 2001
%K book, text, c2001, c200x, c20xx, game theory, edited papers, paper,
   beautiful mind, collected work
%X us isbn:0691095272.

%A S. Nasar
%T A Beautiful Mind: The Life of Mathematical Genius and
   Nobel Laureate John Nash
%I TouchstoneBooks
%P 464
%M NOV
%D 2001
%K book, c2001, c200x, c20xx, biography, John Nash, maths, mathematics,
   mathematician, cooperative game theory, Nobel, NobelPrize,
   Abel, prize, AbelPrize
%X pb '02;  uk us isbn:0743224574.  Feature film '01 ~ '02.
   See [<A HREF="http://www.nobel.se/economics/laureates/1994/nash-autobio.html">www.nobel.se</A>][6/2'02].
   NB. Economics Nobel prize -- no Nobel P. for Maths.
   (But in 2015 Nash was awarded the Abel Prize (with Louis Nirenberg) for
    his work on nonlinear partial differential equations.)
   (Also see JN@[<A HREF="http://en.wikipedia.org/wiki/John_Forbes_Nash,_Jr.">wikip</A>]['15].)

%A S. M. Cherry
%T Hyperencryption: Much hype about little that is new
%J IEEE Spectrum
%V 38
%N 4
%M APR
%D 2001
%P 87
%K c2001, c200x, c20xx, hyper-encryption, cypher, cipher, security
%X issn:0018-9235

%A J. Kanndorp
%A J. Kubler
%T The Algorithmic Beauty of Seaweeds and Sponges
%I SpringerVerlag
%P 251
%M JAN
%D 2002
%K book, text, c2002, c200x, c20xx, sponge, biology, biol, seaweed, sea weed
%X about us$50.   uk us isbn:3540677003.

%T The Subversion of Australian Universities
%E J. Biggs
%A R. E. Davies
%K book, 2002, c200x, c20xx, zz0522, Australia, University, academia, quality,
   academic research, management, KPI, KPIs, politics, Dawkins
%X "The theme of this book is that Australian universities have become subverted
   and that this is a catastrophe for society. The traditional university is the
   only institution in society that is dedicated, through research and teaching,
   to the creation, maintenance, and propagation of knowledge in the basic
   disciplines. ..."
   -- at [<A HREF="https://documents.uow.edu.au/~bmartin/dissent/documents/sau/sau00.pdf">UoW</A>]['22].

%A C. C. Lee
%A D. Richard
%A A. Sharma
%T Zen and The Art of Foosball: A Beginner's Guide to Table Soccer
%I iUniverse
%M FEB
%D 2002
%K book, c2002, c200x, c20xx, table football, soccer, foosball, ITSF,
   banzini, fireball garlando, leonhart, roberto
%X 1st ed 2002; pb us $13; uk us isbn:0595217052; uk us isbn13:978-0595217052.
   (Also see [<A HREF="http://www.table-soccer.org/">ITSF</A>]['13],
   and [also search for: foosball].)

%A N. K. Humphrey
%T The illusion of beauty
%J Perception
%V 2
%P 429-439
%D 1973
%K jrnl, quote, quotable, good, beautiful, aesthetics, arts, art, music, poem,
   poetry, like, similarity, rhyme, rhymes, contrast, pattern, attractive,
   classification, good, c1973, c197x, c19xx, zz0702
%X p.434 ... What evidence is there that classification - the core of
   learning - is agreeable to men and to animals also? ...   (via Jon McC')
   -- [<A HREF="http://cogprints.org/1771/">pdf</A>]['06],
      [<A HREF="http://cogprints.soton.ac.uk/documents/disk0/00/00/17/71/">pdf@cogprints</A>][6/'02].

%A J. B. Roebuck
%A R. G. Kessler
%T The Etiology of Alcoholism: Constitutional, Psychological and
   Sociological Approaches
%I Springfield :Thomas
%P 260
%D 1972
%K book, text,  alcohol, abuse, drink, drinking, zz0702
%X [Also search for: Robinson misconduct c1976].

%A D. Robinson
%T From Drinking to Alcoholism
%I JohnWiley
%P 211
%D 1976
%K book, text, Monash University, VC, vice chancellor, alcohol, abuse, drink,
   1976, c1976, c197x, c19xx, Etiology of Alcoholism, Roebuck, Kessler,
   Robinson, plagiarism, scandal, fraud, scientific misconduct, research,
   academic, zzEthics, ethics, zz0702
%X NB. From Drinking to Alcoholism: A Sociological Commentary, 1976.
   "... passages in [the book] are identical to parts of a 1972 work,
   The Etiology of Alcoholism, by a different author." -- [<A HREF="http://www.theage.com.au/text/articles/2002/07/08/1025667114386.htm">The Age</A>][9/7/2002].
  (Roebuck and Kessler '72).
  Robinson was Monash VC from 1996 to 11/7/'02 [<A HREF="http://www.theage.com.au/articles/2002/07/12/1026185107089.html">end</A>][13/7/2002].
  Also see [<A HREF="http://www.nteu.org.au/publications/aur/4602">Aus. Uni. Rev. 46(2), pp.16-22, 2004</A>]['06], Paul Rodan:
     "The rise & fall of David Robinson as Vice-Chancellor of Monash University
     was a parable for the times. The man who defined managerialism in the
     Australian context had in 2002 seemed to be at the peak of his powers; a
     few months later he was gone in disgrace. Paul Rodan reflects on the legacy
     of a management style which, in the end, left DR with nowhere to hide."
  If you have secrets, best not to make enemies.
  (uk us isbn:0471013579; pb uk us isbn:0471013587.)

%A J. A. Eddy
%T The Maunder minimum
%J Science
%V 192
%N 4245
%P 1189-1202
%M JUN
%D 1976
%K jrnl, c1976, c197x, c19xx, zz0114, sun spot, spots, sunspot, sunspots, solar,
   activity, cycle, cycles, minimum, little ice age, Sporer, Maunder
%X "... about 1645 until 1715 was pointed out in the 1890s by G.Sporer and
   E.W.Maunder. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.192.4245.1189">doi:10.1126/science.192.4245.1189</A>]['14],
   MM@[<A HREF="http://en.wikipedia.org/wiki/Maunder_Minimum">wikip</A>]['14].

%A C. Alexander
%A S. Ishikawa
%A M. Silverstein
%T A Pattern Language
%I OUP
%P 1171
%D 1977
%K book, text, OUP, c1977, c197x, c19xx, zz0512, quote, quotation, pattern,
   patterns, compressing, form, beauty, design, building, planning,
   architecture
%X A quote, p. xliv:
   "It is essential then, once you have learned to use the language, that
   you pay attention to the possibility of compressing the many patterns
   which you put together, in the smallest possible space. You may think
   of this process of compressing patterns, as a way to make the cheapest
   possible building which has the necessary patterns in it. It is, also,
   the only way of using a pattern language to make buildings that are
   poems."   -- via P.H..
   hb us$38; uk us isbn:0195019199; uk us isbn13:978-0195019193.

%A D. Robinson
%T Alcoholism Perspective
%D 1979
%K book, text, Monash, VC, drug, alcohol, abuse, alcoholism
%X [Also search for: Robinson misconduct c1976].

%A J. Lovelock
%T Gaia: A New Look at Life on Earth
%I OUP
%P 176
%D 1979
%K book, OUP, c1979, c197x, c19xx, Gaia, climate change, pollution,
   James Lovelock, sustainability
%X "James Lovelock deftly explains his idea that life on earth functions as a
   single organism. Written for the non-scientist, Gaia is a journey through
   time and space in search of evidence with which to support a new and
   radically different model of our planet. In contrast to conventional belief
   that living matter is passive in the face of threats to its existence,
   the book explores the hypothesis that the earth's living matter-air, ocean,
   and land surfaces-forms a complex system that has the capacity to keep the
   Earth a fit place for life. ..."
   1st ed 1979.
   Revised 2000, pb us$13; uk us isbn:0192862189; uk us isbn13:978-0192862181.

%A D. Robinson
%T Drug Use and Misuse
%D 1983
%K book, text, Monash university, VC, drugs, abuse
%X [Also search for: Robinson misconduct 1976].

%A R. Middleton
%T Alexandra David-Neel: Portait of an Adventurer
%I Shambhala
%P 232
%D 1989
%K book, biography, c1989, c198x, c19xx, Alexandra David-Neel, Neal, Tibet,
   travels, Buddhism
%X 1989; pb us$18; uk us isbn:0877734135; uk us isbn13:978-0877734130.
   "... biography explores the inner journey of a woman whose outer life was a
   thrilling story of passion and adventure. Alexandra David-Neel (1868-1969),
   born in Paris to a socially prominent family, once boasted, "I learned to
   run before I could walk!" In the course of a lifetime of more than
   one hundred years, she was an acclaimed operatic soprano, a political
   anarchist, a religious reformer, an intrepid explorer who traveled in Tibet
   for fourteen years, a scholar of Buddhism, and the author of more than forty
   books. But perhaps the most intriguing of all her adventures was the
   spiritual search that led her from a youthful interest in socialism and
   Freemasonry to the teachings of the great sages of India and culminated in
   her initiation into the secret tantric practices of Tibetan Buddhism. This
   book reveals the penetrating insight and courage of a woman who surmounted
   physical, intellectual, and social barriers to pursue her spiritual quest. "
   [Also search for: Alexandra David Neel].

%A D. J. Evans
%A E. G. D. Cohen
%A G. P. Morriss
%T Probability of second law violations in shearing steady states
%J Phys. Rev. Lett.
%V 71
%P 2401-2404
%M OCT
%D 1993
%K thermodynamics, second, 2nd, law, laws, violation, c1993, c199x, c19xx,
   fluctation theorem, system, systems, entropy, order, disorder, zz0702
%X We propose a new definition of natural invariant measure for
   trajectory segments of finite duration for a many-particle system.
   On this basis we give an expression for the probability of fluctuations
   in the shear stress of a fluid in a nonequilibrium steady state far
   from equilibrium. In particular we obtain a formula for the ratio that,
   for a finite time, the shear stress reverse sign, violating the second law
   of thermodynamics. Computer simulations support this formula.
   -- [<A HREF="http://link.aps.org/abstract/PRL/v71/p2401">paper</A>][7/'02],
   -- [<A HREF="http://link.aps.org/abstract/PRL/v71/p3616">Erratum, Nov '93</A>][7/'02].
   Also see [<A HREF="http://link.aps.org/abstract/PRL/v89/e050601">paper</A>][7/'02].

%A C. Sagan
%A W. R. Thompson
%A R. Carlson
%A D. Gurnett
%A C. Hord
%T A search for life on Earth from the Galileo spacecraft
%J Nature
%V 365
%N 6448
%P 715-721
%M OCT
%D 1993
%K jrnl, c1993, c199x, c19xx, zz1013, signs, life, space, planet, earth, detect,
   detection, alien
%X "In its Dec. 1990 fly-by of Earth, the Galileo spacecraft found evidence of
   abundant gaseous oxygen, a widely distributed surface pigment with a sharp
   absorption edge in the red part of the visible spectrum, & atmospheric
   methane in extreme thermodynamic disequilibrium; together, these are strongly
   suggestive of life on Earth. Moreover, the presence of narrow-band, pulsed,
   amplitude-modulated radio transmission seems uniquely attributable to
   intelligence. These observations constitute a control experiment for the
   search for extraterrestrial life by modern interplanetary spacecraft."
   -- [<A HREF="http://dx.doi.org/10.1038/365715a0">doi:10.1038/365715a0</A>]['13].
   (NB. On earth!-) (Also see 20th ann.@[<A HREF="http://dx.doi.org/10.1038/502272a">www</A>].)

%A F. Mittelbach
%A M. Goossens
%A J.Braams
%A D.Carlisle
%A C.Rowley
%T The LaTex Companion
%I AddisonWesley
%P 560
%D 1993
%K book, text, LaTex, c1993, c199x, c19xx, text formatting, markup
%X isbn:0201541998;        [[also see seminar.sty]] via KK.
   And 2nd edn, c2004, 1120p.(!), us$54, isbn:0201362996.

%A D. E. Knuth
%T The Stanford GraphBase: A Platform for Combinatorial Computing
%I ACM Press and
%I AddisonWesley
%D 1993
%K book, text, Stanford GraphBase, sgb, graph base, c1993, c199x, c19xx, maths,
   combinatorial computing, combinatorics
%X uk us isbn:0201542757.
   sgb@[<A HREF="http://www-cs-faculty.stanford.edu/~knuth/sgb.html">stanford.edu</A>]['09].

%A P. Samuelson
%T Self-plagiarism or fair use
%J CACM
%V 37
%N 8
%P 21-25
%M AUG
%D 1994
%K jrnl, cacm, c1994, c199x, c19xx, reuse, publication, cite, citation,
   reference
%X [<A HREF="http://doi.acm.org/10.1145/179606.179731">doi:10.1145/179606.179731</A>]['05].

%A S. Bird
%A T. Mark Ellison
%T One-level phonology: autosegmental representations and rules as
   finite automata
%J Computational Linguistics
%V 20
%N 1
%P 55-90
%M MAR
%D 1994
%K jrnl, natural language, c1994, c199x, c19xx, FSA, rule, II
%X "... present a finite-state model of phonology in which automata are the
   descriptions & tapes (or strings) are the objects being described. This
   provides the formal semantics for an autosegmental phonology without
   structure-changing rules. Logical operations on the phonological domain -
   such as conjunction, disjunction, & negation---make sense since the
   phonological domain consists of descriptions rather than objects. These
   operations as applied to automata are the straightforward operations of
   intersection, union, & complement. If the arrow in a rewrite rule is viewed
   as logical implication, then a phonological rule can also be represented as
   an automaton, ..."
   -- [<A HREF="http://portal.acm.org/ft_gateway.cfm?id=972512&type=pdf&coll=GUIDE&dl=GUIDE&CFID=72844789&CFTOKEN=3224337">pdf</A>]['06],
      [<A HREF="http://markellison.net/">MarkE</A>]['06].

%A A. D. Sokal
%T Transgressing the boundaries: Towards a transformative hermeneutics of
   quantum gravity
%J Social Text
%V #46/47
%P 217-252
%D 1996
%K jrnl, spoof, fake, parody, hoax, bogus, paper, c1996, c199x, c19xx,
   postmodern, postmodernism, pseudoscience, controversial, affair,
   funny, ha ha, haha
%X see [<A HREF="http://www.physics.nyu.edu/faculty/sokal/">sokal</A>]['05].
   [Also search for: postmodernism generator].

%A J. R. Quinlan
%T Learning first-order definitions of functions
%J Artificial Intell. Res.
%V 5
%P 139-161
%D 1996
%K jrnl, AI, II, function, c1996, c199x, c19xx, ILP, FOIL, FFOIL, logic,
   functional relations
%X "First-order learning involves finding a clause-form definition of a
   relation from examples of the relation & relevant background information. In
   this paper, a particular first-order learning system is modified to
   customize it for finding definitions of functional relations. This
   restriction leads to faster learning times &, in some cases, to definitions
   that have higher predictive accuracy. Other first-order learning systems
   might benefit from similar specialization."
   -- [<A HREF="http://arxiv.org/abs/cs.AI/9610102">@arxiv</A>]['05].
   e.g. 5.1 append, last, reverse, lshift, tr;  5.2 qsort, bublesort;
        5.3 ackermann;  5.4 verb past tense

%A E. Bernstein
%A U. Vazirani
%T Quantum complexity theory
%J SIAM J. Comput.
%V 26
%N 5
%P #1411
%D 1997
%K jrnl, c1997, c199x, c19xx, zz1214, quantum computing, computer, algorithm,
   complexity, time, NP, BQP, NPC, BPP, QTM, problem,
   probabilistic, Turing machine
%X "... study quantum computation from a complexity theoretic viewpoint. Our
   first result is the existence of an efficient universal q.Turing m/c in
   Deutsch's model of a q. Turing m/c (QTM) [Proc.Roy.Soc. London Ser.A,
   400 (1985), pp.97-117].  ...  We give the first formal evidence that q.Turing
   m/c violate the modern (complexity theor.) formulation of the Church-Turing
   thesis. We show the existence of a problem, relative to an oracle, that can
   be solved in polynomial time on a q.Turing m/c, but requires superpolynomial
   time on a bounded-error probabilistic Turing m/c, & thus not in the class
   'BPP'. The class 'BQP' of languages that are efficiently decidable (with
   small error-probability) on a q.Turing m/c satisfies 'BPP subseteq BQP
   subseteq Ptime^SP'. Therefore, there is no possibility of giving a math.
   proof that q.Turing m/cs are more powerful than classical probabilistic
   Turing m/cs (in the unrelativized setting) unless there is a major
   breakthrough in complexity theory."
   -- [<A HREF="http://dx.doi.org/10.1137/S0097539796300921">doi:10.1137/S0097539796300921</A>]['14].
   (Also see, "[it] is generally suspected to be false" that
              QC can solve NPC problems in P time"
   -- QC@[<A HREF="http://en.wikipedia.org/wiki/Quantum_computer">wikip</A>][11/'14].)
   [Also search for: complexity quantum computing].

%A G. M. Wang
%A E. M. Sevick
%A E. Mittag
%A D. J. Searles
%A D. J. Evans
%T Experimental demonstration of violations of the second law of
   thermodynamics for small systems and short time scales
%J Phys. Rev. Lett.
%V 89, 050601
%M JUL
%D 2002
%K physics, entropy, thermodynamics, 2nd, law, laws, order, disorder,
   small system, microscopic, violation, fluctuation theorem, particle,
   particles, optical trap, traps, colloid, scale, time, arrow,
   c2002, c200x, c20xx, zz0702
%X "We experimentally demonstrate the fluctuation theorem, which
   predicts appreciable and measurable violations of the second law
   of thermodynamics for small systems over short time scales, by
   following the trajectory of a colloidal particle captured in an
   optical trap that is translated relative to surrounding water
   molecules. From each particle trajectory, we calculate the entropy
   production/consumption over the duration of the trajectory and
   determine the fraction of second law-defying trajectories. Our results
   show entropy consumption can occur over colloidal length and time scales."
   -- [<A HREF="http://link.aps.org/abstract/PRL/v89/e050601">paper</A>][7/'02].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Entropy/Gas/">entropy</A>].)

%E F. Suppe
%T The Structure of Scientific Theories
%I U. Illinois Press
%P 818
%D 1977
%K book, text, Frederick, philosophy of science, theory, theories
%X Matheson lib' 501 S959S2

%T Uniform Requirements for Manuscripts Submitted to Biomedical Journals:
   Writing and Editing for Biomedical Publication
%Q ICMJE
%J BMJ
%D 1978
%K c1978, c1979, c197x, c19xx, zz0618, Vancouver protocol, scientific, academic,
   scholarly, research, papers, publications, manuscipts, journals, NLM, ICMJE,
   journal editors, publish, perish
%X E.g., 'For Debate ...', BMJ, 1, 1334, 20/5/1978 [<A HREF="https://doi.org/10.1136/bmj.1.6123.1334">doi:10.1136/bmj.1.6123.1334</A>]['18].
   And later editions, e.g., at [<A HREF="http://research.ntu.edu.sg/rieo/Documents/Foundational%20Documents/Vancouver%20Protocol.pdf">www</A>]['18].
   Also see [<A HREF="http://www.icmje.org/">icmje.org</A>]['18].
   [Also search for: publish perish].

%T Longshot
%D 1981
%K movie, c1981, c198x, c19xx, foosball, table football, soccer
%X Leif Garrett, Linda Manz, Ralph Seymour; dir: E. W. Swackhamer;
   -- [<A HREF="http://www.imdb.com/title/tt0082676/">imdb</A>]['13].
   [Also search for: foosball].

%A F. Suppe
%T Semantic Conception of Theories and Scientific Realism
%I U. Illinois Press
%P 475
%D 1989
%K book, text, Frederick, philosophy of science, theory, theories
%X Matheson lib' 501 S959S

%A G. D. Birkhoff
%T Aesthetic Measure
%D 1933
%I ?
%K book, text, beauty, arts, art, maths, theory, beautiful,
   taste, (esthetics), aesthetics, esthetic, c1933, c193x, c19xx
%X via Frieder Nake, &  Jon McC
   -- [<A HREF="http://www-gap.dcs.st-and.ac.uk/~history/Mathematicians/Birkhoff.html">biog'</A>][8/'02].
   Birkhoff (1884-1944).

%A A. A. Moles
%T Information Theory and Esthetic Perception
%D 1966
%I U. of Illinois Press
%K book, text, IT, maths, beauty, arts, art, beautiful, taste, aesthetics,
   aesthetic, c1966, c196x, c19xx
%X Translated by Joel E. Cohen from the 1958 french edition,
   via Jon McC.

%A C. H. Bennett
%T Logical reversibility of computation
%J IBM J. of Res. and Dev.
%V 17
%N 6
%P 525-532
%M NOV
%D 1973
%K jrnl, c1973, c197x, c19xx, zz0714, reversible, computing, computer, machine,
   automaton, logic, gate, gates, energy, heat, dissipation, entropy, quantum,
   thermodynamics
%X "The usual general-purpose computing automaton (e.g. a Turing machine) is
   logically irreversible - its transition fn lacks a single-valued inverse.
   Here it is shown that such m/cs may he made logically reversible at every
   step, while retaining their simplicity & their ability to do general
   computations. This result is of great physical interest because it makes
   plausible the existence of thermodynamically reversible computers which could
   perform useful computations at useful speed while dissipating considerably
   less than kT of energy per logical step.  In the first stage of its
   computation the logically reversible automaton parallels the corresponding
   irreversible automaton, except that it saves all intermediate results,
   thereby avoiding the irreversible operation of erasure.  The second stage
   consists of printing out the desired output. The third stage then reversibly
   disposes of all the undesired intermediate results by retracing the steps of
   the first stage in backward order (a process which is only possible because
   the first stage has been carried out reversibly), thereby restoring the
   machine (except for the now-written output tape) to its original condition.
   The final machine configuration thus contains the desired output & a
   reconstructed copy of the input, but no other undesired data. The foregoing
   results are demonstrated explicitly using a type of three-tape Turing m/c.
   The biosynthesis of messenger RNA is discussed as a physical example of
   reversible computation."
   -- copy@[<A HREF="http://www.math.ucsd.edu/~sbuss/CourseWeb/Math268_2013W/Bennett_Reversibiity.pdf">ucsd</A>]['14].
   [Also search for: Landauer c196x].
   (Also see rev.comp@[<A HREF="http://en.wikipedia.org/wiki/Reversible_computing">wikip</A>]['14].)

%A S. M. Stigler
%T Stigler's law of eponymy
%J Trans. of the New York Acad. of Sci.
%V 39
%N 1
%S 2
%P 147-157
%M APR
%D 1980
%K jrnl, c1980, c198x, c19xx, zz0814, scientific research, publish, perish,
   credit, originator, naming, impact, discovery, reward, reputation, laws,
   Matthew effect, principle, adage, funny, quote, quotable
%X -- [<A HREF="http://dx.doi.org/10.1111/j.2164-0947.1980.tb02775.x">doi:10.1111/j.2164-0947.1980.tb02775.x</A>]['14].
   (Also see law@[<A HREF="http://en.wikipedia.org/wiki/Stigler%27s_law">wikip</A>]['14], which includes
      "'Everything of importance has been said before by
      somebody who did not discover it' is an adage
      attributed to Alfred North Whitehead[5].")
   [Also search for: Matthew effect]  and  [also search for: funny law].

%A A. Vergis
%A K. Steiglitz
%A B. Dickinson
%T The complexity of analog computation
%J Math. Comput. Simulation
%V 28
%N 2
%P 91-113
%M APR
%D 1986
%K jrnl, c1986, c198x, c19xx, zz1117, computing, computability, NPC, analog,
   analogue, algorithm, computer, Churchs, strong Church thesis, quantum
%X "We ask if analog computers can solve NP-complete problems efficiently.
   Regarding this as unlikely, we formulate a strong version of Church's
   Thesis: that any analog computer can be simulated efficiently (in
   polynomial time) by a digital computer. ...  We conclude with a comment on
   the recently discovered connection between spin glasses and combinatorial
   optimization."
   -- [<A HREF="https://doi.org/10.1016/0378-4754(86)90105-9">doi:10.1016/0378-4754(86)90105-9</A>]['17].  (ref in Shor 1995.)
   [Also search for: analogue computing].

%A C. G. Lord
%A M. R. Lepper
%A E. Preston
%T Considering the opposite: a corrective strategy for social judgment
%J J. Pers. Soc. Psychol.
%V 48
%N 6
%P 1231-1243
%M DEC
%D 1984
%K jrnl, c1984, c198x, c19xx, zz0217, human behaviour, psychology, anchoring,
   confirmation bias, biases, belief, beliefs, perseverance, debias,
   reasoning, politics, Francis Bacon
%X "It is proposed that several biases in social judgment result from a failure
   - first noted by Francis Bacon - to consider possibilities at odds with
   beliefs & perceptions of the moment. Individuals who are induced to consider
   the opposite, therefore, should display less bias in social judgment. In two
   separate but conceptually parallel experiments, this reasoning was applied to
   two domains - biased assimilation of new evidence on social issues & biased
   hypothesis testing of personality impressions. Subjects were induced to
   consider the opposite in two ways: through explicit instructions to do so &
   through stimulus materials that made opposite possibilities more salient. In
   both experiments the induction of a consider-the-opposite strategy had
   greater corrective effect than more demand-laden alternative instructions to
   be as fair & unbiased as possible. The results are viewed as consistent with
   previous research on perseverance, hindsight, & logical problem solving, &
   are thought to suggest an effective method of retraining social judgment."
   -- abs@[<A HREF="https://www.ncbi.nlm.nih.gov/pubmed/6527215">ncbi</A>]['17],
      pdf@[<A HREF="http://synapse.princeton.edu/~sam/lord_lepper_preston84_JPSP_considering-the-opposite.pdf">pr'ncet'n</A>]['17].

%A R. K. Merton
%T The Matthew effect in science, II. Cumulative advantage and the symbolism
   of intellectual property
%I ISIS
%V 79
%P 606-623
%D 1988
%K c1988, c198x, c19xx, zz0814, Matthew effect, principle, law, funny, laws,
   publish, perish, credit, impact, citation, scientific research, luck,
   investigators, inequality, rich get richer, cumulative advantage
%X "... We begin by noting a theme that runs through Harriet Zuckerman's
   hours-long interviews with Nobel laureates in the early 1960s.  It is
   repeatedly suggested in these interviews that eminent scientists get
   disproportionately great credit for their contributions to science while
   relatively unknown ones tend to get disproportionately little for their
   occasionally comparable contributions.  ..."
   -- pdf@[<A HREF="http://garfield.library.upenn.edu/merton/matthewii.pdf">U.Penn</A>]['14].
   [Also search for: publish perish]  and  [also search for: Stigler law].

%A H. M. Baum
%A A. K. Lund
%A J. K. Wells
%T The mortality consequences of raising the speed limit to 65mph on rural
   interstates
%J Am. J. Public Health
%V 79
%P 1392-1395
%M OCT
%D 1989
%K jrnl, AJPH, c1989, c198x, c19xx, road traffic, speed, speeding, limit, drive,
   driving, car, cars, US, USA, death, fatal, fatality, mortality, rates,
   accident, accidents, crash, safety, interstate, road, roads, stats
%X "As of April 1987, states were permitted to raise the speed limit on rural
   interstates to 65mph without incurring federal sanctions; 38 states [did] in
   1987. Fatality data for the months when the new limit was in effect in 1987
   were compared with fatalities in the same months of 1982-86 on rural
   interstates & other rural roads. Fatalities on rural interstates in the
   states with increased speed limits in 1987 were conservatively estimated to
   be 15% higher than they would have been if the states had retained the 55mph
   limit (95% CI=6,24). Among states that retained the 55mph limit, fatalities
   on rural interstates were 6% lower than expected (95% CI=-23,13)."
   -- [<A HREF="http://ajph.aphapublications.org/cgi/content/abstract/79/10/1392">abs</A>]['11].

%T Learning in Graphical Models (Adaptive Computation and Machine Learning)
%E M. I. Jordan
%I MITpress
%P 648
%D 1998
%K book, text, model, probability, statistics, stats, model
%X about us$63; isbn:0262600323.

%A K. Marriott
%A P. J. Stuckey
%T Programming with Constraints: an Introduction
%I MITpress
%P 476
%M MAR
%D 1998
%K book, text, intro, c1998, c199x, c19xx, constraint, CLP, CLPR
%X auth2@uniMelb; us$70; isbn:0262133415; isbn13:9780262133418.

%A R. Doll
%T Uncovering the effects of smoking: Historical perspective
%J Stat Methods Med Res
%V 7
%N 2
%M JUN
%P 87-117
%D 1998
%K jrnl, quit, health, mortality, stats, statistics, c1998, c199x, c19xx,
   1950, c195x, medical, smoke, smoking, tobacco, cigarette, cigarettes,
   lung cancer, cause, causality, effect, zz0704
%X "Tobacco was introduced into Europe from America at the end of the fifteen
   century. At first used primarily for medicinal purposes [...]  it can now be
   seen that medical evidence of the harm done by smoking has been accumulating
   for 200 years, at first in relation to cancers of the lip and mouth, and
   then in relation to vascular disease and cancer of the lung. The evidence
   was generally ignored until five case-control studies relating smoking to
   the development of lung cancer were published in 1950. [...]  The
   interpretation that smoking caused these various diseases was vigorously
   debated for some years but came to be generally accepted in respect of lung
   cancer by the late 1950s and of many other diseases in the subsequent two
   decades. ..."       [Also search for: Doll 1950].
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=9654637&dopt=Abstract">ncbi</A>][6/'04].
   [Also search for: smoking cause cancer].

%A R. P. Taylor
%A A. P. Micolich
%A D. Jonas
%T Fractal analysis of Pollock's drip paintings
%J Nature
%V 399
%P 422
%M JUN
%D 1999
%K jrnl, art, artwork, artworks, painting, abstract, Jackson Pollock,
   Blue Poles, chaos, chaotic, fractals, drip, drips, c1999, c199x, c19xx,
   zz1002
%X ...we describe an analysis of Pollock's patterns which shows, 1st,
   that they are fractal, reflecting the fingerprint of nature, &
   2nd, that the fractal dimensions increased during Pollock's career. ...
   Refs:
    Mandelbrot B. B.  The Fractal Geometry of Nature (Freeman, New York, '77)
    Ott, E.  Chaos in Dynamical Systems (Cambridge Univ. Press, '93)
   Nature:[<A HREF="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v399/n6735/full/399422a0_fs.html">www</A>][9/'02].
   UNSW:[<A HREF="http://www.phys.unsw.edu.au/PHYSICS_!/FRACTAL_EXPRESSIONISM/fractal_taylor.html">article</A>][9/'02].
        [<A HREF="http://www.phys.unsw.edu.au/STAFF/RESEARCH/taylor.html#fractal">Taylor</A>][9/'02].

%A S. Travers
%T Tomorrow To Be Brave
%I CorgiAdult
%P 352
%D 2000
%K book, Sue, Susan, world war two, La Miss, free, French Foreign Legion,
   ww2, wwII, woman, women, north africa, Koenig, biography, memoir,
   c2000, c200x, c20xx
%X Susan Travers (23/9/1909-18/12/2003) was the only ( pb, isbn:0552148148; )
   woman to have joined the French Foreign Legion.   ( hb, isbn:0743200012; )

%A M. Hirvensalo
%T Computing with quanta - impacts of quantum theory on computation
%J Theor. Computer Science
%V 287
%N 1
%P 267-298
%D 2002
%K TCS, jrnl, c2002, c200x, c20xx, quantum computer, physics, intro,
   introduction, survey, TR386, TR 386, zz1002
%O Preliminary version as TUCS TR386, Dec, 2000.
%X  ...survey article to quantum computing. ... introduction on the theory ...
   Hilbert space formalism of quantum physics. ...
   -- [<A HREF="http://www.math.utu.fi/staff/hirvensalo.htm">home</A>][10/'02].
   -- [<A HREF="http://www.tucs.fi/Publications/techreports/TR386.php">TUCS TR386</A>][10/'02].
   -- [<A HREF="http://www.elsevier.com/gej-ng//10/41/16/197/21/30/abstract.html">abs'</A>][10/'02].
   -- [<A HREF="http://www.mathematicsweb.org/mathematicsweb/show/Abstract.htt?Pu=gej%2Dng%2F10%2F41%2F16%2F258%2F27%2F42">abs'</A>][10/'02].

%A M. A. Nielsen
%A I. L. Chuang
%T Quantum Computation and Quantum Information
%I CUP
%D 2000
%K book, text, good, intro, CUP, cqc, computer, computing, physics, theory,
   qbit, qubit, qbism, qubism, quantum, information, c2000, c200x, c20xx, viaRDK
%X Anniv. ed 2011; us$71; uk us isbn:1107002176; uk us isbn13:978-1107002173.
     "... quantum algs., q.teleportation, q.cryptography & q.error-correction.
      Q.mechanics & comp.sci. are introduced before moving on to describe
      what a q.computer is, how it can be used to solve problems faster than
      'classical' computers & its real-world implementation. It concludes with
      an in-depth treatment of q.information. ..."
   Ref in Sci-Am '02.
   Also see [<A HREF="http://www.qubit.org/">qubit.org</A>][11/'02].
   [Also search for: Qbism physics].

%A R. Peto
%A S. Darby
%A H. Deo
%A P. Silcocks
%A E. Whitley
%A R. Doll
%T Smoking, smoking cessation, and lung cancer in the UK since 1950:
   Combination of national statistics with two case-control studies
%J British Med. J.
%P 323-329
%V 321
%M AUG
%D 2000
%K jrnl, BMJ, medical, medicine, smoking, tobacco, cigarettes, health, death,
   c1950, c195x, c19xx, 1950s, c2000, c200x, c20xx, stats, statistics,
   cigaratte, lung cancer, cause, mortality, health, quit, quitting
%X "To relate UK national trends since 1950 in smoking, in smoking cessation,
   & in lung cancer to the contrasting results from two large case-control
   studies centred around 1950 & 1990. [...]"
   -- [<A HREF="http://bmj.bmjjournals.com/cgi/content/full/321/7257/323">paper</A>][6/'04];
   [Also search for: Doll BMJ].

%A S. Baron-Cohen
%T Autism: deficits in folk psychology exist alongside superiority in
   folk physics
%E S. Baron-Cohen
%E H. Tager-Flusberg
%E D. Cohen
%B Understanding Other Minds: Perspectives from autism and
   developmental cognitive neuroscience
%I OUP
%D 2000
%K autism, autistic, Asperger's, BaronCohen, Tager-Flusberg, psychology
%X www.psychiatry.cam.ac.uk

%A S. Baron-Cohen
%T Theory of mind and autism: a fifteen-year review
%B Understanding Other Minds: Perspectives from autism and
   developmental cognitive neuroscience
%I OUP
%D 2000
%K autism, autistic, Asperger's, mind, psychology, BaronCohen
%X [<A HREF="http://www.psychiatry.cam.ac.uk">www</A>]['04].

%A S. Baron-Cohen
%T The cognitive neuroscience of autism: Implications for the evolution of
   the male brain
%E M. Gazzaniga
%B The Cognitive Neuroscience
%I MITpress, 2nd edn
%D 2000
%K autism, autistic, Asperger's, development
%X www.psychiatry.cam.ac.uk

%T Complex Systems
%E T. R. J. Bossomaier
%E D. G. Green
%I CUP
%M JUL
%D 2000
%K book, text, CUP, c2000, c200x, c20xx, system, L-systems, self-organisation,
   Alife
%X uk us isbn:0521462452.
   -- [<A HREF="http://titles.cambridge.org/catalogue.asp?isbn=0521462452">cup</A>]['04].
   [Also search for: Alife].

%A H. Cobban
%T The Moral Architecture of World Peace: Nobel Laureates Discuss
   our Global Future
%I U. Press of Virginia
%D 2000
%K book, Helena Cobban, war, c2000, c200x, c20xx, Dalai Lama, Tutu, culham,
   politics, conflict, prize, NobelPrize,
%X <!-- Hcobban at aol com, 1/2005 -->us$25, isbn:0813919878.
   -- [<A HREF="http://www.people.virginia.edu/~hc3z/">auth</A>]['05],
      [<A HREF="http://www.upress.virginia.edu/books/cobban.html">press</A>]['05].

%A M. Prior
%A A. Sanson
%A D. Smart
%A F. Oberklaid
%T Pathways from infancy to adolescence:
   Australian temperament project 1983-2000
%I Australian Institute of Family Studies
%D 2000
%K book, report, c2000, c200x, c20xx, AIFS, family, child, development,
   adolescent, adolescents, pathway, behaviour, parent, parents
%X au$16.50, isbn:0642394784.
   -- [<A HREF="http://www.aifs.gov.au/atp/">@aifs</A>]['05].
   "... initial sample comprised 2443 families from urban and rural areas
   of [Vic]. ...  born Sept'82 to Jan.'83. ..."

%A A. Purvis
%A A. Hector
%T Getting the measure of biodiversity
%J Nature
%V 405
%P 212-219
%M MAY
%D 2000
%K jrnl, diversity, biology, biological, biol, c2000, c200x, c20xx, ecology,
   review, survey, intro, introduction, evolution, taxa, ImperialCollege
%X "...'biodiversity' is a simple contraction of 'biological diversity', & at
   1st sight the concept is simple too: biod. is the sum total of all biotic
   variation from the level of genes to ecosystems. The challenge comes in
   measuring such a broad concept in ways that are useful. ... although biod.
   can never be fully captured by a single number, study of particular facets
   has led to rapid, exciting & sometimes alarming discoveries. Phylogenetic &
   temporal analyses are shedding light on the ecological & evolutionary
   processes that have shaped current biod.. There is no doubt that humans are
   now destroying this d. at an alarming rate. A vital question now being
   tackled is how badly this loss affects ecosystem functioning. Although
   current research efforts are impressive, they are tiny in comparison to the
   amount of unknown diversity & the urgency and importance of the task."
   -- [<A HREF="http://dx.doi.org/10.1038/35012221">doi:10.1038/35012221</A>]['05],
      [<A HREF="http://www.bio.ic.ac.uk/research/apurvis/ajpurvis.htm">ajp</A>]['05].

%A J. T. Kim
%T LindEvol: Artificial models for natural plant evolution
%J Kunstliche Intelligenz, Special Issue on Textmining
%V 1/2000
%P 26-32
%D 2000
%K Alife, A-life, plant, model, LindEvol, DDC, c2000, c200x, c20xx, uniEA, UEA,
   biodiversity, diversity, distance distribution complexity, DDC
%X [<A HREF="http://www.cmp.uea.ac.uk/people/jtk">auth@UEA</A>]['07].
   Inc. 'distance distribution complexity' (DDC) =
        entropy of rel. abundances of distance values between genomes.
   [Also search for: Alife].

%A T. D. Gedeon
%T Clustering significant words using their co-occurrence in
   document sub-collections
%J Proc. 7th European Congress on Intelligent Techniques and Soft Computing
%P 302-306
%D 1999
%K conf, EUFIT99, EUFIT, c1999, c199x, c19xx, word, collection, index
%X auth @ CS ANU as of ['05].

%A M. Moore
%T Stupid White Men ... and Other Sorry Excuses for the State of the Nation!
%I ReganBooks
%M FEB
%D 2002
%K book, popular, fun, funn, funny, ha ha, haha, politics, satire, social,
   commentary, USA, America, c2002, c200x, c20xx, zz1202
%X isbn:0060392452.

%A D. Anderson
%A R. Johnson
%A L. Saha
%T Changes in academic work: Implications for universities of the changing
   age distribution and work roles of academic staff
%I Commonealth Dept. of Education, Science and Training (Australia)
%P 168
%M DEC
%D 2002
%K DEST, DETYA, CEDAM, ANU, higher education, ed, teaching, university,
   standards, plagiarism, cheat, cheating, copying, work load, workload,
   quality, au, G8, c2002, c200x, c20xx, zz0103
%X [summary] "... the overall picture is of frustration and disillusionment,
   to the point where many respondents to a questionnaire said they would not
   recommend an academic career to anyone.
   [p.36] ...perception of academics is that standards are lower than they were
   10 or 20 years ago but that the decline is not dramatic.  ... many
   respondents believe the top students to be as good as they ever were ...
   a proportion of new students are less able than previously and not well
   prepared for university study.
   [p.44, 4.6] ... Judging from media accounts ... plagiarism may have increased
   in recent years. ... we were told that the practice has increased because
   ... of wide availability of electronic text. "
   -- [<A HREF="http://www.detya.gov.au/highered/otherpub/academic_work.pdf">.pdf</A>][1/'03],
   -- [<A HREF="http://www.anu.edu.au/cedam/agerole/academicwork.html">at ANU</A>][1/'03] [Authors at `CEDAM', ANU].

%A H. J. Morowitz
%T The Emergence of Everything: How the World Became Complex
%I OUP
%P 209
%M NOV
%D 2002
%K book, complex systems, zz0103, c2002, c200x, c20xx, OUP
%X about us$28; uk us isbn:019513513X.

%T Tragically I was an Only Twin - The Complete Peter Cook
%E W. Cook
%I Century (RandomHouse)
%P 468
%M OCT
%D 2002
%K book, good, comedy, funny, fun, haha, ha ha, beyond the fringe, complete,
   not only but also, Pete, Dud, Derek, Clive, zz0203, c2002, c200x, c20xx
%X `The funniest man who ever drew breath' -- Stephen Fry.
   Not only, uk us isbn:0712623981. stg18.   Ed. W.Cook (no relation).
   but also, uk us isbn:0099443252.

%A B. Schwartz
%A A. Ward
%A J. Monterosso
%A S. Lyubomirsky
%A K. White
%A D. R. Lehman
%T Maximizing versus satisficing: Happiness is a matter of choice
%J J. of Personality & Social Psychology
%V 83
%N 5
%P 1178-1197
%M NOV
%D 2002
%K jrnl, happy, happiness, contentment, choice, choices, freedom, consumer,
   well being, wellbeing, human, c2002, c200x, c20xx, zz0304
%X "Can people feel worse off as the options they face increase? [...] studies
   suggest that some people - maximizers - can. [...] maximization scale, which
   measures individual differences in desire to maximize. 7 samples ...
   negative correlations between maximization & happiness, optimism,
   self esteem, & life satisfaction, & positive correlations between
   maximization and depression, perfectionism, & regret. ... maximizers
   less satisfied than nonmaximizers (satisficers) with consumer decisions, &
   more likely to engage in social comparison. ... maximizers more adversely
   affected by upward social comparison. ... maximizers more sensitive to
   regret & less satisfied [...]. The interaction between maximizing & choice
   is discussed in terms of regret, adaptation, and self-blame."
   -- [<A HREF="http://www.swarthmore.edu/SocSci/award1/">Ward home</A>][3/'04].
   See [<A HREF="http://www.psycinfo.com/psycarticles/">psycinfo.com</A>][3/'04] ?account?
   [Also search for: happiness well being].

%T Why Bother?: Sir Arthur Streeb-Greebling Interviewed by Chris Morris
%I BBC Audio
%S BBC Radio Collection (spoken word)
%M MAR
%D 1999
%K Peter Cook, CD, funny, fun, haha, ha ha, Sir Arthur Streeb-Greebling,
   interview, beeb, BBC radio, c1999, c199x, c19xx
%X "Originally broadcast on Radio 4 in January 1994, this is a collection of
   five ten-minute interviews with Peter Cook's comic creation, Sir Arthur
   Streeb-Greebling, who reminisces about his life and career as statesman,
   scholar and tycoon. They formed Cook's final radio series."
   Audio, asin:0563558601.
   [Also search for: Peter Cook].

%A J. R. Petit
%A et al ...
%A M. Stievenard
%T Climate and atmospheric history of the past 420,000 years from the Vostok
   ice core, Antarctica
%J Nature
%V 399
%N 6735
%P 429-436
%M JUN
%D 1999
%K jrnl, c1999, c199x, c19xx, climate, variability, change, CO2, Lake Vostok,
   Antarctica, ice core, ice age, ages, interglacial, level, temperature, dust,
   MIS 11, MIS11, greenhouse gas, gases, record
%X "The recent completion of drilling at Vostok station in E.Antarctica has
   allowed the extn of the ice record of atmospheric composition & climate to
   the past four glacial-interglacial cycles. The succession of changes through
   each climate cycle & termination was similar, & atmospheric & climate
   properties oscillated between stable bounds. Interglacial periods differed
   in temporal evolution & duration. Atmospheric concentrations of CO2 & methane
   correlate well with Antarctic air-temp. throughout the record. Present-day
   atmospheric burdens of these two important greenhouse gases seem to have been
   unprecedented during the past 420,000 years."
   -- [<A HREF="http://dx.doi.org/10.1038/20859">doi:10.1038/20859</A>]['13].
   (Also see Vostak@[<A HREF="http://en.wikipedia.org/wiki/Vostok,_Antarctica">wikip</A>][13],
   and ice_age@[<A HREF="http://en.wikipedia.org/wiki/Ice_age">wikip</A>][13].)

%A N. Chomsky
%T Powers and Prospects: Reflections on human nature and the social order
%I SouthEnd
%P 244
%M JUL
%D 1999
%K book, text, Noam Chomsky, c1999, c199x, c19xx, zz0214, power, prospect,
   power, prospect, AI, Turing test, intelligence, mind, convergence,
   democracy, politics
%X 1st ed 1999; hb us$38; uk us isbn:0896085368; uk us isbn13:978-0896085367.
   Also see excerpts
   "... Adopting this approach, suppose we are interested in deciding whether
   a programmed computer can play chess or understand Chinese. We construct a
   variant of the Turing test, & see whether a jury can be fooled into
   thinking that a human is carrying out the observed performance. If so, we
   will have 'empirically established' that the computer can play chess, ...
   according to proponents of this version of [AI], while their critics deny
   that this result would establish the conclusion.
   There is a great deal of often heated debate about these matters in the
   literature of the cognitive sciences, [AI], & philosophy of mind, but it is
   hard to see that any serious question has been posed. The question of whether
   a computer is playing chess, ... is like the question of whether robots can
   murder or airplanes can fly ...
   There is no answer to the question whether airplanes really fly (though
   perhaps not space shuttles). Fooling people into mistaking a submarine for
   a whale doesn't show that submarines really swim; nor does it fail to
   establish the fact. There is no fact, no meaningful question to be answered,
   as all agree, in this case. The same is true of computer programs, as Turing
   took pains to make clear in the 1950 paper ... Here he pointed out that the
   question whether m/cs think 'may be too meaningless to deserve discussion,'
   being a question of decision, not fact, though he speculated that in 50 y.,
   usage may have 'altered so much that one will be able to speak of machines
   thinking without expecting to be contradicted' - as in the case of airplanes
   flying (in English, at least), but not submarines swimming. Such alteration
   of usage amounts to the replacement of one lexical item by another one with
   somewhat different properties. There is no empirical question as to whether
   this is the right or wrong decision. ..."   [via ArunK & ErikN].
   -- [<A HREF="http://www.chomsky.info/books/prospects01.htm">www</A>]['14].
   [Also search for: AlanTuring c1950].

%A V. S. Ramachandran
%T Phantoms in the Brain: Probing the Mysteries of the Human Mind
%I HarperPerennial
%D 1999
%K book, text, c1999, c199x, c19xx, mind, brain, hallucination, phantom,
   voices
%X 1st ed 1999. uk us isbn:0688172172.
   [Also search for: psychology hallucination].

%A J. Kruger
%A D. Dunning
%T Unskilled and unaware of it: How difficulties in recognizing one's own
   incompetence lead to inflated self-assessments
%J J. of Personality and Social Psychology
%V 77
%N 6
%P 1121-1134
%M DEC
%D 1999
%K jrnl, c1999, c199x, c19xx, zz0716, human, behaviour, psychology, confidence,
   beliefs, overconfidence, competence, incompetence, level, skill, expertise,
   ability, performance, judgement, IgNobel, Dunning Kruger effect,
   quote, quotable
%X "People tend to hold overly favorable views of their abilities in many
   social & intellectual domains. [We] suggest that this overestimation occurs,
   in part, because people who are unskilled in these domains suffer a dual
   burden: Not only do these people reach erroneous conclusions & make
   unfortunate choices, but their incompetence robs them of the metacognitive
   ability to realize it. Across 4 studies, ... found that participants scoring
   in the bottom quartile on tests of humor, grammar, & logic grossly overest.
   their test performance & ability. Although their test scores put them in the
   12th percentile, they estimated themselves to be in the 62nd. Several
   analyses linked this miscalibration to deficits in metacognitive skill, or
   the capacity to distinguish accuracy from error. Paradoxically, improving the
   skills of the participants, & thus increasing their metacognitive competence,
   helped them recognize the limitations of their abilities."  (via AK.)
   -- [<A HREF="http://dx.doi.org/10.1037/0022-3514.77.6.1121">doi:10.1037/0022-3514.77.6.1121</A>]['16].
   Also see DKe@[<A HREF="https://en.wikipedia.org/wiki/Dunning%E2%80%93Kruger_effect">wikip</A>]['16] ...
   "Real knowledge is to know the extent of one's ignorance", Confucius.
   "The Foole doth thinke he is wise, but the wise man knowes himselfe to
    be a Foole", Shakespeare.
   "Ignorance more frequently begets confidence than does knowledge",
    Charles Darwin.
   "One of the painful things about our time is that those who feel certainty
    are stupid, and those with any imagination and understanding are filled with
    doubt and indecision", Bertrand Russell.
   (And different, but [also search for: Peter principle].)

%A P. V. Spade
%T The Cambridge Companion to Ockham
%I CUP
%D 1999
%K book, text, c1999, c199x, c19xx, zz1117, William of Ockham, Occam,
   Ochham's razor, Ockhams, monk, philosophy, religion
%X uk us isbn13:978-0521582445.
   [<A HREF="https://doi.org/10.1017/CCOL052158244X">doi:10.1017/CCOL052158244X</A>]['17].
   (Also see Ockham@[<A HREF="http://www.allisons.org/ll/Images/People/Ockham/">www</A>].)

%A L. Kurke
%T Ancient Greek board games and how to play them
%J Classical Philology
%V 94
%N 3
%P 247-267
%M JUL
%D 1999
%K jrnl, c1999, c199x, c19xx, zz1223, ancient, Greeks, board game, games, old,
   pessoi, historical, history
%X "THE PAULY-WISSOWA ARTICLE on ancient board games ('lusoria tabula') is over
   a thousand columns long. It meticulously catalogues the literary &
   archaeological evidence, details the shapes of boards & pieces, &
   reconstructs the forms of play ..."
   -- [<A HREF="https://www.jstor.org/stable/270405">jstor:270405</A>]['23].
   (Also see board-games@[<A HREF="https://en.wikipedia.org/wiki/Board_game">wikip</A>]['23].)

%A E. Farhi
%A J. Goldstone
%A S. Gutmann
%A M. Sipser
%T Quantum computation by adiabatic evolution
%J arXiv
%M JAN
%D 2000
%K arXiv, TR, c2000, c200x, c20xx, Dwave, zz0514, quantum computing,
   annealing, controversial, adiabatic, Rose
%X "We give a quantum alg. for ... the satisfiability problem, based on
   adiabatic evolution. The evoln of the quantum state is governed by a time-
   -dependent Hamiltonian that interpolates between an initial H., whose ground
   state is easy to construct, & a final H., whose ground state encodes the
   satisfying assignment. To ensure that the system evolves to the desired final
   ground state, the evoln time must be big enough. The time required depends on
   the min. energy difference between the two lowest states of the interpolating
   H.. We are unable to est. this gap in general. We give some special symmetric
   cases of the sat.problem where the symmetry allows us to est. the gap & we
   show that, in these cases, our alg. runs in polynomial time."
   -- [<A HREF="http://arxiv.org/abs/quant-ph/0001106">arXiv</A>]['14].
   [Also search for: Dwave quantum computing] and
   [also  search for: quantum annealing].
   (Also see [<A HREF="http://www.bbc.com/news/science-environment-27264552">bbc</A>][19/5/'14].)

%A S. Brenner
%T Hard cases
%J Current Biology
%V 10
%N 4
%P R127
%M FEB
%D 2000
%K news, views, c2000, c200x, c20xx, Science, Nature, scientific research,
   impact factor, journal, publish, perish, Nascence, peer review,
   referees, refereeing
%X "Excerpt from the transcript of the trial of T.Cobley et al. vs the Editors
   and Publishers of Nascence, before Lord Justice Abel.
      Mr R. Gument Q.C.: May it please your Lordship I appear for the
   plaintiffs, T.Cobley et al. in this action.
      The facts are straightforward and simply recounted. On or about the 10th
   of October 2000, the plaintiffs submitted a typescript of a scientific paper
   to the editors of the journal Nascence. ... The plaintiffs claim that by not
   being able to publish in Nascence, they have suffered injury to their
   professional careers and are claiming compensatory damages. It can be argued
   that this is the fate of many scientists and that their claims should be
   rejected just as their paper was, but we intend to establish that the
   plaintiffs were wrongfully excluded, that they were unable to confront the
   negative referee directly and that the Editor was negligent in not checking
   the validity of this referee's statements. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/S0960-9822(00)00394-8">doi:10.1016/S0960-9822(00)00394-8</A>]['14].

%A S. Mertens
%T A physicist's approach to number partitioning
%J TCS
%V 265
%N 1-2
%P 79-108
%D 2001
%K jrnl, TCS, c2001, c200x, c20xx, NP, NPC, hard problems, phase transition,
   number, set, partitioning, partition
%X "The statistical physics approach to the number partioning problem, a
   classical NP-hard problem, is both simple and rewarding. Very basic notions
   & methods from stat.mech. are enough to obtain analytical results for the
   phase boundary that separates the "easy-to-solve" from the "hard-to-solve"
   phase of the NPP as well as for the probability distributions of the optimal
   & sub-optimal solns. [and] it can be shown that solving a NPP of size N to
   some extent corr. to locating the minimum in an unsorted list of O(2**N)
   numbers. Considering this correspondence it is not surprising that known
   heuristics for NPP are not sig. better than simple random search. "
   -- [<A HREF="http://dx.doi.org/10.1016/S0304-3975(01)00153-0">doi:10.1016/S0304-3975(01)00153-0</A>]['10].
     (Given a (multi)set, S, of N +ve ints, partition S into S1 and S2,
      s.t. the sum of numbers in S1 and in S2 are the same -- if possible.
      Related: minimise the difference.)

%A S. Baron-Cohen
%A S. Wheelwright
%A R. Skinner
%A J. Martin
%A E. Clubley
%T The autism spectrum quotient (AQ): evidence from Asperger syndrome/
   high-functioning autism, males and females, scientists and mathematicians
%J J. Autism & Developmental Disorders
%V 31
%N 1
%P 5-17
%M FEB
%D 2001
%K jrnl, autistic, Asperger's syndrome, AQ, EQ, c2001, c200x, c20xx, science,
   FQ, scientist, mathematics, mathematician, engineering, engineer, maths,
   Cambridge, study, BaronCohen, Aspergers, engineers, psychology, stats,
   questionaire, survey, test, statistics, zz1004
%X "...a new instrument to assess this: the Autism-Spectrum Quotient (AQ).
   Individuals score in the range 0-50.  Four groups of subjects were assessed:
   1: 58 adults with Asperger syndrome (AS) or high-functioning autism (HFA);
   2: 174 randomly selected controls.   3: 840 students in Cam U.; &
   4: 16 winners of the UK Mathematics Olympiad. The adults with AS/HFA had a
   mean AQ score of 35.8 (SD=6.5), significantly higher than Group 2 controls
   (M=16.4, SD=6.3). 80% of the adults with AS/HFA scored 32+, v. 2% of
   controls. Among the controls, men scored slightly but significantly higher
   than women. No women scored extremely highly (AQ score 34+) whereas 4% of
   men did so. Twice as many men (40%) as women (21%) scored at intermediate
   levels (AQ score 20+). Among the AS/HFA group, male & female scores did not
   differ significantly. The students in Cambridge University did not differ
   from the randomly selected control group, but scientists (including
   mathematicians) scored significantly higher than both humanities & social
   sci students, confirming an earlier study that autistic conditions are
   associated with scientific skills. Within the sciences, mathematicians
   scored highest. This was replicated in Group 4, the Mathematics Olympiad
   winners scoring sig'y higher than the male Cam humanities students...."
   -- [<A HREF="http://dx.doi.org/10.1023/A:1005653411471">doi:10.1023/A:1005653411471</A>][10/'04].
   [Also see B-C & W c2004] [<A HREF="http://www.autismresearchcentre.com/papers/2001_BCetal_AQ.pdf">paper.pdf@autismresearchcentre.com</A>]['04] (subsc'n)
   (Erratum: J Autism Dev Disord 2001 Dec;31(6):603 (auths @ psych cam u).)

%A E. Farhi
%A et al
%A D. Preda
%T A quantum adiabatic evolution algorithm applied to random instances of an
   NP-Complete problem
%J arXiv
%M APR
%D 2001
%K jrnl, c2001, c200x, c20xx, zz0223, MIT, quantum computing, annealing, NPC,
   adiabatic, Hamiltonian
%X "A quantum system will stay near its instantaneous ground state if the
   Hamiltonian that governs its evolution varies slowly enough. This q.adiabatic
   behavior is the basis of a new class of algs. for q.computing. We test one
   such alg. by applying it to randomly generated, hard, instances of an NPC
   problem. For the small examples that we can simulate, the q.adiabatic alg.
   works well, & provides evidence that q.computers (if large ones can be built)
   may be able to outperform ordinary computers on hard sets of instances of NPC
   problems."
   -- [<A HREF="https://doi.org/10.48550/arXiv.quant-ph/0104129">arXiv</A>]['23] (13 refs);
   also see [<A HREF="https://doi.org/10.1126/science.1057726">doi:10.1126/science.1057726</A>]['23] APR 2001.
   [Also search for: quantum annealing].

%A B. Briedis
%A T. D. Gedeon
%T Approximating vectors for similarity searching
%J J. of System Research and Information Sys.
%V 10
%P 89-112
%D 2001
%K jrnl, JSRIS, approximate, vector, c2001, c200c, c20xx, search
%X TG @ anu ['04].

%A S. Levy
%T Hackers: Heroes of the Computer Revolution
%I Penguin
%P 464
%D 2001
%K book, c2001, c200x, c20xx, MIT, hack, hacker, hacking, computer, cracking,
   hero
%X "... follows members of an MIT model railroad club - a group of brilliant
   budding electrical engineers and computer innovators - from the late 1950s to
   the mid-1980s. These eccentric characters used the term "hack" to describe a
   clever way of improving the electronic system that ran their massive
   railroad. And as they started designing clever ways to improve computer
   systems, "hack" moved over with them. ..."
   2nd ed 2001; pb us$11; uk us isbn:0141000511; uk us isbn13:978-0141000510.

%A M. Gladwell
%T The Tipping Point
%I BackBay
%P 301
%M JAN
%D 2002
%K book, c2002, c200x, c20xx, tipping point, change, behaviour, social,
   marketing, sales, advertising, popular, trend, trends
%X "The tipping point is that magic moment when an idea, trend, or social
   behavior crosses a threshold, tips, and spreads like wildfire. Just as a
   single sick person can start an epidemic of the flu, so too can a small but
   precisely targeted push cause a fashion trend, ..."
   1st ed 2002; pb us$11; uk us isbn:0316346624; uk us isbn13:978-0316346627.

%T Biometric Authentication
%E D. Maltoni
%E A. K. Jain
%I Springer
%S LNCS
%V 2359
%D 2002
%K face, faces, recognition, finger print, prints, c2002, c200x, c20xx,
   fingerprint, signature, biometrics, verification, verify, authenticate
%X issn:0302-9743

%A Y. Z. Ding
%A M. O. Rabin
%T Hyper-encryption and everlasting security
%J 19th Annual Symp. on Theoretical Aspects of Comp. Sci.
%P 1-26 ?
%D 2002
%I SpringerVerlag
%S LNCS
%V 2285
%K conf, hyperencryption, security, cypher, cipher, c2002, c200x, c20xx,
   bounded, storage model

%A G. Luttgen
%A W. Vogler
%T Bisimulation on speed: Worst-case efficiency
%J Information and Computation
%P ?-?
%V ?
%D 2002 to appear
%K CCS, TACS, time, asynchronous systems, process algebra, algebras,
   Gerald Luttgen, uniYork, c2002, c200x, c20xx, timing, performance, jrnl
%X "...novel bisim'n based faster than preorder... relative speed of sys's
   components are indeterminate. ... TACS ..."
   -- [<A HREF="http://www-users.cs.york.ac.uk/~luettgen/publications/IandC2002.pdf">pp.pdf@cs.york.ac.uk</A>][9/'04].

%A D. H. Rothman
%T Atmospheric carbon dioxide levels for the last 500 million years
%J PNAS
%V 99
%N 7
%P 4167-4171
%M APR
%D 2002
%K jrnl, PNSA, c2002, c200x, c20xx, climate, variability, change, CO2,
   atmosphere, greenhouse gas, gases
%X "The last 500 million y. of the strontium-isotope record are shown to
   correlate significantly with the concurrent record of isotopic fractionation
   between inorganic & organic carbon after the effects of recycled sediment are
   removed from the strontium signal. The correlation is shown to result from
   the common dependence of both signals on weathering & magmatic processes.
   Because the long-term evolution of carbon dioxide levels depends similarly on
   weathering & magmatism, the relative fluctuations of CO2 levels are inferred
   from the shared fluctuations of the isotopic records. The resulting CO2
   signal exhibits no systematic correspondence with the geologic record of
   climatic variations at tectonic time scales."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.022055499">doi:10.1073/pnas.022055499</A>]['13].
   (Also see CO2@[<A HREF="http://en.wikipedia.org/wiki/Carbon_dioxide_in_Earth%27s_atmosphere">wikip</A>]['13].)
   [Also search for: cause global warming].

%E S. J. Lomonaco jr.
%T Quantum Computation: A Grand Mathematical Challenge for the
   Twenty-First Century and the Millenium
%I AMS
%V 58
%P 358
%D 2002
%O Proc. Symp. in Applied Math, 2000
%K conf, c2002, c200x, c20xx, 21C, Shor, factoring, factors, Grover, search,
   book, quantum computing, computer, algorithm, zz0904
%X us$70; us isbn:0821820842;
   review in [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_47/Issue_02/470270.sgm.abs.html">compj@oup.co.uk</A>][p.270,v47(2),Mar,'04].
   "...2 q-algs (Shor's factoring alg, and Grover's search alg) are rep'd in a
   math rigorous way. ...  in a strict sense it could be stated that the rep'd
   q-algs are the only ones that exist! ..."
   [Also search for: quantum computing].

%A H. S. Warren jr.
%T Hacker's Delight
%I AddisonWesley
%P 306
%D 2002
%K book, text, c2002, c200x, c20xx, hacker's delight, hackers, code, source,
   algorithms, tricks, techniques, efficient, fast, computer programming
%X 1st ed 2002, hb us$31; uk us isbn:0201914654; uk us isbn13:978-0201914658.
   "A collection useful programming advice the author has collected over
   the years; small algorithms that make the programmer's task easier."

%A A. Pedahzur
%A A. Perliger
%A L. Weinberg
%T Altruism and fatalism: The characteristics of Palestinian suicide terrorists
%J Deviant Behavior: An Interdisciplinary J.
%V 24
%P 405-422
%D 2002
%K terrorism, terror, c2002, c200x, c20xx, bomb, bomber, database, data base,
   threat, behaviour
%X "... Based on a newly established database compiled for this  purpose which
   includes info. based on terrorists from '93 until the beginning of '02, fit
   the "altruistic" type as well as some elements from the "fatalistic" &
   represent a combination of both types; thus they can be labeled under a new
   category of "fatalistic altruistic" suicide." -- auth1,2@u.haifa, 3@u.Nevada
   -- [<A HREF="http://www.comm.cornell.edu/als481/readings/characteristics.pdf">pdf@cornell</A>][10/'05].
     [<A HREF="http://terrorismexperts.org/terrorism_research_suicide1.htm">www</A>][10/'05].
     [<A HREF="http://dx.doi.org/10.1080/01639620390195240">doi:10.1080/01639620390195240</A>]['02]?

%A A. B. Krueger
%A J. Maleckova
%T Education, poverty, political violence and terrorism: Is there a
   causal connection?
%I National Bureau of Economic Res.
%R NBER Working Paper No. 9074
%M JUL
%D 2002
%K TR, NBER, terrorist, c2002, c200x, c20xx, stats, model, Hezbollah, militant,
   Lebanon, conflict, background, living, school, schooling
%X "... analyze data on support for attacks against Israeli targets from public
   opinion polls conducted in the West Bank & Gaza Strip. These polls indicate
   that support for violent attacks does not decrease among those with higher
   education & higher living standards. ... stat. analysis of the determinants
   of participation in Hezbollah militant activities in Lebanon. ... suggests
   that having a living standard above the poverty line or a 2ndry school or
   higher ed. is +ve assoc. with participation in Hezbollah. ...Jewish settlers
   who attacked Palestinians in the West Bank in the early '80s were
   overwhelmingly from high-paying occupations. ..."
   -- [<A HREF="http://papers.nber.org/papers/W9074">nber</A>]['05].
      [<A HREF="http://www.pcpsr.org/survey/cprspolls/94/poll13a.html">CPRS poll #13</A>]['05].

%A D. Michie
%T Colossus and the breaking of the wartime "fish" codes
%J Cryptologia
%V 26
%N 1
%P 17-58
%D 2002
%K jrnl, c2002, c200x, c20xx, WWII, WW2, cryptology, German, Fish, Tunny,
   Lorenz, Testery, code, breaking, cypher, cipher, Ultra, Donald Michie,
   Bletchley Park, Colossus computer, history, WW2, WWII, cryptanalysis
%X [<A HREF="http://dx.doi.org/10.1080/0161-110291890740">doi:10.1080/0161-110291890740</A>]['10],
   dm@[<A HREF="http://www.aiai.ed.ac.uk/~dm/">ed ac uk</A>]['10],
   [Also search for: Lorenz Testery]  and  [also search for: Bletchley Park].
   (According to J.Robets, Colossus did only one of the code-breaking steps.)
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">B.Park</A>].)

%A B. Foster
%A M. Foster
%T The Secret Lives of Alexandra David-Neel: A Biography of the Explorer of
   Tibet and Its Forbidden Practices
%I OverlookTP
%P 352
%D 2002
%K book, text, biography, c2002, c200x, c20xx, Alexandra David-Neel, Tibet,
   Lhasa, Buddhism, trek, travel, travels
%X 2002; pb us$47; uk us isbn:1585673293; uk us isbn13:978-1585673292.
   "... David-Neel (18681969), the French Tibetophile who was the first European
   woman to explore the once forbidden (to foreigners) city of Lhasa. ... opens
   as a movie might, on David-Neel's surreptitious departure from Lhasa in
   May 1924, after having entered illegally following a perilous journey.
   Succeeding chapters flash back to her childhood, marriage, and first journeys
   east, culminating in the great trek by foot to Lhasa. The final chapters on
   the end of her life, back in France, also review her major writings, which
   include autobiography, novels, translations of Tibetan texts, and studies of
   Buddhism. ..."
   [Also search for: Alexandra David Neel].

%A A. G. Bedeian
%T The Dean's Disease: How the darker side of power manifests itself in the
   office of Dean
%J Academy  of Management Learning and Education
%V 1
%N 2
%P 164-173
%D 2002
%K jrnl, c2002, c200x, c20xx, zz0619, university, management, faculty, dean,
   deans, deanlet, deanitis, power, ethics, corrupts, academic, academia,
   research, impact, KPI, KPIs, higher education
%X "Commentators since the time of Greek dramatist Sophocles have noted that the
   exercise of power often produces strong psychological changes in people. As
   power holders, deans comprise far too few exceptions to this insight. Early
   in their tenure new deans are generally grateful for the confidence placed in
   them by their former colleagues & are eager to work together in changing
   "the system" to eliminate unjust privileges and practices. But soon feelings
   of overwhelming gratitude & oneness become faint memories. Within months of
   taking office, such feelings undergo a transformation so subtle that those
   affected are unaware of changes in their thinkingand behavior. ..."
   -- [<A HREF="https://doi.org/10.5465/AMLE.2002.8509359">doi:10.5465/AMLE.2002.8509359</A>]['19],
      [<A HREF="https://pdfs.semanticscholar.org/8f68/045fc589816a327607b4267e96ad7673bf2f.pdf">sem'schol</A>]['19].
   [Also search for: university management].

%A J. Skoyles
%A D. Sagan
%T Up from Dragons
%I McGrawHill
%D 2002
%K book, c2002, c200x, c20xx, modern, human, brain, mind, thought, evolution,
   behaviour, psychology, neuroscience, ape, apes, consciousness, conscious,
   prefrontal cortex
%X 1st ed 2002; hb uk us isbn:0071378251.

%A G. Heut
%T Sri Yantra geometry
%J TCS
%V 281
%N 1-2
%P 609-628
%M JUN
%D 2002
%K jrnl, TCS, c2002, c200x, c20xx, zz0710, Sri Yantra geometry, tantric, tantra,
   Hindu, Hinduism, sacred diagram, vahni, Purusha, sakti, lotus, padma, yantra,
   symbol
%X "... Sri Yantra is an under-determined Euclidean plane geometry problem with
   4 real params, admitting an infinity of solns around the Classical S.Y. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/S0304-3975(02)00028-2">doi:10.1016/S0304-3975(02)00028-2</A>]['10],
   inc. p'stscript source.

%A L. Prechelt
%A G. Malpohl
%A M. Philippsen
%T Finding plagiarisms among a set of programs with JPlag
%J J. Universal Computer Science
%V 8
%N 11
%D 2002
%K jrnl, eJrnl, c2002, c200x, c20xx, zz0622, JPlag, plagiarism detector,
   program, teaching, greedy string tiling
%X "... web service that finds pairs of similar programs among a given set
  of programs. ...  Greedy String Tiling ..."
   -- [<A HREF="http://www.ipd.kit.edu/tichy/uploads/publikationen/16/finding_plagiarisms_among_a_set_of_progr_638847.pdf">www</A>['22].
   Also see jplag@[<A HREF="https://github.com/jplag/jplag">github</A>]['22] &
   see TR2000-1@[<A HREF="https://publikationen.bibliothek.kit.edu/542000">kit.edu</A>]['22].
   [Also search for: plagiarism detector].

%A N. T. Spark
%T The fastest man on earth, why everything you know about
   Murphy's law is wrong
%J Annals of Improbable Research
%V 9
%N 5
%M SEP/ OCT
%D 2003
%K jrnl, Murphy, Murphys, laws, Stapp, c2003, c200x, c20xx, zz1003,
   igNobel, prize, prizes, physics, www, HREF, http, funny, fun, Stapp,
   c1949, c194x, stuff up
%X Was at
   www.improbable.com/airchives/paperair/volume9/v9i5/murphy/murphy0.html 2003
   but try [<A HREF="https://www.improbable.com/">improbable</A>]['22]?
   ... The late John Paul Stapp, the late Edward A. Murphy, Jr., and
   George Nichols, for jointly giving birth in 1949 to Murphy's Law,
   the basic engineering principle that "If there are two or more ways to
   do something, and one of those ways can result in a catastrophe, someone
   will do it" (or, in other words: "If anything can go wrong, it will")
   -- from 2003 IgNobel prizes for Physics [<A HREF="http://www.improbable.com/ig/ig-pastwinners.html#ig2003">ig</A>][10/'03].
   [Also search for: Murphy law]  and  [also search for: funny law].

%A R. E. Neapolitan
%T Learning Bayesian Networks
%I PrenticeHall
%P 674
%D 2003
%K book, text, probability, statistics, stats, net, nets, network, Bnet, Bnets,
   AI, II, c2003, c200x, c20xx
%X About us$70; uk us isbn:0130125342.
   (BTW, also see [<A HREF="http://www.allisons.org/ll/Publications/2006AI/">CaMML</A>].)

%A M. Croarken
%T Mary Edwards: Computing for a living in 18th-century England
%J Annals of the History of Computing
%I IEEE
%P 9-15
%V 25
%N 4
%M OCT-DEC
%D 2003
%K jrnl, c2003, c200x, c20xx, woman, women, computer, computor, computing,
   Nautical Almanac, 18C, c18xx, zz0304, table, tables, navigation, www,
   science, STEM
%X "The production of astronomical tables is an ancient activity, one
   requiring a great deal of mathematical computation. During the 18th
   century, production of these tables increased & the British government
   hired human computers to prepare the tables of the annual Nautical Almanac.
   From 1765 to 1811, the Nautical Almanac employed 35 computers; only one,
   Mary Edwards, was a woman, whose story is told here."
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/MAHC.2003.1253886">doi:10.1109/MAHC.2003.1253886</A>]['10] ?subscr?.
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Mary_Edwards_(human_computer)">wikip</A>]['14].)
   [computer, computor = one who computes.]
   [Also search for: women computing].

%A P. Laureti
%A P. Ruch
%A J. Wakeling and Y.-C. Zhang
%T The interactive minority game: A web-based investigation of
   human market interactions
%J Physica A: Statistical Mechanics and its Applications
%P 651-659
%V 331
%N 3-4
%D 2003
%K jrnl, physicaa, games, theory, decision-making, market, markets, model,
   models, prediction, c2003, c200x, c20xx, zz0404
%X "... Hundreds of individuals have played a total of tens of thousands of
   game turns against computer-controlled agents in the web-based interactive
   Minority Game. The analytical understanding of the MG permits fine-tuning
   of the market situations encountered, allowing for investigation of human
   behaviour in a variety of controlled environments. In particular, our
   results indicate a transition in players' decision-making, as the markets
   become more difficult, between deductive behaviour making use of short-term
   trends in the market, & highly repetitive behaviour that ignores entirely
   the market history, yet outperforms random decision-making."
   -- [<A HREF="http://dx.doi.org/10.1016/j.physa.2003.07.002">doi:10.1016/j.physa.2003.07.002</A>][4/'04].

%A L. Soldatova
%A R. Mizoguchi
%T Testing of understanding by use of an ontology methodology
%J Proc. of Joint Workshop of Cognition and Learning,
%W Berlin
%P 202-205
%D 2003
%K conf, Larissa Soldatova, c2003, c200x, c20xx, zzOSP, zOSP04, ontology,
   ontological, systematic, test, teach, teaching, student, learn, Bloom,
   Blooms, model, education
%X "... test composition approach to determine the level of a student's
   understanding, based on a test ontology. Domain independent & domain
   dependent parts of the student's model are described. To improve the
   diagnostic of student knowledge we used the 6-layers Bloom's model of
   understanding. Reusable components & steps of the test construction are
   listed. This approach is an example of "function integration" To validate
   the approach a pedagogical experiment was carried out at Vladivostok State
   Uni., Russia. ..."
   -- [<A HREF="http://www.ei.sanken.osaka-u.ac.jp/pub/larisa/TU.pdf">pdf@osaka-u.ac.jp</A>][8/'04].
   (auth1 @ U. Wales, Aberystwyth 2OO4.)

%A R. Lister
%A J. Leaney
%T Introductory programming, criterion-referencing, and Bloom
%J Proc. 34th SIGCSE Technical Symp. on Comp. Cci. Education
%W Nevada
%P 143-147
%D 2003
%K computer programming, introduction, curriculum design, c2003, c200x, c20xx,
   zz0904, prac, pracs, practical work, norm, criterion, referenced, Bloom,
   CS101, CS1, ability, test, tests, teaching
%X "In the trad' norm-referencing approach to grading, all students in a CS1
   class attempt the same prog' tasks,& those attempts are graded "to a curve".
   The danger is that such tasks are aimed at a hypothetical average student.
   Weaker students can do little of these tasks, & learn little. [But] these
   tasks do not stretch the stronger students, so they too are denied an
   opportunity to learn. Our solution is 2-fold.  1st, we use a criterion-
   referenced approach, where fundamentally different tasks are set, according
   to the ability of the students.  2nd, the differences in the nature of the
   tasks reflect the differing levels of Bloom's taxonomy. Weaker CS1 students
   are simply required to demonstrate knowledge & comprehension; the ability to
   read & understand programs. Middling students attempt traditional tasks,
   while the stronger students are set open-ended tasks at the synthesis &
   evaluation levels."  isbn:158113648X.  auths at U. Tech., Sydney, .au
   -- [<A HREF="http://doi.acm.org/10.1145/611892.611954">doi:10.1145/611892.611954</A>][9/'04].

%A C. Cresswell
%T Mathematics and Sex
%I AllenAndUnwin
%M SEP
%D 2003
%K book, c2003, c200x, c20xx, popular, math, maths, sex, sexual, love,
   marriage, relationships, mate selection
%X .au 9/2003, pb, au$25, isbn:1741141591;  UK early c2005.
   ...For several years a Visiting Fellow at the School of Maths, UNSW...
   [also search for: mate selection].

%A S. Baron-Cohen
%A S. Wheelwright
%T The friendship questionnaire: An investigation of adults with Asperger
   syndrome or high-functioning autism, and normal sex differences.
%J J. of Autism and Developmental Disorders
%V 33
%N 5
%P 509-517
%M OCT
%D 2003
%K jrnl, friend, friends, survey, autism, autistic, male, female, gender,
   FQ, AQ, EQ, difference, brain, men, women, social, relationships,
   theory of mind
%X "...The FQ has a maximum score of 135 & a minimum of zero. In Study 1, we
   carried out a study of n=76 (27 m & 49 f) adults from a general pop'n, to
   test for previously reported sex differences in friendships. This confirmed
   that women scored significantly higher than men. In Study 2, we employed the
   FQ with n=68 adults (51 m, 17 f) with Asperger Syndrome or high-functioning
   autism to test the theory that autism is an extreme form of the m brain. The
   adults with Asperger Syndrome or high-functioning autism scored sig' lower
   on the FQ than both the m & f controls from Study 1.The FQ thus reveals both
   a sex difference in the style of friendship in the general population, &
   provides support for the extreme m brain theory of autism."
   -- [<A HREF="http://dx.doi.org/10.1023/A:1025879411971">doi:10.1023/A:1025879411971</A>]['04] (subsc'n).
   Also look for B-C and W (auths in psych at cam U.).

%A A. M. M. S. Ullah
%T Different facets of a computational equivalent of genetic addition
%J Biosystems
%V 68
%N 1
%P 31-41
%M JAN
%D 2003
%K jrnl, biol, biology, c2003, c200x, c20xx, molecule, system, DAS, simulation
%X "...biol. inspired system called DNA Addition System (DAS). The sys. consists
   of 4 elements: a chain molecule; a set of free (elemental) molecules, all of
   which refer to the elements of DNA; a quasi-free molecule, which is the last
   elemental molecule of the chain molecule; & a molecular machine. When the
   system works, a definite reconfiguration, referred to as addition, takes
   place. Addition actually adds a free molecule to the chain molecule to make
   it grow longer. The molecular machine decides which type of free molecule
   should be added taking into account the informational state of the system. A
   simulation model is also developed based on DAS to help generate chain
   molecule applying successive additions. This model can be used to simulate
   chain molecules that exhibit the characteristics of genetic molecules (i.e.
   molecules with identifiable segments) & behaviors of dynamical systems...."
   auth @ UAE Univ.

%A H. Mayell
%T When did "modern" behaviour emerge in humans?
%J National Geographic News
%M FEB
%D 2003
%K news, views, c2003, c200x, c20xx, human, behaviour, evolution, origins,
   modern, humans, apes, Africa, migration, language, mind, brain
%X "Around 50,000 y. ago, modern humans suddenly started leaving Africa. Over
   the course of the next 20,000 y., Homo sapiens pushed other hominid species
   to extinction & established populations in Australia, Asia, & Europe.
   What spurred Homo sapiens to leave Africa after living there for at least
   70,000 y.? ..."
   -- [<A HREF="http://news.nationalgeographic.com/news/2003/02/0220_030220_humanorigins2.html">Nat.Geog.</A>]['12].

%A W. L. Kuechler
%A M. G. Simkin
%T How well do multiple choice tests evaluate student understanding in
   computer programming classes?
%J Jnl. Information Systems Education
%V 14
%N 4
%P 389-399
%D 2003
%K jrnl, computing, IT, information technology, teaching, test, testing, exam,
   exams, examination, MCQ, question, questions, gender, male, female,
   c2003, c200x, c20xx
%X via R o b y n  M..
   -- [<A HREF="http://www.jise.appstate.edu/14/389-Abstract.pdf">abs.pdf@appstate.edu</A>]['05].
   (ProQuest document ID: 544863081)

%A K. Devlin
%T Why universities require computer science students to take math
%J CACM
%V 48
%N 9
%P 36-39
%M SEP
%D 2003
%K CACM, math, maths, mathematics, Comp Sci, CSci, computer science,
   curriculum, education, discipline, c2003, c200x, c20xx, zz0605,
   University, education
%X "The main benefit of learning and doing mathematics is that it develops the
   ability to reason about formally defined abstract structures like those in
   computer science and its applications. ..."
   -- [<A HREF="http://doi.acm.org/10.1145/903893.903917">doi:10.1145/903893.903917</A>]['05].
   [Also search for: CACM SEP c2003].

%A K. B. Bruce
%A R. L. Scot Drysdale
%A C. Kelemen
%A A. Tucker
%T Why math?
%J CACM
%V 48
%N 9
%P 40-44
%M SEP
%D 2003
%K CACM, math, maths, mathematics, Comp Sci, CSci, computer science,
   curriculum, education, discipline, c2003, c200x, c20xx
%X "The mathematical thinking, as well as the mathematics, in a Comp. Sci.
   education prepares students for all stages of system development, from
   design to the correctness of the final implementation."
   -- [<A HREF="http://doi.acm.org/10.1145/903893.903918">doi:10.1145/903893.903918</A>]['05].
   [Also see: CACM SEP c2003].

%A P. B. Henderson
%T Mathematical reasoning in software engineering education
%J CACM
%V 48
%N 9
%P 45-50
%M SEP
%D 2003
%K CACM, math, maths, mathematics, Comp Sci, CSci, computer science, SWE,
   curriculum, education, discipline, computing, c2003, c200x, c20xx
%X "Discrete mathematics, especially logic, plays an implicit role in software
   engineering similar to the role of continuous mathematics in traditional
   physically based engineering disciplines."
   -- [<A HREF="http://doi.acm.org/10.1145/903893.903919">doi:10.1145/903893.903919</A>]['05].
   [Also see: CACM SEP c2003].

%A V. L. Almstrum
%T What is the attraction to computing?
%J CACM
%V 48
%N 9
%P 51-55
%M SEP
%D 2003
%K CACM, math, maths, mathematics, Comp Sci, CSci, computer science,
   motivation, interests, interest, student, students, enrollment,
   recruit, recruiting, marketing, c2003, c200x, c20xx
%X "The strongest motivators include a sense of accomplishment from solving
   problems and programming; the weakest include being captivated by the Web
   and a passion for playing computer games."
   -- [<A HREF="http://doi.acm.org/10.1145/903893.903920">doi:10.1145/903893.903920</A>]['05].
   [Also see: CACM SEP c2003].

%A D. Kral
%A R. Skrekovski
%T A theorem about the channel assignment problem
%J SIAM J. Discrete Maths
%V 16
%N 3
%P 426-437
%D 2003
%K jrnl, c2003, c200x, c20xx, graph coloring, list-coloring, colouring,
   channel assignment problem, zz1105
%X "A list channel assignment problem is a triple (G,L,w), where G is a graph,
   L is a fn which assigns to each vertex of G a list of ints (colors), & w is
   a fn which assigns to each edge of G a positive int. (its weight).A coloring
   c of the vertices of G is proper if c(v)\in L(v)$ for each vertex v &
   $|c(u)-c(v)|\ge w(uv)$ for each edge uv. A weighted degree $\deg_w(v)$ of a
   vertex v is the sum of the weights of the edges incident with v. If G is
   connected, $|L(v)|>\deg_w(v)$ for at least one v, & $|L(v)|\ge\deg_w(v)$
   for all v, then a proper coloring always exists. A list channel assignment
   problem is balanced if $|L(v)|=\deg_w(v)$ for all v. We characterize all
   balanced list channel assignment problems (G,L,w) which admit a proper
   coloring. An application of this result is that each graph with max. degree
   $\Delta\ge 2$ has an L(2,1)-labeling using ints $0,\ldots,\Delta^2+\Delta-1$"
   -- [<A HREF="http://epubs.siam.org/sam-bin/dbq/article/39944">siam</A>]['05].

%A W. Visser
%A K. Havelund
%A G.Brat, S.Park, F.Lerda
%T Model checking programs
%J Automated Software Engineering J.
%V 10
%N 2
%P ?-?
%M APR
%D 2003
%O Proc. 15th IEEE Int. Conf. on Automated Software Eng. (ASE'00)
%K jrnl, c2003, c200x, c20xx, models, program, verification, Java Pathfinder,
   JPF, analysis, slicing, ASE00
%X [<A HREF="http://ti.arc.nasa.gov/people/wvisser/ase00FinalJournal.pdf">@nasa</A>]['05].
   See [<A HREF="http://javapathfinder.sourceforge.net/">javapathfinder@sourceforge</A>]['05].
   "... we will attempt to give convincing arguments for why we believe it is
   time for the formal methods community to shift some of its attention towards
   the analysis of programs written in modern programming languages. ...we have
   developed a verification & testing environment for [JPF] which integrates
   model checking, program analysis & testing. Part of this work has consisted
   of building a new Java Virtual Machine that interprets Java bytecode. JPF
   uses state compression to handle big states, & partial order reduction,
   slicing, abstraction, & runtime analysis techniques to reduce the state
   space. JPF has been applied to a real-time avionics operating system dev. at
   Honeywell, illustrating & intricate error, & to a model of a spacecraft
   controller, illustrating the combination of abstraction, runtime analysis, &
   slicing with model checking." -- ASE00 ?subscrn?
   -- [<A HREF="http://dx.doi.org/10.1109/ASE.2000.873645">doi:10.1109/ASE.2000.873645</A>]['05].

%A S. Atran
%T Genesis of suicide terrorism
%J Science
%V 299
%N 5612
%P 1534-1539
%M MAR
%D 2003
%K review, survey, introduction, terror, terrorist, c2003, c200x, c20xx,
   origin, cause, characteristics, suicide, bomb, bomber, zz1005
%X "... Recent research indicates [suicide terrorists] have no appreciable
   psychopathology & are as educated & economically well-off as surrounding
   populations. A 1st line of defense is to get the communities from which
   suicide attackers stem to stop the attacks by learning how to minimize the
   receptivity of mostly ordinary people to recruiting organizations."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1078854">10.1126/science.1078854</A>]['05].
   -- [<A HREF="http://www.rcgd.isr.umich.edu/faculty/atran.htm">auth</A>]['05].
   -- [<A HREF="http://www.sitemaker.umich.edu/satran/files/suicide_terrorism_database_2004.xls">2004, inc. 103 cases Iraq, .xls</A>]['05].

%A J. G. Wolff
%T Information compression by multiple alignment, unification and search as a
   unifying principle in computing and cognition.
%J Artificial Intelligence Review
%V 19
%N 3
%P 193-230
%M MAY
%D 2003
%K jrnl, c2003, c200x, c20xx, ICMAUS, SP61, AI
%X "... overview of the idea that info. compression by multiple alignment,
   unification & search(ICMAUS) may serve as a unifying principle in computing
   (including math. & logic) & in such aspects of human cognition as the
   analysis & production of natural lang., fuzzy pattern recognition & best
   match info. retrieval, concept hierarchies with inheritance of attributes,
   probabilistic reasoning, & unsupervised inductive learning. The ICMAUS
   concepts are described together with an outline of the SP61 s/w model in
   which the ICMAUS concepts are currently realised. A range of e.g. presented,
   illustrated with output from the SP61 model."
   -- [<A HREF="http://dx.doi.org/10.1023/A:1022865729144">doi:10.1023/A:1022865729144</A>]['05], auth @ UW Bangor.

%A J. Woodward
%T Evolving Turing complete representations
%J Conf. Evol. Comp.
%M JUN
%D 2003
%K conf, CEC, CEC03, c2003, c200x, c20xx, zz1016, AI, II, automatic, genetic,
   programming, program, programs, automaticProgramming, geneticProgramming,
   inference, learning, learn
%X "Standard GP, chiefly concerned with evolving functions, which are mappings
   from inputs to output, is not Turing Complete. We raise issues resulting from
   attempts at extending standard GP to Turing Complete representations. Firstly
   there is a problem when a contiguous piece of code is moved to a new
   location (in a different program) by crossover. In general its functionality
   will be altered if global memory is used, as other parts of the program may
   access the same piece of memory. Secondly, trad. crossover does not
   respect modules. Crossover can disrupt a group of instructions that were
   working together (e.g. in the body of a loop) in one parent, but end up
   separated in two different offspring after reproduction. A crossover operator
   is proposed that only operates at the boundaries of modules. The
   identification of module boundaries is made easy by using a representation in
   which explicit modules are denned[?], in contrast with other representations
   where the module boundaries would have to be identified by some other means.
   The halting problem is a central issue, however as a consequence of this
   crossover operator we are more likely to produce self terminating programs,
   thus saving time when testing."  [via JG].
   -- [<A HREF="http://dx.doi.org/10.1109/CEC.2003.1299753">doi:10.1109/CEC.2003.1299753</A>]['16]($$$).
   (auth@[<A HREF="https://scholar.google.com/citations?user=iZIjJ80AAAAJ">gScholar</A>]['16], was @ UBirmingham, @ StirlingU as of '16.)

%A U. Ratnayake
%A T. D. Gedeon
%T Extending the recommendation architecture model for text mining
%J Int. J. of Knowledge-Based Intelligent Engineering Systems
%V 7
%N 3
%P 139-148
%M JUL
%D 2003
%K jrnl, c2003, c200x, c20xx, text data mining, AI, connectionist
%X ["The Recommendation Architecture (RA) model is a new connectionist approach
   simulating some aspects of the human brain. Application of the RA to a real
   world problem is a novel research problem and has not been previously
   addressed in literature. Research conducted with simulated data has shown
   much promise for the [RA] model's ability in pattern discovery & pattern
   recognition. This thesis investigates the application of the RA model for
   text mining where pattern discovery and recognition play an important role.
   -- from R's Ph.D. [<A HREF="http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20040713.113844">thesis</A>] abs, c2004.

%A R. Axelrod
%A R. A. Hammond
%T Evolution of ethnocentric behavior
%J Midwest Political Science Convention
%P ?-?
%M APR
%D 2003
%K conf, c2003, c200x, c20xx, alife, racism, evolution, cooperation, IPD,
   iterated prisoners dilemma, prisoner's, in-group, out-group, reciprocity,
   behaviour, tribe, tribal, zz0407
%X "Behaviors associated with ethnocentrism include cooperation with members of
   the in-group, but not out-groups. We show that ethnocentric behavior can
   emerge from a simple evolutionary model of local competition between
   individuals. Our agent-based model treats interactions as 1-move Prisoner's
   Dilemmas, and the inheritance of strategies as genetic, cultural, or (most
   plausibly) both. Results from the model demonstrate that e. behavior can
   evolve even when direct reciprocity is impossible, opportunities for
   "cheating" exist, & agents have minimal cognitive ability. When cooperating
   is relatively costly, ethnocentric behavior can even be necessary to sustain
   cooperation."
   -- [<A HREF="http://www-personal.umich.edu/~axe/">auth@umich</A>]['07] inc pdf.
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A R. D. Gray
%A Q. D. Atkinson
%T Language-tree divergence times support the Anatolian theory of Indo-European
   origin
%J Nature
%V 426
%P 435-439
%M NOV
%D 2003
%K jrnl, c2003, c200x, c20xx, natural language, human, origings, migration,
   phylogeny, phylogenetic tree, evolution, Indo, European, Europe, India,
   languages, Kurgan, Anatolian farming
%X "Languages, like genes, provide vital clues about human history. The origin
   of the Indo-European language family is 'the most intensively studied, yet
   still most recalcitrant, problem of historical linguistics'. Numerous genetic
   studies of Indo-European origins have also produced inconclusive results.
   Here ... test two theories of I.-E. origin: the 'Kurgan expansion' & the
   'Anatolian farming' hypotheses. The K.theory centres on ... expansion into
   Europe & the Near East by Kurgan horsemen beginning in the sixth millennium
   BP. ... the Anatolian theory claims that I.-E. languages expanded with the
   spread of agriculture from Anatolia around 8,000-9,500 years bp. In striking
   agreement with the Anatolian hypothesis, our analysis of a matrix of 87
   languages with 2,449 lexical items produced an est.age range for the initial
   I.-E. divergence of between 7,800 and 9,800 years bp. These results were
   robust to changes in coding procedures, calibration pts, rooting of the trees
   and priors in the bayesian analysis."
   -- [<A HREF="http://dx.doi.org/10.1038/nature02029">doi:10.1038/nature02029</A>]['11].
   [Also search for: natural language evolution].

%A N. Bostrom
%T Are we living in a computer simulation?
%J The Philosophical Quarterly
%V 53
%N 211
%P 243-255
%D 2003
%K jrnl, c2003, c200x, c20xx, zz0916, philosophy, metaphysics, human existence,
   think therefore, life, posthuman, computer simulation
%X "I argue that at least one of the following propositions is true: (1) the
   human species is v.likely to become extinct before reaching a 'posthuman'
   stage; (2) any posthuman civilization is extremely unlikely to run a sig. #
   of simulations of its evolutionary history (or variations thereof); (3) we
   are almost certainly living in a computer simulation. It follows that the
   belief that there is a sig. chance that we shall one day become posthumans
   who run ancestor-simulations is false, unless we are currently living in a
   simulation. I discuss some consequences of this result."
   -- [<A HREF="http://dx.doi.org/10.1111/1467-9213.00309">doi:10.1111/1467-9213.00309</A>]['16],
   NB@[<A HREF="https://en.wikipedia.org/wiki/Nick_Bostrom">wikip</A>]['16],
   NB@[<A HREF="http://www.nickbostrom.com/">www</A>]['16].
   (?Just when was that 'Red Dwarf' episode?)

%A M. Allen
%T Liability for climate change
%J Nature
%V 421
%N 6926
%P 891-892
%M FEB
%D 2003
%K news views, c2003, c200x, c20xx, zz0220, climate change, global warming, CO2,
   world, extreme weather, attribution, cause, causation, causality, storms,
   flooding, flood, floods, temperature, drought
%X -- [<A HREF="https://doi.org/10.1038/421891a">doi:10.1038/421891a</A>]['20].
   [Also search for: extreme weather attribution].

%A N. Hurst
%A K. Marriot
%A P. Moulder
%T Cobweb: A constraint based web browser
%J ACSC
%V 35
%W Adelaide
%P 247-254
%D 2003
%K conf, ACSC, c2003, c200x, c20xx, Cobweb, constraint programming, CLP,
   njHurst, constraints, render, page, www, browser
%X "... Cobweb, which we believe is the first web page renderer based on
   constraint-solving technology. One-way constraints are used to specify
   position and style attributes of the document elements. Our implementation
   demonstrates how constraint solving provides a unifying technology for the
   rendering of web pages. It also demonstrates that constraint solving
   inherently supports viewer interaction with the document and that constraints
   allows more flexible and powerful specification of document layout, in
   particular complex text-flow, than is available with existing technologies."
   -- pdf@[<A HREF="https://dl.acm.org/doi/10.5555/783106.783134">ACM</A>]['22],
      was www.acs.org.au/documents/public/crpit/CRPITV16Hurst.pdf ['10].

%A J. Armstrong
%T The Secret Power of Beauty: Why Happiness is in the Eye of the Beholder
%I Penguin
%P 192
%M JAN
%D 2004
%K book, c2004, c200x, c20xx, beauty, perception, appearance, form
%X about stg13; uk us isbn:0713994746.

%T Regional Security in the Asia Pacific. 9/11 and After
%E D. Wright-Neville
%E M. Vicziany
%E P. Lentini
%I EdwardElgar
%D 2004
%K book, text, terror, terrorism, terrorist, c2004, c200x, c20xx, bomb,
   bombs, threat
%X W.N. is <!--  David.WrightNeville arts monash edu au --> @Mon@sh['05].

%A H. T. Tavani
%T Ethics and Technology
%I Wiley
%D 2004
%P 344
%K book, text, c2004, c200x, c20xx, information, communication, privacy,
   cyberspace, zz0104, copyright, copy-right, intellectual property, theft,
   zzLaw, crime, security
%X uk us isbn:0471249661, (pbk).  uk us isbn:0471452505, (WIE).

%A H. Fisher
%T Why We Love: The Nature and Chemistry of Romantic Love
%I Henry Holt
%P 320
%M FEB
%D 2004
%K book, psychology, behaviour, human, norepinephrine, dopamine, seratonin,
   marriage, divorce, evolution, biology, biol, c2004, c200x, c20xx
%X about us$30;  isbn:0805069135.

%A M. Schneider
%A J. Gersting
%T Invitation to Computer Science
%I Brooks Cole
%M FEB
%D 2004
%P 736
%K book, text, CS, CSci, Comp. Sci., L3ref, L4ref, zz0404
%X pb, au$85, isbn:0534419941.

%A A. Svilaas
%A A. Kaur Sakhi, L. Frost Andersen, T. Svilaas,
   E. C. Strom, D. R. Jacobs, Jr., L. Ose, R. Blomhoff
%T Intakes of antioxidants in coffee, wine, and vegetables are correlated with
   plasma carotenoids in humans
%J J. Nutrition
%V 134
%P 562-567
%D 2004
%K jrnl, drink, drinking, health, medical, human, c2004, c200x, c20xx, intake,
   coffee, tea, diet, antioxidant, beta-carotene, alpha-tocopherol, stats,
   zzCoffee, positive, statistics, human, zz1104
%X "... objective...study was to determine the contribution of various food
   groups to total antioxidant intake ... collected 7-d weighed dietary records
   in a group of 61 adults with corresponding plasma samples, & used data from
   a nationwide survey of 2672 Norwegian adults based on an extensive FFQ. The
   total intake of antioxidants was 17 mmol/d with beta-carotene, alpha-
   tocopherol, & vitamin C contributing < 10%. ... coffee contributed 11.1 mmol,
   followed by fruits (1.8 mmol), tea (1.4 mmol), wine (0.8 mmol), cereals
   (i.e., all grain containing foods; 0.8 mmol), & vegetables (0.4 mmol).
   ...agree with the hypothesis that dietary antioxidants other than the well-
   known antioxidants contribute to our antioxidant defense. Surprisingly, the
   single greatest contributor to the total antioxidant intake was coffee."
   -- [<A HREF="http://www.nutrition.org/cgi/content/abstract/134/3/562">subn or us$8</A>][10/'04].
   [Also search for: zzCoffee].

%A R. Doll
%A R. Peto
%A J. Boreham
%A I. Sutherland
%T Mortality in relation to smoking: 50 years' observations on male
   British doctors
%J British Med. J.
%P ?-?
%V ?
%D 2004
%K jrnl, BMJ, health, medical, medicine, smoking, health, tobacco, cigarettes,
   death rates, rate, c2004, c200x, c20xx, zz0704, statistics, stats, age,
   cigarette, lung cancer, cause, quit, quitting
%X "[...] 34,439 male British doctors. Information about their smoking habits
   was obtained in 1951, & periodically thereafter; cause specific mortality
   was monitored for 50 years.  [...]   A substantial progressive decrease in
   the mortality rates among non-smokers over the past half century (due to
   prevention & improved treatment of disease) has been wholly outweighed,
   among cigarette smokers, by a progressive increase in the smoker v.
   non-smoker death rate ratio due to earlier & more intensive use of
   cigarettes. Among the men born around 1920, prolonged cigarette smoking from
   early adult life tripled age specific mortality rates, but cessation at age
   50 halved the hazard, & cessation at age 30 avoided almost all of it."
   -- [<A HREF="http://dx.doi.org/10.1136/bmj.38142.554479.AE">doi:10.1136/bmj.38142.554479.AE</A>][6/'04] online 6/2004.

%A K. Todd
%T Historical study of correlation between A-level grades and
   subsequent performance
%D 2004
%K maths, mathematics, standards, standard, level, levels, Alevels, Alevel,
   decline, curriculum, UK, science, engineering, c2004, c200x, c20xx, stats,
   statistics, PIP, score, scores, school, schools, university, York, uniYork
%X "The subject of A-Level mathematics has attracted a great deal of political
   and academic controversy. Those who represent the academic community in
   Higher Education have argued for over a decade that the standards of A-Level
   mathematics have been declining and continue to do so. Elsewhere it has been
   argued that much of the decline perceived by those who teach in engineering
   and science departments is more likely to be attributed to the very
   substantial national decline in entry standards to engineering and science
   courses rather than any real change in A-Level standards. Using available
   statistics, a study of the electronics students at York set out to discover
   whether these questions could be answered and the results were published in
   a detailed paper [1] of which the following is a summary."
   "... The long term picture is very clear. A student with an A at A-Level
   mathematics today will, on average, obtain a score on our test which would
   have placed them near the bottom of the cohort fifteen years ago...."
   -- [<A HREF="http://www.mathcentre.ac.uk/resources/casestudies/mathsteam/todd.pdf">pdf@mathcentre.ac.uk</A>][8/'04] auth' at York U.
   [1] An Historical Study of the Correlation between G.C.E. Advanced Level
       Grades and the Subsequent Academic Performance of Well Qualified
       Students in a University Engineering Department,
       Mathematics Today. 37(5), Todd, K. L., October (2001).

%A A. M. Frisch
%A C. Jefferson
%A B. Martinez-Hernandez
%A I. Miguel
%T The rules of modelling: Towards automatic generation of constraint programs
%J Proc. of the 3rd Int. Workshop on Modelling and
   Reformulating Constraint Satisfaction Problems
%D 2004
%K wShop, constraints, programming, program, problem, generate, specification,
   CSP, decision variable, CONJURE, ESSENCE, uniYork, zzOSP, zOSP04
%X "... to apply [CP] to a particular domain, the problem 1st must be modelled
   as a constraint sat' or opt'n problem. ..."
   -- [<A HREF="http://www-users.cs.york.ac.uk/ianm/docs/Rules.pdf">pdf@cs.york.ac.uk/ianm</A>]['04].
   Alan F.,  Chris J.,  Bernadatte M. H.,  Ian M..

%A J. Bigaard
%A K. Frederiksen
%A A. Tjonneland, B. L. Thomsen, K. Overvad, B.L. Heitmann, T. I. Sorensen
%T Waist and hip circumferences and all-cause mortality: usefulness of
   the waist-to-hip ratio?
%J Int. J. Obes. Relat. Metab. Disord.
%P 741-747
%M JUN
%D 2004
%K jrnl, obesity, fat, health, death, rate, rates, medical, stats, statistics,
   health, risk, risks, hip, hips, waist, ratio, BMI, weight
%X "... DESIGN: A Danish prospective cohort study with data collected between
   1993 & 1997. SUBJECTS: A total of 27,179 men & 29,875 women born in D. &
   aged 50-64 ... followed for a median of 6.8 years. MEASUREMENTS: BMI, waist
   & hip circumferences at baseline. RESULTS: The associations between hip
   circumference & all-cause mortality were inverse for both men & women, but
   only after adjustment for waist circumference or BMI, or both. The mortality
   rate ratios of mutually adjusted waist & hip circumferences were 0.63
   (95% CI: 0.56, 0.71), & 0.70 (95% CI: 0.63, 0.79) times higher per 10%
   larger hip circumference in men & women, respectively, & 1.45 (95% CI: 1.34,
   1.57) & 1.22 (95% CI: 1.14, 1.31) times higher per 10% larger waist
   circumference. ...  CONCLUSION: When mutually adjusted, waist & hip circ's
   show opposite associations with all-cause mortality, probably due to
   different effects of adipose tissue in the abdominal & gluteofemoral regions.
   The waist-to-hip ratio cannot always capture these relations adequately."
   -- [<A HREF="http://www.cancer.dk/epi/publikationer/">www.cancer.dk/epi/</A>]['04].

%A M. Ahlgren
%A M. Melbye
%A J. Wohlfahrt
%A T. I. A., Sorensen
%T Growth patterns and the risk of breast cancer in women
%J New England J. Medicine
%P 1619-1626
%V 351
%N 16
%M OCT
%D 2004
%K jrnl, medical, health, women, pattern, height, weight, risk, risks, stats,
   statistics, growth, zz1004
%X "... Adult height & body-mass index influence the risk of b.c. in women.
   Whether these associations reflect growth patterns of the fetus or growth
   during childhood & adolescence is unknown. ...investigated the association
   between growth during childhood & the risk of b.c. in a cohort of 117,415
   Danish women. ... High birth weight, high stature at 14y, low body-mass
   index (BMI) at 14y, & peak growth at an early age were independent risk
   factors for breast cancer. Height at 8y & the increase in h during puberty
   (8 to 14y) were also associated with b.c.. The attributable risks of birth
   weight, h at 14y, BMI at 14y, & age at peak growth were 7%, 15%, 15%, & 9%,
   respectively. No effect of adjusting for age at menarche, age at 1st
   childbirth, & parity was observed. Conclusions: Birth w & growth during
   childhood & adolescence influence the risk of b.c.." [Ahlgren, abk @ ssi dk]
   -- [<A HREF="http://content.nejm.org/cgi/content/short/351/16/1619">nejm.org</A>]['04].

%A S. Baron-Cohen
%A S. Wheelwright
%T The empathy quotient: An investigation of adults with Asperger syndrome or
   high functioning autism, and normal sex differences
%J J. Autism and Developmental Disorders
%V 34
%N 2
%P 163-175
%M APR
%D 2004
%K jrnl, autistic, Aspergers, BaronCohen, EQ, sex, gender, difference, stats,
   men, women, male, female, adult, test, survey, development, AQ, statistics,
   FQ, social difficulties, emotion, theory of mind, c2004, c200x, c20xx,
   sympathy, psychology
%X "...new self-report questionnaire, the Empathy Quotient (EQ), for use with
   adults of normal intelligence. It contains 40 empathy items & 20 filler/
   control items. On each empathy item a person can score 2, 1, or 0, so the EQ
   has a max  score of 80 & a min  of 0.  In Study 1 we employed the EQ with
   n=90 adults (65 m, 25 f) with Asperger Syndrome (AS) or high-functioning
   autism (HFA), who are reported clinically to have difficulties in empathy.
   The adults with AS/HFA scored significantly lower on the EQ than n=90 (65 m,
   25 f) age-matched controls. Of the adults with AS/HFA, 81% scored <= 30 pts
   out of 80, compared with only 12% of controls. In Study 2 we carried out a
   study of n=197 adults from a general population, to test for previously
   reported sex differences (female superiority) in empathy. This confirmed
   that women scored significantly higher than men. ...reveals both a sex diff
   in empathy in the general population & an empathy deficit in AS/HFA."
   -- [<A HREF="http://dx.doi.org/10.1023/B:JADD.0000022607.19833.00">doi:10.1023/B:JADD.0000022607.19833.00</A>][10/'04] (subsc'n)
   Also look for B-c & W c2001 (auths @ psych cam U.).
   -- [<A HREF="http://www.autismresearchcentre.com/papers/2004_BCandSW_EQ.pdf">paper.pdf@autismresearchcentre.com</A>][10/'04].

%A J. Zobel
%T Uni cheats racket: A case study in plagiarism
%J 6th Australian Computing Edn Conf
%P ?-?
%D 2004
%W Dunedin
%K conf, c2004, c200x, c20xx, zz1004, RMIT, ACE, cheat, cheating, copy, copying,
   assignments, fraud, detection, RMIT, discipline, academic, university,
   homework, home work, student, students, tutorials, tute, tutes, prac, pracs,
   mytutor, turnin, turnitin, com, law, legal, court, misconduct, plagiarism
%X "... a further concern was the occasional discovery of senior students
   who were simply unable to write sensible code. ..."    [occasional!?!]
   -- [<A HREF="https://dl.acm.org/doi/10.5555/979968.980016">ACM</A>]['22],
      was goanna.cs.rmit.edu.au/~jz/fulltext/ace04z.pdf ['04],
      was crpit.com/confpapers/CRPITV30Zobel.pdf ]'13].
   [Also search for: plagiarism].

%A J. M. Wicherts
%A C. V. Dolan
%A D. J. Hessen, P. Oosterveld, G. C. M. van Baal, D. I. Boomsma,
%A M. M. Span
%T Are intelligence tests measurement invariant over time? Investigating the
   nature of the Flynn effect
%J Intelligence
%I Norwood
%V 32
%N 5
%P 509-537
%D 2004
%K jrnl, c2004, c200x, c20xx, human, IQ, WAIS, intelligence quotient, increase,
   increasing, change, changing, stats, statistics
%X "The gains of scores on standardized intelligence, tests (i.e., Flynn
   effect) ... extensive debate concerning their nature, causes & implications.
   ...present study is to investigate whether 5 intelligence tests are
   measurement invariant with respect to cohort. Measurement invariance implies
   that gains over the years can be attributed to increases in the latent
   variables that the tests purport to measure.  ...
   ...The results of multigroup confirmatory factor analyses clearly indicate
   that measurement invariance with respect to cohorts is untenable. Uniform
   measurement bias is observed in some, but not all subtests. The implications
   of these findings are discussed."

%A J. M. Sundet
%A D. G. Barlaug
%A T. M. Tojussen
%T The end of the Flynn effect? A study of secular trends in mean
   intelligence test scores of Norwegian conscripts during half a century
%J Intelligence
%I Norwood
%V 32
%N 4
%P 349-362
%D 2004
%K jrnl, human, IQ, WAIS, intelligence quotient, increase, increasing, stats,
   statistics, ability score, scores, tests, height, Norway, c19xx
%X "...reports secular trends in the mean scores of a language, mathematics, &
  a Raven-like test together with a combined general ability (GA) score among
  Norwegian (male) conscripts tested from the mid 1950s to 2002 ...  Secular
  gains in standing height (indicating improved nutrition & health care) were
  also investigated. Substantial gains in GA were apparent from the mid 1950s
  (test years) to the end 1960s-early 1970s, followed by a decreasing gain rate
  & a complete stop from the mid 1990s. The gains seemed to be mainly caused by
  decreasing prevalence of low scorers. ...  the Flynn effect may have come to
  an end in Norway. Height gains were strongly correlated with I' gains until
  the cessation of height gains ..."

%A C. Blair
%A D. Gamson
%A S. Thorne
%A D. Baker
%T Rising mean IQ: Cognitive demand of mathematics education for young
   children, population exposure to formal schooling, and the neurobiology of
   the prefrontal cortex
%J Intelligence
%I Elsevier
%V ?
%N ?
%P ?-?
%D 2004
%K jrnl, quotient, IQ, test, tests, maths, increase, increasing, Flynn effect,
   human, intelligence, gain, cognitive stimulation, stats, statistics
%X "...proposes 1 potential explanation for 100 years of rising population mean
   IQ in the [US] associated with historical changes in access to schooling &
   educational practice. A neurodevelopmental-schooling hypothesis is forwarded
   based on evidence of growth in the population's access to schooling early in
   the last century & the increasing cognitive demands of math' curricula from
   mid-century onward. The fact that these educational changes have been
   widespread, affect individuals early in the lifespan, & are uncorrelated
   with genetic propensity for IQ makes them particularly well suited to
   produce large environmentally driven gains in intelligence between gen's in
   the face of high heritability for intelligence. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.intell.2004.07.008">doi:10.1016/j.intell.2004.07.008</A>][in press, online 10/'04],
   but [also search for: Colom diet 2004].

%A R. Colom
%A J. M. Lluis-Font
%A A. Andres-Pueyo
%T The generational intelligence gains are caused by decreasing variance in the
   lower half of the distribution: Supporting evidence for the nutrition
   hypothesis
%J Intelligence
%I Elsevier
%V ?
%N ?
%P ?-?
%D 2004
%K jrnl, quotient, IQ, test, tests, diet, increase, increasing, Flynn effect,
   human intelligence, gain, cognitive stimulation, stats, statistics,
   c2004, c200x, c20xx, zz1004
%X "Generational intelligence gains are one intriguing finding in science.
   Nutrition & cog' stimulation are among the most remarkable causes of the
   upward trend in I.. The nutrition hypothesis predicts a primary impact on
   the most deprived, producing disproportionate gains at low I. levels. The
   cognitive stimulation hypothesis predicts gains along the I. dist'n. However
   data from the entire distribution are rarely available. ... study compares a
   sample of children tested in 1970 with an equivalent sample tested 30 years
   later. Data for the entire distributions were available. The results are
   consistent with the nutrition hypothesis, because the gains were mainly
   concentrated in the lower & medium halves of the distribution & were
   negligible in the very top half of the distribution. Moreover, an impressive
   gradual decrease in the gains was observed from the lower half to the top
   half of the distribution." (auth1 @ U. Autonoma de Madrid)
   -- [<A HREF="http://dx.doi.org/10.1016/j.intell.2004.07.010">doi:10.1016/j.intell.2004.07.010</A>][in press, online 10/'04],
   but [also search for: Blair Gamson 2004].

%A M. Brosnan
%A et ?
%T Digit ratio and faculty membership: Implications for the
   relationship between prenatal testosterone and academia
%J sub to British J. of Psychology
%D 2004
%K c2004, c200x, c20xx, human development, male, female, side, gender,
   sex hormones, zz1004, academic, department, subject, choice, choices, stats,
   statistics, finger, length
%X [<A HREF="http://staff.bath.ac.uk/pssmjb/">home</A>][10/'04].
   Also see [<A HREF="http://www.newscientist.com/news/news.jsp?id=ns99996564">New Sci't</A>][10/'04].
   "...107 male and female academics surveyed at Bath University, UK, had very
   similar ratios [length 1st digit : 3rd] - 0.987 for men and 0.984 for women.
   This suggests the two groups were exposed to the same levels of oestrogen
   and testosterone in the womb. ...  chemistry, comp sci, math and physics
   all had average ratios of over 0.995 - close to the female average - despite
   81% of those subjects being m. ... economics, education, management, social
   and policy sciences had an average ratio below 0.98, the male average,
   despite only 66% of this sample being male.

%A E. J. Okello
%A S. U. Savelev
%A E. K. Perry
%T In vitro anti-beta-secretase and dual anti-cholinesterase activities of
   Camellia sinensis L. (tea) relevant to treatment of dementia
%J Phytotherapy Research
%V 18
%N 8
%P 624-627
%M OCT
%D 2004
%K jrnl, tea, Alzheimer's, Alzheimers, medical, biol, biology, brain, green,
   black tea, amyloidosis, acetylcholinesterase, cholinesterase, secretase,
   AChE, senile, senility, health
%X "The primary target of licensed drugs for the treatment of Alzheimer's ...
   is the inhibition of the enzyme acetylcholinesterase, although preventing
   beta-amyloidosis is a prime target for drugs in development. The in vitro
   dual anti-cholinesterase & beta-secretase activities of Camellia sinensis L.
   extract (tea) is reported. Green & black tea inhibited human
   acetylcholinesterase (AChE) with IC50 values of 0.03 mg/mL & 0.06 mg/mL resp
   & human butyrylcholinesterase (BuChE) with IC50 values 0.05 mg/mL. Green tea
   at a final assay concentration of 0.03 mg/mL inhibited beta-secretase by 38%.
   These novel findings suggest that tea infusions contain biologically active
   principles, perhaps acting synergistically, that may be used to retard the
   progression of the disease assuming that these principles, yet to be
   identified, reach the brain."
   -- [<A HREF="http://dx.doi.org/10.1002/ptr.1519">doi:10.1002/ptr.1519</A>][10/'04].

%A S. C. Renaud
%A R. Gueguen
%A P. Conard, D. Lanzmann-Petithory, J.-M. Orgogozo, O. Henry
%T Moderate wine drinkers have lower hypertension-related mortality: a
   prospective cohort study in French men
%J Amer. J. Clinical Nutrition
%V 80
%N 3
%P 621-625
%M SEP
%D 2004
%K jrnl, health, medical, drink, drinking, alcohol, wine, c2004, c200x, c20xx,
   drinker, France, male, stats, statistics
%X "...36,583 healthy middle-aged men who had normal results on an
   electrocardiogram & were not taking drugs for cardiovascular disease risk
   factors. [they] underwent a comprehensive health appraisal at the Center for
   Preventive Medicine between 1 Jan. 1978 & 31 Dec. 1985. Mortality from all
   causes & from specific causes during a 13-21-y follow-up was recorded. ...
   In a Cox model adjusted for 6 confounding variables, moderate wine drinkers
   (those who consumed < 60 g alcohol/d & no beer) with systolic [bp] (SBP) of
   158, 139, or 116mm Hg had sig. lower risks of death from all causes by 23%,
   27%, & 37%, resp., than did abstainers. Even for the highest quartile of
   [bp], moderate wine drinkers were protected from all-cause mortality. No
   sig. reduction in all-cause mortality in relation to SBP was observed in
   other drinkers (those who consumed 60g alcohol/d or who consumed beer &
   wine). ...  A moderate intake of wine is associated with a lower risk of
   mortality from all causes in persons with hypertension."
   -- [<A HREF="http://www.ajcn.org/cgi/content/abstract/80/3/621">subs or us$8</A>][10/'04].

%A T. den Heijer
%A S. E. Vermeer, E. J. van Dijk, N. D. Prins,
   P. J. Koudstall, C. M. van Duijn, A. Hoffman, M. M. B. Bretler
%T Light to moderate alcohol intake protects against dementia in older persons
%J Amer. J. Clinical Nutrition
%V 80
%P 992-997
%M OCT
%D 2004
%K jrnl, health, medical, drink, drinking, senile, human, stats, brain,
   hippocampus, amygdala, lesions, infarcts, c2004, c200x, c20xx, statistics,
   Alzheimer, old, age, ageing
%X "... a population-based sample of 1074 older persons without dementia (aged
   60-90 y) we made brain MRIs ... rated white matter lesions & brain infarcts.
   In a subset of 509 people, hippocampal & amygdalar volumes on MRI were
   measured. Alcohol intake was assessed by using a structured questionnaire.
   We categorized a. intake as lifetime abstention & very light (< 1 drink/
   wk), light (1 drink/wk to < 1 drink/d), moderate (1 drink/d to < 4 drinks/d),
   & heavy (>=4 drinks/d) intakes ... Persons whose a. consumption was light
   to moderate had less severe white matter lesions and brain infarcts on MRI
   than did abstainers or heavy drinkers. Abstainers & very light drinkers had
   smaller hippocampal and amygdalar volumes on MRI than did light-to-moderate
   drinkers, but only if the former carried an apolipoprotein (APOE) ?4 allele.
   ... Light-to-moderate alcohol intake is associated with a lower prevalence of
   vascular brain findings and, in APOE ?4 carriers, hippocampal and amygdalar
   atrophy on MRI"
   -- [<A HREF="http://www.ajcn.org/cgi/content/abstract/80/4/992">subs or us$8</A>][10/'04].

%A A. Zampelas
%A D. B. Panagiotakos
%A C. Pitsavos, C. Chrysohoou, C. Stefanadis
%T Associations between coffee consumption and inflammatory markers in
   healthy persons: the ATTICA study
%J Amer. J. Clinical Nutrition
%V 80
%N 4
%P 862-867
%M OCT
%D 2004
%K jrnl, health, medical, cardiovascular disease, CVD, coffee, statistics,
   zzCoffee, human health, risk, risks, heart, stats
%X "...A relation exists between moderate-to-high coffee consumption &
   increased inflammation process. This relation could explain, in part, the
   effect of increased coffee intake on the cardiovascular system."
   -- [<A HREF="http://www.ajcn.org/cgi/content/abstract/80/4/862">subs or us$8</A>][10/'04].
   [Also search for: zzCoffee].

%A A. Ruano-Ravina
%A A. Figueiras
%A J. M. Barros-Dios
%T Type of wine and risk of lung cancer: A case-control study in Spain
%J Thorax
%V 59
%P 981-985
%M NOV
%D 2004
%K jrnl, red, white, wine, health, medical, c2004, c200x, c20xx, statistics,
   stats, alcohol, drink, drinking
%X By news-paper reports claims red wine beneficial:  c1999-c2000 132 patients
   with LC, 187 for minor surgery, 1/3 with LC drank red, 1/2 others drank red.
   -- [<A HREF="http://thorax.bmjjournals.com/">jrnl home</A>]['04].
   [But beware the liver.-]

%A J. Soares
%A M. A. Kliem
%A R.Betarbet,J.T.Greenamyre, B.Yamamoto, T.Wichmann
%T 1-methyl-4-pPhenyl-1,2,3,6-tetrahydropyridine-induced Parkinsonism and
   lesions of the external pallidal segment
%J J. Neuroscience
%P 6417-6426
%V 24
%N 29
%M JUL
%D 2004
%K jrnl, medical, human, health, c2004, c200x, c20xx, MPTP, brain, exposure,
   rotenone, pesticide, chronic, GPe, GPi, STN, Parkinson's disease, lesion,
   Parkinsons
%X "...experiments reexamined the notion that reduced activity in the external
   pallidal segment (GPe) results in the abnormalities of neuronal discharge in
   the subthalamic nucleus (STN) & the internal pallidal segment (GPi) & in the
   development of parkinsonian motor signs. Extracellular recording in 2 rhesus
   monkeys, which had been rendered P by treatment with 1-methyl-4-phenyl-1,2,
   3,6-tetrahydropyridine (MPTP), revealed that the average neuronal discharge
   rate decreased in GPe but increased in STN & GPi. After MPTP, neurons in all
   three nuclei tended to discharge in oscillatory bursts. ..."
   -- [<A HREF="http://dx.doi.org/10.1523/JNEUROSCI.0836-04.2004">doi:10.1523/JNEUROSCI.0836-04.2004</A>][11/'04].
   T.J.Gr'y at Emory U., Atlanta. [<A HREF="http://www.jneurosci.org/cgi/content/abstract/24/29/6417">jrnl</A>][11/'04].

%A C. Twardy
%A K. Korb
%T A criterion for probabilistic causality
%J Philosophy of Science
%V 71
%N 3
%P 241-262
%M JUL
%D 2004
%K jrnl, criteria, cause, effect, CTwardy, KBKorb, c2004, c200x, c20xx
%X auths@csse.monash ['04].

%A C. Twardy
%T Argument maps improve critical thinking
%J Teaching Philosophy
%V 27
%N 2
%P 95-116
%M JUN
%D 2004
%K jrnl, map, CTwardy, c2004, c200x, c20xx
%X auths@csse.monash ['04].

%A J. Patrick
%T The Scamseek project: Text mining for financial scams on the internet
%J Proc 3rd Australasian Data Mining Conf.
%W Carins
%P 33-38
%M DEC
%D 2004
%K conf, scam, scams, www, ASIC, c2004, c200x, c20xx, document, web page, pages,
   capital markets, ScamAlert, internet, world wide web, financial, investment
%X "... retrieves potential scam candidate documents from the Internet and
   classifies them as to their potential risk of containing an illegal
   investment proposals or advice. ... uses the semantic model of language,
   Systemic Functional Grammar, to model the semantics of the scam classes and
   uses unigrams ... ASIC operates the system on a 24/7 basis. The estimate of
   savings in human effort in its monitoring role is the order of 100 to 1...."
   -- [<A HREF="http://www.cs.usyd.edu.au/~lkmrl/scamseek_summary.pdf">2pages.pdf</A>]['04],
      [<A HREF="http://www.cs.usyd.edu.au/~lkmrl/scamseek.htm">project-page</A>]['04] (auth @ U. Syd. '04).

%A J. Jaffar
%A A. E. Santosa
%A R. H. C. Yap
%A K. Q. Zhu
%T Scalable distributed depth-first search with greedy work stealing
%J ICTAI
%P 98-103
%D 2004
%K conf, ICTAI, c2004, AI, c2004, c200x, c20xx, parallel, CP,
   constraint programming, NatUniSing
%X "... parallelization of depth-first combinatorial search algs. on a network
   of computers. Our arch. is intended for a distributed setting & uses a work
   stealing strategy coupled with a small number of primitives for the
   processors [workers] to obtain new work & to communicate to other workers.
   These primitives are a minimal imposition & integrate easily with constraint
   programming systems. The main contribution is an adaptive architecture which
   allows workers to incrementally join & leave & has good scaling properties
   as the number of workers increases. Our empirical results illustrate that
   near-linear speedup for backtrack search is achieved for up to 61 workers.
   It suggests that near-linear speedup is possible with even more workers...."
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/ICTAI.2004.107">doi:10.1109/ICTAI.2004.107</A>]['05]($ub$cribe) auths@N.U.S.

%A D. Wright-Neville
%T Dangerous dynamics: Activists, militants and terrorists in Southeast Asia
%J The Pacific Review
%V 17
%N 1
%P 27-46
%M MAR
%D 2004
%K jrnl, terror, terrorism, activist, militant, terrorist, c2004, c200x, c20xx,
   Jemaah Islamiyah, JI, islam
%X "... accepting that al-Qaeda & the indigenous SE Asian group Jemaah
   Islamiyah have emerged as a potent threat to regional security, it
   interrogates the view that this renders SE Asia more dangerous than many
   other parts of the world. ... suggests that this exaggerated sense of threat
   rests largely on a failure to account for nuanced differences in the nature
   of Islamist politics in the region. As a small step towards redressing this
   problem ... outlines a typology of Islamist organizations. ... suggests that
   a person's location within this typology is more than a function of
   religiosity but reflects instead relative degrees of social & political
   alienation." --  auth@mon@sh['05].
   -- [<A HREF="http://dx.doi.org/10.1080/0951274042000182401">doi:10.1080/0951274042000182401</A>]['05].

%A S. Atran
%T Individual factors in suicide terrorism
%J Science
%M APR
%D 2004
%K letter, terror, terrorist, factor, c2004, c200x, c20xx
%X [<A HREF="http://www.rcgd.isr.umich.edu/roots/AtranSciLet0401204.pdf">pdf</A>]['05].
   -- [<A HREF="http://www.rcgd.isr.umich.edu/roots/AtranSciSom040204.pdf">extra</A>]['05].
   [Also search for: Atran c2003].

%E E. P. Lazear
%T The Peter Principle: A Theory of Decline
%J J. of Political Economy
%V 112
%N 1
%P pS141-S163
%M FEB
%D 2004
%K eJrnl, c2004, c200x, c20xx, Peter Principle, level of incompetence, job,
   work, promotion, promoted, management
%X "Some have observed that individuals perform worse after being promoted. The
   Peter Principle, ... This view is unnecessary & inconsistent with the data.
   It is argued that ability appears lower after promotion purely as a
   statistical matter. Being promoted is evidence that a standard has been met.
   Regression to the mean implies that future ability will be lower, on average.
   Firms optimally account for the regression bias in making promotion decisions
   but the effect is never eliminated. Rather than evidence of a mistake, the
   Peter principle is a necessary consequence of any promotion rule. [&], firms
   that take it into account appropriately adopt an optimal strategy. Usually,
   firms inflate the promotion criterion to offset the Peter principle effect, &
   the more important the transitory component is relative to total variation in
   ability, the larger the amount that the standard is inflated. The same logic
   applies to other situations. For example, it explains why movie sequels are
   worse than the original film on which they are based & why second visits to
   restaurants are less rewarding than the first."
   -- [<A HREF="http://ideas.repec.org/p/iza/izadps/dp759.html">www</A>]['09],
      [<A HREF="http://client.norc.org/jole/SOLEweb/lazear.pdf">www</A>]['09],
      [<A HREF="http://faculty-gsb.stanford.edu/lazear/">auth</A>]['09].
   [Also search for: Peter Principle].

%A D. E. Bryant
%T Embeddings of partial Steiner triple systems
%J J. Comb. Theory, Ser.A
%V 106
%N 1
%P 77-108
%D 2004
%K jrnl, embedding, c2004, c200x, c20xx, combinatorial maths, math, STS, pSTS
%X (A partial STS on a set U of u points is a collection of 3-subsets,
   called triples, of U s.t. any 2-subset of U is contained in at most
   one triple.  If "at most"->"exactly" we have a STS -- P.J.C@mer'n.)

%A H. Thimbleby
%T User interface design with matrix algebra
%J ACM Trans. on Computer-Human Interaction (TOCHI)
%V 11
%N 2
%P 181-236
%M JUN
%D 2004
%K jrnl, TOCHI, HCI, c2004, c200x, c20xx, zz0105, GUI, point and click, Harold,
   interfaces, UCLIC, interactive, interaction
%X "It is usually very hard, both for designers and users, to reason reliably
   about user interfaces. ... shows that 'push button' and 'point and click'
   user interfaces are algebraic structures. Users effectively do algebra when
   they interact, and therefore we can be precise about some important design
   issues and issues of usability. Matrix algebra, in particular, is useful for
   explicit calculation and for proof of various user interface properties. With
   matrix algebra, we are able to undertake with ease unusally thorough reviews
   of real user interfaces: this article examines a mobile phone, a handheld
   calculator and a digital multimeter as case studies, and draws general
   conclusions about the approach and its relevance to design."
   -- [<A HREF="http://doi.acm.org/10.1145/1005361.1005364">doi:10.1145/1005361.1005364</A>]['04].
   auth @ UCLIC, U. Coll. London Interaction Centre.

%A M. Sageman
%T Understanding Terror Networks
%I U.PennsylvaniaPress
%P 220
%D 2004
%K book, text, c2004, c200x, c20xx, terrorism, terrorist, suicide bomb, bomber,
   network, stats, recruit, recruitment, FPRI
%X isbn:0812238087, hb, us$30.
   "... analysed biographies of 172 terrorists, all members of the global
   Salafi jihad. He found that "discipleship", where an authority figure such
   as an imam or teacher holds enough loyalty & emotional sway to prescribe in
   followers both belief & action, accounted for only 8% of his sample. ...
   Of the 150 jihadi terrorists for which there was recruitment information,
   75% had pre-existing social bonds to members already involved in global
   jihad or had decided to join the jihad with a group of family members or
   friends. ... interpersonal relationships were at the centre of these
   individuals' radicalisation...  84% joined the jihad as immigrants ..."
   --N.Argo, The Aus. 19/4/'06.
   Also see [<A HREF="http://www.fpri.org/enotes/20041101.middleeast.sageman.understandingterrornetworks.html">fpri</A>]['06].

%A D. H. Meadows
%A J. Randers
%A D. L. Meadows
%T Limits to Growth: The 30-Year Update
%I ChelseaGreen
%P 368
%D 2004
%O (Global Env. Change, 18(3), pp.397-411, AUG 2008)
%K book, text, c2004, c200x, c20xx, zz1208, Club of Rome, Limit, economic,
   Limits to Growth, of, economy, boom, bust, recession, bull, bear, ecology,
   steady state, environmental, resources, population, indutrial, collapse,
   zzPrediction, prediction, zz0124, zz0134
%X pb us$15; uk us isbn:193149858X; uk us isbn13:978-1931498586.
   (1st ed 1972, Universe Books, uk us isbn:0876631650.)
   (Also see: G. Turner,
     'A comparison of 'The Limits to Growth' with 30 years of reality'
     CSIRO, [<A HREF="http://dx.doi.org/10.1016/j.gloenvcha.2008.05.001">doi:10.1016/j.gloenvcha.2008.05.001</A>], 2008 (52 pages).
     Was www.csiro.au/files/files/plje.pdf 2004.)
   [Also search for: limits growth resources], [also search for: zzPrediction].

%A M. M. Kaminski
%T Games Prisoners Play
%I PrincetonUP
%P 215
%D 2004
%K book, text, c2004, c200x, c20xx, zz1112, Poland, Polish, Solidarity,
   politics, political, prison, culture, subculture, Bialoleka, Rakowieka,
   jail, prisoner, grypsman, maths, game, theory
%X 2004 hb, us$48; uk us isbn:0691117217; uk us isbn13:978-0691117218;
   2010 pb, us$19; uk us isbn:0691149321; uk us isbn13:978-0691149325.
   "On March 11, 1985, a van was pulled over in Warsaw for a routine traffic
   check that turned out to be anything but routine. Inside was Marek Kaminski,
   a Warsaw Uni. student who also ran an underground press for Solidarity. The
   police discovered illegal books in the vehicle, and in a matter of hours
   five secret police escorted Kaminski to jail. A sociology and mathematics
   major one day, Kaminski was the next a political prisoner trying to adjust
   to a bizarre and dangerous new world. ..."  (via AlanD.)

%A A. Joux
%T Multicollisions in iterated hash functions. Application to cascaded
   constructions
%J CRYPTO
%I SpringerVerlag
%P 306-316
%S LNCS
%V 3152
%D 2004
%K conf, CRYPTO, c2004, c200x, c20xx, zz1213, cryptography, hash, function,
   hashing, cryptographic, multi collision, collisions, attack
%X "... study the existence of multicollisions in iterated hash fns. We show
   th at finding multicollisions, i.e.  r-tuples of messages that all hash to
   the same value, is not much harder than finding ordinary collisions, i.e.
   pairs ..., even for extremely large values of r. More precisely, the ratio of
   the complexities of the attacks is ~ equal to the logarithm of r. Then, using
   large multi-collisions as a tool, we solve a long standing open problem &
   prove that concatenating the results of several iterated hash fns in order to
   build a larger one does not yield a secure construction. We also discuss the
   potential impact of our attack on several published schemes.  Quite
   surprisingly, for subtle reasons, the schemes we study happen to be immune
   to our attack."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-28628-8_19">doi:10.1007/978-3-540-28628-8_19</A>]['13],
    pdf@[<A HREF="http://www.iacr.org/cryptodb/archive/2004/CRYPTO/1472/1472.pdf">iacr</A>]['13].
   (Also see cr.hash.fn@[<A HREF="https://en.wikipedia.org/wiki/Cryptographic_hash_function">wikip</A>]['13].)

%A S. Perkowitz
%T Digital People: From Bionic Humans to Androids
%I JosephHenryPress
%P 248
%D 2004
%K book, c2004, c200x, c20xx, android, robot, automata, technology, singularity,
   Alife, AI, human
%X 2004, pb us$16; uk us isbn:0309096197; uk us isbn13:978-0309096195.
         hb us$25; uk us isbn:0309089875; uk us isbn13:978-0309089876.
   "Robots, androids, and bionic people pervade popular culture, from classics
   like Frankenstein and R.U.R. to modern tales such as The Six Million Dollar
   Man, The Terminator, and A.I. ..."
   [Also search for: android].

%A D. K. Simonton
%T Creativity in Science: Chance, Logic, Genius, and Zeitgeist
%I CUP
%P 232
%D 2004
%K book, text, CUP, c2004, c200x, c20xx, zz1114, science, research, scientific,
   human creativity, breakthrough, innovation, idea, ideas, luck
%X 1st ed 2004; hb us$66; uk us isbn:0521835798; uk us isbn13:978-0521835794.
   "... Where do major scientific breakthroughs come from? ... provides an
   answer, not by choosing one explanation & ignoring the others, but rather by
   unifying all four perspectives into a single theory in which chance plays the
   primary role, but with the significant involvement of logic, genius &
   zeitgeist."

%T Growing Up in Australia, 2004 annual report
%I Australian Institute of Family Studies
%K report, AIFS, gov, family, families, child, children, c2004, c200x, c20xx,
   LSAC, Longitudinal Study of Australian Children, development, work, stats,
   Australian Temperament Project, ATP, society, social trends
%X [<A HREF="http://www.aifs.gov.au/growingup/pubs/ar/annualreport2004.html">report</A>]['05].
     [<A HREF="http://www.aifs.gov.au/growingup/pubs/ar/annualreport2004.html#use">public use</A>]['05].
     [<A HREF="http://www.aifs.gov.au/growingup/">LSAC</A>]['05].
   -- [<A HREF="http://www.aifs.gov.au/atp/">Australian Temperament Project</A>]['05].
      "...sample of [.au] children born in [Vic] between Sept.1982 & Jan.1983.
      ... 2443 families from urban and rural areas ... .  Approx. [2/3] of the
      families are still participating in the study after 21y..
      13 waves of data have been collected ..."
   -- [<A HREF="http://www.aifs.gov.au/">aifs.gov.au</A>]['05].

%T Poe's law
%D 2005
%K Poe, Poes law, c2005, c200x, c20xx, zz0221, funny laws, ha ha, haha,
   adage, maxim, parody, irony, creationism, flat earth, Qanon
%X "Poe's law is an adage of Internet culture stating that, without a clear
   indicator of the author's intent, it is impossible to create a parody of
   extreme views so obviously exaggerated that it cannot be mistaken by some
   readers for a sincere expression of the views being parodied. The original
   statement, by Nathan Poe, read:
     Without a winking smiley or other blatant display of humor, it is utterly
     impossible to parody a Creationist in such a way that someone won't
     mistake for the genuine article.
   -- PL@[<A HREF="https://en.wikipedia.org/wiki/Poe%27s_law">wikip</A>]['21].
   [Also search for: funny law].

%A C. Stoll
%T The Cuckoo's Egg: Tracking a Spy Through the Maze of Computer Espionage
%I Pocket
%P 416
%D 2005
%K book, text, c2005, c200x, c20xx, computer, hacker, hacking, spy, spies
%X "... Clifford Stoll becomes, almost unwillingly, a one-man security force
   trying to track down faceless criminals who've invaded the university
   computer lab he stewards. What first appears as a 75-cent accounting error in
   a computer log is eventually revealed to be a ring of industrial espionage,
   primarily thanks to Stoll's persistence and intellectual tenacity. ..."
   1st ed 2005; pb us$11; uk us isbn:1416507787; uk us isbn13:978-1416507789.

%A B. J. Winkel
%A C. Deavors
%A D. Kahn
%T The German Enigma Cipher Machine: Beginnings, Success, and Ultimate Failure
%I ArtechPubl
%P 439
%D 2005
%K book, text, c2005, c200x, c20xx, zz0613, German, Enigma machine,
   cypher, cipher, coding, encryption, cryptography, cryptanalysis,
   ww2, world war II, two, Ultra
%X hb us$140; isbn:1580539963; isbn13:978-1580539968;
   "... contains original essays, historical & technical papers, & translations
   of historical materials & retrospectives concerning the German Enigma Cipher
   m/c. You get a comprehensive view of the Enigma m/c's development, uses,
   role in WWII Allied intelligence, & cryptanalysis. From The Commercial
   Enigma: Beginnings of Machine Cryptography & An Enigma Chronology to The Road
   to German Diplomatic Ciphers 1941 1945 & the Geheimschreiber ..."
   [Also search for: enigma machine] and [also search for: Bletchley Park].

%A P. Walther
%A et al
%T Experimental one-way quantum computing
%J Nature
%V 434
%N 7030
%P 169-176
%M MAR
%D 2005
%K jrnl, quantum computing, qbit, qbits, qubits, qubit, entanglement,
   c2005, c200x, c20xx, computer, bit, bits, photon, photons,
   Grover's search algorithm, zz0305
%X "... new model requires qubits to be initialized in a highly entangled
   cluster state. ... the quantum computation proceeds by a sequence of single-
   qubit measurements with classical feedforward of their outcomes. Because of
   the essential role of measurement, a one-way quantum computer is
   irreversible. In the one-way quantum computer, the order & choices of
   measurements determine the algorithm computed. We have experimentally
   realized four-qubit cluster states encoded into the polarization state of
   four photons. We characterize the quantum state fully by implementing
   experimental four-qubit quantum state tomography. Using this cluster state,
   we demonstrate the feasibility of one-way quantum computing through a
   universal set of one- & two-qubit operations. Finally, our implementation of
   Grover's search algorithm..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03347">doi:10.1038/nature03347</A>]['05].

%A C. Collberg
%A S. Kobourov
%T Self-plagiarism in computer science
%J CACM
%V 48
%N 4
%P 88-94
%D 2005
%K cacm, copy, use, reuse, c2005, c200x, c20xx, CSci
%X "... Self-plagiarism occurs when authors reuse portions of their previous
   writings in subsequent research papers. ...
   ... present the results of an automated search for self-plagiarism in CS,
   recount some personal anecdotes, relate what some of our colleagues think
   about the issue, and discuss possible ways of addressing the problem."
   -- [<A HREF="http://doi.acm.org/10.1145/1053291.1053293">doi:10.1145/1053291.1053293</A>]['05].

%A A. Aspuru-Guzik
%A A. D. Dutoi
%A P. J. Love
%A M. Head-Gordon
%T Simulated quantum computation of molecular energies
%J Science
%V 309
%N 5741
%P 1704-1707
%M SEP
%D 2005
%K jrnl, quantum computer, bit, bits, qbits, qubits, c2005, c200x, c20xx,
   qubit, energy, molecule, phase-estimation algorithm
%X "...calc. time for the energy of atoms & molecules scales exponentially with
   system size on a classical computer but polynomially using quantum algs..
   ... such algs. can be applied to problems of chemical interest using modest
   numbers of QBs. Calc. of the water & lithium hydride molecular ground-state
   energies have been carried out on a quantum c. simulator using a recursive
   phase-estimation alg.. [It] reduces the # of QBs ... from about 20 to 4.
   ... # of QBs required scales linearly with the # of basis functions, & the
   # of gates required grows polynomially with the # of QBs."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1113479">doi:10.1126/science.1113479</A>]['05].
   [Also search for: quantum phase].

%A R. Pape
%T Dying to Win: The Strategic Logic of Suicide Terrorism
%I Random House
%D 2005
%P 352
%K book, text, terror, terrorism, terrorist, c2005, c200x, c20xx, cause,
   causes, origin, threat, bomb, bombs, bombing, Tamil Tigers, Hindu,
   Islam, Islamic, muslim, Al-Qaeda, AlQaeda, fundamentalism,
   uniChicago, Chicago project
%X <!-- r-pape uchicago edu -->auth@u.chic@go;  hb, us$26, isbn:1400063175.
   315 cases analysed c1980-c2003.
   -- [<A HREF="http://political-science.uchicago.edu/faculty/pape.html">auth</A>][9/'05].
   Also see [<A HREF="http://www.mfa.gov.il/MFA/Terrorism-%20Obstacle%20to%20Peace/Palestinian%20terror%20since%202000/Suicide%20and%20Other%20Bombing%20Attacks%20in%20Israel%20Since">mfa.gov.il</A>][9/'05].

%A A. Baronchelli
%A M. Felici
%A E.Caglioti, V.Loreto, L.Steels
%T Sharp transition towards shared vocabularies in multi-agent systems
%J arXiv
%P 17
%M SEP
%D 2005
%K vocabulary, word, words, name, names, naming, game, c2005, c200x, c20xx,
   agents, system, language, evolution, semiotic dynamics
%X "... how very large populations are able to converge on the use of a
   particular word or grammatical construction without global coordination? ...
   ... helps to understand why new language constructs usually propagate along
   an S-shaped curve with a rather sudden trans. towards global agreement. ..."
   -- [<A HREF="http://arxiv.org/abs/physics/0509075">arxiv</A>]['05].

%A J. Mervis
%T National Science Foundation: Board suggests how to thrive under stress
%J Science
%V 310
%N 5750
%P 956
%M NOV
%D 2005
%K news, policy, research grant, grants, council, NSF, c2005, c200x, c20xx
%X "... One essential step, according to the draft plan ... strengthen the hand
   of program officers in choosing from among a surfeit of good research
   proposals. ... experiments with the potential to radically change a field
   rather than simply add incrementally to what is known. "Often a program
   officer will get a mixed set of reviews," says Washington. "We shouldn't
   allow one negative review to kill a proposal if the program officer thinks
   that it's worth taking the risk."... suggested that NSF should fund a larger
   and more diverse pool of researchers, even if it means suboptimal funding of
   individual grants and fewer large awards. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.310.5750.956b">doi:10.1126/science.310.5750.956b</A>]['05].

%A J. Baugh
%A O. Moussa
%A C. A. Ryan,   A. Nayak,   R. Laflamme
%T Experimental implementation of heat-bath algorithmic cooling using
   solid-state nuclear magnetic resonance.
%J Nature
%V 438
%P 470-473
%M NOV
%D 2005
%K quantum computing, c2005, c200x, c20xx, qubit, qubits, NMR
%X "...report the experimental realization of multi-step cooling of a quantum
   sys. via heat-bath algorithmic cooling. The experiment was carried out using
   nuclear magnetic resonance of a solid-state ensemble 3-qubit system. We
   demonstrate the repeated repolarization of a particular qubit to an
   effective spin-bath temperature, and alternating logical operations within
   the 3-qubit subspace to ultimately cool a 2nd qubit below this temp...."
   -- [<A HREF="http://dx.doi.org/10.1038/nature04272">doi:10.1038/nature04272</A>]['05].

%A K. W. Wong
%A D. Tikk
%A T. D. Gedeon
%A L. T. Koczy
%T Fuzzy rule interpolation for multidimensional input spaces with
   applications: A case study
%J IEEE Trans. on Fuzzy Systems
%V 13
%N 6
%P ?-? (13p)
%D 2005
%K jrnl, c2005, c200x, c20xx, rules, space
%X TG @ anu ['04].

%A M. Bloom
%T Dying To Kill: The Allure of Suicide Terror
%I ColumbiaU.P.
%P 280
%D 2005
%K book, text, c2005, c200x, c20xx, terrorism, terrorist, bomb, bomber
%X isbn:0231133200, hb, us$25.

%A A. Pedahzur
%T Suicide Terrorism
%I PolityPress
%P 261
%D 2005
%K book, c2005, c200x, c20xx, bomb, bomber, terrorist
%X isbn:0745633838, pb, us$25.

%A W. A. Searcy
%A S. Nowicki
%T The Evolution of Animal Communication: Reliability and Deception in
   Signaling Systems
%I Princeton U.P.
%S Monographs in Behavior and Ecology
%P 288
%D 2005
%K book, text, c2005, c200x, c20xx, signalling, signal, signals, lies, lying,
   liar, liars, deceit, behaviour, honesty, dishonesty, trust, zz0107
%X us$33, isbn:0691070954; isbn13:978-0691070957.
   [also search for: prisoners dilemma].

%A M. Abrahams
%T The Ig Nobel Prizes 2: An All-New Collection of the World's Unlikeliest
   Research
%I Dutton
%P 272
%D 2005
%K book, c2005, c200x, c20xx, Ig Nobel, IgNobel, prize, prizes, gene pool,
   stuff up, ups, doh, AIR, annals improbable research, funny, haha, ha ha
%X hb us$3; uk us isbn:0525949127; uk us isbn13:978-0525949121.
   (Also see [<A HREF="http://www.improbable.com/">improbable.com</A>][2021].)

%A R. K. Standish
%T Complexity of networks
%M AUG
%D 2005
%J arXiv.org
%K TR, c2005, c200x, c20xx, network, graph, graphs, complexity, information,
   ecoLab, compress, food web, webs
%X "... example might be ... the complexity of a food web ...
    [Here] a complexity measure of n/ws is proposed based on the 'complexity is
    information content' paradigm. ... one must fix 2 things: a rep'n language,
    in which strings of symbols from some alphabet describe, or stand for the
    objects being considered; & a means of determining when 2 such desc'ns refer
    to the same object. [Then] the info.content of an object can be computed in
    principle from the # of equiv. desc'ns describing a particular object.
    I propose a simple rep'n lang. for undirected graphs that can be encoded as
    a bitstring, & equivalence is a topological equiv.. [And] an algorithm for
    computing the complexity of an arbitrary undirected network."
    -- pdf@[<A HREF="http://arxiv.org/abs/cs.IT/0508075">arXiv</A>]['10],
    RKS@[<A HREF="http://www.hpcoders.com.au/rks.html">hpcoders</A>]['10].
       (Also see 'Network Complexity of Foodwebs', Alife12, pp.337-343, 2010,
       -- pdf@[<A HREF="http://mitpress.mit.edu/books/chapters/0262290758chap62.pdf">mit</A>]['10].)
    [Also search for: food web], and [also search for: compress graph].

%A K. D. Mitnick
%A W. L. Simon
%T The Art of Intrusion: The Real Stories Behind the Exploits of Hackers,
   Intruders and Deceivers
%I Wiley
%P 288
%D 2005
%K book, c2005, c200x, c20xx, computer, hacker, hacking, intrusion, exploit,
   fraud, slot machine
%X "... In 1995, [Mitnick] was arrested for illegal computer snooping, convicted
   and held without bail for two years before being released in 2002. ... "
   1st ed 2005; pb us$12; uk us isbn:0471782661; uk us isbn13:978-0471782667.
   [Also search for: hacker computer book].

%A M. vos Savant
%T Art of Spelling: The Madness and the Method
%I BarnesAndNoble
%P 208
%D 2005
%K book, text, Marilyn, c2005, c200x, c20xx, vosSavant, spell, spelling,
   English language
%X "... offers some suggestions for spelling improvement, supplying common roots
   like anim-, arch-, and spec- and a list of 500 commonly misspelled words. She
   also includes a few quizzes, with answers in the back of the book. This is
   not a how-to book, however, for more than half of it examines what spelling
   ability tells us about intelligence and personality. Vos Savant points out
   that while it is true that spelling errors reveal a lot about the writer,
   spelling and intelligence do not necessarily go hand in hand: some highly
   educated people spell poorly ..."
   2005; hb us$11; uk us isbn:0760776008; uk us isbn13:9780760776001.

%A S. Mitton
%T Fred Hoyle
%I AurumPress
%P 320
%D 2005
%K book, c2005, c200x, c20xx, astronomer, Fred Hoyle, biography, science,
   steady state
%X 1st ed 2005; hb;       uk us isbn:1854109618; uk us isbn13:978-1854109613.
   pb  ed 2011; pb us$34; uk us isbn:0521189470; uk us isbn13:978-0521189477.
   "Fred Hoyle (1915-2001) ... Written from personal accounts and interviews
   with Hoyle's contemporaries, this book gives valuable personal insights into
   Fred Hoyle and his unforgettable life."

%A Alexandra David-Neel
%T My Journey to Lhasa: The Classic Story of the Only Western Woman Who
   Succeeded in Entering the Forbidden City
%I HarperPerennial
%D 2005
%K book, text, c1924, c192x, c19xx, Tibet, Lhasa, explorer, exploration,
   travel, travels, traveller
%X A reprint, of course, 2005, uk us isbn13:978-0060596552.
   "... Born in 1868, David-Neel eschewed the dances, dinners, & formal
   marriages common to women of her era & social standing in order to indulge
   her fierce independence & insatiable intellectual curiosity. Her interest
   in comparative religions dated back to early childhood; even as a student in
   a Catholic convent school, she kept statues of both Christ & the Buddha in
   her room. She made her first trip to Asia in 1891, then supported herself as
   a light-opera singer & journalist before marrying a seemingly conventional
   man, Philip Neel. Fortunately for both Alexandra David-Neel & for
   posterity, Philip was less stodgy than his position as a well-off engineer
   might imply; though he did not accompany her, he supported his wife's
   explorations & even acted as her literary agent when she began to write
   about the places she visited. Alexandra & Philip remained the closest of
   friends until his death in 1941."
   [Also search for: Alexandra David Neel].

%A J. Walsh
%A J. Cripps Clark
%T Pathways in real life learning
%J Information and Communication Tech. and Real-Life Learning
%I IFIP
%V 182
%P 159-166
%D 2005
%K conf, c2005, c200x, c20xx, julia walsh, teaching, coaching, teacher,
   teachers, expert
%X "The pathway to expertise is a long journey, & few make it. Regardless of
   discipline, the journey is similar; what differentiates the journey is the
   knowledge that underpins the profession. This research explores expert
   teachers & the knowledge that underpins the teaching profession. Much
   research in teacher education has concentrated on individual elements of
   expert teaching. There has been less emphasis on understanding the complex
   real-life process of expert teaching in its entirety. The model presented
   here looks at an integrated approach to understanding the development of
   expert teachers through real-life learning experiences & related factors."
   -- [<A HREF="http://dx.doi.org/10.1007/0-387-25997-X_18">doi:10.1007/0-387-25997-X_18</A>]['12].

%A P. Nicholson
%A J. Walsh
%T Virtual experts: who's online?
%J 8th IFIP World Conf. on Computers in Education: 40 Years of Computers in
   Education: What Works?
%E Pittman, Joyce
%P 1-6
%M JUL
%D 2005
%K conf, WCCE, WCCE8, c2005, c200x, c20xx, Julia Walsh, eLearning, online, web,
   net, teaching, intelligent agent, agents
%X "There will be between 30 & 80 million online students in the world by 2025.
   Globally, school systems are investing huge resources in the development of
   online education programs in order to meet this demand. Related implications
   for online teaching have been largely ignored despite evidence of the greatly
   increased workload for online teachers & widespread student dissatisfaction
   with online leaming experiences. ... Intelligent software agents that can
   automate many routine online tasks & some aspects of learner interaction have
   enormous potential to [help]. ... Currently there is little progress being
   made in this area because of the lack of an agent role model ...  we discuss
   key foundational elements of the nature & basis for implementing elements of
   edu.expertise in s/w & how this could be used in developing agent persona
   models for specific edu.roles & a model for implementing pedagogical
   constructs in intelligent educational software."      (auth1@Deakin U., '12.)
   details@[<A HREF="http://dro.deakin.edu.au/view/DU:30005884">deakin</A>]['12].

%A J. E. Hirsch
%T An index to quantify an individual's scientific research output
%J PNAS
%V 102
%N 46
%P 16569-16572
%M NOV
%D 2005
%K jrnl, PNAS, JEHirsch, c2005, c200x, c20xx, zz0807, index, impact factor,
   h index, Hindex, KPI, KPIs, metric, metrics, success, citation, citations,
   researcher, quality, productivity, publish, perish, publication,
   publications, Gindex, coercive, manipulation, abuse, bibliometrics, science,
   scientific research, ethics
%X "I propose the index h, defined as the no. of papers with citation no. >= h,
   as a useful index to characterize the scientific output of a researcher."
   [Max. h s.t. his/her top h papers have at least h citations each.]
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0507655102">doi:10.1073/pnas.0507655102</A>]['07].
   Also see [<A HREF="http://dx.doi.org/10.1038/448737a">doi:10.1038/448737a</A>]['07].
  [Also search for: Hirsch Hindex]  and  [also search for: publish perish].
  [[Such an index is of course open to manipulation:
      Imagine an academic, X, whose mission when on a programme committee
      is to cause submitting authors to add references, often of little or
      no genuine relevance, to X's own work.  All it takes is a lazy,
      compliant, weak, or stressed editor to let it happen. Maybe you know X?]]
  * [Also search for: Hirsch c2020] *.

%A D. Raynaud
%A J.-M. Barnola
%A R. Souchez
%A R. Lorrain
%A J.-R. Petit
%A P. Duval
%A V. Y. Lipenkov
%T Palaeoclimatology:  The record for marine isotopic stage 11
%J Nature
%V 436
%P 39-40
%M JUL
%D 2005
%K jrnl, c2005, c200x, c20xx, climate, variability, change, CO2, Lake Vostok,
   Antarctica, ice core, ice age, ages, interglacial, level, temperature, dust,
   MIS 11, MIS11, greenhouse gas, gases, record
%X "The marine isotopic stage 11 (MIS 11) is an extraordinarily long
   interglacial period in the Earth's history that occurred some 400,000 y. ago
   & lasted for about 30,000 y.. During this period there were weak,
   astronomically induced changes in the distn of solar energy reaching the
   Earth. ... similar to those of today's interglacial period & they rendered
   the climate susceptible to other forcing - [eg] to changes in the level of
   atmospheric CO2. Here we use ice-core data from the Antarctic Vostok core to
   reconstruct a complete atmospheric CO2 record for MIS 11. ... indicates that
   values for CO2 throughout the interglacial period were close to the Earth's
   pre-industrial levels & that both solar energy & carbon dioxide may have
   helped to make MIS 11 exceptionally long. Anomalies in the oceanic carbonate
   system recorded in marine sediments at the time, [eg] while coral reefs were
   forming, apparently left no signature on atmospheric CO2 concentrations."
   -- [<A HREF="http://dx.doi.org/10.1038/43639b">doi:10.1038/43639b</A>]['13].
   (Also see Vostak@[<A HREF="http://en.wikipedia.org/wiki/Vostok,_Antarctica">wikip</A>][13],
   and ice_age@[<A HREF="http://en.wikipedia.org/wiki/Ice_age">wikip</A>][13].)

%A J. Stribling
%A D. Aguayo
%A M. Krohn
%T Rooter: A methodology for the typical unification of access points and
   redundancy
%J WMSCI
%D 2005
%K bogus, conf, spoof, random, paper, generator, c2005, c200x, c20xx, zz0115,
   SCIgen, conference, scam, bot, SCI, IIIS, WMSCI, WSEAS
%X About the program that generated the paper...
      "SCIgen is a program that generates random Comp. Sci. research papers,
   including graphs, figures, & citations. It uses a hand-written context-free
   grammar to form all elements of the papers. Our aim here is to maximize
   amusement, rather than coherence.  One useful purpose for such a program is
   to auto-generate submissions to conferences that you suspect might have very
   low submission standards. A prime example, which you may recognize from spam
   in your inbox, is SCI/IIIS & its dozens of co-located conferences (check out
   the very broad conference description on the WMSCI 2005 website). There's
   also a list of known bogus conferences. Using SCIgen to generate submissions
   for conferences like this gives us pleasure to no end. In fact, one of our
   papers was accepted to SCI 2005! ..."
   -- SCIgen@[<A HREF="http://pdos.csail.mit.edu/scigen/">mit</A>]['15].
   [Also search for: postmodernism generator].

%A H. G. Frankfurt
%T On Bullshit
%I PrincetonUP
%P 80
%D 2005
%K book, text, essay, c2005, c200x, c20xx, zz0713, spin, PR, management speak,
   writing, truth, hype, lies, lying, false claims, mendacity, obfuscation,
   evasion, exaggeration, manipulation, trendy, bandwagon, pithy, philosophy,
   Zimmer, banned, Markowetz, systems biology, MolBio
%X 1st ed 2005; pb us$10; us isbn:0691122946; us isbn13:978-0691122946.
   'One of the most salient features of our culture is that there is so much
   bullshit. Everyone knows this. Each of us contributes his share. But we tend
   to take the situation for granted. Most people are rather confident of their
   ability to recognize bullshit & to avoid being taken in by it. So the
   phenomenon has not aroused much deliberate concern. We have no clear
   understanding of what bullshit is, why there is so much of it, or what
   functions it serves. And we lack a conscientiously developed appreciation of
   what it means to us. In other words, as HF writes, "we have no theory."
   F., one of the world's most influential moral philosophers, attempts to build
   such a theory here. ...'
   -- [<A HREF="http://press.princeton.edu/titles/7929.html">P</A>]['13].
   (Also see C.Zimmer's 'List of Banned Words'
      [<A HREF="http://blogs.discovermagazine.com/loom/2009/11/30/the-index-of-banned-words-the-continually-updated-edition/">www</A>][30/11/2009], and
   F.Markowetz's 'On Systems Biology and Bullshit'
      [<A HREF="http://scientificbsides.wordpress.com/2012/02/27/on-systems-biology-and-bullshit/">w.press</A>][27/2/2012].)

%A R. M. Colomb
%T Formal versus material ontologies for information systems interoperation in
   the semantic web
%J COMPJ
%V 49
%N 1
%P 4-19
%M JAN
%D 2006
%K jrnl, COMPJ, ontology, SUMO, SUO, c2006, c200x, c20xx, database, zz0106
%X "... argues that, for the purposes of information systems interoperation &
   the semantic web, application-independent upper ontologies are unlikely to be
   successful because of semantic heterogeneity. However, the paper argues for a
   distinction in upper ontologies between formal & material ontologies, based
   on analogies with concepts in Kant's synthetic a priori, & that formal
   ontologies whose focus is on how we see the world are more likely to be
   successfully developed in the absence of applications than are material
   ontologies, which attempt to catalog the world a priori."  [28 refs]
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxh147">doi:10.1093/comjnl/bxh147</A>]['06].

%A P. Mellars
%T Why did modern human populations disperse from
   Africa ca.60,000 years ago?  A new model
%J PNAS
%V 103
%N 25
%P 9381-9386
%M JUN
%D 2006
%K jrnl, PNAS, c2006, c200x, c20xx, brain, modern, human, behaviour,
   evolution, language, Africa, migration, mitochondria
%X "Recent research has provided inc. support for the origins of anatomically
   & genetically 'modern' human populations in Africa between 150,000 & 200,000
   y.ago, followed by a major dispersal ... to both Asia & Europe sometime after
   ca.65,000 ... Studies of both the mitochondrial DNA (mtDNA) mismatch patterns
   in modern African popns & related mtDNA lineage-analysis patterns point to a
   major demographic expansion [~] 80,000 to 60,000 B.P., probably deriving from
   a small geographical region of Africa. Recent archaeological discoveries in
   S. & E. Africa suggest that, at ~ the same time, there was a major increase
   in the complexity of the technological, economic, social, & cognitive
   behavior of certain African groups, which could have led to a major
   demographic expansion of these groups in competition with other, adjacent
   groups. It is suggested that this complex of behavioral changes (possibly
   triggered by the rapid environmental changes around the transition from
   oxygen isotope stage 5 to stage 4) could have led not only to the expansion
   of the L2 & L3 mitochondrial lineages over the whole of Africa but also to
   the ensuing dispersal of these modern popns over most regions of Asia,
   Australasia, & Europe, & their replacement (with or without interbreeding) of
   the preceding 'archaic' popns in these regions."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0510792103">doi:10.1073/pnas.0510792103</A>]['12].

%A G. Lekakos
%A G. M. Giaglis
%T Improving the prediction accuracy of recommendation algorithms:
   Approaches anchored on human factors
%J Interacting with Computers
%V 18
%N 3
%P 410-431
%M MAY
%D 2006
%K c2006, c200x, c20xx, recommender, algorithm, nearest neighbour
%X "[RS] ... special class of personalized systems that aim at predicting a
   user's interest on available products & services by relying on previously
   rated items or item features. Human factors associated with a user's
   personality or lifestyle, ... [We] demonstrate how the concept of lifestyle
   can be incorporated in the [RS] to improve the prediction accuracy by
   efficiently managing the problem of limited data availability. We propose 2
   approaches: one relying on lifestyle alone & another integrating lifestyle
   within the nearest neighbor approach. Both approaches are empirically tested
   in the domain of recommendations for personalized [TV] ads. & are shown to
   outperform existing nearest neighborhood approaches in most cases."
   -- [<A HREF="http://dx.doi.org/10.1016/j.intcom.2005.11.004">doi:10.1016/j.intcom.2005.11.004</A>]['06].
      [<A HREF="http://sense.eltrun.gr/members/m_glekakos.html">auth1</A>]['06].

%A R. K. Standish
%T Theory of Nothing
%I BookSurge
%P 262
%D 2006
%K book, text, c2006, c200x, c20xx, theory, everything, nothing, AI,
   complex systems, reality, observer, physics, mind, cognitive science
%X "... The necessity for observed reality to be consistent with the observer's
   existence implies a strong connection between fundamental physics and
   cognitive science. A revolutionary understanding of why physics has the
   form it does, and why our minds are the way they are is forged. ..."
   1st ed 2006;  pb us$16; uk us isbn:1921019638; uk us isbn13:978-1921019630.
   RKS@[<A HREF="http://www.hpcoders.com.au/rks.html">hpcoders</A>]['10].

%A S. Bringsjord
%A A. Shilliday
%A J. Taylor
%A B. van Heuveln
%A J. Baumes
%A K. Ross
%T A new Godelian argument for hypercomputing minds based on the
   busy beaver problem
%J J. of Applied Math. and Comp.
%V 176
%N 2
%P 516-530
%M MAY
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0406, theory, computation, computable,
   human, mind, AI, limit, limited, hypercompute, Godel
%X An argument (not a proof) that humans are not limited "at or below
   the Turing limit"
   -- [<A HREF="https://doi.org/10.1016/j.amc.2005.09.071">doi:10.1016/j.amc.2005.09.071</A>]['24] via Charles T.,
      [<A HREF="http://kryten.mm.rpi.edu/laihyper11.pdf">pdf</A>]['06].
   [Also search for: Busy Beaver].

%A K. L. Kuntz
%A D. W. Larson
%T Influence of microhabitat constraints and rock-climbing disturbance on
   cliff-face vegetation communities
%J Conservation Biology
%V 20
%N 3
%P 821-852
%M JUN
%D 2006
%K jrnl, biol, c2006, c200x, c20xx, climb, damage, harm, plant, plants,
   stats, statistics, cause, effect, causality, example, zz0706
%X "[some say] rock climbing has significant -ve effects on cliff biota.
   Most ... not controlled for variation in microsite characteristics when
   comparing areas with & without climbing presence. ...
   We solved these problems by sampling climbing areas used by advanced "sport"
   climbers & quantifying differences in microtopography between climbed &
   control cliffs. ...  our results were consistent with the majority of prior
   work on impacts of climbing (i.e., sport-climbed cliff faces supported a
   lower mean richness of vascular plants & bryophytes & sig. different
   frequencies of individual species when compared with pristine cliff faces).
   ... the differences in vegetation were not related to climbing disturbance
   but rather to the selection by sport climbers of cliff faces with microsite
   characteristics that support less vegetation. Climbed sites had not diverged
   toward a separate vegetation community; instead, they supported a subset of
   the species found on pristine cliff faces. ..."
   -- [<A HREF="http://dx.doi.org/10.1111/j.1523-1739.2006.00367.x">pdf</A>]['06].

%A S. Dehnadi
%T Testing programming aptitude
%J PPIG Annual conf.
%W Brighton
%P ?-?
%M SEP
%D 2006
%K conf, c2006, c200x, c20xx, zz1006, teaching, teach, programming,
   student, students, skill, skills, ability
%X "An initial cognitive study of early learning of programming aimed to
   extract experimental test data to establish novices' understanding process
   has been carried out by us.This empirical study was inspired by the notion
   that different people bring different patterns of knowledge in any new
   learning process, & demonstrated that how each student tackles the problem
   in a different way based on their mental model. The initial study suggests
   that success in the first stage of an introductory programming course is
   predictable, by noting consistency in use of the mental models which
   students apply to a basic programming problem even before they have had any
   contact with programming notation, but the consistency/inconsistency
   measurement was somewhat subjective. In this paper I present an objective
   marking method which hope will lead us to more precise & more finely-
   graduated predictions. This method is being trailed in at least 1 exp..."
   -- [<A HREF="http://www.cs.mdx.ac.uk/research/PhDArea/saeed/">www</A>]['06].
   (sup. is R. Bornat)

%A P. Caravelas
%A G. Lekakos
%T MoRe: A movie recommendation system combining collaborative filtering and
   content-based filtering
%J EuroITV
%W Athens
%P ?-?
%M MAY
%D 2006
%K conf, c2006, c200x, c20xx, recommender, movies, rating, ratings
%X auth2  ELTRUN.Athens.gr, Athens U of Econ and Biz  (via I.Z.)
   -- [<A HREF="http://sense.eltrun.gr/members/m_glekakos.html">auth2</A>]['06].

%A V. Devedzic
%T Semantic Web and Education
%I Springer
%P 365
%M OCT
%D 2006
%K book, c2006, c200x, c20xx
%X au$153; uk us isbn:0387354166.

%A M. Stollberg
%A D. Roman
%A J. de Bruijn, D.Fensel, H.Lausen, A.Polleres, J.Domingue
%T Enabling Semantic Web Services: The Web Service Modelling Ontology
%I Springer
%P 192
%M OCT
%D 2006
%K book, c2006, c200x, c20xx, WSMO, OWL-S, OWLs, WSDL-S, WSDLs. deBruijn
%X hb au$67; uk us isbn:3540345191.

%A M. Berry
%T Greetings in Jesus Name
%I HarbourBooks
%P 512
%M OCT
%D 2006
%K book, c2006, c200x, c20xx, zz0912, internet, www, web, site, scam, email,
   spam, fraud, phishing, advice fee, 419, 419scam, 419eater, 419ers, defn,
   Nigerian, lottery, bank account, bequest, will, pigeon drop,
   confidence trick, con man, conman, tricks, baiting
%X 1st ed 2006; uk us isbn:1905128088; uk us isbn13:978-1905128082.
   Also see 419eater@[<A HREF="http://en.wikipedia.org/wiki/419eater.com">wkip</A>]['12].
   and N_scam@[<A HREF="http://en.wikipedia.org/wiki/Nigerian_scam">wikip</A>]['12].

%A T. Freeth
%A et al
%T Decoding the ancient Greek astronomical calculator known as the
   Antikythera Mechanism
%J Nature
%V 444
%P 587-591
%M NOV
%D 2006
%K jrnl, history, c2006, c200x, c20xx, archaeology, zz1206
%X "... geared device, constructed around the end of the second century bc. It
   is known that it calculated & displayed celestial information, particularly
   cycles such as the phases of the moon and a luni-solar calendar. ...
   technically more complex than any known device for at least a millennium
   afterwards. ... The mechanism predicted lunar & solar eclipses on the basis
   of Babylonian arithmetic-progression cycles. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature05357">doi:10.1038/nature05357</A>]['06].
   Also see [<A HREF="http://dx.doi.org/10.1038/455867a">doi:10.1038/455867a</A>]['08].
      (Andrew Carol recreated the mechanism in *lego*
       -- Lego@[<A HREF="http://acarol.woz.org/">woz.org</A>]['10].)
   [Also search for: Antikythera mechanism] and
   [also search for: Archimedes sphere].

%A L. N. Soldatova
%A R. D. King
%T An ontology of scientific experiments
%J J. of the Royal Society Interface
%V 3
%N 11
%P 795-803
%D 2006
%K jrnl, experiment, c2006, c200x, c20xx, OWL-DL, OWLDL, EXPO, SUMO
%X "... no general ontology of experiments exists. We propose the ontology EXPO
   ... . EXPO links the SUMO (the Suggested Upper Merged Ontology) with subject-
   specific ontologies of experiments by formalizing the generic concepts of
   experimental design, methodology & results representation. EXPO is expressed
   in the W3C standard ontology language OWL-DL. We demonstrate the utility of
   EXPO & its ability to describe different experimental domains, by applying it
   to 2 exp's: one in high-energy physics & the other in phylogenetics. ..."
   -- [<A HREF="http://dx.doi.org/10.1098/rsif.2006.0134">doi:10.1098/rsif.2006.0134</A>]['06].
   -- [<A HREF="http://users.aber.ac.uk/lss/Inteface.pdf">pdf@aber</A>]['07].
   (Also see [<A HREF="http://www.newscientisttech.com/article/dn9288-translator-lets-computers-understand-experiments-.html">New Sci.</A>]['06])

%A L. Soldatova
%A A. Clare
%A A. Sparkes
%A R. D. King
%T An ontology for a robot scientist
%J Bioinformatics
%V 22
%P 464-471
%D 2006
%O ISMB06
%K conf, MolBio, ISMB, c2006, c200x, c20xx, EXPO, OWL, experiment, AClare,
   RDKing
%X "... Robot Scientists provide a unique test bed for the development of
   methodologies for the curation & annotation of scientific experiments:
   because the experiments are conceived & executed automatically by computer,
   it is possible to completely capture & digitally curate all aspects of the
   scientific process. This new ability brings with it significant technical
   challenges. To meet these we apply an ontology driven approach to the
   representation of all the Robot Scientist's data & metadata. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl207">doi:10.1093/bioinformatics/btl207</A>]['06].

%A N. Hurst
%A K. Marriot
%A D. Albrecht
%T Solving the simple continuous table layout problem
%J DocEng 2006
%W Amsterdam
%P ?-?
%D 2006
%K conf, c2006, c200x, c20xx, njHurst, document, tables
%X [<A HREF="http://njhurst.com/publications/hma-2006.pdf">pdf</A>]['07].

%T SR-71 Blackbird Pilot's Flight Manual
%I Luli.com
%D 2006
%K book, c2006, c200x, c20xx, SR-71, SR71, Blackbird, Habu, sled, spy plane,
   Lockheed, skunk works, M21, YF-12A, YF12A, A-12, A12, aircraft
%X "... this Flight Operating Handbook provides a revealing look into the
   cockpit of one of history's great planes. Just recently declassified, this
   book contains all the basic pilot's instructions for the SR-71 and two-seat
   training model. ..."
   2006, us$22; us isbn:1411699378; us isbn13:978-1411699373.

%A J. Richter
%T CLR via C# (pro developer)
%I Microsoft
%P 736
%D 2006
%K book, text, c2006, c200x, c20xx, microsnot, programming, introduction,
   CLR, Common Language, Runtime, Csharp, C#, cc, .net, dot net, dotNet
%X 2nd ed 2006; pb us$38; uk us isbn:0735621632; uk us isbn13:978-0735621633.

%A J. Lovelock
%T The Revenge of Gaia
%I BasicBooks
%P 208
%D 2006
%K book, c2006, c200x, c20xx, James Lovelock, Gaia, renewable, energy,
   climate change
%X The Revenge of Gaia, Earth's Climate Crisis and the Fate of Humanity.
   "... Lovelock diagnoses the Earth as suffering from a fever. Its atmospheric
   & oceanic temperatures are rising. The infecting agent is a complex organism
   that has emerged only recently in Earth's history, although it spread
   rapidly. It's Homo sapiens - ourselves. Humans have usurped woods & prairies,
   cutting down forests & turning rangeland into farms for our sustainance. ...
   Gaia's revenge will be to exterminate her affliction. ..."
   1st ed 2006, hb us$12; uk us isbn:046504168X; uk us isbn13:978-0465041688.

%A N. Shadbolt
%A T.Brody
%A L. Carr
%A S. Harnad
%T The open research web: A preview of the optimal and the inevitable
%B Open Access: Key Strategic, Technical and Economic Aspects
%E N. Jacobs
%I Chandos
%D 2006
%K c2006, c200x, c20xx, www, web, OA, open access, publication, research,
   impact factor, quality, ranking, rankings, Research Assessment Exercise, RAE,
   ac uk, academic, eprint, eprints, citebase, g-factor, gFactor, rank
%X "... GNU EPrints and Citebase, together with the growing webwide database of
   Open Access (OA) articles, ... Research Assessment Exercise's recent
   transition to metrics  ..."
   -- [<A HREF="http://eprints.ecs.soton.ac.uk/12453/">s'hampton uk</A>]['09],
      [<A HREF="http://eprints.ecs.soton.ac.uk/12369/">www</A>]['09].
   (Also see [<A HREF="http://openaccess.eprints.org/">eprints.org</A>]['09],
   and [<A HREF="http://www.universitymetrics.com/node/3#What">u.m.</A>]['09].)

%A N. T. Spark
%T A History of Murphy's Law
%I PeriscopeFilm
%P 68
%D 2006
%K book, c2006, c200x, c20xx, zz1209, Murphy's, Murphys, law, laws, stuff up,
   funny, rocket sled, speed
%X 1st ed 2006; pb us$16; us isbn:0978638891; us isbn13:978-0978638894.
   "... Tipped off by his next door neighbor that Murphy may have worked at
   Edwards Air Force Base, and that the Law may have come into being after
   a rocket sled experiment went awry ..."
   [Also search for: Murphy law].

%A L. Egghe
%T Theory and practise of the g-index
%J Scientometrics
%V 69
%N 1
%P 131-152
%D 2006
%K jrnl, c2006, c200x, c20xx, publish, perish, research, publication,
   publications, G index, Gindex, Hindex, citation, citations, metric, metrics,
   modified, bibliometrics, impact factor, quality, KPI, KPIs, practice
%X "Given a set of articles ranked in decreasing order of the # of citations
   that they received, the g-index is the unique largest number such that
   the top g articles together received at least g**2 citations."
   -- [<A HREF="https://documentserver.uhasselt.be//bitstream/1942/981/1/theory%20%26%20practice.pdf">uhasselt.be</A>]['22],
      [<A HREF="http://dx.doi.org/10.1007/s11192-006-0144-7">doi:10.1007/s11192-006-0144-7</A>]['10].
   [Also search for: Hindex] and [also search for: Gindex].

%A P. Seibt
%T Algorithmic Information Theory: Mathematics of Digital Information Processing
%I SpringerVerlag
%P 444
%D 2006
%K book, text, c2006, c200x, c20xx, information
%X 1st ed c2006; hb us$116; uk us isbn:3540332189; uk us isbn13:978-3540332183.
   "... five topics: Data Compression, Cryptography, Sampling (Signal Theory),
   Error Control Codes, Data Reduction. ..."

%A B. Rosenblum
%A F. Kuttner
%A F. Kuttner
%T Quantum Enigma: Physics Encounters Consciousness
%I OUP
%D 2006
%K book, text, OUP, c2006, c200x, c20xx, quantum, quanta, conscious, mind,
   free will, observer
%X 1st ed 2006; hb us$52; uk us isbn:019517559X; uk us isbn13:978-0195175592.
   2nd ed 2011; pb us$12; uk us isbn:0199753814; uk us isbn13:978-0199753819.
   "... exploring consciousness itself - and encounter quantum mechanics.
   Free will and anthropic principles become crucial issues, and the connection
   of consciousness with the cosmos suggested by some leading q.cosmologists ...
   ... In the few decades since the Bell's theorem experiments established the
   existence of entanglement (Einstein's "spooky action"), interest in the
   foundations, and the mysteries, of quantum mechanics has accelerated. In
   recent years, physicists, philosophers, computer engineers, and even
   biologists have expanded our realization of the significance of quantum
   phenomena. This 2nd edition includes such advances. The authors have also
   drawn on many responses from readers and instructors to improve the clarity
   of the book's explanations."

%A D. R. Poulter
%A F. P. McKenna
%T Is speeding a "real" antisocial behaviour? A comparison with other
   antisocial behaviors
%J Accident Analysis and Prevention
%V 39
%N 2
%P 384-389
%M MAR
%D 2006
%K jrnl, c2006, c200x, c20xx, accidents, road safety, speed, speeding, limit,
   uk, survey, public, human behaviour, traffic,  car, cars, driving
%X "The relationship between speed and crashes has been well established in the
   literature ...  The extent to which the public regard speeding as a problem
   that requires enforcement is less clear. Analysis was conducted on public
   perceptions of antisocial behaviors including speeding traffic. The data was
   collected as part of the British Crime Survey, a face-to-face interview ...
   Results revealed that speeding traffic was perceived as the greatest problem
   in local communities, regardless of whether respondents were male or female,
   young, middle aged, or old. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.aap.2006.08.015">doi:10.1016/j.aap.2006.08.015</A>]['11].

%T Colossus: The Secrets of Bletchley Park's Codebreaking Computers
%E B. Jack Copeland et al
%I OUP
%P 480
%D 2006
%K book, text, OUP, c2006, c200x, c20xx, code, codes, breaking, Bletchley Park,
   WW2, WWII, Ultra, history, computing, computer, Colossus, Enigma, Lorenz,
   cryptanalysis, cypher, cipher
%X 1st ed 2006; hb stg13; uk us isbn:019284055X; uk us isbn13:978-0192840554.
   [Also search for: Bletchley Park]  &  [also search for: Roberts Lorenz].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">B.Park</A>].)

%A C. Anderson
%T The Long Tail: Why the Future of Business is Selling Less of More
%I HachetteBooks
%P 267
%M JUL
%D 2006
%K book, c2006, c200x, c20xx, zz0116, business, marketing, choice, products,
   inventory, demand, hits, misses, hit, blockbuster, popular culture,
   movies, pop, iTunes, Amazon, Netflix
%X 1st ed  2006; hb us$25; uk us isbn:1401302378; uk us isbn13:978-1401302375.
   Revised 2008; pb us$14; uk us isbn:1401309666; uk us isbn13:978-1401309664.
   "... shows how the future of commerce and culture isn't in hits, the
   high-volume head of a traditional demand curve, but in what used to be
   regarded as misses--the endlessly long tail of that same curve. ..."
   (But soon there were alternative opinions.)
   [Also search for: Elberse c2013] - contrary.

%A L. Gollogly
%A H. Moomen
%T Ethical dilemmas in scientific publication: pitfalls and solutions for
   editors
%J Revista de Saude Publica
%V 40 (N Esp)
%P 24-29
%M AUG
%D 2006
%K jrnl, c2006, c200x, c20xx, zz1211, ICMJE, Vancouver, publish, perish,
   science, research, dLd, editor, editors, editorial, conduct, ethics, fraud,
   abuse, fabrication, falsification, duplication, gift, guest author,
   ghost authorship, plagiarism, authors, review, referees, refereeing,
   coercive citation, publications, bias, policy, policies, conduct, academic,
   misconduct, corrupt, zzEthics, journals
%X "Editors of sci.js. need to be conversant with the mechanisms by which
   sci. misconduct is amplified by publn practices. ... provides defns, ways to
   document the extent of the problem, & examples of editorial attempts to
   counter fraud. Fabrication, falsification, duplication, ghost authorship,
   gift authorship, lack of ethics approval, non-disclosure, 'salami' publns,
   conflicts of interest, auto-citation, duplicate submission, duplicate
   publns, & plagiarism are common problems. Editorial misconduct includes
   failure to observe due process, undue delay in reaching decisions &
   communicating these to authors, inappropriate review procs., & confounding a
   journal's content with its advertising or promotional potential. Editors also
   can be admonished by their peers for failure to investigate suspected
   misconduct, failure to retract when indicated, & failure to abide voluntarily
   by the six main sources of relevant international guidelines on research,
   its reporting & editorial practice. Editors are in a good posn to promulgate
   reasonable standards of practice, & can start by using consensus guidelines
   on publication ethics to state explicitly how their js. function. Reviewers,
   eds., authors & readers all then have a better chance to understand, & abide
   by, the rules of publishing."
   -- [<A HREF="http://dx.doi.org/10.1590/S0034-89102006000400004">doi:10.1590/S0034-89102006000400004</A>]['11].
   [Also search for: publish perish].

%A S. B. Seymore
%T How does my work become our work?  Dilution of authorship in
   scientific papers, and the need for the academy to obey copyright law
%J Richmond J. of Law and Tech.
%V 12
%N 3
%D 2006
%K TR, c2006, c200x, c20xx, zz1219, university, research, ethics, publication,
   paper, scientific, publish, perish, author, guest, gift, authorship, faculty,
   student, copyright, law, ICMJE, intellectual property, IP
%X "Professors enjoy a world of extensive institutional autonomy & individual
   academic freedom. Universities & courts defer to a prof's judgment for
   'genuinely academic decisions' unless they depart from academic norms.
   Unis., courts, & professional societies should intervene, however, when
   academic norms & custom do not comport with the law. The need to 'publish or
   perish,' both in academic science & increasingly in industry, has led
   professors to publish papers whose authorship is suspect. ..."
   -- [<A HREF="http://scholarship.richmond.edu/jolt/vol12/iss3/4">www</A>]['19].
   [Also search for: publish perish].

%A P. Foukai
%A S. Frohlich
%A H. Spruit
%A T. M. L. Wigley
%T Variations in solar luminosity and their effect on the Earth's climate
%J Nature
%V 443
%P 161-166
%M SEP
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0713, sun, solar, influence, earth, climate,
   change, CO2, global warming, temperature, rise, minimum, sunspot, spots,
   cycle, cycles, Maunder, luminosity
%X "Variations in the Sun's total energy output (luminosity) are caused by
   changing dark (sunspot) & bright structures on the solar disk during the
   11-year sunspot cycle. The var'ns measured from spacecraft since 1978 are too
   small to have contributed appreciably to accelerated global warming over the
   past 30 years. ... we show that detailed analysis of these small output
   var'ns has greatly advanced our understanding of solar luminosity change, &
   this new understanding indicates that brightening of the Sun is unlikely to
   have had a sig.influence on global warming since the 17th C. Additional
   climate forcing by changes in the Sun's output of ultraviolet light, & of
   magnetized plasmas, cannot be ruled out. The suggested mechanisms are,
   however, too complex to evaluate meaningfully at present."  [78 refs.]
   -- [<A HREF="http://dx.doi.org/10.1038/nature05072">doi:10.1038/nature05072</A>]['13].
   (I.e., sun has only a small effect.)

%E K. Doya
%E S. Ishii
%E A. Pouget
%E R. P. N. Rao
%E Bayesian Brain: Probabilistic Approaches to Neural Coding
%S Computational Neuroscience
%I MITpress
%P 340
%D 2007
%K book, text, c2007, c200x, c20xx, brain, neuroscience, neural spikes
%X 1st ed 2007; hb us$47; uk us isbn:026204238X; uk us isbn13:978-0262042383.

%A R. Gitzel
%A I. Ott
%A M. Schader
%T Ontological extension to the MOF metamodel as a basis for code generation
%J COMPJ
%V 50
%N 1
%P 93-115
%M JAN
%D 2007
%K jrnl, COMPJ, c2007, c200x, c20xx, zz0207, ontology, non-linear, OMEGA,
   metamodeling
%X "...ontological metamodel extension for generative architectures (OMEGA), an
   extension to the Meta Object Facility metamodel which allows non-linear
   metamodeling. The article begins with a discussion of non-linear metamodeling
   in general & briefly describes several options available to the designers of
   a metamodeling framework supporting orthogonal metamodeling...."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxl052">doi:10.1093/comjnl/bxl052</A>]['07].

%T Emergence of Communication and Language
%E C.Lyon
%E C.L.Nehaniv
%E A.Cangelosi
%P 400
%I SpringerVerlag
%D 2007
%K book, text, c2007, c200x, c20xx, Alife, AI, evolution, intelligent agents,
   agent, digital organism, simulation
%X "...principal theme is the importance of studies involving artificial agents,
   their contribution to the body of knowledge on the emergence of communication
   and language, and the role of simulations in exploring some of the most
   significant issues. ..."
   hb euro77; uk us isbn13:978-1846284915.

%A P. J. Lu
%A P. J. Steinhardt
%T Decagonal and quasi-crystalline tilings in medieval Islamic architecture
%J Science
%V 315
%N 5815
%P 1106-1110
%M FEB
%D 2007
%K jrnl, c2007, c200x, c20xx, zz0207, quasi crystal, quasicrystal, aperiodic,
   2D, tile, tiles, tiling, girih, Penrose
%X "... show that by 1200C.E. a conceptual breakthrough occurred in which girih
   patterns were reconceived as tessellations of a special set of equilateral
   polygons ("girih tiles") decorated with lines. These tiles enabled the
   creation of increasingly complex periodic girih patterns, & by the 15th c.,
   the tessellation approach was combined with self-similar transformations to
   construct nearly perfect quasi-crystalline Penrose patterns, five centuries
   before their discovery in the West."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1135491">doi:10.1126/science.1135491</A>]['07],
      [<A HREF="http://www.sciencemag.org/cgi/content/abstract/315/5815/1106">sciencemag</A>]['07].
   [Also search for: aperiodic tiling].

%A M. Demir
%A L. A. Weitekamp
%T I am so happy 'cause today I found my friend: Friendship and
   personality as predictors of happiness
%J J. of Happiness Studies
%V 8
%N 2
%D 2007
%K jrnl, c2007, c200x, c20xx, zz0614, happiness, well being, wellbeing,
   friend, friends, friendship, companionship, quality, number of,
   stats, predict
%X "... investigated the rel. between personality, # of friends, best friendship
   quality & happiness among 423 young adults (n=300 women). The main interest
   was to examine whether friendship contributed to h. while controlling for
   personality. [error: 'Friendship', corr:'Study'] variables accounted for 58%
   of the variance in h.. ... revealed that f'ship quality predicted h. above
   & beyond the influence of personality & # of friends, but f'ship conflict
   was not a sig. predictor. Additional analyses revealed that the companionship
   & self-validation features of f'ship quality were predictive of h. while
   controlling for gender & personality. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/s10902-006-9012-7">doi:10.1007/s10902-006-9012-7</A>]['14].
   [Also search for: happiness well being].

%A G. Palla
%A A.-L. Barabasi
%A T. Vicsek
%T Quantifying social group evolution
%J Nature
%V 446
%P 664-667
%M APR
%D 2007
%K jrnl, c2007, c200x, c20xx, clique percolation, groups, society, zz0407,
   small, large, overlapping, social networks, cFinder
%X "... an algorithm based on clique percolation that allows us to investigate
   the time dependence of overlapping communities on a large scale, & thus
   uncover basic relationships characterizing community evolution. Our focus is
   on networks capturing the collaboration between scientists & the calls
   between mobile phone users. We find that large groups persist for longer if
   they are capable of dynamically altering their membership, suggesting that
   an ability to change the group composition results in better adaptability.
   The behaviour of small groups displays the opposite tendency - the condition
   for stability is that their composition remains unchanged. We also show that
   knowledge of the time commitment of members to a given community can be used
   for estimating the community's lifetime. These findings offer insight into
   the fundamental differences between the dynamics of small groups & large
   institutions."
   -- [<A HREF="http://dx.doi.org/10.1038/nature05670">doi:10.1038/nature05670</A>]['07],
      [<A HREF="http://angel.elte.hu/~pallag/publ.html">auth1</A>]['07].

%A P. Grunwald
%T A review of "Statistical and Inductive Inference by Minimum Message Length"
%J COMPJ
%V 50
%N 3
%P 369-370
%M MAY
%D 2007
%K review, COMPJ, c2007, c200x, c20xx, MDL, Wallace, Rissanen, description,
   zz0407
%X [<A HREF="http://dx.doi.org/10.1093/comjnl/bxl027">doi:10.1093/comjnl/bxl027</A>]['07].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">C.S.Wallace's publications</A>].)

%A M. Peters
%A G. Rhodes
%A L. W. Simmons
%T Contributions of the face and body to overall attractiveness
%J Animal Behaviour
%V ?
%N ?
%P ?
%D 2007
%K jrnl, c2007, c200x, c20xx, zz0507, stats, beauty, attractive, male, female,
   facial, mate, selection
%X "... found that the face & body did not interact when an overall
   attractiveness judgement was made. We also investigated the indep. contrib.
   of rated attractiveness of the face & the body to ratings of overall
   attractiveness. Face & body attractiveness each made sig. indep.
   contributions to overall attractiveness in males & females. For both sexes,
   face attractiveness predicted overall attractiveness more strongly than did
   body attractiveness, & this difference was significant in males. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.anbehav.2006.07.012">doi:0.1016/j.anbehav.2006.07.012</A>]['07] (in press 5/'07) auths @ UWA
   [also search for: beauty].

%A D. Butler
%T Academics strike back at spurious rankings
%J Nature
%V 447
%P 514-515
%M MAY
%D 2007
%K news, c2007, c200x, c20xx, college, THES, university ranking, rank, rating,
   ratings, ISI, impact factors, stats, citations, counts, zz0607, misuse,
   wrong, errors, mistakes
%X "... After cleaning up ISI data on all UK papers for such effects, the
   Leeds-based consultancy Evidence Ltd, found the true number of papers from
   [Uni] Oxford, for example, to be 40% higher than listed by ISI ...
   ... One, for example, weights citations on the basis of their sci. field, so
   that a uni. that does well in a heavily cited field doesn't get an
   artificial extra boost..."
   -- [<A HREF="http://dx.doi.org/10.1038/447514b">doi:10.1038/447514b</A>]['07].

%A K.-T. Jeang
%T Impact factor, H index, peer comparisons, and retrovirology: Is it
   time to individualize citation metrics?
%J Retrovirology
%V 4
%N 42
%M JUN
%D 2007
%K editorial, essay, jrnl, ejrnl, c2007, c200x, c20xx, h index, Hindex,
   peer comparison, impact factors, zz0607, JIF, IF, publication, publications,
   citation, index, modified bibliometrics, metrics, citations, ISI,
   publish, perish
%X "... Although historically journal IF has been a convenient quantitative
   shorthand, has its (mis)use contributed to inaccurate perceptions of the
   quality of scientific articles? Is now the time that equally convenient but
   more individually accurate metrics be adopted?"  [11 refs]
   -- [<A HREF="http://dx.doi.org/10.1186/1742-4690-4-42">doi:10.1186/1742-4690-4-42</A>]['07].
  [Also search for: Hindex] and [also search for: Gindex].

%A P. Ball
%T Achievement index climbs the ranks
%J Nature
%V 448
%P 737
%M AUG
%D 2007
%K news, views, c2007, c200x, c20xx, zz0807, key performance indicator,
   KPI, KPIs, Hirsch, indicators, research, researcher, prediction, predicting,
   success, impact factor, metric, metrics, h index, Hindex, publish, perish
%X "... h-index was first proposed in 2005 by Hirsch ... the h-index offers an
   alternative: it is the number n of a researcher's papers that have all
   received at least n citations. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/448737a">doi:10.1038/448737a</A>]['07].
   [Also search for: Hindex] and [also search for: Gindex].
   [Also search for: publish perish].

%A D. C. Marinescu
%A G. M. Marinescu
%T The Boole lecture quantum information: A glimpse at the strange and
   intriguing future of information
%J COMPJ
%V 50
%N 1
%P 505-521
%M SEP
%D 2007
%K jrnl, COMPJ, c2007, c200x, c20xx, computing, physics, computer,
   quantum theory, information, Qbism, qubit, decoherence, zz0907
%X [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm017">doi:10.1093/comjnl/bxm017</A>]['07].
   [Also search for: Qbism physics].

%A D. C. Dennett
%T Breaking the Spell: Religion as a Natural Phenomenon
%I Penguin
%P 448
%D 2007
%K book, text, c2007, c200x, c20xx, zz0907, religious belief, faith
%X pb, us$16, isbn:0143038338; isbn13:978-0143038337.

%A J. Schaeffer
%A N. Burch
%A Y. Bjornsson
%A A. Kishimoto
%A M. Muller
%A R. Lake
%A P. Lu
%A S. Sutphen
%T Checkers is solved
%J Science
%V 317
%N 5844
%P 1518-1522
%M SEP
%D 2007
%K jrnl, c2007, c200x, c20xx, zz0907, chequers, draughts, solve, solved,
   board, game, fair, win, loss, lose, draw
%X "... roughly 500 billion billion possible posns (5 x 10^20). The task of
   solving the game, determining the final result in a game with no mistakes
   made by either player, is daunting. Since 1989, almost continuously, dozens
   of computers have been working on solving checkers, applying state-of-the-art
   AI techs. to the proving process. ...announces that checkers is now solved:
   Perfect play by both sides leads to a draw. This is the most challenging
   popular game to be solved to date, roughly 1 million times as complex as
   Connect 4. AI technology has been used to generate strong heuristic-based
   game-playing programs, such as Deep Blue for chess. Solving a game takes
   this to the next level by replacing the heuristics with perfection."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1144079">doi:10.1126/science.1144079</A>]['07].

%A K. Marriot
%A P. Moulder
%A N. Hurst
%T Automatic float placement in multi-column documents
%J DocEng 2007 to appear
%W Winnipeg
%D 2007
%K conf, c2007, c200x, c20xx, document, layout, njHurst

%A N. Hurst
%A K. Marriot
%T Approximating text by its area
%J DocEng 2007 to appear
%W Winnipeg
%D 2007
%K conf, c2007, c200x, c20xx, document, layout, njHurst, zz1007

%A N. Hurst
%A P. Harrison
%T Low-cost active heat storage
%J ReNew Winter (to appear)
%W Melbourne .au
%D 2007
%K conf, c2007, c200x, c20xx, environment, environmental, building, energy use,
   njHurst
%X [<A HREF="http://njhurst.com/">njh</A>]['07].

%A J.-K. Choi
%A S. Bowles
%T The coevolution of parochial altruism and war
%J Science
%V 318
%N 5850
%P 636-640
%M OCT
%D 2007
%K jrnl, c2007, c200x, c20xx, zz1107, Alife, simulation, agent based,
   prisoners, prisoner's dilemma, IPD, tribe, tribalism, conflict, wars, human,
   evolution, altruism, cooperation, hostility, behaviour, racism, racist
%X "Altruism - benefiting fellow group members at a cost to oneself- &
   parochialism - hostility toward individuals not of one's own ethnic, racial,
   or other group - are common human behaviors. The intersection of the two -
   which we term "parochial altruism" - is puzzling from an evol. perspective
   because altruistic or parochial b. reduces one's payoffs by comparison to
   what one would gain by eschewing these bs.. But parochial altruism could
   have evolved if parochialism promoted intergroup hostilities & the
   combination of altruism & parochialism contributed to success in these
   conflicts. Our game-theoretic analysis & agent-based simulations show that
   under conditions likely to have been experienced by late Pleistocene & early
   Holocene humans, neither parochialism nor altruism would have been viable
   singly, but by promoting group conflict, they could have evolved jointly."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1144237">doi:10.1126/science.1144237</A>]['07] [29 refs].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A C. A. Conway
%A B. C. Jones
%A L. M. DeBruine
%A A. C. Little
%T Evidence for adaptive design in human gaze preference
%J Proc. Royal Soc. B
%V ?
%P ?
%D 2007
%K jrnl, PRSB, c2007, c200x, c20xx, zz1107, human attraction, attractive, face,
   faces, attractiveness, perception, smile, smiles, smiling
%X "... found that participants demonstrated stronger preferences for direct
   gaze when judging the attractiveness of happy faces than that of disgusted
   faces, & that this effect of expression on the strength of attraction to
   direct gaze was particularly pronounced for judgements of opposite-sex faces
   (study 1). By contrast, no such opposite-sex bias in preferences for direct
   gaze was observed when participants judged the same faces for likeability
   (study 2). Collectively, these findings for a context-sensitive opposite-sex
   bias in preferences for perceiver-directed smiles, but not perceiver-directed
   disgust, suggest gaze preference functions, at least in part, to facilitate
   efficient allocation of mating effort, & evince adaptive design in the
   perceptual mechanisms that underpin face preferences."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2007.1073">doi:10.1098/rspb.2007.1073</A>]['07].

%A S. Taylor
%T Storm and Conquest: The Battle for the Indian Ocean, 1808-10
%I AllenAndUnwin
%P 352
%D 2007
%K book, Mauritius, c2007, c200x, c20xx, history, Indian Ocean, 19C,
   UK, France, navy, naval
%X 2007. uk us isbn:0571224661; uk us isbn13:978-0571224661.

%A N. D. Mermin
%T Quantum Computer Science: An Introduction
%I CUP
%P 236
%D 2007
%K book, text, c2007, c200x, c20xx, computation, computing, computers, L4Ref
%X hb, us$41, uk us isbn:0521876583; isbn13:978-0521876582.
   [Also search for: quantum computer].

%A V. Swami
%A D. Einon
%A A. Furnham
%T Cultural signicance of leg-to-body ratio preferences? Evidence
   from Britain and rural Malaysia
%J Asian J. of Social Psychology
%N 10
%P 265-269
%D 2007
%K jrnl, c2007, c200x, c20xx, beauty, leg to body ratio, long legs, LBR,
   attractiveness
%X "The leg-to-body ratio (LBR) has been suggested as an under-researched
   aesthetic criterion in humans. In the present study, 54 rural Malaysians and
   80 Britons rated for physical attractiveness a set of line drawings that
   varied in 5 levels of LBR. The results showed that, for British participants,
   a higher LBR was preferred in women but a lower LBR was preferred in men.
   Malaysian participants, in contrast, rated medium female LBR and low male LBR
   as the most attractive. These results are discussed in terms of cross-
   -cultural differences in media exposure, which may moderate judgements of
   attractiveness of various body components."
   -- [<A HREF="http://dx.doi.org/10.1111/j.1467-839X.2007.00235.x">doi:10.1111/j.1467-839X.2007.00235.x</A>][1/'08].

%T Beautiful Code: Leading Programmers Explain How They Think
%E A. Oram
%E G. Wilson
%I O'Reilly
%P 618
%D 2007
%K book, text, c2007, c200x, c20xx, computer programming, programs, style,
   problem solving
%X pb, us$39, uk us isbn:0596510047; uk us isbn13:978-0596510046.

%A H. K. Schutte
%A J. G. Svec
%T Reaction of Folia Phoniatrica et Logopaedica on the current trend of
   impact factor measures
%J Folia Phoniatrica et Logopaedica
%V 59
%P 281-285
%D 2007
%K jrnl, c2007, c200x, c20xx, science citation index, journal impact factor,
   KPI, KPIs, JIF, ISI, factors, measure, cite, citations, spoofing, game,
   gaming, publications, papers, publish, perish, admiration, grudging
%X "... applying [JIF] universally leads to highly disturbing trends ..."
   -- [<A HREF="http://dx.doi.org/10.1159/000108334">doi:10.1159/000108334</A>]['08].
   (Also see
   "... The Swiss j. Folia Phoniatrica et Logopaedica has a good reputation
   among voice researchers but, with an impact factor of 0.655 in 2007,
   publication in it was unlikely to bring honour or grant money to the
   authors' institutions.  Now two investigators, one Dutch and one Czech, have
   taken on the system and fought back. They published a paper called 'Reaction
   of Folia Phoniatrica et Logopaedica on the current trend of impact factor
   measures' (H. K. Schutte and J. G. Svec Svec, ... 2007). This cited all the
   papers published in the j. in the prev. two years. As 'impact factor' is
   defined as the # of citations to articles in a j. in the past two years,
   divided by the total # of papers published in that j. over the same period,
   their strategy dramatically increased Folia's impact factor this year
   to 1.439. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/455167b">doi:10.1038/455167b</A>]['08].-)
   [Also search for: publish perish].

%A G. G. Szpiro
%T Poincare's Prize: The Hundred-Year Quest to Solve One of Math's
   Greatest Puzzles
%I Dutton
%P 320
%D 2007
%K book, c2007, c200x, c20xx, Poincare, topology, maths, conjecture, puzzle,
   question, topological, invariant, space, geometry, Grigori Perelman
%X "... Szpiro accords pride of place to Grigori Perelman, the reclusive
   titan who finally pierced the mystery - and then spurned the awards. ..."
   1st ed 2007; hb us$19; uk us isbn:0525950249; uk us isbn13:978-0525950240.
   (pb us$15; uk us isbn:0452289645.)

%A E. Garfield
%T The evolution of the Science Citation Index
%J Int. J. Microbio.
%V 10
%P 65-69
%D 2007
%K jrnl, c2007, c200x, c20xx, zz0320, Science Citation Index, history, SCI, ISI,
   KPI, KPIs, bibliometrics, publish, perish, scientific reseach, impact,
   quality, JIF, journal, journals
%X "The Science Citation Index (SCI) was first promulgated in Science in
   1955, as an up-to-date tool to facilitate the dissemination and retrieval
   of scientific literature. Its practicalrealization was possible thanks to
   the already-existing information service, Current Contents. ..."
   -- pdf@[<A HREF="http://garfield.library.upenn.edu/papers/barcelona2007a.pdf">upenn</A>]['20],
      [<A HREF="https://doi.org/10.2436/20.1501.01.10">doi:10.2436/20.1501.01.10</A>]['20] -- but the jrnl cheats on the doi.
   (Also see SCI@[<A HREF="https://en.wikipedia.org/wiki/Science_Citation_Index">wikip</A>]['20].)
   [Also search for: publish perish].

%A M. Kuijsten
%T Reflections on the Dawn of Consciousness:
   Julian Jaynes's Bicameral Mind Theory Revisited
%I Julian Jaynes Soc.
%D 2007
%K book, c2007, c200x, c20xx, psychology, bicameral mind, consciousness
%X 1st ed 2007. isbn:0979074401.
   [Also search for: Bicameral Mind].

%A P. Sorokowski
%A B. Pawlowski
%T Adaptive preferences for leg length in a potential partner
%J Evolution of Human Behaviour
%V ?
%N ?
%P ?-?
%D 2008 to appear
%K jrnl, c2008, c200x, c20xx, zz0108, beauty, attractiveness, mate selection,
   leg to body ratio, long legs, LBR
%X "... study how leg length influences attractiveness in men & women. Stimuli
   consisted of seven different pictures of a man & seven pictures of a woman
   in which the ratio between leg length & height was varied from the avg.
   phenotype by elongating & shortening the legs. 100 men & 118 women were asked
   to assess the attractiveness of the silhouettes using a 7-point scale. We
   found that male & female pictures with shorter than avg legs were perceived
   as less attractive by both sexes. Although longer legs appeared to be more
   attractive, this was true only for the slight (5%) leg length increase;
   excessively long legs decreased body attractiveness for both sexes. Because
   leg length conveys biological quality, we hypothesize that such preferences
   reflect the workings of evolved mate-selection mechanisms. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.evolhumbehav.2007.09.002">doi:10.1016/j.evolhumbehav.2007.09.002</A>]['1/'08].
   [also search for: mate selection].

%A R. H. Graham
%T Flying the SR-71 Blackbird: In the Cockpit on a Secret Operational Mission
%I ZenithPress
%D 2008
%K book, c2008, c200x, c20xx, SR-71, SR71, Blackbird, sled, spy plane, aircraft
%X "... Retired SR-71 pilot and squadron leader Graham takes readers along on
   an operational mission ..."
   1st ed 2008, us$18; uk us isbn:0760332398; uk us isbn13:978-0760332399.

%A A. Buunk
%A J. Park
%A R. Zurriaga
%A L. Klavina
%A K. Massar
%T Height predicts jealousy differently for men and women
%J Evolution and Human Behavior
%V 29
%N 2
%P 133-139
%M MAR
%D 2008
%K jrnl, c2008, c200x, c20xx, male, female, man, woman, tall, short, jealous,
   emotion, beauty, attractive, attractiveness, zz0308
%X "Because male height is assoc. with attractiveness, dominance, & reproductive
   success, taller men may be less jealous. And because female ht has a
   curvilinear relationship with health & reproductive success (with average-
   -height females having the advantages), female ht may have a curvilinear
   relationship with jealousy. In Study1, male ht was found to be
   negatively correlated with self-reported global jealousy, whereas female
   ht was curvilinearly related to jealousy, with average-ht women
   reporting the lowest levels of jealousy. In Study2, male ht was found to be
   -vely correlated with jealousy in response to socially influential,
   physically dominant, & physically attractive rivals. Female ht was -vely
   correlated with jealousy in response to physically attractive, physically
   dominant, & high-social-status rivals; in addition, quadratic effects
   revealed that approx. avg-ht women tend to be less jealous of physically
   attractive rivals but more jealous of rivals with "masculine"
   characteristics of physical dominance & social status."
   -- [<A HREF="http://dx.doi.org/10.1016/j.evolhumbehav.2007.11.006">doi:10.1016/j.evolhumbehav.2007.11.006</A>]['08].

%A S. A. Marglin
%T The Dismal Science: How Thinking Like an Economist Undermines Community
%I HarvardUP
%P 375
%M JAN
%D 2008
%K book, text, c2008, c200x, c20xx, economics, free trade, market economy,
   capitalism, morality, moral philosophy
%X hb, us$35, stg23, us isbn:0674026543; us isbn13:978-0674026544.
   (Reviewed in [<A HREF="http://dx.doi.org/10.1126/science.1157088">doi:10.1126/science.1157088</A>]['08].)

%A S. M. Jaeggi
%A M. Buschkuehl
%A J. Jonides
%A W. J. Perrig
%T Improving fluid intelligence with training on working memory
%J PNAS
%V ?
%N ?
%P ?
%D 2008
%K jrnl, PNAS, c2008, c200x, c20xx, zz0508, fluid intelligence, Gf, IQ,
   improve, test, cognitive training, transfer, individual differences,
   executive processes, control processes
%X "Fluid intelligence (Gf) refers to the ability to reason & to solve new
   problems indep. of previously acquired knowledge. ... critical for a wide
   variety of cognitive tasks, & ... considered one of the most important
   factors in learning. ... closely related to professional & edu.  success,
   esp. in complex & demanding envs.. ... present evidence for transfer from
   training on a demanding working memory task to [Gf]. This transfer results
   even though the trained task is entirely different from the I.test itself.
   [show] the extent of gain in I. critically depends on the amount of training:
   the more training, the more improvement in Gf. ... the training effect is
   dosage-dependent. Thus, in contrast to many previous studies, we conclude
   that it is possible to improve Gf without practicing the testing tasks
   themselves, opening a wide range of applications."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0801268105">doi:10.1073/pnas.0801268105</A>]['08], online 4/2008.
   I can feel a video/computer "game" coming on.

%A A. Politi
%A M. J. Cryan
%A J. G. Rarity
%A S. Yu
%A J. L. O'Brien
%T Silica-on-silicon waveguide quantum circuits
%J Science
%P 646-649
%M MAY
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0508, quantum computing, computer, gate, gates,
   circuit, wave guide
%X "Quantum circuits - in which individual photons interfere, entangle, and
   form logic gates - have been realized on silicon chips."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1155441">doi:10.1126/science.1155441</A>]['08].

%A E. C. Hayden
%T Chemistry: Designer debacle
%J Nature
%V 453
%N 7193
%P 275
%M MAY
%D 2008
%K news article, c2008, c200x, c20xx, biochemistry, protein structure,
   Homme Hellinga, Duke University, DukeUni, triose phosphate isomerase (TIM),
   novo, novoTIM, designer proteins, enzyme, enzymes,
   publication, retraction, inquiry, investigation
%X [<A HREF="http://dx.doi.org/10.1038/453275a">doi:10.1038/453275a</A>]['08].

%A E. Marris
%T Language: The language barrier
%J Nature
%V 453
%N 7194
%P 446
%M MAY
%D 2008
%K news, views, c2008, c200x, c20xx, zz0508, human, natural, language,
   evolution, linguistics
%X "Some researchers think that the evolution of languages can be understood
   by treating them like genomes - but many linguists don't want to hear about
   it. ..."  [5 refs]
   -- [<A HREF="http://dx.doi.org/10.1038/453446a">doi:10.1038/453446a</A>]['08].
   [Also search for: natural language evolution].

%A P. Norton
%T Fighting Traffic: The Dawn of the Motor Age in the American City
%I MITpress
%P 396
%D 2008
%K book, c2008, c200x, c20xx, road traffic, motor car, cars, automobile
%X "Before the advent of the automobile, users of city streets were diverse and
   included children at play and pedestrians at large. By 1930, most streets
   were primarily motor thoroughfares where children did not belong and where
   pedestrians were condemned as "jaywalkers." In Fighting Traffic,
   PN argues that to accommodate automobiles, the American city required
   not only a physical change but also a social one: before the city could be
   reconstructed for the sake of motorists, its streets had to be socially
   reconstructed as places where motorists belonged. It was not an evolution,
   he writes, but a bloody and sometimes violent revolution."
   hb, us$28, uk us isbn:0262141000; uk us isbn13:978-0262141000.

%A M. Schreiber
%T A modification of the h-index: The hm-index accounts for multi-authored
   manuscripts
%J J. Informetrics
%V 2
%N 3
%P 211-216
%M JUL
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0919, publish, perish, Hindex, hmIndex,
   modified bibliometrics, authorship, multiple authors, author, trends,
   papers, citations, KPI, KPIs
%X "In order to take multiple co-authorship appropriately into account, a
   straightforward modification of the Hirsch index was recently proposed.
   Fractionalised counting of the papers yields an appropriate measure which is
   called the hm-index. The effect of this procedure is compared in the present
   work with other variants of the h-index and found to be superior to the
   fractionalised counting of citations and to the normalization of the h-index
   with the avg # of authors in the h-core. Three fictitious examples for model
   cases and one empirical case are analysed."
   -- [<A HREF="https://doi.org/10.1016/j.joi.2008.05.001">doi:10.1016/j.joi.2008.05.001</A>]['19].
   [Also search for: hmIndex] and [also search for: Hindex].

%A R. P. Brent
%T Some comments on C. S. Wallace's random number generators
%J COMPJ
%V 51
%N 5
%P 579-584
%M SEP
%D 2008
%K jrnl, COMPJ, c2008, c200x, c20xx, zz0908, RNG, PRNG, pseudo random numbers,
   generator, algorithm, normal, Gaussian, distribution, RPBrent
%X "We outline some of Chris Wallace's contributions to pseudo-random number
   generation. In particular, we consider his recent idea for generating
   normally distributed variates without relying on a source of uniform random
   numbers & compare it with more conventional methods for generating normal
   random numbers. Implementations of Wallace's idea can be very fast
   (approximately as fast as good uniform generators). We discuss the
   statistical quality of the output, & mention how certain pitfalls can be
   avoided."  Online Feb 2008.
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm122">doi:10.1093/comjnl/bxm122</A>][6/'08].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">C.S.Wallace's publications</A>].)

%A D. Dowe
%T Foreword re C. S. Wallace
%J COMPJ
%V 51
%N 5
%P 523-560
%M SEP
%D 2008
%K jrnl, COMPJ, c2008, c200x, c20xx, biog
%X [326 refs], [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm117">doi:10.1093/comjnl/bxm117</A>][6/'08].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">C.S.Wallace's publications</A>].)

%A M. J. Currie
%A J. K. Mapel
%A T. D. Heidel
%A S. Goffri
%A M. A. Baldo
%T High-efficiency organic solar concentrators for photovoltaics
%J Science
%V 321
%N 5886
%P 226-228
%M JUL
%D 2008
%K c2008, c200x, c20xx, zz0708, solar cell, PV, cells, photovoltaic,
   sustainability, electricity
%X "The cost of photovoltaic power can be reduced with organic solar
   concentrators. ... planar waveguides with a thin-film organic coating on the
   face & inorganic solar cells attached to the edges. Light is absorbed by the
   coating & reemitted into waveguide modes for collection by the solar cells.
   We report single- & tandem-waveguide organic solar c. with quantum
   efficiencies > 50% & projected power conversion efficiencies as high as 6.8%.
   The exploitation of near-field energy transfer, solid-state solvation, &
   phosphorescence enables 10-fold increases in the power obtained from
   photovoltaic cells, without the need for solar tracking."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1158342">doi:10.1126/science.1158342</A>]['08].

%A S. C. Glotzer
%A A. S. Keys
%T Materials science: A tale of two tilings
%J Nature
%V 454
%P 420-421
%M JUL
%D 2008
%K jrnl, c2008, c200x, c20xx, quasicrystal, tiling, quasi crystal
%X "What do you get when you cross a crystal with a quasicrystal? The answer is
   a structure that links the ancient tiles of Archimedes, the iconic Fibonacci
   sequence of numbers and a book from the seventeenth century.
   Quasicrystals are mosaic-like arrangements of atoms that have symmetries once
   thought to be impossible for crystals to adopt. Primarily observed in
   certain metal alloys, these unusual structures are stronger & less deformable
   than analogous regular crystals, & have unusual frictional, catalytic &
   optical properties. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/454420a">doi:10.1038/454420a</A>]['08].
   (See Mikhael, this issue.)

%A J. Mikhael
%A J. Roth
%A L. Helden
%A C. Bechinger
%T Archimedean-like tiling on decagonal quasicrystalline surfaces
%J Nature
%V 454
%P 501-504
%M JUL
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0708, quasi, quasicrystal, crystal, tiling,
   5-fold, 5fold, symmetry, surface
%X "... In comparison with crystals, quasicrystalline surfaces exhibit much
   larger structural & chemical complexity leading, for example, to unusual
   frictional, catalytical or optical properties. Deposition of thin films on
   such substrates can lead to structures that may have typical quasicrystalline
   properties. Recent experiments have indeed showed 5-fold symmetries in the
   diffraction pattern of metallic layers adsorbed on quasicrystals. Here we
   report a real-space investigation of the phase behaviour of a colloidal
   monolayer interacting with a quasicrystalline decagonal substrate created by
   interfering five laser beams. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07074">doi:10.1038/nature07074</A>]['08].

%A T. Freeth
%A A. Jones
%A J. M. Steele
%A Y. Bitsakis
%T Calendars with Olympiad display and eclipse prediction on the Antikythera
   mechanism
%J Nature
%V 454
%P 614-617
%M JUL
%D 2008
%K jrnl, c2008, c200x, c20xx, Antikythera mechanism, Greek, geared, Metonic,
   Saros, Callippic, calendar, glyph, Exeligmos
%X "Previous research on the Antikythera Mechanism established a highly complex
   ancient Greek geared mechanism with front and back output dials. The upper
   back dial is a 19-year calendar, based on the Metonic cycle, arranged as a
   5-turn spiral. The lower back dial is a Saros eclipse-prediction dial,
   arranged as a 4-turn spiral of 223 lunar months, with glyphs indicating
   eclipse predictions. Here we add surprising findings concerning these back
   dials. Though no month names on the Metonic calendar were previously known,
   we have now identified all 12 months, which are unexpectedly of Corinthian
   origin ... "
   -- [<A HREF="http://dx.doi.org/10.1038/nature07130">doi:10.1038/nature07130</A>]['11],
   video@[<A HREF="http://www.nature.com/nature/videoarchive/antikythera/">nature</A>]['11].
   [Also search for: Antikythera mechanism].

%A M. W. Kanan
%A D. G. Nocera
%T In situ formation of an oxygen-evolving catalyst in neutral water containing
   phosphate and CO2
%J Science
%V 321
%N 5892
%P 1072-1075
%K jrnl, c2008, c200x, c20xx, photosynthesis, water, H2O, H2, O2, CO2, catalyst,
   energy, source, fuel, sunlight, water splitting, artificial leaf,
   MIT, Sun Catalytix
%X "... natural photosynthesis, energy from sunlight is used to rearrange the
   bonds of water to oxygen & hydrogen equivs.. [An] artificial systems that
   perform 'water splitting' requires catalysts that produce oxygen from water
   without the need for excessive driving potentials. ... report such a catalyst
   that forms upon the oxidative polarization of an inert indium tin oxide
   electrode in phosphate-buffered water containing cobalt (II) ions. A variety
   of analytical techniques indicates the presence of phosphate in an approx.
   1:2 ratio with cobalt in this material. The pH dependence of the catalytic
   activity also implicates the hydrogen phosphate ion as the proton acceptor in
   the oxygen-producing reaction. This catalyst not only forms in situ from
   earth-abundant materials ... operates in neutral water under ambient condns."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1162018">doi:10.1126/science.1162018</A>]['11].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.332.6025.25">doi:10.1126/science.332.6025.25</A>]['11] (2011).)

%A S. Licht
%A H. Wub
%A X. Yub
%A Y. Wang
%T Renewable highest capacity VB2/air energy storage
%J Chemical Commun.
%I Royal Soc. of Chem.
%P 3257-3259
%M JUN
%D 2008
%K jrnl, c2008, c200x, c20xx, chemical, electric, energy storage, battery,
   fuel cell, vanadium boride, VB, VB2, vehicle, vehicles
%X "The first renewable electrochemical energy system which stores more energy
   than gasoline is presented, & with an order of magnitude higher capacity
   than lithium-ion batteries, VB2 opens a pathway towards electric vehicles
   with a viable driving range."
   -- [<A HREF="http://dx.doi.org/10.1039/b807929c">doi:10.1039/b807929c</A>]['08].

%A S. L. Titus
%A J. A. Wells
%A L. J. Rhoades
%T Repairing research integrity
%J Nature
%V 453
%P 980-982
%M JUN
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0808, research, ethics, ethical, misconduct,
   fraud, fabrication, falsification, plagiarism, scientific, science, academic,
   zzEthics
%X "A survey suggests that many research misconduct incidents in the [USA]
   go unreported ... fabrication, falsification or plagiarism in proposing,
   performing or reviewing research, or in reporting research results ..."
   -- [<A HREF="http://dx.doi.org/10.1038/453980a">doi:10.1038/453980a</A>]['08].
   [Also search for: academic misconduct].

%A B. Winther-Jensen
%A O. Winther-Jensen
%A M. Forsyth
%A D. R. MacFarlane
%T High rates of oxygen reduction over a vapor phase-polymerized PEDOT electrode
%J Science
%V 321
%N 5889
%P 671-674
%M AUG
%D 2008
%K jrnl, c2008, c200x, c20xx, Pt, monashUni, fuel cell, cells, Goretex, gortex,
   PEDOT, poly 3,4-ethylenedioxythiophene, catalyst, catalytic, O2, vapour
%X "... describe an air electrode based on a porous material coated with
   poly(3,4-ethylenedioxythiophene) (PEDOT), which acts as an O2 reduction
   catalyst. Continuous operation for 1500hrs was demonstrated without material
   degradation or deterioration in performance. O2 conv. rates were comparable
   with those of Pt-catalyzed electrodes of the same geometry, & the electrode
   was not sensitive to CO. ..."  [32 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1159267">doi:10.1126/science.1159267</A>]['08].

%T Bioenergy
%I ASMpress
%E J. D. Wall
%E C. S. Harwood
%E A. Demain
%P 454
%D 2008
%K book, Microbial fuels, c2008, c200x, c20xx, renewable energy, microbes,
   biofuels, bioelectricity, fuel, fuels, sustainability
%X hb, us$120, us isbn:1555814786; us isbn13:978-1555814786.

%A M. E. Mann
%A Z. Zhang
%A M. K. Hughes
%A R. S. Bradley
%A S. K. Miller
%A S. Rutherford
%A F. Ni
%T Proxy-based reconstructions of hemispheric and global surface temperature
   variations over the past two millennia
%J PNAS
%V ?
%P ?-?
%D 2008
%K PNAS, jrnl, c2008, c200x, c20xx, zz0908, stats, global warming, temperature,
   climate change, rise, data, evidence, reconstruction, variation
%X "... reconstruct surface temp. at hemispheric & global scale for much of the
   last 2,000 y. using a greatly expanded set of proxy data for decadal-to-
   -centennial climate changes, recently updated instrumental data, &
   complementary methods that have been thoroughly tested & validated with model
   simulation experiments. ... extend previous concls. that recent N.Hemisphere
   surface temp. increases are likely anomalous in a long-term context. Recent
   warmth appears anomalous for at least the past 1,300 y. whether or not tree-
   -ring data are used. If tree-ring data are used, the concl. can be extended
   to at least the past 1,700 years, but with additional strong caveats. The
   reconstructed amplitude of change over past centuries is greater than
   hitherto reported, with somewhat greater Medieval warmth in the N.Hemisphere,
   albeit still not reaching recent levels."    -- online Sept 2008.
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0805721105">doi:10.1073/pnas.0805721105</A>]['08].

%A K. R. Foster
%A H. Kokko
%T The evolution of superstitious and superstition-like behaviour
%J Proc. the Royal Soc. B
%V ?
%N ?
%P ?-?
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0908, belief, Alife, simulation, belief,
   superstition, superstitious, cause and effect, human, animal behaviour
%X "Superstitious behaviours, which arise through the incorrect assignment of
   cause & effect, receive considerable attention in psychology & popular
   culture. ... develop a simple model to define the condition under which
   natural selection will favour assigning causality between 2 events. This
   leads to an intuitive inequality - akin to an amalgam of Hamilton's rule &
   Pascal's wager - that shows that nat.seln can favour strategies that lead to
   frequent errors in assessment as long as the occasional correct response
   carries a large fitness benefit. It follows that incorrect responses are the
   most common when the probability that 2 events are really associated is low
   to moderate ... nat.seln will rarely favour making very weak associations.
   Extending the model to include multiple events identifies conditions
   under which nat. sel. can favour assoc. events that are never causally
   related. Specifically, limitations on assigning causal probs. to pairs
   of events can favour strategies that lump non-causal associations with
   causal ones. We conclude that behaviours which are, or appear, superstitious
   are an inevitable feature of adaptive behaviour in all organisms, ..."
   Online 9 Sept 2008 [<A HREF="http://dx.doi.org/10.1098/rspb.2008.0981">doi:10.1098/rspb.2008.0981</A>]['08].

%A T. Opatrny
%T Playing the system to give low-impact journal more clout
%J Nature
%V 455
%N 167
%M SEP
%D 2008
%K correspondence, c2008, c200x, c20xx, science citation, citations, factors,
   impact factor, spoofing, Folia Phoniatrica et Logopaedica,
   ISI, IF, publications, journal, journals, self, funny, haha, ha ha
%X "... Swiss j. Folia Phoniatrica et Logopaedica has a good reputation among
   voice researchers but, with an impact factor of 0.655 in 2007 ... Now two
   investigators, one Dutch & one Czech, have taken on the sys. & fought back.
   They published a paper called 'Reaction of Folia Phoniatrica et Logopaedica
   on the current trend of impact factor measures' (H. K. Schutte & J. G. Svec
   Folia Phoniatr. Logo. 59, 281-285; 2007). This cited all the papers
   publ. in the j. in the previous 2y.. As [IF] is def. as the # of citations
   to articles in a j. in the past two years, divided by the total # of papers
   published in that j. over the same period, their strategy dramatically
   increased Folia's impact factor this year to 1.439. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/455167b">doi:10.1038/455167b</A>]['08].
   Also see [<A HREF="http://dx.doi.org/10.1159/000108334">doi:10.1159/000108334</A>]['08],
   and [<A HREF="http://dx.doi.org/10.1038/455729b">doi:10.1038/455729b</A>][10/'08].

%A R. N. Barger
%T Computer Ethics: A Case-based Approach
%I CUP
%D 2008
%K book, text, CUP, c2008, c200x, c20xx, L2Ref, L3Ref, zz1008, ethics, ethical,
   computing, zzEthics
%X "Computer Ethics: A Case-based Approach teaches students to solve ethical
   dilemmas in the field of computing, taking a philosophical, rather than a
   legal, approach to the topic. It first examines the principles of Idealism,
   Realism, Pragmatism, Existentialism, and Philosophical Analysis, explaining
   how each of them might be adopted as a basis for solving computing dilemmas.
   The book then presents a worksheet of key questions to be used in solving
   dilemmas. Twenty-nine cases, drawn from the real-life experiences of computer
   professionals, are included in the book as a means to let students experiment
   with solving ethical dilemmas and identify the philosophical underpinnings of
   the solutions."
   1st ed 2008, hb us$85; uk us isbn:0521882516; uk us isbn13:978-0521882514.

%A J. Marchant
%T Decoding the Heavens: Solving the Mystery of the World's First Computer
%I William Heinemann / Da Capo Press
%P 330
%D 2008 / 2009
%K book, c2008, c200x, c20xx, zz1008, Antikythera Mechanism, calculator,
   astronomical, astronomy, ancient, computing, history, Greek, Greece
%X 1st ed 2008, stg13, us$25;
   uk us isbn:043401835X; uk us isbn13:978-0434018352.
   "In 1900 a group of sponge divers blown off course in the Mediterranean
   discovered an Ancient Greek shipwreck dating from around 70BC. Lying
   unnoticed for months amongst their hard-won haul was what appeared to be a
   formless lump of corroded rock, which turned out to be the most stunning
   scientific artefact we have from antiquity. For more than a century this
   'Antikythera mechanism' puzzled academics, but now, more than 2000 years
   after the device was lost at sea, scientists have pieced together its
   intricate workings. Unmatched in complexity for 1000 years, it was able to
   predict eclipses & track the paths of the Sun & the Moon through the zodiac,
   & probably even showed ancient astronomers the movements of the five known
   planets. ..."
   (Reviewed [<A HREF="http://dx.doi.org/10.1038/455867a">doi:10.1038/455867a</A>]['08].)
   [Also search for: Antikythera mechanism].

%A J. A. Abreu
%A J. Beer
%A F. Steinhilber
%A S. M. Tobias
%A N. O. Weiss
%T For how long will the current grand maximum of solar activity persist?
%J Geophys. res. Lett.
%V 35
%P L20109
%M OCT
%D 2008
%K eJrnl, c2008, c200x, c20xx, zz0109, sun, solar, activity, maximum, spot,
   spots, sunspot, sunspots, cycles, minimum, GRIP, Be
%X "... The sunspot record since 1610 shows irregular 11-y. cycles of activity;
   ... modulated on longer timescales & were interrupted by the Maunder min. in
   the 17th C.. ... not easily predicted - even in the short-term. Recent
   activity has been abnormally high for at least 8 cycles: is this grand max.
   likely to terminate soon or even to be followed by another (Maunder-like)
   grand minimum? ... use, as a measure of the Sun's open magnetic field, a
   composite record of the solar modulation fn Phi, reconstructed principally
   from the proxy record of cosmogenic 10-Be ... icecore from Greenland. ...
   extends back for almost 10,000 y., ... statistical analysis of this record
   & calc. the life expectancy of the current grand max.. ... only expected to
   last for a further 15-36 y., with the more reliable methods yielding shorter
   expectancies, & we therefore predict a decline in solar activity within the
   next 2 or 3 cycles. ... not able, however, to predict the level of the
   ensuing minimum."   [so: 2023 - 2044].
   -- [<A HREF="http://dx.doi.org/10.1029/2008GL035442">doi:10.1029/2008GL035442</A>]['09].

%E M. Brynin
%E J. Ermisch
%T Changing Relationships
%I Routledge
%S Adv. in Sociology
%D 2008
%K book, text, c2008, c200x, c20xx, zz0209, relationship, human behaviour,
   behavior, family, families, friend, love
%X 1st ed 2008, hb us$95; uk us isbn:0415965233; uk us isbn13:978-0415965231.
   "Some relationships are within the family - such as between parents &
   children, grandparents and children and between siblings - while others are
   between friends. In some cases, these distinctions are blurred (are
   short-term partners family members? Are family members seen as such when
   relations become unfriendly? Does divorce, if amicable, replace a family
   with a friendship?). ... quantitative, stat. analysis ..."
   Ed1@[<A HREF="http://www.iser.essex.ac.uk/people/brins">U.Essex</A>]['09].

%A Q. Schiermeier
%T Self-publishing editor set to retire
%J Nature
%V 456
%P 432
%M NOV
%D 2008
%K news, views, c2008, c200x, c20xx, z1222, Mohamed El Naschie, ElNaschie,
   publish, perish, academia, academic conduct, controversial, publishing,
   journal, JIF, editor, publications, self citation
%X "The editor of a theoretical-physics j., who was facing growing criticism
   that he used its pages to publish numerous papers written by himself, is set
   to retire early next year. ..."
   -- [<A HREF="https://doi.org/10.1038/456432a">doi:10.1038/456432a</A>]['22].
   (Didn't F. do a bit of that?)
   [Also search for: KCChou].

%A S. J. Green
%A J. Brendsel
%T Key discoveries often originate with lone researchers
%J Nature
%V 456
%P 315
%M NOV
%D 2008
%K corr, c2008, c200x, c20xx, key, discovery, research, idea, ideas, innovation,
   researcher, lone, team, teams, Uzzi
%X [<A HREF="http://dx.doi.org/10.1038/456315a">doi:10.1038/456315a</A>]['08].

%A D. H. Wolpert
%T Physical limits of inference
%J Physica D
%V 237
%P 1257-1281
%D 2008
%O '07 CNLS conf. on unconventional computation
%K c2008, c200x, c20xx, zz0509, limit, inference, model, prediction, learn,
   laws of nature, II, inference device, devices, machine, prediction, TM, UTM,
   strong, universal, physics, theories, theory of almost everything,
   jrnl, complexity, universe, computer
%X "I show that physical devices that perform observation, prediction, or
   recollection share an underlying math. structure. ... devices with that
   structure 'inference devices'. I present a set of existence & impossibility
   results concerning inference devices. ... In a limited sense, the
   impossibility results establish that Laplace was wrong to claim that even in
   a classical, non-chaotic universe the future can be unerringly predicted,
   given sufficient knowledge of the present. Alternatively, these impossibility
   results can be viewed as a non-quantum mechanical 'uncertainty principle'.
   Next I explore the close connections between the math. of inference devices
   & of Turing m/cs. In particular, the impossibility results for inference
   devices are similar to the Halting theorem for TM's. Furthermore, one can
   define an analog of Universal TM's (UTM's) for inference devices. I call
   those analogs 'strong inference devices'. I use strong inference devices to
   define the 'inference complexity' of an inference task, which is the analog
   of the Kolmogorov complexity of computing a string. However no universe can
   contain more than one strong inference device. So whereas the K.complexity
   of a string is arbitrary up to specification of the UTM, there is no such
   arbitrariness in the inference complexity of an inference task. I end
   by discussing the philosophical implications of these results, e.g., for
   whether the universe 'is' a computer."
   -- arXiv:0708.1362v2@[<A HREF="http://arxiv.org/abs/0708.1362">arXiv</A>]['09],
      dhw@[<A HREF="http://ti.arc.nasa.gov/profile/dhw/">nasa</A>]['09].
   (Also see comment@[<A HREF="http://dx.doi.org/10.1038/455884">doi:10.1038/455884</A>]['09], Nature.)

%A D. Fouqueta
%A T. B. Johansson
%T European renewable energy policy at crossroads - Focus on electricity
   support mechanisms
%J Energy Policy
%V 36
%N 11
%P 4079-4092
%M NOV
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0909, renewable energy, feed in tarrif, FIT,
   tradable green certificates, TGC, tarrifs, electricity, generation,
   sustainability, sustainable, energy, policy, mechanism, solar, Europe
%X "... 2 major categories, tradable green certificates (TGC) & feed-in tariffs
   (FiT). Experiences ... suggest that FiT deliver larger & faster penetration
   of RE than TGC, at lower cost. ... In a TGC system, a target for RE
   penetration is set by public authorities seeking to minimise cost for
   achieving this target. The certificate price is set by the market. In a FiT
   system, public auths. set an effective price but are not limiting the
   quantity installed. This has led to impressive growth rates, particularly in
   Denmark, Germany, & Spain. It is found that investor risks are much lower in
   a FiT system, & that innovation incentives are larger. ... it therefore
   appears that, at least for the time being, continued reliance on national
   systems, especially FiT would be preferred."
   -- [<A HREF="http://dx.doi.org/10.1016/j.enpol.2008.06.023">doi:10.1016/j.enpol.2008.06.023</A>]['09].
   (Also see [<A HREF="http://www.globalchange.umd.edu/energytrends/germany/6/">globalchange.umd.edu</A>]['09].)

%A N. Sperling
%T This Book Warps Space and Time: Selections from The Journal of
   Irreproducible Results
%I AndrewsMcMeel
%D 2008
%K book, c2008, c200x, c20xx, zz1209, AIR, annals, irreproducible results,
   research, funny, ha ha, haha
%X pb us$10; uk us isbn:0740777130; uk us isbn13:978-0740777134.
   [Also search for: IgNobel].

%A C. Goodall
%T Ten Technologies to Save the Planet
%I GreenProfile
%P 302
%D 2008
%K book, c2008, c200x, c20xx, zz1208, renewable, sustainability, sustainable,
   CO2, energy, climate change, global warming, algae
%X "... introducing the innovators & innovations that will tackle climate
   change head-on. ... slash global greenhouse emissions. But how do we actually
   achieve that? ... Goodall profiles 10 technologies to watch, explaining how
   they work & telling the stories of the inventors & entrepreneurs driving them
   forward. ... e.g. Algae, for example, can soak up carbon dioxide & produce
   fuel, while charcoal made from waste vegetable & forestry matter can lock
   carbon into soils & reduce the need for fertilizers. Cutting-edge &
   accessible, this is popular science at its most crucial."
   1st ed 2008, pb stg7.00; uk isbn:84668868X; uk isbn13:978-1846688683.

%A M. Nakahara
%A T. Ohmi
%T Quantum Computing: From Linear Algebra to Physical Realizations
%I CRCpress
%D 2008
%K book, text, c2008, c200x, c20xx, zz0210, quantum computing, computer,
   DiVincenzo criteria
%X "... two sections, with the first devoted to the theoretical aspects of
   quantum computing and the second focused on several candidates of a working
   quantum computer, evaluating them according to the DiVincenzo criteria."
   1st ed 2008, hb us$64; uk us isbn:0750309830; uk us isbn13:978-0750309837.
   [Also search for: quantum computing]  and  [also search for: DiVincenzo].

%A R. Bamford
%A K. J. Gibson
%A A. J. Thornton
%A J. Bradford
%A R. Bingham
%A L. Gargate
%A L. O. Silva
%A R. A. Fonseca
%A M. Hapgood
%A C. Norberg
%A T. Todd
%A R. Stamper
%T The interaction of a flowing plasma with a dipole magnetic field:
   measurements and modelling of a diamagnetic cavity relevant to
   spacecraft protection
%J Plasma Physics and Controlled Fusion
%V 50
%N 12
%P 124025
%M DEC
%D 2008
%K jrnl, c2008, c200x, c20xx, space travel, craft, radiation, protection,
   shield, shielding, plasma, solar wind, cosmic, particle, magnetic field,
   magnetosphere
%X "... dipole-like magnetic field & plasma, surrounding a spacecraft forming a
   'mini magnetosphere'. Initial lab.experiments have been ... determine the
   effectiveness of a magnetized plasma barrier to be able to expel an impacting
   low beta, supersonic flowing energetic plasma representing the solar wind.
   Optical & Langmuir probe data of the plasma density, the plasma flow velocity
   & the intensity of the dipole field clearly show the creation of a narrow
   transport barrier region & diamagnetic cavity virtually devoid of energetic
   plasma particles. This demonstrates the potential viability of being able to
   create a small 'hole' in a solar wind plasma, of the order of the ion Larmor
   orbit width, in which an inhabited spacecraft could reside in rel.safety.
   The experimental results have been quantitatively compared with a 3D
   particle-in-cell 'hybrid' code simulation ..."
   -- [<A HREF="http://dx.doi.org/10.1088/0741-3335/50/12/124025">doi:10.1088/0741-3335/50/12/124025</A>]['10].
   (Also see [<A HREF="http://dx.doi.org/10.1088/0741-3335/50/7/074017">doi:10.1088/0741-3335/50/7/07401</A>].)

%A J. Erickson
%T Hacking: The Art of Exploitation
%I NoStarch
%P 488
%D 2008
%K book, text, c2008, c200x, c20xx, zz0610, hacker, hacking, exploit,
   computer, computers, cracking
%X 2nd ed 2008; pb us$33; uk us isbn:1593271441; uk us isbn13:978-1593271442.

%A J. H. Ausubel
%A P. E. Waggoner
%T Dematerialization: Variety, caution, and persistence
%J PNAS
%V 105
%N 35
%P ?-?
%M SEP
%D 2008
%K jrnl, PNAS, c2008, c200x, c20xx, zz0712, earth, human, consumption, use,
   peak, oil, resources, energy, food, GDP, growth, economics, sustainability
%X "Dematerialization, represented by declining consumption per GDP of energy
   or of goods, offers some hope for rising environmental quality with
   development. ... We observe that combinations of low income elasticity for
   staples & of learning by producers cause a variety of dematerializations
   & declining intensities of impact, from energy use & carbon emission to
   food consumption & fertilizer use, globally & in countries ranging from
   the United States & France to China, India, Brazil, & Indonesia. ...
   substantial declining intensity of impact, and especially, dematerialization
   persisted between 1980 and 2006. "
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0806099105">doi:10.1073/pnas.0806099105</A>]['12].
   (Contentious.)

%A S. Larsson
%T The Girl with the Dragon Tattoo
%I Knopf
%D 2008
%P 480
%K book, novel, crime, thriller, c2008, c200x, c20xx, Salander, Blomkvist,
   hacker, hacking, The Girl with the Dragon Tattoo, Men who Hate Women
%X hb us$17; uk us isbn:0307269752; uk us isbn13:978-0307269751.
   1st book of the trilogy.
   [Also search for: Larsson Dragon Tattoo].

%A D. Levy
%T Love and Sex with Robots: The Evolution of Human-Robot Relationships
%I HarperPerennial
%P 352
%D 2008
%K book, c2008, c200x, c20xx, AI, robot, android, human, relationship, Roxy,
   Roxxy, Roxxxy, sex doll, sexbot, robotics, humanoid, gynoid,
   prediction, controversial, zz0150, zzPrediction
%X 1st ed 2008; pb us$6; uk us isbn:0061359807.
   "... addresses the question of love with robots, and moves on to consider the
   mechanics of actually having sex with them. In order to put the reader at
   ease with the possibility of human-robot love, Levy compares the phenomenon
   to the ways in which humans fall in love with each other, their pets, and
   even their motorcycles. From there, Levy argues, it is a short emotional step
   to the affection people can be expected to display towards robots. ..."
   (Also see [<A HREF="http://www.bbc.co.uk/news/business-23637225">bbc</A>][27/8/2013],
   and "... David Levy ... believes that there will be a huge market for dolls
       such as Roxxy and predicts that by 2050, intimate relationships between
       robots and humans will be commonplace. ..."
       -- [<A HREF="http://www.bbc.com/news/technology-34118482">15/9/2015</A>].
   [Also search for: zzPrediction] and [also search for: sex robot].)

%A C. H. Tienken
%T Rankings of international achievement test performance and
   economic strength: Correlation or conjecture?
%J Int. J, Ed. Policy and Leadership
%V 3
%N 4
%D 2008
%K c2008, c200x, c20xx, zz0113, education, school, schools, mathematics,
   science, tests, stats, score, scores, rank, ranking, rankings, performance,
   TIMSS, Growth Competitiveness Index, GCI, economics
%X "... presents results from a series of Spearman Rho calcns conducted to
   investigate relationships between countries' rankings on int. tests of
   math. & sci. & future economic competitiveness as measured by the 2006 World
   Economic Forum's Growth Competitiveness Index (GCI). ... investigated ...
   relationships between int. test rankings from three different time periods
   during the last 50 years of U.S. ed. policy development (i.e., 1957-1982,
   1983-2000, & 2001-2006) & 2006 GCI ranks. It extends prev. research on the
   topic by investigating how GCI rankings in the top 50% & bottom 50% relate to
   rankings on int. tests for the countries that participated in each test. The
   study found that the relationship between ranks on int. tests of math. &
   sci. & future economic strength is stronger among nations with lower-
   -performing economies. Nations with strong economies, such as the US,
   demonstrate a weaker, nonsignificant relationship."
   -- @[<A HREF="http://journals.sfu.ca/ijepl/index.php/ijepl/article/view/110">sfu</A>]['13].

%A C. Anderseon
%T The end of theory: The data deluge makes the scientific method obsolete
%J Wired
%M JUN
%D 2008
%K views, opinion, c2008, c200x, c20xx, zz0122, big data, bigData, theory,
   hypothesis, explanation, inference, science, scientific method, correlation
%X "'All models are wrong, but some are useful.' So proclaimed statistician
   George Box 30 years ago, & he was right. But what choice did we have? ..."
   -- [<A HREF="https://www.wired.com/2008/06/pb-theory/">www</A>]['22].

%A P. Roth
%T The EMBO Journal 2009: new initiatives
%J EMBO
%V 28
%P 1-3
%M JAN
%D 2009
%K c2009, c200x, c20xx, zz0610, publish, publication, journal, journals, policy,
   RPF, scientific, papers, review, reviewing, referee, referees, refereeing,
   editorial, process, transparent, fair, open, initiative, comment, openness
%X "... editorial process. Instead of just saying so, we will make it visible.
   ... cite primary literature whenever possible.  On publication of a paper,
   there will be an additional supplementary editorial process file linked to it
   on the web. This file will contain all dates relevant to the processing of
   the article at the j., showing the mechanics of the process. It will also
   contain all pertinent communication regarding the article between the
   corresponding author and the editorial office, inc. the referees' comments as
   part of the decision letter."
   -- [<A HREF="http://dx.doi.org/10.1038/emboj.2008.250">doi:10.1038/emboj.2008.250</A>]['10].
   And update Oct. 2009:
   -- [<A HREF="http://www.nature.com/emboj/about/emboj_review_process.html">emboj</A>]['10].
   (Also see progress@[<A HREF="http://dx.doi.org/10.1038/468029a">doi:10.1038/468029a</A>][4/11/2010].)

%A P. W. Singer
%T Wired for War: The Robotics Revolution and Conflict in the 21st Century
%I Penguin
%P 512
%D 2009
%K book, c2009, c200x, c20xx, zz1109, wired, war, robot, robots, robotic,
   robotics, mil, military, electronic, warfare, war, Predator, drone, drones,
   UAV, unmanned, autonomous, lethal, cyber, bot, bots, Terminator, T2, ethics,
   future, futurist, zzEthics
%X 1st ed 2009; hb us$20; uk us isbn:1594201986; uk us isbn13:978-1594201981.

%T Experts still needed
%J Nature
%V 457
%P 7-8
%M JAN
%D 2009
%K c2009, c200x, c20xx, zz0109, editorial, expert, research assessment exercise,
   RAE, research excellence framework, REF, metrics, KPI, KPIs, United Kingdom,
   UK, university, universities
%X There are good reasons to be suspicious of metric-based research assessment.
   ... Many countries are keen to measure their universities' res. performance
   with minimal burdens on the participants. Not least of these is the UK, which
   last month announced the results of its 6th & final (RAE, see p.13).
   The RAE relied heavily on expert peer review of research publications, &
   attention in Britain & beyond is now focused on what form the replacement
   system will take. The proposed successor, the Research Excellence Framework
   (REF), is opaque. Little is known about how it will work other than a central
   principle: it will assess research quality using metrics, inc. publication
   citations. It may also take into account the # of p/g completing their
   studies & the amount of research income won by universities. There will be a
   smattering of 'light-touch expert review', although the exact form that this
   will take is not yet clear - it might simply be used to interpret the metrics
   results. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/457007b">doi:10.1038/457007b</A>]['09],
   also see [<A HREF="http://dx.doi.org/10.1038/457013a">doi:10.1038/457013a</A>]['09].

%A V. J. Stenger
%T Quantum Gods: Creation, Chaos, and the Search for Cosmic Consciousness
%I PrometheusBooks
%P 292
%D 2009
%K book, c2009, c200x, c20xx, zz0509, quantum theory, mechanics, religion,
   consciousness, physics, theology, religion, spirituality, God, pseudoscience,
   pseudo science, quasi, cosmic
%X 1st ed, c2009, hb us$18; uk us isbn:1591027136; uk us isbn13:978-1591027133.
   (Also see [<A HREF="http://www.newscientist.com/article/mg20227041.600-quantum-gods-dont-deserve-your-faith.html">New Sci.</A>]['09].)

%A R. Wilkinson
%A K. Pickett
%T The Spirit Level: Why More Equal Societies Almost Always Do Better
%I AllenLane
%P 320
%D 2009
%K book, c2009, c200x, c20xx, zz0509, human, society, social, inequality,
   equality, equal, welfare, capitalism, wellbeing, well being, poor, poverty,
   wealth, stress, envy, mental illness
%X "... emphasise that it is not the poor and the deprived in isolation who
   suffer from the effects of inequality, but also the bulk of that nation's
   population. According to their findings. incidences of mental illness, for
   example, are 500% higher across the whole population spectrum in the most
   unequal societies than they in the most equal ones. ..."
   1st ed 2009, hb stg13; uk isbn:1846140390; uk isbn13:978-1846140396.

%A S. N. Riduan
%A Y. Zhang
%A J. Y. Ying
%T Conversion of carbon dioxide into methanol with silanes over N-heterocyclic
   carbene catalysts
%J Angewandte Chemie
%V 48
%N 18
%P 3322-3325
%D 2009
%K jrnl, c2009, c200x, c20xx, carbon dioxide, CO2, convert, methanol, methane,
   conversion, catalyst, silanes, NHC, carbene
%X "Carbon dioxide was reduced with silane using a stable N-heterocyclic carbene
   organocatalyst to provide methanol under very mild conditions. Dry air can
   serve as the feedstock, & the organocatalyst is much more efficient than
   transition-metal catalysts for this reaction. This approach offers a very
   promising protocol for chemical CO2 activation & fixation." (online 3/'09.)
   -- [<A HREF="http://dx.doi.org/10.1002/anie.200806058">doi:10.1002/anie.200806058</A>]['09].

%A R. Arkin
%T Governing Lethal Behavior in Autonomous Robots
%I ChapmanHall
%P 256
%M MAY
%D 2009
%K book, text, c2009, c200x, c20xx, zz1209, mil, military, war, warfare, robot,
   cyber, combat, robotics, autonomous, unmanned, robots, lethal, robot,
   ethics, UAV
%X "... Governing Lethal Behavior in Autonomous Robots explores how to produce
   an artificial conscience in a new class of robots, humane-oids, which are
   robots that can potentially perform more ethically than humans in the
   battlefield. The author examines the philosophical basis, motivation, theory,
   and design recommendations for the implementation of an ethical control and
   reasoning system in autonomous robot systems, taking into account the Laws
   of War and Rules of Engagement ..."
   1st ed 2009; hb us$51; uk us isbn:1420085948; uk us isbn13:978-1420085945.

%A P.-M. Binder
%T Computation: The edge of reductionism
%J Nature
%V 459
%P 332-334
%M MAY
%D 2009
%K news, views, c2009, c200x, c20xx, zz0509, reductionism, simulation,
   emergence, complex systems, emergent, cellular automaton, Wolfram,
   decidability
%X "Research at the frontier between CompSci & physics illustrates the
   shortcomings of the reductionist approach to science, which explains
   macroscopic behaviour using microscopic principles. ... But there are hints
   that finite objects may, after all, have undecidable properties. One hint
   comes from certain mappings of a solid square onto itself, which have been
   shown to be undecidable ... A second hint comes from a new level of
   computation that is more powerful than a Turing machine ... hopes ... will
   lead to a better understanding of the 'computer' in which we live."
   -- [<A HREF="http://dx.doi.org/10.1038/459332a">doi:10.1038/459332a</A>]['09].
   [Also search for: model computation Turing].

%A J. E. Campbell
%A D. B. Lobell
%A C. B. Field
%T Greater transportation energy and GHG offsets from bioelectricity than
   ethanol
%J Science
%V 324
%N 5930
%P 1055-1057
%M MAY
%D 2009
%O (Originally publ. Science Express, 7 May 2009)
%K jrnl, c2009, c200x, c20xx, greenhouse gas, gases, CO2, bio fuel, fuels,
   biofuel, biofuels, electric, electricity, car, cars, automobile, transport,
   biomass, bioelectricity, green, sustainable, sustainability
%X "The quantity of land available to grow biofuel crops without affecting food
   prices or greenhouse gas (GHG) emissions from land conversion is limited.
   [so] bioenergy should maximize land-use efficiency when addr. transportation
   & climate change goals. Biomass could power either int.combustion or elec.
   vehicles, but the relative land-use efficiency of these 2 energy pathways is
   not well quantified. ... show that bioelectricity outperforms ethanol across
   a range of feedstocks, conversion techs., & vehicle classes. Bioelectricity
   produces an average of 81% more transp. kms & 108% more emissions offsets
   per unit area of cropland than does cellulosic ethanol. ... suggest that
   alternative bioenergy pathways have large diffs. in how efficiently ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1168885">doi:10.1126/science.1168885</A>]['09].

%A R. P. N. Rao
%A N. Yadav
%A M. N. Vahia
%A H. Joglekar
%A R. Adhikari
%A I. Mahadevan
%T Entropic evidence for linguistic structure in the Indus script
%J Science
%V 324
%N 5931
%P 1165
%M MAY
%D 2009
%K jrnl, c2009, c200x, c20xx, lingustics, natural, human language, written,
   entropy
%X "... The hypothesis that the script encodes language has recently been
   questioned. Here, we present evidence for the linguistic hypothesis by
   showing that the script's conditional entropy is closer to those of natural
   languages than various types of nonlinguistic systems."
   --  [<A HREF="http://dx.doi.org/10.1126/science.1170391">doi:10.1126/science.1170391</A>]['10].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Notes/Information/">entropy</A>].)

%A D. Fanelli
%T How many scientists fabricate and falsify research? A systematic review and
   meta-analysis of survey data
%J PLoS ONE
%V 4
%N 5
%P e5738
%M MAY
%D 2009
%K jrnl, eJrnl, c2009, c200x, c20xx, zz0216, academic, scientific, research,
   ethics, fraud, misconduct, plagiarism, fabrication, falsification,
   manipulation, University
%X "The freq. with which scientists fabricate & falsify data, or commit other
   forms of scientific misconduct is a matter of controversy. ... This is the
   first meta-analysis of these surveys. ... A pooled weighted average of 1.97%
   (N=7, 95%CI: 0.86-4.45) of scientists admitted to have fabricated, falsified
   or modified data or results at least once -  a serious form of misconduct by
   any standard -  & up to 33.7% admitted other questionable research practices.
   In surveys asking about the behaviour of colleagues, admission rates were
   14.12% (N=12, 95% CI: 9.91-19.72) for falsification, & up to 72% for other
   questionable research practices. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0005738">doi:10.1371/journal.pone.0005738</A>]['16].
   [Also search for: research academic misconduct].

%A J. Tyrangiel
%T Auto-Tune: Why pop music sounds perfect
%J Time
%M FEB
%D 2009
%K magazine, news, c2009, c200x, c20xx, zz0609, Antares, auto tune, autotune,
   music, note, pitch, adjust, perfect, correct, correction, shift, transpose,
   transposition, studio, singing, Hildebrand, Cher, Believe, pop song, tune
%X "... Auto-Tune's inventor is a man named Andy Hildebrand, ...
   autocorrelation ... Auto-Tune was born in late 1996. ...
   1998 Cher hit 'Believe.' ..."
   -- 5 Feb 2009 [<A HREF="http://www.time.com/time/magazine/article/0,9171,1877372-2,00.html">time</A>]['09].
      [<A HREF="http://www.antarestech.com/">Antares</A>]['09].

%A R. J. Goettle
%A A. Fawcett
%T The structural effects of cap and trade climate policy
%J Energy Economics
%V 31
%N Supplement 2
%P S244-S253
%M JUL
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1209, cap and trade, emissions, ETS, costs,
   cost, greenhouse gas, gases, climate change, CO2, IGEM, economics, economy,
   model, mitigation, scheme
%X "The Inter-temporal General Equilibrium Model (IGEM) explores the cost to the
   U.S. economy of increasingly more stringent cap & trade regimes. The economy-
   -wide losses are small with energy, agriculture, chemicals, high tech
   manufacturing & trade being most affected. The availability of lower cost
   offsets substantially reduces these economic losses. The economy becomes less
   capital but more labor intensive. Household welfare losses are smaller for
   full consumption (goods, services & leisure). A more inelastic trade-off
   between consumption & leisure dramatically reduces policy costs as do more
   favorable revenue recycling options. Induced technical change yields a small,
   measurable reduction in policy costs."
   "... The overall economic impacts of these alternatives are estimated to be
   small even in the most restrictive of cases. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.eneco.2009.06.016">doi:10.1016/j.eneco.2009.06.016</A>]['09].

%A E. S. Reich
%T Plastic Fantastic: How the Biggest Fraud in Physics Shook the
   Scientific World
%I Macmillan
%P 272
%D 2009
%K book, c2009 c200x, c20xx, zz0809, scientific fraud, peer review, ethics,
   falsification, misconduct, Schon, science, Bell Labs, zzEthics
%X "... saga of physicist Hendrik Schon. At Bell Labs in the late 1990s,
   Schon's apparent discoveries about atomic-scale devices called field-effect
   transistors earned him a stellar peer-group reputation - until his research
   was exposed as faked in c2002. ..."
   1st ed 2009, hb us$18; uk us isbn:0230224679; uk us isbn13:978-0230224674.

%A R. F. Service
%T Transportation Research: Hydrogen cars: Fad or the future?
%J Science
%V 324
%N 5932
%P 1257-1259
%M JUN
%D 2009
%K news, views, c2009, c200x, c20xx, zz0609, car, automobile, hydrogen, H2,
   fuel, fuels, cell, cells, emission, emissions, transport
%X "... Last month, Energy Secretary Steven Chu announced that the Dept of
   Energy (DOE) was putting the brakes on research into automotive hydrogen
   fuel cells. Chu cites the cost and durability of vehicle fuel cells, the
   inability to store large volumes of hydrogen fuel, the absence of a
   carbon-free way of generating the hydrogen, and the need to build a
   nationwide refueling infrastructure. The issue came down to a simple
   question, says Chu: "Is it likely in the next 10 or 15 or even 20 years that
   we will convert to a H.-car economy? The answer, we felt, was no." ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.324_1257">doi:10.1126/science.324_1257</A>]['09].

%A R. F. Service
%T ExxonMobil fuels Venter's efforts to run vehicles on algae-based oil
%J Science
%V 325
%N 5939
%P 379
%M JUL
%D 2009
%K news, views c2009, c200x, c20xx, zz1009, alga, algae, algal, oil, fuel,
   fuels, bio, biofuel, sustainable, energy, ExxonMobil, Exxon, Exon, Mobil,
   photosynthesis
%X "... [EM] will spend up to $600 million over 5 to 6 years to produce biofuels
   from algae. Half the money will go to Synthetic Genomics Inc. (SGI) ...
   a founder of Sapphire Energy, thinks the tallest hurdle is scaling up the
   process ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.325_379a">doi:10.1126/science.325_379a</A>]['09].
   (Also see [<A HREF="http://www.nature.com/news/2009/090923/full/461460a.html">nature</A>][9/'09].)

%A S. A. Greenberg
%T How citation distortions create unfounded authority: analysis of a citation
   network
%J BMJ
%M JUL
%V 339
%D 2009
%K jrnl, BMJ, c2009, c200x, c20xx, zz1013, publish, perish, cite,
   citation, bias, misuse, distortion, fact, scientific, research
%X "... A complete citation n/wk was constructed from all PubMed indexed English
   literature papers addressing the belief that beta amyloid, a protein
   accumulated in the brain in Alzheimer's disease, is produced by & injures
   skeletal muscle of patients with inclusion body myositis. Social n/wk theory
   & graph theory were used to analyse this network. ... Citation is both an
   impartial scholarly method & a powerful form of social comm'n. Through
   distortions in its social use that include bias, amplification, & invention,
   citation can be used to generate info. cascades resulting in unfounded
   authority of claims. Construction & analysis of a claim specific citation
   n/wk may clarify the nature of a published belief system & expose distorted
   methods of social citation." (BMJ 2009;339:b2680)
   -- [<A HREF="http://dx.doi.org/10.1136/bmj.b2680">doi:10.1136/bmj.b2680</A>]['13].
   [Also search for: publish perish].

%A M. Sivak
%A O. Tsimhoni
%T Fuel efficiency of vehicles on US roads: 1923-2006
%J Energy Policy
%V 37
%N 8
%P 3168-3170
%M AUG
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0709, road transport, transportation, car, cars,
   truck, trucks, vehicle, vehicles, motor, oil shock, mpg, fuel consumption,
   efficiency, US, USA
%X "... Information about distances driven & fuel consumed was used to calculate
   the on-the-road fuel efficiency of the overall fleet & of different classes
   of vehicles. The overall fleet fuel efficiency decreased from 14mpg in 1923
   to 11.9mpg in '73. Starting in '74, efficiency increased rapidly to 16.9mpg
   in '91. Thereafter, improvements have been small, with efficiency reaching
   17.2mpg in 2006. ..."
   "CARS: ... data for '36 through '91 follow a pattern similar to that of all
   vehicles. As with the overall fleet, there were major improvements from
   '73 to '91 (from 13.4 to 21.2mpg). ... improvements from '91 to the
   present were substantially smaller than those prior to '91 (achieving
   22.4mpg in '06) ..."  [auths @ U.Mich.]
   -- [<A HREF="http://dx.doi.org/10.1016/j.enpol.2009.04.001">doi:10.1016/j.enpol.2009.04.001</A>]['09].

%T National algal biofuels technology roadmap (draft report, 2009)
%I U.S. Department of Energy Biomass Program
%P 214
%D 2009
%K TR, c2009, c200x, c20xx, biofuel, biofuels, alga, algae, algal, renewable,
   energy, fuel, fuels, biodiesel, DOE, gov, oleaginous, species,
   Pseudochlorococcum sp., Haematococcus pluvialis
%X pdf@[<A HREF="https://e-center.doe.gov/iips/faopor.nsf/UNID/79E3ABCACC9AC14A852575CA00799D99/$file/AlgalBiofuels_Roadmap_7.pdf">doe.gov</A>]['09].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.326.5958.1345-a">doi:10.1126/science.326.5958.1345-a</A>]['09].)

%A L. Itti
%A P. Baldi
%T Bayesian surprise attracts human attention
%J Vision Res.
%B 49
%N 10
%P 1033-1036
%M JUN
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0809, predict, prediction, Bayesian surprise,
   human behaviour, vision, gaze, attention, prior beliefs
%X "We propose a formal Bayesian defn of surprise to capture subjective aspects
   of sensory information. ... differences between posterior & prior beliefs
  ... test the framework by quantifying the extent to which humans may orient
  attention & gaze towards surprising events or items while watching TV. ...
  simple computational model where a low-level, sensory form of surprise is
  computed by simple simulated early visual neurons. [BS] is a strong attractor
  of human attention, with 72% of all gaze shifts directed towards locations
  more surprising than the avg., ... rising to 84% when focusing the analysis
  onto regions simultaneously selected by all observers..."
  -- [<A HREF="http://dx.doi.org/10.1016/j.visres.2008.09.007">doi:10.1016/j.visres.2008.09.007</A>]['09],
  -- NIPS06 pdf@[<A HREF="http://ilab.usc.edu/publications/doc/Itti_Baldi06nips.pdf">usc</A>]['09],
  [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/18834898">n c b i</A>]['09].

%A C. R. Sunstein
%T Going to Extremes: How Like Minds Unite and Divide
%I OUP
%P 208
%D 2009
%K book, OUP, c2009, c200x, c20xx, zz0909, human behaviour, society, extremism,
   politics, opinion, opinions
%X 1st ed, 2009, hb, us$21.95, stg13,
   uk us isbn:0195378016; uk us isbn13:978-0195378016.

%A E. Pennisi
%T On the origin of cooperation
%J Science
%V 325
%N 5945
%P 1196-1199
%M SEP
%D 2009
%K essay, views, c2009, c200x, c20xx, cooperation, prisoner, prisoners dilemma,
   evolution, cooperate
%X "... Darwin suggested that selection might favor families whose members were
   cooperative, ... But cheaters - those who benefit without making sacrifices
   - are likely to evolve because they will have an edge over individuals ...
   ... finding that even single-celled organisms have sophisticated means of
   working together. As genomics has come of age, researchers are getting down
   to the genetic nuts and bolts of cooperation in a variety of systems ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.325_1196">doi:10.1126/science.325_1196</A>]['09].

%A A. Politi
%A J. C. F. Matthews
%A J. L. O'Brien
%T Shor's quantum factoring algorithm on a photonic chip
%J Science
%V 325
%N 5945
%P 1221
%M SEP
%D 2009
%K brevia, c2009, c200x, c20xx, zz0909, Shor, Shors, algorithm, computing,
   quantum computer, primes, prime factoring, factorisation, factorization,
   factors
%X "Shor's quantum factoring alg. finds the prime factors of a large # exp.
   faster than any other known method ... requires a quantum computer, a device
   that harnesses the massive ||-ism afforded by quantum superposition & ent'
   of quantum bits (or qubits). We report the demonstration of a compiled
   version of S's alg. on an integrated waveguide silica-on-silicon chip that
   guides 4 single-photon qubits through the computation to factor 15."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1173731">10.1126/science.1173731</A>]['09].
   (NB. 4 qubits, factors 15 = 3 x 5.)
   [Also search for: Shor algorithm quantum].

%A D. G. Rand
%A A. Dreber
%A T. Ellingsen
%A D. Fudenberg
%A M. A. Nowak
%T Positive interactions promote public cooperation
%J Science
%V 325
%N 5945
%P 1272-1275
%M SEP
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0909, behaviour, cooperation, cooperate,
   altruism, public goods game, good, punishment, reward, identity, repeated,
   iterated, interaction, greed, selfish
%X "The public goods game ... Each participant chooses how much to contribute to
   a common pool that returns benefits to all participants equally. The ideal
   outcome occurs if everybody contributes the max. amount, but the self-
   -interested strategy is not to contribute anything. Most previous studies
   have found punishment to be more effective than reward ... The typical design
   of these studies, however, represses future consequences for today's actions.
   In an exp.setting, we compare public goods games followed by punishment,
   reward, or both in the setting of truly repeated games, in which player
   identities persist from round to round. We show that reward is as effective
   as punishment for maintaining public cooperation & leads to higher total
   earnings. Moreover, when both options are available, reward leads to
   increased contributions & payoff, whereas punishment has no effect on
   contributions & leads to lower payoff. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1177418">doi:10.1126/science.1177418</A>]['09].
   [Also search for: public goods game].

%A D. Greenfield
%A S. Moore
%T Implications of electronics technology trends for algorithm design
%J COMPJ
%V 52
%N 6
%P 690-698
%M AUG
%D 2009
%K COMPJ, jrnl, c2009, c200x, c20xx, zz0909, computer architecture, Cmp,
   communication, data, parallel
%X "Scaling of electronics technology has brought us to a pivotal point ...
   Technology scaling favours transistors over wires which has led us into an
   era where communication takes more time & consumes more power than the comp'n
   itself. ... pushes us toward a comm'n-centric approach to alg. design. ...
   need to be able to predict data movement both in time & space. We demonstrate
   that algs. exhibit fractal like comm'n behaviour which is likely to help with
   such an analysis. [&] successfully exploiting these fractal properties will
   allow us to reduce comm'n ... increasing performance & power efficiency."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxp013">doi:10.1093/comjnl/bxp013</A>]['09].

%A P. H. Frampton
%T Did Time Begin? Will Time End?: Maybe the Big Bang Never Occurred
%I World Scientific
%P 116
%D 2009
%K book, text, c2009, c200x, c20xx, zz1209, time, big bang, physics, cosmology,
   dark matter, energy, beginning, end, universe, entropy
%X "... Recent observational discoveries, especially that the expansion rate of
   the universe is accelerating, have revolutionized the understanding of the
   energy content of the universe (only a small fraction of about 4% is normal
   matter; the remainder is about 24% dark matter and 72% dark energy). Thus the
   dark side of the universe, especially dark energy, leads to new possibilities
   for the beginning and end of the universe. This book emphasizes the notion of
   entropy and describes how it is theoretically possible that the universe may
   end in a finite time. ..."
   1st ed 2009; hb us$22; uk us isbn:9814280585; uk us isbn13:978-9814280587.

%A D. Reich
%A K. Thangaraj
%A N. Patterson
%A A. L. Price
%A L. Singh
%T Reconstructing Indian population history
%J Nature
%V 461
%P 489-494
%M SEP
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1009, India, Indian, population, groups,
   populations, history, migration, origin, origins, genetics, north, south,
   human, Indians, Indo European, Asian, racial
%X "... analyse 25 diverse groups in India to provide strong evidence for two
   ancient populations, genetically divergent, that are ancestral to most
   Indians today. One, the 'Ancestral North Indians' (ANI), is genetically close
   to Middle Easterners, Central Asians, and Europeans, whereas the other, the
   'Ancestral South Indians' (ASI), is as distinct from ANI and East Asians as
   they are from each other. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08365">doi:10.1038/nature08365</A>]['09].

%A J. E. Hirsch
%T An index to quantify an individual's scientific research output that takes
   into account the effect of multiple coauthorship
%J arXiv
%M FEB
%D 2010
%K TR, c2010, c201x, c20xx, zz1222, JEHirsch, Hbar, Hindex, hCore, publish,
   perish, modified bibliometrics, multi, multiple, author, authors,
   coauthorship
%X "I propose the index ('hbar'), defined as the number # papers of an
   individual that have citation count larger than or equal to the h of all
   coauthors of each paper, as a useful index to characterize the scientific
   output of a researcher that takes into account the effect of multiple
   coauthorship. The bar is higher for hbar."
   -- 0911.3144@[<A HREF="https://arxiv.org/abs/0911.3144">arXiv</A>].
     "... A scientist has index hbar if hbar of his/her papers belong to his/her
     hbar core. A paper belongs to the hbar core of a sci't if it has >= hbar
     citations [&] belongs to the hbar-core of each of [its] coauthors ..."
   (The claimed benefits of Hbar over H seem doubtful to me.)
   [Also search for: modified Hindex]  and  [also search for: Hirsch Hindex].

%A F. Pearce
%T Peoplequake: Mass Migration, Ageing Nations and the Coming Population Crash
%I EdenProject
%M FEB
%D 2010
%K book, c2010, c201x, c20xx, zz0110, population, resources, sustainability,
   renewable, ecology, human behaviour, climate change, eco systems, ecosystems,
   ageing, Eden Project
%X 1st ed 2010; pb stg10; uk isbn:1905811349; uk isbn13:978-1905811342.

%A E. Hoffman
%T Time
%I Profile Books
%P 224
%D 2009
%K book, time, c2009, c200x, c20xx, zz1109, arrow, perception, circadian
%X 1st ed 2009; pb stg7; uk us isbn:1846680387; uk us isbn13:978-1846680380.
   [Also search for: arrow time].

%A A. Little
%T Power Trip: A Journey Through Our Fossil-Fuel Past in Search of a
   Renewable Future
%I HarperCollins
%P 446
%M OCT
%D 2009
%K book, c2009, c200x, c20xx, renewable energy, climate change, resources
%X "... during the summer blackout of 2003, when a massive line of electrical
   cable shorted, leaving six major metropolitan areas without power for days.
   Reflecting on the impact of the power outage, Little examines the role
   fossil fuels plays in her own life ..."
   1st ed 2009, hb us$21; uk us isbn:0061353256; uk us isbn13:978-0061353253.

%A C. Gershenson
%A L. A. Pineda
%T Why does public transport not arrive on time? The pervasiveness of
   equal headway instability
%J PLoS ONE
%V 4
%N 10
%P e7292
%M OCT
%D 2009
%K jrnl, eJrnl, c2009, c200x, c20xx, zz1109, bus, buses, busses, grouping,
   platooning, why do buses all come at once,  equal headway instability,
   delay, delays, late, train, trains, systems, travel time, arrival, together
%X "The equal headway instability phenomenon is pervasive in public transport
   systems. This instability is characterized by an aggregation of vehicles
   that causes inefficient service.  ...  the phenomenon is apparent in many
   transport systems and can be modeled and rectified in abstraction."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0007292">doi:10.1371/journal.pone.0007292</A>]['09].

%T Cycling in the UK: An Introduction to the National Cycle Network
%Q Sustrans
%I AA publ.
%D 2009
%K book, guide, c2009, c200x, c20xx, cycle, network, route, routes, maps,
   bicycle, bike, cycling, touring, UK, England, Scotland, Wales
%X "National Cycle Network, is now around 12,000 miles and
   runs within one mile of 55 per cent of the UK population."
   -- [<A HREF="http://www.theaa.com/motoring_advice/news/national-cycle-network.html">AA</A>]['09].
   (And 'Cycling in the UK: The Official Guide to the National Cycle Network',
    3rd ed 2006; pb stg12; uk isbn:1901389510; uk isbn13:978-1901389517.)

%A A. Le Goff
%A V. Artero
%A B. Jousselme
%A P. D. Tran
%A N. Guillet
%A R. Metaye
%A A. Fihri
%A S. Palacin
%A M. Fontecave
%T From hydrogenases to noble metal-free catalytic nanomaterials for H2
   production and uptake
%J Science
%V 326
%N 5958
%P 1384-1387
%M DEC
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1209, electricty, hydrogen, catalyst, hydrogen,
   H2, water, energy, storage, store, electrical, fuel cell, interconversion,
   electrolysis, cheap, catalyst, nickel bisdiphosphine, hydrogenase, mimic
%X "... show that the covalent attachment of a nickel bisdiphosphine-based
   mimic of the active site of hydrogenase enzymes onto multiwalled carbon
   nanotubes results in a high-surface area cathode material with high catalytic
   activity under the strongly acidic conditions required in proton exchange
   membrane technology. Hydrogen evolves from aqueous sulfuric acid solution
   with very low overvoltages (20 millivolts), & the catalyst exhibits
   exceptional stability (more than 100,000 turnovers). The same catalyst is
   also very efficient for hydrogen oxidation in this environment, exhibiting
   current densities similar to those observed for hydrogenase-based materials."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1179773">doi:10.1126/science.1179773</A>]['09].
   (about 100 x less efficient than a platinum based one, as yet)

%A S. Pincock
%T Culture clash at Australian synchrotron
%J Nature
%V 462
%P 706-707
%M DEC
%D 2009
%K news, c2009, c200x, c20xx, zz1209, SAC, Australia, synchroton, Melbourne,
   Victoria, politics, academic management, Catherine Walter, Lamb, director,
   scientific, science, research, funding, grants, scandal, strike
%X "... staff went on strike in recent weeks, relations between the board that
   oversees the facility and the scientists who use it have broken down. ...
   board director and lawyer Catherine Walter ... According to scientists on the
   SAC, Walter has routinely ignored advice ... facility director, chemist
   Robert Lamb of the U. of Melbourne, was dismissed without explanation ... "
   -- [<A HREF="http://dx.doi.org/10.1038/462706b">doi:10.1038/462706b</A>]['09].

%A D. Garcia-Castellanos
%A F. Estrada
%A I. Jimenez-Munt
%A C. Gorini
%A M. Fernandez
%A J. Verges
%A R. De Vicente
%T Catastrophic flood of the Mediterranean after the Messinian salinity crisis
%J Nature
%V 462
%P 778-781
%M DEC
%D 2009
%K jrnl, c2009, c200x, c20xx, Mediterranean sea, Straits, Gibraltar Strait,
   Messinian salinity crisis, Zanclean, level, rise, fall
%X "The M. Sea became disconnected from the world's oceans & mostly desiccated
   by evaporation about 5.6-million years ago during the Messinian salinity
   crisis. The Atlantic waters found a way through the present Gibraltar Strait
   & rapidly refilled the Med. 5.33-m.y. ago ... the Zanclean flood. ...
   Although the flood started at low water discharges that may have lasted for
   up to several thousand y., our results suggest that 90% of the water was
   transferred in a short period ranging from a few months to 2 y.. ... may have
   involved peak rates of sea level rise in the Med. of > 10 metres/day."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08555">doi:10.1038/nature08555</A>]['09].

%E T. Hey
%E S. Tansley
%E K. Tolle
%T The Fourth Paradigm: Data-Intensive Scientific Discovery
%I Microsoft
%P 287
%M OCT
%D 2009
%K book, text, c2009, c200x, c20xx, zz1209, Jim Gray, data intensive, analysis,
   eScience
%X "... Data-Intensive Scientific Discovery, the collection of essays expands
   on the vision of pioneering computer scientist Jim Gray for a new, fourth
   paradigm of discovery based on data-intensive science and offers insights
   into how it can be fully realized."
   1st ed 2009; uk us isbn:0982544200; uk us isbn13:978-0982544204.
   (Also see [<A HREF="http://research.microsoft.com/en-us/collaboration/fourthparadigm/">msnot</A>]['09].)

%A B. R. Komisaruk
%A B. Whipple
%A C. Beyer-Flores
%A S. Nasserzadeh
%T Orgasm Answer Guide
%I JohnHopkinsUP
%P 176
%M NOV
%D 2009
%K book, text, c2009, c200x, c20xx, orgasm, sex, sexuality
%X 1st ed 2009; hb us$36; us isbn:080189395X; us isbn13:978-0801893957.
   "... answers common questions many people have about one of life's most
   fascinating experiences. In an accessible question-and-answer format, 4 of
   the world's leading sexuality experts address every aspect of orgasms: how
   they happen, why they don't, and what can be done to enhance s. experiences.
   The authors provide clear & informed anss. to > 80 common questions. ..."

%A B. Lovell
%T Challenged by Carbon: The Oil Industry and Climate Change
%I CUP
%P 230
%D 2009
%K book, CUP, c2009, c200x, c20xx, oil, CO2, climate change, risk, risks,
   fossil fuels, carbon
%X "Is there a low-carbon future for the oil industry? Faced with compelling
   new geological evidence, the petroleum industry can no longer ignore the
   consequences of climate change brought on by consumption of its products ..."
   1st ed 2009; hb us$90; uk us isbn:0521197015; uk us isbn13:9780521197014.
   [Also search for: climate change book].

%A A. Trees
%T Decoding Love: Why It Takes Twelve Frogs to Find a Prince, and
   Other Revelations from the Science of Attraction
%I Avery
%P 272
%D 2009
%K book, popular, c2009, c200x, c20xx, love, mate, selection, date, dating,
   attraction, attractive, human behaviour
%X 1st ed 2009; hb us$10; uk us isbn:1583333312.
          2010; pb us$10; uk us isbn:1583333746; uk us isbn13:978-1583333747.
   [also search for: mate selection].

%A S. M. Gorelick
%T Oil Panic and the Global Crisis: Predictions and Myths
%I Wiley
%P 256
%D 2009
%K book, text, c2009, c200x, c20xx, zz0510, peak oil, crude, hydrocarbons,
   global, energy, reserve, reserves, fuel, fuels, fossil, production, economics
%X 1st ed 2009; hb us$47; uk us isbn:1405195487; uk us isbn13:978-1405195485.
   [Also search for: peak oil fossil fuel].

%A C. M. Reinhart
%A K. Rogoff
%T This Time is Different
%I PrincetonUP
%P 496
%D 2009
%K book, text, c2009, c200x, c20xx, economy, economics, economist, boom, bust,
   bubble, global financial crisis, GFC, depression, recession, debt,
   Wall St, street, banking, money
%X This Time is Different (not); Eight Centuries of Financial Folly.
   1st ed; hb us$20; uk us isbn:0691142165; uk us isbn13:978-0691142166.
   [Also search for: Reinhart Rogoff].

%A N. D. Kristof
%A S. WuDunn
%T Half the Sky: Turning oppression into opportunity for women worldwide
%I Knopf
%D 2009
%P 320
%K book, c2009, c200x, c20xx, zz0210, women, womens, health, oppression,
   welfare, education, equality, gender, girls
%X 1st ed 2009; pb us$14; uk us isbn:0307267148; uk us isbn13:978-0307267146.

%A N. Lane
%T Life Ascending: The Ten Great Inventions of Evolution
%I WWNorton
%P 352
%D 2009
%K book, text, c2009, c200x, c20xx, zz0910, biol, biology, life, origins,
   evolution, cell, cells, DNA, sex, consciousness, death, science
%X 1st ed 2009; hb us$20; uk us isbn:0393065960; uk us isbn13:978-0393065961.
   "... what were the great biological inventions that led to Earth as we
   know it. ... the origin of life, the creation of DNA, photosynthesis,
   the evolution of complex cells, sex, movement, sight, warm bloodedness,
   consciousness and death ..."

%A S. Larsson
%T The Girl Who Played with Fire
%P 503
%K Knopf
%D 2009
%K book, novel, crime, thriller, c2009, c200x, c20xx, Salander, Dragon Tattoo
%X hb us$17; uk us isbn:0307269981; uk us isbn13:978-0307269980.
   2nd book of the trilogy.
   [Also search for: Larsson Dragon Tattoo].

%A S. Larsson
%T The Girl Who Kicked the Hornet's Nest
%I Knopf
%D 2009
%P 576
%K book, novel, crime, thriller, c2009, c200x, c20xx, Salander, Dragon Tattoo
%X hb us$12; uk us isbn:030726999X; uk us isbn13:978-0307269997.
   3rd book of the trilogy.
   [Also search for: Larsson Dragon Tattoo].

%A J. Hannam
%T God's Philosophers: How the Medieval World Laid the Foundations of
   Modern Science
%I IconBooks
%P 320
%D 2009
%K book, text, c2009, c200x, c20xx, zz0910, God, religion, medieval, science,
   history, c12xx, philosophy, metaphysics, Copernicus, Buridan, Oresme,
   Bradwardine, Bacon, Aquinas, Christianity, Islam, scholar, scholars, clock
%X 1st ed 2009; hb stg10; uk us isbn:1848310706; uk us isbn13:978-1848310704.
   "... showing that medieval people did not think the earth is flat, nor did
   Columbus 'prove' that it is a sphere; the Inquisition burnt nobody for their
   science nor was Copernicus afraid of persecution; no Pope tried to ban human
   dissection or the number zero. "God's Philosophers" is a celebration of the
   forgotten scientific achievements of the Middle Ages - advances which were
   often made thanks to, rather than in spite of, the influence of Christianity
   & Islam. Decisive progress was also made in technology: spectacles & the
   mechanical clock, for instance, were both invented in 13C Europe. Charting
   an epic journey through six centuries of history, "G.'s P." brings back to
   light the discoveries of neglected geniuses like John Buridan, Nicole Oresme
   & Thomas Bradwardine, as well as putting into context the contrib. of more
   familiar figures like Roger Bacon, William of Ockham & St Thomas Aquinas."

%A B. Goldacre
%T Bad Science
%I Harper
%P 288
%D 2009
%K book, c2009, c200x, c20xx, zz1111, science, funny, sceptic, skeptic, ads,
   advertsing, snake oil, pseudo, principles, bullshit, scare, scares, MMR,
   homeopathy, myths, mythbuster, critical thinking, scientific, good, funny,
   research methods, quacks, quackery, big pharma
%X reprnt 2009; pb stg5; uk us isbn:000728487X; uk us isbn13:978-0007284870.
   "... takes us on a hilarious, invigorating and informative journey through
   the bad science we're fed by the worst of the hacks and the quacks! When
   Dr B.G. saw someone on daytime TV dipping her feet in an 'Aqua Detox'
   footbath, releasing her toxins into the water and turning it brown, he
   thought he'd try the same at home. ..."

%A L. Fisher
%T The Perfect Swarm: The Science of Complexity in Everyday Life
%I BasicBooks
%P 288
%M DEC
%D 2009
%K book, text, c2009, c200x, c20xx, zz0311, complexity, emergence, swarm, flock,
   shoal, behaviour
%X 1st ed 2009; hb us$14; uk us isbn:046501884X; uk us isbn13:978-0465018840.
   '... process of "self-organization" reveals itself in the inanimate worlds of
   crystals and seashells, but as Len Fisher shows, it is also evident in living
   organisms, from fish to ants to human beings. The coordinated movements of
   fish in shoals, for example, arise from the simple rule: "Follow the fish in
   front." Traffic flow arises from simple rules: "Keep your distance" and
   "Keep to the right." ...'

%A K. B. Wray
%T Did professionalization afford better opportunities for young scientists?
%J Scientometrics
%V 81
%N 3
%P 757-764
%M DEC
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1114, science, scientific, research, career,
   researcher, scientist, old, young, age, grant, grants
%X "... professionalization of science, a process that unfolded between 1600 &
   1899, afforded better opportunities for young scientists to make sig.
   discoveries. My analysis suggests that the professionalization of the scis.
   did make it a little easier for scientists to make sig. contributions at a
   younger age. But, I also argue that it is easy to exaggerate the effects of
   professionalization. Older & middle age scis. continued to play an important
   role in making sig. discoveries throughout the history of modern science."
   -- [<A HREF="http://dx.doi.org/10.1007/s11192-008-2254-x">doi:10.1007/s11192-008-2254-x</A>]['14].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.346.6212.929 ">www</A>][21/11/'14] on NIH.)

%A J. Camilo Bohorquez
%A S. Gourley
%A A. R. Dixon
%A M. Spagat
%A N. F. Johnson
%T Common ecology quantifies human insurgency
%J Nature
%V 462
%P 911-914
%M DEC
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1012, violence, war, insurgent, conflict,
   terrorism, terrorist, internal interactions, network, stats, model
%X "Many collective human activities, inc. violence, have been shown to exhibit
   universal patterns. The size distn of casualties both in whole wars from 1816
   to 1980 & terrorist attacks have separately been shown to follow approx.
   power-law distns. ... Here we show that the sizes & timing of violent events
   within different insurgent conflicts exhibit remarkable similarities. We
   propose a unified model of human insurgency ... Our model treats each
   insurgent pop'n as an ecology of dynamically evolving, self-organized groups
   following common decision-making processes. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08631">doi:10.1038/nature08631</A>]['12].

%A A. Golec de Zavala
%A A. Cichocka
%A R. Eidelson
%A N. Jayawickreme
%T Collective narcissism and its social consequences
%J J. of Personality and Social Psychology
%V 97
%N 6
%P 1074-1096
%M DEC
%D 2009
%K jrnl, psychology, c2009, c200x, c20xx, zz0317, human behaviour, politics,
   democracy, personality, collective narcissism, ingroup, outgroup, them,
   aggression, war, patriotism, conspiracy, intolerance, offence, anger,
   grudge, hostility, brexit, Trump, zzTrump, altright
%X "... introduces the concept of collective narcissism [CN] - an emotional
   investment in an unrealistic belief about the in group's greatness- aiming to
   explain how feelings about an ingroup shape a tendency to aggress against
   outgroups. ... 5 studies indicate that collective, but not individual,
   narcissism predicts intergroup aggressiveness. CN is related to high private
   & low public collective self-esteem & low implicit group esteem. It predicts
   perceived threat from outgroups, unwillingness to forgive outgroups,
   preference for military aggression over & above social dominance orientation,
   right-wing authoritarianism, & blind patriotism. The relationship between
   [CN] & aggressiveness is mediated by perceived threat from outgroups &
   perceived insult to the ingroup. In sum, the results indicate that [CN] is a
   form of high but ambivalent group esteem related to sensitivity to threats to
   the ingroup's image & retaliatory aggression."
   -- [<A HREF="http://dx.doi.org/10.1037/a0016904">doi:10.1037/a0016904</A>]['17],
   pdf@[<A HREF="https://www.researchgate.net/publication/40455337_Collective_Narcissism_and_Its_Social_Consequences">Res'Gate</A>]['17].
   (Also see "Welcome to the age of collective narcissism"
   -- the [<A HREF="https://theconversation.com/welcome-to-the-age-of-collective-narcissism-71196">Conversation</A>][25/1/2017].)

%A E. Knill
%T Physics: Quantum computing
%J Nature
%V 463
%P 441-443
%M JAN
%D 2010
%K news, views, c2010, c201x, c20xx, zz0210, intro, progress, survey,
   quantum computing, computer
%X "... I am optimistic that I will be able to perform interesting computations
   on quantum devices in my lifetime, but would not be disappointed if we
   encounter unexpected obstacles along the way."
   -- [<A HREF="http://dx.doi.org/10.1038/463441a">doi:10.1038/463441a</A>]['10] .
   [Also search for: quantum computing].

%A A. J. Oswald
%A S. Wu
%T Objective confirmation of subjective measures of human well-being:
   evidence from the U.S.A.
%J Science
%V 327
%N 5965
%P 576-579
%M JAN
%D 2010
%K jrnl, c2010, c201x, c20xx, happiness, happy, well being, wellbeing, survey,
   stats, USA, subjective, objective,
%X "... Yet there is little scientific evidence that such [survey] data are
   meaningful. This study examines a 2OO5-2OO8 Behavioral Risk Factor
   Surveillance System random sample of 1.3 million U.S. citizens. Life
   satisfaction in each U.S. state is measured. Across America, people's answers
   trace out the same pattern of quality of life as previously estimated, from
   solely nonsubjective data, in one branch of economics (so-called
   "compensating differentials" neoclassical theory, originally from Adam
   Smith). There is a state-by-state match (r=0.6, P < 0.001) between subjective
   and objective well-being. This result has some potential to help to unify
   disciplines."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1180606">doi:10.1126/science.1180606</A>]['10].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.1186315">persp'ves</A>].)
   [Also search for: happiness well being].

%A K. van Deemter
%T Not Exactly: In Praise of Vagueness
%I OUP
%P 368
%D 2010
%K book, text, OUP, c2010, c201x, c20xx, zz0210, logic, AI, precision,
   measurement, categories, quantity, size, degree, natural language, TENDUM
%X "Not everything is black and white. Our daily lives are full of vagueness or
   fuzziness. Language is the most obvious example ...  looks at the principles
   of measurement, and how we choose categories; the vagueness lurking behind
   what seems at first sight crisp concepts such as that of the biological
   'species'; uncertainties in grammar and the impact of vagueness on the
   programmes of Chomsky and Montague; vagueness and mathematical logic;
   computers, vague descriptions, and Natural Language Generation in AI ..."
   1st ed 2010, hb stg17; uk us isbn:0199545901; uk us isbn13:978-0199545902.
   (Also see [<A HREF="http://www.csd.abdn.ac.uk/~kvdeemte/NotExactly">www</A>]['10].)

%A C. M. Reinhart
%A K. S. Rogoff
%T Growth in a time of debt
%J Amer. Economic Rev.
%V 100
%N 2
%P 573-578
%M MAY
%D 2010
%K jrnl, c2010, c201x, c20xx, zz1113, economics, debt, growth, GDP, economy,
   national, right wing, politics, austerity, controversial, policy,
   error, errors
%X -- [<A HREF="http://dx.doi.org/10.1257/aer.100.2.573">doi:10.1257/aer.100.2.573</A>]['13];
   also see [<A HREF="http://en.wikipedia.org/wiki/Growth_in_a_Time_of_Debt">wikip</A>]['13] and
      T.Herndon, M.Ash, R.Pollin, Does High Public Debt Consistently Stifle
      Economic Growth? A Critique of Reinhart and Rogoff. Political Economy
      Res. Inst., U. Massachusetts, Amherst, April 2013,
      [<A HREF="http://www.peri.umass.edu/fileadmin/pdf/working_papers/working_papers_301-350/WP322.pdf">www</A>]['13].

%A P. Thagard
%T The Brain and the Meaning of Life
%I PrincetonUP
%P 292
%M FEB
%D 2010
%K book, text, c2010, c201x, c20xx, zz0310, meaning of life, brain, mind,
   reality, thought, free will, philosophy, rational
%X "... Thagard argues that minds are brains and that reality is what science
   can discover. Brains come to know reality through a combination of perception
   and reasoning. Just as important, our brains evaluate aspects of reality
   through emotions that can produce both good and bad decisions. Our cognitive
   and emotional abilities allow us to understand reality, decide effectively,
   act morally, and pursue the vital needs of love, work, and play. Wisdom
   consists of knowing what matters, why it matters, and how to achieve it. ..."
   1st ed; hb us$24; uk us isbn:0691142726; uk us isbn13:9780691142722.

%A D. Goodstein
%T Scientific fraud, and how not to do it
%I PrincetonUP
%P 184
%M FEB
%D 2010
%K book, text, c2010, c201x, c20xx, zz0410, science, fraud, ethics, ethical,
   scientific research, academic, misconduct, scandal, fabrication,
   falsification, Millikan, Fleischmann, Pons, Ninov, Schon, Bednorz, Muller
%X "... a tour of real controversies from the front lines of science & helps
   readers determine for themselves whether or not fraud occurred ... inc. ...
   Robert A. Millikan, whose historic measurement of the electron's charge
   has been maligned by accusations of fraud; Martin Fleischmann & Stanley Pons
   & their "discovery" of cold fusion; Victor Ninov & the supposed discovery of
   element 118; Jan Hendrik Schon from Bell Labs & his work in semiconductors;
   & J. Georg Bednorz & Karl Muller's discovery of high-temp. superconductivity,
   a seemingly impossible accomplishment that turned out to be real."
   1st ed 2010; hb us$18; us isbn:0691139660; us isbn13:978-0691139661.
   [Also search for: scientific misconduct].

%A D. Butler
%T University rankings smarten up
%J Nature
%V 464
%P 16-17
%M MAR
%D 2010
%K news, c2010, c201x, c20xx, zz0510, uni, university, ranking, rankings,
   rank, ranks, rating, ratings, quality, higher education, research, THES
%X "Systems for ranking the world's higher-education and research institutions
   are about to become more sophisticated ..."
   -- [<A HREF="http://dx.doi.org/10.1038/464016a">doi:10.1038/464016a</A>].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/2008-rankings/">ITrankings</A>].)

%A P. Parsons
%T The Science of Doctor Who
%I JohnHopkinsUP
%P 320
%M JUN
%D 2010
%K book, c2010, c201x, c20xx, zz0610, Doctor Who, the, Dr, TARDIS, Time Lord,
   BBC TV, Sci Fi, SciFi
%X 1st ed 2010; hb us$19; us isbn:080189560X; us isbn13:9780801895609.

%A R. Lee
%A P. Jonathan
%A P. Ziman
%T Pictish symbols revealed as a written language through application of
   Shannon entropy
%J PRSS A
%V ?
%P ?-?
%M ?
%D 2010
%K PRSS, PRSSA, jrnl, c2010, c201x, c20xx, zz0410, Pictish, Pict, Picts,
   Scotland, iron age, symbol, symbols, natural, human, written, writing,
   linguistics, language, entropy, Dtree, petroglyph, petroglyphs
%X "... Picts, a Scottish, Iron Age culture, left a few hundred stones expertly
   carved with highly stylized petroglyph symbols. Although the symbol scripts
   are assumed to convey information, owing to the short (one to three symbols),
   small (less than 1000 syms.) & often fragmented nature of many symbol sets,
   it has been impossible to conclude whether they represent forms of written
   language. This paper reports on a 2-param. decision-tree technique that
   distinguishes between the different character sets of human communication
   systems when sample sizes are small, thus enabling the type of communication
   expressed by these small symbol corpuses to be determined. Using the
   technique on the Pictish symbols established that it is unlikely that they
   are random or sematographic (heraldic) characters, but that they exhibit the
   characteristics of written languages."   (online Mar 2010.)
   -- [<A HREF="http://dx.doi.org/10.1098/rspa.2010.0041">doi:10.1098/rspa.2010.0041</A>]['10].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Notes/Information/">entropy</A>].)

%A S. Pironio
%A et al ...
%A C. Monroe
%T Random numbers certified by Bell's theorem
%J Nature
%V 464
%P 1021-1024
%M APR
%D 2010
%K jrnl, c2010, c201x, c20xx, zz0410, Bell, Bells, inequality, theorem, RNG,
   QRNG, random number, numbers, quantum theory, theoretic, information,
   non local, locality
%X "... inspired by earlier work on non-locality-based & device-indep., quantum
   information processing, we show that the non-local correlations of entangled
   quantum particles can be used to certify the presence of genuine randomness.
   It is thereby possible to design a cryptographically secure random #
   generator that does not require any assumption about the internal working of
   the device. Such a strong form of randomness generation is impossible
   classically & possible in quantum sys. only if certified by a Bell inequality
   violation. We carry out a proof-of-concept demo. of this proposal in a sys.
   of 2 entangled atoms separated by approx. 1 metre. The observed Bell
   inequality violation, featuring near perfect detection efficiency,
   guarantees that 42 new random #s are generated with 99% confidence. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09008">doi:10.1038/nature09008</A>]['10].
   [Also search for: quantum RNG].

%A L. Rendell
%A et al ...
%A K. N. Laland
%T Why copy others? Insights from the social learning strategies tournament
%J Science
%V 328
%N 5975
%P 208-213
%M APR
%D 2010
%K jrnl, c2010, c201x, c20xx, zz0510, discountmachine, Cownden, Lillicrap,
   social learning, AI, II, Alife, copy, copiers, imitate, imitation, game,
   Cultaptation, computer tournament, competition, behaviour
%X "Social learning ... is widespread in nature & is central to the remarkable
   success of humanity [but] unclear why copying is profitable & how to copy
   most effectively. ... we organized a computer tournament in which entrants
   submitted strategies specifying how to use social learning & its asocial
   alternative (eg, trial-and-error learning) ...  Most current theory
   predicts the emergence of mixed strategies that rely on some combination of
   the 2 types of learning. In the tournament, however, strategies that relied
   heavily on social learning were found to be remarkably successful, even when
   asocial info. was no more costly than social info.. ... because individuals
   frequently demonstrated the highest-payoff behavior in their repertoire,
   inadvertently filtering info. for copiers. The winning strategy
   (discountmachine) relied nearly exclusively on social learning & weighted
   info. according to the time since acquisition."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1184719">doi:10.1126/science.1184719</A>]['10],
   @[<A HREF="http://lalandlab.st-andrews.ac.uk/tournaments/sociallearning.html">st-andr'ws</A>]['10], &
   -- [<A HREF="http://www.intercult.su.se/cultaptation/tournament.php">cultaption</A>]['08].

%A P. H. Gleick
%A et al
%T Climate change and the integrity of science
%J Science
%V 328
%N 5979
%P 689-690
%M MAY
%D 2010
%K jrnl, letter, c2010, c201x, c20xx, zz0510, climate change, global warming,
   CO2, greenhouse gas, gases, effect, IPCC, fossil fuels, politics, business
%X "We are deeply disturbed by the recent escalation of political assaults on
   scientists in general and on climate scientists in particular. All citizens
   should understand some basic scientific facts. ...
   Society has 2 choices: We can ignore the science & hide our heads in the sand
   & hope we are lucky or we can act in the public interest to reduce the threat
   of global climate change quickly & substantively. The good news is that smart
   & effective actions are possible. But delay must not be an option."
   -- [<A HREF="http://dx.doi.org/10.1126/science.328.5979.689">doi:10.1126/science.328.5979.689</A>]['10].

%A C. Chabris
%A D. Simons
%T The Invisible Gorilla: And Other Ways Our Intuitions Deceive Us
%I Crown
%P 320
%M MAY
%D 2010
%K book, text, c2010, c201x, c20xx, zz0710, intuition, cognitive psychology,
   human, behaviour, brain, failings, inattention, irrational
%X hb, us$18; uk us isbn:0307459659; uk us isbn13:978-0307459657.

%A D. Clery
%T Laser fusion poised to ignite
%J Science
%V 328
%N 5980
%P 808-809
%M MAY
%D 2010
%K news, c2010, c201x, c20xx, inertial, nuclear, fusion power, laser, US NIF,
   LLNL, CLF, Nuckolls
%X "In 1960, John Nuckolls, a physicist at (LLNL) in Cal. ... he heard that
   Theodore Maiman had built the first successful optical laser ...
   Within days Nuckolls was working out how to implode his fuel capsule with a
   laser.  Today, the direct result of N.'s initiative is sitting in a cavernous
   hall 10 stories high and large enough to cover 3 football fields: the
   $3.5 billion National Ignition Facility. NIF was completed in 2009, and test
   firing of its giant laser has been going on since last summer. Shots aimed at
   igniting fusion fuel could begin later this year. ...  Laser, or inertial,
   fusion energy "needs ignition to be successful," says Mike Dunne, dir. of the
   Central Laser Facility at the Rutherford Appleton Laboratory in Didcot, U.K.
   "There's a lot of belief. The question is when?"  ...  To give NIF the best
   chance of success, LLNL researchers built a laser designed to produce 1-off
   pulses with the highest energy curr.poss.: 1.8 megajoules in a flash
   lasting about 20nanosecs.. [But] NIF can fire only 2 or 3 /day. ...
   an inertial fusion power station would need to explode a fuel capsule about
   10 x /sec, a feat no high-energy lasers can now achieve. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.328.5980.808">doi:10.1126/science.328.5980.808</A>]['10].
   Also see [<A HREF="http://dx.doi.org/10.1038/467893a">doi:10.1038/467893a</A>][10/'10].
   [Also search for: nuclear fusion power].

%A K. Sigmund
%T The Calculus of Selfishness
%I PrincetonUP
%P 184
%D 2010
%K book, text, c2010, c201x, c20xx, zz0610, selfish, cooperation, cooperate,
   cheat, defect, self interest, behaviour, game theory
%X "How does cooperation emerge among selfish individuals? When do people share
   resources, punish those they consider unfair, and engage in joint
   enterprises? Such questions fascinate philosophers, biologists, and alike,
   for the invisible hand that should turn selfish efforts into public benefit
   is not always at work. The Calculus of Selfishness looks at social dilemmas
   where cooperative motivations are subverted and self-interest becomes
   self-defeating. ..."
   1st ed 2010, hb us$35; uk us isbn:0691142750; uk us isbn13:978-0691142753.
   (Reviewed@[<A HREF="http://dx.doi.org/10.1126/science.1189117">doi:10.1126/science.1189117</A>]['10].)

%A W. Stacey
%T The Quest for a Fusion Energy Reactor: An Insider's Account of the
   INTOR Workshop
%I OUP
%P 208
%M MAR
%D 2010
%K book, text, c2010, c201x, c20xx, nuclear, fusion power, reactor,
   INTOR, ITER, Tokomak
%X "... The Workshop led to the International Thermonuclear Experimental Reactor
   (ITER), construction of which began in 2009 with the goal of demonstrating
   the scientific and technical feasibility of fusion power."
   1st ed 2010; hb us$25; uk us isbn:0199733848; uk us isbn13:978-0199733842.
   [Also search for: nuclear fusion power].

%A A.-L. Barabasi
%T Bursts: The Hidden Pattern Behind Everything We Do
%I Dutton (Penguin)
%P 310
%D 2010
%K book, text, c2010, c201x, c20xx, zz0610, network, networks, complex, linked
%X 1st ed 2010; hb us$18; uk us isbn:0525951601; uk us isbn13:978-0525951605;
          also, pb us$12; uk us isbn:0452297184; uk us isbn13:978-0452297180.
   "... Linked- explains how the digital age has yielded a massive, previously
   unavailable data set that proves the daily pattern of human activity isn't
   random, it's "bursty." We work and fight and play in short flourishes of
   activity followed by next to nothing. ..."

%A N. Oreskes
%A E. M. Conway
%T Merchants of Doubt: How a Handful of Scientists Obscured the Truth on
   Issues from Tobacco Smoke to Global Warming
%I Bloomsbury
%P 368
%D 2010
%K book, text, c2010, c201x, c20xx, zz1110, global warming, climate change, CO2,
   greenhouse gas, fossil fuel, coal, smoking, tobacco, lung cancer, cause,
   science, scientific research, public policy, politics, business, industry,
   risks, evidence, lobbying, spin, lies, right wing, deception, denial, denier,
   deny, bullshit, misinformation, obfuscation, PR
%X "... ranging from the risks of smoking to the reality of global warming. The
   people the authors accuse in this carefully documented book are themselves
   scientists - ...  vested interests like the tobacco industry ..."
   1st ed 2010; hb us$18; uk us isbn:1596916109; uk us isbn13:978-1596916104.
   [Also search for: Oreskes Conway].

%T How to improve the use of metrics
%J Nature
%V 465
%P 870-872
%M JUN
%D 2010
%K opinion, views, c2010, c201x, c20xx, zz0610, ranking, rankings, research,
   metric, metrics, publishing, peer review, rank
%X "Since the invention of the science citation index in the 1960s, quantitative
   measuring of the performance of researchers has become ever more prevalent,
   controversial & influential. 6 commentators tell Nature what changes might
   ensure that individuals are assessed more fairly. ...
     Get experts on board ...          Use ranking to help search ...
     Motivate people with prizes ...   Learn from game theory ...
     Accentuate the positive ...       Reward effort, not luck ...
   --[<A HREF="http://dx.doi.org/10.1038/465870a">doi:10.1038/465870a</A>]['10].

%A P. T. Greenland
%A S. A. Lynch
%A A. F. G. van der Meer
%A B. N. Murdin
%A C. R. Pidgeon
%A B. Redlich
%A N. Q. Vinh
%A G. Aeppli
%T Coherent control of Rydberg states in silicon
%J Nature
%V 465
%P 1057-1061
%M JUN
%D 2010
%K jrnl, c2010, c201x, c20xx, zz0710, quantum, computer, silicon, phosphorus,
   laser, superposition
%X "Laser cooling and electromagnetic traps ... can be used in the quantum
   control of one atom by another, are excited Rydberg states, where wavefns are
   expanded from their ground-state extents of less than 0.1-nm to several
   nanometres & even beyond; this allows atoms far enough apart to be
   non-interacting in their ground states to strongly interact in their excited
   states. ... demonstrate the coherent control of impurity wavefns in the most
   ubiquitous donor in a semiconductor, namely phosphorus-doped silicon. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09112">doi:10.1038/nature09112</A>]['10].

%A J. Smith
%A J. D. Van Dyken
%A P. C. Zee
%T A generalization of Hamilton's rule for the evolution of microbial
   cooperation
%J Science
%V 328
%N 5986
%P 1700-1703
%M JUN
%D 2010
%K report, c2010, c201x, c20xx, zz0710, cooperate, cheat, evolution,
   Myxococcus xanthus, bacteria, bacterial, sporulation, microbes
%X "H's rule states that coop'n will evolve if the fitness cost to actors < the
   benefit to recipients multiplied by their genetic relatedness. This rule
   makes many simplifying assumptions, however, & does not accurately describe
   social evolution in organisms such as microbes where sel'n is both strong &
   nonadditive. We derived a generalization of H's rule & measured its params.
   in Myxococcus xanthus bacteria. Nonadditivity made cooperative sporulation
   remarkably resistant to exploitation by cheater strains. Sel'n was driven by
   higher-order moments of pop'n structure, not relatedness. These results
   provide an empirically testable cooperation principle applicable to both
   microbes & multicellular organisms & show how nonlinear interactions among
   cells insulate bacteria against cheaters."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1189675">doi:10.1126/science.1189675</A>][1'0].
   [Also search for: Hamilton rule].

%A O. Harman
%T The Price of Altruism: George Price and the Search for the Origins of
   Kindness
%I Norton
%P 464
%M JUN
%D 2010
%K book, text, c2010, c201x, c20xx, zz0710, Oren, Price, biography, altruism,
   cooperate, cooperation, social, human, animal, behaviour
%X 1st ed 2010; hb stg15; uk us isbn:0393067785; uk us isbn13:978-0393067781.
   "... The Price of Altruism tells for the first time the moving story of the
   eccentric American genius George Price (1922-75), as he strives to answer
   evolution's greatest riddle. An original & penetrating picture of 20th
   century thought, it is also a deeply personal journey. From the heights of
   the Manhattan Project to the inspired equn that explains altruism to the
   depths of homelessness & despair, P's life embodies the paradoxes of
   Darwin's enigma. His tragic suicide in a squatter's flat, among the
   vagabonds to whom he gave all his possessions, provides the ultimate
   contemplation on the possibility of genuine benevolence."

%A N. Carr
%T The Shallows: What the Internet Is Doing to Our Brains
%I NortonCo.
%P 280
%D 2010
%K book, text, c2010, c201x, c20xx, internet, www, wwweb, human, brain,
   change, risks, society, technology, googling
%X hb us$15; pb us$9; uk us isbn:0393339750; uk us isbn13:978-039333975.
   "Is Google making us stupid? ...Our brains, the historical and scientific
   evidence reveals, change in response to our experiences. The technologies we
   use to find, store, and share information can literally reroute our neural
   pathways. Building on the insights of thinkers from Plato to McLuhan ..."

%A A. Johns
%T Piracy: The Intellectual Property Wars from Gutenberg to Gates
%I U. Chicago Press
%P 640
%D 2010
%K book, text, c2010, c201x, c20xx, zz0811, piracy, pirate, IP, copyright,
   intellectual property, patent, patents, law, legal, rights, microsoft,
   zzLaw, bootleg, music, movie, downloads, bill gates
%X 1st ed; hb us$23; us isbn:0226401189; us isbn13:978-0226401188.

%A C. d'Oliveira
%A S. Carson
%A K. James
%A J. Lazarus
%T MIT opencourseware: Unlocking knowledge, empowering minds
%J Science
%V 329
%N 5991
%P 525-526
%M JUL
%D 2010
%K essay, c2010, c201x, c20xx, zz0810, open course ware, courseware, consortium,
   courses, teaching, education, material, lecture notes, internet,
   www, ocw, MIT
%X "... In 2000, a faculty committee at (MIT) ... Rather than using the Internet
   to make money through distance learning, MIT should simply take the core
   academic materials already created on campus - the syllabi, lecture notes,
   assignments, and exams - and share them with the world. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.11826962">doi:10.1126/science.11826962</A>]['10],
   ocw@[<A HREF="http://ocw.mit.edu/">mit</A>]['10],
   &   [<A HREF="http://ocwconsortium.org/">consortium</A>]['10].

%A H. F. Moed
%T Measuring contextual citation impact of scientific journals
%J J. Informetrics
%V 4
%N 3
%P 265-277
%M JUL
%D 2010
%K jrnl, c2010, c201x, c20xx, zz1212, modified bibliometrics, adjusted JIF,
   SNIF, SNIP, source normalized impact, journals, ranking, academia, research
%X "... A j's subject field is defined as the set of papers citing that j..
   SNIP is defined as the ratio of the j's citation count per paper & the
   citation potential in its subject field. ..."
   -- [<A HREF="https://doi.org/10.1016/j.joi.2010.01.002">doi:10.1016/j.joi.2010.01.002</A>]['22],
   0911.2632@[<A HREF="https://arxiv.org/abs/0911.2632">arXiv</A>]['22].
   Also see, "... SNIP=RIP/(R/M), where RIP=raw impact per paper,
      R = citation potential and M = median database citation potential."
   -- Jranking@[<A HREF="https://en.wikipedia.org/wiki/Journal_ranking#SNIP">wikip</A>]['22].
   [Also search for: modified bibliometrics], maybe add in JIF.

%A A. Schirmer
%A M. A. Rude
%A X. Li
%A E. Popova
%A S. B. del Cardayr
%T Microbial biosynthesis of alkanes
%J Science
%V 329
%N 5991
%P 559-562
%M JUL
%D 2010
%K jrnl, MolBio, c2010, c201x, c20xx, microbe, bacterial, synthesis, synthesize,
   alkane, biofuel, biofuels, biodiesel, diesel, hydrocarbon, renewable,
   sustainable, fuel, fuels, alkenes, acyl, aldehyde decarbonylase,
   diiron enzyme, Ecoli, cyanobacteria
%X "... describe the discovery of an alkane biosynthesis pathway from
   cyanobacteria. ... consists of an acyl-acyl carrier protein reductase & an
   aldehyde decarbonylase, which together convert intermediates of fatty acid
   metabolism to alkanes & alkenes. ... fungible hydrocarbon fuels." [27 refs].
   "... Ten of these strains produced alkanes ... PCC7002, did not produce
   alkanes. ... The 10 genomes of the a.producing cy. were intersected, & the
   PCC7002 genome was subtracted ... Seventeen genes common to the 10 producing
   strains remained ..."  then inserted into Ecoli ... .
   -- [<A HREF="http://dx.doi.org/10.1126/science.1187936">doi:10.1126/science.1187936</A>]['10].

%A N. Eagle
%A M. Macy
%A R. Claxton
%T Network diversity and economic development
%J Science
%V 328
%N 5981
%P 1029-1031
%M MAY
%D 2010
%K c2010, c201x, c20xx, zz0810, social, network, networks, economic,
   communication, telephone, development, uk, stats, policy, socioeconomic,
   census, region, regional, diversity
%X "Social networks form the backbone of social & economic life. Until recently,
   however, data have not been available to study the social impact of a
   national n/w struct.. ... combined the most complete record of a national
   commn n/w with national census data on the socioeconomic well-being of
   communities. These data make possible a population-level investigation of
   the relation between the struct. of social n/ws & access to socioeconomic
   opportunity. We find that the diversity of individuals' relationships is
   strongly correlated with the economic development of communities."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1186605">doi:10.1126/science.1186605</A>][1'0].

%A E. Simpson
%T Edward Simpson: Bayes at Bletchley Park
%J Significance
%V 7
%N 2
%P 76-80
%M JUN
%D 2010
%K jrnl, c2001, c201x, c20xx, zz0816, Bletchley Park, WWII, WW2, German, Enigma,
   Tunny, Lorenz, Japan, JN 25, JN25, JN11, code breaking, cypher, cipher,
   cryptanalysis, Banburismus, Banburisms, ban, Bayesian statistics, stats,
   history, computing, biog, autobiography, Edward Simpson, paradox
%X "Edward Simpson CB ceased being an active statistician in 1947, when he
   joined the Civil Service. But statistics owes him much. He is the Simpson of
   Simpson's index of diversity & of Simpson's paradox, the bizarre apparent
   contradiction which he published in 1951 & which has puzzled students of
   statistics ever since. Perhaps more importantly, for the world as well as for
   statistics, from 1942 to 1945 he was a code breaker at Bletchley Park, where
   Alan Turing & others broke enemy ciphers & the world's first modern computer
   was developed. Here Edward Simpson tells the hitherto unpublished story of
   the part that Bayesian statistics played in breaking two of the enemy
   ciphers."  [via T.S.]
   -- [<A HREF="http://dx.doi.org/10.1111/j.1740-9713.2010.00424.x">doi:10.1111/j.1740-9713.2010.00424.x</A>]['16].
   [Also search for: Bletchley Park].

%A S. Karlin
%T Red-Hot Robots. Roxxxy and Rocky, the world's first sex robots, are
   ready to leave the lab
%I IEEE Spectrum
%M JUN
%D 2010
%K news, views, c2010, c201x, c20xx, zz0816, technology, Hines, sex robot, doll,
   Roxxy, Roxxxy, sexbot, controversial, campaignagainstsexrobots
%X "It's been a whirlwind 5 months for Douglas Hines, the self-professe
   computer geek who - after wading in obscurity for two decades in the
   computer-systems trenches - created a media frenzy with Roxxxy, the world's
   first sex robot. ..."     [?real or spoof?]
   -- [<A HREF="http://spectrum.ieee.org/robotics/humanoids/redhot-robots">www</A>]['16].
   (Also see the bbc[<A HREF="http://www.bbc.com/news/technology-34118482">5/9/2015</A>]['16].)
   [Also search for: sex robot].

%A H. Ledford
%T Harvard probe kept under wraps
%J Nature
%V 466
%P 908-909
%M AUG
%D 2010
%K news, c2010, c201x, c20xx, Harvard, University, academic, scandal, fraud,
   scientific, misconduct, Marc Hauser, publication, papers, paper,
   investigation, probe, psychology, evolutionary psychologist, fabrication
%X [9 refs].
   -- [<A HREF="http://dx.doi.org/10.1038/466908a">doi:10.1038/466908a</A>]['10].
   (Also see Sci.[<A HREF="http://dx.doi.org/10.1126/science.329.5994.890-b">doi:10.1126/science.329.5994.890-b</A>]['10],
    and Nat. [<A HREF="http://dx.doi.org/10.1038/4661023a">doi:10.1038/4661023a</A>].)
   [Also search for: academic misconduct].

%A G. Dudek
%A M. Jenkin
%T Computational Principles of Mobile Robotics
%I CUP
%P 408
%D 2010
%K book, text, CUP, c2010, c201x, c20xx, zz0810, mobile robot, robotics, robots,
   autonomous, SLAM, localization, mapping, multi, computing
%X 2nd ed 2010; pb us$47; uk us isbn:0521692121; uk us isbn13:978-0521692120.
   "... new edition includes advances in robotics and intelligent machines over
   the last ten years, including significant coverage of SLAM (simultaneous
   localization and mapping) and multi-robot systems. ..."
   1st ed 2000; pb; uk us isbn:0521568765; uk us isbn13:978-0521568760.

%A A. Dorin
%A K. B. Korb
%T Network measures of ecosystem complexity
%J Proc. 12th Int. Conf. on the Synthesis and Simulation of Living Systems
%P 323-328
%M AUG
%D 2010
%K conf, c2010, c201x, c20xx, Monash, aland, Alife, Alife12, network, measure
%X pdf@[<A HREF="http://mitpress.mit.edu/books/chapters/0262290758chap60.pdf">mit</A>]['10],
   procs@[<A HREF="http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=12433&mode=toc">mit</A>]['10].

%A J. McCormack
%T Enhancing creativity with niche construction
%J Proc. 12th Int. Conf. on the Synthesis and Simulation of Living Systems
%P 525-532
%M AUG
%D 2010
%K conf, c2010, c201x, c20xx, zz0910, jon, jonmc, Monash, Alife, Alife12,
   niche, creativity, novelty
%X pdf@[<A HREF="http://mitpress.mit.edu/books/chapters/0262290758chap99.pdf">mit</A>]['10].

%A M. Hvistendahl
%T Of population projections and projectiles
%J Science
%V 329
%N 5998
%P 1460
%M SEP
%D 2010
%K news, views, c2010, c201x, c20xx, zz0910, China, one child policy,
   population, growth, projection, prediction, Song Jian, Geert Jan Olsder
%X "China's one-child policy was based on the projections of a 1970s missile
   scientist & a series of equns developed by a Dutch mathematician to
   control population on a fictional island. ... Song Jian, a Soviet-trained
   military scientist ... he met Geert Jan Olsder, a specialist in differential
   game theory. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.329.5998.1460">doi:10.1126/science.329.5998.1460</A>]['10].

%A D. Siegel
%A P. Baveye
%T Battling the paper glut
%J Science
%P 1466
%M SEP
%D 2010
%K views, c2010, c201x, c20xx, zz0910, publish, publication, perish, adacdemic,
   papers, glut, jrnls, flood, Hindex, Gindex, KPI, least publishable unit, LPU,
   KPIs, topN, top3, scientific research, metric, measure, quality, impact,
   productivity, implausibly prolific
%X "... As soon as the 'publish or perish' concept (the imperative to publish
   work constantly to further or sustain an academic career) surfaced in the
   United States in the early 1950s, academics criticized it openly as a recipe
   for disaster. Nevertheless, in the early to mid-1980s, administrators in
   universities systematically began to use the # of articles published per year
   by individual faculty members as a measure of their productivity. ...
   "least publishable units" ... Multi-authored manuscripts increased regardless
   of true contribution to the work. ... Researchers have reacted to this
   publication glut by developing bibliometric indices, such as the h- &
   g-indexes, ... As the medical community proposed 25 years ago, researchers
   should never be allowed to include more than three publications per year in
   activity reports; in research proposals, principal investigators should cite
   no more than 10 papers. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.329.5998.1466-a">doi:10.1126/science.329.5998.1466-a</A>]['10].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.331.6013.29-b">doi:10.1126/science.331.6013.29-b</A>]['11], claws out.)
   [Also search for: implausibly prolific].

%A E. Lupton
%T Thinking with Type, 2nd revised and expanded edition: A Critical Guide for
   Designers, Writers, Editors, & Students
%I PrincetonArchitecturalPress
%P 224
%M OCT
%D 2010
%K book, text, c2010, c201x, c20xx, zz0320, typeface, typefaces, style sheets,
   font, fonts
%X 2nd ed 2010; pb us$13; uk us isbn:1568989695; uk us isbn13:978-1568989693.

%A M. Neeley
%A et al
%T Generation of three-qubit entangled states using superconducting phase qubits
%J Nature
%V 467
%P 570-573
%M SEP
%D 2010
%K jrnl, c2010, c201x, c20xx, physics, quantum computing, computer, circuit,
   entanglement, qubit, qubits, qbit, qbit, three
%X "... Unlike the two-qubit case, where all maximally entangled two-qubit
   states are equivalent up to local changes of basis, three qubits can be
   entangled in two fundamentally different ways. These are typified by the
   states |GHZ> = (|000>+|111>)/sqrt(2) & |W> = (|001>+|010>+|100>)/sqrt(3).
   Here we demo. the operation of three coupled superconducting phase qubits &
   use them to create & measure |GHZ> & |W> states. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09418">doi:10.1038/nature09418</A>]['10].
   Also comments in news:
   -- [<A HREF="http://dx.doi.org/10.1038/467513a ">doi:10.1038/467513a</A>]['10].
   [Also search for: quantum computing].

%A L. DiCarlo
%A M. D. Reed
%A L. Sun
%A B. R. Johnson
%A J. M. Chow
%A J. M. Gambetta
%A L. Frunzio
%A S. M. Girvin
%A M. H. Devoret
%A R. J. Schoelkopf
%T Preparation and measurement of three-qubit entanglement in a superconducting
   circuit
%J Nature
%V 467
%P 574-578
%M SEP
%D 2010
%K jrnl, c2010, c201x, c20xx, physics, quantum computing, computer,
   entanglement, qubit, qubits, qbit, qbit
   "... Although entanglement in superconducting circuits has been limited so
   far to two qubits, the extension of entanglement to three, eight and ten
   qubits has been achieved among spins, ions and photons, resp. ...
   demonstrate deterministic production of three-qubit Greenberger-Horne-
   -Zeilinger (GHZ) states with fidelity of 88 per cent, measured with
   quantum state tomography. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09416">doi:10.1038/nature09416</A>]['10].
   Also comments in news:
   -- [<A HREF="http://dx.doi.org/10.1038/467513a ">doi:10.1038/467513a</A>]['10].
   [Also search for: quantum computing].

%A S. M. Shearer
%T Beautiful: The Life of Hedy Lamarr
%I StMartinsPress
%P 480
%M SEP
%D 2010
%K book, biog, biography, c2010, c201x, c20xx, Hedy Kiesler, Lamarr, actress,
   Hollywood, MGM, WW2, WWII, inventor, spread spectrum, frequency hopping,
   CDMA, communications
%X 1st ed 2010; hb us$23; uk us isbn:0312550987; uk us isbn13:978-0312550981.
   "As a teenage actress in 1920s Austria, performing on the stage & in film in
   light comedies & musicals, Hedy Kiesler, with her exotic beauty, was heralded
   across Europe by her mentor, Max Reinhardt. However, it was her nude scene, &
   surprising dramatic ability, in Ecstasy that made her a star. Ecstasy's
   notoriety followed her for the rest of her life. ... "
      Also see [<A HREF="http://en.wikipedia.org/wiki/Hedy_Lamarr">wikip</A>],
   "... Lamarr also co-invented - with composer George Antheil - an early
   technique for spread spectrum communications & freq.hopping, necessary to
   wireless communication from the pre-computer age to the present day. ..."
   (Hedwig Eva Maria Kiesler, b.1913, d.2000.)

%A A. Guillot
%A J.-A. Meyer
%T How to Catch a Robot Rat: When Biology Inspires Innovation
%I MITpress
%P 232
%D 2010
%K book, text, MITpress, c2010, c201x, c20xx, zz1010, robot, robotics, AI
%X 1st ed 2010; us$23; uk us isbn:0262014521; uk us isbn13:978-0262014526.
   "... describe how natural structures, materials & behaviours are being
   adapted for nanotechnology and electronics. From an aerial drone that flies
   like an albatross to a robot salamander, they examine machines with animal
   traits and look ahead to hybrid systems, such as neuroprostheses that
   translate the thoughts of people with quadriplegia into mechanical motion."

%A C. Thurau
%A C. Bauckhage
%T Analyzing the evolution of social groups in World of Warcraft
%J Conference on Computational Intelligence and Games
%I IEEE
%P 170-177
%M AUG
%D 2010
%K conf, c2010, c201x, c20xx, zz1010, social, groups, data analysis, mining,
   visualisation visualization, computer games, MMORPG, World of Warcraft, WoW,
   Convex-Hull Non Negative Matrix Factorization, CH-NMF, NMF
%X "... investigates the evol. of social structures in the game [WoW]. We
   analyze 192 million recordings of 18 m. characters belonging to 1.4 m. teams,
   spanning a period of 4 years. Using a recent matrix factorization method, we
   extract lower dimensional data embeddings. The embeddings provide intuitively
   interpretable categorizations & we find a tendency towards guilds comprised
   of casual gamers. To our knowledge, this is the first study considering such
   a vast amount of data for analyzing groups in MMORPGs."
      "... Given a non-neg. input matrix V, NMF aims [for] two non-neg. matrix
      factors W and H s.t.  V ~ W H.  Convex NMF ... additionally restrict the
      cols. of W to be convex combinations of the data pts gathered in V, [so]
      W represents meaningful 'cluster centroids'. ..." [8 refs].
   -- pdf@[<A HREF="http://game.itu.dk/cig2010/proceedings/papers/cig10_022_079.pdf">itu.dk</A>]['10].

%A B. Headey
%A R. Muffels
%A G. G. Wagner
%T Long-running German panel survey shows that personal and economic choices,
   not just genes, matter for happiness
%J PNAS
%V ?
%N ?
%P ?-?
%M ?
%D 2010
%K jrnl, PNAS, c2010, c201x, c20xx, happiness, happy, survey, study, well being,
   wellbeing, dataset, German socio-economic panel, SOEP, longitudinal survey,
   marriage, money, set-point theory, choice approach
%X "... A direct test of the most widely accepted psychological theory,
   set-point theory, shows it to be flawed. Results are then given, using the
   economists' newer 'choice approach' - an approach also favored by +ve
   psychologists - which yields substantial payoffs in explaining long-term
   changes in happiness. Data come from the German Socio-Economic Panel
   (1984-2008), a unique 25-y prospective longitudinal survey. This dataset
   enables direct tests of theories explaining long-term happiness."
   "... partner personality traits, esp. neuroticism, had a substantial effect
   on life satisfaction. ... women whose partners give high priority to family
   goals are sig.happier than women whose partners give family matters lower
   priority ... being underworked is much worse than being over-worked ...
   Being involuntarily unemployed is worst ..."  Online Oct 2010; auth1@melbu.
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1008612107">doi:10.1073/pnas.1008612107</A>]['10].
   [Also search for: happiness well being].

%A Z. Merali
%T Computational science: ... Error ... why scientific programming
   does not compute
%J Nature
%V 467
%P 775-777
%M OCT
%D 2010
%K news, views, c2010, c201x, c20xx, SWE, software engineering, source code,
   scientific computing, documentation, quality assurance
%X "... A quarter of a century ago, most of the computing work done by
   scientists was relatively straightforward. But as computers & programming
   tools have grown more complex, scientists have hit a "steep learning curve"
   ... As a general rule, researchers do not test or document their programs
   rigorously, & they rarely release their codes, making it almost impossible
   to reproduce & verify published results generated by scientific s/w,
   say computer scientists. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/467775a">doi:10.1038/467775a</A>]['10].

%A A. A. Lacis
%A G. A. Schmidt
%A D. Rind
%A R. A. Ruedy
%T Atmospheric CO2: Principal control knob governing earth's temperature
%J Science
%V 330
%N 6002
%P 356-359
%M OCT
%D 2010
%K jrnl, c2010, c201x, c20xx, climate, change, cause, global warming, CO2,
   greenhouse, gas, gases, atmosphere, temperature, stable, stability,
   earth, ice
%X "Ample physical evidence shows that carbon dioxide (CO2) is the single most
   important climate-relevant greenhouse gas in Earth's atmosphere. This is
   because CO2, like ozone, N2O, CH4, & chlorofluorocarbons, does not
   condense & precipitate from the atmosphere at current climate temperatures,
   whereas water vapor can & does. Noncondensing greenhouse gases, which
   account for 25% of the total terrestrial greenhouse effect, thus serve to
   provide the stable temperature structure that sustains the current levels of
   atmospheric water vapor & clouds via feedback processes that account for
   the remaining 75% of the greenhouse effect. Without the radiative forcing
   supplied by CO2 & the other noncondensing greenhouse gases, the terrestrial
   greenhouse would collapse, plunging the global climate into an icebound
   Earth state."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1190653">doi:10.1126/science.1190653</A>]['10],
   at [<A HREF="http://pubs.giss.nasa.gov/abs/la09300d.html">nasa</A>]['13].
   [Also search for: cause global warming].

%A G. Benford
%A and the Editors of Popular Mechanics
%T The Wonderful Future That Never Was: Flying Cars, Mail Delivery by
   Parachute, and Other Predictions from the Past
%I Hearst
%P 208
%D 2010
%K book, c2010, c201x, c20xx, future, prediction, predictions, futurology,
   futurist, science, flying car, cars, technobabble, technobable,
   leisure society
%X "Between 1903 and 1969, scientists and other experts made hundreds of
   predictions in Popular Mechanics magazine about what the future would hold.
   ... Skyscrapers so tall they'll have their own climate  . Underground
   pneumatic tubes to replace garbage trucks  . Rooftop lakes that serve
   as air conditioning systems  . Clothes made from asbestos & aluminum
   . Mail sorted by robots & delivered by parachutes."
   1st ed 2010; hb us$16; uk us isbn:1588168220; uk us isbn13:978-1588168221.
   [Also search for: zzPrediction].

%A L. Vinicius
%T Modular Evolution.  How Natural Selection Produces Biological Complexity
%I CUP
%P 248
%D 2010
%K book, text, CUP, c2010, c201x, c20xx, zz1110, biol, biology, information,
   organization, evolution, complexity
%X 1st ed 2010; hb us$70; uk us isbn:0521429641; uk us isbn13:978-0521429641.
   "... new explanation for the tendency of life to become more complex through
   evolution, ... introduction to the key debates in evol.theory, inc. the role
   of genes & sex in evoln, the adaptive reasons for senescence & death & the
   origin of neural info.. ... argues that biol.complexity increased through the
   process of 'modularity transfer': modular phenotypes (proteins, somatic
   cells, learned behaviours) evolved into new modular info.carriers (regulatory
   proteins, neural cells, words), giving rise to new info.systems & higher
   levels of biol.organisation. ..."

%A M. Blencowe
%T Quantum computing: Quantum RAM
%J Nature
%V 468
%P 44-45
%M NOV
%D 2010
%K news, views, c2010, c201x, c20xx, quantum computing, computer, RAM, hybrid
%X "Hybrid quantum systems have been suggested ... research shows that they
   offer a robust solution to developing a form of random access memory for
   such a machine. ... the four teams describe work towards realizing a hybrid
   quantum-computer architecture that combines qubits of both types described
   above: superconducting qubits and spin qubits. ... step towards realizing a
   quantum RAM."
   [Points to 4 res. papers.]

%A S. Winchester
%T Atlantic: Great Sea Battles, Heroic Discoveries, Titanic Storms, and
   a Vast Ocean of a Million Stories
%I Harper
%P 512
%M OCT
%D 2010
%K book, c2010, c201x, c20xx, Atlantic ocean, exploration, history, historical,
   Columbus, Viking, Vikings, America, Americas, geography
%X "Blending history & anecdote, geography & reminiscence, science & exposition,
   the NYT bestselling auth. of Krakatoa tells the breathtaking saga of the
   magnificent Atlantic O., ..."
   1st ed 2010; hb us$15; uk us isbn:0061702587; uk us isbn13:978-0061702587.

%A D. Rustagi
%A S. Engel
%A M. Kosfeld
%T Conditional cooperation and costly monitoring explain success in forest
   commons management
%J Science
%V 330
%N 6006
%P 961-965
%M NOV
%D 2010
%K jrnl, c2010, c201x, c20xx, zz1110, human behaviour, cooperation, common land,
   commons (tragedy), resource management, conditional, Ethiopia, Oromo,
   forest, woodlands, grazing, clan, clans
%X "Recent evidence suggests that prosocial behaviors like conditional
   coop. & costly norm enforcement can stabilize large-scale coop. for commons
   management. However, field evidence on the extent to which variation in these
   behaviors among actual commons users accounts for natural commons outcomes is
   altogether missing. Here, we combine experimental measures of cond.coop. &
   survey measures on costly monitoring among 49 forest user groups in Ethiopia
   with measures of natural forest commons outcomes to show that (i) groups vary
   in cond.cooperator share, (ii) groups with larger cond.cooperator share are
   more successful in forest commons management, & (iii) costly monitoring is a
   key instrument with which cond.cooperators enforce cooperation. Our findings
   are consistent with models of gene-culture coevolution on human cooperation
   & provide external validity to laboratory experiments on social dilemmas."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1193649">doi:10.1126/science.1193649</A>]['10].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.1198349">doi:10.1126/science.1198349</A>]['10].)
   [Also search for: tragedy commons].

%A S. E. Page
%T Diversity and Complexity
%I PrincetonUP
%S Primers in Complex Systems
%P 296
%D 2010
%K book, text, c2010, c201x, c20xx, complex systems, zz0211
%X 1st ed 2010; pb us$18; us isbn:0691137676; us isbn13:978-0691137674.
   "... explains how diversity underpins system level robustness, allowing for
   multiple responses to external shocks & internal adaptations; how it
   provides the seeds for large events by creating outliers that fuel tipping
   points; & how it drives novelty & innovation. Page looks at the different
   kinds of diversity - variations within & across types, & distinct
   community compositions & interaction structures - & covers the evolution
   of diversity within complex systems & the factors that determine the
   amount of maintained diversity within a system. ..."

%A B. Bryson
%T Seeing Further: The Story of Science and the Royal Society
%I HarperPress
%P 496
%D 2010
%K book, c2010, c201x, c20xx, Bill Bryson, science, scientific, royal society,
   history, Boyle, Wren
%X "... The origins of the Royal Soc. lie in an "invisible college" of
   natural philosophers who began meeting in the mid-1640s to discuss the ideas
   of Francis Bacon. Its official foundation date is 28 November 1660, when
   12 of them met at Gresham College after a lecture by Christopher Wren, the
   Gresham Professor of Astronomy, and decided to found a College for the
   Promoting of Physico-Mathematicall Experimentall Learning.  This group
   included Wren himself, Robert Boyle, John Wilkins, Sir Robert Moray, and
   William, Viscount Brouncker.  ..."
   1st ed 2010; hb us$25; uk us isbn:0007302568; uk us isbn13:978-0007302567.
   (William Morrow; isbn:0061999768; isbn13:978-0061999765.)

%A E. Winsberg
%T Science in the Age of Computer Simulation
%I U. ChicagoPress
%P 168
%D 2010
%K book, text, c2010, c201x, c20xx, computer simulation, simulate, physics,
   philosophy of science, scientific, stats
%X "... Computer simulation was first pioneered as a scientific tool in
   meteorology and nuclear physics in the period following WWII, but it has
   grown rapidly to become indispensible in a wide variety of sci.disciplines,
   inc. astrophysics, high-energy physics, climate science, engineering,
   ecology, and economics. Digital computer simulation helps study phenomena of
   great complexity, but how much do we know about the limits and possibilities
   of this new scientific practice? How do simulations compare to traditional
   experiments? And are they reliable? ..."
   1st ed 2010; hb us$66; us isbn:0226902021; us isbn13:978-0226902029.

%T Information and the Nature of Reality: From Physics to Metaphysics
%E P. Davies
%A N. H. Gregersen
%I CUP
%P 398
%M DEC
%D 2010
%K book, text, c2010, c201x, c20xx, zz1210, information, reality, physics,
   quantum theory, universe, nature, II, AIC, entropy
%X "Many scientists regard mass & energy as the primary currency of nature.
   In recent years, however, the concept of information has gained importance.
   Why? ... eminent scientists, philosophers & theologians chart various
   aspects of info., from quantum info. to biological & digital info., [to]
   understand how nature works. Beginning with a historical treatment of the
   topic, the book also examines physical & biol. approaches to info., & its
   philosophical, theological & ethical implications."
   1st ed 2010; hb us$20; uk us isbn:0521762251; uk us isbn13:978-0521762250.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)
   [Also search for: Qbism physics].

%T Darwin
%E W. Brown
%E A. C. Fabian
%I CUP
%P 224
%D 2010
%K book, text, CUP, Charles Darwin, c2010, c201x, c20xx, intelligent,
   evolution, biol, biology, design
%X "Leading authorities from the history of science, economics, philosophy and
   English literature as well as the biological sciences field provide accounts
   of the influence of the thoughts, ideas, research and writing of Darwin on
   the arts, society and science. Written for the non-specialist reader
   interested in any of these disciplines."
   1st ed 2010; pb us$22, stg13;
   uk us isbn:0521131952; uk us isbn13:978-0521131957.

%A N. Graves
%A A. G. Barnett
%A P. Clarke
%T Cutting random funding decisions
%J Nature
%V 469
%N 7330
%P 299
%M JAN
%D 2011
%K c2011, c201x, c20xx, zz0914, NHMRC, ARC, grant, grants, funding, peer review,
   reviewers, science, scientific research, University, quality, ERA, Australia,
   academia, management, randomness, inconsistency, variability
%X "We find that for one-third of grant applications in 2009 to Australia's
   National Health and Medical Research Council, success is random owing to
   variability among peer reviewers. Increased competition for restricted
   res. budgets means we must rectify this element of chance in selection. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/469299c">doi:10.1038/469299c</A>]['14].
   [Also search for: peer review].

%A M. New
%A D. Liverman
%A H. Schroder
%A K. Anderson
%T Four degrees and beyond: The potential for a global temperature increase of
   four degrees and its implications
%J Phil. Trans. R. Soc. A
%V 369
%P 6-19
%M JAN
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0111, climate change, global, warming,
   temperature, rise, increase, CO2, gas, greenhouse, gases, Copenhagen Accord,
   IPCC, Kyoto
%X "... need for accelerated and focused research that improves understanding
   of how the climate system might behave under a 4C warming, what the impacts
   of such changes might be and how best to adapt to what would be
   unprecedented changes in the world we live in."
   -- [<A HREF="http://dx.doi.org/10.1098/rsta.2010.0303">doi:10.1098/rsta.2010.0303</A>]['10],
   special-issue@[<A HREF="http://rsta.royalsocietypublishing.org/content/369/1934">R.Soc.</A>]['10].

%A A.-W. Harzing
%T The Publish or Perish Book: Your Guide to Effective and
   Responsible Citation Analysis
%I TarmaSoftWare
%P 250
%D 2010
%K book, text, c2010, c201x, c20xx, publish, perish, publication, publications,
   bibliometrics, bibliometrics, measure, cite, citation, citations, papers,
   impact factor, IF, JIF, JIFs, Hindex, ISI, scientific research, metrics
%X 1st ed 2010; pb us$30; uk us isbn:0980848512; uk us isbn13:978-0980848519.
   "Citations are not only a reflection of the impact that a particular piece
   of academic work has generated. Citations can also be used to tell stories
   about academics, journals and fields of research. This book is meant to help
   you create effective stories, but also to teach you how to be a responsible
   user of research metrics."
   [Also search for: Hindex]  and  [also search for: publish perish].

%A A. R. Poteete
%A M. A. Janssen
%A E. Ostrom
%T Working Together: Collective Action, the Commons, and Multiple Methods in
   Practice
%I PrincetonUP
%P 370
%D 2010
%K book, text, c2010, c201x, c20xx, tragedy of the commons, human behaviour,
   economics, natural resource, resources, regulation, collective action,
   cooperation, control, exploitation, system
%X 1st ed 2010; pb us$31; uk us isbn:0691146047; uk us isbn13:978-0691146041;
                hb us$85; uk us isbn:0691146039; uk us isbn13:978-0691146034.
   "... provide numerous examples of collaborative, multimethod research related
   to collective action and the commons. They examine the pros and cons of case
   studies, meta-analyses, large-N field research, experiments and modeling, and
   empirically grounded agent-based models, and they consider how these methods
   contribute to research on collective action for the management of natural
   resources. Using their findings, the authors outline a revised theory of
   collective action that includes three elements: individual decision making,
   microsituational conditions, and features of the broader social-ecological
   context. ..."
   [Also search for: tragedy commons].
   Ostrom won the 2009 Nobel prize in Economics
   -- [<A HREF="http://elinorostrom.indiana.edu/">indi.</A>]['11].

%A B. Bahrami
%A K. Olsen
%A P. E. Latham
%A A. Roepstorff
%A G. Rees
%A C. D. Frith
%T Optimally interacting minds
%V 329
%N 5995
%P 1081-1085
%M AUG
%D 2010
%K jrnl, c2010, c201x, c20xx, mind, minds, cooperating, cooperating, decision,
   making, group, joint, when are two heads better than one, confidence,
   confident, crowd, sourcing
%X "... addressed this q. in the context of a collective low-level perceptual
   decision-making task. For two observers of nearly equal visual sensitivity,
   two heads were definitely better than one, provided they were given the
   opportunity to communicate freely, even in the absence of any feedback about
   decision outcomes. But for observers with very different v.sensitivities, two
   heads were actually worse than the better one. These seemingly discrepant
   patterns of group behavior can be explained by a model in which two heads are
   Bayes optimal under the assumption that individuals accurately communicate
   their level of confidence on every trial."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1185718">doi:10.1126/science.1185718</A>]['12].
   (Also see Koriat, [<A HREF="http://dx.doi.org/10.1126/science.1216549">doi:10.1126/science.1216549</A>][4/2012],
   and [<A HREF="http://dx.doi.org/10.1126/science.1221403">views</A>].)

%A B. E. Harcourt
%T Risk as a proxy for race
%J Criminology and Public Policy (Forthcoming)
%M SEP
%D 2010
%O U. Chicago, Public Law working paper 323
%K c2010, c201x, c20xx, zz0619, law, crime, prevention, AI, bias, biases,
   USA, race, racial, racism, racist, algorithm, stereotype,
   face, facial recognition, risk, risks, prediction
%X "Today, an increasing chorus argues that risk-assessment instruments are a
   politically feasible way to resolve our problem of mass incarceration and
   reduce prison populations. In this essay, I argue against this progressive
   argument for prediction: using risk-assessment tools to decrease prison
   populations would unquestionably aggravate the already intolerable racial
   imbalance in our prison populations and will not address the real source of
   mass incarceration, namely the admissions process. ..."
   -- [<A HREF="https://papers.ssrn.com/sol3/papers.cfm?abstract_id=1677654">www</A>]['19].
   Also see
   propublica@[<A HREF="https://www.propublica.org/article/machine-bias-risk-assessments-in-criminal-sentencing">www</A>]['19].

%A J. D. Neelin
%T Climate Change and Climate Modeling
%I CUP
%P 304
%D 2010
%K book, text, CUP, c2010, c201x, c20xx, climate change, global warming, CO2,
   modeling, modelling
%X pb us$53; uk us isbn:0521602432; uk us isbn13:978-0521602433.
   "... key is understanding what aspects of climate science are well understood
   and where quantitative uncertainties arise. This textbook will inform the
   future users of climate models and the decision-makers of tomorrow by
   providing the depth they need, while requiring no background in atmospheric
   science and only basic calculus and physics. Developed from a course that the
   author teaches at UCLA ..."

%A R. Stannard
%T The End of Discovery: Are We Approaching the Boundaries of the Knowable?
%I OUP
%P 224
%D 2010
%K book, text, c2010, c201x, c20xx, zz0612, science, philosophy, research,
   cosmology, determinism, mind, consciousness, time
%X 1st ed 2010; hb us$15; uk us isbn:0199585245; uk us isbn13:978-0199585243.
   "... a list of sci. problems that he thinks may never be resolved. An
   infamous problem is string theory ... that minuscule vibrating 'strings' are
   the lowest possible denominators of existence passes all the math. smell
   tests, but the odds of its being experimentally proven anytime soon are about
   as minuscule as strings themselves. Or take consciousness: will we ever
   understand the interplay between free will & determinism? And is it true that
   we live in a 'block universe' in which our entire lives are already embedded
   in time - and that we just haven't reached the frames in our future? ..."

%A D. Barrett
%T Supernormal Stimuli: How Primal Urges Overran Their Evolutionary Purpose
%I WWNorton
%D 2010
%K book, text, c2010, c201x, c20xx, hyperstimulus, stimulus, urge, junk food,
   evolution, human, animal, behaviour, greed, sexuality, psychology
%X 1st ed 2010; hb us$16; uk us isbn:039306848X; uk us isbn13:978-0393068481.
   "Our instincts - for food, sex, or territorial protection - evolved for life
   on the savannahs 10,000y. ago, not in today's world of densely populated
   cities, technological innovations, & pollution. We now have access to a glut
   of larger-than-life objects, from candy to pornography to atomic weapons -
   that gratify these gut instincts with often-dangerous results. Animal
   biologists coined the term 'supernormal stimuli' ..."
   [Also search for: hyperstimulus].

%A G. Davis
%T The Republic of Learning: Higher Education Transforms Australia
%I ABCbooks, HarperCollins
%P 127
%M NOV
%D 2010
%K book, text, c2010, c201x, c20xx, zz0519, university, management,
   faculty, teaching, research, administration, Melbourne, Australia,
   BoyerLectures
%X pb; uk us isbn:0733328741; uk us isbn13:978-0733328749.
   (as of 2019, auth is the ex VC of Melbourne University.)
   (Also see the abc[<A HREF="https://www.abc.net.au/radionational/programs/boyerlectures/series/boyer-lectures-2010-the-republic-of-learning/2981312">14/11/2010</A>]['19].)
   [Also search for: university management].

%A M. Mobbs
%T Sustainable House
%I UNSWpress
%P 288
%M DEC
%D 2010
%K book, text, c2010, c201x, c20xx, sustainability, houses, housing, home,
   building, resources, water, green, energy, heating, cooling, Australia
%X 2nd ed 2010; us$30; isbn:192070552X; isbn13:978-1920705527.
   "... advice & step-by-step instructions on achieving an environmentally
   friendly home. Fully revised & updated, this new edition provides tips for
   working with councils, builders, & engineers while renovating not only
   kitchens, bathrooms, gardens, & waste systems but also water and energy
   supplies. ..."
   [Also search for: Mobbs book].

%A D. H. Freedman
%T Wrong: Why experts keep failing us a and how to know when not to trust them
%I LittleBrown
%P 304
%D 2010
%K book, c2010, c201x, c20xx, zz0213, expert, prediction, predictions,
   futurology, futurist, guru, gurus, future, confidence
%X 1st ed 2010; hb us$10; uk us isbn:0316087912; uk us isbn13:978-0316087919.
   "... Actually, those experts are a big reason we're in this mess. ... such
   expert counsel usually turns out to be wrong - often wildly so. Wrong reveals
   the dangerously distorted ways experts come up with their advice, & why the
   most heavily flawed conclusions end up getting the most attention-all the
   more so in the online era. But there's hope: Wrong spells out the means by
   which every individual & organization can do a better job of unearthing the
   crucial bits of right within a vast avalanche of misleading pronouncements."
   [Also search for: zzPrediction].

%A E. Morozov
%T The Net Delusion: How Not to Liberate the World
%I AllenLane
%P 432
%M JAN
%D 2011
%K book, text, c2011, c201x, c20xx, zz0411, www, web, internet,
   social media, politics, protest, dissent, oppression, regime, freedom,
   democracy, human rights, china, russia, open, closed, society
%X 1st ed 2010; pb us$18; uk us isbn:1846143535; uk us isbn13:978-1846143533.
   "Does free information mean free people? At the start of the twenty-first
   century we were promised that the internet would liberate the world. We could
   come together as never before, & from Iran's 'twitter revolution' to Facebook
   'activism', technological innovation would spread democracy to oppressed
   peoples everywhere. We couldn't have been more wrong. [EM] destroys this
   myth, arguing that 'internet freedom' is an illusion, & that technology has
   failed to help protect people's rights. Not only that - in many cases the
   internet is actually helping authoritarian regimes. From China to Russia to
   Iran, oppressive governments are using cyberspace to stifle dissent:
   planting clandestine propaganda ..."

%A C. Edmondson
%T Fast Car Physics
%I JohnHopkinsUP
%P 248
%M JAN
%D 2011
%K book, text, c2011, c201x, c20xx, physics, fast, racing, car, cars,
   motor sports, motorsport
%X 1st ed 2011; pb us$30; us isbn:0801898234; us isbn13:978-0801898235.

%E J. C. Lagarias
%T The Ultimate Challenge: The 3x+1 Problem
%I Amer. Math. Soc.
%P 348
%M JAN
%D 2011
%K book, text, c2011, c201x, c20xx, zz0111, 3x+1 problem, puzzle, maths,
   3Xplus1, problem, Collatz, Syracuse, Kakutani, Hasse, Ulam
%X 1st ed 2011; hb stg.43; uk us isbn:0821849409; uk us isbn13:978-0821849408.
   [Also search for: Collatz problem].

%A S. Turkle
%T Alone Together: Why We Expect More from Technology and Less from Each Other
%I BasicBooks
%P 384
%D 2011
%K book, c2011, c201x, c20xx, zz0211, technology, society, social, web, net,
   internet, freedom, delusion
%X 1st ed 2011; hb us$17; uk us isbn:0465010210; uk us isbn13:978-0465010219.
   "... In the third & final vol. of a trilogy dissecting the interface between
   humans & technology, Turkle suggests that we seem determined to give human
   qualities to objects and content to treat each other as things. ..."
   [Also search for: technology society].

%E D. Archer
%E R. Pierrehumbert
%T The Warming Papers
%I Wiley
%P 432
%M JAN
%D 2011
%K book, text, c2011, c201x, c20xx, zz0311, climate change, global warming,
   cause, CO2, greenhouse gas, gases, science
%X 1st ed 2011; pb us$76; uk us isbn:1405196165; uk us isbn13:978-1405196161.
   "... a compendium of the classic sci.papers that constitute the foundation of
   the global warming forecast. ... ranges from Fourier and Arrhenius in the
   19th Century to Manabe and Hansen in modern times. A. + P. provide intros.
   and commentary which places the papers in their context and provide students
   with tools to develop and extend their understanding of the subject. ..."

%A D. Leigh
%A L. Harding
%T WikiLeaks: Inside Julian Assange's War on Secrecy
%I PublicAffairs
%P 352
%M FEB
%D 2011
%K book, c2011, c201x, c20xx, zz0211, Wikileaks, Wiki leaks, Julian Assange,
   Iraq war, US, USA, government, diplomatic cables, leak, security, politics,
   open, whistle blower, blowers, zzLaw, law, legal, freedom of speech
%X 1st ed 2011; pb us$10; us isbn:161039061X; us isbn13:978-1610390613;
   and Guardian books     uk isbn:0852652399; uk isbn13:978-0852652398.
   "A team of journalists with unparalleled inside access provides the first
   full, in-depth account of WikiLeaks, its founder Julian Assange, & the
   ethical, legal, & political controversies it has both uncovered & provoked."
   [Also search for: WikiLeaks].

%A D. Domscheit-Berg
%T Inside WikiLeaks: My Time with Julian Assange at the World's Most
   Dangerous Website
%I JonathanCape
%P 304
%M FEB
%D 2011
%K book, c2011, c201x, c20xx, Chaos, Wikileaks, Wiki leaks, Julian Assange,
   government cables, leak, security, politics, open, OpenLeaks
%X 1st ed 2011; pb stg6; uk us isbn:0224094017; uk us isbn13:978-0224094016;
   Meine Zeit bei der gefahrlichsten Website der Welt.
      (Note that Assange and Domscheit-Berg fell out,
      D-B resigned from WikiLeaks and started OpenLeaks.)
   [Also search for: WikiLeaks].

%A M. L. Sifry
%A A. Rasiej
%T WikiLeaks and the Age of Transparency
%I Counterpoint
%P 224
%M MAR
%D 2011
%K book, c2011, c201x, c20xx, zz0311, Wikileaks, Wiki leaks, Julian Assange,
   government cables, leak, security, politics, open
%X 1st ed 2011; pb us$11; uk us isbn:1582437793; uk us isbn13:978-1582437798.
   "... Now we are told a small, international band of renegades armed with
   nothing more than laptops presents the greatest threat to the U.S. regime
   since the close of the Cold War. WikiLeaks release of a massive trove of
   secret official documents has riled politicians from across the spectrum.
   Even noted free-speech advocate Floyd Abrams blames WikiLeaks founder Julian
   Assange for the certain defeat of federal shield-law legislation protecting
   journalists. ..."
   [Also search for: WikiLeaks].
   (Also see [<A HREF="http://www.guardian.co.uk/technology/2010/dec/10/wikileaks-cables-anonymous-online-war">grauniad</A>]['10].)

%A J. Assange
%T Wikileaks Versus the World: My Story
%I CanongateBooks
%M APR
%D 2011
%K book, text, c2011, c201x, c20xx, zz0411, Wikileaks, Wiki leaks,
   Julian Assange, government cables, leak, security, politics, society,
   open, www, internet
%X 1st ed 2011; pb stg15; uk us isbn:0857861891; uk us isbn13:978-0857861894.
   [Also search for: WikiLeaks].
   (Also see [<A HREF="http://mirror.wikileaks.info/">wikil...info</A>][2/'11].)

%A K. Temme
%A T. J. Osborne
%A K. G. Vollbrecht
%A D. Poulin
%A F. Verstraete
%T Quantum Metropolis sampling
%J Nature
%V 471
%P 87-90
%M MAR
%D 2011
%K jrnl, c2011, c201x, c20xx, quantum computing, simulation,
   Metropolis sampling algorithm
%X "The original motivation to build a q.computer came from Feynman, who
   imagined a m/c capable of simulating generic q. mechanical systems -
   a task that is believed to be intractable for classical computers. ... Part
   of F.'s challenge was met by Lloyd, who showed how to approx. decompose
   the time evolution operator of interacting q.particles into a short
   seq. of elementary gates, suitable for operation on a q.computer.  ...
   Here we demo. how to implement a q.version of the Metropolis alg..
   This alg. permits sampling directly from the eigenstates of the Hamiltonian,
   & thus evades the sign problem present in classical simulations. A small-
   -scale implementation of this alg. should be achievable with today's tech.."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09770">doi:10.1038/nature09770</A>]['11].

%A D. Coyle
%T The Economics of Enough: How to Run the Economy as If the Future Matters
%I PrincetonUP
%P 336
%M MAR
%D 2011
%K book, text, c2011, c201x, c20xx, zz0311, economics, sustainable, resources,
   sustainability, growth, saving, savings, society, wealth, greed
%X hb us$15; uk us isbn:0691145180; us isbn13:978-0691145181.
   "... The top priority must be ensuring that we get a true picture of
   long-term economic prospects, with the development of official statistics on
   national wealth in its broadest sense, including natural and human resources.
   Saving and investment will need to be encouraged over current consumption.
   Above all, governments will need to engage citizens in a process of debate
   about the difficult choices that lie ahead and rebuild a shared commitment
   to the future of our societies. ..."

%A K. R. Hill
%A et al ...
%A B. Wood
%T Co-residence patterns in hunter-gatherer societies show unique human social
   structure
%J Science
%V 331
%N 6022
%P 1286-1289
%M MAR
%D 2011
%K jrnl, c2011, c201x, c20xx, coresidence, society, social, human, behaviour,
   cooperation
%X "... analyzed co-residence patterns among 32 present-day foraging societies
   (total n=5067 individuals, mean experienced band size=28.2 adults). We found
   that hunter-gatherers display a unique social structure where (i) either sex
   may disperse or remain in their natal group, (ii) adult brothers & sisters
   often co-reside, & (iii) most individuals in residential groups are
   genetically unrelated. These patterns produce large interaction networks of
   unrelated adults & suggest that inclusive fitness cannot explain extensive
   cooperation in hunter-gatherer bands. However, large social networks may help
   to explain why humans evolved capacities for social learning that resulted
   in cumulative culture."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1199071">doi:10.1126/science.1199071</A>]['11].

%A P. Atkins
%T On Being: A Scientist's Exploration of the Great Questions of Existence
%I OUP
%P 152
%M MAR
%D 2011
%K book, text, OUP,  c2011, c201x, c20xx, science, why are we here, existence,
   meaning of life, philosophy, philosophical, cosmos, universe, religion,
   debate
%X 1st ed 2011; hb us$14; uk us isbn:0199603367; uk us isbn13:978-0199603367.
   '... "The scientific method can shed light on every & any concept, even those
   that have troubled humans since the earliest stirrings of consciousness," [A]
   writes. He takes a materialist approach to the great questions of being that
   have inspired myth & religion.. ...  "the substrate of existence is nothing
   at all." The total electrical charge of the universe, among other things,
   must be nothing -zero- ..."

%T Chernobyl's legacy
%A M. Peplow
%J Nature
%V 471
%P 562-656
%M MAR
%D 2011
%K news, views, c2011, c201x, c20xx, zz0411, nuclear power, energy, fission,
   melt down, meltdown, reactor, Chernobyl, Pripyat, Ukraine,
   fire, explosion, graphite, iodine131, health, risk, risks
%X "... When Chernobyl's reactor number 4 exploded in the early hours of
   26 April 1986, the ensuing blaze spewed 6.7 tonnes of material from the core
   high into the atmosphere ... Today, a staff of about 3,500 enters the zone
   each day to monitor, clean & guard the site, where remediation work will
   continue for at least another 50 years. ... Of 134 emergency workers
   diagnosed with acute radiation sickness, 28 died from their exposure within
   four months. Another 19 have died since from various causes, & many of the
   surviving workers now have cataracts & skin injuries. ... More than 5,000
   cases of thyroid cancer have so far been seen in people who were children at
   the time ... more than ten-fold increase from normal ... Fewer than 20 of
   these people have died [yet] ..."   [5 refs].
   -- [<A HREF="http://dx.doi.org/10.1038/471562a">doi:10.1038/471562a</A>]['11].
   [Also search for: Chernobyl].
   (Also see [<A HREF="http://www.bbc.co.uk/search/news/chernobyl">bbc</A>][4/'11].)

%T Knowledge, Networks and Nations: Global scientific collaboration in
   the 21st century
%I The Royal Soc.
%P 114
%M MAR
%D 2011
%K report, study, c2011, c201x, c20xx, zz0713, science, research, international,
   scientific, RandD, journals, publishing, publish, perish
%X "Science is a global enterprise. Today there are over 7 million researchers
   around the world, drawing on a combined international R & D spend of over
   us$1000 billion (a 45% increase since 2002), & reading & publishing in around
   25,000 separate scientific journals per year. ..."
   -- [<A HREF="http://royalsociety.org/uploadedFiles/Royal_Society_Content/policy/publications/2011/4294976134.pdf">RS</A>]['13].
   uk isbn13:978-0854038909.
   [Also search for: publish perish].

%A S. J Brams
%T Game Theory and the Humanities: Bridging Two Worlds
%I MITpress
%P 352
%M MAR
%D 2011
%K book, text, c2011, c201x, c20xx, games, humanities, game theory,
   applications, strategy, economics, politics, political, human, behaviour
%X '... examines such topics as Abraham's decision to offer his son for
   sacrifice ...; the outcome and payoff matrix of Pascal's wager on the
   existence of God; and the strategic games played by presidents & Supreme
   Court justices; frustration games, as illustrated by the strategic use of
   sexual abstinence in Aristophanes's Lysistrata; & how info. was slowly
   uncovered in the game played by Hamlet & Claudius. ... also derives
   propositions about "generic games" applicable to a broad class of sit'ns.
   The reader gains not just new insights into the actions of certain literary
   & historical characters but also a larger strategic perspective on the
   choices that make us human.'
   1st ed 2011; hb us$28; us isbn:0262015226; us isbn13:978-0262015226.

%A M. Kaufman
%T First Contact: Scientific Breakthroughs in the Hunt for Life Beyond Earth
%I SimonAndSchuster
%P 224
%M APR
%D 2011
%K book, c2011, c201x, c20xx, extraterrestrial, extra terrestrial, life,
   search, hunt, exoplanet, universe, space, alien, aliens
%X 1st ed 2011; hb us$16; uk us isbn:1439109001; uk us isbn13:978-1439109007.
   [Also search for: exoplanet].

%A Q. D. Atkinson
%T Phonemic diversity supports a serial founder effect model of language
   expansion from Africa
%J Science
%V 332
%N 6027
%P 346-349
%M APR
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0411, natural language, evolution, phylogeny,
   phylogenetic tree, languages, human, origin, migration, Africa,
   phoneme, linguistic diversity
%X "Human genetic & phenotypic diversity declines with distance from Africa, as
   predicted by a serial founder effect in which successive pop'n bottlenecks
   during range expansion progressively reduce diversity, underpinning support
   for an African origin of modern h.. Recent work suggests that a similar
   founder effect may operate on human culture & language. Here I show that the
   # of phonemes used in a global sample of 504 languages is also clinal & fits
   a serial founder-effect model of exp'n from an inferred origin in Africa ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1199295">doi:10.1126/science.1199295</A>]['11].
   [Also search for: natural language evolution].

%A E. Rieffel
%A W. Polak
%T Quantum Computing: A Gentle Introduction
%I MITpress
%P 372
%M APR
%D 2011
%K book, text, intro, c2011, c201x, c20xx, zz0511, quantum, computer, computing
%X 1st ed 2011; hb us$36; uk us isbn:0262015064; uk us isbn13:978-0262015066.
   "... exposition of q.computing & the underlying concepts of q.physics, with
   explanations of the relevant mathematics & numerous examples."
   [Also search for: quantum computing].

%A P. W. Conkling
%A R. Alley
%A W. Broekcer
%A G. Denton
%T The Fate of Greenland: Lessons from Abrupt Climate Change
%I MITpress
%P 224
%M MAY
%D 2011
%K book, text, c2011, c201x, c20xx, zz0511, climate change, global warming,
   CO2, greenhouse gas, gases, Greenland, glaciers, sea level rise
%X 1st ed 2011; hb us$20; uk us isbn:0262015641; uk us isbn13:978-0262015646.
   "... Greenland's ice sheet is melting; ... rapidly melting glaciers has
   become a tourist attraction. ... dramatic color photographs & investigates
   G's climate history for clues about what happens when climate change is
   abrupt rather than gradual.
      Geological evidence suggests that G. has already been affected by two
   dramatic changes in climate: the Medieval Warm Period, when warm temperatures
   in N.Europe enabled Norse exploration & settlements in G.; & the
   Little Ice Age that followed & apparently wiped out the settlements. [Its]
   climate past & present could presage our climate future. Abrupt climate
   change would be cataclysmic: the melting of G's ice shelf would cause sea
   levels to rise twenty-four feet worldwide; lower Manhattan would be
   underwater & Florida's coastline would recede to Orlando."
   [Also search for: climate change].

%A M. Nowak
%A R. Highfield
%T SuperCooperators Altruism, Evolution, and Why We Need Each Other to Succeed
%I FreePress
%P 352
%D 2011
%K book, text, c2011, c201x, c20xx, zz0511, cooperation, defect, cooperate,
   game theory, altruism, evolution, origin, human, behaviour
%X 1st ed 2011; hb us$17; uk us isbn:1439100187; uk us isbn13:978-1439100189.
   "... offers a new explanation for the origin of life & a new theory for the
   origins of language, biology's second greatest information revolution after
   the emergence of genes. SuperCooperators also brings to light his
   game-changing work on disease. ..."
   [Also search for: cooperation] and [also search for: prisoners dilemma].

%A S. Jones
%T The Darwin Archipelago: The Naturalist's Career Beyond Origin of Species
%I YaleUP
%P 248
%D APR
%D 2011
%K book, text, c2011, c201x, c20xx, Charles Darwin, biography, bibliography,
   history, publications, Earthworms, Emotions
%X 2011; hb us$17; uk us isbn:0300155409; uk us isbn13:978-0300155402.
   "... [CD] produced many other books over his long career, exploring specific
   aspects of the theory of evolution by natural selection in greater depth.
   The [author] uses these lesser-known works as springboards to examine how
   their essential ideas have generated whole fields of modern biology. ...
   'Earthworms' ... 'Expression of the Emotions' ...
   'Self-Fertilization and Forms of Flowers' ..."

%A V. J. Stenger
%T The Fallacy of Fine-Tuning: Why the Universe Is Not Designed for Us
%I PrometheusBooks
%P 345
%M APR
%D 2011
%K book, text, c2011, c201x, c20xx, zz0611, universe, cosmology, physics, laws,
   life, anthropomorphic, constants, parameters, intelligent design, God
%X  1st ed 2011; hb us$15; uk us isbn:1616144432; uk us isbn13:978-1616144432.
   "... argues that many of the claims by theists are based on their
   misunderstanding of the science. He looks at the specific parameters &
   shows that plausible reasons can be found for the values they have within the
   existing standard models of physics & cosmology. These models are
   introduced in detail so that the reader has the background needed to
   understand the role of the parameters claimed to be fine-tuned & judge the
   veracity of the arguments.
   He also discusses related issues such as whether or not the universe had a
   beginning, what q.mechanics implies about the involvement of human
   consciousness in affecting reality, & whether evidence can be found in
   nature for a divine plan. ..."

%T Communication with Extraterrestrial Intelligence
%E D. A. Vakoch
%I State Uni. of NY
%P 500
%M APR
%D 2011
%K book, text, conf, c2011, c201x, c20xx, extraterrestrial intelligence, life,
   alien, aliens, space, universe, search, communicate, SETI, CETI
%X 2011; hb us$119; us isbn:1438437935; uk us isbn13:978-1438437934.
   "In April 2010, fifty years to the month after the first experiment in the
   Search for Extraterrestrial Intelligence (SETI), scholars from a range of
   disciplines ..."
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Film/Andromeda/">A for Andromeda</A>].-)
   [Also search for: extraterrestrial life].

%A R. Jayawardhana
%T Strange New Worlds: The Search for Alien Planets and Life beyond
   Our Solar System
%I PrincetonUP
%P 288
%M FEB
%D 2011
%K book, text, c2011, c201x, c20xx, extraterrestrial life, alien,
   space, universe, exoplanet, exoplanets
%X 1st ed 2011; hb us$16; us isbn:0691142548; us isbn13:978-0691142548.
   [Also search for: exoplanet].

%A T. F. Peterson
%T Nightwork: A History of Hacks and Pranks at MIT
%I MITpress
%P 190
%D 2011
%K book, c2011, c201x, c20xx, zz0511, prank, hack, hacking, hacker, computer,
   computing, university, MIT
%X 1st ed 2011; pb us $16; us isbn:0262661373; us isbn13:978-0262661379.
   "... hacking culture has given us such treasures as police cars & cows on
   the Great Dome, a disappearing door to the President's office, & the
   commencement game of 'Al Gore Buzzword Bingo.' Hacks can be technical,
   physical, virtual, or verbal. Often the underlying motivation is to conquer
   the inaccessible & make possible the improbable. Hacks can express
   dissatisfaction with local culture or with administrative decisions, but
   mostly they are remarkably good-spirited. They are also by definition
   ephemeral. ... MIT Museum has amassed a unique collection of hack-related
   pictures, reports, & remnants. ..."

%A Y.-Y. Liu
%A J.-J. Slotine
%A A.-L. Barabasi
%T Controllability of complex networks
%J Nature
%V 473
%P 167-173
%M MAY
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0511, network, networks, graph, control, driver,
   controllability, nodes, node
%X "... we develop analytical tools to study the controllability of an arbitrary
   complex directed network, identifying the set of driver nodes with time-
   -dependent control that can guide the system's entire dynamics. ...
   Counterintuitively, we find that in both model & real systems the driver
   nodes tend to avoid the high-degree nodes."
   -- [<A HREF="http://dx.doi.org/10.1038/nature10011">doi:10.1038/nature10011</A>]['11].
   (Also see comments@[<A HREF="http://dx.doi.org/10.1126/science.332.6031.777">doi:10.1126/science.332.6031.777</A>].)

%A K. Richardson
%A W. Steffen
%A D. Liverman
%T Climate Change. Global Risks, Challenges and Decisions
%I CUP
%P 523
%D 2011
%K book, text, CUP, c2011, c201x, c20xx, zz0611, climate change,
   global warming, CO2, greenhouse gas, gases
%X 1st ed 2011; hb us$91; uk us isbn:0521198364; uk us isbn13:978-052119836.
   "... synthesis of all knowledge relevant to the climate change issue, from
   basic science to the technologies, economic instruments & political
   strategies that can be employed in response to climate change. ..."

%A E. Teglas
%A et al ...
%A L. L. Bonatti
%T Pure reasoning in 12-month-old infants as probabilistic inference
%J Science
%V 332
%N 6033
%P 1054-1059
%M MAY
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0611, Bayesian, reasoning, logic, infant, baby,
   babies, infant, human, behaviour, II
%X "... When 12-month-old infants view complex displays of multiple moving
   objects, they form time-varying expectations about future events that are a
   systematic & rational fn of several stimulus variables. Infants' looking
   times are consistent with a Bayesian ideal observer embodying abstract
   principles of object motion. The model explains infants' statistical
   expectations & classic qualitative findings about object cognition in younger
   babies, not originally viewed as probabilistic inferences."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1196404">doi:10.1126/science.1196404</A>]['11].
   [Also search for: baby logic].

%A M. J. Gelfand
%A et al ...
%A S. Yamaguchi
%T Differences between tight and loose cultures: A 33-nation study
%J Science
%V 332
%N 6033
%P 1100-1104
%M MAY
%D 2011
%K jrnl, c2011, c201x, c20xx, human, behaviour, society, conformism, culture,
   social norms, religion, national differences
%X "With data from 33 nations, we illustrate the diffs. b/ween cultures that are
   tight (have many strong norms & a low tolerance of deviant behavior) v. loose
   (have weak social norms & a high tolerance of dev.b.). Tightness-looseness is
   part of a complex, loosely integrated multilevel system that comprises
   distal ecological & historical threats (e.g., high population density,
   resource scarcity, a history of territorial conflict, & disease &
   environmental threats), broad v. narrow socialization in societal
   institutions (e.g., autocracy, media regulations), the strength of everyday
   recurring situations, & micro-level psychological affordances (e.g.,
   prevention self-guides, high regulatory strength, need for structure). This
   research advances knowledge that can foster cross-cultural understanding in a
   world of increasing global interdependence & has implications for modeling
   cultural change."
   -- [<A HREF="http://dx.doi.org/1126/science.1197754">doi:1126/science.1197754</A>]['11].

%A M. W. Johnson
%A et al ...
%A G. Rose
%T Quantum annealing with manufactured spins
%J Nature
%V 473
%P 194-198
%M MAY
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0611, D-Wave Systems, Dwave, quantum computing,
   computer, annealing, spin
%X "Many interesting but practically intractable problems can be reduced to that
   of finding the ground state of a system of interacting spins; however,
   finding such a ground state remains computationally difficult. It is
   believed that the ground state of some naturally occurring spin systems can
   be effectively attained through a process called quantum annealing. If it
   could be harnessed, quantum annealing might improve on known methods for
   solving certain types of problem. However, physical investigation of quantum
   annealing has been largely confined to microscopic spins in condensed-matter
   systems. Here we use quantum annealing to find the ground state of an
   artificial Ising spin system comprising an array of eight superconducting
   flux quantum bits with programmable spin-spin couplings. We observe a clear
   signature of quantum annealing, distinguishable from classical thermal
   annealing through the temperature dependence of the time at which the system
   dynamics freezes. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature10012">doi:10.1038/nature10012</A>]['11].
   [Also search for: quantum computer] and
   [also search for: Dwave quantum computing].

%A Z. Merali
%T First sale for quantum computing
%J Nature
%V 474
%P 18
%M MAY
%D 2011
%K news, c2011, c201x, c20xx, D-Wave Systems, Dwave, quantum computing,
   annealing, spin, computer, quantumComputer, controversial,
   sale, commercial, company
%X "... Last week, D-Wave Systems of Burnaby in British Columbia, Canada,
   announced the first sale of a commercial quantum computer, to global security
   firm Lockheed Martin,  ... uncertainty persists around how the impressive
   black monolith known as D-Wave One actually works. ... So D-Wave's claims to
   have a working 128-qubit processor - combined with the company's former
   reluctance to publish details of the technique in peer-reviewed journals -
   have long raised eyebrows, ..."
   -- [<A HREF="http://dx.doi.org/10.1038/474018a">doi:10.1038/474018a</A>]['11].
   [Also search for: Dwave quantum computing].

%A M. S. Mahoney
%A T. Haigh
%T Histories of Computing
%I HarvardUP
%P 260
%M JUN
%D 2011
%K book, text, c2011, c201x, c20xx, zz0611, history, science, technology,
   computing, computer, computers
%X 1st ed 2011; hb us$40; uk us isbn:0674055683; uk us isbn13:978-0674055681.
   "... historiography, software engineering, and theoretical
   computer science. ..."
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/">www</A>].)
   [Also search for: history computer book]  (omit 'book' if you like).

%A I. Stewart
%T The Mathematics of Life
%I BasicBooks
%P 340
%M JUN
%D 2011
%K book, text, intro, c2011, c201x, c20xx, maths, biology, science,
   life, patterns
%X 1st ed 2011; hb us$11; uk us isbn:0465022383; uk us isbn13:978-0465022380.
   "... explains how mathematicians and biologists have come to work together
   on some of the most difficult scientific problems that the human race has
   ever tackled, including the nature and origin of life itself."

%A I. E. Drore
%A C. Champod
%A G. Langenburg
%A D. Charlton
%A H. Hunt
%A R. Rosenthal
%T Cognitive issues in fingerprint analysis: Inter- and intra-expert consistency
   and the effect of a 'target' comparison
%J Forensic Science Int.
%V 208
%N 1
%P 10-17
%M MAY
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0112, finger print, prints, fingerprints,
   latent marks, features, analysis, comparison, identification, accuracy,
   reliability, police, crime, investigation
%X "... examined the consistency (both between- & within-experts) in the
   analysis of latent marks, & whether the presence of a 'target' comparison
   print affects this analysis. ... showed that the context of a comparison
   print affected analysis of the latent mark, possibly influencing allocn of
   attention, visual search, & threshold for determining a 'signal'. ... found
   that even without the context of the comparison print there was still a lack
   of consistency in analysing latent marks. Not only was this reflected by
   inconsistency between different experts, but the same experts at different
   times were inconsistent with their own analysis. However, the charact'n of
   these inconsistencies depends on the std & defn of what constitutes
   inconsistent. ... effects were not uniform; the lack of consistency varied
   across fingerprints & experts. ..." [online Dec '10.].
   -- [<A HREF="http://dx.doi.org/10.1016/j.forsciint.2010.10.013">doi:10.1016/j.forsciint.2010.10.013</A>]['12].

%A T. Hartford
%T Adapt: Why Success Always Starts with Failure
%I FSandG
%P 320
%M MAY
%D 2011
%K book, c2011, c201x, c20xx, zz0611, search, adapt, change, optimization, GFC,
   crisis, climate change
%X 1st ed 2011; hb us$18; uk us isbn:0374100969; uk us isbn13:978-0374100964.
   "... H. argues that today's challenges simply cannot be tackled with
   ready-made solutions and expert opinions; the world has become far too
   unpredictable and profoundly complex. Instead, we must adapt. Deftly weaving
   together psychology, evolutionary biology, anthropology, physics, and
   economics, along with compelling stories of hard-won lessons learned in the
   field, H. makes a passionate case for the importance of adaptive
   trial-and-error in tackling issues such as climate change, poverty, and the
   financial crisis."

%A J. Lorenz
%A H. Rauhut
%A F. Schwitzer
%A D. Helbing
%T How social influence can undermine the wisdom of crowd effect
%J PNAS
%V ?
%D 2011
%K jrnl, PNAS, c2011, c201x, c20xx, zz0912, crowd sourcing, wisdom, social,
   group, media, opinion, survey, range reduction, influence, confidence,
   effect, affect, collective judgement
%X '... Already Galton [Galton F (1907) Nature 75:7] found evidence that the
   median estimate of a group can be more accurate than estimates of experts.
   This wisdom of crowd effect ... In contrast, we demo. by exp.evidence (N=144)
   that even mild social influence can undermine the w. of crowd effect in
   simple estimation tasks. ... subjects could reconsider their response to
   factual Qs after having received avg or full information of the responses of
   other subjects. ...  Although groups are initially "wise," knowledge about
   ests. of others narrows the diversity of opinions to such an extent that it
   undermines the wisdom of crowd effect in three different ways. The "social
   influence effect" diminishes the diversity of the crowd without improvements
   of its collective error. The "range redn effect" moves the posn of the truth
   to peripheral regions of the range of ests. ... The "confidence effect"
   boosts individuals' confidence after convergence of their ests despite lack
   of improved accuracy. Examples of the revealed mechanism range from misled
   elites to the recent global financial crisis.'  [online May 20122] via AK.
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1008636108">doi:10.1073/pnas.1008636108</A>]['12].

%T Chimeras and Consciousness: Evolution of the Sensory Self
%E L. Margulis
%E C. A. Asikainen
%E W. E. Krumbein
%I MITpress
%P 321
%M APR
%D 2011
%K book, text, c2011, c201x, c20xx, zz0711, information processing, life,
   conscious, consciousness, cognition
%X 1st ed 2011; pb us$26; uk us isbn:0262515830; uk us isbn13:978-0262515832.
   "... From social bacteria to urban citizens, all living beings participate
   in community life. Nested inside families within communities inside
   ecosystems, each metabolizes, takes in matter, expends energy, and excretes.
   Each of the members of our own and other species, in groups with incessantly
   shifting alliances, receives and processes information. Mergers of radically
   different life forms with myriad purposes - the "chimeras" of the titleâ -
   underlie dramatic metamorphosis and other positive evolutionary change.
   Since early bacteria avoided, produced, and eventually used oxygen, Earth's
   sensory systems have expanded and complexified. The provocative essays in
   this book, going far beyond science but undergirded by the finest science,
   serve to put sensitive, sensible life in its cosmic context."

%A D. L. Eggleston
%T Basic Electronics for Scientists and Engineers
%I CUP
%P ?
%M APR
%D 2011
%K book, text, CUP, c2011, c201x, c20xx, electronic, electronics, L2Ref, L3Ref,
   circuit, circuits, digital, analog, analogue
%X 1st ed 2011; hb us$103; uk us isbn:0521769701; uk us isbn13:978-0521769709.
   "... covers basic electronics for undergraduate students in science and
   engineering.  ... from passive circuits through to semiconductor-based
   analog circuits and basic digital circuits. ..."

%T Fix the PhD
%J Nature
%V 472
%N 7374
%M APR
%D 2011
%K views, c2011, c201x, c20xx, zz0415, university, research, PhD, PhDs,
   scientific, science, academic, postgrad, sausage factory, jobs, supervision,
   IGERT, training
%X 'The world has many problems & it will take a lot of bright, educated people
   to solve them. So, on the face of it, it seems like a good thing that more &
   more people are earning PhDs in science, technology & engineering. Most
   countries, convinced that higher education & scientific research are key to
   economic growth & prosperity, are expanding doctoral ed. in sci.. The
   thought, as one researcher who has studied doctoral-education trends puts it,
   is that you can "grow PhDs like mushrooms." ...'  [via AK].
   -- [<A HREF="http://dx.doi.org/10.1038/472259b">doi:10.1038/472259b</A>]['15].
   [Also search for: postgrad PhD].

%A R. Garnaut
%T The Garnaut Review 2011: Australia in the Global Response to Climate
%I CUP
%P 244
%M JUL
%D 2011
%K book, text, CUP, c2011, c201x, c20xx, zz0220, Australia, climate change,
   global warming, greenhouse gas, gases, CO2, coal, oil, fossil fuel,
   economics, GFC, sustainability, environment, wind, solar, politics, enquiry
%X 1st edn 2011; pb us$43; uk us isbn:1107691680; uk us isbn13:978-1107691681.
   "In this update to the 2008 Garnaut Climate Change Review, Ross Garnaut
   re-examines the case for action in the aftermath of the global financial
   crisis and recent developments by major countries to reduce emissions and
   prepare for a low-carbon future. He guides the reader through the climate
   change debate, and explains why Australia's contribution is vital to the
   national interest and matters to the global effort. He outlines a set of
   policies through which Australia can contribute its fair share without
   damaging Australian prosperity. The Garnaut Review 2011: Australia in the
   Global Response to Climate Change extends the analysis to contemporary
   economic, political and environmental conditions in a way that is clear and
   easy to understand. It is an essential resource for all who care about the
   future of our economy and environment."
   [Also search for: climate change].

%A M. Duduta
%A et al ...
%A Y.-M. Chang
%T Semi-solid lithium rechargeable flow battery
%J Advanced Energy Materials
%V 1
%N 4
%P 511-516
%M JUL
%D 2011
%K c2011, c201x, c20xx, zz0811, flow battery, batteries, transport, car, cars,
   SSFC, cell, electric, vehicle, vehicles, renewable energy, sustainable,
   24M Technologies
%X "A new kind of flow battery is fueled by semi-solid suspensions of
   high-energy-density lithium storage compounds that are electrically
   'wired' by dilute percolating networks of nanoscale conductor particles.
   Energy densities are an order of magnitude greater than previous flow
   batteries; new applications in trans. & grid-scale storage may result."
   -- [<A HREF="http://dx.doi.org/10.1002/aenm.201100152">doi:10.1002/aenm.201100152</A>]['11].
   (Claim ~ us$250/kWhr.)

%A B. L. Eide
%A F. F. Eide
%T The Dyslexic Advantage: Unlocking the Hidden Potential of the Dyslexic Brain
%I PenguinGroup
%M AUG
%D 2011
%K book, c2011, c201x, c20xx, zz0911, dyslexia, dyslexic, brain, reasoning,
   advantage, advantages, human behaviour
%X 1st ed 2011; hb us$14; uk us isbn:1594630798; uk us isbn13:978-1594630798.
   "... dyslexic people have unique brain structure & organization ...
   differences are responsible for certain challenges with literacy & reading,
   [but] the dyslexic brain also gives a predisposition to important skills,
   & special talents.  While dyslexics typically struggle to decode the written
   word, they often also excel in such areas of reasoning as mechanical
   (required for architects & surgeons), interconnected (artists & inventors);
   narrative (novelists & lawyers), & dynamic (scientists & business pioneers).
   The Dyslexic Advantage provides the first complete portrait of dyslexia."

%A M. Brooks
%T Free Radicals: The Secret Anarchy of Science
%I ProfileBooks
%P 288
%M JUL
%D 2011
%K book, c2011, c201x, c20xx, zz0811, free radicals, radical, science,
   scientists, popular, scientific process, new ideas
%X 1st ed 2011; pb stg7; uk us isbn:1846684056; uk us isbn13:978-1846684050.
   "Scientists present themselves as cool, logical and level-headed, but the
   truth is they will do anything: Take drugs, steal, lie and even cheat - in
   the pursuit of new discoveries."

%A D. Butler
%T Computing giants launch free science metrics
%J NatureNews
%V 476
%P 18
%M AUG
%D 2011
%K news, views, c2011, c201x, c20xx, zz0811, google, scholar, GSC, microsoft,
   citations, MAS, publish, perish, index, papers, impact, JIF, Hindex,
   bibliometrics
%X "... Google Scholar last month added [beta test] Google Scholar Citations
   (GSC), which lets a researcher create a personal profile showing all their
   articles in the Google Scholar database (<A HREF="http://go.nature.com/7wkpea">www</A>).
   The profile also shows plots of the # of citations these papers have received
   over time, and other citation metrics including the popular h-index ..."
   -- [<A HREF="http://dx.doi.org/10.1038/476018a">doi:10.1038/476018a</A>]['11].
   [Also search for: publish perish].

%A B. Sparrow
%A J. Liu
%A D. M. Wegner
%T Google effects on memory: Cognitive consequences of having information at
   our fingertips
%J Science
%V 333
%N 6043
%P 776-778
%M AUG
%D 2011
%K jrnl, c2011, c201x, c20xx, internet, www, web, google, information, memory,
   remember, remembering, facts, human behaviour, cognition
%X "... four studies suggest that when faced with difficult questions, people
   are primed to think about computers and that when people expect to have
   future access to information, they have lower rates of recall of the info.
   itself and enhanced recall instead for where to access it. The Internet has
   become a primary form of external or transactive memory, where info. is
   stored collectively outside ourselves."  [13 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1207745">doi:10.1126/science.1207745</A>]['11].

%A P. Ginsparg
%T ArXiv at 20
%J Nature
%V 476
%P 145-147
%M AUG
%D 2011
%K news, views, c2011, c201x, c20xx, 1991, ArXiv org, preprint, preprints,
   server, www, online, papers, publish, perish, publications, reports,
   science
%X "Twenty years ago this month, I launched an electronic bulletin board
   intended to serve a few hundred friends and colleagues working in a subfield
   of theoretical high-energy physics. ... now contains close to 700,000 full
   texts, receives 75,000 new texts each year, and serves roughly 1 million
   full-text downloads to about 400,000 distinct users every week ...
   mathematics, nonlinear sciences, computer science, statistics and ..."
   -- [<A HREF="http://dx.doi.org/10.1038/476145a">doi:10.1038/476145a</A>]['11],
      [<A HREF="http://arxiv.org/">arxiv</A>]['11].

%T Origami 5: Fifth International Meeting of Origami Science, Mathematics, and
   Education
%E P. Wang-Iverson
%E R. J. Lang
%E M. Yim
%I CRCpress
%M JUL
%D 2011
%K wShop, OSME, c2011, c201x, c20xx, Origami, fold, folding, paper, sheet,
   maths
%X 5OSME 2011; us$60; uk us isbn:1568817142; uk us isbn13:978-1568817149.
   "... begins with a section on origami history, art, and design. ...
   followed by sections on origami in education, origami science, engineering,
   and technology, and culminates with a section on origami mathematics -
   the pairing that inspired the original meeting. ..."

%A K. Mitnick
%T Ghost in the Wires: My Adventures as the World's Most Wanted Hacker
%I LittleBrownCo
%P 474
%M AUG
%D 2011
%K book, c2011, c201x, c20xx, hacker, hacking, Mitnick, mittnick, wire,
   computer, security
%X 1st ed 2011; hb us$14; uk us isbn:0316037702; uk us isbn13:978-0316037709;
   other 2011, uk us isbn:1441793739; uk us isbn13:978-1441793737.
   "... M. bypassed security systems and blazed into major organizations inc.
   Motorola, Sun Microsystems, and Pacific Bell. But as the FBI's net began to
   tighten, Kevin went on the run, engaging in an increasingly sophisticated
   cat and mouse game that led through false identities, a host of cities,
   plenty of close shaves, and an ultimate showdown with the Feds ..."

%A Y. Bhattacharjee
%T Exoplanetary Research: A distant glimpse of alien life?
%J Science
%V 333
%N 6045
%P 930-932
%M AUG
%D 2011
%K news, views, c2011, c201x, c20xx, alien life, exoplanet, exo planets, ET,
   extraterrestrial, Goldilocks planet, space, spectrum, Kepler-10b, Gliese 229B
%X '... "The expectation is that we will start to find a dozen Earth-like
   planets a year," Gaudi says ...'
   -- [<A HREF="http://dx.doi.org/10.1126/science.333.6045.930">doi:10.1126/science.333.6045.930</A>]['11].
   (i.e., not yet, but the search, and techniques)
   [Also search for: exoplanet].

%A R. F. Service
%T Algae's second try
%J Science
%V 333
%N 6047
%P 1238-1239
%M SEP
%D 2011
%K news, views, c2011, c201x, c20xx, zz0911, alga, algae, algal, bio fuel,
   fuels, biofuel, renewable, alternative, biofuels,
   Solazyme, Exxon Mobil, Sheehan
%X "Fifteen years ago, the United States gave up on algae-based biofuels. Now
   synthetic biology has helped revitalize the field. ...  The effort at the
   National Renewable Energy Laboratory (NREL) in Golden, Co., surveyed more
   than 3000 algal strains for their ability to produce oils ...  (DOE) killed
   the program in 1996, opting instead to focus its limited funds on turning
   agricultural wastes and other 'cellulosic' material into ethanol.
   Fifteen years later, the algae biofuels business is thriving. Since 2000,
   more than $2 billion in private funds have flooded into the field. In May,
   Solazyme, an algae biofuels company in South S.F., Cal., raised $227 million
   on the stock market. Last year, ExxonMobil announced it would invest up to
   $600 million ...    ... [now] the cheapest algal fuels cost ~ $2.25/l ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.333.6047.1238">doi:10.1126/science.333.6047.1238</A>]['11].

%A J. L. Powell
%T The Inquisition of Climate Science
%I ColumbiaUP
%P 248
%D 2011
%K book, c2011, c201x, c20xx, climate change, global warming, denial, denier,
   politics, business
%X 1st ed 2011; hb us$28; uk us isbn:0231157185; uk us isbn13:978-0231157186.
   "... the climate science denial movement and the deniers themselves,
   exposing their lack of credentials, their extensive industry funding, and
   their failure to provide any alternative theory to explain the observed
   evidence of warming. In this book, readers meet the most prominent deniers
   while dissecting their credentials, arguments, and lack of objectivity. ..."

%A R. H. Frank
%T The Darwin Economy: Liberty, Competition, and the Common Good
%I PrincetonUP
%P 256
%M SEP
%D 2011
%K book, text, c2011, c201x, c20xx, zz1011, economics, Smith, Darwin,
   competition, economic, business, regulation, taxation, government
%X 1st ed 2011; hb us$17; uk us isbn:0691153191; uk us isbn13:978-0691153193.
   "Who was the greater economist--Adam Smith or Charles Darwin? The Q. seems
   absurd. ... Frank argues, is that Darwin's understanding of competition
   describes economic reality far more accurately than Smith's. & the
   consequences of this fact are profound. ... failure to recognize that we live
   in Darwin's world rather than Smith's is putting us all at risk by preventing
   us from seeing that competition alone will not solve our problems. ..."

%A D. Colquhoun
%T Publish-or-perish: Peer review and the corruption of science
%I The Guardian
%M 5th SEP
%D 2011
%K news, newspaper, c2011, c201x, c20xx, zz0911, publish, perish, publications,
   science, scientific research, university management, administration,
   KPI, KPIs, impact, JIF, misuse, audit culture, Imperial College
%X '... Peer review is the process that decides whether your work gets published
   in an academic journal. It doesn't work very well any more, mainly as a
   result of the enormous number of papers that are being published (an est.
   1.3 million papers in 23,750 journals in 2006). There simply aren't enough
   competent people to do the job. ...
   Not long ago, Imperial College's medicine department were told that their
   "productivity" target for publications was to "publish three papers per annum
   including one in a prestigious journal with an impact factor of at least
   five." The effect of instructions like that is to reduce the quality of
   science and to demoralise the victims of this sort of mismanagement. ...
   David Colquhoun is prof. of pharmacology at University College London ...'
   -- [<A HREF="http://www.guardian.co.uk/science/2011/sep/05/publish-perish-peer-review-science">www</A>]['11];
   auth@[<A HREF="http://www.dcscience.net/">blog</A>]['11].
   [Also search for: publish perish].

%A L. Kaltenegger
%A S. Udry
%A F. Pepe
%T A habitable planet around HD 85512?
%J Arxiv
%M AUG
%D 2011
%K arxiv, c2011, c201x, c20xx, zz0911, space, exo planets, exoplanet, ET,
   HD 85512, HD85512, HD85512b, HARPS, GTO, habitable zone, Goldilocks,
   extraterrestrial, alien life, superearth, super earth
%X "... assess the habitability of HD85512b, a 3.6M_Earth planet orbiting a K5V
   star. The radial velocity data and orbital parameters for HD 85512 b have
   just been published, based on data from the dedicated HARPS-upgrade GTO
   program.  ... To first order the limits of the Habitable Zone depend on the
   effective stellar flux distribution in wavelength and time, the planet's
   Bond albedo, and greenhouse gas effects in this approach. We also discuss the
   dependence of habitability on the measurement accuracies.  ... We find that
   HD 85512 b could be potentially habitable if the planet exhibits more than
   50% cloud coverage. HD 85512 b is, with Gl 581 d, the best candidate for
   exploring habitability to date, a planet on the edge of habitability."
   -- @[<A HREF="http://arxiv.org/abs/1108.3561">arxiv</A>]['11].
   [Also search for: exoplanet].

%A D. D. P. Johnson
%A J. H. Fowler
%T The evolution of overconfidence
%J Nature
%V 477
%P 317-320
%M SEP
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0911, over confidence, self image,
   human behaviour, overconfidence, overconfident, evolution,
   evolutionarily stable, bluff, bluffing, strategy, game theory
%X "... we present an evolutionary model showing that, counterintuitively,
   overconfidence maximizes individual fitness and populations tend to become
   overconfident, as long as benefits from contested resources are sufficiently
   large compared with the cost of competition. In contrast, unbiased strategies
   are only stable under limited conditions. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature10384">doi:10.1038/nature10384</A>]['11].

%A T. C. Pataky
%A T. Mu
%A K. Bosch
%A D. Rosenbaum
%A J. Y. Goulermas
%T Gait recognition: highly unique dynamic plantar pressure patterns among
   104 individuals
%J J. Royal Soc. Interface
%V ?
%P ?-?
%M SEP
%D 2011
%K jrnl, JRSI, c2011, c201x, c20xx, zz0911, biometric, biometrics,
   gait, recognition, identification
%X "... has been shown that both humans & computers are v.good at recognizing
   known gait patterns. [So] unsurprising that dynamic foot pressure patterns,
   which indirectly reflect the accelerations of all body parts, are also unique
   & that prev.studies have achieved moderate-to-high classification rates
   (CRs) using foot pressure vars.. However, these studies are limited by small
   sample sizes (n < 30), moderate CRs (CR ~90%), or both. Here we show, using
   relatively simple image proc. & feature extraction, that dynamic foot
   pressures can be used to identify n=104 subjects with a CR of 99.6%. Our
   key innovation was improved & automated spatial alignment which, by itself,
   improved CR to over 98% ..."  (online Sept 2011).
   -- [<A HREF="http://dx.doi.org/10.1098/rsif.2011.0430">10.1098/rsif.2011.0430</A>]['11].

%A N. Graves
%A A. G Barnett
%A P. Clarke
%T Funding grant proposals for scientific research: retrospective analysis of
   scores by members of grant review panel
%J BMJ
%V 343
%M SEP
%D 2011
%K jrnl, BMJ, c2011, c201x, c20xx, zz0413, peer review, publish, perish,
   science, research, NHMRC, ARC, grant, grants, funding, application, success,
   score, randomness, cost, reviewers, cost, predicting, reproducibility,
   inconsistency, stats, analysis
%X "Objective: To quantify randomness & cost when choosing health & medical
   research projects for funding. ...  Results: 59% of 620 funded grants were
   sometimes not funded when random variability was taken into account. Only 9%
   (n=255) of grant proposals were always funded, 61% (n=1662) never funded, &
   29% (n=788) sometimes funded. The extra cost per grant effectively funded
   from the most effective system was $A18,541 ..."
   -- [<A HREF="http://dx.doi.org/10.1136/bmj.d4797">doi:10.1136/bmj.d4797</A>]['13].
   [Also search for: peer review]  and  [also search for: publish perish].

%A S. Fuller
%T Humanity 2.0: What it Means to be Human Past, Present and Future
%I PagraveMacmillan
%P 280
%M NOV
%D 2011
%K book, c2011, c201x, c20xx, zz1011, human, humanity, future, futurology,
   futurist, life, society, social, convergence, tipping point, AI, technology
%X 1st ed 2100; pb us$21; uk us isbn:0230233430; uk us isbn13:978-0230233430.
   "... historical, philosophical and theological moments that have shaped our
   understandings of humanity.  Tackling head on the twin taboos that have
   always hovered over the scientific study of humanity - race and religion -
   ... argues that far from disappearing, they are being reinvented. ... argues
   that these new developments will force us to decide which features of our
   current way of life - not least our bodies - are truly needed to remain
   human ..."

%T Origins of Altruism and Cooperation
%E R. W. Sussman
%E C. R. Cloninger
%I SpringerVerlag
%S Developments in Primatology: Progress and Prospects Series
%V 36
%M AUG
%D 2011
%K book, text, c2011, c201x, c20xx, zz1011, animal, primate, human, behaviour,
   society, social, groups, altruism, cooperation, cooperate, origin, evolution
%X 1st ed 2011; us$140; uk us isbn:1441995196; uk us isbn13:978-1441995193.
   "... Although cooperation & altruism are often thought of as ways to
   attenuate competition & aggression within groups, or are related to the
   action of 'selfish genes', there is increasing evidence that these behaviors
   are the result of biological mechanisms that have developed through natural
   selection in group-living species. This evidence leads to the conclusion that
   cooperative & altruistic behavior are not just by-products of competition
   but are rather the glue that underlies the ability for primates & humans
   to live in groups. ..."

%A S. Pinker
%T Decline of violence: Taming the devil within us
%J Nature
%V 478
%P 309-311
%M OCT
%D 2011
%K essay, book, text, c2011, c201x, c20xx, zz1011, human behaviour,
   society, social, violence, risk, risks, murder, homicide, rate,
   civilisation, crime, war
%X '"The twentieth century was the bloodiest in history." This frequently
   asserted claim ... rarely backed up by numbers, and it is almost certainly
   an illusion. ... The obsolescence of major war is just one of many historical
   declines of violence. European homicide rates have dropped at least 30-fold
   since the Middle Ages, from about 40 per 100,000 people per year in the
   fourteenth century to 1.3 at the end of the twentieth. ... "
   -- [<A HREF="http://dx.doi.org/10.1038/478309a">doi:10.1038/478309a</A>]['11].
   (Also see auth's book: uk us isbn:0670022950; uk us isbn13:978-0670022953;
   'The Better Angels of Our Nature: Why Violence Has Declined'; Penguin, 2011.)

%A M. Pavlou
%A E. P. Diamandis
%T The athletes of science
%J Nature
%V 478
%P 419
%M OCT
%D 2011
%K views, c2011, c201x, c20xx, zz1111, publish and perish, impact, KPI, KPIs,
   Hindex, Gindex, ranking, rankings, research, metrics, publications, citation,
   citations, everything, count, counted, quote, quotable, cite, science, ISI,
   SCI, academic
%X '... adapted from a saying by Albert Einstein[?]: "Many of the things you
   can count, don't count. Many of the things you can't count, do count. ...'
   -- [<A HREF="http://dx.doi.org/10.1038/nj7369-419a">doi:10.1038/nj7369-419a</A>]['11].
   *BUT* [also search for: count quote] and [also search for: publish perish].

%A W. Isaacson
%T Steve Jobs
%I SimonAndSchuster
%P 656
%M OCT
%D 2011
%K book, c2011, c201x, c20xx, zz1011, Steve Jobs, Apple, computers, computer,
   personnal, biography, obit, PC, AppleII, Lisa, Mac, NeXT, OSX, iMac, iPhone,
   iPad, tablet, iTunes, Pixar, technology
%X 1st ed 2011; hb us$18; uk us isbn:1451648537; uk us isbn13:978-1451648539.
   Steve Jobs, 1955-2011.
   "Based on more than forty interviews with Jobs conducted over two years -
   as well as interviews with more than a hundred family members, friends,
   adversaries, competitors, and colleagues ... "
   (Also see obit@[<A HREF="http://dx.doi.org/10.1038/479042a">doi:10.1038/479042a</A>]['11] in Nature,
   and [<A HREF="http://dx.doi.org/10.1126/science.1216019">doi:10.1126/science.1216019</A>]['11] in Science.)

%A P. Cauwels
%A D. Sornette
%T Quis pendit ipsa pretia: Facebook valuation and diagnostic of a bubble based
   on nonlinear demographic dynamics
%J arXiv
%M OCT
%D 2011
%K TR, c2011, c201x, c20xx, zz0512, facebook, social media, network, internet,
   www, groupcon, value, Facebook, Meta, price, float, IPO, shares, finance,
   financial model, zzPrediction, economics, bubble
%X "We present a novel methodology to determine the fundamental value of firms
   in the social-networking sector based on two ingredients: (i) revenues &
   profits are inherently linked to its user basis through a direct channel that
   has no equivalent in other sectors; (ii) the growth of the # of users can be
   calibrated with standard logistic growth models & allows for reliable
   extrapolations of the size of the business at long time horizons. We
   illustrate the methodology with a detailed analysis of facebook  ...
   To prove the wider applicability of our methodology, the analysis is repeated
   on Groupon, the well-known deal-of-the-day website which is expected to go
   public in Nov 2011. The results are in line with the facebook analysis.
   Customer growth will plateau. By not taking this fundamental property of the
   growth process into consideration, ests. of its IPO are wildly overpriced."
   -- @[<A HREF="http://arxiv.org/abs/1110.1319">arXiv</A>][12']. auths@ethz.
      (Facebook Float, 18 May 2012: The shares opened at us$38, and
       fell to $29 by the 29 May; see [<A HREF="http://www.allisons.org/ll/Computing/Misc/Events/">/Misc/Events/</A>].
       However, on 3/1/24 we were still suffering from long-Facebook and
       Meta's(!) shareprice was us$346.)

%E A. Wokaun
%E E. Wilhelm
%T Transition to Hydrogen: Pathways Toward Clean Transportation
%I CUP
%P 272
%M NOV
%D 2011
%K book, text, CUP, c2011, c201x, c20xx, zz0112, energy, fuel, fuels, hydrogen,
   economy, clean, renewable, climate change, greenhouse gases, H2, CO2,
   transport, car, cars, truck, vehicle, vehicles
%X 1st ed 2011; hb us$101; uk us isbn:0521192889; uk us isbn13:978-0521192880.
   "... Using hydrogen as a fuel offers a possible solution to satisfying global
   mobility needs, inc. sustainability of supply & the potential reduction
   of greenhouse gas emissions. ... focuses on research issues that are at the
   intersection of hydrogen & transportation, since the study of vehicles &
   energy-carriers is inseparable. It concentrates on light duty vehicles (cars
   & light trucks), set in the context of other competing technologies, the
   larger energy sector and the overall economy. ..."

%A D. Oswald
%A C. Paar
%T Breaking Mifare DESFire MF3ICD40: Power Analysis and Templates in the
   Real World
%I Workshop on Cryptographic Hardware and Embedded Systems (CHES)
%P ?-?
%D 2011
%K wShop, CHES, c2011, c201x, c20xx, zz1111, 3DES, contactless, smart, card,
   cards, wireless, RFID, side channel analysis, NXP, chip, transit, payWave,
   Visa, payPass, Mastercard, AMEX, NFC, tap and go, pay, credit, cash,
   security, fraud, attack, theft, crime, bank, banking
%X wShop 28 Sept - 1 Oct 2011.
   Also see:
      Amir Moradi, Oliver Mischke, Christof Paar, Yang Li,
      Kazuo Ohta, Kazuo Sakiyama,
      "On the Power of Fault Sensitivity Analysis and Collision Side-Channel
      Attack in a Combined Setting,"
   same workshop.
   (*Also see 'Choice' [<A HREF="https://www.choice.com.au/money/credit-cards-and-loans/credit-cards/articles/visa-paywave-and-mastercard-paypass-security">www</A>][28/4/2015].*)
   [Also search for: bank card security].

%A S. Shultz
%A C. Opie
%A Q. D. Atkinson
%T Stepwise evolution of stable sociality in primates
%J Nature
%V 479
%P 219-222
%M NOV
%D 2011
%K jrnl, c2011, c201x, c20xx, zz1111, social, cooperation, animal bahaviour,
   evolution, primate, family, tribe
%X "... primate social behaviour shows strong evidence for phylogenetic inertia,
   permitting the use of B@yesian comparative methods to infer changes in social
   behaviour ... a model of primate social evolution, whereby sociality
   progresses from solitary foraging individuals directly to large multi-
   -male/multi-female aggregations (~ 52 m.years ago), with pair-living
   (~ 16Myr ago) or single-male harem systems (~ 16Myr ago)
   derivative from this 2nd stage. ... fits the data sig.better than the two
   widely accepted alternatives (an unstructured model implied by the
   socioecological hypothesis or a model that allows linear stepwise changes in
   social complexity through time). We also find strong support for the
   co-evolution of social living with a change from nocturnal to diurnal
   activity patterns, but not with sex-biased dispersal. This supports
   suggestions that social living may arise because of increased predation risk
   assoc. with diurnal activity. Sociality based on loose aggregation is
   followed by a 2nd shift to stable or bonded groups. This structuring
   facilitates the evolution of cooperative behaviours and may provide the
   scaffold for other distinctive anthropoid traits including coalition
   formation, cooperative resource defence and large brains."
   -- [<A HREF="http://dx.doi.org/10.1038/nature10601">doi:10.1038/nature10601</A>]['11].

%A W. deBuys
%T A Great Aridness: Climate Change and the Future of the American Southwest
%I OUP
%P 384
%M NOV
%D 2011
%K book, text, OUP, c2011, c201x, c20xx, zz1211, climate change, global warming,
   risk, risks, US, USA, America, arid, rainfall
%X 1st ed 2011; hb us$18; uk us isbn:0199778922; uk us isbn13:978-0199778928.
   "... paints a compelling picture of what the Southwest might look like when
   the heat turns up and the water runs out. This semi-arid land, vulnerable to
   water shortages, rising temperatures, wildfires, and a host of other
   environmental challenges, is poised to bear the heaviest consequences of
   global environmental change in the United States. Examining interrelated
   factors such as vanishing wildlife, forest die backs, and the
   over-allocation of the already stressed Colorado River ..."

%A E. Casey
%A G. Fellows
%A M. Geiger
%A G. Stellatos
%T The growing impact of full disk encryption on digital forensics
%J Digital Investigation
%V ?
%P ?-?
%M ?
%D 2011
%K jrnl, c2011, c201x, c20xx, zz1211, digital, computer, forensic, crime,
   police, law, investigation, investigators, FDE, full disc, encrypt,
   encryption, security
%X "The increasing use of full disk encryption (FDE) can sig. hamper digital
   investigations, potentially preventing access to all digital evidence in a
   case. The practice of shutting down an evidential computer is not an
   acceptable technique when dealing with FDE or even volume encryption because
   it may result in all data on the device being rendered inaccessible for
   forensic examination. To address this challenge, there is a pressing need for
   more effective on-scene capabilities to detect & preserve encryption prior to
   pulling the plug. [And] to give digital investigators the best chance of
   obtaining decrypted data in the field, prosecutors need to prepare search
   warrants with FDE in mind. ... describes how FDE has hampered past inv's., &
   how circumventing FDE has benefited certain cases. ... provide guidance for
   gathering items at the crime scene that may be useful for accessing encrypted
   data, & for performing on-scene forensic acquisitions of live computer syss..
   ... increase the chances of acquiring digital evidence in an unencrypted
   state or capturing an encryption key or passphrase. ..."  [online Nov 2011].
   -- [<A HREF="http://dx.doi.org/10.1016/j.diin.2011.09.005">doi:10.1016/j.diin.2011.09.005</A>]['11].

%A T. W. Deacon
%T Incomplete Nature: How Mind Emerged from Matter
%I WWNorton
%P 624
%M NOV
%D 2011
%K book, text, c2011, c201x, c20xx, zz1211, life, mind, sentient, matter, brain,
   body, thought, consciousness, philosophy
%X 1st ed 2011; hb us$16; uk us isbn:0393049914; uk us isbn13:978-0393049916.
   "As physicists work toward completing a theory of the universe & biologists
   unravel the molecular complexity of life, a glaring incompleteness in this
   scientific vision becomes apparent. The 'Theory of Everything' that appears
   to be emerging includes everything but us: the feelings, meanings,
   consciousness, & purposes that make us (& many of our animal cousins) what we
   are. These most immediate & incontrovertible phenomena are left unexplained
   by the natural sciences because they lack the physical properties - such as
   mass, momentum, charge, & location - that are assumed to be nec. for
   something to have physical consequences in the world. This is an unacceptable
   omission. We need a 'theory of everything' that does not leave it absurd that
   we exist."
   [Also search for: mind consciousness].

%A S. Adams
%T How's That Underling Thing Working Out for You?
%I AndrewsMcMeelPub
%P 128
%M NOV
%D 2011
%K book, Scott Adams, cartoon strip, c2011, c201x, c20xx, zz0212, funny, haha,
   ha ha, IT, computing, satire, workplace, job, work, office, worker, the,
   Alice, Asok, Ashok, Catbert, Carol, Dilbert, Dogbert, Ted, Wally, boss,
   WDG, Elbonia, Elbonian, bureaucracy
%X 1st ed 2011; us$9; uk us isbn:1449408192; uk us isbn13:978-1449408190.
   "... If you agree that every indeterminable project has to have at least one
   WDG (Worthless Dumb Guy), or are subjected to results-free sensitivity
   training, questionable employee surveys, & freelance consultants that seem
   to offer little more than exorbitant invoices, then chances are you find the
   corporate cubicle culture philosophy represented inside How's That Underling
   Thing Working Out for You? alive & well inside your own work environment..."
   (Also see [<A HREF="http://www.dilbert.com/">www</A>].)

%A P. Schilperoord
%T The Extraordinary Life of Josef Ganz: The Jewish Engineer Behind Hitler's
   Volkswagen
%I RVP
%P 352
%M DEC
%D 2011
%K book, c2011, c201x, c20xx, car, cars, automobile history, VW, Volkswagen,
   people's car, peoples, Beetle, Mai, May bug, Maikaefer, Maikafer, WW2, WWII
%X 1st ed 2011; hb us$19; uk us isbn:1614122016; uk us isbn13:978-1614122012.
   "... Josef Ganz, a Jewish designer from Frankfurt, who in May 1931 created a
   revolutionary small car: the Maikafer (German for May Bug). Seven years later
   Hitler introduced the Volkswagen. He not only 'took' the concept of G's
   family car, he even used the same nickname. ...  incorporated many of the
   features of Ganz's original [M.] , yet until recently Ganz received no
   recognition for his pioneering work. ... forced to flee Germany while Porsche
   created the [VW] for Hitler using many of his groundbreaking ideas. Ganz was
   hunted by the Nazis even beyond Germany's borders & narrowly escaped
   assassination. After [WW2] ... moved to Australia where he died in 1967 ..."
   ?Contentious?

%A A. G. Haldane
%A R. M. May
%T Systemic risk in banking ecosystems
%J Nature
%V 469
%N 7330
%P 351-355
%M JAN
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0815, economics, risk, bank, banks, stability,
   global financial crisis, GFC, instability, markets, crash, derivatives,
   finance, feedback, interactions, species, ecology, food web, network
%X "In the run-up to the recent financial crisis, an increasingly elaborate set
   of financial instruments emerged, intended to optimize returns to individual
   instns with seemingly minimal risk. Essentially no attention was given to
   their possible effects on the stability of the system as a whole. Drawing
   analogies with the dynamics of ecological food webs & with networks within
   which infectious diseases spread, we explore the interplay between complexity
   & stability in deliberately simplified models of financial n/wks. We suggest
   some policy lessons that can be drawn from such models, with the explicit
   aim of minimizing systemic risk."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09659">doi:10.1038/nature09659</A>]['15].

%A M. E. Ireland
%A R. B. Slatcher
%A P. W. Eastwick
%A L. E. Scissors
%A E. J. Finkel
%A J. W. Pennebaker
%T Language style matching predicts relationship initiation and stability
%J Psych. Sci.
%V 22
%N 1
%P 39-44
%M JAN
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0214, stats, human behaviour, psychology,
   speed dating, date, romance, romantic, love, talk, talking, styles, speech,
   relationships, dyads, couples, LSM
%X "... investigated whether similarity in dyads' use of fn words, called
   language style matching (LSM), predicts outcomes for romantic relationships.
   In Study 1, greater LSM in transcripts of 40 speed dates predicted increased
   likelihood of mutual romantic interest (odds ratio=3.05). Overall, 33.3% of
   pairs with LSM above the median mutually desired future contact, compared
   with 9.1% of pairs with LSM at or below the median. In Study 2, LSM in 86
   couples' instant messages positively predicted relationship stability at a
   3-month follow-up (odds ratio=1.95). Specifically, 76.7% of couples with LSM
   greater than the median were still dating at the follow-up, [v.] 53.5% of
   couples with LSM at or below the median. LSM appears to reflect implicit
   interpersonal processes central to romantic relationships. "
   -- [<A HREF="http://dx.doi.org/10.1177/0956797610392928">doi:10.1177/0956797610392928</A>]['14],
   pdf@[<A HREF="http://homepage.psy.utexas.edu/HomePage/Faculty/Pennebaker/Reprints/Ireland_et.al_LSM&relationships.pdf">uTexas</A>]['14].

%A M. Smith
%T The Secrets of Station X: The Fight to Break the Enigma Cypher
%I BitebackPubl
%P 240
%D 2011
%K book, c2011, c201x, c20xx, station X, stationX, Bletchley Park,
   world war II, ww2, wwII, Enigma machine, cypher, cipher, bombe, Ultra,
   code breaking, codes, cryptanalysis
%X pb us$13; uk us isbn:1849540950; uk us isbn13:978-1849540957.
   [Also search for: Bletchley Park].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">B.Park</A>].)

%A B. Ginsberg
%T The Fall of the Faculty: The Rise of the All-Administrative University and
   Why it Matters
%I OUP
%P 264
%M AUG
%D 2011
%K book, text, OUP, university, tertiary education, administration, policy,
   bureaucracy, KPIs, faculty, dean, deanlet, deanitis, management,
   managerialism, USA
%X 1st ed 2011; hb us$25; isbn:019978244X; isbn13:978-0199782444.
   "... examines the fallout of rampant administrative blight that now plagues
   the nation's universities. In the past decade, universities have added layers
   of administrators & staffers to their payrolls every year even while laying
   off full-time faculty in increasing numbers - ostensibly because of budget
   cuts. In a further irony, many of the newly minted - and non-academic -
   administrators are career managers who downplay the importance of teaching &
   research, as evidenced by their tireless advocacy for a banal 'life skills'
   curriculum. Consequently, students are denied a more enriching educational
   experience - one defined by intellectual rigor. Ginsberg also reveals how the
   legitimate grievances of minority groups & liberal activists, which were
   traditionally championed by faculty members, have, in the hands of
   admins., been reduced to chess pieces in a game of power politics. ..."
   [Also search for: university management].

%A Nanyang Xu
%A Jing Zhu
%A Dawei Lu
%A Xianyi Zhou
%A Xinhua Peng
%A Jiangfeng Du
%T Quantum factorization of 143 on a Dipolar-Coupling NMR system
%J arXiv
%M NOV
%D 2011
%K TR,  c2011, c201x, c20xx, zz1214, quantum computing, integer factorization,
   (not) Shor, adiabatic, factorisation, factoring
%X "... report an improved adiabatic factoring alg. & its experimental
   realization to factor the number 143 on a liquid crystal NMR q.processor
   with dipole-dipole couplings. We believe this to be the largest number
   factored in q.-computation realizations, which shows the practical
   importance of adiabatic q.algs.."
   -- 1111.3726@[<A HREF="http://arxiv.org/abs/1111.3726">arXiv</A>]['14].
   [4 qubits, 143=13*11, way to go.]
   [Also search for: quantum computing factorization].

%A R. H. Gray
%T The Elusive WOW: Searching for Extraterrestrial Intelligence
%I PalmerSquarePress
%P 266
%M DEC
%D 2011
%K SETI, c2011, c201x, c20xx, zz1114, 1977, c1977, c197x, wow signal, radio,
   6EQUJ5, Ehman, SETI, Big Ear, 21cm hydrogen line, extraterrestrial,
   extra terrestrial, transmission, alien, life, intelligence, search
%X 1st ed 2011, hb us$25; us isbn:0983958440; us isbn13:978-0983958444.
   Also see
   "The Wow! signal was a strong narrowband radio signal detected by
   Jerry R. Ehman on August 15, 1977, while he was working on a SETI project at
   the Big Ear radio telescope of The Ohio State University, ... It lasted for
   the full 72-second window that [fixed] Big Ear was able to observe it, but
   has not been detected again. ... The location of the signal [was] in the
   constellation Sagittarius, near the Chi Sagittarii star group. ..."
   -- wow@[<A HREF="http://en.wikipedia.org/wiki/Wow!_signal">wikip</A>]['14].
   (*Also see archive@[<A HREF="http://archive.seti.org/epo/news/features/interstellar-signal-from-the-70s.php">seti</A>][11/'14].*)
   [Also search for: extraterrestrial life].

%A A. Yadin
%T Reducing the dropout rate in an introductory programming course
%J Inroads
%I ACM
%V 2
%N 4
%P 71-76
%M DEC
%D 2011
%K c2011, c201x, c20xx, zz0317, university education, teaching, curriculum,
   introductory, computer programming, course, first year, computer science, CS,
   CSci, CSC 101, CS101, L1Ref, drop out, Python, microworld
%X "... (1) Python ... (2) visualization environment (micro-world) ...
   (3) individual assignments ..."  (via J.G.)
   -- [<A HREF="http://dx.doi.org/10.1145/2038876.2038894">doi:2038876.2038894</A>]['17].

%A J. H. Williams
%A A. DeBenedictis
%A R. Ghanadan
%A A. Mahone
%A J. Moore
%A W. R. Morrow III
%A S. Price
%A M. S. Torn
%T The technology path to deep greenhouse gas emissions cuts by 2050: The
   pivotal role of electricity
%J Science
%V 335
%N 6064
%P 53-59
%M JAN
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0112, climate change, CO2, greenhouse gas, GHG,
   emissions, cut, cuts, cutting, mitigation, renewable energy, electricity
%X "Several states & countries have adopted targets for deep reductions in
   greenhouse gas emissions by 2050, but there has been little physically
   realistic modeling of the energy & economic transformations required. We
   analyzed the infrastructure & technology path required to meet California's
   goal of an 80% redn below 1990 levels, using detailed modeling of
   infrastructure stocks, resource constraints, & elec.system operability. We
   found that tech.feasible levels of energy efficiency & decarbonized energy
   supply alone are not sufficient; widespread electrification of trans'n &
   other sectors is required. Decarbonized elec. would become the dominant form
   of energy supply, posing challenges & opportunities for economic growth &
   climate policy. This trans'n demands technologies that are not yet
   commercialized, [&] coordination of investment, tech.development, &
   infrastructure deployment."  [online Nov 2011].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1208365">doi:10.1126/science.1208365</A>]['12].

%A W. Poundstone
%T Are You Smart Enough to Work at Google?
%I LittleBrownAndCo
%P 304
%M JAN
%D 2012
%K book, c2012, c201x, c20xx, new economy, industries, dotcom, interview,
   interviews, interviewing, question, questions, job, jobs, work, google,
   aptitude test, tests, OEIS
%X 1st ed 2012; pb us$13; uk us isbn:031609997X; uk us isbn13:978-0316099974.
     Trick Questions, Zen-like Riddles, Insanely Difficult Puzzles, and
     Other Devious Interviewing Techniques You Need to Know to Get a Job
     Anywhere in the New Economy. ...
     'What's the next number in this sequence - 10, 9, 60, 90, 70, 66, ...?'[*]
     'How would you weigh your head?'<!-- [*]96, # of letters in name -->
   ([*]Also see A052196@[<A HREF="http://oeis.org/A052196">OEIS</A>]['11].)
     <!--  [*] even better, 'ten googol'!  -->

%A G. McGuire
%A B. Tugemann
%A G. Civario
%T There is no 16-clue Sudoku: Solving the Sudoku minimum number of
   clues problem
%J arXiv
%P 36
%M JAN
%D 2012
%K TR, c2012, c201x, c20xx, zz0112, Sudoku, number, puzzle, problem, clue,
   hitting set, NPC, vertex cover, problem
%X "We apply our new hitting set enumeration alg. ... [to] What is the smallest
   number of clues (givens) that a s.puzzle may have? It was conjectured that
   the answer is 17. We have performed an exhaustive search for a 16-clue s.
   puzzle, & we did not find one, thereby proving that the answer is indeed 17.
   ... The hitting set problem is computationally hard; it is one of Karp's
   twenty-one classic NPC problems. We have designed a new alg. that allows us
   to efficiently enum. hitting sets of a suitable size. Hitting set problems
   have applicns in many areas of sci., such as bioinformatics & s/w testing. "
   -- @[<A HREF="http://arxiv.org/abs/1201.0749">arXiv</A>]['12].
   Auths @ U.Coll.Dublin [2012].

%A S. Edelman
%T The Happiness of Pursuit: What Neuroscience Can Teach Us About the Good Life
%I BasicBooks
%P 256
%M JAN
%D 2012
%K book, text, c2012, c201x, c20xx, zz0212, happiness, happy, joy, pursuit,
   brain, mind, wetware, human, behaviour, greed, contentment, well being,
   wellbeing
%X 1st ed 2012; hb us$17; uk us isbn:0465022243; uk us isbn13:978-0465022243.
   "When fishing for happiness, catch and release. Remember these seven words -
   they are the keys to being happy. So says [SE], an expert on psychology & the
   mind.  ... offers a fundamental understanding of pleasure & joy via the
   brain. Using the concept of the mind as a computing device, he unpacks how
   the human brain is highly active, involved in patterned n/ws, & constantly
   learning from experience. As our brains predict the future through pursuit of
   experience, we are rewarded both in real time and in the long run. ..."
   [Also search for: happiness well being].

%A S. Barz
%A E. Kashefi
%A A. Broadbent
%A J. F. Fitzsimons
%A A. Zeilinger
%A P. Walther
%T Demonstration of blind quantum computing
%J Science
%V 335
%N 6066
%P 303-308
%M JAN
%D 2012
%K jrnl, c2012, c201x, c201xx, zz0212, quantum computing, computer, secret,
   secrecy, security, blind, server
%X "Quantum computers, besides offering substantial computational speedups,
   are also expected to preserve the privacy of a compn. ... an experimental
   demo of blind quantum c. in which the input, compn, & output all remain
   unknown to the computer. We exploit the conceptual f/wk of measurement-based
   quantum c. that enables a client to delegate a compn to a quantum server.
   Various blind delegated computations, inc. one- and two-qubit gates & the
   Deutsch and Grover quantum algs., are demonstrated. The client only needs
   to be able to prepare & transmit individual photonic qubits. Our demo. is
   crucial for unconditionally secure quantum cloud computing & might become a
   key ingredient for real-life applicns, esp. when considering the challenges
   of making powerful quantum computers widely available"
   -- [<A HREF="http://dx.doi.org/10.1126/science.1214707">doi:10.1126/science.1214707</A>]['12],
   & [<A HREF="http://dx.doi.org/10.1126/science.1216922">persp</A>]['12].
   [Also search for: quantum computing].

%A J. Murray
%A D. King
%T Climate policy: Oil's tipping point has passed
%J Nature
%V 481
%P 433-435
%M JAN
%D 2012
%K news, views, c2012, c201x, c20xx, peak oil, fossil fuel, fuels, production,
   demand, petrol, economics, economy
%X "The economic pain of a flattening supply will trump the environment as a
   reason to curb the use of fossil fuels, ... From 2005 onwards, conventional
   crude-oil production has not risen to match increased demand. ...
   [Prodn] ~ constant for the past 7 y., despite an increase in price of
   ~15% per year (at Brent crude ... from ~us$15/barrel in '98 to > $140/b
   '08 ..."
   -- [<A HREF="http://dx.doi.org/10.1038/481433a">doi:10.1038/481433a</A>]['12],
   pdf@[<A HREF="http://www.ocean.washington.edu/people/faculty/jmurray/MurrayKing2012.pdf">wash.</A>]['12],
      auth1@[<A HREF="http://www.ocean.washington.edu/people/faculty/jmurray/jmurray.html">wash.</A>]['12].
   [Also search for: peak oil fossil fuel].

%A A. W. Wilhite
%A E. A. Fong
%T Scientific publications: Coercive citation in academic publishing
%J Science
%V 335
%N 6068
%P 542-543
%M FEB
%D 2012
%K news, views, c2012, c201x, c20xx, zz0212, publish, perish, coercive, rank,
   citation, citations, abuse, refs, papers, coercion, impact factor, science,
   ranking, academia
%X "... impact factors continue to be a primary means by which academics
   'quantify the quality of science.' One side effect of impact factors is the
   incentive they create for eds. to coerce authors to add citations to their
   journal. ... Coercive self-citation refers to requests that (i) give no
   indication that the manuscript was lacking in attribution; (ii) make no
   suggestion as to specific articles, authors, or a body of work requiring
   review; & (iii) only guide authors to add citations from the editor's j..
   This quote from an editor as a condition for publication highlights the
   problem: 'you cite Leukemia [once in 42 refs.]. Consequently, we kindly ask
   you to add refs. of articles published in Leukemia to your present article.'
   ... the message is clear: Add citations or risk rejection."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1212540">doi:10.1126/science.1212540</A>]['12].
   [Also search for: publish perish] & [also search for: coercive citation].

%A R. van Noorden
%T Researchers feel pressure to cite superfluous papers
%J Nature
%V ?
%P ?-?
%M FEB
%D 2012
%K news, views, c2013, c201x, c20xx, zz0913, publish, perish, impact factor,
   scientific research, journals, self citation, padding, references, referees,
   refereeing, coercive, coercion, coerce, journal, JIF, editor
%X "One in five academics in a variety of social science & business fields say
   they have been asked to pad their papers with superfluous references in order
   to get published. The figures, from a survey published today in Science[1],
   also suggest that journal editors strategically target junior faculty, who
   in turn were more willing to acquiesce. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature.2012.9968">doi:10.1038/nature.2012.9968</A>]['13], and see
   [1][<A HREF="http://dx.doi.org/10.1126/science.1212540">doi:10.1126/science.1212540</A>]['13].
   (A reviewer of a paper may act so as to boost his/her own "impact".)
   [Also search for: publish perish].

%A M. Lockwood
%T Solar Influence on Global and Regional Climates
%J Surveys in Geophysics
%V 33
%N 3
%P 503-534
%M FEB
%D 2012
%K c2012, c201x, c20xx, zz0114, climate change, global warming, Maunder minimum,
   sun, solar, cycle, flux, activity, jet stream blocking, severe winter,
   Europe, winters, cause
%X " ... The best estimates of the solar influence on the global mean air
   surface temp. show relatively small effects, compared with the response to
   anthropogenic changes (& broadly in line with their respective radiative
   forcings). However, the situation is more interesting when one looks at
   regional & season variations around the global means. ... recent research
   indicates that winters in Eurasia may have some dependence on the Sun, with
   more cold winters occurring when the solar activity is low. Advances in
   modelling 'top-down' mechanisms, whereby stratospheric changes influence the
   underlying troposphere, offer promising explanations of the observed
   phenomena. In contrast, the suggested modulation of low-altitude clouds by
   galactic cosmic rays provides an increasingly inadequate explanation of
   observations."
   -- [<A HREF="http://dx.doi.org/10.1007/s10712-012-9181-3">doi:10.1007/s10712-012-9181-3</A>]['14],
   pdf@[<A HREF="http://www.eiscat.rl.ac.uk/Members/mike/publications/pdfs/2012/286_Lockwood_SurvGeophys2012.pdf">rl.ac.uk</A>]['14].
   Also see
   '... "If we take all the sci. that we know relating to how the Sun emits heat
   & light & how that heat & light powers our climate system, & we look at the
   climate system globally, the difference that it makes even going back into
   Maunder Minimum conditions is very small. I've done a number of studies that
   show at the very most it might buy you about five years before you reach a
   certain global avg. temp. level. But that's not to say, on a more regional
   basis there aren't changes to the patterns of our weather that we'll have to
   get used to." ...'  [[i.e., cold winters in Europe]]
   -- [<A HREF="http://www.bbc.co.uk/news/science-environment-25743806">bbc</A>][18/1/2014],
   and [<A HREF="http://news.bbc.co.uk/2/hi/science/nature/8615789.stm">bbc</A>][14/4/2010].
   [Also search for: cause global warming].

%T Turing centenary: Is the brain a good model for machine intelligence?
%J Nature
%V 482
%P 462-463
%M FEB
%D 2012
%K news, jrnl, c2012, c201x, c20xx, zz0312, Alan Turing, test, special issue,
   human, artificial, intelligence, AI, II, learning, brain, mind, thought,
   computer, computing, power, machine, intelligent, convergence, singularity
%X "To celebrate the centenary of the year of Alan Turing's birth, four
   scientists & entrepreneurs assess the divide between neuroscience and
   computing. ..."
   "... Turing used a person as the basis for his model. ..."
   "... we need to better understand the brain's workings at the
   algorithmic level ..."
   "... In terms of processing power, the brain can reach about 10-50 petaflops
   - equivalent to hundreds of thousands of the most advanced Intel Core i7
   CPUs. Yet signals in the brain are transmitted at a snail's pace ..."
   -- [<A HREF="http://dx.doi.org/10.1038/482462a">doi:10.1038/482462a</A>]['12].
   [Also search for: Turing c193x], and similar.
   (Also see csw on Machine [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/1993-08-10/">Inference</A>].)

%A G. Dyson
%T Turing's Cathedral: The Origins of the Digital Universe
%I Pantheon
%P 432
%M MAR
%D 2012
%K book, text, c2012, c201x, c20xx, zz0312, Turing, computer, computers, origin,
   origins, computing, machine, history, von Neumann, architecture,
   stored program, vonNeumann, Institute for Advanced Study, IAS
%X 1st ed 2012; hb us$18; uk us isbn:0375422773; uk us isbn13:978-0375422775.
   "... focuses on a small group of men & women, led by John von Neumann at the
   Inst. for Advanced Study in Princeton, NJ, who built [c '45-'52] one of
   the 1st computers to realize Alan Turing's vision of a Universal Machine. ...
   would break the distn between numbers that mean things & numbers that do
   things - & our universe would never be the same.  Using five kilobytes of
   memory ...  achieved unprecedented success in both weather prediction &
   nuclear weapons design, while tackling, in their spare time, problems ranging
   from the evolution of viruses to the evol. of stars. ... sheds important new
   light on how the digital universe exploded in the aftermath of WWII. ..."
   (Also see review@[<A HREF="http://www.guardian.co.uk/technology/2012/feb/26/first-computers-john-von-neumann">The_G</A>]['12].)
   [Also search for: Manchester Baby] & [also search for: history computer].

%A M. Balter
%T Reviewer's deja vu, French science sleuthing uncover plagiarized papers
%J Science
%V 6073
%N 6073
%P 1157-1158
%M MAR
%D 2012
%K news, c2012, c201x, c20xx, plagiarism, fraud, publication, paper, papers,
   academic, misconduct, Serge Valentin Pangou, Jansen, turnitin
%X "... thought a paper he was asked to review for the Int. J. of Biodiversity
   and Conservation (IJBC) seemed familiar. Suspicious, he ran it through the
   Turnitin anti plagiarism software ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.335.6073.1157">doi:10.1126/science.335.6073.1157</A>]['12].
   [Also search for: misconduct plagiarism].

%A C. Koch
%T Consciousness: Confessions of a Romantic Reductionist
%I MITpress
%P 184
%M MAR
%D 2012
%K book, text, c2012, c201x, c20xx, zz0312, brain, mind, conscious, science
%X 1st ed 2120; hb us$16; uk us isbn:0262017490; uk us isbn13:978-0262017497.
   "... part scientific overview, part memoir, part futurist speculation
   describes Koch's search for an empirical explanation for consciousness.
   K. recounts not only the birth of the modern sci. of consciousness but also
   the subterranean motivation for his quest-his instinctual (if 'romantic')
   belief that life is meaningful. ..."

%A S. Harris
%T Free Will
%I FreePress
%P 96
%M MAR
%D 2012
%K book, text, c2012, c201x, c20xx, free will, determinism, mind, consciousness,
   morality
%X 1st ed 2012; pb us$10; uk us isbn:1451683405; uk us isbn13:978-1451683400.
   "... argues that this truth about the human mind does not undermine morality
   or diminish the importance of social & political freedom, but it can & should
   change the way we think about some of the most important questions in life."
      "... asserts that the course of human life is all down to luck, & that
   will power is a 'biol. phenomenon.' ... not in charge of our own minds
   ... thought & intention simply arise. ..."

%A D. Franklin
%A J. Andrews
%T Megachange: The World in 2050
%I Wiley
%P 320
%M MAR
%D 2012
%K book, text, c2012, c201x, c20xx, zz0312, mega change, changes, trend, trends,
   world, economics, prediction, futurology, zzPrediction, zz0150, c205x
%X 1st ed 2012; hb us$22; uk us isbn:1118180445; uk us isbn13:978-1118180440.
   "... Groups the 'megatrends' that are shaping our world into several
   categories: People, Life and Death, Economy and Business, & Knowledge ..."
   [Also search for: zzPrediction].

%A A. Casadevall
%A F. C. Fang
%T Reforming science: Methodological and cultural reforms
%J Infection and Immunity
%V 80
%N 3
%P 891-896
%M MAR
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0412, publish, perish, science, scientific,
   reform, research, literature, publications, journals, ethics, fraud,
   corrupt, dysfunction, exploitation, abuse, misuse, impact, promotion,
   Matthew effect
%X "... signs of dysfunction in the sci. community as well as threats from
   diverse antiscience & political forces. Incentives in the current system
   place scientists under tremendous stress, discourage cooperation, encourage
   poor scientific practices, and deter new talent from entering the field. ..."
      "A romantic ideal depicts scis. as intrepid & objective explorers in the
   relentless pursuit of truth ... realities of sci. can be quite different ...
   pyramid scheme with a small # of principal investigators presiding over an
   army of research scis., postdocs, students, & technicians who have little
   autonomy & increasingly uncertain career prospects ..." [online Dec 2011].
   -- [<A HREF="http://dx.doi.org/10.1128/IAI.06183-11">doi:10.1128/IAI.06183-11</A>]['12].
   [Also search for: publish perish].

%A J. Zalasiewicz
%A M. Williams
%T The Goldilocks Planet: The 4 billion year story of Earth's climate
%I OUP
%P
%M MAR
%D 2012
%K book, text, c2012, c201x, c20xx, earth, atmosphere, biosphere, geology,
   climate change, past, global warming
%X 1st ed 2012; hb stg.11; uk us isbn:0199593574; uk us isbn13:978-0199593576.
   "... Earth's climate has continuously altered over its 4.5 billion-year
   history. ... read from clues preserved in the Earth's strata ... the story
   of the E.'s climate is now being reconstructed in ever-greater detail ...
   Changes in global & regional climate range from bitterly cold to sweltering
   hot, from arid to humid, & they have impacted hugely upon the planet's
   evolving animal & plant communities, & upon its physical landscapes of the
   Earth. And yet, through all of this, the E. has remained consistently
   habitable for life for over three billion years ..."
   [Also search for: climate change].

%T Electronic Textbooks: Why the Rush?
%J Science
%V 335
%N 6076
%P 1569-1571
%M MAR
%D 2012
%K views, c2012, c201x, c20xx, zz0412, electronic book, books, eBook, eBooks,
   textbook, school, university, education
%X "... electronic textbook sales have not followed the upward trend of e-books
   ... Reading electronic textbooks takes longer, on average, than reading
   print, & many students report higher levels of fatigue upon completion. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.335.6076.1569">doi:10.1126/science.335.6076.1569</A>]['12].

%A P. J. Wyatt
%T Commentary: Too many authors, too few creators
%J Physics Today
%V 65
%N 4
%P 9
%D 2012
%K news, views, c2012, c201x, c20xx, zz1122, multiple authors, authorship,
   trends, physics, science, STEM, academia, university, scientific research,
   postgraduate, papers, publications, KPI, KPIs
%X "A few years ago, Robert Fefferman, dean of physical sciences at the U. of
   Chicago, made an interesting remark. ... that Enrico Fermi, wanting to
   encourage individual creativity & innovation, required his PhD students to
   select their problem, solve it, & submit the results for publ'n in their name
   alone. ... Over the years, publication lists were increasing. Some colleagues
   boasted more than 300 publications & one close to 800! ... single-author
   papers had become relatively rare. Were Albert Einstein, Enrico Fermi,
   Richard Feynman, & other great scientists just lucky ... Although the data
   sets selected are relatively small, they show the downward trend of
   individual creativity. ... It has long been evident that some profs
   established groups of grad. students whose main activities were often focused
   on publishing res. results. Authorship of such articles expanded to include
   all members of the group despite only the peripheral or negligible
   contributions by some ..."
   -- [<A HREF="https://doi.org/10.1063/PT.3.1499">doi:10.1063/PT.3.1499</A>]['22].

%A J. Long
%T Darwin's Devices: What Evolving Robots Can Teach Us About the History of
   Life and the Future of Technology
%I BasicBooks
%P 288
%M APR
%D 2012
%K book, text, c2012, c201x, c20xx, robot, evolving, evolve, evolution, Alife
%X 1st ed 2012; hb us$17; uk us isbn:0465021417; uk us isbn13:978-0465021413.
   "... creates robots that look and behave like extinct animals, subjects them
   to evolutionary pressures, lets them compete for mates & resources, & mutates
   their 'genes'. In short, he lets robots play the game of life. ..."

%A R. F. Service
%T Biofuels and city air: A marginal effect
   (News Focus: American Chemical Society Spring Meeting)
%J Science
%V 336
%N 6079
%P 292-293
%M APR
%D 2012
%K news, c2012, c201x, c20xx, zz0412, fuel, fuels, petrol, gasoline, ethanol,
   sugar, bio, biofuel, biofuels, transport, transportation, renewable, car,
   cars, trucks, pollution, air quality, Geiger, Salvo
%X '... gas prices in Brazil are tightly regulated. The cost of ethanol, however
   varies wildly with the cost of sugar cane. ... for two of the past three
   winters, world hikes in the price of sugar have made gasoline a better value,
   prompting 1.5 million drivers - about 26% of the total of 5.8million cars &
   light trucks - to switch for a couple of months. ... decided to see whether
   this change affected air quality. To their surprise, it didn't. ... "Any
   discernible change may require an even larger share of vehicles to switch
   fuels, or change to a new fuel altogether," Geiger says. ...'
   -- [<A HREF="http://dx.doi.org/10.1126/science.336.6079.292-b">doi:10.1126/science.336.6079.292-b</A>]['12].

%A M. Baucells
%A R. Sarin
%T Engineering Happiness: A New Approach for Building a Joyful Life Paperback
%I UniCalPress
%P 248
%M MAR
%D 2012
%K book, text, c2013, c201x, c20xx, happy, happiness, joy, human, psychology,
   research, reality, expectations, well being, wellbeing, aspiration
%X 1st ed 2012; pb us$22; uk us isbn:0520268210; uk us isbn13:978-0520268210.
   "... their own research with the latest thinking in the behavioral & social
   sciences - including management science, psychology, & economics - they
   offer a new approach to the puzzle of happiness. ..."
   "Happiness equals Reality minus Expectations"
   [Also search for: happiness well being].

%A W. M. Fitch
%T The Three Failures of Creationism: Logic, Rhetoric, and Science
%I UCalPress
%P 194
%M MAR
%D 2012
%K book, text, c2012, c201x, c20xx, zz0512, science, sci, evolution, creation,
   US, USA, creationism, intelligent design, reason
%X 1st ed 2012; pb us$25; uk us isbn:0520270533; uk us isbn13:978-0520270534.
   "... explains the basics of logic and rhetoric at the heart of sci. thinking,
   shows what a logical syllogism is, and tells how one can detect that an
   argument is logically fallacious, and therefore invalid, or even duplicitous.
   F. takes his readers through the arguments used by creationists to question
   the science of evolution. He clearly delineates the fallacies in logic that
   characterize creationist thinking, and explores the basic statistics that
   creationists tend to ignore, including elementary genetics, the age of the
   Earth, and fossil dating. ..."

%A A. Abbott
%T Plagiarism charge for Romanian minister
%J Nature
%V 485
%N 7398
%P ?-?
%M MAY
%D 2012
%K news, c2012, c201x, c20xx, Ioan Mang, Romania, science, research,
   education, academic, ethics, plagiarism, fraud
%X "Romania's new government was thrown into turmoil last week after its
   education and research minister, Ioan Mang, was accused of extensive
   plagiarism in at least eight of his academic papers. ... Mang is a computer
   scientist at the University of Oradea ..."
   -- [<A HREF="http://dx.doi.org/10.1038/485289a">doi:10.1038/485289a</A>]['12].
   [Also search for: plagiarism].

%A L. R. Hochberg
%A et al ...
%A J. P. Donaghue
%T Reach and grasp by people with tetraplegia using a neurally controlled
   robotic arm
%J Nature
%V 485
%N 7398
%P 372-375
%M MAY
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0512, robotic, arm, quadriplegic, spinal cord,
   nerve, neural, control, electrode, implant, brain, movement, human
%X "... demonstrate the ability of two people with long-standing tetraplegia
   to use neural interface system-based control of a robotic arm to perform
   three-dimensional reach and grasp movements. Participants controlled the arm
   and hand over a broad space without explicit training, using signals decoded
   from a small, local population of motor cortex (MI) neurons recorded from a
   96-channel microelectrode array. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11076">doi:10.1038/nature11076</A>]['12].

%A K. M. Walter Anthony
%A P. Anthony
%A G. Grosse
%A J. Chanton
%T Geologic methane seeps along boundaries of arctic permafrost thaw and
   melting glaciers
%J Nature Geoscience
%V ?
%P ?-?
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0512, methane, seep, seeps, perma frost,
   permafrost, arctic, global warming, greenhouse gas, gases, Alaska, Greenland
%X "Methane, a potent greenhouse gas, accumulates in subsurface hydrocarbon
   reservoirs, such as coal beds & natural gas deposits. In the Arctic,
   permafrost & glaciers form a 'cryosphere cap' that traps gas leaking from
   these reservoirs ... With a carbon store of over 1,200 Pg, the Arctic
   geologic methane reservoir is large [v.] the global atmospheric methane pool
   of around 5 Pg.  ... document the release of 14C-depleted methane to the
   atmosphere from abundant gas seeps concentrated along boundaries of
   permafrost thaw & receding glaciers in Alaska & Greenland ..."
   -- [<A HREF="http://dx.doi.org/10.1038/Ngeo1480">doi:10.1038/Ngeo1480</A>][12'] online May 2012.
   auth1@[<A HREF="http://ine.uaf.edu/werc/people/katey-walter-anthony/">uaf</A>]['12],
   and [<A HREF="http://www.youtube.com/watch?v=YegdEOSQotE">youtube</A>]['12].

%A N. A. Downie
%T The Ultimate Book of Saturday Science: The Very Best Backyard Science
   Experiments You Can Do Yourself
%I PrincetonUP
%P 576
%M MAY
%D 2012
%K book, text, c2012, c201x, c20xx, zz0612, science, home, school, kids,
   experiment
%X 1st ed 2012; pn us$20; uk us isbn:0691149666; isbn13:978-0691149660.
   "... may be the only book that encourages hands-on sci. learning through the
   use of high-velocity, air-driven carrots. ... such marvels as the Helevator -
   a contraption that's half helicopter, half elevator - & the Rocket Railroad,
   which pumps propellant up from its own track. The Riddle of the Sands
   demonstrates why some granular materials form steep cones when poured while
   others collapse in an avalanche. The Sunbeam Exploder creates a combustible
   delivery system out of sunlight, while the Red Hot Memory experiment shows
   you how to store data as heat. ..."

%A D. Butler
%T Scientists: your number is up
%J Nature
%V 485
%N 7400
%P ?-?
%M MAY
%D 2012
%K news, ORCID, c2012, c201x, c20xx, zz0612, scientific research, number, name,
   Open Researcher Contributor, unique, id, publish, publication, author
%X "ORCID scheme will give researchers unique identifiers to improve tracking
   of publications. ... when scientists and their patrons see the practical
   benefits of ORCID, it will become the de facto standard author identifier in
   research, much as the digital object identifier (DOI) has become for papers
   and data."
   -- [<A HREF="http://dx.doi.org/10.1038/485564a">doi:10.1038/485564a</A>]['12],
   alt [<A HREF="http://www.nature.com/news/scientists-your-number-is-up-1.10740">www</A>]['12].
   [Also search for: ORCID].

%A J. Randers
%T A Global Forecast for the Next Forty Years 2052
%I ChelseaGreen
%P 304
%M JUN
%D 2012
%K book, text, c2012, c201x, c20xx, zz0612, zzPrediction, 2052, c2052, c205x,
   world, sustainability, society, resources, Limits to Growth, zz0152
%X 1st ed 2012; pb us$16; uk us isbn:1603584218; uk us isbn13:978-1603584210.
   "Forty years ago, 'The Limits to Growth' ...  limitations of planet Earth.
   It predicted that during the first half of the 21st c. the ongoing growth in
   the human ecological footprint would stop-either through catastrophic
   'overshoot and collapse'-or through well-managed 'peak and decline.'
   So, where are we now? ... The good news: we will see impressive advances in
   resource efficiency, and an increasing focus on human well-being rather than
   per capita income growth. But this change might not come as we expect ..."
   [Also search for: limits growth resources].

%A D. F. Dufty
%T How to Build an Android: The True Story of Philip K. Dick's Robotic
   Resurrection
%I HoltAndCo
%P 288
%M JUN
%D 2012
%K book, c2012, c201x, c20xx, zz0612, android, robot, head, google
%X 1st ed 2012; hb us$17; uk us isbn:0805095519; uk us isbn13:978-080509551.
   "In late Jan. 2006, a young robotocist on the way to Google HQ lost an
   overnight bag on a flight somewhere between Dallas & Las Vegas. In it was a
   fully functional head of the android replica of Philip K. Dick, cult
   science-fiction writer & counterculture guru. It has never been recovered.
   In a story that echoes some of the most paranoid fantasies of a Dick novel,
   readers get a fascinating inside look at the scientists & technology that
   made this amazing android possible. ..."     (Uhh?)

%A P. Jansen
%A P.-M. Forget
%T Predatory publishers and plagiarism prevention
%J Science
%V 336
%N 6087
%P 1380
%M JUN
%D 2012
%K c2012, c201x, c20xx, zz0612, publish, perish, science, plagiarism, ethics,
   dodgy, predatory, publisher, journal, journals, scam, misconduct, publishing,
   publish, perish, crossCheck, eBlast
%X "M. Balter ("Reviewer's Deja Vu, French sci. sleuthing uncover plagiarized
   papers ...) ... Publishers can easily prevent publishing plagiarism by
   systematically running submitted manuscripts through software such as
   CrossCheck and eBlast or by running strings of words that are
   unlikely to be repeated by chance through search engines. ..." [5 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.336.6087.1380-a">doi:10.1126/science.336.6087.1380-a</A>]['12].
   (Takes a stab at open-access (e)journals.)
   [Also search for: publish perish].

%A J. Bering
%T Why Is the Penis Shaped Like That?: And Other Reflections on Being Human
%I SciAm
%P 320
%M JUL
%D 2012
%K book, c2012, c201x, c20xx, zz0812, sex, penis, human behaviour, reproduction,
   free will, life, death, cannibalism, taboo, taboos
%X 1st ed 2012; pb us$10; uk us isbn:0374532923; uk us isbn13:978-0374532925.

%A J. Lang
%T Titanic: A Fresh Look at the Evidence by a Former Chief Inspector of
   Marine Accidents
%I RowmanAndLittlefield
%P 304
%M JUL
%D 2012
%K book, c2012, c201x, c20xx, RMS Titanic, ship wreck, shipwreck, iceberg,
   accident, sinking
%X 1st ed 2012; hb us$35; uk us isbn:1442218908; uk us isbn13:978-1442218901.
   "The sinking of the Titanic on her maiden voyage in April 1912 was one of the
   defining moments of the 20C. ...  examines the events ... from that
   completely new perspective. ... brings the standards of a 21C accident
   investigation to bear on the events ..."

%A Z. Peng
%A S. A. Freunberger
%A Y. Chen
%A P. G. Bruce
%T A reversible and higher-rate Li-O2 battery
%J Science
%V 337
%N 6094
%P 563-566
%M AUG
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0812, Li O, Li2O2, Li2 O2, LiO2, battery,
   dimethyl sulfoxide, energy density, batteries
%X "... LiO2 ... theoretically, its specific energy far exceeds ... lithium-ion
   cells. Operation of the rechargeable Li-O2 battery depends critically on
   repeated & highly reversible formation/decomposition of lithium peroxide
   (Li2O2) at the cathode upon cycling. Here, we show that this process is
   possible with the use of a dimethyl sulfoxide electrolyte & a porous gold
   electrode (95% capacity retention from cycles 1 to 100), whereas previously
   only partial Li2O2 formation/decomposition & limited cycling could occur.
   Furthermore, we present data indicating that the kinetics of Li2O2 oxidation
   on charge is approximately 10 times faster than on carbon electrodes. "
   -- [<A HREF="http://dx.doi.org/10.1126/science.1223985">doi:10.1126/science.1223985</A>]['12].

%A R. A. Kerr
%T Oil resources. Are world oil's prospects not declining all that fast?
%J Science
%V 337
%N 6095
%P 633
%A AUG
%D 2012
%K news, views, c2012, c201x, c20xx, crude oil, peak oil, Maugeri, supply,
   reserves, hydrocarbons, resources, risks, OPEC
%X "Lately the buzz in the oil patch has been all about growing abundance. New,
   more capable technology is coming on line: mining the oil sands of Alberta,
   wringing oil from beneath North Dakota by fracking, drilling down to the
   superdeep deposits beneath the Gulf of Mexico. Then, in June, a new report
   called Oil: The Next Revolution
   (report@[<A HREF="http://belfercenter.ksg.harvard.edu/publication/22144/oil.html">hrvd</A>])
   from a Harvard Uni. researcher really fanned the flames of oil optimism ...
   The ultimate arbiter will be the drill. ... Despite encouragement from high
   prices, non-OPEC crude production has been flat since 2003."
   -- [<A HREF="http://dx.doi.org/10.1126/science.337.6095.633">doi:10.1126/science.337.6095.633</A>]['12].

%A R. Bouckaert
%A et al ...
%A Q. D. Atkinson
%T Mapping the origins and expansion of the Indo-European language family
%J Science
%V 337
%N 6097
%P 957-960
%M AUG
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0812, origin, indo european, natural, language,
   human, prehistory, migration, europe, Pontic steppes, steppe, Anatolia,
   Bayesian, II
%X "... two competing hyps. for the origin of the Indo-European language family.
   The conventional view places the homeland in the Pontic steppes about 6000
   y.ago. An alt.hyp. claims that the langs. spread from Anatolia with the
   expansion of farming 8000 to 9500 y.ago. We used Bayesian phylogeographic
   approaches, together with basic vocabulary data from 103 ancient &
   contemp. Indo-European langs., to explicitly model the expansion of the
   f. & test these hyps.. ... decisive support for an Anatolian origin over a
   steppe origin. Both the inferred timing & root locn of the I.-E. lang. trees
   fit with an agricultural expn from Anatolia beginning 8000 - 9500 y.ago. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1219669">doi:10.1126/science.1219669</A>]['12].
   Also see [<A HREF="http://dx.doi.org/10.1126/science.337.6097.902">news</A>]['12].
   [Also search for: natural language evolution] and
   [also search for: Bayesian inference II].

%T Computers and Creativity
%E J. McCormack
%E M. d'Inverno
%I Springer
%P 454
%M AUG
%D 2012
%K book, text, c2012, c201x, c20xx, zz1012, dInverno, computer, creativity,
   creative, computing, visual, art, arts, sound, music, novelty, AI
%X 1st ed 2012; hb us$129; uk us isbn:364231726X; uk us isbn13:978-3642317262.
   "... introduces new theories and ideas on creativity from the perspectives
   of science and art. Featuring contributions from leading researchers,
   theorists and artists working in artificial intelligence, generative art,
   creative computing, music composition, and cybernetics, the book examines
   the relationship between computation and creativity from both analytic and
   practical perspectives. ..."

%A C. Boehm
%T Moral Origins: The Evolution of Virtue, Altruism, and Shame
%I BasicBooks
%M MAY
%D 2012
%P 426
%K book, text, c2012, c201x, c20xx, zz0912, human behaviour, social, morality,
   ethics, zzEthics, origin, virtue, altruism, cooperation, shame, groups,
   bullies
%X 1st ed 2012; us$28; uk us isbn:0465020488; uk us isbn13:978-0465020485.
   "... Tracing the development of altruism & group social control over 6 m.y.,
   Boehm argues that our moral sense is a sophisticated defense mechanism that
   enables individuals to survive & thrive in groups. One of the biggest risks
   of group living is the possibility of being punished for our misdeeds by
   those around us. Bullies, thieves, free-riders, & especially psychopaths -
   those who make it difficult for others to go about their lives - are the most
   likely to suffer this fate. Getting by requires getting along ..."

%A M. Bond
%A O. Choudary
%A S. J. Murdoch
%A S. Skorobogatov
%A R. Anderson
%T Chip and skim: Cloning EMV cards with the pre-play attack
%I Cambridge U.
%J ? crypto conf Sept. 2012 ?
%D 2012
%K TR, c2012, c201x, c20xx, zz0912, EMV, credit card, cards, chip, pin, bank,
   banking, authentication, clone, cloning, fraud, POS, ATM, preplay, attack,
   attacks, skimming, risks, security flaw, vulnerability, weakness,
   disputed transactions, refund, crime, cybercrime, Visa, MasterCard, AMEX
%X "... cards contain a chip so they can execute an authentication protocol.
   This protocol requires point-of-sale (POS) terminals or ATMs to generate a
   nonce, called the unpredictable number, for each transn to ensure it is
   fresh. ... discovered that some EMV implementers have merely used counters,
   timestamps or home-grown algs. to supply this #. This exposes them to a
   'pre-play' attack which is indistinguishable from card cloning from the
   standpoint of the logs available to the card-issuing bank, & can be carried
   out even if it is impossible to clone a card physically ...
   Card cloning is the very type of fraud that EMV was supposed to prevent. We
   describe how we detected the vulnerability, a survey methodology we dev. to
   chart the scope of the weakness, evidence from ATM & terminal experiments in
   the field, & our implementation of proof-of-concept attacks. We found flaws
   in widely-used ATMs from the largest manufacturers. We can now explain at
   least some of the increasing # of frauds in which victims are refused refunds
   by banks which claim that EMV cards cannot be cloned & that a customer
   involved in a dispute must therefore be mistaken or complicit. Pre-play
   attacks may also be carried out by malware in an ATM or POS terminal, or by
   a man-in-the-middle between the terminal & the acquirer. We explore the
   design & implementation mistakes that enabled the flaw to evade detection
   until now: shortcomings of the EMV specification, of the EMV kernel
   certification process, of implementation testing, formal analysis, or
   monitoring customer complaints. Finally we discuss countermeasures."
   -- pdf@[<A HREF="http://www.cl.cam.ac.uk/~rja14/Papers/unattack.pdf">cam</A>]['12],
   & [<A HREF="http://www.bbc.com/news/technology-19559124">bbc</A>][11/9/'12].
   [Also search for: bank card security].

%A D. Krioukov
%T The proof of innocence
%J Annals of Improbable Research
%V 18
%N 4
%P 12-14
%M JUL/AUG
%D 2012
%K jrnl, AIR, c2012, c201x, c20xx, zz0414, traffic, ticket, fine,
   stop sign, stats, statistics
%X "We show that if a car stops at a stop sign, an observer, e.g., a police
   officer, located at a certain distance perpendicular to the car trajectory,
   must have an illusion that the car does not stop, if the following three
   conditions are satisfied: (1) the observer measures not the linear but
   angular speed of the car; (2) the car decelerates and subsequently
   accelerates relatively fast; and (3) there is a short-time obstruction of
   the observer's view of the car by an external object, e.g., another car,
   at the moment when both cars are near the stop sign."
   -- 1204.0162@[<A HREF="http://arxiv.org/abs/1204.0162">arXiv</A>][14].
      ("A way to fight your traffic tickets. The paper was awarded a special
      prize [AIR] of $400 that the author did not have to pay to the state of
      California.  In view of enormous, extremely surprising and completely
      unexpected public interest to this work, we have added an appendix
      answering the two most common questions.")

%A D. W. Dunstan
%A B. Howard
%A G. N. Healy
%A N. Owen
%T Too much sitting - a health hazard
%J Diabetes Res. & Clinical Practice
%V 97
%N 3
%P 368-376
%M SEP
%D 2012
%K jrnl, c2012, c201x, c20xx, zz1115, human, health, risk, risks, work,
   desk, job, exercise, sit, sitting, television, TV, viewing time, death,
   mortality
%X "... prolonged sitting has been engineered into our lives across many
   settings ... new evidence that too much sitting (also known as sedentary
   behavior - which involves v.low energy expenditure, such as television
   viewing & desk-bound work) is [unhealthy], inc. cardio-metabolic risk
   biomarkers, type 2 diabetes & premature mortality. ... associations remain
   even after accounting for time spent in leisure time physical activity. ...
   evidence from epidemiological & experimental studies that makes a persuasive
   case that too much sitting should now be considered an important stand-alone
   component of the physical activity & health eqn ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.diabres.2012.05.020">doi:10.1016/j.diabres.2012.05.020</A>]['15].

%T Honorary Authorship
%J Science
%V 337
%N 6101
%P 1453
%M SEP
%D 2012
%K buzz, news, c2012, c201x, c20xx, zz0912, publish, perish, ethics, zzEthics,
   publications, grants, academic research, academia, scientific, guest author,
   authors, coercive authorship
%X "... Honorary authorship remains common; researchers add the names of
   prominent scientists to boost their paper's credibility, & senior scientists
   demand that their names be added to the work of younger researchers. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.337.6101.1453-a">doi:10.1126/science.337.6101.1453-a</A>]['12].
   [Also search for: publish perish].

%T Losing Humanity: The Case against Killer Robots
%I Human Rights Watch
%P 50
%M NOV
%D 2012
%K HRW, report, c2012, c201x, c20xx, zz0313, robot, robots, drone, drones, USA,
   mil, military, ethics, accountability, law, AI, autonomous weapon system,
   zzLaw, zzEthics, weapons, systems, Taranis, SGR, SGR1
%X isbn:1564329852.
   "This 50-page report outlines concerns about these fully autonomous weapons,
   which would inherently lack human qualities that provide legal and non-legal
   checks on the killing of civilians. In addition, the obstacles to holding
   anyone accountable for harm caused by the weapons would weaken the law's
   power to deter future violations."
   -- [<A HREF="http://www.hrw.org/reports/2012/11/19/losing-humanity-0">www</A>]['13].

%A X. Dumusque
%A et al ...
%A S. Udry
%T An Earth-mass planet orbiting α Centauri B
%J Nature
%V 491
%P 207-211
%M NOV
%D 2012
%K jrnl, c2012, c201x, c20xx, astronomy, exo-planet, exoplanet, alpha centauri
%X "Exoplanets down to the size of Earth have been found, but not in the
   habitable zone - that is, at a distance from the parent star at which water,
   if present, would be liquid. ... Here we report the detection of an
   Earth-mass planet orbiting our neighbour star α Centauri B, a member
   of the closest stellar system to the Sun. The planet has an orbital period of
   3.236 days and is about 0.04 astronomical units from the star (one
   astronomical unit is the Earth-Sun distance)."    online 18/10/'12)
   -- [<A HREF="http://dx.doi.org/10.1038/nature11572">doi:10.1038/nature11572</A>]['12].
   (Alpha Centauri is "only" ~4.4 light years from earth.)
   [Also search for: exoplanet].

%A E. Martin-Lopez
%E et al ...
%A J. L. O'Brien
%T Experimental realization of Shor's quantum factoring algorithm using qubit
   recycling
%J Nature Photonics
%V ?
%P ?-?
%M OCT
%D 2012
%K jrnl, c2012, c201x, c20xx, zz1012, Shor's algorithm, quantum computing,
   qubit, recycle, photon, factor, prime, primes, oBrien
%X "... demonstrate a scalable version of Shor's alg. in which the n-qubit
   control register is replaced by a single qubit that is recycled n times: the
   total # of qubits is one-third of that req. in the std protocol. Encoding
   the work reg. in higher-dimensional states, we implement a two-photon
   compiled alg. to factor N=21. The alg. output is distinguishable from
   noise, in contrast to prev.demonstrations. These results point to larger-
   -scale implementations of Shor's alg. by harnessing scalable resource
   reductions applicable to all physical architectures." (online 21 Oct '12.)
   -- [<A HREF="http://dx.doi.org/10.1038/nphoton.2012.259">doi:10.1038/nphoton.2012.259</A>]['12]  (N=21).
   [Also search for: Shor algorithm quantum].

%A E. Marshall
%T Want to tear down your rival? Here's what might work best
%J Science
%V 338
%N 6106
%P 465
%K news, views, politics, c2012, c201x, c20xx, zz1012, Krupnikov, political,
   ad, advert, negative, attack, opponent, election, US, USA, propaganda
%X "... If you want to attack your political opponent, do it after voters have
   made up their minds.  That's the conclusion of a new and controversial study
   on the impact of negative advertising in political campaigns. October is the
   critical month for election propaganda, says Yanna Krupnikov ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.338.6106.465">doi:10.1126/science.338.6106.465</A>]['12].

%A M. Pasta
%A C. D. Wessells
%A R. A. Huggins
%A Y. Cui
%T A high-rate and long cycle life aqueous electrolyte battery for
   grid-scale energy storage
%J NatureComms
%V 3
%N 1149
%M OCT
%D 2012
%K c2012, c201x, c20xx, battery, technology, batteries, high power, energy,
   storage, grid, carbon polypyrrole anode, electrodes
%X "... demonstrate a new type of safe, fast, inexpensive, long-life aqueous
   electrolyte battery, which relies on the insertion of potassium ions into a
   copper hexacyanoferrate cathode & a novel activated carbon/polypyrrole
   hybrid anode. The cathode reacts rapidly with very little hysteresis. The
   hybrid anode uses an electrochemically active additive to tune its potential.
   This high-rate, high-efficiency cell has a 95% round-trip energy efficiency
   when cycled at a 5C rate, & a 79% energy efficiency at 50C. It also has
   zero-capacity loss after 1,000 deep-discharge cycles."
   -- [<A HREF="http://dx.doi.org/10.1038/ncomms2139">doi:10.1038/ncomms2139</A>]['12].
   (auths@Dept of Materials Sci & Eng, Stanford.)

%A P. J. Nahin
%T The Logician and the Engineer: How George Boole and Claude Shannon Created
   the Information Age
%I PrincetonUP
%P 244
%M OCT
%D 2012
%K book, text, c2012, c201x, c20xx, zz1112, history, science, Boole, Shannon,
   Boolean logic, bool, technology, IT
%X 1st ed 2012; hb us$15; uk us isbn:0691151008; uk us isbn13:978-0691151007.
   "... How did a system of mathematics established in the Victorian era become
   the basis for such incredible technological achievements a century later?
   ... [PN] combines engaging problems and a colorful historical narrative to
   tell the remarkable story of how two men in different eras ..."
   [George Boole (1815-1864), Claude Shannon (1916-2001).]

%A M. Mobbs
%T Sustainable Food
%I Choice Books
%M NOV
%D 2012
%K book, text, c2012, c201x, c20xx, sustainability, green, self sufficiency,
   water, food, Australia, community, garden, vegetables, meat, chooks
%X 1st ed 2012, pb au$45; isbn:1920705546; isbn13:978-1920705541.
   "After renovating his inner-city Sydney terrace and making it almost entirely
   self-sufficient in energy, water and waste disposal, MM realised his house
   was sustainable, but he wasn't. While his house saves 100,000 litres of dam
   water a year, the same amount of water is used to produce ten days' worth of
   food for the average Australian. ..."
   [Also search for: Mobbs book].

%A J. Sheffield
%A E. F. Wood
%A M. L. Roderick
%T Little change in global drought over the past 60 years
%J Nature
%V 491
%P 435-438
%M NOV
%D 2012
%K jrnl, c2012, c201x, c20xx, zz1112, weather, stats, climate, drought,
   rainfall, precipitation, change, Palmer Drought Severity Index, PDSI
%X "Drought is expected to increase in frequency & severity in the future as
   a result of climate change ... Here we show that the previously reported
   increase in global drought is overestimated because the PDSI uses a
   simplified model of potential evaporation that responds only to changes in
   temp. & thus responds incorrectly to global warming in recent decades. More
   realistic calcns, based on the underlying physical principles that take into
   account changes in available energy, humidity & wind speed, suggest that
   there has been little change in drought over the past 60 years. The results
   have implications for how we interpret the impact of global warming on the
   hydrological cycle & its extremes, & may help to explain why palaeoclimate
   drought reconstructions based on tree-ring data diverge from the PDSI-based
   drought record in recent years."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11575">doi:10.1038/nature11575</A>]['12].

%A J. Wilkins
%A B. J. Schoville
%A K. S. Brown
%A M. Chazan
%T Evidence for early hafted hunting technology
%J Science
%V 338
%N 6109
%P 942-946
%M NOV
%D 2012
%K jrnl, c2012, c201x, c20xx, zz1112, early human, evolution, hominins,
   hominid, Neandertals, Africa, KP1, tool, tools, making, spear, spears,
   tips, stone, working
%X "...  Multiple lines of evidence indicate that ~500,000-year-old stone points
   from the archaeological site of Kathu Pan 1 (KP1), S.Africa, functioned as
   spear tips. KP1 points exhibit fracture types diagnostic of impact.
   Modification near the base of some pts is consistent with hafting ... data
   indicate that the pts could function well as spear tips. Shape analysis
   demonstrates that the smaller retouched points are as symmetrical as larger
   retouched points, which fits expectations for spear tips. The dist'n of edge
   damage is similar to that in an experimental sample of spear tips & is
   inconsistent with expectations for cutting or scraping tools. Thus, early
   humans were manufacturing hafted multicomponent tools ~200,000 years earlier
   than previously thought. "
   -- [<A HREF="http://dx.doi.org/10.1126/science.1227608">doi:10.1126/science.1227608</A>]['12].

%A D. Yeomans
%T Near-Earth Objects: Finding Them Before They Find Us
%I PrincetonUP
%P 192
%M NOV
%D 2012
%K book, text, c2012, c201x, c20xx, zz1212, SpaceGuard, astronomy, solar system,
   asteroid, comet, near earth object, NEO, impact, mass extinction, tracking
%X 1st ed 2012; hb us$16;
   "Of all the natural disasters that could befall us, only an Earth impact by
   a large comet or asteroid has the potential to end civilization in a single
   blow. Yet these near-Earth objects also offer tantalizing clues to our solar
   system's origins, and someday could even serve as stepping-stones for space
   exploration. ..."

%A H. P. de Vladar
%T The game of active search for extra-terrestrial intelligence: breaking the
   'Great Silence'
%J Int. J. of Astrobiology
%V ?
%P ?-?
%M NOV
%D 2012
%K jrnl, c2012, c201x, c20xx, alien, intelligence, life, extraterrestrial,
   universe, SETI, active, risk, prisoner's dilemma, prisoners
%X "... have engaged in an active messaging only rarely. This suggests ...
   that if other civilizations exist & take a similar approach to ours, namely
   listening but not broadcasting, the result is a silent universe. A simple
   game theoretical model, the prisoner's dilemma, explains this sitn: each
   player (civilization) can passively search (defect), or actively search &
   broadcast (cooperate). In order to maximize the payoff (or, equivalently,
   minimize the risks) the best strategy is not to broadcast. In fact, the
   active search has been opposed on the basis that it might be dangerous to
   expose ourselves. ... I develop a game-theoretical f'work where civilizations
   can be of different types, & explicitly apply it to a sitn where societies
   are either interested in establishing a two-way commn or belligerent & in
   urge to exploit ours. ... gives a quantitative soln (a mixed-strategy), which
   is how frequent we should perform the active SETI. ... is roughly
   proportional to the inverse of the risk, & can be [v.]small. However, given
   the immense amount of stars being scanned, it supports active SETI. The model
   is compared with simulations, & the possible actions are evaluated through
   the San Marino scale, measuring the risks of messaging."  (online 11/2012)
   -- [<A HREF="http://dx.doi.org/10.1017/S1473550412000407">doi:10.1017/S1473550412000407</A>]['12].
   [Also search for: prisoners dilemma] and
   [also search for: extraterrestrial life].

%A J. R. Flynn
%T Are We Getting Smarter?: Rising IQ in the Twenty-First Century
%I CUP
%D 2012
%K book, text, CUP, c2012, c201x, c20xx, zz0213, human, IQ, 20C, 21C,
   intelligence, smart, clever, test, tests, result, results, score, scores,
   increase, increasing, change, changing, trend, psychometrics, Flynn effect
%X 1st ed 2012; pb us$15; uk us isbn:1107609178; uk us isbn13:978-1107609174.
   "Q gains are persisting into the 21st century, particularly in the developing
   world: the 'Flynn effect' marches on! ... aims to make sense of the continued
   rise in IQ scores and considers what this tells us about our intelligence,
   our minds and society."
   Also see a [<A HREF="http://dx.doi.org/10.1126/science.1232678">review</A>]['13].
   [Also search for: human intelligence IQ].

%A J. But
%A R. Shobbrook
%T Web - based lecture technologies and their effects on student performance
%J AAEE Conf.
%M DEC
%D 2012
%K conf, AAEE, c2012, c201x, c20xx, zz0714, teaching, education, university,
   learning, lecture, lectures, audio, recordings, student performance,
   internet, web, www, WBLT, Swinburne
%X "Pressure to use Web - Based Learning Technologies lecture recordings (WBLT)
   has been placed on lecturers (Chang 2007) with the assumption that WBLT is
   beneficial to student learning. Prior to 2007, most available research into
   the use of WBLT relied on student surveys. Little research had been conducted
   into the impact of using WBLT on student performance ... Our results showed
   that whenever WBLT was available there were no positive effects on the
   overall exam performance.  For some groups of students, negative effects were
   observable.  These results are similar to the findings of subsequent research
   by others (Williams, et al. 2012; McNulty, 2011; Figlio, 2010).  ..."
   -- pdf@[<A HREF="http://www.aaee.com.au/conferences/2012/documents/abstracts/aaee2012-submission-111.pdf">www</A>]['14].

%A J. Tollefson
%T Methane leaks erode green credentials of natural gas
%J Nature
%V 493
%N 7430
%P ?-?
%M JAN
%D 2013
%K news, c2013, c201x, c20xx, zz0113, greenhouse gas, gases, climate change,
   natural gas, methane, coal seam, leak, fracking, fugitive emissions, energy,
   resources
%X "Scientists are once again reporting alarmingly high methane emissions from
   an oil and gas field, underscoring questions about the environmental benefits
   of the boom in natural-gas production that is transforming the US energy
   system. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/493012a">doi:10.1038/493012a</A>]['12].

%A D. R. Powell
%A T. Seeman
%T VAGUE: a graphical user interface for the Velvet assembler
%J J. Bioinformatics
%V 29
%N 2
%P 264-265
%D 2014
%K jrnl, MolBio, c2013, c201x, c20xx, zz0115, Velvet, sequence assembly,
   assembler, DNA, Torsten, VBC, MonashUni
%X "... Most of the problems experienced by new users of Velvet revolve around
   constructing syntactically & semantically correct command lines, getting
   input files into acceptable formats & assessing the output. ... present
   Velvet Assembler Graphical User Environment (VAGUE), a multi-platform
   graphical front-end for V.. VAGUE aims to make seq. assembly accessible to a
   wider audience & to facilitate better usage amongst existing users of V.."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bts664">doi:10.1093/bioinformatics/bts664</A>]['14].

%A S. Wilson
%T Legal limits to data re-identification
%J Science
%V 339
%N 6120
%P 647
%M FEB
%D 2013
%K views, c2013, c201x, c20xx, zz0213, data, privacy, protection, identity,
   reidentify, reidentifying, identify, law, legal, OECD Privacy Principles
%X "... The OECD Privacy Principles are enacted in over 80 countries worldwide
   -- [<A HREF="http://oecdprivacy.org">www</A>]. Privacy Principle No.1 states:
   'There should be limits to the collection of personal data and any such data
   should be obtained by lawful and fair means and, where appropriate, with the
   knowledge or consent of the data subject.' ... re-identifying the information
   later signifies a new collection. The new collection of personal information
   requires its own consent ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.339.6120.647-a">doi:10.1126/science.339.6120.647-a</A>]['13].

%A K. Kupferschmidt
%A G. Vogel
%T Plagiarism hunters take down research minister
%J Science
%V 339
%N 6121
%P 747
%M FEB
%D 2013
%K news, c2013, c201x, c20xx, science, academic, plagiarism, ethics, politics,
   germany, germany, minister, Annette Schavan, University of Dusseldorf
%X "When Annette Schavan, Germany's minister for sci. & education, resigned on
   9 February, even politicians from opposition parties called the move
   'tragic.' She is the latest in a string of officials here who have stepped
   down amid plagiarism allegations. But Schavan's case, centering on her 1980
   dissertation in education studies, was less clear-cut than others, & it has
   opened up a debate in German academia. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.339.6121.747">doi:10.1126/science.339.6121.747</A>]['13].
   [Also search for: plagiarism].

%A A. M. Childs
%A D. Gosset
%A Z. Webb
%T Universal computation by multiparticle quantum walk
%J Science
%V 339
%N 6121
%P 791-794
%M FEB
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0213, quantum, computer, computing,
   random walk
%X "A quantum walk is a time-homogeneous quantum-mechanical process on a graph
   defined by analogy to classical random walk. The quantum walker is a particle
   that moves from a given vertex to adjacent vertices in quantum superposition.
   We consider a generalization to interacting systems with more than one walker
   such as the Bose-Hubbard model & systems of fermions or distinguishable
   particles with nearest-neighbor interactions, & show that multiparticle
   quantum walk is capable of universal quantum computation. Our construction
   could, in principle, be used as an architecture for building a scalable
   quantum computer with no need for time-dependent control."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1229957">doi:10.1126/science.1229957</A>]['13].

%A A. Vaks
%A et al ...
%A G. M. Henderson
%T Speleothems reveal 500,000-year history of Siberian permafrost
%J Science
%V ?
%P ?-?
%M FEB
%D 2013
%K jrnl, c2013, c201x, c20xx, methane, release, global warming, climate change,
   greenhouse gas, CH4, carbon, gases, permafrost, thaw, thawing,
   MIS, MIS11, Speleothem
%X "Soils in permafrost regions contain twice as much carbon as the atmosphere
   ... we date periods of speleothem growth in a north-south transect of caves
   in Siberia to reconstruct the history of permafrost in past climate states.
   Speleothem growth is restricted to full interglacial conditions in all
   studied caves. In the northernmost cave (at 60N), no growth has occurred
   since Marine Isotopic Stage (MIS) 11. Growth at that time indicates that
   global climates only slightly warmer than today are sufficient to thaw
   significant regions of permafrost. " [online 21 Feb 2013].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1228729">doi:10.1126/science.1228729</A>]['13].

%A A. A. Anderson
%A D. Brossard
%A D. A. Scheufele
%A M. A. Xenos
%A P. Ladwig
%T The "nasty effect:" Online incivility and risk perceptions of
   emerging technologies
%J J. Computer-Mediated Communication
%V ?
%P ?-?
%D 2013
%K jrnl, c2013, c201x, c20xx, zz1013, social media, web, www, blog, comment,
   blogs, comments, blogging, online, articles, trolls, spambot, spambots,
   aggressive, aggression, nasty, rude, rudeness, perception
%X "Uncivil discourse is a growing concern in American rhetoric, & this trend
   has expanded beyond traditional media to online sources, such as audience
   comments. Using an experiment given to a sample representative of the U.S.
   population, we examine the effects online incivility on perceptions toward a
   particular issue - namely, an emerging technology, nanotechnology. We found
   that exposure to uncivil blog comments can polarize risk perceptions of
   nanotechnology along the lines of religiosity & issue support."
   -- [<A HREF="http://dx.doi.org/10.1111/jcc4.12009">doi:10.1111/jcc4.12009</A>]['13].
   (Also see [<A HREF="http://www.theguardian.com/technology/2013/sep/25/popular-science-youtube-comments">The_G.</A>], [<A HREF="http://www.bbc.co.uk/news/technology-24240038">bbc</A>], 9/2013.)
   [Also search for: nasty social media].

%A L. Schneps
%A C. Colmez
%T Math on Trial: How Numbers Get Used and Abused in the Courtroom
%I BasicBooks
%P 272
%M MAR
%D 2013
%K book, c2013, c201x, c20xx, zz0313, law, court, legal, trial, evidence,
   zzLaw, expert witness, probability, statistics, stats, injustice, justice,
   Sally Clark
%X 1st ed 2013; hb us$16; uk us isbn:0465032923; uk us isbn13:978-0465032921.
   "... stories of Sally Clark, who was accused of murdering her children by
   a dr with a faulty sense of calcn; of 19C tycoon Hetty Green, whose
   dispute over her aunt's will became a signal case in the forensic use of
   mathematics; and of the case of Amanda Knox, in which a judge's
   misunderstanding of probability led him to discount critical evidence - which
   might have kept her in jail. Offering a fresh angle on cases from the
   19C Dreyfus affair to the murder trial of Dutch nurse Lucia de Berk ..."

%A S. A. Marcott
%A J. D. Shakun
%A P. U. Clark
%A A. C. Mix
%T A reconstruction of regional and global temperature for the past 11,300 years
%J Science
%V 339
%N 6124
%P 1198-1201
%M MAR
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0313, climate change, global warming,
   temperature, record, historical, ice age, ages, holocene, IPCC
%X "Surface temp. reconstructions of the past 1500 y. suggest that recent
   warming is unprecedented in that time. ... provide a broader perspective by
   recon. regional & global temp. anomalies for the past 11,300 y. from 73
   globally distributed records. Early Holocene (10,000 to 5000 y. ago) warmth
   is followed by ~0.7C cooling through the middle to late Holocene (< 5000 y.
   ago), culminating in the coolest temps. of the Holocene during the Little
   Ice Age, about 200 y. ago. This cooling is largely assoc. with ~2C change in
   the N.Atlantic. Current global temps. of the past decade have not yet
   exceeded peak interglacial values but are warmer than during ~75% of the
   Holocene ... . Intergovernmental Panel on Climate Change model projections
   for 2100 exceed the full distribution of Holocene temp. under all plausible
   greenhouse gas emission scenarios."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1228026">doi:10.1126/science.1228026</A>]['13].

%A K. Weaver
%T Lab life: Scientists are snobs
%J Nature
%V 495
%P 167-168
%M MAR
%D 2013
%K comment, views, c2013, c201x, c20xx, zz0313, publish, perish, grant,
   funding, citations, citing, KPI, KPIs, rank, ranking, impact factor
%X "It is a mistake to dismiss the people and projects coming out of
   lesser-known institutions, argues Keith Weaver - they have strengths too ...
   Of potentially greater impact is the effect this scientific snobbery has on
   citation practices. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/495167a">doi:10.1038/495167a</A>]['13], amen.

%A L. Fortnow
%T The Golden Ticket: P, NP, and the Search for the Impossible
%I PrincetonUP
%P 188
%M MAR
%D 2013
%K book, text, c2013, c201x, c20xx, zz0413, algorithm, complexity, P, NP, NPC
%X 1st ed 2013; hb us$16; uk us isbn:0691156492; uk us isbn13:978-0691156491.
   "The P-NP problem is the most important open problem in computer science, if
   not all of mathematics. ... a nontechnical intr. to P-NP, its rich history,
   and its algorithmic implications for everything we do with computers and
   beyond. ... traces how the problem arose during the Cold War on both sides of
   the Iron Curtain, and gives examples of the problem from a variety of
   disciplines, inc. economics, physics, and biology. He explores problems that
   capture the full difficulty of the P-NP dilemma, from discovering the
   shortest route through all the rides at Disney World to finding large groups
   of friends on Facebook."

%A A. Acerbi
%A V. Lampos
%A P. Garnett
%A R. A. Bentley
%T The expression of emotions in 20th century books
%J PLoS One
%V 8
%N 3
%P e59030
%M MAR
%D 2013
%K jrnl, eJrnl, c2013, c201x, c20xx, zz0413, book, English, American, 20C,
   literature, word, words, emotion, emotional, mood, moods, happiness, sadness,
   happy, sad, frequency, frequencies, counts, stats
%X "We report here trends in the usage of 'mood' words, ... carrying emotional
   content, in 20C English language books, using the data set provided by Google
   that includes word freqs. in ~4% of all books published up to the year 2008.
   ... evidence for distinct historical periods of +ve and -ve moods, underlain
   by a general decrease in the use of emotion-related words through time.
   ... American English has become decidedly more 'emotional' than British
   English in the last half-century, as a part of a more general increase of
   the stylistic divergence between the two variants of English language."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0059030">doi:10.1371/journal.pone.0059030</A>]'[13].

%A J. M. Collins
%T The New World Champion Paper Airplane Book: Featuring the Guinness World
   Record-Breaking Design, with Tear-Out Planes to Fold and Fly
%I TenSpeed
%P 160
%M MAR
%D 2013
%K book, c2013, c201x, c20xx, zz0413, paper plane, airplane, record, distance,
   greatest
%X 1st ed 2013; pb us$14; uk us isbn:1607743884; uk us isbn13:978-1607743880.
   "On Feb. 26, 2012, my paper airplane design, Suzanne, flying 226 feet and
   10 inches, broke the old paper airplane world record for distance by
   19 feet and 6 inches. ... The old mark had stood for nine years. ..."
   (Also see [<A HREF="http://www.youtube.com/watch?v=wedcZp07raE">u-bend</A>].)

%A D. L. Herbert
%A A. G. Barnett
%A N. Graves
%T Funding: Australia's grant system wastes time
%J Nature
%V 495
%P 314
%M MAR
%D 2013
%K views, c2013, c201x, c20xx, zz00413, peer review, publish perish, ARC, NHMRC,
   grant, grants, funding, stats, analysis, Australia, au, QUT, University,
   science, research, KIP, KPIs, funding, time, waste, applications,
   quote, quotable
%X "We found that scientists in Australia spent more than five centuries' worth
   of time preparing research-grant proposals for consideration by the largest
   funding scheme of 2012. Because just 20.5% of these applications were
   successful, the equivalent of some four centuries of effort returned no
   immediate benefit to researchers and wasted ..."
   -- [<A HREF="http://dx.doi.org/10.1038/495314d">doi:10.1038/495314d</A>]['13].
   [Also search for: research funding]  and [also search for: publish perish].

%A M. McCullogh
%T Ambient Commons: Attention in the Age of Embodied Information
%I MITpress
%P 368
%M MAR
%D 2013
%K book, text, c2013, c201x, c20xx, zz0513, internet, www, connected, society
%X 1st ed 2013; hb us$18; uk us isbn:0262018802; uk us isbn13:978-0262018807.
   "... Sensors, processors, & memory ... smart phones but also built into
   everyday objects. Amid this flood, your attention practices matter more than
   ever. ... it is worth remembering that underneath all these augmentations &
   data flows, fixed forms persist, ... Mc. describes what he calls the Ambient:
   an increasing tendency to perceive information superabundance whole, where
   individual signals matter less & at least some mediation assumes
   inhabitable form. ..."

%A M. R. Allen
%A J. F. B. Mitchell
%A P. A. Stott
%T Test of a decadal climate forecast
%J Nature Geoscience
%V 6
%P 243-244
%M MAR
%D 2013
%K jrnl, c2013, c201x, c20xx, anthropogenic climate change, global warming,
   simulation, prediction, zzPrediction, testing, verification, IPCC, zz0136
%X "...  Here we assess one of the first probabilistic climate forecasts with a
   full uncertainty assessment that was based on climate models & data up to
   1996. Using observations of global temp. over the ensuing 16 y., we find that
   the original forecast is performing sig. better than a hypothetical alt.
   based on the assumption that decade-to-decade temp. fluctuations consist of a
   random walk, that is, a seq. of random fluctuations with no externally driven
   warming trend. The original climate forecast also outperforms a very simple
   interpretation of the climate models used for the latest Assessment of the
   Intergovernmental Panel on Climate Change (IPCC), supporting the conclusions
   of previous assessments that the spread of such an ensemble is not, on its
   own, an adequate measure of forecast uncertainty ..."
   -- [<A HREF="http://dx.doi.org/10.1038/ngeo1788">doi:10.1038/ngeo1788</A>]['13].
   Original prediction was made in
      M.R.Allen, P.A.Stott, J.F.Mitchell, R.Schnur, T.L.Delworth,
      Quantifying the uncertainty in forecasts of anthropogenic climate change,
      Nature 407(6804), pp.617-620, Oct 2000.
      -- [<A HREF="http://dx.doi.org/10.1038/35036559">doi:10.1038/35036559</A>]['13].
   (Also check back after 2036.)

%A P. Sabin
%T The Bet: Paul Ehrlich, Julian Simon, and Our Gamble over Earth's Future
%I YaleUP
%P 320
%M MAR
%D 2013
%K book, c2013, c201x, c20xx, zz0913, population bomb, growth, sustainability,
   limits, growth, food supply, metal prices, earth, resources, Ehrlich, Simon
%X 1st ed 2013; hb us$17; uk us isbn:0300176481; uk us isbn13:978-0300176483.
   "In 1980, the iconoclastic economist Julian Simon challenged celebrity
   biologist Paul Ehrlich to a bet. Their wager on the future prices of five
   metals captured the public's imagination as a test of coming prosperity or
   doom. Ehrlich, author of the landmark book The Population Bomb ..."
   [Also search for: limits growth resources].

%A J. Bonnet
%A P. Yin
%A M. E. Ortiz
%A P. Subsoontorn
%A D. Endy
%T Amplifying genetic logic gates
%J Science
%V ?
%P ?-?
%M ?
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0412, biological computing, logic gate, gates,
   transcriptor, transcriptors, nand, xor, RNA polymerase
%X "... developed a three-terminal device architecture, termed the transcriptor,
   that uses bacteriophage serine integrases to control the flow of RNA
   polymerase along DNA. Integrase-mediated inversion or deletion of DNA
   encoding transcription terminators or a promoter modulate transcription
   rates. We realize permanent amplifying AND, NAND, OR, XOR, NOR, & XNOR gates
   actuated across common control signal ranges & sequential logic supporting
   autonomous cell-cell communication of DNA encoding distinct logic gate
   states. The single-layer digital logic architecture developed here enables
   engineering of amplifying logic gates to control transcription rates within
   & across diverse organisms."  (online Mar 2013.)
   -- [<A HREF="http://dx.doi.org/10.1126/science.1232758">doi:10.1126/science.1232758</A>]['13].

%A S. Boixo
%A T. F. Ronnow
%A S. V. Isakov
%A Z. Wang
%A D. Wecker
%A D. A. Lidar
%A J. M. Martinis
%A M. Troyer
%T Quantum annealing with more than one hundred qubits
%J arXiv
%M APR
%D 2013
%K TR, arXiv, c2013, c201x, c20xx, zz0513, adiabatic, quantum computing,
   computer, Dwave, D wave, One, Two, Dwave2, qubit, qbit, annealing, annealer
%X "... A quantum annealer, in particular, finds solutions to hard optimisation
   problems by evolving a known initial config. towards the ground state of a
   Hamiltonian that encodes an opt'n problem. ... present results from
   experiments on a 108 qubit D-Wave One device based on superconducting flux
   qubits. The correlations between the device & a simulated q.annealer
   demonstrate that the device performs quantum annealing: unlike classical
   thermal annealing it exhibits a bimodal sep'n of hard & easy problems, with
   small-gap avoided level crossings characterizing the hard problems. To assess
   the compnl power of the q.annealer we compare it to optimised classical algs.
   We discuss how quantum speedup could be detected on devices scaled to [more]
   qubits where the limits of classical algorithms are reached."
   -- 1304.4595@[<A HREF="http://arxiv.org/abs/1304.4595">arXiv</A>]['13].
   (Also see [<A HREF="http://www.bbc.co.uk/news/science-environment-22554494">bbc</A>][16/5/2013] & [<A HREF="http://www.bbc.com/future/story/20130516-big-bets-on-quantum-computers">2</A>][16/5/2013], and
   Nature@[<A HREF="http://dx.doi.org/10.1038/498286a">doi:10.1038/498286a</A>][20/6/2013].)
   [Also search for: Dwave quantum computing].

%A S. K. Pell
%T Jonesing for a privacy mandate, getting a technology fix -- Doctrine to
   follow
%J N. Carolina J. of Law and Tech.
%V 14
%N 2
%M MAY
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0913, Jones Court, Fourth Amendment, law, US,
   USA, privacy, government, power, NSA, GCHQ, encryption, backdoor, back door,
   cyber security, email, interception, Intelligence, spy, spying, going dark,
   Edgehill, Tempora, Bullrun, MANASSAS, cell phone, mobile phones, internet,
   state surveillance
%X "While the Jones Court held unanimously that the government's use of a GPS
   device to track Antoine Jones' vehicle for 28 days was a Fourth Amendment
   search, the Justices disagreed on the facts & rationale supporting the
   holding. ... the majority opinion does nothing to constrain gvmt use of other
   tracking technologies, including cell phones, which merely involve the
   transmission of electronic signals without physical trespass. ...  the Jones
   opinions leave us still jonesing for a privacy mandate. As of the writing of
   this Article, Congress has not been successful in passing legislation that
   would regulate gvmt use of tracking technologies. A third regulator of g.
   power has emerged, however, in the form of technology itself, specifically
   in new(ish) methods an individual or group of individuals can use to make it
   more difficult, in some cases perhaps impossible, for law enforcement to
   obtain the information it seeks. ... Moreover, at a time when cybersecurity
   is a national security priority & recommended 'best practices' include the
   use of encryption technologies to protect, among other things, US
   intellectual property, law enforcement is likely to face continued instances
   of 'Going Dark' as it attempts to intercept communications in the face of the
   increasing availability & use of encryption technologies. ..."
   -- [<A HREF="http://ssrn.com/abstract=2262397">www</A>]['13],
      biog@[<A HREF="http://www.netcaucus.org/biography/stephanie-pell.shtml">netcaucus.org</A>]['13].
   auth@Stanford Law School Center for Internet and Society.
   (Also see the G. [<A HREF="http://www.theguardian.com/world/2013/sep/05/nsa-gchq-encryption-codes-security">www</A>][6/9/2013],
   -- [<A HREF="http://www.theguardian.com/world/the-nsa-files">indx</A>]['13].)

%A W. J. Borucki
%A et al ...
%A J. N. Winn
%T Kepler-62: A five-planet system with planets of 1.4 and 1.6 Earth radii in
   the habitable zone
%J Science
%V 340
%N 6132
%P 587-590
%M MAY
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0513, astronomy, exoplanet, exoplanets,
   exo planet, planets, space, Goldilocks, star, Kepler 62, Kepler62
%X "... detection of five planets - Kepler-62b, c, d, e, and f - of size 1.31,
   0.54, 1.95, 1.61 & 1.41 Earth radii (R*), orbiting a K2V star at periods of
   5.7, 12.4, 18.2, 122.4, & 267.3 days, resp.. The outermost planets,
   Kepler-62e & -62f, are super-Earth-size (1.25 R* < planet radius <= 2.0 R*)
   planets in the habitable zone of their host star, resp. receiving 1.2+/-0.2
   times & 0.41+/- 0.05 times the solar flux at Earth's orbit. Theor.models of
   Kepler-62e & -62f for a stellar age of ~7billion y. suggest that both planets
   could be solid, either with a rocky composition or composed of mostly solid
   water in their bulk."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1234702">doi:10.1126/science.1234702</A>]['13].
   [Also search for: exoplanet].

%A J. Vrigham-Grette
%A et al ...
%A U. Herzschuh
%T Pliocene warmth, polar amplification, and stepped pleistocene cooling
   recorded in NE Arctic Russia
%J Science
%V ?
%P ?-?
%M MAY
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0513, climate change, CO2, greenhouse gas,
   gasses, levels, global warming, earth, sea-level, temperature,
   Lake El'gygytgyn, Elgygytgyn, Russia, Pliocene, Pleistocene, forcing
%X "... Evidence from Lake El'gygytgyn, NE Arctic Russia, shows that 3.6-3.4
   million y. ago, summer temps. were ~8C warmer than today when pCO2 was ~400
   ppm. Multiproxy evidence suggests extreme warmth & polar amplification during
   the middle Pliocene, sudden stepped cooling events during the Pliocene-
   -Pleistocene transition, & warmer than present Arctic summers until ~2.2Ma,
   after the onset of N.Hemispheric glaciation. Our data are consistent with
   sea-level records & other proxies indicating that Arctic cooling was
   insufficient to support large-scale ice sheets until the early Pleistocene."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1233137">doi:10.1126/science.1233137</A>]['13].
   [NB. The CO2 level in 2013 is again ~400ppm.]

%A M. M. Wilde
%T Quantum Information Theory
%I CUP
%M JUN
%D 2013
%K book, text, CUP, c2013, c201x, c20xx, zz0613, quantum theory, physics,
   computing, Qbism, entanglement, Holevo, superactivation
%X 1st ed 2013; hb us$68; uk us isbn:1107034256; uk us isbn13:978-1107034259.
   "... for graduate-level courses ... tools nec. for understanding
   important results in q. I. theory, including capacity thms for classical,
   entanglement-assisted, private & quantum comm'n. [&] recent developments such
   as superadditivity of private, coherent & Holevo info., & the superactivation
   of quantum capacity. ..."
   [Also search for: Qbism physics].

%A C. McGeoch
%A C. Wang
%T Experimental evaluation of an adiabatic quantum system for combinatorial
   optimization
%J Int. Conf. on Computing Frontiers
%I ACM
%P ?-?
%M MAY
%D 2013
%K conf, CF2013, c2013, c201x, c20xx, zz0513, quantum computing, computer,
   annealing, Dwave, D-wave,
%X "... an experimental study of a novel computing system (alg. + platform)
   that carries out quantum annealing, a type of adiabatic quantum computation,
   to solve opt. problems. We compare [it] to three conventional s/ware solvers,
   using instances from three NP-hard problem domains. ... describe experiments
   to learn how performance of the quantum annealing alg. depends on input."
   -- pdf@[<A HREF="http://www.cs.amherst.edu/ccm/cf14-mcgeoch.pdf">amherst</A>]['13].
   -- [<A HREF="http://www.computingfrontiers.org/2013/">CF2013</A>]['13] Ischia, Italy, 14-16 May.
   [Also search for: Dwave quantum computing].

%A B. Alberts
%T Impact factor distortions
%J Science
%V 340
%N 6134
%P 787
%M MAY
%D 2013
%K editorial, c2013, c201x, c20xx, zz0513, KPI, KPIs, publish perish,
   San Francisco Declaration On Research Assessment, DORA, ASCB, publications,
   journals, JIF, JIFs, impact factor, conferences, science, scientific, papers,
   contribution, reading, university, academic, research quality, metric,
   distortion, misuse, CORE, ERA, ARC, quality, rank, ranking
%X '... San Francisco declaration on research Assessment (DORA), ...
   states that the impact factor must not be used as "a surrogate measure of the
   quality of individual research articles, to assess an individual scientist's
   contributions, or in hiring, promotion, or funding decisions." ...
   endorsed by more than 150 leading scientists and 75 scientific
   organizations.  ...   analyzing the scientific contributions of other
   researchers. To do so in a meaningful way requires the actual reading of a
   small selected set of each researcher's publications, a task that must not
   be passed by default to journal editors.'
   -- [<A HREF="http://dx.doi.org/10.1126/science.1240319">doi:10.1126/science.1240319</A>]['13].
   "The [SF] Declaration on Research Assessment (DORA), initiated by the Amer.
   Soc. for Cell Biology (ASCB) together with a group of editors & publishers
   of scholarly journals, recognizes the need to improve the ways in which the
   outputs of scientific research are evaluated. The group met in Dec. 2012
   during the ASCB Annual Meeting in [SF] & subsequently circulated a draft
   decln among various stakeholders. DORA as it now stands has benefited from
   input by many of the original signers listed below. It is a worldwide
   initiative covering all scholarly disciplines. We encourage individuals &
   organizations who are concerned about the appropriate assessment of
   scientific research to sign DORA."
   -- DORA@[<A HREF="http://am.ascb.org/dora/">ASCB</A>]['14].
   [Also search for: publish perish].

%A M. P. Pearson
%T Stonehenge - A New Understanding: Solving the Mysteries of the
   Greatest Stone Age Monument
%I ?
%P 432
%M MAY
%D 2013
%K book, text, c2013, c201x, c20xx, zz0513, stonehenge, henge, stone circle,
   prehistoric, Neolithic, megalithic
%X hb us$19; uk us isbn:1615190791; uk us isbn13:978-1615190799.
   "... dating, filling gaps in our knowledge about its builders and how they
   lived, clarifying the monument's significance both celestially and as a
   burial ground, and contextualizing Stonehenge - which sits at the center of
   one of the densest prehistoric settlements in history - within the broader
   landscape of the Neolithic Age."
   [Also search for: stone circle].

%A M. Livio
%T Brilliant Blunders: From Darwin to Einstein - Colossal Mistakes by Great
   Scientists That Changed Our Understanding of Life and the Universe
%I SimonAndSchuster
%P 352
%M MAY
%D 2013
%K book, c2013, c201x, c20xx, zz0713, mistake, blunder, errors, wrong, science,
   scientific, research, theory, discovery
%X 1st ed 2013; hb us$19; uk us isbn:1439192367; uk us isbn13:978-1439192368.
   "... Lord Kelvin, Britain's leading scientific intellect at the time,
   gravely miscalculated the age of the earth. Linus Pauling, the world's
   premier chemist (who would win the Nobel Prize in chem.) constructed an
   erroneous model for DNA in his haste to beat the competition to publn.
   Astrophysicist Fred Hoyle dismissed the idea of a 'Big Bang' origin to the
   universe (ironically, the caustic name he gave to this event endured long
   after his erroneous objections were disproven). And Albert Einstein, whose
   name is synonymous with genius, speculated incorrectly about the forces that
   hold the universe in equilibrium - and that speculation opened the door to
   brilliant conceptual leaps. ..."

%A R. J. Deibert
%T Black Code: Inside the Battle for Cyberspace
%I Signal
%P 320
%M MAY
%D 2013
%K book, c2013, c201x, c20xx, zz1013, internet, www, security, cyber, privacy,
   civil rights, NSA, crime, scam, scams, Koobface
%X 1st ed 2013; hb us$20; uk us isbn:0771025335; uk us isbn13:978-0771025334.
   "... lifts the lid on cyberspace and shows what's at stake for Internet users
   and citizens. As cyberspace develops in unprecedented ways, powerful agents
   are scrambling for control. Predatory cyber criminal gangs such as Koobface
   have made social media their stalking ground. The discovery of Stuxnet, a
   computer worm reportedly developed by Israel and the United States and aimed
   at Iran's nuclear facilities, showed that state cyberwar is now a very real
   possibility. Governments and corporations are in collusion and are setting
   the rules of the road behind closed doors. ..."
   [Also search for: NSA internet].

%A A. V. Bell
%T Evolutionary thinking in microeconomic models: Prestige bias and market
   bubbles
%J PLoS One
%V 8
%N 3
%P e59805
%M MAR
%D 2013
%K jrnl, eJrnl, c2013, c201x, c20zz, zz0815, economics, human behaviour, market,
   bubble, envy, bias, social learning
%X "Evolutionary models broadly support a number of social learning strategies
   likely important in economic behavior. ... show how prestige bias, or copying
   of famed (& likely successful) individuals, influences price equilibria &
   investor disposition in a way that exacerbates or creates market bubbles. I
   discuss how integrating the social learning & demographic forces important
   in cultural evolution with economic models provides a fruitful line of
   inquiry into real-world behavior."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0059805">10.1371/journal.pone.0059805</A>]['15].

%A V. I. shCherbak
%A M. A. Makukov
%T The "Wow! signal" of the terrestrial genetic code
%J Icarus
%V 224
%N 1
%P 228-242
%M MAY
%D 2013
%K c2013, c201x, c20xx, zz1214, wow, ET, alien intelligence, message,
   number 37, number37, SET, extraterrestrial, genetic code, controversial
%X "... Genomic DNA is already used on Earth to store non-biol. info.. Though
   smaller in capacity, but stronger in noise immunity is the genetic code. ...
   a flexible mapping between codons & AAs, & this flexibility allows modifying
   the code artificially. But once fixed, the code might stay unchanged over
   cosmological timescales; in fact, it is the most durable construct known.
   Therefore it represents an exceptionally reliable storage for an intelligent
   signature  ...  A statistically strong intelligent-like 'signal' in the
   genetic code is then a testable consequence of such scenario. Here we show
   that the terrestrial code displays a thorough precision-type orderliness ...
   The patterns are profound to the extent that the code mapping itself is
   uniquely deduced from their algebraic representation. The signal displays
   readily recognizable hallmarks of artificiality, among which are the symbol
   of zero, the privileged decimal syntax & semantical symmetries. ...
   Overall, while the code is nearly optimized biologically, its limited
   capacity is used extremely efficiently to pass non-biological information."
   -- [<A HREF="http://dx.doi.org/10.1016/j.icarus.2013.02.017">doi:10.1016/j.icarus.2013.02.017</A>]['14],
      1303.6739@[<A HREF="http://arxiv.org/abs/1303.6739">arXiv</A>]['14].
   (Or, the code could just have evolved to minimise the effects of mutations.
   [Also search for: Swanson code c1984].   Hmm, May is close to April.)
   [Also search for: extraterrestrial life] and
   [also search for: SETI wow signal].

%A M. Kirschner
%T A perverted view of "impact"
%J Science
%V 340
%N 6138
%P 1265
%M JUN
%D 2013
%K editorial, views, c2013, c201x, c20xx, zz0613, impact factor, grant, grants,
   funding, career, ranking, rankings, significance, science,
   scientific research, publish perish, ARC, NIH, university, misuse, career
%X 'Scientists Often Face Vexing Professional Decisions: Whom to Hire, what to
   fund, what to publish, & whom to promote. Because science is about the
   unknown ... the US National Institutes of Health has elevated "significance"
   to an explicit criterion in funding decisions. ... [Scientists] should work
   hard to encourage risk & exploration, while at the same time rewarding
   careful, thoughtful investigation. And they should reemphasize humility,
   banishing the words "impact" & "significance" & seeing them for what they
   really are: ways of asserting bias without being forced to defend it.'
   -- [<A HREF="http://dx.doi.org/10.1126/science.1240456">doi:10.1126/science.1240456</A>]['13].
   [Also search for: publish perish].

%A A. Cho
%T Network science at center of surveillance dispute
%J Science
%V 340
%N 6138
%P 1272
%M JUN
%D 2013
%K news, views, c2013, c201x, c20xx, zz0613, Prism, US, USA, NSA, CIA, networks,
   analysis, communication, computer, cryptography, links, state, surveillance,
   government, big brother, UK GCHQ, spy, spying, spooks, Verizon,
   social, privacy, Edward Snowden, internet
%X "Last week, civil libertarians cried foul when press reports revealed that,
   in its efforts to ferret out terrorists, the U.S. National Security Agency
   (NSA) is collecting cell phone records and Internet data from companies such
   as Verizon, Facebook, and Skype. ... clear that NSA is performing network
   analysis, a type of science that aims to identify social groups from the
   connections among people. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.340.6138.1272">doi:10.1126/science.340.6138.1272</A>]['13].
   Also see [<A HREF="http://www.guardian.co.uk/world/2013/jun/10/nsa-spying-scandal-what-we-have-learned">Guardian</A>][6/2013] and
   -- [<A HREF="http://www.bbc.co.uk/news/world-us-canada-22850901">bbc</A>][6/2013].
   [Also search for: NSA cryptography].

%T Medium-Term Renewable Energy Market Report 2013 -- Market trends and
   projections to 2018
%I IEA
%P 217
%M JUN
%D 2013
%K IEA, report, c2013, c201x, c20xx, zz0713, MTREMR, energy, renewable, wind,
   solar, fossil fuels, nuclear, electricity, projections, predictions, OECD
%X "... renewable sources worldwide will exceed that from gas and be twice
   that from nuclear by 2016 ..."
   -- [<A HREF="http://iea.org/newsroomandevents/pressreleases/2013/june/name,39156,en.html">iea</A>]['13],
   and [<A HREF="http://www.iea.org/w/bookshop/add.aspx?id=453">bookshop</A>]['13].
   euro100, uk us isbn13:978-9264191181.

%A R. Martin
%T How We Do It: The Evolution and Future of Human Reproduction
%I BasicBooks
%P 320
%M JUN
%D 2013
%K book, text, c2013, c201x, c20xx, biology, biol, sex, human, reproduction,
   procreation, contraception, pregnancy, IVF, babies, birth, obstetrics,
   midwife, parenting, breast feeding
%X 1st ed 2013; hb us$18; uk us isbn:0465030157; uk us isbn13:978-0465030156.
   "... examines the procreative history of humans as well as that of our
   primate kin to reveal what is really natural when it comes to making and
   raising babies, and distinguish which behaviors we ought to continue - and
   which we should not. Although it is not realistic to raise our children like
   our ancestors did ... investigation reveals surprising consequences of - and
   suggests ways to improve upon - the way we do things now. ..."

%A K. Cue
%T MeLand: 10 Ways Self-Obsession Makes You Stupid
%I ConnorCourt
%P 262
%D JUN
%D 2013
%K book, c2013, c201x, c20xx, zz0813, education, teaching, school, self esteem,
   quotable, students, pupils, realistic, standards, schools, self obsession,
   obsessed, quality, mathspig, maths
%X 1st ed 2013; pb us$20; uk us isbn:1922168106; uk us isbn13:978-1922168108.
   '... globalised, market-driven, click-on click-off culture we not only fail
   to answer these questions, we can't even focus on them for long. ... shows
   how our mass-marketing culture spreads self-obsession and how, paradoxically,
   this self-obsession erodes your individuality, undermines your identity and,
   ultimately, diminishes your self-respect. ...'
   (Auth is mathspig@[<A HREF="http://mathspig.wordpress.com/">wPress</A>]['13].)
   '... As a maths teacher I cannot turn to a student and say "Don't
   you worry about algebra, Charlie, I know you don't like it". ...'

%A J. A. Smolin
%A G. Smith
%A A. Vargo
%T Oversimplifying quantum factoring
%J Nature
%V 499
%P 163-165
%K c2013, c201x, c20xx, zz0713, Schor's, Shor, algorithm, primes, factoring,
   quantum computing
%X "Shor's quantum factoring alg. exponentially outperforms known classical
   methods. Previous experimental implementations have used simplifications
   dependent on knowing the factors in advance. However, as we show here, all
   composite #s admit simplification of the alg. to a circuit equivalent to
   flipping coins. The difficulty of a particular experiment therefore depends
   on the level of simplification chosen, not the size of the # factored. Valid
   implementations should not make use of the answer sought. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12290">doi:10.1038/nature12290</A>]['13].
   [Also search for: Shor algorithm quantum].

%A A. Barbon
%T A Brief History of the Philosophy of Time
%I OUP
%P 200
%M JUL
%D 2013
%K book, text, OUP, c2013, c201x, c20xx, zz0713, arrow, time, free will, science
%X 1st ed 2013; pb us$16; uk us isbn:0199301085; uk us isbn13:978-0199301089.
   "... covers subjects such as time and change, the experience of time,
   physical and metaphysical approaches to the nature of time, the direction of
   time, time travel, time and freedom of the will, and scientific and
   philosophical approaches to eternity and the beginning of time. ..."

%A I. Kubiszewski
%A et al ...
%A T. Jackson
%T Beyond GDP: Measuring and achieving global genuine progress
%J Ecological Economics
%V 93
%P 57-68
%M SEP
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0913, GPI, Genuine Progress Indicator, GDP,
   growth, happiness, welfare, footprint, HDI, biocapacity, GINI, satisfaction,
   Gross Domestic Product, GDP, social, society, wellbeing, well being, stats,
   1970s, 1978
%X "... economic welfare, as est. by the Genuine Progress Indicator (GPI), has
   actually decreased since 1978. We synthesized ests. of GPI over the 1950-2003
   time period for 17 countries for which GPI has been est.. ...
   compared GPI with Gross Domestic Product (GDP), Human Development Index
   (HDI), Ecological Footprint, Biocapacity, Gini coeff., & Life Satisfaction
   scores. ... sig. variation among these countries, but some major trends. We
   also est. a global GPI/capita over the 1950-2003 period. Global GPI/capita
   peaked in 1978, about the same time that global Ecological Footprint exceeded
   global Biocapacity. Life Satisfaction in almost all countries has also not
   improved sig. since 1975. Globally, GPI/capita does not inc. beyond a
   GDP/capita of ~ $7000/capita. If we distributed income more equitably around
   the planet, the current world GDP ($67 trillion/yr) could support 9.6 billion
   people at $7000/capita. While GPI is not the perfect economic welfare
   indicator, it is a far better approxn than GDP. Development policies need to
   shift to better account for real welfare & not merely GDP growth."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ecolecon.2013.04.019">doi:10.1016/j.ecolecon.2013.04.019</A>]['13].
   [Also search for: happiness well being].

%A J. E. Mayfield
%T The Engine of Complexity: Evolution as Computation
%I ColumbiaUP
%P 416
%M JUL
%D 2013
%K book, text, c2013, c201x, c20xx, zz0713, complex, evolution, biol,
   information theory
%X 1st ed 2013; hb us$34; uk us isbn:0231163045; uk us isbn13:978-0231163040.
   "... concepts from multiple disciplines to offer a new approach to
   understanding how evolution works and how complex organisms, structures,
   organizations, and social orders can and do arise based on information theory
   and computational science. ..."
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%T The Pitch Drop Experiment
%M JUL
%D 2013
%K pitch drop, experiment, tar, c2013, c201x, c20xx, zz0713, viscous, viscosity,
   Parnell, Poiseuille's law
%X 2013 Dublin "It took seven decades, but the pitch has finally been caught in
   the act. ... last week a Webcam was on hand to witness the magic moment. ..."
   -- [<A HREF="http://news.cnet.com/8301-17938_105-57594322-1/69-year-experiment-captures-pitch-tar-drop/">cNet</A>]['13],
   since 1944 @[<A HREF="http://www.tcd.ie/Physics/tar-experiment/">tcd.ie</A>]['13], and
   since 1927 @[<A HREF="http://smp.uq.edu.au/content/pitch-drop-experiment">UQ</A>]['13].

%A M. A. Wakefield
%A L. Hayes
%A S. Durkin
%A R. Borland
%T Introduction effects of the Australian plain packaging policy on adult
   smokers: A cross-sectional study
%J BMJ Open
%V 3
%N 7
%P e003175
%M JUL
%D 2013
%K jrnl, eJrnl, c2013, c201x, c20xx, zz0713, public health, Melbourne, smoking,
   government policy, cigarettes, cigarette, pack, packs, plain packaging,
   health warnings, tobacco, quit, quitting, smoker, law, stats,
   Melbourne, Victoria, Australia
%X "... Participants 536 cigarette smokers with a usual brand, of whom 72.3%
   were smoking from a plain pack & 27.7% were smoking from a branded pack. ...
   ... Compared with branded pack smokers, those s. from plain packs perceived
   their cigarettes to be lower in quality ((AdjOR)=1.66, p=0.045), tended to
   perceive their cigarettes as less satisfying than a year ago (AdjOR=1.70,
   p=0.052), were more likely to have thought about quitting at least once a day
   in the past wk (AdjOR=1.81, p=0.013) & to rate quitting as a higher priority
   in their lives (F=13.11, df=1, p < 0.001). ..."
   -- [<A HREF="http://dx.doi.org/10.1136/bmjopen-2013-003175">doi:10.1136/bmjopen-2013-003175</A>]['13].
   [Also search for: smoking cigarettes].

%A G. Whiteman
%A C. Hope
%A P. Wadhams
%T Climate science: Vast costs of Arctic change
%J Nature
%V 499
%P 401-403
%M JUL
%D 2013
%K news, views, c2013, c201x, c20xx, global warming, climate change, methane,
   greenhouse gas, gases, arctic, thaw, permafrost, hydrates, Siberia, PAGE09
%X "... As the amount of Arctic sea ice declines ... thawing of offshore
   permafrost releases methane. A 50-gigatonne (Gt) reservoir of m., stored in
   the form of hydrates, exists on the East Siberian Arctic Shelf. ... The
   m. pulse will bring forward by 15-35 years the avg. date at which the global
   mean temp. rise exceeds 2C above pre-industrial levels - to 2035 for the
   business-as-usual scenario and to 2040 for the low-emissions case ..."
   -- [<A HREF="http://dx.doi.org/10.1038/499401a">doi:10.1038/499401a</A>]['13].

%A M. Maleszewska
%T Too much hype
%J Nature
%V 500
%P 113
%M JUL
%D 2013
%K views, c2013, c201x, c20xx, zz0813, publish, perish, hype, LPU, science,
   research, ethics, postgrad, PhD, university, academia, academic, misuse
%X "If you had asked me a few years ago what makes a scientist, I would have
   said curiosity. Now, after almost three years pursuing my PhD, I would
   probably say political skills. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nj7460-113a">doi:10.1038/nj7460-113a</A>]['13].
   [Also search for: publish perish].

%A C. Goldblatt
%A T. D. Robinson
%A K. J. Zahnle
%A D. Crisp
%T Low simulated radiation limit for runaway greenhouse climates
%J Nature Geoscience
%V 6
%P 661-667
%M JUL
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0813, climate change, Earth, Venus, H20,
   water vapour, cloud, clouds, greenhouse gas, forcing, albedo, troposphere,
   atmosphere, climate
%X "The atmospheres of terrestrial planets are expected to be in long-term
   radiation balance: an increase in the absorption of solar rad'n warms the
   surface & troposphere, which leads to a matching increase in the emission of
   thermal r.. Warming a wet planet such as Earth would make the atmosphere
   moist & optically thick such that only thermal r. emitted from the upper
   troposphere can escape to space. Hence, for a hot moist a., there is an upper
   limit on the thermal emission that is unrelated to surface temp.. If the
   solar rad'n absorbed exceeds this limit, the planet will heat uncontrollably
   & the entire ocean will evaporate - the so-called runaway greenhouse. Here we
   model the solar & thermal radiative transfer in incipient & complete runaway
   greenhouse atmospheres ... find a thermal radiation limit of 282Wm2 (lower
   than prev. reported) & that 294Wm2 of solar radn is absorbed (higher than
   prev. reported). Therefore, a steam atmosphere induced by such a runaway
   greenhouse may be a stable state for a planet receiving a similar amount of
   solar radiation as Earth today. Avoiding a runaway greenhouse on Earth
   requires that the a. is subsaturated with water, & that the albedo effect of
   clouds exceeds their greenhouse effect. A runaway greenhouse could in theory
   be triggered by increased greenhouse forcing, but anthropogenic emissions are
   probably insufficient."  [[That's nice!]]
   -- [<A HREF="http://dx.doi.org/10.1038/ngeo1892">doi:10.1038/ngeo1892</A>]['13].

%T Report to the President: MIT and the Prosecution of Aaron Swartz
%E H. Abelson
%I MIT
%M JUL
%D 2013
%K report, c2013, c201x, c20zz, zz0813, Aaron Swartz, suicide, computer,
   hacking, hacker, computing, internet, JSTOR, security, open access, ethics,
   CFAA, Computer Fraud and Abuse Act, MIT, University, US Government, USA,
   Obama, American, law, legal, cyber laws, prosecution, felony, wire fraud,
   zzLaw, zzEthics
%X "In January 2013, MIT President L. Rafael Reif asked Professor Hal Abelson to
   lead a thorough analysis of MIT's involvement in the Aaron Swartz matter,
   from the time that MIT first perceived unusual activity on its network in
   fall 2010 up to the time of Aaron Swartz's suicide on January 11, 2013.  On
   July 26, 2013, Professor Abelson and his team submitted their report to
   President Reif. Through this site, President Reif is sharing their report
   with the community. This site offers direct access to their report, a letter
   from President Reif in response and a variety of documents that MIT has
   previously committed to releasing publicly."
   -- [<A HREF="http://swartz-report.mit.edu/">MIT</A>][7/2013],
   &  [<A HREF="http://web.mit.edu/newsoffice/2013/mit-releases-swartz-report-0730.html">www</A>][30/7/2013].
   Also see [<A HREF="http://www.theguardian.com/technology/2013/aug/04/bradley-manning-case-credibility-computer-fraud-law">The G.</A>][4/8/2013],
   and [<A HREF="http://www.theguardian.com/technology/aaron-swartz">www</A>][2013].

%A J. Couzin-Frankel
%T The web's faceless judges
%J Science
%V 341
%N 6146
%P 606-608
%M AUG
%D 2013
%K news, views, c2013, c201x, c20xx, zz0813, publish, perish,
   PubPeer, web site, www, HREF, scientific research, papers, publications
%X "Many scientists long for a place for unfettered discussion about published
   papers, and PubPeer is one of the latest websites trying to fill that gap.
   These sites can help to clarify experiments, suggest avenues for follow-up
   work, and catch errors. But PubPeer's founders and most of its commenters
   choose to remain anonymous, which may foster free discussion but doesn't
   always elevate it."
   -- [<A HREF="http://dx.doi.org/10.1126/science.341.6146.606">doi:10.1126/science.341.6146.606</A>]['13].
   [Also search for: publish perish].

%A C. Nodder
%T Evil by Design: Interaction Design To Lead Us Into Temptation
%I Wiley
%P 320
%M JUN
%D 2013
%K book, c2013, c201x, c20xx, zz0813, marketing, marketting, advertising, ads,
   persuasion, sins, pride, sloth, gluttony, anger, envy, lust, greed
%X 1st ed 2013; pb us$26; uk us isbn:1118422147; uk us isbn13:978-1118422144.

%A E. Zuckerman
%T Rewire: Digital Cosmopolitans in the Age of Connection
%I WWNorton
%P 288
%M JUN
%D 2013
%K book, c2013, c201x, c20xx, zz0813, social media, internet, www, online,
   human behaviour, Facebook
%X 1st ed 2013; hb us$18; uk us isbn:0393082830; ;uk us isbn13:978-0393082838.
   "... explains why the technological ability to communicate with someone does
   not inevitably lead to increased human connection. At the most basic level,
   our human tendency to 'flock together' means that most of our interactions,
   online or off, are with a small set of people with whom we have much in
   common. In examining this fundamental tendency, Z. draws on his own work as
   well as the latest res. in psychology & sociology to consider technology's
   role in disconnecting ourselves from the rest of the world. ..."

%A C. Macilwain
%T Halt the avalanche of performance metrics
%J Nature
%V 500
%N 7462
%P ?
%M AUG
%D 2013
%K views, c2013, c201x, c20xx, zz0813, publish, perish, scientific research,
   DORA, quality, performance, impact, measures, citations, ranking, rankings,
   misuse, assessment, Snowball, snowballmetrics, grants, academic, education,
   University management, VC, Deans, KPI, KPIs
%X "... power has moved from the depts to the vice-chancellor. And U.leaders,
   flanked by research managers & associated flunkies, want to use metrics to
   shift that balance still further. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/500255a">doi:10.1038/500255a</A>]['13].
   [Also search for: publish perish] & [also search for: publish perish misuse].

%A R. van Noorden
%T Brazilian citation scheme outed
%J Nature
%V 500
%N 7464
%P ?-?
%M AUG
%D 2013
%K news, c2013, c201x, c20xx, zz0913, publish, perish, journal, journals, JIF,
   rank, ranking, score, scores, impact factor, citations, citation stacking,
   abuse, gaming, scamming, spoofing, boost, rank, padding, science,
   scientific research, CAPES, SciELO, ISI, Reuters, anti, algorithm
%X "Mauricio Rocha-e-Silva thought that he had spotted an easy way to raise the
   profiles of Brazilian journals. From 2009, he & several other editors
   published articles containing hundreds of references to papers in each
   others' journals - in order, he says, to elevate the journals' impact
   factors.  Because each article avoided citing papers published by its own
   journal, the agreement flew under the radar ... until 19 June ..."
   -- [<A HREF="http://dx.doi.org/10.1038/500510a">doi:10.1038/500510a</A>]['13].
      (?I wonder if the algorithms extend to the activities of
      individual authors/referees?  As of 2O2O, yes they did.)
   [Also search for: publish perish]  and  [also search for: citation abuse].

%A O. Picard
%A M. Lord
%A A. Blondin-Masse
%A O. Marcotte
%A M. Lopes
%A S. Harnad
%T Hidden structure and function in the lexicon
%J arXiv
%M AUG
%D 2013
%K TR, c2013, c201x, c20xx, zz0913, natural language, word, words, definition,
   meaning, core, kernel, human, learning, English, dictionary, lexicon
%X "How many words are needed to define all the words in a dictionary?
   Graph-theoretic analysis reveals that about 10% of a d. is a unique Kernel of
   words that define one another & all the rest, but this is not the smallest
   such subset. The Kernel consists of one huge strongly connected component
   (SCC), about half its size, the Core, surrounded by many small SCCs, the
   Satellites. Core words can define one another but not the rest of the d.. The
   Kernel also contains many overlapping Minimal Grounding Sets (MGSs), each
   about the same size as the Core, each part-Core, part-Satellite. MGS words
   can define all the rest of the d.. They are learned earlier, more concrete &
   more freq. than the rest of the d.. Satellite words, not correl. with age
   or freq., are less concrete (more abstract) words also needed for full
   lexical power. "
   -- 1308.2428@[<A HREF="http://arxiv.org/abs/1308.2428">arXiv</A>]['13].

%A B. Frohlich
%A J. F. Dynes
%A M. Lucamarini
%A A. W. Sharpe
%A Z. Yuan
%A A. J. Shields
%T A quantum access network
%J Nature
%V 501,
%P 69-72
%M SEP
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0913, quantum, communication, computing,
   network, node, key distribution, QKD, encryption
%X "... introduce & experimentally demonstrate the concept of a 'quantum access
   network': based on simple & cost-effective telecomm. technologies, the scheme
   can greatly expand the # of users in q.networks & therefore vastly broaden
   their appeal. We show that a high-speed single-photon detector positioned at
   a network node can be shared between up to 64 users for exchanging secret
   keys with the node, thereby sig. reducing the hardware requirements for each
   user added to the network. This point-to-multipoint architecture removes one
   of the main obstacles restricting the widespread application of QKD. It
   presents a viable method for realizing multi-user QKD networks with efficient
   use of resources, & brings QKD closer to becoming a widespread technology."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12493">doi:10.1038/nature12493</A>]['13].
   [Also search for: quantum communication].

%A D. Wodarz
%A N. L. Komarova
%T Dependence of the firearm-related homicide rate on gun availability:
   A mathematical analysis
%J PLoS One
%V 8
%N 7
%P e71606
%M JUL
%D 2013
%K jrnl, eJrnl, c2013, c201x, c20xx, zz0913, gun, guns, murder, shot, homicide,
   shooting, USA, stats, model, public safety, risk, risks, law, laws, NRA
%X "... The parameters that need to be measured include the fraction of
   offenders that illegally possess a gun, the degree of protection provided by
   gun ownership, & the fraction of the population who take up their right to
   own a gun & carry it when attacked. Limited data available in the
   literature were used to demonstrate how the model can be parameterized, &
   this preliminary analysis suggests that a ban of private firearm possession,
   or possibly a partial reduction in gun availability, might lower the rate of
   firearm-induced homicides. This, however, should not be seen as a policy
   recommendation, due to the limited data available to inform & parameterize
   the model. However, the model clearly defines what needs to be measured, &
   provides a basis for a scientific discussion about assumptions & data."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0071606">doi:10.1371/journal.pone.0071606</A>]['13].

%A Y. Kosaka
%A S.-P. Xie
%T Recent global-warming hiatus tied to equatorial Pacific surface cooling
%J Nature
%V 501
%N 7467
%P 403-407
%M SEP
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0913, global warming, earth, temperature,
   Pacific, ocean, oceans, sea, surface, natural, la Nina, el Nino, ENSO,
   circulation, drought, USA, trend, trends, variation
%X "... present a novel method of uncovering mechanisms for global temp. change
   by prescribing, in addition to radiative forcing, the obs. history of sea
   surface temp. over the central to eastern tropical Pacific in a climate
   model. Although the surface temp. prescription is limited to only 8.2% of the
   global surface, our model reproduces the annual-mean global temp. remarkably
   well with correl. coeff. r=0.97 for 1970-2012 (includes the current hiatus
   & a period of accelerated global warming). ... inc. the intensified Walker
   circulation, the winter cooling in NW North America & the prolonged drought
   in the S. USA. Our results show that the current hiatus is part of natural
   climate variability, tied specifically to a La-Nina-like decadal cooling.
   Although similar decadal hiatus events may occur in the future, the multi-
   -decadal warming trend is v.likely to continue with greenhouse gas increase."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12534">doi:10.1038/nature12534</A>]['13] (30 refs).

%A L. Dayton
%T Will new government overcome 'symbolically challenged' start?
%J Science
%V 341
%N 6153
%P 1439
%M SEP
%D 2013
%K news, views, c2013, c201x, c20xx, zz1013, Australia, Australian, Government,
   Abbott, Liberal, education, policy, university, science, politics, minister,
   scientific research, technology, grants, NHMRC, au, ARC, CO2, climate change
%X "... Fresh off its victory in the 7 Sept. elections, the new conservative
   government began dismantling climate change science and mitigation programs,
   and it eliminated the science minister post - leaving the country without a
   science minister for the first time in more than 80 years. ... The government
   has not tipped whether it will follow through on a campaign threat to
   micromanage Australian Research Council (ARC) grants ... by terminating
   grants in areas such as anthropology and philosophy and instead funding
   projects in dementia, bowel cancer, diabetes, and tropical health. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.341.6153.1439">doi:10.1126/science.341.6153.1439</A>]['13].
   [Also search for: cause global warming] and
   [also search for: mitigation global warming].

%A F. Lavigne
%A et al ...
%A E. de Belizal
%T Source of the great A.D. 1257 mystery eruption unveiled, Samalas volcano,
   Rinjani Volcanic Complex, Indonesia
%J PNAS
%V ?
%P ?-?
%M SEP
%D 2013
%K jrnl, PNAS, c2013, c201x, c20xx, zz1113, AD1257, 1257 AD, volcano, volcanic,
   Samalas, Mount Rinjani, Lombok Island, Indonesia
%X "Based on ice core archives of sulfate & tephra deposition, one of the
   largest volcanic eruptions of the historic period & of the past 7,000y
   occurred in A.D. 1257. However the source of this 'mystery eruption'
   remained unknown. ... new evidence from radiocarbon dates, tephra
   geochemistry, stratigraphic data, a medieval chronicle, this study argues
   that the source of this eruption is Samalas volcano, part of the Mount
   Rinjani Volcanic Complex on Lombok Island, Indonesia. These results solve a
   conundrum that has puzzled glaciologists, volcanologists, & climatologists
   for more than three decades. [&] the identification of this volcano gives
   rise to the existence of a forgotten Pompeii in the Far East." (online 30/9.)
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1307520110">doi:10.1073/pnas.1307520110</A>]['13].

%A E. Schlosser
%T Command and Control: Nuclear Weapons, the Damascus Accident, and
   the Illusion of Safety
%I PenguinPress
%P 656
%M SEP
%D 2013
%K book, c2013, c201x, c20xx, zz0915, risk, risks, atomic bomb, nuclear arms,
   weapons, Titan missile, warhead, accident, cold war, military, Arkansas,
   America, USA, Russia
%X 1st ed 2013; hb us$22; uk us isbn:1594202273; uk is isbn13:978-1594202278.
   "... interweaves the minute-by-minute story of an accident at a
   nuclear missile silo in rural Arkansas ..."
   (Also see [<A HREF="http://www.abc.net.au/news/2015-09-02/americas-history-of-nuclear-weapons-eric-schlosser/6745318">abc</A>][2/9/2015].)

%A P. K. Jonason
%A A. Jones
%A M. Lyons
%T Creatures of the night: Chronotypes and the Dark Triad traits
%J Personality and Individual Differences
%V 55
%N 5
%P 538-541
%M SEP
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0914, UWS, IgNobel prize, psychology, human,
   personality, trait, manipulative, psychopathy, psychopath, narcissism,
   Machiavellianism, chronotype, office
%X "In this study (N=263) we provide a basic test of a niche-specialization
   hypothesis of the Dark Triad (i.e., narcissism, psychopathy, &
   Machiavellianism). We propose that in order to best enact a 'cheater
   strategy' those high on the Dark Triad traits should have optimal cognitive
   performance &, thus, have a night-time chronotype. Such a disposition will
   take advantage of the low light, the limited monitoring, & the lessened
   cognitive processing of morning-type people. The Dark Triad composite was
   correlated with an eveningness disposition. This link worked through links
   with the 'darker' aspects of the Dark Triad (i.e., Machiavellianism,
   secondary psychopathy, & exploitive narcissism); correlations that were
   invariant across the sexes. While we replicated sex differences in the Dark
   Triad, we failed to replicate sex differences in chronotype, suggesting
   eveningness may not be a sexually selected trait as some have argued but is
   a trait under natural selective pressures to enable effective exploitations
   of conspecifics by both sexes."
   -- [<A HREF="http://dx.doi.org/10.1016/j.paid.2013.05.001">doi:10.1016/j.paid.2013.05.001</A>]['14].
   (Also see the 2014 IgNobel Prizes
    [<A HREF="http://www.improbable.com/">improbable.com</A>][2021], and e.g.,
    The_G@[<A HREF="http://www.theguardian.com/science/2014/sep/19/ig-nobel-prize-british-researchers-win">www</A>][19/9/2014].)

%A J. Bohannon
%T Who's afraid of peer review?
%J Science
%V 342
%N 6154
%P 60-65
%M OCT
%D 2013
%K jrnl, news, c2013, c201x, c20xx, zz1013, scientific, research, paper, papers,
   publications, publish, perish, open access, journals, DOAJ, spoof, sting,
   peer review, reviewing, refereeing, PLoS One
%X "A spoof paper concocted by Science reveals little or no scrutiny at many
   open-access journals.  On 4 July, good news arrived in the inbox of Ocorrafoo
   Cobange, a biologist at the Wassee Inst. of Medicine in Asmara. It was the
   official letter of acceptance for a paper he had submitted 2 months earlier
   to the J. of Natural Pharmaceuticals, describing the anticancer properties of
   a chemical that Cobange had extracted from a lichen.  In fact, it should have
   been promptly rejected. Any reviewer with more than a high-school knowledge
   of chemistry & the ability to understand a basic data plot should have
   spotted the paper's short-comings immediately ...
   PLoS ONE, was the only J. that called attention to the paper's potential
   ethical problems [&] rejected the paper 2 weeks later on the basis of
   its scientific quality. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.342.6154.60">doi:10.1126/science.342.6154.60</A>]['13].
   [Also search for: publish perish].

%A J. Huang
%A C. Piech
%A A. Nguyen
%A L. Guibas.
%T Syntactic and functional variability of a million code submissions in a
   machine learning MOOC
%J Workshop on Massive Open Online Courses (MOOCshop),
   16th Int. Conf. on A.I. in Education (AIED 2013)
%M JUL
%D 2013
%K wkShop, c2013, c201x, c20xx, zz1113, codeweb, MOOC, online course, courses,
   marking, teaching, students, submission, computer programming, source code,
   automatic
%X "We parsed each of 40,000 student submissions into an Abstract Syntax Tree
   (AST) ... by adapting the parsing module from the Octave source code. ASTs
   allow us to capture the structure of each student's code while ignoring
   irrelevant information such as whitespace & comments ([&] to some extent,
   variable names).  We next computed the tree edit distance between every pair
   of unique trees, which counts the minimum number of edit operations (e.g.,
   deletes, inserts, replaces) required to transform one tree into the other
   Reasoning that small edit distances between ASTs are meaningful while larger
   distances less so, we finally dropped edges whose edit distances were above
   a threshold & and used gephi to visualize the resulting graph"
   -- codeweb@[<A HREF="http://www.stanford.edu/~jhuang11/research/pubs/moocshop13/codeweb.html">stanf'd</A>]['13].
   [Also search for: tree edit distance]  and  [also search for: Octave PLD].

%A M. Eigen
%T From Strange Simplicity to Complex Familiarity: A Treatise on Matter,
   Information, Life and Thought
%I OUP
%P 704
%M JUL
%D 2013
%K book, text, OUP, c2013, c201x, c20xx, zz1013, life, matter, complexity,
   science, Alife, entropy, information, self organisation
%X '... argument for the almost lost idea of a unity of all natural sciences.
   It starts with the "strange" physics of matter, inc. particle physics, atomic
   physics & quantum mechanics, cosmology, relativity & their consequences
   (Ch I), & it continues by describing the properties of material systems that
   are best understood by statistical & phase-space concepts (Ch II). These lead
   to entropy & to the classical picture of quantitative info., initially devoid
   of value & meaning (Ch III). Finally, "information space" & dynamics within
   it are introduced as a basis for semantics (Ch IV), leading to an exploration
   of life & thought as new problems in physics (Ch V).  ...'
   1st ed 2013; hb us$176; uk us isbn:019857021X; uk us isbn13:978-0198570219.

%A D. Wang
%A C. Song
%A A.-L. Barabasi
%T Quantifying long-term scientific impact
%J Science
%V 342
%N 6154
%P 127-132
%M OCT
%D 2013
%K jrnl, c2013, c201x, c20xx, zz1013, publish, perish, science, research,
   bibliometrics, impact factor, citation, citations, KPI, KPIs, Hindex, Gindex,
   controversial
%X "The lack of predictability of citation-based measures frequently used to
   gauge impact, from impact factors to short-term citations, raises a
   fundamental question: Is there long-term predictability in citation patterns?
   Here, we derive a mechanistic model for the citation dynamics of individual
   papers, allowing us to collapse the citation histories of papers from
   different journals & disciplines into a single curve, indicating that all
   papers tend to follow the same universal temporal pattern. The observed
   patterns not only help us uncover basic mechanisms that govern scientific
   impact but also offer reliable measures of influence that may have potential
   policy implications."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1237825">doi:10.1126/science.1237825</A>]['13].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.1245218">views</A>]['13].
   *And, "We replicate their analysis but find discouraging results ..."
   -- [<A HREF="http://dx.doi.org/ 10.1126/science.1248770">comment</A>][11/7/'14].)
   [Also search for: publish perish].

%A A. Finkbeiner
%T Researchers split over NSA hacking
%J Nature
%V 502
%N 7470
%P ?
%M OCT
%D 2013
%K news, c2013, c201x, c20xx, zz1013, NSA, USA, computer security, cryptography,
   standards, privacy, spying, Snowden, US, Prism, big brother, Internet,
   state, surveillance
%X "The US National Security Agency (NSA) has upset a great many people this
   year. Since June, newspapers have been using documents leaked by former
   intelligence worker Edward Snowden to show how the secretive but powerful
   agency has spied on the communications of US citizens & foreign governments.
   Last month, the media reported that the NSA, which is based in Fort Meade,
   Maryland, had undermined Internet security standards. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/502152a">doi:10.1038/502152a</A>]['13].
   (Also see [<A HREF="http://www.guardian.co.uk/world/2013/jun/10/nsa-spying-scandal-what-we-have-learned">Guardian</A>][6/2013].)
   [Also search for: NSA cryptography].

%A D. Edmonds
%T Would You Kill the Fat Man?: The Trolley Problem and What Your Answer Tells
   Us about Right and Wrong
%I PrincetonUP
%P 240
%M OCT
%D 2013
%K book, text, c2013, c201x, c20xx, zz1013, philosophy, utility, utilitarianism,
   morality, ethics
%X 1st ed 2013; hb us$15; uk us isbn:0691154023; uk us isbn13:978-0691154022.
   "A runaway train is racing toward five men who are tied to the track. Unless
   the train is stopped, it will inevitably kill all five men. You are standing
   on a footbridge looking down on the unfolding disaster. However, a fat man,
   a stranger, is standing next to you: if you push him off the bridge, he will
   topple onto the line &, although he will die, his chunky body will stop the
   train, saving 5 lives. Would you kill the fat man? The Q may seem bizarre.
   But it's one var'n of a puzzle that has baffled moral philosophers ..."

%A S. Power
%A et al ...
%A K. Keay
%T Robust twenty-first-century projections of El-Nino and related precipitation
   variability
%J Nature
%V 502
%N 7472
%P 541-545
%M OCT
%D 2013
%K jrnl, climate, c2013, c201x, c20xx, zz1013, change, El Nino, La Nina, ENSO,
   rainfall, ocean, temperature, variability, CO2, model
%X "... Given that further human-forced changes in the Earth's climate system
   seem inevitable ... we show that there are in fact robust projected changes
   in the spatial patterns of year-to-year ENSO-driven variability in both
   surface temperature & precipitation. These changes are evident in the two
   most recent generations of climate models, using four different scenarios for
   CO2 & other radiatively active gases. By the mid- to late 21st century, the
   projections include an intensification of both El-Nino-driven drying in the
   W. Pacific Ocean & rainfall increases in the central & E. equatorial Pacific.
   Experiments with an Atmospheric General Circulation Model reveal that robust
   projected changes in precipitation anomalies during El-Nino years are
   primarily det. by a nonlinear response to surface global warming. Uncertain
   projected changes in the amplitude of ENSO-driven surface temp. variability
   have only a secondary role. Projected changes in key characteristics of ENSO
   are consequently much clearer than previously realized."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12580">doi:10.1038/nature12580</A>]['13].

%A J. Laghari
%T Climate change: Melting glaciers bring energy uncertainty
%J Nature
%V 502
%N 7473
%P ?-?
%M OCT
%D 2013
%K news, views, c2013, c201x, c20xx, zz1113, Himalaya, Himalayan, glacier,
   repreat, melt, melting, water
%X "... Between 2003 and 2009, Himalayan glaciers lost an estimated 174
   gigatonnes of water each year, and contributed to catastrophic floods of
   the Indus, Ganges and Brahmaputra rivers. ... near the [Indus]'s source, in
   mountains in the Indian-administered state of Jammu and Kashmir, the glaciers
   are thinning at an alarming rate of 0.7 metres per year. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/502617a">doi:10.1038/502617a</A>]['13].

%A E. A. Petigura
%A A. W. Howard
%A G. W. Marcy
%T Prevalence of Earth-size planets orbiting Sun-like stars
%J PNAS
%V ?
%P ?-?
%M NOV
%D 2013
%K jrnl, PNAS, c2013, c201x, c20xx, zz1113, exoplanet, exo planet, planets,
   rocky, surface water, stats, alien, space, universe, NASA, Kepler telescope
%X "... used the [NASA] Kepler telescope to survey 42,000 Sun-like stars for
   periodic dimmings that occur when a planet crosses in front of its host star.
   We found 603 planets, 10 of which are Earth size and orbit in the habitable
   zone, where conditions permit surface liquid water. We measured the
   detectability of these planets by injecting synthetic planet-caused dimmings
   into Kepler brightness measurements. We find that 22% of Sun-like stars
   harbor Earth-size planets orbiting in their habitable zones. The nearest such
   planet may be within 12 light-years."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1319909110">doi:10.1073/pnas.1319909110</A>]['13].
   [Also search for: exoplanet].

%A F. Estrada
%A P. Perron
%A B. Martinez-Lopez
%T Statistically derived contributions of diverse human influences to
   twentieth-century temperature changes
%J Nature Geoscience
%V ?
%P ?-?
%M NOV
%D 2013
%K jrnl, c2013, c201x, c20xx, zz1113, climate change, global warming,
   pause, chlorofluorocarbons, CFC, CFCs, methane, ozone hole,
   greenhouse gas, gases
%X "The warming of the climate sys. is unequivocal as evidenced by an increase
   in global temps. by 0.8Â°C over the past century. However, the attribution
   of the obs. warming to human activities remains less clear ... apparent
   slow-down in warming since the late 1990s. ... analyse radiative forcing &
   temp. time series with state-of-the-art stat.methods to address this Q
   without climate model simulations. We show that long-term trends in total
   radiative forcing & temperatures have largely been determined by atmospheric
   greenhouse gas concentrations, & modulated by other radiative factors. We
   identify a pronounced increase in the growth rates of both temps. & radiative
   forcing c1960, which marks the onset of sustained global warming. Our
   analyses also reveal a contribution of human interventions to two periods
   when global warming slowed down. Our stat.analysis suggests that the
   reduction in the emissions of ozone-depleting substances under the Montreal
   Protocol, as well as a reduction in methane emissions, contributed to the
   lower rate of warming since the 1990s. [&] identify a contribution from the
   two world wars & the Great Depression to the documented cooling in the
   mid-twentieth century, through lower carbon dioxide emissions. We conclude
   that reductions in greenhouse gas emissions are effective in slowing the
   rate of warming in the short term."
   -- [<A HREF="http://dx.doi.org/10.1038/ngeo1999">doi:10.1038/ngeo1999</A>]['13].
   Also see [<A HREF="http://www.bbc.co.uk/news/science-environment-24874060">bbc</A>][10/11/2013].

%A M. Derex
%A M.-P. Beugin
%A B. Godelle
%A M. Raymond
%T Experimental evidence for the influence of group size on cultural complexity
%J Nature
%V 503
%N 7476
%P 389-391
%M NOV
%D 2013
%K jrnl, c2013, c201x, c20xx, zz1113, human behaviour, culture, society,
   interaction, population, social, group, size
%X "... accumulation of beneficial cultural innovations across generations is
   puzzling because transmission events are generally imperfect, although there
   is large variance in fidelity. ... perfect cultural transmission &
   innovations should be more frequent in a large population. [So] a large popn
   size may be a prereq. for the evoln of cultural complexity, although
   anthropological studies have produced mixed results & empirical evidence is
   lacking. ... use a dual-task computer game to show that cultural evoln
   strongly depends on popn size, as players in larger groups maintained higher
   cultural complexity. ... when group size increases, cultural knowledge is
   less deteriorated, improvements to existing cultural traits are more
   frequent, & cultural trait diversity is maintained more often. ... demo. how
   changes in group size can generate both adaptive cultural evolution &
   maladaptive losses of culturally acquired skills. As humans live in habitats
   for which they are ill-suited without specific cultural adaptations, it
   suggests that, in our evolutionary past, group-size reduction may have
   exposed human societies to significant risks, including societal collapse."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12774">doi:10.1038/nature12774</A>]['13], online 14 Nov 2013.

%A E. Proto
%A A. Rustichini
%T A reassessment of the relationship between GDP and life satisfaction
%J PLoS One
%V 8
%N 11
%P e79358
%M NOV
%D 2013
%K jrnl, eJrnl, c2013, c201x, c20xx, zz1213, happiness, life, satisfaction,
   Easterlin paradox, GDP, gross national product, well being, wellbeing,
   wealth, income, aspiration, wants, social science, human behaviour,
   economics, Easterlin paradox
%X "The scientific debate on the relation between Gross Domestic Product (GDP)
   & self reported indices of life satisfaction is still open. ...  appears to
   be strictly monotonically increasing with income when one studies this
   relation at a point in time across nations. Here, we analyze the relation
   between per capita GDP & life satisfaction without imposing a functional form
   & eliminating potentially confounding country-specific factors. We show that
   ... increases in country with a per capita GDP below 15,000 USD (2005 in
   Purchasing Power Parity), then it flattens for richer countries. ...
   In countries with an income above 17,000 USD the probability of reporting the
   highest level of life satisfaction changes within a range of 2% maximum. ...
   life satisfaction seems to peak at around 30,000 USD & then slightly but
   sig. decline among the richest countries. ... suggest an explanation of the
   Easterlin paradox ...  [by] aspiration levels. We assume that a gap between
   aspiration & realized income is negatively perceived; & aspirations to higher
   income increase with income. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0079358">doi:10.1371/journal.pone.0079358</A>]['13],
   & @[<A HREF="http://wrap.warwick.ac.uk/44785/">warw'ck</A>]['13].
   (Also see The G. [<A HREF="http://www.theguardian.com/world/2013/nov/27/happiness-study-uk-life-satisfaction">www</A>][27/11/2013].)
   [Also search for: happiness wellbeing] and
   [also search for: Easterlin paradox].

%A J. K. McNulty
%A M. A. Olson
%A A. L. Meltzer
%A M. J. Shaffer
%T Though they may be unaware, newlyweds implicitly know whether their marriage
   will be satisfying
%J Science
%V 342
%N 6162
%P 1119-1120
%M NOV
%D 2013
%K jrnl, c2013, c201x, c20xx, zz1213, marriage, human, mate selection, partner,
   spouse, wife, husband, newlywed, love test, attitude, satisfaction,
   psychology, subconscious, automatic processes, conscious attitudes
%X "For decades, social psychological theories have posited that the automatic
   processes captured by implicit measures have implications for social
   outcomes. Yet few studies have demo. any long-term implications of automatic
   processes, & some scholars have begun to question the relevance & even the
   validity of these theories. At baseline of our longitudinal study, 135
   newlywed couples (270 individuals) completed an explicit measure of their
   conscious attitudes toward their relationship & an implicit measure of their
   aut. attitudes toward their partner. They then reported their marital
   satisfaction every 6 months for the next 4 years. We found no correlation
   between spouses' aut. & conscious attitudes, which suggests that spouses were
   unaware of their aut. attitudes. Further, spouses' aut. attitudes, not their
   conscious ones, predicted changes in their marital satisfaction, s.t. spouses
   with more +ve aut. attitudes were less likely to experience declines in
   marital satisfaction over time."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1243140">doi:10.1126/science.1243140</A>]['13].
   (Also see [<A HREF="http://www.bbc.co.uk/news/science-environment-25129117">bbc</A>][29/11/2013].)

%A T. Suddendorf
%T The Gap: The Science of What Separates Us from Other Animals
%I BasicBooks
%P 368
%M NOV
%D 2013
%K book, text, c2013, c201x, c20xx, zz0214, animal, apes, human, behaviour,
   language, intelligence, brain, mind
%X 1st ed 2013; hb us$22; uk us isbn:0465030149; uk us isbn13:978-0465030149.
   "... provides a definitive account of the mental qualities that separate
   humans from other animals, as well as how these differences arose. Drawing on
   two decades of research on apes, children, & human evolution, he surveys
   the abilities most often cited as uniquely human - language, intelligence,
   morality, culture, theory of mind, & mental time travel - & finds that
   two traits account for most of the ways in which our minds appear so
   distinct: Namely, our open-ended ability to imagine & reflect on scenarios,
   & our insatiable drive to link our minds together. ..."

%T PISA 2012 Results: What Students Know and Can do: Student Performance in
   Mathematics, Reading and Science (Volume I)
%I OECD
%M DEC
%D 2013
%K Pisa, report, c2013, c201x, c20xx, zz1213, education, student, rank, ranking,
   rankings, school, teaching, nations, reading, maths, science
%X "15 year old students"
   keyFindings@[<A HREF="http://www.oecd.org/pisa/keyfindings/pisa-2012-results-volume-i.htm">oecd</A>]['13],
   au@[<A HREF="http://gpseducation.oecd.org/CountryProfile?primaryCountry=AUS&treshold=10&topic=PI">oecd</A>]['13],
   ozpisa@[<A HREF="http://www.acer.edu.au/ozpisa/">acer.edu.au</A>]['13].
   Also see
   "... Australia's mean performance placed us at equal 14th for reading, 19th
   for maths, & equal 16th for science, among participating countries. ...
   Maths has been Australia's weakest area of performance since PISA 2003. ..."
   -- [<A HREF="http://www.abc.net.au/news/2013-12-04/buckingham-pisa-panic/5133364">abc</A>][4/12/2013].

%A N. G. Shakeshaft
%A M. Trzaskowski
%A A. McMillan
%A K. Rimfeld
%A E. Krapohl
%A C. M. A. Haworth
%A P. S. Dale
%A R. Plomin
%T Strong genetic influence on a UK rationwide test of educational achievement
   at the end of compulsory education at age 16
%J PLoS One
%V 8
%N 12
%P e80341
%M DEC
%D 2013
%K jrnl, eJrnl, c2913, c201x, c20xx, zz1213, school, education, academic,
   results, performance, teaching, home, scores, children, genes,
   UK, GCSE, exam, exams, twins, twin study
%X "... UK-wide examination, called the General Certificate of Secondary
   Education (GCSE). In a national twin sample of 11,117 16-year-olds,
   heritability was substantial for overall GCSE performance for compulsory core
   subjects (58%) [&] for each of them individually: English (52%), maths (55%)
   & sci. (58%). In contrast, the overall effects of shared environment, which
   includes all family & school influences shared by members of twin pairs
   growing up in the same family & attending the same school, accounts for about
   36% of the variance of mean GCSE scores. The significance of these findings
   is that individual differences in educational achievement at the end of
   compulsory education are not primarily an index of the quality of teachers or
   schools: much more of the variance of GCSE scores can be attributed to
   genetics than to school or family environment. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0080341">doi:10.1371/journal.pone.0080341</A>]['13].

%A K. Schuchmann
%A V. Muller
%T Direct and reversible hydrogenation of CO2 to formate by a bacterial carbon
   dioxide reductase
%J Science
%V 342
%N 6164
%P 1382-1385
%M DEC
%D 2013
%K jrnl, c2013, c201x, c20xx, hydrogen, alternative fuel, fuels, storage,
   energy, CO2, formate, dihydrogen, hydrogenation, Acetobacterium woodii,
   reductase
%X "... An increasingly considered alternative for the direct handling of
   hydrogen is to use CO2 as an intermediate storage material. However, CO2 is
   thermodynamically stable, & developed chemical catalysts often require high
   temps., pressures, &/or additives for high catalytic rates. ... present the
   discovery of a bacterial hydrogen-dependent CO2 reductase from Acetobacterium
   woodii directly catalyzing the hydrogenation of CO2. [&] demonstrate a
   whole-cell system able to produce formate as the sole end product from
   dihydrogen (H2) & CO2 as well as syngas. ... opens biotechnological
   alternatives for efficient CO2 hydrogenation either by using the isolated
   enzyme or by employing whole-cell catalysis."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1244758">doi:10.1126/science.1244758</A>]['13].

%A R. Bendlin
%A S. Krehbiel
%A C. Peikert
%T How to share a lattice trapdoor: Threshold protocols for signatures and
   (H)IBE
%J 11th Int. Conf. on Applied Cryptography and Network Security
%P 218-236
%M JUN
%D 2013
%K conf, ACNS, c2013, c201x, c20xx, zz0214, lattice based cryptography, code,
   encryption, hard, public key, protocol, signature, delegation, GPV, IBE
%X "We develop secure threshold protocols for two important ops. in lattice
   cryptography, namely, generating a hard lattice L together with a 'strong'
   trapdoor, & sampling from a discrete Gaussian distn over a desired coset of
   L using the trapdoor. ... e.g.,, they are exactly the key-generation &
   signing ops (resp.) for the GPV sig.scheme ...
   & they are the public parameter ... also provide a protocol for trapdoor
   delegation, which is used in lattice-based hierarchical IBE schemes. ..."
   -- pdf@[<A HREF="http://www.cc.gatech.edu/~cpeikert/pubs/threshtrap.pdf">gatech</A>]['14],
      auth3@[<A HREF="http://www.cc.gatech.edu/~cpeikert/">gatech</A>]['14],
      [<A HREF="http://dx.doi.org/10.1007/978-3-642-38980-1_14">doi:10.1007/978-3-642-38980-1_14</A>]['14].
   Also see 'Quantum Spy Games' -- [<A HREF="http://dx.doi.org/10.1126/science.343.6170.482">news</A>][31/1/'14].
   [Also search for: public key encryption].

%A J. Marsden
%A D. Budden
%A H. Craig
%A P. Mascato
%T Language individuation and marker words: Shakespeare and his Maxwell's demon
%J PLoS One
%V 8
%N 6
%P e66813
%M JUN
%D 2013
%K jrnl, eJrnl, c2013, c201x, c20xx, zz0414, Shakespeare, Fletcher, Jonson,
   Middleton, literature, writing, style, styles, play, plays, word, words,
   author, stats, CM1 score, frequency, vocabulary, linguistic analysis
%X "... corpus containing 55,055 unique words was generated from 168 plays from
   the Shakespearean era (16th & 17th C) of undisputed authorship. ... results
   suggest that different authors, while adhering to the structural &
   grammatical bounds of a common language, develop measurably distinct styles
   by the tendency to over-utilise or avoid particular common words & phrasings.
   Considering language & the potential of words as an abstract chaotic system
   with a high entropy, similarities can be drawn to the Maxwell's Demon thought
   experiment; authors subconsciously favour or filter certain words, modifying
   the probability profile in ways that could reflect their individuality &
   style."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0066813">doi:10.1371/journal.pone.0066813</A>]['14],
   auth3@[<A HREF="http://www.newcastle.edu.au/profile/hugh-craig">Uni.NC</A>]['14].

%A J.-M. Fortin
%A D. J. Currie
%T Big science vs. little science: How scientific impact scales with funding
%J PLoS One
%V ?
%P ?-?
%M JUN
%D 2013
%K jrnl, eJrnl, c2013, c201x, c20xx, zz0214, publish, perish, grant, grants,
   peer review, impact factor, citations, track record, scientific, funding,
   money, research, application, ARC, NHMRC, NSERC, health
%X "... examine the scientific impact of individual university-based researchers
   in three disciplines funded by the Nat. Sci. & Eng. Res. Council of Canada
   (NSERC). We considered four indices of sci.impact: numbers #s articles
   published, #s of citations to those articles, the most cited article, & the
   # of highly cited articles, each measured over a four-year period [v] the
   amount of NSERC funding received. Impact is +vely, but only weakly, related
   to funding. Researchers who received additional funds from a 2nd federal
   granting council, the Canadian Insts. for Health Res., were not more
   productive than those who received only NSERC funding. Impact was generally
   a decelerating fn of funding. Impact per dollar was therefore lower for large
   grant-holders. This is inconsistent with the hypothesis that larger grants
   lead to larger discoveries. [&] the impact of researchers who received
   increases in funding did not predictably increase. We conclude that sci.
   impact (as reflected by publns) is only weakly limited by funding. We suggest
   that funding strategies that target diversity, rather than 'excellence', are
   likely to prove to be more productive."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0065263">doi:10.1371/journal.pone.0065263</A>]['14].
   [Also search for: research funding]  and  [also search for: publish perish].

%A K. Johnson
%T Dear Code Breaker: The Letters of Margaret Rock (Bletchley Park Code Breaker)
   and John Rock (Parachute & Glider Forces Pioneer)
%I BookTower
%P 198
%M AUG
%D 2013
%K book, text, c2013, c201x, c20xx, zz1114, Bletchley Park, WW2, WWII,
   world war two, cryptanalysis, woman, female, cryptanalyst, codes
%X 1st ed 2013; pb; uk isbn:0955716454; uk isbn13:978-0955716454.
   "... This touching book of letters is a unique glimpse into the lives of
   Margaret Rock, Bletchley Park Code Breaker, and her brother, John Rock,
   British Parachute and Glider Forces Pioneer. ..."
   [Also search for: Bletchley Park].

%A D. L. Paulhus
%A B. G. Westlake
%A S. S. Calvez
%A P. D. Harm
%T Self-presentation style in job interviews: The role of personality and
   culture
%J J. of Applied Social Psychology
%V 43
%N 10
%P 2042-2059
%M OCT
%D 2013
%K jrnl, c2013, c201x, 20xx, zz0716, human behaviour, self promoter, narcissist,
   narcissists, job interview, applicant, ethnic, ethnicity, jobs, work,
   confidence, vain, vanity, ego, egoist, egoistical, self esteem
%X "Chronic self-promoters may thrive in job interviews where such behavior is
   encouraged. In Study 1, 72 participants were videotaped as they simulated the
   job applicant role. Accountability was manipulated by the expectation of
   expert versus nonexpert interviewers. As accountability increased,
   self-promotion tended to decrease among non-narcissists but increase among
   narcissists. Ingratiation showed no interaction or main effects. In Study 2,
   222 raters evaluated applicant videos varying in narcissism (high vs. low) &
   ethnicity (European heritage vs. East Asian heritage). Chronic self-promoters
   (i.e., Euro.-heritage narcissists) were given the most +ve evaluations.
   Detailed behavior analyses indicated that the n. advantage was
   derived primarily from frequent self-praise & the Euro.-heritage advantage
   from use of active ingratiation tactics. In sum, self-presentation styles
   that pay off in the (Western) interview context are highly selective."
   -- [<A HREF="http://dx.doi.org/10.1111/jasp.12157">doi:10.1111/jasp.12157</A>]['16].

%A A. Elberse
%T Blockbusters: Hit-making, Risk-taking, and the Big Business of Entertainment
%I HenryHolt
%P 320
%M OCT
%D 2013
%K book, c2013, c201x, c20xx, zz0116, business, marketing, choice, products,
   inventory, demand, hits, misses, hit, blockbuster, popular culture,
   entertainment, pop, TV, movies, iTunes, Amazon, Netflix, long tail (not)
%X 1st ed 2016; hb us$23; uk us isbn:0805094334; uk us isbn13:978-0805094336.
   (kindle, asin:B00C74OXLO.)
   "... explains a powerful truth about the fiercely competitive world of
   entertainment: building a business around blockbuster products - the movies,
   television shows, songs, and books that are hugely expensive to produce and
   market - is the surest path to long-term success. ..."
   (Also see,
    "... In 2011, eight million different songs sold at least one copy.
    'But people don't realize that about one-third of these songs
    sold exactly one copy.' ..."
    -- mag@[<A HREF="http://harvardmagazine.com/2014/01/the-way-of-the-blockbuster">hrvd</A>]['16].)
   [Also search for: Anderson c2006] - contrary.

%A M. A. Woodley
%A J. te Nijenhuis
%A R. Murphy
%T Were the Victorians cleverer than us? The decline in general intelligence
   estimated from a meta-analysis of the slowing of simple reaction time
%J Intelligence
%V 41
%N 6
%P 843-850
%M NOV-DEC
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0814, IQ, decline, rise, fall, Flynn effect,
   human, general intelligence, change, changing, eugenics,
   European, Western, Victorian, populations, controversial
%X "The Victorian era was marked by an explosion of innovation & genius ...
   The presence of dysgenic fertility for IQ amongst W.nations, starting in the
   19th C., suggests that these trends might be related to declining IQ. ...
   We tested the hyp. that the Vs. were cleverer than modern popns, using high-
   -quality instruments, namely measures of simple visual reaction time in a
   meta-analytic study. ...  used the data on the secular slowing of simple
   reaction time described in a meta-analysis of 14 age-matched studies from
   W.countries conducted between 1889 & 2004 to est. the decline in g [gen.
   intel] that may have resulted from the presence of dysgenic fertility. Using
   psychometric meta-analysis we computed the true correln between simple
   reaction time & g, yielding a decline of -1.16 IQ points / decade or -13.35
   IQ points since V.times. ... strongly indicate that with respect to g the
   Vs. were substantially cleverer than modern W.poplns."
   -- [<A HREF="http://dx.doi.org/10.1016/j.intell.2013.04.006">doi:10.1016/j.intell.2013.04.006</A>]['14].
   (?So, a reverse Flynn effect?)   [Also search for: human intelligence IQ].

%A C. Arthur
%T Academics should not remain silent on hacking
%J Nature
%V 504
%N 7480
%M DEC
%D 2013
%K news, views, c2013, c201x, c20xx, zz1213, NIST Dual EC DRBG, random numbers,
   cryptography, Snowden files, OpenAudit, encryption, communications, security,
   privacy, big brother, spy, spying, state surveillance,
   US, USA, NSA, prism, Microsoft, Windows, TrueCrypt, backdoor,
   British, UK, GCHQ
%X "The revelation that US & British spy agencies have undermined a commonly
   used encryption code should alarm researchers, says Charles Arthur. ... "
   -- [<A HREF="http://dx.doi.org/10.1038/504333a">doi:10.1038/504333a</A>]['13].
       "The National Security Agency should be banned from attempting to
       undermine the security of the internet and stripped of its power to
       collect telephone records in bulk, a White House review panel
       recommended on Wednesday. ..."
       -- The_G.@[<A HREF="http://www.theguardian.com/world/2013/dec/18/nsa-bulk-collection-phone-date-obama-review-panel">www</A>][18/12/2013].
   Also see [<A HREF="http://www.OpenAudit.org">openaudit</A>]['13].
   And, "The Windows version of TrueCrypt 7.0a deviates from the Linux version
   in that it fills the last 65,024 bytes of the header with random values
   whereas the Linux version fills this with encrypted zero bytes. From the
   point of view of a security analysis the behavior of the Windows version
   is problematic ..."
   -- [<A HREF="http://blog.cryptographyengineering.com/2013/10/lets-audit-truecrypt.html">cryptographyengineering.com</A>][10/2013].
    = [<A HREF="http://go.nature.com/nsvdjh">nat're</A>][19/12/2013].
   [Also search for: NSA cryptography].

%T ASPIRES: Young people's science and career aspirations age 10-14
%I Dept. Ed. and Prof. Studies, Kings Coll., London
%M DEC
%D 2013
%K TR, c2013, c201x, c20xx, zz1214, school, university, education, career,
   gender, children, boys, girls, women, students, scientist, engineer,
   STEM, science, technology, engineering, mathematics, computing, GCSE,
   uk, stats
%X "... Gender issues are evident from a young age. Girls are less likely than
   boys to aspire to sci. careers, even though a higher percentage of girls
   than boys rate sci. as their favourite subject. Girls are far more likely to
   aspire to arts-related & 'caring' careers.  Among 12-13 year old students,
   18% of boys & 12% of girls aspire to become scientists - in comparison, 64%
   of girls aspire to careers in the arts. ... Those 'girly' girls who do aspire
   to sci. careers at age 10/11 tend to either drop or change these aspirations
   over time.  ...  often referred to as the 'leaky pipeline', whereby women &
   girls participate in progressively smaller #s as they move along the sci.
   qualifications & career 'ladder'. ..."
   -- pdf@[<A HREF="http://www.kcl.ac.uk/sspp/departments/education/research/aspires/ASPIRES-final-report-December-2013.pdf">12/2013</A>]['14].
   (And, Aspires2, age 14-19, 2014+ [<A HREF="http://www.kcl.ac.uk/sspp/departments/education/research/aspires/index.aspx">kcl</A>]['14].)
   [Also search for: STEM education].

%A D. Kahneman
%T Thinking Fast and Slow
%I FarrarStrausGiroux
%P 512
%D 2013
%K book, c2013, c201x, c20xx, zz0715, human behaviour, decision, making,
   thought, bias, biases, intuition, logical, confidence, risk, economics,
   financial
%X reprint 2013; pb us$8; uk us isbn:0374533555; uk us isbn13:978-0374533557.
   "... explains the two systems that drive the way we think. System #1 is fast,
   intuitive, & emotional; #2 is slower, more deliberative, & more logical.
   The impact of overconfidence on corporate strategies, the difficulties of
   predicting what will make us happy in the future, the profound effect of
   cognitive biases on everything from playing the stock market to planning our
   next vacation ..."
   [Also search for: human behaviour biases] & [also search for: Kahneman book].

%A D. Aitkenhead
%T Peter Higgs: I wouldn't be productive enough for today's academic system
%J The Guardian
%M DEC
%D 2013
%K news, interview, c2013, c201x, c20xx, physics, Higgs boson, mass,
   2013 Nobel prize winner, NobelPrize, publish, perish, KPI, KPIs,
   Edinburgh University, scientific research, science, management, impact,
   publications, papers, quote, quotable
%X '... published fewer than 10 papers after his groundbreaking work, which
   identified the mechanism by which subatomic material acquires mass, was
   published in 1964. ...  authorities then took the view, he later learned,
   that he "might get a Nobel prize - and if he doesn't we can always get rid
   of him". Higgs said he became "an embarrassment to the department when they
   did research assessment exercises". A message would go around the dept
   saying: "Please give a list of your recent publications." Higgs said:
   "I would send back a statement: 'None.'" ...'
   -- The G [<A HREF="https://www.theguardian.com/science/2013/dec/06/peter-higgs-boson-academic-system">7/12/2013</A>]['20].

%A J. P. A. Ioannidis
%T Research accomplishments that are too good to be true
%J Intensive Care Medicine
%V 40
%N 1
%P 99-101
%M JAN
%D 2014
%K conf, ESICM, c2014, c201x, c20xx, zz1114, publish, perish, science,
   University, academic, scientific research, impact, ethics, scandal, fake,
   fraud, abuse, misconduct, corrupt, falsify, falsification, fabricate,
   fabrication, Dean, Stapel, Tilburg, Boldt, hydroxylethyl starch,
   quote, quotable
%X "We are all proud of successes in sci. res.. Society at large expects to
   reap great benefits from these breakthroughs. However, sometimes research
   accomplishments are just too good to be true: single studies with
   extravagant results ...  Vignette 1: A famous prof. states (verbatim) in
   his inaugural speech on being installed in a prestigious university:
     'The freedom we have in the design of our experiments is so enormous that
     when an experiment does not give us what we are looking for, we blame the
     experiment, not our theory. (At least, that is the way I work). Is this
     problematic? No.' The researcher claims essentially that he can always get
   significant results. In fact, he does. He publishes ferociously & climbs
   fast the academic ladder[1]. ...
   ... Vignette 1: This is Diederik Stapel, dean of the School of Social &
   Behavioral Scis. at Tilburg U., & the quote is from his inauguration at
   Groningen. After decades of publishing dozens of spectacular papers, he
   admitted to propelling his career with fake data [1, 3]. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/s00134-013-3100-z">doi:10.1007/s00134-013-3100-z</A>]['14];
   auth@[<A HREF="https://med.stanford.edu/profiles/john-ioannidis">Stanf.</A>]['14].
   [Also search for: publish perish] and
   [also search for: scientific research misconduct].

%A Betty Medsger
%T The Burglary: The Discovery of J. Edgar Hoover's Secret FBI
%I Knopf
%M JAN
%D 2014
%K book, c2014, c201x, c20xx, zz0113, 1971, big brother, FBI, J Edgar Hoover,
   US, USA, state, government, Cointelpro, surveillance, illegal, spying, law,
   privacy, burglary, documents, Bonnie Raines, Forsyth, civil rights movement
%X "... A small group of activists - eight men and women - the Citizens
   Commission to Investigate the FBI, inspired by Daniel Berrigan's rebellious
   Catholic peace movement, set out to use a more active, but nonviolent, method
   of civil disobedience to provide hard evidence once and for all that the
   government was operating outside the laws of the land. ..."
   1st ed 2014; hb us$22; uk us isbn:0307962954; uk us isbn13:978-0307962959.
   (Also see [<A HREF="http://www.theguardian.com/world/2014/jan/07/fbi-office-break-in-1971-come-forward-documents">the G.</A>][7/1/2014].)

%A S. M. Bellovin
%A R. M. Hutchins
%A T. Jebara
%A S. Zimmeck
%T When enough is enough: Location tracking, mosaic theory, and machine learning
%J NYU J. of Law & Liberty
%V 8
%D 2014
%O U. of Maryland Legal Studies Res. Paper No.2013-51.
%K law, c2014, c201x, c20xx, zz0614, legal, privacy, tracking, surveillance,
   USA, fourth amendment, police, state, computer, technology, GPS,
   mosaic theory
%X "Since 1967, when it decided Katz v. United States, the Supreme Court has
   tied the right to be free of unwanted government scrutiny to the concept of
   reasonable expectations of privacy. ... Mosaic theorists advocate a
   cumulative approach to the evaluation of data collection. ... searches are
   'analyzed as a collective seq. of steps rather than as individual steps.'
   ... In 2001, the Supreme Court asked 'what limits there are upon the power
   of technology to shrink the realm of guaranteed privacy.' ... we explore an
   answer & investigate what lessons there are in the power of technology to
   protect the realm of guaranteed privacy. After all, as technology takes away,
   it also gives. The objective understanding of data compilation & analysis
   that is revealed by machine learning provides important 4th Amendment
   insights. We should begin to consider these insights more closely."
   -- [<A HREF="http://ssrn.com/abstract=2320019">www</A>]['14],
      [<A HREF="http://dx.doi.org/10.2139/ssrn.2320019">doi:10.2139/ssrn.2320019</A>]['14].

%A H. D. Matthews
%A et al
%T National contributions to observed global warming
%J Env. Res. Lett.
%V 9
%N 1
%P 014010
%M JAN
%D 2014
%K jrnl, eJrnl, c2014, c201x, c20xx, zz0114, climate change, CO2, greenhouse,
   gas, gases, emissions, methane, land use, clearing, deforestation,
   emitters
%X "There is considerable interest in identifying national contributions to
   global warming as a way of allocating historical responsibility for observed
   climate change. ... present a new estimate of national contributions to
   observed c.w., inc. CO2 emissions from fossil fuels & land-use change, ...
   also that there are vast disparities in both total and per-capita climate
   contributions among countries, and that across most developed countries,
   per-capita contributions are not currently consistent with attempts to
   restrict global temperature change to less than 2C above pre-industrial
   temperatures."
   -- [<A HREF="http://dx.doi.org/10.1088/1748-9326/9/1/014010">doi:10.1088/1748-9326/9/1/014010</A>]['14].

%A T. F. Ronnow
%A et al ...
%A M. Troyer
%T Defining and detecting quantum speedup
%J arXiv
%M JAN
%D 2014
%K TR, c2014, c201x, c20xx, zz0114, Dwave, D wave, two, Dwave2,
   quantum computing, computer, annealer, speed
%X "... show how to define & measure quantum speedup in various scenarios, & how
   to avoid pitfalls that might mask or fake quantum speedup. We illustrate our
   discussion with data from a randomized benchmark test on a D-Wave Two device
   with up to 503 qubits. Comparing the performance of the device on random spin
   glass instances with limited precision to simulated classical & q.annealers,
   we find no evidence of q.speedup when the entire data set is considered, &
   obtain inconclusive results when comparing subsets of instances on an
   instance-by-instance basis. Our results for one particular benchmark do not
   rule out the possibility of speedup for other classes of problems &
   illustrate that q.speedup is elusive & can depend on the question posed."
   -- 1401.2910@[<A HREF="http://arxiv.org/abs/1401.2910">arXiv</A>]['14].
   [Also search for: quantum computer] and
   [also search for: Dwave quantum computing].

%A J. Cannarella
%A J. A. Spechler
%T Epidemiological modeling of online social network dynamics
%J arXiv
%M JAN
%D 2014
%K TR, c2014, c201x, c20xx, zz0114, internet, www, social media, facebook, Meta,
   myspace, online, networks, OSN, SIR, irSIR, prediction, decline, abandonment,
   zz0124, zzPrediction
%X 'The last decade has seen the rise of immense online social networks (OSNs)
   such as MySpace and Facebook. ... we use epidemiological models to explain
   user adoption & abandonment of OSNs ... modify the traditional SIR model of
   disease spread by incorporating infectious recovery dynamics such s.t.
   contact between a recovered & infected member of the popn is required for
   recovery. The proposed infectious recovery SIR model (irSIR model) is
   validated using publicly available Google search query data for "MySpace" as
   a case study of an OSN that has exhibited both adoption & abandonment phases.
   The irSIR model is then applied to search query data for "Facebook," which is
   just beginning to show the onset of an abandonment phase. Extrapolating the
   best fit model into the future predicts a rapid decline in Facebook activity
   in the next few years.'
   -- 1401.4208@[<A HREF="http://arxiv.org/abs/1401.4208">arXiv</A>]['14].
   And check back c2017
   -- [<A HREF="http://www.abc.net.au/news/2014-01-23/facebook-could-fade-out-like-a-disease-researchers/5214524">abc</A>]['14].
   Also see [<A HREF="http://www.theguardian.com/technology/2014/jan/24/facebook-princeton-university-demise">the_G.</A>][24/1/2014].
   (30 July 2015: "Half the world's estimated online population now
    check into ... Facebook at least once a month. ... [its shares now]
    trading at around us$97 ..."
    -- [<A HREF="http://www.bbc.com/news/business-33712729">bbc</A>].
    And, 3/1/24, Meta's(!) shareprice us$346, & we still have long-Facebook.)
   [Also search for: zzPrediction] -- I do like a prediction.

%A J. Haig
%A J. Nott
%A G.-J. Reichart
%T Australian tropical cyclone activity lower than at any time over the
   past 550-1,500 years
%J Nature
%V 505
%P 667-671
%M JAN
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0214, climate change, weather, meteorology,
   cyclones, hurricane, storm, storms, frequency, Australia, CAI, stats
%X "... show, on the basis of a new tropical cyclone activity index (CAI), that
   the present low levels of storm activity on the mid west & NE coasts of
   Australia are unprecedented over the past 550 to 1,500 y.. ... & long-term
   palaeotempest (prehistoric tropical cyclone) records derived from the
   18-O/16-O ratio of seasonally accreting carbonate layers of actively growing
   stalagmites. ... reveal a repeated multicentennial cycle of tropical cyclone
   activity, the most recent of which commenced around AD1700. The present cycle
   inc. a sharp decrease in activity after 1960 in WA. This is in contrast to
   the increasing freq. & destructiveness of Northern Hemisphere tropical
   cyclones since 1970 in the Atlantic Ocean & the W N Pacific Ocean. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12882">doi:10.1038/nature12882</A>]['14].
   [Note however, the cyclones that do occur will be much stronger.]

%A H. S. Dent jr
%T The Demographic Cliff: How to Survive and Prosper During the
   Great Deflation of 2014-2019
%I PortfolioHC
%P 368
%M JAN
%D 2014
%K book, c2014, c201x, c20xx, zz0214, economics, economy, investment, housing,
   cycle, boom, demography, population, bust, prediction, zz0120, zzPrediction
%X 1st ed 2014; hb us$18; uk us isbn:1591847273; uk us isbn13:978-1591847274.
   "... With his track record of accurately predicting Japan's collapse in 1989,
   the dot-com bubble-bust in 2000 and the housing bust in 2006 to 2007 (among
   many other things), he has appeared on Good Morning America and PBS, and is
   a regular guest on CNBC and Fox Business[*]. ..."
   [*Is that a good thing?]  Also see
   -- [<A HREF="http://www.theguardian.com/business/2014/feb/14/australia-housing-bubble-ready-burst">The_G.</A>][13/2/2014].
   [Also search for: zzPrediction].  Must check back in 2020.

%A E. G. Nisbet
%A E. J. Dlugokencky
%A P. Bousquet
%T Methane on the rise again
%J Science
%V 343
%N 6170
%P 493-495
%M JAN
%D 2014
%K news, views, c2014, c201x, c20xx, zz0214, climate change, greenhouse gas,
   gases, CH4, methane, global warming, cause
%X "Roughly one-fifth of the increase in radiative forcing by human-linked
   greenhouse gases since 1750 is due to methane. The past three decades have
   seen prolonged periods of increasing atmospheric methane, but the growth rate
   slowed in the 1990s, & from 1999 to 2006, the m.burden (that is, the total
   amount of m. in the air) was nearly constant. Yet strong growth resumed in
   2007. The reasons for these observed changes remain poorly understood
   because of limited knowledge of what controls the global m.budget."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1247828">doi:10.1126/science.1247828</A>]['14].
   [Also search for: cause global warming].

%A L. Harding
%T The Snowden Files: The Inside Story of the World's Most Wanted Man
%I VintagePubl
%P 352
%M FEB
%D 2014
%K book, c2014, c201x, c20xx, zz0214, internet, security, privacy, spying,
   spies, spooks, NSA, US, intelligence, USA, UK, GCHQ, eavesdropping,
   communications, meta data, metadata, PRISM, big brother, state surveillance,
   the Guardian, Grauniad, whistle blower
%X 1st ed 2014; pb us$11; uk us isbn:0804173524; uk us isbn13:978-0804173520.
   [Also search for: NSA cryptography].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/1984/">1984</A>].)

%A H. Shema
%A J. Bar-Ilan
%T Do blog citations correlate with a higher number of future citations?
   Research blogs as a potential source for alternative metrics
%J J. Assoc. for Info. Sci. and Tech.
%V ?
%P ?-?
%M FEB
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0214, www, internet, science, blog, blogging,
   impact factor, publish, perish
%X "... examines ... blog posts aggregated at ResearchBlogging.org, which
   discuss peer-reviewed articles & provide full bibliographic refs.. Articles
   reviewed in these blogs therefore receive 'blog citations.' We hypothesized
   that articles receiving blog citations close to their publn time receive more
   j. citations later than the articles in the same j. published in the same
   year that did not receive such blog citations. Stat. sig. evidence for
   articles published in 2009 & 2010 support this hypothesis for seven of 12
   journals (58%) in 2009 & 13 of 19 journals (68%) in 2010. ..." (online Jan.)
   -- [<A HREF="http://dx.doi.org/10.1002/asi.23037">doi:10.1002/asi.23037</A>]['14].
   [Also search for: publish perish].

%A I.-U. Park
%A M. W. Peacey
%A M. R. Munafo
%T Modelling the effects of subjective and objective decision making in
   scientific peer review
%J Nature
%V 506
%P 93-96
%M FEB
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0214, scientific, research, publish, perish,
   peer review, reviewing, refereeing, referees, herding, bias, papers, model
%X "... Given the increasing concern surrounding the reproducibility of much
   published research, it is critical to understand whether peer review is
   intrinsically susceptible to failure, or [if] other extrinsic factors are
   responsible that distort scientists' decisions. ... show that even when
   scis. are motivated to promote the truth, their behaviour may be influenced,
   & even dominated, by info. gleaned from their peers' behaviour, rather than
   by their personal dispositions. ... known as herding, subjects the sci.
   community to an inherent risk of converging on an incorrect answer & raises
   the possibility that, under certain condns, sci. may not be self-correcting.
   ... demo. that exercising some subjectivity in reviewer decisions ... serves
   to curb the herding process, can be beneficial for the sci.community in
   processing available info. to est. truth more accurately. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12786">doi:10.1038/nature12786</A>]['14].
   [Also search for: publish perish]  and  [also search for: refereeing].

%A J. Mervis
%T Peering into peer review
%J Science
%V 343
%N 6171
%P 596-598
%M FEB
%D 2014
%K news, views, c2014, c201x, c20xx, zz0214, publish, perish, NIH, scientific,
   science, research, grant, grants, peer review, ARC, refereeing, application,
   funding, impact factor
%X "Most scientists have the greatest respect[?] for peer review at the National
   Institutes of Health (NIH). But two recent studies of cardiovascular research
   suggest it's falling short in meeting its main mission - to help NIH
   officials decide what research is likely to have the biggest impact."
   -- [<A HREF="http://dx.doi.org/10.1126/science.343.6171.596">doi:10.1126/science.343.6171.596</A>]['14].
   [Also search for: research funding]  and  [also search for: publish perish].
      (Also see 'Making Every Scientist a Research Funder' @
      [<A HREF="http://dx.doi.org/10.1126/10.1126/science.343.6171.598">Sci.</A>]['14].)

%A M. Ramscar
%A P. Hendrix
%A C. Shaoul
%A P. Milin
%A H. Baayen
%T The myth of cognitive decline: Non-linear dynamics of lifelong learning
%J Topics in Cognitive Sci.
%V 6
%N 1
%P 5-42
%M JAN
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0414, brain, age, aging, ageing, learning,
   cognition, memory, recall, adult, human
%X "As adults age, their performance on many psychometric tests changes
   systematically ... widely taken to reveal that cognitive information-
   -processing capacities decline across adulthood. Contrary to this, we suggest
   that older adults'; changing perf. reflects memory search demands, which
   escalate as experience grows. A series of simulations show how the perf.
   patterns observed across adulthood emerge naturally in learning models as
   they acquire knowledge. The simulations correctly identify greater variation
   in the cog. perf. of older adults, & successfully predict that older adults
   will show greater sensitivity to fine-grained differences in the properties
   of test stimuli than younger adults. ... indicate that older adults';
   performance on cognitive tests reflects the predictable consequences of
   learning on info.-proc., & not cognitive decline. We consider the
   implications of this for our scientific & cultural understanding of aging."
   -- [<A HREF="http://dx.doi.org/10.1111/tops.12078">doi:10.1111/tops.12078</A>]['14].
   (Also see auth1@[<A HREF="http://michaelramscar.wordpress.com/access-articles/">w'rdpr'ss</A>]['14].)

%A W. Cai
%A et al ...
%A M. H. England ...
%A F.-F. Jin
%T Increasing frequency of extreme El Nino events due to greenhouse warming
%J Nature Climate Change
%V 4
%P 111-116
%M JAN
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0214, climate, change, global warming,
   temperature, El Nino, Pacific
%K "... present climate modelling evidence for a doubling in the occurrences in
   the future in response to greenhouse warming. We est. the change by
   aggregating results from climate models in the Coupled Model Intercomparison
   Project phases 3 (CMIP3) & 5 (CMIP5) multi-model databases, & a perturbed
   physics ensemble. The increased freq. arises from a projected surface warming
   over the eastern equatorial Pacific that occurs faster than in the
   surrounding ocean waters, facilitating more occurrences of atmospheric
   convection in the eastern equatorial region."
   -- [<A HREF="http://dx.doi.org/10.1038/nclimate2100">doi:10.1038/nclimate2100</A>]['14].

%A S. W. Shin
%A G. Smith
%A J. A. Smolin
%A U. Vazirani
%T How "Quantum" is the D-Wave machine?
%J arXiv
%M JAN
%D 2014
%K arXiv, TR, c2014, c201x, c20xx, zz0514, Dwave, quantum computing,
   controversial
%X "... outline a simple classical model, & show that it achieves excellent
   correlation with published [I/O] behavior of the D-Wave One m/c on 108
   qubits. While raising questions about "how quantum" the D-Wave m/c is, the
   new model also provides additional algorithmic insights into the nature of
   the native computational problem solved by the D-Wave machine."
   -- 1401.7087@[<A HREF="http://arxiv.org/abs/1401.7087">arXiv</A>]['14].
   [Also search for: Dwave quantum computing].
   (Also see, "... concluding that a simple, classical computing model of
   interacting magnets could explain behaviour in D-Wave's machines. ..."
   -- [<A HREF="http://www.bbc.com/news/science-environment-27264552">bbc</A>][19/5/'14].)

%A M. H. England
%A S. McGregor
%A P. Spence
%A G. A. Meehl
%A A. Timmermann
%A W. Cai
%A A. Sen Gupta
%A M. J. McPhaden
%A A. Purich
%A A. Santoso
%T Recent intensification of wind-driven circulation in the Pacific and the
   ongoing warming hiatus
%J Nature Climate Change
%V ?
%P ?-?
%M FEB
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0214, climate, change, global warming, ocean,
   subsurface, mixing, temperature, rise, increase, hiatus, pause,
   trade winds, tropical, Pacific
%X "Despite ongoing increases in atmospheric greenhouse gases, the Earth's
   global avg. surface air temp. has remained more or less steady since 2001.
   ... we show that a pronounced strengthening in Pacific trade winds over the
   past two decades - unprecedented in observations/reanalysis data & not
   captured by climate models - is sufficient to account for the cooling of the
   tropical P. & a substantial slowdown in surface warming through increased
   subsurface ocean heat uptake. The extra uptake has come about through
   increased subduction in the Pacific shallow overturning cells, enhancing
   heat convergence in the equatorial thermocline. [&] the accelerated trade
   winds have incr. equatorial upwelling in the central & eastern P., lowering
   sea surface temp. there, which drives further cooling in other regions. The
   net effect of these anomalous winds is a cooling in the 2012 global avg.
   surface air temp. of 0.1-0.2C, which can account for much of the hiatus in
   surface warming observed since 2001. ... could persist for much of the
   present decade if the trade wind trends continue, however rapid warming is
   expected to resume once the anomalous wind trends abate."
   -- [<A HREF="http://dx.doi.org/10.1038/nclimate2106">doi:10.1038/nclimate2106</A>]['14],
   & auth1@[<A HREF="http://web.science.unsw.edu.au/~matthew/">unsw</A>]['14].
      (Also see '... "Over the last 50 years, 90% of the extra heat that's
                been stored by the earth is found in the ocean. ..." ...'
      -- [<A HREF="http://www.abc.net.au/news/2014-02-10/scientists-find-explanation-for-global-warming-pause/5248456">abc</A>][10/2/2014].)
      (Also see perspective@[<A HREF="http://dx.doi.org/10.1126/science.1248115">www</A>][28/2/2014]</A>.)

%A K. Pistone
%A I. Eisenman
%A V. Ramanathan
%T Observational determination of albedo decrease caused by vanishing
   Arctic sea ice
%J PNAS
%P ?-?
%M FEB
%D 2014
%K jrnl, PNAS, c2014, c201x, c20xx, zz0214, global warming, climate change, CO2,
   Arctic, polar, sea ice, melt, cover, summer, albedo, reflection, CERES
%X "The decline of Arctic sea ice has been documented in over 30y ... The
   resulting darkening of the Arctic & its amplification of global warming was
   hypothesized almost 50y ago but has yet to be verified with direct obs.. This
   study uses satellite radiation budget measurements along with satellite
   microwave sea ice data to document the Arctic-wide decrease in planetary
   albedo & its amplifying effect on the warming. ... reveals a striking
   relationship between planetary albedo & sea ice cover, quantities inferred
   from two indep. satellite instruments. We find that the Arctic planetary
   albedo has decreased from 0.52 to 0.48 between 1979 & 2011, corr.to an
   additional 6.4 +/- 0.9 W/m2 of solar energy input into the A.Ocean region
   since 1979. Avgd over the globe, this a. decr. corr.to a forcing that is 25%
   as large as that due to the change in CO2 during this period, considerably
   larger than expectations from models & other less direct recent ests..
   Changes in cloudiness appear to play a negligible role in obs. Arctic
   darkening, thus reducing the possibility of Arctic cloud albedo feedbacks
   mitigating future Arctic warming." [online Feb 2014].
   -- pdf@[<A HREF="http://eisenman.ucsd.edu/publications/Pistone-Eisenman-Ramanathan-2014.pdf">ucsd</A>]['14].

%A E. Szeng
%T How academia and publishing are destroying scientific innovation:
   A conversation with Sydney Brenner
%J King's review
%M FEB
%D 2014
%K news, views, c2014, c201x, c20xx, zz0314, publish, perish, KPI, KPIs,
   scientific research, impact, peer review, misuse, reviewing, refereeing,
   Sydney Brenner, Peter Higgs, grant, grants, funding, ARC, NIH, NHMRC,
   quote, quotable, Nobel prize, NobelPrize
%X "I recently had the privilege of speaking with Professor Sydney Brenner, a
   prof. of Genetic medicine at the Univ. of Cambridge & Nobel Laureate in
   Physiology or Medicine in 2002 ...
   SB: 'Today the Americans have developed a new culture in science
       based on the slavery of graduate students. Now graduate students
       of American institutions are afraid. He just performs. He's got
       to perform. ... .'
   ... 'A Fred Sanger would not survive today's world of science. With
   continuous reporting & appraisals, some committee would note that
   he published little of import between insulin in 1952 & his
   first paper on RNA sequencing in 1967 with another long gap until
   DNA sequencing in 1977. He would be labelled as unproductive, &
   his modest personal support would be denied. We no longer have a
   culture that allows individuals to embark on long-term - & what
   would be considered today extremely risky - projects.'
      I found this particularly striking given that another recent Nobel
   prize winner, Peter Higgs, who identified the particle that bears
   his name, the Higgs boson, similarly remarked in an interview with
   the Guardian that, 'he doubts a similar breakthrough could be
   achieved in today's academic culture, because of the expectations
   on academics to collaborate & keep churning out papers. He said
   that: "it's difficult to imagine how I would ever have enough peace
   & quiet in the present sort of climate to do what I did in 1964."'
   ... 'I think peer review is hindering science. In fact, I think it
   has become a completely corrupt system. ...' ..."
   -- [<A HREF="http://kingsreview.co.uk/magazine/blog/2014/02/24/how-academia-and-publishing-are-destroying-scientific-innovation-a-conversation-with-sydney-brenner/">www</A>]['14].
   [Also search for: peer review].

%A K. Cowtan
%A R. G. Way
%T Coverage bias in the HadCRUT4 temperature series and its impact on
   recent temperature trends
%J Quarterly J. of the Royal Meteorological Soc.
%V ?
%P ?-?
%M FEB
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0514, climate change, global warming, pause,
   hiatus, missing heat, Arctic, temperature, trends, HadCRUT4, data set,
   sea ice
%X "Incomplete global coverage is a potential source of bias ... The widely used
   Hadley Centre's Climatic Reseach Unit ver.4 (HadCRUT4) dataset covers on
   avg. ~ 84% of the globe ... unsampled regions being concentrated at the poles
   & over Africa. ... [suggest] that HadCRUT4 is subject to bias due to its
   treatment of unobserved regions. ...  The widely quoted trend since 1997 in
   the hybrid global reconstruction is two and a half times *greater* than the
   corr.trend in the coverage-biased HadCRUT4 data. Coverage bias causes a cool
   bias in recent temps. relative to the late 1990s, which increases from around
   1998 to the present. Trends starting in 1997 or 1998 are particularly biased
   with respect to the global trend. The issue is exacerbated by the strong
   El Nino event of 1997-1998, which also tends to suppress trends starting
   during those years."
   -- [<A HREF="http://dx.doi.org/10.1002/qj.2297">doi:10.1002/qj.2297</A>]['14].
   [I.e., maybe no pause at all.]
   (Also see news@[<A HREF="http://www.york.ac.uk/news-and-events/news/2013/research/global-warming/">York</A>]['13].)

%A M. Parker
%T University, Ltd: Changing a business school
%J Organization
%M MAR
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0419, university, management, faculty, teaching,
   research, administration, deans, change, managerialism, KIP, KPIs, impact,
   league tables, Leicester, UK
%X "... recounts two years in the change management of a European business
   school. Using evidence gained whilst I was an employee, I describe the
   condns & institutional mechanisms which allowed an 'earth shattering' change
   programme to take place. This involved discounting the past & claiming that
   anyone who is against change is either self-interested or doesn't
   understand the 'real world'. The lack of collective & successful resistance
   is of particular concern here, since it suggests that (in certain contexts)
   academics are incapable of preventing their own institutions changing around
   them. Exit appears to be the only choice, when loyalty is questioned &
   voice impossible. I conclude with some observations on the relationship
   between the managerial business school & the idea of the university."
   -- [<A HREF="https://doi.org/10.1177/1350508413502646">doi:10.1177/1350508413502646</A>]['19]
   or [<A HREF="https://lra.le.ac.uk/bitstream/2381/37149/4/University,%20Ltd%20v4%20complete.pdf">le.ac.uk</A>]['19].
   [Also search for: university management].

%A J. Ruths
%A D. Ruths
%T Control profiles of complex networks
%J Science
%V 343
%N 6177
%P 1373-1376
%P 1373-1376
%M MAR
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0314, control, network, system, random
%X "Studying the control properties of complex networks provides insight into
   how designers & engineers can influence these systems to achieve a desired
   behavior. Topology of a n/w has been shown to strongly correlate with certain
   control properties; here we uncover the fundamental structures that explain
   the basis of this correlation. We develop the control profile, a statistic
   that quantifies the different proportions of control-inducing structures
   present in a n/w. We find that standard random n/w models do not reproduce
   the kinds of control profiles that are observed in real-world n/ws. The
   profiles of real n/ws form three well-def. clusters that provide insight into
   the high-level organization & function of complex systems."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1242063">doi:10.1126/science.1242063</A>]['14].

%A J. A. Secord
%T Visions of Science: Books and Readers at the Dawn of the Victorian Age
%I UChicagoPress
%D 2014
%K book, text, c2014, c201x, c20xx, zz0414, Victorian, c18xx, UK, science,
   Babbage, Lyell, Somerville, Carlyle, ideas, scientific, history
%X 1st ed 2014; hb us$24; uk us isbn:022620328X; uk us isbn13:978-0226203287.
   "The first half of the nineteenth century witnessed an extraordinary
   transformation in British political, literary, and intellectual life. ...
   explores seven key books - among them Charles Babbage's Reflections on
   the Decline of Science, Charles Lyell's Principles of Geology,
   Mary Somerville's Connexion of the Physical Sciences, and Thomas Carlyle's
   Sartor Resartus - and shows how literature that reflects on the wider
   meaning of science can be revelatory when granted a close reading and
   explored in tandem with an understanding of the physical qualities of
   books. ..."

%A P. Ginsparg
%T Automated screening: ArXiv screens spot fake papers
%J Nature
%V 508
%N 7494
%P 44
%M APR
%D 2014
%K news, c2014, c201x, c20xx, zz0414, fake, spam, spoof, hoax, gibberish,
   computer generated, SCIgen, Mathgen, paper, papers, publications,
   arXiv, Labbe
%X "Unlike the computer-generated nonsense papers in some peer-reviewed
   subscription services... the 500 or so preprints received daily by the
   automated repository arXiv are not pre-screened by humans. But sometimes
   automated assessment can be better than human diligence at enforcing stds."
   -- [<A HREF="http://dx.doi.org/10.1038/508044a">doi:10.1038/508044a</A>]['14].

%A A. B. Kao
%A I. D. Couzin
%T Decision accuracy in complex environments is often maximized by small group
   sizes
%J Proc. Royal Soc. B
%V 281
%N 1784
%P ?
%M JUN
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0815, economics, human, group, behaviour,
   groups, social, size, decision making, crowd, crowds, herd, effects
%X "... demo., using two simple models, that taking this natural complexity
   into account considerably alters the relationship between group size &
   decision-making accuracy. In only a minority of environments do we observe
   the typical wisdom of crowds phenomenon (whereby collective accuracy
   increases monotonically with group size). When the wisdom of crowds is not
   observed, we find that a finite, & often small, group size maximizes decision
   accuracy. We reveal that, counterintuitively, it is the noise inherent in
   these small groups that enhances their accuracy, allowing individuals in such
   groups to avoid the detrimental effects of correlated info. while exploiting
   the benefits of collective decision-making. Our results demonstrate that the
   conventional view of the wisdom of crowds may not be informative in complex &
   realistic environments, & that being in small groups can maximize decision
   accuracy across many contexts."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2013.3305">doi:10.1098/rspb.2013.3305</A>]['15].

%A L. Allen
%A J. Scott
%A A. Brand
%A M. Hlava
%A M. Altman
%T Publishing: Credit where credit is due
%J Nature
%V 508
%N 7496
%P 312-313
%P APR
%D 2014
%K news, views, c2014, c201x, c20xx, zz0414, publish, perish, papers,
   scientific, research, authors, authorship, contribution, role, roles,
   taxonomy
%X "Liz Allen, Amy Brand, Jo Scott, Micah Altman and Marjorie Hlava are
   trialling digital taxonomies to help researchers to identify their
   contributions to collaborative projects. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/508312a">doi:10.1038/508312a</A>]['14].

%A Z. Wang
%A B. Xu
%A H.-J. Zhow
%T Social cycling and conditional responses in the Rock-Paper-Scissors game
%J arXiv
%M APR
%D 2014
%K arXiv, c2014, c201x, c20xx, zz0514, rock paper scissors, RPS, game theory,
   NE, equilibrium, strategy, human players, behaviour
%X "... we observe population-level cyclic motions in a lab. experiment of the
   discrete-time iterated RPS game under the trad. random pairwise-matching
   protocol. The cycling direction & frequency are not sensitive to the payoff
   parameter a. This collective behavior contradicts with the NE theory but it
   is quantitatively explained by a microscopic model of win-lose-tie
   conditional response without any adjustable parameter. Our theoretical
   calculations reveal that this new strategy may offer higher payoffs to
   individual players in comparison with the NE mixed strategy, suggesting that
   high social efficiency is achievable through optimized conditional response."
   -- 1404.5199@[<A HREF="http://arxiv.org/abs/1404.5199">arXiv</A>]['14].

%A W. MacAskill
%T Replaceability, career choice, and making a difference
%J Ethical Theory and Moral Practice
%V 17
%N 2
%M APR
%D 2014
%P 269-283
%K jrnl, c2014, c201x, c20xx, zz0815, effective charity, altruism, philanthropy,
   ethics, being good, doing, philosophy, utility, utilitarian, donating,
   donation
%X "In this paper I defend the idea that deliberately pursuing a lucrative
   career in order to donate a large proportion of one's earnings is typically
   ethically preferable to a career within the charity sector."
   -- WM@[<A HREF="http://www.williammacaskill.com/">www</A>]['15],
      [<A HREF="http://cambridge.academia.edu/WilliamMacAskill">www</A>]['15].
   Also see The G. [<A HREF="http://www.theguardian.com/books/2015/aug/20/doing-good-better-william-macaskill-review">www</A>][20/8/2015].

%A E. V. Quintana
%A et al ...
%A F. Selsis
%T An earth-sized planet in the habitable zone of a cool star
%J Science
%V 344
%N 6181
%P 277-280
%K jrnl, c2014, c201x, c20xx, zz0414, astronomy, exo planet, exoplanet,
   Kepler-186f, Kepler 186f, water
%X "... Although planets that are Earth-sized & smaller have been detected,
   these planets reside in orbits that are too close to their host star to allow
   liquid water on their surfaces. We present the detection of Kepler-186f, a
   1.11+/-0.14 Earth-radius planet that is the outermost of five planets, all
   roughly Earth-sized, that transit a 0.47+/-0.05 solar-radius star. The
   intensity & spectrum of the star's radiation place Kepler-186f in the stellar
   habitable zone, implying that if Kepler-186f has an Earth-like atmosphere &
   water at its surface, then some of this w. is likely to be in liquid form."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1249403">doi:10.1126/science.1249403</A>]['14].

%A R. F. Service
%T Perovskite solar cells keep on surging
%J Science
%V 344
%N 6183
%P 458
%M MAY
%D 2014
%K news, c2014, c201x, c20xx, solar cell, cells, Perovskite, energy, electrical,
   efficiency, efficient, photovoltaic, PV
%X "... At a meeting here last week, three research groups reported besting the
   previous efficiency record in cheap, easy-to-make crystalline materials
   called perovskites. One group's cells turn just shy of 20% of incoming solar
   energy into electricity. That's up from 16.2% efficiency reported in Feb. &
   3.8% just 5 years ago ... Layering p.cells on top of conventional solar cells
   to make 'tandem' cells could push the efficiency up to 32%. That could make
   solar elec. as cheap as elec. produced from coal or natural gas, according
   to ests. from the [DOE]. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.344.6183.458">doi:10.1126/science.344.6183.458</A>]['14].
   (Also see perovskite@[<A HREF="http://en.wikipedia.org/wiki/Perovskite">wikip</A>]['14].)

%T Dirty Secrets: Our ASIO Files
%E M. Burgmann
%I UNSWpress
%P 384
%M MAY
%D 2014
%K book, text, c2014, c201x, c20xx, zz0514, ASIO, Australia, security, spooks,
   spies, spying, secret, state, surveillance, file, privacy, student,
   politics, Adams, Wheatley, Kirby, Cundall, Foley, Summers, Vietnam war,
   persons of interest, person, protest, protesters
%X 1st ed 2014; pb au$40; uk us isbn:1742231403; uk us isbn13:978-1742231402.
   "In this moving, funny and sometimes chilling book, leading Australians open
   their ASIO files and read what the state's security apparatus said about
   them. Writers from across the political spectrum including Mark Aarons,
   Phillip Adams, Nadia Wheatley, Michael Kirby, Peter Cundall, Gary Foley and
   Anne Summers confront - and in some cases reclaim - their pasts. Reflecting
   on the interpretations, observations and proclamations that anonymous
   officials make about your personal life is not easy. Yet we see outrage mixed
   with humour, not least as ASIO officers got basic information wrong a lot of
   the time, though many writers have to contend with personal betrayal. ..."
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/1984/">more</A>].)
   [Also search for: privacy state surveillance].

%A G. Greenwald
%T No Place to Hide: Edward Snowden, the NSA, and the U.S. Surveillance State
%I MetropolitanBooks
%P 272
%M MAY
%D 2014
%K book, c2014, c201x, c20xx, zz0614, US, USA, NSA, spying, state, surveillance,
   spooks, Prism, government, privacy, security, GCHQ, The Guardian, internet,
   phone, Snowden, whistleblower
%X 1st ed 2014; hb us$16; uk us isbn:162779073X; uk us isbn13:978-1627790734.
   "In May 2013, Glenn Greenwald set out for Hong Kong to meet an anonymous
   source who claimed to have astonishing evidence of pervasive government
   spying ..."
   (Also see
   -- [<A HREF="http://www.theguardian.com/world/nsa">TheG</A>]['14],
   -- [<A HREF="http://www.allisons.org/ll/Computing/Misc/1984/">more</A>].)
   [Also search for: privacy state surveillance].

%A T. Lanting
%A et al ...
%A G. Rose
%T Entanglement in a quantum annealing processor
%J Phys. Rev. X
%V 4
%M MAY
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0614, Dwave, quantum computer, computing,
   annealing, qubits, controversial
%X "Entanglement lies at the core of quantum algs. designed to solve problems
   that are intractable by classical approaches. One such alg., quantum
   annealing (QA), provides a promising path to a practical q.processor. ...
   built a series of architecturally scalable QA processors consisting of
   n/ws of manufactured interacting spins (qubits). Here, we use qubit tunneling
   spectroscopy to measure the energy eigenspectrum of two- & eight-qubit
   systems within one such processor, demonstrating quantum coherence in these
   systems. We present experimental evidence that, during a critical portion of
   QA, the qubits become entangled & entanglement persists even as these systems
   reach equilibrium with a thermal environment. ... provide an encouraging sign
   that QA is a viable technology for large-scale quantum computing."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevX.4.021041">doi:10.1103/PhysRevX.4.021041</A>]['14];
   also see [<A HREF="http://www.bbc.com/news/science-environment-27632140">bbc</A>][30/5/2014].
   [Also search for: Dwave quantum computing].

%T Beyond Bibliometrics: Harnessing Multidimensional Indicators of
   Scholarly Impact
%E B. Cronin
%E C. R. Sugimoto
%I MITpress
%P 480
%M MAY
%D 2014
%K c2014, c201x, c20xx, zz0714, publish, perish, bibliometrics, KPI, KPIs,
   impact, altmetrics, altmetric, webometrics, scientometrics, influmetrics,
   publications, publishing, papers, citations, academic,
   scholar, university, scientific research, quality (ha)
%X 1st ed 2014; hb us$56; uk us isbn:0262026791; isbn13:978-0262026796.
   "... describes recent theoretical & practical advances in metrics-based
   research, examining a variety of alt. metrics -- or 'altmetrics' -- while
   also considering the ethical & cultural consequences of relying on metrics to
   assess the quality of scholarship. Once the domain of information scientists
   & mathematicians, b. is now a fast-growing, multidisciplinary field that
   ranges from webometrics to scientometrics to influmetrics[!]. ..."
   [Also search for: publish perish].

%A J. E. Oliver
%A T. Wood
%T Medical conspiracy theories and health behaviors in the United States
%J JAMA Intern. Med.
%D 174
%N 5
%P 817-818
%M MAY
%D 2014
%K jrnl, c2014, c201x, c20xx, zz1214, conspiracy theory, human behaviour, USA,
   medicine, health, flouridation, anti vaccination, denier, deniers, beliefs,
   ideology, alt-right, altRight, psychology, public health, policy
%X "Over the past 50 years, numerous conspiracy theories have materialized
   around public health matters such as water fluoridation, vaccines, cell
   phones, & alternative medicine. What remains unclear is whether the American
   public supports these conspiracy theories or whether they correlate with
   actual health behaviors."
   -- [<A HREF="http://dx.doi.org/10.1001/jamainternmed.2014.190">doi:10.1001/jamainternmed.2014.190</A>]['14].

%A M. Howard
%A J. Wallman
%A V. Veitch
%A J. Emerson
%T Contextuality supplies the 'magic' for quantum computation
%J Nature
%V 510
%N 7505
%P 351-355
%M JUN
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0614, quantum computing, physics, computer,
   mechanics, information theory, contextuality, nonlocality
%X "... prove a remarkable equiv. between the onset of contextuality & the
   possibility of universal quantum computation via 'magic state' distillation,
   which is the leading model for experimentally realizing a fault-tolerant
   q.computer. This is a conceptually satisfying link, because contextuality,
   which precludes a simple 'hidden variable' model of q.mechanics, provides one
   of the fundamental characterizations of uniquely q. phenomena. [&] this
   connection suggests a unifying paradigm for the resources of q.information:
   the non-locality of q.theory is a particular kind of contextuality, & non-
   -locality is already known to be a critical resource for achieving advantages
   with q.communication. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13460">doi:10.1038/nature13460</A>]['14].
   [Also search for: quantum information computing] and
   [also search for: Qbism physics].

%A J. Adams
%T Bibliometrics: The citation game
%J Nature
%N 510
%P 470-471
%M JUN
%D 2014
%K views, c2014, c201x, c20xx, zz0614, publish, perish, citations, journals,
   impact, scientific research, scientist, academic, publications, papers,
   Hindex, game, gaming, JIF, misuse, altmetrics
%X "Bibliometrics has a problem. ... the field -  which tracks schoarly impact
   ... from j.papers to citns, data sets & tweets - has a lot of problems. Its
   indicators need better interp'n, its tools are widely misused, its relevance
   is often questioned & its analyses lack timeliness. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/510470a">doi:10.1038/510470a</A>]['14].
   [Also search for: publish perish].

%A J. E. Stiglitz
%A B. C. Greenwald
%T Creating a Learning Society: A New Approach to Growth, Development, and
   Social Progress
%I ColumbiaUP
%S Kenneth J. Arrow Lecture Series
%P 680
%M JUN
%D 2014
%K book, text, c2014, c201x, c20xx, zz0714, society, politics, higher education,
   economics, growth, progress, government, policy
%X 1st ed 2014; hb us$24; us isbn:0231152140; us isbn13:978-0231152143.
   "It has long been recognized that an improved standard of living results from
   advances in technology, not from the accumulation of capital. It has also
   become clear that what truly separates developed from less-developed
   countries is not just a gap in resources or output but a gap in knowledge.
   In fact, the pace at which developing countries grow is largely a fn of the
   pace at which they close that gap. ..."
   (Also see The_G.@[<A HREF="http://www.theguardian.com/business/2014/jul/09/australia-american-path-to-inequality">9/7/2014</A>].)

%A R. Wilson
%A J. Mack
%T Declines in high school mathematics and science participation: Evidence of
   students' and future teachers' disengagement with maths
%J Int. J. of Innovation in Sci. and Math. Education
%V ?
%P ?-?
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0714, maths, science, STEM, education, PISA,
   high school, schooling, HSC, gender, teaching, Australia, NSW, university,
   decline, technology, numeracy, skills, training
%X auth1@[<A HREF="http://sydney.edu.au/education_social_work/about/staff/profiles/rachel.wilson.php">U.Syd</A>]['14].
   (Also see Fin. Rev. [<A HREF="http://www.afr.com/p/national/education/australia_maths_crisis_I3P1MZ7bcKJKqiyOSnGDVM">7/6/2014</A>], and
    also relevant "... In 2001 some 19.7% of boys and 16.8% of girls studied
    a math/science combination in the HSC however by 2011 only 18.6% of boys
    and 13.8% of girls studied maths/science. ..."
    -- [<A HREF="http://ojs-prod.library.usyd.edu.au/index.php/IISME/article/view/7043">ACSME2013</A>]['14].)
   [Also search for: STEM education].

%A T. L. Delworth
%A F. Zeng
%T Regional rainfall decline in Australia attributed to anthropogenic greenhouse
   gases and ozone levels
%J Nature Geoscience
%V ?
%P ?-?
%M JUL
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0714, climate change, global warming, austral,
   CO2, ozone, greenhouse gas,  Australia, WA, Perth, rainfall, dry, drying,
   drought
%X "Precipitation in austral autumn & winter has declined over parts of S &
   esp. SW Australia in the past few decades. According to observations &
   climate models, at least part of this decline is assoc. with changes in
   large-scale atmos. circln, inc. a poleward movement of the W winds
   & increasing atmospheric surface pressure over parts of S Australia. ... use
   a high-res. global climate model to analyse the causes of this rainfall
   decline. ... Simulations of future climate with this model suggest amplified
   winter drying over most parts of S Australia in the coming decades in
   response to a high-end scenario of changes in radiative forcing. ... most
   pronounced over SW Australia, with total redn in austral autumn & winter
   precipitation of ~ 40% by the late 21C."  [online 13/7/'14.]
   -- [<A HREF="http://dx.doi.org/10.1038/ngeo2201">doi:10.1038/ngeo2201</A>]['14].

%A J. P. A. Ioannidis
%A K. W. Boyack
%A R. Klavans
%T Estimates of the continuously publishing core in the scientific workforce
%J PLoS One
%V 9
%N 7
%P e101968
%M JUL
%D 2014
%K jrnl, eJrnl, c2014, c201x, c20xx, zz0714, publish, perish, Scopus, UCP,
   scientific research, scientists, publications, papers, impact, citations
%X "... Using the entire Scopus DB, we est. that there are 15,153,100 publishing
   scientists (distinct author ids.) in the period 1996-2011. However, only
   150,608 (< 1%) of them have published something in each & every year in this
   16-y. period (uninterrupted, cts presence [UCP] in the lit.). This small core
   of scis. with UCP are far more cited than others, & they account for 41.7% of
   all papers in the same period & 87.1% of all papers with > 1000 citations in
   the same period. Skipping even a single year substantially affected the avg.
   citation impact. We also studied the birth & death dynamics of membership in
   this influential UCP core, by imputing & estimating UCP-births & UCP-deaths.
   We est. that 16,877 scientists would qualify for UCP-birth in 1997 (no
   publication in 1996, UCP in 1997-2012) & 9,673 scientists had their UCP-death
   in 2010.  ...
   ... there is mounting evidence that the current scientific enterprise may be
   focusing more on disciplines that require incremental cts contributions ...
   ... In many disciplines, doctoral students may be enrolled in high numbers,
   offering a cheap workforce ..."   [26 refs.]
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0101698">doi:10.1371/journal.pone.0101698</A>][11/7/'14].
   (Also see ES@[<A HREF="http://news.sciencemag.org/scientific-community/2014/07/1-scientific-publishing">scimag</A>]['14].)
   [Also search for: publish perish].

%A J. Mervis
%T Research Grants. A radical change in peer review
%J Science
%V 345
%N 6194
%P 248-249
%M JUL
%D 2014
%K news, views, c2014, c201x, c20xx, zz0714, reviewing, refereeing, grant,
   peer review, grants, funding, research, application, NSF, ARC, NHMRC
%X The NSF ran "... an experiment that not only allowed more than 100
   applicants to double as reviewers, but also required them to assess seven
   competing proposals as the price for submitting their own. ... applicants
   assessed the quality of seven proposals and then ranked the proposals from
   best to worst. NSF also employed a novel scoring system aimed at dissuading
   a reviewer from downgrading a competitor's proposal in order to boost their
   own; reviewers earned bonus points on their own applications if their
   assessments of other proposals closely matched what their colleagues
   thought. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.345.6194.248">doi:10.1126/science.345.6194.248</A>]['14].
   [Obviously designed by someone with a good understanding of game theory.]

%A R. J. W. Vernon
%A C. A. M. Sutherland
%A A. W. Young
%A T. Hartley
%T Modeling first impressions from highly variable facial images
%J PNAS
%V ?
%N ?
%P ?-?
%M JUL
%D 2014
%K jrnl, PNAS, c2014, c201x, c20xx, zz0814, human, face, faces, appearance,
   stats, model, impression, approachability, trustworthiness, dominance
%X "... create a quantitative model that can predict first impressions of prev.
   unseen ambient images of faces ... from a linear combination of facial
   attributes, explaining 58% of the variance in raters' impressions despite the
   considerable variability of the photos.. Reversing this process, we then
   demonstrate that face-like images can be generated that yield predictable
   social trait impressions in naive raters because they capture key aspects of
   the systematic variation in the relevant physical features of real faces."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1409860111">doi:10.1073/pnas.1409860111</A>]['14],
      [<A HREF="http://www.pnas.org/content/early/2014/07/23/1409860111">www</A>]['14], [online July 2014].

%A N. Hall
%T The Kardashian index: A measure of discrepant social media profile for
   scientists
%J Genome Biol.
%V 15
%N 7
%P 424
%M JUL
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0814, publish, perish, impact, KPI, KPIs,
   citations, Kindex, Hindex, gIndex, science, University, scientific research,
   funny, ha ha, haha, Kim Kardashian, fame, celebrity, social media,
   Twitter, tweet, followers, altMetrics, academia
%X "In the era of social media there are now many different ways that a
   scientist can build their public profile; the publn of high-quality sci.
   papers being just one. While social media is a valuable tool for outreach &
   the sharing of ideas, there is a danger that this form of comm'n is gaining
   too high a value & that we are losing sight of key metrics of sci.value, such
   as citation indices. To help quantify this, I propose the 'Kardashian Index',
   a measure of discrepancy between a scientist's social media profile &
   publication record based on the direct comparison of # of citations &
   Twitter followers."  [via TS & AK.]
   '... K_index = (# followers) / ("correct" # followers for citations) ...'
   -- [<A HREF="http://dx.doi.org/10.1186/s13059-014-0424-0">doi:10.1186/s13059-014-0424-0</A>]['14].
   [Also search for: publish perish].

%A M. Abrahams
%T This is Improbable Too: Synchronized Cows, Speedy Brain Extractors and
   More WTF Research
%I OneworldPub.
%P 336
%M JUL
%D 2014
%K book, c2014, c201x, c20xx, zz0914, IgNobel prize, prizes, awards,
   improbable, scientific research, funny, haha, ha ha
%X 1st ed 2014; pb us$13; uk us isbn:1780743610; uk us isbn13:978-1780743615.
   "... odd questions that researchers are asking, such as: What's the best way
   to get a monkey to floss regularly? How much dandruff do soldiers in
   Pakistan's army have? If you add an extra henchman to your bank-robbing gang,
   how much more money will you earn? Why is it so impossible to estimate the
   number of stupid people in circulation? How many dimples will be found on the
   cheeks of 28,282 Greek children? Who is the Einstein of pork carcasses? ..."

%A P. G. Sekeris
%T The tragedy of the commons in a violent world
%J RAND J. of Economics
%V 45
%N 3
%P 521-532
%M JUL
%D 2014
%K jrnl, c2014, c201x, c20xx, zz114, economics, tragedy of the commons,
   game theory, conflict, war, warfare, violence, cooperation, cooperate,
   natural resources, public goods, good, over exploitation, agreement,
   disagreement, sharing
%X "... we graft on a standard natural-resource exploitation game the
   possibility to appropriate the resource through violent means. Because
   conflict emerges endogenously as resources get depleted, the threat
   supporting the cooperative outcome is no longer subgame perfect, & thus
   credible. The unique equilibrium is such that players exploit
   noncooperatively the resource when it is abundant, & they revert to conflict
   when it becomes scarce. The players' utility is shown to be lower even if
   conflict wastes no resources."
   -- [<A HREF="http://dx.doi.org/10.1111/1756-2171.12060">doi:10.1111/1756-2171.12060</A>]['14].
   (Also see TheWarGame(1967)@[<A HREF="https://en.wikipedia.org/wiki/The_War_Game">wikip</A>]['23].)
   [Also search for: tragedy commons].

%A A. B. Kao
%A N. Miller
%A C. Torney
%A A. Hartnett
%A I. D. Couzin
%T Collective learning and optimal consensus decisions in social animal groups
%J PLoS Comput. Biol.
%V 10
%N 8
%P e1003762
%M AUG
%D 2014
%K jrnl, eJrnl, c2014, c201x, c20xx, zz0815, economics, human behaviour, market,
   collective, group,  social, decision making
%X "... decisions both individually & as part of a collective. Reaching
   consensus nec. means that a single option is chosen by the group... This
   decision-making process decouples the otherwise direct relationship between
   animals' preferences & their experiences ... Instead, because an individual's
   learned preferences influence what others experience, & therefore learn about
   collective decisions couple the learning processes between social organisms.
   ... model collective learning within animal groups ... behavior that is
   fundamentally different from that learned in isolation ...  Because these
   properties make min. cogn. demands on individuals, collective learning & the
   capabilities it affords, may be widespread among grp-living organisms. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pcbi.1003762">doi:10.1371/journal.pcbi.1003762</A>]['15].

%A R. B. Rutledge
%A N. Skandali
%A P. Dayan
%A R. J. Dolan
%T A computational and neural model of momentary subjective well-being
%J PNAS
%V ?
%P ?-?
%M AUG
%D 2014
%K jrnl, PNAS, c2014, c201x, c20xx, zz0814, happiness, well being, wellbeing,
   psychology, striatum, insula, reward, gain, momentary, joy, model
%X "... Using comp.modeling, we show that emotional reactivity in the form of
   momentary happiness in response to outcomes of a probabilistic reward task is
   explained not by current task earnings, but by the combined influence of
   recent reward expectns & predn errors arising from those expectns. The
   robustness of this account was evident in a large-scale replication involving
   18,420 participants. Using functional MRI, we show that the very same
   influences account for task-dependent striatal activity in a manner akin to
   the influences underpinning changes in happiness." [Online 8/2014.]
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1407535111">doi:10.1073/pnas.1407535111</A>]['14],
      [<A HREF="http://www.pnas.org/content/early/2014/07/31/1407535111">early</A>]['14].
   [Also search for: happiness well being].

%A C. Scharf
%T The Copernicus Complex: Our Cosmic Significance in a Universe of Planets and
   Probabilities
%I ScientificAmerican
%P 288
%M SEP
%D 2014
%K book, c2014, c201x, c20xx, zz0814, intelligence, life, universe, space,
   alien, astrophysics, planet, exoplanet, extra terrestrial, extraterrestrial
%X 1st ed 2014; hb us$19; uk us isbn:0374129215; uk us isbn13:978-0374129217.
   "... we do occupy an unusual time in a 14-billion-year-old universe, in a
   somewhat unusual type of solar sys. surrounded by an ocean of unimaginable
   planetary diversity: hot Jupiters with orbits of less than a day, planet-size
   rocks spinning around dead stars, and a wealth of alien super-Earths. Yet
   life here is built from the most common chemistry in the universe ..."

%A V. Callier
%A N. L. Vanderford
%T Ailing academia needs culture change
%J Science
%V 345
%N 6199
%P 885
%M AUG
%D 2014
%K views, comment, c2014, c201x, c20xx, zz0814, university, academia, academic,
   postdoc, career, PhD, postgrad, grant, grants, funding, peer review,
   science, scientific research, NSF, NIH, ARC
%X "... the pressure felt by many postdocs, in part because there are not
   enough jobs available in academia. ... research enterprise has become
   unsustainable in its current form. R.funding levels/mechanisms, the
   peer-review process, & the methods of training Ph.D.s are flawed, & these
   issues are crippling the pipeline of future, successful academic researchers.
   ... the value system in academia perpetuates these issues & thus prevents
   +ve change.  Universities & individual faculty are addicted to grant funding
   & to the cheap labor provided by Ph.D. trainees ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.345.6199.885-b">doi:10.1126/science.345.6199.885-b</A>]['14].
   [Also search for: postgrad PhD].

%A R. D. Norris
%A J. M. Norris
%A R. D. Lorenz
%A J. Ray
%A B. Jackson
%T Sliding rocks on racetrack playa, Death Valley National Park: First
   observation of rocks in motion
%J PLoS One
%V 9
%N 8
%P e105948
%M AUG
%D 2014
%K jrnl, eJrnl, c2014, c201x, c20xx, zz0914, Death Valley, USA, Playa, tracks,
   rock, rocks, move, moving, slide, sliding, slithering, ice, Source Hill
%X "The engraved trails of rocks on the nearly flat, dry mud surface of
   Racetrack Playa, Death Valley National Park ... We recorded the 1st direct
   sci.obs. of rock movements using GPS-instrumented rocks & photography ...
   The largest obs. rock movement involved > 60 rocks on Dec. 20, 2013 & some
   instrumented rocks moved up to 224m between Dec. 2013 & Jan. 2014 in multiple
   move events. ... the process of rock movement that we have observed occurs
   when the thin, 3 to 6mm, 'windowpane' ice sheet covering the playa pool
   begins to melt in late morning sun & breaks up under light winds of ~4-5m/s.
   Floating ice panels 10s of meters in size push multiple rocks at low speeds
   of 2-5m/min. along trajectories det. by the dirn & velocity of the wind as
   well as that of the water flowing under the ice."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0105948">doi:10.1371/journal.pone.0105948</A>]['14],
      [<A HREF="https://scripps.ucsd.edu/news/mystery-solved-sailing-stones-death-valley-seen-action-first-time">UCSD</A>]['14],
      video@[<A HREF="https://www.youtube.com/watch?feature=player_embedded&v=uyHcs7B27Zk">uBend</A>]['14].

%A D. M. Markowitz
%A J. T. Hancock
%T Linguistic traces of a scientific fraud: The case of Diederik Stapel
%J PLoS One
%V 9
%N 8
%P e105937
%M AUG
%D 2014
%K jrnl, eJrnl, c2014, c021x, c20xx, zz0914, Stapel, scientific research,
   University, fraud, academic, misconduct, scandal, publications, papers,
   language, use, words, word, usage, writing, style, stats
%X "...investigated the linguistic patterns of fraudulent (N=24; 170,008 words)
   & genuine publns (N=25; 189,705 words) first-authored by social psychologist
   Diederik Stapel.  ... S's fraudulent papers contained linguistic changes in
   sci.-related discourse dimensions, inc. more terms pertaining to methods,
   investigation, & certainty than his genuine papers. His writing style also
   matched patterns in other deceptive language, including fewer adjectives in
   fraudulent publns relative to genuine publns. Using differences in language
   dimensions we were able to classify S's publns with above chance accuracy.
   Beyond these discourse dimensions, S included fewer co-authors when reporting
   fake data than genuine data ..."  [33 refs.]
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0105937">doi:10.1371/journal.pone.0105937</A>]['14].
   [Also search for: scientific misconduct].

%A M. Braga
%A M. Paccagnella
%A M. Pellizzari
%T Evaluating students' evaluations of professors
%J Economics of Ed. Rev.
%V 41
%P 71-88
%M AUG
%D 2014
%K jrnl, c2014, c201x, c20xx, zz1014, teaching, education, lecturing, college,
   university, tertiary, teacher, professor, prof, lecturer, student, pupil,
   learning, review, course, evaluation, assessment, survey, SETU, opinion,
   quality, good, effectiveness, performance, ability, grades, weather,
   KPI, KPIs, stats
%X "... contrasts measures of teacher effectiveness with the students' eval. for
   the same teachers using admin. data from Bocconi U.. The effectiveness
   measures are est. by comparing the performance in follow-on coursework of
   students who are randomly assigned to teachers. We find that teacher quality
   matters substantially & that our measure of effectiveness is -vely correlated
   with the students' eval. of professors. A simple theory rationalizes this
   result under the assumption that students evaluate profs. based on their
   realized utility, an assumption that is supported by additional evidence
   that the evaluations respond to meteorological conditions."
      ("... Assuming that the weather affects utility & not teaching quality
       ... Our results show that students evaluate professors more negatively
       on rainy & cold days. ...")
      ("... The results, thus, suggest that the -ve correlns reported in table-8
       are mostly due to classes with a particularly low incidence of
       high ability students. ...")
      ("... good teachers are those who require their students to exert effort;
       students dislike it, especially the least able ones ...")
   -- [<A HREF="http://dx.doi.org/10.1016/j.econedurev.2014.04.002">doi:10.1016/j.econedurev.2014.04.002</A>]['14].
   (Teacher effectiveness is negatively correlated with students' evaluations!-)

%A W. Poundstone
%T How to Predict the Unpredictable: The Art of Outsmarting Almost Everyone
%I Oneworld
%P 304
%M SEP
%D 2014
%K book, c2014, c201x, c20xx, zz0914, game, games, playing, random, randmoness,
   predictable, surprising, representativeness, Kahneman
%X 1st ed 2014; pb stg.7; uk us isbn:1780744072; uk us isbn13:978-1780744070.
   "We are hard-wired to believe that the world is more predictable than it is.
   We chase 'winning streaks' that are often just illusions, & we are all too
   predictable exactly when we try hardest not to be. In the 1970s, Daniel
   Kahneman & Amos Tversky coined the phrase 'representativeness' to describe
   the psychology of this behaviour. Since then representativeness has been used
   by auditors to catch people fiddling their tax returns & by hedge fund
   managers to reap billions from the emotions of small investors. ..."
   [Also search for: economics human behaviour bias].

%A M. R. Raupach
%A et al ...
%A C. Le Quere
%T Sharing a quota on cumulative carbon emissions
%J Nature Climate Change
%V ?
%P ?-?
%M SEP
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0914, climate change, global warming, carbon,
   CO2, greenhouse gas, gases, temperature rise, share, fossil fuel, fuels,
   coal, emission, reduction
%X "Any limit on future g.w. is assoc. with a quota on cumulative global CO2
   emissions. We translate this global C quota to regional & national scales,
   on a spectrum of sharing principles that extends from continuation of the
   present distribution of emissions to an equal per-capita distn of cumulative
   emissions. A blend of these endpoints emerges as the most viable option. For
   a C quota consistent with a 2 deg C warming limit (rel. to pre-industrial
   levels), the necessary long-term mitigation rates are very challenging
   (typically over 5% per year), both because of strong limits on future
   emissions from the global C quota & also the likely short-term persistence in
   emissions growth in many regions."  [online Sept 2014.]
   -- [<A HREF="http://dx.doi.org/10.1038/nclimate2384">doi:10.1038/nclimate2384</A>]['14],
   C.LeQ@[<A HREF="http://www.tyndall.ac.uk/people/corinne-le-quere">ac.uk</A>]['14].

%A P. Gerland
%A et al ...
&A J. Wilmoth
%T World population stabilization unlikely this century
%J Science
%V 346
%N 6206
%P 234-237
%M SEP
%D 2014
%K jrnl, c2014, c201x, c20xx, zz1114, world, population, growth, people,
   demographics, billions, billion, stats, UN, model, public policy, resources,
   prediction, zzPrediction
%X "The [UN] recently released popn projections based on data until 2012 & a
   Bayesian probabilistic methodology. ... reveals that, contrary to prev.
   literature, the world popn is unlikely to stop growing this century. ... an
   80% prob. that world popn, now 7.2 billion ... will increase to between 9.6
   & 12.3 billion in 2100. This uncertainty is much smaller than the range from
   the trad. UN high & low variants. Much of the increase is expected to happen
   in Africa, in part due to higher fertility rates & a recent slowdown in the
   pace of fertility decline. Also, the ratio of working-age people to older
   people is likely to decline substantially in all countries, even those that
   currently have young populations."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1257469">doi:10.1126/science.1257469</A>]['14].
   (Also see
   [<A HREF="http://dx.doi.org/10.1073/pnas.1410465111">PNAS</A>][9/2014] and
   [<A HREF="http://www.bbc.com/news/science-environment-29788754">bbc</A>][27/10/2014].)

%A A. van de Rijt
%A S. Moon Kang
%A M. Restivo
%A A. Patil
%T Field experiments of success-breeds-success dynamics
%J PNAS
%V 111
%N 19
%P 6934-6939
%M SEP
%D 2014
%K jrnl, PNAS, c2014, c201x, c20xx, zz0220, deRijt, success, luck, social,
   feedback, Matthew effect, principle, preferential attachment,
   rich get richer, human behaviour, experiment, grants, kickstarter, Hindex
%X "... Some scholars have suggested such inequality merely reflects
   hard-to-observe personal differences in ability. Others have proposed that
   one fortunate success may trigger another, thus producing arbitrary
   differentiation. We conducted randomized experiments through intervention in
   live social systems to test for success-breeds-success dynamics. Results show
   that different kinds of success (money, quality ratings, awards, and
   endorsements) when bestowed upon arbitrarily selected recipients all produced
   significant improvements in subsequent rates of success as compared with the
   control group of nonrecipients. However, greater amounts of initial success
   failed to produce much greater subsequent success, suggesting limits ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.1316836111">doi:10.1073/pnas.1316836111</A>][20].
   (Also see Sci Show, ABC radio[<A HREF="https://www.abc.net.au/radionational/programs/scienceshow/the-new-science-of-success/11928636">www</A>][8/2/20].)
   [Also search for: success luck].

%A V. Evans
%T The Language Myth: Why Language Is Not an Instinct
%I CUP
%M SEP
%D 2014
%K book, text, CUP, c2014, c201x, c20xx, zz1014, natural language, human,
   learning, learn, acquire, universal, grammar, Chomsky
%X 1st ed 2014; pb us$23; uk us isbn:1107619750; uk us isbn13:978-1107619753;
                hb us$73; uk us isbn:1107043964; uk us isbn13:978-1107043961.
   "... Debunking the notion of a language 'instinct', E. demonstrates that
   language is related to other animal forms of communication; that languages
   exhibit staggering diversity; that we learn our mother tongue drawing on
   general properties & abilities of the human mind, rather than an inborn
   'universal' grammar; that language is not autonomous but is closely related
   to other aspects of our mental lives; & that, ultimately, language & the
   mind reflect and draw upon the way we interact with others in the world ..."
   (I.e., attempts to rebut Chomsky.)

%A A. Yong
%T Critique of Hirsch's citation index: A combinatorial Fermi problem
%J Notices of the AMS
%V 61
%N 9
%P 1040-1050
%M OCT
%D 2014
%K jrnl, c2014, c201x, c20xx, zz1014, scientific research, university, KPI,
   KPIs, Hirsch, Hindex, H index, scholar, impact, citations, publications,
   publish perish, Durfee square, Fields medalists, medal
%X H_index ~ sqrt(n_Citations/5)
   "... Whether it be Fields medalists, Abel Prize laureates, job promotion, or
   grant candidates, clearly, the quality of a researcher cannot be fully
   measured by numerics. However, in reality, the h-index is used, formally or
   informally, for comparisons. ..."
   -- pdf@[<A HREF="http://dx.doi.org/10.1090/noti1164">doi:10.1090/noti1164</A>]['14].
   [Also search for: publish perish]  and  [also search for: Hirsch Hindex].

%A M. S. Tame
%A B. A. Bell
%A C. Di Franco
%A W. J. Wadsworth
%A J. G. Rarity
%T Experimental realization of a one-way quantum computer algorithm solving
   Simon's problem
%J arXiv
%M OCT
%D 2014
%O ? to appear Phys. Rev. Lett. ?
%K arXiv, c2014, c201x, c20xx, zz1014, Simon, Simon's, problem, simons, one way,
   quantum, computer, computing, algorithm, run, demo, Shor, diFranco
%X "... experimental demo. of a one-way implementation of a quantum alg. solving
   Simon's Problem - a black box period-finding problem which has an exponential
   gap between the classical & quantum runtime. Using an all-optical setup &
   modifying the bases of single-qubit measurements on a five-qubit cluster
   state, key representative fns of the logical two-qubit version's black box
   can be queried & solved. To the best of our knowledge, this work represents
   the 1st experimental realization of the q.alg. solving S's Problem. The
   experimental results are in excellent agreement with the theoretical model,
   demonstrating the successful performance of the alg.. With a view to scaling
   up to larger numbers of qubits, we analyze the resource requirements for an
   n-qubit version. ..."
   -- 1410.3859@[<A HREF="http://arxiv.org/abs/1410.3859">arXiv</A>]['14].
   [Way to go before being practical!]
   (Also see
      "[SP] was also the inspiration for Shor's alg.. Both problems are
       special cases of the abelian hidden subgroup problem, which is now known
       to have efficient quantum algorithms. ..."
      -- S's.P@[<A HREF="http://en.wikipedia.org/wiki/Simon%27s_problem">wikip</A>]['14].)

%A R. Van Noorden
%A B, Maher
%A R. Nuzzo
%T The top 100 papers
%J Nature
%V 514
%N 7524
%P ?-?
%M OCT
%D 2014
%K jrnl, news, views, c2014, c201x, c20xx, zz1114, publish, perish, paper,
   cite, citations, impact, SCI, science, scientifc research
%X "... [SCI] lists papers published from 1900 to the present day. The exercise
   revealed some surprises, not least that it takes a staggering
   12,119 citations to rank in the top 100 ..."
   -- [<A HREF="http://dx.doi.org/10.1038/514550a">doi:10.1038/514550a</A>]['14].
   (Also see [<A HREF="http://dx.doi.org/10.1038/514561a">www</A>]['14].)
   [Also search for: publish perish].

%A M. O. Reidl
%T The Lovelace 2.0 test of artificial creativity and intelligence
%J arXiv
%M OCT
%D 2014
%K arXiv, TR, c2014, c201x, c20xx, zz1214, AI, computer, creativity,
   imagination, intelligence, art, Turing, Lovelace2, test
%X "Observing that the creation of certain types of artistic artifacts
   necessitate intelligence, we present the Lovelace 2.0 Test of creativity as
   an alternative to the Turing Test as a means of determining whether an agent
   is intelligent. The Lovelace 2.0 Test builds off prior tests of creativity
   & additionally provides a means of directly comparing the relative
   intelligence of different agents."
   -- 1410.6142@[<A HREF="http://arxiv.org/abs/1410.6142">arXiv</A>]['14].
   [Also search for: Turing test AI].

%A L. Pachter
%T To some a citation is worth $3 per year
%M OCT
%D 2014
%K blog, c2014, c201x, c20xx, zz1219, university, ranking, rankings, impact,
   USNWR, rating, research, gaming, scamming, buying, adjunct, management,
   quality, KPI, KPIs, KAU, King Abdulaziz University, Saudi Arabia, grudging
%X "Earlier this week US News and World Report (USNWR) released, for the first
   time, a global ranking of universities including rankings by subject area.
   In mathematics, the top ten unis. are:
   1. Berkeley; 2. Stanford; 3. Princeton; 4. UCLA; 5. U. of Oxford;
   6. Harvard; 7. King Abdulaziz University [KAU](*);
   8. Pierre and Marie Curie - Paris 6; 9. U. of Hong Kong;
   10. U. of Cambridge; ... Even more surprising is the entry at #7
   that I have boldfaced: the math department at King Abdulaziz U. (KAU)
   in Jeddah, Saudi Arabia. ... KAU employs (as adjunct faculty) more than a
   quarter of the highly cited mathematicians at Thomson Reuters. ...
   profs. are hired as adjunct pros. at KAU for $72,000 per year in return for
   agreeing (apparently by contract) to add KAU as a secondary affiliation..."
   -- [<A HREF="https://liorpachter.wordpress.com/2014/10/31/to-some-a-citation-is-worth-3-per-year/">www</A>]['19].
      (I must confess to feeling a little grudging admiration of KAU
      for exploiting such a weak measure.)
   Also see Y.Bhattacharjee in Science, Dec 2011,
   [<A HREF="https://doi.org/10.1126/science.334.6061.1344">www</A>]['19].
   [Also search for: university rankings].

%A K. Howard
%T Women Codebreakers at Bletchley Park
%D 2014
%K book, c2014, c201x, c20xx, zz1114, Bletchley Park, world war two, WWII, WW2,
   StationX, cryptanalysis, Margaret Rock, Joan Clarke, Mavis Lever, Ruth Briggs,
   hut 8, hut8, Enigma, Imitation Game movie, women, www, code, cypher, cipher,
   science, maths, STEM
%X ebook ~ Nov 2014?
   WCb@[<A HREF="http://www.bletchleyparkresearch.co.uk/research-notes/women-codebreakers/">B.Park</A>]['14,17'],
   JC@[<A HREF="http://en.wikipedia.org/wiki/Joan_Clarke">wikip</A>]['14],
   JC@[<A HREF="http://www-history.mcs.st-and.ac.uk/Biographies/Clarke_Joan.html">StAndr</A>]['14].
   (Also see, "Joan Clarke's ingenious work as a codebreaker during WW2 ...
    ... The only woman to work in the nerve centre of the quest to crack
    German Enigma ciphers, Clarke rose to deputy head of Hut 8, and
    would be its longest-serving member. She was also Turing's
    lifelong friend and confidante and, briefly, his fiancee. ...
    ... The 'Imitation Game' [movie 2014] ..."
    -- [<A HREF="http://www.bbc.com/news/technology-29840653">bbc</A>][10/11/'14] and see
    JC@[<A HREF="https://en.wikipedia.org/wiki/Joan_Clarke">wikip</A>]['24].)
   [Also search for: Bletchley Park].

%A C. Ferguson
%A A. Marcus
%A I. Oransky
%T Publishing: The peer-review scam
%J Nature
%V 515
%N 7528
%P 480-482
%M NOV
%D 2014
%K news, views, c2014, c201x, c20xx, zz1214, publish, perish, papers, science,
   scientific research, publications, scam, fraud, misconduct, university,
   academic, peer review, refereeing, ring, Hyung-In Moon, Dongguk University,
   journal, Enzyme Inhibition and Medicinal Chemistry, ScholarOne,
   impact, citation, abuse,
   Peter Chen, National Pingtung University of Education
%X "When a handful of authors were caught reviewing their own papers, it exposed
   weaknesses in modern publishing systems. ... Most j. eds. know how much
   effort it takes to persuade busy researchers to review a paper. That is why
   the ed. of The J. of Enzyme Inhibition & Medicinal Chem. was puzzled by the
   reviews for manuscripts by one author - Hyung-In Moon, a medicinal-plant
   researcher then at Dongguk Uni. in Gyeongju, South Korea. The reviews
   themselves were not remarkable ... What was unusual was how quickly they were
   completed - often within 24 hours. ... [J.s] invite authors to suggest
   potential reviewers for their papers. So Moon provided names ... often with
   bogus e-mail addresses that would go directly to him or his colleagues. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/515480a">doi:10.1038/515480a</A>]['14].
   [Also search for: publish perish] and [also search for: peer review abuse].

%A S. Boixo
%A et al ...
%A H. Neven
%T Computational role of collective tunneling in a quantum annealer
%J arXiv
%M NOV
%D 2014
%K arXiv, TR, c2014, c201x, c20xx, zz1214, quantum, computer, computing, Dwave,
   Dwave2, D-wave Two, annealing, tuneling, tunnelling, NASA Ames
%X "... present the first experimental evidence of a computational role of
   multiqubit quantum tunneling in the evolution of a programmable q.annealer.
   We develop a theor. model based on a NIBA Quantum Master Equation to describe
   the multiqubit dissipative tunneling effects under the complex noise
   characteristics of such q.devices. ... show that the collective effect of the
   q.environment is suppressed in the 'critical' phase during the evolution
   where q.tunneling 'decides' the right path to soln. In a later stage
   dissipation facilitates the multiqubit tunneling leading to the soln state.
   The predictions of the model accurately describe the experimental data from
   the D-Wave Two q.annealer at NASA Ames. In our computational primitive the
   temperature dependence of the prob. of success in the q.model is opposite to
   that of the classical paths with thermal hopping. Specifically, we provide an
   analysis of an optimization problem with sixteen qubits, demonstrating eight
   qubit tunneling that increases success probabilities. [&] report results for
   larger problems with <=200 qubits that contain the primitive as subproblems."
   -- 1411.4036@[<A HREF="http://arxiv.org/abs/1411.4036">arXiv</A>]['14].
   [Also search for: Dwave quantum computing].

%A O. Causa
%A A. de Serres
%A N. Ruiz
%T Can growth-enhancing policies lift all boats? An analysis based on
   household disposable incomes?
%I OECD Economics Dept
%S Working Papers
%M DEC ?
%D 2014
%K TR, c2014, c201x, c20xx, zz1214, stats, economics, economic growth,
   inequality, income, wealth, rich, poor, poverty, trickle down,
   Thatcherism, Reaganomics, politics, deSerres
%X Also see [<A HREF="http://www.oecd.org/forum/oecdyearbook/growth-and-inequality-close-relationship.htm">OECD</A>]['14].
   And, "... rising inequality in the two decades after 1985 shaved
   nine percentage points off UK growth between 1990 and 2000 ..."
   -- The_G.@[<A HREF="http://www.theguardian.com/business/2014/dec/09/revealed-wealth-gap-oecd-report">www</A>][9/12/2014].

%A J. E. Terrell
%T A Talent for Friendship: Rediscovery of a Remarkable Trait
%I OUP
%P 320
%M DEC
%D 2014
%K book, text, OUP, c2014, c201x, c20xx, zz1214, human, behaviour, society,
   societies, social, culture, anthropology, friendship, friend, friends
%X 1st ed 2014; hb us$25; uk us isbn:0199386455; uk us isbn:978-0199386451.
   "... a new way to understand friendship. JT argues that the ability to make
   friends is an evolved human trait not unlike our ability to walk upright on
   two legs or our capacity for speech and complex abstract reasoning. ..."
   (Also see auth@[<A HREF="https://www.fieldmuseum.org/about/staff/profile/306">fieldmuseum</A>].)

%A K. Siler
%A K. Lee
%A L. Bero
%T Measuring the effectiveness of scientific gatekeeping
%J PNAS
%V ?
%P ?-?
%M DEC
%D 2014
%K jrnl, PNAS, c2014, c201x, c20xx, zz0115, peer review, publish, perish,
   referee, refereeing, impact, science, stats, scientific research, paper,
   paper, editor, publications, quality
%X "... dataset of 1,008 manuscripts submitted to three elite medical journals,
   we show differences in citation outcomes for articles that received different
   appraisals from editors & peer reviewers. Among rejected articles,
   desk-rejected manuscripts, deemed as unworthy of peer review by editors,
   received fewer citations than those sent for peer review. Among both rejected
   & accepted articles, manuscripts with lower scores from peer reviewers
   received relatively fewer citations when they were eventually published.
   However, hindsight reveals numerous questionable gatekeeping decisions. Of
   the 808 eventually published articles in our dataset, our three focal
   journals rejected many highly cited manuscripts, including the 14 most
   popular; roughly the top 2%. Of those 14 articles, 12 were desk-rejected.
   This finding raises concerns regarding whether peer review is ill-suited to
   recognize & gestate the most impactful ideas & research. Despite this finding
   results show that in our case studies, on the whole, there was value added in
   peer review. Editors & peer reviewers generally - but not always - made good
   decisions regarding the identification & promotion of quality in scientific
   manuscripts."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1418218112">doi:10.1073/pnas.1418218112</A>]['14].
   [Also search for: publish perish].

%A E. Gibney
%T Quantum computer quest
%J Nature
%V 516
%N 7529
%P 24-26
%M DEC
%D 2014
%K news, views, c2014, c201x, c20xx, zz0217, quantum computing, computer
%X "After a 30-year struggle to harness quantum weirdness for computing,
   physicists finally have their goal in reach. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/516024a">doi:10.1038/516024a</A>]['17].

%A R. Munroe
%T What If? Serious Scientific Answers to Absurd Hypothetical Questions
%I MarinerBooks
%P 320
%D 2014
%K book, c2014, c201x, c20xx, zz0118, xkcd, science, predictions, myths, fun,
   funny, haha, ha ha, www, HREF, popular, scientific, question, answer,
   QandA, urban myth, popular, sceptic
%X 1st ed 2014; pb us$10; uk us isbn:0544456866; uk us isbn13:978-0544456860.
   "... His responses are masterpieces of clarity and wit, gleefully and
   accurately explaining everything from the relativistic effects of a baseball
   pitched at near the speed of light to the many horrible ways you could die
   while building a periodic table out of all the actual elements. ..."
   (Also see [<A HREF="https://what-if.xkcd.com/">what-if.xkcd.com</A>]['17].)

%T Brandolini's law
%D 2015
%K Brandolini, c2015, c201x, c20xx, zz0221, funny, laws, haha, ha ha,
   bullshit, fake news, fakeNews, rumours, misinformation, disinformation,
   lies, postTruth, Qanon, conspiracy, conspiracist
%X "Brandolini's law, also known as the bullshit asymmetry principle ...
   The amount of energy needed to refute bullshit is an order of magnitude
   larger than to produce it."
   -- BL@[<A HREF="https://en.wikipedia.org/wiki/Brandolini%27s_law">wikip</A>]['21].
   [Also search for: funny law].

%A C. McGlade
%A P. Ekins
%T The geographical distribution of fossil fuels unused when limiting
   global warming to 2 deg. C
%J Nature
%V 517
%N 7533
%P 187-190
%M JAN
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0115, climate change, global warming, CO2,
   carbon bubble, greenhouse gas, gases, fossil fuel, fuels, oil, gas, coal,
   limits, divestment, reserves, energy, resources, exploration, stats, model
%X "... It has been est. that to have at least a 50% chance of keeping warming
   below 2deg.C throughout the 21C, the cumulative carbon emissions between 2011
   & 2050 need to be limited to around 1,100 gigatonnes of CO2. However, the
   greenhouse gas emissions contained in present estimates of global fossil fuel
   reserves are around three times higher than this and so the unabated use of
   all current fossil fuel reserves is incompatible with a warming limit of
   2deg.C. ... model ... Our results suggest that, globally, a third of oil
   reserves, half of gas reserves and over 80% of current coal reserves should
   remain unused from 2010 to 2050 ... to meet the target of 2deg.C. We show
   that development of resources in the Arctic & any increase in unconventional
   oil production are incommensurate with efforts to limit average global
   warming to 2deg.C. Our results show that policy makers' instincts to exploit
   rapidly & completely their territorial fossil fuels are, in aggregate,
   inconsistent with their commitments to this temp.limit. Implementation of
   this policy commitment would also render unnecessary continued substantial
   expenditure on fossil fuel exploration, because any new discoveries could not
   lead to increased aggregate production."
   -- [<A HREF="http://dx.doi.org/10.1038/nature14016">doi:10.1038/nature14016</A>]['15].
   (Also see [<A HREF="http://www.bbc.com/news/business-32322269">bbc</A>][16/4/2015].)

%A R. Werner
%T The focus on bibliometrics makes papers less useful
%J Nature
%V 517
%N 7543
%P ?-?
%M JAN
%D 2015
%K views, c2015, c201x, c20xx, zz0115, publish, perish, impact, journal, paper,
   papers, bibliometrics, hiring, funding, merit, Physical Review Letters, PRL,
   science, scientific research, proxy, quality, good scientist, quality, JIF
%X "How do we recognize a good scientist? There is an entire industry -
   bibliometrics - that would have us believe that it is easy: count journal
   articles, sort them according to the impact factors of the journals, and
   count all the citations. ... example is the distortion in the journal
   landscape - and with it the changes in the style of papers - that arose when
   the journal impact factor began to be taken seriously as a proxy for
   reputation. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/517245a">doi:10.1038/517245a</A>]['15].
   [Also search for: publish perish].

%A M. Goodman
%T Future Crimes: Everything is Connected, Everyone is Vulnerable and
   What We Can Do About It
%I Doubleday
%M FEB
%D 2015
%K book, c2015, c201x, c20xx, zz0415, internet, online, crime, hacking, hacked,
   technology, security, theft, banking, risks
%X 1st ed 2015; hb us$21; uk us isbn:0385539002; uk us isbn13:978-0385539005.
   "... ways criminals, corporations, and even countries are using new and
   emerging technologies against you ..."

%A M. Smith
%T The Debs of Bletchley Park and Other Stories
%I AurumPress
%P 304
%M MAR
%D 2015
%K book, c2015, c201x, c20xx, zz0115, WW2, WWII, world war two, Enigma, code,
   deb, woman, women, Webb, Every, Pitt-Lewis, Dilly Knox, blockF, decryption,
   code breakers, codebreaker, codes, maths, science, STEM, www
%X "... a total of twelve thousand people worked there of whom nine thousand
   were women. Their roles ranged from some of the leading codebreakers,
   cracking German messages that others could not break, through the debutantes
   who chauffeured the codebreakers to and from work, to women like Baroness
   Trumpington who were employed as filing clerks, to the mass of girls from
   ordinary working families who operated machines or listed endless streams of
   figures, largely unaware of the major impact their work was having on the
   war. ..."
   1st ed 2015; hb us$22; uk us isbn:1781313873; uk us isbn13:978-1781313879.
   (Also see, "... The Imitation Game - about which they had mixed opinions.
      - Over dramatised," Body said. "And that's putting it mildly."'
      -- The_G.@[<A HREF="http://www.theguardian.com/uk-news/2015/jan/20/bletchley-park-women-meet-codebreakers-book-launch">www</A>]['15].)
   [Also search for: Bletchley Park] & [also search for: women computing].

%A T. P. Howard
%A et al ...
%A J. Love
%T Synthesis of customized petroleum-replica fuel molecules by targeted
   modification of free fatty acid pools in Escherichia coli
%J PNAS
%V 110
%N 19
%P 7636-7641
%M JAN
%D 2015
%K jrnl, PNAS, c2015, c201x, c20xx, zz0115, Ecoli, biofuel, biofuels, biodiesel,
   diesel, sustainable. renewable, petroleum
%X "... report on prodn of such petroleum-replica hydrocarbons in E.coli. The
   activity of the fatty acid (FA) reductase complex from Photorhabdus
   luminescens was coupled with aldehyde decarbonylase from Nostoc punctiforme
   to use free FAs as substrates for alkane biosynthesis. This combination of
   genes enabled rational alterations to hydrocarbon chain length (Cn) & the
   production of branched alkanes through upstream genetic & exogenous
   manipulations of the FA pool. Genetic components for targeted manipulation of
   the FA pool included expression of a thioesterase from Cinnamomum camphora
   (camphor) to alter alkane C_n & expression of the branched-chain alpha-keto
   acid dehydrogenase complex & beta-keto acyl-acyl carrier protein synthase III
   from Bacillus subtilis to synthesize branched (iso-) alkanes. Rather than
   simply reconstituting existing metabolic routes to alkane prodn found in
   nature, these results demonstrate the ability to design & implement
   artificial molecular pathways for the prodn of renewable, industrially
   relevant fuel molecules."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1215966110">doi:10.1073/pnas.1215966110</A>]['15].
   (Also see [<A HREF="http://www.bbc.com/news/science-environment-22253746">bbc</A>]['15].)

%A M. Lesk
%T How many scientific papers are not original?
%J PNAS
%V 112
%N 1
%P 6-7
%M JAN
%D 2015
%K jrnl, PNAS, c2015, c201x, c20xx, zz0618, MLesk, publish, perish, science,
   research, paper, papers, publications, plagiarism, fraud, original,
   refereeing
%X "Is plagiarism afflicting science ... In 1830, Charles Babbage deplored
   unreliable science. He discussed hoaxes, forgeries, data trimming, and
   'cooking' (selecting data to match a theory) ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.1422282112">doi:10.1073/pnas.1422282112</A>]['18].

%A J. Langford
%T The NIPS experiment
%M JAN
%D 2015
%K blog, views, news, c2015, c201x, c20xx, zz0515, publish, publication,
   peer, review, reviewing, paper, papers, referee, refereeing, fair, noise,
   noisy
%X "Corinna Cortes & Neil Lawrence ran the NIPS experiment, where 1/10th of
   papers sub. to the Neural Info. Proc. Sys. Foundation (NIPS) went through the
   NIPS review process twice, & then the accept/reject decision was compared.
   ... The 26% disagreement rate presented at the NIPS conf. understates the
   meaning in my opinion, given the 22% acceptance rate. The immediate
   implication is that between half & two-thirds of papers accepted at NIPS
   would have been rejected if reviewed a second time. ..."
   -- @[<A HREF="http://cacm.acm.org/blogs/blog-cacm/181996-the-nips-experiment/fulltext">acm</A>]['15],
      @[<A HREF="http://hunch.net/?p=467864">hunch</A>]['15].
   [Also search for: peer reviewing].

%A H. D. Nghiem
%A H. T. Nguyen
%A R. Khanam
%A L. B. Connolly
%T Does school type affect cognitive and non-cognitive development in
   children? Evidence from Australian primary schools
%J Labor Economics
%V 33
%P 55-65
%M APR
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0415, private, Catholic, state, public, labour,
   independent, primary school, schools, education, LSAC, Australia, stats
%X "... effects of primary school choices on cognitive & non-cog. development in
   children using data from the Longitudinal Study of A. Children (LSAC). We
   militate against the measurement problems that are assoc. with individual
   unobserved heterogeneity by exploiting the richness of LSAC data & applying
   contemporary econometric approaches. We find that sending children to
   Catholic or other indep. primary schools has no sig. effect on their
   cognitive & non-cog. outcomes. The literature now has evidence from three
   different continents that the returns to attending Catholic primary schools
   are no different than public schools."
   -- [<A HREF="http://dx.doi.org/10.1016/j.labeco.2015.02.009">doi:10.1016/j.labeco.2015.02.009</A>]['15].
   (Also see the ABC[<A HREF="http://www.abc.net.au/news/2015-04-14/study-finds-no-academic-edge-for-private-school-students/6390936">14/4/2015</A>].)

%A E. C. Hayden
%T Rule rewrite aims to clean up scientific software
%J Nature
%V 520
%N 7547
%P 276-277
%M APR
%D 2015
%K news, views, c2015, c201x, c20xx, zz0415, scientific research,
   computer software, availability, peer review, replication, results,
   Barzel, Barabasi, Kellis, controversial, MolBio, biological, regulatory,
   networks, systems
%X "Nature Biotechnology asks peer reviewers to check accessibility of code used
   in computational studies ... In announcing its policy, [NB] cited two of its
   studies that were called into question by scientists who could not replicate
   the conclusions. Both papers[2,3] had reported new methods for analysing
   connections within networks, but neither provided sufficient documentation of
   their tools or approach. The j. has now published more info. about how
   s/w was used in each analysis. ..."
     [2]Barzel, B. & Barabasi, A.-L. Nature Biotechnol. 31, 720-725, 2013.
     [3]Feizi, S., Marbach, D., Medard, M. & Kellis, M.,
        Nature Biotech. 31, 726-733, 2013.
   -- [<A HREF="http://dx.doi.org/10.1038/520276a">doi:10.1038/520276a</A>]['15].

%A D. Hicks,
%A P. Wouters,
%A L. Waltman,
%A S. de Rijcke
%A I. Rafols
%T Bibliometrics: The Leiden Manifesto for research metrics
%J Nature
%V 520
%N 7548
%P 429-431
%M APR
%D 2015
%K views, c2015, c201x, c20xx, zz0515, publish, perish, bibliometrics,
   impact, citations, altmetrics, science, management, scientific research, ISI,
   InCites, SciVal, journals, JIF, KPI, KPIs, Hindex, misuse
%X "... The problem is that evaluation is now led by the data rather than by
   judgement. Metrics have proliferated: usually well intentioned, not always
   well informed, often ill applied. We risk damaging the system with the very
   tools designed to improve it ..."
  -- [<A HREF="http://dx.doi.org/10.1038/520429a">doi:10.1038/520429a</A>]['15].
   Also see "The Leiden Ranking 2011/2012..." (DEC 2012)
   -- [<A HREF="https://doi.org/10.1002/asi.22708">10.1002/asi.22708</A>]['23].
   [Also search for: publish perish].

%A M. Dyble
%A et al ...
%A A. B. Migliano
%T Sex equality can explain the unique social structure of hunter-gatherer bands
%J Science
%V 348
%N 6236
%P 796-798
%M MAY
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0515, human, behaviour, hunter gatherer,
   society, social, culture, cooperation, sex, gender, men, women, pair bonding,
   mates, Agta, Mbendjele BaYaka, agent based
%X "The social organization of mobile hunter-gatherers has several derived
   features, inc. low within-camp relatedness & fluid meta-groups. Although
   these features have been proposed to have provided the selective context for
   the evoln of human hypercooperation & cumulative culture, how such a
   distinctive social system may have emerged remains unclear. We present an
   agent-based model suggesting that, even if all individuals in a community
   seek to live with as many kin as possible, within-camp relatedness is reduced
   if men & women have equal influence in selecting camp members. Our model
   closely approx. observed patterns of co-residence among Agta & Mbendjele
   BaYaka hunter-gatherers. Our results suggest that pair-bonding & increased
   sex egalitarianism in human evolutionary history may have had a
   transformative effect on human social organization."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaa5139">doi:10.1126/science.aaa5139</A>]['15].

%A M. Kwiek
%T Academic top earners. Research productivity, prestige generation, and
   salary patterns in European universities
%J Sci. and Public Policy
%M MAY
%D 2017
%K c2017, c201x, c20xx, zz0717, scientific research, university, academic,
   salary, work, jobs, success, funding, grants, Europe
%X "... While, in the Anglo-Saxon countries, the U.research mission typically
   pays off at an individual level, in Continental Europe, it pays off only in
   combination with administrative & related duties. Seeking future financial
   rewards solely through res. does not seem to be a viable strategy in Europe,
   but seeking satisfaction in res. through solving res. puzzles is also
   becoming difficult, with the growing emphasis on the 'relevance' &
   'applicability' of fundable research. Thus, both the traditional 'investment
   motivation' & 'consumption motivation' to perform research decrease, creating
   severe policy implications. The primary data come from 8,466 usable cases."
   -- [<A HREF="https://doi.org/10.1093/scipol/scx020">doi:10.1093/scipol/scx020</A>]['17].

%A E. Gibney
%T UK universities slow to publish reports of misconduct investigations
%J Nature
%V 521
%V 7552
%P ?-?
%M MAY
%D 2015
%K news, c2015, c201x, c20xx, zz0515, publish, perish, science, scientific,
   research, misconduct, academic, university, management, administration,
   UK, investigation, concordat, integrity, UKRIO
%X "Few institutions have followed research integrity guidelines to the letter.
   Just a fraction of universities in the UK have made public the extent of
   their investigations into research misconduct, a survey has found - even
   though all have been told that they should do so. ... 21 investigations, of
   which 4 upheld the allegations of misconduct & 3 were ongoing. Of the 11
   cases in which a type of misconduct was specified, 5 were investigations into
   plagiarism, 2 into falsification, 2 into questions over authorship, one into
   fabrication & one into breach of confidentiality. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature.2015.17559">doi:10.1038/nature.2015.17559</A>]['15].
   Also see editorial@[<A HREF="http://dx.doi.org/10.1038/521259a">www</A>]['15].
   [Also search for: research misconduct].

%A C. Hidalgo
%T Why Information Grows: The Evolution of Order, from Atoms to Economies
%I BasicBooks
%P 256
%M JUN
%D 2015
%K book, text, c2015, c201x, c20xx, zz0615, information, economics, order,
   growth, networks
%X 1st ed 2015, hb us$17; uk us isbn:0465048994; isbn13:978-0465048991.
   "... understanding the nature of economic growth demands transcending the
   social sciences and including the natural sciences of information, networks,
   and complexity. To understand the growth of economies, H. argues, we first
   need to understand the growth of order. ..."

%A T. R. Karl
%A et al ...
%A H.-M. Zhang
%T Possible artifacts of data biases in the recent global surface warming hiatus
%J Science
%V 348
%N 6242
%P 1469-1472
%M JUN
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0615, climate change, global warming, hiatus,
   pause, surface, temperature, no slowdown, CO2, greenhouse gases, bias,
   IPCC, NOAA, 21C
%X "... apparent decrease in the upward trend of global surface temps. since
   1998, a phenomenon that has been dubbed the global warming 'hiatus.' Here we
   present an updated global surface temp. analysis that reveals that global
   trends are higher than reported by the IPCC, esp. in recent decades, & that
   the central est. for the rate of warming during the first 15y. of the 21st
   century is at least as great as the last half of the 20th c.. ... do not
   support the notion of a 'slowdown' in the increase of global surface temp.."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaa5632">doi:10.1126/science.aaa5632</A>]['15].
   (Slightly higher (0.116C/decade) in fact.)
   (Also see bbc@[<A HREF="http://www.bbc.com/news/science-environment-33006179">5/6/2015</A>].)

%T Australia's future workforce?
%I Committee for Economic Development of Australia (CEDA)
%P 258
%M JUN
%D 2015
%K report, c2015, c201x, c20xx, zz0615, prediction, zz0125, zz0135,
   zzPrediction, work, job, jobs, automation, robotics, technology, disruption,
   economics, skills, education, Australia
%X 2015; isbn:0858013002.
   "... focuses on what jobs and skills we need to develop to ensure our economy
   continues to grow and diversify. ... The high probability that 40% of
   Australia's workforce, more than five million people, could be replaced by
   automation within the next 10 to 20 years; ..."
   -- [<A HREF="http://www.ceda.com.au/research-and-policy/policy-priorities/workforce">www</A>]['15],
   p.r.@[<A HREF="http://www.ceda.com.au/2015/06/16/five-million-Aussie-jobs-gone-in-10-to-15-years">www</A>]['15],
   pdf@[<A HREF="http://adminpanel.ceda.com.au/FOLDERS/Service/Files/Documents/26792~Futureworkforce_June2015.pdf">www</A>]['15] (258pp).
   (Check prediction in 2030.)
   [Also search for: zzPrediction].

%A P. Moriarty
%T The use of raw grant income as a performance target has got to go - now
%J Times Higher Ed
%M JUN
%D 2015
%K news, newspaper, c2015, c201x, c20xx, zz0615, higher education, university,
   research, management, academic, grant, income, target, grants, funding,
   KPI, KPIs, scientific research, Nottingham, Professor, Grimm,
   Imperial College London, ICL, ARC, THES, UK
%X "This mendacious metric is dangerous for individuals & the sector, & bad news
   for the taxpayer ... An analysis of research income targets in last week's
   Times Higher Education (Grant goals set for staff at one in six campuses,
   11 June) revealed that quite a few UK universities are esp. keen to
   incentivise academics to rip off the taxpayer. ... The use of raw grant
   income as a performance target has got to go. Now. It's blatantly flawed &
   immoral because it encourages us to overstate the publicly funded resources
   we need for our work. But there's a simple solution. Here's my advice to
   senior university managers: put aside the fixation on flawed metrics & trust
   your staff. ..."  [via AK.]
   -- [<A HREF="https://www.timeshighereducation.co.uk/the-use-of-raw-grant-income-performance-as-a-target-has-got-go-now">www</A>][18/6/2015] -- paywalled '20.
   (Also see, "... I am of the opinion that you [Grimm] are struggling to
       fulfil the metrics of a Professorial post at Imperial College which
       include maintaining established funding in a programme of research
       with an attributable share of research spend of stg.200k p.a.
       ...  imperial.ac.uk/.../ordinances/... ..."
   -- DC's Improbable Science,
      [<A HREF="http://www.dcscience.net/2014/12/01/publish-and-perish-at-imperial-college-london-the-death-of-stefan-grimm/">www</A>][1/12/14].)
   [Also search for: University KPIs].

%A Y. N. Harari
%T Sapiens: A Brief History of Humankind
%I HarperPubl
%P 464
%M FEB
%D 2015
%K book, c2015, c201x, c20xx, zz0715, human, homo sapiens, history, evolution
%X 1st ed 2015; hb us$20; uk us isbn:0062316095; uk us isbn13:978-0062316097.
   "... One hundred thousand years ago, at least six different species of humans
   inhabited Earth. Yet today there is only one - homo sapiens. What happened to
   the others? And what may happen to us? ..."

%A J. Iqbal
%T The women whom science forgot
%I BBC
%M JUN
%D 2015
%K c2015, c201x, c20xx, zz0715, science, scientific research, gender, woman,
   women, STEM, www, Marie Curie, X-rays, Dorothy Hodgkin, penicillin,
   crystallography, Esther Lederberg, microbiology, Rosalind Franklin,
   DNA helix, Ida Tacke, rhenium, masurium technetium, chemistry, Lise Meitner,
   meitnerium, nuclear fission, Chien-Shiung Wu, physics, law of parity,
   Henrietta Leavitt, astronomy, period luminosity
%X bbc [<A HREF="http://www.bbc.com/news/science-environment-33157396">19/6/2015</A>].
   [Also search for: women STEM].

%A M. Wen
%A N. Baym
%A O. Tamuz
%A J. Teevan
%A S. Dumais
%A A. Kalai
%T OMG UR funny! Computer-aided humor with an application to chat
%J 6th Int. Conf. on Computational Creativity
%W Park City, UT
%M JUN
%D 2015
%K conf, ICCC, c2015, c201x, c20xx, zz0715, humour, humor, funny, ha ha, haha,
   joke, jokes, chat, chatroom, chatBot, generator, funny, sense of humour,
   emoticons, images, CAH, CAHOOTS
%X "... explore Computer-Aided Humor (CAH), where a computer & a human
   collaborate to be humorous. CAH systems support people's natural desire to be
   funny by helping them express their own idiosyncratic sense of humor.
   [AI] research has tried for years to create systems that are funny, but found
   the problem to be extremely hard. We show that by combining the strengths of
   a computer & a human, CAH can foster h. better than either alone.  We present
   CAHOOTS, an online chat system that suggests humorous images to its users to
   include in the conversation. We compare CAHOOTS to a regular chat system, &
   to a system that automatically inserts funny images using an artificial
   humor-bot. Users report that CAHOOTS made their conversations more enjoyable
   & funny, & helped them to express their personal senses of humor.
   Computer-Aided Humor offers an example of how systems can algorithmically
   augment human intelligence to create rich, creative experiences."
   -- pdf@[<A HREF="http://research.microsoft.com/en-us/um/people/teevan/publications/papers/iccc15-humor.pdf">m/s</A>]['15].
   auth1@[<A HREF="https://sites.google.com/site/wenmiaomiao98/">www</A>]['15] is @CMU; others at m/s res..

%A L. Brodbeck
%A S. Hauser
%A F. Iida
%T Morphological evolution of physical robots through model-free phenotype
   development
%J PLoS One
%V 10
%N 6
%P e0128444
%M JUN
%D 2015
%K jrnl, eJrnl, c2015, c201x, c20xx, zz0815, AI, artificial, robot, evolution,
   self assembly, building, Pallab
%X "... report model-free development & evaluation of phenotypes in the
   artificial evoln of physical systems, in which a mother robot autonomously
   designs & assembles locomotion agents. The locomotion agents are
   automatically placed in the testing environment & their locomotion behavior
   is analyzed in the real world. This feedback is used for the design of the
   next iteration. Through experiments with a total of 500 autonomously built
   locomotion agents, this article shows diversification of morphology &
   behavior of physical robots for the improvement of functionality with limited
   resources."  [28 refs.]
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0128444">doi:10.1371/journal.pone.0128444</A>]['15].
   (?Run for the hills?-)

%A R. Barends
%A et al ...
%A J. M. Martinis
%T Digitized adiabatic quantum computing with a superconducting circuit
%J Nature
%V 534
%P 222-226
%M JUN
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0916, quantum computing, computer, adiabatic,
   digital, Ising problem, google, UCSB
%X "... adiabatic q.computing, a system is slowly evolved from the ground state
   of a simple initial Hamiltonian to a final H. that encodes a computational
   problem. The appeal of this approach lies in the combination of simplicity &
   generality; in principle, any problem can be encoded. In practice,
   applications are restricted by limited connectivity, available interactions
   & noise. A complementary approach is digital q.computing, which enables the
   construction of arbitrary interactions & is compatible with error correction,
   but uses q.circuit algs. that are problem-specific. Here we combine the
   advantages of both approaches by implementing digitized adiabatic q.computing
   in a superconducting system. We tomographically probe the system during the
   digitized evolution & explore the scaling of errors with system size. We then
   let the full system find the soln to random instances of the one-dimensional
   Ising problem as well as problem Hamiltonians that involve more complex
   interactions. This digital q.simulation of the adiabatic alg. consists of up
   to nine qubits & up to 1,000 q.logic gates. The demonstration of digitized
   adiabatic q.computing in the solid state opens a path to synthesizing
   long-range correlations & solving complex comp. problems. When combined with
   fault-tolerance, ... becomes a general-purpose alg. that is scalable."
   -- [<A HREF="http://dx.doi.org/10.1038/nature17658">doi:10.1038/nature17658</A>]['16].

%A W. MacAskill
%T Doing Good Better: How Effective Altruism Can Help You Make a Difference
%I Gotham
%P 272
%M JUL
%D 2015
%K book, text, c2015, c201x, c20xx, zz0915, effective charity, ethics,
   philosophy, rational, giving, philanthropy, donating, doing, being good
%X 1st ed 2015; hb us$15; uk us isbn:1592409105; uk us isbn13:978-1592409105.
   "Most of us want to make a difference. We donate our time & money to
   charities ... Unfortunately, we often base these decisions on assumptions &
   emotions rather than facts. As a result, even our best intentions often lead
   to ineffective - & sometimes downright harmful - outcomes. How can we do
   better? ... How many people benefit, & by how much? Is this the most
   effective thing I can do? Is this area neglected? What would have happened
   otherwise? What are the chances of success, & how good would success be? ..."
   Also see WM@[<A HREF="http://www.williammacaskill.com/">www</A>]['15],
    WM@[<A HREF="http://cambridge.academia.edu/WilliamMacAskill">www</A>]['15],
    & The G. [<A HREF="http://www.theguardian.com/books/2015/aug/20/doing-good-better-william-macaskill-review">www</A>][20/8/2015].

%A S. Reardon
%T US vaccine researcher sentenced to prison for fraud
%J Nature
%V 523
%N 7559
%P ?-?
%M JUL
%D 2015
%K news, c2015, c201x, c20xx, zz0715, scientific research, fraud, academic,
   misconduct, Dong-Pyou Han, Iowa State University, HIV, vaccine, trial,
   ethics, zzEthics, prison, jail, gaol, NIH, NSF
%X "... on 1 July, Dong-Pyou Han, a former biomedical scientist at Iowa State
   University in Ames, was sentenced to 57 months for fabricating & falsifying
   data in HIV vaccine trials. Han has also been fined US$7.2 million & will be
   subject to three years of supervised release after he leaves prison. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature.2015.17660">doi:10.1038/nature.2015.17660</A>]['15].
   [Also search for: academic research misconduct].

%T The Metric Tide: Report of the Independent Review of the Role of Metrics in
   Research Assessment and Management
%I HEFCE
%M JUL
%D 2015
%K report, TR, c2015, c201x, c20xx, zz0715, scientific research, university,
   management, academic, academia, excellence, peer review, refereeing,
   KPI, KPIs, JIF, impact, uk, review, grant, grants, funding, HEFCE, UK, ARC
%X "... investigate the current & potential future roles that quantitative
   indicators can play in the assessment & management of research. ... There is
   legitimate concern that some indicators can be misused or 'gamed': journal
   impact factors, university rankings & citation counts being three prominent
   examples. ... Analysis concluded that that no metric can currently provide
   a like-for-like replacement for REF peer review. ..."
   -- [<A HREF="https://apo.org.au/node/56066">apo</A>]['22],
      [<A HREF="https://doi.org/10.13140/RG.2.1.4929.1363">doi:10.13140/RG.2.1.4929.1363</A>]['22],
      [<A HREF="http://www.hefce.ac.uk/pubs/rereports/Year/2015/metrictide/">MTide</A>]['15],
     @[<A HREF="http://www.hefce.ac.uk/rsrch/metrics/">ms</A>]['15],
     @[<A HREF="http://www.hefce.ac.uk/">hefce</A>]['15].
   [Also search for: Campbell law]  and  [also search for: Goodhart law].

%A M. Pais-Vieira
%A G. Chiuffa
%A M. Lebedev
%A A. Yadav
%A M. A. L. Nicolelis
%T Building an organic computing device with multiple interconnected brains
%J Sci. Rep.
%V 5
%P e11869
%M JUL
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0715, organic computer, rat brains, brainnet,
   brainnets, brain machine, interface, implant, controversial
%X "... Brainets, i.e. n/wks formed by multiple animal brains, cooperating &
   exchanging info. in real time through direct brain-to-brain interfaces ...
   describe the 1st experimental demo. of such a Brainet ... four adult rat
   brains. ... concurrently recording the extracellular electrical activity
   generated by popns of cortical neurons distrib. across multiple rats
   chronically implanted with multi-electrode arrays. ... Using this approach,
   different Brainet architectures solved a number # useful comp. problems, such
   as discrete classn, image proc., storage & retrieval of tactile info., & even
   weather forecasting. Brainets consistently performed at the same or higher
   levels than single rats in these tasks. ... propose that Brainets could be
   used to investigate animal social behaviors as well as a test bed for
   exploring the properties & potential applications of organic computers."
   -- [<A HREF="http://dx.doi.org/10.1038/srep11869">doi:10.1038/srep11869</A>]['15].
   (?Is this nice? ?The Borg?)

%A A. Ambainis
%A A. Yakaryilmaz
%T Automata and quantum computing
%J arXiv
%P pp.32
%M JUL
%D 2015
%O to appear in 'Automata: From Mathematics to Applications'
%K TR, c2015, c201x, c20xx, zz0715, quantum computing, computer,
   finite state automaton, FSA, machine, FSM, QFSA, QFSM
%X "Q. comp. is a new model of compn, based on q.physics. Q.comps. can be
   exponentially faster than conventional computers for problems such as
   factoring. Besides full-scale q.comps., more restricted models such as
   q. versions of finite automata have been studied. ... survey various models
   of q. finite automata & their properties. We also provide some open questions
   & new directions for researchers."
   -- 1507.01988@[<A HREF="http://arxiv.org/abs/1507.01988">arXiv</A>][7/'15].

%A S. E. Bradforth
%A et al
%T University learning: Improve undergraduate science education
%J Nature
%V 523
%N 7560
%P 282-284
%M JUL
%D 2015
%K views, c2015, c201x, c20xx, zz0715, university, teaching, science, AAU, STEM,
   education, learning, assessment
%X "Undergraduate students are not being taught science, technology, engineering
   and mathematics (STEM) subjects as well as they need to be. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/523282a">doi:10.1038/523282a</A>]['15].

%T Search for extraterrestrial intelligence gets a $100-million boost
   Russian billionaire Yuri Milner announces most comprehensive hunt for
   alien life
%J Nature
%V 523
%N 7561
%P 392-393
%M JUL
%D 2015
%K news, views, Breakthrough Listen, Milner, c2015, c201x, c20xx, zz1220, SETI,
   search, radio, signal, BLC, BLC1, extraterrestrial life, intelligence, space,
   alien
%X "You could say that the silence has been deafening. Since its beginnings more
   than half a century ago, the dedicated search for extraterrestrial
   intelligence (SETI) has failed to detect the presence of alien civilizations.
   But at London's Royal Society today (20 July), Russian billionaire Yuri
   Milner announced a shot in the arm for SETI: a US$100-million decadal project
   to provide the most comprehensive hunt for alien communications so far. ..."
   -- [<A HREF="https://doi.org/10.1038/nature.2015.18016">doi:10.1038/nature.2015.18016</A>]['20].
   (Also see [<A HREF="https://en.wikipedia.org/wiki/Breakthrough_Listen">wikip</A>]['20].)
   [Also search for: extraterrestrial life].

%A A. Chatwin-Davies
%A A. S. Jermyn
%A S. M. Carroll
%T How to recover a qubit that has fallen into a black hole
%J arXiv
%M JUL
%D 2015
%K TR, c2015, c201x, c20xx, zz0715, physics, black hole, quantum, information,
   qubit, radiation
%X "... algorithm for the retrieval of a qubit, encoded in spin angular
   momentum, that has been dropped into a no-firewall unitary black hole.
   Retrieval is achieved analogously to quantum teleportation by collecting
   Hawking radiation & performing measurements on the black hole. Importantly,
   these methods only require the ability to perform measurements from outside
   the event horizon & to collect the H.radiation emitted after the state of
   interest is dropped into the black hole."
   -- 1507.03592@[<A HREF="http://arxiv.org/abs/1507.03592">arXiv</A>]['15].

%A S. Boixo
%A et al ...
%A H. Neven
%T Characterizing quantum supremacy in near-term devices
%J arXiv
%M JUL
%D 2016
%K TR, c2016, c201x, c20xx, zz0916, quantum computing, simulation, qubits,
   google
%X "...study the task of sampling from the output distributions of
   (pseudo-)random q.circuits, a natural task for benchmarking q.computers.
   Crucially, sampling this distribution classically requires a direct numerical
   simulation of the circuit, with computational cost exponential in the # of
   qubits. ... study the convergence to the chaotic regime using extensive
   supercomputer simulations, modeling circuits with up to 42 qubits - the
   largest q.circuits simulated to date for a computational task that approaches
   quantum supremacy. ..."
   -- 1608.00263@[<A HREF="http://arxiv.org/abs/1608.00263">arXiv</A>]['16].

%A P. A. Stott
%A N. Christidis
%A F. E. Otto
%A et al ...
%A F. W. Zwiers
%T Attribution of extreme weather and climate-related events
%J Wiley Interdisciplinary Reviews: Climate Change
%V 7
%P 1
%P 23-41
%D 2016
%K c2016, c201x, c20xx, zz0220, extreme, world, weather attribution, WWA,
   climate change, global warming, CO2, human activity, cause, causality, stats
%X "... Event attribution studies seek to determine to what extent anthropogenic
   climate change has altered the probability or magnitude of particular
   events. ..."
   -- [<A HREF="https://doi.org/10.1002/wcc.380">doi:10.1002/wcc.380</A>]['20].
   [Also search for: extreme weather attribution].

%A A. Letchford
%A H. S. Moat
%A T. Preis
%T The advantage of shorter titles: Should scientists keep it snappy?
%I The Royal Soc.
%V 2
%N 8
%M AUG
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0316, scientific, paper, title, short, length,
   publications, impact, citations
%X "... investigate whether any of this variance [in citations] can be explained
   by a simple metric of one aspect of the paper's presentation: the length of
   its title. Our analysis provides evidence that journals which publish papers
   with shorter titles receive more citations per paper. These results are
   consistent with the intriguing hypothesis that papers with shorter titles may
   be easier to understand, and hence attract more citations."
   -- [<A HREF="http://dx.doi.org/10.1098/rsos.150266">doi:10.1098/rsos.150266</A>]['16].
   (Also see [<A HREF="https://royalsociety.org/news/2015/08/advantage-shorter-titles/">www</A>]['16].)

%A J. E. Coxworth
%A P. S. Kim
%A J. S. McQueend
%A K. Hawkes
%T Grandmothering life histories and human pair bonding
%J PNAS
%V 112
%N 38
%P 11806-11811
%M SEP
%D 2015
%K jrnl, PNAS, c2015, c201x, c20xx, zz0915, human behaviour, social, monogamy,
   mate selection, mating, guarding, pair bond, bonding, parenting, grandmother,
   lifespan, fertile, male, female, fertility, sex ratios, Hazda
%X "... develop an alternative argument that connects the evolution of human
   pair bonds to the male-biased mating sex ratios that accompanied the evoln of
   human life history. We simulate an agent-based model of the grandmother
   hypothesis, compare simulated sex ratios to data on great apes & human
   hunter-gatherers, & note associations between a preponderance of males & mate
   guarding across taxa. Then we explore a recent model that highlights the
   importance of mating sex ratios for differences between birds & mammals &
   conclude that lessons for human evoln cannot ignore mammalian reproductive
   constraints. In contradiction to our claim that male-biased sex ratios are
   characteristically human, female-biased ratios are reported in some populns.
   We consider the likelihood that fertile men are undercounted & conclude that
   the mate-guarding hypothesis for human pair bonds gains strength from
   explicit links with our grandmothering life history." (online 8/9/2015.)
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1599993112">doi:10.1073/pnas.1599993112</A>]['15].
   (Also see abc[<A HREF="http://www.abc.net.au/science/articles/2015/09/08/4307665.htm">8/9/2015</A>].)

%A C. Cesare
%T Online security braces for quantum revolution; Encryption fix begins in
   preparation for arrival of futuristic computers
%J Nature
%V 525
%N 7568
%P 167-168
%M SEP
%D 2015
%K news, c2015, c201x, c20xx, zz0915, quantum computing, cryptography,
   security, codebreaking, IQC, NSA, cryptosystem, encryption, RSA,
   McEliece, PQCRYPTO
%X "It is an inevitability that cryptographers dread: the arrival of powerful
   quantum computers that can break the security of the Internet. Although these
   devices are thought to be a decade or more away, researchers are adamant
   that preparations must begin now. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/525167a">doi:10.1038/525167a</A>]['15].

%A D. Sarewitz
%T Reproducibility will not cure what ails science
%J Nature
%V 525
%N 7568
%P 159
%M SEP
%D 2015
%K news, views, c2015, c201x, c20xx, zz0915, science, stats, America, US, CO2,
   politics, Republican, Environmental Protection Agency, EPA, climate change,
   law, laws, act
%X "A bill to make data for environmental regulation more transparent reveals
   the fuzzy boundary between science and ideology. ... Consider, for example,
   the Secret Science Reform Act of 2015, a US bill that would 'prohibit the
   Environmental Protection Agency from proposing, finalizing, or disseminating
   regulations or assessments based upon science that is not transparent or
   reproducible.' Passed in March by the House of Representatives essentially
   along party lines (Republicans in favour, Democrats opposed) & now awaiting
   action by the Senate, the bill has been vigorously opposed by many scientific
   & environmental organizations.They argue, probably correctly, that the bill's
   intent is to block & even roll back environmental regulations by requiring
   that all data on which the rules are based be made publicly available for
   independent replication. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/525159a">doi:10.1038/525159a</A>]['15].

%A R. Hil
%T Selling Students Short: Why You Won't Get the University Education You
   Deserve
%I AllenAndUnwin
%P 240
%M SEP
%D 2015
%K book, text, c2015, c201x, c20xx, zz0116, education system, tertiary, higher,
   University, Universities, Australia, grades, overseas, student, fee, fees,
   HECS debt, staff, teach, teaching, lecture, course, MOOCS, academic research,
   Go8, KPI, KPIs
%X 1st ed 2015; pb us$25; uk us isbn:1743318898; uk us isbn13:978-1743318898.
   "Today more students than ever before go to U., & what they experience there
   is vastly different from even a decade ago. The hi-tech libraries ... hide
   a less attractive reality. Today's Us. are vocationally driven, they use
   technology to offset staffing costs, class sizes have blown out, & staff are
   rewarded more for research than teaching. Students are less well prepared,
   they work longer hours in part-time jobs, & their education leaves them in
   debt for years. Drawing on research studies & his own interviews with 70 u/g
   students from Us. around .au, ... lifts the lid on the U. experience. ...
   argues Us. are turning out a consumer popln which is often unable to perform
   some of the most basic professional duties, & has little capacity to engage
   critically with the world around them."
   (Also see [<A HREF="http://www.abc.net.au/radionational/programs/bigideas/what-students-really-think-of-university/7002078">abc</A>][10/1/2016],
   and [<A HREF="http://www.allisons.org/ll/Computing/Misc/2008-rankings/">www</A>].)

%A J. Marchant
%T Archimedes' legendary sphere brought to life; Recreation of a
   2,000-year-old model of the Universe to appear in exhibition
%J Nature
%V 526
%N 7571
%P 19
%M SEP
%D 2015
%K news, c2015, c201x, c20xx, zz1015, ancient, Greek, heavens, stars, planets,
   model, history, Archimedes, sphere,
   M. Wright, reconstruction, gear wheel, gears, geared
%X "A mechanical model of the Universe attributed to the ancient Greek
   mathematician and polymath Archimedes has been reconstructed after
   more than two millennia. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature.2015.18431">doi:10.1038/nature.2015.18431</A>]['15].
   [Also search for: Antikythera mechanism].

%A M. McNutt
%T Climate warning, 50 years later
%J Science
%V 350
%N 6262
%P 721
%M NOV
%D 2015
%K news, views, editorial, c1965, c196x, c19xx, c2015, c201x, c20xx, zz1115,
   climate change, global warming, CO2, greenhouse gas, gases, atmosphere,
   PCAST, 1965, risk, prediction, zzPrediction
%X "Long before geophysicist Michael Mann's hockeystick graph became the icon
   for anthropogenic global warming, the U.S. President's Science Advisory
   Committee [now known as the President's Council of Advisors on Science &
   Technology (PCAST)] cautioned President Lyndon B. Johnson that the continued
   release of CO2 to the atmosphere from burning fossil fuels would 'almost
   certainly cause significant changes' and 'could be deleterious from the point
   of view of human beings.' The committee's report concluded that there could
   be 'marked changes in climate, not controllable through local or even
   national efforts.' In recognition of the 50th anniversary of that first
   official warning from scientists to policy-makers, the American Association
   for the Advancement of Science (AAAS), the Carnegie Institution for Science,
   the American Meteorological Society, & the Linden Trust for Conservation
   sponsored a 1-day climate symposium on 29 October. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aad7927">doi:10.1126/science.aad7927</A>]['15].
   (2023 was the world's hottest year on record.)

%A M. Hvistendahl
%T China pursues fraudsters in science publishing
%J Science
%V 350
%N 6264
%P 1015
%M NOV
%D 2015
%K news, c2015, c201x, c20xx, zz1115, academic misconduct, fraud, scandal,
   publishing, fake, peer review, ghostwritten, paper, papers,
   China, CAST, scientific research
%X "China's main basic research agency is cracking down on scientists who used
   fake peer reviews to publish papers, demanding that serious offenders return
   research funding. ...  investigated dozens of scientists involved in
   peer-review scams. ...  ghostwritten or fraudulent papers. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.350.6264.1015">doi:10.1126/science.350.6264.1015</A>['15].


%A R. Susskind
%A D. Susskind
%T The Future of the Professions: How Technology Will Transform the Work of
   Human Experts
%I OUP
%P 256
%M JAN
%D 2016
%K book, OUP, c2016, c201x, c20xx, 21C, zz1215, prediction, zzPrediction, work,
   automation, job, profession, lawyers
%X 1st ed 2016; hb us$25; uk us isbn:0198713398; uk us isbn13:978-0198713395.
   "... predicts the decline of today's professions & describes the people &
   systems that will replace them. In an Internet society, according to [RS, DS]
   we will neither need nor want doctors, teachers, accountants, architects,
   the clergy, consultants, lawyers, & many others, to work as they did in the
   20th century. ..."
   [Also search for: zzPrediction].

%A J. Gould
%T How to build a better PhD
%J Nature
%V 528
%N 7580
%P 22-25
%M DEC
%D 2015
%K news, views, c2015, c201x, c20xx, zz1215, scientific research, academic,
   University, PhD, doctorate, jobs, graduate, postdoc
%X "There are too many PhD students for too few academic jobs -
   but with imagination, the problem could be solved.
   'Since 1977, we've been recommending that graduate departments partke
   in birth control, but no one has been listening,' ...
   In 2003, 21,343 science graduate students in the USA received a doctorate.
   By 2013, this had increased by almost 41% - and the life sciences showed the
   greatest growth. That trend is mirrored elsewhere. According to a 2014
   report looking at the 34 countries that make up the Organisation for
   Economic Co-operation and Development, the proportion of people who leave
   tertiary education with a doctorate has doubled from 0.8% to 1.6% over the
   past 17 years. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/528022a">doi:10.1038/528022a</A>]['15].

%A M. Valenzuela
%A Vu Ha
%A O. Etzioni
%T Identifying meaningful citations
%J Workshop on Scholarly Big Data: AI Perspectives, Challenges, and Ideas
%D 2015
%K wkShop, c2015, c201x, c20xx, zz0418, modified bibliometrics, papers, impact,
   scientific research, cite, important, significant, citations, references,
   semanticscholar, knowledge, science
%X "We introduce the novel task of identifying important citations in scholarly
   literature, i.e., citations that indicate that the cited work is used(!) or
   extended in the new effort. We believe this task is a crucial component in
   algorithms that detect & follow research topics & in methods that measure the
   quality of publications. We model this task as a supervised classification
   problem at two levels of detail: a coarse one with classes (important vs.
   non-important), & a more detailed one with four importance classes. We
   annotate a dataset of approximately 450 citations with this information, &
   release it publicly. We propose a supervised classification approach that
   addresses this task with a battery of features that range from citation
   counts to where the citation appears in the body of the paper, & show that,
   our approach achieves a precision of 65% for a recall of 90%."
   -- [<A HREF="https://ai2-website.s3.amazonaws.com/publications/ValenzuelaHaMeaningfulCitations.pdf">am'zonaws</A>]['22],
      [<A HREF="https://www.aaai.org/ocs/index.php/WS/AAAIW15/paper/download/10185/10244">AAAI</A>]['18],
    @ [<A HREF="https://www.semanticscholar.org/paper/Identifying-Meaningful-Citations-Valenzuela-Ha/1c7be3fc28296a97607d426f9168ad4836407e4b">SScclr</A>]['22].
   (Also see semanticscholar@[<A HREF="https://www.semanticscholar.org/">www</A>]['18].)
   [Also search for: modified bibliometrics].

%A B. Liu
%A S. Floud
%A K. Pirie
%A J. Green
%A R. Peto
%A V. Beral
%T Does happiness itself directly affect mortality? The prospective UK million
   women study
%J The Lancet
%V ?
%N ?
%P ?-?
%M DEC
%D 2015
%K jrnl, c2015, c201x, c20xx, zz1215, human, happiness, wellbeing, longevity,
   women, health, ageing, mortality, lifespan, stats
%X "... Of 719,671 women in the main analyses (median age 59 years ...
   Self-rated poor health at baseline was strongly assoc. with unhappiness. ...
   In middle-aged women, poor health can cause unhappiness. After allowing
   for this association & adjusting for potential confounders, happiness &
   related measures of wellbeing do not appear to have any direct effect on
   mortality."  [online 9 Dec 2015.]
   -- [<A HREF="http://dx.doi.org/10.1016/S0140-6736(15)01087-9">doi:10.1016/S0140-6736(15)01087-9</A>]['15].
   [Also search for: happiness].

%T All together now, or how Hamsters become co-authors of scientific papers
%I columbus-web
%M DEC
%D 2019
%K views, c2016, c201x, c20xx, zz0319, scientific, university, research,
   impact, JIF, KIP, KPIs, Hindex, publish, perish, guest author,
   multiple authors, trends, hamster, Geim, publications, papers, LPU, LPUs,
   ranking, distortion, misuse, gaming, implausibly, improbably prolific,
   authorship abuse
%X "Recent developments in international research illustrate two well-known
   laws, the Goodhart and the Campbell laws, both developed in the middle of the
   70s. ... Say you write one paper a year. If you team up with a colleague
   doing similar work and write two half-papers instead, both parties end up
   with their names on twice as many papers, but with no increase in workload.
   Find a third researcher to join in and you can get your name on three papers
   a year. And so on. ... Sir Andre Geim, who won the 2010 Nobel Prize in
   physics, listed H.A.M.S. ter Tisha as co-author of a paper he published in
   2001 in Physica B, a peer-reviewed journal! ..."
   -- [<A HREF="https://www.columbus-web.org/en/news-and-events/item/148-all-together-now,-or-how-hamsters-become-co-authors-of-scientific-papers.html">www</A>]['19].
   'Detection of earth rotation with a diamagnetically levitating gyroscope',
      A.K.Geim, H.A.M.S.Ter Tisha, Physica B: Condensed Matter,
      vol.294-295, pp.736-739, 2001
   -- [<A HREF="https://doi.org/10.1016/S0921-4526(00)00753-5">doi:10.1016/S0921-4526(00)00753-5</A>]['22].
   Also see, "... Geim's pet hamster was cited as a co-author in a sci. paper
      for his assistance with the project."
   -- [<A HREF="https://www.abc.net.au/radionational/programs/scienceshow/nobel-prize-winner-co-authored-paper-with-his-pet-v1/10785784">abc</A>][9/2/2019].
   [Also search for: publish perish] & [also search for: implausibly prolific].

%A J. Bohannon
%T Publishers embrace scheme to end name confusion
%J Science
%V 351
%N 6270
%P 213
%M JAN
%D 2016
%K news, c2016, c201x, c20xx, zz0116, ORCID, scientific research, publications,
   journals, name, names, unique, digital, identifier, id, ids, researcherID,
   author, authors, Scopus
%X "Name ambiguity can be a nuisance. If you are a Williams or a Johnson -
   among the most common surnames ... ORCID is so far dodging another problem:
   what to do about assigning numbers to dead scientists. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.351.6270.213">doi:10.1126/science.351.6270.213 </A>]['16].
   (Also see ORCID@[<A HREF="http://orcid.org/">www</A>][2016].)

%A J. Tollefson
%T 2015 declared the hottest year on record. Warming in the Pacific Ocean helps
   to shatter past records, and could bring even faster temperature rises
%J Nature
%V 529
%N 7587
%P 450
%M JAN
%D 2016
%K news, c2016, c201x, c20xx, zz0216, climate change, global warming, earth,
   2015, temperature, rise, record, Pacific ocean, El Nino, ElNino, PDO, NOAA,
   meteorology
%X "It's official: 2015 was the hottest year on record. Global data show that a
   powerful El Nino system, marked by warmed waters in the tropical Pacific
   Ocean, helped to drive atmospheric temperatures well past 2014's record
   highs. Some researchers suggest that broader Pacific trends could spell even
   more dramatic temperature increases in years to come. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature.2016.19216">doi:10.1038/nature.2016.19216</A>]['16].
   (See,
      "The globally averaged temperature over land and ocean surfaces for 2015
      was the highest among all years since record keeping began in 1880. ..."
      -- [<A HREF="http://www.ncdc.noaa.gov/sotc/summary-info/global/201512">noaa</A>][1/2016].)

%T Leading People
%Q Sutton Trust
%M FEB
%D 2016
%K TR, c2016, c201x, c20xx, zz0316, UK, British, class system, public, private,
   independent, state, school, education, Oxbridge, University, professions,
   job, jobs, work, old boys network, privilege, advantage, disadvantage,
   society, social mobility
%X "Over a decade ago, the Sutton Trust published its first report on the
   educational backgrounds of the UK's professional elite, looking at the
   schools & universities attended by top solicitors, barristers & judges. ...
   key:    [profession, independent school, state school].
   today: [[UK population,       7%, 93%],
           [law (judiciary),    74%, 26%],
           [law (barristers),   74%, 26%], ...,
           [medicine,           61%, 39%], ...,
           [law (solicitors),   51%, 49%],
           [politics (cabinet), 50%, 50%], ...,
           [business,           34%, 66%]].
   And all time:
          [[film (Oscars),      67%, 33%],
           [Nobel prizes,       63%, 37%],
           [film (BAFTAs),      42%, 58%],
           [pop music (BRITs),  19%, 81%]]."
   -- [<A HREF="http://www.suttontrust.com/researcharchive/leading-people-2016/">www</A>]['16].

%A A. Cohen
%T Imbeciles: The Supreme Court, American Eugenics, and the Sterilization of
   Carrie Buck
%I Penguin
%P 416
%M MAR
%D 2016
%K book, c2016, c201x, c20xx, zz0316, eugenics, biology, US, USA, America,
   American, law, legal, discrimination, Taft, Brandeis, Wendell Holmes
%X 1st ed 2016; hb us$19; uk us isbn:1594204187; uk us isbn13:978-1594204180.
   "One of America's great miscarriages of justice, the Supreme Court's infamous
   1927 Buck v. Bell ruling made government sterilization of 'undesirable'
   citizens the law of the land. ... led to the sterilization of 70,000
   Americans ..."

%A M. Derex
%A R. Boyd
%T Partial connectivity increases cultural accumulation within groups
%J PNAS
%V ?
%N ?
%P ?-?
%M FEB
%D 2016
%K jrnl, PNAS, c2016, c201x, c20xx, zz0316, creativity, innovation, idea, ideas,
   originality, connectivity, connected, culture,
   population size, social network, groupthink, game
%X "... Recent work suggests that a population's ability to develop complex
   technologies is positively affected by its size & connectedness. Here, we
   present a simple computer-based experiment that compares the accumulation of
   innovations by fully & partially connected groups of the same size in a
   complex fitness landscape. We find that the propensity to learn from
   successful individuals drastically reduces cultural diversity within fully
   connected groups. In comparison, partially connected groups produce more
   diverse solns, & this diversity allows them to develop complex solns that are
   never produced in fully connected groups. These results suggest that
   explanations of ancestral patterns of cultural complexity may need to
   consider levels of populn fragmentation & interaction patterns between
   partially isolated groups."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1518798113">doi:10.1073/pnas.1518798113</A>]['16] (online Feb 2016).

%A J. Gao
%A B. Barzel
%A A.-L. Barabasi
%T Universal resilience patterns in complex networks
%J Nature
%V 530
%N 7590
%P 307-312
%M FEB
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0816, network, resilience
%X "... limitations are rooted in a theoretical gap: the current analytical
   framework of resilience is designed to treat low-dimensional models with a
   few interacting components, & is unsuitable for multi-D systems consisting of
   a large # of components that interact through a complex nwk. Here we bridge
   this theoretical gap by developing a set of analytical tools with which to
   identify the natural control & state parameters of a multi-D complex system,
   helping us derive effective one-D dynamics that accurately predict the
   system's resilience. The proposed analytical framework allows us
   systematically to separate the roles of the system's dynamics & topology,
   collapsing the behaviour of different nwks onto a single universal resilience
   fn. The analytical results unveil the nwk characteristics that can enhance
   or diminish resilience ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature16948">doi:10.1038/nature16948</A>]['16].
   [Also search for: Barzel Barabasi network].

%A T. Monz
%A et al ...
%A R. Blatt
%T Realization of a scalable Shor algorithm
%J Science
%V 351
%N 6277
%P 1068-1070
%M MAR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0316, Shor, shors, Shor's algorithm, factor,
   factorization, factorisation, factoring, integer, quantum computer, computing
%X "... 1994, Peter Shor came up with a quantum alg. that calculates the prime
   factors of a large # vastly more efficiently than a classical computer. For
   general scalability of such algs., h/w, quantum error correction, & the
   algorithmic realization itself need to be extensible. ... present the
   realization of a scalable Shor alg., as proposed by Kitaev. We factor the #15
   by effectively employing & controlling seven qubits & four 'cache qubits'
   & by implementing generalized arith. opns, known as modular multipliers.
   ... has been realized scalably within an ion-trap q.computer & returns
   the correct factors with a confidence level exceeding 99%."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aad9480">doi:10.1126/science.aad9480</A>]['16].
   [Also search for: Shor's algorithm].

%A M. Haythorpe
%T Reducing the generalised Sudoku problem to the Hamiltonian cycle problem
%J arXiv
%M MAR
%D 2016
%K TR, c2016, c201x, c20xx, zz0316, Sudoko, game, puzzle,
   Hamiltonian cycle problem
%X "The generalised Sudoku problem with N symbols is known to be NP-complete,
   & hence is equiv. to any other NPC problem, even for the std restricted
   version where N is a perfect square. In particular, generalised Sudoku is
   quiv. to the, classical, Hamiltonian cycle problem. A constructive alg.
   is given that reduces generalised S. to the H.cycle problem, where the
   resultant instance of H.cycle problem is sparse, & has O(N^3) vertices. The
   H.cycle problem instance so constructed is a directed graph, & so a (known)
   conversion to undirected H.cycle problem is also provided so that it can be
   submitted to the best heuristics. A simple alg. for obtaining the valid
   Sudoku soln from the Hamiltonian cycle is provided. Techniques to reduce
   the size of the resultant graph are also discussed.
   -- 1603.03019@[<A HREF="http://arxiv.org/abs/1603.03019">arXiv</A>]['16].

%A R. E. Zeebe
%A A. Ridgwell
%A J. C. Zachos
%T Anthropogenic carbon release rate unprecedented during the past
   66 million years
%J Nature Geoscience
%V ?
%P ?-?
%M MAR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0316, climate change, global warming, CO2,
   greenhouse gas, gases, emissions, Palaeocene Eocene Thermal Maximum, PETM,
   rate, rates
%X "... The Palaeocene-Eocene Thermal Maximum (PETM) is known at present to have
   the highest carbon release rates of the past 66 million years ... We
   conclude that, given currently available records, the present anthropogenic
   carbon release rate is unprecedented during the past 66 million years.
   We suggest that such a 'no-analogue' state represents a fundamental
   challenge in constraining future climate projections. Also, future ecosystem
   disruptions are likely to exceed the relatively limited extinctions observed
   at the PETM."
   -- [<A HREF="http://dx.doi.org/10.1038/ngeo2681">doi:10.1038/ngeo2681</A>]['16].

%A J. K. McNulty
%T Should spouses be demanding less from marriage? A contextual perspective on
   the implications of interpersonal standards
%J Pers. Soc. Psychol. Bull.
%V 42
%N 4
%P 444-457
%M APR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0416, human behaviour, love, marriage, husband,
   wife, wed, married, spouse, happiness, satisfaction, contentment, standards,
   expectations, hopes, divorce
%X "How much should people ask of their relationships? Whereas several
   perspectives suggest high standards should make actual outcomes feel worse
   by comparison & thus harm relationships, other perspectives suggest high
   standards should motivate people to exert the effort necessary to cultivate
   quality partnerships. The current 4-year longitudinal study of newlywed
   couples reconciled these competing perspectives by testing a prediction
   implicit in Finkel, Hui, Carswell, & Larson's suffocation model of marriage
   - that spouses' standards interact with factors reflective of their
   abilities to meet those standards to predict subsequent satisfaction. Among
   spouses who either reported less severe problems or were in marriages
   observed to be characterized by lower levels of destructive behavior,
   standards were positively associated with satisfaction over time; among
   spouses who reported more severe problems or were in marriages characterized
   by higher levels of destructive behavior, in contrast, standards were
   negatively associated with satisfaction over time."
   -- [<A HREF="http://dx.doi.org/10.1177/0146167216634050">doi:10.1177/0146167216634050</A>]['16].
   (Also see the G. [<A HREF="http://www.theguardian.com/commentisfree/2016/mar/21/secret-happy-marriage-low-expectations">22/3/2016</A>].)

%A L. J. Gunn
%A F. Chapeau-Blondeau
%A M. McDonnell
%A B. Davis
%A A. Allison
%A D. Abbott
%A et al.
%T Too good to be true: when overwhelming evidence fails to convince
%J Proc. of The Royal Society A
%V ?
%M APR ?
%D 2016
%K jrnl, PRSA, c2016, c2016, c20xx, zz0416, stats, evidence, witness, unanimous,
   police line up, lineup, research, archaeology, primality,
   paradox of unanimity, Duhem Quine hypothesis, independence
%X "Is it possible for a large sequence of measurements or observations, which
   support a hypothesis, to counterintuitively decrease our confidence? Can
   unanimous support be too good to be true? The assumption of independence is
   often made in good faith, however rarely is consideration given to whether a
   systemic failure has occurred.  Taking this into account can cause certainty
   in a hypothesis to decrease as the evidence for it becomes apparently
   stronger. We perform a probabilistic Bayesian analysis of this effect with
   examples based on (i) archaeological evidence, (ii) weighing of legal
   evidence, & (iii) cryptographic primality testing.  We find that even with
   surprisingly low systemic failure rates high confidence is very difficult to
   achieve & in particular we find that certain analyses of
   cryptographically-important numerical tests are highly optimistic,
   underestimating their false-negative rate by as much as a factor of 2^80."
   -- 1601.00900@[<A HREF="http://arxiv.org/abs/1601.00900">arXiv</A>][16].
   (Also see phys.org [<A HREF="http://phys.org/news/2016-01-evidence-bad.html">www</A>]['16].)

%A S. Gachter
%A J. F. Schulz
%T Intrinsic honesty and the prevalence of rule violations across societies
%J Nature
%V 531
%P 496-499
%M MAR
%D 2016
%K c2016, c201x, c20xx, zz0416, human behaviour, psychology, national,
   punishment, honesty, honest, corruption, corrupt, misconduct, deceit, fraud,
   cheat, cheating, lying, lies, society, law, legality, antisocial
%X "... we present cross-societal experiments from 23 countries around the world
   that demonstrate a robust link between the prevalence of rule violations &
   intrinsic honesty. We developed an index of the 'prevalence of rule
   violations' (PRV) based on country-level data from the year 2003 of
   corruption, tax evasion & fraudulent politics. We measured intrinsic honesty
   in an anonymous die-rolling experiment. We conducted the experiments with
   2,568 young participants (students) who, due to their young age in 2003,
   could not have influenced PRV in 2003. We find individual intrinsic honesty
   is stronger in the subject pools of low PRV countries than those of high
   PRV countries. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature17160">doi:10.1038/nature17160</A>]['16].

%T Measures of success
%J Science
%V 352
%N 6281
%P 28-30
%M APR
%D 2016
%K view, c2016, c201x, c20xx, zz0416, scientific research, publish and perish,
   scientist, publications, papers, impact, KPI, KPIs, early career, Hindex,
   bibliometrics
%X "In Jan., we asked young scientists this question: Do publns (# & impact)
   convey the true value of an early-career scientist? Out of the almost 200
   (self-selected) scientists who replied, about 75% did not think that publns
   conveyed a scientist's true value. About 25% said that publns were indeed
   the most important metric. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.352.6281.28">doi:10.1126/science.352.6281.28</A>]['16].
   [Also search for: publish perish]  and  [also search for: success luck].

%A J. Jacob
%A et al ...
%A J. F. Sherson
%T Exploring the quantum speed limit with computer games
%J Nature
%V 532
%N 7598
%P 210-213
%M APR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0516, quantum moves, quantumMoves, physics,
   problem, human, game, solve, optimisation, optimization, heuristic,
   gamification
%X "Humans routinely solve problems of immense computational complexity by
   intuitively forming simple, low-dimensional heuristic strategies. ... The
   citizen science games Foldit, EteRNA & EyeWire have been used successfully to
   study protein & RNA folding & neuron mapping ... Here we report on Quantum
   Moves, an online platform gamifying optimization problems in quantum physics.
   We show that human players are able to find solns to difficult problems
   assoc. with the task of quantum computing. Players succeed where purely
   numerical optimization fails, & analyses of their solns provide insights into
   the problem of optimization ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature17620">doi:10.1038/nature17620</A>]['16].

%A J. Bohannon
%T Who's downloading pirated papers? Everyone
%J Science
%V 352
%N 6285
%P 508-512
%M APR
%D 2016
%K news, c2016, c201x, c20xx, zz0516, Sci Hub, SciHub, Elbakyan, Elsevier,
   publisher, scientific publishing, science, research, publish, academic,
   papers, open access, pay wall, payWall, copyright, pirate
%X "...  researchers around the world are turning to Sci-Hub, which hosts
   50 million papers and counting. ..."
   -- [<A HREF="https://doi.org/10.1126/science.aaf5664">doi:10.1126/science.aaf5664</A>]['18].
   [Also search for: research open access].

%A D. Rennie
%T Let's make peer review scientific
%J Nature
%V 535
%N 7610
%P ?-?
%M JUL
%D 2016
%K views, c2016, c201x, c20xx, zz0716, peer review, refereeing, publishing,
   papers, bias, open, CONSORT, scientific research, journals
%X "... Peer review is touted as a demonstration of the self-critical nature of
   science. But it is a human system. Everybody involved brings prejudices,
   misunderstandings and gaps in knowledge ... In 1985, an influential
   commentary1 asserted that 'the arbiters of rigor, quality, and innovation in
   scientific reports' did not 'apply to their own work the standards they use
   in judging the work of others.' ..."
   -- [<A HREF="http://dx.doi.org/10.1038/535031a">doi:10.1038/535031a</A>]['16].

%A M. Biagioli
%T Watch out for cheats in citation game
%J Nature
%V 535
%N 7611
%P 201
%M JUL
%D 2016
%K views, c2016, c201x, c20xx, zz0716, publish, perish, scientific research,
   impact, academic, KPI, KPIs, citation, citations, peer review, reviewing,
   refereeing, papers, publication, abuse, cheat, fraud, misconduct, academic
%X "The focus on impact of published research has created new opportunities for
   misconduct & fraudsters ... It is no longer enough for scientists to publish
   their work. The work must be seen to have an influential shelf life. This
   drive for impact places the academic paper at the centre of a web of metrics
   - typically, where it is published & how many times it is cited - & a good
   score on these metrics becomes a goal that scientists & publishers are
   willing to cheat for. ... fake email addresses of suggested peer reviewers.
   ... 'Review & citation' rings go a step further ... Others hack publisher
   databases to seek more invitations to review papers, & so possibly insert
   more citations to their own work. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/535201a">doi:10.1038/535201a</A>]['16].
   [Also search for: publish perish]  and  [also search for: citation abuse].

%A V. Lariviere
%A et al
%T A simple proposal for the publication of journal citation distributions
%J bioRxiv
%M JUL
%D 2016
%K TR, c2016, c20x, c20xx, zz0716, journal impact factor, JIF, peer review,
   publishing, publication, metrics, rank, ranking, ERA, ARC, NIH, JIF, JIFs,
   scientific research, academic, university, proxy, quality, distribution, skew
%X "Although the Journal Impact Factor (JIF) is widely acknowledged to be a poor
   indicator of the quality of individual papers, it is used routinely to
   evaluate research & researchers. Here, we present a simple method for
   generating the citation distributions that underlie JIFs. Application of this
   straightforward protocol reveals the full extent of the skew of distributions
   & variation in citations received by published papers that is characteristic
   of all sci. journals. Although there are differences among js. across the
   spectrum of JIFs, the citation distns overlap extensively, demonstrating that
   the citation performance of individual papers cannot be inferred from the
   JIF. We propose that this methodology be adopted by all js. as a move to
   greater transparency, one that should help to refocus attention on individual
   pieces of work & counter the inappropriate usage of JIFs during the process
   of research assessment."
   [Also search for: publish perish].
   -- 062109@[<A HREF="http://biorxiv.org/content/early/2016/07/05/062109">biorxiv</A>]['16].

%A T. Cowen
%A B. Southward
%T Is the rate of scientific progress slowing down?
%J GMU Working Paper in Economics No.21-13
%M AUG
%D 2019
%K TR, c2019, c201x, c20xx, zz0123, scientific research, progress, KPI, KPIs,
   impact, publish, perish
%X "... we consider whether the rate of scientific progress has slowed down, &
   more generally what we know about the rate of scientific progress, based on
   these literatures & other metrics ...  If progress in sci. is slowing down,
   as indeed we have some reason to believe, these data may help us figure out
   where the problem has come from. We then could act to speed it up, or at
   least try to figure out how to do so."
   -- [<A HREF="https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3822691">ssrn</A>]['23].
   [Also search for: scientific progress].

%A J. Perkel
%T 'Kudos' promises to help scientists promote their papers to new audiences
%J Nature
%V 536
%N 7614
%P ?-?
%K AUG
%D 2016
%K news, views, c2016, c201x, c20xx, zz0816, scientific research, Kudos, www,
   publications, papers, impact, social media
%X "... Increasingly, researchers across the scientific spectrum are coming to
   the same conclusion. That demand has led to the emergence of an online tool
   for managing the practice: a free site called Kudos, which aims to help
   researchers maximize the reach and impact of their papers on social media,
   and measure the effects of their efforts. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/536113a">doi:10.1038/536113a</A>]['16],
   &  kudos@[<A HREF="https://www.growkudos.com/">www</A>]['16].

%A J. Lu Li
%T Revisiting the trolley problem on the ethics of animal model organisms
%J The Ethical Endeavor
%V 1
%N 1
%P 1
%M AUG
%D 2016
%K c2016, c201x, c20xx, zz0518, trolley problem, tram, railway, tracks,
   ethics, morality, philosophy, mouse, mice, Philippa Foot
%X "Despite the fervor with which researchers have tackled the issue in the past
   few decades, the ethical dilemma Philippa Foot famously put forth in 1967 has
   yet to be resolved. The 'Trolley Problem,' as it is often referred to,
   consists of a dilemma in which five innocent workers in the path of a
   'runaway tram' are destined to be killed; however, there also exists a fork
   in the tracks that leads to a stemming track with an equally innocent single
   person on it ..."
   -- [<A HREF="https://www.researchgate.net/publication/306032239_Revisiting_the_Trolley_Problem_On_The_Ethics_of_Animal_Model_Organisms">www</A>]['18]
      ( theethicalendeavor.weebly.com/ ).


%A G. Anglada-Escude
%A et al
%T A terrestrial planet candidate in a temperate orbit around Proxima Centauri
%J Nature
%V 536
%N 7617
%P 437-440
%M AUG
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0916, astronomy, planet, near, exoplanet,
   Proxima Centauri, GL 551, HIP 70890, goldilocks zone
%X "At a distance of 1.295 parsecs, the red dwarf Proxima Centauri ...
   is the Sun's closest stellar neighbour ... report observations that reveal
   the presence of a small planet with a minimum mass of about 1.3 Earth masses
   orbiting Proxima with a period of ~ 11.2 days at a semi-major-axis distance
   of around 0.05 astronomical units. Its equilibrium temperature is within the
   range where water could be liquid on its surface."
   -- [<A HREF="http://dx.doi.org/10.1038/nature19106">doi:10.1038/nature19106</A>]['16].

%A D. Geman
%A S. Geman
%T Opinion: Science in the age of selfies
%J PNAS
%V 113
%N 34
%P 9384-9387
%M ?
%D 2016
%K views, PNAS, c2016, c201x, c20xx, zz0916, publish and perish, scientific,
   university, management, academic, research, publications, infobabble,
   bandwagon, AI, big, data science, dataScience, LPU, Einstein, quote,
   quotable, impact, KPI, KPIs, misuse, bibliometrics, performance,
   selfy, selfie
%X "A time traveler from 1915 arriving in 1965 would have been astonished by the
   scientific theories & engineering technologies invented during that half
   century. ... Would a visitor from 1965, having traveled the 50 years to 2015,
   be equally dazzled? ... Here there is a paradox: Today, there are many more
   scientists, & much more money is spent on research, yet the pace of
   fundamental innovation, the kinds of theories & engineering practices that
   will feed the pipeline of future progress, appears, to some observers,
   including us, to be slowing ...
   ... outsized claims for artificial intelligence in the 1960s. After all, the
   'knowledge representation' & 'knowledge engineering' of the 1960s are not
   so dissimilar to today's 'data science.' ...
   What has certainly changed is the ... behavior of scientists, partly driven
   by new technology that affects everyone & partly driven by an alteration in
   the system of rewards & incentives. ... Grigori Perelman's proof of the
   Poincare conjecture & Yitang Zhang's contributions to the twin-prime
   conjecture - were the work of iconoclasts with an instinct for solitude ...
   'minimum publishable units' [LPUs] ...
   Albert Einstein remarked that 'an academic career, in which a person is
   forced to produce scientific writings in great amounts, creates a danger of
   intellectual superficiality' ... Discard numerical performance metrics ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1609793113">doi:10.1073/pnas.1609793113</A>]['16], [via RH].
   [Also search for: publish perish].

%A P. E. Smaldino
%A R. McElreath
%T The natural selection of bad science
%J Royal Soc. Open Sci.
%M SEP
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0319, scientific, university, research, stats,
   job, management, selection, methodology, pValue, significance, KPI, KPIs,
   impact, Hindex, papers, publications, realscientists, Campbell, law
%X "Poor research design & data analysis encourage false-positive findings. ...
   The persistence of poor methods results partly from incentives that favour
   them, leading to the natural selection of bad science. ...first present a
   60-year meta-analysis of statistical power in the behavioural sciences &
   show that power has not improved despite repeated demonstrations of the
   necessity of increasing power. ... As in the real world, successful labs
   produce more 'progeny,' such that their methods are more often copied & their
   students are more likely to start labs of their own. Selection for high
   output leads to poorer methods & increasingly high false discovery rates. We
   additionally show that replication slows but does not stop the process of
   methodological deterioration. Improving the quality of research requires
   change at the institutional level."
   -- [<A HREF="https://doi.org/10.1098/rsos.160384">doi:10.1098/rsos.160384</A>]['19].
   Also see Smaldino, Nature, 575, 9, 2019
   [<A HREF="https://doi.org/10.1038/d41586-019-03350-5">doi:10.1038/d41586-019-03350-5</A>]['19] and
   [<A HREF="http://smaldino.com/">smaldino.com</A>]['19].
   (Also see 'Incentive malus ...', The Economist 24/9/2016 [<A HREF="https://www.economist.com/science-and-technology/2016/09/24/incentive-malus">www</A>]['19].)
   Quotes:
   "I've been on a number of search committees. I don't remember anybody looking
   at anybody's papers. Number and IF [impact factor] of pubs are what counts.
   -- Terry McGlynn (realscientists) (21 Oct 2015, 4:12 p.m. Tweet.)
   [Also search for: Campbells law].

%A A. McCook
%T Duke fraud case highlights financial risks for universities
%J Science
%V 353
%N 6303
%P 977-978
%K SEP
%D 2016
%K news, c2016, c201x, c20xx, zz0916, scientific research, academic, fraud,
   misconduct, Duke University, USA, NIH, grant, grants
%X "A whistleblower is accusing a former Duke University researcher, her former
   supervisor, and the university of including fraudulent data in applications
   and reports involving more than 60 grants worth some $200 million. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.353.6303.977">doi:10.1126/science.353.6303.977</A>]['16].
   [Also search for: academic misconduct].

%A The Hon. Mr Justice Burton
%A The Hon. Mr Justice Mitting
%A Sir Richard McLaughlin
%A Mr Charles Flint QC
%A Ms Susan O'Brien QC
%T UKIPTrib 15_110-CH
%M JUL
%D 2016
%K c2016, c201x, c20xx, zz1016, UK, British, national security, spy, spies,
   spooks, government agencies, GCHQ, MI5, MI6, law, bill, powers, BCD, BPD,
   surveillance, privacy, ECHR, Privacy International, bulk data, internet,
   tribunal
%X "... The proceedings were brought on 5th June 2015 relating to the SIAs'
   acquisition, use, retention, disclosure, storage and deletion of Bulk
   Personal Datasets ('BPDs'), ... 101.Accordingly, our conclusion is, in
   respect of Issues 2 and 3, that, subject to the issue of transfer of data,
   and to resolution of Issue 4 below, the s.94 BCD regime did not comply with
   Article 8 [of the European Convention on Human Rights (ECHR)] until November
   4 2015 and thereafter complies, and that the BPD regime did not comply with
   Article 8 until 12 March 2015 and thereafter complies.
   We so decide.  ..." -- Investigatory Powers Tribunal
   [<A HREF="http://www.ipt-uk.com/docs/Bulk_Data_Judgment.pdf">www</A>]['16].
   I.e., British spy agencies collected data illegally.
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/1984/">1984</A>]['16].)

%A E. Gibney
%T Inside Microsoft's quest for a topological quantum computer
%J Nature
%V ?
%N ?
%P ?
%M OCT
%D 2016
%K news, views, c2016, c201x, c20xx, zz0117, quantum computer, computing
   Bocharov, qubits, quasiparticle, non-abelian anyon, anyons, topological
%X --[<A HREF="http://dx.doi.org/10.1038/nature.2016.20774">doi:10.1038/nature.2016.20774</A>]['17].
   (Also see [<A HREF="http://dx.doi.org/10.1038/541009a">1/2017</A>].)

%A A. Cho
%T Odd computer zips through knotty tasks
%J Science
%V 354
%N 6310
%P 269-270
%M OCT
%D 2016
%K news, views, c2016, c201x, c20xx, zz1016, Ising computer, model, machine,
   optical, quantum, Yamamoto, McMahon
%X "A century-old theoretical model of magnetism is giving rise to a hybrid
   computer, part classical and part quantum ...The so-called Ising machine,
   described in 100-bit and 2000-bit versions in two reports this week ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.354.6310.269">doi:10.1126/science.354.6310.269</A>]['16].
   (Also see Stanf'rd[<A HREF="http://news.stanford.edu/2016/10/20/stanford-researchers-create-new-special-purpose-computer/">www</A>][20/10/16].)
   [Also search for: quantum computer] and [also search for: Ising computer].

%A T. Inagaki
%A et al ...
%A H. Takesue
%T A coherent Ising machine for 2000-node optimization problems
%J Science
%V 354
%N 6312
%P 603-606
%M NOV
%D 2016
%K jrnl, c2016, c201x, c20xx, zz1116, Ising computer, model, machine, problem,
   optical, quantum, Yamamoto, McMahon, graph max cut
%X "... Many such problems can be mapped onto ground-state-search problems of
   the Ising model, & various artificial spin systems are now emerging as
   promising approaches. However, physical Ising mcs have suffered from limited
   numbers of spin-spin couplings because of implementations based on localized
   spins, resulting in severe scalability problems. We report a 2,000-spin
   network with all-to-all spin-spin couplings. Using a measurement & feedback
   scheme, we coupled time-multiplexed degenerate optical parametric oscillators
   to implement maximum cut problems on arbitrary graph topologies with up to
   2,000 nodes. Our coherent Ising machine could outperform simulated annealing
   in terms of accuracy & computation time for a 2,000-node complete graph."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aah4243">doi:10.1126/science.aah4243</A>]['16] (online 10/2016).
   [Also search for: Ising computer].

%A P. McMahon
%T A fully-programmable 100-spin coherent Ising machine with all-to-all
   connections
%J Science
%V 354
%N 6312
%P 614-617
%M NOV
%D 2016
%K jrnl, c2016, c201x, c20xx, zz1116, Ising computer, model, machine, problem,
   optical, quantum, Yamamoto, McMahon
%X "... present a scalable optical processor with electronic feedback that can
   be realized at large scale with room-temperature technology. Our prototype
   machine is able to find exact solutions of, or to sample good approximate
   solutions to, a variety of hard instances of Ising problems with up to
   100 spins and 10,000 spin-spin connections."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aah5178">doi:10.1126/science.aah5178</A>]['16] (online 10/2016).
   [Also search for: Ising computer].

%A R. Sinatra
%A D. Wang
%A P. Deville
%A C. Song
%A A.-L. Barabasi
%T Quantifying the evolution of individual scientific impact
%J Science
%V 354
%N 6312
%M NOV
%D 2016
%K jrnl, c2016, c201x, c20xx, zz1116, publications, impact, KPI, KPIs,
   scientific, research, university, career, Hindex, scientist, researcher,
   QQ, factorQ, Qfactor, random, luck, lucky, prizes
%X "Despite the frequent use of numerous quantitative indicators to gauge the
   professional impact of a sci., little is known about how sci. impact emerges
   & evolves in time. ... quantify the changes in impact & productivity
   throughout a career in sci., finding that impact, as measured by influential
   publications, is distributed randomly within a sci.'s seq. of publns. This
   random-impact rule allows us to formulate a stochastic model that uncouples
   the effects of productivity, individual ability, & luck & unveils the
   existence of universal patterns governing the emergence of sci. success. The
   model assigns a unique individual parameter Q to each scientist, which is
   stable during a career, & it accurately predicts the evolution of a sci.'s
   impact, from the h-index to cumulative citations, & indep. recognitions, such
   as prizes."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaf5239">doi:10.1126/science.aaf5239</A>]['16] (via AK).

%A G. Naik
%T The quiet rise of the NIH's hot new metric
%J Nature
%V 539
%N 7628
%P 150
%M NOV
%D 2016
%K news, views, c2016, c201x, c20xx, zz1116, scientific research, impact,
   modified, adjusted, bibliometrics, papers, Hindex, NIH, OPA, ARC, funding,
   Relative Citation Ratio, RCR, grant, grants, outcome, influence
%X "Biomedical funders worldwide are adopting the US agency's free Relative
   Citation Ratio to analyse grant outcomes. ... In 2015, the NIH's Office for
   Portfolio Analysis (OPA) in Bethesda, Maryland, devised the tool to compare
   the performance of articles from different fields more fairly. Now, one of
   the NIH's biggest institutes is using the metric - the Relative Citation
   Ratio, or RCR - to identify whether some types of grant deliver more bang for
   their buck. Other funders have adopted the RCR, which the agency offers
   freely online. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/539150a">doi:10.1038/539150a</A>]['16].
   [Also search for: modified bibliometrics].

%A M. Hoschele
%A A. Zeller
%T Mining input grammars from dynamic taints
%J Automated SWE (ASE) Conf.
%D 2016
%K conf, c2016 c201x, c20xx, zz0419, infer, learn, test, grammar, CFG, grammars,
   program, behaviour, AUTOGRAM, SWE, UniSaarland
%X "Knowing which part of a program processes which parts of an input can
   reveal the structure of the input [&] the structure of the program. In
   a URL http://www.example.com/path/, ... the protocol http, the host
   www.example.com, & the path 'path' would be handled by different fns & stored
   in  different  variables.  Given a set of sample inputs, we use dynamic
   tainting to trace the data flow of each input char, & aggregate those input
   fragments that would be handled by the same fn into lexical & syntactical
   entities.  The result is a CFG that reflects valid input structure. In its
   evaluation, our AUTOGRAM prototype automatically produced readable &
   structurally accurate grammars for inputs like URLs, spread-sheets or
   config. files. ..."
   -- pdf@[<A HREF="https://www.st.cs.uni-saarland.de/models/autogram/ase2016-autogram.pdf">sa'rland</A>]['19].
   Also see AUTOGRAM@[<A HREF="https://www.st.cs.uni-saarland.de/models/autogram/">sa'rland</A>]['19].
   [Also search for: infer grammar].

%A M. Baker
%T Stat-checking software stirs up psychology
%J Nature
%V 540
%N 7631
%P 151-152
%M NOV
%D 2016
%K news, views, statcheck, c2016, c2091x, c20xx, zz1216, stats, papers, Pvalue,
   Hartgerink, Nuijten, Epskamp, scientific research, publication, statistics,
   error, errors, mistake, mistakes, peer review, algorithm, stats
%X "Researchers debate whether using a program to automatically detect
   inconsistencies in papers improves the literature, or raises false alarms.
   M. Nuijten and her colleagues found rampant inconsistencies when they
   unleased statcheck on the psychological literature. The program scans
   articles for statistical results, redoes the calculations and checks that the
   numbers match. It went through 30,717 papers to identify 16,695 that tested
   hypotheses using statistics. In half of those, it found at least one
   potential error (M. B. Nuijten et al. Behav. Res. Methods 48,
   1205-1226; 2016). ..."
   -- [<A HREF="http://dx.doi.org/10.1038/540151a">doi:10.1038/540151a</A>]['16].
   StatCheck@[<A HREF="https://mbnuijten.com/statcheck/quick-install/">mbnuijten</A>]['17].

%A J. M. Fernandez
%A M. P. Monteiro
%T Evolution in the number of authors of computer science publications
%J Scientometrics
%V 110
%N 2
%P 1-11
%M DEC
%D 2016
%K jrnl, c2016, c201x, c20xx, zz1122, bibliometrics, multiple authors, trends,
  authorship, computer science, comp sci, CSci, research, STEM, KPI, KPIs,
  1950s, 2010s, papers, publications
%X "... analyses the evolution in the number of authors of scientific publ'ns in
   comp.sci. (CS). ... collected & mined over 200,000 article references ...
   spanning a 60-year period (1954-2014) ... all CS areas witness an increase in
   the avg # of authors, in every decade, with just one slight exception. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/s11192-016-2214-9">doi:10.1007/s11192-016-2214-9</A>]['22].
   (Fig.1 suggests the avg rises from one or two to three or four.)
   [Also search for: multiple authors trends].

%A J. Copeland
%A J. Bowen
%A M. Sprevak
%A R. Wilson
%T The Turing Guide
%I OUP
%M JAN
%D 2017
%K book, text, OUP, biog, Alan Turing, c2017, c201x, c20xx, zz0117, test, AI,
   WW2, WWII, code breaking, cryptography, cryptanalysis, Bletchley Park
%X 1st ed 2017; hb stg50; uk us isbn:0198747829; uk us isbn13:978-0198747826.
   [Also search for: Turing book].

%A E. Gibney
%T Scepticism surrounds the ultimate potential of D-wave machines, but
   researchers are already finding uses for them
%J Nature
%V 541
%N ?
%P 447-448
%M JAN
%D 2017
%K news, views, c2017, c201x, c20xx, zz0117, Dwave, quantum computer, annealing,
   optimization, optimisation
%X "The company that makes the world's only commercially available quantum
   computers has released its biggest machine yet - & researchers are paying
   close attention. Named 2000Q after the # of q.bits, or qubits ... So far,
   researchers have proved that, for a problem crafted to suit the machine's
   abilities, the q.computer can offer a huge increase in processing speed over
   a classical version of an alg. (V. S. Denchev et al. Phys. Rev. X 6,031015;
   2016 [<A HREF="https://doi.org/10.1103/PhysRevX.6.031015">www</A>]). But the
   computers do not beat every classical alg., & no one has found a problem for
   which they outperform all classical rivals. ... D-Wave is suitable only for
   solving ... optimization problems. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/541447b">doi:10.1038/541447b</A>]['17].
   (Also see, 'Quantum Annealing amid Local Ruggedness and Global Frustration,'
      "... [on] simulated annealing (SA) & quantum Monte Carlo (QMC). The study
      showed the D-Wave 2X to be up to 100 million times faster than the
      classical algs.. ..."
   -- 1701.04579@[<A HREF="https://arxiv.org/abs/1701.04579">arXiv</A>]['17].)
   [Also search for: Dwave quantum]  and  [also search for: quantum computer].

%A D. Prelec
%A H. S. Seung
%A J. McCoy
%T A solution to the single-question crowd wisdom problem
%J Nature
%V 541
%N ?
%P 532-535
%M JAN
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0117, crowd wisdom, crowds
%X "... we propose the following alternative to a democratic vote: select the
   answer that is more popular than people predict. We show that this principle
   yields the best answer under reasonable assumptions about voter behaviour,
   while the standard 'most popular' or 'most confident' principles fail under
   exactly those same assumptions. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature21054">doi:10.1038/nature21054</A>]['17].

%A B. Lekitsch
%A et al ...
%A W. K. Hensinger
%T Blueprint for a microwave trapped ion quantum computer
%J Science Adv.
%V 3
%N 2
%P e1601540
%M FEB
%D 2017
%K c2017, c201x, c20xx, zz0217, quantum computer, gates,
   long-wavelength radiation, ion trapping
%X "... present a blueprint for a trapped ion-based scalable q.computer module,
   making it possible to create a scalable q.computer architecture based on
   long-wavelength radiation q.gates. The modules control all operations as
   stand-alone units, are constructed using silicon microfabrication techniques
   & are within reach of current technology. To perform the required
   q.computations, the modules make use of long-wavelength radiation-based
   q.gate technology. To scale this microwave q.computer architecture to a large
   size, we present a fully scalable design that makes use of ion transport
   between different modules, thereby allowing arbitrarily many modules to be
   connected to construct a large-scale device. A high error-threshold surface
   error correction code can be implemented in the proposed architecture to
   execute fault-tolerant operations. With appropriate adjustments, the proposed
   modules are also suitable for alternative trapped ion q.computer
   architectures, such as schemes using photonic interconnects."
   -- [<A HREF="http://dx.doi.org/10.1126/sciadv.1601540">doi:10.1126/sciadv.1601540</A>]['17].
   (Also see the bbc[<A HREF="http://www.bbc.com/news/science-environment-38811255">1/2/2017</A>].)
   [Also search for: quantum computer].

%A M. M. Wilde
%T Quantum Information Theory
%I CUP
%P 780
%D 2017
%K book, text, CUP, c2017, c201x, c20xx, zz0217, quantum information, qubits,
   communication
%X 2nd ed 2017; hb us$99; uk us isbn:1107176166; uk is isbn13:978-1107176164.
   1st ed 2013; hb us$77; uk us isbn:1107034256; uk us isbn13:978-1107034259.
   "... Beginning with an extensive overview of classical information theory
   suitable for the non-expert, the author then turns his attention to quantum
   mechanics for quantum information theory, and the important protocols of
   teleportation, super-dense coding and entanglement distribution. He develops
   all of the tools necessary for understanding important results in quantum
   information theory ..."
   [Also search for: quantum communication].

%A A. Currin
%A K. Korovin
%A M. Ababi
%A K. Roper
%A D. B. Kell
%A P. J. Day
%A R. D. King
%T Computing exponentially faster: implementing a non-deterministic universal
   Turing machine using DNA
%J J. of the Royal Soc. Interface
%V 14
%N 128
%P ?
%D MAR
%D 2017
%K jrnl, JRS, c2017, c201x, c20xx, zz0317, DNA, computing, biocomputer, PCR,
   controversial, nondeterministic, NUTM, Thue, string rewriting system,
   systems, semiThue, unconventional, RDKing
%X "... demonstrate the first physical design of an NUTM. ... based on Thue
   string rewriting systems, & thereby avoids the limitations of most previous
   DNA computing schemes: all the compn is local (simple edits to strings) so
   there is no need for communication, & there is no need to order operations.
   The design exploits DNA's ability to replicate to execute an exponential
   number of computational paths in P time. Each Thue rewriting step is embodied
   in a DNA edit implemented using a novel combination of polymerase chain
   reactions & site-directed mutagenesis. ... demo. that the design works using
   both computational modelling & in vitro mol.biol. experimentation: the design
   is thermodynamically favourable, microprogramming can be used to encode
   arbitrary Thue rules, all classes of Thue rule can be implemented, &
   non-deterministic rule implementation. In an NUTM, the resource limitation is
   space, which contrasts with classical UTMs & QUTMs where it is time ..."
   -- [<A HREF="http://dx.doi.org/10.1098/rsif.2016.0990">doi:10.1098/rsif.2016.0990</A>]['17].
   &  RK@[<A HREF="https://scholar.google.com/citations?hl=en&user=BgZp7XcAAAAJ">sch'l'r</A>]['18].
   [Also search for: Thue rewriting system] & [Also search for: biocomputer].

%A H. Briggs
%T 'Fake research' comes under scrutiny
%I BBC
%M MAR
%D 2017
%K news, c2017, c201x, c20xx, zz0417, fake research, university, academic,
   scientific, research, science, fraud, misconduct, UK, plagiarism,
   fabrication, piracy, retraction
%X "... Official data points to about 30 allegations of research misconduct
   between 2012 and 2015.  However, figures obtained by the BBC under Freedom of
   Information rules identified hundreds of allegations over a similar time
   period at 23 universities alone. ... at least 300 allegations were reported
   at 23 of the 24 research-intensive Russell Group universities between 2011
   & 2016 among staff & research students.  About a third of allegations of
   plagiarism, fabrication, piracy & misconduct were upheld. More than 30
   research papers had to be retracted. ..."
   -- [<A HREF="http://www.bbc.com/news/science-environment-39357819">bbc</A>][27//3/2017].
   [Also search for: academic research misconduct].

%A P. Stephan
%A R. Veugelers
%A J. Wang
%T Reviewers are blinkered by bibliometrics
%J Nature
%V 544
%N 7651
%P 411-412
%M APR
%D 2017
%K news, views, c2017, c201x, c20xx, zz0517, bibliometrics, journal, impact,
   JIF, JIFs, science, university, academic, scientific research, grant, grants,
   ARC, ERC, NSF, NIH, quality, Leiden manifesto, risk, innovation, novelty,
   publishing, referees, refereeing, peer review, reviewer, REF, papers,
   publish or perish, misuse
%X "There is a disconnect between the research that reviewers purport to admire
   and the research that they actually support. As participants on multiple
   review panels and scientific councils, we have heard many lament
   researchers' reluctance to take risks. Yet we've seen the same panels eschew
   risk and rely on bibliometric indicators for assessments, despite widespread
   agreement that they are imperfect measures ... analysed citations in more
   than 660,000 research articles published in 2001 to see how risky research
   tracks with JIFs and citation counts. Our proxy for risky research is whether
   a paper cites new combinations of journals in its reference list, taking into
   account the likelihood of such combinations. ...  Universities: [should]
   adopt as standard practice a requirement that committees actually read
   candidates' research [[radical!]], as is done in the REF exercise. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/544411a">doi:10.1038/544411a</A>]['17].
   [Also search for: publish perish]  and  [also search for: peer review].

%T Let's talk about sex robots
%J Nature
%V 547
%N 7662
%P 138
%M JUL
%D 2017
%K editorial, news, views, c2017, c201x, c20xx, zz0717, doll, robot, sex,
   sexbot, humanoid, android, Jia Jia, JiaJia, Roxy, Roxxy, Roxxxy, Sinthetics,
   Realdoll, report, human, society
%X "... Enabling robots to read human behaviour and to respond in appropriate
   ways is a burgeoning area of research. As is the study of how humans will
   react to these potentially clever, personalized & ever-available companions.
   But there is another aspect of human-robot relationships that is rarely
   mentioned, & it's one on which robots could have just as great an impact as
   any other. Sex.  That reticence changed, at least in the United Kingdom, last
   week. A flurry of press reports followed the publication of a consultation
   report ..."
   -- [<A HREF="http://dx.doi.org/10.1038/547138a">doi:10.1038/547138a</A>]['17].
   (That report: 'Our Sexual Future with Robots',
   -- Foundation for Responsible Robotics
      [<A HREF="http://responsiblerobotics.org/wp-content/uploads/2017/07/FRR-Consultation-Report-Our-Sexual-Future-with-robots_Final.pdf">www</A>]['17], pp.42 inc. refs.)

%A A. V. Whillians
%A et al
%T Buying time promotes happiness
%J PNAS
%V ?
%P ?-?
%M JUL
%D 2017
%K jrnl, PNAS, c2017, c201x, c20xx, zz0717, happiness, well being, wellbeing,
   satisfaction, time, wealth, society, USA
%X "... provide evidence that using money to buy time can provide a buffer
   against this time famine, thereby promoting happiness. Using large, diverse
   samples from the United States, Canada, Denmark, & The Netherlands (n=6,271),
   we show that individuals who spend money on time-saving services report
   greater life satisfaction. A field experiment provides causal evidence that
   working adults report greater happiness after spending money on a time-saving
   purchase than on a material purchase. Together, these results suggest that
   using money to buy time can protect people from the detrimental effects of
   time pressure on life satisfaction."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1706541114">doi:10.1073/pnas.1706541114</A>]['17].
   [Also search for: happiness well being].

%A P. A.Kirschnera
%A P. Bruyckere
%T The myths of the digital native and the multitasker
%J Teaching and Teacher Ed.
%V 67
%P 135-142
%M OCT
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0817, digital native, multitasking, millennials,
   technology, youth, age, urban myth, education, school, learning, teaching
%X "... have been labelled digital natives & have been ascribed the ability to
   cognitively process multiple sources of information simultaneously (i.e.,
   they can multitask). As a result of this thinking, they are seen by teachers,
   educational administrators, politicians/policy makers, & the media to require
   an educational approach radically different from that of previous
   generations. This article presents scientific evidence showing that there is
   no such thing as a digital native who is information-skilled simply because
   (s)he has never known a world that was not digital. It then proceeds to
   present evidence that one of the alleged abilities of students in this
   generation, the ability to multitask, does not exist & that designing
   education that assumes the presence of this ability hinders rather than helps
   learning. ..."  [online July 2017.]
   -- [<A HREF="https://doi.org/10.1016/j.tate.2017.06.001">doi:10.1016/j.tate.2017.06.001</A>]['17].
   (Also see [<A HREF="https://doi.org/10.1038/547380a">www</A>]['17].)

%A A. Abritis
%A A. McCook
%T Cash incentives for papers go global
%J Science
%V 357
%N 6351
%P 541
%M AUG
%D 2017
%K news, views, c2017, c201x, c20xx, zz0817, publish and perish, journal,
   scientific management, paper, publication, incentive, bonus, reward,
   academic, university, China, impact
%X "... scientists at Chinese institutions stand to make a small fortune if a
   paper they author appears in journals with high citation impacts. A recent
   analysis posted to arXiv showed that, on average, Chinese universities offer
   first authors more than $43,000 for publishing a paper in Science or Nature,
   with the top reward for such a paper receiving a knee-wobbling $165,000."
   -- [<A HREF="https://doi.org/10.1126/science.357.6351.541">doi:10.1126/science.357.6351.541</A>]['17].

%A B. C. G. Karlsson
%A R. Friedman
%T Dilution of whisky - the molecular perspective
%J Sci. Reports
%V 7
%N 6489
%D 2017
%M AUG
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0817, whisky, scotch, water, dilute, taste,
   flavour, alcohol, guaiacol, ethanol, amphipathic, smell
%X "Whisky is distilled to around 70% alcohol by volume (vol-%) then diluted to
   about 40 vol-%, & often drunk after further slight dilution to enhance its
   taste. ... found at the liquid-air interface in mixtures that contain up to
   45 vol-% of ethanol. At ethanol concentrations of 59 vol-% or higher,
   guaiacol is increasingly surrounded by ethanol molecules & is driven to the
   bulk. This indicates that the taste of guaiacol in the whisky would be
   enhanced upon dilution prior to bottling. Our findings may apply to other
   flavour-giving amphipathic molecules & could contribute to optimising the
   production of spirits for desired tastes. Furthermore, it sheds light on the
   molecular structure of water-alcohol mixtures that contain small solutes, &
   reveals that interactions with the water may be negligible already at
   89 vol-% of ethanol."
   -- [<A HREF="https://doi.org/10.1038/s41598-017-06423-5">doi:10.1038/s41598-017-06423-5</A>]['17].
  [Also search for: whisky].

%A C. Guyeux
%A Q. Wang
%A X. Fang
%A J. Bahi
%T Introducing the truly chaotic finite state machines and their applications
   in security field
%J arXiv
%M AUG
%D 2017
%K TR, c2017, c201x, c20xx, zz0817, FSM, FSA, finite state machine, automaton,
   TM, chaos, chaotic, hashing
%X "... explaining how finite state machines can behave chaotically regarding
   the slight alteration of their inputs. This behavior is explained using
   Turing machines and formalized thanks to a special family of discrete
   dynamical systems called chaotic iterations. An illustrative example is
   finally given in the field of hash functions."
   -- 1708.04963@[<A HREF="https://arxiv.org/abs/1708.04963">arXiv</A>]['17].

%A J. Fagone
%T The Woman Who Smashed Codes: A True Story of Love, Spies, and the
   Unlikely Heroine Who Outwitted America's Enemies
%I DeyStreetBooks
%M SEP
%D 2017
%K book, c2017, c201x, c20xx, zz1017, code, codes, cryptography, breaking,
   Elizebeth Smith, Friedman, cypher, cipher, WW2, WWII, Japan, Purple,
   cryptanalysis, maths, women, woman, science, STEM, www
%X 1st ed 2017; hb us$18; uk us isbn:0062430483,; uk us isbn13:978-0062430489.
   "... an American woman and her husband who invented the modern science of
   cryptology together and used it to confront the evils of their time, solving
   puzzles that unmasked Nazi spies and helped win World War II.  In 1916, at
   the height of World War I, brilliant Shakespeare expert Elizebeth Smith went
   to work for an eccentric tycoon on his estate outside Chicago. The tycoon had
   close ties to the U.S. government, and he soon asked Elizebeth to apply her
   language skills to an exciting new venture: code-breaking. There she met the
   man who would become her husband, groundbreaking cryptologist William
   Friedman ..."
   Also see bbc@[<A HREF="http://www.bbc.com/future/story/20171009-the-female-code-breakers-who-were-left-out-of-history-books">10/10/2017</A>] and
   auth@[<A HREF="https://www.jasonfagone.com/woman-who-smashed/">www</A>]['17].
   [Also search for: WW2 code].

%A D. S. Chawla
%T Publishers take academic networking site to court
%J Science
%V 358
%N 6360
%P 161
%M OCT
%D 2017
%K news, views, c2017, c201x, c20xx, zz1017, ResearchGate, publishing, science,
   www, web, papers, articles, copyright, law, STM, ScienceOpen
%X "Scholarly publishing giants Elsevier and the American Chemical Society (ACS)
   last week filed a lawsuit in Germany against ResearchGate, a popular academic
   networking site, alleging copyright infringement on a massive scale. The
   move comes after a larger group of publishers became dissatisfied with
   ResearchGate's response to a request to alter its article-sharing
   practices. ..."
   -- [<A HREF="https://doi.org/10.1126/science.358.6360.161">doi:10.1126/science.358.6360.161 </A>]['17].

%A B. C. Martinson
%T Give researchers a lifetime word limit
%J Nature
%P ?-?
%N 7676
%V 550
%M OCT
%D 2017
%K news, views, c2017, c201x, c20xx, zz1017, publish, perish, publication,
   academic, scientific, research, impact, authorship, paper, papers, citations
%X "A dirty truth pervades academic publishing: we write papers to gain credit
   in an academic marketplace. Almost a quarter of a century ago, academic
   worthies lamented that scholarly publications had become 'the coins academics
   must use to get through the tollgates on their way to academic promotion'
   (D. Rennie and A. Flanagin J. Am. Med. Assoc. 271, 469-471; 1994). In some
   cases, papers in flashy j. truly do bring in hard cash - reportedly more than
   US$40,000 at some unis. in China. And plenty of people reading this will have
   felt they'd better squeeze a paper or two out soon to have any chance of
   getting their next grant proposal funded. ..."
   -- [<A HREF="https://doi.org/10.1038/550303a">doi:10.1038/550303a</A>]['17].
   [Also search for: publish perish].

%A L. Mundy
%T Code Girls: The Untold Story of the American Women Code Breakers of
   World War II
%I HachetteBooks
%P 432
%M OCT
%D 2017
%K book, c2017, c201x, c20xx, zz1017, codes, cyphers, cryptology, cryptanalysis,
   WWII, WW2, cypher, code, breaker, girls, women, mathematics, maths, math,
   science, STEM
%X 1st ed 2017; hb us$17; uk us isbn:0316352535, uk us isbn13:978-0316352536.
   "Recruited by the U.S. Army and Navy from small towns and elite colleges,
   more than ten thousand women served as codebreakers during WWII. ..."
   [Also search for: WW2 code] and [also search for: women STEM].

%T The Lancet commission on pollution and health
%J The Lancet
%M OCT
%D 2017
%K c2017, c201x, c20xx, zz1017, public health, pollution, death, deaths,
   risk, risks, disease, air, water, soil, sustainable, environment
%X [<A HREF="http://www.thelancet.com/commissions/pollution-and-health">www</A>]['17].
   Also see, "Pollution has been linked to nine million deaths worldwide
      in 2015 ... Almost all of these deaths occurred in low- and
      middle-income countries, where pollution could account for up to a
      quarter of deaths. Bangladesh and Somalia were the worst affected. ..."
   -- the bbc[<A HREF="http://www.thelancet.com/commissions/pollution-and-health">20/10/2017</A>].

%T Many junior scientists need to take a hard look at their job prospects
%J Nature
%V 550
%N 7677
%P ?-?
%M OCT
%D 2017
%K news, views, c2017, c201x, c20xx, zz1017, academic, university, research,
   science, scientist, job, jobs, career, careers, prospect, exploitation,
   PhD, PhDs, postgrad, postgraduate, degree, degrees, STEM, UK, US, USA,
   postdoc, editorial
%X Editorial:
   "... For our Careers section this week, Nature surveyed more than 5,700
   early-career scientists worldwide who are working on PhDs. Three-quarters of
   them, they told us, think it's likely that they will pursue an academic
   career when they graduate ... Global figures are hard to come by, but only
   three or four in every hundred PhD students in the United Kingdom will land
   a permanent staff position at a university. It's only a little better in the
   United States. ..."
   -- [<A HREF="https://doi.org/10.1038/550429a">doi:10.1038/550429a</A>]['17].

%T Citation is not the only impact. A look at what we have published highlights
   the variety of editorial judgements in selecting and assessing papers
%J Nature
%V 551
%N 7678
%P 6
%M NOV
%D 2017
%K news, views, editorial, c2017, c201x, c20xx, zz1117, journals, science,
   good, scientific, research, university, academic, publishing, impact,
   rankings, ranking, Hindex, citations, publish, perish
%X "What makes good science? And how do Nature's editors select papers to
   publish? The answers to both questions are many and varied. But they have one
   thing in common: neither is necessarily reflected in citations. ..."
   -- [<A HREF="https://doi.org/10.1038/551006a">doi:10.1038/551006a</A>]['17].

%A A. Csiszar
%T The catalogue that made metrics, and changed science
%J Nature
%V 551
%N 7679
%P 163-165
%M NOV
%D 2017
%K news, views, c2017, c201x, c20xx, zz1117, academic, scientific, research,
   Babbage, Catalogue of Scientific Papers, Garfield, Science Citation Index,
   SCI, ISI, citations, c18xx, history, publish, papers, perish, count, quality,
   impact, Hindex, KPI, KPIs, bibliometrics, altMetrics
%X "In 1830, Charles Babbage had an unusual idea. Exasperated by how little
   recognition science was getting in England, the computer pioneer &
   scientific provocateur suggested that quantifying authorship might be a way
   to identify scientific eminence.  ...  Babbage's suggestion to count authors'
   papers was met with various criticisms. One author did the calculation for
   each fellow in the Royal Society in London, & showed that this was a
   terrible guide to scientific eminence. Another pointed out that 'a far more
   satisfactory criterion' would have been 'the value of those papers'. ...
   When the first volumes of the Catalogue of Scientific Papers appeared at the
   end of 1867 ... [c1930+/-] the phrase publish or perish began to circulate in
   academia. ... In the 1960s, Eugene Garfield launched a radically different
   search tool, known as the Science Citation Index. ..."
   -- [<A HREF="https://doi.org/10.1038/551163a">doi:10.1038/551163a</A>]['17].
   (Also see SCI@[<A HREF="https://en.wikipedia.org/wiki/Science_Citation_Index">wikip</A>]['20].)
   [Also search for: publish perish] and [also search for: citation index SCI].

%A J. Reardon
%T The Postgenomic Condition: Ethics, Justice, and Knowledge after the Genome
%I U. of ChicagoPress
%P 304
%M DEC
%D 2017
%K book, MolBio, c2017, c201x, c20xx, zz1117, science, scientific research,
   ethics, society, genomics, genes, genome, HGP, medicine, human, health,
   commerce, business, big pharma
%X 1st ed 2017; pb  $35, uk us isbn:022651045X, isbn13:978-0226510453.
                hb $105, uk us isbn:022634455X, uk us isbn13:978-0226344553.
   "... how the extensive efforts to transform genomics from high tech
   informatics practiced by a few to meaningful knowledge beneficial to all
   exposed the limits of long-cherished liberal modes of knowing and
   governing life. ..."
   The auth was on the
   abc[<A HREF="http://www.abc.net.au/radionational/programs/bigideas/just-genomics/8838350">13/11/2017</A>]['17].
   (And a review,
   [<A HREF="https://www.nature.com/articles/551296a">www</A>][11/2017].)

%A A. Sommerlad
%A et al ...
%A G. Livingston
%T Marriage and risk of dementia: systematic review and meta-analysis of
   observational studies
%J J. of Neurology, Neurosurgery and Psychiatry
%V ?
%P ?-?
%D 2017
%K jrnl, c2017, c201x, c20xx, zz1217, human, health, psychology, marriage,
   dementia, married, ageing, aging, risks
%X "...  We included 15 studies with 812,047 participants. Compared with those
   who are married, lifelong single (relative risk=1.42 (95% CI 1.07 to 1.90))
   & widowed (1.20 (1.02 to 1.41)) people have elevated risk of dementia. We did
   not find an association in divorced people. ... less education partially
   confounds the risk in widowhood & worse physical health the elevated risk in
   lifelong single people. Compared with studies that used clinical registers
   for ascertaining dementia diagnoses, those which clinically examined all
   participants found higher risk for being unmarried. ..."
   -- [<A HREF="https://doi.org/10.1136/jnnp-2017-316274">doi:10.1136/jnnp-2017-316274</A>]['17].

%A J. Belluz
%A B. Plumer
%A B. Resnick
%T The 7 biggest problems facing science, according to 270 scientists
%J Vox
%M SEP
%D 2016
%K news, views, c2019, c201x, c20xx, zz0519, scientific research, science,
   misuse, KPI, KPIs, university management, jobs, work, Hindex, grants, JIF,
   impact, ethics, ERA, ARC, pHacking, p hacking, peer review,
   perverse incentives
%X "... we sent scientists a survey asking this simple question: If you could
   change one thing about how science works today, what would it be and why?
   We heard back from 270 scientists all over the world, including graduate
   students, senior professors, laboratory heads, and Fields Medalists. They
   told us that, in a variety of ways, their careers are being hijacked by
   perverse incentives. The result is bad science. ..."
   -- [<A HREF="https://www.vox.com/2016/7/14/12016710/science-challeges-research-funding-peer-review-process">www</A>]['19].
   [Also search for: university management].

%A Anon
%T The Secret Lecturer: An Insider's Guide to Working in a Modern University
%P 110
%M NOV
%D 2016
%K book, c2016, c201x, c20xx, zz1217, university, academic, secret lecturer,
   academia, teaching, research, scholar, australia, australian, job, career,
   dean, deanitis, professor, student, ARC, eBook, dumb, funny,
   ha ha, haha, revenge
%X 1st ed 2016; ebook us$7; asin:B01MRFTP66; isbn13:978-1925333848.
   "... a darkly humorous look at what it is really like to work in a modern
   Australian university. Set against a backdrop of rising student numbers and
   falling staff numbers, it draws on extensive insider knowledge to highlight
   the often absurd and farcical decision-making that follows from letting a
   bunch of smart people try to run a business that sells 'education'. ..."
   (Also see [<A HREF="https://www.secretlecturer.com/">www</A>]['17].)
   A sequel: 'Revenge of the Secret Lecturer', 2017.

%A M. A. Edwards
%A S. Roy
%T Academic research in the 21st century: Maintaining scientific integrity in a
   climate of perverse incentives and hypercompetition
%J Environmental Eng. Sci.
%V 34
%N 1
%P ?-?
%M JAN
%D 2017
%K jrnl, c2017, c201x, c20xx, zz1218, publish, perish, scientific, research,
   ethics, integrity, academic, university, KPI, KPIs, grant, grants,
   EPA, NIH, ARC, misconduct, manipulation, abuse
%X "Over the last 50 years, we argue that incentives for academic scientists
   have become increasingly perverse in terms of competition for res.funding,
   development of quantitative metrics to measure performance, & a changing
   business model for higher ed. itself. [&] decreased discretionary funding at
   the federal & state level is creating a hypercompetitive environment between
   gvmt agencies (e.g., EPA, NIH, CDC), for scientists in these agencies, & for
   academics seeking funding from all sources - the combination of perverse
   incentives & decreased funding increases pressures that can lead to unethical
   behavior. If a critical mass of scientists become untrustworthy, a tipping
   point is possible in which the scientific enterprise itself becomes
   inherently corrupt & public trust is lost, risking a new dark age with
   devastating consequences to humanity. Academia & federal agencies should
   better support science as a public good, & incentivize altruistic & ethical
   outcomes, while de-emphasizing output."
   -- [<A HREF="https://doi.org/10.1089/ees.2016.0223">doi:10.1089/ees.2016.0223</A>]['18].
   [Also search for: publish perish]  and  [also search for: misconduct].

%A M. Harvey
%A R. Mailhammer
%T Reconstructing remote relationships
%J Diachronica
%V 34
%N 4
%P 470-515
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0418, linguistics, libguistic, proto-Australian,
   natural, language, evolution, noun, nouns, indigenous, aboriginal, koori,
   Australia, Australian
%X "... Hypotheses on remote relationships commonly involve greater geographical
   & temporal ranges. Consequently, we propose that there are two factors which
   are likely to play a greater role in comparing hypotheses of chance, contact
   & inheritance for remote relationships: (i) spatial distribution of
   corresponding forms; & (ii) language specific unpredictability in related
   paradigms. Concentrated spatial distributions disfavour hypotheses of chance,
   & discontinuous distributions disfavour contact hypotheses, whereas
   hypotheses of inheritance may accommodate both. Higher levels of
   language-specific unpredictability favour remote over recent transmission.
   We consider a remote relationship hypothesis, the Proto-Australian
   hypothesis. We take noun class prefixation as a test dataset for evaluating
   this hypothesis against these two criteria, & we show that inheritance is
   favoured over chance & contact."
   -- [<A HREF="https://doi.org/10.1075/dia.15032.har">doi:10.1075/dia.15032.har</A>]['18].
   auth1@{<A HREF="https://scholar.google.com.au/citations?user=uMZJKykAAAAJ&hl=en">schlr</A>]['18],
   auth2@[<A HREF="https://scholar.google.com/citations?hl=en&user=s5nUrT8AAAAJ&view_op=list_works&sortby=pubdate">schlr</A>]['18].
   (Also see [<A HREF="http://www.abc.net.au/news/2018-03-28/indigenous-language-comes-from-a-single-root-tongue/9594414http://www.abc.net.au/news/2018-03-28/indigenous-language-comes-from-a-single-root-tongue/9594414">abc</A>][28/3/2018].)
   [Also search for: natural language evolution].

%A S. F. Way
%A A. C. Morgan
%A A. Clauset
%A D. B. Larremore
%T The misleading narrative of the canonical faculty productivity trajectory
%J PNAS
%V 114
%N 44
%P E9216-E9223
%M OCT
%D 2017
%K jrnl, PNAS, c2017, c201x, c20xx, zz0619, scientific research, science,
   scientist, university, management, academic, academia, faculty, impact,
   promotion, job, career, ideas, creativity, prediction, predict, publications,
   KPI, KPIs, papers
%X "A scientist may publish tens or hundreds of papers over a career ... Sixty
   years of studies on career productivity patterns in a variety of fields
   suggest an intuitive & universal pattern: Productivity tends to rise
   rapidly to an early peak & then gradually declines. Here, we test the
   universality of this conventional narrative ... We show that the conventional
   narrative confidently describes only one-fifth of faculty, regardless of
   department prestige or researcher gender, & the remaining four-fifths of
   faculty exhibit a rich diversity of productivity patterns. To explain this
   diversity, we introduce a simple model of productivity trajectories &
   explore correlations between its parameters & researcher covariates,
   showing that departmental prestige predicts overall individual productivity
   & the timing of the transition from first- to last-author publications.
   These results demonstrate the unpredictability of productivity over time &
   open the door for new efforts to understand how environmental & individual
   factors shape scientific productivity."
   -- [<A HREF="https://doi.org/10.1073/pnas.1702121114">doi:10.1073/pnas.1702121114</A>]['19].

%A E. A. Fong
%A A. W. Wilhite
%T Authorship and citation manipulation in academic research
%J PLoS One
%V ?
%P ?-?
%M DEC
%D 2017
%K jrnl, eJrnl, c2017, c201x, c20xx, zz1217, academic, university, science,
   publish, perish, scientific research, papers, publications, authorship,
   honorary author, coercive, citation, RLM, citations, grant, grants, ARC, NIH,
   journals, JIF, ethics, misconduct, abuse, fraud, scam, game, manipulation,
   rank, rankings, impact, gaming, Hindex, KPI, KPIs
%X "Some scholars add authors to their research papers or grant proposals even
   when those individuals contribute nothing to the research effort. Some
   journal editors coerce authors to add citations that are not pertinent to
   their work & some authors pad their reference lists with superfluous
   citations. ... Even though the majority of scholars disapprove of such
   tactics, many feel pressured to make such additions while others suggest
   that it is just the way the game is played. ..."
   -- [<A HREF="https://doi.org/10.1371/journal.pone.0187394">doi:10.1371/journal.pone.0187394</A>]['17].
   [Also search for: publish perish]  and  [also search for: citation abuse].

%A J. Smyth
%T The Toxic University: Zombie Leadership, Academic Rock Stars and
   Neoliberal Ideology
%I PalgraveMacmillan
%P 235
%D 2017
%K book, c2017, c201x, c20xx, zz0518, University, tertiary, higher education,
   academic, management, politics, teaching, research, faculty, dean, deanitis,
   jargon, impact, KPI, KPIs, superstars, Federation Uni, Monash, Gippsland,
   Australia, ranking, rating, performance manage, workload, league table,
   tables, neoliberal, neoliberalism, Reaganomics, zombie, leader, leadership
%X 1st ed 2017; hb us$64; uk us isbn:1137549769; uk us isbn13:978-1137549761.
   "This book considers the detrimental changes that have occurred to the
   institution of the university, as a result of the withdrawal of state funding
   and the imposition of neoliberal market reforms on higher education. It
   argues that universities have lost their way, and are currently drowning in
   an impenetrable mush of economic babble, spurious spin-offs of zombie
   economics, management-speak and militaristic-corporate jargon. ...
   meaningless marketing hype ..."
   (Also see, "John Smyth has a call to arms for academics frustrated by trends
   in higher education in the United States, Britain, Australia and
   elsewhere. ..."
   -- [<A HREF="https://www.insidehighered.com/news/2017/07/12/author-discusses-ideas-his-new-book-toxic-university">www</A>][11/12/17].)
   [Also search for: toxic university].

%A Y. Polozhentseva
%A M. Klevtsova
%T KPI-monitoring for university's performance improvement
%J Economic Annals-XXI
%V 163
%N 1-2(1)
%P 71-74
%D 2017
%K jrnl, c2017, c201x, c20xx, zz1019, university, academic, research,
   managament, education, KPI, KPIs, ranking, rankings, THES, Leiden, QS,
   SCImago, ERA, ARC, Stanford, Harvard, Cambridge, Oxford, Toronto, Tokyo,
   Lomonosov, Moscow, europe, uk, usa, russia
%X "Approaches based on KPI-monitoring are used by commercial entities
   worldwide. However, such an approach is new and insufficiently developed for
   universities. Specific features of their functioning necessitate not just
   assessment of their economic efficiency but also consideration of special
   aspects of higher education. Therefore, studying the issues of uni.
   performance monitoring based on the development of a system of indicators is
   challenging in terms of encouraging rapid international development of
   'smart economy'. The article contains analysis of universities' global
   rankings based on the selection of indicators of KPI-monitoring system to
   show development of university competitive strengths related to countries'
   economic development."
   -- [<A HREF="https://pdfs.semanticscholar.org/8103/dd18ed4e4e0f8e57c0708ecbcf95338e72b9.pdf">www</A>]['19].
   [Also search for: university management].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/2008-rankings/">rankings</A>].)

%A M. Enserink
%T Swedish plastics study fabricated, panel finds
%J Science
%V 358
%N 6369
%P 1367
%M DEC
%D 2017
%K news, c2017, c201x, c20xx, zz1217, science, scientific, university, academic,
   research, fraud, misconduct, plastic, pollution, Uppsala, Lonnstedt, Eklov
%X "On 7 Dec., Uppsala U. in Sweden released a long-awaited report by
   its Board for Investigation of Misconduct in Research, which investigated a
   high-profile paper about the effects of microplastics on fish, published in
   Science in June 2016. The panel found that the paper's first author, Oona
   Lonnstedt, committed misconduct by fabricating data in the paper; her lone
   co-author and supervisor, Peter Eklov, bears responsibility for the
   fabrication as well ..."
   -- [<A HREF="https://doi.org/10.1126/science.358.6369.1367">doi: 10.1126/science.358.6369.1367</A>]['17].

%A Captain Jerry Roberts
%T Lorenz: Breaking Hitler's Top Secret Code at Bletchley Park
%I TheHistoryPress
%P 240
%D 2017
%K book, memoir, c2017, c201x, c20xx, zz1124, cryptology, code breaking,
   codeBreaking, broken, double Playfair, Tunny, Testery, Colossus,
   Bill Tutte, Tommy Flowers
%X (Bear in mind that this is a memoir by JR (1920-2014).)
   JR was one of the first codebreakers in the Testery --
   before and after the T. started work on Lorenz.
   The UK only declassified work on the L.code in 2002.
   1st ed 2017; hb, uk us isbn:0750978856; uk us isbn13:978-0750978859.
   [Also search for: Bletchley Park].

%A I. Stengers
%A S. Mucke (transl.)
%T Another Science is Possible: A Manifesto for Slow Science
%I Polity
%P 220
%D 2018 ?
%K book, text. c2018, c201x, c20xx, zz1217, science, scientific research,
   politics, policy
%X 1st ed 2018?; us$65; uk us isbn:1509521801; uk us isbn13:978-1509521807.
   "Like fast food, fast science is quickly prepared, not particularly good,
   and it clogs up the system. ...  researchers should stop seeing themselves as
   the 'thinking, rational brain of humanity' and refuse to allow their
   expertise to be used to shut down the concerns of the public, or to spread
   the belief that scientific progress is inevitable and will resolve all of
   society's problems. Rather, science must engage openly and honestly with an
   intelligent public and be clear about the kind of knowledge it is capable of
   producing. ..."

%T Maths strikes a blow for democracy
%J Nature
%M JAN
%D 2018
%K editorial, c2018, c201x, c20xx, zz0118, Mattingly, US, USA, North Carolina,
   politics, Republican party, gerrymander, drawing electoral boundary,
   boundaries, 2012, election, elections, voting, vote, fair, fairness,
   criteria, Reock, democracy
%X "... In striking down the way that officials in North Carolina unfairly
   partitioned the state into electoral districts, a US federal court last week
   conspicuously cited the work of mathematicians including Jonathan Mattingly,
   an expert in mathematical modelling. ... Mattingly, a researcher at Duke U.
   in Durham, NC ... alg. that produced around 24,000 maps of marginally
   different district configurations that were randomly drawn on the basis of
   geographic criteria. The Republican-drawn boundaries, which had delivered 9
   Republicans to the state's 13 seats in the House of Reps. in Washington DC in
   2012, were more gerrymandered than practically every single one of
   Mattingly's algorithm-derived maps. ..."
   -- [<A HREF="https://www.nature.com/articles/d41586-018-00661-x">www</A>]['18].
   (*Also see [<A HREF="https://doi.org/10.1038/546200a">doi:10.1038/546200a</A>][8/6/2017].*)

%A N. Brown
%A T. Sandholm
%T Superhuman AI for heads-up no-limit poker: Libratus beats top professionals
%J Science
%V 359
%N 6374
%P 418-424
%M JAN
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0118, AI, card, cards, game, playing, poker,
   HUNL, Texas hold'em, Libratus, bluff, bluffing
%X "... present Libratus, an AI that, in a 120,000-hand competition, defeated
   four top human specialist professionals in heads-up no-limit Texas hold'em,
   the leading benchmark & long-standing challenge problem in
   imperfect-information game solving. Our game-theoretic approach features
   application-independent techniques: an alg. for computing a blueprint
   for the overall strategy, an alg. that fleshes out the details of the
   strategy for subgames that are reached during play, & a self-improver
   alg. that fixes potential weaknesses that opponents have identified
   in the blueprint strategy."
   -- [<A HREF="https://doi.org/10.1126/science.aao1733">doi:10.1126/science.aao1733</A>]['18].
   [Also search for: poker AI].

%A O. Kinouchi
%A L. D. H. Soares
%A G. H. Cardoso
%T A simple centrality index for scientific social recognition
%J Physica A: Stat. Mech. and its Applications
%V 491
%P 632-640
%M FEB
%D 2018
%K jrnl, c2018, c201x, c20xx, zz1222, modified bibliometrics, Kindex, graph,
   network, centrality, hub, Hindex, KPI, KPIs, publish, perish
%X "... bipartite n/wk of papers & authors that we call K-index. ... The K-index
   is robust to self-citations, is not limited by the total # of papers
   published by a researcher as occurs for the H-index & can distinguish in a
   consistent way researchers that have the same H-index but very different
   scientific social recognition. ..."
   -- [<A HREF="https://doi.org/10.1016/j.physa.2017.08.072">doi:10.1016/j.physa.2017.08.072</A>]['22],
   1609.05273@[<A HREF="https://arxiv.org/abs/1609.05273">arXiv</A>]['22].
     "If a researcher has K citing papers, each one with at least K citations,
     then their K-index is K."
   [Also search for: publish perish].  (And beware, there is another Kindex:-)

%A J. Z. Muller
%T The Tyranny of Metrics
%I PrincetonUP
%P 240
%M FEB
%D 2018
%K book, c2018, c201x, c20xx, zz0218, publish, perish, bibliometrics, impact,
   Hindex, KIP, KPIs, misuse, teaching, scores, audit culture
%X 1st ed 2018; hb us$19; uk us isbn:0691174954; uk us isbn13:978-0691174952.
   "...  our zeal to instill the evaluation process with scientific rigor,
   we've gone from measuring performance to fixating on measuring itself. The
   result is a tyranny of metrics that threatens the quality of our lives and
   most important institutions. ... Filled with examples from education,
   medicine, business and finance, government, the police and military, and
   philanthropy and foreign aid, this brief and accessible book explains why the
   seemingly irresistible pressure to quantify performance distorts and
   distracts, whether by encouraging "gaming the stats" or
   'teaching to the test." ..."
   [Also search for: bibliometrics misuse].

%A S. Curry
%T Let's move beyond the rhetoric: it's time to change how we judge research
%J Nature
%V 554
%M FEB
%D 2018
%K news, views, c2018, c201x, c20xx, zz0218, publish, perish, DORA, scientific,
   research, academic, modified, impact, quality, journals, JIF, publications,
   ranking, ARC, NIH
%X "... The San Francisco Declaration on Research Assessment (DORA) ... Dec 2012
   it proclaims a pressing need to improve how scientific research is evaluated,
   and asks scientists, funders, institutions and publishers to forswear using
   journal impact factors (JIFs) to judge individual researchers.  DORA's aim is
   a world in which *the content of a research paper matters more than the
   impact factor of the journal in which it appears.[!] ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-018-01642-w">doi:10.1038/d41586-018-01642-w</A>]['18].

%A R. S. Nerem
%A at al
%A G. T. Mitchum
%T Climate-change-driven accelerated sea-level rise detected in the
   altimeter era
%J PNAS
%V ?
%P ?-?
%M FEB
%D 2018
%K jrnl, PNAS, c2018, c201x, c20xx, zz0218, climate change, global warming,
   ice sheet, melt, melting, sea level, rise, rising, TOPEX/Poseidon, Jason,
   Jason1, Jason2, and Jason3, satellite, data
%X "Using a 25y time series of precision satellite altimeter data from
   TOPEX/Poseidon, Jason-1, Jason-2, and Jason-3, we estimate the
   climate-change-driven acceleration of global mean sea level over the last
   25y to be 0.084+/-0.025 mm/y2. Coupled with the average
   climate-change-driven rate of sea level rise over these same 25y of
   2.9 mm/y, simple extrapolation of the quadratic implies global mean sea
   level could rise 65+/-12 cm by 2100 compared with 2005, roughly in
   agreement with the Intergovernmental Panel on Climate Change (IPCC)
   5th Assessment Report (AR5) model projections."
   -- [<A HREF="https://doi.org/10.1073/pnas.1717312115">doi:10.1073/pnas.1717312115</A>]['18].

%A R. Hougaard
%T The Mind of the Leader: How to Lead Yourself, Your People, and
   Your Organization for Extraordinary Results
%I HarvardBuisRev
%P 256
%M MAR
%D 2018
%K book, c2018, c201x, c20xx, zz0818, managing, leader, leadership, bosses,
   management, managing, business, economics, neoliberalism, econobabble
%X "The world is facing a global leadership crisis. Seventy-seven percent of
   leaders think they do a good job of engaging their people, yet 88 percent of
   employees say their leaders don't engage enough. There is also a high level
   of suffering in the workplace: 35 percent of employees would forgo a pay
   raise to see their leaders fired. ... need to develop managers and executives
   who lead with three core mental qualities: mindfulness, selflessness, and
   compassion. ..."
   1st ed 2018; ub us$22; uk us isbn:1633693422; uk us isbn13:978-1633693425.

%A T. F. Watson
%A et al
%A L. M. K. Vandersypen
%T A programmable two-qubit quantum processor in silicon
%J Nature
%V 555
%P 633-637
%M MAR
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0218, quantum computing, computer, qubit,
   qubits, qbit, qbits, dot, dots, silicon, chip, Deutsch Josza algorithm,
   DelftUT, UniWisconsinMadison
%X "Now that it is possible to achieve measurement & control fidelities for
   individual quantum bits (qubits) above the threshold for fault tolerance ...
   using carefully designed control techniques to demonstrate a programmable
   two-qubit quantum processor in a silicon device that can perform the
   Deutsch-Josza algorithm & the Grover search algorithm-canonical examples of
   quantum algorithms that outperform their classical analogues. We characterize
   the entanglement in our processor by using quantum-state tomography of Bell
   states, measuring state fidelities of 85-89% & concurrences of 73-82%.
   These results pave the way for larger-scale quantum computers that
   use spins confined to quantum dots."  (online Feb 2018.)
   -- [<A HREF="https://doi.org/10.1038/nature25766">doi:10.1038/nature25766</A>]['18].
   [Also search for: quantum computing].
   (Also see, "... turned to silicon to suspend single electron qubits whose
    spin was fixed by the use of microwave energy.  In the superposition state,
    the electron was spinning both up and down. ..."
    -- [<A HREF="http://www.bbc.com/news/science-environment-43065485">bbc</A>][14/2/2018].)

%A X. Mi
%A et al ...
%A J. R. petta
%T A coherent spin-photon interface in silicon
%J Nature
%V ?
%P ?-?
%M FEB
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0218, quantum computing, computer, qubit,
   qubits, qbit, qbits, silicon, chip, electron spin, photon,
   PrincetonUni, UniKonstanz, Maryland
%X "Electron spins in silicon quantum dots are attractive systems for quantum
   computing owing to their long coherence times & the promise of rapid scaling
   of the # of dots in a system using semiconductor fabrication techniques. ...
   ... demonstrate strong coupling between a single spin in silicon & a single
   microwave-frequency photon, with spin-photon coupling rates of more than
   10 megahertz. The mechanism that enables the coherent spin-photon
   interactions is based on spin-charge hybridization in the presence of a
   magnetic-field gradient. In addition to spin-photon coupling, we demonstrate
   coherent control & dispersive readout of a single spin. These results open up
   a direct path to entangling single spins using microwave-frequency photons."
   -- [<A HREF="https://doi.org/10.1038/nature25769">doi:10.1038/nature25769</A>]['18].
   [Also search for: quantum computing].
   (Also see [<A HREF="http://www.bbc.com/news/science-environment-43065485">bbc</A>][14/2/2018].)

%A D. J. Carragher
%A et al
%T Visuospatial asymmetries do not modulate the cheerleader effect
%J Sci. Reports
%V 8
%N 2548
%M FEB
%D 2018
%K c2018, c201x, c20xx, zz0318, cheer leader, cheerleader effect,
   attractiveness, groups, human, vision, perception
%X "The cheerleader effect occurs when the same individual appears to be
   more attractive when seen in a group, compared to alone. ..."
   -- [<A HREF="https://doi.org/10.1038/s41598-018-20784-5">doi:10.1038/s41598-018-20784-5</A>]['18].
   (Also see the abc[<A HREF="http://www.abc.net.au/news/2018-03-02/cheerleader-effect-attraction-tinder-facebook-online-dating/9501848">2/3/2018</A>].)

%A A. McCook
%T University is quick to disclose misconduct
%J Science
%V 360
%N 6384
%P 13-14
%M APR
%D 2018
%K news, views, c2018, c201x, c20xx, zz0418, academic, university, scientific,
   research, Ohio State University (OSU), cancer, Ching-Shih Chen, misconduct,
   ethics, Retraction Watch, NIH, grant, grants
%X "... (OSU) in Columbus last week released a detailed account of the
   scientific misbehavior of one of its former faculty members. The 75-page
   report was damning: It concluded that cancer researcher Ching-Shih Chen -
   once lauded as an 'Innovator of the Year' and the winner of millions of
   dollars in federal funding - had committed misconduct in eight papers.
   Chen resigned last September. ..."
   -- [<A HREF="https://doi.org/10.1126/science.360.6384.13">doi:10.1126/science.360.6384.13</A>]['18].
   [Also search for: academic misconduct].

%A J. Brainard
%T NIH looks to punish reviewers who violate confidentiality
%J Science
%V 360
%N 6384
%P 17
%M APR
%D 2018
%K news, views, c2018, c201x, c20xx, zz0418, academic, scientific, research,
   grant, grants, NIH, ARC, peer review, reviewing, ethics, misconduct, scandal,
   cheating, corruption, scam, fraud, reciprocal favour, favor, USA
%X "The U.S. National Institutes of Health (NIH) announced last week it is
   investigating violations of confidentiality rules designed to protect the
   integrity of its peer reviews that score funding applications. A violation
   of NIH rules involving one peer-review panel led the agency recently to
   re-review 60 applications that the committee had evaluated. NIH officials
   were mum about the number of cases and most other details but said at least
   one violation involved 'reciprocal favors' - a term that typically means an
   applicant offered a favor to a reviewer in exchange for a favorable
   evaluation of a proposal, or vice versa. NIH rules suggest possible sanctions
   could include suspending or barring violators from obtaining federal
   research funds."
   -- [<A HREF="https://doi.org/10.1126/science.360.6384.17">doi:10.1126/science.360.6384.17</A>]['18].
   [Also search for: peer review].

%A A. Nunes
%A B. Reimer
%A J. F. Coughlin
%T People must retain control of autonomous vehicles
%J Nature
%V 556
%N ?
%P 169-171
%M APR
%D 2018
%K news, views, c2018, c201x, c20xx, zz0418, autonomous, self driving, car,
   cars, automobile, law, laws, liability, Tesla, accident, collision, casualty,
   safety, driverless, policy, politics, risk, risks
%X "Last month, for the first time, a pedestrian was killed in an accident
   involving a self-driving car. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-018-04158-5">doi:10.1038/d41586-018-04158-5</A>]['18].
   [Also search for: autonomous cars].

%A K. Gross
%A C. T. Bergstrom
%T Contest models highlight inefficiencies of scientific funding
%J arXiv
%D 2018
%K TR, c2018, c201x, c20xx, zz0418, scientific, academic, university, research,
   grant, grants, writing, proposals, ARC, NIH, waste, KPI, KPIs, model
%X "... At a first approximation, the work invested in writing proposals
   provides no value to the funder. Here, we use the economic theory of contests
   to analyze the scientific efficiency of the proposal system, & compare it to
   recently proposed, partially randomized alternatives such as lotteries. We
   find that the effort researchers waste in writing proposals may be comparable
   to the total scientific value of the additional funding, especially when only
   a small percentage of proposals are funded. Moreover, when professional
   pressures motivate investigators to seek funding for reasons that extend
   beyond the value of the proposed science, the entire program can act as a
   drag on scientific progress when paylines are low. We suggest that lost
   efficiency may be recouped at low paylines either by partial lotteries for
   funding, or by funding researchers based on past scientific success instead
   of proposals for future work."
   -- 1804.03732@[<A HREF="https://arxiv.org/abs/1804.03732">arXiv</A>]['18].

%A M. K. McNutt
%A et al ...
%A I. M. Verma
%T Transparency in authors' contributions and responsibilities to promote
   integrity in scientific publication
%J PNAS
%M FEB
%D 2018
%K views, c2018, c201x, c20xx, zz0518, scientific research, university, paper,
   papers, publications, author, authors, authorship, role, roles, CRediT, TACS,
   impact, publish, perish
%X "... propose changes to journal authorship policies & procedures to provide
   insight into which author is responsible for which contributions, better
   assurance that the list is complete, & clearly articulated standards to
   justify earning authorship credit. ... Contributor Roles Taxonomy (CRediT)
   (docs.casrai.org/CRediT) ... ecommend that universities & research
   institutions articulate expectations about author roles & responsibilities
   to provide a point of common understanding for discussion of authorship
   across research teams. ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.1715374115">doi:10.1073/pnas.1715374115</A>]['18].
   [Also search for: publish perish].
   (And sadly, also see [<A HREF="https://doi.org/10.1126/science.aau0036">doi:10.1126/science.aau0036</A>][26/4/2018].)

%T China sets a strong example on how to address scientific fraud
%A Editor
%J Nature
%V 558
%N 7709
%P 162
%M JUN
%D 2018
%K news, views, c2018, c201x, c20xx, zz0618, academic, scientific, research,
   misconduct, fraud, Chinese, law
%X "... One of the most striking conditions is that researchers will be deterred
   from publishing findings in journals that China deems to be of poor academic
   quality, poorly managed and set up merely for profit. ... China is handing
   the responsibility for deterring and investigating scientific misconduct to
   the government's science ministry. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-018-05417-1">doi:10.1038/d41586-018-05417-1</A>]['18].
   And also,
   "China introduces sweeping reforms to crack down on academic misconduct ..."
   by David Cyranoski
   -- [<A HREF="https://doi.org/10.1038/d41586-018-05359-8">doi:10.1038/d41586-018-05359-8</A>]['18].

%A J. Tregoning
%T How will you judge me if not by impact factor?
%J Nature
%V 558
%N 7710
%P ?-?
%M JUN
%D 2018
%K views, c2018, c201x, c20xx, zz0618, publish, perish, impact, KPI, KPIs, JIF,
   publications, journal, scientific research, university, DORA, Hindex
%X "Rumours among junior faculty members are that reports of the death of the
   impact factor are greatly exaggerated. ... Ideally, just putting our research
   out there should be enough for people to descry our brilliance & promote
   it accordingly. But that is not how the system works. ... Although DORA is
   in my heart, impact factors are still on my mind. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-018-05467-5">doi:10.1038/d41586-018-05467-5</A>]['18].
   [Also search for: publish perish]  and  [also search for: Hindex abuse].

%A W. K. T. Cho
%T Algorithms can foster a more democratic society
%J Nature
%V 558
%N 7711
%P ?-?
%M JUN
%D 2018
%K news, views, c2018, c201x, c20xx, zz0618, USA, election, elections,
   politics, gerrymander, America, political, boundaries
%X "Gerrymandering - the manipulation of district boundaries to give one group
   a political advantage ... the contorted shapes of electoral districts defy
   simple explanation and imbue a public perception of a rigged system. And when
   as in Pennsylvania in 2014, a party captures 72% of its US House of
   Representatives seats with only 55.5% of the statewide vote, suspicions are
   piqued. ... In the United States, electoral districts are redrawn every
   ten years. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-018-05498-y">doi:10.1038/d41586-018-05498-y</A>]['18].
   [Also search for: gerrymander].

%A C. Sumner
%A J. E. Scofield
%A E. M. Buchanan
%A M.-Rose Evans
%A M. Shearing
%T The role of personality, authoritarianism and cognition in the
   United Kingdom's 2016 referendum on European Union membership
%I Online Privacy Foundation
%M JUL
%D 2018
%K TR, c2018, c201x, c20xx, zz0718, stats, Brexit, EU, Europe, UK, referendum,
   vote, personality, traits, authoritarianism, conscientiousness, numeracy,
   politics, democracy, psychology, stats
%X "... examined the role of personality traits, cognition & cognitive biases in
   relation to referendum voters' choices. A total of 11,225 participants
   completed questionnaires & controlled experiments ... Participants expressing
   an intent to vote to leave the EU reported sig. higher levels of
   authoritarianism & conscientiousness, & lower levels of openness &
   neuroticism than voters expressing an intent to vote to remain in the EU.
   When compared with Remain voters, Leave voters displayed sig. lower levels of
   numeracy & appeared more reliant on impulsive System 1 thinking. In the
   experimental studies, voters on both sides were found to be susceptible to
   the cognitive biases tested, but often, unexpectedly, to different degrees.
   These results raise important questions regarding the use & framing of
   numerical & non-numerical data for public consumption."
   -- draft n5r67@[<A HREF="https://osf.io/n5r67/download">osf</A>][7/2018],
      project urt63@[<A HREF="https://osf.io/urt63/">osf</A>]['18],
      [<A HREF="https://www.onlineprivacyfoundation.org/opf-research/psychological-biases/personality-authoritarianism-and-cognition-in-brexit/">oPf</A>]['18].
   [Also search for: brexit].

%A B. Bratsberg
%A O. Rogeberg
%T Flynn effect and its reversal are both environmentally caused
%J PNAS
%V 115
%N 26
%P 6674-6678
%M JUN
%D 2018
%K jrnl, PNAS, c2018, c201x, c20xx, zz0719, human, intelligence, IQ,
   Flynn effect, Flyn, reverse, reversal, reversed, decline
%X "Population intelligence quotients increased throughout the 20th century -
   a phenomenon known as the Flynn effect - although recent years have seen a
   slowdown or reversal of this trend in several countries. To distinguish
   between the large set of proposed explanations, we categorize hypothesized
   causal factors by whether they accommodate the existence of within-family
   Flynn effects. Using administrative register data & cognitive ability scores
   from military conscription data covering three decades of Norwegian birth
   cohorts (1962-1991), we show that the observed Flynn effect, its turning
   point, & subsequent decline can all be fully recovered from within-family
   variation. The analysis controls for all factors shared by siblings & finds
   no evidence for prominent causal hypotheses of the decline implicating genes
   & environmental factors that vary between, but not within, families."
   -- [<A HREF="https://doi.org/10.1073/pnas.1718793115">doi:10.1073/pnas.1718793115</A>]['19].
   (Also see the bbc[<A HREF="http://www.bbc.com/future/story/20190709-has-humanity-reached-peak-intelligence">10/4/2019</A>].)
   [Also search for: Flynn effect].

%T What Will the Future of Scientific Publishing Look Like?
%I Lindau Nobel Laureate Meetings
%K c2018, c201x, c20xx, zz0718, publish perish, grants, fellowship, impact,
   JIF, citations, journal, journals, Ropers ceo Springer, Schekman, PNAS,
   eLife, EMBO, open, access, reviewing, referees, LIN, LIN018, Lindau meeting,
   Nobel, NobelPrize, panel discussion, scientific research, university,
   academic, publication, publications, papers
%M JUN
%D 2018
%X "Publish or perish - anyone working in research or academia knows that
   phrase all too well and has felt the pressure and dread caused by it. ...
   the current way of researchers climbing over one another or, worse yet,
   molding their results to fit a promising narrative to get a publication in
   one of the glamour journals, is unsustainable. The rationale behind wanting a
   'big' publication is simple: A paper in a journal with a high glamour factor
   (which is closely correlated to the impact factor of the journal) such as
   Nature, Science or Cell promises high visibility for the leading authors of
   the paper and presumably heightens their value and prospects when applying
   for a new fellowship or grant. ..."
   -- [<A HREF="https://www.lindau-nobel.org/blog-what-will-the-future-of-scientific-publishing-look-like/">www</A>][28/6/2018] inc. the video.  (Via AK).
   [Also search for: publish perish] and check out
   Schekman & eLife, e.g., [<A HREF="https://doi.org/10.7554/eLife.31697">doi:10.7554/eLife.31697</A>][12/10/2017].

%A E. S. Bernstein
%A S. Turban
%T The impact of the 'open' workspace on human collaboration
%J Phil. Trans. of the Royal Soc. B
%V 373
%N 1753
%M JUL
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0718, open plan office, space, openPlan, F2F,
   management, business, organization, company, layout, human behaviour,
   experiment, stats
%X "Organizations' pursuit of increased workplace collaboration has led managers
   to transform traditional office spaces into 'open', transparency-enhancing
   architectures with fewer walls, doors and other spatial boundaries, yet there
   is scant direct empirical research on how human interaction patterns change
   as a result of these architectural changes. In two intervention-based field
   studies of corporate headquarters transitioning to more open office spaces,
   we empirically examined ... In short, rather than prompting increasingly
   vibrant face-to-face collaboration, open architecture appeared to trigger a
   natural human response to socially withdraw from officemates and interact
   instead over email and IM [messaging]. ..."
   -- [<A HREF="https://doi.org/10.1098/rstb.2017.0239">doi:10.1098/rstb.2017.0239</A>]['18].

%A S. Cave
%A K. Dihal
%T Ancient dreams of intelligent machines: 3,000 years of robots
%J Nature
%V 559
%P 473-475
%M JUL
%D 2018
%K c2018, c201x, c20xx, zz0718, robot, gods, robots, android, AI, automaton,
   Alife, Ingenious Devices, HAL, Skynet, Mayor, books, literature
%X "... hopes and fears that have been associated with human-like machines for
   nearly three millennia. ... In her forthcoming book Gods and Robots,
   classicist Adrienne Mayor describes bronze automata that featured at the
   Olympic Games two centuries before the Argonautica - a leaping dolphin and
   eagle in apparent flight. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-018-05773-y">doi:10.1038/d41586-018-05773-y</A>]['18].
   [Also search for: android].

%A A. Mayor
%T Gods and Robots: Myths, Machines, and Ancient Dreams of Technology
%I PrincetonUP
%P 296
%M NOV
%D 2018
%K book, text, c2018, c201x, c20xx, zz0818, robot, robots, android, Greeks,
   Talos, AI, Alife, sinularity, Ingenious Devices, HAL, Skynet
%X "The first robot to walk the earth was a bronze giant called Talos. This
   wondrous machine was created not by MIT Robotics Lab, but by Hephaestus,
   the Greek god of invention. More than 2,500 years ago ..."
   1st ed 2018; hb us$30; uk us isbn:0691183511; uk us isbn13:978-0691183510.
   [Also search for: android].

%A H. Else
%T How Unpaywall is transforming open science
%J Nature
%V 560
%N 7718
%P ?-?
%M AUG
%D 2018
%K news, views, c2018, c201x, c20xx, zz0818, papers, publications, Unpaywall,
   free, open, access, OA, openAccess, online, impact, scientific research,
   Piwowar, Priem, Parra, preprint, preprints, PeerJ
%X "...  a group of computer scientists simply moved to an adjacent hallway.
   There, Heather Piwowar, Jason Priem and Cristhian Parra worked all night on
   software to help academics to illustrate how much of their work was freely
   available on the Internet. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-018-05968-3">doi:10.1038/d41586-018-05968-3</A>].
   Also see, 'The State of OA: A large-scale analysis of the
              prevalence and impact of Open Access articles'
   --  [<A HREF="https://doi.org/10.7287/peerj.preprints.3119v1">10.7287/peerj.preprints.3119v1</A>]['17].
   [Also search for: unpaywall] & [also search for: research open access].

%A J. P. A. Ioannidis
%A R. Klavans
%A K. W. Boyack
%T Thousands of scientists publish a paper every five days
%J Nature
%V 561
%P 167-169
%M SEP
%D 2018
%K news, views, c2018, c201x, c20xx, zz0918, publish, perish, scientific,
   research, paper, papers, Scopus, guest authorship, implausibly prolific,
   questionable, dubious, publication, glut, Hindex, KPI, KPIs
%X "... We searched Scopus for authors who had published more than 72 papers
   (the equivalent of one paper every 5 days) in any one calendar year between
   2000 and 2016, a figure that many would consider implausibly prolific. We
   found more than 9,000 individuals, and made every effort to count only
   'full papers' - articles, conference papers, substantive comments and
   reviews - not editorials, letters to the editor and the like. We hoped that
   this could be a useful exercise in understanding what scientific authorship
   means. ..."
   --  [<A HREF="https://doi.org/10.1038/d41586-018-06185-8">doi:10.1038/d41586-018-06185-8</A>]['18].
   [Also search for: publish perish] & [also search for: implausibly prolific].

%A D. Turing
%T X, Y & Z: The Real Story of How Enigma Was Broken
%I HistoryPress
%P 288
%M SEP
%D 2018
%K book, c2018, c201x, c20xx, Enigma, code, cypher, breaking, decryption,
   cryptography, WW2, WWII, Bletchley Park, XYZ,
   Polish, Poland, Ciezki, Langer, Palluth
%X 1st ed 2018; hb us$21;
   "X, Y & Z describes how French, British and Polish secret services came
   together to unravel the Enigma machine. It tells of how, under the very noses
   of the Germans, Enigma code-breaking continued in Vichy France. ..."
   (D.T. is the nephew of A.T.)
   [Also search for: Bletchley Park].

%A D. Graeber
%T Bullshit Jobs: A Theory
%I AllenLane
%M MAY
%D 2018
%K book, c2018, c201x, c20xx, zz1018, Graeber, LSE, society, neoliberal, work,
   job, jobs, spin, bullshitization, academic, academia, toxic university,
   management, dean, vice chancellor, impact, teaching, higher education,
   faculty
%X 1st ed 2018; hb us$21, uk us isbn:9780241263884, uk us isbn13:978-0241263884.
   (Also see,
   "I would like to write about the bullshitization of academic life: that is,
   the degree to which those involved in teaching and academic management spend
   more and more of their time involved in tasks which they secretly - or not so
   secretly - believe to be entirely pointless. ...",
   -- D.G.@[<A HREF="https://www.chronicle.com/article/Are-You-in-a-BS-Job-In/243318">www</A>][6/5/2018]. And see
   J.Weinberg@[<A HREF="http://dailynous.com/2018/05/08/bullshit-jobs-higher-ed/">8/5/2018</A>]['18].)
   [Also search for: toxic university].

%T Paywall: The Business of Scholarship
%D 2018
%K movie, film, c2018, c201x, c20xx, zz1018, scientific research, publications,
   papers, articles, journal, journals, quality, JIF, open access, openAccess,
   OA, Elsevier, Wiley, Springer Nature, SpringerNature, publishing, publisher,
   SciHub, Sci-Hub
%X "Paywall: The Business of Scholarship is a documentary which focuses on the
   need for open access to research and science, questions the rationale behind
   the $25.2 billion a year that flows into for-profit academic publishers,
   examines the 35-40% profit margin associated with the top academic publisher
   Elsevier ..."
   -- [<A HREF="https://paywallthemovie.com/">paywallthemovie.com</A>]['18].
   (Also see review@[<A HREF="https://doi.org/10.1038/d41586-018-06140-7">4/9/2018</A>].)
   [Also search for: research open access].

%A K. Hall Jamieson
%T Cyberwar: How Russian Hackers and Trolls helped elect a President,
   what we don't, can't, and do know
%I OUP
%P 336
%M OCT
%D 2018
%K book, OUP, c2018, c201x, c20xx, zz1018, USA, US, American, politics,
   Donald Trump, zzTrump, Russia, internet, facebook, twitter, social media,
   troll, hack, president, POTUS, presidential, 2016, election
%X 1st ed 2018; hb us$17; uk us isbn13:978-0190915810; asin:0190915811.
   "... how Donald Trump won the 2016 election looms over his presidency. In
   particular, were the 78,000 voters who gave him an Electoral College victory
   affected by the Russian trolls and hackers? ..."

%A C. Armitage
%T Less prestigious institutions deliver better value for grant money
%J NatureIndex
%M OCT
%D 2018
%K news, views, c2018, c201x, c20xx, zz1018, institution, university, bias,
   scientific research, ARC, NIH, grant, grants, funding, prestige, quality,
   reputation, inequality, Wahls, bioRxiv
%X "Study finds "wasteful" skew in NIH funding towards those at the top.
   An analysis of United States National Institutes of Health (NIH) grant
   allocations finds that prestigious institutions deliver much lower output
   per dollar spent than less prestigious institutions, yet get a
   disproportionate share of funding. ..."
   [* SEE:
   'High cost of bias: Diminishing marginal returns on NIH grant funding to
   institutions', W.P.Wahls, bioRxiv July 2018,
   "... revealed robust inverse correlations between funding (per institution,
   per award, per investigator) and scientific output (publication productivity
   and citation impact productivity). ..."
   -- [<A HREF="https://doi.org/10.1101/367847">doi:10.1101/367847</A>]['18]. *]
   [Also search for: research grants].

%A D. Heaven
%T AI peer reviewers unleashed to ease publishing grind
%J Nature
%V 563
%N 7733
%P 609-610
%M NOV
%D 2018
&K news, views, c2018, c201x, c20xx, zz1118, peer review, reviewing, AI, tools,
   refereeing, science, scientific, research, publication, literature, papers,
   StatReviewer, ScholarOne, UNSILO, PubMed, Clarivate, Wizdom, statcheck
%X "... Now peer review by artificial intelligence (AI) is promising to improve
   the process, boost the quality of published papers - and save reviewers time.
   A handful of academic publishers are piloting AI tools to do anything from
   selecting reviewers to checking statistics and summarizing a paper's
   findings. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-018-07245-9">doi:10.1038/d41586-018-07245-9</A>][22/11/'18].
   [Also search for: peer review].

%A M. Dyakonov
%T The case against quantum computing
%J Spectrum
%I IEEE
%M NOV
%D 2018
%K jrnl, c2018, c201x, c20xx, zz1118, quantum computing, computer, computation,
   noise, errors, practical, Manin, Landauer, research bubble, fad,
   controversial, controversy, prediction, zz1123, zz1128, zz1133, zzPrediction
%X "The proposed strategy relies on manipulating with high precision an
   unimaginably huge # of variables. Q.computing is all the rage. It seems
   like hardly a day goes by without some news outlet describing the
   extraordinary things this technology promises. Most commentators forget, or
   just gloss over, the fact that people have been working on q.computing for
   decades - and without any practical results to show for it. ...
   In light of all this, it's natural to wonder: When will useful q.computers
   be constructed? The most optimistic experts estimate it will take 5 to 10
   years. More cautious ones predict 20 to 30 y.. (Similar predictions have been
   voiced, by the way, for the last 20 years.) I belong to a tiny minority that
   answers, 'Not in the foreseeable future.' ... Could we ever learn to control
   the more than 10^{300} continuously variable parameters defining the q.state
   of such a system?  My answer is simple. No, never. I believe that,
   appearances to the contrary, the q.computing fervor is nearing its end.
   That's because a few decades is the maximum lifetime of any big bubble in
   technology or science. ...   should still heed an admonition that IBM
   physicist Rolf Landauer made decades ago ... 'This scheme, like all other
   schemes for q.computation, relies on speculative technology, does not in its
   current form take into account all possible sources of noise, unreliability
   & manufacturing error, & probably will not work.'"  [!]
   -- [<A HREF="https://spectrum.ieee.org/computing/hardware/the-case-against-quantum-computing">www</A>]['18].
   (?Actually an anti-prediction?i, but worth checking in 2023 [inconclusive],
   2028 & 2033 say?
   MD is well known for, e.g.,
   Dyakonov surface waves@[<A HREf="https://en.wikipedia.org/wiki/Dyakonov_surface_waves">wikip</A>]['18].)
   [Also search for: zzPrediction]  and  [also search for: quantum computer].

%A C. Candia
%A C. Jara-Figueroa
%A C. Rodriguez-Sickert
%A A.-L. Barabasi
%A C. A. Hidalgo
%T The universal decay of collective memory and attention
%J Nature Human Behaviour
%V ?
%P ?-?
%M DEC
%D 2018
%K jrnl, c2018, c201x, c20xx, zz1218, human behaviour, collective memory,
   influence, culture, universal biexponential, distribution, publications,
   papers, citations
%X "Collective memory & attention are sustained by two channels: oral
   communication (communicative memory) & the physical recording of information
   (cultural memory). Here, we use data on the citation of academic articles &
   patents, & on the online attention received by songs, movies & biographies,
   to describe the temporal decay of the attention received by cultural
   products. ... the attention received by cultural products decays following a
   universal biexponential function. ... biographies remain in our communicative
   memory the longest (20-30y.) & music the shortest (~5.6y.). ... show
   that the avg. attention received by cultural products decays following a
   universal biexponential fn."
   -- [<A HREF="https://doi.org/10.1038/s41562-018-0474-5">doi:10.1038/s41562-018-0474-5</A>]['18].

%T Classical and quantum computers are vying for superiority
%J Nature
%V 564
%P 302
%M DEC
%D 2018
%K news, views, editorial, c2018, c201x, c20xx, zz0119, quantum computing,
   classical, computer, algorithm, recommender systems, linear, rival, Ewin Tang
%X Editorial, "... Is a quantum computer even needed? High-profile work by an
   18-year-old computer scientist earlier this year suggests not, at least for
   one specific task. Ewin Tang effectively taught an old computer a new trick
   - one that was previously thought to need a quantum system.  She developed an
   extremely efficient classical alg. - that is, one that can run on an ordinary
   computer - for 'recommendation systems' ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-018-07801-3">doi:10.1038/d41586-018-07801-3</A>]['18], online 18/12/2018.
   See, E.Tang, 'A quantum-inspired classical algorithm for
        recommendation systems', 10 July 2018,
        1807.04271@[<A HREF="https://arxiv.org/abs/1807.04271">arXiv</A>]['19].
   [Also search for: quantum computer] or [also search for: quantum computing].

%A M. Bentert
%A p. Skowron
%T Comparing election methods where each voter ranks only few candidates
%J arXiv
%M JAN
%D 2019
%K TR, c2019, c201x, c20xx, zz0219, election, vote, voting, system, preference,
   preferential, Borda, politics, ranking, rankings
%X "... We ask how well certain election rules (focusing on positional scoring
   rules & the Minimax rule) can be approximated from partial preferences
   collected through one of the following procedures: (i) randomized - we ask
   each voter to rank a random subset of L candidates, & (ii) deterministic - we
   ask each voter to provide a ranking of her L most preferred candidates (the
   L-truncated ballot). We establish theoretical bounds on the approximation
   ratios & we complement our theoretical analysis with computer simulations. We
   find that mostly (apart from the cases when the preferences have no or very
   little structure) it is better to use the randomized approach. While we
   obtain fairly good approximation guarantees for the Borda rule already for
   L=2, for approximating the Minimax rule one needs to ask each voter to
   compare a larger set of candidates in order to obtain good guarantees."
   -- 1901.10848@[<A HREF="https://arxiv.org/abs/1901.10848">arXiv</A>]['19].

%A P. Davies
%T The Demon in the Machine: How Hidden Webs of Information are
   Finally Solving the Mystery of Life
%I AllenLane
%P 320
%M SEP
%D 2018
%K book, text, c2018, c201x, c20xx, zz0219, life, definition, information,
   entropy
%X 1st ed 2018, hb us$17; uk us isbn:024130959X; uk us isbn13:978-0241309599.
   "... proposes a radical vision of biology which sees the underpinnings of
   life as similar to circuits and electronics, arguing that life as we know it
   should really be considered a phenomenon of information storage. ..."
   [Also search for: life definition].

%A K. Devlin
%T Turned On: Science, Sex and Robots
%I BloomsburySigma
%P 288
%M DEC
%D 2018
%K book, c2018, c201x, c20xx, zz0719, AI, sex, robot, robots, sexbot, android,
   humanoid, human, society
%X 1st ed 2018; hb us$23; uk us isbn:1472950895; uk us sibn13:978-1472950895.
   "The idea of the seductive sex robot is the stuff of myth, legend and science
   fiction. From the ancient Greeks to twenty-first century movies ... Sex
   robots are here, and here to stay--and more are coming ..."
   [Also search for: sex robot].

%A P. Azouly
%T Small research teams 'disrupt' science more radically than large ones
%J Nature
%V 566
%N 7743
%P ?
%M FEB
%D 2019
%K news, views, c2019, c201x, c20xx, zz0219, scientific research, progress,
   teams, paper, papers, citation, impact, KPI, KPIs, small, research grant,
   grants, ARC, NIH, publish, perish, Wu, Wang, Evans
%X "The application of a new citation metric prompts a reassessment of the
   relationship between the size of scientific teams and research impact, &
   calls into question the trend to emphasize 'big team' science. ...
   Citation behaviour can also reflect strategic considerations, such as
   currying favour with referees or editor ... Wu and colleagues ... describe &
   validate a citation-based index of 'disruptiveness' that has previously been
   proposed for patents. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-019-00350-3">doi:10.1038/d41586-019-00350-3</A>]['19].
   [Also search for: scientific progress].

%A L. Wu
%A D. Wang
%A J. A. Evans
%T Large teams develop and small teams disrupt science and technology
%J Nature
%V 566
%N ?
%P 378-382
%M FEB
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0219, scientific research, progress, team,
   paper, papers, citation, impact, KPI, KPIs, small, research grant, grants,
   ARC, NIH, disruption, disruptive, new, idea, ideas, creativity, Hindex,
   Sleeping Beauty, SBindex, Web of Science, WOS, software, patent,
   publish, perish
%X "... [trend] today is the growth of large teams in all areas ...
   Here we analyse more than 65 million papers, patents & s/w products that span
   the period 1954-2014, & demonstrate that across this period smaller teams
   have tended to disrupt sci. & tech. with new ideas & opportunities, whereas
   larger teams have tended to develop existing ones. ... Observed differences
   between small & large teams are magnified for higher-impact work, with small
   teams known for disruptive work & large teams for developing work. ...
   science policies should aim to support a diversity of team sizes."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-0941-9">doi:10.1038/s41586-019-0941-9</A>][13/2/'19],
      [<A HREF="https://www.nature.com/articles/s41586-019-0941-9">www</A>]['19].
   [Also search for: scientific progress] and [also search for: publish perish].

%A R. Connell
%T The Good University. What universities actually do and why it's time for
   radical change
%I MonashUP
%P 240
%M FEB
%D 2019
%K book, text, c2019, c201x, c20xx, zz0519, university, management, KPI, KPIs,
   rankings, league tables, ERA, quality, higher education, neoliberal,
   Reaganomics, faculty, teaching, research, ethics, administration,
   Monash, MUP, Australia
%X 1st ed 2019; hb us uk isbn:1786995417; uk us isbn13:978-1786995414;
                pb au$30; isbn13:978-1925835038.
   "The higher ed. industry might seem like it's booming, with over 200 million
   students in universities & colleges worldwide & funds flowing in like never
   before. But the truth is that these institutions have never been unhappier
   places to work. Corporate-style management, cost-cutting governments,
   mobilisations by angry students & strikes by disgruntled staff have all taken
   their toll - in almost every country around the world. It's no wonder that
   there is talk of 'universities in crisis.' ... outlines a practical vision
   for how our unis. can become both more engaging & more productive places,
   driven by social good rather than profit, & helping to build fairer
   societies."
   [Also search for: university management].

%A R. Garwood
%A A. R. T. Spencer
%A M. D. Sutton
%T REvoSim: Organism-level simulation of macro and microevolution
%J Palaeontology
%V 62
%N 3
%P 339-355
%M FEB
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0724, REvoSim, digital organism, evolution,
   Alife
%X "... we present & document a novel model called REvoSim (Rapid Evolutionary
   Simulator) coupled with a s/w implementation of this model. ... can simulate
   pop'ns of 105-107 digital organisms over geological timescales on a typical
   desktop computer, & incorporates spatial & temporal environmental variation,
   recombinant reproduction, mutation & dispersal. ..."
   -- [<A HREF="https://doi.org/10.1111/pala.12420">doi:10.1111/pala.12420</A>]['24].
   Also see digOrg@[<A HREF="https://en.wikipedia.org/wiki/Digital_organism">wikip</A>]['24].
   [Also search for: Alife]  and  [also search for: Alife organism].

%A O. Chang
%A H. Lipson
%T Seven myths in machine learning research
%J arXiv
%M FEB
%D 2019
%K TR, views, c2019, c201x, c20xx, zz0219, AI, risks, stats, myth, myths,
   reproducibility, deep, tensorflow, NN, ANN, image, images, validation,
   training, test, testing
%X "We present seven myths commonly believed to be true in machine learning
   research, circa Feb 2019. This is an archival copy of the blog postat
[crazyoscarchang.github.io/2019/02/16/seven-myths-in-machine-learning-research/]
   Myth 1: TensorFlow is a Tensor manipulation library ...
   Myth 2: Image datasets are representative of real images found in the wild
   Myth 3: Machine Learning researchers do not use the test set for validation
   Myth 4: Every datapoint is used in training a neural network
   Myth 5: We need (batch) normalization to train very deep residual networks
   Myth 6: Attention > Convolution
   Myth 7: Saliency maps are robust ways to interpret neural networks
   -- 1902.06789@[<A HREF="https://arxiv.org/abs/1902.06789">arXiv</A>]['19].
   [Also search for: NN ANN reproducibility].

%A H. Childress
%T The Adjunct Underclass: How America's Colleges Betrayed Their Faculty,
   Their Students, and Their Mission
%I UChicagoPress
%P 208
%M APR
%D 2019
%K book, text, c2019, c20x, c20xx, zz0419, university, academia, job, jobs,
   management, exploitation, prof, professor, dean, deans, deanitis, pay,
   tenure, part-time, teaching, higher education, college, gig economy, USA,
   casual, casualisation
%X 1st ed 2019; hb us$16; uk us isbn:022649666X; uk us isbn13:978-0226496665.
   "... Over the past few decades, the job of college professor has been utterly
   transformed - for the worse. America's colleges & unis. were designed to
   serve students & create knowledge through the teaching, research, & stability
   that come with the longevity of tenured faculty, but higher ed. today is
   dominated by adjuncts. In 1975, only 30% of faculty held temporary or
   part-time posns. By 2011, as unis. faced both a decrease in public support
   & ballooning admin. costs(!), that # topped 50%. Now, some surveys suggest
   that as many as 70% of American professors are working course-to-course, with
   few benefits, little to no security, & extremely low pay. ..."
   [Also search for: University management].

%A H. Else
%T Impact factors are still widely used in academic evaluations
%J Nature
%V ?
%N ?
%M APR
%D 2019
%K news, vews, c2019, c201x, c20xx, zz0419, impact, KPI, KPIs, JIF, DORA,
   journal, university, culture, promotion, hire, hiring, job, jobs, employment,
   management, research, USA
%X "Almost half [~40%] of research-intensive universities consider jrnl impact
   factors when deciding whom to promote, a survey of North American
   institutions has found. ... has been widely criticized as a crude and
   misleading proxy for the quality of scientists' work. ... unhealthy research
   culture ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-019-01151-4">doi:10.1038/d41586-019-01151-4</A>]['19].
   (Also see [<A HREF="https://doi.org/10.1038/d41586-018-01642-w">doi:10.1038/d41586-018-01642-w</A>][2/2019].)
   Probably .uk and .au are much the same as .us?
   [Also search for: university management].

%A A. Finkel
%T To move research from quantity to quality, go beyond good intentions
%J Nature
%V 566
%N 566
%P 297
%M APR
%D 2019
%K news, views, c2019, c201x, c20xx, zz0419, university, management, faculty,
   KPI, KPIs, science, scientific research, Hindex, gIndex, KPI, KPIs, publish,
   perish, publications, papers, journals, JIF, SNIP, citations, bibliometrics,
   audit culture, misuse, impact, quality, ERA, ARC, Australia, chief scientist,
   quote, quotable, Monash, Australia, topN, top5
%X "... Next, institutions must heed growing calls to abandon paper counting and
   similar metrics for evaluating researchers. One alternative approach, the
   Rule of Five, demonstrates a clear commitment to quality: candidates present
   their best five papers over the past five years, accompanied by a description
   of the research, its impact and their individual contribution. The exact
   numbers are immaterial: what matters is the focus on quality. A handful of
   institutions have required reviewers to consider individual contributions
   rather than lists of publications, and the shift has not been easy. Reviewers
   should be admonished for Googling individuals' h-indices and citation lists,
   for example. Perseverance and self-reflection are essential. ..."
   -- [<A HREF="https://www.nature.com/articles/d41586-019-00613-z">doi:10.1038/d41586-019-00613-z</A>]['19].
   (Alan Finkel is Australian chief scientist and was
   Chancellor of Monash University 2008-2016.)
   [Also search for: publish perish] & [also search for: university management].

%T Heath Robinson: WW2 codebreaking machine reconstructed
%I BBC
%M APR
%D 2019
%K news, c2019, c201x, c20xx, zz0519, Heath Robinson, 1943, WW2, WWII,
   code breaker, cracking, automation, history, computing, Bletchley Park
%X "A WW2 codebreaking machine has been reconstructed after a seven-year project
   ... The machine was an early attempt to automate code-cracking &, due to its
   complexity, was named after the illustrator W. Heath Robinson. ... The m/c
   which went into operation at BP in June 1943, is acknowledged as the
   inspiration for Colossus, the world's first programmable computer. ..."
   -- bbc[<A HREF="https://www.bbc.com/news/uk-england-beds-bucks-herts-47813994">6/4/2019</A>].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">B.Park</A>].)
   [Also search for: Bletchley Park].

%T Springer Nature journals unify their policy to encourage preprint sharing
%A editor
%J Nature
%V ?
%P ?-?
%M MAY
%D 2019
%K news, views, c2019, c201x, c20xx, zz0519, scientific research,
   publishing, preprint, preprints, server, arXiv, Springer, Nature,
   journal, policy, journals, plan S planS
%X "For more than two decades, Nature and its sister journals have supported
   pre-publication sharing of manuscripts on preprint servers ... we now make it
   clear that authors may choose any licence for preprints, including Creative
   Commons licences. Licensing choice will not impede consideration at a
   Springer Nature journal, but authors should bear in mind that it could affect
   sharing, adaptation and reuse of the preprint itself."
   -- [<A HREF="https://dx.doi.org/10.1038/d41586-019-01493-z">doi:10.1038/d41586-019-01493-z</A>]['19].
   (Also see, 'Facing Plan S, publishers may set papers free'
   -- Science [<A HREF="https://dx.doi.org/10.1126/science.364.6441.620">doi:10.1126/science.364.6441.620</A>][17/5/2019].)

%A O. E. Williams
%A L. Lacasa
%A V. Latora
%T Quantifying and predicting success in show business
%J NatureComms
%V 10
%N 2256
%M JUN
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0619, showbiz, actor, actors, acting, arts,
   career, job, peak, impact, movie, movies, imdb, films, rich-get-richer,
   hot hands, Matthew effect, stats
%X "In certain artistic endeavours - such as acting in films & TV, where
   unemployment rates hover at around 90% - sustained productivity (simply
   making a living) is probably a better proxy for quantifying success than high
   impact. Drawing on a worldwide database, here we study the temporal profiles
   of activity of actors & actresses. We show that the dynamics of job
   assignment is well described by a 'rich-get-richer' mechanism & we find that,
   while the percentage of a career spent active is unpredictable, such activity
   is clustered. Moreover, productivity tends to be higher towards the beginning
   of a career & there are signals preceding the most productive year.
   Accordingly, we propose a machine learning method which predicts with 85%
   accuracy whether this 'annus mirabilis' has passed, or if better days are
   still to come. We analyse actors & actresses separately, also providing
   compelling evidence of gender bias in show business."
   -- [<A HREF="https://doi.org/10.1038/s41467-019-10213-0">doi:10.1038/s41467-019-10213-0</A>]['19].
   (Also see the abc[<A HREF="https://www.abc.net.au/news/science/2019-06-05/maths-can-predict-if-a-movie-actors-career-is-peaking/11178374">5/6/2019</A>].)

%A R. Giblin
%A J. Kennedy
%A C. Pelletier
%A J. Thomas
%A K. G. Weatherall
%A F. Petitjean
%T What can 100,000 books tell us about the international public library
   e-lending landscape?
%J Inf. Res.
%V 24
%N 3
%M MAR
%D 2019
%O Sydney Law School, Res. Paper #19/21
%K eBook, eBooks, books, c2019, c201x, c20xx, zz0420, public library, libraries,
   lending, eLending, access, availability, licence, price, cost,
   Au, NZ, UK, USA, Canada
%X "We investigated the relative availability of e-books to libraries for
   e-lending in five English-language countries, and analysed their licence
   terms and prices. ..."
   -- [<A HREF="https://ssrn.com/abstract=3354215">www</A>]['20].
   Also see [<A HREF="http://elendingproject.org/">elendingproject</A>]['20].
   [Also search for: eBooks public access].

%A S. B. Kaufman
%A D. B. Yaden
%A E. Hyde
%A E. Tsukayama
%T The light vs. dark triad of personality: Contrasting two very different
   profiles of human nature
%J Front. Psychol.
%V ?
%M MAR
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0519, psychology, human beahaviour, good, evil,
   people, Kantianism, Humanism, Humanity, goodness, agreeable, HEXACO,
   honesty humility
%X "... we contrasted the nomological network of the Dark Triad (a well-studied
   cluster of socially aversive traits) with the nomological network of the
   Light Triad, measured by the 12-item Light Triad Scale (LTS). The LTS is a
   first draft measure of a loving and beneficent orientation toward others
   ('everyday saints') that consists of three facets: Kantianism (treating
   people as ends unto themselves), Humanism (valuing the dignity and worth of
   each individual), and Faith in Humanity (believing in the fundamental
   goodness of humans). ..."
   -- [<A HREF="https://doi.org/10.3389/fpsyg.2019.00467">doi:10.3389/fpsyg.2019.00467</A>]['19].
   (Also see the bbc[<A HREF="https://www.abc.net.au/news/science/2019-05-16/psychopaths-narcissm-the-dark-triad-fascinate-us-the-light-triad/11093104">16/5/2019</A>].)

%A H. Else
%T What universities can learn from one of science's biggest frauds
%J Nature
%V ?
%M JUN
%D 201910.1038/d41586-019-01884-2
%K views, c2019, c201x, c20xx, zz0619, fraud, academic, university,
   scientific research, misconduct, scandal, plagiarism, investigation, Sato,
   Kurume University, Hirosaki
%X "Detailed analysis of misconduct investigations into huge research fraud
   suggests institutional probes aren't rigorous enough. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-019-01884-2">doi:10.1038/d41586-019-01884-2</A>]['19].
   [Also search for: academic misconduct].

%A N. Brown
%A T. Sandholm
%T Superhuman AI for multiplayer poker
%J Science
%V ?
%P eaay2400
%M JUL
%D 2019
%K c2019, c201x, c20xx, zz0719, AI, poker, six player no limit Texas hold'em,
   poker, holdem, professional, Pluribus, card game, cards, games
%X "... present Pluribus, an AI that we show is stronger than top human
   professionals in six-player no-limit Texas hold'em poker, the most popular
   form of poker played by humans."
   -- [<A HREF="https://doi.org/10.1126/science.aay2400">doi:10.1126/science.aay2400</A>]['19].

%A E. Musk
%T An integrated brain-machine interface platform with thousands of channels
%J bioRxiv
%M JUL
%D 2019
%K TR, c2019, c201x, c20xx, zz0719, brain, machine, interface, implant,
   electrode, channel, control, Elon Musk, Neuralink, cyborg, borg, BMI, BMIs
%X "... We have built arrays of small & flexible electrode 'threads', with as
   many as 3,072 electrodes per array distributed across 96 threads. We have
   also built a neurosurgical robot capable of inserting six threads (192
   electrodes) per minute. Each thread can be individually inserted into the
   brain with micron precision for avoidance of surface vasculature & targeting
   specific brain regions. The electrode array is packaged into a small
   implantable device that contains custom chips for low-power on-board
   amplification & digitization: the package for 3,072 channels occupies less
   than (23 x 18.5 x 2) mm3. A single USB-C cable provides full-bandwidth data
   streaming from the device, recording from all channels simultaneously. This
   system has achieved a spiking yield of up to 85.5% in chronically implanted
   electrodes. ..."
   -- 10.1101/703801v2@[<A HREF="https://www.biorxiv.org/content/10.1101/703801v2">bio'xiv</A>]['19].
   (Also see neuralink[<A HREF="https://www.neuralink.com/">www</A>]['19].)

%A Z. Corbyn
%T Margaret Hamilton: "They worried that the men might rebel. They didn't"
%J The Guardian
%M JUL
%D 2019
%K news, c2019, c201x, c20xx, zz0719, grauniad, computer science, Apollo 11,
   NASA, moon landing, 1969, software, Margaret Hamilton, woman, women, science,
   STEM, web, www, HREF
%X "Computer pioneer Margaret Hamilton was critical to landing astronauts on
   the moon for the first time on 20 July 1969 and returning them safely a few
   days later. The young Massachusetts Institute of Technology (MIT) computer
   programmer and working mother led the team that created the onboard flight
   software for the Apollo missions, including Apollo 11. ..."
   -- [<A HREF="https://www.theguardian.com/technology/2019/jul/13/margaret-hamilton-computer-scientist-interview-software-apollo-missions-1969-moon-landing-nasa-women">13/7/2019</A>].
   [Also search for: women science STEM].

%A M. Dillon
%T University of Adelaide to run probe into 'culture' at world-class
   ancient DNA lab
%J ABC
%M JUL
%D 2019
%K news, views, c2019, c201x, c20xx, zz0719, university, Adelaide, Australia,
   Australian, research, ACAD, Ancient DNA, academia, scientific research,
   university management, scientific, culture, toxic, KPI, KPIs
%X '... The university confirmed it was undertaking a "culture check" at the
   Australian Centre for Ancient DNA (ACAD) ... described the culture at ACAD
   as "cut-throat", "competitive" and "everyone was in it for themselves". ...
   "We all developed health problems, I developed really debilitating stomach
   problems that would floor me anything from a week to a month," ...'
   -- [<A HREF="https://www.abc.net.au/news/2019-07-12/culture-check-at-australian-centre-for-ancient-dna/11294652">abc</A>][12/7/2019].

%A P. Schwardmann
%A J. van der Weele
%T Deception and self-deception
%J Nature Human Behaviour
%V ?
%P ?-?
%M JUL
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0919, Trivers, von Hippel, vonHippel,
   human behaviour, psychology, self deception, over confidence, overconfidence,
   confident, skill, ability, deceit, persuasion, Trivers
%X "There is ample evidence that the average person thinks he or she is more
   skilful, more beautiful and kinder than others and that such overconfidence
   may result in substantial personal and social costs. ... [A] theory, first
   advanced by evolutionary biologist Robert Trivers, posits that people
   self-deceive into higher confidence to more effectively persuade or deceive
   others. Here we conduct two experiments (combined n=688) to test this
   strategic self-deception hypothesis. ... Overconfidence emerges from these
   results as the product of an adaptive cognitive technology with important
   social benefits, rather than some deficiency or bias."
   -- [<A HREF="https://doi.org/10.1038/s41562-019-0666-7">doi:10.1038/s41562-019-0666-7</A>]['19].
   (Also see the [<A HREF="https://www.abc.net.au/news/science/2019-07-30/overconfidence-study-help-hindrance/11365430">bbc</A>][30/7/2019].)

%A N. Persily
%T Math on trial
%J Science
%V 365
%N 6453
%P 523
%M AUG
%D 2019
%K news, views, c2019, c201x, c20xx, zz0819, USA, America, politics,
   gerrymander, elections, fairness
%X "Can science help take the partisanship out of politics? To some extent, that
   was the question the U.S. Supreme Court confronted in this year's blockbuster
   partisan gerrymandering case. The Court answered 'no' and, by doing so,
   delivered an object lesson in the limits of math and science to settle the
   most political of constitutional questions. ..."
   -- [<A HREF="https://doi.org/10.1126/science.aay9836">doi:10.1126/science.aay9836</A>]['19].
   [Also search for: gerrymander].

%A J. P. A. Ioannidis
%A J. Baas
%A R. Klavans
%A K. W. Boyack
%T A standardized citation metrics author database annotated for
   scientific field
%J PLoS Biology
%V 17
%N 8
%P e3000384
%M AUG
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz0919, publish, perish, impact, KPI, KPIs,
   scientific, university, academic, research, management, modified,
   bibliometrics, scientist, authorship, modified, Hindex, misuse, hmIndex,
   hm-index, citations, multiple authors, author, trends
%X "Citation metrics are widely used & misused. We have created a publicly
   available database of 100,000 top scientists that provides standardized
   info. on citations, h-index, coauthorship-adjusted hm-index, citations to
   papers in different authorship positions, & a composite indicator. Separate
   data are shown for career-long & single-year impact. Metrics with & without
   self-citations & ratio of citations to citing papers are given. Scientists
   are classified into 22 scientific fields & 176 subfields. Field- &
   subfield-specific percentiles are also provided for all scientists who have
   published at least five papers. Career-long data are updated to end of 2017
   & to end of 2018 for comparison."
   -- [<A HREF="https://doi.org/10.1371/journal.pbio.3000384">doi:10.1371/journal.pbio.3000384</A>]['19], via AK.
   data@[<A HREF="https://data.mendeley.com/datasets/btchxktzyw/1">www</A>]['19].
   auth1@[<A HREF="http://orcid.org/0000-0003-3118-6859">orcid</A>]['19].
   [Also search for: hmIndex]  and  [also search for: publish perish].

%A K. Haustein
%A et al ...
%A A. P. Schurer
%T A limited role for unforced internal variability in twentieth-century warming
%J J. of Climate
%V 32
%N 16
%M AUG
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0120, 20C, climate, variability, surface, ocean,
   temperature, warming, global, change, external forcing, CO2, anthropogenic,
   meteorology, world, extreme weather attribution, WWA, probability,
   model, cause, causality
%X "The early 20C warming (EW; 1910-45) & the mid20C cooling (MC; 1950-80) have
   been linked to both internal variability of the climate system & changes in
   external radiative forcing. The degree to which either of the two factors
   contributed to EW & MC, or both, is still debated. Using a two-box impulse
   response model, we demonstrate that multidecadal ocean variability was
   unlikely to be the driver of observed changes in global mean surface temp.
   (GMST) after AD1850. Instead, virtually all (97%-98%) of the global low-freq.
   variability (> 30 years) can be explained by external forcing. We find
   similarly high % of explained variance for interhemispheric & land-ocean
   temp. evolution. Three key aspects are identified that underpin the
   conclusion of this new study: inhomogeneous anthropogenic aerosol forcing
   (AER), biases in the instrumental sea surface temperature (SST) datasets, &
   inadequate representation of the response to varying forcing factors. Once
   the spatially heterogeneous nature of AER is accounted for, the MC period is
   reconcilable with external drivers. SST biases & imprecise forcing responses
   explain the putative disagreement between models & observations during the
   EW period. As a consequence, Atlantic multidecadal variability (AMV) is found
   to be primarily controlled by external forcing too. ..."
   -- [<A HREF="https://doi.org/10.1175/JCLI-D-18-0555.1">doi:10.1175/JCLI-D-18-0555.1</A>]['19].
   [Also search for: weather attribution].
   (Also see world weather attribution [<A HREF="https://www.worldweatherattribution.org/">www</A>][1/2020].)

%A A. J. Stewart
%A M. Mosleh
%A M. Diakonova
%A A. A. Arechar
%A D. G. Rand
%A J. B. Plotkin
%T Information gerrymandering and undemocratic decisions
%J Nature
%V 573
%P 117-121
%M SEP
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0919, politics, voting, election, gerrymander,
   social media, USA, presidential, president, potus, Trump, zzTrump, brexit,
   democracy, vote, votes, influence
%X "... we develop a voter game as a model system to study information flow in
   collective decisions. Players are assigned to competing groups (parties) &
   placed on an 'influence network' that determines whose voting intentions each
   player can observe. Players are incentivized to vote according to partisan
   interest, but also to coordinate their vote with the entire group. Our
   mathematical analysis uncovers a phenomenon that we call information
   gerrymandering: the structure of the influence network can sway the vote
   outcome towards one party, even when both parties have equal sizes & each
   player has the same influence. A small number of zealots, when strategically
   placed on the influence network, can also induce information gerrymandering &
   thereby bias vote outcomes. We confirm the predicted effects of information
   gerrymandering in social network experiments with n=2,520 human subjects.
   Furthermore, we identify extensive information gerrymandering in real-world
   influence networks, including online political discussions leading up to the
   US federal elections, & in historical patterns of bill co-sponsorship in the
   US Congress & European legislatures. ... also highlights a group-level social
   dilemma: information gerrymandering can enable one party to sway decisions in
   its favour, but when multiple parties engage in gerrymandering the group
   loses its ability to reach consensus & remains trapped in deadlock."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-1507-6">doi:10.1038/s41586-019-1507-6</A>]['19].

%A R. Giblin
%A J. Kennedy
%A K. Weatherall
%A D. Gilbert
%A J. Thomas
%A F. Petitjean
%T Available, but not accessible? Investigating publishers' e-lending licensing
   practices
%J Inf. Res.
%V 24
%N 3
%O paper 837
%M SEP
%D 2019
%K paper837, public library, libraries, c2019, c201x, c20xx, zz0420, eBook,
   eBooks, books, access, accessibilty, availability, literature, aggregator,
   publisher, publishing, copyright, licence, price, cost, Rakuten OverDrive,
   eLending, loans, borrowing, Au, NZ, UK, USA, Canada
%X "We report our mixed-methods investigation of publishers' licensing
   practices, which affect the books public libraries can offer for e-lending.
   ... sampled titles offered by e-book aggregators to public libraries across
   Australia, New Zealand, Canada, the United States and United Kingdom. ...
   licence terms and price ... While availability was better than anticipated,
   licensing practices make it infeasible for libraries to purchase certain
   kinds of e-book, particularly older titles. Confidentiality requirements make
   it difficult for libraries to shop (and aggregators to compete) on price and
   terms."
   -- [<A HREF="http://InformationR.net/ir/24-3/paper837.html">www</A>]['20],
      [<A HREF="https://web.archive.org/web/20190829181741/http://www.informationr.net/ir/24-3/paper837.html">www</A>]['20].
   Also see [<A HREF="http://elendingproject.org/">elendingproject</A>]['20].
   [Also search for: open access research].

%A D. S. Chawala
%T Elsevier investigates hundreds of peer reviewers for manipulating citations
%J Nature
%V 573
%P 174
%M SEP
%D 2019
%K news, views, c2019, c201x, c20xx, zz0919, publish, perish, review,
   citations, coercive citation, Hindex, ethics, cheat, fraud, peer review,
   citation abuse, misuse, Kuo-Chen Chou, KCChou, KuoChenChou, corrupt, scam,
   referee, gaming, refereeing, academic, research, misconduct, manipulation,
   papers, Baas, Fennel, Elsevier
%X "... The publisher is looking into the possibility that some peer reviewers
   are encouraging the authors of work under review to cite the reviewers' own
   research in exchange for positive reviews - a frowned-on[!] practice broadly
   termed coercive citation. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-019-02639-9">doi:10.1038/d41586-019-02639-9</A>]['19].
   (See,  Baas and Fennel, 'When Peer Reviewers Go Rogue - Estimated
    Prevalence of Citation Manipulation by Reviewers Based on the
    Citation Patterns of 69,000 Reviewers', May 2019,
    -- [<A HREF="https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3339568">www</A>]['19].)
   [Also search for: peer review]  and  [also search for: Hindex abuse].

%A C. A. Chapman
%A et al
%T Games academics play and their consequences: How authorship, h-index and
   journal impact factors are shaping the future of academia
%J Proc. Royal Soc. B: Biol. Scis.
%V 286
%N 1916
%P #20192047
%M SEP
%D 2019
%K jrnl, c2019, c201x, c20xx, zz1020, journals, JIF, DORA, impact, gaming, scam,
   academia, faculty, research, quality, university management, peer review,
   ARC, ERA, NSERC, citation cartel, KPI, KPIs, Hindex, publications,
   authorship, gamed, gaming, abuse, ethics, zzEthics
%X "... We first examine how authorship, h-index of individuals & [JIF] factors
   are being used & abused. Second, we speculate on the consequences of the
   continued use of these metrics with the hope of sparking discussions that
   will help our fields move in a +ve dir'n. We would like to see changes in the
   incentive systems, rewarding quality research & guaranteeing transparency.
   Senior faculty should establish the ethical stds, mentoring practices &
   institutional evaluation criteria to create the needed changes."
   -- [<A HREF="http://dx.doi.org/10.1098/rspb.2019.2047">doi:10.1098/rspb.2019.2047</A>]['20].
   [Also search for: university management].

%A T. Tao
%T Almost all orbits of the Collatz map attain almost bounded values
%J arXiv
%M SEP
%D 2019
%K TR, c2019, c201x, c20xx, zz0821, Collatz, problem, Syracuse iteration, 3X+1,
   3Xplus1, 3Nplus1, Tao, Terras, Korec
%X "... Our proof proceeds by establishing an approx. transport property for a
   certain 1st passage random var. assoc. with the Collatz iteration (or more
   precisely, the closely related Syracuse iteration), which in turn follows
   from estimation of the characteristic fn of a certain skew random walk on a
   3-adic cyclic group at high frequs.. This estimation is achieved by studying
   how a certain two-dimensional renewal process interacts with a union of
   triangles assoc. to a given freq.."
   -- 1909.03562@[<A HREF="https://arxiv.org/abs/1909.03562">arXiv</A>]['21].
   Also see CP@[<A HREF="https://en.wikipedia.org/wiki/Collatz_conjecture">wikip</A>]['21].
   [Also search for: Collatz problem].

%A J. Bardin
%A et al ...
%A C. M. Gidney
%T A 28nm bulk-CMOS 4-to-8GHz < 2mW cryogenic pulse modulator for
   scalable quantum computing
%J Proc. 2019 Int. Solid State Circuits Conf.
%A IEEE
%P 456-458
%D 2019
%K conf, c2019, c201x, c20xx, zz1019, google, quantum, computer, computing,
   qubit, qubits
%X "Future q.c. systems will require cryogenic integrated circuits to control
   & measure millions of qubits. ... we report design & measurement of a
   prototype cryogenic CMOS integrated circuit that has been optimized for the
   control of transmon qubits. The circuit has been integrated into a q.
   measurement setup & its performance has been validated through multiple
   quantum control experiments."
   -- pub47965@[<A HREF="https://ai.google/research/pubs/pub47965">g'gle</A>]['19].
   [Also search for: quantum computing].

%T A kinder research culture is possible
%J Nature
%M OCT
%D 2019
%K news, views, c2019, c201x, c20xx, zz1019, scientific, university, research,
   KPI, KPIs, quality, excellence, management, culture, ARC, grants, ERA,
   Farrar, Welcome Trust, biol, biology
%X "Wellcome's director Jeremy Farrar didn't hold back. 'The emphasis on
   excellence in the research system is stifling diverse thinking and positive
   behaviours,' he wrote in a blog post last month. 'The relentless drive for
   research excellence has created a culture in modern science that cares
   exclusively about what is achieved and not about how it is achieved.' These
   are strong words, not least because Farrar acknowledges that the UK
   biomedical funding charity that he leads helped to create such a focus on
   excellence. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-019-02951-4">doi:10.1038/d41586-019-02951-4</A>]['19].
   [Also search for: scientific research management].

%A F. Arute
%A et al ...
%A J. M. Martinis
%T Quantum supremacy using a programmable superconducting processor
%J Nature
%V 574
%P 505-510
%M OCT
%D 2019
%K jrnl, c2019, c201x, c20xx, zz1019, quantum computer, quantumComputer,
   computing, google, Sycamore, 53 qubits, controversial, claim, IBM Summit,
%X "...  we report the use of a processor with programmable superconducting
   qubits to create q.states on 53 qubits, corr. to a computational state-space
   of dimension 253 (~10^16). Measurements from repeated experiments sample the
   resulting prob. distn, which we verify using classical simulations. Our
   Sycamore processor takes about 200 seconds to sample one instance of a
   q.circuit a million times - our benchmarks currently indicate that the
   equivalent task for a state-of-the-art classical supercomputer would take
   ~10,000 years. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-1666-5">doi:10.1038/s41586-019-1666-5</A>]['19].
   Interesting, but not yet useful.
   (Also see the bbc[<A HREF=" https://www.bbc.com/news/science-environment-50154993">23/10/2019</A>], and
   1910.09534@[<A HREF="https://arxiv.org/abs/1910.09534">arXiv</A>][21/10/19]
   [<A HREF="https://www.ibm.com/blogs/research/2019/10/on-quantum-supremacy/">ibm</A>][21/10/2019].)

%T The Chinese Government co-funded at least four University of Queensland
   courses
%I ABC
%M OCT
%D 2019
%K c2019, c201x, c20xx, zz1119, news, views, Australia, Australian, University,
   UQ, Universities, China, Chinese, CCP, Government, Taiwan, Tibet,
   fund, funding, influence, human rights, terrorism, concerns, controversial,
   Confucious Institute, course, soft power, politics
%X "The Chinese Government has co-funded at least four courses at the
   University of Queensland (UQ), including one on China's role in
   'strengthening' responses to 'global security challenges', such as
   human rights, 'mass atrocities prevention' and 'counter-terrorism'. ..."
   -- [<A HREF="https://www.abc.net.au/news/2019-10-15/chinese-government-cofunded-four-university-of-queensland-course/11601946">15/10/2019</A>]['19].
   [Also search for: Chinese Government].

%T Are Australian universities putting our national security at risk by
   working with China?
%I ABC
%M OCT
%D 2019
%K news, views, c2019, c201x, c20xx, zz1119, Australia, Australian, University,
   Universities, China, Chinese, CCP, Government, state, human rights,
   social credit, great firewall, police, surveillance,facial recognition,
   Global Tone Communication (GTCOM), UNSW, UTS, DFAT, ASIO
%X "Australia's top universities could be aiding the Chinese Communist Party's
   mission to develop mass surveillance and military technologies, amid rising
   concerns from Australian intelligence agencies that they are putting national
   security at risk. ..."
   -- [<A HREF="https://www.abc.net.au/news/2019-10-14/chinese-communist-party-gtcom-connection-australian-universities/11586118">4/11/2019</A>]['19].
   [Also search for: Chinese Government].

%A C. Woolston
%T PhDs: the tortuous truth
%J Nature
%M NOV
%D 2019
%K news, views, c2019, c201x, c20xx, zz1119, PhD, university, postgraduate,
   student, research, thesis, survey, satisfaction, harassment, stress, health
%X Nature's survey of more than 6,000 graduate students reveals
   the turbulent nature of doctoral research.
   -- [<A HREF="https:doi.org/10.1038/d41586-019-03459-7">10.1038/d41586-019-03459-7</A>]['19].
   [Also search for: the PhD movie].

%T 100 'most inspiring' novels revealed by BBC Arts
%I BBC
%M NOV
%D 2019
%K best books, c2019, c201x, c20xx, zz1119, good, book, novel, novels,
   literature, survey
%X "A list of the most inspiring novels chosen by a panel of experts has
   been revealed by BBC Arts. ..."
   -- [<A HREF="https://www.bbc.com/news/entertainment-arts-50302788">5/11/2019]</A>]['19].

%A G. Livan
%T Don't follow the leader: how ranking performance reduces meritocracy
%J Royal Soc., Open Sci.
%V 6
%N 191255
%M NOV
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz1119, interesting, ranking, rankings,
   peer, peers, ERA, ARC, KPI, KPIs, university research, Alife, performance,
   inequality, meritocracy, PRF, serendipity, imitation, bast practice,
   bibliometrics, bibliometrics, citations
%X "In the name of meritocracy, modern economies devote increasing amounts of
   resources to quantifying and ranking the performanceof individuals and
   organizations. ... several studies have shown that the imitation of best
   practices often leads to a drop in performance. So, should those lagging
   behind in a ranking imitate top performers or should they instead pursue a
   strategy of their own? I tackle this question by numerically simulating a
   stylized model of a society whose agents seek to climb a ranking either by
   imitating the actions oftop performers or by randomly trying out different
   actions, i.e. via serendipity. The model gives rise to a rich phenomenology,
   showing that the imitation of top performers increases welfare overall, but
   at the cost of higher inequality. Indeed, the imitation of top performers
   turns out to be a self-defeating strategy that consolidates the early
   advantage of a few lucky - and not necessarily  talented - winners, leading
   to a very unequal, homogenized and effectively non-meritocratic society.
   Conversely, serendipity favours meritocratic outcomes and prevents rankings
   from freezing."
   -- [<A HREF="http://dx.doi.org/10.1098/rsos.191255">doi:10.1098/rsos.191255</A>]['19],
      [<A HREF="https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.191255">www</A>]['19].
   [Also search for: Campbell Law] and [also search for: Goodhart Law].

%A C. Smith
%T The hidden stories of Australia's first women working in computing
%I ABC
%D DEC
%D 2019
%K news, views, c2019, c201x, c20xx, zz1219, history, computer, computing, STEM,
   women, www, HREF, Australia, Australian, Astrographic Catalogue, CSIRAC,
   SILLIAC, Pearcey, Semkiw, Kay Thorne, Harcourt, Vorrath, www, HREF
%X -- abc[<A HREF="https://www.abc.net.au/news/science/2019-12-01/women-computing-astronomy-technology/11713282">1/12/2019</A>].
   [Also search for: women computing].

%T Quality over quantity: How the Dutch Research Council is giving
   researchers the opportunity to showcase diverse types of talent
%I DORA
%M NOV
%D 2019
%K news, views, c2019, c201x, c20xx, zz1219, scientific, university, research,
   CV, CVs, management, DORA, NWO Veni, quality, diversity, publish, perish,
   citations, unreliable, KPI, KPIs, ban, Hindex, topN, top10
%X "The Dutch Research Council (NWO) is piloting a narrative CV format in the
   Veni scheme, its major funding instrument for early career researchers. The
   format advances showcasing diverse types of talent and encourages assessment
   of quality rather than quantity. ... The Key output section allows a maximum
   of ten output items. ... banned what we consider unreliable metrics. We
   exclude the use of journal impact factors and any kind of metric that refers
   to journal, publisher, or publication platform, and also ban (H-)indexes,
   citation avgs, totals, & sums, as these measures are sensitive to bias. ..."
   -- [<A HREF="https://sfdora.org/2019/11/14/quality-over-quantity-how-the-dutch-research-council-is-giving-researchers-the-opportunity-to-showcase-diverse-types-of-talent/">www</A>][14/11/2019].
   [Also search for: publish perish].

%A J. Mervis
%T Universities move to stop passing the harasser
%J Science
%M NOV
%D 2019
%K news, views, c2019, c201x, c20xx, zz1219, MeToo, #metoo, meto, harassment,
   abuse, bullying, bully, sexual, university, academic, conduct, misconduct,
   research, management, work, job, jobs, study, staff, faculty
%X "... major research universities are taking steps to penetrate the veil of
   silence that abets the practice of 'passing the harasser.' The Davis and
   San Diego campuses of the U. of Cal. system are conducting pilot programs
   that ask certain faculty candidates to waive some privacy protections ..."
   -- [<A HREF="https://doi.org/10.1126/science.366.6469.1057">doi:10.1126/science.366.6469.1057</A>]['19].
   [Also search for: MeToo].

%A A. Hatch
%T To fix research assessment, swap slogans for definitions
%J Nature
%V 576
%N 9
%M DEC
%D 2019
%K news, views, c2019, c201x, c20xx, zz1219, publish, perish, DORA, university,
   scientific, research, impact, rating, rankings, KPI, KPIs, quality
%X "... My view is that most assessment guidelines permit sliding standards:
   instead of clearly defined terms, they give us feel-good slogans that lack
   any fixed meaning. Facing the problem will get us much of the way towards a
   solution. ...":
   -- [<A HREF="https://doi.org/10.1038/d41586-019-03696-w">doi:10.1038/d41586-019-03696-w</A>]['19].
   [Also search for: publish perish].

%T China due to introduce face scans for mobile users
%I BBC
%D Dec
%D 2019
%K news, bbc, c2019, c201x, c20xx, zz1219, China, mobile phone, phones, face,
   scan, facial recognition, privacy, state, surveillance, identity, Chinese,
   social credit
%X "People in China are now required to have their faces scanned when
   registering new mobile phone services, as the authorities seek to verify the
   identities of the country's hundreds of millions of internet users. ..."
    -- [<A HREF="https://www.bbc.com/news/world-asia-china-50587098">bbc</A>][1/12/2019].

%A C. Wilcox
%T Rude reviews are pervasive and sometimes harmful, study finds
%J Science
%V 366
%N 6472
%P 1433
%M DEC
%D 2019
%K news, views, c2019, c201x, c20xx, zz0120, papers, publications, scientific,
   research, PeerJ, journals, peer review, reviewing, refereeing, conduct,
   misconduct, citations, reviewer2
%X "... Peer reviewers are supposed to ensure that journals publish high-quality
   science ... a new PeerJ study, which surveyed 1106 scientists from 46
   countries and 14 disciplines.  More than half ... reported receiving at least
   one 'unprofessional' review, & a majority ... said they had received multiple
   problematic comments. [Eg] one author received a review that stated: 'The
   phrases I have so far avoided using in this review are 'lipstick on a pig'
   & 'bullshit baffles brains.'' Another reported receiving this missive:
   'The author's last name sounds Spanish. I didn't read the ms because I'm sure
   it's full of bad English.' ..."
   -- [<A HREF="https://doi.org/10.1126/science.aba5502">doi:10.1126/science.aba5502</A>]['20].
   [Also search for: reviewing] and [also search for: publish perish].

%A M. J. Lerchenmueller
%A O. Sorenson
%A A. B. Jena
%T Gender differences in how scientists present the importance of their
   research: observational study
%J BMJ
%V 367
%P l6573
%D 2019
%K BMJ, c2020, c202x, c20xx, zz0220, scientific research, publications, papers,
   title, titles, citations, gender, publish, perish, gender, women, STEM
%X "... this study was to analyze whether men and women differ in how positively
   they frame their research findings and to analyze whether the positive
   framing of research is associated with higher downstream citations. ..."
   -- [<A HREF="http://dx.doi.org/10.1136/bmj.l6573">doi:10.1136/bmj.l6573</A>]['20].
      "... Clinical articles involving a male first or last author were
      more likely to present research findings positively in titles and
      abstracts compared with articles in which both the first and last
      author were women, particularly in the highest impact journals.
      Positive presentation of research findings was associated with
      higher downstream citations. ..."
   [Also search for: publish perish].

%A L. Smolin
%T Einstein's Unfinished Revolution: The Search for What Lies Beyond the Quantum
%I PenguinPress
%D 2019
%K book, c2019, c201x, c20xx, zz0422, physics, philosophy, cosmology,
   consciousness
%X 1st ed 2019; hb us$57; uk us isbn:1594206198; uk us isbn13:978-1594206191.
   "... theoretical physicist Lee Smolin provocatively argues that the problems
   which have bedeviled q.physics since its inception are unsolved & unsolvable
   for the simple reason that the theory is incomplete. ..."

%A J. Adams
%A D. Pendlebury
%A R. Potter
%A M. Szomszor
%T Global Research Report Multi-authorship and research analytics
%I Inst. for Sci. Info. (ISI)
%D 2019
%K bibliometrics, c2019, c201x, c20xx, zz1122, ISI, multiple authors, trends,
   authorship, papers, publications, KPI, KPIs, JIF, citation, citations,
   distortion, hyperauthorship
%X "... The Web of Science has identified a growing # of research articles with
   1,000 or more unique authors across more than 100 different countries. The
   combination of many authors/ many countries creates a complex authorship
   pattern that differs from more typical academic papers & drives elevated
   citation rates. ... Across the Web of Sci., the most frequent # of authors on
   an article is three and 95% of global output has 10 or fewer authors ..."
   -- uk us isbn13:978-1916086869.

%A C. S. Parker
%A et al
%T From invisibility to readability: Recovering the ink of Herculaneum
%J PLoS One
%M MAY
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz0724, scrolls, Herculaneum, papyri,
   papyrus, scroll, ancient Rome, microCT
%X "... we show new experiments indicating a subtle but detectable signature
   from carbon ink in micro-CT. ... This previously 'unseen' evidence of carbon
   inks, which can now successfully be made visible, is a discovery that can
   lead directly to the noninvasive digital recovery of the lost texts of
   Herculaneum."
   -- [<A HREF="https://doi.org/10.1371/journal.pone.0215775">doi:10.1371/journal.pone.0215775</A>]['24].
   Also see Smithsonian [<A HREF="https://www.smithsonianmag.com/history/buried-ash-vesuvius-scrolls-are-being-read-new-xray-technique-180969358/">www</A>][7/2018].

%A E. Worthington
%T Murdoch University drops financial claim against whistleblower academic
   after backlash
%I ABC
%M JAN
%D 2020
%K news, c2020, c202x, c20xx, zz0220, Australia, Murdoch University, WA,
   student, students, welfare, overseas, international, Schroder-Turk,
   whistleblower, academic, scandal, administration, NTEU
%X "... A West Australian university is withdrawing a multi-million-dollar
   financial damages claim filed against a whistleblower academic who spoke on
   the ABC's Four Corners last year. Associate Professor Gerd Schroder-Turk
   was one of three Murdoch University academics who appeared on the program
   raising concerns about the welfare of international students.  He took
   legal action in the Federal Court seeking an injunction to stop the
   university from removing him from his position on the university's senate
   after the broadcast.  In response, Murdoch University counter-sued Dr
   Schroder-Turk for costs and damages.  Murdoch claimed that since
   Dr Schroder-Turk's comments the U.'s reputation had been damaged ..."
   --[<A HREF="https://www.abc.net.au/news/2020-01-13/murdoch-university-drops-financial-claim-against-whistleblower/11863410">abc</A>][13/1/2020].

%A N. Phillips
%A B. Nogrady
%T The race to decipher how climate change influenced Australia's record fires
%J Nature
%V 577
%P 610-612
%M JAN
%D 2020
%K news, views, c2020, c202x, c20xx, zz0220, world, Australia, Victoria, NSW,
   risk, risks, climate change, extreme weather attribution, WWA, bush fires,
   bushfire, drought, cause, causality, CO2, greenhouse gas, gases,
   human activity, Sophie Lewis, Perkins-Kirkpatrick
%X "On 1 January, the air in Canberra was the worst of any city in the world.
   With unprecedented bush fires raging nearby, a thick blanket of smoke
   smothered Australia's capital for weeks, ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-020-00173-7">doi:10.1038/d41586-020-00173-7</A>]['20].
   [Also search for: extreme weather attribution].

%A M. Bagioli
%T Gaming the Metrics: Misconduct and Manipulation in Academic Research
%I MITpress
%P 306
%M JAN
%D 2020
%K book, text, MIT, c2020, c202x, c20xx, zz1120, university management, jobs,
   academia, faculty, rankings, scientific research, impact, KPI, KPIs, JIF,
   gaming, scam, scamming, academic miconduct, fraud, citation ring,
   peer review, publications, audit culture,
   China, Australia, Melbourne, Queensland
%X 2020, pb us$63; asin=B08BT3S9LL; isbn13: 978-0262537933.
   "... Gaming the Metrics examines how the increasing reliance on metrics to
   evaluate scholarly publications has produced radically new forms of academic
   fraud and misconduct. ..."
   "... In China, universities hand substantial cash bonuses to their faculty
   for their publ'ns, indexing them to the j's impact factor. Nature & Science
   articles fetch over $30,000 a piece. Similar schemes can be found on the
   other side of the Equator: Melbourne Business School pays $A15,000 cash for
   every paper published in the Top 40 list compiled by the Financial Times. The
   scheme at Queensland University Business School is more complicated. Payments
   made to the departmental accounts of authors, are ~ : Tier 1 j. - $A12,000;
   Tier 2 j. - $A7500; Tier 3 j. - $A5500; Tier 4 j. - $A2000;
   Professional j. - $A1000. (Macdonald & Kam, 2007) ..."
   Also at [<A HREF="https://mitpress.mit.edu/books/gaming-metrics">MITpress</A>][2020].
   [Also search for: university management].

%A R. Van Noorden
%T Highly cited researcher banned from journal board for citation abuse
%J Nature
%V 578
%P 200-201
%M FEB
%D 2020
%K news, views, VanNorden, c2020, c202x, c20xx, zz0220, publish, perish,
   research, coerce, coercive, citations, papers, gIndex, Hindex, KPI, KPIs,
   impact, university management, JTB, journals, Kuo-Chen Chou, KCChou,
   KuoChenChou, academic misconduct, peer review, research, refereeing, scam,
   abuse, misuse, ethics
%X "A US-based biophysicist [Kuo-Chen Chou] who is one of the world's most
   highly cited researchers has been removed from the editorial board of one
   journal and barred as a reviewer for another, after repeatedly manipulating
   the peer-review process to amass citations to his own work. ... asked authors
   of dozens of papers he was editing to cite a long list of his publications -
   sometimes more than 50 ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-020-00335-7">doi:10.1038/d41586-020-00335-7</A>]['20].
   [Also search for: peer review]  and  [also search for: KuoChenChou].

%A F. Squazzoni
%A et al ...
%A M. Willis
%T Unlock ways to share data on peer review
%J Nature
%V 578
%P 512-514
%M FEB
%D 2020
%K news, views, c2020, c202x, c20xx, zz0320, peer review, reviewing, bias,
   PEERE, scientific literature, journals, papers, research, publish perish
%X "Peer review is the defining feature of scholarly comm'n. In a 2018 survey of
   more than 11,000 researchers, 98% said that they considered PR important or
   extremely important for ensuring the quality & integrity of scholarly comm'n.
   Indeed, now that the 'net & social media have assumed js' original
   role of dissemination, a j's main fn is curation.  ... [a 2018 study] found
   that reviewers tended to favour authors connected to them through
   co-authorship & professional n/wks ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-020-00500-y">doi:10.1038/d41586-020-00500-y</A>]['20].
   [Also search for: peer review].

%A J. M. Pino
%A et al ...
%A B. Neyenhuis
%T Demonstration of the QCCD trapped-ion quantum computer architecture
%J ?
%K news, c2020, c202x, c20xx, zz0320, quantum computing, computer, volume,
   Honeywell, quantum charge coupled device, QCCD, azure
%D 2020
%X "We report on the integration of all necessary ingredients of the trapped-ion
   QCCD (quantum charge-coupled device) architecture into a robust,
   fully-connected, and programmable trapped-ion q.computer. ... employs
   171Yb+ ions for qubits & 138Ba+ ions for sympathetic cooling & is built
   around a Honeywell cryogenic surface trap capable of arbitrary ion
   rearrangement & parallel gate op'ns across multiple zones. As a minimal
   demo., we use two spatially-separated interaction zones in parallel to
   execute arb. four-qubit q.circuits. ... benchmarked at both the component
   level & at the holistic level through a variety of means. Individual
   components including state preparation & measurement, single-qubit gates, &
   two-qubit gates are characterized with randomized benchmarking. Holistic
   tests inc. parallelized randomized benchmarking showing that the cross-talk
   between different gate regions is negligible, a teleported CNOT gate
   utilizing mid-circuit measurement, & a q.volume measurement of 24."
   -- [<A HREF="https://www.honeywell.com/content/dam/honeywell/files/Beta_10_Quantum_3_3_2020.pdf">www</A>]['20].
   Also see, 'Behind the Scenes of a Major Quantum Breakthrough', March 2020,
   "... Thanks to a breakthrough in technology, we're on track to release a
   q.computer with a q.volume of at least 64, twice that of the next alternative
   in the industry. ..."
   -- [<A HREF="https://www.honeywell.com/en-us/newsroom/news/2020/03/behind-the-scenes-of-a-major-quantum-breakthrough">www</A>]['20].

%A D. E. Knuth
%A L. Shustek
%T Let's not dumb down the history of computer science
%J CACM
%V 64
%N 2
%P 33-35
%M FEB
%D 2021
%K CACM, news, views, c2014, c201x, c2021, c202x, c20xx, zz0621, maths,
   computer science, Comp Sci, CompSci, CSci, history, Knuth, Kailath lecture,
   talk, seminar, transcript, seminars, Campbell-Kelly, controversial
%X "Editor's note: On May 7, 2014, Don Knuth delivered that year's Kailath
   Lecture at Stanford U. to a packed auditorium. In it he decried the absence
   of technical content from the histories of CS being written, & he made an
   impassioned plea for historians of CS to get back on track, as the historians
   of maths. have always been. ... This Viewpoint, which we thank Comms. Snr
   Editor Moshe Vardi for suggesting, is a condensed & highly edited transcript
   of the original talk that has provoked so much discussion."
   -- [<A HREf="https://doi.org/10.1145/3442377">doi:10.1145/3442377</A>]['21].
   Video of intro & Knuth's talk @[<A HREF="https://www.youtube.com/watch?v=gAXdDEQveKw">ubend</A>]['21] (via AK).

%A S. Mallapaty
%T China bans cash rewards for publishing papers
%J Nature
%V 579
%N 18
%M FEB
%D 2020
%K news, views, c2020, c202x, c20xx, zz0320, publish, perish, China, journals,
   publications, papers, scientific research, academia, citations, SCI
%X "Chinese institutions have been told to stop paying researchers bonuses for
   publishing in journals, as part of a new national policy to cut perverse
   incentives that encourage scientists to publish lots of papers rather than
   focus on high-impact work.  In an order released last week ... institutions
   must not promote or recruit researchers solely on the basis of the number of
   papers they publish, or their citations. ... Since 2009, articles in these
   [SCI] jrnls written by authors from Chinese institutions increased from some
   120,000/y to 450,000 in 2019. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-020-00574-8">doi:10.1038/d41586-020-00574-8</A>]['20].
   [Also search for: publish perish].

%A J. Brainard
%T Publishers try out alternative pathways to open access
%J Science
%V 367
%N 6483
%P 1179
%M MAR
%D 2020
%K news, views, c2020, c202x, c20xx, zz0320, publishing, scientific research,
   papers, articles, publications, jrnls, open access, openAccess, OA,
   subscribe, costs, fees, APC, APCs, ACM
%X "... article-processing fees (APCs), which can run several thousand dollars
   per paper ... Now, two nonprofit publishers of prominent jrnls have debuted
   new ways to support OA jrnls without shifting the burden entirely to authors.
   ... One approach, called Subscribe to Open ... [Another] ACM is asking the
   instns that publish the most papers in its 59 jrnls to pay more than they do
   now for subsns - in some cases about 10 times as much, or $100,000/y ..."
   -- [<A HREF="https://doi.org/10.1126/science.367.6483.1179">doi:10.1126/science.367.6483.1179</A>]['20].

%A C. Woolston
%T Australian junior scientists report damaging lack of support at work
%J Nature
%V 579
%P 457-458
%M MAR
%D 2020
%K news, views, Christian, Doran, c2020, c202x, c20xx, zz0420, university,
   academia, scientific research, management, ethics, bullying, Australia,
   Australian, scientist, STEM, PhD, postdoc, postgrad, faculty
%X "System built on short-term contracts & grants causes many to consider
   leaving. Four out of five early-career researchers in Australia have
   considered leaving science or their jobs because of factors inc. questionable
   research practices & an absence of institutional support, suggests a survey
   of 658 postdocs & junior faculty members. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-020-00687-0">doi:10.1038/d41586-020-00687-0</A>]['20].
 * Report@[<A HREF="https://www.biorxiv.org/content/10.1101/2020.02.19.955328v1">bioRxiv</A>][20/2/2020].
   [Also search for: University management].

%A J. Taylor
%T Melbourne professor quits after health department pressures her over
   data breach
%J The Guardian
%M MAR
%D 2020
%K newspaper, c2020, c202x, c20xx, zz0521, Australia, University of Melbourne,
   UniMelb, Vanessa Teague, data, privacy, deidentification, reidentification,
   Medicare, medical, federal government, health department, PBS, MBS, data,
   blunder
%X 8 March 2020: "... an open government data website by the federal government,
   of 2.5 million Australians' Medicare & PBS payment history dating back to
   1984 that had supposedly been de-identified so people were anonymous. Teague
   & her colleagues reported that the dataset had several samples where people
   were able to be identified. ... Beauchamp [health dept secretary] also
   requested Teague cease her work on the dataset. ..."
   -- [<A HREF="https://www.theguardian.com/australia-news/2020/mar/08/melbourne-professor-quits-after-health-department-pressures-her-over-data-breach">www</A>][8/3/2020].
   Also see 'MBS/PBS data publication 23 March 2018'
   "On 1 August 2016, the Department of Health published on data.gov.au a
   collection of Medicare Benefits Schedule and Pharmaceutical Benefits Schedule
   related data. The data consisted of claims information for a 10% sample of
   people who had made a claim for payment of Medicare Benefits since 1984, or
   for payment of Pharmaceutical Benefits since 2003. ..."
   -- OAIC .gov.au [<A HREF="https://www.oaic.gov.au/privacy/privacy-decisions/investigation-reports/mbspbs-data-publication/#conclusion">www</A>]['21].
   [Also search for: data reidentification].

%A C. Houston
%T Melbourne Uni pays out $700,000 to PhD student 'groped' by professor
%J The Age
%M APR
%D 2020
%K news, MeToo, c2020, c202x, c20xx, zz0420, University of Melbourne, UniMelb,
   Computer Science, Department, Faculty, Professor Ramamohanarao Rao Kotagiri,
   Prof, Comp Sci Dept, PhD student, academic, misconduct, sexual harassment,
   #metoo, meto, assault, scandal, bullying, management, Go8, Australia,
   Victoria, Supreme Court
%X 11 April 2020:  "The U. of Melbourne has paid $700,000 in compensation to a
   former PhD student who alleges she was sexually assaulted and harassed by a
   professor, amid claims the prestigious institution concealed previous
   complaints ... The accused academic, Professor Ramamohanarao 'Rao' Kotagiri,
   will be 'retiring on April 17 to pursue other opportunities', according to
   an email recently sent to colleagues by a senior university figure. ...
   Between June 2014 and April 2016, the 69-year-old academic is accused of ...
   filed with the court in 2017. ... An indep. investigator appointed by the
   uni. allegedly uncovered other complaints made by at least two former
   students against Prof. K. ..."
   -- The Age [<A HREF="https://www.theage.com.au/national/victoria/melbourne-uni-pays-out-700-000-to-phd-student-groped-by-professor-20200410-p54ixi.html">www</A>][11/4/2020].
   [Also search for: academic misconduct]  and  [also search for: MeToo].

%A R. Van Noorden
%T Nature to join open-access Plan S, publisher says
%J Nature
%M APR
%D 2020
%K journal Nature, c2020, c202x, c20xx, zz0420, open access, OA, Plan S, PlanS,
   publishing, science, scientific literature, papers, research,
   hybrid, transformative journals, free, paywall, paywalls
%X "... Springer Nature says it commits to offering researchers a route to
   publishing open access in Nature and most Nature-branded journals from 2021.'
   ... But Lisa Hinchliffe, a librarian at the U. of Illinois at Urbana-Ch.,
   says the changed rules show that publishers have successfully pushed back
   against Plan S, softening its guidelines and expectations - in particular
   in the case of hybrid journals, which publish some content openly & keep
   other papers behind paywalls. 'The coalition continues to take actions that
   rehabilitate hybrid journals into compliance rather than taking the hard
   line of unacceptability originally promulgated,' she says. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-020-01066-5">doi:10.1038/d41586-020-01066-5</A>]['20].
   [Also search for: research open access].

%A S. Horbach
%A W. Hepkema
%A W. Halffman
%T Hundreds of journals' editorial practices captured in database
%J Nature
%V 582
%N 7810
%P ?-?
%M JUN
%D 2020
%K news, views, c2020, c202x, c20xx, zz0620, PREP, peer review, research,
   Platform for Responsible Editorial Policies, responsiblejournals, journals,
   KPIs, JIF, impact, editor, editorial, practice, policy, refereeing,
   scientific research, reviewing, publishing, ethics
%X "We have launched a Platform for Responsible Editorial Policies
   [<A HREF="http://www.responsiblejournals.org">www</A>]. This facilitates
   transparent review and research into peer-review procedures, thereby
   contributing to open science and optimal journal management."
   -- [<A HREF="https://doi.org/10.1038/d41586-020-01628-7">doi:10.1038/d41586-020-01628-7</A>]['20].

%A M. Trump
%T Too Much And Never Enough: How My Family Created the World's Most
   Dangerous Man
%I SimonAndSchuster
%P 240
%M JUL
%D 2020
%K book, c2020, c202x, c20xx, zz0720, USA, politics, president, Trump, zzTrump,
    Potus, niece, uncle, Trumpery
%X 1st ed 2020; hb us$25; uk us isbn:1982141468; uk us isbn13:978-1982141462.
   "... Donald's only niece, shines a bright light on the dark history of their
   family in order to explain how her uncle became the man who now threatens the
   world's health, economic security, and social fabric. ..."
   (Also see the [<A HREF="https://www.bbc.com/news/world-us-canada-53058811">bbc</A>][16/6/2020].)
   [Also search for: USA President Trump].

%A J. Bolton
%T The Room Where It Happened: A White House Memoir
%I SimonAndSchuster
%P 592
%M JUL
%D 2020
%K book, memoir, c2020, c202x, c20xx, zz0720, USA, politics, president,
   National Security Advisor, Oval Office, West Wing, White House, Washington,
   foreign policy, Trump, zzTrump, Trumpery, Trumpistan, Putin, Ukraine, Russia,
   Xi, China, election, interference
%X 1st ed 2020; hb us$41; uk us isbn:1982148039; uk us isbn13:978-1982148034.
   "... comprehensive and substantial account of the Trump Administration, and
   one of the few to date by a top-level official. With almost daily access to
   the President ..."
   [Also search for: USA President Trump].

%A S. Richie
%T Science Fictions: How Fraud, Bias, Negligence, and Hype Undermine the
   Search for Truth
%I MetropolitanBooks
%P 368
%M JUL
%D 2020
%K book, c2020, c202x, c20xx, zz0720, science, scientific, university, research,
   ethics, fraud, misconduct, manipulation, stats, errors, mistake, peer review,
   reviewing, pressure, impact, KPI, KPIs, Hindex, Phacking
%X 1st ed 2020; hb us$23; uk us isbn:1250222699; uk us isbn13:978-1250222695.
   "... failures in peer review & mistakes in statistics have rendered a
   shocking number of scientific studies useless - or, worse, badly misleading.
   ... reveals the very human biases, misunderstandings, and deceptions that
   undermine the scientific endeavor: from contamination in science labs to the
   secret vaults of failed studies that nobody gets to see; from outright
   cheating with fake data to the more common, but still ruinous, temptation to
   exaggerate mediocre results for a shot at scientific fame. ..."

%A J. D. Wren
%A C. Georgescu
%T Detecting potential reference list manipulation within a citation network
%J bioRxiv
%M AUG
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, publish, perish, KPI, KPIs, Hindex, impact,
   misconduct, gaming, scamming, paper, peer review, reviewing, cite, citation,
   abuse, reference, manipulation, scam, coercive, coercion, RLM,
   Kuo-Chen Chou, KCChou, KuoChenChou, Roukos, journals, JTB, Elsevier,
   modified bibliometrics, Gini, GiniIndex
%X "... reference list manipulation (RLM) could take place during the
   peer-review process (e.g., coercive citation from editors or reviewers), or
   prior to it (e.g., a quid-pro-quo between authors). ... find the freq. of
   non-self citations (NSC) to one author coming from one paper ~ Zipf's law.
   We propose the Gini Index as a simple means of quantifying skew in this
   dist'n ... We estimate between 81 (FDR < 0.05) & 231 (FDR < 0.10) authors are
   outliers on the curve, suggestive of chronic, repeated RLM. Based upon the
   distribution, we est. ~ 3,284 (16%) of all authors may have engaged in RLM
   to some degree ..."
   -- [<A HREF="https://www.biorxiv.org/content/10.1101/2020.08.12.248369v1">bioRxiv</A>]['20],
      [<A HREF="https://doi.org/10.1101/2020.08.12.248369">doi:10.1101/2020.08.12.248369</A>]['20].
   (Also see: "Signs of 'citation hacking' flagged in scientific papers",
   Nature 14/8/2020 [<A HREF="https://doi.org/10.1038/d41586-020-02378-2">www</A>]['20] and
   "Highly cited researcher banned from journal board for citation abuse",
   Nature 6/2/2020 [<A HREF="https://doi.org/10.1038/d41586-020-00335-7">www</A>]['20].)
   [Also search for: Hindex manipulation]  and  [also search for: KuoChenChou].

%Q Google AI Quantum and Collaborators
%T Hartree-Fock on a superconducting qubit quantum computer
%J Science
%V 369
%N 6507
%P 1084-1089
%M AUG
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0820, quantum computer, qubits, chemistry,
   fermion, physics
%X "... We performed several quantum simulations of chemistry with up to
   one dozen qubits, inc. modeling the isomerization mechanism of diazene. ..."
   -- 2004.04174@[<A HREF="https://arxiv.org/abs/2004.04174">arXiv</A>]['20],
      pub49057@[<A HREF="https://research.google/pubs/pub49057/">go'gle</A>]['20],
      [<A HREF="https://doi.org/10.1126/science.abb9811">doi:10.1126/science.abb9811</A>]['20].

%T 'Make research fun again': UK's powerful funding chief is on a mission to
   change scientific culture
%J Nature
%V 584
%P 508
%M AUG
%D 2020
%K news, views, c2020, c202x, c20xx, zz0820, Ottoline Leyser, UK, UKRI,
   scientific research, university, management, impact, KPI, KPIs, grant,
   grants, peer review
%X -- [<A HREF="https://doi.org/10.1038/d41586-020-02424-z">doi:10.1038/d41586-020-02424-z</A>]['20].
   [Also search for: scientific research grants].

%A R. Aldrich
%T GCHQ: Centenary Edition
%I HarperCollins
%P 720
%M AUG
%D 2020
%K book, text, c2020, c202x, c20xx, zz1020, GCHQ, UK, cryptography, MI5,
   spies, intelligence organisation, code breaking, Bletchley Park
%X 2020; pb us$22; uk us isbn: 0008351805; uk us isbn13:978-0008351809.
   "... GCHQ is the largest & most secretive intelligence organisation in the
   UK, and has existed for 100 years - but we still know next to nothing
   about it. ..."

%A J. Lepore
%T Scientists use big data to sway elections and predict riots -
   welcome to the 1960s
%J Nature
%V 585
%P 348-350
%M SEP
%D 2020
%K c196x, 1960s, sixties, USA, politics, analytics, political, Kennedy, JFK,
   election, people machine, Simulmatics, Ithiel de Sola Pool, ComCom,
   behavioural science
%X "... political scientist Ithiel de Sola Pool. He helped to establish the
   Simulmatics Corporation ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-020-02607-8">doi:10.1038/d41586-020-02607-8</A>]['20].

%A R. Cellan-Jones
%T Women in computing - there is good news and bad
%I BBC
%M SEP
%D 2020
%K News, c2020, c202x, c20xx, zz0920, computing CSci, CompSci, GCSE, women,
   girls, STEM, UK, GCSE, ICT, CSci, CompSci, school, schools,
   Durham University, Uni
%X "... The good news: a major university has doubled the number of women
   arriving to study computer science in the space of a year.  The bad: the
   latest GCSE figures show the number of girls getting any kind of computing
   qualification at school continues to decline. ..."
   -- [<A HREF="https://www.bbc.com/news/technology-54204833">bbc</A>][20/9/2020].

%A C. Laufkotter
%A J. Zscheischler
%A T. L. Frolicher
%T High-impact marine heatwaves attributable to human-induced global warming
%J Science
%V 369
%N 6511
%P 1621-1625
%M SEP
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0920, climate change, CO2, attributing, severe,
   attribution, weather events, heatwave, MHW, MHWs, stats, greenhouse gas,
   global warming
%X "... We show that the occurrence probs. of the duration, intensity, &
   cumulative intensity of most documented, large, & impactful MHWs have
   increased more than 20-fold as a result of anthropogenic climate change.
   MHWs that occurred only once every hundreds to thousands of years in the
   preindustrial climate are projected to become decadal to centennial events
   under 1.5C warming conditions & annual to decadal events under 3C warming
   conditions. ..."
   -- [<A HREF="https://doi.org/10.1126/science.aba0690">doi:10.1126/science.aba0690</A>]['20].

%A N. DeVito
%A et al
%T How we learnt to stop worrying and love web scraping
%J Nature
%V 585
%P 621-622
%M SEP
%D 2020
%K views, intro, c2020, c202x, c20xx, zz0920, web scraper, webScraper,
   www, HTML, BeautifulSoup, rvest, data
%X -- [<A HREF="https://doi.org/10.1038/d41586-020-02558-0">doi:10.1038/d41586-020-02558-0</A>]['20].

%A N. N. Trakakis
%T Wayne's world: How universities are crushing academics
%I ABC
%M SEP
%D 2020
%K news, view, research, c2020, c202x, c20xx, zz1020, university management,
   academia, toxic, Grimm, Imperial College London, ICL, ARC, Australia, ERA,
   grants, rankings, leadership, deans, deanitis, Faculty, KPI, KPIs
%X "... The rise & effects of this pathology have been well documented by
   Australian academic John Smyth in his book, The Toxic University. He points,
   for example, to a 2011 study of staff in 16 Australian universities, which
   found that academics feel berated & denigrated, rather than inspired &
   supported, by their research leadership. The malaise, according to Smyth,
   lies largely in the reduction of higher education to a business enterprise,
   driving university leaders to place their faith in 'gaming the market of
   academic casino capitalism' - just consider the ERA scheme. ..."
   -- [<A HREF="https://www.abc.net.au/religion/universities-in-crises-and-what-to-do-about-it/12714252">www</A>][29/9/2020].
   [Also search for: university management].

%A S. Aarobson
%T The busy beaver frontier
%J ACM Sigact news
%V 51
%N 3
%P 32-54
%M SEP
%D 2020
%K survey, c2020, c202x, c20xx, zz1124, non computable, BB, function
%X "The BB fn, with its incomprehensibly rapid growth, has captivated
   generations of comp. scientists, mathematicians, & hobbyists. ... I offer a
   personal view of the BB fn 58 years after its intro., emphasizing
   lesser-known insights, recent progress, & esp. favorite open problems ...
   inc.: when does the BB fn first exceed the Ackermann fn? Is the value of
   BB(20) indep. of set theory? Can we prove that BB(n+1) > 2*BB(n) for large
   enough n? Given BB(n), how many advice bits are needed to compute BB(n+1)?
   Do all BBs halt on all inputs, not just the 0 input? Is it decidable, given
   n, whether BB(n) is even or odd?"
   -- [<A HREF="https://doi.org/10.1145/3427361.3427369">doi:10.1145/3427361.3427369</A>]['24].
   [Also search for: Busy Beaver].

%A B. Devore-McDonald
%A E. D. Berger
%T Mossad: Defeating software plagiarism detection
%J arXiv
%M OCT
%D 2020
%K TR, c2020, c202x, c20xx, zz1020, computer programming, plagiarism, detect,
   detector, detection, student, university, homework, cheat, cheating
%X "... Mossad, that defeats popular s/w plagiarism detection tools. Mossad
   comprises a framework that couples techniques inspired by gen.prog. with
   domain-specific knowledge to effectively undermine plagiarism detectors.
   ... effective at defeating four plagiarism detectors, inc. Moss & JPlag.
   Mossad is both fast & effective: it can, in minutes, generate modified
   versions of programs that are likely to escape detection. More insidiously,
   because of its non-det. approach, Mossad can, from a single program,
   generate dozens of variants ..."
   -- 2010.01700@[<A HREF="https://arxiv.org/abs/2010.01700">arXiv</A>]['20].

%A M. Mejigaard
%A et al
%T Research integrity: Nine ways to move from talk to walk
%J Nature
%V 586
%P 358-360
%M OCT
%D 2020
%K news, views, c2020, c202x, c20xx, zz1120, scientific research, ethics,
   integrity, Delft, Imperial College, University management, Faculty, Dean,
   academic misconduct, academia, KPI, KPIs, impact, JIF, EU, Horizon Europe
%X "In 2018, Delft U. of Tech. in the Netherlands began building a community of
   data champions across all faculties, ... Imperial College London now shuns
   journal-based metrics in staff assessment; it relies more on peer judgement
   of research quality. At Mahidol U. in Bangkok, Thailand, all staff sign the
   university's code of good governance ..."
    -- [<A HREF="https://doi.org/10.1038/d41586-020-02847-8">doi:10.1038/d41586-020-02847-8</A>]['20].
   [Also search for: university management]  and  [also search for: KCChou].

%A L. Schneider
%T Yuqing Zhang 10 years of research fraud, a whistleblower account
%N NOV
%D 2020
%K news, views, c2020, c202x, c20xx, zz1120, Zhang Yuqing, Tianjin university,
   tju, China, .cn, paper mill, PaperMill, scientific research, academia,
   Elsevier journals, allegation, fraud, academic, misconduct, Monash
%X "... at least 50 peer reviewed papers in respectable Elsevier journals: all
   are entirely fabricated, with barely or no experiments ever done. ...
   [...] was admitted to TJU as master student in spring 2015, as doctoral
   student in winter 2016, & to Monash U. as PhD student in summer 2017. Her
   current advisor is Prof. Huanting WANG. ..."
   -- forbetterscience@[<A HREF="https://forbetterscience.com/2020/11/24/yuqing-zhangs-10-years-of-fraud-a-whistleblower-account/">www</A>]['20].
   [Also search for: PaperMill].

%A E. Gadd
%T University rankings need a rethink
%J Nature
%V 587
%P 523
%M NOV
%D 2020
%K news, views, c2020, c202x, c20xx, zz1120, university management, academia,
   faculty, deanitis, ranking, bibliometrics,
   THES, DORA, ARWU, THEWUR, WUR, INORMS, CWTS
%X "Researchers often complain about the indicators that hiring and grant
   committees use to judge them. In the past ten years, initiatives such as the
   San Francisco Declaration on Research Assessment and the Leiden Manifesto
   have pushed universities to rethink how and when to use publications and
   citations to assess research and researchers. The use of rankings to assess
   universities also needs a rethink. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-020-03312-2">doi:10.1038/d41586-020-03312-2</A>][24/11/2020].

%A D. Hope
%A J. Limberg
%T The economic consequences of major tax cuts for the rich
%R WorkingPaper 55
%I LSE
%M DEC
%D 2020
%K TR, LSE, c2020, c202x, c20xx, zz1220, Economics, tax, cut, cuts, rich, poor,
   trickle down, Reaganomics, income inequality, wealth, unemployment, poverty,
   data, OECD
%X "... uses data from 18 OECD countries over the last five decades to est. the
   causal effect of major tax cuts for the rich on income inequality, economic
   growth, & unemployment. First, we use a new encompassing measure of taxes on
   the rich to identify instances of major red'ns in tax progressivity. ... We
   find that major reforms reducing taxes on the rich lead to higher income
   inequality ... The effect remains stable in the medium term. In contrast,
   such reforms do not have any sig. effect on economic growth & unemployment.
   -- pdf@[<A HREF="http://eprints.lse.ac.uk/107919/1/Hope_economic_consequences_of_major_tax_cuts_published.pdf">lse</A>]['20].

%A K. Christian
%A et al
%T Research Culture: A survey of early-career researchers in Australia
%J eLife
%V 10
%P #e60613
%M JAN
%D 2021
%K jrnl, eJrnl, c2021, c202x, c20xx, zz0223, academia, Australia, scientific,
   research, university, postgraduate, postgrad, PhD, postdoc, bullying,
   harassment,  academic, job, supervision, misconduct, STEM, STEMM
%X "... we surveyed 658 ECRs working in Australia to better understand the needs
   & challenges faced by this community. Although most respondents indicated a
   'love of science', many also expressed an intention to leave their research
   position. The responses highlight how job insecurity, workplace culture,
   mentorship & 'questionable research practices' are impacting the job
   satisfaction of ECRs & potentially compromising science in Australia. We also
   make recommendations for addressing some of these concerns."
   -- [<A HREF="https://doi.org/10.7554/eLife.60613">doi:10.7554/eLife.60613</A>]['23].
   Also see [<A HREF="https://doi.org/10.1101/2020.02.19.955328">bioRxiv</A>][2/2020].

%T Open access takes flight
%J Science
%V 371
%N 6524
%P 16-20
%M JAN
%D 2021
%K news, views, c2021, c202x, c20xx, zz0121, publications, journal, open access,
   papers, PlanS, paywall
%X "In 2018, a group of mostly European funders sent shock waves through the
   world of sci. publishing by proposing an unprecedented rule: The scientists
   they funded would be required to make j.articles developed with their support
   immediately free to read when published. ..."
   -- [<A HREF="https://doi.org/10.1126/science.371.6524.16">doi:10.1126/science.371.6524.16</A>]['21].
   [Also search for: open access].

%A J. Slimming
%T Codebreaker Girls: A Secret Life at Bletchley Park
%I PenAndSword
%P 224
%M MAR
%D 2021
%K book, c2021, c202x, c20xx, zz0322, code, women, STEM, Bletchley Park,
   Daisy Lawrence, WW2, WWII, www
%X 1st ed 2021; hb us$57; uk us isbn:1526784114; uk us isbn13:978-1526784117.
   "... tells the true story of Daisy Lawrence. Following extensive research,
   the author uses snippets of information, unpublished photographs and her own
   recollections to describe scenes from her mother's poor, but happy,
   upbringing in London, and the disruptions caused by the outbreak of [WW2]."
   [Also search for: Bletchley Park].

%A T. Freeth
%A et al
%T A model of the cosmos in the ancient Greek Antikythera mechanism
%J Scientific Reports
%V 11
%N #5821
%M MAR
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0321, Antikythera mechanism, ancient, Greek,
   astronomy, device, cosmos, history, computing, calculator
%X "The Antikythera Mechanism, an ancient Greek astronomical calculator, has
   challenged researchers since its discovery in 1901. Now split into 82
   fragments, only a third of the original survives, including 30 corroded
   bronze gear wheels. Microfocus X-ray Computed Tomography (X-ray CT) in 2005
   decoded the structure of the rear of the machine but the front remained
   largely unresolved. X-ray CT also revealed inscriptions describing the
   motions of the Sun, Moon and all five planets known in antiquity ..."
   -- [<A HREF="https://doi.org/10.1038/s41598-021-84310-w">doi:10.1038/s41598-021-84310-w</A>].
   (Also see [<A HREF="https://www.bbc.com/news/science-environment-56377567">bbc</A>]['21].)
   [Also search for: Antikythera mechanism].

%A H. Else
%A R. Van Noorden
%T The fight against fake-paper factories that churn out sham science
%J Nature
%V 591
%P 516-519
%M MAR
%D 2021
%K news, c2021, c202x, c20xx, zz0321, papers, publications, paper mill, China,
   PaperMill, scam, fraud, scientific research, cheating, ghostwriter,
   academia, academic misconduct
%X "When Laura Fisher noticed striking similarities between research papers
   submitted to RSC Advances, she grew suspicious. None of the papers had
   authors or institutions in common, but their charts and titles looked
   alarmingly similar, says Fisher, the executive editor at the journal.
   'I was determined to try to get to the bottom of what was going on.' ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-00733-5">doi:10.1038/d41586-021-00733-5</A>]['21].
   [Also search for: PaperMill].

%T M. Hutson
%T Robo-writers: the rise and risks of language-generating AI
%J Nature
%M MAR
%D 2021
%K news, views, c2021, c202x, c20xx, zz0821, AI, GPT 3, GPT3, robo writer,
   emulating, imitating, funny, haha, ha ha, spoof, satire, natural language,
   NN, generator, LLM, LarLangM, deep, model, risks, OpenAI
%X "... the latest and most powerful in a series of 'large language models':
   AIs that generate fluent streams of text after imbibing billions of words
   from books, articles and websites. GPT-3 had been trained on around 200
   billion words, at an estimated cost of tens of millions of dollars. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-00530-0">doi:10.1038/d41586-021-00530-0</A>]['21].
   [Also search for: GPT]  and  [also search for: postmodernism].
   (Also see V.G.Cerf on LLMs, CACM 66(8) [<A HREF="https://doi.org/10.1145/3606337">www</A>['23] AUG 2023.)

%A J. Pablo Bonilla Ataides
%A D. K. Tuckett
%A S. D. Bartlett
%A S. T. Flammia
%A B. J. Brown
%T The XZZX surface code
%J Nat. Comms.
%V 12
%N 2172
%M APR
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0421, quantum computing, fault tolerant, qubit,
   XZZX surface code
%X "Performing large calculations with a quantum computer will likely require a
   fault-tolerant architecture based on quantum error-correcting codes. ... we
   show that a variant of the surface code - the XZZX code - offers remarkable
   performance for fault-tolerant q.comp'n. The error threshold of this code
   matches what can be achieved with random codes (hashing) for every
   single-qubit Pauli noise channel; it is the first explicit code shown to have
   this universal property. We present numerical evidence that the threshold
   even exceeds this hashing bound for an experimentally relevant range of noise
   parameters. ... show that it is possible to maintain all of these advantages
   when we perform fault-tolerant quantum computation.
   -- [<A HREF="https://doi.org/10.1038/s41467-021-22274-1">doi:10.1038/s41467-021-22274-1</A>]['21].
   Also see [<A HREF="https://www.abc.net.au/news/2021-04-13/sydney-university-student-solves-quantum-computing-problem/100064328">abc</A>]['4/2021].

%A J. W. Weiss
%A J. M. Jacobson
%T Learning on knowledge graph dynamics provides an early warning of
   impactful research
%J NatureBiotech
%M MAR
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0521, DELPHI, publish, perish, JIF, impact,
   quality, bibliometrics, scientific literature, publications, research,
   academia
%X "The sci. ecosystem relies[!] on citation-based metrics that provide only
   imperfect, inconsistent & easily manipulated[!] measures of research quality.
   Here we describe DELPHI (Dynamic Early-warning by Learning to Predict High
   Impact), a framework that provides an early-warning signal for 'impactful'
   research by autonomously learning high-dimensional relationships among
   features calc. across time from the sci. lit.. We prototype this framework &
   deduce its performance & scaling properties on time-structured publication
   graphs from 1980 to 2019 drawn from 42 biotechnology-related journals,
   inc. over 7.8 million individual nodes, 201 million relationships & 3.8
   billion calculated metrics. We demonstrate the framework's performance by
   correctly identifying 19/20 seminal biotechnologies from 1980 to 2014 via a
   blinded retrospective study & provide 50 research papers from 2018 that
   DELPHI predicts will be in the top 5% of time-rescaled node centrality in the
   future. We propose DELPHI as a tool to aid in the construction of
   diversified, impact-optimized funding portfolios."
   -- [<A HREF="https://doi.org/10.1038/s41587-021-00907-6">doi:10.1038/s41587-021-00907-6</A>]['21] (via AK).
   GROAN.  [Also search for: publish perish].

%A R. Van Noorden
%T Hundreds of gibberish papers still lurk in the scientific literature
%J Nature
%V 593
%P ?
%M MAY
%D 2021
%K news, c2021, c202x, c20xx, zz0621, SCIgen, computer generated, fake,
   paper generator, joke, funny, ha ha, haha, hoax, bogus,
   SCIdetect, MATHgen, IOP, IEEE
%X "Nonsensical research papers generated by a computer program are still
   popping up in the scientific literature many years after the problem was
   first seen, a study has revealed. ... The issue began in 2005, when three
   PhD students created paper-generating software called SCIgen for 'maximum
   amusement', & to show that some confs. would accept meaningless papers. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-01436-7">doi:10.1038/d41586-021-01436-7</A>]['21].
   [Also search for: postmodernism].

%A M. Schlapfer
%A et al ...
%A G. B. West
%T The universal visitation law of human mobility
%J Nature
%V 593
%P 522-527
%M MAY
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0621, human behaviour, distance, visit, visits,
   frequency, mobility, law, laws
%X "... we reveal a simple & robust scaling law that captures the temporal &
   spatial spectrum of pop'n movement on the basis of large-scale mobility data
   from diverse cities around the globe. According to this law, the # of
   visitors to any location decreases as the inverse square of the product of
   their visiting freq. & travel dist.. We further show that the spatio-
   temporal flows to different locations give rise to prominent spatial clusters
   with an area dist'n that follows Zipf's law. Finally, we build an individual
   mobility model based on exploration & preferential return to provide a
   mechanistic explanation for the discovered scaling law & the emerging
   spatial structure. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-03480-9">doi:10.1038/s41586-021-03480-9</A>]['21].

%A J. J. Gooley
%T Large-scale digital traces of university students show that morning classes
   are bad for attendance, sleep, and academic performance
%J bioRxiv
%M MAY
%D 2021
%K TR, c2021, c202x, c20xx, zz0621, Duke, NUS, University, Singapore, teaching,
   GPA, results, exams, lecture, lectures, class, classes, student, learning,
   early, morning, behaviour
%X "... Wi-Fi connection data were used to est. attendance rates of 24,678
   students enrolled in lecture courses with start times ranging from 08:00
   to 16:00. ... Analyses of grades in 27,281 s. showed that having morning
   classes on more days of the week resulted in a lower grade pt avg.. ...
   suggest cumulative -ve effects of morning classes on learning. Early morning
   classes force many s. to decide to either sleep more & skip class, or sleep
   less to attend class. Therefore, universities should avoid scheduling early
   morning classes. ..."
   -- [<A HREF="https://doi.org/10.1101/2021.05.14.444124">doi:10.1101/2021.05.14.444124</A>]['21].
   [Also search for: student learning].

%A P. Rovelli
%A C. Curnis
%T The perks of narcissism: Behaving like a star speeds up career advancement
   to the CEO position
%J The Leadership Quarterly
%V 32
%N 3
%P #101489
%M JUN
%D 2021
%K c2021, c202x, c0xx, zz0921, leadership, leader, boss, CEO, dean, management,
   narcissism, narcissistic, personality, psychology, business, power, discord
%X "It is widely acknowledged that narcissism is a peculiar characteristic of
   leaders, such as CEOs. ... Estimates on a sample of 172 individuals partially
   confirm the hypotheses. Highly n. individuals become CEOs quicker, regardless
   of whether the firm is a family business or not. ..."
   -- [<A HREF="https://doi.org/10.1016/j.leaqua.2020.101489">doi:10.1016/j.leaqua.2020.101489</A>]['21].
   Also see [<A HREF="https://www.bbc.com/worklife/article/20210830-how-narcissists-climb-the-career-ladder-quickly">bbc</A>][8/2021].
   [Also search for: narcissism].

%A M. L. Littman
%T Collusion rings threaten the integrity of computer science research
%J CACM
%V 64
%N 6
%M JUN
%D 2021
%P 43-44
%K CACM, news, viwes, c2021, c202x, c20xx, zz0621, scientific research,
   peer review, reviewing, refereeing, academic misconduct, ethics, collusion,
   scam, gaming, fraud, KPI, KPIs
%X "... I want to alert the community to a growing problem that attacks the
   fundamental assumptions that the review process has depended upon. ... I
   became aware of an example in the computer-architecture community where a
   jnr researcher may have taken his own life instead of continuing to engage
   in a possible collusion ring. ..."  [online May '21.]
   -- [<A HREF="https://doi.org/10.1145/3429776">doi:10.1145/3429776</A>]['21].
   [Also search for: academic misconduct]  and  [also search for: peer review].

%A V. Koltun
%A D. Hafner
%T The h-index is no longer an effective correlate of scientific reputation
%J PLoS One
%M JUN
%D 2021
%K jrnl, eJrnl, c2021, c202x, c20xx, zz1221, Hindex, busted, modified,
   bibliometrics, gaming, gamed, scammed, broken, Hindex, hmIndex, Hfrac,
   fractional, multiple authors, authorship, hyperauthorship, trends,
   scientific research, academia, university, management, faculty, deans, KPIs
%X "... A scientist's h-index affects hiring, promotion, & funding decisions, &
   thus shapes the progress of sci.. ... We find that the correlation of the
   h-index with awards that indicate recognition by the scientific community has
   substantially declined. These trends are assoc. with changing authorship
   patterns. We show that these declines can be mitigated by fractional
   allocation of citations among authors, ..."
   -- [<A HREF="https://doi.org/10.1371/journal.pone.0253397">doi:10.1371/journal.pone.0253397</A>]['21].
   [Also search for: hmIndex]  and  [also search for: Campbell law].

%A C. Wagner
%A et al
%T Measuring algorithmically infused societies
%J Nature
%V 595
%P 197-204
%M JUL
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0721, human, behaviour, society, social, data,
   collection, bigdata, privacy, fairness, openess, openness, justice, internet,
   www, tracking
%X "... The emergence of 'algorithmically infused societies' - societies whose
   very fabric is co-shaped by algorithmic & human behaviour - raises three key
   challenges: the insufficient quality of measurements, the complex
   consequences of (mis)measurements, & the limits of existing social theories.
   Here we argue that tackling these challenges requires new social theories
   that account for the impact of alg.systems on social realities. ... the
   development of measurements should be transparent & participatory, & include
   mechanisms to ensure measurement quality & identify possible harms. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-03666-1">doi:10.1038/s41586-021-03666-1</A>]['21] (153 refs).

%A J. de Vrieze
%T Large survey finds questionable research practices are common
%J Science
%V 373
%N 6552
%P 265
%M JUL
%D 2021
%K news, views, deVrieze, c2021, c202x, c20xx, zz0721, scientific, research,
   academia, ethics, fraud, academic, misconduct, Holland, Netherlands, Europe
%X "More than half of Dutch scientists regularly engage in questionable research
   practices, according to new study results that are likely to apply to other
   countries. And one in 12 admitted to committing a more serious form of res.
   misconduct within the past 3 years: fabrication or falsification of res.
   results. At 8%, that is more than double the rate reported in prev. studies.
   The Dutch National Survey on Research Integrity, the largest of its kind to
   date, took special precautions to guarantee the anonymity of respondents, so
   its organizers believe the results are more accurate than previous surveys."
   -- [<A HREF="https://doi.org/10.1126/science.373.6552.265">doi:10.1126/science.373.6552.265</A>]['21].
   [Also search for: scientific research misconduct].

%A S. Kean Little
%T The Icepick Surgeon: Murder, Fraud, Sabotage, Piracy, and Other Dastardly
   Deeds Perpetrated in the Name of Science
%I BrownPubl.
%P 368
%M JUL
%D 2021
%K book, c2021, c202x, c20xx, zz0721, science, scientific research, crime,
   ethics, misconduct
%X 1st ed 2021; hb us$20; uk us isbn:0316496502; isbn13:978-0316496506.
   "... beginning with Cleopatra's dark deeds in ancient Egypt. ... reveals the
   origins of much of modern sci. in the transatlantic slave trade of the 1700s,
   as well as Thomas Edison's mercenary support of the electric chair & the
   warped logic of the spies who infiltrated the Manhattan Project. But the sins
   of sci. aren't all safely buried in the past. Many of them, Kean reminds us,
   still affect us today. ..."
   [Also search for: scientific research ethics].

%A C. Woolston
%T Impact factor abandoned by Dutch university in hiring and promotion decisions
%J Nature
%V 595
%P 462-462
%M JUL
%D 2021
%K news, views, c2021, c202x, c20xx, zz0721, university, academia, impact, JIF,
   research, publications, citations, Hindex, DORA, KPIs, KPI, Netherlands,
   Holland, Dutch, Europe, Utrecht University, hire, hiring, promoting, policy,
   promotion, tenure, scientific research, open science, sci, management
%X "... By early 2022, every department at Utrecht U. in the Netherlands will
   judge its scholars by other standards, including their commitment to teamwork
   & their efforts to promote open science  ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-01759-5">doi:10.1038/d41586-021-01759-5</A>]['21].
     Also see, 'Indicator frameworks for fostering open knowledge practices in
     science and scholarship'
     -- [<A HREF="https://op.europa.eu/en/publication-detail/-/publication/b69944d4-01f3-11ea-8c1f-01aa75ed71a1">EU</A>]['21].
   [Also search for: University management].

%A N. Subbaraman
%T Gun violence is surging - researchers finally have the money to ask why
%J Nature
%V 595
%P 486-488
%M JUL
%D 2021
%K news, views, c2021, c202x, c20xx, zz0721, USA, NRA, politics, gun control,
   research, violence, death
%X "With historically high levels of new funding, US gun-violence research is
   starting to find its footing. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-01966-0">doi:10.1038/d41586-021-01966-0</A>]['21].

%T Emmanuel Macron identified in leaked Pegasus project data
%J TheGuardian
%M JUL
%D 2021
%K news, c2021, c202x, c20xx, zz0721, spy, spying, spyware, abuse, Pegasus,
   NSO, Israel, NSOgroup, privacy, human rights, journalist, politician,
   politics, iPhone, iOS, Safari, iMessage, AndroidPhone, Chrysaor, smartPhone,
   mobile phone, hack, hacking, security, democracy, Guardian, grauniad
%X "The leaked database at the heart of the Pegasus project includes the mobile
   phone numbers of the French president, Emmanuel Macron, and 13 other heads
   of state and heads of government, the Guardian can reveal. ..."
   -- The G [<A HREF="https://www.theguardian.com/world/2021/jul/20/emmanuel-macron-identified-in-leaked-pegasus-project-data">www</A>][21/7/2021].
   Also see [<A HREF="https://www.abc.net.au/news/2021-07-22/how-does-pegasus-spyware-work-and-is-my-phone-at-risk/100315390">abc</A>][22/7/2021], and
   Pegasus@[<A HREF="https://en.wikipedia.org/wiki/Pegasus_(spyware)">wikip</A>]['21].

%A G. Cabanac
%A C. Labbe
%A A. Magazinov
%T Tortured phrases: A dubious writing style emerging in science. Evidence of
   critical issues affecting established journals
%J arXiv
%J JUL
%D 2021
%K TR, c2021, c202x, c20xx, zz0821, academic, research, misconduct, fraud,
   plagiarism, AI generated, GPT 3, GPT3, robo writer, tortured phrases, weird,
   colossal information, profound neural organization, journal, publications,
   papers, fake, scientific literature, editorial practice, peer review,
   PaperMill, journal, refereeing
%X "... Now more complex AI-powered generation techniques produce texts
   indistinguishable from that of humans & the generation of scientific texts
   from a few keywords has been documented. Our study introduces the concept of
   tortured phrases: unexpected weird phrases in lieu of established ones, such
   as 'counterfeit consciousness' instead of [AI]. ..."
   -- 2107.06751@[<A HREF="https://arxiv.org/abs/2107.06751">arXiv</A>]['21].
   [Also search for: GPT3] and [also search for: peer review].

%A Xinwen Jiang
%T A polynomial time algorithm for a NPC problem
%J arXiv
%M AUG
%D 2021
%K TR, c2021, c202x, c20xx, zz0821, MSP, NP, NPC, controversial
%X "It is introduced a so called 'Multi-stage graph Simple Path' problem (MSP
   for short) & proved that SAT problem can be polynomial reducible to MSP
   problem in this small paper. To solve MSP problem, we propose a polynomial
   time alg.. Our result implies NP=P."
   -- 2108.03877@[<A HREF="https://arxiv.org/abs/2108.03877">arXiv</A>]['21].
   [(?breakthrough or crash and burn?-)]

%A C. Watson
%T Preprint ban in grant applications deemed 'plain ludicrous'
%J Nature
%V ?
%P ?-?
%M AUG
%D 2021
%K news, views, c2021, c202x, c20xx, zz0921, Australia, scientifc research,
   academia, career, preprints, applications, management, ARC, grants, funding
%X "The Australian Research Council's decision to reject early-career funding
   applications that mention preprints is hopelessly outdated, say scientists.
   ... At least 23 researchers - 7 of whom Nature contacted for comment - have
   been deemed ineligible because they ref. to preprints in applications ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-02318-8">doi:10.1038/d41586-021-02318-8</A>]['21].

%A H. Nowotny
%T In AI We Trust: Power, Illusion and Control of Predictive Algorithms
%I Polity
%P 200
%M SEP
%D 2021
%K book, text, c2021, c202x, c20xx, zz1021, AI, data analytics, society, bias,
   technology, democracy, risks
%X 1st ed 2021; hb us$41; uk us isbn:1509548815; uk us isbn13:978-1509548811.
   "One of the most persistent concerns about the future is whether it will be
   dominated by the predictive algorithms of AI - and, if so, what this will
   mean for our behaviour, for our institutions and for what it means to
   be human. ..."

%A H. Else
%T China's clampdown on fake-paper factories picks up speed
%J Nature
%V ?
%M SEP
%D 2021
%K news, views, c2021, c202x, c20xx, zz1021, publish, perish, academic,
   misconduct, China, scientific research, fake, paper mill, PaperMill, mills
%X "As part of a misconduct crackdown, Chinese funders are penalizing
   researchers who commission sham journal articles from 'paper mills', but
   some say the measures still don't go far enough. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-02587-3">doi:10.1038/d41586-021-02587-3</A>]['21].
   [Also search for: publish perish]  and  [also search for: PaperMill].

%A D. Hemprich-Bennett
%A D. Rabaiotti
%A E. Kennedy
%T Beware survivorship bias in advice on science careers
%J Nature
%V ?
%M OCT
%D 2021
%K news, views, c2021, c202x, c20xx, zz1021, science, academic, research,
   academia, career, careers, job, jobs, advice, survivor bias, luck,
   chance, fart, farting
%X "A major flaw in much scientific & academic career advice is survivorship
   bias. This is a common logical error, involving drawing conclusions based on
   those who have 'survived' a process - and are thus more visible than those
   who did not. In the case of sci. careers advice, the bias arises because
   those who manage to stick to their chosen career path are there to advise the
   next gen. of researchers on how to stay in their field. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-02634-z">doi:10.1038/d41586-021-02634-z</A>]['21].
   [Also search for: survivor bias].
   (Makes reference to: N. Caruso & D. Rabaiotti, 'Does it Fart',
   1st ed 2018, hb us$26; us us isbn:0316484156; uk us isbn13:978-0316484152.)

%A K. Siler
%A V. Lariviere
%A P. Vincent-Lamarre
%A C. R. Sugimoto
%T Predatory publishers' latest scam: bootlegged and rebranded papers
%J Nature
%V 598
%P 563-565
%M OCT
%D 2021
%K news, views, c2021, c202x, c20xx, zz1021, predatory, dodgy, journal,
   journals, publisher, publishing, scam, deception, fake, bootleg, hijack,
   plagiarism, misconduct, academia, scientific research, paper, OMICS, Hilaris,
   Longdom, iMedPub, Lacuna
%X "To thwart publishing rackets that undermine scholars & scholarly publishing,
   legitimate jrnls should show their workings. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-02906-8">doi:10.1038/d41586-021-02906-8</A>]['21].
   (Also see Lacuna [<A HREF="http://lacunadb.io/">www</A>]['21].)
   [Also search for: misconduct publishing].

%A M. Spring
%T I get abuse and threats online - why can't it be stopped?
%I BBC
%M OCT
%D 2021
%K news, views, c2021, c202x, c20xx, zz1121, disinformation, social media, feed,
   nasty, facebook, meta, twitter, instagram, www, web, abuse, online, hate,
   slur, slurs, misogyny, gender, troll, trolls, trolling, incel, qanon,
   antivax, threat, fake news, fakeNews, conspiracy theories
%X "I'm the BBC's first specialist disinformation reporter - & I receive abusive
   messages on social media daily. Most are too offensive to share unedited. The
   trigger? My coverage of the impact of online conspiracies & fake news. I
   expect to be challenged & criticised - but misogynistic hate directed at me
   has become a very regular occurrence. ..."
   -- [<A HREF="https://www.bbc.com/news/uk-58924168">bbc</A>][18/10/2021].
   [Also search for: nasty social media].

%A Junhui Wu
%A et al
%T Honesty and dishonesty in gossip strategies: a fitness interdependence
   analysis
%J Phil. Trans. of the Royal Soc. B
%M OCT
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0922, gossip, gossiping, lie, lying,
   truth, 2022, c2022, igNobel
%X "... We build formal models to provide the theor. foundation for individuals'
   gossip strategies, taking into account the gossiper's fitness interdependence
   with the receiver & the target. Our models across four different games
   suggest a very simple rule: when there is a perfect match (mismatch) between
   fitness interdependence & the effect of honest gossip, the gossiper should
   always be honest (dishonest); however, in the case of a partial match, the
   gossiper should make a choice based on their fitness interdependence with the
   receiver & the target & the marginal cost/benefit in terms of pay-off
   differences caused by possible choices of the receiver & the target in the
   game. Moreover, gossipers can use this simple rule to make optimal decisions
   even under noise. We discuss empirical examples that support the predictions
   of our model & potential extensions."
   -- [<A HREF="https://doi.org/10.1098/rstb.2020.0300">doi:10.1098/rstb.2020.0300</A>]['22].
   (Also see *2022* IgNobel winners [<A HREF="https://improbable.com/ig/winners/#ig2022">www</A>]['22].)

%A C. Woolston
%T Stagnating salaries present hurdles to career satisfaction
%J Nature
%V 599
%P 519-521
%M DEC
%D 2021
%K news, views, c2021, c202x, c20xx, zz1221, university, scientific, research,
   STEM, science, scientist, researcher, management, faculty, job, jobs, career,
   salary, pay
%X "Fewer than half of respondents to Nature's 2021 salary and satisfaction
   survey feel positive about their prospects. ... High salaries proved to be
   more common in industry than academia. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-021-03041-0">doi:10.1038/d41586-021-03041-0</A>]['21].
   [Also search for: science career].

%A E. Worthington
%T Death threats, ghost researchers and sock puppets: Inside the weird, wild
   world of dodgy academic research
%J ABC
%M JAN
%D 2022
%K news, c2022, c202x, c20xx, zz0222, Artemisia Stricta, academia, university,
   scientific research, fraud, academic misconduct, KPI, KPIs, Ali Nazari, ARC,
   engineering, Swinburne, retraction watch, Shadi Riahi, Ehsan Mohseni,
   Newcastle, Diederik Stapel, Bruce Murdoch, Caroline Barwood, Queensland, UQ
%X "The email arrived on a Saturday morning in July last year. The recipient was
   a person known only as 'Artemisia Stricta', a moniker they adopted when they
   started their secret career as an online sleuth exposing academic fraud.
   The message was from a NSW police constable investigating death threats ..."
   -- [<A HREF="https://www.abc.net.au/news/2022-01-31/on-the-trail-of-dodgy-academic-research/100788052">31/1/2022</A>].

%A R. Imhoff
%A et al
%T Conspiracy mentality and political orientation across 26 countries
%J NatureHumanBehaviour
%V 6
%P 392-403
%M JAN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1122, human behaviour, conspiracy theory,
   stats, psychology, fake news, fakeNews, lies, far, left, right, wing,
   politics, USA, denial, QQ, Qanon, altright
%X "... Prev. res. yielded inconsistent findings on the reln between conspiracy
   mentality [CM] & political orientation, showing a greater CM either among the
   political right (a linear reln) or amongst both the left & right extremes (a
   curvilinear reln). We revisited this relationship across two studies spanning
   26 countries (combined N=104,253) & found overall evidence for both linear &
   quadratic relns, albeit small & heterogeneous across countries. We also
   observed stronger support for CM among voters of opposition parties (that is,
   those deprived of political control).  Nonetheless, the quadratic effect of
   political orientation remained sig. when adjusting for political control
   deprivation. We conclude that CM is assoc. with extreme left- & esp. extreme
   right-wing beliefs, & that this non-linear reln may be strengthened by, but
   is not reducible to, deprivation of political control."
   -- [<A HREF="https://doi.org/10.1038/s41562-021-01258-7">doi:10.1038/s41562-021-01258-7</A>]['22].
  [Also search for: conspiracy theory] & [also search for: left right politics].

%A R. Thoppilan
%A et al
%T LaMDA: Language models for dialog applications
%J arXiv
%M JAN
%D 2022
%K TR, c2022, c202x, c20xx, zz0622, LaMDA, natural language, chatBot, google,
   conversation, dialogue, safety, truth, facts, AI, controversy, controversial
%X "... LaMDA: Language Models for Dialog Applications. ... a family of
   Transformer-based neural language models specialized for dialog, which have
   up to 137B parameters and are pre-trained on 1.56T words of public dialog
   data and web text. ... The 1st challenge, safety[!], involves ensuring that
   the model's responses are consistent with a set of human values ... The
   2nd challenge, factual grounding[!], involves enabling the model to consult
   external knowledge sources ... Finally, we explore the use of LaMDA in the
   domains of education & content recommendations, & analyze their helpfulness
   & role consistency."
   -- [<A HREF="https://arxiv.org/abs/2201.08239">arXiv</A>]['22].
   ("Google engineer put on leave after saying AI chatbot has
    become sentient ..."
    -- The G [<A HREF="https://www.theguardian.com/technology/2022/jun/12/google-engineer-ai-bot-sentient-blake-lemoine">www</A>][13/6/2022].
    Also see the abc@[<A HREF="https://www.abc.net.au/news/2022-06-13/google-ai-lamda-sentient-engineer-blake-lemoine-says/101147222">www</A>][13/6/2022].)
   [Also search for: chatBot]  and  [also search for: AI natural language].

%A E. Ashton
%T Mickey7: A Novel
%I St.Martin's Press
%P 304
%M FEB
%D 2022
%K book, novel, SciFi, c2022, c202x, c20xx, zz0222, uploaded, upload,
   consciousness, immortality, expendable
%X 1st ed 2022; us$18; uk us isbn:250275032; uk us isbn13:978-1250275035.
   "... Mickey7 is an Expendable: a disposable employee on a human expedition
   sent to colonize the ice world Niflheim. Whenever there's a mission that's
   too dangerous - even suicidal - the crew turns to Mickey. After one iteration
   dies, a new body is regenerated with most of his memories intact. ..."

%A D. Kwon
%T The rise of citational justice: how scholars are making references fairer
%J Nature
%M MAR
%D 2022
%K news, views, c2022, c202x, c20xx, zz0322, publish, perish, scientific,
   literature, references, papers, cite, citation, women, colour, STEM,
   academia, KPI, KPIs
%X "An emerging movement aims to push researchers to pay more heed to inequities
   in scholarly citations. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-00793-1">doi:10.1038/d41586-022-00793-1</A>]['22].
   [Also search for: publish perish].

%A W. Van Tilburg
%A E. Igou
%A M. Panjwani
%T Boring people: Stereotype characteristics, interpersonal attributions, and
   social reactions
%J Personality and Social Psychology Bull.
%M MAR
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0422, human, behaviour, psychology, boring,
   dull, person, job, jobs, occupation
%X "... the underlying psychological processes & consequences of perceiving a
   person as 'boring' have been largely unexplored. We examined the stereot.
   features of boring others by having people generate (Study 1) & then rate
   (Study 2) these. We focused on occupations (e.g., data analytics, taxation,
   accounting), hobbies (e.g., sleeping, religion, watching TV), & personal
   characteristics (e.g., lacking humor & opinions, being negative) that people
   ascribed to stereotypically boring others. Experiments then showed that those
   who were ascribed boring characteristics were seen as lacking interpersonal
   warmth & competence (Study 3), were socially avoided (Study 4), & enduring
   their company required compensation (Study 5). These results suggest that
   being stereotyped as a bore may come with substantially -ve interpersonal
   consequences."
   -- [<A HREF="https://doi.org/10.1177/01461672221079104">doi:10.1177/01461672221079104</A>]['22],
      [<A HREF="http://repository.essex.ac.uk/32109/">essex.ac.uk</A>]['22].
   (ignobel candidate?  Not interesting enough?)

%A B. Capra
%T The metaphysics of farts
%J Think
%M MAR
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0622, fart, funny, bum, butt,
   ha ha, haha, philosophy
%X "I consider the metaphysics of farts. I contrast the essential-bum-origin
   view with a phenomenological view, and I argue in favour of the latter."
   -- [<A HREF="https://www.cambridge.org/core/journals/think/article/metaphysics-of-farts/6BD856AD874E9B23DC0AAD80CB465397">www</A>]['22].
   (?Not 1 April, but close? ?ig...?)

%A F. Urbina
%A et al
%T Dual use of artificial-intelligence-powered drug discovery
%J Nat. Mach. Intell.
%V 4
%P 189-191
%M MAR
%D 2022
%K news, views, MolBio, c2022, c202x, c20xx, zz0723, risk, risks, AI,
   biochemical weapon, weapons
%X "An int. security conf. explored how artificial intelligence (AI)
   technologies for drug discovery could be misused for de novo design of
   biochemical weapons. A thought experiment evolved into a comp'l proof."
   -- [<A HREF="https://doi.org/10.1038/s42256-022-00465-9">doi:10.1038/s42256-022-00465-9</A>]['23].

%A D. Singh Chawla
%T Russian site peddles paper authorship in reputable journals for up to
   $5000 a pop
%J Science
%V ?
%M APR
%D 2022
%K news, Abalkina, c2022, c202x, c20xx, zz0422, university, scientific,
   research, paper mill, papers, publications, academic misconduct, KPI, KPIs,
   fake, fraud, author, PaperMill, ghostwriting, Russia, Russian, LLC
%X "Since 2019, Anna Abalkina has been monitoring a website that offers an
   illicit way for scientists to burnish their CVs. The site, operated from
   Russia, openly offers to sell authorship slots on soon-to-be-published
   sci.papers, for fees ranging from several hundred dollars to nearly $5000.
   ..."
   -- [<A HREF="https://doi.org/10.1126/science.abq4090">doi:10.1126/science.abq4090</A>]['22],
   and report at [<A HREF="https://arxiv.org/ftp/arxiv/papers/2112/2112.13322.pdf">arxiv</A>]['22].
   [Also search for: academic misconduct] & [also search for: PaperMill] etc..

%A C. S. O. Siew
%A T. Engelthaler
%A T. T. Hills
%T Nymph piss and gravy orgies: Local and global contrast effects in
   relational humor
%J J. of Experimental Psychology: Learning, Memory, and Cognition
%D 2022
%K jrnl, psychology, humour, c2022, c202x, c20xx, zz0522, funny, ha ha, haha,
   words, phrases, natural language, joke, jokes
%X "How does the relation between two words create humor? In this article, we
   investigated the effect of global & local contrast on the humor of word
   pairs. ... find evidence of both global & local contrast on compound-word
   humor. Specifically, we find that humor arises when there is a violation of
   expectations at the local level, between the individual words that make up
   the word pair, even after accounting for violations at the global level
   relative to the entire language. ... also find that semantic dissimilarity
   increases humor ..."
   -- [<A HREF="https://doi.org/10.1037/xlm0001120">doi:10.1037/xlm0001120</A>]['22],
      3r7fw@[<A HREF="https://psyarxiv.com/3r7fw/">psyarxiv</A>]['22].
   (auth1@[<A HREF="http://hello.csqsiew.xyz/">xyz</A>]['22].)

%A A. George
%A T. Walsh
%T Artificial intelligence is breaking patent law
%J Nature
%M MAY
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0622, AI, law, patent, patents, invention
%X "The patent system assumes that inventors are human. Inventions devised by
   machines require their own intellectual property law and an international
   treaty. In 2020, a machine-learning algorithm helped researchers to develop a
   potent antibiotic that works against many pathogens ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-01391-x">doi:10.1038/d41586-022-01391-x</A>]['22].

%A V. Gewin
%T Has the 'great resignation' hit academia?
%J Nature
%V 606
%P 211-213
%M MAY
%D 2022
%K news, views, c2022, c202x, c20xx, zz0622, university administration,
   leavingacademia, academia, management, KPI, KPIs, jobs, career
%X "... growing wave of researchers using the #leavingacademia hashtag ...
   By May 2021, one in five academic jobs in Australia had been cut. ...`
   -- [<A HREF="https://doi.org/10.1038/d41586-022-01512-6">doi:10.1038/d41586-022-01512-6</A>]['22].
   [Also search for: university administration].

%A Yingchen Wang
%A et al
%T Hertzbleed: Turning power side-channel attacks into remote timing attacks on
   x86
%M JUN
%D 2022
%O 31st USENIX Security Symp., Boston, 10-12 Aug. 2022
%K conf, Hertzbleed, c2022, c202x, c20xx, zz0622, hack, computer security, SIKE,
   attacker, x86, CPU, attack
%X "... we show that on modern Intel (and AMD) x86 CPUs, power side-channel
   attacks can be turned into timing attacks that can be mounted without access
   to any power measurement interface ... we show that this new channel is a
   real threat to the security of cryptographic software ..."
   -- [<A HREF="https://www.hertzbleed.com">hertzbleed.com</A>][6/2022].

%A D. Monroe
%T Building a practical quantum computer
%J CACM
%V 65
%N 7
%P 15-17
%M JUL
%D 2022
%K news, views, c2022, c202x, c20xx, zz0722, quantum computer, progress, survey
%X "... quantum computing has not made practical contributions. Moreover,
   there is still no winner among very different schemes to physically
   implement quantum bits, or qubits. ..."
    -- [<A HREF="https://doi.org/10.1145/3535191">doi:10.1145/3535191</A>]['22].

%A D. S. Chawla
%T Swiss funder unveils new CV format to make grant evaluation fairer
%J Nature
%V 606
%P 1033-1034
%M JUN
%D 2022
%K news, views, c2022, c202x, c20xx, zz0722, hire, fire, KPI, KPIs, SciCV,
   jobs, academia, ARC, NSF, grant, grants, scientific research, management,
   funding, Switzerland, Europe
%X "Switzerland's main research funder is set to roll out a 'narrative' CV
   format for grant applications this year, as part of a move to showcase
   achievements beyond publication lists. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-01599-x">doi:10.1038/d41586-022-01599-x</A>]['22].
   [Also search for: grant funding].

%A E. Gibney
%T Open-source language AI challenges big tech's models
%J Nature
%V 606
%P 850-851
%M JUN
%D 2022
%K news, views, c2022, c202x, c20xx, zz0722, BLOOM, AI, natural language model,
   NN, ANN, BigScience, GPT 3, GPT3, ChatGPT, chatBot, OpenAI, openSource
%X "An international team of around 1,000 largely academic volunteers has tried
   to break big tech's stranglehold on natural-language processing & reduce its
   harms. ... the BLOOM language model will rival in scale those made by firms
   Google & OpenAI, but will be open-source. ... BLOOM has 176 billion params,
   on a par with GPT-3 ... researchers hand-picked nearly 2/3 of their
   341-billion-word data set from 500 sources. [inc.] Semantic Scholar ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-01705-z">doi:10.1038/d41586-022-01705-z</A>]['22].
   Also see BLOOM@[<A HREF="https://en.wikipedia.org/wiki/BLOOM_(language_model)">wikip</A>]['23]
   &  B'gSc'ence@[<A HREF="https://bigscience.huggingface.co/">www</A>]['22]
   v. [<A HREF="https://openai.com/">OpenAI</A>]['22] (NB. not opensource).
   [Also search for: natural language NN].  (Also see GPT4 3/2023.)

%A P. Surendiran
%A et al
%A T. Korten
%T Solving exact cover instances with molecular-motor-powered network-based
   biocomputation
%J Amer. Chem. Soc. Nanoscience
%M JUN
%D 2022
%K c2022, c202x, c20xx, zz0722, bio computer, bioComputer, computing,
   network based biocomputation, NBC, exact cover problem
%X "... An alternative, highly energy efficient, parallel computing paradigm is
   network-based biocomputation (NBC). In NBC a given combinatorial problem is
   encoded into a nanofabricated, modular n/wk. Parallel exploration of the
   n/wk by a very large # of indep. molec.-motor-propelled protein filaments
   solves the encoded problem. Here we demo. a sig. scale-up of this technology
   by solving four instances of Exact Cover ... The difficulty of the largest
   instances solved here is 128 times greater in comparison to the current
   state of the art for NBC."
   -- [<A HREF="https://doi.org/10.1021/acsnanoscienceau.2c00013">doi:10.1021/acsnanoscienceau.2c00013</A>]['22].
   (Last auth@[<A HREF="https://scholar.google.de/citations?user=7A6Oz4AAAAAJ&hl=en">sch'l'r</A>]['22].)
   [Also search for: biocomputer].

%A E. Shein
%T Using makeup to block surveillance
%J CACM
%V 65
%N 7
%P 21-23
%M JUL
%D 2022
%K cacm, c2022, c202x, c20xx, zz0722, Guetta, makeup, surveillance, CCTV,
   camera, disguise, dazzle camouflage, face, facial recognition
%X "Altering one's facial features with a special type of makeup
   can keep them from being recognized by artificial intelligence. ..."
   -- [<A HREF="https://doi.org/10.1145/3535192">doi:10.1145/3535192</A>]['22].

%A P.-H. Kamp
%T Surveillance too cheap to meter
%J CACM
%V 65
%N 7
%P 42-44
%M JUL
%D 2022
%K cacm, c2022, c202x, c20xx, zz0722, Big Brother, bigBrother, privacy,
   state surveillance, mobile phone, internet, meta data, metadata, advertising,
   real time bidding, RTB, tracking, users, facebook, google
%X "Stopping Big Brother would require an expensive overhaul of the entire
    system. ..."
   -- [<A HREF="https://doi.org/10.1145/3511661">doi:10.1145/3511661</A>]['22].

%T Agreement on Reforming Research Assessment
%Q ScienceEurope.org
%M JUL
%D 2022
%K c2022, c202x, c20xx, zz0722, Europe, EU, scientific, research management,
   reform, academia, university, KPI, KPIs, ranking, grant, grants, peer review,
   publish, perish, metrics, JIF, RoRI, DORA
%X "... The Agreement on Reforming Research Assessment sets a shared direction
   for changes in assessment practices for research, researchers & research
   performing organisations, with the overarching goal to maximise the quality
   & impact of research. ... 'Publish or perish' & metrics have led us into a
   blind alley. ..."
   -- [<A HREF="https://scienceeurope.org/news/rra-agreement-final">scienceeurope</A>]['22].
   Also see N'ture@[<A HREF="https://doi.org/10.1038/d41586-022-02037-8">doi:10.1038/d41586-022-02037-8</A>]['22].
   [Also search for: publish perish]  and  [also search for: peer review].

%A M. Onen
%A et al
%T Nanosecond protonic programmable resistors for analog deep learning
%J Science
%V 377
%N 6605
%P 539-543
%M JUL
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0722, analog, analogue, nonStandard, computing,
   non standard, ANN, NN, artificial neuron, proton, synapse
%X "... Nanoscale ionic programmable resistors for analog deep learning are
   1000 times smaller than biological cells ... we generated silicon-compatible
   nanoscale protonic programmable resistors ... This operation regime enabled
   controlled shuttling & intercalation of protons in nanoseconds at room temp.
   in an energy-efficient manner. ... showed symmetric, linear & reversible
   modulation characteristics with many conductance states covering a 20 x
   dynamic range. Thus, the space-time-energy performance of the all-solid-state
   artificial synapses can greatly exceed that of their biol. counterparts."
   -- [<A HREF="https://doi.org/10.1126/science.abp8064">doi:10.1126/science.abp8064</A>]['22].
   [Also search for: analogue computing].

%A S. Babones
%T International student revenue and international rankings success: A case
   study of Australian university research strategies
%J Youth and Globalization
%I BRILL
%V 4
%N 1
%P 56-81
%M JUL
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1122, Australia, academia, University, research,
   Go8, management, THES, ranking, rankings, gaming, bias, KPI, KPIs, money,
   overseas, students, education
%X "The publication of the 1st major int. uni. rankings in 2003 opened up a new
   era in ... generated a potential principal-agency problem, as
   nationally-funded unis. increasingly seek int. validation. ... many [.au]
   unis. seem to have excessively expanded their int. student enrolments as a
   way to generate the funds needed to compete in the 'rankings game'. Second,
   many [.au] universities seem to have prioritized research in fields that
   yield higher returns in rankings outcomes. ... provide circumstantial
   evidence that Go8 universities may have compromised their educational
   missions in the pursuit of rankings success."
   -- [<A HREF="https://doi.org/10.1163/25895745-bja10019">doi:10.1163/25895745-bja10019</A>]['22]
   or [<A HREF="https://brill.com/view/journals/yogo/4/1/article-p56_004.xml">www</A>]['22].
   [Also search for: University management].

%A A. Severin
%A et al
%T Journal impact factor and peer review thoroughness and helpfulness:
   A supervised machine learning study
%J arXix
%M JUL
%D 2022
%K TR, c2022, c202x, c20xx, zz0922, peer review, reviewing, refereeing,
   journal, JIF, scientific papers
%X "... We examined the assoc. between the content of peer review & JIF by
   analysing 10,000 peer review reports submitted to 1,644 medical & life sci.
   journals. ... examined the assoc. between ten groups of journals defined by
   JIF deciles & the content of peer reviews using linear mixed-effects models
   ... peer review in journals with higher JIF tends to be more thorough in
   discussing the methods used but less helpful in terms of suggesting solns &
   providing examples. Differences were modest & variability high, indicating
   that the JIF is a bad predictor for the quality of peer review of an
   individual manuscript."
   -- [<A HREF="https://arxiv.org/abs/2207.09821">arXiv</A>]['22].

%T Status Report on the Third Round of the NIST Post-Quantum Cryptography
   Standardization Process
%I NIST
%M JUL
%D 2022
%K c2022, c202x, c20xx, zz0424, post quantum encryption, lattice problem, NIST,
   CRYSTALS, Kyber, quantum computing, cryptography, encryption, public key
%X "The National Institute of Standards & Technology is in the process of
   selecting public-key cryptographic algs. through a public, competition-like
   process ... summarizes each of the 15 third-round candidate algs. &
   identifies those selected for standardization ..."
   -- [<A HREF="https://doi.org/10.6028/NIST.IR.8413-upd1">doi:10.6028/NIST.IR.8413-upd1</A>]['24].
   Also see Kybr@[<A HREF="https://en.wikipedia.org/wiki/Kyber">wikip</A>]['24].
   [Also search for: post quantum cryptography].

%A A. Cho
%T Ordinary computers can beat Google's quantum computer after all
%J Science
%V 377
%N 6606
%M AUG
%D 2022
%K news, views, c2022, c202x, c20xx, zz0822, quantum computing, computer,
   supremacy, speed, google, Sycamore
%X "... In 2019, Google researchers claimed they had passed a milestone known as
   q.supremacy when their q.computer Sycamore performed in 200 seconds an
   abstruse calculation they said would tie up a supercomputer for 10,000years.
   Now, scientists in China have done the computation in a few hours with
   ordinary processors. A supercomputer, they say, could beat Sy. outright. ..."
   -- [<A HREF="https://doi.org/10.1126/science.ade2364">doi:10.1126/science.ade2364</A>]['22].
   [Also search for: quantum computer]  &  [also search for: quantum supremacy].

%A J. Tollefson
%A R. Van Noorden
%T US government reveals big changes to open-access policy
%J Nature
%M AUG
%D 2022
%K news, views, c2022, c202x, c20xx, zz0922, scientific research, publishing,
   open access, equity, paywall, publishers, papers
%X "US research agencies should make the results of federally funded research
   free to read as soon as they are published, the administration of President
   Joe Biden has announced ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-02351-1">doi:10.1038/d41586-022-02351-1</A>]['22].
   Also, J. Brainard, J. Kaiser, Sci., 26 Aug. 2022,
   "White House requires immediate public access to all U.S.-funded
   research papers by 2025 ..."
   -- [<A HREF="https://doi.org/10.1126/science.ade6076">doi:10.1126/science.ade6076</A>]['22].
   [Also search for: research open access].

%A I. Lazaridis
%E et al
%T The genetic history of the Southern Arc: A bridge between West Asia and
   Europe
%J Science
%V 377
%N 6609
%P ?-?
%M AUG
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1122, linguistics, human, language evolution,
   PIE, evolutionary, genetics, proto Indo European, migration, Anatolia,
   Yamnaya, Asian
%X "By seq. 727 ancient individuals from the S.Arc (Anatolia & its neighbors
   in SE Europe & W.Asia) over 10,000y. ... Two streams of migration
   transmitted Caucasus & Anatolian/Levantine ancestry northward, & the Yamnaya
   pastoralists, formed on the steppe, then spread southward into the Balkans
   & across the Caucasus into Armenia ... Anatolia was transformed by
   intra-West Asian gene flow, with negligible impact of the later Yamnaya
   migrations. This contrasts with all other regions where Indo-European
   languages were spoken, suggesting that the homeland of the Indo-Anatolian
   language family was in West Asia, with only secondary dispersals of
   non-Anatolian Indo-Europeans from the steppe."
   -- [<A HREF="https://doi.org/10.1126/science.abm4247">doi:10.1126/science.abm4247</A>]['22].

%A S. Crafa
%T From legal contracts to legal calculi: the code-driven normativity
%J arXiv
%M SEP
%D 2022
%K TR, c2022, c202x, c20xx, zz0922, law, legal, contract, automation, automatic,
   formal, programming, logic, LP, permission, prohibition, obligation
%X "... we focus on software-based legal contracts; we illustrate the design of
   a legal calculus whose primitives allow a direct formalisation of contracts'
   normative elts (i.e., permissions, prohibitions, obligations, asset transfer,
   judicial enforcement & openness to the external context). We show that
   interpreting legal contracts as interaction protocols between (untrusted)
   parties enables the generalisation of formal methods & tools for concurrent
   systems to the legal setting."
   -- 2209.02353@[<A HREF="https://arxiv.org/abs/2209.02353">arXiv</A>]['22].
   [Also search for: automatic contract programming].

%A M. Le Conte
%T Escape: How a generation shaped, destroyed and survived the internet
%I BlinkPubl
%P 304
%M SEP
%D 2022
%K book, c2022, c202x, c20xx, LeConte, zz0922, internet, www, mail groups,
   social media, web, internet, blog, MSN, Tumblr, myspace, facebook, twitter,
   chat rooms, forums
%X "... [auth] was born in 1991, the same year the WWW was invented. She had
   her first blog at twelve ... MSN, Tumblr and MySpace, to chat rooms, forums
   and blogs; Marie is part of the millennial generation that grew up while the
   internet was growing up with them. Where did it go all wrong? How did the
   internet go from a place where you went to escape real life to where real
   life is shaped? ..."
   1st ed 2022; hb stg5; uk us isbn:1788705157; uk us isbn13:978-1788705158.
   [Also search for: social media].

%A L. Allison
%T Allison's law
%M OCT
%D 2022
%K c2022, c202x, c20xx, zz1022, LAllison, Lloyd, Allisons, funny, laws,
   axiom, principle, Optus, data breach, identity theft, scam, fraud, personal,
   DOB, privacy, security
%X "Any set of private information[*] used to establish the identity of
   an individual who is remote[#] will rapidly become unfit for purpose."
   ... this in the wake of the Optus data breach and
       in the spirit of Goodhart's/Campbell's law.
   (The principle is v.probably out-there from long ago, although
   maybe I can still claim it in an instance of Stigler's law?)
      [*] e.g., date of birth (dob), phone number, pet's name, licence number.
      [#] e.g., phone, email, login.
   [Also search for: funny law].

%A E. Terzon
%T Medibank, Optus hacks and ATO attacks expose identity-theft
   risks, warn cyber security experts
%I ABC
%M OCT
%D 2022
%K news, c2022, c202x, c20xx, zz1022, Optus, Medicare, data breach,
   hack, identity theft, ATO, Australia, Cybersecurity
%X "The Australian Tax Office has revealed it gets 3 million
   attempted hacks on its systems every month ... Medibank has now
   admitted that the personal data of some of its customers has been
   stolen in the cyber attack, inc. Medicare information, policy
   numbers, & some claims data. It follows the breach on telco Optus,
   where hackers claimed to have accessed the data of 9.8 million
   current and former customers, including their passports, drivers
   licences and Medicare card details. ..."
   -- [<A HREF="https://www.abc.net.au/news/2022-10-21/medibank-data-breach-cyber-expert-warning/101557684">ABC</A>][21/10/2022].
   [Also search for: Allison's law].

%A E. Terzon
%A S. Yang
%T Medibank says all customers' personal data compromised by cyber attack
%I ABC
%M OCT
%D 2022
%K news, c2022, c202x, c20xx, zz1022, Australia, Medibank, health data breach,
   healthcare, identity theft, security, privacy, hack
%X "Medibank has confirmed the criminal entity behind the cyber attack on the
   company had access to the data of at least 4 million customers, some of which
   includes health claims. ..."
   -- [<A HREF="https://www.abc.net.au/news/2022-10-26/medibank-hack-criminals-access-hack-data/101578438">abc</A>][26/10/2022].
   [Also search for: medibank].

%A C. Woolston
%T Stress and uncertainty drag down graduate students' satisfaction
%J Nature
%V 610
%P 805-808
%M OCT
%D 2022
%K news, views, c2022, c202x, c20xx, zz1122, scientific, university, research,
   academia, PhD, MSc, postgrad, postgraduate, student, jobs, career,
   well being, management
%X "Scholars in PhD & master's programmes struggle with securing work-life
   balance & support around career training & mental health, finds Nature
   survey. Faced with financial hardships, multiple demands on their time &
   uncertain career prospects, some graduate students are losing faith in their
   chosen career path. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-03394-0">doi:10.1038/d41586-022-03394-0</A>]['22].

%A E. C. R. da Rosa
%A C. Lima
%T Programming with quantum mechanics
%J arXiv
%M OCT
%D 2022
%K TR, tute, intro, survey, c2022, c202x, c20xx, zz1122, quantum computing,
   computer programming language, KET, daRosa
%X "... This tutorial gives a broad view of q.computing, abstracting most of the
   math. formalism & proposing a hands-on with the q. prog. lang. Ket. The
   target audience is undergrad. & grad. students starting in q. computing ..."
   -- 2210.15506@[<A HREF="https://arxiv.org/abs/2210.15506">arXiv</A>]['22].
   [Also search for: quantum programming language].

%A S. M. Fiil-Flynn
%A et al
%T Legal reform to enhance global text and data mining research
%J Science
%V 378
%N 6623
%M DEC
%D 2022
%K news, views, c2022, c202x, c20xx, zz1222, copyright, law, AI, training data,
   internet, www, image, images, text, data mining, TDM, international
%X "... Most text, images, & other materials that TDM [text data mining]
   researchers use are subject to copyright law. Copyright law gives the owner
   of a protected work the legal right to prohibit reproduction, distribution,
   modification, & other forms of exploitation of that work without the owner's
   permission. These rights apply even if the material is readily accessible -
   for example, published on the internet or available in a library. ..."
   -- [<A HREF="https://doi.org/10.1126/science.add6124">doi:10.1126/science.add6124</A>]['22].
   [Also search for: copyright].

%A Bao Yan
%A et al
%T Factoring integers with sublinear resources on a superconducting quantum
   processor
%J arXiv
%M DEC
%D 2022
%K TR, c2022, c202x, c20xx, zz0123, quantum computing, factoring, integers,
   QAOA, integer factorization, factorisation, primes, RSA, RSA2048, encryption,
   cryptology, controversial
%X "... we report a universal q.alg. for int. factorization by combining the
   classical lattice red'n with a q. approximate optimization alg. (QAOA). The
   # of qubits required is O(log(N)/loglog(N)), which is sublinear in the bit
   length of the integer N, making it the most qubit-saving factorization alg.
   to date. We demonstrate [it] experimentally by factoring ints. up to 48
   bits with 10 superconducting qubits, the largest int. factored on a q.device.
   We estimate that a q.circuit with 372 physical qubits & a depth of thousands
   is necessary to challenge RSA-2048 using our algorithm. ..."
   -- [<A HREF="https://doi.org/10.48550/arXiv.2212.12372">doi:10.48550/arXiv.2212.12372</A>]['23].
   [Also search for: quantum computing factorization].
   (Also see, "... 15-digit # 261,980,999,226,229[=]15,538,213x16,860,433 ..."
   -- Nature [<A HREF="https://doi.org/10.1038/d41586-023-00017-0">www</A>][1/2023].)
   AND, "...claims of factoring with q.computers have however been criticized
       for depending heavily on classical comp'n to reduce the # of qubits
       required ..."
       -- IFrecords@[<A HREF="https://en.wikipedia.org/wiki/Integer_factorization_records">wikip</A>]['23].

%A M. Park
%A E. Leahey
%A R. J. Funk
%T Papers and patents are becoming less disruptive over time
%J Nature
%V 613
%P 138-144
%M JAN
%D 2023
%K jrnl, c2023, c2023, c20xx, zz0123, scientific research, progress, impact,
   management, academia, breakthrough, novelty, innovation, disrupt, impact,
   CD, CDindex, publish, perish, paper, patent
%X "... Recent decades have witnessed exponential growth in the volume of new
   scientific & technological knowledge, thereby creating conditions that should
   be ripe for major advances. Yet contrary to this view, studies suggest that
   progress is slowing in several major fields. ... six large-scale datasets,
   together with a new quantitative metric - the CD index ... find that papers
   & patents are increasingly less likely to break with the past in ways that
   push sci. & tech. in new directions. ... link this decline in disruptiveness
   to a narrowing in the use of previous knowledge ..."  [80 refs.]
   -- [<A HREF="https://doi.org/10.1038/s41586-022-05543-x">doi:10.1038/s41586-022-05543-x</A>]['23].
   (Also see comment@[<A HREF="https://doi.org/10.1038/d41586-022-04577-5">www</A>]['23].)
   [Also search for: scientific progress].

%A M. Welsh
%T The end of programming
%J CACM
%V 66
%N 1
%P 34-35
%M JAN
%D 2023
%K views, c2023, c202x, c20xx, zz0123, computer programming, CSci, CompSci,
   prediction, zzPrediction, controversial, deepAI, AI, NN, ANN,
   CoPilot, GPT, GPT2, zz0133
%X "The end of classical computer science is coming, and most of us are
   dinosaurs waiting for the meteor to hit. ... This shift is underscored by the
   fact that nobody actually understands how large AI models work. ..."
   -- [<A HREF="https://doi.org/10.1145/3570220">doi:10.1145/3570220</A>]['23].
   [Also search for: zzPrediction]. Run for the hills? Or check back in 2033?

%A T. Williams
%T Artists angry after discovering artworks used to train AI image
   generators without their consent
%I The Age
%M JAN
%D 2023
%K news, c2023, c202x, c20xx, zz0123, art, ethics, copyright, law, legal, ANN,
   NN, LLM, LarLangM, AI, image generator, Prisma, Lensa, haveibeentrained.com,
   LAION 5B, LAION5B, non-consumptive use, nonConsumptive
%X "Six-time Archibald Prize finalist Kim Leutwyler says "it feels like a
   violation" that their art was used without their consent to train the [AI]
   technology behind increasingly popular text-to-image software. ... An
   artist's individual artworks are protected by copyright law, but their
   overall style is not. ..."
   -- T.W., The Age [<A HREF="https://www.abc.net.au/news/2023-01-10/artists-protesting-artificial-intelligence-image-generators/101786174">10/1/2023</A>].
   [Also search for: AI LLM copyright].

%A J. Kaiser
%T To reduce 'reputational bias,' NIH may revamp how grant proposals are scored
%J Science
%V 379
%M JAN
%D 2023
%K news, views, c2023, c202x, c20xx, zz0123, grant, proposal, grants, NIH, ARC,
   funding, ranking, reputation, scientific research, progress, peer review,
   reviewing, refereeing, importance, rigor, feasibility, expertise, idea, ideas
%X "Researchers familiar with the NIH's peer-review process can cite many cases
   where the reputation of a scientist or their workplace seemed to count for
   more than the strength of their ideas. ... into three factors. Two would be
   scored: importance, & rigor & feasibility. Reviewers would also consider,
   but not directly score, a third factor: expertise & resources. ..."
   -- [<A HREF="https://doi.org/10.1126/science.adg7365">doi:10.1126/science.adg7365</A>]['23].

%A C. A. Gao
%A et al
%T Comparing scientific abstracts generated by ChatGPT to original abstracts
   using an artificial intelligence output detector, plagiarism detector, and
   blinded human reviewers
%K bioRxiv
%M JAN
%D 2023
%K TR, c2023, c202x, c20xx, zz0123, ChatGPT, GPT, chatBot, AI, NN, ANN,
   cheating, publications, paper, papers, reviewing, refereeing, text generator,
   detector, scientific research, university, homework, plagiarism, ethics
%X "...We gathered ten research abstracts from five high impact factor medical
   journals (n=50) & asked ChatGPT to generate research abstracts based on their
   titles & journals. ... Most generated abstracts were detected using the AI
   output detector ... Generated abstracts scored very high on originality using
   the plagiarism detector ... blinded human reviewers correctly identified 68%
   of generated abstracts as being generated by ChatGPT, but incorrectly
   identified 14% of original abstracts as being generated. ..."
   -- [<A HREF="https://doi.org/10.1101/2022.12.23.521610">doi:10.1101/2022.12.23.521610</A>]['23].
   [Also search for: paper generator].

%A H. Else
%T Multimillion-dollar trade in paper authorships alarms publishers
%J Nature
%V 613
%P 617-618
%M JAN
%D 2023
%K news, views, c2023, c202x, c20xx, zz0123, authorship, sell, sale,
   scientific publication, scam, academic misconduct
%X "Research-integrity sleuths have uncovered hundreds of online advertisements
   that offer the chance to buy authorship on research papers to be published in
   reputable jrnls. Publishers are investigating the claims, and have retracted
   dozens of articles over suspicions ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-023-00062-9">doi:10.1038/d41586-023-00062-9</A>]['23].
   [Also search for: authorship misconduct].

%A K. Kirkpatrick
%T Can AI demonstrate creativity?
%J CACM
%V 66
%N 2
%P 21-23
%M FEB
%D 2023
%K news, views, c2023, c202x, c20xx, zz0123, DALL E, DALLE, DALLE2, art,
   image generator, music, creativity, AI, NN, ANN
%X "When fed a sufficient amount of training data, AI techniques can be used to
   generate new ideas in several different ways. Is that creativity?"
   -- [<A HREF="https://dx.doi.org/10.1145/3575665">doi:10.1145/3575665</A>]['23].

%A D. Monroe
%T Post quantum cryptography
%J CACM
%V 66
%N 2
%M FEB
%D 2023
%K news, views, c2023, c202x, c20xx, zz0123, quantum computing, security,
   break, breaking
%X "Cryptographers seek algorithms quantum computers cannot break."
   -- [<A HREF="https://dx.doi.org/10.1145/3575664">doi:10.1145/3575664</A>]['23].

%A H. Holden Thorp
%T Revolt against educational rankings
%J Science
%V 379
%N 6631
%P 419
%M JAN
%D 2023
%K editorial, news, views, c2023, c202x, c20xx, zz0223, university ranking,
   management, academic, academia, deanitis, USA, USnews, T14, KPIs, KPI,
   quote, quotable
%X "The ranking of universities & colleges at the national & global level is a
   well-known dubious practice. Flawed methodologies generate distorted &
   inaccurate profiles of these institutions. Yet, rankings have remained a
   popular ... prestigious law & medical schools have started to walk away from
   this 'evaluation.' ... There are many theories about how higher education in
   the United States lost its way. A reasonable hypothesis is that it started in
   1983 when U.S. News published its first list. It's been downhill ever since.
   Time to turn it around."
   -- [<A HREF="https://doi.org/10.1126/science.adg8723">doi:10.1126/science.adg8723</A>]['23].
   [Also search for: university rankings].

%A N. Oreskes
%A E. M. Conway
%T The Big Myth: How American Business Taught Us to Loathe Government and
   Love the Free Market
%I BloomsburyPubl
%P 576
%M MAY
%D 2023
%K book, text, c2023, c202x, c20xx, zz0223, risks, denial, climate change,
   altRight, science, spin, lies, doubt, USA, politics, economics, reaganomics
%X 1st ed 2023; hb us$63; uk us isbn:1635573572; uk us isbn13:978-1635573572.
   "... In the early 20C, business elites, trade associations, wealthy
   powerbrokers, and media allies set out to build a new American orthodoxy:
   down with 'big government' and up with unfettered markets. ..."
   [Also search for: Oreskes Conway].

%A C. S. de Witt
%A et al
%T Perfectly secure steganography using minimum entropy coupling
%J ICLR
%M MAR
%D 2023
%K conf, ICLR, c2023, c202x, c20xx, zz0323, steganography, secret message,
   hidden, hiding
%X "Steganography is the practice of encoding secret information into innocuous
   content in such a manner that an adversarial third party would not realize
   that there is hidden meaning. ... we show that a s. procedure is perfectly
   secure under ... information theoretic-model of s. if & only if it is induced
   by a coupling. Furthermore, we show that, among perfectly secure procedures,
   a procedure is maximally efficient if & only if it is induced by a minimum
   entropy coupling ..."
   -- [<A HREF="https://arxiv.org/abs/2210.14889">arXiv</A>]['23].
   [Also search for: steganography].

%A K. Sanderson
%T GPT-4 is here: what scientists think
%J Nature
%V 615
%N ?
%P 773
%M MAR
%D 2023
%K news, views, c2023, c202x, c20xx, zz0423, ChatGPT, ChatGPT4, chat gpt 4,
   GPT4, chatBot, AI, NN, ANN
%X NB. OpenAI is not "open".
   "Researchers are excited about the AI - but many are frustrated that its
   underlying engineering is cloaked in secrecy. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-023-00816-5">doi:10.1038/d41586-023-00816-5</A>]['23].
   [Also search for: ChatGPT]  and  [also search for: chatBot].

%A M. Catanzaro
%T Saudi universities entice top scientists to switch affiliations - sometimes
   with cash
%J Nature
%M MAY
%D 2023
%K news, views, c2023, c202x, c20xx, zz0623, Saudi Arabia, academia,
   university rankings, gaming, manipulation, THES
%X "Some institutions arrange for highly cited researchers to change their main
   affiliations, which boosts their position in global university rankings. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-023-01523-x">doi:10.1038/d41586-023-01523-x</A>]['23].
   [Also search for: gaming university rankings] and
   [also search for: Saudi Arabia].

%A E. M. Dworak
%A W. Revelle
%A D. M. Condon
%T Looking for Flynn effects in a recent online U.S. adult sample: Examining
   shifts within the SAPA Project
%J Intelligence
%V 98
%M MAY-JUN
%D 2023
%K jrnl, c2023, c202x, c20xx, zz1223, IQ, Flynn effect, reverse, reversal,
   reversed, decline, USA, SAPA
%X "... 13y of cross-sectional data from a subsample of adults (n=394,378) ...
   showed a pattern consistent with a reversed Flynn effect from 2006 to 2018
   when stratified across age, education, or gender. ... A reversed F.effect was
   also present from 2011 to 2018 for composite ability scores from 60 items ...
   [but] three-dimensional rotn scores showed evidence of a F.effect with the
   largest slopes occurring across age stratified regressions."
   -- [<A HREF="https://doi.org/10.1016/j.intell.2023.101734">doi:10.1016/j.intell.2023.101734</A>]['23].
   [Also search for: Flynn effect IQ], and maybe include: reverse.

%T The Garage Girls and their secret war machine
%I ABC
%M JUN
%D 2023
%O 'Breaking the Code: Cyber Secrets Revealed', ABC News Channel 4/6/2023 &
   ABC1 5/6/2023a & ABC iview
%K news, c2023, c202x, c20xx, zz0623, WW2, WWII, code breaking, Japan, codes,
   1945, Hiroshima, Australia, Central Bureau, women, www, codebreakers, STEM,
   TypeX
%X "Not long after an American atomic bomb exploded over Hiroshima, a horrified
   Japanese officer radioed back to Imperial Navy headquarters in Tokyo to
   report what he had witnessed. ...  his extraordinary witness account was
   intercepted by an Australian signalman stationed near the Philippines. From
   there, it passed into the hands of a secret unit of women codebreakers whose
   work in a garage at the back of a Brisbane mansion was kept top secret for
   decades. ..."
   -- [<A HREF="https://www.abc.net.au/news/2023-06-03/garage-girls-world-war-2-spying-in-australia/102411022">ABC</A>][3/6/2023].

%A F. Joelving
%T Did a 'nasty' publishing scheme help an Indian dental school win high
   rankings? Prodigious self-citation enables Saveetha Dental College to top
   global lists, investigation finds
%M JUN
%D 2023
%K news, views, c2023, c202x, c20xx, zz0623, gaming, QS, university, rankings,
   academia, ranking, citation, citations, publising, dentistry,
   Saveetha, India, SIMATS, scamming, Varghese
%X "... the dental college, part of the larger Saveetha Inst. of Medical &
   Tech. Sci. (SIMATS), appears to have quietly pursued self-citation at an
   industrial scale ..."
   -- [<A HREF="https://doi.org/10.1126/science.adj1231">doi:10.1126/science.adj1231</A>]['23].
   [Also search for: gaming rankings academia].

%A P. Samuelson
%T Generative AI meets copyright.  Ongoing lawsuits could affect everyone who
   uses generative AI
%J Science
%V 381
%N 6654
%M JUL
%D 2023
%K new, views, c2023, c202x, c20xx, zz0723, AI, LLM, chatGPT, OpenAI, chatGPT,
   copyright law, USA, StabilityAI, Getty, Codex, Copilot, gBARD, BARD,
   training data, LAION
%X "... some professional artists, writers, & programmers fiercely object to the
   use of their creations as training data for generative AI systems & to
   outputs that may compete with or displace their works. Lack of attribution &
   compensation for use of their original creations are other sources of
   aggravation to critics of generative AI. Copyright lawsuits that are now
   underway in the United States ..."
   -- [<A HREF="https://doi.org/10.1126/science.adi0656">doi:10.1126/science.adi0656</A>]['23].
   [Also search for: AI LLM copyright].

%A M. Mitchell
%T How do we know how smart AI systems are?
%J Science
%V 381
%N 6654
%M JUL
%D 2023
%K news, views, c2023, c202x, c20xx, zz0723, AI, NN, ANN, chatBot, chatGPT,
   intelligence, understanding, cleverness, clever, smartness, OpenAI, GPT4,
   exam, flaws, pitfalls, leakage, overfitting, test set, testing data
%X "... We humans, however, are prone to anthropomorphism ... earlier this year,
   OpenAI reported that its most advanced AI system, GPT-4, scored highly on the
   Uniform Bar Exam, the Graduate Record Exam ... One problem is known as 'data
   contamination.' ... critics noted that for one of the coding benchmarks,
   GPT-4's performance on problems published before 2021 was substantially
   better than on problems published after 2021 - GPT-4's training cutoff. This
   is a strong indication that the earlier problems were in GPT-4's training
   data. ... Second is the problem of robustness. ... Third is the problem of
   flawed benchmarks. ..."
   -- [<A HREF="https://doi.org/10.1126/science.adj5957">doi:10.1126/science.adj5957</A>]['23].

%A A. Heidt
%T Artificial-intelligence search engines wrangle academic literature
%J Nature
%V 620
%P 456-457
%M AUG
%D 2023
%K news, views, c2023, c202x, c20xx, zz0823, internet, www, search engine,
   scientific literature, research, publications, bias, AI, chatBot
%X "Developers want to free scientists to focus on discovery & innovation by
   helping them to draw connections from a massive body of literature. ... the
   programs remain relatively untested & run the risk of perpetuating existing
   biases in the academic publishing process. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-023-01907-z">doi:10.1038/d41586-023-01907-z</A>]['23].
   [Also search for: laws Matthew principle].

%A S. Ambrogio
%A et al
%T An analog-AI chip for energy-efficient speech recognition and transcription
%J Nature
%V 620
%P 768-775
%M AUG
%D 2023
%K jrnl, c2023, c202x, c20xx, zz0823, analogue, tiles, NN, ANN, computing,
   multiplication
%X "... Analog in-memory computing (analog-AI) can provide better energy
   efficiency by performing matrix-vector mult'ns in parallel on 'memory tiles'.
   However, analog-AI has yet to demonstrate SW-equiv. accuracy on models that
   require many such tiles & efficient communication of NN activations between
   the tiles. Here we present an analog-AI chip that combines 35 million
   phase-change memory devices across 34 tiles, massively parallel inter-tile
   comm'n & analog, low-power peripheral circuitry that can achieve up to
   12.4 tera-operations per sec. per watt (TOPS/W) chip-sustained performance.
   We demonstrate fully end-to-end SWeq accuracy for a small keyword-spotting
   n/wk & near-SWeq accuracy on the much larger MLPerf8 recurrent NN transducer
   (RNNT), with more than 45 million weights mapped onto more than 140 million
   phase-change memory devices across five chips."
   -- [<A HREF="https://doi.org/10.1038/s41586-023-06337-5">doi:10.1038/s41586-023-06337-5</A>]['23].
   [Also search for: analogue computing].

%A M. Joseph
%A G. Sekar
%A R. Balasubramanian
%T Revisiting the software-efficient stream ciphers RCR-64 and RCR-32
%J COMPJ
%V ?
%N ?
%P ?-?
%M AUG
%D 2023
%K jrnl, COMPJ, c2023, c202x, c20xx, zz0923, cryptography, encryption, cipher,
   stream, RCR 32 64, RCR64, RCR32, Sekar, security, cryptanalytic attacks
%X "... The RCR ciphers have remained unbroken since they were publ. in 2007.
   ... we present arguments that not only support the designers' security claims
   but suggest, in general, that the ciphers are secure against several classes
   of cryptanalytic attacks. We find that the ciphers are best used with 256-bit
   keys & 384-bit IVs. ..."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxad084">doi:10.1093/comjnl/bxad084</A>]['23].
   [Also search for: RCR cryptography].

%A O. Regev
%T An efficient quantum factoring algorithm
%J arXiv
%M SEP
%D 2023
%K TR, c2023, c202x, c20xx, zz0923, Shor's algorithm, factorisation, algorithm,
   integers, factorization, quantum computing
%X "We show that n-bit ints. can be factorized by indep. running a q.circuit
   with ~O(n^{3/2}) gates for sqrt(n)+4 times, & then using polynomial-time
   classical post-processing. The correctness of the alg. relies on a #-theor.
   heuristic assumption reminiscent of those used in subexponential classical
   factorization algs.. It is currently not clear if [it] can lead to improved
   physical implementations in practice."
   -- [<A HREF="https://arxiv.org/abs/2308.06572">arxiv:2308.06572</A>]['23].
   [Also search for: integer factorisation algorithm] and
   [also seach for: factorisation quantum Shor].
   (Also see comment@[<A HREF="https://doi.org/10.1126/science.adk9418">www</A>][19/9/2023].)

%A N. Jones
%T How to stop AI deepfakes from sinking society - and science
%J Nature
%V 621
%P 676-679
%M SEP
%D 2023
%K news, views, c2023, c202x, c20xx, zz0923, LarLangM, LLM, AI, ANN, generative,
   deepFake, fake, images, papers, fakeNews, SynthID, C2A
%X "Deceptive videos & images created using generative AI could sway elections,
   crash stock markets & ruin reputations. Researchers are developing methods to
   limit their harm. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-023-02990-y">doi:10.1038/d41586-023-02990-y</A>]['23].
   [Also search for: LLmodel AI].

%A T. Recuber
%T The Digital Departed: How We Face Death, Commemorate Life, and
   Chase Virtual Immortality
%I NYUpress
%P 290
%M SEP
%D 2023
%K book, text, c2023, c202x, c20xx, zz0124, life, death, dead, memorial,
   social media
%X 1st ed 2023; hb us$165; uk us isbn:1479814946; uk us isbn13:978-1479814947.
   "... the social meaning of digital death From blogs written by terminally ill
   authors to online notes left by those considering suicide, technology has
   become a medium for the dead and the dying to cope with the anxiety of death.
   Services like artificial intelligence chatbots ..."

%A S. Arai
%A H. Oshiyama
%A H. Nishimori
%T Effectiveness of quantum annealing for continuous-variable optimization
%J Phys Rev A
%V 108
%N 4
%M OCT
%D 2023
%K jrnl, c2023, c202x, c20xx, zz1023, Dwave, 2000Q, quantum annealing,
   computing, optimisation
%X "... We test the performance of quantum annealing applied to a 1D
   cts-variable fn with a rugged energy landscape. ... we conclude that the
   hardware realization of quantum annealing has the potential to sig.
   outperform the best classical algs. if thermal noise & other imperfections
   are sufficiently suppressed & the device operates coherently, as demonstrated
   in recent short-time quantum simulations."
   -- [<A HREF="https://doi.org/10.1103/PhysRevA.108.042403">doi:10.1103/PhysRevA.108.042403</A>]['23].

%A S. Choi
%A et al
%T The quantum tortoise and the classical hare: A simple framework for
   understanding which problems quantum computing will accelerate (and
   which it will not)
%J arXiv
%M OCT
%D 2023
%K TR, news, views, c2023, c202x, c20xx, zz1023, quantum computing, supremacy,
   speedup
%X "... Our analysis reveals that many problems, particularly those of small to
   moderate size that can be important for typical businesses, will not benefit
   from q.computing. Conversely, larger problems or those with particularly big
   algorithmic gains will benefit from near-term q.c.. Since v.large algorithmic
   gains are rare in practice & theorized to be rare even in principle, our
   analysis suggests that the benefits from q.c. will flow either to users of
   these rare cases, or practitioners processing very large data."
   -- [<A HREF="https://arxiv.org/abs/2310.15505">arxiv:2310.15505</A>]['23].

%A J. M. Parrilla
%T ChatGPT use shows that the grant-application system is broken
%J Nature
%V 623
%N 443
%M OCT
%D 2023
%K news, views, c2023, c202x, c20xx, zz1123, chatGPT, AI, academia, university,
   scientific, research, management, grant, grants, writing, proposals,
   funding, ERA, ARC, NIH, wastes, waste, time
%X "I've always hated writing grants. ... for a 90-95% chance of getting
   rejected. ... A 2023 Nature survey of 1,600 researchers found that more than
   25% use AI to help them write manuscripts & that more than 15% use the
   tech. to help them write grant proposals. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-023-03238-5">doi:10.1038/d41586-023-03238-5</A>]['23].
   [Also search for: research funding waste].

%A H. Takizawa
%T Othello is solved
%J arXiv
%M OCT
%D 2023
%K TR, c2023, c202x, c20xx, zz1023, Othello, solved, board game, theory, draw
%X "... Othello has roughly ten octodecillion (10 to the 58th power) possible
   game records & ten octillion (10 to the 28th power) possible game position.
   ... announces a sig. milestone: O. is now solved, computationally proved that
   perfect play by both players lead to a draw. Strong O. s/w has long been
   built using heuristically designed search techniques. Solving a game provides
   the soln which enables s/w to play the game perfectly."
   -- [<A HREF="https://arxiv.org/abs/2310.19387">arxiv:2310.19387</A>]['23].
   (Proof depends on a program.)
   [Also search for: Othello game].

%A K. Sanderson
%T Who should pay for open-access publishing? APC alternatives emerge
%J Nature
%M NOV
%D 2023
%K news, views, c2023, c202x, c20xx, zz1123, publication, journals, publishing,
   open access, science, research, papers, costs, charges, APCs
%X "Article-processing charges levied by publishers on authors have become an
   integral - and sometimes unpopular - part of the open-access revolution.
   Other options are being explored. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-023-03506-4">doi:10.1038/d41586-023-03506-4</A>]['23].
   [Also search for: open access publishing].

%A Y. Stephanou
%T A Theory of Truth
%M OCT
%D 2023
%K book, text, c2023, c202x, c20xx, zz1223, truth, philosophy, logic,
   liar paradox, paradoxes
%X 1st ed 2023; hb $154; uk us isbn:1009437186; uk us isbn13:978-1009437189
   "How should we treat the liar & kindred paradoxes? A Theory of Truth argues
   that we should diverge from classical logic, & presents a new formal theory
   of truth. ... deviates from classical logic significantly, & endorses
   principles like 'No sentence is both true & false' & 'No sentence is neither
   true nor false'. ..."
   [Also search for: logic paradox].

%A U. Sabbagh
%T The postdoc experience is broken. Funders such as the NIH must help to
   reimagine it
%J Nature
%V 624
%P 475
%M DEC
%D 2023
%K news, views, c2023, c202x, c20xx, zz1223, postdoc, postdocs, postgrad, PhD,
   academia, jobs, career, careers, exploitation, scientific research
%X "It's not breaking news that postdocs feel undervalued and demoralized. In a
   Nature survey of 3,838 postdocs in 93 countries earlier this year, only 40%
   were satisfied with their salaries, & just 34% with their career-advancement
   prospects ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-023-04028-9">doi:10.1038/d41586-023-04028-9</A>]['23].
   [Also search for: postdoc]

%A J. P. A. Ioannidis
%A T. A. Collins
%A J. Baas
%T Evolving patterns of extremely productive publishing behavior across science
%J bioRxiv
%D DEC
%D 2023
%K TR, c2023, c202x, c20xx, zz0124, implausibly prolific, papers, publications,
   academia, academic, Saudi Arabia, China, publish, perish, paper mill, ARC,
   University rankings, management, misconduct, fake, authorship, guest author
%X "... Extremely productive (EP) authors were defined as those with > 60 full
   papers (articles, reviews, conf. papers) published in a single calendar year
   & indexed in Scopus. ... While Physics had much higher #s of EP authors in
   the past, in 2022 the number of EP authors was almost similar in non-Physics
   & Physics disciplines (1,226 vs. 1,480). ..."
   -- [<A HREF="https://doi.org/10.1101/2023.11.23.568476">doi:10.1101/2023.11.23.568476</A>]['24].
   (Also see G.Conroy@[<A HREF="https://doi.org/10.1038/d41586-023-03865-y">www</A>]['24].)
    [Also seach for: implausibly prolific].

%A M. Catanzaro
%T Citation cartels help some mathematicians - and their universities - climb
   the rankings
%J Science
%M JAN
%D 2024
%K news, c2024, c202x, c20xx, zz0224, university ranking, rankings, academia,
   publications, fraud, citation cartel, citations, China, Egypt, Saudi Arabia,
   rankings, manipulation, gaming, maths, bibliometrics, Clarivate, Docampo
%X "Cliques of mathematicians at institutions in China, Saudi Arabia, &
   elsewhere have been artificially boosting their colleagues' citation counts
   by churning out low-quality papers that repeatedly reference their work,
   according to an unpublished analysis seen by Science. ..."
   -- [<A HREF="https://doi.org/10.1126/science.zcl2s6d">doi:10.1126/science.zcl2s6d</A>]['24].
   [Also search for: university ranking].

%A M. Kozlov
%T Dana-Farber retractions: meet the blogger who spotted problems in dozens of
   cancer papers
%J Nature
%V 626
%P 16-17
%M JAN
%D 2024
%K news, c2024, c202x, c20xx, zz0224, academic research, publications, papers,
   scientific, misconduct, images, figures, paper retraction, DFCI, Sholto David
%X "The prestigious Dana-Farber Cancer Institute (DFCI) in Boston, Mass.,
   acknowledged this week that it would seek retractions for 6 papers &
   corrections for an additional 31 ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-024-00202-9">doi:10.1038/d41586-024-00202-9</A>]['24].
   [Also search for: paper retraction].

%A A. M. Lindkvist
%A L. Koppel
%A G. Tinghog
%T Bounded research ethicality: researchers rate themselves and their field as
   better than others at following good research practice
%J Sci. Reports
%V 14
%N 3050
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0324, scientific research, academia, university,
   ethics, survey, Sweded, Linkoping
%X "Bounded ethicality refers to people's limited capacity to consistently
   behave in line with their ethical standards. Here, we present results from a
   pre-registered, large-scale (N=11,050) survey of researchers in Sweden,
   suggesting that researchers too are boundedly ethical. Specifically,
   researchers on average rated themselves as better than other researchers in
   their field at following good research practice, and rated researchers in
   their own field as better than researchers in other fields ..."
   -- [<A HREF="https://doi.org/10.1038/s41598-024-53450-0">doi:10.1038/s41598-024-53450-0</A>]['24].
   [Also search for: scientific research ethics].

%A L. Messeri
%A M. J. Crockett
%T Artificial intelligence and illusions of understanding in scientific research
%J Nature
%V 627
%P 39-58
%M MAR
%D 2024
%K news, views, c0224, c202x, c20xx, zz0324, AI, chatGPT, scientific research
%X "... we develop a taxonomy of scientists' visions for AI, observing that
   their appeal comes from promises to improve productivity & objectivity by
   overcoming human shortcomings. But proposed AI solutions can also exploit our
   cognitive limitations, making us vulnerable to illusions of understanding in
   which we believe we understand more about the world than we actually do ...
   The proliferation of AI tools in science risks introducing a phase of
   scientific enquiry in which we produce more but understand less. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07146-0">doi:10.1038/s41586-024-07146-0</A>]['24].

%A W. Liang
%A et al
%T Monitoring AI-modified content at scale: A case study on the impact of
   chatGPT on AI conference peer reviews
%J arXiv
%M MAR
%D 2024
%K TR, c2024, c202x, c20xx, zz0424, publications, peer review, conf, AI,
   LarLangM, large language model, LLM, review, reviewing, refereeing, academia,
   Gray, papers. contamination, scientific research
%X "We present an approach for estimating the fraction of text in a large corpus
   which is likely to be substantially modified or produced by a large language
   model (LLM). ... ICLR 2024, NeurIPS 2023, CoRL 2023 & EMNLP 2023. Our results
   suggest that between 6.5% & 16.9% of text submitted as peer reviews to these
   confs. could have been substantially modified by LLMs ..."
   -- [<A HREF="https://arxiv.org/abs/2403.07183">arxiv:2403.07183</A>]['24].
 Also see,
   "ChatGPT 'contamination': estimating the prevalence of LLMs in the
   scholarly literature ... It is estimated that at least 60,000 papers
   (slightly over 1% of all articles) were LLM-assisted, though this #
   could be extended & refined by analysis of other characteristics of the
   papers or by identification of further indicative keywords. ..."
   -- [<A HREF="https://arxiv.org/abs/2403.16887">arxiv:2403.16887</A>]['24]
   &  [<A HREF="https://doi.org/10.1038/d41586-024-01051-2">Nature2024</A>]['24].

%A Yilei Chen
%T Quantum algorithms for lattice problems
%J Cryptology Archive
%M APR
%D 2024
%K TR, c2024, c202x, c20xx, zz0424, quantum, algorithm, lattice problem,
   learning with errors, LWE, shortest vector problem, GapSVP, shortest, SIVP
%X "We show a polynomial time q.alg. for solving the learning with errors
   problem (LWE) with certain polynomial modulus-noise ratios. Combining with
   the reductions from lattice problems to LWE ... obtain polynomial time
   q.algs. for solving the decisional shortest vector problem (GapSVP) & the
   shortest indep. vector problem (SIVP) for all-dimensional lattices within
   approx'n factors of ~Omega(n^{4.5}). ..."
   -- [<A HREF="https://eprint.iacr.org/2024/555">iacr:2024.555</A>]['24].
   Could have consequences for "post quantum" cryptography.
   ?Will it be "confirmed"?  No...
   *** 'Update: Scientists Spot Mistake in Proposed PQC-Cracking Algorithm'
   -- [<A HREF="https://thequantuminsider.com/2024/04/20/update-scientists-spot-mistake-in-proposed-pqc-cracking-algorithm/">www</A>][20/4/2024].

%A H. Farrell
%A C. Shalizi
%T Opinion: Bias, skew, and search engines are sufficient to explain
   online toxicity
%J CACM
%M APR
%D 2024
%K CACM, news, views, c2024, c202x, c20xx, zz0424, internet, www, web2.0,
   search engine, google, social media, USA politics, democracy, toxicity,
   Qanon, twitter, XX, Xtwitter, meta, facebook, hate
%X "Social media would still be a mess even without engagement algs.."
   -- [<A HREF="https://dx.doi.org/10.1145/3624715">doi:10.1145/3624715</A>]['24].

%A L. Besser
%T Wiley's 'fake science' scandal is just the latest chapter in a broader
   crisis of trust universities must address
%I ABC
%M MAY
%D 2024
%K news, views, c2024, c202x, c20xx, zz0524, Wiley, Hindawi, publications,
  journals, fake science, papers, academia, plagiarism, scam, academic,
  university, research, misconduct, authorship, paper mill
%X "... In March, [Wiley] revealed to the NYSE a $US9 million ($13.5 million)
   plunge in research revenue after being forced to "pause" the publication of
   so-called "special issue" journals by its Hindawi imprint, which it had
   acquired in 2021 for US$298 million ($450 million).  Its statement noted the
   Hindawi program, which comprised some 250 journals, had been "suspended
   temporarily due to the presence in certain special issues of compromised
   articles". ..."
   -- [<A HREF="https://www.abc.net.au/news/2024-05-21/wiley-hindawi-articles-scandal-broader-crisis-trust-universities/103868662">abc</A>][21/5/2024].

%A R. F. Service
%T Compound interest
%J Science
%V 384
%N 6699
%M MAY
%D 2024
%K news, views, c2024, c202x, c20xx, zz0624, quantum computing, applications,
   chemistry
%X "... The achievement shows how quantum computers are tentatively moving
   from the realm of mere promise to tackling real-world challenges. ..."
   -- [<A HREF="https://doi.org/10.1126/science.zlxq0ls">doi:10.1126/science.zlxq0lsdoi</A>]['24].
   [Also search for: quantum computing applications].

%A M. R. Dougherty
%A D. A. Illingworth
%A R. Nguyen
%T A memory-theoretic account of citation propagation
%J Royal Soc., Open Sci.
%M MAY
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0624, scientific research, literature,
   publication, references, cite, citation, count, Hindex, bibliometrics,
   academia, university, management, hiring, firing, tenure, impact, job, jobs,
   publish, perish, Matthew effect
%X "Despite the common assumption that citations are indicative of an article's
   scientific merit, increasing evidence indicates that c.counts are largely
   driven by variables unrelated to quality. ... we treat people's decisions of
   what to cite as an instance of memory retrieval & show that observed c.
   patterns are well accounted for by a model of memory. ...  magnified over
   time & can lead to the emergence of highly cited papers. ... occurs even when
   there is no variation in the starting point exposure probabilities ...  We
   discuss the implications of the model within the context of research
   evaluation & hiring, tenure & promotion decisions."
   -- [<A HREF="https://doi.org/10.1098/rsos.231521">doi:10.1098/rsos.231521</A>]['24].
   [Also search for: scientific citation].

%A R. Rojas
%T The first computer program
%J CACM
%V 67
%N 6
%P 78-81
%M JUN
%D 2024
%K jrnl, CACM, c2024, c202x, c20xx, zz0624, Babbage, history, computing,
   computer, analytical engine, program
%X "Mathematician and inventor Charles Babbage's code sketches are the first
   attempt to specify how to mechanize complex algorithms with a computer."
   -- [<A HREF="https://doi.org/10.1145/3624731">doi:10.1145/3624731</A>]['24].
      (Also see, The computer programs of Charles Babbage,
      IEEE Annals of the History of Computing 43, 1 (2021), 618,
      [<A HREF="https://doi.org/10.1109/MAHC.2020.3045717">doi:10.1109/MAHC.2020.3045717</A>]['24].)
   [Also search for: history Babbage].

%A S. Ragavan
%A V. Vaikuntanathan
%T Space-efficient and noise-robust quantum factoring
%J arXiv
%M FEB
%D 2024
%K TR, c2025, c202x, c20xx, zz0624, quantum, integer factorisation, algorithm,
   Shor, Regev, factorization, factoring
%X "... Our main result constructs a quantum factoring circuit using O(n log n)
   qubits & O(n^{3/2} log n) gates ...achieved by implementing efficient &
   reversible exponentiation with Fibonacci numbers in the exponent, rather than
   the usual powers of 2 ..."
   -- [<A HREF="https://arxiv.org/abs/2310.00899">arxiv:abs/2310.00899</A>]['24].

%A Xinqu Zhang
%A Peng Wang
%T Research misconduct in China: towards an institutional analysis
%J SagePub
%M APR
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0624, China, academia, university, management,
   research, academic, misconduct, ethics, ranking, rankings, double first,
   journals, papers, paper mill, Q1, Q2, publications, authorship
%X "Unethical research practices are prevalent in China, but little research has
   focused on the causes ... this article focuses on China's Double First-Class
   University Initiative & its impact on elite Unis. that respond to the policy
   by generating new incentive structures to promote research quality &
   productivity as well as granting faculties & depts greater flexibility in
   terms of setting high promotion criteria concerning research productivity.
   This generates enormous institutional tensions and strains ..."
   -- [<A HREF="https://doi.org/10.1177/17470161241247720">doi:10.1177/17470161241247720</A>]['24].
   [Also search for: academic misconduct].

%A A. Liesenfeld
%A M. Dingemanse
%T Rethinking open source generative AI: open-washing and the EU AI Act
%J FAccT '24: Proc. of the 2024 ACM Conf. on Fairness, Accountability, and
   Transparency
%M JUN
%D 2024
%P 1774-1787
%K conf, FAccT, c2024, c202x, c20xx, zz0624, opensource, openSource, AI, ANN,
   chatGPT, EU, Europe, Europen, law, chatbot, openness, openWashing, washing,
   LarLangM, LLM, chat, BLOOMZ, Llama2, Llama3, openAI
%X "The past year has seen a steep rise in generative AI systems that claim to
   be open. But how open are they really? ... upcoming EU AI Act that regulates
   open source systems differently, creating an urgent need for practical
   openness assessment. ... 14 dimensions of openness, from training datasets to
   sci. and tech. doc'n and from licensing to access methods. Surveying over 45
   generative AI systems ... argue that openness in generative AI is necessarily
   composite (consisting of multiple elements) and gradient (coming in degrees)
   ..."
   -- [<A HREF="https://doi.org/10.1145/3630106.3659005">doi:10.1145/3630106.3659005</A>]['24].
   Also see E.Gibney [<A HREF="https://doi.org/10.1038/d41586-024-02012-5">news</A>]['23].
   (NB. openAI isn't (open).)

%A Rong Fu
%A et al
%T Achieving energetic superiority through system-level quantum circuit
%J arXiv
%M JUN
%D 2024
%K TR, c2024, c202x, c20xx, zz0724, quantum, google, sycamore, conventional,
   computing, GPU, supremacy
%X "... present a groundbreaking large-scale sys. tech. that leverages
   optimization on global, node, & device levels ... enable accommodating
   large-scale tensor n/wks with up to tens of terabytes of memory, reaching up
   to 2304 GPUs with a peak computing power of 561 PFLOPS half-precision. ...
   achieved a time-to-soln of 14.22 sec. with energy consumption of 2.39kWh
   which achieved fidelity of 0.002 & our most remarkable result is a
   time-to-soln of 17.18 sec., with energy consumption of only 0.29kWh which
   achieved a XEB of 0.002 after post-processing, outperforming Google's
   q.processor Sycamore in both speed & energy efficiency, which recorded
   600 sec. & 4.3kWh, resp.."
   -- [<A HREF="https://arxiv.org/abs/2407.00769v1">arxiv:2407.00769v1</A>]['24].
   ... simulated it.
   [Also search for: quantum supremacy].

%A S. Egozi
%A Y. Ram
%T Prestige bias in cultural evolutionary dynamics
%J Royal Soc. Open Sci.
%M JUL
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0724, evolution, genetic drift, prestige bias,
   success bias, natural selection, drift, society, culture, rich get richer,
   reputation, Kardashian, Matthew effect, principle
%X "If the traits of more successful individuals are more likely to be adopted,
   the resulting cultural transmission is described as success biased. [v.] if
   the traits of 'prestigious' individuals - those who have already been copied
   many times - are more likely to be adopted, this is described as
   prestige-biased cultural transmission. In this case, prestige can be a
   convenient proxy for success. ... results show that success bias effectively
   plays the role of natural selection, whereas prestige bias effectively plays
   the role of genetic drift. Prestige bias, which may be strong in highly
   social communities, also accelerates the evolutionary dynamics, as expected
   in a rich-get-richer process. ..."
   -- [<A HREF="https://doi.org/10.1098/rsos.230650">doi:10.1098/rsos.230650</A>]['24].
   [Also search for: Matthew effect].

%A J. Blu Buhs
%T Think to New Worlds: The Cultural History of Charles Fort and His Followers
%I Univ. Chicago Press
%M JUL
%D 2024
%K book, c2024, c202x, c20xx, zz0724, Fortean, conspiracy theories, Qanon, UFO,
   UFOs, antivax
%X "Flying saucers. Bigfoot. Frogs raining from the sky. Such phenomena
   fascinated Charles Fort, the maverick writer who scanned newspapers, jrns,
   & magazines for reports of bizarre occurrences: dogs that talked,
   vampires, ..."
   1st ed 2024, hb us$32; uk us isbn:0226831485; uk us isbn13:978-0226831480.

%A M. Kozlov
%T 'Publish or Perish' is now a card game - not just an academic's life ..."
%J Nature
%M AUG
%D 2024
%K news, views, c2024, c202x, c20xx, zz0824, academia, publish, perish,
   bibliometrics, Hindex, JIF, publications, papers, citations, funny, haha,
   ha ha, university research
%X "A player wins by racking up more citations than the competition, even if
   that means engaging in a little light plagiarism. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-024-02511-5">doi:/10.1038/d41586-024-02511-5</A>]['24].
   [Also search for: publish perish].

%A H. Ibrahim
%A et al
%T Google Scholar is manipulatable
%M FEB
%D 2024
%K TR, c2024, c202x, c20xx, zz0924, duh, manipulable, surprise, google, scholar,
   Hindex, academia, fraud, scam, gaming, misconduct, publish, perish,
   citation, ring, bibliometrics, paper mill, university, scientific research
%X "... scientists may be incentivized to inflate their citation counts[!] ...
   A we compile a dataset of ~1.6 million profiles on G. S. to examine instances
   of citation fraud on the platform. We survey faculty at highly-ranked unis.
   & confirm that G.S. is widely used when evaluating scientists. Intrigued by a
   citation-boosting service that we unravelled during our investigation, we
   contacted the service while undercover as a fictional author, & managed to
   purchase 50 citations ..."
   -- [<A HREF="https://arxiv.org/abs/2402.04607">arxiv:2402.04607</A>]['24],
   also see [<A HREF="https://doi.org/10.1038/d41586-024-01672-7">www</A>]['24].

%A M. Mitchell
%T The Turing Test and our shifting conceptions of intelligence
%J Science
%M AUG
%D 2024
%K news, views, c2024, c202x, c20xx, zz0924, human, AI, intelligence, thinking,
   AGI, LLM, LarLangM
%X "'Can machines think?' So asked Alan Turing in his 1950 paper,
   'Computing Machinery and Intelligence.' Turing quickly noted that, given the
   difficulty of defining thinking ..."
   -- [<A HREF="https://doi.org/10.1126/science.adq9356">doi:10.1126/science.adq9356</A>]['24].

%A R. Gittins
%T The most deplorable thing unis copied from big business, aside from
   vice-chancellor pay
%J The Age
%M AUG
%D 2024
%K news, views, c2024, c202x, c20xx, zz0924, Australia, University, VC, Go8,
   gig, uni, academia, management, privatisation, Monash, Melbourne
%X "... Successive federal governments have engineered a kind of backdoor
   privatisation of our universities. They remain owned by the states and
   heavily regulated by the feds, but have increasingly been told to pay their
   own way. ..."
   -- [<A HREF="https://www.theage.com.au/national/the-most-deplorable-thing-unis-copied-from-big-business-aside-from-vice-chancellor-pay-20240806-p5jzyl.html">www</A>][7/8/2024].

%A D. Normile
%T China's scientists often cite work from their own nation. Is that skewing
   global research rankings?
%J Science
%V 386
%N 6717
%M OCT
%D 2024
%K jrnl, c2024, c202x, c20xx, zz1024, scientific research, impact, ranking,
   gaming, citations, citation stacking, Hindex, home country, bias
%X "... Overall, they found that 62% of citations to China's top 10% of papers
   came from within the country. The United States had the second-highest rate
   of home bias at 24%. Other developed nations had same-country citations
   ranging from Italy's 13% to Canada's 6%. ..."
   -- [<A HREF="https://doi.org/10.1126/science.zwtuywu">doi:10.1126/science.zwtuywu</A>]['24].

%A A. Gronlund
%A K. Green Larsen
%T An exponential separation between quantum and quantum-inspired classical
   algorithms for machine learning
%J arXiv
%M NOV
%D 2024
%K TR, c2024, c202x, c20xx, zz1124, computing, AI, advantage
%X "... we present the first such provable exponential sep'n between q. &
   q.-inspired classical algs.. We prove the sep'n for the basic problem of
   solving a linear system when the input matrix is well-conditioned & has
   sparse rows & columns."
   -- [<A HREF="https://arxiv.org/abs/2411.02087v2">arxiv:2411.02087v2</A>]['24].

%A B. Singler
%A F. Watts
%T The Cambridge Companion to Religion and Artificial Intelligence
%I CUP
%P 338
%M NOV
%D 2024
%K book, text, c2024, c202x, c20xx, zz1124, society, religion, philosophy,
   human, versus, AI
%X "... explores the fields of Religion & AI comprehensively & provides an
   authoritative guide to their symbiotic relationship. It examines est.
   topics, such as transhumanism, together with new & emerging fields, notably,
   computer simulations of religion. Specific chapters are devoted to Judaism,
   Christianity, Islam, Hinduism, & Buddhism ..."
   1st ed 2024; pb us$47; uk us isbn:1009013653; uk us isbn13:978-1316516034.
   (Also see auth1 at [<A HREF="https://bvlsingler.com">www</A>].)  (well!?)


%T The theory of splines and their applications
%E Ahlberg
%E Nilson
%E Walsh
%I AcademicPress
%V 38
%S Math. in Sci. and Eng.
%D 1967
%K book, text, c1967, c196x, c19xx, spline, splines, computer graphics, CAD,
   cubic, curve, curves, fit, fitting, interpolation, approximation,
   smooth, lofting, aided, design
%X 1st ed 1967; hb us$290; uk us isbn:0120447509; uk us isbn13:978-0120447503.

%A J. L. Bentley
%A D. Wood
%T An optimal algorithm for reporting intersections of rectangles
%J IEEE Trans. on Computers
%V C-29
%D 1980
%P 571-577
%K jrnl, c1980, c198x, c19xx, rectangle, square, polygon, intersection,
   intersect, overlap, interval graph
%X from the H@skell mailing list 11/'03, and: [<A HREF="http://citeseer.nj.nec.com/context/2049538/0">citeseer</A>][11/'03].

%A M. A. Fischler
%A R. C. Bolles
%T Random sample consensus: a paradigm for model fitting with applications to
   image analysis and automated cartography
%J CACM
%V 24
%N 6
%P 381-395
%M JUN
%D 1981
%K jrnl, CACM, c1981, c198x, c19xx, zz0807, computer graphics, line fitting,
   Random Sample Consensus, RANSAC, RAN SAC, Location Determination Problem,
   fit, LDP, image processing, shape, sampling, outliers, outlier
%X "... fitting a model to experimental data is introduced. RANSAC is capable of
   interpreting/smoothing data containing a significant % of gross errors, & is
   thus ideally suited for applications in automated image analysis where
   interpretation is based on the data provided by error-prone feature
   detectors. ... describes the application of RANSAC to the Location
   Determination Problem (LDP): Given an image depicting a set of landmarks with
   known locations, determine that point in space from which the image was
   obtained. ..."
   -- [<A HREF="http://doi.acm.org/10.1145/358669.358692">doi:10.1145/358669.358692</A>]['07],
   [<A HREF="http://en.wikipedia.org/wiki/RANSAC">R...@wikip</A>]['07],
   [also search for: MLESAC].

%A J. D. Foley
%A A. van Dam
%A S. Feiner
%A J. F. Hughes
%T Computer Graphics Principles and Practice
%I AddisonWesley
%D 1990
%K book, text, vanDam, computing, computer graphics, 1982, 1990, 1996,
   c1990, c199x, c19xx
%X 1996, 2nd edition in C, uk us isbn:0201848406; uk us isbn13:978-0201848403.
   1990, 2nd edn..
   1982, 1st edn..

%A W. Newman
%A R. Sproull
%T Principles of Interactive Computer Graphics
%I McGrawHill
%D 1979
%K book, text, computing, computer graphics

%A J. Neider
%A T. Davis
%A M. Woo
%T OpenGL Programming Guide
%I AddisonWesley
%D 1993
%K book, text, open GL, computer graphics, computing, SGI, c1993, c199x, c19xx,
   red book
%X 4th edn, OpenGL ver1.4, 11/2OO3, isbn:0321173481, 800p, with D. Schreiner.
   [Also search for: OpenGL].

%A J. Wernecke
%T The Inventor Mentor
%I AddisonWesley
%D 1994
%K computer graphics, computing, SGI, C++, CplusPlus, book, text
%X <A HREF="http://www.sgi.com/tech/Inventor.html">SGI Inventor web page</A> ['95].

%A J. Wernecke
%T The Inventor Toolmaker
%I AddisonWesley
%M APR
%D 1994
%K tool maker kit, toolkit, SGI, C++, CplusPlus,
   interactive 3D computer graphics, computing, book, text
%X isbn:0 201 62493 1;    This is NOT an introduction
   <A HREF="http://www.sgi.com/tech/Inventor.html">SGI Inventor web page</A> ['95].

%A M. Irani
%A S. Peleg
%T Improving resolution by image registration
%J Graphical models and image processing
%M MAY
%D 1991
%P ?-?
%K image processing, IP, merge merging images, composite, computing
%X see also <A HREF="http://www.sgi.com/grafica/merge/index.html">SGI</A>[3/95].

%A S. Mann
%A R. W. Picard
%T Virtual bellows: constructing high quality stills from video
%J IEEE Int. Conf. on Image Processing
%M NOV
%D 1994
%P ?-?
%K IP, merge merging images, composite, computing
%X see also <A HREF="http://www.sgi.com/grafica/merge/index.html">SGI</A>[3/95].

%A V. Caglioti
%T On the uncertainty of straight lines in digital images
%J Graphical Models and Image Processing
%V 55
%N 4
%M JUL
%D 1993
%P 255-270
%K CVGIP, IP, image, line, fit, fitting, edge, uncertainty, estimation
%X considers (i) noise and (ii) discretization - staircasing etc..

%A M. V. Wickerhauser
%T Adapted Wavelet Analysis from Theory to Software
%I A.K.Peters Ltd.
%D 1994
%P 486
%K computer graphics, image processing, IP, wavelet, wavelets
%X isbn:1-56881-041-5; review Comp Rev Jul 95 p.356.

%A G. Glaeser
%T Fast Algorithms for 3D-Graphics
%I SpringerVerlag
%D 1994
%P 306
%K computer graphics, algorithm, 3D, text, book, zz1195
%X in Hargrave.

%A M. Vetterli
%A J. Kovacevic
%T Wavelets and Subband Coding
%I PrenticeHall
%D 1995
%K book, text, wavelet, sub band, image processing, IP, zz0596
%X isbn:0-13-097080-8;  reviewed in Comp Rev p111 Feb 96.

%A J. G. Dunham
%T Optimum uniform piecewise linear approximation of planar curves
%J IEEE Trans. Patt. Analysis and Machine Intell.
%V 8
%N 1
%P 67-75
%M JAN
%D 1986
%K jrnl, c1986, c198x, c19xx, curve, fit, fitting, continuous, polygon, line,
   approximation, image processing
%X ref from TR by  B a n e r j e e   et al  '96.

%A M. Soumekh
%T Fourier Array Imaging
%I PrenticeHall
%D 1994
%P 559
%K book, text, Fourier analysis, image processing, IP
%X isbn:0-13-063769-6.

%A A. Kalvin
%A E. Schonberg
%A J. T. Schwartz
%A M. Sharir
%T Two dimensional, model based, boundary matching using footprints
%J Int. J. Robotics Research
%I SagePubl.
%V 5
%N 4
%P 38-55
%D 1986
%K IJRR, jrnl, c1986, c198x, c19xx, curve matching, match, geometric hashing,
   GH, curve, outline, shape recognition, foot print, filter, approximate, 2D,
   zz0596
%X [NB.  K i s h o n  and  W o l f s o n  '87  attribute
    this paper as giving the 1st defn of geometric hashing.]
   "... describe a technique for geometrically hashing 2D model objects. Used
   in conjunction with other methods for recognizing partially obscured &
   over-lapping objects, this technique enables us to recognize overlapping 2D
   objects selected from [DBs] without sig, perf. degredation when the DB is
   enlarged. ... based on ... a synthetic attribute of an object ..."
   -- [<A HREF="http://dx.doi.org/10.1177/027836498600500403">doi:10.1177/027836498600500403</A>]['09], issn:0278-3649.

%A H. Wolfson
%A E. Schonberg
%A A. Kalvin
%A Y. Lamdan
%T Solving jigsaw puzzles by computer
%J Annals of Operations Res.
%D 1987
%K AOR, jig saw, puzzle, OR, shape recognition, shapes, match, matching
%X K i s h o n  and  W o l f s o n  '87  list this as `to appear' at that time
   in  the volume `Approaches to Intelligent Decision Support'
   of the series  Annals of Operations Research '87.

%A H. J. Wolfson
%T On curve matching
%J IEEE Trans. Pattern Analysis and Mach. Int.
%V 12
%N 5
%P 483-489
%M MAY
%D 1990
%K jrnl, IEEE, AI, MI, shape, shapes, curves, recognition, match, matching, 2D
%X 16 refs.

%A P. Clifford
%A G. Nicholls
%T A Metropolis sampler for polygonal image reconstruction
%I Dept. of Statistics, Oxford Univ.
%M DEC
%D 1994
%K stats, TR, polygon fitting, fit, shape, image processing, IP,
   sampling, Monte Carlo, Markov model, Arak process, zz0996
%X 1000 data points, 120 edges, 5 minutes Sun Sparc 2
   <A HREF="http://www.stats.ox.ac.uk/%7Eclifford/papers/">[wwweb]</A>
   <A HREF="mailto:clifford@stats.ox.ac.uk">[email author]</A>          [9/'96].

%A T. Arak
%A P. Clifford
%A D. Surgailis
%T Point based polygonal models for random graphs
%J Adv. in Appl. Prob.
%V 25
%P 348-372
%D 1993
%K polygon fitting, fit, image processing, IP, graph, model, probability
%X ref in Clifford and N' '94.

%A U. Grenander
%T General Pattern Theory
%I OUP
%D 1993
%K book, text, Oxford, patterns, image processing, IP, fit, fitting
%X ref in   C l i f f o r d   and N'   '94

%A P. Cheeseman
%A B. Kanefsky
%A R. Kraft
%A J. Stutz
%T Super-resolved surface reconstruction from multiple images
%R FIA-94-12
%I AI Research Branch, NASA Ames
%M DEC
%D 1994
%K TR 12, TR12, image reconstruction, montage, overlap, processing, IP,
   Mars, Martian data, Viking
%X NASA Ames Research Centre, Mail Stop 269-2, Moffett Field, CA 94035, USA
   Given a set of images of a surface taken from roughly the same direction
   and with similar lighting, infer a super-resolved 2-D surface model.
   Applied to the Viking Mars data.  Some extensions are discussed,
   including 3-D surface reconstruction and the resolution of diffraction
   blurred images.
   -- <A HREF="http://ic-www.arc.nasa.gov/ic/projects/bayes-group/group/">[wb]</A>.

%A Jin-Long Chen
%A G. C. Stockman
%T Determining pose of 3D objects with curved surfaces
%J IEEE Trans. Pattern Anal. Mach. Intell.
%P 52-57
%V 18
%N 1
%M JAN
%D 1996
%K jrnl, AI, computer vision, view, model based

%A Weidong Kou
%T Digital Image Compression Algorithms and Standards
%I Kluwer
%D 1995
%K book, text, processing, CCITT, JBIG, JPEG, MPEG, zz0197
%X uk us isbn:0-7923-9128-3.

%A R. Scheifler
%A J. Gettys
%T The X window system
%J ACM Trans Graphics
%V 5
%N 2
%P 79-109
%D 1986
%K jrnl, X windows, Xwindows, computer graphics

%A S. W. Thomas
%T X and PEX programming
%J Advances in Computer Graphics VI: Images: Synthesis, Analysis and Interaction
%E G. Garcia
%E I. Herman
%P 269-307
%I SpringerVerlag
%D 1991
%O Eurographics '90
%K conf, Eurographics6, X windows, Xwindows, protocol, Xlib, PHIGS, PEX,
   good, tute, tutorial, introduction
%X Includes a tutorial on X windows.
   Hargrave 006.6 A244/6,   12 refs.

%A D. Young
%T X Window System Programming and Applications with Xt
%I PrenticeHall
%D 1989
%K book, text, X windows, Xwindows, Xt, Xtools, Xtoolkit, Unix, OSF, Motif,
   computer graphics, GUI, GUIs
%X also OSF/Motif edition 1990.

%A A. Nye
%T X Protocol Reference Manual
%I O'Reilly & Assoc.
%S The X windows system series
%N 0
%D 1988
%K book, text, Xprotocol, Xlib, X windows, Xwindows, Unix

%A A. Nye
%T Xlib Programming Manual
%I O'Reilly & Assoc.
%D 1988
%S The X windows system series
%N 1
%K book, text, Xlib, X windows, Xwindows, computer graphics, Unix

%A A. Nye
%T The Xlib Reference Manual
%I O'Reilly & Assoc.
%D 1988
%S The X windows system series
%N 2
%K book, text, computer graphics, Xlib, X windows, Xwindows, Unix

%A A. Nye
%T X Window System User's Guide
%I O'Reilly & Assoc.
%S The X windows system series
%N 3
%D 1989
%K book, text, Xwindows, X windows, Unix

%A A. Nye
%A T. O'Reilly
%T X Toolkit Intrinsics Programming Manual
%I O'Reilly & Assoc.
%S The X windows system series
%N 4
%D 1989
%K book, text, computer graphics, X windows, Xwindows, Unix

%A T. O'Reilly
%T X Toolkit Intrinsics Reference Manual
%I O'Reilly & Assoc.
%S The X windows system series
%N 5
%D 1990
%K book, text, computer graphics, X windows, Xwindows, Xtools, Xtoolkit, Unix

%A S. T. Barnard
%T Stochastic stereo matching over scale
%J Int. Jrnl. of Computer Vision
%P 17-32
%V 3
%D 1989
%K jrnl, stereo vision, depth

%A A. J. Maeder
%T Animation techniques for chain-coded objects
%J Proc. 1st Conf. on Visualization '90
%I IEEE
%P 67-73
%D 1990
%K conf, object, chain code, computer graphics, shape, c1990, c199x, c19xx,
   shapes, AJMaeder
%X "Chain coding is a common boundary representation for objects used in image
   analysis. When animating digital image sequences for visualization, it is
   often convenient to retain this representation. Methods for scaling,
   rotation and elastic deformation of objects based solely on chain code
   elements are discussed here. Quantized methods transform groups of chain
   code elements into other groups while incremental methods construct the
   transformed chain code element by element."   isbn:0818620838.
   -- [<A HREF="http://portal.acm.org/citation.cfm?id=949531.949542">acm</A>][11/'04].

%A D. V. Papadimitriou
%A T. J. Dennis
%T A stereo disparity algorithm for 3D model construction
%J Image Proc. and its Applications
%P 178-182
%D 1995
%K 3D, 3-D, stereo vision, computer, matching

%A P. L. Rosin
%A G. A. W. West
%T Nonparametric segmentation of curves into various representations
%J IEEE Transactions on Pattern Analysis and Machine Intelligence
%V 17
%N 12
%P 1140-1153
%M DEC
%D 1995
%K jrnl, c1995, c199x, c19xx, segment, curve, fit, fitting, approximation,
   line, lines, arc, arcs, poynomial
%X "...an alg. for segmenting connected pts into a combination of rep'ns such as
   lines, circular, elliptical & superelliptical arcs, & polynomials. The alg.
   has a number of interesting properties including being scale invariant,
   nonparametric, general purpose, & efficient."
   [<A HREF="http://dx.doi.org/10.1109/34.476507">doi:10.1109/34.476507</A>]['07].

%A A. K. Dalmia
%A M. Trivedi
%T High speed extraction of 3D structure of selectable quaility using
   a translating camera.
%J Computer Vision and Image Understanding
%V 64
%P 97-110
%D 1996
%K jrnl, image processing, stereo vision, matching

%A R. F. Rohmfeld
%T Classifications of curve-curve intersections from the CAD/CAM viewpoint
%J Proc. Computer Graphics International (CGI'96)
%I IEEE
%P 230-?
%D 1996
%K conf, c1996, c199x, c19xx, zz0307, intersection point, intersection path,
   CGI96, self intersection, transversal intersection, Jordan curve theorem,
   Boolean operation
%X "... most circumstances, the key property of an intersection point is the
   behavior of the curves in a neighborhood of that intersection pt. ...presents
   the classification of intersection pts from the differential geometric point
   of view in terms of the movement of particles along curves. The movement is
   evaluated in the neighborhood of an intersection pt under the constraint that
   the particle moves along one curve with respect to the other. Applications of
   this classification & an universal algorithm for boolean operations on areas
   enclosed by continuous, simple curves ..."
   [<A HREF="http://doi.ieeecomputersociety.org/10.1109/CGI.1996.511865">doi:10.1109/CGI.1996.511865</A>]['07].
   isbn:0818675187.

%A K. Popat
%A R. W. Picard
%T Cluster based probability model and its application to image and
   texture processing
%J IEEE Trans. Image Processing
%V 6
%N 2
%P 268-284
%M FEB
%D 1997
%O MIT Media Lab TR351
%K jrnl, TR 351, TR351, images, IP, compress, compression, restoration,
   classification
%X <A HREF="http://www-white.media.mit.edu/people/popat/profile.html">[www]</A>
   [11/'97].

%A D. Coco
%T Creating humans for games
%J Computer Graphics World
%P 26-32
%M OCT
%D 1997
%K magazine, human, model, modelling, figure, avatar, animation, game,
   Apocalypse, Blade Runner, BladeRunner, Tomb Raider, Lara Croft
%X Not a refereed journal - a magazine.
   Short article on human models in Apocalypse, Blade Runner.
   Also Lara Croft from Tomb Raider.

%A Z. Xiang
%T Color quantization by minimizing the maximum intercluster distance
%J ACM Trans. Graphics
%P 260-276
%V 16
%N 3
%M JUL
%D 1997
%K ACM, jrnl, computer graphics, colour, colours, quantisation, quantize,
   quantise, cluster, clustering, reduce, zz1297

%A J. K. Hodgins
%A N. S. Pollard
%T Adapting simulated behaviours for new characters
%J SIGGRAPH 97
%I Addison Wesley
%P 153-162
%D 1997
%K ACM, SIGGRAPH97, conf, character, walk, walking, zz1297
%X has a walking man, adapts it to walking woman, child, creature ...
   similarly cycling

%A H. C. Yun
%A B. K. Guenter
%A R. M. Mersereau
%T Lossless compression of computer-generated animation frames
%J ACM Trans. Graphics
%V 16
%N 4
%P 359-396
%M OCT
%D 1997
%K jrnl, TOGS, computer graphics, data compression, image,
   motion prediction, zz0398
%X Note *computer generated* images.  Uses transformation information
   available in the animation script, ... motion prediction ....

%A M. C. Lin
%T Efficient collision detection for animation and robotics
%I U. California, Berkeley
%M DEC
%D 1993
%K PhD thesis, Lin-Canny, computer graphics, collide, detect, zz1298
%X see also  Cohen et al '95,  VClip '98

%A J. D. Cohen
%A M. C. Lin
%A D. Manocha
%A M. K. Ponamgi
%T I-collide: an interactive and exact collision-detection system for
   large scaled environments
%J ACM Symp. on Interactive 3D Graphics
%M APR
%D 1995
%P 189-196
%K conf, computer graphics, animation, Icollide, Lin-Canny,
   collide, detect, zz1298
%X see also  Lin '93, and  VClip  '98

%A A. J. Hanson
%T Rotations for N-dimensional graphics
%J Graphics Gems V
%P 55-64
%D 1995
%K c1995, c199x, c19xx, zz0414, computer graphics, rotation, ND, 3D, 4D,
   rolling ball, Arcball
%X "... described a fundamental family of techniques for dealing with the
   geometry of N-dimensional models in the context of graphics applications.
   Here, we build on that framework to look in more detail at the treatment of
   rotns in N-D Eucidean space. ... give a previously overlooked but
   v.natural N-D extension of the 3D rolling ball technique described in an
   earlier Gem (H. 1992), along with the corr. analog of the Virtual Sphere
   method (Chen et al. 1988). ... discuss a practical method for specifying &
   understanding the params. of N-D rotns in terms of nested hyperspheres.
   Finally, we give the 4D extension of 3D quaternion orientation splines."
   -- pp.55-64 in uk us isbn:0125434553, uk us isbn13:978-0125434553,
      10.1.1.35.112@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.35.112">c'tse'r</A>]['14],
      pdf@[<A HREF="http://www.cs.indiana.edu/pub/techreports/TR406.pdf">ind'ana</A>]['14].

%A B. Mirtich
%T V-Clip: fast and robust polyhedral collision detection
%J ACM Trans. on Graphics
%V 17
%N 3
%M JUL
%D 1998
%P 177-208
%O PhD thesis, U. California, Berkeley, Dec '96
%K jrnl, TOGS, ACM, polyhedra, polyhedron, collide, detect, animation,
   computer graphics, motion, Voronoi-clip, vclip, v-clip, zz1298
%X ... tracks closest pair of features between convex polyhedra ...
   reminiscent of Lin-Canny ...
   Improvements: simple coding, robustness, no numerical tolerances,
   no cycling problems.  Handles penetrating polyhedra and therefore [ok]
   with nonconvex polyhedra described as hierarchies of convex pieces.
   Tests with V-Clip, Lin-Canny and enhanced GJK algorithms...
   See also  Icollide '95.

%A C. de Boor
%T A Practical Guide to Splines
%I SpringerVerlag
%D 1978
%K book, text, deBoor, cubic, spline, curve, curves, smooth, lines, fit, fitting
%X a ref in a paper.

%A E. R. Gansner
%A S. C. North
%T An open graph visualization system and its applications to
   software engineering
%J SPE
%V 30
%N 11
%P 1203-1233
%M SEP
%D 2000
%K jrnl, SPE, c2000, c200x, c20xx, graph visualization, graphviz, viz, draw,
   drawing, layout
%X (Special issue on discrete algorithm engineering)
   "... package of practical tools & libraries for manipulating graphs & their
   drawings. Our design, which is aimed at facilitating the combination of the
   package components with other tools, includes stream & event interfaces for
   graph operations, high-quality static & dynamic layout algorithms, & the
   ability to handle sizeable graphs. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N">doi:10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N</A>]['09],
   [<A HREF="http://www.graphviz.org/">graphviz.org</A>]['09].

%A D. Robin
%T Wooden mirror
%J SIGGRAPH
%D 2000
%O IEEE Spectrum, 38(3), pp.69, '01.
%K conf, c2000, c200x, c20xx, computer graphics, generated, mirrors, virtual,
   wood, art
%X "... Wood, motors, video camera, computer ..."
   [<A HREF="http://www.siggraph.org/artdesign/gallery/S00/interactive/thumbnail16.html">www</A>]['07],
   [<A HREF="http://smoothware.com/danny/">auth</A>]['07].

%T Final Fantasy - The Spirits Within
%D 2001
%K DVD, c2001, c200x, c20xx, film, movie, movies, computer generated images,
   cgi, animation, scifi, aliens
%X "Earth is a desolate wasteland in Final Fantasy: The Spirits Within.
   Humanity has been decimated by an invasion of Phantoms, insubstantial aliens
   that extract and devour the spirits of living things. The few remaining
   humans have retreated to a handful of cities that are protected by massive
   bio-energy shields. ..."
   DVD, us$8; asin:B00003CY5D.

%A T. Moller
%A E. Haines
%A T. Akenine-Moller
%T Real-Time Rendering
%I AKPeters
%P 900
%D 2002
%K book, text, c2002, c200x, c20xx, computer graphics, render, rendering, CGI,
   animation, animated, game, games, movies, pixar
%X 2nd ed, hb, us$55, uk us isbn:1568811829; uk us isbn13:978-1568811826.

%A T. Geraud
%T Segmentation of curvilinear objects using a watershed-based curve
   adjacency graph
%J Pattern Recognition and Image Analysis, 1st Iberian Conf.
%I SpringerVerlag
%S LNCS
%V 2652
%P 279-286
%M JUN
%D 2003
%K conf, shape, image, processing, images, region, c2003, c200x, c20xx, zz0204,
   regions, segment, segmenting, 2D, Markov, Markovian random field
%X "...presents a general framework to segment curvilinear objects in 2D
   images. A pre-processing step relies on mathematical morphology to obtain
   a connected line which encloses curvilinear objects. Then, a graph is
   constructed from this line and a Markovian Random Field is defined to
   perform objects segmentation. Applications of our framework are numerous:
   they go from simple surve segmentation to complex road network extraction
   in satellite images."
   -- [<A HREF="http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=2652&spage=279">OpenURL</A>][2/'04],
      [<A HREF="http://www.springerlink.com/link.asp?id=2ageykpkbdhkrae7">met@press</A>][2/'04],
      [<A HREF="http://dx.doi.org/10.1007/978-3-540-44871-6_33">doi:10.1007/978-3-540-44871-6_33</A>][14].
   isnn:03029743.

%A A. Maeder
%A C. Fookes
%T A visual attention approach to personal identification
%J ANZIIS
%P ?-?
%M DEC
%D 2003
%K conf, identity, gaze, track, tracking, c2003, c200x, c20xx, zz0204,
   ajmaeder, ajm, biometric, biometrics
%X authors at qut.edu.au

%A Neng-Fa Zhou
%T CGLIB - a constraint-based graphics library
%J SPE
%V 33
%N 13
%P 1199-1216
%D 2003
%K jrnl, SPE, c2003, c200x, c20xx, CGLIB, b-prolog, prolog, LP, CLP, layout
%X "...and a set of constraints including not-overlap, grid, table and
   tree constraints..."
   [<A HREF="http://dx.doi.org/10.1002/spe.539">doi:10.1002/spe.539</A>][2/'04].

%T OpenGL(R) Reference Manual: The Official Reference Document to
   OpenGL, Version 1.4
%E D. Schreiner
%I AddisonWesley
%P 784
%D 2004
%K book, text, OpenGL, v1.4 ver1.4, computer graphics, c2004, c200x, c20xx
%X us$50, 4th edn, 2004, isbn:032117383X
   [Also search for: OpenGL].

%A L. von Ahn
%A L. Dabbish
%T Labeling images with a computer game
%J Proc. SIGCHI Conf. on Human factors in Computing Systems
%P 319-326
%D 2004
%K conf, c2004, c200x, c20xx, image, images, labelling, labeling, game,
   describe, describing, description, www, web, vonAhn
%X "... game that is fun & can be used to create valuable output. When people
   play the game they help determine the contents of images by providing
   meaningful labels for them. [If] played as much as popular online games, we
   estimate that most images on the Web can be labeled in a few months. Having
   proper labels associated with each image on the Web would allow for more
   accurate image search, improve the accessibility of sites (by providing
   descriptions of images to visually impaired individuals), & help users block
   inappropriate images. ..."    -- in isbn:1581137028.
   [<A HREF="http://doi.acm.org/10.1145/985692.985733">doi:10.1145/985692.985733</A>]['08], and
   [<A HREF="http://www.gwap.com/gwap/">the game</A>]['08].

%T OpenGL(R) Programming Guide: The Official Guide to Learning OpenGL(R),
   Version 2
%A OpenGL Architecture Review Board
%A D. Shreiner
%A et al
%I AddisonWesley
%P 896
%D 2005
%K book, text, c2005, c200x, c20xx, computer graphics, open GL R, openGL,
   OpenGL2, OpenGLR
%X 5th ed, pb, us$48, uk us isbn:0321335732; uk us isbn13:978-0321335739.

%A S. Rabin
%T Introduction to Game Development
%I CharlesRiver Media
%S Game Development Series
%P 978
%D 2005
%K book, text, c2005, c200x, c20xx, computer graphics, games, CGI
%X hb, us$44, uk us isbn:1584503777; uk us isbn13:978-1584503774.

%T GPU Gems 2: Programming Techniques for High-Performance Graphics and
   General-Purpose Computation
%E M. Pharr
%I AddisonWesley
%P 880
%D 2005
%K book, text, c2005, c200x, c20xx, graphics processing, processor, Nvidia,
   unit, GP, GPU, GPgpu, programming, Gems2, rendering, GeForce,
   Streaming Architectures, stream reduction
%X "... also learn new methods for using the substantial processing power of the
   GPU in other computationally intensive appl'ns, such as scientific computing
   & finance. 20 of the book's 48 Chs. are devoted to GPGPU programming ..."
      "... Part 4, General Purpose Computation on GPUs, a primer:
        Streaming Architectures and Technology Trends;
        The GeForce 6 Series GPU Architecture;
        Mapping Computational Concepts to GPUs;
        GPU Computation Strategies and Tips;
        Implementing Efficient Parallel Data Structures on GPUs;
        Flow Control Idioms;
        GPU Program Optimization;
        Stream Reduction Operations for GPGPU Applications."
      "... Part 6: Simulation and Numerical Algorithms ..."
   2005; us$60; uk is isbn:0321335597; uk us isbn13:978-0321335593.
   [Also search for: GPU gems3].

%A Y.-W. Chow
%A R. Pose
%A M. Regan
%A J. Phillips
%T Human visual perception of region warping distortions
%J Proc. Twenty-Ninth Australasian Computer Science Conf. (ACSC 2006)
%P 217-226
%M JAN
%D 2006
%K conf, ACSC2006, ACSC29, ACSC, c2006, c200x, c20xx, computer graphics,
   virtual reality, rendering, VR, distortion
%X "... investigates the distortions caused by the implementation of a
   technique known as region warping from the human visual perception
   perspective. ... to facilitate priority rendering for a virtual reality
   Address Recalculation Pipeline (ARP) system. The ARP is a graphics display
   architecture designed to reduce user head rotational latency in immersive
   Head Mounted Display (HMD) virtual reality. ..."
   -- [<A HREF="https://dl.acm.org/doi/abs/10.1145/1174429.1174490">ACM</A>]['22],
      was crpit.com/confpapers/CRPITV48Chow.pdf ['06].

%A E. Langetepe
%A G. Zachmann
%T Geometric Data Structures for Computer Graphics
%I AKPeters
%P 350
%M FEB
%D 2006
%K book, text, c2006, c200x, c20xx, data structure, computer graphics,
   CGI, geometry, algorithm, algorithms
%X hb, us$64, uk us isbn:1568812353; uk us isbn13:978-1568812359.

%A M. A. Bekos
%A M. Kaufmann
%A A. Symvonis
%A A. Wolff
%T Boundary labeling: Models and efficient algorithms for rectangular maps
%J Computational Geometry: Theory and Applications
%V 36
%N 3
%P 215-236
%M APR
%D 2007
%K jrnl, c2007, c200x, c20xx, label, labels, labelling, diagram, diagrams
%X "... model for labeling point sites with large labels. ... labels are placed
   around an axis-parallel rectangle that contains the point sites, each label
   is connected to its corr. site through a polygonal line called leader, & no
   2 leaders intersect. Although BL is commonly used, e.g., for tech. drawings &
   ill'ns in medical atlases, this problem has not yet been studied in the
   literature. The problem is interesting in that it is a mixture of a label-
   -placement & a graph-drawing problem. In this paper we investigate several
   variants of [BL]. We consider labels of identical or different size, straight
   -line or rectilinear leaders, fixed or sliding ports for attaching leaders to
   sites & attaching labels to 1, 2 or all  sides of the bounding rectangle...."
   [<A HREF="http://dx.doi.org/10.1016/j.comgeo.2006.05.003">doi:10.1016/j.comgeo.2006.05.003</A>]['07].

%A A. Powers
%T Cinema 4D: The Artist's Project Sourcebook
%I FocalPress
%P 368
%D 2007
%K book, text, c2007, c200x, c20xx, Cinema 4D, Cinema4D, computer graphics,
   artist, artists, 3D
%X 2nd ed 2007; pb us$33; uk us isbn:024080953X; uk us isbn13:978-0240809533.

%A A. Davison
%T Pro Java 6 3D Game Development: Java 3D, JOGL, JInput and JOAL APIs
%I Apress
%P 528
%D 2007
%K book, text, c2007, c200x, c20xx, Java, game, games, development, API,
   program, programming, computer graphics, cgi, Java6, 3D, Java3D, JOGL,
   JInput, JOAL
%X hb, us$44, uk us isbn:1590598172; uk us isbn13:978-1590598177.

%A E. Angel
%T OpenGL: A Primer (3rd ed)
%I AddisonWesley
%P 230
%D 2007
%K book, text, c2007, c200x, c20xx, OpenGL, Open GL, computer graphics CGI
%X 3rd ed 2007, pb; uk us isbn:0321398114; uk us isbn13:978-0321398116.
   [Also search for: OpenGL].

%A L. Ammeraal
%A K. Zhang
%T Computer Graphics for Java Programmers
%I Wiley
%P 386
%D 2007
%K book, text, c2007, c200x, c20xx, programming, computer, CGI, Java, 3D, 2D
%X "... from classic graphics algorithms to perspective drawings and
   hidden-line elimination ..."
   pb, us$48, uk us isbn:0470031603; uk us isbn13:978-0470031605.

%T GPU Gems 3
%E H. Nguyen
%I AddisonWesley
%P 1008
%D 2007
%K book, text, c2007, c200x, c20xx, graphics processing, processor, Nvidia,
   unit, GPU, Gems3, rendering, computer graphics, programming
%X ". Geometry . Light and Shadows . Rendering . Image Effects
    . Physics Simulation . GPU Computing".
   2007; us$58; uk us isbn:# 0321515269; uk us isbn13:978-0321515261.
   [Also search for: GPU Gems].

%A E. Angel
%T Computer Graphics: A Top Down Approach with OpenGL (5th ed)
%I AddisonWesley
%P 864
%D 2008
%K book, text, c2008, c200x, c20xx, zz0408, computer graphics, CGI, Open GL,
   OpenGL, X-windows, Xwindows, game, games L3Ref, interactive, modelling
%X 5th ed, us$114, uk us isbn:0321535863; uk us isbn13:978-0321535863.
   [1st(?) ed 1998.]    (Prescribed text for CSE3313.)
   [Also search for: OpenGL].

%A B. Fry
%T Visualizing Data
%I OReilly
%P 382
%D 2008
%K book, text, c2008, c200x, c20xx, visualizing, visualize, visualising,
   visualise, data, stats, computer graphics
%X "Ben Fry received his doctorate from the Aesthetics and Computation Group at
   MIT Media Lab. and was the 06-07 Nierenberg Chair of Design for the
   Carnegie Mellon School of Design. ..."
   pb us$24; uk us isbn:0596514557; uk us isbn13:978-0596514556.

%A S. Colton
%T The painting fool: Stories from building an automated painter
%B Computers and Creativity
%E J. McCormack and M. d'Inverno
%I SpringerVerlag
%P ?-?
%D 2012 ?
%K c2012, c201x, c20xx, computer graphics, art, paint, ImperialCollege
%X SC@[<A HREF="www.doc.ic.ac.uk/~sgc/">IC</A>]['13].

%A D. Fattal
%A Z. Peng
%A T. Tran
%A S. Vo
%A M. Fiorentino
%A J. Brug
%A R. G. Beausoleil
%T A multi-directional backlight for a wide-angle, glasses-free
   three-dimensional display
%J Nature
%V 495
%P 348-351
%M MAR
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0313, computer graphics, three D, 3D, display,
   glasses free, multi-directional, diffractive backlight
%X "Multiview three-dimensional (3D) displays can project the correct
   perspectives of a 3D image in many spatial directions simultaneously ...
   we introduce a multi-directional diffractive backlight technology that
   permits the rendering of high-resolution, full-parallax 3D images in a very
   wide view zone (up to 180 degrees in principle) at an observation distance of
   up to a metre. The key to our design is a guided-wave illumination ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11972">doi:10.1038/nature11972</A>]['13].

%A P. Tresset
%A F. F. Leymarie
%T Portrait drawing by Paul the robot
%J Computers and Graphics
%V 37
%N 5
%P 348-363
%M AUG
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0513, computer graphics, art, Paul, robot,
   drawing, sketch, sketching, Victoria Albert museum
%X "... Paul, a robotic installation that produces observational face drawings
   of people. Paul is a naive drawer: it does not have high level knowledge of
   the structures constitutive of the human face (such as the mouth, nose, eyes)
   nor the capability of learning expertise based on experience as a human
   would. However, P. is able to draw using the equiv. of an artist's stylistic
   signature based on a # of processes mimicking drawing skills & technique,
   which together form a drawing cycle. [&] present here our first efforts in
   implementing two different versions of visual feedback to permit the robot to
   iteratively augment & improve a drawing which initially is built from a
   process of salient lines recovery. [1.] we refer to as computational as it
   involves a purely internal (memory-based) repn of regions to render via
   shading by the robot. [2.] physical as it involves the use of a camera as an
   'eye' taking new snapshots of the artefact in progress. This is then analysed
   to take decisions on where & how to render shading next. A main point ... in
   this work is the issue of embodiment of graphical systems, [here] a robotic
   platform. ... arguments in favour of such a posn for the graphics community
   to reflect upon. Finally, we emphasise that the drawings produced by P. have
   been considered of interest by fine art professionals in recent int. art
   fairs & exhibitions, as well as by the public at large. One drawing is now
   in the Victoria & Albert museum colln. We identify a number of factors that
   may account for such perceived qualities of the produced drawings."[May '13]
   -- [<A HREF="http://dx.doi.org/10.1016/j.cag.2013.01.012">doi:10.1016/j.cag.2013.01.012</A>]['13].


%A J. A. Todd
%A H. S. M. Coxeter
%T A practical method for enumerating cosets of a finite abstract group
%J Proc. Edinb. Math. Soc., II., Ser. 5
%P 26-34
%D 1936
%K c1936, c193x, c19xx, Todd, Coxeter, algorithm, group, finite, groups, coset,
   generator, generators, enumerate, enumeration, membership, word problem,
   maths, mathematics
%X "An important problem in finite-group theory is the determination of an
   abstract definition for a given group G, that is, a set of relations
   f_i(S_1, ... S_k) = E, (i=1, ..., n),   --(1)
   between k generating operations S_1, .., S_k of G, s.t. every other relation
   between S_1, ..., S_k is an algebraic consequence of (1).
   The # of groups for which abstract definitions are actually known is
   relatively small, but a remarkable feature of the results already obtained is
   the extreme simplicity of the relations (1) in the case of several groups of
   quite high order. This fact constitutes an additional incentive to the search
   for abstract definitions, and many elegant results have doubtless yet to be
   discovered."
   -- [<A HREF="http://dx.doi.org/10.1017/S0013091500008221">doi:10.1017/S0013091500008221</A>]['14].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Todd-Coxeter_algorithm">wikip</A>]['09].)
   [Also search for: group Todd Coxeter],  and
   [also search for: group word problem].

%A P. S. Novikov
%T Uber die algorithmische Unentscheidbarkeit des Wortproblems in der
   Gruppentheorie
   (On the algorithmic unsolvability of the word problem in group theory)
%J Tr. Mat. Inst. Steklova
%V 44
%P 1-143
%D 1955
%K c1955, c195x, c19xx, zz0514, group, maths, mathematics, groups,
   unsolvable, uncomputable, word problem
%X [<A HREF="https://zbmath.org/?format=complete&q=an:0068.01301">zbMath</A>]['14].
   (Also see wordP@[<A HREF="http://en.wikipedia.org/wiki/Word_problem_for_groups">wikip</A>]['14].)
   [Also search for: group word problem].

%A W. W. Boone
%T The word problem
%J PNAS
%V 44
%N 10
%P 1061-1065
%D 1958
%K PNAS, c1958, c195x, c19xx, zz0514, group, word problem, maths, mathematics,
   groups, unsolvable, uncomputable, word problem, generators
%X "There is exhibited a group given by a finite # of generators and a
   finite # of defining relations and having an unsolvable word problem. ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.44.10.1061">doi:10.1073/pnas.44.10.1061</A>]['14].
   (Also see wordP@[<A HREF="http://en.wikipedia.org/wiki/Word_problem_for_groups">wikip</A>]['14].)
   [Also search for: group word problem].

%A J. J. Cannon
%T Computers in group theory: a survey
%J CACM
%V 12
%N 1
%P 3-12
%M JAN
%D 1969
%K jrnl, CACM, c1969, c196x, c19xx, group theory, coset enumeration, subgroup,
   lattices, automorphism groups, character tables, table, permutation, perm,
   groups, algorithm, maths, mathematics
%X "Computers are being applied to an increasingly diverse range of problems in
   group theory. The most important areas of application at present are coset
   enumeration, sub-group lattices, automorphism groups of finite groups,
   character tables, and commutator calculus. ..."
   -- [<A HREF="http://doi.acm.org/10.1145/362835.362837">doi:10.1145/362835.362837</A>]['09].

%A J. J. Cannon
%T Computing local structure of a large finite groups
%J Computers in Algebra and Number Theory
%I SIAM - AMS
%W New York
%D 1970
%P 161-176
%K c1970, c197x, c19xx, group, groups, finite structure, maths
%X groups order 10^4 to 10^8
   Centralizers, Sylow subgroups, the Fitting subgroup, elementary subgroups
   and normal subgroup lattice can be found upto 10^8.
   Also normalizers, derived series and lower central series for smaller order.

%A J. J. Canon
%A L. A. Dimino
%A G. Havas
%A J. M. Watson
%T Implementation and analysis of the Todd-Coxeter algorithm
%J Mathematics of Computation
%V 27
%N 123
%M Jul
%D 1973
%K jrnl, c1973, c197x, c19xx, Todd, Coxeter, algorithm, maths, group, groups,
   generator, generators, coset, cosets, enumeration, representative

%A M. Furst
%A J. Hopcroft
%A E. Luks
%T Polynomial time algorithms for permutation groups
%J Proc. 21st Annual Symposium on the Foundations of Computer Science
%I IEEE
%P 36-41
%M OCT
%D 1980
%K conf, c1980, c198x, c19xx, perm, permutation, group, generator, algorithm,
   word problem, membership, equality, inclusion, closure, solvability,
   intersection, maths, mathematics, FOCS 21, FOCS21, FOCS80
%X builds data-structure in O(n**6) time (p.38).
   Membership testing,
   equality testing,
   inclusion testing  - all polynomial time.
   Normal closure of a subgroup polynomial time.
   Can use latter to test for solvability.
   Describe approach to group intersection.
   -- $ @ [<A HREF="http://doi.ieeecomputersociety.org/10.1109/SFCS.1980.34">doi:10.1109/SFCS.1980.34</A>]['10],
      $ @ [<A HREF="http://dx.doi.org/10.1109/SFCS.1980.34">doi:10.1109/SFCS.1980.34</A>]['10].
   [Also search for: group word problem] & [also search for: permutation group].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Group/">Groups</A>].)

%A M. P. J. Curran
%T Topics in Group Theory and Computation
%I AcademicPress
%D 1977
%K book, text, c1977, c197x, c19xx, maths, mathematics, group, groups, subgroup,
   perm, permutation

%A J. R. Driscoll
%A M. L. Furst
%T Computing short generator sequences
%J Info. and Comput.
%V 72
%N 2
%P 117-132
%M FEB
%D 1987
%K jrnl, c1987, c198x, c19xx,  maths, group, groups, perm, permutation,
   generator, sequence, diameter, group theory, membership, cycle, cycles
%X Diameter is longest product of generators needed to reach some element.
   Show diameter of perm group of order n generated by cycles
   of bounded degree is O(n^2). This is best possible bound.
   Such short products can be found in polynomial time.
   -- [<A HREF="http://dx.doi.org/10.1016/0890-5401(87)90043-5">doi:10.1016/0890-5401(87)90043-5</A>]['14].
   [Also search for: group generator sequence].

%A A. K. Head
%T The Galois unsolvability of the sextic equation of anisotropic elasticity
%J J. of Elasticity
%V 9
%N 1
%P 9-20
%M JAN
%D 1979
%I Sijtoff and Noordhoff, Netherlands
%K jrnl, c1979, c197x, c19xx, permutation, symmetry, maths, group, sextic,
   exact solution, solutions, Galois theory, crystallography
%X "By an approx. numerical application of Galois theory it is proved that the
   sextic equn of anisotropic elasticity for cubic symmetry is in general
   unsolvable in radicals, elementary transcendental fns, or elliptic modular
   fns & that its group is the full symmetric group. ..."
   -- [<A HREF="https://doi.org/10.1007/BF00040976">doi:10.1007/BF00040976</A>]['20].

%A A. K. Head
%T The monodromic Galois groups of the sextic equation of anisotropic
   elasticity
%I CSIRO Division of MAaterial Science,
   University of Melbourne
   Parkville, Australia 3052
%D 1978
%K c1978, c197x, c19xx, permutation, symmetry, maths, group, sextic,
   exact solution, solutions
%X elasticity of cubic crystals has sextic equation
   would like exact solutions in radicals but this impossible in general
   (nice for Nuclear reactors etc.!)

%A M. Jerrum
%T A compact representation for permutation groups
%J J. of Algorithms
%V 7
%P 60-78
%M MAR
%D 1986
%O Proc 23rd IEEE FOCS Symposium, pp.126-133, 1982
%K jrnl, c1986, c198x, c19xx, permutation, perm, maths, group, subgroup,
   coset representative, block, strong, generator, set, FOCS 23, FOCS23, FOCS82,
   isomorph rejection, membership, word problem, jrnl, generators,
   representatives, representation
%X A permutation group of order n can be represented in O(n^2) space.
   given generators, algorithm constructs data structure in O(n^5) time.
   fast membership test.
   Uses an efficient algorithm for generating coset representatives.
   -- [<A HREF="http://dx.doi.org/10.1016/0196-6774(86)90038-6">doi:10.1016/0196-6774(86)90038-6</A>]['05],
   auth@[<A HREF="http://homepages.inf.ed.ac.uk/mrj/">ed</A>]['05].
   [Also search for: group word problem].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Group/">Groups</A>].)

%A R. J. Lipton
%A L. Sneider
%A Y. Zalcstein
%T The complexity of word and isomorphism problems for finite groups
%I Dept. Computer Science, Yale University
%M MAR
%D 1977
%K c1977, c197x, c19xx, maths, methematics, finite group, subgroup,
   word problem, isomorphism, membership
%X word problems:
      the evaluation of w1 o w2 o ... o wk
      can be done in
      (1) O(T^2) in an arbitrary groupoid
      (2) O(Tlog^2 T) in an arbitrary semigroup
      (3) O(Tlog T) in an abelian group.
   isomorphism problems:
      the isomorphism problem for finite groups can be solved in polylogspace
      ie., in c log^2 T    where T is length of input tape and has
           multiplication table of group.
      The isomorphism problem for finite abelian groups can be solved
      in polynomial time.
      The isomorphism problem for groups in Gk, k fixed,
      is in nondeterminsitic and hence polynomial time.
      (Gk = class of all groups generated by sets of cardinality <= k).
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Group/">Groups</A>].)

%A C. C. Sims
%T Some group theoretic algorithms
%J Proc. 18th Summer Research Institute of the Australian Mathematical Society
%P 108-124
%M JAN
%D 1978
%E M. F. Newman
%O Springer Verlag, LNM 697
%K c1978, c197x, c19xx,  maths, group, groups, subgroup, finite presentation,
   order, permutation, generators, algorithm
%X [Also search for: Sims group] and [also search for: permutation group].

%A C. C. Sims
%T Computational methods in the study of permutation groups
%P 169-183
%B Computational Problems in Abstract Algebra
%E J. Leech
%E J. Howlett
%I Pergamon Press
%D 1967
%K c1967, c196x, c19xx, maths, group, subgroup, perm, degree, coset,
   representatives, generators, algorithm
%X [Also search for: Sims group] and [also search for: permutation group].

%A C. C. Sims
%T Computation with permutation groups
%J Proc. 2nd Symposium on Symbolic and Algebraic Manipulation
%P 23-28
%M Mar
%D 1971
%K conf, c1971, c197x, c19xx, permutation group, maths, groups, perm, subgroup,
   finite presentation, order, generators, algorithm, symmetry, theory
%X "... intro. to some computational techniques which have proved useful in the
   study of large permutation groups. In particular they have been used to study
   the Suzuki simple group of degree 1782 & order 448,345,497,600 & the simple
   group G2(5) of order 5,859,000,000 in a representation of degree 3906. Many
   of the algs. discussed here are still in a developmental state & no claim is
   made that the most efficient solutions have been found."  [3 refs].
   -- [<A HREF="http://doi.acm.org/10.1145/800204.806264">doi:10.1145/800204.806264</A>]['10], inc. pdf.
   [Also search for: permutation group].

%A M. R. Jerrum
%T The complexity of finding minimum-length generator sequences
%J Theoretical Computer Science
%I SpringerVerlag
%V 36
%M APR
%P 265-289
%D 1985
%K TCS, conf, c1985, c198x, c19xx, PSpace, complete, permutation, generator,
   sequence, representation, maths, group, groups
%X "... no computationally feasible soln to this problem is known ..."
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-13345-3_24">doi:10.1007/3-540-13345-3_24</A>]['10],
   From driscoll OF cannon.dartmouth.edu (Jim Driscoll)  15 sept 90.
   [Also search for: group generator sequence],
   [also search for: permutation group word problem].

%A D. Kornhauser
%A G. Miller
%A P. Spirakis
%T Coordinating pebble motion on graphs, the diameter of permutations groups,
   and applications
%J Proc. 25th FOCS
%D 1984
%P 241-250
%K conf, c1984, c198x, c19xx, generators, maths, graph, group, subgroup, perm,
   permutation, membership, expression, FOCS 25, FOCS25, FOCS84
%X generators given according to generalizations of Sam Lloyd's 15-puzzle.
   From: driscoll OF cannon.dartmouth.edu (Jim Driscoll)  15 sept 90

%A A. Fiat
%A S. Moses
%A A. Shamir
%A I. Shimshoni
%A G. Tardos
%T Planning and learning in permutation groups
%J 30th FOCS
%P 274-279
%D 1989
%K expression, generators, maths, group, target, perm, permutation, short,
   membership, word problem, c1989, c198x, c19xx, FOCS 30, FOCS30, FOCS89,
   Rubik, Rubik's cube
%X From: driscoll OF cannon.dartmouth.edu (Jim Driscoll)  15 sept 90
   includes application to Rubik's cube.
   [Also search for: group word problem].

%A P. McKenzie
%T Permutations of bounded degree generate groups of polynomial diameter
%J IPL
%V 19
%D 1984
%P 253-254
%K jrnl, IPL, c1984, c198x, c19xx, expression, generators, perm, permutation,
   maths, group, target, membership, short
%X Although the latter does not give algorithms, asymptotically efficient
   ones can be given.
   From driscoll OF cannon.dartmouth.edu (Jim Driscoll)  15 sept 90

%A Babai
%A et al
%T On the diameter of finite groups
%J 31st FOCS
%D 1990
%K conf, c1990, c199x, c19xx, perm, permutation, maths, group, subgroup,
   generators, diameter, membership, word problem, short, expression
%X but I haven't been in touch with them
   and don't know what their results are.  - Jim.
   From: driscoll OF cannon.dartmouth.edu (Jim Driscoll)  15 sept 90.

%A K. D. Blaha
%T Minimum bases for permutation groups
%J J. Algorithms
%V 13
%P 297-306
%M JUN
%D 1992
%K maths, group, subgroup, permutation, base, bases, minimum, minimal,
   generator set, perm, NP, NP-hard hard,
   jrnl, J Alg, JAlg, JA, c1992, c199x, c19xx
%X Given generators for a perm group G in 1..n
   find a minimum set of generators.
   Shown to be NP-hard.
   If M is the actual min size then shows that the greedy alg
   in general finds a set of size <= O(M*log log n)  - sharp bound.
   [Also search for: permutation group].

%A L. Babai
%A E. M. Fuks
%A A. Seress
%T Fast management of permutation groups
%J Proc. 29th IEEE Symp. Foundations of Comp. Sci.
%P 272-282
%D 1988
%K conf, c1988, c19xx, c19xx, maths, mathematics, group, groups, permutation,
   membership, word problem, subgroup, generator, perm,
   FOCS 29 FOCS29 FOCS88
%X "... provide an order-of-magnitude improvement in the worst-case analysis of
   the basic permutation-group problems, inc. membership testing & computing the
   order of the group. For deeper questions about the g., inc. finding
   composition factors, an improvement of up to four orders of magnitude is
   realized. These and other essential investigations are all accomplished in
   O(n/sup 4/log/sup c/n) time. ..."
   -- [<A HREF="https://doi.org/10.1109/SFCS.1988.21943">doi:10.1109/SFCS.1988.21943</A>]['20].
   via rgep OF owl.pmms.cam.ac.uk (Richard Pinch)  11/93.
   [Also search for: permutation group].

%A W. M. Kantor
%A E. M. Luks
%T Computing in quotient groups
%J Proc. 22nd ACM Symp. Theory of Comp.
%P 524-534
%D 1990
%K maths, group, groups, permutation, membership, subgroup, generator, perm,
   conf, c1990, c199x, c19xx, STOC 22 STOC22 STOC90
%X via rgep OF owl.pmms.cam.ac.uk (Richard Pinch)  11/93.

%A G. Butler
%T Fundamental Algorithms for Permutation Groups
%I SpringerVerlag
%S LNCS
%V 559
%P 238
%M DEC
%D 1991
%K book, text, c1991, c199x, c19xx, perm, maths, group, subgroup, coset,
   generators, expression, membership, word problem
%X 1st ed 1991, pb us$35; uk us isbn:0387549552; uk us isbn13:978-0387549552.
   "... algorithms for permutation groups with reference to aspects of
   combinatorial group theory, soluble groups, and p-groups where appropriate.
   ... begins with a constructive introduction to group theory and algorithms
   for computing with small groups, followed by a gradual discussion of the
   basic ideas of Sims for computing with very large permutation groups, ..."
   From plisonek OF risc.uni-linz.ac.at (Petr Lisonek)  11/93.
   [Also search for: permutation group].

%A R. Korf
%T Learning to Solve Problems by Searching for Macro Operators
%I Pitman
%D 1985
%O PhD thesis CMU 85? 83?
%K combinatorial search, Rubik, Rubic, Rubik's cube, permutation, group, maths,
   operator
%X via: Jalal Maleki   2/94
        Organization: CIS Dept, Univ of Linkoping, Sweden
        jalma OF ida.liu.se (Jalal Maleki).

%A W. P. Thurston
%T Conway's tiling groups
%J Am. Math. Monthly
%P 757-773
%M OCT
%D 1990
%K AMM, c1990, c199x, c19xx, tile, tiled, tiling, domino, dominoe, polyomino,
   Conway, maths, group
%X You will find there an algorithm for the construction of tilings by
   dominoes of any holefree polyomino. Two of these tilings are the
   "highest" and "lowest" according to an height function defined in
   the Cayley graph of the finitely generated group
   G = { a,b | a_{2}ba{-2}b_{-1} = ab_{2}a_{-1}b_{-2} = e }
   The essential thing is that any tiling can be obtained from any
   other tiling just by repeatedly replacing tilings of 2 x 2 squares
   by two horizontal dominoes by tilings by two vertical dominoes
   (and the reverse).
   Jim Propp from M.I.T. has also done nice work on enumerating tilings
   by dominoes of special figures (the aztec diamond in particular).
 Philippe Aigrain
 email: aigrain OF irit.irit.fr
 Institut de Recherche en Informatique de Toulouse            (7/94).

%A D. E. Knuth
%T Efficient representation of perm groups
%J Combinatorica
%V 11
%N 1
%P 33-43
%M MAR
%D 1991
%K jrnl, c1991, c199x, c19xx, perm, permutation, group, maths, groups,
   representation, strong generator set, SGS, base, BSGS, generating,
   Schreier-Sims, membership
%X "... presents an elementary version of Sims's alg. for computing strong
   generators of a given perm group, together with a proof of correctness & some
   notes about appropriate low level data structs.. Upper & lower bounds on the
   running time are also obtained. (Following a suggestion of V.Pratt, we
   adopt the convention that perm=permutation, perhaps thereby saving millions
   of syllables in future research.)"
   -- [<A HREF="http://dx.doi.org/10.1007/BF01375471">doi:10.1007/BF01375471</A>]['10],
   or P123@[<A HREF="http://www-cs-faculty.stanford.edu/~knuth/preprints.html">stanf</A>]['10].
     ("a strong generating set ... is a g.set that clearly exhibits the perm'n
     structure as described by a stabilizer chain [which] is a seq. of subgrps,
     each containing the next & each stabilizing 1 more pt."
     -- [<A HREF="http://en.wikipedia.org/wiki/Strong_generating_set">wikip</A>]['10].)
   [Also search for: maths group representation].

%A L. Babai
%A G. Cooperman
%A L. Finkelstein
%A E. Luks
%A A. Seress
%T Fast Monte Carlo algorithms for permutation groups
%J Annual ACM Symp. on Theory of Computing
%P 90-100
%D 1991
%K conf, STOC, c1991, c199x, c19xx, permutation, group, maths, groups,
   randomised, algorithm, representation, membership, problem,
   strong generatin set, SGS
%X "... key idea is that under certain condns, random subproducts of the
   generators successfully emulate truly random elts of a group. We achieve a
   nearly optimal O(n3 log c n) asymptotic running time for membership testing,
   where n is the size of the perm.domain. ...is an improvement of 2 orders of
   mag. [v.] known elementary algs. & 1 order of mag. [v.] algs. which depend on
   heavy use of group theory.  An even greater speedup is achieved for normal
   closures, a key ingredient of algs. in computational group theory, now
   constructible in Monte Carlo time O(n2 log c n), i.e., essentially linear
   time (as a fn of the input length).  As a by-product, for low rank systems of
   linear equns we achieve a speedup over Gaussian elimination.  [OTOH] some of
   the new techniques are so general, that they allow polynomial time implns in
   the very general model of black box groups (grp ops. performed by an oracle).
   In particular, the normal closure alg. leads to polynomial time MCalgorithms
   to test solvability & nilpotence of such groups, & a # of further applns to
   matrix grps. ... randomized algs are not heuristic: the probability of error
   is guaranteed not to exceed a bound >0, prescribed by the user. The cost of
   this requirement is a factor of j log j in the running time."
   -- [<A HREF="https://doi.org/10.1145/103418.103435">doi:10.1145/103418.103435</A>]['10],
   pdf@[<A HREF="http://people.cs.uchicago.edu/~laci/lasvegas79.pdf">uchicago</A>]['22],
   ps.gz@[<A HREF="http://www.ccs.neu.edu/home/gene/papers/jcss95.ps.gz">neu</A>]['10].
   [Also search for: permutation group]  &  [also search for: group membership].

%A C. C. Sims
%T Computation with Finitely Presented Groups
%I CUP
%P 624
%D 1994
%K book, text, CUP, c1994, c199x, c19xx, group, groups, theory, maths, Comp Sci,
   subgroup, permutation, quotient, finitely presented
%X 1st ed 1994; hb us$200; uk us isbn:0521432138; uk us isbn13:978-0521432139.
          2010; pb us$60;  uk us isbn:0521135079; uk us isbn13:978-0521135078.
   "... methods for working with elements, subgroups, & quotient groups of a
   finitely presented group. ... emphasizes the connection with fundamental
   algs. from theoretical comp.sci., particularly the theory of automata &
   formal languages, from computational number theory, & from computational
   commutative algebra. The LLL lattice reduction alg. & various algs. for
   Hermite & Smith normal forms are used to study the Abelian quotients of a
   finitely presented group. The work of Baumslag, Cannonito, & Miller on
   computing non-Abelian polycyclic quotients is described as a generalization
   of Buchberger's Grobner basis methods to right ideals in the integral group
   ring of a polycyclic group."
   [Also search for: permutation group].

%A A. Seress
%T Permutation Group Algorithms
%I CUP
%P 276
%M AUG
%D 2003
%K book, text, CUP, c2003, c200x, c20xx, group, groups, algorithm, permutations,
   c2003, c200x, c20xx, zz0703, maths, mathematics, CSC, Comp Sci, theory
%X 1st ed 2003; hb us$93; uk us isbn:052166103X; uk us isbn13:978-0521661034.
   "Permutation group algorithms are indispensable in the proofs of many deep
   results, including the construction and study of sporadic finite simple
   groups. This work describes the theory behind permutation group algs., up to
   the most recent developments based on the classification of finite simple
   groups. ..."
   [Also search for: permutation group].

%A D. F. Holt
%A B. Eick
%A E. A. O'Brien
%T A Handbook of Computational Group Theory
%I ChapmanHall
%P 536
%D 2005
%K book, text, c2005, c200x, c20xx, OBrien, maths, group, groups, permutation,
   coset, representation, algorithm
%X 1st ed 2005; hb us$95; uk us isbn:1584883723; uk us isbn13:978-1584883722.

%A G. Havas
%A C. Ramsay
%T On proofs in finitely presented groups
%J Groups, St Andrews
%D 2005
%O London Mathematical Society, Lect. Note Series, Vol.340, pp.457-474, 2007
%K conf, c2005, c200x, c20xx, maths, group, proof
%X Auths @ UQ c2009.

%A J. Meier
%T Groups, Graphs and Trees. An Introduction to the Geometry of Infinite Groups
%I CUP
%P 256
%D 2008
%K CUP, book, text, c2008, c200x, c20xx, group, theory, groups, graph, tree,
   Thompsons, maths, mathematics
%X 2008, hb us$101; uk us isbn:0521895456; uk us isbn13:978-0521895453.
   2008, pb us$40;  uk us isbn:0521719771; uk is isbn13:978-0521719773.
   "...presents the modern, geometric approach to group theory, ...
   ... Topics include group actions, the construction of Cayley graphs, &
   connections to formal language theory & geometry. Theorems are balanced by
   specific examples such as Baumslag-Solitar groups, the Lamplighter group &
   Thompson's group."

%A E. M. Luks
%T Group isomorphism with fixed subnormal chains
%J arXiv
%M OCT
%D 2015
%K TR, c2015, c201x, c20xx, zz1115, maths, group, isomorphism, chain, problem,
   algorithm, groups, Pgroup
%X "In recent work, Rosenbaum & Wagner showed that isomorphism of explicitly
   listed p-groups of order n could be tested in n^((1/2)log_p n + O(p)) time,
   ~ square root of the classical bnd. The O(p) term is entirely due to an
   n^O(p) cost of testing for isomorphisms that match fixed composition series
   in the two groups. We focus here on the fixed-composition-series subproblem
   & exhibit a polynomial-time algorithm that is valid for general groups. A
   subsequent paper will construct canonical forms within the same time bound."
   -- 1511.00151@[<A HREF="http://arxiv.org/abs/1511.00151">arXiv</A>]['15].
   [Also search for: group isomorphism].

%A A. Nies
%A K. Tent 
%T Describing finite groups by short first-order sentences
%J Israel J. of Math.
%V 221
%P 85-115
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0921, maths, finite group, sentence,
   straight line program, straightLineProgram
%X "We say that a class of finite structures for a finite 1st-order signature is
   r-compressible for an unbounded fn r: N->N^+ if each struct. G in the class
   has a 1st-order desc'n of size at most O(r(|G|)). We show that the class of
   finite simple groups is log-compressible, & the class of all finite gs. is
   log^3-compressible. ... we obtain that the class of all finite transitive
   perm'n gs. is log^3-comp.. The results rely on the classification of finite
   simple groups, the bi-interpretability of the twisted Ree groups with finite
   difference fields, the existence of profinite presentations with few relators
   for finite groups, & group cohomology. We also indicate why the results are
   close to optimal."
   -- [<A HREF="https://doi.org/10.1007/s11856-017-1563-2">doi:10.1007/s11856-017-1563-2</A>]['21].
   (Also see SLP@[<A HREF="https://en.wikipedia.org/wiki/Straight-line_program">wikip</A>]['21].)

%A B. Das
%A S. Sharma
%A P. R. Vaidyanathan
%T Space efficient representations of finite groups
%J arXiv
%M FEB
%D 2020
%K TR, c2020, c202x, c20xx, zz0320, maths, group, representation
%X "The Cayley table rep'n of a group uses O(n^2) words for a g. of order n &
   answers multiplication queries in time O(1). It is interesting to ask if
   there is a o(n^2)-space rep'n of groups that still has O(1) query-time. We
   show that for any d, 1/log(n) <= d <= 1, there is an O(n^{1+d}/d)-space
   rep'n for groups of order n with O(1/d) query-time. ... We construct data
   structures in their model for Hamiltonian groups & some other classes of g.
   with const. query-time."
   -- 2002.11391@[<A HREF="https://arxiv.org/abs/2002.11391">aXiv</A>]['20].
   [Also search for: maths group representation] and see: Das group 2024.


%A S. Dzeroski
%A N. Lavrac
%T Refinement graphs for FOIL and LINUS
%B Inductive Logic Programming
%E S. Muggleton
%P 319-334
%I AcademicPress
%D 1992
%K refinement graph, ILP, LP, c1992, c199x, c19xx

%A D. Conklin
%A I. H. Witten
%T Complexity-based induction
%J Machine Learning
%V 16
%N 3
%P 203-225
%M SEP
%D 1994
%K jrnl, ILP, c1994, c199x, c19xx, inductive logic programming, model, proof,
   automaticProgramming, complexity, inductive inference, LP, II,
   minimum message length, MML, encoding, description, MDL, proof, model,
   justification, complexity, data compression, SLP, probability, probabilistic,
   logical, theory, theories
%X Has a nice explanation and comparison of
   1. proof complexity - code an example as the choices in its proof  versus
   2. model complexity - give examples as set of provable things,
   and 2 examples where they give different results.
   -- [<A HREF="https://doi.org/10.1007/BF00993307">doi:10.1007/BF00993307</A>]['22].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)
   [Also search for: ILP probability].

%A A. Srinivasan
%A S. Muggleton
%A M. Bain
%T The justification of logical theories based on data compression
%E K. Furukawa, D. Michie, and S. Muggleton
%J Machine Intelligence
%V 13
%P 87-121
%I OUP
%D 1994
%K ILP, logic, theory, inductive logic programming, proof, MML, MDL
%X -- [<A HREF="http://www.doc.ic.ac.uk/~shm/Papers/mi13just.pdf">mi13just.pdf</A>][8/'04]
   [Also search for: complexity ILP SEP 1994].

%A S. Muggleton
%A A. Srinivasan
%T Mode-directed inverse resolution
%J Machine Intelligence
%V 14
%I OUP
%D 1994
%K inductive logic programming, LP, ILP, AI, OUP
%X ref [7] from ILP94 p.230.

%A A. Srinivasan
%A S. H. Muggleton
%A R. D. King
%A M. J. E. Sternberg
%T Mutagenesis: ILP experiments in a non-determinate biological domain
%J Proc. 4th Int. Workshop on Inductive Logic Programming
%E S. Wrobel
%W Bad Honnef / Bonn
%M SEP
%D 1994
%P 217-232
%K LP, ILP, ILP4, ILP94, c1994, c199x, c19xx, RDKing, AI, conf, Progol,
   MolBio, biology, computing
%X ... to discovering structural features that can lead to mutagenicity in
   small molecules. ...
   Progol allows the construction of hypotheses with bounded non-determinacy
   by performing a best-first search within the subsumption lattice.
   isbn:3-88457-237-7.

%A S. Wrobel
%T Concept Formation and Knowledge Revision
%I Kluwer Academic Publishers
%P 256
%D 1995
%K book, text, AI, inductive logic programming, ILP, MOBAL,
   inductive inference, II, concept
%X See [<A HREF="http://nathan.gmd.de/persons/stefan.wrobel/kluwerbook.html]">WWW (2/'95)</A>].
      1. Introduction.
      2. The Psychology of Concepts and Concept Formation.
      3. Concept Representation in a Paraconsistent Logic with Higher-
         Order Elements.
      4. Knowledge Revision as a Concept Formation Context.
      5. Demand-Driven Concept Formation.
      6. Embeddedness.
      7. Conclusion.
      A. MOBAL Software Info Page. B. Glossary of Symbols.
   isbn:0-7923-9500-X.
   Dr. Stefan Wrobel, GMD  email: teuber@gmd.de  (2/'95).

%A I. Bratko
%A S. Muggleton
%T Applications of inductive logic programming
%J CACM
%V 38
%N 11
%P 65-70
%D 1995
%K jrnl, CACM, ILP, LP, induction, c1995, c199x, c19xx
%X -- [<A HREF="http://www-users.cs.york.ac.uk/~stephen/jnl.html">www</A>][1/'02].

%A S. Muggleton
%T Stochastic logic programs
%J Advances in Inductive Logic Programming
%I IOS
%P 254-264
%E L. de Raedt
%D 1996
%K SLP, SLPs, ILP, LP, c1996, c199x, c19xx, AI, II, stochatsic, probabilistic,
   log-linear

%A S. Muggleton
%T Learning from positive data
%J Proc. 6th Int. Workshop on Inductive Logic Programming
%I SpringerVerlag
%S LNAI
%V 1314
%D 1997
%K wkShop, c1997, c199x, c19xx, zz0418, Inductive Logic Programming, ILP,
   Progol, Inverse Entailment, compression, information, AI, II
%X progol@[<A HREF="http://www.doc.ic.ac.uk/~shm/progol.html">ic</A>]['18].
   (Also see ILP@[<A HREF="https://en.wikipedia.org/wiki/Inductive_logic_programming">wikip</A>]['18].)

%A S. Muggleton
%T Scientific knowledge discovery using inductive logic programming
%J CACM
%V 42
%N 11
%P 42-46
%M NOV
%D 1999
%K jrnl, CACM, ILP, LP, program, zz0102, c1999, c199x, c19xx
%X -- [<A HREF="http://www-users.cs.york.ac.uk/~stephen/jnl.html">www</A>][1/'02].

%A M. Turcotte
%A S. H. Muggleton
%A M. J. E. Sternberg
%T Automated discovery of structural signatures of protein fold and function
%J Jrnl. of Molec. Biol.
%V 306
%P 591-605
%D 2001
%K jrnl, JMB, MolBio, c2001, c200x, c20xx, ILP, inductive, induction, II,
   protein, fold, folding, structure
%X "... To search systematically for protein fold signatures, we have explored
   the use of Inductive Logic Programming (ILP). ILP is a machine learning
   technique which derives rules from observation & encoded principles. The
   derived rules are readily interpreted in terms of concepts used by experts.
   For 20 populated folds in SCOP, 59 rules were found automatically. ..."
   -- [<A HREF="https://doi.org/10.1006/jmbi.2000.4414">doi:10.1006/jmbi.2000.4414</A>]['22],
      [<A HREF="http://www-users.cs.york.ac.uk/~stephen/jnl.html">www</A>][1/'02].

%A M. Turcotte
%A S. H. Muggleton
%A M. J. E. Sternberg
%T The effect of relational background knowledge on learning of
   protein three-dimensional fold signatures
%J Machine Learning
%V 1, 2
%P 81-96
%M APR-MAY
%D 2001
%K jrnl, MolBio, c2001, c200x, c20xx, 3D, structure, protein, fold, folding,
   ILP, LP, Progol
%X "... application [of ILP] in structural molecular biology, that of
   constructing readable descriptions of the major protein folds. ..."
   -- [<A HREF="https://doi.org/10.1023/A:1007672817406">doi:10.1023/A:1007672817406</A>]['22].

%A J. W. Lloyd
%T Logic for Learning. Learning Comprehensible Theories from Structured Data
%I Springer
%S Cognitive Technologies
%P 256
%D 2003
%K book, text, machine learning, programming, LP, Alkemy, Escher, FLP,
   decision tree, trees, DTree, c2003, c200x, c20xx, AI, JWLloyd
%X 1 Intro;        2 Logic;    3 Individuals;    4 Predicates;
   5 Computation;  6 Learning, 6.1 D Trees, 6.2 Illustrations.
   "Probabi1ity' is not discussed although "accuracy" comes into the D.Ts..
   h.b.; isbn:3540420274.  Machine learning, algorithmic learning,
   artificial intelligence, computational learning, computational logic,
   higher-order logic, knowledge representation, predicate construction
   [auth@ANU '03][<A HREF="http://users.rsise.anu.edu.au/~jwl/LogicforLearning/">contents@anu</A>]['05] <!-- see email 15/7/05 --> .

%A V. Santos Costa
%A D. Page
%A M. Qazi
%A J. Cussens
%T CLP(BN): Constraint logic programming for probabilistic knowledge
%J Proc. of the 19th Annual Conf. on Uncertainty in Artificial Intelligence
%P ?-?
%M AUG
%D 2003
%I MorganKaufman
%K conf, CLP, CLPbn, AI, LP, UAI, UAI03, probability, data mining,
   c2003, c200x, c20xx
%X (ref at www.informatik.uni-freiburg.de/~kersting/plmr/ )

%A S. Dzeroski
%T Multi-relational data mining: an introduction
%J ACM SIGKDD Explorations Newsletter
%V 5
%N 1
%M JUL
%D 2003
%P 1-16
%K c2003, c200x, c20xx, relational data base, database, discovery, relations,
   MRDM, zzOSP, zOSP04
%X "Data mining algorithms look for patterns in data. [...] multi-relational
   data mining (MRDM) approaches look for patterns that involve multiple tables
   (relations) from a relational [DB]. ... most common types of patterns &
   approaches considered in data mining have been extended to the
   multi-relational case & MRDM now encompasses multi-relational (MR)
   association rule discovery, MR decision trees & MR distance-based methods,
   among others. MRDM approaches have been successfully applied to a number of
   problems in a variety of areas, most notably in the area of bioinformatics.
   [...] introduction to MRDM, ..."
   -- [<A HREF="http://doi.acm.org/10.1145/959242.959245">doi:10.1145/959242.959245</A>][8/'04].

%A D. P. Enot
%A R. D. King
%T Application of inductive logic programming to structure-based drug design
%J 7th Euro. Conf. Principles & Practice of Knowledge Discovery in Databases
%P 156-167
%M SEP
%D 2003
%I SpringerVerlag
%S LNCS
%V 2838
%K conf, David Enot, MolBio, ILP, LP, aber, c2003, c200x, c20xx, zzOSP, zOSP04,
   PKDD, 3D, protein, drug design, Glycogen Phosphorylase inhibitors,
   HIV protease, RDKing
%X "...data available on the 3D structure of protein-ligand complexes. The
   extraction of knowledge from this data is central to the design of new
   drugs. We extended the application of ... (ILP) in drug design to deal with
   such structure-based drug design (SBDD) problems. We first expanded the ILP
   pharmacophore representation to deal with protein active sites. Applying a
   combination of the ILP algorithm Aleph, & linear regression, we then formed
   quantitative models that can be interpretated chemically. We applied this
   approach to 2 test cases: Glycogen Phosphorylase inhibitors, & HIV protease
   inhibitors. In both cases we observed a significant (P < 0.05) improvement
   over both standard approaches, & use of only the ligand. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/b13634">doi:10.1007/b13634</A>]['04]
   uk us isbn:3540200851.  auths @ at U. Wales Aberystwyth c2004.

%A A. Srinivasan
%A R. D. King
%A M. E. Bain
%T An empirical study of the use of relevance information in
   inductive logic programming.
%J J. Machine Learning Res.
%V 4
%P 269-282
%M DEC
%D 2003
%K jrnl, c2003, c200x, c20xx, zz0206, AI, LP, RDKing
%X "... When using [ILP] systems, it is typically assumed that sufficient human
   expertise is at hand to rule out irrelevant background information. Such
   irrelevant information can, & typically does, hinder an ILP system's search
   for good models. Here, we provide evidence that if expertise is available
   that can provide a partial-ordering on sets of [bg] predicates in terms of
   relevance to the analysis task, then this can be used to good effect by an
   ILP system. In particular, using data from biochemical domains, we
   investigate an incremental strategy of including sets of predicates in
   decreasing order of relevance. Results obtained suggest that: (a) the
   incremental approach identifies, in substantially less time, a model that is
   comparable in predictive accuracy to that obtained with all [bg] information
   in place; & (b) the incremental approach using the relevance ordering
   performs better than one that does not (that is, one that adds sets of
   predicates randomly). ..."
   -- [<A HREF="http://portal.acm.org/citation.cfm?id=945387">acm</A>]['06].

%A A. Amin
%T Recognition of hand-printed characters based on structural description and
   inductive logic programming
%J Pattern Recognition Lett.
%V 24
%P 3187-3196
%D 2003
%K jrnl, hand writing, ILP, c2003, c200x, c20xx, arabic character, uniNSW,
   handwriting, written, handwritten
%X "... automatic recognition of hand-printed Arabic characters using machine
   learning. Conventional methods have relied on hand-constructed dictionaries
   which are tedious to construct & difficult to make tolerant to variation in
   writing styles. [M. L.] can generalize over the large degree of variation
   between writing styles & recognition rules can be constructed by example.
   ... tested on a sample of handwritten characters from several individuals
   whose writing ranged from acceptable to poor in quality & the average
   correct recognitions rate obtained using cross-validation was 86.65%"
   -- [<A HREF="http://dx.doi.org/10.1016/j.patrec.2003.08.004">doi:10.1016/j.patrec.2003.08.004</A>]['05],
      [<A HREF="http://www.cse.unsw.edu.au/~amin/">auth</A>]['05].

%A U. Schmid
%T Inductive Synthesis of Functional Programs
%I SpringerVerlag
%P 420
%D 2003
%K book, text, c2003, c200x, c20xx, program, FP, II, program, programming,
   universal planning, fold, folding of finite programs, schema abstraction,
   analogical reasoning
%X uk us isbn:3540401741; uk us isbn13:9783540401742.
   @springer [<A HREF="http://dx.doi.org/10.1007/b12055">doi:10.1007/b12055</A>]['07].
   Review in JFP [<A HREF="http://dx.doi.org/10.1017/S0956796807006296">doi:10.1017/S0956796807006296</A>]['07].

%A R. D. King
%A P. H. Wise
%A A. Clare
%T Confirmation of data mining based predictions of protein function
%J Bioinformatics
%P 1110-1118
%M MAY
%D 2004
%K jrnl, MolBio, prediction, proteins, DMP, Genepredictions, gene,
   c2004, c200x, c20xx, RDKing, AClare
%X "... examined the updated (20.02.02) Riley group genome annotation, and
   examined the scientific literature for direct experimental derivations of
   ORF function. Both tests confirmed the DMP predictions. Accuracy varied
   between rules, and with the detail of prediction, but they were generally
   significantly better than random. For voting rules, accuracies of 75-100%
   were obtained. Twenty-one of these DMP predictions have been confirmed by
   direct experimentation. The DMP rules also have interesting biological
   explanations. DMP is, to the best of our knowledge, the first non-SIM based
   prediction method to have been tested directly on new data."
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/20/7/1110?etoc">online</A>] 5 Feb 2004,
      [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bth047">doi:10.1093/bioinformatics/bth047</A>][6/'04].

%A R. D. King
%A K. E. Whelan
%A F. M. Jones,  P. G. K. Reiser,  C. H. Bryant, S. H. Muggleton,  D. B. Kell
%A S. G. Oliver
%T Functional genomic hypothesis generation and experimentation by a
   robot scientist
%J Nature
%P 247-252
%V 427
%M JAN
%D 2004
%K jrnl, MolBio, progol, ASE, ILP, Saccharomyces cerevisiae, yeast, genes,
   functional genomics, zz0204, c2004, c200x, c20xx, aber, zzOSP, zOSP04,
   bioinformatics, gene function, predict, prediction, AI, II, auxotrophic,
   protein, metabolite, metabolic, pathway, pathways, model, RDKing
%X "...[can we] automate the scientific process is of both great theoretical
   interest & increasing practical importance because, in many scie. areas,
   data are being generated much faster than they can be effectively analysed.
   We describe a physically implemented robotic system that applies techniques
   from artificial intelligence to carry out cycles of scientific exp'n.
   [It] automatically originates hypotheses to explain observations, devises
   experiments to test these hypotheses, physically runs the experiments using
   a lab' robot, interprets the results to falsify hypotheses inconsistent with
   the data, & then repeats the cycle. ...apply the system to the determination
   of gene function using deletion mutants of yeast (Saccharomyces cerevisiae)
   & auxotrophic growth experiments. We built & tested a detailed logical model
   (involving genes, proteins & metabolites) of the aromatic amino acid
   synthesis pathway. In biological experiments that automatically reconstruct
   parts of this model, ... intelligent experiment selection strategy is
   competitive with human performance & significantly outperforms, with a cost
   decrease of 3-fold & 100-fold (respectively), both cheapest &
   random-experiment selection." 15 Jan 2004
   -- [<A HREF="http://dx.doi.org/10.1038/nature02236">doi:10.1038/nature02236</A>][1/'04].
   [Also search for: robot scientist].

%A N. Angelopoulos
%A J. Cussens
%T On the implementation of MCMC proposals over stochastic logic programs
%J Colloquium on Implementation of Constraint and Logic Programming Systems,
   Satellite Workshop to ICLP04
%W Saint-Malo, .fr
%P ?-?
%D 2004
%K wShop, ILP, LP, MCMC, SLP, AI, c2004, c200x, c20xx, uniYork, Monte Carlo,
   complexity, proposal, probabilistic, Nicos Angelopoulos, zzOSP, zOSP04,
   probability, prior, program
%X "... issues that arise in an MCMC alg' which uses a prob' ext'n of
   [LP] ... challenges ... in extending the underlying logic engine to
   facilitate such alg's.  ... core issues ... analyse the possibility of
   integration with Prolog. ... "  [10 refs]
   -- [<A HREF="http://www-users.cs.york.ac.uk/nicos/pbs/Ciclops04.ps.gz">pp.ps@cs.york.ac.uk</A>][9/'04]
   fig 1, [pr =] 1/2 :: nat(0).                 (So pr(nat(n)) = 1/2**n.)
          [pr =] 1/2 :: nat(s(X)) :- nat(X).
   "...expressing prob' distn's over theories of stat' models [B.nets] while
   the MCMC alg'provides a versatile tool of Bayesian learning.
   ... ways in which the Prolog enginine can be improved for ...
   [Also search for: ILP probability].

%A L. De Raedt
%T Statistical relational learning: An inductive logic programming perspective
%J ECML
%P 3-5
%D 2005
%K conf, c2005, c200x, c20xx, deRaedt, relation, relations, ILP, PRISM, nFOIL,
   FOIL, Bnet
%X "... The main contribution of this talk is the introduction of three
   probabilistic inductive logic programming settings ... PRISM ... Bayesian
   ... proofs ..."
   -- [<A HREF="http://dx.doi.org/10.1007/11564126_3">doi:10.1007/11564126_3</A>]['06].

%T 18th Int. Conf. in Inductive Logic Programming
%I SpringerVerlag
%S LNCS
%V 5194
%E F. Zelezny
%E N. Lavrac
%D 2008
%K conf, c2008, c200x, c20xx, ILP, LP, AI, LNAI, LNCS
%X uk us isbn:3540859276; uk us isbn13:978-3540859277.

%T Probabilistic Inductive Logic Programming
%E L. De Raedt
%E P. Frasconi
%E K. Kersting
%E S. H. Muggleton
%I SpringerVerlag
%S LNAI
%V 4911
%P 341
%D 2008
%K book, c2008, c200x, c20xx, zz0210, deRaedt, AI, II, ILP, PILP, probabilistic,
   probability, PRISM, CLPbn, deRaedt
%X "... such as relational sequence learning techniques, using kernels with
   logical representations, Markov logic, the PRISM system, CLP(BN), B.logic
   programs, and the independent choice logic. The third part provides a
   detailed account of some show-case applications of probabilistic inductive
   logic programming. The final part touches upon some theor.investigations and
   includes chapters on behavioural comparison of probabilistic logic prog.
   representations and a model-theoretic expressivity analysis."
   1st ed 2008; pb us$48; uk us isbn:3540786511; uk us isbn13:978-3540786511.
   -- [<A HREF="https://doi.org/10.1007/978-3-540-78652-8">doi:10.1007/978-3-540-78652-8</A>]['22].
   [Also search for: ILP probability].

%A A. Cropper
%A R. Morel
%A S. H. Muggleton
%T Learning higher-order logic programs
%J arXiv
%M JUL
%D 2019
%K TR, c2019, c201x, c20xx, zz0719, LP, ILP, MIL, ASP, inductive logic program,
   AI, II, learn, high, higher, first, second, order
%X "A key feature of inductive logic programming (ILP) is its ability to learn
   first-order programs, which are intrinsically more expressive than
   propositional programs. In this paper, we introduce techniques to learn
   higher-order programs. Specifically, we extend meta-interpretive learning
   (MIL) to support learning higher-order programs by allowing for
   higher-order definitions to be used as background knowledge. Our
   theoretical results show that learning higher-order programs, rather than
   first-order programs, can reduce the textual complexity required to express
   programs which in turn reduces the size of the hypothesis space and sample
   complexity. ..."
   -- 1907.10953@[<A HREF="https://arxiv.org/abs/1907.10953">arXiv</A>]['19].
   [Also search for: logic ILP].

%A F. Dagnino
%A D. Ancona
%A E. Zucca
%T Flexible coinductive logic programming
%J arXiv
%M AUG
%D 2020
%K TR, conf, ICLP, ICLP2019, LP, ILP, c2020, c202x, c20xx, zz0820, coinduction,
   coLP, inductive logic programming, coClause
%X "Recursive defns of predicates are usually interpreted either inductively or
   coinductively. Recently, a more powerful approach has been proposed, called
   flexible coinduction, to express a variety of intermediate interpretations,
   nec. in some cases to get the correct meaning. We provide a detailed formal
   a/c of an extension of LP supporting flexible coinduction. ... coclauses,
   clauses with a special meaning used to tune the interpretation of predicates.
   As usual, the declarative semantics can be expressed as a fixed pt which,
   however, is not nec. the least, nor the greatest one, but is determined by
   the coclauses. ... the op.semantics is a combination of std SLD resolution &
   coSLD res'n. We prove that the op.semantics is sound & complete ..."
   -- 2008.02140@[<A HREF="https://arxiv.org/abs/2008.02140">arXiv</A>][5/8/2020].
      (Also see coI@[<A HREF="https://en.wikipedia.org/wiki/Coinduction ">wikip</A>]['20].)
   [Also search for: LP ILP]  and  [also search for: coinduction].

%A S. Patsantzis
%A S. H. Muggleton
%T Top program construction and reduction for polynomial time meta-interpretive
   learning
%J arXiv
%K JAN
%D 2021
%O to appear in Machine Learning J., Spec. Issue on Learning & Reasoning
%K TR, c2021, c202x, c20xx, zz0121, inductive logic programming, ILP, LP, AI,
   top program, topProgram, Louise, Metagol, MIL
%X "Meta-Interpretive Learners, like most ILP systems, learn by searching for a
   correct hypothesis in the hyp.space, the powerset of all constructible
   clauses. We show how this exponentially-growing search can be replaced by the
   construction of a Top program: the set of clauses in all correct hypotheses
   that is itself a correct hypothesis. We give an alg. for Top program
   construction & show that it constructs a correct Top program in polynomial
   time & from a finite # of examples. ...  Louise, that constructs a Top
   program & then reduces it by removing redundant clauses. ..."
   -- 2101.05050@[<A HREF="https://arxiv.org/abs/2101.05050">arXiv</A>]['21].
   [Also search for: LP ILP].

%A Ruoyu Wang
%A D. Sun
%A R. Wong
%A R. Ranjan
%T Horn rule discovery with batched caching and rule identifier for proficient
   compressor of knowledge data
%J SPE
%M NOV
%D 2022
%K jrnl, SPE, c2022, c202x, c20xx, zz1222, SInC, Prolog, ILP, LP, Horn clause,
   rule, discovery, AI, II, compress, data, compression
%X "... [here] proposes SInC, a semantic inductive compressor, to efficiently
   induce 1st-order Horn rules & semantically compress knowledge bases. SInC
  Â improves the scalability of top-down rule mining by batching correlated
   records in the cache & further optimizes the pruning of duplication &
   specialization via an identifier structure of Horn rules. ... evaluated on
   real-world & synthetic datasets & compared against the state-of-the-art. The
   results show that the batched caching speed up the rule mining procedure by
   more than two orders while consuming fewer than three times memory space. The
   identifier technique speeds up the duplication & specialization pruning by
   orders of magnitude with less than 5â° & 15% error rates, resp.. SInC
  Â outperforms the state-of-the-art from the perspective of overall compression
   on both scalability & compression effect."
   -- [<A HREF="https://doi.org/10.1002/spe.3165">doi:10.1002/spe.3165</A>]['22].
   [Also search for: AI II compression]  &  [also search for: ILP LP].

%A S. H. Muggleton
%T Hypothesizing an algorithm from one example: the role of specificity
%J Phil. Trans. of the Royal Soc., A
%V 381
%N 2251
%M JUN
%D 2023
%K jrnl, c2023, c202x, c20xx, zz0723, prolog, LP, ILP, II, AI, inference,
   program, generator, DeepLog, automatic programming
%X "Stat. mc. learning usually achieves high-accuracy models by employing tens
   of thousands of examples. By contrast, both children & adult humans typically
   learn new concepts from either one or a small # of instances. ... This paper
   explores ways in which this apparent disparity between human & mc. learning
   can be reconciled by considering algs. involving a preference for specificity
   combined with program minimality. It is shown how this can be efficiently
   enacted using hierarchical search based on identification of certificates &
   push-down automata to support hypothesizing compactly expressed maximal
   efficiency algs.. Early results of a new system called DeepLog indicate that
   such approaches can support efficient top-down construction of relatively
   complex logic programs from a single example."
   -- [<A HREF="https://doi.org/10.1098/rsta.2022.0046">doi:10.1098/rsta.2022.0046</A>]['23].
   [Also search for: prolog ILP].

%A C. Hocquette
%A S. Dumancic
%A A. Cropper
%T Learning logic programs by discovering higher-order abstractions
%J arXiv
%M AUG
%D 2023
%K TR, c2023, c202x, c20xx, zz0823, LP, ILP, II, AI, compress, logic program,
   Stevie
%X "... introduce an approach to discover higher-order abstractions, such as
   map, filter, & fold. We focus on inductive logic programming ... the goal is
   to compress a logic program by introducing higher-order abstn. We implement
   our approach in STEVIE ... STEVIE can improve predictive accuracies by 27% &
   reduce learning times by 47%. We also show that STEVIE can discover
   abstractions that transfer to different domains."
   -- [<A HREF="https://arxiv.org/abs/2308.08334">arXiv:2308.08334</A>]['23].
   [Also search for: logic LP ILP].


%A R. O. Duda
%A P. E. Hart
%T Pattern Classification and Scene Analysis
%I Wiley
%D 1973
%K book, text, image processing, IP, supervised classification,
   nearest neighbour
%X from a ref, includes Nearest Neighbour:
   To classify a query, x, find the "most similar" example in the
   training set and predict that x is of the same class as the example.

%A G. Strang
%A T. Nguyen
%T Wavelets and Filter Banks
%I Wellesley_Cambridge Press
%D 1996
%K book, text, wavelet, image processing, IP, 2D, images, zz0500

%A E. J. Stollnitz
%A T. D. DeRose
%A D. H. Salesin
%T Wavelets for Computer Graphics: Theory and Applications
%I MorganKauffman
%D 1996
%K Harr wavelet, Book, image processing, IP, images, zz1200
%X a ref.

%A A. P. Paplinski
%T Directional filtering in edge detection
%J IEEE Trans. Image Processing
%V 7
%N 4
%P 611-615
%M APR
%D 1998
%K jrnl, IEEE, filter, filters, IP, 2D, edge detection, conjugate images,
   directional, Monash, zz0498
%X [18 refs] (<A HREF="http://www.csse.monash.edu.au/">CSSE Monash</A>).

%A P. J. Olver
%T Joint invariant signatures
%J Found. Comput. Math.
%V 1
%P 3-67
%D 1999
%K c1999, c199x, c19xx, curve, shape, object, signature, recognition,
   differential invariant, moving frames
%X "A new, alg. theory of moving frames is applied to classify joint invariants
   & joint differential invariants of transformation groups. Equivalence &
   symmetry properties of submanifolds are completely det. by their joint
   signatures, which are parametrized by a suitable colln of joint invariants
   &/or joint diffl invariants. A variety of fundamental geometric examples are
   dev. in detail. Applications to object recognition problems in computer
   vision & the design of invariant numerical approximations are indicated."
   -- pdf@[<A HREF="http://www.math.umn.edu/~olver/mf_/ji.pdf">umn</A>]['12].
   [Also search for: curve signature].

%A H. Gomez Moreno
%A S. Maldonado Bascon
%A F. Lopez Ferreras,  M. Utrilla Manso,  P. Gil Jimenez
%T A modified median filter for the removal of impulse noise based on
   the support vector machines
%J Advances in signal processing and computer technologies
%E N. Mastorakis
%I WSES Press, USA
%P 9-14
%D 2001
%K conf, SCM, machine, image processing, IP, noisy
%X via H.W. isbn:9608052378.  Also see 2OO3 paper by 4/5 authors.

%A R. D. Morris
%A V. N. Smelyansky
%A P. C. Cheeseman
%T Matching images to models - camera calibration for 3-D surface reconstruction
%J Proc.  Third Int. Workshop on Energy Minimization Methods in
   Computer Vision and Pattern Recognition (EMMCVPR)
%I SpringerVerlag
%P 105-117
%D 2001
%K wShop, c2001, c200x, c20xx, image processing, model, models, 3D, surface,
   camera, images
%X [<A HREF="http://dx.doi.org/10.1007/3-540-44745-8_8">doi:10.1007/3-540-44745-8_8</A>]['09].

%A H. Gomez Moreno
%A S. Maldonado Bascon
%A F. Lopez Ferreras,  P. Gil Jimenez
%T Removal of impulse noise in images by means of the use of
   support vector machines
%I SpringerVerlag
%S LNCS
%V 2687
%P 536-543
%D 2003
%K SVM, machine, image processing, IP, noisy
%K via H.W.

%A F. Yang
%A T. Jiang
%T Pixon-based image segmentation with Markov random fields
%J IEEE Trans on Image Proc.
%V 12
%N 12
%P 1552-1559
%M DEC
%D 2003
%K jrnl, c2003, c200x, c20xx, MRF, field, image processing, segment
%X "... novel pixon-based adaptive scale method for image seg..  ... a pixon-
   -based image model is combined with a Markov random field (MRF) model under
   a Bayesian framework. We introduce a new pixon scheme that is more suitable
   for image segmentation than the "fuzzy" pixon scheme. The anisotropic
   diffusion eqn is successfully used to form the pixons in our new pixon
   scheme. Experimental results demonstrate that our alg. performs fairly well &
   computational costs decrease dramatically compared with the pixel-based MRF
   alg.."  [29 refs]
   [<A HREF="http://dx.doi.org/10.1109/TIP.2003.817242">doi:10.1109/TIP.2003.817242</A>]['07]

%A C. Fookes
%A A. J. Maeder
%T Quadrature-based image registration method using mutual information
%J Proc. of the 2004 IEEE Int. Symp. on Biomedical Imaging: From Nano to Macro
%W Arlington, VA, USA
%P 728-731
%M APR
%D 2004
%K conf, processing, register, AJMaeder, c2004, c200x, c20xx, correlation
%X ajm @ csiro e-health Qld as of 2OO5.

%A V. N. Smelyansky
%A P. Cheeseman
%A D. A. Maluf
%A R. D. Morris
%T Bayesian super-resolved surface reconstruction from images
%J Conf. Computer Vision and Pattern Recognition
%I IEEE
%P 1375-1782
%D 2000
%K conf, CVPR, 3D, 3-D, c2000, c200x, c20xx, image processing, zz0605,
   superresolved, resolution, improvement, reconstruction, surface, model
%X "...formulate the 3D reconstruction problem as the problem of inferring the
   parameters of a surface model from image data, and show how B. methods can
   be used to est. the parameters of this model given the image data. Thus we
   recover the 3D description of the scene. ..."
   -- [<A HREF="http://www.robinmorris.org/sigproc/cvpr00.ps.gz">p.s.gz</A>]['05],
      [<A HREF="http://ase.arc.nasa.gov/publications/pdf/1999-0202.pdf">??nasa??</A>]['05].

%A Y. Rubner
%A C. Tomasi
%A L. J. Guibas
%T The earth mover's distance as a metric for image retrieval
%J Int. J. of Computer Vision
%V 40
%N 2
%P 99-121
%M NOV
%D 2000
%K jrnl, c2000, c200x, c20xx, zz0214, image processing, earth mover distance,
   EMD, transport, transportation problem, histogram matching, match,
   distributions
%X "We investigate the properties of a metric between two distns, the Earth
   Mover's Distance (EMD), for content-based image retrieval. ... based on the
   minimal cost that must be paid to transform one distn into the other ...
   combine this idea with a representation scheme for distns that is based on
   vector quantization. ...  The EMD is based on a soln to the transportation
   problem from linear optimization, for which efficient algs are available, &
   also allows naturally for partial matching. It is more robust than histogram
   matching techniques, in that it can operate on variable-length rep's of the
   distns that avoid quantization & other binning problems typical of
   histograms. When used to compare distns with the same overall mass, the EMD
   is a true metric. ... we focus on applications to color & texture, & we
   compare the retrieval performance of the EMD with that of other distances."
   -- [<A HREF="http://dx.doi.org/10.1023/A:1026543900054">doi:10.1023/A:1026543900054</A>]['14], via njh.
   [Also search for: transportation problem] and
   [also search for: histogram distance].

%A B. Janvier
%A E. Bruno
%A T. Pun
%A S. Marchand-Maillet
%T Information theoretic temporal segmentation of video and applications:
   multiscale keyframes selection abd shot boundaries detection
%J Multimedia Tools and Applications
%I KluwerAcademic
%P ?-?
%D 2005 to appear
%K c200x, c20xx, MML, MDL, image processing, keyframe, temporal, time,
   segments, shots
%X [<A HREF="http://vision.unige.ch/publications/postscript/2005/janvier_itts.pdf">pdf</A>]['06].

%A B. Yang
%A F. Gu
%A X. Niu
%T Block mean value based image perceptual hashing
%J Int. Conf. on Intelligent Information Hiding and Multimedia
%P 167-172
%D 2006
%M DEC
%D 2006
%K conf, c2006, c200x, c20xx, zz0616, image, perceptual, hash, hashing,
   identify, content, identification, transformation
%X "Image perceptual hashing has been proposed to identify or authenticate image
   contents in a robust way against distortions caused by compression, noise,
   common signal processing & geometrical modifications, while still holding a
   good discriminability for different ones in sense of human perception. We
   propose & compare four normalized block mean value based image perceptual
   hashing algs. which demonstrate higher performances than other existing algs.
   in robustness and discriminalibility & simplicity for implementation.
   Overlapped blocking & rotation operations are employed to enhance the
   robustness to geometrical distortions. To evaluate the proposed algs'
   robustness & discriminability, given fixed modifications, identification
   ratio is used; & given fixed content classification, receiver operating
   curves is obtained."
   -- [<A HREF="http://dx.doi.org/10.1109/IIH-MSP.2006.265125">doi:10.1109/IIH-MSP.2006.265125</A>]['16], $ieee$,
   or pdf@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.97.6496">citeseer</A>]['16].

%A D. Brinkman
%A P. J. Olver
%T Invariant histograms
%J Amer. Math. Monthly
%I MAA
%P 4-24
%M JAN
%D 2012
%K c2012, c201x, c20xx, zz0912, curve, curves, shape, recognition, similarity,
   point, sets, local, distance set, signature, signatures, invariant,
   global, local, histogram
%X "We introduce & study a Euclidean-invariant distance histogram fn for
   curves. For a sufficiently regular plane curve, we prove that the cumulative
   distance histograms based on discretizing the curve by either uniformly
   spaced or randomly chosen sample pts converge to our histogram fn. ... serves
   as a simple, noise-resistant shape classifier for regular curves under the
   Euclidean group of rigid motions. Extensions of the underlying ideas to
   higher-dim. submanifolds, as well as to area histogram fns invariant under
   the group of planar area-preserving affine transfns, are discussed."
 p.20: "... calc. the average diff. between two hist.plots, normalized wrt
   delta l. Our working hypothesis is that diffs. < 1% represent histogram
   approximations that cannot be distinguished. ..."
   -- [<A HREF="http://dx.doi.org/10.4169/amer.math.monthly.119.01.004">doi:10.4169/amer.math.monthly.119.01.004</A>]['12]
    & [<A HREF="http://www.jstor.org/stable/10.4169/amer.math.monthly.119.01.004">Jstor</A>]['12];
   auth1@[<A HREF="http://www.damtp.cam.ac.uk/people/d.brinkman/">cam</A>]['12];
     "The distance histogram of a finite set of pts, P={z1,...,zn},
      is  nu_P(r) = #{(i,j) | 1 <= i < j <= n, d(zi,zj) = r}."
   [Also search for: curve signature].

%A M. Cuturi
%T Sinkhorn Distances: Lightspeed computation of optimal transport
%J Advances in Neural Info. Proc. Sys.
%V 26
%D 2013
%K conf, c2013, c201x, c20xx, zz0214, image, Sinkhorn distance, histogram,
   transportation, transport, problem, MNIST
%X "Optimal transportation distances are a fundamental family of parameterized
   distances for histograms in the probability simplex. ... their computation
   involves the resolution of a linear program whose cost is prohibitive
   whenever the histograms' dimension exceeds a few hundreds. ... new family of
   optimal transportation distances that look at transportation problems from a
   max.-ent. perspective. We smooth the classical optimal transportation problem
   with an entropic regularization term, & show that the resulting optimum is
   also a distance which can be computed through Sinkhorn's matrix scaling alg.
   at a speed that is several orders of magnitude faster than that of
   transportation solvers. We also report improved performance on the MNIST
   benchmark problem over competing distances."
   -- paper@[<A HREF="http://papers.nips.cc/paper/4927-sinkhorn-distances-lightspeed-computation-of-optimal-transport">nips</A>]['14],
   pdf@[<A HREF="http://machinelearning.wustl.edu/mlpapers/paper_files/NIPS2013_4927.pdf">wustl</A>]['14].
   [Also search for: transportation problem] and
   [also search for: histogram distance].

%A D. J. rezende
%A et al ...
%A N. Heess
%T Unsupervised learning of 3D structure from image
%J arXiv
%M JUL
%D 2016
%O NIPS 2016
%K conf, NIPS, c2016, c201x, c20xx, zz1016, image, 2D, 3D, images, ShapeNet,
   deepmind, deep learning
%X "A key goal of computer vision is to recover the underlying 3D structure from
   2D observations of the world. ... we learn strong deep generative models of
   3D structures, & recover these structures from 3D & 2D images via
   probabilistic inference. We demonstrate high-quality samples & report
   log-likelihoods on several datasets, inc. ShapeNet [2], & establish the first
   benchmarks in the literature. We also show how these models & their inference
   networks can be trained end-to-end from 2D images. This demonstrates for the
   first time the feasibility of learning to infer 3D representations of the
   world in a purely unsupervised manner."
   -- 1607.00662@[<A HREF="https://arxiv.org/abs/1607.00662">arXiv</A>]['16]
   (Also see deepmind@[<A HREF="https://deepmind.com/">www</A>]['16].)

%A K. Madi
%A E. Paquet
%A H. Kheddouci
%T New graph distance based on stable marriage formulation for deformable 3D
   objects recognition
%J IEEE/ACS 16th Int. Conf. on Comp. Systems and Appl. (AICCSA)
%P 1-8 
%M NOV
%D 2019
%K conf, c2019, c201x, c20xx, zz1122, maths, graph edit distance, GED,
   similarity, match, matching, 3D, object recognition, stable marriage problem
%X "We propose a novel fast g.matching approach based on a new formulation of
   the SMP, to measure the dist. between graphs. ... is optimal in terms of
   execution time, i.e. ... O(n^2). ... based on the decomposition of graphs
   into a set of substructs. which are subss. matched with the SM alg.. ... we
   address the problem of comparing deformable 3D objects rep. by graphs, we use
   a triangle-stars decomposition for triangular tessellations ... proposed
   approach is based on computing an approx'n of Graph Edit Dist. which is
   fault-tolerant to noise & distortion ..."
   -- [<A HREF="https://doi.org/10.1109/AICCSA47632.2019.9035320">doi:10.1109/AICCSA47632.2019.9035320</A>]['22],
      pdf@[<A HREF="https://www.researchgate.net/publication/338623269_New_Graph_Distance_based_on_Stable_Marriage_formulation_for_Deformable_3D_Objects_Recognition">resg'te</A>]['22] (open).
   (Also see Gmatch@[<A HREF="https://en.wikipedia.org/wiki/Graph_matching">wikip</A>]['22].)
   [Also search for: graph edit distance GED] and
   [also search for: stable marriage problem].


%A J. R. Neil
%A C. S. Wallace
%A K. B. Korb
%T Learning Bayesian networks with restricted causal interactions
%J UAI99
%P 486-493
%D 1999
%K conf, UAI, UAI15, UAI99, network, local models, model, c1999, c199x, c19xx,
   AI, II, stats, MML, MDL, log linear, logLinear, LLM, analysis, LLA, logit,
   cause, interaction, CSW, CSWallace
%X "A major problem for the learning of Bayesian networks (BNs) is the
   exponential number of parameters needed for conditional probability tables.
   Recent research reduces this complexity by modeling local structure in the
   probability tables. We examine the use of log-linear local models. While
   log-linear models in this context are not new (Wh'ttaker, '90;
   Bunt'ne, '91; Ne@l, '92; Heck'rman and Me'k, '97), for structure learning
   they are generally subsumed under a naive Bayes model. We describe an
   alternative interpretation, and use a Minimum Message Length (MML)
   (W@llace, '87) metric for structure learning of networks exhibiting causal
   independence, which we term first-order networks (FONs).
   We also investigate local model selection on a node-by-node basis."
   isbn:1-55860-614-9.      Auth's at Mon@sh U., .au
   [Also search for: Bayesian network].
   (Also see [<A HREF="/~lloyd/tildeImages/People/Wallace/">CSW</A>.])

%A K. B. Korb
%T The frame problem: An AI fairy tale
%J Minds and Machines
%I Kluwer
%V 8
%N 3
%P 317-351
%M AUG
%D 1998
%K kbk, jrnl, MAM, AI, frame problem, zz0601
%X "I analyze the frame problem & its relation to other epistemological
   problems for artificial intelligence, such as the problem of induction, the
   qualification problem & the "general" AI problem. I dispute the claim that
   extensions to logic (default logic & circumscriptive logic) will ever
   offer a viable way out of the problem. In the discussion it will become
   clear that the original frame problem is really a fairy tale: as originally
   presented, & as tools for its solution are circumscribed by Pat Hayes, the
   problem is entertaining, but incapable of resolution. The solution to the
   frame problem becomes available, & even apparent, when we remove artificial
   restrictions on its treatment & understand the interrelation between the
   frame problem & the many other problems for artificial epistemology. I
   present the solution to the frame problem: an adequate theory & method for
   the machine induction of causal structure. Whereas this solution is clearly
   satisfactory in principle, & in practice real progress has been made in
   recent years in its application, its ultimate implementation is in prospect
   only for future generations of AI researchers." --
   [<A HREF="http://dx.doi.org/10.1023/A:1008286921835">doi:10.1023/A:1008286921835</A>][/01/'04]
   [<A HREF="http://www.wkap.nl/oasis.htm/168538">online</A>][6/'01]

%A K. B. Korb
%T Inductive learning and defeasible inference
%J Journal of Experimental and Theoretical Artificial Intelligence.
%D 1994 to appear
%K kbk, JETAI, inductive inference, II, machine, learn, Monash
%X <A HREF="/~korb/">kbk home page</A> ('94)

%A K. B. Korb
%T The meanings of "Meaning"
%J Special Supplement of Stanford Humanities Review `Bridging the Gap'.
%V 4
%N 1
%P 75-78
%D 1994
%K kbk, meaning, inductive inference, II, Monash
%X <A HREF="/~korb/">kbk home page</A> ('94)

%A K. B. Korb
%T Stephen Jay Gould on intelligence
%J Cognition
%V 52
%P 111-23
%D 1994
%O TR 93/174, Dept. Computer Science, Monash University
%K kbk, Monash
%X <A HREF="/~korb/">kbk home page</A> ('94)

%A K. B. Korb
%T Infinitely many resolutions of Hempel's paradox
%B Theoretical Aspects of Reasoning about Knowledge V.
%E R. Facid
%I Morgan-Kaufmann
%W Asilomar, California
%P 138-49
%D 1994
%O Australasian Assoc. for the History, Philosophy and Social Studies
   of Science Conf., LaTrobe Univ., Melbourne, 1993
%K kbk, Hempel, AI, Monash
%X <A HREF="/~korb/">kbk home page</A> ('94)

%A K. B. Korb
%T A pragmatic Bayesian acceptance theory
%J AAAI spring symposium series: Goal-driven learning
%E M. desJardins
%E A. Ram
%E L. Hunter
%E F. J. Provost
%W Stanford
%P 128-30
%D 1994
%K kbk, AI, Bayes, inductive inference, II, Monash
%X <A HREF="/~korb/">kbk home page</A> ('94)

%A C. S. Wallace
%A K. B. Korb
%T A Bayesian learning agent
%J Research conference: Faculty of Computing and Information Technology
%I Monash University, Melbourne
%E C. S. Wallace
%P 19
%D 1994
%K CSW, CSWallace, KBK, AI, Bayes, FCIT, inductive inference, II, machine,
   learn, Monash, c1994, c199x, c19xx
%X Also see [<A HREF="/~lloyd/tildeImages/People/Wallace/">CSW</A>].
   <A HREF="/~korb/">kbk home page</A> ('94)

%A K. B. Korb
%T Stage effects in the Cartesian theater: A review of Daniel Dennett's
   "Consciousness Explained"
%J Psyche
%V 1
%N 1
%P 29-39
%D 1993
%K kbk, AI, Dennett, conscious, mind, Monash
%X <A HREF="/~korb/">kbk home page</A> ('94)

%A K. B. Korb
%T The Collapse of Collective Defeat: Lessons from the Lottery Paradox
%J PSA
%V 1
%P 230-236
%D 1992
%K kbk, inductive inference, II, Monash
%X <A HREF="/~korb/">kbk home page</A> ('94)

%A K. B. Korb
%T Searle's AI Program
%J J. of Experimental and Theoretical Artificial Intelligence
%V 3
%P 283-296
%D 1991
%K kbk, JETAI, AI
%X <A HREF="/~korb/">kbk home page</A> ('94)

%A K. B. Korb
%T Explaining Science
%J British Journal for the Philosophy of Science
%V 42
%P 239-253
%D 1991
%K kbk, inductive inference, II
%X <A HREF="/~korb/">kbk home page</A> ('94)


%T Studies in Stemmatology
%E P. van Reenen
%E M. van Mulken
%E J. Dyk
%I JohnBenjamins
%P 311
%D 1996
%K book, text, c1996, c199x, c19xx, stemmatology, stematology, stemmatics,
   stematics, stemma, natural language, NLP, textual criticism, copy-text,
   text, document, writing
%X hb us$131; uk us isbn:1556195079; uk us isbn13:978-1556195075.
   "... three parts which cover:
      methodological approaches;
      subject-related observations; and
      applications to manuscript traditions."
   Also see [<A HREF="http://en.wikipedia.org/wiki/Stemmatology">wikip</A>]['11],
   stemma: "family tree".
   [Also search for: stemmatology].

%A D. Watson
%T Death Sentence (the decay of public language)
%I RandomHouse
%M NOV
%D 2003
%K book, english, language, gobbledegook, newspeak, new-speak, corporate, Don,
   obfuscate, jargon, RMIT, mission statement, c2003, c200x, c20xx, zz1103,
   technobabble, spin
%X "..in public life the language has never been held in less regard. It
   withers in the dungeons of the technocratic mind. It is butchered by the
   media. In politics it lacks all qualifications for the main game. Don Watson
   Almost 60 years ago, George Orwell described the decay of language and why
   this threatened democratic society. But compared to what we now endure, the
   public language of Orwell's day brimmed with life and truth. Today's
   corporations, government departments, news media, and, perhaps most
   dangerously, politicians speak to each other and to us in cliched,
   impenetrable, lifeless sludge. Don Watson can bear it no longer. In
   Death Sentence, part diatribe, part cool reflection on the state of
   Australia's public language, he takes a blowtorch to the words and
   their users who kill joy, imagination and clarity. Scathing, funny and
   brilliant, D' S' is a small book of profound weight and timelines."
   ppbk, about au$30, isbn:174051206.
   "People always laugh like buggery when you speak it.
   They begin to get hysterical" -- Don Watson.
   The vision thing, e.g. [<A HREF="http://www.infotech.monash.edu.au/aimsvalues/ourvision/">fit</A>][11/'03],
   e.g. "...The system as described is designed as a comprehensive planning
   approach leading to a coherent set of artefacts comprising the Strategic
   Plan and a complete set of mutually consistent subplans with outcomes
   (outputs) specified in some detail. ..." -[<A HREF="http://www.business.rmit.edu.au/esg/itc/html/rmit_context.html">bus'rmit</A>][11/'03].

%A P-Y. Oudeyer
%T The self-organization of speech sounds
%J J. Theor. Biol
%P 435-449
%V 233
%N 3
%D 2005
%K jrnl, JTB, sound, language, evolution, origin, origins, c2005, c200x, c20xx,
   zz0305, artificial, linguistic
%X Also see [<A HREF="http://arxiv.org/list/cs.LG/new">@arxiv</A>]['05]...
   "... How then may a speech code [SC] be formed prior to the existence of
   linguistic interactions? Moreover, the human SC is discrete & compositional,
   shared by all the individuals of a community but different across communities
   & phoneme inventories are characterized by statistical regularities. How can
   a SC with these properties form? ...approach these questions in the paper,
   using the "methodology of the artificial". We build a society of artificial
   agents, & detail a mechanism that shows the formation of a discrete SC
   without pre-supposing the existence of linguistic capacities or of
   coordinated interactions. ... based on a low-level model of sensory-motor
   interactions. ... certain very simple & non language-specific neural devices
   leads to the formation of a SC [with] properties similar to the human SC..."

%A Z. Solan
%A D. Horn
%A E. Ruppin
%A S. Edelman
%T Unsupervised learning of natural languages
%J PNAS
%V ?
%P ?-?
%D 2005 (to appear)
%K PNAS, jrnl, language, ADIOS, c2005, c200x, c200x, CFG, learn, zz0805,
   learning, syntax, inference, II
%X "... problem, fundamental to linguistics, bioinformatics & certain other
   disciplines, of using corpora of raw symbolic sequential data to infer
   underlying rules that govern their production. Given a corpus of strings
   (such as text, transcribed speech, chromosome or protein seq. data, sheet
   music, etc.), our unsupervised alg. recursively distills from it
   hierarchically structured patterns. The ADIOS (Automatic DIstillation of
   Structure) alg. relies on a statistical method for pattern extraction & on
   structured generalization, 2 processes that have been implicated in language
   acquisition. It has been evaluated on artificial CFGs with thousands of rules
   on natural languages as diverse as English & Chinese, & on protein data
   correlating sequence with function. This is the 1st time [!?] an unsup. alg.
   is shown capable of learning complex syntax, generating grammatical novel
   sentences, & proving useful in other fields that call for structure
   discovery from raw data, such as bioinformatics."
   [<A HREF="http://dx.doi.org/10.1073/pnas.0409746102">doi:10.1073/pnas.0409746102</A>]['05]
   [<A HREF="http://adios.tau.ac.il/">ADIOS</A>]['05] (corne11).

%A M. Dunn
%A et al
%T Structural phylogenetics and the reconstruction of ancient language history
%J Science
%V 309
%N 5743
%P 2972-2075
%M SEP
%D 2005
%K jrnl, language, natural, evolution, phylogenetic, c2005, c200x, c20xx,
   linguistics
%X "...  application of biological cladistic methods, not to vocabulary (as has
   been previously tried) but to language structure (sound systems and grammar)
   may extend the time depths at which language data can be used. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1114615">doi:10.1126/science.1114615</A>]['05].
   [Also search for: natural language evolution].

%A T. Roos
%A T. Heikkila
%T Evaluating methods for computer-assisted stemmatology using artificial
   benchmark data sets
%J Literary and Linguistic Computing
%V 24
%N 4
%P 417-433
%D 2009
%K jrnl, c2009, c200x, c20xx, stemmatology, copy text, textual, criticism,
   version, versions
%X "Given a collection of imperfect copies of a textual document, the aim of
   stemmatology is to reconstruct the history of the text, indicating for each
   variant the source text from it was copied. We describe an experiment
   involving three artificial benchmark data sets to which a # of computer-
   -assisted stemmatology methods were applied. Contrary to earlier similar
   experiments, we propose & use a numerical criterion to evaluate all the
   solns. Moreover, our primary data set is sig.larger than used before. The
   results suggest the superiority of two computer-assisted methods amongst
   those tested: the maximum parsimony method implemented in the PAUP* s/w
   package & a related compression-based method we have proposed ..."
      'No book is published without some discrepancy in each one of the
      copies. Scribes take a secret oath to omit, to interpolate, to change.'
      (Jorge Luis Borges: The Lottery in Babylon, in Labyrinths:
      Selected Stories & Other Writings, 1962)"
   -- [<A HREF="http://dx.doi.org/10.1093/llc/fqp002">doi:10.1093/llc/fqp002</A>]['11].
   [Also search for: stemmatology].  (auths @ U.Helsinki ['09].)

%A S. Gakkhar
%A M. Marcolli
%T Syntactic structures and the general Markov models
%J arXiv
%M APR
%D 2021
%K TR, c2021, c202x, c20xx, zz0521, syntax, syntactic structures, Markov model,
   evolution, trees, human, natural language, linguistics
%X "... studying syntactic structures data from Longobardi (2017b), Collins
   (2010), Ceolin et al. (2020) & Koopman (2011) using general Markov models
   initiated in Shu et al. (2017), exploring the question of how consistent the
   data is with the idea that general Markov models. The ideas explored ... are
   more generally applicable than to the setting of syntactic structures, & can
   be used when analyzing consistency of data with general Markov models.
   Additionally, we give an interpretation of the methods of Ceolin et al.
   (2020) as an infinite sites evolutionary model & compare it to the Markov
   model & explore each in the context of evolutionary processes acting on human
   language syntax.
   -- 2104.08462@[<A HREF="https://arxiv.org/abs/2104.08462">arXiv</A>]['21].
   [Also search for: natural language evolution].

%A S. D'Alonzo
%A M. Tegmark
%T Machine-learning media bias
%J arXiv
%M AUG
%D 2021
%K TR, c2021, c202x, c20xx, zz0522, natural language, phrases, media, press,
   news, newspapers, bias, biases, left right, establishment, politics
%X "... an automated method for measuring media bias. Inferring which newspaper
   published a given article, based only on the freqs. with which it uses
   different phrases, leads to a conditional probability distn whose analysis
   lets us automatically map newspapers & phrases into a bias space. By
   analyzing ~ a million articles from roughly a hundred newspapers for bias in
   dozens of news topics, our method maps newspapers into a 2D bias landscape
   that agrees well with prev. bias class'ns based on human judgement. One
   dimension can be interpreted as traditional left-right bias, the other as
   establishment bias. This means that although news bias is inherently
   political, its measurement need not be."
   -- 2109.00024@[<A HREF="https://arxiv.org/abs/2109.00024">arXiv</A>]['22].

%A M. Robbeets
%A et al
%T Triangulation supports agricultural spread of the Transeurasian languages
%J Nature
%V ?
%P ?-?
%M NOV
%D 2021
%K jrnl, MolBio, ancient DNA, Transeurasian, Tunguscic, Mongolian, Turkik,
   Turkish, Korean, Japanese, natural language, linguistics, human, evolution,
   phylogeny, spread, farming, agriculture
%X "... 'triangulating. genetics, archaeology & linguistics in a unified
   perspective. We report wide-ranging datasets from these disciplines, inc. a
   comprehensive Transeurasian agropastoral & basic vocabulary; an
   archaeological database of 255 Neolithic-Bronze Age sites from NE Asia; & a
   collection of ancient genomes from Korea, the Ryukyu islands & early cereal
   farmers in Japan, complementing prev. published genomes from East Asia. ...
   show that the early spread of Transeurasian speakers was driven by ag.."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-04108-8">doi:10.1038/s41586-021-04108-8</A>]['21].
   [Also search for: natural language evolution].

%A M. H. Christiansen
%A N. Chater
%T The Language Game: How Improvisation Created Language and Changed the World
%I BasicBooks
%P 304
%M FEB
%D 2022
%K book, c2022, c202x, c20xx, zz0422, learning, evolution, linguistics,
   natural language
%X 1st ed 2022; hb us$17; uk us isbn:1541674987; uk us isbn13:978-1541674981.
   "... shows how people learn to talk not by acquiring fixed meanings & rules,
   but by picking up, reusing, & recombining countless linguistic fragments in
   novel ways. Talking is verbal charades- an improvisational game of spinning
   intricate patterns of words to get the message across. Each improvisation
   builds on the last, creating the richly layered patterns that comprise a
   language. The patterns in l. are not wired into our brains or our genes ..."


%A E. Nagel
%A J. R. Newman
%D Godel's Proof
%I NYUP
%D 1958
%P 118
%K book, text, c1958, c195x, c19xx, maths, incompleteness, logic, theory,
   foundations, mathematics, decision problem, STEM, KurtGodel, Kurt
%X Also see, 'In Retrospect: Godel's proof', A. Hodges,
   [<A HREF="http://dx.doi.org/10.1038/454829a">doi:10.1038/454829a</A>]['08].

%T Symposium on Logic in Computer Science
%I IEEE
%W Ithaca, NY
%M Jun
%D 1987
%K logic, ieee
%X sponsored by the computer society of the ieee
   technical committee on mathematical foundations of computing
   Hargrave lib, Monash: H005,131 S989/2

%A R. Fagin
%A J. Y. Halpern
%T I'm OK if you're OK: on the notion of trusting in communication
%J Symposium on Logic in Computer Science
%W Ithaca, NY
%M Jun
%D 1987
%P 280-292
%K FOCS, logic, ieee, honest
%X consider notions of truth and honesty for messages in distributed systems.
   (a) Formally, a message 'm' sent by 'p' at time 't' is 'trusting' if
   p knows at time t that if every message sent up to time t is true
   then m is true.
   Want something weaker than trusting.
   (b) Message m sent be p is trusting*  if p knows that if all previous
       messages are trusting* then m is true.
       - this is a recursive defn of trusting*.
   Papers shows in general trusting* not well defined.
   There is a 'complete consistent notion of trusting*' in a system if
   there is a way of marking some messages as trusting* so as to
   satisfy equation for trusting*.
   In systems were messages are well founded, eg. with a global clock and
   rounds of communication, there is a unique consistent notion
   of trusting*.

%A M. J. C. Gordon
%T Programming Language Theory and its Implementation
%I PrenticeHall
%S Int. Series in Computer Science.
%D 1988
%K logic, theory, program, verification, text, book, c1988, c198x, c19xx
%X 1. program specification
   2. Floyd - Hoare logic
   3. Mechanizing program verification
   4. intro to lambda calculus
   5. representing things in l.c.
   6. functional programs
   7. theorems about l.c.
   8. combinators
   9. lisp
  10. a theorem prover
  11. a program verifier
  12. a l.c. toolkit
  pb; uk us isbn:0137304099; uk us isbn13:978-0137304097.

%A L. C. Paulson
%A A. W. Smith
%T Logic programming, functional programming and inductive definitions
%B Extensions of Logic Programming.
%E P. Schroeder-Heister
%I SpringerVerlag
%S LNCS
%V 475
%P 283-309
%D 1989
%K logic functional declarative programming language, Prolog, FP, LP, FLP,
   constraint, equational theory theories, narrowing

%T Coq
%D 1989
%K Coq, Coc, c1989, c198x, c19xx, zz0823, theorem prover, proof assistant,
   maths, logic, FP, type, dependent types, Gallina, SSReflect
%X "Coq is an interactive theorem prover first released in 1989. It allows for
   expressing mathematical assertions, mechanically checks proofs of these
   assertions ... When viewed as a prog. lang., Coq implements a dependently
   typed functional prog. lang. ... viewed as a logical system, it implements a
   higher-order type theory. ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Coq">wikip</A>]['23];
      [<A HREF="http://coq.inria.fr/">coq.inria.fr</A>]['23].
   [Also search for: Coq]  and  [also search for: proof assistant].

%E M. Bruynooghe
%E M. Wirsing
%T Programming Language Implementation and Logic Programming
%I SpringerVerlag
%S LNCS
%V 631
%M AUG
%D 1992
%O Proc. 4th Int. Symp. PLILP '92.
%W Leuven, Belgium
%K logic programming language implementation, LP, FP, FLP,
   Prolog, FP, HOL, PLILP
%X includes some papers on logic+functional programming.

%E G. Burn
%E S. Gay
%E M. Ryan
%T Theory and Formal Methods
%I SpringerVerlag
%C London
%S Workshops in Computing
%V ???
%D 1993
%K wShop, c1993, c199x, c19xx, SV, WC, IC, functional programming FP,
   type types
%O Proc. of the First Imperial College Department of Computing
   Workshop on Theory and Formal Methods
   Isle of Thorns Conference
   Centre, Chelwood Gate, Sussex, UK, 29-31 March 1993
%X isbn:3-540-19842-3;   (via enews)
   OVERVIEW PAPERS
   Geoffrey Burn    The Abstract Interpretation of Functional Languages
   Roy Crole        Deriving Category Theory from Type Theory
   Steve Vickers    Geometric Logic in Computer Science
   Chris Hankin     Graph Rewriting Systems and Abstract Interpretation
 RESEARCH PAPERS
   Samson Abramsky  Interaction Categories
   Mark Dawson      Animating LU
   Abbas Edalat     Dynamical Systems, Measures and Fractals via Domain Theory
   Abbas Edalat     Self-Duality, Minimal Invariant Objects and Karoubi
                    Invariance in Information Categories
   Lindsay Errington, Chris Hankin and Thomas Jensen
                    Reasoning about GAMMA Programs
   Jose  Fiadeiro and Tom Maibaum
         Generalising Interpretation between Theories in the Context
         of (pi-)Institutions
   Simon Gay and Raja   Nagarajan Modelling SIGNAL in Interaction Categories
   Reinhold Heckmann    Product Operations in Strong Monads
   Michael Huth         On the Equivalence of State-transition Systems
   Stuart Kent          Towards a Modal Logic of Durative Actions
   Marta Kwiatkowska    Concurrency, Fairness, and Logical Complexity
   Marta Kwiatkowska and Iain Phillips
                    Concurrency and Conflict in CSP
   Sarah Liebert    A Complete Axiom System for CCS with a Stability Operator
   Ian Mackie, Leopoldo Roman and Samson Abramsky
                    An Internal Language for Autonomous Categories
   Juarez Muylaert Filho and Geoffrey Burn
              Continuation-passing Transformation and Abstract Interpretation
   Iain Phillips    A Note on the Expressiveness of Process Algebra
   Mark Ryan        Prioritising Preference Relations
   David Sands      Laws of Parallel Synchronised Termination
   Zvi Schreiber    Implementing Process Calculi in C
   Paul Taylor      An Exact Interpretation of While
   Irek Ulidowski   Congruences for tau-respecting Formats of Rules
%P 336 (approx)

%A Roland Yap Hock Chuan
%T A constraint logic programming framework for constructing DNA restriction
   maps
%J Artificial Intelligence in Medicine
%V 5
%P 447-464
%D 1993
%K Monash, jrnl, MolBio, AIM, site, map, mapping, RSM, CLP, CLPR, CLP(R), LP
%X 19 refs.
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Mapping/">mapping</A>].)

%A J. Jaffar
%A P. J. Stuckey
%T Semantics of infinite tree logic programming
%J Theoretical Computer Science
%V 46
%D 1986
%P 141-158
%K TCS, jrnl, LP, logic programming, Prolog, infinite tree unification, unify,
   T theory
%O TR 54 Monash University June 1985

%A T. Nicholson
%A N. Foo
%T A denotational semantics for Prolog
%I Basser-Department-of-Computer-Science, University-of-Sydney
%R 240
%M Aug
%D 1984
%K TR 240, TR240,  denotational semantics, definition, DS, theory, Prolog,
   logic programming LP
%X (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A N. D. North
%T A formal definition of Prolog including non-logical features
%J Logic Programming Conference
%D 1987
%M May
%K conf, LP, denotational semantics, Prolog
%X (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A N. D. Jones
%A A. Mycroft
%T Stepwise development of operational and denotational semantics For Prolog
%J A.I. Conference?
%D 1983
%K denotational semantics Prolog logic programming LP

%A D. Miller
%T A theory of modules for logic programming
%J Symposium on Logic Programming
%D 1986
%M Sep
%I IEEE
%P 106-114
%X adds implications  D=>G  as goals in Prolog logic programming
   parametric modules
   explains some uses af assert
   sound and complete for intuitionistic logic not classical logic
%K theory logic intuitionistic Prolog LP

%A A. Bundy
%A B. Welham
%T Using meta-level inference for selective application of multiple
   rewrite rule sets in algebraic manipulation
%J Artificial Intelligence
%P 189-211
%V 16
%D 1981
%K AI, jrnl, inference, rule, rewrite, meta, meta-level, algebra, algebraic

%A M. H. Van Emden
%A R. A. Kowalski
%T The semantics of predicate logic as a programming language
%J JACM
%V 23
%N 4
%P 733-742
%M Oct
%D 1976
%K jrnl, JACM, predicate, logic program, programming, Prolog, LP,
   semantics, SL, resolution

%A L. M. Periera
%A L. F. Monteiro
%T The semantics of parallelism and coroutining in logic programming
%J Colloquia Mathemtica Societatis Janos Bolyai
%W Salgotarjan, Hungary
%D 1978
%P 611-657
%K Prolog logic programming coroutine coroutining parallel parallelism LP

%A H. A. Blair
%T The recursion-theoretic complexity of the semantics of predicate logic
   as a programming language
%J Information and Control
%D to appear as of 1983
%K Prolog logic programming complexity LP

%A T. Sato
%T Negation and semantics of Prolog programs
%J First International Logic Programming Conference
%M Sep
%D 1982
%W Marseille
%P 169-174
%K Prolog logic programming LP negation semantics theory

%A R. Kowalski
%T Algorithm = logic + control
%J CACM
%M Jul
%D 1979
%V 22
%N 7
%P 424-435
%K jrnl, CACM, logic programming, LP, Prolog

%A M. Bruynooghe
%T The memory management of Prolog implementations
%R CW 21
%M Jun
%D 1980
%I Applied-Maths-and-Programming-Division,
   Katholieke-Universiteit-Leuven
%O Logic Programming Workshop, Debrecen, Hungary, July 1980
%K Prolog LP implementation memory management structure sharing
   logic programming
%X Prolog execution, stack, space saving on bindings of variables,
   structure sharing

%A L. M. Pereira
%A A. Porto
%T Selective backtracking
%B Logic Programming
%E Clark
%E Tarnlund
%D ???
%K Horn clause logic programming LP Prolog
   selective intelligent backtracking  optimise

%A D. H. Warren
%A L. M. Pereira
%A F. Pereira
%T Prolog - the language and its implementation compared with Lisp
%J Proc. of the Symposium on Artificial Intelligence and
   Programming languages
%M Aug
%D 1977
%P 109-115
%K Prolog implementation logic programming LP Lisp comparison
%X (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A C. T. Haynes
%T Logic continuations
%J J. of Logic Programming
%D 1987
%V 4
%P 157-176
%K jrnl, c1987, c198x, c19xx, LP, logic, program, Prolog, scheme, continuation
%X embed logic prog in scheme
   success and failure continuations
   extra control transfers are possible cf. Prolog

%A Sergot et al
%T British nationality act ...
%J CACM
%V 29
%N 5
%P 370-386
%M May
%D 1986
%K jrnl, CACM,  LP, Prolog, logic programming, British nationality act, law,
   legal, citizen, citizenship, negation, c1986, c198x, c19xx
%O Imperial College  Technical Report
%X [Also search for: law LP logic].

%A J. G. Cleary
%T Logical arithmetic
%I Dept.-Computer-Science, University-of-Calgary
%D 1987 ?
%K logic programming, LP, real arithmetic, interval, inequality
%X introduces real arithmetic into logic programming Prolog, better than  'is'.

%A M. Bruynooghe
%A L. M. Pereira
%T Deduction revision by intelligent backtracking
%B Current Issues in Prolog Implementation
%P 194-215
%D ???
%K logic programming LP intelligent backtrack search culprit

%A P. T. Cox
%T Finding backtrack points for intelligent backtracking
%B Implementations of Prolog
%E J. A. Campbell
%I Ellis-Horwood
%D 1984
%P 216-233
%K logic programming LP intelligent backtrack Prolog  failure thrash thrashing

%A J. W. Lloyd
%A R. W. Topor
%T Making Prolog more expressive
%J J. Logic Programming.
%V 3
%D 1984
%P 225-240
%K jrnl, LP, Prolog, logic programming, extended, JWLloyd, c1984, c198x, c19xx,
   RWTopor
%X extended program can have arbitrary first-order formula in its body.
   results   soundness of negation as failure
             SLDNF resolution for extended programs.
   (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A P. Leith
%T Fundamental errors in legal logic programming
%J COMPJ
%V 29
%N 6
%D 1986
%P 545-552
%K jrnl, COMPJ, c1986, c198x, c19xx, LP, logic programming, Prolog,
   British nationality act, law, legal, automation, legol,
   expert system, AI, artificial intelligence, mind
%X argues the Prolog translation of the British nationality act
   is unsound,   the world is not logical,
   law is interpreted by lawyers and judges.
   the "core of certainty" that is the set of later cases that can
   be interpreted unambiguously using the rules [created] can be extremely
   small.  Leith: logic programmers have a false epistomology: they
   see the world in terms of a computational model and fail to stand
   outside that model. Thus whenever they attempt to apply their model
   to the world they will always fail. For the world is not a logical world.
   Reviewed in  Computing Reviews  Dec 1987 V28 N12 p.648.
   [Also search for: law LP logic].

%A U. S. Reddy
%T Transformation of Logic Programs into Functional Programs
%J Proc. SLP-84
%W Atlantic City, NJ
%M Feb
%D 1984
%K LP logic programming, modes, determinacy, control, static analysis

%A C. S. Mellish
%T Some Global Optimizations for a Prolog Compiler
%J J. Logic Programming
%V 2
%N 1
%M Apr
%D 1985
%K LP logic programming, modes, determinacy, control, static analysis
   optimise, Prolog

%A S. K. Debray
%A D. S. Warren
%T Detection and Optimization of Functional Computations in Prolog
%J Proc. 3rd ICLP
%W London
%M Jul
%D 1986
%K LP logic programming, modes, determinacy, control, static analysis
   Prolog, optimise

%A G. Smolka
%T Making Control and Data Flow in Logic Programs Explicit
%J Proc. 1984 Symp. on Lisp and Func. Prog
%W Austin, TX
%M Aug
%D 1984
%K LP logic programming, modes, determinacy, control, static analysis

%A Shapiro
%A Takeuchi
%T Object Oriented programming in Concurrent Prolog
%J New Generation Computing
%V 1
%N 1
%D 1983
%K logic programming LP, OOP OOPS OO
%X via enews

%A Kahn
%A Tribble et al.
%T Objects in Concurrent Logic Programming Languages
%J OOPSLA '86
%O SIGPLAN
%N 11
%D 1986
%K logic programming LP Prolog, object oriented OO OOP OOPS
%X via enews

%A Kahn et al.
%T Vulcan: Logical Concurrent Objects
%E Shapiro
%B Concurrent Prolog
%I MIT-Press
%D 1987
%K logic programming LP Prolog, object oriented OO OOP OOPS
%X via enews

%A Davison
%T Objects and Meta Objects in Parlog
%R Research Report
%I Imperial-College
%D 1987
%K logic programming LP Prolog, object oriented OO OOP OOPS
%X via enews

%A Davison
%A Polka
%T A Parlog Object Oriented Language
%R Research Report
%I Imperial-College
%D 1988
%K logic programming LP Prolog, object oriented OO OOP OOPS
%X via enews

%A S. K. Debray
%A P. Mishra
%T Denotational and operational semantics for Prolog
%J J. Logic Programming
%D 1988
%V 5
%N 1
%M Mar
%P 61-91
%K logic programming LP denotational semantics, Prolog, cut
%X gives denotational semantics DS and operational semantics
   for Prolog, show equivalent.
   Prove some transformations of Prolog programs are correct.
   [Also search for: Prolog semantics].

%A T. Sato
%T An algorithm for intelligent backtracking
%B RIMS Symposia on Software Science and Engineering
%I SpringerVerlag
%V 147
%S LNCS
%D 1982
%E E. Goto
%E K. Furukawa
%E R. Nakajima
%E I. Nakata
%E A. Yonezawa
%K logic programming LP Prolog, backtrack, failure, trashing

%A P. Leith
%T Legal expert systems: misunderstanding the legal process
%J Computers and the Law
%N 49
%M Sep
%D 1986
%K logic programming, LP, Prolog, law, legal, British nationality act
%X critical of the Prolog program and attempts to automate the law.
   [Also search for: law LP logic].

%A H. A. Blair
%T The undecidability of two completeness notions for the negation
   as failure rule in logic programming
%P 164-168
%D 1983 ?
%J ???
%K logic programming LP Prolog, negation, not, failure

%A M. Sato
%T A formal theory of symbolic expressions
%D 1984 ?
%J ???
%K Prolog

%A A. Colmerauer
%T Prolog and infinite trees
%J ???
%D ?84?
%P 231-251
%K logic programming LP Prolog, infinite tree

%A D. A. Wolfram
%A M. J. Maher
%A J-L. Lassez
%T A unified treatment of resolution strategies for logic programs
%J ???
%P 263-276
%D 1984 ?
%K logic programming LP Prolog, resolution

%A J-L. Lassez
%A M. Maher
%T The denotational semantics of Horn clauses as a production system
%J ???
%D 1984 ?
%K logic programming LP Prolog, horn clause

%A K. L. Clark
%T An introduction to logic programming
%I Imperial-College
%M Apr
%D 1981
%K LP Prolog
%X (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>.)

%A M. Sato
%A T. Sakurai
%T Qute: a Prolog/lisp type language for logic programming
%I Dept-Information-Science, University-of-Tokyo
%K LP Prolog
%D ????

%A R. S. Boyer
%A J. S. Moore
%T The sharing of structure in theorem-proving programs
%B Machine Intelligence
%V 7
%P 101-116
%D 1972
%K jrnl, c1972, c197x, c19xx, automatic theorem proving, maths, prover, proof,
   assistant
%X auth2@[<A HREF="http://www.cs.utexas.edu/~moore/best-ideas/structure-sharing/index.html">uTexas</A>]['13].
   [Also search for: theorem proving].

%A A. Porto
%T Epilog: a language for extended programming in logic
%I Departmento-de-Informatica, Univesidad-Nova-de-Lisboa
%D 1983
%K logic programming LP Prolog

%A H. Ait-Kaci
%T Warren's Abstract Machine: A Tutorial Reconstruction
%I MITpress
%D 1991
%K book, c1991, c199x, c19xx, Warren, abstract, machine, Prolog, logic,
   LP, language implementation
%X hb, us isbn:0262011239;
   pb, us isbn:0262510588;

%A U. Nilsson
%A J. Maluszynski
%T Logic, Programming and Prolog
%I Wiley
%P 289
%M APR
%D 1990
%K Logic Programming, LP, text book, c1990, c199x, c19xx
%X pb, uk us isbn:0471926256; uk us isbn13:978-0471926252.
   (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>.)

%A M. Hanus
%T The integration of functions into logic programming: a survey
%R MPI-I-94-201
%I Max-Plank-Institut Fuer Informatik
%D 1994
%O J. Func. Prog. to appear
%K JFP, logic, function, functional programming, LP, FP, LFP, FLP,
   TR 94 201 TR201
%X ... Early research concentrated on the definition and improvement of
   execution principles for such [FP+LP] integrated languages, while more
   recently efficient implementations of these execution principles have
   been developed so that these languages became relevant for practical
   applications. In this paper we survey the development of the operational
   semantics as well as the improvement of the implementation of functional
   logic languages.    <A HREF="http://www.mpi-sb.mpg.de/">MPI home</A> (9/'94)
   [Also search for: LFP FLP].

%A G. Nadathur
%A D. Miller
%T An overview of lambda prolog
%J Proc. 5th Int. Conf. and Symp. on Logic Programming
%W Seattle
%P 810-827
%D 1988
%I MITpress
%K logic, function, functional programming, LP, FP, LFP, FLP, lambda-prolog
%X [Also search for: LFP FLP].

%A J. Lloyd
%T Combining functional and logic programming languages
%J Proc. Int. Logic Prog. Symp.
%P ?-?
%D 1994
%K ILPS94, ILPS, logic, LP, FP, LFP, FLP, conf, Godel, Escher, JWLloyd,
   c1994, c199x, c19xx
%X In this paper, I outline a proposal for a combined functional & logic
   programming language.  The main aim of the proposal is to combine in a
   practical & comprehensive way the best ideas of existing functional &
   logic languages, such as Godel, Haskell, & lambdaProlog.  I consider
   here only the core of the language, leaving aside many important issues such
   as the module system, meta-programming, & input/output.  The logic of the
   language is Church's simple theory of types.  I discuss the somewhat unusual
   computational model of the language & illustrate its main ideas with
   various programs.  I conclude with some remarks on what needs to be done to
   complete the design & implementation.
   email: jwl at miki.bristol.ac.uk (John Lloyd)
   <A HREF="ftp://ftp.cs.bris.ac.uk/">FTP</A> see /goedel/jwl_papers. (9/'94)
   [Also search for: LFP FLP].

%A E. Tick
%T Determinacy testing for nondeterminate logic programming languages
%J TOPLAS
%V 16
%N 1
%P 3-24
%M JAN
%D 1994
%K LP, nondeterministic, non, deterministic, zz0595

%A N. E. Fuchs
%A R. Schwitter
%T Specifying logic programs in controlled natural language
%I Dept. Comp. Sci., Uni. Zurich
%R 95.17
%D 1995
%O CLNLP 95, workshop on comp' logic for nat' lang' proc', Edinburgh 1995,
%K TR17, TR 17, CLNLP, CLNLP95, logic programming, LP, computing,
   AI, natural language processing, zz0695
%X ... we propose controlled natural language as a declarative &
   application-specific specification language.
   ... automatically translated into Prolog clauses, ...
   <A HREF="http://www.ifi.unizh.ch/techreports/">www</A>
   (File pub/techreports/ifi-95.17.ps.Z)
   - Norbert E. Fuchs    email: fuchs at ifi.unizh.ch   [6/'95]

%A F. G. McCabe
%T Logic and Objects
%I PrenticeHall
%S Comp. Sci.
%D ?
%K book, text, c199x, c19xx, logic, functional programming, LP, FP, LFP,
   computing, zz0695
%X McCabe L and O system merges functional, logic and object-oriented
   programming in a very nice way. There is an implementation of the system
   for LPA MacProlog somewhere in src.doc.ic.ac.uk
   via <!-- email: pmoura at mat.uc.pt --> (Paulo Jorge Lopes de Moura)  [6/'95]
   [Also search for: LFP FLP].

%E C. Beierle
%E L. Pluemer
%T Logic Programming: Formal Methods and Practical Applications
%I NorthHolland
%D 1995
%P 418
%K book, text, c1995, c199x, c19xx, Logic Programming, LP, computing
%X hb; uk us isbn:0444820922; uk us isbn13:978-0444820921.
   (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A W. F. Clocksin
%T Clause and Effect: Prolog Programming for the Working Programmer
%I SpringerVerlag
%P 143
%M OCT
%D 1997
%K book, text, c1997, c199x, c19xx, Prolog, logic programming, LP, AI
%X pb; uk us isbn:3540629718; uk us isbn13:978-3540629719.
   (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A A. Brodsky
%A C. Lassez
%A J-L. Lassez
%A M. J. Maher
%T Separability of polyhedra for optimal filtering of spatial and constraint
   data
%J J. of Automated Reasoning
%P 83-104
%V 23
%N 1
%D 1999
%K jrnl, constraints, programming, space, JLLassez, MJMaher, polyhedron,
   c1999, c199x, c19xx
%X [<A HREF="http://www.cse.unsw.edu.au/~mmaher/pubs/cdb/filter.ps">pp.ps@cse.unsw.edu.au</A>]['04]

%A J. M. Spivey
%A S. Seres
%T Embedding Prolog in Haskell
%I Dept of Comp. Sci., U. of Utrecht
%R UU-CS-1999-28
%D 1999
%O Proc. of 1999 Haskell workshop, E.Meijer ed., pp.25-38
%K TR, wShop, c1999, c199x, c19xx, LFP, FLP, prolog, LP, Haskell, FP
%X Also see wShop@[<A HREF="http://www.cs.uu.nl/research/techreps/UU-CS-1999-28.html">uu.nl</A>]['12],
   or [<A HREF="http://lambda-the-ultimate.org/node/112">www</A>]['12].
   [Also search for: LFP FLP].

%A M. Newborn
%T Automated Theorem Proving: Theory and Practice
%I Springer
%P 231
%M DEC
%D 2000
%K book, text, c2000 c200x, c20xx, theorem proving, prove, prover, automatic,
   maths, proof, assistant, semantic tree, resolution, refutation,
   symbolic logic
%X 1st ed 2000; hb us$130; uk us isbn:0387950753; uk us isbn13:978-0387950754.
   "... text and s/w package introduces readers to automated theorem proving,
   while providing two approaches implemented as easy-to-use programs. These are
   semantic-tree theorem proving & resolution-refutation theorem proving. The
   early chapters introduce first-order predicate calculus, well-formed formulae
   & their transformation to clauses. Then the author goes on to show how the
   two methods work & provides numerous examples ..."
   [Also search for: theorem proving].
   (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A D. Billington
%A A. Rock
%T Propositional plausible logic: Introduction and implementation
%J Studia Logica
%V 67
%P 243-269
%D 2001
%K jrnl, c2001, c200c, c20xx, AI, uniGriffith, Qld, defeasible, logics,
   Phobos, non-monotonic, nonMonotonic, reasoning, ARock
%X "... examples .., coherence result ... implementation in Haskell"
   [<A HREF="http://www.cit.gu.edu.au/~arock/publications/BilRoc2001.pdf">pdf</A>]['05]
   "P.L. is a knowledge rep'n method based on rules and priorities. There may be
   conflicts between rules in the sense that they support opposite conclusions
   A and not A. Priorities may help resolve such conflicts; if they fail then
   neither A nor not A are derived."
   -- [<A HREF="http://www.cit.gu.edu.au/~arock/plausible/Plausible.cgi">www</A>]['05].

%A M. J. Maher
%A A. Rock
%A G.Antoniou
%A D. Billington
%A T. Miller
%T Efficient defeasible reasoning systems
%J Int. J. A.I. Tools
%V 10
%N 4
%P 482-501
%D 2001
%K jrnl, IJAIT, c2001, c200c, c20xx, AI, Deimos, logic, logics, non-monotonic,
   Deimos, nonMonotonic, reasoning, ARock, MJMaher
%X "D.L. is a knowledge rep'n method based on rules and priorities. There may be
   conflicts between rules in the sense that they support opposite conclusions
   A and not A. Priorities may help resolve such conflicts; if they fail then
   neither A nor not A are derived."
   -- [<A HREF="http://www.cit.gu.edu.au/~arock/defeasible/Defeasible.cgi">www</A>]['05].

%A P. Blackbrun
%A M. de Rijke
%A Y. Venema
%T Modal Logic
%I CUP
%D 2002
%K book, text, CUP, c2002, c200x, c20xx, deRijke, maths, logic, modal,
   logics, theory
%X 1st ed 2002; uk us isbn:0521527147.

%A M. J. Maher
%T A synthesis of constraint satisfaction and constraint solving
%J Int. Conf. on Principles and Practice of Constraint Programming
%P 525-538
%D 2003
%K conf, constraints, c2003, c200x, c20xx, MJMaher
%X [<A HREF="http://www.cse.unsw.edu.au/~mmaher/pubs/cp/synth.ps">pp.ps@cse.unsw.edu.au</A>]['04]
   [<A HREF="http://www.cse.unsw.edu.au/~mmaher/">@unsw</A>]['04]
   [<A HREF="http://nicta.com.au/director/research/programs/krr/people/michael_maher.cfm">mjm, nicta</A>]['04]

%A C. S. Mellish
%A W. F. Clocksin
%T Programming in Prolog: Using the ISO Standard
%I SpringerVerlag
%P 293
%M JUL
%D 2003
%K book, text, c2003, c200x, c20xx, logic programming, LP
%X pb; uk us isbn:3540006788; uk us isbn13:978-3540006787.
   (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A S. Ferre
%A O. Ridoux
%T Introduction to logical information systems
%J Information Processing and Management
%V 40
%N 3
%P 383-419
%D 2004
%K jrnl, logic, LIS, system, programming, LP, data base, zzOSP, zOSP04,
   c2004, c200x, c20xx, logics, concept lattice, aber
%X "... can be given an abstract spec' that does not depend on the choice of
   a particular logic, and ... . ... logic plays in a LIS the role of a schema
   in databases. ..."
   [<A HREF="http://dx.doi.org/10.1016/S0306-4573(03)00018-9">doi:10.1016/S0306-4573(03)00018-9</A>][8/'04]
   [<A HREF="http://users.aber.ac.uk/sbf/ipm2004.ps.gz">ps@aber.ac.uk(pp.45)</A>][7/'04]
   Auth1 at U. Wales Aberystwyth 2OO2-'04 & U. Rennes1, fr. / IRISA late '04.

%A M. Huth
%A M. Ryan
%T Logic in Computer Science, Modelling and Reasoning about Systems
%I CUP
%P 2004
%K book, text, CUP, c2004, c200x, c20xx, system, verification, SAT, prover,
   model checking, LTL, NuSMV, CTL, logic, maths, L3Ref, L4Ref
%X "...extra and expanded sections on SAT solvers, existential/universal
   second-order logic, micro-models, programming by contract and total
   correctness. The coverage of model-checking ... substantially updated. ..."
   2nd ed, 2004, stg30, uk us isbn:052154310X; uk us isbn13:978-0521543101;
   [<A HREF="http://www.cs.bham.ac.uk/research/projects/lics/toc.html">toc</A>]['08].

%A M. A. Bramer
%T Logic programming with Prolog
%I SpringerVerlag
%P 223
%M AUG
%D 2005
%K book, text, c2005, c200x, c20xx, logic programming, program, computer, LP
%X pb; uk us isbn:1852339381; uk us isbn13:978-1852339388.
   (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A P. Blackburn
%A J. Bos
%A K. Striegnitz
%T Learn Prolog Now!
%I CollegePublns
%D 2006
%K book, text, c2006, c200x, c20xx, Prolog, logic programming, LP, L2Ref, L3Ref
%X "... a very high level language, good for knowledge rich applications such
   as artificial intelligence, natural language processing, and the semantic
   web. So by studying Prolog, you gain insight into how sophisticated tasks
   can be handled computationally. ..."
   1st ed 2006; pb us$23; uk us isbn:1904987176; uk us isbn13:978-1904987178.
   (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A J. Harrison
%T Handbook of Practical Logic and Automated Reasoning
%I CUP
%P 702
%D 2009
%K book, text, CUP, c2009, c200x, c20xx, zz0112, L4Ref, L5Ref, handbook,
   logic, OCaml, automated, automatic, maths, theorem proving, prover, ATP
%X 1st ed 2009; hb us$128; uk us isbn:0521899575; uk us isbn13:978-0521899574.
   "... self-contained and broad-based account of the concepts, the machinery
   and the use of automated reasoning. The mathematical logic foundations are
   described in conjunction with practical application, all with the minimum of
   prerequisites. The approach is constructive, concrete and algorithmic: a key
   feature is that methods are described with reference to actual
   implementations (for which code is supplied) ..."
   [Also search for: theorem proving].

%A N. S. Yanofsky
%T The Outer Limits of Reason: What Science, Mathematics, and
   Logic Cannot Tell Us
%I MITpress
%P 424
%M AUG
%D 2013
%K book, text, c2013, c201x, c20xx, zz1113, logic, computability, unsolvable,
   maths, mathematics, philosophy, paradoxes, provability, intuition
%X 1st ed 2013; hb us$23; uk us isbn:0262019353; uk us isbn13:978-0262019354.
   "... investigates what cannot be known. Rather than exploring the amazing
   facts that science, mathematics, and reason have revealed to us, this work
   studies what science, mathematics, and reason tell us cannot be revealed.
   In The Outer Limits of Reason, N.Y. considers what cannot be predicted
   described, or known, and what will never be understood. He discusses the
   limitations of computers, physics, logic, and our own thought processes. ..."

%A D. P. Friedman
%A C. Eastlund
%T The Little Prover
%I MITpress
%P 248
%D 2015
%K CompSci, CSCI, book, text, c2015, c201x, c20xx, zz0920, program, proof,
   logic. correctness, maths, theorem proving, prover, proof,
   computer programming
%X 1st ed 2015; pb us$40; uk us Isbn:0262527952; uk us isbn13:978-0262527958.
   "... a gentle intro. to the nuts & bolts of formal proofs about programs.
   Following on from The Little Schemer, it is an excellent guide for both
   thoughtful FP'ers wondering what it really means to know that a program is
   correct & do-it-yourselfers who want a taste of how proof assistants like
   ACL2 do their work. ...â
   [Also search for: theorem proving].

%A K. Bansal
%A S. M. Loos
%A M. N. Rabe
%A C. Szegedy
%A S. Wilcox
%T HOList: An environment for machine learning of higher-order theorem proving
   (extended version)
%J arXiv
%M APR
%D 2019
%K TR, c2019, c201x, c20xx, zz0519, HOList, HOL light, maths, mathematical,
   automated, theorem, proving, maths, proof, prove, prover, assistant,
   HOList, HOL light
%X "We present an environment, benchmark, and deep learning driven automated
   theorem prover for higher-order logic. Higher-order interactive theorem
   provers enable the formalization of arbitrary mathematical theories and
   thereby present an interesting, open-ended challenge for deep learning. We
   provide an open-source framework based on the HOL Light theorem prover that
   can be used as a reinforcement learning environment. HOL Light comes with a
   broad coverage of basic mathematical theorems on calculus and the formal
   proof of the Kepler conjecture, from which we derive a challenging benchmark
   for automated reasoning. We also present a deep reinforcement learning driven
   automated theorem prover, DeepHOL, with strong initial results on this
   benchmark."
   -- 1904.03241@[<A HREF="https://arxiv.org/abs/1904.03241">arXiv</A>]['19].
   (Also see RL@[<A HREF="https://en.wikipedia.org/wiki/Reinforcement_learning">wikip</A>]['22].)
   [Also search for: theorem proving].

%A P. Tarau
%A J. Wielemaker
%A T. Schrijvers
%T Lazy stream programming in prolog
%X arXiv
%M JUL
%D 2019
%K TR, c2019, c201x, c20xx, zz0819, LP, prolog, logic, lazy, stream, streams,
   list, lists, generator, generators
%X "... Prolog has so far been lacking ... we present {\em lazy stream
   generators} as a unified Prolog interface for stateful computations on both
   finite and infinite sequences of data that are produced incrementally through
   I/O and/or algorithmically. We expose stream generators to the application
   programmer in two ways: 1) through an abstract sequence manipulation API,
   convenient for defining custom generators, and 2) as idiomatic lazy lists,
   compatible with many existing list predicates. We define an algebra of stream
   generator operations that extends Prolog via an embedded language interpreter
   provides a compact notation for composing generators and supports moving
   between the two isomorphic representations. ..."
   -- 1907.11354@[<A HREF="https://arxiv.org/abs/1907.11354">arXiv</A>]['19].

%A M. Hamana
%T How to prove decidability of equational theories with second-order
   computation analyser SOL
%J JFP
%V 29
%P #e20
%M DEC
%D 2019
%K jrnl, JFP, FP, c2019, c201x, c20xx, zz0120, theorem proving, prover, solver,
   maths, proof, SOL, second order, logic, decidability, decidable
%X "We present a general methodology of proving the decidability of equational
   theory of programming language concepts in the framework of second-order
   algebraic theories. ... a Haskell-based analysis tool, i.e. 2nd-Order Lab.,
   which assists the proofs of confluence & strong normalisation of computation
   rules derived from 2nd-order algebraic theories. To cover various examples in
   prog.lang. theory, we combine & extend both syntactical & semantical results
   of the 2nd-order computation in a non-trivial manner. We demo. how to prove
   decidability of various algebraic theories in the literature. It includes the
   equational theories of monad & \-calculi, Plotkin & Power's theory of states
   & bits, & Stark's theory of pi-calculus. We also demo. how this [it] can
   solve the coherence of monoidal categories."
   -- [<A HREF="https://doi.org/10.1017/S0956796819000157">doi:10.1017/S0956796819000157</A>]['20].
   [NB. not the SOL of the 1980s.]
   [Also search for: theorem proving].

%A W. Drabent
%T A note on occur-check
%J arXiv
%M SEP
%D 2021
%K TR, c2021, c202x, c20xx, zz0921, logic programming, LP, Prolog, unification,
   occurs, occur, check
%X "Most known results on avoiding the occur-check are based on the notion of
   'not subject to occur-check' (NSTO). It means that unification is performed
   only on such pairs of atoms for which the occur-check never succeeds in any
   run of a nondet. unification alg.. Here we show that this requirement is too
   strong. We show how to weaken it, & present some related sufficient condns
   under which the occur-check may be safely omitted. We show examples for which
   the proposed approach provides more general results than the approaches based
   on well-moded & nicely moded programs (this inc. cases to which the latter
   approaches are inapplicable).
   -- 2109.08278@[<A HREF="https://arxiv.org/abs/2109.08278">arXiv</A>]['21].

%A G.-A. Silber
%T Towards an automatic consolidation of French law
%J arXiv
%M JAN
%D 2023
%K TR, c2023, c202x, c20xx, zz0123, Legistix, law, legal, Europe, European,
   France, French, grammar, computing, automation
%X "We present preliminary results about Legistix, a tool we are developing to
   automatically consolidate the French & European law. Legistix is based both
   on regular expressions used in several compound grammars, similar to the
   successive passes of a compiler, & on a new specialized language of
   functional type, allowing to describe the changes applied to the texts.
   Instead of creating manually a full consolidated version of a text at each
   modification date, Legistix generates automatically programs from legal
   documents written in natural language to automatically create the
   consolidated versions."
   -- [<A HREF="https://arxiv.org/abs/2301.06469">arXiv</A>]['23].
   [Also search for: law legal automation].

%A A. Bentkamp
%A et al
%T Mechanical mathematics
%J CACM
%V 66
%N 4
%M APR
%D 2023
%K jrnl, CACM, c2023, c202x, c20xx, zz0423, survey, intro, maths, logic, LP,
   theorem, proving, prover, proof assistant, automatic, algorithm, high,
   higher order
%X -- [<A HREF="https://dx.doi.org/10.1145/3557998">doi:10.1145/3557998</A>]['23].
   [Also search for: theorem proving].


%A I. Newton
%T Philosophiae Naturalis Principia Mathematica
%D 1687
%K book, text, c1687, c168x, c16xx, Sir Isaac Newton, maths, mathematics,
   differential, integral, calculus, infinitesimal, fluxions, Newtonian,
   laws of motion, classical, gravity, gravitation, Principia Mathematica
%X 1st ed 1687, 2nd ed 1713, 3rd ed 1726.
   AKA 'Principia Mathematica'. 3 volumes.
   1st ed scanned@[<A HREF="http://cudl.lib.cam.ac.uk/view/PR-ADV-B-00039-00001/">Cam.U.</A>]['12].

%A G. de L'Hospital
%T L'Analyse des Infiniment Petits pour l'Intelligence des Lignes Courbes
%D 1696
%K L'Hospital's, L'Hospitals, l'Hopital's, l'Hopitals, rule, limit, limits,
   defn, definition, book, c1696, c169x, c16xx,
%X "Analysis of the Infinitely Small to Learn about Curved Lines."
   H's rule:  lim :- limit as x tends to c or to infinity.
              If lim f(x) and lim g(x) are both zero, or both +-infinite,
              then lim{f(x)/g(x)} = lim{f'(x)/g'(x)}.
   [Also search for: infinitesimal calculus].

%A A. de Segner
%T Enumeratio modorum, quibus figurae planae rectilineae per diagonales
   dividuntur in triangula
%J Novi commentarii academiae scientiarum Petropolitanae
%V 7
%P 203-209
%D 1758-1759
%K c1758, c175x, c17xx, zz0119, Catalan number, numbers, de Segner, deSegner,
   Dyck path, paths, maths, polygon, triangulation
%X "C_0=1, C_{n+1}=SUM_{i=0..n} C_i.C_{n-i}, for n > 0."
  See a copy at
  [<A HREF="http://www.math.ucla.edu/~pak/lectures/Cat/Segner1.pdf">ucla</A>][23/1/'19],
  from
  [<A HREF="https://archive.org/details/novicommentariia07impe/page/204">archive.org</A>][23/1/'19].
  Also see
  Cnums@[<A HREF="https://en.wikipedia.org/wiki/Catalan_number">wikip</A>]['19],
  Dwrds@[<A HREF="https://en.wikipedia.org/wiki/Dyck_language">wikip</A>]['19]
  (Walther Franz Anton von Dyck 1856-1943).

%A W. R. Hamilton
%T On quaternions, or on a new system of imaginaries in algebra
%J Philosophical Magazine
%V 25
%N 3
%P 489-495
%D 1844
%K jrnl, maths, c1844, c184x, c18xx, quaternion, complex, imaginary, number,
   numbers
%X Qs. devised by H. in 1843
   -- Q@[<A HREF="http://en.wikipedia.org/wiki/Quaternions">wikip</A>].
   [Also search for: Hamilton quaternion].
   (Also see [<A HREF="http://www.allisons.org/ll/Maths/Quaternion/">quaternions</A>].)

%A C. G. J. Jacobi
%T Uber ein leichtes Verfahren, die in der Theorie der Sakularstorngen
   vorkommenden Gleichungen numerische aufzulosen
%J Crelle's J.
%V 30
%P 51-94
%D 1846
%K jrnl, c1846, c184x, c18xx, maths, Eigen value, values, Eigenvalue,
   Eigenvalues, algorithm, Jacobi, Givens, rotation, numerical computing,
   real symmetric, matrix
%X alg@[<A HREF="http://en.wikipedia.org/wiki/Jacobi_eigenvalue_algorithm">wikip</A>]['11], and
   others@[<A HREF="http://en.wikipedia.org/wiki/Eigenvalue_algorithm">wikip</A>]['11].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Numerical/Eigen-Value/">Eigen-Values</A>].)

%A G. Boole
%T An Investigation of the Laws of Thought on Which are Founded the
   Mathematical Theories of Logic and Probabilities
%P 355
%D 1854
%K book, c1854, c185x, c18xx, zz0424, Boole, maths, boolean, logic, algebra,
   probability, reasoning, propositional calculus
%X pdf@[<A HREF="https://www.gutenberg.org/files/15114/15114-pdf.pdf">Gut'nberg</A>]['24].

%A B. Riemann
%T Ueber die Anzahl der Primzahlen unter einer gegebenen Grosse
   (on the number of primes less than a given magnitude)
%I Monatsberichte der Berliner Akademie
%D 1859
%K c1859, c185x, c18xx, Riemann hypothesis, generalized, reimann, zeta function,
   critical strip, zeroes, prime number, primes, numbers, distribution, gap,
   gaps
%X "zeta(s) has [trivial] zeros at the negative even integers"
   The RH is that "The real part of every non-trivial zero of the Riemann
   zeta function is 1/2.  Thus, if the hypothesis is correct, all the
   non-trivial zeros lie on the critical line consisting of the complex numbers
   1/2+i*t, where t is a real number and i is the imaginary unit."
   "zeta(s) = SUM_{n=1..inf} 1/n^s"
   [1859]: "In Gesammelte Werke, Teubner, Leipzig (1892), Reprinted by Dover,
   N.Y. (1953). Original manuscript (with English translation). Reprinted in
   (Borwein et al. 2008) and (Edwards 1974)"
   -- RH@[<A HREF="https://en.wikipedia.org/wiki/Riemann_hypothesis#CITEREFRiemann1859">wikip</A>]['18].
   [Also search for: prime number distribution].

%A W. R. Hamilton
%T Elements of Quaternions
%I LongmansGreen
%D 1866
%K book, text, c1866, 186x, c18xx, zz0711, quaternion, complex, imaginary,
   number, maths, numbers, rotation, rotations, vectors
%X Qs. devised by H. in 1843.
   1st edn 1866, posthumously, ed. by his son.  2nd edn 1899.
   CUP reproduction 2009; uk us isbn:1108001718; uk us isbn13:978-1108001717.
      "This is an *exact* reproduction of a book published before 1923 ...
      not an OCR'd book [it] may have occasional imperfections such as missing
      or blurred pages, poor pictures, errant marks, etc. that were either part
      of the original artifact, or were intro. by the scanning process. We
      believe this work is culturally important ..."  -- CUP.
   (See Q@[<A HREF="http://en.wikipedia.org/wiki/Quaternions">wikip</A>].)
   [Also search for: Hamilton quaternion].

%A J. J. Sylvester
%T Chemistry and Algebra
%J Nature
%V 17
%N 432
%P 284-284
%M FEB
%D 1878
%K jrnl, c1878, c187x, c18xx, zz0714, maths, graph, chemical compound,
   chemistry, molecule, molecules, compound
%X "... an analogy that has recently forcibly impressed me between branches
   of human knowledge apparently so dissimilar as modern chemistry and
   modern algebra. ..."
   -- [<A HREF="http://www.nature.com/nature/journal/v17/n432/abs/017284a0.html">www</A>]['14],
      [<A HREF="http://dx.doi.org/10.1038/017284a0">doi:10.1038/017284a0</A>]['14].
   [Also search for: Sylvester c18xx].

%A J. J. Sylvester
%T On an application of the new atomic theory to the graphical representation
   of the invariants and covariants of binary quantics
   - with three appendices
%J Amer. J. of Mathematics, Pure & Applied
%V 1
%N 1
%P 64-90
%D 1878
%K jrnl, c1878, c187x, c18xx, zz0714, origin, maths, graph, chemical compound,
   chemistry, molecule, molecules, compound
%X "Thus, ex. gr. O2 (oxygen combined with itself) will represent a quadratic
   invariant of a quadric. Its graph is seen in Fig.1, (a).  Potash, a
   combination of potassium, oxygen and hydrogen, having for its graph that of
   Fig.2", p.65  [i.e.,  fig.1 O=O,  fig.2  K-O-K, etc.]
   -- 2369436@[<A HREF="http://www.jstor.org/stable/2369436">Jstor</A>]['14].
   ?Origin of the term "graph" in this sense.?
   [Also search for: Sylvester c18xx].

%A A. Cayley
%T Desiderata and suggestions: No.2. The theory of groups: Graphical
   representation
%J Amr. J. Maths.
%V 1
%N 2
%P 174-176
%D 1878
%K jrnl, maths, c1878, c187x, c18xx, zz0220, group, graph, diagram, permutation,
   generators, representation theory, theorem
%X -- [<A HREF="https://doi.org/10.2307/2369306">doi:10.2307/2369306</A>]['20],
      2369306@[<A HREF="https://www.jstor.org/stable/2369306">Jstore</A>]['20].
   Also see CayleyG@[<A HREF="https://en.wikipedia.org/wiki/Cayley_graph">wikip</A>]['20].
   [Also search for: permutation group].

%A H. Pade
%T Sur la representation approchee d'une fonction par des fractions rationelles
   Thesis, Ann. 'Ecole Nor. (3), 9
%P 1-93 supplement
%D 1892
%K c1892, c189x, c18xx, zz0614, Pade approximation, approximate, approximant,
   numerical method, analysis, computing, function,
   Wynn epsilon algorithm, convergence, stability
%X "Given a function f and two integers m >=  0 and n >= 1, the Pade
    approximant of order [m/n] is the rational function
       R(x) = (a_0 + a_1 x + ... + a_m x^m) / (1 + b_0 + b_1 x + ... + b_n x^n)
    which agrees with f(x) to the highest possible order, which amounts to
       f(0)=R(0), f'(0)=R'(0), ..., f^(m+n)(0)=R^(m+n)(0). ..."
    -- [<A HREF="http://en.wikipedia.org/wiki/Pade_approximant">wikip</A>]['14]
    ([<A HREF="http://en.wikipedia.org/wiki/Pad%C3%A9_approximant">w</A>]['14]).
   (Also see P.Wynn, SIAM J. Num. Anal., 3(1), pp.91-122, 1966
      [<A HREF="http://epubs.siam.org/doi/abs/10.1137/0703007">www</A>]['14] or
      2949688@[<A HREF="http://www.jstor.org/stable/2949688">Jstor</A>]['14].)

%T Prime number theorem
%D 1896
%K c1896, c189x, c18xx, zz1020, prime number theorem, PrimeNumberTheorem, PNT,
   primes, numbers, distribution, Hadamard, de la Vallee Poussin, Riemann zeta
%X "... proved independently by Jacques Hadamard & Charles Jean de la Vallee
   Poussin in 1896 using ideas introduced by Bernhard Riemann (in particular,
   the Riemann zeta function) ... pi(N) ~ N/log(N) where pi(N) is the
   prime-counting fn ... for large enough N, the probability that a random
   int. not greater than N is prime is very close to 1/log(N).  [So] a random
   int. with at most 2n digits (for large enough n) is about half as likely to
   be prime as a random int. with at most n digits. ..."   [[NB. N=2^n.]]
   -- PNT@[<A HREF="https://en.wikipedia.org/wiki/Prime_number_theorem">wikip</A>]['20].
   [Also search for: prime number distribution].

%A G. H. Hardy
%T A Course of Pure Mathematics
%I CUP
%S Cambridge Mathematical Library
%P 522
%D 1908
%K c1908, c2008, c200x, c20xx, 2008, zz0408, CUP, book, text, G H Hardy, maths,
   GHHardy, pure, theory
%X 100th anniversary ed 2008, with a foreword by
   T.W.Korner;    uk us isbn:0521720559; uk us isbn13:978-0521720557.
   [10th ed 1993; uk us isbn:0521092272; uk us isbn13:978-0521092272.]

%A J. Mercer
%T Functions of positive and negative type and their connection with the
   theory of integral equations
%J Philos. Trans. Royal Soc. (A)
%V 83
%N 559
%P 69-70
%M NOV
%D 1909
%K jrnl, PTRS, c1909, c190x, c19xx, Mercer's theorem, Mercers, kernel function,
   positive definite, SVM, SVMs, machine
%X "... any continuous, symmetric, positive semi-definite kernel function
   K(x,y) can be expressed as a dot product in a high-dimensional space. ..."
   -- [<A HREF="http://www.jstor.org/pss/93056">Jstor</A>]['09],
      [<A HREF="http://rsta.royalsocietypublishing.org/content/209/441-458/415.full.pdf+html">PTRS</A>]['10], and
   thm@[<A HREF="http://en.wikipedia.org/wiki/Mercer's_theorem">wikip</A>]['09].

%A G. H. Hardy
%A S. Ramanujan
%T The normal number of prime factors of a number n
%J Quarterly J. of Math.
%V 48
%P 76-92
%D 1917
%K jrnl, maths, c1917, c191x, c19xx, zz0323, GHHardy, number theory,
   prime factors
%X -- [<A HREF="https://zbmath.org/?format=complete&q=an:46.0262.03">www</A>]['23].
   "... Roughly speaking, this means that most numbers have about this
   [log(log(n))] number of distinct prime factors. ..."
   -- HRthm@[<A HREF="https://en.wikipedia.org/wiki/Hardy%E2%80%93Ramanujan_theorem">wikip</A>]['23].
   [Also search for: Hardy maths].

%A S. Gershgorin
%T Uber die abgrenzung der Eigenwerte einer matrix
%J Izv. Akad. Nauk. USSR Otd. Fiz.-Mat. Nauk
%V 7
%P 749-754
%D 1931
%K jrnl, c1931, c193x, c19xx, Eigen value, eigenvalue, vector, spectrum, circle,
   matrix, theorem, Gerschgorin, Gershgorin
%X "... Every eigenvalue of A lies within at least one of the
   Gershgorin discs D(aii,Ri). ..."
      where aii is a diagonal elt of the natrix,
      and   Ri = sum[j!=i] |aij|
   -- thm@[<A HREF="http://en.wikipedia.org/wiki/Gershgorin_circle_theorem">wikip</A>]['11].
   [Also search for: Eigenvalue].

%A H. Whitney
%T Congruent graphs and the connectivity of graphs
%J Amer. J. Math.
%V 54
%P 150-168
%D 1932
%K jrnl, c1932, c193x, c19xx, congruent, isomorphic, isomorphism, mathematics,
   maths, graph, connectivity, K3, K13, line graphs, MCS
%X "other than K[3] and K[1,3] any 2 connected graphs having
   isomorphic line graphs are themselves isomorphic"   -- a ref.
   'Line Graph' (or edge graph), L(G),  of G:
      An edge, (u,v), of G is a vertex of L(G),
      and (u,v) and (v,w) are connected by an edge in L(G).
   -- 2371086@[<A HREF="https://www.jstor.org/stable/2371086">Jstor</A>]['19],
      [<A HREF="https://doi.org/10.2307/2371086">doi:10.2307/2371086</A>]['19].
   [Is relevant to the (MCS) MCIS and MCES problems.]

%A C. S. Meijer
%A Uber Whittakersche bzw. Besselsche Funktionen und deren Produkte
%J Nieuw Archief voor Wiskunde (2)
%V 2
%V 18
%N 4
%P 10-39
%D 1936
%K jrnl, c1936, c193x, c19xx, zz1219, Meijer, G function, Gfunction, Gfunctions,
   general, functions, hypergeometric
%X Also see MGF@[<A HREF="https://en.wikipedia.org/wiki/Meijer_G-function">wikip</A>]['19].
   [Also search for: Meijer Gfunction].

%A G. Polya
%T Kombinatorische anzahlbestimmungen fur gruppen, graphen und
   chemische verbindungen
%J Acta Mathematica
%I SpringerVerlag
%V 68
%N 1
%P 145-254
%D 1937
%K jrnl, c1937, c193x, c19xx, maths, graph, group, chemical compound,
   combinatorial enumeration
%X -- [<A HREF="http://dx.doi.org/10.1007/BF02546665">doi:10.1007/BF02546665</A>]['10].
   [Also search for: Polya c1987].

%A P. Erdos
%A M. Kac
%T The Gaussian law of errors in the theory of additive number theoretic
   functions
%J Amer. J. Math.
%V 62
%P 738-742
%D 1940
%K jrnl, number theory, c1940, c194x, c19xx, prime number, primes, numbers,
   AMS, distribution, theory
%X "If an arith. fn satisfies $f(m)+f(n)=f(mn)$ for $(m,n)=1$ and
   $f(p^\alpha)=f(p)$, $|f(p)|\leq 1$ for all prime numbers $p$, put
   $$ A_n=\sum_{p < n}p^{-1}f(p),\quad B_n{}^2=\sum_{p < n}p^{-1}f^2(p). $$
   Suppose that $B_n\rightarrow\infty$ as $n\rightarrow\infty$. If $K_n$ denotes
   for a real $\omega$, the number of integers $m$ between $l$ and $n$ for which
   $f(m) < A_n+\omega\sqrt 2B_n$, then
   $$ \lim_{n\rightarrow\infty}\frac{K_n}{n}=\pi^{-\frac 1{2}}\int_{-\infty}^{+\infty}\exp(-u^2)\,du. $$
   The analogy of this thm to a classical stat. limit thm is obvious. The proof
   consists in the justification of the interchange of 2 limiting processes.
   The one is $n\rightarrow\infty$ of the thm; the other consists in letting
   $l\rightarrow\infty$ in the case when only the first $l$ primes are
   considered. The interchange is based on some of the deeper "elementary"
   arithmetical methods, in particular on a method of Vigo Brun's classical
   memoir concerning the sieve of Eratosthenes"
   -- [<A HREF="http://www.ams.org/mathscinet-getitem?mr=2:42c">ams</A>]['05]

%A N. G. de Bruijn
%T A combinatorial problem
%J Koninklijke Nederlandse Akademie v. Wetenschappen
%V 49
%P 758-764
%D 1946
%K jrnl, c1946, c194x, c19xx, de Bruijn, deBruijn, maths, graph, graphs, Good
%X [<A HREF="http://en.wikipedia.org/wiki/De_bruijn_graph">wikip</A>]['08]:
   "... an n-dimensional de Bruijn graph of m symbols is a directed graph
   representing overlaps between seqs. of symbols. It has m**n vertices,
   consisting of all possible length-n seqs. of the given symbols ... If one of
   the vertices can be expressed by shifting all symbols by 1 place to the left
   & adding a new symbol at the end of another vertex, then the latter has a
   directed edge to the former ... discovered indep. by I.J.Good (1946)...".
   [Also search for: Good c1946].

%A I. J. Good
%T Normal recurring decimals
%J J. of the London Math. Soc.
%V 21
%N 3
%P 167-169
%D 1946
%K jrnl, IJGood, c1946, c194x, c19xx, deBruijn, de Bruijn, maths, graph, graphs,
   Good, decimal, number
%X pdf:[<A HREF="http://dx.doi.org/10.1112/jlms/s1-21.3.167">doi:10.1112/jlms/s1-21.3.167</A>]['08].
   [Also search for: de Bruijn graph c1946]  and  [also search for: IJGood].

%A M. K. Wood
%A G. B. Dantzig
%T Programming of interdependent activities: I General discussion
%J Econometrica
%V 17
%N 3/4
%P 193-199
%M JUL-OCT
%D 1949
%I The Econometric Soc.
%K jrnl, c1949, c194x, c19xx, zz0221, linear programming, simplex algorithm
%X "... concerned with improved techniques of program planning, particularly as
   they apply to the scheduling of activities over time within an organization
   or economy in which the activities must share in the use of limited amounts
   of various commodities. The contemplated use of electronic computers for
   rapidly computing programs and the assumptions underlying the math. model
   are discussed. The paper is concluded by an illustrative example."
   -- [<A HREF="https://doi.org/10.2307/1905522">doi:10.2307/1905522</A>]['21],
   or 1905522@[<A HREF="https://www.jstor.org/stable/1905522">Jst'r</A>]['21].
   [Also search for: Dantzig linear programming].

%A G. B. Dantzig
%T Programming of interdependent activities: II Mathematical model
%J Econometrica
%V 17
%N 3/4
%P 200-211
%M JUL-OCT
%D 1949
%I The Econometric Society
%K jrnl, c1949, c194x, c19xx, zz0221, linear programming, simplex algorithm
%X "Activities (or production processes) are considered as building blocks out
   of which a technology is constructed. Postulates are developed by which
   activities may be combined. The main part of the paper is concerned with
   the discrete type model and the use of a linear maximization function for
   finding the "optimum" program. The math. problem associated with this
   approach is developed first in general notation and then in term sof a
   dynamic system of equations expressed in matrix notation. Typical problems
   from the fields of inter-industry relations, transportation nutrition,
   warehouse storage, and air transport are given in the last section.
   -- [<A HREF="https://doi.org/10.2307/1905523">doi:10.2307/1905523</A>]['21],
   or 190552@[<A HREF="https://www.jstor.org/stable/1905523">Jst'r</A>]['21].
   [Also search for: Dantzig linear programming].

%A T. van Aardenne-Ehrenfest
%A N. G. de Bruijn
%T Circuits and trees in oriented linear graphs
%J Simon Stevin : Wisen Natuurkundig Tijdschrift
%V 28
%P 203-217
%D 1951
%K c1951, c195x, c19xx, deBruijn, maths, directed, graph, Eulerian, circuit,
   closed, path, paths, trail, trails, tree, number, count, counting,
   enumerate, enumerating, arborescence, BEST theorem
%X pdf@[<A HREF="http://repository.tue.nl/597493">tue.nl</A>]['12].
   And...
      BEST thm: the # of Eul.Circ. in a directed graph G = < V, E >,
         ec(G) = t[w](G) PROD[v in V] (deg(v)-1)!
      where deg(v) = indeg(v) = outdeg(v) [necc. for a E.circuit],
      and t[w](G) is the number of arborescences, which are trees directed
      towards the root at a fixed vertex w in G [which] can be computed as a
      determinant, by the version of the matrix tree theorem for dir.graphs.
      ... t[v](G)=t[w](G) for every 2 vertices v & w in a connected Eul.graph G.
      -- [<A HREF="http://en.wikipedia.org/wiki/BEST_theorem">wikip</A>]['12].

%A A. Moessner
%T Eine Bemerkung uber die Potenzen der naturlichen Zahlen
%D 1952
%S Sitzungsberichte
%D 1951,3
%K jrnl, maths, c1952, c195x, c19xx, zz0721, number, numbers, powers, Moessner,
   theorem, magic, integer, sequences, triangles, Perron, Kozen, Silva
%X -- [<A HREF="https://publikationen.badw.de/de/003383662">www</A>]['21].
   Also see MM@[<A HREF="https://en.wikipedia.org/wiki/Moessner%27s_theorem">wikip</A>]['21] and
   "On Moessner's Theorem", D. Kozen & A. Silva,
   The Amer. Math. Monthly, 120(2), 131-139, 2013
   -- [<A HREF="https://doi.org/10.4169/amer.math.monthly.120.02.131">doi:10.4169/amer.math.monthly.120.02.131</A>]['21].  (via AK)

%A K.Mahler
%A J. Popken
%T On a maximum problem in arithmetic
%J Nieuw Archief voor Wiskunde
%V 1
%P 1-15
%D 1953
%K jrnl, c1953, c95x, c19xx, zz0823, integer complexity, ones, arithmetic,
   integerComplexity
%X "In number theory, the IC of an int. is the smallest # of ones that can be
   used to represent it using ones & any # of additions, multiplications, &
   parentheses. It is always within a constant factor of the log of the given
   int.. [eg] 11 may be represented using 8 ones [at best]:
   11=(1+1+1)x(1+1+1)+1+1. ..."
   -- [<A HREF="https://mathscinet.ams.org/mathscinet-getitem?mr=0053986">www</A>],
      IC@[<A HREF="https://en.wikipedia.org/wiki/Integer_complexity">wikip</A>]['23].
   [Also search for: integer complexity ones].

%A F. Harary
%A G. E. Uhlenbeck
%T On the number of Husimi trees, I
%J PNAS
%V 39
%N 4
%P 315-322
%M APR
%D 1955
%K jrnl, PNAS, c1953, c195x, c19xx, zz0220, Husimi tree, cactus graph, cacti,
   block, cycles, maths, count, counting
%X "... A H.tree is a connected graph s.t. no line [edge] lies on more
   than one cycle. ..."
   --  [<A HREF="https://doi.org/10.1073/pnas.39.4.315">doi:10.1073/pnas.39.4.315</A>]['20].
   Also see, "Meanwhile, ... H.tree commonly came to refer to gs. in which every
   block is a complete g. ... This usage had little to do with the work of H.,
   & the more pertinent term block g. is now used for this family; however,
   because of this ambiguity this phrase has become less frequently used to
   refer to cactus graphs."
   -- CactusGraph@[<A HREF="https://en.wikipedia.org/wiki/Cactus_graph">wikip</A>]['20].

%T Kolmogorov-Arnold representation theorem
%D 1956 / 1957
%K c1956, c195x, c19xx, zz1122, Kolmogorov Arnold representation theorem,
   function representation, represent, sum, multivariate, composition,
   ANN, NN, Hilbert's 13th
%X "... the K.-A. representation thm (or superposition thm) states that every
   multivariate cts fn can be rep. as a superposition of the two-argument
   addition & cts fns of one variable. It solved a more constrained, yet more
   general form of Hilbert's thirteenth problem ...
   f(X) = f(x1,...,xn) = SUM_{q=0..2n} G_q(SUM_{p=1..n}H_{q,p}(x_p)) ..."
   -- KA@[<A HREF="https://en.wikipedia.org/wiki/Kolmogorov%E2%80%93Arnold_representation_theorem">wikip</A>]['22].
   (Also see
    Kurkova 1991 [<A HREF="https://doi.org/10.1162/neco.1991.3.4.617">doi:10.1162/neco.1991.3.4.617</A>]['22] N.C. 3(4) 12/1991, and
    Arnold  2009 [<A HREF="https://doi.org/10.1007/978-3-642-01742-1_5">doi:10.1007/978-3-642-01742-1_5</A>]['22].)

%A P. J. Kelly
%T A congruence theorem for trees
%J Pacific J. Math.
%V 7
%N 1
%P 961-968
%D 1957
%K jrnl, c1957, c195x, c19xx, zz0115, maths, graph, graphs, tree,
   reconstruction conjecture, Kelly, Ulam, subgraphs
%X "... It is natural to wonder if any two graphs must be isomorphic when they
   have the same composition in terms of (n-1)-point subgraphs. The
   author has considered the question for graphs having at most one join for an
   y pair of points, with no point joined to itself.  Actual in - spection shows
   that the theorem is valid for all such graphs up to order seven.  It also
   holds for any two such graphs of general, finite order if either is
   disconnected or its transpose is disconnected. (The transpose is obtained by
   reversing the join relationship between every pair of vertices.) However, the
   author was unable to prove or disprove the general case. As a final comment,
   it is not true that the same composition in terms of (n-2)-point subgraphs
   implies isomorphism."
   -- 1103043674@[<A HREF="http://projecteuclid.org/euclid.pjm/1103043674">pr'jecteuclid</A>]['14].
   (Also see,
      "... For a graph G, the deck of G, denoted D(G), is the multiset of all
      vertex-deleted subgraphs of G. Each graph in D(G) is called a card. Two
      graphs that have the same deck are said to be hypomorphic. With these
      definitions, the conjecture can be stated as: Reconstruction Conjecture:
      Any two hypomorphic graphs on at >= 3 vertices are isomorphic.  ..."
   and variations
   -- conjecture@[<A HREF="http://en.wikipedia.org/wiki/Reconstruction_conjecture">wikip</A>]['14].)

%A K. T. Chen
%A R. H. Fox
%A R. C. Lyndon
%T Free differential calculus, IV. The quotient groups of the lower central
   series
%J Annals of Mathematics
%S 2
%V 68
%N 1
%P 81-95
%M JUL
%D 1958
%K jrnl, c1958, c195x, c19xx, zz1109, quotient, maths, group, groups, theory,
   Lyndon word, words, LyndonWord, string, strings
%X @[<A HREF="http://www.jstor.org/stable/1970044">Jstor</A>]['09].
   [A word, w = a[0],a[1],...,a[n-1], is a LW if it is *strictly*
    lexicographically less than all of its cyclic rotations.]
   [Also search for: Lyndon word factor algorithm].

%A J. W. Tukey
%T The teaching of concrete mathematics
%J American Math. Monthly
%V 65
%K JAN
%D 1958
%P 1
%K jrnl, origin, word, terminology, software, bit, bits, c1958, c195x, c19xx,
   information
%X T is credited with originating the terms 'bit' 1946(?)
      'Sequential conversion of continuous data to digital data',
      Bell Labs Memorandum Sept 1947,
      (also H. S. Tropp, `Origin of the term Bit',
            Annals History of Computing, 6, pp.152-155, 1984.)
   and also `software' (above); apparently article is in Jstor.
   [Also search for: origin ban]

%A M. Kac
%T Statistical Independence in Probability, Analysis and Number Theory
%I Wiley
%D 1959
%K book, text, stats, prime numbers, c1959, c195x, c19xx, dependent,
   independent, statistics, primes, maths, theory
%X [Also search for: Kac Erdos c1940]

%A E. P. Wigner
%T The unreasonable effectiveness of mathematics in the natural sciences
%J Comm. on Pure and Appl. Maths
%V 13
%N 1
%P 1-14
%M FEB
%D 1960
%O Richard Courant lecture in Math. Sci., delivered at New York Univ.,
   11 May 1959
%K lecture, seminar, talk, c1960, c196x, c19xx, zz0820, science, maths, model,
   prediction, predict, effective, useful, mathematics, seminars,
   physics, quote, quotable
%X -- [<A HREF="https://doi.org/10.1002/cpa.3160130102">doi:10.1002/cpa.3160130102</A>]['20],
      [<A HREF="https://en.wikipedia.org/wiki/The_Unreasonable_Effectiveness_of_Mathematics_in_the_Natural_Sciences">wikip</A>]['20].

%A C. W. Clenshaw
%A A. R. Curtis
%T A method for numerical integration on an automatic computer
%J Numerische Mathematik
%V 2
%P 197-205
%D 1960
%K jrnl, c1960, c196x, c19xx, zz1013, integration, quadrature,
   numerical method
%X "A new method for ... of a 'well behaved' function ... expanding the
   integrand in a series of Chebyshev polynomials and integ. this series
   term by term ..."
   -- [<A HREF="http:http://www.digizeitschriften.de/dms/resolveppn/?PPN=GDZPPN001163442">www</A>]['13].
   (Also see C-C@[<A HREF="http://en.wikipedia.org/wiki/Clenshaw-Curtis_quadrature">wikip</A>]['13],
   "... Equivalently, they employ a change of variables x=cos theta and use a
   discrete cosine transform (DCT) approximation for the cosine series....".)

%A J. G. F. Francis
%T The QR transformation, I
%J COMPJ
%V 4
%N 3
%P 265-271
%D 1961
%K jrnl, COMPJ, c1961, c196x, c19xx, transformation, decomposition, QR, LR,
   eigenvector,  eigenvectors, eigenvalue, eigenvalues, Eigen value, maths,
   matrix, matrices, algorithm, numerical
%X "The LR transformation, due to Rutishauser, ... for finding the eigenvalues
   of symmetric band matrices. Little attention, however, has been paid to its
   application to the more difficult problem of finding eigenvalues of general
   unsymmetric matrices. If the matrices are large two important difficulties
   are likely to occur. 1st, triangular decomp. ... is by no means always
   numerically stable, & 2nd, the amount of computation required by the method
   is likely to be very great. ... describes an alg. similar to the LR trans.
   except that ... all unitary and can thus be expected to by numerically
   stable. ... shown that there are various advantages in 1st converting the
   matrix to almost-triangular form; in particular, the amount of work involved
   in the algorithm can then be greatly reduced.
   Pt.1 ... largely concerned with proof of convergence, & the theor.aspect.
   Pt.2 ... Jan. discussed practical comp. & gives results of experiments."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/4.3.265">doi:10.1093/comjnl/4.3.265</A>]['11].  Also,
     "... write the matrix, A, as a product of an orthogonal matrix & an upper
     triangular matrix, multiply the factors in the other order, & iterate. ...
     A[0] = A,  Q[.] orthogonal,  R[.] upper triangular, note
     A[k+1] = R[k] Q[k] = Q[k]^T Q[k] R[k] Q[k]
            = Q[k]^T A[k] Q[k] = Q[k]^(-1) A[k] Q[k],
     so all the A[.] have the same eigenvalues. ..."
     -- [<A HREF="http://en.wikipedia.org/wiki/QR_algorithm">wikip</A>]['11].
   [Also search for: QR transformation].
   [Also search for: matrix decomposition].

%A S. Parter
%T The use of linear graphs in Gauss elimination
%V 3
%N 2
%P 119-130
%M APR
%D 1961
%K jrnl, c1961, c196x, c19xx, zz1218, maths, graph, Gaussian, elimination,
   sparse, matrix, system, equations, solve
%X "A proc. to study the effect of sparseness in G.elimination & to choose an
   elimination scheme if practical ... The associations between graphs &
   matrices are developed & illustrated, & properties of special graphs, the
   trees, are discussed. The occasional breakdown of the G.proc. is also
   illustrated."
   -- [<A HREF="https://doi.org/10.1137/1003021">doi:10.1137/1003021</A>]['18],
      2027387@[<A HREF="https://www.jstor.org/stable/2027387">Jstor</A>]['18].
   [Also search for: elimination].

%A D. H. Lehmer
%T A machine method for solving polynomial equations
%J JACM
%V 8
%N 2
%P 151-162
%M APR
%D 1961
%K jrnl, JACM, c1961, c196x, c19xx, equation, root finding, roots, zero, zeroes,
   Schur, bisection method, complex number, plane, numbers, winding
%X -- [<A HREF="http://doi.acm.org/10.1145/321062.321064">doi:10.1145/321062.321064</A>]['07].
   "... extending the 1D bracketing used by the bisection method to find the
   roots of a fn of 1 complex var. inside any rectangular region ... rectangle
   is quadrisected into 4, congruent 1/4 rectangles. The argument principle is
   then applied to the boundary of each quarter to find the winding # (about the
   origin) for the boundary. Given that the function is analytic within each of
   these quarters, a nonzero winding number N (always an integer) identifies
   N zeros of the fn inside the quarter in question, each zero counted as many
   times as its multiplicity. Analogously with the bisection method, the alg.
   is then applied recursively to any quarter whose boundary has nonzero winding
   number ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Lehmer-Schur_algorithm">LW@wikip</A>]['07].

%A J. G. F. Francis
%T The QR transformation - part 2
%J COMPJ
%V 4
%N 4
%P 332-345
%D 1962
%K jrnl, COMPJ, c1962, c196x, c19xx, QR transformation, matrix, eigenvector,
   eigenvalue
%X "... consider the practical application of the QR transformation. Two
   versions of the alg. have been programmed for the Pegasus computer; these
   are described and an attempt is made to evaluate the method. Some results and
   detailed algorithms are given in appendices. Part 1 was published on
   pp.265-271 of this vol. (Oct. 1961)."
   -- [<A HREF="http://comjnl.oxfordjournals.org/content/4/4/332.abstract">compj</A>]['11].
   [Also search for: QR transformation].
   [Also search for: matrix decomposition].

%A G. Dantzig
%T Linear Programming and Extensions
%I PrincetonUP
%P 656
%D 1963
%O updated '97 and '03.
%K book, text, linear programming, simplex method, c196x, c196x, c19xx,
   algorithm, LinearProgramming, linear inequalities, transportation problem
%X c1998, 648pp., pb us$60, uk us isbn:0691059136.
   [Also search for: linearProgramming].

%A C. Lanczos
%T A precision approximation of the Gamma function
%J J. SIAM Numerical Analysis (B)
%V 1
%P 86-89
%D 1964
%K jrnl, c1964, c196x, c19xx, numerical algorithm, factorial
%X -- [<A HREF="https://www.jstor.org/stable/2949767">jstor:2949767</A>]['24].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Lanczos_approximation">wikip</A>]['07].)

%A M. Abramowitz
%A I. Stegun
%T Handbook of Mathematical Functions with Formulas, Graphs, and
   Mathematical Tables
%I DoverPubl
%P 1064
%D 1964
%K book, text, good, c1964, c196x, c19xx, zz0912, www, HREF, NIST, mathematical,
   maths, applied, numerical, methods, recipes, function, formula, formulae,
   approximation, series, logGamma, psi, diGamma, polyGamma, log gamma,
   Bessel function, modified
%X uk us isbn:0-486-61272-4.
   "An electronic copy of the tenth printing [1972] ..."
   -- [<A HREF="http://people.math.sfu.ca/~cbm/aands/">sfu</A>]['12]
         (polyGamma@[<A HREF="http://people.math.sfu.ca/~cbm/aands/page_260.htm">sec.6.4;p.260</A>]['12]),
      [<A HREF="http://www.nr.com/aands/">nr.com</A>]['12].
   "... first published in 1964, the 1046 page Handbook has been one
   of the most comprehensive ..."
   -- A&S@[<A HREF="http://en.wikipedia.org/wiki/Abramowitz_and_Stegun">wikip</A>]['12].

%A R. L. Adler
%A A. G. Konheim
%A M. H. McAndrew
%T Topological entropy
%I Trans. of the American Math. Soc.
%V 114
%N 2
%P 309-319
%M FEB
%D 1965
%K jrnl, AMS, c1965, c196x, c19xx, maths, topological entropy, information
%X -- paper@[<A HREF="http://www.jstor.org/stable/1994177">Jstor</A>]['11].
   (Also see TE@[<A HREF="http://en.wikipedia.org/wiki/Topological_entropy">wikip</A>]['11].)

%A G. Golub
%A W. Kahan
%T Calculating the singular values and pseudo-inverse of a matrix
%J J. SIAM: Series B, Numerical Analysis
%I SIAM
%V 2
%N 2
%P 205-224
%D 1965
%K jrnl, c1965, c196x, c19xx, singular value decomposition, SVD, pseudo inverse,
   scientific, numerical method, methods, matrix, matrices,
   Householder transformation, QR
%X "A numerically stable and fairly fast scheme is described to compute the
   unitary matrices U and V which transform a given matrix A into a diagonal
   form S = U^* A V, thus exhibiting A's singular values on S's diagonal. The
   scheme 1st transforms A to a bidiagonal matrix J, then diagonalizes J. The
   scheme described here is complicated but does not suffer from the
   computational difficulties which occasionally afflict some previously known
   methods. Some applications are mentioned, in particular the use of the
   pseudo-inverse A^I = V S^IU* to solve least squares problems in a way which
   dampens spurious oscillation and cancellation."
   -- [<A HREF="http://www.jstor.org/stable/2949777">@Jstor</A>]['08],
   [<A HREF="http://dx.doi.org/10.1137/0702016">doi:10.1137/0702016</A>]['13].
   NB. U is unitary if, U U^* = U^* U = I, where ^* is conjugate transpose.
   Also see SVD@[<A HREF="http://en.wikipedia.org/wiki/Singular_value_decomposition">wiki</A>]['13].

%A P. H. Schonemann
%T A generalized solution of the orthogonal Procrustes problem
%J Psychometrika
%V 21
%P 1
%P ?-?
%M MAR
%D 1966
%K jrnl, c1966, c196x, c19xx, zz1113, stats, maths, orthogonal matrix,
   Procrustes problem, nearest, approximation, least squares, linear, SVD,
   line fitting
%X "A soln T of the least-squares problem, A T = B+E, given A and B, s.t.
   trace(E' E) = minimum and T' T = I, is presented. ... compared to a less
   gen. soln Green[5]. The pres. soln ... applicable to matrices A and B which
   are of less than full column rank. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/BF02289451">www</A>]['13], or
      [<A HREF="http://www2.psych.purdue.edu/~phs/pdf/3.pdf">purdue</A>]['13].
   ("equivalent to finding the nearest orthogonal matrix to a given matrix
    M=A^T B. To do this find this orth.matrix R using SVD, M=U S V*, R=U V*."
   -- OPP@[<A HREF="http://en.wikipedia.org/wiki/Orthogonal_Procrustes_problem">wikip</A>]['13].)
   [Also search for: Procrustes].

%A A. Mukhopadhyay
%T The square root of a graph
%J J. Combin. Theory
%V 2
%N 3
%P 290-295
%M MAY
%D 1967
%K jrnl, c1967, c196x, c19xx, zz0914, maths, graph, square root, sqrt
%X "... presents a soln to the problem of characterizing graphs that have at
   least one square-root graph. The characterization is stated in terms of
   existence of a set of complete subgraphs of the given graph satisfying
   certain properties."
   -- [<A HREF="http://dx.doi.org/10.1016/S0021-9800(67)80030-9">doi:10.1016/S0021-9800(67)80030-9</A>]['14].
   [Also search for: sqrt graph maths].

%A B. Weisfeiler
%A A. Leman
%T The reduction of a graph to canonical form and the algebra which
   appears therein
%J NTI, Ser.2
%D 1968
%O English trans. by G.Ryabov
%K c1968, c196x, c19xx, zz1120, WL, graph, graphs, isomorphism, maths,
   canonical, automorphism, certificate, algorithm
%X "We consider an alg. for the reduction of a given finite multigraph G to
   canonical form. Therein the new invariant of a graph appears - the
   algebra A(G). ..."
   -- [<A HREF=" https://www.iti.zcu.cz/wl2018/pdf/wl_paper_translation.pdf">www</A>]['20].
    [Also search for: maths graph isomorphism].

%A F. Harary
%T Graph Theory
%I AddisonWesley
%D 1969
%K book, text, c1969, c196x, c19xx, Harary, maths, graph, graphs
%X 1st ed 1969.
   On demand ed 1994; us$71; uk us isbn:0201410338; uk us isbn13:978-0201410334.

%A G. Spencer-Brown
%T Laws of Form
%I AllenAndUnwin
%D 1969
%K book, c1969, c196x, c19xx, distinction, distinctions, calling, crossing,
   spatial forms, maths, philosophy, primary, boundary algebra, zz0407
%X reprinted by Cognizer c1994: isbn:0963989901; isbn13:9780963989901.
   (Hard to know what to make of it.-)
   Review by [<A HREF="http://dx.doi.org/10.1038/2231392b0">Varley@nature</A>]['07] '69.
   [<A HREF="http://en.wikipedia.org/wiki/Laws_of_Form">LOF@wikip</A>]['07],
   [<A HREF="http://www.lawsofform.org/">lawsofform.org</A>]['07].

%A R. P. Langlands
%T Problems in the theory of automorphic forms
%S Lectures in modern analysis and applications, III, Lecture Notes in Maths
%V 170
%P 18-61
%D 1970
%K conf, maths, c1970, c197x, c19xx, zz0524, Langlands conjecture, program,
   programme, reductive groups, group representation, theory, number field
%X "There has recently been much interest, if not a tremendous amount of
   progress, in the arithmetic theory of automorphic forms. In this lecture I
   would like to present the views not of a number theorist but of a student of
   group representations ..."
   -- [<A HREF="https://doi.org/10.1007/BFb0079065">doi:10.1007/BFb0079065</A>]['24].
   Also see Lprogram@[<A HREF="https://en.wikipedia.org/wiki/Langlands_program">wikip</A>]['24].

%A G. Golub
%A C. Reinsch
%T Singular value decomposition and least squares solutions
%J Num. Math.
%V 14
%N 5
%P 403-420
%M APR
%D 1970
%K jrnl, c1970, c197x, c19xx, SVD, matrix, matrices, pseudo inverse, solution,
   linear algebra
%X pdf: [<A HREF="http://dx.doi.org/10.1007/BF02163027">doi:10.1007/BF02163027</A>]['08].
   (Also see SVD@[<A HREF="https://en.wikipedia.org/wiki/Singular_value_decomposition">wikip</A>]['16].)

%A S. MacLane
%T Categories for the Working Mathematician
%D 1971
%I SpringerVerlag
%K book, text, introduction, intro, category theory, maths, methematics,
   natural transformations, c1971, c197x, c19xx, adjoint functor, functors,
   monads, monoidal
%X pp272;                  c1994;  isbn:0387900357.
   pp314;  us$65;  2nd edn c1998;  isbn:0387984038.

%A H. Kuki
%T Complex gamma function with error control
%J CACM
%V 15
%N 4
%P 262-272
%M APR
%D 1972
%K jrnl, CACM, c1972, c197x, c19xx, factorial, Gamma, log gamma, continuous
%X [<A HREF="http://doi.acm.org/10.1145/361284.361296">doi:10.1145/361284.361296</A>]['07]
   Also see algorithm 421, Fortran: [<A HREF="http://doi.acm.org/10.1145/361284.361298">doi:10.1145/361284.361298</A>]['07]
   (NB. Gamma n = (n-1)! when n is an +int)

%A H. Kuki
%T Algorithm 421: complex gamma function with error control [S14]
%J CACM
%V 15
%N 4
%P 271-272
%M APR
%D 1972
%K algorithm, CACM, c1972, c197x, c19xx, factorial, Gamma, log gamma, logGamma,
   lnGamma, gammaLog, gammaLn
%X "... Fortran program computes either the gamma function or the loggamma
   function of a complex variable in double precision. In addition, it
   provides an error estimate of the computed answer. ..."
   [<A HREF="http://doi.acm.org/10.1145/361284.361298">doi:10.1145/361284.361298</A>]['07]
   accompanying paper [<A HREF="http://doi.acm.org/10.1145/361284.361296">doi:10.1145/361284.361296</A>].
   (NB. Gamma n = (n-1)! when n is an +int.)

%A D. J. Rose
%T A graph-theoretic study of the numerical solution of sparse positive
   definite systems of linear equations
%B Graph theory and computing
%I AcademicPress, NewYork
%P 183-217
%D 1972
%K chapter, c1972, c197x, c19xx, zz1118, sparse matrix, matrices, fill in,
   fillin, equation, chordal, triangulation, completion, maths, graph,
   elimination game
%X "... an overview of a graph-theoretic study of the numerical soln of sparse
   +ve definite systems of linear equns. By following the formulation of
   elimination as a combinatorial process a considerable insight into the
   elimination process by studying the evolution of the cycle structure & the
   vertex-separator, or cut-set, structure of a graph under elimination can be
   gained. ... A g.-theor. approach for dealing with sparse systems in regard to
   Gaussian elimination is to attempt to find permutation matrices P, Q s.t.
   A=PMQ, which is block lower triangular, as in this case it is necessary only
   to decompose the diagonal blocks of PMQ. ..."
   -- [<A HREF="https://doi.org/10.1016/B978-1-4832-3187-7.50018-0">doi:10.1016/B978-1-4832-3187-7.50018-0</A>]['18].
   (Also see,
   "... If a chordal completion of a graph is given, a seq. of steps in which
   to perform Gaussian elimination to achieve this fill-in pattern can be found
   by computing an elimination ordering of the resulting chordal graph. In this
   way, the minimum fill-in problem can be seen as equivalent to the minimum
   chordal completion problem. ..."
   -- chordal@[<A HREF="https://en.wikipedia.org/wiki/Chordal_completion">wikip</A>]['18].)
   [Also search for: graph triangulation], or try minimum/minimal, fillin, etc..

%A F. Black
%A M. Scholes
%T The pricing of options and corporate liabilities
%J J. of Political Economy
%V 81
%N 3
%P 637-654
%M MAY-JUN
%D 1973
%K jrnl, c1973, c197x, c19xx, Black, Scholes, Merton, economics, option,
   options, put, call, trading, derivatives, liability, finance, market,
   valuation, discount, corporate bond, default, price, risk, risks, security,
   securities, delta hedge, hedging, financial instrument, banking, GFC
%X 1831029@[<A HREF="http://www.jstor.org/stable/1831029">Jstor</A>].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Black-Scholes">wikip</A>].)

%A F. Harary
%A R. C. Read
%T Is the null-graph a pointless concept?
%J Proc. of the Capital Conf. on Graph Theory & Combinatorics
%W George Washington U., 1973
%I SpringerVerlag
%S LNM
%V 406
%P 37-44
%M JUN
%D 1973
%K conf, c2014, c201x, c20xx, zz0814, maths, empty, null, graph, network,
   graphs, no, zero, vertices, defn
%X "The graph with no points & no lines is discussed critically. Arguments for
   & against its official admittance as a g. are presented. This is accompanied
   by an extensive survey of the literature. Paradoxical properties of the
   null-graph are noted. No conclusion is reached."  [NB. 'no points']
      Null-graph:  no vertices (& no edges), probably not ok.
      Empty-graph: no edges, is ok if |V| > 0.
   -- [<A HREF="http://dx.doi.org/10.1007/BFb0066433">doi:10.1007/BFb0066433</A>]['14].
   (Also see null_G@[<A HREF="http://en.wikipedia.org/wiki/Null_graph">wikip</A>]['14].)

%A R. W. Robinson
%T Counting labeled acyclic digraphs
%B New Directions in the Theory of Graphs
%I AcademicPress
%P 239-273
%D 1973
%K conf, c1973, c197x, c19xx, maths, graph, graphs, DAG, DAGs, count,
   directed, enumerate, labelled, labeled, A003024
%X "The # of DAGs on n labelled vertices, a_n, is
    1, 1, 3, 25, 543, 29281, 3781503, ... (sequence A003024 in the OEIS),
    a_n = SUM_{k=1}^n (-1)^{k-1} n_C_k 2^{k(n-k)} a_{n-k}"
   -- DAG@[<A HREF="https://en.wikipedia.org/wiki/Directed_acyclic_graph">wikip</A>]['18].
   NB. "labeled vertices".
   (Conf, uk us isbn:012324255X; uk us isbn13:978-0123242556.)
   [Also search for: counting unlabeled DAGs].
   (Also see, Harary, Frank; Palmer, Edgar M. (1973),
   'Graphical Enumeration,' AcademicPress, p.19, uk us isbn:0123242452.)

%A R. Sherman Lehman
%T Factoring large integers
%J Math. of Comp.
%V 28
%N 126
%P 637-646
%M APR
%D 1974
%K jrnl, c1974, c197x, c19xx, zz0823, integer, factorisation, factorization,
   algorithm, Fermat, method, squares
%X "A modification of F.'s difference of squares method is used for factoring
   large ints. ... permits factoring $n$ in $O(n^{1/3})$ elementary ops., where
   +, -, x, div, or the extraction of a square root is considered as an
   elementary op.. A principal part is played by the use of a dissection of the
   continuum similar to the Farey dissection. This has been programmed for
   n <= 1.05 x 10^{20} on the CDC 6400."
   -- [<A HREF="https://doi.org/10.2307/2005940">doi:10.2307/2005940</A>]['23],
      [<A HREF="https://www.jstor.org/stable/2005940">jstor:2005940</A>]['23].
   [Also search for: integer factorisation algorithm].
   (Also see FFM@[<A HREF="https://en.wikipedia.org/wiki/Fermat%27s_factorization_method">wikip</A>]['23].)

%A V. Chvatal
%T A combinatorial theorem in plane geometry
%J J. of Combinatorial Theory, Ser. B
%I Elsevier
%V 18
%N 1
%P 39-41
%M FEB
%D 1975
%K jrnl, c1975, c197x, c19xx, maths, geometry, art gallery problem,
   museum problem, theorem, defn, definition, guards, guarding,
   watchman, watchmen
%X [<A HREF="http://dx.doi.org/10.1016/0095-8956(75)90061-1">doi:10.1016/0095-8956(75)90061-1</A>]['12].
   "... originates from a real-world problem of guarding an art gallery with
   the min. number of guards which together can observe the whole gallery. ..."
   "... floor(n/3) guards are always sufficient, and sometimes necessary, to
   guard a simple polygon with n vertices. ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Art_gallery_problem">wikip</A>]['12].
   [Also search for: art gallery problem].

%A E. Szemeredi
%T On sets of integers containing no k elements in arithmetic progression
%J Acta Arithmetica
%V 27
%P 199-245
%D 1975
%K jrnl, c1975, c197x, c19xx, zz0312, Maths, theorem, Erdos Turan conjecture,
   arithmetic progressions, set, integer, element, series, density,
   combinatorics
%X "... density d, 0 < d < 1, for every integer k there is a number N(d,k)
   s.t.  every subset of {1, ..., N} of cardinality dN contains an arithmetic
   progression of length k, provided that N > N(d,k). ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Szemeredi%27s_theorem">wikip</A>]['12],
      [<A HREF="http://www.ams.org/mathscinet-getitem?mr=0369312">ams</A>]['12].
   (In 2012 E.S. won the Abel prize, us$1m, [<A HREF="http://www.abelprize.no/c54147/seksjon/vis.html?tid=54148&strukt_tid=54147">www</A>]['12].)

%A H. Barrow
%A R. Burstall
%T Subgraph isomorphism, matching relational structures and maximal cliques
%J IPL
%V 4
%N 4
%P 83-84
%D 1976
%K jrnl, IPL, c1976, c197x, c19xx, zz0920, maths, graph, maximal clique,
   matching
%X -- [<A HREF="https://doi.org/10.1016/0020-0190(76)90049-1">doi:10.1016/0020-0190(76)90049-1</A>]['20].
   (Also see MCS@[<A HREF="https://en.wikipedia.org/wiki/Maximum_common_subgraph">wikip</A>]['20].)
   [Also search for: graphAlignment].

%A T. Ohtsuki
%A L. K. Cheung
%A T. Fujisawa
%T Minimal triangulation of a graph and optimal pivoting order in a
   sparse matrix
%V 54
%N 3
%P 622-633
%M JUN
%D 1976
%K jrnl, c1976, c197x, c19xx, zz1018, maths, graph, triangulated, chordal,
   sparse, matrix factorisation, factorization, fill in, fillIn, elimination,
   minimal, OCF vertex
%X "... problem of finding a minimal triangulation of an undirected graph
   G=(V,E), where a tri. is a set T such that every cycle in G=(V,E U T) has a
   chord. A tri. T is minimal (minimum) if no tri. F exists such that F is a
   proper subset of T (|F| < |T|) & an ordering alpha is optimal (optimum) if a
   minimal (minimum) tri. is generated by alpha. A minimum tri. (optimum
   ordering) is nec. minimal (optimal), but the converse is not nec. true. A
   nec. & sufficient condition for a tri. to be minimal is presented. This leads
   to an alg. for finding an optimal ordering alpha which produces a minimal set
   of 'fill-in' when the process is viewed as triangular factorization of a
   sparse matrix.
   -- [<A HREF="https://doi.org/10.1016/0022-247X(76)90182-7">doi:10.1016/0022-247X(76)90182-7</A>]['18].
   [Also search for: minimal triangulation] and [also search for: elimination].

%A R. W. Robinson
%T Counting unlabeled acyclic digraphs
%J Combinatorial Maths. V: Proc. 5th Australian Conf.
%P 24-26
%M AUG
%D 1976
%K conf, c1976, c197x, c19xx, maths, graph, graphs, DAG, DAGs, count,
   directed, enumerate, unlabeled, unlabelled
%X "The previously known ways to count acyclic digraphs, both labeled & unlab'd,
   are reviewed. Then a new method of enumerating unlabeled acyclic digraphs is
   developed. It involves computing the sum of the cyclic indices of the
   automorphism groups of the acyclic digraphs, achieving a considerable gain in
   efficiency through an application of the inclusion-exclusion principle.
   Numerical results are reported on, & a table of the #s of unlabeled acyclic
   digraphs on up to 18 points [vertices] is included."  (1976 but online 2006.)
   NB. "unlabeled DAGs".   Conf, uk us isbn13:978-3540085249.
   -- [<A HREF="https://doi.org/10.1007/BFb0069178">doi:10.1007/BFb0069178</A>]['18].
   [Also search for: Counting labeled DAGs].

%A S. M. Ulam
%T Adventures of a Mathematician
%I Scribner, N.Y.
%P 281
%D 1976
%K book, text, math, maths, Ulam, c1976, c197x, c19xx

%A J. Moses
%T An introduction to the Risch integration algorithm
%J ACM/CSC-ER
%I ACM
%P 425-428
%D 1976
%K symbolic integration, integrate, c1976, c197x, c19xx, zz0307, integrability,
   integral, elementary functions, function, exponential, logarithmic,
   algebraic, algebra
%X "Risch's decision procedure for determining the integrability in closed form
   of the elementary functions of the calculus is presented via examples. The
   exponential & logarithmic cases of the algorithms had been implemented for
   the MACSYMA system several years ago. The implementation of the algebraic
   case of the algorithm is the subject of current research."
   -- pdf@[<A HREF="http://doi.acm.org/10.1145/800191.805632">doi:10.1145/800191.805632</A>]['07] [6 refs].

%A D. E. Knuth
%T Big Omicron and big Omega and big Theta
%J SIGACT
%I ACM
%V 8
%N 2
%P 18-24
%D 1976
%K big Oh, O, bigO, bigOh, complexity, algorithm, c1976, c197x, c19xx,
   math, maths, algorithmic, analysis, time, space, is order, origins,
   history, notation, little
%X pdf: [<A HREF=" http://doi.acm.org/10.1145/1008328.1008329">doi:10.1145/1008328.1008329</A>]['05] [9 refs].

%A M. Gardner
%T Mathematical Games, Nov. 1977, in which joining sets of points by
   lines leads into diverse (and diverting) paths
%J Sci. Amer.
%M NOV
%D 1977
%K c1977, c197x, c19xx, zz0219, Graham's number, Grahams, large, big, enormous,
   vast, integers, Ramsey theory, g64, graphs, maths, uparrow notation
%X SciAm pdf@[<A HREF="https://www.scientificamerican.com/article/mathematical-games-1977-11/">www</A>]['19] us$8,
   also [<A HREF="https://doi.org/10.1038/scientificamerican1177-18">doi:10.1038/scientificamerican1177-18</A>]['19] us$8.
   (Also see,
   "Graham's number is an enormous number that arises as an upper bound on the
   answer of a problem in the mathematical field of Ramsey theory. It is named
   after mathematician Ronald Graham, who used the number as a simplified
   explanation of the upper bounds of the problem he was working on in
   conversations with popular science writer Martin Gardner. ..."
   -- GNum@[<A HREF="https://en.wikipedia.org/wiki/Graham%27s_number">wikip</A>]['19].)

%A E. Szemeredi
%T Regular partitions of graphs
%B Problemes combinatoires et theorie des graphes,
   Colloq. Internat. CNRS, Univ. Orsay, Orsay, 1976
%P 399-401
%D 1978
%K conf, c1978, c197x, c19xx, zz1018, maths, graph, regularity lemma, edges,
   regular, partition
%X Also a 1975 TR,
   "A crucial lemma in recent work of the author (showing that k-term
   arithmetic progression-free sets of integers must have density zero) stated
   (approximately) that any large bipartite graph can be decomposed into
   relatively few 'nearly regular' bipartite subgraphs. In this note the author
   generalizes this result to arbitrary graphs, at the same time strengthening
   and simplifying the original bipartite result."
   -- STAN-CS-75-489@TR@[<A HREF="http://i.stanford.edu/pub/cstr/reports/cs/tr/75/489/CS-TR-75-489.pdf">stanf.</A>][10/'18].
   Also see, "In maths, the Szemeredi regularity lemma states that every large
     enough graph can be divided into subsets of about the same size so that the
     edges between different subsets behave almost randomly. ..."
     -- SRL@[<A HREF="https://en.wikipedia.org/wiki/Szemer%C3%A9di_regularity_lemma">wikip</A>]['18].

%A N. Stern
%T Age and achievement in mathematics: A case-study in the sociology of science
%J Social Studies of Science
%V 1
%N 1
%P ?-?
%M FEB
%D 1978
%K jrnl, c1978, c197x, c19xx, zz0118, mathematics, maths, mathematician,
   age, impact, importance
%X "... An analysis is performed to determine whether citations are a rough
   measure of quality in mathematics. Citations to work published by
   mathematicians who have been elected to the US National Academy of Sciences
   are compared with those to the work of a random sample of university-based
   American mathematicians. The study examines productivity & citation counts,
   to determine if there is a relationship between a m's age & achievement, & to
   test the claim that younger ms are more apt to do important work. Finally,
   this paper explores the difficulties peculiar to the sociological study of
   maths, which account for the reluctance of most sociologists of science to
   study this field."
   -- [<A HREF="https://doi.org/10.1177/030631277800800105">doi:10.1177/030631277800800105</A>]['18].
   (Also see [<A HREF="https://www.nature.com/articles/d41586-018-00513-8">www</A>][12/1/2018].)

%A H. Fredericksen
%A J. Maiorana
%T Necklaces of beads in k colors and k-ary de Bruijn sequences
%J Discrete Maths
%V 23
%N 3
%P 207-210
%D 1978
%K jrnl, necklace, c1978, c197x, c19xx, sequence, combinatorial, generate
   bead, colour, colours, color, FKM algorithm, de Bruijn, deBruijn
%X (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Recn/Necklaces/">necklaces</A>].)

%A S. Fisk
%T A short proof of Chvatal's watchman theorem
%J J. of Combinatorial Theory, Series B
%V 24
%N 3
%P 374
%M JUN
%D 1978
%K jrnl, c1978, c197x, c19xx, art gallery problem, museum, three, proof
%X "This note contains a short proof of Chvatal's Watchman Theorem using the
   existence of a three-coloring of a triangulated polygon."
   -- [<A HREF="http://dx.doi.org/10.1016/0095-8956(78)90059-X">doi:10.1016/0095-8956(78)90059-X</A>]['12].
   [Also search for: art gallery problem].

%T Statistics Problem Solver
%I REA
%D 1978
%P 1080
%K book, text, REA, c1978, c197x, 19xx, stats, statistics, introduction, teach,
   course, teaching, probability, learning
%X "Beginning with basic probability and through binomial, normal, joint,
   discrete, and continuous distributions. Other sections deal with sampling,
   confidence intervals, hypothesis testing, regression, and correlation
   analysis. An extensive number of applications are included."
   pb us$20; us isbn:087891515X; us isbn13:978-0878915156.

%A R. S. Stepleman
%A N. D. Winarsky
%T Adaptive numerical differentiation
%J Math. of Computation
%V 33
%N 148
%P 1257-1264
%M OCT
%D 1979
%K jrnl, c1979, c197x, c19xx, derivative, numerical computation, computing,
   methods, finite difference, differences, approximation
%X "... d(h) = (f(x+h)-f(x-h)/(2h) is a delicate task. ... yield efficiently
   the theoretical max. # of digits for the given machine precision."
      "... for essentially all diff. f ... d(h[i]) tends monot. to f'.  Under
   stronger hypotheses |d(h[i])-d(h[i+1])| <= |d(h[i])-d(h[i-1])|  ... The basic
   idea ...  choose {h[i] -> 0 monot. ... Let h[j] be the 1st h[i] ... s.t.
   either of the above criteria are violated, then approx f' by d(h[j-1])."
   -- [<A HREF="http://links.jstor.org/sici?sici=0025-5718%28197910%2933%3A148%3C1257%3AAND%3E2.0.CO%3B2-F">paper@Jstor</A>]['08].

%A R. R. Stoll
%T Set Theory and Logic
%I DoverPubl.
%P 496
%D 1979
%K book, text, c1979, c197x, c19xx, maths, logic, set, theory, sets,
   relations, relation, relational, boolean algebra
%X pb us$13; uk us isbn:0486638294; uk us isbn13:978-0486638294.
   "... explains sets and relations, the natural number sequence and its
   generalization, extension of natural numbers to real numbers, logic,
   informal axiomatic mathematics, Boolean algebras, informal axiomatic set
   theory, several algebraic theories, and first-order theories. ..."

%A D. M. Cvetkovic
%A M. Doob
%A H. Sachs
%T Spectra of Graphs
%A AcademicPress
%P 451
%D 1980
%K book, text, c1980, c198x, c19xx, maths, graph, graphs, theory, spectrum,
   spectra, spectral, analysis
%X 3rd ed 1998; uk us isbn:3527296859; uk us isbn13:978-3527296859.
   Ref in Biggs c1993.

%A B. D. McKay
%T Graph Isomorphism (1980 ?)
%B Encyclopedia of Algorithms
%E M.-Y. Kao
%I SpringerVerlag
%V 7
%P ?-?
%D 1980 (?)
%K c1980, c198x, c19xx, survey, intro, mathematics, maths, graph, isomorphism,
   automorphism, symmetry group, matching, problem, algorithm
%X "The problem of determining isomorphism of 2 combinatorial structures is a
   ubiquitous one, with applications in many areas. The paradigm case [here] is
   isomorphism of 2 graphs. ...  Graph isomorphism is closely related to many
   other types of isomorphism of combinatorial structures. In the section
   entitled 'Applications', several examples are given."
   ed 2008(!); uk us isbn:0387301623; uk us isbn13:978-0387307701.
   -- [<A HREF="http://dx.doi.org/10.1007/978-0-387-30162-4_172">doi:10.1007/978-0-387-30162-4_172</A>]['10],
   online@[<A HREF="http://www.springerlink.com/content/u635g14250p5j215/fulltext.html">html</A>]['10].

%T Linear Algebra Problem Solver
%I REA
%D 1980
%P 1024
%K book, text, c1980, c198x, c19xx, REA, linear algebra, introduction, teaching,
   course
%X "For linear algebra courses, as well as for courses in computers, physics,
   engineering, and sciences which use linear algebra. Concentrations on
   solutions to applied problems in economics, mechanics, electricity,
   chemistry, geometry, business, probability, graph theory, and
   linear programming."
   pb us$20; us isbn:0878915184; us isbn13:978-0878915187.

%A M. Yannakakis
%T Computing the minimum fill-in is NP-complete
%J SIAM J. Alg. Disc. Methods
%V 2
%N 1
%P 77-79
%M MAR
%D 1981
%K jrnl, c1981, c198x, c19xx, zz1018, maths, graph, graphs, minimum, fill-in,
   fillin, chordal, triangulation, triangulated, elimination, NPC,
   linear arrangement, OLAP
%X "We show that the following problem is NP-complete. Given a graph, find the
   minimum # of edges (fill-in) whose addition makes the graph chordal. This
   problem arises in the solution of sparse symmetric positive definite systems
   of linear equations by Gaussian elimination."
   -- [<A HREF="https://doi.org/10.1137/0602010">doi:10.1137/0602010</A>]['18].
   (NB. 'minimum' not 'minimal'. Proof by reduction from
    the 'optimal linear arrangement problem'.)

%A J. E. Dennis
%A D. M. Gay
%A R. E. Welsch
%T Algorithm 573 NL2SOL - An adaptive nonlinear least-squares algorithm [E4]
%J TOMS
%I ACM
%V 7
%N 3
%P 369-383
%M SEP
%D 1981
%K jrnl, TOMS, c1981, c198x, functionMin, c19xx, optimise, optimisation,
   optimize, optimization, function, max, min, maximize, maximise, minimize,
   minimise, minimisation, minimization, maximization, quasi-Newton,
   numerical methods, algorithm
%X "... The alg. amounts to a variation on Newton's method in which part of the
   Hessian matrix is computed exactly and part is approximated by a secant
   (quasi-Newton) updating method. ..."
   -- [<A HREF="http://doi.acm.org/10.1145/355958.355966">doi:10.1145/355958.355966</A>]['07].
   [Also search for: functionMin].

%T Advanced Calculus Problem Solver
%I REA
%D 1981
%P 1056
%K book, text, REA, c1981, c198x, c19xx, maths, mathematics, calculus,
   differential, differentiation, integration,introduction, teaching, help
%X "The theoretical aspects of calculus are emphasized. Advanced theories of
   differentiation, integration, sequences, series, and transforms are dealt
   with extensively."
   pb us$28; us isbn:0878915338; isbn13:978-0878915330.

%A L. M. Adleman
%A C. Pomerance
%A R. S. Rumely
%T On distinguishing prime numbers from composite numbers
%J Ann. Math.
%V 117
%N 1
%P 173-206
%D 1983
%K jrnl, maths, prime number, primality, c1983, c198x, c19xx, Bosma,
   test, testing
%X O( (ln n)**(c*log(log(log n))) )-time for some c > 0.
   MRNUMBER = {MR683806 (84e:10008)} [<A HREF="http://www.ams.org/mathscinet-getitem?mr=84e:10008">ams</A>]['05].
   [Also search for: primality].

%A E. S. Barnes
%A N. J. A. Sloane
%T The optimal lattice quantizer in three dimensions
%J J. on Algebraic and Discrete Methods
%I SIAM
%V 4
%N 1
%P 30-41
%D 1983
%K jrnl, SIAM, c1983, c198x, c19xx, zz0408, 3D, dimension, lattice konstant, G3,
   lattices, cubic, quantize, quantization, quantise
%X "The body-centered cubic lattice is shown to have the smallest mean squared
   error of any lattice quantizer in three dimensions, assuming that the input
   to the quantizer has a uniform distribution."
   "Thm 1. For any 3-D lattice L, G(L) >= 19/(192 . 2**(1/3)) = 0.0785433...,
   with equality iff L is equiv. to the body centered cubic lattice D*[3].
   Furthermore for no other lattice is G(L) a local minimum."  [p.1]
   -- [<A HREF="http://www.att.com/~njas/doc/optimal.pdf">pdf@att.com</A>]['08].
   [Also search for: lattice constant]    (via enesm).

%A C. Beeri
%A R. Fagin
%A D. Maier
%A M. Yannakakis
%T On the desirability of acyclic database schemes
%J JACM
%V 30
%N 3
%P 479-513
%M JUL
%D 1983
%K jrnl, JACM, c1983, c198x, c19xx, zz0518, maths, graph, acyclic, DB, DBMS,
   chordal, triangulation, hypergraph, dependency, dependencies, acyclicity,
   simplicial, join, properties
%X "A class of database schemes, called acyclic, was recently introduced. ...
   shown that this class has a # of desirable properties. In particular, several
   desirable properties that have been studied by other researchers in very
   different terms are all shown to be eqmvalent to acylicity.  [&] several
   equiv. characterisations of the class in terms of graphs & hypergraphs are
   given, & a simple alg. for determining acyclicity is presented.  Also given
   are several equivalent characterizations of those sets M of multivalued
   dependencies s.t. M is the set of multivalued dependencies that are the
   consequences of a given join dependency.  Several characterizations for a
   conflict-free (in the sense of Lien) set of multivalued dependencies are
   provided."
   -- pdf@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/citations;jsessionid=56904DE8E1E821E70D98F36E4C5C2597?doi=10.1.1.69.4653">c'teseer</A>]['18].

%A R. E. Tarjan
%A M. Yannakakis
%T Simple linear-time algorithms to test chordality of graphs, test acyclicity
   of hyper-graphs, and selectively reduce acyclic hypergraphs
%J SIAM J. on Comp.
%V 13
%N 3
%P 566-579
%D 1984
%K jrnl, c1984, c198x, c19xx, zz0521, simplicial, chordal, graph, graphs, maths,
   acyclic, algorithm, test
%X "Chordal gs. arise naturally in the study of Gaussian elim'n on sparse
   symmetric matrices; acyclic hypergraphs arise in the study of rel'l data
   bases. Rose, Tarjan & Lueker [SIAM J.Comput., 5 ('76), pp. 266-283] have
   given a linear-time alg. to test whether a graph is chordal, which Y. has
   modified to test whether a hypergraph is acyclic. Here we develop a
   simplified linear-time test for g.chordality & hyperg. acyclicity. The test
   uses a new kind of g. (& hyperg.) search, which we call maximum cardinality
   search. A variant of the method gives a way to selectively reduce acyclic
   hypergs., which is needed for evaluating queries in acyclic rel. DBs."
   -- [<A HREF="https://doi.org/10.1137/0213035">doi"10.1137/0213035</A>]['21].
   [Also search for: chordal].

%A A. V. Goldberg
%T Finding a maximum density subgraph
%I EECS, U.Cal.Berkeley
%R UCB/CSD-84-171
%D 1984
%K TR, c1984, c198x, c19xx, zz1119, densest subgraph, problem, fast, algorithm,
   maximum density, dense, maths, graph, minimum capacity cut, network flow,
   max, generalized clique
%X pdf@[<A HREF="https://www2.eecs.berkeley.edu/Pubs/TechRpts/1984/5956.html">ucb</A>]['19].
   (Also see,
   "... G={E,V}, S={E_S,V_S} is a subgraph of G,
   the density of S equals |E_S|/|V_S| ..."
   -- DSg@[<A HREF="https://en.wikipedia.org/wiki/Dense_subgraph">wikip</A>]['19].
   [Also search for: Dense Subgraph problem].

%A G. Chartrand
%T Introductory Graph Theory
%I DoverPubl
%P 320
%M DEC
%D 1984
%K book, text, c1984, c198x, c19xx, maths, graph, graphs
%X 1st ed 1984; pb us$100; uk us isbn:0486247759; uk us isbn13:978-0486247755.
   "... covers all basics of theory and application, inc. mathematical models,
   elementary concepts of graph theory, transportation problems, connection
   problems, party problems, diagraphs and math.models, games and puzzles,
   graphs and social psychology, planar graphs and coloring problems, and
   graphs and other mathematics."

%A R. Halin
%T On the representation of triangulated graphs in trees
%J Europ. J. Combinatorics
%V 5
%P 23-28
%D 1983
%K jrnl, c1983, c198x, c19xx, maths, graph, triangulated graphs, simplicial,
   chordal, intersection graph, tree, decomposition, treeDecomposition,
   junction, clique, join trees, infinite
%X "The intersection graph of a family of subtrees of a tree is always a
   triangulated g., & v.v. every finite triangulated g. can be rep. in this way.
   The analogous statement is in general not  true for infinite triangulated
   gs..  A characterization of the gs. which are 'tree-representable' in this
   sense is given by means of simplicial decompositions."
   -- [<A HREF="https://doi.org/10.1016/S0195-6698(84)80014-1">doi:10.1016/S0195-6698(84)80014-1</A>]['18].
      (Also see,
      "In graph theory, a 'tree decomposition' is a mapping of a graph into
      a tree that can be used to define the treewidth of the graph and speed
      up solving certain computational problems on the graph. ... also called
      junction trees, clique trees, or join trees ..."
      -- TD@[<A HREF="https://en.wikipedia.org/wiki/Tree_decomposition">wikip</A>]['18].)
   [Also search for: graph decomposition]  and  [also search for: simplicial].

%A R. E. Tarjan
%T Decomposition by clique separators
%J Discrete Math.
%V 55
%N 2
%P 221-232
%M JUL
%D 1985
%K jrnl, c1985, c198x, c19xx, zz0618, maths, graph, graphs, separator, clique,
   complete, colouring, coloring, simplicial, binary, tree, decomposition,
   algorithm, fill-in, Gaussian elimination, maximum clique, colouring,
   coloring, independent set
%X "... finding cliques (complete graphs) whose removal disconnects the graph.
   We give an O(nm)-time algorithm for finding a decomposition of an n-vertex,
   m-edge graph. We describe how such a decomposition can be used in
   divide-and-conquer algorithms for various graph problems, such as
   graph coloring and finding maximum independent sets. We survey classes of
   graphs for which such divide-and-conquer algs. are especially useful."
   "... The binary decomposition tree of a graph is far from unique ..."
   -- [<A HREF="https://doi.org/10.1016/0012-365X(85)90051-2">doi:10.1016/0012-365X(85)90051-2</A>]['18].
      Finds a use in 'optimal decomp by ...', H.-G. Leimer, 1993,
      Discr. Maths., 113, 99-123.
   [Also search for: decomposition defn]  and  [also search for: Leimer c1993].

%A L. Babai
%T Trading group theory for randomness
%J Proc, ACM Symp. on Theory of Computing
%P 421-429
%D 1985
%K conf, STOC, STOC17, c1985, c198x, c19xx, zz0115, theory, maths, complexity,
   classes, NP, coNP, NPC, AM, AMk, games, Goldwasser
%X "In a prev. paper [BS] we proved, using the elts of the theory of nilpotent
   groups, that some of the fundamental comp. problems in matrix groups belong
   to NP. ... were also shown to belong to coNP, assuming an unproven hypothesis
   concerning finite simple groups. The aim [here] is to replace most of the
   (proven & unproven) group theory of [BS] by elementary combinatorial
   arguments. The result we prove is that relative to a random oracle B, the
   mentioned matrix group problems belong to (NP*coNP)B. The problems we
   consider are membership in & order of a matrix group given by a list of
   generators. These problems can be viewed as multidimensional versions of a
   close relative of the discrete logarithm problem. Hence NP*coNP might be the
   lowest natural complexity class they may fit in. We remark that the results
   remain valid for black box groups where group ops. are performed by an
   oracle. The tools we introduce seem in their own right. We define a new
   hierarchy of complexity classes AM(k) 'just above NP', introducing Arthur vs.
   Merlin games, the bounded-away version of Papdimitriou's Games against
   Nature. We prove that in spite of their analogy with the polynomial time
   hierarchy, the finite levels of this hierarchy collapse to AM=AM(2). Using a
   combinatorial lemma on finite groups [BE], we construct a game by which the
   nondet. player (Merlin) is able to convince the random player (Arthur) about
   the relation [G]=N provided Arthur trusts conclns based on stat. evidence
   (such as a Slowly-Strassen type 'proof' of primality). One can prove that AM
   consists precisely of those languages which belong to NPB for almost every
   oracle B.  Our hierarchy has an interesting, still unclarified reln to
   another hierarchy obtained by removing the central ingredient from the User
   vs. Expert games of Goldwasser, Micali & Rackoff."
   -- [<A HREF="http://dx.doi.org/10.1145/22145.22192">doi:10.1145/22145.22192</A>]['15],
    & [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.130.3397">c'teseer</A>]['15].
   (Also see KWRegan's [<A HREF="http://rjlipton.wordpress.com/2011/06/28/name-that-graph/">blog</A>][28/6/'11].)

%A N. C. Wormald
%T Counting labelled chordal graphs
%J Graphs and Combinatorics
%V 1
%N 1
%P 193-200
%D 1985
%K jrnl, c1985, c198x, c19xx, zz1114, maths, graph, chordal, count, counting,
   number, triangulated
%X "An equn is derived which is sat. by special types of gen. fns for labelled
   c.graphs. This enables calc. of the # of labelled c.graphs with given #s of
   cliques of given sizes. From this is determined the # of n-vertex labelled
   chordal graphs with given connectivity. Calculations were completed for
   N <= 13."  (via FPj)
   -- [<A HREF="http://dx.doi.org/10.1007/BF02582944">doi:10.1007/BF02582944</A>]['14].

%A J. H. Conway
%A R. T. Curtis
%A S. P. Norton
%A R. A. Parker
%A R. A. Wilson
%T Atlas of Finite Groups. Maximal Subgroups and Ordinary Characters for
   Simple Groups. With computational assistance from J. G. Thackray
%I OUP
%D 1985
%K book, text, OUP, c1985, c198x, c19xx, zz0121, maths, group, simple groups,
   finite, monster, symmetry, sporadic, Lie, classification of, atlas,
   JHConway, John Horton Conway
%X 1st ed 1985; isbn:0198531990.
   Also see, "... The classification theorem states that the list of finite
   simple groups consists of 18 countably infinite families plus 26 exceptions
   that do not follow such a systematic pattern. ..."
   --  SGs@[<A HREF="https://en.wikipedia.org/wiki/Sporadic_group">wikip</A>]['21].

%A H. Fredericksen
%A I. J. Kessler
%T An algorithm for generating necklaces of beads in two colors
%J Discrete Maths
%V 61
%N ?
%P 181-188
%D 1986
%K jrnl, necklace, c1986, c198x, c19xx, sequence, combinatorial, generate
   bead, colour, colours, color, FKM
%X (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Recn/Necklaces/">necklaces</A>].)

%A H. Yserentant
%T On the multilevel splitting of finite element spaces
%J Numerische Mathematik
%V 49
%N 4
%P 379-412
%M JUL
%D 1986
%K jrnl, c1986, c198x, c19xx, sparse grid, grids, numerical approximation
%X [<A HREF="http://dx.doi.org/10.1007/BF01389538">doi:10.1007/BF01389538</A>]['07]

%A H.-J. Boehm
%A R. Cartwright
%A M. Riggle
%A M. J. O'Donnell
%T Exact real arithmetic: A case study in higher order programming
%J ACM Conference on LISP and Functional Programming
%P 162-173
%D 1986
%K conf, c1986, c198x, c19xx, real number, system, numbers, computer arithmetic,
   FP, high, reals, computer
%X pdf: [<A HREF="http://doi.acm.org/10.1145/319838.319860">doi:10.1145/319838.319860</A>]['07]. isbn:0897912004.
   [Also search for: computer arithmetic]  and  [also search for: FP numbers].

%A H.-J. Bandelt
%A H. Martyn Mulder
%T Distance-hereditary graphs
%J J. of Combinatorial Theory, Series B
%V 41
%N 2
%P 182-208
%M OCT
%D 1986
%K jrnl, c1986, c198x, c19xx, distance hereditary, completely separable,
   maths, graph, graphs, ptolemaic, theory
%X "Distance-hereditary graphs ... are connected graphs in which all induced
   paths are isometric. Examples of such g. are provided by complete
   multipartite gs. & ptolemaic gs.. Every finite distance-hereditary g. is
   obtained from K1 by iterating the following 2 operations: adding pendant
   vertices & splitting vertices. Moreover, distance-hereditary gs. are
   characterized in terms of the dist. fn d, or via forbidden isometric subgs.."
   [<A HREF="http://dx.doi.org/10.1016/0095-8956(86)90043-2">doi:10.1016/0095-8956(86)90043-2</A>]['08].

%A R. Diestel
%T Simplicial decomposition of graphs - some uniqueness results
%J J. Comb. Theory
%V 42
%S B
%P 133-145
%M APR
%D 1987
%K jrnl, JCT, c1983, c198x, c19xx, zz0618, maths, graph, simplicial,
   decomposition, decompose, prime, primes, simplices, cliques, attachment
%X "A simplicial decomposition of a graph G is the recursively defined analog to
   writing G as the union of two proper subgraphs overlapping in a complete
   graph (a 'simplex' [clique]). We consider simplicial decompositions into
   primes, i.e., into graphs that cannot be decomposed further in this way. Such
   decompositions can be used for characterizing suitable graph properties by
   giving a list of B of possible primes of their members g eps G, together with
   an explicit rule stating how exactly one must assemble the elements of B to
   obtain the members of G. For such characterizations results are needed
   asserting the independence of the factors as well as of the 'simplices of
   attachment' from the decomposition chosen. We prove such uniqueness results
   by characterizing both prime factors and simplices of attachment without
   reference to any particular decomposition. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0095-8956(87)90035-9">doi:10.1016/0095-8956(87)90035-9</A>]['18].
   [Also search for: simplicial]

%A R. Diestel
%T Simplicial decompositions of graphs: A survey of applications
%J Discr. Maths
%V 75
%N 1-3
%P 121-144
%M MAY
%D 1989
%K jrnl, survey, c1989, c198x, c19xx, simplicial graph decomposition, maths,
   algorithm, extremal, chordal, interval, separating
%X "We survey applications of simplicial decompositions (decompositions by
   separating complete subgraphs) to problems in graph theory. Among the areas
   of application are excluded minor theorems, extremal graph theorems, chordal
   and interval graphs, infinite graph theory and algorithmic aspects."
   -- [<A HREF="http://dx.doi.org/10.1016/0012-365X(89)90084-8">doi:10.1016/0012-365X(89)90084-8</A>]['18].
   [Also search for: simplicial].

%A T. S. Verma
%A J. Pearl
%T An algorithm for deciding if a set of observed independencies has a causal
   explanation
%J UAI
%D 1992
%K conf, UAI, UAI92, UAI1992, c1992, c199x, c19xx, zz0618, maths, graph, DAG,
   recovery, reconstruction, DAGs, partially directed, partiallyDAG, PDAG,
   causal model, models, d-separation, dSeparation, collider, DAGisomorphic
%X "... address the question of deciding whether there exists a causal model
   that explains ALL the observed dependencies & independencies. Formally, given
   a list M of conditional independence statements, it is required to decide
   whether there exists a directed acyclic graph (DAG) D that is perfectly
   consistent with M, namely, every statement in M, & no other, is reflected via
   d-separation in D. We present & analyze an effective alg. that tests for the
   existence of such a day, and produces one, if it exists."
   -- 1303.543@[<A HREF="https://arxiv.org/abs/1303.5435">arXiv</A>]['18],
      [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.49.5025">c'tes'er</A>]['18].
   [Also search for: PDAG]  and  [also search for: graph recovery algorithm].

%A C. D. Savage
%A T. M. Wang
%T A new algorithm for generating necklaces
%J Proc., 28th Annual Allerton Conf. on Communication, Control, and Computing
%P ?-?
%D 1992
%K conf, necklace, necklaces, c1992, c199x, c19xx, colors, colours, bead,
   beads, combinatorial, generate, permutations
%X "... generating the smallest [lex. earliest] rep. of all the
   n-bead necklaces of k-colours. ...  O(n*N(n,k))-time
   where N(n,k) is the # of necklaces with n beads of k colours. ..."
   -- [<A HREF="http://www.csc.ncsu.edu/faculty/savage/AVAILABLE_FOR_MAILING/necklace_allerton.ps">.ps</A>]['05].
   (A necklace is invariant under rotation, but not reflection, here;
   also see [<A HREF="http://www.allisons.org/ll/AlgDS/Recn/Necklaces/">necklaces</A>].)

%A W. H. Press
%A B. P. Flannery
%A S. A. Teukolsky
%A W. T. Vetterling
%T LU decomposition and its applications
%B Numerical Recipes in FORTRAN: The Art of Scientific Computing (2nd ed.)
%I CUP
%P 34-42
%D 1992
%K chapter, CUP, c1992, c199x, c19xx, numerical algorithm, LU decomposition,
   LU factorization, LDU, LUP, matrix, matrices
%X In book:
     2nd ed 1992; pb us$27; uk us isbn:0521437210; uk us isbn13:978-0521437219;
     1st ed 1989; hb us$50; uk us isbn:0521383307; uk us isbn13:978-0521383301.
   "... matrix A=LU where L and U are lower and upper triangular matrices ..."
   LU@[<A HREF="http://en.wikipedia.org/wiki/LU_decomposition">wikip</A>]['11].
   [Also search for: matrix decomposition].

%A F. K. Hwang
%A D. S. Richards
%A P. Winter
%T The Steiner Tree Problem
%I Elsevier NorthHolland
%S Annals of Discrete Maths.
%V 53
%D 1992
%K book, text, c1992, c199x, c19xx, Steiner tree problem, trees, optimisation,
   optimization, minimum, points, vertices
%X "The Steiner problem asks for a shortest network which spans a given set of
   points. Min. spanning networks have been well-studied when all connections
   are required to be between the given points. The novelty of the Steiner tree
   problem is that new auxiliary pts can be introduced between the original pts
   so that a spanning n/w of all the pts will be shorter than otherwise poss..
   These new pts are called Steiner pts ..."
   1st ed 1992, hb; uk us isbn:0-444-89098X; uk us isbn13:978-0444890986.
   [Also search for: Steiner Tree].

%A D. Dor
%A M. Tarsi
%T A simple algorithm to constract a consistent extension of a
   partially oriented graph
%R R-185
%I Cog. Sys. Lab., UCLA
%M OCT
%D 1992
%K TR, TR185, c1992, c199x, c19xx, Dorit, zz0718, maths, partially oriented,
   directed, graph, PDAG, hybrid, DAG, extension, causal, Vstructure, collider,
   independencies
%X "A partially directed acyclic graph, (pdag), is a g. which contains both
   directed & undir. edges, with no dir. cycle in its dir. subgraph. An oriented
   extension of a pdag G is a fully dir. acyclic graph (DAG) on the same
   underlying set of edges, with the same orientation on the directed subg. of
   G & the same set of vee-structures.  A vee-struct. is formed by two edges,
   directed toward a common head, while their tails are nonadjacent. A simple
   polynomial-time alg. is presented, to solve the following problem: Given a
   pdag, does it admit an oriented extension?  The problem was stated by Verma
   & Pearl, while studying the existence of causal explanation to a given set of
   observed independencies."          (Note, "polynomial-time".)
   "extend( G: pdag )
     { G' := G; A := G;
       while A is not empty do
        { Select a vertex x in A s.t.
          (a) x is a sink (no edge x -> y) and
          (b) for every vertex y adjacent to x with (x,y) undirected,
              y is adjacent to all other vertices which are adjacent to x;
          If no such x can be found then return (false, _); /*else...*/
          direct all edges involving x to x in G';
          A := A-x; /*remove x and all edges involving x*/
        }
       return (true, G');
     }"
   -- pdf@[<A HREF="ftp://ftp.cs.ucla.edu/pub/stat_ser/r185-dor-tarsi.pdf">ucla</A>]['18].
   [Also search for: PDAG]  and  [also search for: graph recovery algorithm].

%A N. Biggs
%T Algebraic Graph Theory
%P CUP
%P 213
%D 1993
%K c1993, c199x, c19xx, CUP, graph theory, graphs, book, text, characteristic,
   chromatic, polynomial, spectrum, spectral, spectra, eigenvalue, eigenvalues,
   maths
%X "...applications of linear algebra & matrix theory to the study of graphs;
   algebraic constructions such as adjacency matrix & the incidence matrix &
   their applications are discussed in depth. There follows an extensive account
   of the theory of chromatic polynomials, a subject that has strong links with
   the "interaction models" studied in theoretical physics & the th. of knots.
   ...last part deals with symmetry & regularity properties. ... are important
   connections with other branches of alg. combinatorics & group theory. ..."
   "The spectrum of a graph G is the set of numbers which are eigenvalues of
   [the adj. matrix] A(G) with their multiplicities"
   "characteristic polynomial, X(G;lambda), of G [is] det(lambda.I-A(G))"
   "X(G;lambda) = lambda^n + c[1]lambda^(n-1) + ... + c[n], ...
   -c[1] is the sum of the zeroes (ie of the eigenvalues) = 0,
   -c[2] is the # of edges of G,
   -c[2] is twice the # of triangles in G."
   2nd ed 1993, pb us$40; uk us isbn:0521458978; uk us isbn13:978-0521458979.
   1st ed 1974.
   -- <!-- email hillman at math washington edu --> C.Hillman 12/'94.

%A C. D. Godsil
%T Algebraic Combinatorics
%I ChapmanAndHall
%D 1993
%K c1993, c199x, c19xx, maths, mathematics, Graph theory, book, text
%X <!-- email: hillman@math.washington.edu --> via Christopher Hillman 12/'94.

%A G. W. Mackey
%T The scope and history of commutative and noncommutative harmonic analysis
%I American Mathematical Society
%D c 1992
%K mathematics, Harmonic analysis, AMS, book, text
%X <!-- email: hillman@math.washington.edu --> Christopher Hillman 12/'94

%A J. O. Coplien
%T To iterate is human, to recurse, divine
%J C++ Report
%V 10
%N 7
%P 43-51
%M JUL/AUG
%D 1998
%K cc, cplusplus, OO, OOP, recursive, recursion, iteration, Deutsch, Heller,
   haha, ha ha, quote, quotation, quotable, c1998, c199x, c19xx, zz0803
%X [The] title ... variously attributed to
   L. Peter Deutsch and Robert Heller. ...
   -- [<A HREF="http://www1.bell-labs.com/user/cope/Patterns/C%2b%2bReport/SpaceIII-1.html">paper</A>][8/'03].

%A L. H. Kauffman
%T On Knots
%I PrincetonUP
%D 1987
%K c1987, c198x, c19xx, mathematics, Knot theory, book, text
%X <!-- email: hillman@math.washington.edu --> Christopher Hillman 12/'94.

%A L. H. Kauffman
%T Knots and Physics
%I World Scientific
%D 1991
%K c1991, c199x, c19xx, mathematics, Knot polynomials, Mathematical physics,
   book, text
%X <!-- email: hillman@math.washington.edu --> Christopher Hillman 12/'94.

%A G. Polya
%A R. C. Read
%T Combinatorial Enumeration of Groups, Graphs, and Chemical Compounds
%I SpringerVerlag
%P 148
%D 1987
%K book, text, c1987, c198x, c19xx, mathematics, maths, group, graph theory,
   compound, cycle decomposition, enumerate
%X "This is a translation of the 1937 paper by Polya where he showed his theorem
   on enumeration modulo a group. This is his prototypical example: one colours
   the vertices of an octahedron (say, three red, two blue, one yellow); in how
   many ways can this be done, taking into account rotational equivalence? ...
   ... [and] a 40-page supplement by Read on 'The legacy of Polya's paper'."
   1st ed 1987; hb us$127; uk us isbn:0387964134; uk us isbn13:978-0387964133.
 * G. Polya, 'Kombinatorische Anzahlbestimmungen fur Gruppen, Graphen
      und Chemische Verbindungen',
      Acta Mathematica (Springer Verlag), 68(1), pp.145-254, 1937.
   -- [<A HREF="http://dx.doi.org/10.1007/BF02546665">doi:10.1007/BF02546665</A>]['10].

%A D. M. Berman
%A K. W. Holladay
%T Homomorphism polynomials of chemical graphs
%J J. Math. Chemistry
%V 1
%N 4
%P 405-414
%M NOV
%D 1987
%K jrnl, c1987, c198x, c19xx, maths, graph, chemical compound, compounds,
   structure, structures, homomorphic, homomorphism polynomial, Randicacute
%X "... a graph G is homomorphic to a graph H if there is a mapping p from the
   Vs. of G onto the Vs. of H s.t. p(u) and p(nu) are adjacent in H whenever u
   & nu are adj. in G. The homomorphism polynomial of a graph G is a p. in 2
   variables that counts the # of homomorphisms of G onto the complete graph of
   each order. This polynomial can be computed recursively in an analog to the
   chromatic polynomial. ... present some results regarding the homomorphism
   polynomials of the graphs of chemical compounds - in particular, alkane
   isomers. The coeffs. of the homomorphism polynomial can be used to predict
   the rankings of compounds with respect to several chemical properties.
   ... seem to refine [results] by Randicacute et al. from path lengths."
   -- [<A HREF="http://dx.doi.org/10.1007/BF01205069">doi:10.1007/BF01205069</A>]['08] [13 refs] via KM.

%A S. W. Bent
%A U. Manber
%T On non-intersecting Eulerian circuits
%J Discrete Appl. Math.
%V 18
%P 87-94
%D 1987
%K jrnl, c1987, c198x, c198xx, zz0715, maths, graph, Eulerian circuit,
   flame cutting, plane
%X "The following Q. arises in flame-cutting & similar applications. 'Given a
   graph drawn in the plane, is there an E.circuit in which successive edges
   always belong to a common face?' We prove that this Q & related ones are
   NP-complete."
   -- [<A HREF="http://dx.doi.org/10.1016/0166-218X(87)90045-X">doi:10.1016/0166-218X(87)90045-X</A>]['15].

%A A. Griewank
%T Evaluating Derivatives: Principles and Techniques of Algorithmic
   Differentiation
%I SIAM
%P 390
%D 1987
%K book, text, c1987, c198x, c19xx, zz0108, automatic differentiating,
   derivative, partial, differantiation, differentiate, numerical computation,
   computing, methods, algorithm, automatic, AD, forward, reverse mode,
   dual numbers, algebra
%X "Algorithmic, or automatic, differentiation (AD) is concerned with the
   accurate & efficient evaluation of derivatives for functions defined by
   computer programs. No truncation errors are incurred, & the resulting
   numerical derivative values can be used for all scientific computations that
   are based on linear, quadratic, or even higher order approxs. to nonlinear
   scalar or vector fns. ... has been applied to optimization, param.
   identification, eqn solving, the numerical integration of differential eqns,
   & combinations thereof. Apart from quantifying sensitivities numerically,
   AD techniques can also provide structural information, e.g., sparsity
   pattern & generic rank of Jacobian matrices."
   uk us isbn:0898714516; uk us isbn13:978-0898714517; us$64.
   Also see [<A HREF="http://en.wikipedia.org/wiki/Automatic_differentiation">AD@wikip</A>]['08].
   See [<A HREF="http://www.autodiff.org/">autodiff.org</A>]['08].
   [Also search for: automatic differentiation].

%A A. Pelc
%T Prefix search with a lie
%J J. Combinatorial Theory
%S A
%V 48
%N 2
%P 165-173
%M JUL
%D 1988
%K jrnl, Ulam, game, faulty feedback, lie, lies, c1988, c198x, c19xx

%A M. Dehon
%T Classifying geometries with Cayley
%J J. Symb. Comput.
%V 17
%N 3
%P 259-276
%M AMR
%D 1994
%K JSC, jrnl, c1994, c199x, c19xx, Cayley, geometry, group, groups,
   mathematics, maths, zz1295
%X review Comp Rev p539 Oct '95.

%A K. -K. Lau
%T Linear Programming, a Computational Approach
%I ChartwellBratt
%D 1984
%P 119
%K book, text, good, LinearProgramming, simplex method, revised, dual,
   parametric programming
%X <!-- via Kim M' --> uk us isbn:0-86238-071-5.
   [Also search for: linearProgramming].

%A W. T. Tutte
%T Graph Theory
%I LongmanHE
%P 333
%D 1984
%K book, text, c1984, c198x, c19xx, graph theory, maths, mathematics
%X 1st ed 1984; uk us isbn:0201135205; uk us isbn13:978-0201135206.
   [Also search for: Tutte book].

%A W. B. Johnson
%A J. Lindenstrauss
%T Extensions of Lipschitz mappings into a Hilbert space
%J Conf. in Modern Analysis and Probability
%I Amer. Math. Soc.
%V 26
%P 189-206
%D 1984
%O Conf. was held in 1982, book publ. 1984
%K conf, c1984, c198x, c19xx, maths, transform, mapping, points, lemma, space,
   high dimension, dimensionality, reduction, embed, embedding,
   manifold learning
%X [<A HREF="http://dx.doi.org/10.1090/conm/026/737400">doi:10.1090/conm/026/737400</A>]['12] ($subn), uk us isbn13:978-0-8218-5030-5.
   "... a small set of pts in a high-dim. space can be embedded into a space of
   much lower dimn in such a way that distances between the pts are nearly
   preserved. ..."
   -- J-L-lemma@[<A HREF="http://en.wikipedia.org/wiki/Johnson-Lindenstrauss_lemma">wikip</A>]['12].
   [Also search for: dimension reduction].

%A L. Babai
%A E. Szemeredi
%T On the complexity of matrix group problems I
%J FOCS
%I IEEE
%D 1984
%K conf, FOCS, FOCS84, FOCS25, c1984, c198x, c19xx, zz0718, matrix, group,
   straight line program, straightLineProgram, maths, word, problem,
   reachability, subgroup, NPB, black box
%X "We build a theory of black box groups, & apply it to matrix grps over finite
   fields. Elts of a black box grp are encoded by strings of uniform length &
   grp operations are performd by an oracle. Subgrps are given by a list of
   generators. We prove that for such subgrps, membership & divisor of the order
   are in NP^B. (B is the grp box oracle.) Under a plausible math. hypothesis on
   short presentations of finite simple grps, non membership & exact order will
   also be in NP^B & thus in NP^B intersection coNP^B."
   -- [<A HREF="https://doi.org/10.1109/SFCS.1984.715919">doi:10.1109/SFCS.1984.715919</A>]['18] (uk us isbn:081860591X),
      pdf@[<A HREF="https://www.computer.org/csdl/proceedings/focs/1984/0591/00/0715919.pdf">c'mputer.org</A>]['18].
   (alludes to a second, later paper.)
   (And, "Babai & Szemeredi (1984) ... prove that every elt of a finite group
         G has an SLP of length O(log^2 |G|) in every generating set. ..."
         -- SLP@[<A HREF="https://en.wikipedia.org/wiki/Straight-line_program">wikip</A>]['18].
   (auth EM@[<A HREF="https://users.renyi.hu/~szemered/">r'nyi.hu</A>]['18].)
   [Also search for: group word problem].

%A J. A. Paulos
%T The Narrative of Numbers
%I BasicBooks N.Y.
%D 1998
%K book, text, number, math, maths, mathematics, zz0499
%X reviewed in Scientific American Feb '99 p82.
   Apparently it includes the ``[cheating|unfaithful] [wives|husbands]'' puzzle
   but changed to suit the Asian Financial Crisis of '97/'98!
   [Hint, search for: unfaithful].

%A J. H. Conway
%A N. J. A. Sloane
%T Voronoi regions of lattices, second moments of polytopes and quantization
%J IEEE Trans. Information Theory
%V IT-28
%N 2
%P 211-226
%M MAR
%D 1982
%K jrnl, CS82, c1982, c198x, c19xx, maths, lattice, constant, diagram, polytope,
   region, E8, Gn, code, encoding, quantizer, quantize, quantise,
   squared error, channel, JHConway
%X "If a pt is picked at random inside a regular simplex, octahedron, 600-cell,
   or other polytope, what is its avg squared dist. from the centroid?
   In n-dim. space, what is the avg sqd dist of a random pt from the closest
   pt of the lattice A_n (or D_n, E_n, A_n^* or D_n^*)? The ans. are given here
   together with a descn of the Voronoi (or nearest neighbor) regions of these
   lattices. ... have applicns to quantization & to the design of signals for
   the Gaussian channel. [E.g.] a quantizer based on the eight-D lattice E8 has
   a mean-squared error/symbol of 0.0717 ... when applied to uniformly
   distributed data, compared with 0.08333 ... the best one-D quantizer."
   -- [<A HREF="http://dx.doi.org/10.1109/TIT.1982.1056483">doi:10.1109/TIT.1982.1056483</A>]['12],
    * pdf@[<A HREF="http://neilsloane.com/doc/Me82.pdf">neilsloane</A>]['15]*.
   [Also search for: lattice constant].

%A P. Erdos
%A R. Laskar
%T On maximum chordal subgraph
%J Congerssus Numerantium
%V 39
%P 367-373
%D 1983
%K c1983, c198x, c19xx, maths, graph, subgraphs, chordal, maximum, largest
%X "... 1) what is the minimal set of new edges to be added to the graph to make
   it chordal? [see Rose, T & L 1976]  2) What is the minimal set of edges to be
   deleted from the graph to make the resulting g. a maximum chordal subg.? ...
   This note determines asymptotically the minimum number of edges to be deleted
   from the g. such that the resulting g. is a maximum chordal subgraph. ..."
   -- pdf@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.436.2885&rep=rep1&type=pdf">cit'seer</A>]['18].
   Note, "maximum chordal subgraph", not "maximal...".
   [Also search for: maximum chordal subgraph] and/or try "maximal", and
   [also search for: induced chordal subgraph].

%A J. H. Conway
%A N. J. A. Sloane
%T Sphere Packings, Lattices and Groups
%I SpringerVerlag
%P 633
%D 1988
%K book, CS88, text, c1988, c198x, c19xx, zz0699, laminated, lattice, group,
   maths, polytope, polytopes, packing, constant, constants, G1, G2,
   Voronoi regions, quantization, tiling, space, codes, john conway, JHConway
%X 1st ed 1988(!), uk us isbn:038796617X, uk us isbn13:9780387966175;
   3rd ed, pp.888(?), Dec c1998, uk us isbn:0387985859.
   Includes a table of bounds on mean sq err', G, (p61) for n=0..8, 12, 16, 24.
   i.e. "lattice constants", G0=0, G1=1/12, G2=5/(36sqrt(3)), limit 1/(2 pi e).
   dimn: kappa[n];
      1: 0.083333 = 1/12;
      2: 0.080188 = 5/(36 sqrt(3));
      3: 0.078543 = 19/(192 . 2**(1/3));
      4: 0.076603;
      5: 0.075625;
      6: 0.074244;
      7: 0.073116;
      8: 0.071682;
   -- [<A HREF="https://doi.org/10.1007/978-1-4757-6568-7">doi:10.1007/978-1-4757-6568-7</A>]['17].
   [Also search for: lattice constant]  and  [also search for: Zador lattice].
   (The constants are used in [<A HREF="http://www.allisons.org/ll/MML/Notes/Fisher/">MML</A>] inference.)

%A J. Vuillemin
%T Exact real computer arithmetic with continued fractions
%J ACM Conf. on LISP and Functional Programming
%W Snowbird
%P 14-27
%D 1988
%K conf, c1988, c198x, c19xx, real numbers, real number, computer arithmetic,
   fraction, FP
%X "... by continued fractions. This deals with the subtle points of undecidable
   comparison an integer division, as well as representing the infinite 1/0 &
   undefined 0/0 numbers.  2 general algs. for performing arithmetic ops. are
   introduced. The algebraic alg., which computes sums & products of continued
   fractions as a special case, basically operates in a positional manner,
   producing 1 term of output for each term of input. The transcendental alg.
   uses a general formula of Gauss to compute the continued fractions of
   exponentials, logarithms, trigonometric functions, as well as a wide class of
   special functions. A prototype system has been implemented in LeLisp, & the
   performance of these algorithms is promising."
   -- [<A HREF="http://doi.acm.org/10.1145/62678.62681">doi:/10.1145/62678.62681</A>]['07]
   [Also search for: computer arithmetic].

%A J. Oesterle
%T Novelle approaches du "theorem de Fermat"
%J Asterisque, Seminaire Bourbaki, exp 694
%V 161
%P 165-186
%D 1988
%K maths, seminar, c1988, c198x, c19xx, zz0420, ABC conjecture, defn,
   prime number, theory, numbers, square free, radical, number theory,
   Fermat's, Fermats, last theorem, diophantine, Masser, Mochizuki
%X '... three +ve integers, a, b & c [...], which have no common factor &
   satisfy a+b=c. If d denotes the product of the distinct prime factors of abc,
   the conjecture essentially states that d is rarely much smaller than c. ...
   the radical n, rad(n), is the product of the distinct prime factors of n. ...
   it turns out that "usually" c < rad(abc). The abc conjecture deals with the
   exceptions. Specifically, it states that for every eps > 0, there exist only
   finitely many triples (a,b,c) of +ve coprime ints with a+b=c s.t.
   c > rad(abc)**(1+eps). ...'
   -- [<A HREF="http://en.wikipedia.org/wiki/Abc_conjecture">wikip</A>].
   (2012: Possible proof by Mochizuki@[<A HREF="http://www.kurims.kyoto-u.ac.jp/~motizuki/top-english.html">Kyoto-U</A>]['17]
   -- various.
    2020: Also see [<A HREF="https://doi.org/10.1038/d41586-020-00998-2">www</A>][4/2020].)

%A P. M. Dearing
%A D. R. Shier
%A D. D. Warner
%T Maximal chordal subgraphs
%J Discr. Appl. Maths.
%V 20
%N 3
%P 181-190
%M JUL
%D 1988
%K jrnl, c1988, c198x, c19xx, zz0818, maths, graph, maximal, chordal, subgraph,
   finding, algorithm
%X "An alg. for finding maximal chordal subgraphs is developed that has
   worst-case time complexity of O(|E|d), where |E| is the # of edges in G &
   d is the max. vertex degree in G. ...  Two examples are given that illustrate
   potential applications of maximal chordal subgs..  One provides an
   alternative formulation to the maximum indep. set problem on a g.. The other
   involves a novel splitting scheme for solving large sparse systems of linear
   equns. "
   -- [<A HREF="https://doi.org/10.1016/0166-218X(88)90075-3">doi:10.1016/0166-218X(88)90075-3</A>]['18].
   Note 1, "maximal...", not "maximum...".  Note 2, allows deleting edges.
   [Also search for: maximal chordal subgraph] and/or try "maximum",  and
   [also search for: induced chordal subgraph].

%A R. Diestel
%T Simplicial decompositions, tree-decompositions and graph minors
%J Ars Combinatoria
%V 25C
%P 97-104
%D 1988
%K jrnl, c1988, c198x, c19xx, zz0618, maths, graph, graphs, tree, simplicial,
   decomposition, decompose, minor, primes, Robertson, Seymour, Halin,
   uniqueness, simplices, attachment
%X "... gives a summary of open problems and recent results concerning the
   existence and uniqueness of simplicial decompositions (Halin) &
   tree-decompositions (Robertson/Seymour) into primes."  (15 refs.)
   And,
   "... it is not difficult to show that every finite graph admits a
   simplicial decomp. into primes (see Halin[11]). Moreover, Halin[9] was
   able to extend this result to graphs of any cardinality which do not contain
   an infinite simplex. ... When Halin posed the above problem in [9], he also
   showed that gs. not admitting a simp.decomposition into primes exist ..."
   -- [<A HREF="https://www.math.uni-hamburg.de/home/diestel/papers/Ars.pdf">UniH</A>]['18],
   at [<A HREF="https://www.math.uni-hamburg.de/home/diestel/papers/allpapers.html">publns</A>]['18].
   (Simplicial tree-decomposition v. simplicial-d. v. tree-d.)
   [Also search for: Diestel graph] and [also search for: graph decomposition].

%A W. Bosma
%A M.-P. van der Hulst
%T Faster primality testing
%J Adv. in Cryptology, Proc. Eurocrypt '89
%W Houthalen
%I SpringerVerlag
%P 652-656
%M APR
%D 1989
%K conf, prime, primes, primality, test, testing, c1989, c198x, c19xx
%X [Also search for: primality].

%A A. E. Brouwer
%A A. M. Cohen
%A A. Neumaier
%T Distance-Regular Graphs
%I SpringerVerlag
%P 495
%D 1989
%K book, text, c1989, c198x, c19xx, distance regular, maths, graph, graphs,
   theory
%X uk us isbn:0387506195; uk us isbn13:978-0387506197.
   ref in Biggs c1993.

%A J. Dongarra
%A J. Du Croz
%A S. Hammarling
%A I. Duff
%T A set of level 3 basic linear algebra subprograms
%T TOMS
%I ACM
%V 16
%N 1
%P 1-17
%D 1990
%K jrnl, TOMS, c1990, c199x, c19xx, algorithm, algorithms, numerical, method,
   methods, optimization, optimisation, sub programs, BLAS
%X "... describes an extension to the set of Basic Linear Algebra Subprograms.
   The extensions are targeted at matrix-vector operations that should provide
   for efficient & portable implementations of algs. for high-perf. computers."
   pdf: [<A HREF="http://doi.acm.org/10.1145/77626.79170">doi:10.1145/77626.79170</A>]['08].

%A M. Naor
%T Succinct representation of general unlabeled graphs
%J Discr. Applied Math.
%V 28
%N 3
%P 303-307
%M SEP
%D 1990
%K jrnl, c1990, c199x, c19xx, zz0820, maths, graph, compress, encode, decode
%X "We show that general unlabeled graphs on n nodes can be represented by
   (^n_2)-nlog2(n)+O(n) bits which is optimal up to the O(n) term. Both the
   encoding & decoding require linear time."
   -- [<A HREF="https://doi.org/10.1016/0166-218X(90)90011-Z">doi:10.1016/0166-218X(90)90011-Z</A>]['20].
   [Also search for: graph compress].

%A T. S. Verma
%A J. Pearl
%T Deciding morality of graphs is NP-complete
%J UAI
%P 391-399
%D 1993
%K conf, UAI, UAI93, UAI1993, c1993, c199x, c19xx, zz0718, maths, graph, DAG,
   causal, explanation, recovery algorithm, moral, NPC
%X "In order to find a causal explanation for data presented in the form of
   covariance & concentration matrices it is necessary to decide if the graph
   formed by such associations is a projection of a directed acyclic graph
   (DAG). We show that the general problem of deciding whether such a dag exists
   is NP-complete."
   -- [<A HREF="https://doi.org/10.1016/B978-1-4832-1451-1.50052-4">doi:10.1016/B978-1-4832-1451-1.50052-4</A>]['18],
      1303.1501@[<A HREF="https://arxiv.org/abs/1303.1501">arXiv</A>]['18].
   [Also search for: graph recovery algorithm].

%A J. Pearl
%A N. Wermuth
%T When can association graphs admit a causal interpretation?
%B Selecting Models from Data: AI and Statistics IV
%P 205-214
%S LNS
%V 89
%I Springer
%D 1994
%K c1994, c199x, c19xx, association, covariance, concentration, graph, maths,
   DAG, causal, explanation, recovery algorithm
%X "We discuss essentially linear structures which are adequately represented by
   assoc. graphs called covariance graphs & concentration gs.. These do not
   explicitly indicate a process by which data could be generated in a stepwise
   fashion. Therefore, on their own, they do not suggest a causal
   interpretation. By contrast, each DAG describes such a process & may offer a
   causal interpretation whenever this process is in agreement with substantive
   knowledge about causation among the variables under study. We derive
   conditions & procedures to decide for any given covariance g. or conc. graph
   whether all their pairwise independencies can be implied by some DAG."
   -- [<A HREF="https://doi.org/10.1007/978-1-4612-2660-4_21">doi:10.1007/978-1-4612-2660-4_21</A>]['18].
   [Also search for: Pearl c199x].

%A C. Kenyon
%A V. King
%T On boolean decision trees with faulty nodes
%J Random Struct. Algorithms
%V 5
%P 453-464
%D 1994
%K decision, classification tree, node, faulty feedback, c1994, c199x, c19xx,
   DTree, Ulam game, noise
%X from an online ref.

%A J. H. Conway
%A N. J. A. Sloane
%T What are all the best sphere packings in low dimensions?
%J Discrete & Computational Geometry
%V 13
%N 3
%P 383-403
%M JUN
%D 1995
%K jrnl, CS95, c1995, c199x, c19xx, zz1215, maths, lattice cosntant, constants,
   dimension, JHConway
%X "We describe what may be all the best packings of nonoverlapping equal
   spheres in dimensions n <= 10, where 'best' means both having the highest
   density & not permitting any local improvement. For example, the best
   five-d. sphere packings are parametrized by the 4-colorings of the one-d.
   integer lattice. We also find what we believe to be the exact #s of 'uniform'
   packings among these, that is, those in which the automorphism group acts
   transitively. These assertions depend on certain plausible but as yet
   unproved postulates.  Our work may be regarded as a continuation of
   Laszlo  Fejes Toth's work on solid packings."
   -- [<A HREF="http://dx.doi.org/10.1007/BF02574051">doi:10.1007/BF02574051</A>]['15].
   [Also search for: lattice constant].

%A A. Wiles
%T Modular elliptic curves and Fermat's last theorem
%J Annals of Maths.
%V 141
%N 3
%P 443-551
%M MAY
%D 1995
%K jrnl, maths, c1995, c199x, c19xx, zz0316, Fermat, Fermat's last theorem,
   number theory, Shimura, Taniyama, Weil, Frey, modularity conjecture,
   semistable elliptic curve, Abel Prize, AbelPrize
%X "An elliptic curve over Q is said to be modular if it has a finite covering
   by a modular curve of the form X_0(N). ..."
   -- [<A HREF="http://dx.doi.org/10.2307/2118559">doi:10.2307/2118559</A>]['16],
      2118559@[<A HREF="http://www.jstor.org/stable/2118559">Jstor</A>]['16].
   ("The Norwegian Academy of Science & Letters has decided to award the Abel
   Prize for 2016 to Sir Andrew J. Wiles (62), U. of Oxford, 'for his stunning
   proof of Fermat's Last Theorem by way of the modularity conjecture for
   semistable elliptic curves, opening a new era in number theory.' ..."
   -- [<A HREF="http://www.abelprize.no/nyheter/vis.html?tid=67106">abelprize.no</A>]['16];
      AW@[<A HREF="https://en.wikipedia.org/wiki/Andrew_Wiles">wikip</A>]['16].)

%A N. Alon
%A R. Yuster
%A U. Zwick
%T Color-coding
%J JACM
%V 42
%N 4
%M JUL
%D 1995
%K Jrnl, JACM, c1995, c199x, c19xx, zz0920, Noga, NAlon, maths, graph, path,
   cycle, colour coding, randomized algorithm, randomised
%X "We describe a novel randomized method, the method of color-coding for
   finding simple paths & cycles of a specified length k, & other small
   subgraphs, within a given graph G=(V,E). The randomized algs obtained using
   this method can be derandomized using families of perfect hash fns ..."
   -- [<A HREF="https://doi.org/10.1145/210332.210337">doi:10.1145/210332.210337</A>]['20],
      [<A HREF="http://courses.cs.tau.ac.il/combsem/09a/papers/ColorCoding.pdf">ac.il</A>]['20].

%A Tjalling J. Ypma
%T Historical development of the Newton-Raphson method
%J SIAM Review
%V 37
%N 4
%P 531-551
%M DEC
%D 1995
%K jrnl, c1995, c199x, c19xx, solve, solution, zero, zeroes, equation,
   root finding, roots, optimization, optimisation, optimise, optimize,
   function, numerical methods, intro, introduction
%X SIAM Rev: [<A HREF="http://dx.doi.org/10.1137/1037125">doi:10.1137/1037125</A>]['07]
   [<A HREF="http://links.jstor.org/sici?sici=0036-1445%28199512%2937%3A4%3C531%3AHDOTNM%3E2.0.CO%3B2-4">paper@Jstor</A>]['07]
   NR is iterative: x[n+1] = x[n] - f(x[n])/f'(x[n]).
   See [<A HREF="http://en.wikipedia.org/wiki/Newton's_method">NR@wikip</A>]['07]

%A H. T. Siegelmann
%T Computation beyond the Turing limit
%J Science
%V 268
%N 5210
%P 545-548
%M APR
%D 1995
%K jrnl, c1995, c199x, c19xx, model, models of, computation, super Turing,
   machine, thesis, computability
%X "Extensive efforts have been made to prove the Church-Turing thesis, which
   suggests that all realizable dynamical & physical sys. cannot be more
   powerful than classical models of comp'n. A simply described but highly
   chaotic dynamical sys. called the analog shift map is presented here, which
   has computational power beyond the Turing limit (super-Turing); it computes
   exactly like neural networks & analog machines. This dynamical system is
   conjectured to describe natural physical phenomena."
   -- [<A HREF="http://dx.doi.org/10.1126/science.268.5210.545">doi:10.1126/science.268.5210.545</A>]['09].
   [Also search for: model computation Turing].

%A G. Simonyi
%T Graph entropy: a survey
%J Combinatorial Optimization
%I DIMACS
%V 20
%P 399-441
%D 1995
%K jrnl, c1995, c199x, c19xx, zz0816, maths, graph, entropy, compress,
   information, vertex packing polytope, characeristic, survey, intro
%X Graph entropy is a functional on a graph with a probability distribution on
   its vertex set. This survey article discusses its main properties, its
   remarkable connections to well-investigated combinatorial objects, eg,
   perfect graphs, as well as several applications of its sub-additivity in
   different areas including formula complexity and the design of sorting
   algorithms. Its origin in information theory and its connections to graph
   capacity concepts are also discussed."
      "... the vertex packing polytope VP(G) of G is the convex hull of
      the characeristic vectors of the stable sets of G.
      Let G be a graph on vertex set V(G)={1,...,n} and let P=(p_1,...,p_n)
      be a prob. distn on V(G) .... The entropy of G wrt P is then def as
         H(G,P)=min_{a in VP(G), a > 0} SUM_{i=1..n} p_i log(1/a_i). ..."
   -- pdf@[<A HREF="http://www.renyi.hu/~simonyi/grams.pdf">renyi.hu</A>]['16],
      [<A HREF="https://books.google.com.au/books?hl=en&lr=&id=Mhf4Zmq1Q3cC&oi=fnd&pg=PA399&dq=info:vh6sRffaxYEJ:scholar.google.com&ots=wM5CZirWfL&sig=HHvvJqcFI4aATScM55YQr7QqKC8&redir_esc=y#v=onepage&q&f=false">www</A>]['16].
   [Also search for: compress graph] and
   [also search for: graph entropy survey].

%A A. Tarski
%T Introduction to Logic
%I DoverPubl.
%P 239
%D 1995
%K book, text, c1995, c199x, c19xx, maths, logic, deduction, deductive, method,
   logical, reasoning, L3Ref, L4Ref
%X 2nd? ed 1995, pb us$8; us usk isbn:048628462X; uk us isbn13:978-0486284620.
   "This classic undergraduate treatment examines the deductive method in
   its first part and explores applications of logic and methodology in
   constructing mathematical theories in its second part.
   Exercises appear throughout."

%A M. Studeny
%T On separation criterion and recovery algorithm for chain graphs
%J UAI
%D 1996
%O Int. J. Approx. Reasoning, 17(2-3), pp.265-293, Aug-Oct, 1997,
   doi:10.1016/S0888-613X(97)00018-2
%K conf, UAI96, UAI1996, c1996, c199x, c19xx, zz0618, maths, chain graph,
   chainGraph, hybrid, DAG, DAGs, recovery, reconstruction, causal model,
   dependency, criteria
%X "Chain graphs (CGs) give a natural unifying point of view on Markov and
   Bayesian networks & enlarge the potential of graphical models for
   description of conditional in dependence structures. ... a didrect graphical
   separation criterion for CGs which generalizes the d-separation criterion
   for B.n/wks is introduced (recalled). It is equiv. to the classic
   moralization criterion for CGs & complete m the sense that for every CG there
   exists a prob.distn satisfying exactly independencies derivable from the CG
   by the separation criterion. Every class of Markov equivalent CGs can be
   uniquely described by a natural representative, called the largest CG. A
   recovery alg., which on basis of the (cond.) dependency model given by a CG
   finds the corresponding largest CG, is p.
   -- 1302.3606@[<A HREF="https://arxiv.org/abs/1302.3606">arXiv</A>]['18],
      IJAR@[<A HREF="https://doi.org/10.1016/S0888-613X(97)00018-2">doi:10.1016/S0888-613X(97)00018-2</A>]['18].
   [Also search for: chainGraph] & [also search for: graph recovery algorithm].

%A M. Ajtai
%T Generating hard instances of lattice problems (extended abstract)
%J Proc. 28th annual ACM symp. on Theory of Computing (STOC)
%P 99-108
%M JUL
%D 1996
%K conf, c1996, c199x, c19xx, zz1220, hard, lattice, problem, cryptography,
   based, public key encryption, short, shortest vector problem, SVP
%X "We give a random class of lattices in Z^n s.t. if there is a probabilistic
   polynomial time alg. which finds a short vector in a random lattice with a
   prob. of at least 1/2 then there is also a prob. polynomial time alg. which
   solves the following three lattice problems in every lattice in Z^n with a
   prob. exponentially close to one. (1) Find the length of a shortest nonzero
   vector in an n-dim. lattice, approximately, up to a polynomial factor.
   (2) Find the shortest nonzero vector in an n-dim. lattice L where the
   shortest vector v is unique in the sense that any other vector whose length
   is at most n c kvk is parallel to v, where c is a sufficiently large absolute
   constant. (3) Find a basis b_1,...,b_n in the n-dim. lattice L whose length,
   defined as max n i=1 kb i k, is the smallest possible up to a polynomial
   factor ..."
   -- [<A HREF="https://doi.org/10.1145/237814.237838">doi:10.1145/237814.237838</A>]['20],
      [<A HREF="https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.40.2489">c'teseer</A>]['20].
   Also see LBC@[<A HREF="https://en.wikipedia.org/wiki/Lattice-based_cryptography">wikip</A>]['20].
   [Also search for: lattice based cryptography].

%A P. D. Straffin
%T Game Theory and Strategy
%I Math. Assoc. of America
%D 1996
%K book, text, c1996, c199x, c19xx, math, maths, game theory, games, discrete
%X us$27; us isbn:0883856379; us isbn13:978-0883856376.

%A C. Ding
%A D. Pei
%A A. Salomaa
%T Chinese Remainder Theorem. Applications in Computing, Coding, Cryptography
%I WorldScientific
%P 224
%D 1996
%K book, text, c1996, c199x, c19xx, zz0715, maths, Chinese Remainder theorem,
   CRT, Sun Tzu, Sunzi, residue, congruent, modulo
%X 1996, hb us$71; uk us isbn:9810228279; uk us isbn13:978-9810228279.
   (Also see CRT@[<A HREF="https://en.wikipedia.org/wiki/Chinese_remainder_theorem">wikip</A>]['15].)

%A H. S. Wilf
%T On crossing numbers, and some unsolved problems
%P 557-562
%B Combinatorics, Geometry and Probability, a tribute to Paul Erdos
%E B. Bollobas
%A A. Thomason
%I CUP
%D 1997
%K chapter, c1997, c199x, c19xx, zz1211, maths, graph, rectilinear crossing,
   number, problem, matrix, matrices, triangular, permutation, rows, columns
%X In, hb, stg133; uk us isbn:0521584728; uk us isbn13:978-0521584722;
   pb, uk us isbn13:978-0521607667.
   "... 1. ... a connection between the rectilinear crossing # problem
   for graphs and an old question in geometric probability that was asked
   by J.J.Sylvester.   2. ... propose a # of unsolved problems in comb. &
   graph th., ..."
   -- [<A HREF="http://dx.doi.org/10.1017/CBO9780511662034.049">doi:10.1017/CBO9780511662034.049</A>]['11].
     '... considers the complexity of transforming an NxM(?) binary matrix into
     a triangular matrix by permutations of the rows and columns of A, and
     concludes that the problem falls in difficulty between a known easy case
     and a known hard case of the general NP-complete problem.' -- njh.

%A G. J. Chaitin
%T The Limits of Mathematics: A course on information theory and the
   limits of formal reasoning
%I SpringerVerlag
%D 1998
%K book, text, c1998, c199x, c19xx, zz0809, information theory, foundations,
   theory, formal, logic, decidability, completeness, incompleteness, theorem,
   randomness, Omega, Hilbert
%X 1st ed, hb us$33; uk us isbn:981308359X; uk us isbn13:978-9813083592.
   "... final version of a course on algorithmic information theory and the
   epistemology of mathematics and physics. ... thesis that mathematics is
   quasi-empirical. ..."
   chaitin@[<A HREF="http://www.umcs.maine.edu/~chaitin/">maine.edu</A>]['09].

%A J. Kleinberg
%T Authoritative sources in a hyperlinked environment
%C Proc. 9th ACM-SIAM Symp. on Discrete Algorithms
%P 668-677
%D 1998
%O Extended version in J. ACM, vol.46, 1999.
%K conf, c1998, c199x, c19xx, web, www, hyper-links, link structure, ranking,
   eigenvectors, matrix, graph, graphs, citation, citations, page rank, google,
   link, pageRank, pageRanking, source hyper text, hypertext, web, www,
   search engine
%X  Also appears as IBM Research Report RJ 10076, May 1997
   ... alg's ... extract info from the link structure...
   ...connections with eigenvectors of certain matrics associated with
   the link graph...
   [<A HREF="http://www.cs.cornell.edu/home/kleinber/auth.pdf">.pdf</A>][11/'03]
   [Also see: search engine c1998]

%A M. Greibel
%T Adaptive sparse grid multilevel methods for elliptic PDEs based on
   finite differences
%J Computing
%V 61
%N 2
%P 151-179
%D 1998
%K jrnl, c1998, c199x, c19xx, sparse grids, numerical approximation
%X "... multilevel approach for the solution of PDEs. ... based on a multiscale
   basis which is constructed from a 1-D multiscale basis by the tensor product
   approach. Together with the use of hash tables as data structure, this allows
   in a simple way for adaptive refinement and is, due to the tensor product
   approach, well suited for higher dimensional problems. Also, the adaptive
   treatment of PDEs, the discretization (involving finite differences) and the
   solution (here by preconditioned BiCG) can be programmed easily. We describe
   the basic features of the method, discuss the discretization, the solution
   and the refinement procedures and report on the results of different
   numerical experiments."
   [also search for: sparse grids].

%A H. Bunke
%A K. Shearer
%T A graph distance metric based on the maximal common subgraph
%J Pattern Recognition Letters
%V 19
%N 3-4
%P 255-259
%M MAR
%D 1998
%K jrnl, c1998, c199x, c19xx, maths, graph, graphs, maximal common subgraph,
   MCS, similar, similarity, approximate
%X "... a new distance measure on graphs is proposed. It is based on the
   MCS of 2 graphs. The new measure is superior to edit distance based measures
   in that no particular edit operations together with their costs need to be
   defined. It is formally shown that the new distance measure is a metric.
   Potential[!] algs. for the efficient comp'n of the new m. are discussed."
   -- [<A HREF="http://dx.doi.org/10.1016/S0167-8655(97)00179-7">doi:10.1016/S0167-8655(97)00179-7</A>]['08].
   [Also search for: MCS graph].

%A L. D. Andersen
%A H. Fleischner
%A S. Regner
%T Algorithms and outerplanar conditions for A-trails in plane Eulerian graphs
%J Discr. Appl. Maths.
%V 85
%N 2
%P 99-112
%M JUN
%D 1998
%K jrnl, c998, c199x, c19xx, zz0715, algorithm, maths, graph, outerplanar,
   A-trail, Atrail, Atrails, Eulerian, multigraph
%X "The problem of finding A-trails in plane Eulerian graphs is NP-complete even
   for 3-connected graphs, as shown by the first two authors in an earlier
   paper. ... we discuss sufficient conditions for the existence of an A-trail
   in a 2-connected plane E.graph. They generalize the result that
   simple 2-connected outerplane E.graphs always have A-trails; we give a
   polynomial alg. for finding A-trails in such graphs & show that this alg.
   also works for certain multigraphs."
   -- [<A HREF="http://dx.doi.org/10.1016/S0166-218X(97)00141-8">doi:10.1016/S0166-218X(97)00141-8</A>]['15].
   (NB. 'An Eulerian graph is a g. containing an E.cycle' - various.)

%A Claire Voisin
%T Mirror Symmetry
%I AMS
%P 120
%D 1999
%K book, maths, STEM, woman, women, mathematician, algebraic geometry,
   Crafoord Prize, string theory
%X "... book reflecting the discovery of the mirror symmetry phenomenon. The
   first chapter is devoted to the geometry of Calabi-Yau manifolds, and the
   second describes, as motivation, the ideas from quantum field theory that
   led to the discovery of mirror symmetry. ..."
   pb us$36; uk us isbn13: 978-0821819470.
   wikip: [<A HREF="https://en.wikipedia.org/wiki/Claire_Voisin">www</A>]['24],
   home: [<A HREF="https://webusers.imj-prg.fr/~claire.voisin/">www</A>]['24],
   nature 2024: [<A HREF="https://doi.org/10.1038/d41586-024-00402-3">www</A>]['24].

%A E. Deutsch
%T Dyck path enumeration
%J Discr. Math.
%V 204
%N 1-3
%P 167-202
%M JUN
%D 1999
%K jrnl, c1999, c199x, c19xx, zz1118, Dyck path, paths, word, words, enumerate,
   generate, Narayana, function, Fine number, numbers
%X "An elementary technique is used for the enumeration of Dyck paths according
   to various parameters. For several of the considered parameters the
   generating fn is expressed in terms of the Narayana fn. Many enumeration
   results are obtained, some of which involve the Fine numbers."
   -- [<A HREF="https://doi.org/10.1016/S0012-365X(98)00371-9">doi:10.1016/S0012-365X(98)00371-9</A>]['18].
   [Also search for: Dyck paths].

%A V. S. Dimitrov
%A G. A. Jullien
%A W. C. Miller
%T Theory and applications of the double-base number system
%J IEEE Trans. on Comp.
%V 48
%N 10
%P 1098-1106
%M OCT
%D 1999
%K jrnl, c1999, c199x, c19xx, zz1221, double base number system, DBNS, CDBNR,
   MDLNS, integers, computer arithmetic
%X "... we analyze some of the main properties of a double base number system,
   using bases 2 & 3; in particular, we emphasize the sparseness of the rep'n.
   A simple geometric interp'n allows an efficient implemen'n of the basic
   arithmetic ops. & we introduce an index calculus for logarithmic-like
   arithmetic with considerable h/w reductions in lookup table size. We discuss
   the application of this # system in the area of digital signal processing; we
   illustrate the discussion with [egs] of finite impulse response filtering."
   -- [<A HREF="https://doi.org/10.1109/12.805158">doi:10.1109/12.805158</A>]['21],
   pdf@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.111.721&rep=rep1&type=pdf">c'teseer</A>]['21].
   "... digits only 0,1 and requiring o(log N) nonzero digits ... DBNS ...
    using bases 2 and 3 ... x = SUM_{i,j} d_{i,j} 2^i 3^j  ..."
    (Generalises to: Multi-Dimensional Logarithmic Number System (MDLNS).)
   [Also search for: computer arithmetic].

%A M. Fitting
%A R. L. Mendelsohn
%T First-Order Modal Logic (Synthese Library)
%I Springer
%P 308
%M NOV
%D 1999
%K book, text, c1999, c199x, c19xx, philosophy, maths, logic,
   possible world model, model
%X pb, us$40, uk us isbn:0792353358; isbn13:978-0792353355.

%A D. Hilbert
%A W. Ackermann
%T Principles of Mathematical Logic
%E R. E. Luce
%A (translators) L. M. Hammond, G. G. Leckie, F. Steinhardt
%I AMS
%P 172
%D 1999
%K book, text, c1999, c199x, c19xx, translation, symbolic logic, mathematics,
   maths, completeness, predicate calculus
%X "... translation is based on the second German edition, & has been modified
   according to the criticisms of Church & Quine. In particular, the authors'
   original formulation of Godel's completeness proof for the predicate calculus
   has been updated. ..."
   hb, us$23, us isbn:0821820249; us isbn13:978-0821820247.

%A Copeland
%A Proudfoot
%T Alan Turing's forgotten ideas in Computer Science
%J Scientific American Mag.
%P ?-?
%M APR
%D 1999
%K c1999, c199x, c19xx, Alan Turing, AlanTuring, biographical, Comp Sci, CSci,
   computation
%X 'Alan Mathison Turing conceived of the modern computer in 1935. Today all
   digital computers are, in essence, "Turing machines." ... also pioneered the
   field of [AI], proposing the famous & widely debated Turing test ... .
   During WWII, Turing was instrumental in breaking the German Enigma code in
   part of a top-secret British operation that historians say shortened the war
   in Europe by 2 years. When he died at the age of 41, Turing was doing the
   earliest work on what would now be called artificial life, simulating the
   chemistry of biological growth.
   Throughout his remarkable career, T. had no great interest in publicizing his
   ideas. Consequently, important aspects of his work have been neglected or
   forgotten over the years. ... few people - even those knowledgeable about
   CS - are familiar with Turing's fascinating anticipation of connectionism,
   or neuronlike comp.. Also neglected are his groundbreaking theor. concepts
   in the exciting area of "hypercomputation." According to some experts,
   hyperc.s might one day solve problems heretofore deemed intractable.'
   [Also search for: AlanTuring].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/">www</A>].)

%A L. P. Cordella
%T Performance evaluation of the VF graph matching algorithm
%J Proc. Int. Conf. on Image Analysis and Processing
%I IEEE
%P 1172-1177
%D 1999
%K conf, c1999, c199x, c19xx, zz0716, VF, VF2, maths, graph, subgraph,
   isomorphism, Ullman
%X "... performance of a graph matching alg. tailored for dealing with large
   graphs in computer vision without using information about the topology of the
   graphs to be matched. [It] presented in more detail in other papers (&
   publicly available on the WWW as VF), is now discussed with reference to its
   computational complexity & memory requirements. ... is compared with the one
   proposed by Ullmann (1976): experimental results confirmed the theoretical
   expectations, highlighting the overall efficiency of the algorithm. ..."
   -- [<A HREF="http://dx.doi.org/10.1109/ICIAP.1999.797762">doi:10.1109/ICIAP.1999.797762</A>]['16] $.
   [Also search for: maths subgraph isomorphism] and
   [also search for: subgraph VF].

%A J. R. Magnus
%A H. Neudecker
%T Matrix Differential Calculus with Applications in Statistics and Econometrics
%I Wiley
%P 422
%D 1999
%K book, text, c1999, c199x, c19xx, matrix, matrices, calculus, log, exp,
   algebra, differential, differentiate, stats, economics
%X "... Contains the essentials of multivariable calculus with an
   emphasis on the use of differentials. Many new examples and exercises ..."
   2nd ed 1999, pb us$112; uk us isbn:047198633X; uk us isbn13:978-0471986331.
   3rd ed 2007, download from [<A HREF="http://center.uvt.nl/staff/magnus/mdc/">M@uvt</A>]['08].

%A J. KcKee
%T Speeding Fermat's factoring method
%J Math. Comp.
%V 68
%P 1729-1737
%D 1999
%K jrnl, c1999, c199x, c19xx, zz0823, integer, factorisation, factorization,
   algorithm, Fermat, squares
%X "A factoring method is presented which, heuristically, splits composite in
   O(n^{1/4-e}) steps. There are two ideas: an int. appr'n to sqrt(q/p) provides
   an O(n^{1/2_e}) alg. in which is represented as the difference of two
   rational squares; observing that if a prime m divides a square, then m^2
   divides that square, a heuristic speed-up to O(n^{1/4+e}) steps is achieved.
   The method is well-suited for use with small computers: the storage required
   is negligible, and one never needs to work with numbers larger than itself."
   -- [<A HREF="https://www.ams.org/journals/mcom/1999-68-228/S0025-5718-99-01133-3/home.html">www</A>]['23].
   [Also search for: integer factorisation algorithm].
   (Also see FFM@[<A HREF="https://en.wikipedia.org/wiki/Fermat%27s_factorization_method">wikip</A>]['23].)

%A J. Kleinberg
%T The small-world phenomenon: An algorithmic perspective
%J Proc. 32nd ACM Symp. on Theory of Computing
%P ?-?
%D 2000
%O Cornell Computer Science Technical Report 99-1776, Oct. '99
%K conf, TOC, small world, degree separation, networks, maths, graph, graphs,
   c2000, c200x, c20xx
%X [<A HREF="http://www.cs.cornell.edu/home/kleinber/swn.pdf">.pdf</A>][11/'03].

%A C. Deppe
%T Solution of Ulam's searching game with three lies or an optimal
   adaptive strategy for binary three-error-correcting codes
%J Discrete Math.
%V 224
%N 1-3
%P 79-98
%D 2000
%K jrnl, Ulam, Ulams, binary search, noise, noisy, c2000, c200x, c20xx,
   faulty feedback
%X [<A HREF="http://www.mathematik.uni-bielefeld.de/ahlswede/papers/deppe.html">auth</A>][8/'04]
   Also see Deppe c2004

%A C. Hall
%A J. O'Donnell
%T Discrete Mathematics Using a Computer
%I Springer
%P 360
%D 2000
%K book, text, math, maths, c2000, c200x, c20xx, functional prpgramming, FP,
   l1Ref, L2Ref
%X "... introduces the main topics of discrete math. with a strong emphasis on
   applications to comp.sci.. It uses computer progs. to implement & illustrate
   the math. ideas, helping the reader to gain a concrete understanding of the
   abstract math.. The programs are also useful for practical calculations, and
   they can serve as a foundation for larger software packages. ..."
   isbn:1852330899.

%A K. Cattell
%A F. Ruskey
%A J. Sawada
%A M. Serra
%A C. R. Miers
%T Fast algorithms to generate necklaces, unlabelled necklaces and
   irreducible polynomials over GF(2)
%J J. Algorithms
%V 37
%N 2
%P 267-282
%D 2000
%K jrnl, c2000, c200x, c20xx, necklace, polynomial, bead, beads, colour,
   colours, color, colors, GF2, irreducible primitive polynomial, equivalence,
   class, algorithm, combinatorics, enumerate, enumerating, generating, zzRWT,
   Lyndon word, LyndonWord, maths
%X "... A k-ary n. is an equiv.class of k-ary strings under rotn (the cyclic
   group). A k-ary unlabeled n. is an equiv. class of k-ary strings under rotn
   & permn of alphabet symbols. ... new, fast, simple, recursive algs. for
   generating (i.e., listing) all n. & binary unlabeled ns.. Generalization ...
   to the case where no substring 0**t occurs for fixed t. All these algs. have
   optimal running times ... their running times are proportional to the # of
   ns. produced. As an applic., we describe the implementation of a fast alg.
   for listing all degree n irreducible & primitive polynomials over GF(2)."
   -- [<A HREF="http://www.cs.uvic.ca/~ruskey/Publications/">auth2</A>]['06], [22 refs] (via rwt).
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Recn/Necklaces/">necklaces</A>].)

%A P. Gowland
%A D. Lester
%T A survey of exact arithmetic implementations
%J Computability and Complexity in Analysis, 4th Int. Workshop
%I SpringerVerlag
%S LNCS
%V 2064
%P 30-?
%D 2000
%K wShop, c2000, c200x, c20xx, CCA, exact real arithmetic, computer, real,
   reals, implementation
%X "... survey of practical systems for exact arithmetic. We describe some of
   the methods used in their implementation, and suggest reasons for the
   performance differences displayed by some of the competing systems at this
   years CCA Exact Arithmetic Competition. ..."
   -- [<A HREF="http://www.springerlink.com/content/dnkph5hxfr96k7vd/">pdf@springerlink</A>]['07].
   [Also search for: computer arithmetic].

%A W. T. Tutte
%T Graph Theory
%I CUP
%P 360
%M JAN
%D 2001
%K book, text, CUP, c2001, c200x, c20xx, graph theory, maths, mathematics,
   graphs
%X pb us$53; uk us isbn:0521794897; uk us isbn13:978-0521794893.
   "... for the nonspecialist, this classic text by a world expert is an
   invaluable reference tool for those interested in a basic understanding
   of the subject. ..."
   [Also search for: Tutte book].

%A L. P. Cordella
%A P. Foggia
%A C. Sansone
%A M. Vento
%T An improved algorithm for matching large graphs
%J 3rd IAPR-TC15 Workshop on Graph-based Representations in Pattern Recognition
%W Cuen
%P 149-159
%D 2001
%K conf, c2001, c200x, c20xx, zz0716, VF, VF2, maths, graph subgraph,
   isomorphism
%X "... improved version of a graph matching alg. is presented, which is able to
   efficiently solve the graph isomorphism & graph-subgraph isomorphism problems
   on Attributed Relational Graphs. This version is particularly suited to work
   with very large graphs, since its memory requirements are quite smaller than
   those of other algorithms of the same kind . ..."
   -- [<A HREF="http://lalg.fri.uni-lj.si/pub/amalfi/papers/vf-algorithm.pdf">www</A>]['16].
   [Also search for: maths subgraph isomorphism] and
   [also search for: subgraph VF].

%A G. Priest
%T Logic: A Very Short Introduction
%I OUP
%P 144
%D 2001
%K book, text, OUP, c2001, c200x, c20xx, maths, logic, formal, philosophy,
   theory, paradox, intro, L2Ref, L3Ref
%X pb us$7; uk us isbn:0192893203; uk us isbn13:978-0192893208.
   "... explores the philosophical roots of the subject, explaining how modern
   formal logic deals with issues ranging from the existence of God and the
   reality of time to paradoxes of probability and decision theory. Along the
   way, the basics of formal logic are explained in simple, non-technical terms
   showing that logic is a powerful and exciting part of modern philosophy."

%A I. Poernomo
%A J. N. Crossley
%T Fred: An approach to generating real, correct reusable programs from proofs
%J J. of Universal Comp. Sci.
%I Springer
%V 7
%N 1
%P 71-88
%D 2001
%K proof, program, logic, maths, theory, constructive, JNCrossley
%X [IP's Ph D done @ csse monash <!-- jnc --> u, c2OO4.  At kcl.ac.uk c2OO4.]
   "... our system has a number of novel features designed to make it v easy to
   use & as close as possible to ordinary mathematical terminology & practice.
   These features include 1. the use of Henkin's technique [Hen50] to reduce
   higher-order logic to many-sorted (1st-order) logic; 2. the free use of new
   rules for induction subject to certain conditions; 3. the extensive use of
   previously programmed (total, recursive) functions; 4. the use of templates
   to make the reasoning much closer to normal mathematical proofs & 5. a
   conceptual distinction between the computational type theory (for rep.
   programs) & the logical type theory (for reasoning about programs).
     As an example of our system we give a constructive proof of the well known
   theorem that every graph of even parity, which is non-trivial in the sense
   that it does not consist of isolated vertices, has a cycle. Given such a
   graph as input, the extracted program produces a cycle as promised."
   -- [<A HREF="http://www.jucs.org/jucs_7_1/fred_an_approach_to">jucs</A>]['04].

%A S. Jukna
%T Extremal Combinatorics: With Applications in Computer Science
%I Springer
%P 375
%D 2001
%K book, text, intro, introduction, c2001, c200x, c20xx,
   combinatorics, combinatorial, Ramsey theory
%X "... intro. to extremal combinatorics ... Strong emphasis is made on theorems
   with particularly elegant & informative proofs which may be called gems of
   the theory. A wide spectrum of most powerful comb. tools is presented:
   methods of extremal set theory, the linear algebra method, the
   probabilistic method and fragments of Ramsey theory. ..."
   1st ed 2001, hb us$60; uk us isbn:3540663134; uk us isbn13:978-3540663133.

%A B. Gutkin
%A U. Smilansky
%T Can one hear the shape of a graph?
%J J. Physics A: Math. and General
%V 34
%N 31
%P 6061
%D 2001
%K eJrnl, c2001, c200x, c20xx, maths, physics, metric, graph, spectrum
%X "We show that the spectrum of the Schrodinger operator on a finite, metric
   graph determines uniquely the connectivity matrix and the bond lengths,
   provided that the lengths are non-commensurate and the connectivity is simple
   (no parallel bonds between vertices and no loops connecting a vertex to
   itself). That is, one can hear the shape of the graph! We also consider a
   related inversion problem: a compact graph can be converted into a scattering
   system by attaching to its vertices leads to infinity. We show that the
   scattering phase determines uniquely the compact part of the graph, under
   similar conditions as above."
   -- [<A HREF="http://dx.doi.org/10.1088/0305-4470/34/31/301">doi:10.1088/0305-4470/34/31/301</A>]['11].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Hearing_the_shape_of_a_drum">wikip</A>]'11].)

%A C. Godsil
%A G. Royle
%T Algebraic Graph Theory
%I Springer
%P 464
%D 2001
%K book, text, c2001, c200x, c20xx, L5Ref, maths, mathematics, graph, graphs,
   ArunM
%X "aimed at graduate students and researchers in graph theory, combinatorics,
   or discrete mathematics in general. However, all the necessary graph theory
   is developed from scratch, so the only pre-requisite for reading it is a
   1st course in linear algebra and a small amount of elementary group theory."
   1st ed 2001, pb us$41; uk us isbn:0387952209; uk is isbn13:978-0387952208.
   (Rec. by ArunM.)

%A J. Garcke
%A M. Griebel
%T Classification with sparse grids using simplicial basis functions
%J Intell. Data Analysis
%V 6
%N 6
%P 483-502
%D 2002
%K jrnl, c2002, c200x, c20xx, sparse grid, function, numerical approximation,
   regularization network, classify, cluster, clustering
%X "...based on the regularization network approach but in contrast to other
   methods, which employ ansatz functions associated to data points, we use a
   grid in the usually high-dimensional feature space for the minimization
   process.  ...  The method computes a nonlinear classifier but scales only
   linearly with the number of data points and is well suited for data mining
   applications where the amount of data is very large, but where the dimension
   of the feature space is moderately high. ...'
   [<A HREF="http://citeseer.ist.psu.edu/388914.html">@citeseer</A>]['07],
   [also search for: sparse grids]

%A A. Pelc
%T Searching games with errors - fifty years of coping with liars
%J Theoretical Comp. Sci.
%P 71-109
%V 270
%N 1-2
%M JAN
%D 2002
%K jrnl, TCS, Ulam, Ulams, game, noise, faulty feedback, error, liar,
   c2002, c200x, c20xx
%X "...survey on searching with errors, considered in the framework of 2-person
   games. The Responder thinks of an object in the search space, & the
   Questioner has to find it by asking questions to which the Responder
   provides answers, some of which are erroneous. We give a taxonomy of such
   games, depending on the type of questions allowed, on the degree of
   interactivity between the players, and on the imposed limitations on errors.
   We survey the existing results concerning such games, concentrating on the
   issue of optimizing the Questioner's querying strategy, & pointing out open
   problems. We show the relations between searching games with errors &
   problems concerning communication through a noisy channel & error-correcting
   codes. Finally, we discuss other search & computation problems with faulty
   feedback which are related to searching with errors"
   -- [<A HREF="http://dx.doi.org/10.1016/S0304-3975(01)00303-6">doi:10.1016/S0304-3975(01)00303-6</A>]['04].

%A C. S. Calude
%T Information and Randomness. An Algorithmic Perspective (2nd ed.)
%I SpringerVerlag
%S TTCS
%P 490
%D 2002
%K book, text, random, randomness, string, sequence, Omega numbers,
   c2002, c200x, c20xx, l4ref, l5ref, zz0604
%X 2nd ed 2002; uk us isbn:3540434666.
   [<A HREF="http://www.cs.auckland.ac.nz/~cristian/">auth</A>][5/'04]

%A C. S. Calude
%A M. Dumitrescu
%T Entropic measures, Markov information sources and complexity
%J Applied Math. and Comp'n.
%V 132
%N 2-3
%P 369-384
%D 2002
%K jrnl, c2002, c200x, c20xx, entropy, measure, source, random,
   algorithmic probability, zz0604, introduction
%X "...entropy plays a major part in communication theory. The Shannon entropy
   is a measure of uncertainty with respect to a priori probability
   distribution. In algorithmic information theory the information content of a
   message is measured in terms of the size in bits of the smallest program for
   computing that message. This paper discusses the classical entropy and
   entropy rate for discrete or continuous Markov sources, with finite or
   continuous alphabets, and their relations to program-size complexity and
   algorithmic probability. The accent is on ideas, constructions and results;
   no proofs will be given."
   -- [<A HREF="http://dx.doi.org/10.1016/S0096-3003(01)00199-0">doi:10.1016/S0096-3003(01)00199-0</A>][5/'04],
      [<A HREF="http://www.cs.auckland.ac.nz/~cristian/">auth-1</A>][5/'04].

%A J. C. Baez
%T The octonions
%J Bull. Amer. Math. Soc.
%V 39
%P 145-205
%D 2002
%K jrnl, AMS, octonion, quaternion, complex, number, numbers, Fano plane,
   normed division algebra, norm, maths, c2002, c200x, c20xx, zz1102
%X "The octonions are the largest of the four normed division algebras. While
   somewhat neglected due to their nonassociativity, they stand at the
   crossroads of many interesting fields of mathematics. Here we describe them
   and their relation to Clifford algebras and spinors, Bott periodicity,
   projective and Lorentzian geometry, Jordan algebras, and the exceptional Lie
   groups.  We also touch upon their applications in quantum logic, special
   relativity and supersymmetry."
   -- math/0105155@[<A HREF="https://arxiv.org/abs/math/0105155">wikip</A>]['22],
      [<A HREF="https://doi.org/10.1090/S0273-0979-01-00934-X">doi:10.1090/S0273-0979-01-00934-X</A>]['22].
   [Also search for: quaternion]  and  [also search for: octonian].

%A S. O. Ehmety
%A L. C. Paulson
%T Program Composition in Isabelle/UNITY
%J Formal Methods for Parallel Programming: Theory and Application.
%E M. Charpentier
%E B. Sanders
%D 2002
%K c2002, c200x, c20xx, zz1205, automated, automatic, theorem prover, proving,
   prove, uniCambridge, Isabelle, UNITY
%X [<A HREF="http://www.cl.cam.ac.uk/users/lcp/papers/UNITY/ehmety-composition.pdf">pdf</A>]['05]
   'Isabelle is a popular generic theorem proving environment developed at
   Cambridge University.'
   [Also search for: theorem proving].

%A I. T. Jolliffe
%T Principal Component Analysis
%I SpringerVerlag
%S Series in Statistics
%P 502
%D 2002
%K book, text, c2002, c200x, c20xx, principal component analysis, PCA, stats
%X "The central idea of principal component analysis (PCA) is to reduce the
   dimensionality of a data set consisting of a large number of interrelated
   variables, while retaining as much as possible of the variation present in
   the data set. ..."
   hb, 2nd ed, us$79, 2002; uk us isbn:0387954422; uk us isbn13:978-0387954424.

%A B. Chazelle
%T The Discrepancy Method: Randomness and Complexity
%I CUP
%P 494
%M JAN
%D 2002
%K book, text, CUP, c2002, c200x, c20xx, zz0214, maths, random, randomness,
   sequence
%X 1st ed 2002; pb us$52; uk us isbn:0521003571; uk us isbn13:978-0521003575.
   "The discrepancy method has produced the most fruitful line of attack on a
   pivotal computer science question: What is the computational power of random
   bits? [&] played a major role in recent developments in complexity theory.
   ... tells the story of the d.method in a few succinct indep. vignettes. The
   chs. explore such topics as communication complexity, pseudo-randomness,
   rapidly mixing Markov chains, pts on a sphere, derandomization, convex hulls
   & Voronoi diagrams, linear prog., geometric sampling & VC-dimn theory,
   min. spanning trees, circuit complexity, & multidim. searching. The math.
   treatment is thorough & self-contained, with minimal prereqs..
   [<A HREF="http://www.cs.princeton.edu/~chazelle/book.html">www</A>]['14]."
   [Also search for: discrepancy method].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Erd%C5%91s_discrepancy_problem">wikip</A>]['14].)

%A D. Micciancio
%A S. Goldwasser
%T Complexity of Lattice Problems: A Cryptographic Perspective
%I Springer
%P 220
%M MAR
%D 2002
%K book, text, c2002, c200x, c20xx, zz0408, lattices, problem, packing,
   constant, constants, lattice based cryptography, closest vector problem,
   short, shortest vector, SVP
%X "... particular emphasis on problems that are related to the construction of
   cryptographic functions. Specific topics covered are the strongest known
   inapproximability result for the shortest vector problem; the relations
   between this and other computational lattice problems; an exposition of how
   cryptographic functions can be built and proven secure based on worst-case
   hardness assumptions about lattice problems; and a study of the limits of
   non-approximability of lattice problems. ..."
      Approximation algs,  closest vector problem,    shortest vector problem,
      sphere packings,     basis reduction problems,  cryptographic functions,
      interactive proof systems.
   hb us$111; uk us isbn:0792376889; uk us isbn13:978-0792376880.
   [Also search for: lattice based cryptography].

%A S. Dasgupta
%A A. Gupta
%T An elementary proof of a theorem of Johnson and Lindenstrauss
%J Random Structures & Algorithms
%V 22
%N 1
%M JAN
%D 2003
%K jrnl, c2003, c200x, c20xx, zz0916, viaNjh, maths, Johnson, Lindenstrauss,
   high, low dimension, embedding, random, dimension reduction
%X "A result of J. & L. [13] shows that a set of n points in high dimensional
   Euclidean space can be mapped into an O(log n/e^2)-dimensional Euclidean
   space such that the distance between any two points changes by only a factor
   of (1 +/- e). In this note, we prove this theorem using elementary
   probabilistic techniques."
   -- [<A HREF="http://dx.doi.org/10.1002/rsa.10073">doi:10.1002/rsa.10073</A>]['16].
   (Also see J-L@[<A HREF="https://en.wikipedia.org/wiki/Johnson%E2%80%93Lindenstrauss_lemma">wikip</A>]['16].)

%A C. Moler
%A C. F. Van Loan
%T Nineteen dubious ways to compute the exponential of a matrix, twenty-five
   years later
%J SIAM Review
%V 45
%N 1
%P 3-49
%D 2003
%K jrnl, c2003, c200x, c20xx, zz0614, numerical methods, computing, analysis,
   algorithm, square, matrix, exponential, exp, log, survey, intro
%X "In principle, the exp. of a m. could be computed in many ways. Methods
   involving approxn theory, differential equns, the m.eigenvalues, & the
   m.characteristic polynomial have been proposed. In practice, consideration
   of computational stability & efficiency indicates that some of the methods
   are preferable to others but that none are completely satisfactory.  Most
   of this paper was originally published in 1978. An update, with a separate
   bibliography, describes a few recent developments."
   -- [<A HREF="http://dx.doi.org/10.1137/S00361445024180">doi:10.1137/S00361445024180</A>]['14].
   ("... exp(M) = SUM_(k=0..) {(1/k!) M^k}. ..."
    -- M.E.@[<A HREF="http://en.wikipedia.org/wiki/Matrix_exponential">wikip</A>]['14].)

%A P. Bose
%A A. Maheshwari
%A P. Morin
%T Fast approximations for sums of distances, clustering and the
   Fermat-Weber problem
%J Comp. Geometry: Theory and Applications
%V 24
%N 3
%P 135-146
%M APR
%D 2003
%K c2003, c200x, c20xx, zz0513, maths, geometry, geometric median, algorithm,
   nD, 1-median, 1median, point, approximation, sum, distance
%X "... two data structs. that preprocess a set S of n pts in R^d (d constant)
   so that the sum of Euclidean distances of pts in S to a query pt q can be
   quickly approximated to within a factor of epsilon. This preprocessing
   technique has several applicns in clustering & facility locn. ... derive an
   O(n log n) time deterministic & O(n) time randomized epsilon-approx. alg. for
   the so called Fermat-Weber problem in any fixed dimension."
   -- [<A HREF="http://dx.doi.org/10.1016/S0925-7721(02)00102-5">doi:10.1016/S0925-7721(02)00102-5</A>]['13].
   (Also see GM@[<A HREF="http://en.wikipedia.org/wiki/Geometric_median">wikip</A>]['13].)
   [Also search for: geometric median].

%A D. Crawford
%T editorial
%J CACM
%V 46
%N 9
%P 7
%M SEP
%D 2003
%K CACM, ACM, maths, mathematics, computer science, comp sci, compsci, CS,
   CSci, education, syllabus, courses, theory, special issue, zz0903, SWE
%X Why math?
   This simple, yet age-old question has puzzled generations of computer
   science students pursuing what many believed is the stuff of precision and
   logic. Isn't building computer systems and software rooted in real-life
   reasoning, they argue; while mathematics orbits around an abstract world?
     This month's special section dispels those myths in a series of articles
   investigating the mathematical reasoning in software engineering and how math
   benefits computing practitioners and students alike.  Guest editor Keith
   Devlin contends that once students-and educators-accept the fact that
   computing entails constructing, manipulating, and reasoning about
   abstractions, it becomes obvious that the ability to handle abstractions in a
   precise manner is a critical prerequisite for writing programs.
   ... issn:00010782. [<A HREF="http://portal.acm.org/citation.cfm?id=903903">www</A>][9/'03],
   [<A HREF="http://doi.acm.org/10.1145/903893.903903">http://doi.acm.org/10.1145/903893.903903</A>][9/'03],
   [<A HREF="http://dx.doi.org/10.1145/903893.903903">doi:10.1145/903893.903903</A>][9/'03].

%A P. Bartlett
%T Undirected graphical models: Chordal graphs, decomposable graphs,
   junction trees, and factorizations
%I Berkeley
%M OCT
%D 2003
%K notes, c2003, c200x, c20xx, zz0518, maths, graph, chordal,
   recursively simplicial, junction tree, decomposable, model
%X "... G = < V, E > an undirected graph ...
   The following are equivalent
   1. G is chordal.                 2. G is decomposable.
   3. G is recursively simplicial.  4. G has a junction tree. ...
   ... the classic paper on the graph-theoretic equivalences
   presented here is C. Beeri et al, JACM 1983 ..."
   -- pdf@[<A HREF="https://people.eecs.berkeley.edu/~bartlett/courses/2009fall-cs281a/graphnotes.pdf">berk'ley</A>]['25/5/18].
   [Also search for: decomposition defn], [also search for: factorization defn],
   [Also search for: Beeri graph c1983].

%A D. Kempe
%A A. Dobra
%A J. Gehrke
%T Computing aggregate information using gossip
%J FOCS
%P ?-?
%D 2003
%K conf, FOCS, graph, graphs, uniform gossip, sum, average, random sample,
   decentralized protocol, distributed, zz1103, c2003, c200x, c20xx
%X "We present and analyze simple algorithms for decentralized protocols to
   compute aggregate functions, such as sums, averages, random samples,
   quantiles, etc. We show that when using Uniform Gossip for communication,
   the protocols converge to the true answer exponentially fast. We give a
   general framework that separates the details of the protocol from the
   communication mechanism, and analyze their mutual influence. In particular,
   we also analyze the convergence speed for flooding."
   [<A HREF="http://www-rcf.usc.edu/~dkempe/publications/aggregation.pdf">pdf@usc</A>]['05],
   [<A HREF="http://www.cs.cornell.edu/kempe/publications/aggregation.pdf">.pdf</A>][11/'03].

%A D. Kempe
%A J. Kleinberg
%A E. Tardos
%T Maximizing the spread of influence in a social network
%J KDD
%C Washington DC.
%P ?-?
%D 2003
%K conf, infuential, impact, networks, www, link, links, graph, graphs,
   marketing, marektting, advertising, spread, spreading, idea, ideas, zz1103,
   c2003, c200x, c20xx
%X "We study the problem of how to spread an innovation in a network, such
   as a social network. We consider several standard models from the sociology
   literature, and provide a constant-factor approximation algorithm for the
   problem of how to spend a given marketing budget to reach as large a
   fraction of the network as possible in expectation."
   [<A HREF="http://www-rcf.usc.edu/~dkempe/publications/spread.pdf">pdf@usc</A>]['05],
   [<A HREF="http://www.cs.cornell.edu/kempe/publications/spread.pdf">.pdf</A>][11/'03].
   [Also search for: influence network].

%A J. Sawada
%T A fast algorithm to generate necklaces with fixed content
%J Theor. Comp. Sci.
%I Elsevier
%V 301
%N 1-3
%P 477-489
%M MAY
%D 2003
%K jrnl, TCS, necklace, generating, c2003, c200x, c20xx, zz0605,
   combinatorial, Lyndon word, words, LyndonWord
%X "We develop a fast algorithm for listing all necklaces with fixed content.
   By fixed content, we mean the number of occurrences of each alphabet symbol
   is fixed. Initially, we construct a simple but inefficient algorithm by
   making some basic modifications to a recursive necklace generation alg..
   We then improve it by using two classic comb. optimization techniques. An
   analysis using straight forward bounding techniques is used to prove that
   the algorithm runs in constant amortized time."
   Paper: [<A HREF="http://dx.doi.org/10.1016/S0304-3975(03)00049-5">doi:10.1016/S0304-3975(03)00049-5</A>]['05].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Recn/Necklaces/">necklaces</A>].)

%A G. E. Farr
%T The Go polynomials of a graph
%J Theor. Comp. Sci.
%V 306
%N 1-3
%P 1-18
%M SEP
%D 2003
%K jrnl, TCS, polynomial, game, board, c2003, c200x, c20xx, GFarr, graphs,
   maths, theory, colouring, coloring, zz0205
%X "...for each vertex of a graph, we either leave it uncoloured or choose a
   colour uniformly at random from a set of available colours, with the choices
   for the vs. being independent & identically distributed. We ask for the
   prob. that the resulting partial assignment of colours has the following
   property: for every colour class, each component of the subgraph it induces
   has a vertex that is adjacent to an uncoloured vertex. In Go terms, we are
   requiring that every group is uncaptured. This definition leads to Go
   polynomials for a graph. Although these polynomials are based on properties
   that are less "local" in nature than those used to define more traditional
   graph polynomials such as the chromatic polynomial we show that they satisfy
   recursive relations based on local modifications similar in spirit to the
   deletion-contraction relation for the chromatic polynomial. ...show that they
   are #P-hard to compute in general, using a result on linear forms in
   logarithms from transcendental number theory. We also briefly record some
   correlation inequalities."  (auth@cs.mon@sh)
   [<A HREF="http://dx.doi.org/10.1016/S0304-3975(02)00831-9">doi:10.1016/S0304-3975(02)00831-9</A>]['05].

%A W. V. Quine
%T Mathematical Logic (Revised Ed.)
%I HarvardUP
%P 358
%D 2003
%K book, text, c2003, c200x, c20xx, mathematics, logic, theory, CSci, CSC
%X pb, us$28, us isbn:0674554515; us isbn13:978-0674554511.

%A S. S. Epp
%T Discrete Mathematics with Applications
%I BrooksCole
%P 928
%D 2003
%K book, text, c2003, c200x, c20xx, math, maths, comp sci, Discrete Mathematics
%X 3rd ed c2003; hb, us$150; us isbn:0534359450; us isbn13:978-0534359454.

%A S. Pemmaraju
%A S. Skiena
%T Computational Discrete Mathematics: Combinatorics and Graph Theory with
   Mathematica
%I CUP
%P 494
%D 2003
%K book, text, CUP, c2003, c200x, c20xx, mathematica, mathworld, maths,
   combinatorica
%X "With examples of all 450 functions in action plus tutorial text on the
   mathematics, this book is the definitive guide to Experimenting with
   Combinatorica, a widely used software package for teaching and research in
   discrete mathematics. ..."
   1st ed 2003; hb us$90; uk us isbn:0521806860; uk us isbn13:978-0521806862.

%A R. Fagin
%A R. Kumar
%A D. Sivakumar
%T Comparing top k lists
%J SIAM J. Discrete Math.
%V 17
%N 1
%P 134-160
%D 2003
%K jrnl, SIAM, c2003, c200x, c20xx, zz0513, permutation, partial, ranking,
   rankings, top k list, almost metric, distance, measure,
   rank aggregation problem, Kendall's tau, Spearman's footrule, rho
%X "... introduce various distance measures between 'top k lists.' Some of these
   dist.measures are metrics, while others are not. For each of these latter
   d.measures, we show that they are 'almost' a metric in the following two
   seemingly unrelated aspects: (i) they satisfy a relaxed version of the
   polygonal (hence, triangle) inequality, & (ii) there is a metric with +ve
   const. multiples that bound our measure above & below. This is not a
   coincidence - we show that these two notions of almost being a metric are the
   same. Based on the 2nd notion, we define two d.measures to be equivalent if
   they are bounded above & below by const. multiples of each other. We thereby
   identify a large & robust equivalence class of d.measures.  Besides the
   applications to the task of identifying good notions of (dis)similarity
   between two top k lists, our results imply polynomial-time constant-factor
   approxn algs. for the rank aggregation problem with respect to a large class
   of distance measures."
      "Kendall's tau turns out to be = to the # of exchanges needed in a
      bubble sort to convert one perm. to the other."
   -- [<A HREF="http://dx.doi.org/10.1137/S0895480102412856">doi:10.1137/S0895480102412856</A>]['13].
   [Also search for: permutation rank distance].

%A G. B. Dantzig
%A M. N. Thapa
%T Linear Programming 2: Theory and Extensions
%I Springer
%S Op. Res.
%P 456
%M JUL
%D 2003
%K book, text, c2003, c200x, c20xx, linear programming, LinearProgramming,
   optimisation, optimization, constrained, simplex, algorithm, interior point,
   methods, GUB, integer
%X 1st ed 2003; hb us$109; uk us isbn:0387986138; uk us isbn13:978-0387986135.
   "... the founder of this subject with his invention of the simplex alg. in
   the 1940s. In this 2nd vol. ... expanded to inc. such additional advanced
   topics as variants of the simplex method; interior point methods, GUB,
   decomposition, integer programming, & game theory. ..."
   [Also search for: linearProgramming].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Simplex_algorithm">wikip</A>]['12].)

%A L. A. Levin
%T The tale of one-way functions
%J Problems of Info. Transmission
%V 39
%P 92-103
%M JAN
%D 2003
%K jrnl, c2003, c200x, c20xx, zz0123, one way function, OWF, AUG 2003,
   cryptography
%X "... discusses & refines a number of concepts relevant to this problem. For
   instance, it gives the first combinatorial complete owf, i.e., a fn which is
   one-way if any fn is. There are surprisingly many subtleties in basic defns.
   ..."
   -- [<A HREF="https://doi.org/10.1023/A:1023634616182">doi:10.1023/A:1023634616182</A>]['23],
      cs/0012023@[<A HREF="https://arxiv.org/abs/cs/0012023">arXiv</A>]['23].
   Also see OWF@[<A HREF="https://en.wikipedia.org/wiki/One-way_function">wikip</A>]['23].

%A D. Kempe
%A J. Kleinberg
%A E. Tardos
%T Influential nodes in a diffusion model for social networks
%J Sub. to SODA 2004
%D 2004 ?
%K c200x, c20xx, graph, graphs, node, gossip, influence, impact, society,
   network, small world, degree, degrees, separation, who knows
%X [<A HREF="http://www-rcf.usc.edu/~dkempe/">@usc</A>]['05],
   [<A HREF="http://www.cs.washington.edu/homes/kempe/">home-page</A>][11/'03],
   [<A HREF="http://www.cs.cornell.edu/kempe/publications/">publ'ns</A>][11/'03].
   [Also search for: influence network].

%A P. Wegner
%A E. Eberbach
%T New models of computation
%J COMPJ
%V 47
%N 1
%P 4-9
%M JAN
%D 2004
%K jrnl, compj, theory, maths, Turing machine, thesis, UTM, c2004, c200x, c20xx,
   model, interaction, pi-calculus, super Turing, computability, zz0104,
   computation, Cockshott, Michaelson, zz0307
%X "...examines the limitations of TM's as a complete model of comp'n, &
   presents several models that extend [TMs]. Dynamic interaction of clients
   and servers on the Internet, an infinite adaptation from evolutionary
   computation, and robots sensing and acting are some examples of areas that
   cannot be properly described using Turing Machines and algorithms. They
   require new models of computation going beyond Turing Machines. We refer to
   such new models as superTuring models of computation. Three superTuring
   models of computation, namely Interaction Machines, the [pi-]calculus and
   the $-calculus are presented and explained, focussing on why they are better
   for the solution of computational problems. We expect that superTuring
   computation will become the central programming paradigm in the future."
   -- [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_47/Issue_01/470004.sgm.abs.html">www</A>][1/'04]  (28 refs)
   [Also search for: model computation Turing].
   Also see P.Cockshott & G.Michaelson,
            'Are There New Models of Computation?' Reply to Wegner and Eberbach,
            COMPJ, 50(2), pp.232-247, 2007,
            -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxl062">doi:10.1093/comjnl/bxl062</A>]['07].

%T Galois Connections and Applications
%E K. Denecke
%E M. Erne
%E S. L. Wismath
%I Kluwer
%S Math. and its Applications
%V 565
%P 501
%M FEB
%D 2004
%K book, text, classical, general, Galois theory, connection, maths,
   mathematics, algebra, c2004, c200x, c20xx
%X us$160, au$250; uk us isbn:1402018975.

%A C. Deppe
%T Strategies for the Renyi-Ulam-Game with fixed number of lies
%J TCS
%V 314
%N 1-2
%P 45-55
%M FEB
%D 2004
%K jrnl, lie, lies, liar, binary search, error correcting codes, Ulams, games,
   TCS, c2004, c200x, c20xx, faulty feedback
%X "...finding the minimal number L[l](M) of binary questions needed to find an
   unknown element of a set of cardinality M with a sequential strategy if at
   most l of the answers are lies. [If] l=0, |log M| questions are needed. Thus
   1 more question is necessary if the number of elements is doubled. We show
   that for every fixed l and sufficiently large M, then L[l](2M)<=L[l](M)+2
   and moreover L[l](3M/2)<=L[l](M)+1. ...bounds are sharp in infinitely many
   cases. [So] at most 1 question more than the information theoretic lower
   bound is needed to successfully find the unknown number. 1 of our strategies
   uses the minimum amount of adaptiveness during the search process."
   -- [<A HREF="http://www.mathematik.uni-bielefeld.de/ahlswede/papers/deppe.html">auth</A>][8/'04].
     Also see Deppe c2000
     -- [<A HREF="http://dx.doi.org/10.1016/j.tcs.2003.10.036">doi:10.1016/j.tcs.2003.10.036</A>][8/'04].

%A D. Kempe
%A J. Kleinberg
%A A. Demers
%T Spatial gossip and resource location protocols
%J JACM
%V 51
%N 6
%P 943-967
%M NOV
%D 2004
%K jrnl, JACM, c2004, c200x, c20xx, geographic, protocol, zz0205, distributed,
   information
%X [<A HREF="http://www-rcf.usc.edu/~dkempe/publications/gossip.pdf">pdf@usc</A>]['05].

%A K. Doets
%A J. van Eijck
%T The Haskell Road to Logic, Maths and Programming
%I King's Coll. Publ., London
%P 444
%M MAY
%D 2004
%K book, text, functional programming, FP, c2004, c200x, c20xx, math, maths,
   logic, mathematics, computer programming, Haskell, ghc
%X stg14, us$25, uk isbn:0954300696; uk isbn13:978-0954300692.
   (Also see [<A HREF="http://www.allisons.org/ll/FP/">FP</A>].)
   [Also search for: Haskell book FP].

%A H. J. Bungartz
%A M. Greibel
%T Sparse grids
%J Acta Numerica
%N 13
%P 147-269
%D 2004
%K jrnl, c2004, c200x, c20xx, sparse grid, numerical approximation, computation
%X us$110; isbn:0521838118; isbn13:9780521838115.
   [Also search for: sparse grids].

%A F. Chung
%T Laplacians and the Cheeger inequality for directed graphs
%J Annals of Combinatorics
%V 9
%N 1
%P 1-19
%M APR
%D 2005
%K jrnl, c2005, c200x, c20xx, zz0716, maths, graph, Cheeger inequality,
   conductance, circulation
%X "We consider Laplacians for directed graphs & examine their eigenvalues. We
   introduce a notion of a circulation in a directed g. & its connection with
   the Rayleigh quotient. We then define a Cheeger const. & establish the
   Cheeger inequality for directed gs.. These relns can be used to deal with
   various problems that often arise in the study of non-reversible Markov
   chains including bounding the rate of convergence & deriving comparison
   theorems."
   -- [<A HREF="http://dx.doi.org/10.1007/s00026-005-0237-z">doi:10.1007/s00026-005-0237-z</A>]['16].
   [Also search for: graph conductance Cheeger].

%A G. Gottlob
%A G. Greco
%A F. Scarcello
%T Pure Nash equilibria: Hard and easy games
%J J. A.I. Res.
%V 24,
%P 357-406
%D 2005
%K JAIR, jrnl, eJrnl, c2005, c200x, c20xx, zz0614, game theory, Nash equilbrium,
   NPH, payoff
%X "... complexity issues rel.to pure Nash equilibria of strategic games. We
   show that, even in very restrictive settings, determining whether a game has
   a pure Nash Equilibrium is NP-hard, while deciding whether a game has a
   strong Nash equilibrium is SigmaP2-complete. We then study practically
   relevant restns that lower the complexity. ... interested in quantitative &
   qualitative restns of the way each player's payoff depends on moves of other
   players. We say that a game has small neighborhood if the utility fn for each
   player depends only on (the actions of) a logarithmically small # of other
   players. The dependency structure of a game G can be expressed by a graph
   DG(G) or by a hypergraph H(G). By relating N.equilibrium problems to [CSPs]
   we show that if G has small neighborhood & if H(G) has bounded hypertree
   width (or if DG(G) has bounded treewidth), then finding pure Nash & Pareto
   equilibria is feasible in polynomial time. If the game is graphical, then
   these problems are LOGCFL-complete & thus in the class NC2 of highly
   parallelizable problems."
   -- [<A HREF="http://dx.doi.org/10.1613/jair.1683">doi:10.1613/jair.1683</A>]['14].

%A W. Hodges
%T Logic (2nd ed)
%I Penguin
%P 304
%D 2005
%K book, text, c2005, c200x, c20xx, maths, logic, predicate, deductive,
   intro, reasoning, mathematices, formal, L2Ref, L3Ref
%X 2nd ed 2005; pb us$13; uk us isbn:0141003146; uk us isbn13:978-0141003146.
   "If a man supports Arsenal one day and Spurs the next then he is fickle
   but not necessarily illogical. From this starting point, and assuming no
   previous knowledge of logic, Wilfrid Hodges takes the reader through the
   whole gamut of logical expressions in a simple and lively way. ..."

%A R. Bagnara
%A P. M. Hill
%A E. Ricci
%A E. Zaffanella
%T Precise widening operators for convex polyhedra
%J Science of Computer Programming
%V 58
%N 1-2
%P 28-56
%D 2005
%K jrnl, c2005, 200x, c20xx, zz0307, widen, widening, abstract interpretation,
   PPL, polyhedron, convex, NNC, Cousot, Halbwachs, standard
%X "... static analysis via abstract interpretation, convex polyhedra
   constitute the most used abstract domain among those capturing numerical
   relational information. Since the domain of convex polyhedra admits infinite
   ascending chains, it has to be used in conjunction with appropriate
   mechanisms for enforcing & accelerating the convergence of fixpoint
   computations. Widening operators provide a simple & general characterization
   for such mechanisms. For the domain of convex polyhedra, the original
   widening operator proposed by Cousot & Halbwachs amply deserves the name of
   standard widening ..."
   [also search for: PPL].

%A R. Diestel
%T Graph Theory
%I SpringerVerlag
%S Graduate Texts in Mathematics
%V 173
%P 415
%D 2005
%K book, text, c2006, c200x, c20xx, l4ref, l5ref, math, maths, graph theory,
   graphs, subgraph
%X 5th ed 2016, hb us$71; uk us isbn:3662536218; uk us isbn13: 978-3662536216;
   3rd ed 2005, hb      ; uk us isbn:3540261826;
   3rd ed 2006, pb us$45; uk us isbn:3540261834; uk us isbn13:978-3540261834;
   also see [<A HREF="http://diestel-graph-theory.com/">www</A>]['10].

%A D. C. Lay
%T Linear Algebra and Its Applications
%I AddisonWesley
%P 576
%D 2005
%K book, text, c2005, c200x, c20xx, numerical, scientific, method, methods
%X 3rd ed, hb; uk us isbn:0321287134; uk us isbn13:978-0321287137.

%A K. Edwards
%A G. Farr
%T On monochromatic component size for improper colourings
%J Discrete Appl. Maths.
%V 148
%N 1
%P 89-105
%M APR
%D 2005
%K jrnl, c2005, c200x, c20xx, GFarr, maths, graph, colour, color, colouring,
   coloring, improper, monochromatic, components
%X "... improper lambda-colourings of & focuses on the sizes of the
   monochromatic components ... . Consider the following three simple ops.,
   which should, heuristically, help reduce m.component size: (a) assign to a
   vertex the colour that is least popular among its neighbours; (b) change the
   colours of any two adjacent differently coloured vertices, if doing so
   reduces the number of monochromatic edges; & (c) change the colour of a
   vertex, if by so doing you can reduce the size of the largest monochromatic
   component containing it without increasing the # of monochromatic edges. If a
   colouring cannot be further improved by these operations, then we regard it
   as locally optimal. We show that, for such a locally optimal 2-colouring of a
   g. of max. degree 4, the max. monochromatic component size is
   O(2^((2 log2 n)(1/2))). The opn-set (a)-(c) appears to be one of the simplest
   that achieves a o(n) bound on m.component size. Recent work by Alon, Ding,
   Oporowski & Vertigan, & then Haxell, Szabo & Tardos, has shown that some
   algs. can do much better, achieving a const.bound on m.component size.
   However, the simplicity of our opn-set, & of the assoc. local search alg.,
   make the alg., & our locally opt.colourings, of interest in their own right."
   -- [<A HREF="http://dx.doi.org/10.1016/j.dam.2004.10.005">doi:10.1016/j.dam.2004.10.005</A>]['11].

%A B. Barak
%A A. Sahai
%T How to play almost any mental game over the Net - concurrent composition
   using super-polynomial simulation.
%J Proc. 46th FOCS
%I IEEE
%D 2005
%K conf, FOCS, c2005, c200x, c20xx, security, zero knowledge proof, proofs
%X [<A HREF="http://www.cs.princeton.edu/~boaz/Papers/conc-comp.pdf">pdf@princeton</A>]['07],
   [<A HREF="http://www.cs.princeton.edu/~boaz/">boaz@princeton</A>]['07].

%A S. Khot
%T Hardness of approximating the shortest vector problem in lattices
%J JACM
%V 52
%N 5
%M SEP
%D 2005
%K jrnl, JACM, c2005, c200x, c20xx, zz1020, short, shortest vector problem, SVP,
   lattice, closest, CVP
%X "Let p > 1 be any fixed real. We show that assuming NP not subset RP, there
   is no polynomial time algorithm that approximates the Shortest Vector Problem
   (SVP) in l_p norm within a constant factor. ...
   -- [<A HREF="https://doi.org/10.1145/1089023.1089027">doi:10.1145/1089023.1089027</A>]['20].
   Also see
      LP@[<A HREF="https://en.wikipedia.org/wiki/Lattice_problem">wikip</A>]['20].
   [Also search for: shortest vector lattice].

%A J. W. Garson
%T Modal Logic for Philosophers
%I CUP
%P 470
%D 2006
%K book, text, CUP, c2006, c200x, c20xx, maths, philosophy, logic,
   quantified, designator
%X pb, us$34, uk us isbn:0521682290; isbn13:978-0521682299.

%A M. Davis
%T The Church-Turing Thesis: Consensus and opposition
%J Proc. Computability in Europe 2006
%S LNCS
%V 3988
%P 125-132
%D 2006
%K conf, c1006, c200x, c20xx, Church, thesis, model, models of computation,
   super, machine, Turing, Church, thesis
%X pdf@[<A HREF="http://people.cs.uchicago.edu/~simon/TEACH/28000/DavisUniversal.pdf">uchicago</A>]['09].
   [Also search for: model computation Turing].

%A E. Althaus
%A R. Naujoks
%T Computing Steiner minimum trees in Hamming metric
%J Proc. 17th annual ACM-SIAM symposium on Discrete algorithms
%P 172-181
%D 2006
%K conf, c2006, c200x, c20xx, Steiner tree, trees, Hamming distance,
   phylogenetic, evolutionary, family
%X "... a branch and bound method developed by Penny and Hendy have been the
   fastest for more than 20 years. [Here] describe a new pruning approach that
   is superior to previous methods and its implementation."   [19 refs].
   "...call a topology spanning all terminals a full-t. otherwise a partial-t..
   ... 1st we construct all rooted topologies of all subsets of the terminals up
   to cardinality n/2, which we cannot provably exclude from being part of an
   optimal topology. [2nd] construct the full topologies by combining all poss.
   triples of partial topologies whose terminals are a partition of T. ...
   partial topologies spanning k terminals are constructed by combining all
   partial topologies spanning i & k-i terminals (1 <= i < k/2) whose terminal
   sets are disjoint."
   -- [<A HREF="http://doi.acm.org/10.1145/1109557.1109578">doi:10.1145/1109557.1109578</A>]['09], uk us isbn:0898716055,
   pdf@[<A HREF="http://www.mpi-inf.mpg.de/~althaus/hamming_conf.pdf">mpg.de</A>]['09].
   [Also search for: Steiner phylogenetic tree], and
   [also search for: phylogenetic tree MolBio].

%A K. Briggs
%T Implementing exact real arithmetic in Python, C++ and C
%J Theor. Comp. Sci.
%V 351
%N 1
%P 74-81
%M FEB
%D 2006
%K jrnl, TCS, c2006, c200x, c20xx, zz0807, cc, Boehm, computer arithmetic,
   real, reals, scaled integer, floating point, rational, mpfs
%X "... efficient implementation of the scaled-integer exact real arith. model
   intro. by Boehm ['86] & others. ... represents a real # with a automatically
   controlled level of precision by a rational with implicit denominator. I
   describe 3 practical codes, in python, C++ & C. These allow the convenient
   use of this computational paradigm in commonly used imperative languages."
   -- [<A HREF="http://dx.doi.org/10.1016/j.tcs.2005.09.058">doi:10.1016/j.tcs.2005.09.058</A>]['07],
      [<A HREF="http://keithbriggs.info/">keithbriggs.info</A>]['07] & see.../mpfs.html.
   [Also search for: computer arithmetic].

%A P. Heggernes
%T Minimal triangulations of graphs: A survey
%J Disc. Maths.
%V 306
%N 3
%P 297-317
%M FEB
%D 2006
%K jrnl, intro, c2006, c200x, c20xx, zz0913, minimal triangulation,
   triangulated, graph, maths, separator, separators, chordal, edges,
   decomposable model, stats, algorithm
%X "Any given graph can be embedded in a chordal graph by adding edges, & the
   resulting c.g. is called a triangulation of the input g.. ... study minimal
   triangulations, which are the result of adding an inclusion minimal set of
   edges to produce a tri.. This topic was first studied [in] sparse matrices &
   vertex elimination in graphs. Today we know that minimal t. are closely
   related to minimal separators of the input graph. Since the 1st papers
   presenting minimal tri. algs. appeared in 1976, several characterizations of
   min. tris. have been proved, & a variety of algs. exist for computing minimal
   tris. of both general & restricted graph classes. ... presents & ties
   together these results in a unified modern notation, keeping an emphasis on
   the algs.."    [via F.P.]
   -- [<A HREF="http://dx.doi.org/10.1016/j.disc.2005.12.003">doi:10.1016/j.disc.2005.12.003</A>]['13].
   [Also search for: chordal graph] and
   [also search for: minimal triangulation].

%A A. Berry
%A A. Sigayret
%A C. Sinoquet
%T Maximal sub-triangulation in pre-processing phylogenetic data
%J Soft Computing
%V 10
%N 5
%P 461-468
%M MAR
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0913, chordal, graph, maths, family, tree,
   2pair, 2 pairs, triangulation, subtriangualtion, dissimilarity, phylogeny,
   sandwich family
%X "... propose a new method for pre-processing the corr. dissimilarity matrix,
   which is related to the property that the distance matrix of a phylogeny
   (called an additive matrix) describes a sandwich family of chordal graphs.
   As experimental data often yield distance values which are known to be
   under-estimated, we address the issue of correcting the data by increasing
   the distances which are incorrect. This is done by computing, for each graph
   of the sandwich family, a maximal chordal subgraph."  [via F.P.]
   -- [<A HREF="http://dx.doi.org/10.1007/s00500-005-0507-7">doi:10.1007/s00500-005-0507-7</A>]['13].
   [Also search for: graph triangulation].

%A I. Bezakova
%A A. Kalai
%A R. Santhanam
%T Graph model selection using maximum likelihood
%J ICML
%P 105-112
%M JUN
%D 2006
%K conf, ICML, ICML06, ICML23, c2006, c200x, c20xx, zz0420, maths, graph, model,
   graphModel, random, probability, likelihood, power law,
   preferential attachment, small world
%X "... propose a model seln criterion for graph models. Since each model is in
   fact a prob. distn over graphs, we suggest using [M.L.] to compare g.models &
   select their parameters. Interestingly, for the case of g.ms., computing
   likelihoods is a difficult algorithmic task. However, we design & implement
   MCMC algs for computing the [M.L.] for 4 popular models: a power-law random
   g.m., a preferential attachment m., a small-world m., & a uniform random
   g.m.. We hope that this novel use of M.L. will objectify comparisons between
   graph models."  [via K.L.]
   -- [<A HREF="https://doi.org/10.1145/1143844.1143858">doi:10.1145/1143844.1143858</A>]['20].
   [Also search for: graphModel].

%A F. R. K. Chung
%T Spectral Graph Theory
%I AMS
%S Regional Conference Series in Mathematics
%V 92
%P 207
%D 1996
%K book, text, AMS, CBMS, c1996, c199x, c19xx, spectral, maths, graph, spectrum,
   eigenvalues, eigenvectors
%X 1st ed 1992; pb us$25; us isbn:0821803158; us isbn13:978-0821803158.
   "... based on 10 lectures given at the CBMS workshop on spectral graph theory
   in June '94 at Fresno State U.. Chung's well-written exposition can be
   likened to a conversation with a good teacher--one who not only gives you the
   facts, but tells you what is really going on, why it is worth doing, and how
   it is rel. to familiar ideas in other areas. ..."
   (Also see auth@[<A HREF="http://www.math.ucsd.edu/~fan/research/revised.html">ucsd</A>].)

%A M. Hegland
%A C. Burden
%A L. Santoso
%A S. MacNamara
%A H. Booth
%T A solver for the stochastic master equation applied to
   gene regulatory networks
%J J. Computational and Applied Maths.
%V ?
%N ?
%P ?-?
%D 2007 to appear
%K jrnl, c2007, c200x, c20xx, ANuni, MolBio, genes, regulation, regulate,
   network, equations, curse, dimensionality, sparse grid, grids, approximate,
   numerical approximation
%X "An important driver of gene regulatory networks is noise arising from the
   stochastic nature of interactions of genes, their products & regulators. ...
   such systems are stochastic & can be modelled by the chemical master equns..
   ... curse of dimensionality which occurs when one attempts to integrate these
   equns.. While stochastic simulation techniques effectively address the curse,
   many repeated simulations are required to provide precise information about
   stationary points, bifurcation phenomena & other properties of the stochastic
   processes. An alternative way to address the curse of dimensionality is
   provided by sparse grid approximations. The sparse grid methodology is
   applied & the application demonstrated to work efficiently for up to 10
   proteins. As sparse grid methods have been developed for the approximation of
   smooth functions, a variant for infinite sequences had to be developed
   together with a multiresolution analysis similar to Haar wavelets. Error
   bounds are provided which confirm the effectiveness of sparse grid
   approximations for smooth high-dimensional probability distributions."
   [<A HREF="http://dx.doi.org/10.1016/j.cam.2006.02.053">doi:10.1016/j.cam.2006.02.053</A>]['07].

%A S. E. Schaeffer
%T Graph clustering
%J Comp. Sci. Rev.
%V 1
%N 1
%P 27-64
%M AUG
%D 2007
%K jrnl, c2007, c200x, c20xx, zz0716, maths, graph, clustering, cluster
%X "...  finding sets of 'related' vertices in graphs. We review the many
   defins for what is a cluster in a g. & measures of cluster quality. ...
   present global algs. for producing a clustering for the entire vertex set of
   an input g., after which we discuss the task of identifying a cluster for a
   specific seed vertex by local computation. Some ideas on the application
   areas of g.clustering algs. are given. We also address the problematics of
   evaluating clusterings & benchmarking cluster algs.."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cosrev.2007.05.001">doi:10.1016/j.cosrev.2007.05.001</A>]['16],
   or [<A HREF="http://dollar.biz.uiowa.edu/~nstreet/graphClustering.pdf">uiowa</A>]['16].
   [Also search for: maths graph clustering].

%A B. Chazelle
%T Computing: The security of knowing nothing
%J Nature
%V 446
%P 992-993
%M APR
%D 2007
%K news, c2007, c200x, c200x, zero knowledge proof, proofs, security, survey
%X [5 refs] [<A HREF="http://dx.doi.org/:10.1038/446992a">doi:doi:10.1038/446992a</A>]['07]
   Also see:  B a r a k  c2005.

%A N. Chen
%A N. Wang
%A B. Shi
%T A new algorithm for encoding and decoding the Hilbert order
%J SPE
%V 37
%P 897-908
%M JUN
%D 2007
%K jrnl, SPE, c2007, c200x, c20xx, space filling curve, curves, zz0607, coding
%X "An iterative alg. is described, based on the replication process of the
   Hilbert matrix, for encoding & decoding the Hilbert order. The time
   complexity ... is smaller than those published previously, & the space
   complexity is bounded by a constant. ... wider applicability when compared
   with existing algs. for certain machine-word lengths. A new variant of the
   Hilbert curve is suggested to overcome a shortcoming of the trad. Hilbert
   curve for the mapping problem. The proposed coding alg. for the trad. Hilbert
   curve are also applicable to the new variant without increasing the time &
   space complexities."                    [[Hilbert's is the "square" curve.]]
   "... A coding proc. is based on a 1-1 mapping between z & (x,y) given the
   resolution n, where z is called the Hilbert code & (x,y) is the coord.
   at z on the Hilbert curve ... z in [0,4**n). ..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.793">doi:10.1002/spe.793</A>]['07].

%A G. E. Farr
%T On the Ashkin-Teller model and Tutte-Whitney functions
%J Combinatorics Probability and Computing
%V 16, ed 2
%I CUP
%P 251-260
%D 2007
%K c2007, c200x, c20xx, CUP, function, maths, GFarr, statistical mechanics,
   graph
%X "The partition fns of the Ising & Potts models in statistical mechanics are
   well known to be partial evaluations of the Tutte-Whitney polynomial of the
   appropriate graph. ... we show that the symmetric Ashkin-Teller partition fn
   can be obtained from a generalized T-W fn which is intermediate in a precise
   sense between the usual T-W polynomialof the graph & that of its dual."
   -- [<A HREF="https://doi.org/10.1017/S0963548306007966">doi:10.1017/S0963548306007966</A>]['24].
   (Also see Ashkin-Teller, 1943, [<A HREF="https://doi.org/10.1103/PhysRev.64.178">doi:10.1103/PhysRev.64.178</A>]['24].)

%A W. H. Press
%A S. A. Teukolsky
%A W. T. Vetterling
%A B. P. Flannery
%T Numerical Recipes: The Art of Scientific Computing
%I CUP
%P 1256
%D 2007
%K book, text, c2007, c200x, c20xx, recipe, scientific computing,
   numerical methods, method, linear algebra, interpolation, integration,
   optimization, optimisation, minimise, maximise,
   ODE, PDE, Quasi-Newton, QuasiNewton
%X hb, 3rd ed, us$58; uk us isbn:0521880688; uk us isbn13:978-0521880688.
   E.g., Sec.10.9. Quasi-Newton or Variable Metric Methods in Multidimensions,
         [<A HREF="http://apps.nrbook.com/empanel/index.html#pg=521">p.521</A>]['14].

%A M. H. Albert
%A R. E. L. Aldred
%A M. D. Atkinson
%A H.P. van Ditmarsch
%A C.C. Handley
%A D.A. Holton
%A D. J. McCaughan
%A C. W. Monteith
%T Cyclically closed pattern classes of permutations
%J Austral. J. Comb.
%V 38
%P 87-100
%D 2007
%K jrnl, c2007, c200x, c20xx, maths, permutation, pattern, class, cycle,
   cyclic, closure, closed, superpermutation
%X "The cyclic closure of a perm. pattern class is def. as the set of all the
   cyclic rot'ns of its perms..  E.g.s of finitely based classes whose cyclic
   closure is also finitely based are given as well as an e.g. where the cyclic
   closure is not f.b..  Some enumeratons of cyclic closures are computed."
     ("A perm. pi is said to be a 'superpermutation' of (or pattern within) a
     perm. sigma if sigma has a subseq that is order isomorphic to pi.)
   -- pdf@[<A HREF="http://www.cs.otago.ac.nz/staffpriv/mike/Papers/CyclicClosure/CyclicJournal.pdf">otago</A>]['10];
   lastAuth@[<A HREF="http://cs.anu.edu.au/~monteith/">anu</A>]['10]
   (sup is B. M c K a y).

%A B. Fuchs
%A W. Kern
%A D. Molle
%A S. Richter
%A P. Rossmanith
%A X. Wang
%T Dynamic programming for minimum Steiner trees
%J Theory of Computing Systems
%I SpringerNY
%V 41
%N 3
%P 493-500
%M OCT
%D 2007
%K c2007, c200x, c20xx, minimum, Steiner tree, trees, dynamic programming,
   algorithm, Dreyfus-Wagner, parameterized, full set
%X "... new dynamic programming alg. that solves the minimum Steiner tree
   problem on graphs with k terminals in time O*(c^k) for any c > 2. This
   improves the running time of the previously fastest parameterized alg. by
   Dreyfus-Wagner of order O*(3^k) and the so-called "full set dynamic
   programming" algorithm solving rectilinear instances in time O*(2.38^k)."
   -- [<A HREF="http://dx.doi.org/10.1007/s00224-007-1324-4">doi:10.1007/s00224-007-1324-4</A>]['07], or
   ps@[<A HREF="http://tcs.rwth-aachen.de/pub/papers/jsteiner.ps">aachen</A>]['09],
   ps@[<A HREF="http://www.zaik.uni-koeln.de/~ftp/paper/zaik2005-492.ps.gz">koeln</A>]['09].
   (NB. The "S. t. problem on *graphs*.")

%A M. Aigner
%T A Course in Enumeration
%I Springer
%S Graduate Texts in Math.
%D 2007
%K book, text, maths, c2007, c200x, c20xx, L5Ref, enumerate, combinatorics
%X 1st ed 2007; hb us$72; uk us isbn:3540390324; uk us isbn13:978-3540390329.
   "Combinatorial enumeration is a readily accessible subject full of easily
   stated, but sometimes tantalizingly difficult problems. ... leads the reader
   in a leisurely way from basic notions of combinatorial enumeration to a
   variety of topics, ranging from algebra to statistical physics. ... organized
   in 3 parts: Basics, Methods, & Topics. The aim is to introduce readers to a
   fascinating field, & to offer a sophisticated source of information for
   professional mathematicians desiring to learn more. There are 666 exercises,
   & every chapter ends with a highlight section, discussing in detail a
   particularly beautiful or famous result."

%A K. Morgan
%A G. Farr
%T Approximation algorithms for the maximum induced planar and
   outerplanar subgraph problems
%J J. of Graph Algorithms and Applications
%V 11
%P 165-193
%D 2007
%K c2007, c200x, c20xx, maths, GFarr, graph, planar, outerplanar,
   Maximum Induced Planar Subgraph problem, MIPS
%X "... finding the largest subset of vertices of a g. that induces a planar
   subg. is known as the Maximum Induced Planar Subgraph problem (MIPS). ...
   new approximation algs. for MIPS ... The results of an extensive study of the
   performance of these and existing MIPS approximation algs. on randomly
   gen.graphs ... . Efficient algs. for finding large induced outerplanar graphs
   are also given. One of these algs. is shown to find an induced outerplanar
   subg. with at least 3n/(d+5/3) vertices for gs. of n vertices with maximum
   degree at most d. The results ... indicate that most existing algs. perform
   substantially better than the existing lower bounds indicate."
   -- pdf@[<A HREF="http://www.cs.brown.edu/publications/jgaa/accepted/2007/MorganFarr2007.11.1.pdf">br'wn</A>]['10].

%A L. A. Zager
%A G. C. Verghese
%T Graph similarity scoring and matching
%J Appl. Math. Lett.
%V 21
%N 1
%P 86-94
%M JAN
%D 2008
%K jrnl, AML, c2008, c200x, c20xx, zz0920, maths, graph, similarity, matching,
   graphAlignment
%X "We outline a class of g.similarity measures that uses the struct. sim. of
   local n'hoods to derive pairwise sim.scores for the nodes of two different
   gs., & present a related sim.measure that uses a linear update to generate
   both node & edge sim.scores. ... then applied to the task of g.matching."
   -- [<A HREF="https://doi.org/10.1016/j.aml.2007.01.006">doi:10.1016/j.aml.2007.01.006</A>]['20].
   [Also search for: graphAlignment]  and  [also search for: graph MCS].

%A J. Nie
%A P. A. Parrilo
%A B. Sturmfels
%T Semi-definite representation of the k-ellipse
%J IMA Vols. in Math. & its Applicns
%V 146
%P 117-132
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0513, SemiDefinite, programming, SDP, problem,
   geometric median, 1median
%X "The k-ellipse is the plane algebraic curve consisting of all pts whose sum
   of distances from k given pts is a fixed number. The polynomial equn defining
   the k-ellipse has degree 2^k if k is odd & degree 2^k-binom k k/2 if k is
   even. We express this polyn. equn as the determinant of a symmetric matrix of
   linear polyns.. Our repn extends to weighted k-ellipses & k-ellipsoids in
   arbitrary dimensions, & it leads to new geometric applicns of semidefinite
   programming."
   -- 0702005@[<A HREF="http://arxiv.org/abs/math/0702005">arXiv</A>]['13].
   (Also see GM@[<A HREF="http://en.wikipedia.org/wiki/Geometric_median">wikip</A>]['13].)
   [Also search for: geometric median]  and  [also search for: Semidefinite].

%A K. Edwards
%A G. Farr
%T Planarization and fragmentability of some classes of graphs
%J Discrete Mathematics
%V 308
%P 2396-2406
%D 2008
%K jrnl,c2008, c200x, c20xx, maths, GFarr, graph, nearly planar, planarization,
   vertex removal, Maximum Induced Planar Subgraph problem
%X "The coefficient of fragmentability of a class of graphs measures the
   proportion of vertices that need to be removed from the gs. in the class [to]
   leave behind bounded sized components. ...  we give fragmentability bounds
   for some classes of gs. of bounded avg. degree, as well as classes of given
   thickness, the class of k-colourable graphs, & the class of n-dimensional
   cubes. [To] establish the fragmentability results for bounded average degree,
   we prove that the proportion of vertices that must be removed from a g. of
   avg. degree at most d in order to leave behind a planar subg. (in fact, a
   series-parallel subgraph) is at most (d-2)/(d+1), provided d >= 4 or the g.
   is connected d >= 2. ... yields an alg. for finding large induced planar
   subgs. & (under certain condns) a LWB on the size of the induced planar subg.
   it finds. This bound is similar in form to the one we found for a previous
   alg. we developed for that problem, but applies to a larger class of gs.."
   -- pdf@[<A HREF="http://www.csse.monash.edu.au/~gfarr/research/planfrag-revised.pdf">mon@sh</A>]['10].

%A J. W. Eaton
%A D. Bateman
%A S. Hauberg
%T GNU Octave Manual Version 3
%I NetworkTheory
%D 2008
%K book, text, c2008, c200x, c20xx, Gnu Octave, numerical, methods, computing,
   algorithm, matrix, matrices, sparse, vectors, non, linear, nonlinear,
   problem
%X 3rd ed 2008; pb us$30; isbn:095461206X; isbn13:978-0954612061.
   "... guide to GNU Octave, an interactive environment for num. comp.. GNU
   Octave provides a convenient command-line interface for solving linear &
   nonlinear problems using vectors & matrices. This updated edition of the
   manual covers v.3 of [it], & includes documentation for new features such as
   sparse matrices, linear programming and computational geometry."
   See man@[<A HREF="http://www.network-theory.co.uk/octave/manual/">net.-theo.</A>]['14].

%T The Princeton Companion to Mathematics
%E T. Gowers
%E J. Barrow-Green
%E I. Leader
%I PrincetonUP
%P 1008
%D 2008
%K book, text, c2008, c200x, c20xx, maths, survey, L4Ref, L5Ref
%X 1st ed 2008; hb us$72; uk us isbn:0691118809; uk us isbn13:978-0691118802.
   "... TG, a recipient of the Fields Medal, it presents nearly 200 entries,
   written especially for this book by some of the world's leading
   mathematicians, that introduce basic mathematical tools and vocabulary; trace
   the development of modern mathematics; explain essential terms and concepts;
   examine core ideas in major areas of mathematics; describe the achievements
   of scores of famous mathematicians; explore the impact of mathematics on
   other disciplines such as biology, finance, and music ..."

%A F. Ruskey
%T Generating balanced parenthesis strings by prefix shifts
%J CATS, Wollongong
%V 77
%P 107-115
%M JAN
%D 2008
%K conf, CATS, c2008, c200x, c20xx, zz1118, trees, Dyck word, words, path,
   paths, generate, enumerate, rank, ranking, unranking, CoolCat, CoolLex,
   prefix shift, loopless, parentheses, brackets, Catalan numbers, Kasa
%X "We show that the set B_n of balanced parentheses strings with n left & n
   right parentheses can be generated by prefix shifts. If b_1,b_2,...,b_{2n} is
   a member of B_n, then the k-th prefix shift is the string b_1, b_k, b_2,
   ..., b_{k-1}, b_{k+1}, ..., b_{2n}. Prefix shift algs. are also known for
   combinations, & permutations of a multiset; the combination alg. appears in
   fascicles of Knuth, vol.4. We show that the alg. is closely related to the
   combination alg., & like it, has a loopless implementation, & a ranking alg.
   that uses O(n) arithmetic ops.. [&] the alg. can be directly translated to
   generate all binary trees by a loopless implementation that makes a constant
   # of pointer changes for each successively generated tree."
   -- pdf@[<A HREF="https://webhome.cs.uvic.ca/~ruskey/Publications/Coollex/CoolCat.html">uvic.ca</A>]['18],
      pdf@[<A HREF="https://dl.acm.org/citation.cfm?id=1379361.1379382">acm.org</A>]['19],
      [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.205.3821">c'teseer</A>]['19].
   [Also search for: Dyck paths].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Recn/Brackets/">parentheses</A>].)

%A J. Nocedal
%A S. Wright
%T Numerical Optimization
%I SpringerVerlag
%P 580
%D 2009
%K book, text, c2009, c200x, c20xx, numerical methods, computing, linear,
   quadratic, programming, LinearProgramming, QuadraticProgramming, methods,
   optimisation, constraint, optimize, optimise, minimize, maximize, problem
%X 2nd ed 2009; hb us$77; uk us isbn:0387303030; uk us isbn13:978-0387303031.
   "... mathematical programming covers numerical methods for finite-dimensional
   optimization problems. It begins with very simple ideas progressing through
   more complicated concepts, concentrating on methods for both unconstrained
   and constrained optimization."
   [Also search for: linearProgramming].

%A Z. Kasa
%T Generating and ranking of Dyck words
%J Acta Universitatis Sapientiae, Informatica
%V 1
%N 1
%P 109-118
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1118, Dyck word, words, path, paths, generate,
   enumerate, Catalan numbers, PosDyckWords, ranking, unranking, nth
%X "A new alg. to generate all Dyck words is presented ... used in ranking &
   unranking Dyck words. We emphasize the importance of using Dyck words in
   encoding objects related to Catalan numbers. As a consequence of formulas
   used in the ranking alg. we can obtain a recursive formula for the nth
   Catalan number."  [7 refs.]
   -- [<A HREF="http://www.acta.sapientia.ro/acta-info/C1-1/info1-9.pdf">www</A>]['18] and
   1002.2625@[<A HREF="https://arxiv.org/abs/1002.2625">arXiv</A>][2/2010].
   [Also search for: Dyck paths]  and  [also search for: Ruskey Dyck].

%A L. Fortnow
%T Viewpoint: Time for computer science to grow up
%J CACM
%V 52
%N 8
%P 33-35
%M AUG
%D 2009
%K CACM, news, views, c2009, c200x, c20xx, zz0621, computer science, Comp Sci,
   CompSci, CSci, scientific, university, academic, research, conference,
   conferences, journals, papers, KPI, KPIs
%X "Unlike every other academic field, CS uses confs rather than journals as the
   main publn venue. While this made sense for a young discipline, our field has
   matured & the conf. model has fractured the discipline & skewered it toward
   short-term, deadline-driven research. ..."
   -- [<A HREF="https://doi.org/10.1145/1536616.1536631">doi:10.1145/1536616.1536631</A>]['21]  (via GF).

%A P. Boldi
%A M. Santini
%A S. Vigna
%T Permuting Web and Social Graphs
%J Internet Math.
%V 6
%N 3
%P 257-283
%D 2009
%K eJrnl, jrnl, c2009, c200x, c20xx, zz0817, maths, graph, network, web, WWW,
   compress, social, webGraph, transposed, shingle orderings, backlink
%X "... it has been clear that the ordering of the nodes of a web graph has a
   fundamental influence on the comp. rate (usually expressed as the # of bits
   per link). ... LINK database, for instance, investigated three different
   approaches: an extrinsic ordering (URL ordering) & two intrinsic orderings
   based on the rows of the adjacency matrix (lexicographic & Gray code); they
   concluded that URL ordering has many advantages in spite of a small penalty
   in comp.. ... we approach this issue in a more systematic way, testing some
   known orderings & proposing some new ones. Our experiments are made in the
   WebGraph framework, & show that the comp. technique & the structure of the
   graph can produce sig. different results. ... show that for a transposed web
   graph, URL ordering is sig. less effective, & that some new mixed orderings
   combining host information & Gray/lexicographic orderings outperform all
   previous methods: in some large transposed graphs they yield the quite
   incredible comp. rate of 1 bit per link. We experiment with these simple
   ideas on some nonweb social n/wks & obtain results that are extremely
   promising & are v.close to those recently achieved using shingle orderings &
   backlink comp. schemes."
   [Also search for: compress graph].

%A S. Torquato
%A Y. Jiao
%T Dense packings of the Platonic and Archimedean solids
%J Nature
%V 460
%P 876-879
%M AUG
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0310, Platonic, Archimedean, solid, solids,
   polyhedron, polyhedra, lattice, pack, packing, packed, tile, tiled, tiling,
   3D, space
%X "... we formulate the generation of dense packings of polyhedra as an
   optimization problem, using an adaptive fundamental cell subject to periodic
   boundary conditions (... the 'adaptive shrinking cell' scheme). Using a
   variety of multi-particle initial configurations, we find the densest known
   packings of the 4 non-tiling Platonic solids (the tetrah., octah., dodecah.
   & icosah.) in 3D Euclidean space. The densities are 0.782.., 0.947.., 0.904..
   & 0.836.., resp.. ...  conjecture that the densest packings of the Platonic
   & Archimedean solids with central symmetry are given by their corr. densest
   lattice packings. This is the analogue of Kepler's sphere conjecture for
   these solids."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08239">doi:10.1038/nature08239</A>].
   [["...the truncated tetrahedron is the only 'non-chiral' Archimedean solid
     that is not centrally symmetric. This subtle distinction does not affect
     any of the results, conclusions or conjectures in our paper." 25/2/'10.]]

%A P. Van Mieghem
%T Graph Spectra for Complex Networks
%I CUP
%P 362
%M JAN
%D 2011
%K book, text, CUP, c2011, c201x, c20xx, vanMieghem, maths, graph, spectra,
   spectrum, complex, network
%X 1st ed 2011; hb us$103; uk us isbn:052119458X; uk us isbn13:978-0521194587.
   "... provides a concise intro. to the theory of graph spectra & its
   applications to the study of complex n/ws. Covering a range of types of
   graphs & topics important to the analysis of complex systems, this guide
   provides the math.foundation needed to understand & apply spectral insight to
   real-world systems. In particular, the general properties of both the
   adjacency & Laplacian spectrum of graphs are derived & applied to complex
   n/ws. ..."

%A E. Even-Dar
%A A. Shapira
%T A note on maximizing the spread of influence in social networks
%J IPL
%V 111
%N 4
%D 2011
%K jrnl, IPL, c2011, c201x, c20xx, social network, influence, node, spread,
   viral marketing, advertising, EvenDar
%X "... given a social n/w rep. as a graph & are required to find the set of the
   most 'influential' individuals that by introducing them with a new technology
   we maximize the expected # of individuals in the n/w, later in time, that
   adopt the new t.. ... has applications in viral marketing ... provide very
   simple & efficient algs. for solving this problem. An interesting special
   case of our result is that the most natural heuristic soln, which picks the
   nodes in the n/w with the highest degree, is indeed the optimal solution."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2010.11.015">doi:10.1016/j.ipl.2010.11.015</A>]['12].
   [Also search for: influence network].

%A J. H. Conway
%A Y. Jiau
%A S. Torquato
%T New family of tilings of three-dimensional Euclidean space by tetrahedra and
   octahedra
%J PNAS
%V 109
%N 21
%P ?-?
%M JUN
%D 2011
%K jrnl, PNAS, c2011, c201x, c20xx, zz0512, JHConway, maths, tiling,
   tessellation, tetrahedron, octahedron, 3D, R3, space, Delaunay,
   face-centered cubic, fcc, lattice, polyhedra, optimal lattice packing,
   symmetry, symmetric, octet truss
%X "It is well known that two regular tetrahedra can be combined with a single
   regular octahedron to tile (fill) [3D] Euclidean space R^3. ...
   was believed that such a tiling, which is the Delaunay tessellation of the
   face-centered cubic (fcc) lattice, & its closely related stacking variants,
   are the only tessellations of R3 that involve two different regular
   polyhedra. Here we identify & analyze a unique family comprised of a
   noncountably infinite # of periodic tilings of R3 whose smallest repeat
   tiling unit consists of one regular octahedron & six smaller regular
   tetrahedra. ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1105594108">doi:10.1073/pnas.1105594108</A>]['12].

%T Interior-point methods for large-scale cone programming
%B Optimization for Machine Learning
%E S. Sra
%E S. Nowozin
%E S. J. Wright
%I MITpress
%D 2011
%K c2011, c201x, c20xx, CVXOpt, zz0613, interior-point solver,
   convex optimization, cone programming, conic, conelp, coneqp
%X "The use of CVXOPT to develop customized interior-point solvers is
   decribed in the ... chapter on Optimization for Machine Learning."
   -- [<A HREF="http://cvxopt.org/documentation/index.html">cvxopt</A>]['13].
   (Ch in hb us$32, uk us isbn:026201646X, uk us isbn13:978-0262016469.)
   (Also see con@[<A HREF="http://en.wikipedia.org/wiki/Conic_programming">wikip</A>]['13],
   cvx@[<A HREF="http://en.wikipedia.org/wiki/Convex_optimization">wikip</A>]['13].)

%A V. Becher
%A P. A. Heiber
%T On extending de Bruijn sequences
%J IPL
%V 111
%N 18
%P 930-932
%M SEP
%D 2011
%K jrnl, IPL, c2011, c201x, c20xx, zz0911, de Bruijn, deBruijn, sequence,
   sequences, order, length, incremental, extend, extending
%X "We give a complete proof of the following theorem: Every de Bruijn seq. of
   order n in at least three symbols can be extended to a deB.seq. of order n+1.
   Every deB.seq. of order n in two symbols cannot be extended to order n+1, but
   it can be extended to order n+2."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2011.06.013">doi:10.1016/j.ipl.2011.06.013</A>]['11].
   (Also see deB@[<A HREF="http://en.wikipedia.org/wiki/De_Bruijn_sequence">wikip</A>]['11].)

%A M. P. H. Stumpf
%A M. A. Porter
%T Critical truths about power laws
%J Science
%V 335
%N 6069
%P 665-666
%M FEB
%D 2012
%K views, c2012, c201x, c20xx, power law, laws, maths, mathematics, stats
%X "... A striking feature that has attracted considerable attention is the
   apparent ubiquity of power-law relationships in empirical data. ... power
   laws have been reported in areas ranging from finance & molec.biology to
   geophysics & the Internet, the data are typically insufficient & the
   mechanistic insights are almost always too limited for the identification of
   power-law behavior to be scientifically useful ... . Indeed, even most
   statistically 'successful' calculations of power laws offer little more than
   anecdotal value.  By power-law behavior, one typically means that some
   physical quantity or probability distribution y(x) satisfies
      y(x) propTo x**(-lambda), for x > x0, ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1216142">doi:10.1126/science.1216142</A>]['12].

%A E. Mossel
%A J. Neeman
%A A. Sly
%T Stochastic block models and reconstruction
%J arXiv
%M FEB
%D 2012
%K TR, c2012, c201x, c20xx, zz0620, maths, graph, model, graphModel,
   stochastic block model,  SBM, Decelle, Krzkala, Moore, Zdeborova,
   planted partition model, PPM, community, communities, network
%X "The planted partition model (also known as the stochastic blockmodel) is a
   classical cluster-exhibiting random g.model that has been extensively studied
   in stats., physics, & comp.sci.. In its simplest form, the PPM is a model for
   random gs. on n nodes with two equal-sized clusters, with an between-class
   edge prob. of q & a within-class edge prob. of p. ... We prove half of
   [DKMZ's] prediction, showing that it is indeed impossible to cluster if
   (a-b)^2 < 2(a+b). [&] show that it is impossible even to est. the model
   params. from the g. when (a-b)^2 < 2(a+b); [but] we provide a simple &
   efficient alg. for est. a & b when (a-b)^2 > 2(a+b). Following D. et al, our
   work establishes a rigorous connection between the clustering problem,
   spin-glass models on the Bethe latt. & the so called reconstruction problem.
   This connection points to fascinating applications & open problems."
   -- 1202.1499@[<A HREF="https://arxiv.org/abs/1202.1499">arXiv</A>]['20].
   (Also see SBM@[<A HREF="https://en.wikipedia.org/wiki/Stochastic_block_model">wikip</A>]['20].)
   [Also search for: graphModel]  and  [also search for: community network].

%A D. Niederman
%T The Puzzler's Dilemma: From the Lighthouse of Alexandria to Monty Hall, a
   Fresh Look at Classic Conundrums of Logic, Mathematics, and Life
%I PerigreeTrade
%P 224
%M MAR
%D 2012
%K book, c2012, c201x, c20xx, zz0312, maths, mathematical puzzle, puzzles,
   puzzler, puzzlers, conundrum, problems
%X 1st ed 2012; pb us$11; uk us isbn:0399537295; uk us isbn13:978-0399537295.

%A K. Imai
%A T. Hatsuda
%A K. Sato
%T A universal semi-totalistic cellular automaton on kite and dart Penrose
   tilings
%J arXiv
%M AUG
%D 2012
%O conf: Automata2012
%K TR, c2012, c201x, c20xx, zz0912, Penrose tiling, 2D, machine, automaton,
   cellular automata, Turing, TM, UTM, game of life, quasiperiodic, aperiodic
%X "... investigate certain properties of semi-totalistic cellular automata
   (CA) on the well known quasi-periodic kite and dart 2D tiling of the plane
   presented by Roger Penrose. We show that, despite the irregularity of the
   underlying grid, it is possible to devise a semi-totalistic CA capable of
   simulating any boolean circuit on this aperiodic tiling."
   -- pdf@[<A HREF="http://arxiv.org/abs/1208.2771v1">arXiv</A>]['12].
   (auths@Hiroshima U.)
   [Also search for: aperiodic tiling].

%A B. Farzad
%A M. Karimi
%T Square-root finding problem in graphs, a complete dichotomy theorem
%J arXiv
%M OCT
%D 2012
%K arXiv, TR, c2012, c201x, c20xx, zz0914, maths, graph,
   square root of a graph, sqrt
%X "Graph G is the square of graph H if two vertices x,y have an edge in G if
   and only if x,y are of dist. <= two in H. Given H it is easy to compute its
   square H^2. Determining if a given graph G is the square of some graph is not
   easy in general. Motwani & Sudan proved that it is NPC to det. if a given
   graph G is the square of some graph. The graph introduced in their reduction
   is a graph that contains many triangles & is relatively dense. Farzad et al.
   proved the NP-completeness for finding a square root for girth 4 while they
   gave a polynomial time alg. for computing a square root of girth at least
   six. Adamaszek & Adamaszek proved that if a graph has a square root of girth
   six then this square root is unique up to isomorphism. ... we consider the
   characterization & recognition problem of graphs that are square of graphs of
   girth at least five. We introduce a family of graphs with exponentially many
   non-isomorphic square roots, & ... prove that the square root finding problem
   is NPC for square roots of girth five. This proof is providing the complete
   dichotomy thm for sqrt problem in terms of the girth of the square roots. "
   -- 1210.7684@[<A HREF="http://arxiv.org/abs/1210.7684">arXiv</A>]['14].
   [Also search for: sqrt graph maths].

%A M. Coons
%T An arithmetical excursion via Stoneham numbers
%J arXiv
%M DEC
%D 2012
%K TR, c2012, c201x, c20xx, zz0313, Stoneham number, maths, number theory, prime
%X "Let p be a prime & b a primitive root of p^2. ... give an explicit formula
   for the number of times a value in {0,1,...,b-1} occurs in the periodic part
   of the base b expansion of 1/p^m.  [So] we prove two recent conjectures of
   Francisco Aragon, David Bailey, Jonathan Borwein, & Peter Borwein concerning
   the base b expansion of Stoneham numbers. "
   -- [<A HREF="http://arxiv.org/abs/1212.3449">arXiv</A>]['13].

%A A. Mowshowitz
%A M. Dehmer
%T Entropy and the complexity of graphs revisited
%J Entropy
%V 14
%N 3
%D 2012
%P 559-570
%K jrnl, c2012, c201x, c20xx, zz0816, maths, graph, compress, entropy,
   information, Korner, survey, intro
%X "... presents a taxonomy & overview of approaches to the measurement of
   graph & network complexity. ... distinguishes between deterministic (e.g.,
   Kolmogorov complexity) & probabilistic approaches with a view to placing
   entropy-based probabilistic measurement in context. Entropy-based measurement
   is the main focus of the paper. Relationships between the different entropy
   fns used to measure complexity are examined; & intrinsic (e.g., classical
   measures) & extrinsic (e.g., Korner entropy) variants of entropy-based models
   are discussed in some detail."  [49 refs.]
   -- [<A HREF="http://dx.doi.org/10.3390/e14030559">doi:10.3390/e14030559</A>]['16].
   [Also search for: graph entropy survey].

%A V. Lyubashevsky
%A C. Peikert
%A O. Regev
%T On ideal lattices and learning with errors over rings
%J Cryptology ePrint Archive: Report 2012/230
%D 2012
%K TR, c2012, c201x, c20xx, zz0920, ring learning with errors, RLWE, LWE,
   problem, lattice, ring, homomorphic encryption, pseudorandom
%X "The 'learning with errors' (LWE) problem is to distinguish random linear
   equations, which have been perturbed by a small amount of noise, from truly
   uniform ones. The problem has been shown to be as hard as worst-case lattice
   problems ... we show that the ring-LWE distribution is pseudorandom, assuming
   that worst-case problems on ideal lattices are hard for polynomial-time
   quantum algs.. Applications include the first truly practical lattice-based
   public-key cryptosystem ..."
   -- 2012/230@[<A HREF="https://eprint.iacr.org/2012/230">iacr</A>]['20].
   Also see RLWE@[<A HREF="https://en.wikipedia.org/wiki/Ring_learning_with_errors">wikip</A>]['20] (learning with errors over rings).
   [Also search for: homomorphic encryption].

%A H.-F. Yu
%A C.-J. Hsieh
%A S. Si
%A I. Dhillon
%T Scalable coordinate descent approaches to parallel matrix factorization for
   recommender systems
%J ICDM
%P 765-774
%D 2012
%K conf, ICDM, ICDM12, c2012, c201x, c20xx, matrix, decomposition, recommender,
   ALS, SGD, CCD, CCD++, CCDplusplus
%X "MF when the matrix has missing values ... To handle web-scale datasets
   with millions of users & billions of ratings, scalability ... Alternating
   Least Squares (ALS) & Stochastic Gradient Descent (SGD) are two popular ...
   There has been a recent flurry of activity to parallelize these algs..
   However, due to the cubic time complexity in the target rank, ALS is not
   scalable to large-scale datasets. [But] SGD conducts efficient updates but
   usually suffers from slow convergence that is sensitive to the params..
   Coordinate descent, a classical opt. approach, has been used for many other
   large-scale problems, but its application to MF for recommender syss. has not
   been explored thoroughly. ... show that c.descent based methods have a more
   efficient update rule [v] ALS, & are faster & have more stable convergence
   than SGD. We study different update seqs. & propose the CCD++ alg., which
   updates rank-one factors one by one. [&] CCD++ can be easily parallelized on
   both multi-core & distributed systems. We empirically show that CCD++ is
   much faster ... [E.g.] on a synthetic dataset with 2billion ratings, CCD++
   is 4 x faster than both ... with 20 machines."
   -- [<A HREF="http://dx.doi.org/10.1109/ICDM.2012.168">doi:10.1109/ICDM.2012.168</A>]['12].
   [Also search for: matrix decomposition].

%A J. Kiusalaas
%T Numerical Methods in Engineering with Python 3
%I CUP
%P 440
%D 2013
%K book, text, CUP, c2013, c201x, c20xx, zz0313, numerical methods, recipes,
   Python III, Python3
%X 3rd ed 2013; hb us$94; uk us isbn:1107033853; uk us isbn13:978-1107033856.
   "... intr. to numerical methods for students in eng.. It covers the usual
   topics found in an eng. course: solution of equns, interpolation and data
   fitting, soln of differential equns, eigenvalue problems, and optimization.
   The algs. are implemented in Python 3. ..."

%A J. I. Latorre
%A G. Sierra
%T Quantum computation of prime number functions
%J arXiv
%M FEB
%D 2013
%K TR, c2013, c201x, c20xx, zz0313, Riemann hypothesis, prime, primes, numbers,
   counting, count, frequency, quantum computing
%X "We propose a quantum circuit that creates a pure state corr.to the quantum
   superposition of all prime numbers less than 2^n, where n is the # of qubits
   of the register. This Prime state can be built using Grover's alg., whose
   oracle is a quantum implementation of the classical Miller-Rabin primality
   test. The Prime state is highly entangled, and its entanglement measures
   encode number theoretical fns such as the distribution of twin primes or the
   Chebyshev bias. [alg.] can be further combined with the quantum Fourier
   transform to yield an est. of the prime counting fn, more efficiently than
   any classical alg. and with an error below the bound that allows for the
   verification of the Riemann hypothesis. Arith. properties of prime numbers
   are then, in principle, amenable to experimental verifications on q.systems."
   -- [<A HREF="http://arxiv.org/abs/1302.6245">arXiv</A>]['13].
   [Also search for: Miller Rabin primality].

%A R. Beals
%A J. Szmigielski
%T Meijer G-Functions: A Gentle Introduction
%J Notices of the Amer. Math. Soc..
%V 60
%N 7
%P 866-872
%M AUG
%D 2013
%K jrnl,  c2013, c201x, c20xx, zz1219, AMS, Meijer, G function, functions,
   Gfunction, Gfunctions, general, hypergeometric, GHGE, Meijer
%X "The Meijer G-functions are a remarkable family of fns of one variable, each
   of them determined by finitely many indices. ... Most special fns, & many
   products of special fns, are G-fns or are expressible as products of
   G-fns with elementary fns. ..."
   -- pdf@[<A HREF="https://doi.org/10.1090/noti1016">doi:10.1090/noti1016</A>]['19].
   Also see MGF@[<A HREF="https://en.wikipedia.org/wiki/Meijer_G-function">wikip</A>]['19].
   [Also search for: Meijer Gfunction].

%A A. S. Posamentier
%A I. Lehmann
%T Magnificent Mistakes in Mathematics
%I PrometheusBooks
%M AUG
%D 2013
%K book, c2013, c201x, c20xx, zz0713, maths, math, blunder, blunders, mistake,
   errors, error
%X 1st ed 2013; hb us$17; uk us isbn:1616147474; uk us isbn13:978-1616147471.
   "Requiring no more than high-school-level math ... better grasp of this
   fundamental, all-important science. Veteran math educators demonstrate how
   some 'magnificent mistakes' had profound consequences for our understanding
   of mathematics' key concepts. In the 19C, English mathematician William
   Shanks spent fifteen years calculating the value of pi, setting a record for
   the # of decimal places. Later, his calculation was reproduced using large
   wooden numerals to decorate the cupola of a hall in the Palais de la
   Decouverte in Paris. However, in 1946, with the aid of a mechanical desk
   calculator that ran for seventy hours, it was discovered that there was a
   mistake in the 528th decimal place. ..."

%A S. Singh
%T The Simpsons and Their Mathematical Secrets
%I BloomsburyUSA
%P 272
%M OCT
%D 2013
%K book, c2013, c201x, c20xx, zz1013, the Simpsons, Bart, Lisa, Homer, Marge,
   Futurama, TV, cartoon, series, funny, freeze frame gag, maths, joke, jokes
%X 1st ed 2013; hb us$20; us isbn:1620402777; us isbn13:978-1620402771.
   "You may have watched hundreds of episodes of The Simpsons (and its sister
   show Futurama) without ever realizing that cleverly embedded in many plots
   are subtle references to mathematics ..."
   (Also see The G. [<A HREF="http://www.theguardian.com/tv-and-radio/2013/sep/22/the-simpsons-secret-formula-maths-simon-singh">www</A>].)

%A B. Konev
%A A. Lisitsa
%T A SAT attack on the Erdos discrepancy conjecture
%J arXiv
%M FEB
%D 2014
%K TR, c2014, c201x, c20xx, zz0214, Erdos, maths, discrepancy, method, sequence,
   Boolean satisfiability, combinatorics
%X "In 1930s Paul Erdos conjectured that for any +ve int. C in any infinite
   +1 -1 sequence (x_n) there exists a subseq. x_d, x_{2d}, ..., x_{kd} for some
   +ve ints. k & d, s.t. |x_d + x_{2d} + ... + x_{kd}| > C.  ... referred to as
   one of the major open problems in combinatorial number theory & discrepancy
   theory. For ... C=1 a human proof of the conjecture exists; for C=2 a bespoke
   computer program had generated seqs. of length 1124 having discrepancy 2, but
   the status of the conjecture remained open even for such a small bound. We
   show that by encoding the problem into Boolean satisfiability & applying the
   state of the art SAT solvers, one can obtain a seq. of length 1160 with
   discrepancy 2 & a proof of the Erdos discrepancy conjecture for C=2,
   claiming that no seq. of length 1161 & discrepancy 2 exists. We also present
   our partial results for the case of C=3. "
   -- 1402.2184@[<A HREF="http://arxiv.org/abs/1402.2184">arXiv</A>]['14].
   Also see [<A HREF="http://en.wikipedia.org/wiki/Erd%C5%91s_discrepancy_problem">wikip</A>]['14].
   [Also search for: discrepancy method].

%A Y. Zhang
%T Bounded gaps between primes
%J Annals of Mathematics
%V 179
%N 3
%P 1121-1174
%M MAY
%D 2014
%K jrnl, c2014, c201x, c20xx, zz1017, Yitang Zhang, twin, consecutive, prime,
   primes, gap, gaps, finite bound, Bombieri Vinogradov
%X "It is proved that lim inf_{n->inf} (p_{n+1} - p_n) < 7 x 10^7,
   where p_n is the n-th prime.  Our method is a refinement of the recent work
   of Goldston, Pintz and Yildirim on the small gaps between consecutive primes.
   A major ingredient of the proof is a stronger version of the
   Bombieri-Vinogradov theorem that is applicable when the moduli are free from
   large prime divisors only, but it is adequate for our purpose."
   -- [<A HREF="https://doi.org/10.4007/annals.2014.179.3.7">doi:10.4007/annals.2014.179.3.7</A>]['17].
   (Also see twin-prime@[<A HREF="https://en.wikipedia.org/wiki/Twin_prime">wikip</A>]['17].)

%A J. Ellenberg
%T How Not to Be Wrong: The Power of Mathematical Thinking
%I PenguinPress
%P 480
%M MAY
%D 2014
%K book, text, c2014, c201x, c20xx, zz0614, popular, maths, mathematics, logic
%X 1st ed 2014; hb us$20; uk us isbn:1594205221; uk us isbn13:978-1594205224.
   "... Math is not confined to abstract incidents that never occur in real
   life, but rather touches everything we do - the whole world is shot through
   with it. ..."

%A D. Lokshtanov
%A M. Pilipczuk
%A M. Pilipczuk
%A S. Saurabh
%T Fixed-parameter tractable canonization and isomorphism test for graphs of
   bounded treewidth
%J Proc. of Symp. on Foundations of Comp. Sci. (FOCS)
%P 186-195
%D 2014
%K conf, FOCS, c2014, c201x, c20xx, zz0115, maths, graph, canonical,
   labelling, renumbering, canonization, tree width, treewidth
%X "We give a fixed-param. tractable alg. that, given a param. k & two graphs
   G1, G2, either concludes that one of these graphs has treewidth at least k,
   or determines whether G1 & G2 are isomorphic. The running time ... on an
   n-vertex graph is 2^O(k^5 log k).n^5, & this is the first fixed-param. alg.
   for G.Iso. parameterized by treewidth.  [It] in fact solves the more general
   canonization problem. We namely design a procedure working in
   2^O(k^5 log k).n^5 time that, for a given graph G ... either concludes that
   the treewidth of G is at least k, or: *finds in an isomorphic-invariant way
   a graph c(G) that is isomorphic to G; *finds an isomorphism-invariant
   construction term -- an algebraic expression that encodes G together with a
   tree decomposition of G of width O(k^4).  Hence, the isomorphism test reduces
   to verifying whether the computed isomorphic copies or the construction terms
   for G1 & G2 are equal."
   -- 1404.0818@[<A HREF="http://arxiv.org/abs/1404.0818">arXiv</A>]['15],
   pdf@[<A HREF="http://www.ii.uib.no/~daniello/papers/tw-iso.pdf">uib.no</A>]['15].
   [Also search for: maths graph canonical].

%A J. R. Lee
%A S. O. Gharan
%A L. Trevisan
%T Multiway spectral partitioning and higher-order Cheeger inequalities
%J JACM
%V 61
%N 6
%P ?-?
%M NOV
%D 2014
%K jrnl, JACM, c2014, c201x, c20xx, zz0716, maths, graph, spectral, Cheeger,
   conductance, connected component, eigenvalue, partition
%X "... the # of connected components in an undirected graph is equal to the
   multiplicity of the eigenvalue zero in the Laplacian matrix of the g. ...
   the g. is disconnected iff there are >= two eigenvalues equal to zero.
   Cheeger's inequality & its variants provide an approx. version of the latter
   fact; ... a g. has a sparse cut iff there are >= two eigenvalues that are
   close to zero.  It has been conjectured that an analogous characterization
   holds for higher multiplicities: There are k eigenvalues close to zero iff
   the vertex set can be partitioned into k subsets, each defining a sparse cut.
   We resolve this conjecture +vly. ... provides a theoretical justification for
   clustering algs. that use the bottom k eigenvectors to embed the vertices
   into R^k, & then apply geometric considerations to the embedding.  [&] show
   that these techniques yield a nearly optimal quantitative connection between
   the expansion of sets of size approx n/k & lambda k, the kth smallest
   eigenvalue of the normalized Laplacian, where n is the # of vertices. ...
   show that in every g. there are >= k/2 disjoint sets (one of which will have
   size <= 2n/k), each having expansion at most O(sqrt lambda k log k). Louis,
   Raghavendra, Tetali, & Vempala have indep. proved a slightly weaker version
   of this last result. The sqrt log k bound is tight, up to const. factors, for
   the 'noisy hypercube' graphs."
   -- [<A HREF="http://dx.doi.org/10.1145/2665063">doi:10.1145/2665063</A>]['16].
   [Also search for: graph partition].

%A M. Bowling
%A N. Burch
%A M. Johanson
%A O. Tammelin
%T Heads-up limit hold'em poker is solved
%J Science
%V 347
%N 6218
%P 145-149
%M JAN
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0115, CFR+, CFR, game theory, card, poker, AI,
   Texas holdem, hold em, imperfect information
%X "... announce that heads-up limit Texas hold'em is now essentially weakly
   solved. Furthermore, this computation formally proves the common wisdom that
   the dealer in the game holds a substantial advantage. This result was enabled
   by a new algorithm, CFR+, which is capable of solving extensive-form games
   orders of magnitude larger than previously possible."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1259433">doi:10.1126/science.1259433</A>]['15].
   (Also see [<A HREF="http://www.bbc.com/news/science-environment-30718558">bbc</A>][8/1/2015].)
   [Also search for: poker AI].

%A N. K. Ahmed
%A J. Neville
%A R. A. Rossi
%A N. Duffield
%T Efficient graphlet counting for large networks
%J ICDM
%P ?-?
%D 2015
%K conf, c2015, c201x, c20xx, zz0119, maths, induced, subgraph, graphlet,
%X (NB. in this, graphlet = small(!) vertex induced subgraph.)
   "... we propose a fast, efficient, & parallel alg. for counting graphlets of
   size k={3,4}-nodes ... algs. leverages a # of proven combinatorial arguments
   for different graphlets. For each edge, we count a few graphlets, & with
   these counts along with the combinatorial arguments, we obtain the exact
   counts of others in constant time. On a large collection of 300+ n/wks from a
   variety of domains, our graphlet counting strategies are on average 460x
   faster than current methods. ..."
   -- [<A HREF="http://dx.doi.org/10.1109/ICDM.2015.141">doi:10.1109/ICDM.2015.141</A>]['19].
   [Also search for: graph count subgraph].

%A G. Lu
%A B. Li
%A L. Wang
%T Some new properties for degree-based graph entropies
%J Entropy
%V 17
%N 12
%P 8217-8227
%M DEC
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0816, maths, graph entropy, degree, power
%X "The graph entropies inspired by Shannon's entropy concept become the
   information-theoretic quantities for measuring the structural information of
   graphs & complex n/ws. ... continue studying some new properties of the graph
   entropies based on information functionals involving vertex degrees. We prove
   the monotonicity of the g.entropies wrt the power exponent. Considering only
   the max. & min. degrees of the (n, m)-graph, we obtain some upper & lower
   bounds for the degree-based g.entropy. These bounds have different
   performances to restrict the degree-based g.entropy in different kinds of
   graphs. [&] the degree-based g.entropy can be estimated by these bounds."
   -- [<A HREF="http://dx.doi.org/10.3390/e17127871">doi:10.3390/e17127871</A>]['16].

%A M. Mohri
%A M. Riley
%A A. T. Suresh
%T Automata and graph compression
%J arXiv
%M FEB
%D 2015
%K TR, c2015, c201x, c20xx, LZA, automaton, graph, compress
%X "... extends to graph compression. Similar to stationary ergodic processes,
   we formulate a probabilistic process of graph & automata generation that
   captures real world phenomena & provide a universal compression scheme LZA
   for this probabilistic model. Further, we show that LZA sig. outperforms
   other compression techniques such as gzip & the UNIX compress command for
   several synthetic and real data sets."
   -- 1502.07288@[<A HREF="http://arxiv.org/abs/1502.07288">arXiv</A>]['15].
   [Also search for: graph compress].

%A S. Martiniani
%A K. Julian Schrenk
%A J. D. Stevenson
%A D. J. Wales
%A D. Frenkel
%T Turning intractable counting into sampling: Computing the configurational
   entropy of three-dimensional jammed packings
%J Phys. Rev. E
%V 93
%N 1
%P 012906 (16pp)
%M JAN
%D 2016
%K jrnl, eJrnl, c2016, c201x, c20xx, zz0216, maths, counting, 3D, spheres,
   sphere, balls, jammed packing, configuration, entropy, energy, minima,
   attraction
%X "We present a numerical calcln of the total # of disordered jammed
   configurations Omega  of N repulsive, 3D spheres in a fixed volume V. To make
   these ... tractable, we increase the comp. efficiency of the approach of Xu
   et al ... & we extend the method to allow computation of the configurational
   entropy as a function of pressure. ... computes the configurational entropy
   by sampling the absolute volume of basins of attraction of the stable
   packings in the potential energy landscape. We find a surprisingly strong
   correlation between the pressure of a configuration & the volume of its basin
   of attraction in the potential energy landscape. This relation is well
   described by a power law. Our methodology to compute the number of minima in
   the potential energy landscape should be applicable to a wide range of other
   enumeration problems in statistical physics, string theory, cosmology, &
   machine learning that aim to find the distribution of the extrema of a scalar
   cost fn that depends on many degrees of freedom."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevE.93.012906">doi:10.1103/PhysRevE.93.012906</A>]['16].

%A R. J. Lemke Oliver
%A K. Soundararajan
%T Unexpected biases in the distribution of consecutive primes
%J arXiv
%M MAR
%D 2016
%K TR, maths, number theory, c2016, c201x, c20xx, zz0316, prime, primes,
   modulo, mod, bias, Hardy-Littlewood conjectures
%X "While the seq. of primes is v.well distributed in the reduced residue
   classes (mod q), the distn of pairs of consec. primes among the permissible
   phi(q)^2 pairs of reduced residue classes (mod q) is surprisingly erratic.
   ... proposes a conjectural explanation for this phenomenon, based on the
   Hardy-Littlewood conjectures. The conjectures are then compared to numerical
   data, & the observed fit is very good."
   -- 1603.03720@[<A HREF="http://arxiv.org/abs/1603.03720">arXiv</A>]['16].

%A M. Viazovska
%T The sphere packing problem in dimension 8
%J arXiv
%M MAR
%D 2016
%K TR, c2016, c201x, c20xx, zz0416, spheres, 8D, space, E8, lattice,
   quantization
%X "... we prove that no packing of unit balls in Euclidean space R8 has
   density greater than that of the E8-lattice packing.:
  -- 1603.04246v1@[<A HREF="http://arxiv.org/abs/1603.04246v1">arXiv</A>]['16].
   [Also search for: sphere packing].

%A H. Cohn
%A A. Kumar
%A S. D. Miller
%A D. Radchenko
%A M. Viazovska
%T The sphere packing problem in dimension 24
%J arXiv
%M MAR
%D 2016
%K TR, c2016, c201x, c20xx, zz0416, spheres, 24D, space, Leech, lattice,
   periodic, quantization
%X "Building on Viazovska's recent solution of the sphere packing problem in
   eight dimensions, we prove that the Leech lattice is the densest packing of
   congruent spheres in twenty-four D., and that it is the unique optimal
   periodic packing. ... we find an optimal auxiliary fn for the linear prog.
   bounds, which is an analogue of V.'s fn for the eight-D case."
   -- 1603.06518v1@[<A HREF="http://arxiv.org/abs/1603.06518v1">arXiv</A>]['16].
   [Also search for: sphere packing].

%A K. Topley
%T Computationally efficient bounds for the sum of Catalan numbers
%J arXiv
%M MAR
%D 2016
%K TR, c2016, c201x, c20xx, zz0519, sum, cummulative, Catalan number,
   bound, Dyck paths, asymptotic, approximations
%X "Easily computable lower & upper bounds are found for the sum of Catalan #s.
   The lwb is proven to be tighter than the upb, which previously was declared
   to be only an asymptotic. The avg. of these bounds is proven to be also an
   upb, & empirically it is shown that the avg. is superior to the prev. upb by
   a factor greater than (9/2)."
   -- [<A HREF="https://arxiv.org/abs/1601.04223">arXiv</A>]['5/19].

%A Jianliang Gao
%A Ping Liu
%A Xuedan Kang
%A Lixia Zhang
%A Jianxin Wang
%T PRS: Parallel relaxation simulation for massive graphs
%J COMPJ
%V 59
%N 6
%P 848-860
%M JUN
%D 2016
%K jrnl, COMPJ, c2016, c201x, c20xx, zz0716, maths, graph, motif, pattern,
   relaxation simulation
%X "...  Graph pattern matching is traditionally defined in terms of subgraph
   isom. or g.simulation. These notions, however, often impose too strong
   constraint to identify meaningful matches. ... propose a new g. pattern
   matching based on a notion of relaxation simulation, which extends
   g.simulation by allowing partially absent vertices. We show that relaxation
   simulation is able to find sig. matches which traditional approaches of
   g.pattern matching fail to catch. We propose two parallel algs. to apply
   relaxation simulation to massive graph since the g. in practice is
   considerably large. The algs. are based on Bulk Synchronous Parallel model &
   can be easily deployed on cloud computing platforms. Finally,
   we experimentally verify the effectiveness & efficiency of these algs., using
   real-life data & synthesis data. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxu159">doi:10.1093/comjnl/bxu159</A>]['16].

%A I. Bliznets
%A F. V. Fomin
%A M. Pilipczuk
%A Y. Villanger
%T Largest chordal and interval subgraphs faster than 2^n
%J Algorithmica
%V 76
%N 2
%P 569-594
%M OCT
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0818, maths, graph, chordal, induced subgraph
   interval, maximum, largest, count, counting, enumerate, enumerating,
   problem, property, hereditary, clique path
%X "We prove that in a g. with n vertices, *induced* chordal & interval subgs.
   with the maximum # of vertices can be found in time O(2^{lambda n}) for some
   lambda < 1. These are the first algs. breaking the trivial 2^n.n^{O(1)} bound
   of the brute-force search for these problems."
     ("... Interval gs. form a subclass of chordal gs. admitting a decomposition
      into a clique path instead of less restrictive clique tree. ...")
   -- [<A HREF="https://doi.org/10.1007/s00453-015-0054-2">doi:10.1007/s00453-015-0054-2</A>]['18].
   Note 1, "... *induced* [property-] subgraph ...", and
   note 2, "maximum # of ver...", not "maximal...".
   [also search for: maximum chordal subgraph] and/or try "maximal",  and
   [also search for: induced chordal subgraph].

%A V. Patel
%A G. Regts
%T Deterministic polynomial-time approximation algorithms for partition
   functions and graph polynomials
%J arXiv
%M JUL
%D 2016
%K TR, c2016, c201x, c20xx, zz0716, maths, degree, graph, graphs, partition,
   function, Tutte, independence, polynomial, spin, coloring, colouring,
   Barvinok, permanent
%X "... give the first deterministic polynomial-time approximation alg. for
   computing complex-valued evaluations of the Tutte polynomial & the
   independence polynomial on bounded degree graphs, as well for computing
   partition fns of complex-valued spin & edge-coloring models on bounded degree
   graphs. ... builds on a recent line of work init. by A.Barvinok, Computing
   the permanent of (some) complex matrices, Foundations of Comp. Math. (2014)
   1-14. A.Barvinok, Computing the partition fn for cliques in a graph, Theory
   of Comp. 11 (2015), Article 13, pp.339-355), which provides a new alg.
   approach besides the existing correlation decay method for these types of
   problems. "
   -- 1607.01167@[<A HREF="http://arxiv.org/abs/1607.01167">arXiv</A>]['16].
   [Also search for: graph partition].

%A A. R. Benson
%A D. F. Gleich
%A J. Leskovec
%T Higher-order organization of complex networks
%J Science
%V 353
%N 6295
%P 163-166
%M JUL
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0616, network, graph, clustering, subgraphs,
   conductance, bifan, bi-fan
%X "... higher-order organization of complex n/wks - at the level of small n/wk
   subgraphs - remains largely unknown. Here, we develop a generalized framework
   for clustering n/wks on the basis of higher-order connectivity patterns. [It]
   provides mathematical guarantees on the optimality of obtained clusters &
   scales to n/wks with billions of edges. ... reveals higher-order organization
   in a # of n/wks, inc. information propagation units in neuronal n/wks & hub
   structure in transportation n/wks. Results show that n/wks exhibit rich
   higher-order organizational structures that are exposed by clustering based
   on higher-order connectivity patterns."  [29 refs.]
      "... For triangular motifs, the alg. scales to networks with
      billions of edges &, typically, only takes several hours to
      process graphs of such size. On smaller n/wks with hundreds
      of thousands of edges, [it] can process motifs up to size 9 ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aad9029">doi:10.1126/science.aad9029</A>]['16].
   [Also search for: graph conductance Cheeger].

%A V. Jelinek
%A J. Kyncl
%T Hardness of permutation pattern matching
%J arXiv
%M AUG
%D 2016
%K TR, c2016, c201x, c20xx, zz0816, permutation matching problem, PPM, NPC
%X "Permutation Pattern Matching (or PPM) is a decision problem whose input is
   a pair of perms. pi & tau, represented as seq. of ints., & the task is to
   determine whether tau contains a subseq. order-isomorphic to pi. Bose, Buss &
   Lubiw proved that PPM is NP-complete on general inputs. We show that PPM is
   NP-complete even when pi has no decreasing subseq. of length 3 & tau has no
   decreasing subseq. of length 4. This provides the first known example of PPM
   being hard when one or both of pi & tau are restricted to a proper hereditary
   class of permutations. ... also obtain analogous hardness & tractability
   results for the class of so-called skew-merged patterns. ... we deduce a
   complexity dichotomy for the PPM problem restricted to pi belonging to
   Av(rho), where Av(rho) denotes the class of perms. avoiding a perm. rho.
   Specifically, we show that the problem is polynomial when rho is in the set
   {1, 12, 21, 132, 213, 231, 312}, & it is NP-complete for any other rho."
   -- 1608.00529@[<A HREF="http://arxiv.org/abs/1608.00529">arXiv</A>]['16].

%A M. W. Mahoney
%T Lecture Notes on Spectral Graph Methods
%J arXiv
%P 257pp
%M AUG
%D 2016
%K TR, c2016, c201x, c20xx, zz0816, maths, spectral. spectrum, graph, intro,
   notes
%X "These are lecture notes that are based on the lectures from a class I taught
   on the topic of Spectral Graph Methods at UC Berkeley during the Spring 2015
   semester."
   -- 1608.04845@[<A HREF="http://arxiv.org/abs/1608.04845">arXiv</A>]['16].

%A T. Clunes
%T How to raise a genius: lessons from a 45-year study of super-smart children
%J Nature
%V 537
%N 7619
%P 152-155
%M SEP
%D 2016
%K news, c2016, c201x, c20xx, zz0916, education, intelligence, smart, genius,
   gifted, giftedness, IQ, child, children, clever, STEM, math, mathematics,
   maths, mathematically, precocious, SMPY, UVanderbilt
%X "A long-running investigation of exceptional children reveals what it takes
   to produce the scientists who will lead the twenty-first century. ...
   Study of Mathematically Precocious Youth (SMPY) ..."
   -- [<A HREF="http://dx.doi.org/10.1038/537152a">doi:10.1038/537152a</A>]['16].
   Also see [<A HREF="https://my.vanderbilt.edu/smpy/">SMPY</A>]['16].

%A T. Godin
%T An analogue to Dixon's theorem for automaton groups
%J arXiv
%M OCT
%D 2016
%K TR, c2016, c201x, c20xx, zz1016, maths, group, groups, permutation,
   Dixon, theorem, random, automata, automaton
%X "Dixon's famous theorem states that the group generated by two random
   permutations of a finite set is generically either the whole symmetric group
   or the alternating group. In the context of random generation of finite
   groups this means that it is hopeless to wish for a uniform distn - or even a
   non-trivial one - by drawing random perms. & looking at the generated group.
   Mealy automata are a powerful tool to generate groups, inc. all finite groups
   & many interesting infinite ones, whence the idea of generating random finite
   groups by drawing random Mealy automata. ... show that, for a special class
   of Mealy automata that generate only finite groups, the distn is far from
   being uniform since the obtained groups are generically a semi-direct product
   between a direct product of alternating groups & a group generated by a tuple
   of transpositions."
   -- 1610.03301@[<A HREF="https://arxiv.org/abs/1610.03301">arXiv</A>]['16].

%A N. Kriege
%A F. Kurpicz
%A P. Mutzel
%T On maximum common subgraph problems in series-parallel graphs
%J arXiv
%M AUG
%D 2017
%K TR, c2017, c201x, c20xx, zz0817, maths, graph, problem, algorithm,
   maximum common connected subgraph, MCS, MCSG
%X "The complexity of the maximum common connected subgraph problem in partial
   k-trees is still not fully understood. Polynomial-time solns are known for
   degree-bounded outerplanar g., a subclass of the partial 2-trees. [But] the
   problem is known to be NP-hard in vertex-labeled partial 11-trees of bounded
   degree. We consider series-parallel g., i.e., partial 2-trees. We show that
   the problem remains NP-hard in biconnected series-parallel g. with all but
   one vertex of degree 3 or less. A +ve complexity result is presented for a
   related problem of high practical relevance which asks for a max. common
   connected subg. that preserves blocks & bridges of the input g.. We present a
   polynomial time alg. for this problem in series-parallel g., which utilizes a
   combination of BC- & SP-tree data structures to decompose both graphs."
   -- 1708.02772@[<A HREF="https://arxiv.org/abs/1708.02772">arXiv</A>]['17].
   [Also search for: graph MCS].

%A N. Sitchinava
%A D. Strash
%T Reconstructing generalized staircase polygons with uniform step length
%J ArXiv
%M SEP
%D 2017
%K TR, c2017, c201x, c20xx, zz0917, visibility graph, polygon
%X "... construct a polygon that has a given visibility graph ... unknown
   complexity (although VG recognition is known to be in PSPACE). We show that
   two classes of uniform step length polygons can be reconstructed efficiently
   by finding & removing rectangles formed between consecutive convex boundary
   vertices called tabs. ... give an O(n^2 m)-time reconstruction alg. for
   orthogonally convex polygons, where n & m are the # of vertices & edges in
   the visibility graph, resp.. [&] show that reconstructing a monotone chain of
   staircases (a histogram) is fixed-parameter tractable, when parameterized on
   the # of tabs, & polynomially solvable in time O(n^2 m) under reasonable
   alignment restrictions."
   -- 1708.09842@[<A HREF="https://arxiv.org/abs/1708.09842">arXiv</A>]['17].

%A I. Stewart
%T Significant Figures: Lives and Works of Trailblazing Mathematicians
%I ProfileBooks
%D 2017
%K book, text, biog, biography, c2017, c201x, c20xx, zz1017, maths, math,
   mathematician, Poincare, Lovelace, Gauss, Ramanujan
%X 1st ed 2017; pb us$12; isbn:1781258996; isbn13:978-1781258996.

%A E. Duesbury
%A J. Holliday
%A P. Willett
%T Comparison of maximum common subgraph isomorphism algorithms for the
   alignment of 2D chemical structures
%J Spec. Issue: Cheminformatics in Drug Discovery
%M OCT
%D 2017
%K c2017, c201x, c20xx, zz0920, maths, graph, MCS, similarity, graphAlignment,
   matching, large, maximum common subgraph, MCSG, chemical molecule, fMCS,
   MaxCliquesSeq, ChemAxon, ChemAxon_MCS, algorithm, MolBio, chemical, compound,
   molecule
%X "The identification of the largest substructure in common when two (or more)
   molecules are overlaid ... The fastest exact algs. for the connected &
   disconnected problems were found to be the fMCS & MaxCliqueSeq algs., resp.,
   while the ChemAxon_MCS alg. was the fastest approximate alg. for both types
   of problem."
   -- [<A HREF="https://doi.org/10.1002/cmdc.201700482">doi:10.1002/cmdc.201700482</A>]['20].
   [Also search for: graphAlignment]  and  [also search for: MCS graph].
   Also see MCS@[<A HREF="https://en.wikipedia.org/wiki/Maximum_common_subgraph">wikip</A>]['20].

%A T. Gannon
%T Mathematics: A pariah finds a home
%J Nature
%V ?
%N ?
%P ?-?
%M OCT
%D 2017
%K news, c2017, c201xm, c20xx, zz1017, maths, mathematics, group theory,
   finite simple groups, sporadic, O'Nan, ONan, pariah moonshine, Selmer,
   Tate Shafarevich, elliptic curve, Duncan, Mertens, Ono, physics
%X "Pariahs are fundamental building blocks in a branch of mathematics called
   group theory, but seem to be unconnected from both physics & other areas of
   maths. Such a connection has now been identified. ... there are also 26
   isolated groups called the sporadics. ... The largest is known as the
   monster; it contains about 8 x 1053 elements & all but 6 of the other
   sporadics. The remaining 6 are jokingly called the pariahs. It could have
   been that every sporadic is completely disconnected from all other areas of
   maths & sci.. But the monster is not irrelevant: its representations show up
   in modular functions. ..."
   -- [<A HREF="https://dx.doi.org/10.1038/nature24147">doi:10.1038/nature24147</A>]['17].
   This news is about:
      Duncan JFR, Mertens MH, Ono K. 'Pariah moonshine,'
      Nat.Commun., 8(1):670, Sept., 2017,
      [<A HREF="https://dx.doi.org/10.1038/s41467-017-00660-y">doi:10.1038/s41467-017-00660-y.</A>]['17].

%A N. S. Yanofsky
%T Theoretical Computer Science for the working category theorist
%J arXiv
%M OCT
%D 2017
%K TR, c2017, c201x, c20xx, zz1017, maths, mathematics, category theory,
   functor
%X 'Theoretical computer science discusses foundational issues about
    computations. It asks & answers questions such as "What is a computation?",
   "What is computable?", "What is efficiently computable?","What is
   information?", "What is random?", "What is an algorithm?", etc. We will
   present many of the major themes & theorems with the basic language of
   category theory. Surprisingly, many interesting theorems & concepts of
   theoretical comp. sci. are easy consequences of functoriality & composition
   when you look at the right categories & functors connecting them.'
   -- 1710.03090@[<A HREF="https://arxiv.org/abs/1710.03090">arXiv</A>]['17].

%A K. Cordwell
%A et al
%T On algorithms to calculate integer complexity
%J arXiv
%P 8p.
%M JUN
%D 2017
%K TR, c2017, c201x, c20xx, zz0823, integer complexity, ones, arithmetic,
   algorithm, integerComplexity
%X "... Currently, the fastest known alg. runs in time O(n^1.230175) & was given
   by J.Arias de Reyna & J.van de Lune in 2014. [it] makes use of a recursive
   defn given by Guy & iterates through products, f(d)+f(n/d), for d|n, & sums,
   f(a)+f(n-a), for a up to some fn of n. The rate-limiting factor is iterating
   through the sums. We discuss potential improvements to [it] via a method that
   provides a strong uniform bound on the # of summands that must be calculated
   for almost all n. We also develop code to run J.Arias de Reyna & J. van de
   Lune's analysis in higher bases & thus reduce their runtime ... to
   O(n^1.222911236). ..."
   -- [<A HREF="https://arxiv.org/abs/1706.08424">arxiv:1706.08424</A>]['23].
   [Also search for: integer complexity ones].

%A D. Darling
%A A. Banerjee
%T Weird Maths: At the Edge of Infinity and Beyond
%I OneWorld Publ.
%P 288
%M FEB
%D 2018
%K book, c2018, c201x, c20xx, zz0118, maths, mathematics, random
%X 1st ed 2018; pb stg.12; uk us isbn:1786072645, uk us isbn13:978-178607264.
   "Is anything truly random? Does infinity actually exist? Could we ever
   see into other dimensions? ... would we like alien music? ..."

%A N. Gillis
%T Multiplicative updates for polynomial root finding
%J IPL
%V 132
%P 14-18
%M APR
%D 2018
%K jrnl, IPL, c2018, c201x, c20xx, zz0418, polynomial, root, roots, find,
   finding, solve, solving, nonnegative, factorization, factorisation,
   multiplicative updates, algorithm
%X "Let f(x)=p(x)-q(x) be a polynomial with real coeffs. whose roots have
   nonnegative real part, where p & q are polynomials with nonnegative coeffs..
   ... prove the following: Given an initial point x0, the multiplicative update
   x_(t+1) = x_t p(x_t)/q(x_t) (t=0,1,...) monotonically and linearly converges
   to the largest (resp. smallest) real roots of f smaller (resp. larger) than
   x0 if p(x0) < q(x0) (resp. q(x0) < p(x0)). The motivation to study this alg.
   comes from the multiplicative updates proposed ... to solve optimization
   problems with nonnegativity constraints; in particular many variants of
   nonnegative matrix factorization."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2017.11.008">doi:10.1016/j.ipl.2017.11.008</A>]['18].

%A A. Conte
%A et al
%T A fast discovery algorithm for large common connected induced subgraphs
%J Spec. Issue of Discr. Maths (sub.)
%M MAY
%D 2018
%K TR, c2018, c201x, c20xx, zz0920, maths, graph, common subgraph, MCS, MCSG,
   MolBio, protein, chemical, molecule
%X "... fast alg. for the classical problem of finding common subgraphs, which
   are useful for detecting struct. relationships between biol. macromolecules.
   Although the cost is potentially high for this hard problem, we improve
   performance by several orders of mag. [v] known algs. We validate our
   findings with experiments on proteins with thousands of atoms."
   -- hal-02338435@[<A HREF="https://hal.inria.fr/hal-02338435/document">inria</A>]['20].
   [Also search for: graph MCS].

%A L. Chindelevitch
%A J. Paulo Pereira Zanetti
%A J. Meidanis
%T On the rank-distance median of 3 permutations
%J BMC Bioinformatics
%V 19
%N supp.6
%M MAY
%D 2018
%O RECOMB Comparative Genomics Satellite Workshop: bioinformatics
%K wkShop, c2018, c201x, c20xx, zz0518, rank distance, permutation, algorithm,
   double cut join, DCJ, genomes, sorting, reversals, reversal, inversion,
   transposition, median, rearrangement distance, comparison
%X "... provides the first proof that, wrt the rank distance, the problem of
   finding the median of 3 genomes, as well as the median of 3 permutations, is
   exactly solvable in polynomial time, a result which should be contrasted with
   its NP-hardness for the DCJ (double cut-and-join) distance and most other
   families of genome rearrangement operations. This result, backed by our
   experimental tests, indicates that the rank distance is a viable alternative
   to the DCJ distance widely used in genome comparisons."
   -- [<A HREF="https://doi.org/10.1186/s12859-018-2131-4">doi:10.1186/s12859-018-2131-4</A>]['18].
   [Also search for: permutation rank distance].

%T Machine learning leads mathematicians to unsolvable problem
%J Nature
%M JAN
%D 2019
%K news, views, c2019, c201x, c20xx, zz0119, machine learning, AI, II,
   learnability, learnable, compression, PAC, VC, estimating the maximum, EMX,
   Godel, incompleteness, continuum hypothesis, Shai Ben-David, Pavel Hrubes,
   Shay Moran, Amir Shpilka, Amir Yehudayoff, logic, paradox
%X ("A team of researchers has stumbled on a question that is mathematically
   unanswerable because it is linked to logical paradoxes discovered by Austrian
   mathematician Kurt Godel ... were working on a machine-learning problem, show
   that the question of 'learnability' - whether an algorithm can extract a
   pattern from limited data - is linked to a paradox known as the continuum
   hypothesis. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-019-00083-3">doi:10.1038/d41586-019-00083-3</A>]['19].
   More: 'Unprovability comes to machine learning', L. Reyzin,
   Nature, 565 pp 166-167, 7/1/2019,
   [<A HREF="https://doi.org/10.1038/d41586-019-00012-4">doi:10.1038/d41586-019-00012-4</A>]'19].)
   *** And the paper in question:
   'Learnability can be undecidable',
   Shai Ben-David, Pavel Hrubes, Shay Moran, Amir Shpilka, Amir Yehudayoff,
   Nature Machine Intelligence, 1, pp.44-48, 7/1/2019,
   "...  We show that, in some cases, a solution to the 'estimating the maximum'
   problem is equivalent to the continuum hypothesis. The main idea is to prove
   an equivalence between learnability and compression."
   -- [<A HREF="https://doi.org/10.1038/s42256-018-0002-3">doi:10.1038/s42256-018-0002-3</A>]['19]  ***.

%A S. Plouffe
%T A set of formulas for primes
%J arXiv
%M JAN
%D 2019
%K TR, c2019, c201x, c20xx, zz0119, maths, prime, primes, number, numbers,
   Mills, Wright
%X "A new set of formulas for primes is presented. These formulas are more
   efficient and grow much slower than the two known formulas of Mills and
   Wright."
   -- 1901.01849@[<A HREF="https://arxiv.org/abs/1901.01849">arXiv</A>]['19].
%J arXiv
%M JAN
%D 2019

%A M. Equi
%A R. Grossi
%A C. Makinen
%T On the complexity of exact pattern matching in graphs: Binary strings and
   bounded degree
%J arXiv
%M JAN
%D 2019
%K TR , c2019, c201x, c20xx, zz0119, maths, graph, string, labelled,
   Strong Exponential Time Hypothesis, SETH, Backurs, Indyk
%X "Exact pattern matching in labeled graphs is the problem of searching paths
   of a graph G=(V,E) that spell the same string as the pattern P[1..m]. ... We
   describe a simple conditional lower bound that, for any constant e > 0, an
   O(|E|^{1-e}m)-time or an O(|E|m^{1-e})-time alg. for exact p.matching on
   graphs, with node labels & patterns drawn from a binary alphabet, cannot be
   achieved unless the Strong Exponential Time Hypothesis (\seth) is false. The
   result holds even if restricted to undirected gs. of max. degree three or
   DAGs of max. sum of indegree & outdegree three. ..."
   -- 901.05264@[<A HREF="https://arxiv.org/abs/1901.05264">arXiv</A>]['19].

%A A. R. Booker
%T Cracking the problem with 33
%I U. Bristol
%D 2019
%K TR, c2019, c201x, c20xx, zz0319, maths, number theory, sum, three, cubes,
   cube, integer, Mordell, Heath-Brown, HeathBrown, conjecture, 33, 42,
   UniBristol, UBristol
%X "Inspired by the Numberphile video 'The uncracked problem with 33' by
   Tim Browning and Brady Haran, we investigate solutions to x^3+y^3+z^3=k
   for a few small values of k.  We find the first known solution for k=33."
   "Let k be a +ve int with k .ne +/-4 (mod 9). ..."
   "33 = 8866128975287528^3 + (-8778405442862239)^3 + (-2736111468807040)^3."
   -- pdf@[<A HREF="https://people.maths.bris.ac.uk/~maarb/papers/cubesv1.pdf">bris</A>]['19].
   (Also see, sums of three cubes,
   "... k cannot equal 4 or 5 modulo 9 [but] it is unknown whether this nec.
   condn is sufficient. ... Through ... searches, it was discovered that
   all k < 100 that are unequal to 4 or 5 modulo 9 have a soln, with two
   exceptions, 33 and 42 ... Heath-Brown conjectured [such k have] infinitely
   many representations as sums of three cubea. ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Sums_of_three_cubes">wikip</A>]['19].
   So of 2-digit numbers, 33 done, 42 still unknown.)

%A C. Schofield
%A J. B. Wang
%A Y. Li
%T Quantum walk inspired algorithm for graph similarity and isomorphism
%J arXiv
%M FEB
%D 2019
%K TR, c2019, c201x, c20xx, zz0319, graph, maths, network, similarity,
   isomorphism, labelled, coined, quantumWalk, inspired, algorithm
%X "... networks can be v.large, [so] scalability & efficiency of the alg. are
   key concerns. More importantly, for gs. with unknown labeling, this
   g.similarity problem requires exponential time to solve using existing algs..
   ... we propose a quantum walk inspired alg., which provides a soln to the
   g.similarity problem without prior knowledge on graph labeling. [It] is
   capable of distinguishing between minor structural differences, such as
   between strongly regular gs. with the same parameters. [It] has polynomial
   complexity, scaling with O(n^9).
   -- 1902.11105@[<A HREF="https://arxiv.org/abs/1902.11105">arXiv</A>]['19].
   (?"unknown labelling"  So, labels unknown but not absent?
   auth1 & 2 @ UWA, auth3 @ UWtrloo.  Does not mention  B a b a i (2015).)
   [Also search for: graph isomorphism]  &  [also search for: graph similarity].

%A V. A. Traag
%A L. Waltman
%A N. J. van Eck
%A From Louvain to Leiden: Guaranteeing well-connected communities
%J Sci. Reps.
%V 9
%N 5233
%M MAR
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0820, vanEck, network, maths, graph,
   Louvain algorithm, louvian, modularity, modular, Leiden,
   community, detection, networks
%X "... We show that this [Lo.] alg. has a major defect that largely went
   unnoticed until now: the Lo.alg. may yield arbitrarily badly connected
   communities. In the worst case, communities may even be disconnected, esp.
   when running [it] iteratively. ... we introduce the Leiden alg.. We prove
   that the Le.alg. yields communities that are guaranteed to be connected. [&]
   prove that, when the Le.alg. is applied iteratively, it converges to a
   partition in which all subsets of all communities are locally optimally
   assigned. ... [&] runs faster ..."
   -- [<A HREF="https://doi.org/10.1038/s41598-019-41695-z">doi:10.1038/s41598-019-41695-z</A>]['20].
   (Also see Louvain@[<A HREF="https://en.wikipedia.org/wiki/Louvain_modularity">wikip</A>]['20].)
   [Also search for: community network].

%A A. Arman
%A P. Gao
%A N. Wormald
%T Fast uniform generation of random graphs with given degree sequences
%J arXiv
%M MAY
%D 2019
%K TR, c2019, c201x, c20xx, zz0519, generate, sample, random, graph, maths,
   degree sequence
%X "... provide an alg. that generates a graph with given degree seq. uniformly
   at random. Provided that D^4=O(m), where D is the maximal degree & m is the
   # of edges, the alg. runs in expected time O(m). ... sig. improves the prev.
   most efficient uniform sampler, which runs in expected time O(m^2D^2) for the
   same family of degree seqs.. ...uses a novel ingredient which progressively
   relaxes restrictions on an object being generated uniformly at random, & we
   use this to give fast algs. for uniform sampling of graphs with other degree
   seqs. as well. Using the same method, we also obtain algs. with expected run
   time which is (i) linear for power-law degree seqs. in cases where the prev.
   best was O(n^{4.081}), and (ii) O(nd+d^4) for d-regular graphs when
   d=o(sqrt(n)), where the prev. best was O(nd^3)."
   -- 1905.03446@[<A HREF="https://arxiv.org/abs/1905.03446">arXiv</A>]['19].
   [Also search for: random graph].

%A D. B. Blumenthal
%T New Techniques for Graph Edit Distance
%J arXiv
%M AUG
%D 2019
%K PhD thesis, c2019, c201x, c20xx, zz0819, maths, graph, edit distance, GED,
   algorithm, QAP, LSAPE
%X "... widely used measure is the graph edit distance (GED) ... hard to
   compute. ... In this thesis, new results and techniques ...  several
   reductions from GED to the quadratic assignment problem (QAP) are presented.
   Secondly, solvers for the linear sum assignment problem with error-correction
   (LSAPE) are discussed. ... Thirdly, exact algorithms for computing GED are
   presented in a systematic way, and improvements of existing algorithms as
   well as a new mixed integer programming (MIP) based approach ... Fourthly, a
   detailed overview of heuristic algorithms ..."
   -- 1908.00265@[<A HREF="https://arxiv.org/abs/1908.00265">arXiv</A>]['19].
   [Also search for: graph edit distance GED].

%A G. Gutierres
%A R. Mamede
%A J. L. Santos
%T Optimal Gray code for involutions
%J IPL
%V 148
%P 19-22
%M AUG
%D 2019
%K jrnl, IPL, c2019, c201x, c20xx, zz0919, Gray code, involution, group
%X "We present a Gray code for the set of involutions of the symmetric group,
   where the difference between two consecutive involutions is a transposition,
   or a rotation of three letters. Our code improves previous constructions, &
   it is proven to be optimal in relation to the Hamming distance between
   consecutive elements of the code. We also show that the transitions made
   using a transposition are more frequent than those made using a rotation of
   three elements."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2019.04.003">doi:10.1016/j.ipl.2019.04.003</A>]['19].

%A J. Malik
%A O. Suchy
%A T. Valla
%T Efficient implementation of color coding algorithm for subgraph isomorphism
   problem
%J arXiv
%M AUG
%D 2019
%K TR, c2019, c201x, c20xx, zz0919, maths, graph, subgraph, isomorphism,
   algorithm, color, colour, heuristic
%X "We consider the subgraph isomorphism problem where, given two graphs G
   (source g.) & F (pattern g.), one is to decide whether there is a (not
   nec. induced) subgraph of G isomorphic to F. While many practical heuristic
   algs. have been developed for the problem, as pointed out by McCreesh et al.
   [JAIR 2018], for each of them there are rather small instances which they
   cannot cope. ... A seminal paper by Alon, Yuster & Zwick [JACM '95]
   introduced the color coding approach to solve the problem, where the main
   part is a dynamic programming over color subsets & partial mappings. As with
   many exp.-time DPAs, the memory requirements constitute the main limiting
   factor ... grow exponentially with the treewidth of the pattern g., all
   existing implementations based on the color coding principle restrict
   themselves to specific pattern gs., e.g., paths or trees. In contrast, we
   provide an efficient implementation of the alg. sig. reducing its memory
   req. so that it can be used for pattern gs. of larger treewidth. [&] our
   implementation not only decides the existence of an isomorphic subg., but it
   also enumerates all such subgs. (or given number of them). We provide an
   extensive experimental comparison of our implementation to other available
   solvers for the problem."
   -- 1908.11248@[<A HREF="https://arxiv.org/abs/1908.11248">arXiv</A>]['19].
   [Also search for: subgraph isomorphism].

%A N. V. C. Gudapati
%A E. Malaguti
%A M. Monaci
%T In search of dense subgraphs: How good is greedy peeling?
%J arXiv
%M NOV
%D 2019
%O Networks, vol.77, no.4, pp.572-586, March 2021
%K TR, c2019, c201x, c20xx, zz1119, maths, graph, subgraph, dense, densest,
   maximum, density, problem, algorithm, heuristic, large, Goldberg
%X "The problem of finding the densest subgraph ... Depending on the application
   finding dense subgraphs can be used to determine regions of high importance
   ... The densest subgraph extraction problem is a fundamentally a non-linear
   optimization problem. Nevertheless, it can be solved in polynomial time by an
   exact alg. based on the iterative soln of a series of maximum flow
   sub-problems. ... the computing time required ... on v.large graphs could be
   prohibitive. ... We provide an efficient implementation of a greedy heuristic
   from the literature that is extremely fast & has some nice theoretical
   properties. We also introduce a new heurisitic alg. that is built on top of
   the greedy & the exact methods. ..."
   -- 1911.02356@[<A HREF="https://arxiv.org/abs/1911.02356">arXiv</A>]['19].
   [Also search for: Dense Subgraph problem].
   (Also see DSg@[<A HREF="https://en.wikipedia.org/wiki/Dense_subgraph">wikip</A>]['19].)

%T SymPy
%D ? 2009+ on ?
%K TR, c201x, c20xx, zz0220, Python, symbolic maths, mathematics, SymPy, mpmath,
   galgebra, computer algebra, library
%X "SymPy is a Python library for symbolic mathematics. It aims to become a
   full-featured computer algebra system (CAS) while keeping the code as simple
   as possible in order to be comprehensible and easily extensible. SymPy is
   written entirely in Python."
   -- [<A HREF="https://www.sympy.org/en/index.html">www</A>]['20],  (via njh).

%A L. Piccirillo
%T The Conway knot is not slice
%J Annals of Mathematics
%V 191
%N 2
%M MAR
%D 2020
%K maths, jrnl, c2020, c202x, c20xx, zz0820, maths, knot theory, slice,
   Conway, JHConway, 4ball, 11n34, Crossings, Lisa Piccirillo, women, STEM
%X "A knot is said to be slice if it bounds a smooth properly embedded disk in
   the 4-ball. We demonstrate that the Conway knot, 11n34 in the Rolfsen tables,
   is not slice. This completes the class'n of slice knots under 13 crossings,
   & gives the 1st example of a non-slice knot which is both topologically slice
   & a positive mutant of a slice knot."
   -- [<A HREF="https://doi.org/10.4007/annals.2020.191.2.5">doi:10.4007/annals.2020.191.2.5</A>]['20],
      [<A HREF="https://arxiv.org/abs/1808.02923">arXiv</A>]['20], and
   Auth@[<A HREF="https://en.wikipedia.org/wiki/Lisa_Piccirillo">wikip</A>]['20].

%A E. Barszcz
%T A blind permutation similarity algorithm
%J arXiv
%M MAR
%D 2020
%K TR, c2020, c202x, c20xx, zz0420, matrix, matrices, blind, permutation,
   similar, similarity, algorithm, invertible, transformation
%X "... a polynomial blind alg. that determines when two square matrices, A &
   B, are permutation similar. The shifted & translated matrices (A+bI+gJ) &
   (B+bI+gJ) are used to color the vertices of two square, edge weighted, rook's
   graphs. Then the orbits are found by repeated symbolic squaring of the vertex
   colored & edge weighted adjacency matrices. Multisets of the diagonal symbols
   from non-permutation similar matrices are distinct within a few iterations,
   typically four or less."
   -- 2003.11998@[<A HREF="https://arxiv.org/abs/2003.11998">arXiv</A>]['20].
   (Also see, "... In the definition of similarity, if the matrix P can be
    chosen to be a permutation matrix then A and B are permutation-similar ..."
   -- MSim@[<A HREF="https://en.wikipedia.org/wiki/Matrix_similarity">wikip</A>]['20].)

%A M. P. Deisenroth
%T Mathematics for Machine Learning
%I CUP
%P 398
%M APR
%D 2020
%K CUP, book, text, c2020, c202x, c20xx, zz0921, AI, maths, algebra, stats
%X 1st ed 2020; pb us$46; uk us isbn:110845514X; uk us isbn13:978-1108455145.
   "... linear algebra, analytic geometry, matrix decompositions, vector
   calculus, optimization, probability and statistics. ..."
   [Also search for: machine learning book].

%A M. Yannakakis
%T Planar graphs that need four pages
%J arXiv
%M MAY
%D 2020
%K TR, c2020, c202x, c20xx, zz0620, planar graph, maths, embed, book embedding
%X "We show that there are planar graphs that require four pages in any
   book embedding."
   -- 2005.14111@[<A HREF="https://arxiv.org/abs/2005.14111">arXiv</A>]['20].
   [Also search for: planar graph].
   Also see, "a book embedding is a generalization of p.embedding of a g. to
     embeddings into a book, a colln of half-planes all having the same line as
     their boundary. Usually, the vertices of the g. are required to lie on this
     boundary line, called the spine, & the edges are required to stay within a
     single half-plane. ..."
   -- BE@[<A HREF="https://en.wikipedia.org/wiki/Book_embedding">wikip</A>]['20].)

%A G. Hall
%A L. Massoulie
%T Partial recovery in the graph alignment problem
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0720, maths, graph, alignment, matching,
   graphAlignment, MCES, approximate, noisy isomorphism
%X "... the graph alignment problem ... recovering, given two graphs, a
   one-to-one mapping between nodes that maximizes edge overlap. ... can be
   viewed as a noisy version of the well-known graph isomorphism problem &
   appears in many applications, inc. social network deanonymization & cellular
   biology. Our focus here is on partial recovery, i.e., we look for a 1-to-1
   mapping which is correct on a fraction of the nodes of the g. rather than on
   all of them, & we assume that the two input gs to the problem are correlated
   ErdosRenyi gs of parameters (n,q,s). Our main contribution is then to give
   nec. & suff. conditions on (n,q,s) under which partial recovery is possible
   with high prob. as the # of nodes n goes to infinity. These conditions are
   compact, easily interpretable, & cover [most] of the parameter space."
   -- 2007.00533@[<A HREF="https://arxiv.org/abs/2007.00533">arXiv</A>]['20].
   [Also search for: graphAlignment].

%A D. Q. Huynh
%T Metrics for 3D rotations: Comparison and analysis
%J J. Math Imaging Vis.
%V 35
%P 155-164
%M JUN
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0820, maths, Matrix Lie group, Lie algebra,
   Quaternion, SO3, 3D rotation, distance, similarity, norm, UWA
%X "3D rotations arise in many computer vision ... evaluation of the distance
   between two 3D rotns is often an essential task. ... presents a detailed
   analysis of six fns for measuring dist. between 3D rotns that have been
   proposed in the lit.. ... we demonstrate that five of them are biinvariant
   metrics on SO(3) but that only four of them are boundedly equiv. to each
   other. We conclude that it is both spatially & computationally more efficient
   to use q. for 3D rotns. Lastly, by treating the two rotns as a true & an est.
   rotn matrix, we illustrate the geometry assoc. with iso-error measures."
   -- [<A HREF="https://doi.org/10.1007/s10851-009-0161-2">doi:10.1007/s10851-009-0161-2</A>]['20] (online 18/6/2009).

%A B. A. Burton
%T The next 350 million knots
%J 36th Int. Symp. on Comp. Geometry (SoCG)
%M JUN
%D 2020
%K conf, c2020, c202x, c20xx, zz0722, maths, geometry, prime knot, knots,
   enumeration, counting, combinatorial
%X "The tabulation of all prime knots up to a given number of crossings ...
   extend the tables from 16 to 19 crossings, with a total of 352,152,252
   distinct non-trivial prime knots. we describe the many different algorithmic
   components in this process, which draw on graph theory, hyperbolic geometry,
   knot polynomials, normal surface theory, and computational algebra. ..."
   -- pdf@[<A HREF="https://drops.dagstuhl.de/opus/volltexte/2020/12183">dagstuhl</A>]['22].
   (Also see BB@[<A HREF="https://smp.uq.edu.au/profile/225/benjamin-burton">UQ</A>]['22].)

%A A. Gaikwad
%A S. Maity
%A S. K. Tripathi
%T The satisfactory partition problem
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, maths, satisfactory partition problem, SPP,
   adequate, network, community, graph, vertex, vertices, modularity,
   Gerber, Kobler
%X "The Satisfactory Partition problem consists in deciding if the set of
   vertices of a given undirected g. can be partitioned into two nonempty parts
   s.t. each vertex has at least as many neighbours in its part as in the other
   part. ... its parameterized complexity remains open until now. ... It is
   known that the SP problem [&] a variant where the parts are required to be
   of the same cardinality, are NP-complete. ...  showing that (1) the problem
   is FPT when parameterized by the neighbourhood diversity of the input g.,
   (2) it can be solved in O(n^{8cw})) where cw is the clique-width, (3) a
   generalized version ... is W[1]-hard when parameterized by the treewidth."
   -- 2007.14339@[<A HREF="https://arxiv.org/abs/2007.14339">arXiv</A>][28/7/20].
   (Also see Mod@[<A HREF="https://en.wikipedia.org/wiki/Modularity_(networks)">wikip</A>]['20].)
   [Also search for: network modularity] and [also search for: graph partition].

%A I. Kontoyiannis
%A Y. Heng Lim
%A K. Papakonstantinopoulou
%A W. Szpankowski
%T Compression and symmetry of small-world graphs and structures
%J arXiv
%M JUL
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, maths, graph, model, graphModel, compress
%X "... a graph can be examined at three levels. Its structure can be described
   as the unlabeled version of the g.; then the labeling of its structure can be
   added; & finally, given the structure & labeling, the contents of the labels
   can be described ... we focus on a class of small-world gs.. These are
   geometric random gs. ... establish the degree dist'n of this model ... derive
   the relevant entropy & structural entropy of these random gs., in connection
   with g.compression."
   -- 2007.15981@[<A HREF="https://arxiv.org/abs/2007.15981">arXiv</A>]['20].
   [Also search for: graphModel].

%A R. K. Gautam
%A A. S. Kare
%A S. D. Bhavani
%T Faster heuristics for graph burning
%J arXiv
%M AUG
%D 2020
%K TR, c2020, c202x, c20xx, zz0820, maths, graph, burn, burning, NPH, heuristic
%X "Graph burning is a process of info. spreading through the n/wk by an agent
   in discrete steps. The problem is to find an optimal seq. of nodes which have
   to be given info. so that the n/wk is covered in least # of steps. G.burning
   problem is NP-Hard for which two approx'n algs. & a few heuristics have been
   proposed ...  we propose three heuristics, namely, Backbone Based Greedy
   Heuristic (BBGH), Improved Cutting Corners Heuristic (ICCH) & Component Based
   Recursive Heuristic (CBRH). These are mainly based on Eigenvector centrality
   measure. ..."
   -- 2008.08811@[<A HREF="https://arxiv.org/abs/2008.08811">arXiv</A>]['20].

%A M. Bressan
%A S. Leucci
%A A. Panconesi
%T Faster motif counting via succinct color coding and adaptive sampling
%J arXiv
%M SEP
%D 2020
%K TR, c2020, c202x, c20xx, zz0920, maths, graph, motif, network, motifs,
   pattern, count, frequent, colour
%X "... the problem of computing the dist'n of induced connected subgs., aka
   graphlets or motifs, in large gs.. The current state-of-the-art algs. est.
   the motif counts via uniform sampling, by leveraging the color coding
   technique by Alon, Yuster & Zwick ... We extend the applicability of this
   approach, by introducing a set of alg. optimizations & techniques that reduce
   the running time & space usage ... improve the accuracy of the counts. ...
   first show how to optimize color coding ...  For 8-node motifs, we can build
   [a] table in one hour for a g. with 65M nodes & 1.8B edges, which is 2000
   times larger than the state of the art. We then intro. a novel adaptive
   sampling scheme that breaks the 'additive error barrier' of uniform sampling,
   ... allows us to count not only the most freq. motifs, but also extremely
   rare ones. [eg], on one graph we accurately count nearly 10,000 distinct
   8-node motifs ..."
   -- 2009.03052@[<A HREF="https://arxiv.org/abs/2009.03052">arXiv</A>]['20].
   [Also search for: NAlon graph].

%A M. Grohe
%A P. Schweitzer
%T The graph isomorphism problem
%J CACM
%V 63
%N 11
%P 128-134
%M NOV
%D 2020
%K jrnl, survey, CACM, c2020, c202x, c20xx, zz1120, graph isomorphism, maths,
   color refinement, colour, dimension, WL, Weisfeiler Leman, algorithm,
   certificate, k-indistinguishability, Babai
%X "... in a recent breakthrough Babai proved that GI is solvable in
   quasipolynomial time. This means that on n-vertex input graphs, Babai's
   alg. runs in time n^{p(log n)} for some polynomial p(X). This can be
   interpreted as the problem being almost efficiently solvable - theoretically.
   ... we will survey both theoretical & practical aspects of the GI problem,
   paying particular attention to the developments that led to Babai's result."
   -- [<A HREF="https://doi.org/10.1145/3372123">doi:10.1145/3372123</A>]['20] and
 * see 2011.01366v1@[<A HREF="https://arxiv.org/abs/2011.01366v1.pdf">arXiv</A>]['20] * (82 refs).
   [Also search for: maths graph isomorphism]  and
   [also search for: graph color refinement]   and
   [also search for: Weisfeiler Leman].

%A S. Kiefer
%T The Weisfeiler-Leman algorithm: an exploration of its power
%J ACM SIGLOG
%M NOV
%D 2020
%K c2020, c202x, c20xx, zz1120, graph isomorphism problem, maths, intro, survey,
   Weisfeiler Leman, algorithm, WL, 2WL, 3WL, dimension, certificate
%X "... (WL) alg. is still an important combinatorial technique whenever graphs
   or other relational structures are to be classified. However, despite its
   simple algebraic description & its variety of applications, we still lack a
   precise understanding of the expressive power of [it]. This column introduces
   the reader to the basic concepts of the WL alg. & discusses its dimension as
   a parameter to capture the structural complexity of an input g.. Specifically
   I present a survey of work regarding the WL dimension ..."
   -- [<A HREF="https://doi.org/10.1145/3436980.3436982">doi:10.1145/3436980.3436982</A>]['20],
      [<A HREF="https://dl.acm.org/doi/10.1145/3436980.3436982">www</A>]['20].
   [Also search for: maths graph isomorphism].

%A M. Anders
%A P. Schweitzer
%T Engineering a fast probabilistic isomorphism test
%J arXiv
%M NOV
%D 2020
%K TR, c2020, c202x, c20xx, zz1120, DEJAVU, maths, graph isomorphism, problem,
   probabilistic algorithm
%X "We engineer a new probabilistic Monte-Carlo alg. for isomorphism testing.
   Most notably, as opposed to all other solvers, it implicitly exploits the
   presence of symmetries without explicitly computing them. ... Our results
   demonstrate that, with current algs., isomorphism testing is in practice
   easier than the related problems of computing the automorphism group or
   canonically labeling a g.. The results also show that prob.algs. for
   isomorphism testing can be engineered to outperform deterministic approaches,
   even asymptotically."
     ["... Our solver clearly gains advantages by not computing canonical
      labelings & automorphism groups ... suggests that with the currently
      available alg. approaches, in practice, isomorphism testing is
      substantially easier than automorphism group comp'n & canonical
      labeling. ..."]
   -- 2011.09375@[<A HREF="https://arxiv.org/abs/2011.09375">arXiv</A>]['20].
   [Also search for: maths graph isomorphism].

%A I. Ullisch
%T A closed-form solution to the geometric goat problem
%J The Mathematical Intelligencer
%V 42
%P 12-16
%D 2020
%K c2020, c202x, c20xx, zz1220, geometric goat problem, tethered-bull,
   women, STEM, maths, puzzle, Ladies Diary, Woman's Almanack
%X via DS
   -- [<A HREF="https://doi.org/10.1007/s00283-020-09966-0">doi:10.1007/s00283-020-09966-0</A>]['20].
   "The goat problem is a problem in recreational maths known since the 18th
   century. It was 1st published in 1748 in England, in the yearly publ'n
   The Ladies Diary: or, the Woman's Almanack ..."
   -- GP@[<A HREF="https://en.wikipedia.org/wiki/Goat_problem">wikip</A>]['20].
   Also see the LD@[<A HREF="https://en.wikipedia.org/wiki/The_Ladies%27_Diary ">wikip</A>]['20].

%A S. P. Dwivedi
%T Some algorithms on exact, approximate and error-tolerant graph matching
%J arXiv
%M DEC
%D 2020
%K TR, c2020, c202x, c20xx, zz0121, maths, graph, matching,
   graph, geometric edit distance, GED, algorithm, IIT, phd thesis
%X "... present an extensive survey of various exact & inexact graph matching
   techniques. Graph matching using the concept of homeomorphism is presented.
   A category of GM-algs. is presented, which reduces the g.size by removing the
   less important nodes using some measure of relevance. We present an approach
   to error-tolerant GM using node contraction where the given g. is transformed
   into another g. by contracting smaller degree nodes. We use this scheme to
   extend the notion of graph edit distance ..."
   -- [<A HREF="https://arxiv.org/abs/2012.15279">arXiv</A>]['21].
   Also see GED@[<A HREF="https://en.wikipedia.org/wiki/Graph_edit_distance">wikip</A>]['21].
   (*Beware, there's another meaning to 'graph matching'.*)
   [Also search for: maths graph matching] and
   [also search for: graph edit distance GED].

%A M. Henk
%A D. M. Wills
%T Packings, sausages and catastrophes
%J Beitr Algebra Geom.
%V 62
%P 265-280
%D 2021
%K jrnl, c2021, c202x, c20xx, zz1223, maths, sphere packing, convex bodies,
   finite packings, parametric density, sausage conjecture, catastrophe
%X "... survey we give an overview about some of the main results on parametric
   densities, a concept which uniï¬es the theory of ï¬nite (free) packings & the
   classical theory of inï¬nite packings."
   -- [<A HREF="https://doi.org/10.1007/s13366-020-00502-x">doi:10.1007/s13366-020-00502-x</A>]['23].
   (Also see FSP@[<A HREF="https://en.wikipedia.org/wiki/Finite_sphere_packing">wikip</A>]['23].)

%T Generating conjectures on fundamental constants with the Ramanujan Machine
%J Nature
%V 590
%P 67-73
%M FEB
%D 2021
%K jrnl, Ramanujan Machine, c2021, c202x, c20xx, zz0321, AI, maths, conjecture,
   equations
%X "... Our algs. find dozens of well known formulas as well as previously
   unknown ones, such as continued fraction representations of pi, e, Catalan's
   constant, and values of the Riemann zeta fn. Several conjectures found by our
   algs. were (in retrospect) simple to prove, whereas others remain as yet
   unproved. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-03229-4">doi:10.1038/s41586-021-03229-4</A>]['21].
   Also see [<A HREF="http://www.ramanujanmachine.com/">ramanujanmachine</A>]['21].

%A D. Aspero
%A R. Schindler
%T Martin's Maximum++ implies Woodin's axiom (*)
%J Ann. of Math. (2)
%V 193
%N 2
%P 793-835
%M MAY
%D 2021
%K jrnl, maths, c2021, c202x, c20xx, zz0722, continuum hypothesis, CH, infinity,
   infinities, aleph, aleph2, power set, sets, theory, ZF, axiom of choice, AC,
   ZFC, forcing axioms, Aspero, UEA
%X "We show that Martin's Maximum++ implies Woodin's Pmax axiom (*). This
   answers a q. from the 1990s & amalgamates two prominent axioms of set theory
   which were both known to imply that there are aleph_2 many real numbers."
   -- [<A HREF="https://doi.org/10.4007/annals.2021.193.3.3">doi:10.4007/annals.2021.193.3.3</A>]['22],
   pp@[<A HREF="https://annals.math.princeton.edu/2021/193-3/p03">pr'nceton</A>]['22].
   (Also see [<A HREF="https://www.quantamagazine.org/how-many-numbers-exist-infinity-proof-moves-math-closer-to-an-answer-20210715/">q'mag</A>][15/7/2021]
   and CH@[<A HREF="https://en.wikipedia.org/wiki/Continuum_hypothesis">wikip</A>]['22].)

%A N. Veldt
%A A. R. Benson
%A J. Kleinberg
%T The generalized mean densest subgraph problem
%J arXiv
%M JUN
%D 2021
%K TR, c2021, c202x, c20xx, zz0621, mean, densest, dense, subgraph, DSG,
   core, kcore, peeling, algorithm, generalised, graph, maths
%X "... introduce a new family of dense subgraph objectives, parameterized by a
   single param. p, based on computing generalized means of degree seqs. of a
   subgraph. ... captures both the std DSG problem & the maximum k-core as
   special cases & provides a way to interpolate between & extrapolate beyond
   these two objectives when searching for other notions of DSGs. ... first show
   that our objective can be minimized in polynomial time for all p>=1 using
   repeated submodular minimization. ... prove that the std peeling alg. can
   perform arbitrarily poorly on our generalized objective, but we then design a
   more sophisticated peeling method which for p>=1 has an approx'n guarantee
   that is always >=1/2 & converges to 1 as p -> inf. ... show that this alg.
   obtains extremely good approx'ns to the optimal soln, scales to large graphs,
   & highlights a range of different meaningful notions of density ... [&], it
   is typically able to approx. the DSG problem better than the std peeling
   alg., by better accounting for how the removal of one node affects other
   nodes in its neighborhood."
   -- 2106.00909@[<A HREF="https://arxiv.org/abs/2106.00909">arXiv</A>]['21].
   [Also search for: dense subgraph problem].

%A Lek-Heng Lim
%T Tensors in computations
%J arXiv
%M JUN
%D 2021
%O Acta Numerica, vol.30, pp.555-764, MAY 2021
%K TR, c2021, c202x, c20xx, zz0621, tensor, tensors, intro, numerical methods,
   equivariance, multilinearity, separability
%X "The notion of a tensor captures three great ideas: equivariance,
   multilinearity, separability. But trying to be 3 things at once makes the
   notion difficult to understand. We will explain tensors in an accessible &
   elementary way through the lens of linear algebra & numerical linear algebra,
   elucidated with examples from computational & applied mathematics.'
   -- 2106.08090@[<A HREF="https://arxiv.org/abs/2106.08090">arXiv</A>]['21],
      [<A HREF="https://doi.org/10.1017/S0962492921000076">doi:10.1017/S0962492921000076</A>]['22], Acta Numerica, CUP, AUG. 2021.
   [Also search for: tensor].

%A R. Lewis
%A D. Thiruvady
%A K. Morgan
%T The maximum happy induced subgraph problem: Bounds and algorithms
%J Computers & Op. Res.
%V 126
%P 1-15
%V 126
%P #105114
%M FEB
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0821, happy vertex, set, algorithm graph, maths,
   happy induced subgraph, happy vertices problem, colouring
%X "... a combinatorial opt'n problem that takes as input a g. in which some of
   the vertices have been preassigned to colours. The aim is to then identify
   the largest induced subg. in which all remaining vs. are able to assume the
   same colour as all of their neighbours. ... shares similarities with the
   g.colouring problem, vertex cut problems, & the maximum happy vertices
   problem. It is NP-hard in general. ... we derive a # of upper & lwbs & also
   show how certain problem instances can be broken up into smaller subproblems.
   ... propose one exact & two heuristic algs. ... & use these to investigate
   the factors that make some problem instances more difficult to solve than
   others."
   -- [<A HREF="https://doi.org/10.1016/j.cor.2020.105114">doi:10.1016/j.cor.2020.105114</A>]['21].
   [Also search for: happy set graph].

%A V. Dujmovic
%A L. Esperet
%A C. Gavoille
%A G. Joret
%A P. Micek
%A P. Morin
%T Adjacency labelling for planar graphs (and beyond)
%J JACM
%V 68
%N 6
%P #42, 1-33
%M DEC
%D 2021
%K jrnl, JACM, c2021, c202x, c20xx, zz021, maths, graph, graphs, planar,
   vertex, adjacent, adjacency, label, labelling, schemes, information, bits,
   genus
%X "We show that there exists an adjacency labelling scheme for planar graphs
   where each vertex of an n-vertex planar g. G is assigned a
   (1+o(1))log_2(n)-bit label & the labels of two vertices u & v are sufficient
   to determine if uv is an edge of G. ... equivalent, interpretation of this
   result is that, for every +ve integer n, there exists a g. U_n with
   n^{1+o(1)} vertices such s.t. every n-vertex planar g. is an induced subg.
   of U_n. ..."  [online Nov 2021].
   -- [<A HREF="https://doi.org/10.1145/3477542">doi:10.1145/3477542</A>]['21].
   [Also search for: planar graph].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/Graph/">graphs</A>].)

%A A. Davies
%A et al
%T Advancing mathematics by guiding human intuition with AI
%J Nature
%V 700
%P 70-74
%M DEC
%D 2021
%K jrnl, c2021, c202x, c20xx, zz1221, maths, mathematics, DeepMind, AI,
   Birch, Swinnerton, Dyer, theorem, theorems, aided
%X "... Since the 1960s, mathematicians have used computers to assist in the
   discovery of patterns & formulation of conjectures, most famously in the
   Birch & Swinnerton-Dyer conjecture, a Millennium Prize Problem. Here we
   provide examples of new fundamental results in pure maths that have been
   discovered with the assistance of machine learning - demonstrating a method
   by which machine learning can aid mathematicians in discovering new
   conjectures & theorems. ... led to meaningful math. contributions on
   important open problems: a new connection between the algebraic & geometric
   structure of knots, & a candidate alg. predicted by the combinatorial
   invariance conjecture for symmetric groups. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-04086-x">doi:10.1038/s41586-021-04086-x</A>]['21].

%A P. Indyk
%A T. Wagner
%T Optimal (Euclidean) metric compression
%J SIAM J. Comput.
%V 51
%N 3
%P ?-?
%M JUN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0722, Euclidean, distance, pairwise, distances,
   compress, lossy compression, dimension reduction, quantization
%X "... problem of representing all distances between n pts in R^d, with arb.
   small distortion, using as few bits as possible. We give asymptotically tight
   bounds for this problem, for Euclidean metrics, for L_1 (... Manhattan)...,
   & for general metrics. Our bounds for E.metrics mark the 1st improvement over
   compression schemes based on discretizing the classical dimensionality red'n
   theorem of Johnson & Lindenstrauss [Contemp.Math. 26 (1984), pp.189-206].
   Since it is known that no better dim'n red'n is possible, our results
   establish that Euc.metric compr'n is possible beyond dim.red.."
   -- [<A HREF="https://doi.org/10.1137/20M1371324">doi:10.1137/20M1371324</A>]['22].

%A D. Larsen
%T Bertrand's postulate for Carmichael numbers
%J Int. Math. Res. Notices
%M JUL
%D 2022
%K jrnl, c2022, c202x, c20xx, zz1022, Carmichael numbers, maths, young students,
   number theory
%X "Alford et al. [1] proved that there are infinitely many Carmichael numbers.
   In the same paper, they ask if a statement analogous to Bertrand's postulate
   could be proven for C. #s. In this paper, we answer this q., proving the
   stronger statement that for all d > 0 & x suff. large in terms of d, there
   exist at least log(x)/e^(log log x)^2+d) C. #s between x &
   x+x/((log(x))^(1/(2+d)))â "
   -- [<A HREF="https://arxiv.org/abs/2111.06963">arXiv:2111.06963</A>]['22],
      [<A HREF="https://doi.org/10.1093/imrn/rnac203">doi:10.1093/imrn/rnac203</A>]['22],
      CN@[<A HREF="https://en.wikipedia.org/wiki/Carmichael_number">wikip</A>][wikip</A>]['22].

%A S. K. Bera
%A L. Gishboliner
%T Counting subgraphs in degenerate graphs
%J JACM
%V 69
%N 3
%M JUN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0722, count, counting, subgraph, algorithm,
   instance, maths, graph, bounded degeneracy, degenerate,
   Bera, Pashanasangi, Seshadhri
%X "... problem of counting the # of copies of a fixed graph H within an input
   graph G. ... focus on solving this problem when the input G has bounded
   degeneracy. This is a rich family of graphs, containing all g. without a
   fixed minor (e.g., planar g.), [&] graphs generated by various random
   processes ... say that H is easy if there is a linear-time alg. for counting
   the # of copies of H in an input G of bnd deg.. ... Bressan has recently
   introduced a framework for counting subgraphs in deg.g., from which one can
   extract a suff. cond'n for a graph H to be easy. Here, we show that this
   suff. cond'n is also necessary, thus fully answering the Bera-Pashanasangi-
   Seshadhri problem. [&] resolve two closely related problems; namely
   characterizing the graphs that are easy with respect to counting induced
   copies, & wrt counting homomorphisms."
   -- [<A HREF="https://doi.org/10.1145/3520240">doi:10.1145/3520240</A>]['22].
   [Also search for: count subgraph].

%A D. Chakraborty
%A D. Das
%A R. Krauthgamer
%T Clustering permutations: New techniques with streaming applications
%J arXiv
%M DEC
%D 2022
%K TR, c2022, c202x, c20xx, zz1222, permutation, ranking, cluster, clustering,
   Ulam distance, edit distance, k median, Kmedian, perm, rankings, algorithm
%X "We study the classical metric k-median clustering problem over a set of
   input rankings (i.e., permutations) ..., from social-choice theory to web
   search & databases. A folklore alg. provides a 2-approximate soln in
   polynomial time for all k=O(1), & works irrespective of the underlying dist.
   measure, so long it is a metric; however, going below the 2-factor is a
   notorious challenge. We consider the Ulam dist., a variant of the well-known
   edit-dist. metric, where strings are restricted to be permutations. ..."
   -- 2212.01821@[<A HREF="https://arxiv.org/abs/2212.01821">arXiv</A>]['22].
   [Also search for: permutation distance].

%A F. Lombardi
%A E. Onofri
%T Graph contraction on attribute-based coloring
%J Procedia Computer Science
%V 201
%P 429-436
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0424, maths, graph, contraction, cluster,
   colouring
%X "... the problem of contracting possibly large colored graphs into much
   smaller representatives. It also provides a novel serial but parallelizable
   alg. to tackle this task. ..."
   -- [<A HREF="https://doi.org/10.1016/j.procs.2022.03.056">doi:10.1016/j.procs.2022.03.056</A>]['24].
   [Also search for: graph compression].

%A D. Smith
%A et al
%T An aperiodic monotile
%J arXiv
%M MAR
%D 2023
%K TR, c2023, c202x, c20xx, zz0323, maths, tiling, aperiodic, monotile, 2D,
   space
%X "A longstanding open problem asks for an aperiodic monotile, also known as an
   'einstein"... We answer this problem for topological disk tiles by exhibiting
   a continuum of combinatorially equivalent aperiodic polygons. ..."
   -- [<A HREF="https://doi.org/10.48550/arXiv.2303.10798">arXiv</A>]['23].
   Also see APT@[<A HREF="https://en.wikipedia.org/wiki/Aperiodic_tiling">wikip</A>]['23].
   [Also search for: aperiodic tiling].

%A J. P. Aguilera
%A F. Pakhomov
%A A. Weiermann
%T Modern perspectives in Proof Theory
%J Phil. Trans. Royal Soc. A
%M APR
%D 2023
%K jrnl, c2023, c202x, c20xx, zz0623, maths, proof, inconsistent, consistency,
   incompleteness theorem, logic, provability, logics
%X "The articles collected in this volume form a snapshot of the state of
   Proof Theory at the beginning of the year 2023. ..."
   -- [<A HREF="https://doi.org/10.1098/rsta.2022.0020">doi:10.1098/rsta.2022.0020</A>]['23].

%A C. Jakel
%T A computation of the ninth Dedekind number
%J arXiv
%M APR
%D 2023
%O Int. Wshop on Boolean Fns & their Applications (BFA), Sep., 2023
%K TR, c2023, c202x, c20xx, zz0723, ninth, Dedekind number, numbers, antichain,
   lattice, A000372, monotone Boolean functions
%X "... present an alg. to compute the 9th Dedekind Number. The key aspects are
   the use of matrix multiplication & symmetries in the free distributive
   lattice, which are detected with techniques from Formal Concept Analysis."
   -- [<A HREF="https://arxiv.org/abs/2304.00895">arxiv:2304.00895</A>]['23].
   286386577668298411128469151667598498812366
   (Also see
   "... monotonic if, for every combination of inputs, switching one of the
   inputs from false to true can only cause the output to switch from false to
   true & not from true to false ..."
   -- DN@[<A HREF="https://en.wikipedia.org/wiki/Dedekind_number">wikip</A>]['23];
   "The number d(n) of monotone Boolean fns of n variables ..."
   -- [<A HREF="https://mathworld.wolfram.com/DedekindNumber.html">w'lfram</A>]['23].)

%A J. Arai
%A Y. Fujiwara
%A M. Onizuka
%T GuP: Fast subgraph matching by guard-based pruning
%J arXiv
%M JUN
%D 2023
%K TR, c2023, c202x, c20xx, zz0623, GuP, graph, maths, subgraph, search,
   isomorphic, quard, query, algorithm
%X "Subgraph matching, which finds subgraphs isomorphic to a query ... In this
   paper, we propose GuP, a [SG M] alg. with pruning based on guards. Guards are
   a pattern of intermediate search states that never find isomorphic SGs. GuP
   attaches a guard on each candidate vertex & edge & filters out them
   adaptively to the search state. ... GuP can efficiently solve various queries
   inc. those that the state-of-the-art methods could not solve in practical
   time."
   -- 2306.06557@[ <A HREF="https://arxiv.org/abs/2306.06557">arXiv</A>]['23].
   [Also search for: subgraph search].

%A R. Steinfeld
%T Post-quantum zero-knowledge proofs and applications
%J Proc. 10th ACM Asia Public-Key Cryptography Workshop (APKC)
%M JUL
%D 2023
%K conf, c2023, c202x, c20xx, zz0923, lattice based encryption, cryptography,
   ZKP, MonashUni
%X "Lattice-based cryptography is one of the most promising candidates for
   designing post-quantum cryptographic algs. that resist emerging q.computing
   attacks. ... discuss some recent developments in design & analysis of
   practical lattice-based post-quantum ZKPs and their applications. ..."
   -- [<A HREF="https://doi.org/10.1145/3591866.3593075">doi:10.1145/3591866.3593075</A>]['23] (5 refs),
      [<A HREF="https://scholar.google.com/citations?user=Xv7eWKcAAAAJ&hl=en">auth</A>]['23].

%A H. Eto
%A et al
%T Happy set problem on subclasses of co-comparability graphs
%J Algorithmica
%V 85
%P 3327-3347
%M NOV
%D 2023
%K jrnl, c2023, c202x, c20xx, zz1123, maths, interval, permutation, trapezoid,
   graph, maximum happy set, vertex, vertices, problem, algorithm
%X "... For a graph G & its vertex subset S, a vertex v in S is happy if all v's
   neighbors in G are contained in S. Given a graph G & a non-negative int. k,
   Maximum Happy Set is the problem of finding a vertex subset S of G s.t.
   |S|=k & the # of happy vertices in S is maximized. ... is NP-hard ... give
   an alg. for n-vertex interval graphs whose running time is O(n^2+k^3n) ..."
   -- [<A HREF="https://doi.org/10.1007/s00453-022-01081-0">doi:10.1007/s00453-022-01081-0</A>]['23] (online 12/2022).
   [Also search for: happy set graph].

%A L. Guth
%A J. Maynard
%T New large value estimates for Dirichlet polynomials
%J arXiv
%M MAY
%D 2024
%K TR, c2024, c202x, c20xx, zz0824, Riemann hypothesis, zeta function, prime,
   primes, number, numbers, polynomial
%X "We prove new bounds for how often Dirichlet polynomials can take large
   values. This gives improved estimates for a Dirichlet polynomial of length N
   taking values of size close to N^{3/4}, which is the critical situation for
   several estimates in analytic ..."
   -- [<A HREF="https://arxiv.org/pdf/2405.20552">arxiv:2405.20552</A>]['24],
   also see [<A HREF="https://doi.org/10.1126/science.z0p8ow7">www</A>]['24].

%A K.-M. Klein
%A J. Reuter
%T Faster lattice basis computation - the generalization of the Euclidean
   algorithm
%M AUG
%D 2024
%K TR, c2024, c202x, c20xx, zz0924, lattice, basis, algorithm, pivoting
%X "... our main result, we obtain an alg. to compute a lattice basis for given
   vectors A1,...,An in Z^d in time [bit ops] LS+O^~((n-d)d^2 . log(||A||))
   where LS is the time required to obtain the exact fractional solution of a
   certain system of linear equalities. ...
   -- [<A HREF="https://arxiv.org/abs/2408.06685">arxiv:2408.06685</A>]['24].

%A S. Dutta
%A A. Bhattacharya
%T RSVP: Beyond Weisfeiler Lehman graph isomorphism test
%M SEP
%D 2024
%K TR, c2024, c202x, c20xx, zz1024, Weisfeiler Lehman graph, maths, graphs,
   heuristic, Miyazaki, Paulus, hypohamiltonian
%X "... we propose a novel polynomial-time g.iso. testing heuristic, RSVP, &
   depict its enhanced discriminative power compared to the Weisfeiler-Lehman
   approach for several challenging classes of graphs. Bounded by a run-time
   complexity of O(e^2+ev^2+v^3) ... Similar to the WL test, our proposed
   alg. is prone to only one-sided errors, where isomorphic g. will never be
   determined to be non-isomorphic, although the reverse can happen."
   -- [<A HREF="https://arxiv.org/abs/2409.20157v1">arXiv:2409.20157v1</A>]['24].
   [Also search for: Weisfeiler Lehman].


%E J. Corner
%T Popular Television in Britain
%I British Film Institute
%D 1991
%K book, text, c1991, c199x, c19xx, TV, telly, BFI, BBC, England, UK
%X hb, isbn:0-85170-269-4; pb, isbn:0-85170-270-8;  [in main lib']
   essays on Brit TV.

%A R. Fulton
%T The Encyclopedia of TV Science Fiction
%P 593
%I Boxtree Ltd and ITV books
%D 1990
%K Science Fiction, c1990, c199x, c19xx, Scifi, SF, book, text, television,
   telly, TV
%X short entries on a great many TV science fiction programmes from
   'Stranger From Space' (BBC, 1951) and 'Quatermass' (BBC 1953) onwards.

%A J. Leman
%T Wise scientists and female androids: class and gender in science fiction
%P 108-124
%B Popular Television in Britain
%E J. Corner
%I British Film Institute
%D 1991
%K c1991, c199x, c19xx, TV, telly, series, serial, 1961, SciFi, SF,
   A for Andromeda, Hoyle, Julie Christie, Quatermass, women, men, computer,
   android, gynoid, computing, science, scientist, BFI, BBC, England, UK
%X hb, uk isbn:0-85170-269-4;  pb, uk isbn:0-85170-270-8; [in main lib.].
   An essay, as the title says, on class and gender in TV SF particularly the
   2 TV series 'Quatermass' (1953, 1955, 1958) and 'A for Andromeda' (1961).
   Picture of Julie Christie ('Christine' in A for A) at a computer teletype
   (terminal) on p.120.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Film/Andromeda/">A-for-A</A>].)

%A T. Vahimagi
%T British Television: An Illustrated Guide
%I OUP
%D 1994
%K 1994, c199x, c19xx, TV, telly, book, text, England, UK, Britain, BBC, ITV,
   British Film Institute, BFI
%X Short one column entries (+ a picture) on many British television
   programmes from 1936 to 1992.  Great for nostalgia.

%T The Smoking Gun: A Dossier of Secret, Surprising, and Salacious Documents
%E W. Bastone
%E D. Green
%E B. Glauber
%I LittleBrown
%D 2001
%K c2001, c200x, c20xx, book, fun, funn, funny, haha, ha ha, joke, document,
   Sid Vicious, JFK, conspiracy theory, theories
%X '... scandalous, or bizarre news stories of recent years....
   What Sid Vicious told police...,
   A CIA memo on the use of "trained cats" as assassins... '
   About us$11; uk us isbn:0316611107.

%A T. C. Hoad
%A J. Zobel
%T Video similarity detection for digital rights management
%J 26th Australasian Computer Science Conf. (ACSC)
%P 237-245
%M FEB
%D 2003
%K conf, c2003, c200x, c20xx, zz0203, ACSC, ACSC2003, similarity, fingerprint,
   copyright, protection, video, videos, footage, films, movies, TV, monitoring,
   DPA, cut, cuts, shot, youtube, www
%X Detect "cuts" between "shots".  Use a DPA on the sequence of shot lengths.
   (Apparently typical broadcasts have about 1200 cuts per hour!)


%A L. M. Terman
%T A new approach to the study of genius
%J Psychological Review
%V 29
%N 4
%P 310-318
%D 1922
%K jrnl, c1922, c192x, c19xx, zz1120, human, intelligence, ability, gifted,
   genius, cleverness, creativity, precocity, IQ, talent, threshold, hypothesis
%X "Three stages in the study of genius during the last century are noted. In
   the first, the method is impressionistic & anecdotal. In the second, the
   method is inductive, the cases being selected on the basis of objective
   criteria & treated statistically. In the third, marked by Cattell's study of
   living American men of science, the selection of cases is accomplished by
   vastly improved methods. The next step in the study of genius is an
   examination of gifted children. This work has been commenced at Stanford
   U.. The writer presents concisely a # of sig., but tentative, conclusions.â
   -- [<A HREF="https://doi.org/10.1037/h0071072">www</A>]['20],
   auth@[<A HREF="https://en.wikipedia.org/wiki/Lewis_Terman">wikip</A>]['20],
   see [<A HREF="https://doi.org/10.3102%2F0034654316675476">www</A>]['20].

%A J. von Neumann
%T The Computer and the Brain
%I YaleUP
%D 1958
%K book, text, c1958, c195x, c19xx, computer, brain, size, estimate, sizes,
   mind, thought, consciousness, vonNeumann, John von Neumann
%X Unfinished, published after JvN's death.
   "... the views of one of the greatest mathematicians of the 20C on the
   analogies between computing machines and the living human brain. John von
   Neumann concludes that the brain operates in part digitally, in part
   analogically, but uses a peculiar statistical language unlike that employed
   in the operation of man-made computers. This edn includes a new foreword by
   2 eminent figures in the fields of philosophy, neuroscience & consciousness."
   1st ed 1958; hb;      uk us isbn:0300007930; uk us isbn13:978-0300007930.
   2nd ed 2000; pb us$9; uk us isbn:0300084730; uk us isbn13:978-0300084733.
    (In one summary JnV concludes:
     Comparison factor for size:  10^8 vs 10^9 in favour of nature v. computer.
     Comparison factor for speed: 10^4 vs 10^5 in favour of computer v. nature.
     Computer now typically has 10^5 or 10^6 bits ...,
     Human ~10^10 nerve cells * 14 inputs requires 14 * 10^10 bits/sec ...,
     over a lifetime total required memory capacity (human) = 2.8 x 10^20 bits
     -- A.D., 4/'12.)
   (Also see JvN@[<A HREF="http://en.wikipedia.org/wiki/Von_neumann">wikip</A>].)
   [Also search for: brain size estimate].

%A W. G. Chase
%A H. A. Simon
%T Perception in chess
%J Cog. Psychology
%V 4
%P 55-81
%D 1973
%K jrnl, c1975, c197x, c19xx, zz0319, human, behaviour, skill, practice,
   learning, chess, master, grand master, game, deGroot, playing, chunk,
   chunking, mastery, training, goal, goals
%X "This paper develops a technique for isolating and studying the perceptual
   structures that chess players perceive. Three chess players of varying
   strength - from master to novice - were confronted with two tasks:
   (1) A perception task, where the player reproduces a chess position in plain
   view, and (2) de Groot's( 1965) short-term recall task, where the player
   reproduces a chess position after viewing it for 5sec. The successive glances
   at the position in the perceptual task and long pauses in tbe memory task
   were used to segment the structures in the reconstruction protocol. The size
   and nature of these structures were then analyzed as a function of chess
   skill."
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.601.272
4&rep=rep1&type=pdf">c'teseer</A>]['19].
   (Also see the
   [<A HREF="http://www.bbc.com/capital/story/20190318-how-to-master-new-skills-
with-deliberate-practice">bbc</A>][19/3/2019].)

%A T. V. P. Bliss
%A T. Lomo
%T Long-lasting potentiation of synaptic transmission in the dentate area of
   the anaesthetized rabbit following stimulation of the perforant path
%J J. Physiology
%V 232
%N 2
%P 331-356
%M JUL
%D 1973
%K jrnl, c1973, c197x, c19xx, zz0316, brain, memory, nerve, synapse, neuron,
   neuroscience
%X "1. The after-effects of repetitive stimulation of the perforant path fibres
   to the dentate area of the hippocampal formation have been examined with
   extracellular micro-electrodes in rabbits anaesthetized with urethane. ..."
   -- [<A HREF="http://dx.doi.org/10.1113/jphysiol.1973.sp010273">doi:10.1113/jphysiol.1973.sp010273</A>]['16].
   (Also see the 2016 "brain prize"
    -- [<A HREF="http://www.bbc.com/news/science-environment-35686351">bbc</A>][3/2016].)

%A A. J. DeLong
%T Phenomenological space-time: Toward an experiential relativity
%J Science
%V 213
%N 4508
%P 681-683
%M AUG
%D 1981
%K jrnl, c1981, c198x, c19xx, zz0719, human, mind, perception, time, arrow,
   scale, size, psychology
%X "Subjects observing differently scaled environments undergo systematic shifts
   in the experience of time. The experience of temporal duration is compressed
   relative to the clock in the same proportion as scale-model environments
   being observed are compressed relative to the full-sized environment. This
   research suggests that spatial scale may be a principal mediator in the
   experience of time."
   -- [<A HREF="https://doi.org/10.1126/science.7256273">doi:10.1126/science.7256273</A>]['19].

%A Richard E. Cytowic
%T The Man Who Tasted Shapes: A Neurologist Reveals the Illusion of the
   Rational Mind
%I Jeremy Tarcher / PutnamPubl.
%P 256
%D 1993
%K text, book, c1993, c199x, c19xx, mind, brain, disorder, sense, senses,
   synesthesia, neurology
%X via enews; From: "Richard E. Cytowic MD" (p00907 of psilink.com)
   hardback, release date Aug '93.
   uk us isbn:0-87477-738-0; us$21.95 / us$28.95 (US).
     Cytowic has an open-minded and imaginative way of looking at
   neurology, hie patients, and society. During more than a decade,
   he has studied 42 people with synesthesia, a rare condition that
   haphazardly blends the five senses, and Michael, his first
   patient, plays a major role in the book's first part, "A Medical
   Mystery Tale."
     Cytowic graphically describes his growing knowledge of the
   condition and his gradually changing beliefs about the ways the
   brain functions, study of which has shifted its emphasis from
   spot localization of functions to functional pathways at the same
   time that the general emphasis in brain study has shifted from
   the cortex to the limbic system. The major theme throughout is
   that the brain runs more on emotion than on reason, but Cytowic
   also shows how artificial intelligence has gotten into a blind alley.
     The brief essays that make up the book's second part contain
   expansions of some of Cytowic's lines of thought. "The Man Who
   Tasted Shapes" will appeal to all medical detective fans; indeed,
   to any reader who likes an intriguing story and is not afraid to
   think. --William Beatty.

%E B. Dahlbom
%T Dennett and his Critics
%I Blackwell
%D 1993
%P 247
%K Dennett, text, book, c1993, c199x, c19xx, mind, AI
%X uk us isbn:0-631-18549-6.
   chapters by Dawkins, Dennett and others.

%A C. Seife
%T Cold numbers unmake the quantum mind
%J Science
%V 287
%N 5454
%P 791
%M FEB
%D 2000
%K views, c2000, c200x, c20xx, zz0414, brain, consciousness, quantum mind,
   Penrose, Tegmark
%X "Calculations show that collapsing wave functions in the scaffolding of the
   brain cannot explain the mystery of consciousness. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.287.5454.791">doi:10.1126/science.287.5454.791</A>]['14].
   (Also see MT@[<A HREF="http://space.mit.edu/home/tegmark/brain.html">mit</A>]['14]
   and QMind@[<A HREF="http://en.wikipedia.org/wiki/Quantum_mind">wikip</A>]['14].)
   [Also search for: quantum mind brain].

%A M. Tegmark
%T Importance of quantum decoherence in brain processes
%J Phys. Rev. E
%V 61
%P 4194
%M APR
%D 2000
%K c2000, c200x, c20xx, conscious, consciousness, quantum mind, brain,
   Penrose, microtubule, neural, decoherence
%X "Based on a calculation of neural decoherence rates, we argue that the
   degrees of freedom of the human brain that relate to cognitive processes
   should be thought of as a classical rather than quantum system, i.e., that
   there is nothing fundamentally wrong with the current classical approach to
   neural n/w simulations. We find that the decoherence time scales (~10^-13 -
   10^-20s) are typically much shorter than the relevant dynamical time scales
   (~10^-3 - 10^-1s), both for regular neuron firing & for kinklike polarization
   excitations in microtubules. This conclusion disagrees with suggestions by
   Penrose and others that the brain acts as a quantum computer, & that
   q.coherence is related to consciousness in a fundamental way."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevE.61.4194">doi:10.1103/PhysRevE.61.4194</A>]['14].
   (Also see QM@[<A HREF="http://en.wikipedia.org/wiki/Quantum_mind">wikip</A>]['14].)
   [Also search for: quantum mind brain].

%T Atom and Archetype: The Pauli/Jung Letters, 1932-1958
%E C. A. Meier
%I PrincetonUP
%P 312
%D 2001
%K book, text, c2001, c200x, c20xx, Pauli, Jung, mind, psychology, physics,
   quantum mechanics, theory, uncertainty principle, observation
%X trans 2001; hb us$166; uk us isbn:0691012075; uk us isbn13:978-0691012070.
   '... For Pauli, the creativity of science included considerations of the
   psyche. In science, he subscribed to the quantum uncertainty theory that the
   position and presence of the observer changes the perception and reality of
   what is observed. To that thesis--that one cannot measure the wave and the
   particle at the same time--he added a psychological dimension, observing that
   insofar as the scientist must opt to know "which aspect of nature we want to
   make visible . . . we simultaneously make a sacrifice, . . . [a] coupling of
   choice and sacrifice." ...'
   -- [<A HREF="http://press.princeton.edu/chapters/s7042.html">.P.UP</A>]['13].

%A S. Adams
%T When Body Language Goes Bad
%I AndrewsMcMeel
%P 128
%M MAR
%D 2003
%K book, c2003, c200x, c20xx, Dilbert, funny, ha ha, haha
%X about us$9. us isbn:0740732986.
   (Also see [<A HREF="http://www.dilbert.com/">dilbert</A>]['12].)

%A N. Chater
%A P. M. B. Vitanyi
%T The generalized universal law of generalization
%J J. Math. Psych.
%V 47
%P 346-369
%D 2003
%K jrnl, c2003, c200x, c20xx, zz0518, animal, behaviour, psychology,
   generalization, generalise, generalize, efficient coding,
   compression, information
%X "... We show that, nonetheless, the Universal Law of Generalization can be
   derived in the more complex setting of arbitrary stimuli, using a much more
   universal measure of dist.. This universal dist. is defined as the
   length of the shortest program that transforms the representations of the two
   items of interest into one another: The algorithmic information dist.. It
   is universal in the sense that it minorizes every computable dist.: It is
   the smallest computable dist.. We show that the Universal Law of
   Generalization holds with probability going to one-provided the probabilities
   concerned are computable. We also give a mathematically more appealing form
   of the Universal Law."
   -- [<A HREF="https://doi.org/10.1016/S0022-2496(03)00013-0">doi:10.1016/S0022-2496(03)00013-0</A>]['18].
   [Also search for: MML] and [also search for: universal law generalization].

%A Gray
%T Consciousness: Creeping up on the Hard Problem
%P 360
%I OUP
%M AUG
%D 2004
%K book, text, OUP, c2004, c200x, c20xx, zz0815, brain, mind, consciousness,
   neuroscience, human behaviour, self awarness, free will
%X "... analyses these core issues & reviews the evidence from both
   introspection & experiment. To many its conclusions will be surprising &
   even unsettling: The entire perceived world is constructed by the brain. The
   relationship between the world we perceive & the underlying physical reality
   is not as close as we might think. Much of our behaviour is accomplished with
   little or no participation from conscious experience. Our conscious
   experience of our behaviour lags the behaviour itself by around a fifth of a
   second - we become aware of what we do only after we have done it. The lag in
   conscious experience applies also to the decision to act - we only become
   aware of our decisions after they have been formed. The self is as much a
   creation of the brain as is the rest of the perceived world. Written by a
   leading scientist, this analysis of how conscious experience relates to brain
   & behaviour is accessible & compelling. It will have major implications for
   our understanding of human nature."
   1st ed 2004; hb us$70; uk us isbn:0198520905; uk us isbn13:978-0198520900.
   [Also search for: mind conscioussness].

%A J. Hawkins
%A S. Blakeslee
%T On Intelligence
%I TimesBooks
%P 272
%M SEP
%D 2004
%K book, text, c2004, c200x, c20xx, zz0614, AI, ANN, brain, mind, cortex,
   memory, consciousness, human, creativity, imagination, computer, machine,
   artificial intelligence
%X 1st ed 2004; hb us$6; uk us isbn:0805074562; uk us isbn13:978-0805074567.
   "... Most people think that computers are getting smarter, and that maybe
   someday, they'll be as smart as we humans are. But H explains why the way we
   build computers today won't take us down that path. He shows, using nicely
   accessible examples, that our brains are memory-driven systems that use our
   five senses and our perception of time, space, and consciousness in a way
   that's totally unlike the relatively simple structures of even the most
   complex computer chip. ..." -amaz.
   There is a section on 'Testable Predictions':
      1. We should find cells ... [for] anticipation of a sensory event...
      2. The more spacially specific a predn can be the closer to
         the primary sensory cortex we should find cells... ...
      11. Invariant repns should be found in all cortical areas.

%A F. C. Crick
%A C. Koch
%T What is the function of the claustrum?
%J Phil. Trans of the Royal Soc., B
%V 360
%N 1458
%P 1271-1279
%M JUN
%D 2005
%K jrnl, c2005, c200x, c20xx, zz0714, human, brain, seat of, consciousness,
   conscious, mind, claustrum, neocortex, cortex, insula
%X "The c. is a thin, irregular, sheet-like neuronal struct. hidden beneath the
   inner surface of the neocortex in the general region of the insula. Its fn is
   enigmatic. Its anatomy is quite remarkable in that it receives input from
   almost all regions of cortex & projects back to almost all regions of cortex.
   ... summarize what is known about the c., speculate on its possible relns to
   the processes that give rise to integrated conscious percepts, propose
   mechanisms that enable info. to travel widely within the c. & discuss
   experiments to address these Qs."
   -- [<A HREF="http://dx.doi.org/10.1098/rstb.2005.1661">doi:10.1098/rstb.2005.1661</A>]['14].
   [Also search for: claustrum]  and [also search for: consciousness].

%A P. Hut
%A M. Alford
%A M. Tegmark
%T On math, matter and mind
%J arXiv
%M JAN
%D 2006
%K TR, c2006, c200x, c20xx, brain, quantum mind, Penrose, science, physics
%X "We discuss the nature of reality in the ontological context of Penrose's
   math-matter-mind triangle. ... suggests the circularity of the widespread
   view that math arises from the mind, the mind arises out of matter, & that
   matter can be explained in terms of math. Non-physicists should be wary of
   any claim that modern physics leads us to any particular resolution of this
   circularity, since even the sample of three theor. physicists writing this
   paper hold three divergent views. Some physicists believe that current
   physics has already found the basic framework for a complete description of
   reality, & only has to fill in the details. Others suspect that no single
   framework, from physics or other sources, will ever capture reality. Yet
   others guess that reality might be approached arbitrarily closely by some
   form of future physics, but probably based on completely different
   frameworks. We will designate these three approaches as the fundamentalist,
   secular & mystic views of the world, as seen by practicing physicists. We
   present & contrast each of these views, which arguably form broad categories
   capturing most if not all interpretations of physics. We argue that this
   diversity in the physics community is more useful than an ontological
   monoculture, since it motivates physicists to tackle unsolved problems with
   a wide variety of approaches."
   -- 0510188@[<A HREF="http://arxiv.org/abs/physics/0510188">arXiv</A>]['14].
   [Also search for: quantum mind brain].

%A B. De Martino
%A D. Kumaran
%A B. Seymour
%A R. J. Dolan
%T Frames, biases, and rational decision-making in the human brain
%J Science
%V 313
%N 5787
%P 684-687
%M AUG
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0715, deMartino, human behaviour, risk, risks,
   loss, economics, brain, amygdala, decision making, frame problem, framing,
   bias, rationality, rational
%X ".. manner in which options are presented. This so-called 'framing effect'
   represents a striking violation of std economic accounts of human rationality
   although its underlying neurobiology is not understood. We found that the
   framing effect was specifically assoc. with amygdala activity, suggesting a
   key role for an emotional system in mediating decision biases. [&] across
   individuals, orbital & medial prefrontal cortex activity predicted a reduced
   susceptibility to the framing effect. This finding highlights the importance
   of incorporating emotional processes within models of human choice & suggests
   how the brain may modulate the effect of these biasing influences to approx.
   rationality."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1128356">doi:10.1126/science.1128356</A>]['15].

%A M. Minsky
%T The Emotion Machine: Commonsense Thinking, Artificial Intelligence, and
   the Future of the Human Mind
%I SimonAndSchuster
%P 400
%D 2006
%K book, text, Marvin Minsky, c2006, c200x, c20xx, zz0119, AI, human, mind,
   emotions, instinct, thought, consciousness, zzPrediction
%X reprint 2007, pb us$14; uk us isbn:0743276647, uk us isbn13: 978-0743276641.
   "... argues persuasively that emotions, intuitions, and feelings are not
   distinct things, but different ways of thinking. ... shows how our minds
   progress from simple, instinctive kinds of thought to more complex forms,
   such as consciousness or self-awareness. ..."
   (M.M., 1927-2016, MM@[<A HREF="https://en.wikipedia.org/wiki/Marvin_Minsky">wikip</A>]['19].)

%A K. D. Vohs
%A J. W. Schooler
%T The value of believing in free will
%J Psych. Sci.
%V 19
%N 1
%P 49-54
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0914, human, free will, behaviour, cheat,
   cheating, belief
%X 91974@[<A HREF="http://assets.csom.umn.edu/assets/91974.pdf">csom.umn</A>]['14].

%A E. M. Izhikevich
%A G. M. Edelman
%T Large-scale model of mammalian thalamocortical systems
%J PNAS
%V 105
%N 9
%P 3593-3598
%M MAR
%D 2008
%K PNAS, jrnl, c2008, c200x, c20xx, brain, simulation, neuron, neurons,
   network, NN, chip, activity, spiking, waves, dendrite
%X "... a detailed large-scale thalamocortical model based on experimental
   measures in several mammalian species. The model spans three anatomical
   scales. (i) It is based on global (white-matter) thalamocortical anatomy
   obtained by means of diffusion tensor imaging (DTI) of a human brain.
   (ii) It includes multiple thalamic nuclei and six-layered cortical
   microcircuitry based on in vitro labeling and 3D reconstruction of single
   neurons of cat visual cortex. (iii) It has 22 basic types of neurons with
   appropriate laminar distribution of their branching dendritic trees. The
   model simulates one million multicompartmental spiking neurons calibrated to
   reproduce known types of responses recorded in vitro in rats. It has almost
   half a billion synapses with appropriate receptor kinetics, short-term
   plasticity, and long-term dendritic spike-timing-dependent synaptic
   plasticity (dendritic STDP). The model exhibits behavioral regimes of normal
   brain activity that were not explicitly built-in but emerged spontaneously as
   the result of interactions among anatomical and dynamic processes. ...
   spontaneous activity, sensitivity to changes in individual neurons, emergence
   of waves and rhythms, and functional connectivity on different scales."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0712231105">doi:10.1073/pnas.0712231105</A>]['13],
      [<A HREF="http://www.izhikevich.org/publications/large-scale_model_of_human_brain.htm">www</A>]['13].
   [Also search for: brain simulation].

%A G. Tononi
%T Consciousness as Integrated Information: a Provisional Manifesto
%J Biol. Bull.
%V 215
%N 3
%P 216-242
%M DEC
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0514, brain, mind, consciousness,
   unconsciousness, IIT, qualia
%X "The integrated information theory (IIT) starts from phenomenology & makes
   use of thought experiments to claim that consciousness is II. Specifically:
   (i) the quantity of consciousness corresponds to the amount of integrated
   information generated by a complex of elements; (ii) the quality of
   experience is specified by the set of informational relationships gen. within
   that complex. II (phi) is def. as the amount of info. gen. by a complex of
   elts, above & beyond the info. gen. by its parts. Qualia space (Q) is a space
   where each axis represents a poss. state of the complex, each pt is a prob.
   distn of its states, & arrows between pts represent the informational
   relationships among its elts gen. by causal mechanisms (connections).
   Together, the set of informational relationships within a complex constitute
   a shape in Q that completely & univocally specifies a particular experience.
   Several observations concerning the neural substrate of consciousness fall
   naturally into place within the IIT framework. Among them are the assoc. of
   consciousness with certain neural systems rather than with others; the fact
   that neural processes underlying consciousness can influence or be influenced
   by neural processes that remain unconscious; the reduction of consciousness
   during dreamless sleep & generalized seizures; & the distinct role of
   different cortical architectures in affecting the quality of experience.
   Equating consciousness with integrated information carries several
   implications for our view of nature."
   -- [<A HREF="http://www.biolbull.org/content/215/3/216">biolBull</A>]['14],
      [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/19098144">p'bm'd</A>]['14].
   [Also search for: Tononi consciousness IIT].

%A S. Vazire
%A E. N. Carlson
%T Others sometimes know us better than we know ourselves
%J Current Directions in Psychological Sc.
%V 20
%N 2
%P 104-108
%M APR
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0916, mind, psychology, self, judgement,
   delusion, perception, personality
%X "... People's perceptions of their own personalities, while largely accurate,
   contain important omissions. Some of these blind spots are likely due to a
   simple lack of information, whereas others are due to motivated distortions
   in our self-perceptions. Perhaps for these reasons, others can perceive some
   aspects of personality better than the self can. This is esp. true for
   traits that are v.desirable or undesirable, when motivational factors are
   most likely to distort self-perceptions. Therefore, much can be learned about
   a person's personality from how he or she is seen by others. Future research
   should examine how people can tap into others' knowledge to improve
   self-knowledge."
   -- [<A HREF="http://dx.doi.org/10.1177/0963721411402478">doi:10.1177/0963721411402478</A>]['16].
   (... students' self-reports of intelligence bore almost no relation to
    results from IQ tests ... -- N.S.)

%A R. Pechey
%A P. Hallian
%T The prevalence of delusion-like beliefs relative to sociocultural beliefs in
   the general population
%J Psychopathology
%V 44
%N 2
%P 106-115
%M JAN
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0415, psychology, human, belief, beliefs,
   delusion, delusions, Cardiff Beliefs Questionnaire, CBQ, DLB, reality,
   religion, God, soul, intelligent design, astrology, paranoia, persecution,
   dysmorphia, magic, deluded, rationality, UCardiff, UniCardiff
%X "... Strong belief in 1 or more DLB was reported by 39% of the [1000]
   participants (91% reporting 'weak', 'moderate' or 'strong' belief in at least
   1 DLB). Moreover, 25% endorsed at least 1 bizarre DLB (76% one or more at any
   strength). Endorsements of DLB were strongly corr. with paranormal &
   religious beliefs but not general political/social beliefs. Conclusions: Both
   bizarre & non-bizarre DLB are frequently found in the general popn, lending
   support to the psychosis continuum account & need to revise key clinical
   criteria used to diagnose delusions. The good psychometric properties
   demonstrated by the CBQ indicate that this measure is a useful tool to
   investigate the wider continuum of beliefs held in the general population."
   -- [<A HREF="http://dx.doi.org/10.1159/000319788">doi:10.1159/000319788</A>]['15].

%A B. Hood
%T The Self Illusion: Why There is No 'You' Inside Your Head
%I ConstablePubl.
%P 272
%M APR
%D 2012
%K book, text, c2012, c201x, c20xx, mind, brain, self, consciousness,
   conscious
%X 1st ed 2012; pb stg.7; uk us isbn:1780330073; uk us isbn13:978-1780330075.
   "... that sovereignty of the self is increasingly under threat from sci. as
   our understanding of the brain advances. Rather than a single entity, the
   self is really a constellation of mechanisms & experiences that create the
   illusion of the internal you. We only emerge as a product of those around us
   as part of the different storylines we inhabit from the cot to the grave. It
   is an every changing character, created by the brain to provide a coherent
   interface between the multitude of internal processes & the external world
   demands that require different selves."

%A B. Hood
%T The Self Illusion: How the Social Brain Creates Identity
%I OUP
%P 368
%M MAY
%D 2012
%K book, text, c2012, c201x, c20xx, zz0512, brain, mind, self, consciousness
%X 1st ed 2012; hb us$20; uk us isbn:019989759X; uk us isbn13:978-0199897599.
   "... reveals how the self emerges during childhood & how the architecture
   of the developing brain enables us to become social animals dependent on each
   other. Humans spend proportionally the greatest amount of time in childhood
   compared to any other animal. It's not only to learn from others, Hood notes,
   but also to learn to become like others. We learn to become our self. Even as
   adults we are continually developing & elaborating this story, learning to
   become different selves in different situations - the work self, the home
   self, the parent self. ..."

%A T. Nagel
%T Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is
   Almost Certainly False
%I OUP
%P 144
%M SEP
%D 2012
%K book, text, OUP, c2012, c201x, c20xx, zz1012, mind, cosmos, theory,
   philosophy, nature, consciousness, body, reducibility, reductionism,
   materialistic, science, determinism, theism, God
%X 1st ed 2012; hb us$22; uk us isbn:0199919755; uk us isbn13:978-0199919758.
   "The modern materialist approach to life has conspicuously failed to explain
   such central mind-related features of our world as consciousness,
   intentionality, meaning, & value. ... An adequate conception of nature would
   have to explain the appearance in the universe of materially irreducible
   conscious minds, as such.  Nagel's skepticism is not based on religious
   belief or on a belief in any definite alternative. ... to recognize its
   limits is the first step in looking for alternatives, or at least in being
   open to their possibility."  <!-- BTW, it is not pro god -->

%A C. Aliasmith
%A et al ...
%A D. Rasmussen
%T A large-scale model of the functioning brain
%J Science
%V 338
%N 6111
%P 1202-1205
%M NOV
%D 2012
%K news, c2012, c201x, c20xx, zz1212, Spaun, brain, mind, simulation, modelling,
   neurons, neural, visual
%X "... present a 2.5-million-neuron model of the brain (called 'Spaun') that
   bridges this gap by exhibiting many different behaviors. The model is
   presented only with visual image sequences, & it draws all of its responses
   with a physically modeled arm. Although simplified, the model captures many
   aspects of neuroanatomy, neurophysiology, & psychological behavior, which we
   demonstrate via eight diverse tasks. "
   -- [<A HREF="http://dx.doi.org/10.1126/science.1225266">doi:10.1126/science.1225266</A>]['12].
   [Also search for: brain simulation].

%A R. Kurzweil
%T How to Create a Mind: The Secret of Human Thought Revealed
%I Viking
%P 352
%M NOV
%D 2012
%K book, text, c2012, c201x, c20xx, zz0213, brain, mind, AI, HMM, HHMM,
   intelligence, simulation
%X 1st ed 2012; hb us$16; uk us isbn:0670025291; uk us isbn13:978-0670025299.
   "... K. presents a provocative exploration of the most important project in
   human-machine civilization - reverse engineering the brain to understand
   precisely how it works and using that knowledge to create even more
   intelligent machines.  ... discusses how the brain functions, how the mind
   emerges from the brain, & the implications of vastly increasing the powers of
   our intelligence in addressing the world's problems. ..."
   [Also search for: brain simulation].

%A R. Preissl
%A T. M. Wong
%A P. Datta
%A R. Singh
%A S. Esser
%A W. Risk
%A H. Simon
%A M. Flickner
%A D. Modha
%T Compass - A Scalable Simulator for an Architecture for Cognitive Computing
%J Int. Conf. for High Performance Computing, Networking, Storage and Analysis
%M NOV
%D 2012
%K conf, c2012, c201x, c20xx, brain, simulation, size, estimate, complexity,
   neuron, neurons, SyNAPSE, synapses, IBM, TrueNorth, True North
%X "... developing TrueNorth, a novel modular, non-von Neumann, ultra-low power,
   compact architecture. ... consists of a scalable network of neurosynaptic
   cores, with each core containing neurons, dendrites, synapses, & axons. To
   set sail for TrueNorth, we have developed Compass, a multithreaded, massively
   parallel functional simulator & a parallel compiler that maps a network of
   long-distance pathways in the Macaque monkey brain to TrueNorth. ... demo
   near-perfect weak scaling on a 16 rack IBM Blue Gene/Q (262144 CPUs, 256 TB
   memory), achieving an unprecedented scale of 256 million neurosynaptic cores
   containing 65 billion neurons & 16 trillion synapses running only 388 x
   slower than real-time with an average spiking rate of 8.1 Hz. By using
   emerging PGAS communication primitives, we also demonstrate 2 x better real-
   -time performance over MPI primitives on a 4 rack Blue Gene/P (16384 CPUs,
   16 TB memory)."
   -- [<A HREF="http://sc12.supercomputing.org/schedule/event_detail.php?evid=pap649">www</A>]['13],
      pdf@[<A HREF="http://www.modha.org/blog/SC12/SC2012_Compass.pdf">www</A>]['13].
   (Also see [<A HREF="http://www.bbc.com/future/story/20130207-will-we-ever-simulate-the-brain">bbc</A>][8/2/2013].)
   [Also search for: brain simulation] and
   [also search for: brain size estimate].

%A S. Kouider
%A et al ...
%A G. Dehaene-Lambertz
%T A neural marker of perceptual consciousness in infants
%J Science
%V 340
%N 6130
%P 376-380
%M APR
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0413, brain, mind, baby, consciousness,
   child, children, development
%X "... demonstrating conscious access in infants remains challenging ...
   circumvent this problem, we studied whether an electrophysiological signature
   of consciousness found in adults, corr.to a late nonlinear cortical response
   [~300ms] to brief pictures, already exists in infants. We recorded event-
   -related potentials while 5-, 12-, and 15-month-old infants (N=80) viewed
   masked faces at various levels of visibility. In all age groups, we found a
   late slow wave showing a nonlinear profile at the expected perceptual
   thresholds. However, this late component shifted from a weak & delayed
   response in 5-month-olds (starting ~900ms) to a more sustained & faster
   response in older infants (~750ms). ... reveal that the brain mechanisms
   underlying the threshold for conscious perception are already present in
   infancy but undergo a slow acceleration during development."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1232509">doi:10.1126/science.1232509</A>]['13].

%A D. Hofstadter
%A E. Sander
%T Surfaces and Essences: Analogy as the Fuel and Fire of Thinking
%I BasicBooks
%P 592
%D 2013
%K book, text, c2013, c201x, c20xx, zz0413, mind, brain, analogies, thought,
   similarity
%X 1st ed 2013; hb us$21; uk us isbn:0465018475; uk us isbn13:978-0465018475.
   "... The answer to all these questions, of course, is analogy-making - the
   meat and potatoes, the heart and soul, the fuel and fire, the gist and the
   crux, the lifeblood and the wellsprings of thought. Analogy-making, far from
   happening at rare intervals, occurs at all moments, defining thinking from
   top to toe, from the tiniest and most fleeting thoughts to the most creative
   scientific insights. ..."
   [Also search for: Hofstadter book].

%A H. M. Ravven
%T The Self Beyond Itself: An Alternative History of Ethics, the
   New Brain Sciences, and the Myth of Free Will
%I NewPress
%P 528
%M MAY
%D 2013
%K book, text, c2013, c201x, c20xxx, zz0513, brain, mind, fuman, free will,
   self, ethics, morality, society
%X 1st ed 2013; hb us$20; uk us isbn:1595585370; uk us isbn13:978-1595585370.
   "... review of modern neuro-scientific research into the brain's capacity for
   decision-making - from mirror neurons and self-mapping to surprising new
   understandings of the dynamics of group psychology. ... points to the
   profound, virtually inescapable social influences on moral choices. ... shows
   that it is possible to build a theory of ethics that doesn't rely on free
   will yet still holds both individuals and groups responsible for the
   decisions that help create a good society. ..."
   [Also search for: brain mind].

%A J. Kagan
%T The Human Spark: The Science of Human Development
%I BasicBooks
%P 352
%M JUN
%D 2013
%K book, text, c2013, c201x, c20xx, zz0613, human development, psychology,
   neuroscience, nurture, behaviour
%X 1st ed 2013; hb us$20; uk us isbn:0465029825, isbn13:978-046502982.
   "... Kagan offers an unflinching examination of personal, moral, & cultural
   development that solidifies his place as one of the most influential
   psychologists of the past century. In this definitive analysis of the factors
   that shape the human mind, Kagan explores the tension between biology & the
   environment. He reviews major advances in the science of development over the
   past three decades & offers pointed critiques & new syntheses. In so doing,
   Kagan calls out the shortcomings of the modern fad for neuroscience ..."

%A C. Eliasmith
%T How to Build a Brain: A Neural Architecture for Biological Cognition
%I OUP
%S on Cognitive Models and Architectures
%P 480
%M JUN
%D 2013
%K book, text, OUP, c2013, c201x, c20xx, zz0713, brain, cognition,
   semantic pointer architecture, perception, model, simulation, Nengo
%X 1st ed 2013; hb us$80; uk us isbn:0199794545; uk us isbn13:978-0199794546.
   "... provides a detailed guided exploration of a new cognitive architecture
   that takes biological detail seriously, while addressing cognitive phenomena.
   The Semantic Pointer Architecture (SPA) introduced in this book provides a
   set of tools for constructing a wide range of biologically constrained
   perceptual, cognitive, and motor models.  ..."
   [Also search for: brain simulation].

%A B. De Martino
%A J. P. O'Doherty
%A D. Ray
%A P. Bossaerts
%A C. Camerer
%T In the mind of the market: theory of mind biases value computation during
   financial bubbles
%J Neuron
%V 79
%N 6
%P 1222-1231
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0715, brain, theory of mind, ToM, finance,
   economics, market bubble, financial, stock exchange, share, shares, market,
   boom, bust, investor, trader, human behaviour, dorsomedial prefrontal cortex,
   ventromedial, deMartino, ODoherty
%X "... show that ToM can also be maladaptive when people interact with complex
   modern institutions like financial markets. We tested participants who were
   investing in an experimental bubble market, a sitn in which the price of an
   asset is much higher than its underlying fundamental value. We describe a
   mechanism by which social signals computed in the dorsomedial prefrontal
   cortex affect value computations in ventromedial prefrontal cortex, thereby
   increasing an individual's propensity to 'ride' financial bubbles & lose
   money. These regions compute a financial metric that signals variations in
   order flow intensity, prompting inference about other traders' intentions.
   ... suggest that incorporating inferences about the intentions of others when
   making value judgments in a complex financial market could lead to the
   formation of market bubbles."
   -- [<A HREF="http://dx.doi.org/10.1016/j.neuron.2013.07.003">doi:10.1016/j.neuron.2013.07.003</A>]['15].

%A M.-C. Lai
%A et al ...
%A S. Baron-Cohen
%T Biological sex affects the neurobiology of autism
%J Brain
%V ?
%P ?-?
%M AUG
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0813, brain, autism, male, female, gender,
   autistic, adult
%X "... We found that the neuroanatomy of autism differed between adult males
   & females, evidenced by minimal spatial overlap (not different from that
   occurred under random condn) in both grey & white matter, & substantially
   large white matter regions showing sig. sex x diagnosis interactions in the
   2 x 2 factorial design. These suggest that a. manifests differently by
   biol.sex. [&] atypical brain areas in females with a. substantially &
   non-randomly (P < 0.001) overlapped with areas that were sexually dimorphic
   in neurotypical controls, in both grey & white matter, suggesting neural
   x masculinization. This was not seen in males with autism. How diffs in
   neuroanatomy relate to the similarities in cognition between males & females
   with autism remains to be understood. Future res. should stratify by
   biological sex to reduce heterogeneity & to provide greater insight into
   the neurobiology of autism."  [online Aug 2013.]
   -- [<A HREF="http://dx.doi.org/10.1093/brain/awt216">doi:10.1093/brain/awt216</A>]['13].

%A T. Suddendorf
%T The Gap: The Science of What Separates Us from Other Animals
%I BasicBooks
%P 368
%M NOV
%D 2013
%K book, text, c2013, c201x, c20xx, zz0514, human, animal, brain, mind,
   imagination
%X 1st ed 2103; hb us%22; uk us isbn:0465030149; uk us isbn13:978-0465030149.
   "... finds that two traits account for most of the ways in which our minds
   appear so distinct: Namely, our open-ended ability to imagine and reflect on
   scenarios, and our insatiable drive to link our minds together. These two
   traits explain how our species was able to amplify qualities that we
   inherited in parallel with our animal counterparts; transforming animal
   communication into language, memory into mental time travel, sociality into
   mind reading, problem solving into abstract reasoning, traditions into
   culture, and empathy into morality. ..."

%A S. Dehaene
%T Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts
%I VikingAdult
%P 352
%M JAN
%D 2014
%K book, text, c2014, c201x, c20xx, zz0114, brain, mind, consciousness,
   thought, awareness, conscious, human
%X 1st ed 2014; hb us$20; uk us isbn:0670025437; uk us isbn13:978-0670025435.
   "... describes the pioneering work his lab and the labs of other cognitive
   neuroscientists worldwide have accomplished in defining, testing, and
   explaining the brain events behind a conscious state. We can now pin down
   the neurons that fire when a person reports becoming aware of a piece of
   information and understand the crucial role unconscious computations play in
   how we make decisions. The emerging theory enables a test of consciousness
   in animals, babies, and those with severe brain injuries. ..."

%A M. Tegmark
%T Consciousness as a state of matter
%J arXiv
%M JAN
%D 2014
%K TR, c2014, c201x, c20xx, zz0414, brain, quantum mind, consciousness,
   matter, state, observer, perceptronium, Tononi, IIT, arrow, time
%X '... hypothesis that consciousness can be understood as a state of matter,
   "perceptronium", with distinctive info. proc. abilities. We explore five
   basic principles that may distinguish conscious matter from other physical
   systems such as solids, liquids & gases: the information, integration,
   independence, dynamics & utility principles. If such principles can identify
   conscious entities, then they can help solve the quantum factorization
   problem: why do conscious observers like us perceive the particular Hilbert
   space factorization corr. to classical space (rather than Fourier space,
   say), & more generally, why do we perceive the world around us as a dynamic
   hierarchy of objects that are strongly integrated & relatively independent?
   Tensor factorization of matrices is found to play a central role, & our
   technical results include a theorem about Hamiltonian separability (defined
   using Hilbert-Schmidt superoperators) being maximized in the energy
   eigenbasis. ... generalizes Giulio Tononi's integrated info.framework for
   neural-network-based consciousness to arbitrary quantum systems, & we find
   interesting links to error-correcting codes, condensed matter criticality, &
   the Quantum Darwinism program, as well as an interesting connection between
   the emergence of consciousness & the emergence of time. "
   -- 1401.1219@[<A HREF="http://arxiv.org/abs/1401.1219">arXiv</A>]['14].
   [Also search for: quantum mind brain]  and  [also search for: arrow time].

%A S. Hameroff
%A R. Penrose
%T Consciousness in the universe: A review of the 'Orch OR' theory
%J Physics of Life Reviews
%V 11
%N 1
%P 39-78
%M MAR
%D 2014
%K jrnl, c2014, c201x, c20xx, zz1122, consciousness, brain, mind, quantum,
   OrchOr, objective reduction, microtubule, controversial
%X "... We proposed in the mid 1990's that consciousness depends on biologically
   'orchestrated' coherent q.processes in collections of microtubules within
   brain neurons ... & that the cts Schrodinger evolution of each such process
   terminates in accordance with the specific Diosi-Penrose (DP) scheme of
   'objective reduction' ('OR') of the q.state. This orchestrated OR activity
   ('Orch OR') is taken to result in moments of conscious awareness &/or
   choice. ..."
   -- [<A HREF="https://doi.org/10.1016/j.plrev.2013.08.002">doi:10.1016/j.plrev.2013.08.002</A>]['22] (online 8/2013).
   (Also see Qconc@[<A HREF="https://en.wikipedia.org/wiki/Quantum_mind">wikip</A>]['22].)
   [Also search for: quantum brain mind].

%A M. Oizumi
%A L. Albantakis
%A G. Tononi
%T From the phenomenology to the mechanisms of consciousness: Integrated
   information theory 3.0
%J PLoS Comp. Biol.
%V 10
%N 5
%P e1003588
%M MAY
%D 2014
%K jrnl, eJrnl, IIT, c2014, c201x, c20xx, zz0114, brain, mind, consciousness,
   MICS, phenomenological, theory, unconsciousness, zomby, zombies
%X "... [ver.] 3.0 ... several advances over previous formulations. IIT starts
   from phenomenological axioms: information says that each experience is
   specific - it is what it is by how it differs from alternative experiences;
   integration says that it is unified - irreducible to non-interdependent
   components; exclusion says that it has unique borders & a particular
   spatio-temporal grain. These axioms are formalized into postulates that
   prescribe how physical mechanisms, such as neurons or logic gates, must be
   configured to generate experience (phenomenology). ... used to define
   intrinsic info. as 'differences that make a difference' within a system, &
   integrated info. as info. spec. by a whole that cannot be reduced to that
   specified by its parts. By applying the postulates both at the level of
   individual mechanisms & at the level of systems of mechanisms, IIT arrives at
   an identity: an experience is a maximally irreducible conceptual structure
   (MICS, a constellation of concepts in qualia space), & the set of elts that
   generates it constitutes a complex. ... a MICS specifies the quality of an
   experience & integrated info. phi^Max its quantity. From the theory follow
   several results, inc.: a system of mechanisms may condense into a major
   complex & non-overlapping minor complexes; the concepts that specify the
   quality of an experience are always about the complex itself & relate only
   indirectly to the external env.; anatomical connectivity influences complexes
   & assoc. MICS; a complex can generate a MICS even if its elts are inactive;
   simple sys. can be minimally conscious; complicated sys. can be unconscious;
   there can be true 'zombies' -  unconscious feed-forward sys. that are
   functionally equivalent to conscious complexes."  [online May 2014.]
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pcbi.1003588">doi:10.1371/journal.pcbi.1003588</A>]['14].
   [Also search for: Maguire mind consciousness].

%A P. Maguire
%A P. Moser
%A R. Maguire
%A V. Griffith
%T Is consciousness computable? Quantifying integrated information using
   algorithmic Information theory
%J arXiv
%M MAY
%D 2014
%K arXiv, c2014, c201x, c20xx, zz0514, AI, mind, brain, consciousness, AIT,
   lossless, lossy, compression, Tononi, IIT, Griffith, memories, noncomputable,
   unitary
%X "... we review Tononi's (2008) theory of consciousness as integrated
   information. We argue that prev. formalizations of integrated info. (e.g.
   Griffith, 2014) depend on info. loss. Since lossy integration would
   necessitate cts damage to existing memories, we propose it is more natural
   to frame consciousness as a lossless integrative process & provide a
   formalization of this idea using alg.info.theory. We prove that complete
   lossless integration requires noncomputable fns. This result implies that
   if unitary consciousness exists, it cannot be modelled computationally."
   -- 1405.0126@[<A HREF="http://arxiv.org/abs/1405.0126">arXiv</A>][5/'14].

%A M. Donoso
%A A. G. E. Collins
%A E. Koechlin
%T Foundations of human reasoning in the prefrontal cortex
%J Science
%V 344
%N 6191
%P 1481-1486
%M JUN
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0714, human, brain, prefrontal cortex,
   thought, reasoning, probabilistic inference
%X "The prefrontal cortex (PFC) subserves reasoning in the service of adaptive
   behavior. Little is known, however, about the architecture of reasoning
   processes in the PFC. Using computational modeling & neuroimaging, we show
   here that the human PFC has two concurrent inferential tracks: (i) one from
   ventromedial to dorsomedial PFC regions that makes probabilistic inferences
   about the reliability of the ongoing behavioral strategy & arbitrates between
   adjusting this strategy v. exploring new ones from long-term memory, &
   (ii) another from polar to lateral PFC regions that makes probabilistic
   inferences about the reliability of two or three alternative strategies &
   arbitrates between exploring new strategies versus exploiting these
   alternative ones. The two tracks interact &, along with the striatum, realize
   hypothesis testing for accepting versus rejecting newly created strategies."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1252254">doi:10.1126/science.1252254</A>]['14].

%A T. D. Wilson
%A D. A. Reinhard
%A E. C. Westgate
%A D. T. Gilbert
%A N. Ellerbeck
%A C. Hahn
%A C. L. Brown
%A A. Shaked
%T Just think: The challenges of the disengaged mind
%J Science
%V 345
%N 6192
%P 75-77
%M JUL
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0714, psychology, human behaviour, thinking,
   thought, think, challenge, bored, boredom, quiet, isolation, contemplation,
   inaction, inactivity, electric shock, shocks, challenge
%X "In 11 studies, we found that participants typically did not enjoy spending
   6 to 15 minutes in a room by themselves with nothing to do but think, that
   they enjoyed doing mundane external activities much more, & that many
   preferred to administer electric shocks to themselves instead of being left
   alone with their thoughts. Most people seem to prefer to be doing something
   rather than nothing, even if that something is negative."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1250830">doi:10.1126/science.1250830</A>]['14].
      (Also see, "... 18 of 42 people, more of them men than women,
       chose to give themselves at least one mild shock on the ankle
       when left alone for 15 minutes. ..."
      -- bbc@[<A HREF="http://www.bbc.com/news/science-environment-28130690">4/7/2014</A>].)

%A M. Z. Koubeissi
%A F. Bartolomei
%A A. Beltagyd
%A F. Picard
%T Electrical stimulation of a small brain area reversibly disrupts
   consciousness
%J Epilepsy & Behavior
%V 37
%P 32-35
%M AUG
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0714, human, brain, claustrum, mind,
   consciousness, seat, medial parietal, claustrum, insula, epilepsy
%X "... describe a region in the human brain where electrical stimn reproducibly
   disrupted consciousness. A 54y.o. woman with intractable epilepsy underwent
   depth electrode implantation & electrical stimulation mapping. The electrode
   whose stimulation disrupted consciousness was between the left claustrum &
   anterior-dorsal insula. Stimulation of electrodes within 5mm did not affect
   c.. ...  Stimulation of the claustral electrode reproducibly resulted in a
   complete arrest of volitional behavior, unresponsiveness, & amnesia without
   negative motor symptoms or mere aphasia. The disruption of c. did not outlast
   the stimn & occurred without any epileptiform discharges. We found a sig.
   increase in correlation for interactions affecting medial parietal &
   posterior frontal channels during stimns that disrupted c. [v.] those that
   did not. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.yebeh.2014.05.027">doi:10.1016/j.yebeh.2014.05.027</A>]['14],
      [<A HREF="http://www.sciencedirect.com/science/article/pii/S1525505014002017">sci.dir.</A>].
   [Also search for: claustrum]  and  [Also search for: consciousness].

%A E. Underwood
%T Researchers aim for an electrical memory prosthesis
%J Science
%V 345
%N 6194
%P 250
%M JUL
%D 2014
%K news, c2014, c201x, c20xx, zz0714, memory, loss, brain injury, prosthesis,
   implant, DARPA, controversial
%X "Last fall, Geoffrey Ling, a top biotechnology research official at the
   Defense Advanced Research Projects Agency (DARPA), challenged neuroscientists
   to do something extraordinary: Develop an implantable device that can reverse
   memory loss in veterans with traumatic brain injuries. Dangling up to
   $40million ... two academic teams have made the lunge. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.345.6194.250">doi:10.1126/science.345.6194.250</A>]['14].

%A E. Nahmias
%A G. Shepard
%A S. Reuter
%T It's OK if 'my brain made me do it': People's intuitions about free will and
   neuroscientific prediction
%J Cognition
%V 133
%N 2
%P 502-516
%M NOV
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0914, human, free will, mind
%X "... provide evidence suggesting that most people do not view the possibility
   of neuro-prediction as a threat to free will unless it also raises concerns
   about manipulation of the agent's behavior. In Experiment 1 two scenarios
   described future brain imaging technology that allows perfect predn of
   decisions & actions based on earlier neural activity, & this possibility did
   not undermine most people's attributions of free will or responsibility,
   except in the scenario that also allowed manipulation. In Experiment 2 the
   scenarios increased the salience of the physicalist implications of neuro-
   -prediction, while in Experiment 3 the scenarios suggested dualism, with
   perfect prediction by mindreaders. The patterns of results for these two
   experiments were similar to the results in Experiment 1, suggesting that
   participants do not understand free will to require specific metaphysical
   conditions regarding the mind'body relation. Most people seem to understand
   free will in a way that is not threatened by perfect predn based on neural
   info., suggesting that they believe that just because 'my brain made me do
   it,' that does not mean that I didn't do it of my own free will."
   -- [<A HREF="http://dx.doi.org/10.1016/j.cognition.2014.07.009">doi:10.1016/j.cognition.2014.07.009</A>]['14].

%A G. Tononi
%A C. Koch
%T Consciousness: Here, there and everywhere?
%J Phil. Trans. B
%I Royal Soc.
%M MAY
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0419, human, brain, mind, consciousness,
   conscious, thought, information, quale, philosophy, AI, NN, ANN,
%X "... we need not only more data but also a theory of consciousness one that
   says what experience is & what type of physical systems can have it.
   Integrated information theory (IIT) does so by starting from experience
   itself via five phenomenological axioms: intrinsic existence, composition,
   information, integration & exclusion. From these it derives five postulates
   about the properties required of physical mechanisms to support
   consciousness. The theory provides a principled account of both the quantity
   & the quality of an individual experience (a quale), & a calculus to evaluate
   whether or not a particular physical system is c. & of what. ... The theory
   holds that c. is a fundamental property possessed by physical systems having
   specific causal properties. It predicts that c. is graded, is common among
   biological organisms & can occur in some very simple systems. Conversely, it
   predicts that feed-forward networks, even complex ones, are not c., nor are
   aggregates such as groups of individuals or heaps of sand. Also, in sharp
   contrast to widespread functionalist beliefs, IIT implies that digital
   computers, even if their behaviour were to be functionally equivalent to
   ours, & even if they were to run faithful simulations of the human brain,
   would experience next to nothing."
   -- [<A HREF="https://doi.org/10.1098/rstb.2014.0167">doi:10.1098/rstb.2014.0167</A>]['19].
   Also see the bbc[<A HREF="http://www.bbc.com/future/story/20190326-are-we-close-to-solving-the-puzzle-of-consciousness">27/3/2019</A>].
   [Also search for: consciousness].

%A T. Aflalo
%A et al ...
%A R. A. Andersen
%T Decoding motor imagery from the posterior parietal cortex of a
   tetraplegic human
%J Science
%V 348
%N 6237
%P 906-910
%M MAY
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0615, human, brain implant, tetraplegic, PPC,
   mind control, robotic arm, intention, planning, posterior parietal cortex,
   PPC, electrodes, action, prosthetic, prosthesis, paralyzed, Erik Sorto
%X "... studies have suggested that popns of neurons in the posterior parietal
   cortex (PPC) may represent high-level aspects of action planning that can be
   used to control external devices as part of a brain-machine interface.
   However, there is no direct neuron-recording evidence that human PPC is
   involved in action planning, & the suitability of these signals for
   neuroprosthetic control has not been tested. We recorded neural popns
   activity with arrays of microelectrodes implanted in the PPC of a tetraplegic
   subject. Motor imagery could be decoded from these neural popns, inc.
   imagined goals, trajectories, & types of movement. These findings indicate
   that the PPC of humans represents high-level, cognitive aspects of action &
   that the PPC can be a rich source for cognitive control signals for neural
   prosthetics that assist paralyzed patients. "
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaa5417">doi:10.1126/science.aaa5417</A>]['15].

%A S. M. Frankland
%A J. D. Greene
%T An architecture for encoding sentence meaning in left mid-superior temporal
   cortex
%J PNAS
%V 112
%N 37
%P 11732-11737
%M AUG
%D 2015
%K jrnl, PNAS, c2015, c201x, c20xx, zz0915, human, brain, word, words, language,
   thought, abstract, thoughts, temporal cortex, lmSTC, superior temporal gyrus
%X "...  Here, in two functional mag. resonance imaging (fMRI) experiments using
   multivoxel pattern analysis (MVPA), we identify a region of left mid-superior
   temporal cortex (lmSTC) that flexibly encodes 'who did what to whom' in
   visually presented sentences. We find that lmSTC represents the current
   values of abstract semantic variables ('Who did it?' and 'To whom was it
   done?') in distinct subregions. Experiment 1 first identifies a broad region
   of lmSTC whose activity patterns (i) facilitate decoding of structure-depdt
   sentence meaning ('Who did what to whom?') & (ii) predict affect-related
   amygdala responses that depend on this info. (e.g., 'the baby kicked the
   grandfather' vs. 'the gf. kicked the baby'). Exp.2 then identifies distinct,
   but neighboring, subregions of lmSTC whose activity patterns carry info.
   about the identity of the current 'agent' ... & the current 'patient'
   ('To whom was it done?'). These neighboring subregions lie along the upper
   bank of the superior temporal sulcus & the lateral bank of the superior
   temporal gyrus, respectively. At a high level, these regions may fn like
   topographically defined data registers, encoding the fluctuating values of
   abstract semantic variables. This functional architecture, which in key
   respects resembles that of a classical computer, may play a critical role in
   enabling humans to flexibly generate complex thoughts." (online 24 Aug 2015.)
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1421236112">doi:10.1073/pnas.1421236112</A>]['15].

%A D. Eagleman
%T The Brain: The Story of You
%I PantheonPubl
%P 224
%M OCT
%D 2015
%K book, text, c2015, c201x, c20xx, zz1015, mind, brain, neuroscience
%X "... What is reality? Who are 'you'? How do you make decisions? Why does
   your brain need other people? How is technology poised to change what it
   means to be human?  In the course of his investigations, E. guides us through
   the world of extreme sports, criminal justice, facial expressions, genocide,
   brain surgery, gut feelings, robotics, and the search for immortality. ..."
   1st ed 2015; hb us$20; uk us isbn:1101870532; uk us isbn13:978-1101870532.

%A E. Sternberg
%T NeuroLogic: The Brain's Hidden Rationale Behind Our Irrational Behavior
%I PantheonPubl
%P 320
%M JAN
%D 2016
%K book, text, c2016, c201x, c20xx, zz0216, human, brain, mind, consciousness,
   conscious, unconscious, thought, neurology
%X 1st ed 2016; hb us$19; uk us isbn:0307908771; uk is isbn13:978-0307908773.
   "... explores the brain's internal system of reasoning, from its unconscious
   depths to conscious decision making, and illuminates how it explains our most
   outlandish as well as our most stereotyped behaviors. From sleepwalking
   murderers, contagious yawning, and the brains of sports fans to false
   memories, subliminal messages, and the secret of ticklishness ..."

%A F. de Waal
%T Are We Smart Enough to Know How Smart Animals are?
%I WWNorton
%P 352
%M APR
%D 2016
%M book, text, c2016, c201x, c20xx, zz0516, animal, human, mind, intelligence,
   deWaal, behaviour, tools, chimpanzees, bonobos, elephants
%X 1st ed 2016; hb us$17; uk us isbn:0393246183; uk us isbn13:978-0393246186.
   "... What separates your mind from an animal's? Maybe you think it's your
   ability to design tools, your sense of self, or your grasp of past & future
   - all traits that have helped us define ourselves as the planet's preeminent
   species. But in recent decades, these claims have eroded, or even been
   disproven outright, by a revolution in the study of animal cognition. Take
   the way octopuses use coconut shells as tools; elephants that classify humans
   by age, gender, & language; or Ayumu, the young male chimp. at Kyoto U. whose
   flash memory puts that of humans to shame. Based on research involving crows,
   dolphins, parrots, sheep, wasps, bats, whales, & of course chimpanzees &
   bonobos, Frans de Waal explores both the scope & the depth of animal
   intelligence. ..."
   [Also search for: deWaal animal behaviour].

%A A. B. Barron
%A C. Klein
%T What insects can tell us about the origins of consciousness
%J PNAS
%V ?
%N ?
%M APR
%D 2016
%K jrnl, PNAS, c2016, c201x, c20xx, zz0416, invertebrate, insect, conscious,
   consciousness, evolution, brain, mind, subjective experience,
   MacquarieUni, MacquarieU
%X "... Here we propose that at least one invertebrate clade, the insects, has a
   capacity for the most basic aspect of consciousness: subjective experience.
   In vertebrates the capacity for subjective experience is supported by
   integrated structures in the midbrain that create a neural simulation of the
   state of the mobile animal in space. This integrated & egocentric repn of
   the world from the animal's perspective is suff. for subjective experience.
   Structures in the insect brain perform analogous fns. [So] argue the insect
   brain also supports a capacity for subjective experience. In both vertebrates
   & insects this form of behavioral control system evolved as an efficient soln
   to basic problems of sensory reafference & true navigation. The brain
   structures that support subjective experience in v. & insects are v.different
   from each other, but in both cases they are basal to each clade. Hence we
   propose the origins of subjective experience can be traced to the Cambrian."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1520084113">doi:10.1073/pnas.1520084113</A>]['16] (online 4/2016).

%A A. G. Huth
%A W. A. de Heer
%A T. L. Griffiths
%A F. E. Theunissen
%A J. L. Gallant
%T Natural speech reveals the semantic maps that tile human cerebral cortex
%J Nature
%V 532
%P 453-458
%M APR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0516, human, brain, map, semantics, word, words,
   language, meaning, fMRI
%X "The meaning of language is represented in regions of the cerebral cortex
   collectively known as the 'semantic system'. However, little of the semantic
   system has been mapped comprehensively ...  we systematically map semantic
   selectivity across the cortex using voxel-wise modelling of functional MRI
   (fMRI) data collected while subjects listened to hours of narrative stories.
   We show that the semantic system is organized into intricate patterns that
   seem to be consistent across individuals. We then use a novel generative
   model to create a detailed semantic atlas. Our results suggest that most
   areas within the sem.sys. represent info. about specific semantic domains, or
   groups of related concepts, & our atlas shows which domains are represented
   in each area. ... demonstrates that data-driven methods - commonplace in
   studies of human neuroanatomy & functional connectivity - provide a powerful
   & efficient means for mapping functional representations in the brain."
   -- [<A HREF="http://dx.doi.org/10.1038/nature17637">doi:10.1038/nature17637</A>]['16].

%A R. Guevara Erra
%A D. M. Mateos
%A R. Wennberg
%A J. L. Perez Velazquez
%T Towards a statistical mechanics of consciousness: maximization of number of
   connections is associated with conscious awareness
%J arXiv
%M JUN
%D 2016
%O Phys. Rev. E 94, 052402, 8 Nov. 2016
%K jrnl, c2016, c201x, c20xx, zz0223, brain, activity, mind, consciousness,
   entropy, connections, networks, LZcomplexity
%X "It has been said that complexity lies between order & disorder. In the case
   of brain activity, & physiology in general, complexity issues are being
   considered with increased emphasis. ... analysing neurophysiological
   recordings in conscious & unconscious states. We find a surprisingly simple
   result: normal wakeful states are characterised by the greatest # of possible
   configurations of interactions between brain n/wks, representing highest
   entropy values. ... consciousness could be the result of an optimization of
   information processing. ..."
   -- 1606.00821@[<A HREF="https://arxiv.org/abs/1606.00821">arXiv</A>]['23].
   Also see [<A HREF="https://physicsworld.com/a/consciousness-is-tied-to-entropy-say-researchers/">comment</A>]['23].

%A M. J. Vansteensel
%A et al ...
%A N. F. Ramsey
%T Fully implanted brain-computer interface in a locked-in patient with ALS
%J NEJM
%V ?
%P ?-?
%M NOV
%D 2016
%K jrnl, NEJM, c2016, c201x, c20xx, zz1116, human, medicine, locked in syndrome,
   ALS, brain, implant, mind, control
%X "... a fully implanted brain-computer interface that consists of subdural
   electrodes placed over the motor cortex & a transmitter placed subcutaneously
   in the left side of the thorax. By attempting to move the hand on the side
   opposite the implanted electrodes, the patient accurately & independently
   controlled a computer typing program 28 weeks after electrode placement, at
   the equivalent of two letters per minute. The brain-computer interface
   offered autonomous communication that supplemented & at times supplanted the
   patient's eye-tracking device."
   -- [<A HREF="http://dx.doi.org/10.1056/NEJMoa1608085">doi:10.1056/NEJMoa1608085</A>]['16].
   (Also see [<A HREF="http://neuroprosthesis.eu/">www</A>]['16].)

%A D. B. Fischer
%A et al ...
%A J. C. Geerling
%T A human brain network derived from coma-causing brainstem lesions
%J Neurology
%V ?
%P ?-?
%M NOV
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0417, human, brain, stem, mind, seat of,
   consciousness, rostral dorsolateral pontine tegmentum, anterior insula,
   pregenual anterior cingulate cortex, pACC
%X "To characterize a brainstem location specific to coma-causing lesions, & its
   functional connectivity network. ... We compared 12 coma-causing brainstem
   lesions to 24 control brainstem lesions ... A small region in the rostral
   dorsolateral pontine tegmentum was sig. assoc. with coma-causing lesions. In
   healthy adults, this brainstem site was functionally connected to the ventral
   anterior insula (AI) & pregenual anterior cingulate cortex (pACC). These
   cortical areas aligned poorly with previously defined resting-state networks,
   better matching the distribution of von Economo neurons. Finally,
   connectivity between the AI and pACC was disrupted in patients with disorders
   of consciousness, & to a greater degree than other brain networks. ... This
   network of brain regions may have a role in the maintenance of human
   consciousness."
   -- [<A HREF="http://dx.doi.org/10.1212/WNL.0000000000003404">doi:10.1212/WNL.0000000000003404</A>]['17].
   (Also see sci-daily, 4/11/2016 [<A HREF="http://www.sciencedaily.com/releases/2016/11/161104190535.htm">www</A>]['17].)
   [Also search for: mind consciousness].

%A P. Godfrey-Smith
%T Other Minds: The Octopus, the Sea, and the Deep Origins of Consciousness
%I FarrarStrausGiroux
%P 272
%M DEC
%D 2016
%K book, text, c2016, c201x, c20xx, zz0417, brain, mind, minds, intelligence,
   consciousness, philosophy, evolution, ET, alien,
   cephalopod, octopus, squid, cuttlefish
%X 1st ed 2016; hb us$17; uk us isbn:0374227764; uk us isbn13:978-0374227760.
   "... a very distant branch of the tree of life has also sprouted higher
   intelligence: the cephalopods, consisting of the squid, the cuttlefish, and
   above all the octopus. In captivity, octopuses have been known to identify
   individual human keepers, raid neighboring tanks for food, turn off
   lightbulbs by spouting jets of water, plug drains, and make daring escapes.
   How is it that a creature with such gifts evolved through an evolutionary
   lineage so radically distant from our own? What does it mean that evolution
   built minds not once but at least twice? The octopus is the closest we will
   come to meeting an intelligent alien. What can we learn from the
   encounter? ..."
   [Also search for: brain mind]  and  [also search for: octopus]  etc..

%A T. Kitamura
%A S. K. Ogawa
%A D. S. Roy
%A T. Okuyama
%A M. D. Morrissey
%A L. M. Smith
%A R. L. Redondo
%A S. Tonegawa
%T Engrams and circuits crucial for systems consolidation of a memory
%J Science
%V 356
%N 6333
%P ?-?
%M APR
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0417, brain, mind, fear, memory, human, biol,
   long term, short, episodic, neocortex, prefrontal, hippocampus,
   entorhinal cortex, amygdala
%X "Episodic memories initially require rapid synaptic plasticity within the
   hippocampus for their formation & are gradually consolidated in neocortical
   n/wks for permanent storage. However, the engrams & circuits that support
   neocortical memory consolidation have thus far been unknown. We found that
   neocortical prefrontal memory engram cells, which are critical for remote
   contextual fear memory, were rapidly generated during initial learning
   through inputs from both the hippocampal-entorhinal cortex n/wk & the
   basolateral amygdala. After their generation, the prefrontal engram cells,
   with support from hippocampal memory engram cells, became functionally mature
   with time. Whereas hippocampal engram cells gradually became silent with
   time, engram cells in the basolateral amygdala, which were necessary for fear
   memory, were maintained. Our data provide new insights into the functional
   reorganization of engrams & circuits underlying systems consolidation of
   memory."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aam6808">doi:10.1126/science.aam6808</A>]['17].
   (Also see the bbc[<A HREF="http://www.bbc.com/news/health-39518580">7/4/2017</A>].)

%A A. Antinori
%A O. L. Carter
%A L. D. Smillie
%T Seeing it both ways: Openness to experience and binocular rivalry suppression
%J J. of Research in Personality
%V 68
%P 15-22
%M JUN
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0417, human, psychology, personality,
   openness, binocular rivalry, mixed percept, perception
%X "Openness to experience is characterised by flexible & inclusive cognition.
   ... investigated whether this extends to basic visual perception, s.t. open
   people combine information more flexibly, even at low-levels of perceptual
   processing. We used binocular rivalry, where the brain alternates between
   perceptual solns & times where neither soln is fully suppressed, mixed
   percept. Study 1 showed that openness is +vely assoc. with duration of mixed
   percept & ruled out the possibility of response bias. Study 2 showed that
   mixed percept increased following a +ve mood induction particularly for open
   people. ... openness is linked to differences in low-level visual perceptual
   experience. ..."
   -- [<A HREF="http://doi.org/10.1016/j.jrp.2017.03.005">doi:10.1016/j.jrp.2017.03.005</A>]['17].

%A E. Travers
%A C. D. Frith
%A N. Shea
%T Learning rapidly about the relevance of visual cues requires conscious
   awareness
%J Quarterly J. of Experimental Psychology
%M JUN
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0717, brain, mind, consciousness, human,
   behaviour, learning, psychology, cognition, awareness, cue
%X "Humans have been shown capable of performing many cognitive tasks using
   info. of which they are not consciously aware. This raises Qs about what role
   consciousness actually plays in cognition. Here, we explored whether
   participants can learn cue-target contingencies in an attentional learning
   task when the cues were presented below the level of c.awareness, & how this
   differs from learning about c.cues. Participants' manual (Experiment 1) &
   saccadic (Exp.2) response speeds were influenced by both c. & unc. cues.
   However, participants were only able to adapt to reversals of the cue-target
   contingencies (Exp.1) or changes in the reliability of the cues (Exp.2) when
   consciously aware of the cues. Therefore, although visual cues can be
   processed unconsciously, learning about cues over a few trials requires
   c.awareness of them. Finally, we discuss implications for cognitive theories
   of consciousness."
   -- 7becr@[<A HREF="https://osf.io/preprints/psyarxiv/7becr/">psyarxiv</A>]['17],
   or e4cz7@[<A HREF="https://osf.io/e4cz7/">osf.io</A>]['17],
   or [<A HREF="https://doi.org/10.17605/OSF.IO/E4CZ7">doi10.17605/OSF.IO/E4CZ7</A>]['17].
   [Also search for: consciousness].

%A T. Suddendorf
%A J. Crimston
%A J. Redshaw
%T Preparatory responses to socially determined, mutually exclusive
   possibilities in chimpanzees and children
%J Biol. Lett.
%M JUN
%D 2017
%K jrnl, biology, biol, c2017, c201x, c20xx, zz0623, human, child, chimp,
   planning, anticipation, learning, uncertainty, intelligence, cognition,
   chimpanzee
%X "Recent research suggests that between age 2 & 4 children gradually begin to
   demonstrate a capacity to prepare for two simple, mutually exclusive
   alternatives of an immediate future event. ... While 4-year-olds demonstrated
   competence, chimpanzees & the younger children instead tended to cover only
   one exit. These results substantiate the conclusion that the capacity for
   simultaneous preparation for mutually exclusive event outcomes develops
   relatively late in children & they are also in line with the possibility that
   our close animal relatives lack this capacity."
   -- [<A HREF="https://doi.org/10.1098/rsbl.2017.0170">doi:10.1098/rsbl.2017.0170</A>]['23].

%A C. Kabadayi
%A M. Osvath
%T Ravens parallel great apes in flexible planning for tool-use and bartering
%J Science
%V 357
%N 6347
%P 202-204
%M JUL
%D 2017
%K c2017, c201x, c20xx, zz0717, animal, bird, raven, crow, corvid, corvids,
   behaviour, planning, learning, intelligence, memory
%X "... Corvids, however, have shown evidence of planning their food hoarding,
   although this has been suggested to reflect a specific caching adaptation
   rather than domain-general planning. Here, we show that ravens plan for
   events unrelated to caching - tool-use and bartering - with delays of up to
   17 hours, exert self-control, and consider temporal distance to future
   events. Their performance parallels that seen in apes and suggests that
   planning evolved independently in corvids, which opens new avenues for the
   study of cognitive evolution."
   -- [<A HREF="http://doi.org/10.1126/science.aam8138">doi:10.1126/science.aam8138</A>]['17].

%A W. Arthur
%T Life through Time and Space
%I HarvardUP
%P 296
%M AUG
%D 2017
%K book, c2017, c201x, c20xx, zz0817, intelligence, life, intelligent, brain,
   space, extraterrestrial, evolution
%X 1st ed 2017; hb us$23; uk us isbn:0674975863; uk us isbn13:978-0674975866.
   "All humans share three origins: the beginning of our individual lives, the
   appearance of life on Earth, and the formation of our planetary home. WA
   combines embryological, evolutionary, and cosmological perspectives to tell
   the story of life on Earth and its potential to exist elsewhere in the
   universe."

%A A. Genevsky
%A C. Yoon
%A B. Knutson
%T When brain beats behavior: Neuroforecasting crowdfunding outcomes
%J J. Neuroscience
%V ?
%P ?-?
%M AUG
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0817, brain, mind, neuro, neuroscience,
   nucleus accumbens, NAcc, medial prefrontal cortex, MPFC, consciousness,
   judgement, FMRI, predict, crowdfunding
%X "...  To test whether neural activity could forecast market-level
   crowdfunding outcomes weeks later, 30 human subjects (14 female) decided
   whether to fund proposed projects ... while undergoing scanning with
   functional magnetic resonance imaging (FMRI). Although activity in both the
   nucleus accumbens (NAcc) & medial prefrontal cortex (MPFC) predicted
   individual choices to fund on a trial-to-trial basis in the neuroimaging
   sample, only NAcc activity generalized to forecast market funding outcomes
   weeks later on the internet. Behavioral measures from the neuroimaging
   sample, however, did not forecast market funding outcomes. This pattern of
   associations replicated in a 2nd study. ... demonstrate that a
   subset of the neural predictors of individual choice can generalize to
   forecast market-level c.f. outcomes - even better than choice itself."
   -- [<A HREF="http://doi.org/10.1523/JNEUROSCI.1633-16.2017">doi:10.1523/JNEUROSCI.1633-16.2017</A>]['17].

%A S. Dehaene
%A H. Lau
%A S. Kouide
%T What is consciousness, and could machines have it?
%J Science
%V 358
%N 6362
%P 486-492
%M OCT
%D 2017
%K jrnl, views, AI, c2017, c201x, c20xx, zz1017, consciousness, brain, mind,
   robot, AI, unconscious, self awareness, android
%X "...  We suggest that the word 'consciousness' conflates two different types
   of information-processing computations in the brain: the selection of
   information for global broadcasting, thus making it flexibly available for
   computation and report (C1, consciousness in the first sense), and the
   self-monitoring of those computations, leading to a subjective sense of
   certainty or error (C2, consciousness in the second sense). We argue that
   despite their recent successes, current machines are still mostly
   implementing computations that reflect unconscious processing (C0) in the
   human brain. We review the psychological and neural science of unconscious
   (C0) and conscious computations (C1 and C2) and outline how they may inspire
   novel machine architectures."
   -- [<A HREF="https://doi.org/10.1126/science.aan8871">doi:10.1126/science.aan8871</A>]['17].

%A F. Knolle
%A R. P. Goncalves
%A A. J. Morton
%T Sheep recognize familiar faces and unfamiliar human faces from
   two-dimensional images
%J Royal Society Open Science
%M NOV
%D 2017
%K c2017, c201x, c20xx, zz1117, face recognition, sheep, celebrity, face, faces,
   photographs, Huntington's disease, Ovis aries
%X "... trained eight sheep (Ovis aries) to recognize the faces of four
   celebrities ... After training, the sheep chose the 'learned-familiar' faces
   rather than the unfamiliar faces sig. above chance. We then tested whether
   the sheep could recognize the four celebrity faces if they were presented in
   different perspectives. This ... has previously been shown only in humans.
   Sheep successfully recognized the four celebrity faces from tilted images.
   Interestingly, there was a drop in performance with the tilted images (from
   79.22+/-7.5% to 66.5+/-4.1%) of a magnitude similar to that seen when humans
   perform this task. Finally, we asked whether sheep could recognize a very
   familiar handler from photographs. Sheep identified the h. in 71.8+/-2.3% of
   the trials without pretraining. Together these data show that sheep have
   advanced face-recognition abilities, comparable with those of humans and
   non-human primates."
   -- [<A HREF="https://doi.org/10.1098/rsos.171228">doi:10.1098/rsos.171228</A>]['17],
   auth3@[<A HREF="https://www.pdn.cam.ac.uk/directory/jenny-morton">cam.ac</A>]['17].
   (Also see, "Sheep can recognise images of Barack Obama and Emma Watson,
   Cambridge University study finds ..."
   -- abc[<A HREF="http://www.abc.net.au/news/2017-11-09/sheep-have-good-facial-recognition-systems-study/9132750">9/11/2017</A>].)
   (It is serious research, but is it a chance for an igNobel?)

%A N. Birbaumer
%T Your Brain Knows More Than You Think
%I ScribePubl
%P 263
%M SEP
%D 2017
%K book, text, c2018, c201x, c20xx, zz0318, brain, plasticity, neuroplasticity,
   damage, locked in syndrome, volition, epilepsy, stroke, psychopath,
   addiction
%X 1st ed 2017; pb us$23; uk us isbn:1911344382; uk us isbn13:978-1911344384.
   "... arguing that neuroplasticity - the virtually limitless capacity of the
   brain to remould itself - is enough to overcome almost any condition, however
   life-limiting it seems. Like the fathers and mothers of psychiatry, Birbaumer
   explores the sometimes-wild frontiers of a new way of thinking about our
   brains and behaviour. Through actual cases from his research and practice,
   he shows how we can change through brain training alone - and without risky
   drugs - if we simply open our minds."
   (Author on 'All in the mind', ABC radio 4/3/'18
   -- [<A HREF="http://www.abc.net.au/radionational/programs/allinthemind/frontiers-of-the-changeable-brain/9489666">abc</A>]['18].)

%A F. Hindriks
%A I. Douven
%T Nozick's experience machine: An empirical study
%J Philos. Psych.
%V 31
%N 2
%M DEC
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0324, AI, the matrix movie, SciFi, philosophy,
   Nozick, psychology, simulation, happiness, reality
%X "... In this thought experiment, people can choose to plug into a m/c that
   induces exclusively pleasurable experiences. We test Nozick's hypothesis that
   people will reject this offer. We also contrast Nozick's experience m/c
   scenario with scenarios that are less artificial, & offer options which are
   less invasive or disruptive than being connected to a m/c, specifically
   scenarios in which people are offered an experience pill or a pill that
   improves overall functioning."
   -- [<A HREF="https://doi.org/10.1080/09515089.2017.1406600">doi:10.1080/09515089.2017.1406600</A>]['24].
   Also see the [<A HREF="https://www.bbc.com/future/article/20240321-experience-machines-thought-experiment-that-inspired-matrixs-greatest-question">bbc</A>][24/3/2024</A>].

%A R. J. Sternberg
%T Speculations on the role of successful intelligence in solving contemporary
   world problems
%J J. Intelligence
%V 6
%N 1
%P 4
%M JAN
%D 2018
%K jrnl, c2018, c20x, c20xx, zz0719, human intelligence, IQ, creativity,
   wisdom, smartness, clever, cleverness, wise, wisdom, society, commonsense,
   common sense, Flynn effect, SAT, ACT, GRE, foolishness, school, education
%X "... I argue that conventional views of intelligence and its measurement have
   contributed toward at least some of the societal problems of today. I
   suggest that to escape from a degenerative process, society needs to consider
   the importance not only of intelligence, as conventionally defined but also
   of successful intelligence, involving in addition to conventional analytical
   intelligence, common sense, creativity, and wisdom."
   -- [<A HREF="https://dx.doi.org/10.3390/jintelligence6010004">doi:10.3390/jintelligence6010004</A>]['19].
   (Also see the bbc[<A HREF="http://www.bbc.com/future/story/20190709-has-humanity-reached-peak-intelligence">10/4/2019</A>].)

%A K. R. Jensen
%T An Evolution of Minds
%I Indep.
%P 337
%M MAR
%D 2018
%K book, c2018, c201x, c20xx, zz0322, mind, minds
%X pb us$17; uk us isbn:1980506892; uk us isbn13:978-1980506898.
   "What does it take to walk on water, raise the dead, manipulate matter, and
   have command over nature? Searching for the enigmatic powers of the prophets,
   a group of neuroscientists believe themselves to have found the answer,
   coming up with a plan to induce enlightenment ..."
   (Oh yeah?!)

%A N. Cesana-Arlotti
%A et al ...
%A L. L. Bonatti
%T Precursors of logical reasoning in preverbal human infants
%J Science
%V 359
%N 6381
%P 1263-1266
%M MAR
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0418, human development, baby, babbies, infant,
   logic, reasoning, brain, mind
%X "Infants are able to entertain hypotheses about complex events & to modify
   them rationally when faced with inconsistent evidence. These capacities
   suggest that infants can use elementary logical representations to frame &
   prune hypotheses. By presenting scenes containing ambiguities about the
   identity of an object, here we show that 12- & 19-month-old infants look
   longer at outcomes that are inconsistent with a logical inference necessary
   to resolve such ambiguities. At the moment of a potential deduction,
   infants' pupils dilated, & their eyes moved toward the ambiguous object when
   inferences could be computed, in contrast to transparent scenes not requiring
   inferences to identify the object. These oculomotor markers resembled those
   of adults inspecting similar scenes, suggesting that intuitive & stable
   logical structures involved in the interpretation of dynamic scenes may be
   part of the fabric of the human mind."
   -- [<A HREF="https://doi.org/10.1126/science.aao3539">doi:10.1126/science.aao3539</A>]['18].
   [Also search for: baby logic].

%A M. S. Gazzaniga
%T The Consciousness Instinct: Unraveling the Mystery of How the Brain Makes
   the Mind
%I FarrarStrausGiroux
%P 288
%M APR
%D 2018
%K book, c2018, c201x, c20xx, zz0418, brain, mind, consciousness,
   meat machine
%X 1st ed 2018; hb us$22; uk us isbn:0374715505; uk us isbn13:978-0374715502.
   "... Gazzaniga asserts that this model has it backward - brains make machines
   but they cannot be reduced to one. New research suggests the brain is
   actually a confederation of independent modules working together. ..."

%A C. Koch
%T What is consciousness?
%J Nature
%V 558
%P S8-S12
%M MAY
%D 2018
%K news, views, essay, c2018, c201x, c20xx, zz1020, mind, consciousness, NCC,
   neuronal correlates of consciousness, brain, cerebellum, Tononi
%X "Consciousness is everything you experience. It is the tune stuck in your
   head ... What is it about a highly excitable piece of brain matter that gives
   rise to consciousness? Once we can understand that, we hope to get closer to
   solving the more fundamental problem. We seek, in particular, the neuronal
   correlates of consciousness (NCC), defined as the minimal neuronal mechanisms
   jointly sufficient for any specific conscious experience. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-018-05097-x">doi:10.1038/d41586-018-05097-x</A>]['20].
   [Also search for: Consciousness].

%A C. R. Sims
%T Efficient coding explains the universal law of generalization in
   human perception
%J Science
%V 360
%N 6389
%P 652-656
%M MAY
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0518, animal behaviour, generalization,
   generalise, generalize, efficient coding, compression, information
%X "... will learn to avoid preying on that species again by generalizing its
   past experience to new perceptual stimuli. ... Here, I challenge existing
   theoretical explanations for the universal law and offer an alternative
   account based on the principle of efficient coding. I show that the universal
   law emerges inevitably from any information processing system (whether
   biological or artificial) that minimizes the cost of perceptual error subject
   to constraints on the ability to process or transmit information."
   -- [<A HREF="https://doi.org/10.1126/science.aaq1118">doi:10.1126/science.aaq1118</A>]['18].
   [Also search for: MML] and [also search for: universal law generalization].

%A L. Beaulieu-Laroche
%A et al
%A M. T. Harnett
%T Enhanced dendritic compartmentalization in human cortical neurons
%J Cell
%V 175
%N 3
%P 643-651
%M OCT
%D 2018
%K jrnl, c2018, c201x, c20xx, zz1018, human, brain, neuron, neurons, rodent,
   rat, cortex, dendrite, cognition
%X "... Cortical neurons are larger in humans than in other species, but it is
   unclear how their size affects synaptic integration. ..."
   -- [<A HREF="https://doi.org/10.1016/j.cell.2018.08.045">doi:10.1016/j.cell.2018.08.045</A>]['18].

%A G. Savulich
%A E. Thorp
%A T. Piercy
%A K. A. Peterson
%A J. D. Pickard
%A B. J. Sahakian
%T Improvements in attention following cognitive training with the novel
   'Decoder' game on an iPad
%J Front. in Behav. Neurosci.
%M JAN
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0119, decoder, human brain, attention, ADHD,
   game, cognitive training, improve, concentration, visual, RVP,
   Trail Making Test, TMT
%X "... aimed to investigate the effects of cognitive training in 75 healthy
   young adults randomly assigned to a Cognitive Training (8h of playing Decoder
   over 4 weeks; n=25), Active Control (8h of playing Bingo over 4 w; n=25) or
   Passive Control (continuation of activities of daily living; n=25) group.
   Results indicated that cognitive training with Decoder was superior to both
   control groups in terms of increased target sensitivity (A') on the Cambridge
   Neuropsychological Test Automated Battery Rapid Visual Information processing
   (CANTAB RVP) test, indicating sig. improved sustained visual attention.
   Individuals playing Decoder also showed sig. better performance on the Trail
   Making Test (TMT) compared with those playing Bingo. ..."
   -- [<A HREF="https://doi.org/10.3389/fnbeh.2019.00002">doi:10.3389/fnbeh.2019.00002</A>]['19].
   (Also see the [<A HREF="https://www.abc.net.au/news/2019-01-22/cambridge-uni-develops-app-with-ritalin-like-effects/10737268">abc</A>][23/1/2019].)

%A R. Pryluk
%A Y. Kfir
%A H. Gelbard-Sagiv
%A I. Fried
%A R. Paz
%T A tradeoff in the neural code across regions and species
%J Cell
%V 176
%N 3
%P 597-609 E18
%M JAN
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0119, human, monkey, primate, brain, brains,
   amygdala, cingulate, cortex, neurons, neuron, evolution, difference,
   psychopathologies, psychiatric, psychiatry, psychology, mental, health
%X "... we find that human neurons better utilize information capacity
   (efficient coding) than macaque neurons in both regions, and that cingulate
   neurons are more efficient than amygdala neurons in both species. In contrast
   we find more overlap in the neural vocabulary & more synchronized activity
   (robustness coding) in monkeys in both regions & in the amygdala of both
   species. Our findings demonstrate a tradeoff between robustness & efficiency
   across species and regions.  ..."
   -- [<A HREF="https://doi.org/10.1016/j.cell.2018.12.032">doi:10.1016/j.cell.2018.12.032</A>][24/1/2019].

$A A. Demertzi
%A et al
%T Human consciousness is supported by dynamic complex patterns of
   brain signal coordination
%J ScienceAdvances
%V 5
%N 2
%M FEB
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0723, brain, consciousness,  mind
%X "... we determined whether dynamic signal coordination provides specific &
   generalizable patterns pertaining to conscious & unconscious states after
   brain damage. ... results establish that c. rests on the brain's ability to
   sustain rich brain dynamics & pave the way for determining specific &
   generalizable fingerprints of c. & unc. states."
   -- [<A HREF="https://doi.org/10.1126/sciadv.aat7603">doi:10.1126/sciadv.aat7603</A>]['23].
   [Also search for: consciousness].
   (Also see IInfoTh@[<A HREF="https://en.wikipedia.org/wiki/Integrated_information_theory">wikip</A>]['23].)

%A D. Toker
%A F. T. Sommer
%T Information integration in large brain networks
%J PLoS Comp. Biol.
%V ?
%M FEB
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0419, human, monkey, brain, mind, consciousness,
   information, anterior, posterior, cortex
%X "... info. flow in the massively recurrent n/wks of the rest of the brain
   have been lacking. To address this, recent work in info.theory has produced
   a sound measure of network-wide 'integrated info.', which can be estimated
   from time-series data. But, a computational hurdle has stymied attempts to
   measure large-scale info. integration in real brains. Specifically, the
   measurement of integrated info. involves a combinatorial search for the
   informational 'weakest link' of a n/wk, a process whose computation time
   explodes super-exponentially with n/wk size. Here, we show that spectral
   clustering, applied on the correlation matrix of time-series data, provides
   an approximate but robust soln to the search for the informational weakest
   link of large n/wks. ... We evaluate this soln in brain-like systems of
   coupled oscillators as well as in high-density electrocortigraphy data from
   two macaque monkeys, & show that the informational 'weakest link' of the
   monkey cortex splits posterior sensory areas from anterior association areas.
   Finally, we use our soln to provide evidence in support of the long-standing
   hypothesis that info. integration is maximized by n/wks with a high global
   efficiency, & that modular n/wk structures promote the segregation of info.."
   -- [<A HREF=" https://doi.org/10.1371/journal.pcbi.1006807">doi:10.1371/journal.pcbi.1006807</A>]['19].
   Also see bbc[<A HREF="http://www.bbc.com/future/story/20190326-are-we-close-to-solving-the-puzzle-of-consciousness">27/3/2019</A>].
   [Also search for: consciousness].

%A M. Lang
%A et al ...
%A J. Henrich
%T Moralizing gods, impartiality and religious parochialism across 15 societies
%J Proc. Royal Soc. B
%V 286
%N 1898
%P id=20190202
%M MAR
%D 2019
%K jrnl, PRS, PRSB, c2019, c201x, c20xx, zz0319, human behaviour, society,
   civilisation, cooperation, cooperate, sharing, ingroup, outgroup,
   God, Gods, religious belief, religion
%X "... One hypothesis points to culturally evolved beliefs in punishing,
   interventionist gods that facilitate the extension of cooperative behaviour
   toward geographically distant co-religionists. [&] another hyp. points to
   such mechanisms being constrained to the religious ingroup, possibly at the
   expense of religious outgroups. To test ... we administered two behavioural
   experiments & a set of interviews to a sample of 2228 participants from 15
   diverse populations. ... included foragers, pastoralists, horticulturalists,
   & wage labourers, practicing Buddhism, Christianity, & Hinduism, but also
   forms of animism ... The effects of punishing & monitoring gods on outgroup
   allocations revealed between-site variability, suggesting that in the absence
   of intergroup hostility, moralizing gods may be implicated in cooperative
   behaviour toward outgroups. These results provide support for the hypothesis
   that beliefs in monitoring & punitive gods help expand the circle of
   sustainable social interaction, & open questions about the treatment of
   religious outgroups."
   -- [<A HREF="https://doi.org/10.1098/rspb.2019.0202">doi:10.1098/rspb.2019.0202</A>]['19].
   [Also search for: moralizing gods].

% H. Whitegouse
%A et al...
%A P. Turchin
%T [7/7/'21, RETRACTED ARTICLE:] Complex societies precede moralizing gods
   throughout world history
%J Nature
%V 568
%P 226-229
%M MAR
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0721, human behaviour, society, God, Gods,
   cooperation, religious belief, religion, retracted, retraction,
   missing data, stats
%X "The origins of religion and of complex societies represent evolutionary
   puzzles. The 'moralizing gods' hypothesis offers a soln to both puzzles by
   proposing that belief in morally concerned supernatural agents culturally
   evolved to facilitate coop'n among strangers in large-scale societies. ...
   Our analyses not only confirm the assoc. between moralizing gods & social
   complexity, but also reveal that moralizing gods follow - rather than
   precede - large increases in social complexity. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-1043-4">doi:10.1038/s41586-019-1043-4</A>]['21], but ...
   *** 'Treatment of missing data determined conclusions regarding moralizing
   gods', B.Beheim et al, Nature, 595, E29-E34, 2021
   -- [<A HREF="https://doi.org/10.1038/s41586-021-03655-4">doi:10.1038/s41586-021-03655-4</A>]['21].
   [Also search for: moralizing gods].

%A F. Mollica
%A S. T. Piantadosi
%J Humans store about 1.5 megabytes of information during language acquisition
%J Royal Soc. Open Sci.
%V 6
%N 3
%P MAR
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0419, human, brain, mind, natural language,
   linguistics, learn, knowledge, information theory, content
%X "... provide estimates at several levels of linguistic analysis: phonemes,
   wordforms, lexical semantics, word frequency and syntax. Our best guess is
   that the average English-speaking adult has learned 12.5 million bits of
   information, the majority of which is lexical semantics. Interestingly, very
   little of this information is syntactic, even in our upper bound analyses.
   Generally, our results suggest that learners possess remarkable inferential
   mechanisms capable of extracting, on average, nearly 2000 bits of information
   about how language works each day for 18 years."
   -- [<A HREF="https://doi.org/10.1098/rsos.181393">doi:10.1098/rsos.181393</A>]['19],
      [<A HREF="https://mollicaf.github.io/papers.html">mollicaf</A>]['19].
   [Also search for: natural language information].

%A H. Critchlow
%T The Science of Fate: Why Your Future is More Predictable Than You Think
%I HodderAndStoughton
%P 256
%M MAY
%D 2019
%K book, text, c2019, c201x, c20xx, zz0619, free will, freewill, mind,
   determinism
%X 1st ed 2019; uk us isbn:1473659280; uk is isbn13: 978-1473659285.

%A F. Gesiarz
%A D. Cahill
%A T. Sharot
%T Evidence accumulation is biased by motivation: A computational account
%J PLoS Comp. Biol.
%V 15
%N 6
%P e1007089
%M JUN
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz0719, human, behaviour, mind, bias,
   psychology, decision making, judgement, model
%X "To make good judgments people gather information. ... an agent needs to
   solve is when to continue sampling data and when to stop gathering evidence.
   ... Results show that participants' judgments were biased towards believing
   they were in the desirable state. They required a smaller proportion of
   supporting evidence to reach that conclusion and ceased gathering samples
   earlier when reaching the desirable conclusion. The findings were replicated
   in an additional sample of participants. ... modeled the data using a
   drift-diffusion model. ... found that a valence-dependent model, with both a
   response bias & a process bias, fit the data better than a range of other..."
    -- [<A HREF="https://doi.org/10.1371/journal.pcbi.1007089">doi:10.1371/journal.pcbi.1007089</A>]['19].

%A J. Kleiner
%T Mathematical models of consciousness
%J arXiv
%M JUL
%D 2019
%K TR, c2019, c201x, c20xx, zz0520, mind, conscious, consciousness, model
%X "... promising math. models have been suggested which aim to describe
   conscious experience & its relation to the physical domain. Whereas the
   axioms & metaphysical ideas of these theories have been carefully motivated,
   their math. formalism has not. ... we aim to remedy this sit'n. We give an
   account of what warrants math. representation of phenomenal experience,
   derive a general math. f/wk which takes into account consciousness' epistemic
   context & study which math. structures some of the key characteristics of
   c.experience imply, showing precisely where math. approaches allow to go
   beyond what the std methodology can do. The result is a general math. f/wk
   for models of c. that can be employed in the theory-building process."
   -- 1907.03223@[<A HREF="https://arxiv.org/abs/1907.03223">arXiv</A>]['20],
      auth@[<A HREF="https://jkleiner.de/">www</A>]['20].
   [Also search for: consciousness mind].

%A M. S. A. Graziano
%T Rethinking Consciousness: A Scientific Theory of Subjective Experience
%I WWNorton
%D 2019
%K book, text, c2019, c201x, c20xx, zz0919, AI, human, mind, conscious,
   consciousness, Attention Schema Theory, AST, PrincetonU, PrincetonUni
%X auth@[<A HREF="https://grazianolab.princeton.edu/">prin'ton</A>]['19].
   Also see AST@[<A HREF="https://en.wikipedia.org/wiki/Attention_schema_theory">wikip</A>]['19].
   [Also search for: consciousness mind].

%A C. Koch
%T The Feeling of Life Itself: Why Consciousness Is Widespread but
   Can't Be Computed
%M SEP
%D 2019
%K book, c2019, c201x, c20xx, zz1119, brain, mind, consciousness, computer,
   computed, being
%X 1st ed 2019; hb us$19; uk us isbn:0262042819; uk us isbn13:978-0262042819.
   "An argument that consciousness, more widespread than previously assumed, is
   the feeling of being alive, not a type of computation or a clever hack. ...
   Koch argues that programmable computers will not have consciousness. Even a
   perfect software model of the brain is not conscious. Its simulation is fake
   consciousness. Consciousness is not a special type of computation - it is
   not a clever hack. Consciousness is about being."
   [Also search for: Koch consciousness].

%A J. M. Shine
%A et al ...
%A R. A. Poldrack
%T Human cognition involves the dynamic integration of neural activity and
   neuromodulatory systems
%J Nature Neuroscience
%V 22
%P 289-296
%D 2019
%K jrnl, c2019, c201x, c20xx, zz1119, human, brain, expertise, skill,
   adaption, repetition, thalmus, cognition, neuroscience
%X "... we investigated the spatial, dynamic, & molecular signatures of
   system-wide neural activity across a range of cognitive tasks. We found that
   neuronal activity converged onto a low-dimensional manifold that facilitates
   the execution of diverse task states. Flow within this attractor space was
   associated with dissociable cognitive functions, unique patterns of
   network-level topology, & individual differences in fluid intelligence.
   The axes of the low-dimensional neurocognitive architecture aligned with
   regional differences in the density of neuromodulatory receptors, which in
   turn relate to distinct signatures of network controllability estimated from
   the structural connectome. ..."
   -- [<A HREF="https://doi.org/10.1038/s41593-018-0312-0">doi:10.1038/s41593-018-0312-0</A>]['19].
   (Also see the [<A HREF="https://www.abc.net.au/news/science/2019-11-01/brain-less-complicated/11658342">abc</A>][1/11/2019].)
   [Also search for: brain connectome].

%A M. S. A. Graziano
%T We are machines that claim to be conscious
%J J. of Consciousness Studies
%V 26
%N 10
%P 94-104
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0721, human, brain, mind, consciousness,
   awareness, attention schema theory, materialist
%X "The attention schema theory explains how a biological, info.processing
   machine can claim to have consciousness, & how, by introspection (by
   assessing its internal data), it cannot determine that it is a machine whose
   claims are based on computations. The theory directly addresses Chalmers'
   meta-problem of c., the problem of why we think we have a
   difficult-to-explain c. in the first place."
   -- [<A HREF="https://www.ingentaconnect.com/contentone/imp/jcs/2019/00000026/f0020009/art00008">www</A>]['21] --$.
   Also see AST@[<A HREF="https://en.wikipedia.org/wiki/Attention_schema_theory">wikip</A>]['21] and
   G@[<A HREF="https://grazianolab.princeton.edu/">pr'ncet'n</A>]['21].
   Also search for: consciousness mind]  and  [also search for: mind Graziano].

%A D. Robson
%T The Intelligence Trap - Why Smart People Make Dumb Mistakes
%M JUN
%D 2020
%K book, text, c2020, c202x, c20xx, zz1221, smart, clever, intelligence, IQ,
   human behaviour, psychology, thinking, expertise, functional stupidity,
   mistake, blunder, judgement
%X 1st ed 2020; hb us$44; uk us isbn:0393651428; uk us isbn13:978-0393651423.
   "... reveals the surprising ways that even the brightest minds & most
   talented organizations can go wrong - from some of Thomas Edison's worst
   ideas to failures at NASA, Nokia, & the FBI. And he offers practical advice
   to avoid mistakes based on the timeless lessons of Benjamin Franklin,
   Richard Feynman, & Daniel Kahneman."

%A S. M. Fleming
%T Know Thyself: The Science of Self-Awareness
%I BasicBooks
%P 304
%M APR
%D 2021
%K book, text, c2021, c202x, c20xx, zz0521, mind, self, consciousness,
   awareness, metacognition, thought, thinking
%X 1st ed 2021; hb us $20; uk us isbn:1541672844; uk us isbn13:978-1541672840
   "... Metacognition, or thinking about thinking, is the most important tool
   we have for understanding our own mind. ..."

%A J. A. Olson
%A ...
%A M. E. Webb
%T Naming unrelated words predicts creativity
%J PNAS
%V 118
%N 25
%P #e2022340118;
%M JUN
%D 2021
%K jrnl, PNAS, c2021, c202x, c20xx, zz0721, divergent association task, DAT,
   human, creative, creativity, imagination, test, naming unrelated words,
   UniMelb
%X "Several theories posit that creative people are able to generate more
   divergent ideas. If this is correct, simply naming unrelated words & then
   measuring the semantic dist. between them could serve as an objective measure
   of divergent thinking. ... we asked 8,914 participants to name 10 words that
   are as different from each other as possible. A computational alg. then est.
   the avg. semantic dist. between the words ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.2022340118">doi:10.1073/pnas.2022340118</A>]['21].
      ("... Scores peaked in young adulthood, & females showed slightly
      higher overall scores than males. ..." :-)
   (Also see the test @[<A HREF="https://www.datcreativity.com/">www</A>]['21].)

%A O. Gunturkun
%T The conscious crow
%J Learning & Behavior
%V 49
%P 3-4
%M FEB
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0422, animal, bird, crow, crows, behaviour,
   brain, neuron, consciousness
%X "Nieder, Wagener, & Rinnert (Science, 369(6511), 1626-1629, 2020) demo. that
   some neurons in a prefrontal-like brain area of carrion crows signal neither
   the physical stimulus nor the intended action but the upcoming choice. This
   pattern of results implies that neural computations for consciousness can be
   generated by nonmammalian brains in similar ways as in primates."
   -- [<A HREF="https://doi.org/10.3758/s13420-021-00466-5">doi:10.3758/s13420-021-00466-5</A>]['22],
      [<A HREF="https://www.bio.psy.ruhr-uni-bochum.de/papers/2021_G%C3%BCnt%C3%BCrk%C3%BCn_TheConsciousCrow.pdf">www</A>]['22].

%A J. C. Peterson
%A et al
%T Using large-scale experiments and machine learning to discover theories of
   human decision-making
%J Science
%V 372
%N 6547
%P 1209-1214
%M JUN
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0122, human thought, decision making, choice,
   behaviour
%X "... using large datasets to power machine-learning algs. that are
   constrained to produce interpretable psychological theories. Conducting the
   largest experiment on risky choice to date & analyzing the results using
   gradient-based optimization of differentiable decision theories implemented
   through [ANNs], we were able to recapitulate historical discoveries,
   establish that there is room to improve on existing theories, & discover a
   new, more accurate model of human decision-making in a form that preserves
   the insights from centuries of research."
   -- [<A HREF="https://doi.org/10.1126/science.abe2629">doi:10.1126/science.abe2629</A>]['22].
   [Also search for: human decision making].

%A A. Damasio
%T Feeling & Knowing: Making Minds Conscious
%I Pantheon
%P 256
%D 2021
%K book, text, c2021, c202x, c20xx, zz1121, mind, consciousness, feelings, AI,
   neuroscience
%X 1st ed 2021; hb us$17; uk us isbn:1524747556; uk us isbn13:978-1524747558.
   "... helps us understand why being conscious is not the same as sensing, why
   nervous systems are essential for the development of feelings, and why
   feeling opens the way to consciousness writ large.  ..."
   [Also search for: mind consciousness].

%A Z. Z. Bronfman
%A S. Ginsburg
%A E. Jablonka
%T When will robots be sentient?
%J J. of Artificial Intel. and Consciousness
%V 8
%N 2
%P 1-2
%D 2021
%K jrnl, c2021, c202x, c20xx, zz1121, AI, robot, computers, mind, conscious,
   consciousness, self aware, awareness, sentient
%X "... Taking an evolutionary approach, we previously suggested that the
   emergence of consciousness was entailed by the evolution of an open-ended
   domain-general form of learning, which we call unlimited associative learning
   (UAL). Here, we outline the UAL theory & discuss the constraints &
   affordances that seem nec. for constructing an AI m/c exhibiting UAL. We
   argue that a m/c that is capable of domain-general learning requires the
   dynamics of a UAL architecture & that a UAL arch. requires, in turn, that the
   m/c is highly sensitive to the environment & has an ultimate value (like
   self-persistence) that provides shared context to all its behaviors &
   learning outputs. ..."
   -- [<A HREF="https://doi.org/10.1142/S2705078521500168">doi:10.1142/S2705078521500168</A>]['21].
   [Also search for: mind consciousness].

%A A. Seth
%T Being You: A New Science of Consciousness
%I PenguinRandomHouse
%P 352
%M OCT
%D 2021
%K book, c2021, c202x, c20xx, zz0522, brain, consciousness, mind
%X 1st ed 2021; hb us$28; uk us isbn:0571337708; uk us isbn13:978-1524742874.
   "...  puts forward an exhilarating new theory about how we experience the
   world that should encourage us to view ourselves as less apart from & more
   a part of the rest of nature. ..."

%A C. Lacaux
%A et al ...
%A D. Oudiette
%T Sleep onset is a creative sweet spot
%J Sci. Adv.
%V 7
%N 50
%P ?-?
%M DEC
%D 2021
%K jrnl, c2021, c202x, c20xx, zz1221, human, brain, mind, creativity, creative,
   sleep, onset
%X "... we show that the brain activity common to the twilight zone between
   sleep & wakefulness (nonrapid eye movement sleep stage 1 or N1) ignites
   creative sparks. Participants (N=103) were exposed to math. problems without
   knowing that a hidden rule allowed solving them almost instantly. We found
   that spending at least 15s in N1 during a resting period tripled the chance
   to discover the hidden rule (83% v. 30% when participants remained awake), &
   this effect vanished if subjects reached deeper sleep. Our findings suggest
   that there is a creative sweet spot within the sleep-onset period, & hitting
   it requires individuals balancing falling asleep easily [v.] falling asleep
   too deeply."
   -- [<A HREF="https://doi.org/10.1126/sciadv.abj5866">doi:10.1126/sciadv.abj5866</A>]['21].
   [Also search for: human creativity].

%A S. Pinker
%T Rationality: What It Is, Why It Seems Scarce, Why It Matters
%I Viking
%P 432
%M SEP
%D 2021
%K book, text, c2021, c202x, c20xx, zz1221, thought, rational, rationality,
   irrationality, decision making, problem solving, human behaviour
%X 1st ed 2021; hb us$15; uk us isbn:0525561994; isbn13:978-0525561996.
   "... rejects the cynical cliche that humans are simply irrational-cavemen out
   of time[*] saddled with biases, fallacies, & illusions. After all, we
   discovered the laws of nature, lengthened & enriched our lives, & set out the
   benchmarks for rationality itself.  We actually think in ways that are
   sensible in the low-tech contexts in which we spend most of our lives, but
   fail to take advantage of[*] the powerful tools of reasoning we've discovered
   over the millennia: logic, critical thinking, probability, correlation &
   causation ..."
   ([*] don't they contradict?-)

%A G. Leuenberger
%T The substrate-prior of consciousness
%D 2021
%K essay, c2021, c202x, c20xx, zz0324, philosophy, brain, mind, consciousness
%X "... Given functionally equivalent minds, how does the expected quantity of
   their conscious experience differ across different substrates & how could we
   calculate this?  We argue that a realistic digital brain emulation would be
   orders of magnitude less conscious than a real biological brain. On the other
   hand, a mind running on neuromorphic hardware or a quantum computer could in
   principle be more conscious than than a biological brain."
   -- pdf@[<A HREF="https://philpapers.org/archive/LEUTSO-5.pdf">philpapers.org</A>]['24].

%A D. J. Chalmers
%T Reality+: Virtual Worlds and the Problems of Philosophy
%I WWNorton (us) & AllenLane (uk)
%P 544
%M JAN
%D 2022
%K book, text, c2022, c202x, c20xx, zz0222, virtual reality, meta, metaverse,
   world, TheMatrix, simulation, reality
%X 1st ed 2022; hb us$22; uk us isbn:0393635805; uk us isbn13:978-0393635805.
   "... I first argue that we can't know we're not in a simulation like the
   Matrix. This is a modern-day version of Rene Descartes's idea that we might
   be in the grip of an evil demon producing sensations of an external world.
   ... I argue that in principle we can lead meaningful lives inside
   metaverse-style virtual worlds. These worlds needn't be illusions,
   hallucinations, or fictions. ..."

%A J. Birch
%A et al ...
%A O. Zacks
%T How should we study animal consciousness scientifically?
%J J. of Consciousness Studies
%V 29
%N 3-4
%P 8-28
%M MAR
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0622, mind, conscious, consciousness, animals,
   intelligence, cognition, unlimited associative learning, UAL, Marta Halina
%X "A conscious being has a subjective point of view on the world & on its own
   body. This idea of a 'point of view' is easiest to grasp in the case of
   vision. ..."
   -- [<A HREF="https://doi.org/10.53765/20512201.29.3.008">doi:10.53765/20512201.29.3.008</A>]['22]
    in [<A HREF="https://www.ingentaconnect.com/content/imp/jcs/2022/00000029/f0020003">www</A>]['22].

%A P. Ball
%T The Book of Minds: How to Understand Ourselves and Other Beings, from
   Animals to AI to Aliens
%I UniChicagoPress
%M JUN
%D 2022
%K book, c2022, c202x, c20xx, zz0722, mind, brain, animal, alien, consciousness
%X 1st ed 2022; hb us$19; uk us isbn:022679587X; uk us isbn13:978-0226795874.
   "... explore what sorts of minds we might expect to find in the universe. In
   so doing, he offers for the first time a unified way of thinking about what
   minds are and what they can do ..."
   [Also search for: mind book].

%A N. Humphrey
%T Sentience: The Invention of Consciousness
%M MAR
%D 2023
%K book, text, c2023, c202x, c20xx, zz1122, consciousness, self, sentient, mind
%X 1st ed 2023; hb us$25; uk us isbn:0262047942; uk us isbn13:978-0262047944.
   "... Conscious sensations ground our sense of self. They are crucial to our
   idea of ourselves as psychic beings: present, existent, & mattering. But is
   it only humans who feel this way? Do other animals? Will future m/chs.? ..."
   [Also search for: mind book].

%A A. Clark
%T The Experience Machine. How Our Minds Predict and Shape Reality
%I PenguinBooks
%P 304
%M MAY
%D 2023
%K book, text, c2023, c202x, c20xx, zz0623, brain, mind, experience, prediction
%X 1st ed 2023; hb us$20, uk us isbn:1524748455; uk us isbn13:9780241394526.
   "... work on the predictive brain to explore its fascinating mechanics &
   implications. Among the most stunning of these is the realization that
   experience itself, because it is guided by prior expectation, is a kind of
   controlled hallucination. We don't passively take in the world around us;
   instead our mind is constantly making and refining predictions about what
   we expect to see. ..."
   [Also search for: mind book].

%A S. Winchester
%T Knowing What We Know. The Transmission of Knowledge: From Ancient Wisdom to
   Modern Magic
%I WilliamCollins
%P 400
%M MAY
%D 2023
%K book, text, c2023, c202x, c20xx, zz0723,  AI, GPT, knowledge, information,
   epistemology, wisdom, human, thought, mind, www, internet, HAL, encyclopedia,
   printing press, AI, chatBot, chatGPT
%X 1st ed 2023; hb us$30;  uk us isbn:0008484384; uk us isbn13:978-0008484385.
   "... With so much knowledge at our fingertips, what is there left for our
   brains to do? At a time when we seem to be stripping all value from the idea
   of knowing things - no need for math, no need for map-reading, no need for
   memorization - are we risking our ability to think? As we empty our minds,
   will we one day be incapable of thoughtfulness? ..."

%T An adversarial collaboration to critically evaluate theories of consciousness
%Q Cogitate Consortium
%J bioRxiv
%M JUN
%D 2023
%K TR, c2023, c202x, c20xx, zz0723, brain, mind, cognition, consciousness,
   integrated information, global neuronal workspace, GNWT, Melloni
%X "... we present an open science adversarial collaboration which directly
   juxtaposes Integrated Information Theory (IIT) & Global Neuronal Workspace
   Theory (GNWT) ... results confirm some predictions of IIT & GNWT, while
   substantially challenging both theories: for IIT, a lack of sustained
   synchronization within posterior cortex contradicts the claim that network
   connectivity specifies consciousness. GNWT is challenged by the general lack
   of ignition at stimulus offset & limited representation of certain conscious
   dimensions in prefrontal cortex. ..."
   -- [<A HREF="https://doi.org/10.1101/2023.06.23.546249">bioRxiv:10.1101/2023.06.23.546249</A>]['23].
   (See comment at [<A HREF="https://www.science.org/content/article/search-neural-basis-consciousness-yields-first-results">www</A>][6/2023], and
   news & views 17/1/24@[<A HREF="https://doi.org/10.1038/d41586-024-00107-7">doi:10.1038/d41586-024-00107-7</A>]['24].)
   [Also search for: consciousness].

%A P. Butlin
%A et al
%T Consciousness in artificial intelligence: Insights from the science of
   consciousness
%J arXiv
%P 120p.
%M AUG
%D 2023
%K TR, AI, c2023, c202x, c20xx, zz0823, conscious, sentience, sentient
%X "... We survey several prominent sci. theories of c., inc. recurrent
   processing theory, global workspace theory, higher-order theories, predictive
   processing, & attention schema theory. ... we derive 'indicator properties'
   of c., elucidated in computational terms that allow us to assess AI systems
   for these properties. We use these indicator properties to assess several
   recent AI systems, & we discuss how future systems might implement them. Our
   analysis suggests that no current AI systems are conscious, but also suggests
   that there are no obvious technical barriers to building AI systems which
   satisfy these indicators."
   -- [<A HREF="https://arxiv.org/abs/2308.08708">arxiv:2308.08708</A>]['23].
   (Also see comment@[<A HREF="https://doi.org/10.1126/science.adk4451">doi:10.1126/science.adk4451</A>]['23].)

%A S. Fleming
%A et al
%T The integrated information theory of consciousness as pseudoscience
%J PsyArXiv
%M SEP
%D 2023
%K TR, c2023, c202x, c20xx, zz0923, mind, consciousness, controversial,
   integrated information theory
%X "The media, inc. news articles in both Nature & Science, have recently
   celebrated the Integrated Information Theory (IIT) as a 'leading' &
   empirically tested theory of consciousness. We are writing as researchers
   with some relevant expertise to express our concerns. ..." 
   -- [<A HREF="https://doi.org/10.31234/osf.io/zsr78">doi:10.31234/osf.io/zsr78</A>]['23],
      [<A HREF="https://psyarxiv.com/zsr78/">www</A>]['23].
   [Also search for: consciousness integrated information theory].

%A D. C. Dennett
%T I've Been Thinking
%I WWNorton / AllenLane
%P 434
%M OCT
%D 2023
%K book, memoir, c2023, c202x, c20xx, zz1123, mind, consciousness, free will,
   thought, AI
%X 1st ed 2023; hb us$31; uk us isbn:0393868052; uk us isbn13:978-0393868050.
   "... What is consciousness and how did it come about? What distinguishes
   human minds from the minds of animals? ..."

D. K. F. Pang
%T The staggering complexity of the human brain
%J Psych. Tody
%M DEP
%D 2023
%K news, views, c2023, c202x, c20xx, zz0324, human, brain, neurons, synapses,
   complexity, size, estimate
%X "... The brain contains around 86 billion neurons, 85 billion other cells,
   & over 100 trillion connections. ... The total length of this complex fibre
   n/w is est. to be ~500,000km or over 310,000 miles long (Science Daily,
   2017). ..."
   [<A HREF="https://www.psychologytoday.com/us/blog/consciousness-and-beyond/202309/the-staggering-complexity-of-the-human-brain">www</A>]['24].
   [Also search for: brain complexity].

%A J. E. LeDoux
%T The Four Realms of Existence: A New Theory of Being Human
%M JAN
%D 2024
%K book, memoir, c2023, c202x, c20xx, zz1123, mind, consciousness, thought,
   philosophy, AI
%X "... argues that we have hit an epistemological wall-that ideas like the self
   are increasingly barriers to discovery and understanding. He offers a new
   framework of who we are, theorizing four realms of existence - bodily,
   neural, cognitive, and conscious. ..."
   1st ed 2024; hb us$42; uk us isbn:0674261259; uk us isbn13:978-0674261259.

%A K. J. Mitchell
%T Free Agents: How Evolution Gave Us Free Will
%I Princeton Univ. Press
%P 352
%M JAN
%D 2024
%K book, text, c2023, c202x, c20xx, zz1123, mind, consciousness, thought, AI
%X 1st ed 2023; hb us$38; uk us isbn:0691226237; uk usisbn13:978-0691226231.
   "... the emergence of nervous systems provided a means to learn about the
   world, granting sentient animals the capacity to model, predict, and
   simulate. Mitchell reveals how these faculties reached their peak in humans
   with our abilities to imagine and to be introspective ..."

%A C. Ranganath
%T Why We Remember
%I Faber(uk), Doubleday(usa)
%P 304
%M FEB
%D 2024
%K book, text, c2024, c202x, c20xx, zz0524, memory, memories, forget,
   forgetting, human, brain, psychology, neuroscience
%X 1st ed 2024; uk us isbn:038554863X; uk us isbn13:978-0385548632.
   Also see [<A HREF="https://www.bbc.com/future/article/20240514-why-forgetting-is-beneficial">bbc</A>][17/5/2024].


%A C. S. Wallace
%A D. M. Boulton
%T An information measure for classification
%J COMPJ
%V 11
%N 2
%M AUG
%D 1968
%P 185-194
%K WB68, zzMML, CSW, CSWallace, jrnl, COMPJ, MML, MDL, II, c1968, c196x, c19xx,
   Monash, COMPJ, SNOB, classification, class, taxonomy, cluster,
   clustering, EM algorithm, information theory, stats, IT, coding, encoding,
   minimum message length, AIC, BIC, inductive inference, minimum description
   length, probability distribution, origin, prior, multistate, multi-state,
   categorical, multinomial, complexity, binomial, normal, Gaussian, discrete,
   stochastic, algorithmic complexity, Bayes, Bayesian, Occam, Ockham, Occam's,
   razor, Rissanen, statistics, search, mixture modelling, split, merge, kill,
   EM algorithm, learning, SMEM, expectation, maximization, maximisation, model,
   citerion, seal skull, seals, skulls, Chaitin, Solomonoff, Kolmogorov,
   Figueiredo, Jain
%X "This paper derives a measure of the goodness of a classification based on
   information theory.  A classification is regarded as a method of economical
   statistical encoding of the available attribute information.
      The measure may be used to compare the relative goodness of
   classifications produced by different methods or as the basis of a
   classification procedure.
      A classification program, 'SNOB', has been written for the University
   of Sydney KDF-9 computer, and first tests show good agreement with
   conventional taxonomy.
   (An example classifies species of seal based on measurements of skulls.)"
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/11.2.185">doi:10.1093/comjnl/11.2.185</A>]['14].
   Appendix has derivation of optimal encoding for multistate data.
   [Also search for: MML].  See [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>],
   and [<A HREF="/~lloyd/tildeMML/Structured/1968-WB-CJ/">paper</A>].

%A D. M. Boulton
%A C. S. Wallace
%T The information content of a multistate distribution
%J J. Theor. Biol.
%V 23
%P 269-278
%D 1969
%K BW69, zzMML, CSW, CSWallace, c1969, c196x, c19xx, Minimum Message Length,
   JTB, jrnl, Encoding, MML, information, theory, IT, SC, NML, content, entropy,
   prior, adaptive code, MDL, compress, compression, BIC, string, sequence,
   multistate, multi state, multi-state, multinomial, binomial, coding,
   description, inductive inference, II, Monash, jrnl, Bayes, Bayesian, Occam,
   Occam's, Ockham razor, categorical
%X Also see Wallace & Boulton COMPJ (Computer J.) 1968.
   [<A HREF="http://dx.doi.org/10.1016/0022-5193(69)90041-1">doi:10.1016/0022-5193(69)90041-1</A>]['06],
   [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].  [Also search for: MML].

%A D. M. Boulton
%A C. S. Wallace
%T An information measure for hierarchic classification
%J COMPJ
%P 254-261
%V 16
%N 3
%M AUG
%D 1973
%K BW73, CSW, Monash, jrnl, hierarchic, tree, family, class, classification,
   Minimum Message Length Encoding, MML, class, description, code, coding, MDL,
   encoding, mixture model, inductive inference, II, Computer Journal, SNOB,
   information, theory, IT, Bayes, Bayesian, Occam Occam's Ockham razor,
   c1973, c197x, c19xx, CSWallace, algorithm, extimation
%X "The information measure has been developed as a criterion of merit for
   intrinsic classifications. The information measure for non-hierarchic
   classifications has been described previously and a program developed which
   searched for that classification optimising the information measure.
   However, hierarchic classifications are often of practical importance and
   this paper develops the information measure for hierarchic classifications.
   Two algorithms are outlined for generating hierarchic classifications which
   minimise the information measure. One of these has been programmed and first
   tests show a good agreement with conventional taxonomy."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/16.3.254">doi:10.1093/comjnl/16.3.254</A>]['05].
   Also Wallace and Boulton COMPJ (Computer J.) 1968,
   and [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>],
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_16/Issue_03/160254.sgm.abs.html">paper</A>][12/'03].

%A H. Akaike
%T Information theory and an extension of the maximum likelihood principle
%J Proc. of the 2nd Int. Symp. on Information Theory
%E Petrov B. N. and Csaki F.
%P 267-281
%D 1973
%K conf, Akaike Information Criterion, criteria, AIC, model, modelling,
   parameters, complexity, overfitting, c1973, c197x, c19xx
%X via j o s h.   [Also search for: AIC].

%A D. M. Boulton
%T The Information Measure Criterion for Intrinsic Classification
%I Dept. of Computer Science, Monash University
%D 1975
%K PhD thesis, minimum message length, MML, description, MDL, BIC Bayesian,
   information theory, criterion, criteria, inductive inference, II, AI, AIC,
   unsupervised classification, clustering, cluster, mixture modelling, model,
   algorithm, Snob, c1975, c197x, c19xx
%X <!-- sup'r C.S.Wallace, CSW;  Gop@l has a copy --> ref is from  Comp. Sci. Mon@sh tr 91/151.
   [Also search for: Boulton MML].

%A J. Patrick
%A C. S. Wallace
%T Stone circle geometries: An information theory approach
%P 231-264
%B Archaeoastronomy in the Old World
%E D. Heggie
%I CUP
%D 1982
%O Int. Symp. on Archaeoastronomy, Queen's College, Oxford, Sept. 4-9, 1981.
%K PW82, CSW, CSWallace, c1982, c198x, c19xx, Monash, inductive inference,
   II, IT, standing, megalithic, yard, stonehenge, stone circle, henge, stones,
   circles, minimum message length encoding, MML, minimum description length,
   standing, Thom, conf, chapter, MDL, Occam, Occam's, Ockham, razor, occams
%X "This article discusses the techniques of A.Thom in deriving geometric
   designs to fit stone circles & from this background argues for an alternative
   defn of an hypothesis in scientific research. The defn that is advocated
   herein is a union of Solomonoff's application of Information Theory to
   inductive inference, Wallace's Information measures & Halstead's software
   science measures. This approach is applied to the comparison of Thom's
   hypothesis against the authors' hypothesis that stone circles are meant to be
   roughly circular & locally smooth to the eye. The authors' hypothesis is
   modelled by a fourier series wrapped around a circle. The results from 65
   Irish sites show that the authors' hypothesis is favoured at odds of better
   than 780:1 compared to Thom's hypothesis."
   -- [<A HREF="http://dx.doi.org/10.1017/CBO9780511898310.016">doi:10.1017/CBO9780511898310.016</A>][11/'11].
   (In: hb us$52, uk us isbn:0521125308, uk us isbn13:978-0521125307.)
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)
   [Also search for: megalithic stone circle].

%A C. S. Wallace
%T On the identification of outliers in a simple model
%I Dept. Computer Science, Monash University
%D 1984 ?
%K CSWallace, CSW, c1984, c198x, c19xx, description of outliers, outlier, stats,
   statistics, minimum message length, MML, MDL, noise, noisy, data, discordancy
%X "We suppose that we are given a set of 'N' observations {yi, i=1,...,N} which
   are thought to arise independently from some process of known form & unknown
   (vector) parameter theta. However, we may have reason to suspect that some
   small fraction of the N obs. are in some sense contaminated or erroneous,
   i.e., that they arise from a process different from the main process.
   Any such obs. is called an "outlier". We will then be interested in methods
   for identifying or at least estimating the # of the outliers, & for
   estimating theta in a way which is minimally upset by the outliers. . . ."
   -- [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/Outlier/">More (click)</A>].
   (Written in the 1980s.)

%A M. P. Georgeff
%A C. S. Wallace
%T A general selection criterion for inductive inference
%J European Conf. on Artificial Intelligence
%P 473-482
%W Pisa
%M SEP
%D 1984
%I Elsevier Sci. Publ.
%C New York
%O TR 32, CS Monash March 1983
%K GW84, zzMML, CSW, conf, ECCAI, ECCAI84, information theory, IT, II, Bayesian,
   language, minimum message length, MML, encoding, description, Occam, Ockham,
   curve, Occam's razor, MDL, simplicity, hypothesis, line, lines, fit, fitting,
   infer, inferring, string, strings, probabilistic finite state automaton,
   automata, PFSA, FSA, Hidden Markov Models, HMM, TR32, TR 32,
   c1984, c198x, c19xx, complexity, Kolmogorov, Solomonoff, AIC, CSWallace
%X The nature of theories, structural descriptions,
   inference of line segments,
   There are more examples, including inference of probabilistic
   finite state automata (PFSA) for languages in the technical report.
   -- [<A HREF="http://www.allisons.org/ll/MML/Structured/TR32/">TR 32</A>],
   or [<A HREF="/~lloyd/tildeMML/Structured/TR32/">TR 32</A>].

%A C. S. Wallace
%A P. R. Freeman
%T Estimation and inference by compact coding
%J J. of the Royal Statistical Soc. series B
%V 49
%N 3
%D 1987
%P 240-265
%K WF87, zzMML, CSW, CSWallace, Monash, jrnl, JRSS, RSS, JRSSB, MML87, stats,
   strict minimum message length encoding, MML, SMML, inductive inference, II,
   information theory, IT, minimum description length, MDL, Jorma Rissanen,
   SNOB, mixture model, modelling, classification, class, classification,
   cluster, clustering, probability distribution, normal, stochastic, prior,
   Bayes, Bayesian, Occam, Occam's, Occams, Ockham, razor, algorithm,
   estimation, algorithmic complexity, AC, AIC, BIC, Fisher information,
   Kolmogorov, c1987, c198x, c19xx
%X "The systematic variation within a set of data, as represented by a usual
   stat. model, may be used to encode the data in a more compact form than would
   be possible if they were considered to be purely random. The encoded form has
   two parts. The 1st states the inferred estimates of the unknown parameters
   in the model, the 2nd states the data using an optimal code based on the data
   prob. distn implied by those param. estimates. Choosing the model & the
   estimates that give the most compact coding leads to an interesting general
   inference procedure. In its strict form it has great generality & several
   nice properties but is computationally infeasible. An approx. form is
   developed and its relation to other methods is explored."
   -- There was a special session of the Royal Stat. Soc. and
   Vol.49 No.3 pp.223-265 includes  Rissanen 's paper, W + F, and discussion.
   -- [<A HREF="http://www.allisons.org/ll/MML/Structured/1987-WF-JRSS.html">paper</A>],
      [<A HREF="http://www.allisons.org/ll/MML/">MML</A>],
   or [<A HREF="/~lloyd/tildeMML/Structured/1987-WF-JRSS.html">paper</A>],
   2985992@[<A HREF="http://www.jstor.org/stable/2985992">Jstor</A>]['14].

%A J. D. Patrick
%A P. R. Freeman
%T A cluster analysis of astronomical orientations
%B Records in Stone
%E C. L. N. Ruggles
%I CUP
%P 252-261
%D 1988
%K megalithic, pre-history, prehistory, minimum message length, description,
   MML, c1988, c198x, c19xx, MDL, II, AI, clustering, CUP, c1988, c198x, c19xx,
   site, sites, circle, circles, stones, astronomy, unsupervised classification,
   Thom, Ruggles, skyscape, paleoastronomy, archaeoastronomy
%X "An information-theoretic clustering method has been applied to Ruggles'
   dataset of 276 megalithic alignments in western Scotland. While there is
   strong evidence that the data are clustered rather than forming a single
   homogeneous set, there are only weak indications that the clustering is
   related to any kind of astronomical intention. Some relations between
   direction of indication and geographical area, horizon distance and whether
   the indication is one-site or inter-site have also been noted."
   (Ref from Comp Sci Mon@sh tr 91/151.)
   In: pp.537; stg33; uk us isbn:0521531306; uk us isbn13:978-0521531306.
   -- [<A HREF="https://doi.org/10.1017/S0003598X00075839">doi:10.1017/S0003598X00075839</A>]['24].
   (Was www.cambridge.org/uk/catalogue/catalogue.asp?isbn=0521531306 ['05].)
   [Also search for: megalithic MML].

%A C. S. Wallace
%T Classification by minimum-message-length encoding
%B Advances in Computing and Information - ICCI '90
%I SpringerVerlag
%S LNCS
%V 468
%P 72-81
%M MAY
%D 1990
%K Wal90, zzMML, CSW, Monash, conf, ICCI 90, ICCI90, inductive inference, II,
   SNOB, class, classify, classes, classification, cluster, clustering, mixture,
   model, modelling, c1990, c199x, c19xx, minimum message length encoding, MML,
   description, MDL, dld, bits back, mmld, Bayes, Bayesian, Occam, Ockham razor,
   Snob2, fractional, soft assignment, bit borrowing, Hinton, Camp, CSWallace
%X 'Although classification is perhaps the oldest practical application of MML
   inference, the early algorithm was subject to weakly inconsistent estimation.
   The same problem is inherent in any MML inference which infers many discrete
   "nuisance" parameters. A solution has been found using a novel coding trick,
   which could be useful in many inductive inferences.'
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-53504-7_63">doi:10.1007/3-540-53504-7_63</A>]['11]; uk us isbn:3540535047.
   Note, sec.3 "partial assignment," p.75, includes a discussion of
      partial- / fractional- / soft-assignment of a datum to a cluster (class).
   And on p.81,
      "... a more detailed descn of the program is given by ...
      Wallace, 'An improved program for classification',
      Monash U., Comp. Sci. TR 47 (1984)."
         {It actually says by "Wallace & Patrick" but TR47 (1984) is
         actually by Wallace alone; I have a copy -- L.A. 16/7/'14.}
   [Also search for: Wallace 1986 ACSC9], and
   see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].

%A J. J. Oliver
%A C. S. Wallace
%T Inferring decision graphs
%J IJCAI-91, workshop 8
%P ???-???
%M JAN
%D 1991
%O TR 92/170, Dept Computer Science, Monash U.
%K OW91, CSW, IJCAI, IJCAI91, MML, minimum message length encoding,
   classification, inductive inference, II, machine learning,
   disjunctive decision tree DTree, DGraph, graph graphs, description, DAG,
   Monash, conf, MDL, c1991, c199x, c19xx, Bayes, Bayesian,
   Occam Occam's Ockham razor, CSWallace, TR 170, TR170
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/DGraph/">MML</A>].)
   [Also search for: Dgraph]  and  [also search for: Dtree].

%A T. M. Cover
%A J. A. Thomas
%T Elements of Information Theory
%I Wiley & Sons, N.Y.
%P 542
%D 1991
%K book, text, entropy, relative entropy, KL-distance, mutual information,
   channel capacity, probability, stats, statistics, c1991, c199x, c19xx, L4Ref
%X us$94; isbn:0471062596.
   [<A HREF="http://yreka.stanford.edu/~cover/">T.C.</A>][8/'04],
   [<A HREF="http://www-isl.stanford.edu/~jat/eit2/">eit2</A>][8/'04].

%A C. S. Wallace
%A J. D. Patrick
%T Coding decision trees
%J Machine Learning
%V 11
%P 7-22
%D 1993
%K WP93, CSW, CSWallace, c1993, c199x, c19xx, Monash, DTree, decision tree,
   trees, Quinlan, Rivest, classification, minimum message length encoding,
   MML, description, classification tree, CTree, MDL, inductive inference, II,
   jrnl, TR 91 153 TR91/153 TR153, information theory, Bayes, Bayesian, Occam,
   Occam's, Ockham, razor, code
%O TR 91/153, Comp. Sci., Monash U.
%X "Quinlan & Rivest have suggested a [D]-tree inference method using the
   [MDL] idea. We show that there is an error in their derivation of message
   lengths, which fortunately has no effect on the final inference. We further
   suggest 2 improvements to their coding techniques, one removing an
   inefficiency in the description of non-binary trees, & one improving the
   coding of leaves. We argue that these improvements are superior to similarly
   motivated proposals in the original paper.
   Empirical tests confirm the good results reported by Quinlan & Rivest, &
   show our coding proposals to lead to useful improvements in the performance
   of the method."
   -- [<A HREF="http://dx.doi.org/10.1023/A:1022646101185">doi:10.1023/A:1022646101185</A>][8/'04].
   [Also search for: decision graph]  with J. O l i v e r,  and
   see [<A HREF="http://www.allisons.org/ll/MML/Structured/DTree/">MML</A>].
   (Also see, sec.2.1.14, sec.2.1.15 & sec.2.1.16 of [CSWallace book], 2005,
   on codes for integers.)

%A C. S. Wallace
%A P. R. Freeman
%T Single-factor analysis by minimum message length estimation
%J J. of the Royal Statistical Soc. series B
%V 54
%N 1
%P 195-209
%D 1992
%K WF92, zzMML, CSW, CSWallace, jrnl, JRSS, RSS, JRSSB, single factor analysis,
   FactorAnalaysis, mixture model, classification, FA, MML,
   minimum description length, encoding, inductive inference, II, multivariate,
   estimate, stats, statistics, MDL, nuisance, hidden, factors, load, loadings,
   Bayes, Bayesian, Occam, Occam's, Monash, SNOB, Ockham razor,
   dimension reduction, c1992, c199x, c19xx
%X "The minimum message length (MML) technique is applied to the problem of
   estimating the parameters of a multivariate Gaussian model in which the
   correlation structure is modelled by a single common factor. Implicit
   estimator equations are derived and compared with those obtained from a
   maximum likelihood (ML) analysis. Unlike ML, the MML estimators remain
   consistent when used to estimate both the factor loadings and the factor
   scores. Tests on simulated data show the MML estimates to be on average more
   accurate than the ML estimates when the former exist. If the data show
   little evidence for a factor, the MML estimate collapses. It is shown that
   the condition for the existence of an MML estimate is essentially that the
   log-likelihood ratio in favour of the factor model exceeds the value
   expected under the null (no-factor) hypotheses."
   Also see [<A HREF="http://www.allisons.org/ll/MML/Notes/SNOB-factor/">factor-snob</A>],
      [<A HREF="/~lloyd/tildeMML/Structured/1992-WF-JRSS.html">paper</A>],
      2345956@[<A HREF="http://www.jstor.org/stable/2345956">Jstor</A>]['14].
   [Also search for: MML multiple factor analysis].

%A C. S. Wallace
%T Multiple factor analysis by MML estimation
%R 95/218
%I Dept. Comp. Sci., Monash U.
%M MAR
%D 1995
%K Wal95, zzMML, CSW, CSWallace, TR 218, TR218, minimum message length, MML,
   FA, FactorAnalysis, description, multiple factor analysis, factors, MDL,
   inductive inference, II, statistics, stats, factors, dimension,
   dimensionality reduction, Monash, c1995, c199x, c19xx
%X Also see (i) the single factor paper:  JRSS(B) 54(1), pp.195-209, '92.
   and (ii) Proc. Bien' Stat' Conf',  Brisbane, '98.
   Ordering TR 95/218: Faculty of Info. Tech. (Clayton), Monash Uni., .au 3800.
   Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/Multi-Factor/">multi-F</A>],
   and [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/FactorSnob/">factor Snob</A>].

%A C. S. Wallace
%T False oracles and SMML estimators
%R TR 128
%I Dept. Computer Science, Monash University
%D 1989
%K Wal89, zzMML, CSW, CSWallace, TR 128, TR128, oracle, c1989, c198x, c19xx,
   strict minimum message length, encoding, MML, inductive inference, II, BIC,
   description, information theory, IT, foundations, AIC, AICc, MDL, oracle,
   Monash, csse, point, estimator, estimation, estimate, Bayesian, theoretical,
   Kolmogorov complexity, SMML, foundations, statistics, stats, methodology
%X "An attempt is made to formalize the notion of the empirical comparison
   of two estimators for the same problem. By "empirical", we mean that the
   comparison be based on the estimates produced by the estimator for some set
   of data, not on how they produce them. Defining the `oracle' as an estimator
   which gives the true values of the unknown parameters, we define `false
   oracle' as an estimator which no fair empirical criterion can be expected to
   reject in favour of the oracle, and argue that false oracles exist, but are
   stochastic functions of the data. Further, we show that Strict Minimum
   Message Length estimators closely imitate false oracles despite being
   deterministic functions. Some practical consequences are exhibited."
   (Ordering TR89/128: Faculty of Info. Tech. (Clayton), Monash Uni., .au 3800.)
   [Also search for: ISIS96] and see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/False-Oracles/">False-Oracles</A>].

%A D. P. McKenzie
%A P. D. McGorry
%A C. S. Wallace
%T Constructing minimal diagnostic decision trees
%J Australian Soc. for Psychiatric Res. Conf., Adelaide.
%D 1992
%K conf, CSWallace, Monash, MML, MDL, DTree, tree, c1992, c199x, c19xx
%X Poster. [Also search for: McKenzie c1993]
   See [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A D. P. McKenzie
%A L. H. Low
%T The construction of computerized classification systems using
   machine learning algorithms: An overview
%J Computers in Human Behaviour
%V 8
%N 2/3
%P 155-167
%D 1992
%K discriminant function, decision, classification, tree, trees, ID3,
   c1992, c199x, c19xx

%A D. P. McKenzie
%A P. D. McGorry
%A C. S. Wallace
%A L. H. Low
%A D. L. Copolov
%A B. S. Singh
%T Constructing a minimal length diagnostic decision tree
%J Methods in Information in Medicine.
%V 32
%N 2
%P 161-166
%M APR
%D 1993
%K CSW, CSWallace, Monash, supervised classification jrnl, c1993, c199x, c19xx,
   DTree, trees, minimum message length encoding, MML, inductive inference, II,
   Bayes, Bayesian, calssification, medical, diagnose, description, MDL
%X "CTs & discriminant function analysis ... to ascertain whether a small # of
   diagnostic decision rules could be extracted from a large inventory of items.
   Several models, involving up to 17 symptoms, that led to a broad psychiatric
   diagnosis were then tested on a small validation sample of 53 patients. All
   methods, with the exception of CART used without any pruning, generated
   identical trees involving four items. Almost 90% of the validation sample
   was able to be correctly classified by all methods although poor
   classification performance was noted in the case of 1 particular diagnosis,
   Schizoaffective Psychosis. In contrast, stepwise LDA originally selected 17
   items, although 3 out of the first 4 items selected were identical to those
   chosen by the tree-building methods. Although more research is required,
   there are indications that the latter methods may be usefully employed in
   constructing parsimonious decision trees."
   Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A C. S. Wallace
%A D. L. Dowe
%T Estimation of the von Mises concentration parameter using minimum message
   length
%J Proc. 12th. Aust. Stat. Soc. Conf.
%P ??-??
%D 1994
%K CSW, DLD, Monash, conf, vonMises, minimum message length encoding, MML,
   Bayes, Bayesian, SNOB, class, classify, classification, cluster, circle,
   circular, probability distribution, angle, direction, description,
   CSWallace, TR193, TR 193, zz0795, c1994, c199x, c19xx
%O W & D,
     'MML estimation of the von Mises concentration parameter,' TR 93/193,
     Dept. Comp. Sci., Monash Uni., Clayton 3168, Australia, pp.20,  1993;
   also
   D, O, B & W,
     'Bayesian estimation of the Von Mises concentration parameter',
     Proc. 15th Int. Wkshop on Max Ent. and B. Methods, Santa Fe, '95
%X (Was [<A HREF="ftp://ftp.csse.monash.edu.au/publications/1993/TR193.ps.gz">TR193</A>]['94].)
   [Also search for: vonMises direction], and
   [also search for: probability distribution circle], and
   also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A C. S. Wallace
%A D. L. Dowe
%T Intrinsic classification by MML - the Snob program
%J Proc. 7th Australian Joint Conf. on Artificial Intelligence
%W Armidale, NSW, Australia
%I World Scientific
%P 37-44
%M NOV
%D 1994
%K AJCAI, AJCAI7, ACAI7, AI, CSW, CSWallace, DLD, monash, conf, class,
   clustering, cluster, inductive inference, SNOB, c1994, c199x, c19xx,
   minimum message length MML, description, encoding, MDL, von Mises, vonMises
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A C. S. Wallace
%T Multiple factor analysis by MML estimation
%J Proc. of the 14th Biennial Statistical Conf.
%W Brisbane
%P 144
%M JUL
%D 1998
%K Wal98, zzMML, CSW, CSWallace, minimum message length, MML, description,
   c1998, c199x, c19xx, factors, MDL, MFA, multiple factor, multivariate,
   Gaussian, normal, AIC, maximum likelihood, conf, common, score, scores,
   FactorAnalysis, dimension, dimensionality reduction,
   ratio, test, tests, stats, statistics, FA
%X "... The [MML] estimator has been extensively tested and compared to the
   maximum likelihood and AIC estimators.  The MML estimator is found to be
   substantially more accurate, to provide consistent estimates of the factor
   scores and to recover the number of common factors more reliably than a
   likelihood ratio test among maximum likelihood models."
   Also see (i) the single-factor paper JRSS 1992, and (ii) TR 95/218,
   and [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/Multi-Factor/">MML-factors</A>].

-------------------------------------------------------------------------------

%A L. A. Levin
%T Laws of information conservation (nongrowth) and aspects of the
   foundation of probability theory
%J Probl. Peredachi Inf.  (Problems Inform. Transmission)
%V 10
%N 3
%P 30-35
%D 1974
%K jrnl, c1974, c197x, c19xx, information theory, probability, stats, MML, MDL,
   AIT, algorithmic, coding theorem, Kolmogorov, complexity
%X "A new alt. defn is given for the algorithmic quantity of info. defined by
   Kolmogorov. The nongrowth of this quantity is proved for random & certain
   other processes, The established properties are used to investigate problems
   related to the approach of
      [A.N.Kolmogorov, Probl.Peredachi Inf., 1965, vol.1, no.1, pp.3-7],
      [P.Martin-Lof, Inf.Control, 1966, vol.9, no.6, pp.602-619]
   with bearing on the foundation of probability theory."
   -- ppi1039@mathnet.[<A HREF="http://mi.mathnet.ru/ppi1039">.ru</A>]['14].

%A J. Rissanen
%T Parameter estimation by shortest description of data
%J Proc JACE Conf RSME
%P 593-?
%D 1976
%K conf, minimum description length, MDL, inductive inference, II,
   c1976, c197x, c19xx
%X via GF.   See [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].
   [Also search for: MML  MDL  inductive inference II].

%A J. Rissanen
%T Modeling by shortest data description
%J Automatica
%V 14
%N 5
%P 465-471
%D 1978
%K shortest, minimum description length, modelling, encoding, MDL, MML,
   model, modelling, inductive inference, II, c1978, c197x, c19xx
%X "The # of digits it takes to write down an observed seq. x1,...,xN of a
   time series depends on the model with its params. that one assumes to have
   gen. the obs. data. Accordingly, by finding the model which minimizes the
   desc.len. one obtains ests. of both the integer-valued structure params. &
   the real-valued system params."
   Quote: "Following a suggestion by Boul ton & Wall ace (private corr.)" p.470.
   -- [<A HREF="http://dx.doi.org/10.1016/0005-1098(78)90005-5">doi:10.1016/0005-1098(78)90005-5</A>]['12].
   [Also search for:  MML  inductive inference II], and
   see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A J. Rissanen
%T Stochastic complexity
%J J. of the Royal Statistical Soc. series B
%V 49
%N 3
%D 1987
%P 223-239 & 252-265
%K c1987, c198x, c19xx JRSS, jrnl, RSS, JRSSB, MDL, minimum description length,
   encoding, coding, MML, inductive inference II, Occam, Occam's, Ockham razor,
   AI
%X (W a l l a c e  and  F r e e m a n 's paper and comparative discussion
   of MDL and MML follows in the same issue JRSS(B) 49(3) pp240-265 1987.
       Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].
       [Also search for:  MML  inductive inference II].)
   "It is argued that all the useful information in observed data that can be
   extracted with a selected class of modeled distributions, will be obtained
   if we calculate the stochastic complexity, defined to be the shortest
   description length of the data. The same quantity also determines the
   greatest lower bound for prediction errors when the data are sequentially
   predicted. An abstract definition of stochastic complexity is given along
   with 2 fundamental thms which justify the notion. Further, 3 explicit model
   selection criteria to approx. the stochastic complexity are described & the
   assoc. optimal models are interpreted to define asymptotically sufficient
   statistics for the data."
   -- 2985991@[<A HREF="http://www.jstor.org/stable/2985991">Jstor</A>]['14],
   or [<A HREF="http://links.jstor.org/sici?sici=0035-9246%281987%2949%3A3%3C223%3ASC%3E2.0.CO%3B2-U">Jstor</A>]['06].

%A J. Rissanen
%T Stochastic Complexity in Statistical Inquiry
%I World Scientific Publ. Co.
%D 1989
%K MML, MDL, minimum message, description, length encoding,
   inductive inference, II, statistics, Occam, Occam's, Ockham razor,
   c1989, c198x, c19xx
%X Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A G. J. Chaitin
%T Information-Theoretic Incompleteness
%I World Scientific
%D 1992
%K text, book, information theory, theoretic, IT, c1992, c199x, c19xx
%X collection of more popular articles.

%A E. Papp
%A D. L. Dowe
%A S. J. D. Cox
%T Spectral classification of radiometric data using an information theory
   approach
%J Proc. Advanced Remote Sensing Conf.
%W Sydney
%M JUL
%D 1993
%P 223-232
%K DLD, minimum message length encoding, MML,
   inductive inference II, Earth Sciences, image processing, IP, PARSC,
   Monash, conf, description, MDL
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A D. L. Dowe
%A N. Krusel
%T A decision tree model of bushfire activity
%J Proc. 6th Australian Joint Conf. on A.I.
%E C. Rowles
%E et al
%M NOV
%D 1993
%P 287-292
%K DLD, minimum message length encoding, MML, Monash, description, MDL,
   DTree, conf, inductive inference II,  bush fire,
   AAI AAI6 AAI93 AJCAI AJCAI6 AJCAI93
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A N. Krusel
%A D. L. Dowe
%T Predicting bushfire activity in the mallee region of north west Victoria
   using a decision tree model
%J Proc. Inst. Australian Geographers (IAG) Conf.
%P ?-?
%M SEP
%D 1993
%K DLD, Monash, conf, inductive inference, II, MML, MDL, DTree
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A D. L. Dowe
%A N. Krusel
%T Decision tree models of bushfire activity
%J AI Applications
%V 8
%N 3
%P 71-72
%D 1994
%K DLD, MML, MDL, Monash, jrnl, DTree, inductive inference, II, bush fire
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A A. R. Barron
%A T. M. Cover
%T Minimum complexity density estimation
%J IEEE Trans. on Info. Theory
%V 37
%N 4
%P 1034-1054
%M JUL
%D 1991
%K Minimum Message Length encoding, MML, description, MDL,
   information theory, IT, content, inductive inference II, review, survey,
   Occam, Occam's, Ockham, razor, jrnl, TIT, c1991, c199x, c19xx
%X Theorem 1: The minimum complexity criterion will find the true
      distribution if it is on the `list of distributions' considered for
      all sufficient large sample sizes and with probability one.
   Theorem 2: If the true distribution is not on the list, then
      consistency will hold, provided the true density is approximated by a
      sequence of densities on the list in the relative entropy sense.
   The index of resolvability is introduced, which bounds the rate of
   convergence of minimum complexity density estimators.
   This paper points out that AIC is not strongly consistent in finite
   dimensional cases!
   --  [<A HREF="http://dx.doi.org/10.1109/18.86996">doi:10.1109/18.86996</A>]['09],
   pdf@[<A HREF="http://www.stanford.edu/~cover/papers/barron_cover_91.pdf">stanf</A>]['09].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A M. Li
%T Minimum description length based 2D shape description
%J IEEE 4th Int. Conf. on Computer Vision.
%W Berlin
%D 1992
%P 512-517
%K minimum message length encoding, MML, description,  MDL,
   2-D, curve, line, ellipse, IP image processing, inductive inference, II
%X 17 refs.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A R. A. Baxter
%A D. L. Dowe
%T Model selection in linear regression using the MML criterion
%J Proc. 4th IEEE Data Compression Conf.
%W Snowbird, Utah
%E J. A. Storer
%W M. Cohn
%P 498
%M MAR
%D 1994
%O Dept. Computer Science, Monash University, '93
%K DCC, DCC4, DCC94, DLD, Monash, II, inductive inference,
   minimum message length encoding, MML, description, MDL, CAICF,
   curve polynomial fit fitting, Akaike, Bozdogan, CAICF, Rissanen,
   Occam Occam's Ockham razor
%X compares several methods - including Akaike,  Bozdogan (CAICF),
   Rissanen -  both analytically and experimentally.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%E S. Muggleton
%T Inductive Logic Programming
%I AcademicPress
%C London
%S APIC
%N 38
%D 1992
%K text, book, ILP, LP, induction, inference, II, prolog, Golem, Foil, Linus,
   MML, MDL, machine learning, c1992, c199x, c19xx
%X uk us isbn:0125097158.

%A N. Lavrac
%A S. Dzeroski
%T Inductive Logic Programming: Techniques and Applications
%I EllisHorwood (SimonAndSchuster)
%S Artificial Intelligence
%D 1994
%K text, book, c1994, c199x, c19xx, artificial intelligence, AI, induction,
   inference, MML, II, machine learning, logic, logic programming, LP, ILP,
   machine learning, Linus, Golem, mFoil, Foil, deductive databases
%X From: saso@cs.kuleuven.ac.be (Saso Dzeroski) 11/93
   20+294 pp.  Hardcover $53.95,  isbn:0-13-457870-8.
    PART I: INTRODUCTION TO ILP
    1 Introduction  3
    2 Inductive logic programming  23
    3 Basic ILP techniques  39
    PART II: EMPIRICAL ILP
    4 An overview of empirical ILP systems  67
    5 LINUS: Using attribute-value learners in an ILP framework  81
    6 Experiments in learning relations with LINUS  123
    7 ILP as search of refinement graphs  137
    8 Handling imperfect data in ILP  153
    9 mFOIL: Extending noise-handling in FOIL  173
    10 Experiments in learning relations from noisy examples  183
    PART IV: APPLICATIONS OF ILP
    11 Learning rules for early diagnosis of rheumatic diseases  199
    12 Finite element mesh design  217
    13 Learning qualitative models of dynamic systems  227
    14 Other ILP applications  243.

%A M. J. Pazzani
%A C. A. Brunk
%A G. Silverstein
%T An information-based approach to integrated empirical and explanation-based
   learning
%P 373-394
%B Inductive Logic Programming
%E S. Muggleton
%I AcadamicPress
%D 1992
%K information theory, explanation based, inductive inference II, MML, MDL,
   FOIL, FOCL, machine learning, logic programming,LP, ILP, c1992, c199x, c19xx

%A S. Muggleton
%T A strategy for constructing new predicates in first order logic
%J 3rd European Working Session on Learning (EWSL 88)
%W Glasgow
%D 1988
%P 123-130
%K EWSL 88 EWSL88 EWSL3, CIGOL, GOLEM, inductive inference, II, logic
   programming, LP, ILP, algorithmic complexity, information theory, MML, MDL

%A P. M. Murphy
%A M. J. Pazzani
%T Exploring the Decision Forest: An Empirical Investigation of Occam's
   Razor in Decision Tree Induction
%J J. of AI Research
%V 1
%P 257-275
%D 1994
%K AI, JAIR, classification, tree, trees, minimum message length encoding,
   MML, MDL, Occam, Occam's, Ockham, razor
%X We report on a series of experiments in which all decision
   trees consistent with the training data are constructed. These
   experiments were run to gain an understanding of the properties of the
   set of consistent decision trees and the factors that affect the
   accuracy of individual trees. In particular, we investigated the
   relationship between the size of a decision tree consistent with some
   training data and the accuracy of the tree on test data. The
   experiments were performed on a massively parallel Maspar computer.
   The results of the experiments on several artificial and two real
   world problems indicate that, for many of the problems investigated,
   smaller consistent decision trees are on average less accurate than
   the average accuracy of slightly larger trees.  [BUT ... no noise]

%A W. Jeffreys
%A J. Berger
%T Ockham's razor and Bayesian analysis
%J American Scientist
%V 80
%P 64-??
%M JAN
%D 1993
%K minimum message length encoding, MML, Occam Occam's Ockham
   Ockhams, philosophy of science, explanation, theory, hypothesis, MDL,
   Bayes, Bayesian, probability, distribution, conditional, description
%X via rohan B a x t e r:
   (I have it if you're interested, fairly high level account
   parallelling the MacKay neural network approach: the variance of the
   posterior distribution is given an Ockham interpretation...).

%A G. Schwarz
%T Estimating the dimension of a model
%J The Annals of Statistics
%I IMS
%V 6
%N 2
%P 461-464
%M MAR
%D 1978
%K AS, statistics, stats, number, parameter, parameters, estimate, estimation,
   model, selection, complexity, penalty, fit, fitting, over, over-fitting,
   noise, Bayes, Bayesian, BIC, c1978, c197x, c19xx
%X "The problem of selecting one of a number of models of different dimensions
   is treated by finding its Bayes solution, & evaluating the leading terms of
   its asymptotic expansion. These terms are a valid large-sample criterion
   beyond the Bayesian context, since they do not depend on the a priori
   distribution."
   -- 1176344136@[<A HREF="http://projecteuclid.org/euclid.aos/1176344136">pr'jecteuclid</A>]['14] (open),
      [<A HREF="http://dx.doi.org/10.1214/aos/1176344136">doi:10.1214/aos/1176344136</A>]['14],
      2958889@[<A HREF="http://www.jstor.org/stable/2958889">Jstor</A>]['14].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A L. Brillouin
%T Science and Information Theory
%I AcademicPress, N.Y.
%P 320
%D 1956
%K book, text, MML, entropy, content, MDL, c1956, c195x, c19xx, capacity,
   channel, communication, thermodynamics, negative, computation, math, theory
%X <!-- R. K i n g has a copy --> uk us isbn:0121349500.  A 2nd edn c1962.

%A E. T. Jaynes
%T Information theory and statistical mechanics
%I Phys. Rev.
%P 620-630
%V 106
%N 4
%D 1957
%K jrnl, statistics, physics, maximum entropy, max ent, c1957, c195x, c19xx
%X via G. F a r r.   See also follow paper, same title + II.

%A E. T. Jaynes
%T Information theory and statistical mechanics II
%I Phys. Rev.
%P 171-190
%V 108
%N 2
%D 1957
%K jrnl, statistics, physics, maximum entropy, max ent, c1957, c195x, c19xx
%X via G. F a r r

%A E. T. Jaynes
%T Papers on Probability, Statistics and Statistical Physics
%I Reidel
%D 1982
%K book, text, c1982, c198x, c19xx, mechanics, maximum entropy, max ent
%X via G. F a r r

%A P. Zador
%T Asymptotic quantization error of continuous signals and the quantization
   dimension
%J IEEE Trans. on Information Theory
%V IT-28
%N 2
%P 139-149
%M MAR
%D 1982
%K jrnl, c1982, c198x, c19xx, signal, zz0807, code book, books, discretization,
   quantisation, discretisation, Bennet, lattice constant, constants
%X "Extensions of the limiting quantization error formula of Bennet are proved.
   These are of the form D_{s,k}(N,F)=N^{-beta}B, where N is the # of output
   levels, D_{s,k}(N,F) is the sth moment of the metric distance between
   quantizer input & output, beta, B>0, k=s/beta is the signal space dimn, &
   F is the signal distribution. If a suitably well-behaved k-dimn signal dens.
   f(x) exists, B=b_{s,k}[int f^{rho}(x)dx]^{1/rho}, rho=k/(s+k), & b_{s,k}
   does not depend on f. For k=1, s=2 this reduces to Bennett's formula. If F
   is the Cantor distribution on [0,1], 0 < k=s/ beta=log 2/log 3 < 1 & this k
   equals the fractal dimension of the Cantor set[12,13]. Random quantization,
   optimal quantization in the presence of an output information constraint, &
   quantization noise in high dim. spaces are also investigated."
   -- [<A HREF="https://doi.org/10.1109/TIT.1982.1056490">doi:10.1109/TIT.1982.1056490</A>]['17],
      [<A HREF="http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1056490">pdf@ieee</A>]['07] ?subscr?.
   Ref from CSW, TR 128, p.11: (G is the gamma fn, on lattice const k_J)
     Z shows (G(J/2+1)^(2/J).G(2/J+1))/(J.pi) > k_J > (G(J/2+1)^2/J)/((J+2).pi)

%A E. T. Jaynes
%T Probability Theory - the Logic of Science
%I Physics, Washington University, St. Louis, MO 63130, USA
%D 1994
%K text, book, probability, statistics, inductive inference, II,
   Bayesian, maximum entropy, model, theory, hypothesis, c1994, c199x, c19xx,
   www, HREF, http
%X [<A HREF="http://omega.albany.edu:8008/JaynesBook.html">Book</A>] (8/'94)
   URL for ALL (!) chapters -  file://bayes.wustl.edu/Jaynes.book
   New version:
      [<A HREF="http://bayes.wustl.edu/">web</A>] [5/'96]
      [<A HREF="ftp://bayes.wustl.edu/">ftp</A>].

%A J. D. Patrick
%T Snob: a program for discriminating between classes
%R 91/151
%I Computer Science, Monash University
%P 19
%D 1991
%K SNOB, class, classes, classify, classification, mixture modelling, cluster,
   clustering, model, minimum message length, MML, encoding, description, MDL,
   measure, WIM, inductive inference, II, applications, EM algorithm, smem,
   TR151, TR 151, c1991, c199x, c19xx
%X "The problem addressed by Snob is known variously as 'classification',
   'intrinsic classification' (to distinguish it from the case when the number
   and nature of the classes are known a priori), 'clustering', 'unsupervised
   pattern recognition', or 'numerical taxonomy'. The decision statistic used by
   Snob to allocate objects to classes, to divide classes and to merge classes
   is called the Wallace Information Measure (WIM)...."
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.71.9615">cites'r</A>]['14],
      [<A HREF="ftp://ftp.csse.monash.edu.au/publications/1991/TR151.ps.gz">TR 91/151</A>]['04],
      [<A HREF="ftp://ftp.csse.monash.edu.au/publications/1991/TR151.abstract.ps.gz">abs.</A>]['04].
   Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A J. D. Zakis
%A I. Cosic
%A D. L. Dowe
%T Classification of protein spectra derived for the resonant recognition
   model using the minimum message length principle
%J ACSC-17
%P 209-216
%M JAN
%D 1994
%K DLD, Monash, conf, MML, MDL, MolBio, description, ACSC, ACSC17, ACSC94
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. J. Oliver
%A D. J. Hand
%T Averaging over decision stumps
%J Machine Learning: ECML-94
%W Catania, Sicily
%E F. Bergadano
%E L. D. Raedt
%I SpringerVerlag
%S LNAI
%V 784
%P 231-241
%D 1994
%K conf, DJHand, c1994, c199x, c19xx,classification, decision tree, trees,
   DTree, II, stats, ECML, ECML94
%X See the '96 jrnl paper,
   [<A HREF="http://stats.ma.ic.ac.uk/~djhand/">~djhand/</A>][1/'04].
   [Also search for: Dtree].

%A R. S. Forsyth
%A D. D. Clarke
%A R. L. Wright
%T Overfitting revisited: an information-theoretic approach to simplifying
   discrimination trees
%J J. Expt. Theor. Artif. Intell.
%V 6
%P 289-302
%D 1994
%K jrnl, decision, classification, tree, DTree, overfit, zz0599
%X On this subject see also
      W a l l a c e and P a t r i c k, Machine Learning 11 pp7-22 1993.
   Quotes  E i n s t e i n:
      everything should be as simple as possible but no simpler. (no ref).

%A G. Wolff
%T Towards a Theory of Cognition and Computing
%I Ellis Horwood
%M MAY
%D 1991
%K book, text, language, learning, computing, as, compression,
   AI, II, MML, MDL, zz0695, c1991, c199x, c19xx
%X 1st ed 1991; hb us$16; uk us isbn:0139250255; isbn13:978-0139250255.
   Author was at Elec Eng, Uni of Wales at Bangor
   [<A HREF="http://www.sees.bangor.ac.uk/~gerry/lang_learn.html">web page</A>][6/'95].

%A B. McCowan
%A S. F. Hanser
%A L. R. Doyle
%T Quantitative tools for comparing animal communication systems:
   Information theory applied to bottlenosed dolphin whistle repertoires
%J Animal Behaviour
%V 57
%N 2
%P 409-419
%M FEB
%D 1999
%K jrnl, communication, language, message, information content, Zipf, Zipfs law,
   bottle nosed dolphins, Tursiops truncatus, biology, biol, sounds, whistles,
   entropy, c1999, c199x, c19xx
%X ... applied ... information theory stat[s] to a statistically
   categorized set of bottlenose dolphin Tursiops truncatus, whistle
   vocalizations.  1st we use the 1st-order entropic relation in a Zipf-type
   diagram (Zipf '49 Human Behavior and the Principle of Least Effort) to
   illustrate the application of temporal statistics as comparative indicators
   of repertoire complexity, and as possible predictive indicators of
   acquisition/learning in animal vocal repertoires.  2nd we illustrate the
   need for more extensive temporal data sets when examining the higher
   entropic orders, indicative of higher levels of internal informational
   structure, of such vocalizations, which could begin to allow the statistical
   reconstruction of repertoire organization. 3rd we propose using
   `communication capacity' as a measure of the degree of temporal structure
   and complexity of statistical correlation, ...  the slope of Shannon
   entropies, and illustrate how it potentially can be used to compare the
   organizational complexity of vocal repertoires across [many] species. ...
   .pdf [<A HREF="http://dx.doi.org/10.1006/anbe.1998.1000">doi:10.1006/anbe.1998.1000</A>][7/'03].
   [Also search for: Hanser].

%A J. G. Wolff
%T Probabilistic reasoning as information compression by multiple alignment,
   unification and search: An introduction and overview
%J J. of Universal Computer Science
%V 5
%N 7
%P 418-462
%D 1999
%K jrnl, AI, ICMAUS
%X At: [<A HREF="http://www.iicm.edu/jucs_5_7">www</A>],
     - [<A HREF="mailto:gerry@sees.bangor.ac.uk">email</A>].
   See also Wolff, same jrnl, 5(11) pp777-815, 1999.

%A J. G. Wolff
%T Computing as information compression by multiple alignment,
   unification and search
%J J. of Universal Computer Science
%V 5
%N 11
%P 777-815
%D 1999
%K jrnl, AI, machine learning, ICMAUS
%X At: [<A HREF="http://www.iicm.edu/jucs_5_11">www</A>] [1/'00]
   From: Dr J G Wolff, School of Informatics, University of Wales,
         Dean Street, Bangor, Gwynedd, LL57 1UT, UK.
         tel:+44-1248-382691.  fax:+44-1248-361429.
         [<A HREF="mailto:gerry@sees.bangor.ac.uk">email</A>].
         [<A HREF="http://www.sees.bangor.ac.uk/~gerry/">www</A>] [1/'00]
   This paper argues that the operations of a `Universal Turing Machine'
   (UTM) and equivalent mechanisms such as the `Post Canonical System'
   (PCS) - which are widely accepted as definitions of the concept of
   `computing' - may be interpreted as information compression by
   multiple alignment, unification and search (ICMAUS).  [...]

%A G. W. Hart
%T Minimum information estimation of structure
%I Dept. Elec. Eng. and Comp. Sci., MIT
%P 230
%D 1987
%K zz0795, c1987, c198x, c19xx, PhD thesis, minimum message length, MML,
   inductive inference, II, Bayes, description, MDL, phrase structured grammar,
   PSG, FSM, hidden Markov model, HMM, cluster, clustering, waveform, wave form
%X auth sent copy 7/95 (thanks!)
   Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A D. W. Kissane
%A S. Bloch
%A W. I. Burns
%A J. D. Patrick
%A C. S. Wallace
%A D. P. McKenzie
%T Perceptions of family functioning and cancer
%J Psycho-oncology
%V 3
%P 259-269
%D 1994
%K jrnl, psychooncology, medical, minimum message length, MML, description, MDL,
   application, grief, CSW, CSWallace, c1994, c199x, c19xx, psychology,
   families
%X "Family function was assessed in 102 families (342 members) of palliative
   care patients & grouped into classes by a computer-based taxonomic program.
   Five classes were defined through the dimensions of cohesiveness, conflict &
   expressiveness of the Family Environment Scale (FES). One third of families
   we named supportive for their high cohesiveness; a further 21% resolved
   conflict effectively; both of these classes contained low psychological
   morbidity. Two classes (15%) were clearly dysfunctional: hostile families
   (6%) were distinguished by high conflict while sullen families (9%) displayed
   moderate conflict, poor cohesion & limited expressiveness. These two classes
   had significantly higher levels of psychological morbidity & poorer social
   functioning. The remaining class (31%) had intermediate levels of cohesion,
   expressiveness & conflict (termed ordinary) yet more moderate psychosocial
   morbidity. Screening of families with the FES would facilitate a more
   family-centred approach to treatment, with relatively early identification
   of families at-risk; preventive interventions would also then be feasible."
   -- [<A HREF="http://dx.doi.org/10.1002/pon.2960030403">doi:10.1002/pon.2960030403</A>]['14].
   Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A R. Solomonoff
%T A preliminary report on a general theory of inductive inference
%I Zator Co
%R ZTB 138
%D 1962
%K TR ZTB 138, TRztb138, c1962, c196x, c19xx, II, AI, MML, MDL,
   sequence, series, UTM
%X "Some preliminary work is presented on a very general new theory of II. The
   extrapolation of an ordered seq. of symbols is implemented by computing the
   apriori probabilities of various sequences of symbols. The apriori
   probability of a seq. is obtained by considering a UTM whose output is the
   seq. in question.  An approximation to the apriori probability is given by
   the shortest input to the machine that will give the desired output. A more
   exact formulation is given, & it is made somewhat plausible that
   extrapolation probabilities obtained will be largely independent of just
   which UTM was used, providing that the seq. to be extrapolated has an
   adequate amount of information in it.  Some examples are worked out to show
   the application of the method to specific problems. Applications of the
   method to curve fitting & other continuous problems are discussed to some
   extent. Some alternative theories of II are presented whose validities
   appear to be corollaries of the validity of the first method described."
   -- [<A HREF="http://world.std.com/~rjs/z138.ps">tr.ps@std.com</A>][10/'04].
   [Also search for: MML].

%A H. P. Kamer
%T A note on the self-consistency of definitions of generalization and
   inductive inference
%J JACM
%P 280-281
%V 9
%N 2
%M APR
%D 1962
%K jrnl, JACM, II, AI, sequence, series, generalisation, c1962, c196x, c19xx
%X f(1)=E1, f(2)=E2, ..., f(n)=En. Generalization f(n+1)=?
   Q: A seq of events E1, E2, ..., En is given and the generalization f* is
   found.
   Is this 'self consistent', i.e. is f* also a gen' of E1, ..., En, f*(n+1) ?
   A: yes  ...  shows the self-consistency of every defn of gen'n based on the
   min'n of "complexity" or any numerical index, regardless of how this measure
   is defined.
   [<A HREF="http://doi.acm.org/10.1145/321119.321125">doi:10.1145/321119.321125</A>] Refs. Solomonoff 1962.

%A L. Staiger
%T Kolmogorov complexity and Hausdorff dimension
%J Inf. Comput.
%V 103
%N 2
%P 159-194
%D 1993
%O Proc. Fundamentals of Computation Theor, LNCS V.380, pp.34-343, '89
%K jrnl, c1993, c199x, c19xx, information theory, MML, MDL, Martin_loef, Lof,
   string, strings, entropy
%X "...develops several formal relationships between program-size complexity of
   infinite strings & various measures of information content. The idea is to
   bound the complexity of a maximally complex string in a prescribed set of
   strings by the Hausdorff dimension as well as the entropy of that set. Then
   the Hausdorff d. gives lower bounds to the Kolmogorov complexity, & under
   various recursivity conditions the entropy gives upper bounds. ... can be
   used to generalize important thms of P.Martin-Loef on K. c.. ..."
   [<A HREF="http://users.informatik.uni-halle.de/~staiger/Papers/fct89.ps.gz">.ps</A>]['07]
   [<A HREF="http://users.informatik.uni-halle.de/~staiger/">auth@uni-halle.de</A>]['07]
   (seminar @ Monash 2/'07, vis. G.F.)

%A R. J. Solomonoff
%T The discovery of algorithmic probability: a guide for the programming of
   true creativity
%B Computational Learning Theory: Euro-COLT 95
%E P. Vitanyi
%I SpringerVerlag
%P 1-22
%D 1995
%K inductive inference, II, minimum message length, MML, Bayes, AI,
   CSci, description, scientific discovery, learning, MDL, information theory,
   history, Occam's razor, AI, conf, COLT, COLT95, zz0795, c1995, c199x, c19xx
%X <!-- author email: rjs@world.std.com -->     Hargrave 6.31 E89.312
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. Rissanen
%T Stochastic complexity in learning
%B Computational Learning Theory: Euro-COLT 95
%E P. Vitanyi
%I SpringerVerlag
%P 198-209
%D 1995
%K inductive inference, II, minimum description length, MDL, conf, COLT95,
   COLT, c1995, c199x, c19xx
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. J. Oliver
%A D. J. Hand
%T Averaging over decision trees
%J J. of Classification
%V 13
%P 281-297
%D 1996
%K jrnl, tree, dtree, c1996, c199x, c19xx, inductive inference, II,
   DJHand, jono, stats
%X [<A HREF="http://stats.ma.ic.ac.uk/~djhand/">~djhand/</A>][1/'04].
   [Also search for: Dtree].

%A D. W. Kissane
%A S. Bloch
%A D. L. Dowe
%A R. D. Snyder
%A P. Onghena
%A D. P. McKenzie
%A C. S. Wallace
%T The Melbourne family grief study, I: Perceptions of family functioning
   in bereavement
%J American Journal of Psychiatry
%V 153
%P 650-658
%D 1996
%K DLD, CSW, CSWallace, Monash, jrnl, AJP, psychiatry, psychology, grief,
   application, SNOB, application, MML, II, c1996, c199x, c19xx
%X Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A D. W. Kissane
%A S. Bloch
%A P. Onghena
%A D. P. McKenzie
%A R. D. Snyder
%A D. L. Dowe
%T The Melbourne family grief study, II: Psychosocial morbidity and grief
   in bereaved families
%J American Journal of Psychiatry
%V 153
%P 659-666
%D 1996
%K DLD, Monash, jrnl, AJP, psychiatry, psychology, grief,
   SNOB, application, MML, application, II, zz0696
%X also see part I, pp.650-658,
   and [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A R. Solomonoff
%T Does algorithmic probability solve the problem of induction?
%I ISIS96
%M AUG
%D 1996
%W Melbourne
%K conf, ISIS 96, ISIS96, inductive inference, ALP, MML, MDL, minimum
   message description length, complexity, AI, philosophy of science,
   machine learning, Bayesian, prior,  c1996, c199x, c19xx
%X invited talk at ISIS 96,  17 refs,   search for: ISIS
   [<A HREF="mailto:rjs@world.std.com">rjs</A>][9/'96]

%A J. J. Oliver
%A R. A. Baxter
%A C. S. Wallace
%T Unsupervised learning using MML
%J Machine Learning: Proc. 13th Int. Conf. (ICML 96)
%E L. Saitta
%I MorganKaufmann
%P 364-372
%D 1996
%K conf, ICML96, ICML13, minimum message length, MML, description, MDL, Snob,
   classification, model, multivariate, stats, statistics, inductive inference,
   CSW, CSWallace, clustering, II, AI, zz1296, c1996, c199x, c19xx
%X Snob has been widely used for mixture modelling and uses the minimum
   message length criterion. The message length formulas in Snob are
   based on early work. This paper updates the message length formula
   based on general recent work.  The MML criterion is compared to other
   prominent criterion in a series of Monte Carlo experiments.  (via rohan)
   [Also search for: MML],  and
   see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A R. A. Baxter
%A J. J. Oliver
%A D. Hand
%T Fitting finite Gaussian mixture models using minimum message length
   estimation
%J IMS Bull.
%V 25
%N 2
%P ??
%D 1996
%K jrnl, minimum message length, MML, description, MDL, classification,
   model, modelling, multivariate, stats, statistics, inductive inference,
   DJHand, jono, II, zz1296, normal, c1996, c199x, c19xx
%X to other Bayesian model selection criterion for the problem of
   choosing the number of components of a mixture model. Results are
   given for artificial and real data sets.    (via rohan)
   [Also search for: MML mixture model].

%A R. A. Baxter
%A J. J. Oliver
%T The kindest cut: minimum message length segmentation
%J Proc. 7th Int. Workshop on Algorithmic Learning Theory
%S LCNS
%V 1160
%I SpringerVerlag
%P 83-90
%D 1996
%E S. Arikawa
%E A. K. Sharma
%K conf, ALT96, ALT7, minimum message length, MML, description, MDL,
   segmentation, segment, piece-wise, curve fitting, c1996, c199x, c19xx
%X difficult problem, one not suited to many inference methods. A boundary
   is partly discrete and partly continuous. A minimum message length
   formula is derived for estimating boundary points and Monte Carlo
   experiments performed.    (via rohan)
   [Also search for: MML segmentation].

%A D. J. Hand
%A J. J. Oliver
%A A. D. Lunn
%T Discriminant analysis when the classes arise from a continuum
%J Pattern Recognition
%V 31
%P 641-650
%D 1998
%K jrnl, DJHand, jono, class, classification, stats, statistics,
   c1998, c199x, c19xx
%X [<A HREF="http://stats.ma.ic.ac.uk/~djhand/">~djhand/</A>][1/'04].

%A J. J. Oliver
%A R. A. Baxter
%A C. S. Wallace
%T Minimum message length segmentation
%J Res. and Dev. in Knowledge Discovery and Data Mining (PAKDD-98)
%P 222-233
%D 1998
%K conf, segment, cut point, points, cutpoint, MML, MDL, series approximation,
   jono, CSW, CSWallace, Monash, c1998, c199x, c19xx
%X Also see:  Baxter Oliver c1996.
   And [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A D. L. Dowe
%A R. A. Baxter
%A J. J. Oliver
%A C. S. Wallace
%T Point estimation using the Kullback-Leibler loss function and MML
%J 2nd Pacific-Asia Conf. on Knowledge Discovery and Data Mining (PAKDD98)
%S LNAI
%V 1394
%P 87-95
%M APR
%D 1998
%K conf, PAKDD, PAKDD2, CSW, CSWallace, MML, MDL, KL, c1998, c199x, c19xx
%X Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A R. A. Baxter
%A J. J. Oliver
%T Overlapping mixture models
%J 6th Int. Workshop on Artificial Intelligence and Statistics
%W Ft. Lauderdale, Florida
%D 1997
%O TR ??
%K conf, AIS6, AIS97, c1997, c199x, c19xx, model, modelling, stats
%X also a TR (via rohan).
   [Also search for: MML mixture model].

%A C. S. Wallace
%T False oracles and SMML estimators
%J Proc. Int. Conf. on Information, Statistics and Induction in Science
%I World Scientific
%P 304-316
%D 1996
%K Wal96, zzMML, conf, ISIS, ISI96, strict, minimum message length encoding,
   SMML, MML, inductive inference, II, description, information theory, IT,
   foundations, MDL, statistics, Bayes, Bayesian, estimate, AI,
   CSW, CSWallace, c1996, c199x, c19xx, zz1296, TR 128, TR128
%O TR 89/128, Dept. Comp. Sci., Monash Univ., '89
%X "MML and MDL inductive inference techniques are based on the information-
   -theoretic notion of transmitting data concisely. Both methods are
   universally applicable, consistent and efficient. MML [LA: ie MML87] is a
   Bayesian technique and is invariant under parameter transformations; however
   it is a quadratic approximation to a slightly more efficient two-part coding
   technique, Strict MML (SMML), which maps from the data space onto a
   countable, discretized subset of the parameter space. It is shown that the
   posterior distribution of the parameter vector is a "false oracle" in that
   no fair comparison between the true ("oracular") parameter vector and a
   sampling from the posterior will enable us to distinguish one from the other.
   It is further shown that the invariant, consistent and efficient Bayesian
   SMML point estimation technique closely approximates (and converges to) a
   false oracle. Hence, SMML inductions are practically indistiguishable from
   the truth in the absence of data other than that used in the induction."
   -- [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/False-Oracles/">paper@www</A>].
   [Also search for: TR128 CSW].

%A R. A. Baxter
%T MML and the likelihood principle
%J Proc. Int. Conf. on Information, Statistics and Induction in Science
%I World Scientific
%P 292-303
%D 1996
%K strict, minimum message length encoding, MML, inductive inference, II,
   description, information theory, IT, foundations, MDL, statistics,
   Bayes, Bayesian, estimate, conf, c1996, c199x, c19xx
%X The Likelihood Principle states that a sensible estimate should not
   depend on data unseen (i.e. the size of the data space). MML breaches
   the Likelihood Principle in the strict sense...any coding method must
   have a proper probability distribution over possible data.
   If we change the set of possible data, this distribution changes
   and the estimate changes. Two classical Likelihood Principle examples
   are considered and the MML estimate is found not too change much.
   [Also search for: MML]             (via rohan).

%A C. S. Wallace
%A D. L. Dowe
%T MML mixture modelling of multi-state, Poisson, von Mises circular
   and Gaussian distributions
%J Proc 28th Symp. on the Interface
%P 608-613
%D 1997
%O Preliminary papers of the 6th Int Workshop on AI and Stats,
      Ft. Lauderdale, Florida, 529-536, Jan 1997
%K MML, MDL, inductive inference, II, clustering, classification, class,
   cluster, normal, periodic, Snob, conf, AIS6, AIS97, CSW, DLD,
   vonMises, zz0197, CSWallace, c1997, c199x, c19xx
%X [Also search for: MML SNOB]  and  [also search for: vonMises direction]
   and see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A D. L. Dowe
%A J. J. Oliver
%A C. S. Wallace
%T MML estimation of the parameters of the spherical Fisher distribution
%J Proc. 7th Int w'shop on Alg. Learning Complexity
%D 1996
%W Sydney
%S LNAI
%N 1160
%P 213-227
%O TR 97/272, Dept. Comp Sci. Monash University
%K ALT, ALT96, ALT7, conf, MML, MDL, probability, DLD, CSW, CSWallace,
   c1996, c199x, c19xx
%X [Also search for: MML vonMises].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A D. L. Dowe
%A C. S. Wallace
%T Resolving the Neyman-Scott problem by Minimum Message Length (abstract)
%J Proc. Sydney Int. Stat. Congress
%P 197-198
%D 1996
%O TR 97/307, Department of Computer Science, Monash University, Australia,
   Feb 1997
%K abstract, conf, SISC, SISC96, TR 307, TR307, MML, description, MDL, DLD, CSW,
   CSWallace, c1996, c199x, c19xx
%X authors at Comp. Sci., Monash University, Vic, oz
   also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T MML inference of predictive trees, graphs and nets
%B Computational Learning and Probabilistic Reasoning
%E A. Gammerman
%I Wiley
%P 43-66
%D 1996
%K minimum message length, MML, MDL, description, DTree, c1996, c199x, c19xx,
   inductive inference, II, CSW, CSWallace, chapter
%X isbn:0-471-96279-1.
   Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A S. R. Eddy
%T Profile hidden Markov models (review)
%J Bioinformatics
%V 14
%N 9
%P 755-763
%D 1998
%K MolBio, jrnl, HMM, profiles, protein, survey, zz0199
%X Beware: what many (mostly) protein biologists call hidden MM's
   are really a special case (subset) of general HMM's.
   [also search for: HMM].

%A P. Grunwald
%A P. Kontkanen
%A P. Myllymaki
%A T. Silander
%A H. Tirri
%T Minimum encoding approaches for predictive modeling
%J UAI98
%P 183-192
%D 1998
%K conf, c1998, c199x, c19xx, modelling, UAI, UAI98, MML, MDL
%X Compares some min' encoding schemes on small data sets.
   NB. They seem to have confused `inference' with `prediction'.
  ?The ref's include one of the newer reports by  B a x t e r & O l i v e r '94
   but the paper does not seem to take it into account?

%T Special issue on Clustering and Classification
%E F. Murtagh
%J COMPJ
%V 41
%N 8
%D 1998
%K jrnl, COMPJ, cluster, class, classify, clusters, classes, MML, MDL,
   data mining, knowledge discovery, KD, DM, zz0499, c1998, c199x, c19xx
%X Editorial p517.
   8 papers:
   M i r k i n,  L i & J a i n,  G i l l e t et al,  O k a,  H u b e r t et al,
   F r a l e y & R a f t e r y,  W i t t e r & B e r r y, W a l l a c e
   Hint [also search for: COMPJ classify 1998].

%A B. Mirkin
%T Least-squares structuring, clustering and data processing issues
%J COMPJ
%V 41
%N 8
%P 518-536
%D 1998
%K jrnl, COMPJ, cluster, class, clustering, classification, classify

%A Y. H. Li
%A A. K. Jain
%T Classification of text documents
%J COMPJ
%V 41
%N 8
%P 537-546
%D 1998
%K jrnl, COMPJ, cluster, class, clustering, classification, classify,
   rainbow, retrieval, web, www, document, Bayes, similarity, zz0499
%X ... 83% "classification accuracy" on a 7-class test set.  [29 refs].

%A V. J. Gillet
%A D. J. Wild
%A P. Willett
%A J. Bradshaw
%T Similarity and dissimilarity methods for processing chemical
   structure databases
%J COMPJ
%V 41
%N 8
%P 547-558
%D 1998
%K jrnl, COMPJ, cluster, class, clustering, classification, classify,
   chemistry, chemicals, compounds
%X [71 refs].

%A R. Oka
%T Spotting method for classification of real world data
%J COMPJ
%V 41
%N 8
%P 559-565
%D 1998
%K jrnl, COMPJ, cluster, class, clustering, classification, classify
%X [18 refs]

%A L. Hubert
%A P. Arabie
%A J. Meulman
%T The representation of symmetric proximity data: dimensions and
   classifications
%J COMPJ
%V 41
%N 8
%P 566-577
%D 1998
%K jrnl, COMPJ, cluster, class, clustering, classification, classify
%X [17 refs]

%A C. Fraley
%A A. E. Raftery
%T How many clusters? Which clustering method? Answers via model-based
   cluster analysis
%J COMPJ
%V 41
%N 8
%P 578-588
%D 1998
%K jrnl, COMPJ, cluster, class, clustering, classification, classify
%X [66 refs]

%A S. Deerwester
%A S. Dumais
%A G. Furnas
%A T. Landauer
%A R. Harshman
%T Indexing by latent semantic analysis
%J J. Am. Soc. for Inf. Sci.
%V 41
%N 6
%P 391-407
%D 1990
%K jrnl, JASIS, information retrieval, document, latent semantic analysis
%X ref in  B e r r y et al '96

%A D. I. Witter
%A M. W. Berry
%T Downdating the latent semantic indexing model for conceptual information
   retrieval
%J COMPJ
%V 41
%N 8
%D 1998
%P 589-601
%K jrnl, COMPJ, cluster, class, clustering, classification, classify,
   document, retrieval
%X [20 refs]

%A C. S. Wallace
%T Intrinsic classification of spatially correlated data
%J COMPJ
%V 41
%N 8
%P 602-611
%D 1998
%K jrnl, COMPJ, cluster, class, clustering, classification, region, geographic,
   classify, data mining, mine, knowledge discovery, KD, DM, AI, HMM, Markov,
   random field, mixture modelling, spatial, fields, model, pattern, 2D, 3D,
   Monte Carlo, MCMC, Gibbs sampling, minimum message length encoding, MML, EM,
   SNOB, correlation, Markov, inductive inference, minimum description length,
   II, zz0499, c1998, c199x, c19xx, MDL, CSWallace, CSW, Monash
%X "Intrinsic classification, or unsupervised learning of a classification,
   was the earliest application of what is now termed minimum message length
   (MML) or minimum description length (MDL) inference. The MML algorithm
   Snob[1] and its relatives have been used successfully in many domains. These
   algorithms treat the things to be classified as independent random
   selections from an unknown population whose class structure, if any, is to
   be estimated. This work extends MML classification to domains where the
   things have a known spatial arrangement and it may be expected that the
   classes of neighbouring things are correlated. Two cases are considered.
   In the first, the things are arranged in a sequence and the correlation
   between the classes of successive things modelled by a first-order Markov
   process. An algorithm for this case is constructed by combining the Snob
   algorithm with a simple dynamic programming algorithm. The method has been
   applied to the classification of protein secondary structure. In the second
   case, the things are arranged on a two-dimensional (2D) square grid, like
   the pixels of an image. Correlation is modelled by a prior over patterns
   of class assignments whose log probability depends on the number of adjacent
   mismatched pixel pairs. The algorithm uses Gibbs sampling from the pattern
   posterior & a thermodynamic relation to calculate message length." [17 refs]
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/41.8.602">doi:10.1093/comjnl/41.8.602</A>]['05].
   [Also search for: Edgoose DCC 1998], and
   see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>],
   and [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A P. Grunwald
%T The minimum description length principle and reasoning under uncertainty
%I U. of Amsterdam
%D 1998
%K PhD thesis, c1998, c199x, c19xx, MML, MDL
%X [<A HREF="http://homepages.cwi.nl/~pdg/publicationpage.html">PG@cwi</A>][8/'05].

%A M. Viswanathan
%A C. S. Wallace
%T A note on the comparison of polynomial selection methods
%J Proc. 7th Int. Workshop on Artif. Intell. and Stats.
%W Ft. Lauderdale
%M JAN
%D 1999
%P 169-177
%I MorganKauffman
%K conf, fitting, basis functions, minimum message length, description, MDL,
   Murli, CSW, CSWallace, MML, SVM, zz1099, c1999, c199x, c19xx, curve, fit,
   regression, method, structural risk minimisation, SRM, minimization, AIS
%X "Minimum Message Length (MML) & Structural Risk Minimisation (SRM) are 2
   computational learning principles that have achieved wide acclaim in recent
   years. ...former is based on Bayesian learning & the latter on the classical
   theory of VC-dimension, they are similar in their attempt to define a
   trade-off between model complexity & goodness of fit to the data. A recent
   empirical study by Wallace compared the perf. of std model sel. methods in a
   1-D polynomial regression framework. ... strong evidence in support of the
   MML & SRM based methods over the other std approaches. [here] present a
   detailed empirical evaluation of 3 model sel. methods which include an MML
   based approach & 2 SRM based methods. ... suggest that the MML-based approach
   ...has higher predictive accuracy & also raise questions on the inductive
   capabilities of [SRM]."  [11 Refs].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A M. Viswanathan
%A C. S. Wallace
%A D. L. Dowe
%A K. B. Korb
%T Finding cutpoints in noisy binary sequences - a revised empirical evaluation
%J Proc 12th Australian Joint Conf. on Artif. Intell.
%W Melbourne
%P 405-416
%D 1999
%K conf, AI, cut point, points, segmentation, MML, MDL, minimum message length,
   Kearns, series, Murli, CSW, CSWallace, DLD, description, zz1099, segment,
   c1999, c199x, c19xx
%X ... Kearns et al ... risk minimization, MDL, cross validation, ...
   inefficiency in the [original] MDL approach, ... give revised MDL method &
   another based on minimum message length (MML) principle.  [8 Refs].
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-46695-9_34">doi:10.1007/3-540-46695-9_34</A>]['09].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A A. Gammerman
%A V. Vovk
%T Kolmogorov complexity: sources, theory and applications
%J COMPJ
%V 42
%N 4
%P 252-255
%D 1999
%K jrnl, COMPJ, algorithmic information theory, MML, MDL, c1999, c199x, c19xx
%X special issue of the COMPJ on KC.   [also search for: MML MDL]

%A R. Solomonoff
%T Two kinds of probabilistic induction
%J COMPJ
%V 42
%N 4
%P 256-259
%D 1999
%K jrnl, COMPJ, inductive inference, II, AI, MML, MDL, c1999, c199x, c19xx,
   minimum message description length, Kolmogorov, complexity, zz1099
%X [<A HREF="mailto:rjs@world.std.com">email rjs</A>].
   Problems in probabilistic induction are of two general kinds. In the first,
   we have a linearly ordered sequence of symbols that must be extrapolated.
   In the second we want to extrapolate an unordered set of finite strings.
   A very general formal solution to the first kind of problem is well known
   and much work has been done in obtaining good approximations to it
   [1, 3, 4, 5, 6, 9, 10]. Though the second kind of problem is of much
   practical importance, no general solution has been published. We present
   two general solutions for unordered data. We also show how machines can be
   constructed to summarize sequential and unordered data in optimum ways.
   (This was a special issue of the COMPJ and the other papers
   therefore related.)
   See [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_42/Issue_04/">COMPJ at OUP</A>][10/1999].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. Rissanen
%T Hypothesis selection and testing by the MDL principle
%J COMPJ
%V 42
%N 1
%D 1999
%P 260-269
%K jrnl, COMPJ, minimum descrition length, MDL, inductive inference,
   AI, complexity, zz1099, c1999, c199x, c19xx
%X [<A HREF="mailto:rissanen@almaden.ibm.com">email r</A>].
   The central idea of the MDL (Minimum Description Length) principle is to
   represent a class of models (hypotheses) by a universal model capable of
   imitating the behavior of any model in the class. The principle calls for a
   model class whose representative assigns the largest probability or density
   to the observed data. Two examples of universal models for parametric
   classes ${\cal M}$ are the normalized maximum likelihood (NML) model
   \[ \hat f (x^n\mid{\cal M})=f(x^n\mid\hat \theta(x^n))\bigg/\int_\Omega
   f(y^n\mid\hat\theta(y^n))\,{\rm d}y^n, \] where $\Omega$ is
   an appropriately selected set, and a mixture \[ f_w(x^n\mid
   {\cal M})=\int f(x^n\mid\theta)w(\theta)\,{\rm d}\theta \]
   as a convex linear functional of the models. In this
   interpretation a Bayes factor $B-f_w(x^n\mid{\cal M}_1)/f_v
   (x^n\mid{\cal M}_2)$ is the ratio of mixture representatives of two model
   classes. However, mixtures need not be the best representatives, and as will
   be shown the NML model provides a strictly better test for the mean being
   zero in the Gaussian cases where the variance is known or taken as a param..
   Also see discussion
      by `D a w i d' p.323-326,
      by `R...' p.327-329,
      by `W a l l a c e' and `D o w e' p.330-337,
      by `C l a r k e' p.338-339, and
      by `S h e n' p.340-342 in the same issue and a
      rejoinder by `R...' pp3.43-344, and by `W and D' p.345-347'.
   See [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_42/Issue_04/">COMPJ at OUP</A>][10/1999],
   and also [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A L. A. Levin
%T Robust measures of information
%J COMPJ
%V 42
%N 4
%P 284-286
%D 1999
%K jrnl, COMPJ, c1999, c199x, c19xx, NP, NPC, complexity, measure, zz1099
%X The usual (ie easily computable) prob dists share a remarkable feature.
   They are concentrated on strings which do not differ noticeably
   in any robust characteristic, except their informational size (KC).
   The formalization of this statement distinguishes a class of
   homogeneous prob' measures suggesting various applic'ns.
   ... it may explain why the average case NP-completeness results
   are so measure-indep't and may lead to their gen'n to this wider and
   more invariant class of measure.  It also demonstrates a sharp
   difference between the pseudorandom strings and the objects known before.

%A V. V. Vyugin
%T Algorithmic complexity and stochastic properties of finite binary sequences
%J COMPJ
%V 42
%N 4
%P 294-317
%D 1999
%K jrnl, COMPJ, c1999, c199x, c19xx, statistical, Kolmogorov complexity
%X [also search for: MML MDL].

%A V. Vovk
%A A. Gammerman
%T Complexity approximation principle
%J COMPJ
%V 42
%N 4
%P 318-322
%D 1999
%K jrnl, COMPJ, CAP
%X [also search for: MML MDL]

%A R. A. Baxter
%A J. J. Oliver
%T Finding overlapping components with MML
%J Stats and Comp.
%I Kluwer
%V 10
%N 1
%P 5-16
%M JAN
%D 2000
%K jrnl, MML, MDL, mixture model, models, modelling, statistics, Normal,
   unsupervised classification, Gaussian, clustering, soft, overlap,
   learning, alorithm, discovery, c2000, c200x, c20xx, zz0701, jono, ultimode
%X "We use minimum message length (MML) estimation for mixture modelling. MML
   estimates are derived to choose the # of components in the m.model to best
   describe the data & to est. the parameters of the component densities for
   Gaussian m.models. An empirical comparison of criteria prominent in the
   literature for estimating the # of components in a data set is performed."
   -- [<A HREF="https://doi.org/10.1023/A:1008928315401">doi:doi.org/10.1023/A:1008928315401</A>]['23],
    ? 10.1.1.12.6240@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.12.6240">c'teseer</A>]['18],ps@[<A HREF="http://www.act.cmis.csiro.au/rohanb/PAPERS/overlapping_mixtures.ps">cs'ro</A>][5/'04].
   [Also search for: MML mixture model].

%A G. E. Farr
%A C. S. Wallace
%T Algorithmic and combinatorial problems in strict minimum message length
   inference
%J Res. in Combinatorial Algorithms
%P 50-58
%D 1997
%K jrnl, MML, SMML, c1997, c199x, c19xx, zz0801, binomial, trinomial,
   multinomial distribution, inductive inference, II, AI, GFarr, CSW, CSWallace
%X Construction of the SMML estimator is NP-hard for most distributions.
   The only two dist' for which it has been constructed are
   binomial & trinomial.
   Also see: Farr and Wallace, Comp. Jrnl., Vol.45(3), '02,
   and [<A HREF="http://www.allisons.org/ll/MML/">MML</A>],
   or [also search for: MML].

%A G. W. Rumantir
%T Minimum message length criterion for second-order polynomial
   model discovery
%J PAKDD 2000
%I SpringerVerlag
%S LNAI
%V 1805
%P 40-48
%M APR
%D 2000
%K conf, PAKDD00, PAKDD2000, polynomials, regression, inductive inference, II,
   minimum message length, MML, description, MDL, zz0202
%X author at  M o n a s h  uni  2/'02.

%A G. W. Rumantir
%T Tropical cyclone intensity forecasting model: Balancing complexity and
   goodness of fit
%J PRICAI 2000
%I SpringerVerlag
%S LNAI
%V 1886
%P 230-240
%D 2000
%K conf, PRICAI00, PRICAI2000, weather, minimum message length, MML,
   predict, prediction, forecast, description, over fitting, overfitting,
   inductive inference, II, MDL, zz0202
%X author at  M o n a s h  uni  2/'02.

%A D. L. Donoho
%T (Wald Lecture 1) Counting bits with Kolmogorov and Shannon
%I Dept. of Stats., Stanford Univ.
%R 38
%D 2000
%K TR, c2000, c200x, c20xx, information theory, stats, rate distortion,
   Gaussian process, GaussianProcess, epsilon entropy, ellipsoids, MML, MDL,
   inductive inference, Donoho, donohue, donahue
%X "Shannon's rate-distortion theory describes the # of bits needed to approx.
   represent typical realizations of a stochastic process X=(X(t):t in T ),
   while Kolmogorov's eps-entropy describes the # of bits needed to approx.
   represent an arbitrary member f=(f(t):t in T) of a fn class F. For many
   stochastic processes a great deal is known about the behavior of the rate
   distortion fn, while for few functional classes F has there been success..."
   -- cached@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.26.2909">c'teseer</A>]['21],
      was [<A HREF="http://www-stat.stanford.edu/reports/abstracts/00-38.ps">TR@stanford</A>]['07].
   (auth@[<A HREF="https://statweb.stanford.edu/~donoho/">Stanf</A>]['18].)
   Also see GP@[<A HREF="https://en.wikipedia.org/wiki/Gaussian_process">wikip</A>]['21].
   [Also search for: GaussianProcess].

%A G. W. Rumantir
%A C. S. Wallace
%T Sampling highly correlated data for polynomial regression and model discovery
%J IDA 2001
%S SpringerVerlag
%S LNCS
%V 2189
%P 370-377
%M SEP
%D 2001
%K conf, IDA01, IDA2001, polynomials, regression, inductive inference, II,
   Intelligent Data Analysis, minimum message length, MML, description, MDL,
   GWR, GWRumantir, CSW, CSWallace, c2001, c200x, c20xx, zz0202, models
%X "The usual way of conducting empirical comparisons among competing polynomial
   model selection criteria is by generating artificial data from created true
   models with specified link weights. The robustness of each model seln
   criterion is then judged by its ability to recover the true model from its
   sample data sets with varying sizes and degrees of noise.
   If we have a set of multivariate real data & have empirically found a poly.
   regression model that is so far seen as the right model represented by the
   data, we would like to be able to replicate the multivariate data
   artificially to enable us to run multiple experiments to achieve two
   objectives. First, to see if the model selection criteria can recover the
   model that is seen to be the right model. Second, to find out the min. sample
   size required to recover the right model. ...
   proposes a methodology to replicate real multivariate data using its
   covariance matrix and a polynomial regression model seen as the right model
   represented by the data. The sample data sets generated are then used for
   model discovery experiments."
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-44816-0_37">doi:10.1007/3-540-44816-0_37</A>]['11].
   Author at  M o n a s h  uni  2/'02.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A G. E. Farr
%A C. S. Wallace
%T The complexity of strict minimum message length inference
%J COMPJ
%V 45
%N 3
%P 285-292
%D 2002
%K CompJ, Jrnl, zz0897, zz0602, c2002, c200x, c20xx, algorithmic complexity, NP,
   NPC, NPH, theory, SMML, MDL, MML, AI, II, GFarr, CSW, CSWallace, binomial,
   trinomial, multinomial, probability distribution, information theory
%X "Strict Minimum Message Length (SMML) inference is an information-theoretic
   criterion for inductive inference introduced by Wallace & Boulton & is known
   to possess several desirable statistical properties. ...  we examine its
   computational complexity. We give an efficient alg. for the binomial case &
   indeed for any SMML problem that is essentially 1D in character. The problem
   in general is shown to be NP-hard. A heuristic is discussed which gives good
   results for binomial & trinomial SMML inf.. The complexity of the trinomial
   case remains open & is worth further investigation."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/45.3.285">doi:10.1093/comjnl/45.3.285</A>]['05]
   (Also see [<A HREF="http://www.allisons.org/ll/MML/SMML/Binomial/">SMML</A>].

%A L. Kornienko
%A D. L. Dowe
%A D. W. Albrecht
%T Message length formulation of support vector machines for binary
   classification - a preliminary scheme
%J Proc. 15th Australian Joint Conf. on A.I.
%I SpringerVerlag
%S LNAI
%V 2557
%P 119-130
%M DEC
%D 2002
%K conf, AI, AI2002, MML, MDL, AI, SVM, DLDowe, DWAlbrecht, machine, zz1202,
   LKornienko, hyperplane, c2002, c200x, c20xx
%X "... preliminary ... extrinsic binary class'n by reformulating the
   [SVM] approach in a Bayesian Message Length framework. ... uses the [MML]
   principle as a way of costing each hyperplane via a 2-part message. This
   message defines a separating hyperplane. The length of this message is used
   as an objective function for a search through the hypothesis space of
   possible hyperplanes used to dichotomise a set of data points.
      2 prelim. MML implementations ... differ in the (Bayesian) coding
   schemes used and the search procedures. The generalisation ability of
   these 2 reform. on both artificial and real data sets are compared against
   ... SVMlight, the Lagrangian Support Vector Machine & SMOBR.
      ...all impls. improved as the size of the data sets increased.  [MML]
   tended to perform best on the insep. data sets & the real data set. ..."
   Hint1 [also search for: MML], hint2 [also search for: SVM],
   uk us isbn:3540001972.
   [<A HREF="http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=2557&spage=119">openUrl</A>]['05],
   [<A HREF="http://www.springerlink.com/link.asp?id=0u05ufd81q1tknub">met@press</A>]['05].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A S. F. Hanser
%A L. Doyle
%A J. Jenkins
%A B. McCowan
%T Information theory applied to animal communication systems and
   its possible application to SETI
%J Bioastronomy
%P ?-?
%V 7
%D 2002
%K system, information content, compressibility, communication,
   intelligence, animals, messages, SETI
%X is it a conf?  V6 '99?  V5 '96?
   Hint, [also search for: Hanser].

%A B. McCowan
%A L. Doyle
%A S. F. Hanser
%T Using information theory to assess the diversity, complexity, and
   development of communicative repertoires
%J J. Comparative Psychology
%P 166-172
%V 116
%D 2002
%K jrnl, JCP, information content, compressibility, communication,
   intelligence, animals, messages
%X [also search for: Hanser].

%A I. Zukerman
%A S. George
%T A minimum message length approach for argument interpretation
%J Proc. 3rd SIGdial Workshop on Discourse and Dialogue
%W Philadelphia
%I Assoc. Computational Linguistics
%P 211-220
%M JUL
%D 2002
%K wShop, natural language processing, NLP, MML, MDL, Monash
%X [<A HREF="http://acl.ldc.upenn.edu/W/W02/W02-0227.pdf">pp.pdf@upenn.edu</A>]['04].

%T Pattern Detection and Discovery
%E D. J. Hand
%E N. M. Adams
%E R. J. Bolton
%I Springer
%D 2002
%K book, DJHand, c2002, c200x, c20xx, statistics, stats
%X [<A HREF="http://stats.ma.ic.ac.uk/~djhand/">~djhand/</A>][1/'04].

%A D. L. Donoho
%T The Kolmogorov Sampler
%I Dept. of Stats., Stanford U.
%R 2002-4
%P 42
%M JAN
%D 2002
%K TR, TR4, c2002, c200x, c20xx, statistics, inference, II, MML, MDL, minimum,
   message, description, length, complexity, estimator, MKCE, theory,
   Bayesian, theoretical, Bprocess, StanfordUni, StanfordU
%X "Given noisy observations X[i] = T[i]+Z[i], i=1..n, ...
   consider the Minimum Kolmogorov Complexity Estimator (MKCE), ...
   ... show that the MKCE behaves as a sample from the posterior distribution.
   ... Our proof combines ideas from information theory to get what seems an
   essentially novel conclusion: that when the loss level is equal to the true
   underlying noise level, optimal lossy compression of random process data
   must exhibit reconstructions which look like samples from the correct
   Bayesian posterior. ..."
   -- [<A HREF="https://statweb.stanford.edu/~donoho/Reports/2002/KolmogorovSampler.pdf">pdf</A>]['18],
      [<A HREF="http://www-stat.stanford.edu/~donoho/Reports/2002/KolmogorovSampler.pdf">pdf</A>]['06].
   (auth@[<A HREF="https://statweb.stanford.edu/~donoho/">Stanf</A>]['18].)
   [Also search for: MML]  and  [also search for: oracle inductive inference].

%A Y. Agusta
%A D. Dowe
%T MML clustering of continuous-valued data using Gaussian and t-distributions
%J 15th Australian Joint AI Conf.
%P 143-154
%D 2002
%K conf, c2002, c200x, c20xx, Student, Students, t distribution, tDistribution,
   Agu02, Yudi
%X [<A HREF="http://www.springerlink.com/content/ny4nahk82rg7cm14/">@springer</A>]['06].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Continuous/T/">MML</A>] and
    [also search for: Student MML].)

%A C. S. Calude
%A S. Marcus
%A L. Staiger
%T A topological characterization of random sequences
%J Information Process. Lett.
%V 88
%N 5
%P 245-250
%M DEC
%D 2003
%K jrnl, IPL, c2003, c200x, c20xx, Kolmogorov complexity, MML, MDL,
   information theory, string, strings, sequence
%X "...The set of random sequences is large in the sense of measure,
   but small in the sense of category.  ... "
   [<A HREF="http://dx.doi.org/10.1016/j.ipl.2003.07.002">doi:10.1016/j.ipl.2003.07.002</A>]['07]
   [Also search for: Staiger].

%A E. T. Jaynes
%T Probability Theory
%E G. L. Bretthorst
%I CUP
%P 758
%D 2003
%K book, text, c2003, c200x, c20xx, CUP, inductive inference, II, stats,
   statistics, zz0603,
%X ... dispels the imaginary distinction between probability theory and
   statistical inference, leaving a logical unity and simplicity, which
   provides greater technical power and flexibility in applications. This
   book goes beyond the conventional mathematics of probability theory,
   viewing the subject in a wider context. ... applications of probability
   theory to ... physics, mathematics, economics, chemistry and biology. ...
   2003 stg45;  uk us isbn:0521592712.

%A R. J. Bolton
%A D. J. Hand
%A A. R. Webb
%T Projection techniques for nonlinear principal components analysis
%J Statistics and Computing
%V 13
%P 267-276
%D 2003
%K jrnl, non-linear, component, stats, statistics, c2003, c200x, c20xx, zz0104,
   PCA, DJHand
%X [<A HREF="http://stats.ma.ic.ac.uk/~djhand/">~djhand/</A>][1/'04].

%A G. W. Rumantir
%A C. S. Wallace
%T Minimum message length criterion for second-order polynomial model selection
   applied to tropical cyclone intensity forecasting
%J Int. Symp. Intell. Data Analysis, IDA 2003
%P 486-496
%I SpringerVerlag
%S LNCS
%V 2810
%D 2003
%K conf, IDA, IDA2003, CSW, CSWallace, MML, MDL, models, c2003, c200x, c20xx,
   weather, climate, regression, II, AI, minimum message length, description,
   AIC, SRM, SC, forecast, cyclones, hurricane, storm, strength
%X "... tries to merge polynomial model seln research & tropical cyclone
   forecasting res.. The contributions of the work are 4-fold. First, a new
   criterion based on the [MML] principle specifically formulated for the task
   of polynomial model seln up to the 2nd order is presented. Second, a
   programmed optimisation search alg. for 2nd-order polynomial models that can
   be used in conjunction with any model selection criterion is developed.
   Third, critical examinations of the differences in performance of the various
   criteria ... . Fourth, a novel strategy which uses a synergy between the new
   criterion built based on the MML principle & other model seln criteria namely
   [MDL], Corrected Akaike's Information Criterion, Structured Risk Minimization
   & Stochastic Complexity is proposed. The forecasting model developed using
   this new automated strategy has better performance than the benchmark models
   SHIFOR (Statistical HurrIcane FORcasting) & SHIFOR94 ..."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-45231-7_45">doi:10.1007/978-3-540-45231-7_45</A>]['11].
      [Also search for: polynomial regression] and
      [also search for: polynomial MML].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A M. Viswanathan
%A C. S. Wallace
%T An optimal approach to mining Boolean functions from noisy data
%J Intelligent Data Engineering and Automated Learning
%P 717-724
%I SpringerVerlag
%S LNCS
%V 2690
%M SEP
%D 2003
%O 4th Int. Conf. Intelligent Data Engineering and Automated Learning,
   IDEAL 2003, Hong Kong, China, March 21-23
%K minimum message length, MML, segmentation, description, CSW, CSWallace, MDL,
   Kearns, Murli, boolean, binary function, guaranteed risk minimization,
   conf, IDEAL, AI, II, cross validation, c2003, c200x, c20xx
%X "Data Mining of binary seqs. ... The inference task in this paper, a
   specialized version of the segmentation problem, is the estimation of a
   predefined Boolean function on the real interval [0,1] from a noisy random
   sample. The framework for this problem was introduced by Kearns et al (1997)
   .... This paper presents an optimal approach to mining for Boolean fns from
   noisy data samples based on the [MML] principle. [It] is shown to be optimal
   in comparison to well-known model selection methods based on Guaranteed Risk
   Minimization, Minimum Description Length (MDL) Principle & Cross Validation
   after a thorough empirical evaluation with varying levels of noisy data."
   [<A HREF="http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=2690&spage=717">openurl</A>]['04],  isbn:354040550X.
   Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A J. Comley
%A D. L. Dowe
%T General Bayesian networks and asymmetric languages
%J Hawaii Int. Conf. Statistics and Related Fields (HICS-2)
%M JUN
%D 2003
%K conf, HICS, HICS2, joshc, JComley, DLD, DLDowe, network, dTree,
   c2003, c200x, c20xx, MDL, MML
%X Also see J. Comley's thesis c2005,
   and [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].
   [Also search for: network local structure].

%A G. W. Rumantir
%T A hybrid statistical and feedforward network model for time-series
   forecasting with a limited amount of data
%J Soft Computing Systems: Design, Management and Applications,
   Frontiers in Artificial Intelligence and Applications
%I IOSpress
%P ?-?
%D 2003 (in press)
%K conf, II, AI, GWRumantir, nn, timeSeries, prediction, c2003, c200x, c20xx
%X [<A HREF="http://www.multimedia.monash.edu.au/research/rumantir.html">auth</A>]['04].

%A A. C. Bickerstaffe
%A P. E. Tischer
%T An MML approach for discovering structure in discrete one-dimensional data
%J Proc. Advances in Computer Science and Technology
%W US Virgin Islands
%P ?-?
%D 2004
%K conf, c2004, c200x, c20xx, zz0607, 1D, sequence, discrete, time series, MDL,
   adrianb, description, minimum message length, MML, Markov model, models
%X "... determining the optimal order, lag, & state transition probs. for a
   Markov model given a seq. of discrete data symbols. ...uses [MML] encoding to
   trade-off model complexity against goodness of fit to the data. The encoding
   scheme does not make the assumption of data being waveform in nature - we
   assume no correlation between symbol labels & thus, our method is invariant
   to linear transformations of symbol labels. Experiments using synthetic data
   indicate that our approach to Markov modelling is capable of inferring
   appropriately simple models which capture periodicity & sub-structure present
   in the data. The proposed scheme of Markov modelling compares well against
   elementary correlation coefficient tests & a more complex periodicity
   transform (PT) approach."
   [<A HREF="http://www.actapress.com/PaperInfo.aspx?PaperID=17288">@actapress</A>]['07].

%A G. W. Rumantir
%T A Bayesian framework for tropical cyclone causal and risk analysis
%J Proc. 2nd Int. Conf. on Knowledge Economy and Development in Sci. and Tech.
%W Beijing
%P ?-?
%D 2004 (accepted)
%K conf, MML, MDL, cyclones, cause, model, models, c2004, c200x, c20xx, risks,
   weather, application, GWRumantir
%X auth @ monash '05.

%A J. W. Comley
%A D. L. Dowe
%T Minimum message length and generalized Bayesian nets with asymmetric
   languages
%B Advances in Minimum Description Length: Theory and Applications
%I MITpress
%E P.Grunwald, I.J.Myung, M.A.Pitts
%P 265-294
%M MAY
%D 2005
%K chapter, JWComley, DLDowe, DLD, c2005, c200x, c20xx, net MML, MDL, implicit
%X In, us isbn:0262072629. (via dld 7/6/05).
   [Also search for: Comley thesis c2005] and
   [also search for: network local structure], and
   see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].

%A D. F. Schmidt
%A A. P. Paplinski
%A G. S. Lowe
%T Adaptive control of hydraulic systems with MML inferred RBF networks
%J IEEE Int. Conf. on Robotics and Automation
%P 101-106
%M APR
%D 2005
%K conf, c2005, c200x, c20xx, zz0106, minimum message length, description,
   nonlinear, non-linear, network, system, MDL, ICRA, ICRA05
%X auths@Mon@sh ['05].

%A N. Bouguila
%A D. Ziou
%T MML-based approach for high-dimensional unsupervised learning using the
   generalized Dirichlet mixture
%J IEEE Workshop on Learning in Vision and Pattern Recognition (LCVPR'05)
%P CD-rom
%D 2005
%K wShop, c2005, c200x, c20xx, CVPR05, AI, MDL, AIC, MMDL, HSEM, stats
%X "... determining the structure of high-dimensional data, without prior
   knowledge of the number of clusters. Data are represented by a finite
   mixture model based on the generalized Dirichlet distribution. The g. D.
   distribution has a more general covariance structure than the D. d. ...
   ... The number of clusters is determined using the (MML) principle.
   Parameters est. is done by a hybrid stochastic expectation-maximization
   (HSEM) alg.. ..."
   -- [<A HREF="http://csdl2.computer.org/persagen/DLAbsToc.jsp?resourcePath=/dl/proceedings/&toc=comp/proceedings/cvpr/2005/2372/03/23723toc.xml&DOI=10.1109/CVPR.2005.493#additionalInfo">ieee</A>] ?$ub$cription?,
      [<A HREF="http://www.dmi.usherb.ca/~bouguila/">auth1</A>]['05].
   (Also see D@[<A HREF="https://en.wikipedia.org/wiki/Dirichlet_distribution">wikip</A>]['18].)

%A S. de Rooij
%A P. Grunwald
%T MDL model selection using the ML plug-in code
%J Proc. of the Int. Symp. on Information Theory (ISIT)
%P ?-?
%M SEP
%D 2005
%K conf, c2005, c200x, c20xx, prequential ML code, deRooij
%X [<A HREF="http://homepages.cwi.nl/~rooij/research/isit_prequential.ps">.ps</A>]['05].

%A P. Grunwald
%A S. de Rooij
%T Asymptotic log-loss of prequential maximum likelihood codes
%J 18th Annual Conf. on Learning Theory (COLT)
%I SpringerVerlag
%P 652-667
%D 2005
%K conf, c2005, c200x, c20xx, code, coding, minimum description length, MDL,
   encoding, adaptive, Dawid, Rissanen
%X "...analyze the Dawid-Rissanen prequential maximum likelihood codes relative
   to 1-parameter exponential family models M.  If data are i.i.d. according to
   an (essentially) arbitrary P, then the redundancy grows at rate 1/2 cln n.
   We show that c = s1**2/s2**2, where s1**2 is the variance of P, and s2**2 is
   the variance of the distribution M* in M that is closest to P in KL-div..
   This shows that prequential codes behave quite differently from other
   important universal codes such as the 2-part MDL, Shtarkov & Bayes codes, for
   which c=1. This behavior is undesirable in an MDL model selection setting."
   pdf: [<A HREF="http://dx.doi.org/10.1007/11503415_44">doi:10.1007/11503415_44</A>]['07]; isbn:3540265562.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A M. Viswanathan
%A Y.-K. Yang
%A T. K. Whangbo
%T Minimum message length and classical methods for model selection in
   univariate polynomial regression
%J ETRI J.
%V 27
%N 6
%P 747-758
%M DEC
%D 2005
%K jrnl, Murli, c2005, c200x, c20xx, MML, MDL, polynomial, fitting, Akaike, FPE,
   AIC, Schwartz, SCH, SRM, criteria, criterion, model selection,
   statistical test, stats, testing, polynomials
%X "... presents an empirical study of the [FPE, AIC, SCH, GCV, MML, MDL, SRM]
   principles in the context of model selection, where the models under
   consideration are univariate polynomials. ... includes a detailed empirical
   evaluation of the model selection methods on six target functions, with
   varying sample sizes and added Gaussian noise. The results from the study
   appear to provide strong evidence in support of the MML- and SRM- based
   methods over the other standard approaches (FPE, AIC, SCH and GCV)."
   -- [<A HREF="http://dx.doi.org/10.4218/etrij.05.0104.0180">doi:10.4218/etrij.05.0104.0180</A>]['11].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A Y. Agusta
%T Minimum message length mixture modelling for uncorrelated and
   correlated continuous data applied to mutual funds classification
%I Monash University
%D 2005
%K PhD thesis, c2005, c200x, c20xx, t-distribution, tDistribution, Yudi,
   mutual fund, Agu05, MML, csse
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].)

%A S. de Rooij
%A P.D. Grunwald
%T An empirical study of MDL model selection with infinite parametric
   complexity
%J J. Math. Psychology
%V 50
%N 2
%P 180-192
%D 2006
%K jrnl, deRoij, c2006, c200x, c20xx, MDL, NML, II, Poisson, Geometric,
   distribution, model selection
%X "Parametric complexity is a central concept in MDL model seln. In practice
   it often turns out to be infinite, even for quite simple models such as the
   Poisson & Geometric families. In such cases, MDL model selection as based on
   NML & Bayesian inference based on Jeffreys' prior cannot be used. Several
   ways to resolve this problem have been proposed. ... experiments to compare
   & evaluate their behaviour on small sample sizes. We find interestingly poor
   behaviour for the plug-in predictive code; a restricted NML model performs
   quite well but it is questionable if the results validate its theoretical
   motivation. The Bayesian model with the improper Jeffreys' prior is the most
   dependable."
   -- [<A HREF="http://www.cwi.nl/~pdg/ftp/modselstudy.pdf">pdf</A>]['06].
   [Also search for: geometric Poisson].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Discrete/Integers/Geometric/">geom. & P.</A>].)

%A J. Rissanen
%T The structure function and distinguishable models of data
%J COMPJ
%V 49
%N 6
%P 657-664
%M NOV
%D 2006
%K COMPJ, jrnl, c2006, c200x, c20xx, MDL, model
%X [<A HREF="http://dx.doi.org/10.1093/comjnl/bxl045">doi:10.1093/comjnl/bxl045</A>]['06].

%A R. T. O'Donnell
%A A. E. Nicholson
%A B. Han
%A K. B. Korb
%A M. J. Alam
%A L. R. Hope
%T Causal discovery with prior information
%J 19th ACS Australian Joint Conf. on Artificial Intelligence (AI2006)
%I SpringerVerlag
%S LNCS
%V 4304
%P 1162-1167
%M DEC
%D 2006
%K conf, priors, c2006, c200x, c20xx, Bayesian networks, CaMML, MML, MDL,
   minimum message length, description, network, KBKorb, annn, rodo,
   experts, Bnet, Bnets
%X "Bayesian networks (BNs) are rapidly becoming a leading tool in applied [AI].
   BNs may be built by eliciting expert knowledge or learned via causal
   discovery programs. A hybrid approach is to incorporate prior information
   elicited from experts into the causal discovery process. We present several
   ways of using expert information as prior probabilities in the CaMML causal
   discovery program."   uk us isbn13:978-3540497875.
   -- [<A HREF="http://dx.doi.org/10.1007/11941439_141">doi:10.1007/11941439_141</A>]['06]
   [Also search for: CaMML],  [and for: causal model], and
   see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].

%A T. Maheswaran
%A J. G. Sanjayan
%A D. Dowe
%A P. J. Tan
%T MML mixture models of heterogeneous Poisson processes with uniform outliers
   for bridge deterioration
%J 19th ACS Australian Joint Conf. on Artificial Intelligence (AI2006)
%I SpringerVerlag
%S LNCS
%V 4304
%P 322-331
%M DEC
%D 2006
%K conf, c2006, c200x, c20xx, MML, MDL, stats, bridges, engineering, outlier
%X "Effectiveness of maintenance programs of existing concrete bridges is highly
   dependent on the accuracy of the deterioration parameters utilised in the
   asset mgmt models of the bridge assets..."  uk us isbn13:978-3-540-49787-5.
   -- [<A HREF="http://dx.doi.org/10.1007/11941439">doi:10.1007/11941439</A>]['06].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Discrete/Integers/Poisson/">MML/Poisson</A>].)
   [Also search for: outlier MML].

%A J. Rissanen
%T Information and Complexity in Statistical Modeling
%I Springer
%S Information Science and Statistics
%P 142
%D 2007
%K book, text, c2007, c200x, c20xx, model, modelling, theory, stats,
   minimum description length, encoding, MDL, NML, SC, Rissanen, Rissannen
%X "No statistical model is "true" or "false," "right" or "wrong"; the models
   just have varying performance, which can be assessed. The main theme in this
   book is to teach modeling based on the principle that the objective is to
   extract the information from data that can be learned with suggested classes
   of probability models. The intuitive and fundamental concepts of complexity,
   learnable information, and noise are formalized, which provides a firm
   information theoretic foundation for statistical modeling. Although the
   prerequisites include only basic probability calculus and statistics, a
   moderate level of mathematical proficiency would be beneficial."
   hb, us$45; isbn:0387366105; isbn13:9780387366104.
   [Also search for: MDL].
   (Also see a [<A HREF="http://www.allisons.org/ll/MML/2005book.html">related book</A>].)

%A P. D. Grunwald
%T The Minimum Description Length Principle
%I MITpress
%D 2007
%P 703
%K book, text, c2007, c200x, c20xx, MDL, MML, II, AI
%X hb, us$37, uk us isbn:0262072815; uk us isbn13:9780262072816.
   (Also see a [<A HREF="http://www.allisons.org/ll/MML/2005book.html">relevant book</A>].)
   [Also search for: II minimum length].

%A R. J. Solomonoff
%T Three kinds of probabilistic induction: Universal distributions and
   convergence theorems
%J COMPJ
%V 51
%N 5
%P 566-570
%M SEP
%D 2008
%K jrnl, COMPJ, c2008, c200x, c20xx, zz0908, MML, MDL, II, kind, theorem,
   distribution
%X "... describe 3 kinds of prob. induction problems, & give general solutions
   for each, with assoc. convergence thms which show that they tend to give good
   prob. ests.. The 1st kind extrapolates a seq. of strings &/or numbers. The
   2nd extrapolates an unordered set of strings &/or numbers. The 3rd
   extrapolates an unordered set of ordered pairs of elements that may be
   strings &/or numbers. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm120">doi:10.1093/comjnl/bxm120</A>]['08].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A M. A. Jorgensen
%A G. J. McLachlan
%T Wallace's approach to unsupervised learning: The Snob program
%J COMPJ
%V 51
%N 5
%P 571-578
%M SEP
%D 2008
%K jrnl, COMPJ, c2008, c200x, c20xx, zz0908, Wallace, Snob, mixture modelling,
   model, intro, survey, hard, total, soft, partial assignment, MML, MDL, AIC,
   Bayesian, BIC, complexity, information, clustering, cluster, class, Gaussian,
   classification, expectation maximization, SMEM, EM algorithm, maximisation
%X "We describe the Snob program for unsupervised learning as it has evolved
   from its beginning in the 1960s until its present form. Snob uses the
   minimum message length principle ...  pay particular attention to the
   revision of Snob in the 1980s where definite assignment of things to
   classes was abandoned."  Online Jan 2008.
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm121">doi:10.1093/comjnl/bxm121</A>][6/'08].
   [Also search for: Wallace Snob MML].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">C.S.Wallace's publications</A>].)

%A R. J. Solomonoff
%T The probability of "undefined" (non-converging) output in generating the
   universal probability distribution
%J IPL
%V 106
%N 6
%P 238-240
%M JUN
%D 2008
%K jrnl, IPL, c2008, c200x, c20xx, information theory, MML, MDL, AIC, BIC,
   Kolmogorov complexity, loop, diverge, divergent, non-converging
%X "... to generate a universal prob. dist. to extrapolate a binary string x of
   length i, we feed random bits into a universal device, M. When we find an
   input string that gives an output matching x, we continue the successful
   input with random bits until M produces a zero or one as output. The relative
   probs. of these 2 continuations can give a normalized prediction for the
   prob. of the symbol following x. There is, however, a prob., P[i+1](u) that
   the continued random input string will not generate any output for the
   (i+1)th symbol.
   We will show E[mu]SUM[i=1..n] P[i]mu <= k[mu]ln(2). Here E[mu] is the
   expected value with respect to mu, the prob.dist. that created x.  k[mu] is
   the Kolmogorov complexity of mu with respect to M. n is any +ve int.. Usually
   we do not know mu & so we do not know k[mu]. However, if mu is the uniform
   dist., we can usually find a good upper bound for k[mu].
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2007.11.018">doi:10.1016/j.ipl.2007.11.018</A>]['08].

%A E. Makalic
%A D. F. Schmidt
%T Minimum message length shrinkage estimation
%J Statistics & Probability Letters
%V 79
%N 9
%P 1155-1161
%M MAY
%D 2009
%O Tech. Report 229, FIT, Monash U., Sept. 2008,
   pdf@[<A HREF="http://www.csse.monash.edu.au/publications/2008/tr-2008-229-full.pdf">monash</A>]['08].
%K jrnl, stats, c2009, c200x, c20xx, zz1109, minimum description length, mmld,
   MDL, message, MML, shrinkage estimation, estimate, model, statistics, normal,
   hierarchical, Bayesian, James, Stine, estimator, multivariate, Gaussian,
   hyperparameters, parameter, probability, dowe, enesm, DEnes
%X "... considers estimation of the mean of a multivariate Gaussian dist'n with
   known variance within the Minimum Message Length (MML) framework.
   Interestingly, the resulting MML estimator exactly coincides with the
   positive-part James-Stein estimator under the choice of an uninformative
   prior. A new approach for estimating parameters & hyperparameters in general
   hierarchical Bayes models is also presented."
   -- [<A HREF="http://dx.doi.org/10.1016/j.spl.2008.12.021">doi:10.1016/j.spl.2008.12.021</A>]['09],
   & @[<A HREF="http://www.csse.monash.edu.au/~dschmidt/MMLShrinkageEstimationMakalicSchmidt2008-SPL-final.pdf">mon@sh</A>]['08].

%A D. F. Schmidt
%A E. Makalic
%T Universal models for the exponential distribution
%J IEEE Trans. Information Theory
%V 55
%N 7
%P 3087-3090
%M JUL
%D 2009
%K jrnl, stats, c2009, c200x, c20xx, zz1109, enesm, minimum description length,
   MML, message, sequential normalized maximum likelihood, SNML, MDL,
   conditional, CNML, Bayes mixture, code, BMC, normalised, model, aic,
   information theory, statistics, exponential distribution, AIT, SC,
   probability, universal model, DEnes
%X "... problem of constructing info.theoretic universal models for data
   distributed according to the exponential dist'n. The universal models
   examined inc. the sequential normalized maximum likelihood (SNML) code,
   conditional normalized maximum likelihood (CNML) code, the minimum message
   length (MML) code, & the Bayes mixture code (BMC). The CNML code yields a
   code length identical to the Bayesian mixture code, & within O(1) of the MML
   code length, with suitable data driven priors. "
   -- [<A HREF="http://dx.doi.org/10.1109/TIT.2009.2018331">doi:10.1109/TIT.2009.2018331</A>]['09],
   & @[<A HREF="http://www.csse.monash.edu.au/~dschmidt/SchmidtMakalic_UniversalModelsForExponential_2009.pdf">mon@sh</A>]['09].

%A D. F. Schmidt
%A E. Makalic
%T MML invariant linear regression
%J Australasian Conf. on Artificial Intelligence
%I SpringerVerlag
%S LNCS
%V 5866
%P 312-321
%D 2009
%K conf, c2009, c200x, c20xx, zz0410, enesm, minimum message length, MML,
   description, linear regression, MDL, minimax, squared error loss, SC, NLM,
   information, model, stats
%X "... derives 2 new info.theoretic linear regression criteria based on the
   minimum message length principle. Both ... invariant to full rank affine
   transformations of the design matrix & yield estimates that are minimax with
   respect to squared error loss. The new criteria are compared against state of
   the art info.theoretic model seln criteria on both real & synthetic data &
   show good performance in all cases."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-10439-8_32">doi:10.1007/978-3-642-10439-8_32</A>]['10],
   uk us isbn13:978-3642104381.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A E. Makalic
%A D. F. Schmidt
%T Fast computation of the Kullback-Leibler divergence and exact Fisher
   information matrix for the first-order moving average model
%J IEEE Signal Processing Letters
%V 17
%N 4
%P 391-393
%M APR
%D 2010
%K jrnl, c2010, c201x, c20xx, zz0610, enesm, Kullback-Leibler divergence, KL,
   distance, MML, MDL, first order, moving average model, time series, DEnes
%X "... two first-order Gaussian moving average models in O[n](1) time
   as the sample size -> infinity. ... also Fisher I.M. in O[n](1) time ..."
   -- [<A HREF="http://dx.doi.org/10.1109/LSP.2009.2039659">doi:10.1109/LSP.2009.2039659</A>]['10]; issn:1070-9908.
   auth1@[<A HREF="http://www.emakalic.org/">www</A>]['10].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A P. Miettinen
%A J. Vreeken
%T Model order selection for boolean matrix factorization
%J KDD '11
%P 51-59
%D 2011
%K conf, KDD, KDD11, c2011, c201x, c20xx, zz0413, binary, Boolean, matrix,
   matrices, BMF, factor, factors, factorization, decomposition, MDL
%X "Matrix factorizations ... data m. is approximated by a product of >=2 factor
   matrices ... often used to separate global struct. from noise. [But] requires
   solving the 'model order seln problem' ... where fine-grained struct. stops,
   & noise starts, i.e., what is the proper size of the factor matrices. Boolean
   m.factorization (BMF) ... has received increased attention ... has desirable
   properties, such as high interpretability & natural sparsity. ... we propose
   to use the [MDL] principle for this task. ... has numerous benefits, e.g., it
   is automatic, does not require a likelihood fn, is fast, &, as experiments
   show, is highly accurate. ... formulate the desc.length fn for BMF in general
   - making it applicable for any BMF alg.. We extend an existing alg. for BMF
   to use MDL to identify the best [BMF], analyze the complexity of the problem
   ... experimental evaln ..."
   -- [<A HREF="http://dx.doi.org/10.1145/2020408.2020424">doi:10.1145/2020408.2020424</A>]['13] via njh. uk us isbn13:978-1450308137.
   [Also search for: MDL factors]  and  [also search for: matrix decomposition].

%A S. M. Moser
%A P.-N. Chen
%T A Student's Guide to Coding and Information Theory
%I CUP
%P 206
%M FEB
%D 2012
%K book, text, CUP, c2012, c201x, c20xx, zz0412, intro, information theory,
   L3Ref, L4Ref
%X 1st ed 2012; hb us$85; uk us isbn:1107015839; uk us isbn13:978-1107015838;
                pb us$30; uk us isbn:1107601967; uk us isbn13:978-1107601963.
   "... introducing beginners to the engineering background of modern comm.sys.,
   from mobile phones to data storage. Assuming only basic knowledge of high-
   -school maths. & inc. many practical e.g.s & ex. to aid understanding ...
   ideal for anyone who needs a quick intr. to the subject."
   [Also search for: information theory book].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Notes/Information/">MML</A>].)

%A P. Rocchi
%T What is information? Beyond the jungle of information theories
%J COMPJ
%V 55
%N 7
%M JUL
%D 2012
%O ? ACM 2011-2011 ?
%K jrnl, Compj, c2012, c201x, c20xx, zz0812, information, theory, origin,
   Hartley, analog, analogue
%X "Digital experts rigorously apply the principles of sharpness & semantics
   whereas analog experts pay less attention to these principles. ... put
   fwd a way to distinguish the digital paradigm from the analog paradigm: the
   former adheres to these principle through precise rules; the latter adheres
   to them in generic and imprecise terms."
      "... radio engineer R.V.L. Hartley was the 1st to develop a th. of info.
   that was not centered on humans. In his 1928 paper, he intr. the word
   'information' ...    we have inventoried over twenty-five information
   theories proposed during the last six decades. ... "  [12 refs].
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxs079">doi:10.1093/comjnl/bxs079</A>]['12].

%A J. Gleick
%T The Information: A History, a Theory, a Flood
%I Vintage
%P 544
%D 2012
%K book, text, c2012, c201x, c20xx, zz1212, information theory, IT,
   communication, encoding, codes, message, computing, technology
%X pb us$12; uk us isbn:1400096235; uk us isbn13:978-1400096237.
   "...  from the language of Africa's talking drums to the invention of written
   alphabets; from the electronic transmission of code to the origins of
   information theory, into the new information age and the current deluge of
   news, tweets, images, and blogs. Along the way, G. profiles key innovators,
   inc. Charles Babbage, Ada Lovelace, Samuel Morse, and Claude Shannon ..."
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A D. F. Schmidt
%A E. Makalic
%T Minimum message length inference and mixture modelling of inverse Gaussian
   distributions
%J 25th Australasian Joint Conf. AI
%W Sydney
%I SpringerVerlag
%S LNCS
%V 7691
%P 672-682
%M DEC
%D 2012
%K conf, AI2012, c2012, c201x, c20xx, zz1016, stats, II, MML, mdl, information,
   inverse Gaussian, inverseGaussian, normal
%X "... problem of modelling continuous, +ve data by finite mixtures of inverse
   Gaussian distns using the minimum message length (MML) principle. We derive
   a message length expression for the inverse Gaussian distn, & prove that the
   param. estimator obtained by minimising this message length is superior to
   the regular max. likelihood estimator in terms of Kullback-Leibler
   divergence. Experiments on real data demonstrate the potential benefits of
   using inverse Gaussian mixture models for modelling cts, +ve data,
   particularly when the data is concentrated close to the origin or exhibits a
   strong positive skew."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-35101-3_57">doi:10.1007/978-3-642-35101-3_57</A>]['16],  uk us isbn13:978-3642351013.
   ("... pdf(x) = sqrt(lambda/(2 pi x^3)).exp(-lambda(x-mu^2)/(2 mu^2 x)),
    for x > 0, ... mean = mu, variance = mu^3 / lambda ...
    ... The name can be misleading: it is an 'inverse' only in that, while
    the G. describes a Brownian Motion's level at a fixed time, the inverse G.
    describes the distn of the time a Brownian Motion with +ve drift takes to
    reach a fixed positive level. ..."
    -- IG@[<A HREF="https://en.wikipedia.org/wiki/Inverse_Gaussian_distribution">wikip</A>].)
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A D. F. Schmidt
%A E. Makalic
%T Minimum message length ridge regression for generalized linear models
%J 26th Australasian Joint Conf. AI
%W Dunedin
%I SpringerVerlag
%S LNCS
%V 8272
%P 408-420
%M DEC
%D 2013
%K conf, AI2013, c2013, c201x, c20xx, zz1016, MML, mdl, aic, ridge regression,
   Tikhonov regularization, generalized linear model, GLM, stats
%X "... ridge parameter estimation criterion for generalized linear models based
   on the minimum message length principle. The criterion is highly general in
   nature, & handles a range of target distributions, inc. the normal, binomial,
   Poisson, geometric & gamma distributions. Estimation of the regression
   parameters, the ridge hyperparameter & the set of covariates assoc. with the
   targets is all performed within the same framework ..."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-319-03680-9_41">doi:10.1007/978-3-319-03680-9_41</A>]['16],  uk us isbn13:978-3319036793.
   (Also see RR@[<A HREF="https://en.wikipedia.org/wiki/Ridge_regression">wikip</A>]['16].)
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. G. Dowty
%T SMML estimators for 1-dimensional continuous data
%J COMPJ
%V 58
%N 1
%P 126-133
%M JAN
%D 2015
%K jrnl, COMPJ, c2014, c201x, c20xx, zz0115, MML, SMML, mmld, mdl, model, aic,
   strict minimum message length, information, description, 1D, distribution,
   AI, II, stats, statistics
%X "A method is given for calculating the strict minimum message length (SMML)
   estimator for 1-D exponential families with cts sufficient stats.. A set of
   n eqns are found that the n cut-points of the SMML est. must satisfy. These
   eqns can be solved using Newton's method & this approach is used to produce
   new results & to replicate results that C.S.Wallace obtained. A rigorous
   proof is also given that the length of the 2-part code corr. to the SMML
   est. is a cts fn of the data, even though this length is composed of step
   functions."   [Online 23 Dec.,'13.]
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxt145">doi:10.1093/comjnl/bxt145</A>]['14].
   [Also search for: MML SMML].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/SMML/">SMML</A>].)

%A J. G. Dowty
%T SMML estimators for linear regression and tessellations of hyperbolic space
%J arXiv
%M MAR
%D 2014
%K TR, c2014, c201x, c20xx, zz0115, MML, SMML, strict minimum message length,
   linear regression, II, stats
%X "The strict minimum message length (SMML) principle links data compression
   with inductive inference. The corr. estimators have many useful properties
   but they can be hard to calculate. We investigate SMML estimators for linear
   regression models & we show that they have close connections to hyperbolic
   geometry. When equipped with the Fisher info. metric, the linear regn model
   with p covariates & a sample size of n becomes a Riemannian manifold, & we
   show that this is isometric to (p+1)-dim. hyperbolic space H^(p+1) equipped
   with a metric tensor which is 2n times the usual metric tensor on H^(p+1).
   A natural identification then allows us to also view the set of sufficient
   statistics for the linear regn model as a hyperbolic space. We show that the
   partition of an SMML est. corr. to a tessellation of this hyperbolic space."
   -- 1403.2201@[<A HREF="http://arxiv.org/abs/1403.2201">arXiv</A>]['15].
   [Also search for: MML SMML].

%A G. Barmpalias
%A R. G. Downey
%A Kobayashi compressibility
%J arXiv
%M AUG
%D 2016
%K TR, c2016, c201x, c20xx, zz0816, Kobayashi compressibility, binary,
   sequences
%X "Kobayashi introduced a uniform notion of compressibility of infinite binary
   seqs. in terms of relative Turing computations with sub-linear use of the
   oracle. K.compressibility has remained a relatively obscure notion, with the
   exception of some work on resource bounded Kolmogorov complexity. The main
   goal of this note is to show that it is relevant to a # of topics in current
   research on algorithmic randomness. We prove that K.compressibility can be
   used in order to define Martin-Loef randomness, a strong version of finite
   randomness & Kurtz randomness, strictly in terms of Turing redns. [&] these
   randomness notions naturally corr. to Turing reducibility, weak truth-table
   reducibility & truth-table reducibility respectively. Finally we discuss
   Kobayashi's main result from his 1981 tech.rep. regarding the compressibility
   of computably enumerable sets ..."
   -- 1608.00692@[<A HREF="http://arxiv.org/abs/1608.00692">arXiv</A>]['16].

%A D. Ellman
%T What can logic contribute to information theory?
%X arXiv
%M SEP
%D 2016
%K TR, c2016, c201x, c20xx, zz0916, maths, logic, probability, partition,
   subset, logical entropy
%X "Logical probability theory was developed as a quantitative measure based on
   Boole's logic of subsets. But info. theory was developed into a mature theory
   by Claude Shannon with no such connection to logic. But a recent development
   in logic changes this situation. In category theory, the notion of a subset
   is dual to the notion of a quotient set or partition, & recently the logic of
   partitions has been developed in a parallel relationship to the Boolean logic
   of subsets (subset logic is usually mis-specified as the special case of
   propositional logic). What then is the quantitative measure based on
   partition logic in the same sense that logical prob. theory is based on
   subset logic? It is a measure of information that is named "logical entropy"
   in view of that logical basis. This paper develops the notion of logical
   entropy & the basic notions of the resulting logical info. theory. Then an
   extensive comp'n is made with the corr. notions based on Shannon entropy."
   -- 1609.02422@[<A HREF="http://arxiv.org/abs/1609.02422">arXiv</A>]['16].
   (Also see [<A HREF="http://arxiv.org/abs/1301.5607">2013</A>].)

%A D. F. Schmidt
%A E. Makalic
%A J. L. Hopper
%T Approximating message lengths of hierarchical Bayesian models using
   posterior sampling
%J Australasian Joint Conf. in AI
%W Hobart
%P 482-294
%M NOV
%D 2016
%K conf, AJCAI, AI, c2016, c201x, c20xx, zz0418, II, MML, MMLh, dowe, MDL,
   EnesM, dfschmidt
%X "... we adapt ideas from the information theoretic minimum message length
   principle & propose a powerful yet simple model selection criteria for
   general hierarchical Bayesian models called MML-h. Computation of this
   criterion requires only that a set of samples from the posterior distribution
   be available. The flexibility of this new algorithm is demonstrated by a
   novel application to state-of-the-art Bayesian hierarchical regression
   estimation. Simulations show that the MML-h criterion is able to adaptively
   select between classic ridge regression & sparse horseshoe regression
   estimators, & the resulting procedure exhibits excellent robustness to the
   underlying structure of the regression coefficients."
   -- [<A HREF="https://doi.org/10.1007/978-3-319-50127-7_41">doi:10.1007/978-3-319-50127-7_41</A>]['18].
   (Conf., print pp.729, uk us isbn:3319501267; uk us isbn13:978-3-319-50126-0.)

%A M. Andreev
%T Busy beavers and Kolmogorov complexity
%J arXiv
%M MAR
%D 2017
%K TR, c2017, c201x, c20xx, zz0317, busy beaver, machine, Rado
%X "The idea to find the 'maximal number that can be named' can be traced back
   to Archimedes (see his Psammit). From the viewpoint of compn theory the
   natural q. is 'which # can be described by at most n bits?' This
   q. led to the defn of the so-called 'b.b.' #s (intro. by T.
   Rado). ... consider different versions of the b.b.-like notions
   defined in terms of Kolmogorov complexity. We show that [they] differ
   depending on the version of complexity used (plain, prefix, or a priori
   complexities) & find out how these notions are related, providing matching
   lower & upper bounds."
   -- 1703.05170@[<A HREF="https://arxiv.org/abs/1703.05170">arXiv</A>]['17].
   [Also search for: busy beaver].

%A C. K. Wong
%A E. Makalic
%A D. F. Schmidt
%T Minimum message length inference of the Poisson and geometric models using
   heavy-tailed prior distributions
%J arXiv
%M AUG
%D 2017
%K TR, c2017, c201x, c20xx, zz0817, MML, MDL, Poisson, geometric, DEnes,
   prior, Bayesian, normalized maximum likelihood
%X "[MML] is a general Bayesian principle for model selection & parameter
   estimation that is based on information theory. This paper applies [MML] to
   a small-sample model seln problem involving Poisson & geometric data models.
   Since MML is a Bayesian principle, it requires prior distributions for all
   model params.. We introduce three candidate prior distns for the unknown
   model parameters with both light- & heavy-tails. The performance of the MML
   methods is compared with objective Bayesian inference & [MDL] techniques
   based on the normalized maximum likelihood code. Simulations show that our
   MML approach with a heavy-tail prior distribution provides an excellent
   performance in all tests."
   -- 1708.02742@[<A HREF="https://arxiv.org/abs/1708.02742">arXiv</A>]['17].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A C. K. Wong
%A E. Makalic
%A D. F. Schmidt
%T A minimum message length criterion for robust linear regression
%J arXiv
%M FEB
%D 2018
%K TR, c2018, c201x, c20xx, zz0518, MML, mdl, robust linear regression, DEnes,
   Student-t distribution, StudentT, scale mixture, scaleMixture
%X "... inference of linear regression models with Student-t errors. A new
   criterion for var. selection & parameter estimation in Student-t regression
   is proposed. By exploiting properties of the regression model, we derive a
   suitable non-informative proper uniform prior distn for the regression
   coefficients that leads to a simple & easy-to-apply criterion.  ... does not
   require spec. of hyperparameters & is invariant under both full rank
   transformations of the design matrix & linear transformations of the
   outcomes. We comp are the proposed criterion with several ..."
   -- 1802.03141@[<A HREF="https://arxiv.org/abs/1802.03141.pdf">arXiv</A>]['18].
   [Also search for: scaleMixture].

%A V. Palade
%A J. G. Wolff
%T A roadmap for the development of the 'SP Machine' for artificial intelligence
%J COMPJ
%M NOV
%D 2019
%K jrnl, COMPJ, c2019, c201x, c20xx, zz1119, AI, SP machine, SPmachine
%X "... describes a roadmap for the development of the SP Machine, based on the
   SP Theory of Intelligence and its realization in the SP Computer Model. The
   SP Machine will be developed initially as a software virtual machine with
   high levels of parallel processing, hosted on a high-performance computer.
   The system should help users visualize knowledge structures and processing.
   Research is needed into how the system may discover low-level features in
   speech and in images. ... A computer model is needed of SP-Neural, the
   version of the SP Theory expressed in terms of neurons and their
   interconnections. The SP Machine has potential in many areas of application,
   several of which may be realized on short-to-medium timescales."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxy126">doi:10.1093/comjnl/bxy126</A>]['19].

%A E. Makalic
%A D. F. Schmidt
%T MML probabilistic principal component analysis
%J arXiv
%M SEP
%D 2022
%K TR, c2022, c202x, c20xx, zz1022, MML, probabilistic, dimension reduction,
   dimensionality, principal component analysis, PCA, stats
%X "... A key question in PCA decomposition of data is deciding how many factors
   to retain. This manuscript describes a new approach to automatically
   selecting the # of principal components based on the Bayesian minimum message
   length method of inductive inference. We also derive a new est. of the
   isotropic residual variance & demonstrate, via numerical experiments, that it
   improves on the usual maximum likelihood approach."
   -- 2209.14559@[<A HREF="https://arxiv.org/abs/2209.14559">arXiv</A>]['22].
   [Also search for: dimension reduction] &
   [also search for: MML dimension reduction].


%A F. P. Brooks
%A A. L. Hopkins
%A P. G. Newmann
%A W. V. Wright
%T An experiment in musical composition
%J IRE Trans. on Electronic Computers
%V 6
%N 1
%P 175-182
%M SEP
%D 1957
%O F. Brooks, et al., "An experiment in musical composition",
   Machine Models of Music, S.Schwanauer and D.Levitt, eds.,
   MITpress, pp.23-40, '93
%K jrnl, music, computer, c1957, c195x, c19xx, hymn, hymns, zz0805, compose,
   composing

%A J. A. Moorer
%T Music and computer composition
%J CACM
%V 15
%N 2
%P 104-113
%M FEB
%D 1972
%K jrnl, CACM, c1972, c197x, c19xx, computer music, Illiac suite, piece,
   compose, composing
%X "... simulating human composition of Western popular music by computer and
   some relevant theories of music and harmony are given. Problems with this
   kind of program and several schemes that are known not to work are discussed.
   Several previous computer compositions are discussed, including the ILLIAC
   Suite. A program to generate short melody fragments was written to simulate
   some of the aspects of human composition. 5 samples of its output are
   presented and discussed. It was discovered that although the fragments show
   many of the characteristics of popular melodies, they have a strangely alien
   sound. It is theorized that this is because the relevant probabilities which
   would discriminate against unfamiliar sequences were not used."
   -- pdf@[<A HREF=" http://doi.acm.org/10.1145/361254.361265">doi:10.1145/361254.361265</A>]['05].

%A O. Karolyi
%T Introducing Music
%P Penguin
%P 176
%D 1991
%K book, text, good, music, introduction, melody, chords, progressions,
   cadence, scales, harmony, theory, c1965, c196x, c19xx, zz1103
%X Lovely little book, was a Pelican book 1965; Penguin 1991, isbn:0140135200.
   Author is in Dept. of English studies, [<A HREF="http://www.stir.ac.uk/">U. Stirling</A>], as of '03.

%A B. Vercoe
%T Csound: A manual for the audio processing system and supporting programs
%R ?
%I MIT Media Lab
%D 1986
%K TR, c1986, c198x, c19xx, Csound, music, sound file, files
%X [also search for: Csound book] '99.

%A D. Cope
%T Experiments in Music Intelligence
%J Proc. Int. Computer Music Conf.
%W San Francisco
%D 1987
%I Computer Music Assoc. ?
%P ?-?
%K conf, ICMC, music, computer, computers, generated, AI
%X <A HREF="http://arts.ucsc.edu/faculty/cope/">[cope home]</A>[5/'03].

%A C. Anderton
%T The Electronic Musician's Dictionary
%I New York; London: Amsco
%D 1988
%K book, computer music, c1998, c198x, c19xx
%X from a ref list

%A D. Cope
%T Recombinant music: Using the computer to explore musical style
%J Computer
%I IEEE
%V 24
%N 7
%P 22-28
%M JUL
%D 1991
%K jrnl, music, musical, computer, style, compose, composer, analysis,
   genre, c1991, c199x, c19xx, zz0503
%X ... Experiments in Musical Intelligence (EMI) ... One subprogram of EMI is
   an expert system that uses pattern recognition processes to create
   recombinant music, i.e. music written in the styles of various composers
   by means of a contextual recombination of elements in the music of those
   composers.  ... separates and analyzes musical pitches and durations and
   then mixes and recombines the patterns of these pitches and durations so
   that while each new composition is different, it substantially conforms to
   the style of the original. ...pattern matching ...analyzing each component
   ... reassembling the parts sensitively. ...
   -- [<A HREF="http://www.computer.org/computer/co1991/r7022abs.htm">abstr@ct</A>][5/'03] (needs subsc'n),
      [<A HREF="http://ieeexplore.ieee.org/iel1/2/2777/00084830.pdf?isNumber=2777&prod=JNL&arnumber=84830&arNumber=84830&arSt=22&ared=28&arAuthor=Cope%2C+D">paper@ieeexplore</A>][5/'03], issn:0018-9162,
      [<A HREF="http://arts.ucsc.edu/faculty/cope/">cope home</A>][5/'03].

%A D. Cope
%T Computers and Musical Style
%I A-R Editions, Madison, Wis.
%D 1991
%K book, text, c1991, c199x, c19xx, music, computer, composition, melody
%X The book includes (LISP) source ...
   applied to examples from musical literature, (Bach,
   Mozart, Schubert, Stravinsky and many others). ...; isbn:0895792567.
   [<A HREF="http://arts.ucsc.edu/faculty/cope/">cope home</A>][8/'97].
   [<A HREF="http://www.faqs.org/faqs/music/midi/bibliography/preamble.html">www.faqs.org/faqs/music/midi/bibliography/preamble.html</A>][7/'02].
   ? also The Computer Music and Digital Audio Series,
     Vol. 6, Oxford University Press, Oxford ?

%A L. Spector
%A A. Alpern
%T Criticism, Culture, and the Automatic Generation of Artworks
%J AAAI-94 to appear
%D 1994
%K AAAI 94 AI, art, arts, music, melody, bebop, jazz,
   evolve, evolving, genetic algorithm GA
%X Researchers wishing to create computational systems that themselves
   generate artworks face two interacting challenges. The first is that
   the standards by which artistic output is judged are notoriously
   difficult to quantify. The larger AI community is currently involved
   in a rich internal dialogue on methodological issues, standards, and
   rigor, and hence murkiness with regard to the assessment of output
   must be faced squarely. The second challenge is that any artwork exists
   within an extraordinarily rich cultural and historical context, and it
   is rare that an artist who is ignorant of this context will produce
   acceptable works. In this paper we assert that these considerations
   argue for case-based AI/Art systems that take critical criteria as
   parameters. We describe an example system that produces new bebop jazz
   melodies from a case-base of melodies, using genetic programming
   techniques and a fitness function based on user-provided critical
   criteria. We discuss the role that such techniques may play in future
   work on AI and the arts.
   content areas: AI and the Arts, Genetic Algorithms, Case-based Reasoning
   address: School of Communications and Cognitive Science,
   Hampshire College, Amherst, MA 01002
   email: LSPECTOR OF hamp.hampshire.edu                        (7/94).

%T Math and Music: Harmonious Connections
%E T. H. Garland
%E C. V. Kahn
%E K. Stenstedt
%I DaleSeymourPub
%D 1995
%P 168
%K book, text, c1995, c199x, c19xx, mathematics, harmony
%X reviews say for beginners, us$22; isbn:0866518290.

%A C. Roads
%T The Computer Music Tutorial
%D 1996
%I MITpress
%P 904
%K book, good, text, music, computer, musical, book, compose, composition,
   midi, acoustics, c1996, c199x, c19xx,
%X the most comprehensive text on computer music (IMHO) - J.Mc. 3/'03;
   isbn:0262680823.  us$65.

%A J. McCartney
%T SuperCollider: A new real time synthesis language
%J Proc. Int. Computer Music Conf.
%W Hong-Kong
%P ?-?
%D 1996
%K conf, ICMC, ICMC96, Super-Collider, SC3, sound, sounds, music
%X ...environment for real time audio synthesis which runs on a Power Mac
   with no additional hardware.  ... built in prog lang with real time
   incremental garbage collection, 1st class functions/closures, a small O.O.
   class system, a mini GUI builder for creating a patch control panel, a GUI
   for creating wave tables and breakpoint envelopes, MIDI control, a large
   library of signal processing and synthesis functions, and a large library of
   functions for list processing of musical data. The user can write both the
   synthesis and compositional algorithms for their piece in the same lang'...
   [<A HREF="http://www.audiosynth.com/icmc96paper.html">paper</A>][11/'02].
   [<A HREF="http://www.audiosynth.com/">audiosynth.com</A>][11/'02] James not Paul:-)

%A D. Cope
%T Experiments in Musical Intelligence
%I A-R Editions
%D 1996
%K book, text, computer, computers, generated, music, Mozart, emi, ucsc, zz0897,
   c1996, c199x, c19xx
%X from New Scientist about Aug '97
   <A HREF="http://arts.ucsc.edu/faculty/cope/">[cope home]</A>[8/'97].

%A R. E. Prather
%T Harmonic analysis from the computer representation of a musical score
%J CACM
%V 39
%N 12es
%P n.a.
%M DEC
%D 1996
%K jrnl-es, cacm, computer music, c1996, c199x, c19xx
%X in electronic supplement to Dec 1996 issue
   [<A HREF="http://dx.doi.org/10.1145/272682.272716">doi:10.1145/272682.272716</A>]['05].
   [<A HREF="http://portal.acm.org/toc.cfm?id=272682">es</A>]['05].

%A M. Bellgard
%A C. P. Tsang
%T On the use of an effective Boltzmann machine for musical style recognition
   and harmonisation
%J Int. Computer Music Conf.
%W Hong Kong
%I Int. Computer Music Assoc.,
%P 461-464
%D 1996
%K conf, c1996, c199x, c19xx, uniWA, UWA, genre, styles
%X isbn:9628509217.

%T Beyond MIDI: The Handbook of Musical Codes
%E E. Selfridge-Field
%I MITpress
%P 630
%M AUG
%D 1997
%K book, text, reference, music, midi file, files, format, musical, computer,
   c1997, c199x, c19xx, zz0503
%X about us$65. isbn:0262193949.
   Also see [<A HREF="http://www.ccarh.org/publications/books/beyondmidi/">ccarh.org</A>][5/'03].

%A D. Gatherer
%T The evolution of music: A comparison of Darwinian and dialectical methods
%J J. of Social & Evolutionary Sys.
%V 20
%N 1
%P 75-92
%D 1997
%K jrnl, music, musical, jazz, computer, 20C, theory, c1997, c199x, c19xx
%X "M. provides a challenging system for the analysis of cultural evol.. The
   dialectical approach to m. seeks to identify the internal stylistic tensions
   & contradictions (in terms of thesis & antithesis) which give rise to new
   m. forms (synthesis). The Darwinian alternative to dialectics, which in its
   most reductionist form is becoming known as memetics, seeks to interpret the
   evol. of m. by examining the adaptiveness of its various component parts in
   the selective environment of culture. This essay compares the memetic &
   dialectical approaches with special reference to the development of jazz in
   the era of recorded sound, in the light of Benzon's classification of m.
   styles into evol. Ranks (Benzon 1993). It is concluded that the basic
   postulate of memetics is falsifiable & therefore that memetics qualifies as
   scientific in the Popperian sense, rather than being simply a pseudo-sci.
   metanarrative for cultural evolution. Some suggestions for empirical analysis
   are provided. In contrast, the dialectical perspective is not scientific in
   the Popperian sense, but does provide a good explanatory framework for the
   history of jazz in the years 1900-1970, & shows how transitions between
   Ranks may be generated. However, dialectics is considerably less successful
   in the construction of a model to explain the period since 1970."
   -- [<A HREF="http://cogprints.org/4354/">cogprints</A>]['05] via Ch@rles.T.

%A T. Crawford
%A C. Iliopoulos
%A R. Raman
%T String matching techniques for musical similarity and melodic recognition
%J Computing in Musicology
%V 11
%P 71-100
%D 1998
%K jrnl, match, sequence, music, edit distance, LCS, melody, tune, approximate,
   matching, recognise, c1998, c199x, c19xx
%X [<A HREF="http://www.kcl.ac.uk/kis/schools/hums/music/ttc/String_matching.html">abs</A>][2/'03].
   ref in  M a k i n e n  et al '03.  Authors at King's Coll. Lond.
   [Also search for: music match].

%A M. Gogins
%T Music graphs for algorithmic composition and synthesis with an extensible
   implementation in Java
%J Proc. Int. Computer Music Conf.
%M SEP
%D 1998
%K conf, ICMC
%X [<A HREF="http://www.pipeline.com/~gogins/Silence/Gogins.pdf">paper</A>][11/'02].
   [Also search for: Csound book].

%A M. Gogins
%T Creating and using a platform-independent graphical user interface for
   Csound in Java
%P ?-?
%B The Csound Book
%E R. C. Boulanger
%D 1999
%X [<A HREF="http://www.pipeline.com/~gogins/">Gogins</A>][11/'02].
   [Also search for: Csound book].

%T The Csound Book: Perspectives in Software Synthesis, Sound Design,
   Signal Processing, and Programming
%E R. C. Boulanger
%I MITpress
%P 740
%M OCT
%D 1999
%K Csound, book, text, Barry Vercoe, sound, sounds, computer,
   music, Java, c1999, c199x, c19xx, zz1102
%X about us$55.  isbn:0262522616.  book+CDRom.
   [<A HREF="http://mitpress.mit.edu/e-books/csound/frontpage.html">MIT press</A>][11/'02].
   [Also search for: Csound].

%A A. Copland
%T What to Listen for in Music
%I Penguin
%P 288
%M MAR
%D 1999
%K book, text, good, Aaron Copland, music, musical, appreciation, structure,
   about, zz0303, c193x, c1999, c199x, c19xx, opera, sonata, fugue, copeland
%X "... Copland's series of lectures at the New School in New York City
   in the late 1930s,... " (recommended by JMc and AD)
   ppbk; uk us isbn:0451628802.

%A M. Das
%A D. M. Howard
%A S. L. Smith
%T Motion curves in music: The statistical analysis of midi data
%J 25th Euromicro Conference (EUROMICRO '99) Vol.2
%M SEP
%P 2013-2019
%D 1999
%K conf, MIDI, tempo, change, changes, Truslit, acceleration, zz0403, c1999,
   c199x, c19xx
%X ...analysis of multivariate MIDI data allows for the statistical analysis
   of motion in music.  ...analyzing the kinematic motion components within
   music, [i.e.] music velocity (i.e. tempo) & music acceleration/
   deceleration (i.e. tempo change), based upon Truslit's definition of
   predominant up-down motion types ('38).  ...variables of music velocity &
   acceleration are mathematically defined & extracted from MIDI encodings.
   Analysis of music velocity indicates that the differing motion types have
   specific & consistent velocity profiles, & that these profiles can be
   expressed mathematically & analyzed statistically. ...relating the open
   motion velocity curve to the beta distribution. ...
   -- [<A HREF="http://www.computer.org/proceedings/euromicro/0321/volume2/03212013abs.htm">paper</A>][4/'03] authors at ohm.york.ac.uk.

%A E. Cambouropoulos
%T From MIDI to traditional musical notation
%J Proc. AAAI2000 Workshop on A.I. and Music
%W Austin, TX
%P ?-?
%M JUL
%D 2000
%K wShop, computer music, midi, score, track, tracking, beat, timing,
   transcription, quantisation, time, signature, pitch spelling, zz0804
%X "... designed to extract the musical score from a MIDI performance ... .
   The proposed system comprises of a number of modules that perform the
   following tasks: identification of elementary musical objects, calculation
   of accent (salience) of musical events, beat induction, beat tracking, onset
   quantisation, streaming, duration quantisation and pitch spelling. The
   system has been applied on 13 complete Mozart sonata performances giving
   very encouraging results."   Also see same author in 2OO3.
   -- [<A HREF="http://www.ai.univie.ac.at/cgi-bin/tr-online?number+2000-15">univie.ac.at</A>][8/'04].
   [<A HREF="http://www.ai.univie.ac.at/~emilios/pub.html">auth</A>][8/'04].

%A D. Cope
%T The Algorithmic Composer
%I A-R Editions
%P 130
%D 2000
%K book, text, Alice, SARA, music, musical, computer, composition, compose,
   c2000, c200x, c20xx, zz0503, generation, generate
%X ...and SARA, and fundamental issues, such as Markov chains, randomness and
   association nets. He also takes up the aspect of inference with regard to
   tonality, non-pitch elements, variation, texture and the ensuing rules that
   can be derived. ...  isbn:0895794543.  us$50.
   [<A HREF="http://arts.ucsc.edu/faculty/cope/">cope home</A>][5/'03].

%A D. Cope
%T Facing the music: Perspectives on machine composed music
%J Leonardo Music J.
%I MITpress
%V 9
%P 79-87
%D 2000
%K jrnl, musical, computer, c2000, c200x, c20xx, compose, composition
%X ... processes [] in creating Experiments in Musical Intelligence, a computer
   program for the simulation of musical styles. ... outlines ... problems
   listeners face when attempting to deal with successful output from such
   programs. These problems involve redefining terms, debating human- v.
   computer-creativity and, ultimately, grappling with the meaning of music.
   ... includes an e.g. from the computer-composed opera Mahler. ... argues
   that such music should be considered integral to mainstream human-composed
   music since it results from a collaboration between humans and the machines
   they have created.
   [<A HREF="http://arts.ucsc.edu/faculty/cope/">cope home</A>][5/'03].
   [<A HREF="http://mitpress.mit.edu/catalog/item/default.asp?tid=5577&ttype=6">pdf@jrnl</A>][8/'04].

%A C. Anderton
%T The quantification of emotion
%J EQ magazine
%N 3
%D 2000
%K EQ magazine, music, musical, rythm, drum, drumming, drums, style, funky,
   cool, moving, emotions, computer, analysis, c2000, c200x,
   c20xx,  Ernest Cholakis, DNA Groove Templates, template
%X Why some musical performances are emotionally moving and others are not...
   ...  Ernest Cholakis ...
   [<A HREF="http://www.numericalsound.com/eqsndgra.pdf">.pdf</A>][3/'03] at
   [<A HREF="http://www.numericalsound.com/">numericalsound.com</A>][3/'03].

%A D. Phillips
%T Linux Music and Sound
%I NoStarch
%P 408
%M SEP
%D 2000
%K book, text, Linux, Unix, music, sound, sounds, midi, mod, mp3
%X about us$28.  isbn:1-886411-34-4.
   [<A HREF="http://linux-sound.org/">linux-sound</A>][11/'02],
   [<A HREF="http://www.nostarch.com/lms.htm">nostarch</A>][11/'02].

%A A. Glinsky
%A R. Moog
%T Theremin: Ether Music and Espionage (Music in American Life)
%I U. IllinoisPress
%P 464
%M OCT
%D 2000
%K book, electronic, music, musical instrument, Theremin, theramin, sound,
   sounds, Lev Sergeyevich Termen
%X about us$35.  Lev Sergeyevich Termen (1896-1993).  us isbn:0252025822.
   [Also search for: electronic music].

%T Music and Emotion: Theory and Research
%E P. N. Juslin
%E J. A. Sloboda
%I OUP
%M AUG
%D 2001
%K book, text, music, OUP, c2001, c200x, c20xx, zz1203, psychology, brain,
   aesthetics, effect, sociology, musicology
%X stg24; isbn:0192631888.
   [<A HREF="http://www.keele.ac.uk/depts/ps/musacts.htm">www.keele.ac.uk/depts/ps/musacts.htm</A>][12/'03].

%A D. Cope
%T Virtual Music, Computer Synthesis of Musical Style
%I MITpress
%M APR
%D 2001
%P 292
%K book, text, musical, computer, creativity, c2001, c200x, c20xx, zz0503
%X ... 1. Experiments in Musical Intelligence, ... Hofstadter. ...
   2. from the creation of a database to the completion of a new work
   in the style of Mozart. ... 3. perspectives and analyses by [various] ...
   4. author's responses to these commentaries ... and implications of
   artificial creativity.  isbn:026203283X.  us$50 cloth.
   [<A HREF="http://arts.ucsc.edu/faculty/cope/">cope home</A>][5/'03].

%A W. Chai
%A B. Vercoe
%T Folk music classification using hidden Markov models
%J Proc. of Int. Conf. on Artificial Intelligence
%P ?-?
%M JUN
%D 2001
%K conf, music, musical, computer, HMM, c2001, c200x, c20xx, zz0503
%X off the web: [<A HREF="http://web.media.mit.edu/~chaiwei/papers/chai_ICAI183.pdf">.pdf</A>][5/'03].

%A E. R. Miranda
%T Composing Music with Computers
%D 2001
%S Music Technology Series
%I Focal Press, Oxford, Boston
%K book, text, musical, computer, c2001, c200x, c20xx
%X - via J.Mc. 3/'03.

%A H.-H. Shih
%A S. S. Narayanan
%A C.-C. J. Kuo
%T Automatic main melody extraction from MIDI files with a modified
   Lempel-Ziv algorithm
%J Int. Symp. on Intell. Multimedia, Video and Speech Processing
%P 9-12
%M MAY
%D 2001
%K music, musical, conf, tune, theme, repetitive patterns, c2001, c200x,
   c20xx, bar, bars, LZ, LZ78
%X ... dictionary based approach ... for audio DB management ... tempo info
   and music score is decomposed into bars. ... Each bar is indexed ...
   LZ78 to extract repetitive patterns. ...
   -- [<A HREF="http://viola.usc.edu/newextra/people/maverick/papers/isimp.pdf">.pdf</A>][1/'03].

%A D. Temperley
%T The Cognition of Basic Musical Structures
%I MITpress
%P 360
%D 2001
%K book, text, music, computational theory, c2001, c200x, c20xx
%X stg30,  isbn:0262201348.

%A W. L. Benzon
%T Beethoven's Anvil: Music in Mind and Culture
%I BasicBooks
%D 2001
%K book, speculative, Beethoven, music, brain, art, c2001, c200x, c20xx,
   culture
%X isbn:0465015433.

%A K. Balasubramanian
%T Combinatorial enumeration of ragas (scales of integer sequences) of Indian
   music
%J J. of Integer Sequences
%V 5
%N 2
%P 02.2.6
%D 2002
%K music, c2002, c200x, c20xx, raga, ragas, India, scales, Carnatic
%X "It is shown that a combinatorial method based on the principle of inclusion
   and exclusion (Sieve formula) yields generating functions for the enumeration
   of integer seqs. chosen from 12 musical tones for the ragas (scales) of the
   Indian music system. Mathematical & computational schemes are pres. for the
   enum. & construction of int.seqs. pertinent to Indian music."  [15 refs].
   -- [<A HREF="http://www.cs.uwaterloo.ca/journals/JIS/VOL5/Balasubramanian/bala6.html">www</A>]['11].

%A F. Samagaio
%T The Mellotron Book
%I ArtistPro.com
%M FEB
%D 2002
%K book, electronic music, musical instrument, sound, sounds, tape loop,
   sampler, c2002, c200x, c20xx
%X about us$25.  isbn:1931140146.
   [Also search for: electronic music].

%A T. Pinch
%A F. Trocco
%T Analog Days: The Invention and Impact of the Moog Synthesizer
%I HarvardUP
%P 352
%M OCT
%D 2002
%K Bob Moog, book, pop music, sound, sounds, keyboards, electronic,
   musical instrument, synthesizer, synthesized, c2002, c200x, c20xx
%X about us$30.  isbn:0674008898.
   [Also search for: electronic music].

%A R. Bod
%T A unified model of structural organization in language and music
%J J. Artificial Intelligence Res.
%V 17
%P 289-308
%D 2002
%K jrnl, JAIR, AI, computer music, musical, data oriented parsing, DOP,
   Essen folksong, folk song, c2002, c200x, c200xx, zz0503
%X [<A HREF="http://turing.wins.uva.nl/~rens/jair02.pdf">.pdf</A>][5/'03].

%A N. Hu
%A R. B. Dannenberg
%A A. L. Lewis
%T A probabilistic model of melodic similarity
%J Proc. Int. Computer Music Conf.
%W San Francisco
%P ?-?
%D 2002
%K conf, music, match, matching, edit distance, approximate, pitch distances,
   melody, transposition, musical, note, notes, DPA, c2002, c200x, c20xx
%X Melodic similarity is an important concept for music databases,
   musicological studies, and interactive music systems. Dynamic programming
   is commonly used to compare melodies, often with a distance function based
   on pitch differences measured in semitones. This approach computes an
   "edit distance" as a measure of melodic dissimilarity. The problem can also
   be viewed in probabilistic terms: What is the probability that a melody is
   a "mutation" of another melody, given a table of mutation probabilities?
   We explain this approach and demonstrate how it can be used to search a
   database of melodies. Our experiments show that the probabilistic model
   performs better than a typical "edit distance" comparison.
   4 pages [<A HREF="http://www.cs.cmu.edu/~rbd/papers/icmc02melodicsimilarity.pdf">.pdf</A>][2/'03].
   [Also search for: music match].

%A C. Anderton
%T The link between music and emotional response
%J SOS (Sound on Sound) magazine
%M MAY
%D 2002
%K magazine, music, Ernest Cholakis, style, emotion, cool, funky, c2002,
   c200x, c20xx, computer analysis, drum, drumming, timing, variations,
   DNA groove template, templates
%X ... at a recent AES convention, when Ernest Cholakis showed me his
   notes on trying to quantify emotional responses in music ...
   [<A HREF="http://www.sospubs.co.uk/sos/may02/articles/cholakis.asp">html</A>][3/'03].
   [<A HREF="http://www.numericalsound.com/">numericalsound.com</A>][3/'03].

%A E. Cambouropoulos
%T Pitch spelling: A computational model
%J Music Perception
%I UCalPress
%P 411-429
%N 4
%V 20
%D 2003
%K jrnl, computer music, musical, c2003, c200x, c20xx, midi, pitch class,
   key signature, pitches, transcription, score, notation, zz0804
%X "... task ... is pitch spelling, that is, how traditional score notation can
   be derived from a simple unstructured 12-tone representation (e.g., pitch-
   class set or MIDI pitch representation). This study provides useful insights
   both into the domain of pitch perception & into musicological aspects of
   score notation strategies. ...model is described that transcribes polyphonic
   MIDI pitch files into the Western traditional music notation. Input to the
   proposed algorithm is merely a sequence of MIDI pitch numbers in the order
   they appear in a MIDI file. No a priori knowledge such as key signature,
   tonal centers, time signature, chords, or voice separation is required.
   Output of the algorithm is a sequence of "correctly" spelled pitches. The
   algorithm is based on an interval optimization approach that takes into
   account the frequency of occurrence of pitch intervals within the major-
   minor tonal scale framework. The algorithm was evaluated on 10 complete
   piano sonatas by Mozart & had a success rate of 98.8% (634 pitches were
   spelled incorrectly out of a total of 54,418 notes); it was tested
   additionally on three Chopin waltzes & had a slightly worse success rate.
   The proposed pitch interval optimization approach is also compared with &
   tested against other pitch-spelling strategies."
   -- [<A HREF="http://dx.doi.org/10.1525/mp.2003.20.4.411">doi:10.1525/mp.2003.20.4.411</A>][8/'04].

%A R. Cilibrasi
%A P. Vitanyi
%A R. de Wolf
%T Algorithmic clustering of music
%J arXiv.org
%D 2003
%K music, cluster, unsupervised, classification, AI, compression, zip,
   Rudi Cilibrasi, zz0403
%X ...automatic method for music classification, based ...compression of
   strings that represent the music pieces.  ...uses no background knowledge
   about music whatsoever: it is completely general and can, without change,
   be used in different areas like linguistic classification and genomics.
   It is based on an ideal theory of the information content in individual
   objects (Kolmogorov complexity), information distance, and a universal
   similarity metric. Experiments show that the method distinguishes reasonably
   well between various musical genres and can even cluster pieces by composer.
   -- [<A HREF="http://arXiv.org/abs/cs/0303025">www</A>][4/'03].
   [<A HREF="http://www.cwi.nl/~paulv/papers/music.ps">www.cwi.nl</A>][4/'03].

%A A. C. Bickerstaffe
%A E. Makalic
%T MML classification of music genres
%J AI2003, Advances in Artificial Intelligence
%E T. D. Gedeon
%E L. C. C. Fung
%I SpringerVerlag
%S LNAI
%V 2903
%P 1063-1071
%D 2003
%X conf, AI2003, computer, music, analysis, MDL, genre, c2003, c200x, c20xx,
   enesm, musical, ACBickerstaffe, EMakalic
%X "... applies 4 different classification methods to the task of
   distinguishing between rock & classical music styles. Each method uses the
   [MML] principle of statistical inference. The 1st, an unsupervised learning
   tool called Snob performed very poorly. 3 supervised classification methods,
   namely [DT], [DG] & [ANN], performed significantly better. The defining
   attributes of the 2 musical genres were found to be pitch mean & standard
   deviation, duration mean & standard deviation, along with counts of distinct
   pitches & rhythms per piece. ..."
   -- [<A HREF="http://springerlink.metapress.com/openurl.asp?genre=article&issn=0302-9743&volume=2903&spage=1063">openURL</A>]['05].
   [<A HREF="http://springerlink.metapress.com/link.asp?id=wrcflqp6np6f9mt1">met@press</A>]['05].
   issn:03029743, isbn:3540206469.

%A N. Collins
%A A. McLean
%A J. Rohrhuber
%A A. Ward
%A Live coding in laptop performance
%J Organised Sound
%V 8
%N 3
%P 321-330
%D 2003
%K jrnl, computer music, c2003, c200x, c20xx, art, Perl, REALbasic,
   SuperCollider
%X "Seeking new forms of expression in computer music, a small number of laptop
   composers are braving the challenges of coding music on the fly. Not content
   to submit meekly to the rigid interfaces of performance software like Ableton
   Live or Reason, they work with programming languages, building their own
   custom software, tweaking or writing the programs themselves as they perform.
   Often this activity takes place within some established language for computer
   music like SuperCollider, but there is no reason to stop errant minds
   pursuing their innovations in general scripting languages like Perl. This
   paper presents an introduction to the field of live coding, of real-time
   scripting during laptop music performance, and the improvisatory power &
   risks involved. We look at 2 test cases, the command-line music of slub
   utilising, amongst a grab-bag of technologies, Perl & REALbasic, & Julian
   Rohrhuber's Just In Time library for SuperCollider. We try to give a flavour
   of an exciting but hazardous world at the forefront of live laptop perf.."
   -- [<A HREF="http://dx.doi.org/10.1017/S135577180300030X">doi:10.1017/S135577180300030X</A>]['07].
   [<A HREF="http://doc.gold.ac.uk/~ma503am/alex/">auth2@gold.ac.uk</A>]['07].

%A S. E. Trehub
%T The developmental origins of musicality
%J Nature Neuroscience
%V 6
%N 7
%P 669-673
%M JUL
%D 2003
%K jrnl, music, perception, fourth, fifth, child, baby, babies, infants,
   c2003, c200x, c20xx, zz1003
%X ... available evidence indicates that infants are sensitive to a number
   of sound features that are fundamental to music across cultures. Their
   discrimination of pitch and timing differences and their perception of
   equivalence classes are similar, in many respects, to those of listeners
   who have had many years of exposure to music. Whether these perceptual
   skills are unique to human listeners is not known. What is unique is the
   intense human interest in music, which is evident from the early days of
   life. Also unique is the importance of music in social contexts. ...
   -- [<A HREF="http://dx.doi.org/10.1038/nn1084">paper</A>][10/'03].

%A O. Celma
%A M. Ramirez
%A P. Herrera
%T Semantic interaction with music content using FOAF
%J 1st Workshop on Friend of a Friend, Social Networking and the Semantic Web
%D 2004
%K wShop, music, SIMAC, c2004, c200x, c20xx, semanticaudio, www, zz0106
%X [<A HREF="http://www.iua.upf.es/mtg/publications/SWADFOAF2004-CelmaRamirezHerrrera.pdf">pdf@iua.upf.es</A>]['05].
   also [<A HREF="http://www.semanticaudio.com/">semanticaudio</A>]['05].

%A A. C. Bickerstaffe
%A D. L. Dow e
%T MML-based compressive models for musical melody
%J Proc. 4th Int. ICSC Symp. on Engineering of Intelligence Systems (EIS)
%W Madeira, Portugal
%P 6
%M FEB
%D 2004
%K conf, c2004, c200x, c20xx, MDL, computer music, dld, adrianB, monash
%X ICSC Academic Press, Canada, isbn:3906454355.

%A S. Koelsch
%A E. Kasper
%A D. Sammler, K. Schulze, T. Gunter
%A A. D. Friederici
%T Music, language and meaning: brain signatures of semantic processing
%J Nature Neuroscience
%P 302-307
%M MAR
%D 2004
%K jrnl, music, perception, brain, mind, signature, semantics, zz0304,
   EEG, ERP, N400
%X "... We compared processing of semantic meaning in language and music, ...
   results indicate that both music and language can prime the meaning of a
   word, and that music can, as language, determine physiological indices of
   semantic processing."  (auth1: koelsch Of cns mpg de)
   -- [<A HREF="http://dx.doi.org/10.1038/nn1197">abs</A>][3/'04].

%A J. F. Paiement
%A D. Eck
%A S. Bengio
%A D. Barber
%T A graphical model for chord progressions
%J Proc. Int. Conf. on Machine Learning ICML'05
%P ?-?
%D 2005
%K conf, computer music, c2005, c200x, c20xx, progression, chords, modeling
%X "Chord progressions are the building blocks from which tonal music is
   constructed. Inferring chord progs. is thus an essential step towards
   modeling long term dependencies in music. ... a distributed rep. for chords
   is designed such that Euclidean dist. roughly correspond to psychoacoustic
   dissimilarities. Parameters in the graphical m. are learnt with the EM alg.
   & the classical Junction Tree alg.. Various model architectures are compared
   in terms of conditional out-of-sample likelihood. Both perceptual & stat.
   evidence show that binary trees related to meter are well suited to capture
   chord dependencies."
   -- [<A HREF="http://www.machinelearning.org/proceedings/icml2005/papers/081_ChordProgession_PaiementEtAl.pdf">pdf@conf</A>]['05].
   [<A HREF="http://www.idiap.ch/~paiement/articles/chords.pdf">pdf</A>]['05].

%A M. J. Salganik
%A P. Sheridan Dodds
%A D. J. Watts
%T Experimental study of inequality and unpredictability in an
   artificial cultural market
%J Science
%V 311
%N 5762
%P 854-856
%M FEB
%D 2006
%K jrnl, c2006, c200x, c20xx, hit, song, hits, success, popular, popularity,
   pop, sociology, predicting, predict, prediction, music, media, gIndex,
   Music Lab, MusicLab, hit, hits, social, likes, luck, Matthew effect
%X "... hit songs, books, & movies are many times more successful than average,
   suggesting that 'the best' alternatives are qualitatively different from
   'the rest'; yet experts routinely fail to predict which products will
   succeed. ... Increasing the strength of social influence increased both
   inequality & unpredictability of success. Success was also only partly
   determined by quality: The best songs rarely did poorly, & the worst rarely
   did well, but any other result was possible."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1121066">doi:10.1126/science.1121066</A>]['06].
   [Also search for: success luck].

%T Evolutionary Computer Music
%E E. R. Miranda
%E J. A. Biles
%I Springer
%M MAR
%P 259
%D 2007
%K book, text, computer music, c2007, c200x, c20xx, zz0507, generate,
   generation, musical
%X pb us$99; uk us isbn:1846285992; uk us isbn13:978-1846285998.

%A C. Callender
%A I. Quinn
%A D. Tymoczko
%T Generalized voice-leading spaces
%J Science
%V 320
%N 5874
%P 346-348
%M APR
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0408, music, space, pitch, chord, harmony,
   transformation, maths, symmetry, transposition, inversion
%X "...Western musicians traditionally classify pitch seqs. by disregarding the
   effects of 5 musical transformations: octave shift, permutation,
   transposition, inversion, & cardinality change. We model this process
   mathematically, showing that it produces 32 equiv. relations on chords,
   243 equiv. relations on chord seqs., & 32 families of geometrical quotient
   spaces, in which both chords & chord seqs. are represented. This model
   reveals connections between music-theoretical concepts, yields new
   analytical tools, unifies existing geometrical representations, & suggests a
   way to understand similarity between chord types. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1153021">doi:10.1126/science.1153021</A>]['08].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.1155463">doi:10.1126/science.1155463</A>]['08].)

%A B. Parker
%T Good Vibrations: The Physics of Music
%I JohnHopkinsUP
%P 288
%M NOV
%D 2009
%K book, text, c2009, c200x, c20xx, zz0110, physics, music, musical, sound,
   instrument, wave, waves, harmonics
%X 1st ed 2009; hb us$18; us isbn:0801892643; us isbn13:978-0801892646.
   "... details the science of how instruments, the acoustics of rooms,
   electronics, and humans create and alter the varied sounds we hear. Using
   physics as a base, Parker discusses the history of music, how sounds are made
   and perceived, and the various effects of acting on sounds. ..."

%A N. J. Hudson
%T Hypothesis. Musical beauty and information compression: Complex to the
   ear but simple to the mind?
%J BMC Research Notes
%V 4
%N 9
%P ?
%M JAN
%D 2011
%K eJrnl, c2011, c201x, c20xx, zz1112, arts, music, beauty, compression,
   information theory, IT, appreciation, taste, pleasure, Beethoven, pattern
%X '... Presentation of the Hypothesis: The entire life-long sensory data stream
   of a human is enormous. The adaptive solution to this problem of scale is
   information compression, thought to have evolved to better handle, interpret
   & store sensory data. In modern humans highly sophisticated information
   compression is clearly manifest in philosophical, mathematical & sci.
   insights. [e.g.] the Laws of Physics explain apparently complex observations
   with simple rules. Deep cognitive insights are reported as intrinsically
   satisfying, implying that at some point in evolution, the practice of
   successful information compression became linked to the physiological reward
   system. I hypothesise that the establishment of this "compression & pleasure"
   connection paved the way for musical appreciation, which subsequently became
   free (perhaps even inevitable) to emerge once audio compression had become
   intrinsically pleasurable in its own right. ...'  (34 refs, auth@csiro Qld.)
   -- [<A HREF="http://www.biomedcentral.com/1756-0500/4/9">bmc</A>]['12],
      [<A HREF="http://dx.doi.org/10.1186/1756-0500-4-9">doi:10.1186/1756-0500-4-9</A>]['12].
   [Also search for: arts beauty],  [also search for: arts information theory],
   and also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/1993-08-10/">Inductive-Inference</A>].)

%A M. Mauch
%A R. M MacCallum
%A M. Levy
%A A. M Leroi
%T The evolution of popular music: USA 1960-2010
%J Royal Soc. Open Sci. J.
%V 2
%N 5
%P ?-?
%M MAY
%D 2015
%K pop music, c2015, c201x, c20xx, zz0515, evolution, sixties, human culture,
   social, society, arts, trend, taste, fashion, US Billboard Hot 100, chart,
   charts, top 10, hit, hits, tunes, rock and roll, folk, Motown, blues,
   hip hop, hipHop, jazz, soul, country, rap, funk, disco, techno,
   1960s, Beatles
%X 'In modern societies, cultural change seems ceaseless. The flux of fashion is
   esp. obvious for popular music. ... we investigate the US Billboard Hot 100
   between 1960 & 2010. Using Music Information Retrieval (MIR) & text-mining
   tools we analyse the musical properties of ~17,000 recordings that appeared
   in the charts & demo. quantitative trends in their harmonic & timbral
   properties. ... use these properties to produce an audio-based classification
   of musical styles & study the evoln of musical diversity & disparity, testing
   & rejecting several classical theories of cultural change. ... investigate
   whether pop musical evoln has been gradual or punctuated. We show that,
   although pop music has evolved continuously, it did so with particular
   rapidity during three stylistic "revolutions" around 1964, 1983 & 1991. We
   conclude by discussing how our study points the way to a quantitative sci.
   of cultural change.'
   -- [<A HREF="https://doi.org/10.1098/rsos.150081">doi:10.1098/rsos.150081</A>]['15],
      1502.05417@[<A HREF="http://arxiv.org/abs/1502.05417">arXiv</A>]['15],
      matthiasmauch.[<A HREF="http://matthiasmauch.net/">net</A>]['15].
   Also see [<A HREF="http://www.bbc.com/news/science-environment-32599916">bbc</A>][6/5/2015].

%A A. M. Khalili
%T On the mathematics of beauty: beautiful music
%J arXiv
%M JUL
%D 2017
%K TR, c2017, c201x, c20xx, zz0717, music, beauty, Dyson distribution,
   regularity, randomness
%X "...  we will study the simplest kind of beauty that can be found in a simple
   piece of music & can be appreciated universally. The proposed model suggest
   that there is a link between beautiful music & the Dyson distribution which
   seems to be the result of a deeper optimisation process between randomness &
   regularity. Then we show that beautiful music need to satisfy a more
   fundamental law that seeks to deliver the highest amount of information
   using the least amount of energy. The proposed model is tested on a set of
   beautiful music pieces."
   -- 1707.06510@[<A HREF="https://arxiv.org/abs/1707.06510">arXiv</A>]['17].

%A P. Hudak
%A D. Quick
%T The Haskell School of Music: From Signals to Symphonies
%I CUP
%P 398
%M OCT
%D 2018
%K book, text, c2018, c201x, c20xx, zz1219, computer, FP, Haskell, music,
   generation, synthesis, euterpea
%X "... explores the fundamentals of computer music & functional programming
   through the Haskell programming language ... learn how to use the Euterpea
   library for Haskell (www.euterpea.com) to represent & create their own
   music with code ... Other topics covered include the basics of signal-based
   systems in Haskell, sound synthesis, & virtual instrument design."
   1st ed 2018; hb $49; uk us isbn:1108416756; uk us isbn13:978-1108416757.

%A T. Daikoku
%A et al
%T Bodily maps of uncertainty and surprise in musical chord progression and the
   underlying emotional response
%J iScience
%M APR
%D 2024
%K ejrnl, c2024, c202x, c20xx, zz0424, music, meoldy, tune, chord progression,
   human, response, emotion
%X "... This study examined how the perception of musical chord elicits bodily
   sensations and emotions through the brainâs predictive processing. ..."
   -- [<A HREF="https://doi.org/10.1016/j.isci.2024.109498">doi:10.1016/j.isci.2024.109498</A>]['24].


%A H. A. Simon
%T On a class of skew distribution functions
%J Biometrika
%V 42
%N 3-4
%P 425-440
%D 1955
%K jrnl, c1955, c195x, c19xx, zz0115, word, words, Yule, distribution
%X "... discusses a number of related stochastic processes that lead to a class
   of highly skewed distributions (the Yule distn) possessing characteristic
   properties that distinguish them from such well-known fns as the negative
   binomial and Fisher's logarithmic series. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/biomet/42.3-4.425">doi:10.1093/biomet/42.3-4.425.</A>]['15].
   [Also search for: Yule c192x].

%A E. N. Gilbert
%T Random graphs
%J Annals of Math. Stats.
%I Inst. Math. Stats.
%V 30
%P 1141-1144
%M DEC
%D 1959
%K jrnl, c1959, c195x, c19xx, maths, random, graph, randomGraph, model, graphs,
   network, networks, graphModel, ERmodel
%X "... N pts ... for all pairs of pts make random choices, indep. of each
   other, whether or not to join the pts by a line [edge]. ... prob. p. ...
   ... The prob. P(N) that the graph is connected & also the prob. R(N) that
   two specific points, say 1 and 2, are connected, will be found. ...
   [and] *asymptotically* P(N) ~ 1-N(1-p)**(N-1), R(N) ~ 1-2(1-p)**(N-1) ..."
   -- pdf@[<A HREF="http://www.jstor.org/stable/2237458">Jstor</A>]['10].
   [Also search for: graphModel] and [also search for: random graph].
   (Also see [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_11">graph-models</A>]['20].)

%A P. Erdos
%A A. Renyi
%T On random graphs
%J Publ. Math. Debrecen
%V 6
%P 290-297
%D 1959
%K jrnl, c1959, c195x, c19xx, random, maths, graph, randomGraph, model, graphs,
   network, networks, graphModel, ERmodel
%X "... N vertices ... [ER] assigns equal probability to
   all graphs with exactly M edges ..."
   -- ER@[<A HREF="http://en.wikipedia.org/wiki/Erd%C5%91s%E2%80%93R%C3%A9nyi_model">wikp</A>]['14],
      rndmG@[<A HREF="http://en.wikipedia.org/wiki/Random_graph">wikip</A>]['08],
      pdf@[<A HREF="http://www.renyi.hu/~p_erdos/1959-11.pdf">.hu</A>]['14].
   [Also search for: Gilbert c1959]  and  [also search for: graphModel].
   (Also see [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_11">graph-models</A>]['20].)

%A P. Erdos
%T Graph theory and probability
%J Canad. J. Math.
%V 11
%P 34-38
%D 1959
%K jrnl, c1959, c195x, c19xx, maths, graph, graphModel, complete,
   independent set
%X "A well-known theorem of Ramsay (8; 9) states that to every n there exists a
   smallest integer g(n) so that every graph of g(n) vertices contains either
   a set of n independent points or a complete graph of order n, but there
   exists a graph of g(n)-1 vertices which does not contain a complete subgraph
   of n vertices and also does not contain a set of n independent points. ..."
   -- pdf@[<A HREF="http://dx.doi.org/10.4153/CJM-1959-003-9">doi:10.4153/CJM-1959-003-9</A>]['14].
   [Also search for: graphModel].

%A H. Galperin
%A A. Wigderson
%T Succinct representations of graphs
%J Inf. and Control
%V 56
%P 183-198
%M MAR
%D 1983
%K jrnl, c1983, c198x, c19xx, zz0415, graph, network, succinct, data structure,
   representation, compress, algorithm complexity, NP hard, NPH
%X "For a fixed graph property Q, the complexity of the problem: Given a g. G,
   does G have property Q? is usually investigated as a fn of |V|, the # of
   vertices in G, with the assumption that the input size is polynomial in |V|.
   In this paper the complexity of these problems is investigated when the input
   g. is given by a succinct repn. By a succinct repn it is meant that the input
   size is polylog in |V|. It is shown that g.problems which are approached this
   way become intractable. Actually, no 'nontrivial' problem could be found
   which can be solved in polynomial time. The main result is characterizing a
   large class of g.properties for which the resp. 'succinct problem' is
   NP-hard. Trying to locate these problems within the P-Time hierarchy shows
   that the succinct versions of polynomially equiv. problems may not be
   polynomially equivalent."
   -- [<A HREF="http://dx.doi.org/10.1016/S0019-9958(83)80004-7">doi:10.1016/S0019-9958(83)80004-7</A>]['15].
   [Also search for: compress graph].

%A P. Bonacich
%T Power and centrality: A family of measures
%J Amer. J. of Sociology
%V 92
%N 5
%P 1170-1182
%M MAR
%D 1987
%K jrnl, c1987, c198x, c19xx, zz0415, social, graph, network, centrality,
   importance, important node
%X "Although network centrality is gen. assumed to produce power, recent res.
   shows that this is not the case in exchange n/wks. ... proposes a gen'n of
   the concept of c. that accounts for the usual +ve reln b/ween power &
   centrality & Cook et al's recent exceptional results."
      "... c(a,b). The param b reflects the degree to which an individual's
   status is a fn of the statuses of those to whom (s)he is connected. ..."
   -- @[<A HREF="http://www.jstor.org/stable/2780000">Jstor</A>]['15].
   (Also see centrality@[<A HREF="http://en.wikipedia.org/wiki/Centrality">wikip</A>]['15].)

%A C. J. Fidge
%T Timestamps in message-passing systems that preserve the partial ordering
%J Proc. of the 11th Australian Comp. Sci. Conf.
%P 56-66
%M FEB
%D 1988
%O ACSC, 10(1), pp.56-66, Feb 1988
%K conf, ACSC88, c1988, c198x, c19xx, zz0414, computer network, distributed,
   vector clock, clocks, event, events, timestamp, system
%X "Timestamping is a common method of totally ordering events in concurrent
   programs.  However, for applications requiring access to the global state,
   a total ordering is inappropriate. ... presents algorithms for timestamping
   events in both synchronous and asynchronous message passing programs that
   allow for access to the partial ordering inherent in a parallel system. The
   algs. do not change the communications graph or require a central timestamp
   issuing authority."
   -- pdf@[<A HREF="http://zoo.cs.yale.edu/classes/cs426/2012/lab/bib/fidge88timestamps.pdf">yale</A>]['13].
   Also see VC@[<A HREF="https://en.wikipedia.org/wiki/Vector_clock">wikip</A>]['14].

%A F. Mattern
%T Virtual time and global states of distributed systems
%J Proc. Workshop on Parallel and Distributed Algs.
%W Chateau de Bonas, France
%I Elsevier
%P 215-226
%M OCT
%D 1988
%K conf, ACSC88, c1988, c198x, c19xx, zz0414, computer network, distributed,
   vector clock, clocks, timestamp, system
%X [Also search for: Fidge c1988].
   Also see VC@[<A HREF="https://en.wikipedia.org/wiki/Vector_clock">wikip</A>]['14].

%A L. D. Trindell
%T NetView: a Professional's Guide to SNA Network Management
%I McGrawHill
%D 1993
%P 632
%K book, text, SNA, computer, network
%X uk us isbn:0-07-041984-1.

%A M. A. Miller
%T Managing Internetworks with SNMP: the Definitive Guide to the
   Simple Network Management Protocol and SNMP Version 2.
%I M & T Books, NY
%D 1993
%K book, text, InterNet, Network, computer, SNMP, SNMP2
%X uk us isbn:1-55851-304-3.

%A H. C. Rao
%A L. L. Peterson
%T Accessing files on the internet: the Jade file system
%J IEEE Trans. Softw. Eng.
%V 19
%N ?
%M JUN
%D 1993
%P 613-624
%K InterNet, network, computer, filing, address, path, IEEE, jrnl
%X Jade provides a uniform Unix pathname across different machines and OpSys.
   Reviewed in Comp. Rev. 35(10) p530 Oct '94

%T Integrated Network Management,  IFIP TC6/WG6.6 Symp. on
%I NorthHolland
%D 1989, 1993
%K computer networks, IFIP, symposium
%X No 1: Boston        May 1989  Hargrave lib', book, H004.65 I23/1
   No 2: ???
   No 3: San Francisco Apr 1993  Hargrave lib', book, H004.65 I23/3

%A M. P. Consens
%A M. Z. Hasan
%T Supporting network management through declaratively specified data
   visualization.
%J Integrated Network Management 3: IFIP TC6/WG6.6 Symp. on
%W San Francisco
%I NorthHolland
%M APR
%D 1993
%P 725-738
%K computer networks, visualization, GUI, GUIs
%X Hargrave lib', book, H004.65 I23/3

%T IEEE Network Operations and Management Symposium
%D 1994
%K computer networks, NOMS, NOMS94, IEEE, GUI, GUIs
%X 1994: 3 vols, vol 3 includes GUIs, Hargrave lib' periodical H004.605 I59.1

%A W. Stallings
%T ISDN and Broadband ISDN
%I Macmillan
%D 1992
%K book, text, ISDN, computer networks
%X from an hons report

%A H. Helgert
%T Integrated Services Digital Networks: Architectures/ Protocols/ Standards
%I Addison-Wesley
%D 1991
%K book, text, ISDN, computer networks
%X from an hons report

%A S. Hardwick
%T ISDN Design, A Practical Approach
%I AcademicPress
%D 1989
%K book, text, ISDN, computer networks
%X from an hons report

%A D. J. Cook
%A L. B. Holder
%T Substructure discovery using minimum description length and background
   knowledge
%J JAIR
%V 1
%P 231-255
%D 1994
%K jrnl, JAIR, c1994, c199x, c199x, SUBDUE, mdl, frequent, pattern,
   network, graph, mining, compress
%X "The ability to identify interesting & repetitive substructures is an
   essential component to discovering knowledge in structural data. ... new
   version of our Subdue substructure discovery system based on [MDL] principle.
   [It] discovers subst. that compress the original data & represent structural
   concepts in the data. By replacing prev.-discovered substs. in the data,
   multiple passes of Subdue produce a hierarchical descn of the structural
   regularities in the data. ... uses a computationally-bounded inexact graph
   match that identifies similar, but not identical, instances of a substructure
   & an approx. measure of closeness of two substs. when under comp.constraints.
   [&] to the [MDL] principle, other background knowledge can be used by Subdue
   to guide the search towards more appropriate substs.. Experiments ..."
      -- examples on vertex-labelled, edge-labelled graphs, chem cmpds &
         electronic circuits
   -- [<A HREF="http://www.jair.org/papers/paper43.html">jair</A>]['14].
   [Also search for: MML]  and  [also search for: compress graph].

%A R. Canetti
%A C. Dwork
%A M. Naor
%A R. Ostrovsky
%T Deniable encryption
%J Proc. 17th Annual Int. Cryptology Conf. on Advances in Cryptology
%I SpringerVerlag
%S LNCS
%V 1294
%P 90-104
%D 1997
%K crypto97, conf, c1997, c199x, c19xx, deniable encryption, encryptions,
   file system
%X "Consider a situation in which the transmission of encrypted messages is
   intercepted by an adversary who can later ask the sender to reveal the random
   choices (and also the secret key, if one exists) ...  An encryption scheme is
   deniable if the sender can generate `fake random choices' that will make the
   ciphertext `look like' an encryption of a different cleartext, thus keeping
   the real cleartext private. Analogous requirements can be formulated with
   respect to attacking the receiver & with respect to attacking both parties.
   ... introduce deniable encryption & propose constructions of schemes with
   polynomial deniability. In addition to being interesting by itself, &
   having several applications, d.e. provides a simplified & elegant
   construction of adaptively secure multiparty computation."
   -- in: uk us isbn:3540633847; uk us isbn13:978-3540633846.
   -- ps@[<A HREF="http://eprint.iacr.org/1996/002">iacr</A>]['10].

%A C. Hunt
%T TCP/IP Network Administration (2nd ed)
%I OReilly
%P 612
%D 1998
%K book, text, TCP, IP, TCPIP, computer communications, network,
   networks, zz0399
%X 2nd ed 1998, is$33; uk us isbn:1-56592-322-7; rev' in Comp Rev Sep 98 p.439.

%A D. J. Watts
%A S. H. Strogatz
%T Collective dynamics of 'small-world' networks
%J Nature
%V 393
%P 440-442
%M JUN
%D 1998
%K jrnl, c1998, c199x, c19xx, maths, graph, graphs, small world network,
   networks, clustered, hub, clustering coefficient, graphModel, WSmodel
%X "... explore simple models of n/ws that can be tuned through this middle
   ground: Regular n/ws 'rewired' to introduce increasing amounts of disorder.
   We find that these systems can be highly clustered, like regular lattices,
   yet have small characteristic path lengths, like random graphs. We call them
   'small-world' n/ws, by analogy with the small-world phenomenon (popularly
   known as six degrees of separation). The neural n/w of the worm
   Caenorhabditis elegans, the power grid of W. United States, & the
   collaboration graph of film actors are shown to be small-world n/ws. Models
   of dynamical systems with small-world coupling display enhanced signal-
   -propagation speed, computational power, & synchronizability. In particular,
   infectious diseases spread more easily in small-w. n/w [v] regular lattices."
   -- [<A HREF="http://dx.doi.org/10.1038/30918">doi:10.1038/30918</A>]['08].
   (Also see WS.model@[<A HREF="http://en.wikipedia.org/wiki/Watts_and_Strogatz_model">wikip</A>]['14].)
   [Also search for: clustering coefficient graph] and
   [also search for: graphModel].

%A A.-L. Barabasi
%A R. Albert
%T Emergence of scaling in random networks
%J Science
%V 286
%N 5439
%P 509-512
%M OCT
%D 1999
%K jrnl, c1999, c199x, c19xx, scale free, scaling, graph, graphs, network,
   networks, power law, preferential attachment, preferentially, attach,
   hub, hubs, vertex, degree, distribution, small world, graphModel, BAmodel,
   controversy, controversial, Pachter
%X "Sys. as diverse as genetic n/ws or the [www] are best described as n/ws with
   complex topology. A common property of many large n/ws is that the vertex
   connectivities follow a scale-free power-law distn. ... found to be a
   consequence of 2 generic mechanisms:  (i) networks expand continuously by the
   addition of new vertices, &  (ii) new vertices attach preferentially to sites
   that are already well connected. A model based on these 2 ingredients
   reproduces the observed stationary scale-free distns, which indicates that
   the development of large n/ws is governed by robust self-organizing
   phenomena that go beyond the particulars of the individual systems."
   -- [<A HREF="http://dx.doi.org/10.1126/science.286.5439.509">doi:10.1126/science.286.5439.509</A>]['08].
   (*BUT see Lior Pachter @[<A HREF="http://liorpachter.wordpress.com/2014/02/10/the-network-nonsense-of-albert-laszlo-barabasi/">w'rdpress</A>][10/2/2014]
   for a strong(!) counter view.*)
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Barab%C3%A1si%E2%80%93Albert_model">wikip</A>]['14],
   was [<A HREF="http://en.wikipedia.org/wiki/BA_model">wikip</A>]['08].)
   [Also search for: graphModel] and [also search for: Solla Price c197x].
   (Also see [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_11">graph-models</A>]['20].)

%A A.-L. Barabasi
%A V. W. Freeh
%A H. Jeong
%A J. B. Brockman
%T Parasitic computing
%J Nature
%V 412
%P 894-897
%D 2001
%K SAT, 3-SAT, 3SAT, NP, NPC, TCP IP, TCPIP, protocol, checksum, CRC, parasite,
   communication, HTTP, www, zz0902, c2001, c200x, c20xx
%X code a [TSP, possible_solution] as a TCP packet s.t. the checksum
   is valid iff the possible_solution is a genuine solution.
   code all possible [problem, solution] pairs.:
      [...] The parasite node injects each message into the network at the
      IP level [...], bypassing TCP. After receiving the message, the target
      server verifies the data integrity of the TCP segment by calculating a
      TCP checksum.  The construction of the message [...] ensures that the
      TCP checksum fails for all messages containing an invalid solution to the
      posed SAT problem. Thus, a message that passes the TCP checksum contains
      a correct solution. The target server will respond to each message it
      receives (even if it does not understand the request). As a result, all
      messages containing invalid solutions are dropped in the TCP layer. Only
      a message which encodes a valid solution 'reaches' the target server,
      which sends a response to the 'request' it received. [...]
   [<A HREF="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v412/n6850/abs/412894a0_fs.html">Nature</A>][8/'02]
   [<A HREF="http://www.nd.edu/~parasite/">www</A>][8/'02]

%A M. E. J. Newman
%T The structure of scientific collaboration networks
%J PNAS
%V 98
%N 2
%P 404-409
%M JAN
%D 2001
%K jrnl, PNAS, c2001, c200x, c20xx, network, co author, authors, coauthor,
   coauthors, science, scientists, collaborate, joint paper, papers,
   publications, small world, worlds, degrees of separation
%X "... Two scientists are considered connected if they have authored a paper
   together & explicit n/ws of such connections are constructed by using data
   drawn from a number of DBs, inc. MEDLINE (biomedical res.), the Los Alamos
   e-Print Archive (physics), & NCSTRL (comp.sci.). I show that these
   collaboration n/ws form "small worlds", in which randomly chosen pairs of
   scientists are typically separated by only a short path of intermediate
   acquaintances. I further give results for mean & distribution of numbers of
   collaborators of authors, demonstrate the presence of clustering in the n/ws,
   & highlight a number of apparent differences in the patterns of collaboration
   between the fields studied. ..."   (via AK).
   [<A HREF="http://www.pnas.org/cgi/doi/10.1073/pnas.021544898">doi:10.1073/pnas.021544898</A>]['08].

%A D. Alderson
%A J. C. Doyle
%A L. Li
%A W. Willinger
%T Towards a theory of scale-free graphs: Definition, properties, and
   implications
%J Internet Maths.
%V 2
%N 4
%P 431-523
%D 2005
%K jrnl, c2005, c200x, c20xx, zz0420, maths, graph, model, graphModel,
   scale free, scaleFree, internet, www
%X "... there is unfortunately no consistent, precise definition of scale-free
   graphs & few rigorous proofs of many of their claimed properties. In fact, it
   is easily shown that the existing theory has many inherent contradictions &
   that the most celebrated claims regarding the Internet & biology are
   verifiably false. ... we introduce a structural metric that allows us to
   differentiate between all simple, connected gs. having an identical degree
   seq., which is of particular interest when that seq. satisfies a power law
   relationship. We demonstrate that the proposed structural metric yields
   considerable insight into the claimed properties of SF graphs & provides one
   possible measure of the extent to which a g. is scale-free. This structural
   view can be related to previously studied g. properties such as the various
   notions of self-similarity, likelihood, betweenness & assortativity. ...
   clarifies much of the confusion surrounding the sensational qualitative
   claims in the current literature, & offers a rigorous & quantitative
   alternative, while suggesting the potential for a rich & interesting theory.
   This paper is aimed at readers familiar with the basics of Internet
   technology & comfortable with a theorem-proof style of exposition, but who
   may be unfamiliar with the existing literature on scale-free networks.
   -- 1150477667@[<A HREF="https://projecteuclid.org/euclid.im/1150477667">eucl'd</A>]['20].
   [Also search for: graphModel].

%A R. W. Smith
%T Advanced Linux Networking
%I AddisonWesley
%P 784
%M JUN
%D 2002
%K book, text, Linux, Unix, computer, networks, network, server, servers,
   client, www, ftp, smtp, TCP/IP, TCPIP, dhcp, c2002, c200x, c20xx, zz0103,
   protocols, protocol
%X au$106.  uk us isbn:0201774232.

%A M. Girvan
%A M. E. J. Newman
%T Community structure in social and biological networks
%J PNAS
%V 99
%N 12
%P 7821-7826
%M JUN
%D 2002
%K jrnl, PNAS, c2002, c200x, c20xx, zz0415, graph, network, model, communities,
   community, detection, algorithm, detecting, discovery, centrality
%X "... Researchers have concentrated particularly on a few properties that seem
   to be common to many networks: the small-world property, power-law degree
   distns, & n/wk transitivity. ... we highlight another property that is found
   in many n/wks ... community structure, in which n/wk nodes are joined
   together in tightly knit groups, between which there are only looser
   connections. We propose a method for detecting such communities, built around
   the idea of using centrality indices to find community boundaries. We test
   our method on computer-gen. & real-world graphs whose comm.str. is already
   known & find that the method detects this known struct. with high sensitivity
   & reliability. ... apply the method to two n/wks whose comm.str. is not well
   known - a collaboration network & a food web - & find that it detects sig. &
   informative community divisions in both cases."
   -- [<A HREF="https://arxiv.org/abs/cond-mat/0112110">arXiv</A>]['20],
      [<A HREF="http://dx.doi.org/10.1073/pnas.122653799">doi:10.1073/pnas.122653799</A>]['15].
   (I.e., dense subgraphs with rel. few links between them.)
   (Also see ComStr@[<A HREF="https://en.wikipedia.org/wiki/Community_structure">wikip</A>]['20].)
   [Also search for: community network].

%A A. Inokuchi
%A T. Washio
%A H. Motodo
%T An Apriori-based algorithm for mining frequent substructures from graph data
%J PKDD
%P 13-23
%M JUL
%D 2002
%K conf, PKDD, c2002, c200x, c20xx, zz1114, AGM, apriori, graph, mining,
   network, pattern, substructure, frequent, apriori, transaction
%X "... novel approach named AGM to efficiently mine the association rules among
   the frequently appearing sub-structures in a given graph data set. A graph
   transaction [?!] is represented by an adjacency matrix, & the freq. patterns
   appearing in the matrices are mined through the extended alg. of the basket
   analysis. Its performance has been evaluated for the artificial simuln data
   & the carcinogenesis data of Oxford U. & NTP. Its high efficiency has been
   confirmed for the size of a real-world problem ..."  [14 refs]
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-45372-5_2">doi:10.1007/3-540-45372-5_2</A>]['14].
   [?Does "A graph transaction [?!] is represented by an adjacency matrix"
     mean "graph transaction"="graph"?!]
   [Also search for: graph mining].

%A G. Caldarelli
%A A. Capocci
%A P. De Los Rios
%A M. A. Munoz
%T Scale-free networks from varying vertex intrinsic fitness
%J Phys. Rev. Lett.
%V 89
%P e258702
%M DEC
%D 2002
%K jrnl, eJrnl, c2002, c200x, c20xx, zz1214, graph, network, graphModel, model,
   rich get richer, scale-free, power-law, hub, hubs, preferential attachment
%X "A new mechanism leading to scale-free n/ws is proposed ... It is shown that,
   in many cases of interest, the connectivity power-law behavior is neither
   related to dynamical properties nor to preferential attachment. Assigning a
   quenched fitness value x_i to every vertex, & drawing links among vertices
   with a prob. depending on the fitnesses of the two involved sites, gives
   rise to what we call a good-get-richer mechanism, in which sites with larger
   fitness are more likely to become hubs (i.e., to be highly connected)."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.89.258702">doi:10.1103/PhysRevLett.89.258702</A>]['14].
   (Also see SFN@[<A HREF="http://en.wikipedia.org/wiki/Scale-free_network">wikip</A>]['14].)
   [Also search for: graphModel].

%A X. Yan
%A J. Han
%T CloseGraph: Mining closed frequent graph patterns
%J Proc. Int. Conf. Knowledge Discovery & Data Mining
%D 2003
%K conf, KDD, c2003, c200x, c20xx, zz0814, CloseGraph, gSpan, closed,
   maths, graph, motif, pattern, viaFPj
%X "... A graph g is 'closed' in a database of there exists no proper
   supergraph of g that has the same support as g. ..."
   -- gSpan@[<A HREF="http://www.cs.ucsb.edu/~xyan/software/gSpan.htm">ucsb</A>]['14].

%A Y. Shaked
%A A. Wool
%T Cracking the Bluetooth PIN
%J Proc. 3rd USENIX/ACM Conf. Mobile Systems, Applications, and
   Services (MobiSys)
%W Seattle, WA
%P ?-?
%M JUN
%D 2005
%K conf, wireless, radio, network, networks, blue tooth, c2005, c200x, c20xx,
   security, computer, device, devices, hack, crack, pairing, link, PIN, key
%X "...describes the implementation of an attack on the Bluetooth security
   mechanism. ... passive attack, in which an attacker can find the PIN used
   during the pairing process. We then describe the cracking speed we can
   achieve through three optimizations methods. Our fastest opt. employs an
   algebraic representation of a central cryptographic primitive (SAFER+) used
   in Bluetooth. Our results show that a 4-digit PIN can be cracked in less than
   0.3 sec on an old Pentium III 450MHz computer, & in 0.06 sec on a Pentium IV
   3Ghz HT computer."
   -- [<A HREF="http://www.eng.tau.ac.il/~yash/shaked-wool-mobisys05/">www</A>]['05].

%A N. S. Ketkar
%A L. B. Holder
%A D. J. Cook
%T Subdue: Compression-based frequent pattern discovery in graph data
%J Proc. 1st Int. Workshop on Open Source DataMining
%P ?-?
%D 2005
%K wShop, OSDM, c2005, c200x, c20xx, zz0814, SUBDUE, graph, mining, AI, II,
   frequent, interesting, interest, subgraph, pattern, motif, gSpan, FSG,
   compress, information, viaFPj
%X "... describe the graph-based data mining system Subdue which focuses on the
   discovery of sub-graphs which are not only f. but also compress the g.
   dataset, using a heuristic alg.. The rationale behind the use of a compn
   methodology for frequent pattern discovery is to produce a fewer # of highly
   interesting patterns than to generate a large # of patterns from which
   interesting patterns need to be identified. We perform an experimental
   comparison of Subdue with the g.mining systems gSpan & FSG on the Chemical
   Toxicity & the Chemical Compounds datasets that are provided with gSpan. We
   present results on the performance on the Subdue system on the Mutagenesis &
   the KDD 2003 Citation Graph dataset. An analysis of the results indicates
   that Subdue can efficiently discover best-compressing frequent patterns which
   are fewer in number but can be of higher interest.."  [via FP.]
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.88.8451">c'teseer</A>]['14],
      pdf@[<A HREF="http://ailab.wsu.edu/subdue/papers/KetkarOSDM05.pdf">wsu</A>]['14]
      Subdue@[<A HREF="http://ailab.wsu.edu/subdue/">wsu</A>]['14].
   [[Uses "transaction" probably to mean a "graph"?  Does not explain
     just how compression is done (presumably involves adj. mat.).
     The examples seem to involve finding one(?) subgraph (e.g.,
     a C-ring) common to some given graphs.]]
   [Also search for: chemical compound compress]   and
   [also search for: graph information complexity] and
   [also search for: compress graph].

%A J. C. Doyle
%A D. L. Alderson
%A L. Li
%A S. Low
%A M. Roughan
%A S. Shalunov
%A R. Tanaka
%A W. Willinger
%T The "robust yet fragile" nature of the Internet
%J PNAS
%V 102
%N 41
%P 14497-14502
%M OCT
%D 2005
%K jrnl, PNAS, network, networks, TCPIP, TCP IP, c2005, c200x, c20xx, zz0407,
   graph, graphs, complex, scale free, model, models, tolerance, HOTnet
%X "... relevant beyond either the Internet or the 2 specific approaches
   focused on here (i.e. scale-free networks & highly optimized tolerance NWs)."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0501426102">doi:10.1073/pnas.0501426102</A>]['07].

%A M. A. Moritz
%A M. E. Morais
%A L. A. Summerell
%A J. M. Carlson
%A J. Doyle
%T Wildfires, complexity, and highly optimized tolerance
%J PNAS
%V 102
%N 50
%P 17912-17917
%M DEC
%D 2005
%K PNAS, jrnl, c2005, c200x, c20xx, wildfire, complex, bushfire, sensitivity,
   fire management, ecology
%X "Recent, large fires in the western USA ...  Here, we examine historical fire
   catalogs & a detailed fire simulation model; both are in agreement with a
   highly optimized tolerance [HOT] model. Highly optimized tolerance suggests
   robustness tradeoffs underlie resilience in different fire-prone ecosystems.
   Understanding these mechanisms may provide new insights into the structure of
   ecological systems & be key in evaluating fire management strategies &
   sensitivities to climate change."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0508985102">10.1073/pnas.0508985102</A>]['07]

%A F. Schreiber
%A H. Schwobbermeyer
%T Frequency concepts and pattern detection for the analysis of motifs in
   networks
%J Trans. on Computational Sys. Biol. III
%I SpringerVerlag
%S LNCS
%V 3737
%P 89-104
%D 2005
%K MolBio, c2005, c200x, c20xx, zz0515, FPF, Mavisto, downward, closure,
   network, motif, pattern
%X "... presents 1) three different concepts for the determination of pattern
   freq. & 2) an alg. to compute these freqs.. The different concepts of pattern
   freq. depend on the reuse of n/w elts. The presented alg. finds all or highly
   frequent patterns under consideration of these concepts. ...  demonstrated
   by applying it to biological data."
   -- [<A HREF="http://dx.doi.org/10.1007/11599128_7">doi:10.1007/11599128_7</A>]['15].  (auth1 at mon@sh c2O14.)
   (*** Also see "... exploits the downward closure property ..."
    -- motifs@[<A HREF="http://en.wikipedia.org/wiki/Network_motif">wikip</A>]['15].)
   [Also search for: network motif].

%A N. Lin
%A H. Zhao
%T Are scale-free networks robust to measurement errors?
%J BMC Bioinformatics
%V 16
%N 6
%P 119
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, scale free, networks, error, parameter,
   Saccharomyces cerevisiae, protein interaction, network, yeast
%X "... addresses the impact of erroneous links on n/w topological inference &
   explores possible error mechanisms for scale-free n/ws with an emphasis on
   S.cerevisiae protein interaction n/ws. ... show that the ignorance of
   erroneous links in n/w analysis may lead to biased ests. of the scale
   param. & recommend robust estimators in such scenarios. ... in the presence
   of erroneous links, the connectivity distribution of scale-free n/ws is still
   scale-free for the middle range connectivities, but can be greatly distorted
   for low & high connecitivities. ..."  (via AK).
   [<A HREF="http://dx.doi.org/10.1186/1471-2105-6-119">doi:10.1186/1471-2105-6-119</A>]['08].

%A T. Y. Wong
%A K. T. Law
%A J. C. S. Lui
%A M. H. Wong
%T An efficient distributed algorithm to identify and traceback DDoS traffic
%J COMPJ
%V 49
%N 4
%P 418-442
%M JUL
%D 2006
%K jrnl, COMPJ, c2006, c200x, c20xx, zz0707, network, denial of service attack,
   internet, trace back, attackers, attacker, router, routers, ICMP
%X [<A HREF="http://dx.doi.org/10.1093/comjnl/bxl026">doi:10.1093/comjnl/bxl026</A>]['06]

%A T. Ho
%A D. S. Lun
%T Network Coding: An Introduction
%I CUP
%P 184
%D 2008
%K book, text, CUP, c2008, c200x, c20xx, zz0709, network, networks, encoding,
   coded, communications, multicast, security, intro
%X 1st ed 2008; hb us$43; uk us isbn:052187310X; uk us isbn13:978-0521873109.
   1 the network model
   2 lossless multicast network coding
   3 inter-session network coding
   4 network coding in lossy networks
   5 subgraph selection
   6 security against adversarial errors,
   (Rev'd by I. G e i l in [<A HREF="http://comjnl.oxfordjournals.org/cgi/reprint/52/4/510">C.J.</A>]['09].)

%A G. Buehrer
%A K. Chellapilla
%T A scalable pattern mining approach to web graph compression with communities
%J Proc. Int. Conf. on Web Search and Data Mining
%P 95-106
%D 2008
%K conf, WSDM, c2008, c200x, c20xx, zz0415, graph, network, web, www, frequent,
   pattern, biclique, compress, compression, PageRank, link server
%X "... a compression scheme for the web graph specifically designed to
   accommodate community queries & other random access algs. on link servers. We
   use a freq. pattern mining approach to extract meaningful connectivity
   formations. ... achieves graph compn without sacrificing r.a. by gen.
   virtual nodes from frequent itemsets in vertex adjacency lists. ...
   guarantees scalability by bounding the pattern mining complexity to
   O(E log E). We facilitate global mining, relaxing the requirement for the
   graph to be sorted by URL, enabling discovery for both inter-domain [&]
   intra-domain patterns. [So] allows incremental g. updates. [&] it not only
   facilitates [&] expedite g. compns such as PageRank & local random walks by
   implementing them directly on the compressed g.. We demo. ... approach on
   several publicly available large web g. data sets. Experimental results
   indicate that the proposed alg. achieves a 10- to 15-fold compn on most real
   word web g. data sets."
   -- [<A HREF="http://dx.doi.org/10.1145/1341531.1341547">doi:10.1145/1341531.1341547</A>]['15].
   [Also search for: compress graph].

%A Y. Asano
%A Y. Miyawaki
%A T. Nishizeki
%T Efficient compression of web graphs
%J COCOON
%P 1-11
%D 2008
%K conf, c2008, c200x, c20xx, zz0415, web graph, network, compress, www,
   internet, pages, links, succinct
%X "Several methods have been proposed for compressing the linkage data of a Web
   graph. Among them, the method proposed by Boldi & Vigna is known as the most
   efficient one. ... we propose a new method to compress a W.graph. [It] is
   more efficient than theirs wrt the size of the compressed data.  Eg, our
   method needs only 1.99 bits per link to compress a Web graph containing
   3,216,152 links connecting 325,557 pages [v.] 2.84 bits per link to
   compress the same W.graph."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-69733-6_1">doi:10.1007/978-3-540-69733-6_1</A>]['15],
      pdf@[<A HREF="http://www.ecei.tohoku.ac.jp/alg/nishizeki/sub/j/DVD/PDF_J/J179.pdf">tohoku</A>]['14].
   [Also search for: compress graph].

%A S. Navlakha
%A R. Rastogi
%A N. Shrivastava
%T Graph summarization with bounded error
%J SIGMOD Int. Conf.
%I ACM
%P 419-432
%D 2008
%P conf, c2008, c200x, c20xx, zz0415, network, graph, summary, compress, MDL,
   error, aggregate, supernode, superedge
%X "We propose a highly compact two-part repn of a given graph G consisting of a
   graph summary & a set of corrections. The g.summary is an aggregate g. in
   which each node corresponds to a set of nodes in G, & each edge represents
   the edges between all pair of nodes in the two sets. On the other hand, the
   corrections portion specifies the list of edge-corrns that should be applied
   to the summary to recreate G. Our repn allow for both lossless & lossy g.
   compression with bounds on the introduced error. [&] in combination with the
   MDL principle, they yield highly intuitive coarse-level summaries of the
   input graph G. We develop algs. to construct highly compressed
   g.representations with small sizes & guaranteed accuracy, & validate our
   approach through an extensive set of experiments with multiple real-life
   g. data sets.  To the best of our knowledge, this is the first work to
   compute g.summaries using the MDL principle, & use the summaries (along with
   corrections) to compress graphs with bounded error."
   -- "... if two nodes have edges to the same set (or v.similar set) of other
      nodes, then we can collapse them into a supernode & replace the two edges
      going to each common neighbor with a single superedge."  [& corrections]
   -- [<A HREF="http://dx.doi.org/10.1145/1376616.1376661">doi:10.1145/1376616.1376661</A>]['15].
   ("each node corr ... in the two sets." - sounds like bipartite cliques.)
   [Also search for: compress graph] and [also search for: compress graph mml].

%A D. Achlioptas
%A R. M. D'Souza
%A J. Spencer
%T Explosive percolation in random networks
%J Science
%V 323
%N 5920
%P 1453-1455
%M MAR
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0309, random, network, networks, graphs,
   ERmodel, graphModel, connected, connectivity, percolation, discontinuous,
   dSouza
%X "... a critical point, the addition of a small # of connections causes a
   sizable fraction of the n/w to suddenly become linked together. Typically
   such transitions are continuous, so that the % of the n/w linked together
   tends to zero right above the transition point. Whether percolation
   transitions could be discontinuous has been an open question. ... show that
   incorporating a limited amount of choice in the classic Erdos-Renyi n/w
   formation model causes its percolation transition to become disc.. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1167782">doi:10.1126/science.1167782</A>]['09].
   (And "perspective": [<A HREF="http://dx.doi.org/10.1126/science.1171297">doi:10.1126/science.1171297</A>]['09].)

%A J. B. Glattfelder
%A S. Battiston
%T Backbone of complex networks of corporations: The flow of control
%J arXiv
%D 2009
%K report, c2009, c200x, c20xx, ETHZ, network, interconnections, economics,
   economy, finance, trade, transnational, company, companies, corporation,
   TNC, share market, capitalism, wealth, rich, power, wealth
%X "... methodology to extract the backbone of complex networks based on the
   weight & direction of links, as well as on nontopological properties of
   nodes. ... can be applied in general to networks in which mass or energy is
   flowing along the links. In particular, the procedure enables us to address
   important questions in economics, namely, how control & wealth are structured
   & concentrated across national markets. We report on the first cross-country
   investigation of ownership networks, focusing on the stock markets of 48
   countries around the world. On the one hand, our analysis confirms results
   expected on the basis of the literature on corporate control, namely, that
   in Anglo-Saxon countries control tends to be dispersed among numerous
   shareholders. On the other hand, it also reveals that in the same countries,
   control is found to be highly concentrated at the global level, namely, lying
   in the hands of very few important shareholders. Interestingly, the exact
   opposite is observed for European countries. ..."
   -- @[<A HREF="http://arxiv.org/abs/0902.0878">arXiv</A>]['11],
   auth1@[<A HREF="http://www.sg.ethz.ch/people/formercoll/jglattfelder">ethz</A>]['11].
   [Also search for: economics network].

%A F. Chierichetti
%A R. Kumar
%A S. Lattanzi
%A M. Mitzen-macher
%A A. Panconesi
%A P. Raghavan
%T On compressing social networks
%J KDD
%P 219-228
%D 2009
%K conf, KDD, c2009, c200x, c20xx, zz0415, network, graph, social, communities,
   compress, web, Boldi, shingle, heuristic, shingles, MLogA, MLogGapA,
   Jaccard coefficient
%X "Motivated ... the Web graph that support efficient data structs. for in
   memory adjacency queries, we study the extent to which a large n/wk can be
   compressed. Boldi & Vigna (WWW 2004), showed that Web graphs can be
   compd down to  three bits  of storage / edge; we study the compressibility
   of social n/wks where again adj.queries are a fundamental primitive. ...
   propose simple combinatorial formulations that encapsulate efficient
   compressibility of graphs. We show that some of the problems are NP-hard yet
   admit effective heuristics, some of which can exploit properties of social
   n/wks such as link reciprocity. Our extensive experiments show that social
   n/wks & the Web g. exhibit vastly different compressibility characteristics."
   -- "... s a perm ... M_s(A) = smallest element in A according to s; we call
      it the shingle. ... heuristic is to treat the out-neighbors out(u) of a
      node u as a set & compute the shingle M_s(out(u)) of this set for a
      suitabe perm. (or hash fn) s. The nodes ... ordered by the shingles. ..."
   -- [<A HREF="http://dx.doi.org/10.1145/1557019.1557049">doi:10.1145/1557019.1557049</A>]['15],
      pdf@[<A HREF="http://www.eecs.harvard.edu/~michaelm/postscripts/kdd2009.pdf">h@rv@rd</A>]['15].
   [Also search for: compress graph].

%A A. Apostolico
%A G. Drovandi
%T Graph compression by BFS
%J Algorithms
%V 2
%N 3
%P 1031-1044
%M AUG
%D 2009
%K jrnl, c2009, c200x, c20xx, zz0415, network, graph, compress, web,
   BFS, breadth first search, succinct
%X "The Web Graph ... This paper introduces a compression scheme that combines
   efficient storage with fast retrieval for the information in a node. [It]
   exploits the properties of the Web Graph without assuming an ordering of the
   URLs, so that it may be applied to more general graphs. Tests on some
   datasets of use achieve space savings of about 10% over existing methods."
   -- [<A HREF="http://dx.doi.org/10.3390/a2031031">doi:10.3390/a2031031</A>]['15].
   [Also search for: compress graph].

%A S. Omidi
%A F. Schreiber
%A A. Masoudi-Nejad
%T MODA: An efficient algorithm for network motif discovery in
   biological networks
%J Genes & Genetic Systems
%V 84
%N 5
%P 385-395
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1114, MODA, network, pattern, motif,
   discover, Falk
%X "... Unfortunately, n/w motif discovery is a computationally hard problem &
   finding rather large motifs (> 8 nodes) by means of current algs. is
   impractical as it demands too much comp.effort. ... present a new alg. (MODA)
   that incorporates techniques such as a pattern growth approach for extracting
   larger motifs efficiently.  ... tested our alg. & found it able to identify
   larger motifs with > 8 nodes more efficiently than most of the current
   state-of-the-art motif discovery algs.. While most of the algs. rely on
   induced subgraphs as motifs of the n/ws, MODA is able to extract both induced
   & non-induced subgraphs simultaneously. The MODA source code is freely
   available at [<A HREF="http://LBB.ut.ac.ir/Download/LBBsoft/MODA/">www</A>]['09]."
   -- [<A HREF="http://dx.doi.org/10.1266/ggs.84.385">doi:10.1266/ggs.84.385</A>]['14],
      20154426@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/20154426">p'bmed</A>]['14].
   (FalkS., auth2 @monash c2O14.
   *** [Also search for: enumerate subgraph graph]. ***)

%A Wei Chen
%A Zhenming Liu
%A Xiaorui Sun
%A Yajun Wang
%T Community detection in social networks through community formation games
%J IJCAI
%P 2576-2581
%D 2010
%O Data Mining and Knowledge Discovery, 21(2), 2010
%K conf, IJCAI, c2010, c201x, c20xx, zz0620, Newman, community formation game,
   social network, modularity, media, overlapping, community detection,
   detecting, discovery, communities, cohesion, sociogram, analysis
%X "... The dynamics ofcommunity formation is framed as a strategic game called
   community formation game: Given a social network, each node is selfish &
   selects communities to join or leave based on her own utility measurement. A
   community struct. can be interpreted as an equilibrium of this game. We
   formulate the agentsâ utility by the combination of a gain fn & a loss fn.
   Each agent can select multiple communities ..."
   -- [<A HREF="https://www.ijcai.org/Proceedings/11/Papers/429.pdf">www</A>]['20].
   (Also see SocialNA@[<A HREF="https://en.wikipedia.org/wiki/Social_network_analysis">wikip</A>]['20].)
   [Also search for: community network].

%A R. Cohen
%A S. Havlin
%T Complex Networks: Structure, Robustness and Function
%I CUP
%P 248
%D 2010
%K book, text, L4Ref, L5Ref, CUP, c2010, c201x, c20xx, zz1010, complex, network,
   robust, stability, epidemic
%X "... graduate-level textbook is a step-by-step presentation of the structure
   & function of complex networks. Using a range of [eg], from the stability
   of the internet to efficient methods of immunizing populations, & from
   epidemic spreading to how one might efficiently search for individuals ..."
   1st ed 2010; hb us$47; uk us isbn:0521841569; uk us isbn13:978-0521841566.

%A O. Riordan
%A L. Warnke
%T Explosive percolation is continuous
%J Science
%V 333
%N 6040
%P 322-324
%M JUL
%D 2011
%K jrnl, c2011, c201x, c20xx, network, graph, random, Achlioptas process,
   growth, phase transition
%X "'Explosive percolation' is said to occur in an evolving network when a
   macroscopic connected component emerges in a # of steps that is  '< <'  than
   the sys.size. Recent predictions based on simulations suggested that certain
   Achlioptas processes (much-studied local modifications of the classical
   mean-field growth model of Erdos & Renyi) exhibit this phenomenon, undergoing
   a phase transition that is discontinuous in the scaling limit. We show that,
   in fact, all Achlioptas processes have continuous phase transitions, although
   related models in which the # of nodes sampled may grow with the n/w size
   can indeed exhibit explosive percolation."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1206241">doi:10.1126/science.1206241</A>]['11].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.1208712">persp.</A>].)
   [Also search for: random graph]  and  [also search for: graphModel].

%A U. Kang
%A C. Faloutsos
%T Beyond 'caveman communities': Hubs and spokes for graph compression and
   mining
%J ICDM
%I IEEE
%P 300-309
%M DEC
%D 2011
%K cond, ICDM, c2011, c201x, c20xx, zz0415, network, graph, hub, spoke,
   power law, network, web, graph, model, community, compress,
   slash burn, slashburn, cut, cuts
%X "... We show that the block-diagonal mental image of the 'cavemen graph' is
   the wrong paradigm, in full agreement with earlier results that real world
   graphs have no good cuts. Instead, we propose to envision gs. as a colln of
   hubs connecting spokes, with super-hubs connecting the hubs, & so on,
   recursively. ... propose the Slash Burn method (burn the hubs, & slash the
   remaining g. into smaller connected components). Our view point has several
   advantages: (a) it avoids the 'no good cuts' problem, (b) it gives better
   compression, & (c) it leads to faster exec. times for matrix-vector ops.,
   which are the back-bone of most g.processing tools. Experimental results show
   that our [SB] method consistently outperforms other methods on all datasets,
   giving good compression & faster running time."
   -- [<A HREF="http://dx.doi.org/10.1109/ICDM.2011.26">doi:10.1109/ICDM.2011.26</A>['15],
      10.1.1.208.660@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.208.660">citeseer</A>]['15].
   It's good for "power law" networks.
   [Also search for: compress graph]  and  [also search for: graphModel].

%A S. Vitali
%A J. B. Glattfelder
%A S. Battiston
%T The network of global corporate control
%J arXiv
%M JUL
%D 2011
%O ?PLoS One ?to appear?
%K TR, arXiv, c2011, c201x, c20xx, zz0812, economics, world, TNC, company,
   transnational corporations, power, finance, control, stability, instability,
   unstable, network, competition, Orbis, connected, interconnected, society,
   global, business, holdings, Barclays, JPMorgan, J P Morgan, Merrill Lynch,
   superentity, super entity
%X "The structure of the control n/work of transnational corps. affects global
   market competition & financial stability. So far, only small national samples
   were studied & there was no appropriate methodology to assess control
   globally. We present the first investigation of the architecture of the
   internl ownership n/work, along with the computation of the control held by
   each global player. We find that transnational corps. form a giant bow-tie
   structure & that a large portion of control flows to a small tightly-knit
   core of financial instns. This core can be seen as an economic 'super-entity'
   that raises new important issues both for researchers & policy makers."
   (Rank   Economic actor name
    1      BARCLAYS PLC;
    2      CAPITAL GROUP COMPANIES INC, THE;
    3      FMR CORP;
    4      AXA;
    5      STATE STREET CORPORATION;
    6      JPMORGAN CHASE & CO.;
    7      LEGAL & GENERAL GROUP PLC;
    8      VANGUARD GROUP, INC., THE;
    9      UBS AG;
   10      MERRILL LYNCH & CO., INC.;
   ... .)
   -- 1107.5728@[<A HREF="http://arxiv.org/abs/1107.5728">arXiv</A>][12'],
   auth2@[<A HREF="http://www.sg.ethz.ch/people/formercoll/jglattfelder">ethz</A>]['12].
   (Also see company DB orbis@[<A HREF="http://www.bvdinfo.com/Products/Company-Information/International/Orbis">www</A>]['12].)
   [Also search for: economics network].

%A C. Hernandez
%A G. Navarro
%T Compressed representation of web and social networks via sense subgraphs
%J String Proc. and Info. Retrieval
%I SpringerVerlag
%S LNCS
%V 7608
%P 264-276
%D 2012
%K conf, c2012, c201x, c20xx, zz0415, network, graph, dense subgraph, pattern,
   compress, succinct, data structure, web, social, biclique
%X "... propose a novel compressed structure aiming to reduce storage & support
   efficient navigation over web & social graph compressed repns. [It] uses
   clustering & mining for finding dense subgraphs & represents them using
   compact data structs.. We perform experiments using a wide range of web &
   social n/ws & compare our results with the best known techniques. ... also
   enables mining queries based on dense subgs., such as cliques & bicliques."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-34109-0_28">doi:10.1007/978-3-642-34109-0_28</A>]['15].
   [Also search for: compress graph].

%A S. Battiston
%A M. Puliga
%A R. Kaushik
%A P. Tasca
%A G. Caldarelli
%T DebtRank: Too central to fail? Financial networks, the FED and systemic risk
%J Nature Scientific Reports
%V 2
%N 541
%M AUG
%D 2012
%K c2012, c201x, c20xx, zz0812, economics, big business, bank, banks, banking,
   DebtRank, FOC, FOCproject, finance, GFC, crisis, crises, risk, fail, failure,
   network, graph, holding, debt rank, interconnected
%X "Systemic risk ... depends on the n/wk of financial exposures among
   institutions. ... introduce, DebtRank, a novel measure of systemic impact
   inspired by feedback-centrality. [eg] analyse a new & unique dataset on the
   USD 1.2 trillion FED emergency loans program to global financial instns
   during 2008-2010. We find that a group of 22 instns, which received most of
   the funds, form a strongly connected graph where each of the nodes becomes
   systemically important at the peak of the crisis. Moreover, a systemic
   default could have been triggered even by small dispersed shocks. ... suggest
   that the debate on too-big-to-fail instns should include the even more
   serious issue of too-central-to-fail."
   -- [<A HREF="http://dx.doi.org/10.1038/srep00541">doi:10.1038/srep00541</A>]['12],
   or [<A HREF="http://www.nature.com/srep/2012/120802/srep00541/full/srep00541.html">nature</A>]['12],
   &  focproject@[<A HREF="http://www.focproject.net/">www</A>]['12].
   [Also search for: economics network].

%A F. Papadopoulos
%A M. Kitsak
%A M. A. Serrano
%A M. Boguna
%A D. Krioukov
%T Popularity versus similarity in growing networks
%J Nature
%V 489
%N 7417
%P 537-540
%M SEP
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0912, network, graph, growth, popularity,
   preferential attachment, attraction, edge, connection, rich get richer,
   power law, laws
%X "The principle that 'popularity is attractive' underlies pref.attachment
   ... the resulting distribution of the number of connections possessed by
   nodes follows power laws ... Pref.a. has been directly validated for some
   real n/wks (inc. the 'net), ...  we show that popularity is just one
   dimn of attractiveness; another d. is similarity. We develop a framework in
   which new connections optimize certain trade-offs between popularity &
   similarity, instead of simply preferring popular nodes. ... has a geometric
   interp. in which pop.pref. emerges from local optimization. [v.] pref.a.,
   our optimization framework accurately describes the large-scale evoln of
   technological (the 'net), social (trust relationships between people) &
   biol. (E.coli metabolic) n/wks, predicting the prob. of new links with
   high precision. ... can thus be used for predicting new links in evolving
   n/wks, & provides a different perspective on pref.a. as an emergent
   phenomenon."  [online Sept 2012].
   -- [<A HREF="http://dx.doi.org/10.1038/nature11459">doi:10.1038/nature11459</A>]['12].

%A X. Li
%A D. S. Stones
%A H. Wang
%A H. Deng
%A X. Liu
%A G. Wang
%T NetMODE: Network motif detection without Nauty
%J PLoS One
%V ?
%M DEC
%D 2012
%K eJrnl, PLoS, c2012, c201x, c20xx, zz0115, NetMODE, network, networks, motif,
   pattern, subgraph, discovery, enumerate
%X "A motif in a n/w is a connected graph that occurs sig. more frequently as an
   induced subgraph than would be expected in a similar randomized n/w. ...
   Classifying the subgraphs encountered, for instance, is typically performed
   using a graph canonical labeling package, such as Nauty ... we describe an
   implementation of a n/w motif detection package, which we call NetMODE.
   NetMODE can only perform motif detection for k-node subgraphs when k <= 6,
   but does so without the use of Nauty. ... has an initial pretreatment phase,
   where k-node graph data is stored in memory (k <= 5). For k=6 we take a novel
   approach, which relates to the Reconstruction Conjecture for directed graphs.
   ... NetMODE can perform up to ~30 times faster than its predecessors when
   k <= 5 and up to ~20 times faster when k=6 ... also (a) includes a method for
   generating comparison graphs uniformly at random, (b) can interface with
   external packages (e.g. R), & (c) can utilize multi-core architectures.
   NetMODE is available from netmode.sf.net."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0050093">doi:10.1371/journal.pone.0050093</A>]['14].
   [Also search for: graph reconstruction conjecture] and
   [also search for: enumerate subgraph graph].

%A A. Farzan
%A J. I. Munro
%T Succinct encoding of arbitrary graphs
%J Theor. Comp. Sci.
%V 513
%P 38-52
%M NOV
%D 2013
%K jrnl, TCS, c2013, c201x, c20xx, zz0415, maths, graph, network, compress,
   compression, succinct encoding, data structure,
   adjacency, neighborhood, degree
%X "... problem of encoding graphs with n vertices & m edges compactly
   supporting adjacency, neighborhood & degree queries in const. time in the
   Theta(log n)-bit word RAM model. ... prove a lwb in the cell probe model
   indicating it is impossible to achieve the info.-theory lwb up to lower order
   terms unless the graph is either too sparse (m=o(n**delta) for any constant
   delta > 0) or too dense (m=omega(**(2-delta) ...). ... present a succinct
   encoding of graphs supporting aforementioned queries in const. time. The
   space requirement of the encoding is within a multiplicative 1+eps factor of
   the info.-theory lwb for any arb. small const. eps > 0. This is the best
   achievable space bound according to our lwb where it applies. The space
   requirement of the repn achieves the info.-theory lwb tightly within lower
   order terms where the graph is very sparse (m=o(n**delta ...) or v.dense
   (m > n**2/lg**(1-delta)(n) ...)."
   -- [<A HREF="http://dx.doi.org/10.1016/j.tcs.2013.09.031">doi:10.1016/j.tcs.2013.09.031</A>]['15].
   [Also search for: compress graph].

%A F. Nourbakhsh
%A S. Rota Bulo
%A M. Pelillo
%T A matrix factorization approach to graph compression with partial information
%J Int. J. Mach. Learning and Cyberetics
%V SpringerVeralg
%V ?
%P 1-14
%M AUG
%D 2014
%K jrnl, IJMLC, c2014, c201x, c20xx, zz0415, network, graph, compress, lossy,
   reconstruction error, matrix, factorization
%X "... the problem of encoding a graph of order n into a graph of order k < n
   in a way to minimize reconstruction error. This encoding is characterized in
   terms of a particular factorization of the adj.matrix of the original g.. The
   factn is determined as the soln of a discrete optn problem, which is for
   convenience relaxed into a cts, but equiv., one. Our formulation does not
   require to have the full g., but it can factorize the g. also in the presence
   of partial info.. We propose a multiplicative update rule for the optn task
   resembling the ones introduced for nonnegative matrix f., & convergence
   properties are proven. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/s13042-014-0286-5">doi:10.1007/s13042-014-0286-5</A>]['15].
   [Also search for: compress graph].

%A R. S. Farr
%A J. L. Harer
%A T. M. A. Fink
%T Easily repairable networks: Reconnecting nodes after damage
%J Phys. Rev. Lett.
%V 113
%P 138701
%M SEP
%D 2014
%K jrnl, eJrnl, c2014, c201x, c20xx, zz1014, network, fault, damage, repair,
   reconnect, maths, graph
%X "We introduce a simple class of distribution networks that withstand damage
   by being repairable instead of redundant. Instead of asking how hard it is to
   disconnect nodes through damage, we ask how easy it is to reconnect nodes
   after damage. We prove that optimal n/ws on regular lattices have an expected
   cost of reconnection proportional to the lattice length, & that such n/ws
   have exactly three levels of structural hierarchy. We extend our results to
   n/ws subject to repeated attacks, in which the repairs themselves must be
   repairable. We find that, in exchange for a modest increase in repair cost,
   such n/ws are able to withstand any number of attacks."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.113.138701">doi:10.1103/PhysRevLett.113.138701</A>]['14].

%A J. Leskovec
%A A. Krevl
%T SNAP datasets: Stanford large network dataset collection
%M JUN
%D 2014
%K TR, c2014, c201x, c20xx, zz1020, network repository, networkRepository,
   networks, graphs, data, dataset, datasets, SNAP
%X -- [<A HREF="http://snap.stanford.edu/data/">www</A>]['20].
   [Also search for: networkRepository].

%A E. Estrada
%A P. A. Knight
%T A First Course in Network Theory
%I OUP
%P 272
%M MAR
%D 2015
%K book, text, OUP, c2015, c201x, c20xx, zz0515, networks
%X 1st ed 2015; pb us$30; uk us isbn:0198726465; uk us isbn13:978-0198726463.
   "... of interest in various disciplines ranging from physics & maths., to
   biol. & sociology. ... useful tools for modern practitioners of network
   theory. These include degree distributions, random n/wks, n/wk fragments,
   centrality measures, clusters & communities, communicability, & local &
   global properties ..."

%A S. Maneth
%A F. Peternek
%T A survey on methods and systems for graph compression
%J arXiv
%M APR
%D 2015
%K TR, c2015, c201x, c20xx, graph, compress
%X "... an informal survey (meant to accompany another paper) on graph
   compression methods. We focus on lossless methods, briefly list available
   pproaches, and compare them where possible or give some indicators on their
   compression ratios. We also mention some relevant results from the field of
   lossy compression and algorithms specialized for the use on large graphs
   Note: The comparison is by no means complete. ..."
   -- 1504.00616@[<A HREF="http://arxiv.org/abs/1504.00616">arXiv</A>]['15].
   [Also search for: graph compress].

%A R. L. Lumsdaine
%A D. N. Rockmore
%A N. Foti
%A G. Leibon
%A J. D. Farmer
%T The intrafirm complexity of systemically important financial institutions
%J arXiv
%M MAY
%D 2015
%K arXiv, TR, c2015, c201x, c20xx, zz0515, firm, firms, companies, bank, banks,
   banking, multinational, transnational, financial institution, control,
   network, SIFI, stability, connected, interconnected,
   economics, law, regulation
%X "... we take on the challenges of measuring the complexity of a financial
   institution & to that end explore the use of the structure of an individual
   firm's control hierarchy as a proxy for inst. complexity. The control
   hierarchy is a n/wk representation of the institution & its subsidiaries. We
   show that this math. representation (& various assoc. metrics) provides a
   consistent way to compare the complexity of firms with often very disparate
   business models & as such may provide the foundation for determining a SIFI
   [systemically important financial institutions] designation. ..."
   -- 1505.02305@[<A HREF="http://arxiv.org/abs/1505.02305">arXiv</A>]['15].
   [Also search for: economics network].

%A F. Morone
%A H. A. Makse
%T Influence maximization in complex networks through optimal percolation
%J Nature
%V 524
%N 7563
%P 65-68
%M AUG
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0815, network, collective, influence, CI,
   influencer, opinion, social, contagion, epidemic, centrality, hubs
%X "... a specific set of structural nodes, much smaller than the total size,
   which, if activated, would cause the spread of info. to the whole n/wk ...
   or, if immunized, would prevent the diffusion of a large scale epidemic.
   Localizing this optimal, that is, minimal, set of structural nodes, called
   influencers ... map the problem onto optimal percolation in random n/wks to
   identify the minimal set of influencers, which arises by minimizing the
   energy of a many-body sys., where the form of the interactions is fixed by
   the non-backtracking matrix of the n/wk. ... much smaller than the one
   predicted by prev. heuristic centralities. Remarkably, a large # of prev.
   neglected weakly connected nodes emerges among the optimal influencers. These
   are topologically tagged as low-degree nodes surrounded by hierarchical
   coronas of hubs, & are uncovered only through the optimal collective
   interplay of all the influencers in the n/wk. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature14604">doi:10.1038/nature14604</A>]['15].
   [Also search for: influence network].

%A R. A. Rossi
%A N. K. Ahmed
%T An interactive data repository with visual analytics
%J SIGKDD Explor.
%V 17
%N 2
%P 37-41
%D 2016
%K TR, c2016, c201x, c20xx, zz1020, Network repository, NetworkRepository,
   networks, database, graphs, data, dataset, datasets, GraphViz, collection
%X -- [<A HREF="http://networkrepository.com">www</A>]['20].
   [Also search for: NetworkRepository].

%A A. Grover
%A J. Leskovec
%T node2vec: Scalable feature learning for networks
%J KDD
%P 855-864
%M AUG
%D 2016
%K Conf, KDD, c2016, c201x, c20xx, zz1220, node2vec, graph, network, feature,
   neighbourhood, node, embed, embedding, Gensi, word2vec, algorithm, SNAP
%X "... we propose node2vec, an algorithmic framework for learning cts feature
   rep'ns for nodes in networks. In node2vec, we learn a mapping of nodes to a
   low-dimensional space of features that maximizes the likelihood of preserving
   n/wk neighborhoods of nodes ..."
   -- [<A HREF="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5108654/">ncb'</A>]['20],
      [<A HREF="https://doi.org/10.1145/2939672.2939754">doi:10.1145/2939672.2939754</A>]['20].
   Also see snap@[<A HREF="https://snap.stanford.edu/node2vec/">www</A>]['20].

%A K. Lee
%A D. Hoon Lee
%A J. Hwan Park
%A M. Yung
%T CCA security for self-updatable encryption: Protecting cloud data when
   clients read/write ciphertexts
%J COMPJ
%V 62
%N 4
%P 545-562
%M APR
%D 2019
%K jrnl, COMPJ, c2019, c201x, c20xx, zz0419, encryption, chosen ciphertext, CCA,
   cyphertext, SUE, public-key, cloud server, revocable, RS-ABE, RSABE,
   networks, computer security
%X "Self-updatable encryption (SUE) is a new kind of public-key encryption,
   motivated by cloud computing, which enables anyone (i.e., cloud server with
   no access to private keys) to update a past ciphertext to a future ciphertext
   by using a public key. The main applications of SUE are revocable-storage
   attribute-based encryption (RS-ABE) that provides an efficient & secure
   access control to encrypted data stored in cloud storage. ... a new threat
   s.t. a revoked user still can access past ciphertexts ... RS-ABE solves this
   problem by combining user revocation & ciphertext updating functionalities.
   We propose the first SUE & RS-ABE schemes secure against a relevant form of
   chosen-ciphertext security (CCA). Due to the fact that some ciphertexts are
   easily derived from others, we employ a different notion of CCA that avoids
   easy challenge related messages. Specifically, we define 'time extended
   challenge' CCA security for SUE which excludes ciphertexts that are easily
   derived from the challenge (over time periods) from being queried on. We then
   propose an efficient SUE scheme with such CCA security, & we also present an
   RS-ABE scheme with this CCA security."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxy122">doi:10.1093/comjnl/bxy122</A>]['19].

%A Jiahao Guo
%A P. Singh
%A K. E. Bassler
%T Reduced network extremal ensemble learning (RenEEL) scheme for
   community detection in complex networks
%J Sci. Rep.
%V 9
%P #14234
%M OCT
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz0820, community detection, algorithm,
   network
%X "... ensemble learning scheme for community detection ... found by a
   conventional base alg., to find a node partition that maximizes modularity.
   At each iter'n, core groups of nodes that are in the same community in every
   ensemble part'n are identified & used to form a reduced n/wk. Partitions of
   the reduced n/wk are then found & used to update the ensemble. ..."
   -- [<A HREF="https://doi.org/10.1038/s41598-019-50739-3">doi:10.1038/s41598-019-50739-3</A>]['20].
   (Also see ComStr@[<A HREF="https://en.wikipedia.org/wiki/Community_structure">wikip</A>]['20].)
   [Also search for: community network].

%A D. Nguyen
%A A. Vullikanti
%T Differentially private densest subgraph detection
%X arXiv
%M MAY
%D 2021
%K TR, c2021, c202x, c20xx, zz0521, differential privacy, dense subgraph
%X "Densest subgraph detection ... However, in many domains, the n/wk is private
   & returning a densest SG can reveal info. about the n/wk. Differential
   privacy ... handle such settings. We study the densest SG problem in the edge
   privacy model, in which the edges of the g. are private. We present the first
   sequential & parallel DP algs. for this problem. We show that our algs. have
   an additive approximation guarantee. We evaluate [them] on a large # of
   real-world n/wks, & observe a good privacy-accuracy tradeoff when the n/wk
   has high density."
   -- 2105.13287@[<A HREF="https://arxiv.org/abs/2105.13287">arXiv</A>]['21].
      (I am told: It's a typical g.DP problem. Adding noise to the answers of
      an existing subgraph mining alg., so the true answer is protected.)
   [Also search for: differential privacy].


%A M. Wright
%T Interior methods for constrained optimization
%J Acta Mathematica
%D 1992
%K jrnl, constraint, c1992, c199x, c19xx, programming, minimize, survey,
   method, point, constraints, nonlinear, non-linear
%X Ref from: [<A HREF="http://www-unix.mcs.anl.gov/otc/Guide/faq/nonlinear-programming-faq.html">www</A>]['05]

%A J. J. More
%A S. J. Wright
%T Optimization Software Guide
%I SIAM
%D 1993
%K book, c1993, c199x, c19xx, NEOS, linear, non, Nonlinear, NLP, quadratic, QP,
   constrained, constraint, constraints, programming, optimisation, optimise,
   optimize, problem, algorithm
%X Ref from: [<A HREF="http://www.optimization-online.org/">optimization-online.org</A>]['05]
   [<A HREF="http://www-fp.mcs.anl.gov/otc/Guide/">www</A>]['05]

%A H. Muehlenbein
%A G. Paass
%T From recombination of genes to the estimation of distributions I,
   binary parameters
%J Proc. Fourth Conf. Parallel Problem Solving from Nature
%I Springer
%S LNCS
%V 1141
%P 178-188
%D 1996
%K conf, c1996, c199x, c19xx, estimation of distribution algorithm, EDA, zz0707,
   optimise, optimisation, optimization, search, BGA
%X "The Breeder [GA] (BGA) is based on the equn for the response to selection.
   ...to use this equn for prediction, the variance of the fitness of the pop'n
   has to be estimated. For the usual sexual recombination the computation can
   be difficult. [we] state the problem & investigate several modifications of
   sexual recombination. The 1st method is gene pool recombination, which leads
   to marginal distribution algs..  [also] discuss more sophisticated methods,
   based on estimating the distribution of promising points."
   [<A HREF="http://dx.doi.org/10.1007/3-540-61723-X_982">doi:10.1007/3-540-61723-X_982</A>]['07]
   Also see part II. [Also search for: estimation distribution algorithm]

%A H. Muehlenbein
%A G. Paass
%T From recombination of genes to the estimation of distributions II,
   continuous parameters
%J Proc. Fourth Conf. Parallel Problem Solving from Nature
%I Springer
%S LNCS
%V 1141,
%P 188-197
%D 1996
%K conf, c1996, c199x, c19xx, estimation of distribution algorithm,
   optimise, optimisation, optimization, search
%X [<A HREF="http://dx.doi.org/10.1007/3-540-61723-X_983">doi:10.1007/3-540-61723-X_983</A>]['07]
   Also see part I. [Also search for: estimation distribution algorithm]

%A T. Fruhwirth
%T Theory and practice of constraint handling rules
%J J. Logic Prog.
%V 37
%N 1-3
%P 95-138
%M OCT
%D 1998
%K jrnl, c1998, c199x, c19xx, zz0210, JLP, LP, constraint, constraint,
   programming, Constraint Handling Rules, CHR, language, handler, multiheaded,
   guarded rule, rules
%X "... a declarative language extension especially designed for writing
   user-defined constraints. CHR are essentially a committed-choice language
   consisting of multi-headed guarded rules that rewrite constraints into
   simpler ones until they are solved. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/S0743-1066(98)10005-5">doi:10.1016/S0743-1066(98)10005-5</A>]['10];
   see [<A HREF="http://en.wikipedia.org/wiki/Constraint_Handling_Rules">wikip</A>]['10].
   [Also search for: Constraint Handling Rules CHR].

%A M. Pelikan
%A D. E. Goldberg
%A E. Cantu-Paz
%T BOA: The Bayesian optimization algorithm
%J Proc. of the Genetic and Evolutionary Computation Conf. GECCO-99
%I MorganKaufmann
%W Orlando
%V 1
%P 525-532
%D 1999
%K conf, GECCO 99, GECCO99, c1999, c199x, c19xx, BOA, EDA, zz0707,
   estimation of distribution algorithm, Bayesian network, networks
%X "...based on the concepts of genetic algs. that uses an est. of the joint
   distribution of promising solns in order to generate new candidate
   solns is proposed. The proposed alg. is called the Bayesian optimization alg.
   (BOA). To est. the distribution of promising solns, techniques for modeling
   multivariate data by Bayesian networks are used. The proposed alg. identifies
   reproduces & mixes building blocks up to a specified order. It is indep. of
   the ordering of the variables in the strings representing the solns. Moreover
   prior information about the problem can be incorporated into the alg..
   However, the prior information is not essential. Preliminary experiments show
   that the BOA outperforms the simple GA even on decomposable fns with tight
   building blocks as the problem size grows."
   [<A HREF="ftp://ftp-illigal.ge.uiuc.edu/pub/papers/Publications/pelikan/boa.ps.Z">paper.ps.Z</A>]['07]
   [<A HREF="http://www.cs.umsl.edu/~pelikan/">pelikan@umsl</A>]['07]

%A P. Larranaga
%A J. A. Lozano
%T Estimation of Distribution Algorithms
%I Kluwer Academic
%D 2002
%K book, text, c2002, c200x, c20xx, estimation of distribution algorithm,
   optimise, optimize, optimisation, optimization, search
%X [Also search for: estimation distribution algorithm].

%A S. Boyd
%A L. Vandenberghe
%T Convex Optimization
%I CUP
%P 730
%D 2004
%K book, text, c2004, c200x, c20xx, CUP, convex optimisation, optimize,
   numerical, maths, economics, CVXOPT
%X hb, us$72; uk us isbn:0521833787; uk is isbn13:978-0521833783.
   "... focus is on recognizing convex optimization problems and then finding
   the most appropriate technique for solving them. The text contains many
   worked examples and homework exercises ...  fields such as engineering,
   computer science, mathematics, statistics, finance, and economics."
   Also see [<A HREF="http://abel.ee.ucla.edu/cvxopt/">www</A>]['08].
   [Also search for: CVXOPT].

%A M. Pelikan
%T Hierarchical Bayesian Optimization Algorithms
%I SpringerVerlag
%D 2005
%K book, text, c2005, c200x, c20xx, BOA, algorithm, zz0707
%X [<A HREF="http://www.cs.umsl.edu/~pelikan/">pelikan@umsl</A>]['07].

%A J. Dahl
%A L. Vandenberghe
%T CVXOPT User's Guide
%M APR
%D 2008
%K manual, c2008, c200x, c20xx, CVXOPT, BLAS, LAPACK, SVD, Python, .py,
   numerical, concave, optimisation algorithms, algorithm, matrix, matrices,
   users manual
%X Release 1.0, April 24, 2008 at [<A HREF="http://abel.ee.ucla.edu/cvxopt/">www</A>]['08].
   [Also search for: CVXOPT] & [also search for: BLAS numerical].
   See book by  B o y d  and V., c2004.   Also see NumPy.

%A J. Sneyers
%A T. Schrijvers
%A B. Demoen
%T The computational power and complexity of constraint handling rules
%J ACM Trans. Program. Lang. Syst.
%V 31
%N 2
%P 8
%D 2009
%K jrnl, TOPLAS, c2009, c200x, c20xx, zz0210, language, machine,
   constraint handling rules, rule, CHR, constraints, programming, JCHR
%X "Constraint Handling Rules (CHR) is a high-level rule-based programming lang.
   which is increasingly used for general-purpose programming. We introduce the
   CHR machine, a model of computation based on the operational semantics of
   CHR. Its computational power & time complexity properties are compared to
   those of the well-understood Turing m/c & RAM-machine. This allows us to
   prove the interesting result that every alg. can be implemented in CHR with
   the best known time & space complexity. We also investigate the practical
   relevance of this result & the constant factors involved. Finally we expand
   the scope of the discussion to other (declarative) programming languages."
   -- [<A HREF="http://doi.acm.org/10.1145/1462166.1462169">doi:10.1145/1462166.1462169</A>],
   pdf@[<A HREF="http://www.cs.kuleuven.ac.be/~dtai/publications/files/41821.pdf">kuleuven</A>]['10],
   CHR@[<A HREF="http://www.cs.kuleuven.be/~dtai/projects/CHR/">home</A>]['10].
   "introduced in 1991 by Thom Fruhwirth"
   -- [<A HREF="http://en.wikipedia.org/wiki/Constraint_Handling_Rules">wikip</A>]['10].
   (Also J@va, JCHR, 2005.)   [Also search for: constraint handling rules CHR].

%A Ziming Liu
%A M. Tegmark
%T Machine learning hidden symmetries
%J Phys. Rev. Lett.
%V 128
%N 18
%M MAY
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0522, symmetry, transformation,
   dimension reduction, asymmetry, PDE
%X "We present an automated method for finding hidden symmetries, defined as
   symmetries that become manifest only in a new coord. sys. that must be
   discovered. Its core idea is to quantify asymmetry as violation of certain
   partial differential eqns, & to numerically minimize such violation over the
   space of all invertible transformations, parametrized as invertible neural
   networks. For example, our method rediscovers the famous Gullstrand-Painleve
   metric that manifests hidden translational symmetry in the Schwarzschild
   metric of nonrotating black holes, as well as Hamiltonicity, modularity, &
   other simplifying traits not traditionally viewed as symmetries."
    -- [<A HREF="https://doi.org/10.1103/PhysRevLett.128.180201">doi:10.1103/PhysRevLett.128.180201</A>]['22].
   (auth2 [<A HREF="https://scholar.google.com/citations?hl=en&user=eBXEZxgAAAAJ&view_op=list_works&sortby=pubdate">www</A>].)


%A D. Burns
%A E. N. Hawkins
%A D. R. Judd
%A J. L. Venn
%T The Egdon system for the KDF9
%J COMPJ
%V 8
%N 4
%P 297-302
%M JAN
%D 1966
%K COMPJ, jrnl, c1966, c196x, c19xx, zz0224, KDF9, KDF 9, operating system, OS,
   multiprogramming, timesharing, kernel, COSEC, COTAN, Thomas Hardy,
   computing, c1966, c196x, c19xx, English Electric
%X "An operating system based on the use of high-level languages & on the use of
   a discfile for program storage is described. The use of the discfile & the
   fact that only a small fraction of a program has to be recompiled when an
    error is corrected means that a very quick turnround is provided to users."
   -- [<A HREF="https://doi.org/10.1093/comjnl/8.4.297">doi:10.1093/comjnl/8.4.297</A>]['24].
   (Also see,
   "... The EGDON O.S. was so named because one was going to UKAEA Winfrith: in
   Thomas Hardy's book The Return of the Native Winfrith Heath is called Egdon
   Heath. EGDON Fortran was called EGTRAN. Eldon was so named because Leeds U's.
   computer was located in a converted Eldon chapel. ..."
   -- KDF9@[<A HREF="https://en.wikipedia.org/wiki/English_Electric_KDF9">wikip</A>]['24].)
   [Also search for: KDF9].

%A E. W. Dijkstra
%T Co-operating sequential processes
%B Programming Languages
%E F. Genuys
%I Academic Press N.Y.
%P 43-112
%D 1968
%K book, text, cooperating, process, parallel, concurrent, semaphore,
   semaphores, synchronise, synchronize, synchronization, c1968, c196x, c19xx
%X [<A HREF="http://www.cs.utexas.edu/~EWD/transcriptions/EWD01xx/EWD123.html">csp</A>]['12],
   pdf@[<A HREF="http://www.cs.utexas.edu/users/EWD/ewd01xx/EWD123.PDF">utex</A>]['12] (1.7MB),
   ewd@[<A HREF="http://www.cs.utexas.edu/~EWD/">utex</A>]['12] (1930-2002).

%A P. C. Poole
%T Some aspects of the EGDON 3 operating system for the KDF9
%J IFIP Congress (1)
%P 531-535
%D 1968
%K conf, c1968, c196x, c19xx, IFIP, Egdon, Egdon3, KDF9, KDK 9, COTAN,
   operating system, OS, kernel, PCPoole
%X [Also seach for: KDF9].

%A P. C. Poole
%A T. Lang
%T The development of on-line computing facilities for the KDF9 part 1;
   COSEC - a single on-line console
%J COMPJ
%V 11
%N 1
%P 5-11
%M MAY
%D 1968
%K COMPJ, jrnl, KDF9, KDF 9, Egdon, COTAN, COSEC, operating system, OS, kernel,
   online, Culham online task activation network, laboratory,
   UKAEA, PCPoole, c1968, c196x, c19xx
%X "... describes the first stage of a project to provide multi-access
   facilities in the Egdon system operating on a KDF9. Initially, on-line access
   was obtained through the single monitor console & a user could interrupt a
   b/g job to initiate such foreground tasks as program amendment & execution."
   -- [<A HREF="https://doi.org/10.1093/comjnl/11.1.5">doi:10.1093/comjnl/11.1.5</A>]['24].
   [Also search for: KDF9].

%A P. C. Poole
%T Developing a multi-access system online
%J SPE
%V 1
%N 1
%P 39-50
%M JAN
%D 1971
%K SPE, jrnl, KDF 9, KDF9, COTAN, COSEC, operating system, OS, shell, PCPoole,
   multiuser, multiaccess, time sharing, timesharing, c1971, c197x, c19xx,
   zz1001
%X "COTAN is a multi-access system designed to operate on linked KDF9-PDP8
   computers. It supports 20 remote teletypes & provides the online user with
   both remote job entry & interactive capabilities. The development of COTAN
   relied heavily on the continuing availability of online access from an early
   stage in the project. Access was first obtained through the monitor console
   on the KDF9 & this was then used to 'bootstrap' the implementation of the
   multi-access facilities. The new s/w was checked out in a real time, online
   test bed called an 'environmental simulator'. This provided a close
   approximation to the ultimate operating conditions & enabled the system to be
   brought to a high degree of reliability before being placed in service."
   -- [<A HREF="https://doi.org/10.1002/spe.4380010104">doi:10.1002/spe.4380010104</A>]['24].
   [Also search for: KDF9].

%A D. F. Hartley
%A B. Landy
%A R. M. Needham
%T The structure of a multiprogramming supervisor
%J COMPJ
%V 11
%N 3
%D 1968
%P 247-255
%K COMPJ, jrnl, Titan, Atlas, Cambridge, operating system, OS, kernel
%X [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_11/Issue_03/110247.sgm.abs.html">paper</A>][9/'01]
   [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_11/Issue_03/">issue</A>][9/'01]

%A M. Anderson
%A R. D. Pose
%A C. S. Wallace
%T A password capability system
%J COMPJ
%V 29
%N 1
%M Feb
%D 1986
%P 1-8
%K jrnl, COMPJ, Monash, CSW, CSWallace, multiprocessor, multi processor, OS,
   operating system, capabilities, c1986, c198x, c19xx, concurrent, money,
   charging
%X A tightly coupled multiprocessor.
   supports a uniform virtual memory
   unusual capability mechanism and the introduction of a money mechanism.
   simple and flexible solution to the confinement problem.
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/29.1.1">doi:10.1093/comjnl/29.1.1</A>]['05],
   CSW's [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">publns</A>].

%A C. Hazari
%A H. Zedan
%T A distributed algorithm for distributed termination
%J IPL
%V 24
%N 5
%M Mar
%D 1987
%P 293-297
%K jrnl, IPL, concurrent parallel distributed termination algorithm theory
   deadlock Occam

%A M. Elizabeth
%A C. Hull
%T Implementations of the CSP notation for concurrent systems
%J COMPJ
%M Dec
%D 1986
%V 29
%N 6
%P 500-505
%K jrnl, COMPJ, CSP concurrent parallel message operating system implementation
   survey  COSPOL Barter   CSP80   Occam

%A H. C. Lauer
%A R. M. Needham
%T On the duality of operating system structures
%J Proc. 2nd International Symposium on Operating Systems
%I IRIA
%M Oct
%D 1978
%O ACM Operating System Review V13 N2 P3-19 1979
%K conf, message process procedure, c1978, c197x, c19xx
%X operating systems:
   cat-1: small fixed no of processes pass messages
   cat-2: large, rapidly changing no of small processes, shared data
   Show 2 categories are dual.

%A S. J. Mullender
%A P. M. B. Vitanyi
%T Distributed match-making for processes in computer networks
%J ACM Operating System Review
%V 20
%N 2
%P 54-64
%M Apr
%D 1986
%O 4th PODC Conf. Proc. ACM 1985
%K process service request client server match making  match-making
%X large no of processors
   processes migrate
   want distributed matching of client and server
   algorithms given and complexity investigated.

%A C. Morgan
%A B. Sufrin
%T Specification of the Unix filing system
%J IEEE Trans. Software Engineering
%V SE-10
%N 2
%M Mar
%D 1984
%K jrnl, specification theory set Unix file system

%E D. Beech
%J Command Language Directions: Proc. 79 IFIP Working Conf.
   on Command Languages
%I North Holland
%D 1980
%K conf, new directions 1979 trends shell  command language

%A T. A. Dolatta
%A J. R. Mashey
%T Using a command language as the primary programming tool
%J Command Language Directions: Proc. 79 IFIP Working Conf.
   on Command Languages
%E D. Beech
%I North Holland
%D 1980
%K conf, shell  command language

%T Proceedings of the Eleventh ACM Symposium on Operating System Principles
%M Nov
%D 1987
%W Austin
%O SigOps V21 N5
%K SOSP SOSP11
%X J. Howard et al Scale and performance in a distributed file system  p1 ExAbs
   M. Nelson, B. Welch, J. Ousterhout
      Caching in the Sprite network file system p 3 ExABs
   D. Nichols  Using idle workstations in a shared computing environment p3
   E. Zayas  Attacking the process migration  bottleneck p13
   G. Varghese  T. Lauck  Hashed and hierarchical timing wheels: data
      structures for the efficient implementation of a timer facility p25
   J. Mogul, R. Rashid, M. Accetta
      The packet filter: an efficient mechanism for user level network code p39
   M. Schwartz, J. Zahorjan, D. Notkin
      A name service for evolving heterogeneous systems p52
   M. Young et al,  The duality of memory and communication in the
      implementation of a multiprocessor operating system         p63
         Mach is a multiprocessor operating system at CMU.
         Unix 4.3bsd compatible. multiprocessor computers.
   D. Jefferson et al,  Time Warp operating system  p77
         on Hypercube multiprocessor
   A.Birrell et al,  Synchronisation primitives for a multiprocessor:
      a formal specification  p94
         Threads synchronisation primitives
         Taos operating system
   D. Terry, D. Swinehart.
      Managing stored voice in the etherphone system p103 ExAbs
   E. Jul, et al Fine-grained mobility in the emerald system p105 ExAbs
   R. Haskin et al, Recovery management in quicksilver p107 ExAbs
   A Chang, M Mergen. 801 storage: architecture and programming p109 ExAbs
   B. Lisvov et al Implementation of Argus p111
   K. Birman, T. Joseph.
      Exploiting virtual synchrony in distributed systems p123
   R. Finlayson, D. Cheriton. Log files: an extended
      file service exploiting write-only storage p139
   A. Birrell, M. Jones, E. Wobber.
      A simple and efficient implementation of a small database p149
   R. Hagmann. Reimplementing the cedar file system using logging and
      group commit p155

%A C. H. Russell
%A P. J. Waterman
%T Variations on Unix for parallel processing computers
%J CACM
%V 30
%N 12
%M Dec
%D 1987
%P 1048-1055
%K jrnl, parallel multi multiprocessor unix operating system
   Mach  Butterfly  Ultra Ultracomputer

%A L. A. Stabile
%T FP and its use as a command language
%J Fall COMPCON
%W Washington DC
%D 1980
%P 301-306
%K conf, functional programming, FP, shell, command language, unix
%X Backus FP used as a Unix shell or command language.
   [Also search for: Backus FP].

%A W. Stoye
%T Message based functional operating systems
%J Science of Computer Programming
%V 6
%N 3
%M May
%D 1986
%P 291-311
%K jrnl, message, operating system, OS, functional programming, FP, applicative
%X see also Stoye's PhD thesis
   [see complab Cambridge]

%A P. H. Salus
%T A Quarter Century of Unix
%I AddisonWesley
%D 1994
%K book, text, computer, computing, history, operating system, OS,
   Unix, X windows, Xwindows, c1994, c199x, c19xx
%X uk us isbn:0 201 54777 5.

%A N. Wirth
%T Ceres-net: a low cost computer network
%J SPE
%V 20
%N 1
%P 13-24
%M ???
%D 1990
%K jrnl, SPE, Ceres, net, network, Oberon, OS, computing

%A V. J. Fazio
%A R. D. Pose
%A J. R. Wells
%T Monash secure RISC multiprocessor: performance simualtion
%J 18th Australian Computer Science Conf.
%M FEB
%D 1995
%P 161-165
%K multi, Monash, conf, secure, security, operating system, computing,
   ACSC, ACSC18, ACSC95
%X isbn:0157 3055
   see <A HREF="http://www.csse.monash.edu.au/">CSci Monash</A>

%A W. R. Stevens
%T Unix Network Programming
%I PrenticeHall
%D 1990
%K Unix, network, operating system, systems, communication, socket, sockets,
   stream, streams, port, computing, book, text
%X uk us isbn:0-13-949876-1.

%A R. M. Cardell-Oliver
%T The Formal Verification of Hard Real-Time Systems
%I U. of Cambridge
%D 1992
%O U. of Cambridge, Computer Laboratory, Technical Report 255, May 1992
%K PhD thesis, real time, operating system, OS, program verification, proof,
   TR255, TR 255, Cambridge, Rachel, UWA, c1992, c199x, c19xx
%X [<A HREF="http://www.csse.uwa.edu.au/~rachel/">CO home</A>][5/'03].

%A W. R. Stevens
%T Advanced Programming in the Unix Environment
%I AddisonWesley
%D 1992
%K Unix, network, operating system, systems, communication, socket, sockets,
   stream, streams, port, computing, book, text
%X uk us isbn:0-201-56317-7.

%A H-J. Boehm
%A A. J. Demers
%T Implementing multiple locks using Lamport's mutual exclusion algorithm
%J ACM Lett. Prog. Lang. and Sys.
%V 2
%N 1-4
%P 46-58
%M MAR-DEC
%D 1993
%K jrnl, mutual exclusion, spin lock, parallel, concurrent, jrnl
%X review in Computing Surveys p257 May '95

%A M. G. Sobell
%T Hands-On Unix
%I Benjamin/Cummings
%D 1995
%K book, text, c1995, c199x, c19xx, Unix, operating system, OS, shell,
   programming, system five, systemV, system5, computing, CSci, zz0895
%X Also see Hands-On Linux 1998.

%A R. Cardell-Oliver
%T An equivalence theorem for the operational and temporal semantics of
   real-time, concurrent programs
%J J. of Logic and Computation
%V 8
%N 4
%P 545-567
%M AUG
%D 1998
%K jrnl, real time, operating systems, programs, programming, proof,
   verification, theory, logic, RTS, c1998, c199x, c19xx
%X [<A HREF="http://www.csse.uwa.edu.au/~rachel/">CO home</A>][5/'03].

%A M. G. Sobell
%T Hands-On Linux
%I AddisonWesley
%D 1998
%P 1015
%K book, text, Unix, Linux, operating system, manual, OS, shell, programming,
   Caldera openLinux, pc, bash, fvwm windows manager, zz0998
%X review in ACM Comp Rev p238 May '98;
   CD included;  uk us isbn:0-201-32569-1;  us$54.95;
   Also see Hands-On Unix 1995.

%A J. Mohr
%T Linux User's Resource: A Guide to Running your Business on Linux
%I PrenticeHall
%P 800
%D 1998
%K book, text, c1998, c199x, c19xx, Linux, Unix, introduction, OS, MS, DOS
%X uk us isbn:0-13-842378-4;  us$50;  rev Comp Rev p.451 Sept 98.

%A M. Welsh
%A L. Kaufman
%T Running Linux
%I OReilly
%P 630
%D 1995
%K book, text, Linux, Unix, operating system, OS, Intel, Wintel, ms, msn, DOS,
   c1995, c2002, c199x, c200x
%X uk us isbn:1565921518; about au$60  5/'99.
   uk us isbn:0596002726; fourth edn, about us$45, pp.692, Dec 2002.

%A J. P. Heckman
%T Linux in a Nutshell
%I OReilly
%P 438
%D 1997
%K book, text, manual, c1997, c199x, c19xx, Linux, Unix, GNU, operating system,
   OS
%X uk us isbn:1-56592-167-4.

%A O. Kirch
%T Linux Network Administrator's Guide
%I OReilly
%D 1995
%P 370
%K book, text, operating system, Linux, manual
%X uk us isbn:1-56592-087-2.

%A J. Tranter
%T Linux Multimedia Guide
%I OReilly
%D 1996
%P 386
%K book, text, multi-media, multiMedia
%X uk us isbn:1-56592-219-0.

%A A. Rubini
%T Linux Device Drivers
%I OReilly
%D 1998
%P 432
%K book, text, devices, driver, Intel, i486, pentium, hardware, c1998, c199x
%X 1st edn,        uk us isbn:1565922921, 1998.
   2nd edn, pp592, uk us isbn:0596000081, June 2001

%A L. Torvalds
%A D. Diamond
%T Just for Fun: The Story of an Accidental Revolutionary
%I Harper-Business
%P 288
%M MAY
%D 2001
%K book, text, Linus Torvalds, autobiography, biography, history,
   Linux, Unix, operating system, open source, software, opensource, gnu,
   OS, c2001, c200x, c20xx
%X us isbn:0066620724.  About us$18.

%A W. A. Wulf
%A R. Levin
%A S. P. Harbison
%T Hydra / C.mmp: An Experimental Computer System
%I McGrawHill
%D 1981
%K Hydra, book, text, CM*, Cmmp, operating system, OS, multiprocessor,
   CSci, computing
%X uk us isbn:0 07 072120 3;  (ref sigplan 30(7) p36).

%A S. J. Mullender
%A C. van Rossum
%A A. S. Tanenbaum
%A R. van Renesse
%A H. van Stavern
%T Amoeba: a distributed operating system for the 1990s
%I IEEE Computer
%V 23
%N 5
%P 44-53
%M MAY
%D 1990
%K jrnl, Amoeba, operating system, OS, CSci, computing,
   vanRossum, vanRenesse, vanStavern, c1990, c199x, c19xx
%X ref sigplan 30(7) p.36.

%A M. Spasojevic
%A M. Satyanarayanan
%T An empirical study of a wide area distributed file system
%J TOCS
%V 14
%N 2
%P 200-222
%M MAY
%D 1996
%K TOCS, jrnl, CSci, wide area, Andrew, Andrews file system, ADF,
   distributed, files, WAFS, WADFS, network, zz0796
%X study of the Andrews File System, in the field.

%A C. Huitema
%T IPv6: The New Internet Protocol
%I PrenticeHall
%D 1996
%P 188
%K book, text, IP 6, IPV6, computer network, networks, routing, protocols,
   layer, communications, internet engineering task force, 1998, zz0898
%X 2nd ed 1998; 247pp, us$39; uk us isbn:0-13-850505-5.
   1st ed 1996; us$40; uk us isbn:0-12-241936-X.
   See A.C.M. Comp. Rev. p181 APR '98.

%A B. W. Kernighan
%A R. Pike
%T The Unix Programming Environment
%I PrenticeHall
%D 1984
%K book, text, manual, Unix, operating system, OS, API, shell, make,
   L3Ref, zz0197
%X hb; uk us isbn:0139376992.
   pb; uk us isbn:013937681X.

%A A. Schulman
%T Unauthorized Windows 95
%I IDG Books
%P 608
%D 1994
%K book, text, windows 95, windows95, win95, microsoft, micro soft, MS, 1995,
   operating system, OS, OLE, unauthorised, zz1197
%X us isbn:1-56-884-1698;  $29.99 US.
   <A HREF="http://www.sonic.net/~undoc/">[web]</A>[11/1997].

%A P. Kelly
%A P. Donham
%A D. Collier-Brown
%T Using Samba
%I OReilly
%D 1999
%P 300
%K book, text, samba, Microsoft Windows, MS, win95, win98, NT, NT4, xp, server,
   Unix, Linux, client, zz0599
%X uk us isbn:1-56592-449-5.

%A S. S. Miller
%T Windows NT Security Guide
%I DigitalPress
%D 1998
%P 322
%K book, win, NT, winNT, zz0799
%X isbn:1-55558-211-7;  us$40;
   mediocre review in ACM Comp Rev 40(2) Feb '99 pp.93.

%A C. S. McDonald
%A T. I. Dix
%T Support for graphs of processes in a command interpreter
%J SPE
%V 18
%N 10
%P 1011-1016
%D 1988
%K jrnl, SPE, graph, shell, sh, csh, process, pipe, pipes, command language,
   operating system, OS, c1988, c198x, c19xx
%X Chris McDonald - UWA;  Dix - Monash.

%A T. Gerdsmeier
%A R. Cardell-Oliver
%T A method for verifying real-time properties of Ada programs
%J 7th IEEE Int. Conf. on Engineering Complex Computer Systems (ICECCS 2001)
%W Skovde, Sweden
%P 35-47
%I IEEE Press
%M JUN
%D 2001
%K conf, ICECCS, real time systems, RTS, Ada, programming language
%X [<A HREF="http://www.csse.uwa.edu.au/~rachel/">CO home</A>][5/'03].

%A D. Pogue
%T Mac OS X: The Missing Manual, Second Edition
%I OReilly
%M OCT
%D 2002
%P 725
%K book, text, operating system, OS, Mac, Apple, OS-X, OSX, Unix, BSD, ms, msn,
   manual, c2002, c200x, c20xx, zz1202
%X Max OS-X 10.2 ...; uk us isbn:0596004508.

%A M. Gagne
%T Moving to Linux: Kiss the Blue Screen of Death Goodbye!
%I AddisonWesley
%P 368
%M AUG
%D 2003
%K book, text, operating system, systems, Linux, Unix, ms, bill gates, csharp,
   microsoft, pc, windows, kernel, Knoppix, msn, c2003, c200x, c20xx, xp,
   zz1104, BSOD, cd, cd-rom, cdrom
%X book + CD, us35, uk us isbn:0321159985.

%A Kyung-Suk Lhee
%A S. J. Chapin
%T Buffer overflow and format string overflow vulnerabilities
%J SPE
%V 33
%N 5
%P 423-460
%M APR
%D 2003
%K jrnl, SPE, computer security, hack, hackers, attack, exploiting,
   web services, server, format string overflow, c2003, c200x, c20xx,
   c, cc, library
%X [<A HREF="http://dx.doi.org/10.1002/spe.515">doi:10.1002/spe.515</A>][1/'04].

%A A. Silberschatz
%A P. B. Galvin
%A G. Gagne
%T Operating System Concepts
%I Wiley
%D 2004
%K book, text, c2004, c200x, c20xx, OpSys, OS, file system, NUMA, ZFS,
   memory management
%X 8th ed 2008; hb us$122; uk us isbn:0470128720; uk us isbn13:978-0470128725.
      "... Process, memory, and storage management.  Protection and security.
       Distributed systems.  Special-purpose systems. ..."
   7th ed 2004, hb  us$89; uk us isbn:0471694665; uk us isbn13:978-0471694663.

%A R. Love
%T Linux Kernel Development
%I Novell
%D 2005
%K book, c2005, c200x, c20xx, unix, Linux, kernel, OS, OpSys, windows
%X pb us$32; 2nd ed 2005; uk us isbn:0672327201; uk us isbn13:978-0672327209.

%A D. Bovet
%A M. Cesati
%T Understanding the Linux Kernel
%I OReilly
%P 942
%D 2005
%K book, text, c2005, c200x, c20xx, operating system, systems,
   Linux, unix, kernel, kernels
%X 3rd ed 2005, pb us$33; uk us isbn:0596005652; uk us isbn13:978-0596005658.

%A G. Kroah-Hartman
%T Linux Kernel in a Nutshell
%I OReilly
%P 198
%D 2005
%K book, c2006, c200x, c20xx, unix, Linux, kernel, operating system, systems,
   OS, OpSys
%X pb us$26; uk us isbn:0596100795; isbn13:978-0596100797.

%A A. S. Tanenbaum
%A A. S. Woodhull
%T Operating Systems Design and Implementation
%I PrenticeHall
%P 1080
%D 2006
%K book, text, c2006, c200x, c20xx, operating system, systems, OS, Op Sys,
   OpSys, minix, unix, posix, file system, security
%X "Most books on OS deal with theory while ignoring practice. While the usual
   principles are covered in detail, the book describes a small, but real
   UNIX-like operating system: MINIX. ...demonstrates how it works while
   illustrating the principles behind it. Operating Systems: Design &
   Implementation 2nd Ed. provides the MINIX source code. The relevant
   selections of the MINIX code are described in detail. When it 1st came out,
   MINIX caused something of a revolution. Within weeks, it had its own
   newsgroup on USENET, with 40,000 people. Most wanted to make MINIX bigger &
   fancier. Instead, Linux was created. That has become quite popular, very
   large, & complicated. MINIX, on the other hand, has remained small & suitable
   for instruction & example. The book has been revised to include updates in
   MINIX, which started out as a v7 unix clone for a floppy-disk only 8088. It
   is now aimed at 386, 486, & pentium machines & is based on the international
   posix standard instead of on v7. There are now also versions of MINIX for the
   Macintosh & SPARC available. Professional programmers will find this book to
   be a valuable resource & reference book."
   3rd ed 2006, hb us$98; uk us isbn:0131429388; uk us isbn13:978-0131429383.

%A M. D. Castro
%A R. D. Pose
%A C. Kopp
%T Password-capabilities and the Walnut kernel
%J COMPJ
%V 51
%N 5
%P 595-607
%M SEP
%D 2008
%K jrnl, COMPJ, c2008, c200x, c20xx, capability, operating system, OS, OpSys,
   kernel, Walnut, password capability system, model,
   CSW, CSWallace, RDP, Computer Science, Monash University, Uni, MonashUni
%X "The Walnut kernel is a capability-based OS system kernel that was developed
   in the Dept of Comp. Sci. at Monash University during the 1990s. This kernel
   is heir to many of the ideas that were implemented in the Password-Capability
   System. Focusing on the programmer's view, this paper describes the
   password-capability model & the features of the Walnut kernel & the design
   decisions taken in creating it. An ANSI compliant standard I/O library is
   used as an example of the expressive power of the system."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm124">doi:10.1093/comjnl/bxm124</A>]['08].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">C.S.Wallace's publications</A>].)

%A D. Pogue
%T Mac OS X Snow Leopard: The Missing Manual
%I Pogue Press
%D 2009
%P 912
%K book, c2009, c200x, c20xx, zz1209, Max, Apple, OS X, OSX, Snow Leopard,
   iMac, manual, computer, computers, operating system,
   Finder, Safari, iChat, iPhoto
%X 1st ed 2009; pb us$23; us isbn:0596153287; us isbn13:978-0596153281.

%A E. Bott
%A C. Siechert
%A C. Stinson
%T Windows7 Inside Out
%I Microsoft Press
%P 1000
%M SEP
%D 2009
%K book, manual, c2009, c200x, c20xx, Windows 7, Windows7, operating system, OS
%X 1st ed 2009; pb is$31;
   [Also search for: operating system manual].


%A S. Forrest
%T Genetic algorithms: principles of natural selection applied to computation
%J Science
%V 261
%M AUG
%D 1993
%P 872-878
%K GA
%X 64 refs.   eg. TSP.

%A D. Tilman
%T Competition and biodiversity in spatially structured habitats
%J Ecology
%V 75
%N 1
%P 2-16
%M JAN
%D 1994
%K species, GA, space, spatial

%A M. Oliphant
%T Evolving cooperation in the non-iterated prisoner's dilemma: The importance
   of spatial organization
%J Proc. of Artificial Life IV
%E Brooks
%E Maes
%I MITpress
%P 349-352
%D 1994
%K conf, Alife, c1994, c199x, c19xx, IPD, prisoners dilemma, space, position,
   geographical, location
%X "Most work on evolving cooperation in the Prisoner's Dilemma treats the
   non-iterated game as an undesirable simple case that should be risen above.
   It has been taken as a given that populations evolving to play the
   non-iterated game will always converge on defection. This paper questions
   this assumption, & demonstrates that organizing a population spatially
   dramatically changes the nature of the game & allows cooperation to emerge."
   -- 170@[<A HREF="http://cogprints.org/170/">cogprints</A>][13], via AlanD.

%A P. J. Angeline
%T An alternative interpretation of the iterated prisoner's dilemma and the
   evolution of non-mutual cooperation
%J Proc. of Artificial Life IV
%E Brooks
%E Maes
%I MITpress
%P 353-358
%D 1994
%K conf, Alife, c1994, c199x, c19xx, IPD, prisoners dilemma, nonmutual
%X "... traditional definition of the game, constraints are provided that limit
   the cooperation between players to mutual cooperation, i.e. both players
   deciding to "cooperate" on a single play. This paper demonstrates that by
   modifying the traditional constraints, successful strategies must embody the
   ability to coordinate their interactions over several consecutive plays, a
   much more complex & potentially more interesting behavior. This form of
   interaction is termed nonmutual cooperation. This paper demonstrate the
   evolution of non-mutually cooperative agents, represented as Finite State
   Machines, under two distinct payoff schemes & discusses the implications of
   these results."
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.48.7583">cites'er</A>]['13], via AlanD.

%A M. Huston
%T A general hypothesis of species diversity
%J American Naturalist
%V 113
%N 1
%M JAN
%D 1979
%P 81-101
%K GA, evolution

%A M. J. Wade
%A F. Breden
%T The evolution of cheating and selfish behaviour
%J Behavioral Ecology and Sociobiology
%V 7
%N ?
%P 167-172
%M ?
%D 1980
%K c1980, c198x, c19xx, cheat, cooperate, cooperation, altruism, GA, behaviour,
   behavioural, cheat, defect

%A M. W. Feldman
%A E. A. C. Thomas
%T Behavior-dependent contexts for repeated plays of the prisoner's dilemma II:
   dynamical aspects of the evolution of cooperation
%J JTB
%V 128
%N ?
%P 297-315
%M ?
%D 1987
%K prisoner, iterated, PD, IPD, behaviour, tit-for-tat, TFT, cooperate, defect,
   behaviour, JTB
%X ... stable polymorphisms may reults, and may involve more strategies
   than just TFT and all-defect. The tendency for clustering amongst like
   strategists to enhance their initial increase when rare is also
   explored dynamically.
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A L. A. Dugatkin
%T Do guppies play tit for tat during predator inspection visits?
%J Behavioral Ecology and Sociobiology
%V 23
%N ?
%P 395-399
%M ?
%D 1988
%K behaviour, prisoner's dilemma, tit-for-tat, TFT, PD, IPD,
   cooperate, defect, altruism, guppy, animal, fish, predator, behaviour

%A A. Grafen
%T Biological signals as handicaps
%J JTB
%V 144
%P 517-546
%D 1990
%K jrnl, JTB, c1990, c199x, c19xx, signal, signalling, handicap principle,
   model, animal behaviour, communication, mate attraction, displays,
   peacock, peacocks tail

%A D. S. Wilson
%A L. A. Dugatkin
%T Nepotism vs tit for tat, or, why should you be nice to your rotten brother
%J Evol. Ecology
%V 5
%N ?
%P 291-299
%M ?
%D 1991
%K c1991, c199x, c19xx, prisoner's dilemma, PD, IPD, altruism, cooperate,
   defect, TFT, kin, animal behaviour, kin, kinship, sibling

%A M. S. Dawkins
%A T. Guilford
%T The corruption of honest signaling
%J Animal Behaviour
%V 41
%P 865-873
%D 1991
%K jrnl, c1991, c199x, c19xx, animal behaviour, signal, signals, communication,
   honesty, deceit, liars, lying, mimic, mimicry, signalling
%X from a ref

%A L. A. Dugatkin
%A M. Alfieri
%T Guppies and the tit for tat strategy: preference based on past interaction
%J Behavioral Ecology and Sociobiology
%V 28
%N ?
%P 243-246
%M ?
%D 1991
%K behaviour, fish, guppy, PD, IPD, TFT

%A L. A. Dugatkin
%T Dynamics of the tit for tat strategy during predator inspection in the guppy
   (poecilia reticulata).
%J Behavioral Ecology and Sociobiology
%V 29
%N ?
%P 127-132
%M ?
%D 1991
%K behaviour, fish, TFT

%A H. C. J. Godfray
%T Signalling of need by offspring to their parents
%J Nature
%V 352
%P 328-330
%D 1991
%K jrnl, c1991, c199x, c19xx, parent, signal, signals, animal behaviour,
   communication, honesty, deceit, begging, chick, chicks

%A L. A. Dugatkin
%A M. Alfieri
%T Interpopulational [!] differences in the use of the tit-for-tat
   strategy during predator inspection in the guppy, poecilia reticulata
%J Evol. Ecology
%V 6
%N ?
%P 519-526
%M ?
%D 1992
%K prisoner's dilemma, PD, IPD, TFT, fish, cooperate, altruism
%X see Dugatkin 1988 and 1991.

%A M. Milinski
%T Tit for tat in sticklebacks and the evolution of cooperation
%J Nature
%V 325
%M JAN
%D 1987
%P 433-435
%K prisoner's dilemma, PD, IPD, fish, behaviour, cooperate, defect, TFT

%A M. Milinski
%A D. Pfluger
%A D. Kulling
%A R. Kettler
%T Do sticklebacks really cooperate repeatedly in reciprocal pairs?
%J Behavioral Ecology and Sociobiology
%V ?
%N ?
%P 17-21
%M ?
%D 1990 ?
%K behaviour, fish, behaviour, altruism, PD, IPD, TFT

%A R. Axelrod
%T Effective choice in the prisoner's dilemma
%J J. Conflict Resolution
%V 24
%N 1
%M MAR
%D 1980
%P 3-25
%K jrnl, c1980, c198x, c19xx, iterated prisoner dilemma, PD, IPD, TFT, defect,
   altruism, genetic, algorithm, GA, competition, tit for tat

%A R. Axelrod
%T More effective choice in the prisoner's dilemma
%J J. Conflict Resolution
%V 24
%N 3
%M SEP
%D 1980
%P 379-403
%K jrnl, c1980, c198x, c19xx, iterated prisoner dilemma, PD, IPD, TFT, defect,
   altruism, genetic algorithm, GA, competition, tit for tat

%A M. Nowak
%T An evolutionary stable strategy may be inaccessible
%J JTB
%V 142
%N ?
%P 237-241
%M ?
%D 1990
%K jrnl, JTB, c1990, c199x, c19xx, ESS, iterated prisoner's prisoner dilemma,
   PD, IPD, game theory

%A M. A. Nowak
%A K. Sigmund
%T Tit for tat in heterogeneous populations
%J Nature
%V 355
%P 250-253
%M JAN
%D 1992
%K iterated prisoner's prisoner dilemma, PD, IPD, game theory

%A H. C. J. Godfray
%T The evolution of forgiveness
%J Nature
%V 355
%M JAN
%D 1990
%P 206-207
%K iterated prisoner's prisoner dilemma, PD, IPD, tit for tat, TFT,
   cooperate, defect, forgive, generous, altruism
%X (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A K. Sigmund
%T On prisoners and cells
%J Nature
%V 359
%M OCT
%D 1992 ?
%P 774
%K iterated prisoner's prisoner dilemma, PD, IPD,
   cooperate, game of life, cellular automata

%A W. F. Harms
%T Adaption and Moral Realism
%J Biology and Philosophy
%V 15
%P 699-712
%D 2000
%K jrnl, c2000, c200x, c20xx, process, evolution, animal behaviour,
   communication, signal, signalling, honesty, deceit

%A S. F. Brosnan
%A F. B. M. de Waal
%T Monkeys reject unequal pay
%J Nature
%V 425
%P 297-299
%M SEP
%D 2003
%K jrnl, c2003, c200x, c20xx, zz0313, deWaal, animal behaviour, cooperation,
   cooperate, primate, monkey, capuchin, reward, fair, fairness, inequity,
   equity
%X "During the evolution of cooperation it may have become critical for
   individuals to compare their own efforts and pay-offs with those of others.
   ... we are not the only cooperative animals, hence inequity aversion may not
   be uniquely human. Many highly cooperative nonhuman species seem guided by a
   set of expectations about the outcome of cooperation and the division of
   resources. Here we demonstrate that a nonhuman primate, the brown capuchin
   monkey (Cebus apella), responds negatively to unequal reward distribution in
   exchanges with a human experimenter. Monkeys refused to participate if they
   witnessed a conspecific obtain a more attractive reward for equal effort, an
   effect amplified if the partner received such a reward without any effort at
   all. ... support an early evolutionary origin of inequity aversion."
   -- [<A HREF="http://dx.doi.org/10.1038/nature01963">doi:10.1038/nature01963</A>]['13],
   SB@[<A HREF="http://www2.gsu.edu/~wwwpsy/brosnan.html">gsu</A>]['15].
   [Also search for: deWaal cooperation].

%A H. Oosterbeek
%A R. Sloof
%A G. van de Kuilen
%T Cultural differences in ultimatum game experiments: Evidence from a
   meta-analysis
%J Experimental Economics
%V 7
%P 171-188
%M JUN
%D 2004
%K jrnl, c2004, c200x, c20xx, zz1222, game theory, ultimatum, ultimatumGame,
   threat, ultimate, offer, human behaviour, sharing, fairness, fair, unfair,
   punishment, responder, economics, negotiation, strategy, Hofsted, Inglehart
%X "... meta-analysis of 37 papers with 75 results ... find that on avg the
   proposer offers 40% of the pie to the responder. This share is smaller for
   larger pie sizes & larger when a strategy method is used or when subjects are
   inexperienced. On avg 16% of the offers is rejected. The rejection rate is
   lower for larger pie sizes & for larger shares offered. Responders are less
   willing to accept an offer when the strategy method is employed. As the
   results come from different countries, meta-analysis provides an alt. way to
   investigate whether bargaining behavior in ultimatum games differs across
   countries. We find differences in behavior of responders (& not of proposers)
   across g.regions. With one exception, these differences cannot be attributed
   to various cultural traits on which for inst. the cultural classifications of
   Hofstede (1991) & Inglehart (2000) are based."
    -- [<A HREF="https://doi.org/10.1023/B:EXEC.0000026978.14316.74">doi:10.1023/B:EXEC.0000026978.14316.74</A>]['22].
   (Also see UG@[<A HREF="https://en.wikipedia.org/wiki/Ultimatum_game">wikip</A>]['22].)
   [Also search for: ultimatum game].

%A W. F. Harms
%T Information and Meaning in Evolutionary Processes
%I CUP
%D 2004
%K book, text, CUP, c2004, c200x, c20xx, process, evolution, animal behaviour,
   communication, honesty, deceit, lies

%A D. S. Wilson
%T Human groups as adaptive units: toward a permanent consensus
%E P. Carruthers et al
%B The Innate Mind: Culture and Cognition
%I OUP
%D 2006
%K chapter, OUP, c2006, c200x, c20xx, zz1219, group selection, cooperation,
   altruism, kin, PD, IPD, human, animal, behaviour
%X "... The founding fathers of the human social sciences spoke about groups as
   organisms as if it were common sense (Wegner 1986). ... groups can evolve
   into adaptive units that are designed to maximize their contribution to the
   total gene pool to the extent that selection among groups prevails against
   selection within groups. ..."    (In uk us isbn13:978-0195310146.)
   Also see groupSel@[<A HREF="https://en.wikipedia.org/wiki/Group_selection">wikip</A>]['19].
   [Also search for: cooperation behaviour].

%A B. Herrmann
%A C. Thoni
%A S. Gachter
%T Antisocial punishment across societies
%J Science
%V 319
%N 5868
%P 1362-1367
%M MAR
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0308, game theory, anti social, cooperate,
   cooperation, defect, defection, cheat, cheating, fair play, fairness,
   justice, society, IPD, human, behaviour
%X "We document the widespread existence of antisocial punishment, that is, the
   sanctioning of people who behave prosocially. Our evidence comes from public
   goods experiments that we conducted in 16 comparable participant pools around
   the world. However, there is a huge cross-societal variation. Some
   participant pools punished the high contributors as much as they punished the
   low contributors, whereas in others people only punished low contributors.
   In some participant pools, antisocial punishment was strong enough to remove
   the cooperation-enhancing effect of punishment. We also show that weak norms
   of civic cooperation and the weakness of the rule of law in a country are
   significant predictors of antisocial punishment. Our results show that
   punishment opportunities are socially beneficial only if complemented by
   strong social norms of cooperation."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1153808">doi:10.1126/science.1153808</A>]['08].

%A M. Ackermann
%A B. Stecher
%A N. E. Freed
%A P. Songhet
%A W.-D. Hardt
%A M. Doebeli
%T Self-destructive cooperation mediated by phenotypic noise
%J Nature
%V 454
%P 987-990
%M AUG
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0808, cooperation, cooperate, defect,
   phenotypic noise, assortment, public goods, prisoners dilemma
%X "In many biological e.g. ... individuals that cooperate cannot benefit from
   the resulting public good. This is esp. clear in cases of self-destructive
   cooperation, where individuals die when helping others. If self-destructive
   cooperation is genetically encoded, these genes can only be maintained if
   they are expressed by just a fraction of their carriers, whereas the other
   fraction benefits from the public good. One mechanism that can mediate this
   differentiation into 2 phenotypically different sub-pops. is phenotypic
   noise. Here we show that noisy expression of self-destructive c. can evolve
   if individuals that have a higher prob. for self-destruction have, on avg.,
   access to larger public goods. This sitn, which we refer to as assortment..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07067">doi:10.1038/nature07067</A>]['08].
   [29 refs]  [Also search for: cooperation].

%A R. M. Seymour
%A P. D. Sozou
%T Duration of courtship effort as a costly signal
%J JTB
%V 256
%N 1
%P 1-13
%M JAN
%D 2009
%K jrnl, JTB, c2009, c200x, c20xx, zz0209, mate choice, selection, male, female,
   human behaviour, signalling, sex, sexual, date, dating, dates, game theory,
   courting, courtship, length
%X "We consider a male & a female in a courtship encounter over continuous time.
   Both parties pay participation costs per unit time. The game ends when either
   one or other of the parties quits or the female accepts the male as a mate.
   We assume that there is a binary variable which determines whether the male
   is a "good" or "bad" type from the female's point of view, according to
   either his condition or his willingness to care for the young after mating.
   This variable is not directly observable by the female, but has fitness
   consequences for her: she gets a +ve fitness payoff from mating with a
   "good" male but a -ve fitness payoff from mating with a "bad" male. [And] a
   "good" male has a higher ratio of fitness benefit from mating to fitness cost
   per unit time of courtship than a "bad" male. ... under suitable assumptions,
   there are evolutionarily stable equilibrium behaviours in which time-extended
   courtship takes place. A "good" male is willing to court for longer than a
   "bad" male; in this way the duration of a male's courtship signals his type,
   & acts as a costly handicap. By not being willing to mate immediately the
   female achieves a degree of screening because the posterior prob. that the
   male is "good", conditional on his not having quit the game, increases ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jtbi.2008.09.026">doi:10.1016/j.jtbi.2008.09.026</A>]['09].

%A F. de Waal
%T The Age of Empathy: Nature's Lessons for a Kinder Society
%I Broadway
%P 304
%M SEP
%D 2010
%K book, text, deWaal, c2010, c201x, c20xx, zz1212, empathy, morality, society,
   social, animal, monkey, chimp, human, behaviour, evolution, origins,
   altruism, cooperation, ethics, fairness, fair, kindness, compassion, trust,
   cucumber, grape, grapes
%X 1st ed 2010; pb us$10; uk us isbn:0307407772; uk us isbn13:978-0307407771.
   "By studying social behaviors in animals, such as bonding, the herd instinct,
   the forming of trusting alliances, expressions of consolation, and conflict
   resolution, Frans de Waal demonstrates that animals - and humans - are
   'preprogrammed to reach out.' He has found that chimpanzees care for mates
   that are wounded by leopards, elephants offer 'reassuring rumbles' to
   youngsters in distress, and dolphins support sick companions near the water's
   surface to prevent them from drowning. From day one humans have innate
   sensitivities to faces, bodies, and voices; we've been designed to feel for
   one another."
   (Also see the 'Science Show', ABC radio, 23/6/2012
   [<A HREF="http://www.abc.net.au/radionational/programs/scienceshow/frans-de-waal---the-origins-of-morality/4051518#transcript">abc</A>]['12].)

%A F. C. Santosa
%A J. M. Pacheco
%T Risk of collective failure provides an escape from the tragedy of the commons
%J PNAS
%V 108
%N 26
%P 10421-10425
%M JUN
%D 2011
%K jrnl, PNAS, c2011, c201x, c20xx, zz0916, tragedy of the commons, behaviour,
   public good, goods, resource management, cooperation, risk, risks
%X "From group hunting to global warming, how to deal with collective action may
   be formulated in terms of a public goods game of cooperation. In most cases,
   contributions depend on the risk of future losses. ... introduce an
   evolutionary dynamics approach to a broad class of cooperation problems in
   which attempting to minimize future losses turns the risk of failure into a
   central issue in individual decisions. We find that decisions within small
   groups under high risk & stringent requirements to success sig. raise the
   chances of coordinating actions & escaping the tragedy of the commons. We
   also offer insights on the scale at which public goods problems of coop'n
   are best solved. Instead of large-scale endeavors involving most of the
   population, which as we argue, may be counterproductive to achieve coop'n,
   the joint combination of local agreements within groups that are small [v]
   the pop'n at risk is prone to sig. raise the prob. of success. [&] our model
   predicts that, if one takes into consideration that groups of different sizes
   are interwoven in complex n/wk of contacts, the chances for global
   coordination in an overall cooperating state are further enhanced." [via KK.]
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1015648108">doi:10.1073/pnas.1015648108</A>]['16].
   [Also search for: tragedy commons].

%A W. H. Press
%A F. J. Dyson
%T Iterated prisoner's dilemma contains strategies that dominate any
   evolutionary opponent
%J PNAS
%V 109
%N 26
%P 10409-10413
%M JUN
%D 2012
%K jrnl, PNAS, c2012, c201x, c20xx, zz0813, IPD, PD, game theory, ultimatum,
   iterated prisoner's dilemma, theory of mind, strategy, zero-determinant, ZD,
   stable, stability, memory
%X "... generally assumed that there exists no simple ultimatum strategy whereby
   one player can enforce a unilateral claim to an unfair share of rewards. ...
   show that such strategies unexpectedly do exist. In particular, a player X
   who is witting of these strategies can (i) deterministically set her
   opponent Y's score, independently of his strategy or response, or
   (ii) enforce an extortionate linear reln between her & his scores. Against
   such a player, an evolutionary player's best response is to accede to the
   extortion. Only a player with a theory of mind about his opponent can do
   better, in which case IPD is an Ultimatum Game."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1206569109">doi:10.1073/pnas.1206569109</A>]['13].
   [Also search for: ZD IPD game]  and  [also search for: IPD game].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].)

%A V. D. L. R. Goulart
%A R. J. Young
%T Selfish behaviour as an antipredator response in schooling fish?
%J Animal Behaviour
%V ?
%N ?
%P ?-?
%M JUL
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0713, animal, fish, school, behaviour, selfish,
   selfishness, two spot, Astyanax bimaculatus, game theory, cooperation,
   predation
%X "One widely acknowledged benefit of group living is an increase in the
   efficiency of predator avoidance. Experiments have demo. a variety of
   mechanisms involved, such as 'the selfish herd'. ... we exposed groups of
   two-spot astyanax, Astyanax bimaculatus, to three predatory stimuli
   ('active search', 'avian pecking' & 'sit-and-wait') & one nonpredatory
   control stimulus. ... found that fish were more likely to chase & attack a
   group member when exposed to an active search predator model. ... not
   observed for the control or the other predators. This response could reduce
   an individual's predation risk by making the other (i.e. the attacked)
   individual more vulnerable to predation. We showed that this trait was an
   innate response & as such a result of natural seln rather than a learning
   process. This study shows how group living may result in active selfishness,
   an additional cost of group living."
   -- [<A HREF="http://dx.doi.org/10.1016/j.anbehav.2013.05.041">doi:10.1016/j.anbehav.2013.05.041</A>]['13].
   [Also search for: IPD].

%A C. Adami
%A A. Hintze
%T Evolutionary instability of zero-determinant strategies demonstrates that
   winning is not everything
%J NatureComms
%V 4
%P article#2193
%M AUG
%D 2013
%O 1208.2666 @ arXiv, Aug., 2012
%K eJrnl, c2013, c201x, c20xx, zz0813, iterated prisoner's dilemma, IPD, PD,
   game theory, zero determinant strategy, ZD, strategies, weakly dominant,
   Dyson, extortion, evolutionarily stable, evolutionary stability, unstable,
   ultimatum, golden balls, memory
%X "Zero-determinant strategies are a new class of probabilistic & conditional
   s. that are able to unilaterally set the expected payoff of an opponent in
   iterated plays of the PD irrespective of the opponent's strategy (coercive
   strategies), or else to set the ratio between the player's & their opponent's
   expected payoff (extortionate s.). ... show that zero-det. s. are at most
   weakly dominant, are not evol.stable, & will instead evolve into less
   coercive s.. We show that zero-det. s. with an informational advantage over
   other players that allows them to recognize each other can be evol.stable
   (& able to exploit other players). However, such an advantage is bound to be
   short-lived as opposing strategies evolve to counteract the recognition."
   -- [<A HREF="http://arxiv.org/abs/1208.2666">arXiv</A>]['12],
      [<A HREF="http://dx.doi.org/10.1038/ncomms3193">doi:10.1038/ncomms3193</A>]['13].
   [Also search for: ZD IPD game]  and  [also search for: IPD game].

%A O. P. Hauser
%A D. G. Rand
%A A. Peysakhovich
%A M. A. Nowak
%T Cooperating with the future
%J Nature
%V 511
%P 220-223
%M JUL
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0714, game theory, games, resource, resources,
   public goods, good, exploitation, sustainability, voting, behaviour,
   generations, cooperation, selfishness, greed, psychology, behaviour,
   economics, growth, conservation, preservation, tragedy, commons
%X "Overexploitation of renewable resources today has a high cost on the welfare
   of future generations. Unlike in other public goods games, however, future
   generations cannot reciprocate actions made today. What mechanisms can
   maintain cooperation with the future? ... devise a new experimental paradigm,
   the 'Intergenerational Goods Game'. A line-up of successive groups
   (generations) can each either extract a resource to exhaustion or leave
   something for the next group. Exhausting the resource maximizes the payoff
   for the present gen., but leaves all future gens. empty-handed. ... show that
   the resource is almost always destroyed if extraction decisions are made
   individually. This failure to cooperate with the future is driven primarily
   by a minority of individuals who extract far more than what is sustainable.
   In contrast, when extractions are democratically decided by vote, the
   resource is consistently sustained. Voting is effective for two reasons.
   First, it allows a majority of cooperators to restrain defectors. Second, it
   reassures conditional cooperators that their efforts are not futile. Voting,
   however, only promotes sustainability if it is binding for all involved. Our
   results have implications for policy interventions designed to sustain
   intergenerational public goods."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13530">doi:10.1038/nature13530</A>]['14].
   [Also search for: tragedy commons] and [also search for: public goods game].

%A S. F. Brosnan
%A F. B. M. de Waal
%T Evolution of responses to (un)fairness
%J Science
%V 346
%N 6207
%P ?-?
%M OCT
%D 2014
%K review, c2014, c201x, c20xx, zz1014, deWaal, animal, behaviour, ape, human,
   fair, fairness, unfairness, reward, cooperation, equity, inequity, ethics
%X "The human sense of fairness is an evol. puzzle. To study this, we can look
   to other species, in which this can be translated empirically into responses
   to reward distn. Passive & active protest against receiving less than a
   partner for the same task is widespread in species that cooperate outside
   kinship & mating bonds. There is less evidence that nonhuman species seek to
   equalize outcomes to their own detriment, yet the latter has been documented
   in our closest relatives, the apes. This reaction probably reflects an
   attempt to forestall partner dissatisfaction with obtained outcomes & its
   -ve impact on future cooperation. We hypothesize that it is the evolution of
   this response that allowed the development of a complete sense of fairness in
   humans, which aims not at equality for its own sake but for the sake of
   continued cooperation."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1251776">doi:10.1126/science.1251776</A>]['14],
   SB@[<A HREF="http://www2.gsu.edu/~wwwpsy/brosnan.html">gsu</A>]['15].
   [Also search for: animal fairness] and
   [also search for: evolution cooperation].

%A D. W. Pfaff
%T The Altruistic Brain: How We Are Naturally Good
%I OUP
%P 312
%M JAN
%D 2015
%K book, text, OUP, c2015, c201x, c20xx, zz0215, altruism, human, animal,
   behaviour, empathy, fairness, goodness, morality, ethics
%X 1st ed 2015; hb us$22; uk us isbn:0199377464; uk us isbn13:978-0199377466.

%A I. Morris
%T Foragers, Farmers, and Fossil Fuels: How Human Values Evolve
%I PrincetonUP
%P 400
%D 2015
%K book, text, c2015, c201x, c20xx, zz0515, human behaviour, morality, ethics,
   origins, society, energy, forager, farmer, fuel, value
%X 1st ed 2015; hb us$22; us isbn:0691160392, us isbn13:978-0691160399.
   "... new argument about the evolution of human values ... driven by the most
   basic force of all: energy. Humans have found three main ways to get the
   energy they need - from foraging, farming, and fossil fuels. ..."

%A H. P. de Vladar
%A E. Szathmary
%T Beyond Hamilton's rule
%J Science
%V 356
%N 6337
%P 485-486
%M MAY
%D 2017
%K news, views, c2017, c201x, c20xx, zz0517, human, animal, behaviour,
   Hamilton's rule, HR, Hamilton, relatedness, kin, society, altruism,
   cooperation,
%X "Why do worker bees give up their own reproduction in favor of other
   offspring of the queen? Does this make sense from a Darwinian point of view,
   which prescribes maximization of reproductive success? ... Most experts in
   evolution agree that the first detailed, and essentially correct,
   explanation for altruistic behavior was given by Hamilton in 1964. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aam6322">doi:10.1126/science.aam6322</A>]['17]  (12 refs).
   [Also search for: Hamilton rule].

%A F. LeRon Shults
%A et al ...
%A M. Toft
%T A generative model of the mutual escalation of anxiety between religious
   groups
%J J. of Artificial Societies and Social Simulation
%V 21
%N 4
%P 7
%M OCT
%D 2018
%K jrnl, eJrnl, JASSS, c2018, c201x, c20xx, zz1018, Alife, simulation,
   cooperation, behaviour, human behaviour, society, social, conflict, hate,
   threat, religion, xenophobia, inGroup, outGroup, Gujurat, Troubles, Bogside,
   Conflict Archive, CAIN
%X "... model of the emergence & escalation of xenophobic anxiety in which
   individuals from two different religious groups encounter various hazards
   within an artificial society. ... results identify some of the conditions &
   mechanisms that engender the intensification of anxiety within & between
   religious groups. ... Trace validation techniques show that the most common
   conditions under which longer periods of mutually escalating xenophobic
   anxiety occur are those in which the difference in the size of the groups is
   not too large & the agents experience social & contagion hazards at a level
   of intensity that meets or exceeds their thresholds for those hazards. Under
   these conditions agents will encounter out-group members more regularly, &
   perceive them as threats, generating mutually escalating xenophobic anxiety.
   The model's capacity to grow the macro-level emergence of this phenomenon
   from micro-level agent behaviors & interactions provides the foundation for
   future work in this domain."
   -- [<A HREF="http://jasss.soc.surrey.ac.uk/21/4/7.html">www</A>]['18],
      [<A HREF="https://doi.org/10.18564/jasss.3840">doi:10.18564/jasss.3840</A>]['18].
   (Also see the bbc[<A HREF="https://www.bbc.com/news/technology-46035542">31/10/2018</A>].)

%A K. Smith
%A T. Larroucau
%T Hunter-gatherers maintain assortativity in cooperation despite high levels
   of residential change and mixing
%J Current Biol.
%V 28
%N 19
%P P3152-3157.e4
%M OCT
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0119, UPenn, human behaviour, society,
   cooperation, IPD, share, sharing, help, Hadza, hunter gatherer,
   cooperative, selfish, culture, reciprocity
%X "... we analyze four years of data (2010, 2013, 2014, 2016) tracking
   residence & levels of cooperation elicited from a public goods game in Hadza
   hunter-gatherers of Tanzania. Data were collected from 56 camps, comprising
   383 unique individuals, 137 of whom we have data for two or more years.
   Despite significant residential mixing, we observe a robust pattern of
   assortment that is necessary for cooperation to evolve; in every year, Hadza
   camps exhibit high between-camp & low within-camp variation in cooperation.
   We find little evidence that cooperative behavior within individuals is
   stable over time or that similarity in cooperation between dyads predicts
   their future cohabitation. Both sets of findings are inconsistent with models
   that assume stable cooperative & selfish types, including partner choice
   models. Consistent with social norms, culture, & reciprocity theories,
   the strongest predictor of an individual's level of cooperation is the
   mean cooperation of their current campmates. ..."
   -- [<A HREF="https://doi.org/10.1016/j.cub.2018.07.064">doi:10.1016/j.cub.2018.07.064</A>]['19],
      313064@[<A HREF="https://doi.org/10.1101/313064">biorXiv</A>][22/5/2018].
   So, "predictor ... mean cooperation of their current campmates"!
   (Also see the abc[<A HREF="https://www.abc.net.au/news/2019-01-09/competition-versus-cooperation--human-instinct/10590490">9/1/2019</A>].)
   [Also search for: human cooperation].

%A R. Wrangham
%T The Goodness Paradox: The Strange Relationship Between Virtue and Violence in
   Human Evolution
%I PantheonPress
%P 400
%M JAN
%D 2019
%K book, text, c2019, c201x, c20xx, zz0319, human behaviour, primate,
   cooperation, cooperate, aggression
%X 1st ed 2019; hb us$ ; uk us isbn:1101870907; uk us isbn13:978-1101870907.
   "How does the intensity of violence among humans compare with the aggressive
   behavior of other primates? How did humans domesticate themselves? And how
   were the acquisition of language and the practice of capital punishment
   determining factors in the rise of culture and civilization? ..."

%A C. Alos-Ferrer
%A J. GarcÃa-Segarra
%A A. Ritschel
%T Generous with individuals and selfish to the masses
%J NatureHumanBehaviour
%P 1-9
%M JUL
%D 2021
%K eJrnl, c2021, c202x, c20xx, zz0821, human behaviour, generosity, theft,
   big robber, Dictator, Ultimatum, Trust, games, selfish, selfishness, charity,
   prosocial, altruism, antisocial, cooperation
%X "... We design an experimental setting, the 'Big Robber' game, where a
   'robber' can obtain a large personal gain by appropriating the earnings of a
   large group of 'victims'. In a large lab. experiment (N=640), more than half
   of all robbers took as much as poss. & almost nobody declined to rob. However
   the same participants simultaneously displayed std, predominantly prosocial
   behaviour in Dictator, Ultimatum & Trust games. Thus, we provide direct
   empirical evidence showing that individual selfishness in high-impact
   decisions affecting a large group is compatible with prosociality in
   bilateral low-stakes interactions. That is, human beings can simultaneously
   be generous with others and selfish with large groups."
   -- [<A HREF="https://doi.org/10.1038/s41562-021-01170-0">doi:10.1038/s41562-021-01170-0</A>]['21].
   [Also search for: cooperation human behaviour] and
   [also search for: ultimatum game].

%A T. Bonnemain
%A et al
%T Pedestrians in static crowds are not grains, but game players
%J arXiv
%M JAN
%D 2022
%K TR, c2022, c202x, c20xx, zz0222, crowd, human behaviour, game theory,
   metro, underground, tube, boarding
%X "The short-term ('operational') dynamics of pedestrian crowds are generally
   thought to involve no anticipation, except perhaps the avoidance of the most
   imminent collisions. We show that current models rooted in this belief fail
   ... We identify the missing ingredient as the pedestrians' ability to plan
   ahead far enough beyond the next interaction, which explains why instead of
   walking away from the intruder they accept to temporarily move transversely
   towards denser regions ... a minimal model based on mean-field game theory
   ... situations such as partial metro boarding. ..."
   -- 2201.08592@[<A HREF="https://arxiv.org/abs/2201.08592">arXiv</A>]['22].
   auth1@[<A HREF="https://scholar.google.fr/citations?hl=fr&user=QBtXRxoAAAAJ">schlr</A>]['22].

%A R. Koster
%A et al
%T Human-centred mechanism design with democratic AI
%J NutureHumanBehaviour
%M JUL
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0722, AI, economic game, distribute, money,
   fairness, fair, social, society, behaviour, poliocy
%X "... A large group of humans played an online investment game that involved
   deciding whether to keep a monetary endowment or to share it with others for
   collective benefit. Shared revenue was returned to players under two
   different redistribution mechanisms, one designed by the AI & the other by
   humans. The AI discovered a mechanism that redressed initial wealth
   imbalance, sanctioned free riders & successfully won the majority vote. By
   optimizing for human preferences, Democratic AI offers a proof of concept for
   value-aligned policy innovation."
   -- [<A HREF="https://doi.org/10.1038/s41562-022-01383-x">doi:10.1038/s41562-022-01383-x</A>]['22].

%A C. Efferson
%A et al
%T Super-additive cooperation
%J Nature
%V 626
%P 1034-1041
%M FEB
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0324, human, animal, behaviour, cooperation,
   reciprocity, PD, IPD, social
%X "Repeated interactions provide an evolutionary explanation for one-shot human
   cooperation that is counterintuitive but orthodox. Intergroup competition
   provides an explanation that is intuitive but heterodox. Here, using models
   & a behavioural experiment, we show that neither mechanism reliably supports
   cooperation. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07077-w">doi:10.1038/s41586-024-07077-w</A>]['24].
  (Also see [<A HREF="https://doi.org/10.1038/d41586-024-00308-0">doi:10.1038/d41586-024-00308-0</A>]['24].)
   [Also search for: PD IPD].

%A J. Silvertown
%T Selfish Genes to Social Beings: A Cooperative History of Life
%I OUP
%P 256
%D 2024
%K book, text, c2024, c202x, c20xx, zz0424, PD, IPD, human behaviour, animal,
   cooperation
%X "... show how cooperation is key to the cells forming our organs, to
   symbiosis between organisms, to genes that band together, to the dawn of life
   itself. Cooperation has enabled life to thrive and become complex. Without it
   life would never have begun."
   1st ed 2024; hb stg.20; uk us isbn:0198876394; uk us isbn13:978-0198876397.

%A T. Johnson
%T Empirically testing a relationship between cooperation and the prime numbers
%J Royal Soc. Open Sc.
%M JUN
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0624, prime number, PD, IPD, cooperation,
   prisoner's dilemma, prey
%X "Theoretical models suggest a relationship between cooperation & the prime
   numbers. In environments where agents play multiple one-shot prisoner's
   dilemma games per generation, cooperators evolve to fixation more freq. when
   cooperating on a cyclical schedule with a prime-# period length. ... I find
   v.modest evidence of cyclicality at prime-numbered time intervals ...
   findings cast doubt on the hypothesis of increased cooperation at
   prime-number time points - at least among humans playing public goods games."
   -- [<a HREF="https://doi.org/10.1098/rsos.231425">doi:10.1098/rsos.231425</A>]['24].

%A N. E. Glynatsi
%A et al
%T Evolution of reciprocity with limited payoff memory
%J Proc. Royal Soc. B
%M JUN
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0624, PD, IPD, cooperation
%X "Direct reciprocity is a mechanism for the evolution of cooperation in
   repeated social interactions. ... we consider the evol'n of conditional
   behaviours when individuals learn based on more recent experiences. Even in
   the most extreme case that they only take into account their very last
   interaction, we find that cooperation can still evolve ... While our results
   suggest that some rudimentary form of payoff memory is necessary, it
   suffices to remember a few interactions."
    -- [<A HREF="https://doi.org/10.1098/rspb.2023.2493">doi:10.1098/rspb.2023.2493</A>]['24].
   [Also search for: IPD cooperation].
   Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/IPD/">IPD</A>].



%A J. C. Maxwell
%T Illustrations of the dynamical theory of gases. Part I. On the motions &
   collisions of perfectly elastic spheres
%J The London, Edinburgh, and Dublin Philosophical Mag. and J. of Sci.,
%S 4
%V 19
%P 19-32
%D 1860
%K jrnl, c1860, c186x, c18xx, zz1024, physics, statistical mechanics,
   ideal, gas, particles, energy, velocity, distribution
%X "... two spheres moving in opposite dirns with velcities inversely as their
   masses strike one another ..."
   -- [<A HREF="https://www.biodiversitylibrary.org/item/53795#page/33/mode/1up">biodiversitylibrary.org</A>]['24].
   And part-2:
   'Illustrations of the dynamical theory of gases. Part II. On the process of
   diffusion of two or more kinds of moving particles among one another',
   vol.20, pp.21-37, 1860
   -- [<A HREF="https://www.biodiversitylibrary.org/item/20012#page/37/mode/1up">biodiversitylibrary.org</A>]['24].
   Also see the 'Maxwell-Boltzmann distribution'
   -- [<A HREF="https://en.wikipedia.org/wiki/Maxwell-Boltzmann_distribution">wikip</A>]['24],
   and the 'Boltzmann distribution' (no M).

%A W. Thomson
%T Kinetic theory of the dissipation of energy
%J Nature
%V 9
%N 232
%P 441-444
%M APR
%D 1874
%K jrnl, Thomson, Baron Kelvin, c1874, c197x, c18xx, zz0314, science, physics,
   entropy, thermodynamics, 2nd, second law, energy, dynamics, reversibility,
   reversibile, reversal, heat, 1852, dissipation, dissipative, arrow, time,
   irreversibility, time reversal, Loschmidt's paradox
%X "In abstract dynamics an instantaneous reversal of the motion of every moving
   particle of a system causes the system to move backwards, each particle of it
   along its old path - and at the same speed as before when again in the same
   position - that is to say, in mathematical language, any solution remains a
   soln when t is changed into -t. In physical dynamics, this simple & perfect
   reversibility fails on account of forces depending on friction of solids;
   imperfect fluidity of fluids; imperfect elasticity of solids; inequalities of
   temperature & consequent conduction of heat produced by stresses in solids &
   fluids; imperfect magnetic retentiveness; residual electric polarisation of
   dielectrics; generation of heat by electric currents induced by motion;
   diffusion of fluids, solution of solids in fluids, & other chemical changes;
   & absorption of radiant heat & light. Consideration of these agencies in
   connection with the all-pervading law of the conservation of energy proved
   for them by Joule, led me twenty-three years ago to the theory of the
   dissipation of energy, which I communicated first to the Royal Society of
   Edinburgh in 1852, in a paper entitled 'On a Universal Tendency in Nature to
   the Dissipation of Mechanical Energy.'"
   -- [<A HREF="http://dx.doi.org/10.1038/009441c0">doi:10.1038/009441c0</A>]['14] may $$$,
   & in S.Brush (ed.), 'Kinetic Theory', vol.2, Pergamon, pp.176-187, 1966.
   [Also search for: arrow time].
   (Also see the [<A HREF="http://www.allisons.org/ll/MML/Entropy/Gas/">Ideal_Gas</A>] & [<A HREF="http://en.wikipedia.org/wiki/Loschmidt's_paradox">wikip</A>]['14].)

%T Flatland: A Romance of Many Dimensions
%P 83
%I Dover
%D 1880
%O 1992
%K book, text, c1880, c188x, c18xx, flat land, planiverse, one, two, three,
   four, dimension, 1D, 2D, 3D, 4D, geometry, space
%X E. A. Abbott (Illustrator), B. Hoffmann (Intro); isbn:048627263X.
   (pb, 12pp; uk us isbn:0064635732; 1983.)

%A L. Boltzmann
%T Further studies on the thermal equilibrium of gas molecules
   (orig: Weitere Studien uber das Wormegleichgewicht unter Gasmolekulen)
%J Sitzungsberichte Akad. Wiss., Vienna, part II,
%V 66
%P 275-370
%D 1872
%O (trans:)  The Kinetic Theory of Gases, History of Modern Physical Sciences,
   pp.262-349, 2003
%K jrnl, physics, x1872, c187x, c18xx, zz1024, thermodanamics, gas, heat,
   entropy
%X "According to the mechanical theory of heat, the thermal properties of gases
   & other substances obey perfectly definite laws in spite of the fact that
   these substances are composed of large numbers of molecules in states of
   rapid irregular motion. The explanation of these properties must be based on
   prob. theory ..."
   -- [<A HREF="https://doi.org/10.1142/9781848161337_0015">doi:10.1142/9781848161337_0015</A>]['24].
   [Also search for: Boltzmann physics].

%A L. E. Boltzmann
%T Vorlesungen uber Gastheorie
%D 1910
%C Leipzig
%K book, text, statistical physics, mechanics, c1910, c191x, c19xx, gas theory,
   thermodynamics, entropy, Htheorem, dispersion, gases, ideal gas
%X ref from vonMises p.234 1957: 2 vols, 2nd impression, Leipzig, 1910.
   (Also see LEB@[<A HREF="https://en.wikipedia.org/wiki/Ludwig_Boltzmann">wikip</A>]['24], 1844-1906 and
   [<A HREF="http://www.allisons.org/ll/MML/Entropy/Gas/">gas</A>gas</A>].)

%A J. E. Jones
%T On the determination of molecular fields.-I. From the variation of the
   viscosity of a gas with temperature
%J Proc. of the Royal Soc. of London
%S Ser.A, containing Papers of a Mathematical and Physical Character
%V 106
%N 738
%P 441-462
%M OCT
%D 1924
%K conf, physics, MolBio, c1924, c192x, c19xx, zz1122, Lennard Jones,
   atomic forces, force, potential field, molecular, molecules, atoms,
   attraction, repulse, van der Waals, vanDerWaals
%X "... we cannot hope to make a direct calculation of the nature of the forces
   called into play during an encounter between molecules in a gas. ... the
   field in the neighbourood of a hydrogen atom, assumed to consist of a -ve
   charge in motion in circular orbit about a +ve nucleus, & has shown how the
   pulsating field gives rise on the whole to a force of repulsion, as well as
   one of attraction n a unit negative charge. ..."
   -- [<A HREF="https://doi.org/10.1098/rspa.1924.0081">doi:10.1098/rspa.1924.0081</A>]['22].
   * Also see LJ@[<A HREF="https://en.wikipedia.org/wiki/Lennard-Jones_potential">wikip</A>]['22].
   [Also search for: molecule potential].

%A C. Davisson
%A L. H. Germer
%T The scattering of electrons by a single crystal of nickel
%J Nature
%V 119
%P 558-560
%M APR
%D 1927
%K jrnl, c1927, c192x, c19xx, physics, quantum effect, effects, theory,
   mechanics, wave, particle, duality, uncertainty, wave function,
   electron, wave length, wavelength
%X "... directing a narrow beam of electrons normally against a target cut from
   a single crystal of nickel, & are measuring the intensity of scattering
   (# of electrons per unit solid angle with speeds near that of the bombarding
   electrons) in various directions in front of the target. The experimental
   arrangement is s.t. the intensity of scattering can be measured in any
   latitude from the equator (plane of the target) to within 20A of the pole
   (incident beam) & in any azimuth. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/119558a0">doi:10.1038/119558a0</A>]['09],
   &  "In 1927, D. & G. bombarded a single crystal of nickel with a beam of
   electrons, & observed several beams of scattered electrons that were almost
   as well defined as the incident beam. The phenomenological similarities with
   X-ray diff'n were striking, & showed that a wavelength could indeed be assoc.
   with the electrons.   Nature 119, 558-560 (1927)"
   -- [<A HREF="http://www.nature.com/physics/looking-back/davisson/index.html">www</A>][11/'09].

%A P. M. Morse
%T Diatomic molecules according to the wave mechanics. II. Vibrational levels
%J Phys. Rev.
%V 34
%N 1
%P 57-64
%M JUL
%D 1929
%K jrnl, physics, MolBio, c1929, c192x, c19xx, zz1024, chemical bond, diatomic,
   potential energy
%X "An exact solution is obtained for the Schroedinger eqn ... diatomic ..."
   -- [<A HREF="https://link.aps.org/doi/10.1103/PhysRev.34.57">doi:10.1103/PhysRev.34.57</A>]['24].
   (Also see PMP@[<A HREF="https://en.wikipedia.org/wiki/Morse_potential">wikip</A>]['24].
   [Also search for: molecule potential].

%A P. A. M. Dirac
%T A new notation for quantum mechanics
%J Math. Proc. of the Cambridge Philosophical Soc.
%V 35
%N 3
%P 416-418
%M JUL
%D 1939
%K jrnl, c1939, c193x, c19xx, zz0323, quantum physics, mechanics, braket,
   bra ket notation, defn, vector, vectors, inner product, Hilbert space
%X -- [<A HREF="https://doi.org/10.1017/S0305004100021162">doi:10.1017/S0305004100021162</A>]['23].
   Also see, "... A ket is of the form |v>. ... it denotes a vector, v, in an
   abstract (complex) vector space V, & physically it represents a state of some
   quantum system.
   A bra is of the form < f| ... denotes a linear form f:V->C, i.e. a linear map
   that maps each vector in V to a number in the complex plane C. Letting the
   linear functional < f| act on a vector |v> is written as < f|v> in C. ..."
   -- BK@[<A HREF="https://en.wikipedia.org/wiki/Bra%E2%80%93ket_notation">wikip</A>]['23].

%A L. Meitner
%A O. R. Frisch
%T Disintegration of Uranium by neutrons: A new type of nuclear reaction
%J Nature
%V 143
%P 239-240
%M FEB
%D 1939
%K jrnl, Physics, c1939, c193x, c19xx, zz0414, nuclear fission, atom, atomic,
   neutron, nucleus, split, splitting, chain reaction, Hahn,
   woman, women, www, STEM, scientist
%X "In making chemical assignments, it was always assumed that these
   radioactive bodies had atomic numbers near that of the element bombarded,
   since only particles with one or two charges were known to be emitted from
   nuclei. A body, for example, with similar properties to those of osmium was
   assumed to be eka-osmium (Z=94) rather than osmium (Z=76) or
   ruthenium (Z=44)."
   -- [<A HREF="http://dx.doi.org/10.1038/143239a0">doi:10.1038/143239a0</A>]['14].
   Also see "... Meitner was part of the team that discovered nuclear fission,
   an achievement for which her colleague Otto Hahn was awarded the Nobel
   Prize. Meitner is often mentioned as one of the most glaring examples of
   women's scientific achievement overlooked by the Nobel committee. ..."
   -- LM@[<A HREF="http://en.wikipedia.org/wiki/Lise_Meitner">wikip</A>]['14].

%A J. R. Oppenheimer
%A H. Snyder
%T On continued gravitational contraction
%J Phys. Rev.
%I APS
%V 56
%P 455-459
%M SEP
%D 1939
%K jrnl, physics, c1939, c193x, c19xx, zz0724, black hole, holes, gravity,
   gravitational field equations, cosmology
%X "When all thermonuclear sources of energy are exhausted a sufficiently heavy
   star will collapse. Unless fission due to rotation, the radiation of mass, or
   the blowing off of mass by radiation, reduce the star's mass to the order of
   that of the sun, this contraction will continue indefinitely. ... we study
   the solns of the gravitational field equns which describe this process. ..."
   -- [<A HREF="https://doi.org/10.1103/PhysRev.56.455">doi:10.1103/PhysRev.56.455</A>]['24].

%A E. Schrodinger
%T What is Life?
%I MacmillanCo
%P 91
%D 1945
%K book, Erwin Schrodinger, c1945, c194x, c19xx, zz0219, life, definition,
   mind, matter, philosophy, schroedinger
%X 1945, hb us$45, asin:B000JTFNAO.
   And a CUP reprint 2012, also with 'Mind and Matter', pp.200,
   pb us$15; uk us isbn:1107683653, uk us isbn13:978-1107604667.
   [Also search for: life definition].

%A Y. G. Sinai
%T On the notion of entropy of a dynamical system
%J Doklady of Russian Acad. of Sci.
%V 124
%P 768-771
%D 1959
%K jrnl, c1959, c195x, c19xx, zz0414, maths, physics, dynamic system, entropy,
   Kolmogorov Sinai, metric, ergodic, ergodicity, theory, measure, theoretic
%X "... The measure-theoretic entropy of a dynamical system (X,B,T,m) wrt a
   partition Q={Q_1, ..., Q_k} is def. as
      h_m(T,Q) = lim_N->inf (1/N) H (OR_n=0..N T^-n Q).
   Finally, the Kolmogorov-Sinai or metric or measure-theoretic entropy of
   a dynamical system (X,B,T,m) is def. as
      h_m(T) = SUP_Q h_m(T, Q),
   where the supremum is taken over all finite measurable partitions. ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Measure-preserving_dynamical_system">wikip</A>]['14].
   See Sinai@[<A HREF="http://www.math.princeton.edu/directory/yakov-sinai">Pr'nc't'n</A>]['14].

%A P. Dirac
%T The Evolution of the Physicist's Picture of Nature
%J Sci. Am.
%M MAY
%D 1963
%O Sci. Amer., (reprinted) June 2010
%K physics, cosmology, c1963, c196x, c19xx, zz0318, theory, Dirac, essay,
   relativity, quantum mechanics, theory
%X "In this article I should like to discuss the development of general
   physical theory: how it developed in the past and how one may expect it
   to develop in the future. One can look on this continual development as
   a process of evolution, a process that has been going on for several
   centuries. ..."
   -- [<A HREF="https://blogs.scientificamerican.com/guest-blog/the-evolution-of-the-physicists-picture-of-nature/">www</A>]['18].

%A J. S. Bell
%T On the Einstein Podolsky Rosen paradox
%J Physics
%V 1
%N 3
%P 195-200
%D 1964
%K jrnl, c1966, c196x, c19xx, Bell, Bells inequality, quantum mechanics, theory,
   physics, hidden variable, variables, theorem, non locality, local,
   entanglement
%X "... [hidden variables] formulated math. and shown to be incompatible with
   the stat. predns of q.mech.. It is the requirement of locality, or more
   precisely that the result of a measurement in one sys. be unaffected by the
   ops on a distant sys. with which it has interacted in the past that creates
   the essential difficulty. ..."
   -- [<A HREF="http://www.informationphilosopher.com/solutions/scientists/bell/Bell_On_EPR.pdf">www</A>]['14].
   (Also see 50th@[<A HREF="http://dx.doi.org/10.1038/510467a">nat're</A>][19/6/2014]
   and [<A HREF="http://en.wikipedia.org/wiki/Bell's_theorem">wikip</A>]['10].)
   [Also search for: Bell c1966] & [also search for: Bell's inequality].

%A Y. Aharonov
%A P. G. Bergmann
%A J. L. Lebowitz
%T Time symmetry in the quantum process of measurement
%J Phys. Rev.
%V 1
%N B1410
%M JUN
%D 1964
%K jrnl, c1964, c196x, c19xx, zz1122, physics, time, arrow, irreversibility,
   measurement, retrodiction, prediction, coherence, quantum
%X "We examine the assertion that the 'reduction of the wave packet,' implicit
   in the q.theory of measurement introduces into the foundations of q.physics
   a time-asymmetric element, which in turn leads to irreversibility. ..."
   -- [<A HREF="https://doi.org/10.1103/PhysRev.134.B1410">doi:10.1103/PhysRev.134.B1410</A>]['22].
   [Also search for: time arrow physics].

%A A. A. Penzias
%A R. W. Wilson
%T A measurement of excess antenna temperature at 4080 Mc/s
%J Astrophysical J.
%V 142
%P 419-421
%D 1965
%K jrnl, astronomy, c1965, c196x, c19xx, big bang, universe, cosmic,
   microwave background radiation, CMB, physics, cosmology
%X "Measurements of the effective zenith noise temp. of the 20-foot
   horn-reflector antenna (Crawford, Hogg, & Hunt 1961) at the Crawford Hill
   Lab., Holmdel, New Jersey, at 4080 Mc/s have yielded a value of about
   3.5K higher than expected. This excess temp. is, within the limits of our
   observations, isotropic, unpolarized, & free from seasonal variations
   (July, 1964 - April, 1965). A possible explanation for the observed excess
   noise temperature is the one given by Dicke, Peebles, Roll, & Wilkinson
   (1965) in a companion letter in this issue."
   -- [<A HREF="http://dx.doi.org/10.1086/148307">doi:10.1086/148307</A>]['14].
   Also see CMBR@[<A HREF="http://en.wikipedia.org/wiki/Cosmic_microwave_background_radiation">wikip</A>]['14].

%A J. S. Bell
%T On the problem of hidden variables in quantum mechanics
%J Rev. Mod. Phys.
%V 38
%N 3
%P 447-452
%D 1966
%K jrnl, c1966, c196x, c19xx, Bell, Bells inequality, quantum mechanics, theory,
   physics, hidden variable, theorem
%X "The demonstrations of von Neumann and others, that q.mechanics does
   not permit a hidden variable interpretation, are reconsidered. It is shown
   that their essential axioms are unreasonable. It is urged that in further
   examination of this problem an interesting axiom would be that mutually
   distant systems are indep. of one another."
   -- [<A HREF="http://rmp.aps.org/abstract/RMP/v38/i3/p447_1">aps</A>]['10],
      [<A HREF="http://dx.doi.org/10.1103/RevModPhys.38.447">doi:10.1103/RevModPhys.38.447</A>]['10].
   [Also search for: Bell c1966] & [also search for: Bell's inequality].

%A A. Hewish
%A S. J. Bell
%A J. D. H. Pilkington
%A P. F. Scott
%A R. A. Collins
%T Observation of a rapidly pulsating radio source
%J Nature
%V 217
%P 709-713
%M FEB
%D 1968
%K jrnl, c1968, c196x, c19xx, pulsar, pulsars, radio astronomy, signal,
   Jocelyn Bell, little green men, Nobel prize
%X "Unusual signals from pulsating radio sources have been recorded at the
   Mullard Radio Astronomy Observatory. The radiation seems to come from local
   objects within the galaxy, and may be associated with oscillations of white
   dwarf or neutron stars."
   -- [<A HREF="http://dx.doi.org/10.1038/217709a0">doi:10.1038/217709a0</A>]['10].
   [Also search for: Bell pulsar].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/Film/Andromeda/era/">A for A.</A>].-)

%A S. W. Hawking
%A R. Penrose
%T The singularities of gravitational collapse and cosmology
%J Proc. Royal Soc. (A)
%V 314
%N 1519
%P 529-548
%M JAN
%D 1970
%K jrnl, c1970, c197x, c19xx, physics, space, time, black hole, holes
%X "A new theorem on space-time singularities is presented which largely
   incorporates & generalizes the previously known results. [It] implies that
   space-time s. are to be expected if either the universe is spatially closed
   or there is an 'object' undergoing relativistic gravitational collapse
   (existence of a trapped surface) or there is a point p whose past null cone
   encounters sufficient matter that the divergence of the null rays through p
   changes sign somewhere to the past of p (i.e. there is a min.apparent solid
   angle, as viewed from p for small objects of given size). The thm applies if
   the following four physical assumptions are made: (i) Einstein's equns hold
   (with zero or -ve cosmological constant), (ii) the energy density is nowhere
   < minus each principal pressure nor less than minus the sum of the three
   principal pressures (the 'energy condition'), (iii) there are no closed
   timelike curves, (iv) every timelike or null geodesic enters a region where
   the curvature is not specially alined with the geodesic. (This last condition
   would hold in any sufficiently general physically realistic model.) In common
   with earlier results, timelike or null geodesic incompleteness is used here
   as the indication of the presence of space-time singularities. No assumption
   concerning existence of a global Cauchy hypersurface is required for the
   present theorem."
   -- [<A HREF="http://dx.doi.org/10.1098/rspa.1970.0021">doi:10.1098/rspa.1970.  0021</A>].

%A J. P. Christiansen
%T Numerical simulation of hydrodynamics by the method of point vortices
%J J. Comp. Physics
%V 13
%N 2
%P 363-379
%D 1973
%O J. Comp. Physics,  Special issue: commemoration of the 30th anniversary,
   135(2), pp.189-197, Aug., c1997
%K jrnl, computer program, numerical methods, vortex, c1973, c197x, c19xx,
   hydrodynamic, flow, plasma, nuclear, fusion, power, JPChristiansen
%X [<A HREF="http://dx.doi.org/10.1006/jcph.1997.5701">jcph.1997</A>]['04].

%A J. D. Bekenstein
%T Generalized second law of thermodynamics in black-hole physics
%J Phys. Rev.
%V D9
%P 3292-3300
%M JUN
%D 1974
%K black holes, surface area, 2nd, generalization, GSL, laws,
   information, entropy, Sbh, c1974, c197x, c19xx
%X Studies the author's (see abstr. A44989 of 1973) suggested generalization
   of the second law of thermodynamics to regions containing black-holes:
   'the black-hole entropy plus the common entropy in the black-hole exterior
   never decreases'. The black-hole entropy is defined as
   Sbh=(1/2)ln2(2 pi alpha /h) where alpha is the rationalized black-hole area.
   The infall of an entropy-bearing system into a large and more
   massive black-hole is studied; an upper bound for the entropy of the system
   and a lower bound for the increase of the black-hole entropy are obtained.
   Quantum effects and the significantly statistical nature of the generalized
   second law are discussed.

%A C. Marchal
%A D. G. Saari
%T On the final evolution of the n-body problem
%J J. Differential Equns
%V 20
%N 1
%P 150-186
%M JAN
%D 1976
%K jrnl, c1976, c197x, c19xx, zz0115, Newtonian, n body, nBody, physics,
   gravity, gravitational, time, arrow
%X "... main result gives the asymptotic properties of the distances between
   particles as time (t) approaches infinity. It is shown how particles can
   separate into subsystems between which the distances are asymptotic to
   constant multiples of time, & within which the mutual distances are at most
   of the order t^(2/3). Each subsystem behaves asymptotically like a pure
   n-body problem in the sense that an energy & an angular momentum relationship
   are asymptotically satisfied. These techniques allow some three-body results
   found by Birkhoff & by Sundman to be extended to the n-body problem. Finally,
   some n-body results are derived for a motion which expands faster than time."
   -- [<A HREF="http://dx.doi.org/10.1016/0022-0396(76)90101-7">doi:10.1016/0022-0396(76)90101-7</A>]['15].
   [Also search for: arrow time].

%A D. Bohm
%T Wholeness and the Implicate Order
%I RoutledgePubl
%D 1980
%K book, text, physics, philosophy, c1980, c198x, c19xx, zz0123, quantum,
   weirdness, reality, wave, particle, duality
%X isbn:0744800005;
   Routledge 2002, uk us isbn:0415289793; isbn13:978-0415289795.
   Also see DB@[<A HREF="https://en.wikipedia.org/wiki/David_Bohm">wikip</A>]['23].
   [Also search for: physics Bohm].

%A J. D. Bekenstein
%T Black hole thermodynamics
%J Physics Today
%V 33
%N 1
%P 24-31
%M JAN
%D 1980
%K physics, c1980, c198x, c19xx, cosmology, black holes
%X papers only on-line from about '95.

%A E. Fredkin
%A T. Toffoli
%T Conservative logic
%J Int. J. Theor. Physics
%N 3-4
%P 219-253
%M APR
%D 1982
%I SpringerVerlag
%K conf, c1982, c198x, c19xx, zz0714, model, computing, physics, energy, mass,
   conservation, computer, computing, computation, logic, gate, gates,
   reversible, reversibility, laws, power dissipation, CNOT gate
%X "CL is a comprehensive model of compn which explicitly reflects a # of
   fundamental principles of physics, such as the reversibility of the dynamical
   laws & the conservation of certain additive quantities ... Because it more
   closely mirrors physics than trad. models of compn, CL is in a better posn to
   provide indications concerning the realization of high-performance computing
   systems ...  resources' actually offered by nature. ... In particular, CL
   shows that it is ideally possible to build seq.circuits with zero internal
   power dissipation. After establishing a general framework, we discuss two
   specific models of compn. The first uses binary vars. & is the
   conservative-logic counterpart of switching theory; [it] proves that
   universal computing capabilities are compatible with the reversibility &
   conservation constraints. The 2nd model, which is a refinement of the 1st,
   constitutes a substantial breakthrough in establishing a corr. between compn
   & physics. In fact, this model is based on elastic collisions of identical
   'balls' & thus is formally identical with the atomic model that underlies the
   (classical) kinetic theory of perfect gases. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/BF01857727">doi:10.1007/BF01857727</A>]['14].
   [Also search for: reversible computing].
   (Also see F.gate@[<A HREF="http://en.wikipedia.org/wiki/Fredkin_gate">wikip</A>]['14].)
   (?In uk us isbn:1852335408, 2002?)

%A W. H. Zurek
%T Environment-induced superselection rules
%J Phys. Rev. D
%V 26
%N 1862
%M OCT
%D 1982
%K eJrnl, c1982, c198x, c19xx, zz0821, physics, quantum mechanics, system,
   apparatus, measurement, observable
%X "We show how the correlations of a q.system with other q.systems may cause
   one of its observables to behave in a classical manner. In particular,
   'reduction of the wave packet,' postulated by von Neumann to explain
   definiteness of an outcome of an individual observation, can be explained
   when a realistic model of an apparatus is adopted. Instead of an isolated
   q.apparatus with a # of states equal to the # of possible distinct outcomes
   of the measurement, discussed by von N., we consider an apparatus interacting
   with other physical systems, described here summarily as 'environment.' ..."
   -- [<A HREF="https://doi.org/10.1103/PhysRevD.26.1862">doi:10.1103/PhysRevD.26.1862</A>]['21].

%A R. P. Feynman
%T Simulating Physics with Computers
%J IJTP
%V 21
%N 6/7
%P 467-488
%D 1982
%K IJTP, jrnl, c1982, c19xx, c19xx, quantum computing, computer, science,
   quantumComputer, science, quomplexity, qomplexity, complexity, NP, NPC, BQP
%X Feynman points out the curious problem that it appears to be impossible
   to simulate a general quantum physical system on a probabilistic Turing
   Machine without an exponential slowdown, even if the quantum physical
   system to be simulated is discrete (like some kind of quantum cellular
   automaton).
   -- [<A HREF="http://dx.doi.org/10.1007/BF02650179">doi:10.1007/BF02650179</A>]['14].
   (Also see QC@[<A HREF="http://en.wikipedia.org/wiki/Quantum_computer">wikip</A>]['14].)
   [Also search for: Feynman quantum computing].

%A N. Herbert
%T Quantum Reality
%I Doubleday
%P 256
%D 1985
%K book, text, physics, philosophy, c1985, c198x, c19xx, Fundamental Fysiks,
   quantum mechanics, quon, quons, wave function, waves, measurement,
   interpretation, Copenhagen, three polarizers
%X uk us isbn:0385187041; uk us isbn13:978-0385187046.
   -- [<A HREF="https://en.wikipedia.org/wiki/Quantum_Reality">wikip</A>]['2].
   [Also search for: quantum reality mechanics].

%A A. Peres
%T Reversible logic and quantum computers
%J Phys. Rev. A
%V 32
%P 3266-3276
%M DEC
%D 1985
%K c1985, c198x, c19xx, quantum computing, computer, quantumComputer,
   correction, error correcting codes, qubit
%X "... concerned with the const'n of a quantum-mechanical Hamiltonian
   describing a computer. This H. generates a dynamical evolution which mimics
   a seq. of elementary logical steps. This can be achieved if each logical step
   is locally reversible (global reversibility is insufficient). Computational
   errors due to noise can be corrected by means of redundancy. In particular,
   reversible error-correcting codes can be embedded in the H. itself. An
   estimate is given for the minimum amount of entropy which must be dissipated
   at a given noise level and tolerated error rate."
   -- [<A HREF="https://doi.org/10.1103/PhysRevA.32.3266">10.1103/PhysRevA.32.3266</A>]['21].

%A R. P. Feynman
%T Quantum mechanical computers
%J Foundations of Physics
%V 16
%N 6
%P 507-531
%D 1986
%O Conf. on Lasers & Electro-Optics 1984
%K physics, conf, jrnl, c1984, c1986, c198x c19xx, quantum computing, mechanics,
   computer, science, reversible, energy, complexity, NPC, gate, gates, CNOT
%X "The physical limitations, due to quantum mechanics, on the functioning of
   computers are analyzed."
   -- [<A HREF="https://doi.org/10.1007/BF01886518">doi:10.1007/BF01886518</A>]['17].
   ("A computer is imagined in which all the parts are simple two-state objects
    obeying quantum mechanical laws. A time-indep. Hamiltonian for such a system
    is written & analyzed. The comp'n is done in logically reversible steps.
    It is used to study possible limitations on computers due to fundamental
    physical laws. ..."
    -- 1984 Conf [<A HREF="https://doi.org/10.1364/CLEO.1984.TUAA2">doi:10.1364/CLEO.1984.TUAA2</A>]['24].)
   [Also search for: Feynman quantum computing],
   [also search for: quantum computing].

%A A. K. Dewdney
%T Armchair Universe: An Exploration of Computer Worlds
%I WHFreeman
%D 1988
%P 330
%K book, world, physics, introduction, fun, good, scientific american, articles
%X uk us isbn:0716719398.
   collection of A.K. Dewdney's articles from the `Computer Recreations'
   column of Scientific American.

%A N. D. Mermin
%T What's wrong with these equations?
%J Phys. Today
%V 42
%N 10
%P 9
%D 1989
%K physics, c1989, c198x, c19xx, quantum theory, weird, weirdness, shut up,
   calculate, understanding, zz0913
%X "shut up and calculate!"
   -- [<A HREF="http://dx.doi.org/10.1063/1.2811173">doi:10.1063/1.2811173</A>]['13].
   (Also see [<A HREF="http://dx.doi.org/10.1038/501154a">www</A>][9/'13].)

%A A. K. Dewdney
%T The Magic Machine: A Handbook of Computer Sorcery
%I Freeman
%P 357
%D 1990
%K book, text, introduction, fun, AI, fractals, biomorphs, computers
%X isbn:0716721449.

%A A. K. Dewdney
%T The Planiverse: Computer Contact With a Two-Dimensional World
%I Copernicus
%D 2000
%K book, text, flatland, 2D, science fiction, sciFi
%X isbn:0387989161.  About us$22.  [Also search for: Flatland].

%A J. Oppenheim
%A B. Reznik
%A W. Unruh
%T Temporal ordering in quantum mechanics
%J arXiv
%M MAR
%D 2000
%K TR, physics, c2000, c200x, c20xx, zz0323, quantum, time, arrow, future, past
%X "We examine the measurability of the temporal ordering of two events, [&]
   event coincidences. In classical mechanics, a measurement of the
   order-of-arrival of two particles is shown to be equiv. to a measurement
   involving only one particle (in higher dimensions). In q.mechanics, we find
   that diffraction effects introduce a minimum inaccuracy to which the temporal
   order-of-arrival can be determined unambiguously. The min. inaccuracy of the
   measurement is given by dt=1/E where E is the total kinetic energy of the two
   particles. Similar restrictions apply to the case of coincidence
   measurements. We show that these limitations are much weaker than limitations
   on measuring the time-of-arrival of a particle to a fixed location."
   -- quant-ph/0003130@[<A HREF="https://doi.org/10.48550/arXiv.quant-ph/0003130">arXiv</A>]['23].

%A D. P. DiVincenzo
%T The physical implementation of quantum computation
%J Fortschritte der Physik
%V 48
%N 9-11
%P 771-783
%M OCT
%D 2000
%K jrnl, c2000, c200x, c20xx, zz0323, quantum computing, computer, requirements,
   criteria
%X "... requirements for the physical implementation of q.computation are
   discussed. These five requirements, plus two relating to the communication of
   q.info., are extensively explored & related to the many schemes in atomic
   physics, quantum optics, nuclear & electron magnetic resonance spectroscopy,
   superconducting electronics, & q.-dot physics, for achieving q.computing."
   -- [<A HREF="https://doi.org/10.1002/1521-3978(200009)48:9/11<771::AID-PROP771>3.0.CO;2-E">www</A>]['23] and
   quant-ph/0002077@[<A HREF="https://arxiv.org/abs/quant-ph/0002077">arXiv</A>]['23].
   [Also search for: DiVincenzo quantum].

%A L. Hardy
%T Quantum theory from five reasonable axioms
%J arXiv
%M JAN
%D 2001
%K TR, c2001, c201x, c20xx, pyysics, quantum theory, probability, uncertainty,
   axiom, zz0913
%X "The usual formulation of quantum t. is based on rather obscure axioms
   (employing complex Hilbert spaces, Hermitean operators, & the trace rule for
   calculating probabilities). ... it is shown that quantum t. can be derived
   from five very reasonable axioms. The first four of these are obviously
   consistent with both q.theory & classical p.theory. Axiom 5
   (which requires that there exists continuous reversible transformations
   between pure states) rules out classical p.theory. If Axiom 5 (or even just
   the word 'continuous' from Axiom 5) is dropped then we obtain classical
   p.theory instead. ... provides some insight into the reasons q.theory
   is the way it is. [Eg,] it explains the need for complex #s & where the
   trace formula comes from. We also gain insight into the relationship between
   q.theory & classical p.theory."  [auth@Oxf.U.]
   -- 0101012@[<A HREF="http://arxiv.org/abs/quant-ph/0101012">arXiv</A>]['13].
   (Also see [<A HREF="http://dx.doi.org/10.1038/501154a">www</A>][9/'13].)

%A A. K. Dewdney
%T The (New) Turing Omnibus: 66 Excursions in Computer Science
%I Freeman
%D 2001
%K book, text, CS, CSci, computers
%X isbn:0805071660.  About us$25.

%A C. A. Fuchs
%T Quantum foundations in the light of quantum information
%J arXiv
%M JUN
%D 2001
%K TR, c2001, c201x, c20xx, physics, quantum theory, probability, rule,
   Copenhagen interpretation, personal information, belief, zz0913
%X "... reports three almost trivial thms that nevertheless appear to have sig.
   import for quantum foundations studies. 1) A Gleason-like derivation of the
   quantum probability law, but based on the +ve operator-valued measures as the
   basic notion of measurement (see also Busch, quant-ph/9909073). Of note, this
   thm also works for 2-D vector spaces & for vector spaces over the rational
   #s, where the standard Gleason thm fails. 2) A way of rewriting the quantum
   collapse rule so that it looks almost precisely identical to Bayes rule for
   updating probabilities in classical prob.theory.  And 3) a derivation of the
   tensor-product rule for combining quantum systems (& with it the very notion
   of quantum entanglement) from Gleason-like considerations for local
   measurements on bipartite systems along with classical communication. "
   -- 0106166@[<A HREF="http://arxiv.org/abs/quant-ph/0106166">arXiv</A>]['13].
   (Also see [<A HREF="http://dx.doi.org/10.1038/501154a">www</A>][9/'13].)

%A T. N. Palmer
%T A local deterministic model of quantum spin measurement
%J Proc. Royal Soc. London
%P ?-?
%M MAR
%D 1995
%K physics, quantum, theory, c1995, c199x, c19xx, Bell's inequality, Bells,
   Kochen_specker, random, deterministic, locality, theorem, entanglement
%X "The conventional view, that Einstein was wrong to believe that quantum
   physics is local & deterministic, is challenged. A parametrised model, Q,
   for the state vector evolution of spin 1/2 particles during measurement is
   developed. ... Although the evolution of Q's state vector is uncomputable,
   the probability that the system will evolve to one of the two attractors is
   computable. ... Bell's theorem & a version of the Bell-Kochen_specker
   quantum entanglement paradox are discussed. It is shown that proving an
   inconsistency with locality demands the existence of definite truth values
   to certain counterfactual propositions. In Q these deterministic propositions
   are physically uncomputable & no non-algorithmic solution is either known or
   suspected. Adapting the mathematical formalist approach, the non-existence of
   definite truth values to such counterfactual propositions is posited. No
   inconsistency with experiment is found. Hence Q is not necessarily
   constrained by Bell's inequality."
   "accepted for Proc. of the Royal Society of London (Proc.Roy.Soc.A)"
   -- [<A HREF="http://arxiv.org/abs/quant-ph/9505025">pp@arxiv</A>][9/'04] auth @ ECMWF.int.

%A P. Davies
%T About Time: Einstein's Unfinished Revolution
%I Viking
%P 316
%D 1995 ?
%K time, physics, popular, book, text, science
%X reviewed NewScientist, p42 13 May 1995.

%A J. Gribbin
%T Schrodinger's Kittens and the Search for Reality
%I Weidenfeld & Nicolson
%P 261
%D 1995 ?
%K quantum mechanics, theory, physics, popular, book, text, science
%X reviewd New Scientist, p42 13 May 1995.

&A D. P. DiVincenzo
%T Topics in quantum computers
%D DEC
%D 1996
%K TR, c1996, c199x, c19xx, zz0323, quantum computer, computing, features,
   requirements, criteria, intro, Di Vincenzo
%X "I provide an intro. to q.computers, describing how they might be realized
   using language accessible to a solid state physicist. A listing of the
   minimal requirements for creating a q.computer is given. I also discuss
   several recent developments in the area of q.error correction, a subject of
   importance not only to q.computation, but also to some aspects of the
   foundations of q.theory."
   -- cond-mat/9612126@[<A HREF="https://arxiv.org/abs/cond-mat/9612126">arXiv</A>]['23].
   Also see QC@[<A HREF="https://en.wikipedia.org/wiki/Quantum_computing">wikip</A>]['23].

%A D. Deutsch
%T The Fabric of Reality
%I Viking
%P 390
%D 1997
%K book, text, physics, c1998, c199x, c19xx, zz0916, time, space, cosmology,
   DDeutsch
%X "Quantum physics, evolution, computation, and knowledge ... [DD] shows that
   they are so closely intertwined that we cannot properly understand any one of
   them without reference to the other three. Considered jointly, they reveal a
   unifed fabric of reality that is objective and comprehensible, and in which
   human actions and ideas play essential roles."
   1st ed 1998; us$38; uk us isbn:0713990619; uk us isbn13:978-0713990614.
   Also see DD@[<A HREF="http://www.daviddeutsch.org.uk/">www</A>]['16].
   [Also search for: time arrow].

%A E. F. Taylor
%A S. Vokos
%A J. M. O'Meara
%T Teaching Feynman's sum-over-paths quantum theory
%J Computers in Physics
%V 12
%N 2
%P 190-199
%M MAR/APR
%D 1998
%K physics, c1998, c199x, c19xx, zz0218, quantum theory, intro, introduction,
   teaching, schools
%X "We outline an intro. to q.mechanics based on the sum-over-paths method
   originated by Richard P. F.. Students use s/w with a graphics interface
   to model sums assoc. with multiple paths for photons & electrons, leading to
   the concepts of electron wavefunction, the propagator, bound states, &
   stationary states. Material in the first portion of this outline has been
   tried with an audience of high-school science teachers. These students were
   enthusiastic about the treatment, & we feel that it has promise for the
   education of physicists & other scientists, as well as for distribution to a
   wider audience."
   -- [<A HREF="https://doi.org/10.1063/1.168652">doi:10.1063/1.168652</A>]['18].

%A J. M. Maldacena
%T The large N limit of superconformal field theories and supergravity
%J arXiv
%D 1997
%O Adv. Theor. Math. Phys. 2: 231-252, 1998
%K TR, jrnl, physics, c1997, c199x, c19xx, zz0523, holographic principle,
   universe, cosmology, string theory, gravity, speculative, Mtheory
%X "We show that the large N limit of certain conformal field theories in
   various dimensions include in their Hilbert space a sector describing
   supergravity on the product of Anti-deSitter spacetimes, spheres & other
   compact manifolds. ..."
   -- [<A HREF="https://arxiv.org/abs/hep-th/9711200">arxiv:hep-th/9711200</A>]['23].
   Also see JM@[<A HREF="https://en.wikipedia.org/wiki/Juan_Maldacena">wikip</A>]['23].

%A I. I. Shapiro
%T A century of relativity
%I SpringerVerlag
%P 69-88
%D 1999
%K chapter, physics, c1999, c199x, c19xx, zz0115, gravity, space,
   relativity, quantum theory
%X "Except for quantum mechanics - a more than modest exception - relativity has
   been the most profound conceptual advance in 20th century physics. Both in
   developing special and general relativity, Albert Einstein's hallmark was to
   anchor his theory on a few simple but profound principles. The results have
   provided endless fascination and puzzlement to the general public, and have
   had an enormous impact on our conceptual framework for understanding nature."
   -- [<A HREF="http://dx.doi.org/10.1007/978-1-4612-1512-7_6">doi:10.1007/978-1-4612-1512-7_6</A>]['15], in
   1st ed 1999, hb us$57; uk us isbn:0387986626; uk us isbn13:978-0387986623.
   ($And [<A HREF="http://journals.aps.org/rmp/abstract/10.1103/RevModPhys.71.S41">Rev.Mod.Phys</A>]['14].$)

%A J. Barbour
%T The End of Time: The Next Revolution in Physics
%I OUP
%P 384
%D 1999
%K book, text, c1999, c199x, c19xx, arrow, time, cosmology, universe, illusion,
   unreality, eternalism, block
%X "... if nothing happened, if nothing changed, then time would stop. For time
   is nothing but change. It is change that we perceive occurring all around us,
   not time. Put simply, time does not exist. ..."
   hb, uk us isbn:0297819852;
   pb, us $9, uk us isbn:0195145925; uk us isbn13:978-0195145922.
   Also see JB@[<A HREF="https://en.wikipedia.org/wiki/Julian_Barbour">wikip</A>]['21].
   [Also search for: time arrow].

%A H. Ollivier
%A W. H. Zurek
%T Quantum discord: A measure of the quantumness of correlations
%J Phys. Rev. Lett.
%V 88
%N 1
%P 017901 (4p)
%D 2001
%K jrnl, eJrnl, c2001, c200x, c20xx, zz1113, physics, quantum theory, discord,
   nonclassical, correlation, states, entanglement, mutual information
%X "Two classically identical expressions for the mutual info. generally differ
   when the systems involved are quantum. This diff. defines the q.discord. It
   can be used as a measure of the quantumness of correlations. Separability of
   the density matrix describing a pair of systems does not guarantee vanishing
   of the discord, thus showing that absence of entanglement does not imply
   classicality. We relate this to the quantum superposition principle, &
   consider the vanishing of discord as a criterion for the preferred
   effectively classical states of a system, i.e., the pointer states."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.88.017901">doi:10.1103/PhysRevLett.88.017901</A>]['13];
   also see d@[<A HREF="http://en.wikipedia.org/wiki/Quantum_discord">wikip</A>]['13].

%A J. P. Christiansen
%T Transport from non-classical orbits
%I EURATOM/UKAEA, Culham Science Centre
%R UKAEA FUS 466
%P 24
%M OCT
%D 2001
%K TR 466, TR466, plasma, nuclear, fusion, power, tokamak, tokomak,
   c2001, c200x, c20xx, orbit, JET, MAST, UKAEA, Culham, UK,
   jes, jess, JPChristiansen
%X [<A HREF="http://www.fusion.org.uk/techdocs/ukaea-fus-466.pdf">pdf@fusion.org.uk</A>]['04].

%A L. M. K. Vandersypen
%A et al
%T Experimental realization of Shor's quantum factoring algorithm using
   nuclear magnetic resonance
%J arXiv
%M DEC
%D 2001
%K TR, c2001, c200x, c20xx, zz0324, quantum computing, qubit, qubits, NMR, spin
%X "... Here we report an impl'n of the simplest instance of Shor's alg.:
   factorization of N=15 (whose prime factors are 3 & 5). We use seven spin-1/2
   nuclei in a molecule as q.bits, which can be manipulated with room temp.
   liquid state nuclear magnetic resonance techniques. ..."
   -- [<A HREF="https://arxiv.org/abs/quant-ph/0112176">arxiv:quant-ph/0112176</A>]['24].

%A R. Schutzhold
%T Pattern recognition on a quantum computer
%I Dept. Physics and Astronomy, U. British Columbia
%M AUG
%D 2002
%K UBC, quantum computing, computer, patterns, FFT, Fourier transform, zz0902,
   c2002, c200x, c20xx, quomplexity, qomplexity
%X By means of a simple example it is demonstrated that the task of finding
   certain patterns in an otherwise (macroscopically) unstructured data set
   can be accomplished efficiently by a quantum computer.  Employing the
   powerful tool of the quantum Fourier transform the quantum algorithm
   exhibits an exponential speed-up [v.] its classical counterpart.
   -- [<A HREF="http://arXiv.org/abs/quant-ph/0208063">arXiv</A>][9/'02],
   schuetz@physics.ubc.ca  27/8/'02.

%A L. Grover
%A T. Rudolph
%T Creating superpositions that correspond to efficiently integrable
   probability distributions
%M AUG
%D 2002
%K TR, c2002, c200x, c20xx, zz0224, quantum computing, probability distribution,
   integration, quantum, superposition, computing
%X "We give a simple & efficient process for generating a q.superposition of
   states which form a discrete approx. of any efficiently integrable (such as
   log concave) probability density fns."
   -- [<A HREF="https://arxiv.org/abs/quant-ph/0208112">doi:quant-ph/0208112</A>]['24].
   [Also search for: quantum computing]  and  [also search for: Grover quantum].

%A U. H Danielsson
%T Holography, inflation and quantum fluctuations in the early Universe
%J J. Cosmology and Astroparticle Physics
%V ?
%D 2003
%K jrnl, c2003, c200x, c20xx, cosmology, physics, black hole, holes, entropy,
   universe, zz0703
%X ...the relevance of holographic entropy bounds in the context of inflation
   is investigated. We distinguish between entropy on large and small scales
   and confront the entropy of quantum fluctuations in an inflating cosmology
   with the appropriate entropy bounds. In conclusion we do not find any
   constraints on inflation from holography, but some suggestions for future
   studies are given.   [elec jrnl]
   -- [<A HREF="http://dx.doi.org/10.1088/1475-7516/2003/03/002">DOI:10.1088/1475-7516/2003/03/002</A>][7/'03].

%A J. Harvey
%A et al
%T An analysis of the forces required to drag sheep over various surfaces
%J Applied Ergonomics
%V 33
%N 6
%P 523-531
%M NOV
%D 2002
%K jrnl, igNobel prize, 2003, physics, prizes, zz1003, c2002, c200x, c20xx,
   http, www, HREF, ignoble
%X The 2003 Ig Nobel Prize Winners for Physics
   [<A HREF="http://www.culvenor.com/">culvenor.com</A>][10/'03]
   [<A HREF="http://www.improbable.com/ig/ig-pastwinners.html#ig2003">ig</A>][10/'03].

%A D. N. Spergel
%A L. Verde
%A H. V. Peiris
%A et al
%T First year Wilkinson microwave anisotropy probe (WMAP) observations:
   Determination of cosmological parameters
%J arxiv.org
%M JUN
%D 2003
%K online, astrophysics, astro-physics, cosmology, parameter, WMAP, data,
   micro-wave, universe, geometry, c2003, c200x, c20xx, model, stats, statistics
%X "WMAP precision data enables accurate testing of cosmological models. We
   find that the emerging standard model of cosmology, a flat Lambda-dominated
   universe seeded by nearly scale-invariant adiabatic Gaussian fluctuations,
   fits the WMAP data. ..."
   -- [<A HREF="http://arxiv.org/abs/astro-ph/0302209">arxiv.org</A>][7/'04],
      [<A HREF="http://lambda.gsfc.nasa.gov/product/map/">wmap</A>][7/'04].

%A S. Ghosh
%A T. F. Rosenbaum
%A G. Aeppli
%A S. N. Coppersmith
%T Entangled quantum state of magnetic dipoles
%J Nature
%V 425
%P 48-51
%M SEP
%D 2003
%K jrnl, quantum theory, physics, entagled, particles, atoms, magnetic salt,
   magnetic, field, effects, quantum entanglement, macroscopic, c2003, c200x,
   c20xx, dipole, magnets, moments, susceptibility, zz0404
%X "... show that a much simpler material system -- namely, the insulating
   magnetic salt LiHoxY1-xF4 -- can also display such a power law. Moreover, by
   comparing the results of numerical simulations of this system with
   susceptibility and specific-heat data, we show that both energy level
   splitting and quantum entanglement are crucial to describing its behaviour.
   ..." [<A HREF="http://dx.doi.org/10.1038/nature01888">doi:10.1038/nature01888</A>][4/'04].

%A G. T. Hoang
%A J. Jacquinot
%T Controlled fusion: The next step
%J Physicsweb
%M JAN
%D 2004
%K physics web, news, nuclear fusion, power, energy, tokamak, tokomak,
   International Thermonuclear Experimental Reactor, ITER, deuterium, TFTR,
   Joint European Torus, JET, magnetic confinement, deuterium, tritium, plasma,
   Tore Supra, survey, intro, introduction, EFDA, Culham,
%X "... A fusion reactor burning just 1 kg of fuel per day could produce a
   sustained power output of 1 GW. ... plasma temperature, T, must be extremely
   high - typically about 10 keV, which corresponds to almost 108K. However,
   the density of the plasma, n, can be relatively low at about 10**20/m3. The
   resulting pressure in the plasma is therefore only about one atmosphere. ...
   The next big step in fusion research will be the International Thermonuclear
   Experimental Reactor (ITER), which is designed to produce up to 500 MW of
   fusion power. [10x more out than in.] ... A commercial fusion reactor would
   be only slightly larger than ITER & would produce ... about 4 GW. ..."
   -- [<A HREF="https://physicsworld.com/a/controlled-fusion-the-next-step/">www</A>]['22].
   Also see JET@[<A HREF="https://ccfe.ukaea.uk/research/joint-european-torus/">ukaea</A>]['22] at [<A HREF="https://ccfe.ukaea.uk/">ccfe</A>]['22],
   [<A HREF="http://www.jet.efda.org/">jet.efda.org</A>]['04],
   [<A HREF="http://www.ukaea.org.uk/fusion/">ukaea.org.uk/fusion/</A>]['04],
   JET@[<A HREF="https://en.wikipedia.org/wiki/Joint_European_Torus">wikip</A>]['24].
   [Also search for: nuclear fusion power].

%A C. Brukner
%A S. Taylor
%A S. Cheung
%A V. Vedral
%T Quantum entanglement in time
%J arxiv.org
%M FEB
%D 2004
%K online, quantum theory, physics, theoretical, Bell inequality, locality,
   realism, causality, past, present, future, zz0504, c2004, c200x, c20xx,
   cause, effect, time
%X "The temporal Bell inequalities are derived from the assumptions of realism
   and locality in time. It is shown that quantum mechanics violates these
   inequalities and thus is in conflict with the two assumptions. This can be
   used for performing certain tasks that are not possible classically. Our
   results open up a possibility for introducing the notion of entanglement in
   time in quantum physics."
   -- [<A HREF="http://www.arxiv.org/abs/quant-ph/0402127">arxiv.org</A>][4/'04].
   Also VV@[<A HREF="https://www.vlatkovedral.com/">www</A>]['22]
     or [<A HREF="https://scholar.google.com/citations?user=d0ruO6gAAAAJ">sc'lar</A>]['22].

%A J. B. Hartle
%T General relativity and quantum cosmology
%J arXiv.org
%M FEB
%D 2004
%K online, physics, laws, time, cause and effect, now, present, past, future,
   the, remember, arrow, information gathering and utilizing systems, IGUSes,
   space time, spacetime, 4D, relativity, c2004, c200x, c20xx
%X "The world is four-dimensional ... spacetime that has no unique division
   into space and time. Yet our subjective experience is divided into present,
   past, and future. This paper discusses the origin of this division in terms
   of simple models of information gathering and utilizing systems (IGUSes).
   Past, present, and future are not properties of four-dimensional spacetime
   but notions describing how individual IGUSes process information. Their
   origin is to be found in how these IGUSes evolved or were constructed. The
   past, present, and future of an IGUS is consistent with the four-dimensional
   laws of physics and can be described in four-dimensional terms. ...
   speculate why the present, past, and future organization might be favored
   by evolution and therefore a cognitive universal."
   -- [<A HREF="http://www.arxiv.org/abs/gr-qc/0403001">arxiv.org</A>][4/'04].
   [Also search for: arrow time].

%A A. R. Liddle
%T How many cosmological parameters?
%J arXiv
%M MAY
%D 2004
%K online, astro-physics, astrophysics, WMAP data, concordance model, AIC, BIC,
   parameter, cosmology, stats, statistics, models, zz0704, c2004, c200x, c20xx,
   Wilkinson Microwave Anisotropy Probe
%X "Constraints on cosmological parameters depend on the set of parameters
   chosen to define the model which is compared with observational data. I use
   the Akaike & Bayesian information criteria to carry out cosmological model
   selection, in order to determine the parameter set providing the preferred
   fit to the data. Applying the information criteria to the current
   cosmological data sets indicates, for example, that spatially-flat models
   are statistically preferred to closed models, & that possible running of the
   spectral index has lower significance than inferred from its confidence
   limits. I also discuss some problems of statistical assessment arising from
   there being a large number of `candidate' cosmological parameters that can
   be investigated for possible cosmological implications, & argue that 95%
   confidence is too low a threshold to robustly identify the need for new
   parameters in model fitting. The best present description of cosmological
   data uses a scale-invariant (n=1) spectrum of Gaussian adiabatic
   perturbations in a spatially-flat Universe, with the cosmological model
   requiring only five fundamental parameters to fully specify it."
   -- [<A HREF="http://www.arxiv.org/abs/astro-ph/0401198">pdf, ps@arxiv.org</A>][7/'04],
      [<A HREF="http://lambda.gsfc.nasa.gov/product/map/">wmap</A>][7/'04].

%A D. M. D. Smith
%A N. F. Johnson
%T Evolution management in a complex adaptive system: Engineering the future
%J arxiv
%D 2004
%K economics, market, markets, prediction, control, c2004, c200x, c20xx,
   financial, OCCF, uniOxford
%X "examine the feasibility of predicting & subsequently managing the future
   evolution of a Complex Adaptive System. Our archetypal system mimics a
   competitive pop'n of mechanical, biological, informational or human objects.
   ... short-term prediction yields corridors along which the system will, with
   very high probability, evolve. We then show how small amounts of 'population
   engineering' can be undertaken in order to steer the system away from any
   undesired regimes which have been predicted. Despite the sys's many degrees
   of freedom & inherent stochasticity, this dynamical 'soft' control over
   future risk requires only minimal knowledge about the pop's composition."
   -- [<A HREF="http://arxiv.org/abs/cond-mat/0409036">arxiv.org/abs/cond-mat/0409036</A>][9/'04],
   auths@Ox.U. [<A HREF="http://www.maths.ox.ac.uk/~smithdm/">S</A>]['04] [<A HREF="http://www.lincoln.ox.ac.uk/fellows/johnson/">J</A>]['04],
   [<A HREF="http://www.occf.ox.ac.uk/">occf.ox</A>]['04].

%A T. N. Palmer
%T A granular permutation-based representation of complex numbers and
   quaternions: Elements of a possible realistic quantum theory
%J Proc.: Mathematical, Physical and Engineering Sciences
%I Royal Soc.
%P 1039-1055
%V 460
%N 2044
%M APR
%D 2004
%K jrnl, physics, quantum, theory, c2004, c200x, c20xx, Bell inequality,
   number, quaternion, non, determinism, deterministic, locality, random,
   measurement, entanglement, probability
%X "It is suggested that the long-standing conceptual difficulties of quantum
   theory (the measurement problem and associated concept of probability on the
   one hand and the notions of entanglement and non-locality on the other)
   arise fundamentally from the role played by the continuum field C of complex
   numbers in the axioms of standard quantum theory. An alternative
   representation  [...]  Based on this formalism, finite samples of values of
   r on the rational meridians are used to define a frequentist-based
   probability measure consistent with quantum-theoretic probability and
   correlation. The granularity of r is crucial in accounting for the theory's
   evasion of the Bell inequalities. Standard quantum phenomena are discussed
   from the perspective of the proposed theory. Some emphasis is given to the
   issues of contextuality and non-locality in the proposed theory."
   -- [<A HREF="http://dx.doi.org/10.1098/rspa.2003.1189">doi:10.1098/rspa.2003.1189</A>][9/'04]; issn:13645021, paper.

%A S. M. Carroll
%A J. Chen
%T Spontaneous inflation and the origin of the arrow of time
%J arXiv
%M OCT
%D 2004
%K TR, c2004, c200x, c20xx, zz1022, time, arrow, physics, cosmology, universe,
   big bang, de Sitter, deSitter, thermodynamics
%X "We suggest that spontaneous eternal inflation can provide a natural
   expl'n for the thermodynamic arrow of time ... In the absence of inflation,
   we argue that systems coupled to gravity usually evolve asymptotically to the
   vacuum, which is the only natural state in a thermodynamic sense. In the
   presence of a small +ve vacuum energy & an appropriate inflaton field, the
   de Sitter vacuum is unstable to the spontaneous onset of inflation at a
   higher energy scale. Starting from de Sitter, inflation can increase the
   total entropy of the universe without bound, creating universes similar to
   ours in the process. An important consequence of this picture is that
   inflation occurs asymptotically both fwds & backwards in time, implying a
   universe that is (statistically) time-symmetric on ultra-large scales."
   -- hep-th/0410270@[<A HREF="https://arxiv.org/abs/hep-th/0410270">arXiv</A>]['22].
   [Also search for: time arrow].

%A H. Ollivier
%A D. Poulin
%A W. H. Zurek
%T Objective properties from subjective quantum states: Environment as
   a witness
%J Physical Rev. Lett.
%V 93
%M NOV
%D 2004
%O 220401
%K quantum mechanics, theory, decoherence, coherence, observer, state,
   einselection, classical, physics
%X "We study the emergence of objective properties in open quantum systems.
   ... the environment is promoted from a passive role of a reservoir
   selectively destroying quantum coherence to an active role of amplifier
   selectively proliferating information about the system. We show that only
   preferred pointer states of the system can leave a redundant and therefore
   easily detectable imprint on the environment. Observers who - as is almost
   always the case - discover the state of the system indirectly (by probing a
   fraction of its environment) will find out only about the corresponding
   pointer observable. Many observers can act in this fashion independently and
   without perturbing the system. They will agree about its state. In this
   operational sense, preferred pointer states exist objectively."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.93.220401">doi:10.1103/PhysRevLett.93.220401</A>]['04].
  Also see [<A HREF="http://www.arxiv.org/abs/quant-ph/0105127">zurek</A>]['04].

%A A. Valentini
%A H. Westerman
%T Dynamical origin of quantum probabilities
%J Proc. Royal Soc., A (Math., Physical and Eng. Sci.)
%V 461
%N 2053
%P 253-272
%M JAN
%D 2005
%K jrnl, physics, c2005, c200x, c20xx, zz0414, quantum theory, mechanics,
   hidden variables, dynamic, wave function, causal, non local, nonlocal,
   light speed, de Broglie, deBroglie, Bohm, controversial
%X "We study the origin of the Born prob. rule rho=|psi|^2 in the de Broglie-
   -Bohm pilot-wave formulation of q.theory. It is argued that quantum prob.
   arise dynamically, & have a status similar to thermal probs. in ordinary
   statistical mechanics. ... illustrated by numerical sim'n for a 2D system. We
   show that a simple initial ensemble, with a non-std distribution
   rho != |psi|^2 of particle posns, evolves towards the quantum distribution to
   high accuracy. The relaxation process who -> |psi|^2 is quantified in terms
   of a coarse-grained H-function (equal to minus the relative entropy of rho
   wrt |psi|^2), which is found to decrease approx. exponentially over time,
   with a time constant that accords with a simple theoretical estimate."
   -- [<A HREF="http://dx.doi.org/10.1098/rspa.2004.1394">doi:10.1098/rspa.2004.1394</A>]['14],
      [<A HREF="http://rspa.royalsocietypublishing.org/content/461/2053/253">rspa</A>]['14].
   Also see AV@[<A HREF="http://en.wikipedia.org/wiki/Antony_Valentini">wikip</A>]['14].

%A G. Brumfiel
%T Fusion energy: Just around the corner
%J Nature
%V 436
%P 318-320
%M JUL
%D 2005
%K nuclear fusion, reactor, Tokamak, hydrogen, deuterium, tritium, power, ITER,
   c2005, c200x, c20xx, torus, plasma, magnetic confinment, Cadarache
%X "... Cadarache, southern France ... construction to begin in 2006,
   and operation in 2016 ... costs of US$5.5 billion ... outer radius
   of 6.2 metres and a plasma volume of 840 m^3 ..."
   -- [<A HREF="http://dx.doi.org/10.1038/436318a">doi:10.1038/436318a</A>]['05],
      [<A HREF="http://www.iter.org/">iter.org</A>]['05],
      [<A HREF="http://fusion.org.uk/">fusion.org.uk</A>]['05].
   [Also search for: nuclear fusion power].

%A S. W. Hawking
%T Information loss in black holes
%J arXiv
%M JUL
%D 2005
%K TR, physics, c2005, c200x, c20xx, zz1021, black hole, paradox, information,
   loss, unitary, unitarity, cosmology
%T "The question of whether information is lost in black holes is investigated
   using Euclidean path integrals. The formation & evaporation of black holes is
   regarded as a scattering problem with all measurements being made at
   infinity. This seems to be well formulated only in asymptotically AdS
   spacetimes. The path integral over metrics with trivial topology is unitary &
   information preserving. On the other hand, the path integral over metrics
   with non-trivial topologies leads to correlation functions that decay to
   zero. Thus at late times only the unitary information preserving path
   integrals over trivial topologies will contribute. Elementary quantum gravity
   interactions do not lose information or quantum coherence.
   -- hep-th/0507171@[<A HREF="https://arxiv.org/abs/hep-th/0507171">arXiv</A>]['21].
   [Also search for: black hole paradox].
   (Also see BHoleP@[<A HREF="https://en.wikipedia.org/wiki/Black_hole_information_paradox">wikip</A>]['21].)

%A M. Horodecki
%A J. Oppenheim
%A A. Winter
%T Partial quantum information
%J Nature
%V 436
%P 673-678
%M AUG
%D 2005
%K letter, information, quantum computing, c2005, c200x, c20xx, zz0805,
   conditional entropy, positive, negative, physics, entanglement
%X "Information - be it classical or quantum - is measured by the amount of
   communication needed to convey it. In the classical case, if the receiver
   has some prior information about the messages being conveyed, less
   communication is needed.  ...  In the classical case, partial information
   must always be +ve, but we find that in the quantum world this physical
   quantity can be negative. If the partial information is +ve, its sender
   needs to communicate this number of quantum bits to the receiver; if it is
   -ve, then sender & receiver instead gain the corresponding potential
   for future quantum communication. We introduce a protocol that we term
   'quantum state merging' which optimally transfers partial information. We
   show how it enables a systematic understanding of quantum network theory,
   & discuss several important applications including distributed compression,
   noiseless coding with side information, multiple access channels &
   assisted entanglement distillation."
   -- [<A HREF="http://dx.doi.org/10.1038/nature03909">doi:10.1038/nature03909</A>]['05],
   quant-ph/0505062@[<A HREF="https://doi.org/10.48550/arXiv.quant-ph/0505062">arXiv</A>]['23].
   Also see [<A HREF="https://www.ucl.ac.uk/oppenheim/negative-information.shtml ">ucl.ac.uk</A>]['23].

%A K. G. Libbrech
%T The physics of snow crystals
%J Rep. Prog. Phys.
%V 68
%N 4
%P 855-895
%M MAR
%D 2005
%K jrnl, physics, c2005, c2200x, c20xx, zz1223, snowflake, snow flake, flakes
%X "... ï¬rst part of this review focuses on understanding the dramatic
   variations seen in snow crystal morphology as a fn of temp., a mystery that
   has remained largely unsolved since its discovery 75 years ago ... The second
   part of this review examines pattern formation in snow crystals, with
   special emphasis on the growth of snow crystal dendrites. ..."
   -- [<A HREF="http://dx.doi.org/10.1088/0034-4885/68/4/R03">doi:10.1088/0034-4885/68/4/R03</A>]['23].
   * Also see KL@[<A HREF="https://scholar.google.com/citations?user=ElYGFcQAAAAJ">sch'lar</A>]['23].

%A J. Conway
%A S. Kochen
%T The free will theorem
%J Foundations of Physics
%V 36
%P 1441-1473
%D 2006
%K jrnl, Physics, maths, c2006, c200x, c20xx, zz0420, free will theorem, FWT,
   spin, fin, experiment, measurement, quantum mechanics, entanglement,
   determinism, information, past, cause, causal, causality,
   elementary particles
%X "On the basis of three physical axioms, we prove that if the choice of a
   particular type of spin 1 experiment is not a fn of the information
   accessible to the experimenters, then its outcome is equally not a fn of the
   info. accessible to the particles. We show that this result is robust, &
   deduce that neither hidden variable theories nor mechanisms of the GRW type
   for wave fn collapse can be made relativistic & causal. We also establish the
   consistency of our axioms & discuss the philosophical implications."
   -- [<A HREF="https://doi.org/10.1007/s10701-006-9068-6">doi:10.1007/s10701-006-9068-6</A>]['20].
   "... states that if we have a free will in the sense that our choices are
   not a function of the past, then, subject to certain assumptions, so must
   some elementary particles. ..."
   -- FWT@[<A HREF="https://en.wikipedia.org/wiki/Free_will_theorem">wikip</A>]['20].
   [Also search for: Conway Kochen free will] & [also search for: maths Conway].

%A S. S. Afshar
%A E. Flores
%A K. F. McDonald
%A E. Knoesel
%T Paradox in Wave-Particle Duality
%J Foundations of Physics
%V 37
%P 295-305
%M JAN
%D 2007
%K jrnl, physics, c2007, c200x, c20xx, zz0722, quantum theory, wave, particle,
   double slit experiment, pin holes, Bohr's Principle of Complementarity,
   controversial
%X "We report on the simultaneous determination of complementary wave & particle
   aspects of light in a double-slit type 'welcher-weg' experiment beyond the
   limitations set by Bohr's Principle of Complementarity. Applying classical
   logic, we verify the presence of sharp interference in the single photon
   regime, while reliably maintaining the info. about the particular pinhole
   through which each individual photon had passed. ... poses interesting
   questions on the validity of Complementarity in cases where measurements
   techniques that avoid Heisenberg's uncertainty principle & q.entanglement are
   employed. We further argue that the application of classical concepts of
   waves & particles as embodied in Complementarity leads to a logical
   inconsistency in the interpretation of this experiment."
   -- [<A HREF="https://doi.org/10.1007/s10701-006-9102-8">doi:10.1007/s10701-006-9102-8</A>]['22],
      quant-ph/0702188@[<A HREF="https://doi.org/10.48550/arXiv.quant-ph/0702188">arXiv</A>]['22].
   Also see A_Experiment@[<A HREF="https://en.wikipedia.org/wiki/Afshar_experiment">wikip</A>]['22].

%A N. S. Yanofsky
%A M. A. Mannucci
%T Quantum Computing for Computer Scientists
%I CUP
%D 2007
%K book, text, CUP, c2007, c200x, c20xx, zz1008, computer science,
   CSci, L4Ref, L5Ref, computer, computation
%X "In the 1990s it was realized that quantum physics has some spectacular
   applications in computer science. This book is a concise introduction
   to quantum computation, developing the basic elements of this new branch
   of computational theory without assuming any background in physics. ..."
   1st ed 2008, hb us$36; uk us isbn:0521876583; uk us isbn13:978-0521876582.

%A V. Jacques
%A E. Wu
%A F. Grosshans
%A F. Treussart
%A P. Grangier
%A A. Aspect
%A J.-F. Roch
%T Experimental realization of Wheeler's delayed-choice gedanken experiment
%J Science
%V 315
%N 5814
%P 966-968
%M FEB
%D 2007
%K jrnl, Physics, c2007, c200x, c20xx, quantum, theory, mechanics, wave,
   particle, duality, Wheeler, beam splitter, light, interference,
   single photon, double slit, delayed choice, interferometer
%X "... the config. of a two-path interferometer is chosen after a single-photon
   pulse has entered it: Either the interferometer is closed (that is, the two
   paths are recombined) & the interference is observed, or the [it] remains
   open & the path followed by the photon is measured.  We report an almost
   ideal realization of that gedanken experiment with single photons allowing
   unambiguous which-way measurements. The choice between open & closed configs.
   made by a q.random number generator, is relativistically separated from the
   entry of the photon into the i.. "
   -- [<A HREF="http://dx.doi.org/10.1126/science.1136303">doi:10.1126/science.1136303</A>]['13],
      0610241@[<A HREF="http://arxiv.org/abs/quant-ph/0610241">arXiv</A>]['13].
   [Also search for: physics quantum delayed choice].

%A S. Gerlich
%A et al
%T A Kapitza-Dirac-Talbot-Lau interferometer for highly polarizable molecules
%J NaturePhysics
%V 3
%P 711-715
%D 2007
%K eJrnl, physics, c2007, c200x, c20xx, zz0821, particle, molecule, wave,
   matter, quantum mechanics, interference
%X "... Here, we describe the first experimental realization of a new set-up
   that solves this problem [the strongly dispersive effect of the interaction
   between the diffracted molecule & the grating wall] by combining the
   advantages of a so-called Talbot-Lau interferometer with the benefits of an
   optical phase grating."
   -- [<A HREF="https://doi.org/10.1038/nphys701">doi:10.1038/nphys701</A>]['21].
   [Also search for: quantum molecule wave].

%A A. G. Lisi
%T An exceptionally simple theory of everything
%J arXiv
%M NOV
%D 2007
%K arXiv, c2007, c200x, c20xx, zz0412, physics, theory, E8, particles, forces,
   G2, F4, strong, electroweak, gravity, boson, fermion, boson,
   Higgs, particle, force
%X "All fields of the std model & gravity are unified as an E8 principal bundle
   connection. A non-compact real form of the E8 Lie algebra has G2 & F4
   subalgebras which break down to strong su(3), electroweak su(2) x u(1),
   gravitational so(3,1), the frame-Higgs, & 3 generations of fermions related
   by triality. The interactions & dynamics of these 1-form & Grassmann valued
   parts of an E8 superconnection are described by the curvature & action over
   a 4D base manifold. "
   -- 0711.0770@[<A HREF="http://arxiv.org/abs/0711.0770">arXiv</A>].
   (Also see auth@[<A HREF="http://deferentialgeometry.org/epe/">www</A>].)
   [Also search for: Higgs boson physics].

%A N. Perra
%A V. Zlatic
%A A. Chessa
%A C. Conti
%A D. Donato
%A G. Caldarelli
%T Schroedinger-like PageRank equation and localization in the www
%J arXiv Physics
%M JUL
%D 2008
%K TR, c2008, c200x, c20xx, zz0808, search engine, page rank, google, ranking,
   graph, graphs, diffusion, schrodinger, equation, world wide web, pages
%X "... show that the PageRank can be expressed in terms of a wave fn obeying a
   Schroedinger-like equn. ... the topological disorder given by the unbalance
   of outgoing & ingoing links between pages, induces wave fn & potential
   structuring. This allows to directly localize the pages with the largest
   score. ...[so] can now compute the PageRank without iterative techniques.
   For most of the cases of interest our method is faster ..."  [5pp, 17 refs].
   -- [<A HREF="http://arxiv.org/abs/0807.4325v1">@arxiv</A>]['08].

%A A. Ashtekar
%A V. Taveras
%A M. Varadarajan
%T Information is not lost in the evaporation of 2-dimensional black holes
%J arXiv
%D 2008
%K TR, c2008, c200x, c20xx, 2D, black hole, evaporate, Hawking evaporation
%X "We analyze Hawking evaporation of the Callen-Giddings-Harvey-Strominger
   (CGHS) black holes from a quantum geometry perspective & show that info. is
   not lost, primarily because the quantum space-time is sufficiently larger
   than the classical.  Using suitable approximations to extract physics from
   quantum space-times we establish that: i)future null infinity of the quantum
   space-time is sufficiently long for the the past vacuum to evolve to a pure
   state in the future; ii) this state has a finite norm in the future Fock
   space; & iii) all the information comes out at future infinity; there are
   no remnants."
   -- [<A HREF="http://arxiv.org/abs/0801.1811">arxiv.org/abs/0801.1811</A>]['08],
      [<A HREF="http://cgpg.gravity.psu.edu/people/Ashtekar/">auth1</A>]['08].

%A D. Salart
%A A. Baas
%A C. Branciard
%A N. Gisin
%A H. Zbinden
%T Testing the speed of 'spooky action at a distance'
%J Nature
%V 454
%P 861-864
%M AUG
%D 2008
%K jrnl, c2008, c200x, c20xx, quantum mechanics, theory, state, entanglement,
   Bell, inequalities, inequality, test
%X "... Quantum physics predicts an entirely different kind of cause for some
   correlations, named entanglement. This reveals itself in correlations that
   violate Bell inequalities (implying that they cannot be described by common
   causes) between space-like separated events (implying that they cannot be
   described by classical communication). ... We performed a Bell test over
   more than 24 hours between two villages separated by 18km & approx. east-west
   oriented, with the source located precisely in the middle. We continuously
   observed two-photon interferences well above the Bell inequality threshold.
   Taking advantage of the Earth's rotation, the configuration of our experiment
   allowed us to determine, for any hypothetically privileged frame, a lower
   bound for the speed of the influence. For example, if such a privileged
   reference frame exists & is such that the Earth's speed in this frame is
   less than 10**(-3) times that of the speed of light, then the speed of the
   influence would have to exceed that of light by at least four orders of
   magnitude."
   -- [<A HREF="http://dx.doi.org/10.1038/nature07121">doi:10.1038/nature07121</A>]['10].

%A M. H. Brennan
%T Data processing in the early cosmic ray experiments in Sydney
%J COMPJ
%V 51
%N 5
%P 561-565
%M SEP
%D 2008
%K jrnl, COMPJ, c2008, c200x, c20xx, CSWallace, SILLIAC, physics
%X "The cosmic ray air shower experiment set up at the University of Sydney in
   the late 1950s was one of the first complex experiments in Australia to
   utilize the power of an electronic computer to process & analyse the
   experimental data. The paper provides a brief overview of the design &
   construction of the equipment for the experiment & the use of the computer
   SILLIAC in the processing & analysis of the data. The central role of
   Chris Wallace in this latter aspect is given special attention."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm119">doi:10.1093/comjnl/bxm119</A>][08].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">C.S.Wallace's publications</A>].)

%A C. Castelnovo
%A R. Moessner
%A L. Sondhi
%T Magnetic monopoles in spin ice
%J Nature
%V 451
%N 7174
%M JAN
%D 2008
%K jrnl, physics, c2008, c200x, c20xx, zz0814, magnetic monopole, spin ice
%X "... no elem.particles with a net mag.charge have ever been obs., despite
   intensive & prolonged searches ... pursue an alt. strategy, namely that of
   realizing them not as elementary but rather as emergent particles - that is,
   as manifestations of the correlns present in a strongly interacting many-body
   sys.. The most prominent eg of emergent quasiparticles are the ones with
   fractional electric charge e/3 in quantum Hall phys.. ... propose that mag.
   monopoles emerge in a class of exotic magnets known collectively as spin ice:
   the dipole moment of the underlying electronic degrees of freedom
   fractionalises into monopoles. ... account for a mysterious phase transn
   obs. experimentally in spin ice in a mag.field which is a liquid-gas
   transn of the mag.monopoles. These m. can also be detected by other means,
   eg, in an experiment modelled after the Stanford mag.monopole search."
   -- [<A HREF="http://dx.doi.org/10.1038/nature06433">doi:10.1038/nature06433</A>]['14].
   [Also search for: magnetic monopole].

%A S. M. Carroll
%T What if time really exists
%I arXiv
%M NOV
%D 2008
%K TR, c2008, c200x, c20xx, zz1121, quatum physics, cosmology, time, times,
   exist, exists, arrow, universe, reality
%X "Despite the obvious utility of the concept, it has often been argued that
   time does not exist. I take the opposite perspective: let's imagine that time
   does exist, & the universe is described by a quantum state obeying ordinary
   time-dep. q.mechanics. Reconciling this simple picture with the known facts
   about our universe turns out to be a non-trivial task, but by taking it
   seriously we can infer deep facts about the fundamental nature of reality.
   The arrow of time finds a plausible explanation in a 'Heraclitean universe,'
   described by a q.state eternally evolving in an infinite-dimensional Hilbert
   space."
   -- 0811.3772@[<A HREF="https://arxiv.org/abs/0811.3772">arXiv</A>]['21].
   [Also search for: time arrow].

%A J. H. Conway
%A S. Kochen
%T The strong free will theorem
%J Notices of the AMS
%V 56
%N 2
%P 226-232
%M FEB
%D 2009
%K jrnl, maths, physics, c2009, c200x, c20xx, zz0420, strong free will theorem,
   SWFT, FWT, quantum, information, cause, causality, past, determinism, spin,
   fin, min, experiment, measurement, rGRWf
%X "... [the FWT] asserts, roughly, that if indeed we humans have free will,
   then elementary particles already have their own small share of this valuable
   commodity. ...
   -- [<A HREF="http://www.ams.org/notices/200902/rtx090200226p.pdf">www</A>]['20].
   Also see,
   "... In their later 2009 paper, "The Strong Free Will Theorem", C. & K.
   replace the Fin axiom by a weaker one called Min, thereby strengthening the
   theorem. Min asserts only that two experimenters separated in a space-like
   way can make choices of measurements indep. of each other. In particular it
   is not postulated that the speed of transfer of all info. is subject to a
   maximum limit, but only of the particular info. about choices of
   measurements. In 2017, K. argued that Min could be replaced by Lin -
   experimentally testable Lorentz covariance. ..."
   -- FWT@[<A HREF="https://en.wikipedia.org/wiki/Free_will_theorem">wikip</A>]['20].
   [Also search for: Conway Kochen free will].

%A D. Clery
%T Fusion's great bright hope
%J Science
%V 324
%N 5925
%P 326-330
%M APR
%D 2009
%K news, c2009, c200x, c20xx, physics, nuclear, fusion, inertial confinement,
   laser, power, inertial, LLNL, NIF
%X "... LLNL's National Ignition Facility (NIF) ... in '10 the power of those
   [laser] beams will be directed at a small beryllium sphere filled with
   hydrogen isotopes. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.324.5925.326">doi:10.1126/science.324.5925.326</A>]['09].
   [Also search for: nuclear fusion power].

%A L. Maccone
%T Quantum solution to the arrow-of-time dilemma
%J Phys. Rev. Lett.
%V 103
%N 080401
%D 2009
%K c2009, c200x, c20xx, zz0909, laws of physics, reversibility, symmetry,
   quantum theory, arrow of time, entropy, second law, thermodynamics, energy,
   information, direction
%X "The arrow-of-time dilemma states that the laws of physics are invariant for
   time inversion, [but] phenomena we see everyday are not (i.e., entropy
   increases). I show that, within a quantum mechanical framework, all phenomena
   which leave a trail of info. behind (& hence can be studied by physics) are
   those where entropy necessarily increases or remains constant. All phenomena
   where the entropy decreases must not leave any info. of their having
   happened. This situation is completely indistinguishable from their not
   having happened at all. In the light of this obs'n, the 2nd law of
   thermodynamics is reduced to a mere tautology: physics cannot study those
   processes where entropy has decreased, even if they were commonplace."
   -- [<A HREF="http://link.aps.org/doi/10.1103/PhysRevLett.103.080401">doi:10.1103/PhysRevLett.103.080401</A>]['09].
   [Also search for: arrow time] and
   [also search for: thermodynamics information energy].

%A M. Zwolak
%A H. T. Quan
%A W. H. Zurek
%T Quantum Darwinism in a hazy environment
%J arXiv
%M OCT
%D 2009
%K TR, c2009, c200x, c20xx, zz0821, physics, quantum Darwinism, weirdness,
   observer, measurement
%X "Q.Darwinism recognizes that we - the observers - acquire our info about the
   'systems of interest' indirectly from their imprints on the environment.
   Here, we show that info about a system can be acquired from a mixed-state, or
   hazy, environment, but the storage capacity of an environment fragment is
   suppressed by its initial entropy. In the case of good decoherence, the
   mutual info between the system & the fragment is given solely by the
   fragment's entropy increase. For fairly mixed environments, this means a
   reduction by a factor 1-h, where h is the haziness of the env., i.e., the
   initial entropy of an env. qubit. Thus, even such hazy envs. eventually
   reveal the state of the system, although now the intercepted env. fragment
   must be larger by ~1/(1-h) to gain the same information about the system."
   -- [<A HREF="https://arxiv.org/abs/0904.0418">arXiv</A>]['21],
      auth3@[<A HREF="https://public.lanl.gov/whz/articles.html">lanl</A>]['21].

%A S. T. Bramwell
%A S. R. Giblin
%A S. Calder
%A R. Aldus
%A D. Prabhakaran
%A T. Fennell
%T Measurement of the charge and current of magnetic monopoles in spin ice
%J Nature
%V 461
%P 956-959
%M OCT
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1009, magnetic monopole, spin ice, Dy2Ti2O7,
   magnetism, magnet, electromagnetism, electromagnetic, charge, charges,
   magnetricity, monopoles
%X "...a real material, the 'spin ice' Dy2Ti2O7 ... experimental measurements
   prove that magnetic charges exist in this material, interact via a Coulomb
   potential, & have measurable currents. We further characterize deviations
   from Ohm's law, & determine the elementary unit of magnetic charge to be
   5 mu B A^-1, which is equal to that recently predicted using the microscopic
   theory of spin ice. Our measurement of magnetic charge & magnetic current
   establishes an instance of a perfect symmetry b/w electricity & magnetism."
   -- [<A HREF="http://dx.doi.org/10.1038/nature08500">doi:10.1038/nature08500</A>]['09] (30 refs).
   [Also search for: magnetic monopole].

%A N. Gisi
%T (Perspectives, Physics)  Quantum nonlocality: How does nature do it?
%J Science
%V 326
%N 5958
%P 1357-1358
%M DEC
%D 2009
%K perspective, c2009, c200x, c20xx, Bell's, Bells, inequality, quantum theory,
   nonlocal, non locality, entanglement, information, space, time
%X "... it is important to state that the nonlocal correlations of quantum
   physics are nonsignaling. That is, they do not communicate information. ...
   To put the tension in other words: No story in space-time can tell us how
   nonlocal correlations happen; hence, nonlocal quantum correlations seem to
   emerge, somehow, from outside space-time." [16 refs].
   -- [<A HREF="http://dx.doi.org/10.1126/science.1182103">doi:10.1126/science.1182103</A>]['09].

%A B. Cox
%A J. Forshaw
%T Why does E = m c**2? (And why should we care?)
%I DaCapo Press
%P 264
%D 2010
%K book, text, c2010, c201x, c20xx, physics, Einstein, relativity, E, e = mc2,
   mass, speed of light, energy
%X 1st ed 2009; hb us$13; uk us isbn:0306817586; uk us isbn13:978-0306817588.

%A W. Edelstein
%A A. Edelstein
%T Speed kills: Highly relativistic spaceflight would be fatal for people and
   instruments
%J Bull. of the Amer. Physical Soc.
%V 55
%N 1
%M APR
%D 2010
%K conf, D13.00008, c2010, c201x, c20xx, zz0210, Star Trek, space travel,
   flight, speed of light, interstellar hydrogen, warp speed, Sci Fi, SciFi
%X "... As spaceship velocities approach the speed of light, interstellar
   hydrogen, although only present on average at a density of about 2 atoms per
   cm^3, impinges on the spacecraft and turns into intense radiation that would
   quickly kill passengers and destroy instrumentation. In addition, the energy
   loss of ionizing radiation passing through the ship's hull represents an
   increasing heat load which necessitates large expenditures of energy to cool
   the ship. Preventing this irradiation by the use of material or
   electromagnetic shields is a daunting and, as far as we know, unsolvable
   problem. The presence of interstellar hydrogen is yet another formidable
   obstacle to interstellar travel."
   -- [<A HREF="http://meetings.aps.org/Meeting/APR10/Event/115032">www</A>]['10].

%A S. Carroll
%T From Eternity to Here: The Quest for the Ultimate Theory of Time
%I Dutton
%P 448
%M JAN
%D 2010
%K book, text, c2010, c201x, c20xx, zz0310, arrow of time, direction, physics,
   multiverse, universe
%X 1st ed 2010; hb us$18; uk us isbn:0525951334; uk us isbn13:978-0525951339.
   [Also search for: arrow time].

%A M. Brooks
%T The Big Questions: Physics
%I QuercusPubl
%P 208
%M FEB
%D 2010
%K book, text, c2010, c201x, c20xx, zz0115, science, physics, intro, popular,
   cosmology, gravity, quantum, universe, time
%X hb; 1st ed 2010; uk us isbn:1849161461; uk us isbn13:978-1849161466.
   [<A HREF="http://www.michaelbrooks.org/">auth</A>]['15].

%A G. F. R. Ellis
%A T. Rothman
%T Time and spacetime: The crystallizing block universe
%J Int. J. of Theor. Physics
%V 49
%N 5
%P 988-1003
%M MAY
%D 2010
%K jrnl, physics, c2010, c201x, c20xx, zz0716, quantum theory, time, arrow,
   space time, present, past, weirdness, delayed choice, retrocausality,
   indeterminacy, CBU, EBU, causality
%X "The nature of the future is completely different from the nature of the
   past. When q. effects are significant, the future shows all the signs of
   q. weirdness, including duality, uncertainty, & entanglement. With the
   passage of time, after the time-irreversible process of state-vector
   reduction has taken place, the past emerges, with the previous q.
   uncertainty replaced by the classical certainty of definite particle
   identities & states. The present time is where this transition largely takes
   place, but the process does not take place uniformly: evidence from delayed
   choice & related experiments shows that isolated patches of q.
   indeterminacy remain, & that their transition from probability to certainty
   only takes place later. Thus, when q. effects are sig., the picture of a
   classical Evolving Block Universe ('EBU') cedes place to one of a
   Crystallizing Block Universe ('CBU'), which reflects this q. transition
   from indeterminacy to certainty, while nevertheless resembling the EBU on
   large enough scales."
   -- [<A HREF="http://dx.doi.org/10.1007/s10773-010-0278-5">doi:10.1007/s10773-010-0278-5</A>]['16].
   (Also see the bbc [<A HREF="http://www.bbc.com/earth/story/20160708-the-past-is-not-set-in-stone-so-we-may-be-able-to-change-it">12/7/2016</A>].)
   [Also search for: physics time arrow] and
   [also search for: time retrocausality].

%A U. Sinha
%A C. Couteau
%A T. Jennewein
%A R. Laflamme
%A G. Weihs
%T Ruling out multi-order interference in quantum mechanics
%J Science
%V 329
%N 5990
%P 418-421
%M JUL
%D 2010
%K jrnl, c2010, c201x, c20xx, zz0710, physics, quantum, theory, mechanics,
   Born's, rule, Borns, pair, pairs, paths, multipath, interference
%X "Quantum mechanics & gravitation [...] seem to be incompatible theories.
   There are suggestions that one of these theories must be generalized to
   achieve unification. [e.g.,] Born's rule - one of the axioms of quantum
   mechanics - could be violated. B's rule predicts that quantum interference,
   as shown by a double-slit diffraction experiment, occurs from pairs of paths.
   A generalized version of quantum mechanics might allow multipath (i.e.,
   higher-order) interference ... . We performed a 3-slit experiment with
   photons & bounded the magnitude of 3-path interference to < 10**2 of the
   expected 2-path interference, thus ruling out third- & higher-order
   interference & providing a bound on the accuracy of B's rule. ...
   consistent with the postulate both in semiclassical & quantum regimes."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1190545">doi:10.1126/science.1190545</A>]['10].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.1192624">doi:10.1126/science.1192624</A>]['10].)

%A D. M. Toyli
%A C. D. Weis
%A G. D. Fuchs
%A T. Schenkel
%A D. D. Awschalom
%T Chip-scale nanofabrication of single spins and spin arrays in diamond
%J Nano Lett.
%M JUL
%D 2010
%P ?-?
%K c2010, c201x, c20xx, physics, quantum, theory, mechanics, computing, bits,
   qubit, qubits, spin, diamond, nano fabrication, nitrogen vacancy
%X online 23 July 2010.
   "... technique to nanofabricate nitrogen vacancy (NV) centers in diamond
   based on broad-beam nitrogen implantation through apertures in electron beam
   lithography resist. This method enables high-throughput nanofabrication of
   single NV centers on sub-100-nm length scales. ..."
   -- [<A HREF="http://dx.doi.org/10.1021/nl102066q">doi:10.1021/nl102066q</A>]['10].
   (Also see news@[<A HREF="http://dx.doi.org/10.1126/science.329.5992.616-b">Sci.</A>].)

%A R. Penrose
%T Cycles of Time: An Extraordinary New View of the Universe
%I BodleyHead
%P 320
%M SEP
%D 2010
%K book, text, c2010, c201x, c20xx, physics, cosmology, big bang, universe, end,
   beginning, time, space, cycle, conformal transformation, Penrose diagram,
   thermodynamics
%X hb stg14; uk us isbn:0224080369; uk us isbn13:978-0224080361.
   (A review @ [<A HREF="http://dx.doi.org/10.1126/science.1203148">doi:10.1126/science.1203148</A>].)
   [Also search for: arrow time].

%A J. A. Dunningham
%T Introductory Quantum Physics and Relativity
%I Imperial Coll. Press
%P 200
%D 2010
%K book, text, L1Ref, L2Ref, c2010, c201x, c20xx, quantum theory, mechanics,
   physics
%X 1st ed 2010; pb stg29; uk isbn:1848165153; uk isbn13:978-1848165151.
   "...based on the lecture courses taught by D. and V. at the U. of Leeds. ...
   contains all the necessary material for quantum physics & relativity in the
   1st 2 years of a typical physics degree course. The choice of topics complies
   fully with the Inst. of Physics guidelines, but the coverage also includes
   more interesting and up-to-date applications, such as Bose condensation and
   global positioning system (GPS)."
   Also [<A HREF="https://www.vlatkovedral.com/">www</A>]['22]
     or [<A HREF="https://scholar.google.com/citations?user=d0ruO6gAAAAJ">sc'lar</A>]['22].

%A J. van Dongen
%T Einstein's Unification
%I CUP
%P 224
%D 2010
%K book, text, c2010, c201x, c20xx, CUP, Einstein, unified field theory,
   physics, relativity, forces, electromagnetism, gravity, quantum theory
%X 1st ed 2010; hb us$68; uk us isbn:0521883466; uk us isbn13:978-0521883467.
   "Shedding new light on Einstein's later work, this book explores E's belief
   that he could find a unified theory of all of nature's forces by repeating
   the methods he used when formulating general relativity. [For] physicists,
   historians and philosophers of science."

%A D. Deutsch
%T The Beginning of Infinity: Explanations That Transform the World
%I AllenLane / VikingPress
%P 496
%D 2011
%K book, c2011, c201x, c20xx, zz0514, physics, information, philosophy,
   universal constructor, creativity, quantum, cosmology, multiverse, DDeutsch
%X 1st ed 2011;  hb; uk us isbn:0670022756; uk us isbn13:978-0670022755.
   Penguin 2012, pb; uk us isbn:0143121359, uk us isbn13:978-0143121350.
   "... argues that explanations have a fundamental place in the universe - and
   that improving them is the basic regulating principle of all successful human
   endeavor. Taking us on a journey through every fundamental field of science,
   as well as the history of civilization, art, moral values, and the theory of
   political institutions ..."
   (Also see DD@[<A HREF="http://www.daviddeutsch.org.uk/">www</A>]['16],
             DD@[<A HREF="http://www.physics.ox.ac.uk/al/people/Deutsch.htm">oxf</A>]['14].)

%A A. Winter
%T Quantum mechanics: The usefulness of uselessness
%J Nature
%V 466
%P 1053-1054
%M AUG
%D 2010
%K news, c2010, c201x, c20xx, zz0910, physics, quantum theory, mechanics, Bell,
   Bells, inequality, inequalities, facet, no, non signalling, correlations,
   classical, Almeida, Pironio, guess your neighbours input, game, advantage,
   neighbour, nonlocal
%X "Why play games that quantum dice don't help you win? Writing in Phys. Rev.
   Letters, Almeida et al.
      [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.104.230404">doi:10.1103/PhysRevLett.104.230404</A>]['10]
   provide a surprising twist on the foundations of quantum mechanics and tell
   us why we should be at least interested in this question. ... It is a curious
   property of both classical and quantum correlations that they are
   'no-signalling': the choice of input at one site cannot have an observable
   effect at another site. ... their game results in a Bell inequality that is
   true even for quantum correlations, yet it is non-trivial because its viol'n
   is consistent with no signalling. In fact, it is a 'facet inequality',
   meaning that it is not implied by any other Bell inequality ..."
   -- [<A HREF="http://dx.doi.org/10.1038/4661053a">doi:10.1038/4661053a </A>]['10].

%A S. Hawking
%A L. Mlodinow
%T The Grand Design
%I BantamPress
%P 208
%D 2010
%K book, text, c2010, c201x, c20xx, zz0910, physics, universe, time, god,
   creation, origin, history, big bang, mTheory, cosmology, intelligent
%X 1st ed 2010; hb stg.10; uk us isbn:0593058291; uk us isbn13:978-0593058299.
   "... explains the latest thoughts about model-dependent realism (the idea
   that there is no one version of reality), & about the multiverse concept
   of reality in which there are many universes. There are new ideas about the
   top-down theory of cosmology (the idea that there is no one history of the
   universe, but that every possible history exists). It concludes with a
   riveting assessment of m-theory, & discusses whether it is the unified
   theory Einstein spent a lifetime searching for. This is the first major
   work in nearly a decade by one of the world's greatest thinkers. ..."
   2010; pb us$14; uk us isbn:0553840886; uk us isbn13:978-0553840889.

%A G. Jannes
%A R. Piquet
%A P. Maissa
%A C. Mathis
%A G. Rousseaux
%T The circular jump is a white hole
%J arXiv
%M OCT
%D 2010
%K physics, c2010, c201x, c20xx, white hole, simulation, Hawking radiation,
   circular hydraulic jump, gravitational fountain, black
%X "... experimental demo. that the circular hydraulic jump represents
   a hydrodynamic white hole or gravitational fountain (the time-reverse of a
   black hole) by measuring the angle of the Mach cone created by an object in
   the 'supersonic' inner flow region. We emphasise the general character of
   this gravitational analogy by showing theoretically that the white hole
   horizon constitutes a stationary & spatial saddle-node bifurcation within
   dynamical-systems theory. Some perspectives are outlined on the usefulness of
   the [cj] as an experimentally viable white hole model for analogue gravity,
   in particular [wrt] the ... debate on the robustness of Hawking radiation."
   -- 1010.1701v1@[<A HREF="http://arxiv.org/abs/1010.1701v1">arXiv</A>]['10].

%A S. Toyabe
%A T. Sagawa
%A M. Ueda
%A E. Muneyuki
%A M. Sano
%T Experimental demonstration of information-to-energy conversion and
   validation of the generalized Jarzynski equality
%J Nature Physics
%M NOV
%D 2010
%K eJrnl, c2010, c201x, c20xx, zz1110, information, energy, conversion, bit,
   convert, Brownian motion, particle, location, staircase, Maxwell's demon,
   Jarzynski equality, Szilard engine, physics, thermodynamics
%X "... An experimental demonstration of this information-to-energy conversion,
   however, has been elusive. Here we demonstrate that a non-equilibrium
   feedback manipulation of a Brownian particle on the basis of info. about its
   locn achieves a Szilard type I-to-E conv..  Using real-time feedback control,
   the particle is made to climb up a spiral-staircase-like potential exerted by
   an electric field & gains free energy larger than the amount of work done on
   it. This enables us to verify the generalized Jarzynski equality, & suggests
   a new fundamental principle of an info-to-heat engine that converts info.
   into energy by feedback control."
   -- [<A HREF="http://dx.doi.org/10.1038/nphys1821">doi:10.1038/nphys1821</A>]['10].
   "... at room temp., one bit of info. converts to ~3 x 10**-21 joules." --NS.
   [Also search for: thermodynamics information energy].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Entropy/Gas/">Gas</A>].)

%A J. Oppenheim
%A S. Wehner
%T The uncertainty principle determines the nonlocality of quantum mechanics
%J Science
%V 330
%N 6007
%P 1072-1074
%M NOV
%D 2010
%K jrnl, physics, c2010, c201x, c20xx, zz1110, quantum mechanics, theory,
   uncertainty principle, non locality, steering, spooky action
%X 'Two central concepts of quantum mechanics are Heisenberg's uncertainty
   principle & a subtle form of nonlocality that Einstein famously called
   "spooky action at a distance." These two fundamental features have thus far
   been distinct concepts. We show that they are inextricably & quantitatively
   linked: Quantum mechanics cannot be more nonlocal with measurements that
   respect the uncertainty principle. In fact, the link between uncertainty &
   nonlocality holds for all physical theories. More specifically, the degree of
   nonlocality of any theory is determined by two factors: the strength of the
   uncertainty principle & the strength of a property called "steering," which
   determines which states can be prepared at one location given a measurement
   at another.'
   -- [<A HREF="http://dx.doi.org/10.1126/science.1192065">doi:10.1126/science.1192065</A>]['10].

%A V. Vedral
%T Decoding Reality: The Universe as Quantum Information
%I OUP
%P 256
%D 2010
%K book, text, OUP, c2010, c201x, c20xx, quantum, information, qubism, qbism,
   theory, universe, reality, cosmology, cosmos, physics
%X 1st ed 2010; hb us$24; uk us isbn:0199237697; uk us isbn13:978-0199237692;
                pb us$13; uk us isbn:0199695741; uk us isbn13:978-0199695744.
   "... The most fundamental definition of reality is not matter or energy, he
   writes, but information - and it is the processing of information that lies
   at the root of all physical, biological, economic, & social phenomena. ..."
   Also VV@[<A HREF="https://www.vlatkovedral.com/">www</A>]['22]
     or [<A HREF="https://scholar.google.com/citations?user=d0ruO6gAAAAJ">sc'lar</A>]['22].

%A G. Mauro D'Ariano
%A A. Tosini
%T Space-time and special relativity from causal networks
%J arXiv
%M AUG
%D 2010
%K TR, physics, c2010, c201x, c20xx, zz0415, quantum theory, relativity, space,
   events, event, space time, network, qubit
%X "We show how the Minkowskian space-time emerges from a topologically
   homogeneous causal network, presenting a simple analytical derivation of the
   Lorentz transformations, with metric as pure event-counting. The derivation
   holds generally for d=1 space dimension, however, it can be extended to
   d > 1 for special causal networks."  [12 refs].
   -- 1008.4805@[<A HREF="http://www.qubit.it/research/publications/1008.4805.pdf">qubit</A>]['15],
      auth1@[<A HREF="http://www.qubit.it/people/dariano/">qubit</A>]['15].

%A M. Van Raamsdonk
%T Building up spacetime with quantum entanglement
   (Essay awarded by the Gravity Research Foundation)
%J General Relativity and Gravitation
%V 42
%N 10
%P 2323-2329
%M OCT
%D 2010
%K jrnl, physics, c2010, c201x, c20xx, zz1115, VanRaamsdonk, quantum theory,
   space time, gravity, relativity, spacetime, cosmology, entanglement, weird
%X "In this essay, we argue that the emergence of classically connected
   spacetimes is intimately related to the quantum entanglement of degrees of
   freedom in a non-perturbative description of quantum gravity. Disentangling
   the degrees of freedom associated with two regions of spacetime results in
   these regions pulling apart & pinching off from each other in a way that can
   be quantified by standard measures of entanglement."
   10.1007/s10714-010-1034-0
   -- [<A HREF="http://dx.doi.org/10.1007/s10714-010-1034-0">doi:10.1007/s10714-010-1034-0</A>]['15].
   (Also see
   feature@[<A HREF="http://dx.doi.org/10.1038/527290a">10.1038/527290a</A>][16/11/'15].)

%A D. Kaiser
%T How the Hippies Saved Physics: Science, Counterculture, and the
   Quantum Revival
%I Norton
%P 372
%M JUN
%D 2011
%K book, c2011, c201x, c20xx, zz0811, quantum physics, mechanics, Bells, 1970s,
   Berkeley, Sarfatti, Sirag, Wolf, spooky action, Fundamental Fysiks Group,
   science, ideas, process
%X 1st ed 2011; hb us$13; uk us isbn:0393076369; uk us isbn13:978-0393076363.
   "... For physicists, the 1970s were a time of stagnation. Jobs became scarce,
   and conformity was encouraged, sometimes stifling exploration of the
   mysteries of the physical world. Dissatisfied, underemployed, and eternally
   curious, an eccentric group of physicists in Berkeley, California, banded
   together to throw off the constraints of the physics mainstream and explore
   the wilder side of science. Dubbing themselves the 'Fundamental Fysiks Group'
   they pursued an audacious, speculative approach to physics. They studied
   quantum entanglement and Bell's Theorem through the lens of Eastern mysticism
   & psychic mind-reading, discussing the latest research while lounging in
   hot tubs. Some even dabbled with LSD to enhance their creativity. Unlikely as
   it may seem, these iconoclasts spun modern physics in a new dirn, ..." (!)

%A A. Cho
%T Furtive approach rolls back the limits of quantum uncertainty
%J Science
%V 333
%N 6043
%P 690-693
%M AUG
%D 2011
%K news, c2011, c201x, c20xx, zz0811, physics, quantum theory, mechanics,
   uncertainty principle, weak measurement, Vaidman, Aharonov, postselection,
   Hosten, Kwiat
%X "You cannot measure a quantum particle without disturbing it. Or can you?
   Weird "weak measurements" are opening new vistas in quantum physics.  ... "
   -- [<A HREF="http://dx.doi.org/10.1126/science.333.6043.690">doi:10.1126/science.333.6043.690</A>]['11].
   [Also search for: weak measurement quantum physics].

%A L. Peliti
%T Statistical Mechanics in a Nutshell
%I PrincetonUP
%P 416
%M AUG
%D 2011
%K book, text, c2011, c201x, c20xx, statistical mechanics, physics, dynamics,
   thermodynamics, generalized Brownian motion, stochastic, complex, simulation
%X 1st ed 2011; hb us$65; uk us isbn:0691145296; uk us isbn13:978-0691145297.
   "... including the theory of phase transitions, generalized Brownian motion
   and stochastic dynamics, the methods underlying Monte Carlo simulations,
   complex systems ..."
   [Also search for: statistical mechanics].

%A M. Tegmark
%T How unitary cosmology generalizes thermodynamics and solves the inflationary
   entropy problem
%J arXiv
%M AUG
%D 2011
%K TR, c2011, c201x, c20xx, zz0117, physics, themodynamics, quantum mechanics,
   cosmology, universe, inflation, entropy, entanglement, qubits, observer
%X 'We analyze cosmology assuming unitary q.mechanics, using a tripartite
   partition into system, observer & environment degrees of freedom. This
   generalizes the second law of thermodynamics to "The system's entropy can't
   decrease unless it interacts with the observer, & it can't increase unless
   it interacts with the environment." ...'
   -- 1108.3080@[<A HREF="https://arxiv.org/abs/1108.3080">arXiv</A>]['17].

%Q The OPERA Collaboration
%T Measurement of the neutrino velocity with the OPERA detector in the CNGS beam
%J Arxiv
%M SEP
%D 2011
%K report, TR, c2011, c201x, c20xx, zz1011, physics, speed of light, relativity,
   muon neutrino, velocity, faster, supraluminal, anomaly, CERN, Opera,
   experiment, CNGS, tachyon
%X "... measured the velocity of neutrinos from the CERN CNGS beam over a
   baseline of about 730km with much higher accuracy than prev.studies conducted
   with accelerator neutrinos. The measurement is based on high-statistics data
   taken by OPERA in the years 2009, 2010 & 2011. Dedicated upgrades of the CNGS
   timing system and of the OPERA detector, as well as a high precision geodesy
   campaign for the measurement of the neutrino baseline, allowed reaching
   comparable systematic & statistical accuracies. An early arrival time of
   CNGS muon neutrinos with respect to the one computed assuming the speed of
   light in vacuum of (60.7 \pm 6.9 (stat.) \pm 7.4 (sys.)) ns was measured.
   This anomaly corresponds to a relative difference of the muon neutrino
   velocity with respect to the speed of light
   (v-c)/c = (2.48 \pm 0.28 (stat.) \pm 0.30 (sys.)) \times 10-5. "
   -- report@[<A HREF="http://arxiv.org/abs/1109.4897">arxiv</A>]['11].
   (Also see comment@[<A HREF="http://dx.doi.org/10.1126/science.333.6051.1809">doi:10.1126/science.333.6051.1809</A>]['11].)

%A D. Deutsch
%T Vindication of quantum locality
%J arXiv
%P
%M SEP
%D 2011
%K TR, c2011, c201x, c20xx, zz0916, physics, time, quantum, mechanics,
   relativity, theory, locality, information, DDeutsch, Hayden, Wallace,
   Timpson
%X "In a previous paper [<A HREF="http://arxiv.org/abs/quant-ph/9906007">arXiv:quant-ph/9906007</A>]
   Hayden & I proved, using the Heisenberg picture, that q.physics satisfies
   Einstein's criterion of locality. Wallace & Timpson have argued that certain
   transformations of the Heisenberg-picture description of a q.system must be
   regarded as leaving invariant the factual situation being described, & that
   taking this into account reveals that Einstein's criterion is violated after
   all. Here I vindicate the proof & explain some misconceptions that have led
   to this & other criticisms of it."
   -- 1109.6223@[<A HREF="http://arxiv.org/abs/1109.6223">arXiv</A>]['16].

%A M. Mariantoni
%A et al ...
%A J. M. Martinis
%T Implementing the quantum von Neumann architecture with superconducting
   circuits
%J Science
%V 334
%N 6052
%P 61-65
%M OCT
%D 2011
%K jrnl, c2011, c201x, c20xx, zz1011, quantum computing, computer, circuit,
   CPU, memory, algorithm
%X "... a CPU and a memory holding instructions and data. We demonstrate a
   q.CPU that exchanges data with a quantum random-access memory
   integrated on a chip, with instructions stored on a classical computer. We
   test our quantum m/c by executing codes that involve seven quantum elements:
   Two superconducting qubits coupled through a quantum bus, two quantum
   memories, and two zeroing registers. Two vital algs. for quantum computing
   are demonstrated, the quantum Fourier transform, with 66% process fidelity,
   and the three-qubit Toffoli-class OR phase gate, with 98% phase fidelity.
   ... illustrate a potentially viable approach to factoring numbers and
   implementing simple quantum error correction codes. "
   -- [<A HREF="http://dx.doi.org/10.1126/science.1208517">doi:10.1126/science.1208517</A>]['11].

%A S. Hawking
%T The Dreams That Stuff Is Made Of: The Most Astounding Papers of
   Quantum Physics and How They Shook the Scientific World
%I RunningPress
%P 1088
%M OCT
%D 2011
%K book, text, c2011, c201x, c20xx, quantum physics, mechanics, uncertainty,
   principle, cosmology, science
%X 1st ed 2011; hb us$19; uk us isbn:0762434341; uk us isbn13:978-0762434343.
   "... compiles the essential works from the scientists who sparked the
   paradigm shift that changed the face of physics forever, pushing our
   understanding of the universe on to an entirely new level of comprehension.
   Gathered in this anthology is the scholarship that shocked and befuddled
   the scientific world, including works by Niels Bohr, Max Planck, Werner
   Heisenberg, Max Born, Erwin Schrodinger, J. Robert Oppenheimer,
   Richard Feynman ... and S.H.."

%A B. Cox
%A J. Forshaw
%T The Quantum Universe: (And Why Anything That Can Happen, Does)
%I DaCapoPress
%P 256
%M JAN
%D 2012
%K book, text, c2012, c201x, c20xx, zz0112, quantum, physics, universe
%X 1st ed 2012; hb us$15; uk us isbn:0306819643; uk us isbn13:978-0306819643.
   "... The subatomic realm has a reputation for weirdness, spawning any number
   of profound misunderstandings, journeys into Eastern mysticism, and woolly
   pronouncements on the interconnectedness of all things. Cox and Forshaw's
   contention? There is no need for quantum mechanics to be viewed this way.
   ... asks what observations of the natural world made it necessary, how it was
   constructed, and why we are confident that, for all its apparent strangeness,
   it is a good theory. ..."

%A M. F. Pusey
%A J. Barrett
%A T. Rudolph
%T The quantum state cannot be interpreted statistically
%I LANL
%M NOV
%D 2011
%K LANL, preprint, c2011, c201x, c20xx, zz1111, science, physics,
   quantum theory, mechanics, interpretation, wave function, waveFunction,
   probabilistic, statistical, physical, reality
%X "Quantum states are the key math.objects in quantum theory. [so] surprising
   that physicists have been unable to agree on what a QS represents. There are
   at least two opposing schools of thought ... One is that a pure state is a
   physical property of system, much like posn & momentum in classical
   mechanics.  Another is that even a pure state has only a statistical sig.,
   akin to a prob.distn in stat.mechanics. ... show that, given only v.mild
   assumptions, the stat. interp. of the QS is inconsistent with the predictions
   of quantum theory. ... holds even in the presence of small amounts of
   experimental noise, & is therefore amenable to experimental test using
   present or near-future technology. If the predictions of quantum theory are
   confirmed, such a test would show that distinct QSs must corr. to physically
   distinct states of reality."
   -- [<A HREF="http://lanl.arxiv.org/abs/1111.3328">www</A>]['11].
   (Also see comment@[<A HREF="http://dx.doi.org/10.1038/nature.2011.9392">doi:10.1038/nature.2011.9392</A>]['11].)
   [Also search for: quantum waveFunction reality].

%A G. Dvali
%A C. Gomez
%T Black hole's quantum N-portrait
%J arXiv
%M DEC
%D 2011
%K TR, c2011, c201x, c20xx, quantum, theory, mechanics, black holes, gravity,
   physics, cosmology, graviton, t'Hooft-Polyakov monopole
%X "We establish a quantum measure of classicality in the form of the
   occupation number, $N$, of gravitons in a gravitational field. ... The black
   hole is a leaky bound-state in form of a cold Bose-condensate of $N$ weakly
   --interacting soft gravitons of wave-length $\sqrt{N}$ times the Planck
   length and of quantum interaction strength 1/N. ..."
   -- [<A HREF="http://arxiv.org/abs/1112.3359">www</A>]['12].

%A E. Sanders
%T Swimming against the tide: explaining the Higgs
%I CERN
%D 2012
%K physics, news, CERN, LHC, c2012, c201x, c20xx, Higgs boson, particle, field,
   mass, standard model, theory, God particle
%X [<A HREF="http://cdsweb.cern.ch/record/1420890">www</A>]['12].
   Also see [<A HREF="http://cms.web.cern.ch/news/about-higgs-boson">about</A>]['12],
   1207.7235@[<A HREF="http://arxiv.org/abs/1207.7235">arxiv</A>][31/7/'12].
   [Also search for: Higgs boson physics].

%A H. Price
%T Does time-symmetry imply retrocausality? How the quantum world says "Maybe"?
%J Studies in History and Philosophy of Science Part B:
   Studies in History and Philosophy of Modern Physics
%V 43
%N 2
%P 75-83
%M MAY
%D 2012
%K jrnl, physics, c2012, c201x, c20xx, zz0716, quantum mechanics, time,
   retrocausality, time symmetry
%X "It has often been suggested that retrocausality offers a soln to some of the
   puzzles of quantum mechanics: e.g., that it allows a Lorentz-invariant
   explanation of Bell correlations, & other manifestations of quantum
   nonlocality, without action-at-a-distance.  Some writers have argued that
   time-symmetry counts in favour of such a view ...  Under these
   assumptions, the combination of time-symmetry without retrocausality is
   unavailable in q.mechanics, for reasons intimately connected with the
   differences between classical & q.physics (esp. the role of discreteness in
   the latter). Not all interpretations of q.mechanics share these assumptions,
   however, & in those that do not, time-symmetry does not entail retroc.."
   -- [<A HREF="http://dx.doi.org/10.1016/j.shpsb.2011.12.003">doi:10.1016/j.shpsb.2011.12.003</A>]['16].
   (Also see the bbc [<A HREF="http://www.bbc.com/earth/story/20160708-the-past-is-not-set-in-stone-so-we-may-be-able-to-change-it">12/7/2016</A>].)
   [Also search for: time retrocausality].

%A C. C. Berry
%A K. M. Bruno
%T The Quantum Divide: Why Schrodinger's Cat is Either Dead or Alive
%I OUP
%P 197
%M MAR
%D 2013
%K book, text, OUP, c2013, c201x, c20xx, zz0613, quantum theory, physics,
   superposition, state, states
%X 2013; hb us$37; uk us isbn:0199666563; uk us isbn13:978-0199666560.
   "... presents a discussion of the strikingly counter-intuitive phenomena of
   the quantum world that defy explanation in terms of everyday "common sense"
   reasoning, and it provides the corresponding quantum mechanical explanations
   with a very elementary use of associated formalism. Most, but certainly not
   all, of the experiments it describes are optical experiments involving a very
   small number of photons (particles of light). The book begins with
   experiments on the wave-particle duality of electrons ..."

%A A. Berut
%A et al ...
%A E. Lutz
%T Experimental verification of Landauer's principle linking information
   and thermodynamics
%J Nature
%V 483
%P 187-189
%M MAR
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0312, information, physics, energy, bit, change,
   thermodynamics, irreversible, computation, computing, bits, change, set,
   reset, erase, Landauer, limit, bound, Maxwell, Maxwell's demon, theory
%X "In 1961, Rolf Landauer argued that the erasure of information is a
   dissipative process. A minimal quantity of heat, proportional to the thermal
   energy & called the Landauer bound, is necessarily produced when a classical
   bit of information is deleted. A direct consequence of this logically
   irreversible transformation is that the entropy of the environment increases
   by a finite amount. ...  [we] experimentally show the existence of the
   L.bound in a generic model of a one-bit memory. Using a system of a single
   colloidal particle trapped in a modulated double-well potential, we establish
   that the mean dissipated heat saturates at the Landauer bound in the limit of
   long erasure cycles. This result demonstrates the intimate link between
   information theory & thermodynamics. It further highlights the ultimate
   physical limit of irreversible computation."
   -- [<A HREF="http://dx.doi.org/10.1038/nature10872">doi:10.1038/nature10872</A>]['12]
   (and [<A HREF="http://dx.doi.org/10.1038/nature.2012.10186">comment</A>]).
   [Also search for: thermodynamics information energy].

%A A. Hodges
%T Beyond Turing's Machines
%J Science
%V 336
%N 6078
%P 163-164
%M APR
%D 2012
%K views, c2012, c201x, c20xx, Alan Turing, machine, test, centenary, computing,
   computable, mechanical, quantum Zeno effect, intuition, brain, Comp Sci, CSci
%X "... In 1951, however, Turing gave a radio talk ... suggesting that the
   nature of quantum mechanics might make simulation of the physical brain
   impossible. ... renewed interest in quantum theory & noted a problem about
   the observation of quantum sys. (now known as the quantum Zeno effect).
   With his death, this train of thought was lost ...  Since the 1980s, quantum
   comp. has given a practical techno.arena in which computation & q.physics
   interact excitingly ...
   Perhaps the best-known body of ideas is that of Roger Penrose ...
   The problem remains: Does computation with discrete symbols give a complete
   account of the physical world? If it does, how can we make this connection
   manifest? If it does not, where does computation fail, & what would this
   tell us about fundamental sci.?"
   -- [<A HREF="http://dx.doi.org/10.1126/science.1218417">doi:10.1126/science.1218417</A>]['12].

%A J. W. Britton,
%A et al ...
%A J. J. Bollinger
%T Engineered two-dimensional Ising interactions in a trapped-ion quantum
   simulator with hundreds of spins
%J Nature
%V 484
%P 489-492
%M APR
%D 2012
%K physics, c2012, cw01x, c20xx, zz0412, quantum, 2D, spin, quibit, quibits,
   computer, computing, beryllium
%X "... calculations involving N-body entanglement become intractable for as few
   as N~30 particles ... Here we demonstrate a variable-range Ising-type spin-
   spin interaction, J[i,j], on a naturally occurring, [2D] triangular crystal
   lattice of hundreds of spin-half particles (beryllium ions stored in a
   Penning trap). ... This demonstration, coupled with the high spin count,
   excellent quantum control and low technical complexity of the Penning trap,
   brings within reach the simulation of otherwise computationally intractable
   problems in quantum magnetism."
   -- [<A HREF="http://dx.doi.org/10.1038/nature10981">doi:10.1038/nature10981</A>]['12].
   (Also see [<A HREF="http://www.abc.net.au/news/2012-04-26/super-computer/3972832">abc</A>][4/2012].)

%A A. Cho
%T Textbook electrodynamics may contradict relativity
%J Science
%V 336
%N 6080
%P 404
%M APR
%D 2012
%K news, views, c2012, c201x, c20xx, zz0512, Mansuripur, sci, physics, magnetic,
   electric, field, electro, electromagnetism, relativity, Lorentz force,
   Maxwell law
%X "A basic equn of electricity & magnetism is wrong, 1 scientist claims. The
   classic formula for the force exerted by electric & magnetic fields - the
   so-called Lorentz force - clashes with E.'s special theory of rel., says
   Masud Mansuripur, ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.336.6080.404">doi:10.1126/science.336.6080.404</A>]['12].
   M. Mansuripur, 'Maxwell's macroscopic equations, energy-momentum posulates,
   the Lorentz law of force, and interesting connections with the Doppler
   shift,' (inv.), Int. Photonics W.shop, U. Sao Carlos, Sao Paulo, Brazil,
   Feb. 2012.
   M. Mansuripur, 'The trouble with the Lorentz law of force,'
   sub. to Phys. Rev. Lett., Jan. 2012.
   M@[<A HREF="http://www.optics.arizona.edu/masud/">ariz</A>]['12].
   Also see [<A HREF="http://link.aps.org/doi/10.1103/PhysRevE.79.026608">doi:10.1103/PhysRevE.79.026608</A>]['12], 2009.

%A A. Mithani
%A A. Vilenkin
%T Did the universe have a beginning?
%J arXiv
%M APR
%D 2012
%K arXiv, c2012, c201x, c20xx, physics, cosmology, cosmos, universe, time,
   beginning, past, start, origins, inflation, emergent
%X "We discuss three candidate scenarios which seem to allow the possibility
   that the universe could have existed forever with no initial singularity:
   eternal infation,  cyclic evolution,  & the emergent universe.
   The first two of these scenarios are geodesically incomplete to the past,
   & thus cannot describe a universe without a beginning. The third, although
   it is stable with respect to classical perturbations, can collapse quantum
   mechanically, & therefore cannot have an eternal past."
   -- [<A HREF="http://arxiv.org/abs/arXiv:1204.4658">arXiv</A>]['12],
   auth2@[<A HREF="http://cosmos2.phy.tufts.edu/vilenkin.html">tufts</A>]['12].

%A M. F. Pusey
%A J. Barrett
%A T. Rudolph
%T On the reality of the quantum state
%J Nature Physics
%V 8
%P 475-478
%M MAY
%D 2012
%K jrnl, physics, c2012, c201x, c20xx, quantum, theory, mechanics, state,
   wave function, waveFunction, reality, physical, information, property,
   particle, probability, nogo theorem
%X "Quantum states are the key math. objects in quantum theory. [So ...]
   surprising that physicists have been unable to agree on what a QS truly
   represents. One possibility is that a pure QS corr.directly to reality.
   However, there is a long history of suggestions that a QS (even a pure state)
   represents only knowledge or info. about some aspect of reality. ... show
   that any model in which a QS represents mere info. about an underlying
   physical state of the sys., & in which systems that are prepared indep. have
   indep. physical states, must make predns that contradict those of Q.theory."
   -- [<A HREF="http://dx.doi.org/10.1038/nphys2309">doi:10.1038/nphys2309</A>]['12] (online May 2012).
     (Also see [<A HREF="http://dx.doi.org/10.1038/485157a">comment</A>][12],
     & [<A HREF="http://dx.doi.org/10.1038/nature.2011.9392">news</A>][11/'12].)
   [Also search for: quantum waveFunction reality].

%A V. Vedral
%T An information-theoretic equality implying the Jarzynski relation
%J J. Phys. A: Math. Theor.
%V 45
%N 27
%P e2001
%M JUN
%D 2012
%K jrnl, c2012, c201x, c20xx, zz1012, physics, information theory, measurement,
   thermodynamics, energy, Jarzynski relation, classical, quantum
%X "We derive a general information-theoretic equality for a system undergoing
   two projective measurements separated by a general temporal evolution. The
   equality implies the non-negativity of the mutual info. between the
   measurement outcomes of the earlier & later projective measurements. We show
   that it also contains the Jarzynski reln between the avg. exponential of the
   thermodynamical work & the exponential of the difference between the initial
   & final free energy. Our result elucidates the information-theoretic
   underpinning of thermodynamics & explains why the Jarzynski reln holds
   identically both quantumly as well as classically."
   -- [<A HREF="http://dx.doi.org/10.1088/1751-8113/45/27/272001">doi:10.1088/1751-8113/45/27/272001</A>]['12].
   Also VV@[<A HREF="https://www.vlatkovedral.com/">www</A>]['22]
     or [<A HREF="https://scholar.google.com/citations?user=d0ruO6gAAAAJ">sc'lar</A>]['22].
   [Also search for: thermodynamics information energy].

%A C. A. Fuchs
%T Interview with a quantum Bayesian
%J arXiv
%M JUL
%D 2012
%K TR, c2012, c201x, c20xx, zz0913, physics, quantum theory, information,
   Bayesian, Bayesianism, Qbism, qubism, qbist, qubist, probability,
   uncertainty, weirdness, Schlosshauer, interviews, elegance
%X "This paper collects into one place (most of) my answers to the questions
   Maximilian Schlosshauer posed in his interview volume, 'Elegance and
   Enigma: The Quantum Interviews' (Springer, Frontiers Collection, 2011)."
   -- 1207.2141@[<A HREF="http://arxiv.org/abs/1207.2141">arXiv</A>]['13].
   (Also see [<A HREF="http://dx.doi.org/10.1038/501154a">www</A>][9/'13], and
    QB@[<A HREF="http://en.wikipedia.org/wiki/Quantum_Bayesianism">wikip</A>]['14].)
   [Also search for: Qbism physics].

%A A. Shapere
%A F. Wilczek
%T Constraints on chronologies
%J arXiv
%M AUG
%D 2012
%K physics, c2012, c20x, c20xx, quantum theory, relativity, entanglement,
   space time, spacetime, simultaneous, events, ordering, order, inertial frame,
   chronology
%X "The time ordering of two spacelike separated events is arbitrary, when all
   inertial frames are taken into account, but for three or more events it is
   not generally so. We determine the structure of possible time orderings, or
   chronologies, for multiple events in any number of dimensions, analytically
   & exhaustively for three events in four space-time dimensions,
   algorithmically in other cases. We also formulate an alternative criterion,
   based on convexity, for determining the allowed chronologies of a set of
   events. We show how the metric of a Lorentz invariant spacetime can be
   partially reconstructed from a knowledge of the chronologies it supports.
   Finally, we propose a different but related criterion for allowed
   chronologies in curved spacetimes."  [sub. Aug 2012].
   -- [<A HREF="http://arxiv.org/abs/1208.3841">arXiv</A>]['12].

%A L. A. Rozema
%A A. Darabi
%A D. H. Mahler
%A A. Hayat
%A Y. Soudagar
%A A. M. Steinberg
%T Violation of Heisenberg's measurement-disturbance relationship by weak
   measurements
%J Phys. Rev. Lett.
%I Amer. Phys. Soc.
%V 109
%N 10
%P e100404
%M SEP
%D 2012
%K jrnl, eJrnl, c2012, c201x, c20xx, zz0912, Physics, quantum theory, mechanics,
   Heisenberg, uncertainty, principle, Lund, Weisman, Ozawa, observation
%X 'While there is a rigorously proven reln. about uncertainties intrinsic to
   any quantum system, often ref. to as "Heisenberg's uncertainty principle,"
   H. originally formulated his ideas in terms of a reln. between the precision
   of a measurement & the disturbance it must create. Although this latter
   reln. is not rigorously proven, it is commonly believed (& taught) as an
   aspect of the broader [UP]. ... experimentally observe a violation of H's
   "measurement-disturbance relationship," using weak measurements to
   characterize a q.sys. before & after it interacts with a measurement
   apparatus. ... implements a 2010 proposal of Lund & Wiseman to confirm a
   revised measurement-disturbance relationship derived by Ozawa in 2003. ..."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.109.100404">doi:10.1103/PhysRevLett.109.100404</A>]['12].
   [Also search for: weak measurement quantum physics].

%T Observation of a new particle in the search for the Standard Model
   Higgs boson with the ATLAS detector at the LHC
%Q ATLAS Collaboration
%J Physics Lett. B
%V 716
%N 1
%P 1-29
%M SEP
%D 2012
%K jrnl, physics, c2012, c201x, c20xx, standard model, particle, Higgs, boson,
   ATLAS, LHC, CERN, mass
%X "A search for the Standard Model Higgs boson in proton-proton collisions with
   the ATLAS detector ... Clear evidence for the production of a neutral boson
   with a measured mass of 126+/- ... compatible with the production and decay
   of the Standard Model Higgs boson."
   -- [<A HREF="10.1016/j.physletb.2012.08.020">doi:10.1016/j.physletb.2012.08.020</A>]['12].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.338.6114.1558">news</A>][12/2012].)
   [Also search for: Higgs boson physics].

%T Observation of a new boson at a mass of 125 GeV with the CMS experiment at
   the LHC
%Q CMS Collaboration
%J Physics Lett. B
%V 716
%N 1
%P 30-61
%M SEP
%D 2012
%K jrnl, physics, c2012, c201x, c20xx, standard model, particle, Higgs, boson,
   CMS, LHC, CERN, mass
%X "... proton-proton collisions at sqrt(s)=7 and 8 TeV in the Compact Muon
   Solenoid experiment at the LHC ...  An excess of events is observed above the
   expected background, with a local sig. of 5.0 SDs, at a mass near 125GeV,
   signalling the production of a new particle. The expected sig. for a standard
   model Higgs boson of that mass is 5.8 SDs. ...  The decay to two photons
   indicates that the new particle is a boson with spin different from one."
   -- [<A HREF="http://dx.doi.org/10.1016/j.physletb.2012.08.021">doi:10.1016/j.physletb.2012.08.021</A>]['12].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.338.6114.1558">news</A>][12/2012].)
   [Also search for: Higgs boson physics].

%A R. Vijay
%A C. Macklin
%A D. H. Slichter
%A S. J. Weber
%A K. W. Murch
%A R. Naik
%A A. N. Korotkov
%A I. Siddiqi
%T Stabilizing Rabi oscillations in a superconducting qubit using quantum
   feedback
%J Nature
%V 490
%P 77-80
%M OCT
%D 2012
%K jrnl, physics, c2012, c201x, c20xx, zz1012, quantum, computing, qubit,
   weak, measurement, state, quantum theory, Schrodinger's cat, Schrodingers,
   Rabi oscillations
%X "The act of measurement bridges the quantum and classical worlds by
   projecting a superposition of possible states into a single (probabilistic)
   outcome. ... we implement quantum feedback control in a solid-state system,
   namely a superconducting quantum bit (qubit) coupled to a microwave cavity.
   A weak measurement of the qubit is implemented by probing the cavity with
   microwave photons, maintaining its average occupation at less than one
   photon. ... demonstrate quantum feedback control by inhibiting the decay of
   Rabi oscillations, allowing them to persist indefinitely ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature11505">doi:10.1038/nature11505</A>]['12].
   [Also search for: weak measurement quantum physics].

%A D. Deutsch
%T Constructor Theory
%J arXiv
%M OCT
%D 2012
%K Science, Physics, c2012, c201x, c20xx, zz1112, quantum theory, mechanics,
   laws, everything, entropy, computing, physical transformation, time, arrow,
   DDeutsch
%X "Constructor theory is the theory of which physical transformations can be
   caused to happen and which cannot, and why. Several converging motivations
   for expecting it to be a fundamental branch of physics are discussed. Some
   principles of the theory are proposed and its potential for solving various
   problems and achieving various unifications is explored."
   -- at [<A HREF="http://arxiv.org/abs/1210.7439">arXiv</A>]['12].
   [Also search for: time arrow].

%A M. Schlosshauer
%A J. Kofler
%A A. Zeilinger
%A A snapshot of foundational attitudes toward quantum mechanics
%J arXiv
%P 17
%M JAN
%D 2013
%K TR, arXiv, c2013, c201x, c20xx, zz0814, physics, philosophy, quantum theory,
   mechanics, foundations, information, Qbism, state, states, observer,
   consciousness, reality, local realism, reconstruction, determinism,
   randomness, opinion, opinions, poll, Tegmark, survey
%X "... foundations of q.mechanics themselves remain hotly debated in the
   sci.community, & no consensus on essential Qs has been reached. ... present
   the results of a poll carried out among 33 participants of a conf. on the
   foundations of q.mechanics. The participants completed a questionnaire
   containing 16 multiple-choice Qs probing opinions on q.-foundational issues.
   Participants included physicists, philosophers, & mathematicians. We describe
   our findings, identify commonly held views, & determine strong, medium, &
   weak correlations between the answers. ..."  [via AK.]
   -- 1301.1069@[<A HREF="http://arxiv.org/abs/1301.1069">arXiv</A>]['14].
   [Also search for: Qbism physics].

%A S. Braun
%A et al ...
%A U. Schneider
%T Negative absolute temperature for motional degrees of freedom
%J Science
%V 339
%N 6115
%P 52-55
%M JAN
%D 2013
%K jrnl, Physics, c2013, c201x, c20xx, zz0113, negative, temperature, entropy,
   thermodynamics, Kelvin, absolute zero, bosons, cold, pressure
%X "... negative temperatures - in which high-energy states are more occupied
   than low-energy states - are also possible. ... have been demonstrated in
   localized systems with finite, discrete spectra. Here, we prepared a -ve
   temp. state for motional degrees of freedom. By tailoring the Bose-Hubbard
   Hamiltonian, we created an attractively interacting ensemble of ultracold
   bosons at -ve temp. that is stable against collapse for arbitrary atom
   numbers. The quasimomentum distribution develops sharp peaks at the upper
   band edge, revealing thermal equilibrium & bosonic coherence over several
   lattice sites. Negative temps. imply -ve pressures & open up new parameter
   regimes for cold atoms, enabling fundamentally new many-body states."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1227831">doi:10.1126/science.1227831</A>]['13].

%A A. Almheiri
%A D. Marolf
%A J. Polchinski
%A J. Sully
%T Black holes: Complementarity or firewalls?
%J J. High Energy Phys.
%V 2013
%N 2
%M FEB
%D 2013
%K jrnl, physics, c2013, c201x, c20xx, zz0615, AMPS, black hole, falling into,
   infalling, event horizon, Hawking radiation, information, quantum
%X "We argue that the following three statements cannot all be true: (i) Hawking
   radiation is in a pure state, (ii) the info. carried by the radiation is
   emitted from the region near the horizon, with low energy effective field
   theory valid beyond some microscopic distance from the horizon, & (iii) the
   infalling observer encounters nothing unusual at the horizon. Perhaps the
   most conservative resolution is that the infalling observer burns up at the
   horizon. Alternatives would seem to require novel dynamics that nevertheless
   cause notable violations of semiclassical physics at macroscopic distances
   from the horizon."
   -- [<A HREF="http://dx.doi.org/10.1007/JHEP02(2013)062">doi:10.1007/JHEP02(2013)062</A>]['15].
   (Also see bbc@[<A HREF="http://www.bbc.com/earth/story/20150525-a-black-hole-would-clone-you">25/5/'15</A>]['15].)

%E W. M. Haynes
%T Handbook of Chemistry and Physics
%I CRC press
%P 2650
%D 2013
%K book, text, CRC, c2013, c201x, c20xx, zz0113, science, physics, chemistry,
   tables, formula, formulae, formulas, maths, mathematical,
   Bessel function, modified, kind
%X 94th ed, 2013; hb us$166; uk us isbn:1466571144; uk us isbn13:978-1466571143.
   "... resource consisting of tables of data, its usefulness spans every
   discipline. New tables have been added and others updated, inc. the math.
   tables in Appendix A. ..."
   86th ed, 2005; uk us isbn:0849304865; uk us isbn13:978-0849304866. ... .
   (Also see Bessel-fns@[<A HREF="http://en.wikipedia.org/wiki/Bessel_function">wikip</A>]['13].)

%A E. Jan R. Vesseur
%A T. Coenen
%A H. Caglayan
%A N. Engheta
%A A. Polman
%T Experimental verification of n=0 structures for visible light
%J Phys. Rev. Lett.
%V 110
%N 1
%P e013902
%M JAN
%D 2013
%K jrnl, eJrnl, c2013, c201x, c20xx, zz0113, physics, light, refractive index,
   speed, nanomaterial
%X "... a metal-dielectric nanostructure with an effective refractive index n=0
   in the visible spectral range. Light is excited in the material at deep
   subwavelength resolution by a 30-keV electron beam. From the measured
   spatially and angle-resolved emission patterns, a vanishing phase advance,
   corresponding to an effective eps=0 and n=0, is directly observed at the
   cutoff freq.. The wavelength at which this condn is observed can be tuned
   over the entire visible or near-infrared spectral range by varying the
   waveguide width. This n=0 plasmonic nanostructure may serve as a new building
   block in nanoscale optical integrated circuits & to control spontaneous
   emission as experimentally demonstrated by the strongly enhanced radiative
   optical density of states over the entire n=0 structure."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.110.013902">doi:10.1103/PhysRevLett.110.013902</A>]['13].
   (Refractive index is ~0 (speed near infinite), glass = 1.5, space = 1.0.)

%A D. S. Hajdukovic
%T Can observations inside the Solar System reveal the gravitational properties
   of the quantum vacuum?
%J Astrophysics and Space Sci.
%V 343
%N 2
%P 505-509
%M FEB
%D 2013
%K jrnl, c2013, c201x, c20xx, physics, astronomy, quantum gravity, virtual,
   gravitational dipole, dipoles, precession, perihelion, Eris, Dysnomia
%X "... It was recently proposed that the quantum vacuum contains the virtual
   gravitational dipoles; we argue that this hyp. might be tested within the
   Solar System. ... the quantum vacuum ('enriched' with the grav.dipoles)
   induces a retrograde precession of the perihelion. It is obvious that this
   phenomenon might eventually be revealed by more accurate studies of orbits of
   planets & orbits of the artificial Earth satellites. However, we suggest that
   potentially the best 'laboratory' for the study of the grav. properties of
   the q.vacuum is the recently discovered dwarf planet Eris with its satellite
   named Dysnomia; the distance of nearly 100AU from the Sun makes it the unique
   system in which the precession of the p. of Dysnomia (around Eris) is
   strongly dominated by the quantum vacuum."
   -- [<A HREF="http://dx.doi.org/10.1007/s10509-012-1303-3">doi:10.1007/s10509-012-1303-3</A>]['13].

%A V. D'Ambrosio
%A I. Herbauts
%A E. Amselem
%A E. Nagali
%A M. Bourennane
%A F. Sciarrino
%A A. Cabello
%T Experimental implementation of a Kochen-Specker set of quantum tests
%J Phys. Rev. X
%V 3
%N 1
%P 011012 (10p)
%D 2013
%K jrnl, eJrnl, Physics, c2013, c201x, c20xx, zz0413, quantum theory, mechanics,
   contextuality, context, computer, computing, KS theorem, sets, test, tests
%X "The conflict between classical & quantum physics can be identified through a
   series of yes-no tests on quantum systems, without it being necessary that
   these systems be in special quantum states. Kochen-Specker (KS) sets of
   yes-no tests have this property & provide a quantum-v.-classical advantage
   that is free of the initialization problem that affects some q.computers.
   ... report the first experimental implementation of a complete KS set that
   consists of 18 yes-no tests on 4D quantum sys. & show how to use the KS set
   to obtain a state-indep. quantum advantage. ... demonstrate the unique power
   of this KS set for solving a task while avoiding the problem of state
   initialization. ... done by showing that, for 28 different q.states encoded
   in the orbital-angular-momentum & polarization degrees of freedom of single
   photons, the KS set provides an impossible-to-beat soln. [Then] generate
   maximally contextual quantum correlns by performing compatible seq.
   measurements of the polarization & path of single photons. ... state indep.
   is demo. for 15 different initial states. Max. contextuality & state indep.
   follow from the fact that the seqs. of measurements project any initial
   q.state onto one of the KS set's eigenstates. ... show that KS sets can be
   used for q.-info. processing & q.compn ..."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevX.3.011012">doi:10.1103/PhysRevX.3.011012</A>]['13].
   (Also see [<A HREF="http://dx.doi.org/10.1038/496282a">doi:10.1038/496282a</A>]['13].)

%A C. Monroe
%A J. Kim
%T Scaling the ion trap quantum processor
%J Science
%V 339
%N 6124
%P 1164-1169
%M MAR
%D 2013
%K jrnl, c2013, c201x, c20xx, zz1020, IonQ, quantum computer, computing,
   trap, trapped, ion
%X "Trapped atomic ions are standards for q.info. processing, serving as q.
   memories, hosts of q.gates in q.computers and simulators, and nodes of
   q.comm'n n/wks.  Q.bits ...
   -- [<A HREF="https://doi.org/10.1126/science.1231298">doi:10.1126/science.1231298</A>]['20].
   Also see IonQ@[<A HREF="https://en.wikipedia.org/wiki/IonQ">wikip</A>]['20].
   [Also search for: quantum computer].

%A Z. Merali
%T Astrophysics: Fire in the hole! Will an astronaut who falls into a
   black hole be crushed or burned to a crisp?
%J Nature
%V 496
%N 7443
%P ?-?
%M APR
%D 2013
%K news, views, c2013, c201x, c20xx, zz0413, physics, black hole, holes,
   event horizon, Polchinski
%X "In March 2012, Joseph Polchinski began to contemplate suicide -  at least
   in mathematical form. A string theorist ... pondering what would happen to
   an astronaut who dived into a black hole. Obviously, he would die.
   But how? ... According to the then-accepted account, he wouldn't feel
   anything special at first, even when his fall took him through the black
   hole's event horizon: ... But eventually ... As his plunge carried him
   inexorably downwards, the difference in forces would quickly increase and
   rip him apart, before finally crushing his remnants into the black hole's
   infinitely dense core. ... But Polchinski's calculations ... quantum effects
   would turn the event horizon into a seething maelstrom of particles. Anyone
   who fell into it would hit a wall of fire and be burned to a crisp in an
   instant. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/496020a">doi:10.1038/496020a</A>]['13].

%A J. J. Pla
%A et al ...
%A A. Morello
%T High-fidelity readout and control of a nuclear spin qubit in silicon
%J Nature
%V 496
%P 334-338
%K APR
%D 2013
%K jrnl, Physics, c2013, c201x, c20xx, zz0413, quantum computing, qubit, qubits,
   atom, nucleus, spin
%X "... demonstrate electrical detection & coherent manipulation of a single
   31P nuclear spin qubit with sufficiently high fidelities for fault-tolerant
   quantum computing ... we find a nuclear spin coherence time of 60msec &
   a one-qubit gate control fidelity exceeding 98% ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12011">doi:10.1038/nature12011</A>]['13],
      [<A HREF="https://arxiv.org/abs/1302.0047">arxiv:1302.0047</A>]['24].

%A B. W. Reichardt
%A F. Unger
%A U. Vazirani
%T Classical command of quantum systems
%J Nature
%V 496
%P 456-460
%M APR
%D 2013
%K jrnl, physics, c2013, c201x, c20xx, zz0413, quantum theory, mechanics,
   computing, computer, cryptography, test, Clauser, Horne, Shimony, Holt
%X "... In 1969, Clauser, Horne, Shimony & Holt proposed an experimental test
   that can be passed by a quantum-mechanical sys. but not by a sys. restricted
   to classical physics. Here we extend this test to enable the characterization
   of a large quantum sys.. We describe a scheme that can be used to det. the
   initial state & to classically command the sys. to evolve according to
   desired dynamics. The bipartite sys. is treated as two black boxes, with no
   assumptions about their inner workings except that they obey quantum physics.
   The scheme works even if the sys. is explicitly designed to undermine it; any
   misbehaviour is detected. Among its applicns, our scheme makes it possible to
   test whether a claimed quantum computer is truly quantum. It also advances
   towards a goal of quantum cryptography: namely, the use of 'untrusted'
   devices to establish a shared random key, with security based on the validity
   of quantum physics."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12035">doi:10.1038/nature12035</A>]['13].

%A S. Nimmrichter
%A K. Hornberger
%T Macroscopicity of mechanical quantum superposition states
%J Phys. Rev. Lett.
%V 110
%N 16
%P 160403 (5p)
%M APR
%D 2013
%K Physics, c2013, c201x, c20xx, zz0513, quantum theory, state,
   macroscopic, experiment, Schrodinger's cat
%X "We propose an experimentally accessible, objective measure for the
   macroscopicity of superposition states in mechanical quantum systems. Based
   on the observable consequences of a minimal, macrorealist extension of
   quantum mechanics, it allows one to quantify the degree of macroscopicity
   achieved in different experiments."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.110.160403">doi:10.1103/PhysRevLett.110.160403</A>]['13].

%A A. Aleksandrova
%A V. Borish
%A W. K. Wootters
%T Real-vector-space quantum theory with a universal quantum bit
%J arXiv
%M APR
%D 2013
%K arXiv, TR, c2013, c201x, c20xx, zz0214, quantum theory, physics, bit, uBit,
   u bit, real, complex, numbers, Stueckelberg, effective, standard, information
%X "We explore a model of the world based on real-vector-space quantum theory.
   ... the familiar complex phase appearing in quantum states is replaced by a
   single binary object that we call the ubit, which is not localized & which
   can interact with any object in the world. Ordinary complex-vector-space
   quantum theory can be recovered from this model if we simply impose a certain
   restriction on the sets of allowed measurements & transformations
   (Stueckelberg's rule), but in this paper we try to obtain the std theory, or
   a close approx. to it, without invoking such a restriction. We look
   particularly at the effective theory that applies to a subsystem when the
   ubit is interacting with a much larger environment. In a certain limit it
   turns out that the ubit-environment interaction has the effect of enforcing
   S's rule automatically, & we obtain a one-parameter family of effective
   theories - modifications of std quantum theory - that all satisfy this rule.
   The one param. is the ratio s/omega, where s quantifies the strength of the
   ubit's interaction with the rest of the world & omega is the ubit's rotn
   rate. We find that when this param. is small but not zero, the effective
   theory is similar to std q.theory but is characterized by spontaneous
   decoherence of isolated systems."
   -- 1210.4535@[<A HREF="http://arxiv.org/abs/1210.4535">arXiv</A>]['14].
   (Also see 1301.2018@[<A HREF="http://arxiv.org/abs/1301.2018">arXiv</A>]['14].)

%A S. Aaronson
%T Quantum Computing since Democritus
%I CUP
%P 398
%M APR
%D 2013
%K book, text, CUP, c2013, c201x, c20xx, zz0518, quantum computing, computer
%X 1st ed 2013; pb us$32; uk us isbn:0521199565; uk us isbn13:978-0521199568.
   "... Beginning in antiquity with Democritus, it progresses through logic and
   set theory, computability and complexity theory, quantum computing,
   cryptography, the information content of quantum states and the
   interpretation of quantum mechanics. ..."
   (Also see SA@[<A HREF="https://scottaaronson.com/">www</A>]['18].)
   [Also search for: Aaronson quantum].

%A J. Leslie
%A R. L. Kuhn
%T The Mystery of Existence
%I WileyBlackwell
%P 328
%M APR
%D 2013
%K book, text, c2013, c201x, c20xx, zz0813, science, physics, cosmology,
   existence, why, universe, philosophy
%X 1st ed 2013; hb us$76; uk us isbn:0470673540; uk us isbn13:978-0470673546;
                pb us$20; uk us isbn:0470673559; uk us isbn13:978-0470673553.
   "... includes the thoughts of dozens of luminaries from Plato & Aristotle
   to Aquinas & Leibniz to modern thinkers such as physicists Stephen Hawking
   & Steven Weinberg, philosophers Robert Nozick & Derek Parfit, philosophers
   of religion Alvin Plantinga & Richard Swinburne, & the Dalai Lama. ..."

%A D. Harlow
%A P. Hayden
%T Quantum computation vs. firewalls
%J J. High Energy Phys.
%V 2013
%N ?
%M JUN
%D 2013
%K jrnl, physics, c2013, c201x, c20xx, zz0615, black hole, quantum, information,
   Almheiri, AMPS, thought experiment, event horizon, infalling, nonlocality,
   locality
%X "... discuss q. computational restrictions on the types of thought
   experiments recently used by Almheiri, Marolf, Polchinski, & Sully [AMPS] to
   argue against the smoothness of black hole horizons. We argue that the q.
   compns required to do these experiments would take a time which is
   exponential in the entropy of the black hole under study, & we show that for
   a wide variety of BHs this prevents the experiments from being done. We
   interpret our results as motivating a broader type of nonlocality than is
   usually considered in the context of BH thought experiments, & claim that
   once this type of nonlocality is allowed there may be no need for firewalls.
   Our results do not threaten the unitarity of BH evaporation or the ability of
   advanced civilizations to test it."
   -- [<A HREF="http://dx.doi.org/10.1007/JHEP06(2013)085">doi:10.1007/JHEP06(2013)085</A>]['15].
   [Also search for: black hole event horizon].

%A P. Busch
%A P. Lahti
%A R. F. Werner
%T Proof of Heisenberg's error-disturbance relation
%J arXiv
%M JUN
%D 2013
%K arXiv, physics, c2013, c201x, c20xx, zz0713, quantum theory, measurement,
   Heisenberg, uncertainty principle, Ozawa, weak, Steinberg, Rozema
%X 'While the slogan "no measurement without disturbance" has established itself
   under the name Heisenberg effect in the consciousness of the scientifically
   interested public, a precise statement of this fundamental feature of the
   quantum world has remained elusive, & serious attempts at rigorous
   formulations of it as a consequence of q.theory have led to seemingly
   conflicting preliminary results. Here we show that despite recent claims to
   the contrary [Rozema et al, Phys. Rev. Lett. 109, 100404 (2012)], Heisenberg-
   -type inequalities can be proven that describe a trade-off between the
   precision of a position measurement & the necessary resulting disturbance of
   momentum (& vice versa). More generally, these inequalities are instances of
   an uncertainty relation for the imprecisions of any joint measurement of
   position and momentum.'
   -- 1306.1565@[<A HREF="http://arxiv.org/abs/1306.1565">arXiv</A>]['13].
   Also see news@Nature.[<A HREF="http://dx.doi.org/10.1038/498419a">doi:10.1038/498419a</A>][6/'13].
   [Also search for: weak measurement quantum physics].

%A D. Clery
%T A Piece of the Sun: The Quest for Fusion Energy
%I Overlook
%P 320
%M JUN
%D 2013
%K book, c2013, c201x, c20xx, nuclear, fusion, power, enery, JET, ITER
%X 1st ed 2013; hb us$19; uk us isbn:1468304933; uk us isbn13:978-1468304930.
   "... Skeptics say it will never work but, as A Piece of the Sun makes clear,
   large-scale nuclear fusion is scientifically possible - and has many
   advantages over other options. Fusion is clean, green and virtually limitless
   and C. argues passionately and eloquently that the only thing keeping us from
   proving its worth is our politicians' shortsightedness. The world energy
   industry is worth trillions of dollars, divert just a tiny fraction of that
   into researching fusion and we would soon know if it is workable."
   Also see JET@[<A HREF="https://en.wikipedia.org/wiki/Joint_European_Torus">wikip</A>]['24].

%A R. Pohl
%A et al
%T The size of the proton
%J Nature
%V 466
%N 7303
%P 213-216
%M JUN
%D 2013
%K jrnl, c2013, c201x, c20xx, science, physics, particle, proton, size
%X "... The root-mean-square charge radius, rp, has been determined with an
   accuracy of 2% (at best) ... we find rp = 0.84184(67)fm, which differs by
   5.0 std dev. from the CODATA value of 0.8768(69)fm. ... implies that either
   the Rydberg constant has to be shifted by -110kHz/c (4.9 s.d.), or the
   calculations of the QED effects in atomic hydrogen or muonic hydrogen atoms
   are insufficient."
   -- [<A HREF="http://dx.doi.org/10.1038/nature09250">doi:10.1038/nature09250</A>]['13].

%A G. Heinze
%A C. Hubrich
%A T. Halfmann
%T Stopped light and image storage by electromagnetically induced transparency
   up to the regime of one minute
%J Phys. Rev. Lett.
%V 111
%N 3
%P (5p) 033601
%M JUL
%D 2013
%K jrnl, Physics, EIT, c2013, c201x, c20xx, zz0713, light, speed, halted, slow,
   slowed, stopped, stop, stopping
%X "The maximal storage durn is an important benchmark for memories. In
   quantized media, storage times are typically ltd due to stochastic
   interactions with the environment. Also, optical memories based on
   electromagnetically induced transparency (EIT) suffer strongly from such
   decoherent effects.  ...  present a self-learning evolutionary strategy to
   efficiently drive an EIT-based memory. By combination of the self-learning
   loop for optimized optical preparation & improved dynamical decoupling, we
   extend EIT storage times in a doped solid above 40s. [&] demonstrate storage
   of images by EIT for 1min. ... set a new benchmark for EIT-based memories.
   The concepts are also applicable to other storage protocols."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.111.033601">doi:10.1103/PhysRevLett.111.033601</A>]['13].

%A D. Goldberg
%T The Universe in the Rearview Mirror: How Hidden Symmetries Shape Reality
%I DuttonAdult
%P 336
%M JUL
%D 2013
%K book, c2013, c301x, c20xx, zz0813, science, physics, symmetry, conservation,
   Emmy Noether, maths, STEM, women
%X 1st ed 2013; hb us$19; uk us isbn:0525953663; uk us isbn13:978-0525953661.
   "... an unsung genius and Nazi holocaust escapee named Emmy Noether - the
   other Einstein. She was unrecognized, even unpaid, throughout most of her
   career simply because she was a woman. Nevertheless, her theorem relating
   conservation laws to symmetries is widely regarded to be as important as
   Einstein's notion of the speed of light. Einstein himself said she was 'the
   most significant creative mathematical genius thus far produced since the
   higher education of women began.' ..."

%A Z. Merali
%T Theoretical physics: The origins of space and time
%J Nature
%V 500
%N 7464
%P 516-519
%M AUG
%D 2013
%K news, views, c2013, c201x, c20xx, zz0813, science, physics, cosmology,
   space, time, origin, relativity, quantum theory, quanta, information,
   gravity, black hole, thermodynamics, loop, holographic principle, theories
%X "Many researchers believe that physics will not be complete until it can
   explain not just the behaviour of space and time, but where these entities
   come from. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/500516a">doi:10.1038/500516a</A>]['13].

%A L. Smolin
%T Time Reborn: From the Crisis in Physics to the Future of the Universe
%I HoughtonMifflinHarcourt
%P 352
%D 2013
%K book, text, c2013, c201x, c20xx, zz0913, time, arrow,
   relativity, physics, science, quantum, cosmology
%X 1st ed 2013; hb us$20; asin:0547511728; uk us isbn13:978-0547511726.
   (Review@[<A HREF="http://dx.doi.org/10.1126/science.1239717">www</A>]['13].)
   [Also search for: time arrow].

%A A. R. Liddle
%A M. Cortes
%T Cosmic microwave background anomalies in an open universe
%J Phys. Rev. Lett.
%V 111
%N 11
%M SEP
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0913, physics, cosmology, universe, origin,
   CMB, anomaly, WMAP, open, curvature, inflation, big bang, Erickcek, theory
%X "We argue that the observed large-scale cosmic microwave anomalies,
   discovered by WMAP & confirmed by the Planck satellite, are most naturally
   explained in the context of a marginally open universe. ..."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.111.111302">doi:10.1103/PhysRevLett.111.111302</A>]['13].

%A C. Rovelli
%T Relative information at the foundation of physics
%M OCT
%D 2013
%O in "It from Bit or Bit from It? On Physics and information", Springer,
      the Frontiers Collection, 2015
%K physics, c2013, c201x, c20xx, zz1022, relative information, entropy, quantum,
   thermodynamics, essay, philosophy
%X "Shannon's notion of relative info. between two physical systems can function
   as foundation for statistical mechanics & q.mechanics, without referring to
   subjectivism or idealism. It can also represent a key missing elt in the
   foundation of the naturalistic picture of the world, providing the
   conceptual tool for dealing with its apparent limitations. I comment on the
   relation between these ideas & Democritus."
   -- [<A HREF="https://doi.org/10.1007/978-3-319-12946-4_7">doi:10.1007/978-3-319-12946-4_7</A>]['22].
   Also see CR@[<A HREF="https://en.wikipedia.org/wiki/Carlo_Rovelli">wikip</A>]['22].
   [Also search for: quantum information].

%A B. K. Tippett
%A D. Tsang
%T The blue box white paper
%J arXiv
%M OCT
%D 2013
%K arXiv, c2013, c201x, c20xx, zz1113, Tardis, Dr Who, Doctor, police box,
   time travel, space, relativity, SciFi, fiction, UK, TV, worm hole, wormhole
%X "This white paper is an explanation of Ben & Dave's TARDIS time machine,
   written for laypeople who are interested in time travel, but have no
   technical knowledge of Einstein's Theory of General Relativity. ..."
   -- 1310.7983@[<A HREF="http://arxiv.org/abs/1310.7983">arXiv</A>][29/10/2013].

%A B. Vlastakis
%A et al ...
%A R. J. Schoelkopf
%T Deterministically encoding quantum information using 100-photon Schrodinger
   cat states
%J Science
%V 342
%N 6158
%P 607-610
%M NOV
%D 2013
%K jrnl, physics, c2013, c201x, c20xx, zz1113, quantum theory, mechanics,
   information, memory, computing, qubit, qubits, Schrodinger cat, state
%X "In contrast to a single quantum bit, an oscillator can store multiple
   excitations & coherences provided one has the ability to generate &
   manipulate complex multiphoton states. We demonstrate multiphoton control by
   using a superconducting transmon qubit coupled to a waveguide cavity
   resonator with a highly ideal off-resonant coupling. This dispersive
   interaction is much greater than decoherence rates & higher-order
   nonlinearities to allow simultaneous manipulation of hundreds of photons.
   With a tool set of conditional qubit-photon logic, we mapped an arbitrary
   qubit state to a superposition of coherent states, known as a 'cat state.'
   We created cat states as large as 111 photons & extended this protocol to
   create superpositions of up to four coherent states. This control creates a
   powerful interface between discrete & continuous variable quantum computation
   & could enable applications in metrology & quantum information processing."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1243289">doi:10.1126/science.1243289</A>]['13].

%A C. Stoughton
%T Quantum geometry and the Fermilab holometer
%J Time and Matter Conf.
%W Venice
%P ?-?
%D 2013
%K conf, c2013, c201x, c20xx, zz0914, physics, quantum, mechanics, information,
   space, uncertainty, Hogan, Fermilab E-990, E990, holometer, hologram,
   holographic noise, fluctuations, principle
%X "Recent ... proposes a quantum aspect of geometry with posn operators
   obeying the commutator [X_i, X_j] = i l'_p e_ijk X_k. This leads to an
   uncertainty in transverse distance after propagating a distance D of
   < x_bottom **2 > - L l'_p, with l'_p ~ the Planck length. ..."
   -- pdf@[<A HREF="http://holometer.fnal.gov/tam2013-proceedings-stoughton.pdf">fnal.gov</A>]['14],
  & holometer@[<A HREF="http://holometer.fnal.gov/">fnal</A>]['14].

%A E. Moreva
%A et al
%T Time from quantum entanglement: an experimental illustration
%J arXiv
%M OCT
%D 2013
%K TR, c2013, c201x, c20xx, zz0624, physics, arrow, time, quantum, emergent,
   entanglement, experiment
%X "...to provide an insight into how this phenomenon [time emergent] can occur,
   ... an experiment that illustrates Page and Wootters' mechanism of "static"
   time, & Gambini et al. subsequent refinements. A static, entangled state
   between a clock system & the rest of the universe is perceived as evolving by
   internal observers that test the correlations between the two subsystems. We
   implement this mechanism using an entangled state of the polarization of two
   photons, one of which is used as a clock to gauge the evolution of the 2nd:
   an "internal" observer that becomes correlated with the clock photon sees the
   other system evolve, while an "external" observer that only observes global
   properties of the two photons can prove it is static."
   -- [<A HREF="https://arxiv.org/abs/1310.4691">arxiv:1310.4691</A>]['24].
   Also see time@[<A HREF="https://en.wikipedia.org/wiki/Problem_of_time">wikip</A>]['24].
   [Also search for: arrow time].

%A G. Smith
%A J. A. Smolin
%T An exactly solvable model for quantum communications
%J Nature
%V 504
%N 7479
%P 263-267
%M DEC
%D 2013
%K jrnl, c2013, c201x, c20xx, zz1213, quantum, communication, computing,
   information, noise, noisy, channel, rate, capacity
%X "... Accurate models of physical communication devices must include quantum
   effects, but these typically make the theory intractable. [so] communication
   capacities - the max. possible rates of data transmission - are not known,
   even for transmission between two users connected by an electromagnetic
   waveguide with Gaussian noise. ... present an exactly solvable model of
   communication with a fully quantum electromagnetic field. This gives explicit
   expressions for all point-to-point capacities of noisy quantum channels ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12669">doi:10.1038/nature12669</A>]['13].
   [Also search for: quantum communication].

%A M. W. Ray
%A E. Ruokokoski
%A S. Kandel
%A M. Mottonen
%A D. S. Hall
%T Observation of Dirac monopoles in a synthetic magnetic field
%J Nature
%V 505
%N 7485
%M JAN
%D 2014
%K jrnl, physics, c2014, c201x, c20xx, zz0814, Dirac, magnetic monopole,
   quantum
%X "... Dirac's 1931 development of a theory of monopoles consistent with both
   q.mechanics & the gauge invariance of the electromag. field ... Here we
   demonstrate the controlled creation of D. monopoles in the synthetic mag.
   field produced by a spinor Bose-Einstein condensate. Monopoles are
   identified, in both experiments & matching numerical simulations, at the
   termini of vortex lines within the condensate. By directly imaging such a
   vortex line, the presence of a m. may be discerned from the experimental data
   alone. These real-space images provide conclusive & long-awaited exp.
   evidence of the existence of D.ms.. Our result provides an unprecedented
   opportunity to observe & manipulate these q.mechanical entities in a
   controlled environment."
   -- [<A HREF="http://dx.doi.org/10.1038/nature12954">doi:10.1038/nature12954</A>]['14].
   (Also see MM@[<A HREF="http://en.wikipedia.org/wiki/Magnetic_monopole">wikip</A>]['14], and
   discussion @ CERN [<A HREF="http://home.web.cern.ch/cern-people/opinion/2014/02/observation-authentic-make-believe-monopoles">5/2</A>][2014].)
   [Also search for: magnetic monopole].

%A P. G. Ferreira
%T The Perfect Theory: A Century of Geniuses and the Battle over
   General Relativity
%I HoughtonMifflinHarcourt
%P 304
%M FEB
%D 2014
%K book, text, physics, c2014, c201x, c20xx, zz0814, general relativity,
   quantum, cosmology, theory, test, tests
%X 1st ed 2014; hb us$21; uk us isbn:0547554893; uk us isbn13:978-0547554891.
   "... Though eclipsed for decades by q.mechanics, Einstein's theory -
   crystallized in 10 elegant field equns - ultimately enthralls a phalanx of
   conceptual pioneers. ... or testing the limits of string theory, these
   pioneers take Einstein's formulas as their sure guide. Predictably, strong-
   -willed scientists clash over their reading of these fiendishly entangled
   formulas: Eddington v. Chandrasekhar over black holes, Hawking v.
   Bekenstein over cosmic entropy, Oppenheimer v. Wheeler over stellar-
   -collapse singularities, Godel v. Robertson over rotating space-time. ..."

%A O. A. Hurricane
%A et al ...
%A R. Tommasini
%T Fuel gain exceeding unity in an inertially confined fusion implosion
%J Nature
%V 506
%N 7488
%P 343-348
%M FEB
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0214, inertial, laser, fusion, power, nuclear,
   energy, hohlraum, gain, US NIF
%X "... report the achievement of fusion fuel gains exceeding unity on the
   US National Ignition Facility using a 'high-foot' implosion method, which is
   a manipulation of the laser pulse shape in a way that reduces instability in
   the implosion. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature13008">doi:10.1038/nature13008</A>]['14].
   (BUT "the fuel gain ... less than 1% of the total energy entering the system"
    -- New_Sci.)
   [Also search for: nuclear fusion power].

%A N. D. Mermin
%T Physics: QBism puts the scientist back into science
%J Nature
%V 507
%N 7493
%P ?-?
%M MAR
%D 2014
%K news, views, c2014, c201x, c20xx, zz0414, physics, quantum theory,
   information, wave function, Qbism, Bohr, observer, now
%X [<A HREF="http://dx.doi.org/10.1038/507421a">doi:10.1038/507421a</A>]['14].
   [Also search for: Qbism physics].

%A C. Brukner
%T Quantum causality
%J Nature Physics
%V 10
%N 4
%P 259-263
%M APR
%D 2014
%K jrnl, physics, c2014, c201x, c20xx, zz0815, quantum theory, mechanics,
   uncertainty, information, cause, effect, causality
%X "Traditionally, q.theory assumes the existence of a fixed b/g causal struct..
   But if the laws of q.mechanics are applied to the causal relations, then one
   could imagine situations in which the causal order of events is not always
   fixed, but is subject to quantum uncertainty. Such indefinite causal struct.
   could make new q.infomation processing tasks possible & provide
   methodological tools in q.theories of gravity. Here, I review recent
   theoretical progress in this emerging area."
   -- [<A HREF="http://dx.doi.org/10.1038/nphys2930">doi:10.1038/nphys2930</A>]['15],
   auth@[<A HREF="http://www.quantumfoundations.org/caslav-brukner.html">www</A>]['15] and
      [<A HREF="https://scholar.google.com.au/citations?user=YVhdrsoAAAAJ">sch'l'r</A>]['15].

%A L. Mlodinow
%A T. A. Brun
%T Relation between the psychological and thermodynamic arrows of time
%J Phys. Rev. E
%V 89
%N 052102
%M MAY
%D 2014
%K jrnl, physics, c2014, c201x, c20xx, zz0716, quantum mechanics, time arrow,
   psychological, thermodynamics, past, present, future, memory, system
%X "... lay out an argument that generically the psychological arrow of time
   should align with the thermodynamic arrow of time where that arrow is well
   defined. [It] applies to any physical sys. that can act as a memory, in the
   sense of preserving a record of the state of some other sys.. This result
   follows from two principles: the robustness of the thermodynamic arrow of
   time to small perturbations in the state, & the principle that a memory
   should not have to be fine-tuned to match the state of the sys. being
   recorded. This argument applies even if the memory system itself is
   completely reversible & nondissipative. We make the argument with a
   paradigmatic system, & then formulate it more broadly for any sys. that can
   be considered a memory. We illustrate these principles for a few other e.g.
   systems & compare our criteria to earlier treatments of this problem."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevE.89.052102">doi:10.1103/PhysRevE.89.052102</A>]['16].
   (Also see the bbc [<A HREF="http://www.bbc.com/earth/story/20160708-the-past-is-not-set-in-stone-so-we-may-be-able-to-change-it">12/7/2016</A>].)
   [Also search for: physics time arrow].

%A D. Deutsch
%A C. Marletto
%T Constructor theory of information
%J arXiv
%M MAY
%D 2014
%K TR, c2014, c201x, c20xx, zz0421, quantum physics, classical, information,
   theory, qubits
%X "We present a theory of information expressed solely in terms of which
   transformations of physical systems are possible & which are impossible -
   i.e. in constructor-theoretic terms. Although it includes conjectured laws of
   physics that are directly about info., indep. of the details of particular
   physical instantiations, it does not regard info. as an a priori
   mathematical or logical concept, but as something whose nature & properties
   are determined by the laws of physics alone. It does not suffer from the
   circularity at the foundations of existing info.theory (namely that info. &
   distinguishability are each defined in terms of the other). It explains the
   relationship between classical & quantum info., & reveals the single,
   constructor-theoretic property underlying the most distinctive phenomena
   assoc. with the latter, inc. the lack of in-principle distinguishability of
   some states, the impossibility of cloning, the existence of pairs of
   variables that cannot simultaneously have sharp values, the fact that
   measurement processes can be both deterministic & unpredictable, the
   irreducible perturbation caused by measurement, & entanglement (locally
   inaccessible information).
   -- 1405.5563@[<A HREF="https://arxiv.org/abs/1405.5563">arXiv</A>]['21].
   Also see [<A HREF="https://www.edge.org/memberbio/chiara_marletto">www</A>]['21] & [<A HREF="https://www.wolfson.ox.ac.uk/person/chiara-marletto">www</A>]['21].
   [Also search for: Marletto].

%A C. Marletto
%T Constructor theory of life
%J arXiv
%M JUL
%D 2014
%K TR, c2014, c201x, c20xx, zz0421, life, reproduction, replication, replicator,
   natural selection, Darwinian, evolution
%X "Neo-Darwinian evol. theory explains how the appearance of purposive design
   in the sophisticated adaptations of living organisms can have come about
   without their intentionally being designed. The explanation relies crucially
   on the possibility of certain physical processes: mainly, gene replication &
   natural selection. ... I show that for those processes to be possible without
   the design of biological adaptations being encoded in the laws of physics,
   those laws must have certain other properties. ..."
   -- 1407.0681@[<A HREF="https://arxiv.org/abs/1407.0681">arXiv</A>]['21].
   [Also search for: Marletto constructor]

%A P. Komar
%A E. M. Kessler
%A M. Bishof
%A L. Jiang
%A A. S. Sorensen
%A J. Ye
%A M. D. Lukin
%T A quantum network of clocks
%J Nature Physics
%V ?
%P ?-?
%M JUN
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0614, science, physics, atomic clock, clocks,
   world clock, standard, time, measurement,  nonlocal, quantum entanglement
%X "... By combining precision metrology & quantum n/ws, we propose a q.,
   cooperative protocol for operating a n/w of geographically remote optical
   atomic clocks. Using nonlocal entangled states, we demonstrate an optimal
   utilization of global resources, & show that such a n/w can be operated near
   the fundamental precision limit set by quantum theory. [&] the internal
   structure of the n/w, combined with q. communication techniques, guarantees
   security both from internal & external threats. Realization of such a global
   q.n/w of clocks may allow construction of a real-time single international
   time scale (world clock) with unprecedented stability & accuracy."
   -- [<A HREF="http://dx.doi.org/10.1038/nphys3000">doi:10.1038/nphys3000</A>]['14].

%A E. Weisz
%A H. K. Choi
%A I. Sivan
%A M. Heiblum
%A Y. Gefen
%A D. Mahalu
%A V. Umansky
%T An electronic quantum eraser
%J Science
%V 344
%N 6190
%P 1363-1366
%M JUN
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0614, physics, quantum mechanics, information,
   erase, erased, electron, which path, detector, Schrodingers cat
%X "The quantum eraser is a device that illustrates the q. principle of
   complementarity & shows how a dephased system can regain its lost q. behavior
   by erasing the 'which-path' info. already obtained about it. Thus far, q.
   erasers were constructed predominantly in optical systems. ... present a
   realization of a q. eraser in a mesoscopic electronic device. The use of
   interacting electrons, instead of noninteracting photons, allows control over
   the extracted info. & a smooth variation of the degree of q. erasure. The
   demonstrated sys. can serve as a 1st step toward a variety of more complex
   setups."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1248459">doi:10.1126/science.1248459</A>]['14].
   (Also see [<A HREF="http://www.sciencemag.org/content/344/6190/1344.summary">comment</A>].)

%A G. Vallone
%A D. Bacco
%A D. Dequal
%A S. Gaiarin
%A V. Luceri
%A G. Bianco
%A P. Villoresi
%T Experimental satellite quantum communications
%J arXiv
%M JUN
%D 2014
%K TR, arXiv, c2014, c201x, c20xx, zz0714, communication, secure,
   cryptography, qubits, quantum key distribution, QKD
%X "... demonstrated the faithful transmission of qubits from space to ground by
   exploiting satellite corner cube retroreflectors acting as transmitter in
   orbit, obtaining a low error rate suitable for QKD. We also propose a two-way
   QKD protocol exploiting modulated retroreflectors that necessitates a minimal
   payload on satellite, thus facilitating the expansion of Space Quantum
   Communications."
   -- 1406.4051@[<A HREF="http://arxiv.org/abs/1406.4051">arXiv</A>]['14].
   [Also search for: quantum communication].

%A A. Cho
%T Breakthrough lost in coin toss?
%J Science
%V 346
%N 6205
%P 22-23
%M OCT
%D 2014
%K physics, c2014, c201x, c20xx, zz1014, quantum mechanics, weak, measurement
%X 'For 26 years, physicists have argued over an unorthodox q.measurement
   technique that seems to circumvent one of the central tenets of q.mechanics.
   "Anomalous weak values" bend the rule that you can't measure a q. particle
   without disturbing it, devotees say, & provide deep insights into q. reality.
   Skeptics counter that the whole enterprise is just standard q.mechanics
   misinterpreted. Now, two theorists say that anomalous weak values aren't even
   a q. phenomenon. To prove it, they propose a thought experiment in which two
   people, Alice & Bob, produce an anomalous weak value classically, by
   exchanging a coin. The theorists argue that because anomalous weak values
   aren't inherently quantum mechanical they offer no novel insight into the
   quantum realm. The inventors of the technique dismiss the analysis.'
   -- [<A HREF="http://dx.doi.org/10.1126/science.346.6205.22">doi:10.1126/science.346.6205.22</A>]['14].
   [Also search for: weak measurement quantum physics].

%A J. Barbour
%A T. Koslowski
%A F. Mercati
%T Identification of a gravitational arrow of time
%J Phys. Rev. Lett.
%V 113
%N 181101
%M OCT
%D 2014
%K jrnl, eJrnl, Physics, c2014, c201x, c20xx, zz1214, the arrow of time,
   forwards, backwards, direction, entropy, complexity, universe, gravity,
   n-body, nBody, laws, thermodynamics, past, future, symmetry
%X "It is widely believed that special initial condns must be imposed on any
   time-symmetric law if its solns are to exhibit behavior of any kind that
   defines an 'arrow of time.' We show that this is not so. The simplest
   nontrivial time-symmetric law that can be used to model a dynamically closed
   universe is the Newtonian N-body problem with vanishing total energy &
   angular momentum. Because of special properties of this system (likely to be
   shared by any law of the Universe), its typical solns all divide at a
   uniquely defined point into two halves. In each, a well-defined measure of
   shape complexity fluctuates but grows irreversibly between rising bounds from
   that point. Structures that store dynamical info. are created as the
   complexity grows & act as 'records.' Each soln can be viewed as having a
   single past & two distinct futures emerging from it. Any internal observer
   must be in one half of the solns & will only be aware of the records of one
   branch & deduce a unique past & future direction from inspection of the
   available records.
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.113.181101">doi:10.1103/PhysRevLett.113.181101</A>]['14].
   (Also see [<A HREF="http://dx.doi.org/10.1103/Physics.7.111">comment</A>]['15].)
   * [Also search for: time arrow] * .

%A J. M. Lukens
%A A. J. Metcalf
%A D. E. Leaird
%A A. M. Weiner
%T Temporal cloaking for data suppression and retrieval
%J Optica
%V 1
%N 6
%P 372-375
%M DEC
%D 2014
%K jrnl, eJrnl, c2014, c201x, c20xx, zz1214, optics, optical, communication,
   temporal, cloak, hide, secret, time cloaking, data, telecommunications,
   light, channel
%X "Recent research on time cloaking has revealed a fascinating approach to hide
   temporal events from an interrogating optical field ...  we report a temporal
   cloak with the new capability not only to hide optical data, but also to
   concurrently transmit it along another wavelength channel for subsequent
   readout, masking the info. from one observer while directing it to another.
   [&] the cloak succeeds in passing modulated data unscathed through a
   scrambling event, providing a new form of tampering resistance. ..."
   -- [<A HREF="http://dx.doi.org/10.1364/OPTICA.1.000372">doi:10.1364/OPTICA.1.000372</A>]['14].

%A C. Fields
%T Effective dark energy from decoherence
%J arXiv
%M FEB
%D 2015
%K TR, c2015, c201x, c20xx, zz1219, physics, cosmology, dark energy, universe,
   bit, bits, energy, information, cosmological constant, decoherence, Landauer,
   controversial
%X "... observers obtain pointer-state information about quantum systems by
   interacting with a local sample of the surrounding environment, e.g. a local
   sample of the ambient photon field. Because the environment encodes such
   pointer state information uniformly & hence redundantly throughout its entire
   volume, the information is equally available to all observers regardless of
   their location. This framework is applied to the observation of stellar
   center-of-mass positions, which are assumed to be encoded by the ambient
   photon field in a way that is uniformly accessible to all possible observers.
   Assuming Landauer's Principle, constructing such environmental encodings
   requires (ln2)kT per encoded bit. For the observed 1024 stars & a uniform
   binary encoding of center-of-mass positions into voxels with a linear
   dimension of 5km, the free energy required at the current CMB temperature
   T = 2.7K is ~2.5 10^{â27} kg m^{â3}, strikingly close to the observed value
   of Omega_{Dealta rho_c}. Decreasing the voxel size to (lP)^3 results in a
   free energy requirement 10^{117} times larger."
   -- 1502.03424@[<A HREF="https://arxiv.org/abs/1502.03424">arXiv</A>]['19].
   (Also see [<A HREF="https://medium.com/the-physics-arxiv-blog/how-the-nature-of-information-could-resolve-one-of-the-great-paradoxes-of-cosmology-8c16fc714756">www</A>][18/2/'15].)

%A D. Giovannini
%A et al
%A M. J. Padgett
%T Spatially structured photons that travel in free space slower than the speed of light
%J Science
%V 347
%N 6224
%P 857-860
%M FEB
%D 2015
%K jrnl, physics, c2015, c201x, c20xx, zz0215, speed of light, particle, wave,
   plane waves, beam, vacuum, slow
%X "... light beams have finite transverse size, which leads to a modification
   of their wave vectors resulting in a change to their phase & group
   velocities. We study the group velocity of single photons by measuring a
   change in their arrival time that results from changing the beam's transverse
   spatial structure. Using time-correlated photon pairs, we show a reduction in
   the group velocity of photons in both a Bessel beam & photons in a focused
   Gaussian beam. In both cases, the delay is several micrometers over a
   propagation distance of ~1 meter. Our work highlights that, even in free
   space, the invariance of the speed of light only applies to plane waves."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaa3035">doi:10.1126/science.aaa3035</A>]['15].

%A A. Ananthaswamy
%T Purifying Physics: The Quest to Explain Why the "Quantum" Exists
%J FQXI
%M FEB
%D 2015
%K views, TR, physics, c2015, c201x, c20xx, zz1217, quantum theory, Chiribella,
   D'Ariano, dAriano, Perinotti, pure, mixed, purification principle,
   space time, arrow, irreversible, reversible
%X "... In 2010, Chiribella, D'Ariano and Perinotti identified a more
   commonplace set of alternative postulates [for Q.theory] from which all other
   physical properties - both classical and quantum - could be derived
   (Phys. Rev. A 84, 012311 (2011)). ... should be easy to grasp. For instance,
   their first postulate pertains to causality and says that the outcome of an
   experiment should not depend on operations made after the experiment has been
   completed ... Their five axioms are valid both for classical and q.systems.
   It is the sixth postulate, dubbed 'the purification principle,' which lies at
   the heart of the team's alternative take on q.theory. It marks out why
   particles behave so differently at the subatomic level compared with objects
   we see around us. ... [if] two entangled particles are taken together, they
   are said to be in a pure state - that means that you know all there is to
   know about the system. But if you study the evolution of any one of the
   entangled pair in isolation, you are said to be dealing with a particle in a
   mixed state; you'd never know all there is to know about that one particle
   until you include information about its partner. ..."
   -- 199@[<A HREF="http://fqxi.org/community/articles/display/199">fqxi</A>]['17]
   (& [<A HREF="https://plus.maths.org/content/purifying-physics-quest-explain-why-quantum-exists">www</A>]['17]).

%A M. Ringbauer
%A at el ...
%A A. Fedrizzi
%T Measurements on the reality of the wavefunction
%J Nature Physics
%V 11
%N 3
%P 249-254
%M FEB
%D 2015
%K jrnl, physics, c2015, c201x, c20xx, zz0515, quantum theory, wave function,
   waveFunction, reality, weirdness, nogo theorem, Copenhagen interpretation
%X "... it is still unclear what the wavefunction actually is: does it merely
   represent our limited knowledge of a system, or is it in direct corr. to
   reality? Recent no-go theorems argued that if there was any objective reality
   then the w.fn must be real. However, that conclusion relied on debatable
   assumptions. Here we follow a different approach without these assumptions &
   experimentally bound the degree to which knowledge interpretations can
   explain quantum phenomena. Using single photons, we find that no knowledge
   interp. can fully explain the limited distinguishability of non-orthogonal
   quantum states in three & four dimensions. Assuming that a notion of
   objective reality exists, our results thus strengthen the view that the
   w.fn should directly correspond to this reality."
   -- [<A HREF="http://dx.doi.org/10.1038/nphys3233">doi:10.1038/nphys3233</A>]['15].
   Also see news@[<A HREF="http://dx.doi.org/10.1038/521278a">20/5/15</A>].
   [Also search for: quantum waveFunction reality].

%A T. E. Gureyev
%A F. de Hoog
%A Ya I. Nesterets
%A D. M. Paganin
%T On the noise-resolution duality, Heisenberg uncertainty and Shannon's
   information
%J arXiv
%M MAR
%D 2015
%K TR, c2015, c201x, c20xx, quantum, physics, mechanics, noise, MonashU, arXiv,
   imaging, images
%X "Several variations of the Heisenberg uncertainty inequality are derived on
   the basis of 'noise-resolution duality' recently proposed by the authors. The
   same approach leads to a related inequality that provides an upper limit for
   the info. capacity of imaging systems in terms of the # of imaging quanta
   (particles) used in the experiment. These results can be useful in the
   context of biomedical imaging constrained by the radiation dose delivered to
   the sample, or in imaging (e.g. astronomical) problems under 'low light'
   conditions."
   -- 1503.04367@[<A HREF="http://arxiv.org/abs/1503.04367">arXiv</A>]['15].
   (auth4 is @ monashU, 2015.)

%A B. Heim
%A T. F. Ronnow
%A S. V. Isakov
%A M. Troyer
%T Quantum versus classical annealing of Ising spin glasses
%J Science
%V 348
%N 6231
%P 215-217
%M APR
%D 2015
%K jrnl, physics, c2015, c201x, c20xx, zz0415, quantum mechanics, annealing,
   QA, QMC, speedup, classical, Monte Carlo, Ising spin glass
%X "Quantum annealers use q.fluctuations to escape local minima & find
   low-energy configurations of a physical system. Strong evidence for
   superiority of q.annealing (QA) has come from comparing QA implemented
   through q. Monte Carlo (QMC) simulations to classical annealing. ...
   revisit the question of when q. speedup may be expected. Although a better
   scaling is seen for QA in 2D Ising spin glasses, this advantage is due to
   time discretization artifacts & measurements that are not possible on a
   physical q. annealer. Simulations in the physically relevant continuous time
   limit, on the other hand, do not show superiority. Our results imply that
   care must be taken when using QMC simulations to assess the potential for
   q. speedup."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaa4170">doi:10.1126/science.aaa4170</A>]['15]   (auths @ ethz.ch, and #3 @ google).

%A J.âY. Haw
%A et al
%T Maximization of extractable randomness in a quantum random-number generator
%J Phys. Rev. Applied
%V 3
%N #054004
%M MAY
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0323, quantum RNG, QRNG
%X "... we propose & experimentally demonstrate an approach that produces
   side-information-indep. randomness that is quantified by min-entropy
   conditioned on this classical noise. We present a method for maximizing the
   conditional min entropy of the # seq. generated from a given
   quantum-to-classical-noise ratio. The detected photocurrent in our experiment
   is shown to have a real-time [RNG] rate of 14â(Mbit/s)/MHz. ..."
   -- [<A HREF="https://doi.org/10.1103/PhysRevApplied.3.054004">doi:10.1103/PhysRevApplied.3.054004</A>]['23].
   (Also see QRNG@[<A HREF="https://qrng.anu.edu.au/">ANU</A>]['23].)
   [Also search for: quantum RNG].

%A A. G. Manning
%A R. I. Khakimov
%A R. G. Dall
%A A. G. Truscott
%T Wheeler's delayed-choice gedanken experiment with a single atom
%J Nature Physics
%V 11
%P 539-542
%M MAY
%D 2015
%K physics, jrnl, c2015, c201x, c20xx, zz0716, quantum mechanics, weirdness,
   entanglement, atom, particle, wave, Wheeler, delayed choice, Bell, Bell's,
   double slit, interferometer
%X "The wave-particle dual nature of light & matter & the fact that the choice
   of measurement determines which one of these two seemingly incompatible
   behaviours we observe are e.g.s of the counterintuitive features of
   q.mechanics. They are illustrated by Wheeler's famous 'delayed-choice'
   experiment, recently demonstrated in a single-photon experiment. Here, we use
   a single ultracold metastable helium atom in a Mach-Zehnder interferometer to
   create an atomic analogue of Wheeler's original proposal. Our experiment
   confirms Bohr's view that it does not make sense to ascribe the wave or
   particle behaviour to a massive particle before the measurement takes place.
   This result is encouraging for current work towards entanglement & Bell's
   theorem tests in macroscopic systems of massive particles."
   -- [<A HREF="http://dx.doi.org/10.1038/nphys3343">doi:10.1038/nphys3343</A>]['16].
   [Also search for: physics quantum delayed choice].

%A J. Carolan
%A et al ...
%A A. Laing
%T Universal linear optics
%J Science
%V 349
%N 6249
%P 711-716
%M AUG
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0815, physics, quantum, mechanics, optics,
   optical, photon, photonics, computing, linear, LPU, circuit, wave guide,
   gate, computing
%X "... demo. a single reprogrammable optical circuit that is sufficient to
   implement all poss. linear optical protocols up to the size of that circuit.
   Our six-mode universal system consists of a cascade of 15 Mach-Zehnder
   interferometers with 30 thermo-optic phase shifters integrated into a single
   photonic chip that is electrically & optically interfaced for arbitrary
   setting of all phase shifters, input of up to six photons, & their
   measurement with a 12-single-photon detector system. We programmed this
   system to implement heralded q.logic & entangling gates, boson sampling with
   verification tests, & six-dimensional complex Hadamards. We implemented 100
   Haar random unitaries with an avg fidelity of 0.999+/-0.001. ... can be
   rapidly reprogrammed to implement these & any other linear optical protocol,
   pointing the way to applicns across fundamental sci. & q.technologies."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aab3642">doi:10.1126/science.aab3642</A>]['15].

%A A. Berera
%A R. V. Buniy
%A T. W. Kephart
%A H. Pas
%A J. G. Rosa
%T Knotty inflation and the dimensionality of spacetime
%J arXiv
%M AUG
%D 2015
%K TR, physics, c2015, c201x, c20xx, zz0915, space time, cosmology, dimension,
   dimensions, 3D, universe, inflation, big bang, QCD, knots
%X "We suggest a structure for the vacuum comprised of a network of tightly
   knotted/linked flux tubes formed in a QCD-like cosmological phase transition
   & show that such a n/wk can drive cosmological inflation. As the n/wk can be
   topologically stable only in three space dimensions, this scenario provides a
   dynamical explanation for the existence of exactly three large spatial
   dimensions in our Universe."
   -- 1508.01458@[<A HREF="http://arxiv.org/abs/1508.01458">arXiv</A>]['15].

%A B. Hensen
%A et al ...
%A R. Hanson
%T Experimental loophole-free violation of a Bell inequality using entangled
   electron spins separated by 1.3km
%J arXiv
%M AUG
%D 2015
%O Loophole-free Bell inequality violation using
   electron spins separated by 1.3 kilometres,
   Nature, 526 (7575), pp.682-686, Oct 2015
%K TR, physics, c2015, c201x, c20xx, zz0915, quantum theory, mechanics, reality,
   locality, local, realism, weirdness, CHSH, Bell, Bells, inequality,
   entanglement swapping, electron spin
%X "... numerous ingenious Bell inequality tests have been reported. However,
   because of experimental limitations, all experiments to date required
   additional assumptions to obtain a contradiction with local realism,
   resulting in loopholes. Here we report on a B.experiment that is free of any
   such additional assumption & thus directly tests the principles underlying
   B's inequality. We employ an event-ready scheme that enables the generation
   of high-fidelity entanglement between distant electron spins. Efficient spin
   readout avoids the fair sampling assumption (detection loophole), while the
   use of fast random basis seln & readout combined with a spatial separation of
   1.3km ensure the required locality condns. We perform 245 trials testing the
   CHSH-Bell inequality S <= 2 & find S=2.42+/-0.20. A null hypothesis test
   yields a probability of p=0.039 that a local-realist model for space-like
   separated sites produces data with a violation at least as large as observed,
   even when allowing for memory in the devices. This result rules out large
   classes of local realist theories, & paves the way for implementing
   device-indept quantum-secure communication & randomness certification."
   -- 1508.05949@[<A HREF="http://arxiv.org/abs/1508.05949">arXiv</A>]['15].
   (Also see news@[<A HREF="http://dx.doi.org/10.1038/nature.2015.18255">n@ture</A>][3/9/'15].)
   [Also search for: quantum Bell inequality].


%A D. Clery
%T Twisted logic
%J Science
%V 350
%N 6259
%P 369-371
%M OCT
%D 2015
%K news, c2015, c201x, c20xx, zz1015, physics, nuclear fusion, tokomak,
   stellarator, reactor, Wendelstein 7-X, W7-X, W7X, helical, LHD
%X "... lab in Germany's [NE] corner, researchers are preparing to switch on a
   fusion device called a stellarator, the largest ever built. The 1 billion
   euro machine, known as Wendelstein 7-X (W7-X), appears now as a 16-meter-wide
   ring of gleaming metal bristling with devices of all shapes and sizes ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.350.6259.369">doi:10.1126/science.350.6259.369</A>]['15].
   [Also search for: nuclear fusion power].

%A T. B. Batalhao
%A A. M. Souza
%A R. S. Sarthour
%A I. S. Oliveira
%A M. Paternostro
%A E. Lutz
%A R. M. Serra
%T Irreversibility and the arrow of time in a quenched quantum system
%J Phys. Rev. Lett.
%V 115
%N 190601
%M NOV
%D 2015
%K physics, c2015, c20x, c20xx, zz0716, quantum, theory, time, arrow,
   irreversibility, theormodynamics, entropy, small system
%X "... Using a nuclear magnetic resonance setup, we measure the nonequilibrium
   entropy produced in an isolated spin-1/2 system following fast quenches of an
   external magnetic field. We experimentally demonstrate that it is equal to
   the entropic distance, expressed by the Kullback-Leibler divergence, between
   a microscopic process & its time reversal. Our result addresses the concept
   of irreversibility from a microscopic quantum standpoint."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.115.190601">doi:10.1103/PhysRevLett.115.190601</A]['16].
   [Also search for: time arrow] and
   [also search for: small system entropy].

%A T. S. Cubitt
%A D. Perez-Garcia
%A M. M. Wolf
%T Undecidability of the spectral gap
%J Nature
%V 528
%N 7581
%P 207-211
%M DEC
%D 2015
%K jrnl, c2015, c201x, c20xx, zz1215, physics, quantum, theory, Hamiltonian,
   undecidability, mathematics, spectral gap, gapped, gapless,
   quasi-periodic tiling, quasiperiodic, aperiodic
%X "The spectral gap - the energy difference between the ground state & first
   excited state of a system ... the general spectral gap problem: given the
   Hamiltonian of a quantum many-body system, is it gapped or gapless? Here we
   prove that this is an undecidable problem. ... construct families of quantum
   spin systems on a [2D] lattice with translationally invariant,
   nearest-neighbour interactions, for which the spectral gap problem is
   undecidable. This result extends to undecidability of other low-energy
   properties, such as the existence of algebraically decaying ground-state
   correlations. The proof combines Hamiltonian complexity techniques with
   aperiodic tilings, to construct a H. whose ground state encodes the evolution
   of a quantum phase-estimation alg. followed by a universal Turing machine.
   The spectral gap depends on the outcome of the corr. 'halting problem'. Our
   result implies that there exists no alg. to determine whether an arbitrary
   model is gapped or gapless, & that there exist models for which the presence
   or absence of a spectral gap is independent of the axioms of mathematics."
   -- [<A HREF="http://dx.doi.org/10.1038/nature16059">doi:10.1038/nature16059</A>]['15].
   (Also see full 146p version
   1502.04573@[<A HREF="http://arxiv.org/abs/1502.04573">arXiv</A>]['15],
   and comment
   [<A HREF="http://dx.doi.org/10.1038/nature.2015.18983">doi:10.1038/nature.2015.18983</A>]['15].)

%A S. Barz
%T Quantum computing with photons: introduction to the circuit model, the
   one-way quantum computer, and the fundamental principles of photonic
   experiments
%J J. Physics B: Atomic, Molec. and Opt. Physics
%V 48
%N 8
%D 2015
%K jrnl, Physics, c2015, c201x, c20xx, zz0324, quantum computing, photon,
   photonics, light, polarisation, polarization, polarised, gate, gates
%X "... tutorial reviews the fundamental tools of photonic q.info. processing.
   The basics of theoretical q.computing are presented & the q.circuit model as
   well as measurement-based models of q.computing are introduced. Furthermore,
   it is shown how these concepts can be implemented experimentally using
   photonic qubits, where information is encoded in the photons' polarization."
   -- [<A HREF="https://doi.org/10.1088/0953-4075/48/8/083001 ">doi:10.1088/0953-4075/48/8/083001 </A>]['24].
   [Also search for: quantum computing], maybe add 'photon'.
   Also see ph@[<A HREF="https://en.wikipedia.org/wiki/Linear_optical_quantum_computing">wikip</A>]'24].

%A S. W. Hawking
%A M. J. Perry
%A A. Strominger
%T Soft hair on black holes
%J arXiv
%P 22pp
%M JAN
%D 2016
%K TR, c2016, c201x, c20xx, zz0216, physics, black hole, information, loss,
   radiation, horizon, quantum, firewall, space time, spaceTime, vacuum
%X "It has recently been shown that BMS supertranslation symmetries imply an
   infinite # of conservation laws for all gravitational theories in
   asymptotically Minkowskian spacetimes. These laws require black holes to
   carry a large amount of soft (i.e. zero-energy) supertranslation hair. The
   presence of a Maxwell field similarly implies soft electric hair. This paper
   gives an explicit description of soft hair in terms of soft gravitons or
   photons on the black hole horizon, & shows that complete information about
   their quantum state is stored on a holographic plate at the future boundary
   of the horizon. Charge conservation is used to give an infinite # of exact
   relations between the evaporation products of black holes which have
   different soft hair but are otherwise identical. It is further argued that
   soft hair which is spatially localized to much less than a Planck length
   cannot be excited in a physically realizable process, giving an effective #
   of soft degrees of freedom proportional to the horizon area in Planck units."
   -- 1601.00921@[<A HREF="http://arxiv.org/abs/1601.00921">arXiv</A>]['16].
   (Also see comment@[<A HREF="http://www.nature.com/news/hawking-s-latest-black-hole-paper-splits-physicists-1.19236">www</A>][27/1/2016].)

%T Observation of gravitational waves from a binary black hole merger
%A B. P. Abbott
%A et al
%Q LIGO Scientific Collaboration and Virgo Collaboration
%J Phys. Rev. Lett.
%V 116
%P 061102
%M FEB
%D 2016
%K physics, jrnl, c2016, c201x, c20xx, zz0216, cosmology, black holes,
   merger, gravititational waves, gravity wave, ripple, relativity, LIGO
%X "On September 14, 2015 at 09:50:45 UTC the two detectors of the Laser
   Interferometer Gravitational-Wave Observatory simultaneously observed a
   transient gravitational-wave signal. The signal sweeps upwards in freq. from
   35 to 250 Hz with a peak g.-wave strain of 1.0x10^-21. It matches the
   waveform pred. by gen. relativity for the inspiral & merger of a pair of
   black holes & the ringdown of the resulting single black hole. The signal was
   obs. with a matched-filter SNR of 24 & a false alarm rate est. to be < 1
   event per 203,000 years, equiv. to a sig. > 5.1 sigma. The source lies at a
   luminosity dist. of 410^{+160}_{1-80} Mpc corr. to a redshift
   z=0.09^{+0.03}_{-0.04}. ... the initial black hole masses are 36^{+5}_{-4}M
   & 29^{+4}_{-4}M, & the final black hole mass is 62^{+4}_{-4}M, with
   3.0^{+0.5}_{-0.5}Mc^2 radiated in g.waves. All uncertainties define 90%
   credible intervals. These obs. demo. the existence of binary stellar-mass
   black hole systems. This is the first direct detection of g.waves & the
   first obs. of a binary black hole merger."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.116.061102">doi:10.1103/PhysRevLett.116.061102</A>]['16].

%A D. H. Mahler
%A L. Rozema
%A K. Fisher
%A L. Vermeyden
%A K. J. Resch
%A H. M. Wiseman
%A A. Steinberg
%T Experimental nonlocal and surreal Bohmian trajectories
%J Sci. Advances
%V 2
%N 2
%P e1501466
%M FEB
%D 2016
%K eJrnl, jrnl, c2016, c201x, c20xx, zz0216, physics, quantum theory, weirdness,
   Bohm, Bohmian, interferometer, two slit, surreal trajectory, weak measurement
%X "Experimental nonlocal & surreal Bohmian trajectories Weak measurement allows
   one to empirically determine a set of average trajectories for an ensemble
   of quantum particles. However, when two particles are entangled, the
   trajectories of the first particle can depend nonlocally on the posn of the
   2nd particle. [&] the theory describing these trajectories, called Bohmian
   mechanics, predicts trajectories that were at first deemed 'surreal' when
   the 2nd particle is used to probe the position of the 1st particle. We
   entangle two photons & determine a set of B.trajectories for one of them
   using weak measurements & postseln. We show that the trajectories seem
   surreal only if one ignores their manifest nonlocality."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1501466">doi:10.1126/science.1501466</A>]['16].
   [Also search for: Bohm physics].

%A C. Wang
%A et al ...
%A R. J. Schoelkopf
%T A Schrodinger cat living in two boxes
%J Science
%V 352
%N 6289
%P 1087-1091
%M MAY
%D 2016
%K jrnl, physics, c2016, c201x, c20xx, zz1216, quantum physics, uncertainty,
   superposition, states
%X "Q.superpositions of distinct coherent states in a single-mode harmonic
   oscillator, known as 'cat states,' have been an elegant demonstration of
   S's famous cat paradox. Here, we realize a two-mode cat state of
   electromagnetic fields in two microwave cavities bridged by a
   superconducting artificial atom, which can also be viewed as an entangled
   pair of single-cavity cat states. We present full q.state tomography of this
   complex cat state over a Hilbert space exceeding 100 dimensions via quantum
   nondemolition measurements of the joint photon number parity. The ability to
   manipulate such multicavity quantum states paves the way for logical
   operations between redundantly encoded qubits for fault-tolerant quantum
   computation and communication."
  -- [<A HREF="http://dx.doi.org/10.1126/science.aaf2941">doi:10.1126/science.aaf2941</A>]['16].

%A D. Almada
%A K. Ch'ng
%A S. Kintner
%A B. Morrison
%A K. B. Wharton
%T Are retrocausal accounts of entanglement unnaturally fine-tuned?
%J Int. J. of Quantum Foundations (accepted)
%D 2016
%K jrnl, physics, c2016, c201x, c20xx, zz0716, quantum theory, time arrow,
   retrocausality
%X "An explicit retrocausal model is used to analyze the general Wood-Spekkens
   argument that any causal explanation of Bell-inequality violations must be
   unnaturally fine-tuned to avoid signaling. The no-signaling aspects of the
   model turn out to be robust under variation of the only free parameter, even
   as the probabilities deviate from standard quantum theory. The ultimate
   reason for this robustness is then traced to a symmetry assumed by the
   original model. A broader conclusion is that symmetry-based restrictions seem
   a natural & acceptable form of fine-tuning, not an unnatural model-rigging.
   And if the Wood-Spekkens argument is indicating the presence of hidden
   symmetries, this might even be interpreted as supporting time-symmetric
   retrocausal models."
   -- 1510.03706@[<A HREF="http://arxiv.org/abs/1510.03706">arXiv</A>]['16].
   (Also see the bbc [<A HREF="http://www.bbc.com/earth/story/20160708-the-past-is-not-set-in-stone-so-we-may-be-able-to-change-it">12/7/2016</A>].)
   [Also search for: time retrocausality].

%A S. Carroll
%T The Big Picture: On the Origins of Life, Meaning, and the Universe Itself
%I Dutton
%P 480
%D 2016
%K book, c2016, c201x, c20xx, zz1016, time, cosmology
%X 1st ed 2016; yb us$18; uk us isbn:0525954821; uk us isbn13:978-0525954828.
   "... learn the difference between how the world works at the quantum level,
   the cosmic level, & the human level - & how each connects to the other. ..."
   [Also search for: time arrow].

%A B. Bradlyn
%A J. Cano
%A Z. Wang
%A M. G. Vergniory
%A C. Felser
%A R. J. Cava
%A B. A. Bernevig
%T Beyond Dirac and Weyl fermions: Unconventional quasiparticles in conventional
   crystals
%J Science
%V 353
%N 6299
%M AUG
%D 2016
%K jrnl, physics, c2016, c201x, c20xx, zz0816, quantum mechanics, theory,
   lattice, space, particles, Dirac, Weyl, Majorana, fermion, crystal,
   symmetry
%X "Condensed-matter systems have recently become a fertile ground for the
   discovery of fermionic particles & phenomena predicted in high-energy phys.;
   examples include Majorana fermions, as well as Dirac & Weyl semimetals.
   However, fermions in condensed-matter systems are not constrained by
   Poincare symmetry. Instead, they must only respect the crystal symmetry of
   one of the 230 space groups. Hence, there is the potential to find & classify
   free fermionic excitations in solid-state systems that have no high-energy
   counterparts. ...We found that three space groups exhibit symmetry-protected
   three-band crossings. In two cases, this results in a threefold degenerate
   point node, whereas the third case results in a line node away from the
   high-symmetry point. These crossings are required to have a nonzero Chern
   number & hence display surface Fermi arcs. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaf5037">doi:10.1126/science.aaf5037</A>]['16].
   Also see comments by C. Beenakker, pp.539-540 ...
   "We observe space as a continuum, but we might entertain the thought that
   there is an underlying lattice and that space is actually a crystal. Which
   particles would inhabit such a lattice world? This question was first raised
   by Werner Heisenberg in 1930 ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aag2865">doi:10.1126/science.aag2865</A>]['16].

%A J. Steinhauer
%T Observation of quantum Hawking radiation and its entanglement in an analogue
   black hole
%J Nature Physics
%V ?
%N ?
%P ?-?
%M AUG
%D 2016
%K jrnl, physics, c2016, c201x, c20xx, zz0816, Hawking radiation, quantum,
   black hole, Bose-Einstein condensate
%X "We observe spontaneous Hawking radiation, stimulated by quantum vacuum
   fluctuations, emanating from an analogue black hole in an atomic
   Bose-Einstein condensate. Correlations are observed between the H.particles
   outside the black hole & the partner particles inside. ... indicate an
   approx. thermal distribution of H.radiation. We find that the high-energy
   pairs are entangled, while the low-energy pairs are not, within the
   reasonable assumption that excitations with different freqs. are not
   correlated. The entanglement verifies the quantum nature of the H.radiation.
   The results are consistent with a driven oscillation experiment & a
   numerical simulation."
   -- [<A HREF="http://dx.doi.org/10.1038/nphys3863">doi:10.1038/nphys3863</A>]['16].
   (Also see the bbc[<A HREF="http://www.bbc.com/news/science-environment-37088877">16/8/2016</A>].)

%A A. M. Kaufman
%A M. E. Tai
%A A. Lukin
%A M. Rispoli
%A R. Schittko
%A P. M. Preiss
%A M. Greiner
%T Quantum thermalization through entanglement in an isolated many-body system
%J Science
19 Aug 2016:
%V 353
%N 6301
%P 794-800
%M AUG
%D 2016
%K jrnl, physics, c2016, c201x, c20xx, zz0816, quantum mechanics, entropy,
   local, thermal, thermalization, entanglement, thermodynamics
%X "Statistical mechanics relies on the maximization of entropy in a system at
   thermal equilibrium. However, an isolated quantum many-body system
   initialized in a pure state remains pure during Schrodinger evolution, & in
   this sense it has static, zero entropy. We experimentally studied the
   emergence of stat.mechanics in a q.state & observed the fundamental role of
   q.entanglement in facilitating this emergence. Microscopy of an evolving
   q.system indicates that the full q.state remains pure, whereas thermalization
   occurs on a local scale. We directly measured entanglement entropy, which
   assumes the role of the thermal entropy in thermalization. The entanglement
   creates local entropy that validates the use of statistical physics for local
   observables. Our measurements are consistent with the eigenstate
   thermalization hypothesis."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaf6725">doi:10.1126/science.aaf6725</A>]['16].
   (Also see, 'Thermalization in small quantum systems,' pp.752-753,
      [<A HREF="http://dx.doi.org/10.1126/science.aah5776">doi:10.1126/science.aah5776</A>]['16].)

%A R. A. Muller
%T Now The Physics of Time
%P 368
%I NortonCo
%M SEP
%D 2016
%K book, c2016, c201x, c20xx, zz1016, time, arrow, now
%X 1st ed 2016; hb us $18;
   "... does more than poke holes in past ideas; he crafts his own revolutionary
   theory, one that makes testable predictions. He begins by laying out - with
   the refreshing clarity that made Physics for Future Presidents so
   successful - a firm and remarkably clear explanation of the physics building
   blocks of his theory: relativity, entropy, entanglement, antimatter, and the
   Big Bang. With the stage then set, he reveals a startling way forward. ..."
   [Also search for: arrow time].

%A R. F. Service
%T Perovskite solar cells gear up to go commercial
%J Science
%V 354
%N 6317
%P 1214-1215
%M DEC
%D 2016
%K news, c2016, c201x, c20xx, zz1216, solar energy, renewable, solar cells,
   perovskites, silicon, cell
%X "Cheap photovoltaic materials called perovskites are continuing their march
   to commercialization. ...new results on tandem solar photovoltaics in which
   perovskite cells are layered atop conventional silicon solar cells. ... And
   it's expected they will continue to improve over the next year, perhaps
   converting as much as 30% of incoming light energy into electricity. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.354.6317.1214">doi:10.1126/science.354.6317.1214</A>]['16].

%A J. V.Koski
%A J. P.Pekola
%T Maxwell's demons realized in electronic circuits,
   Demons de Maxwell realises avec des circuits electroniques
%J Comptes Rendus Physique
%V 17
%N 10
%P 1130-1138
%M DEC
%D 2016
%K jrnl, physics, c2016, c201x, c20xx, zz0922, Maxwell, demon, thermodynamics,
   entropy, energy, information, Szilard engine, quantum
%X "We review recent progress in making the former gedanken experiments of
   Maxwell's demon into real experiments in a lab. ... focus on realizations
   based on single-electron tunneling in electronic circuits. We first present
   how stochastic thermodynamics can be investigated in these circuits. Next we
   review recent experiments on an electron-based Szilard engine. Finally, we
   report on experiments on single-electron tunneling-based cooling, overviewing
   the recent realization of a Coulomb gap refrigerator, as well as an
   autonomous Maxwell's demon."
   -- [<A HREF="https://doi.org/10.1016/j.crhy.2016.08.011">doi:10.1016/j.crhy.2016.08.011</A>]['22].
   Also see MD@[<A HREF="https://en.wikipedia.org/wiki/Maxwell%27s_demon">wikip</A>]['22].
   [Also search for: thermodynamics information].

%A P. Chen
%A G. Mourou
%T Accelerating plasma mirrors to investigate the black hole information
   loss paradox
%J Phys. Rev. Lett.
%V 118
%P 045001
%M JAN
%D 2017
%K physics, c2017, c201x, c20xx, zz0117, Hawking evaporation, radiation,
   black hole, paradox, information loss, preservation, experiment,
   plasma mirror, unitarity, cosmology
%X "The question of whether Hawking evaporation violates unitarity, & therefore
   results in the loss of info., has remained unresolved since Hawking's
   seminal discovery. ...  A conception of such an experiment is proposed & a
   self-consistent set of physical parameters is presented. Critical issues,
   such as how the black hole unitarity may be preserved, can be addressed
   through the entanglement between the analog Hawking radiation photons &
   their partner modes.
   -- [<A HREF="https://doi.org/10.1103/PhysRevLett.118.045001">10.1103/PhysRevLett.118.045001</A>]['17].
   [Also search for: black hole paradox].
   (Also see BHoleP@[<A HREF="https://en.wikipedia.org/wiki/Black_hole_information_paradox">wikip</A>]['21].)

%A E. Gibney
%T The quest to crystallize time
%J Nature
%V 543
%N 7644
%P 164-166
%M MAR
%D 2017
%K news, c2017, c201x, c20xx, zz0517, physics, Wilczek, time cystal, timeCrystal
%X "Bizarre forms of matter called time crystals were supposed to be physically
   impossible. Now theyâre not. ... Time crystals are hypothetical structures
   that pulse without requiring any energy - like a ticking clock that never
   needs winding. The pattern repeats in time in much the same way that the
   atoms of a crystal repeat in space. The idea was so challenging that when
   Nobel prizewinning physicist Frank Wilczek proposed the provocative concept
   in 2012, other researchers quickly proved there was no way to create time
   crystals.  But there was a loophole ..."
   -- [<A HREF="https://doi.org/10.1038/543164a">doi:10.1038/543164a</A>]['17].
   [Also search for: timeCrystal].

%A J. Zhang
%A et al ...
%A C. Monroe
%T Observation of a discrete time crystal
%J Nature
%V 543
%N 7644
%P 217-220
%M MAR
%D 2017
%K news, c2017, c201x, c20xx, zz0517, physics, Wilczek, discrete, time cystal,
   timeCrystal
%X "Spontaneous symmetry breaking ... An example is the breaking of spatial
   translational symmetry, which underlies the formation of crystals & the
   phase transition from liquid to solid. Using the analogy of crystals in
   space, the breaking of t. s. in time & the emergence of a 'time crystal' was
   recently proposed but was later shown to be forbidden in thermal equilibrium.
   However, non-equilibrium Floquet systems, which are subject to a periodic
   drive, can exhibit persistent time correlations at an emergent subharmonic
   freq. This new phase of matter has been dubbed a 'discrete time crystal'. ...
   present the experimental observation of a discrete time crystal, in an
   interacting spin chain of trapped atomic ions. We apply a periodic
   Hamiltonian to the system under many-body localization condns, & observe a
   subharmonic temporal response that is robust to external perturbations. ..."
   -- [<A HREF="https://doi.org/10.1038/nature21413">doi:10.1038/nature21413</A>]['17].
   [Also search for: timeCrystal].

%A S. Choi
%A et al ...
%A M. D. Lukin
%T Observation of discrete time-crystalline order in a disordered dipolar
   many-body system
%J Nature
%V 543
%N 7644
%P 221-225
%M MAR
%D 2017
%K news, c2017, c201x, c20xx, zz0517, physics, Wilczek, discrete, time cystal,
   timeCrystal
%X "... advances in the controlled manipulation of isolated many-body systems
   have enabled detailed studies of non-equilibrium phases in strongly
   interacting quantum matter ... report the experimental observation of such
   discrete time-crystalline order in a driven, disordered ensemble of about one
   million dipolar spin impurities in diamond at room temperature. We observe
   long-lived temporal correlations, experimentally identify the phase boundary
   & find that the temporal order is protected by strong interactions. ..."
   -- [<A HREF="https://doi.org/10.1038/nature21426">doi:10.1038/nature21426</A>]['15].
   [Also search for: timeCrystal].

%A J. Yin
%A et al
%T Satellite-based entanglement distribution over 1200 kilometers
%J Science
%V 356
%N 6343
%P 1140-1144
%M JUN
%D 2017
%K jrnl, physics, c2017, c201x, c20xx, zz0617, quantum, data transmission,
   secure, communication, space, satellite, key distribution, encryption,
   entangled, photons
%X "... Owing to channel loss, however, the previously achieved distance
   was limited to ~100km. Here we demonstrate satellite-based distribution of
   entangled photon pairs to two locations separated by 1203km on Earth, through
   two satellite-to-ground downlinks with a summed length varying from 1600 to
   2400km. We observed a survival of two-photon entanglement & a violation of
   Bell inequality by 2.37+/-0.09 under strict Einstein locality conditions. The
   obtained effective link efficiency is orders of magnitude higher than that of
   the direct bidirectional transmission of the two photons through
   telecommunication fibers."
   -- [<A HREF="https://doi.org/10.1126/science.aan3211">doi:10.1126/science.aan3211</A>]['17].
   [Also search for: quantum communication].

%A P. Ball
%T How quantum trickery can scramble cause and effect
%J Nature
%V 546
%P 590-592
%M JUN
%D 2017
%K views, c2017, c201x, c20xx, zz0717, physics, quantum theory, mechanics,
   qubit, qubits, information, paths, Walther, causal, ambiguity, causality,
   indeterminacy, Copenhagen interpretation, superposition, Chiribella, Brukner
%X "... Albert Einstein is heading out for his daily stroll & has to pass
   through two doorways. First he walks through the green door, & then through
   the red one. Or wait - did he go through the red first & then the green? ...
   Walther's group has shown that it is impossible to say in which order these
   photons pass through a pair of gates as they zip around the lab. It's not
   that this information gets lost or jumbled - it simply doesn't exist. In
   Walther's experiments, there is no well-defined order of events. This finding
   in 2015 ..."   [11 refs.]
   -- [<A HREF="https://doi.org/10.1038/546590a">doi:10.1038/546590a</A>]['17].

%A D. Castelvecchi
%T The strange topology that is reshaping physics
%J Nature
%V 547
%N 7663
%P ?-?
%M JUL
%D 2017
%K news, views, c2017, c201x, c20xx, zz0717, physics, quantum, chemistry,
   topology, topological, effects, Thouless, Hall effect, insulator, Hasan
%X "Topological effects might be hiding inside perfectly ordinary materials,
   waiting to reveal bizarre new particles or bolster quantum computing. ...
   In the past decade, they have found that topology provides unique insight
   into the physics of materials, such as how some insulators can sneakily
   conduct electricity along a single-atom layer on their surfaces. ... Some of
   the most fundamental properties of subatomic particles are, at their heart,
   topological. Take the spin of the electron, for example ..."
   -- [<A HREF="https://doi.org/10.1038/547272a">doi:10.1038/547272a</A>]['17].
   Also see 'Topological quantum chemistry',
   -- [<A HREF="https://doi.org/10.1038/nature23268">doi:10.1038/nature23268</A>]['17].

%A J.-M. A Allen
%A J. Barrett
%A D. C. Horsman
%A C. M. Lee
%A R. W. Spekkens
%T Quantum common causes and quantum causal models
%J Physical Rev. X
%V 7
%N 3
%M JUL
%D 2017
%K jrnl, physics, c2017, c201x, c20xx, zz0618, quantum, common cause, causality,
   Reichenbach's principle, Reichenbachs, model
%X "Reichenbach's principle asserts that if two observed variables are found to
   be correlated, then there should be a causal explanation of these
   correlations. [&] if the explanation is in terms of a common cause, then the
   cond. prob. distn over the vars. given the complete common cause
   should factorize. The principle is generalized by the formalism of causal
   models, in which the causal relationships among vars. constrain the form
   of their joint prob. distn. In the quantum case, however, the observed
   correlations in Bell experiments cannot be explained in the manner R.'s
   principle would seem to demand. Motivated by this, we introduce a quantum
   counterpart to the principle. We demonstrate that under the assumption that
   quantum dynamics is fundamentally unitary ..."
   -- [<A HREF="https://doi.org/10.1103/PhysRevX.7.031021">doi:10.1103/PhysRevX.7.031021</A>]['18].
   (Also see auth3@[<A HREF="https://scholar.google.ca/citations?user=dQrta_AAAAAJ&hl=en">sch'l'r</A>]['18].)

%A A. Alonso-Serrano
%A M. Visser
%T Entropy budget for Hawking evaporation
%J Universe
%V 3
%P 58
%M JUL
%D 2017
%K c2017, c201x, c20xx, zz0218, physics, entropy, information, black hole,
   cosmology, Hawking, radiation, evaporation
%X "Blackbody radiation, emitted from a furnace & described by a Planck
   spectrum, contains (on avg.) an entropy of 3.9 +/- 2.5 bits per photon.
   Since normal physical burning is a unitary process, this amount of entropy is
   compensated by the same amount of 'hidden information' in correlations
   between the photons. The importance of this result lies in the posterior
   extension of this argument to the H.radiation from black holes, demonstrating
   that the assumption of unitarity leads to a perfectly reasonable
   entropy/information budget for the evaporation process. In order to carry out
   this calculation we adopt a variant of the 'average subsystem' approach, but
   consider a tripartite pure system that includes the influence of the rest of
   the universe, & which allows 'young' black holes to still have a non-zero
   entropy; which we identify with the standard Bekenstein entropy."
   -- [<A HREF="https://doi.org/10.3390/universe3030058">doi:10.3390/universe3030058</A>]['18];
   auth1[<A HREF="https://www.researchgate.net/profile/Ana_Alonso-Serrano">www</A>]['18].

%A A. Tilloy
%T Ghirardi-Rimini-Weber model with massive flashes
%J arXiv
%M SEP
%D 2017
%K TR, c2017, c201x, c20xx, zz0917, physics, quantum theory, gravity, GRW,
   flashes, collapse, cosmology
%X "... a modification of the Ghirardi-Rimini-Weber (GRW) model in which the
   flashes (or collapse space-time events) source a classical gravitational
   field. The resulting semi-classical theory of Newtonian g. preserves the
   statistical interpretation of quantum states of matter in contrast with mean
   field approaches. It can be seen as a discrete version of recent proposals of
   consistent hybrid quantum classical theories. The model seems to be in
   agreement with known experimental data & introduces new falsifiable
   predictions: (1) particles do not attract themselves, (2) the 1/r
   gravitational potential of Newtonian gravity is cut-off at short (<= 0-7m)
   distances, & (3) gravity makes spatial superpositions decohere at a rate
   inversely proportional to that coming from the vanilla GRW model. Together,
   the last two predictions make the model experimentally falsifiable for all
   values of its parameters."
   -- [<A HREF="https://arxiv.org/abs/1709.03809">arXiv</A>]['17].

%A Z. Merali
%T The new thermodynamics: how quantum physics is bending the rules
%J Nature
%V 551
%N 7678
%P 20-22
%M NOV
%D 2017
%K news, c2017, c201x, c20xx, zz1117, physics, quantum, thermodynamics,
   Kosloff, Schaetz, Riera, Bera
%X "... There is reason to suspect that the laws of thermodynamics, which are
   based on how large numbers of particles behave, are different in the quantum
   realm. There is reason to suspect that the laws of thermodynamics, which are
   based on how large numbers of particles behave, are different in the q.realm.
   ... Thermodynamic quantities such as temperature and heat are statistical in
   nature and defined in reference to the average motion of large ensembles of
   particles. But back in the 1980s, Kosloff began pondering whether this
   picture would continue to make sense for much smaller systems. ..."
   -- [<A HREF="https://doi.org/10.1038/551020a">doi:10.1038/551020a</A>]['17].

%A D. M. Zajac
%A et al
%T Resonantly driven CNOT gate for electron spins
%J Science
%V 359
%N 6374
%P 439-442
%M JAN
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0118, quantum computing, CNOT, controlled NOT,
   gate, qubit, qubits, silicon, dots
%X "Single-qubit rotations & two-qubit CNOT operations are crucial ingredients
   for universal quantum computing.  ... demonstrate an efficient resonantly
   driven CNOT gate for electron spins in silicon. Our platform achieves
   single-qubit rotations with fidelities greater than 99%, as verified by
   randomized benchmarking. Gate control of the exchange coupling allows a
   quantum CNOT gate to be implemented with resonant driving in ~200
   nanoseconds. We used the CNOT gate to generate a Bell state with 78% fidelity
   (corrected for errors in state preparation & measurement). Our quantum dot
   device architecture enables multi-qubit algorithms in silicon."
   -- [<A HREF="https://doi.org/10.1126/science.aao5965">doi:10.1126/science.aao5965</A>]['18].

%A V. M. Schafer
%A et al ...
%A D. M. Lucas
%T Fast quantum logic gates with trapped-ion qubits
%J Nature
%V 555
%P 75-78
%M MAR
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0318, quantum computing, gate, gates, qubit,
   optical
%X "... the essential two-qubit logic gate that is used to generate quantum
   entanglement has hitherto always been performed in an adiabatic regime (in
   which the gate is slow compared with the characteristic motional frequencies
   of the ions in the trap ... Here we implement one such method, which uses
   amplitude-shaped laser pulses to drive the motion of the ions along
   trajectories designed so that the gate operation is insensitive to the
   optical phase of the pulses. This enables fast (megahertz-rate) quantum logic
   that is robust to fluctuations in the optical phase, which would otherwise be
   an important source of experimental error. We demonstrate entanglement
   generation for gate times as short as 480 nanoseconds ..."
   -- [<A HREF="https://doi.org/10.1038/nature25737">doi:10.1038/nature25737</A>]['18].
   [Also search for: quantum gate].

%A P. Ball
%T Beyond Weird: Why Everything you Thought you knew about Quantum Physics is
   Different
%I ChicagoUP
%D 2018
%K book, physics, c2018, c201x, c20xx, zz0418, quantum, theory, weirdness,
   intro, information
%X 1st ed 2018; hb us$26; uk us isbn: 022655838X; uk us isbn13:978-0226558387.
   (Also see a review [<A HREF="https://doi.org/10.1038/d41586-018-03272-8">doi:10.1038/d41586-018-03272-8</A>]['18].)

%A A. Becker
%T What Is Real?: The Unfinished Quest for the Meaning of Quantum Physics
%I BasicBooks
%% MAR
%D 2018
%K book, text, c2018, c201x, c20xx, zz0418, physics, quantum mechanics,
   reality, Copenhagen
%X 1st ed 2018; us$25; uk us isbn:0465096050; uk us isbn13:978-0465096053.

%A P. Bierhorst
%A et al ...
%A L. K. Shalm
%T Experimentally generated randomness certified by the impossibility of
   superluminal signals
%J Nature
%V 556
%P 223-226
%M APR
%D 2018
%K jrnl, physics, c2018, c201x, c20xx, zz0418, random numbers, RNG, quantum,
   QRNG, Bell test, number, cryptography
%X "... present certified randomness obtained from a photonic Bell experiment &
   extract 1,024 random bits that are uniformly distributed to within 10^(â12).
   These random bits could not have been predicted according to any physical
   theory that prohibits faster-than-light (superluminal) signalling ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-018-0019-0">doi:10.1038/s41586-018-0019-0</A>]['18].
   [Also search for: quantum RNG].

%A S. W. Hawking
%A T. J. Hertog
%T A smooth exit from eternal inflation?
%J J. of High Energy Physics
%V 147
%M APR
%D 2018
%K jrnl, physics, c2018, c201x, c20xx, zz0518, cosmology, universe, inflation,
   big bang, bigBang, string theory, multiverse, quantum gravity
%X "The usual theory of inflation breaks down in eternal inflation. We derive a
   dual description of eternal inflation in terms of a deformed Euclidean CFT
   located at the threshold of eternal inflation. The partition function gives
   the amplitude of different geometries of the threshold surface in the
   no-boundary state. Its local and global behavior in dual toy models shows
   that the amplitude is low for surfaces which are not nearly conformal to the
   round three-sphere and essentially zero for surfaces with negative curvature.
   Based on this we conjecture that the exit from eternal inflation does not
   produce an infinite fractal-like multiverse, but is finite and reasonably
   smooth."
   -- [<A HREF="https://doi.org/10.1007/JHEP04(2018)147">doi:10.1007/JHEP04(2018)147</A>]['18],
      1707.07702@[<A HREF="https://arxiv.org/abs/1707.07702">arXiv</A>]['18].
   (Also see [<A HREF="http://www.cam.ac.uk/research/news/taming-the-multiverse-stephen-hawkings-final-theory-about-the-big-bang?utm_medium=email&utm_source=EN0518">www</A>][2/5/2018.)

%A C. Rovelli
%T The Order of Time
%I RiverheadBooks
%P 256
%M MAY
%D 2018
%K book, text, c2018, c201x, c20xx, zz0418, physics, arrow of time, past,
   future, philosophy
%X 1st ed 2018; hb us$18; uk us isbn:073521610X; uk us isbn13:978-0735216105.
   "... Why do we remember the past and not the future? What does it mean for
   time to "flow"? Do we exist in time or does time exist in us? In lyric,
   accessible prose, [CR] invites us to consider questions about the nature of
   time that continue to puzzle physicists and philosophers alike. ..."
   Also see CR@[<A HREF="https://en.wikipedia.org/wiki/Carlo_Rovelli">wikip</A>]['22].
   [Also search for: arrow time].

%T Challenging local realism with human choices
%Q The BIG Bell Test Collaboration
%J Nature
%V 557
%P 212-216
%M MAY
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0518, quantum theory, mechanics, physics,
   Bell test, local realism, freedom of choice, loophole
%X "... We recruited about 100,000 human participants to play an online video
   game that incentivizes fast, sustained input of unpredictable selections and
   illustrates Bell-test methodology ... The observed correlations strongly
   contradict local realism and other realistic positions in bipartite and
   tripartite scenarios. Project outcomes include closing the
   âfreedom-of-choice loopholeâ (the possibility that the setting choices are
   influenced by âhidden variablesâ to correlate with the particle
   properties) ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-018-0085-3">doi:10.1038/s41586-018-0085-3</A>]['18].

%A S. Aaronson
%T PDQP/qpoly = ALL
%D 2018
%K TR, c2018, c201x, c20xx, zz0618, quantum computing, computer, information.
   quomplexity, qomplexity, advice, UTexasA, UTexas, PDQP, qpoly,
   non-collapsing measurements, Raz
%X "We show that combining two different hypothetical enhancements to quantum
   computation - namely, quantum advice and non-collapsing measurements - would
   let a quantum computer solve any decision problem whatsoever in polynomial
   time, even though neither enhancement yields extravagant power by itself.
   This complements a related result due to Raz. The proof uses locally
   decodable codes."
   -- 1805.08577@[<A HREF="https://arxiv.org/abs/1805.08577">arXiv</A>]['18],
      pdf@[<A HREF="https://scottaaronson.com/papers/">www</A>]['18].
   Says, "to appear in Quantum Information and Computation, 2018".

%A S. Hossenfelder
%T Lost in Math: How Beauty Leads Physics Astray
%I BasicBooks
%P 304
%M JUN
%D 2018
%K book, text, physics, c2018, c201x, c20xx, zz0618, maths, theory, theories,
   Sabine Hossenfelder
%X 1st ed 2018; hb us$23; uk us isbn:0465094252; uk us isbn13:978-0465094257.
   "... physicists believe the best theories are beautiful, natural, and
   elegant, and this standard separates popular theories from disposable ones.
   This is why, Sabine Hossenfelder argues, we have not seen a major
   breakthrough in the foundations of physics for more than four decades. The
   belief in beauty has become so dogmatic that it now conflicts with scientific
   objectivity: observation has been unable to confirm mindboggling theories,
   like supersymmetry or grand unification, invented by physicists based on
   aesthetic criteria. ..."
   [Also search for: Sabine Hossenfelder].

%Q Gravity Collaboration
%T Detection of the gravitational redshift in the orbit of the star S2 near
   the Galactic centre massive black hole
%J Astronomy and Astrophysics
%V 615
%P L15
%M JUL
%D 2018
%K jrnl, eJrnl, c2018, c201x, c20xx, zz0818, physics, relativity, gravity,
   light, redshift, relativistic, black hole, blackHole
%X "The highly elliptical, 16-year-period orbit of the star S2 around the
   massive black hole candidate Sgr A* is a sensitive probe ...  Near pericentre
   at 120 AU ~1400 Schwarzschild radii, the star has an orbital speed of
   ~7650 km/s, s.t. the first-order effects of Special & General Relativity have
   now become detectable with current capabilities. ... From data up to & inc.
   pericentre, we robustly detect the combined gravitational redshift &
   relativistic transverse Doppler effect for S2 of z = Del L / L ~200km/s/c
   with different statistical analysis methods. When parameterising the
   post-Newtonian contribution from these effects by a factor f, with f=0 &
   f=1 corr. to the Newtonian & general relativistic limits, resp., we find from
   posterior fitting with different weighting schemes
   f=0.90 +/- 0.09_{stat} +/- 0.15_{sys}. The S2 data are inconsistent with
   pure Newtonian dynamics."
   -- [<A HREF="https://doi.org/10.1051/0004-6361/201833718">doi:10.1051/0004-6361/201833718</A>]['18].
   (Also see the [<A HREF="https://www.bbc.com/news/science-environment-44967491">bbc</A>][26/7/2018].)

%A A. Ananthaswamy
%T Through Two Doors at Once: The Elegant Experiment That Captures the
   Enigma of Our Quantum Reality
%I DuttonPubl
%P 3014
%M AUG
%D 2018
%K book, c2018, c201x, c20xx, zz0818, physics, quantum theory, mechanics,
   diffraction, interference, pattern, double slit, slits, wave, particle
%X 1st ed 2018; hb us$25; uk us isbn:1101986093; isbn13:978-1101986097.
   "... How can a single particle behave both like a particle and a wave? Does
   a particle exist before we look at it, or does the very act of looking
   create reality? ..."
   (Also see [<A HREF="https://doi.org/10.1038/d41586-018-05892-6">review</A>]['18].)

%A A. Almheiri
%A R. Mahajan
%A J. Maldacena
%A Y. Zhao
%T The Page curve of Hawking radiation from semiclassical geometry
%J arXiv
%M AUG
%D 2019
%K TR, c2019, c201x, c20xx, zz1119, physics, black hole, quantum theory,
   holes, information, entropy, RT HRT, EP, EPR, Hawking radiation, Page curve,
   entanglement
%X "We consider a gravity theory coupled to matter, where the matter has a
   higher-dimensional holographic dual. In such a theory, finding quantum
   extremal surfaces becomes equivalent to finding the RT/HRT surfaces in the
   higher-dimensional theory. Using this we compute the entropy of Hawking
   radiation and argue that it follows the Page curve, as suggested by recent
   computations of the entropy and entanglement wedges for old black holes. The
   higher-dimensional geometry connects the radiation to the black hole
   interior in the spirit of ER=EPR. The black hole interior then becomes part
   of the entanglement wedge of the radiation. Inspired by this, we propose a
   new rule for computing the entropy of quantum systems entangled with
   gravitational systems which involves searching for "islands" in determining
   the entanglement wedge."
   -- 1908.10996@[<A HREF="https://arxiv.org/abs/1908.10996">arXiv</A>][19].

%A D. Frauchiger
%A R. Renner
%T Quantum theory cannot consistently describe the use of itself
%J NatureCommunications
%V 9
%N 3711
%M SEP
%D 2018
%K quantum physics, c2018, c201x, c20xx, zz1018, theory, macroscopic,
   consistent, consistency, inconsistent, Schrodinger, Schrodinger's cat
%X "... we propose a Gedankenexperiment to investigate the question whether
   quantum theory can, in principle, have universal [macroscopic] validity. The
   idea is that, if the answer was yes, it must be possible to employ QT to
   model complex systems that include agents who are themselves using QT.
   Analysing the experiment under this presumption, we find that one agent, upon
   observing a particular measurement outcome, must conclude that another agent
   has predicted the opposite outcome with certainty. The agents' conclusions,
   although all derived within QT, are thus inconsistent. This indicates that
   QT cannot be extrapolated to complex systems, at least not in a
   straightforward manner."
   -- [<A HREF="https://doi.org/10.1038/s41467-018-05739-8">doi:10.1038/s41467-018-05739-8</A>]['18].
   Also see F&R 1604.07422@[<A HREF="https://arxiv.org/abs/1604.07422">arXiv</A>][25/4/18].
   (Also see FW@[<A HREF="https://phys.org/news/2018-09-errors-quantum-world.html">www</A>][19/9/2018] and
    DC@[<A HREF="https://doi.org/10.1038/d41586-018-06749-8">doi:10.1038/d41586-018-06749-8</A>][18/9/2018].)

%A S. Bravyi
%A D. Gosset
%A R. Konig
%T Quantum advantage with shallow circuits
%J Science
%V 362
%N 6412
%P 308-311
%M OCT
%D 2018
%K jrnl, c2018, c201x, c20xx, zz1018, quantum, algorithm, computer, circuit,
   speed, advantage, locality, nonlocality
%X "... Whether a quantum advantage can be rigorously proven in some setting or
   demonstrated experimentally using near-term devices is the subject of active
   debate. We show that parallel quantum algs. running in a constant time period
   are strictly more powerful than their classical counterparts; they are
   provably better at solving certain linear algebra problems assoc. with binary
   quadratic forms. ... gives an unconditional proof of a computational q.adv.
   & simultaneously pinpoints its origin: It is a consequence of quantum
   nonlocality. The proposed q.alg. is a suitable candidate for near-future
   experimental realizations, as it requires only constant-depth q.circuits with
   nearest-neighbor gates on a two-dimensional grid of qubits (quantum bits)."
   -- [<A HREF="https://doi.org/10.1126/science.aar3106">doi10.1126/science.aar3106</A>]['18].

%A Y. Liu
%A et al ...
%A J.-W. Pan
%T Device-independent quantum random-number generation
%T Nature
%V 562
%P 548-551
%M OCT
%D 2018
%K jrnl, c2018, c201x, c20xx, zz1018, physics, quantum, random number,
   generator, generation, QRNG, RNG, DIQRNG
%X "... Device-independent quantum random-number generation (DIQRNG) based on
   the loophole-free violation of a Bell inequality produces genuine,
   unpredictable randomness without requiring any assumptions about the inner
   workings of the devices ... Here we present DIQRNG that is secure against
   quantum and classical adversaries. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-018-0559-3">doi:10.1038/s41586-018-0559-3</A>]['18].
   [Also search for: random RNG] and [also search for: quantum RNG].

%A J. van Apeldoorn
%A S. Gribling
%T Simon's problem for linear functions
%J arXiv
%M OCT
%D 2018
%K TR, c2018, c201x, c20xx, zz1118, Simons problem, quantum computing,
   classical, algorithm, linear function, vanApeldoorn
%X "Simon's prob. [is]: determine if a fn f:{0,1}^n -> {0,1}^n is 1-to-1 or if
   there exists a unique s in {0,1}^n s.t. f(x)=f(x+s) for all x in {0,1}^n,
   given the promise that exactly one of the two holds. A classical alg. that
   can solve this problem for every f requires 2^{Omega(n)} queries to f. Simon
   showed that there is a quantum alg. that can solve this promise problem for
   every f using only O(n) quantum queries to f. A matching lwb on the # of
   q.queries was given by Koiran et al., even for functions f:F^n_p -> F^n_p.
   We give a short proof that O(n) q.queries is optimal even when we are
   additionally promised that f is linear. This is somewhat surprising because
   for linear fns there even exists a classical n-query alg.."
   -- 1810.12030@[<A HREF="https://arxiv.org/abs/1810.12030">arXiv</A>]['18].

%A E. K. Chen
%T Quantum mechanics in a time-asymmetric universe: On the nature of the
   initial quantum state
%J British J. for the Philosophy of Sci., axy068
%M OCT
%D 2018
%K jrnl, c2020, c202x, c20xx, zz0920, Eddy Keming Chen, physics, arrow of time,
   asymmetric, past, future, quantum mechanics
%X "In a q.universe with a strong arrow of time, we postulate a low-entropy
   boundary condition (the past hypothesis, PH) to account for the temporal
   asymmetry. In this article, I show that the PH also contains enough info. to
   simplify the q.ontology and define a natural initial condition. First, I
   introduce 'density-matrix realism', the thesis that the q.state of the
   universe is objective and impure. This stands in sharp contrast to
   wave-function realism ..."
   -- 1712.01666@[<A HREF="https://arxiv.org/abs/1712.01666">arXiv</A>]['20],
      [<A HREF="https://doi.org/10.1093/bjps/axy068">doi:10.1093/bjps/axy068</A>]['20],
      EKC@[<A HREF="https://www.eddykemingchen.net/">.net</A>]['20],
      EKC@[<A HREF="http://ucsd.academia.edu/EddyKemingChen">acad.</A>]['20].

%A A. Kempf
%T Quantum Gravity, Information Theory and the CMB
%J Foundn Physics
%V 48
%N 10
%M OCT
%P 1191-1203
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0219, Achim Kempf, quantum physics,
   information theory, CMB, fluctuations, field, fields, discrete, continuous,
   empty space, spacetime
%X "We review connections between the metric of spacetime[s.t.] & the quantum
   fluctuations of fields. We start with the finding that the s.t.metric can be
   expressed entirely in terms of the 2-pt correlator of the fluctuations of
   q.fields. We then discuss the open question whether the knowledge of only the
   spectra of the q.fluctuations of fields also suffices to determine the
   s.t.metric. ... of interest because spectra are geometric invariants & their
   quantization would, therefore, have the benefit of not requiring the modding
   out of diffeomorphisms. [&] we discuss the fact that spacetime at the Planck
   scale need not nec. be either discrete or cts. Instead, results from
   information theory show that spacetime may be simultaneously discrete & cts
   in the same way that information can. Finally, we review the recent finding
   that a covariant natural ultraviolet cutoff at the Planck scale implies a
   signature in the cosmic microwave background (CMB) that may become
   observable."  [57 refs.]
   -- [<A HREF="https://doi.org/10.1007/s10701-018-0163-2">doi:10.1007/s10701-018-0163-2</A>]['19].
   (AK at [<A HREF="https://uwaterloo.ca/physics-of-information-lab/">uwaterloo</A>]['19].)

%A M. Buchanan
%T In search of lost memories
%J NaturePhysics
%V 15
%P 420
%M MAY
%D 2019
%K physics, jrnl, c2019, c201x, c20xx, zz0123, quantum mechanics, particle,
   pilot, wave, guide, duality, weirdness, Bohm, Bohmian, deBroglie, Couder
%X "In 1980, the physicist David Bohm published a book entitled Wholeness & the
   Implicate Order, in which he speculated about hidden structures that might
   somehow lie behind the mystery of q.entanglement - the weird linking together
   of distant & apparently indep. systems. As a suggestive analogy for the kind
   of structures he had in mind, Bohm referred to a famous memory effect in
   fluids. Place a blob of ink into a viscous liquid confined in the narrow gap
   between two cylindrical walls, & start rotating the inner cylinder. Shearing
   in the fluid will smear the ink out into increasingly fine ribbons, which
   eventually vanish. The ink is apparently gone, leaving only a featureless
   expanse of fluid. But ..."
   -- [<A HREF="https://doi.org/10.1038/s41567-019-0521-9">doi:10.1038/s41567-019-0521-9</A>]['23].
   Also see W-P@[<A HREF="https://en.wikipedia.org/wiki/Wave%E2%80%93particle_duality">wikip</A>]['23] and
   Yves Couder video@[<A HREF="https://www.youtube.com/watch?v=W9yWv5dqSKk">ubend</A>]['23].
   [Also search for: physics Bohm].

%T Time and Causality Across the Sciences
%E S. Kleinberg
%I CUP
%P 282
%M NOV
%D 2019
%K book, text, c2019, c201x, c20xx, zz1119, time, arrow, philosophy, causality,
   cause, effect
%X 1st ed 2019; hb us$65; uk us isbn:1108476678; uk us isbn13:978-1108476676.
   "...  explores what that means for both the metaphysics and epistemology of
   causes - what they are and how we can find them. Across psychology, biology,
   and the social sciences, common themes emerge, suggesting that time plays a
   critical role in our understanding. The increasing availability of large time
   series datasets allows us to ask new questions about causality, necessitating
   new methods for modeling dynamic systems and incorporating mechanistic
   information into causal models."
   [Also search for: time arrow].

%A Z. K. Minev
%A et al ...
%A M. H. Devoret
%T To catch and reverse a quantum jump mid-flight
%J Nature
%V 570
%P 200-204
%M JUN
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0619, physics, quantum theory, discrete,
   continuous, jump
%X "In quantum physics, measurements can fundamentally yield discrete & random
   results. Emblematic of this feature is Bohr's 1913 proposal of q.jumps
   between two discrete energy levels of an atom. ... Despite the
   non-deterministic character of q.physics, is it possible to know if a q.jump
   is about to occur? Here we answer this question affirmatively: we
   experimentally demonstrate that the jump from the ground state to an excited
   state of a superconducting artificial three-level atom can be tracked as it
   follows a predictable 'flight', by monitoring the popln of an auxiliary
   energy level coupled to the ground state. The experimental results
   demonstrate that the evolution of each completed jump is cts, coherent &
   deterministic. We exploit these features, using real-time monitoring &
   feedback, to catch & reverse q.jumps mid-flight - thus deterministically
   preventing their completion. Our findings, which agree with theoretical
   predictions essentially without adjustable parameters, support the modern
   q.trajectory theory & should provide new ground for the exploration of
   real-time intervention techniques in the control of q.systems, such as the
   early detection of error syndromes in q.error correction."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-1287-z">doi:10.1038/s41586-019-1287-z</A>]['19].

%A G. Milburn
%A S. Shrapnel
%T Classical and quantum causal interventions
%J Entropy
%V 20
%N 9
%P 687
%M SEP
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0919, causal, network, model, cause, causality,
   intervention, intervene, classical, quantum
%X "... Causal models are representational devices that can be used as oracles
   for future interventions, to predict how values of some variables will change
   in response to interventions on others. Recent work has generalised concepts
   from this field to situations involving quantum systems, resulting in a new
   notion of quantum c.structure. A key concept in both the classical & q.
   context is that of an intervention. Interventions are the controlled
   operations required to identify causal structure & ultimately the feature
   that endows causal models with empirical meaning. Although interventions are
   a crucial feature of both the c. & q. causal modelling frameworks, to date
   there has been no discussion of their physical basis. ... we consider
   interventions from a physical perspective & show that, in both the c. & q.
   case, they are constrained by the thermodynamics of measurement & feedback
   in open systems. We demonstrate that the perfect 'atomic' or 'surgical'
   interventions characterised by Pearl's famous do-calculus are physically
   impossible, & this is the case for both c. & q. systems."
   -- [<A HREF="https://doi.org/10.3390/e20090687">doi:10.3390/e20090687</A>]['19],
    & [<A HREF="https://espace.library.uq.edu.au/view/UQ:d2e8e2d">UQ</A>]['19].
   auth2@[<A HREF="https://orcid.org/0000-0001-8407-7176">orcid</A>]['19],
   auth2@[<A HREF="https://researchers.uq.edu.au/researcher/16630">UQ</A>]['19].
   [Also search for: quantum causal model] & [also search for: causal model].

%A W. A. Borders
%A et al
%A S. Datta
%T Integer factorization using stochastic magnetic tunnel junctions
%J Nature
%V 573
%P 390-393
%M SEP
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0919, integers, factor, factorisation,
   probabilistic, adiabatic, p bit, pBit, qBit, factors, factorisation,
   computer, computing, Shor, algorithm, prime, composite, number, numbers,
   spintronics
%X "... Probabilistic computing is another unconventional computation scheme
   that shares similar concepts with quantum computing but is not limited by the
   above challenges. The key role is played by a probabilistic bit (a p-bit) -
   a robust, classical entity fluctuating in time between 0 & 1, which interacts
   with other p-bits in the same system using principles inspired by neural
   networks. ... a proof-of-concept experiment for prob.computing using
   spintronics technology, and demonstrate int.factorization, an [e.g.] of the
   optimization class of problems addressed by adiabatic and gated q.computing.
   ... The p-bits are electrically connected to form a functional asynchronous
   n/wk, to which a modified adiabatic q.computing alg. that implements three- &
   four-body interactions is applied. Factorization of integers up to 945 is
   demonstrated with this rudimentary asynchronous probabilistic computer using
   eight correlated p-bits, & the results show good agreement with theoretical
   predictions, thus providing a potentially scalable h/w approach to the
   difficult problems of optimization & sampling."
   -- [<A HREF="https://doi.org/10.1038/s41586-019-1557-9">doi:10.1038/s41586-019-1557-9</A>]['19].
   [Also search for: quantum computing] and
   [also search for: integer factorization algorithm].

%A C. de Rham
%A A. J. Tolley
%T The speed of gravity
%J arXiv
%M SEP
%D 2019
%K TR, physics, c2019, c201x, c20xx, zz0720, deRham, speed, mass, gravity,
   light, cosmology, relativity, gravitational waves, quantum
%X "Within the std effective field theory of General Relativity, we show that
   the speed of gravitational waves deviates, ever so slightly, from luminality
   on cosmological & other spontaneously Lorentz-breaking backgrounds. This
   effect results from loop contributions from massive fields of any spin ...
   speed of grav.waves is in general superluminal at low-energies on NEC
   preserving backgrounds, meaning grav.waves travel faster than allowed by the
   metric to which photons & Std Model fields are minimally coupled. We show
   that departure of the speed from unity increases in the IR & argue that the
   speed inevitably returns to luminal at high energies as required by Lorentz
   invariance ..."
   -- 1909.00881@[<A HREF="https://arxiv.org/abs/1909.00881">arXiv</A>]['20],
      CdeR@[<A HREF="https://www.imperial.ac.uk/people/c.de-rham">Imp.C.</A>]['20].

%A Y. Y. Fein
%A et al
%T Quantum superposition of molecules beyond 25 kDa
%J NaturePhysics
%V 15
%P 1242-1245
%M SEP
%D 2019
%K eJrnl, physics, c2019, c201x, c20xx, zz0821, quantum, mechanics, particle,
   wave, duality, matter, large, molecule, interference
%X "Matter-wave interference experiments ... By increasing the mass of the
   interfering particles ... stringent bounds can be placed on modified q.
   theories such as objective collapse models. ... report interference of a
   molecular library of functionalized oligoporphyrins with masses beyond
   25,000âDa & consisting of up to 2,000 atoms ... results show excellent
   agreement with q.theory & cannot be explained classically. The interference
   fringes reach more than 90% of the expected visibility & the resulting
   macroscopicity value of 14.1 represents an order of magnitude increase over
   previous experiments."
   -- [<A HREF="https://doi.org/10.1038/s41567-019-0663-9">doi:10.1038/s41567-019-0663-9</A>]['21].
   [Also search for: quantum molecule wave].

%A E. Di Valentino
%A A. Melchiorri
%A J. Silk
%T Planck evidence for a closed Universe and a possible crisis for cosmology
%J NatureAstronomy
%V 4
%P 196-203
%M NOV
%D 2019
%O (online 11/2019, vol.4 '20)
%K jrnl, c2019, c201x, c20xx, zz1119, physics, universe, curvature, positive,
   cosmology, flat, open, curved, closed, cosmological constant, lensing,
   microwave background
%X "The recent Planck Legacy 2018 release has confirmed the presence of an
   enhanced lensing amplitude in cosmic microwave background power spectra
   compared with that predicted in the standard L cold dark matter model, where
   L is the cosmological const. ... we further investigate the evidence for
   a closed Universe from Planck, showing that positive curvature naturally
   explains the anomalous lensing amplitude ..."
   -- [<A HREF="https://doi.org/10.1038/s41550-019-0906-9">doi:10.1038/s41550-019-0906-9</A>]['19] (online 11/2019).
   (Also see auth2[<A HREF="https://scholar.google.it/citations?user=wOEchpYAAAAJ&hl=en">www</A>]['19].)

%A J. E. Hirsch
%T Superconductivity, what the H? The Emperor has no clothes
%J Physics and Society
%M JAN
%D 2020
%K publish, perish, JEHirsch, TR, c2020, c202x, c20xx, zz0820, news, views,
   physics, superconductor, citations, publications, Hindex, misuse, abuse,
   jrnl, KPI, KPIs, impact, university, scientific research, bibliometrics, wry,
   quote, quotable, controversial
%X "... For better or for worse, I am most famous (or infamous) for the
   invention of the Hindex. ... In a nutshell, my observation is that about half
   the scientific community loves the Hindex & half hates it, & the Hindex of
   the scientist itself is a great predictor of whether s/he belongs to the 1st
   or the 2nd group, in addition to its other virtues. I am not completely
   unhappy with the impact of my paper, which is by far my most highly cited
   one. As Oscar Wilde said, 'There is only one thing in life worse than being
   talked about ...'. ...  But I have now come to believe that it can also fail
   spectacularly & have severe unintended -ve consequences. I can understand how
   the sorcerer's apprentice must have felt. ..."
   -- 2001.09496@[<A HREF="https://arxiv.org/abs/2001.09496">arXiv</A>]['20].
   [Also search for: publish perish]  and  [also search for: Hirsch Hindex].

%A Zhengfeng Ji
%A A. Natarajan
%A T. Vidick
%A J. Wright
%A H. Yuen
%T MIP* = RE
%J arXiv
%M JAN
%D 2020
%K TR, c2020, c202x, c20xx, zz0220, MIP, RE, spooky, quantum prover, computing,
   physics, entanglement, game, Halting Problem, entangled value,
   undecidability, Tsirelson, commuting, correlation, Connes, embedding,
   conjecture
%X "We show that the class MIP* of languages that can be decided by a classical
   verifier interacting with multiple all-powerful quantum provers sharing
   entanglement is equal to the class RE of rec. enum. langs.. ... builds upon
   the q. low-degree test of (Natarajan & Vidick, FOCS 2018) by integrating
   recent developments from (Natarajan & Wright, FOCS 2019) & combining them
   with the recursive compression framework of (Fitzsimons et al., STOC 2019).
   An immediate byproduct of our result is that there is an efficient reduction
   from the Halting Problem to the problem of deciding whether a two-player
   nonlocal game has entangled value 1 or at most 1/2. Using a known connection,
   undecidability of the entangled value implies a -ve answer to Tsirelson's
   problem: we show, by providing an explicit e.g., that the closure C_{qa} of
   the set of q.tensor product correlations is strictly included in the set
   C_{qc} of q.commuting correlns. Following work of (Fritz, Rev. Math. Phys.
   2012) & (Junge et al., J. Math. Phys. 2011) our results provide a refutation
   of Connes' embedding conjecture from the theory of von Neumann algebras."
   -- 2001.04383@[<A HREF="https://arxiv.org/abs/2001.04383">arXiv</A>]['20].
   (I'm glad that's clear.)  Not yet peer reviewed.
   (Also see discussion at [<A HREF="https://doi.org/10.1038/d41586-020-00120-6">doi:10.1038/d41586-020-00120-6</A>]['20].)

%A B. Greene
%T Until the End of Time: Mind, Matter, and Our Search for Meaning in an
   Evolving Universe
%I Knopf
%P 448
%M FEB
%D 2020
%K book, text, c2020, c202x, c20xx, zz0220, time, entropy, meaning, human,
   science, physics, cosmology, free will
%X "... explores how life and mind emerged from the initial chaos, and how our
   minds, in coming to understand their own impermanence, seek in different ways
   to give meaning to experience: in narrative, myth, religion, creative
   expression, science, the quest for truth ..."
   1st ed 2020; hb us$21; uk us isbn:1524731676; uk us isbn13:978-1524731670.
   [Also search for: consciousness]  and  [also search for: arrow time].

%A L. Henriet
%A et al ...
%A C. Jurczak
%T Quantum computing with neutral atoms
%J arXiv
%M JUN
%D 2020
%O Quantum J., vol.4, p.327, Sep. 2020
%K TR, c2020, c202x, c20xx, zz0122, quantum, computing, qubit, neutral atom
%X "... review the main characteristics of these devices from atoms/qubits to
   application interfaces, & propose a class'n of a wide variety of tasks that
   can already be addressed in a computationally efficient manner in the Noisy
   Intermediate Scale Quantum era we are in. We illustrate how applic'ns ranging
   from optimization challenges to simulation of q.systems can be explored
   either at the digital level (programming gate-based circuits) or at the
   analog level (programming Hamiltonian seqs.). We give evidence of the
   intrinsic scalability of neutral atom q.processors in the 100-1,000 qubits
   range & intro. prospects for universal fault tolerant q.computing &
   applications beyond q.computing."
   -- [<A HREF="https://arxiv.org/abs/2006.12326">arXiv</A>]['22] and in
      QJ[<A HREF="https://doi.org/10.22331/q-2020-09-21-327">doi:10.22331/q-2020-09-21-327</A>]['22].
   [Also search for: quantum computing].

%A Kok-Wei Bong
%A et al ...
%A H. M. Wiseman
%T A strong no-go theorem on the Wigner's friend paradox
%J Nat. Physics
%V ?
%M AUG
%D 2020
%K jrnl, physics, c2020, c202x, c20xx, zz0820, quantum theory, Wigner, friend,
   paradox, measurement, collapse, fact, facts, observation, observer,
   observed, event, events, determinism, superdeterminism, locality,
   objectivity, weirdness, absoluteness, inequality, theorem, Bell,
   inequalities, Bells, KokWeiBong, HMWiseman, GriffithUni
%X "Does quantum theory apply at all scales, inc. that of observers? ... Here,
   by building on a scenario with two separated but entangled friends introduced
   by Brukner, we prove that if q.evol'n is controllable on the scale of an
   observer, then one of 'No-Superdeterminism', 'Locality' or 'Absoluteness of
   Observed Events' - that every observed event exists absolutely, not
   relatively - must be false. We show that although the violation of Bell-type
   inequalities in such scenarios is not in general suff. to demo. the
   contradiction between those three assumptions, new inequalities can be
   derive ..."
   -- [<A HREF="https://doi.org/10.1038/s41567-020-0990-x">doi:10.1038/s41567-020-0990-x</A>][17/8/2020].
   Also see, "Testing the reality of Wigner's friend's observations", 4/2020,
   at 1907.05607@[<A HREF="https://arxiv.org/abs/1907.05607">arXiv</A>]['20], and
   WF@[<A HREF="https://en.wikipedia.org/wiki/Wigner%27s_friend">wikip</A>]['20].

%A M. Van Raamsdonk
%T Spacetime from bits
%J Science
%V 370
%N 6513
%P 198-202
%M OCT
%D 2020
%K jrnl, physics, c2020, c202x, c20xx, zz1020, cosmology, space, time, bits,
   spacetime, conformal field theory, quantum, entanglement, gravity,
   vanRaamsdonk
%X "... Here, I demonstrate that this nongravitational system can be replaced
   with an arbitrarily large collection of noninteracting systems ('bits')
   placed in a highly entangled state. This construction makes manifest the
   idea that spacetime geometry emerges from entanglement between the
   fundamental degrees of freedom of quantum gravity and that removing this
   entanglement is tantamount to disintegrating spacetime. ..."
   -- [<A HREF="https://doi.org/10.1126/science.aay9560">doi:10.1126/science.aay9560</A>]['20].  (That's cleared it up.-)
   [Also search for: Raamsdonk physics].

%A S. Hossenfelder
%T Superdeterminism: A guide for the perplexed
%J arXiv
%M OCT
%D 2020
%K TR, physics, c2020, c202x, c20xx, zz0521, determinism, superdeterminism,
   quantum mechanics, weirdnes, predestination, predetermined, free will,
   Sabine Hossenfelder
%X "Superdeterminism is presently the only known consistent description of
   nature that is local, deterministic, and can give rise to the observed
   correlations of quantum mechanics. I here want to explain what makes this
   approach promising and offer the reader some advice for how to avoid common
   pitfalls. In particular, I explain why superdeterminism is not a threat to
   science, is not necessarily finetuned, what the relevance of future input is,
   and what the open problems are."
   -- 2010.01324@[<A HREF="https://arxiv.org/abs/2010.01324">arXiv</A>]['21].
   [Also search for: superdeterminism] & [also search for: Sabine Hossenfelder].

%A J. J. Halliwell
%A C. Mawby
%T Conditions for macrorealism for systems described by many-valued variables
%J Physical Rev. A: Atomic, Molecular and Optical Physics
%V 102
%P 012209-1-012209-15
%D 2020
%K jrnl, physics, c2020, c202x, c20xx, zz1112, macrorealism, quantum physics,
   reality, Fine's theorem, Leggett-Garg, NSIT, variable
%X "Macrorealism (MR) is the view that a system evolving in time possesses
   definite properties indep. of past or future measurements & is traditionally
   tested for systems described at each time by a single dichotomic variable Q.
   A # of necessary & suff. condns for MR have been derived for a dichotomic
   variable using sets of Leggett-Garg (LG) inequalities, or the stronger no
   signaling in time (NSIT) condns, or a combination thereof. Here we extend
   this framework by establishing nec. & suff. conditions for macrorealism for
   measurements made at two & three times for systems described by variables
   taking three or more values at each time. Our results include a
   generalization of Fine's theorem to many-valued variables for measurements at
   three pairs of times & we derive the corr. complete set of LG ineqs. ..."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevA.102.012209">doi:10.1103/PhysRevA.102.012209</A>]['21],
      [<A HREF="http://hdl.handle.net/10044/1/81473">www</A>][21], and
      auth1@[<A HREF="https://www.imperial.ac.uk/people/j.halliwell">imp.col</A>]['21].
   [Also search for: quantum physics reality].

%A A. N. Pearson
%A et al
%T Measuring the thermodynamic cost of timekeeping
%J Phys. Rev. X
%V 11
%N 021029
%M MAY
%D 2021
%K jrnl, physics, c2021, c202x, c20xx, zz0521, time, thermodynamics, entropy,
   clock, clocks, accuracy
%X "All clocks, in some form or another, use the evolution of nature toward
   higher entropy states to quantify the passage of time. Because of the stat.
   nature of the second law & corr. entropy flows, fluctuations fundamentally
   limit the performance of any clock. This suggests a deep relation between the
   increase in entropy & the quality of clock ticks. Indeed, minimal models for
   autonomous clocks in the quantum realm revealed that a linear reln can be
   derived, where for a limited regime every bit of entropy linearly increases
   the accuracy of quantum clocks. But can such a linear relation persist as we
   move toward a more classical system? We answer this in the affirmative by
   presenting the first experimental investigation of this thermodynamic reln in
   a nanoscale clock. We stochastically drive a nanometer-thick membrane & read
   out its displacement with a radio-freq. cavity, allowing us to identify the
   ticks of a clock. We show theoretically that the max. possible accuracy for
   this classical clock is proportional to the entropy created per tick, similar
   to the known limit for a weakly coupled q.clock but with a different
   proportionality const.. We measure both the accuracy & the entropy. Once
   nonthermal noise is accounted for, we find that there is a linear reln
   between accuracy & entropy and that the clock operates within an order of
   magnitude of the theoretical bound."
   -- [<A HREF="https://link.aps.org/doi/10.1103/PhysRevX.11.021029">doi:10.1103/PhysRevX.11.021029</A>]['21].
   [Also search for: physics time].

%A K. Mack
%T The End of Everything
%I Scribner
%P 256
%M MAY
%D 2021
%K book, text, c2021, c202x, c20xx, zz0622, time, cosmology, universe
%X 1st ed 2021; pb us$10; uk us isbn:1982103558; uk us isbn13:978-1982103552.
   "... tour through five of the cosmos's possible finales: the Big Crunch,
   Heat Death, the Big Rip, Vacuum Decay (the one that could happen at any
   moment!), and the Bounce. ..."

%A E. Distante
%A et al ...
%A S. Welte
%T Detecting an itinerant optical photon twice without destroying it
%J Phys. Rev. Lett.
%V 126
%N #253603
%M JUN
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0721, physics, quantum, photon, detect, track,
   detector, state
%X "Nondestructive quantum measurements are central for quantum physics applns
   ... Employing the toolbox of cavity quantum electrodynamics, we here
   concatenate two identical nondestructive photon detectors to repeatedly
   detect & track a single photon propagating through a 60m long optical fiber.
   By demonstrating that the combined signal-to-noise ratio of the two detectors
   surpasses each single one by about 2 orders of magnitude, we experimentally
   verify a key practical benefit of cascaded nondemolition detectors compared
   to conventional absorbing devices."
   -- [<A HREF="https://doi.org/10.1103/PhysRevLett.126.253603">doi:10.1103/PhysRevLett.126.253603</A>]['21].

%A N. Wolchover
%T Eternal change for no energy: A time crystal finally made real[1]
%J QuantaMagazine
%M JUL
%D 2021
%K news, views, c2021. c202x, c20xx, zz0821, physics, time crystal, Floquet,
   quantum, computing, qubits
%X "... A novel phase of matter that physicists have strived to realize for many
   years, a time crystal is an object whose parts move in a regular, repeating
   cycle, sustaining this constant change without burning any energy. ...
   The time crystal is a new category of phases of matter, expanding the defn of
   what a phase is. ... On July 5, a team based at the Delft Uni. of Tech.[2] in
   the [,n]] reported that they built a Floquet time crystal not in a
   q.processor, but out of the nuclear spins of carbon atoms in a diamond. ..."
   -- [<A HREF="https://www.quantamagazine.org/first-time-crystal-built-using-googles-quantum-computer-20210730/">www</A>]['21].
   [1] 2107.13571@[<A HREF="https://arxiv.org/abs/2107.13571">arXiv</A>]['21].
   [2] 2107.00736@[<A HREF="https://arxiv.org/abs/2107.00736">arXiv</A>]['21].
   [Also search for: physics time].

%A E. Adlam
%T Determinism beyond time evolution
%J arXiv
%M OCT
%D 2021
%K TR, physics, c2021, c202x, c20xx, zz0122, time, arrow, determinism, chance
%X "... we use a constraint-based framework to set out a generalization of
   determinism which does not presuppose temporal directedness, distinguishing
   between strong, weak & delocalised global determinism. We discuss some
   interesting consequences of these generalized notions of determinism, & we
   show that this approach sheds new light on the long-standing debate
   surrounding the nature of objective chance."
   -- 2110.07656@[<A HREF="https://arxiv.org/abs/2110.07656">arXiv</A>]['22],
      auth@[<A HREF="https://scholar.google.com/citations?user=RlTqjZMAAAAJ">sch'lar</A>]['22].
   [Also search for: time arrow].

%A M. O. Renou
%A et al ...
%A M. Navascues
%T Quantum theory based on real numbers can be experimentally falsified
%J Nature
%M DEC
%D 2021
%K jrnl, physics, c2021, c202x, c20xx, zz1221, quantum theory, real,
   complex numbers, number, experiment
%X "... Although most theories of physics are based on real numbers, q.theory
   was the 1st to be formulated in terms of operators acting on complex Hilbert
   spaces. This has puzzled countless physicists, inc. the fathers of the
   theory, for whom a real version of q.theory, in terms of real operators,
   seemed much more natural. In fact, prev. studies have shown that such a
   'real q.theory' can reproduce the outcomes of any multipartite experiment,
   as long as the parts share arbitrary real q.states. Here we investigate
   whether complex #s are actually needed in the q.formalism. We show this to be
   the case by proving that real & complex Hilbert-space formulations
   of q.theory make different predictions in n/wk scenarios comprising
   independent states & measurements. This allows us to devise a Bell-like
   experiment, the successful realization of which would disprove real q.theory,
   in the same way as standard Bell experiments disproved local physics."
   -- [<A HREF="https://doi.org/10.1038/s41586-021-04160-4">doi:10.1038/s41586-021-04160-4</A>]['21].
   (Does that make complex numbers real?-)

%A K. S. Lee
%A et al ...
%A R.Dumke
%T Entanglement between superconducting qubits and a tardigrade
%J arXiv
%M DEC
%D 2021
%K TR, physics, c2021, c202x, c20xx, zz1221, quantum, entanglement, entangled,
   life, lifeform, live, living animal, tardigrade, qubit, igNobel
%X "... We observe coupling between the animal in cryptobiosis & a
   superconducting q.bit & prepare a highly entangled state between this
   combined system & another qubit. The tardigrade itself is shown to be
   entangled with the remaining subsystems. The animal is then observed to
   return to its active form after 420 hours at sub 10mK temperatures & pressure
   of 6x10^{â6} mbar, setting a new record for the conditions that a complex
   form of life can survive."
   -- [<A HREF="https://arxiv.org/abs/2112.07978">arXiv</A>]['21].
   Also see news@[<A HREF="https://www.improbable.com/2021/12/16/ig-nobel-winners-leap-from-magnetized-cockroaches-to-entangled-tardigrades/">igs</A>]['21].
   (What's next, S's cat?)

%A V. Baumann
%A et al ...
%A C. Brukner
%T Generalized probability rules from a timeless formulation of
   Wigner's friend scenarios
%J Quantum
%V 5
%P 524
%D 2021
%K quantum physics, c2021, c202x, c20xx, zz0222, theory, reality, cosmology,
   Wigner, Wigner's friend, entanglement
%X "The q.measurement problem can be regarded as the tension between the two
   alt. dynamics prescribed by q.mechanics: the unitary evolution of the wave fn
   & the state-update rule (or 'collapse') at the instant a measurement takes
   place. The notorious Wigner's friend gedankenexperiment ... in which
   different observers (one of whom is observed by the other) describe one & the
   same interaction differently, one - the Friend - via state-update & the other
   - Wigner - unitarily. This can lead to W. & his friend assigning different
   probs. to the outcome of the same subs. measurement. ... we apply the
   Page-Wootters mechanism (PWM) as a timeless description of W.'s friend-like
   scenarios. We show that the std rules to assign two-time cond. probs. within
   the PWM need to be modified ... identify 3 main defns of such modified rules
   to assign two-time cond.probs., all of which reduce to std q.theory for
   non-W's friend scenarios. However, when applied to the W's friend setup each
   rule assigns different cond.probs., potentially resolving the
   prob.-assignment paradox in a different manner. Moreover, one rule imposes
   strict limits on when a joint prob.distn for the measurement outcomes of W &
   his Friend is well-defined, which single out those cases where W's
   measurement does not disturb the Friend's memory & such a prob. has an
   operational meaning in terms of collectible statistics. Interestingly, the
   same limits guarantee that said measurement outcomes fulfill the consistency
   condition of the consistent histories framework."
   -- [<A HREF="https://doi.org/10.22331/q-2021-08-16-524">doi:10.22331/q-2021-08-16-524</A>]['21],
      1911.09696v4@[<A HREF="https://arxiv.org/abs/1911.09696v4">arXiv</A>]['22],
      lastAuth@[<A HREF="https://www.iqoqi-vienna.at/people/staff/caslav-brukner">v.at</A>]['22].
   [Also search for: Wigner friend].
   (Also see [<A HREF="https://www.newscientist.com/article/mg25333720-800-do-we-create-space-time-a-new-perspective-on-the-fabric-of-reality/">NewSci</A>][2/2/'22].)

%A E. Gibney
%T Nuclear-fusion reactor smashes energy record
%J Nature
%M FEB
%D 2022
%K news, views, c2022, c202x, c20xx, zz0222, physics, nuclear fusion power,
   UK, Culham, JET, ITER, Tokomak
%X "The experimental Joint European Torus has doubled the record for the amount
   of energy made from fusing atoms -- the process that powers the Sun. ...
   [on] 21/12/2021, JET's tokamak produced 59 megajoules of energy over a fusion
   'pulse' of five seconds, more than double the 21.7 megajoules released in
   1997 over around four seconds. Although the 1997 experiment still retains the
   record for 'peak power', it was over a fraction of a sec. & its avg. power
   then was less than half that of today, ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-00391-1">doi:10.1038/d41586-022-00391-1</A>]['22].
   Also see JET@[<A HREF="https://en.wikipedia.org/wiki/Joint_European_Torus">wikip</A>]['24].
   [Also search for: nuclear fusion power].

%A X. Calmet
%A R. Casadio
%A S. D.âH. Hsu
%A F. Kuipers
%T Quantum hair from gravity
%J Phys. Rev. Lett.
%V 128
%N 111301
%M MAR
%D 2022
%K jrnl, physics, c2022, c202x, c20xx, zz0322, quantum theory, relativity,
   gravity, information loss, no, yes, hair, hairy, black hole, blackhole,
   Hawking, paradox, controversial
%X "We explore the relationship between the quantum state of a compact matter
   source & of its asymptotic graviton field. ... there is a one to one map
   between graviton states on the boundary of spacetime & the matter src states.
   Effective field theory allows us to compute a purely q.gravitational effect
   which causes the subleading asymptotic behavior of the graviton state to
   depend on the internal structure of the src. This establishes the existence
   of ubiquitous quantum hair due to gravitational effects."
   -- [<A HREF="https://doi.org/10.1103/PhysRevLett.128.111301">doi:10.1103/PhysRevLett.128.111301</A>]['22].

%A S. Baron
%A K. Miller
%A J. Tallant
%T Out of Time: A Philosophical Study of Timelessness
%I OUP
%P 288
%M APR
%D 2022
%K book, text, OUP, c2022, c202x, c20xx, zz0422, time, timelessness, physics,
   quantum, gravity, space, cause, causal, causation
%X 1st ed 2022; us%68; uk us isbn:0192864882; uk us hb isbn13:978-0192864888.
   "The idea that time does not exist is, for many, unthinkable: time must
   exist. Almost every experience we have tells us so. There has been plenty of
   debate around what time is like, but not whether it exists. The goal of this
   book is to make the absence of time thinkable. Time might not exist.
   Beginning with an empirically flavoured examination of the 'folk' concept of
   time, the book explores the implications this has for our understanding of
   agency, and the extent to which our best physics and best metaphysics are
   compatible with a timeless conception of reality."
   (Also see [<A HREF="https://www.abc.net.au/news/2022-04-17/time-might-not-exist/100993982">abc</A>]['17/4/2022].)
   [Also search for: physics time].

%A N. Furey
%A M. J. Hughes
%T One generation of standard model Weyl representations as a single copy of
   R x C x H x O
%J Physics Lett. B
%V 827
%M APR
%D 2022
%K jrnl, particle physics, maths, c2022, c202x, c20xx, zz0822, complex,
   quaternion, quaternions, octonion, octonions, numbers, division algebra,
   fermion, symmetry, breaking, 32D, Higgs, SU5, SU_5, SU3, SU_3, SU2, SU_2,
   standard model
%X "Peering in from the outside, A = R x C x H x O looks to be an ideal math.
   structure for particle physics. It is 32-D: exactly the size of one full
   generation of fermions. Furthermore, as alluded to earlier in [1], it
   supplies a richer algebraic structure, which can be used, e.g., to replace
   SU(5) with the SU(3)xSU(2)xU(1)/Z_6 symmetry of the std model. ... In this
   article, we solve the fermion doubling problem in the context of A. ..."
   -- [<A HREF="https://doi.org/10.1016/j.physletb.2022.137186">doi:10.1016/j.physletb.2022.137186</A>]['22].
   (Also see auth1@[<A HREF="https://www.furey.space/">www</A>]['22],
    CF@[<A HREF="https://en.wikipedia.org/wiki/Cohl_Furey">wikip</A>]['2] &
    article@[<A HREF="https://www.quantamagazine.org/the-octonion-math-that-could-underpin-physics-20180720/">QuantaMag</A>][8/2022].)

%A L. Postler
%A et al
%T Demonstration of fault-tolerant universal quantum gate operations
%J Nature
%V 605
%P 675-680
%M MAY
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0622, quantum computing, gate, gates, error,
   fault, detection, qubit
%X "... Here we demonstrate a fault-tolerant universal set of gates on two
   logical qubits in a trapped-ion quantum computer. ... make use of the
   recently introduced paradigm of flag fault tolerance, where the absence or
   presence of dangerous errors is heralded by the use of auxiliary flag
   qubits. We perform a logical two-qubit controlled-NOT gate between two
   instances of the seven-qubit colour code ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-04721-1">doi:10.1038/s41586-022-04721-1</A>]['22].

%A G. Schilling
%T The Elephant in the Universe: Our Hundred-Year Search for Dark Matter
%I HarvardUP
%P 376
%M MAY
%D 2022
%K book, physics, cosmology, c2022, c202x, c20xx, zz0722, universe, dark matter
%X 1st ed 2022; hb us$26; uk us isbn:0674248996; uk us isbn 13:978-0674248991.
   "... explores the fascinating history of the search for dark matter. Evidence
   for its existence comes from a wealth of astronomical observations. ...
   Yet so far dark matter has escaped every experiment. ..."

%A L. S. Madsen
%A et al
%T Quantum computational advantage with a programmable photonic processor
%J Nature
%V 606
%P 75-81
%M JUN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0622, physics, photonic, quantum computing,
   Gaussian boson sampling, GBS
%X "... we report quantum computational advantage using Borealis, a photonic
   processor offering dynamic programmability on all gates implemented. We
   carry out Gaussian boson sampling (GBS) on 216 squeezed modes entangled with
   3D connectivity ... Borealis requires only 36âmu s. This runtime advantage is
   over 50 million times ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-04725-x">doi:10.1038/s41586-022-04725-x</A>]['22].

%A S.Ebadi
%A et al
%T Quantum optimization of maximum independent set using Rydberg atom arrays
%J Science
%V 376
%N 6598
%M JUN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0622, quantum computing, speedup, algorithm,
   maximum independent set problem
%X "... Using Rydberg atom arrays with up to 289 qubits in two spatial dim., we
   experimentally investigate q.algs. for solving the max. indep. set problem.
   ... find that the problem hardness is controlled by the soln degeneracy & #
   of local minima, & we experimentally benchmark the q.alg.'s performance v.
   classical sim.annealing. On the hardest graphs, we observe a superlinear
   q.speedup in finding exact solns in the deep circuit regime ..."
   -- [<A HREF="https://www.science.org/doi/10.1126/science.abo6587">doi:10.1126/science.abo6587</A>][22'].
   [Also search for: quantum computing algorithm].

%A S. Hossenfelder
%T Existential Physics: A Scientist's Guide to Life's Biggest Questions
%I Viking
%P 272
%M AUG
%D 2022
%K book, c2022, c202x, c20xx, zz0722, physics, quantum theory, mechaniscs,
   philosophy, weird, nonlocal, locality, realism, Sabine Hossenfelder
%X 1st ed 2022; hb us$28; uk us isbn:1984879456. uk us isbn13:978-1984879455.
   "... H. takes on the biggest Qs in physics: Does the past still exist? Do
   particles think? Was the universe made for us? Has physics ruled out free
   will? Will we ever have a theory of everything? ..."
   (Also see auth@[<A HREF="https://sabinehossenfelder.com/">www</A>]['22].)
   [Also search for: Sabine Hossenfelder].
   (A video by SH on QM [<A HREF="https://www.youtube.com/watch?v=hpkgPJo_z6Y">ubend</A>]['23].)

%A D. P. Nadlinget
%A et al
%T Experimental quantum key distribution certified by Bell's theorem
%J Nature
%V 607
%P 682-686
%M JUL
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0722, post quantum, communication, secure, key,
   encryption, Bennett-Brassard, Ekert, entanglement, DIQKD
%X "Cryptographic key exchange protocols traditionally rely on comp.conjectures
   such as the hardness of prime factorization to provide security against
   eavesdropping attacks. Remarkably, q.key dist'n protocols such as the
   Bennett-Brassard scheme provide info.-theoretic security against such attacks
   a much stronger form of security ... However, q.protocols realized so far are
   subject to a new class of attacks exploiting a mismatch between the q.states
   or measurements implemented & their theoretical modelling, as demonstrated in
   numerous experiments ... we present the experimental realization of a
   complete q.key distribution protocol immune to these vulnerabilities,
   following Ekert's pioneering proposal to use entanglement to bound an
   adversary's info. from Bell's theorem. ...  we obtain 95,628 key bits with
   device-indep. security from 1.5âmillion Bell pairs created during eight hours
   of run time. We take steps to ensure that info. on the measurement results is
   inaccessible to an eavesdropper. These measurements are performed without
   space-like separation. ... shows that provably secure cryptography under
   general assumptions is possible with real-world devices, & paves the way for
   further q.info. applications based on the device-independence principle."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-04941-5">doi:10.1038/s41586-022-04941-5</A>]['22]. (Also see in same issue.)
   [Also search for: quantum communication].

%A Wei Zhange
%A et al
%T A device-independent quantum key distribution system for distant users
%V 607
%P 687-691
%M JUL
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0722, post quantum, communication, secure, key,
   encryption, entanglement
%X "Device-indep. q.key distribution (DIQKD) enables the generation of secret
   keys over an untrusted channel using uncharacterized & potentially untrusted
   devices ... can be certified by a statistical test using a Bell inequality
   ... we present an experimental system that enables for DIQKD between two
   distant users. The experiment is based on the generation & analysis of
   event-ready entanglement between two indep'ly trapped single rubidium atoms
   located in buildings 400âmetre apart ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-022-04891-y">doi:10.1038/s41586-022-04891-y</A>]['22]. (Also see in same issue.)
   [Also search for: quantum communication].

%A N. Furey
%A M. J. Hughes
%T Division algebraic symmetry breaking
%J Physics Lett. B
%V 831
%M AUG
%D 2022
%K jrnl, physics, maths, c2022, c202x, c20xx, zz0822, Cohl Nichol,
   standard model, octonion, octonions, quaternion, quaternions, complex,
   numbers, symmetries, SU_2, SU2
%X "Reframing certain well-known particle models in terms of normed division
   algebras leads to two new results for BSM physics. (1) We identify a seq. of
   complex structures which induces a cascade of breaking symmetries:
   Spin(10) -> Pati-Salam -> Left-Right symmetric -> Std model + B-L (both
   pre- & post-Higgs-mechanism). These complex structures derive from the
   octonions, then from the quaternions, then from the complex numbers. (2) We
   provide, also for the 1st time we believe, an explicit demonstration of
   left-right symmetric Higgs representations stemming from quaternionic
   triality, tri(H). Upon the breaking of su(2)_R, our Higgs reduces to the
   familiar std model Higgs."
   -- [<A HREF="https://doi.org/10.1016/j.physletb.2022.137186">doi:10.1016/j.physletb.2022.137186</A>]['22].
   (Also see auth1@[<A HREF="https://www.furey.space/">www</A>]['22],
    CF@[<A HREF="https://en.wikipedia.org/wiki/Cohl_Furey">wikip</A>]['2] &
    article@[<A HREF="https://www.quantamagazine.org/the-octonion-math-that-could-underpin-physics-20180720/">QuantaMag</A>][8/2022].)

%A B. Cox
%A J. Forshaw
%T Black Holes: The Key to Understanding the Universe
%I MarinerBooks
%M MAR
%D 2023
%K book, text, C2023, c202x, c20xx, information, black hole, physics, cosmology,
   space time
%X 1st ed 2023; hb us$29; uk us isbn:0062936697; uk us isbn13:978-0062936691.
   "... holes as the key to our understanding of the fundamentals of our
   universe and perhaps all other universes. ..."

%A D. Castelvicchi
%A E. Gibney
%T 'Spooky' quantum-entanglement experiments win physics Nobel
%J Nature
%V ?
%P ?-?
%M OCT
%D 2022
%K news, c2022, c202x, c20xx, zz1022, Nobel prize, physics, quantum,
   John Clauser, Anton Zeilinger, Alain Aspect, computing, information,
   entanglement, Bell's inequality
%X "Three q.physicists have won the 2022 Nobel Prize in Physics for their
   experiments with entangled photons, in which particles of light become
   inextricably linked. Such experiments have laid the foundations for an
   abundance of q.technologies, inc. q.computers & communications. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-03088-7">doi:10.1038/d41586-022-03088-7</A>]['22].
   * Also see the [<A HREF="https://www.bbc.com/news/science-environment-63121287">bbc</A>][5/10/2022].
   [Also search for: Bell's inequality].

%A M. Henriques
%T Why does time go forwards, not backwards?
%I BBC
%M OCT
%D 2022
%K c2022, c202x, c20xx, zz1122, time, arrow, physics, entropy, thermodynamics,
   universe, big bang, bigBang, reversibility, clocks
%X "... The issue is that Newton's laws work about twice as well as we might
   expect them to. They describe the world we move through every day - the world
   of people, the hands that move around a clock & even the apocryphal fall of
   certain apples - but they also account perfectly well for a world in which
   people walk backwards, clocks tick back afternoon to morning, & fruit soars
   up from the ground to its tree-branch. ..."
   -- [<A HREF="https://www.bbc.com/future/article/20221003-why-does-time-go-forwards-not-backwards">bbc</A>][10/2022].
   [Also search for: time arrow].
   Also see [<A HREF="http://www.allisons.org/ll/MML/Entropy/Gas/">Ideal Gas</A>].

%A Kunkun Wang
%A Ruqiao Xia
%A L. Bresque
%A Peng Xue
%T Experimental demonstration of a quantum engine driven by entanglement and
   local measurements
%J Phys. Rev. Res.
%V 4
%P L032042
%M SEP
%D 2022
%K jrnl, c2022, c202x, c20xx, physics, quantum, information, thermodynamics,
   engine, fueled, measurement, energy
%X "... Recently, a two-qubit engine was put forward as an appropriate platform
   to tackle these challenges. Here we achieve an experimental simulation &
   provide the direct experimental proof of these findings using single photons
   & linear optics. Encoding the qubits by polarization & transverse spatial
   modes of single photons, entanglement is created through the interaction
   between them. We show that, upon local measurement, classical mutual info.
   can be extracted in order to fuel a quantum measurement engine. ..."
   -- [<A HREF="https://doi.org/10.1103/PhysRevResearch.4.L032042">doi:10.1103/PhysRevResearch.4.L032042</A>]['22].
   Also see auth3@[<A HREF="https://orcid.org/0000-0002-1978-690X">orC'd</A>]['22].
   [Also search for: quantum information thermodynamics].

%T IBM Unveils 400 Qubit-Plus Quantum Processor and Next-Generation
   IBM Quantum System Two
%M NOV
%D 2022
%K news, c2022, c202x, c20xx, zz1122, quantum computer, quantumComputer,
   computing, Osprey, IBM
%X "... "The new 433 qubit 'Osprey' processor brings us a step closer to the
   point where q.computers will be used to tackle previously unsolvable
   problems," said Dr. DarÃo Gil, Senior Vice President ..."
   -- [<A HREF="https://newsroom.ibm.com/2022-11-09-IBM-Unveils-400-Qubit-Plus-Quantum-Processor-and-Next-Generation-IBM-Quantum-System-Two">ibm</A>][9/11/2022].
   "... 433-Qubit Osprey Chip ..."
   [<A HREF="https://spectrum.ieee.org/ibm-quantum-computer-osprey">ieee</A>]['22].
   [Also search for: quantum computer].

%T Breakthrough in nuclear fusion energy announced
%I BBC
%M DEC
%D 2022
%K news, physics, c2022, c202x, c20xx, zz1222, nuclear fusion power,
   inertial confinement, LLNL, NIF
%X "... lasers had input 2.05 megajoules (MJ) of energy *to the target*,
   which had then produced 3.15 MJ of fusion energy output. ..."
   -- [<A HREF="https://www.bbc.com/news/science-environment-63950962">bbc</A>]['13/12/2022].
   But, "each laser shot requires about 300MJ of energy from the grid"
   -- Phys. Today [<A HREF="https://doi.org/10.1063/PT.6.2.20221213a">doi:10.1063/PT.6.2.20221213a</A>][13/12/2022].
   Also see [<A HREF="https://www.llnl.gov/">llnl</A>]['22] and
   NIF@[<A HREF="https://en.wikipedia.org/wiki/National_Ignition_Facility">wikip</A>]['22].
   [Also search for: nuclear fusion power].

%A M. Akhtar
%A et al ...
%A W. K. Hensinger
%T A high-fidelity quantum matter-link between ion-trap microchip modules
%J NatureComms
%V 14
%N #531
%M FEB
%D 2023
%K jrnl, c2023, c202x, c20xx, zz0223, quantum computer, computing, qubits,
   USussex, UniSussex
%X "... we present the demonstration of a quantum matter-link in which ion
   qubits are transferred between adjacent QC modules. Ion transport between
   adjacent modules is realised at a rate of 2424/sec & with an infidelity
   associated with ion loss during transport below 7x10^{-8}. [&] we show that
   the link does not measurably impact the phase coherence of the qubit. ..."
   -- [<A HREF="https://doi.org/10.1038/s41467-022-35285-3">doi:10.1038/s41467-022-35285-3</A>]['23].
   Also see the bbc[<A HREF="https://www.bbc.com/news/science-environment-64492456">9/2/2023</A>].
   [Also search for: quantum computer].

%A T. Hertog
%T On the Origin of Time: Stephen Hawking's Final Theory
%I PenguinBooks
%P 330
%M MAR
%D 2023
%K book, text, physics, c2023, c202x, c20xx, zz0323, time, arrow, cosmology,
   hologram, holographic projection, big bang, causality, laws
%X 1st ed 2023; uk us isbn:0593128443; uk us isbn13:978-0593128442.
   "... new theory of the cosmos that could account for the emergence of life.
   ... They were startled to find a deeper level of evolution in which the
   physical laws themselves transform & simplify until particles, forces, & even
   time itself fades away. This discovery led them to a revolutionary idea: The
   laws of physics are not set in stone but are born & co-evolve as the universe
   they govern takes shape. ..."
   (Also see [<A HREF="https://www.sciencefocus.com/space/stephen-hawking-final-theory/ ">www</A>]['23].)
   [Also search for: time arrow]  and  [also search for: Hawking physics].

%A D. H. Wolpert
%T What can we know about that which we cannot even imagine?
%J arXiv
%P 30
%M AUG
%D 2022
%O 'A sliver of reality,' Aeon mag., 2022
%K essay, TR, c2022, c202x, c20xx, zz0423, mind, intelligence, concept,
   concepts, ideas, imagination, physics, cosmology, epistemics, reality,
   maths, SFI
%X "In this essay I will consider a seq. of questions, ending with one about the
   breadth & depth of the epistemic limitations of our our sci. & maths.. I will
   then suggest a possible way to circumvent such limitations. I begin by
   considering questions about the biological function of intelligence. ..."
   -- [<A HREF="https://arxiv.org/abs/2208.03886">arXiv:2208.03886</A>]['23].
   Also see article@[<A HREF="https://aeon.co/essays/ten-questions-about-the-hard-limits-of-human-intelligence">aeon.co</A>]['23]
   and DHW@[<A HREF="https://www.santafe.edu/people/profile/david-wolpert">santafe</A>]['23].
   [Also search for: Wigner lecture].

%A T. Jones
%T Simulation of, and with, First Generation Quantum Computers
%I Oxford U.
%D 2022
%K c2022, c202x, c20xx, zz0923, quantum computing, computer, DPhil, thesis,
   phd, simulation, Tyson Jones
%X "... thesis is about utilising 1st gen. q.computers & predicting their
   behaviour using classical computers. It develops novel q.algs. to perform
   variational minimisation, Hamiltonian diagonalisation, & approximate circuit
   recompilation, all intendedly compatible with near-future machines. It also
   devises classical algs. for efficiently simulating q.variational algs.,
   emulating q.computers using high-performance supercomputing facilities ..."
   -- at [<A HREF="https://ora.ox.ac.uk/objects/uuid:b666f280-249c-4218-8112-f88d348f198f">ox.ac.uk</A>]['23].
   (Also see TJ@[<A HREF="https://tysonjones.io/index.html">www</A>]['23].)

%A G. F. Lewis
%A B. J. Brewer
%T Detection of the cosmological time dilation of high-redshift quasars
%J Nature Astronomy
%V 475
%M JUL
%D 2023
%K jrnl, astronomy, c2023, c202x, c20xx, zz0723, physics, time, dilation,
   expansion, cosmology, quasar
%X "... owing to the expansion of space, observations of the distant cosmos
   should be time dilated & appear to run slower than events in the local
   universe. ... present the identification of cosmic time dilation in a sample
   of 190 quasars monitored for over two decades ..."  [42 refs]
   -- [<A HREF="https://doi.org/10.1038/s41550-023-02029-2">doi:10.1038/s41550-023-02029-2</A>]['23],
   auth1@[<A HREF="https://www.sydney.edu.au/science/about/our-people/academic-staff/geraint-lewis.html">USydney</A>][2023].

%A Kaizhe Wang
%A et al
%T Centrifugal flows drive reverse rotation of Feynman's sprinkler
%J Physical Rev. Lett.
%V 132
%N 4, #044003
%M JAN
%D 2024
%K physics, c2024, c202x, c20xx, zz0224, Feynman, sprinkler, rotation, rotate,
   fluid, hydrodynamics
%X "... reversibility in hydromechanical sprinklers that auto-rotate while
   ejecting fluid from S-shaped tubes raises fundamental [Qs] that remain
   unresolved. ... report on precision experiments that reveal robust &
   persistent reverse rotn under suction & a model that accounts for the
   observed motions. We implement an ultralow friction bearing in an apparatus
   that allows for free rotn under ejection & suction for a range of flow rates
   & arb. long times. Flow measurements reveal a rocketlike mechanism shared by
   the rev. & fwd modes that involves angular momentum flux, whose subtle
   manifestation in the reverse case stems from centrifugal effects for flows in
   curved conduits. These findings answer F's long-standing Q by providing
   quantitatively accurate explanations of both modes, & they suggest further
   inquiries into flux-based force generation & the roles of geometry &
   Reynolds number."
   -- [<A HREF="https://doi.org/10.1103/PhysRevLett.132.044003">doi:10.1103/PhysRevLett.132.044003</A>]['24].

%A E. Gibney
%T Pioneering nuclear-fusion reactor shuts down: what scientists will learn
%J Nature
%V 626
%P 13-14
%M JAN
%D 2024
%K news, c2024, c202x, c20xx, zz0224, physics, nuclear, fusion power, energy,
   Culham, UK, UKAEA, JET, Joint European Torus, tokamak, ITER
%X "Scientists have begun to decommission one of the world's foremost
   nuclear-fusion reactors, 40 years after it began operations. Researchers will
   study the 17-year process of dismantling the Joint European Torus (JET) near
   Oxford ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-024-00135-3">doi:10.1038/d41586-024-00135-3</A>]['24].
   Also see JET@[<A HREF="https://ccfe.ukaea.uk/programmes/joint-european-torus/">ukaea</A>]['24],
   JET@[<A HREF="https://en.wikipedia.org/wiki/Joint_European_Torus">wikip</A>]['24].
   (?Slightly premature ... also see fusion JET c2024.)
   [Also search for: fusion power JET].

%T Breaking new ground: JET Tokamak's latest fusion energy record shows
   mastery of fusion processes
%I EUROfusion
%M FEB
%D 2024
%K news, c2024, c202x, c20xx, zz0224, physics, nuclear, fusion power, energy,
   deuterium tritium, Culham, UK, UKAEA, JET, Joint European Torus, tokamak,
   ITER
%X "... (JET) facility have set a new world energy record of 69 megajoules
   released in sustained & controlled fusion energy. ... 69.26 megajoules of
   heat released during a single pulse ... Released over six seconds from only
   0.21 milligrams of fuel ... 20 times the amount of energy released in a
   recent shot at the U.S. National Ignition Facility (NIF) at Lawrence
   Livermore National Laboratory [LLNL] in Oct. 2023 ..."
   -- [<A HREF="https://euro-fusion.org/eurofusion-news/dte3record/">www</A>]['24].
   Also see the [<A HREF="https://www.bbc.com/news/science-environment-68233330">bbc</A>]['9/2/2024].

%A N. C. J. Papadopoulos
%A et al
%T Reductive quantum phase estimation
%J arXiv
%M FEB
%D 2024
%L TR, c2024, c202x, c20xx, zz0224, quantum computing, phase estimation,
   algorithm, QPE, RQPE
%X "... two well-known methods have been developed in distinct contexts, namely,
   Ramsey interferometry (RI) in atomic & molecular physics & quantum phase
   est. (QPE) in q.computing. We demonstrate that these canonical examples are
   instances of a larger class of phase est. protocols, which we call reductive
   q.phase est. (RQPE) circuits. ... present an explicit alg. that allows one to
   create an RQPE circuit. [It] distinguishes an arbitrary set of phases with a
   fewer # of qubits & unitary applications ..."
   -- [<A HREF="https://arxiv.org/abs/2402.04471">arxiv:2402.04471</A>]['24].
   [Also search for: quantum phase].

%A J. Verstraten
%A et al
%T In-situ imaging of a single-atom wave packet in continuous space
%J arXiv
%M APR
%D 2024
%K TR, c2024, c202x, c20xx, zz0424, quantum physics, atom, wave packet, image
%X "... we use quantum gas microscopy to image the in-situ spatial distribution
   of deterministically prepared single-atom wave packets as they expand in a
   plane. We achieve this by controllably projecting the expanding wavefunction
   onto the sites of a deep optical lattice & subsequently performing
   single-atom imaging ...
   -- [<A HREF="https://arxiv.org/abs/2404.05699">arxiv:2404.05699</A>]['24].

%A S. Neyens
%A et al
%T Probing single electrons across 300-mm spin qubit wafers
%J Nature
%V 629
%P 80-95
%M MAY
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0524, quantum computing, computer, qubit,
   qubits, spin
%X "... we present a testing process using a cryogenic 300-mm wafer prober to
   collect high-volume data on the performance of hundreds of
   industry-manufactured spin qubit devices at 1.6âK. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07275-6">doi:10.1038/s41586-024-07275-6</A>]['24].
   [Also search for: quantum computer].

%A A. Forrest
%T Escape from Shadow Physics: The Quest to End the Dark Ages of Quantum Theory
%I KayBasicBooks
%P 496
%D 2024
%K physics, c2024, c202x, c20xx, zz0624, quantum, mechanics, determinism,
   pilot wave
%X 1st ed 2024; hb us$30; uk us isbn:1541675789 ISBN-13:978-1541675780.
   "... Kay takes up Einstein's torch: reality isn't mysterious or dependent on
   human measurement, but predictable & independent of us. ... research with
   little drops of oil. These droplets behave as particles do in the
   long-overlooked q.theory of pilot waves; crucially, they showcase q.behavior
   while being described by classical physics. ..."

%A A. Barzegar
%A D. Oriti
%T Epistemic-pragmatist interpretations of quantum mechanics: A comparative
   assessment
%J Foundations of Physics
%V 54
%N 5
%P 1-34
%M OCT
%D 2024
%K jrnl, c2024, c202x, c20xx, zz1024, quantum, physics, philosophy, reality,
   Copenhagen interpretation
%X "... we investigate similarities & differences between the main
   neo-Copenhagen (or 'epistemic-pragmatist') interpretations of q.mechanics
   ... & the simultaneous avoidance of hidden variables, while maintaining the
   q.formalism unchanged. We argue that there is a single general interpretive
   f/wk in which the core claims that the various interpretations in the class
   are committed to, & which they emphasize to varying degrees, can be rep.. We
   also identify, however, remaining differences ..."
   -- [<A HREF="https://arxiv.org/abs/2210.13620">arxiv:2210.13620</A>]['24],
      [<A HREF="https://doi.org/10.1007/s10701-024-00804-3">doi:10.1007/s10701-024-00804-3</A>]['24].

%A A. Constantin
%A D. Bartlett
%A H. Desmond
%A P. G. Ferreira
%T Statistical patterns in the equations of physics and the emergence of a
   meta-law of nature
%J arXiv
%M AUG
%D 2024
%K TR, c2024, c202x, c20xx, zz1024, physics, law, pattern
%X "... Zipf's law states that the freq. of any word in a large corpus of text
   is roughly inversely prop. to its rank in the freq. table, we investigate
   whether similar patterns for the dist'n of operators emerge in the eqns of
   physics. We analyse three corpora of formulae & find, using sophisticated
   implicit-likelihood methods, that the freq. of operators as a fn of their
   rank in the freq. table is best described by an exponential law with a stable
   exponent, in contrast with Zipf's inverse power-law. Understanding the
   underlying reasons behind this stat. pattern may shed light on Nature's modus
   operandi or reveal recurrent patterns in physicists' attempts to formalise
   the laws of Nature ..."
   -- [<A HREF="https://arxiv.org/abs/2408.11065">arxiv:2408.11065</A>]['24].
   (?curiosity or something deep?)

%A A. Aspect
%T Einstein and the Quantum Revolutions
%I Uni. Chicago Press
%D 2024
%K book, text, physics, c2024, c202x, c20xx, zz1124, quantum, entanglement,
   Bell's inequality
%X 1st ed 2024; hb $27; uk us isbn:0226832015; uk us isbn13:978-0226832012.
   "... [AA] a co-recipient of the 2022 Nobel Prize in Phys. 'for experiments
   with entangled photons, establishing the violation of Bell inequalities &
   pioneering q.information sci.. ...' ..."
   (Also see comment: [<A HREF="https://doi.org/10.1038/d41586-024-03473-4">www</A>]['24].)

%A T. Ord
%T Bounds on the rates of growth and convergence of all physical processes
%J arXiv
%M OCT
%D 2024
%K TR, c2024, c202x, c20xx, zz1124, physics, computable, thesis, Busy Beaver,
   limit, rate
%X "The upper limit on what is computable in our universe is unknown, but widely
   believed to be set by the Turing machine - with a fn being physically
   comp. iff it is T.-computable. I show how this apparently mild assumption
   leads to generous yet binding limits on how quickly or slowly any directly
   measurable physical phenomenon can grow or converge - limits that are
   intimately connected to Rado's Busy Beaver fn. I conjecture that these limits
   are novel physical laws governing which rates of growth & convergence are
   possible in our universe." 
   -- [<A HREF="https://arxiv.org/abs/2410.10928v1">arxiv:2410.10928v1</A>]['24].
   [Also search for: busy beaver].


%A M. Kaufmann
%A P. Manolios
%A J. Strother Moore
%T Computer-Aided Reasoning: An Approach
%I KluwerAcademic
%M JUN
%D 2000
%K ACL2, ACL, book, text, introduction, intro, verification, Lisp, proof,
   computer programming language definition, PLD, specification. logic,
   industrial strength, Boyer-Moore theorem proving, automated, automatic,
   prover, Nqthm, c2000, c200x, c20xx
%X "How to use ACL2"  v2.8 c2004;
   hb; uk us isbn:0792377443; uk us isbn13:978-0792377443.
   -- [<A HREF="http://www.cs.utexas.edu/users/moore/acl2/">...moore/acl2/</A>]['04]; uk us isbn:0792377443.
   -- [<A HREF="http://www.cs.utexas.edu/users/moore/acl2/acl2-doc.html#User's-Manual">User's-Manual</A>]['04].
   [Also search for: theorem proving].

%T Computer-Aided Reasoning: ACL2 Case Studies
%E M. Kaufmann
%E P. Manolios
%E J. Strother Moore
%I KluwerAcademic
%M JUN
%D 2000
%K ACL2, ACL, Nqthm, computer programming language, c2000, c200x, c20xx,
   study, book, text, verification, automatic, automated, theorem proving,
   prover, proved, properties
%X "What can be done with ACL2"  v2.8 c2004.
   hb; uk us isbn:0792377443; uk us isbn13:978-0792377443.
   -- [<A HREF="http://www.cs.utexas.edu/users/moore/acl2/">...moore/acl2/</A>]['04]; isbn:0792378490.
   [Also search for: theorem proving].

%A P. Sewell
%A J. J. Leifer
%A K. Wansbrough
%A F. Z. Nardelli
%A M. Allen-Williams
%A P. Habouzit
%A V. Vafeiadis
%T Acute: High-level programming language design for distributed computation
%J J. Functional Programming
%V 17
%P 547-612
%D 2007
%K Acute, jrnl, JFP, FP, c2007, c200x, c20xx, parallel, distributed, languages,
   PLD, definition, channel, channels, threads, ML, SML, zz0807
%X "... describe an experimental language, Acute, which extends an ML core to
   support distributed development, deployment, & execution, allowing type-safe
   interaction between separately built programs. ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796807006442">doi:10.1017/S0956796807006442</A>]['07].


%T Military Standard Ada Programming Language
%I American-National-Standards-Institute-Inc.
%M FEB
%D 1983
%K Ada, imperative, parallel, concurrent, programming language definition, PLD,
   computing, ANSI, MIL-STD, 1815A, c1983, c198x, c19xx
%X <IMG SRC="/~lloyd/tildeImages/Vehicles/tank.small.gif"> .


%A A. Abel
%A S. Adelsberger
%A A. Stzer
%T Interactive programming in Agda - Objects and graphical user interfaces
%J JFP
%V 27
%P e8
%M JAN
%D 2017
%K jrnl, JFP, FP, c2017, c201x, c20xx, zz0617, Agda, ooAgda, OOP, copattern,
   copatterns, coinductive type, types, GUI, GUIs, computer programming language
%X "We develop a methodology for writing interactive and object-based programs
   (in the sense of Wegner) in dependently typed FP languages. The methodology
   is implemented in the ooAgda library. ooAgda provides a syntax similar to the
   one used in object-oriented programming languages, thanks to Agda's copattern
   matching facility. The library allows for the development of graphical user
   interfaces (GUIs), including the use of action listeners ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796816000319">doi:10.1017/S0956796816000319</A>]['17]  (54pp).
   (Also see Agda@[<A HREF="https://en.wikipedia.org/wiki/Agda_(programming_language)">wikip</A>][17].)

%A A. Vezzosi
%A A. Mortberg
%A A. Abel
%T Cubical Agda: A dependently typed programming language with univalence and
   higher inductive types
%J JFP
%M APR
%D 2021
%K jrnl, FP, JFP, c2021, c202x, c20xx, zz0421, type, dependent, dependant,
   types, system, Agda, functional programming language
%X "... Cubical type theory provides a solution by giving computational meaning
   to Homotopy Type Theory and Univalent Foundations, in particular to the
   univalence axiom and higher inductive types (HITs). ... describes an ext'n of
   the dependently typed functional [PL] Agda with cubical primitives, making it
   into a full-blown proof assistant with native support for univalence and ..."
   -- [<A HREF="https://doi.org/10.1017/S0956796821000034">doi:10.1017/S0956796821000034</A>]['21].
   [Also search for: Agda].


%A J. W. Backus
%A F. L. Bauer
%A J. Green
%A C. Katz
%A J. McCarthy
%A P. Naur
%A A. J. Perlis
%A H. Rutishauer
%A K. Samelson
%A B. Vauquois
%A J. H. Wegstein
%A A. van Wijngarden
%A M. Woodger
%T Revised Report on the algorithmic language ALGOL 60
%I IFIP
%O CACM, Vol.6, No.1, Jan. 1963
%K Algol 60, Algol60, Algol-60, imperative programming language definition,
   c1963, c196x, c19xx, A60, PLD, L3Ref, L4Ref, c1963, c196x, c19xx, quote,
   quotable, quip, IFIP
%X ''Here is a language so far ahead of its time, that it was not only an
   improvement on its predecessors, but also on on nearly all its successors.''
    -- C. A. R. Tony Hoare, 'Hints on Programming Language Design',
       Stanford AI Lab., Memo AIM-224, STAN-CS-73-403, Dec '73.  [p27]
       (thanks to Doug Merritt for finding this 4/'04).
   (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/Algol60/">Algol60</A>].)


%A A. van Wijngaarden
%T Orthogonal design and description of a formal language
%I Stichting Mathematisch Centrum
%D 1965
%K Algol68, Algol 68, TR, c1965, c196x, c19xx, zz0724, vanWijngaarden,
   orthogonality, orthogonal, programming language design, IFIP WG2.1
%X "Amsterdam, 4th April 1972: One of the basic documents in the history of
   ALGOL 68 is MR 76, Orthogonal design and description of a formal language.
   It was only made available to members of the IFIP WG 2.1 at its meeting in
   St. Pierre de Chartreuse in October 1965. ..."
   -- [<A HREF="https://ir.cwi.nl/pub/9208">ir.cwi.nl/pub/9208</A>]['24].
   [Also search for: Algol68].

%A C. H. Lindsey
%T ALGOL 68 with fewer tears
%J COMPJ
%V 15
%N 2
%P 176-188
%M MAY
%D 1972
%K COMPJ, jrnl, Algol 68, Algol68, A68, computer programming language, PL,
   c1972, c197x, c19xx
%X [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_15/Issue_02/150176.sgm.abs.html">paper</A>][9/'01],
   -- [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_15/Issue_02/">issue</A>][9/'01].
   (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/Algol68/">Algol68</A>].)

%E A. van Wijngaarden
%E B. J. Mailloux
%E J. E. L. Peck
%E C. H. A. Koster
%E M. Sintzoff
%E C. H. Lindsey
%E L. G. L. T. Meertens
%E R. G. Fisker
%T Revised Report on the Algorithmic Language Algol 68
%I SpringerVerlag
%D 1976
%O Acta Informatica, 5, pp.1-236 (1975)<!-- from the www -->;
   SIGPLAN Notices, 12(5), pp.1-70 (1977).
%K Algol 68, Algol68, Algol-68, A68, imperative programming language definition,
   PLD, orthogonal, design, orthogonality, quote, quotable, two 2 level grammar,
   grammars, 2LVWGG 2LG, formal theory, book, text, vanWijngaarden,
   c1976, c197x, c19xx, zz0724
%X [<A HREF="https://doi.org/10.1145/954652.1781176">doi:10.1145/954652.1781176</A>]['24] abs ACM,
   [<A HREF="https://dl.acm.org/doi/pdf/10.1145/954652.1781176">ACM</A>]['24] pdf in full, and
   [<A HREF="https://doi.org/10.1007/978-3-642-95279-1">doi:10.1007/978-3-642-95279-1</A>]['24] (Springer).
      A quote: "0.1.2. Orthogonal design: The number of independent primitive
      concepts has been minimized in order that the language be easy to
      describe, to learn, and to implement. On the other hand, these concepts
      have been applied "orthogonally" in order to maximize the expressive power
      of the language while trying to avoid deleterious superfluities."
   Also see books on A68 by  1. Lindsey and van der Meulen,  2. Pagan.
   (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/Algol68/">Algol68</A>].)

%A C. H. Lindsey
%T A History of Algol 68
%J ACM SIGPLAN Notices
%V 28
%N 3
%P 97-132
%D 1993
%K algol-68, algol, a68, alogol68, programming language, development,
   c1993, c199x, c19xx, computing, computer


%A L. Cardelli
%T Amber
%B Combinators and Functional Languages
%I SpringerVerlag
%S LNCS
%V 242
%E G. Cousineau
%E P-L. Curien
%E B. Robinet
%D 1985
%K Amber, functional programming language definition, FP, PLD,
   applicative, mac implementation, graphics, process, data type, types,
   polymorphic, polymorphism, channel, persistent persistence,
   object, objects, OO, OOP, OOPS, c1985, c198x, c19xx


%A K. E. Iverson
%T A Programming Language
%I Wiley
%D 1962
%K APL, text book, applicative, operator, operators, one liner, one-liner,
   c1962, c196x, c19xx, programming language definition, PLD, www, HREF, FTP
%X [<A HREF="http://www.acm.org/sigapl/">www.acm.org/sigapl</A>][10/'01],
   -- [<A HREF="ftp://watserv1.uwaterloo.ca/languages/apl/">FTP APL</A>][10/'01],
   -- [<A HREF="news:comp.lang.apl">comp.lang.apl newsgroup</A>],
   also see the programming language 'J'.

%A N. D. Thomson
%A R. P. Polivka
%T APL2 in Depth
%I SpringerVerlag
%D 1995
%K APL, APL2, book, text, programming language, zz0995, c1995, c199x, c19xx
%X uk us isbn:0-387-94213-0;  $39.95.
   Olivier Lefevre  <!-- email: lefevre at ACFcluster.nyu.edu --> [9/95].


%A R. A. Brooker
%T The Autocode programs developed for the Manchester University computers
%J COMPJ
%V 1
%N 1
%P 15-21
%D 1958
%K Autocode, jrnl, COMPJ, c1968, c195x, c19xx, computer architecture,
   programming language, program
%X "...describes 2 programs written for the Manchester University Computers,
   which enable these machines to accept programs written in a simplified form."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/1.1.15">doi:10.1093/comjnl/1.1.15</A>]['05] See issue #3.

%A R. A. Brooker
%T Further Autocode facilities for the Manchester (Mercury) computer
%J COMPJ
%V 1
%N 3
%P 124-127
%D 1958
%K Autocode, jrnl, COMPJ, c1958, c195x, c19xx, computers, Manchester,
   Ferranti Mercury
%X [<A HREF="http://dx.doi.org/10.1093/comjnl/1.3.124">doi:10.1093/comjnl/1.3.124</A>]['05]  See issue #1.


%A S. C. Johnson
%A B. W. Kernighan
%T The programming language B
%R TR 8
%I AT and T Bell Labs
%M JAN
%D 1973
%K TR, c1973, c197x, c19xx, zz0624, B, bb, C, cc, programming language
%X "B is a computer language designed by D. M. Ritchie and K. L. Thompson,
   for primarily non-numeric applications such as system programming. ..."
   -- paper@[<A HREF="https://www.bell-labs.com/usr/dmr/www/bintro.html">bellLabs</A>][2024].
   "[B was] parent of C (and child of BCPL)" according to Ritchie 1993.
   (Beware there are other language(s) called 'B'.)
   [Also search for: BB CC language].

%A S. Schneider
%T The B-Method
%I Palgrave Macmillan
%P 384
%M JUL
%D 2001
%P 384
%K B, BB, SEES, USES, book, text, software engineering, c2001, c200x, c20xx,
   SWE
%X about stg25;  uk us isbn:033379284X; uk us isbn13:978-0333792841.
   (B comes after Z, I think.-)


%A J. G. Kemeny
%A T. E. Kurtz
%T Basic Programming (2nd ed)
%I Wiley
%D 1967
%K BASIC, book, text, imperative programming language definition, PLD,
   c1967, c196x, c19xx
%X uk us isbn:0-471-46830-4.   library of congress cat' card number 70 138911.


%A R. J. W. Housden
%T A note on list-processing in BCL
%J COMPJ
%V 12
%N 4
%P 332-341
%M NOV
%D 1969
%K BCL, computer programming language, list, lists, definition, PLD, Lisp,
   jrnl, COMPJ, c1969, c196x, c19xx
%X ...BCL a general purpose language with special emphasis on data structures.
   The basic LISP functions are defined in BCL and examples given of
   recursive functions. A program to input and
   differentiate polynomial expression is described.
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/12.4.332">doi:0.1093/comjnl/12.4.332</A>]['05].


%A M. Richards
%T The portability of the BCPL compiler
%J SPE
%V 1
%P 135-146
%D 1971
%K jrnl, SPE, BCPL, basic CPL, ocode, boot strap, bootstrap,
   c1971, c197x, c19xx, systems programming implementation language,
   imperative, programming language definition, PLD
%X [Also search for: BCPL language] and [also search for: CPL language].

%A M. Richards
%T How BCPL evolved from CPL
%J COMPJ
%V 56
%N 5
%P 664-670
%M MAY
%D 2013
%K jrnl, COMPJ, c2013, c201x, c20xx, zz0513, programming language history,
   CPL, BCPL, development
%X "... how the programming language BCPL developed from the work on the design
   & implementation of Combined Programming Language (CPL). It shows that BCPL
   is essentially just CPL with all the difficult bits removed & with just a few
   extensions. The CPL project lasted from early 1962 to December 1966 & the
   first outline of BCPL appeared in 1966. Its first compiler was implemented at
   MIT in early 1967 &, surprisingly, the language is still used commercially &
   by individuals all over the world."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxs026">doi:10.1093/comjnl/bxs026</A>]['13].
   [Also search for: BCPL language] and [also search for: CPL language].


%A O. Lehrmann Madsen
%A B. Moller-Pedersen
%A K. Nygaard
%T Object-Oriented Programming in the BETA Programming Language
%I AddisonWesley
%P 350
%M JUN
%D 1993
%K book, text, c1993, c199x, c19xx, BETA, programming language definition, PLD,
   object oriented, OO, OOP, Mjolner System, Simula, origins
%X "In the beginning there was Simula - designed by Kristen Nygaard and
   Ole-Johan Dahl at the Norwegian Computing Center in the 1960s, the first
   language to introduce the techniques now known as [OOP]. Spreading from the
   use of Simula in an expanding range of applications, OOP has achieved great
   importance with the commercial success of languages like Java, C++,
   Smalltalk, and Eiffel. Now, from the birthplace of OOP, comes the BETA
   programming language, for which this book is the definitive guide."
      uk us isbn:0201624303.
   Reprinted by Mjolner Informatics with permission from Addison-Wesley
   2000 Mjolner Informatics A/S.
   -- [<A HREF="http://www.daimi.au.dk/~beta/">beta@daimi.au.dk</A>][5/'08].

%A B. Kernighan
%A D. Ritchie
%T The C Programming Language
%I PrenticeHall
%D 1978
%O Bell-Labs
%K C, cc, classic, imperative programming language definition, PLD, unix,
   c1978, c197x, c19xx, good, book, text, Kernighan, Kernigan
%X Brian Kernighan and Dennis Ritchie; see also ANSI C ('89) and C++.
   pb; uk us isbn:0131101633; uk us isbn13:978-0131101630.
   <IMG SRC="/~lloyd/tildeImages/Vehicles/indian.small.gif">
   The last good thing written in C was Franz Schubert's Ninth Symphony
   -- <!-- email: gvw at cs.vu.nl --> Gregory V. Wilson.
   [Also search for: cc language].

%T ANSI C
%D 1989
%K C, cc, imperative programming language definition, ANSI, ANSI-C, ANSIC,
   c1989, c198x, c19xx
%X American National Standard X3.159, 1989.
   [Also search for: cc language].

%A D. Ritchie
%T The development of the C language
%J Second History of Programming Languages Conference
%W Cambridge, Mass.
%P ?-?
%M APR
%D 1993
%O Sigplan, 26(3), pp.201-208, 1993
%K conf, B, bb, C, cc, imperative programming language, Unix, 2nd,
   c1993, c199x, c19xx
%X BCPL to B to C.
   "... [C's] parent B and its grandparent BCPL" ..."
   -- [<A HREF="https://doi.org/10.1145/155360.155580">doi:10.1145/155360.155580</A>]['24],
      paper@[<A HREF="https://www.bell-labs.com/usr/dmr/www/chist.html">BellLabs</A>]['24].
   [Also search for: BCPL language], and for CPL.
   Via enews,  email: oz at nexus.yorku.ca (ozan s. yigit,   '94 ?).

%A P. van der Linden
%T Expert C Programming
%I PrenticeHall
%P 353
%D 1994
%K book, text, c1994, c199x, c19xx, vanDerLinden, C, CC, computer programming
%X 1st ed 1994; pb us$31; uk us isbn:0131774298; uk us isbn13:978-0131774292.


%A B. Stroustrup
%T The C++ Programming Language
%I AddisonWesley
%P 1030
%D 2000
%K book, text, c2000, c200x, c20xx, zz0318, C++, Cpp, Cplusplus, C plus plus,
   computer, standard library, OO OOP, programming language, PLD,
   C++98, Cpp98, C++11, Cpp11
%X "...six parts: Introduction: Chapters 1 through 3 give an overview of the
   C++ language, the key programming styles it supports, and
   the C++ standard library. "
   3rd ed, 2000; hb, us$52; uk us isbn:0201700735; uk us isbn13:978-0201700732.
   C++11, 1368 pages ...
   4th ed, 2014; hb, us$68; uk us isbn:0321958322; uk us isbn13:978-0321958327.

%A B. Stroustrup
%T Programming: Principles and Practice Using C++
%I AddisonWesley
%P 1088
%D 2008
%K book, text, c2008, c200x, c20xx, zz0508, Cpp, Cplusplus, C plus plus, C++,
   computer programming
%X pb, us$60; uk us isbn:0321543726; uk us isbn13:978-0321543721.

%A N. M. Josuttis
%T The C++ Standard Library: A Tutorial and Reference
%I AddisonWesley
%P 832
%D 1999
%K book, text, c1999, c199x, c19xx, zz0408, Cplusplus, Cpp, C plus plus, C++,
   template, templates, STL, OO, OOP, objects, introduction, intro
%X "... pairs and auto_ptr, numeric limits, the Standard Template Library (STL)
   basics, containers, iterators, algorithms, vectors, lists, deques, strings,
   sets, multisets, bitsets, maps, multimaps, stacks, queues, iterator adapters,
   function objects, element requirements, value and reference semantics,
   complex numbers, valarrays, stream classes, stream manipulators and
   formatting, file I/O, internationalization, and locales. ..."
   hb, us$59; uk us isbn:0201379260; uk us isbn13:978-0201379266.

%A P. J. Plauger
%T The Draft Standard C++ Library
%I PrenticeHall
%P 590
%D 1995
%K C, Cpp, C++, Cplusplus, C plus plus, programming language, book, text,
   zz0196, c1995, c199x, c19xx
%X tb; uk us isbn:0131170031; uk us isbn13:978-0131170032.
   [also search for: Cplusplus].

%A K. E. Macphee
%A T. I. Dix
%T A framework for dynamic checks of C arrays via a C++ class
%J Proc. of the Eleventh Aust. Software Eng. Conf.  (ASWEC-98)
%W Adelaide, .au
%P 57-65
%D 1998
%K IEEE, conf, TIDix, Katriona, cc, c++, Cpp, c plus plus, cplusplus,
   array, bound, bounds, check, TIDix, c1998, c199x, c19xx
%X uk us isbn:0818691875.

%A S. Meyers
%T Effective Modern C++: 42 Specific Ways to Improve Your Use of C++11 and C++14
%I OReilly
%D 2014
%K book, text, c2014, c201x, c20xx, zz0318, C++, Cpp, CplusPlus, C plus plus,
   C++11, Cpp11, C++14, Cpp14, programming language
%X "... auto declarations, range-based for loops, lambda expressions, and
   rvalue references change the face of C++, to say nothing of the new
   concurrency features. And then there are the idiomatic changes. 0 and
   typedefs are out, nullptr and alias declarations are in. ..."
   1st ed 2014; pb, us$40; uk us isbn:1491903996; uk us isbn13:978-149190399.


%A O. Cornes
%A et al
%T Professional C# programming
%I WroxPress
%D 2001
%P 1200
%K C#, book, manual, C-sharp, Csharp, computer programming language, Microsoft,
   MS, dot net, .net, zz0901, c2001, c200x, c20xx
%X isbn:1-86100-499-0.  About US$60, au$128.

%A E. Gunnerson
%T A Programmer's Introduction to C#
%I Apress
%P 540
%M JUN
%D 2001
%K C#, book, text, c2001, c200x, c20xx, C-sharp, Csharp, programming language,
   dot net, .net, c2001, c200x, c20xx
%X pb; uk us isbn:1893115623; uk us isbn13:978-1893115620.

%A A. Hejlsberg
%A P. Golde
%A S. Wiltamuth
%T C# Language Specification
%I AddisonWesley
%P 432
%M OCT
%D 2003
%K book, C#, C-sharp, Csharp, programming language definition, PLD
%X us$30; uk us isbn:0321154916; uk us isbn13:978-0321154910978-0321154910..

%A J. Albahari
%A B. Albahari
%T C# 3.0 in a Nutshell: A Desktop Quick Reference
%I OReilly
%P 858
%D 2007
%K book, text, guide, c2007, c200x, c20xx, zz0408, programming, source code,
   cc, Csharp, C Sharp, C#, microsoft, dot net, .net, LINQ
%X pb; uk us isbn:0596527578; uk us isbn13:978-0596527570.

%A A. Troelsen
%T Pro C# 2008 and the .NET 3.5 Platform
%I Apress
%P 1370
%D 2007
%K book, text, c2007, c200x, c20xx, C#, Csharp, C sharp, dot net, .net,
   net3.5, OO, OOP, computer programming, microsoft, API, APIs, LINQ
%X 4th ed, hb, us$38; uk us isbn:1590598849; uk us isbn13:978-1590598849.



%T Caml Light
%D 1997
%K CAML, Caml light, Inria, functional programming language, FP, zz0301,
   c1997, c199x, c19xx
%X [<A HREF="http://caml.inria.fr/">caml.inria</A>],
   -- [<A HREF="http://caml.inria.fr/distrib-caml-light-eng.html">distrib</A>][3/01],
   [also search for: OCaml].


%A R. Plasmeijer
%A M. van Eekelen
%T Clean language report version 2.0
%D 2002
%K Clean, functional programming language, FP, uniqueness type, typing, types,
   programming language definition, PLD, c2002, c200x, c20xx,
   destructive update
%X [<A HREF="http://www.cs.ru.nl/~clean/">clean</A>]['05],
     -- [<A HREF="http://www.cs.ru.nl/~clean/contents/contents.html">contents</A>]['05],
   -- [<A HREF="ftp://ftp.cs.kun.nl/">FTP, see /pub/Clean</A>][11/94].



%A L. VanderHart
%A S. Sierra
%T Practical Clojure
%I Apress
%P 232
%M JUN
%D 2010
%K book, text, c2010, c201x, c20xx, zz0411, Clojure, Lisp, JVM, FP,
   programming language definition, PLD,
%X 1st ed 2011; pb us$31; uk us isbn:1430272317; isbn13:978-1430272311.
   "... demonstrates the use of the language through examples, including
   features such as STM and immutability, which may be new to programmers
   coming from other languages. ..."
   [Also search for: clojure programming language].

%A M. Fogus
%A C. Houser
%T The Joy of Clojure: Thinking the Clojure Way
%I ManningPubl.
%P 300
%M MAR
%D 2011
%K book, text, C2011, c201x, c20xx, Clojure, programming language, JVM, Lisp
%X 1st ed 2011; pb us$29; uk us isbn:1935182641; uk us isbn13:978-1935182641.
   "... Clojure is a dynamic programming language that targets the
   Java Virtual Machine. ..."
   [Also search for: clojure programming language].

%A A. Rathore
%T Clojure in Action
%I ManningPubl.
%P 475
%M MAR
%D 2011
%K book, text, C2011, c201x, c20xx, Clojure, programming language, JVM, Lisp
%X 1st ed 2011; pb is$31; uk us isbn:1935182595; uk us isbn13:978-1935182597.
   "Clojure is a new version of Lisp that runs on the Java Virtual Machine.
   It is a functional language, which means that it is ideal for the growing
   need for concurrent programming and for specialized tasks like creating
   domain specific languages. ..."
   [Also search for: clojure programming language].



%A J. Jaffar
%A S. Michaylov
%A P. J. Stuckey
%A R. H. C. Yap
%T The CLP(R) language and system
%J TOPLAS
%V 14
%N 3
%M JUL
%D 1992
%K CLP, CLPR, CLP(R), constraint logic programming language definition, PLD,
   jrnl, TOPLAS, LP, Prolog, Monash, Melbourne, c1992, c199x, c19xx
%X [<A HREF="http://www.cs.monash.edu.au/">CSci Monash home</A>]


%A B. Liskov
%A J. Guttag
%T Abstraction and Specification in Program Development
%I MITpress
%D 1986
%K CLU, programming language, abstract datatype data type, ADT,
   module, modular, OO OOP, c1986, c198x, c19xx
%X <!-- email: mday at note.lcs.mit.edu (Mark Day) (9/'94) --> .
   us isbn:0262121123;   CLU is in an appendix

%A B. Liskov
%A R. Atkinson
%A T. Bloom
%A E. Moss
%A J. Craig Schaffert
%A R. Scheifler
%A A. Snyder
%T CLU Reference Manual
%I SpringerVerlag
%D 1979
%O MIT/LCS/TR-225
%K CLU, imperative programming language definition, PLD, module, modular,
   abstract datatype data type, ADT, OO OOP, c1979, c197x, c19xx,
   book, text, MIT, TR 225, TR225
%X There are two portable CLU implementations, both of which compile CLU to C.
   pclu is the implementation done at MIT.  You can get it by anonymous
   ftp from    ftp.lcs.mit.edu    in the pub/pclu directory.
   CLU2C is the implementation done at Tokyo Institute of Technology.
   You can get it by anonymous ftp from ftp.is.titech.ac.jp in the
   pub/clu2c directory.
   -- <!-- email: mday at note.lcs.mit.edu --> (Mark Day) (9/'94).


%T Cobol
%I CODASYL Committee
%D 1960
%K Cobol, COmmon Business Oriented Language, programming definition, PLD,
   c1960, c196x, c19xx
%X ANS X3.23-1968; and ANS X3.23-1974.


%A A. Hillegass
%T Cocoa Programming for Mac OS X
%I AddisonWesley
%P 464
%D 2008
%K book, c2008, c200x, c20xx, Apple, MAC, OSX, Xcode, interface builder,
   Objective C, ObjectiveC, windows
%X 3rd ed 2008, pb, us$30, uk us isbn:0321503619; uk us isbn13:978-0321503619.


%A D. W. Barron
%A J. N. Buxton
%A D. F. Hartley
%A E. Nixon
%A C. Strachey
%T The main features of CPL
%J COMPJ
%V 6
%N 2
%P 134-143
%M JUL
%D 1963
%K COMPJ, jrnl, CPL, programming language definition, PLD, BCPL,
   c1963, c196x, c19xx, Titan, Atlas
%X "... provides an informal account of CPL, a new PL currently being
   implemented for the Titan at Cambridge & the Atlas at London University.
   ... based on, & contains the concepts of, ALGOL 60. In addition there are
   extended data descriptions, cmd & expression structures, provision for
   manipulating non-numerical objects, & comprehensive IO facilities. However,
   CPL is not just another proposal for the extension of ALGOL 60, but has been
   designed from 1st principles & has a logically coherent structure."
   NB. CPL = Combined Programming Language
   broken?[<A HREF="http://dx.doi.org/10.1093/comjnl/6.2.134">doi:10.1093/comjnl/6.2.134</A>]['05],
   -- [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_06/Issue_02/060134.sgm.abs.html">paper</A>][8/'01],
   -- [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_06/Issue_02/">issue</A>][8/'01];
   [also search for: BCPL language].

%A G. F. Coulouris
%A T. J. Goodey
%A R. W. Hill
%A R. W. Keeling
%A D. Levin
%T The London CPL1 compiler
%J COMPJ
%V 11
%N 1
%P 26-30
%D 1968
%K jrnl, COMPJ, CPL, compile, programming language, c1968, c196x, c19xx
%X [<A HREF="http://dx.doi.org/10.1093/comjnl/11.1.26">doi:10.1093/comjnl/11.1.26</A>]['05].
   [Also search for: CPL language].


%A M. Hanus
%T Report on Curry (ver.0.8.2)
%I Inst. fur Informatik, Christian-Albrechts Universitat, .de
%D 2006
%K Curry, programming language definition, PLD, functional, logic, concurrent,
   residuation, narrowing, FP, LP, LFP, FLP, multiparadigm, multi-paradigm,
   c2006, c200x, c20xx
%X "... Curry: An Integrated Functional Logic Language
   (Version 0.8.2 of March 28, 2006) ..."
   -- [<A HREF="http://www.informatik.uni-kiel.de/~mh/curry/">curry@uni-kiel.de</A>]['07],
   -- [<A HREF="http://danae.uni-muenster.de/~lux/curry/">@uni-muenster</A>]['07].


%A V. Vepsalainen
%T ECMAScript - The journey of a programming language from an idea to a standard
%J arXiv
%M MAY
%D 2023
%O EURAS conf 2023
%K ECMAScript, c2023, c202x, c20xx, zz0523, programming language, web, www,
   browser, HTML, javascript
%X "A sig. portion of the web is powered by ECMAScript. ... we will go through
   the movements that led to the dominant posn of ECMAScript, evaluate the
   factors leading to it, & consider its evolution using the Futures Triangle
   framework & the theory of standards wars."
   -- [<A HREF="https://arxiv.org/abs/2305.01373">arxiv:2305.01373</A>]['23].
   [Also search for: javascript].

%A B. Meyer
%T Eiffel, The Language
%I PrenticeHall
%P 300
%D 1992
%K text, book, Eiffel, object oriented, OO, OOP, c1992, c199x, c19xx,
   imperative programming language definition, PLD
%X pb; uk us isbn:0132479257; uk us isbn13:978-0132479257.

%A J. Armstrong
%A R. Virding
%A M. Williams
%T Concurrent Programming in Erlang
%I PrenticeHall
%P 350
%D 1993
%K Erlang, text, book, parallel, concurrent, asynchronous message passing,
   functional, applicative, FP, programming language definition, PLD,
   www, HREF, FTP, c1993, c199x, c19xx
%X pb; uk us isbn:0-132857928; uk us isbn13:978-0132857925.
   2nd edn'96.
   -- [<A HREF="ftp://euagate.eua.ericsson.se:/pub/eua/erlang/info">Erlang info</A>].

%A J. W. Lloyd
%T Programming in an integrated functional and logic language
%J J. F. and L. Programming
%V 1999
%N 3
%M MAR
%D 1999
%K jrnl, JFLP, c1999, c199x, c19xx, zz0623, LP, FP, LFP, FLP, Escher,
   programming language definition, PLD
%X "Escher is a general-purpose, declarative prog. lang. that integrates the
   best features of both functional & logic prog. langs. It has types & modules,
   higher-order & meta-prog..."
   -- [<A HREF="http://danae.uni-muenster.de/lehre/kuchen/JFLP/articles/1999/A99-03/A99-03.html">uniMuenster</A>]['23],
      [<A HREF="https://www.semanticscholar.org/paper/Programming-in-an-Integrated-Functional-and-Logic-Lloyd/be123de6355749b88f7ad107dbdf526340cfbe44">semSchol</A>]['23],
      [<A HREF="https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=31d9a554f61ced1304ecd0ded9fca6fee2173b99">c'teseer</A>]['23].
   [Also search for: FLP FP LP].

%A J. Armstrong
%T EX11 - A GUI in a concurrent functional language
%J 3rd ACM SIGPLAN Erlang Workshop.
%W Snowbird
%P ?-?
%M SEP
%D 2004
%K wShop, c2004, c200x, c20xx, Erlang, FP, programming
%X [<A HREF="http://www.erlang.se/workshop/2004/ex11.pdf">pdf</A>]['04],
   -- [<A HREF="http://www.erlang.se/publications/index.shtml">erlang.se</A>]['05].


%A M. Metcalf
%A J. K. Reid
%T The F Programming Language
%I OUP
%D 1996
%K F, book, text, OUP, c1996, c199x, c19xx, FF, programming language definition,
   PLD, numerical, scientific
%X "[F] is a dramatic new development in scientific programming. Building on the
   well established strengths of the Fortran family of languages, it retains the
   powerful numerical & data abstraction capabilities of its parent language,
   Fortran 90. This book is the defining document for the language, setting out
   the complete syntax & semantics of F in a readable but thorough way. It
   begins with an introductory chapter, then describes the features of F:
   language elements, expressions & assignments, control constructs, program
   units and procedures, array features, intrinsic procedures & input/output
   facilities. ...".   pb; uk us isbn:198500262; uk us isbn13:978-0198500261.
   [Also search for: FF book]. (!-)

%A R. Pickering
%T Foundations of F#
%I Apress
%P 360
%D 2007
%K book, text, c2007, c200x, c20xx, zz0511, F, FF, Fsharp, F sharp,
   programming language, dot net, dotnet
%X 1st ed 2007; hb us$33; uk us isbn:1590597575; uk us isbn13:978-1590597576.
   [Also search for: FF book]. (!-)


%A J. Backus
%T Fortran
%D 1954
%K Fortran, imperative programming language definition, PLD,
   c1954, c195x, c19xx, FORmula TRANslation, history, origins
%X Fortran I   design 1954, compiler 1957;  FORmula TRANslation.
   Fortran II (with subroutines) 1958.
   Fortran IV 1962.
   Fortran 66, Fortran IV standardised ASA X3.9-1966.
   Fortran 77.
   Fortran 90 / 95 array proc, ADTs, modules, pointers.

%A W. E. Mayo
%A M. Cwiakala
%T Programming with FORTRAN 77
%I McGrawHill
%S Schaum's Outline's series
%P 352
%D 1995
%K book, text, c1995, c199x, c19xx, imperative programming language,
   fortran77, f77, g77, zz0607
%X ppb, us$14; uk us isbn:0070411557; uk us isbn13:978-0070411555.
   [Also search for: fortran95],
   -- [<A HREF="http://www.gnu.org/software/gcc/fortran/">fortran@gnu</A>]['07].

%A M. Metcalf
%A J. Reid
%T Fortran 90/95 Explained
%I OUP
%P 368
%M JUN
%D 1999
%K book, text, OUP, Fortran, Fortran90, Fortran95, f90, f95,
   c1999, c199x, c19xx, imperative programming language, zz1299
%X stg18, Au$46, paperback; uk us isbn:0198505582; uk us isbn13:978-0198505587.
   Now has array processing, ADTs, modules, pointers.
   [also search for: Fortran95]
   -- [<A HREF="http://www.gnu.org/software/gcc/fortran/">fortran@gnu</A>]['07]
   -- [<A HREF="http://www.g95.org/">g95.org</A>['08].

%A M. Counihan
%T Fortran 95
%I UCLpress
%D 1996
%P 401
%K book, text, programming language, Fortran95, Fortran90, f95, zz0399,
   c1996, c199x, c19xx
%X us$38; rev in Comp Rev p448 Sep 98;
   pb; uk us isbn:1857283678; uk us isbn13:978-1857283679.
   Proposed standard for Fortran-95.
   -- [<A HREF="http://www.gnu.org/software/gcc/fortran/">fortran@gnu</A>]['07]
   -- [<A HREF="http://www.g95.org/">g95.org</A>['08].

%A I. Chivers
%A J. Sleightholme
%T Introduction to Programming with Fortran: With coverage of
   Fortran 90, 95, 2003 and 77.
%I SpringerVerlag
%P 592
%M DEC
%D 2005
%K book, text, c2005, c200x, c20xx, fortran2003, f2003, fortran95, f95,
   fortran90, f90, fortran77, f77, g77, imperative programming language,
   scientific computing
%X pb, us$56; uk us isbn:1846280532; uk us isbn13:978-1846280535.
   -- [<A HREF="http://www.gnu.org/software/gcc/fortran/">fortran@gnu</A>]['07]
   -- [<A HREF="http://www.g95.org/">g95.org</A>['08].

%A M. Metcalf
%A J. Reid
%A M. Cohen
%T Modern Fortran Explained
%I OUP
%P 512
%M MAY
%D 2011
%K book, text, OUP, c2011, c201x, c20xx, zz0611, Fortran90, f90, Fortran95, f95,
   Fortran2003, Fortran2008, f2008, Fortran, coarray, coarrays,
   computer programming language, scientific
%X 4th ed 2011; pb us$54; uk us isbn:0199601429; uk us isbn13:978-0199601424.
   "Modern Fortran Explained expands on its predecessor, Fortran 95/2003
   Explained. The opening chapters contain a complete description of Fortran 95,
   extended by Fortran 2003 allocatable array features. Coverage of the other
   additional features of Fortran 2003 follows, before new chapters on coarrays
   and the many other enhancements of Fortran 2008. The distinction between the
   three language levels is maintained throughout, allowing readers to
   understand and amend legacy code as well as the new features."

%T The state of Fortran
%M MAR
%D 2022
%K Fortran, TR, c2022, c202x, c20xx, zz0422, computer programming language,
   scientific computing
%X "A community of developers has formed to modernize the Fortran ecosystem. ...
   we describe the high-level features of Fortran that continue to make it a
   good choice for scientists & engineers in the 21st century. Ongoing efforts
   inc. the development of a Fortran std library & package manager, the
   fostering of a friendly & welcoming online community, improved compiler
   support, & language feature development. The lessons learned are common
   across contemporary prog.langs. & help reduce the learning curve & increase
   adoption of Fortran."
   -- 2203.15110@[<A HREF="https://arxiv.org/abs/2203.15110">arXiv</A>]['22].

%A E. Allen
%A D. Chase
%A V. Luchango
%A J-W. Maessen
%A S. Ryu
%A G. L. Steel jr.
%A S. Tobin-Hochstadt
%R The Fortress Language Specification, version 0.618
%I Sun Microsystems
%M APR
%D 2005
%P 111
%K Fortress, programming language definition, PLD, c2005, c200x, c20xx,
   object, OO, OOP, trait, traits
%X "...secure Fortran..." not compatible, except for intended applic. domain.
   [also search for: Sisal] - attempt to wean scientists off Fortran.
   -- [<A HREF="http://research.sun.com/projects/plrg/fortress0618.pdf">pdf</A>][4/'05].



%A J. H. Conway
%T FRACTRAN: A simple universal programming language for arithmetic
%B Open Problems in Communication and Computation
%I Springer Verlag
%P 4-26
%D 1987
%K c1987, c198x, c19xx, zz0821, John Horton Conway, JHConway, JHC, FRACTRAN,
   PLD, game, computing, complete, integers
%X "To play the fraction game corresponding to a given list f1,f2,...,fk of
   fractions & starting int. N, you repeatedly multiply the int. you have at any
   stage (initially N) by the earliest f_i in the list for which the answer is
   integral. Whenever there is no such f_i, the game stops."
   -- [<A HREF="https://doi.org/10.1007/978-1-4612-4808-8_2">doi:10.1007/978-1-4612-4808-8_2</A>]['21].
   Also see F@[<A HREF="https://en.wikipedia.org/wiki/FRACTRAN">wikip</A>]['21].


%A J. C. Reynolds
%T GEDANKEN - a simple typless language based on the principle of completeness
   and reference concept
%J CACM
%V 13
%N 5
%M May
%D 1970
%K Gedanken, programming language definition, PLD, complete, orthogonal,
   label variable, labels, reference, ref, value, values, jrnl,
   c1970, c197x, c19xx
%X "GEDANKEN is an experimental [PL] with the following characteristics. (1) Any
   value which is permitted in some context of the language is permissible in
   any other meaningful context. ... fns & labels are permissible results of
   fns & values of variables. (2) Assignment & indirect addressing are
   formalized by introducing values, called references, which in turn possess
   other values. The assignment op. always affects the relation between some
   reference & its value. (3) All compound data structures are treated as fns.
   (4) Type declarations are not permitted. ..."
   -- [<A HREF="https://doi.org/10.1145/362349.362364">doi:10.1145/362349.362364</A>]['24].

%T Go
%Q google
%D 2009
%K Go, Golang, gccgo, programming language, c2009, c200x, c20xx, zz1109, google,
   concurrent, garbage collected, goroutine, go coroutine, godoc
%X "... type safe and memory safe. Go has pointers but no pointer arithmetic.
   For random access, use slices, which know their limits. ... promotes writing
   systems and servers as sets of lightweight communicating processes, called
   goroutines ... open source. ... Go has types and methods and allows an
   object-oriented style of programming, there is no type hierarchy. The concept
   of 'interface' in Go provides a different approach ..."
   -- [<A HREF="http://golang.org/">goloang.org</A>][11/'09], and see
      [<A HREF="http://en.wikipedia.org/wiki/Go_(programming_language)">wikip</A>]['13].


%A P. M. Hill
%A J. W. Lloyd
%T The Godel Programming Language
%I MITpress
%P 368
%D 1994
%S Logic Programming Series
%K Godel, LP, text, book, c1994, c199x, c19xx, PMHill, JWLloyd
%X review in Comp reviews Aug 95 p400;
   hb; uk us isbn:0262082292; uk us isbn13:978-0262082297.
   (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)


%A M. P. Jones
%T Gofer
%I CS, Yale
%P 122 ?
%M AUG
%D 1995
%K Gofer, functional programming language, FP, c1995, c199x, c19xx
%X email: jones-mark at cs.yale.edu   ['91].


%A R. Balter
%A S. Lacourte
%A M. Riveill
%T The Guide language
%J COMPJ
%V 37
%N 6
%P 519-530
%M ?
%D 1994
%K Guide, programming language, comandos, object oriented, OO, OOP,
   jrnl, COMPJ, c1994, c199x, c19xx


%T Report on the Programming Language Haskell, version 1.2
%A P. Hudak
%A S. Peyton Jones
%A P. Wadler, B. Boutel, J. Fairbairn, J. Fasel, M. M. Guzman,
   K. Hammond, J. Hughes, T. Johnsson, D. Kieburtz, R. Nikhil, W. Partian,
   J. Peterson
%J Sigplan
%V 27
%N 5
%M MAY
%D 1992
%O Hudak, Wadler, Arvind, Boutel, Fairbairn, Fasel, Hughes, Johnsson,
   Kieburtz, Nikhil, Peyton Jones, Reeve, Wise, Young;   Version 1.0:
   Functional Programming (Languages?) and Computer Architecture 89,
   pp123, 1989, c1992, c199x, c19xx
%K Haskell, functional programming language definition, FP, Peyton-Jones,
   lazy, non-strict, polymorphic data type, types, signature, module, channel,
   class, FPCA, FPCA89, L4Ref
%X eds: P. Hudak - Yale University,  P. Wadler University of Glasgow
   Owes a debt to:  ML, SML, LML, Miranda, SASL, Hope, ...
   -- [<A HREF="http:/cgi-bin/glookbib?Haskell%20functional%20FP%20www%20HREF+~lloyd/public_html/INDEX">Haskell on the www</A>].
   See also Gofer (M.P.Jones ~ 92),
   -- [<A HREF="http://www.haskell.org/">haskell.org</A> ][2/'00],
   -- [<A HREF="http://www.haskell.org/tutorial/goodies.html">goodies</A>],
   -- [<A HREF="http://www.haskell.org/tutorial/classes.html">classes</A>].

%T Report on the Programming Language Haskell 98
%A S. Peyton Jones (ed)
%A J. Hughes (ed)
%A L. Augustsson, D. Barton, B. Boutel, W. Burton, J. Fasel,
   K. Hammond, R. Hinze, P. Hudak, T. Johnsson, M. Jones, J. Launchbury,
   E. Meijer, J. Peterson, A. Reid, C. Runciman, P. Wadler
%M FEB
%D 1999
%K Haskell, nonstrict, lazy, FP, polymorphic types, monad, monads, monadic,
   functional programming language definition, c1999, c199x, c19xx,
   Glasgow, ghc, hs, Haskell1, 1.4, Haskell98, www, HREF, http, org
%X [<A HREF="http://www.haskell.org/">haskell.org</A>][7/'02]
     -- [<A HREF="http://www.haskell.org/ghc/">/ghc</A>][7/'02]
     -- [<A HREF="http://www.haskell.org/ghc/documentation.html">doc'</A>][7/'02]
   NB. revised report, a CUP book, c2003.

%T Haskell 98 Language and Libraries, the Revised Report
%E S. Peyton Jones
%E et al
%I CUP
%M APR
%D 2003
%P 272
%K book, text, Haskell, Haskell98, computer programming language definition,
   H98, PLD, functional programming, FP, c2003, c200x, c20xx, zz0303, standard,
   polymorphic type, types, checking, classes, class, library, libraries,
   prelude, preludes, CUP, www, http, HREF, onlinereport
%X Preface;   1. Introduction;    2. Lexical structure;    3. Expressions;
   4. Declarations and bindings;  5. Modules;              6. Basic types;
   7. Input/output;               Appendix A. Standard prelude;
   Appendix B. Syntax;            Appendix C. Literate comments;
   Appendix D. Derived instances; Appendix E. Compiler pragmas;
   Bibliography; Index of prelude functions and types.
   stg35.00, hb; uk us isbn:0521826144; uk us isbn13:978-0521826143.
   (Also see [<A HREF="http://www.haskell.org/">haskell.org</A>][7/'02].)

%A P. Hudak
%A J. H. Fasel
%T A gentle introduction to Haskell
%J Sigplan
%V 27
%N 5
%P T1-T53
%M MAY
%D 1992
%K Haskell, c1992, c199x, c19xx, examples, functional programming, FP
%X report for v1.2 follows in same issue;
   [also search for: gentle Haskell98].

%A P. Hudak
%A J. Peterson
%A J. Fasel
%T A gentle introduction to Haskell, version 98
%M SEP
%D 1999
%K Haskell98, H98, functional programming language, FP, c1999, c199x, c19xx
%X [<A HREF="http://haskell.cs.yale.edu/tutorial/">www</A>][8/'02].

%A P. Hudak
%T The Haskell School of Expression: Learning Functional Programming through
   Multimedia
%I CUP
%M JAN
%D 2000
%P 363
%K Haskell, Haskell98, H98, book, text, functional programming language, FP,
   multi media, animation, robot, music description, MDL, soe, SOEGraphics,
   HGL, graphics library, source code, c2000, c200x, c20xx, zz0301, MIDI,
   music, Haskore, L3Ref
%X 1. Problem Solving, Programming, and Calculation
   2. A Module of Shapes: Part I      3. Simple Graphics
   4. Shapes II: Drawing Shapes       5. Polymorphic & Higher-Order Functions
   6. Shapes III: Perimeters of Shapes   7. Trees
   8. A Module of Regions             9. More About Higher-Order Functions
  10. Drawing Regions                11. Proof by Induction
  12. Qualified Types                13. A Module of Simple Animations
  14. Programming With Streams       15. A Module of Reactive Animations
  16. Communicating With the Outside World   17. Rendering Reactive Animations
  18. Higher-Order Types             19. An Imperative Robot Language
  20. Functional Music Composition   21. Interpreting Functional Music
  22. From Performance to MIDI       23. A Tour of the PreludeList Module
  24. A Tour of Haskell's Standard Type Classes
   hb; uk us isbn:0521643384; uk us isbn13:978-0521643382; $75 hb.
   pb; uk us isbn:0521644089; uk us isbn13:978-0521644082; $30 pb.
  -- [<A HREF="http://haskell.cs.yale.edu/soe/">soe</A>][3/01],
     [<A HREF="mailto:paul.hudak of yale edu">author</A>][3/01].


%A R. Burstall
%A D. MacQueen
%A D. Sannella
%T Hope: an experimental applicative language
%J Proc. 1980 LISP Conference
%P 136-143
%D 1980
%K Hope, functional programming language, FP, conf, zz0995, c1980, c198x, c19xx
%X <!-- email: dts at uyea.dcs.ed.ac.uk --> Don Sannella  [9/'95]


%A M. P. Jones
%T The Hugs 98 User Manual
%D ?
%K hugs, gugs98, functional programming language definition, PLD, FP,
   Gofer, zz0301, c199x, c19xx
%X [<A HREF="http://www.cse.ogi.edu/PacSoft/projects/Hugs/pages/hugsman/index.html">ogi</A>][3/01]
   -- [<A HREF="http://haskell.cs.yale.edu/hugs/">yale</A>][3/01]
   [Also search for: Gofer language] and [also search for: Haskell language].


%A R. E. Griswold
%A M. T. Griswold
%T The Icon Programming Language
%I PrenticeHall
%P 313
%M APR
%D 1990
%K Icon, programming language definition, PLD, text book, goal oriented, L3Ref,
   coroutine, coexpression, generator, SL5, www, HREF, FTP, c1990, c199x, c19xx
%X 2nd edn published 1990; 3rd edn '96,
   pb; uk us isbn:1573980013; uk us isbn13:978-1573980012.
   -- [<A HREF="http://www.cs.arizona.edu/icon/ftp/doc/lb1up.pdf">.pdf</A>]['03]
   -- [<A HREF="http://www.cs.arizona.edu/icon/">Icon at Arizona</A>]['03]
   -- [<A HREF="ftp://ftp.cs.arizona.edu/icon/">ftp.cs.arizona.edu/icon/</A>]['03]
   -- see books and articles on Icon and SL5.
   (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/Icon/">Icon</A>].)


%A R. S. Nikhil
%T Id language reference manual (version 90.1)
%R Computation Structure Group Memo 284-2
%I Laboratory-for-Computer-Science-MIT
%M JUL
%D 1991
%K Id, functional programming language definition, FP, PLD,
   non-strict, lenient, lazy, speculative evaluation, c1991, c199x, c19xx,
   TR 284-2, parallel, concurrent

%A W. Brady
%T Idris, a general-purpose dependently typed programming language:
   Design and implementation
%J J. Functional Programming
%V ?
%P ?-?
%M OCT
%D 2013
%K jrnl, JFP, c2013, c201x, c20xx, zz1113, Idris, FP, functional programming,
   language, dependently typed, dependent type, dependentType, types, check,
   checking, checker, system, TT, UTT
%X "Many components of a dependently typed prog. lang. are by now well
   understood, [e.g.,] the underlying type theory, t.checking, unification &
   evaln. How to combine these components into a realistic & usable high-level
   lang. is, however, folklore, discovered anew by successive language
   implementors. ... I describe the impl'n of Idris, a new dependently typed
   FP language. Idris is intended to be a general-purpose prog. lang. & as such
   provides high-level concepts such as implicit syntax, type classes & do
   notation. I describe the high-level lang. & the underlying type theory, &
   present a tactic-based method for elaborating concrete high-level syntax with
   implicit args & type classes into a fully explicit t.theory. [&] show how
   this method facilitates the impl'n of new high-level lang. constructs."
   -- [<A HREF="http://dx.doi.org/10.1017/S095679681300018X">doi:10.1017/S095679681300018X</A>]['13] (online Oct 2013).
   [Also search for: dependent type].

%A K. E. Iverson
%T J Introduction and Dictionary
%I Iverson-Software-Inc.,
%C 33 Major St., Toronto, Ontario, Canada M5S 2K9
%D 1993
%K J, jj, applicative programming language definition, PLD, L3Ref,
   APL, verb, adverb, adjective, noun, operator, c1993, c199x, c19xx
%X isbn:1-895721-06-7;
   -- [<A HREF="ftp://watserv1.waterloo.ca/languages/j/">FTP J</A>][12/'03]
   also see APL and [<A HREF="news:comp.lang.apl">comp.lang.apl newsgroup</A>].
   Also see [<A HREF="http://www.allisons.org/ll/ProgLang/J/">J directory</A>].

%A M. C. Rinard
%A M. S. Lam
%T The design, implementation and evaluation of Jade
%J TOPLAS
%V 20
%N 3
%P 483-545
%M MAY
%D 1998
%O Rinard's PhD Thesis, Comp Sci, Stanford 1994
%K jrnl, TOPLAS, ACM, programming language, concurrent, c1998, c199x, c19xx,
   parallel, computing, implicit, zz1298
%X ... implitly parallel ... for exploiting task-level concurrency.
   Start with a program ... in a standard serial, imperative language, ...
   use Jade constructs to declare ...
   We have implemented Jade as an extension to C, ...
   -- [<A HREF="http://www.cag.lcs.mit.edu/~rinard">~rinard</A>]12/1998],
   -- [<A HREF="http://suif.stanford.edu/~scales/sam.html">SAM</A>][12/1998].


%A J. Gosling
%A B. Joy
%A G. Steele
%T The Java Language Specification
%I AddisonWesley
%D 1997
%K Java, Sun Microsystems, book, text, computer, zz1097, c1997, c199x, c19xx,
   programming language definition, PLD, net, object oriented, OOP, OO,
   classes, threads, generics, SE8
%X 3rd ed, c2005, us$50; uk us isbn:0321246780; uk us isbn13:9780321246783;
   inc. "generics", [<A HREF="http://java.sun.com/docs/books/jls/third_edition/html/j3TOC.html">@sun</A>]['07].
   ((?)1st ed; uk us isbn:0201634511; uk us isbn13:978-0201634518.)
   (And, Gosling, Joy, Steele jr, Bracha, Buckley,
         'Java SE 8 Edition', 2014, pb us$51, 792pp,
         uk us isbn:013390069X; uk us isbn13:978-0133900699.)

%A I. Palmer
%T Essential Java 3D Fast
%I SpringerVerlag
%S Essential
%M APR
%D 2001
%P 280
%K Java, 3D, 3 D, computer graphics, book, text, c2001, c200x, c20xx,
   multimedia, applications, applets, animation
%X pb; uk us isbn:1852333944; uk us isbn13:978-1852333942.

%A A. Walsh
%T Java 3D Jump Start
%I PrenticeHall
%M AUG
%D 2001
%K book, Sun, Java, 3D, 3 D, ms, microsoft, windows, graphics, text,
   c2001, c200x, c20xx, 3D computer graphics, animation
%X pb; uk us isbn:0130340766; uk us isbn13:978-0130340764; about au$74.

%A G. Kirby
%A R. Morrison
%A D. Stemple
%T Linguistic reflection in Java
%J SPE
%V 28
%N 10
%P 1045-1077
%M AUG
%D 1998
%K jrnl, SPE, programming language, Java, reflect, reflection,
   class, object oriented, OO, OOP, PJama, orthogonal persistence,
   persistent, zz1199, c1998, c199x, c19xx
%X includes ways around absence of constructor for class Class
   such as write new compiler, write class to file use javac and load, ...
   -- [<A HREF="https://arxiv.org/abs/cs/9810027">arxiv:cs/9810027</A>]['24].
   Also see <A HREF="http://www.sunlabs.com/research/forest/opj.main.html">[PJama]</A>[11/1999].
   [33 refs].

%A T. Lindholm
%A F. Yellin
%T The Java Virtual Machine Specification
%I AddisonWesley
%P 475
%M SEP
%D 1996
%K Java, interpreter, byte code, implementation, programming language, Sun,
   computer, book, text, c1996, c199x, c19xx
%X pb; uk us isbn:020163452X; uk us isbn13:978-0201634525.

%A D. Lea
%T Concurrent Programming in Java: Design Principles and Patterns
%I AddisonWesley
%D 1997 ?
%K Java, concurrent, parallel, thread, threads, programming language,
   book, text
%X isbn:0-201-69581-2.

%A K. Arnold
%A J. Gosling
%T The Java Programming Language
%I AddisonWesley
%D 1996
%K Java, computer programming language, book, text, applet, Sun, zz1097
%X pb; uk us isbn:0201634538; uk us isbn13:978-0201634532.
   [also search for: Java PLD]

%A J. Gosling
%A F. Yellin
%A The Java Team (!)
%T The Java Application Programming Interface Volume 1: Core Packages
%I AddisonWesley
%D 1996
%K Java, API, Sun, www, applet, application, package, book, text
%X pb; uk us isbn:0201634538; uk us isbn13:978-0201634532.
   Vol 2 covers window toolkit and applets.

%A J. Gosling
%A F. Yellin
%A The Java Team (!)
%T The Java Application Programming Interface Volume 2: Window Toolkit and
   Applets
%I AddisonWesley
%D 1997 ?
%K Java, API, Sun, application, package, awt, applet, widget, book, text
%X isbn:0-201-63459-7;

%A T. Saulpaugh
%A T. Clements
%A C. A. Mirho
%T Inside the JavaOS Operating System
%I AddisonWesley
%P 184
%D 1999
%K Java, OS, x1999, c199x, c19xx, unix, windows, Operating System, OpSys,
   book, text, Sun
%X pb; uk us isbn:0201183935; uk us isbn13:978-0201183931.

%A G. Hamilton
%A R. Cattell
%A M. Fisher
%T JDBC Database Access with Java: A Tutorial and Annotated Reference
%I AddisonWesley
%D 1997
%K Java, database, data base, computer, databases, bases, JDBC, DBMS,
   book, text, c1997, c199x, c19xx, Sun
%X pb; uk us isbn:0201309955; uk us isbn13:978-0201309959.

%A D. Flanagan
%T Java in a Nutshell
%I OReilly and Assoc.
%P 435
%D 1996
%K Java, nut shell, book, text, good, programming language, applet, API,
   Java1.1, zz1296, c1996, c199x, c19xx
%X Lots of stuff from the API, a bit terse but the best the I've seen - LA.
   2nd ed 1997, 628pp, Java 1.1,
   pb; uk us isbn:156592262X; uk us isbn13:978-1565922624.

%A P. H. Winston
%A S. Narasimhan
%T On To Java
%I AddisonWesley
%P 328
%D 1996
%K Java, book, text, c1996, c199x, c19xx, programming language, applet, zz0697
%X To p226 is about the Java language itself, p227-314 covers applets.
   tb; uk us isbn:020149826X; uk us isbn13:978-0201498264.
   Says programs available at [<A HREF="http://www.ascent.com/books">www</A>].

%A B. Boone
%T Java Essentials for C and C++ Programmers
%I AddisonWesley
%D 1996
%P 311
%K Java, book, text, programming language, zz0697, cc, c#, csharp,
   c1996, c199x, c19xx
%X pb; uk us isbn:020147946X; uk us isbn13:978-0201479461.

%A H. Sowizral
%A K. Rushforth
%A M. Deering
%T Java 3D API Specification
%P 482
%D 1998
%I AddisonWesley
%K Java, Java3D, programming language, book, text, 3-D, 3D, computer graphics,
   c1998, c199x, c19xx, living worlds, software package, animation, zz1298
%X pb; uk us isbn:0201325764; uk us isbn13:978-0201325768; about US$40;
   [also search for: Java3D].

%A D. Selman
%T Java 3D Programming
%I ManningPubCo
%P 400
%M APR
%D 2002
%K book, text, c2002, c200x, c20xx, Java3D, computer graphics, animations
%X pb; uk us isbn:1930110359; uk us isbn13:978-1930110359.
   -- [<A HREF="http://www.manning.com/selman/">book</A>]['06]
   Also see [<A HREF="http://www.j3d.org/">j3d.org</A>],
   [also search for: Java3D].

%A T. Ritchey
%T Java!
%I New Riders
%P 366
%M OCT
%D 1995
%K Java, book, text, Sun, world wide web, hot java,
   programming language, zz1095
%X $35, u us isbn:156205533X; uk us isbn13:978-1562055332; with CD.
   About 360 pages.  There does seem to be
   technical content and lots of examples.  There also is a CD with 'ready-to-
   use java applets' that is otherwise not described.
   -- David N. Smith <!-- email: dnsmith at watson.ibm.com --> [10/95]
   Waste of money - L.

%A John December
%T Presenting Java
%I Sams Publ.
%P 207
%D 1996
%K Java, book, c1996, c199x, c19xx,text, Sun, world wide web, hot java,
   programming language, zz1095
%X $25; uk us isbn:1575210398; uk us isbn13:978-1575210391.
   It reads like the Sun WWW pages. Incredible hype...  But would make
   a great present for your local Java True Believer since it has little in
   the way of real content to confuse the issue. (That is, unless you
   count a Visit to the Rolling Stones home page as Real Content.)
   - David N. Smith <!-- email: dnsmith at watson.ibm.com --> [10/95].

%A D. Lea
%T Concurrent Programming Using Java
%I AddisonWesley
%D 1996
%K Java, book, c1996, c199x, c19xx, text, parallel, thread, threads,
   programming language, zz0397
%X pb; uk us isbn:0201695812; uk us isbn13:978-0201695816; stg29.95,  us$35.

%A K. Walrath
%A M. Campione
%A A. Huml
%A S. Zakhour
%T The JFC Swing Tutorial
%I PrenticeHall
%P 800
%M SEP
%D 2003
%K Java, book, text, c2003, c200x, c20xx, graphics, widget, widgets,
   graphical user interface, GUI, JFC, swing, library, class, classes, applet,
   applets, frame, frames, scroll, components, windows, OO, OOP, programming,
   introduction, zz1103
%X 2nd ed, c2004; uk us isbn:0201914670; uk us isbn13:978-020191467.

%A P. Chan
%T The Java Developers Almanac
%I AddisonWesley
%P 861
%D 1999
%K Java, book, text, c1999, c199x, c19xx, programming language, applet, applets,
   applications, OO, OOP, class, classes
%X pb; uk us isbn:0201432986; uk us isbn13:978-0201432985.
   inc' Java 1.0, 1.1 and 1.2.
   NB. It is a reference not an introduction.

%A S. C. Wang
%T Interdisciplinary Programming in Java Programming Language
%I Kluwer
%S Eng. & CS
%V 743
%P 282
%M AUG
%D 2003
%K book, text, c2003, c200x, c20xx, cc, csharp, programming language,
   applications, applets
%X h.b. us$140; uk us isbn:1402075138; us us isbn13:978-1402075131.

%A C. S. Lindsey
%A J. S. Tolliver
%A T. Lindblad
%T JavaTech, an Introduction to Scientific and Technical Computing with Java
%I CUP
%P 726
%D 2005
%K book, text, CUP, c2005, c200x, c20xx, distributed computing, concurrent,
   RMI, CORBA, web services
%X us$90; uk us isbn:0521821134; uk us isbn13:9780521821131.

%A J. Magee
%A J. Kramer
%T Concurrency: State Models and Java Programs
%I Wiley
%P 434
%D 2006
%K book, text, c2006, c200x, c20xx, Java, concurrent, concurrency, parallel,
   state model, program, programming, L3ref, L4Ref, LTSA
%X "... informal descriptions, illustrative examples, abstract models and
   concrete Java examples. These combine to provide problem patterns and
   associated solution techniques which enable students to recognise problems
   and arrive at solutions."
   2nd ed 2006; hb stg30; uk us isbn:0470093552; uk us isbn13:978-0470093559.

%A Y. Wang
%A K. B. Kent
%A G. Johnson
%T Improving J9 virtual machine with LTTng for efficient and effective tracing
%J SPE
%V 45
%N 7
%P 973-987
%M JUL
%D 2015
%K jrnl, SPE, c2015, c201x, c20xx, zz0815, Java, IBM, J9, JVM, LTTng
%X "... propose the integration of LTTng, an effective open-source tracing
   toolset, with J9 to improve its tracing fns. ... the tracing component is not
   only decoupled from the VM but also performed efficiently at both user &
   kernel levels to achieve a high-throughput result. To validate the integn &
   its impact performance, some empirical study results based on SpecJBB2005 &
   SQLBenchmark (supported by instrumented MariaDB) are also presented."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.2282">doi:10.1002/spe.2282</A>]['15].
   (Also see J9@[<A HREF="https://en.wikipedia.org/wiki/IBM_J9">wikip</A>]['15].)


%A M. Farber
%T A formal specification of the jq language
%J arXiv
%m APR
%d 2024
%K JQ, TR, json, c2024, c202x, c20xx, zz0424, definition
%X "jq is a widely used tool that provides a programming language to manipulate
   JSON data. ..."
   -- [<A HREF="https://arxiv.org/abs/2403.20132">arxiv:2403.20132</A>]['24].


%A D. Flanagan
%T JavaScript, the Definitive Guide
%I OReilly
%D 1996
%K book, text, Java script, JavaScript, programming language, explorer, web,
   c1996, c199x, c19xx, 2006, 2011, Netscape, Jscript, ECMAscript, scripting,
   SVG, page, pages, HTML, www, web development
%X 6th ed 2011; pb us$31; uk us isbn:0596805527; uk us isbn13:978-0596805524.
      "... JavaScript language (v. 1.0 - v. 1.5) and its relatives, JScript and
      ECMAScript, as well as the W3C DOM standards they're often used to
      manipulate. ..."
   5th ed 2006; uk us isbn:0596101996; uk us isbn13:978-0596101992.
      Modest title!  Also see the author's book on Java.
      "... Tutorial sections show how to program in JavaScript, while
      reference sections summarize syntax ..."

%A C. Easttom
%T Advanced JavaScript
%I WordwarePubl.
%D 2001
%P 650
%K JavaScript, programming, book, text, c2001, c200x, c20xx, Jscript,
   HTML, explorer, netscape
%X pb us$55, au$117; uk us isbn:155622852X; uk us isbn13:978-1556228520.

%A J. Pollock
%T JavaScript 2.0
%I McGrawHill
%P 624
%M FEB
%D 2004
%K book, c2004, c200x, c20xx, www, web, explorer, netscape, browser,
   JavaScript2, js, js2, Jscript, Jscript2
%X pb us$25; uk us isbn:0072227907; uk us isbn13:978-0072227901.

%A S. Power
%T Learning JavaScript
%I OReilly
%P 396
%D 2008
%K book, text, c2008, 200x, c20xx, XML, JSON, Ajax, web developer, page, pages,
   JavaScript, scripting
%X 2nd ed 2008; pb us$23; uk us isbn:0596521871; uk us isbn13:978-0596521875.

%A D. Crockford
%T JavaScript: The Good Parts
%I OReilly
%P 170
%D 2008
%K book, text, JavaScript, c2008, c200x, c20xx, www, HTML, web pages, design
%X pb us$20; uk us isbn:0596517742; uk us isbn13:978-0596517748.


%A P. Brinch Hansen
%T Joyce - a programming language for distributed systems
%J SPE
%V 17
%N 1
%M JAN
%D 1987
%P 29-50
%K Joyce, programming language definition PLD, c1987, c198x, c19xx, SPE,
   distributed, parallel, communication,
   synchronisation, channel, message, CSP, agent, agents, polling
%X secure programming language Joyce based on CSP and Pascal.
   unbounded recursive activation of communicating agents.
   synchronous channels.
   A channel can transfer messages of different types between two or more
   agents.
   A compiler can check message types and ensure that agents use disjoint sets
   of variables only.

%A A. W. Keen
%A T. Ge
%A J. T. Maris
%T R. A. Olsson
%T JR: Flexible distributed programming in an extended Java
%J ACM Trans. on Prog. Languages and Sys.
%V 26
%N 3
%P 578-608
%M MAY
%D 2004
%K jrnl, TOPLAS, c2004, c200x, c20xx, zz0916, JR, java, SR, parallel,
   concurrent, parallel, operations, programming language definition, PLD
%X "... The JR programming language extends Java to provide a rich concurrency
   model, based on that of SR.  JR provides dynamic remote virtual machine
   creation, dynamic remote object creation, remote method invocation,
   asynchronous communication, rendezvous, & dynamic process creation. JR's
   concurrency model stems from the addition of operations (a generalization of
   procedures) & JR supports the redefinition of operations through inheritance.
   JR programs are written in an extended Java & then translated into standard
   Java programs. The JR run-time support sys. is also written in std Java. ..."
   -- [<A HREF="http://dx.doi.org/10.1145/982158.982162">doi:10.1145/982158.982162</A>]['16].

%A E. C. R. Da Rosa
%A R. De Santiago
%T Ket quantum programming
%J J. on Emerging Technologies in Comp. Sys.
%V 18
%N 1
%P #12 (p.1-25)
%M OCT
%D 2022
%K jrnl, c2021, c202x, c20xx, zz1122, KET, quantum programming language, PLD,
   QPL, Libket, KBW, computing, daRosa
%X "... We present a runtime architecture for classical-quantum execution that
   mitigates the limitation of interaction between classical & q.computers
   originated from the cloud-based model of q.computation provided by several
   vendors, which implies a q.computer processing in batch. ... introduce (i)
   runtime q.code generation to enable generic q.programming & dynamic
   q.execution; & (ii) the concept of futures to handle dynamic interaction
   between classical & q.computers. ... have implemented the Ket Q.Programming
   f/wk that features a Python-embedded classical-q. prog. lang. named Ket  ..."
   -- [<A HREF="https://doi.org/10.1145/3474224">doi:10.1145/3474224</A>]['22].
   Also see q'ket@[<A HREF="https://quantumket.org/">www</A>]['22].

%T KOKA
%D 2024
%K Koka, c2024, c202x, c20xx, zz0824, programming language definition, PLD,
   effects, effect handlers, Perceus
%X "... Koka distinguishes itself through effect typing, effect handlers, and
   Perceus memory management: ..."
   -- [<A HREF="https://koka-lang.github.io/koka/doc/book.html#why">book</A>]['24].  via njh.


%A J. McCarthy-et-al
%T Lisp 1.5 Programmer's Manual
%I MITpress
%P 112
%D 1962
%K Lisp, text, book, functional, applicative, programming language definition,
   good, FP, PLD, lambda calculus, eval, quote, c1962, c196x, c19xx,
   L3Ref, L4Ref
%X Should be read by anyone calling themselves a Computer Scientist.
   uk us isbn:0262130114; uk us isbn13:978-0262130110.

%A P. Graham
%T ANSI Common Lisp
%I PrenticeHall
%D 1996 ?
%K Lisp, text, book, functional, applicative, programming language definition,
   FP, ANSI, c199x, c19xx, zz0996
%X uk us isbn:0-13-370875-6;          Hargrave: H 005.133 L771 GRA.A

%A R. Wilensky
%T Common LISPcraft
%I Norton
%D 1984
%K Common Lisp, book, text, programming language, FP, AI
%X isbn:0-393-95544-3,   also 1986.

%A R. F. Richards
%T M programming: A Comprehensive Guide
%I Digital_Press
%D 1997
%P 407
%K M, MM, programming language definition, PLD, procedural,
   book, text, MUMPS, Comprehensive Health Care System, DOD, zz0998
%X MUMPS created at Massachusetts General Hospital 1967;  used for
   DOD health care sys';  ANSI standards 1984, 1990, 1995.
   isbn:1-55558-167-6;  us$39.95;      - ACM Comp Rev p237 May '98.

%A D. A. Turner
%T Miranda: a non strict functional language with polymorphic types
%B Functional Programming Languages and Computer Architecture
%I SpringerVerlag
%S LNCS
%V 201
%E J. P. Jouannaud
%M SEP
%D 1985
%K Miranda, functional programming language definition, FP, PLD,
   lazy, non-strict, FPCA, FPCA85, FPLCA, FPLCA85, c1985, c198x, c19xx

%A C. Clack
%A C. Myers
%A E. Poon
%T Programming with Miranda
%I PrenticeHall
%M OCT
%D 1994
%K Miranda, text, book, functional programming, FP, Meyers, c1994, c199x, c19xx
%X Also see their book on Standard ML
   -- [<A HREF="http://www.cs.ucl.ac.uk/people/clack.papers/Books/progmira.html">a www page</A>],
   -- [<A HREF="http://www.cs.ucl.ac.uk/">CSci UCL</A>]['94].

%A S. Thompson
%T Miranda: The Craft of Functional Programming
%I AddisonWesley
%D 1995
%P 480
%K Miranda, book, text, functional programming language, FP, CSci,
   computing, zz0595, c1995, c199x, c19xx
%X pb; uk us isbn:0201422794; uk us isbn13:978-0201422795; 21.95 pounds stg.
   <A HREF="http://www.ukc.ac.uk/computer_science/Miranda_craft/">www page</A> [5/'95]
   email: S.J.Thompson at ukc.ac.uk  [5/'95].

%A The little MLer.
%I MITpress
%P 200
%D 1997
%K book, text, c1997, c199x, c19xx, FP, functional programming language,
   ML, SML, NJ, Standard ML, SMLNJ
%X pb; uk us isbn:026256114X; uk us isbn13:978-0262561143; us$25.

%A N. Wirth
%T Modula: a language for modular multiprogramming
%J SPE
%V 7
%P 3-35
%D 1977
%K Modula, module, imperative programming language definition, PLD,
   c1977, c197x, c19xx
%X see also Modula-2.

%A N. Wirth
%T Programming in Modula-2
%I SpringerVerlag
%D 1982
%K text, book, module, Modula, Modula-2, Modula2, Modula-II,
   imperative programming language definition, PLD, c1982, c198x, c19xx
%X 2nd edn 1983; uk us isbn:3540122060.

%A N. Wirth
%T The Programming Language Oberon
%J SPE
%V 18
%N 7
%P 671-690
%M JUL
%D 1988
%K Oberon, programming language definition, PLD, operating system,
   www, HREF, FTP, c1988, c198x, c19xx
%X see book by Wirth and Gutknecht '92
   via: the programming language list,
   -- [<A HREF="ftp://neptune.inf.ethz.ch/">ftp: neptune.inf.ethz.ch</A>]['?96?].

%A H. Mossenbock
%T Object-Oriented Programming in Oberon-2
%I SpringerVerlag
%D 1993
%K Oberon, Oberon-2, Oberon2, object oriented, OO, OOP, programming language,
   c1993, c199x, c19xx
%X pb; uk us isbn:038756411X; uk us isbn13:978-0387564111.

%A H. Mossenbock
%A N. Wirth
%T The programming language Oberon-2
%J Structured Programming
%V 12
%N 4
%P ?-?
%D 1991
%K jrnl, Oberon, Oberon-2, programming language, c1991, c199x, c19xx
%X from the refs in a paper [also search for: Oberon].

%A M. Reiser
%T The Oberon System. User Guide and Programmer's Manual
%I AddissonWesley
%P 350
%D 1991
%K Oberon, programming language, book, text, c1991, c199x, c19xx
%X pb; uk us isbn:0201544229; uk us isbn13:978-0201544220.

%A M. Reiser
%A N. Wirth
%T Programming in Oberon. Steps beyond Pascal and Modula-2
%I AddisonWesley
%D 1992
%K Oberon, book, c1992, c199x, c19xx, programming language, OO, OOP
%X pb; uk us isbn:0201565439; uk us isbn13:978-0201565430.


%A M. Dalrymple
%A S. Knaster
%T Learn Objective-C on the Mac
%I Apress
%P 360
%D 2009
%K ObjectiveC, book, text, c2009, c200x, c20xx, programming language,
   Objective C, cc, object oriented, Mac, developer, computer programming
%X pb us$23; uk us isbn:1430218150; uk us isbn13:978-1430218159.


%A D. Remy
%A J. Vouillon
%T Objective ML: An effective object-oriented extension to ML
%J Theory and Practice of Object Systems
%V 4
%N 1
%P 27-50
%D 1998
%K OCAML, OCaml, CAML, caml, object oriented programming language definition,
   OOP, PLD, module system, modules, functional, FP, zz0301,
   jrnl, c1998, c199x, c19xx
%X [<A HREF="http://caml.inria.fr/ocaml/papers.html">caml.inria.fr</A>][3/'01]
   inc' ps paper.   [Also search for: CAML].

%A J. Whitington
%T OCaml from the Very Beginning
%I CoherentPress
%P 204
%M JUN
%D 2013
%K book, text, c2013, c201x, c20xx, zz0913, objective, CAML, OCAML, FP,
   object oriented programming language definition, PLD, computer, OOP
%X 1st ed 2013; pb us$35; uk us isbn: 0957671105; uk us isbn13:978-0957671102.
   "... [for] new programmers, & experienced programmers eager to explore
   functional languages such as OCaml. It is suitable both for formal use
   within an undergraduate or graduate curriculum, & for the interested
   amateur. ..."

%A E. Chailloux
%A P. Manoury
%A B. Pagano
%T Developing Applications with Objectice Caml
%O Developement d'applications avec Objective Caml, OReilly, France
%D 2002?
%K OCaml, Caml, object oriented, OO, OOP, book, text,
   functional programming, FP, zz0802
%X [<A HREF="http://caml.inria.fr/oreilly-book/">www</A>][8/'02].

%T Occam 2 Reference Manual
%I PrenticeHall
%D 1988
%K Occam, programming language definition, PLD, c1988, c198x, c19xx,
   parallel, concurrent, message passing, transputer, Inmos
%X pb; uk us isbn:0136293123; uk us isbn13:978-0136293125; via enews.

%T Octave
%D 1988
%K Octave, c1988, c198x, c19xx, programming language definition, PLD,
   matlab, mat lab, mathlab, numerical computing, scientific
%X "Octave was originally conceived (~1988) to be companion s/w for an u/grad-
   -level textbook on chemical reactor design being written by J.B.Rawlings of
   the U. of Wisconsin-Madison & J.G.Ekerdt of the U.Texas. ..."
    -- octave@[<A HREF="http://www.gnu.org/software/octave/">gnu</A>]['11].
   "O. built with MATLAB compatibility ... shares many features with [it]."
    -- octave@[<A HREF="http://en.wikipedia.org/wiki/GNU_Octave">wikip</A>]['11].
 .+  Elt by elt +, also .-, .*, ./, .\, .^ (.**), etc..
 x'  Complex conjugate transpose; same as .' for reals; conj(x.') for complex.
 x.' Transpose.
 x/y Right divison, is equiv. (inverse(y')*x')'.
 x\y Left division, is equiv. inverse(x)*y.

%A M. Henz
%A G. Smolka
%A J. Wurtz
%T Object-oriented concurrent constraint programming in Oz
%J Principles and Practice of Constraint Programming
%E V. Saraswat
%E P. van Hentenryck
%I MITpress
%P 27-48
%D 1995
%K Oz, computer programming language, constraint, OO, OOP, logic, LP,
   dfki, vanHentenryck, c1995, c199x, c19xx
%X (paper is chapter 2 of the book)
   About Oz:  Oz is a concurrent constraint programming language designed for
   applications that require complex symbolic computations, organization into
   multiple agents, and soft real-time control. It is based on a new
   computation model providing a uniform foundation for higher-order
   functional programming, constraint logic programming, and concurrent
   objects with multiple inheritance. From functional languages Oz inherits
   full compositionality, and from logic languages Oz inherits logic variables
   and constraints (including feature and finite domain constraints). Search in
   Oz is encapsulated (no backtracking) and includes one, best and all solution
   strategies. [...]
   -- [<A HREF="http://ps-www.dfki.uni-sb.de:80/oz/">Oz on www at dfki (2/'95)</A>].

%A P. Van Roy
%A S. Haridi
%T Ideas for the future of Prolog inspired by Oz
%J arXiv
%M FEB
%D 2023
%K TR, c2023, c202x, c20xx, logic, programming language, LP, FP, Oz, Prolog,
   green, blue, cut, cuts, bagof 3, bagof3, setof 3, setof3
%X "... There is a sig. subset of Oz that is a syntactic variant of Prolog: pure
   Prolog programs with green or blue cuts & bagof/3 or setof/3 can be
   translated directly to Oz. Because of this close relationship between P. & Oz
   we propose that the extensions made by Oz to LP can be an inspiration for the
   future evolution of P.. We explain three extensions, namely deterministic LP,
   lazy concurrent FP, & purely functional distributed computing. We briefly
   present these extensions & we explain how they can help P. evolve in its next
   50 years."
   -- 2302.00558@[<A HREF="https://arxiv.org/abs/2302.00558">arXiv</A>]['23].
   [Also search for: Oz programming language].


%A N. Wirth
%T The programming language Pascal
%J Acta Informatica
%V 1
%P 35-63
%D 1971
%K Pascal, jrnl, imperative programming language definition, PLD,
   c1971, c197x, c19xx, recursive
%X British standard 1982; Australian standard 1983; ISO ?
   <IMG SRC="/~lloyd/tildeImages/Vehicles/vw.beetle.gif">
   see book by Jensen and Wirth,
   and [<A HREF="http://www.allisons.org/ll/ProgLang/Pascal">Pascal</A>].

%T Australian Standard 2580-1983 Programming Language PASCAL
%I Standards-Association-of-Australia
%D 1983
%O British Standard BS 6192: 1982
%K Pascal, imperative programming language definition, AS, ASO, ISO, BS,
   standard 2580,  6192, c1983, c198x, c19xx
%X isbn:0-7262-2770-6;
   see book:
   Jensen and Wirth, Pascal user manual and report, Springer-Verlag, '75.

%A J. S. Rohl
%A H. J. Barrett
%T Programming via Pascal
%I CUP
%D 1980
%K book, text, Pascal, computer programming language, c1980, c198x, c19xx
%X pb; uk us isbn:052135661X; uk us isbn13:978-0521356619.

%A L. Wall
%A R. L. Schwartz
%T Programming Perl
%I OReilly
%D 1992
%K Perl, book, text, c1992, c199x, c19xx, string processing,
   programming language, computing
%X 3rd ed 2000, pb us$33; uk us isbn:0596000278; uk us isbn13:978-0596000271.

%A R. L. Schwartz
%T Learning Perl
%I OReilly
%D 1993
%K Perl, book, text, string processing, programming language,
   computing, zz0695, c1993, c199x, c19xx
%X 4th ed, c2005; uk us isbn:0596101058; uk us isbn13:978-0596101053.

%A N. Chapman
%T Perl: The Programmer's Companion
%I Wiley
%M OCT
%D 1997
%P 250
%K Perl, book, c1997, c199x, c19xx, scripts, book, text, string processing,
   programming language, web development, zz0198
%X pb, stg22.50; uk us isbn:047197563X; uk us isbn13:978-0471975632.

%A D. Conway
%T Object Oriented Perl
%I Manning
%P 512
%M AUG
%D 1999
%K book, text, c1999, c199x, c19xx, good, programming language,
   OO, OOP, object, objects, class, classes
%X pb; uk us isbn:1884777791; uk us isbn13:978-1884777790.

%A D. Conway
%T Perl Best Practices
%I OReilly
%P 542
%M JUL
%D 2005
%K book, text, c2005, c200x, c20xx, Perl, practice, programming, software,
   source code, guide, good, L2Ref, L3Ref, OReilly, Damian Conway
%X pb; uk us isbn:0596001738; uk us isbn13:978-0596001735.

%A A. L. Johnson
%T Elements of Programming with Perl
%I Manning
%P 368
%M OCT
%D 1999
%K book, text, programming language, OO, OOP
%X pb; uk us isbn:1884777805; uk us isbn13:978-1884777806.

%A C. Dichter
%A M. Pease
%T Software Engineering with Perl: Prototyping and Toolsmithing for better
   Software - sooner.
%I PrenticeHall
%P 282
%D 1995
%K Perl, book, c1995, c199x, c19xx, text, zz0197
%X us$39; uk us isbn:013016965X.

%A R. Burstall
%A Collins
%A R. Popplestone
%T Programming in Pop-2
%I Edinburgh-Univ.-Press
%D 1968
%K POP POP2 POP-2 POP-11 POP-II, text, book, EUP UP,
   programming language definition, PLD, c1968, c196x, c19xx
%X The original silver book.  Pop-11 is a close derivative of Pop-2.
   Most Pop systems have a compatibility library.  This book contains mainly
   small procedures and their descriptions. (currently out of print).
   [From Laventhol87].

%A A. B. Downey
%T Python for Software Design: How to Think Like a Computer Scientist
%I CUP
%P 270
%D 2009
%K book, text, Python, CUP, c2009, c200x, c20xx, computer programming language,
   swampy, L2Ref, L3Ref, software design
%X 1st ed 2009; pb us$33; uk us isbn:0521725968; uk us isbn13:978-0521725965.
   "... starts with the most basic concepts and gradually adds new material.
   Some of the ideas students find most challenging, like recursion and object-
   -oriented programming, are divided into a sequence of smaller steps and
   introduced over the course of several chapters. The focus is on the
   programming process, with special emphasis on debugging. ..."
   [Also search for: Python book].

%A G. van Rossum
%A F. L. Drake, Jr.
%T Python Language Reference Manual
%I Network Theory Ltd.
%P 144
%D 2003
%K book, text, c2003, c200x, c20xx, programming language definition, PLD,
   vanRossum, duck typing, duckTyping, Python2, Python3
%X us$20; pb; uk us isbn:0954161785; uk us isbn13:978-0954161781.
   [Also search for: NumPy] and [also search for: SimPy].
   Also see [<A HREF="https://www.python.org/">python.org</A>]['23] and
   "... Python2 2000, Python3 2008,
   -- python@[<A HREF="https://en.wikipedia.org/wiki/Python_(programming_language)">wikip</A>]['23] and
      SyAndSe@[<A HREF="https://en.wikipedia.org/wiki/Python_syntax_and_semantics">wikip</A>]['23].

%T NumPy, and SimPy
%K Python, library, package, computing, computer, code,
   maths, algebra, symbolic, numerical, methods, recipes,
   approximations, gamma, functions
%X Initial release 1995
      NumPy@[<A HREF="http://en.wikipedia.org/wiki/NumPy">wikip</A>]['12];
   Initial release 2007
      SimPy@[<A HREF="http://en.wikipedia.org/wiki/SymPy">wikip</A>]['12].
   [Also search for: Python book].

%A Mark Lutz
%T Python Pocket Reference
%I OReilly
%P 75
%M NOV
%D 1998
%K Python, book, text, c1998, c199x, c19xx, programming language, book, text
%X pb; uk us isbn:1565925009; uk us isbn13:978-1565925007.
   -- [<A HREF="http://www.python.org/">python.org</A>][9/'03].
   [Also search for: Python book].

%A Mark Lutz
%T Programming Python (2nd edn)
%I OReilly
%P 1292
%M MAR
%D 2001
%K Python, book, text, c2001, c200x, c20xx, programming language, script
%X pb; uk us isbn:0596000855; uk us isbn13:978-0596000851.
   -- [<A HREF="http://www.python.org/">python.org</A>][9/'03].
   [Also search for: Python book].

%E G. van Rossum
%E F. L. Drake, Jr.
%T An Introduction to Python
%I Network Theory Ltd
%P 124
%M SEP
%D 2003
%K Python, book, text, programming language
%X pb; uk us isbn:0954161769; uk us isbn13:978-0954161767.
   -- [<A HREF="http://www.python.org/">python.org</A>][9/'03].
   [Also search for: Python book].

%A A. Martelli
%T Python in a Nutshell
%I OReilly
%P 654
%M MAR
%D 2003
%K Python, book, text, python2.2, C, CC, Numeric, Tkinter, Cheetah,
   programming language, c2003, c200x, c20xx
%X "...desktop reference for Python 2.2. Covers the language itself,
   built-in types and functions, the standard library, and crucial
   third-party extensions such as Numeric, Tkinter, twisted.internet,
   Cheetah. Also covers Extending and Embedding Python, with C, Java,
   and other languages and tools.
   Includes information on what parts were new in Python 2.2
   (doesn't cover 2.3, as it was not yet finalized when the book was published,
   but does mention a few 2.3 additions that were already known at the time)."
   pb; uk us isbn:0596001886; uk us isbn13:978-0596001889.
   -- [<A HREF="http://www.python.org/">python.org</A>][9/'03].
   [Also search for: Python book].

%A T. Herman
%T A Functional Start to Computing with Python
%I Chapman & Hall / CRC
%S Textbooks in Computing
%V Book 10
%P 427
%D 2013
%K book, text, Python, programming language, FP, computer programming
%X 1st ed 2013; pb us$68; uk us isbn:1466504552; uk us isbn13:978-1466504554.
   "... learn computing without having to use loops, variables, and object
   abstractions at the start. Requiring no prior programming experience, ...
   draws on Python's flexible data types and operations as well as its capacity
   for defining new functions. Along with the specifics of Python, the text
   covers important concepts of computing, inc. software engineering motivation,
   algorithms behind syntax rules, advanced functional programming ideas, and,
   briefly, finite state machines. ..."
   [Also search for: Python programming language book].


%A K. Singhal
%A K. Hietala
%A S. Marshall
%A R. Rand
%T Q# as a quantum algorithmic language
%J arXiv
%M JUN
%D 2022
%K TR, c022, c202x, c20xx, zz0622, Q#, Qsharp, quantum computing, programming,
   programming language, PLD
%X "Q# is a standalone domain-specific prog.lang. from M'crosoft for writing &
   running quantum programs. ... designed without a formal spec., which can
   naturally lead to ambiguity in its interpretation. We aim to provide a formal
   l.defn for Q# ... This paper presents lambda Q#, an idealized version of Q#
   that illustrates how we may view Q# as a quantum A1gol (alg. lang.). We show
   the safety properties enforced by lambda Q#'s type system & present its
   equational semantics based on a fully complete algebraic theory by Staton."
   -- 2206.03532@[<A HREF="https://arxiv.org/abs/2206.03532">arXiv</A>]['22].
   [Also search for: quantum programming language].

%A R. Rudiger
%T Quantum programming languages: An introductory overview
%J COMPJ
%V 50
%N 2
%P 134-150
%D 2007
%K jrnl, COMPJ, c2007, c200x, c20xx, quantum computing, zz0407, computation,
   language
%X "...overview of the novel field of quantum programming languages (QPLs) from
   a pragmatic perspective. ... short summary of basic notations of quantum
   mechanics, some of the goals & design issues are surveyed, which motivate the
   res. in this area. Then, several of the approaches are described in more
   detail. The article concludes with a brief survey..."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxl057">doi:10.1093/comjnl/bxl057</A>]['07].
   [Also search for: quantum programming language].

%A A. S. Green
%A P. L. Lumsdaine
%A N. J. Ross
%A P. Selinger
%A B. Valiron
%T An introduction to quantum programming in Quipper
%J 5th Int. Conf. on Reversible Computation
%I SpringerVerlag
%M JUL
%D 2013
%K conf, c2013, c201x, c20xx, zz0713, Quipper, computer programming language,
   quantum computing, Fourier Transform, QFT
%X "Quipper is a recently developed programming language for expressing quantum
   computations. ... brief tutorial intr. to the language, through a demo. of
   how to make use of some of its key features. We illustrate many of Q's
   language features by developing a few well known e.g. of Q.compn, inc.
   quantum teleportation, the quantum Fourier transform, & a quantum circuit
   for addition."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-38986-3_10">doi:10.1007/978-3-642-38986-3_10</A>]['13],
   & 1304.5485@[<A HREF="http://arxiv.org/abs/1304.5485">arXiv</A>]['13].
   (In uk us isbn:3642389856; uk us isbn13:978-3642389856.)
   [Also search for: quantum programming language].


%T Ruby
%D ?
%K Ruby, programming language
%X [<A HREF="http://www.ruby-lang.org/">ruby-lang.org</A>]['07].

%A D. Thomas
%A C. Fowler
%A A. Hunt
%T Programming Ruby: The Pragmatic Programmers' Guide (2nd ed)
%I PragmaticBookshelf
%P 829
%D 2004
%K book, text, c2004, c200x, c20xx, Ruby, programming language
%X "... installation, packaging, documenting Ruby source code, threading and
   synchronization, and enhancing Ruby's capabilities using C-language
   extensions. Programming for the World Wide Web is easy in Ruby, with new
   chapters on XML/RPC, SOAP, distributed Ruby, templating systems, and other
   web services. ..."
   2nd ed, pb, us$30, us isbn:0974514055; us isbn13:978-0974514055.


%A A. Demers
%A J. Donahue
%T Report on the programming language Russell
%I Comp. Sci., Cornell Univ.
%R 79-371
%D 1979
%K Russell, TR371, TR 371, programming language definition, PLD,
   parametric type, types, system, c1979, c197x, c19xx
%X [Also search for: Russell TR431].

%A Alan J. Demers and James E. Donahue
%T The Russell semantics: An exercise in abstract data types
%I Comp. Sci., Cornell Univ.
%R 80-431
%M SEP
%D 1980
%K Russell, TR431, TR 431, programming language, ADT, c1980, c198x, c19xx
%X [<A HREF="http://cs-tr.cs.cornell.edu/">search</A>][10/'01],
   [<A HREF="http://cs-tr.cs.cornell.edu/Dienst/UI/1.0/ShowComposite/ncstrl.cornell/TR80-431">paper</A>][10/'01].
   [Also search for: Russell TR371].


%A G. Hoare
%T The Rust Programming Language
%D 2010
%K Rust, rustc, c2010, c201x, c20xx, zz0216, computer programming language,
   definition, PLD, type, types, traits
%X "Rust is a systems programming language that runs blazingly fast,
    prevents segfaults, and guarantees thread safety."
   -- [<A HREF="https://www.rust-lang.org/">rust-lang.org</A>]['16].
   "The type system supports a mechanism similar to type classes, called
   'traits', inspired directly by the Haskell language. This is a facility
   for ad-hoc polymorphism, achieved by adding constraints to type variable
   declarations."
   -- rust@[<A HREF="https://en.wikipedia.org/wiki/Rust_(programming_language)">wikip</A>]['16].
   [Also search for: Rust programming language].

%A S. Klabnik
%A C. Nichols
%T The Rust Programming Language
%P 490
%M AUG
%D 2019
%K book, text, c2020, c202x, c20xx, zz1220, Rust, programming language
%X 2nd ed 2019; uk us isbn:1718500440; uk us isbn13:978-1718500440.
   "... Rust offers the control and performance of a low-level language with the
   helpful abstractions of a high level one, and does this all without having a
   garbage collector. ..."
   [Also search for: Rust programming language].


%T Scala Language Specification - the Scala language reference document
%M MAR
%D 2007
%K Scala, programming language definition, PLD, c2007, c200x, c20xx, FP, OOP,
   functional programming, object oriented, OO, component, components, zz0407,
   Odersky
%X "Scala is a general purpose programming language designed to express common
   programming patterns in a concise, elegant, and type-safe way. It smoothly
   integrates features of object-oriented & functional languages. It is also
   fully interoperable with Java."
   -- [<A HREF="http://www.scala-lang.org/">scala-lang.org</A>]['07],
      [<A HREF="http://www.scala-lang.org/docu/manuals.html">manuals</A>]['07].
   "... every value is an object ... every op. is a method ...
   functions are 1st class values ..."  -- the S. overview.
   [Also search for: Scala programming language].

%A C. K. K. Loverdos
%A A. Syropoulos
%T Steps in Scala: An Introduction to Object-Functional Programming
%I CUP
%P 504
%M NOV
%D 2010
%K Scala, book, text, CUP, c2010, c201x, c20xx, zz1012, OO, object oriented,
   FP, functional programming language
%X 1st ed 2010; pb us$45; uk us isbn:0521747589; uk us isbn13:978-0521747585.
      "... shows how to use the dual-object and functional-oriented natures
      combined at Scala's core, and so write code that is less 'boilerplate',
      giving a genuine increase in productivity."
   [Also search for: Scala programming language].

%A M. C. Lewis
%T Introduction to the Art of Programming Using Scala
%I ChapmanAndHall
%P 936
%M NOV
%D 2012
%K Scala, book, text, c2012, c201x, c20xx, zz1114, L1Ref, L2Ref, CS1, CS2,
   FP, functional programming language, computer programming
%X 1st ed 2012; pb us$76; uk us isbn:1439896666; uk us isbn13:978-1439896662.
   "... presents many concepts from CS1 and CS2 using a modern,
   JVM-based language that works well for both programming in the
   small and programming in the large. ..."
   [Also search for: Scala programming language].


%A G. L. Steele
%A G. J. Sussman
%T The revised report on Scheme, a dialect of Lisp
%I MIT
%R AI Memo 452
%D 1978
%K Scheme, book, text, reference, c1978, c197x, c19xx, functional, applicative,
   Scheme, Schemer,Lisp, programming language, FP, definition, PLD
%X See book by Dybvig;  also see JFP c2009.

%A M. Sperber
%A R. K. Dybvig
%A M. Flatt
%A A. van Straaten
%A R. Findler
%A J. Matthews
%T Revised report on the algorithmic language Scheme
%J JFP
%V 19, Suppl.S1
%P 1-301
%M AUG
%D 2009
%K Scheme, c2009, c200x, c20xx, zz0809, revised, functional, applicative, Lisp,
   programming language, FP, definition, PLD
%X [<A HREF="http://dx.doi.org/10.1017/S0956796809990074">doi:10.1017/S0956796809990074</A>]['09].

%A R. Kent Dybvig
%T The Scheme Programming Language
%I MITpress
%P 307
%D 1987
%K text, book, Scheme, functional programming, FP, applicative, language, lisp,
   c1987, c198x, c19xx
%X 4th ed 2009, pb us$35; uk us isbn:026251298X; uk us isbn13:978-0262512985.
   3rd ed 2OO3, pb us$35; uk us isbn:0262541483; uk us isbn13:978-0262541480.

%A D. Friedman
%A M. Felleison
%T The Seasoned Schemer
%I MITpress
%P 224
%D 1995
%K book, text, c1995, c199x, c19xx, Scheme, programming language, Lisp,
   L3Ref, L4Ref
%X 1st ed 1995, pb us$17; uk us isbn:026256100X; uk us isbn13:978-0262561006.
   [Also search for: Scheme book programming language].

%A D. P. Friedman
%T The Little Schemer
%I MITpress
%D 1996
%K book, text, c1996, c199x, c19xx, Scheme, programming language, Lisp, FP,
   L2ref, L3Ref
%X 4th ed, pb, stg17, us$27; uk us isbn:0262560992; uk us isbn13:978-0262560993.
   [Also search for: Seasoned Schemer].

%A D. P. Friedman
%A W. E. Byrd
%A O. Kiselyov
%T The Reasoned Schemer
%I MITpress
%D 2005
%K book, text, c2005, c200x, c20xx, Scheme, Lisp, FP, programming
%X ed 2005, pb us$25; uk us isbn:0262562146; uk us isbn13:978-0262562140.

%A J. Schwartz
%T The SETL language and examples of its use
%I Computer-Science-Dept., Courant-Institute-of-Math.-Sciences, N.Y.
%D 1971
%K Setl, set, programming language definition, PLD, c1971, c197x, c19xx

%A J. Palme
%T Experience from the standardization of the SIMULA programming language
%J SPE
%V 6
%N 3
%P 405-409
%M JUL
%D 1976
%K Simula, programming language, coroutine, class,
   OO, OOP, OOPS, c1976, c197x, c19xx, jrnl, SPE
%X See also:
   <A HREF="ftp://ftp.germany.eu.net/pub/programming/languages/simula">FTP</A>
   from <!-- email: claird at Starbase.NeoSoft.COM --> Cameron Laird [3/'95].

%T SIMULA Standard. DATA processing - Programming languages - SIMULA
%D 1987
%K Simula, Simula87, programming language definition, PLD, coroutine, class,
   OO, OOP, OOPS, c1987, c198x, c19xx, standard, standards
%X Swedish Standard SS 63 61 14,
   SIS, Box 3295, Stockholm, Sweden.  uk us isbn:9171622349.
   [also search for: Simula].
   Also see [<A HREF="http://www.isima.fr/asu/">isima.fr</A>]['05].

%A K. Nygaard
%A O. -J. Dahl
%T The development of the Simula languages
%J ACM Sigplan History of Programming Languages Conf.
%M JUN
%D 1987
%O ACM Sigplan Notices 13(8) Aug 87 p245-272
%K Simula, conf, object oriented, OO, OOP, inheritance, concatenation, zz0297
%X ref in   T a i v a l s a a r i   '96.

%A J. McGraw
%A S. Skedzielewski
%A S. Allan
%A R. Oldehoeft
%A J. Glauert
%A C. Kirkham
%A B. Noyce
%A R. Thomas
%T SISAL: Streams and iteration in a single assignment language,
   language reference manual version 1.2
%I Lawrence-Livermore-National-Laboratory
%M MAR
%D 1985
%K Sisal, LLNL, applicative programming language definition, PLD, functional,
   FP, stream, array, parallel, concurrent, multi-processor,
   c1985, c198x, c19xx
%X free of side-effects,
   serious attempt to wean Fortran programmers to something for which it is
   easier to write parallel implementation.

%A A. Goldberg
%A D. Robson
%T Smalltalk-80: The Language and its Implementation
%I AddisonWesley
%P 608
%D 1983
%K book, text, Smalltalk, Smalltalk80, small talk, c1983, c198x, c19xx,
   programming language definition, PLD, object oriented, OO, OOP
%X pb; uk us isbn:0201136880; uk us isbn13:978-0201136883.

%A W. Lalonde
%T Discovering Smalltalk
%I Benjamin-Cummings
%P 554
%D 1994
%K Smalltalk, small talk, object oriented computer programming language,
   book, text, OO, OOP, zz0595
%X pb; uk us isbn:0805327207; uk us isbn13:978-0805327205.
   reviewed Comp' Reviews p94 Feb 1995.

%A R. Milner
%T The Standard ML Core Language (Revised)
%D 1985
%I Dept.-Computer-Science, University-of-Edinburgh
%K SML,  Standard ML, functional, applicative, programming language definition,
   FP, PLD, polymorphism, polymorphic, data type, types, inference,
   c1985, c198x, c19xx
%X <A HREF="http://www.dcs.ed.ac.uk/">Dept CSci Edinburgh home</A>
   see various books on SML
   see Lazy ML [LML]
   Subject: Linux SML 0.93 Source      (8/'94)
    I accidentally found the Linux "sml" binary pre-compiled on tsx-11.mit.edu
    To whoever made this binary, thank you much!  I got through patching
    the signal stuff, but the assembler wouldn't make it through "as".  Where
    can I find the source patched for Linux?  I'd like to build the debugging
    and no-share versions on sml.
    Rose Hoskins/AT&T CFO     Michael S. Garnett/AT&T CSG
    (email: Rose Hoskins       email: pickles at cnj.digex.net)

%A R. Milner
%A M. Tofte
%A R. M. Harper
%T The Definition of Standard ML
%I MITpress
%D 1990
%K book, text, standard ML, ML, SML, NJ, functional programming, language, FP,
   c1990, c199x, c19xx
%X pb; uk us isbn:0262631814; uk us isbn13:978-0262631815.

%A R. Griswold
%A J. Poage
%A I. Polonsky
%T The Snobol 4 Programming Language
%I PrenticeHall
%D 1971
%K Snobol, text, book, snobol4, pattern, string match, processing,
   programming language definition, PLD, c1971, c197x, c19xx,
   www, HREF, FTP
%X pb; uk us isbn:0138153736; uk us isbn13:978-0138153731.
   See also SL5 and Icon (Griswold),
   -- [<A HREF="http://cs.arizona.edu/">cs.arizona.edu</A>]['03].

%T Stan Modelling Language, ver.3.9.0
%D DEC
%D 2015
%K Stan, c2015, c201x, c20xx, zz0220, probabilistic programming language, PLD,
   stats, probability, model
%X "Stan is a state-of-the-art platform for statistical modeling and
   high-performance statistical computation. Thousands of users rely on Stan
   for statistical modeling, data analysis, and prediction in the social,
   biological, and physical sciences, engineering, and business. ..."
   -- Stan@[<A HREF="https://mc-stan.org/">www</A>]['20] home.
   "Stan is a probabilistic programming language for statistical inference
   written in C++. ..."
   -- Stan@[<A HREF="https://en.wikipedia.org/wiki/Stan_(software)">wikip</A>]['20]  (via njh).

%A P. Brinch Hansen
%T Interference control in SuperPascal - a block structures parallel language
%J COMPJ
%V 37
%N 5
%P 399-406
%M ?
%D 1994
%K jrnl, SuperPascal, super Pascal, Per BrinchHansen,
   computer programming language, data parallel, forall
%X algorithmic parallelism: PARALLEL S1, S2, ..., Sn END
   data parallelism:        FORALL i= e1 TO e2 DO s

%A J. K. Ousterhout
%T Tcl and Tk Toolkit
%I AddisonWesley
%P 458
%D 1994
%K Tcl, Tk, book, text, tool command language, programming,
   X windows, XWindows, c1994, c199x, c19xx
%X pb; uk us isbn:020163337X; uk us isbn13:978-0201633375.

%A R. C. Holt
%A P. A. Matthews
%A J. A. Rosselet
%A J. R. Cordy
%T The Turing Programming Language, Design and Definition
%I PrenticeHall
%D 1988
%K Turing, text book, c1988, c198x, c19xx,
   imperative, programming language definition, PLD
%X similar to C, Pascal -ish.
   -- [<A HREF="/~lloyd/tildeProgLang/Turing">Turing</A>].


%A J. W. Cooper
%T Visual Basic for DOS: Building Scientific and Technical Applications
%I Wiley
%D 1993
%P 401
%K VisualBasic, book, text, VB, DOS, VBDOS, programming language
%X isbn:0-471-59772-4.

%A K. Gurganus
%A D. Alexander
%T Microsoft Visual C++: Windows primer
%I AcademicPress
%P 346
%D 1994
%K VisualC++, book, text, c1994, c199x, c19xx, ms, micro soft,
   programming language
%X reviewed Computing Reviews, p.234 May c1995,
   pb; uk us isbn:0123086507; uk us isbn13:978-0123086501.


%A R. L. Drechsler
%A J. M. Mocenigo
%T The Yoix(r) scripting language: A different way of writing Java(tm)
   applications
%J SPE
%V 37
%N 6
%P 643-667
%M MAY
%D 2007
%K jrnl, SPE, c2007, c200x, c20xx, programming language definition, PDL, script,
   YOIX, zz0507
%X "... scripting language implemented in Java & providing access to many Java
   capabilities. The result provides a mechanism for fast & efficient
   development, deployment & maintenance of client/server applications. The
   Yoix interpreter does not rely on Java reflection classes to access Java
   capabilities, but rather uses programmatic methods. This approach allowed us
   to deliver the complex aspects of Java functionality more simply & succinctly
   at the Yoix level as well as achieve consistent behavior & portability across
   platforms. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.784">doi:10.1002/spe.784</A>]['07],
   -- [<A HREF="http://www.research.att.com/sw/tools/yoix/">yoix@att</A>]['07],
   -- [<A HREF="http://www.yoix.org/">yoix.org</A>]['07].


%A M. Luck
%A M. d'Inverno
%T A conceptual framework for agent definition and development
%J COMPJ
%V 44
%N 1
%P 1-20
%D 2001
%K Z, ZZ, jrnl, COMPJ, agents, c2001, c200x, c20xx, specification language,
   programming, dIverno, zz0406
%X "... applying formal methods to provide a defining framework for agent
   systems. The Z specification language is used to provide an accessible &
   unified formal account of agent systems, allowing us to escape from the
   terminological chaos that surrounds agents. ... precisely & unambiguously
   provides meanings for common concepts & terms, enables alternative models of
   particular classes of system to be described within it, & provides a
   foundation for subsequent development of increasingly more refined concepts"
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/44.1.1">doi:10.1093/comjnl/44.1.1</A>]['06],
   -- [<A HREF="http://www.ecs.soton.ac.uk/~mml/">auth1@U.South@mpton</A>]['06],
      [<A HREF="http://www2.wmin.ac.uk/~dinverm/">auth2@U.Westm'nster</A>]['06].

-------------------------------------------------------------------------------

%A C. A. R. Hoare
%T Hints on programming language design
%I Stanford AI Lab.
%R AIM 224
%O STAN CS 73 403
%M DEC
%D 1973
%K TR 224, AIM224, STANCS73403, CS403, languages, algol 60, algol60, A60,
   c1973, c197x, c19xx, Tony Hoare, syntax, semantics, POPL, quote, quotable
%X Based on a keynote address SIGACT/SIGPLAN POPL Oct 1973.
   Incuding, on Algol-60,  "Here is a language so far ahead of its time,
      that it was not only an improvement on its predecessors, but also on
      nearly all its successors."  [p.27]
   -- [<A HREF="http://www.cs.berkeley.edu/~necula/cs263/handouts/hoarehints.pdf">.pdf</A>][4/'04].

%A P. Brinch Hansen
%T A Joyce implementation
%J SPE
%V 17
%N 4
%M Apr
%D 1987
%P 267-276
%K Joyce, programming language, distributed, parallel, communication,
   synchronisation, channel, message, CSP, agent, agents, polling,
   implementation, IBM PC

%A A. S. Tanenbaum
%T A tutorial on Algol 68
%J ACM Computing Surveys
%M JUN
%D 1976
%V 8
%N 2
%K algol, algol68, algol-68, c1976, c197x, c19xx, tute, tutorial,
   introduction, programming language

%A Lindsey
%A van der Meulen
%T Informal Introduction to Algol 68
%I North-Holland
%D 1971
%K algol, algol68, algol-68, introduction, manual, programming language,
   text, book, c1971, c197x, c19xx

%A F. G. Pagan
%T A Practical Guide to Algol 68
%I Wiley
%D 1976
%K algol, algol68, algol-68, introduction, book, manual, programming language,
   text, book, c1976, c197x, c19xx

%A D. R. Hanson
%A R. E. Griswold
%T The SL5 procedure mechanism
%J CACM
%V 21
%N 5
%M May
%D 1978
%P 392
%K SL5, backtrack, coroutine, control, procedure, call, closure, bind,
   binding, activation record, stack, heap, c1978, c197x, c19xx
%X [Also search for: Icon programming language].

%A T. Takaoka
%T The semantics of new while loop
%J COMPJ
%V 29
%N 1
%M FEB
%D 1986
%P 33-35
%K axiom, proof, rule, semantics, Hoare-style,
   while, nwhile, loop, construct, command, statement
%X nwhile B do S
   terminates as soon as B becomes false ( procedures not mentioned)

%A D. L. Parnas
%T A generalized control structure and its formal definition
%J CACM
%V 26
%N 8
%P 572-581
%M AUG
%D 1983
%K if, while, it ti,   general, generalised,
   control structure, loop, conditional, nondeterminism, non determinism
%X it P1 -> N1 ^  |
      ...
      Pm -> Nm ^  |
      Q1 -> T1 v  |
      ...
      Qn -> Tn v
   ti.
   The Pi -> Ni are non-terminating parts, the Qj -> Tj terminating parts.
   If multiple guards Pi and Qj are true, choice is non-deterministic.
   Gives examples and argument about use of formal program design
   methods and program proof.

%A R. E. Griswold
%T An overview of the Icon programming language
%I Dept-Computer-Science, University-of-Arizona
%M FEB
%D 1983
%K Icon, programming language, control, string, pattern match, goal

%A R. Salter
%T Concurrent applicative implementations of nondeterministic algorithms
%J Computer Languages
%V 8
%N 2
%P 61-68
%D 1983
%K nondeterministic, non-deterministic, non deterministic,
   nondeterminism, non-determinism, non determinism,
   backtrack, backtracking,  coroutine,
   concurrent, concurrency, parallel, multi, multiprocessor,
   suspend, suspended, structure, structures,
   applicative, functional, language,   frons
%X utilise concurrency in place of backtracking
   in implementation of nondet algorithms.
   use Friedman Wise multiprogramming primitive frons.
   Suspensions - control disciplines embodied as conceptual data structures
   which in reality manifest themselves only for purposes of control (eek !)
   eight queens 8 queens
   also a coroutine controlled backtracking problem
   good sequences of Dijkstra  - no two adjacent substrings equal
   eg 2123123 is not good,
      1213231 is good.

%A G. Lindstrom
%T Backtracking in a generalized control setting
%J Trans Program Sys ?TOPLAS?
%V 1
%P 8-26
%D 1979
%K functional, applicative, language, backtrack, nondeterminism,
   non determinism, coroutine

%A J. R. Bitner
%A E. M. Reingold
%T Backtrack programming techniques
%J CACM
%V 18
%N 11
%P 651-656
%M NOV
%D 1975
%K backtrack, backtracking, nondeterminism, non determinism,
   n-queens, eight, 8 queens, nqueens, tiling,
   macro, macros
%X macros used to speed up combinatorial algorithms,
   nqueens,
   tiling with pentominoes.

%A R. W. Floyd
%T Nondeterministic algorithms
%J JACM
%V 14
%N 4
%P 636-644
%M OCT
%D 1967
%K nonDeterminism, non determinism, backtrack, backtracking, eight, 8 queens,
   8queens, choice, fail, nqueens, c1967, c196x, c19xx, non-deterministic,
   simple cycles, cycle, graph
%X "Programs to solve combinatorial search problems may often be simply written
   by using multiple-valued functions. Such programs, although impossible to
   execute directly on conventional computers, may be converted in a mechanical
   way into conventional backtracking programs. The process is illustrated with
   algorithms to find all solutions to the 8 queens problem on the chessboard,
   and to find all simple cycles in a network."
   -- Important seminal paper near the start of things,
      [<A HREF="http://doi.acm.org/10.1145/321420.321422">doi:10.1145/321420.321422</A>]['05].

%A J. Cohen
%T Nondeterministic algorithms
%J ACM  Surveys
%V 11
%P 79-94
%D 1979
%K nondeterminism, non determinism, nondeterministic, non deterministic,
   backtrack, backtracking, eight, 8 queens, nqueens,
   survey, algorithm, algorithms, c1979, c197x, c19xx

%A S. B. Wampler
%A R. E. Griswold
%T Co-expressions in Icon
%J COMPJ
%V 26
%N 1
%D 1983
%M JAN
%P 72-78
%K icon, c1983, c198x, c19xx, programming language, generator,
   coexpression, coroutine

%A P. Henderson
%T Functional Programming: Application and Implementation
%I PrenticeHall
%P 368
%D 1980
%K functional, applicative programming, FP, lisp, lispkit, book

%A M. Felleisen
%T Reflections on Landin's J operator: a partly historical note
%J Computer Languages
%P 197-207
%V 12
%N 3/4
%D 1987
%K J, J-operator, lambda calculus, algol, algol-60, continuations, scheme,
   functional, applicative programming, FP, control, jump
%X Landin's J-operator was the first attempt to extend the lambda calculus
   with a non functional control facility. We show in this note how the
   extended language can be embedded in Scheme. This finally clarifies
   the relationship between the J- and the call/cc-operator. Beyond
   the historical perspective the note simultaneously provides insight into
   the programming with continuations and the construction of language
   embeddings for the clarification of semantic issues. [author].

%A P. J. Landin
%T A correspondence between Algol 60 and Church's lambda notation
%J CACM
%V 8
%N 2
%P 89-101; 158-165
%D 1965
%K Algol, 60 Algol-60, lambda calculus, Church,
   functional programming language, FP

%A P. J. Landin
%T An abstract machine for designers of computing languages
%J Proc. IFIP Congress
%P 438-439
%D 1965
%K SECD, lambda calculus, programming, programming, functional, FP

%A G. D. Plotkin
%T Call-by-name, call-by-value- and the lambda-calculus
%J Theoretical Computer Science
%V 1
%P 125-159
%D 1975
%K jrnl, TCS, c1975, c197x, c19xx, lambda calculus, call by value, call by need,
   normal order, lazy evaluation, functional programming, FP

%A J. C. Reynolds
%T Definitional interpreters for higher-order programming languages
%J Proc. ACM Annual Conference
%P 717-740
%D 1972
%K definition, semantics, interpreter, conf, c1972, c197x, c19xx

%A D. Kozen
%T Semantics of probabilistic programs
%J JCSS
%V 22
%N 3
%P 328-350
%D 1981
%K jrnl, JCSS, c1981, c198x, c19xx, zz0823, probabilistic programming language
%X "... presents two complementary but equivalent semantics for a high level
   probabilistic prog. lang.. One of these interprets programs as partial
   measurable fns on a measurable space. The other interprets programs as
   cts linear operators on a Banach space of measures. It is shown how the
   ordered domains of Scott & others are embedded naturally into these spaces.
   We use the semantics to prove a general result about prob.programs, namely,
   that a program's behavior is completely det. by its action on fixed inputs."
   -- [<A HREF="https://doi.org/10.1016/0022-0000(81)90036-2">doi:10.1016/0022-0000(81)90036-2</A>]['23].
   [Also search for: probabilistic programming].

%A L. V. Atkinson
%A J. J. McGregor
%A S. D. North
%T Context sensitive editing as an approach to incremental compilation
%J COMPJ
%V 24
%N 3
%D 1981
%M AUG
%P 222-229
%K edit, editing, program, editor, compiler
%X an incremental compiler fpor a block structured language
   1 pass subset of Algol-60
   performs minimal recompilation after edits
   correct errors when detected
   semantic errors checked.

%A A. Adam
%A P. Gloess
%A J-P. Laurent
%T An interactive tool for program manipulation
%J IEEE 5th International Conference on Software Engineering ???
%M MAR
%D 1981
%K program editor, edit, debug, debugging, transformation
%X interactive system for understanding programs
   information about control structure and data flow.

%A R. A. Brooker
%A D. Morris
%T A general translation program for phrase structure languages
%J JACM
%V 9
%D 1962
%P 1-10
%K parse, parser, CC, compiler, compiler-compiler, LL(1)

%A J. N. Brownlee
%T An Algol based implementation of Snobol4 patterns
%J CACM
%V 20
%N 7
%M JUL
%D 1977
%P 527-529
%K snobol, snobol4, pattern match, matching, string processing

%A J. P. Banatre
%A J. P. Routeau
%A L. Trilling
%T An event-driven compiling technique
%J CACM
%V 22
%N 1
%M JAN
%D 1979
%P 34-42
%K compile, compiler, compiling, technique, one pass, onepass, event, process,
   parallelism
%X forward references resolved using events and processes,
   used on an Algol68 compiler.

%A J. Bishop
%A D. Barron
%T Procedure calling and structured architecture
%J ???
%D 1978
%K stack, call, entry, exit, procedure, thunk, closure, link, linkage,
   static, dynamic, display, programming language

%A J. M. Bishop
%A D. W. Barron
%T Principles of descriptors
%J COMPJ
%V 24
%N 3
%P 210-221
%M AUG
%D 1981
%K descriptor, vector, array, block, object

%A P. J. Brown
%T Throw-away compiling
%J SPE
%V 6
%P 423-434
%D 1976
%K jrnl, SPE, c1976, c197x, c19xx, compiler, interpreter, basic, throw away
%X for use with small memory
   compile what you can, run it,
   if drop off the end, throw away and compile next bit.

%A D. G. Bobrow
%A B. Wegbreit
%T Model for control structures for artificial intelligence programming
   languages
%J IEEE Transactions on Computers
%V C-25
%N 4
%M Apr
%D 1976
%P 347-353
%K search, backtrack, nondeterminism, coroutine, control structure, stack

%A R. J. Cichelli
%T Pascal I - interactive, conversational PascalS
%P 34-44
%J SIGPLAN
%V 15
%N 1
%M JAN
%D 1980
%K Pascal, PascalI, PascalS, interact, incremental

%A R. W. Conway
%A T. R. Wilcox
%T Design and implementation of a diagnostic compiler for PL/1
%J CACM
%M MAR
%D 1973
%V 16
%N 3
%P 169-179
%K compiler, debug, debugger, diagnose, error, programming language, one, 1,
   PL1, PLC, PL/C

%A J. Cohen
%A E. Carton
%T Non-deterministic Fortran
%J COMPJ
%V 17
%N 1
%P 44-51
%D 1974
%K nondeterminism, backtrack, fortran, n-queens, nqueens, c1974, c197x, c19xx,
   jrnl, COMPJ, non-determinism, nondeterministic
%X "... extensions to FORTRAN that enable programmers to write Floyd's
   non-deterministic algorithms. ...also describes a syntax-directed translator
   of non-deterministic F. programs into standard F.. It is shown that is
   suitable conventions are made as the form of input programs, there exists a
   simple finite-state grammar that can be used to drive the translation. Two
   examples are given: (1) a program to solve the 8 queens problem & (2) a
   selective top-down parser that can be useful in syntax-directed trans.."
   -- [<A HREF="http://comjnl.oxfordjournals.org/cgi/content/abstract/17/1/44">paper@oup</A>]['05].

%A J. Cohen
%T Garbage collection of linked data structures
%J Computing Surveys
%V 13
%N 3
%M SEP
%D 1981
%P 341-367
%K garbage collect, list, tree, mark, marking, scan, compact, reference count,
   parallel, real time, lisp, functional, applicative programming, FP,
%X survey on garbage collection, good bibliography.

%A K. Delcour
%A A. J. W. Duijvestain
%T Enclosures: an access control mechanism with applications in
   parallel programming and other areas of system programming
%J IPL
%V 5
%N 5
%M NOV
%D 1976
%K enclosure, monitor, protected region, protection, access, scope, module

%A F. DeRemer
%A T. Pennello
%T Efficient computation of LALR(1) look-ahead sets
%J TOPLAS
%V 4
%N 4
%M OCT
%D 1982
%P 615-649
%K algorithm, LALR, lookahead set, parser, parsing, bottom up, yacc, LR, jrnl

%A M. C. Er
%T Optimizing procedure calls and returns
%J SPE
%V 13
%P 921-939
%D 1983
%K optimise, optimize, procedure, function call, return, tail recursion


%A D. P. Friedman
%A M. Felleisen
%T The little LISPer
%I MITpress
%P 200
%D 1986
%K Scheme, lisp,  programming, applicative, functional language, FP,
   book, text, L3Ref, L4Ref, c1986, c198x, c19x
%X 2nd ed, c1987, pb; uk us isbn:0262560380; uk us isbn13:978-0262560382.

%A H. Abelson
%A G. Sussman
%A J. Sussman
%T Structure and Interpretation of Computer Programs
%I MITpress and also McGraw-Hill
%D 1985
%K Scheme, lisp, functional, applicative programming, language,
   introductory, L2Ref, L3Ref, book, text, c1985, c198x, c19xx
%X 2nd ed c1997, hb us$69; uk us isbn:0070004846; uk us isbn13:978-0070004849.

%A J. E. Sammet
%T Programming languages: history and future
%J CACM
%V 15
%M JUL
%D 1972

%E R. Wexelblat
%T History of Programming Languages
%I AcademicPress
%D 1981
%K text, book, history, survey

%A P. J. Landin
%T The mechanical evaluation of expressions
%J COMPJ
%V 6
%N 4
%D 1963
%K lambda calculus, functional applicative programming language, FP, SECD,
   jrnl, COMPJ, c1963, c196x, c19xx

%A M. Richards
%T BCPL: a tool for compiler writing and system programming
%J Proc. Spring Joint Computer Conference
%D 1969
%K conf, BCPL, basic CPL, programming language, c1969, c196x, c196x
%X [Also search for: BCPL language].

%A P. J. Landin
%T The next 700 programming languages
%J CACM
%V 9
%N 3
%P 157-166
%K jrnl, cacm, acm, PL, language, design, c1966, c196x, c19xx
%X "A family of unimplemented computing languages is described that is intended
   to span differences of application area by a unified framework. This
   framework dictates the rules about the uses of user-coined names, & the
   conventions about characterizing functional relationships. Within this
   framework the design of a specific language splits into two independent
   parts. One is the choice of written appearances of programs (or more
   generally, their physical representation). The other is the choice of the
   abstract entities (such as numbers, character-strings, list of them,
   functional relations among them) that can be referred to in the language.
   The system is biased towards "expressions" rather than "statements." It
   includes a nonprocedural (purely functional) subsystem that aims to expand
   the class of users' needs that can be met by a single print-instruction,
   without sacrificing the important properties that make conventional
   right-hand-side expressions easy to construct & understand."
   -- [<A HREF="http://doi.acm.org/10.1145/365230.365257">paper</A>][2/'04].

%A N. Wirth
%A C. A. R. Hoare
%T A contribution to the development of Algol
%J CACM
%M JUN
%D 1966
%K algol, algol-60, algol-68, Pascal, Algol-W, programming language
%X ?The schism?
   [Also search for: algol programming language].

%A W. A. Wulf
%A D. B. Russel
%A A. Nico Habermann
%T Bliss: a language for systems programming
%J CACM
%M DEC
%D 1971
%K bliss

%A Per Brinch Hansen
%T The programming language concurrent Pascal
%J IEEE Transactions on Software Engineering
%M JUN
%D 1975

%A J. C. Cleaveland
%A R. C. Uzgalis
%T Grammars for programming languages: what every programmer should know about
   grammar
%I American-Elsevier
%D 1976
%K 2-LVWG, two level, VWG, grammar

%A B. W. Lampson et al
%T Report on the programming language Euclid
%J Sigplan
%M FEB
%D 1977
%K Euclid

%A K. Jensen
%A N. Wirth
%T The Programming Language Pascal
%I SpringerVerlag
%D 1975
%K text, book, Pascal, c1975, c197x, c19xx, L1Ref, L2Ref

%A W. A. Wulf
%A R. L. London
%A M. Shaw
%T Abstraction and verification in Alphard: introduction to
   language and methodology
%I USC-Information-Science-UCLA
%M AUG
%D 1976
%K Alphard,  abstract data type, datatype

%A J. Feldman
%A D. Gries
%T Translator writing systems
%J CACM
%P 77-113
%V 11
%N 2
%M FEB
%D 1968
%K compiler-compiler, TWS, parse, parser, parsing, generator
%X survey  state of the art in 1968 (!).

%A D. A. Fisher
%T DoD's common programming language effort
%J IEEE Computer
%D 1978
%M MAR
%P 24-33
%K Ada, c1978, c197x, c19xx, DOD, Department of Defense, iron-man, tin-man

%A D. Gries
%A N. Gehani
%T Some ideas on data types in a high level language
%J CACM
%M JUN
%D 1977
%V 20
%N 6
%P 414-420
%K data, type, datatype, generic procedure
%X data type is a set of values plus operations.
   need iteration over any finite set.
   domain of array is data type.
   parameters of datatypes.

%A J. V. Guttag
%A E. Horowitz
%A D. R. Musser
%T Abstract data types and software validation
%J CACM
%M DEC
%D 1978
%V 21
%N 12
%P 1048-1064
%K abstract data type, datatype, data structure, specification
%X data abstraction algebraic axioms   axiomatisation.
   proof
   semi automatic tools for such proofs.
   examples: stack, dictionary table.

%A J. Guttag
%T Abstract data types and the development of data structures
%J CACM
%V 20
%N 6
%M JUN
%D 1977
%P 396-404
%K abstract data type, datatype, axiom, algebra

%A C. Ghezzi
%A D. Mandrioli
%T Incremental parsing
%J TOPLAS
%V 1
%M JUL
%D 1979
%N 1
%P 58-70
%K incremental parsing, LR grammar, LR parser, threaded tree

%A A Burns
%T Concurrent Programming in Ada
%I CUP
%D 1985
%K text, book, task, concurrent, parallel, Ada
%X hb; uk us isbn:0521300339; uk us isbn13:978-0521300339.
   (Reviewed in Computing Reviews Jan c1988 p.50.)

%A S. H. Kaisler
%T Interlisp: the language and its usage
%I Wiley
%D 1986
%K text, book, Interlisp, Lisp
%X uk us isbn:0-471-81644-2;
   reviewed in Computing Reviews Jan 1988 p51, unfavourably.

%A J. B. Goodenough
%T Exception handling: Issues and a proposed notation
%J CACM
%V 18
%N 12
%M DEC
%D 1975
%P 683-696
%K exit, exception, raise, throw, catch, handle, error condition

%A R. E. Griswold
%A D. R. Hanson
%T Language facilities for programmable backtracking
%J SIGPLAN
%V 12
%N 8
%M AUG
%D 1977
%O also SIGART No64, joint symposium on AI and Programming Languages
%P 94-99
%K SL5, backtrack, nondeterminism
%X see also Snobol4 and Icon.

%A S. L. Gerhart
%A L. Yelowitz
%T Control structure abstraction of the backtracking
   programming technique
%J IEEE Transactions on Software Engineering
%V SE-2
%N 4
%M DEC
%D 1976
%P 285-292
%K backtracking, nondeterminism, control

%A P. Brinch-Hansen
%A J. Staunstrup
%T Specification and implementation of mutual exclusion
%C IEEE Trans. Software Engineering
%V SE-4
%N 5
%M SEP
%D 1978
%P 365-370
%K concurrent, parallel, guarded region, mutual exclusion

%A R. J. W. Housden
%T Teaching top-down analysis using Algol-68 phrases
%I School-of-Computing-Studies, Uni.-East-Anglia
%J Liverpool Conference on Experience with Algol-68
%D 1975
%K Algol, Algol68, top down, phrase structure, parse, parser, grammar

%A C. A. R. Hoare
%T Monitors: an operating system structuring concept
%J CACM
%V 17
%N 10
%M OCT
%D 1974
%P 549-557
%K monitor, c1974, c197x, c19xx, parallel, concurrent, mutual exclusion

%A R. G. Herriot
%T Towards the ideal programming language
%J Proc. of the ACM Conf. on Language Design for Reliable Software
%M MAR
%D 1977
%O Sigplan V12 No3
%P 56-62
%X class, template and instance,
   some ideas taken from English clauses.

%A D. Harel
%T And/or programs: A new approach to structured programming
%J TOPLAS
%V 2
%N 1
%M JAN
%D 1980
%P 1-17
%K alternation, and/or, and or, program verification

%A S.J. Allan
%A R.R. Oldehoeft
%T HEP SISAL: parallel functional programming
%B Parallel MIMD computation: HEP supercomputer and its applications
%E Janusz S. Kowalik
%I MITpress
%C Cambridge, Massachusetts
%D 1985
%P 123-150
%K Sisal, applicative, FP

%A R.R. Oldehoeft
%A S.J. Allan
%T Execution support for HEP SISAL
%B Parallel MIMD computation: HEP supercomputer and its applications
%E Janusz S. Kowalik
%I MITpress
%C Cambridge, Massachusetts
%D 1985
%P 151-180

%A Rodney R. Oldehoeft
%A David C. Cann
%T Applicative parallelism on a shared-memory multiprocessor
%J IEEE Software
%K ieee_soft
%V 5
%N 1
%M JAN
%D 1988
%P 62-68
%K SISAL, performance, functional programming

%A R.R. Oldehoeft
%A D.C. Cann
%A S.J. Allan
%T SISAL: initial MIMD performance results
%J Proceedings of the Conference on Algorithms and Hardware for
   Parallel Processing
%C Aachen, West Germany
%M SEP
%D 1986
%E W. Handler
%E D. Haupt
%E R. Jeltsch
%E W. Juling
%E O. Lange
%O published as Lecture Notes in Computer Science LNCS 237
   by Springer-Verlag
%K conpar, conpar86, LNCS237
%P 120-127

%A Thomas Gross
%A Alan Sussman
%T Mapping a single-assignment language onto the Warp systolic array
%J Proceedings of the 1987 Symposium on
   Functional Programming Languages and Computer Architecture
%C Portland, Oregon
%M SEP
%D 1987
%E Gilles Kahn
%O published as Lecture Notes in Computer Science 274
   by Springer-Verlag
%K fpca, fplca, fpca87, fplca87, K, SISAL, IF1, W2
%P 347-363

%A Stephen J. Allan
%A R.R. Oldehoeft
%T Parallelism in SISAL: exploiting the HEP architecture
%J Proceedings of the 19th Annual Hawaii International Conference on
   System Sciences,
   Volume 2
%E Bruce D. Shriver
%C Honolulu, Hawaii
%M JAN
%D 1986
%K hicss, hawaii19, hicss19, hawaii86, hicss86
%P 538-548

%A S.K. Skedzielewski
%A R.K. Yates
%A R.R. Oldehoeft
%T DI: an interactive debugging interpreter for applicative languages
   (extended abstract)
%J Proceedings of the SIGPLAN '87 Symposium
   on Interpreters and Interpretive Techniques
%C St. Paul, Minnesota
%M JUN
%D 1987
%O published as SIGPLAN Notices 22:7
%K iit, iit87, SISAL
%P 102-112

%A J.L. Gaudiot
%A L.T. Lee
%T Multiprocessor systems programming in a high-level data-flow language
%J Proceedings of the Conference on Parallel Architectures and Languages Europe,
   Volume I: Parallel Architectures
%E J.W. de Bakker
%E A.J. Nijman
%E P.C. Treleaven
%C Eindhoven, Netherlands
%M JUN
%D 1987
%O published as Lecture Notes in Computer Science 258
   by Springer-Verlag
%K parle, parle87, SISAL, TX16, Inmos transputer, occam, IF1
%P 134-151

%A A.P.W. Bohm
%A J. Sargeant
%T Efficient dataflow code generation for SISAL
%J Proceedings of the Second International Conference on Parallel Computing
%C Berlin
%M SEP
%D 1985
%E M. Feilmeier
%E G. Joubert
%E U. Schendel
%K Sisal, pc pc2, FP, programming language
%P 339
%O published as "Parallel computing 85" by North-Holland   and
   Technical Report UMCS-85-10-3
   Department of Computer Science, University of Manchester, 1985
%X The efficiency of dataflow code generated from a high level language
   can be improved drastically by both conventional and dataflow-specific
   optimisations.
   Such techniques are used in implementing the functional language SISAL
   on the Manchester Dataflow Machine.

%A P. Brinch Hansen
%T Structured multiprogramming
%J CACM
%V 15
%N 7
%M JUL
%D 1972
%P 574-578
%K structured, multiprogramming, multi, parallel, concurrent, critical region

%A P. Brinch Hansen
%T Distributed processes: a concurrent programming concept
%J CACM
%V 21
%N 11
%M NOV
%D 1978
%P 934-941
%K concurrent, parallel, process, critical region, guard, guarded regions,
   concurrent Pascal

%A R. Haskell
%T Efficient implementation of a class of recursively defined functions
%J COMPJ
%M FEB
%D 1975
%P 23-29
%V 18
%N 1
%K recursion, stack, two stacks, tail recursion, function
%X a method eval' rec functions using 2 or more stacks.
   claims simpler linkage.
   goto or iterative recursion uses bounded storage.

%A R. S. Barton
%T A new approach to the functional design of a computer
%J Proc. Western Joint Comp. Conf.
%D 1961
%P 393-396
%K conf, cactus, stack, computer architecture, CS, CSci
%X enews: R.Evans [11/'95].

%A E. A. Hauck
%A B. A. Dent
%T Burroughs B6500/7500 stack mechanism
%J AFIPS Spring Joint Conference Proceedings
%V 32
%D 1968
%P 245-251
%K Burrough , 6500, 7500, B6500, B7500, cactus, stack, display,
   c1968, c196x, c19xx, zero address, tag, tagged, descriptor,
   computer architecture
%X tagged words
   descriptors,   reverse polish or zero address code.

%A A. Hassitt
%A J. W. Lageschulte
%A L. E. Lyon
%T Implementation of a high level language machine
%J CACM
%V 16
%N 4
%M Apr
%D 1973
%P 199-212
%K APL, microcode, microprogramming
%X microprogrammed a IBM 360 to execute APL code.

%A W. J. Hansen
%T User engineering principles for interactive systems
%J AFIPS Fall Joint Conference Proceedings
%D 1971
%V 39
%P 523-532
%K Emily, holophrasting, edit, editor
%X Emily text editor.

%A R. J. W. Housden
%T An implementation of phrase structures in Algol
%J SPE
%V 2
%P 231-240
%D 1972
%K phrase structure, parser, top down syntax analysis, fastback
%X phrase structures added to algol60.

%A R. J. W. Housden
%T Phrase structures in FORTRAN
%J COMPJ
%P 224-228
%V 14
%N 3
%D 1971
%K phrase structure, top down syntax analysis, parse, parser, grammar, fastback
%X phrase structures added to Fortran.

%A F. Chow
%A M. Himelstein
%A E. Killian
%A L. Weber
%T Engineering a RISC compiler
   system
%J Digest of Papers of the Thirtyfirst IEEE Computer Society
   International Conference (CompCon 86 Spring)
%M FEB
%D 1986
%P 132-137
%K C, compiler, register allocation, optimise, optimize, 31, 31st, CompCon
%X via enews
   It describes the MIPS C compiler which has the optimization you mentioned.
   optimises leaf functions and register allocation.

%A P. Jorrand
%T Data types and extensible languages
%J Proc. International Symposium on Extensible Languages
%O Sigplan V16 No12
%M DEC
%D 1971
%P 75-83
%K datatype, data type, conversion, coercion, inheritance
%X programmer can define new types and coercions.
   int - real - complex
   and then what of pair(int) - pair(real) - pair(complex)  etc.

%A E. T. Irons
%T Experience with an extensible language
%J CACM
%V 13
%N 1
%M JAN
%D 1970
%P 31-40
%K extensible programming language

%A K. E. Iverson
%T Notation as a tool of thought
%J CACM
%M AUG
%D 1980
%V 23
%N 8
%P 444-465
%K APL, notation, operators, programming language, ACM Turing award lecture,
   L3Ref, L4Ref, c1980, c198x, c19xx, jrnl
%X Also see languages 'APL' and 'J'.

%A K. E. Iverson
%T Operators
%J TOPLAS
%V 1
%N 2
%M OCT
%D 1979
%P 161-176
%K operator, APL, J, JJ, expression
%X Also see languages 'APL' and 'J'.

%A K. E. Iverson
%T Programming in J
%I Iverson-Software-Inc.,
%C 33 major St., Toronto, Ontario, Canada M5S 2K9
%D 1992
%K J, JJ, programming language, APL, applicative, verb, adverb, adjective, noun,
   operator
%X Also see language 'APL'.

%A R. K. W. Hui
%T An Implementation of J
%I Iverson-Software-Inc.,
%C 33 Major St., Toronto, Ontario, Canada M5S 2K9
%D 1992
%K J, JJ, c1992, c199x, c19xx, programming language, APL, applicative, verb,
   adverb, adjective, noun, operator

%A K. E. Iverson
%T Calculus
%I Iverson-Software-Inc.,
%C 33 major St., Toronto, Ontario, Canada M5S 2K9
%D 1993
%K J, JJ, programming language, APL, applicative, verb, adverb, adjective, noun,
   operator
%X isbn:1-895721-05-9.

%A P. R. Kosinski
%T A data flow language for operating systems programming
%J ????
%D ????
%O IBM Yorktown Heights, pre  1980
%P 89-94

%A W. H. Kaubisch
%A R. H. Perrott
%A C. A. R. Hoare
%T Quasiparellel programming
%J SPE
%V 6
%P 341-356
%D 1976
%N 3
%M JUL
%K Simone, coroutine, operating system, simulation, language
%X simone extension of pascal, like simula but without classes.

%A R. F. Keller
%T On control constructs for constructing programs
%J Sigplan
%M SEP
%D 1977
%P 36-44
%V 12
%N 9
%K while, incase, forcase

%A R. Krzemien
%A A. Lukasiewicz
%T Automatic generation of lexical analyzers in a compiler-compiler
%J IPL
%V 4
%N 6
%M MAR
%D 1976
%K compiler, parser generator, regular grammar language, FSA, FSM

%A S. Rao Kosaraju
%T Analysis of structured programs
%J J. of Computer and System Sciences
%V 9
%P 232-255
%D 1974
%X compare structural complexity of various classes of structured programs.
   reducibility of classes of programs.

%A R. B. Kieburtz
%A A. Silberschatz
%T Comments on "communicating sequential processes"
%J TOPLAS
%V 1
%N 2
%M OCT
%D 1979
%P 218-225
%K concurrent, parallel communication, process, message passing,
   CSP, CCS

%A D. E. Knuth
%T Top-down syntax analysis
%J Acta Informatica
%V 1
%P 79-110
%D 1971
%K top down, parse, parser, parsing

%A D. E. Knuth
%A J. L. McNeley
%T A formal definition of SOL
%J IEEE Transaction on Electronic Computers
%M AUG
%D 1964
%P 10-15
%K SOL
%X SOL is a general purpose algorithmic language
   useful for describing and simulating complex systems.
   includes parallel computations
   random quantities can be computed nicely
   statistics gathered automatically.

%A J. L. W. Kessels
%T A conceptual framework for a nonprocedural language
%J CACM
%V 20
%N 12
%M DEC
%D 1977
%P 906-913
%K parallel programming, non procedural, data flow, applicative language

%A G. Lee
%T DOPLs: a new type of programming language
%J Proceedings of the Symposium on Language Design and Programming Methodology.
%W Sydney
%M SEP
%D 1979
%P 169-189
%K DOPL

%A G. Lee
%T DOPLs: a new style of programming
%I Dept. Computer Science, University of Western Australia
%M JUL
%D 1980
%K DOPL

%A G. Lee
%T Using DOPLs to define programming languages
%I Dept. Computer Science, University of Western Australia
%D 1980
%K DOPL, Description oriented programming languages

%A A. M. Lister
%A K. J. Maynard
%T An implementation of monitors
%J SPE
%V 6
%N 3
%M JUL
%D 1976
%P 377-385
%K monitor, operating system, mutual exclusion, synchronisation, BCPL
%X shows how to implement monitors in BCPL.
   Scope rules provide most of the requisite compile time checking.

%A L. Lamport
%T Concurrent reading and writing
%J CACM
%V 20
%N 11
%M NOV
%D 1977
%P 806-811
%K reader, writer, reading and writing, multiprocessor, parallel, shared data
%X defines readers and writers problem.

%A H. F. Ledgard
%A R. W. Taylor
%T Two views of data abstraction
%J CACM
%M JUN
%D 1977
%V 20
%N 6
%P 382-384
%K abstract data type

%A C. H. Lindsey
%T Making the hardware suit the language
%B Algol 68 implementation
%E J. E. L. Peck
%I NorthHolland
%P 347-365
%D 1970
%K Algol, Algol-68, A68, MU5, descriptor, stack, environment,
   programming language
%X [Also search for: Algol68].

%A T. E. Lindquist
%T The correctness of simple programs written in the language KL-1
%I Cyclone-Computer-Laboratory, Iowa-State-University
%D 1977
%K incase, forcase, Keller, KL1, KL-1

%A R. Halstead
%T Parallel Symbolic Computing
%J IEEE Computer
%V 19
%N 8
%M AUG
%D 1986
%P 35-43
%K parallel Lisp, multilisp
%X via enews

%A R. Halstead
%T Parallel Computing Using Multilisp
%B Parallel Computation and Computers for Artificial Intelligence
%E J. Kowalik
%I Kluwer-Academic Publishers
%D 1987
%K parallel lips, multi, lisp, multilisp
%X Describes exception handling implementation: exception values, catch/throw,
   unwind-protect.
   via enews.

%A R. Halstead
%A J. Loaiza
%T Exception Handling in Multilisp
%J 1985 Int'l. Conf. on Parallel Processing
%W St. Charles, Ill.
%M AUG
%D 1985
%P 822-830
%K parallel Lisp, multi, lisp, multilisp
%X Discusses the three major ways to use
   futures and describes other "lessons from experience".
   via enews.

%A R. Halstead
%T An Assessment of Multilisp: Lessons From Experience
%J Int. J. of Parallel Programming
%V 15
%N 6
%M DEC
%D 1986
%I PlenumPress, New York
%K IJPP, multi, multilisp, parallel Lisp
%X Multilisp is available from the Parallel Processing Group at
   M.I.T. The present implementation is a byte-code interpreter
   which runs on uniprocessor machines supporting UNIX (BSD 4.2)
   and the multiprocessor Encore Multimax (and our Concert
   Multiprocessor). Little work should be necessary to port the
   implementation to other shared memory multiprocessors, which
   like the Multimax, support UNIX.
   I'll post details on how to obtain this implementation of
   Multilisp if people express interest.
   Randy Osborne   email: ran at vx.lcs.mit.edu    3 June 1988.

%A L. Meertens
%T A space saving technique for assigning Algol 68  multiple values
%J IPL
%V 5
%N 4
%M OCT
%D 1976
%P 97-99
%K Algol 68, Algol-68, Algol68, multiple, array, structure,
   programming language

%A K. Kendal
%A R. Conradi
%A P. Holager
%A O. Solberg
%A G. Green
%T Mary a system for software development on microcomputers
%B Minicomputer Software
%E J. R. Bell
%E C. G. Bell
%I North-Holland
%P 15-27
%D 1976
%K Mary, programming language

%A Z. Manna
%T The correctness of nondeterministic program
%J Artificial Intelligence
%D 1970
%V 1
%P 1-26
%K correctness, verification, nondeterminism, logic
%X by satisfiability and validity of formulae in first order logic.

%A C. Montangero
%A G. Pacini
%A F. Turini
%T Two-level control structure for nondeterministic programming
%J CACM
%V 20
%N 10
%M OCT
%D 1977
%P 725-730
%K nondeterminism, backtracking, control structure

%A A. G. Middleton
%T On the use of macros for iteration
%J COMPJ
%P 170-172
%V 19
%N 2
%D 1976
%M May
%K macro, iteration, loop

%A O. L. Madsen
%A B. B. Kristensen
%T LR-parsing of extended context free grammars
%J Acta Informatica
%V 7
%P 61-73
%D 1976
%N 1
%K context free grammar, CFG, parser, parse, LR parser
%X CFG with repetition *,   alternation |, and parenthesis  =>  ECFG.

%A J. McCarthy
%T Recursive functions of symbolic expressions and their computation by
   machine, part 1
%J CACM
%V 3
%P 184-195
%D 1960
%K jrnl, CACM, c1960, c196x, c19xx, Lisp, FP, expression, garbage collection,
   tracing, GC
%X [Also search for: McCarthy Lisp book].

%A J. R. McGraw
%T The VAL language: description and analysis
%J TOPLAS
%V 4
%N 1
%M JAN
%D 1982
%P 44-82
%K Val, data flow, dataflow, programming language

%A J. R. McGraw
%T Data flow computing - software development
%J IEEE Transactions on Computers
%V C-29
%N 12
%M DEC
%D 1980
%P 1095-1103
%K dataflow, data flow, applicative, programming language, VAL

%A R. B. E. Napper
%A R. N. Fisher
%T Alec - a user extensible scientific programming language
%J COMPJ
%V 19
%N 1
%D 1976
%P 25-31
%K extensible programming language, RCC, CC, Alec, c1976, c197x, c19xx

%A F. G. Pagan
%T Towards complete programming language descriptions that are both
   formal and understandable
%J SPE
%V 14
%N 3
%P 199-206
%M MAR
%D 1984
%K description, definition, semantics, metalanguage

%A R. H. Pierce
%A J. Rowell
%T A transformation-directed compiling system
%J COMPJ
%V 20
%N 2
%P 109-115
%M May
%D 1977
%K LL(1), TWS
%X parser generator plus semantic processing by transformation grammar.

%A J. L. Peterson
%T Petri nets
%J Computing Surveys
%V 9
%N 3
%M SEP
%D 1977
%K asynchronous, concurrent, parallel, petri net

%A J. S. Rohl
%T Test your own PTQ
%I Dept-Computer-Science-UWA
%D ????
%K Pascal
%X '82 ish

%A B. K. Kosen
%T High-level data flow analysis
%J CACM
%M OCT
%D 1977
%V 20
%N 10
%P 712-724
%K data flow, dataflow, analysis, control flow

%A M. Richards
%T Intcode - an interpretive machine
%I Computing Laboratory, Cambridge University
%M AUG
%D 1970
%K intcode, BCPL, portability, bootstrapping, boot strap

%A J. A. Self
%T Embedding non-determinism
%J SPE
%V 5
%P 221-227
%D 1975
%K non-determinism, backtrack, select, choice, fail, programming language
%X added to BCPL.

%A G. L. Steele
%T Multiprocessing compactifying garbage collection
%J CACM
%M SEP
%D 1975
%V 18
%N 9
%P 495-508
%K GC, garbage collection, parallel, multi processor, concurrent

%A L. G. Valiant
%T General context-free recognition in less than cubic time
%J J. Comp. and Sys. Sci.
%V 10
%N 2
%P 308-314
%M APR
%D 1975
%K jrnl, JCSS, c1975, c197x, c19xx, zz0415, CFG, CF grammar, parse, parser,
   parsing, complexity, time
%X "An algorithm for general context-free recognition is given that requires
   less than n3 time asymptotically for input strings of length n.
   By a succession of reductions we show that context-free recognition, for n
   character input strings, can be carried out at least as fast as
   multiplication for nxn Boolean matrices. Using Strassen's method for matrix
   multiplication, an indirect algorithm for general context-free recognition
   can be derived that has time complexity O(n^2.81).  ..."
   -- [<A HREF="http://dx.doi.org/10.1016/S0022-0000(75)80046-8">doi:10.1016/S0022-0000(75)80046-8</A>]['15].
   [And later faster as matrix mult. was shown to be faster.]

%A T. A. Standish
%T Extensibility in programming language design
%J AFIPS Conference Proceedings
%V 44
%D 1975
%P 287-290
%K extensible

%A C. Strachey
%T A general purpose macrogenerator
%J COMPJ
%V 8
%D 1965
%P 225-241
%K COMPJ, jrnl, macro, generator, macros, expansion, processor, GPM,
   c1965, c196x, c19xx
%X [<A HREF="http://dx.doi.org/10.1093/comjnl/8.3.225">doi:10.1093/comjnl/8.3.225</A>]['05],
   [<A HREF="http://comjnl.oxfordjournals.org/cgi/content/abstract/8/3/225">jrnl</A>]['05].

%A C. Strachey
%T Fundamental concepts of programming languages
%J Int. Summer School in Comp. Prog.
%C Copenhagen
%D 1967
%O Higher-Order & Symbolic Computation (HOSC), Kluwer, v13(1/2), pp.11-49, 2000
%K conf, c1967, c196x, c19xx, CPL, programming language, function,
   first class value, type, types, polymorphism, polymorphic, parametric,
   ad hoc, adhoc, semantics, L-value, R-value, values,  Lvalues, Rvalues,
   parameter passing, binding, citizen, orthogonal design, computer, CS, CSci,
   quote, quotable
%X "This paper forms the substance of a course of lectures given at the
   Int. Summer School in Comp. Prog. at Copenhagen in Aug., 1967.  ..."
   (finally published in a special issue of HOSC 13(1/2) 2000;  abs and .pdf:)
   -- [<A HREF="http://dx.doi.org/10.1023/A:1010000313106">doi:10.1023/A:1010000313106</A>][05/'04],
      [<A HREF="https://web.archive.org/web/20100216060948/http://www.cs.cmu.edu/~crary/819-f09/Strachey67.pdf">wayb'ck-mc</A>]['24],
   was[<A HREF="http://www.wkap.nl/oasis.htm/257993">abstract</A>][10/'01],
   was[<A HREF="http://www.wkap.nl/">Kluwer</A>][10/'01].
   (Also, "functions as first-class citizens [was] coined by Strackey 1967"
    -- [<A HREF="https://en.wikipedia.org/wiki/First-class_function">wikip</A>]['24].)

%A E. Shapiro
%A G. Collins
%A L. Johnson
%A J. Ruttenberg
%T Pases: a programming environment for Pascal
%J SIGPLAN
%V 16
%N 8
%M AUG
%D 1981
%P 50-57
%K screen editor, interpreter, Pascal

%A P. Wegner
%T programming languages - the first 25 years
%J IEEE Transactions on Computers
%V C25
%N 12
%M DEC
%D 1976
%P 1207-1225
%K c1976, c197x, c19xx, history, programming language

%A T. Winograd
%T Beyond programming languages
%J CACM
%M JUL
%D 1979
%V 22
%N 7
%K c1979, c197x, c19xx, programming language

%A L. M. Wegner
%T On parsing 2-level grammars
%J Acta Informatica
%V 14
%P 175-193
%D 1980
%K two level, vanwijngaarden, van wijngaarden, grammar

%A L. Wegner
%T Bracketted two-level grammars - a decidable and practical approach to
   language definition
%D 82??
%I Universitat-Karlsruhe
%K 2-level, two level van wijngaarden

%A A. I. Wasserman
%A S. Gutz
%T The future of programming
%J CACM
%V 25
%N 3
%P 196-206
%M MAR
%D 1982
%K jrnl, CACM, c1982, c198x, c19xx, human factors, computer programming,
   prediction, zzPrediction, SWE
%X "The nature of programming is changing. These changes will accelerate as
   improved s/w development practices and more sophisticated development tools
   and environments are produced. This paper surveys the most likely changes in
   the programming task and in the nature of s/w over the short term, the medium
   term, and the long term. In the short term, the focus is on gains in
   programmer productivity through improved tools and integrated development
   environments. In the medium term, programmers will be able to take advantage
   of libraries of software components and to make use of packages that generate
   programs automatically for certain kinds of common systems. Over the longer
   term, the nature of programming will change even more significantly as
   programmers become able to describe desired functions in a nonprocedural way,
   perhaps through a set of rules or formal spec. languages. As these changes
   occur, the job of the application programmer will become increasingly
   analysis-oriented and software developers will be able to attack a large
   # of application areas which could not previously be addressed effectively."
   -- [<A HREF="https://doi.org/10.1145/358453.358459">doi:10.1145/358453.358459</A>]['17].

%A H. Wettstein
%T The implementation of synchronizing operations in various environments
%J SPE
%V 7
%P 115-126
%D 1977
%K SPE, jrnl, critical region, process synchronise, locking, lock, semaphore

%A B. Wegbreit
%T The treatment of data types in EL1
%J CACM
%M MAY
%D 1974
%V 17
%N 5
%P 251-264
%K EL1, data type, datatype, generic, conversion, coercion,
   programming language

%A H. Weber
%T A microprogrammed implementation of Euler on IBM system/360 model 30
%J CACM
%V 10
%N 9
%M SEP
%D 1967
%P 549-558
%K Euler, microprogram

%A J. W. Davidson
%A C. W. Fraser
%T Eliminating redundant object code
%J Ninth Annual Symposium on Principles of Programming Languages
%P 128-132
%D 1982
%K POPL, POPL9, POPL82, logically adjacent, code generation, optimise

%A Kranz
%A Kelsey
%A Rees
%A Hudak
%A Philbin
%A Adams
%T Orbit: an optimising compiler for Scheme
%J CACM
%P 219
%D 1986
%K jrnl, CACM, programming language, Scheme, c1986, c198x, c19xx, compile

%A R. Sethi
%A J. Ullman
%T The generation of optimal code for arithmetic expressions
%J JACM
%V 17
%N 4
%P 715-728
%M OCT
%D 1970
%K jrnl, JACM, compile, register, allocation, expression, optimise,
   optimize, optimisation, compile, compiling, compiler, expression,
   c1970, c197x, c19xx
%X "... evaluating arithmetic exps. on a machine with N >= 1 g.p. registers
   is considered. It is initially assumed that no algebraic laws apply to the
   operators and operands in the expression. An alg. for evaluation of exps.
   under this assumption is proposed, and it is shown to take the shortest
   possible number of instructions. It is then assumed that certain operators
   are commutative or both comm. and assoc.. ... a procedure is given for
   finding an exp. equivalent to a given 1 and having the shortest possible
   evaluation seq.. ...shown that the algs. presented here also min. the # of
   storage references in the evaluation."
   -- [<A HREF="http://doi.acm.org/10.1145/321607.321620">doi:10.1145/321607.321620</A>]['05].

%A P. Z. Ingerman
%T Thunks: a way of compiling procedure statements with some comments on
   procedure declarations
%J CACM
%V 4
%N 1
%P 55-58
%M JAN
%D 1961
%K Algol 60, call by name, call-by-name, by-name, FP, parameter, passing,
   jrnl, thunk, think, pass, closure, lazy, algol-60, c1961, c196x, c19xx,
   programming language, languages, L3Ref, L4Ref
%X [<A HREF="http://doi.acm.org/10.1145/366062.366084">doi:10.1145/366062.366084</A>]['05].

%A D. A. Watt
%T Programming Language Concepts and Paradigms
%I PrenticeHall
%S Int. Series in Computer Science
%D 1990
%K text, book, good, programming language, paradigm, logic, functional, FP, LP,
   object oriented, OO, OP, declarative, concept, L3Ref, c1990, c199x, c19xx
%X 2nd ed, c2OO4, pb; uk us isbn:0470853204; uk us isbn13:978-0470853207; 492pp.

%A R. Gregory
%A Andrews
%A R. A. Olsson
%T The SR Programming Language: Concurrency in Practice
%I Benjamin/Cummings
%D 1993
%K SR, programming language, parallel, concurrent, process, implementation,
   c1993, c199x, c19xx
%X isbn:0-8053-0088-0;  via enews.

%A M. E. Bermudez
%A G. Logothetis
%T Simple computation of LALR(1) lookahead sets
%J IPL
%V 31
%P 233-238
%D 1989
%K parse, parser, syntax, LR, LR(1), LALR, LALR(1), limited lookahead set, sets
%X via enews.

%E J. Anderson
%T Pop-11 Comes of Age
%I EllisHorwood
%D 1989
%K Pop, Pop-11, Pop11, c1989, c198x, c19xx, programming language, languages
%X A collection of papers on the history of dialects of Pop, the
   features and benefits of the language, and some applications using
   Pop-11.

%A Barrett, R
%A Ramsay, A
%A Sloman, A
%T POP-11: a Practical Language for Artificial Intelligence
%I EllisHorwood
%C Chichester
%D 1985
%K text, book, Pop, Pop-11, Pop11, programming language
%X This was the first book published on Pop-11.  The authors were or are
   involved with Poplog development.  An introduction to the language.

%A Barrett
%A Ramsay
%T Artificial Intelligence in Practice: Examples in Pop-11
%I EllisHorwood
%D 1987
%K text, book, Pop, Pop-11, Pop11
%X A book of large example AI programs with sources in Pop-11.  Based on
   research at Sussex University.

%A du Boulay, J. B. H.
%A Elsom-Cook, M. T.
%A Khabaza, T.
%A Taylor, J.
%T Poplog and the Learner: An Artificial Intelligence Environment Used
   in Education,
%B Directory of Computer Training 1986, published by Badegmore part
   Enterprises for Hoskyns Education.
%D 1986
%K Poplog, Pop, Pop-11, logic, LP

%A du Boulay, J. B. H.
%T POPLOG for beginners: a powerful environment for learning
   programming
%E Hawley, R.
%B Artificial Intelligence Programming Environments
%I EllisHorwood,
%D 1987
%K Pop, Pop-11

%A Burton
%A Shadbolt
%T POP-11 Programming for Artificial Intelligence
%I AddisonWesley
%D 1987
%K text, book, Pop, Pop-11, Pop11, AI
%X Artificial intelligence for cognitive psychologists, based on teaching
   material from the University of Nottingham. [From Laventhol87].

%A Davies
%T Popler - Implementation of a POP-2-based PLANNER
%P 28-49
%B Implementations of Prolog
%E Campbell, J. A.
%I Wiley
%D 1983
%C New York
%K text, book, Pop, Pop-11, Planner
%X Describes a Planner-type language developed for a Pop-2 language
   environment.  Work done during the early 1970s.

%A Davies, D.J.M.
%T POP-10 Users' Manual
%R Computer Science Report #25
%I University-of-W.-Ontario
%D 1976
%K Pop, Pop-10, Pop10

%A Green, T.
%A Guest, D.
%T An Easily Implemented Language for the Computer Control of
   Complex Experiments
%J International Journal of Man-Machine Studies
%V 6
%D 1974
%P 335-359
%X This paper describes glue, a dialect of Pop-2, used for controlling
   psychology experiments.  [From Hardy84]
%K Pop, Pop-11

%A Gazdar, G.
%A Mellish, C.
%T Natural Language Processing in POP-11
%I AddisonWesley
%D 1989
%X Versions for Prolog and Common Lisp also available. The programming
   examples are now part of the Poplog Contrib Library
   (See HELP * CONTRIB)
%K text, book, Pop, Pop11, Pop-11

%A Hardy, S.
%A Mellish, C.
%T Integrating Prolog in the Poplog environment
%P 147-162
%B Implementations of Prolog
%E Campbell, J. A.
%I Wiley
%D 1983
%C New York
%K Pop, Pop-11, LP
%X This paper describes the way in which PROLOG has been implemented in
   the Poplog system and outlines the advantages of putting a Prolog
   compiler into a good programming environment.

%A Hardy, S.
%T A New Software Environment for List-Processing and Logic Programming
%P 110-136
%B Artificial Intelligence: Tools, Techniques, and Applications
%E O'Shea, Tim
%E Eisenstadt, Marc
%I Harper-and-Row
%C New York
%D 1984
%K Pop, Pop-11
%X An overview of Poplog with some descriptions of using coroutines as
   the basis of producer/consumers.

%A Khabaza, T.
%T Towards an Intelligent Help File Finder
%E Hawley, R.
%B Artificial Intelligence Programming Environments
%I EllisHorwood
%D 1987
%K Pop, Pop-11
%X Describes a project aimed at improving access for POPLOG help files.

%A Laventhol J.
%T Programming in POP-11
%I Blackwell-Scientific-Publications-Ltd.
%D 1987
%K Pop, Pop-11, programming language
%X An introduction to Pop-11, adhering to the AlphaPop subset.

%A Noble, Hugh M.
%T Natural Language Processing
%I Blackwell-Scientific-Publications
%C Oxford
%D 1988
%K Pop, Pop-11
%X This is a practical introduction to Natural Language Processing
   with worked examples in POP (and a few in Prolog).

%A Ian Rogers
%D 1990
%R Cognitive Science Research Report 171
%T Embedding X into the Poplog Environment
%I University-of-Sussex
%C Brighton
%K Pop, Pop-11
%X Also in the proceedings of "The European X Window System Conference"
   November 1990 - CEP Consultants Ltd.; uk isbn:0-905941-44-6.

%A Sharples et. al.
%T Computers and Thought
%I MITpress
%D 1989
%K Pop, Pop-11
%X Based on teaching material from the School of Cognitive and Computing
   Sciences at the University of Sussex.

%A Robert Smith
%A Aaron Sloman
%A John Gibson
%D January 1990
%R Cognitive Science Research Report 153
%T POPLOG's Two-level Virtual Machine Support for Interactive Languages
%I Univ.-of-Sussex
%C Brighton
%K Pop, Pop-11
%X To appear (1991?) in a volume edited by D.Sleeman and N.O.Bernson
   Price: 1.00
   (Actually it appeared as
   Research Directions in Cognitive Science Volume 5: Artificial
    Intelligence,
   eds D. Sleeman and N. Bernsen, Lawrence Earlbaum Associates, 1992)

%A R. E. Griswold
%T Programming with generators
%J COMPJ
%V 31
%N 3
%D 1988
%K jrnl, COMPJ, generator, Icon, programming language, back track,
   backtracking, c1988, c198x, c19xx
%X [<A HREF="http://comjnl.oxfordjournals.org/cgi/content/abstract/31/3/220">compj</A>]['05].

%A R. E. Griswold
%T String scanning in the Icon programming language
%J COMPJ
%V 33
%N 2
%P 98-107
%M APR
%D 1990
%K Icon, programming language, string, scan, jrnl, COMPJ, c1990, c199x, c19xx,
   strings, scan, processing
%X "As a consequence of the primary historical role of computers as a tool for
   numerical computation, most programming languages have minimal facilities
   for string manipulation. ...discusses some of the language design &
   implementation issues involved in incorporating string scanning, analysis &
   synthesis facilities into a general-purpose programming language & describes
   how they have been introduced in the Icon programming language."
   -- [<A HREF="http://comjnl.oxfordjournals.org/cgi/content/abstract/33/2/98">compj</A>]['05].

%A D. G. Bobrow
%A B. Wegbreit
%T A model and stack implementation of multiple environments
%J CACM
%V 16
%N 10
%P 591-603
%M OCT
%D 1973
%K stack, stacks, cactus, spaghetti, concurrent, parallel, environment,
   jrnl, CACM, c1973, c197x, c19xx, programming language, implementation
%X via enews.

%A J. G. Hook
%T Understanding Russell: A First Attempt
%B ???
%I SpringerVerlag
%S LNCS
%V 173
%P ???-???
%D ???
%K Russell, programming language

%A A. J. Demers
%A J. E. Donahue
%T Data Types Parameters and Type Checking
%J Proc. 7th POPL
%W Las Vegas
%D 1980
%P ???-???
%K Russell, POPL, POPL7, POPL80, type, types, check, checking

%A A. J. Demers
%A J. E. Donahue
%T Making Variables Abstract: An Equational Theory for Russell
%J Proc. 10th POPL
%W Austin
%D 1983
%K Russell, programming language, POPL, POPL10, POPL83,
   variable, type, types, check, checking

%A Woodward
%A Bond
%T Guide to Algol 68 for users of RS Systems
%I Arnold
%D 1983
%K text, book, programming language, algol 68, algol68, algol-68, a68,
   algol68R, algol68RS, 68R 68RS, rs rsre, c1983, c198x, c19xx
%X uk isbn:0-7131-3490-9.
   (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/">www</A>].)

%A C. D. Marlin
%T Coroutines
%I SpringerVerlag
%S LNCS
%N 95
%D 1980
%K programming language, coroutine, LNCS95, text, book, c1980, c198x, c19xx

%A D. Merrit
%T Adventures in Prolog
%I SpringerVerlag
%D ???
%K introduction, introductory, text, book, thin, small, programming language,
   logic, LP, Merritt
%X via scott gilbert <!--  email: scott at caslon.cs.arizona.edu --> '94.

%A I. Bratko
%T Prolog, Programming for Artificial Intelligence (2nd edn)
%I AddissonWesley
%P 597
%D 1990
%K introduction, introductory, text, book, c1990, c199x, c19xx,
   programming language, logic, LP, AI
%X 4th ed, c2008, pb; uk us isbn:0321417461; uk us isbn13:978-0321417466.
   via kim marriott.
   (Also see <A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A L. Sterling
%A E. Shapiro
%T The Art of Prolog
%I MITpress
%D 1986
%P 437
%K introduction, introductory, text, book, c1986, c198x, c19xx,
   programming language, logic, LP
%X 2nd ed, c1994, pb; uk us isbn:0262691639; uk us isbn13:978-0262691635.
   hbk via kim marriott
   (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A A. Celentano
%T Incremental LR Parsers
%J Acta Informatica
%V 10
%N ?
%P 307-321
%D 1978
%K parse, parser, parsing

%A P. Degano
%A S. Mannucci
%A B. Mojana
%T Efficient incremental LR Parsing for syntax directed editors
%J TOPLAS
%V 10
%N 3
%P 345-373
%M JUL
%D 1988
%K parse, parser, editor, c1988, c198x, c19xx

%A C. Ghezzi
%A D. Mandrioli
%T Augmenting parsers to support incrementality
%J JACM
%V 27
%N 3
%P 564-579
%M JUL
%D 1980
%K parse, parser, parsing, incremental

%A W. Li
%A C. McDonald
%T A specification driven language editor
%J ACSC 15
%P 561-572
%D 1992
%K ACSC, ACSC15, ACSC92, UWA, syntax, directed, edit, editor,
   parse, parser, parsing, incremental

%A J. Park
%A K. Choe
%A C. Chang
%T A new analysis of LALR formalisms
%J TOPLAS
%V 7
%N 1
%P 159-175
%M JAN
%D 1985
%K LR, parse, parser, parsing

%A B. Meyer
%T Object-Oriented Software Construction
%I PrenticeHall
%D 1988
%K OO, OOP, book, text, c1988, c198x, c19xx
%X see the book on Eiffel '92

%A T. MacKenzie
%A T. I. Dix
%T A distributed memory multiprocessor implementation of C-with-Ease
%J Int. Conf. on Parallel and Distributed Systems
%W Hinchu, Taiwan
%D 1994
%P 250-257
%K conf, C, cc, Ease, parallel, distributed, multi, programming language,
   TIDix, Monash, conf, ICPDS, c1994, c199x, c19xx

%A H. Leiss
%T On Kilbury's modification of Earley's algorithm
%J TOPLAS
%V 12
%N 4
%P 610-640
%M OCT
%D 1990
%K parse, parser, parsing, Early, lookahead
%X Ted Pedersen  <!-- pedersen at seas.smu.edu --> [2/'95].

%A G. E. Blelloch
%A G. W. Sabot
%T Compiling collection-oriented languages onto massively parallel computers
%J J. Parallel and Distributed Computing
%V 8
%P 119-134
%M FEB
%D 1990
%K jrnl, c1990, c199x, c19xx, data parallel, compile, computer, language,
   code vectorisation, vectorization, CM2, CM-2, compiler, nested parallelism,
   vector, array, operations, instructions, instruction
%X "... compiling the nested parallelism (||) of collection-oriented langs.
   onto existing || hardware. Programmers of || mcs encounter nested ||ism
   whenever they write a rtn that performs || operations, & then want to
   call that rtn itself in ||.  ...  A compiler that translates a subset of a
   collection-oriented lang., Paralation Lisp, into the instruction set of a
   flat virtual mc is presented.  ... have implemented the instructions on
   the Connection Machine computer (CM-2), a massively ||, single-instruction
   computer.  ...  a quicksort example. ... has been tested on the CM-2. ...
   the compiled sort is only x3 slower than that of the fastest CM-2 sort."
   -- [<A HREF="http://dx.doi.org/10.1016/0743-7315(90)90087-6">doi:10.1016/0743-7315(90)90087-6</A>]['08].

%A A. P. W. Bohm
%A R. R. Oldehoeft
%T Two issues in parallel language design
%J TOPLAS
%V 16
%N 6
%P 1675-1683
%M NOV
%D 1994
%K parallel, concurrent, programming language, computer, zz0595

%A M. M. Brandis
%A H. Mossenbock
%T Single-pass generation of static single-assignment form for structured
   languages
%J TOPLAS
%V 16
%N 6
%P 1684-1698
%M NOV
%D 1994
%K static single assignment, SSA, optimise, optimize, optimization,
   flow of control, programming language, computer, zz0595
%X 15 refs

%A B. H. Liskov
%A J. M. Wing
%T A behavioral notion of subtyping
%J TOPLAS
%V 16
%N 1
%P 1811-1841
%M NOV
%D 1994
%K datatype, type, types, subtype, Larch, programming language, computer,
   behavioural, zz0595, c1994, c199x, c19xx, typing, jrnl, TOPLAS
%X ... higher level supertypes capture the behavior that all of their
   subtypes have in common. ...

%A J. S. Conery
%A M. Lynch
%A T. Hovland
%T Optimizing irregular computations on SIMD machines
%J Proc. 5th Symp. Frontiers of Massively Parallel Comp.
%P 222-230
%D 1995
%K parallel computing, SIMD, conf
%X unchecked.

%A J. S. Conery
%T Continuation based control in the implementation of parallel logic programs
%J Lisp and Symbolic. Comp.
%V 7
%N 1
%P 111-133
%D 1994
%K jrnl, LSC, logic programming, LP, continuation, jrnl

%A R. P. Gabriel
%T Performance and Evaluation of Lisp Systems,
%I MITpress
%D 1985
%K Lisp, book, text, performance, speed, space, bench mark, benchmark,
   computing, applicative
%X - Dietmar Logoz <!-- email: logoz at ibm.net --> [10/'95].

%A J. B. Johnson
%T The contour model of block structured processes
%J ACM Symp. on Data Structures in Programming Languages (Sigplan 6(2))
%M FEB
%D 1971
%K conf, sigplan, cactus, stack, process, CSci
%X enews: D. Sand [11/'95].

%A P. T. Breuer
%A J. P. Bowen
%T Decompilation: the enumeration of types and grammars
%J TOPLAS
%V 16
%N 5
%M SEP
%D 1994
%P 1613-1647
%K TOPLAS, jrnl, decompilation, reverse engineering, programming language,
   uncompiling, computing, CS, CSci
%X review: Comp Rev' Sep 95 p481-482.

%A M. Burnett
%A A. Ambler
%T Interactive visual data abstraction in a declarative visual programming
   language.
%J J. of Visual Languages and Computing
%V ?
%P 29-60
%M MAR
%D 1994
%K jrnl, JVLC, Forms, GUI, guis, functional, applicative,
   programming, FP, zz1195
%X Forms: side-effect free OOP
   M. Burnett,  email: burnett at cs.orst.edu    [11/'95].

%T Visual Object-Oriented Programming: Concepts and Environments
%E M. Burnett
%E A. Goldberg
%E T. Lewis
%I PrenticeHall/Manning Publ.
%D 1995
%K book, text, GUI, guis, OO, OOP, programming languages, Forms, zz1195
%X Forms: side-effect free,  See chapter 7
   M. Burnett,  email: burnett at cs.orst.edu    [11/'95].

%A J. G. Hays
%A M. M. Burnett
%T A guided tour of Forms/3
%R 95-60-6
%I Comp. Sci., Oregon State Univ.
%M JUN
%D 1995
%K TR, programming language, guide, Forms, Forms3, ftp
%X <A HREF="ftp://ftp.cs.orst.edu/pub/burnett/Tour.Forms.ps">[postscript]</A>['95].
   M. Burnett,  email: burnett at cs.orst.edu    [11/'95].

%A R. Morrison
%T A method of implementing procedure entry and exit in block structured
   high level languages
%J SPE
%V 9
%N 5
%P 535-537
%D 1977
%K SPE, jrnl, programming language, routine, subroutine, entry sequence, code,
   exit sequence, stack, zz0196, c1977, c197x, c19xx
%X ref morr79 in  D a v i e `An intro to func' sys' using Hask'll'.

%A R. Morrison
%T The string as a simple data type
%J SIGPLAN Notices
%V 17
%N 3
%D 1982
%K SIGPLAN, jrnl, string, data type, datatype
%X ref morr82 in  D a v i e `An intro to func' sys' using Hask'll'.

%A C. A. Finseth
%T The Craft of Text Editing: Emacs for the Modern World
%I SpringerVerlag
%D 1991
%K book, text, c1991, c199x, c19xx, Emacs, text editor, editing, programmable
%X hb us$50; uk us isbn:0387976167; uk us isbn13:978-0387976167.

%E G.-R. Perrin
%E A. Darte
%T The Data Parallel Programming Model.  Foundations, HPF Realization,
   and Scientific Applications
%I SpringerVerlag
%S LNCS
%V 1132
%D 1996
%P 284
%K book, text, SIMD, zz0297
%X uk us isbn:3-540-61736-1;   A$53.50 [1/'96].

%A A. Taivalsaari
%T On the notion of inheritance
%J Comp. Surveys
%V 28
%N 3
%M SEP
%D 1996
%P 438-479
%K ACM, Comp Surveys, c1996, c199x, c19xx, jrnl, object oriented, survey,
   OO, OOP, programming languages, zz0297

%A M. Walicki
%A S. Meldal
%T Algebraic approaches to nondeterminism: an overview
%J ACM Computing Surveys
%V 29
%N 1
%P 30-81
%K jrnl, survey, non determinism, programming languages, semantics,
   bounded, unbounded, zz0997
%X 4.5 pages of references.

%A G. Booch
%T Object-Oriented Analysis and Design with Applications
%I AddisonWesley
%P 608
%D 1993
%K OO, OOP, c1993, c199x, c19xx, software engineering, SWE, book, text,
   computer programming
%X 2nd edn, hb; uk us isbn:0805353402; uk us isbn13:978-0805353402.

%A G. Booch
%T Object Solutions: Managing the Object-Oriented Project (OBT)
%I AddisonWesley
%P 336
%D 1995
%K book, text, c1995, c199x, c19xx, OO, OOP
%X pb; uk us isbn:0805305947; uk us isbn13:978-0805305944.

%A G. Booch
%A J. Rumbaugh
%A I. Jacobson
%T The Unified Modeling Language User Guide
%I ?
%D 1998
%K book, text, L3Ref, object oriented, OO, OOP, modelling, UML,
   software engineering, SWE, zz0200
%X Hargrave 005.12 B724U.  See also  Booch '94.

%A P. Sallis
%A et al
%T Software Engineering: Practice, Management, Improvement
%I AddisonWesley
%P 216
%D 1994
%K SWE, OO, OOP, computer programming, book, text, c1994, c199x, c19xx
%X hb; uk us isbn:0201539594; uk us isbn13:978-0201539592.

%A E. Gamma
%A R. Helm
%A R. Johnson
%A J. Vlissides
%T Design Patterns: Elements of Reusable Object-Oriented Software
%I AddisonWesley
%D 1995
%K book, text, object oriented, OO, OOP, reuse, computer programming, zz0998,
   c1995, c199x, c19xx
%X foreword by Grady Booch;  recommended by Damain C.
   hb; uk us isbn:0201633612; uk us isbn13:978-0201633610.

%A G. N. C. Kirby
%T Reflection and Hyper-Programming in Persistent Programming Systems
%I Dept. Math and Computational Sciences, U. of St. Andrews
%D 1993
%R CS/93/3
%K PhD thesis, TR 93 3, computer programming languages, persistence, reflect,
   reflection, type system, datatype, class, OO, OOP, Lisp, POP-2,
   Napier, Napier88, PS-algol, PSalgol, hyperprogramming, zz1098
%X U' St A', Dept Math & Comp Sci, North Haugh, St Andrews, Scotland KY16 9SS;
   175 pages.

%A T. Kuhne
%T A Functional Pattern System for Object-Oriented Design
%I Kovac
%P 328
%D 1999
%K book, text, programming, paradigm, FP, OO, OOP, c1999, c199x, c19xx,
   patterns, language, Eiffel
%X "Design patterns inspired by FP concepts can advance OO design. This thesis
   promotes the idea that concepts from the world of FP can be captured with
   design pattern descriptions. These can then be used to benefit from FP
   concepts with ordinary OO languages. The functional patterns are evaluated
   for their impact on language design and a new approach to a dual-paradigm
   language is presented". us isbn:3860647709; us isbn13:978-3860647707.
   -- [<A HREF="http://www.mm.informatik.tu-darmstadt.de/~kuehne/fps/">site</A>]['05].

%A P. W. O'Hearn
%A J. C. Reynolds
%T From Algol to polymorphic linear lambda-calculus
%J JACM
%V 47
%N 1
%P 167-223
%M JAN
%D 2000
%K jrnl, JACM, c2000, c200x, c20xx, OHearn, A60, Algol60, Algol 60,
   functional programming language, FP, linear type, types, typed, system,
   logic, zz0600
%X In a linearly typed functional language, one can define functions that
   consume their arguments in the process of computing their results.
   ... translating two variations of Algol 60 into a purely functional Lang'
   with polymorphic linear types.  On the one hand ... semantic analysis
   ... in terms of a model of the linear language.  On the other hand,
   ... demo' that linearly typed FL can be at least as expressive as Algol.

%A J. Aycock
%A R. N. Horspool
%T Practical Earley parsing
%J COMPJ
%V 45
%N 6
%P 620-630
%D 2002
%K jrnl, compj, parser, parse, algorithm, empty production, rule, rules,
   CFG, FSA, FSM, Earleys, c12002, c200x, c20xx
%X Earley's parsing algorithm is a general algorithm, able to handle any
   context-free grammar. As with most parsing algorithms, however, the presence
   of grammar rules having empty right-hand sides complicates matters. By
   analyzing why Earley's algorithm struggles with these grammar rules, we have
   devised a simple solution to the problem. Our empty-rule solution leads to a
   new type of finite automaton expressly suited for use in Earley parsers and
   to a new statement of Earley's algorithm. We show that this new form of
   Earley parser is much more time efficient in practice than the original.
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/45.6.620">doi:10.1093/comjnl/45.6.620</A>]['05],
   &  [<A HREF="http://comjnl.oxfordjournals.org/cgi/content/abstract/45/6/620">jrnl</A>]['05].

%A K. C. Louden
%T Programming Languages: Principles and Practice
%I CourseTech.
%P 720
%D 2002
%K book, text, c2002, c200x, c20xx, programming language, languages, paradigm,
   paradigms, L3Ref
%X 2nd ed 2002; hb us$116; uk us isbn:0534953417; uk us isbn13:978-0534953416.
   "... provides students with an overview of key issues in the study of
   programming languages. Rather than focus on individual language issues ...
   focuses on language paradigms & concepts that are common to all languages."
   [Also search for: programming languages text book].

%A K. B. Bruce
%T Foundations of Object-Oriented Languages: Types and Semantics
%I MITpress
%P 404
%D 2002
%K book, text, OO, OOP, class, classes, objects, programming languages, zz0703,
   c2002, c200x, c20xx, type, check, system
%X Reviewed in CompJ 46(4) p463.
   us$45, stg30; us isbn:026202523X; us isbn13:978-0262025232.

%A B. Omer
%T Classical concepts in quantum programming
%J arXiv
%M APR
%D 2003
%O QS2002 proc.
%K conf, c2003, c200x, c20xx, zz0224, quantum programming language, QCL,
   state, gate, program
%X "... investigates, how classical concepts like h/w abstraction, hierarchical
   programs, data types, memory management, flow of control & structured
   programming can be used in q.computing. The experimental language QCL will be
   introduced as an [eg], how elements like irreversible fns, local variables &
   conditional branching, which have no direct q. counterparts, can be
   implemented ..."
   -- [<A HREF="https://arxiv.org/abs/quant-ph/0211100">arxiv:quant-ph/0211100</A>]['24].
   [Also search for: quantum Omer].

%A S. Steinert
%T Graph programs for graph algorithms
%I U. Oldenburgh, Dept fur Informatik
%R 7/03
%D 2003
%K TR 7, TR7, program, algorithm, graphs
%X also see: uniYork, [<A HREF="http://www-users.cs.york.ac.uk/~sandra/publications/steinert03.ps.gz">.ps.gz@york</A>]['04].

%A A. Bakewell
%A D. Plump
%A C. Runciman
%T Specifying pointer structures by graph reduction
%J Int. Workshop Applications of Graph Transformations with
   Industrial Relevance(!)
%D 2003
%O pp.30-44, LNCS, v.3062, SpringerVerlag, 2OO4
%K wShop, graphs, rewriting, rewrite, c2003, c200x, c20xx, zzOSP, zOSP04,
   transformation, pointers, AGTIVE2003, AGTIVE, uniYork, Detlef Plump,
   FP, specification, GSR, PGSR
%X "... like various forms of balanced trees that cannot be handled by existing
   methods. ... mainly interested in PGRSs -- poly' terminating GRSs ...
   ... cyclic lists, trees, balanced trees and red-black trees. ..."
   -- [<A HREF="http://www-users.cs.york.ac.uk/~det/Papers/agtive.04.ps.gz">.ps.gz@york</A>][9/'04]
  Also see B,P&R, `Specifying pointer structures by graph reduction',
           Math. Struct's in Comp. Sci, to appear (as of '04).

%A D. Plump
%A S. Steinert
%T Towards graph programs for graph algorithms
%J Proc. Int. Conf. on Graph Transformation
%P ?-?
%D 2004
%I SpringerVerlag
%S LNCS
%K conf, ICGT, graphs, program, transformations, algorithm, path, paths,
   uniYork, c2004, c200x, c20xx, Detlef Plump, double pushout rule, rules,
   schemata, language
%X "... we introduce conditional rule schemata which are instantiated to
   (conditional) double pushout rules over ordinary graphs. ... case study ...
   two versions of Dijkstra's shortest path alg'. ..."
   -- [<A HREF="http://www-users.cs.york.ac.uk/~det/Papers/icgt.04.ps.gz">.ps.gz@york</A>][9/'04],
   -- [<A HREF="http://www-users.cs.york.ac.uk/~det/">Detlef.P@york</A>]['04],
   -- [<A HREF="http://www-users.cs.york.ac.uk/~sandra/">Sandra.S@york</A>]['04].

%A R. Finkel
%A V. W. Marek
%A M. Truszczyski
%T Constraint Lingo: Towards high-level constraint programming
%J SPE
%V 34
%N 15
%P 1481-1504
%M OCT
%D 2004
%K jrnl, SPE, clp, c2004, c200x, c20xx, zz1204, graph, graphs, coloring,
   colouring, independent sets, constraints, language
%X "... such problems include logic puzzles solvable on a hatch grid and
   combinatorial problems such as graph coloring and independent sets. The
   proper abs. for these problems are rows, columns, entries, & their
   interactions. We present a higher-level language, Constraint Lingo dedicated
   to problems in this domain. ... describe how we translate programs from
   Constraint Lingo into lower-level logic formalisms such as the logic of
   propositional schemata. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.623">doi:10.1002/spe.623</A>]['04].

%A M. Felleisen
%T Functional objects
%J Object-Oriented Programming (ECOOP)
%I Springer
%S LNCS
%V 3086
%D 2004
%K conf, ECOOP, c2004, c200x, c20xx, zz0524, OOP, FP, function, functions,
   object, class
%X Sadly just a 1/2 page abstract at the doi:-(
   "At ï¬rst glance, OOP has little or nothing in common with FP. One grew out of
   the procedural tradition ... computing proceeds via method calls. The other
   is a radical departure from conventional programming.  It emphasizes an
   (almost) purely math. approach. ... Still, nobody can overlook the
   similarities of the two approaches considering the development of design
   patterns & notions of eï¬ective object-oriented programming practices.  In my
   talk, I will compare and contrast the two ideas of programming & PL-design.
   I will present & defend the thesis that good OOP heavily 'borrows' from FP
   & that the future of OOP is to study FP & language design even more." :-(
   -- [<A HREF="https://doi.org/10.1007/978-3-540-24851-4_12">doi:10.1007/978-3-540-24851-4_12</A>]['24].
   Although there are lecture slides at
   [<A HREF="https://pdfs.semanticscholar.org/416a/955f7c1c3e202f8bc0e2397466a1d048b081.pdf">www</A>]['24], hmmm?

%A P. van Roy
%A S. Haridi
%T Concepts, Techniques, and Models of Computer Programming
%I MITpress
%P 930
%D 2004
%K book, text, c2004, c200x, c20xx, vanRoy, paradigm, computer, programming,
   languages
%X "... presents all major programming paradigms in a uniform framework that
   shows their deep relationships and how and where to use them together. ..."
   1st ed c2004, us$55; uk us isbn:0262220695; uk is isbn13:978-0262220699.

%A S. Park
%A F. Pfenning
%T A probabilistic language based on sampling functions
%J POPL
%V 40
%P 171-182
%D 2005
%O TOPLAS, 31(1), pp.4:1-4:46, Dec. 2008
%K conf, POPL, c2005, c200x, c20xx, zz1012, function, probability, simulation,
   programming language, FP, lambdaO, lambda_O, robotics
%X "As probabilistic compns play an inc. role in solving various problems,
   researchers have designed probabilistic languages which treat prob.distns as
   primitive datatypes. ... Rich expressiveness of lambdaO is due to its use of
   sampling fns ... mappings from the unit interval (0,1] ...  enables
   programmers to formally express & reason about sampling methods developed in
   simulation theory. [e.g.] robotics: robot localization, people tracking, &
   robotic mapping. ..."   (via D.P.)
   -- [<A HREF="http://dx.doi.org/10.1145/1047659.1040320">doi:10.1145/1047659.1040320</A>]['12],
   and TOPLAS@[<A HREF="http://dx.doi.org/10.1145/1452044.1452048">doi:10.1145/1452044.1452048</A>]['12].
   [Also search for: FP probability].

%A K. Lee
%T Programming Languages: An Active Learning Approach
%I SpringerVerlag
%P 282
%D 2008
%K book, text, L3ref, c2008, c200x, c20xx, zz0908, programming language,
   compiler, compilation, Ruby, OO, OOP, FP, LP
%X "... introduces students to 3 programming paradigms: object-oriented/
   imperative languages using C++ and Ruby, functional languages using Standard
   ML, & logic programming using Prolog. This interactive textbook is intended
   to be used in & outside of class. Each chapter follows a pattern of
   presenting a topic followed by a practice exercise or exercises that
   encourage students to try what they have just read. This textbook is
   best-suited for students with a 2-3 course intr. to imperative programming."
   hb, us$129; uk us isbn:0387794212; uk us isbn13:978-0387794211.

%A D. P. Friedman
%A M. Wand
%T Essentials of Programming Languages
%I MITpress
%P 416
%D 2008
%K book, text, 3rd ed, c2008, c200x, c20xx, programming languages, comparative,
   L3Ref, L4Ref, language
%X 3rd ed 2008; hb us$41; uk us isbn:0262062798; uk us isbn13:978-0262062794.
   2nd ed 2001.

%A R. M. Stallman
%Q GCC Development Community
%T Using the Gnu Compiler Collection: A Gnu Manual for Gcc Version 4.3.3
%I CreateSpace
%D 2009
%K book, text, c2009, c200x, c20xx, Gnu, gnu, CC, gcc, compiler, Unix,
   opensource, open, software, free, programming languages, L2Ref, L3Ref
%X 2009; pb us$32; uk us isbn:144141276X; uk us isbn13:978-1441412768.

%A B. Omer
%T Structured quantum programming
%I Inst. for Theor. Physics, Vienna U. of Tech.
%P 72, 92-107
%M MAY
%D 1999
%K thesis, c1999, c199x, c19xx, zz0224, quantum computing,
   programming language, program
%X "... This thesis investigates how the classical formalism of structured
   programming can be adapted to the field of q.computing, based on the
   m/c model of a universal computer with a q.oracle allowing the application
   of unitary gates & the measurement of single qubits ..."
   -- Archived from the original (PDF) on March 27, 2022,
      pdf@[<A HREF="https://web.archive.org/web/20220327170025/tph.tuwien.ac.at/~oemer/doc/structquprog.pdf">www</A>]['24].
   [Also search for: quantum Omer].

%A B. A. Tate
%T Seven Languages in Seven Weeks: A Pragmatic Guide to Learning Programming
   Languages
%I PragmaticBookshelf
%P 328
%D 2010
%K book, text, c2012, c201x, c20xx, zz1013, computer programming language,
   Clojure, Haskell, Io, Prolog, Scala, Erlang, Ruby, comparative, L3Ref, L4Ref
%X 1st ed 2010; pb us$23; uk us isbn:193435659X; uk us isbn13:978-1934356593.
   "... Clojure, Haskell, Io, Prolog, Scala, Erlang, and Ruby ..." (via F.P.)
   (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/">P.Langs</A>].)

%A B. G. Ryder
%A B. Wiedermann
%T Language design and analyzability: a retrospective
%J SPE
%V 42
%N 1
%P 3-18
%M JAN
%D 2012
%K jrnl, SPE, c2012, c201x, c20xx, programming language, languages, procedural,
   scripting, computer program, static analysis
%X "... in '71, most languages in commercial use were procedural (e.g.,
   FORTRAN, ALGOL, PL/I) & on the whole were easier to analyze than languages
   of today such as JavaScript & Python. Modern languages include dynamic
   features, which enhance prototyping of approaches, often resulting in
   programs that are difficult for software tools or humans to understand.
   ... explore the relationship between language features & the ability of
   static analysis to precisely determine control flow & data flow in programs,
   thus enabling program optimization, transformation & understanding."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.1133">doi:10.1002/spe.1133</A>]['12].
   [Also search for: static analysis program].

%A L. Bergstrom
%A M. Fluet
%A M. Rainey
%A J. Reppy
%A A. Shaw
%T Lazy tree splitting
%J JFP
%V 22
%N 4-5
%P 382-438
%M SEP
%D 2012
%K jrnl, JFP, FP, c2012, c201x, c20xx, zz1012, parallel ML, PML, Manticore,
   nested data parallelism, NDP, lazy tree splitting, LTS
%X "Nested data-parallelism (NDP) ... programming irregular parallel applns in
   a declarative style. ... describe the implementation of NDP in Parallel ML
   (PML), which is a part of the Manticore system. ... If we have too many small
   chunks of work, the overhead will be too high, but if we do not have enough
   chunks of work, processors will be idle. Recently, the technique of Lazy
   Binary Splitting was proposed ... for nested parallel loops over flat arrays.
   ... uses binary trees to represent parallel arrays. ... which we call Lazy
   Tree Splitting (LTS), has the key advantage of performance robustness ..."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796812000172">doi:10.1017/S0956796812000172</A>]['12].

%A R. Harper
%T Practical Foundations for Programming Languages
%I CUP
%D 2012
%K book, text, c2012, c201x, c20xx, zz0714, programming language, principles,
   features, type, types
%X 1st ed 2012; hb us$64; uk us isbn:1107029570; uk us isbn13:978-1107029576.
   "Types are the central organizing principle of the theory of PLs. ...
   offers a fresh perspective on the fundamentals of these languages through
   the use of type theory. Whereas most textbooks on the subject emphasize
   taxonomy, Harper instead emphasizes genetics, examining the building blocks
   from which all programming languages are constructed. Language features are
   manifestations of type structure. The syntax of a language is governed by
   the constructs that define its types, and its semantics is determined by
   the interactions among those constructs. The soundness of a language design
   - the absence of ill-defined programs - follows naturally. ..."

%A J. Sieka
%T J2C
%D 2015
%K java, C++, J2C, j2c, c2015, c201x, c20xx, zz1217, Jacek Sieka, arnetheduck,
   programming language, convertor, converter, translate, convert, translator,
   CplusPlus, cc
%X "J2C will convert Java code into hopefully compilable C++(11) code.  It
   works on source level, translating Java source code constructs into their
   rough equivalents in C++ . The output will be reasonably valid C++ code that
   looks a lot like its Java counterpart & hopefully works mostly the same ..."
   -- j2c@[<A HREF="https://bitbucket.org/arnetheduck/j2c">bitbucket</A>]['17].
     ((Also see another "Java to C++ Converter"
       -- [<A HREF="https://www.tangiblesoftwaresolutions.com/product_details/java_to_cplusplus_converter_details.html">tangiblesoftwaresolutions</A>]['17], and
       "Java and C++ Equivalents"
       -- [<A HREF="https://www.tangiblesoftwaresolutions.com/java-and-cplus-equivalents.html">www</A>]['17].
       And a stackoverflow discussion
       -- [<A HREF="https://stackoverflow.com/questions/556807/does-a-java-to-c-converter-tool-exist">www</A>]['17].))

%A M. Abadi
%A G. D. Plotkin
%T A simple differentiable programming language
%J arXiv
%M NOV
%D 2019
%K TR, c2019, c201x, c20xx, zz1119, programming language, automatic,
   differentiation, differentiable, derivative, reverse mode, semantics
%X "Automatic differentiation plays a prominent role in scientific computing
   and in modern machine learning, often in the context of powerful programming
   systems. The relation of the various embodiments of automatic differentiation
   to the mathematical notion of derivative is not always entirely clear -
   discrepancies can arise, sometimes inadvertently. In order to study automatic
   differentiation in such programming contexts, we define a small but
   expressive programming language that includes a construct for reverse-mode
   differentiation. We give operational and denotational semantics for this
   language. The operational semantics employs popular implementation
   techniques, while the denotational semantics employs notions of
   differentiation familiar from real analysis. We establish that these
   semantics coincide."
   -- 1911.04523@[<A HREF="https://arxiv.org/abs/1911.04523">arXiv</A>]['19].
   [Also search for: automatic differentiation].
   (Also see AD@[<A HREF="https://en.wikipedia.org/wiki/Automatic_differentiation">wikip</A>]['19].)

%A O. Manzyuk
%A B. A. Pearlmutter
%A A. A. Radul
%A D. R. Rush
%T Perturbation confusion in forward automatic differentiation of
   higher-order functions
%J JFP
%V 29
%P e12
%M SEP
%D 2019
%K jrnl, JFP, FP, c2019, c201x, c20xx, zz1219, automatic differentiation, bug,
   error, implementation, maths, high order function, tags, curried
%X "... a technique for augmenting computer programs to compute derivatives. The
   essence of AD in its forward accumulation mode is to attach perturbations to
   each number, & propagate these through the computation by overloading the
   arithmetic operators. ... The essence of the bug is as follows: a unique
   tag is needed for each derivative calculation, but in existing
   implementations unique tags are created when taking the derivative of a fn at
   a point. When taking derivatives of higher-order fns, these need not corr.!
   We exhibit a simple example: a higher-order fn f whose derivative at a pt x,
   namely fâ²(x), is itself a fn which calculates a derivative. This situation
   arises naturally when taking derivatives of curried fns. Two potential solns
   are presented, & their deficiencies discussed. ..."
   -- [<A HREF="https://doi.org/10.1017/S095679681900008X">doi:10.1017/S095679681900008X</A>]['19].
   Also see [<A HREF="http://en.wikipedia.org/wiki/Automatic_differentiation">AD@wikip</A>]['08].
   [Also search for: automatic differentiation].

%A F. Dahlqvist
%A R. Salvia
%A G. A. Constantinides
%T A probabilistic approach to floating point arithmetic
%J arXiv
%M DEC
%D 2019
%K TR, c2019, c201x, c20xx, zz1219, floating point arithmetic, precision,
   accuracy, distribution, rounding error, Kozen
%X "Finite-precision floating point arithmetic unavoidably introduces rounding
   errors .., worst-case analysis might be overly conservative because
   worst-case errors can be extremely rare events in practice. Here we develop a
   probabilistic model of rounding errors with which it becomes possible to
   estimate the likelihood that the rounding error of an alg. lies within a
   given interval. ... show how to compute the distribution of rounding errors.
   We do this exactly for low precision arithmetic, for high precision arith.
   we derive a simple approxn. The model is then entirely compositional ..."
   -- 1912.00867@[<A HREF="https://arxiv.org/abs/1912.00867">arXiv</A>]['19].

%A E. D. Berger
%A C. Hollenbeck
%A P. Maj
%A O. Vitek
%A J. Vitek
%T On the impact of programming languages on code quality: A reproduction study
%J TOPLAS
%V 41
%N 4
%M DEC
%D 2019
%K jrnl, TOPLAS, c2019, c201x, c20xx, zz1219, programming language, languages,
   Ray, Posnett, Devanbu, Filkov, c2014, github, software, errors, bugs,
   defects, static, dynamic, types, checking, typing, FP, rebuttal,
   language wars, controversy, controversial, fuss
%X "In a 2014 article, Ray, Posnett, Devanbu, and Filkov claimed to have
   uncovered a stat. sig. assoc. between 11 programming languages & s/w defects
   in 729 projects hosted on GitHub. Specifically, their work answered four
   research Qs relating to s/w defects & PLs. With data & code provided by the
   authors, the present article first attempts to conduct an experimental
   repetition of the original study. The repetition is only partially
   successful, due to missing code & issues with the class'n of languages. The
   2nd part of this work focuses on their main claim, the assoc. between bugs
   & languages, & performs a complete, independent reanalysis of the data & of
   the statistical modeling steps undertaken by Ray et al. in 2014. ...
   uncovers a # of serious flaws that reduce the # of languages with an assoc.
   with defects down from 11 to only 4. Moreover, the practical effect size is
   exceedingly small. ... thus undermine the conclusions of the original study.
   Correcting the record is important, as many subsequent works have cited the
   2014 article & have asserted, without evidence, a causal link between the
   choice of PL for a given task and the # of s/w defects. Causation is not
   supported by the data at hand; &, in our opinion, even after fixing the
   methodological flaws we uncovered, too many unaccounted sources of bias
   remain to hope for a meaningful comparison of bug rates across languages."
   -- [<A HREF="https://doi.org/10.1145/3340571">doi:10.1145/3340571</A>]['19].
   Also see the original paper by Ray et al,
   'A Large Scale Study of Programming Languages and Code Quality in Github',
   FSE14, Nov. 2014 [<A HREF="https://web.cs.ucdavis.edu/~filkov/papers/lang_github.pdf">www</A>]['19] &
   CACM 60(10), pp.91-100, Oct 2017 [<A HREF="https://doi.org/10.1145/3126905">doi:10.1145/3126905</A>]['19],
   Ray et al, 'Rebuttal to Berger et al., TOPLAS 2019'
   [<A HREF="https://arxiv.org/abs/1911.07393">arXiv</A>][18/11/2019],
   and finally(?) Berger et al,
   'FSE/CACM Rebuttal: Correcting A Large-Scale Study of
   Programming Languages and Code Quality in GitHub ...',
   1911.11894@[<A HREF="https://arxiv.org/abs/1911.11894">arXiv</A>][27/11/2019].

%A C. R. Harris
%A et al
%T Array programming with NumPy
%J Nature
%V 585
%P 357-362
%M SEP
%D 2020
%K review, c2020, c202x, c20xx, zz0920, Python, NumPy, numerical methods,
   algorithms, array, arrays
%X "... NumPy is the primary array programming library for the
   Python language ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2649-2">doi:10.1038/s41586-020-2649-2</A>]['20].

%A J. Jacobs
%T Paradoxes of probabilistic programming and how to condition on events of
   measure zero with infinitesimal probabilities
%J arXiv
%M JAN
%D 2021
%O Proc. ACM Prog.Lang. 5, POPL, #58, JAN 2021
%K conf, c2021, c202x, c20xx, zz0121, probabilistic programming language, STAN,
   Anglican, observe, probability, simulation, sampling, stats
%X "... run by accumulating likelihood at each observe statement, & using the
   likelihood to steer random choices & weigh results with inference algs. such
   as importance sampling or MCMC. We argue that naive LH-accumulation does not
   give desirable semantics & leads to paradoxes when an observe statement is
   used to condition on a measure-zero event ... show that the paradoxes
   disappear if we explicitly model measure-zero events as a limit of +ve
   measure events, & that we can execute these type of prob.programs by
   accumulating infinitesimal probs. rather than prob.densities. ..."
   -- 2101.03391@[<A HREF="https://arxiv.org/abs/2101.03391">arXiv</A>]['21].
   Also see conf@[<A HREF="https://doi.org/10.1145/3434339">doi:10.1145/3434339</A>]['21].
   [Also search for: probabilistic programming language].

%A C. Helbling
%A F. Aksoy
%T Solving the funarg problem with static types
%X arXiv
%M AUG
%D 2021
%K TR, c2021, c202x, c20xx, zz0821, programming language, funarg, closure,
   thunk, heap, stack, type, prenex, Juniper, Arduino, FP
%X "The difficulty assoc. with storing closures in a stack-based environment is
   known as the funarg problem. ... 1st identified with ... Lisp in the 1970s
   ... The modern soln ... is to allocate closures on the heap, or to apply
   static analysis to determine when cs. can be stack allocated. ...  embedded
   sys. often have limited memory resources where heap allocation may cause
   memory fragmentation. We present a simple extension to the prenex fragment of
   System F that allows closures to be stack-allocated. ...  [eg] in the Juniper
   functional reactive p.l., which is designed to run on extremely resource
   limited Arduino devices. We also discuss other solns present in other p.ls
   that solve the funarg problem but haven't been formally discussed in the
   literature."
   -- 2108.07389@[<A HREF="https://arxiv.org/abs/2108.07389">arXiv</A>]['21].

%A V. Choudhury
%A J. Karwowski
%A A. Sabry
%T Symmetries in reversible programming: From symmetric rig groupoids to
   reversible programming languages
%J arXiv
%M OCT
%D 2021
%K TR, c2021, c202x, c20xx, zz1021, reversible, computing, information, PL,
   rig groupoid, circuit, logic, symmetry, quantum computing
%X "The Pi family of reversible prog. langs. for boolean circuits is presented
   as a syntax of combinators witnessing type isomorphisms of algebraic
   datatypes. ... We establish a corr. between the syntactic groupoid of the
   language & a formally presented univalent subuniverse of finite types. ...
   Using the formalisation of our results, we show how to perform
   normalisation-by-eval'n, verification, & synthesis of reversible logic gates,
   motivated by examples from quantum computing."
   -- 2110.05404@[<A HREF="https://arxiv.org/abs/2110.05404">arXiv</A>]['21].
   [Also search for: reversible computing].

%A L. Bergmans
%A X. Schrijen
%A E. Ouwehand
%A M. Bruntink
%T Measuring source code conciseness across programming languages using
   compression
%J arXiv
%M NOV
%D 2021
%K TR, c2021, c202x, c20xx, zz1121, programming language, succinct, concise,
   brief, brevity, software, metrics, compress, compression
%X "... we present a model for measuring the conciseness of PLs in a consistent,
   objective & evidence-based way. We present the approach, explain how it is
   founded on info. theor. principles, present detailed analysis steps & show
   the quantitative results of applying this model to a large benchmark of
   diverse commercial s/w applications. We demonstrate that our metric for
   language conciseness is strongly correlated with both an alternative
   analytical approach, & with a large scale developer survey, & show how its
   results can be applied to improve s/w metrics for multi-lang. applications."
   -- 2111.09728@[<A HREF="https://arxiv.org/abs/2111.09728">arXiv</A>]['21].

%A F. Krawiec
%A et al ...
%A A. Fitzgibbon
%T Provably correct, asymptotically efficient, higher-order reverse-mode
   automatic differentiation
%J POPL
%V 6
%P #48, 1-30
%M JAN
%D 2022
%K conf, c2022, c202x, c20xx, zz0922, FP, automatic differentiation, forward,
   reverse
%X "... give a simple & efficient impl'n of reverse-mode auto.diff., which both
   extends easily to higher-order fns, & has run time & memory consumption
   linear in the run time of the original program. [&] to a formal description
   of the translation, we also describe an implementation of this alg., & prove
   its correctness by means of a logical relations argument."
   -- [<A HREF="https://doi.org/10.1145/3498710">doi:10.1145/3498710</A>]['22].
   (Also see AD@[<A HREF="https://en.wikipedia.org/wiki/Automatic_differentiation">wikip</A>]'22].)
   [Also search for: automatic differentiation].

%A H. Earley
%T The alef-calculus: A declarative model of reversible programming
%K arXiv
%M JUN
%D 2022
%K TR, c2022, c202x, c20xx, zz0622, reversible computing, computation,
   programming language, alefCalculus
%X "A novel model of reversible computing, the N-calculus, is introduced. It is
   declarative, reversible-Turing complete, & has a local term-rewriting
   semantics. Unlike prev. demonstrated reversible term-rewriting systems, it
   does not require the accumulation of history data. Terms in the N-calculus,
   in combination with the program defns, encapsulate all program state. An
   interpreter was also written."
   -- 2206.05957@[<A HREF="https://arxiv.org/abs/2206.05957">arXiv</A>]['22].
   [Also search for: reversible computing].

%A J. Huckelheim
%A et al
%T Understanding automatic differentiation pitfalls
%J arXiv
%M MAY
%D 2023
%K TR, c2023, c202x, c20xx, zz0623, automatic differentiation, autodiff,
   backpropagation, backprop, ANN, problems, errors
%X "Automatic differentiation, also known as backpropagation, AD, autodiff, or
   algorithmic differentiation ... the derivatives computed by AD could be
   interpreted as incorrect. ... we broadly categorize problematic usages of AD
   ..."
   -- 2305.07546@[<A HREF="https://arxiv.org/abs/2305.07546">arXiv</A>]['23].
   Also see [<A HREF="http://en.wikipedia.org/wiki/Automatic_differentiation">AD@wikip</A>]['08].
   [Also search for: automatic differentiation].

%A A. Herten
%T Many cores, many models: GPU programming model vs. vendor compatibility
   overview
%J arXiv
%M SEP
%D 2023
%K TR, c2023, c202x, c20xx, zz0923, GPU, programming languages, parallel, HPC,
   survey, introduction, Aurora, El Capitan, JUPITER, NVIDIA, CUDA
%X "... The current HPC GPU landscape features three vendors (AMD, Intel,
   NVIDIA), each with native & derived programming models. The choices are
   ample, but not all models are supported on all platforms, especially if
   support for Fortran is needed; in addition, some restrictions might apply.
   ... hard for sci. programmers to navigate this abundance of choices & limits.
   This paper gives a guide by ..."
   -- [<a HREF="https://arxiv.org/abs/2309.05445">arxiv:2309.05445</A>]['23].

%A D. Stein
%A S.Staton
%T Probabilistic programming with exact conditions
%J JACM
%M FEB
%D 2024
%K jrnl, JACM, c2024, c202x, c20xx, zz0224, Gaussian, programming language,
   STAN, model
%X "We spell out the paradigm of exact conditioning as an intuitive & powerful
   way of conditioning on observations in probabilistic programs. This is
   contrasted with likelihood-based scoring known from languages such as Stan.
   ... cases of discrete & Gaussian probability ..."
   "Prob.prog. is a prog.paradigm that uses code to formulate generative
   statistical models & perform inference on them ..."
   -- [<A HREF="https://doi.org/10.1145/3632170">doi:10.1145/3632170</A>]['24].

%A S. Graf
%A S. Peyton Jones
%A S. Keidel
%T Abstracting denotational interpreters
%J arXiv
%M MAR
%D 2024
%K TR, c2024, c202x, c20xx, zz0324, abstract, semantics, static analysis,
   interpreter, datatype, type, types, trace, traces, PeytonJones
%X "... By parameterising our denotational interpreter over the semantic domain
   & then varying it, we recover dynamic semantics with different evaluation
   strategies as well as summary-based static analyses such as type analysis,
   all from the same generic interpreter. ..."
   -- [<A HREF="https://arxiv.org/abs/2403.02778">arxiv:2403.02778</A>]['24].



%A K. C. R. C. Arnold
%T Screen updating and cursor movement optimzation: a library package
%I Computer Science, University of California at Berkeley
%K Unix, terminal, C, cursor, screen, VDU, curses, computing
%P ??
%D 19??

%A N. A. B. Gray
%T Programming with Class: A Practical Introduction to
   Object-Oriented Programming with C++
%M JUN
%D 1994
%P 680
%I Wiley
%K book, text, computer programming language, Cpp, CplusPlus, xx, OO, OOP
%X isbn:0471 94350 9; ppb.    isbn:0471 94358 4; disk

%A S. P. Harbison
%A G. L. Steele jr.
%T C: A Reference Manual
%I PrenticeHall
%D 1991
%K C, cc, ANSI C, ANSIC, book, text, imperative programming language, Unix
%X 4th edn 1995,
   isbn:0-13-326232-4, (case);
   isbn:0-13-326224-3, (pbk);

%A A. Kelley
%A I. Pohl
%T C by Dissection: Essentials of C Programming (2nd edn)
%K C, cc, book, text, computer programming language
%D 1992

%A S. B. Lippman
%T A C++ Primer
%I AddisonWesley
%D 1991
%K book, text, computer programming language, cc, Cpp, CplusPlus, OO, OOP
%O AT and T Bell Labs (1989)

%A I. Pohl
%T C++ for C Programmers
%I Benjamin-Cummings
%D 1994
%K book, text, computer programming language, cc, Cpp, CplusPlus, OO, OOP

%A I. Pohl
%T C++ for Pascal Programmers
%I Benjamin-Cummings
%D 1994
%K book, text, computer programming language, cc, Cpp, CplusPlus, OO, OOP

%A J. Shapiro
%T A C++ Toolkit
%I PrenticeHall
%D 1990
%K book, text, computer programming language, cc, Cpp, CplusPlus, OO, OOP

%A P. H. Winston
%T On to C++
%I AddisonWesley
%P 305
%D 1994
%K book, text, computer programming language, cc, Cpp, CplusPlus, OO, OOP, good
%X isbn:0-201-58043-8; ppb    (mercifully brief)

%A J. Siek
%A L.-Q. Lee
%A A. Lumsdaine
%T The Boost Graph Library: User Guide and Reference Manual
%I AddisonWesley
%P 321
%D 2002
%K book, text, C++, cc, Boost, library, package, c2002, c200x, c20xx,
   graph, graphs, BGL, Cpp, CplusPlus, OO, OOP
%X "The Boost Graph Library (BGL) is the first C++ library to apply the
   principles of generic programming to the construction of the advanced
   data structures and algorithms used in graph computations. Problems in
   such diverse areas as Internet packet routing, ..."
   pb us$37; uk us isbn:0201729148; uk us isbn13:978-0201729146.
   [Also search for: Cplusplus boost].
   (Also see [<A HREF="http://www.boost.org/">boost.org</A>]['09].)

%A David Abrahams
%A A. K. Gurtovoy
%T C++ Template Metaprogramming: Concepts, Tools, and Techniques from
   Boost and Beyond
%I AddisonWesley
%P 400
%D 2004
%K book, text, C++, cc, Boost, library, c2004, c200x, c20xx, template,
   templates, Metaprogramming, Cpp, CplusPlus, OO, OOP, in depth series
%X "... Since the introduction of templates, C++ programmers have discovered
   surprising and powerful ways to perform computation at compile-time. While
   the excitement generated by these capabilities among C++ experts has reached
   the community at large, their practical application remains out-of-reach for
   many programmers. Literature on C++ template metaprogramming has focused
   primarily on details of low-level "tricks" at the expense of strong idioms
   and abstractions ..."
   1st ed 2004; pb us$44; uk us isbn:# 0321227255; uk us isbn13:978-0321227256.
   [Also search for: Cplusplus boost].
   (Also see [<A HREF="http://www.boost.org/">boost.org</A>]['09].)

%A D. Ryan Stephens
%A C. Diggins
%A J. Turkanis
%A J. Cogswell
%T C++ Cookbook
%I OReilly
%P 592
%D 2005
%K book, text, C++, cc, c2005, c200x, c20xx, zz0609, template, Cpp, CplusPlus,
   library, Boost, OO, OOP, programming, introduction
%X 1st ed 2005; pb us$30; uk us isbn:# 0596007612; uk us isbn13:978-0596007614.
   [Also search for: Cplusplus library].
   (Also see [<A HREF="http://www.boost.org/">boost.org</A>]['09].)

%A B. Karlsson
%T Beyond the C++ Standard Library: An Introduction to Boost
%I AddisonWesley
%P 432
%D 2005
%K book, text, C++, cc, Boost, library, intro, c2005, c200x, c20xx, zz0509,
   Cpp, CplusPlus, OO, OOP, standard, template, libraries, programming language,
   package
%X "Introducing the Boost libraries: the next breakthrough in C++ programming
   Boost takes you far beyond the C++ Standard Library, making C++ programming
   more elegant, robust, and productive. Now, for the first time, a leading
   Boost expert systematically introduces the broad set of Boost libraries and
   teaches best practices for their use. Writing for intermediate-to-advanced
   C++ developers, ..."
   1st ed 2005, pb us$50; uk us isbn:0321133544; uk us isbn13:978-0321133540.
   [Also search for: Cplusplus boost].
   (Also see [<A HREF="http://www.boost.org/">boost.org</A>]['09].)


%A T. Kasami
%T An efficient recognition and syntax analysis algorithm for
   context-free languages
%R AFCRL-65-758
%I Air Force Cambridge Res. Lab., Bedford Mass.
%D 1965
%K TR, c1965, c196x, c19xx, parse, parser, parsing, CYK, CKY, algorithm,
   language, CFG, grammar, Cocke, Younger, Kasami, dynamic programming
%X ?does anyone have a copy plsz?   CYK = Cocke, Younger, Kasami.
   [Also search for: CYK parsing].

%A D. H. Younger
%T Recognition and parsing of context-free languages in time n^3
%J Inf. and Control
%V 10
%N 2
%P 189-208
%D 1967
%K jrnl, c1967, c196x, c19xx, parse, parser, parsing, CYK algorithm, CFG,
   Cocke, Younger, Kasami, language, dynamic programming
%X CYK = Cocke, Younger, Kasami.     [Also search for: CYK parsing].

%A D. Gries
%T Compiler Construction for Digital Computers
%I Wiley
%D 1971
%K book, text, c1971, c197x, c19xx, compilers, compilation, parse, parser,
   parsing, code generation
%X uk us isbn:0471327719.

%A R. S. Glanville
%A S. L. Graham
%T A new method for compiler code generation
%J Symp. on Principles of Programming Languages
%I ACM
%P 231-254
%D 1978
%K symp, popl, generator, compilers, c1978, c197x, c19xx, table driven, tree,
   SIGACT-SIGPLAN, popl5
%X "...translate a relatively low-level intermediate representation of a
   program into assembly code or m/c code for a target computer. The alg. is
   table driven. A construction alg. is used to produce the table from a
   functional description of the target m/c. The method produces high quality
   code for many commercially available computers. By replacing the table, it
   is possible to retarget a compiler for another kind of computer...."
   -- [<A HREF="http://doi.acm.org/10.1145/512760.512785">doi:10.1145/512760.512785</A>]['04].

%A R. Bornat
%T Understanding and Writing Compilers
%I Macmillan
%P 396
%D 1979
%K book, text, good, c1979, c197x, c19xx, L3Ref, compiler, compilation, parser,
   parsing, parse, code generation, programming languages, language,
   implementation
%X isbn:0333217322.
   [<A HREF="http://www.cs.mdx.ac.uk/staffpages/r_bornat/">bornat</A>]['06]

%A S. L. Graham
%A R. R. Henry
%A R. A. Schulman
%T An experiment in table driven code generation
%J Symp. on Compiler Construction
%I ACM
%P 32-43
%D 1982
%K symp, Sigplan, c1982, c198x, c19xx, compilers, maximal munch, tree, trees,
   C, cc, Vax-11, Vax11
%X "...local code generator... using a parser-like inst'n pattern matcher. The
   code generator replaces the 2nd pass of the UNIX portable C-compiler. ...
   describes the design of the code generator & the special considerations
   imposed by the pattern matching process. We summarize the structure of the
   m/c description grammar & its assoc. semantic actions, [&] the tools ...
   to manipulate the large VAX description. ...this approach makes the inst'n
   selection phase of the compiler easier & faster to implement, & more likely
   to be correct than traditional techniques." uk us isbn:0897910745.
   -- [<A HREF="http://portal.acm.org/citation.cfm?id=806978">inc pdf</A>]['04].

%A A. V. Aho
%A R. Sethi
%A J. D. Ullman
%T Compilers: Principles, Techniques and Tools
%I AddisonWesley
%P 796
%D 1986
%K book, text, good, c1986, c198x, c19xx, dragon book, parse, parser, parsing,
   compile, compiler, compilation, programming languages, language,
   implementation
%X 1st ed 1986; hb us$28; The "Dragon Book", uk us isbn:0201100886.
   2nd ed 2006; hb us$106; uk us isbn:0321486811; uk us isbn13:978-0321486813;
      1000 p., by A. V. Aho, M. S. Lam, R. Sethi, J. D. Ullman.
   (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/">Prog Langs</A>].)

%A W. M. Meleis
%A E. S. Davidson
%T Optimal Register Allocation for a Multiple-Issue Machine
%J Proc. 1994 Int. Conf. on Supercomputing (ICS)
%W Manchester, UK
%P 107-116
%D 1994
%K ICS, ICS94, conf, register, allocation, compiler, optimization, code,
   computing, c1994, c199x, c19xx
%X via email: Alexandre Eichenberger (alexe of eecs.umich.edu) [2/'95].

%A P. Briggs
%T Register Allocation via Graph Coloring
%R 92-183
%I Rice University, Houston, Texas, USA
%D 1992
%K PhD thesis, register allocation, compiler, optimization, code,
   colouring, computing
%X via email: Alexandre Eichenberger (alexe of eecs.umich.edu) [2/'95].

%A D. Callahan
%A B. Koblenz
%T Register allocation via hierarchical graph coloring
%J Proc. ACM SIGPLAN '91 Conf. Programming Language Design and Implementation.
%W Toronto, Canada.
%P ?-?
%M JUN
%D 1991
%K PLDI, PLDI91, register allocation, compiler, optimization, code,
   colouring, computing
%X via email: Alexandre Eichenberger (alexe of eecs.umich.edu) [2/'95].

%A L. Hendren
%A G. Gao
%A E. Altman
%A C. Mukerji
%T A register allocation framework based on hierarchical cyclic interval graphs
%J Proc.  4th Int. Conf. Compiler Construction
%S LNCS
%V 641
%I SpringerVerlag
%P ?-?
%D 1992
%K ICCC, ICCC4, ICCC92, conf, register allocation, compiler, optimization,
   code, computing
%X via email: Alexandre Eichenberger (alexe of eecs.umich.edu) [2/'95].

%A A. W. Appel
%T Axiomatic bootstrapping: a guide for compiler hackers
%J TOPLAS
%V 16
%N 6
%P 1699-1718
%M NOV
%D 1994
%K bootstrap, boot strap, axiom, compile, SML, FP, zz0595
%X compiler for language L is implemented in L,
   then it should be able to compile itself.
   ... here I attempt an axiomatic clarification of b' using Standard ML
   of New Jersey as a case study. ... .

%A A. Appel
%T Modern Compiler Implementation in C
%I CUP
%D 1998
%P 560
%K book, text, c1998, c199x, c19xx, compile, programming language, CC
%X us$54.95, au$82.25; uk us isbn:052158390X.
   ppb, uk us isbn:0521607655.  See also ... in Java or ML.

%A A. Appel
%T Modern Compiler Implementation in Java
%I CUP
%D 1998
%P 560
%K book, text, c1998, c199x, c19xx, compile, programming language, zz0498
%X US$54.95, Au$82.25, ppb; uk us isbn:0521583888.
   [Also search for: Appel book ML] and [also search for: Appel book CC].

%A A. Appel
%T Modern Compiler Implementation in ML
%I CUP
%D 1998
%P 560
%K book, text, compile, programming language, c1998, c199x, c19xx, compilation,
   SML, CUP, MLlex, MLyacc
%X c2004 ed, pb, us$55, uk us isbn:0521607647; uk us isbn13:978-0521607643.
   (pb, us$54.95, au$82.25, uk us isbn:0521582741; also see ... in C or Java,
     [<A HREF="http://www.cs.princeton.edu/~appel/modern/ml/">@princeton</A>]['05].)

%E K. Pingali
%E U. Banerjee
%E D. Gelernter
%E A. Nicolau
%E D. Padua
%T Languages and Compilers for Parallel Computing
%I SpringerVerlag
%S LNCS
%V 892
%M AUG
%D 1994
%K conf, book, text, computer, CSci, zz0595

%E T. Gyimothy
%T Compiler Construction: 6th International Conference CC '96
%I SpringerVerlag
%S LNCS
%N 1060
%D 1996
%K compiler, conf, LNCS 1060, CC96, CC6, programming language implementation,
   CSci, zz0796

%A R. Wilhelm
%A D. Maurer
%T Compiler Design
%I AddisonWesley
%D 1995
%P 599
%K book, text, compilers, compilation programming languages, L3Ref, zz0297
%X uk us isbn:0-201-42290-5.
      1: intro           2: imperative langs    3: func' langs
      4: logic langs     5: OO langs            6: compiler structure
      7: lexical         8: syntax              9: sematics
     10: abs' interp'   11: tree patt' match   12: code gen'
   translated from the German
   <A HREF="http://www.cs.uni-sb.de/users/martin/COMP">[http]</A> [2/'97]
   <A HREF="ftp://ftp.cs.uni-sb.de/pub/compiler">[ftp]</A>  - from book.

%A J. P. Bennett
%T Introduction to Compiling Techniques: a first course using
   ANSI C, Lex and Yacc
%I McGrawHill
%D 1990
%P 242
%K book, text, lex, yacc, compilers, programming languages, cc, L3Ref
%X uk us isbn:0-07-707215-4.

%A T. Pittman
%A J. Peters
%T The Art of Compiler Design
%I PrenticeHall
%D 1992
%P 420
%K book, text, programming languages, compilation
%X uk us isbn:0-13-046160-1.

%A R. Morgan
%T Building an Optimizing Compiler
%I DigitalPress
%P 450
%D 1998
%K book, text, compile, compilation, compilers, programming languages
%X uk us isbn:1-55558-179-X.

%A W. Pugh
%A D. Wonnacott
%T Constraint-based array dependence analysis
%J TOPLAS
%P 635-678
%V 20
%N 3
%M MAY
%D 1998
%K jrnl, TOPLAS, arrays, dependency, programming, c1998, c199x, c19xx,
   Presburger arithmetic
%X "...need to ask about the flow of values in arrays, to check the legality of
   array privatization, & about the conditions under which a dependence exists,
   to obtain information about conditional parallelism. In some cases, we must
   answer these questions about code containing nonlinear terms in loop bounds
   or subscripts. This article describes techniques for phrasing these questions
   in terms of systems of contstraints. Conditional dependence analysis can be
   performed with a constraint operation we call the "gist" operation. When
   subscripts & loop bounds are affine, questions about the flow of values in
   array variables can be phrased in terms of Presburger Arithmetic. When the
   constraints describing a dependence are not affine, we introduce
   uninterpreted function symbols to represent the nonaffine terms...."
   -- [<A HREF="http://doi.acm.org/10.1145/291889.291900">doi:10.1145/291889.291900</A>]['05] auth1 at umd.edu.

%A M. Madhavan
%A P. Shankar
%A S. Rai, & U. Ramakrishnan
%T Extending Graham-Glanville techniques for optimal code generation
%J TOPLAS
%V 22
%N 6
%P 973-1001
%M NOV
%D 2000
%K jrnl, compiler, compilers, c2000, c200x, c20xx, code generator, tree, trees,
   table driven
%X "...combines the advantages of the Graham-Glanville parsing technique & the
   bottom-up tree parsing approach. M/c descs. are similar to Yacc specs.. The
   construction effectively generates a pushdown automaton as the matching
   device. [It] is able to handle ambigious grammars, & can be used to generate
   locally optimal code without the use of heuristics. Cost computations are
   performed at preproc. time. The class of regular tree grammars augmented
   with costs that can be handled by our system properly includes those that
   can be handled by bottom-up systems based on finite-state tree parsing
   automata. Parsing time is linear in the size of the subject tree...."
   -- [<A HREF="http://doi.acm.org/10.1145/371880.371881">doi:10.1145/371880.371881</A>]['04].

%A W. Pugh
%T The Java memory model is fatally flawed
%J Concurrency: Practice and Experience
%P 1-11
%V 12
%N 1
%D 2000
%K Java, programming language, concurrent, parallel, thread, threads,
   OO, OOP, c2000, c200x, c20xx
%X [<A HREF="http://www.cs.umd.edu/~pugh/papers/jmm2.pdf">@umd</A>]['05].

%A P. G. Joisha
%A P. Banerjee
%T A translator system for the MATLAB language
%J SPE
%V 37
%N 5
%P 535-578
%D 2007
%K jrnl, SPE, c2007, c200x, c20xx, compile, translate, C, CC, compiler,
   MATLAB, zz0307
%X "A whole-program MATLAB to C translation system is presented. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.781">doi:10.1002/spe.781</A>]['07].

%A J.-P. Bernardy
%A K. Claessen
%T Efficient parallel and incremental parsing of practical context-free
   languages
%J JFP
%V 25
%P e10 (39pp.)
%M JUL
%D 2015
%K jrnl, JFP, c2015, c201x, c20xx, zz0815, FP, parse, parsing, parser,
   algorithm, CFG, grammar, Valiant
%X We present a divide-and-conquer alg. for parsing context-free languages
   efficiently. [It] is an instance of Valiant's (1975; General CF recognition
   in less than cubic time. J. Comput. Syst. Sci. 10(2), 308-314), who reduced
   the problem of parsing to matrix multiplications. ... while the conquer step
   of V's is O(n^3), it improves to O(log^2 n) under certain condns satisfied by
   many useful inputs that occur in practice, & if one uses a sparse repn of
   matrices. ... because the multns involve an overwhelming majority of empty
   matrices. ... relevant to modern computing: divide-&-conquer algs. with a
   polylogarithmic conquer step can be parallelized relatively easily."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796815000131">doi:10.1017/S0956796815000131</A>]['15].
   [Also search for: Valiant c1975].

%A P. Bahr
%A G. Hutton
%T Calculating correct compilers
%J JFP
%V 25
%P e14 (47pp)
%M SEP
%D 2015
%K jrnl, JFP, c2015, c201x, c20xx, zz1115, FP, Coq, proof, verification,
   compiler, compilation, compiling, programming language, implementation
%X "... a new approach to the problem of calculating compilers. ... develop a
   simple but general technique that allows us to derive correct compilers from
   high-level semantics by systematic calc'n, with all details of the
   implementation of the compilers falling naturally out of the calc'n process.
   ... based upon the use of std equational reasoning techniques, & has been
   applied to calculate compilers for a wide range of language features & their
   combination, inc. arithmetic expressions, exceptions, state, various forms of
   lambda calculi, bounded & unbounded loops, non-determinism & interrupts. All
   the calculations in the article have been formalised using the Coq proof
   assistant, which serves as a convenient interactive tool for developing &
   verifying the calculations."  (online Sept 2015.)
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796815000180">doi:10.1017/S0956796815000180</A>]['15].


%A Tony Abbott
%T Quote
%D 2013
%K Abbott, suppository, quote, quotable, funny, haha, ha ha, c2013, zz0813,
   Liberal party, Australia, election, campaign, politics, ABC, SBS, tax, GST,
   marriage, same sex, coal, NSA, ASIO, non core promise, promises, lies
%X "No one, however smart, however well-educated, however
    experienced, is the suppository of all wisdom."
    -- Tony Abbott, Liberal leader,
       campaigning for the Australian Federal election, 12 August 2013.
 * "It is an absolute principle of democracy that governments should not and
    must not say one thing before an election and do the opposite afterwards."
    -- Tony Abbott, 22 August 2011.
 * And, "no cuts to education" "no cuts to health", "no change to pensions",
        "no change to the GST", "no cuts to the ABC or SBS",
   -- Tony Abbott, 6 September 2013,
      [<A HREF="https://www.youtube.com/watch?v=wAHNXdHai0g">'uTube</A>]['14],
      [<A HREF="http://www.abc.net.au/news/2014-04-22/berg-election-promises-are-there-for-the-breaking/5403160">abc</A>]['14].
    (The Lib.-Nat. coalition won that election, 7 Sept 2013, so TA became PM.
     Also see [<A HREF="http://www.bbc.co.uk/news/world-asia-23677992">bbc</A>]['13].)
 * "We stand for lower, simpler, fairer taxes, not great big new taxes
    that damage Australia's economy, not great big new taxes ..."
   -- Tony Abbott, 28 October 2013,
      [<A HREF="http://www.abc.net.au/news/2014-05-01/fact-file-what-tony-abbott-promised-on-tax/5420226">abc</A>] Fact Check 1/5/2014.
 * '"From time immemorial, in every culture that's been known, marriage or
   that kind of solemnised relationship has been between a man and a woman,"
   Mr Abbott said on October 25, 2013. ... [But] A significant body of
   academic work shows that marriage and "other solemnised relationships" have
   not always been between "a man and a woman".  Mr Abbott is incorrect.'
   -- [<A HREF="http://www.abc.net.au/news/2013-11-01/tony-abbott-incorrect-history-marriage/5053844">abc</A>] Fact Check 1/11/2013.
 * '"Mr Abbott said he was "worried and concerned" by the ABC taking a lead in
   reporting leaks from Snowden, a former US NSA contractor.'
   -- [<A HREF="http://www.abc.net.au/news/2014-01-29/tony-abbott-steps-up-criticism-of-abc/5224676">abc</A>][29/1/2014],
      [<A HREF="http://www.allisons.org/ll/Computing/Misc/1984/">more</A>].
 * "Coal is good for humanity" -- T.A. 13/10/2014,
      [<A HREF="http://www.abc.net.au/news/2014-10-13/coal-is-good-for-humanity-pm-tony-abbott-says/5810244">abc</A>]['14],
      [<A HREF="https://www.youtube.com/watch?v=VBiJfWbffZU">'uTube</A>]['14].
 * (14/9/2015: The Libs replaced TA with Malcolm Turnbull as leader, and PM.)

%A Franklin Pierce Adams
%T Quote
%D 1881-1960
%K Adams, quote, quotable, good old days, bad memory, faulty, zz0119,
   nostalgia, funny, haha
%X "Nothing is more responsible for the good old days than a bad memory."
   -- is attributed to Franklin Pierce Adams (1881-1960) by a
   number of quotation web-sites.

%A anon
%T Lies, damned lies, and statistics
%K anon, damned lies, statistics, stats, quote, quotable, funny, Mark Twain,
   Benjamin Disraeli, Charles Dilke
%X -- LDLS@[<A HREF="https://en.wikipedia.org/wiki/Lies,_damned_lies,_and_statistics">wikip</A>]['20].
   Attributed to several, different people.
   *Popularised* by Mark Twain and others.

%A John Arbuthnot
%T Quote
%D 1692
%K Arbuthnot, quote, quotable, reason, reasoning, mathematics, maths, logic,
   c1692, c169x, c16xx
%X "When a Mathematical Reasoning can be had it's as great a folly
   to make use of any other, as to grope for a thing in the dark,
   when you have a Candle standing by you."
   [from a  P h i l i p  W a d l e r  email].

%A Archilochus
%T Quote
%K Archilochus, quote, quotable, fox, hedgehog, trick, tricks
%X The poet A. wrote "The fox has many tricks, and the hedgehog one great one".

%A V. I. Arnol'd
%T Quote
%K quote, obfuscation, jargon, maths, Arnold
%X "It is almost impossible for me to read contemporary mathematicians who,
   instead of saying 'Petya washed his hands,' write simply:
     'There is a $t_1 < 0$ such that the image of $t_1$ under the natural
     mapping $t_1 \mapsto {\rm Petya}(t_1)$ belongs to the set of dirty hands,
     and a $t_2$, $t_1 < t_2 \leq 0$, such that the image of $t_2$ under the
     above-mentioned mapping belongs to the complement of the set defined in
     the preceding sentence.'
   via A.K.;  also see [<A HREF="http://www-zeuthen.desy.de/~kolanosk/eep06/skripte/lie.pdf">pdf</A>]['09] or [<A HREF="http://math.ucr.edu/home/baez/lie/node1.html">www</A>]['09].

%A Lawrence (Yogi) Berra (1925-2015)
%T Quote
%K Berra, quote, quotable, Yogiisms, bear, malapropism, witticism,
   wit, funny, ha ha, haha, baseball
%X The future ain't what it used to be.
 * It ain't over till it's over
 * It's like deja vu all over again.
 * When you come to a fork in the road, take it.
 * No one goes there nowadays, itâs too crowded.
 * You can observe a lot by just watching.
 * If you don't know where you are going, you'll end up someplace else.
 * Baseball is ninety percent mental and the other half is physical.
 * Always go to other people's funerals, otherwise they won't come to yours.
 * A nickel ain't worth a dime anymore.               [via AK]
   More YB@[<A HREF="https://en.wikipedia.org/wiki/Yogi_Berra">wikip</A>]['20].

%A George Brandis
%D 2014
%T Quote
%K Brandis, quote, quotable, c2014, zz0514, attorney general, Australia,
   politics, Liberal party, Racial Discrimination Act, hatred, 18C, offensive,
   bigot, biggot, Andrew Bolt
%X "People do have a right to be bigots, you know.
    In a free country, people do have rights to say things
    that other people find offensive or insulting or bigoted."
    -- p.1797@[<A HREF="http://parlinfo.aph.gov.au/parlInfo/search/display/display.w3p;query=Id%3A%22chamber%2Fhansards%2F6a5b8de8-212b-46a9-b00f-61b865fe92a2%2F0026%22">hansard</A>][24/3/2014],
       [<A HREF="http://www.abc.net.au/news/2014-04-30/george-brandis-ill-informed-on-right-to-be-bigots/5375302">abc</A>]['14].

%A Nils Bohr
%T Quote
%K Bohr, quote, quotable, funny, predict, prediction, future, model,
   over fitting, overfit, overfitting, stats, modeling, modelling, theory
%X "Prediction is very difficult, especially if it's about the future."
   -- This quote serves as a warning of the importance of testing a
      forecasting model out-of-sample. It's often easy to find a model that fits
      the past data well -- perhaps too well! -- but quite another matter to
      find a model that correctly identifies those features of the past data
      which will be replicated in the future
      (was at www.lsp.ups-tlse.fr/Stephen/STATS/quotes.html [2002].)
   {BUT see [<A HREF="http://en.wikiquote.org/wiki/Niels_Bohr">wikiq</A>]['14].}

%A C. Caleb
%K Caleb, c1820, c182x, c18xx, zz1023, plagiarism, quote, quotable, copy,
   copying, research, three
%X "If we steal thoughts from the moderns, it will be cried down as
   plagiarism; if from the ancients, it will cried up as erudition."
   -- quoteinvestigator
   and several(!) variations inc.:
   "If you copy from one book, that's plagiarism: if you copy from
   many books, thatâs research." (1930).

%A W. B. Cameron
%T Informal Sociology: A Casual Introduction to Sociological Thinking
%I RandomHouse
%S Studies in Sociology
%V 21
%P 170
%D 1963
%K Cameron, book, text, c1963, c196x, c19xx, Sociology
%X asin:B0006AYNI4.
   [Also search for: Cameron quote counting].

%A W. B. Cameron
%T Quote
%K Cameron, quote, quotable, c1963, c196x, c19xx, funny, count, counts,
   counting, counted, everything, KPI, KPIs, Einstein
%X "not everything that can be counted counts, and
   not everything that counts can be counted."
     (Quote Investigator attributes it to W. B. Cameron, 'Informal
     Sociology: A Casual Introduction to Sociological Thinking' (1963),
     -- [<A HREF="https://quoteinvestigator.com/2010/05/26/everything-counts-einstein/">www</A>]['18],
     although many think it is due to Einstein.
     Note, QI's page contains a "picture of Einstein at blackboard
     with *fictitious* writing constructed at hetemeel.com.")
   [Also search for: Campbell law]  and  [also search for: Goodhart law].

%A Howard Carter
%D ??? - 1939 ?
%T Quote
%K Carter, quote, quotable, rubbish, ball balls, Tutankhamen, Tutankhamun
%X In reply to rubbish: "The answer to that is spherical and in the plural."

%A Robert R. Coveyou
%D ? 1960s ?
%K Coveyou, quote, quotable, funny, Coveyou, pseudo random number generators,
   generation, numbers, too important, left to chance, RNG, PRNG, c19xx
%X "The generation of random numbers is too important to be left to chance."
   Many 'net sources attribute this to
   mathematician Robert R. Coveyou of the Oak Ridge National Laboratory
   ? in the 1950s and 1960s ?

%A Ronald Coase
%K Coase, quote, quotable, economics, economist, statistics, stats, data, model,
   funny, haha
%X "If you torture the data enough, nature will always confess."

%A E. Dijkstra
%D ?
%T Quote
%K Dijkstra, Edsger, EWD, c19xx, zz0220, quote, quotable, SE, SWE, SWEng,
   computer programming, proof, verification, logic, formal,
   Software Engineering, crisis
%X "The required techniques of effective reasoning are pretty formal, but
   as long as programming is done by people that don't master them, the
   software crisis will remain with us and will be considered an incurable
   disease. And you know what incurable diseases do: they invite the quacks
   and charlatans in, who in this case take the form of Software Engineering
   gurus."
   -- [<A HREF="http://www.cs.utexas.edu/users/EWD/transcriptions/EWD13xx/EWD1305.html">www</A>]['20]  (via AK).

%A A. Einstein
%D 1933 ?
%T Quote
%K Einstein, quote, quotable, simple, simplicity, II, AI, theory, theories,
   KISS, Occam's razor, occams, c193x, c19xx
%X ... wrote in 1933 "The supreme goal of all theory is to make the irreducible
   basic elements as simple and as few as possible without having to surrender
   the adequate representation of a single datum of experience"
   often paraphrased as
   "Theories should be as simple as possible, but no simpler."
   --[<A HREF="http://en.wikipedia.org/wiki/Occam's_Razor">wikip</A>]['07]
   And
   "Das Oberste Ziel aller Theorie ist, die nicht reduzierbaren grundlegenden
   Elemente zu bilden, wie einfach und nur moglich, ohne zu mussen, die
   ausreichende Darstellung eines Einzelnen Bezugspunktes der Erfahrung zu
   ubergeben." -- Albert Einstein (1933)
   --[<A HREF="http://en.wikiquote.org/wiki/Talk:Albert_Einstein">wikiq</A>]['07].
   ?Where was E. writing?

%A R. Feynman
%T Probability and Uncertainty - The Quantum Mechanical View of Nature
%M NOV
%D 1964
%K Feynman, quote, quotable, Feynman, quantum, theory, mechanics, nobody,
   understands, understanding, physics, weirdness, c1964, c196x, c19xx, zz0814
%X Lecture, includes: "... I think I can safely say that
                       nobody understands quantum theory. ..." at 7:40+.
   -- [<A HREF="http://www.youtube.com/watch?feature=player_detailpage&v=hUJfjRoxCbk#t=457">7.40</A>]['14], via A.K.,
      [<A HREF="https://www.youtube.com/watch?v=x5RQ3QF9GGI">uBend</A>]['14].

%A Flanders and Swan
%K Flanders, Swan, quote, quotable, entropy, first, second, law, thermodynamics,
   physics, heat, funny, haha
%X The First Law of Thermodynamics:  Heat is work and work is heat. ...
   The Second Law of Thermodymamics: Heat cannot of itself pass from
   one body to a hotter body. ...
   Heat is work and work's a curse.
   And all the heat in the Universe.
   Is gonna cooool down 'cos it can't increase.
   Then there'll be no more work and there'll be perfect peace.
   Really?
   Yeah -- that's entropy, man!

%A Peter Goldsworthy
%T The biology of poetry
%D 2002
%K Goldsworthy, quote, quotable, poem, poetry, arts, art, beauty, pattern,
   motif, metaphor, emotion, patterns, c2002, c200x, c20xx
%X "... But when we start talking about the emotional power of poetry, we start
   talking about metaphor above all.  Metaphor is the key basic building block
   of poetry.  An this is no surprise - because metaphor is a kind of pattern
   seeking - and our brains are formatted at seeking patterns.  Logic
   doesn't come naturally to the human brain.  Our brains have to be trained -
   Pavloved - into logic.  Culturally constructed, if you like.  But our
   brains very naturally seek patterns.  That's what they do best. ..."
      [From 'The biology of poetry', the Judith Wright memorial lecture,
      Balmain Town Hall, Australian Poetry Festival, 2002, as re-printed
      in the 'Adelaide Review', Feb, 2003.]
   (See .doc@[<A HREF="http://petergoldsworthy.com/s/JudithWrightLecture.doc">www</A>][11/2017].)

%T G. H. Hardy and the Riemann Hypothesis (story)
%K Hardy, quote, quotable, c19xx, zz1123, story, Bohr, Riemann Hypothesis
%X "Hardy stayed in Denmark with Bohr until the very end of the summer vacation,
   & when he was obliged to return to England to start his lectures there was
   only a very small boat available... The North Sea can be pretty rough, & the
   probability that such a small boat would sink was not exactly zero. Still,
   Hardy took the boat, but sent a postcard to Bohr: 'I proved the Riemann
   Hypothesis. G.H. Hardy.' If the boat sinks & Hardy drowns, everybody must
   believe that he has proved the Riemann Hypothesis. Yet God would not let
   Hardy have such a great honor & so He will not let the boat sink."
   -- [<A HREF="https://home.cc.umanitoba.ca/~mcleod/Riemann/Hardy.html">mcleod</A>]['23].

%A Philip Hodgins
%D 2002
%T Quote
%K Hodgins, aphorism, quote, quotable, obituary, die, gallows humour, humor,
   ha ha, haha
%X 'an obituary to die for'
   -- attributed to the poet P.H. by Peter Goldsworthy (2002) in
   'The biology of poetry', the Judith Wright memorial lecturer;
   it was PH's response (with a bottle of wine) to PG's obituary of
   PH sent to PH shortly before his death.

%A Donald E. Knuth
%D 1977
%T Quote
%K Knuth, quote, quotable, c1977, c197x, c19xx, verification, proof, deque,
   correctness, bug, bugs, testing, program, programming, SWE, SWeng, code
%X "Beware of bugs in the above code; I have only
   proved it correct, not tried it."   -- Donald E. Knuth.
      Final sentence of a letter written to Peter van Emde Boas titled
   "Notes on the van Emde Boas construction of priority deques:
   An instructive use of", 1977.                [Via Geoff W., '06].

%A Pierre Laplace
%D 1819
%T Quote
%K Laplace, quote, quotable, probability theory, c1819, c181x, c18xx
%X Probability theory is nothing but common sense reduced to calculation.
   [from R u s s e l l and N o r v i g '95, p.458].

%A Arthur Lesk
%T On Deans
%D pre-2014
%K Lesk, University, Faculty, Dean, Deans, deanitis, tertiary education,
   research, academia, university management, KPI, KPIs, quality (not),
   publications, papers, impact, publish, perish, count, zz0614,
   funny, ha ha, haha, quote, quotable, ALesk, AMLesk
%X Deans are  unable to read,
   Deans are unable to weigh,
   Counting is roughly their speed,
   So publish a little each day.

%A James Maxwell
%D 1850
%T Quote
%K Maxwell, quote, quotable, probability, inductive inference,
   II, c1850, c185x, c18xx
%X The true logic for this world is the calculus of Probabilities, which
   takes account of the magnitude of the probability which is, or
   ought to be, in any reasonable man's mind.
   [from R u s s e l l and N o r v i g '95, p.458].

%A J. von Neumann
%D 1951
%K Neumann von, quote, pseudo random number generators, RNG, PRNG, c1951, c195x,
   c19xx, vonNeumann, generation, quotable, funny
%X Anyone who considers arithmetical methods of producing random digits is,
   of course, in a state of sin.     [via enews].

%A J. von Neumann
%K Neumann von, quote, quotable, funny, stats, statistics, overfitting,
   over fitting, parameters, c195x, c19xx
%X "with four parameters I can fit an elephant, and with five I can
   make him wiggle his trunk."
   Attributed to J vN by Fermi
   -- [<A HREF="https://statmodeling.stat.columbia.edu/2017/07/22/a-stunned-dyson/">www</A>]['21].

%A J. R. Oppenheimer
%T Quote
%K Oppenheimer Robert, quote, quotable, death, destroyer of worlds,
   Krishna, Arjuna, Bhagwat Gita, atom bomb, atomic, Abomb, WW2, WWII,
   Manhattan Project, Los Alomos, LosAlomos, test, c1945, c194x, c19xx
%X "Now I am become death, destroyer of worlds."
   e.g., utube[<A HREF="https://www.youtube.com/watch?v=dus_M4sn0_I">www</A>]['20].
   [Also search for: Manhattan Project bomb].

%A Blaise Pascal
%D 1656
%T Quote
%K Pascal, quote, quotable, funny, letter, writing, short, shorter, long,
   longer, succinct, brief, brevity, MML, time, busy, Mark Twain
%X Often attributed to Mark Twain, and others, but apparenly due to Pascal:
      "Je n'ai fait celle-ci plus longue parceque je n'ai pas eu le loisir de
      la faire plus courte."
   "I have made this letter longer than usual, because I lack the time to
   make it short."
   Blaise Pascal, Lettres Provinciales (1656-1657), no. 16.
   -- I.M.Richmond, Dept of French, U. W.Ontario  [1991].

%A Plato
%D c. 428-348 BC
%T Quote
%K Plato, quote, quotable, class, classification, feathered, featherless,
   man, Diogenes
%X "Seeing that the human race falls into the same classification as the
   feathered creatures, we must divide the biped class into featherless
   and feathered" - Plato
 and then ...
   "Plato having defined man to be a two-legged animal without feathers,
   Diogenes the Cynic plucked a cock and brought it into the Academy, and said,
   'This is Plato's man.' On which account this addition was made to the
   definition: 'With broad flat nails.'"
                              - From Diogenes Laertius,
                              Lives of Eminent Philosophers, Diogenes, sec.6
   via enews.

%A Drummond Rennie
%D 2010 ?
%T Quote
%K Rennie, quote, quotable, publish, perish, authors, authorship, gift, gifted,
   guest, priority, credit, contribution, publications, papers, Venkatraman
%X "If scientists want to convey this information by the way their names are
   ordered, the method is similar to sending smoke signals, in code, on a dark,
   windy night."
   Attributed to DR by V.Venkatraman in 'Conventions of Scientific Authorship',
   Science, APR, 2010
   -- [<A HREF="https://doi.org/10.1126/science.caredit.a1000039">doi:10.1126/science.caredit.a1000039</A>]['18].
   [Also search for: publish perish].

%A William Shakespeare
%T Let me not to marriage of true minds admit impediments
%K Shakespeare, sonnet 116, sonnet116, CXVI, love, time, sonnets, c15xx, c16xx
%X William Shakespeare (1564 - 1616), Sonnet 116:
      Let me not to the marriage of true minds
      Admit impediments. Love is not love
      Which alters when it alteration finds,
      Or bends with the remover to remove:
      O no! it is an ever-fixed mark
      That looks on tempests and is never shaken;
      It is the star to every wandering bark,
      Whose worth's unknown, although his height be taken.
      Love's not Time's fool, though rosy lips and cheeks
      Within his bending sickle's compass come:
      Love alters not with his brief hours and weeks,
      But bears it out even to the edge of doom.
      If this be error and upon me proved,
      I never writ, nor no man ever loved.

%A Socrates
%T Quote
%K Socrates, Socratic, Plato, wisdom, knowledge, over confidence, overconfident,
   experience, paradox, Dunning Kruger effect, law, zz1019
%X '"I know that I know nothing" is a saying derived from Plato's account of the
   Greek philosopher Socrates. It is also called the Socratic paradox. The
   phrase is not one that Socrates himself is ever recorded as saying.
   This saying is also connected or conflated with the answer to a question
   Socrates (according to Xenophon) or Chaerephon (according to Plato) is said
   to have posed to the Pythia, the Oracle of Delphi, in which the oracle stated
   something to the effect of "Socrates is the wisest."'
   -- [<A HREF="https://en.wikipedia.org/wiki/I_know_that_I_know_nothing">wikip</A>]['19].

%A Elizabeth Taylor (27/2/1932 - 23/3/2011)
%T Quote
%K Taylor, vice, vices, virtue, virtues, annoying, funny, haha, quote, quotable
%X "The problem with people who have no vices is that generally you can
   be pretty sure they're going to have some pretty annoying virtues."
       (? Quoted in The Seven Deadly Sins, Steven Schwartz p.23, 2000 ?)

%A Donald J. Trump
%T D. Trump quotes
%K Trump, DJT, Trumpism, Trumpisms, Trumpery, Trumpistan, Trumped, zzTrump,
   potus, c2017, c201x, c20xx, quote, quotable, funny, ha ha, haha, US, USA,
   America, American, politics, president, Mexico, wall, Russia, politics,
   fake news, fakeNews, newspeak, covid19
%X * "The concept of global warming was created by and for the Chinese
     in order to make U.S. manufacturing non-competitive.",
     Twitter [<A HREF="https://twitter.com/realdonaldtrump/status/265895292191248385?lang=en">6/11/2012</A>].
   * "Trump boasts that he's 'like, really smart' and a
     'very stable genius' amid questions over his mental fitness",
     e.g., see The Washington Post [<A HREF="https://www.washingtonpost.com/news/post-politics/wp/2018/01/06/trump-boasts-that-hes-like-really-smart-and-a-very-stable-genius-amid-questions-over-his-mental-fitness">6/1/2018</A>].
   * "'In the end, Mexico is going to pay for the wall,' the US president
     told supporters at a campaign-style rally in Nashville. ...",
     e.g., see The G [<A HREF="https://www.theguardian.com/us-news/2018/may/29/mexico-president-trump-border-wall-twitter">30/5/2018</A>]['18].
   * "They really like me in the UK", e.g., CNN[<A HREF="http://edition.cnn.com/TRANSCRIPTS/1807/13/cnr.19.html">13/7/2018</A>],
     in fact 10s of 1000s protested against him, e.g., abc[<A HREF="http://www.abc.net.au/news/2018-07-14/brits-turn-up-in-hordes-to-march-at-donald-trump-protest/9993820">14/7/2018</A>].
   * "I don't see any reason why it would be" [Russia that interfered in the
     presidential election], on 16/7/2018, e.g., bbc[<A HREF="https://www.bbc.co.uk/news/world-us-canada-44864739">17/7/2018</A>].
   * "And we're building a wall in Colorado", e.g., bbc[<A HREF="https://www.bbc.com/news/av/50160803/trump-kidding-about-colorado-border-wall">24/10/2019</A>].
   * "I never understood wind. You know, I know windmills very much."
     -- TheG[<A HREF="https://www.theguardian.com/us-news/2019/dec/23/trump-bizarre-tirade-windmills">23/12/2019</A>].
   * "I like this stuff.  I really get it.  People are surprised that I
      understand it.  Every one of these doctors said, 'How do you know
      so much about this?'  Maybe I have a natural ability.  Maybe I should
      have done that instead of running for President. ..."
      in
      'Remarks by President Trump After Tour of the
      Centers for Disease Control and Prevention, Atlanta, GA, 6 March 2020,
      -- wh[<A HREF="https://www.whitehouse.gov/briefings-statements/remarks-president-trump-tour-centers-disease-control-prevention-atlanta-ga/">.gov</A>][7/3/2020].
   * "And then I see the disinfectant where it knocks it [SARS-CoV-2] out in a
     minute. One minute. And is there a way we can do something like that, by
     injection inside or almost a cleaning? So it'd be interesting to
     check that."
     -- bbc[<A HREF="https://www.bbc.com/news/world-us-canada-52407177">24/4/2020</A>].
   * "It is what it is." (covid-19 death toll) -- cnn[<A HREF="https://edition.cnn.com/2020/08/04/politics/trump-covid-death-toll-is-what-it-is/index.html">4/8/2020</A>].
   * "I said, 'You didn't pay, you're delinquent?' No, I would not protect you
     [your country]. In fact, I would encourage them [Russia] to do whatever the
     hell they want. You got to pay. You got to pay your bills."
     -- The_G[<A HREF="https://www.theguardian.com/us-news/2024/feb/11/donald-trump-says-he-would-encourage-russia-to-attack-nato-countries-who-dont-pay-bills">12/2/2024</A>] and see the
        bbc[<A HREF="https://www.bbc.com/news/world-us-canada-68286645">15/2/2024</A>].
   * "I'm going to be a dictator for day one", e.g., [<A HREF="https://www.pbs.org/wnet/preserving-democracy/video/behind-trumps-hold-over-the-gop/">pbs</A>]['24].
   (Also see, 'A Ladybird book about Donald Trump', Oct. 2019,
   $16; uk us isbn:0241422728; uk us isbn13:978-0241422724.)
   [Also search for: Trumpery].

%A Xi Jinping
%K Xi Jinping, c202x, c20xx, China, PRC, CCP, president, Xi Jinping, quote,
   quotable, media, politics
%X * Xi Jinping told senior Communist Party officials it was important to
     present an image of a "credible, loveable and respectable China", according
     to a report by state-run news agency Xinhua.
     -- bbc[<A HREF="https://www.bbc.com/news/world-asia-china-57327177">3/6/2021</A>].
   * The country needed to create a team of professionals and adopt "precise
     communication methods" for different regions, [Xi] said.
     -- reuters[<A HREF="https://www.reuters.com/world/china/chinas-xi-calls-greater-global-media-reach-2021-06-01/">2/6/2021</A>].
   * China's response was "scientific and effective". He told officials to
     "unswervingly adhere to the general policy of dynamic zero-Covid".
     -- The G [<A HREF="https://www.theguardian.com/world/2022/may/06/xi-jinping-attacks-doubters-as-he-doubles-down-on-chinas-zero-covid-policy">6/5/2022</A>].

%A Mark Zuckerberg
%T Zuckerberg quotes
%K Zuckerberg emails, Facebook, www, social media, sharing, quote, quotable,
   c2012, c201x, c20xx, zz0920, UK, privacy
%X "That may be good for the world, but it's not good for us,"
   Zuckerberg wrote in a 2012 email.
   -- [<A HREF="https://www.theguardian.com/technology/2018/dec/05/facebook-emails-analysis-user-data-parliament">The-G</A>][5/12/2018], J.C.Wong.
   [Also search for: Facebook].



%T Computer Models
%A James Hacker
%M JAN
%D 2013
%K c2013, c201x, c20xx, zz0614, quote, quotable, quotation, funny, ha ha, haha,
   computer model, statistical, stats, British, uk, TV, PM, Yes Prime Minister,
   James Hacker, Poisoned Chalice, Europe, euro, global financial crisis, GFC
%X "Computer models, Humphrey, are no different from fashion models -
   seductive, unreliable, easily corrupted and they lead sensible people
   to make fools of themselves." -- PM James Hacker (now David Haig) to
   Humphrey Appleby (now Henry Goodman) in the TV series 'Yes Prime Minister'
   (revived), ep.2, 'The Poisoned Chalice', S01E02, 22 January 2013.
   [Also search for: stats quote].

%T Economists
%T Quote
%K quote, quotable, economist, c19xx, predict, prediction, predicting, economy,
   economics, dismal, stats
%X "An economist is someone who can predict the past, 50% of the time."
   I read it, alas I cannot remember where -- LA.

%T Fortran
%D 19??
%K quote, quotable, programming language, languages, Fortran, c19xx
%X "I don't know what the language of the year 2000 will
   look like, but it will be called Fortran."
   I have seen this attributed to Seymour Cray, Tony Hoare & many others -- LA.


%A M. Nelson
%T Arithmetic Coding + Statistical Modeling = Data Compression
%J Dr. Dobbs J.
%M FEB
%D 1991
%K c1991, c199x, c19xx, zz0916, arithmetic coding, statistical modeling,
   data compression, modelling, quote, quotable
%X "... article first appeared in the February, 1991 issue of Dr. Dobb's J. ..."
   -- [<A HREF="http://marknelson.us/1991/02/01/arithmetic-coding-statistical-modeling-data-compression/">www</A>]['16].
   [Also search for: arithmetic coding compression].


%A L. Menand
%T Notable Quotables
%J The New Yorker
%M FEB
%D 2007
%K views, c2007, c200x, c20xx, zz1119, quotes, quotable, quote, quotations
%X -- [<A HREF="https://www.newyorker.com/magazine/2007/02/19/notable-quotables">19-26/2/2007</A>]['19].


%A C. A. R. Hoare
%T An axiomatic basis for computer programming
%J CACM
%V 12
%N 10
%M OCT
%D 1969
%P 576-583
%K jrnl, CACM, c1969, c196x, c19xx, axiom, axiomatic, proof, precondition,
   postcondition, invariant, verification, correctness

%A C. A. R. Hoare
%T An axiomatic definition of the programming language Pascal
%J Acta Informatica
%V 2
%P 335-355
%D 1973
%K axiomatic, proof, Pascal
%X The axiomatic definition method proposed in reference [5] is extended
   and applied to define the meaning of the programming language Pascal.
   The whole language is covered with the exception of real arithmetic
   and go to statements.

%A A. W. Mazurkiewicz
%T Proving algorithms by tail functions
%J Information and Control
%V 18
%P 220-226
%D 1971
%K jrnl, c1971, c197x, c19xx, continuation
%X tail function of an algorithm descibes all possible
   computations defined by the algorithm.
   Seems to be origin of continuation.

%A R. Milne
%A C. Strachey
%T A Theory of Programming Language Semantics
%I ChapmanHall
%D 1976
%O 2 vols
%K text, book, c1976, c197x, c19xx, textbook, denotational semantics, DS,
   theory
%X Principia Informatica !

%A D. Scott
%T Data types as lattices
%J SIAM Journal of Computing
%V 5
%N 3
%M SEP
%D 1976
%P 522-587
%K jrnl, c1976, c197x, c19xx, denotational semantics, DS, model theory lattice,
   CPO Pw power set power-set lambda calculus  fixed point

%A P. Cousot
%A R. Cousot
%T Abstract interpretation: A unified lattice model for static analysis of
   programs by construction of approximate fixpoints
%J Proc, 4th ACM Symp. on Principles of Prog. Langs.
%P 238-252
%D 1977
%K conf, POPL, FP, c1977, c197x, c19xx, zz0719, abstract interpretation,
   program analysis, programming languages
%X pdf@[<A HREF="https://www.di.ens.fr/~cousot/publications.www/CousotCousot-POPL-77-ACM-p238--252-1977.pdf">ens.fr</A>]['19].
   [Also search for: abstract interpretation].

%A D. S. Scott
%T Logic and programming languages
%J CACM
%V 20
%N 9
%P 634-641
%M SEP
%D 1977
%K logic, denotational semantics, DS,  lambda calculus model lattice, L4Ref,
   jrnl, ACM, CACM, c1977, c197x, c19xx, language, Dana Scott
%X Turing award lecture
   [<A HREF="http://doi.acm.org/10.1145/359810.359826">doi:10.1145/359810.359826</A>]['07]

%A R. D. Tennent
%T The denotational semantics of programming language
%J CACM
%M AUG
%D 1976
%P 437-453
%K CACM, jrnl, c1976, c197x, c19xx, denotational semantics, DS,
   gedanken tutorial introduction
%X good introduction.

%A R. D. Tennent
%T Language design methods based on semantic principles
%J Acta Informatica
%V 8
%P 97-112
%D 1977
%K jrnl, c1977, c197x, c19xx, denotation semantics, DS, orthogonal,
   programming language, orthogonality module, array parameter,
   declaration, L4REF
%X "Two language design methods based on principles derived from the
   denotational approach to prog. lang. semantics are described & illustrated by
   an application to the language Pascal. ...[1] the correspondence between
   parametric & declarative mechanisms, & [2] a principle of abstraction for
   prog. langs adapted from set theory. Several useful extensions &
   generalizations of Pascal emerge by applying these principles, inc. a soln to
   the array parameter problem, & a modularization facility."
   -- [<A HREF="https://doi.org/10.1007/BF00289243">doi:10.1007/BF00289243</A>]['24].

%A F. G. Pagan
%T Formal Specification of Programming Language Semantics
%I PrenticeHall
%D 1981
%K denotational semantics, c1981, c198x, c19xx, DS
%X includes 2LVWG  Attribute Grammars.

%A F. G. Pagan
%T A style for writing the syntactic portions of complete definitions
   of programming languages
%J COMPJ
%V 24
%N 2
%M MAY
%D 1981
%P 143-147
%K COMPJ, c1981, c198x, c19xx

%A F. G. Pagan
%T In interpreter oriented definitions of programming languages
%J COMPJ
%V 19
%N 2
%M MAY
%D 1976
%P 151-155
%K COMPJ, c1976, c197x, c19xx, algol, algol68

%A F. G. Pagan
%T A highly structured interpreter for a Snobol4 subset
%J SPE
%V 9
%P 281-312
%D 1979
%K Snobol Snobol4 semantics interpreter algol algol68

%A F. G. Pagan
%T Algol 68 as a metalanguage for denotational semantics
%J COMPJ
%V 22
%N 1
%M FEB
%D 1979
%P 63-66
%K denotational semantics, DS, algol algol68

%A M. J. C. Gordon
%T The Denotational Description of Programming Languages
%I SpringerVerlag
%D 1979
%K text, book, c1979, c197x, c19xx, semantics, DS, ML, SML, L4REF

%A J. E. Stoy
%T Denotational Semantics the Scott Strachey Approach to Programming
   Language Theory
%I MITpress
%D 1977
%K DS, text, book, c1977, c197x, c19xx
%X hard to get,  [also search for: Denotational Semantics]

%A A. D. McGettrick
%T The Definition of Programming Language
%S Cambridge Computer Science Texts V-11
%I CUP
%D 1980s
%K c198x, c19xx, CUP, text, book, denotational semantics, DS
%X includes various formalisms

%A J. E. Donahue
%T Complementary Definitions of Programming Language Semantics
%S LNCS V 42
%I SpringerVerlag
%D 1976
%K text, book, c1976, c197x, c197xx, axiomatics, denotational semantics, DS,
   Pascal

%A D. Schmidt
%T Denotational semantics
%I Bacon and Allyn
%D 1986
%K text, book, DS, c1986, c198x, c19xx

%A L. C. Paulson
%T A compiler generator for semantic grammars
%M DEC
%D 1981
%I Dept Computer Science, Stanford University
%K denotational semantics, DS, PhD thesis

%A P. D. Mosses
%T Compiler generation using denotational semantics
%J Mathematical Foundations of Computer Science
%D 1976
%I SpringerVerlag
%S LNCS V 45
%K c1976, c197x, c19xx, DS, MFCS, MFCS76

%A F. C. Belz
%A E. K. Blum
%A D. Heimbigner
%T A multi processing implementation oriented formal definition of Ada
   in Semanol
%J Proceedings ACM Symposium on the Ada Programming Language
%M NOV
%D 1980
%K Ada semantics parallel communication Semanol
%W Boston
%P 202-212

%A E. R. Anderson
%A F. C. Belz
%A E. K. Blum
%T Semanol (73) a metalanguage for programming the semantics
   of programming languages
%J Acta Informatica
%V 6
%P 109-131
%D 1976

%A E. A. Ashcroft
%A W. W. Wadge
%T Lucid, a nonprocedural language with iteration
%J CACM
%M JUL
%D 1977
%V 20
%N 7
%P 519-526
%K semantics  single assignment

%A E. A. Ashcroft
%A W. W. Wadge
%T A summary of Lucid for programmers (1981 version)
%R CS-82-57
%I Faculty of Mathematics, University of Waterloo
%D 1982
%K Lucid single assignment
%O (LA has)

%A E. A. Ashcroft
%A W. W. Wadge
%T R for semantics
%J TOPLAS
%V 4
%N 2
%M APR
%D 1982
%P 283-294
%K jrnl, c1982, c198x, c19xx, denotational semantics, DS,
   presciption prescriptive Lucid

%A M. Wand
%T First order identities as a defining language
%J Acta Informatica
%V 14
%P 337-357
%D 1980
%K denotational operational semantics logic algebra first-order

%T Semantics directed compiler generation
%S LNCS V 94
%I SpringerVerlag
%E N. D. Jones
%M JAN
%D 1980
%K semantics denotational, DS, operational translator

%A A. P. Ershov
%T Mixed computation: Potential applications and problems for study
%J Theoretical Computer Science
%V 18
%P 41-67
%D 1982
%K TCS, partial evaluation  mix mixed computation compiler generator

%A N. D. Jones
%A P. Sestoft
%A H. Sondergaard
%T An experiment  in partial evaluation: The generation of a compiler generator
%D 1985
%P 124-140
%B Rewriting Techniques and Applications
%E J. P. Jouannaud
%I SpringerVerlag
%S LNCS
%V 202
%K c1985, c198x, c19xx, partial evaluation, compiler generator, mix,
   mixed computation

%A P. Sestoft
%T The structure of a self-applicable partial evaluator
%P 236-256
%B Programs as Data Objects
%I SpringerVerlag
%S LNCS
%V 217
%D 1986
%E N. D. Jones
%E H. Ganzinger
%K self application partial evaluation compiler generator mix mixed

%A M. J. Beeson
%T Foundations of Constructive Mathematics
%D ?
%K text book foundations theory constructive mathematics
   computability lambda calculus combinators combinatory logic
   s k i

%A E. Astesiano
%A G. Reggio
%T Comparing direct and continuation semantics for concurrent languages
   - revisiting an old problem from a new viewpoint
%P 311-322
%B STACS 87, 4th Annual Symposium on Theoretical Aspects of Computer Science
%I SpringerVerlag
%S LNCS
%V 247
%M FEB
%D 1987
%E F. J. Brandenburg
%E G. Vidal-Naquet
%E M. Wirsig
%W Passau
%K denotational direct continuation vdm semantics, DS,
   concurrent parallel language
   when raise send create process

%A M. J. C. Gordon
%T Register transfer systems and their behaviour
%B Computer Hardware Description Languages and Their Applications
%E M. Breuer
%E R. Hartenstein
%P 23-36
%I North Holland
%D 1981
%K semantics hardware register synchronous
%X register systems defined in denotational semantics style
   memories, gates, combinational and sequential circuits, state, states
   related to CCS

%A N. Francez
%A C. A. R. Hoare
%A D. J. Lehmann
%A W. P. de Roever
%T Semantics of nondeterminism, concurrency and communication
%M AUG
%D 1978
%K nondeterminism, concurrent, parallel, communicate, message
   CSP CCS, theory,
%X input actions, output actions, parallel composition, nondeterministic
   choice, sequential composition.
   trees, trace traces

%A D. A. Watt
%T Executable semantic descriptions
%J SPE
%V 16
%N 1
%P 13-43
%M JAN
%D 1986
%K denotational semantics, DS, ML, executable, semantic algebra

%A J. Diller
%T Modified realization and the formulae as types notion
%B To H. B. Curry: Essays in Combinatory Logic, Lambda Calculus and Formalism
%E J. P. Seldin
%E J. R. Hindley
%I AcademicPress
%D 1980
%P 491-501
%K realizability, constructive mathematics, theory, intuitionistic mathematics
   type, datatype

%A W. A. Howard
%T The formulae as types notion of construction
%B To H. B. Curry: Essays in Combinatory Logic, Lambda Calculus and Formalism
%E J. P. Seldin
%E J. R. Hindley
%I AcademicPress
%D 1980
%P 479-490
%K realizability, constructive mathematics, theory, intuitionistic mathematics
   type, datatype

%A F. Nielson
%T Strictness analysis and denotational abstract interpretation
%J Information and Control
%V 76
%N 1
%M JAN
%D 1988
%P 29-92
%K abstract interpretation, strict, strictness, symbolic evaluation,
   partial evaluation, semantics, DS, non-standard semantics
%X long paper !

%A D. A. Schmidt
%T Detecting global variables in denotational specifications
%J TOPLAS
%V 7
%N 2
%M APR
%D 1985
%P 299-310
%K semantics, DS, single threading, optimize, optimise, imperative,
   side effect, functional, applicative
%X sufficient criteria given for replacing all occurrences of the store
   argument in a denotational semantics by a single global variable.
   useful for transforming semantics to compilers and interpreters
   for imperative machines, for optimizing applicative programs

%A P. Sestoft
%A H. Sondergaard
%T A bibliography on partial evaluation
%J Sigplan
%V 23
%N 2
%M FEB
%D 1988
%P 19-27
%K c1988, c198x, c19xx, partial evaluation, compiler compiler, mix,
   mixed computation

%A A. Glacalone
%A T. W. Doeppner
%A M. J. Braca
%T Towards a formally based programming environment
%J Integrated Interactive Computing Systems
%I North Holland
%E P. Degano
%E E. Sandwell
%D 1983
%P 363-374
%K programming environment, shell, pipe, CCS
%X formal system to manipulate spec's of modules and
   implementation environment.
   based on CCS and inspired by Unix shell.

%A Z. Manna
%A A. Shamir
%T The optimal approach to recursive programs
%J CACM
%V 20
%N 11
%M NOV
%D 1977
%P 824-831
%K optimal fixed point, recursion, recursive

%E D. H. Pitt
%E A. Poigne
%E D. E. Rydeheard
%T Category Theory and Computer Science
%I SpringerVerlag
%S LNCS
%V 283
%M SEP
%D 1987
%K category theory

%T GRAAL: a functional programming system with uncurryfied combinators
   and its reduction machine
%A P. Bellot
%B ESOP 86
%S LNCS
%V 213
%I SpringerVerlag
%P 82-98
%O European Symposium on Programming, Proceedings
%M MAR
%D 1986
%W Saarbrucken, Federal Republic of Germany
%K GRAAL, functional programming, FP, applicative, uncurried, ski, ESOP ESOP86

%T A safe approach to parallel combinator reduction
%A C. L. Hankin
%A G. L. Burn
%A S. L. Peyton Jones
%B ESOP 86
%S LNCS
%V 213
%I SpringerVerlag
%P 99-110
%M MAR
%D 1986
%O European Symposium on Programming, Proceedings
%W Saarbrucken, Federal Republic of Germany
%K SKI, functional programming, FP, combinators, parallel, ESOP ESOP86

%T Design and implementation of a generic, logic and functional programming
   language
%A Didier Bert
%A Rachid Echahed
%B ESOP 86
%S LNCS
%V 213
%I SpringerVerlag
%P 119-132
%D 1986
%O European Symposium on Programming, Proceedings
%M MAR
%W Saarbrucken, Federal Republic of Germany
%K functional, FP, applicative, language, prolog, LP, FLP, LFP, ESOP ESOP86

%T Rewriting with a nondeterministic choice operator: from algebra to proofs
%A Stephane Kaplan
%B ESOP 86
%S LNCS
%V 213
%I SpringerVerlag
%P 351-374
%D 1986
%O European Symposium on Programming, Proceedings
%M MAR
%W Saarbrucken, Federal Republic of Germany
%K nondeterminism, or, choice, ESOP ESOP86

%T Pragmatic aspects of two-level denotational meta-languages
%A Hanne R Nielson
%A Flemming Nielson
%B ESOP 86
%S LNCS
%V 213
%I SpringerVerlag
%P 133-143
%D 1986
%O European Symposium on Programming, Proceedings
%M MAR
%W Saarbrucken, Federal Republic of Germany
%K two level, denotational semantics, DS, compile time, run time, compiletime,
   runtime, ESOP ESOP86

%A G. F. Stewart
%T An algebraic model for string patterns
%J 2nd ACM Symposium on Principles of Programming Languages
%M JAN
%D 1975
%P 167-184
%K algebra, string, pattern, snobol, POPL, POPL2, POPL75

%A R. Weyhrauch
%A R. Milner
%T Program semantics and correctness in a mechanized logic
%J First USA-Japan Computer Conference
%D 1972
%P 384-392
%K LCF, logic for computable functions, ML, SML

%A M. Hennessy
%T The Semantics of Programming Languages:
   an elementary introduction using structural operational semantics
%I Wiley
%D 1990
%K c1990, c199x, c19xx, book, text, operational semantics

%A G. Winskel
%T The Formal Semantics of Programming Languages: An Introduction
%I MITpress
%S Foundations of Computing series
%M FEB
%D 1993
%P 384
%K text, book, denotational, DS, programming language definition
%X us isbn:0-262-23169-7;  WINFH              us$40.00.

%A A. W. Appel
%T Semantics-Directed Code Generation
%J Twelfth ACM Symp. on Principles of Programming Languages
%I ACM Press
%C New York
%P 315-24
%D 1985
%K compile, compiler, code generation, semantics, POPL, POPL12, POPL85
%X <!-- email: appel@dynastar.princeton.edu (Andrew Appel)   '94 --> .
   <A HREF="http://www.cs.Princeton.EDU:80/faculty/appel/papers/sdcg.ps">Appel</A>

%A R. A. Frost
%T Constructing programs as executable attribute grammars
%J COMPJ
%V 35
%N 4
%P 376-389
%D 1992 ?
%K attribute grammar, AG, semantics, code generation, compile compiler,
   functional programming, FP, lazy
%X via: Richard Frost
   <!-- email: richard@CS.UWindsor.Ca  Wed Apr  6 23:32:19 1994 --> .
        School of Computer Science, University of Windsor, ONT N9B 3P4, CANADA

%A P. D. Mosses
%T Action Semantics
%I CUP
%S Tracts in Theor. Comp. Sci.
%V 26
%P 372
%D 1992
%K book, text, c1992, c199x, c19xx, programming languages,
   denotational operational
%X "A modular hybrid of denotational and operational semantics, developed
   since '85, with D. W@tt (Gl@sgow) 6-'00 ... "
   [<A HREF="http://www.brics.dk/~pdm/">home</A>]['04]
   U Wales, Swansea from '05.
   Also see MSOS [<A HREF="http://www.daimi.au.dk/jwig-cnn/dSem/">course</A>]['05]

%A R. Cartwright
%A M. Felleisen
%T Extensible denotational language specifications
%J Symposium on Theoretical Aspects of Computer Software
%W Sendai
%M APR
%D 1994
%P ???-???
%O Extended direct semantics, TR 90-105 Rice University, Jan '90
%K conf, STACS, STACS94, TACS TACS94, TR105 TR 90 105,
   direct denotational semantics, DS, extend, extended, orthogonal,
   interpreter, Scheme, control
%X authors at Dept. Comp. Sci., Rice University, Houston, Texas TX 77251 1892
          and Dept. Comp. Sci., CMU, Pittsburgh, PA 15213 3890
   Traditional denotational semantics assigns radically different meanings to
   one and the same phrase depending on the rest of the programming language.
   [eg.] If the language is purely functional, the denotation of a numeral is
   a function from environments to integers. But, in a functional language
   with imperative control operators, a numeral denotes a function from
   environments AND continuations to integers.
    ...
   accomodate orthogonal extensions of a language without changing the
   denotations of existing phrases.
    ...
   In general, the denotation of a phrase in a functional language is always
   a projection of the denotation of the same phrase in the semantics of an
   extended language - no matter what the extension is. Based on extended
   direct semantics, it is also possible to construct interpreters for complete
   languages by composing interpreters for language fragments.
   29 refs

%T Partial Evaluation
%E O. Danvy
%E R. Glck
%E T. Thiemann
%I SpringerVerlag
%S LNCS
%V 1110
%P 514
%D 1996
%K LNCS, book, conf, programming languages, mix, mixed, zz0996
%X ... International Seminar on Partial Evaluation held in Dagstuhl Castle,
   Germany in February 1996. The 24 strictly refereed full papers included
   evaluate the progress achieved in the field during the last decade. ...
   uk us isbn:3-540-61580-6.
   <A HREF="mailto:glueck@diku.dk">Robert Glueck</A> [9/'96].

%A A. Gordon
%A A. Pitts
%T Higher Order Operational Techniques in Semantics
%I CUP
%D 1998
%P 398
%K book, text, CUP, programming language, semantics, zz0498
%X stg40, au$98.50, uk us isbn:0521631688.

%A J. C. Reynolds
%T Theories of Programming Languages
%I CUP
%D 1998
%P 500
%K book, text, theory, semantics, computer, language, definitions,
   computing, CS, CSci, zz0399
%X uk us isbn:0-521-59414-6;  us$50.

%A C. A. R. Hoare
%T The ideal of program correctness
%J COMPJ
%V 50
%N 3
%P 254-260
%D 2007
%K COMPJ, jrnl, tony, c2007, c200x, c20xx, verification, software engineering
%X 3rd Computer J. Lecture
   "The ideal of verified software has long been the goal of research in
   Computer Science. This article argues that the time is ripe to embark on a
   Grand Challenge project to construct a program verifier, based on a sound &
   complete theory of programming, and evaluated by experimental application to
   a large and representative sample of useful computer software. ..."
   -- [<A HREF="dx.doi.org/10.1093/comjnl/bxl078">doi:10.1093/comjnl/bxl078</A>]['07].


%A L. Paccioli
%T Summa de Arithmetic, Geometria et Proportionalita
%D 1494
%K book, 15C, Luca Paccioli, dice, balla, odds, risk, probability,
   c1494, c149x, c14xx
%X "... A and B are playing a fair game of balla. They agree to continue
   until one has won six rounds. The game actually stops when A has won
   five and B three. How should the stakes be divided?"
    - from  B e r n s t e i n  "Against the..." [c1996].

%A G. Cardano
%T Liber de Ludo Aleae (Book on Games of Chance)
%D 1663
%K book, Girolamo Cardano, dice, probability, risk, odds, c1663, c166x, c16xx
%X He wrote Ars Magna (the Great Art) in 1545.
   Wrote L' de L' A in 1525, rewrote 1565, published after his death 1663.
    - from B e r n s t e i n "Against the..." [c1996].

%A J. Graunt
%T Natural and Political Observations made upon the Bills of Mortality
%D 1662
%K book, William Petty, birth, death, life tables, mortality,
   life expectancy, risk, c1662, c166x, c16xx
%X data for London 1604-1661.
    - from B e r n s t e i n "Against the..." [c1996] pp.75.

%A D. Bernoulli
%T Specimen Theoriae Novae de Mensura Sortis
   (Exposition of a New Theory on the Measurement of Risk)
%J Papers of the Imperial Acad. Sci., St. Petersburg
%D 1738
%O Trans. L. Sommer, Econometrica, 22 pp.23-26 1954
%K Daniel Bernoulli, probability, risk, expected gain, expectation,
   utility, uncertainty, ducats, c1738, c173x, c17xx
%X In real life, utility is not the same as (math) expected gain.
    - from B e r n s t e i n "Against the..." [c196] pp.104.

%A J. Bernoulli
%T Ars Conjectandi (the Art of Conjecture)
%D 1713
%K book, Jacob Bernoulli, probability, confidence, level, interval,
   prior, a priori, apriori, a posteriori, aposteriori,
   moral certainty, uncertainty, risk, c1713, c171x, c17xx
%X ed. by N.B.;  pub. after J.B.'s death.
    - from B e r n s t e i n "Against the..." [c1996] pp.118.

%A A. de Moivre
%T The Doctrine of Chances
%D 1718, 1738, 1756
%K Abraham de Moivre, deMoivre, probability, risk,
   normal distribution, Gaussian, 18C, c1718, c1738, c1756, c171x, c17xx
%X ... de M's distribution is known today as the normal curve...
    - from B e r n s t e i n "Against the..." [c1996] pp.126.

%A Sir John Sinclair
%T Statistical Account of Scotland
%D 1791-1799
%K stats, book, zz0202, c1791, c179x, c17xx, Thurso, Dunbartonshire, Scotland,
   GB, UK, statistics, statistical, word, origin, history
%X JS (1754 - 1835) born Thurso Castle.
   ... had heard ["statistics"] from the Germans who used it to refer to a
   collection of facts about the political strength of a country.
   - [<A HREF="http://edina.ed.ac.uk/StatAcc/shortintro.html">www</A>][1/'02]
   For a social and economic record of the parishes of Dunbartonshire,
   together with masses of statistical material, see Sir John Sinclair's
   Statistical Account of Scotland [21 vols] which was compiled in the 1790s.
   Follow-up works to this were the New Statistical Account (also known
   as the Second Statistical Account) which was prepared in the 1830s and
   1840s; and more recently the Third Statistical Account which has been
   prepared since the Second World War. --
   Online@[<A HREF="http://edina.ac.uk/cgi/StatAcc/StatAcc.cgi">Stat.Acc.S.</A>][1/'02].

%A P. S. Laplace
%T Essai philosophique des probabilites
%D 1814
%O introduction in Theorie analytique des probabilites.
%K probability, statistics, stats, history, c1814, c181x, c18xx, 19C
%X ref from vonMises l957 ... point of view of unlimited determinism ...
   Pierre Simon (later Marquis de) Laplace 1749-1827.

%A P. S. Laplace
%T Theorie analytique des probabilites
%I Mme Ve Courcier (Paris)
%P 850
%D 1820
%K book, text, probability, c1820, c182x, c18xx, 19C, history
%X @[<A HREF="http://www.archive.org/details/theorieanaldepro00laplrich">arch'.org</A>]['10].
   Pierre Simon (later Marquis de) Laplace 1749-1827.

%A S. D. Poisson
%T Recherches sur la probabilite des judgements en matiere criminelle et
   en matiere civile
%D 1837
%K book, c1837, c183x, c18xx, 19C, probability, stats, statistics, history,
   law, justice, criminal, civil, court, courts
%X see Ch5, from vonMises l957.
   Simeon Denis Poisson 1781-1840.

%A C. S. Peirce
%T The Probability of Induction
%J Popular Sci. Monthly
%V 12
%P 705-718
%M APR
%D 1878
%O 'The Essential Peirce, Volume 1: Selected Philosophical Writings' (1867-1893)
   N. Houser and C. Kloesel (eds), IndianaUP, 1992
%K c1878, c187x, c18xx, zz0214, Sanders Peirce, philosophy, belief, evidence,
   information theory, weight, weigh, chance, odds, log, probability, induction,
   inference, doctrine of chances, science, stats, statistics, Bayesian,
   Charles Sanders Peirce
%X "... Any quantity which varies with the chance might, therefore, serve
   as a thermometer for the proper intensity of belief. ...
   ... Now there is one quantity which, more simply than any other
   fulfills these conditions; it is the logarithm of the chance. ... It is
   that our belief ought to be proportional to the weight of evidence, ..."
   -- pp.158-159, 'The probability of induction,' 1878,
      in, uk us isbn:0253207215; uk us isbn13:978-0253207210.
   See [<A HREF="http://www.peirce.org/writings.html">peirce.org</A>]['14].
   [Also search for: IJGood Turing ban] and
   [also search for: information theory].

%A F. Galton
%T Hereditary Genius: An Inquiry into Its Laws and Consequences
%D 1869
%I Macmillan, London
%K Francis Galton, eugenics, 19C, c1869, c186x, c18xx, regression to the mean,
   quality, intelligence, stats, statistics
%X eugenics c1883.
   "... eminently gifted mean are raised as much above mediocrity as
   idiots are depressed below it ..."
   -- from B e r n s t e i n "Against the..." [c1996] pp.163.
   "I propose to show in this book that a man's natural abilities are derived
   by inheritance, under exactly the same limitations as are the form and
   physical features of the whole organic world. Consequently, as it is easy,
   notwithstanding those limitations, to obtain by careful selection a
   permanent breed of dogs or horses gifted with peculiar powers of running, or
   of doing anything else, so it would be quite practicable to produce a
   highly-gifted race of men by judicious marriages during several consecutive
   generations. ..."
   -- pdf@[<A HREF="http://galton.org/books/hereditary-genius/">galton.org</A>]['14],
      @[<A HREF="http://books.google.com.au/books/about/Hereditary_genius.html?id=BngwYJc1p94C">googlebooks</A>].
   (And 2014, hb us$50; uk us isbn:1494154323; uk us isbn13:978-1494154325.)

%A F. Galton
%T Inquiries into Human Faculty and Development
%I Macmillan, London
%D 1883
%K Regression to the mean, Reversion to the mean, Francis Galton, eugenics,
   probability, statistics, stats, distribution, 19C, c1883, c188x, c18xx,
   quality, intelligence
%X ... the child inherits partly from his parents, partly from his ancestry.
   ... The law is even handed ...  If it discourages the extravagant
   expectations of gifted parents that their children ... discountenances
   extravagant fears ...
   - from B e r n s t e i n "Against the..." [c1996] pp.167.

%A F. Galton
%T Section H. Anthropology. Opening Address by Francis Galton
%J Nature
%V 82
%P 507-510
%D 1885
%K views, c1885, c188x, c18xx, zz1117, regression, stats
%X Contains the first use of the term 'regression' according to David (1995).
   See pdf@[<A HREF="https://doi.org/10.1038/032502a0">doi:10.1038/032502a0</A>]['17],
       pdf@[<A HREF="https://www.nature.com/nature/journal/v32/n830/pdf/032502a0.pdf">n'ture</A>]['17].

%A J. Bertrand
%T Calcul des probabilites
%D 1888
%K Bertrand, paradox, Bertrands, c1888, c188x, c18xx, probability, prior,
   equilateral triangle, circle, arc, side, longer, puzzle, geometry,
   geometric, Bayesian
%X Includes Bertrand's paradox:
   Consider an equilateral triangle inscribed in a circle. Suppose a chord of
   the circle is chosen at random. What is the probability that the chord is
   longer than a side of the triangle?
   1. random endpoints.  Rotate the triangle so an endpoint is a vertex.
      The ans is 1/3.
   2. random radius.  Choose a point on the radius and construct a chord
      thru the pt and perp to the radius.  Rotate triangle so a side is
      parallel to the chord; the side bisects the radius.
      The ans is 1/2.
   3. random midpoint.  Choose a pt in the circle.  Construct a chord with the
      pt as its midpoint. The chord is longer than a side if the midpoint is
      inside a circle inscribed in the triangle (& 1/2 dia of the orig circle).
      The ans is 1/4.  (areas, (1/2)**2=1/4)
   How can this be?!
   (Well of course it all comes down to different prob. distributions over
   "the random chord", or equivalently its midpoint.)
   -- [<A HREF="http://en.wikipedia.org/wiki/Bertrand%27s_paradox_(probability)">wikip</A>]['10].

%A F. Galton
%T Kinship and correlation
%J North American Review
%V 150
%P 419-431
%D 1890
%K jrnl, c1890, c189x, c18xx, Gal90, Gal89, zz1117, Galton, kinship, heredity
%X Reprinted in Statist. Sci., Vol.4, No.2, 1989, pp.81-86,
   [<A HREF="https://doi.org/10.1214/ss/1177012581">doi:10.1214/ss/1177012581</A>]['17],
   1177012581@[<A HREF="https://projecteuclid.org/euclid.ss/1177012581">eucl'd</A>]['17],
   2245330@[<A HREF="http://www.jstor.org/stable/2245330">Jstor</A>]['17].

%A V. Pareto
%T Cours d'Economie Politique
%I Droz:Geneva
%D 1896
%K Pareto's, Paretos, law, probability distribution, c1896, c189x, c18xx
%X From a ref in a 2OO3 paper by W. L i;   also see  Z i p f.

%A P. Jaccard
%T Etude comparative de la distribution florale dans une portion des Alpes et
   des Jura
%J Bulletin de la Societe vaudoise des sciences naturelles
%V 37
%P 547-579
%D 1901
%K jrnl, c1901, c1902, c19xx, zz1220, Jaccard index, Tanimoto coefficient,
   distance, similar, similarity, classification, plants, flowers, attributes,
   features, stats, search, chemical compound
%X "... Jaccard index = Tanimoto index, but J_distance != T_distance ..."
   -- JI@[<A HREF="https://en.wikipedia.org/wiki/Jaccard_index">wikip</A>]['20].

%A K. Pearson
%T On lines and planes of closest fit to systems of points in space
%J Philosophical Magazine
%V 2
%N 11
%P 559-572
%D 1901
%K jrnl, c1901, c190x, c19xx, principal components analysis, PCA, covariance,
   singular value decomposition, SVD, eigenvalue decomposition, EVD,
   total squared reconstruction error, TLS, TLSE
%X Also see
   "... data matrix, X, with zero empirical mean (sample mean subtracted) ...
   X has 'n' rows (data) and 'k' columns (variables) ...
   loadings (unit vector) w_(k)=(w_1,..,w_p)_(k), map each row X_(i) to
   princ. comp. scores t_(i)=(t_1,...,t_p)_(i) where t_k(i)=x_(i).w_(k) s.t. the
   variables of t successively inherit the maximum possible variance from x ...
   w_(1)=argmax_||w||=1 {SUM_i (t_1)_(i) **2} = argmax_||w||=1 (x_(i).w)**2 ...
   kth component found by subtracting the first k-1 principal comps. from X ...
   [so] T=XW where W is a pxp matrix whose cols are the eigenvectors of X^T X...
   Keeping only the first L principal components ... T_L=X W_L (n rows, L cols)
   ... minimising total squared reconstr. error ||T-T_L||**2. ...
   1st p.c. ~ line through the mean and minimizes the sum of squares of the
   distances of the points from the line ..."
   -- PCA@[<A HREF="http://en.wikipedia.org/wiki/Principal_components#cite_note-1">wikip</A>]['13].
   [Also search for: principal components PCA].

%A Student
%T The probable error of a mean
%J Biometrika
%V 6
%N 1
%P 1-25
%D 1908
%K W.S.Gosset, jrnl, c1908, c190x, c19xx, zz0408, stats, normal, Gaussian,
   Student's t-distribution, students, probability, tDistribution
%X 'Any experiment may he regarded as forming an individual of a "population"
   of experiments which might he performed under the same conditions. A series
   of experiments is a sample drawn from this population. ...'
   By William Sealy Gosset writing as "Student".
   -- [<A HREF="http://www.york.ac.uk/depts/maths/histstat/student.pdf">pdf@york</A>]['08],
   &  [<A HREF="http://biomet.oxfordjournals.org/cgi/reprint/6/1/1">subscription</A>]['08].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Continuous/T/">t-Distn</A>].)

%A F. Galton
%T Kantsaywhere
%D 1910 +/-
%K novel, c1910, c190x, c19xx, zz1016, Sir Francis Galton, eugenic, eugenics,
   utopian, Kantsaywhere, Allfancy, archive, UCL
%X "... UCL Special Collections holds the manuscript fragment of Sir Francis
   Galton's unpublished utopian novel The Eugenic College of Kantsaywhere
   (c.1910), part of the Galton Archive ...  presented as 'Extracts from the
   J. of the late Professor I. Donoghue'. Donoghue, from Dunno Weir, is a Prof.
   of vital statistics who arrives in Kantsaywhere and submits to a series
   of examinations for a eugenics degree in order to be eligible to marry the
   object of his affections, Miss Allfancy. ..."
   -- [<A HREF="http://www.ucl.ac.uk/library/special-collections/kantsaywhere">ucl</A>]['16],
      [<A HREF="http://www.ucl.ac.uk/library/special-coll/ksw.shtml">ucl</A>][2011].
   [Also search for: Francis Galton].

%A J. M. Keynes
%T Treatise on Probability
%D 1921
%K stats, statistics, foundations, c1921, c192x, c19xx, subjective,
   subjectivist
%X ref from vonMises l957:  Treatise on Probability, London, 1921.

%A R. V. L. Hartley
%T Transmission of information
%J Bell System Technical J.
%V 7
%N 3
%P 535-563
%D 1928
%K jrnl, c1928, c192x, c19xx, Hartley, ban, deciban, unit, information theory,
   data communication, transmission, Shannon
%X "Quantitative measure of information is developed, based on physical as
   contrasted with psychological considerations; how rate of transmission of
   this information over system is limited by distortion resulting from storage
   of energy is discussed from transient viewpoint; several illustrations of
   application of this principle to practical systems; in case of picture
   transmission and television, special variation of intensity is analyzed by
   steady-state method."
     ('In the opening paragraph of his landmark paper, "A Math. Theory of
     Comm'n", Shannon credits Hartley's "Transmission of Info.", and work by
     Nyquist, as forming the basis for a general theory of communication.')

%A R. von Mises
%T Probability Statistics and Truth
%I Springer
%D 1928
%O orig. in German; in English by George Allen & Unwin 1957; Dover 1981
%K book, text, foundations, theory, probability, stats, c1928, c192x, c19xx,
   vonMises, history, 1957, c1957, frequencies, frequentist, collectives,
   zzOSP, zOSP04, distribution, statistics
%X <!-- Ross K' copy -->  Six lectures on the foundations of
   probability and statistics.  Favours Bayes;  for only *limited* use of
   max. likelihood;  gives Fisher a "serve"  -- see p.157.
   2nd rev. English ed, NY, Dover, 1981, ...
   2nd ed 1981, us$10; uk us isbn:0486242145; uk us isbn13:978-0486242149.

%A J. Todhunter
%T A History of the Mathematical Theory of Probability, from the time of
   Pascal to that of Laplace
%I G.E.Stechert ?
%C N.Y.
%D 1931
%K book, probability, stats, statistics, theory, foundations,
   c1931, c193x, c19xx
%X ref in vonMises p227 l957.

%A H. Jeffreys
%T Scientific Inference
%I Cambridge
%D 1931
%K book, probability, stats, statistics, learning, c1931, c193x, c19xx
%X ref in vonMises p23O l957 "esp. pp.8-35".

%A A. Kolmogorov
%T Grundbegriffe der Wahrscheinlichkeitsrechnung
   (= Foundations of the Theory of Probability)
%I Springer
%D 1933
%K book, text, c1933, c193x, c19xx, probability, theory, axioms, foundations,
   history
%X 1933: Grundbegriffe der Wahrscheinlichkeitsrechnung, Berlin, J.Springer.
   Trans. 1956: Foundations of the Theory of Probability,
     (2nd ed.). New York: Chelsea.
     2nd ed 1956; uk us isbn:0828400237;
   and [<A HREF="http://www.mathematik.com/Kolmogorov/index.html">www</A>].
   (Also see: Publications of A. N. Kolmogorov,
     Ann. Probab., 17(3), pp.945-964, 1989.
     Full-text: Open access PDF File (2110kB);
   -- [<A HREF="http://projecteuclid.org/euclid.aop/1176991252">p.e.</A>]['10],
      [<A HREF="http://dx.doi.org/10.1214/aop/1176991252">doi:10.1214/aop/1176991252</A>]['10].)

%A E. Anderson
%T The irises of the Gaspe Peninsula
%J Bulletin of the American Iris Soc.
%V 59
%P 2-5
%D 1935
%K jrnl, Fisher's, Fishers, Iris data set, dataset, stats, statistics,
   numerical taxonomy, species L. Versicolor, L. Verginica, L. Setosa,
   c1935, c193x, c19xx
%X [Also search for: Fisher c1936]
   -- [<A HREF="ftp://ftp.ics.uci.edu/pub/machine-learning-databases/iris/">iris</A>][11/'04],
   at [<A HREF="http://www.ics.uci.edu/~mlearn/MLSummary.html">UCI</A>][11/'04].
   (Also see
   [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_5">doi:10.1007/978-3-319-76433-7_5</A>] on discriminating, and
   [<A HREF="http://www.irises.org/">AIS</A>]['05].)

%A P. C. Mahalanobis
%T On the generalised distance in statistics
%J Proc. of the Nat. Inst. of Sci. of India
%V 2
%N 1
%P 49-55
%D 1936
%K stats, c1936, c193x, c19xx, zz0213, Gaussian, Mahalanobis distance,
   distances
%X [<A HREF="http://www.new.dli.ernet.in/rawdataupload/upload/insa/INSA_1/20006193_49.pdf">.in</A>]['03],
   [<A HREF="http://en.wikipedia.org/wiki/Mahalanobis_distance">wikip</A>]['13].
   [Also search for: Mahalanobis distance].

%A E. Anderson
%T The species problem in Iris
%J Ann. Missouri Bot. Gard.
%V 23
%P 457-509
%D 1936
%K irises, iris, flower, flowers, petal, sepal, Fisher, stats, data set,
   c1936, c193x, c19xx
%X -- 2394164@[<A HREF="http://www.jstor.org/stable/2394164">Jstor</A>]['16].
   Also see [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_5">doi:10.1007/978-3-319-76433-7_5</A>] on discriminating.

%A R. A. Fisher
%T The use of multiple measurements in taxonomic problems
%J Annals of Eugenics
%V 7
%N II
%P 179-188
%D 1936
%K jrnl, RAFisher, Iris data set, dataset, c1936, c193x, c19xx, stats,
   statistics, numerical taxonomy, species, irises, problem, classes,
   classification, clustering,  linear discriminant analysis, LDA
%X "When two or more populations have been measured in several characters,
   x1,...,x8, special interest attaches to certain linear fns of the
   measurements by which the popns are best discriminated. ... use has already
   been made of this fact in craniometry ... . In the present paper the
   application of the same principle will be illustrated on a taxonomic problem;
   some questions connected with the precision of the processes employed will
   also be discussed."
   -- [<A HREF="http://dx.doi.org/10.1111/j.1469-1809.1936.tb02137.x">doi:10.1111/j.1469-1809.1936.tb02137.x</A>]['16].
   [Also search for: Anderson Iris c193x]
      "... fifty plants each of the 2 species [IS] and [IVe] ...  measured
      by Dr E. Anderson to whom I am indebted for the use of the data. ..."
      (The table includes a 3rd species, IVi, which comes in later, p.185.)
   -- [<A HREF="http://www.library.adelaide.edu.au/digitised/fisher/138.pdf">paper</A>]['05].
   (Also see
   [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_5">ch-5</A>] and
   [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_8">ch-8</A>] of book.)

%A J. Neyman
%T Outline of a theory of statistical estimation based on the classical theory
   of probability
%J Philosophical Trans. of the Royal Society of London
%S A
%V 236
%N 767
%P 333-380
%M AUG
%D 1937
%K jrnl, c1937, c193x, c19xx, stats, statistics, probability, inference,
   parameter, estimation, problem, estimate, data, experiment, science,
   confidence interval, intervals, frequentist, foundations
%X "We shall distinguish two aspects of the problem of estimation: (i) the
   practical & (ii) the theoretical. ..."
   -- @[<A HREF="http://www.jstor.org/stable/91337">Jstor</A>]['11].

%A M. Kendall
%T A new measure of rank correlation
%J Biometrika
%V 30
%N 1/2
%P 81-93
%M JUN
%D 1938
%K jrnl, tau, c1938, c193x, c19xx, stats, partially sorted, partial, ordering,
   ranking, concordant, discordant, disorder, pair, pairs, Kendalls, index of,
   ranks, top k list, lists, distance, permutation
%X -- [<A HREF="http://links.jstor.org/sici?sici=0006-3444%28193806%2930%3A1%2F2%3C81%3AANMORC%3E2.0.CO%3B2-G">paper@jstor</A>]['07].
   "... tau = 2P/(n(n-1)/2)-1 = 4P/(n(n-1))-1
   where n is the number of items, and P is the sum, over all the items,
   of items ranked after the given item by both rankings. ..."
   -- [<A HREF="http://en.wikipedia.org/wiki/Kendall's_tau">wikip</A>]['07]
   Also see: M.Kendall, Rank Correlation Methods, Charles Griffin Ltd., '48.
   [Also search for: permutation rank distance].

%A F. Benford
%T The law of anomalous numbers
%J Proc. Amer. Philosophical Soc.
%V 78
%N 4
%P 551-572
%M MAR
%D 1938
%K jrnl, c1938, c193x, c19xx, zz0914, Benford's law, Benfords, Newcomb,
   number, numbers, leading, first, digit, digits, law, one, nine
%X "It has been observed that the first pages of a table of common logarithms
   show more wear than do the last pages indicating that more used numbers
   begin with the digit 1 than with the digit 9. ..."
   -- 984802@[<A HREF="http://www.jstor.org/stable/984802">Jstor</A>]['14].
   Also see
     "... one occurs as the leading digit about 30% of the time ...
     goes back to 1881, when the American astronomer Simon Newcomb noticed that
     in log tables ... the earlier pages ... were much more worn than the
     other pages ..."
   -- B@[<A HREF="http://en.wikipedia.org/wiki/Benford%27s_law">wikip</A>]['14].

%A A. Church
%T On the concept of a random sequence
%J Bull. of the Amer. Math. Soc.
%V 46
%N 2
%P 130-135
%D 1940
%K jrnl, c1940, c194x, c19xx, zz0214, random sequence, string, randomness,
   vonMises, vonMises
%X "... It is therefore suggested that this defn of effective calculability
   be employed in order to define a random sequence as follows:
   An infinite seq. ax, a2, ... of O's and 1's is a random sequence
   if the two following conditions are satisfied :
   (1) If f(r) is the number of 1's among the first r terms of a1, a2, ...
       then f(r)/r approaches a limit p as r approaches infinity.
   (2) If phi is any effectively calculable fn of +ve ints.,
       if b_i = 1 , b_n+i = 2b_n-a_n, c_n = phi(b_n), & the ints. n such that
       c_n = 1 form in order of magnitude an infinite sequence n_1, n_2, ...,
       and if g(r) is the number of 1's among the first r terms of
       a_n1, a_n2, ..., then g(r)/r approaches the same limit p as
       r approaches infinity. ..."
   -- 1183502434@[<A HREF="http://projecteuclid.org/euclid.bams/1183502434">projecteuclid</A>]['14].

%A R. A. Fisher
%T The negative binomial distribution
%J Annals of Eugenics
%V 11
%N 1
%P 182-187
%D 1941
%K jrnl, c1941, c194x, c19xx, zz1017, RAFisher, Fisher, information matrix, F,
   informationMatrix, max likelihood, second derivatives, stats, statistics, II,
   frequentist, Edgeworth
%X "... (q-p)^{-k}, q=1+p, k positive ...".
   David (1995) nominates this paper as having the first(?)
   use of the term "(Fisher) Information Matrix".
   -- [<A HREF="https://doi.org/10.1111/j.1469-1809.1941.tb02284.x">doi:10.1111/j.1469-1809.1941.tb02284.x</A>]['17].
   [Also search for: David terms statistics].
   (*But also read,
      "... The Fisher information was discussed by several early statisticians,
      notably F.Y.Edgeworth. [E.g.,] Savage says: 'In it [Fisher information],
      he [Fisher] was to some extent anticipated (Edgeworth 1908-9 esp. 502,
      507-8, 662, 677-8, 82-5 & references he [Edgeworth] cites including
      Pearson & Filon 1898 [...]).' There are a number of early historical
      sources & a number of reviews of this early work. ..."
      -- [<A HREF="https://en.wikipedia.org/wiki/Fisher_information#History">wikip</A>][10/2017].*)

%A G. Polya
%T Heuristic reasoning and the theory of probability
%J Amer. Math. Monthly
%V 48
%P 450-465
%D 1941
%K jrnl, c1941, c194x, c19xx, stats, statistics, learning, inference, II, AI
%X ref in vonMises p23O l957

%A A. Wald
%T A method of estimating plane vulnerability based on damage of survivors
%I Statistical Res. Group, Columbia U.
%R CRC 432
%D 1943
%K TR, c1943, c194x, c19xx, zz0614, stats, statistics, sample, selection bias,
   data, survivor, survivorship, airplane, bomber, bombers, fuselage, engine,
   armour, Abraham Wald, WW2, WWII, world war two
%X "Denote by P_i (i = 1,2,..., ad inf.) the probability that a plane
   will be downed by i hits. ...
   ... Thus, for the observed data of this hypothetical example, the
   engine area is the most vulnerable in the sense that a hit there
   is most likely to down the plane. The fuselage has a relatively
   low vulnerability. ..."  -- Reprint from July 1980, crc 432,
      pdf@[<A HREF="http://cna.org/sites/default/files/research/0204320000.pdf">CNA</A>]['14], Center for Naval Analyses.
   (Downed planes do not return to base - where bullet holes are counted.
   Also see AW@[<A HREF="http://en.wikipedia.org/wiki/Abraham_Wald">wikip</A>]['14].
   Apparently this example is used in Ellenberg's book,
   'How not to be Wrong' (2014), [also search for: Ellenberg book wrong].)

%A J. B. S. Haldane
%T On a method of estimating frequencies
%J Biometrika
%V 33
%N 3
%P 222-225
%M NOV
%D 1945
%K jrnl, c1945, c194x, c19xx, zz0907, frequency, estimate, estimator,
   negative binomial, probability distribution, unbiased
%X "... If the freq. of an attr. is est. by counting a sample until m members
   possessing this attr. are found, & if the total # in the sample is n, then
   (m-1)/(n-1) is an unbiased est. of the freq., & its variance is v. approx.
   m(n-m)/(n^2 (n-1))."  [4 refs]
   -- [<A HREF="http://links.jstor.org/sici?sici=0006-3444%28194511%2933%3A3%3C222%3AOAMOEF%3E2.0.CO%3B2-W">paper@Jstor</A>]['07].

%A C. R. Rao
%T Information and the accuracy attainable in the estimation of
   statistical parameters
%J Bulletin of the Calcutta Math. Soc.
%V 37
%P 81-89
%D 1945
%K jrnl, c1945, c194x, c19xx, zz1219, stats, Cramer Rao Bound, CRB, limit,
   statistics, efficient, efficiency, Calyampudi Radakrishna Rao
%X Reprinted(?),
   "The earliest method of estimation of statistical parameters is the method
   of least squares due to Markoff. A set of observations whose expectations
   are linear functions of a number of unknown parameters being given, the
   problem which Markoff posed for solution is to find out a linear function of
   observations whose expectation is an assigned linear function of the unknown
   parameters and whose variance is a minimum. There is no assumption about the
   distribution of the observations except that each has a finite variance.",
   in
   'Breakthroughs in Statistics', pp.235-247, Springer, 1992
   -- [<A HREF="https://doi.org/10.1007/978-1-4612-0919-5_16">doi:10.1007/978-1-4612-0919-5_16</A>]['19].
   Also see [<A HREF="https://en.wikipedia.org/wiki/Cram%C3%A9r%E2%80%93Rao_bound">wikip</A>]['19].
   [Also search for: Cramer Rao stats].

%A H. Jeffreys
%T An invariant form for the prior probability in estimation problems
%J Proc. Royal Soc. London (A)
%V 186
%P 453-461
%D 1946
%K jrnl, PRS, PRSL, c1946, c194x, c19xx, probability distribution, distance,
   cross entropy, Kullback Leibler, KL, divergence
%X from  R a m a n' s  thesis '97 Includes symmetric form of cross-entropy,
   c.f. K-L distance on probability distributions.

%A H. Cramer
%T Math. Methods of Statistics
%I PrincetonUP
%D 1946
%K book, text, stats, c1946, c194x, c19xx, zz1219, Cramer Rao Bound, CRB, limit,
   CRLB, inequality, statistics, estimation, variance, Cramer, kramer,
   efficient, efficiency
%X Also see, "... [CRB] expresses a lower bound on the variance of unbiased
   estimators of a deterministic (fixed, though unknown) parameter. ...
   In its simplest form, the bound states that the variance of any unbiased
   estimator is at least as high as the inverse of the Fisher information. An
   unbiased estimator which achieves this lower bound is said to be (fully)
   efficient. ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Cram%C3%A9r%E2%80%93Rao_bound">wikip</A>]['19].
   [Also search for: Cramer Rao stats].

%A W. Weaver
%T Science and Complexity
%J Amer. Scientist
%V 36
%N 4
%P 536
%D 1948
%K c1948, c194x, c19xx, definition, defn, organized, disorganized, complexity,
   complex, organised, history
%X ... Disorganized Complexity ... statistical techniques ...
    v. Organized Complexity    ...
   pdf@[<A HREF="http://www.ceptualinstitute.com/genre/weaver/weaver-1947b.htm">ceptualinstitute.com</A>]['10].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Complexity">wikip</A>]['10]
   and [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A W. Weaver
%T Probability, rarity, interest, and surprise
%J The Scientific Monthly
%V 67
%N 6
%P 390-392
%M DEC
%D 1948
%K jrnl, c1948, c194x, c19xx, zz0724, probability, stats, surprisal, surprising,
   interesting, rare, unusual
%X "... expectation of Q, E(Q) = p_1.Q_1+...+p_n.Q_n ...
   E(p) = p_1^2+...+p_n^2 ...;
   surprise index, SI_j = E(p)/p_i^2 ..."
   -- [<A HREF="https://www.jstor.org/stable/22339">jstor:22339</A>]['24] via ArunK.
   Also see SA@[<A HREF="https://en.wikipedia.org/wiki/Surprisal_analysis">wikip</A>]['24].

%A M. G. Kendall
%T On the reconciliation of theories of probability
%J Biometrika
%V 36
%N 1/2
%P 101-106
%M JUN
%D 1949
%K jrnl, c1949, c194x, c19xx, zz0214, stats, statistics, probability, theory,
   frequentist, origins, frequencies, frequency
%X "1. Few branches of scientific method have been subject to so much difference
   opinion of as the theory of probability. ...
   FREQUENCY AND NON-FREQUENCY THEORIES
   3. Although there are many shades of opinion about the appropriate
   foundations of a theory of probability we may broadly distinguish
   two main attitudes. One takes probability  as 'a degree of rational belief',
   or some similar idea ... The second defines probability in terms of
   frequencies of occurrence of events ... In practice both approaches seem to
   lead to the same kind of direct theory, and it would be rare for exponents
   of the two to reach different mathematical conclusions from the same
   premisses. But this pragmatic reconciliation,though perhaps comforting to
   the onlooker, is not enough. ..."
   -- pdf@[<A HREF="http://www.jstor.org/stable/2332534">Jstor</A>]['14].

%A N. Metropolis
%A S. Ulam
%T The Monte Carlo Method
%J J. Amer. Stat. Assoc.
%V 44
%P 335-341
%D 1949
%K jrnl, JASA, monteCarlo, las vegas, lasVegas, algorithm, estimation,
   c1949, c194x, c19xx, mathematical physics, statistical,
   differential equations
%X "We shall present here the motivation and a general description of a method
   dealing with a class of problems in mathematical physics. The method is,
   essentially, a statistical approach to the study of differential equations,
   or more generally, of integro-differential equations that occur in various
   branches of the natural sciences."
   -- [<A HREF="http://links.jstor.org/sici?sici=0162-1459%28194909%2944%3A247%3C335%3ATMCM%3E2.0.CO%3B2-3">@JStor</A>]['05].
   [Also search for: Monte Carlo Method] &
   [also search for: Metropolis Hastings].

%A C. Eisenhart
%T The reliability of measured values - fundamental concepts
%J Photogrammetric Engineering
%V XVIII
%P 542-554 and 558-565
%D 1952
%K jrnl, c1952, c195x, c19xx, stats, precision, accuracy, error, errors,
   measurement, AoM
%X [Also search for: accuracy precision defn].

%A M. Mandelbrot
%T An information theory of the statistical structure of language
%B Communication Theory
%E W. Jackson
%I AcadPress N.Y.
%D 1953
%P 486-502
%K c1953, c195x, c19xx, word, frequency, frequencies, rank,
   probability distribution, Zipf, law
%X f = k / (r + alpha)**beta, f = word freq', r = rank of word,
   alpha and beta depend on the corpus being analyzed.      [-- from the web]
   ? Is it in a book or a jrnl ?    Also see Zipf's law '49.

%A R. A. Fisher
%T Dispersion on a sphere
%J Proc. of the Royal Soc. of London (A)
%S Series A, Mathematical and Physical Sciences
%V 217
%N 1130
%P 295-305
%M MAY
%D 1953
%K jrnl, stats, c1953, c195x, c19xx, angle, solid angles, sphere, spheres,
   spherical, probability distribution, spherical, vMF, von Mises, vonMises,
   circle, direction, directional, periodic, Fisher, RAFisher
%X "Any topological framework requires the development of a theory of errors of
   characteristic & appropriate mathematical form. ... develops a form of theory
   which appears to be appropriate to measurements of position on a sphere. The
   primary problems of estimation as applied to the true dirn, & the precision
   of observations, are discussed in the subcases which arise. The simultaneous
   distribution of the amplitude & direction of the vector sum of a # of random
   unit vectors of given precision, is demonstrated. From this is derived the
   test of significance appropriate to a worker whose knowledge of precision
   lies entirely in the internal evidence of the sample. This is the analogue of
   'Student's' test in the Gaussian theory of errors. The general formulae
   obtained are illustrated using measurements of the direction of remanent
   magnetization in the directly & inversely magnetized lava flows obtained in
   Iceland by Mr J. Hospers."
   -- [<A HREF="http://dx.doi.org/10.1098/rspa.1953.0064">doi:10.1098/rspa.1953.0064</A>],
      [<A HREF="http://www.jstor.org/stable/i206720">Jstor</A>]['11],
   pdf@[<A HREF="http://digital.library.adelaide.edu.au/dspace/handle/2440/15264">u.Adel</A>],
    & [<A HREF="http://hdl.handle.net/2440/15264">handle</A>]['11].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Von_Mises-Fisher_distribution">wikip</A>]['11].)
   [Also search for: vonMises direction].

%A P. J. Clark
%A F. C. Evans
%T Distance to nearest neighbour as a measure of spatial relationships in
   populations
%J Ecology
%V 35
%P 445-453
%D 1954
%K jrnl, c1954, c195x, c19xx, space, 2D, relationship, neighbours, population
%X for a population-density of d per unit area then
   expected distance to n.n. is 1/(2 sqrt(d))  -- p712 Cr@wley.

%A H. A. Simon
%T On a class of skew distribution functions
%J Biometrika
%V 42
%N 3-4
%P 425-440
%D 1955
%K jrnl, c1955, c195x, c19xx, zz0115, stats, probability, skew, skewed,
   distribution, long tail, word, frequencies, words, Yule, negative binomial
%X "... paper to analyse a class of distribution functions that appears in a
   wide range of empirical data - particularly data describing sociological,
   biological and economic phenomena. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/biomet/42.3-4.425">doi:10.1093/biomet/42.3-4.425.</A>]['15].

%A D. D. McCracken
%T The Monte Carlo method
%J Scientific American
%V 192
%N 5
%P 90-96
%M MAY
%D 1955
%K monte carlo, montecarlo, las vegas, lasvegas, stochastic, algorithm,
   estimation, random, c1955, c195x, c19xx

%A J. Aitchison
%T On the distribution of a positive random variable having a discrete
   probability mass at the origin
%J J. Amer. Stat. Soc.
%V 50
%N 271
%P 901-908
%M SEP
%D 1955
%K jrnl, c1955, c195x, c19xx, zz1206, zero inflated, distribution, sample,
   zeroes, distributions, count, counts, stats
%X [<A HREF="http://links.jstor.org/sici?sici=0162-1459%28195509%2950%3A271%3C901%3AOTDOAP%3E2.0.CO%3B2-M">@Jstor</A>]['06].

%A H. E. Robbins
%T An empirical Bayes approach to statistics
%J Berkeley Symp. on Maths, Stats & Prob.
%V 3.1
%D 1956
%K jrnl, c1959, c195x, c19xx, zz0422, empirical Bayes method, EBM, stats
%X "Let X be a random var. which for simplicity we shall assume to have discrete
   values x & which has a prob.distn depending in a known way on an unknown real
   parameter A,  p(x|l) = Pr(X=x|A=l). A itself being a random var. with apriori
   distn fn G(l) = Pr(A<=l). ..."
   -- [<A HREF="https://doi.org/10.1007/978-1-4612-0919-5_26">doi:10.1007/978-1-4612-0919-5_26</A>]['22],
      [<A HREF="https://projecteuclid.org/proceedings/berkeley-symposium-on-mathematical-statistics-and-probability/proceedings-of-the-third-berkeley-symposium-on-mathematical-statistics-and/Chapter/An-Empirical-Bayes-Approach-to-Statistics/bsmsp/1200501653?tab=ChapterArticleLink">eucl'd</A>]['22].
   Also see, "... procedures for statistical inference in which the prior
   distribution is estimated from the data. ..."
   -- EBM@[<A HREF="https://en.wikipedia.org/wiki/Empirical_Bayes_method">wikip</A>]['22].
   [Also search for: empirical Bayes stats].

%A G. S. Watson
%A E. J. Williams
%T On the construction of significance tests on the circle and the sphere
%J Biometrika
%V 43
%P 344-352
%M DEC
%D 1956
%K jrnl, stats, c1956, c195x, c19xx, zz0714, direction, directional, statistics,
   stats, probability distribution, test, von Mises, vonMises, vMF, circle,
   sphere, periodic, 2D, 3D
%X "A number of papers ... in two and three dimensions, proportional to
      exp(kappa cos(theta)) ..."
   -- 2332913@[<A HREF="http://www.jstor.org/stable/2332913">Jstor</A>]['14].
   [Also search for: vonMises direction].

%A M. Kupperman
%T Probabilities of hypotheses and information-statistics in sampling from
   exponential-class populations
%J Annals of Math. Stats.
%V 29
%N 2
%P 571-575
%M JUN
%D 1958
%K jrnl, c1958, c195x, c19xx, zz0413, sampling, probability distribution,
   prior, posterior, KL distance, statistic
%X "This paper is concerned with inequalities connecting probabilities of
   hypotheses using Bayes' theorem (a posteriori probabilities), a priori
   probabilities, and Kullback-Leibler information-statistics in sampling from
   populations belonging to the exponential class of populations. As a corollary
   it is shown that if it is known that the a priori probabilities are all
   equal, the choice of the hypothesis with the minimum Kullback-Leibler
   information-statistic is the same as the choice of the hypothesis with the
   maximum a posteriori probability, and conversely."
   -- 1177706633@[<A HREF="http://projecteuclid.org/euclid.aoms/1177706633">projEuclid</A>]['13] &
      1177706462@[<A HREF="http://projecteuclid.org/euclid.aoms/1177706462">correction</A>]['13], or
   2237349@[<A HREF="http://www.jstor.org/stable/2237349">Jstor</A>]['13].

%A W. D. Fisher
%T On grouping for maximum homogeneity
%J J. Amer. Stat. Assoc.
%V 53
%N 284
%P 789-798
%M DEC
%D 1958
%K jrnl, JASA, stats, time series, timeSeries, segment, segmentation,
   grouping problem, dynamic programming, DP, DPA, c1958, c195x, c19xx,
   classification
%X Given a set of arb' no's, what is a practical proc' for grouping
   them so that the variance within groups is minimized?  ...
   Given a[1], a[2], ...a[K], and weights w[1], w[2], ...,w[K],
   minimise D=SUM{i=1..K} w[i]*sqr(a[i]-abar[i]),
   where abar[i] is the mean of those a's in the group elt' i assigned to.
   e.g. data: Levels in Lake Michigan - Huron, 1860-1955.
   NB. User nominates the number of groups.     [via dean m' 4/99]
   -- [<A HREF="http://links.jstor.org/sici?sici=0162-1459%28195812%2953%3A284%3C789%3AOGFMH%3E2.0.CO%3B2-O">@JStor</A>]['05].

%A J. S. Hicks
%A R. F. Wheeling
%T An efficient methods for generating uniformly distributed points on the
   surface of an n-dimensional sphere
%J CACM
%V 2
%N 4
%P 17-19
%M APR
%D 1959
%K jrnl, CACM, c1959, c195x, c19xx, zz1113, uniform probability distribution,
   sphere, random vectors, directions, point, picking, generate, generator,
   RVG, PRVG, PRNG
%X "... inductively transform points from the surface of an (n-1)-sphere to the
   surface of an n-sphere in such a manner that uniformity ... is preserved
   ... noting that the diametric cross section of the n-sphere is the
   (n-1)-sphere. ..."
   -- [<A HREF="http://dx.doi.org/10.1145/377939.377945">doi:10.1145/377939.377945</A>]['13].
   [Also search for: PRVG sphere].

%A K. Popper
%T The propensity interpretation of probability
%J British J. for the Philosophy of Science
%P 24-42
%V 10
%D 1959
%K jrnl, c1959, c195x, c19xx, propensity, plausibility, frequentist,
   probability, prob
%X (ref from K & N book (p.348) '04.)

%A G. Rasch
%T Probabilistic models for some intelligence and attainment tests
%I Copenhagen, Denmark: Danmarks Paedogogische Institut,
%D 1960
%K model, stats, test, c1960, c196x, c19xx
%X Also see [<A HREF="http://www.rasch.org/memo24.htm">memo24</A>]['06]

%A M. W. Birch
%T Maximum likelihood in three-way contingency tables
%J J. Royal Stat. Soc. B
%V 25
%P 220-233
%D 1963
%K jrnl, JRSS, c1963, c196x, c19xx, stats, statistics, probability, CPT,
   contingency table, discrete, 3way, three, independence, dependence, margin,
   zero, zeros
%X "Interactions in a 3-way and many-way CTs are def. as certain linear combns
   of the log of the expected frequencies. Max-LH est is discussed for many-way
   tables & the solns given for 3-way tables in the cases of greatest interest."
      m_ij. = SUM_k=1..t m_ijk;  m_i.. = SUM_j=1..s,k=1..t m_ijk;  etc..
      I, II & III mutually indep:  m_ijk = m_i.. m_.j. m_..k / (m_...)^2;
      I and II indep (marginally): m_ijk = m_ij. m_..k / m_...; etc.
   -- 2984562@[<A HREF="http://www.jstor.org/stable/2984562">Jstor</A>]['13].

%A N. L. Johnson
%T Paths and chains of random straight line segments
%J Technometrics
%V 8
%N 2
%P 303-317
%M MAY
%D 1966
%K jrnl, stats, c1966, c196x, c19xx, zz0714, line segment, points, path, chain,
   directions, direction, orientation, Rayleigh, distance, length
%X "Classical problems assoc. with paths composed of straight line segments with
   indep. orientations, which have a continuous distribution, are discussed.
   Moment formulas are obtained for the distance between initial & terminal
   pts, & a new approx'n discussed. The Rayleigh approx'n is used to derive
   approx'ns to other characteristics of the random path."
   -- 1266363@[<A HREF="http://www.jstor.org/stable/1266363">Jstor</A>]['14].

%A G. Rasch
%T An item analysis which takes individual differences into account
%J British J. of Mathematical and Statistical Psychology
%V 19
%P 49-57
%D 1966
%K jrnl, c1966, c196x, c19xx, model, models, stats, difference
%X Also see [<A HREF="http://www.rasch.org/memo24.htm">memo24</A>]['06]

%A N. Gilbert
%A T. C. E. Wells
%T Analysis of quadrat data
%J J. Ecology
%V 54
%N 3
%P 675-685
%M NOV
%D 1966
%K jrnl, c1966, c196x, c19xx, stats, quadrat, transect, rabbit, rabbits, UK,
   myxomatosis, ecological, zz0607
%X [NB. "quadrat" : quadrat frame ... pins ... spacing]
   -- [<A HREF="http://links.jstor.org/sici?sici=0022-0477%28196611%2954%3A3%3C675%3AAOQD%3E2.0.CO%3B2-S">@Jstor</A>]['07].

%A J. MacQueen
%T Some methods for classification and analysis of multivariate observations
%J Proc. 5th Berkeley Symp. on Math. Statist. and Prob.
%I Univ. of Calif. Press
%V 1
%P 281-297
%D 1967
%K c1967, c1968, c19xx, zz0518, k means, kmeans, clustering, classification
%X -- 1200512992@[<A HREF="http://projecteuclid.org/euclid.bsmsp/1200512992">projecteuclid</A>]['18].
   Also see kmeans@[<A HREF="https://en.wikipedia.org/wiki/K-means_clustering">wikip</A>]['18].

%A L. E. Baum
%A J. A. Eagon
%T An inequality with applications to statistical estimation for
   probabilistic functions of Markov processes and to a model of ecology
%J Bull. Amer. Math. Soc.
%V 73
%P 360-363
%D 1967
%K jrnl, stats, AMS, BAMS, expectation maximization, EM algorithm, process, HMM,
   model, Welch, c1967, c196x, c19xx
%X ... In other words the posteriori estimate of transition probabilities
   increases the likelihood of the given observation y. (p.362) ...
   Baum - Welch method; later came to be known as expectation maximization.
  [Also search for: EM algorithm stats] & [also search for: EM algorithm c196x].

%A V. Levenstein
%T in Russian
%D 1968
%K c1968, c196x, c19xx, zz1118, universal, integer code, codes,
   intCodes, Levenstein, Levenshtein, Elias
%X (?Levenstein or Levenshtein?)
   "... The code of zero is '0'.  To code n > 0 ...
   1. Init the step count variable C = 1, and code word CW = ''.
   2. Take the binary value of n without its leading 1, prepend to the CW.
   3. Let M = the # of bits prepended in step 2.
   4. If M != 0 increment C by 1, go to and exec step 2 with M instead of n.
   5. If M = 0 prepend C '1's followed by a '0' to CW. Stop."
   -- [<A HREF="https://books.google.com.au/books?id=81AfzW6vux4C&pg=PA80&dq=%22Levenstein+coding%22&hl=en&ei=tYKZTIfzKJScsQP-1eWpAw&sa=X&oi=book_result&ct=result&redir_esc=y#v=onepage&q&f=false">www</A>]['18],
   "... The Levenstein code of a +ve int. is always one bit longer than the
   Elias omega code of that int.. [But] there is a L.code for zero ..."
   -- LCode@[<A HREF="https://en.wikipedia.org/wiki/Levenshtein_coding">wikip</A>]['18].
   [Also search for: integer code]  and  [also search for: Elias omega c1975].

%A S. Watanabe
%T Knowing and Guessing: A Quantitative Study of Inference and Information
%I Wiley
%P 376-377
%D 1969
%K c1969, c196x, c19xx, Ugly Duckling theorem, argument, prior, biases
%X p.376: sec.7.6.
   See [<A HREF="http://en.wikipedia.org/wiki/Ugly_duckling_theorem">wikip</A>]['08],
   "... if we have no preconceived bias about which categories are better, then
   by perfectly fair means of measuring, everything is equally similar (or
   equally dissimilar). ... Thus, we need some kind of inductive bias to make
   such judgments; some way to prefer certain categories over others."

%A W. T. Williams
%T The problem of attribute-weighting in numerical classification
%J Taxon.
%V 18
%P 369-374
%D 1969
%K jrnl, c1969, c196x, c19xx, variable, weight, weights, taxonomy, class,
   clustering, dependent characters
%X via MBD ['06].

%A J. C. Gower
%A J. S. Ross
%T Minimum spanning tree and single-linkage cluster analysis
%J J. Royal Stat. Soc. C, Applied Statistics
%V 18
%N 1
%P 54-64
%D 1969
%K jrnl, trees, MST, single link, linkage, c1969, c196x, c19xx, clusters, SLCA,
   classification, clustering, hierarchical, dendrogram
%X "(MST) & single linkage cluster analysis (SLCA) are explained ... shown that
   all the info. req. for the SLCA of a set of pts. is contained in their MST.
   Known algs. for finding the MST are discussed. ... efficient even when there
   are very many pts.; this makes a SLCA practicable when other methods of
   cluster analysis are not. ... computing procedures are published in the Alg.
   sect. of the same issue of App. Stats.. The use of the MST in the interp. of
   vector diagrams arising in multiv. analysis is illustrated by [e.g.]"
   -- [<A HREF="http://links.jstor.org/sici?sici=0035-9254%281969%2918%3A1%3C54%3AMSTASL%3E2.0.CO%3B2-9">paper@jStor</A>]['05].
   [Also search for: single link].

%A C. W. J.  Granger
%T Investigating causal relations by econometric models and cross-spectral
   methods
%J Econometrica
%V 37
%N 3
%P 424-438
%M JUL
%D 1969
%K jrnl, c1969, c196x, c19xx, stats, econometric model, Granger causality,
   time series analysis, method, timeSeries, correlation
%X paper@[<A HREF="http://www.jstor.org/stable/1912791">Jstor</A>][12/'09].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Granger_causality">wikip</A>].)

%A I. Fellegi
%A A. Sunter
%T A theory for record linkage
%J J. Amer. Stat. Assoc.
%V 64
%N 328
%P 1183-1210
%M DEC
%D 1969
%K jrnl, JASA, c1969, c196x, c19xx, record, data, link, linkage, RL, PRL, GIRLS,
   data, match, matching
%X -- [<A HREF="http://dx.doi.org/10.2307/2286061">doi:10.2307/2286061</A>]['10].
   [Also search for: record linkage data].

%A B. L. van der Waerden
%T Mathematical Statistics
%I SpringerVerlag
%S Grundlehren der Mathematischen Wissenschaften
%V 156
%D 1969
%K book, text, c1969, c196x, c19xx, zz0214, vanderWaerden,
   Beta probability distribution, random, RNG, PRNG
%X 1st ed 1969; uk us isbn:3540045074; uk us isbn13:978-3662221396;
   -- [<A HREF="http://link.springer.com/book/10.1007/978-3-662-22137-2">spr'nger</A>]['14].
   'The Gamma(alpha,beta) distribution's pdf is
       pdf(x)=(x^(alpha-1)(1-x)^(beta-1))/B(alpha,beta),
       where B(x,y)=(G(x).G(y))/G(x+y), and G is the Gamma function.'
   "If X~Gamma(alpha,theta) and Y~Gamma(beta,theta) independently
       then (X/(X+Y))~Beta(alpha,beta)" -- vdW cited in
   -- [<A HREF="http://en.wikipedia.org/wiki/Beta_distribution">wikip</A>]['14].
   So, [also search for: Gamma PRNG].

%A L. E. Baum
%A T. Petrie
%A G. Soules
%A N. Weiss
%T A maximization technique occurring in the statistical analysis of
   probabilistic functions of Markov chains
%J Ann. Math. Stat.
%V 41
%P 164-171
%D 1970
%K jrnl, AMS, model, HMM, expectation maximization, c1970, c197x, c19xx,
   EM, Welch
%X see also Baum and Eagon '67.
   Baum - Welch; later came to be known as expectation maximization (EM).
   [Also search for: Baum EM c196x].

%A S. W. Golomb
%T Run-length encodings
%J IEEE Trans. Inform. Theory
%V IT-12
%P 399-401
%D 1966
%K jrnl, IT12, run length encoding, code, integer, zz0999, c1966, c196x, c19xx

%A G. E. P. Box
%A G. M. Jenkins
%T Time Series Analysis, Forecasting and Control
%I HoldenDay
%D 1970
%K book, text, predict, prediction, model, modelling, stats, statistics,
   autocorrelation, linear, estimation, c1970, c197x, c19xx, AR, ARMA, ARIMA,
   nonstationarity, time series models, timeSeries, lag
%X 3rd edn, PrenticeHall, pp.592, us$90, isbn:0130607746, c1994.
   Also see [<A HREF="http://en.wikipedia.org/wiki/Autoregressive">wikip</A>]['05]
   AR(p):     X[t] = c+SUM[i=1..p]{a[i]*X[t-i]}+e[t], e[t]~N(0,s)     --autoreg
     "...constant term is omitted by many...for simplicity...
     constraints are necessary...[for] the model [to] remain stationary. ..."
   ARMA(p,q): X[t] = e[t]+SUM[i=1..p]{a[i]*X[t-i]}+SUM[i=1..q]{b[i]*e[t-1]}
     autoregressive, moving average.            [Also search for: Yule Walker].

%A D. G. Willis
%T Computational complexity and probability constructions
%J JACM
%V 17
%N 2
%P 241-259
%M APR
%D 1970
%K jrnl, JACM, c1970, c197x, c19xx, zz0519, information theory, code, codes,
   maths, inductive inference, II, stats, probability, UTM
%X "There exist constructive correspondences between Turing machines having
   finitely determinable behavior & computable probability measures on their
   output seqs.. These correspondences determine limits on the relative
   accuracies with which different computable probability measures predict
   events. Using any UTM as a basis, it is possible to construct an infinite
   hierarchy of increasingly accurate computable prob.measures which are indep.
   of any probability assumptions. The relationship of such measures to real
   events is considered."
   -- [<A HREF="https://doi.org/10.1145/321574.321578">doi:10.1145/321574.321578</A>]['19].
   [Also search for: information theory].

&A L. A. Goodman
%T Partitioning of chi-square, analysis of marginal contingency tables, and
   estimation of expected frequencies in multidimensional contingency tables
%J J. Amer. Stat. Assoc.
%V 66
%N 334
%P 339-334
%M JUN
%D 1971
%K jrnl, c1971, c197x, c19xx, stats, statistics, probability, table, CPT,
   discrete, chi square, squared, hypotheses, margin, multidimensional
%X "... marginal ... ignoring one or more of the tables dimensions ..."
   -- 2283933@[<A HREF="http://www.jstor.org/stable/2283933">Jstor</A>]['13].
   [Also search for: stats CPT].

%A J. A. Hartigan
%T Direct clustering of a matrix
%J J. Amer. Stat. Soc
%V 67
%N 337
%P 123-129
%M MAR
%D 1972
%K jrnl, c1972, c197x, c19xx, zz0415, cluster, cocluster, coclustering,
   bicluster, biclustering, matrix, array, rows, columns, cols, stats
%X "Clustering algs. ... article presents a model, and a technique, for
   clustering cases [rows] and variables [cols] simultaneously. The principle
   advantage ... is the direct interpretation of the clusters in the data."
   -- 2284710@[<A HREF="http://www.jstor.org/stable/2284710">Jstor</A>]['15].
   (*Also see "... most interesting variants of this problem are NP-complete."
   -- bicl@[<A HREF="http://en.wikipedia.org/wiki/Biclustering">wikip</A>]['15].*)
   [Also search for: biclustering] and [also search for: coclustering].

%A P. Elias
%T Minimum times and memories needed to compute the values of a function
%J J. Comput. Sys. Sci.
%V 9
%N 2
%P 196-212
%M OCT
%D 1974
%K jrnl, c1974, c197x, c19xx, zz0619, universal code, integer codes,
   FSA, FSM, UTM, time, space, intCodes
%X "A deterministic sequential device receives one input symbol at a time,
   prints output syms. from left to right on an output tape, & halts for some
   input seqs.. Such a device can be used to compute some repn of the value of a
   fn when some repn of the arg. of the fn is supplied as input. Lower bounds to
   the times required to find the values of the fn & to averages of those times
   follow, even if the device is v.powerful. The bounds can be attained by
   sufficiently powerful devices (which may not be finitely describable) & can
   be approached by finite-state mcs when the appropriate repns of the range &
   the domain are chosen. A speedup theorem permits almost all values to be
   computed more rapidly, but does not reduce the avg time to find a value. A
   universal three-state automaton computes the values of any properly
   represented fn taking at most twice the avg time required by the best
   computer for that fn."
   -- [<A HREF="https://doi.org/10.1016/S0022-0000(74)80007-3">doi:10.1016/S0022-0000(74)80007-3</A>]['19].
   Also see Elias 1975 which attributes the 1st universal code to this paper.
   Also see [<A HREF="http://www.allisons.org/ll/MML/Discrete/Integers/">Integer Codes</A>].
   [Also search for: intCodes].

%A S. J. Haberman
%T Analysis of Frequency Data
%I U. ChicagoPress
%S Stat. res. monographs
%P 432
%D 1974
%K book, text, c1974, c197x, c19xx, zz0614, stats, frequencies,
   associations, log linear analysis, LLA
%X 1st ed 1974; hb us$7; uk us isbn:0226311848, uk us isbn13:978-0226311845.

%A C. Bingham
%T An antipodally symmetric distribution on the sphere
%J Annals of Stats.
%I Inst. of Math. Stats.
%V 2
%N 6
%P 1201-1225
%M NOV
%D 1974
%K jrnl, c1974, c197x, c19xx, zz0814, stats, statistics, direction, directional,
   n-D, nD, unit sphere, n-sphere, probability distribution, Fisher, Kent
%X "The distribution $\Psi(\mathbf{x}; Z, M) = \operatorname{const}.
   \exp(\mathrm{tr} (ZM^T \mathbf{xx}^T M))$ on the unit sphere in three-space
   is discussed. It is parametrized by the diagonal shape & conc. matrix Z &
   the orthog. orientation matrix M. Psi is applicable in the stat. analysis of
   measurements of random undirected axes. Exact & asymptotic sampling distns
   are derived. Max. likelihood estimators for Z & M are found & their
   asymptotic properties elucidated. Inference procs., inc. tests for isotropy
   & circular symmetry, are proposed. The application of psi is illustrated by
   a numerical example."
   -- [<A HREF="http://www.jstor.org/stable/2958339">Jstor</A>]['14].
   The 'Bingham distribution'.
   Also see B@[<A HREF="http://en.wikipedia.org/wiki/Bingham_distribution">wikip</A>]['14].
   [Also search for: direction probability distribution].

%A P. Elias
%T Universal codeword sets and representations of the integers
%J IEEE Trans. Inform. Theory
%V IT-21
%N 2
%P 194-203
%M MAR
%D 1975
%K jrnl, IT21, c1975, c197x, c19xx, zz099, intCodes, set, integer,
   int, ints, number, numbers, universal, code, word, codes, encoding,
   gamma, delta, omega, logstar, log star
%X "Countable prefix codeword sets are constructed with the universal property
   that assigning messages in order of decreasing prob. to codewords in order of
   incr. length gives an avg. code-word length, for any message set with +ve
   entropy, less than a constant times the optimal avg. codeword length for that
   source. Some of the sets also have the asymptotically optimal property that
   the ratio of avg. codeword length to entropy approaches one uniformly as
   entropy increases. An application is the construction of a uniformly
   universal seq. of codes for countable memoryless sources, in which the n-th
   code has a ratio of avg. codeword length to source rate bounded by a fn of n
   for all sources with +ve rate; the bound is less than two for n=0 &
   approaches one as n increases."
   -- [<A HREF="http://dx.doi.org/10.1109/TIT.1975.1055349">doi:10.1109/TIT.1975.1055349</A>]['15].  (via G.F.)
   Note: Elias attributes the 1st universal code to Elias 1974.
   (Also see
   gamma@[<A HREF="https://en.wikipedia.org/wiki/Elias_gamma_coding">wikip</A>]['18],
   delta@[<A HREF="https://en.wikipedia.org/wiki/Elias_delta_coding">wikip</A>]['18],
   omega@[<A HREF="https://en.wikipedia.org/wiki/Elias_omega_coding">wikip</A>]['18] ("recursive"),
   U.Cs@[<A HREF="https://en.wikipedia.org/wiki/Universal_code_(data_compression)">wikip</A>]['18], and
   [<A HREF="http://www.allisons.org/ll/MML/Discrete/Integers/">Integer_Codes</A>].)
   * [Also search for: Levenstein code c1968].

%A K. V. Mardia
%A P. J. Zemroch
%T Algorithm AS 86: The von Mises distribution function
%J J. of the Royal Statistical Society (C)
%S Applied Statistics
%V 24
%N 2
%P 268-272
%D 1975
%K JRSS, jrnl, AS86, c1975, c197x, c19xx, stats, vonMises, circle, circular,
   probability distribution, angle, angles, angular, direction, directional,
   periodic, Bessel functions I0
%X "The distribution function of the vonM random var Z on the circle with
   mean dirn mu and conc.param. K (>=0) is
   G(theta; mu, K) = P(0 < Z <= theta)
   = integral[0,theta] (1/(2 pi I0(K)))exp{K cos(Z-mu)} dZ,
     0 < theta <= 2 pi.  ..."
   -- [<A HREF="http://www.jstor.org/stable/2346578">Jstor</A>]['11].
   [Also search for: vonMises direction].

%A K. V. Mardia
%A S. A. M. El-Atoum
%T Bayesian inference for the von Mises - Fisher distribution
%J Biometrika
%V 63
%N 1
%P 203-206
%M APR
%D 1976
%K jrnl, c1976, c197x, c19xx, ElAtoum, Bayesian, estimator, direction, stats,
   vonMises, Fisher, vMF, directional, probability distribution, circular,
   spherical, hyper
%X "... give a theoretical discussion of Bayesian inference for the
   von Mises - Fisher distribution. The choice of particular priors is
   considered and the admissibility of certian B.estimators studied. For
   the multisample case ests. are given. Some problems of testing hypotheses
   are summarized in the form of posterior odds against the null hypothesis."
   -- [<A HREF="http://dx.doi.org/ 10.1093/biomet/63.1.203">doi: 10.1093/biomet/63.1.203</A>]['12]($),
   &  [<A HREF="http://www.jstor.org/stable/2335106">Jstor</A>]['12]($),
   KVM@[<A HREF="http://www1.maths.leeds.ac.uk/~sta6kvm/">Leeds</A>]['10].
   (Also see vMF@[<A HREF="http://en.wikipedia.org/wiki/Von_Mises%E2%80%93Fisher_distribution">wikip</A>]['12].)
   [Also search for: vonMises direction].

%A G. W. Hill
%T Algorithm 518, Incomplete Bessel function I0: The von Mises distribution
%J ACM Trans. on Mathematical Software
%V 3
%N 3
%P 279-284
%M SEP
%D 1977
%K jrnl, TOMS, stats, c1977, c197x, c19xx, stats, vonMises, circle, circular,
   probability distribution, angle, direction, Bessel function I0
%X "... computes the left tail area of the Von Mises distribution, which is
   equal to the incomplete modified Bessel function of the first kind and
   zero-th order (I0) ..."
   -- [<A HREF="http://dx.doi.org/10.1145/355744.355753">doi:10.1145/355744.355753</A>]['11] inc. pdf.
   [Also search for: stats AS86] and [also search for: vonMises direction].

%A R. Daley
%T On the inference of optimal descriptions
%J Theor. Comput. Sci.
%V 4
%N 3
%P 301-319
%M JUN
%D 1977
%K jrnl, TCS, c1977, c197x, c19xx, zz0306, description, inference, II, model,
   binary sequence, minimum, message, MML, length, MDL, encoding
%X "... The min description of x[1..n] is a program of min length which
   computes x[1..n], which we denote here by M(x[1..n]). The inference problem
   for x is then solvable iff there exists a rec. fn psi s.t. for each n
   psi(x[1..n]) = M(x[1..n]).  ... this is not an inductive inference problem.
   There is no inference in the limit. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0304-3975(77)90015-9 ">doi:10.1016/0304-3975(77)90015-9</A>]['06].

%A S. H. Leung-Yan-Cheong
%A T. M. Cover
%T Some equivalences between Shannon entropy and Kolmogorov complexity
%J IEEE Trand. Inf. Th.
%V IT-24
%N 3
%P 331
%M MAY
%D 1978
%K jrnl, c1978, c197x, c19xx, zz1118, LeungYanCheong, entropy, information,
   integer, integers, log*, logStar, code, intCodes
%X "It is known that the expected codeword length, L_{UD}, of the best uniquely
   decodable (UD) code satisfies H(X) <= L_{UD} < H(X)+1.  Let X be a random
   var. which can take on pi values. Then it is shown that the avg. codeword
   length L_{1:1}, for the best one-to-one (not nec. uniquely decodable) code
   for X is shorter than the avg. codeword length L_{UD}, for the best udquely
   decodable code by no more than (log_2 log_2 n)+3.  Let Y be a random var.
   taking on a finite or countable # of values & having entropy H. Then it is
   proved that L_{1:1} >= H-log_2(H+l)-log_2 log_2(H+l)- ... -6. Some relations
   are established among the Kolmogorov, Chaitin, & extension complexities.
   Finally it is shown that, for all computable probability distributions, the
   universal prefix codes assoc. with the conditional Chaitin complexity have
   expected codeword length within a constant of the Shannon entropy."
   -- [<A HREF="https://doi.org/10.1109/TIT.1978.1055891">doi:10.1109/TIT.1978.1055891</A>]['18],
   pdf@[<A HREF="https://pdfs.semanticscholar.org/c6ae/ce82c4c2076eb22db65a16e6c376b94df37b.pdf">sem'ntic'</A>][11/'18],
   pdf@[<A HREF="http://www-isl.stanford.edu/people/cover/papers/transIT/0331leun.pdf">stanf'd</A>]['19],
   and auth2@[<A HREF="http://www-isl.stanford.edu/people/cover/">stanf'd</A>]['19].
   [Also search for: logStar code]  and  [also search for: integer code].

%A D. E. Denning
%A P. J. Denning
%A M. D. Schwartz
%T The tracker: A threat to statistical database security
%J TODS
%I ACM
%P V
%N 1
%P 76-96
%M MAR
%D 1979
%K TODS, jrnl, c1979, c197x, c19xx, zz0620, differential privacy, stats,
   Schlorer, privacy, survey, database, databases, general tracker, security,
   query sets, queries
%X "The query programs of certain databases report raw statistics for query
   sets, which are groups of records specified implicitly by a characteristic
   formula. ...  Many users & designers believe that the individual records will
   remain confidential as long as query programs refuse to report the statistics
   of query sets which are too small. It is shown that the compromise of small
   query sets can in fact almost always be accomplished with the help of
   characteristic formulas called trackers. Schlorer's individual tracker is
   reviewed ...  The general tracker is introduced: It permits calculating
   statistics for arbitrary query sets ...  Almost all databases have a general
   tracker, & general ts. are almost always easy to find. Security is not
   guaranteed by the lack of a general tracker."
   -- [<A HREF="https://doi.org/10.1145/320064.320069">doi:10.1145/320064.320069</A>]['20].
   (Also see DP@[<A HREF="https://en.wikipedia.org/wiki/Differential_privacy">wikip</A>]['20].)
   [Also search for: differential privacy].

%A A. D. Gordon
%A R. A. Reyment
%T Slotting of borehole sequences
%J Mathematical Geology
%V 11
%N 3
%P 309-327
%M JUN
%D 1979
%K jrnl, c1979, c197x, c19xx, slotting problem, sequence, time series,
   sequence, timeSeries, stratigraphic correlation, geophysical logs, log,
   similarity coefficient, zz0507
%X "... comparing & correlating borehole sequences using information from 1 or
   more physical logs recorded from the boreholes. ... is illustrated by a small
   worked example. Ways are described whereby constraints may be imposed on the
   comparison to allow the incorporation of relevant information, such as the
   presence of marker beds in the stratigraphic sequences. ..."  [9 refs]
   -- [<A HREF="http://dx.doi.org/10.1007/BF01034996">doi:10.1007/BF01034996</A>]['07].
   (Also see [<A HREF="http://www.chrono.qub.ac.uk/inqua/news8/nl8-mc.htm">INQUA newsl 8 7/'93</A>]['07].)

%A R. Perline
%A B. D. Wright
%A H. Wainer
%T The Rasch model as additive conjoint measurement
%J Applied Psychological Measurement
%V 3
%N 2
%P 237-255
%D 1979
%K jrnl, c1979, c197x, c19xx, stats
%X "...present R.'s psychometric model as a special case of +ve conjoint
   measurement. ... Because the theory of conjoint measurement has been
   formulated deterministically, there have been some difficulties in its
   application. ... Rasch model, which is a stochastic model, does not suffer
   from this fault. The exposition centers on the analyses of 2 data sets, each
   of which was analyzed using Rasch scaling methods as well as some of the
   methods of conjoint measurement. ..."
   -- from the web:[<A HREF="http://www.rasch.org/memo24.htm">memo24</A>]['06].
   [Also search for: Rasch model].

%A D. Collett
%T Outliers in circular data
%J J. of the Royal Stat. Soc. C (Applied Stats)
%I OUP
%V 29
%N 1
%P 50-57
%D 1980
%K jrnl, JRSS, c1980, c198x, c19xx, zz0823, statistics, stats, circular,
   outlier, surprise, discordancy, discord, model, robust, von Mises, vonMises,
   directional, circular, probability distribution
%X "... we investigate problems connected with the appearance of surprising
   values in samples of univariate data that are circular or directional. We
   examine how their presence might be detected & describe possible tests of
   discordancy. The relative performance of the test procedures is investigated
   using MonteCarlo methods. A practical application of the discordancy tests
   is included."
   -- [<A HREF="https://doi.org/10.2307/2346410">doi:10.2307/2346410</A>]['23],
      [<A HREF="https://www.jstor.org/stable/2346410">jstor:2346410</A>]['23] (via P.A. '23).
   (Also see outlier@[<A HREF="https://en.wikipedia.org/wiki/Outlier">wikip</A>]['23].)
   [Also search for: stats outlier].

%A D. G. Kendall
%A W. S. Kendall
%T Alignments in two-dimensional random sets of points
%J Adv. Appl. Probab.
%V 12
%P 380-424
%D 1980
%K jrnl, c1980, c198x, c19xx, 2D, points, point, set, alignment, align,
   ley line, straight lines, matching, pontogram
%X "Let n pts in the plane be generated by some specified random mechanism &
   suppose that N(e) of the C(n,3) resulting triads form triangles with largest
   angle >= pi-e. The main object of the paper is to obtain asymptotic formulae
   for E(N(e)) & Var(N(e)) when e->0, & to solve the assoc. ... This problem is
   solved by the intro. of a plot to be called the pontogram & by the intro. of
   simulation-based sig.tests constructed by random lateral perturbations of
   the data."
   -- [<A HREF="https://doi.org/10.2307/1426603">doi:10.2307/1426603</A>]['22],
      1426603@[<A HREF="https://www.jstor.org/stable/1426603">jStor</A>]['22]. via M.D.['05].
   Also see ARP@[<A HREF="https://en.wikipedia.org/wiki/Alignments_of_random_points">wikip</A>]['22].

%A D. Knoke
%A P. J. Burke
%T Log-Linear Models
%I SAGEpubl
%S Quantitative Applications in the Social Sciences
%V 20
%P 80
%M AUG
%D 1980
%K book, text, intro, c1980, c198x, c19xx, zz0314, viaFPj, stats, statistics,
   II, log linear, logLinear, LLA, logLinearModel, graphical model, models,
   crosstabulation, categorical variables, chi2
%X 1st ed 1980; pb us$16; uk us isbn:080391492X; uk us isbn13:978-0803914926.
   "Discusses the innovative log-linear model of statistical analysis. This
   model makes no distinction between independent and dependent variables, but
   is used to examine relationships among categoric variables by analyzing
   expected cell frequencies."
   (At lib.[<A HREF="http://dx.doi.org.ezproxy.lib.monash.edu.au/10.4135/9781412984843">mon@sh</A>]['14],
       lib.[<A HREF="http://srmo.sagepub.com.ezproxy.lib.monash.edu.au/view/log-linear-models/SAGE.xml">mon@sh</A>]['14],
   SAGE [<A HREF="http://dx.doi.org/10.4135/9781412984843">doi:10.4135/9781412984843</A>]['14].)
   [Also search for: graphical model] and [also search for: log linear model].
   (Also see LLM@[<A HREF="https://en.wikipedia.org/wiki/Log-linear_model">wikip</A>]['18].)

%A F. Papentin
%T On order and complexity I. General considerations
%J JTB
%V 87
%N 3
%P 421-456
%M DEC
%D 1980
%K jrnl, JTB, c1980, c198x, c19xx, minimal, MML, MDL, complexity, increase,
   decrease, entropy, evolution, compress, information
%X "The length of the shortest possible description ... of a pattern in a given
   language L is used as a measure of its complexity. ... differentiated into
   an organized & an unorganized aspect. Organized complexity - the min.desc. of
   the rules or laws underlying a pattern - taken as a measure of its 2ndry
   order; unorganized complexity - the min. desc. of the random aspects ... - as
   a measure of its primary disorder. The avg. primary disorder of an ensemble
   of patterns is closely related to the entropy of that ensemble (if it is
   definable), whereas secondary order is beyond the entropy concept.
   The procs. for the calculation of the complexity of a pattern are outlined
   & their reln. to formal lang. theory is given. The simplest of all patterns -
   binary seqs. - are studied as a test case. It is found that unorganized
   complexity corr. better to our intuitive notion of 'disorder' than entropy
   does. ... discussed wrt the old controversy as to whether or not order
   inc. or decr. in evoln. ... may be entirely settled if primary order is
   distinguished from 2ndry order: The 1st always tends to decrease in evoln &
   the 2nd to increase. Moreover, the decrease of the 1st is the very driving
   force for the incr. of the 2nd; 2ndry order may, therefore, be said to
   emerge out of primary order."
   -- [<A HREF="http://dx.doi.org/10.1016/0022-5193(80)90230-1">doi:10.1016/0022-5193(80)90230-1</A>]['10].
   [Also search for: Papentin c198x] and
   [also search for: complexity information evolution].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. A. Anderson
%A P. R. Philips
%T Regression, discrimination and measurement models for ordered category
   variables
%J Applied Stats.
%V 30
%P 22-31
%D 1981
%K jrnl, statistics, c1981, c198x, c19xx, variable, ord, attribute, model
%X via MBD '06.

%A Y. M. Babad
%A J. A. Hoffer
%T Even no data has value
%J CACM
%V 27
%N 8
%P 748-756
%M AUG
%D 1981
%K jrnl, cacm, missing value, values, data, c1981, c198x, c19xx
%X "Data that are missing, lost, or incomplete can be very significant in
   certain situations. Programs and languages need to be able to identify and
   manage such data effectively.
   ... erroneous ... missing values ...  outliers ... imputation ..."
   -- [<A HREF="http://doi.acm.org/10.1145/358198.358204">doi:10.1145/358198.358204</A>]['06].

%A J. T. Kent
%T The Fisher-Bingham distribution on the sphere
%J J. Royal Stat. Soc. Series B (Methodological)
%V 44
%N 1
%P 71-80
%D 1982
%K jrnl, JRSS, stats, c1982, c1982, c19xx, Fisher Bingham, von Mises, vonMises,
   Kent, FB5, probability distribution, sphere, direction, directional,
   2sphere, 3D, sphere2
%X "... spherical analogue of the general bivariate normal distribution.
   Estimation, hyp. testing, and confidence regions are also discussed."
   -- [<A HREF="http://www.jstor.org/stable/2984712">Jstor</A>]['13].
      x = (x_1, x_2, x_3), where x is normalised,
      f(x) = c(k,b)^-1 exp{ k g'_(1).x + b[(g'_(2).x)^2 - (g'_(3).x)^2] },
      conc. k>=0, ovalness b>=0, 3x3 orthog. matrix G=(g_(1), g_(2), g_(3)),
      g_(1) mean direction or pole, g_(2) major axis, g_(3) minor axis,
      c(k,b) = 2pi SUM_j=0.. {Gamma(j+1/2)/Gamma(j+1)) b^2j
                                 (k/2)^(-2j-1/2) I_(2j+1/2)(k)}.
      If rotate to the frame of ref. def. by the cols. of G, x -> x*,
      f(x*) = c(k,b)^-1 exp{ k x*_1 + b(x*_2^2 - x*_3^2) }.
   The 'Fisher Bingham', or 'Kent' distribution.
   (Also see K@[<A HREF="http://en.wikipedia.org/wiki/Kent_distribution">wikip</A>]['13].)
   [Also search for: direction probability distribution].

%A S. Lloyd
%T Least squares quantization in PCM
%J IEEE Trans. on Inf. Th.
%V 28
%N 2
%P 129-137
%M MAR
%D 1982
%K jrnl, stats, c1957, c195x, c1982, c198x, c19xx, zz0518,
   least squares, PCM, Lloyd max, k means, kmeans, EM algorithm, clustering
%X "... In this paper the corresponding result for any finite number # quanta is
   derived; that is, necessary conditions are found that the quanta & associated
   quantization intervals of an optimum finite quantization scheme must satisfy.
   The optimization criterion used is that the avg. quantization noise power be
   a minimum. It is shown that the result obtained here goes over into the
   Panter & Dite result as the # of quanta become large. The optimum
   quantization schemes for2^{b}quanta,b=1,2, \cdots, 7, are given numerically
   for Gaussian & for Laplacian distribution of signal amplitudes."
   -- [<A HREF="https://doi.org/10.1109/TIT.1982.1056489">doi:10.1109/TIT.1982.1056489</A>]['18].
   ("... The std alg. was first proposed by Stuart Lloyd in 1957 as
   a technique for pulse-code modulation, though it wasn't
   published outside of Bell Labs until 1982. ..."
   -- kmeans@[<A HREF="https://en.wikipedia.org/wiki/K-means_clustering">wikip</A>]['18].)

%A F. Papentin
%T On order and complexity II. Application to chemical and biochemical
   structures
%J JTB
%V 95
%N 2
%P 225-245
%M MAR
%D 1982
%K jrnl, JTB, c1982, c198x, c19xx, minimal, MML, MDL, chemical compound,
   organized complexity, structure, compress, information
%X "The organized complexity of a variety of chemical & biochem. compounds is
   est. by the method outlined in the 1st paper of this series. The structural
   formulas of these compounds are treated as labelled graphs, the labels of
   the vertices being the different kinds of atoms, & those of the edges being
   the different kinds of bonds. Such a graph is coded for by a linear seq. of
   symbols which in turn is described as short as possible by means of
   additional symbols. The len. of the shortest poss. descn of a structural
   formula ... is taken as a measure for the org.complexity of the underlying
   compound. Upper limits for the org.complexities of protein & RNA molecules
   are also est.."
   -- [<A HREF="http://dx.doi.org/10.1016/0022-5193(82)90241-7">doi:10.1016/0022-5193(82)90241-7</A>]['10].
   [Also search for: Papentin c198x].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/Graph/">MML</A>].)

%A C. F. Jeff Wu
%T On the convergence properties of the EM algorithm
%J Ann. Statist.
%V 11
%N 1
%P 95-103
%M MAR
%D 1983
%K jrnl, stats, c1983, c198x, c19xx, zz0323, EM algorithm, convergence,
   stability
%X "... Several convergence results are obtained under conditions that are
   applicable to many practical situations. Two ... are: (a) if the unobserved
   complete-data spec. can be described by a curved exponential family with
   compact param. space, all the limit pts of any EM seq. are stationary pts of
   the likelihood function; (b) if the likelihood fn is unimodal & a certain
   differentiability condn is satisfied, then any EM seq. converges to the
   unique maximum likelihood est.. A list of key properties of the alg. is
   included."
   -- [<A HREF="https://doi.org/10.1214/aos/1176346060">doi:10.1214/aos/1176346060</A>]['23].
   (Also see EM@[<A HREF="https://en.wikipedia.org/wiki/Expectation%E2%80%93maximization_algorithm">wikip</A>]['23].)
   [Also search for: EM algorithm stats]  &  [also search for snob mixture].

%A I. J. Good
%T Good Thinking: the Foundations of Probability and its Applications
%I U. MinnesotaPress
%P 352
%D 1983
%K book, text, c1983, c198x, c19xx, zz1211, IJGood, publications, papers,
   Bayesian, probability, stats, statistics, inference, causality,
   philosophy, II, AI, randomness
%X 1st ed 1983; pb us$48; uk us isbn:0816611424; uk us isbn13:978-0816611423.
   "... a representative sampling of IJG's writing on a wide range of Qs about
   the foundations of statistical inference, especially where induction
   intersects with philosophy. Good believes that clear reasoning about many
   important practical & philosophical questions is impossible except in
   terms of probability. ... various published sources 23 of Good's articles
   with an emphasis on more philosophical than math.. ... such topics as
   rational decisions, randomness, operational research, measurement of
   knowledge, mathematical discovery, AI, cognitive psychology, chess, &
   the nature of probability itself. ... organized into 5 sections: Bayesian
   Rationality; Probability; Corroboration, Hypothesis Testing, & Simplicity;
   Information & Surprise; & Causality & Explanation. ..."
   [Also search for: IJGood].

%A J. Monahan
%T Algorithm 616: Fast computation of the Hodges-Lehmann location estimator
%J ACM Trans. on Mathematical Software
%V 10
%N 3
%P 265-270
%M SEP
%D 1984
%K jrnl, TOMS, c1984, c198x, c19xx, stats, statistics, estimate, position,
   robust, efficient, rank, ranks, HL, dataplot
%X pdf: [<A HREF="http://doi.acm.org/10.1145/1271.319414">doi:10.1145/1271.319414</A>]['07]
   "... muEst = median (x[i]+x[j])/2,  1 <= i <= j <= n."
   -- [<A HREF="http://www.itl.nist.gov/div898/software/dataplot/refman2/auxillar/hodglehm.htm">www</A>]['07].
   [Also search for: Hodges Lehmann].

%A M. A. Fligner
%A J. S. Verducci
%T Distance based ranking models
%J J. Royal Statist. Soc. B.
%V 48
%P 359-369
%D 1986
%K jrnl, JRSS, model, c1986, c198x, c19xx, rank, ranks, order, partial,
   modal, ordering, order
%X "A class of [RMs] is proposed for which the prob. of a ranking decreases
   with increasing distance from a modal ranking. Some special distances,
   namely those associated with Kendall & Cayley, decompose into a sum of
   independent components under the uniform distribution. These distances lead
   to multiparameter generalizations whose parameters may be interpreted as
   information at various stages in a ranking process. Estimation of model
   params is described, & the results are applied to an example of word
   associations. A censoring argument motivates simple extensions of these
   models to include partial rankings. The generalized Cayley distance model is
   illus. for random arrangements arising from mechanisms other than ranking."
   -- [<A HREF="http://links.jstor.org/sici?sici=0035-9246%281986%2948%3A3%3C359%3ADBRM%3E2.0.CO%3B2-H">@jstor</A>]['05].
   via M.D.['05].

%A F. Santosa
%A W. W. Symes
%T Linear inversion of band-limited reflection seismograms
%J SIAM J. Sci. and Stat. Comput.
%V 7
%N 4
%P 1307-1330
%D 1986
%K jrnl, c1986, c198x, c19xx, zz0719, stats, lasoo, deconvolution,
   estimation, parameter, parameters, shrinkage
%X "... a method for the linear inversion (deconvolution) of band-limited
   reflection seismograms. A large convolution problem is first broken up into a
   sequence of smaller problems. Each small problem is then posed as an
   optimization problem to resolve the ambiguity presented by the band-limited
   nature of the data. A new cost functional is proposed that allows robust
   profile reconstruction in the presence of noise. An algorithm for minimizing
   the cost functional is described. We present numerical experiments ..."
   -- [<A HREF="https://doi.org/10.1137/0907087">doi:10.1137/0907087</A>]['19].
   [Also search for: lasoo stats].
   (Also see lasoo@[<A HREF="https://en.wikipedia.org/wiki/Lasso_(statistics)">wikip</A>]['19].)

%A F. R. Hampel
%A E. M. Ronchetti
%A P. J. Rousseeuw
%A W. A. Stahel
%T Robust Statistics - The Approach Based on Influence Functions
%I Wiley
%P 536
%D 1986
%K stats, book, text, c1986, c198x, c19xx, robust, influence function, location,
   scale, MAD, mean, estimate, estimator, estimators, breakdown point
%X republished in ppb, c2005, isbn:0471735779; isbn13:978-0471735779.
   (robust@[<A HREF="http://en.wikipedia.org/wiki/Robust_statistics">wikip</A>]['07].)

%A R. DerSimonian
%A N. Laird
%T Meta-analysis in clinical trials
%J Controlled Clinical Trials
%V 7
%N 3
%P 177-188
%M SEP
%D 1986
%K conf, c1986, c198x, c19xx, meta analysis, metaAnalysis, stats, statistics,
   clinical trial, der simonian
%X "... examines 8 publ. reviews each reporting results from several related
   trials. Each review pools the results from the relevant trials in order to
   evaluate the efficacy of a certain treatment for a spec. medical condn. ...
   reviews lack consistent assessment of homogeneity of treatment effect before
   pooling. We discuss a random effects approach to combining evidence from a
   series of experiments comparing 2 treatments. ... incorporates the
   heterogeneity of effects in the analysis of the overall treatment efficacy.
   The model can be extended to include relevant covariates which would reduce
   the heterogeneity & allow for more specific therapeutic recommendations. We
   suggest a simple noniterative procedure for characterizing the distribution
   of treatment effects in a series of studies."
   -- [<A HREF="http://dx.doi.org/10.1016/0197-2456(86)90046-2">doi:10.1016/0197-2456(86)90046-2</A>]['08],
      [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/3802833">pub med entry</A>]['08].

%A C. Glymour
%A R. Scheines
%A P. Spirtes
%A K. Kelly
%T Discovering Causal Structure: Artificial Intelligence, Philosophy of
   Science, and Statistical Modeling
%I AcademicPress
%P 412
%D 1987
%K book, text, c1987, c198x, c19xx, TETRAD, cause, effect, causal modelling,
   Bayesian network, learning, AI, inference
%X 1987, hb, uk us isbn13:978-0122869617;
   1987, pb us$73; uk us isbn:1483239500; uk us isbn13:978-1483239507.
   "This book is about a computer program, TETRAD. The program is designed to
   assist in the search for causal explanations of statistical data. There are
   often many millions of possible alternative causal explanations for
   nonexperimental data; human researchers can only consider & evaluate a
   handful of these alternatives & hope that the best explanation they find is
   the best explanation there is. That hope is often in vain. The TETRAD program
   uses artificial intelligence techniques to help the investigator to perform
   a systematic search for alternative causal models using whatever relevant
   knowledge may be available."
   [Also search for: Bayesian network].

%A A. Apostolico
%A A. Fraenkel
%T Robust transmission of unbounded strings using Fibonacci representations
%J IEEE Trans. on Info. Theory
%V 33
%N 2
%P 238-245
%M MAR
%D 1987
%K jrnl, c1987, c198x, c19xx, zz1118, string, Fibonacci, universal, code,
   integer codes, intCodes, Zeckendorf
%X "Families of Fibonacci codes & Fibonacci representations are defined. Their
   main attributes are robustness, manifesting itself by the local containment
   of errors; & simple encoding & decoding. The main application explored is the
   transmission of binary strings in which the length is in an unknown range,
   using robust Fibonacci representations instead of the conventional
   error-sensitive logarithmic ramp representation. Though the former is
   asymptotically longer than the latter, the former is actually shorter for
   very large initial segments of integers."
      ("... In the final Sec.5 we show, however, that a very broad family of
      Fibonacci representations, inc. p_1^m, p_2^m and p_3^m, is universal
      in the sense of Elias[1975]. ...")
   -- [<A HREF="http://dx.doi.org/10.1109/TIT.1987.1057284">doi:10.1109/TIT.1987.1057284</A>]['18], and
      TR85-545[<A HREF="https://docs.lib.purdue.edu/cgi/viewcontent.cgi?article=1463&context=cstech">purd'e</A>]['19].
   (Also see, "... no number has a representation with consecutive 1s. ...
      for a number N, if d(0),...,d(k) are the digits of N's code word, then
      N = SUM_{i=0..k-1} d(i).F(i+2), and d(k-1) = d(k) = 1.
      where F(i) is the ith Fib.number and so F(i+2) is the ith distinct Fib.
      The last bit d(k) ... does not carry place value. ... The only occurence
      if '11' is at the end. ... [is] a self-synchronizing code ..."
   -- FCode@[<A HREF="https://en.wikipedia.org/wiki/Fibonacci_coding">wikip</A>]['18].)
   [Also search for: universal integer code].

%A M. West
%T On scale mixtures of normal distributions
%J Biometrika
%V 74
%N 3
%P 646-648
%M SEP
%D 1987
%K jrnl, c1987, c198x, c19xx, zz0518, scale mixture, scaleMixture, normal,
   stable
%X "The exponential power family of distns of Box & Tiao (1973) is shown to be a
   subset of the class of scale mixtures of normals. The corr. mixing distn. are
   explicitly obtained, identifying a close relationship between the exponential
   power family & a further class of normal scale mixtures, namely the stable
   distributions."
   -- [<A HREF="https://doi.org/10.1093/biomet/74.3.646">doi:10.1093/biomet/74.3.646</A>]['18].
   [Also search for: scaleMixture].
   (Also see locn-test@[<A HREF="https://en.wikipedia.org/wiki/Location_testing_for_Gaussian_scale_mixture_distributions">wikip</A>]['18].)

%A R. J. Beckman
%A M. E. Johnson
%T Fitting the Student-t distribution to grouped data, with application to a
   particle scattering experiment
%J Technometrics
%V 29
%N 1
%P 17-22
%D 1987
%M jrnl, tDistribution, c1987, c198x, c19xx, stats, Students
%X auths @ los alomos '87.

%A N. Metropolis
%T The beginning of the Monte Carlo method
%J Los Alamos Science
%N 15
%P 125-130
%D 1987
%K c1987, c198x, c19xx, monteCarlo, lasVegas, Las Vegas, problem, algorithm,
   estimation, Metropolis, stochastic, optimisation, optimization
%X 00326866@[<A HREF="https://library.lanl.gov/cgi-bin/getfile?00326866.pdf">lanl</A>],
   was [<A HREF="http://jackman.stanford.edu/mcmc/metropolis1.pdf">pdf@jackman.stanford.edu</A>][7/'04].
   Also see MA@[<A HREF="https://en.wikipedia.org/wiki/Monte_Carlo_method">wikip</A>]['23].
   [Also search for: Metropolis Hastings].

%A M. A. Fligner
%A J. S. Verducci
%T Multistage ranking models
%J Amer. Statit. Soc. J.
%V 83
%P 892-901
%D 1988
%K jrnl, c1988, c198x, c19xx, model, rank, ranks, order, ordering, staged
%X series of increasingly constrained models for the modal rank non-null model
   via M.D.['05].

%A I. J. Good
%T The interface between statistics and philosophy of science
%J Statistical Science
%V 3
%N 4
%P 386-397
%D 1988
%K jrnl, IJGood, Gudak, c1988, c198x, c19xx, probability, stats, inference, II
%X Irving John (Jack) Good, 1916-2009, born Isadore Jacob Gudak,
   one of the Bletchley Park cryptanalysts.
   IJG@[<A HREF="http://www.stat.vt.edu/facstaff/ijgood.html">VT</A>]['10].
   [Also search for: IJGood].

%A S. L. Lauritzen
%A D. J. Spiegelhalter
%T Local computations with probabilities on graphical structures and
   their application to expert systems
%J J. Royal Stat. Soc. B
%V 50
%N 2
%P 157-224
%D 1988
%K jrnl, JRSS, bayesian network, causal, networks, stats, c1988, c198x, c19xx,
   L4Ref, system, electromyography, EMG, MUNIN, joint probability distribution,
   Bnet
%X [<A HREF="http://links.jstor.org/sici?sici=0035-9246%281988%2950%3A2%3C157%3ALCWPOG%3E2.0.CO%3B2-Z">at Jstor</A>][1/'04],
   -- [<A HREF="http://www.math.auc.dk/~steffen/">steffen</A>][1/'04].

%A H. Gitay
%A A. D. Q. Agnew
%T Plant community structure, connectance, niche limitation and species guilds
   within a dune slack grassland
%J Plant Ecology
%V 83
%N 1-2
%P 241-248
%M OCT
%D 1989
%K jrnl, c1989, c198x, c19xx, ecology, plant species, dune, dunes, web, zz1205
%X "Species phytomass in 40x40 mm quadrats was used to examine community
   structure in 4 homogeneous areas of veg. in sand dune slacks. ... 9 to 16
   common species in the samples, & most parameters of community structure were
   found to relate consistently to species number. ..."  via M.D.['05]
   -- [<A HREF="http://dx.doi.org/10.1007/BF00031696">doi:10.1007/BF00031696</A>]['05].

%A S. G. Mallat
%T Multiresolution approximations and wavelet orthonormal bases of L^2(R)
%J Trans. of the American Mathematical Soc.
%V 315
%N 1
%P 69-87
%M SEP
%D 1989
%K jrnl, TAMS, AMS, c1989, c198x, c19xx, defn, wavelets, approximation,
   denoising, basis, discrete wavelet transform, DWT, pyramid algorithm,
   Stephane G Mallat
%X " A multiresolution approx. in a seq. of embedded vector spaces (V_j)[j in Z]
   for approx. L^2(R) fns.  ... properties of multires. approx. and prove it is
   characterized by a 2.pi-periodic fn ... . ... can derive a fn psi(x) called
   a WAVELET s.t. (sqrt(2*j).psi(2^jx -k)[(k,j) in Z^2] is an orthonormal basis
   of L^2(R). ... provides a new approach ..."    -- via enesm and DS.
   -- [<A HREF="http://www.jstor.org/stable/2001373">pp@jstor</A>][9/'08].

%A J. A. Nelder
%A P. McCullagh
%T Generalized Linear Models (2nd Edn)
%I CRCpress
%M AUG
%D 1989
%P 532
%O 1st ed., 1983 ?
%K book, text, Wedderburn, statistics, stats, GLM, GLMs, gamma,
   exponential family, logistic, model, c1989, c198x, c19xx
%X 2nd ed 1989, about us$80; isbn:0412317605.
   ... Nelder and Wedderburn wrote the seminal paper on generalized linear
   models in the 1970s. ...
   [Also search for: GAMs stats].

%A C. Chatfield
%T The Analysis of Time Series: An Introduction
%I ChapmanAndHall
%D 1989
%K book, text, c1989, c198x, c19xx, intro, time series, analysis, timeSeries

%A D. J. Spiegelhalter
%A S. L. Lauritzen
%T Sequential updating of conditional probabilities on directed
   graphical structures
%J Networks
%V 20
%P 579-605
%D 1990
%K jrnl, bayesian network, networks, AI, DAG, c1990, c199x, c19xx, Bnet,
   structure, stats
%X Ref in  F r i e d m a n  &  G o l d s z m i d t  '96.
   -- [<A HREF="http://www.math.auc.dk/~steffen/">~steffen</A>][1/'04].

%A F. V. Jensen
%A S. L. Lauritzen
%A K. G. Olesen
%T Bayesian updating in causal probabilistic networks by local computation
%J Computational Statistics Quarterly
%V 4
%P 269-282
%D 1990
%K jrnl, network, net, c1990, c199x, c19xx, join tree, trees, model, zz1205,
   belief updating, update, junction, Bnet
%X join tree clustering or junction tree clustering algorithm
   [also search for: Bayesian network].

%T SAS Language: Reference, version 6, 1st edn
%I SASinst
%D 1990
%P 1042
%K book, text, manual, c1990, c199x, c19xx, stats, statistics

%A G. Williams
%T Inducing and Combining Multiple Decision Trees
%I Australian National U., Canberra,
%D 1990
%K PhD Thesis, ANU, tree, classification, c1990, c199x, c19xx,
   machine learning
%X [<A HREF="http://togaware.redirectme.net/papers/gjwthesis.pdf">pdf</A>]['05] <!-- via Jon P --> .

%A F. M. Malvestuto
%T Approximating discrete probability distributions with decomposable models
%J Transactions on Systems, Man, and Cybernetics
%I IEEE
%V 21
%N 5
%P 1287-1294
%D 1991
%K jrnl, c1991, c199x, c19xx, zz0214, decomposable graphical model, II,
   KL divergence, KL distance, distribution
%X "A heuristic procedure is presented for approximating an n-dimensional
   discrete prob.distribution with a decomposable model of a given complexity.
   It is shown that, WLOG, the search space can be restricted to a suitable
   subclass of decomposable models, whose members are called elementary models.
   The selected elementary model is constructed in an incremental manner
   according to a local-optimality criterion that consists of minimizing a
   suitable cost function. It is shown by an example that the solution computed
   by the procedure is sometimes optimal."
   -- [<A HREF="http://dx.doi.org/10.1109/21.120082">doi:10.1109/21.120082</A>]['14].
   [Also search for: decomposable graphical model].

%A W. Buntine
%T Theory refinement on Bayesian networks
%J UAI '91
%P 52-60
%D 1991
%K conf, UAI, UAI91, AI, network, c1991, c199x, c19xx, theory refinement,
   Bnet, BNets, network, stats, BDe, BDeu
%X 'Theory refinement is the task of updating a domain theory in the light of
   new cases, to be done automatically or with some expert assistance. [...]
   theory refinement under uncertainty is reviewed here in the context of
   Bayesian statistics, a theory of belief revision. [...] reduced to an
   incremental learning task as follows: the learning system is initially
   primed with a partial theory supplied by a domain expert, and thereafter
   maintains its own internal representation of alternative theories which is
   able to be interrogated by the domain expert and able to be incrementally
   refined from data. Algorithms for refinement of Bayesian networks are
   presented to illustrate what is meant by "partial theory", "alternative
   theory representation", etc. The algorithms are an incremental variant of
   batch learning algorithms [...]'
   -- 1303.5709@[<A HREF="https://arxiv.org/abs/1303.5709">arXiv</A>]['20],
      [<A HREF="http://www2.sis.pitt.edu/~dsl/UAI/UAI91/Buntine2.UAI91.html">...pitt.edu/...</A>][1/'04],
      [<A HREF="http://www.hiit.fi/u/buntine/">buntine</A>]['04].
   Note, "BDe" coined later...  [Also search for: Bnet BDe].

%A R. P. Cody
%A J. K. Smith
%T Applied statistics and the SAS programming language
%I PrenticeHall
%D 1991
%K book, text, SAS, c1991, c199x, c19xx, stats
%X [Mos 517.2 C671A3].

%A M. Friendly
%T SAS System for Statistical Graphics
%I SASpress
%P 720
%D 1991
%K book, text, SAS, manual, stats, c1991, c199x, c19xx, data visualisation,
   visualization
%X [<A HREF="http://www.sas.com/apps/pubscat/bookdetails.jsp?pc=56143">@sas</A>]['05]; uk us isbn:1555444415.

%A M. A. Fligner
%A J. S. Verducci
%T Probability Models and Statistical Analysis of Ranking Data
%I SpringerVerlag
%D 1992
%K book, c1992, c199x, c19xx, model, rank, ranks, order, ordering
%X via M.D.['05];  [also search for: Fligner Verducci c1986].

%A A. Gelman
%A D. B. Rubin
%T Inference from iterative simulation using multiple sequences
%J Stat. Sci.
%P 457-472
%V 7
%D 1992
%K SS, stats, statistics, jrnl, Gibbs sampling GS, Markov, chain, termination,
   convergence, converge, c1992, c199x, c19xx
%X see Geyer same issue,
   via: Catherine Scippione.

%A C. J. Geyer
%T Practical Markov chain Monte Carlo
%J Stat. Sci.
%V 7
%P 473-483
%D 1992
%K SS, stats, statistics, jrnl, Gibbs sampling GS, Markov, chain, termination,
   convergence, converge, c1992, c199x, c19xx
%X see Gelman and Rubin same issue.
   via: Catherine Scippione.

%A M. Tanner
%T Tools for Statistical Inference: Methods for the Explanation of Posterior
   Distributions and Likelihood Functions (2nd edn)
%I SpringerVerlag
%D 1993
%K text, book, stats, statistics, probability, Gibbs sampling sample GS,
   Markov, chain, model, Monte Carlo, Monte-Carlo
%X via: Catherine Scippione.

%A B. S. Everitt
%A D. J. Hand
%T Finite Mixture Distributions
%I ChapmanAndHall
%D 1981
%K text, book, c1981, c198x, c19xx, statistics, stats, mixtures, cluster,
   probability distribution, clustering, classification, class, classify,
   DJHand, model, modelling
%X Hargrave Mos517.21 E93F.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/Mixtures/">mixtures</A>].)

%A J. H. Wolfe
%T A computer program for the maximum likelihood analysis of types
%R 65-15
%I U.S. Naval Personnel Res. Activity, San Diego
%D 1965
%K TR, US, NORMIX, c1965, c196x, c19xx
%X (Defense Documentation Centre AD 620 026)  [see paper: Wolfe 1970]
   -- [<A HREF="http://alumnus.caltech.edu/~wolfe/">~wolfe</A>][11/'02].

%A J. W. Tukey
%T The technical tools of statistics
%J Amer. Statistician
%V 19
%N 2
%P 23-28
%M APR
%D 1965
%K jrnl, c1965, c196x, c19xx, zz0713, stats, statistics, quotable
%X -- Jstor [<A HREF="http://dx.doi.org/10.2307/2682374">doi:10.2307/2682374</A>]['13],
      [<A HREF="http://www.jstor.org/stable/2682374">www</A>]['13].
 ('As John Tukey said in '64, "Most uses of the classical tools of statistics
  have been, are, and will be, made by those who know not what they do"'
  -- RvH@[<A HREF="http://dx.doi.org/10.1126/science.341.6144.343-a">www</A>][7/'13].)

%A H. Akaike
%T Fitting autoregressive models for prediction
%J Annals of the Inst. of Stat. Math.
%V 21
%P 243-247
%D 1969
%K jrnl, AISM, c1969, c196x, c19xx, stats, AIC, information criterion,
   criteria, auto regression, time series, timeSeries
%X ref from a  doc' by  W a r r e n  S. S a r l e, 1 9 9 9  [<A HREF="ftp://ftp.sas.com/pub/neural/dojo/dojo.html">*</A>][4/'03].

%A J. H. Wolfe
%T Pattern clustering by multivariate mixture analysis
%J Multivariate Behavioural Research
%V 5
%N ?
%P 329-350
%M JUL
%D 1970
%K EM, likelihood, expectation maximisation, maximization, cluster, classify,
   class, classification, stats, statistics, mixture model, modelling, NORMIX,
   NORMAP, normal, Gaussian, Bernoulli, distribution, multi-variate, model,
   c1970, c197x, c19xx, John Wolfe
%X Cluster analysis ...as a problem in est' params of a mixture of multi-v'
   dist'ns.  The max l.h. theory and num' soln are developed for a fairly
   general class of distributions. ... normals (NORMIX) and multiv'
   Bernoulli dist'ns (Latent classes) ... Fisher Iris data ... artif' data ...
   via: jono at bruce  Thu Aug 25 15:51:21 1994
   EM before the name was invented.            There's a TR in '65.
   -- [<A HREF="http://alumnus.caltech.edu/~wolfe/wolfe70.pdf">paper</A>][11/'02],
      [<A HREF="http://alumnus.caltech.edu/~wolfe/">~wolfe</A>][11/'02].
   [Also search for: EM algorithm c196x] & [also search for: mixture modelling].

%A N. E. Day
%T Estimating the components of a mixture of normal distributions
%J Biometrika
%V 56
%P 463-474
%M DEC
%D 1969
%K EM algorithm, likelihood, expectation maximisation, maximization, cluster,
   classify, mixture model, modelling, class, classification, stats, statistics,
   c1969, c196x, c19xx, parameter estimation, algorithm, learning, discovery
%X "The problem of estimating the components of a mixture of two normal
   distributions, multivariate or otherwise, with common but unknown covariance
   matrices is examined. The maximum likelihood equations are shown to be not
   unduly laborious to solve and the sampling properties of the resulting
   estimates are investigated, mainly by simulation. Moment estimators,
   minimum chi**2 and Bayes estimators are discussed but they appear greatly
   inferior to maximum likelihood except in the univariate case, the
   inferiority lying either in the sampling properties of the estimates or in
   the complexity of the computation. The wider problems obtained by allowing
   the components in the mixture to have different covariance matrices, or by
   having more than two components in the mixture, are briefly discussed,
   as is the relevance of this problem to cluster analysis."
   -- [<A HREF="http://links.jstor.org/sici?sici=0006-3444%28196912%2956%3A3%3C463%3AETCOAM%3E2.0.CO%3B2-B">at Jstor.org</A>][11/'02],
      EM before the name was invented, via: jono  Thu Aug 25 15:51:21 1994.
   [Also search for: EM algorithm c196x].

%A S. Wright
%T Correlation and causation
%J Jrnl. Agricultural Research
%V 20
%P 557-585
%D 1921
%K jrnl, ag res, cause, causes, effect, effects, stats, model, models,
   c1921, c192x, c19xx, causal, correlation, path coefficients
%X ref in notes by KK and AN '02.
   "... an attempt to present a method of measuring the direct influence along
   each separate path in such a system and thus of finding the degree to which
   variation of a given effect is determined by each articular cause. ..."
   [Also search for: Wright causal c19xx].

%A R. A. Fisher
%T On the mathematical foundations of theoretical statistics
%J Philos. Trans. of the Royal Soc., London. A
%V 222
%P 309
%D 1921
%K jrnl, stats, statistics, probability, c1921, c192x, c19xx, RAFisher
%X ref from vonMises1957.

%A R. A. Fisher
%T Statistical Methods for Research Workers
%I OliverAndBoyd
%D 1925 - 1970
%K RAFisher, text, book, statistics, stats, c1925, c192x, c19xx

%A R. A. Fisher
%T The Genetical Theory of Natural Selection
%I OUP
%D 1930
%K RAFisher, book, text, OUP, MolBio, c1930, c193x, c19xx, OUP, genetic,
   genetics, evolution, selection, sexual reproduction, sex, why, sex ratio,
   ratios, population biology, biol, Fisher's principle
%X Later(!), ed J.H.Bennett, OUP, 2000, pp.318, us$50; uk us isbn:0198504403.
   (and  Dover, 1958,  ppb; isbn:0486604667.)
   "F realized that sexual reproduction in particular ... recombination, leads
   to an increase in the genetic variance among offspring. ... the rate of
   evolution is directly proportional to the extant amount of (additive)
   genetic variance present in a population. Therefore, sexual populations can
   respond to selection faster than asexual ps.. ..." -- Schmid-Hempel '01.
   (Also see <A HREF="http://en.wikipedia.org/wiki/Fisher's_principle">wikip</A>]['13].)
   [Also search for: sexual reproduction why].
   Also explains the 1:1 sex ratio (for most species).
   [Also search for: sex ratio biology].

%A R. A. Fisher
%T The concept of inverse probability and the use of likelihood
%J Proc. Cambridge Philos. Soc.
%V 28
%P 257
%D 1932
%K jrnl, stats, probability, statistics, c1932, c193x, c19xx, RAFisher,
   maximum, likelihood principle
%X ref from vonMisesl957.

%A S. Wright
%T The method of path coefficients
%J Annals of Math. Stats.
%V 5
%N 3
%P 161-215
%M SEP
%D 1934
%K jrnl, causal, cause, causes, effect, effects, model, c1934, c193x, c19xx,
   correlation, coefficient, stats, graphical
%X 1177732676@[<A HREF="http://projecteuclid.org/euclid.aoms/1177732676">projecteuclid</A>]['15],
   [<A HREF="http://dx.doi.org/10.1214/aoms/1177732676">doi:10.1214/aoms/1177732676</A>]['15],
   2957502@[<A HREF="http://www.jstor.org/stable/2957502">Jstor</A>]['15].
   (ref in notes by KK and AN '02.)

%A R. A. Fisher
%T The Design of Experiments
%I Oliver-and-Boyd
%D 1935 - 1966
%K RAFisher, text, book, stats, statistics

%A R. A. Fisher
%A F. Yates
%T Statistical Tables for Biological, Agricultural and Medical Research
%I OliverAndBoyd
%D 1938 - 1963
%K RAFisher, c19xx, text, book, stats, statistics

%A D. J. Best
%A N. I. Fisher
%T Efficient simulation of the von Mises distribution
%J J. Royal Stat. Soc., ser.C (Applied Stats.)
%V 28
%N 2
%P 152-157
%D 1979
%K jrnl, c1979, c197x, ca9xx, zz0423, sample, sampling, vonMises, von Mises,
   direction, distribution, random, generate, generation, RNG, PRNG, PRVG, stats
%X "... A wrapped Cauchy is used as an envelope to to give an
   acceptance-rejection method ..."
   -- [<A HREF="https://www.jstor.org/stable/2346732">jstor:2346732</A>]['23].
   (work at CSIRO, NSW, Australia), via AK.
   [Also search for: vonMises PRVG] & [also search for: vonMises distribution].

%A T. Fine
%T Extrapolation when very little is known about the source
%J Inf. and Control
%V 16
%N 4
%P 331-359
%M JUN
%D 1979
%K jrnl, c1970, c197x, c19xx, zz1118, extrapolation, extrapolate, stats,
   series, predict, prediction, AI, II
%X "... propose and examine a nonstatistical approach to extrapolation. The
   basic problem is the association of a real number y to a sequence of real
   numbers x in such a manner that the pair (x, y) conforms with a set of data
   sequences D = (xi, yi), {iti} = 1, M, our prior knowledge of the data source,
   and our objectives. Our aim is to so define the activity of extrapolation
   that we can derive extrapolations with only minimal assumptions about the
   data source. ... The basic principle we adhere to is that the extrapolation
   of x is a function of only those yi for which x is similar to or close to
   xi; extrapolate the output of a system by examination of the outputs of
   similar systems. ..."
   -- [<A HREF="https://doi.org/10.1016/S0019-9958(70)90177-4">doi:10.1016/S0019-9958(70)90177-4</A>]['18].

%A G. E. P. Box
%T Science and Statistics
%J J. of the Amer. Stat. Assoc.
%V 71
%P 791-799
%D 1976
%K jrnl, c1976, c197x, c19xx, zz0915, stats, models, wrong,
   scientific method
%X -- 2286841@[<A HREF="http://www.jstor.org/stable/2286841">Jstor</A>]['15].
   (Also see wrong@[<A HREF="https://en.wikipedia.org/wiki/All_models_are_wrong">wikip</A>]['15].)
   [Also search for: Box stats].

%A G. E. P. Box
%T Robustness in the strategy of scientific model building
%J Robustness in Statistics
%E R. L. Launer
%E G. N. Wilkinson
%I AcademicPress
%P 201-236
%D 1979
%K jrnl, c1976, c197x, c19xx, zz0915, GEPBox, stats, all, models, wrong,
   some useful, model, quote, quotable, scientific method
%X "The philosophy of robust procedures is discussed. It is argued that the
   present emphasis by statistical researchers on ad hoc methods of robust
   estimation is mistaken. Classical methods of estimation should be retained
   using models which more appropriately represent reality. Attention should not
   be confined merely to discrepancies arising from outliers & heavy tailed
   distributions but should be extended to include serial dependence, need for
   transformation & other problems. Some researches of this kind using Bayes
   theorem are discussed. ..."
   (* "All models are wrong but some are useful" (p.2) *)
   -- ADA070213@[<A HREF="http://www.dtic.mil/docs/citations/ADA070213">mil</A>]['15],
      [<A HREF="https://doi.org/10.1016/B978-0-12-438150-6.50018-2">doi:10.1016/B978-0-12-438150-6.50018-2</A>]['17],
      [<A HREF="https://books.google.com/books/about/Robustness_in_the_Strategy_of_Scientific.html?id=B4jMtgAACAAJ">g''gle</A>]['15],.
  (Also see wrong@[<A HREF="https://en.wikipedia.org/wiki/All_models_are_wrong">wikip</A>]['15].)
   [Also search for: Box stats].

%A R. C. H. Cheng
%A G. M. Feast
%T Some simple Gamma variate generators
%J J. of the Royal Stat. Soc., Series C (Applied Statistics)
%V 28
%N 3
%P 290-295
%D 1979
%K jrnl, JRSS, c1979, c197x, c19xx, zz0214, Gamma, probability distribution,
   random, RNG, PRNG, generator
%X "Gamma variates with index alpha > 1 ... two adaptions of Kinderman and
   Monahan's technique ... fast for all alpha > 1 ..."
   -- 2347200@[<A HREF="http://www.jstor.org/stable/2347200">Jstor</A>]['14].
   [Also search for: Gamma PRNG].

%A I. J. Good
%T Studies in the history of probability and statistics XXXVII:
   A. M. Turing's statistical work in world war II
%J Biometrika
%V 66
%N 2
%P 393-396
%M AUG
%D 1979
%K Alan Turing, stats, ban, bans, deciban, nit, nat, bit, nits, nats, bits,
   origin, evidence, weight, likelihood, likeliness, likely, guess, hypothesis,
   inference, II, WW2, WWII, WW II, 1940, 1941, c194x, information theory,
   code breaking, decrypt, cryptanalysis, decypher, cypher, Bletchley Park,
   Ultra, IJGood, c1979, c197x, c19xx, Bandurism, Banburismus, complexity,
   log, Bayes factor, factors, Bayesian, statistics
%X "1. Preamble: ...
    2. Bayes Factors:
       Turing introduced the expression '(Bayes) factors in favour of a
       hypothesis' without the qualification 'Bayes'. The (Bayes) factor in
       favour of the hypothesis H, provided by evidence E, is O(H|E)/O(H),
       the factor by which the initial odds of H must be multiplied to get
       the final odds. It is an easy but important theorem that the Bayes
       factor is equal to pr(E|H)/pr(E|H') where H' denotes the negation
       of H. Perhaps it is fair to say that Bayes only got half-way to the
       Bayes factor. This thm was already familiar to Jeffreys (1939) but
       without Turing's appealing terminology. The result is especially
       'Bayesian' if either H or H' is composite.
    3. Sequential analysis and log factors:
       Turing was one of the independent inventors of sequential analysis for
       which he naturally made use of the logarithm of the Bayes factor H.
       He did not know that the logarithm of a Bayes factor occurred in a
       paper by the famous philosopher Charles Saunders Peirce (1878),
       who had called it weight of evidence. ..."
   -- 2335677@[<A HREF="http://www.jstor.org/stable/2335677">Jstor</A>]['14],
      [<A HREF="http://dx.doi.org/10.1093/biomet/66.2.393">doi:10.1093/biomet/66.2.393</A>]['14], and
      [also search for: Peirce c1878].
   And quoted in Hodges 'Alan T. the Enigma,' p.197:
      "Turing was the first to recognise one value of naming the units
      in terms of which the weight of evidence is measured. When the
      base of the logarithms was e he called the unit a natural ban, and
      simply a ban when the base was 10 ...  Turing introduced the name
      deciban in the self-explanatory sense of one-tenth of a ban, an
      analogy with the decibel. The reason for the name ban was that
      tens of thousands of sheets were printed in the town of Banbury
      on which weights of evidence were entered in decibans for carrying
      out an important process called Bandurisms."
   I.e., 1 ban = 3+ bits;  1 deciban ~ 0.3 bits.
      I.J.Good was another @ B.Park.
      [Also search for: IJGood]  and  [also search for: Bletchley Park].
   Also see Banburismus@[<A HREF="http://en.wikipedia.org/wiki/Banburismus">wikip</A>]['14].

%A G. K. Zipf
%T Selected studies of the Principle of Relative Frequency in Language
%I Harvard U.P.
%D 1932
%K book, text, Zipf's, Zipfs, law, c1932, c193x, c19xx
%X from a ref in a '03 paper by W. L i.
   (Also see Zipf@[<A HREF="http://en.wikipedia.org/wiki/George_Kingsley_Zipf">wikip</A>]['15].)

%A G. K. Zipf
%T Human Behaviour and the Principle of Least Effort
%I AddisonWesley
%D 1949
%K book, text, Zipf's, Zipfs, law, stats, statistics, c1949, c194x, c19xx
%X f = k / r,  f = word frequncy,  r = word rank.
   Also see '68 book.  (ref from a paper)

%A G. K. Zipf
%T The Psycho-Biology of Language: An Introduction to Dynamic Psychology
%I AddisonWesley
%D 1968
%K book, text, Zipf's, Zipfs, law, c1968, c196x, c19xx
%X also see '49 book.  (ref from a paper)
   (Also see,
   "P_n~1/n^a where P_n is the freq of the nth ranked word & 'a' is almost 1."
   -- Zipf@[<A HREF="http://en.wikipedia.org/wiki/George_Kingsley_Zipf">wikip</A>]['15].)

%A R. A. Fisher
%T The Theory of Inbreeding
%I OliverBoyd
%D 1949, 1965
%K RAFisher, text, book, in breed, breeding, inbred, biol, biology, gene, genes

%A R. A. Fisher
%T Contributions to Mathematical Statistics
%I Wiley
%D 1950
%K RAFisher, c1950, c195x, c19xx, text, book, stats

%A I. J. Good
%T Probability and the Weighing of Evidence
%I Griffin, London
%P 119
%D 1950
%K book, text, IJGood, Gudak, c1950, c195x, c19xx, probability, evidence,
   II, inference, information theory, weight, weighting, weighing
%X Irving John (Jack) Good, 1916-2009, born Isadore Jacob Gudak,
   one of the Bletchley Park cryptanalysts.
   asin:B0000CHL1R.
   See [<A HREF="https://books.google.com.au/books/about/Probability_and_the_Weighing_of_Evidence.html?id=k9g0AAAAMAAJ&redir_esc=y">google_books</A>]['16].
   (Review at [<A HREF="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1037253/">ncbi</A>]['16].)
   IJG@[<A HREF="http://www.stat.vt.edu/facstaff/ijgood.html">VT</A>]['10].
   [Also search for: IJGood].

%A R. A. Fisher
%T Statistical Methods and Scientific Inference
%I OliverBoyd
%D 1956, 1959
%K RAFisher, c1956, c195x, c19xx, text, book, stats, statistics,
   inductive inference, II
%X also Hafner, New-York 1973.

%A S. L. Sclove
%T Improved estimators for coefficients in linear regression
%J J. Amer. Stat. Assoc.
%V 63
%N 322
%P 596-606
%M JUN
%D 1968
%K jrnl, JASA, c1968, c196x, c19xx, stats, estimator, estimate, coefficient,
   linear regression, least squares, shrinkage, principal component, components
%X "Point estimators for the coeffs. in orthogonal l.r. which are better than
   the ordinary least squares est. are obtained when at least 3 coeffs. are to
   be est.. The measure of goodness of an est. is the sum, or weighted sum, of
   the component-wise mean squared errors. Some of the new ests. have
   interpretations as ests. which depend upon preliminary tests of significance.
   These ests. may be esp. appropriate when the independent variables fall into
   2 sets or are ordered, as in polynomial regression or regression on principal
   components. The extension of the results to the general case of nonorthogonal
   regression is given; here the measure of goodness of an est. is the mean of a
   quadratic form in the componentwise errors."  -- via enesm and DS.
   -- [<A HREF="http://www.jstor.org/stable/2284030">pp@jstor</A>]['08].

%A N. Abramson
%T Information Theory and Coding
%I McGrawHill
%D 1963
%K book, text, c1963, c196x, c19xx, code, codes, arithmetic coding,
   data compression
%X uk us isbn:0070001456; uk us isbn13:978-0070001459.
   ("... arith.c. first proposed by [Elias '60s] and first
   described by [Abramson 63] ..." -- Salomon & Motta 5th ed 2010.)

%A J. L. Hodges jr.
%A E. L. Lehmann
%T Estimates of location based on rank tests
%J Annals of Math. Stats
%V 34
%N 2
%P 598-611
%M JUN
%D 1963
%K jrnl, c1963, c196x, c19xx, robust, statistics, rank, test, estimate,
   estimator, efficient, LH
%X [<A HREF="http://links.jstor.org/sici?sici=0003-4851%28196306%2934%3A2%3C598%3AEOLBOR%3E2.0.CO%3B2-U">paper@jstor</A>]['07]
   [Also search for: algorithm 616] (which includes the estimator).

%E J. H. Bennett
%T Collected Papers of R. A. Fisher (5 vols)
%I The University-of-Adelaide
%D 1971 - 1974
%K RAFisher, text, book, statistics, stats, c197x, c19xx

%A A. D. Wyner
%T An upper bound on the entropy series
%J Inf. and Control
%V 20
%P 176-181
%D 1972
%K jrnl, c1972, c197x, c19xx, zz0619, intCodes, information, entropy,
   inequality
%X "An upper bound is established for the entropy corr. to a +ve integer valued
   random variable X in terms of the expectation of certain fns of X. In
   particular, we show that the entropy is finite if E log X < inf. Further, if
   Pr{X=n} is non-increasing in n (n=1,2,...), then the entropy is finite only
   if E log X < inf."
   "... Thm 1. If p is s.t. H(p) < inf, the E log X < inf. ...
   Thm 2. ... Thm 3 ..."
   -- [<A HREF="https://doi.org/10.1016/S0019-9958(72)90365-8">doi:10.1016/S0019-9958(72)90365-8</A>]['19].

%A J. A. Nelder
%A R. W. M. Wedderburn
%T Generalized linear models
%J J. Royal Stat. Soc., A,
%V 135
%P 370-384
%D 1972
%K jrnl, JRSS, GLM, GLMs, exponential family, gamma, model, statistics, stats,
   normal, Gaussian, binomial, Poisson, Gamma, distributions,
   c1972, c197x, c19xx
%X ... iterative wighted linear reg'n used ... max LH ests of params ...
   some exponential family and ... normal, binomial, Poisson, Gamma ...
   (in jstor [<A HREF="http://links.jstor.org/sici?sici=0035-9238%281972%29135%3A3%3C370%3AGLM%3E2.0.CO%3B2-X">paper</A>][6/'03])
   [Also search for: GAMs stats].

%A G. Marsaglia
%T Choosing a point from the surface of a sphere
%J Ann. Math. Stat.
%V 43
%P 645-646
%D 1972
%K jrnl, c1972, c197x, c19xx, generate, picking, random vectors, directions,
   sphere, uniform, RVG, PRVG, PRNG
%X Includes method 2:
      Generate X = [x_1, x_2, ..., x_m], where the indep. x_i are
      from N(0,1); then normalise X.
   (paper is set in terms of 3-D and 4-D)
   -- [<A HREF="http://www.jstor.org/stable/2240001">Jstor</A>]['13].
   [Also search for: PRVG sphere].

%A R. W. M. Wedderburn
%T Quasi-likelihood functions, generalized linear models and
   the Gauss-Newton method
%J Biometrika
%V 61
%P 439-447
%D 1974
%K jrnl, GLM, GLMs, statistics, stats, c1974, c197x, c19xx
%X Also see [<A HREF="http://en.wik
pedia.org/wiki/Gauss-Newton_algorithm">Gauss-Newton@wikip</A>]['07].

%A D. F. Andrews
%A C. L. Mallows
%T Scale mixtures of normal distributions
%J J. Royal Stat. Soc.. Series B (Methodological)
%V 36
%N 1
%P 99-102
%D 1974
%K jrnl, JRSS, c1974, c197x, c19xx, zz0518, scale mixture, scaleMixture, stats,
   normal, exponential, logistic
%X "This paper presents necessary & sufficient condns under which a random
   variable X may be generated as the ratio Z/V where Z & V are indep.
   & Z has a std normal distn. This representation is useful in Monte Carlo
   calculations. It is established that when 0.5*V^2 is exponential,
   X is double exponential; & that when V/2 has the asymptotic distribution
   of the Kolmogorov distance statistic, X is logistic."
   -- 2984774@[<A HREF="http://www.jstor.org/stable/2984774">Jstor</A>]['18].
   [Also search for: scaleMixture].
   (Also see locn-test@[<A HREF="https://en.wikipedia.org/wiki/Location_testing_for_Gaussian_scale_mixture_distributions">wikip</A>]['18].)

%A G. J. Cane
%T Linear estimation of parameters of the Cauchy distribution based on
   sample quantiles
%J J. Amer. Stat. Assoc.
%V 69
%N 345
%P 243-245
%M NOV
%D 1974
%K jrnl, c1974, c197x, c19xx, zz0718, Gwenda, Cauchy distribution, pdf,
   estimate, estimator, quantile, heavy, fat tail, tailed, fatTail, half
%X "Asymptotically best linear unbiased estimates (ABLUE) of the location &
   scale params (when both are unknown) of the Cauchy distn, based on k order
   statistics selected from a large sample, are considered. It is shown that the
   joint asymptotic relative efficiency (JARE) of the two ests. is maximized
   when the sample quantiles are equally spaced, & expressions are derived for
   the coefficients used in these estimates. In estimating the scale param.
   using a reasonably large # of quantiles, it is found that not much weight is
   attached to the extreme observations or those close to the median."
   -- [<A HREF="https://doi.org/10.1080/01621459.1974.10480163">doi:10.1080/01621459.1974.10480163</A>]['18],
      2285535@[<A HREF="https://www.jstor.org/stable/2285535">Jstor</A>]['19].
   [Also search for: Cauchy distribution].
   (Also see,
   "... Cauchy.d's  pdf(x|x_0,g) = 1/(pi g {1+((x-x_0)/g)^2})
    ... mean & variance undefined, median=x_0, mode=x_0 ...
    ... [Eg,] the truncated mean of the middle 24% of the sample order stats
    produces an estimate for x_0 that is more efficient than using either the
    sample median or the full sample mean.
    ... maximum likelihood est.... numerical solution ..."
   -- C@[<A HREF="https://en.wikipedia.org/wiki/Cauchy_distribution">wikip</A>]['18].)

%A K. Fukunaga
%A L. Hostetler
%T The estimation of the gradient of a density function, with applications in
   pattern recognition
%J IEEE Trans. on Info. Th.
%V 21
%N 1
%P 32-40
%M JAN
%D 1975
%K jrnl, c1975, c197x, c19xx, zz1112, mean shift, meanShift, pdf, stats,
   procedure, mode seeking, algorithm, density function, kernel
%X "Nonparametric density gradient est. using a generalized kernel approach
   ... Conditions on the kernel fns are derived to guarantee asymptotic
   unbiasedness, consistency, & uniform consistency of the ests.. ...
   generalized to obtain a simple mean-shift est. that can be extended in
   ak-nearest-neighbor approach. Applications of g.est. to patt.rec. ...
   clustering & intrinsic dimensionality problems ..."
   -- [<A HREF="http://dx.doi.org/10.1109/TIT.1975.1055330">doi:10.1109/TIT.1975.1055330</A>]['12].
   (Also see mean-shift@[<A HREF="http://en.wikipedia.org/wiki/Mean_shift">wikip</A>]['12].)
   [Also search for: meanShift].

%A G. J. Chaitin
%T A theory of program size formally identical to information theory
%J JACM
%V 22
%N 3
%P 329-340
%M JUN
%D 1975
%K jrnl, JACM, c1975, c197x, c19xx, zz1118,
%X "A new defn of program-size complexity is made. H(A,B/C,D) is defined to be
   the size in bits of the shortest self-delimiting program for calculating
   strings A & B if one is given a minimal-size self-delimiting program for
   calculating strings C & D.  This differs from previous defns: (1) programs
   are required to be self-delimiting, i.e. no program is a prefix of another, &
   (2) instead of being given C & D directly, one is given a program for
   calculating them that is minimal in size.  Unlike previous defns, this one
   has precisely the formal properties of the entropy concept of info. theory.
   [Eg] H(A,B) = H(A) + H(B/A) + 0(1). Also, if a program of length k is
   assigned measure 2^{-k}, then H(A) = -log2 (the prob. that the std universal
   computer will calculate A) + 0(1)."
   -- [<A HREF="https://doi.org/10.1145/321892.321894">doi:10.1145/321892.321894</A>]['18]
      [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.84.8489&rep=rep1&type=pdf">c'teseer</A>]['18].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">M.M.L.</A>].)

%A D. de Solla Price
%T A general theory of bibliometric and other cumulative advantage processes
%J J. American Soc. for Info. Sci.
%V 27
%N 5
%P 292-306
%M SEP
%D 1976
%K jrnl, c1976, c197x, c19xx, zz1214, SollaPrice, deSollaPrice, graph, network,
   graphModel, power law, preferential attachment, distribution, success,
   rich get richer, Matthew effect, papers, citations, publish, perish,
   Beta, Barabasi, Albert, Bradford Law, Lotka, Pareto, Zipf, stats, model
%X "A Cumulative Advantage Distribution is proposed which models statistically
   the situation in which success breeds success. It differs from the Negative
   Binomial Distn in that lack of success, being a non-event, is not punished
   by increased chance of failure. It is shown that such a stochastic law is
   governed by the Beta fn, containing only one free param., & this is approx.
   by a skew or hyperbolic distn of the type that is widespread in bibliometrics
   & diverse social science phenomena. In particular, this is shown to be an
   appropriate underlying probabilistic theory for the Bradford Law, the Lotka
   Law, the Pareto & Zipf Distns, & for all the empirical results of citation
   frequency analysis. As side results one may derive also the obsolescence
   factor for literature use. The Beta fn is peculiarly elegant for these
   manifold purposes because it yields both the actual & the cumulative distn
   in simple form, & contains a limiting case of an inverse square law to which
   many empirical distributions conform."
   -- [<A HREF="http://dx.doi.org/10.1002/asi.4630270505">doi:10.1002/asi.4630270505</A>]['14].
   (*Also see "... first applied to the growth of networks by Derek de Solla
    Price in 1976[12] who was interested in the networks of citation ..." --
    -- [<A HREF="http://en.wikipedia.org/wiki/Barab%C3%A1si%E2%80%93Albert_model">www</A>]['14].*)
   [Also search for: graphModel] and [also search for: Matthew effect publish].

%A R. Christensen
%T Log-Linear Models and Logistic Regression
%I SpringerVerlag
%S Statistics
%P 485
%D 1997
%K book, text, intro, c1974, c197x, c19xx, log linear model, logLinearModel,
   logLinear, models, analysis, LLA, logistic regression, stats,
   Christensen97, viaFPj
%X 2nd ed 1997; hb us$107; uk us isbn:0387982477; uk us isbn13:978-0387982472.
   "... log-linear models for contingency tables, but in this 2nd ed., greater
   emphasis has been placed on logistic regression. ... such as logistic
   discrimination and generalised linear models, and builds upon the
   relationships between these basic models for continuous data and the
   analogous log-linear and logistic regression models for discrete data. ..."
   -- [<A HREF="https://doi.org/10.1007/b97647">doi:10.1007/b97647</A>]['18].
   [Also search for: log linear model].

%A M. J. Zaki
%A S. Parthasarathy
%A M. Ogihara
%A W. Li
%T New algorithms for fast discovery of association rules
%J ICDM
%P 283-286
%D 1997
%K conf, ICDM, ICDM3, c1997, c199x, c19xx, tidset, tidsets, algorithm, rule,
   frequent itemset, itemsets
%X "... new algs. for fast assoc. mining, which scan the [DB] only once,
   addressing the open Q whether all the rules can be efficiently extracted in a
   single DB pass. ... use novel itemset clustering techniques to approx. the
   set of potentially maximal frequent itemsets. ... make use of efficient
   lattice traversal techniques to generate the frequent itemsets contained in
   each cluster. We propose two clustering schemes based on equiv.classes &
   maximal hypergraph cliques, & study two traversal techniques based on bottom-
   -up & hybrid search. We also use a vertical DB layout to cluster related
   transactions together. Experimental results show improvements of over an
   order of magnitude ..."
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.42.3283">c'teseer</A>]['14],
      pdf@[<A HREF="http://www.cse.ohio-state.edu/dmrl/papers/kdd97.pdf">ohioState</A>]['14],
      [<A HREF="http://dl.acm.org/citation.cfm?id=898240">acm</A>]['14].

%A Y. Boykov
%A O. Veksler
%A R. Zabih
%T Markov random fields with efficient approximations
%J IEEE Computer Vision and Pattern Recognition Conf.
%P ?-?
%D 1998
%K conf, field, c1998, c199x, c19xx, image
%X [also search for: random field].   via Mike D.

%A R. S. Cerveny
%A R. C. Balling
%T Weekly cycles of air pollutants, precipitation and tropical cyclones in
   the coastal NW Atlantic region
%J Nature
%V 394
%P 561-563
%M AUG
%D 1998
%K jrnl, weather patterns, pattern, cycle, cycles, cyclic, weekend, weekends,
   week, weekly, human activity, influence, pollution, rain, precipitation,
   c1998, c199x, c19xx, zz0303
%X Direct human influences on climate have been detected at local scales,
   such as urban temperature increases and precipitation enhancement, and
   at global scales. A possible indication of an anthropogenic effect on
   regional climate is by identification of equivalent weekly cycles in
   climate and pollution variables. Weekly cycles have been observed in
   both global surface temperature and local pollution data sets. Here we
   describe statistical analyses that ...
   -- [<A HREF="http://dx.doi.org/10.1038/29043">doi:10.1038/29043</A>][3/'03]
   Authors at Arizona State U.

%A B. Efron
%T R. A. Fisher in the 21st century
%J Statistical Science
%V 13
%N 2
%P 95-122
%D 1998
%K jrnl, RAFisher, statistics, stats, fiducial, survey, history, essay, zz1298
%X Invited paper pres' at the '96 Fisher lecture.
   Includes several 'comments' by others.

%T Thomas Bayes
%I American Council for Learned Societies
%B Dictionary of Scientific Biography
%D ??
%K Bayes, Bayesian, law, theorem, probability, statistics, MML, MDL, II
%X Thomas Bayes 1702 - 1761.

%A Y. Tashiro
%T On methods for generating uniform random points on the surface of a sphere
%J Annals Inst. of Stat. Math.
%V 29
%N 1
%P 295-300
%D 1977
%K jrnl, c1977, c197x, c19xx, zz1113, uniform probability distribution, sphere,
   generate, direction, directions, vectors, point, RVG, PRVG, PRNG
%X "Some methods for generating random points uniformly distributed on the
   surface of an n-sphere have been proposed to simulate spherical processes on
   computer. A std method is to normalize random pts inside of the sphere ...
   ... we shall offer direct methods for generating uniform random pts on the
   surface of a unit n-sphere, which can be easily combined with Marsaglia's
   idea for getting more improved methods. Our method in even dimensions was
   obtained by M.Sibuya[6], but a differential-geometric view-point will make
   analyses simpler, even in odd dimensions."
   -- [<A HREF="http://dx.doi.org/10.1007/BF02532791">doi:10.1007/BF02532791</A>]['13].
   [Also search for: PRVG sphere].

%A A. P. Dempster
%A N. M. Laird
%A D. B. Rubin
%T Maximum likelihood from incomplete data via the EM algorithm
%J J. Royal Stat. Soc. B
%V 39
%N 1
%P 1-38
%D 1977
%K JRSS, jrnl, EM, expectation maximization, maximisation, c1977, c197x, c19xx,
   stats, statistics, missing, censored, EMalgorithm
%X "A broadly applicable algorithm for computing maximum likelihood estimates
   from incomplete data is presented at various levels of generality. Theory
   showing the monotone behaviour of the likelihood and convergence of the
   algorithm is derived. Many examples are sketched, including missing value
   situations, applications to grouped, censored or truncated data, finite
   mixture models, variance component estimation, hyperparameter estimation,
   iteratively reweighted least squares and factor analysis."
   -- [<A HREF="http://links.jstor.org/sici?sici=0035-9246%281977%2939%3A1%3C1%3AMLFIDV%3E2.0.CO%3B2-Z">at Jstor.org</A>][11/'02],
      ref in a paper by  L a w r e n c e  and  R e i l l y '90.
   [Also search for: EM algorithm c196x] and maybe also leaving out c196x.

%A R. J. A. Little
%A D. B. Rubin
%T Statistical Analysis with Missing Data
%I John-Wiley
%D 1987
%K book, text, stats, statistics, EM
%X ref in a paper by  L a w r e n c e  and  R e i l l y '90.

%A I. Diaconis
%A R. Graham
%T Spearman's footrule as a measure of disarray
%J J. Royal Stat. Soc., Ser.B
%V 39
%P 262-268
%D 1977
%K JRSS, stats, c1977, c197x, c19xx, zz0513, rank, ranking, top k list, lists,
   partial, permutation, distance, disarray, disorder, Spearman footrule,
   Kendall's tau, metric
%X "S's measure of disarray D is the sum of the abs. values of the diffs.
   between the ranks. We treat D as a metric on the set of perms.. The limiting
   mean, variance & normality are established. D is shown to be related to the
   metric I arising from Kendall's tau thru the combinatorial inequality
   I <= D <= 2I."
   -- [<A HREF="http://www.jstor.org/stable/2984804">Jstor</A>]['13].
   [Also search for: rank permutation].

%A T. Gonzalez
%A S. Sahni
%A W. R. Franta
%T An efficient algorithm for the Kolmogorov-Smirnov and Lilliefors tests
%J ACM Trans. Math. Software
%V 3
%N 1
%P 60-64
%M MAR
%D 1977
%K ACM, TOMS, jrnl, stats, statistics, zz1195
%X linear time alg' for the tests: that a random sample X1, X2, ... Xn
      was drawn from a given continuous distribution F(X).
   Divide range of F(X) into n+1 intervals.
   [7 refs].

%A T. Dalenius
%T Towards a methodology for statistical disclosure control
%J Statistik tidskrift
%D 1977
%K c1977, c197x, c19xx, zz0620, stats, differential privacy, disclosure,
   individual, anonymity, security, database, databases
%X Also see DP@[<A HREF="https://en.wikipedia.org/wiki/Differential_privacy">wikip</A>]['20].

%A J. O. Berger
%T Statistical Decision Theory and Bayesian Analysis
%I SpringerVerlag
%D 1993
%K book, text, statistics, stats, Bayes, II, zz1295
%X via R.A.B.

%A P. Cage
%T New algorithm for data compression
%J The C User Journal
%D 1994
%K c1994, c199x, c19xx, zz0624, file, text, compression, algorithm,
   byte pair encoding, digram coding, file, text, compress
%X "... a simple general-purpose data comp. alg., called Byte Pair Encoding
   (BPE) ...finding the most frequently occurring pairs of adjacent bytes in the
   data & replacing all instances of the pair with a byte that was not in the
   original data ... [multi-pass] ..."
   -- [<A HREF="http://www.pennelynn.com/Documents/CUJ/HTML/94HTML/19940045.HTM">www</A>]['24].
   Also see BPE@[<A HREF="https://en.wikipedia.org/wiki/Byte_pair_encoding">wikip</A>]['24].
   [Also search for: text compression].

%A H. A. L. Kiers
%T SIMPLIMAX: Oblique rotation to an optimal target with simple structure
%J Psychometrika
%V 59
%P 567-579
%D 1994
%K jrnl, correlation, factor, factors, analysis, c1994, c199x, c19xx, stats,
   statistics, principal, components, PCA, data, varimax, way
%X [<A HREF="http://ppswmm.ppsw.rug.nl/~kiers/">auth</A>][8/'04]
   -- [<A HREF="http://ppswmm.ppsw.rug.nl/~kiers/main.html">main.html</A>][8/'04].

%A A. T. A. Wood
%T Simulation of the von Mises Fisher distribution
%J Communications in Statistics - Simulation and Computation
%V 23
%N 1
%P 157-164
%D 1994
%K jrnl, c1994, c199x, c19xx, vonMises, vMF, random, vectors, directions,
   directional, probability distribution, sphere, generate, generating,
   RVG, PRVG, PRNG
%X "Ulrich (1984) discussed ... alternative ... given. ... application of the
   vMF-F matric distn for rotations of R^3 or, equivalently, the Bingham distn
   on the unit sphere in R^4. ... leads to sim. the B.distn in R^q when q > 4."
   -- [<A HREF="http://dx.doi.org/10.1080/03610919408813161">doi:10.1080/03610919408813161</A>]['13].
   [Also search for: PRVG sphere].

%A C. Meek
%A C. Glymour
%T Conditioning and Intervening
%J British J. for the Philosophy of Sci.
%V 45
%P 1001-1021
%D 1994
%K jrnl, cause, effect, causality, dominance principle, conditioning,
   intervene, intervening, intervention, AI, II, c1994, c199x, c19xx
%X "The dominance principle superceded the expected utility principle in the
   philosophical work of Robert Nozick. Since his analysis, similar writing has
   concentrated on a comparison between conditioning or intervening to change
   probabilities in realistic cases. It is shown that probabilities generated
   by an intervention can be calculated when causal parts are established and
   existent probabilities follow Markov conditions."   -- via k.k. ['04].

%A M. D. Maltz
%T Deviating from the mean: The declining significance of significance
%J J. of Research in Crime and Delinquency
%V 31
%N 4
%P 434-463
%M NOV
%D 1994
%K jrnl, test, testing, law, c1994, c199x, c19xx, zz1102
%X [<A HREF="http://tigger.uic.edu/~mikem/">auth' home and .pdf</A>][11/'02].

%A J. M. Bernardo
%A A. F. M. Smith
%T Bayesian Theory
%I Wiley
%D 1994
%K book, text, statistics, stats, Bayes, II, conjugate prior, priors,
   c1994, c199x, c19xx, zz1295
%X via R.A.B.

%A D. L. Donoho
%A I. M. Johnstone
%T Ideal spatial adaptation via wavelet shrinkage
%J Biometrika
%V 81
%P 425-455
%D 1994
%K jrnl, statistics, stats, wavelets, data set, sets, c1994, c199x, c19xx
%X data set: [<A HREF="ftp://ftp.sas.com/pub/neural/dojo/dojo.html">sas.com</A>][4/'03].
   (auth@[<A HREF="https://statweb.stanford.edu/~donoho/">Stanf</A>]['18].)

%A L. Brelman
%T Better subset regression using the nonnegative garrote
%J Technometrics
%V 37
%N 4
%P 373-384
%D 1995
%K jrnl, c2995, c199x, c19xx, zz0719, stats, lasoo, nonnegative garrote, garrot,
   garotte, garrotte, nnGarrote, shrinkage
%X "A new method, called the nonnegative (nn) garrote, is proposed for doing
   subset regression. It both shrinks and zeroes coefficients. In tests on real
   and simulated data, it produces lower prediction error than ordinary subset
   selection. It is also compared to ridge regression. If the regression
   equations generated by a procedure do not change drastically with small
   changes in the data, the procedure is called stable. Subset selection is
   unstable, ridge is very stable, and the nn-garrote is intermediate.
   Simulation results illustrate the effects of instability on prediction
   error."
   -- [<A HREF="https://doi.org/10.1080/00401706.1995.10484371">doi:10.1080/00401706.1995.10484371</A>]['19].
   [Also search for: stats lasoo].
   (Also see lasoo@[<A HREF="https://en.wikipedia.org/wiki/Lasso_(statistics)">wikip</A>]['19].)

%A G. Webb
%T OPUS: An efficient admissible algorithm for unordered search
%J J. of Articial Intelligence Res.
%V 3
%P 483-417
%D 1995
%K jrnl, AI, association rule, rules, c1995, c199x, c19xx, apriori,
   frequent item set, sets
%X Also see Y2K conf paper.
   -- [<A HREF="http://www.csse.monash.edu.au/~webb/">~webb</A>][1/'04].

%A M. Boerlijst
%A P. Hogeweg
%T Spatial gradients enhance persistence of hypercycles
%J Physica D
%V 88
%P 29-39
%D 1995
%K jrnl, ecology, c1995, c199x, c19xx, gradient, hypercycle. stats, statistics
%X [<A HREF="http://dx.doi.org/10.1016/0167-2789(95)00178-7">doi:10.1016/0167-2789(95)00178-7</A>]['07]
   -- [<A HREF="http://citeseer.ist.psu.edu/boerlijst95spatial.html">citeseer</A>]['07] via MD.

%A D. L. Donoho
%A I. M. Johnstone
%A G. Kerkyacharian
%A D. Picard
%T Wavelet shrinkage: Asymptopia? (with discussion)
%J J. of the Royal Stat. Soc., Series B
%V 57
%N 2
%P 301-369
%D 1995
%K jrnl, JRSS, JRSSB, c1995, c199x, c19xx, statistics, wavelets, data set,
   training, test cases, benchmark, sets, blocks, bumps, heavisine, doppler,
   denoising, thresholding,
%X "Much recent effort has sought asymptotically minimax methods for recovering
   infinite dimensional objects - curves, densities, spectral densities,
   images - from noisy data. A now rich & complex body of work develops nearly
   or exactly minimax estimators for an array of interesting problems.
   Unfortunately, the results have rarely moved into practice, for a variety of
   reasons - among them being similarity to known methods, computational
   intractability & lack of spatial adaptivity. We discuss a arise from iterated
   mappings of the centre of the interval to which the map is applied.
   Particular attention is paid to the shape of an invariant distribution in the
   tails or in the neighbourhood of a pole of its density. A new technique is
   developed for this application.  It enables us to combine `parametric'
   information, available from the structure of the map, with `nonparametric'
   information obtainable from numerical experiments."
   data set: [<A HREF="ftp://ftp.sas.com/pub/neural/dojo/dojo.html">sas.com</A>][4/'03].
   (auth@[<A HREF="https://statweb.stanford.edu/~donoho/">Stanf</A>]['18].)
   (NB. JRSS gets into jstor.org.)

%A D. L. Donoho
%A I. M. Johnstone
%T Adapting to unknown smoothness via wavelet shrinkage
%J J. Amer. Stat. Assoc.
%V 90
%P 1200-1224
%D 1995
%K jrnl, JASA, statistics, data set, sets, c1995, c199x, c19xx
%X data set: [<A HREF="ftp://ftp.sas.com/pub/neural/dojo/dojo.html">sas.com</A>][4/'03].
   (auth@[<A HREF="https://statweb.stanford.edu/~donoho/">Stanf</A>]['18].)

%A R. J. MacG. Dawson
%T The "unusual episode" data revisited
%J J. of Statistics Education
%V 3
%N 3
%P ?-?
%D 1995
%K jrnl, Titanic, 1912, ship, sinking, ships, passenger, passengers, survival,
   mortality, death, data set, example, dataset, stats, delve, zz0303
%X A certain dataset, giving population at risk and fatalities for
   "an unusual episode," has been used for some time in classrooms as an
   elementary exercise in statistical thinking, the challenge being to deduce
   the context of the data. Unfortunately, the "solution" has frequently been
   circulated orally, with few details. Moreover, discrepancies have been found
   between the dataset and the "solution," which would render the exercise
   somewhat artificial. This paper investigates the discrepancies and includes
   a fully-explained version of the dataset for classroom use.  ...
   ...some differences of opinion on the number lost... 1,490, 1,502, and 1,517
   ... or 1635 and 1595 However, the British Board of Trade Inquiry Report
   ... claims a death toll of 1490. ... Modern sources seem to agree that the
   true numbers are [about] 1,500, but the exact numbers may never be known.
   ... the numbers [in the data set] are for passengers only. ...
   -- [<A HREF="http://www.amstat.org/publications/jse/v3n3/datasets.dawson.html">html</A>][2/'03],
   Also see [<A HREF="http://www.cs.utoronto.ca/~delve/data/summaryTable.html">delve@utoronto</A>][2/'03].

%A W. W. Cohen
%T Learning rules that classify emails
%J Proc. Spring Symp. on Machine Learning for Information Access
%P ?-?
%D 1996
%K conf, spam, junk mail, email, classify, categorize, c1996, c199x, c19xx,
   filter, RIPPER
%X [Also search for: spam email].

%T ISIS - Information, Statistics and Induction in Science
%E D. L. Dowe
%E K. B. Korb
%E J. J. Oliver
%W Melbourne, Australia
%I WorldScientific
%P 396
%M AUG
%D 1996
%K proc, proceedings conference, ISIS, ISIS96, conf, inductive inference, II,
   artificial intelligence, AI, minimum message length, MML, encoding,
   description, MDL, information theory, machine learning, jono, dld, zz0896
%X uk us isbn:981-02-2824-4.
   Sessions: Classification Trees, Graphs and Rules;
      Regression, Foundations of Statistics; Biology; Economics;
      Philosophy of AI; Scientific Discovery; Minimum Encoding Inference;
      Mixture Modelling
   Organized by members of:-  csse, monash.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A G. J. McLachlan
%A T. Krishnan
%T The EM Algorithm and Extensions
%I Wiley
%D 1997
%K book, text, c1997, c199x, c19xx, probability, statistics, maximum likelihood,
   estimation, expectation maximisation, EM, zz0497
%X Hargrave H Mos 517.51 M161E.    uk us isbn:0417123587.
   [Also search for: EM algorithm]  or  [also search for: EM algorithm c196x].

%A L. Dehaspe
%A L. De Raedt
%T Mining association rules with multiple relations
%J Proc. of the 7th Int. Workshop on Inductive Logic Programming
%I SpringerVerlag
%S LNAI
%V 1297
%P 125-132
%D 1997
%O Proc. 9th Dutch Conf. on Art. Intell. (NAIC-97), pp.343-353, 1997
%K conf, de haspe, deRaedt, rule, frequent item sets, set FIS,
   relational data, logic, WARMR, ILP
%X The application of algorithms for efficiently generating association rules
   is so far restricted to cases where information is put together in a single
   relation. We describe how this restriction can be overcome through the
   combination of the available algorithms with standard techniques from the
   field of inductive logic programming. We present the system WARMR, which
   extends APRIORI (Agrawal et. al, 1996) to mine association rules in multiple
   relations. We apply WARMR to the natural language processing task of mining
   part-of-speech tagging rules in a large corpus of English.
   -- [<A HREF="http://www.cs.kuleuven.ac.be/~ldh/publicaties/Dehaspe97a:proc.ps.gz">paper</A>][12/'02].
   Also see L. DeH's thesis '98,  and FARMER '03.

%A L. Dehaspe
%T Frequent Pattern Discovery in First-Order Logic
%K PhD
%I K. U. Leuven
%M DEC
%D 1998
%K PhD, thesis, de haspe, frequent item set, sets, FIS, association rule,
   rules, relational data, data mining, 1st, logics, WARMR, c1998, c199x, c19xx
%X We present a general formulation of the frequent pattern discovery problem,
   where both the database and the patterns are represented in some subset of
   first-order logic. In recent years, the usage and size of databases have
   grown dramatically, due to a constant decrease in the cost of both the
   collection and the storage of huge amounts of data. The need for tools to
   exploit the popular Data Warehouse has grown accordingly and has given rise
   to a rapidly evolving research field at the intersection of statistics,
   databases and machine learning: Data Mining and Knowledge Discovery in
   Databases (KDD). Within KDD, the discovery of frequent patterns has been
   studied in a variety of settings. In its simplest form, known from
   association rule mining, the task is to discover all frequent item sets,
   i.e., all combinations of items that are found in a sufficient number of
   examples. The fundamental task of association rule and frequent set
   discovery has been extended in various directions, allowing more useful
   patterns to be discovered with special purpose algorithms. We discuss a
   unified representation in first-order logic that gives insight to the
   blurred picture of the frequent pattern discovery domain. Within the
   first-order logic formulation a number of dimensions appear that relink
   diverged settings. We present algorithms for frequent pattern discovery in
   first-order logic that are well-suited for exploratory data mining: they
   offer the flexibility required to experiment with standard and --in
   particular-- novel settings not supported by special purpose algorithms.
   We show how frequent patterns in first-order logic can be used as building
   blocks for statistical predictive modeling, and demonstrate the scientific
   and commercial potential of frequent pattern discovery in first-order logic
   via an application in chemical toxicology, where the task is to identify
   cancer-causing chemical substances.
   -- [<A HREF="http://www.cs.kuleuven.ac.be/~ldh/publicaties/dehaspe98:phd.ps.gz">thesis</A>][12/'02]  also see paper '97.

%A A. Gelman
%A J. B. Carlin
%A H. S. Stern
%A D. B. Rubin
%T Bayesian Data Analysis
%I ChapmanAndHall
%D 1995
%K book, text, c1995, c199x, c19xx, zz0798, zz0512, Bayesian, statistics, stats,
   conjugate prior, priors, AI, II, machine learning, probability, simulation,
   inductive inference, model, models, L4Ref, L5Ref
%X 3rd ed 2012; hb us$66; uk us isbn:1439840954; uk us isbn13:978-1439840955.
   2nd ed 2003; hb us$62; uk us isbn:158488388X; uk us isbn13:978-1584883883.
   1st ed 1995; hb us$50; uk us isbn:0412039915; uk us isbn13:978-0412039911.
   "... how to conceptualize, perform, and critique statistical analyses from
   a Bayesian perspective. Using examples largely from the authors' own
   experiences, the book focuses on modern computational tools and obtains
   inferences using computer simulations. Its unique features include thorough
   discussions of the methods for checking Bayesian models and the role of the
   design of data collection in influencing Bayesian statistical analysis."
   (Orig. via Chip L.)

%A S. Kullback
%A R. A. Leibler
%T On information and sufficiency
%J Annals of Math. Stats.
%V 22
%N 1
%P 79-86
%D 1951
%K KL, KL51, jrnl, statistics, stats, distance, divergence, probability,
   distribution, c1951, c195x, c19xx, theory
%X [<A HREF="https://projecteuclid.org/euclid.aoms/1177729694">proje'cl'd</A>]['15],
   [<A HREF="http://dx.doi.org/10.1214/aoms/1177729694">doi:10.1214/aoms/1177729694</A>]['15].

%A E. H. Simpson
%T The interpretation of interaction in contingency tables
%J J. of the Royal Statistical Society, Series B
%V 13
%N 2
%P 238-241
%D 1951
%K jrnl, JRSS, stats, contingency table, Simpson's paradox, c1951, c195x, c19xx,
   second order interaction, three, 3D, two, 2D, Simpsons, probability
%X "The definition of second order interaction in a (2x2x2) table given by
   Bartlett is accepted, but it is shown by an example that the vanishing of
   this second order interaction does not necessarily justify the mechanical
   procedure of forming the three component 2x2 tables and testing each of
   these for significance by standard methods."
   -- [<A HREF="http://links.jstor.org/sici?sici=0035-9246%281951%2913%3A2%3C238%3ATIOIIC%3E2.0.CO%3B2-J">Jstor</A>]['05].

%A H. Robbins
%T Some aspects of the sequential design of experiments
%J Bull. Amer. Math. Soc.
%V 58
%P 527-535
%D 1952
%K jrnl, c1952, c195x, c19xx, zz0316, stats, multi armed bandit, bandits,
   MABandit, resource allocation, investment, experiment, sequential, adaptive
%X -- [<A HREF="http://dx.doi.org/10.1090/S0002-9904-1952-09620-8">doi:10.1090/S0002-9904-1952-09620-8</A>]['16].
   Also see MABandit@[<A HREF="https://en.wikipedia.org/wiki/Multi-armed_bandit">wikip</A>]['16].
   [Also search for: bandit stats].

%A S. Kullback
%T Information Theory and Statistics
%I Wiley
%D 1959
%K book, text, stats, probability distribution, distance, inference, estimate,
   estimators, Leibler, c1959, c195x, c19xx
%X library of congress number 59-5881;
   also see K and L in Annals Math Stats v22 '51.

%A P. Gunwald
%A P. Kontkanen
%A P. Myllymaki
%A T. Silander
%A H. Tirri
%T Minimum encoding approaches for predictive modelling
%J Uncertainty in A.I.
%D 1998
%P 183-192
%K conf, UAI, UAI98, AI, artificial intelligence, message, description,
   MML, MDL, MMLWF, comparison, prediction, predict, zz0798
%X NB. prediction and inference are different.
   See also  B o u l t o n  and  W a l l a c e  '68;
   R i s s a n e n '78;   W a l l a c e  and  F r e e m a n '87.
   16 refs.

%A R. C. Littell
%A G. A. Milliken
%A W. W. Stroup
%A R. D. Wolfinger
%T SAS System for Mixed Methods
%I SAS Inst.
%D 1996
%K SAS, book, stats, statistics, mixed model, models, fixed,
   random, effect, effects, zz1298
%X ... an effect is called *fixed* if [the data] represent all possible
   levels of the factor, or at least all levels about which inference
   is to be mode. ...
   ... Factor effects are *random* if the levels [in the data] represent
   only a random sample of a larger set of potential levels. ...
   ... A *mixed model* is one that contains both fixed and random effects. ...
    - Via  D e a n Mc K' ['98].    Issued by from SAS Inst, Cary, NC, USA.

%A J. Besag
%A P. Clifford
%T Sequential Monte Carlo p-values
%J Biometrika
%V 78
%P 301-304
%D 1991
%K jrnl, pValue, sequence, series, statistics, correlation, correlated, zz0299
%X From a cit'n in a paper.

%A H. Blockeel
%A L. De Raedt
%T Top-down induction of first-order logical decision trees
%J Artificial Intelligence
%V 101
%N 1-2
%P 285-297
%D 1998
%K jrnl, deRaedt, tree, AI, II, dtree, classification, supervised, Tilde, ILP,
   inductive logic programming, TDIDT, c1998, c199x, c19xx, relations,
   relational, predicate, logic, zzOSP, zOSP04
%X "TILDE is a system that from a set of pre-classified examples induces
   decision trees that can be used to classify unseen examples. TILDE
   follows the inductive logic programming paradigm: both the examples and
   the decision trees are represented by means of first order predicate logic.
   However, unlike most ILP systems it uses the learning from interpretations
   setting, which aims more specifically at classification than the classical
   ILP settings."  [<A HREF="http://www.cs.kuleuven.ac.be/~ml/Tilde/">Tilde</A>][12/'03];
   via Am@nda C.

%A D. Percy
%T ?
%J Mathematics Today
%V 35
%P 54-?
%D 1999 ?
%K dart, darts, aim, aiming, probability, statistics, zz0599
%X New Scien't #2182 17/4/1999 p16 reports that David Percy
   of Salford University U.K. suggests that the best aiming point
   for *novices* at darts is the bulls-eye (centre).
  (Presumably this is for the purposes of getting a large total,
   not for starting or finishing.)

%A L. K. Saul
%A M. G. Rahim
%T Maximum likelihood and minimum classification error factor analysis for
   automatic speech recognition
%J IEEE Trans. on Speech and Audio Processing
%V 8
%N 2
%P 115-125
%D 1999
%K jrnl, c1999, c199x, c19xx, HMM, EM
%X "... derive an Expectation-Maximization (EM) algorithm for maximum
   likelihood estimation and a gradient descent algorithm for improved class
   discrimination. Speech recognizers are evaluated on two tasks, one small-
   sized vocabulary (connected alpha-digits) and one medium-sized vocabulary
   (New Jersey town names).  ..."
   -- [<A HREF="http://www.cis.upenn.edu/~lsaul/papers/fa_ieee99.pdf">pdf</A>]['06].
   [Also search for: EM algorithm c196x] and [also search for: FactorAnalysis].

%A J. Hartigan
%T Clustering Algorithms
%I Wiley
%D 1975
%K book, text, statistics, cluster, class, classification, taxonomy,
   algorithm, mixture modeling, modelling, model, c1975, c197x, c19xx
%X hb; uk us isbn:047135645X; uk us isbn13:978-0471356455.
   via deanM.

%A H. E. Williams
%A J. Zobel
%T Compressing integers for fast file access
%J COMPJ
%V 42
%N 3
%P 193-201
%D 1999
%K jrnl, COMPJ, data, compress, compression, integer, number, numbers, files,
   Elias, delta, gamma, Golomb, variable-byte, c1999, c199x, c19xx, code, codes,
   coding, gzip, zip, zz0999
%X "... including the Elias gamma and delta codes, Golomb coding,
   and a variable-byte integer scheme. ...
   Table 2 shows that it is very hard indeed to beat gzip for compression,
   "but because it is adaptive it cannot be used for random access to data ..."
   -- [<A HREF="https://doi.org/10.1093/comjnl/42.3.193">doi:10.1093/comjnl/42.3.193</A>]['18],
   pdf@<A HREF="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.18.3782&rep=rep1&type=pdf">cits''r</A>]['18].
   [Also search for: integer code].

%A C. Croux
%A P. J. Rousseeuw
%T Time-efficient algorithms for two highly robust estimators of scale
%J Computational Stats.
%V 1
%P 411-428
%D 1992
%K jrnl, c1992, c199x, c19xx, Q estimator, estimate, variance, algorithm
%X "... O(n log n) time, O(n) space algs for two ..."
   -- [<A HREF="http://www.agoras.ua.ac.be/abstract/Timeff92.htm">www</A>]['07].

%A H. B. Newcombe
%A M. E. Fair
%A P. Lalonde
%T The use of names for linking personal records
%I J. Amer. Stat. Assoc.
%V 87
%N 420
%P 1193-1204
%M DEC
%D 1992
%L jrnl, JASA, c1992, c199x, c19xx, record linkage, data, name, names, aliases,
   spelling, RL, PRL, CanLink, GIRLS
%X "... anthony ~ tony, joseph ~ joe, william ~ bill, ..."
   "... known as CANLINK or GIRLS (for Generalized Iterative Record
   Linkage System)  ..."
   -- [<A HREF="http://www.jstor.org/stable/2290660">Jstor</A>]['10].
   [Also search for: record linkage data].

%A U. M. Fayyad
%A K. B. Irani
%T On the handling of continuous-valued attributes in decision tree generation
%J Machine Learning
%V 8
%N 1
%P 87-102
%M JAN
%D 1992
%K Dtree, c1992, c199x, c19xx, AI, II, trees, discrete, continuous,
   discretisation, discretization, classification, attribute
%X "... result serves to give a better understanding of the entropy measure, to
   point out that the behavior of the information entropy heuristic possesses
   desirable properties that justify its usage in a formal sense, & to improve
   the efficiency of evaluating continuous-valued attributes for cut value
   selection. Along with the formal proof, we present empirical results that
   demonstrate the theoretically expected reduction in evaluation effort for
   training data sets from real-world domains."
   -- [<A HREF="http://dx.doi.org/10.1023/A:1022638503176">doi:10.1023/A:1022638503176</A>]['08].

%A S. Becker
%A G. E. Hinton
%T Learning mixture-models of spatial coherence
%J Neural Computation
%V 5
%N 2
%P 267-277
%D 1993
%K sequence, series, probability, inference, II, AI, space, 2D, coherent, model
%X via rohan '99.

%A P. Howson
%A P. Urbach
%T Scientific Reasoning: The Bayesian Approach
%I OpenCourt
%D 1993
%O 3rd ed, pp.470, OpenCourt, April 2005
%K book, text, c1993, c199x, c19xx, stats, classical statistics, probability,
   evidence, statistical inference, II, likelihood, significance, controversial,
   hypothesis test, testing, Pvalue, p value, reject null, frequentist,
   philosophy of science
%X 3rd ed 2005; pb us$26; uk us isbn:081269578X; uk us isbn13:978-0812695786.
   "... examine the way in which scientists appeal to probability arguments, &
   demonstrate that the classical approach to statistical inference is full of
   flaws. Arguing the case for the Bayesian method with little more than basic
   algebra, the authors show that it avoids the difficulties of the classical
   system. The book also refutes the major criticisms leveled against Bayesian
   logic, especially that it is too subjective. ..."
   -- via KK, who recommends the 2nd edition...
   ... 2nd ed 1993; asin:B008IT40OW.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Bayes/">Bayes</A>].)

%A P. J. Rousseeuw
%A C. Croux
%T Alternatives to the median absolute deviation
%J J. American Stat. Assoc.
%V 88
%N 424
%P 1273-1283
%M DEC
%D 1993
%K jrnl, c1993, c199x, c19xx, MAD, alternative, estimate, estimator, variance,
   scale, variability, standard deviation, robust, stats, statistics
%X "... median absolute deviation MAD[n] = 1.4826 med[i]{|x[i]-med[j]x[j]|} ...
   We consider the estimator S[n] = 1.1926 med[i]{med[j]|x[i]-x[j]|} and the
   estimator Q[n]... 0.25-quantile of the distances {|x[i]-x[j]|; i < j}. ...
   Both...can be computed in O(n log n) time and O(n) space. ...
   ... Gaussian efficiency of S[n] is 58% ... Q[n] attains 82% ..."
   -- [<A HREF="http://links.jstor.org/sici?sici=0162-1459%28199312%2988%3A424%3C1273%3AATTMAD%3E2.0.CO%3B2-U">paper@Jstor</A>]['07].
   (Also see [<A HREF="http://en.wikipedia.org/wiki/Median_absolute_deviation">MAD@wikip</A>]['07].)
   [Also search for: Rousseeuw c1992] for the algorithm.

%A M. Berthod
%A Z. Kato
%A S. Yu
%A J. Zerubia
%T Bayesian image classification using Markov random-fields
%J Image and Vision Computing
%V 14
%N 4
%P 285-295
%D 1996
%K sequence, series, probability, inference, II, AI, field, 2D, IP
%X via rohan '99.

%A P. Cheeseman
%A M. Self
%A J. Kelly
%A W. Taylor
%A D. Freeman
%A J. Stutz
%T Bayesian classification
%J Seventh National Conference on Artificial Intelligence
%P 607-611
%W Saint Paul, MN
%D 1988
%K autoclass, class, cluster, inference, II, AI, c1988, c198x, c19xx
%X via rohan '99.

%A P. Cheeseman
%A J. Stutz
%T Bayesian classification (AUTOCLASS): Theory and results
%J Advances in Knowledge Discovery and Data Mining
%I AAAI Press/ MIT Press
%D 1996
%K autoclass, probability, inference, II, AI, c1996, c199x, c19xx
%X via rohan '99.

%A P. Cheeseman
%A J. Stutz
%A R. Hanson
%T Bayesian classification with correlation and inheritance
%J Proc. of the Int. Joint Conf. on Artificial Intelligence
%P 692-698
%I MorganKaufmann
%D 1991
%K autoclass, series, probability, inference, II, AI
%X via rohan '99.

%A F. Chen
%A S. Figlewski
%A J. Heisler
%A A. Weigend
%T Uncovering hidden structures in bonds future trading
%J CIFEr'98, New York
%M March
%D 1998
%K c1998, c199x, c19xx, bond, futures, trade, stock exchange, stocks, market,
   time series, timeSeries, probability, inference, II, AI, structure
%X [<A HREF="http://www.stern.nyu.edu/aweigend/Research/Papers/Tradestyles">[www]</A>]['99],
   via rohan '99.

%A S. Chib
%T Calculating posterior distributions and modal estimates in Markov
   mixture-models
%J J. of Econometrics
%V 75
%N 1
%P 79-97
%D 1996
%K model, jrnl, sequence, time series, timeSeries, probability, inference,
   II, AI
%X via rohan '99.

%A U. Holst
%A G. Lindgren
%T Recursive estimation in mixture-models with Markov regime
%J IEEE Transactions on Information Theory
%V 37
%N 6
%P 1683-1690
%D 1991
%K jrnl, time series, timeSeries, probability, model, inference, II, AI
%X via rohan '99.

%A X. D. Huang
%A Y. Ariki
%A M. A. Jack
%T Hidden Markov Models for Speech Recognition
%I Edinburgh Uni. Press, Edinburgh
%D 1990
%K speech, book, text, series, probability, inference, II, AI
%X via rohan '99.

%A T. Hastie
%A R. J. Tibshirani
%T Generalized Additive Models
%I ChapmanHall
%D 1990
%K book, text, c1990, c199x, c19xx, model, linear, stats, statistics, GAM, GAMs
%X hb, us$95, isbn:0412343908.  2nd ed. c1999.
   [Also search for: GLMs stats].

%A M. Kendall
%A J. D. Gibbons
%T Rank Correlation Methods
%I EdwardArnold
%D 1990
%K book, text, c1990, c199x, c19xx, rank correlation, partial, permutation,
   rank, ranking, ordering, ordered, stats, top k list, lists, Kendall tau
%X [Also search for: rank permutation].

%A R. M. Gray
%T Entropy and Information Theory
%I SpringerVerlag
%P 332
%D 1990
%K book, text, c1990, c199x, c19xx, zz0311, information, entropy, coding,
   codes
%X 2nd ed 2011; hb us$85; uk us isbn:1441979697; uk us isbn13:978-1441979698.
      "About one-third of the book is devoted to Shannon source and channel
      coding theorems; the remainder addresses sources, channels, and codes and
      on information and distortion measures and their properties."
   1st ed 1990; hb us$80; uk us isbn:0387973710; uk us isbn13:978-0387973715.
      "... devoted to the theory of probabilistic information measures and their
      application to coding theorems for information sources and noisy channels.
      The eventual goal is a general development of Shannon's math. theory of
      communication ..."
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. H. Bennett
%T Statistical Inference and Analysis Selected Correspondence of R. A. Fisher
%I OUP
%D 1990
%K book, text, OUP, stats, RAFisher, c1990, c199x, c19xx, statistics, Bayesian,
   maximum likelihood, quote, quotable, foundations, frequentist, Senn
%X "[o]ur palace of adamant rests upon foundations of gossamer which have
   to be renewed two or three times a week by the indefatigable labours of
   mathematical logicians, and yet the superstructure seems to be secure and
   quite habitable." -- R.A.Fisher quoted by S.Senn (from Bennett 1990, p.129)
      in 'Names and Games, A Reply to Deborah G. Mayo,'
      RMM, vol.3, pp.19-21, 2012, (via R.B.),
      pdf@[<A HREF="http://www.rmm-journal.de/downloads/Reply_Senn-1.pdf">rmm</A>]['15],
      [<A HREF="http://www.rmm-journal.de/htdocs/volume3.html">vol.3</A>]['15].
   [Also search for: RAFisher].

%A A. Jalali
%A J. Pemberton
%T Mixture-models for time-series
%J J. of Applied Probability
%V 32
%N 1
%P 123-138
%D 1995
%K jrnl, model, time series, timeSeries, probability, inference, II, AI
%X via rohan '99.

%A B. H. Juang
%A S. E. Levinson
%A M. M. Sondhi
%T Maximum-likelihood estimation for multivariate mixture observations
   of Markov-chains
%J IEEE Transactions on Information Theory
%V 32
%N 2
%P 307-309
%D 1986
%K jrnl, model, models, chain, series, probability, inference, II, AI
%X via rohan '99.

%A B. Kanefsky
%A J. Stutz
%A P. Cheeseman
%T An automatic classification of a Landsat/TM image from Kansas (FIFE)
%R FIA-91-26
%I NASA Ames Research Center, Artificial Intelligence Branch
%M SEP
%D 1991
%K TR, autoclass, series, probability, inference, II, AI, IP, model
%X via rohan '99.

%A K. Knill
%A S. Young
%T Hidden Markov models in speech and language processing
%P 27-68
%J Corpus-Based Methods in Language and Speech Processing
%E S. Young
%E G. Bloothooft
%I Kluwer Academic
%D 1997
%K HMM, series, probability, inference, II, AI
%X via rohan '99.

%A K. Koperski
%A J. Han
%A J. Adhikary
%T Mining knowledge in geographical data
%J CACM
%D 1998
%K jrnl, CACM, 2D, image, IP, probability, inference, II, AI
%X [<A HREF="http://db.cs.sfu.ca/sections/publication/smmdb/smmdb.html">www</A>]['98],
   via rohan '99.

%A C.R. Latimer
%T Eye-movement data: cumulative fixation time and cluster analysis
%J Behav. Res. Meth. Inst. Computers
%V 20
%P 437-470
%D 1988
%K jrnl, model, models, series, probability, inference, II, AI
%X via rohan '99.

%A S. E. Levinson
%A L. R. Rabiner
%A M. M. Sondhi
%T An introduction to the application of the theory of probabilistic
   functions of a Markov process to automatic speech recognition
%J Bell System Technical Journal
%V 62
%N 4
%P 1035-1074
%M APR
%D 1983
%K jrnl, series, probability, inference, II, AI
%X via rohan '99.

%A G. Ulrich
%T Computer generation of distributions on the m-sphere
%J J. Royal Statistical Soc., Series C (Appl. Statist.)
%V 33
%N 2
%P 158-163
%D 1984
%K jrnl, c1984, c298x, c19xx, zz1113, statistics, stats, Fisher, von Mises, vMF,
   vonMises, directional, directions, probability, sphere, pseudo random vector,
   generator, generate, RVG, PRVG, PRNG
%X "A technique ... pseudo random vectors from families of distributions on
   unit m-sphere. ... applied to Fisher von Mises ..."
   -- [<A HREF="http://www.jstor.org/stable/2347441">Jstor:2347441</A>]['13].
   [Also search for: PRVG sphere].

%A T. L. Lai
%A H. Robbins
%T Asymptotically efficient adaptive allocation rules
%J Advances in Applied Mathematics
%V 6
%N 1
%P 4-22
%M MAR
%D 1985
%K jrnl, c1985, c198x, c19xx, zz0216, stats, allocation rule,
   MABandit, multi armed bandit, bandits
%X "... How should we sample x1, x2,. . .  sequentially from the k populns
   in order to achieve the greatest possible expected value of the sum
   S=x1+...+x, as n -> infinity? ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0196-8858(85)90002-8">doi:10.1016/0196-8858(85)90002-8</A>]['16].
   Also see MABandit@[<A HREF="https://en.wikipedia.org/wiki/Multi-armed_bandit">wikip</A>]['16].
   [Also search for: bandit stats].

%A L. Devroye
%T Non-Uniform Random Variate Generation
%I SpringerVerlag
%D 1986
%K book, text, c1986, c198x, c19xx, zz0413, random, variable, variables, sample,
   generate, pseudo random number generation, PRNG, probability distribution,
   simplex, exponential, generating, sampling
%X Also see [<A HREF="http://luc.devroye.org/rnbookindex.html">L.D.</A>]['13].
      And,
      "[To generate] a point from the D-dimensional simplex ... generate
      IID random samples from an exponential distribution (which you do by
      sampling X from [0,1] uniformly, and returning -log(X)). Take D samples,
      & then normalize. Voila, the resulting list of numbers is a uniform
      sample from the simplex." -- S.Venkatasubramanian.

%A R. Ng
%A J. Han
%T Efficient and effective clustering method for spatial data mining
%J Proc. of 1994 Int'l Conf. on Very Large Data Bases (VLDB'94)
%P 144-155
%W Santiago, Chile
%M SEP
%D 1994
%K 2D, model, probability, inference, II, AI
%X via rohan '99.

%A J. Besag
%T On the statistical analysis of dirty pictures
%J J. Royal Stat. Soc. B
%V 48
%P 259-302
%D 1986
%K jrnl, JRSS, 2D, Markov field, fields, picture, c1986, c198x, c19xx,
   image, processing, images, IP, zz1099
%X H519.106 R888J.B
   -- [<A HREF="http://links.jstor.org/sici?sici=0035-9246%281986%2948%3A3%3C259%3AOTSAOD%3E2.0.CO%3B2-%23">article at jstor</A>][1/'04],
      [<A HREF="http://www.jstor.org/journals/00359246.html">www</A>][10/'99].
   (monash can)  -- Tor'sten [10/'99].

%A D. K. Panjwani
%A G. Healey
%T Markov random-field model for unsupervised segmentation of textured
   color images
%J IEEE Transactions on Pattern Analysis and Machine Intelligence
%V 17
%N 11
%P 1128-1128  ? or p939-954 ?
%D 1995
%K jrnl, 2D, image, model, models, probability, inference, c1995, c199x, c19xx,
   II, AI
%X via rohan '99.

%A E. Papp
%A R. Baxter
%T Selection of variables for gold exploration from deep drill hole data
   using a novel information theory method
%J Geological Society of Australia Abstracts
%V 37
%M SEP
%D 1994
%K jrnl, mine, mining, geology, model, models, 2D, 3D, series,
   probability, inference, II, AI
%X via rohan '99.

%A C. Meek
%T Causal inference and causal explanation with background knowledge
%J Proc. of the Eleventh Conf. on Uncertainty in A.I.
%I MorganKaufmann
%P 403-410
%D 1995
%K conf, UAI, causal network, networks, TETRAD, c1995, c199x, c19xx, zz0805,
   orientation rules, collider, Bayesian, cause, effect, UAI11
%X [<A HREF="http://www.phil.cmu.edu/projects/tetrad/">TETRAD</A>]['05].

%A J. Y. Park
%A L. Kurz
%T Unsupervised segmentation of textured images
%J Information Sciences
%V 92
%N 1-4
%P 255-276
%D 1996
%K jrnl, IP, probability, inference, II, AI
%X via rohan '99.

%A I. Pilowsky
%A S. Levine
%A D. M. Boulton
%T The classification of depression by numerical taxonomy
%J Brit. J. Psychiatry
%P 937-945
%D 1969
%K jrnl, mixture modelling, model, clustering, probability, inference, II, AI
%X via rohan '99.

%A L. Seymour
%A C. S. Ji
%T Approximate Bayes model selection procedures for Gibbs-Markov random-fields
%J J. Statistical Planning and Inference
%V 51
%N 1
%P 75-97
%D 1996
%K jrnl, model, 2D, series, probability, inference, II, AI
%X via rohan '99.

%A J. Shi
%A J. Malik
%T Normalized cuts and image segmentation
%J IEEE Conf. Computer Vision and Pattern Recognition
%M JUN
%D 1997
%K conf, 2D, image, IP, probability, inference, II, AI
%X via rohan '99.

%A P. Smyth
%A M. Ghil
%A K. Ide
%A J. Roden
%A A. Fraser
%T Detecting atmospheric regimes using cross-validated clustering
%J Third International Conference on Knowledge Discovery and
   Data Mining (KDD-97)
%D 1997
%K conf, probability, inference, II, AI
%X via rohan '99.

%A T. Zhang
%A R. Ramakrishnan
%A M. Livny
%T BIRCH: an efficient data clustering method for very large databases
%J Proceedings of ACM-SIGMOD International Conference of Management of Data
%P 103-114
%M JUN
%D 1996
%K conf, cluster, probability, inference, II, AI
%X via rohan '99.

%A R. Ihaka
%A R. Gentleman
%T R: A language for data analysis and graphics
%J J. of Computational and Graphical Statistics
%V 5
%N 3
%P 299-314
%D 1996
%K jrnl, R, RR, statistics, stats, software, package, platform, SPlus,
   c1996, c199x, c19xx
%X ref' via  r o h a n  2/'00 (not seen).
   -- [<A HREF="http://www.ci.tuwien.ac.at/~hornik/R/" TARGET="external">..../R/</A>][2/'00].

%A I. Parker
%T Transformations and influential observations in minimum sum of absolute
   errors regression
%J Technometrics
%V 30
%N 2
%P 215-220
%M MAY
%D 1988
%K jrnl, c1988, c198x, c19xx, statistics, stats, linear regression, errors,
   absolute, error, MSAE, Laplace probability distribution, stack-loss,
   stackloss, dataset, data-set
%X "The Box-Cox power transformation model is considered for min. sum of abs.
   errors (MSAE) regression.  A long-tailed error distn, specifically the
   Laplace distribution, is included & could accommodate obsns that in the
   normal case are outlying or unduly influencing a choice of transformation.
   The log-likelihood proc. of Box & Cox (1964) for obtaining the optimal
   transformation param. is adapted for Laplace errors & MSAE regrn. Graphical
   methods for detecting the influence of individual obs. on the choice of
   transformation are described.  Application to examples illustrates that this
   approach can provide valuable additional information to the data analyst."
   -- [<A HREF="http://dx.doi.org/10.1080/00401706.1988.10488369">doi:10.1080/00401706.1988.10488369</A>]['13].
   (Also see dataset@[<A HREF="http://www.stat.colostate.edu/~jah/data/stack.loss">ColoS.</A>]['13].)

%A R. K. Guy
%T The strong law of small numbers
%J Amer. Math. Monthly
%V 95
%P 697-712
%D 1988
%K c1988, c198x, c19xx, zz0618, maths, stats, strong, law, small, number,
   examples, series, sequence, pattern, patterns, number theory
%X 'This paper contains 35 examples of patterns, taken largely from number
   theory and discrete mathematics, that seem to appear when one looks at
   several small examples but do not hold up under additional scrutiny,
   supporting the author's proposed law: "There aren't enough small numbers to
   meet the many demands to them."'
   -- pdf@[<A HREF="https://www.maa.org/programs/maa-awards/writing-awards/the-strong-law-of-small-numbers">www</A>]['18].
   [Also search for: Guy strong law].

%A T. A. B. Snijders
%T On cross-validation for predictor evaluation in time series
%P 56-69
%J On Model Uncertainty and its Statistical Implications,
   Proc. of a workshop, Groningen (nl), 1986
%E T. K. Dijkstra
%M SEP
%D 1988
%I SpringerVerlag
%S Lect. Notes in Econ. and Math. Sys.
%V 307
%K cross validation, time series, timeSeries
%X uk us isbn:0387-1936-77;    [via R.B. 2/'00]  (M@theson Mos 517.2 D575.O)

%A G. Ronning
%T Maximum likelihood estimation of Dirichlet distributions
%J J. Statistical Comput. & Simul.
%V 32
%P 215-221
%D 1989
%K jrnl, c1989, c198x, c19xx, zz1214, stats, Dirichlet probability distribution,
   estimator, estimate, concave, dirichelet, Minka
%X "Global concavity of the likelihood fn is proved by means of an inequality
   involving the trigamma fn. The computation of max. likelihood ests. is
   discussed.  ... Newton-Raphson ..."
   -- [<A HREF="http://www.tandfonline.com/doi/pdf/10.1080/00949658908811178">www</A>]['14].
   (Also see D@[<A HREF="https://en.wikipedia.org/wiki/Dirichlet_distribution">wikip</A>]['18].)
   [Also search for: Dirichlet estimate stats].

%A M. K. Varanasi
%A B. Aazhang
%T Parametric generalized Gaussian density estimation
%J J. of the Acoustical Soc. of America
%V 86
%P 1404
%D 1989
%K jrnl, c1989, c198x, c19xx, zz0321, generalized Gaussian density, GGD, normal,
   exponential power, probability distribution, estimate, estimator, gnorm,
   shape parameter, generalised
%X "... compare the large-sample as well as the small-sample properties of
   different methods for estimating the parameters of a three-parameter
   generalized Gaussian distribution. Three estimators, namely, the moment
   method (MM), the maximum-likelihood (ML), & the moment/Newton-step (MNS)
   estimators ..."
   -- [<A HREF="https://doi.org/10.1121/1.398700">doi:10.1121/1.398700</A>]['21].
   Also see,
   "... is either of two families of parametric continuous prob. distn on the
   real line. Both families add a shape parameter to the normal distn ...
   (1) AKA exponential power distn, or the generalized error distn, this is a
       parametric family of symmetric distns. It includes all normal & Laplace
       distns & as limiting cases it includes all cts uniform distns on
       bounded intervals of the real line. ...
   (2) ... a family of continuous prob. distns in which the shape parameter can
       be used to introduce skew. ..."
   -- [<A HREF="https://en.wikipedia.org/wiki/Generalized_normal_distribution">wikip</A>]['21].
   (And see
   gnorm@[<A HREF="https://cran.r-project.org/web/packages/gnorm/vignettes/gnormUse.html">r-project.org</A>]['21].)

%A A. E. Gelfand
%A A. F. M. Smith
%T Sampling-based approaches to calculating marginal densities
%J J. of the Amer. Stat. Assoc.
%V 85
%N 410
%M FEB
%D 1990
%K jrnl, stats, Gibbs sampling, algorithm, c1990, c199x, c19xx, zz1014,
   probability, distribution, joint, posterior, density
%X "Stochastic substitution, the G.sampler, & the sampling-importance-resampling
   alg. can be viewed as three alternative s.- (or [MC]-) based approaches ..."
   -- [<A HREF="https://doi.org/10.1080/01621459.1990.10476213">doi:10.1080/01621459.1990.10476213</A>]['24].
   (Also see GS@[<A HREF="https://en.wikipedia.org/wiki/Gibbs_sampling">wikip</A>]['24] and
   Gibbs@[<A HREF="https://en.wikipedia.org/wiki/Josiah_Willard_Gibbs">wikip</A>]['24], 1839-1903.)
   [Also search for: Gibbs sampling algorithm].

%A R. K. Guy
%T The second strong law of small numbers
%J Mathematics Mag.
%V 63
%N 1
%P 3-20
%M FEB
%D 1990
%K jrnl, c1990, c199x, c19xx, zz0618, maths, number theory, examples,
   strong law, series
%X "... The Second Strong Law of Small Numbers:
   When two numbers look equal, it ain't necessarily so! ..."
   -- [<A HREF="https://doi.org/10.2307/2691503">doi:10.2307/2691503</A>]['18],
   or [<A HREF="http://www.jstor.org/stable/2691503">Jstor</A>]['18].
   [Also search for: Guy strong law].

%A M. Frydenberg
%T The chain graph Markov property
%J Scand. J. Statist.
%V 17
%N 4
%P 333-353
%D 1990
%K jrnl, c1990, c199x, c19xx, zz0515, chain graph, chainGraph, Markov, model,
   causal, conditional independence, II, stats
%X "A new class of graphs, chaingraphs, suitable for modelling conditional i.
   are introduced & their Markov properties are investigated. This class of
   graphs, which includes undirected & directed acyclic graphs, enables
   modelling recursive models with multivariate response vars.. Results
   concerning the equivalence of different defns of their Markov properties inc.
   a factorization of the density are shown. Finally we give a nec. & suff.
   condn for two chain graphs to have the same Markov properties."
   -- 4616181@[<A HREF="http://www.jstor.org/stable/4616181">Jstor</A>]['15].
      ("A chain graph is a graph which may have both directed & undirected
       edges, but without any *directed* cycles (i.e., if we start at any vertex
       & move along the g. respecting the dirns of any arrows, we cannot return
       to the vertex we started from if we have passed an arrow) ..." -- wikip.)
   [Also search for: chainGraph].

%A A. E. Gelfand
%A A. F. M. Smith
%T Sampling-based approaches to calculating marginal densities
%J J. Amer. Stat. Assoc.
%V 65
%N 410
%P 398-409
%D 1990
%K jrnl, c1990, c199x, c19xx, zz1124, posterior, probability density,
   Gibbs, importance
%X "Stochastic substitution, the Gibbs sampler, & the
   sampling-importance-resampling ... will be reviewed, compared, & contrasted
   in reln to various joint prob. structures freq. encountered in applications.
   In particular, the relevance of the approaches to calculating Bayesian
   posterior densities ..."
   -- [<A HREF="https://doi.org/10.1080/01621459.1990.10476213">doi:10.1080/01621459.1990.10476213</A>]['24].
   [Also search for: Metropolis Hastings].

%A J. S. U. Hjorth
%T Computer Intensive Statistical Methods Validation, Model Selection and
   Bootstrap
%I ChapmanAndHall
%D 1994
%K book, stats, statistics, time series
%X [via  r o h a n].

%A A. K. Jain
%A M. N. Murty
%A P. J. Flynn
%T Data clustering: a review
%J ACM Comp. Surveys
%V 31
%N 3
%P 264-323
%M SEP
%D 1999
%K ACM, jrnl, survey, clusters, unsupervised classification, zz0600
%X Remarkably it does not refer to  W a l l a c e  and  B o u l t o n's
   (and other related) work.

%A C. Silverman
%A S. Brin
%A R. Motwani
%A J. Ullman
%T Scalable techniques for mining causal structures
%J Data Mining and Knowledge Discovery
%I KluwerAcademic
%V 4
%N 2-3
%P 163-192
%M JUL
%D 2000
%K jrnl, c2000, c200x, c20xx, structure, model, net, network, Bnet, quotable,
   causal models, Bayesian networks
%X "Mining for association rules in market basket data ...  such rules indicate
   only a stat. relationship between A and B. They do not specify the nature of
   the relationship: whether the presence of A causes the presence of B, or the
   converse ...  we consider the problem of determining casual relationships,
   instead of mere associations .... We identify some problems with the direct
   application of B.learning ideas to mining large DBs ...  both the
   scalability of algs. & the appropriateness of the stat.techniques, &
   introduce some initial ideas for dealing with these problems. ...  The
   results indicate that the approach proposed here is both computationally
   feasible & successful in identifying interesting causal structures. An
   interesting outcome is that it is perhaps easier to infer the lack of
   causality than to infer causality, information that is useful in preventing
   erroneous decision making."
   -- [<A HREF="http://dx.doi.org/10.1023/A:1009891813863a">doi:10.1023/A:1009891813863a</A>]['14].
     [A quote: "In our view, inferring complete causal models (i.e.,
      causal Bayesian networks) is essentially impossible in large-scale
      data mining applications with thousands of variables." -- p.166.]
   [Also search for: Bayesian network].

%A G. I. Webb
%T Efficient search for association rules
%J Knowledge Discovery and Data Mining
%I ACM
%P 99-107
%D 2000
%K conf, rule, frequent item set, sets, FIS, apriori, c2000, c200x, c20xx,
   basket, analysis, OPUS
%X "...argues that for some applications direct search for association rules
   can be more efficient than the 2 stage process of the Apriori algorithm
   which 1st finds large itemsets which are then used to identify associations.
   ... it is argued, Apriori can impose large computational overheads when the
   number of frequent itemsets is very large. This will often be the case when
   association rule analysis is performed on domains other than basket analysis
   or when it is performed for...".   isbn:1581132336.
   -- [<A HREF="http://doi.acm.org/10.1145/347090.347112">doi:10.1145/347090.347112</A>][1/'04].
   Also see '95 jrnl paper.  [<A HREF="http://www.csse.monash.edu.au/~webb/">~webb</A>][1/'04].

%A M. J. Zaki
%T Scalable algorithms for association mining
%J IEEE Trans. on Knowledge and Data Engineering
%V 12
%N 3
%P 372-390
%D 2000
%K jrnl, frequent item set, FIS, sets, algorithm, apriori, c2000, c200x, c20xx,
   rule, rule
%X via Am@nd@ C

%A J. Hipp
%A U. Guntzer
%A G. Nakhaeizadeh
%T Algorithms for association rule mining - a general survey and comparison
%J SIGKDD Explorations
%V 2
%N 1
%P 58-64
%M JUL
%D 2000
%K frequent item set, FIS, sets, rules, algorithm, apriori, c2000, c200x, c20xx
%X via Am@nda C.

%A P. Spirtes
%A G. Glymour
%A S. Kauffman
%A V. Aimalie
%A F. Wimberly
%T Constructing Bayesian network models of gene expression networks from
   microarray data
%J Proc. Atlantic Symp. Comp. Biol., Genome Information Systems & Technology
%P ?-?
%D 2000
%K MolBio, conf, stats, introduction, networks, model, micro arrays
%X [<A HREF="http://www.phil.cmu.edu/projects/genegroup/papers/spirtes2002.pdf">pdf</A>][12/'02].

%A I. H. Witten
%A E. Frank
%T Nuts and bolts: Machine learning algorithms in Java
%P 265-320
%B Data Mining: Practical Machine Learning Tools and
   Techniques with Java Implementations
%I MorganKaufmann
%P 416
%M OCT
%D 1999
%K book, text, WEKA,Weka, API, data mining, Java, c1999, c199x, c19xx, Waikato,
   New Zealand, NZ, inductive inference, II, machine learning, software, arff,
   manual, www, HREF, http
%X us$50; isbn:1558605525. [<A HREF="http://www.cs.waikato.ac.nz/ml/weka/">www</A>][7/00]
   2nd ed, 'Data Mining: Practical machine learning tools & techniques', c2005.
   And "DataSet: ...external rep. of an Instances class is an ARFF file ...;
          nominal attribute (e.g. @attribute outlook {sunny, overcast rainy}),
          real, integer, numeric, string
        Classifier: ...a c. is an arbitrary complex mapping from all-but-one
          [of the] dataset attributes to the class attribute. ...
        Filter: ... transforms datasets, removing or adding attributes, ...
        Filters.supervised: ... take advantage of the class information. ...
        Filters.unsupervised: ... "
   uk us isbn:0120884070.
   --[<A HREF="http://alex.seewald.at/WEKA/">alex.seewald</A>]['05].

%A S. Pincus
%A B. H. Singer
%T Randomness and degrees of irregularity
%J Proc. Natl, Acad. Sci.
%V 93
%P 2083-2088
%M MAR
%D 1996
%K PNAS, jrnl, random, sequence, sequences, approximate entropy, ApEn, zz0800
%X ?via deanm?
   [Also search for:  MML]

%A I. Cadez
%A S. Gaffney
%A P. Smyth
%T A general probabilistic framework for clustering individuals
%R UCI-ICS-00-09
%M MAR
%D 2000
%O KDD-2000 Proc.
%K TR, UCI, conf, classification, www, HREF, http, zz0900
%X [Also search for: classification]
   -- [<A HREF="http://www.ics.uci.edu/~datalab/papers.html">www</A>[8/'00].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A D. Judd
%A P. K. McKinley
%A A. K. Jain
%T Large scale parallel data clustering
%J Proc. Int. Conf. on Pattern Recognition
%C Vienna
%P 488-493
%D 1996
%K conf, image processing, IP, P cluster, Pcluster, class, classification,
   feature
%X ...mean square error clustering ...images 512x512, 20 float features/pixel.
   (a) P-cluster: server sends centroids to clients, and
       divides data into blocks sent to client mc's.
       Client computes partial sum for each block and each thing in its block.
       Server collects sums and calculates new centroids.  Repeat.
   (b) After a couple of passes,
       1. relatively few patterns [things] change their cluster[s], and
       2. movement of centroids [of clusters] decreases... keep partial sums...
       reduce number of distance computations ...  radii (spheres of
       assignment, 1/2 sep'n) for each centroid ...
       maximum movement [of centroid]  effect ...
   At [<A HREF="http://citeseer.nj.nec.com/185700.html">citeseer</A>][11/'00].

%A C. Bhattacharjee
%A P. Bradley
%A M. Smith
%A A. J. Scally
%A B. J. Wilson
%T Do animals bite more during a full moon? Retrospective observational
   analysis
%J British Med. J.
%V 321
%P 1559-1561
%M DEC
%D 2000
%K jrnl, BMJ, statistics, medical, full moon, moons, effect, effects, animal,
   lunar, cyclic, periodic, dog, dogs, bites, risk, risks, myth, myths, model,
   stats, c2000, c200x, c20xx, zz1200
%X ... Number of patients who attended an accident and emergency
   department during 1997 to 1999 after being bitten by an animal.
   The number of bites in each day was compared with the lunar phase in
   each month. Results: The incidence of animal bites rose significantly at
   the time of a full moon. With the period of the full moon as the
   reference period, the incidence rate ratio of the bites for all other
   periods of the lunar cycle was significantly lower (P <0.001).
   Conclusions: The full moon is associated with a significant increase
   in animal bites to humans.
   -- [<A HREF="http://www.bmj.com/cgi/content/abstract/321/7276/1559">www</A>][12/00],
      cbhattacharjee at hotmail.com [12/00].
   See also Chapman and Morwell same issue of BMJ
   [Also search for: lunar stats].

%A S. Chapman
%A S. Morwell
%T Barking mad? Another lunatic hypothesis bites the dust
%J British Med. J.
%V 321
%P 1561-1563
%M DEC
%D 2000
%K jrnl, BMJ, statistics, medical, full moon, moons, effect, effects, animal,
   lunar, phase, month, periodic, cyclic, stats, model, animals, dog, dogs,
   bite, bites, risk, risks, myth, myths, c2000, c200x, c20xx, zz1200
%X ... 2 peak clusters of admissions were unrelated to the time of the
   full moon. Dog bites are no more frequent on full moons than at any
   other time of the month. Sceptics rejoice.
   -- [<A HREF="http://www.bmj.com/cgi/content/abstract/321/7276/1561">www</A>][12/00],
      simonc at health.usyd.edu.au [12/00]
   See also Bhattacharjee et al same issue of BMJ.
   [Also search for: lunar stats].

%A P. D. Grunwald
%A P. M. B. Vitanyi
%T Kolmogorov complexity and information theory: With an interpretation in
   terms of questions and answers
%J J. of Logic, Language, and Info. (Special Issue on Connecting the
   Different Faces of Information)
%V 12
%N 4
%P 497-529
%D 2003
%K jrnl, c2003, c200x, c20xx, zz0519, information theory, universal code, codes,
   Shannon, entropy, Kolmogorov complexity, algorithmic, intro
%X "We compare the elementary theories of Shannon information & Kolmogorov
   complexity, the extent to which they have a common purpose, & where they are
   fundamentally different. We discuss & relate the basic notions of both
   theories: Shannon entropy, Kolmogorov complexity, Shannon mutual information
   & Kolmogorov ('algorithmic') mutual information. We explain how universal
   coding may be viewed as a middle ground between the two theories. We consider
   Shannon's rate distortion theory, which quantifies useful (in a certain
   sense) information. We use the communication of information as our guiding
   motif, & we explain how it relates to sequential question-answer sessions"
   -- 40167357@[<A HREF="https://www.jstor.org/stable/40167357">Jstor</A>]['19].
   [Also search for: information theory inference].

%A C. E. Frangakis
%A E. Petridou
%T Modelling risk factors for injuries from dog bites in Greece: a case-only
   design and analysis
%J Accident Analysis and Prevention
%P 435-438
%V 35
%N 3
%M MAY
%D 2003
%K jrnl, dog bite, bites, full moon, biting, moons, effect, effects, animal,
   lunar, cyclic, periodic, model, stats, Greece, weekend, men, male, bitten,
   risk, risks, myth, myths
   %X "...hospitals from Greece ... dog bites. Our goal is 3-fold: (a) to inv.
   if surrogate factors of leisure time are associated with increased risk of
   injury from bites; (b) to address ... contradictory results on putative
   assoc. of lunar periods and injuries from dog bites; & (c) to offer a
   general methodology for addressing similar case-only designs with combined
   factors of which some can exhibit cyclical patterns. ... used a case-only
   design of our dataset, & ... controlled simultaneously for weekday/'end
   effects, season of year (winter, spring/fall, summer), & lunar periods,
   because any one of these factors can contribute to the degree of exposure to
   injuries from dog bites. We found that increased risk of injury from bites
   was assoc. with w'ends versus w'days (RR=1.19, 95% CI: 1.10-1.29), summer
   v. winter (RR=1.24, 95% CI: 1.11-1.39), & fall or spring v. winter (RR=1.31,
   95% CI: 1.19-1.45). ...support the hypothesis that longer leisure time at
   these levels of factors does increase the risk of having a bite injury. ...
   after controlling for these factors, risk of bite injury was not associated
   with moon periods,..."
   -- [<A HREF="http://biosun01.biostat.jhsph.edu/~cfrangak/pub.html">Frangakis</A>][5/'02],
      [<A HREF="http://dx.doi.org/10.1016/S0001-4575(02)00015-5">doi:10.1016/S0001-4575(02)00015-5</A>]['05].
   [Also search for: dog bite] and [also search for: lunar stats].

%A C. Raison
%A H. Klein
%A M. Steckler
%T The moon and madness reconsidered
%J J. Affective Disorders
%V 53
%P 99-106
%D 1999
%K jrnl, c1999, c199x, c19xx, moon, full, phase, lunar, perioidic, cyclic,
   stats, model, psychology, risk, risks, myth, myths, zz0701
%X Perhaps the moon once had an effect - natural light, less sleep at
   full moon, but now ..., artificial light, no lunar effect?
   [Also search for: dog bite] and [also search for: lunar stats].

%A J. Rotton
%A I. Kelly
%T Much ado about the full moon: A meta-analysis of lunar-lunacy research
%J Psych. Bull.
%V 97
%P 286-306
%D 1985
%K jrnl, c1985, c198x, c19xx, lunar, stats, phase, madness, psychology,
   risk, risks, myth, myths, zz0701
%X Conclude most work has poor methodology.
   [Also search for: lunar stats]  and  [also search for: dog bite].

%A P. Domingos
%T The role of Occam's razor in knowledge discovery
%J Data Mining and Knowledge Discovery
%I Kluwer
%V 3
%N 4
%P 409-425
%D 1999
%K Occam, Occams, razor, inference, learning, AI, II, c1996, c199x, c19xx,
   simplicity, KDD, problems, limits, against, rebuttal, Bayes, Bayesian, AIC,
   BIC, MML, MDL, complexity, model, models, prediction, accuracy, zz0804,
   generalization error, training set, zzOSP, zOSP04
%X "Many KDD systems incorporate an implicit or explicit preference for simpler
   models, but this use of "Occam's razor" has been strongly criticized by
   several authors (e.g. Schaffer 1993, Webb 1996). This controversy arises
   partly because Occam's razor has been interpreted in 2 quite different ways.
   The 1st interpretation (simplicity is a goal in itself) is essentially
   correct, but is at heart a preference for more comprehensible models. The
   2nd interpretation (simplicity leads to greater accuracy) is much more
   problematic. A critical review of the theoretical arguments for and against
   it shows that it is unfounded as a universal principle, and demonstrably
   false. A review of empirical evidence shows that it also fails as a
   practical heuristic. This article argues that its continued use in KDD risks
   causing significant opportunities to be missed, and should therefore be
   restricted to the comparatively few applications where it is appropriate..."
   -- [<A HREF="http://www.cs.washington.edu/homes/pedrod/papers/dmkd99.pdf">.pdf</A>][7/'04],
      [<A HREF="http://www.cs.washington.edu/homes/pedrod/">auth@cs.washington</A>][7/'04].
   p2 s1: 1st Razor: Given 2 models with the same generalization error the
    simpler one should be preferred because simplicity is desirable in itself.
    2nd Razor: Given 2 models with the same training-set error the simpler one
    should be preferred because it is likely to have lower gen'n error. [...]
    The 1st is largely uncontroversial while the 2nd, taken literally is false.
   p5 s2.3: "... belief is a result of circular reasoning: models are more
    probable apriori because they have shorter codes, but they have shorter
    codes because they are more probable apriori. Care should be taken to avoid
    confusion between assigning the shortest codes to the apriori most
    probable hypotheses and considering that the syntactically simplest models
    in the representation being used (e.g. the decision trees with the fewest
    nodes) are the a priori most probable ones."
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%E R. Sun
%E C. Lee Giles
%T Sequence Learning, Paradigms, Algorithms and Applications
%I SpringerVerlag
%S LNAI
%V 1828
%M NOV
%D 2000
%K book, LNCS, LNAI, LNAI1828, sequence, sequences, time series, timeSeries,
   analysis, AI, model, zz0601
%X [Also search for: sequence analysis].

%A M. B. Dale
%T Mt. Glorious revisited: secondary succession in subtropical rainforest
%J Community Ecology
%P 181-193
%N 2
%V 1
%D 2000
%K jrnl, vegetation
%X [<A HREF="http://ramet.elte.hu/~podani/ce1v1.html">jrnl</A>][2/'04].

%A J. Lafferty
%A A. McCallum
%A F. Pereira
%T Conditional random fields: Probabilistic models for segmenting and
   labeling sequence data
%J Proc. of 18th Int. Conf. on  Machine Learning
%P 282-289
%D 2001
%K conf, ICML, ICML18, c2001, c200x, c20xx, zz0306, field, model, labelling,
   segment, segmentation, CRF
%X "We present conditional random fields, a framework for building prob. models
   to segment & label seq. data. [CRFs] offer several advantages over
   hidden Markov models & stochastic grammars for such tasks, inc. the ability
   to relax strong independence assumptions made in those models. CRFs also
   avoid a fundamental limitation of maximum ent. Markov models (MEMMs) & other
   discriminative Markov models based on directed graphical models, which can be
   biased towards states with few successor states. We present iterative
   parameter est. algs. for CRFs & compare the performance of the resulting
   models to HMMs & MEMMs on synthetic & natural-language data."
   -- [<A HREF="http://www.cis.upenn.edu/~pereira/papers/crf.pdf">pdf@upenn</A>]['06] via M.D.
   [also search for: random field],  [also search for: segmentation].

%A D. Mackay
%T Probabilistic multidimensional scaling using a city-block metric
%J J. Math. Psychology
%V 45
%N 2
%P 249-264
%M APR
%D 2001
%K jrnl, probabilistic, multidimensional scaling, c2001, c200x, c20xx,
   multivariate, scale
%X "Using a prob. model, exact & approx. prob. density fns.(PDFs) for
   city-block distances & distance ratios are developed. The model assumes
   that stimuli can be represented by random vectors having multivariate normal
   dist'ns. Comparisons with the more common Euclidean PDFs are presented.
   The potential ability of the proposed model to correctly detect Euclidean &
   city-block metrics is briefly investigated. These results are then
   contrasted to those obtained using a deterministic, nonmetric model."
   -- [<A HREF="http://dx.doi.org/10.1006/jmps.2000.1311">doi:10.1006/jmps.2000.1311</A>]['05]   -- via Mike D@le

%A D. Mackay
%D 2001
%T Probabilistic unfolding models for sensory data
%J Food Quality Preference
%V 12
%P 427-436
%K jrnl, probabilistic, multidimensional scaling, c2001, c200x, c20xx
%X [search for: probabilistic scaling]

%A J. M. Eagles
%A J. E. Andrew
%A M. I. Johnston
%A E. A. Easton
%A H. R. Millar
%T Season of birth in females with anorexia nervosa in Northeast Scotland
%J Int. J. Eating Disorders
%I Wiley
%V 30
%N 2
%P 167-175
%M SEP
%D 2001
%K jrnl, anorexia, anorexic, date, born, birth, season, month
%X ... 446 anorexic patients ... 5,766 female control ...
   This provides further evidence that birth dates of anorexics peak
   in the late spring and early summer. There are parallels with the
   epidemiology of schizophrenia. The evidence suggests that a seasonally
   fluctuating factor, most plausibly an intrauterine effect of common
   infectious agents during the winter months, is of etiological significance.
    - 1st author at Royal Cornhill Hospital, Aberdeen, UK
   -- [<A HREF="http://www3.interscience.wiley.com/cgi-bin/abstract/84504707/">paper</A>][8/'01]

%A M. B. Dale
%T Functional synonyms and environmental homologues:
   an empirical approach to guild delimitation.
%J Community Ecology
%P 67-80
%N 1
%V 2
%D 2001
%K jrnl, vegetation
%X [<A HREF="http://ramet.elte.hu/~podani/ce1v1.html">jrnl</A>][2/'04]

%A M. B. Dale
%T Minimum message length clustering, environmental heterogeneity and
   the variable Poisson model.
%J Community Ecology
%P 171-180
%N 2
%V 2
%D 2001
%K jrnl, vegetation
%X [<A HREF="http://ramet.elte.hu/~podani/ce1v1.html">jrnl</A>][2/'04]

%A M. B. Dale
%A L. Salmina
%A L. Mucina
%T Minimum message length clustering: an explicationand some applications to
   vegetation data.
%J Community Ecology
%P 231-?
%N 2
%V 2
%D 2001
%K jrnl, description, classification, MML, MDL, biol, biology
%X [<A HREF="http://ramet.elte.hu/~podani/ce1v1.html">jrnl</A>][2/'04]

%A S. Z. Li
%T Markov Random Field Modeling in Image Analysis
%I Springer
%S Comp. Sci. Workbench
%D 2001
%K book, text, fields, images, model, zz0901
%X isbn:4-431-70309-8;    H621.367 L693M 2001.

%A D. J. Hand
%A H. Mannila
%A P. Smyth
%T Principles of Data Mining
%I MITpress
%P 425
%M AUG
%D 2001
%K book, text, DJHand, statistics, data analysis, zz1101
%X 1. foundations, provides a tutorial overview of the principles
      underlying data mining algorithms and their application.
   2. data mining algorithms, shows how algorithms are constructed to solve
      specific problems in a principled manner. The algorithms covered include
      trees and rules for classification and regression, association rules,
      belief networks, classical statistical models, nonlinear models such as
      neural networks, and local "memory-based" models.
   3. shows how all of the preceding analysis fits together when applied
      to real-world data mining problems. Topics include the role of metadata,
      how to handle missing data, and data preprocessing.  isbn:026208290X.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. F. Geweke
%T Bayesian inference of econometric models using Monte Carlo integration
%J Econometrica
%V 57
%P 1317-1339
%M NOV
%D 1989
%K jrnl, leighf, montecarlo, las vegas, lasvegas, stochastic, integrate, stats,
   MCMC, importance sampling, economics, inductive inference, II, model, zz0202
%X It's in [<A HREF="http://www.jstor.org/">jstor</A>]['02].
   Home [<A HREF="http://www.biz.uiowa.edu/faculty/jgeweke/">JGeweke</A>]['02]
   ref from l.f.

%A A. Narayanan
%T Algorithm AS 266: Maximum likelihood estimation of the parameters of the
   Dirichlet distribution
%J J. Royal Stat. Soc., Series C (Applied Stats.)
%V 40
%N 2
%P 365-374
%D 1991
%K jrnl, JRSS, c1991, c199x, c19xx, zz1114, Dirichlet probability distribution,
   parameter, estimator, estimate, DIRICH, stats, AS 266, AS266
%X "A subroutine ... for the max.likelihood est. of the params. of the D..
   ... [Also] present an example to illustrate use of the Dirichlet
   distribution in the study of correlations between proportions
   (Mosimann, 1962). ...  uses a Newton-Raphson method to maximize
   the log-likelihood function ..."   [15 refs.]
   -- [<A HREF="https://doi.org/10.2307/2347605">doi:10.2307/2347605</A>]['17],
      2347605@[<A HREF="http://www.jstor.org/stable/2347605">Jstor</A>]['14].
   (Also see D@[<A HREF="https://en.wikipedia.org/wiki/Dirichlet_distribution">wikip</A>]['18].)
   [Also search for: Ronning 1989] and
   [also search for: Dirichlet estimate stats].
      [Note, the Dirichlet is often used as a prior for the multistate
      (categorical) and multinomial probability distributions.]

%A W. R. Gilks
%A A. Thomas
%A D. J. Spiegelhalter
%T A language and program for complex Bayesian modelling
%J The Statistician
%V 43
%P 169-178
%D 1994
%K jrnl, BUGS, Bayesian inference Using Gibbs Sampling,
   Markov Chain, Monte Carlo, mcmc, Coda
%X [<A HREF="http://www.mrc-bsu.cam.ac.uk/bugs/">BUGS</A>][/'02]

%A R. Agrawal
%A R. Srikant
%T Fast algorithms for mining association rules
%J Proc. 20th Int. Conf. Very Large Data Bases (VLDB)
%I MorganKaufmann
%P 487-499
%D 1994
%K conf, VLDB, KDD, data mining, association rule, frequent item set, sets,
   FIS, customer, buyer, apriori algorithm, apriorihybrid
%X ...problem of discovering association rules between items in a large [DB] of
   sales transactions. ...two new alg's for [the] problem that are
   fundamentally different from the known algorithms. Experiments with
   synthetic [& ] real-life data...  these algorithms outperform the known
   algorithms by factors ranging from three for small problems to more than an
   order of magnitude for large problems. ...    isbn:1558601538.
   -- [<A HREF="http://www.almaden.ibm.com/cs/people/ragrawal/papers/vldb94_rj.ps">paper</A>][12/'02].

%A B. F. J. Manly
%T Multivariate Statistical Methods: A Primer (2nd edn)
%I Chapman & Hall
%P 232
%D 1994
%K bookm text, stats, statistics, sparrows, zzOSP, zOSP04, c1994, c199x, c19xx
%X 2nd edn 1994, us$50, isbn:0412603004.
   ? clustering data, examples?

%A V. Barnett
%A T. Lewis
%T Outliers in Statistical Data
%I Wiley
%D 1994
%K book, text, stats, c1994, c199x, c19xx, zz0823, outlier, outliers
%X 3rd ed 1994; uk us isbn:0471930946; uk us isbn13:978-0471930945.
   "... Important features of this new edn are comprehensive updating of
   methodology & tables; major expansion of topics including time series,
   contingency tables, multivariate analysis & regression data (particularly
   influence & robustness, diagnostics, multiple outliers, non-linear models,
   L_1-norm methods); & richer coverage of practical fields ..."
   (Also see outlier@[<A HREF="https://en.wikipedia.org/wiki/Outlier">wikip</A>]['23].)
   [Also search for: stats outlier].

%A W. R. Gilks
%A S. Richardson
%A D. J. Spiegelhalter
%T Markov Chain Monte Carlo in Practice
%I ChapmanHall
%D 1996
%K book, text, good, montecarlo, las vegas, Chains, lasvegas, stats, statistics,
   model, models, MCMC, bugs, reversible jump, L5Ref
%X isbn:0412055511;  Rec'd by L'F'.   [Also search for: BUGS]

%A B. Pearlmutter
%A L. Parra
%T Maximum likelihood blind source separation: A context-sensitive
   generalization of ICA.
%J Advances in Neural Information Processing Systems
%V 9
%I MITpress
%P 613-619
%D 1997
%K contextual ICA, cICA, c1997, c199x, c19xx, ANN, NN
%X [<A HREF="http://newton.bme.columbia.edu/~lparra/publish/nips96.ps.gz">.ps.gz</A>]['05]

%A S. Richardson
%A P. Green
%T On Bayesian analysis of mixtures with an unknown number of components
%J JRSS
%V 59
%P 731-792
%D 1997
%K jrnl, JRSS, mixture model, models, modelling, c1997, c199x, c19xx,
   reversible jump, MCMC
%X [<A HREF="http://www.stats.bris.ac.uk/~peter/Research.html">P.G.</A>]['02]
   -- [<A HREF="http://links.jstor.org/sici?sici=0035-9246%281997%2959%3A4%3C731%3AOBAOMW%3E2.0.CO%3B2-B">at jstor</A>][1/'04]
   [Also search for: mixture model]  and [also search for: mcmc].

%A S. Della Pietra
%A V. Della Pietra
%A J. Lafferty
%T Inducing features of random fields
%J IEEE Trans. Pattern Analysis and Machine Intelligence
%V 19
%N 4
%P 1-13
%M APR
%D 1997
%K jrnl, c1997, c199x, c19xx, DellaPietra, Markov random field
%X via M.D.

%A N. Friedman
%A D. Geiger
%A M. Goldszmidt
%T Bayesian network classifiers
%J J. Mach. Learning
%V 29
%N 2-3
%P 131-163
%M NOV
%D 1997
%K jrnl, JML, c1997, c199x, c19xx, zz0814, Tree Augmented Naive Bayes, TAN,
   supervised classification, classifier, AI, II
%X "... a surprisingly simple Bayesian classifier with strong assumptions of
   independence among features, called naive Bayes, is competitive with state-
   -of-the-art c. such as C4.5. ... raises the Q. of whether a c. with less
   restrictive assumptions can perform even better. ... we evaluate approaches
   for inducing classifiers from data, based on the theory of learning B. n/ws.
   These n/ws are factored representations of prob. distns that generalize the
   naive B. c. & explicitly represent statements about independence. Among these
   approaches we single out a method we call Tree Augmented Naive Bayes (TAN),
   which outperforms n.B., yet at the same time maintains the computational
   simplicity (no search involved) & robustness that characterize n.B.. We
   experimentally tested these approaches, using problems from the U. of Cal. at
   Irvine repository, & compared them to C4.5, n.B., & wrapper methods for
   feature selection."
   -- [<A HREF="http://dx.doi.org/10.1023/A:1007465528199">doi:10.1023/A:1007465528199</A>]['14].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].)

%A X.-L. Meng
%A D. van Dyk
%T The EM algorithm - an old folk-song sung to a fast new tune
%J JRSS (B)
%V 59
%N 3
%P 511-567
%D 1997
%K jrnl, JRSS, c1997, c199x, c19xx, zz0618, vanDyk, EM algorithm, EMalgorithm,
   stats, history, Dempster, Laird, Rubin
%X "Celebrating the 20th anniversary of the presentation of the paper by
   Dempster, Laird & Rubin which popularized the EM alg., ... after a brief
   historical a/c, strategies that aim to make the EM alg. converge faster while
   maintaining its simplicity & stability ... show, through both empirical &
   theoretical evidence, the potential for a dramatic redn in computational
   time with little increase in human effort. We also discuss the intrinsic
   connection between EM-type algs. & the Gibbs sampler ..."
   -- [<A HREF="https://doi.org/10.1111/1467-9868.00082">doi:10.1111/1467-9868.00082</A>]['18],
   or 2346009@[<A HREF="http://www.jstor.org/stable/2346009">Jstor</A>]['18].
   [Also search for: EM algorithm].

%A D. D'Costa
%A A. P. Kershaw
%T An expanded recent pollen database from south-eastern Australia and its
   potential for refinement of palaeoclimatic estimates
%J Aust. J. Bot.
%V 45
%P 583-605
%D 1997
%K climate, c1997, c199x, c19xx, DB, estimate, ancient, past, BIOCLIM,
   palaeo climatic, count, counts, history, historic
%X "71 pollen spectra from prior to the period of European impact were extracted
   from fossil pollen diagrams on mainland SE .au in '91 to use as a modern
   ref. for refinement of vegetation & climatic histories cons. from the region.
   ... presents results of an extension of this recent database to 135 spectra,
   derived from additional fossil pollen sites on the mainland & also from sites
   in Tasmania. The sites include those of almost all late Quaternary pollen
   studies ever undertaken. Ests. of climate for each site, derived by BIOCLIM,
   have allowed an examination of patterns of representation of individual
   recorded taxa in relation to regional variation in major climatic parameters.
   Pollen taxa show variable representation in relation to their inferred
   presence & abundance in parent vegetation due to differential pollen
   production & dispersal characteristics.  However, patterns of pollen
   representation do appear to relate, in broad terms, to climatic variation.
   It is considered that this modern pollen & climate database should lead to
   more certain interpretation of future pollen records including some
   quantification of palaeoclimatic conditions."
   auths@monash in '97;    via Rohan B. '07

%A T. C. M. Lee
%T Tree-based wavelet regression for correlated data using the
   minimum description length principle.
%J Australian and New Zealand J. of Statistics
%V 44
%N 1
%P 23-39
%D 2002
%K jrnl, regression, trees, DTree, MDL, stats, wavelets

%A D. G. T. Denison
%A B. K. Mallick
%A A. F. M. Smith
%T Automatic Bayesian curve fitting
%J J. Royal Statist. Soc. Series B
%V 60
%P 333-350
%D 1998
%K jrnl, JRSS, JRSSB, stats, fit, curves, line, model, c1998, c199x, c19xx
%X jstor has to '97 inc' as of '02.
   -- [<A HREF="http://stats.ma.ic.ac.uk/~dgtd/tech.html">pub's</A>][2/'02].

%A G. K. Robinson
%T That BLUP is a good thing - The estimation of random effects
%J Statistical Science
%V 6
%N 1
%P 15-51
%D 1991
%K jrnl, stats, statistics, BLUP, effect
%X G.R.: [<A HREF="http://www.cmis.csiro.au/Geoff.Robinson/">www</A>][2/'02]

%A P. L. Bernstein
%T Against the Gods: The Remarkable Story of Risk
%I Wiley
%P 400
%D 1996
%K book, text, probability, risks, statistics, stats, history, origins, good,
   trial of the pyx, trials, 1279, 13C, 1600, 1604, 1661, 17C, games, odds,
   chance, c1996, c199x, c19xx, zz0302
%X isbn:0471295639.  (ppbk edn  Aug '98,  about us$17)
   "... mentions sampling; King Edward I of England tested the weight of the
   coin by the "Trial of the Pyx" in 1279.  A sample of coins was weighed to
   ensure that the correct amount of gold had been used.
   Also: Graunt, a haberdashery merchant, who examined the birth and death
   records of London from 1604 to 1661 and drew conclusions about the
   population profile and size, about the causes of death and about life
   expectancy at various ages from these records.  He talks about bias on
   death certificates, about venereal disease in 1662, Graunt noted that
   "onely hated persons, and such, whose very Noses were eaten of, were
   reported - to have died of this too frequent Maladie". -- [via D. G l a s s]
   [M a t h e s o n  Libr'y main coll'n  # 368 B531A][3/'02].
   [Also search for: probability statistics history], and maybe add book.

%A M. Sawhney
%A J. Eliashberg
%T A parsimonious model for forecasting gross box-office revenues of motion
   pictures.
%J Marketing Sci.
%V 15
%N 2
%P 113-131
%D 1996
%K c1996, c199x, c19xx, movie, movies, film, films, picture, success,
   popular, financial, flop
%X [<A HREF="http://knowledge.wharton.upenn.edu/index.cfm?fa=viewPaper&id=785">abs + pdf</A>]['06]

%A A. Moore
%T Very fast EM-based mixture model clustering using multiresolution kd-trees
%J Adv. in Neural Inf. Proc. Systems
%I MITpress
%V 11
%P ?-?
%D 1998
%K clustering, clusters, unsupervised classification, models, KD tree, KDtree,
   sufficient statistics, stats, multi-resolution, c1998, c199x, c19xx, zz0103,
   leighf, EM algorithm, estimation, discovery, expectation
%X Clustering is important in many fields including manufacturing, biology,
   finance, and astronomy. Mixture models are a popular approach due to their
   statistical foundations, and EM is a very popular method for finding mixture
   models. EM, however, requires many accesses of the data, and thus has been
   dismissed as impractical (e.g. (Zhang, Ramakrishnan, & Livny, 1996)) for
   data mining of enormous datasets. We present a new algorithm, based on the
   multiresolution kd-trees of [] which dramatically reduce [time]...
   ([requires] class densities are monotinic in M@halanobis distance)...
   -- [<A HREF="http://www.ri.cmu.edu/pub_files/pub1/moore_andrew_1998_2/moore_andrew_1998_2.ps.gz">.ps</A>][1/'03]  ref from l.f.
      [<A HREF="http://www.autonlab.org/papers/fastem.ps">.ps</A>][1/'03].
   [Also search for: EM algorithm c196x].

%A Jianming Ye
%T On measuring and correcting the effects of data mining and model selection
%J J. Amer. Stat. Assoc.,  Theory and Methods.
%V 93
%N 441
%P 120-131
%M MAR
%D 1998
%K jrnl, JASA, inductive inference, II, stats, models, Akaike, AIC, zz0502
%X via  J u l e s.

%A A. Moore
%A M. S. Lee
%T Cached sufficient statistics for efficient machine learning with
   large datasets
%J J. Artificial Intelligence Res.
%V 8
%P 67-91
%D 1998
%K jrnl, JAIR, stats, c1998, c199x, c19xx, zz1205, sparse, ADtree, ADtrees,
   AD tree, dataset, trees, algorithm, frequencies, frequency,
   contingency table, tables, categorical, CPT, counting, AI,
   conjunctive query, queries, conjunction, frequent item set, sets
%X "... new algs. & DS for quick counting for ... datasets. We focus on the
   counting task of constructing contingency tables, but our approach is also
   applicable to counting the number of records in a dataset that match
   conjunctive queries. Subject to certain assumptions, the costs of these
   operations can be shown to be independent of the number of records in the
   dataset & loglinear in the number of non-zero entries in the contingency
   table. We provide a very sparse data structure, the ADtree, ..."
  [p.74: Given an ADtree, to compute a c.t. for n attrs (out of M) of arity k,
         (1+n(k-1))k^(n-1) ops in worst case, is indep of M, & of #data R,
         v. O(nR+k^n) for running through the data counting.]
  [p.89, appx.B: To build an ADtree, for M binary (say) attrs, and R data,
         (SUM_k=0..flr(log2(R)) {R/2^k M_choose k}), at worst.]
  [p.86, ?use pay for building?: Results suggest yes if used > 00s of times.]
   -- [<A HREF="http://dx.doi.org/10.1613/jair.453">doi:10.1613/jair.453</A>]['05]
    & [<A HREF="http://www.autonlab.org/autonweb/papers/y1998/14687.html">autonlab.org</A>]['05].

%A P. Pantel
%A D. Lin
%T SpamCop: A spam classification and organization program
%J Learning for Text Categorization: 1998 Workshop
%P ?-?
%D 1998
%O AAAI Tech. Rep. WS-98-05
%K spam, cop, email, mail, junk, filter, filtering,
   spamcop, x1998, c199x, c19xx, zz0303
%X ...simple, yet highly accurate, spam filtering program, called SpamCop,
   which is able to identify about 92% of the spams while misclassifying only
   about 1.16% of the nonspam e-mails. ...
   -- [<A HREF="http://www.cs.ualberta.ca/~ppantel/Download/Papers/aaai98.ps">paper</A>][3/'03].
   [Also search for: spam email].

%A F. C. Duckworth
%A A. J. Lewis
%T A fair method of resetting the target in interrupted one-day cricket matches
%J J. Operational Research Soc.
%V 49
%N 3
%P 220-227
%M MAR
%D 1998
%K jrnl, c1998, c199x, c19xx, zz1108, game, cricket, match, score,
   interrupted, method
%X "A method is described for setting revised target scores for the team batting
   2nd when a limited-overs cricket match has been forcibly shortened after it
   has commenced. It is designed so that neither team benefits or suffers from
   the shortening of the game & so is totally fair to both. It is easy to
   apply, requring nothing more than a single table of numbers & a pocket
   calculator, & is capable of dealing with any number of interruptions at
   any stage of either or both innings. The method is based on a simple model
   involving a 2-factor relationship giving the number of runs which can be
   scored on avg. in the remainder of an innings as a function of the number of
   overs remaining & the number of wickets fallen. It is shown how the
   relationship enables the target score in an interrupted match to be
   recalculated to reflect the relative run scoring resources available to the
   two teams, that is overs & wickets in combination. The method was used in
   several int. & domestic 1-day competitions & tournaments in 1997."
   -- [<A HREF="http://www.jstor.org/stable/3010471">@Jstor</A>].

%T AutoMatch: Generalized record linkage system [computer program], version 4.2
%Q Kennebunkport (ME): Matchware Technologies Inc.
%D 1998
%K automatch, program, c1998, c199x, c19xx, names, aliases, synonyms, spelling,
   record linkage, link, data
%X "... AutoMatch, a probabilistic matching program, was used to link patients
   with more than one hospitalization in the data subset. Variables used in the
   linking process included the following: last name, first name, date of birth,
   municipality, zip code, race/Hispanic origin, hospital, medical record
   number, and insurer identification number. ..."
   -- from [<A HREF="http://www.cdc.gov/pcd/issues/2004/apr/03_0009.htm">cdc</A>]['10].
   [Also search for: record linkage data].

%A P. M. Djuric
%T Asymptotic MAP criteria for model selection
%J IEEE Trans Signal Proc.
%V 46
%N 10
%P 2726-2735
%M OCT
%D 1998
%K jrnl, c1998, c199x, c19xx, AMAP, criterion, stats, AIC
%X "... we show that identical penalization for every parameter is not
   appropriate & that the penalty has to depend on the model structure & type of
   model parameters. The approach to showing this is Bayesian, & it relies on
   large sample theory. We derive maximum a posteriori (MAP) rules for several
   different families of competing models & obtain forms that are similar to
   AIC & naive MDL. For some families, however, we find that the derived
   penalties are different. In those cases, our extensive simulations show that
   the MAP rule outperforms AIC & naive MDL."  [23 refs].
   -- [<A HREF="http://dx.doi.org/10.1109/78.72037">doi:10.1109/78.72037</A>]['07] ?subscr?
   [Also search for: minimum length].

%A R. M. Neal
%A G. E. Hinton
%T A view of the EM algorithm that justifies incremental, sparse, and
   other variants
%J Proc. NATO Adv. Study Inst. on Learning in Graphical Models
%E M. I. Jordan
%I Kluwer Academic Publ.
%P 355-368
%D 1998
%K wShop, c1998, c199x, c19xx, zz0614, EM algorithm, incremental, statistics,
   stats, II, expectation, soft assignment
%X "The EM alg. performs max.LH estn for data in which some vars. are
   unobserved. We present a fn that resembles -ve free energy & show that the
   M step maximizes this fn wrt the model parameters & the E step maximizes it
   wrt the distn over the unobserved vars.. ... it is easy to justify an
   incremental variant of the EM alg. in which the distn for only one of the
   unobserved vars. is recalculated in each E step. This variant is shown
   empirically to give faster convergence in a mixture estn problem. A variant
   of the alg. that exploits sparse conditional distributions is also described,
   & a wide range of other variant algorithms are also seen to be possible."
   -- pdf, ps @[<A HREF="http://www.cs.toronto.edu/~radford/em.abstract.html">toronto</A>]['14].
   (There were earlier drafts since 1993.)
   (See [<A HREF="http://dl.acm.org/citation.cfm?id=299082">dl.acm</A>]['14].)
   [Also search for: EM algorithm c196x]  and
   [also search for: II soft assignment].

%A R. D. Shachter
%T Bayes-ball: The rational pastime (for determining irrelevance and requisite
   information in belief networks and influence diagrams
%T Proc. 14th Conf. in Uncertainty in Artificial Intelligence
%P 480-487
%D 1998
%K conf, UAI, c1998, c199x, c19xx, Bayes ball, Bayess, Bayesian, belief network,
   influence diagram
%X "... statements of conditional irrelevance (or independence) can be verified
   in time linear in the size of the graph. To resolve a particular inference
   query or decision problem, only some of the possible states & prob.
   distributions must be specified, the 'requisite information'. ... presents a
   new, simple, & efficient 'Bayes-ball' alg. which is well suited to both new
   students of belief n/wks & state of the art implementations. The Bayes-ball
   alg. determines irrelevant sets & requisite info. more efficiently than
   existing methods, & is linear in the size of the graph for belief n/wks &
   influence diagrams."
   -- @[<A HREF="http://jmvidal.cse.sc.edu/lib/shachter98a.html">sc</A>]['13].

%A H. Yamamoto
%T New recursive universal code of positive integers
%J Int. Symp. in Info. Theory
%M AUG
%D 1998
%O ?IEEE Trans. on Info. Th. 46:717-723?
%K conf, c1998, c199x, c19xx, zz0723, universal code, integer, intCodes,
%X "A new recursive universal code of +ve ints. is proposed, the codeword length
   of which is shorter than log_2^(n)} bits in almost all sufficiently large
   +ve integers."
   -- [<A HREF="https://doi.org/10.1109/ISIT.1998.708950">doi:10.1109/ISIT.1998.708950</A>]['23].
   [Also search for: universal code integer].

%A N. Friedman
%A I. Nachman
%A D. Pe'er
%T Learning Bayesian network structure from massive datasets:
   The "sparse candidate" algorithm
%J Proc. 15th Conf. on Uncertainty in AI
%P ?-?
%D 1999
%K conf, UAI, UAI99, c1999, c199x, c19xx, zz0614, Peer, sparse candidate, SCA,
   net, nets, Bnet, large, dataset, variable, candidate parents, parent
%X "Learning BNs is often cast as an opt.problem, where the computational task
   is to find a struct. that maximizes a statistically motivated score. ...
   Since the search space is extremely large, such search procs. can spend most
   of the time examining candidates that are extremely unreasonable. ...
   becomes critical when we deal with data sets that are large either in the
   # of instances, or the # of attributes. ... introduce an alg. that achieves
   faster learning by restricting the search space. [it] restricts the parents
   of each var. to belong to a small subset of candidates. We then search for a
   n/w that satisfies these constraints. The learned n/w is then used for
   selecting better candidates for the next iteration. We evaluate this alg.
   both on synthetic & real-life data. ... show that it is sig. faster than
   alternative search procs. w/out loss of quality in the learned structures."
   -- 1301.6696@[<A HREF="http://arxiv.org/abs/1301.6696">arXiv</A>]['14].
   [Also search for: Bayesian network].

%A R. G. Cowell
%A A. P. Dawid
%A S. L. Lauritzen
%A D. J. Spiegelhalter
%T Probabilistic Networks and Expert Systems
%I SpringerVerlag
%S Information Sci. and Stats.
%D 1999
%K book, text, network, system, c1999, c199x, c19xx, graphical model,
   models, Bnet
%X "Probabilistic expert systems are graphical networks that support the
   modelling of uncertainty and decisions in large complex domains, while
   retaining ease of calculation. ..."
   Reprinted 2OO3, euro88, uk us isbn:0387987673.

%A D. J. C. MacKay
%T Maximum likelihood and covariant algorithms for independent component
   analysis
%D 1999
%K TR, c1999, c199x, c19xx, Bell, Sejnowski, ICA
%X "Bell & Sejnowski ('95) have derived a blind signal processing algorithm for
   a non-linear feedforward network from an information maximization viewpoint.
   This paper first shows that the same algo. can be viewed as a max.l. alg.
   for the opt. of a linear generative model. Second, a covariant version of
   the alg. is derived. ... simpler & somewhat more biologically plausible,
   involving no matrix inversions; & it converges in a smaller number of
   iterations. Third ...gives a partial proof of the `folk-theorem' that any
   mixture of sources with high-kurtosis histograms is separable by the classic
   ICA alg.. Fourth, a collection of formulae are given that may be useful for
   the adaptation of the non-linearity in the ICA algorithm."
   "unpublished" [<A HREF="http://www.inference.phy.cam.ac.uk/mackay/abstracts/ica.html">inc. .ps</A>]['05], '96, revised '99.
   auth @ Dept Phys, C@vendish Lab, U. Camb.

%A S. J. Julier
%T The scaled unscented transformation
%D 1999
%O preprint sub. to Elsevier Preprint (rev. 3) Jan 1999
%K transform, sample, mean covariance, UT, c1999, c199x, c19xx, Kalman filter
%X "... the scaled unscented transformation, a new method of applying the
   unscented transform to a nonlinear system. A set of samples are
   deterministically chosen which match the mean & covariance of a (not
   necessarily Gaussian) probability distribution. Each point in the set is
   scaled by a user-specified constant. A method is derived which preserves the
   2nd order accuracy in mean & covariance, giving performance as good as
   2nd order truncated filter."
   -- [<A HREF="http://www.cs.unc.edu/~welch/kalman/media/pdf/ACC02-IEEE1357.PDF">pdf@cs.unc.edu</A>]['05]
   [Also search for: Julier c2002].

%A S. A. Ravid
%T Information, blockbusters, and stars: A study of the film industry
%J J. Business
%V 72
%N 4
%P 463-492
%M OCT
%D 1999
%K c1999, c199x, c19xx, movie, movies, film, films, blockbuster, star,
   financial, success, popular, flop, motion pictures, rating, ratings
%X "... 2 alt. explanations for the role of stars in MPs. Either informed
   insiders signal project quality by hiring an expensive star, or stars
   capture their expected economic rent.  ... tested on a sample of movies
   produced in the 1990s. Means comparisons suggest that star-studded films
   bring in higher revenues. However, regressions show that any big budget
   investment increases revenues. Sequels, highly visible films & "family
   oriented" ratings also contribute to revenues. A higher return on investment
   is correlated only with G or PG ratings and marginally with sequels. This is
   consistent with the 'rent capture' hypothesis."
   -- [<A HREF="http://links.jstor.org/sici?sici=0021-9398%28199910%2972%3A4%3C463%3AIBASAS%3E2.0.CO%3B2-A">@Jstor</A>]['05],
      [<A HREF="http://ideas.repec.org/a/ucp/jnlbus/v72y1999i4p463-92.html">ideas.repec.org</A>]['05].

%A J. A. Hoeting
%A D. Madigan
%A A. E. Raftery
%A C. T. Volinsky
%T Bayesian model averaging: A tutorial
%J Statistical Sci.
%V 14
%N 4
%P 382-417
%D 1999
%O correction, 15, pp.193-195, 1999
%K jrnl, c1999, c199x, c19xx, zz0206, BMA, stats, average, mixture, models,
   MCMC, prediction, weighted, introduction
%X "... (BMA) provides a coherent mechanism for accounting for this
   model uncertainty. Several methods for implementing ..."
   -- [<A HREF="http://www.stat.colostate.edu/~jah/papers/statsci.pdf">pdf@colostate</A>]['06],
   paper pp.382-401, comments by M.Clyde pp.401-403, D.Draper pp.405-409
   and E.I.George pp.409-412, and rejoinder pp.412-417.
   [Also search for: mixture modelling].

%A L. K. Saul
%M M. I. Jordan
%T Mixed memory Markov models: Decomposing complex stochastic processes as
   mixtures of simpler ones
%J Machine Learning
%V 37
%N 1
%P 75-87
%D 1999
%K jrnl, c1999, c199x, c19xx, zz0808, process, mixture model, timeSeries,
   discrete time series
%X "... MMs whose state spaces arise from the Cartesian product of 2 or more
   discrete random variables. We show how to parameterize the transition
   matrices of these models as a convex combination - or mixture - of simpler
   dynamical models. The params in these models admit a simple prob. interp. &
   can be fitted iteratively by an EM procedure. We derive a set of generalized
   Baum-Welch updates for factorial HMMs that make use of this param'n. ..."
   pdf: [<A HREF="http://dx.doi.org/10.1023/A:1007649326333">doi:10.1023/A:1007649326333</A>]['08] via MD.

%A N. H. Saji
%A B. N. Goswami
%A P. N. Vinayachandran
%A T. Yamagata
%T A dipole mode in the tropical Indian Ocean
%J Nature
%V 401
%P 360-363
%D 1999
%K jrnl, c1999, c199x, c19xx, weather, climate, predict, prediction, model,
   Indian ocean, dipole, IOD, sea surface, temperature, SST, rainfall, rain
%X "... IOD ... defined by an index that is the diff. between SST in the W.
   (50deg-70degE, 10degS-10degN) and E. (90deg-110degE, 10deg-0degS) tropical
   Indian Oceans. A +ve IOD occurs when the W. basin is warmer than average &
   the E. basin is cool ... showed a modulation in Australian seasonal rainfall
   with IOD positive and negative years. ..." -- BOM ('09).

%A M. Adams
%T The dead grandmother / exam syndrome
%J Annals of Improbable Research
%V 5
%N 6
%P 3-6
%M NOV/DEC
%D 1999
%K jrnl, AIR, c1999, c199x, c19xx, zz0414, dead, death, deaths, grand mother,
   grandmother, grandparent, life expectancy, parent, graveyard, granny,
   grannies, student, college, university, exam, examination, test, syndrome,
   funny, ha ha, haha
%X "It has long been theorized that the week prior to an exam is an extremely
   dangerous time for the relatives of college students. Ever since I began my
   teaching career, I heard vague comments, incomplete references & unfinished
   remarks, all alluding to the 'Dead Grandmother Problem.' Few colleagues
   would ever be explicit in their description of what they knew, but I quickly
   discovered that anyone who was involved in teaching at the college level
   would react to any mention of the concept. ..."
   -- pdf@[<A HREF="http://www.improbable.com/airchives/paperair/volume5/v5i6/GrandmotherEffect%205-6.pdf">improbable.com</A>]['14,'21] and
     [<A HREF="http://www.easternct.edu/~adams/Resources/Grannies.pdf">pdf</A>]@[<A HREF="http://www.easternct.edu/~adams/">~adams</A>]['14].

%A W. E. Winkler
%T The state of record linkage and current research problems
%R RR99/04
%I US Bureau of the Census
%D 1999
%K TR 04, TR4, records, name, names, identity, match, matching, problem,
   c1999, c199x, c19xx, record, linkage, data
%X "...overview of methods & systems developed for record linkage. Modern RL
   begins with the pioneering work of Newcombe & is especially based on the
   formal mathematical model of Fellegi & Sunter. In their seminal work,
   Fellegi & Sunter introduced many powerful ideas for estimating RL
   parameters & other ideas that still influence record linkage today. Record
   linkage research is characterized by its synergism of statistics, computer
   science, & operations research. Many difficult algorithms have been
   developed & put in software systems. RL practice is still very limited.
   Some limits are due to existing software. Other limits are due to the
   difficulty in automatically estimating matching parameters & error rates,
   with current research highlighted by the work of Larsen & Rubin. Still other
   limits are due to the inability do auxiliary programming to clean-up &
   adjust for data-specific anomalies. The evaluation of matching results also
   necessitates auxiliary analyses...."
   -- [<A HREF="http://www.census.gov/srd/www/byyear.html">reports</A>]['05].
   [Also search for: record linkage data].

%A Te-Won Lee
%A M. Girolami
%A A. J. Bell
%A T. J. Sejnowski
%T A unifying information-theoretic framework for independent component analysis
%J Int. J. Computers and Math.
%V 39
%N 11
%P 1-21
%M MAR
%D 2000
%K jrnl, IJCM, ICA, blind separation, mixed sources, c1999, c199x, c19xx,
   stats, components, infomax
%X "We show that different theories recently proposed for Independent Component
   Analysis (ICA) lead to the same iterative learning alg. for blind separation
   of mixed independent sources. We review those theories & suggest that
   information th. can be used to unify several lines of research. Pearlmutter
   and Parra ('96) and Cardoso ('97) showed that the infomax approach of Bell &
   Sejnowski ('95) and the max.l. est. approach are equivalent. ..."
   -- [<A HREF="http://www.sloan.salk.edu/~tewon/Blind/WWW/Public/ijmc99.ps.gz">www</A>]['04].

%A A. Pfeffer
%T A Bayesian language for cumulative learning
%J AAAI Workshop on Learning Statistical Models from Relational Data
%P ?-?
%M JUL
%D 2000
%K conf, IBAL, agent, agents, scope, observations, zz0703
%X ... 1st-order rep'n lang' ... observations as an integral part
   of a language.  ... key semantic concept is a scope, which consists
   of models and observations.  The meaning of a scope is the knowledge
   state of an agent. ...
   -- [<A HREF="http://www.eecs.harvard.edu/~avi/Papers/cumulative.ps">.ps</A>][7/'03] via c.t.

%A R. H. Shumway
%A D. S. Stoffer
%T Time Series Analysis and Its Applications
%I Springer
%S Texts in Stats.
%P 549
%D 2000
%K book, text, statistics, time series analysis, timeSeries, c2000, c200x, c20xx
%X corrected printing 2001, original 2000. hb euro85, stg 60.
   isbn:0387989501.

%T Data Analysis, Classification, and Related Methods
%E H. A. L. Kiers
%E J.-P. Rasson
%E P. J. F. Groenen
%E M. Schader
%I Springer
%D 2000
%K stats, statistics, II, c2000, c200x, c20xx
%X [<A HREF="http://ppswmm.ppsw.rug.nl/~kiers/">kiers</A>][8/'04],
   [<A HREF="http://ppswmm.ppsw.rug.nl/~kiers/main.html">main.html</A>][8/'04].

%A A. McCallum
%A K. Nigam
%A L. Ungar
%T Efficient clustering of high-dimensional data sets with application to
   reference matching
%J KDD
%P ?-?
%D 2000
%K conf, KDD, knowledge discovery, set, record linkage, citations, blocking,
   distance metric, data
%X "...grouping bibliographic citations ... reduces comp. time by more than
   on order of magnitude and decreases error in comparison to a previously
   used algorithm by 25%."    ...edit-distance ... fields found by a H MM...
   -- [<A HREF="http://www.cs.umass.edu/~mccallum/papers/canopy-kdd2000.ps">pp.ps@cs.umass.edu</A>]['05], AM @ umass['05].

%A S. van Dongen
%T Graph clustering by flow simulation
%I U. of Utrecht
%D 2000
%K PhD thesis, vanDongen, graphs, Markov cluster, MCL, grouping, link, linkage,
   c2000, c200x, c20xx, partitioning, matrix, random walk, walks
%X "Cluster analysis is the math. study of methods for recognizing natural
   groups within a class of entities. ... Markov cluster process ... graph
   clustering which has connections to the clearly scoped field of graph
   partitioning. ..."
   -- [<A HREF="http://micans.org/mcl/lit/svdthesis.pdf.gz">thesis.pdf.gz</A>]['05]
   "The MCL alg. simulates random walks through a graph (e.g. of seqs. as
   vertices, & edges as pairwise matches). By iteratively re-computing random
   walks & favouring those with higher probability (which tend to be
   intra-cluster walks) over those with low prob. (which tend to be
   inter-cluster walks), MCL partitions the graph into segments that can be
   interpreted as clusters" -- H@rlow et al '04.

%A G. J. McLachlan
%A D. Peel
%T Finite Mixture Models
%I Wiley
%D 2000
%K book, text, statistics, stats, mixture model, modelling, EM algorithm,
   cluster, clustering, estimation, c2000, c200x, c20xx, zz0801
%X uk us isbn:0471006262; uk us isbn13:978-0471006268.
   -- [<A HREF="http://www.maths.uq.edu.au/~gjm/">home</A>][8/'01].
   "... include identifiability problems, actual fitting of finite mixtures
   through use of the EM alg., properties of the max. LH estimators so obtained,
   assessment of the # of components to be used in the mixture, and the
   applicability of asymptotic theory ..."
   [Also search for: mixture model]  or  [also search for: EM algorithm c196x].

%A P. H. S. Torr
%A A. Zisserman
%T MLESAC: a new robust estimator with application to estimating image geometry
%J Computer Vision and Image Understanding
%V 78
%N 1
%P 138-156
%M APR
%D 2000
%D 2000
%K jrnl, c2000, c200x, c20xx, zz0807, MLESAC, MLE SAC, multiple view relations,
   point correspondence, location, RANSAC
%X "... robustly estimating multiple view relations from point correspondences.
   The method comprises two parts, the first is a new robust estimator MLESAC
   ... a generalization of the RANSAC estimator. It adopts the same sampling
   strategy as R... to gen. putative solns, but chooses the soln to max the
   likelihood rather than just the number of inliers. The 2nd part to the alg.
   is a general purpose method for auto. parametrizing these relns, using the
   output of MLESAC.  ... overcomes the difficulty of non-linear constraints &
   conducts a constrained optimization. ..."
   -- [<A HREF="www.robots.ox.ac.uk/~vgg/publications/papers/torr00.pdf">pdf@oxford</A>]['07],
      [<A HREF="http://openurl.ingenta.com/content?genre=article&issn=1077-3142&volume=78&issue=1&spage=138&epage=156">openurl</A>]['07].
   [Also search for: RANSAC].

%A F. Murtagh
%A J-L. Starck
%A M. W. Berry
%T Overcoming the curse of dimensionality in clustering by means of the wavelet
   transform
%J COMPJ
%V 43
%N 2
%P 107-120
%D 2000
%K COMPJ, jrnl, high dimension, data space, cluster, exploration, zz0500
%X N things with M attributes, put in NxM matrix, try to diagonalise (permute
   rows and cols), or at least get big values near diagonal, use wavelet
   transform to model/remove noise,  look for clusters in filtered result.
   28 refs.  [Also search for: mixture modelling].

%A G. Marsaglia
%A Wai Wan Tsang
%T A simple method for generating Gamma variables
%J ACM Trand on Math Software
%V 26
%N 3
%P 363-372
%M SEP
%D 2000
%K jrnl, TOMS, c2000, c200x, c20xx, zz0214, Gamma, probability distribution,
   random variable, RNG, PRNG, pseudorandom, generator
%X "... generating a Gamma variate as the cube of a suitably scaled normal
   variate. It is fast and simple ... In brief: generate a normal variate x &
   a uniform variate U until (ln U < 0.5 x^2 + d - dv + d ln(v))
   then return (d v).  Here, the Gamma parameter is alpha >= 1, &
   v=(1+x/sqrt(9d))^3 with d=alpha-1/3. The efficiency is high, exceeding
   0.951, 0.981, 0.992, 0.996 at alpha = 1, 2, 4, 8. ...  return (d v) if
   (U < 1 - 0.0331x^4). ...  show how to boost an alpha < 1 into an
   alpha > 1. ..."
   Note if "alpha < 1, one can use g_alpha = (g_(alpha+1) U^(1/alpha)),
            with U uniform in (0,1) ..."
   -- [<A HREF="http://dx.doi.org/10.1145/358407.358414">doi:10.1145/358407.358414</A>]['14].
   [Also search for: Gamma PRNG].

%A N. Ueda
%A R. Nakano
%A Z. Ghahramani
%A G. E. Hinton
%T SMEM algorithm for mixture models
%J Neural Comput.
%V 12
%N 9
%P 2109-2128
%M SEP
%D 2000
%K c2000, c200x, c20xx, zz1214, stats, SMEM, EM, algorithm, split, merge,
   mixture model, modelling, estimation, learning
%X "... a split-and-merge expectation-maximization (SMEM) alg. to overcome the
   local maxima problem in param. est. of finite mixture models. ... local
   maxima often involve having too many components of a MM in one part of the
   space & too few in another, widely separated part of the space. To escape
   from such configurations, we repeatedly perform simultaneous s.-and-m. ops.
   using a new criterion for efficiently selecting the s.-and-m. candidates.
   We apply the proposed alg. to the training of gaussian mixtures & mixtures of
   factor analyzers using synthetic & real data & show the effectiveness of
   using the s.-and-m. ops. to improve the likelihood of both the training data
   & of held-out test data. We also show the practical usefulness of the
   proposed alg. by applying it to image compression & pattern recognition
   problems."
   -- [<A HREF="http://dx.doi.org/10.1162/089976600300015088">doi:10.1162/089976600300015088</A>]['14].
   [Also search for: Snob mixture model],  c1968 and later.

%A M. A. Stephens
%T Tests of fit for the Laplace distribution, with applications
%J Technometrics
%V 42
%N 4
%P 417-424
%M NOV
%D 2000
%K jrnl, c2000, c200x, c20xx, stats, statistics, Laplace distribution, L1, test,
   absolute error, linear regression, stackloss, stack-loss, dataset, data-set
%X "Tests are given for the Laplace or double exponential distn. The test
   statistics are based on the empirical distn fn & inc. the families of Cramer-
   -von Mises & Kolmogorov-Smirnov. Asymptotic theory is given, & asymptotic
   pts are calc., for the C.-vonM. family, & Monte Carlo pts for finite samples
   are given for all the statistics. Power studies suggest that the Watson
   statistic is the most powerful for the common problem of testing Laplace
   v. other symmetric distns. An applicn of the Laplace d. is in LAD (or L1)
   regression. This is also discussed in the article, with two examples."
   -- [<A HREF="http://dx.doi.org/10.1080/00401706.2000.10485715">doi:10.1080/00401706.2000.10485715</A>]['13],
   & pdf@[<A HREF="http://www.stats.uwo.ca/faculty/aim/2004/04-259/ExtraReading/TestsFitLaplaceDistribution.pdf">uwo</A>]['13].

%A T. P. Minka
%T Estimating a Dirichlet distribution
%D 2000
%K TR, c2000, c200x, c20xx, zz0718, estimate, estimator, estimating, stats
%X "The D.distn & its compound variant, the Dirichlet-multinomial, are two of
   the most basic models for proportional data, such as the mix of vocabulary
   words in a text document. Yet the max.-likelihood est. of these distns is not
   available in closed-form. ... describes simple & efficient iterative schemes
   for obtaining param. ests. in these models. In each case, a fixed-point
   iteration & a Newton-Raphson (or generalized N.-R.) iteration is provided."
   -- pdf@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.220.175">c'teseer</A>]['18],
   and revised 2003, 2009, 2012
   -- pdf@[<A HREF="https://tminka.github.io/papers/dirichlet/">g'th'b</A>]['18].
   [Also search for: Dirichlet estimate stats].

%A T. Hastie
%A R. Tibshirani
%A J. Friedman
%T The Elements of Statistical Learning
%I Springer
%S Stats.
%P 533
%D 2001
%K book, text, data mining
%X isbn:0387952845.  euro80, stg56.  Corrected 2002.
   [Also search for: inductive inference].

%A J. S. Liu
%T Monte Carlo Strategies in Scientific Computing
%I Springer
%S Stats
%P 343
%D 2001
%K book, text, montecarlo, Las Vegas, LasVegas, science
%X isbn:0387952306.  euro70, stg50.

%A C. P. Robert
%T The Bayesian Choice. From Decision Theoretic Foundations to
   Computational Implementation
%I Springer
%S Stats
%P 604
%D 2001
%K book, text, c2001, c200x, c20xx, statistics, stats, Stein effect,
   Monte Carlo, Gibbs sampling, MCMC
%X 2nd ed 2007(?), uk us isbn:0387952314.  euro90, stg63.
   "paperback edition, a reprint of the 2001 edition" ...
   uk us isbn:0387715983; uk us isbn13:978-0387715988.

%A F. R. Kschischang
%A B. J. Frey
%A H.-A. Loeliger
%T Factor graphs and the sum-product algorithm
%J IEEE Trans. on Info. Theory
%V 47
%N 2
%P 498-519
%M JUL
%D 2001
%K jrnl, intro, survey, c1998, c199x, c19xx, zz0721, factor graph, factorGraph,
   dynamic programming, DPA, marginal
%X "A factor graph is a bipartite g. that expresses how a 'global' fn of many
   variables factors into a product of 'local' fns. FGs subsume many other
   graphical models inc. B.n/wks, Markov random fields, & Tanner gs..
   ... the sum-product alg. operates in FGs to compute either exactly or approx.
   various marginal fns by distributed message-passing in the g.. ...
   [Many algs] can be derived as specic instances of the sum-product alg., inc.
   the fwd/bwd alg., the Viterbi alg., the iterative 'turbo' decoding alg.,
   Pearl's belief propagation alg. for BNs, the Kalman filter, & certain fast
   F.transform algs."
   -- [<A HREF="https://doi.org/10.1109/18.910572">doi:10.1109/18.910572</A>]['21].
   ***NB. Longer version (76p, 1998) at [<A HREF="https://www.cs.toronto.edu/~radford/csc2506/factor.pdf">utoronto</A>][2O21].
   (Also see FG@[<A HREF="https://en.wikipedia.org/wiki/Factor_graph">wikip</A>].)

%A P. Dalgaard
%T Introductory Statistics with R
%I Springer
%S Stats
%P 285
%D 2002 to appear
%K book, text, R, RR, S Plus SPlus, stats, data mining, software, package
%X uk us isbn:0387954759.

%A F. B. Jensen
%T Bayesian Networks and Decision Graphs
%I Springer
%P 268
%D 2001
%K book, text, network, c2001, c200x, c20xx, net, nets, graph, Bnet, network
%X euro75, stg53. uk us isbn:0387952594.
   [Also search for: Dgraph decision]

%A H. Liu
%A F. Hussain
%A C. L. Tan
%A M. Dash
%T Discretization: An enabling technique
%J Data Mining and Knowledge Discovery
%V 6
%P 393-423
%D 2002
%K c2002, c200x, c20xx, zz0106, continuous, discrete, quantization,
   quantisation
%X "... paper aims at a systematic study of discretization methods with their
   history of development, effect on classification, and trade-off between
   speed and accuracy. ..."
   -- [<A HREF="http://www.comp.nus.edu.sg/~tancl/Papers/Journals/DMKD-Liu-2002.pdf">pdf</A>]['05].

%A D. P. Farrington
%A B. C. Welsh
%T The effects of improved lighting on street crime: A systematic review
%I Home Office (UK)
%R Research Study 251
%P 61
%D 2002
%K report, light, lights, stats, theft, assault, survey, police, policing,
   Marchant, c2002, c200x, c20xx
%X [<A HREF="http://www.homeoffice.gov.uk/rds/pdfs2/hors251.pdf">.pdf</A>][5/'04].
   See criticism by Marchant and reply by auths in Brit. J. Crim'ogy, 2OO4.

%A A. Lanterman
%T Schwarz, Wallace, and Rissanen: Intertwining themes in theories of
   model order estimation
%J Int. Statistical Rev.
%V 69
%N 2
%P 185-212
%M AUG
%D 2001
%K jrnl, stats, c2001, c200x, c20xx, theory, minimum message length, MML,
   models, model, selection, estimate, fit, zz0702, description, MDL,
   comparison, compare, survey
%X "Investigators interested in model order estimation have tended to divide
   themselves into widely separated camps; this survey of the contributions of
   Schwarz, Wallace, Rissanen, & their coworkers attempts to build bridges
   between the various viewpoints, illuminating connections which may have
   previously gone unnoticed & clarifying misconceptions which seem to have
   propagated in the applied literature. Our tour begins with Schwarz's
   approximation of Bayesian integrals via Laplace's method. We then introduce
   the concepts underlying Rissanen's minimum description length principle via
   a Bayesian scenario with a known prior; this provides the groundwork for
   understanding his more complex non-Bayesian MDL which employs a 'universal'
   encoding of the integers. Rissanen's method of parameter truncation is
   contrasted with that employed in various versions of Wallace's minimum
   message length criteria. Rissanen's more recent notion of stochastic
   complexity is outlined in terms of Bernardo's information-theoretic
   derivation of the Jeffreys prior."
   -- paper@[<A HREF="http://www.jstor.org/stable/1403813">Jstor</A>]['14].
   [Also search for: compare MML MDL].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>] and [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">C.S.Wallace</A>].)

%A M. A. T. Figueiredo
%A A. K. Jain
%T Unsupervised learning of finite mixture models
%J IEEE Trans. on Patt. Analysis and Machine Intell.
%P 381-396
%V 24
%N 3
%M MAR
%D 2002
%K jrnl, IEEE, Trans, PAMI, model, classification, minimum message length,
   MML, description, MDL, selection, expectation maximization, EM algorithm,
   estimation, model, BIC, AIC, c2002, c200x, c20xx, clustering, modelling
%X ... unsupervised algorithm for learning a finite mixture model from
   multivariate data. ... `unsupervised' ... 1) [can select] the number of
   components and 2) ... does not require careful initialization. ...
   ... we do not use a model selection criterion to choose one among a set
   of preestimated candidate models; [but] integrate estimation and model
   selection in a single algorithm. ...
   -- [<A HREF="http://dx.doi.org/10.1109/34.990138">doi:10.1109/34.990138</A>]['06],
      [<A HREF="http://red.lx.it.pt/~mtf/">1</A>][<A HREF="http://www.cse.msu.edu/~jain/">2</A>][7/2'02].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>] and
   [also search for: Snob MML].)

%A P. J. Green
%T Reversible jump Markov chain Monte Carlo computation and Bayesian
   model determination
%J Biometrika
%V 82
%P 711-732
%D 1995
%O Workshop on Model Criticism of Highly Structured Stochastic Systems,
   Weisbaden, Sept 1994
%K jrnl, Peter, MCMC, stochastic, statistics, AI, II, estimation,
   model selection, spaces, models, c1995, c199x, c19xx
%X [<A HREF="http://www.stats.bris.ac.uk/~peter/">~peter</A>][7/'02],
   ... proposes a new framework for the construction of reversible
   Markov chain samplers that jump between parameter subspaces of
   differing dimensionality, which is flexible and entirely constructive.
   It should therefore have wide applicability in model determination problems.
   The methodology is illustrated with applications to multiple
   change-point analysis in one and two dimensions, and to a Bayesian
   comparison of binomial experiments.
   -- [<A HREF="http://www.stats.bris.ac.uk/~peter/abstracts/revjump.html">abs</A>][7/'02].

%A Y. Cheng
%T Mean shift, mode seeking, and clustering
%J IEEE Trans. on Patt. Anal. and M.I.
%V 17
%N 8
%P 790-799
%D 1995
%K c1995, c199x, c19xx, mean shift, meanShift, stats, mode seeking, kernel,
   k-means, kmeans
%X "Mean shift, a simple interactive proc. that shifts each data point to the
   avg. of data pts in its neighborhood is generalized & analyzed ... makes some
   k-means like clustering algs. its special cases. It is shown that m.s. is a
   mode-seeking process on the surface constructed with a 'shadow' kernal. For
   Gaussian kernels, mean shift is a gradient mapping. Convergence is studied
   for mean shift iterations. Cluster analysis is treated as a deterministic
   problem of finding a fixed pt of m.s. that characterizes the data.
   Appl'ns in clustering & Hough transform are demo'd. ... also considered as
   an evolutionary strategy that performs multistart global optimization"
   -- [<A HREF="http://dx.doi.org/10.1109/34.400568">doi:10.1109/34.400568</A>]['12].
   [Also search for: meanShift].

%A D. Heckerman
%A D. Geiger
%A D. M. Chickering
%T Learning Bayesian Networks: The combination of knowledge and statistical data
%J Mach. Learning
%V 20
%P 197-243
%D 1995
%K jrnl, c1995, c199x, c19xx, zz0629, Bnet, Bnets, BDe, BDeu
%X "... from a combination of prior knowledge & statistical data. First ...
   develop a methodology for assessing informative priors needed for learning.
   ... is derived from a set of assumptions made previously as weil as the
   assumption of likelihood equivalence, which says that data should not help
   to discriminate n/wk stuctures that represent the same assertions of
   cond.indep.. ... Second, using these priors, we show how to compute the
   relative posterior probabilities of n/wk structs. given data. Third, we
   describe search methods for identifying n/wk structs. with high posterior
   prob.. ..."
   -- pdf@[<A HREF="http://www.cs.technion.ac.il/~dang/journal_papers/heckerman1995learning.pdf">technion</A>]['20].
   Coined "BDe" and "BDeu" but see...  [Also search for: Bnet BDe].

%A M. Seno
%A G. Karypis
%T LPMiner: An algorithm for finding frequent itemsets using length-decreasing
   support constraint
%J 1st IEEE Conf. on Data Mining
%P ?-?
%M AUG
%D 2001
%K conf, c2001, c200x, c20xx, frequent item set, sets, itemset, FIS, support,
   frequent pattern growth, FPgrowth, association rule, rules
%X "... 2 orders of magnitude faster than `FP-growth' alg'..."
   -- [<A HREF="http://www-users.cs.umn.edu/~karypis/publications/Papers/Postscript/lpm.ps">paper</A>][12/'02]  [9 refs].

%A A. Pfeffer
%T IBAL: An integrated Bayesian agent language
%J IJCAI
%P ?-?
%D 2001
%K conf, IBAL, programming, agents, zz0703, c2001, c200x, c20xx
%X "... IBAL, a rational programming language for prob' & decision theoretic
   agents.  ... declarative ... Bayesian param est'n ...  rich type system ...
   -- [<A HREF="http://www.eecs.harvard.edu/~avi/Papers/ibal.ijcai01.ps">.ps</A>][7/'03] via c.t.

%A A. J. Dobson
%T An Introduction to Generalized Linear Models (2nd edn)
%I ChapmanAndHall
%P 240
%M NOV
%D 2001
%K book, text, statistics, stats, GLM, GLMs, model, c2001, c200x, c20xx, intro
%X 2nd ed 2001, about us$45. uk us isbn:1584881658.
   [Also search for: GAMs stats].
   (Dobson teaches biostats at the U.Qld [<A HREF="http://www.sph.uq.edu.au/">.sph.uq</A>]['05].)

%A C. E. McCulloch
%A S. R. Searle
%T Generalized, Linear, and Mixed Models
%I Wiley
%M JAN
%D 2001
%P 358
%K book, text, statistics, stats, model, GLM, GLMs, c2001, c200x, c20xx
%X about stg67, euro95, hb.; uk us isbn:0-471-19364-X.
   [Also search for: GAMs stats].

%A A. Deshpande
%A M. Garofalakis
%A M. I. Jordan
%T Efficient stepwise selection in decomposable models
%J UAI
%P 128-135
%D 2001
%K conf, UAI, UAI01, UAI17, c2001, c200x, c20xx, zz0913, decomposable model,
   stats, chordal, graph, maths, forward selection, search, edges, eligible,
   log linear, LLA
%X "... efficient alg. for performing stepwise seln in the class of decomposable
   models. ... fwd selection proc., but we also discuss how backward seln. & the
   combination of the two can be performed efficiently. ... (1) a simple
   characterization for the edges that can be added to a decomposable model
   while retaining its decomposability & (2) an efficient alg. for enumerating
   all such edges for a given decomposable model in O(n^2) time, where n is the
   # of vars. in the model.  We also analyze the complexity of the overall
   stepwise seln proc. (includes the complexity of enumerating eligible edges as
   well as the complexity of deciding how to "progress"). We use the KL
   divergence of the model from the saturated model as our metric, but the
   results we present here extend to many other metrics as well."
   -- pdf@[<A HREF="http://dl.acm.org/citation.cfm?id=2074039">acm</A>]['13].
   (?Q. about implementation?)
   [Also search for: stats chordal model] or decomposable ... .

%A C. Yang
%A U. Fayyad
%A P. Bradley
%T Efficient discovery of error-tolerant frequent itemsets in high dimensions
%J Proc. 7th ACM SIGKDD Int. Conf. on Knowledge Discovery and Data Mining
%W San Francisco
%I ACM
%P 194-203
%D 2001
%K conf, frequent item set, sets, FIS, error, support, association rule, rules,
   data mining, KDD01, KDD 01, consumer, customer, buyer, product, digiMine,
   ETI, ETIs, itemset, block, blocks, submatrix, sub matrix, one, ones,
   apriori algorithm, zz1202
%X ...generalization [of FIS] allowing for the notion of errors in the itemset
   definition. We motivate the problem and present an efficient algorithm that
   identifies error-tolerant frequent clusters of items in transactional data
   (customer-purchase data, web browsing data, text, etc.). The algorithm
   exploits sparseness of the underlying data to find large groups of items
   that are correlated over database records (rows). The notion of transaction
   coverage allows us to extend the algorithm and view it as a fast clustering
   algorithm for discovering segments of similar transactions in binary sparse
   data. We evaluate the new algorithm on three real-world applications:
   clustering high-dimensional data, query selectivity estimation and
   collaborative filtering. ...   isbn:158113391X.
   -- [<A HREF="http://doi.acm.org/10.1145/502512.502539">paper</A>][12/'02].

%A C. Li
%A G. Biswas
%A M. B. Dale
%A P. E. R. Dale
%T Building models of ecological dynamics using HMM based temporal
   data clustering.
%J 4th Int. Conf. Intell. Data Analysis
%P 53-62
%M SEP
%D 2001
%I SpringerVerlag
%S LNCS
%V 2189
%K conf, mike dale, IDA, IDA4, advances, time series, c2001, c200x, c20xx,
   timeSeries, ecology, model, BIC, hidden Markov model
%X "...temporal data clustering system that is based on the Hidden Markov
   Model(HMM) methodology. ... explicit HMM model size selection procedure is
   incorporated into the clustering process, i.e., the sizes of the individual
   HMMs are dynamically determined for each cluster. ... (i) the HMM model size
   selection algorithm is effective in re-discovering the structure of the
   generating HMMs, (ii) the HMM clustering with model size selection
   significantly outperforms HMM clustering using uniform HMM model sizes for
   re-discovering clustering partition structures, (iii) it is able to produce
   interpretable and "interesting" models for real world data."
   Adv' in I D A; isbn:3540425810.   [Also see paper in I D A '02]
   -- [<A HREF="http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=2189&spage=53">openurl</A>][2/'04],
   &  [<A HREF="http://www.springerlink.com/link.asp?id=l338tkudlrhexvyc">met@press</A>][2/'04].

%A B. Li
%A G. Biswas
%A M. B. Dale
%A P. E. R. Dale
%T Matryoshka: A HMM based temporal data clustering methodology for
   modeling systems dynamics
%J Intell. Data Analysis
%V 6
%N 3
%P 281-308
%D 2002
%K IDA, hidden Markov model, cluster, unsupervised classification, II,
   timeSeries, time series, models, system, zz1002, BIC
%X "...temporal data clustering system ...based on the ... (HMM) methodology.
   The proposed methodology improves upon existing HMM clustering methods in
   two ways. First, an explicit HMM model size selection procedure is
   incorporated into the clustering process, i.e., the sizes of the individual
   HMMs are dynamically determined for each cluster. This improves the
   interpretability of cluster models, and the quality of the final clustering
   partition results. Second, a partition selection method is developed to
   ensure an objective, data-driven selection of the number of clusters in the
   partition. The result is a heuristic sequential search control algorithm
   that is computationally feasible. Experiments with artificially generated
   data and real world ecology data show that: (i) the HMM model size selection
   algorithm is effective in re-discovering the structure of the generating
   HMMs, (ii) the HMM clustering with model size selection significantly
   outperforms HMM clustering using uniform HMM model sizes for re-discovering
   clustering partition structures, (iii) it is able to produce interpretable
   and "interesting" models for real world data."
   -- [<A HREF="http://iospress.metapress.com/link.asp?id=hqj233f6rhv7kvf3">met@press</A>][2/'04]
      [<A HREF="http://iospress.metapress.com/openurl.asp?genre=article&issn=1088-467X&volume=6&issue=3&spage=281">issn</A>][2/'04]
   via P.T.  H 6.305 I61.4;  biswas at vuse.vanderbilt.edu

%A S. Hawkins
%A G. Williams
%A R. A. Baxter
%T Feature selection for pathology laboratory surveillance
%J Topics in Health Information Management
%V 22
%N 1
%P 14-24
%D 2001
%K jrnl, health, tests, testing, monitoring, lab, Rohan Baxter
%X [<A HREF="http://www.act.cmis.CSIRO.AU/rohanb/">rohan</A>][11/'02]

%A S. L. Lauritzen
%T Graphical Models
%I Clarendon Press, 0xford
%P 298
%D 1996
%K book, text, stats, statistics, model, c1996, c199x, c19xx, L4Ref
%X [<A HREF="http://www.math.auc.dk/~steffen/">~steffen</A>][1/'04]

%A R. Tibshirani
%T Regression shrinkage and selection via the lasso
%J J. Royal Stat. Soc..,  Series B (Methodological)
%V 58
%N 1
%P 267-288
%D 1996
%K jrnl, JRSS, c1996, c199x, c19xx, stats, shringage, lasoo, estimate,
   estimation, selection, linear model, models, L1, penalized, penalised,
   least angle regression, LAR, LARs, regularization
%X "We propose a new method for est. in linear models. The 'lasso' minimizes the
   residual sum of squares subject to the sum of the absolute value of the
   coefficients being less than a constant. Because of the nature of this
   constraint it tends to produce some coefficients that are exactly 0 & hence
   gives interpretable models. ... studies suggest that the lasso enjoys some of
   the favourable properties of both subset selection & ridge regression. It
   produces interpretable models like subset selection & exhibits the stability
   of ridge regression. ... an interesting relationship with recent work in
   adaptive fn est. by Donoho & Johnstone. The lasso idea is quite general & can
   be applied in a variety of stat. models: extensions to gen.regression models
   & tree-based models are briefly described."
   -- pdf@[<A HREF="http://www-stat.stanford.edu/~tibs/lasso/lasso.pdf">Stanf'd</A>]['09],
      [<A HREF="https://www.jstor.org/stable/2346178">Jstor</A>]['19].
   TR June '94, ps@[<A HREF="http://www-stat.stanford.edu/~tibs/ftp/lasso.ps">Stanf'd</A>]['09].
   [Also search for: lasoo stats].
   (Also see [<A HREF="http://www-stat.stanford.edu/~tibs/lasso.html">lasso</A>]['09],
   and lasoo@[<A HREF="https://en.wikipedia.org/wiki/Lasso_(statistics)">wikip</A>]['19].)

%A D. M. Chickering
%T Learning Bayesian Networks is NP-Complete
%J Learning from Data: Artificial Intelligence and Statistics V
%I SpringerVerlag
%P 121-130
%D 1996
%K conf, c1996, c199x, c19xx, net, nets, Bnets, NPC, BDe metric
%X "Algs. for learning BNs from data have two components: a scoring metric & a
   search proc.. The scoring metric computes a score reflecting the goodness-
   -of-fit of the structure to the data. The search proc. tries to identify
   n/w structures with high scores. Heckerman et al. (1995) introduce a B.
   metric, called the BDe metric, that computes the rel. posterior prob. of a
   n/w structure given data. ... show that the search problem of identifying a
   B. n/w - among those where each node has at most K parents - that has a
   rel. posterior prob. greater than a given constant is NP-complete,
   when the BDe metric is used."
   -- pdf@[<A HREF="http://maxchickering.com/publications/lns96.pdf">maxch'.com</A>]['14].
   uk us isbn:0387947361.

%A M. A. Upal
%A E. M. Neufeld
%T Comparison of unsupervised classifiers
%J Proc. of the Information, Statistics and Induction in Science (ISIS)
%I World Scientific
%P 342-353
%D 1996
%K conf, c1996, c199x, c19xx, classification, classifier, clustering,
   performance
%X "... traditional metrics such as precision and recall cannot be directly
   applied to [UCs]. The performance evaluation framework I developed for
   evaluating the classifier performance involved (a) designing a simulator to
   generate training and testing data that could be systematically varied along
   various dimensions of interest, and (b) measuring the performance of various
   systems on the simulated data using a number of novel metrics. ..."
   -- [<A HREF="http://www.eecs.utoledo.edu/~aupal/">Upal</A>]['06]

%A K. Murphy
%T The Bayes net toolbox for Matlab
%J Computing Sci. and Stat.
%W Costa Mesa, Orange County, California
%V 33
%N ?
%P ?-?
%D 2001
%K conf, Bayesian network, BNT, Kevin Murphy, stats, c2001, c200x, c20xx,
   Interface, Interface01, Bnet
%X [<A HREF="http://www.ai.mit.edu/~murphyk/Papers/bnt.ps.gz">paper</A>][12/'02]
   -- [<A HREF="http://www.ai.mit.edu/~murphyk/">M' home</A>][12/'02]
      [<A HREF="http://www.galaxy.gmu.edu/stats/IFNA.html">IFNA</A>][12/'02].

%A J. Williamson
%T Bayesian networks for logical reasoning
%J Using Uncertainty Within Computation, Papers from the AAAI Fall Symposium
%I AAAI
%P 136-142
%M NOV
%D 2001
%K conf, causal, network, logic, logical deduction, c2001, c200x, c20xx,
   AI, AAAI, Bnet
%X "By identifying and pursuing analogies between causal and logical
   influences I show how the Bayesian network formalism can be applied
   to reasoning about logical deduction."
   -- [<A HREF="http://www-users.cs.york.ac.uk/~tw/fall/Proceedings/williamson-letter.ps">.ps@cs.york</A>][7/'04]
      [<A HREF="http://www.aaai.org/Press/Reports/Symposia/Fall/fs-01-04.html">contents</A>][7/'04]; us isbn:157735138X.

%A K.-R. Muller
%A S. Mika
%A G.Ratsch, K.Tsuda, B.Scholkopf
%T An introduction to kernel-based learning algorithms
%J IEEE Neural Networks
%V 12
%N 2
%P 181-201
%M MAY
%D 2001
%K jrnl, kernels, intro c2001, c200x, c20xx, SVM, support vector machines, SVMs
%X [<A HREF="http://mlg.anu.edu.au/~raetsch/ps/review.pdf">pdf@anu</A>]['05]
   (Also see [<A HREF="http://www.kernel-machines.org/">.kernel-machines.org</A>]['05].)

%A J. Cussens
%T Parameter estimation in stochastic logic programs
%J Machine Learning
%K Kluwer
%V 44
%N 3
%P 245-271
%M SEP
%D 2001
%K jrnl, program, LP, AI, II, probability, probabilistic, c2001, c200x, c20xx,
   SLP, SLPs, FAM, failure-adjusted maximisation, log-linear, logLinear, LLA,
   model, probabilistic, distribution, UniYork, zzOSP, zOSP04
%X "... (SLPs) are logic programs with parameterised clauses which define a
   log-linear distribution over refutations of goals. The log-linear
   distribution provides, by marginalisation, a distribution over variable
   bindings, allowing SLPs to compactly represent quite complex distributions.
   We analyse the fundamental statistical properties of SLPs addressing issues
   concerning infinite derivations, `unnormalised' SLPs and impure SLPs. After
   detailing existing approaches to parameter estimation for log-linear models
   and their application to SLPs, we present a new algorithm called
   failure-adjusted maximisation (FAM). FAM is an instance of the EM algorithm
   that applies specifically to normalised SLPs and provides a closed-form for
   computing parameter updates within an iterative maximisation approach. We
   empirically show that FAM works on some small examples and discuss methods
   for applying it to bigger problems" auth @ U.York<!-- A C M dig library -->.
   -- [<A HREF="ftp://ftp.cs.york.ac.uk/pub/ML_GROUP/Papers/jcslpmlj.ps.gz">preprint</A>][7/'04]
      [<A HREF="http://dx.doi.org/10.1023/A:1010924021315">abs' doi:10.1023/A:1010924021315</A>][7/'04]
   [Also search for: log linear model].

%A M. Denny
%T Introduction to importance sampling in rare-event simulations
%J Eur. J. Phys.
%V 22
%P 403-411
%D 2001
%K jrnl, c2001, c200x, c20xx, zz0406, simulation, Monte Carlo, sample, stats
%X "... Where unlikely events are to be simulated, the importance sampling
   technique can considerably ease the processing burdon, without compromising
   statistical significance. Here a comparison of importance sampling and
   standard Monte Carlo simulations is given. Emphasis is on variance reduction,
   and on the simulation gain of importance sampling, which is calculated
   explicitly for a simple example."
   -- [<A HREF="http://dx.doi.org/10.1088/0143-0807/22/4/315">doi:10.1088/0143-0807/22/4/315</A>]['06]

%A J. Li
%A H. Shen
%A R. Topor
%T Mining the smallest association rule set for predictions
%J Proc. IEEE Int. Conf. Data Mining
%P ?-?
%M NOV
%D 2001
%K conf, frequent item set, informative, sets, FIS, rules, c2001, c200x, c20xx
%X "... informative rule set... much smaller than both the
   assoc. rule set and the non-redundant assoc. rule set ..."
   -- [<A HREF="http://www.cit.gu.edu.au/~rwt/papers/smallest-ieee.pdf">pdf</A>]['04]
   auths @ griffith Qld. .au as of '04.

%A C. Borgelt
%A R. Kruse
%T Learning graphical models with hypertree structure using a
   simulated annealing approach
%J Proc. 10th IEEE Int. Conf. on Fuzzy Systems (FUZZ-IEEE'01)
%W Melbourne
%P 135-138
%D 2001
%K conf, c2001, c200x, c20xx, model, hyper-tree
%X [<A HREF="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/fieee_01.pdf">pdf</A>]['06]

%A G. Richards
%A V. J. Rayward-Smith
%A P.H.Sonksen,  S.Carey,  C.Weng
%T Data mining for indicators of early mortality in a database of clinical
   records.
%J J. of Artificial Intelligence in Medicine
%V 22
%N 3
%P 215-231
%D 2001
%K jrnl, c2001, c200x, c20xx, AI, health, epidemiology, epidemiological,
   death, diabetic, diabetes, neuropathy, indicator
%X "...database of diabetic patients' clinical records & death certs..
   ...to find rules that describe associations between observations made of
   patients at their 1st visit to the hospital & early mortality.
   Pre-processing was carried out & a knowledge discovery in databases (KDD)
   package, developed by the Lanner Group & [UEA] was used for rule induction
   using simulated annealing.
   The most sig. discovered rules describe an assoc. that was not generally
   known or accepted by the medical community, however, recent independent
   studies confirm their validity."
   -- [<A HREF="http://dx.doi.org/10.1016/S0933-3657(00)00110-X">doi:10.1016/S0933-3657(00)00110-X</A>]['06];  vjrs@UEA ['06]

%A M. Werman
%A D. Keren
%T A Bayesian method for fitting parametric and nonparametric models to noisy
   data
%J IEEE Trans. on Pattern Analysis and Machine Intelligence
%V 23
%N 5
%P 528-534
%M MAY
%D 2001
%K conf, c2001, c200x, c20xx, model, curve, line, fit
%X [<A HREF="http://www.cs.huji.ac.il/~werman/">werman</A>]['07]

%A I. S. Dhillon
%T Co-clustering documents and words using bipartite spectral
   graph partitioning
%J Knowledge Discovery and Data Mining
%P 269-274
%D 2001
%K conf, c2001, c200x, c20xx, coclustering, biclustering, two way, clustering,
   cluster, 2D, 2way, second, left, right, singular, vector, vectors, graphs,
   document, word, KDD
%X "... novel idea of modeling the document collection as a bipartite graph
   between documents and words, using which the simultaneous clustering
   problem can be posed... uses the 2nd left and right singular vectors of an
   appropriately scaled word-document matrix to yield good bipartitionings. ..."
   -- pdf@[<A HREF="http://doi.acm.org/10.1145/502512.502550">doi:10.1145/502512.502550</A>]['06],
   (Also see bicl@[<A HREF="https://en.wikipedia.org/wiki/Biclustering">wikip</A>]['20].)
   [also search for: biclustering] and [also search for: coclustering].

%A M. Kuramochi
%A G. Karypis
%T Frequent subgraph discovery
%J IEEE Int. Conf. on Data Mining
%P ?-?
%D 2001
%O TR 01-028, Dept Comp. Sci./ Army HPC Research Center, U. of Minnesota
%K conf, ICDM, c2001, c200x, c20xx, frequent subgraph, graph, mining,
   chemical compound
%X "... use a graph to model the database objects. Within that model, the
   problem of finding frequent patterns becomes that of discovering subgraphs
   that occur frequently over the entire set of graphs. ... present a
   computationally efficient alg. for finding all frequent subgs. in large graph
   DBs. We evaluated the performance of the alg. ... with synthetic datasets as
   well as a chemical compound dataset. ... show that our alg. scales linearly
   with the # of input transactions & it is able to discover frequent subgs.
   from a set of graph transactions reasonably fast, even though we have to deal
   with comp. hard problems such as canonical labeling of gs. & subg.isomorphism
   which are not necessary for traditional frequent itemset discovery."
   TR pdf@[<A HREF="http://www.cs.unc.edu/Research/datamining/data/kuramochi01frequent.pdf">unc.edu</A>]['09],
   fee: [<A HREF="http://dx.doi.org/10.1109/ICDM.2001.989534">doi:10.1109/ICDM.2001.989534</A>]['11].

%A B. Scholkopf
%A A. J. Smola
%T Learning With Kernels, Support Vector Machines, Regularization,
   Optimization, and Beyond
%I MITpress
%D 2001
%K book, text, c2001, c200x, c20xx, kernel, kernels, machine learning, stats,
   SVM, SVMs
%X "In the '90s, a new type of learning alg. ... SVM. This gave rise to a new
   class of theoretically elegant learning machines ... . Kernel machines
   provide a modular framework that can be adapted to different tasks & domains
   by the choice of the kernel function and the base alg.. ... begins with the
   basics, it also includes the latest research. ..."
   1st ed c2001, hb us$54; uk us isbn:0262194759; uk us isbn13:978-0262194754.
   Also see slides@[<A HREF="http://www.learning-with-kernels.org/">www</A>]['06].

%A J. Blustein
%A A. El-Maazawi
%T Bloom Filters -- a Tutorial, Analysis, and Survey
%J ?
%M JAN
%D 2002
%K TR CS-2002-10, c2002, c200x, c20xx, zz0223, Bloom filter, hashing,
   membership,
%X "Bloom filters use superimposed hash transforms to provide a probabilistic
   membership test. The only types of errors are false +ves ... Non-members are
   typically detected quickly (requiring only two probes in the optimal case).
   This article surveys modern applications of this technique (e.g., in spell
   checking & Web caching s/w) & provides a detailed analysis of their
   performance, in theory & practice. ... concludes with practical advice about
   implementing this useful & intriguing technique. ..."
   -- [<A HREF="https://cdn.dal.ca/content/dam/dalhousie/pdf/faculty/computerscience/technical-reports/CS-2002-10.pdf">dal.ca</A>]['23]
    & [<A HREF="https://www.researchgate.net/publication/238681522_Bloom_Filters_A_Tutorial_Analysis_and_Survey">res'g'te</A>]['23].
   See BF@[<A HREF="https://en.wikipedia.org/wiki/Bloom_filter">wikip</A>]['23].

%A M. B. Dale
%A P. E. R. Dale
%A T. Edgoose
%T Using Markov models to incorporate serial dependence in studies of
   vegetation change
%J Acta Oecologica
%P 261-269
%N 4
%V 23
%M AUG
%D 2002
%K jrnl, ecology, ecological, model, c2002, c200x, c20xx, mike dale, MDL, HMM,
   MML, timeSeries, time series, data, minimum message, description, length,
   II, Biol
%X "...data from an intertidal salt-marsh... 14 years. ... temporal dependency
   .... Markov models. ... results suggest that, in terms of major processes,
   two distinct communities are present with relatively weak linkages between
   them."
   -- [<A HREF="http://dx.doi.org/10.1016/S1146-609X(02)01153-0">doi:10.1016/S1146-609X(02)01153-0</A>][2/'04]

%A J.-M. Gomez Hidalgo
%T Evaluating cost-sensitive unsolicited bulk email categorization
%J Proc. of the 17th Symp. on Applied Computing.
%I ACMpress
%P 615-620
%D 2002
%K spam, junk mail, email, filter, filtering, c2002, c200x, c20xx, zz0303
%X ...discuss cost-sensitive Text Categorization methods for UBE filtering.
   ...evaluated a range of [] methods for the task (C4.5, Naive Bayes, PART,
   Support Vector Machines and Rocchio), made cost sensitive through several
   methods (Threshold Optimization, Instance Weighting, and Meta-Cost).
   ...Receiver Operating Characteristic Convex Hull method for the evaluation,
   ...results do not show a dominant algorithm nor method for making algorithms
   cost-sensitive, but are the best reported on the test collection used, and
   approach real-world hand-crafted classifiers accuracy.
   -- [<A HREF="http://doi.acm.org/10.1145/508791.508911">paper</A>][3/'03].
   [Also search for: spam email].

%A E. Papp
%A R. A. Baxter
%T Factor analysis and factor score imaging of transient electromagnetic
   model responses over simple geometric ore bodies
%J Exploration Geophysics
%V 33
%N 1
%M MAR
%D 2002
%K jrnl, c2002, c200x, c20xx, II, model, factors, scores, mineral exploration,
   RABaxter
%X [<A HREF="http://www.act.cmis.CSIRO.AU/rohanb/">rohan</A>][11/'02].

%A L. Bovens
%A S. Hartmann
%T Bayesian networks and the problem of unreliable instruments
%J Philosophy of Science
%V 69
%P 29-72
%M MAR
%D 2002
%K jrnl, network, instrument, hypothesis, confirmation, confirm, Duhem Quine,
   Phil, Sci, c2002, c200x, c20xx, zz1102, network, Bnet
%X "We appeal to the theory of Bayesian Networks to model different strategies
   for obtaining confirmation for a hypothesis from experimental test results
   provided by less than fully reliable instruments. In particular, we consider
   (i) repeated measurements of a single test consequence of the hypothesis,
   (ii) measurements of multiple test consequences of the hypothesis,
   (iii) theoretical support for the reliability of the instrument, and
   (iv) calibration procedures. We evaluate these strategies on their relative
   merits under idealized conditions and show some surprising repercussions on
   the variety-of-evidence thesis and the Duhem-Quine thesis."
   0031-8248/2002/6901-0002
   -- [<A HREF="http://www.journals.uchicago.edu/PHILSCI/">jrnl</A>][11/'02]
      [<A HREF="http://www.journals.uchicago.edu/PHILSCI/journal/issues/v69n1/690102/brief/690102.html">paper</A>][11/'02] ?needs a cookie?.

%A D. N. Kutach
%T The entropy theory of counterfactuals
%J Philosophy of Science
%V 69
%P 82-104
%M MAR
%D 2002
%K jrnl, Phil, Sci, counter factual, c2002, c200x, c20xx, counterfactual
%X I assess the thesis that counterfactual asymmetries are explained by an
   asymmetry of the global entropy at the temporal boundaries of the
   universe, by developing a method of evaluating counterfactuals that
   includes, as a background assumption, the low entropy of the early universe.
   The resulting theory attempts to vindicate the common practice of holding
   the past mostly fixed under counterfactual supposition while at the same
   time allowing the counterfactual's antecedent to obtain by a natural
   physical development. Although the theory has some success in evaluating
   a wide variety of ordinary counterfactuals, it fails as an explanation of
   counterfactual asymmetry.
   0031-8248/2002/6901-0004. [<A HREF="http://www.journals.uchicago.edu/PHILSCI/">jrnl</A>][11/'02]
   (Also see a [<A HREF="http://www.allisons.org/ll/MML/Entropy/Gas/">gas</A>].)

%A N. Ramsey
%A A. Pfeffer
%T Stochastic lambda calculus and monads of probability distributions
%J Principles of Prog. Langs.
%P 154-165
%M JAN
%D 2002
%K conf, POPL, functional programming, FP, distribution, monad, monadic,
   measure terms, probabilistic, uncertainty, formal, c2002, c200x, c20xx,
   modeling, modelling, IBAL
%X ...distributions are useful for expressing the meanings of probabilistic
   languages, which support formal modeling of and reasoning about uncertainty.
   [PDs] form a monad, ... leads to simple, natural semantics for a stochastic
   lambda calc', as well as ... implementations of common queries. But the
   monadic implementation of the expectation query can be much less efficient
   than current best practices in probabilistic modeling. We therefore present
   a language of measure terms, which can not only denote discrete probability
   distributions but can also support the best known modeling techniques. We
   give a translation of stochastic lambda calculus into measure terms.
   Whether one translates into the probability monad or into measure terms, the
   results of the translations denote the same probability distribution.
   isbn:1-58113-450-9.  [<A HREF="http://doi.acm.org/10.1145/503272.503288">www</A>][12/'02].

%A M. J. Crawley
%T Statistical Computing - an Introduction to Data Analysis using S-plus
%I Wiley
%P 722
%M APR
%D 2002
%K book, text, S, Splus, stats
%X isbn:0471560405.   [Also search for: RR].

%A J. Fox
%T An R and S-Plus Companion to Applied Regression
%I SagePubl.
%P 368
%M AUG
%D 2002
%K book, text, Splus, R, RR, data analysis, data mining, stats, statistics
%X isbn:0761922806.  About stg31.  [Also search for: RR].

%A B. Everitt
%T Handbook of Statistical Analyses using S-Plus
%I CRC
%P 240
%D 2002 ?
%K book, text, Splus, data analysis, data mining, stats, statistics
%X isbn:1584882808.  About stg25.  [Also search for: RR].

%A P. E. R. Dale
%A M. B. Dale
%T Optimal classification to describe environmental change:
   pictures from the exposition
%J Community Ecology
%P 19-29
%N 1
%V 3
%D 2002
%K jrnl, environment, c2002, c200x, c20xx
%X [<A HREF="http://ramet.elte.hu/~podani/ce1v1.html">jrnl</A>][2/'04].

%A M. B. Dale
%T Models, measures and messages: an essay on the role for induction
%J Community Ecology
%P 191-203
%N 2
%V 3
%D 2002
%K jrnl, mml, mdl, measure, message, c2002, c200x, c20xx
%X [<A HREF="http://ramet.elte.hu/~podani/ce1v1.html">jrnl</A>][2/'04]

%A A. McCallum
%A W. Li
%T Early results for named entity recognition with conditional random fields,
   feature induction and web-enhanced lexicons
%J Proc. of the 7th Conf. on Natural Language Learning
%P ?-?
%D 2003
%K conf, CoNLL, c2003, c200x, c20xx, field, name, names, lexicon
%X [also search for: random field]

%A D. Pinto
%A A. McCallum
%A X. Wei
%A W. B. Croft
%T Table extraction using conditional random fields
%J Proc. 26th Int. ACM SIGIR Conf. on Res. and Dev. in Information Retrieval
%W Toronto
%P ?-?
%D 2003
%K conf, c2003, c200x, c20xx, field
%X [<A HREF="http://ciir.cs.umass.edu/pubfiles/ir-276.pdf">pdf</A>]['05] via Mike D.
   [also search for: random field]

%A J. R. Schott
%T Distributions on spheres and random variables distributed on the
   interval (-1,1)
%J Stats and Probability Letters
%V 62
%N 4
%P 391-396
%M MAY
%D 2003
%K jrnl, stats, c2003, c200x, c20xx, zz0411, probability distribution, sphere,
   spherical, circle, solid, angle, angles
%X "... a simple relationship between a random vector having a cts distribution
   on the unit m-sphere & m random vars., m-1 of which have a distn on the
   interval (-1,1), while the final random var. is a discrete one taking on the
   values -1 & 1. This relationship can be particularly useful when these m
   random vars. are indep.distributed. ... it can be used to construct distns
   on the unit m-sphere having specific features as well as to generate random
   vectors having these distns."
   -- [<A HREF="http://dx.doi.org/10.1016/S0167-7152(03)00043-9">doi:10.1016/S0167-7152(03)00043-9</A>]['11] (-- buy$).
   [Also search for: probability distribution sphere stats].

%A B. Fischer
%A J. Schumann
%T Generating data analysis programs from statistical models
%J J. Functional Prog.
%V 13
%N 3
%P 483-508
%M MAY
%D 2003
%K jrnl, JFP, model, AutoBayes, stats, automatic, program synthesis,
   c2003, c200x, c20xx, zz1102
%X ... Statistical approaches to data analysis, which use methods from
   prob' theory and num' analysis, ...difficult to implement: the development
   of a stat' data analysis prog' for [an] application is time-consuming
   and requires substantial knowledge and experience in several areas.
   ...AutoBayes, a program synthesis system for [...] data analysis programs
   from stat' models. A stat' model specifies the properties for each problem
   variable (i.e. observation or parameter) and its dependencies in the form of
   a prob' dist'n. It is a fully declarative problem description, [like] a set
   of differential equ'ns. ...AutoBayes synthesizes optimized [...] C/C++ code
   [for] the Matlab and Octave environments. Code is generated in a
   schema-guided deductive synthesis process. A schema consists of a code
   template and applicability constraints which are checked against the model
   during synthesis using theorem proving technology. AutoBayes augments
   schema-guided synthesis by symbolic-algebraic computation and can thus
   derive closed-form solutions for many problems. It is well-suited for tasks
   like estimating best-fitting model parameters for the given data. Here, we
   describe the system architecture, in particular the schema-guided synthesis
   kernel.  [Give] advanced textbook examples and benchmarks.
   -- [<A HREF="http://ase.arc.nasa.gov/people/fischer/papers/jfp-01.html">paper</A>][11/'02] via Roh@n B'.

%A B. Mezrich
%T Bringing Down the House: The Inside Story of Six MIT Students Who Took Vegas
   for Millions
%I FreePress
%P 257
%M SEP
%D 2002
%K book, gamble, gambling, LasVegas, Black Jack, Blackjack, cards, card games,
   count, counting, LasVegas, casino, casinos, student, dollars, stats
%X isbn:0743225708.

%A T. Chu
%A C. Glymour
%A R. Scheines
%A P. Spirtes
%T A statistical problem for inference to regulatory structure from
   associations of gene expression measurement with microarrays
%J Submitted<!-- Bioinformatics -->.
%D 2002
%K MolBio, gene expression, regulation, difficulty, stats, errors, error terms,
   II, independence, RNA, mRNA, micro arrays
%X ...mRNA transcript... difficulty... if a number of cells from a
   common pop'n are aggregated...  in general inference of genetic
   regulatory structure based on conditional association is unwarranted.
   -- [<A HREF="http://www.phil.cmu.edu/projects/genegroup/papers/chu2002a.pdf">pdf</A>][12/'02].
   Via C.T.: Problem for discovering gene regulatory networks  lies with
   using summed data to estimate individual parameters.  Error terms become
   correlated.

%A B. S. Everitt
%T The Cambridge Dictionary of Statistics
%I CUP
%P 420
%D 2002
%K book, text, stats, definitions, terms, terminology,
   CUP, c2002, c200x, c20xx, zz0703
%X Inc' short bio's on 100+ statisticians.  au$75, hb, isbn:052181099X.

%A M. B. Dale
%A P. E. R. Dale
%A C. Li
%A G. Biswas
%T Assessing impacts of small perturbations using a model-based approach
%J Ecological Modelling
%P 185-199
%N 2-3
%V 156
%M NOV
%D 2002
%K jrnl, ecology, stats, statistics, models, salt marsh, impact,
   runnelling, MML, BIC, MDL, c2002, c200x, c20xx, zz0304, perturbation
%X [<A HREF="http://dx.doi.org/10.1016/S0304-3800(02)00158-8">doi:10.1016/S0304-3800(02)00158-8</A>][2/'04].

%A H. Blockeel
%T Induction of supermodels
%J Proc. of 12th Belgian-Dutch Conf. on Machine Learning
%E M. Wiering
%P 9-15
%D 2002
%K conf, super model, AI, generator, c2002, c200x, c20xx, zz0804, data mining,
   II, apriori, Hendrick Blockeel, zzOSP, zOSP04
%X "It is rarely the case in machine learning & data mining projects that only
   a single inductive process is run. Often, experiments are performed with a
   number of different algorithms, different settings for a single algorithm,
   different feature sets, & so on. While most research focuses on algorithms
   that induce a single model, given this practice it would be useful to look
   for algorithms that induce a kind of modelgenerator or "super"-model, from
   which multiple concrete models can efficiently be generated (this is a kind
   of partial evaluation). Thus one can avoid executing computationally heavy
   induction processes many times in very similar contexts. The process is
   similar to partial evaluation. This paper discusses some possibilities &
   challenges for research on supermodels."
   -- [<A HREF="http://www.cs.kuleuven.ac.be/cgi-bin-dtai/publ_info.pl?id=40128">kuleuven.ac.be</A>][7/'04].

%A D. Wishart
%T Whisky Classified
%I PavilionBooks
%D 2002
%K book, text, classification, stats, statistics, c2002, c200x, c20xx, zz0804,
   single malt, malts, whiskies, Scotland, Scotch, Clustan
%X "This classification is a refreshingly new way of describing single malt
   whiskies.  Rigorously researched with the cooperation of the whisky
   industry, David Wishart's book guides the reader through all the
   complexities and delights of the 'water of life'." isbn:1862055270.
   stg15.00;  us$25, Trafalgar Square Books, Vermont, USA; and
   'Whisky Geclassificeerd', Spectrum Books, The Netherlands.
    --[<A HREF="http://www.st-andrews.ac.uk/~dw4/">@st-andrews</A>][8/'04].

%A W. F. Taylor
%A J. Brice
%A N. Buck
%A E. Prentice-Lane
%T British Household Panel Survey, User Manual
%I U. Essex, Colchester
%D 2002
%K BHPS, 1990s, health, income, employment, marriage, c2002, c200x, c20xx,
   data-archive, dataArchive, uniEssex, data set, sets, dataset, ESRC
%X "... [BHPS] data were made available through the UK Data Archive."
   -- from G@rdner and Osw@ld c2004.
      [<A HREF="http://www.data-archive.ac.uk/findingData/bhpsTitles.asp">data-archive.ac.uk</A>]['04]
      [<A HREF="http://iserwww.essex.ac.uk/ulsc/bhps/">essex.ac.uk</A>]['04]
   "...Access for academic research is open and freely available. Researchers
   carrying out analysis of the data for private sector clients will be charged
   for access..." ['04]

%A J. Patrick
%A C. Whitelaw
%A R. Munro
%T SLINERC: The Sydney language-independent named entity recogniser and
   classifier
%J Proc. of CoNLL-2002
%W Taipei
%P 199-202
%D 2002
%K conf, CoNLL, named entity recogniser, NER, JPatrick, Jon, text analysis,
   processing, data set, sets, Spanish, Dutch, c2002, c200x, c20xx
%X [<A HREF="http://cnts.uia.ac.be/conll2002/pdf/19902pat.pdf">pp.pdf@uia.ac.be</A>]['05]
   -- [<A HREF="http://cnts.uia.ac.be/conll2002/ner/">conf</A>]['05]
   e.g. "[PER Wolff], currently a journalist in [LOC Argentina],
         played with [PER Del Bosque] in the final years of the seventies
         in [ORG Real Madrid]."   -- the problem.

%A E. Takimoto
%A M. K. Warmuth
%T Predicting nearly as well as the best pruning of a planar decision graph
%J Theor. Comp. Sci.
%V 288
%P 217-235
%D 2002
%K jrnl, TCS, graphs, prune, preuned, c2002, c200x, c20xx, zz0405,
   classification, Dgraph
%X "... efficient on-line algorithms that predict nearly as well as the best
   pruning of a planar decision graph. We assume that the graph has no cycles.
   As in the previous work on decision trees, we implicitly maintain one weight
   for each of the prunings (exponentially many). The method works for a large
   class of algorithms that update its weights multiplicatively. It can also be
   used to design algorithms that predict nearly as well as the best convex
   combination of prunings."
   -- [<A HREF="http://dx.doi.org/10.1016/S0304-3975(01)00401-7 ">doi:10.1016/S0304-3975(01)00401-7 </A>]['05]
      [<A HREF="http://www.maruoka.ecei.tohoku.ac.jp/~t2/publications.html">ET</A>]['05].
   [Also search for: Dgraph decision].

%A I. Navarrete
%A A. Sattar
%A R. Wetprasit
%A R. Marin
%T On point-duration networks for temporal reasoning
%J Artificial Intelligence
%V 140
%N 1
%P 39-70
%M SEP
%D 2002
%K jrnl, AI, time, logic, c2002, c200x, c20xx, network, Bnet
%X "...a point-duration network formalism which extends the point algebra model
   to include additional vars. that represent durations between points of time.
   Thereafter the new qualitative model is enlarged for allowing unary metric
   constraints on points & durations, subsuming in this way several point-based
   approaches to temporal reasoning. We deal with some reasoning tasks within
   the new models & we show that the main problem, deciding consistency, is
   NP-complete. However, tractable special cases are identified & we show
   efficient algorithms for checking consistency, finding a solution &
   obtaining the minimal network."
   -- [<A HREF="http://dx.doi.org/10.1016/S0004-3702(02)00226-6">doi:10.1016/S0004-3702(02)00226-6</A>]['04].
   (auth1,4 @ U. de Murci@ .es, auth2 @ Gr'ffith, auth3 @ P of Songl@)

%A M. Khan
%A Q. Ding
%A W. Perrizo
%T K-nearest neighbor classification of spatial data streams using P-trees
%J Pacific-Asian Conf. on Knowledge Discovery and Data Mining
%P 517-528
%D 2002
%K PAKDD, conf, P tree, Ptree, Ptrees, stream, association rule, rules,
   and, or, operations, operation, neighbour, vertical, frequent

%A S. James Press
%T Subjective and Objective Bayesian Statistics: Principles, Models, and
   Applications (2nd ed.)
%I Wiley
%P 600
%M NOV
%D 2002
%K book, text, stats, c2002, c200x, c20xx
%X hb, us$105, isbn:0471348430.

%A S. J. Julier
%A J. K. Uhlmann
%T Reduced sigma point filters for the propagation of means and
   covariances through nonlinear transformations
%J Proc. American Control Conf.
%V 2
%P 887-892
%D 2002
%K conf, unscented transform, UT, transformation, c2002, c200x, c20xx,
    Kalman filter, mean covariance, approximation
%X [<A HREF="http://dx.doi.org/10.1109/ACC.2002.1023128">doi:10.1109/ACC.2002.1023128</A>]['05]; isbn:0780372980.
   [also search for: Julier c1999]

%A R. Herbrich
%A R. C. Williamson
%T Algorithmic luckiness
%J J. of Machine Learning Res.
%V 3
%P 175-212
%M SEP
%D 2002
%K jrnl, JMLR, c2002, c200x, c20xx, stats, luck, algorithmic stability,
   sparsity, Machine Learning, AI, loss function, ANU, NICTA, maximum margin
%X "The trad. methods of stat. learning theory analyse learning algs. only in
   terms of the class of fns from which the alg. draws its hypotheses. The
   luckiness framework (previous paper) introduced a method by which performance
   on the sample received could be captured, but it still essentially used the
   device of considering the class of fns from which the (data-dependent)
   hypotheses were drawn. [Here] for the 1st time, allowed the use of the
   traditional machinery of statistical learning theory in a manner that allowed
   the use of properties of the alg. beyond merely the class of fns. from which
   the h. is drawn. The paper formally subsumes the previous luckiness f/work,
   & ... allows the analysis of sparsity & algorithmic stability. Finally ...
   is applied to the analysis of the max. margin alg. to obtain a new perf.
   bound which interestingly combines 3 key factors: margin, sparsity, & degree
   of clustering of the data."
   pdf@[<A HREF="http://jmlr.csail.mit.edu/papers/v3/herbrich02a.html">mit</A>]['09],
   auth2@[<A HREF="http://users.rsise.anu.edu.au/~williams/home.shtml">anu</A>]['09].

%A M. E. Brand
%T Incremental singular value decomposition of uncertain data with missing
   values
%J European Conf. on Computer Vision (ECCV)
%I SpringerVerlag
%S LNCS
%V 2350
%P 707-720
%D 2002
%K conf, ECCV, c2002, c200x, c20xx, zz0608, singular value decomposition, SVD,
   missing values, data, stats, rank, residual
%X "... [SVD] developed as data arrives, & can handle arbitrary missing/
   untrusted values, correlated uncertainty across rows or columns of the
   measurement matrix, & user priors. Since incomplete data does not uniquely
   specify an SVD, the procedure selects one having minimal rank. For a dense
   p x q matrix of low rank r, the incremental method has time complexity
   O(pqr) & space complexity O((p+q)r)-better than highly optimized batch algs
   such as MATLAB's svd(). In cases of missing data, it produces factorings of
   lower rank & residual than batch SVD algorithms ..."    [23 refs]  via njh.
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-47969-4">doi:10.1007/3-540-47969-4</A>]['08]
      [<A HREF="http://www.merl.com/publications/TR2002-024/">TR2002-024</A>]['08].
   (Also see SVD@[<A HREF="https://en.wikipedia.org/wiki/Singular_value_decomposition">wikip</A>]['16].)

%A P. Spirtes
%A T. Richardson
%T Ancestral graph Markov models
%J Ann. Statist.
%V 30
%N 4
%P 962-1030
%D 2002
%K jrnl, c2002, c200x, c20xx, zz0718, ancestral graph, maths, ancestralGraph,
   graphs, DAG, mixed, hybrid, model, causal, graphical independence
%X "... introduces a class of graphical independence models that is closed under
   marginalization and conditioning but that contains all DAG independence
   models. This class of g., called maximal ancestral gs., has two attractive
   features: there is at most one edge between each pair of vertices; every
   missing edge corresponds to an independence relation. These features lead to
   a simple parameterization of the corr. set of distns in the Gaussian case."
   -- paper@[<A HREF="https://projecteuclid.org/euclid.aos/1031689015">eucl'd</A>]['18].
   [Also search for: ancestralGraph].

%A N. Srebro
%T Maximum likelihood bounded tree-width Markov networks
%J AI
%V 143
%N 1
%P 123-138
%M JAN
%D 2003
%O Proc. 17th Conf. on Uncertainty in AI (UAI2001)
%K jrnl, AI, c2003, c200x, c20xx, zz1218, graph, bounded treewidth, width,
   tree, algorithm, masters MIT, hypertree, NPH, NP-hard, NPhard,
   Markov, network, Chow, Liu
%X "... problem of projecting a distribution onto (or finding a maximum
   likelihood distribution among) Markov networks of bounded tree-width. By
   casting it as the combinatorial optimization problem of finding a maximum
   weight hypertree, we prove that it is NP-hard to solve exactly and provide
   an approximation alg. with a provable performance guarantee."
   -- [<A HREF="https://doi.org/10.1016/S0004-3702(02)00360-0">doi:10.1016/S0004-3702(02)00360-0</A>]['18], and
      1301.2311@[<A HREF="https://arxiv.org/abs/1301.2311">arXiv</A>]['18].
   (And S's masters thesis: "Maximum Likelihood Markov Networks: An
       Algorithmic Approach", MIT, 2000,
       pdf@[<A HREF="http://dspace.mit.edu/bitstream/handle/1721.1/86593/48134046-MIT.pdf">mit</A>]['18].)

%A A. R. Wiseman
%T The Luck Factor
%I RandomHouse
%P 240
%M JAN
%D 2003
%K book, good luck, bad luck, lucky, person, people, probability
%X Why do some people lead happy successful lives whilst other face repeated
   failure and sadness? Why do some find their perfect partner whilst ...
   The right publisher!  About stg10.  ppb, isbn:0712623884.
   Miramax hb, us$24, isbn:0786869143.  Author @ psychology, U. Herts.

%A P. LienHua Chou
%A X. Zhang
%T Efficiently computing the top N averages in iceberg cubes
%J 26th Australasian Computer Science Conference (ACSC)
%P 101-109
%M FEB
%D 2003
%K conf, ACSC, ACSC2003, cube, count, sum, average, OLAP, h-cubing, Hcubing,
   aggregate, LG-tree, LGtree, LGtrees, zz0203, c2003, c200x, c20xx
%X Data cubes ... efficient on-line analytic processing (OLAP) systems.
   ... aggregates of mult-dim' groups ...

%T Statistical Analysis of Gene Expression Microarray Data
%E T. P. Speed
%I ChapmanAndHall
%P 240
%M MAR
%D 2003
%K book, text, MolBio, c2003, c200x, c20xx, micro arrays, gene expression
%X ... and analysis of comparative experiments involving microarrays, with
   focus on two-color cDNA or long oligonucleotide arrays on glass slides
   us$70.  [Also search for: microarray], uk us isbn:1584883278.

%A L. De Raedt
%A K. Kersting
%T Probabilistic logic learning
%J SIGKDD
%I ACM
%P 31-48
%V 5
%N 1
%M JUL
%D 2003
%K SIG, deRaedt, Knowledge Discovery and Data Mining, c2003, c200x, c20xx, AI,
   multi-relational data mining, inductive logic programming, ILP, LP,
   Logical Bayesian Networks, network, LBN, introduction, survey,
   Freiburg, Probabilistic-Logical Model Repository, PLMR
%X "[recently] witnessed an significant interest in probabilistic logic
   learning, i.e. in research lying at the intersection of probabilistic
   reasoning, logical representations, & machine learning. A rich variety of
   different formalisms & learning techniques have been developed. This paper
   provides an introductory survey & overview of the state-of-the-art in
   probabilistic logic learning through the identification of a number of
   important probabilistic, logical & learning concepts."
   -- [<A HREF="https://doi.org/10.1145/959242.959247">doi:10.1145/959242.959247</A>]['22].
   (Also see [<A HREF="https://mlai.cs.uni-bonn.de/?kristian.kersting/plmr/">PLMR</A>]['22],
    was [<A HREF="http://www.informatik.uni-freiburg.de/~kersting/plmr/">www</A>]['03].)

%A J. Maindonald
%A J. Braun
%T Data Analysis and Graphics Using R
%I CUP
%M AUG
%D 2003
%P 400
%K book, text, R, RR, mining, stats, statistics, Splus, S-Plus,
   computer software, programs, platform, package, c2003, c200x, c20xx, zz0703
%X auth.1.@anu; au$140, hb, isbn:0521813360.

%A R. A. Easterlin
%T Explaining happiness
%J PNAS
%V 100
%N 19
%P 11176-11183
%M SEP
%D 2003
%K jrnl, PNAS, c2003, c200x, c20xx, zz0614, happiness, contentment, US, USA,
   General Social Survey, GSS, stats, pecuniary, salary, work, money, happy,
   wealth, marriage, family, health, stuff, hedonic adaption,
   well being, wellbeing, controversial, paradox, economics, social, society
%X "What do social survey data tell us about the determinants of happiness?
   First, that the psychologists' setpoint model is questionable. Life events
   in the nonpecuniary domain, such as marriage, divorce, & serious disability,
   have a lasting effect on h., & do not simply deflect the avg person
   temporarily above or below a setpoint given by genetics & personality.
   Second, mainstream economists' inference that in the pecuniary domain - more
   is better -  based on revealed preference theory, is problematic. An increase
   in income, & thus in the goods at one's disposal, does not bring with it a
   lasting increase in h. because of the -ve effect on utility of hedonic
   adaptation & social comparison. A better theory of h. builds on the evidence
   that adaptation & social comparison affect utility less in the nonpecuniary
   than pecuniary domains. Because individuals fail to anticipate the extent to
   which adaptation & social comparison undermine expected utility in the
   pecuniary domain, they allocate an excessive amount of time to pecuniary
   goals, & shortchange nonpecuniary ends such as family life & health, reducing
   their h.. There is need to devise policies that will yield better-informed
   individual preferences, & thereby increase individual & societal well-being."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1633144100">doi:10.1073/pnas.163314410</A>]['14].
   (Also see GSS@[<A HREF="http://www3.norc.org/gss+website/">norc.org</A>]['14].)
  [Also search for: Easterlin paradox] & [also search for: happiness wellbeing].

%A S. Nijssen
%A J. N. Kok
%T Efficient frequent query discovery in FARMER
%J 13th Int. Conf. on Inductive Logic Programming (ILP 2003)
%I SpringerVerlag
%S LNCS
%V 2838
%P 350-362
%M NOV
%D 2003
%K conf, ILP, ILP13, FARMER, WARMR, data mining, inductive logic programming,
   graph, queries
%X "The upgrade of frequent item set mining to a setup with multiple relations
   - frequent query mining - poses many efficiency problems. Taking Object
   Identity as starting point, we present several optimization techniques for
   frequent query mining algorithms. The resulting algorithm has a better
   performance than a previous ILP algorithm and competes with more specialized
   graph mining algorithms in performance." [<A HREF="http://www.springerlink.com/link.asp?id=eb30gra5kmh5mtmx">springer</A>][12/'03]
   isbn:3540200851;  [<A HREF="http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=2838&spage=350">springer</A>][12/'03]
   -- [<A HREF="http://www.liacs.nl/home/snijssen/farmer/pkdd03.pdf ">.pdf</A>][12/'03]
      [<A HREF="http://www.liacs.nl/home/snijssen/farmer/">farmer</A>][12/'03]
   via Am@nd@ C.  Also see WARMR

%A T. Jefferson
%A K. Shashok
%A E. Wagner
%T Get peered!
%J British Medical J.
%V 327
%N 7429
%P 1439-1441
%M DEC
%D 2003
%K jrnl, BMJ, c2003, c200x, c20xx, zz1203, peer review, fun, funn, funny, ha ha,
   haha, spoof, board game, global, impact factor, JIF, KPI, KPIs, GIF, factors,
   academia, promotion, publications, paper, papers, publish, perish,
   refereeing, reviewing, www, http, HREF
%X Dec 20 [<A HREF="http://dx.doi.org/10.1136/bmj.327.7429.1439">doi:10.1136/bmj327.7429.1439</A>][12/'03].

%A S. Furness
%A J. Connor
%A S. Robinson, R. Norton, S. Ameratunga, R. Jackson
%T Car colour and risk of car crash injury: population based case control study
%J British Medical J.
%V 327
%N 7429
%P 1455-1456
%M DEC
%D 2003
%K jrnl, BMJ, car, cars, auto, autos, colour, color, safe, safety, accident,
   rating, injury, stats, statistics, c2003, c200x, c20xx, zz1203, silver,
   white, yellow, red, black
%X "Globally, road traffic crashes kill about 3000 people a day. Identification
   of modifiable risk factors is an important step in reducing this burden.
   Previous research suggests that white or light coloured cars are less likely
   to be involved in a crash, than cars of other colours.2 We investigated the
   effect of car colour on the risk of a serious injury from a crash, using a
   population based case control study designed to identify and quantify
   modifiable risk factors."
   Dec 20 [<A HREF="http://dx.doi.org/10.1136/bmj.327.7429.1455">doi:10.1136/bmj.327.7429.1455</A>][12/'03]

%A J. A. Hanley
%A E. Turner
%A C. Bellera
%A D. Teltsch
%T How long did their hearts go on? A Titanic study
%J British Medical J.
%V 327
%N 7429
%P 1457-1458
%M DEC
%D 2003
%K jrnl, BMJ, heart, life expectancy, post-traumatic stress, stats, statistics,
   1912, c1912, c191x, c19xx, c2003, c200x, c20xx, fun, funn, zz0104
%X "Several studies have examined post-traumatic stress in people who survive
   disasters but few have looked at longevity. The 1997 film Titanic followed
   one character, apparently fictional, but the longevity of the actual
   survivors, as a group, has not been studied. Did the survivors of the
   sinking of the Titanic have shortened life spans? Or did they outlive those
   for whom 14-15 April 1912 was a less personal night to remember?"
   Dec 20; [<A HREF="http://dx.doi.org/10.1136/bmj.327.7429.1457">doi:10.1136/bmj.327.7429.1457</A>][12/'03] PMID:14684648.

%T Multiple Classifier Systems, 4th Int. Workshop
%E Terry Windeatt
%E F. Roli
%W Guilford
%I Springer
%S LNCS
%V 2709
%D 2003
%K MCS, MCS4, MCS03, book, machine learning, boosting, ensemble strategie
%X isbn:3540403698.

%A M. Rees
%T Our final century
%I Random House (UK)
%P 244
%D 2003
%K book, text, risk, risks, technology, mankind, future, our final hour,
   Sir Martin Rees, zz0704, c2003, c200x, c20xx, environmental disaster,
   science
%X "Our planet may be insignificant on a cosmic scale, but the evolution of
   intelligent life here makes it unusual, it is likely to be unique in our
   galaxy. Yet we may be on the verge of destroying it, of destroying ourselves
   - over the next century the future of life in the cosmos could be either
   jeopardised - or safeguarded for perpetuity. Exploring the threats of
   genetically engineered viruses, nanotechnology, and environmental
   catastrophe, Martin Rees demonstrates the risks we are taking, as well as
   the great difficulties of limiting them."   isbn:0434008095.
   Published in US as `Our Final Hour' by Basic Books, us$18; isbn:0465068626.
   -- [<A HREF="http://www.ast.cam.ac.uk/IoA/staff/mjr/">auth'</A>][7/'04]

%A J. Cussens
%T Individuals, relations and structures in probabilistic models
%J IJCAI Workshop on Learning Statistical Models from Relational Data
%E L. Getoor
%E D. Jensen
%P 32-36
%W Acapulco, Mexico
%M AUG
%D 2003
%K wShop, SRL2003, c2003, c200x, c20xx, relation, base, model, individual,
   multi, uniYork, zzOSP, zOSP04, statistics, stats, Bayesian nets, network,
   PRM, PRMs, structured, succession, inclusion
%X "Relational data is equivalent to non-relational structured data. It is
   this equivalence which permits probabilistic models of relational data.
   Learning of probabilistic models for relational data is possible because
   one item of structured data is generally equivalent to many related data
   items. Succession and inclusion are two relations that have been well
   explored in the statistical literature. A description of the relevant
   statistical approaches is given. The representation of relational data via
   Bayesian nets is examined, and compared with PRMs. The paper ends with some
   cursory remarks on structured objects."
   -- [<A HREF="ftp://ftp.cs.york.ac.uk/pub/aig/Papers/james.cussens/srl03.pdf">pp.pdf@york.ac.uk</A>][9/'04]

%A W. Buntine
%A S. Perttu
%T Is multinomial PCA multi-faceted clustering or dimensionality reduction?
%J AI and Statistics
%P ?-?
%D 2003
%K conf, AIS, principal components analysis, PCA, c2003, c200x, c20xx, zz1220,
   discrete, documents, dimensionality reduction, stats, statistics
%X "Discrete analogues to Principal Components Analysis (PCA) are intended
   to handle discrete or positive-only data, for instance sets of documents.
   The class of methods is appropriately called multinomial PCA because it
   replaces the Gaussian in the probabilistic formulation of PCA with a
   multinomial. Experiments to date, however, have been on small data sets, for
   instance, from early information retrieval collections. This paper
   demonstrates the method on two large data sets and considers 2 extremes of
   behaviour: (1) dimensionality reduction where the feature set (i.e. bag of
   words) is considerably reduced, and (2) multi-faceted clustering (or aspect
   modelling) where clustering is done but items can now belong in several
   clusters at once."
   -- pdf@[<A HREF=" http://cosco.hiit.fi/search/MPCA/ais03_mpca.pdf">hiit.fi</A>]['20],
      [<A HREF="ttp://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.14.1541">cit'seer</A>]['20]
   (was [<A HREF="http://www.hiit.fi/u/buntine/ais03.html">paper</A>][1/'04]).
   [Also search for: multinomial clustering].

%A A. Popescul
%A L. Ungar
%A D. Pennock
%A S. Lawrence
%T Statistical relational learning for document mining
%J Proc. 3rd IEEE Int. Conf. on Data Mining
%W Melbourne
%P 19-22
%M NOV
%D 2003
%K conf, ICDM, papers, publications, pages, documents, zzOSP, zOSP04,
   structural logistic regression, SLR, c2003, c200x, c20xx
%X ... relational data-bases ... refinement graphs which are widely used in
   I.L.P. ...  [Lawrence ~ citeseer]
   -- [<A HREF="http://www.neci.nec.com/~lawrence/papers/relational-icdm03/relational-icdm03.pdf">pdf</A>][8/'04]

%A C. Andrieu
%A N. de Freitas
%A A. Doucet
%A M. I. Jordan
%T An introduction to MCMC for machine learning
%J Machine Learning
%V 50
%N 1-2
%P 5-43
%D 2003
%K jrnl, intro, monte carlo, markov chain, method, methods, AI, deFreitas
%X "This purpose of this introductory paper is threefold. First, it introduces
   the Monte Carlo method with emphasis on probabilistic machine learning.
   Second, it reviews the main building blocks of modern Markov chain Monte
   Carlo simulation, thereby providing and introduction to the remaining papers
   of this special issue. Lastly, it discusses new interesting research
   horizons."   (Auth #3 @ elec & e eng, melbU.)
   -- [<A HREF="http://www.cs.ubc.ca/~nando/papers/mlintro.pdf">pdf@ubc.ca</A>]['04]
      [<A HREF="http://www-dsp.rice.edu/courses/elec631/papers/jordan03mcmc.pdf">pdf@rice.edu</A>]['04]

%A M. Bilenko
%A R. Mooney
%A W. W. Cohen
%A P. Ravikumar
%A S. Fienberg
%T Adaptive name-matching in information integration
%J IEEE Intelligent Sys.
%V 18
%N 5
%P 16-23
%D 2003
%K names, match, approximate, similar, similarity, named entity recognition,
   NER, Jaro metric, survey, introduction, record, linkage, data, records,
   field, fields, identity, data set, sets, measure, measures,
   c2003, c200x, c20xx
%X "... 'William Jefferson Clinton' and 'bill clinton' ..."
   -- [<A HREF="http://www-2.cs.cmu.edu/~wcohen/postscript/intelligent-systems-2003.pdf">pp.pdf@cs.cmu.edu</A>]['05]
   MB & RM @ u tex@s austin, others @ cmu.   [Also search for: Cohen c2004].

%A W. W. Cohen
%A P. Ravikumar
%A S. Fienberg
%T A comparison of string metrics for matching names and records
%J KDD Workshop on Data Cleaning and Object Consolidation
%P ?-?
%D 2003
%K wShop, metric, name, record, approximate, field, fields, c2003, c200x, c20xx,
   record, linkage, data, linking
%X [<A HREF="http://www-2.cs.cmu.edu/~wcohen/postscript/kdd-2003-match-ws.pdf">pp.pdf@cs.cmu.edu</A>]['05].

%A L. Gu
%A R. A. Baxter
%A D. Vickers
%A C. Rainsford
%T Record linkage: Current practice and future directions
%R 03/83
%M April
%D 2003
%I CSIRO Math. and Inf. Sci., GPO Box 664, Canberra 2601, Australia
%K TR83, TR 83, record, linkage, data, name, identity, matching,
   c2003, c200x, c20xx, RABaxter
%X [<A HREF="http://www.act.cmis.csiro.au/rohanb/PAPERS/record_linkage.pdf">tr.pdf@cmis.csiro.au</A>]['05].

%A R. Baxter
%A P. Christen
%A T. Churches
%T A comparison of fast blocking methods for record linkage
%J ACM SIGKDD '03 Workshop on Data Cleaning, Record Linkage, and
   Object Consolidation
%P 25-27
%D 2003
%K wShop, record, linkage, data, name matching, identity,
   c2003, c200x, c20xx, block, method, RABaxter
%X [<A HREF="http://www.act.cmis.csiro.au/rohanb/PAPERS/kdd03clean.pdf">pp.pdf@cmis.csiro.au</A>]['05]
   [Also search for: record linkage data].

%A L. Parra
%A P. Sajda
%T Blind source separation via generalized Eigenvalue decomposition
%J J. of Machine Learning Res.
%V 4
%P 1261-1269
%D 2003
%K jrnl, linear mixture, mixtures, model, unmixing matrix, c2003, c200x, c20xx,
   speech, EEG, non-white noise, nonwhite, non-stationary, nonstationary, ICA
%X "... linear blind source sepn can be formulated as a generalized eigenvalue
   decomposition under the assumptions of non-Gaussian, non-stationary, or
   non-white indep. sources. The soln for the unmixing matrix is given by the
   generalized eigenvectors that simultaneously diagonalize the covariance
   matrix of the observations & an additional symmetric matrix whose form
   depends upon the particular assumptions. The method critically determines the
   mixture coeffs. & is therefore not robust to est.errors. However it
   provides a rather general & unified soln that summarizes the conditions
   for successful blind source separation. ..."
   -- [<A HREF="http://www.jmlr.org/papers/volume4/parra03a/parra03a.pdf">pdf</A>]['05].

%A M. Charikar
%A V. Guruswami
%A A. Wirth
%T Clustering with qualitative information
%J 44th Annual IEEE Symp. on Foundations of Comp. Sci.
%P 524-533
%D 2003
%K conf, FOCS, cluster, classification, c2003, c200x, c20xx,
   approximation algorithm
%X "We considered the problem of clustering elements based on pairwise
   judgements of similarity, both minimizing the number of pairs clustered in
   disagreement with the judgements and maximizing the number in agreement. Our
   main result was a factor 4 approx. alg. for minimization with a complete set
   of judgements -- the previous best had factor 17433. We also showed this
   case is NP-hard to approximate below a certain factor."
   -- [<A HREF="http://www.cs.mu.oz.au/~awirth/pubs/awirthFocs03.pdf">pdf@cs.mu.oz.au</A>]['05]
   [also search for: classification]  auth3 @ mu ['05]

%A G. Forman
%T An extensive empirical study of feature selection metrics for
   text classification
%J J. Machine Learning Res.
%V 3
%P 1289-1305
%M MAR
%D 2003
%K jrnl, c2003, c200x, c20xx, document categorization, information gain,
   trec, Bi-Normal Separation, BNS, binormal, class, skew, tests
%X "...document categorization, news filtering, document routing, &
   personalization. ...effective feature selection is essential to make the
   learning task efficient & more accurate. ... presents an empirical comp'n of
   12 feature selection methods (e.g. Information Gain) evaluated on a benchmark
   of 229 text classification problem instances that were gathered from Reuters,
   TREC, OHSUMED, etc. The results are analyzed from multiple goal perspectives-
   accuracy, F-measure, precision, & recall-since each is appropriate in
   different situations. The results reveal that a new feature selection metric
   we call 'Bi-Normal Separation' (BNS), outperformed the others by a
   substantial margin in most situations. This margin widened in tasks with high
   class skew, which is rampant in text classification problems & is
   particularly challenging for induction algs ... This analysis also revealed,
   for example, that Information Gain & Chi-Squared have correlated failures, &
   so they work poorly together. When choosing optimal pairs of metrics for
   each of the 4 performance goals, BNS is consistently a member of the pair -
   e.g., for greatest recall, the pair BNS + F1-measure yielded the best
   performance on the greatest number of tasks by a considerable margin."
   -- [<A HREF="http://portal.acm.org/ft_gateway.cfm?id=944974&type=pdf&coll=GUIDE&dl=GUIDE&CFID=49589134&CFTOKEN=27295051">pdf</A>]['05]

%A V. Dose
%T Hyperplane priors
%E C. J. Williams
%J Bayesian Inference and Maximum Entropy Methods in Sci. and Eng.,
   vol. Conf. Proc. 659
%P 350-357
%D 2003
%K conf, c2003, c200x, c20xx, prior probability distribution, hyper-plane,
   planes, line, lines, 2D, 3D, fit, fitting, regression
%X [<A HREF="http://www.ipp.mpg.de/OP/Datenanalyse/Publications/Papers/dose03a.pdf">pdf</A>]['05]

%A M. B. Dale
%A M. Anand
%T On continua and communities: correlation, clusters and complexity
%J Community Ecology
%V 4
%P 129-139
%D 2003
%K jrnl, plant community, c2003, c200x, c20xx, cluster, ecology, MML, MDL

%A D. George
%A K. Saito
%A P.Langley, S.Bay, K.Arrigo
%T Discovering ecosystem models from time-series data
%J Proc. of the 6th Int. Conf. on Discovery Science
%W Saporro, Japan
%I Springer
%P 141-152
%D 2003
%K conf, c2003, c200x, c20xx, timeSeries, model, zz0306, IPN, model, process
%X [<A HREF="http://cll.stanford.edu/~langley/papers/eco.ds03.ps">.ps</A>]['06]

%A J. Aitchison
%A J. W. Kay
%T Possible solutions of some essential zero problems in compositional
   data analysis
%J Compositional Data Analysis Workshop
%M OCT
%D 2003
%K wShop, CoDaWork, c2003, c200x, c20xx, zeroes, zero inflated
%X An essential zero: something truly zero not recorded as zero because
     of exp. design or measuring. ...
     2-stage (i) where are zeros, (ii) how distrib non-zeros.
   -- [<A HREF="http://ima.udg.es/Activitats/CoDaWork03/paper_Aitchison_and_Kay.pdf">pdf@wShop</A>]['06].

%A I. S. Dhillon
%A S. Mallela
%A D. S. Modha
%T Information-theoretic co-clustering
%J Proc. 9th ACM SIGKDD Int. Conf. on Knowledge discovery and data mining
%P 89-98
%D 2003
%K conf, c2003, c200x, c20xx, SIGKDD, coclustering, biclustering, two way,
   clustering, cluster
%X "Two-dimensional contingency or co-occurrence tables arise frequently in
   important applications such as text, web-log & market-basket data analysis.
   ... simultaneous clustering of the rows & [of] columns. A novel theoretical
   formulation views the contingency table as an empirical joint probability
   distribution of two discrete random variables & poses the co-clustering
   problem as an optimization problem in information theory - the optimal
   co-clustering maximizes the mutual information between the clustered random
   variables subject to constraints on the number of row & column clusters. We
   present an innovative co-clustering algorithm that monotonically increases
   the preserved mutual information by intertwining both the row & column
   clusterings at all stages. Using the practical example of simultaneous
   word-document clustering, we demonstrate that our algorithm works well in
   practice, especially in the presence of sparsity & high-dimensionality."
   -- pdf@[<A HREF="http://doi.acm.org/10.1145/956750.956764">doi:10.1145/956750.956764</A>]['06].
   (Also see bicl@[<A HREF="https://en.wikipedia.org/wiki/Biclustering">wikip</A>]['20].)
   [Also search for: biclustering] and [also search for: coclustering].

%A R. E. Groff
%A P. P. Khargonekar
%A D. E. Koditschek
%T A local convergence proof for the Minvar algorithm for computing continuous
   piecewise linear approximations
%J SIAM J. Num. Anal.
%V 41
%N 3
%P 983-1007
%D 2003
%K jrnl, stats, c2003, c200x, c20xx, regression, approximation, continuous
%X "... The minvar alg. computes a continuous PL approx. to data. Local
   convergence of minvar is proven for the case when the data generating fn is
   itself a PL fn and available directly rather than through data." [42 refs]
   -- [<A HREF="http://dx.doi.org/10.1137/S0036142902402213">doi:10.1137/S0036142902402213</A>]['07],
   &  [<A HREF=" http://www.eecs.umich.edu/techreports/cse/2002/CSE-TR-464-02.pdf">TR.pdf@umich</A>]['07].

%A D. J. C. MacKay
%T Information Theory, Inference, and Learning Algorithms
%I CUP
%D 2003
%K book, text, CUP, c2003, c200x, c20xx, information, theory, IT, coding,
   machine learning, artificial intelligence, AI, II, MDL
%X "... communication, signal processing, data mining, machine learning,
   pattern recognition, computational neuroscience, bioinformatics, and
   cryptography. This textbook introduces theory in tandem with applications.
   Information theory is taught alongside practical communication systems, such
   as arithmetic coding for data compression and sparse-graph codes for error-
   -correction. A toolbox of inference techniques, ..."
   1st ed 2003, hb us$60; uk us isbn:0521642981; uk us isbn13:978-0521642989.
   --  [<A HREF="http://www.inference.phy.cam.ac.uk/itila/">www</A>]['14],
   pdf@[<A HREF="http://www.inference.phy.cam.ac.uk/itprnn/book.pdf">www</A>]['12], 9MB.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A I. Tsamardinos
%A C. Aliferis
%A A. Statnikov
%A E. Statnikov
%T Algorithms for large scale Markov blanket discovery
%J 16th Int. FLAIRS Conf.
%I AAAIpress
%D 2003
%K conf, FLAIRS, c2003, c200x, c20xx, zz0615, stats, model, graphical, causal,
   AI, II
%X "... new algs. for discovering the Markov Blanket of a target variable T from
   training data. The MB can be used for variable seln for classn, for causal
   discovery, & for Bayesian n/w learning. We introduce a low-order polynomial
   alg. & several variants that soundly induce the MB under certain broad condns
   in datasets with thousands of vars. & compare them to other state-of-the-art
   local & global methods with excellent results."  (via KK.)
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.13.5894">cit'seer</A>]['15],
   pdf@[<A HREF="https://www.aaai.org/Papers/FLAIRS/2003/Flairs03-073.pdf">aaai</A>]['15].
   [Also search for: Markov blanket].

%A A. Berlinet
%A C. Thomas-Agnan
%T Reproducing Kernel Hilbert Spaces in Probability and Statistics
%I Springer
%D 2003
%K book, text, c2003, c200x, c20xx, reproducing kernel Hilbert spaces, space,
   RKHS, kernels, stats
%X "...the theory of reproducing kernel Hilbert spaces (RKHS) has proved to be
   a powerful tool in many fields of Pure & Applied Maths., & in particular in
   Probability & Stats.. ... The fact that reproducing kernels are covariance
   fns explains the early role of RKHS in inference problems on stochastic
   processes. The continuous rise of applications of RKHS theory & the recent
   burst of the field of SVMs attest that the scope of its applications is far
   from being exhausted ... can be used as a textbook at a postgraduate level."
   1st ed c2003, hb us$134; uk us isbn:1402076797; uk us isbn13:978-1402076794.
   Also see kernel@[<A HREF="http://en.wikipedia.org/wiki/Kernel_(mathematics)">wikip</A>]['09].

%A J. H. Ham
%A D. D. Lee
%A L. K. Saul
%T Learning high dimensional correspondences from low dimensional manifolds
%I Dept. Elec. & Sys. Eng., U. Penn.
%M AUG
%D 2003
%O Workshop on The Continuum from Labeled to Unlabeled Data in M.Learning &
   DataMining, at 20th ICML 2003
%K Ham03, wkshop, UPenn, c2003, c200x, c20xx, zz0820, manifold, alignment,
   manifolds, stats, dimension, dimensionality, reduction, PCA, stats,
   FactorAnalysis, match, correspond, correspondence
%X "Many different high-D data sets are characterized by the same underlying
   modes of variability. When ... continuous & few in #, they can be viewed as
   parameterizing a low-D manifold. ... provides a compact shared rep'n of the
   data, suggesting corr. b/ween the high-D examples from different data sets.
   ... difficult to learn using trad. methods in supervised learning. ... we
   generalize three methods in unsupervised learning - principal components
   analysis, factor analysis, & locally linear embedding - to discover subspaces
   & manifolds that provide common low-D repns of different high-D data sets. We
   use the shared repns ... to put high-D examples from different data sets into
   corr.. Finally, we show that a notion of 'self-correspondence' b/ween
   examples in the same dataset can be used to improve the performance of these
   algs on small data sets. ... demonstrated on images & text."
   -- [<A HREF="https://repository.upenn.edu/cgi/viewcontent.cgi?article=1131&context=ese_papers">UPenn</A>]['20].
   Also see MA@[<A HREF="https://en.wikipedia.org/wiki/Manifold_alignment">wikip</A>]['20].
   [Also search for: FactorAnalysis]  and  [also search for: PCA stats].

%A P. Fenwick
%T Universal codes
%B Lossless Compression Handbook Communications, Networking and Multimedia
%P 55-78
%D 2003
%K chapter, c2003, c200x, c20xx, zz1118, integer code, universal, codes,
   intCodes, FK1, Elias, Fibonacci, Goulomb
%X "... self-delimiting & variable in length for different values, are usually
   known as Universal Codes or Variable-length Codes. ...  'Good' codes are
   simple with a minimum of nonnumeric bits such as length indication &
   termination. The complexity & quantity of nonnumeric bits counts against the
   Elias w & higher order Fibonacci codes. For general use, the FK1 code is a
   good choice & the Elias y code is good for skewed distributions. Rice &
   Goulomb codes are excellent where values are confined to a range of 1:10.
   Additive codes are useful for only small values."
   -- [<A HREF="https://doi.org/10.1016/B978-012620861-0/50004-8">doi:10.1016/B978-012620861-0/50004-8</A>]['18] (uk us isbn13:9780126208610.).
   [Also search for: intCodes].

%A L. Frey
%A D. Fisher
%A I. Tsamardinos
%A C. F. Aliferis
%A A. Statnikov
%T Identifying Markov blankets with decision tree induction
%I ICDM
%D 2003
%K conf, ICDM, c2003, c200x, c20xx, zz0418, AI, II, local, Markov blanket,
   decision tree, DTree, C5.0, C5, Bayesian network
%X "... apply decision tree induction to the task of Markov blanket
   identification. Notably, we compare (a) C5.0, a widely used alg. for decision
   rule indn, (b) C5C, which post-processes C5.0 's rule set to retain the
   most freq. referenced variables & (c) PC, a std method for B.n/wk indn.
   C5C performs as well as or better than C5.0 & PC across a # of data sets. Our
   modest variation of an inexpensive, accurate, off-the-shelf indn engine
   mitigates the need for specialized procedures, & establishes baseline
   performance against which specialized algs. can be compared."
   -- [<A HREF="https://doi.org/10.1109/ICDM.2003.1250903">doi:10.1109/ICDM.2003.1250903</A>]['18],
   or [<A HREF="https://pdfs.semanticscholar.org/1d45/bf22cad3202e6d578c845a66116fbaefab3d.pdf">semanticscholar</A>]['18].
   [Also search for: Bayesian network DTree].

%A M. B. Dale
%A P. E. R. Dale
%T Sources of uncertainty in ecological modelling
%J Community Ecology
%V 5
%P 203-226
%D 2004
%K c2004, c200x, c20xx, ecology, model

%A M. B. Dale
%A M. Anand
%T Domain knowledge, evidence, complexity and convergence
%J Int. J. Ecology Environmental Sci.
%V 30
%P 141-158
%D 2004
%K jrnl, c2004, c200x, c20xx, MML, MDL, plant, communities

%A E. G. Learned-Miller
%A J. W. Fisher III
%T ICA using spacings estimates of entropy
%J J. Machine Learning Res.
%V 4
%N 7-8
%P 1271-1295
%D 2004
%K jrnl, JMLR, independant component analysis, stats, ICA, c2004, c200x, c20xx,
   spacing, entropy, outlier
%X "...new alg. for the independent components analysis (ICA) problem based on
  an efficient entropy estimator. Like many previous methods, this alg. directly
  minimizes the measure of departure from independence according to the est.
  Kullback-Leibler divergence between the joint distribution & the product of
  the marginal distributions. We pair this approach with efficient entropy
  estimators from the statistics literature. In particular, the entropy est.
  we use is consistent & exhibits rapid convergence. The alg. based on this
  estimator is simple, computationally efficient, intuitively appealing, &
  outperforms other well known algs.. ...the estimator' relative insensitivity
  to outliers translates into superior performance by our ICA alg. on outlier
  tests. ... favorable comparisons to the Kernel ICA, FAST-ICA, JADE, & extended
  Infomax algs. in extensive simulations. ... public domain source code ..."
  -- [<A HREF="http://mitpress.mit.edu/catalog/item/default.asp?tid=17187&ttype=6">paper</A>]['05],
     [<A HREF="http://www.cs.umass.edu/~elm/papers/learned-miller03a.pdf">pdf</A>]['05].

%A M. Charikar
%A A. Wirth
%T Maximizing quadratic programs: Extending Grothendieck's inequality
%J 45th Annual IEEE Symp. on Foundations of Comp. Sci.
%P 54-60
%D 2004
%K conf, FOCS, program, approximation algorithm, c2004, c200x, c20xx
%X "The first nontrivial approx. alg. for maximizing the correlation (the
   difference between the # of pairs correctly classified & the number
   incorrectly classified) in the clustering framework of the FOCS '03 paper.
   The factor Omega(1/log(n)) alg. is derived from an approx. alg. for
   maximizing a fairly general type of quadratic prog. on the unit hypercube."
   -- [<A HREF="http://www.cs.mu.oz.au/~awirth/pubs/awirthFocs04.pdf">pdf@cs.mu.oz.au</A>]['05],  auth2@mu ['05].

%A K. J. Bowers
%A S. D. Johnson
%A K. Pease
%T Prospective hot-spotting
%J British J. of Criminology
%P ?-?
%V ?
%N ?
%D 2004
%K jrnl, hot spot, crime, burglary, burglaries, stats, map, maps, grid, risk,
   prediction, predicting, future, Kate Bowers, zz0604, c2004, c200x, c20xx
%X "Existing methods predicting [...] future locations of crime are
   intrinsically retrospective. This paper explores the development of a
   mapping procedure that seeks to produce "prospective" hot-spot maps. [...]
   the authors demonstrates that the risk of burglary is communicable, with
   properties within [400m] of a burgled household being at a significantly
   elevated risk of victimization for up to two months after an initial event.
   [...] using this knowledge, recorded crime data can be analysed to generate
   an ever-changing prospective risk surface. One of the central elements of
   this paper examines the issue of how such a risk surface could be evaluated
   to determine its effectiveness & utility in comparison to existing
   methods. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bjc/azh036">doi:10.1093/bjc/azh036</A>][5/'04] online May 2004; auths at U. Coll., Lndn., UK.

%A D. P. Farrington
%A B. C. Welsh
%T Measuring the effects of improved street lighting on crime
%J British J. of Criminology
%P ?-?
%V ?
%N ?
%D 2004
%K jrnl, disagreement, street lights, crime, crimes, theft, assault,
   stats, Marchant
%X "We consider Dr Marchant's criticisms of our systematic review &
   meta-analysis of the effects of improved street lighting on crime. We
   conclude that the Birmingham, Bristol & Dudley evaluations did provide
   evidence that improved lighting caused a decrease in crime. We also find
   that the conclusions of our meta-analysis hold up, even if we greatly
   increase the variance of our effect size measure. We conclude that existing
   evaluations of the highest methodological quality, when analysed together,
   show that improved lighting, on average, caused a significant 20% decrease
   in crime in experimental areas compared with comparable control areas."
   -- [<A HREF="http://dx.doi.org/10.1093/crimin/azh045">doi:10.1093/crimin/azh045</A>][5/'04] online April 2004

%A P. R. Marchant
%T Research note: A demonstration that the claim that brighter lighting reduces
   crime is unfounded
%J British J. of Criminology
%P ?-?
%V ?
%N ?
%D 2004
%K jrnl, disagreement, Farrington, Welsh, street lights, crime, theft, assault,
   crimes, stats
%X "The major systematic review on street lighting & crime, Home Office
   Research Study 251, suggests that claims for the effectiveness of lighting
   against crime are justified. The review at first sight appears to be an
   appropriate statistical synthesis of all studies on street lighting &
   crime across the world. However on close examination, the statistical claims
   & methods are unfounded. In three cases examined there is a clear conflict
   between the evidence & the reviewers' interpretation of this.
   One of the principal problems is easily seen. The time-series of the
   original data from the Bristol study shows no good evidence for the crime
   reduction benefit of lighting. However the review gives the result for the
   same data as being extremely statistically significant. It is suggested that
   such a difference between the newly lit & the control areas occurring
   purely by chance is less than one in a billion, but this is manifestly
   wrong. Two other component studies, Birmingham & Dudley, are examined."
   -- [<A HREF="http://dx.doi.org/10.1093/bjc/azh009">doi:10.1093/bjc/azh009</A>][5/'04] online April 2004

%A An-Wen Chan
%A A. Hrobjartsson
%A M. T. Haahr
%A P. C. Gotzsche
%A D. G. Altman
%T Empirical evidence for selective reporting of outcomes in randomized trials
%J J. Americam Medical Assoc.
%V 291
%N 20
%P 2457-2465
%M MAY
%D 2004
%K jrnl, medicine, stats, statistics, trial, random, drug, drugs, controversial,
   disagreement, publish, publication, referee, referees, bias, commercial,
   JAMA, complete reporting, selective, protocol, zz0604, c2004, c200x, c20xx,
   fishing, selection, protocols, experiment, experimental
%X "...102 trials with 122 published J. articles & 3736 outcomes ... Overall,
   50% of efficacy & 65% of harm outcomes per trial were incompletely reported.
   Statistically significant outcomes had a higher odds of being fully reported
   compared with nonsignificant outcomes for both efficacy (pooled odds ratio,
   2.4; 95% confidence interval [CI], 1.4-4.0) & harm (pooled odds ratio, 4.7;
   95% CI, 1.8-12.0) data. In comparing published articles with protocols, 62%
   of trials had at least 1 primary outcome that was changed, introduced, or
   omitted. 86% percent of survey responders (42/49) denied the existence of
   unreported outcomes despite clear evidence to the contrary.
   ... reporting of trial outcomes is not only frequently incomplete but also
   biased & inconsistent with protocols. Published articles, as well as
   reviews that incorporate them, may therefore be unreliable & overestimate
   the benefits of an intervention. To ensure transparency, planned trials
   should be registered & protocols should be made publicly available prior
   to trial completion."
   -- [<A HREF="http://jama.ama-assn.org/cgi/content/abstract/291/20/2457">jama</A>][6/'04]
   Team @ Centre for Stats in Medicine, Inst. of Health Sci., 0xford

%A C. Hitchcock
%A E. Sober
%T Prediction versus accommodation and the risk of overfitting
%J British J. for the Philosophy of Science
%V 55
%N 1
%P 1-34
%M MAR
%D 2004
%K jrnl, simplicity, generalisation, generalization, c2004, c200x, c20xx, II,
   inference, AI, predict, explain, theory, hypothesis, model, zzOSP, zOSP04,
   Occam, explanation, confirmation, evidence, selection, zz0804
%X "When a scientist uses an observation to formulate a theory, it is no
   surprise that the resulting theory accurately captures that observation.
   However, when the theory makes a novel prediction - when it predicts an
   obs' that was not used in its formulation-this seems to provide more
   substantial confirmation of the theory. This paper presents a new approach
   to the vexed problem of understanding the epistemic difference between
   prediction & accommodation. In fact, there are several problems that need to
   be disentangled; in all of them, the key is the concept of overfitting. We
   float the hypothesis that accommodation is a defective methodology only when
   the methods used to accommodate the data fail to guard against the risk of
   overfitting. We connect our analysis with the proposals that other
   philosophers have made. We also discuss its bearing on the conflict between
   instrumentalism & scientific realism."         [LA: note the "only when"]
   -- [<A HREF="http://www3.oup.co.uk/phisci/hdb/Volume_55/Issue_01/550001.sgm.abs.html">paper</A>][8/'04]

%A G. A. Meehl
%T C. Tebaldi
%T More intense, more frequent, and longer lasting heat waves in the
   21st century
%J Science
%V 305
%P 994-997
%M AUG
%D 2004
%K jrnl, weather, climate, change, global warming, stats, c2004, c200x, c20xx,
   Chicago, Paris, heat waves, wave, frequency, zz0804
%X auths at Nat Centre Atmos Res, Bou1der, Co1orado.
   -- [<A HREF="http://www.sciencemag.org/cgi/reprint/305/5686/994">@Sci</A>][8/'04]

%A D. Blanchflower
%A A. J. Oswald
%T Well-being over time in Britain and the USA
%J J. of Public Economics
%D 2004
%V 88
%P 1359-1386
%K jrnl, c2004, c200x, c20xx, zz0904, stats, statistics, happiness, well being,
   wellbeing, happy, marriage, US, GB, UK, society, social, GSS, survey,
   General Social Surveys, Eurobarometer, ICPSR, gesis.org
%X "... happiness in [US] & [GB]. Reported levels of wellbeing have declined
   over the last quarter of a century in the US; life satisfaction has run
   approximately flat through time in Britain. ...consistent with the Easterlin
   hypothesis (1974, 1995). The happiness of [US], blacks however, has risen.
   White women in the US have been the biggest losers since the 1970s. Well-
   -being equations have a stable structure. Money buys happiness. People care
   also about relative income. Wellbeing is U-shaped in age.  The paper
   estimates the dollar values of events like unemployment & divorce.  They are
   large. A lasting marriage (compared to widow-hood as a `natural' experiment),
   for example, is estimated to be worth $100,000 a year."  ...
   "... information from the General Social Surveys of [US]. ...  GSS data are
   available in most of the years from 1972 to 1998. ...sample averages approx'
   1500 individuals [p.a.].  Different people are interviewed each year:
   the GSS is not a panel."
   -- [<A HREF="http://webapp.icpsr.umich.edu/GSS/">GSS Nat. Opionion Res. C.</A>]['04],
   and also...
   "The Eurobarometer Surveys provide cross-section inf'n on approx' 55,000
   Britons starting from the early 1970s (annual sample is just over 2000...)"
   -- [<A HREF="http://www2.warwick.ac.uk/fac/soc/economics/staff/faculty/oswald/finaldmo30jul.pdf">pp.pdf@warwick.ac.uk</A>][9/'04],
      [<A HREF="http://www2.warwick.ac.uk/fac/soc/economics/staff/faculty/oswald/">O'_home</A>]['04],
      [<A HREF="http://www.gesis.org/en/data_service/eurobarometer/">eurobarometer</A>]['04].
   [Also search for: happiness wellbeing].

%A J. Gardner
%A A. Oswald
%T How is mortality affected by money, marriage, and stress?
%J J. of Health Economics
%P ?-?
%V ?
%D 2004 ?, to appear
%K jrnl, life expectancy, death, income, stats, statistics, c2004, c200x, c20xx,
   risk, risks, GHQ, score, men, women, male, female, health, cause and effect,
   British Household Panel Survey, BHPS, UK, zz0904, 1990s, middle age, aged,
   ageing, aging, mortality, causality, smoking, zzOSP, zOSP04
%X "It is believed that the length of a person's life depends on a mixture of
   economic & social factors. Yet the relative importance of these is still
   debated. We provide recent British evidence that marriage has a strong
   positive effect on longevity. Economics matters less. After controlling for
   health at the start of the 1990s, we cannot find reliable evidence that
   income affects the probability of death in the subsequent decade. Although
   marriage keeps people alive, it does not appear to work through a reduction
   of stress levels. Greater levels of psychological distress (as measured by
   General Health Questionnaire stress scores) cannot explain why unmarried
   people die younger. For women, however, we do find that mental strain is
   dangerous. High GHQ stress scores help to predict the probability of an
   early death."  [...]  "The observed measures of stress appear uncorrelated
   with subsequent male mortality, though they do predict female longevity."
   ... "Married men are predicted to be some -7.2% less likely to die over
   the period than unmarried men. ... Women m. in 1991 are approx' -4.1%
   less likely to die over the period '93-'00 ...  period 1993 to 2000. ...
   The xs mortality of the unmarried ... similar to that of a smoker (5.0%).
   For women, being a smoker increases the risk of death by 5.2%..."
   -- [<A HREF="http://www2.warwick.ac.uk/fac/soc/economics/staff/faculty/oswald/mortalitymarchos2004.pdf">pre.pdf@warwick.ac.uk</A>][9/'04],
      [<A HREF="http://www2.warwick.ac.uk/fac/soc/economics/staff/faculty/oswald/">O_home</A>]['04],
      [<A HREF="http://www.data-archive.ac.uk/findingData/bhpsTitles.asp">data-archive.ac.uk</A>]['04].
   [Also search for: marriage mortality].

%A D. Prelec
%T A Bayesian truth serum for subjective data
%J Science
%V 306
%P 462-466
%D 2004
%K jrnl, survey, surveys, questionaires, human behaviour, stats, statistics,
   data collection, view, views, consensus, truthfulness, bias
%X "Subjective judgments, an essential information source for science & policy,
   are problematic because there are no public criteria for assessing judgmental
   truthfulness. I present a scoring method for eliciting truthful subjective
   data in situations where objective truth is unknowable. The method assigns
   high scores not to the most common answers but to the answers that are more
   common than collectively predicted, with predictions drawn from the same
   population. This simple adjustment in the scoring criterion removes all bias
   in favor of consensus: Truthful answers maximize expected score even for
   respondents who believe that their answer represents a minority view."
   <!-- dprelec at mit edu --> [<A HREF="http://www.sciencemag.org/cgi/content/abstract/306/5695/462">sci</A>]['04]
   Also see [<A HREF="http://www.newscientist.com/news/news.jsp?id=ns99996535">New Sci't</A>]['04]

%A P. Ravikumar
%A W. W. Cohen
%T A hierarchical graphical model for record linkage
%J UAI
%P ?-?
%D 2004
%K conf, UAI, AI, records, link, record linkage, data, match, matching, models,
   identity, c2004, c200x, c20xx
%X [<A HREF="http://www-2.cs.cmu.edu/~wcohen/postscript/uai-2004.pdf">pp.pdf@cs.cmu.edu</A>]['05]
   Also see Cohen c2003.

%A P. Christen
%A T. Churches
%A A. Willmore
%T A probabilistic geocoding system based on a national address file
%J Australasian Data Mining Conf.
%W Cairns
%P ?-?
%M DEC
%D 2004
%K conf, location, data base, database, record linkage, data, location, place,
   Febrl, address, addresses, geocoding, G-NAF, GNAF, c2004, c200x, c20xx
%X [<A HREF="http://datamining.anu.edu.au/publications/2004/aus-dm2004.pdf">pp.pdf@anu.edu.au</A>]['05].
   Also see [<A HREF="http://datamining.anu.edu.au/projects/linkage.html">project</A>]['05].

%A L. Gu
%A R. Baxter
%T Adaptive filtering for efficient record linkage
%J SIAM Int. Conf. on Data Mining
%P 22-24
%D 2004
%K conf, name matching, identity, records, c2004, c200x, c20xx, RABaxter,
   record linkage, data
%X [<A HREF="http://www.act.cmis.csiro.au/rohanb/PAPERS/sdm04.pdf">pp.pdf@cmis.csiro.au</A>]['05].

%A C. M. O'Keefe
%A M. Yung
%A L. Gu
%A R. Baxter
%T Privacy-preserving data linkage protocols
%J ACM Workshop on Privacy in the Electronic Society
%P ?-?
%W Washington DC
%M OCT
%D 2004
%K wShop, record linkage, data, privacy, matching, c2004, c200x, c20xx
%X auths @ CSIRO ACT .au.
   [Also search for: record linkage data].

%A L. J. Fitzgibbon
%A D. L. Dowe
%A F. Vahid
%T Minimum message length autoregressive model order selection
%J Proc. Int. Conf. on Intelligent Sensors and Information Processing
%W Chennai, India
%P 439-444
%M JAN
%D 2004
%K conf, autoregression, MML, description, MDL, c2004, c200x, c20xx, leighf,
   ICISIP, ICISIP04, LJFitzgibbon, DLDowe, FVahid, time series, sensor

%A M. Quist
%A G. Yona
%T Distributional scaling: An algorithm for structure-preserving embedding of
   metric and nonmetric spaces
%J J. Machine Learning Res.
%V 5
%P 399-420
%M APR
%D 2004
%K jmlr, space, non-metric, c2004, c200x, c20xx, multidimensional scaling, MDS,
   embed, embedded, geometry, geometric distortion, properties, Isomap, LLE,
   dimension reduction, multi-dimensional, zz0705, zzMDale, SAMMON, SSTRESS
%X "... embedding general metric and nonmetric spaces into low-dimensional
   Euclidean spaces. As opposed to traditional multidimensional scaling
   techniques, which minimize the distortion of pairwise distances, our
   embedding algorithm seeks a low-dimensional representation of the data that
   preserves the structure (geometry) of the original data ... combines the
   pairwise distortion with what we call the geometric distortion. ...
   different from the Isomap and LLE algs. ..."
   -- [<A HREF="http://jmlr.csail.mit.edu/papers/v5/quist04a.html">pdf etc @jmlr</A>]['05].

%A T. Gartner
%A J. W. Lloyd
%A P. A. Flach
%T Kernels and distances for structured data
%J Machine Learning
%I Springer
%V 57
%N 2
%P 205-232
%M DEC
%D 2004
%K jrnl, kernel, distance, c2004, c200x, c20xx, JWLloyd, Diterpene data set,
   ILP, AI, nearest neighbour
%X "... brings together 2 strands of machine learning of increasing importance:
   kernel methods and highly structured data. ... a general method for
   constructing a kernel following the syntactic structure of the data, as
   defined by its type signature in a higher-order logic. Our main theoretical
   result is the positive definiteness of any kernel thus defined. We report
   encouraging experimental results on a range of real-world data sets. By
   converting our kernel to a distance pseudo-metric for 1-nearest neighbour,
   we were able to improve the best accuracy from the literature on the
   Diterpene data set by more than 10%."
   -- [<A HREF="http://dx.doi.org/10.1023/B:MACH.0000039777.23772.30">doi:10.1023/B:MACH.0000039777.23772.30</A>]['05].

%A W. ten Brinke
%A D. McG. Squire
%A J. Bigelow
%T Similarity: Measurement, ordering and betweenness
%J 8th Int. Conf., KES
%I SpringerVerlag
%S LNCS
%V 3214
%P 996-1002
%D 2004
%K conf, KES, KES8, survey, overview, c2004, c200x, c20xx, zz0805, similar,
   between, ness, retrieval, relevance feedback
%X "... an overview of the challenges of producing a list of retrieval results
   ranked according to perceptual similarity. We explain some of the problems
   in using a metric to measure perceptual similarity, & consider the arguments
   for the desirability of metrics for retrieval. We discuss the use of
   broader definitions of betweenness to produce such a ranking of retrieval
   results. We propose some initial ideas of a notion of projective betweenness
   that makes explicit the intuition that 2 referents should be used when
   producing a similarity ranking, & indicate how it might be used in
   relevance feedback."    -- auths@Monash.U. ['05]. isbn:3540232060.
   -- [<A HREF="http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=3214&spage=996">open-ur1</A>]['05]
      [<A HREF="http://www.springerlink.com/link.asp?id=5nlur0mn9tjk7nb8">met@pres</A>]['05].

%A S. Landau
%A B. S. Everitt
%T A handbook of statistical analyses using SPSS
%I ChapmanHall/CR
%D 2004
%P 354
%K book, text, SPSS, stats, statistics, c2004, c200x, c20xx
%X isbn:1584883693.
   see [<A HREF="http://web1.iop.kcl.ac.uk/iop/departments/BioComp/SPSSBook.shtml">www</A>]['05]

%A W. Jiang
%A B. Turnbull
%T The indirect method: inference based on intermediate statistics -
   a synthesis and examples
%J Statist. Sci.
%V 19
%N 2
%P 239-263
%D 2004
%K jrnl, stats, statistics, estimator, indirect likelihood,
   generalized method of moments, c2004, c200x, c20xx
%X "... In the indirect method, statistical inference is based on an
   intermediate statistic, which typically follows an asymptotic normal dist.,
   but is not necessarily a consistent est. of the param. of interest. This
   int. stat. can be a naive estimator based on a convenient but misspecified
   model, a sample moment or a solution to an estimating equation. We review a
   procedure of indirect inference based on the generalized method of moments,
   which involves adjusting the naive est. to be consistent and asymptotically
   normal. The objective function of this procedure is shown to be
   interpretable as an "indirect likelihood" based on the int. stat.. Many
   properties of the ordinary LH function can be extended to this indirect LH.
   ...often more convenient computationally than max. LH est. when handling
   such model complexities as random effects and measurement error, for example,
   and it can also serve as a basis for robust inference and model selection,
   with less stringent assumptions on the data generating mechanism. Many
   familiar est. techniques can be viewed as examples of this approach. ..."
   -- [<A HREF="http://projecteuclid.org/Dienst/UI/1.0/Summarize/euclid.ss/1105714160">subscrn</A>]['05]
      [<A HREF="http://neyman.stats.nwu.edu/jiang/indirect.pdf">pp.pdf@stats.nwu.edu</A>]['05]

%T Clementine 9.0 User's Guide
%I SPSS
%D 2004
%K manual, book, text, guide, intro, SPSS, Clementine, c2004, c200x, c20xx,
   stats, CLEM, statistics, package, language, script, scripting, data mining,
   platform, software, analysis
%X It is v. hard to find a real language definition
   (v. sales [<A HREF="http://www.spss.com/clementine/">spin</A>]['05]) for C.!
   Also see SAS, SPlus, R, or Weka.

%A K. Hornik
%A F. Leisch
%T R Version 2.0.0
%J Computational Statistics
%V 19
%N 4
%P 661-664
%D 2004
%K jrnl, RR, c2004, c200x, c20xx, stats, package, software, platform, FAQ,
   language, definition, guide, manual
%X [<A HREF="http://www.wu-wien.ac.at/cstat/hornik/">Hornik</A>]['05], also...
   "... Contrary to other implementations of the S language, R has adopted
   an evaluation model in which nested function definitions are lexically
   [statically] scoped. ..."
   -- [<A HREF="http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html#Lexical-scoping">FAQ</A>]['05], ver 2.2.2005-11-20, isbn:3900051089, and...
      [<A HREF="http://www.r-project.org">r-project.org</A>]['05]

%A R. M. Clark
%A R. Thompson
%T Botanical records reveal changing seasons in a warming world
%J Australian Science
%P 37-39
%M OCT
%D 2004
%K climate, record, c2004, c200x, c20xx, global, plant, plants, growth, CO2,
   temperature, RMClark, Malcolm, flowering, bloom, stats, uniMonash, Monash
%X auth1@monash, auth2@geos.edinb.

%A R. H. Carver
%T Doing Data Analysis with Minitab 14
%I Thomson
%D 2004
%K book, text, manual, c2004, c200x, c20xx, minitab14, stats, statistics,
   software
%X [<A HREF="http://minitab.com/">minitab.com</A>]['05] inc. a "guided tour".
   "... Macros, Complete command language, ..."

%A T. Churches
%A P. Christen
%T Some methods for blindfolded record linkage
%J BMC Med. Inf. Decis. Mak.
%V 4
%N 9
%D 2004
%K jrnl, eJrnl, c2004, c200x, c20xx, record linkage, data, privacy, preserving,
   blindfold, blindfolded, q-grams, kmers, kmer. HMAC
%X "... suggested a protocol based on hashed values of sets of consecutive
   letters (q-grams). For each string, the database holders A & B create for
   each record the power set of the q-grams of their identifiers. Each subset of
   the power set is hashed by an HMAC algorithm using a common secret key of the
   database owners. A & B form tuples containing the hash values, the number
   of q-grams in the hashed subset & the total number of q-grams & an
   encryption of the identifiers to a third party C. The number of tuples is
   much larger than the number of records. To calculate the string similarity
   between two strings a & b, C computes a similarity measure based on the
   information in the tuples. [Shown] C is able to determine a similarity
   measure of a & b by selecting the highest similarity coefficient of the
   tuples associated with a & b. ..."  -- from a citing paper.
   [Also search for: record linkage data].

%A K. B. Korb
%A L. R. Hope
%A A. E. Nicholson
%A K. Axnick
%T Varieties of causal intervention
%J Pacific Rim Int. Conf. on AI
%P 322-331
%D 2004
%K conf, c2004, c200x, c20xx, causal model, cause, effect, Bayesian network,
   c2004, c200x, c20xx, intervene, data, experiment, Bnet
%X auths1-3 @ mon@sh ('06).

%A J. M. Keith
%A D. P. Kroese
%A D. Bryant
%T A generalized Markov sampler
%J Methodology and Computing in Applied Probability
%I SpringerVerlag
%V 6
%N 1
%P 29-53
%M MAR
%D 2004
%K MCMC, c2004, c200x, c20xx, MolBio, string, sequence, segmentation, tree
%X "... An example of this type of sampler is the reversible jump MCMC sampler,
   which is a generalization of the Metropolis-Hastings algorithm. Here, we
   present a new MCMC sampler of this type. The new sampler is a generalization
   of the Gibbs sampler, but somewhat surprisingly, it also turns out to
   encompass as particular cases all of the well-known MCMC samplers, including
   those of Metropolis, Barker, and Hastings. Moreover, the new sampler
   generalizes the reversible jump MCMC. [Applied to] ... consensus sequences,
   phylogenetic inference and delineation of isochores via multiple
   change-point analysis."
   -- [<A HREF="http://dx.doi.org/10.1023/B:MCAP.0000012414.14405.15">doi:10.1023/B:MCAP.0000012414.14405.15</A>]['05]

%A W. J. Reed
%A M. Jorgensen
%T The double Pareto-lognormal distribution - A new parametric model for size
   distribution
%J Com. Stats - Theory & Methods
%V 33
%N 8
%P 1733-1753
%D 2004
%K jrnl, probability, stats, power law, tail, tails, c2004, c200x, c20xx,
   log normal
%X "A family of probability densities, which has proved useful in modelling the
   size distributions of various phenomena, including incomes and earnings,
   human settlement sizes, oil-field volumes and particle sizes, is introduced.
   ... exhibits Paretian (power-law) behaviour in both tails, and when plotted
   on logarithmic axes, its density exhibits hyperbolic-type behaviour."
   -- [<A HREF="http://www.math.uvic.ca/faculty/reed/dPlN.3.pdf">pdf</A>]['05]

%A A. Gionis
%A H. Mannila
%A E. Terzi
%T Clustered segmentations
%J Proc. of 3rd Workshop on Mining Temporal and Sequential Data (TDM)
%W Seattle
%P 22-25
%M AUG
%P 2004
%K wShop, segmentation, c2004, c200x, c20xx, TDM, TDM3, TDM04, model, models,
   sequence
%X "... sequence & time-series seg. ... computational genomics, data analysis
   for scientific applications, & telecommunications. In many of these areas
   the sequences involved are multidimensional, & the goal of the segmentation
   is to discover sequence segments with small variability. One of the
   characteristics of existing techniques is that they force all dimensions to
   share the same seg. boundaries. ... [Here] the dimns. of the seqs. are
   allowed to form clusters and be seg. separately within each cluster. ..."
   -- [<A HREF="http://www.cs.helsinki.fi/u/terzi/tdm04.pdf">pdf</A>]['06]
   [Also search for: segmentation]

%A D. Applebaum
%T Levy processes - from probability to finance and quantum groups
%J Notices of the American Math. Soc.
%V 51
%N 11
%P 1336-1347
%M DEC
%D 2004
%K jrnl, c2004, c200x, c20xx, Levy process, group, Brownian motion, increment,
   increment, drift, jump, jumps
%X "... A Levy process X = (X(t), t>=0) is a stochastic process satisfying...
   (L1) X has indep. and stationary increments  (an increment is an X(s)-X(t)).
   (L2) Each X(0)=0 with prob. one,
   (L3) X is stochastically continuous, i.e. for all a>0 and all s>=0,
        lim[t->s]P( |X(t)-X(s)| > a) = 0.
   -- [<A HREF="http://www.ams.org/notices/200411/fea-applebaum.pdf">pdf@ams</A>]['07]
   Also see [<A HREF="http://en.wikipedia.org/wiki/L%C3%A9vy_process">wikip</A>]['07]

%A S. Lyu
%A D. Rockmore
%A H. Farid
%T A digital technique for art authentication
%J Proc. Natl. Acad. Sci
%P ?-?
%M ?
%D 2004 online
%K PNAS, painting, artist, forgery, forger, stats, statistics, zz1204, Bruegel,
   Pietro Perugino, drawing, wavelets
%X "...authenticating works of art, specifically paintings & drawings from high
   -resolution digital scans of the original works. ... builds a stat. model of
   an artist from the scans of a set of authenticated works against which new
   works then are compared. The stat. model consists of 1st- & higher-order
   wavelet statistics. ... preliminary results from our analysis of 13 drawings
   that at various times have been attributed to Pieter Bruegel the Elder;
   these results confirm expert authentications. ..."  online 24/11/'04
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.0406398101">doi:10.1073/pnas.0406398101</A>]

%A S. Altmueller
%A R. M. Haralick
%T Approximating high dimensional probability distributions
%J Proc. 17th Int. Conf. on Pattern Recognition
%I IEEE
%V 2
%P 299-302
%M AUG
%D 2004
%K conf, ICPR, c2004, c200x, c20xx, zz0214, decomposable graphical model,
   distribution, MDL, data mining, II
%X "... approach to estimating high dimensional discrete prob.distributions with
   decomposable graphical models. Starting with the independence assumption we
   add edges & thus gradually increase the complexity of our model. Bounded by
   the min. description length principle we are able to produce highly accurate
   models without overfitting. We discuss the properties & benefits of this
   approach in an experimental evaluation & compare it to the well-studied
   Chow-Liu alg.."
      N discrete variables X={X_1, ..., X_N};
      if A subset {1, ..., N} then X_A is corr subspace;
      dataset D=D_1,...,D_M;  H(Mod) is the model entropy.
      Sec.3: encode...
      (i) cliques of the graph ... SUM_i=1..|C| log(N)+k_i.log(N);
      (ii) prob tables d[(||X_C0||-1) + SUM_i=1..C ||X_Si||(||X_Ci-Si|| - 1)]
           where d is #bits to encode one param, ||X_A|| size of subspace;
      (iii) data M.H(Mod)"
   -- [<A HREF="http://dx.doi.org/10.1109/ICPR.2004.1334178">10.1109/ICPR.2004.1334178</A>]['14]($),
   or pdf@[<A HREF="http://haralick.org/conferences/212820299.pdf">haralick.org</A>]['14].
   [Also search for: decomposable graphical model].

%A G. Li
%A H. Dai
%A Y. Tu
%T Identifying Markov blankets using lasso estimation
%J Advances in Knowledge Discovery and Data Mining
%I SpringerVerlag
%S LNCS
%V 3056
%P 308-318
%D 2004
%K conf, c2004, c200x, c20xx, zz0715, AI, stats, Markov blanket, MML, MDL, AIC,
   lasso tree, causal, viaKelvin
%X "... a novel Markov Blanket identification alg. based on the Lasso estimator.
   For each variable, [it] first generates a Lasso tree, which represents a
   pruned candidate set of possible feature sets. The MML principle is then
   employed to evaluate all those candidate feature sets, & the feature set with
   min. msg. length is chosen as the M.Blanket. ... results show the ability of
   this alg.. [& it] can be used to prune the search space of causal discovery,
   & further reduce the comp. cost of those score-based causal discovery algs.."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-24775-3_39">doi:10.1007/978-3-540-24775-3_39</A>]['15] (auths@deak'n, '04).
   [Also search for: Markov blanket].

%A M. Z. Ashrafi
%A D. Taniar
%A K. A. Smith
%T PPDAM: Privacy-preserving distributed association rule mining algorithm
%J Int. J. of Intelligent Information Technologies
%V 1
%N 1
%P 49-69
%D 2005
%K jrnl, data, stats, c2005, c200x, c20xx, frequent item sets, FIS, rules,
   PPDAM, record linkage, data, privacy, monash, uniMonash
%X "...present a methodology that generates association rules without revealing
   confidential inputs such as statistical properties of individual sites, &
   yet retains a high level of accuracy in the resultant rules. One of the
   important outcomes of the proposed technique is that it reduces the overall
   communication costs. Performance evaluation of our proposed method shows that
   it reduces the communication cost significantly when we compare it with other
   well-known, distributed association-rule-mining algorithms. Nevertheless, the
   global rule model generated by the proposed method is based on the exact
   global support of each item set & hence diminishes inconsistency, which
   indeed occurs when global models are generated from partial support count of
   an item set."
   [Also search for: record linkage data].

%T Models for Intensive Longitudinal Data
%E T. A. Walls
%E J. L. Schafer
%I OUP
%D 2005 (in press)
%K book, text, c2005, c200x, c20xx, model, stats, statistics, ILD
%X "A new class of longitudinal data has emerged as a result of the use of
   technological devices for data collection in diverse areas of sci. inquiry.
   [eg] social scientific studies frequently utilize handheld computers,
   beepers, web interfaces & other technological tools for data collection.
   This class of data is called intensive longitudinal data (ILD)."
   -- [<A HREF="http://methcenter.psu.edu/ild/">methcenter.psu.edu/ild/</A>]['05]

%A A. Wirth
%A Approximation algorithms for clustering
%I Princeton U.
%D 2005
%K PhD thesis, algorithm, c2005, c200x, c20xx
%X "The results in the APPROX '03, F0CS '03 and F0CS '04 papers were collated,
   together with improvements to and analysis of the running times of the
   various new algorithms in the dissertation."  auth@mu ['05]
   -- [<A HREF="http://www.cs.mu.oz.au/~awirth/pubs/awirthPhd.pdf">pdf</A>]['05].
   [Also search for: classification].

%A J. P. A. Ioannidis
%T Why most published research findings are false
%J PLoS Medicine
%V 2
%N 8
%P e124
%M AUG
%D 2005
%K Essay, stats, statistics, c2005, c200x, c20xx, L4Ref, L5Ref, research, bias,
   statistical significance, true, false, replication, findings, results,
   zz0905
%X "... probability that a research claim is true may depend on study power &
   bias, the number of other studies on the same question, &, importantly, the
   ratio of true to no relationships among the relationships probed in each
   scientific field. ... less likely to be true when the studies conducted in a
   field are smaller; when effect sizes are smaller; when there is a greater
   number & lesser preselection of tested relationships; where there is greater
   flexibility in designs, definitions, outcomes, & analytical modes; when
   there is greater financial & other interest & prejudice; and when more teams
   are involved in a scientific field in chase of statistical significance...."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pmed.0020124">doi:10.1371/journal.pmed.0020124</A>]['05].

%A R. Fischer
%A H. Dreier
%A A. Dinklage
%A B. Kurzan
%A E. Pasch
%T Integrated Bayesian experimental design
%E K. Knuth
%J Bayesian Inference and Maximum Entropy Methods in Sci. and Eng.,
   vol. Conf. Proc. ?,
%P ?-?
%D 2005
%K conf, experiment, c2005, c200x, c20xx, data analysis, IBED
%X [<A HREF="http://www.ipp.mpg.de/OP/Datenanalyse/Publications/Papers/fischer05a.pdf">pdf</A>]['05].

%A S. Fienberg
%T When did Bayesian inference become "Bayesian"?
%J Bayesian Analysis
%V 1
%N 1
%P 1-40
%D 2006
%K jrnl, c2006, c200x, c20xx, zz1017, Bayesian, Bayesianism, theorem, stats,
   statistics, frequentist, posterior, inverse probability, inference, II, AI,
   history
%X "While Bayes' theorem has a 250-year history, & the method of inverse
   probability that flowed from it dominated statistical thinking into the
   twentieth century, the adjective "Bayesian" was not part of the stat. lexicon
   until relatively recently. This paper provides an overview of key B.
   developments, beginning with Bayes' posthumously published 1763 paper &
   continuing up through ~ 1970, inc. the period of time when "Bayesian" emerged
   as the label of choice for those who advocated Bayesian methods."
   -- [<A HREF="https://projecteuclid.org/euclid.ba/1340371071">www</A>]['17].

%A C. D. Heth
%A E. H. Cornell
%T A geographic information system for managing search for lost persons
%B Applied spatial cognition: From research to cognitive technology
%P 267-284
%I MahwahNJ: LawrenceErlbaum
%D 2006
%K chapter, c2006, c200x, c20xx, zz0320, lost, missing, person, child, children,
   human wayfinding, search and rescue, stats
%X Also see
   DH@[<A HREF="http://web.psych.ualberta.ca/~dheth/homepage.html">ualberta</A>]['20],
   EHC@[<A HREF="http://www.psych.ualberta.ca/~ecornell/">ualberta</A>]['20].
   [Also search for: missing person].

%A R. M. Jarvis
%A et al
%T PyChem A multivariate analysis package for python
%J <!-- Bio informatics -->sub.
%D 2006
%K PyChem, python, stats, statistics
%X home [<A HREF="http://www-mitchell.ch.cam.ac.uk/noel/">of O'B</A>]['05]
   -- [<A HREF="http://www.redbrick.dcu.ie/~noel/R_classification.html">R & Py @ dcu.ie</A>]['05].

%A Q. Lu
%A X. Yao
%T Clustering and learning Gaussian distribution for continuous optimization
%J IEEE Trans. on Systems, Man and Cybernetics, Part C
%V 35
%N 2
%P 195-204
%M MAY
%D 2005
%K jrnl, EDA, c2005, c200x, c20xx, clustering, uniBirmingham
%X [Also search for:  mixture model] -- <!-- via r o h a n --> .
   -- [<A HREF="http://www.cs.bham.ac.uk/~xin/papers/published_IEEETSMC_LuYa05.pdf">pdf@bham.ac.uk</A>]['05], Xin Yau @ U. Bham ['05]

%A J. Li
%A et al
%T Mining risk patterns in medical data
%J 11th ACM SIGKDD Int. Conf. on Knowledge Discovery & Data Mining (SIGKDD05),
   Industrial and Government Track.
%P ?-?
%M AUG
%D 2005
%X conf, c2005, c200x, c20xx, machine learning, health, pattern, risks
%X ?GW @ ato, as of '05?
   -- [<A HREF="http://www.togaware.com/Graham.Williams/publications.html">ato</A>]['05] <!-- via Jon P --> .

%A F. Klebaner
%T Introduction to Stochastic Calculus with Applications
%I Imp. Coll. Press
%P 432
%D 2005
%K book, text, stats, probability, application, c2005, c200x, c20xx, uniMonash
%X 1st edn c1998,  2nd edn 2005; hb, isbn:1860945554; pb, isbn:186094566X.
   prof @ monash ['05]

%A D. Tjondronegoro
%A Y-P. Chen
%A B. Pham
%T A statistical-driven approach for automatic classification of events in
   AFL video highlights
%J 28th Australasian Computer Science Conf.
%P 209-218
%D 2005
%K conf, ACSC, Binh Pham, BPham, c2005, c200x, c20xx, movie, TV, event, footy,
   highlight, stats, image processing
%X auths@QUT ['05]

%A M. B. Dale
%D 2005
%T On gradients and response curves
%J Community Ecology
%V 6
%P 155-166
%D 2005
%K c2005, c200x, c20xx, curve

%A S. Panagiotidi
%A E. Katsiri
%A J. Darlington
%T On advanced scientific understanding, model componentisation and
   coupling in GENIE
%J UK eScience All Hands Meeting
%W Nottingham UK
%M SEP
%D 2005
%K wShop, c2005, c200x, c20xx, component, models, OLOGEN, coupling semantics,
   ontology, grid computing, simulation, climate, climatic
%X "GENIE .... simulate .... Earth's climate. ..."
   -- [<A HREF="http://www.allhands.org.uk/2005/proceedings/papers/559.pdf">pdf</A>]['06]

%A T. G. Martin
%A et al
%T Zero tolerance ecology: Improving ecological inference by modelling the
   source of zero observations
%J Ecology Letters
%V 8
%N 11
%P 1235-1246
%M NOV
%D 2005
%K jrnl, true, false, zero, zeroes, c2005, c200x, c20xx, zero-inflated,
   excess, model, stats, observation, zz1206
%X "A common feature of ecological datasets is their tendency to contain many
   zero values. ... define and classify the different kinds of zeros that occur
   in ecological data and describe how they arise: either from 'true zero' or
   'false zero' observations. After reviewing recent developments in modelling
   zero-inflated datasets, ..."  --via MD.
   -- [<A HREF="http://dx.doi.org/10.1111/j.1461-0248.2005.00826.x">doi:10.1111/j.1461-0248.2005.00826.x</A>]['06]
      [<A HREF="http://eprint.uq.edu.au/archive/00002964/">@uq</A>]['06]

%A T. Okita
%T Modeling language for constructing solvers in machine learning:
   Reductionist perspectives
%J Int. J. Computational Intell.
%V 2
%N 3
%P 154-160
%D 2005
%K jrnl, IJCI, AI, c2005, c200x, c20xx, solver, languages, modelling,
   perspective, II, zz0706
%X [<A HREF="http://www.enformatika.org/ijci/v2/v2-3-24.pdf">pdf</A>]['05]

%A G. Adomavicius
%A A. Tuzhilin
%T Toward the next generation of recommender systems:
   a survey of the state-of-the-art and possible extensions
%J IEEE Trans. on Knowledge and Data Engineering
%V 17
%N 6
%P 734-749
%M JUN
%D 2005
%K jrnl, system, recommendation, c2005, c200x, c20xx, system,
   content-based, collaborative, hybrid, rating, ratings
%X "... three main categories: content-based, collaborative, and hybrid
   recommendation approaches. This paper also describes various limitations of
   current recommendation methods and discusses possible extensions that can
   improve recommendation capabilities and make recommender systems applicable
   to an even broader range of applications. These extensions include, among
   others, an improvement of understanding of users and items, incorporation of
   the contextual information into the recommendation process, support for
   multicriteria ratings, and a provision of more flexible and less intrusive
   types of recommendations."
   -- [<A HREF="http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=1423975">ieee</A>]['06]

%A M. Jorgensen
%T Minimum message length estimation using EM methods: a case study
%J Comp. Stats. and Data Analysis
%V 49
%N 1
%P 147-167
%M APR
%D 2005
%K jrnl, c2005, c200x, c20xx, method, MML, AIC, description, MDL, II, EM,
   FactorAnalysis, maximum penalized likelihood, uniWaikato
%X "... we consider a modified MML approach based on the EM algorithm & using
   only 'complete data' quantities which considerably simplify the computation
   of the determinant. In the context of the 'single factor analysis' or
   'comparative calibration' example of Wallace & Freeman we study our modified
   estimator & compare it with that of W+F & other alternatives."
   -- [<A HREF="http://dx.doi.org/10.1016/j.csda.2004.05.005">doi:10.1016/j.csda.2004.05.005</A>]['06]
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A I. H. Jermyn
%T Invariant Bayesian estimation on manifolds
%J Annals of Stats.
%V 33
%N 2
%P 583-605
%D 2005
%K jrnl, c2005, c200x, c20xx, manifold, MAP, MSE, MMSE, invariance, MML, MDL,
   parameter, estimate, parameterization, reparameterization
%X "A frequent & well-founded criticism of the max. a posteriori (MAP) & min.
   mean squared error (MMSE) ests. of a cts param., g, taking values in a
   differentiable manifold, G, is that they are not inv. to arb.
   "reparameterizations" of G. ...clarifies the issues surrounding this problem
   by pointing out the difference between coordinate invariance, which is a
   sine qua non for a math'y well-defined problem, & diffeomorphism invariance,
   which is a substantial issue, & then provides a soln. We 1st show that the
   presence of a metric structure on G can be used to define coord.-invariant
   MAP & MMSE estimates, & we argue that this is the natural way to proceed. We
   then discuss the choice of a metric structure on G. By imposing an inv.
   criterion natural within a Bayesian f/w, we show that this choice is
   essentially unique. It does not necessarily corr. to a choice of coordinates.
   In cases of complete prior ignorance, when Jeffreys' prior is used, the inv.
   MAP est. reduces to the max. likelihood est.. The inv. MAP est. coincides
   with the minimum message length (MML) est., but no discretization or approx.
   is used in its derivation."
   -- [<A HREF="http://dx.doi.org/10.1214/009053604000001273">doi:10.1214/009053604000001273</A>]['07]

%A K. G. van der Boogaart
%T Aitchison geometry for probability and likelihood as a new approach to
   mathematical statistics
%J 2nd Compositional Data Analysis Workshop (CoDaWork)
%P ?-?
%D 2005
%W Girona
%K wShop, c2005, c200x, c20xx, vector space, simplex, Hilbert space, algebraic,
   CoDaWork, CoDaWork2, stats, viaMikeD
%X "... generalized the Aitchison vector space structure for the simplex to a
   Hilbert space  structure A**2(P) for freq. distributions & likelihoods on
   arbitrary spaces. Basic concepts of statistics, such as Information &
   Likelihood, can be characterized  concisely & elegantly in the algebraical
   structure of A**2(P)...."  --via Mike D.
   -- [<A HREF="http://www.math-inf.uni-greifswald.de/~boogaart/Publications/BoogaartPublications.html">auth</A>]['06]
      [<A HREF="http://ima.udg.es/Activitats/CoDaWork05/CD/invited-lectures/Boogaart.pdf">abstract.pdf</A>]['06]

%A A. Banerjee
%A X. Guo
%A H. Wang
%T On the optimality of conditional expectation as a Bregman predictor
%J IEEE Trans. Info. Theory
%V 51
%N 7
%P 2664-2669
%M JUL
%D 2005
%K jrnl, c2005, c200x, c20xx, zz0408, stats, information, BLF,
   least mean square error
%X "We consider the problem of predicting a random variable from observations,
   denoted by a random variable. It is well known that the cond. exp'n E[X|Z] is
   the optimal |**2 predictor (also known as "the least-mean-square error"
   predictor) of X among all (Borel measurable) functions of Z. ...provide nec.
   & suff. conds.  for the general loss functions under which the cond. exp'n is
   the unique optimal predictor. We show that E[X|Z] is the optimal predictor
   for all Bregman loss functions (BLFs), of which the L**2 loss function is a
   special case. ...under mild conditions, we show that the BLFs are exhaustive,
   i.e., if for every random variable X, the infimum of E[F(X|y)] over all
   constants is attained by the expectation E[X], then is a BLF."
   -- [<A HREF="http://www.lans.ece.utexas.edu/~abanerjee/papers/05/bgw.pdf">pdf@utexas</A>]['08]
      [<A HREF="http://dx.doi.org/10.1109/TIT.2005.850145">doi:10.1109/TIT.2005.850145</A>]['08] -subscrn.

%A J. M.C. Larrosa
%T Compositional Time Series: Past and Present
%I EconPapers
%M OCT
%D 2005
%K c2005, c200x, c20xx, survey, autoregresive integrate moving average,
   ARIMA, vector autoregression, CVAR
%X "... survey ... comprehends the analysis of several techniques like
   autoregresive integrate moving average (ARIMA) analysis, compositional
   vector autoregression systems (CVAR) and state space techniques but most of
   these are developed under Bayesian frameworks. ..."
   -- [<A HREF="http://econpapers.repec.org/paper/wpawuwpem/0510002.htm">www</A>[3/'08]
   auth: jlarrosa at criba edu ar

%A E. Candes
%A T. Tao
%T The Dantzig selector: Statistical estimation when p is much larger than n
%J arXiv
%D 2005
%O Annals of Stats., Vol.35, No.6, pp.2313-2351, 2007
%K c2005, c200x, c20xx, zz1009, stats, Dantzig selector, estimate, estimation,
   selection, curse, dimensionality, parameters, Terence Tao
%X "... observations y=X beta+z, where  beta in mathbf{R}^p is a param. vector
   of interest, X is a data matrix with possibly far fewer rows than columns,
   n ll p, and the z_i's are i.i.d. N(0,sigma^2). Is it possible to estimate
   beta reliably based on the noisy data y? ... introduce a new estimator - we
   call it the Dantzig selector - which is a soln to the  ell_1-regularization
   problem  [min_{ ~{ b eta} in mathbf{R}^p} | tilde{ beta} |_{ ell_1} quad
   s.t. quad |X^*r |_{ ell_{ infty}} leq(1+t^{-1}) sqrt{2 log p} cdot sigma, ]
   where r is the residual vector y-X tilde{beta} and t is a positive scalar.
   We show that if X obeys a uniform uncertainty principle (with unit-normed
   columns) & if the true param. vector beta is sufficiently sparse (which here
   roughly guarantees that the model is identifiable), then with very large
   probability, [ |hat{beta}-beta|_{ell_2}^2 le C^2 cdot2 log p cdot  Biggl(
    sigma^2+ sum_i min( beta_i^2, sigma^2) Biggr). ] ... result says that it is
   possible nearly to select the best subset of variables by solving a very
   simple convex program ... [can] recast as a convenient linear program (LP)."
   -- pdf@[<A HREF="http://arxiv.org/abs/math/0506081">arXiv</A>] (revised 3/'08),
      [<A HREF="http://dx.doi.org/10.1214/009053606000001523">doi:10.1214/009053606000001523</A>]['09].

%A A. Banerjee
%A I. S. Dhillon
%A J. Ghosh
%A S. Sra
%T Clustering on the unit hypersphere using von Mises - Fisher distributions
%J J. Machine Learning Res.
%V 6
%P 1345-1382
%M SEP
%D 2005
%K jrnl, eJrnl, JMLR, c2005, c200x, c20xx, zz1212, von Mises, vonMises, Fisher,
   vMF, distribution, hyper sphere, L2 norm, direction, directional, stats
%X "... proposes a generative mixture-model approach to clustering directional
   data based on the [vMF] dist., which arises naturally for data distributed
   on the unit hypersphere. ... derive & analyze two variants of the
   [EM] framework for estimating the mean & concentration params. of this
   mixture. Numerical est. of the conc. param. is non-trivial in high dim.
   since it involves functional inversion of ratios of Bessel fns.  We also
   formulate two clustering algs. corr. to the variants of EM that we derive.
   Our approach provides a theor. basis for the use of cosine similarity that
   has been widely employed ... & obtains the spherical kmeans alg. (kmeans
   with cosine similarity) as a special case of both variants. Empirical
   results on clustering of high-D. text & gene-expression data based on a
   mixture of vMF distns. show that the ability to est. the conc. param. for
   each vMF component, which is not present in existing approaches, yields
   superior results, esp. for difficult clustering tasks in high-D spaces."
   -- [<A HREF="http://jmlr.org/papers/v6/banerjee05a.html">jmlr</A>]['14],
      [<A HREF="http://dl.acm.org/citation.cfm?id=1088718">dl.acm</A>]['14],
      pdf@[<A HREF="http://www.lans.ece.utexas.edu/~abanerjee/papers/05/banerjee05a.pdf">uTexas</A>]['12].
   [Also search for: vonMises direction]  and
   [also search for: II soft assignment]  and
   [also search for: mixture modelling].

%A T. Roos
%A H. Wettig
%A P. Grunwald
%A P. Myllymaki
%A H. Tirri
%T On discriminative Bayesian network classifiers and logistic regression
%J Mach. Learning
%V 59
%N 3
%P 267-296
%M JUN
%D 2005
%K jrnl, JML, c2005, c200x, c20xx, zz0814, viaPJ, AI, II, naive Bayes, TAN,
   tree-augmented, logistic regression
%X "Discriminative learning of the parameters in the naive Bayes model is known
   to be equivalent to a logistic regression problem. Here we show that the same
   fact holds for much more general Bayesian network models, as long as the
   corr. n/w structure satisfies a certain graph-theoretic property. ...
   tree-augmented naive Bayes (TAN) as well as for mixed diagnostic-discrim.
   structures. Our results imply that for n/ws satisfying our property, the
   conditional likelihood cannot have local maxima so that the global maximum
   can be found by simple local optimization methods. We also show that if this
   property does not hold, then in general the cond. l.h. can have local,
   non-global maxima. ... empirical experiments with local optimization in a
   conditional naive Bayes model. ... a heuristic strategy for pruning the #
   of params. ... "  [via FB.]
   -- [<A HREF="http://dx.doi.org/10.1007/s10994-005-0471-6">doi:10.1007/s10994-005-0471-6</A>]['14].

%A K. Saha
%A S. Paul
%T Bias-corrected maximum likelihood estimator of the negative binomial
   dispersion parameter
%J Biometrics
%V 61
%N 1
%P 179-185
%M MAR
%D 2005
%K jrnl, c2005, c200x, c20xx, neg, negative binomial distribution, Poisson,
   count, counts, over dispersion, overdispersion, Fisher matrix
%X [<A HREF="http://dx.doi.org/10.1111/j.0006-341X.2005.030833.x">doi:10.1111/j.0006-341X.2005.030833.x</A>]['08]
   Pr(X=x|m,c) = G(x+c^-1)/(x!G(c^-1) (cm/(1+cm))^x (1/(1+cm))^(c^-1),
     x >= 0, (mean) m > 0, c > -1/m, G() Gamma fn.
     As the "dispersion" param  c -> 0, negBin(m,c) -> Poisson(m).
   Paper gives the Fisher info. matrix for n data (p.185):
     I_11 = n/(m(1+cm));        I_12 = I_21 = 0;
     I_22 = (n/c^4) sum[i=1...]{ i! (cb)^(i+1) / ((i+1)d_i) }
     where b = cm/(1+cm); d_i = Prod[j=0..i] (1+jc).

%A P. E. R. Dale
%A M. B. Dale
%A et al
%T Adaptive management of coastal wetlands: processes, conservation,
   restoration, impacts and assessment
%B Adaptive management of coastal wetlands: Processes, impacts and restoration
%E P.E.R. Dale
%D 2006 ? (in press)
%K chapter, wetland, impact, restore, c200x, c20xx
%X Ch.10

%A S. Wernicke
%T Efficient detection of network motifs
%J IEEE/ACM Trans. on Comp. Biol. and Bioinf.
%V 3
%N 4
%P 347-359
%M OCT
%D 2006
%K jrnl, TCBB, c2006, c200x, c20xx, RAND-ESU, RANDesu, fast, network motif,
   detection, discover, frequent subgraph, Fanmod
%X "Motifs in a given n/w are small connected subn/ws that occur in sig. higher
   freqs. than would be expected in random n/ws. ... we present a new alg. for
   n/w motif detection which overcomes .... [and] present an efficient new
   approach for est. the freq. of subgs. in random n/ws that ...  does not
   require the explicit generation of random n/ws. Experiments ... show our new
   algs. to be orders of mag. faster ... "
   -- [<A HREF="http://dx.doi.org/10.1109/TCBB.2006.51">doi:10.1109/TCBB.2006.51</A>]['10],
   pdf@fanmod@[<A HREF="http://theinf1.informatik.uni-jena.de/~wernicke/motifs/index.html">uni-jena</A>]['10].
      (Also see, W.W. & Rasche,
                'FANMOD: a tool for fast network motif detection',
                J. Bioinf., 22(9) pp.1125-1153, online Feb., 2006,
       [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl038">www</A>]['15],
       and motif@[<A HREF="http://en.wikipedia.org/wiki/Network_motif">wikip</A>]['15].)
   [Also search for: network motif] and
   [also search for: enumerate subgraph graph].

%A R. Sharda
%A D. Delen
%T Predicting box-office success of motion pictures with neural networks
%J Expert Systems with Applications
%V 30
%N 2
%P 243-254
%M FEB
%D 2006
%K jrnl, c2006, c200x, c20xx, movie, movies, film, films, flop, blockbuster,
   block-buster, hit, hits, receipts, artificial neural network, ANN, NN,
   stats, zz1205, picture, financial, popular
%X "Predicting box-office receipts of a particular motion picture ...
   NNs in predicting the financial performance of a m. at the boxoffice
   before its theatrical release is explored. ...forecasting problem is
   converted into a classification problem - rather than forecasting the pt est.
   of box-office receipts, a m. based on its box-office receipts in 1 of 9
   categories is classified, ranging from a 'flop' to a 'blockbuster'. ..."
   "834 movies '98 to '02; inputs...
   rating (5xBool), competition (h/m/l, 3xBool), starValue (h/m/l, 3xBool),
   genre (10xBool, 1+), effects (h/m/l, 3xBool), sequel?, #screens (int)."
   -- [<A HREF="http://dx.doi.org/10.1016/j.eswa.2005.07.018">doi:10.1016/j.eswa.2005.07.018</A>][online Aug, '05]
   (C&R trees also seemed to do quite well.)

%A S. Brody
%T Blood pressure reactivity to stress is better for people who recently had
   penile-vaginal intercourse than for people who had other or no sexual
   activity
%J Biological Psychology
%V 71
%N 2
%P 214-222
%M FEB
%D 2006
%K jrnl, sex, c2006, c200x, c20xx, zz0206, stats, masturbation, PVI, health,
   medicine
%X "... For a fortnight, 24 women and 22 men used daily diaries to record PVI,
   masturbation, & partnered sexual behavior in the absence of PVI. Persons who
   reported PVI (but no other sexual activities) had better stress response
   (less reactivity &/or lower baseline levels) than persons reporting other or
   no sexual behaviors. Persons who only masturbated or had partnered sex
   without PVI had 14 mmHg more systolic BP reactivity than those who had PVI
   but not the other behaviors...."
   -- [<A HREF="http://dx.doi.org/10.1016/j.biopsycho.2005.03.005">doi:10.1016/j.biopsycho.2005.03.005</A>]['06] auth@U.Paisley, Scotland.

%A K. B. Korb
%A E. Nyberg
%T The power of intervention
%J Minds and Machines
%P ?-?
%D 2006 ?
%K cause, effect, causal model, c2006, c200x, c20xx
%X auth1 @ mon@sh('06)

%A A. P. Blaisdell
%A K. Sawa
%A K. J. Leising
%A M. R. Waldmann
%T Causal reasoning in rats
%J Science
%V 311
%N 5763
%P 1020-1022
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0206, rat, rodent, cause, effect, model,
   models, cognition, animal, intervention, interventions, network, net
%X "... Empirical research with nonhuman primates appears to support the view
   that causal reasoning is a key cog. faculty that divides h. from animals.
   The claim is that animals approx. causal learning using assoc. processes.
   The present results cast doubt on that conclusion. Rats made causal
   inferences in a basic task that taps into core features of causal reasoning
   without requiring complex physical knowledge. They derived predictions of
   the outcomes of interventions after passive observational learning of
   different kinds of causal models. These competencies cannot be explained by
   current assoc. theories but are consistent with causal Bayes net theories."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1121872">10.1126/science.1121872</A>]['06].

%A B. Zou
%A X. Ma
%A B. Kemme
%A G. Newton
%A D. Precup
%T Data mining using relational database management systems
%J Proc. PAKDD 10
%I SpringerVerlag
%P 657-667
%D 2006
%K conf, PAKDD10, c2006, c200x, c20xx, DBMS, AI, II, zz0506, Weka, WekaDB
%X "... packages are often based on main-memory data structures, limiting the
   amount of data they can handle. [here] we use a relational DB as secondary
   storage ... to eliminate this limitation. Unlike existing approaches, which
   often focus on optimizing a single alg. to work with a DB backend, we
   propose a general approach, which provides a database interface for several
   algorithms at once. We have taken ... Weka, & added a relational storage
   manager as back-tier to the system. The extension is transparent to the algs.
   implemented in Weka, since it is hidden behind Weka's standard main-memory
   data structure interface. Furthermore, some general mining tasks are
   transfered into the database system..."   -- isbn:3540332065.
   -- [<A HREF="http://dx.doi.org/10.1007/11731139_75">doi:10.1007/11731139_75</A>]['06]
      [<A HREF="http://cogprints.org/4851/">@cogprints</A>]['06] via C.T.

%A Y. Guo
%A D. Schuurmans
%T Convex structure learning for Bayesian networks: Polynomial feature
   selection and approximate ordering
%J UAI
%D 2006
%K confPoster, conf, UAI, UAI06, UAI2006, c2006, c200x, c20xx, zz0706, network,
   continuous convex relaxation, ualberta, Bnet
%X "... regularized estimation in an exponential family representation.
   ... problem of optimizing the variable order for a given set of features.
   ... optimal "soft" ordering in polynomial time. ... do not perform a
   discrete search over DAGs nor over variable orders, but instead solve a
   continuous convex relaxation ..."    (via CT)
   -- [<A HREF="http://www.cs.ualberta.ca/~yuhong/research/papers/bnstructgs.pdf">pdf</A>]['06].

%A L. J. Fitzgibbon
%T On sampling stationary autoregressive model parameters uniformly in r^2 value
%J J. of Statistics and Probability Letters
%V 76
%N 4
%P 349-352
%M FEB
%D 2006
%K jrnl, c2006, c200x, c20xx, time series analysis, parameter, log Gamma,
   sample, autocorrelation, stats, leighf, LJFitzgibbon
%X "... describes a method of sampling stationary autoregressive models so that
   they are uniformly distributed in r^2 value. A log-Gamma distribution, whose
   product density is uniformly distributed over [0,1], is used to sample
   partial autocorrelation parameters and obtain the desired result. This
   method can be used for the empirical evaluation of model selection and
   parameter estimation criteria."
   -- [<A HREF="http://dx.doi.org/10.1016/j.spl.2005.08.028">doi:10.1016/j.spl.2005.08.028</A>]['06].

%A A. P. Reynolds
%A G. Richards
%A B. de la Iglesia
%A V. J. Rayward-Smith
%T Clustering rules: A comparison of partitioning and hierarchical clustering
   algorithms
%J J. of Math. Modelling and Algs.
%V 5
%N 4
%P 475-504
%D 2006
%K jrnl, c2006, c200x, c20xx, cluster, classificaction, rule, uniEA, UEA
%X [<A HREF="http://www.cmp.uea.ac.uk/people/showprofile.jsp?id=vjrs">auth4@UEA</A>]['06]

%A M. E. J. Newman
%T Power laws, Pareto distributions and Zipf's law
%J arXiv
%P 28pp
%M MAY
%D 2006
%O Contemporary Physics, 46, pp.323-351, 2005
%K TR, c2006, c200x, c20xx, zz0716, intro, statistics, stats,
   probability distribution, model, inverse, power law, laws,
   Pareto, Zipf, Zipf's law, viaAK
%X "When the prob. of measuring a particular value of some quantity varies
   inversely as a power of that value, the quantity is said to follow a power
   law, also known variously as Zipf's law or the Pareto distn. Power laws
   appear widely in physics, biology, earth & planetary sciences, economics &
   finance, computer science, demography & the social sciences. For instance,
   the distns of the sizes of cities, earthquakes, solar flares, moon craters,
   wars & people's personal fortunes all appear to follow power laws. The
   origin of power-law behaviour has been a topic of debate in the scientific
   community for more than a century. Here we review some of the empirical
   evidence for the existence of power-law forms & the theories proposed to
   explain them."  [ver.1 Dec '04;  ver.3 May '06.]
   -- [<A HREF="https://arxiv.org/abs/cond-mat/0412004">arXiv</A>]['16].

%A C. D. Aliprantis
%A D. Harris
%A R. Tourky
%T Continuous piecewise linear functions
%J Macroeconomic Dynamics
%V 10
%P 77-99
%D 2006
%K jrnl, c2006, c200x, c20xx, function, line, curve, Riesz space, spaces
%X "... fn space of cts piecewise linear fns in the space of cts fns on the
   m-dimensional Euclidean space. [and] special case of 1D cts piecewise linear
   fns. The study is based on the theory of Riesz spaces that has many applicns
   in economics. The work also provides the math. bg to its sister paper
   Aliprantis, Harris, and Tourky (2006), in which we est. multivariate
   cts piecewise linear regressions by means of Riesz ests, that is, by
   estimators of the the Boolean form ??? where X=(X1,X2,...,Xm) is some random
   vector, {E[j]} j in J is a finite family of finite sets."
   -- [<A HREF="http://dx.doi.org/10.1017/S1365100506050103">doi:10.1017/S1365100506050103</A>]['07], auth1@purdue, auth2@melbu

%A Chu-Hsiung Lin
%A Shan-Shan Shen
%T Can the student-t distribution provide accurate value at risk?
%J J. Risk Finance
%V 7
%N 3
%P 292-300
%M JUN
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0707, market, stocks, shares, securities,
   financial risks, value at risk, VaR, Tdistribution
%X  "... investigate how effectively the value at risk (VaR) estimated using
   the student-t distribution captures the market risk. ... main finding [is]
   using the student-t distribution for estimating VaR can improve the VaR
   est. & offer accurate VaR ests. particularly when tail index technique is
   used to determine the degrees of freedom & the confidence level >98.5%. ..."
   -- [<A HREF="http://dx.doi.org/10.1108/15265940610664960">doi:10.1108/15265940610664960</A>]['07]

%A T. Horvath
%A J. Ramon
%A S. Wrobel
%T Frequent subgraph mining in outerplanar graphs
%J Proc. 12th ACM SIGKDD Int. Conf. on Knowledge Discovery and Data Mining
%P 197-206
%D 2006
%K conf, c2006, c200x, c20xx, ACM, dTenuous, tenuous outerplanar graph, graphs,
   bridge, block, frequent subgraph, NCI molecular graph dataset
%X "... frequent pattern discovery in large databases of graph .... While the
   freq. connected subgraph mining problem for tree datasets can be solved in
   incremental polynomial time, it becomes intractable for arbitrary graph DBs.
   Existing approaches have therefore resorted to various heuristic strategies
   & restrictions of the search space, but have not identified a practically
   relevant tractable graph class beyond trees. ... we define the class of so
   called tenuous outerplanar graphs, a strict generalization of trees, develop
   a frequent subgraph mining alg. for tenuous outerplanar graphs that works in
   incremental polynomial time, & evaluate the alg. empirically on the NCI
   molecular graph dataset."
   p.38: "block == biconnected component"
   p.40: "a d-tenuous outerplanar g., G, is an opg s.t. no block of G has > d
     diagonals. ... 94.3% of 250,251  NCI molecules are outerplanar ...
     almost all have <= 5 diags / block ... one cmpd has a block with 11 diags"
   pdf [<A HREF="http://doi.acm.org/10.1145/1150402.1150427">doi:10.1145/1150402.1150427</A>]['08],
   and [<A HREF="http://www.inf.uni-konstanz.de/mlg2006/04.pdf">pdf@uni-konstanz</A>]['08].
   (NCI data set @ [<A HREF="http://cactus.nci.nih.gov/">nci.nih.gov</A>]['08].)

%A D. Chakrabarti
%A C. Faloutsos
%T Graph mining: Laws, generators, and algorithms
%J ACM Computing Surveys
%V 38
%N 1
%P ?-?
%D 2006
%K jrnl, c2006, c200x, c20xx, survey, intro, graph, network, data mining, AI,
   web, www, frequent subgraph, pattern, law, generator, generate
%X "How does the Web look? How could we tell an abnormal social network ...
   data ... cast as a graph; e.gs. range from computer n/wks to sociology to
   biology ...  A lot of these questions boil down to the following: 'How can
   we generate synthetic but realistic graphs?' ... must first understand what
   patterns are common in real-world graphs ...  integration of pts of view
   from physics, math., sociology, and C.Sci.. ..."
   -- [<A HREF="http://doi.acm.org/10.1145/1132952.1132954">doi:10.1145/1132952.1132954</A>]['10].
   [Also search for: complexity graph].

%A C. R. Twardy
%A A. E. Nicholson
%A K. B. Korb
%A J. McNeil
%T Epidemiological data mining of cardiovascular Bayesian networks
%J Electronic J. of Health Informatics (eJHI)
%V 1
%N 1
%P e3
%D 2006
%K jrnl, eJrnl, c2006, c200x, c20xx, annn, KBKorb, network, heart, health,
   medical, edidemiology, stats, Bnet
%X "Although BNs have been used successfully for many medical diagnosis
   problems, there have been few applications to epidemiological data where DM
   methods play a sig. role. ... we look at the application of BNs to
   epidemiological data, specifically assessment of risk for coronary heart
   disease (CHD). We build the BNs: (1) by knowledge eng. BNs from 2
   epidemiological models of CHD in the literature; (2) by applying a causal BN
   learner. We evaluate these BNs using cross-validation. We compared
   performance in predicting CHD events over 10y., measuring area under the ROC
   curve & Bayesian information reward. The knowledge engineered BNs performed
   as well as logistic regression, while being easier to interpret. These BNs
   will serve as the baseline in future efforts to extend BN technology to
   better handle epidemiological data, specifically to model CHD."
   -- [<A HREF="http://www.ejhi.net/ojs/index.php/ejhi/article/view/e1%281%29%3A3">abs@jrnl</A>]['07].

%A C. D. Aliprantis
%A D. Harris
%A R. Tourkya
%T Riesz estimators
%J J. Econometrics
%V 136
%N 2
%P 431-456
%M FEB
%D 2007
%K jrnl, c2007, c200x, c20xx, additive, estimator, estimate, RIESZVAR,
   multivariate continuous piecewise linear regression, piece wise, line,
   fit, fitting, approximation
%X "We consider properties of estimators that can be written as vector lattice
   (Riesz space) operations. Using techniques widely used in economic theory &
   functional analysis, we study the approximation properties of these ests
   paying special attention to additive models. We also provide 2 algs. RIESZVAR
   (i-ii) for the consistent parametric est. of cts multivariate piecewise
   linear fns."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jeconom.2005.11.005">doi:10.1016/j.jeconom.2005.11.005</A>]['07]

%A M. C. Jones
%T Connecting distributions with power tails on the real line, the half line
   and the interval
%J Int. Statistical Rev.
%V 75
%N 1
%P 58-69
%M MAR
%D 2007
%K jrnl, c2007, c200x, c20xx, zz1019, continuous probability distribution,
   symmetry, heavy, tail, fat, tails, transformation, stats
%X "Univariate continuous distributions have three possible types of support
   exemplified by: the whole real line, R, the semi-finite interval, R+, the
   bounded interval (0,1). This paper is about connecting distributions on these
   supports via 'natural' simple transformations in such a way that tail
   properties are preserved. In particular ... focussed on the case where the
   tails (at +/-inf) of densities are heavy, decreasing as a (-ve) power of
   their argument; connections are then especially elegant. At boundaries (0 &
   1), densities behave conformably with a directly related dependence on power
   of argument. The transformation from (0,1) to R is the std odds transn. The
   transn from R+ to R is a novel identity-minus-reciprocal transn. The main
   points of contact with existing distns are with the transfns involved in the
   Birnbaum-Saunders distn &, especially, the Johnson family of distns.
   Relationships between various other existing & newly proposed distns are
   explored."
   -- [<A HREF="https://doi.org/10.1111/j.1751-5823.2007.00006.x">doi:10.1111/j.1751-5823.2007.00006.x</A>]['19].
   [Also search for: probability distribution symmetry].

%A J. R. Hershey
%A P. A. Olsen
%T Approximating the Kullback Leibler divergence between Gaussian mixture models
%J Int. Conf. on Acoustics, Speech and Signal Processing
%I IEEE
%N 4
%P IV 317-320
%M APR
%D 2007
%K conf, ICASS, c2007, c200x, c20xx, zz0115, mixture model, Gaussian, normal,
   distribution, Kullback Leibler, KL, distance, divergence, stats
%X "... The KL divergence between two Gaussian mixture models (GMMs) is
   frequently needed in the fields of speech & image recognition. Unfortunately
   the KL d. between two GMMs is not analytically tractable, nor does any
   efficient comp.alg. exist. Some techniques cope with this problem by
   replacing the KL d. with other fns that can be computed efficiently. We
   introduce two new methods, the variational approximation & the variational
   upper bound, & compare them to existing methods. We discuss seven different
   techniques in total & weigh the benefits of each one against the others. To
   conclude we eval. the performance of each one through numerical experiments."
   -- [<A HREF="http://dx.doi.org/10.1109/ICASSP.2007.366913">doi:10.1109/ICASSP.2007.366913</A>]['14].
   [Also search for: mixture model].

%A M. Cokol
%A I. Iossifov
%A R. Rodriguez-Esteban
%A A. Rzhetsky
%T How many scientific papers should be retracted?
%J EMBO Rep.
%V 8
%N 5
%P 422-423
%M MAY
%D 2007
%K c2007, c200x, c20xx, paper, publishing, ethics, retraction, retracted,
   stats, model, scientific literature, impact factor, IF, PubMed, zz0507
%X "...not all articles that should be retracted are retracted. This is because
   the quality of a scientific article depends, among other things, on the
   effort & time invested in quality control. ... PubMed provides us with a
   'paleontological' record of articles published in 4,348 journals with a
   known impact factor (IF). Of the 9,398,715 articles published between 1950 &
   2004, 596 were retracted. This wave of retraction hits high-impact journals
   significantly harder than lower-impact journals (Fig 1A), suggesting that
   high-impact journals are either more prone to publishing flawed manuscripts
   or scrutinized much more rigorously than low-impact journals. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/sj.embor.7400970">doi:10.1038/sj.embor.7400970</A>]['07]
   Also see [<A HREF="http://dx.doi.org/10.1038/447236b">doi:10.1038/447236b</A>]['07].

%A R. Nevin
%T Understanding international crime trends: The legacy of preschool
   lead exposure
%J Env. Res.
%V 104
%N 3
%P 315-336
%M JUL
%D 2007
%K jrnl, c2007, c200x, c20xx, zz0414, tetraethyl lead, crime, leaded, petrol,
   pollution, unleaded, ULP, trend, crimes, stats, human behaviour, IQ
%X "... very strong assoc. between preschool blood lead & subsequent crime rate
   trends over several decades in the USA, Britain, Canada, France, Australia,
   Finland, Italy, West Germany, & New Zealand. ... characterized by best-fit
   lags (highest R^2 & t-value for blood lead) consistent with neurobehavioral
   damage in the first year of life & the peak age of offending for index crime,
   burglary, & violent crime. The impact of blood lead is also evident in
   age-specific arrest & incarceration trends. Regression analysis of average
   1985-1994 murder rates across USA cities suggests that murder could be
   especially assoc. with more severe cases of childhood lead poisoning."
   -- [<A HREF="http://dx.doi.org/10.1016/j.envres.2007.02.008">doi:10.1016/j.envres.2007.02.008</A>]['14].
   Lag of about 20 years.
   (Also see [<A HREF="http://www.bbc.com/news/magazine-27067615">bbc</A>]['20/4/2014].)

%A S. Shah
%A B. D. Noble
%T A study of e-mail patterns
%J SPE
%V 37
%N 14
%P 1515-1538
%D 2007
%K jrnl, SPE, c2007, c200x, c20xx, mail, email, stats, statistics, zz1007,
   pattern, postmark, benchmark
%X pdf: [<A HREF="http://dx.doi.org/10.1002/spe.816">doi:10.1002/spe.816</A>]['07].

%A R. Bell
%A Y. Koren
%A C. Volinsky
%T Chasing $1,000,000. How we won the Netflix progress prize
%J Statistical Computing and Graphics
%I ASA
%V 18
%N 2
%P 4-12
%M DEC
%D 2007
%K c2007, c200x, c20xx, zz0408, recommender system, systems, netflix, netflicks,
   stats, movie, movies, rate, rating, ratings, ranking, competition, contest,
   collaborative filtering, filter, $1000000, million dollar, dollars, NSVD,
   KorBell, BellKor, sparse data, topic, topics
%X NB. the *progress* prize, not the $1M big one, but close. (@ at and t labs.)
   "... neighborhood aware factorization ... latent factors ...
   nearest neighbour interpolation ... regularization ..."
   -- [<A HREF="http://stat-computing.org/newsletter/v182.pdf">pdf</A>]['08],
      [<A HREF="http://www.netflixprize.com/">.netflixprize.com</A>]['08].

%A P. Kontkanen
%A P. Myllymaki
%T A linear-time algorithm for computing the multinomial stochastic complexity
%J IPL
%V 103
%N 6
%P 227-233
%D 2007
%K jrnl, IPL, c2007, c200x, c20xx, SC, normalised, normalized, NML, MDL,
   minimum, length, likelihood
%X "... The codelength of a given sample of data under the NML distribution is
   called the stochastic complexity, which is the basis for MDL model class
   selection. Unfortunately, in the case of discrete data, straightforward
   computation of the SC requires exp. time with respect to the sample size,
   since the defn involves an exponential sum over all the poss. data samples of
   a fixed size. As a main contribution of this paper, we derive an elegant
   recursion formula which allows efficient computation of the SC in the case of
   n observations of a single multinomial random var. with K values. The time
   complexity of the new method is O(n+K) as opposed to O(n log n log K) [prev]"
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2007.04.003">doi:10.1016/j.ipl.2007.04.003</A>]['08].
   [Also search for: minimum length encoding].

%A M. Greenacre
%T Correspondence Analysis in Practice
%I ChapmanHall
%P 296
%D 2007
%K book, text, c2007, c200x, c20xx, zz0916, stats, correspondence analysis,
   ADE4, orngCA, SVD, detrended, Hirschfeld, Benzecri, dimensionality,
   reduction, embedding, viaPfh
%X 2nd ed 2007; hb us$90; uk us isbn:1584886161, uk us isbn13:978-1584886167.
   "... shows how the versatile method of correspondence analysis (CA) can be
   used for data visualization in a wide variety of situations. ..."
   (Also see "... conceptually similar to principal component analysis [PCA],
      but applies to categorical rather than continuous data ... creates
      orthogonal components ..."
   -- CA@[<A HREF="https://en.wikipedia.org/wiki/Correspondence_analysis">wikip</A>].)

%A D. Salomon
%T Variable-length Codes for Data Compression
%I Springer
%P 196
%D 2007
%K book, text, c2007, c200x, c20xx, zz1118, integer, code, codes, intCodes,
   universal, variable length, VLC, robust, data compression
%X pb us$109; uk us isbn:1846289580; uk us isbn13:9781846289590.
   "Most data compression methods that are based on variable-length codes
   employ the Huffman or Golomb codes. However, there are a large number of
   less-known codes that have useful properties - such as those containing
   certain bit patterns, or those that are robust - and these can be useful.
   This book brings this large set of codes ..."
   (Also see,
   [<A HREF="https://www.springer.com/gp/book/9781846289583">Spr'ng'r</A>]['18],
   [<A HREF="http://www.davidsalomon.name/VLCadvertis/VLCad.html">VLC_ad</A>] at
   [<A HREF="http://www.davidsalomon.name/">davidsalomon.name</A>]['18].)
   [Also search for: universal integer code].

%A G. S. Mudholkar
%A H. Wang
%T IG-symmetry and R-symmetry: Interrelations and applications to the
   inverse Gaussian theory
%J J. of Stat. Planning and Inference
%V 137
%N 11
%P 3655-3671
%M NOV
%D 2007
%K jrnl, c2007, c200x, c20xx, zz1019, stats, inverse Gaussian, Wald, IG,
   symmetry, IGsymmetry, IGsymmetric, analogy, RRIG, Rsymmetry, Rsymmetric,
   probability distribution, symmetric, Tweedie
%X "... [here] first elaborate the importance of the IG distn and of the G-IG
   analogies. Then we consider the IG-related root-reciprocal IG (RRIG) distn
   & introduce a physically transparent, conceptually clear notion of reciprocal
   symmetry (R-symmetry) and use it to explain the IG-symmetry. We study the
   moments & mixture properties of the R-symmetric distns & the relationship of
   R-symmetry with IG-symmetry & note that RRIG distn provides a link, in
   addition to Tweedie's Laplace transform link, between the Gaussian & inverse
   Gaussian distributions. We also give a structural characterization of the
   unimodal R-symmetric distns. This work further expands the long list of G-IG
   analogies. Several applications including product convolution, monotonicity
   of power fns, peakedness & monotone limit thms of R-symmetry are outlined."
   -- [<A HREF="https://doi.org/10.1016/j.jspi.2007.03.041">doi:10.1016/j.jspi.2007.03.041</A>]['19].
   [Also search for: probability distribution symmetry].
   (Also see,
   "... [IG]name can be misleading: it is an 'inverse' only in that, while the
   G. describes a Brownian motion's level at a fixed time, the inverse G
   describes the distn of the time a B.motion with +ve drift takes to reach a
   fixed +ve level.  ..."
   -- inv_G@[<A HREF="https://en.wikipedia.org/wiki/Inverse_Gaussian_distribution">wikip</A>]['19].)

%A K. Baskerville
%A P. Grassberger
%A M. Paczuski
%T Graph animals, subgraph sampling and motif search in large networks
%J arXiv
%D 2007
%K TR, MolBio, c2007, c200x, c20xx, sample, sampling, subgraph, graphs, network,
   networks, interaction, uniCalgary
%X "... generalize a sampling alg. for lattice animals (connected clusters on a
   regular lattice) to a Monte Carlo alg. for `graph animals', i.e. connected
   subgraphs in arbitrary n/ws ... allows subgraphs with up to 10 or more
   nodes to be sampled with very high stats., from arbitrarily large n/ws.  ...
   results for 2 protein interaction n/ws obtained using the TAP high throughput
   method: one of Escherichia coli with 230 nodes & 695 links, & one for yeast
   (...) with roughly 10 x more nodes and links. ... most connected subgraphs
   are strong motifs (Z-scores >10) or anti-motifs (Z-scores < -10) when the
   null model is the ensemble of n/ws with fixed degree seq.. ...  present Zipf
   plots of counts versus rank. They show broad distributions that are not
   power laws [v.] to the case when disconnected subgs. are included."
   -- [<A HREF="http://arxiv.org/abs/q-bio/0702029">@arxiv.org</A>]['08],
      [<A HREF="http://www.ucalgary.ca/complexity/people/faculty/peter">auth2</A>]['08].
   [Also search for: subgraph sampling].

%A D. N. McCloskey
%A S. Ziliak
%T The Cult of Statistical Significance: How the Standard Error Costs Us Jobs,
   Justice, and Lives
%I U. MichiganPress
%P 352
%M FEB
%D 2008
%K book, text, stats, c2008, c200x, c20xx, frequentist, Bayesian, foundations,
   statistical, significance test, tests, confidence interval, intervals,
   likelihood, error, accept, reject, Pvalue, controversial, statistics, stats,
   science, research
%X 1st ed 2008; pb us$23; uk us isbn:0472050079; uk us isbn13:978-0472050079.
   "... show how economists - and other scientists - suffer from a mass delusion
   about statistical analysis. The quest for statistical significance that
   pervades sci. today is a deeply flawed subst. for thoughtful analysis ..."

%A J. Friedman
%A T. Hastie
%A R. Tibshirani
%T Sparse inverse covariance estimation with the graphical lasso
%J J. Biostatistics
%V 9
%N 3
%P 432-441
%D 2008
%K jrnl, c2008, c200x, c20xx, graphical, linear, model, models, stats, lassoo,
   lasso, lasoo, laso, matrix, Gaussian, L1, cell, signaling, signalling, MolBio
%X "... est. sparse graphs by a lasso penalty applied to the inverse covariance
   matrix.  Using a coordinate descent proc. for the lasso, we develop a simple
   alg. - the graphical lasso - that is remarkably fast: It solves a 1000-node
   problem (~500,000 params.) in at most a minute & is 30-4000 x faster than
   competing methods. It also provides a conceptual link between the exact
   problem & the approx. suggested by Meinshausen & Buhlmann ('06). We
   illustrate the method on some cell-signaling data from proteomics." --via DS.
   pdf [<A HREF="http://dx.doi.org/10.1093/biostatistics/kxm045">doi:10.1093/biostatistics/kxm045</A>]['08], and
   TR: [<A HREF="www-stat.stanford.edu/~tibs/ftp/graph.pdf">@stanf</A>]['08].
   [Also search for: lasoo stats].
   (Also see lasoo@[<A HREF="https://en.wikipedia.org/wiki/Lasso_(statistics)">wikip</A>]['19].)

%A S. T. Karamouzis
%A D. Wood Harper
%T An artificial intelligence system suggests arbitrariness of death penalty
%J Int. J. Law and Information
%I OUP
%V 16
%N 1
%P 1-7
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0708, ANN, NN, law, laws, legal, death penalty,
   execution, prisoner, death row, capital punishment, crime, crimes, criminal,
   justice, US, USA, United States
%X "The arguments against the death penalty in the US have centered on due
   process & fairness. Since the death penalty is so rarely rendered &
   subsequently applied, it appears on the surface to be arbitrary. Considering
   the potential utility of determining whether or not a death row inmate is
   actually executed along with the promising behavior of ANNs as classifiers
   led us into the development, training, & testing of an ANN as a tool for
   predicting death penalty outcomes. For our ANN we reconstructed the profiles
   of 1,366 death row inmates by utilizing variables that are independent of the
   substantive characteristics of the crime for which they have been convicted.
   The ANN's successful performance in predicting executions has serious
   implications concerning the fairness of the justice system."
   -- [<A HREF="http://dx.doi.org/10.1093/ijlit/eam006">doi:10.1093/ijlit/eam006</A>]['08].
      [<A HREF="http://academic.regis.edu/skaramou/projects/dp/index.html">auth1</A>]['08].
   (Also see Art. Intell. & Applics., pp.867-870, ACTA Press, '05.)
      [<A HREF="http://www.icpsr.umich.edu/cocoon/MDRC/XDLY/03667.xml">data?</A>]['08].

%A M. S. Joshi
%T C++ Design Patterns and Derivatives Pricing
%I CUP
%D 2008
%K book, text, c2008, c200x, c20xx, zz0308, finance, financial, economics,
   pattern, product, cc
%X Offering practical steps for implementing pricing models for complex
   financial products, this book will transform your understanding of how
   to use C++. ... extra chapters on interfacing C++ with EXCEL, ...
   pb, stg30, au$95, 28/5/2008, uk us isbn:0521721628; isbn13:9780521721622.

%A M. desJardins
%A P. Rathod
%A L. Getoor
%T Learning structured Bayesian networks: Combining abstraction hierarchies and
   tree-structured conditional probability tables
%J Computational Intelligence
%V 24
%N 1
%P 1-22
%M FEB
%D 2008
%K jrnl, c2008, c200x, c20xx, network, Bnet, CPT, CPTs, TABS, des Jardins,
   local structure
%X "... introduce Tree-Abstraction-Based Search (TABS), an approach for
   learning a data distribution by inducing the graph structure & parameters of
   a BN from training data. TABS combines tree structure & attribute-value
   hierarchies to compactly represent conditional probability tables. ..."
   -- [<A HREF="http://dx.doi.org/10.1111/j.1467-8640.2007.00320.x">doi:10.1111/j.1467-8640.2007.00320.x</A>]['08].
   [Also search for: Bnet MML], and/or [also search for: CaMML].

%A J. Vallverdu
%T The false dilemma: Bayesian vs. frequentist
%J Electronic J. for Philosophy (Philosophy of Sci.)
%I Elogos
%P ?-?
%M APR
%D 2008
%K jrnl, eJrnl, E logos, c2008, c200x, c20xx, stats, statistics, school,
   science, II, foundations, frequentist, classical, Bayesian, Bayesianism,
   approaches, controversial, significance test, Pvalue, confidence interval,
   priors, history
%X "There are two main opposing schools of statistical reasoning, frequentist
   & Bayesian approaches. Until recent days, the freq. or classical approach has
   dominated the sci.research, but B. has reappeared with a strong impulse that
   is starting to change the situation. Recently the controversy about the
   primacy of one of the two approaches seems to be unfinished at a
   philosophical level, but sci. practices are giving an increasingly important
   posn to the B.approach. This paper eludes philosophical debate to focus on
   the pragmatic point of view of scientists' day-to-day practices, in which
   B.methodology is v.useful. Several facts & operational values are described
   as the core-set for understanding the change." (issn 1211-0442, 30.4.2008).
   -- pdf@[<A HREF="http://e-logos.vse.cz/index.php?article=196">J.P.</A>]['12].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A P. Spector
%T Data Manipulation with R
%I Springer
%P 154
%D 2008
%K book, text, c2008, c200x, c20xx, R, RR, stats, S, Splus
%X "... the use of databases in R is covered in detail, along with methods for
   extracting data from spreadsheets and datasets created by other programs.
   Character manipulation, while sometimes overlooked within R, is also covered
   in detail, allowing problems that are traditionally solved by scripting
   languages to be carried out entirely within R. For users with experience in
   other languages, guidelines for the effective use of programming constructs
   like loops are provided ..."   (Phil Spector!-)
   pb, us$44, uk us isbn:0387747303; uk us isbn13:978-0387747309.

%A V. Ziegler
%T Approximation algorithms for restricted Bayesian network structures
%J IPL
%V 108
%N 2
%P 60-63
%M SEP
%D 2008
%K jrnl, IPL, c2008, c200x, c20xx, zz0908, BN, networks, structure, algorithm,
   bounded in degree, inDegree
%X "Bayesian network structures with a maximum in-degree of k can be
   approx. wrt a +ve scoring metric up to an factor of 1/k."   [11 refs].
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2008.03.015">doi:10.1016/j.ipl.2008.03.015</A>]['08].

%A J. F. Olsen
%A K. M. Carley
%T Summarization and information loss in network analysis
%J Workshop on Link Analysis, Counter-Terrorism and Security (LACTS)
%D 2008
%K wShop, LACTS, LACTS08, c2008, c200x, c20xx, network, graph, summarization,
   summary
%X "... mathematical framework within which to consider the problem of network
   summarization. ... concept of information entropy is applied in the context
   of n/w summarization. Finally, an O(-E-) alg. ... for computing info.entropy
   in the case of simple deterministic network summarizations."  [4 refs].
   -- [<A HREF="http://research.cs.queensu.ca/~skill/olson.pdf">pds@queensu.ca</A>][9/'08].
   Auths @ Comp. Sci., CMU.

%A S. Trepetin
%T Privacy-preserving string comparisons in record linkage systems: A review
%J Information Security J.
%V 17
%N 5-6
%P 253-266
%M SEP
%D 2008
%K jrnl, c2008, c200x, c20xx, record linkage, data, intro, survey, privacy,
   preserving, approximate match, matching, errors, comparison, anonymized,
   string, strings
%X "... link records whose identifiers are only "close" to each other, not
   equal, because of typical recording errors. ... reviews existing proposals
   for how such anonymized string comparisons might be accomplished, but
   demos. that existing methods have various operational deficiencies. ..."
   -- [<A HREF="http://dx.doi.org/10.1080/19393550802492503">doi:10.1080/19393550802492503</A>]['10],  issn:1939-3555,  [14 refs].
   [Also search for: record linkage data].

%A S. Baxendale
%A J. Fisher
%T Moonstruck? The effect of the lunar cycle on seizures
%J Epilepsy and Behavior
%V 13
%N 3
%P 549-550
%M OCT
%D 2008
%K jrnl, c2008, c200x, c20xx, zz1213, fits, epileptic, seizure, full moon,
   lunar cycle, cyclic, periodic, stats, model, risk, risks, myth, myths
%X "Recent reports on the effects of the lunar cycle on seizure occurrence have
   yielded mixed results. If the moon phase is influential, we hypothesized that
   this would be due to the moon's contribution to nocturnal illumination,
   rather than its waxing or waning state, & that sign.correlations would not be
   apparent if local cloud cover were controlled for. We found a sig. -ve
   correlation between the mean # of seizures & the fraction of the moon
   illuminated by the sun (rho=-0.09, P < 0.05) in 1571 seizures recorded in a
   dedicated epilepsy inpatient unit over 341 days. This corr. disappeared when
   we controlled for the local clarity of the night sky, suggesting that it is
   the brightness of the night & the contribution the moon phase makes to
   nocturnal luminance, rather than the moon phase per se, that may influence
   the occurrence of epileptic seizures."
   -- [<A HREF="http://dx.doi.org/10.1016/j.yebeh.2008.06.009">doi:10.1016/j.yebeh.2008.06.009</A>]['13],
      [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/18602495">pubm'd</A>]['13].
   [Also search for: lunar stats].

%A R. Viana
%T Quick encoding of plane graphs in log2(14)-bits per edge
%J IPL
%V 108
%N 3
%P 150-154
%M OCT
%D 2008
%K IPL, jrnl, c2008, c200x, c20xx, compress, compression, compressed, encode,
   succinct, plane, planar, graph
%X [NB. a "plane graph" is a (planar) graph actually drawn in a (rubber) plane.]
   "... technique to encode any unlabeled & connected plane graph of E edges in
   E log2(14)-bits is proposed. Both loops & multiple edges are allowed. The
   encoding process follows a labeling strategy based on a det.traversal of the
   graph. It improves existing methods which achieve shorter bit-length
   encodings in both time efficiency & simplicity. Besides, it does not impose
   any restriction on the number of loops & multiple edges that are allowed.
   Compared to techniques of similar time requirements, it offers a more compact
   compression solution."  [25 refs].  auth @ Dept.Math., U. of Alcala, Spain.
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2008.04.017">doi:10.1016/j.ipl.2008.04.017</A>][9/'08].
   (Note, log2(14) < 4.)     [Also search for: compress graph].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/Graph/">graphs</A>].)

%A L. van der Maaten
%A G. Hinton
%T Visualizing data using t-SNE
%J JMLR
%P 2579-2605
%V 9
%M NOV
%D 2008
%K JMLR, c2008, c200x, c20xx, zz1215, t-SNE, tSNE, visualization, visualisation,
   data, visualize, visualise, dimensions, reduction, PCA, notPCA, Isomap
%X "... new technique called "t-SNE" that visualizes high-dim. data by giving
   each datapoint a locn in a two or three-d. map. ... a variation of Stochastic
   Neighbor Embedding ... that is much easier to optimize, ...  show how t-SNE
   can use random walks on neighborhood graphs to allow the implicit structure
   of all of the data to influence the way in which a subset of the data is
   displayed. We illustrate ..."
   -- [<A HREF="http://www.jmlr.org/papers/v9/vandermaaten08a.html">www</A>]['15].
   (Also see tSNE@[<A HREF="https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding">wikip</A>]['15], and
    dim_red@[<A HREF="https://en.wikipedia.org/wiki/Nonlinear_dimensionality_reduction">wikip</A>]['21].)
   [Also search for: tSNA]  (c.f. PCA.)

%A M. C. Jones
%T On reciprocal symmetry
%J J. of Statist. Plann. and Inference
%V 138
%N 10
%P 3039-3043
%M OCT
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0919, R reciprocal symmetry,
   Rsymmetry, Rsymmetric, symmetric, probability distribution,
   log symmetric, logSymmetry, logSymmetric, Mudholkar, Wang
%X "On the +ve half line, there are two natural, & complementary, analogues of
   the single notion of symmetry of distns on the real line. One is the
   R-symmetry recently proposed and investigated by Mudholkar & Wang [2007.
   IG-symmetry and R-symmetry: interrelations & applications to the inverse
   Gaussian theory. J. Statist. Plann. Inference 137, 3655-3671]; the other is
   the 'log-symmetry' investigated here. Log-symmetry can be thought of either
   in terms of a random variable having the same distribution as its reciprocal
   or as ordinary symmetry of the distribution of the logged random variable.
   Various properties, analogies, comparisons & consequences are investigated."
      " ... R-symmetry: f(theta.y) = f(theta/y)  --(1.3)...
        log-symmetry: Y/theta~~theta/Y  --(1.4)
            equivalent to log(Y)-log(theta)~~log(theta)-log(Y)  --(1.5) ..."
   -- 22523@[<A HREF="http://oro.open.ac.uk/22523/">open_ac_uk</A>]['19],
      [<A HREF="https://doi.org/10.1016/j.jspi.2007.11.006">doi:10.1016/j.jspi.2007.11.006</A>]['19].
   [Also search for: probability distribution symmetry].

%A M. C. Jones
%A B. C. Arnold
%T Distributions that are both log-symmetric and R-symmetric
%J Electronic J. of Stats.
%V 2
%P 1300-1308
%D 2008
%K jrnl, eJrnl, c2008, c200x, c20xx, zz0919, log symmetric, logSymmetry,
   logSymmetric, R, Rsymmetric, Rsymmetry, reciprocal, doubly, log symmetry,
   probability distribution, log Normal, logNormal, Pakes
%X "Two concepts of symmetry for the distns of positive random variables are
   log-symmetry (symmetry of the d. of log Y) & R-symmetry. ... we characterise
   the distns that have both properties, which we call doubly symmetric. It
   turns out that doubly symmetric ds. constitute a subset of those ds. that are
   moment-equivalent to the log normal distn. They include the lognormal, some
   members of the Berg/Askey class of distns, & a # of others for which we give
   an explicit construction (based on workof A.J.Pakes) & note some properties;
   Stieltjes classes, however, are not doubly symmetric."
    [[Random variable Y from distn F with pdf f(.) is log-symmetric if there
      exists a d>0 s.t. (y^2)f(d.y) = f(d/y), for all y>0; i.e., Y/d~d/Y.
      Distn F is (reciprocal-) R-symmetric if there
      exists a t>0 s.t. f(t.y)=f(t/y), for all y>0.]]
   -- 0810.0102@[<A HREF="https://arxiv.org/abs/0810.0102">arXiv</A>],
      [<A HREF="https://pdfs.semanticscholar.org/f5e1/ed1bc34ea584786a905deaa2ab5da1b50d39.pdf">SemSchol</A>]['19].
   [Also search for: probability distribution symmetry].
      (Also see logNormal@[<A HREF="https://en.wikipedia.org/wiki/Log-normal_distribution">wikip</A>]['19].)

%A E. J. Vladislavleva
%A G. F. Smits
%A D. den Hertog
%T Order of nonlinearity as a complexity measure for models generated by
   symbolic regression via Pareto genetic programming
%I IEEE
%J Trans. on Evolutionary Comp.
%V 13
%N 2
%P 333-349
%M APR
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1016, AI, II, symbolic regression, equations,
   complexity, polynomial, model, fitting, genetic programming,
   geneticProgramming, denHertog
%X "... novel approach to generate data-driven regression models ... models are
   obtained as solns of a genetic programming (GP) process ... [&] a novel
   complexity measure that adopts the notion of the minimal degree of the
   best-fit polynomial, approximating an analytical fn with a certain precision.
   Using nine regression problems, this paper presents & illustrates two
   different strategies for the use of the order of nonlinearity in symbolic
   regression via GP. ... also introduces a novel heuristic of alternating
   several optimization objectives in a 2-D optimization framework. ..."
   -- [<A HREF="http://dx.doi.org/10.1109/TEVC.2008.926486">doi:10.1109/TEVC.2008.926486</A>]['16].
   [Also search for: symbolic regression] and
   [also search for: polynomial fitting].

%A J. Teuhola
%T Tournament coding of integer sequences
%J COMPJ
%V 52
%N 3
%P 368-277
%M MAY
%D 2009
%K jrnl, COMPJ, c2009, c200x, c20xx, zz0708, integer, int, ints, code, codes,
   compress, compression, sequence, series, list
%X "A new, simple non-statistical source coding technique for seqs of ints ...
   ...based on a tournament scheme, with the seq arranged into pairs, where
   maxima ("winners") are encoded recursively, & minima are encoded by
   semi-fixed-length codes using the related maxima to bound the code lengths.
   In the experiments, tournament coding has outperformed the other
   non-statistical methods (gamma, delta, Fibonacci & interpolative coding)
   for uniform distribution of numbers. Also for non-uniform distributions the
   method is quite competitive."  [22 refs].  (Online June 2008.)
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxn030">doi:10.1093/comjnl/bxn030</A>][6/'08].

%A R. Schnell
%A T. Bachteler
%A J. Reiher
%T Privacy-preserving record linkage using Bloom filters
%J BMC Medical Informatics and Decision Making
%V 9
%P 41
%D 2009
%K jrnl, eJrnl, c2009, c200x, c20xx, record linkage, data, privacy, preserve,
   preserving, approximate match, matching, error, errors, RL, PRL,
   Bloom filter, filters
%X "... In many applications, identifiers have to be encrypted due to privacy
   concerns. ... A new protocol for privacy-preserving record linkage with
   encrypted identifiers allowing for errors in identifiers has been developed.
   The protocol is based on Bloom filters on q-grams of identifiers. ..."
     "... we store the q-grams of each name in a separate bit array (a Bloom
     filter) using k multiple cryptographic mappings (hash fns) resp.. Then we
     compare the Bloom filters bit by bit & calculate a similarity coeff.. ...
     Since crypto. (1-way) hash fns are used, the initial input strings (names)
     can not be reconstructed given only the resulting Bloom filters. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1472-6947-9-41">doi:10.1186/1472-6947-9-41</A>]['10], [51 refs].
   [Also search for: record linkage data].

%A K. S. Ng
%A J. W. Lloyd
%A W. T. B. Uther
%T Probabilistic modelling, inference and learning using logical theories
%J Annals of Mathematics and Artificial Intelligence
%D 2009
%K c2009, c200x, c20xx, AI, II, logic
%X "... a study of probabilistic modelling, inference & learning in a logic-
   -based setting. We show how probability densities, being fns, can be
   represented & reasoned with naturally & directly in higher-order logic, an
   expressive formalism not unlike the (informal) everyday language of math..."
          -- [<A HREF="http://dx.doi.org/10.1007/s10472-009-9136-7">doi:10.1007/s10472-009-9136-7</A>]['09].
   (Also see [<A HREF="http://www.allisons.org/ll/FP/IP/">Ind.Prog.</A>] and
            @[<A HREF="http://dx.doi.org/10.1017/S0956796804005301">JFP</A>].)

%A A. Pavlo
%A E. Paulson
%A A. Rasin
%A D. J. Abadi
%A D. J. DeWitt
%A S. Madden
%A M. Stonebraker
%T A comparison of approaches to large-scale data analysis
%J SIGMOD '09
%I ACM
%P ?-?
%D 2009
%K conf, SIGMOD, SIGMOD09, c2009, c200x, c20xx, data analysis, stats,
   mapReduce, MR, DBMS, parallel SQL, data base, bases, database, DBMS
%X "... enthusiasm around the MapReduce (MR) paradigm for large-scale data
   analysis. ... we describe and compare both [the MP & DBMS] paradigms. ...
   evaluate both kinds of systems in terms of performance and development
   complexity. ... define a benchmark ... For each task, we measure each
   system's performance for various degrees of parallelism on a cluster of 100
   nodes. ... reveal some interesting trade-offs. Although the process to load
   data into & tune the execution of parallel DBMSs took much longer than the
   MR system, the observed performance of these DBMSs was strikingly better. We
   speculate about the causes of the dramatic performance difference & consider
   implementation concepts that future systems should take from both kinds of
   architectures."  [21 refs].
   -- [<A HREF="http://doi.acm.org/10.1145/1559845.1559865">doi:10.1145/1559845.1559865</A>]['09],
   pdf@[<A HREF="http://database.cs.brown.edu/sigmod09/benchmarks-sigmod09.pdf">brown</A>]['09],
   more@[<A HREF="http://database.cs.brown.edu/projects/mapreduce-vs-dbms/">brown</A>]['09].
   [Also search for: mapReduce MR].

%A M. D. Reid
%A R. C. Williamson
%T Surrogate regret bounds for proper losses
%J Proc. 26th Int. Conf. on Machine Learning
%P 897-904
%D 2009
%K conf, c2009, c200x, c20xx, stats, loss, losses, function, bound, regret,
   Bregman divergence, convexity, weighted
%X "... tight surrogate bounds for the class of proper (ie F'sher consistent)
   losses. ... generalise the margin-based bounds ... also ... different
   formulation of a duality result of Bregman divergences ..."
   -- pdf@[<A HREF="http://users.rsise.anu.edu.au/~williams/papers/P179.pdf">anu</A>]['09].
   auth2@[<A HREF="http://users.rsise.anu.edu.au/~williams/">anu</A>]['09].
   [Also search for: regret loss stats].

% C. C. Branas
%A et al
%T Investigating the link between gun possession and gun assault
%J American J. of Public Health
%V ?
%N ?
%P ?-?
%D 2009
%K jrnl, c2009, c200x, c20xx, zz1009, gun, guns, assault, attack, crime, death,
   homicide, murder, risk, risks, safety, shot, shooting, shootings, wounded,
   public health, policy, firearm, firearms, armed,
   USA, cause, effect, causal, stats
%X "... individuals in possession of a gun were 4.46 (P < .05) times more likely
   to be shot in an assault than those not in possession. Among gun assaults
   where the victim had at least some chance to resist, this adjusted odds
   ratio increased to 5.45 (P < .05).
   Conclusions. On average, guns did not protect those who possessed them from
   being shot in an assault. ..."  [online Sept. 2009].
   -- [<A HREF="http://dx.doi.org/10.2105/AJPH.2008.143099">doi:10.2105/AJPH.2008.143099</A>]['09].

%A M. Studeny
%A J. Vormeil
%T A reconstruction algorithm for the essential graph
%J Int. J. Approx. Reasoning
%V 50
%N 2
%P 385-413
%M FEB
%D 2009
%K conf, c2009, c200x, c20xx, zz0618, maths, essential graph, essentialGraph,
   chainGraph, standard imset, recovery algorithm, reconstruction
%X "A std graphical representative of a Bayesian n/wk structure is a special
   chain graph, known as an essential graph. An alt. algebraic approach to the
   math. descrn of this statistical model uses instead a certain integer-valued
   vector, known as a standard imset. We give a direct formula for the
   translation of any chain graph describing a Bayesian n/wk structure into the
   standard imset. Moreover, we present a two-stage alg. which makes it possible
   to reconstruct the essential graph on the basis of the std imset. The core of
   this paper is the proof of the correctness of the algorithm."
   -- [<A HREF="https://doi.org/10.1016/j.ijar.2008.09.001">doi:10.1016/j.ijar.2008.09.001</A>]['18].
   [Also search for: chainGraph].

%A W. Aspinall
%T A route to more tractable expert advice
%J Nature
%V 463
%P 294-295
%M JAN
%D 2010
%K opinion, c2010, c201x, c20xx, pooling, pooled, expert, experts, opinions,
   predictions, advice, concensus, uncertainty, weight, weighted, weighing,
   pool, polled, pooling
%X "There are mathematically advanced ways to weigh & pool scientific advice.
   They should be used more to quantify uncertainty & improve decision-making
   ... I also asked each expert a set of eleven 'seed questions', for which
   answers are known, so that their proficiency could be calibrated. ...
   Again the specialists answered with a best estimate & a credible interval.
   Their performance on these seed questions was used to 'weight' their opinion,
   & these weighted opinions were pooled to provide a 'rational consensus' ..."
   -- [<A HREF="http://dx.doi.org/10.1038/463294a">doi:10.1038/463294a</A>]['10].

%A J. Zhang
%T A highly efficient L-estimator for the location parameter of the
   Cauchy distribution
%J Comp. Stats.
%V 25
%N 1
%P 97-105
%M MAR
%D 2010
%K jrnl, c2010, c201x, c20xx, zz0919, Cauchy distribution, estimator, estimate,
   heavy tail
%X "The Cauchy distn is a peculiar d. due to its heavy tail & the difficulty of
   estimating its location parameter. It is often cited as an e.g. of the
   computational failure of the max.likelihood method of estimation. The method
   of moment estimation fails & Bayesian estimation is v.unstable. A new
   unbiased L-estimator based on order statistics is proposed, which is not only
   asymptotically efficient but outperforms existing L-estimators in terms of
   finite-sample efficiency."
   -- [<A HREF="https://doi.org/10.1007/s00180-009-0163-y">doi:10.1007/s00180-009-0163-y</A>]['19].
   [Also search for: Cauchy distribution].
   (Also see C@[<A HREF="https://en.wikipedia.org/wiki/Cauchy_distribution">wikip</A>]['19].)

%A B. J. Tolkamp
%A M. J. Haskell
%A F. M. Langford
%A D. J. Roberts
%A C. A. Morgan
%T Are cows more likely to lie down the longer they stand?
%J Appl. Animal Behav. Sci.
%V 124
%N 1-2
%P 1-10
%M APR
%D 2010
%K jrnl, c2010, c201x, c20xx, zz0913, animal behaviour, cow, cows, cattle,
   lying, standing, IgNobel, Ig Nobel, prize, probability, stats, 2013
%X "... The probability of cows standing up within the next 15 min increased
   (P < 0.001) with lying time in all experiments, which was consistent with
   the first hypothesis. The probability of cows lying down within the next
   15 min did not significantly increase with standing time.  ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.applanim.2010.02.004">doi:10.1016/j.applanim.2010.02.004</A>]['13].
   (Winner of the 2013 IgNobel 'Probability prize'
   -- [<A HREF="http://www.improbable.com/ig/winners/#ig2013">www</A>]['13].)

%A T. Siegfried
%T Odds are, it's wrong
%J ScienceNews
%V 177
%N 1
%P 26
%M MAR
%D 2010
%K c2010, c201x, c20xx, zz0310, statistics, stats, significance test, tests,
   p value, Pvalue, pValues, values, Bayesian, classical, frequentist,
   science, hypothesis testing, controversial, null, views, intro
%X "... But in fact, there is no logical basis for using a P value from a
   single study to draw any conclusion. ...
   ... Correctly phrased, experimental data yielding a P value of .05 means that
   there is only a 5% chance of obtaining the observed (or more extreme) result
   if no real effect exists (that is, if the no-difference hypothesis is
   correct). But many explanations mangle the subtleties in that definition.
   A recent popular book on issues involving science, for example, states a
   commonly held misperception about the meaning of stat.sig. at the .05 level:
     'This means that it is 95% certain that the observed diff. between groups,
      or sets of samples, is real and could not have arisen by chance.' ...
   Most critics of standard statistics advocate the Bayesian approach ..."
   -- [<A HREF="http://www.sciencenews.org/view/feature/id/57091/title/Odds_Are,_Its_Wrong">www</A>]['10].

%A J. Gasthaus
%A F. Wood
%A Y. W. Teh
%T Lossless compression based on the sequence memoizer
%J DCC
%P 337-345
%M MAR
%D 2010
%K conf, c2010, c201x, c20xx, DCC, sequence memoizer
%X "... describe a sequence compression method based on combining a Bayesian
   nonparametric seq. model with entropy encoding. The model, a hierarchy of
   Pitman-Yor processes of unbounded depth previously proposed by Wood et al.
   in the context of language modelling, allows modelling of long-range
   dependencies by allowing conditioning contexts of unbounded length. We show
   that incremental approx. inference can be performed in this model, thereby
   allowing it to be used in a text comp'n setting. The resulting compressor
   reliably outperforms several PPM variants on many types of data ... effective
   in compressing data that exhibits power law properties." [via mark c].
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/DCC.2010.36">doi:10.1109/DCC.2010.36</A>]['11],
      pdf(s)@[<A HREF="http://www.sequencememoizer.com/papers/">s-m-.com</A>]['11].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">bioinf</A>].)

%A D. Salomon
%A G. Motta
%T Handbook of Data Compression
%I Springer
%P 1361
%D 2010
%K book, text, c2010, c201x, c20xx, code, code, coding, data compression,
   compress, lossy, lossless, survey
%X 5th ed 2010; hb us$103; uk us isbn:1848829027; uk us isbn13:978-1848829022.
      Basic Techniques.  Basic VL Codes.      Advanced VL Codes.
      Robust VL Codes.   Statistical Methods. Dictionary Methods.
      Image Compression. Wavelet Methods.     Video Compression.
      Audio Compression. Other Methods.
   Lots of examples and refs.
   (Don't be lazy & cite the book for some method: Cite the original source.)

%A D. C. Montgomery
%A G. C. Runger
%T Applied Statistics and Probability for Engineers, Student Solutions Manual
%I Wiley
%P ?
%D 2006
%K book, text, c2006, c200x, c20xx, stats, statistics
%X 4th edn 2006; pb us$55; uk us isbn:0470099402; uk us isbn13:978-0470099407.

%A G. Peskir
%A A. Shiryaev
%T Optimal Stopping Theory and Free-Boundary Problems
%I Birkhauser
%S Lectures in Maths. (ETH)
%P 500
%D 2006
%K c2006, c200x, c20xx, zz1113, optimal stopping theory, stats, dating,
   secretary problem, when to stop, search, finance, option, options
%X 1st ed 2006; pb us$52; uk us isbn:3764324198; uk us isbn13:978-3764324193.
   "... connection between optimal stopping problems in probability and
   free-boundary problems. It focuses on key examples and the theory of optimal
   stopping is exposed at its basic principles in discrete and continuous time
   covering martingale and Markovian methods. Methods of solution explained
   range from change of time, space, and measure, to more recent ones such as
   local time-space calculus and nonlinear integral equations. A chapter on
   stochastic processes makes the material more accessible. The book will
   appeal to those wishing to master stochastic calculus via fundamental
   examples. Areas of application include financial mathematics, financial
   engineering, and mathematical statistics."
   (Also see Opt.S.@[<A HREF="http://en.wikipedia.org/wiki/Optimal_stopping">wikip</A>]['13].)

%A T. Silander
%A P. Myllymaki
%T A simple approach for finding the globally optimal Bayesian network structure
%J UAI
%P 445-452
%M JUL
%D 2006
%K conf, UAI06, UAI2006, c2006, c200x, c20xx, zz0418, Bayesian network, AI, II,
   dynamic programming
%X "We study the problem of learning the best B.n/wk structure wrt a
   decomposable score such as BDe, BIC or AIC. This problem is known to be
   NP-hard, which means that solving it becomes quickly infeasible as the #
   of variables increases. Nevertheless ... show that it is possible to learn
   the best B.n/wk struct. with over 30 variables, which covers many practically
   interesting cases. Our alg. is less complicated & more efficient than the
   techniques presented earlier ... easily parallelized, & offers a possibility
   for efficient exploration of the best n/wks consistent with different
   variable orderings. ... compare the performance of the alg. to the previous
   state-of-the-art alg.. Free source-code & an online-demo can be found at
   b-course.hiit.fi/bene [not found 4/'18]."
   "... claim feasibility for n < 33 and demonstrate with n=29 ..."
   -- [<A HREF="https://dl.acm.org/citation.cfm?id=3020473">acm</A>]['18].
   Also see paper at
   1206.6875@[<A HREF="https://arxiv.org/abs/1206.6875">arXiv</A>]['18].
   (?Not sure what makes it "DP"?)
   (auth1@[<A HREF="https://scholar.google.com/citations?user=J40N13sAAAAJ&hl=en">schlr</A>]['18].)
   [Also search for: SLL algorithm].

%A I. Tsamardinos
%A L. E. Brown
%A C. F. Aliferis
%T The max-min hill-climbing Bayesian network structure learning algorithm
%J Mach. Learning
%V 65
%N 1
%P 31-78
%M OCT
%D 2006
%K c2006, c200x, c20xx, zz0514, AI, II, net, nets, causal, model, MMHC,
   direct, orient, edges, Sparse Candidate, Three Phase Dependency Analysis,
   Optimal Reinsertion, Greedy Equivalence Search, Greedy
%X "... new alg. for Bayesian n/w structure learning, called Max-Min
   Hill-Climbing (MMHC). [It] combines ideas from local learning,
   constraint-based, & search-and-score techniques in a principled & effective
   way. It first reconstructs the skeleton of a Bayesian n/w & then performs
   a Bayesian-scoring greedy hill-climbing search to orient the edges. In our
   extensive empirical evaluation MMHC outperforms on average & in terms of
   various metrics several prototypical & state-of-the-art algs., namely the
   PC, Sparse Candidate, Three Phase Dependency Analysis, Optimal Reinsertion,
   Greedy Equivalence Search, & Greedy Search. These are the first empirical
   results simultaneously comparing most of the major Bayesian n/w algs. against
   each other. MMHC offers certain theoretical advantages, specifically over the
   Sparse Candidate alg., ..."
   -- [<A HREF="http://dx.doi.org/10.1007/s10994-006-6889-7">doi:10.1007/s10994-006-6889-7</A>]['14],
      10.1.1.110.2806@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.110.2806">c'tse'r</A>]['14],
      [<A HREF="http://discover.mc.vanderbilt.edu/discover/public/supplements/mmhc_paper/journal_paper.pdf">vanderbilt</A>]['14].
   (Also see [<A HREF="http://www.dsl-lab.org/">dsl-lab</A>]['14].)
   [Also search for: Tsamardinos model].

%A C. Dwork
%A F. McSherry
%A K. Nissim
%A A. Smith
%T Calibrating noise to sensitivity in private data analysis
%J Theory of Cryptography Conference TCC
%P 265-284
%D 2006
%K conf, TCC, c2006, c200x, c20xx, zz0620, differential privacy, database,
   databases, noise, query, queries, privacy, preserving,  disclosure,
   security, survey
%X "...  privacy-preserving statistical databases. Consider a trusted server
   that holds a DB of sensitive information. Given a query fn f mapping DBs to
   reals, the so-called true answer is the result of applying f to the DB. To
   protect privacy, the true answer is perturbed by the addition of random noise
   generated according to a carefully chosen distn, & this response, the true
   answer plus noise, is returned to the user. Prev. work focused on the case of
   noisy sums, in which f=SUM_i g(x_i), where x_i denotes the i-th row of the
   DB & g maps DB rows to [0,1]. We extend the study to general fns f, proving
   that privacy can be preserved by calibrating the std dev'n of the noise
   according to the sensitivity of the fn f. Roughly speaking, this is the
   amount that any single argument to f can change its output. The new analysis
   shows that for several particular applications substantially less noise is
   needed than was previously understood to be the case. The 1st step is a v.
   clean characterization of privacy in terms of indistinguishability of
   transcripts. [&] we obtain separation results showing the increased value of
   interactive sanitization mechanisms over non-interactive.
   -- [<A HREF="https://doi.org/10.1007/11681878_14">doi:10.1007/11681878_14</A>]['20].
   (Also see DP@[<A HREF="https://en.wikipedia.org/wiki/Differential_privacy">wikip</A>]['20].)
   [Also search for: differential privacy].

%A S. Nijssen
%A J. N. Kok
%T Frequent subgraph miners: Runtime don't say everything
%J Proc. Int. Workshop on Mining and Leraning with Graphs
%P 173-180
%D 2006
%K wShop, c2006, c200x, c20xx, maths, graph, frequent, subgraph, mining, miner,
   tree, runtime, efficiency
%X "... new alg.s typically compared the runtimes [v.] previous implementations
   to confirm the efficiency of their methods. ... Wolein et al. performed an
   experimental evaluation of re-impl'ns of several depth-first graph miners,
   where also some statistics beyond runtimes were compared. ... we present
   results of an additional experimental comparison of several g.ms., ...
   (1) we compare original impl'ns; (2) we compare these impl'ns on [more]
   measures than runtimes, ...  (3) we include breadth-first graph miners
   & free tree miners in the comparison"
   -- pdf@[<A HREF="http://www.inf.uni-konstanz.de/mlg2006/18.pdf">uni-konstanz.de</A>]['06],
   and [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.84.3816">citseer</A>]['10].

%A C. E. Rasmussen
%A C. K. I. Williams
%Y Gaussian Processes for Machine Learning
%I MITpress
%D 2006
%K book, text, c2006, c200x, c20xx, zz1121, AI, Gaussian process, functions,
   GaussianProcess, learning, fitting, parameters, model, stats
%X "Gaussian processes (GPs) provide a principled, practical, probabilistic
   approach to learning in kernel machines. ... regression and classification
   ... support-vector machines, neural networks, splines, regularization
   networks, relevance vector machines ..."
   -- book@[<A HREF="http://www.gaussianprocess.org/gpml/">www</A>]['21].
   uk us isbn:026218253X.
   Also see, "A GP can be used as a prior prob. dist'n over fns in B.inference"
   -- GP@[<A HREF="https://en.wikipedia.org/wiki/Gaussian_process">wikip</A>]['21].

%A J. Skilling
%T Nested sampling for general Bayesian computation
%J Bayesian Anal.
%V 1
%N 4
%P 833-859
%M DEC
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0323, stats, nested sampling algorithm, sample,
   posterior, simulated annealing, marginal
%X "... sampling within a hard constraint on likelihood value, as opposed to the
   softened likelihood of annealing methods. Progress depends only on the shape
   of the 'nested' contours of likelihood, & not on the likelihood values. This
   invariance (over monotonic re-labelling) allows the method to deal with a
   class of phase-change problems which effectively defeat thermal annealing."
   -- [<A HREF="https://doi.org/10.1214/06-BA127">doi:10.1214/06-BA127</A>]['23].
   (Also see Nsamp@[<A HREF="https://en.wikipedia.org/wiki/Nested_sampling_algorithm">wikip</A>]['23].)

%A L. Kaufman
%A P. J. Rousseeuw
%T Partitioning around medoids (programPAM)
%B Finding Groups in Data
%P 68-125
%M MAY
%D 2008
%K chapter, c2008, c200x, c20xx, zz0916, clustering, subset, representative,
   selection, medoid, medoids
%X -- [<A HREF="http://dx.doi.org/10.1002/9780470316801.ch2">doi:10.1002/9780470316801.ch2</A>]['16].
   [Also search for: representative subset selection].

%A B. Stevenson
%A J. Wolfers
%T Economic growth and subjective well-being: Reassessing the Easterlin paradox
%J NBER
%R Working Paper # 14282
%M AUG
%D 2008
%K TR 14282, TR14282, NBER, c2008, c200x, c20xx, zz0119, happiness, wealth,
   Betsey Stevenson, money, happy, Easterlin paradox, economics, GDP, nation,
   national, well being, wellbeing
%X "The "Easterlin paradox" suggests that there is no link between a society's
   economic development & its avg level of happiness. We re-assess this p.
   analyzing multiple rich datasets spanning many decades. Using recent data on
   a broader array of countries, we establish a clear +ve link between avg
   levels of subjective well-being & GDP per capita across countries, & find no
   evidence of a satiation point beyond which wealthier countries have no
   further increases in subjective well-being. We show that the estimated
   relationship is consistent across many datasets & is similar to the
   relationship between subject well-being & income observed within countries.
   Finally, examining the relationship between changes in subjective well-being
   & income over time within countries we find economic growth assoc. with
   rising happiness. Together these findings indicate a clear role for absolute
   income & a more limited role for relative income comparisons in determining
   happiness."
   -- [<A HREF="https://www.nber.org/papers/w14282">www</A>]['19],
      [<A HREF="https://doi.org/10.3386/w14282">doi:10.3386/w14282</A>]['19].
   [Also search for: Easterlin happiness].

%A J. Vreeken
%A M. van Leeuwen
%A A. Siebes
%T Krimp: Mining itemsets that compress
%J Data Mining and Knowledge Discovery
%V 23
%P 169-214
%I Springer
%D 2010
%K jrnl, c2010, c201x, c20xx, Krimp algorithm, FIS, frequent item set, sets,
   information, compress, II, boolean matrix factorization, BMF, patterns,
   cover
%X "One of the major problems in pattern mining is the explosion of the # of
   results. Tight constraints reveal only common knowledge, while loose
   constraints lead to an explosion in the # of returned ps.. ... caused by
   large groups of ps. essentially describing the same set of transactions. ...
   approach this problem using the MDL principle: the best set of patterns is
   that set that compresses the database best. ... introduce the Krimp alg. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/s10618-010-0202-x">doi:10.1007/s10618-010-0202-x</A>]['13],
   krimp@[<A HREF="http://www.cs.uu.nl/groups/ADA/krimp/">uu.nl</A>]['10].

%A E. Hazan
%A S. Kale
%A M. K. Warmuth
%T Learning rotations with little regret
%J COLT
%D 2010
%K conf, COLT, c2010, c201x, c20xx, rotation, direction, learn, estimate,
   regret, loss, stats, opportunity loss, online, Follow The Perturbed Leader
%X "... online algs. for learning a rotn from pairs of unit vectors in R**n. We
   show that the expected regret of our online alg. [v.] the best fixed rotn
   chosen offline is O(sqrt nL), where L is the loss of the best rotn. [&] give
   a LWB that proves that this expected regret bound is optimal within a const.
   factor. This resolves an open problem posed in COLT 08. Our online alg. for
   choosing a rotn matrix in each trial is based on the Follow-The-Perturbed-
   -Leader paradigm. It adds a random spectral perturbation to the matrix
   characterizing the loss incurred so far & then chooses the best rotn matrix
   for that loss. ... show that any deterministic alg. for learning rotns has
   Omega(T) regret in the worst case."
      "... The loss to the learner, L_t(R_t), is half the squared norm of
      the difference between her predicted vector and the true vector ...
      Regret = SUM_t=1..T L_t(R_t) - min_R SUM_t=1..n L_t(R) ..."
   -- pdf@[<A HREF="http://ie.technion.ac.il/~ehazan/papers/094-HKW.pdf">techn'on</A>]['13].
   And 9/2010 correction@[<A HREF="http://ie.technion.ac.il/~ehazan/papers/rotfix.pdf">techn'on</A>]['13],
      where bound is weaker at O(n sqrt T), but new alg with O(sqrt nT).
   (Also see Regret@[<A HREF="http://en.wikipedia.org/wiki/Regret_(decision_theory)">wikip</A>]['13],
   [also search for: regret loss stats].)

%A B. Efron
%T Large-Scale Inference: Empirical Bayes Methods for Estimation, Testing, and
   Prediction
%I CUP
%P 276
%M SEP
%D 2010
%K book, text, CUP, c2010, c201x, c20xx, zz0613, Bayes, theorem, empirical,
   stats, statistics, probabilty, AI, II, learning, prior
%X 1st ed 2010; hb us$155; uk us isbn:0521192498; uk us isbn13:978-0521192491;
   and    2013  pb  us$34; uk us isbn:110761967X; uk us isbn13:978-1107619678.
   "... Efron, inventor of the bootstrap, shows how information accrues across
   problems in a way that combines Bayesian & frequentist ideas. Estimation,
   testing, & prediction blend in this framework, producing opportunities for
   new methodologies of increased power. New difficulties also arise, easily
   leading to flawed inferences. This book takes a careful look at both the
   promise & pitfalls of large-scale statistical inference, with particular
   attention to false discovery rates, the most successful of the new stat.
   techniques. Emphasis is on the inferential ideas underlying technical
   developments, illustrated using a large number of real examples."
   (Also see B.E. in [<A HREF="http://dx.doi.org/10.1126/science.1236536">doi:10.1126/science.1236536</A>]['13].)

%A C. Aliferis
%A A. Statnikov
%A I. Tsamardinos
%A S. Mani
%A X. Koutsoukos
%T Local causal and Markov blanket induction for causal discovery and
   feature selection for classification. Part I: Algorithms and empirical
   evaluation
%J J. Machine Learning Res.
%V 11
%P 171-234
%D 2010
%K jrnl, eJrnl, JMLR, c2010, c201x, c20xx, zz0514, Markov blanket,
   local structure, variables, causal model, net, nets, algorithm,
   Generalized Local Learning, GLL, conditional, independence, independent
%X "... learning local causal structure around target variables of interest in
   the form of direct causes/effects and Markov blankets applicable to very
   large data sets with relatively small samples.  ... evaluate several algs.
   derived from this framework in terms of predictivity and feature set
   parsimony and compare to other local causal discovery methods ..."
   -- pdf@[<A HREF="http://www.nyuinformatics.org/downloads/tmp/BMS/Paper8.pdf">nyu</A>]['14],
      [<A HREF="http://dl.acm.org/citation.cfm?id=1756013">dl.acm</A>]['14].
   [Also search for: Markov blanket].

%A D. F. Schmidt
%A E. Makalic
%T The behaviour of the Akaike Information Criterion when applied to non-nested
   sequences of models
%J 23rd Australasian Joint Conf. on AI
%D 2010
%K conf, c2010, c201x, c20xx, zz0714, enesm, Akaike Information Criterion, AIC,
   stats, score, citerion, MDL, MML, SureShrink, model, parameters,
   sparse feature selection
%X "... This paper examines a common scenario in which there is more than one
   candidate model with the same # of free params. which violates the condns
   under which AIC was derived. The main result ... is a novel upper bound that
   quantifies the poor performance of the AIC criterion when applied in this
   setting. Crucially, the UPB does not depend on the sample size & will not
   disappear even asymptotically. [&] an AIC-like criterion for sparse feature
   selection in regression models is derived, & simulation results in the case
   of denoising a signal by wavelet thresholding demo. the new AIC approach is
   competitive with SureShrink thresholding."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-17432-2_23">doi:10.1007/978-3-642-17432-2_23</A>]['14],
      [<A HREF="http://dschmidt.org/">dschmidt.org</A>]['14].
   [Also search for: MML Schmidt].

%A C. Aliferis
%A A. Statnikov
%A I. Tsamardinos
%A S. Mani
%A X. Koutsoukos
%T Local causal and Markov blanket induction for causal discovery and
   feature selection for classification. Part II: Analysis and extensions
%J J. Machine Learning Res.
%V 11
%P 235-284
%D 2010
%K jrnl, eJrnl, c2010, c201x, c20xx, Markov blanket, causal model, net, nets,
   Generalized Local Learning, GLL, global, LGL
%X "... investigate the empirical convergence of GLL to the true local
   neighborhood as a function of sample size. ... study how predictivity
   improves with increasing sample size. ... investigate how sensitive are the
   algs. to multiple statistical testing, esp. in the presence of many
   irrelevant features. ... discuss the role of the alg. parameters and also
   show that Markov blanket and causal graph concepts can be used to understand
   deviations from optimality of state-of-the-art non-causal algs.. ...
   parallel and distributed versions of GLL ... and divide-and-conquer
   local-to-global learning (LGL) strategies. ..."
   -- [<A HREF="http://dl.acm.org/citation.cfm?id=1756006.1756014">dl.acm</A>]['14].
   [Also search for: Markov blanket].

%A S. Drefahl
%T How does the age gap between partners affect their survival?
%J Demography
%V 47
%N 2
%P 313-326
%M MAY
%D 2010
%K jrnl, c2010, c201x, c20xx, zz0416, human, aging, ageing, health, mortality,
   life expectancy, risk, risks, marriage, age, difference, older, younger,
   wealth, partner, men, women, male, female, gender, stats, statistics
%X "I use hazard regression methods to examine how the age diff. between spouses
   affects their survival. In many countries, the age difference ... has
   remained relatively stable for several decades. In Denmark, men are, on avg
   about three years older than the women they marry. Previous studies ...
   found that having a younger spouse is beneficial, while having an older
   spouse is detrimental for one's own survival. Most of the observed effects
   could not be explained satisfactorily until now, mainly because of
   methodological drawbacks & insufficiency of the data. The most common
   explanations refer to selection effects, caregiving in later life, & some
   +ve psychological & sociological effects of having a younger spouse. The
   present study extends earlier work by using longitudinal Danish register data
   that include the entire history of key demographic events of the whole popn
   from 1990 onward. Controlling for confounding factors such as edn & wealth,
   results suggest that having a younger spouse is beneficial for men but
   detrimental for women, while having an older spouse is -ve for both sexes."
   "... One of the combinations was stat. sig. (at the .01 level): men with
   high wealth & who are older than their wives experienced a sig. elevated
   risk of dying of about 5%. ..."
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000022/">ncbi</A>]['16].
   [Also search for: marriage mortality].

%A J. M. Noble
%T An algorithm for learning the essential graph
%J arXiv
%M JUL
%D 2010
%K TR, c2010, c201x, c20xx, zz0618, maths, stats, essential graph, DAG,
   essentialGraph, chainGraph, MMPC, parents children, MMHC, immoralities
%X "... learning the essential graph of a Bayesian n/wk. The basis ... is the
   Maximum Minimum Parents and Children alg. developed by previous authors, with
   three substantial modifications. The MMPC alg. is the first stage of the
   Maximum Minimum Hill Climbing alg. for learning the DAG of a Bayesian n/wk...
   two phases; firstly, the MMPC alg. to locate the skeleton & secondly an edge
   orientation phase. The computationally expensive part is the edge orientation
   phase. The first modification introduced to the MMPC alg., which requires
   little additional computational cost, is to obtain the immoralities & hence
   the essential graph. This renders the edge orientation phase, the ...
   expensive part, unnecessary, since the entire Markov structure that can be
   derived from data is present in the essential graph. Secondly, the MMPC alg.
   can accept independence statements that are logically inconsistent with those
   rejected, since with tests for independence, a 'do not reject' conclusion for
   a particular independence statement is taken as 'accept' independence. An
   example is given to illustrate this & a modification is suggested to ensure
   that the conditional independence statements are logically consistent.
   Thirdly, the MMHC alg. makes an assumption of faithfulness. An example of a
   data set is given that does not satisfy this assumption & a modification is
   suggested to deal with some situations where the assumption is not satisfied.
   The example in question also illustrates problems with the 'faithfulness'
   assumption that cannot be tackled by this modification."
   -- 1007.2656@[<A HREF="https://arxiv.org/abs/1007.2656">arXiv</A>]['18].
   [Also search for: essentialGraph].

%A G. Shmueli
%T To explain or to predict?
%J arXiv
%M JAN
%D 2011
%O Stat. Sci., pp.289-310, 25(3), 2010
%K TR, c2011, c201x, c20xx, zz0917, AI, stats, prediction, explain, MDL,
   MML, explanation, model, modelling, modeling, II, statistical, inference
%X "Statistical modeling is a powerful tool for developing & testing theories by
   way of causal explanation, prediction, & description. In many disciplines
   there is near-exclusive use of statistical modeling for causal explanation &
   the assumption that models with high explanatory power are inherently of high
   predictive power. Conflation between explanation & prediction is common, yet
   the distinction must be understood for progressing scientific knowledge.
   While this distinction has been recognized in the philosophy of science, the
   statistical literature lacks a thorough discussion of the many differences
   that arise in the process of modeling for an explanatory versus a predictive
   goal. The purpose of this article is to clarify the distinction between
   explanatory & predictive modeling, to discuss its sources, & to reveal the
   practical implications of the distinction to each step in the modeling
   process."   [via F.Pj.]
   -- 1101.0891@[<A HREF="https://arxiv.org/abs/1101.0891">arXiv</A>]['17].

%A G. Miller
%T ESP paper rekindles discussion about statistics
%J Science
%V 331
%N 6015
%M JAN
%D 2011
%K news, c2011, c201x, c20xx, zz0211, stats, Bayesian, pValue, pValues,
   t test, tTest, skeptic, controversial,
   Bem, psychic, ESP, J Personality & Social Psychology, JPSP
%X "... Daryl Bem, a respected social psychologist & professor emeritus at
   Cornell U., argues that the results of 9 experiments he conducted with more
   than 1000 college students provide stat.sig. evidence of an ability to
   predict future events. Not surprisingly, word that the paper will appear in
   an upcoming issue of the J. of Personality & Social Psychology (JPSP) has
   provoked outrage from pseudoscience debunkers & counteraccusations of
   closed-mindedness from those willing to consider the possibility of
   psychic powers.  ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.331.6015.272">doi:10.1126/science.331.6015.272</A>]['11].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A D. F. Schmidt
%A E. Makalic
%T Estimating the order of an autoregressive model using normalized
   maximum likelihood
%J IEEE Trans. on Signal Processing
%V 59
%N 2
%P 479-487
%D 2011
%K jrnl, c2011, c201x, c20xx, zz0411, enesm, NML, stats, MDL, autoregressive,
   timeSeries, time series analysis
%X pdf@[<A HREF="http://www.emakalic.org/blog/wp-content/uploads/2010/04/ARNML-Final-Proof.pdf">emakalic</A>]['11].

%A T. Hastie
%A R. Tibishirani
%A J. Friedman
%T The Elements of Statistical Learning: Data Mining, Inference, and Prediction
%I SpringerVerlag
%S Series in Statistics
%P 745
%D 2011
%K book, text, c2011, c201x, c20xx, zz0215, stats, AI, II
%X "... While the approach is statistical, the emphasis is on concepts rather
   than mathematics. Many examples are given, with a liberal use of color
   graphics. It is a valuable resource for statisticians and anyone interested
   in data mining in science or industry. ..."
   2nd ed 2011; hb us$83; uk us isbn:0387848576; uk us isbn13:978-0387848570;
   [Also search for: stats inference book].

%A M. J. Flores
%A J. A. Gamez
%A A. M. Martinez
%A J. M. Puerta
%T Handling numeric attributes when comparing Bayesian network classifiers:
   does the discretization method matter?
%J Appl. Intell.
%V 34
%N 3
%P 372-385
%D 2011
%K jrnl, c2011, c201x, c20xx, classifier, discretization, discretisation,
   continuous data, attribute
%X ".... Despite the loss of info. discretization entails, it is a direct
   easy-to-use mechanism that can offer some benefits: sometimes d. improves the
   run time for certain algorithms; it provides a reduction in the value set ...
   ... presents a study of the impact of using different d. strategies on a set
   of representative BN classifiers, with a sign. sample consisting of 26
   datasets. ... have chosen Naive Bayes (NB) together with several other
   semi-Naive Bayes classifiers: Tree-Augmented Naive Bayes (TAN), k-Dependence
   Bayesian (KDB), Aggregating One-Dependence Estimators (AODE) and Hybrid AODE
   (HAODE). [&] included an augmented Bayesian network created by using a hill
   climbing algorithm (BNHC). ... Our main conclusion is that even if a d.method
   produces different results for a particular dataset, it does not really have
   an effect when classifiers are being compared. ... given a set of datasets,
   accuracy values might vary but the classifier ranking is generally
   maintained. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/s10489-011-0286-z">doi:10.1007/s10489-011-0286-z</A>]['13].
   (auth3 @ mon@sh as of 2012+. papers@[<A HREF="http://www.informatik.uni-trier.de/~ley/pers/hd/m/Mart=iacute=nez:Ana_M=.html">dblp</A>]['13].)

%A L. Floridi
%T The Philosophy of Information
%I OUP
%P 360
%D 2011
%K book, text, OUP, c2011, c201x, c20xx, zz0511, information, theory, science,
   philosophy
%X 1st ed 2011; hb us$48; uk us isbn:0199232385; uk us isbn13:978-0199232383.
   "... (1) the critical investigation of the conceptual nature and basic
   principles of information, including its dynamics, utilisation, and sciences,
   and (2) the elaboration and application of information-theoretic and
   computational methodologies to philosophical problems. ..."
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A S. B. McGrayne
%T The Theory That Would Not Die: How Bayes' Rule Cracked the Enigma Code,
   Hunted Down Russian Submarines, and Emerged Triumphant from Two Centuries
   of Controversy
%I YaleUP
%P 336
%M MAY
%D 2011
%K book, text, c2011, c201x, c20xx, zz0511, Bayesian, Bayes, Bayess, theorem,
   rule, probability, stats, statistics, priors, Pvalue, likelihood,
   frequentist, information, Enigma, WWII, WW2
%X 1st ed 2011; hb us$18; uk us isbn:0300169698; uk us isbn13:978-0300169690.
   "... In the first-ever account of Bayes' rule for general readers, ...
   explores this controversial theorem and the human obsessions surrounding it.
   She traces its discovery by an amateur mathematician in the 1740s through its
   development into roughly its modern form by French scientist Pierre Simon
   Laplace. She reveals why respected statisticians rendered it professionally
   taboo for 150 years - at the same time that practitioners relied on it to
   solve crises involving great uncertainty and scanty information, even
   breaking Germany's Enigma code during World War II, and explains how the
   advent of off-the-shelf computer technology in the 1980s proved to be a
   game-changer. Today, Bayes' rule is used everywhere from DNA de-coding to
   Homeland Security. ..."    (Also see
   -- [<A HREF="http://www.allisons.org/ll/MML/">MML</A>] for Bayesian inference,
      [<A HREF="http://www.allisons.org/ll/Images/Computers/BletchleyPark/">Bletchley</A>], and
      [<A HREF="http://www.allisons.org/ll/Images/People/Bayes/">Bayes</A>].)

%A N. G. Poulson
%A J. G. Scott
%T On the half-Cauchy prior for a global scale parameter
%J arXiv
%M APR
%D 2011
%K TR, c2011, c201x, c20xx, zz-919, half Cauchy, halfCauchy, distribution,
   prior, scale, parameter, stats, inverse Gamma, inverseGamma
%X "... argues that the half-Cauchy distribution should replace the
   inverse-Gamma distribution as a default prior for a top-level scale parameter
   in Bayesian hierarchical models, at least for cases where a proper prior is
   necessary. ... Finally, we briefly summarize some open issues in the
   specification of default priors for scale terms in hierarchical models."
   -- 1104.4937@[<A HREF="https://arxiv.org/abs/1104.4937">arXiv</A>]['19].
   [Also search for: Cauchy distribution].
   (Also see C@[<A HREF="https://en.wikipedia.org/wiki/Cauchy_distribution">wikip</A>]['19].)

%A D. Dorling
%T Fair Play: Selected Readings on Social Justice
%I PolicyPress
%P 320
%M OCT
%D 2011
%K book, text, c2011, c201x, c20xx, zz1011, stats, statistics, fair play,
   politics, political, policy, quality of life, education, school, schools, uk,
   teaching, social reform, justice
%X 1st ed 2011; pb us$42; uk us isbn:1847428797; uk us isbn13:978-1847428790.

%A E. Derman
%T Models Behaving Badly: Why Confusing Illusion with Reality Can Lead to
   Disaster, on Wall Street and in Life
%I FreePress
%P 240
%M OCT
%D 2011
%K book, text, c2011, c201x, c20xx, zz1111, risk, quant, shares, stocks, market,
   economics, economy, model, modeller, GFC, financial crisis, crash,
   Wall Street, business, Goldman Sachs, Black Derman Toy interest rate,
   Derman Kani local volatility, modelling
%X 1st ed 2011; hb us$17; uk us isbn:1439164983; uk us isbn13:9781439164983.
   "... [the] reliance traders put on such quantitative analysis was
   catastrophic for the economy, setting off the series of financial crises that
   began to erupt in 2007 with the mortgage crisis and from which we're still
   recovering. Here Derman looks at why people - bankers in particular - still
   put so much faith in these models, and why it's a terrible mistake to do so.
   Though financial models imitate the style of physics by using the language
   of mathematics, ultimately they deal with human beings. Their similarity
   confuses the fundamental difference between the aims and possible
   achievements of the phsyics world and that of the financial world. ..."

%A K. Iwata
%A S. Ishiwata
%A S. Nakano
%T A compact encoding of unordered binary trees
%J Proc. 8th annual conf. on Theory and Applications of Models of Computation
%I SpringerVerlag
%P 106-113
%D 2011
%K conf, TAMC 11, TAMC11, c2011, c201x, c20xx, zz0912, maths, trees,
   encoding, unordered, binary, tree
%X "A naive encoding of ordered binary trees with n vertices needs 2n bits for
   each tree, & it is asymptotically optimal. ... we give a new simple encoding
   of unordered binary trees. The encoding needs at most 4+1.4n bits for each
   tree. Our encoding & decoding algorithms are simple and run in O(n) time."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-20877-5_11">doi:10.1007/978-3-642-20877-5_11</A>]['12].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/Graph/">Ts-and-Gs</A>].)

%A Chang Wang
%A S. Mahadevan
%T Heterogeneous domain adaptation using manifold alignment
%J 22nd Int. Joint Conf. on AI
%D 2011
%K conf, IJCAI, c2011, c201x, c20xx, zz1220, manifold alignment, correspondence,
   labelled, labels
%X "... construct mappings to link different feature spaces in order to transfer
   knowledge across domains. ... can reuse labelled data from multiple source
   domains even in the case when the input domains do not share any common
   features or instances. ..."
   -- [<A HREF="https://web.archive.org/web/20120415030530/http://www-all.cs.umass.edu/~chwang/IJCAI2011-DA.pdf">www</A>]['20].
   Also see MA@[<A HREF="https://en.wikipedia.org/wiki/Manifold_alignment">wikip</A>]['20].
   [Also search for: manifold alignment].

%A D. N. Reshef
%A Y. A. Reshef
%A H. K. Finucane
%A S. R. Grossman
%A G. McVean
%A P. J. Turnbaugh
%A E. S. Lander
%A M. Mitzenmacher
%A P. C. Sabeti
%T Detecting novel associations in large data sets
%J Science
%V 334
%N 6062
%P 1518-1524
%M DEC
%D 2011
%K jrnl, c2011, c201x, c20xx, zz1211, stats, data set, mining,
   maximal information coefficient, MIC, determination, R2
%X "Identifying interesting relationships between pairs of variables in large
   data sets is increasingly important. ... present a measure of dependence for
   two-variable relationships: the maximal information coefficient (MIC). MIC
   captures a wide range of associations both functional & not, & for fnl
   relationships provides a score that roughly equals the coeff. of
   determination (R2) of the data relative to the regression fn. MIC belongs to
   a larger class of maximal info-based nonparametric exploration (MINE)
   statistics for identifying & classifying relationships. We apply MIC & MINE
   to data sets in global health, gene expression, major-league baseball, & the
   human gut microbiota & identify known & novel relationships."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1205438">doi:10.1126/science.1205438</A>]['11].

%A M. Wolkewitz
%A A. Allignol
%A N. Graves
%A A. G. Barnett
%T Death's Dominion. Is 27 really a dangerous age for famous musicians?
   Retrospective cohort study
%J BMJ
%V 343
%P d7799
%M DEC
%D 2011
%K jrnl, BMJ, c2011, c201x, c20xx, zz0916, stats, pop music, rock and roll,
   27 club, 27club, death, risk, risks, music, pop, entertainer, musician,
   rock and roll, human, mortality, lifespan, Jimi Hendrix, Janis Joplin,
   Jim Morrison, MusicianFiles, data, QUT, BMJ 343:d7799
%X "... Musicians (solo artists & band members) who had a number one album in
   the UK between 1956 & 2007 (n=1046 musicians, with 71 deaths, 7%). ... Risk
   of death by age of musician, accounting for time dependent study entry & the
   # of musicians at risk. Risk was estimated using a flexible spline which
   would allow a bump at age 27 to appear. ...  We identified three deaths at
   age 27 amongst 522 musicians at risk, giving a rate of 0.57 deaths per 100
   musician years. Similar death rates were observed at ages 25 (rate=0.56) &
   32 (0.54). There was no peak in risk around age 27, but the risk of death for
   famous musicians throughout their 20s & 30s was two to three times higher
   than the general UK population. ...  The 27 club is unlikely to be a real
   phenomenon. Fame may increase the risk of death among musicians, but this
   risk is not limited to age 27."
   -- [<A HREF="http://dx.doi.org/10.1136/bmj.d7799">doi:10.1136/bmj.d7799</A>]['16].
   (Also see [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_7">doi:10.1007/978-3-319-76433-7_7</A>] on the 27-club.)
      ("Statistical code and data are available at
      [<A HREF="http://www.hlth.qut.edu.au/ph/about/staff/barnett/MusicianFiles.zip">qut</A>]['11] with open access" -- 2011. Server not found 2016.
      But see "Musician mortality data, 1956-2007"
      -- [<A HREF="https://researchdatafinder.qut.edu.au/display/q1">www</A>]['16],
      data@[<A HREF="https://data.researchdatafinder.qut.edu.au/dataset/musician-mortality-data-">www</A>]['16].)
   (Also see abc[<A HREF="http://www.abc.net.au/science/articles/2011/12/21/3394834.htm">21/12/2011</A>].)
   [Also search for: 27club].

%A K. B. Korb
%A E. P. Nyberg
%A L. Hope
%T A new causal power theory
%B Causality in the Sciences
%I OUP
%D 2011
%K chapter, c2011, c201x, c20xx, zz0220, cause, causality, causal power, KBKorb,
   Bnet, Bayesian network, mutual, information, intervention, stats
%X (In, uk us isbn:0199574138; uk us isbn13:978-0199574131.)
   "The causal power of C over E is (roughly) the degree to which changes in C
   cause changes in E. A formal measure of causal power would be v.useful, as an
   aid to understanding & modelling complex stochastic systems. Previous
   attempts to measure causal power, such as those of Good (1961), Cheng (1997),
   & Glymour (2001), while useful, suffer from one fundamental flaw: they only
   give sensible results when applied to v.restricted types of causal system,
   all of which exhibit causal transitivity. Causal Bayesian networks, however,
   are not in general transitive. The chapter develops an information-theoretic
   alternative, causal information, which applies to any kind of causal B. n/w.
   Causal information is based upon three ideas. First ... that the system can
   be rep. causally as a B.n/wk. Second ... uses hypothetical interventions to
   select the causal from the non-causal paths connecting C to E. Third ... a
   variation on the information-theoretic measure mutual information to
   summarize the total causal influence of C on E. ... gives sensible results
   for a much wider variety of complex stochastic systems than prev. attempts &
   promises to simplify the interpretation & application of B.networks."
   -- [<A HREF="https://doi.org/10.1093/acprof:oso/9780199574131.003.0030">doi:10.1093/acprof:oso/9780199574131.003.0030</A>]['20].
   [Also search for: Bnet information].

%A D. Yong
%A Z. Ma
%A A. Buja
%T A sparse SVD method for high-dimensional data
%J arXiv
%M DEC
%D 2011
%K TR, c2011, c201x, c20xx, zz0916, matrix, sparse, SVD, decomposition,
   matrix, factorisation, factorization, approximate
%X "... approximating a large, noisy data table by a low-rank matrix with sparse
   singular vectors. The approximation is obtained from thresholded subspace
   iterations that produce the singular vectors simultaneously, rather than
   successively as in competing proposals. We introduce novel ways to estimate
   thresholding parameters which obviate the need for computationally expensive
   cross-validation. We also introduce a way to sparsely initialize the alg.
   for computational savings that allow our alg. to outperform the vanilla SVD
   on the full data table when the signal is sparse. A comparison with two
   existing sparse SVD methods suggests that [it] is computationally always
   faster & stat. always at least comparable to the better of the two competing
   algs."
   -- 1112.2433@[<A HREF="https://arxiv.org/abs/1112.2433">arXiv</A>]['16].
   (Also see SVD@[<A HREF="https://en.wikipedia.org/wiki/Singular_value_decomposition">wikip</A>]['16].)

%A C. W. Fox
%A S. J. Roberts
%T A tutorial on variational Bayesian inference
%J Art. Intel. Rev.
%V 38
%P 85-95
%D 2012
%K jrnl, c2012, c201x, c20xx, zz1121, variational Bayesian inference, VBI,
   stats
%X "... describes the mean-field VB approx. to inference in graphical models,
   using modern machine learning terminology rather than statistical physics
   concepts. It begins by seeking to find an approximate mean-field dist'n close
   to the target joint in the KL-div. sense. It then derives local node updates
   & reviews the recent Variational Message Passing framework."
   -- [<A HREF="https://doi.org/10.1007/s10462-011-9236-8">doi:10.1007/s10462-011-9236-8</A>]['21].
   Also see VB@[<A HREF="https://en.wikipedia.org/wiki/Variational_Bayesian_methods">wikip</A>]['21].
   [Also search for: VBI variational stats].

%A L. Chindelevitch
%A P.-R. Loh
%A A. Enayetallah
%A B. Berger
%A D. Ziemek
%T Assessing statistical significance in causal graphs
%J BMC Bioinformatics
%V 13
%P 35
%M FEB
%D 2012
%K MolBio, stats, c2012, c201x, c20xx, zz0312, signed causal graph, network,
   model, regulation, cause, ternary variable, test
%X "Causal graphs are an increasingly popular tool for the analysis of bio.
   datasets. ... signed causal graphs - directed graphs whose edges additionally
   have a sign denoting upregulation or downregulation - can be used to model
   regulatory n/works within a cell. ... compute a p-value for agreement between
   observed & model-predicted classifications of gene transcripts as upregulated
   downreg. or neither. Specifically, how likely are the class'ns to agree to
   the same extent under the null distn of the obs'd class'ns being randomized?
   ... we call 'Ternary Dot Product Distribution' owing to its math.form, can be
   viewed as a gen. of Fisher's exact test to ternary vars. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-13-35">doi:10.1186/1471-2105-13-35</A>]['12].
   [Also search for: Bayesian network stats].

%A S. Sra
%T A short note on parameter approximation for von Mises-Fisher distributions:
   and a fast implementation of I_s(x)
%J Comput. Stats.
%V 27
%N 1
%P 177-190
%M MAR
%D 2012
%K jrnl, c2012, c201x, c20xx, stats, statistics, probability, von Mises Fisher,
   distribution, vonMises, vMF, direction, kappa, concentration parameter,
   modified Bessel function, first kind
%X "... Maximum likelihood estimation for the vMF distribution turns out to be
   surprisingly hard because of a difficult transcendental equn that needs to
   be solved for computing the concentration parameter kappa.  ... we show that
   given the same amount of compn as [Tanabe et al] method, one can achieve
   more accurate approx. using a truncated Newton method. A more interesting
   contribution of this paper is a simple alg. for computing I_s(x): the
   modified Bessel fn of the first kind. Surprisingly, our naive implementation
   turns out to be several orders of magnitude faster for large arguments
   common to high-dimensional data ..."
   -- [<A HREF="http://dx.doi.org/10.1007/s00180-011-0232-x">doi:10.1007/s00180-011-0232-x</A>]'12].
   [Also search for: vonMises direction].

%A F. Simini
%A et al ...
%A A.-L. Barabasi
%T A universal model for mobility and migration patterns
%J Nature
%V 484
%P 96-100
%M APR
%D 2012
%K jrnl, stats, c2012, c201x, c20xx, model, gravity law, population movement,
   traffic, phone, trade, radiation model, cargo, shipping, transport processes,
   pattern
%X "... in 1946, but with roots that go back to the 18C, the gravity law is the
   prevailing f/work with which to predict population movement, cargo shipping
   volume & inter-city phone calls, [&] bilateral trade flows between nations.
   ... relies on adjustable parameters that vary from region to region & suffers
   from known analytic inconsistencies. Here we introduce a stochastic process
   capturing local mobility decisions that helps us analytically derive
   commuting & mobility fluxes that require as input only information on the
   popn distn. [This] radiation model predicts mobility patterns in good
   agreement with mob. & trans.patterns obs. ... from long-term migration
   patterns to commn volume between different regions. Given its parameter-free
   nature [it] can be applied in areas where we lack previous mobility
   measurements, sig. improving the predictive accuracy of most of the
   phenomena affected by mobility and transport processes."
   -- [<A HREF="http://dx.doi.org/10.1038/nature10856">doi:10.1038/nature10856</A>]['12].
   [Also search for: graphModel].

%A P. Turchin
%T Dynamics of political instability in the United States, 1780-2010
%J J. of Peace Res.
%V 49
%N 4
%P 577-591
%M JUL
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0912, human, social, behaviour, civil, society,
   stats, cliodynamics, trend, politics, political, unrest, instability, riot,
   lynching, terrorism, violence, USA, Roman
%X "... database on the dynamics of sociopolitical instability in the [US] ...
   1780 [to] 2010. The DB was cons. by digitizing data collected by prev.res.,
   [&] systematic searches of electronic media archives. ... 1,590 political
   violence events such as riots, lynchings, & terrorism. ... Spectral analysis
   detected two main oscillatory modes. The 1st is a v.long-term - secular -
   cycle, taking the form of an instability wave during the 2nd half of the 19th
   c., bracketed by two peaceful periods (the 1st quarter of the 19th c. & the
   middle decades of the 20th c., resp.). The 2nd is a 50-y. oscillation
   superimposed on the secular cycle, with peaks around 1870, 1920, & 1970.
   ... characteristic of the dynamics of political instability in many
   historical societies, such as ancient Rome & medieval & early-modern England,
   France, & Russia. A poss.expln ... is offered by the structural-demographic
   theory ... that labor oversupply leads to falling living stds & elite
   overproduction, & those, in turn, cause a wave of prolonged & intense
   sociopolitical instability."
   -- [<A HREF="http://dx.doi.org/10.1177/0022343312442078">doi:10.1177/0022343312442078</A>]['12].
   (But also see [<A HREF="http://dx.doi.org/10.1038/488024a">news</A>]['12].)

%A B. M. Lo
%A C. M. Visintainer
%A H. A. Best
%A H. A. Beydoun
%T Answering the myth: Use of emergency services on Friday the 13th
%J The American J. of Emergency Medicine
%V 20
%N 6
%P 886-889
%M JUL
%D 2012
%K jrnl, c2012, c201x, c20xx, zz1017, medicine, accident, rate, risk, risks,
   Friday 13, 13th, thirteenth, myth, myths, superstition, hospital,
   emergency, ED, admissions
%X "A total of 49,094 patient encounters were evaluated. Average ED visits for
   Friday the 13th were not increased compared with the F. before & after the
   month before. However, compared with the month after, there were fewer ED
   visits on F. the 13th (150.1 vs 134.7, P = .011). Of the 13 categories
   evaluated, only penetrating trauma was noted to have an increase risk
   associated with F. the 13th (odds ratio, 1.65; 95% confidence interval,
   1.04-2.61). No other category was noted to have an increase risk on F. the
   13th compared with the control dates.  ... Although the fear of F. the 13th
   may exist, there is no worry that an increase in volume occurs [then]
   compared with the other days studies. ..."
   -- [<A HREF="https://doi.org/10.1016/j.ajem.2011.06.008">doi:10.1016/j.ajem.2011.06.008</A>]['17].
   (Also see the abc[<A HREF="http://www.abc.net.au/news/health/2017-10-13/friday-the-13th-and-emergency-departments/9047644">13/10/2017]</A>], yes a Friday.)
   [Also search for: full moon risk].

%A K. P. Murphy
%T Machine Learning: A Probabilistic Perspective
%I MITpress
%P 1104
%S Adaptive Computation and Machine Learning
%M AUG
%D 2012
%K book, text, c2012, c201x, c20xx, zz0913, machine learning, stats, PMTK,
   probability, model
%X 1st ed 2012; hb us$85; uk us isbn:0262018020; uk us isbn13:978-0262018029.
   "... such topics as probability, optimization, and linear algebra as well as
   discussion of recent developments in the field, including conditional random
   fields, L1 regularization, and deep learning. ..."

%A M. S. Morgan
%T The World in the Model: How Economists Work and Think
%I CUP
%P 435
%M SEP
%D 2012
%K book, text, CUP, c2012, c201x, c20xx, zz0313, intro, stats, economic,
   economics, economy, model, models
%X  1st ed 2012; pb us$40; uk us isbn:0521176190; uk us isbn13:978-0521176194.
   Over 200 years, "[E] become a social science based on math. models in place
   of words. ... describes & analyses that change - both historically &
   philosophically - using ... case studies to illuminate the nature & the
   implications of these changes. ... offers a tourist guide to economics by
   focusing chapters on specific models, explaining how economists create them
   & how they reason with them. It is not a technical book; it is written for
   the intelligent person who wants to understand how economics works from the
   inside out. ..."

%A N. Silver
%T The Signal and the Noise: Why So Many Predictions Fail - but Some Don't
%I PenguinPress
%P 544
%M SEP
%D 2012
%K book, text, c2012, c201x, c20xx, zz1012, predict, prediction, model, stats,
   statistics, Bayesian, probability, forecast, forecasting, economic,
   confidence
%X 1st ed 2012; hb us$16; uk us isbn:159420411X; uk us isbn13:978-1594204111.
   "... examines the world of prediction, investigating how we can distinguish
   a true signal from a universe of noisy data. Most predictions fail, often at
   great cost to society, because most of us have a poor understanding of
   probability and uncertainty. Both experts and laypeople mistake more
   confident predictions for more accurate ones. But overconfidence is often
   the reason for failure. If our appreciation of uncertainty improves, our
   predictions can get better too. This is the 'prediction paradox': The more
   humility we have about our ability to make predictions, the more successful
   we can be in planning for the future. ..."
   [Also search for: zzPrediction].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A K. V. Mardia
%A et al
%T Mixtures of concentrated multivariate sine distributions with applications
   to bioinformatics
%J J. Appl. Stats.
%V 39
%N 11
%P 2475-2492
%M AUG
%D 2012
%K jrnl, stats, c2012, c201x, c20xx, zz0922, vonMises, direction, angle, angles,
   mixture model, directional, probability distribution, protein, MolBio, sine
%X "... study a mixture model of multivariate angular dist'ns. The distin
   treated here (multivariate sine dist'n) is a multivariate extension of the
   well-known von Mises distribution on the circle. The density of the sine
   dist'n has an intractable normalizing constant & here we propose to replace
   it in the concentrated case by a simple approx.. We study the EM alg. for
   this dist'n & apply it to a practical example from protein bioinf.."
   -- [<A HREF="https://doi.org/10.1080/02664763.2012.719221">doi:10.1080/02664763.2012.719221</A>]['22].
   [Also search for: vonMises direction]  &  [also search for: mixture model].

%A T. Niinimaki
%A P. Parviainen
%T Local structure discovery in Bayesian networks
%I UAI
%D 2012
%K conf, UAI, UAI2012, c2012, c201x, c20xx, zz0418, AI, II, Bayesian network,
   SLL algorithm, HITON, local structure, global, UHelsinki, UniHelsinki
%X "Learning a Bayesian network structure from data is an NP-hard ...
   present a score-based local learning alg. called SLL. We conjecture that [it]
   is theoretically sound in the sense that it is optimal in the limit of large
   sample size. Empirical results suggest that SLL is competitive when compared
   to the constraint-based HITON alg.. We also study the prospects of
   constructing the n/wk structure for the whole node set based on local results
   by presenting two algs. & comparing them to several heuristics."
   -- 1210.4888@[<A HREF="https://arxiv.org/abs/1210.4888">arXiv</A>]['18].
   (SLL -- Score based Local Learning.)

%A S. Greenland
%A C. Poole
%T Living with p values: Resurrecting a Bayesian perspective on frequentist
   statistics
%J Epidemiology
%V 24
%N 1
%P 62-68
%M JAN
%D 2013
%K jrnl, stats, statistics, c2013, c201x, c20xx, zz0713, Pvalue, value,
   Bayesian, Bayesianism, frequentist, significance, confidence interval,
   null hypothesis, hypotheses, model, prior, posterior, probability
%X "In response to the widespread abuse & misinterpretation of sig.tests of null
   hypotheses, some eds. & authors have strongly discouraged P values. However,
   null P values still thrive in most js. & are routinely misinterpreted as
   probs. of a 'chance finding' or of the null, when they are no such thing.
   This misuse may be lessened by recognizing correct Bayesian interp'ns. [E.g.]
   under weak priors, 95% confidence intervals approx. 95% posterior probability
   intervals, one-sided P values approx. directional posterior probabilities, &
   pt ests. approxs. posterior medians. Furthermore, under certain condns, a
   1-sided P value for a prior median provides an approx. lower bound on the
   posterior prob. that the pt est. is on the wrong side of that median. More
   generally, P values can be incorporated into a modern analysis framework that
   emphasizes measurement of fit, distance, & posterior prob. in place of
   'statistical significance' & accept/reject decisions."
   -- [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/23232611">pubM</A>]['13],
      [<A HREF="http://dx.doi.org/10.1097/EDE.0b013e3182785741">doi:10.1097/EDE.0b013e3182785741</A>]['13].
   (Also see [<A HREF="http://dx.doi.org/10.1126/science.341.6144.343-a">views</A>]['13],
   and [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A R. Campe
%T The Game of Probability: Literature and Calculation from Pascal to Kleist
%I StanfordUP
%S Cultural Memory in the Present
%P 504
%M JAN
%D 2013
%K book, text, c2013, c201x, c20xx, zz0113, intro, history, origins,
   probability, statistics, odds, game chance, gambling
%X 1st ed 2013; pb us$28; uk us isbn:080476865X; uk us isbn13:978-0804768658.
   "... revisits the 17th & 18th-c. 'probabilistic revolution,' providing a
   history of the relations between math. & rhetorical techniques, between the
   scientific & the aesthetic. ... games of chance as the model for probability
   & on the reinterpretation of aesthetic form as verisimilitude (a critical
   question for theoreticians of that new literary genre, the novel), the scope
   alone of C.'s book argues for probability's crucial role in the constitution
   of modernity."
   [Also search for: probability statistics history], and maybe add book.

%A P. Damien
%A P. Dellaportas
%A N. G. Polson
%A D. A. Stephens
%T Bayesian Theory and Applications
%I OUP
%P 700
%M MAR
%D 2013
%K OUP, book, text, c2013, c201x, c20xx, zz0413, stats, AI, II, Bayesian, MCMC
%X 1st ed 2013; hb us$144; uk us isbn:0199695601; uk us isbn13:978-0199695607.
   "The development of hierarchical models and Markov chain Monte Carlo (MCMC)
   techniques forms one of the most profound advances in Bayesian analysis since
   the 1970s and provides the basis for advances in virtually all areas of
   applied and theoretical Bayesian statistics.  ..."
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Bayes/">Bayes</A>].)

%A A. Clauset
%A R. Woodard
%T Estimating the historical and future probabilities of large terrorist events
%J Ann. Appl. Stat.
%V 7
%N 4
%P 1838-1865
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0215, stats, probability, power law, terrorism,
   terrorist, attack, event, 9/11, 911, nine11, prediction, zzPrediction
%X "... the 9/11 terrorist events produced nearly 3000 fatalities, nearly six
   times more than the next largest event. But, was this enormous loss of life
   statistically unlikely given modern terrorism's historical record? Accurately
   estimating the prob. of such an event is complicated by the large
   fluctuations in the empirical distribution's upper tail. We present a generic
   stat. alg. for making such ests., which combines semi-parametric models of
   tail behavior & a nonparametric bootstrap. Applied to a global DB of
   terrorist events, we est. the worldwide historical prob. of observing at
   least one 9/11-sized or larger event since 1968 to be 11-35%. These results
   are robust to conditioning on global variations in economic development,
   domestic v. international events, the type of weapon used & a truncated
   history that stops at 1998. We then use this procedure to make a data-driven
   statistical forecast of at least one similar event over the next decade."
   -- [<A HREF="http://projecteuclid.org/euclid.aoas/1387823295">www</A>]['15].

%A R. P. Browne
%A P. D. McNicholas
%T A mixture of generalized hyperbolic distributions
%J arXiv
%M MAY
%D 2013
%K TR, c2013, c201x, c20xx, zz0513, stats, mixture model, modelling,
   Gaussian, normal, tDistribution, skewT, probability distribution,
   classification, clustering, cluster
%X "... mixture of generalized hyperbolic distns as an alternative to the
   ubiquitous mixture of Gaussian distns as well as their near relatives of
   which the m. of multivariate t & skew-t distns are predominant. The math.
   development of our mixture of generalized hyperbolic distns model relies on
   its reln with the generalized inverse Gaussian distn. The latter is reviewed
   before our MMs are presented along with details of the aforesaid reliance.
   Param. est. is outlined within the [EM] framework before the performance of
   our MMs is illustrated in clustering applicns on simulated & real data. ...
   the ability of our models to recover params. for data from underlying
   Gaussian, t-, & skew-t distns is demonstrated. Finally, the role of these
   models as a superclass as well as the anticipated impact of these models on
   the model-based clustering, classification, & density est. literature is
   discussed with special focus on the role of G. mixtures."
   -- 1305.1036@[<A HREF="http://arxiv.org/abs/1305.1036">arXiv</A>]['13].
   [Also search for: mixture modelling].

%A B. Efron
%T Bayes' theorem in the 21st century
%J Science
%V 340
%N 6137
%P 1177-1178
%M JUN
%D 2013
%K views, c2013, c201x, c20xx, zz0613, Bayes, theorem, II, AI, probability,
   stats, statistics, statistical inference, controversial, priors, Pvalue,
   frequentist, significance test, likelihood
%X 'The term "controversial theorem" sounds like an oxymoron, but Bayes' theorem
   has played this part for two-and-a-half centuries. Twice it has soared to
   scientific celebrity, twice it has crashed, & it is currently enjoying
   another boom. The thm itself is a landmark of logical reasoning & the 1st
   serious triumph of stat.inference, yet is still treated with suspicion by
   most statisticians. There are reasons to believe in the staying power of its
   current popularity, but also some signs of trouble ahead.'
   -- [<A HREF="http://dx.doi.org/10.1126/science.1236536">doi:10.1126/science.1236536</A>]['13].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Bayes/">Bayes</A>] and [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. Tisi
%A G. Whitehouse
%A S. Maughan
%A N. Burdett
%T Interim report on quality of marking
%Q NFER
%M JUN
%D 2013
%K TR, c2013, c201x, c20xx, zz0714, teaching, education, exam marking, test,
   tests, mark, marks, reliability, fair, fairness, reproducibility,
   reproducible, GCSE, GCSEs, NFER, OfQual, uk, stats, model
%X [<A HREF="http://ofqual.gov.uk/documents/review-of-quality-of-marking-in-exams-in-a-levels-gcses-and-other-academic-qualifications-interim-report/">ofqual</A>]['14].
   Also, "A Review of Literature on Marking Reliability Research,"
   [<A HREF="http://ofqual.gov.uk/documents/report-for-ofqual-a-review-of-literature-on-marking-reliability-research-by-nfer/">ofqual</A>]['14].
   All at [<A HREF="http://ofqual.gov.uk/standards/research/quality-of-marking/">ofqual</A>]['14].

%A E. Liberty
%T Simple and deterministic matrix sketching
%J KDD
%D 2013
%K KDD, conf, c2013, c201x, c20xx, zz0916, matrix sketching, sketch,
   factorization, factorisation, approximate, PCA, sparse
%X "A sketch of a matrix A is another matrix B which is sig. smaller than A, but
   still approximates it well. Finding such sketches efficiently is an important
   building block in modern algorithms for approximating, for example, the PCA
   of massive matrices. This task is made more challenging in the streaming
   model, where each row of the input matrix can be processed only once and
   storage is severely limited. ... we adapt a well known streaming alg. for
   approximating item frequencies to the matrix sketching setting. [It] receives
   n rows of a large matrix A in R^{nxm} one after the other, in a streaming
   fashion. It maintains a sketch B in R^{lxm}, l << m ..."
   -- pdf@[<A HREF="http://www.cs.yale.edu/homes/el327/papers/simpleMatrixSketching.pdf">yale</A>]['16].
   [Also search for: matrix sketching] etc. (SVD, ...).

%A I. Chattopadhyaya
%A A. Kuchina
%A G. M. Suel
%A H. Lipson
%A Inverse Gillespie for inferring stochastic reaction mechanisms from
   intermittent samples
%J PNAS
%V 110
%N 32
%P 12990-12995
%M AUG
%D 2013
%K jrnl, PNAS, c2013, c201x, c20xx, zz1016, Eureka, AI, II, inference,
   Gillespies stochastic simulation, symbolic regression
%X "Gillespie stochastic simulation is used extensively to investigate
   stochastic phenomena ... The inverse problem, however, has remained largely
   unsolved: How to reconstruct the underlying reactions de novo from sparse
   observations. A key challenge is that often only aggregate concentrations,
   proportional to the population #s, are observable intermittently. We
   discovered that under specific assumptions, the set of relative popn updates
   in phase space forms a convex polytope whose vertices are indicative of the
   dominant underlying reactions. We demonstrate the validity of this simple
   principle by reconstructing stochastic models (reaction structure plus
   propensities) from a variety of simulated & experimental systems, where
   hundreds & even thousands of reactions may be occurring in between
   observations. In some cases, the inferred models provide mechanistic insight.
   ... can lead to the understanding of a broad range of phenomena ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1214559110">doi:10.1073/pnas.1214559110</A>]['16].
   Also search for: automaticProgramming].

%A A. Konagurthu
%A J. Collier
%T An information measure for comparing top k lists
%J arXiv
%M OCT
%D 2013
%O 2014 IEEE 10th Int. Conf. on e-Sci.
%K conf, TR, c2013, c201x, c20xx, zz0223, ArunK, JHC, top k list, compare,
   MML, MDL, rank, ranking, rankings, distance, partial, permutation, disarray
%X "Comparing the top k elements between two or more ranked results ...
   introduces a new measure to compare any two top k lists based on measuring
   the information these lists convey. Our method investigates the
   compressibility of the lists, & the length of the message to losslessly
   encode them gives a natural & robust measure of their variability. ..."
   -- 1310.0110@[<A HREF="https://doi.org/10.48550/arXiv.1310.0110">doi:10.48550/arXiv.1310.0110</A>]['23] arXiv, and
      [<A HREF="https://doi.org/10.1109/eScience.2014.39">doi:10.1109/eScience.2014.39</A>]['23] IEEE.
    [Also search for: permutation rank distance].

%A S. Bangalore
%A F. H. Masserli
%T Gun ownership and firearm-related deaths
%J Amer. J. Medicine
%V 126
%N 10
%P 873-876
%M OCT
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0913, USA, America, gun ownership, firearms,
   guns, public health, safety, risk, risks, death, crime, rate, homicide,
   murder, stats, shot, mass shooting, shootings
%X "... The number of guns per capita per country was a strong & indep.
   predictor of firearm-related death in a given country, whereas the predictive
   power of the mental illness burden was of borderline significance in a
   multivariable model. Regardless of exact cause & effect, however, the current
   study debunks the widely quoted hypothesis that guns make a nation safer."
   -- [<A HREF="http://dx.doi.org/10.1016/j.amjmed.2013.04.012">doi:10.1016/j.amjmed.2013.04.012</A>]['13], online Sept 2013.

%A V. E. Johnson
%T Revised standards for statistical evidence
%J PNAS
%V ?
%M NOV
%D 2013
%K jrnl, PNAS, c2013, c201x, c20xx, zz0214, statistics, stats, scientific,
   research, reproducibility, controversial, hypothesis testing, p value,
   Pvalue, nonreproducibility, frequentist, comparison, Bayesian, factors,
   evidence
%X "The lack of reproducibility of sci.research undermines public confidence in
   science & leads to the misuse of resources when researchers attempt to
   replicate & extend fallacious research findings. Using recent developments in
   Bayesian hypothesis testing, a root cause of nonreproducibility is traced to
   the conduct of sig.tests at inappropriately high levels of sig..
   Modifications of common stds of evidence are proposed to reduce the rate
   of nonreproducibility of scientific research by a factor of 5 or greater. ...
   ... evidence thresholds required for the declaration of a significant finding
   should be increased to 25 - 50:1, and to 100 - 200:1 for the declaration of a
   highly sig. finding. In terms of classical hypothesis tests, these evidence
   standards mandate the conduct of tests at the 0.005 or 0.001 level of sig.."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1313476110">doi:10.1073/pnas.1313476110</A>]['14]. (Online Nov 2013.)

%A F. Petitjean
%A G. I. Webb
%A A. E. Nicholson
%T Scaling log-linear analysis to high-dimensional data
%J Int. Conf. on Data Mining
%I IEEE
%M DEC
%D 2013
%K conf, ICDM, c2013, c201x, c20xx, zz0214, chordalysis, chordal graph, LLA,
   decomposable graphical model, log linear, logLinear, association discovery,
   analysis, II, statistics, stats, chi squared, chi2, viaFPj
%X "Association discovery is a fundamental data mining task. The primary
   statistical approach to assoc.disc. between vars. is log-linear analysis.
   Classical approaches to log-linear analysis do not scale beyond about ten
   vars.. We develop an efficient approach to log-linear analysis that scales to
   hundreds of vars. by melding the classical statistical machinery of log-
   -linear analysis with advanced data mining techniques from assoc. disc. &
   graphical modeling."
   -- Chordalysis@[<A HREF="http://sourceforge.net/projects/chordalysis/">sourcef'rge</A>]['14] inc. pdf,
      pdf@[<A HREF="http://www.csse.monash.edu.au/~webb/Files/PetitjeanEtAl13.pdf">monash</A>]['14],
      auth1@[<A HREF="http://www.tiny-clues.eu/Research/">.eu</A>]['14].
   [Also search for: decomposable graphical model] and
   [also search for: log linear model].

%A A. E. Biondo
%A A. Pluchino
%A A. Rapisarda
%A D. Helbing
%T Reducing financial avalanches by random investments
%J Phys. Rev. E
%V 88
%N 6
%P e062814 (7)
%M DEC
%D 2013
%K jrnl, eJrnl, c2013, c201x, c20xx, zz0114, stock exchange, market, trade,
   trading, bubble, crash, boom, bust, investor, SP 500, SP500, random strategy,
   stats, technical trader
%X "... consider a community of interacting investors, distributed in a small-
   -world network, who bet on the bullish (increasing) or bearish (decreasing)
   behavior of the market which has been spec. according to the S&P 500
   historical time series. Remarkably, we find that the size of herding-related
   avalanches in the community can be strongly reduced by the presence of a
   rel.small % of traders, randomly distributed inside the n/w, who adopt
   a random investment strategy. ... suggest a promising strategy to limit the
   size of financial bubbles & crashes. We also obtain that the resulting wealth
   distn of all traders corr.to the well-known Pareto power law, while that of
   random traders is exponential. In other words, for technical traders, the
   risk of losses is much greater than the probability of gains compared to
   those of random traders."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevE.88.062814">doi:10.1103/PhysRevE.88.062814</A>]['14].

%A R. Nuzzo
%T Scientific method: Statistical errors
%J Nature
%V 506
%N 7487
%P ?-?
%M FEB
%D 2014
%K news, views, c2014, c201x, c20xx, zz0214, statistics, stats, p value, values,
   Pvalue, Pvalues, error, wrong, Fisher, statistical significance, test,
   scientific research, error, non Bayesian
%X "P values, the 'gold standard' of statistical validity, are not as reliable
   as many scientists assume. ... The irony is that when UK statistician Ronald
   Fisher introduced the P value in the 1920s, he did not mean it to be a
   definitive test. He intended it simply as an informal way to judge whether
   evidence was significant in the old-fashioned sense: worthy of a second look.
   ... an abundance of confusion about what the P value means. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/506150a">doi:10.1038/506150a</A>]['13].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A D. J. Hand
%T The Improbability Principle: Why Coincidences, Miracles, and Rare Events
   Happen Every Day
%I ScientificAmerican
%P 288
%M FEB
%D 2014
%K book, text, DJHand, c2014, c201x, c20xx, zz0314, statistics, stats,
   probability, chance, coincidence, large numbers, rare event, miracle,
   lottery, unexpected
%X 1st ed 2014; hb us$20; uk us isbn:0374175349; uk us isbn13:978-0374175344.
   "... a firm grounding in a powerful set of laws: the laws of inevitability,
   of truly large numbers, of selection, of the probability lever, and of near
   enough. ..."
   [Also search for: DJHand stats].

%A M. Julia Flores
%A J. A. Gomez
%A A. M. Martinez
%T Domains of competence of the semi-naive Bayesian network classifiers
%J Info. Sci.
%V 260
%P 120-148
%M MAR
%D 2014
%K jrnl, c2014, c201x, c20xx, Spain, AI, II, classifier, AODE
%X "... want to discover which type of datasets, defined by certain range
   values of the complexity measures for supervised classn, fits for some of the
   most well-known semi-naive Bayesian n/w classifiers. This study is carried
   out on cts & discrete domains for naive B. & Averaged One-Dependence
   Estimators (AODE), which are two widely used incremental classifiers that
   provide some of the best trade-offs between error performance & efficiency.
   [&] an automatic proc. to advise on the best semi-naive BNC to use for
   classn, based on the values of certain complexity measures, is proposed."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ins.2013.10.007">doi:10.1016/j.ins.2013.10.007</A>]['14].  (NB. supervised classn.)
   auth3<!-- Ana, foosball --> was @ monash ~ c2012-2013.

%A T. Piketty
%T Capital in the Twenty-First Century
%I BelknapPress
%P 696
%M MAR
%D 2014
%K book, text, c2014, c201x, c20xx, zz0514, economics, capital, economic growth,
   trickle down, Reaganomics, Thatcherism, poverty, inequality, society,
   fairness, money, wealth, wealthy, rich, poor, world top income, tax records,
   18C, 21C, database, stats
%X 1st ed 2014; hb us$23; uk us isbn:067443000X; uk us isbn13:978-0674430006.
   "... analyzes a unique collection of data from 20 countries, ranging as far
   back as the 18th century, to uncover key economic & social patterns. ...
   will transform debate & set the agenda for the next generation of thought
   about wealth & inequality.  ... shows that modern economic growth & the
   diffusion of knowledge have allowed us to avoid inequalities on the
   apocalyptic scale predicted by Karl Marx. But we have not modified the deep
   structures of capital & inequality as much as we thought in the optimistic
   decades following WWII. The main driver of inequality - the tendency of
   returns on capital to exceed the rate of economic growth - today threatens to
   generate extreme inequalities that stir discontent & undermine democratic
   values. ..."
      (Also see "... based primarily on a huge database of tax records that P &
      a team of 30 researchers around the globe have assembled from more than
      20 countries, inc. the United States. ..."
      -- [<A HREF="http://dx.doi.org/10.1126/science.344.6186.826">doi:10.1126/science.344.6186.826</A>]['14],
         Sci., 344(6186), pp.826-827, May 2014.)
   (And [<A HREF="http://topincomes.g-mond.parisschoolofeconomics.eu/">database</A>]['14].)

%A M. J. Zaki
%A W. Meira jr
%T Data Mining and Analysis: Fundamental Concepts and Algorithms
%I CUP
%P 624
%M MAY
%D 2014
%K book, text, CUP, c2014, c201x, c20xx, zz0914, Gspan, stats, II,
   machine learning
%X (Sec.11.3, p.288-297, describes the 'Gspan' algorithm;
    [also search for: gSpan graph].)
   1st ed 2014; hb us$59; uk us isbn:0521766338; uk us isbn13:978-0521766333.
   "... book lays the basic foundations of [data analysis, pattern mining,
   clustering, & classification], & also covers cutting-edge topics such
   as kernel methods, high-dimensional data analysis, & complex graphs &
   networks. ..."   [via FPj.]

%A C. de la Fuente Marcos
%A R. de la Fuente Marcos
%T Recent multi-kiloton impact events: Are they truly random?
%J arXiv
%P 6
%M SEP
%D 2014
%K TR, c2014, c201x, c20xx, zz1014, meteor, meteoroid, impact, stats, NEOs,
   asteroid, superbolide, collision, location, year,
   risk, CTBTO, earth, solar system
%X "It is customarily assumed that Earth-striking meteoroids are completely
   random, and that all the impacts must be interpreted as uncorrel. events
   distributed according to Poisson stats.. [so] their impact dates must be
   uniformly spread throughout the year & their impact coords. must be evenly
   scattered on the surface of our planet. Here, we use a time- & yield-limited
   sample of Earth-impacting superbolides detected since 2000 to explore
   statistically this critical though freq. overlooked topic. We show that the
   cadence of these multi-kiloton impact events is incompatible with a random
   fall pattern at the 0.05 sig. level or better. This result is stat.robust &
   consistent with the observed distribution of the longitudes of the ascending
   nodes of near-Earth objects (NEOs). This lack of randomness is induced by
   planetary perturbations, in particular Jupiter's, & suggests that some of the
   recent, most powerful Earth impacts may be associated with resonant groups of
   NEOs &/or very young meteoroid streams. [so] the impact hazard of
   Chelyabinsk-like objects should peak at certain times in the year."
   -- 1409.0452v3@[<A HREF="http://arxiv.org/abs/1409.0452v3">arXiv</A>]['14].
   (Also see "CTBTO Has Detected 26 Major Asteroid Impacts in
              Earth's Atmosphere Since 2000"
   -- [<A HREF="http://newsroom.ctbto.org/2014/04/24/ctbto-detected-26-major-asteroid-impacts-in-earths-atmosphere-since-2000/">ctbto</A>]['14].)

%A D. T. Kenny
%T Stairway to hell: life and death in the pop music industry
%J The Conversation
%D 2014
%K news, c2014, c201x, c20xx, xx0916, 27 club, 27club, myth, myths, music,
   entertainer, musician death, deaths, lifespan, pop, rock and roll,
   Amy Winehouse, uSydney, uSyd
%X "... I've undertaken the first population study of performing pop musicians
   (n=12,665) from all popular genres who died between 1950 and June 2014 of
   whom 90.6% (11,478 musicians) were male. ...
   -- [<A HREF="http://sydney.edu.au/news/arts/2228.html?newsstoryid=14257">uSyd</A>]['16].
   (Also see [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_7">doi:10.1007/978-3-319-76433-7_7</A>] on the 27-club.)
   Also see,
   'The 27 Club is a myth: 56 is the bum note for musicians'
   -- The C@[<A HREF="http://theconversation.com/the-27-club-is-a-myth-56-is-the-bum-note-for-musicians-33586">19/11/2014</A>], and
   'Stairway to hell: life and death in the pop music industry'
   -- The C [<A HREF="https://theconversation.com/stairway-to-hell-life-and-death-in-the-pop-music-industry-32735">27/10/2014</A>].
   [Also search for: 27club music].

%A D. Colquhon
%T An investigation of the false discovery rate and the misinterpretation of
   p-values
%J Royal Soc. Open Sci.
%V ?
%P ?
%M NOV
%D 2014
%K eJrnl, c2014, c201x, c20xx, zz0515, stats, statistics, Pvalue, Pvalues,
   frequentist, errors, mistakes, false, significance test
%X "... If you use p=0.05 to suggest that you have made a discovery, you will be
   wrong at least 30% of the time. If, as is often the case, experiments are
   underpowered, you will be wrong most of the time. ... The simulation method
   is used also to evaluate the extent to which effect sizes are over-estimated,
   esp. in underpowered experiments. ... if you wish to keep your false
   discovery rate below 5%, you need to use a three-sigma rule, or to insist on
   p <= 0.001. And never use the word 'significantâ.'
   '... before anything was known of Lydgate's skill, the judgements on it had
   naturally been divided, depending on a sense of likelihood, situated perhaps
   in the pit of the stomach or in the pineal gland, & differing in its verdicts
   but not less valuable as a guide in the total deficit of evidence. George
   Eliot (Middlemarch, ch.45)' 'The standard approach in teaching, of stressing
   the formal definition of a p-value while warning against its
   misinterpretation, has simply been an abysmal failure. Sellke et al.'"
   -- [<A HREF="http://dx.doi.org/10.1098/rsos.140216">doi:10.1098/rsos.140216</A>]['15].
   [Also search for: Pvalue stats].

%A K. Laskey
%A R. Hanson
%A C. Twardy
%A W. Sun
%A S. Matsumoto
%T SciCast: A combinatorial prediction market for science and technology
   forecasting
%J GTP2014, Fifth Workshop on Game Theoretic Probability, CIMAT
%W Guanajuato
%M NOV
%D 2014
%K wShop, c2014, c201x, c20xx, zz0515, SciCast, CTwardy, prediction, predicting,
   forecasting, science, technology, group, crowd sourced, crowdsourced,
   www, GeorgeMasonUni
%X slides@[<A HREF="http://www.probabilityandfinance.com/GTP2014/Slides/Laskey.pdf">www</A>]['15].
   Also see [<A HREF="http://blog.scicast.org/">blog</A>].[<A HREF="http://scicast.org/">scicast.org</A>]['15].

%A W. Zhang
%A J. Li
%A X. Yong
%T Relational topic factorization for link prediction in document networks
%J Algorithms and Models for the Web Graph
%I SpringerVerlag
%S LNCS
%V 8882
%P 96-107
%M NOV
%D 2014
%K conf, c2013, c201x, c20xx, zz0916, Topic Factorization, network
%X "Link prediction is one of the fundamental problems in complex networks. ...
  focus on link prediction in document n/ws, in which nodes are text documents.
  We propose the rel. t. f. model (RTF), a model that combines topic models &
  matrix factorization. We also develop an efficient Monte Carlo EM alg. for
  learning the parameters. Empirical results show that our model outperforms
  other state-of-the-art ones & can give better understanding of the documents."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-319-13123-8_8">doi:10.1007/978-3-319-13123-8_8</A>]['16], in uk us isbn13:978-3-319-13122-1.

%A F. Petitjean
%A G. Forestier
%A G. Webb
%A A. E. Nicholson
%A Y. Chen
%A E. Keogh
%T Dynamic time warping averaging of time series allows faster and more accurate
   classification
%J ICDM
%P ?-?
%M DEC
%D 2014
%O J. Knowledge and Info. Sys. archive, 47(1), pp.1-26, Apr., 2016
%K conf, ICDM, c2014, c201x, c20xx, FPj, time warp, warping, series, centroid,
   nearest neighbour, timeSeries, time series
%X "... time series classification. However, because the best soln is typically
   the Nearest Neighbor alg. with the relatively expensive Dynamic Time Warping
   as the dist. ...  A commonly used technique to glean the benefits of the
   NN alg., without inheriting its undesirable time complexity, is to use the
   Nearest Centroid alg.. However because of the unique properties of (most)
   time series data, the centroid typically does not resemble any of the
   instances, an unintuitive & underappreciated fact. ... show that we can
   exploit a recent result to allow meaningful averaging of 'warped' times
   series ... allows us to create ultra-efficient Nearest "Centroid" classifiers
   that are at least as accurate as their more lethargic NN cousins."
   -- [<A HREF="https://doi.org/10.1007/s10115-015-0878-8">doi:10.1007/s10115-015-0878-8</A>]['19],
   [<A HREF="https://www.researchgate.net/publication/283943387_Faster_and_more_accurate_classification_of_time_series_by_exploiting_a_novel_dynamic_time_warping_averaging_algorithm">res-gate</A>]['19].
   [Also search for: time warping].

%A Gun Violence Archive
%D 2014
%K GVA, USA, US, America, gun violence, guns, NRA, public safety, data, stats,
   death, shooting, deaths, murder, killed, homicide, location,
   c2014, c201x, c20xx, zz0317
%X "Gun Violence Archive (GVA) is a not for profit corporation formed in
   2013 to provide free online public access to accurate information about
   gun-related violence in the United States. GVA will collect and check
   for accuracy, comprehensive information about gun-related violence in
   the U.S. and then post and disseminate it online."
    *2016, incidents 58,347, deaths 15,068.
    *2015, incidents 53,569, deaths 13,478.
    *2014, incidents 51,836, deaths 12,555.
   -- [<A HREF="http://www.gunviolencearchive.org/">www</A>][2017].
   (Also see The G
   [<A HREF="https://www.theguardian.com/world/2017/mar/20/mapping-gun-murders-micro-level-new-data-2015">www</A>][21/3/2017].)

%A Zuhe Zhang
%A B. Rubinstein
%A C. Dimitrakakis
%T On the differential privacy of Bayesian inference
%D 2015
%K c2015, c201x, c20xx, zz0521, differential privacy, stats, network, BN, Bnet,
   graphical model
%X "... how to communicate findings of Bayesian inference to third parties,
   while preserving the strong guarantee of differential privacy. ... four
   different algs. for private Bayesian inference on probabilistic graphical
   models. These include two mechanisms for adding noise to the Bayesian
   updates, either directly to the posterior parameters, or to their Fourier
   transform so as to preserve update consistency. We also utilise a recently
   introduced posterior sampling mechanism, for which we prove bounds for the
   specific but general case of discrete Bayesian networks ..."
   -- [<A HREF="https://hal.inria.fr/hal-01234215v2/document">inr'a</A>]['21],
   Also see DP@[<A HREF="https://en.wikipedia.org/wiki/Differential_privacy">wikip</A>]['21].
   [Also search for: differential privacy].

%A D. Trafimow
%A M. Marks
%T Editorial
%J Basic and Applied Psychology
%V 37
%N 1
%P 1-2
%D 2015
%K c2015, c201x, c20xx, zz0315, stats, statistics, science, p value, Pvalue,
   NHSTP, significance test, testing, null, hypothesis, frequentist, Bayesian,
   likelihood, controversial, controversial
%X "The Basic and Applied Social Psychology (BASP) 2014 Editorial emphasized
   that the null hypothesis significance testing procedure (NHSTP) is invalid,
   and thus authors would be not required to perform it ..."
   -- [<A HREF="http://dx.doi.org/10.1080/01973533.2015.1012991">doi:10.1080/01973533.2015.1012991</A>]['15].

%A J. T. Leek
%A R. D. Peng
%T What is the question?
%J Science
%V 347
%N 6228
%P 1314-1315
%M MAR
%D 2015
%K views, c2015, c201x, c20xx, zz0315, stats, statistics, big data,
   science, scientific, research, reproducible, reproducibility
%X "... the era of big data has pushed the issue of reproducibility out of the
   pages of academic journals & into the popular consciousness. Just weeks ago,
   a paper about the relationship between tissue-specific cancer incidence &
   stem cell divisions was widely misreported because of misunderstandings about
   the primary statistical argument in the paper. Public pressure has
   contributed to the massive recent adoption of reproducible research tools,
   with corr. improvements in reproducibility. But an analysis can be fully
   reproducible & still be wrong. Even the most spectacularly irreproducible
   analyses - like those underlying the ongoing lawsuits over failed genomic
   signatures for chemotherapy assignment - are ultimately reproducible. Once an
   analysis is reproducible, the key question we want to answer is, 'Is this
   data analysis correct?' We have found that the most frequent failure in data
   analysis is mistaking the type of question being considered."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaa6146">doi:10.1126/science.aaa6146</A>]['15].

%A A. Desai
%A M. Ghashami
%A J. M. Phillips
%T Improved practical matrix sketching with guarantees
%J IEEE Trans. on Knowledge and Data Eng.
%M APR
%D 2015
%K conf, ESA, c2015, c201x, c20xx, zz0916, matrix sketching, sketch,
   approximation, SVD, iSVD, APT
%X "... This paper attempts to categorize & compare most known methods under
   row-wise streaming updates with provable guarantees, & then to tweak some of
   these methods to gain practical improvements while retaining guarantees. ...
   observe that a simple heuristic iSVD, with no guarantees, tends to outperform
   all known approaches in terms of size/error trade-off. We modify the best
   performing method with guarantees FrequentDirections under the size/error
   trade-off to match the performance of iSVD & retain its guarantees. We also
   demonstrate some adversarial datasets where iSVD performs quite poorly. ..."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-662-44777-2_39">doi:10.1007/978-3-662-44777-2_39</A>]['16].
   Also see paper at 1501.06561@[<A HREF="https://arxiv.org/abs/1501.06561">arXiv</A>]['16].

%A J. T. Leek
%A R. D. Peng
%T Statistics: P values are just the tip of the iceberg
%J Nature
%V 520
%N 7549
%P 612
%M APR
%D 2015
%K views, c2015, c201x, c20xx, zz0515, Pvalue, Pvalues, stats, significance,
   tests, hypothesis, test, controversial, controversial, frequentist
%X "There is no statistic more maligned than the P value. Hundreds of papers &
   blogposts have been written about what some statisticians deride as
   'null hypothesis significance testing' ... NHST deems whether the results of
   a data analysis are important on the basis of whether a summary statistic
   (such as a P value) has crossed a threshold. Given the discourse, it is no
   surprise that some hailed as a victory the banning of NHST methods (& all of
   statistical inference) in the J.Basic & Applied Social Psychology in
   February. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/520612a">doi:10.1038/520612a</A>]['15].
   [Also search for: statistics Pvalue controversial].

%A T. Vigen
%T Spurious Correlations
%I HachetteBooks
%P 208
%M MAY
%D 2015
%K book, text, c2015, c201x, c20xx, zz0615, statistics, stats, correlation,
   cause, effect, causation, funny, haha, ha ha
%X 1st ed 2015; hb us$14; uk us isbn:0316339431; uk us isbn13:978-0316339438.
   "... 'correlation does not equal causation' through hilarious graphs inspired
   by V's viral website. Is there a correlation between Nic Cage films and
   swimming pool accidents? What about beef consumption and people getting
   struck by lightning? Absolutely not. But that hasn't stopped millions of
   people from going to tylervigen.com ..."

%A J. Li
%A L. Schmidt
%T A nearly optimal and agnostic algorithm for properly learning a mixture of
   k Gaussians, for any constant k
%J arXiv
%M JUN
%D 2015
%K TR, arXiv, c2015, c201x, c20xx, zz0615, mixture model, modelling, Gaussian,
   normal, stats, statistics
%X "... One notion of learning a GMM is proper learning: here, the goal is to
   find a mixture of k Gaussians M that is close to the density f of the unknown
   distn from which we draw samples. The dist. between M & f is typically
   measured in the total variation or L1-norm. ... The sample complexity of our
   alg. is O~(k/eps^2) & the running time is (k log(1/eps))^O(k^4)+O~(k/eps^2).
   It is well-known that this sample complexity is optimal (up to log factors),
   & it was already achieved by prior work. However, the best known time
   complexity for proper learning a k-GMM was O~(1/eps^(3k-1)). In particular,
   the dependence between 1/eps & k was exponential. We sig. improve this
   dependence by replacing the 1/eps term with a log(1/eps) while only
   increasing the exponent moderately. Hence, for any fixed k, the
   O~(k/eps^2) term dominates our running time, & thus our alg. runs in time
   which is nearly-linear in the # of samples drawn. Achieving a running time of
   poly(k,1/eps) for proper learning of k-GMMs has recently been stated as an
   open problem by multiple researchers, & we make progress on this q.. ..."
   -- 1506.01367@[<A HREF="http://arxiv.org/abs/1506.01367">arXiv</A>]['15].
   [Also search for: mixture model Gaussian].

%A H. G. Schaathun
%A Evaluation of splittable pseudo-random generators
%J JFP
%V 25
%P e6 (20pp)
%M JUN
%D 2015
%K jrnl, JFP, c2015, c201x, c20xx, zz0715, FP, parallel, RNG, PRNG, SPRNG,
   splittable pseudo random number generator, split, Lehmer trees, leapfrog,
   subsequencing, substreaming
%X "Pseudo-random number gen. ... . In the case of seq. proc. the problem is
   v.well researched, but parallel proc. raises new problems whereof far too
   little is currently understood. Splittable pseudo-r. g. (S-PRNG) have been
   proposed to meet the challenges of parallelism. While applicable to any
   programming paradigm, they are designed to be particularly suitable for pure
   func. prog.. ... review & evaluate known constructions of such generators, &
   we identify flaws in several large classes of generators, inc. Lehmer trees,
   the implementation in Haskell's std library, leapfrog, & subsequencing
   (substreaming)."
   -- [<A HREF="http://dx.doi.org/10.1017/S095679681500012X">doi:10.1017/S095679681500012X</A>]['15],
   or [<A HREF="http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=9786785&fulltextType=RA&fileId=S095679681500012X">www</A>]['15].
   [Also search for: PRNG random].

%A P. Kasarapu
%T Modelling of directional data using Kent distributions
%J arXiv
%M JUN
%D 2015
%K TR, arXiv, c2015, c201x, c20xx, zz0715, MML, directional, direction, Kent,
   probability distribution, vonMises Fisher, vMF, direction, R3, sphere, mdl,
   aic, II, minimum message length, stats, Monash, description
%X "... To model asymmetrically distrib. data on a 3D sphere, Kent distns are
   often used. The moment estimates of the params. are typically used in
   modelling tasks involving K.distns. However, these lack a rigorous stat.
   treatment. ... introduce a Bayesian estimation of the params. of the K.distn
   ... employ the Bayesian information-theoretic paradigm of Minimum Message
   Length (MML) to bridge this gap & derive reliable estimators.
   The inferred params. are subs. used in mixture modelling of K.distns.
   ... also addressed using [MML]. We demonstrate the superior performance of
   the derived MML-based param. ests. [v.] the trad. estimators. We apply the
   MML principle to infer mixtures of K.distns to model empirical data
   corr.to protein conformations. We demonstrate the effectiveness of K.
   models to act as improved descriptors of protein structural data [v.]
   commonly used von Mises-Fisher distns. "
   -- 1506.08105@[<A HREF="http://arxiv.org/abs/1506.08105">arXiv</A>]['15].
   [Also search for: direction probability distribution].

%A J.-P. Baudry
%T Gaussian mixture models
%J Stats and Computing
%I SpringerVerlag
%V 25
%N 4
%P 713-726
%M JUN
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0715, model, stats, EM algorithm
%X "... the EM alg. has well-documented drawbacks: its soln could be highly
   dependent from its initial posn & it may fail as a result of degeneracies.
   We stress the practical dangers of theses limitations & how carefully they
   should be dealt with. Our main conclusion is that no method enables to
   address them satisfactory in all situations. But improvements ...
   first, using a penalized log-likelihood of Gaussian mixture models in a
   Bayesian regularization perspective &, second, choosing the best among
   several relevant initialisation strategies. ... also propose new recursive
   initialization strategies ... They are compared with std init. procs. through
   numerical experiments & their effects on model seln criteria are analyzed."
   -- [<A HREF="http://dx.doi.org/10.1007/s11222-015-9561-x">doi:10.1007/s11222-015-9561-x</A>]['15] ($)?
   [Also search for: mixture model].

%T Estimating the reproducibility of psychological science
%Q Open Science Collaboration
%J Science
%V 349
%N 6251
%P ?-?
%M AUG
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0416, Nosek, science, scientific, research,
   reproducible, reproducibility, reliability, project, psycology,
   statistics, stats, significance, CI, study, experiment
%X "... We conducted replications of 100 experimental & correlational studies
   published in three psychology j. using high-powered designs & original
   materials when available. Replication effects were half the magnitude of
   original effects, representing a substantial decline. Ninety-seven percent of
   original studies had statistically sig. results. Thirty-six percent of
   replications had statistically sig. results; 47% of original effect sizes
   were in the 95% [CI] of the replication effect size; 39% of effects were
   subjectively rated to have replicated the original result; & if no bias in
   original results is assumed, combining original & replication results left
   68% with stat. sig. effects. Correlational tests suggest that replication
   success was better predicted by the strength of original evidence than by
   characteristics of the original & replication teams."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aac4716">doi:10.1126/science.aac4716</A>]['16].
   (* Also see,
     'Response to Comment on "Estimating the reproducibility of
      psychological science",'
      -- [<A HREF="http://dx.doi.org/10.1126/science.aad9163">doi:10.1126/science.aad9163</A>][4/3/2016]. *)

%A G. Radick
%T Beyond the "Mendel-Fisher controversy"
%J Science
%V 350
%N 6257
%P 159-160
%M OCT
%D 2015
%K views, c2015, c201x, c20xx, zz1015, Mendel, Mendelian, science, biology,
   genetics, genes, dominant, recessive, pea varieties, stats, statistics
%X "One hundred & fifty years ago, Gregor Mendel delivered his lectures on
   'Experiments on Plant Hybrids,' going on to publish them in 1866. Around the
   world, celebrations of the monk whose work with pea varieties made him the
   father of genetics are under way. Mendel has alas acquired another, less
   auspicious title, as 'the father of scientific misconduct,' owing to
   suspicions that he faked some of his data. The suspicions have turned out to
   be groundless. Along the way, however, they not only damaged Mendel's
   reputation unfairly but, as a look at the history of the controversy shows,
   sent critical discussion of his data down a sidetrack."
   -- [<A HREF="http://dx.doi.org/10.1126/science.aab3846">doi:10.1126/science.aab3846</A>]['15].

%A W. L. Palmer
%A A. Bottle
%A P. Aylin
%T Association between day of delivery and obstetric outcomes: observational
   study
%J BMJ
%V 351
%M NOV
%D 2015
%K jrnl, BMJ, c2015, c201x, c20xx, zz1115, stats, periodic, day, week,
   weekend effect, birth, baby, babies, mother, woman, women, human, health,
   risk, risks, UK, NHS
%X "... maternal & neonatal records (1,332,835 deliveries & 1,349,599 births
   between 1 April 2010 & 31 March 2012) within the nationwide administrative
   dataset for English National Health Service hospitals by day of the week. ...
   Performance across four of the seven measures was sig. worse for women
   admitted, & babies born, at weekends. In particular, the perinatal mortality
   rate was 7.3 per 1000 babies delivered at weekends, 0.9 per 1000 higher than
   for weekdays (adjusted odds ratio 1.07, 95% CI 1.02 to 1.13). ..."
   -- [<A HREF="http://dx.doi.org/10.1136/bmj.h5774">doi:10.1136/bmj.h5774</A>]['15].

%A J. Textor
%A A. Idelberger
%A M. Liskiewicz
%T Learning from pairwise marginal independencies
%J UAI
%D 2015
%K conf, UAI, UAI15, UAI2015, c2015, c201x, c20xx, zz0718, DAG, maths, graph,
   causal, model, graphs, independency, algorithm
%X "We consider graphs that represent pairwise marginal independencies amongst a
   set of variables ([e.g.] the zero entries of a covariance matrix for normal
   data). We characterize the DAGs that faithfully explain a given set of
   independencies, & derive algs. to efficiently enumerate such structures. Our
   results map out the space of faithful causal models for a given set of
   pairwise marginal independence relations. This allows us to show the extent
   to which causal inference is possible without using conditional independence
   tests."
   -- 1508.00280@[<A HREF="https://arxiv.org/abs/1508.00280">arXiv</A>]['18],
      pdf@[<A HREF="http://auai.org/uai2015/proceedings/papers/221.pdf">uai</A>]['18].

%A A. Spencer
%T World of Numbers
%I Xoum Publ., Sydney
%M NOV
%D 2015
%K book, number, c2015, c201x, c20xx, music, 27 club, 27club, Kenny
%X isbn:1921134860; isbn13:9781921134869.
   On p.123 is a histogram (possibly with age 55 duplicated)
   of the number of musicians who died at various ages, taken from
   the work of D.T.Kenny re the '27club' and musician mortality.
   Accompanying text says,
      "144 died at 27 (re the "27 club") and 239 died at mode-age (56)."
   (Also see [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_7">doi:10.1007/978-3-319-76433-7_7</A>] on the 27-club.)
   [Also search for: music 27club]  and  [also search for: Kenny music].

%A E. Sava
%A C.Twardy
%A R. Koester
%A M.Sonwalkar
%T Evaluating lost person behavior models
%J Transactions in Geographic Information Systems
%P 38-53
%N 1
%V 20
%D 2016
%K jrnl, stats, c2016, c201x, c20xx, zz1117, missing people, persons,
   search, rescue, USA, watershed, wilderness, bush, MapScore, model
%X "US wilderness search and rescue consumes thousands of person-hours and
   millions of dollars annually. ... Planning begins with a probability map
   showing where the lost person is likely to be found. The MapScore project
   described here provides a way to evaluate probability maps using actual
   historical searches. In this work we generated probability maps the Euclidean
   distance tables in (Koester 2008), and using Doke's (2012) watershed model.
   Watershed boundaries follow high terrain and may better reflect actual
   barriers to travel. We also created a third model using the joint
   distribution using Euclidean and watershed features. On a metric where random
   maps score 0 and perfect maps score 1, the Euclidean distance model scored
   0.78 (95%CI: 0.74-0.82, on 376 cases). The simple watershed model by itself
   was clearly inferior at 0.61, but the Combined model was slightly better at
   0.81 (95%CI: 0.77-0.84)."
   -- [<A HREF="https://doi.org/10.1111/tgis.12143">doi:10.1111/tgis.12143</A>]['17].
   [Also search for: search rescue].

%E A.-S. Antoniou
%E C. L. Cooper
%T Coping, Personality and the Workplace: Responding to Psychological Crisis and
   Critical Events
%I Routledge
%S Psychological and Behavioural Aspects of Risk
%P 350
%M FEB
%D 2016
%K book, c2016, c201x, c20xx, zz0317, risk, risks, stats, stress,
   Kenny, music, 27 club, 27club
%X "...  Coping, Personality and the Workplace offers theory, research and
   practice on our ability to cope with dangerous situations, critical
   incidents or other work crises. The chapters include perspectives on social
   and health habits and risks; gender and age differences as well as a range of
   different sources of threat: financial, psychological and physical; those
   within and outside the individual's control; immediate and chronic. ..."
   revised ed 2017; hb us$130;
   uk us isbn:1472416821; uk us isbn13: 978-1472416827.
   (I believe it includes a chapter, ' Morbidity and mortality in
    popular musicians: An examination by era, sex and music genre',
    by D.T.Kenny on musicians [also search for: 27club music] .)
   (Also see [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_7">doi:10.1007/978-3-319-76433-7_7</A>] on the 27-club.)

%A L. B. Thingholm
%A L. Andersen
%A E. Makalic
%A M. C. Southey
%A M. Thomassen
%A L. Lotte Hansen
%T Strategies for integrated analysis of genetic, epigenetic, and gene
   expression variation in cancer: Addressing the challenges
%J Front. Genet.
%M FEB
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0720, review, genetic, GWAS,
   UniMelb, UMelb
%X "... review article will provide an introduction to integration strategies
   used for analyzing genetic risk factors for cancer. We critically examine the
   ability of these strategies to handle the complexity of the human genome and
   also accommodate information about the biological and functional interactions
   between the elements that have been measured - making the assessment of
   disease risk against a composite genomic factor possible. The focus of this
   review is to provide an overview and introduction to the main strategies and
   to discuss where there is a need for further development."
   -- [<A HREF="https://doi.org/10.3389/fgene.2016.00002">doi:10.3389/fgene.2016.00002</A>]['20].
   (Also see GWAS@[<A HREF="https://en.wikipedia.org/wiki/Genome-wide_association_study">wikip</A>]['20].)

%A D. F.Schmidt
%A E. Makalic
%T Minimum message length analysis of multiple short time series
%J Stats. and Prob. Lett.
%V 110
%P 318-328
%M MAR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0720, MML, mdl, multiple short time series,
   several, many, timeSeries, trajectory, stats, model, conditional likelihood
%X "... applies the Bayesian minimum message length principle to the multiple
   short time series problem, yielding satisfactory estimates for all model
   parameters as well as a test for autocorrelation. Connections with the method
   of conditional likelihood are also discussed."
   -- [<A HREF="https://doi.org/10.1016/j.spl.2015.09.021">doi:10.1016/j.spl.2015.09.021</A>]['20], and
   2O15 preprint@[<A HREF="https://www.researchgate.net/profile/Daniel_Schmidt7/publication/283535908_Minimum_message_length_analysis_of_multiple_short_time_series/links/5a5ae4364585154502749234/Minimum-message-length-analysis-of-multiple-short-time-series.pdf">r'srchg'te</A>]['20].

%A N. Milosevic
%T Equity forecast: Predicting long term stock price movement using
   machine learning
%J arXiv
%M MAR
%D 2016
%K TR, c2016, c201x, c20xx, zz0316, prediction, stocks, shares, stock exchange,
   equity, equities, price, trading, movement, investment, finance, economics,
   AI
%X "Long term investment is one of the major investment strategies. However,
   calculating intrinsic value of some company & evaluating shares for long term
   investment is not easy ... [!] So far, little help in predicting the dirn of
   the company value over the longer period of time has been provided from the
   machines. ... present a machine learning aided approach to evaluate the
   equity's future price over the long time. [It] is able to correctly predict
   whether some company's value will be 10% higher or not over the period of
   one year in 76.5% of cases."
   -- 1603.00751@[<A HREF="http://arxiv.org/abs/1603.00751">arXiv</A>]['16].

%A M. V. Hauge
%A M. D. Stevenson
%A D. K. Rossmo
%A S. C. Le Comber
%T Tagging Banksy: Using geographic profiling to investigate a
   modern art mystery
%J J. of Spatial Sci.
%V ?
%N ?
%P ?-?
%M MAR
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0316, street art, Banksy, profile, model, stats,
   geographical, location, , incidents, criminology, epidemiology, events,
   incidents, terrorism, graffiti
%X "The pseudonymous artist Banksy is one of the UK's most successful
   contemporary artists, but his identity remains a mystery. ... use a Dirichlet
   process mixture (DPM) model of geographic profiling, a math. tech. developed
   in criminology & finding increasing application within ecology & epidemiology
   to analyse the spatial patterns of B. artworks in Bristol & London. ...
   calculates the probability of 'offender' residence across the study area. ...
   highlights areas assoc. with one prominent candidate (e.g., his home),
   supporting his identification as Banksy. ... support prev. suggestions that
   analysis of minor terrorism-related acts (e.g., graffiti) could be used to
   help locate terrorist bases before more serious incidents occur, & provides
   a fascinating example of the application of the model to a complex,
   real-world problem."  (online 3/2016.)
   -- [<A HREF="http://dx.doi.org/10.1080/14498596.2016.1138246">doi:10.1080/14498596.2016.1138246</A>]['16].
   (Also see [<A HREF="http://www.bbc.com/news/science-environment-35645371">bbc</A>]['4/3/2016].)

%A M. Baker
%T Statisticians issue warning over misuse of P values.  Policy statement aims
   to halt missteps in the quest for certainty
%J Nature
%V 531
%N 7593
%M MAR
%D 2016
%K news, c2016, c201x, c20xx, zz0316, P value, Pvalue, values, stats,
   statistics, misuse, hypothesis, reproduce, replicate, ASA
%X "Misuse of the P value - a common test for judging the strength of scientific
   evidence - is contributing to the number of research findings that cannot be
   reproduced, the American Statistical Association (ASA) warns ..."
   -- [<A HREF="http://dx.doi.org/10.1038/nature.2016.19503">doi:10.1038/nature.2016.19503</A>][16].
   [Also search for: Pvalue stats].

%A D. T. Kenny
%A A. Asher
%T Life expectancy and cause of death in popular musicians: Is the popular
   musician lifestyle the road to ruin?
%J Medical Problems of Performing Artists
%V 31
%N 1
%P 37-44
%M MAR
%D 2016
%K c2016, c201x, c20xx, zz0916, music, musician death, deaths, 27 club, 27club,
   mortality, lifespan, pop, rock and roll, entertainer, uSydney
%X "Does a combination of lifestyle pressures & personality, as reflected in
   genre, lead to the early death of popular musicians? We explored overall
   mortality, cause of death, & changes in patterns of death over time & by
   music genre membership in popular musicians who died between 1950 & 2014. The
   death records of 13,195 popular musicians were coded for age & year of death,
   cause of death, gender, & music genre. ... Results showed that popular
   musicians have shortened life expectancy compared with comparable general
   populations. Results showed excess mortality from violent deaths (suicide,
   homicide, accidental death, including vehicular deaths & drug overdoses) &
   liver disease for each age group studied compared with population mortality
   patterns. These excess deaths were highest for the under-25-year age group &
   reduced chronologically thereafter. ..."
   -- [<A HREF="http://dx.doi.org/10.21091/mppa.2016.1007">doi:10.21091/mppa.2016.1007</A>]['16]($).
   [Also search for: music 27club].
   (Also see [<A HREF="https://doi.org/10.1007/978-3-319-76433-7_7">doi:10.1007/978-3-319-76433-7_7</A>] on the 27-club.)

%A S. N. Goodman
%T Aligning statistical and scientific reasoning
%J Science
%V 352
%N 6290
%P 1180-1181
%M JUN
%D 2016
%K jrnl, c2016, c201x, c20xx, zz0816, statistics, stats, Pvalue, significance,
   hypothesis testing, defn, definition
%X "... recent release of a statement from the American Statistical Association
   (ASA), with the deceptively innocuous title, 'ASA statement on statistical
   significance and p-values' ... The formal defn of P value is the probability
   of an observed data summary (e.g., an average) and its more extreme values,
   given a specified mathematical model and hypothesis (usually the 'null'). The
   problem is that this index by itself is not of particular interest. What
   scientists want is a measure of the credibility of their conclusions, based
   on observed data. The P value neither measures that nor is it part of a
   formula that provides it. ...">  [16 refs.]
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaf5406">doi:10.1126/science.aaf5406</A>]['16].
   [Also search for: Pvalue stats].

%A N. Veldt
%A A. Wirth
%A D. F. Gleich
%T Correlation clustering with low-rank matrices
%J arXiv
%M NOV
%D 2016
%K TR, c2016, c201x, c20xx, zz1216, correlation clustering, low rank, matrix,
   zonotope, similar, similarity
%X "Correlation clustering is a technique for aggregating data based on
   qualitative information about which pairs of objects are labeled 'similar' or
   'dissimilar.' Because the optimization problem is NP-hard ... [But]
   we explore a new approach ... by considering how to solve the problem when
   the data to be clustered can be represented by a low-rank matrix. ...
   We prove in particular that ... can be solved in polynomial time when the
   underlying matrix is +ve semidefinite with small constant rank, but that the
   task remains NP-hard in the presence of even one negative eigenvalue. ...
   we develop an alg. for efficiently solving low-rank +ve semidefinite
   c.c. by employing a procedure for zonotope vertex enumeration. ..."
   -- 1611.07305@[<A HREF="https://arxiv.org/abs/1611.07305">arXiv</A>]['16].

%A E. Makalic
%A D. F. Schmidt
%T High-dimensional Bayesian regularised regression with the BayesReg package
%J arXiv
%M NOV
%D 2016
%K TR, c2016, c201x, c20xx, zz0720, BayesReg, regression, stats, R, RR
%T "B. penalized regression techniques, such as the B. lasso & the B. horseshoe
   estimator ... However, s/w implementing state-of-the-art B.penalized
   regression, outside of general purpose Markov chain M.C. platforms such as
   STAN, is relatively rare. This paper introduces bayesreg, a new toolbox for
   fitting B.penalized regression models with continuous shrinkage prior
   densities. ... features B.linear regression with Gaussian or heavy-tailed
   error models & B. logistic regression with ridge, lasso, horseshoe &
   horseshoe+ ests.. ... is free, open-source & available for use with the
   MATLAB & R numerical platforms."
   -- 1611.06649@[<A HREF="https://arxiv.org/abs/1611.06649">arXiv</A>]['20].

%A A. L. Stephenson
%A et al ...
%A C. H. Goss
%T Survival comparison of patients with cystic fibrosis in Canada and the
   United States: A population-based cohort study
%J Annals of Internal Medicine
%V ?
%M MAR
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0317, human, health, medicine, Cystic Fibrosis,
   disease, illness, Canada, USA, America, politics, health care, insurance,
   cost, Obamacare, stats
%X "In 2011, the median age of survival of patients with cystic fibrosis
   reported in the [US] was 36.8 years, compared with 48.5 y. in Canada. ...
   Median age of survival in patients with [CF] increased in both countries
   between 1990 & 2013; however, in 1995 & 2005, survival in C. increased at a
   faster rate than in the US (P < 0.001). On the basis of contemporary data
   from 2009 to 2013, the median age of survival in C. was 10 y. greater than in
   the US (50.9 vs. 40.6 y., resp.). ... Differential access to transplantation,
   increased posttransplant survival, & differences in health care systems may,
   in part, explain the Canadian survival advantage."
   -- [<A HREF="http://dx.doi.org/10.7326/M16-0858">doi:10.7326/M16-0858</A>]['17].
   (Also see the [<A HREF="http://www.bbc.com/news/world-us-canada-39410236">bbc</A>]['17].

%A D. Hemenway
%T Fight the silencing of gun research
%J Nature
%V 546
%P 345-347
%M JUN
%D 2017
%K news, views, c2017, c201x, c20xx, zz0617, gun, guns, stats, statistics,
   firearm, firearms, US, USA, law, death, gunshot, shooting, NRA, violence,
   homicide, murder, suicide, quote, quotable
%X "In the half-century since the assassination of Martin Luther King, more
   civilians in the United States have been killed with guns than American
   soldiers have died in all US wars since the nation was founded in 1776.
   Currently, on an average day, about 300 Americans are shot and 100 die from
   gunshot wounds - in murders, attempted suicides or accidents ...
   Among the world's two-dozen highest-income countries, the US has avg. rates
   of non-gun crime & violence. But with many more guns & the weakest gun laws,
   it has by far the most gun deaths per capita. An American 5- to 14-year-old
   is more than 18 times more likely to be murdered with a gun, 11 times more
   likely to use a gun to take their own life & 12 times more likely to be
   killed in a gun accident than children of the same age in other high-income
   countries. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/546345a">doi:10.1038/546345a</A>]['17].
   [Also search for: gun usa].

%T White Paper WP-2017-011: Applying Visual Interactive Dimensionality
   Reduction to Criminal Intelligence Analysis
%D 2017
%K TR, c2017, c201x, c20xx, zz0719, VALCRI, crime, criminal investigation,
   police, policing, UK, EU, AI, stats, visual analytics, law, legal
%X "VALCRI provides a challenging and overwhelming high-dimensional dataset that
   comprises of hundreds of extracted semantic features in addition to the
   usual spatiotemporal information or metadata. To overcome the curse of
   dimensionality and to generate low-dimensional representations of these
   semantic features we apply interactive high-dimensional data analysis
   techniques with the goal of obtaining clusters of similar crime reports.
   However, it is still a challenge for crime analysts to make sense of the
   results and to provide useful interactive feedback to the system. Therefore,
   we provide several tightly integrated interactive visualizations that allow
   the analysts to identify clusters of similar crimes from different
   perspectives and interactively focus their analysis on features or crime
   records of particular interest."
   -- [<A HREF="http://valcri.org/publications/white-paper-applying-visual-interactive-dimensionality-reduction-to-criminal-intelligence-analysis/">www</A>]['19]
   at [<A HREF="http://valcri.org/">valcri.org</A>]['19].

%A C. F. Clements
%A et al
%T Body size shifts and early warning signals precede the historic collapse of
   whale stocks
%J Nature Ecology and Evolution
%V 1
%P 0188
%D 2017
%K jrnl, eJrnl, c2017, c201x, c20xx, zz0617, whale, whales, size, stats, animal,
   population size, decline, extinction, loss, marine, environment, ecology,
   whaling, hunting, resources
%X "Predicting population declines is a key challenge in the face of global
   environmental change. ... demonstrate that early warning signals can be
   present not only in the abundance data, but also in the more reliable body
   size data of wild popns. We show that during the period of commercial whaling
   the mean body size of caught whales declined dramatically (by up to 4m over a
   70-year period), leading to early warning signals being detectable up to 40y
   before the global collapse of whale stocks. Combining abundance & body size
   data can reduce the length of the time series required to predict collapse,
   & decrease the chances of false positive early warning signals. ..."
   -- [<A HREF="http://dx.doi.org/10.1038/s41559-017-0188">doi:10.1038/s41559-017-0188</A>]['17].

%A S. Hough
%T Do large (magnitude >= 8) global earthquakes occur on preferred days of the
   calendar year or lunar cycle?
%J Seismological Res. Lett.
%M JAN
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0118, earth quake, earthquake, seismology,
   full, moon, lunar, cycle, month, stats, myth
%X -- [<A HREF="https://doi.org/10.1785/0220170154">doi:10.1785/0220170154</A>['18]?
   or [<A HREF="https://pubs.geoscienceworld.org/ssa/srl/article-abstract/525827/do-large-magnitude-8-global-earthquakes-occur-on">www</A>]['18]?
   Also see [<A HREF="https://phys.org/news/2018-01-great-earthquakes-affected-moon-phases.html">phys.org</A>]['18],
   and [<A HREF="http://www.abc.net.au/news/science/2018-01-17/massive-earthquakes-no-more-likely-to-strike-during-full-moon/9332838">abc</A>][1/2018].
   [Also search for: lunar stats].

%A H. Doi
%A H. Basadonne
%A P. Venuti
%A K. Shinohara
%T Negative correlation between salivary testosterone concentration and
   preference for sophisticated music in males
%J Personality and individual differences
%V 125
%P 106-111
%M APR
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0118, human, personality, male, males,
   testosterone, music, tastes, jazz, classical, rock and roll
%X "... conjectured that testosterone partly determines individual differences
   in music preference. ... investigated the association between salivary
   testosterone concentration & strength of preference for five different music
   types in young males & females. The results revealed a sig. -ve correlation
   between salivary testosterone concentration & preference for sophisticated
   music, such as classical & jazz in males. This relationship was not mediated
   by the big-five personality traits. ... indicate the possibility that
   neuroendocrinological fn can exert influences on music preference patterns."
   -- [<A HREF="https://doi.org/10.1016/j.paid.2017.11.041">doi:10.1016/j.paid.2017.11.041</A>]['18].

%A J. Peters
%A D. Janzing
%A B. Schoelkopf
%T Elements of Causal Inference: Foundations and Learning Algorithms
%I MITpress
%P 288
%D 2017
%K book, text, c2017, c201x, c20xx, zz0218, Scholkopf, Schoelkopf,
   AI, II, causal model, causality, learning
%X 1st ed 2017; hb us$45; uk us isbn:0262037319; uk us isbn13:978-0262037310.
   "... After explaining the need for causal models and discussing some of the
   principles underlying causal inference, the book teaches readers how to use
   causal models: how to compute intervention distributions, how to infer
   causal models from observational and interventional data, and how causal
   ideas could be exploited for classical machine learning problems. ..."
   (Also see [<A HREF="https://mitpress.mit.edu/books/elements-causal-inference">www</A>]['18].)

%A Depeng Xu
%A Shuhan Yuan
%A Xintao Wu
%T Differential privacy preserving causal graph discovery
%J IEEE Symp. on Privacy Aware Computing (PAC)
%D 2017
%K conf, c2017, c201x, c20xx, zz0621, differential privacy, causal graph,
   Bayesian, network, stats
%X "... releasing causal graphs may risk leakage of individual participant's
   privacy. ... we focus on the PC alg. ... propose a DP PC alg. (PrivPC) for
   categorical data. ... For numerical [Cts] data, we further develop a DP
   causal discovery alg. (PrivPC*). The idea is to add noise once onto the
   covariance matrix ..."  [via KL]
   -- [<A HREF="https://doi.org/10.1109/PAC.2017.24">doi:10.1109/PAC.2017.24</A>]['21].
   [Also search for: differential privacy].

%A A. Wood
%A et al
%T Differential privacy: A primer for a non-technical audience
%J Vanderbilt J. of Entertainment and Technology Law
%V V 21
%N 17
%M JAN
%D 2018
%O Berkman Klein Center Research Publication No. 2019-2
%K eJrnl, c2018, c201x, c20xx, zz0521, differential privacy, DBMS, law, legal,
   deidentification, reidentification, data, stats
%X "... primarily studied in the context of the collection, analysis, & release
   of aggregate statistics. These range from simple stat.estimations, such as
   avgs, to machine learning. Tools for differentially private analysis are now
   in early stages of implementation & use across a variety of academic,
   industry, & government settings. Interest in the concept is growing among
   potential users of the tools, as well as within legal & policy communities,
   as it holds promise as a potential approach to satisfying legal requirements
   for privacy protection when handling personal information. ..."
   -- [<A HREF="http://dx.doi.org/10.2139/ssrn.3338027">doi:10.2139/ssrn.3338027</A>]['21],
      [<A HREF="https://en.wikipedia.org/wiki/Differential_privacy">wikip</A>]['21].

%A L. McInnes
%A J. Healy
%A J. Melville
%T UMAP: Uniform manifold approximation and projection for dimension reduction
%J arXiv
%M FEB
%D 2018
%K TR, c2018, c201x, c20xx, zz0121, stats, UMAP, dimension reduction,
   dimensionality, embedding, nonlinear, manifold, learning, t-SNE, tSNE
%X "UMAP (Uniform Manifold Approx. & Projection) is a novel m.learning technique
   for dim'n red'n. ... constructed from a theoretical f/wk based in Riemannian
   geometry & algebraic topology. ... is a practical scalable alg. that applies
   to real world data. The UMAP alg. is competitive with t-SNE for visualization
   quality, & arguably preserves more of the global structure with superior run
   time performance. [&] UMAP has no computational restrictions on embedding
   dimension, making it viable as a general purpose dim.red. technique for
   machine learning."
   -- [<A HREF="https://arxiv.org/abs/1802.03426">arXiv</A>]['21].
   Also see nonLDR@[<A HREF="https://en.wikipedia.org/wiki/Nonlinear_dimensionality_reduction">wikip</A>]['21].
   [Also search for: UMAP].

%A A. Ghassami
%A S. Salehkaleybar
%A N. Kiyavash
%A K. Zhang
%T Counting and sampling from Markov equivalent DAGs using clique trees
%J arXiv
%M FEB
%D 2018
%K TR, c2018, c201x, c20xx, zz0319, Bayesian network, Bnet, causal model, DAG,
   equivalence class, clique tree, enumerate, count, sample, intervention
%X "... using only observational data, the structure of the ground truth DAG is
   identifiable only up to Markov equivalence, based on conditional independence
   relations among the variables. Therefore, the number of DAGs equivalent to
   the ground truth DAG is an indicator of the causal complexity of the
   underlying structure - roughly speaking, it shows how many interventions or
   how much additional information is further needed to recover the underlying
   DAG. ... we propose a new technique for counting the # of DAGs in a Markov
   equiv.class. ... based on the clique tree representation of chordal graphs.
   We show that in the case of bounded degree gs., the proposed alg. is
   polynomial time. [&] that this technique can be utilized for uniform sampling
   from a Markov equiv.class [which] may be needed for finding the best DAG or
   for causal inference given the equivalence class as input. We also extend our
   counting and sampling method to the case where prior knowledge about the
   underlying DAG is available, and present applications of this extension in
   causal experiment design and estimating the causal effect of joint
   interventions."
   -- 1802.01239@[<A HREF="https://arxiv.org/abs/1802.01239">arXiv</A>]['19].
   [Also search for: Bnet intervention] and
   [also search for: DAG Markov equivalence].

%A N. Polson
%A V. Rockova
%T Posterior concentration for sparse deep learning
%J arXiv
%P 23
%M MAR
%D 2018
%K TR, c2018, c201x, c20xx, zz0418, AI, II, ANN, NN, deep learning, sparse,
   neural network, spike and slab, SSDL, dropout, rectified linear, ReLU,
   regularization, posterior, width, depth, sparsity, sparseness, Bayesian
%X "Spike-and-Slab Deep Learning (SS-DL) is a fully Bayesian alternative to
   Dropout for improving generalizability of deep ReLU networks. This new type
   of regularization enables provable recovery of smooth input-output maps with
   unknown levels of smoothness. Indeed, we show that the posterior distribution
   concentrates at the near minimax rate for alpha-Holder smooth maps,
   performing as well as if we knew the smoothness level alpha ahead of time.
   Our result sheds light on architecture design for deep NNs, namely the choice
   of depth, width & sparsity level. These n/wk attributes typically depend on
   unknown smoothness in order to be optimal. We obviate this constraint with
   the fully Bayes construction. As an aside, we show that SS-DL does not
   overfit in the sense that the posterior concentrates on smaller networks with
   fewer (up to the optimal # of) nodes & links. ... provide new theoretical
   justifications for deep ReLU networks from a Bayesian point of view.
   -- 1803.09138@[<A HREF="https://arxiv.org/abs/1803.09138">arXiv</A>]['18].

%A S. R. McCurdy
%T Ridge regression and provable deterministic ridge leverage score sampling
%J arXiv
%M MAR
%D 2018
%K TR, c2018, c201x, c20xx, zz0418, stats, linear, ridge regression,
   matrix sketch, statistical risk
%X "Ridge leverage scores provide a balance between low-rank approximation and
   regularization, and are ubiquitous in randomized linear algebra and machine
   learning. ... We provide provable guarantees for deterministic column
   sampling using ridge leverage scores. The matrix sketch returned by our
   algorithm is a column subset of the original matrix, yielding additional
   interpretability. ... Performing ridge regression with the matrix sketch
   returned by our algorithm and a particular regularization parameter forces
   coefficients to zero and has a provable (1+{epsilon}) bound on the
   statistical risk. As such, it is an interesting alternative to elastic net
   regularization."
   -- 1803.06010@[<A HREF="https://arxiv.org/abs/1803.06010">arXiv</A>]['18].
   [Also search for: ridge regression].

%A W. Lutz
%A E. Kebede
%T Education and health: Redrawing the Preston curve
%J Population and Development Review
%A APR
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0418, health, education, schooling, wealth, GDP,
   income, life expectancy, longevity, stats
%X "... In all of the models the effect of educational attainment on life
   expectancy is highly significant in the expected direction, and the
   standardized coefficients are clearly larger than those of income. ..."
   -- [<A HREF="https://doi.org/10.1111/padr.12141">doi:10.1111/padr.12141</A>]['18].

%A C. Gray
%A L. Mitchell
%A M. Roughan
%T Generating connected random graphs
%J arXiv
%M JUL
%D 2018
%K TR, c2018, c201x, c20xx, zz0718, random, graph, randomGraph, maths, Waxman,
   model, algorithm, generate
%X "... an alg. to produce connected random graphs using a Metropolis-Hastings
   framework. [It] extends to a general f/wk for sampling from a known distn of
   gs., conditioned on a desired property. We demonstrate the method to generate
   connected spatially embedded random gs., specifically the well known Waxman
   n/wk, & illustrate the convergence & practicalities of the alg.."
   -- 1806.11276@[<A HREF="https://arxiv.org/abs/1806.11276">arXiv</A>]['18].
   [Also search for: random graph].

%A V. R. Tabar
%A F. Elahi
%T A novel method for aggregation of Bayesian networks without considering an
   ancestral ordering
%J Applied AI
%V 32
%N 2
%P 214-227
%D 2018
%K jrnl, Bnet, c2018, c201x, c20xx, zz0820, Bnets, network, aggregate, combine,
   merge, Feng, II
%X "... ensures a combined BN meets three important criteria of avoiding cycles,
   preserving cond.independencies ... first combine the BNs using the mods. of
   the method intro. by Feng et al. We then use the sim.ann.alg. for getting an
   acyclic g. in which the minimum arcs have been removed. ..."
   -- [<A HREF="https://doi.org/10.1080/08839514.2018.1451134">doi:10.1080/08839514.2018.1451134</A>]['20].
   [Also search for: Bayesian network].

%A P. Tiwari
%A M. Melucci
%T Binary classifier inspired by quantum theory
%J arXiv
%M MAR
%D 2019
%K TR, c2019, c201x, c20xx, zz0319, binary classifier, AI, II, quantum inspired,
   BCIQT, MNIST
%X "... Current ML models are based on classical theories of probability and
   statistics, which can now be replaced by Quantum Theory (QT) with the aim of
   improving the effectiveness of ML. In this paper, we propose the Binary
   Classifier Inspired by Quantum Theory (BCIQT) model, which outperforms the
   state of the art classification in terms of recall for every category."
   -- 1903.01167@[<A HREF="https://arxiv.org/abs/1903.01167">arXiv</A>]['19].
   [Also search for: quantum inspired].

%A V. Havlicek
%A A. D. Corcoles
%A K. Temme
%A A. W. Harrow
%A A. Kandala
%A J. M. Chow
%A J. M. Gambetta
%T Supervised learning with quantum-enhanced feature spaces
%J Nature
%V 567
%N ?
%P 209-212
%M MAR
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0319, quantum computing, classifier, features,
   algorithm, AI, supervised, kernel, SVM, IBM TJWatson
%X "... Kernel methods for [Mc.L.] are ubiquitous in pattern recognition, with
   [SVMs] being the best known method for classification problems. However,
   there are limitations to the successful soln to such c.problems when the
   feature space becomes large, & the kernel fns become computationally
   expensive to est.. A core elt in the computational speed-ups enabled by
   quantum algs. is the exploitation of an exponentially large q.state space
   through controllable entanglement & interference. ... propose &
   experimentally implement two q.algs. on a superconducting processor. A key
   component in both methods is the use of the q.state space as feature space.
   ... a possible path to quantum advantage. The alg. solve a problem of
   supervised learning: the construction of a classifier. One method, the
   quantum variational classifier, uses a variational quantum circuit to
   classify the data in a way similar to the method of conventional SVMs. The
   other method, a quantum kernel estimator, estimates the kernel fn on the
   q.computer & optimizes a classical SVM. The two methods provide tools for
   exploring the applications of noisy intermediate-scale q.computers to [M.L.]"
   -- [<A HREF="https://doi.org/10.1038/s41586-019-0980-2">doi:10.1038/s41586-019-0980-2</A>]['19]  [29 refs].
   (Also see discussion, pp.179-181
   -- [<A HREF="https://doi.org/10.1038/d41586-019-00771-0">doi:10.1038/d41586-019-00771-0</A>]['19].)

%A V. Amrhein
%A et al
%T Scientists rise up against statistical significance
%J Nature
%V 567
%P 305-307
%M MAR
%D 2019
%K news, views, c2019, c201x, c20xx, zz0319, stats, statistics, statistical,
   significance, test, p value, Pvalue, Pvalues, misuse, confidence interval,
   experiment, ASA, scientific research
%X "When was the last time you heard a seminar speaker claim there was
   'no difference' between two groups because the difference was
   'statistically non-significant'? ...
   -- [<A HREF="https://www.nature.com/articles/d41586-019-00857-9">www</A>]]['19].
   Also see,
   'The ASA's Statement on p-Values: Context, Process, and Purpose'
   [<A HREF="https://doi.org/10.1080/00031305.2016.1154108">doi:10.1080/00031305.2016.1154108</A>]['19].

%A B. Efron
%T Bayes, oracle Bayes and empirical Bayes
%J Statist. Sci.
%V 34
%N 2
%P 177-201
%M MAY
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0422, stats, oracle, empirical Bayes
%X "... concerns the Bayes & frequentist aspects of empirical B. inference. Some
   of the ideas explored go back to Robbins in the 1950s, while others are
   current. Several examples are discussed, real & artificial, illustrating the
   two faces of empirical Bayes methodology: 'oracle Bayes' shows empirical B.
   in its most frequentist mode, while 'finite B. inference' is a fundamentally
   Bayesian application. In either case, modern theory & computation allow us to
   present a sharp finite-sample picture of what is at stake in an empirical B.
   analysis."
   -- [<A HREF="https://doi.org/10.1214/18-STS674">doi:10.1214/18-STS674</A>]'22].
   [Also search for: empirical Bayes stats].

%A C.  Dwork
%T Differential privacy and the US census
%J Proc. 38th ACM SIGMOD-SIGACT-SIGAI Symp. on Principles of Database Systems
%M JUN
%D 2019
%K conf, c2019, c201x, c20xx, zz1120, differential privacy, USA, census,
   security, stats, adversary
%X "... led the US Census Bureau to adopt differential privacy as the
   disclosure avoidance methodology of the 2020 decennial census. ..."
   -- [<A HREF="https://doi.org/10.1145/3294052.3322188">doi:10.1145/3294052.3322188</A>]['20],
   auth[<A HREF="https://www.microsoft.com/en-us/research/people/dwork/">www</A>]['20].
   [Also search for: differential privacy].

%A L. Rocher
%A J. M. Hendrickx
%A Y.-A. de Montjoye
%T Estimating the success of re-identifications in incomplete datasets using
   generative models
%J NatureComms
%V 10
%P 3069
%M JUL
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz0719, stats, data anonymizing,
   anonymising, anonymous, deidentification, reidentification, reidentifying,
   reidentify, dataset, population, privacy, GDPR, identity, Australia,
   myHealth, healthcare, risk, risks, personal, health records, SingHealth
%X "... Anonymizing datasets through de-identification & sampling before sharing
   them has been the main tool used to address those concerns. ... propose a
   generative copula-based method that can accurately est. the likelihood of a
   specific person to be correctly re-identified, even in a heavily incomplete
   dataset. On 210 popns, our method obtains AUC scores for predicting
   individual uniqueness ranging from 0.84 to 0.97, with low false-discovery
   rate. ... we find that 99.98% of Americans would be correctly re-identified
   in any dataset using 15 demographic attributes. Our results suggest that even
   heavily sampled anonymized datasets are unlikely to satisfy the modern stds
   for anonymization set forth by GDPR & seriously challenge the technical &
   legal adequacy of the de-identification release-and-forget model."
   -- [<A HREF="https://doi.org/10.1038/s41467-019-10933-3">doi:10.1038/s41467-019-10933-3</A>]['19].
   [Also search for: data anonymizing].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc4/">more</A>]['18].)

%A S. M. Cooley
%A et al
%T A novel metric reveals previously unrecognized distortion in dimensionality
   reduction of scRNA-Seq data
%J bioRxiv
%M JUL
%D 2019
%K TR, MolBio, c2019, c201x, c20xx, zz0921, tSNE, t-SNU, UMAP, distortion,
   errors, dimensionality reduction, scRNA
%X "... we introduce a straightforward approach to quantifying this distortion
   by comparing the local neighborhoods of points before & after dimensionality
   red'n. We found that popular techniques like t-SNE & UMAP introduce sig.
   distortion even for relatively simple geometries such as simulated
   hyperspheres. For scRNA-Seq data, we found the distortion in local
   neighborhoods was greater than 95% in the 2- & 3-[D] space typically used for
   downstream analysis. This high level of distortion can readily introduce
   important errors into cell type identification, pseudotime ordering, & other
   analyses ..."
   -- 689851v1@[<A HREF="https://www.biorxiv.org/content/10.1101/689851v1">bioRxiv</A>]['21].

%A M. Belkin
%A et al
%T Reconciling modern machine-learning practice and the classical bias-variance
   trade-off
%J PNAS
%V 116
%N 32
%P 15849-15854
%M JUL
%D 2019
%K jrnl, PNAS, c2019, c201x, c20xx, zz0622, NN, ANN, deep, neuralnetwork,
   parameters, overfitting, stats
%X "... one of the central tenets of the field, the bias-variance trade-off,
   appears to be at odds with the observed behavior of methods used in modern
   machine-learning practice. The bias-variance trade-off implies that a model
   should balance underfitting and overfitting ... neural networks are trained
   to exactly fit (i.e., interpolate) the data. Classically, such models would
   be considered overfitted, and yet they often obtain high accuracy on test
   data. ... has raised questions about the mathematical foundations of machine
   learning ... we reconcile the classical understanding and the modern practice
   within a unified performance curve. This 'double-descent' curve ..."
   -- [<A HREF="https://doi.org/10.1073/pnas.1903070116">doi:10.1073/pnas.1903070116</A>]['22].

%A J. Cardinal
%A A. Ooms
%T Sparse regression via range counting
%J arXiv
%M AUG
%D 2019
%K TR, c2019, c201, c20xx, zz07819, sparse regression, linear, problem,
   algorithm, stats
%X "The sparse regression problem, also known as best subset selection problem,
   can be cast as follows: Given a real d x n matrix A, a vector y in R^d, & an
   integer 2<=k<=d, find an affine combination of at most k columns of A that is
   closest to y. We describe a O(n^{k-1}log^{d-k+2}n)-time randomized
   (1+e)-approximation alg. ... also provide a simple O(nd-1+e)-time
   deterministic exact alg.. Finally, we show how to adapt the approximation
   alg. for the sparse linear regression & sparse convex regression problems
   with the same running time, up to polylogarithmic factors."
   -- 1908.00351@[<A HREF="https://arxiv.org/abs/1908.00351">arXiv</A>]['19].

%A A. Dhir
%A C. M.  Lee
%T Integrating overlapping datasets using bivariate causal discovery
%J arXiv
%M NOV
%D 2019
%O AAAI 2020
%K TR, c2019, c201x, c20xx, zz0520, dataset, cause, causal,
   BNet, BNets, network
%X "... Algs. that can discover causal relations from observational data are
   based on the assumption that all vars have been jointly measured in a single
   dataset. In many cases this assumption fails.  ... as cond. indep. tests only
   determine causal structure up to Markov equivalence, the # of consistent
   joint structures returned by these approaches can be quite large. ...
   we adapt and extend these [recent] so-called bivariate causal discovery
   algs. to the problem of learning consistent causal structures from multiple
   datasets withoverlapping variables belonging to the same generating process,
   providing a sound & complete alg. that outperforms prev, approaches on
   synthetic and real data."
   -- 1910.11356@[<A HREF="https://arxiv.org/pdf/1910.11356.pdf">arXiv</A>]'20].
   [Also search for: BNet causal].

%A F. Parracho Silva
%T A probabilistic framework and significance test for the analysis of
   structural orientations in skyscape archaeology
%J J. of Archaeological Sci.
%V 118
%M JUN
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0520, probability, paleoastonomy, megalithic,
   alignments, stone circle, circles, Archaeology
%X "... probabilistic f/wk for the analysis of structural orientations & using
   it to develop a test of stat. sig.. ... based on two simple premises: firstly
   that the measurement of a str.orientation can be modelled as a prob. distn; &
   secondly, that in order to assess the likelihood of celestial al. such a
   distn needs to be coordinate-transformed in a manner not unlike that of
   radiocarbon calibration. A method that aggregates multiple str.orientations &
   quantifies their stat. sig. in the form of a p-value is then introduced.
   Finally, the robustness of the presented methodology over prev. approaches is
   demonstrated using real-world datasets of orientations of ancient Egyptian
   temples & tombs & Scottish Recumbent Stone Circles ..."
   -- [<A HREF="https://doi.org/10.1016/j.jas.2020.105138">doi:10.1016/j.jas.2020.105138</A>]['24],
      33905@[<A HREF="http://eprints.bournemouth.ac.uk/33905/">bournemouth_U</A>]['20],
      auth@[<A HREF="https://staffprofiles.bournemouth.ac.uk/display/fparrachosilva">bournemouth_U</A>]['20].
   * [Also search for: stone circle].

%A S. Tople
%A A. Sharma
%A A. Nori
%T Alleviating privacy attacks via causal learning
%J Proc. of the 37th Int. Conf. on Mach. Learning (PMLR)
%V 119
%P 9537-9547
%D 2020
%K conf, c2020, c202x, c20xx, zz0621, differential privacy, causal model,
   Bayesian network
%X "M.L. models, esp. deep NNs are known to be susceptible to privacy attacks
   such as membership inference where an adversary can detect whether a data
   point was used to train a model. ... exacerbated when a model is used for
   predictions on an unseen data dist'n. ... demonstrate the benefit of
   predictive models that are based on the causal relationships between input
   features & the outcome. ... show that models learnt using causal struct.
   generalize better to unseen data ... establish a theor. link between
   causality & privacy ..."
   -- [<A HREF="http://proceedings.mlr.press/v119/tople20a.html">www</A>]['21],
      1909.12732@[<A HREF="https://arxiv.org/abs/1909.12732">arXiv</A>]['21].
   [Also search for: Bayesian network].

%A T. Ameen ur Rahman
%A et al ...
%T L. R. Varshney
%T The twelvefold way of non-sequential lossless compression
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, data sets, dataset,
   twelvefold, twelve, unordered, equivalence, symmetry, compress
%X "... huge amounts of data that are not simple sequences of distinguishable
   symbols, but have certain equivalence classes for patterns of symbols within
   which lossless rep'n does not require unique indices. As a simple example,
   the ordering of seqs. of scientific data records are often irrelevant & so
   only the histogram or type class must be represented. Such rep'n problems
   arise for biol. data, social graph structure, NN architecture, & elsewhere
   due to the functional process generating or using the data. These
   non-sequential info.sources may be studied implicitly via group theory & some
   may explicitly be characterized using interchange entropies. ..."
   -- [<A HREF="https://doi.org/10.1109/DCC50243.2021.00061">doi:10.1109/DCC50243.2021.00061</A>]['21],
      2011.04069@[<A HREF="https://arxiv.org/abs/2011.04069">arXiv</A>]['21].
   [Also search for: DCC21].

%A S. Bates
%A T. Hastie
%A R. Tibshirani
%T Cross-validation: what does it estimate and how well does it do it?
%J arXiv
%M APR
%D 2021
%K TR, c2021, c202x, c20xx, zz0421, stats, cross validation, estimate, accuracy,
   variance, bootstrap, splitting, model, confidence interval, CI, stats
%X "... one would like to think that cross-validation estimates the prediction
   error for the model at hand, fit to the training data. We prove that this is
   not the case for the linear model fit by ordinary least squares; rather it
   estimates the avg. prediction error of models fit on other unseen training
   sets drawn from the same pop'n. We further show that this phenomenon occurs
   for most popular ests. of prediction error, inc. data splitting,
   bootstrapping, & Mallow's Cp. Next, the std confidence intervals for
   prediction error derived from cross-validation may have coverage far below
   the desired level. Because each data point is used for both training &
   testing, there are correlations among the measured accuracies for each fold,
   & so the usual est. of variance is too small. We introduce a nested
   cross-validation scheme to est. this variance more accurately, & show
   empirically that this modification leads to intervals with approx. correct
   coverage ... Lastly, our analysis also shows that when producing confidence
   intervals for prediction accuracy with simple data splitting, one should not
   re-fit the model on the combined data, since this invalidates the CIs."
   -- 2104.00673@[<A HREF="https://arxiv.org/abs/2104.00673">arXiv</A>]['21]. [50 refs.  via AK]

%A P. Bloem
%T Finding motifs in knowledge graphs using compression
%J arXiv
%M APR
%D 2021
%K TR, c2021, c202x, c20xx, zz0421, maths, graph, network, motif, compress
%X "We introduce a method to find network motifs in knowledge graphs. Network
   motifs are useful patterns or meaningful subunits of the g. that recur
   frequently. We extend the common definition of a n/wk motif to coincide with
   a basic g.pattern. We introduce an approach, inspired by recent work for
   simple gs., to induce these from a given knowledge g., & show that the motifs
   found reflect the basic structure of the g.. Specifically, we show that in
   random gs., no motifs are found, & that when we insert a motif artificially,
   it can be detected. Finally, we show the results of motif induction on three
   real-world knowledge gs.."
   -- 2104.08163@[<A HREF="https://arxiv.org/abs/2104.08163">arXiv</A>]['21].
   [Also search for: graph motif compress].

%A A. Clayton
%T Bernoulli's Fallacy: Statistical Illogic and the Crisis of Modern Science
%I ColumbiaUPress
%P 368
%M AUG
%D 2021
%K book, text, c2021, c202x, c20xx, zz0921, history, foundations, stats,
   statistics, probability, frequentist, Bayesian, Bernoulli
%X "There is a logical flaw in the statistical methods used across experimental
   science. ... traces the history of how statistics went astray, beginning with
   the groundbreaking work of the 17C-century mathematician Jacob Bernoulli ...
   contends that we need to take a Bayesian approach ... B's Fallacy explains
   why something has gone wrong with how we use data - & how to fix it."
   1st ed 2021; hb us$33; uk us isbn:0231199945; uk is isbn13:978-0231199940.
   [Also search for: Bayesian stats book].

%A V. Fulber-Garcia
%A S. Luis Sardi Mergen
%T LUISA: Decoupling the frequency model from the context model in
   prediction-based compression
%J COMPJ
%V 64
%N 9
%P 1437-1450
%M SEP
%D 2021
%K jrnl, compj, c2021, c202x, c20xx, zz0921, Luisa, PPM, strings, compress,
   compression, model
%X "... methods, like prediction by partial matching, achieve a remarkable
    compression ratio ... However, they are not efficient in terms of speed.
   Part of the problem concerns the usage of dynamic entropy encoding, which is
   considerably slower than the static alternatives. ... we propose a
   predn-based comp. method that decouples the context model from the freq.
   model. ... allows static entropy encoding to be used without a sig. overhead
   in the meta-data embedded in the compressed data. The result is a reasonably
   efficient alg. that is particularly suited for small textual files, as the
   experiments show. We also show it is relatively easy to built strategies
   designed to handle specific cases, like the comp'n of files whose symbols are
   only locally frequent."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxaa074">doi:10.1093/comjnl/bxaa074</A>]['21].
   (Also see LUISA@[<A HREF="https://github.com/ViniGarcia/LUISA">gith'b</A>]['21].)
   [Also search for: compress PPM].

%A Wei Yan
%A Sian-Jheng Lin
%T A tighter upper bound of the expansion factor for universal coding of
   integers and its code constructions
%J arXiv
%M SEP
%D 2021
%K TR, c2021, c202x, c20xx, zz1021, universal code, integer, expansion, bound
%X "... K^*_C is the infimum of the set of expansion factors. The optimal UCI
   is defined as a class of UCI possessing the smallest K^*_C. Based on prior
   research, the range of K^*_C for the optimal UCI is 2<=K^*_C<=2.75. Currently
   the code constructions achieve K_C=2.75 for UCI & K_C=3.5 for asymptotically
   optimal UCI. ... we propose a class of UCI, termed i code, to achieve
   K_C=2.5. This further narrows the range of K^*_C to 2<=K^*_C<=2.5. Next, a
   family of asymptotically optimal UCIs is presented, where their expansion
   factor infinitely approaches 2.5. Finally, a more precise range of K^*_C for
   the classic UCIs is discussed."
   -- 2109.08920@[<A HREF="https://arxiv.org/abs/2109.08920">arXiv</A>]['21].
   [Also search for: integer universal code].

%A D. Flusfeder
%T Luck: A Personal Account of Fortune, Chance and Risk in
   Thirteen Investigations
%I 4thEstate
%P 304
%D 2022
%K book, c2022, c202x, c20xx, zz0422, probability, gambling, luck, lucky,
   chance, fortune, risk, randomness
%X hb $22; uk us isbn:0008245177; uk us isbn13:978-0008245177.
   "... take[s] [DF] to Siberia, Versailles, the Old Testament desert; play
   roulette in Baden-Baden with Dostoevsky; visit a Cambridge fairground with
   Wittgenstein; meet the sixteenth-C poet Thomas Bastard, who challenged
   Fortune, and lost ..."
   [Also search for: probability book].

%A Jason E. Goldstick
%A et al
%T Current causes of death in children and adolescents in the United States
%J NEJM
%V ?
%M APR
%D 2022
%K corr, NEJM, c2022, c202x, c20xx, zz0522, USA, gun, guns, deaths, children,
   risks, firearms
%X "... recently released updated official mortality data that showed 45,222
   firearm-related deaths in the United States in 2020 - a new peak. ... in
   2020, firearm-related injuries became the leading cause of death in that
   [1-19y] age group ..."
   -- [<A HREF="https://doi.org/10.1056/NEJMc2201761">doi:10.1056/NEJMc2201761</A>]['22].
   [Also search for: gun deaths].

%A D. A. Redelmeier
%A S. M. Singh
%T Long-term mortality of academy award winning actors and actresses
%J PLoS One
%V 17
%N 4
%P e0266563
%M APR
%D 2022
%K jrnl, eJrnl, c2022, c202x, c20xx, zz0522, movies, films, entertainer, actor,
   actress, Oscar, Oscars, winning, winners, lifespan, death, stats
%X "... Overall, 2,111 individuals were analyzed with 1,122 total deaths
   occurring during a median follow-up of 68.8 years. Comparisons of winners to
   controls yielded a 4.8% relative difference avg. life-span (95% ci: 1.6 to
   7.9, p = 0.004), a 5.1 year absolute increase in life expectancy (95% ci:
   3.0 to 7.2, p < 0.001), & a 41% improvement in mortality hazard (95% ci: 19
   to 68, p < 0.001). The increased survival tended to be greater in recent
   years, for individuals winning at a younger age, & among those with multiple
   wins. The increased survival replicated in secondary analyses comparing
   winners to nominees & was not observed in analyses comparing nominees to
   controls. ..."
   -- [<A HREF="https://doi.org/10.1371/journal.pone.0266563">doi:10.1371/journal.pone.0266563</A>]['22].
   [Also search for: entertainer lifespan].

%A M. Heder
%A B. Megyesi
%T The DECODE database of historical ciphers and keys: Ver.2
%J Int. Conf. on Historical Cryptology  (HistoCrypt)
%P 111-114
%M JUN
%D 2022
%K conf, c2022, x202x, c20xx, zz0923, DECODE< historic, old, ancient, code, key,
   codes, cyphers, cryptology, cryptography
%X "We report recent developments of the DECODE DB aimed for the systematic
   collection & annotation of encrypted sources: ciphertexts, keys & related
   documents. We released a new, more functional graphical user interface,
   revised some metadata features & enlarged the collection & tripled its size."
   -- [<A HREF="http://dx.doi.org/10.3384/ecp188397">doi:10.3384/ecp188397</A>]['23],
      [<A HREF="https://ecp.ep.liu.se/index.php/histocrypt/article/download/397/355">pdf</A>]['23].
   Also see [<A HREF="https://scholar.google.com/citations?user=gI7pNKkAAAAJ&hl=en">auth2</A>]['23].

%A W. Thomson
%T Escape from Model Land: How Mathematical Models Can Lead Us Astray and
   What We Can Do About It
%I BasicBooks
%M DEC
%D 2022
%K book, stats, c2022, c202x, c20xx, zz1222, statistics, model
%X 1st ed 2022; hb us$21; uk us isbn:1541600983, uk us isbn13:978-1541600980.
   "...illuminates the hidden dangers of models ... demonstrates how ms reflect
   the biases, perspectives, & expectations of their creators. ... shows us why
   understanding the limits of ms. is vital to using them well. ..."

%A M. Wienobst
%A et al
%T Efficient enumeration of Markov equivalent DAGs
%J arXiv
%M JAN
%D 2023
%K TR, c2023, c202x, c20xx, zz0223, DAG, Markov, equivalence, class, MEC,
   MPDAG, MPDAGs, causal, Bnet, BN, networks, delay, enumerate, enumerating,
   generate
%X "... an important primitive in causal analysis. ... present the first
   linear-time delay alg.. On the theoretical side, we show that [it] can be
   generalized to enumerate DAGs rep. by models that incorporate background
   knowledge, such as MPDAGs; on the practical side, we provide an efficient
   implementation & evaluate it in a series of experiments. ..."
   -- 2301.12212@[<A HREF="https://arxiv.org/abs/2301.12212">arXiv</A>]['23].
   [Also search for: DAG Markov equivalence].

%A Yang Li
%A et al
%T Private graph data release: A survey
%J Computing Surveys
%V 55
%N 11
%P 1-39
%M FEB
%D 2023
%K jrnl, ACM, c2023, c202x, c20xx, zz0224, KelvinYL, differential privacy,
   graphs, stats, pufferfish privacy, private
%X "... a comprehensive survey of private graph data release algs. that seek to
   achieve the fine balance between privacy & utility, with a specific focus on
   provably private mechanisms. Many ... are natural extensions of the
   Differential Privacy f/wk to graph data, but we also investigate more general
   privacy formulations like Pufferfish Privacy ..."
   -- [<A HREF="https://doi.org/10.1145/3569085">doi:10.1145/3569085</A>]['24].

%A J. Harviainen
%A K. Rychkova
%A M. Koivisto
%T Quantum speedups for Bayesian Network structure learning
%J arXiv
%M MAY
%D 2023
%K TR, c2023, c202x, c20xx, zz0623, Bayesian Network, BN, quantum computing,
   BNSL
%X "... we ask whether BNSL admits a polynomial quantum speedup, that is,
   whether the problem can be solved by a q.alg. in time O(c^n) for some const.
   c less than 2. We answer the question in the affirmative by giving two algs
   achieving c <= 1.817 & c <= 1.982 assuming the # of potential parent sets is,
   respectively, subexponential & O(1.453^n). Both algs assume the availability
   of a quantum random access memory."
   -- 2305.19673@[<A HREF="https://arxiv.org/abs/2305.19673">arXiv</A>]['23].
   [Also search for: Bayesian Network].

%A Allen Liu
%A A. Moltra
%T Robustly learning general mixtures of Gaussians
%J JACM
%V 70
%N 3
%P 1-53
%K MAY
%D 2023
%K jrnl, JACM, c2023, c202x, c20xx, zz0723, mixture model, Gaussian, normal,
   probability distribution, stats, algorithm, robust, learning, estimate,
   estimation, fitting
%X "... we give the first provably robust alg. for learning mixtures of any
   const. # of Gs.. We require only mild assumptions on the mixing weights &
   that the total variation dist. between components is bounded away from zero.
   ... certain generating fns ..."
   -- [<A HREF="https://doi.org/10.1145/3583680">doi:10.1145/3583680</A>]['23].
   [Also search for: estimate mixture model].

%A J. Strappa
%A F. Bromberg
%T Efficient comparison of independence structures of log-linear models
%J COMPJ
%V ?
%M JUN
%D 2023
%K jrnl, COMPJ, c2023, c202x, c20xx, zz0723, log linear model, LogLinearModel,
  structure, stats, independence, AI, II
%X "... presenting the 1st measure for the direct & efficient comparison of
   independence structures of log-linear models. ... relies only on the
   independence structure of the models, which is useful when the interest lies
   in obtaining knowledge from said structure, or when comparing the performance
   of structure learning algs., among other possible uses. We present proof that
   the measure is a metric, & a method for its computation that is efficient in
   the # of variables of the domain."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxad054">doi:10.1093/comjnl/bxad054</A>]['23].
   Also see LLM@[<A HREF="https://en.wikipedia.org/wiki/Log-linear_model">wikip</A>]['23].
   [Also search for: log linear model].

%A M. Drmota
%A W. Szpankowski
%T Analytic Information Theory, from Compression to Learning
%I CUP
%P 400
%M SEP
%D 2023
%K book, text, c2023, c202x, c20xx, zz1023, AI, machine learning, information
%X 1st ed 2023; hb us$140; uk us isbn:1108474446; uk us isbn13:9781108474443.
   "Through i.theory, problems of comm. & compr. can be precisely modeled,
   formulated, & analyzed, & this information can be transformed by means of
   algs.. Also, learning can be viewed as compr. with side information ..."
   [Also search for: Ockham's razor].


%A A. Kolmogorov
%T On tables of random numbers
%J Sankhya: The Indian J. of Statistics, Ser.A
%V 25
%N 4
%D 1963
%O (reprinted Theor. Comp. Sci., 207(2), pp.387-395, 1998)
%K c1963, c196x, c19xx, zz0214, complexity, random, sequence, randomness
%X "The set theoretic axioms of the calculus of probability, in formulating
   which I had the opportunity of playing some part ...
   for a long time I had the following views:
   (1) The frequency concept based on the notion of limiting frequency as the
    number of trials increases to infinity, does not contribute anything to
    substantiate the applicability of the results of probability theory to real
    practical problems where we have always to deal with a finite # of trials.
   (2) The frequency concept applied to a large but finite number of trials
    does not admit a rigorous formal exposition within the framework of pure
    mathematics. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/S0304-3975(98)00075-9">doi:10.1016/S0304-3975(98)00075-9</A>]['14.

%A P. Martin-Lof
%T The definition of random sequences
%J Information and Control
%V 9
%N 6
%P 602-619
%D 1966
%K jrnl, c1966, c196x, c19xx, random, sequence, information theory, UTM,
   Kolmogorov complexity, Chaitin, MML, MDL, AIC, AIT, entropy, randomness
%X "Kolmogorov has defined the conditional complexity of an object y when the
   object x is already given to us as the minimal length of a binary program
   which by means of x computes y on a certain asymptotically optimal machine.
   On the basis of this defn he has proposed to consider those elts of a given
   large finite pop'n to be random whose complexity is maximal. Almost all
   elements of the pop'n have a complexity which is close to the maximal value.
   [Here] shown that the random elts as def. by K. possess all conceivable
   statistical properties of randomness. They can equivalently be considered as
   the elts which withstand a certain universal stochasticity test. The defn is
   extended to infinite binary seqs. & it is shown that the non random seqs.
   form a maximal constructive null set. Finally, the Kollektivs introduced by
   von Alises obtain a defn which seems to satisfy all intuitive requirements."
   -- [<A HREF="http://dx.doi.org/10.1016/S0019-9958(66)80018-9">doi:10.1016/S0019-9958(66)80018-9</A>]['10].
   ([Also search for: Peirce c1878] and [Good Turing ban].)
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A V. I. Levenshtein
%T Binary codes capable of correcting deletions, insertions and reversals
%J Soviet Physics Doklady
%V 10
%N 8
%P 707-710
%M FEB
%D 1966
%O Doklady Akademii Nauk SSSR, V163 No4 845-848 1965
%K string, strings, string-to-string, sequence, edit distance, metric,
   edit-distance, insert, delete, deletion, indel, LCS, LCSS, similarity,
   comparison, error correcting code, codes, dynamic programming algorithm,
   DPA, Sellers, jrnl, c1966, c196x, c19xx
%X Seems to be the first person to define what became known as the
   (simple) edit-distance and show it to be a metric.  Paper mostly about
   constructing optimal codes to transmit such corrections.
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">bio'nformatics</A>].)

%A A. V. Aho
%A D. S. Hirschberg
%A J. D. Ullman
%T Bounds on the complexity of the longest common subsequence problem
%J JACM
%P 1-12
%V 23
%N 1
%D 1976
%K JACM, jrnl, c1976, c197x, c19xx, string, sequence, alignment, bounds,
   longest common subsequence,  LCS, LCSS, complexity, alphabet
%X [basically O(n*n), may be O(n) if |alphabet|=2.]
   "... examined using the decision tree model of compn, in which vertices
   represent "equal-unequal" comparisons. It is shown that unless a bound on the
   total # of distinct symbols is assumed, every soln to the problem can
   consume an amount of time that is proportional to the product of the lengths
   of the 2 strings. A general lwb as a fn of the ratio of |alphabet| to string
   length is derived. The case where comps between symbols of the same string
   are forbidden is also considered and it is shown that this problem is of
   linear complexity for a 2-symbol alphabet & quadratic for an alphabet of
   >=3 symbols."
   -- [<A HREF="http://doi.acm.org/10.1145/321921.321922">doi:10.1145/321921.321922</A>]['10].

%A D. Angluin
%T Finding patterns common to a set of strings
%J J. of Computer and System Sciences
%P 46-62
%V 21
%D 1980
%K jrnl, JCSS, pattern,  infer, inference, string, strings, c1980, c198x, c19xx
%X pattern is seq' of letters, vars, a reversal symbol,
  find "good" patterns. NPC in general, gives
  a polynomial algorithm to find 1-variable patterns.

%A K. Culik (II)
%A D. Wood
%T A note on some tree similarity measures
%J IPL
%P 39-42
%V 15
%N 1
%D 1982
%K IPL, jrnl, c1982, c198x, c19xx, tree, trees, similarity, homology,
   approximate match, matching

%A L. Dumas
%A J. Ninio
%T Efficient algorithms for folding and comparing nucleic acid sequences
%J NAR
%P 197-206
%V 10
%N 1
%D 1982
%K NAR, jrnl, c1982, c198x, c19xx, MolBio, fold, folding, secondary structure,
   RNA, DNA, jrnl, NAR
%X uses 6-tuples, hash-code and chain n each seq'
  simple CompSci stuff.

%A J.-P. Duval
%T Factorizing words over an ordered alphabet
%J J. Algorithms
%V 4
%N 4
%P 363-381
%M DEC
%D 1983
%K jrnl, c1983, c198x, c19xx, Lyndon word, words, necklace, necklaces,
   factor, factors, string, strings, unique, factorisation, factorization,
   factorising, factorizing, smallest, algorithm, LyndonWord
%X "For a totally ordered alphabet A, there is a unique factorization of each
   word in A* : w = w1 w2 ... wn, where (1) the seq. {w[i]} is nonincreasing
   wrt the lexicographic order, & (2) each w[i] is strictly less than any of
   its proper circular shifts [cf. Chen, Fox, Lyndon, Ann. of Math.  68 (1958),
   81-95]. In this paper two algs. for constructing this factorization are
   presented, & their performance is carefully described.  [and] applications"
   (?Factorizes a word in linear time?)
   [[A 'Lyndon word' w is strictly < all its rotations, equivalently,
    is < all its non-triv right factors v, where w=uv,  equivalently,
    is a non-periodic necklace representative.]]
   [Also search for: Chen Fox Lyndon].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/Factors/">Factors</A>].)

%A S. Karlin
%A G. Ghandour
%A F. Ost
%A S. Tavare
%A L. J. Korn
%T New approaches for computer analysis of nucleic acid sequences
%J PNAS
%P 5660-5664
%V 80
%M SEP
%D 1983
%K PNAS, MolBio, DNA, c1983m c198x, c19xx, composition, sequence, string, KGO83,
   expected length, finite alphabet size, repeat, repeated, substring, zz0904
%X Ref'd in M@nber&Myers1993 p.320 for...  "...[if] all strings of N symbols
   are equally likely, the expected length of the longest repeated substring
   is O(log N / log|E|) [KGO83]." where |E| is the alphabet size.
   And equivalently on p.324, as "... 2.log <SUB>|E|</SUB>(N)+O(1) ..."

%A J. W. Fickett
%T Fast optimal alignment
%J NAR
%P 175-179
%V 12
%N 1
%D 1984
%K MolBio, longest common subsequence, LCS, LCSS, edit distance, homology,
   NAR, alignment, string, strings, sequence
%X think of edit-distance matrix as a height-map, get a valley,
  only need to calculate exact heights to a valley width where
  height is that at the end of valley. Mentions a 10x speedup.
  [Also see Ukkonen '83]

%A M. J. Fischer
%A M. S. Paterson
%T String matching and other products
%R MAC TM 41
%I MIT
%M JAN
%D 1974
%O Complexity of Computation, ed R.M.Karp SIAM-AMS Proc. 7, 113-125, 1974.
%K TR, longest common subsequence,  LCS,  LCSS, edit distance, string, strings,
   alignment, sequence, approximate match, matching, search, wild card,
   wild-card, algorithm, c1974, c197x, c19xx, TR
%X Sub-string matching with a don't care (wildcard) symbol.
   mentions Schonhage-Strassen algorithm for multiplying large integers,
   O( |alphabet|^2 * n * log(n)^2 * loglog(n) )  or code alphabet and then
   O( log|alphabet| * -------"--------------- )
   -- [<A HREF="http://www.lcs.mit.edu/publications/specpub.php?id=40">pdf@mit</A>]['07].
   "The string-matching problem considered here is to find all occurrences of a
   given pattern as a substring of another longer string. When the pattern is
   simply a given string of symbols, there is an algorithm due to [KMP] which
   has a running time proportional to the total length of the pattern and long
   string together. This time may be achieved even on a Turing machine. The
   more difficult case where either string may have "don't care" symbols which
   are deemed to match with all symbols is also considered. By exploiting the
   formal similarity of string-matching with integer multiplication, a new alg.
   has been obtained with a running time which is only slightly worse than
   linear."

%A R. N. Goldberg
%T Minimal string difference encodings
%J J. of Algorithms
%P 147-156
%V 3
%D 1982
%K longest common subsequence,  LCS, LCSS,  edit distance
%X allows insert, delete, replace and skip  as edit operations.

%A P. A. V. Hall
%A G. R. Dowling
%T Approximate string matching
%J ACM Computing Surveys
%P 381-402
%V 12
%N 4
%D 1980
%K longest common subsequence, LCS,  edit distance, LCSS, homology, similarity,
   sequence, string, strings, algorithm

%A D. S. Hirschberg
%T A linear space algorithm for computing maximal common subsequences
%J CACM
%V 18
%N 6
%P 341-343
%M JUN
%D 1975
%K jrnl, longest common subsequence,  LCS, LCSS, recursion, divide and conquer,
   edit distance, sequence, string, strings, alignment, similarity, homology,
   cacm, c1975, c197x, c19xx, dynamic programming, DPA
%X pdf [<A HREF="http://doi.acm.org/10.1145/360825.360861">doi:10.1145/360825.360861</A>]['05]
   [Also search for: edit distance]

%A D. S. Hirschberg
%T Algorithms for the longest common subsequence problem
%J JACM
%P 664-675
%V 24
%N 4
%D 1977
%K jrnl, JACM, c1977, c197x, c19xx, longest common subsequence,  LCS, LCSS,
   string, strings, sequence, similarity, homology, alignment,
   approximate match, matching, algorithm
%X two algorithms, fast for similar (and dissimilar) strings.
    (i) O(pn+nlogn) time  where p=|LCS|
   (ii) O(p(m+1-p)logn)
   uses contours. coined term candidates.
   -- [<A HREF="http://doi.acm.org/10.1145/322033.322044">doi:10.1145/322033.322044</A>]['07]

%A D. S. Hirschberg
%T An information theoretic lower bound for the longest common subsequence
   problem
%J IPL
%P 40-41
%V 7
%N 1
%D 1978
%K jrnl, IPL, c1978, c197x, c19xx, bounds, longest common subsequence,  LCS,
   LCSS, string, strings, sequence, alignment, complexity
%X lower bound of O(nlog(n)).

%A J. A. Howell
%A T. F. Smith
%A M. S. Waterman
%T Computation of generating functions for biological molecules
%J SIAM J. Appl. Math.
%P 119-133
%V 39
%N 1
%M AUG
%D 1980
%K MolBio, DNA,  secondary structure
%X secondary structure algorithms.

%A J. Hunt
%A T. Szymanski
%T A fast algorithm for computing longest common subsequences
%J CACM
%P 350-353
%V 20
%N 5
%D 1977
%K jrnl, CACM, c1977, c197x, c19xx, longest common subsequence,  LCS, LCSS,
   string, strings, sequence, alignment, homology, similarity
%X fast for few matches.
   O((r+n)log n) where r = # matching pairs from a and b.
   Chains instances  of chars together.
   Good for large alphabets.
   -- [<A HREF="http://doi.acm.org/10.1145/359581.359603">doi:10.1145/359581.359603</A>]['07].

%A M. Kanehisa
%T Use of statistical criteria for screening potential homologies in
   nucleic acid sequences
%J NAR
%P 203-213
%V 12
%N 1
%D 1984
%K MolBio, homology similarity, string, strings, sequence matching, NAR
%X probability of a perfect m-match is P(m) = p^m   p=1/4
  prob m matches, r mismatches  P(m,r) = (m+r-2)!/((m-2)!r!) p^m (1-p)^r
  also matches with insert / delete.

%A B. Knobe
%A K. Knobe
%T A method for inferring context-free grammars
%J Information and Control
%P 129-146
%V 31
%D 1976
%K c1976, c197x, c19xx, CFG, context free grammar, rule, rules, infer,
   inference, learn, problem, string, strings, example, examples
%X algorithms to deduce a context-free grammar from examples.

%A R. Lowrance
%A R. Wagner
%T An extension of the string-to-string correction problem
%J JACM
%P 177-183
%V 22
%N 2
%D 1975
%K longest common subsequence,  LCS, LCSS, edit distance, string to strings,
   sequence, alignment, homology, similarity, dynamic programming algorithm,
   DPA, jrnl, JACM
%X allows transpositions of characters under certain restrictions. O(mn) time.

%A W. J. Masek
%A M. S. Paterson
%T How to compute string-edit distances quickly
%P 337-349
%B Time Warps, String Edits and Macromolecules:
   the Theory and Practice of Sequence Comparison
%I AddisonWesley
%D 1983
%K chapter, c1983, c198x, c19xx, algorithm, complexity, edit distance,
   similarity, longest common subsequence, LCS, LCSS, warping, fast, string,
   strings, sequence, alignment, dynamic programming algorithm, DPA, 4 Russians
%X "4 Russians" technique,  O(n*n/log(n)) algorithm fastest (beats n^2)
   if n > 200,000  -- of theoretical interest only.
   [Also search for: sequence similarity algorithm complexity].

%A E. M. McCreight
%T A space-economical suffix tree construction algorithm
%J JACM
%P 262-272
%V 23
%N 2
%M APR
%D 1976
%K suffix, prefix, tree, trees, longest common repeated string, strings,
   data structure, dataStructure, DS, c1976, c197x, c19xx, jrnl, JACM
%X "A new alg. is presented for constructing auxiliary digital search trees to
   aid in exact-match substring searching. ... same asymptotic running time
   bound as previously published algs., but is more economical in space. Some
   implementation considerations are discussed, & new work on the modification
   of these search trees in response to incremental changes in the strings they
   index (the update problem) is presented."
   pdf [<A HREF="http://doi.acm.org/10.1145/321941.321946">doi:10.1145/321941.321946</A>]['05]
   O(n) construction of suffix tree.     Also see  P. W e i n e r  '73.

%A N. Nakatsu
%A Y. Kambayashi
%A S. Yajima
%T A longest common subsequence algorithm suitable for similar text strings
%J Acta Informatica
%P 171-179
%V 18
%D 1982
%K longest common subsequence,  LCS, LCSS, string, strings, sequence
%X draws diagrams back to front,  fast for similar strings,
   [Also see Hirschberg, and see Ukkonen '83]

%A S. B. Needleman
%A C. D. Wunsch
%T A general method applicable to the search for similarities in the amino
   acid sequence of two proteins
%J J. Mol. Biol.
%P 443-453
%V 48
%D 1970
%K MolBio, longest common subsequence,  LCS, edit distance,  homology, DNA,
   JMB, string, strings, sequence, alignment, homology, similarity, shuffling,
   shuffle, randomise, randomize, c1970, c197x, c19xx, significance test
%X a seminal paper.
   p446, s3: "whether a particular [match score] found differs significantly
   from a fortuitous match between two random sequences." ...
   "construct two sets of random sequences, from the amino acid composition
   of each of the proteins compared. [...] If the [match] value found for
   the real proteins is significantly different from the values found for
   [...] random sequences, the difference is a function of the sequences
   alone and not of the compositions."
   Algorithm description not precise re gaps. ?complexity? [See  F i t c h '69]

%A G. Osterburg
%A R. Sommer
%T Computer support of DNA sequence analysis
%J Computer Programs in Biomedicine
%P 101-109
%V 13
%D 1980
%K MolBio, DNA, string, strings, sequence
%X software rather than algorithms as such.

%A V. Paetkau
%T A new rule for analyzing homologous coding sequences in DNA
%J NAR
%P 159-173
%V 12
%N 1
%D 1984
%K MolBio, homology,  reading frame,   FITS, coding, ORF, DNA, NAR
%X in reading frame matches more common in similar sequences,
   but out of frame matches are not.

%A D. Sankoff
%A J. B. Kruskal
%T Time Warps, String Edits and Macromolecules:
   the Theory and Practice of Sequence Comparison
%I AddisonWesley
%D 1983
%K MolBio, text, book, c1983, c198x, c19xx, longest common subsequence, LCS,
   LCSS, string, strings, sequence, time warp, warps, warping, edit distance,
   homology,  DNA, evolution, evolutionary,  mutation, similar, similarity,
   multiple alignment
%X uk us isbn:0201078090.
  a survey book, readable.

%A P. H. Sellers
%T On the theory and computation of evolutionary distances
%J SIAM J. Math.
%P 787-793
%V 26
%N 4
%D 1974
%K MolBio, longest common subsequence,  LCS, LCSS, edit distance,
   string, strings, sequence, evolution, evolutionary, similarity, homology,
   alignment, dynamic programming, DPA, algorithm, c1974, c197x, c19xx
%X "... a formal defn of the biol. concept of evol. dist. & an alg. to compute
   it. For any set S of finite seqs. of varying lengths this distance is a
   real-valued fn on $S \times S$, and it is shown to be a metric under
   condns which are wide enough to include the biol. appl'n. The alg.,
   introduced here, lends itself to computer programming & provides a method to
   compute evol. dist. which is shorter than the other methods ..."
   -- [<A HREF="https://doi.org/10.1137/0126070">doi:10.1137/0126070</A>]['17].
   [Also search for: Levenshtein].

%A P. H. Sellers
%T The theory and computation of evolutionary distances: pattern recognition
%J J. of Algorithms
%P 359-373
%V 1
%N 4
%D 1980
%K MolBio, longest common subsequence,  LCS, LCSS,  edit distance, DPA,
   string, strings, sequence, similarity, evolution, evolutionary, alignment
%X global and local similarity.  Good, readable.

%A T. F. Smith
%T Protein constraints induced by multiframe encoding
%J Mathematical Biosciences
%P 17-26
%V 49
%D 1980
%K MolBio, DNA, information
%X conditional probabilities, information per codon.

%A T. F. Smith
%A M. S. Waterman
%A W. M. Fitch
%T Comparative biosequence metrics
%J J. Mol. Evol.
%P 38-46
%V 18
%D 1981
%K MolBio, DNA, edit distance,  longest common subsequence,  LCS, LCSS,
   JME, evolution, evolutionary, string, strings, sequence, metric, alignment
%X survey, chatty, light

%A W. F. Tichy
%T The string-to-string correction problem with block moves
%J ACM Transactions on Computer Systems
%P 309-321
%V 2
%N 4
%M NOV
%D 1984
%K jrnl, longest common subsequence, LCS, LCSS, edit distance,  block, moves,
   move, jrnl, TOCS, string, strings, sequence, alignment, linear, algorithm,
   similar, similarity, c1984, c198x, c19xx,
   LZ, ZL, factorization, factorisation
%X Uses block moves as the edit operation, seeks min' number, gets a
   O(n) linear algorithm if P.Weiner's ('73) data-structure used.
   S source string, T target string.
   Algorithm: find longest prefix of T that is a substring of S,
     this gives the first block move; repeat until done.
   Proof: by induction on number of block moves.
     One block move - T must obviously be a substring of S, alg' finds this.
     Suppose optimal is i block moves and alg' fails, i.e. finds j > i moves.
       T:----Opt1----|--Opt2--|---Opt3---|.....|--Algi--
       T:-----Alg1-----|---Alg2---|.....|-----Algj------  NB. |Alg1| >= |Opt1|
     Delete the substring Alg1. By induction the alg' would find the opt'
     explanation of the rest of T - but it doesn't :- contradiction.
   -- [<A HREF="http://doi.acm.org/10.1145/357401.357404">doi:10.1145/357401.357404</A>]['05]

%A P. van Emde Boas
%T Preserving order in a forest in less than logarithmic time
%J Symp. on Foundations of Computer Science (16th)
%P 75-84
%D 1975
%O 'Preserving ... time and linear space', Inf Proc Lett 6(3):80-82, June '77
%K FOCS, FOCS16, FOCS75, c1975, c197x, c19xx, conf, suffix, prefix, tree, trees,
   string, strings, longest common repeated, data structure, dataStructure, DS,
   algorithm, priority queue
%X stratified binary-tree, on-line priority queue,
   avg and worst case O(log log n).

%A R. A. Wagner
%A M. J. Fischer
%T The string-to-string correction problem
%J JACM
%V 21
%N 1
%P 168-173
%M JAN
%D 1974
%K longest common subsequence,  LCS, LCSS,  edit distance, string to strings,
   sequence, alignment, approximate match, matching, dynamic programming
   algorithm, DPA, c1974, c197x, c19xx, jrnl, JACM, homology
%X "The string-to-string correction problem is to determine the distance between
   2 strings as measured by the minimum cost sequence of 'edit operations'
   needed to change the one string into the other. The edit operations
   investigated allow changing one symbol of a string into another single symbol
   deleting one symbol from a string, or inserting a single symbol into a
   string. An alg. is presented which solves this problem in time proportional
   to the product of the lengths of the two strings. Possible applications are
   to the problems of automatic spelling correction and determining the longest
   subsequence of characters common to two strings."
   -- [<A HREF="http://doi.acm.org/10.1145/321796.321811">doi:10.1145/321796.321811</A>]['05]

%A M. S. Waterman
%T General methods of sequence comparison
%J Bull. Math. Biol.
%P 473-500
%V 46
%N 4
%D 1984
%K BMB, MolBio, DNA, homology, longest common subsequence,  LCS, LCSS,
   edit distance, string, strings, alignment
%X survey.

%A M. S. Waterman
%A T. F. Smith
%T Identification of common molecular subsequences
%J J. Mol. Biol.
%P 195-197
%V 147
%D 1981
%K MolBio, DNA, homology,  longest common subsequence,  LCS, LCSS,
   edit distance, JMB
%X note on distance metrics amino-acid/amino-acid etc.

%A M. S. Waterman
%A T. F. Smith
%A W. A. Beyer.
%T Some biological sequence metrics
%J Advances in Mathematics
%P 367-387
%V 20
%D 1976
%K MolBio, DNA, homology,  longest common subsequence,  LCS, LCSS,
   edit distance, metric
%X multiple inserts and deletes.

%A P. Weiner
%T Linear pattern matching algorithms
%J 14th IEEE Symposium on switching and automata theory
%P 1-11
%D 1973
%K conf, MolBio, suffix, tree, prefix, trees,  common repeated string, strings,
   linear time, data structure, DS, dataStructure, algorithm,
   c1973, c197x, c19xx
%X Builds prefix/suffix tree in linear time.
   [Also search for: suffix tree linear time].

%A R. M. Wharton
%T Grammar enumeration and inference
%J Information and Control
%P 253-272
%V 33
%N 3
%M MAR
%D 1977
%K jrnl, c1977, c197x, c19xx, grammar, context free, CFG, rule, rules, string,
   strings, learn, infer, inferring, inductive inference, II, example, examples
%X [<A HREF="https://doi.org/10.1016/S0019-9958(77)80005-3">doi:10.1016/S0019-9958(77)80005-3</A>]['17].
   [Also search for: infer grammar].

%A R. Wilhelm
%T A modified tree-to-tree correction problem
%J IPL
%P 127-132
%V 12
%N 3
%D 1981
%K IPL, jrnl, c1981, c198x, c19xx, tree to trees, comparison, similarity,
   correction, tree, edit distance, approximate match, matching, treeEdit
%X [Also search for: treeEdit].

%A C. K. Wong
%A A. K. Chandra
%T Bounds for the string editing problem
%J JACM
%P 13-26
%V 23
%N 1
%D 1976
%K bound, longest common subsequence,  LCS, LCSS, edit distance, string,
   strings, sequence, approximate match, matching
%X complexity, O(n^2), see Aho.

%A A. Apostolico
%T Improving the worst-case performance of the Hunt-Szymanski strategy for the
   longest common subsequence of two strings
%J IPL
%V 23
%N 2
%M AUG
%D 1986
%P 63-69
%K Hunt, Szymanski, LCS, LCSS, edit distance, string, strings, sequence,
   approximate match, matching, alignment

%A W. Miller
%A E. W. Myers
%T A file comparison program
%J SPE
%V 15
%N 11
%M NOV
%D 1985
%P 1025-1040
%K file, edit distance, diff, LCS, LCSS, string, strings, sequence, alignment,
   approximate match, matching, c1985, c198x, c19xx, jrnl, SPE
%X lines indivisible, line insert and delete only

%A P. Heckel
%T A technique for isolating differences between files
%J CACM
%M APR
%D 1978
%V 21
%N 4
%P 264-268
%K edit distance, diff, LCS, LCSS, string, strings, sequence,
   alignment, approximate match, matching, c1978, c197x, c19xx

%A W. J. Wilbur
%A D. J. Lipman
%T Rapid similarity searches of nucleic acid and protein banks
%J Proc. of the National Academy of Sci. USA
%V 80
%P 726-730
%M FEB
%D 1983
%K jrnl, PNAS, c1983, c198x, c19xx, MolBio, edit distance, DNA, algorithm,
   string, sequence, LCS, LCSS, alignment, approximate match, matching,
   k tuple, k tuples, kTuple, kTuples
%X makes k-tuples increases alphabet size by power of k,
   this gives a small number of cross matches,
   so can use fast Hirschberg? method.
   NB. heuristic, not strictly an algorithm - but low probability of a miss.
   -- [<A HREF="http://www.pnas.org/cgi/content/abstract/80/3/726">@pnas</A>]['07]

%A M. S. Johnson
%A R. F. Doolittle
%T A method for the simultaneous alignment of three or more amino acid
   sequences
%J J. Mol. Evol.
%D 1986
%V 23
%P 267-278
%K MolBio, align, alignment, DNA, amino acid, homology, three, string, strings,
   sequence, multiple, AA, protein, LCS, LCSS, similarity, JME, heuristic,
   window
%X ... progressive evaluation of selected segments from each sequence.
   windowing type of heuristic

%A D. F. Feng
%A M. S. Johnson
%A R. F. Doolittle
%T Aligning amino acid sequences: comparison of commonly used methods
%J J. Mol. Evol.
%V 21
%P 112-125
%D 1985
%N 2
%K MolBio, DNA, survey, edit distance, homology, similarity, alignment,
   string, strings, sequence, JME
%X includes jumbling to test significance of alignments.
   (not DNA data strings but could get coding regions)
   actually protein data strings:
       hahu alpha-hemoglobin human  141 residues;
       hbhu beta-hemoglobin human   146 residues;
       hghu gamma-hemoglobin human  146 residues
       myhu myoglobin human         153 residues;
       heha hemoglobin  hagfish     148 residues;
       myer myoglobin  gastropod    151 residues;
       hety hemoglobin  earthworm   139 residues;
       haew hemoglobin earthworm    157 residues;
       gpfb leghemoglobin  kidney bean 145 bases;
   full lengths used.
   Also gives some phylogenetic trees.

%A P. Bucher
%A B. Bryan
%T Signal search analysis : a new method to localize and characterize
   functionally important DNA
%J NAR
%V 12
%N 1
%M JAN
%D 1984
%K MolBio, NAR, DNA, homology, pattern, signal, start, stop, signal, motif

%A R. Staden
%T Computer methods to locate signals in nucleic acid sequences
%J NAR
%V 12
%N 1
%D 1984
%M JAN
%P 505-518
%K MolBio, NAR, DNA, pattern, signal, start, stop, motif

%A B. A. Shapiro
%A J. Maizel
%A L. E. Lipkin
%A K. Currey
%A C. Whitney
%T Generating non-overlapping displays of nucleic acid secondary structure
%J NAR
%V 12
%N 1
%M JAN
%D 1984
%P 75-88
%K MolBio, NAR, DNA, secondary structure,  graph, graphics, display,  planar,
   tree

%A M. Rodeh
%A V. R. Pratt
%A S. Even
%T Linear algorithms for data compression via string matching
%J JACM
%V 28
%N 1
%P 16-24
%M JAN
%D 1981
%K linear, algorithm, text, data, compression, string, match, matching,
   compress, jrnl, JACM, c1981, c198x, c19xx
%X [<A HREF="http://doi.acm.org/10.1145/322234.322237">doi:10.1145/322234.322237</A>]['05]

%A T. A. Welch
%T A technique for high-performance data compression
%J IEEE Computer
%V 17
%N 6
%P 8-19
%D 1984
%K c1984, c198x, c19xx, string, data, text compression, algorithm, Lempel, Ziv,
   LV, LZW
%X search for L and Z in '77 and '78

%A F. van Bockstaele
%T Contextual constraints in protein sequences
%D 1987
%I Institut Curie, 11 rue P & M Curie, 75231 Paris cedex 5, France
%K MolBio, DNA, context, grammar, induction, constraint, protein, sequence
%X Determining grammar ruling occurences of symbols in genetic
   sequences.

%A P. Friedland
%A L.H. Kedes
%T Discovering the secrets of DNA
%J CACM
%V 28
%N 11
%P 1164-1186
%M NOV
%D 1985
%K MolBio, DNA, AI, MOLGEN, pattern recognition, signal, signals

%A R. L. Cann
%A M. Stoneking
%A A. C. Wilson
%T Mitochondrial DNA and human evolution
%J Nature
%V 325
%N 1
%M JAN
%D 1987
%P 31-36
%K MolBio, DNA, jrnl, c1987, c198x, c19xx, mitochondria, DNA, mtDNA, ancient,
   human, evolution, evolutionary, ancestry, Eve, out of Africa, hypothesis,
   phylogenetic, tree, trees
%A Mitochondrial DNA from 147 people drawn from five geographical populations
   have been analysed by restriction mapping. All these mitochondrial DNAs stem
   from one woman who is postulated to have lived about 200,000 years ago,
   probably in Africa. All the pop'ns examined except the African pop'n have
   multiple origins implying that each area was colonised repeatedly.
   -- [<A HREF="http://dx.doi.org/10.1038/325031a0">doi:10.1038/325031a0</A>]['07].
      (NB. Mitochondrial DNA is inherited only from the mother.)
      The original tree wobbled a bit in c1992.
   [Also search for: Stoneking c1992 MolBio] and
   [also search for: MolBio Eve human evolution].

%A A. L. Williams
%A I. Tinoco
%T A dynamic programming algorithm for finding alternative RNA secondary
   structures
%J NAR
%V 14
%N 1
%P 299-315
%D 1986 ?
%K MolBio, DNA, DPA, NAR, nucleic acid, RNA, fold, folding, secondary structure

%A K. Stuber
%T Nucleic Acid Secondary Structure Prediction And Display
%J NAR
%V 14
%N 1
%P 317-326
%D 1986 ?
%K MolBio, NAR, DNA, nucleic acid, secondary structure
%X program written in PASCAL for a VAX - cost $US150

%A A. B. Jacobson
%A L. Good
%A J. Simonetti
%A M. Zuker
%T Some Simple Computational  Methods to Improve the Folding of Large RNAs
%J NAR
%V 12
%N 1
%P 45-52
%X Also Zuker & Stiegler Nucl. Acids Res 9,(1)133-
   148 describing the FOLD program which is available from Zuker
   (in Fortran I believe))
%K NAR, MolBio, DNA, RNA, fold, folding, nucleic acid, secondary structure

%A B. A. Shapiro
%A L. E. Lipkin
%A J. Maizel
%T An Interactive Technique for the Display of Nucleic Acid Secondary Structure
%J NAR
%V 10
%N 21
%P 7041-7052
%K NAR, MolBio, DNA, nucleic acid, secondary structure

%A R. Feldman
%T NASSD-Nucleic Acid Structure Synthesis and Display
%J FOCUS
%V 4
%N 1
%P 1,8,9
%X (written in SAIL for a DECsystem-10) [FOCUS
  is available free from Stansens Scientific]
%K MolBio, DNA, nucleic acid, secondary structure

%A C. Papanicolaou
%A M. Gouy
%A J. Ninio
%T An Energy Model that Predicts the
   Correct Folding of Both the tRNA and 5S RNA Molecules
%J NAR
%V 12
%N 1
%P 31-43
%K MolBio, DNA, RNA, fold, folding, SS, nucleic acid, secondary structure

%A R. Nussinov
%A G. Pieczenik
%A J. R. Griggs
%A D. J. Kleitman
%T Algorithms for Loop Matching
%J SIAM J. Appl. Math.
%V 35
%P 68-82
%K MolBio, DNA, RNA, nucleic acid, secondary structure, SS, fold, folding

%A G. P. Nolan
%A C. V. Maina
%A A. A. Szalay
%T Plasmid mapping computer program
%J NAR
%V 12
%N 1(2)
%M JAN
%D 1984
%P 717-729
%K NAR, MolBio, plasmid mapping, map, computer program, restriction site,
   digest, RSM, endonuclease, MPCIRC

%A B. N. Stone
%A G. L. Griesinger
%A J. L. Modelevsky
%T PLASMAP: an interactive computational tool for storage, retrieval
   and device independent graphic display of conventional restriction maps
%J NAR
%M JAN
%D 1984
%P 465-471
%V 12
%N 1(2)
%K MolBio, NAR, RSM, plasmid mapping, map, computer program, restriction site,
   digest, endonuclease

%A R. Durand
%A F. Bregegere
%T An efficient program to construct restriction maps from experimental
   data with realistic error levels
%J NAR
%V 12
%N 1
%M JAN
%D 1984
%P 703-716
%K MolBio, NAR, RSM, plasmid, mapping, map, computer program, restriction site,
   digest, endonuclease

%A G. Zehetner
%A H. Lehrach
%T A computer program package for restriction map analysis and manipulation
%J NAR
%V 14
%N 1
%M JAN
%D 1986
%P 335-348
%K MolBio, NAR, RSM, plasmid, mapping, map, computer program, restriction site,
   digest, endonuclease

%A M. Stefik
%T Planning with constraints (Molgen: Part 1)
%J Artificial Intelligence
%V 16
%D 1981
%P 111-140
%K MolBio, AI, hierarchical, planner, constraint posting, MOLGEN

%A M. Stefik
%T Planning and meta-planning (Molgen: part 2)
%J Artificial Intelligence
%V 16
%D 1981
%P 141-170
%K MolBio, AI, least commitment,    heuristic,
   Meta, plan, planning,   MOLGEN

%A L. J. Guibas
%A A. M. Odlyzko
%T String overlaps, pattern matching, and nontransitive games
%J J. of Combinatorial Theory, Series A
%V 30
%N 2
%P 183-208
%D 1981
%K jrnl, c1981, c198x, c19xx, autocorrelation polynomial, auto correlation,
   word, words, strings, substring, substrings, overlap, overlap, overlapping,
   Penney's game, Penney, nontransitive, frequency, count
%X "... notion of the correlation of 2 strings is introduced, which is a rep'n
   of how the 2nd string can overlap into the 1st. ... used to state & prove a
   formula for the generating fn that enumerates the q-ary strings of length n
   which contain none of a given finite set of patterns. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/0097-3165(81)90005-4">doi:10.1016/0097-3165(81)90005-4</A>]['08].  Also see...
   Penney's game, for a binary seq {H,T}*:
   Player A selects a seq. of H&Ts of length l, & shows this seq. to player B.
   Player B then selects another seq. of length l.  A fair coin is tossed until
   either player's seq. appears as a subseq. of the coin toss outcomes.
   Whoever's seq. appears 1st wins. ..."  If l >= 3, B can win more than A.
   e.g. P1  P2  P2's odds
        HHH THH  7:1,
        HHT THH  3:1, etc.
   game@[<A HREF="http://en.wikipedia.org/wiki/Penney's_game">wikip</A>]['08].
   [Also search for: Conway equation].

%A M. Stefik
%T Inferring DNA structures from segmentation data
%J Artificial Intelligence
%V 11
%D 1978
%P 85-114
%K MolBio, AI, DNA, restriction, enzyme,  GA1,   plasmid, map, mapping

%A W. R. Pearson
%T Automatic construction of restriction site maps
%J NAR
%V 10
%N 1
%M JAN
%D 1982
%P 217-227
%K MolBio, NAR, RSM, DNA, plasmid, map, mapping, digest, phage

%A G. Polner
%A L. Dorgai
%A L. Orosz
%T PMAP, PMAPS: DNA physical map constructing programs
%J NAR
%V 12
%N 1
%M JAN
%D 1984
%P 227-236
%K MolBio, NAR, RSM, plasmid, map, mapping, DNA

%A W. M. Fitch
%A T. F. Smith
%A W. W. Ralph
%T Mapping the order of DNA restriction fragments
%J Gene
%P 19-29
%V 22
%D 1983
%K MolBio, RSM, plasmid, map, mapping, phage, restriction site

%A H. O. Smith
%A M. L. Birnstiel
%T A simple method for DNA restriction site mapping
%J NAR
%D 1976
%V 3
%P 2387-2398
%K NAR, MolBio, RSM, DNA, enzyme, digest, restriction site, map, plasmid, phage

%A E. Ukkonen
%T On approximate string matching
%B Proc. of the Int. Conf. on Foundations of Computation Theory
%E M. Karpinski
%W Borgholm, Sweden
%S LNCS
%V 158
%M AUG
%D 1983
%P 487-495
%I SpringerVerlag
%K MolBio, FCT, FCT83, DNA, edit distance, LCS, LCSS, similarity, alignment,
   DPA, approximate, strings, sequence, match, myers, c1983, c198x, c19xx,
   algorithm, kDifferences, k differences, Myers
%X Time O(k*n) worst case, & O(n+k**2) average, for k differences, space O(k*k).
   based on edit distance,  cost change = indel = 1
   but claims can use for more general costs.
   Uses fact that diagonals in D() increase, store contours for diagonals.
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-12689-9_129">doi:10.1007/3-540-12689-9_129</A>]['07].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Three/">three</A>].)

%A E. Ukkonen
%T Finding approximate patterns in strings
%J J. of Algorithms
%V 6
%D 1985
%P 132-137
%K DNA, edit distance, similarity, difference, pattern, string, strings,
   sequence, match, matching, LCS, LCSS, algorithm, c1985, c198x, c19xx
%X pattern p,  |p|=m
   text t,  |t|=n
   alphabet S
   max edit distance d
   preprocessing time O( m*|S|*K ) where K=min(3^m, 2^d * |S|^d * m^(d+1))
   main running time O(n) if m, d small
   space O( |S|*K )
   (?probably not a practical algorithm except in restricted cases?)

%A Rose et al.
%T Hydrophobicity of amino acid residues in globular proteins
%J Science
%V 229
%P 834-838
%M AUG
%D 1985
%K MolBio, DNA, secondary structure, protein, SS, AA

%A Klein
%A Kanehisa
%A DeLisi
%T The detection and classification of membrane-spanning proteins
%J BBA
%V 815
%P 468-476
%D 1985
%K MolBio, DNA, secondary structure, protein

%A J. Garnier
%A D. J. Osguthorpe
%A B. Robson
%T Analysis of the accuracy and implications of simple methods for
   predicting the secondary structure of globular proteins
%J J. Mol. Biol.
%V 120
%P 97-120
%D 1978
%K MolBio, DNA, secondary structure, prediction, protein, information theory,
   JMB, SS, statistical, inductive inference, II
%X context of -8 to +8 residues
   weights show tendency for formation of   alpha helix, extended, turn or coil
   tables 20 amino acid by position -8 to +8
   linear sum, choose max.
   (I think extended ~ beta sheets.)
   Claim about 60% prediction correct (chance = 25%).
   Suggest hydrophobic/phylic confirms predictions rather than improves them
   ie. that phylic/phobic used in packing secondary structures rather
   than in forming them.

%A Palau
%A Argos
%A Puigdomenech
%T Protein secondary structure: Studies on the limits of prediction accuracy
%J Int. J. Peptide and Protein Research
%V 19
%P 394-401
%D 1982
%K MolBio, DNA, secondary structure, protein, AA, SS

%A Argos
%A Palau
%T Amino acid distribution in protein secondary structures
%J Int. J. Peptide and Protein Research
%V 19
%P 380-393
%D 1982
%K MolBio, DNA, secondary structure, protein, AA, SS

%A Nagano
%T Logical Analysis of the mechanism of protein folding.  Predictions of
   helices, loops and beta structures from primary structure
%J J. Mol. Biol.
%V 75
%P 401-420
%D 1973
%K JMB, MolBio, c1973, c197x, c19xx, DNA, secondary structure, protein, AA, SS

%A Cariani
%A Goel
%T On the computation of the tertiary structure of globular proteins--IV
   Use of secondary structure information
%J Bull. Math. Biol.
%V 47
%N 3
%P 367-407
%D 1985
%K BMB, MolBio, DNA, secondary structure, protein, AA, SS

%A Cid et al.
%T Secondary structure prediction of human salivary proline-rich proteins
%J FEBS Letters
%V 198
%N 1
%P 140-144
%M MAR
%D 1986
%K MolBio, DNA, secondary structure, protein, AA, SS

%A Levitt
%A Greer
%T Automatic identification of secondary structure in globular proteins
%J J. Mol. Biol.
%V 114
%P 181-293
%D 1977
%K JMB, MolBio, c1977, c197x, c19xx, DNA, secondary structure, protein, AA, SS

%A B. A. Wallace
%A M. Cascio
%A D. L. Mielke
%T Evaluation of methods for the prediction of membrane protein secondary
   structures
%J Proc. Natl. Acad. Sci. (USA)
%V 83
%P 9423-9427
%M DEC
%D 1986
%K MolBio, PNAS, DNA, secondary structure, protein, PNAS, AA, SS
%X membrane proteins not well predicted using coeff's from soluble
   proteins.

%A Engelman
%A Steitz
%A Goldman
%T Identifying non-polar transmembrane helices in amino acid sequences of
   membrane proteins
%J Ann. Rev. Biophys. and Biophys. Chem.
%V 15
%P 321-353
%D 1986
%K MolBio, DNA, secondary structure, protein, AA, SS

%A V. I. Lim
%T Algorithms for prediction of alpha helical and beta-structural regions
   in globular proteins
%J J. Mol. Biol.
%V 88
%P 873-894
%D 1974
%K JMB, MolBio, DNA, secondary structure, protein, alpha helix, beta sheet,
   turn, algorithm, prediction, AA, SS
%X claims 80 and 85% accuracy for alpha and beta respectively
   based on 25 proteins.

%A Chou
%A Fasman
%T Prediction of beta-turns
%J Biophys. J.
%V 26
%P 367-384
%M JUN
%D 1979
%K MolBio, DNA, secondary structure, protein, AA, SS

%A R. E. Tarjan
%T Applications of path compression on balanced trees
%J JACM
%V 26
%N 4
%P 690-715
%M OCT
%D 1979
%L jrnl, JACM, c1979, c197x, c19xx, tree, trees, lowest common ancestor, LCA,
   ancestors, least, nearest, algorithm, offline
%X "computes lowest common ancestors for pairs of nodes in a tree, based on
   the union-find data structure."
   -- [<A HREF="http://dx.doi.org/10.1145/322154.322161">doi:0.1145/322154.322161</A>]['08].
   [Also search for: Tarjan c1983].

%A Chou
%A Fasman
%T Prediction of the secondary structure of proteins from their amino acid
   sequence
%J Adv. Enz.
%V 47
%P 45-147
%D 1979
%K MolBio, DNA, secondary structure, protein, AA, SS

%A F. E. Cohen
%A R. M. Abarbanel
%A I. D. Kuntz
%A R. J. Fletterick
%T Turn prediction in proteins using a pattern-matching approach
%J Biochemistry
%V 25
%P 266-275
%D 1986
%K MolBio, c1986, c198x, c19xx, DNA, secondary structure, protein, AA, SS,
   pattern matching
%O also see Cohen et al. Biochemistry 22:4894-4904 1983.
%X claim 95% accurate on test set,  90% on homologous families.

%A M. J. Zvelebil
%AÂ G. J. Barton
%AÂ W. R. Taylor
%AÂ M. J. Sternberg
%T Prediction of protein secondary structure and active sites using
   alignment of homologous sequences
%J J. Mol. Biol.
%V 195
%N 4
%P 957-961
%M JUN
%D 1987
%K JMB, MolBio, jrnl, c1987, c198x, c19xx, DNA, secondary structure, protein,
   AA, SS
%X "The pred'n of protein s.s. (alpha-helices, beta-sheets & coil) is improved
   by 9% to 66% using the information available from a family of homologous
   seqs.. ... averaging the Garnier et al. ..."
   -- [<A HREF="https://doi.org/10.1016/0022-2836(87)90501-8">doi:10.1016/0022-2836(87)90501-8</A>]['22].

%A DeLisi
%A Berzofsky
%T T-cell antigenic sites tend to be amphipathic structures
%J Proc. Natl. Acad. Sci. (USA)
%V 82
%P 7048-7052
%D 1985
%K MolBio, DNA, secondary structure, protein, PNAS, AA, SS
%M OCT

%A Spouge et al.
%T Strong conformational propensities enhance t-cell antigenicity
%J J. Immunology
%V 138
%N 1
%P 204-212
%K MolBio, DNA, secondary structure, protein, AA, SS
%D 1987

%A S. K. Kumar
%A C. P. Rangan
%T A linear space algorithm for the LCS problem
%J Acta Informatica
%V 24
%N 3
%P 353-362
%M JUN
%D 1987
%K LCS, LCSS, longest common subsequence,  linear, space, strings, strings,
   sequence, fast, divide and conquer, alignment, perfect cut, similarity
%X linear-space by divide and conquer like Hirschberg but
   O(n(m-p)) time where string lengths m and n and |LCS|=p
   Uses idea of "perfect cut".

%A W. J. Hsu
%A M. W. Du
%T New algorithms for the LCS problem
%J J. of Computer and System Sciences
%V 29
%P 133-152
%D 1984
%K JCSS, longest common subsequence, LCS, LCSS, JCSS, sequence, string, strings
%X not seen

%A A. Mukhopadhyay
%T A fast algorithm for the longest common subsequence problem
%J Information Science
%V 20
%P 69-82
%D 1980
%K LCS, LCSS, string, strings, sequence
%X via enews

%A R. H. Lathrop
%A T. A. Webster
%A T. F. Smith
%T Ariadne: pattern-directed inference and hierarchical abstraction
   in protein structure recognition
%J CACM
%V 30
%N 11
%M NOV
%D 1987
%P 909-921
%K MolBio, AI, ARIADNE, DNA, protein, tertiary, structure

%A H. S. Bilofsky-et-al
%T The GenBank genetic sequence databank
%J NAR
%D 1986
%M JAN
%P 1-4
%V 14
%N 1
%K NAR, MolBio, DNA, protein, database
%X very general review of the database, size etc.
   5700 entries of DNA and RNA 1967 t0 1986

%A G. H. Hamm
%A G. N. Cameron
%T The EMBL data library
%J NAR
%M JAN
%D 1986
%P 5-9
%V 14
%N 1
%K NAR, MolBio, DNA, protein, database
%X general overview of EMBL DB
   4800 entries,  4.6 million bases  in 1986

%A D. J. Lipman
%A W. R. Pearson
%T Rapid and sensitive protein similarity searches
%J Science
%V 227
%N 4693
%D 1985
%P 1435-1441
%K jrnl, c1985, c198x, c19xx, FASTP, MolBio, DNA, homology, FASTP, search, DBMS
%X "An alg. ... facilitates the search for similarities between newly determined
   amino acid seqs. & s. already available in DBs. Because of the alg.'s
   efficiency on many microcomputers, sensitive protein DB searches may now
   become a routine procedure for molecular biologists. The method efficiently
   identifies regions of similar sequence & then scores the aligned identical
   & differing residues in those regions by means of an AA ... matrix. This ...
   increases sensitivity by giving high scores to those AA replacements which
   occur freq. in evol.. The alg. has been implemented ... to search protein
   DBs very rapidly. E.g., comparison of a 200-AA seq. to the 500,000 residues
   in the NBRF library would take less than 2 min. on a minicomputer & less than
   10 min. on a microcomputer (IBM PC)."
   -- [<A HREF="http://dx.doi.org/10.1126/science.2983426">doi:10.1126/science.2983426</A>]['07]
   [Also search for: Wilbur Lipman c1984]

%A W. J. Wilbur
%A D. J. Lipman
%T ????
%J SIAM J. Appl. Math.
%V 44
%P 556-567
%D 1984
%K jrnl, c1984, c198x, c19xx, SIAM, MolBio, DNA, homology, search, similarity
%X fast search for DNA or protein database for similar matches
   strictly an approximation and not a correct algorithm
   but in practice it works and is very fast,
   [Also search for: Wilbur Lipman PNAS c1983]

%A O. Gotoh
%A Y. Tagashira
%T Sequence search on a supercomputer
%J NAR
%V 14
%N 1
%M JAN
%D 1986
%P 57-64
%K NAR, MolBio, DNA, homology, similarity, search, vectorise, supercomputer
%X programs for searching DNA and protein databases on a
   supercomputer  Hitachi S810-20 vector machine

%A B. A. Shapiro
%A R. Nussinov
%A L. E. Lipkin
%A J. V. Maizel
%T A sequence analysis system encompassing rules for DNA helical distortion
%J NAR
%V 14
%N 1
%M JAN
%D 1986
%P 75-86
%K NAR, MolBio, DNA, structure
%X DNA distortion due to steric clashes between opposing purines and
   pyrimidines can be quantified by 4 sum functions. The distortions
   involve helical twist, roll, torsion angle variations and
   propeller twist.
   Contend these purturbations act as information carriers for the various
   external DNA interactions.
   Describe system incorporating these 4 rules.

%A W. Bains
%T Multan: a program to align multiple DNA sequences
%J NAR
%V 14
%N 1
%M JAN
%D 1986
%P 159-177
%K MolBio, DNA, NAR, alignment, homology, similarity, string, strings, sequence
%X heuristic for aligning upto 50 1Kbase sequences
   concensus set add strings one at a time

%A J-M Claverie
%A L. Bougueleret
%T Heuristic informational analysis of sequences
%J NAR
%V 14
%N 1
%M JAN
%D 1986
%P 179-196
%K jrnl, NAR, c1986, c198x, c19xx, MolBio, DNA, information theory
%X string sequence of overlapping k-tuples.
   get frequencies of k-tuples from some sample.
   map local information content of a string.
   claims can indicate signals and interesting regions

%A A. L. Williams
%A I. Tinoco
%T A dynamic programming algorithm for finding alternative RNA secondary
   structures
%J NAR
%V 14
%N 1
%M JAN
%D 1986
%P 299-315
%K MolBio, DNA, RNA, NAR, secondary structure, SS
%X determines more than one possible secondary structure.
   based on minimising energy but calculations unsure.

%A E. Sobel
%A H. M. Martinez
%T A multiple sequence alignment program
%J NAR
%V 14
%N 1
%M JAN
%D 1986
%P 363-374
%K MolBio, DNA, NAR, homology, similarity, multiple alignment, string, strings,
   sequence
%X heuristic

%A C.-S. Tung
%T Computer graphics program to reveal the dependence of the gross
   three-dimensional structure of the B-DNA double helix on primary structure
%J NAR
%V 14
%N 1
%M JAN
%D 1986
%P 381-387
%K MolBio, DNA, NAR, BDNA, tertiary structure, 3D, helix, twist
%X rules predict local helix parameters (helix twist, angle, relative
   basepair roll angle) from the sequence.
   Uses either Calladine Dickerson parameters or
   Tung Harvey parameters.

%A G. Krishnan
%A R. K. Kaul
%A P. Jagadeeswaran
%T DNA sequence analysis: a procedure to find homologies among many sequences
%J NAR
%V 14
%N 1
%M JAN
%D 1986
%P 543-550
%K MolBio, DNA, NAR, homology, similarity, multiple alignment, string, strings,
   sequence
%X about a program not an algorithm
   multiple nucleic acid sequences
   concensus string
   IBM PC mBasic

%A M. L. Fredman
%T Algorithms for computing evolutionary similarity measures with length
   indepenedent gap penalties
%J Bull. Math. Biol.
%V 46
%N 4
%P 553-566
%D 1984
%K MolBio, string, strings, sequence, similarity, comparison, homology, three,
   BMB, multiple, alignment, gap, gaps, penalty, cost
%X O(n^3) time.
   NB. in terms of similarity not edit-distance.

%A M. Murata
%A J. S. Richardson
%A J. L. Sussman
%T Simultaneous comparison of three protein sequences
%J Proc. Natl. Acad. Sci. (USA)
%V 82
%P 3073-3077
%M MAY
%D 1985
%K MolBio, DNA, sequence, similarity, homology, edit distance, multiple, PNAS,
   alignment, 3, three, string, strings
%X compare 3 sequences for alignment
   extends needleman-wunsch
   decreases time from n^5 ??? to O(n^3)

%A W. H. E. Day
%T Properties of Levenshtein metrics on sequences
%J Bull. Math. Biol.
%V 46
%N 2
%P 327-332
%D 1984
%K BMB, distance, metric, string, sequence, similarity, alignment, Levenstein
%X some survey material
   one version (Levenshtein) L(x,y) = |x|+|y|-2.|LCS(x,y)|

%A P. H. Sellers
%T Pattern recognition in genetic sequences by mismatch density
%J Bull. Math. Biol.
%V 46
%N 4
%P 501-514
%D 1984
%K BMB, segment, substring, pattern alignment, string, strings, sequence
%X a condition of pattern similarity is defined, an algorithm is given
   which scans any set of similarities and screens out those failing.
   when the set contains every pair of segments, one from each of
   two strings of length m and n, time is O(m.n), leaving those pairs
   of segments satisfying the similarity condition.
   Uses concept of match density.

%A M. S. Waterman
%A R. Arratia
%A D. J. Galas
%T Pattern recognition in several sequences: concensus and alignment
%J Bull. Math. Biol.
%V 46
%N 4
%P 515-527
%D 1984
%K BMB, MolBio, alignment, multiple, several, many, sequence, string, strings,
   alignment
%X dynamic programming is O(n^r) for r sequences - too bad r > 3.
   Suggest heuristic to avoid problem based in k-tuples

%A M. S. Waterman
%A M. D. Perlwitz
%T Line geometries for sequence comparisons
%J Bull. Math. Biol.
%V 46
%N 4
%P 567-577
%D 1984
%K BMB, MolBio, align, alignment, sequence, several, many
%X generalises sequence to weighted average sequence
   gives result about geometry of seq alignments
   suggests heuristic for aligning several sequences quickly

%A L. Raiha
%T Approximate sequence comparison: a study with histograms
%I Dept. Computer Science, University of Tampere, Finland
%R A-1988-2
%D 1988
%M JAN
%O Pattern Recognition, vol. 23, #1/2, pp.159-169, Jan., 1990.
%K conf, c1988, c198x, c19xx, Ukkonen, similarity, edit distance, match,
   matching, histogram
%X A dynamic programming algorithm
   to compute distance between 2 sequences.
   alphabet may be infinite.
   Cost function must have at least 2 of the metric properties:
   non-negative values and the triangle inequality.
   Time O(n.min(z+1+s/D, m))  where n length of longer input,
   z is number of items that can be inserted or deleted in the seq' with
   zero cost, s the distance between the seq's, D is the smallest positive
   insert or deletion cost, m length of shorter seq.
   Linear space.
   -- conf paper@[<A HREF="https://doi.org/10.1016/0031-3203(90)90056-Q">doi:10.1016/0031-3203(90)90056-Q</A>]['18].

%E R. M. Miura
%T Some Mathematical Questions in Biology: DNA Sequence Analysis
%S Mathematics in the Life Sciences
%I Am. Math. Soc.
%V 17
%D 1986
%O Proc 1984 Symp. Some Math. Questions in Biology.
%K MolBio, book, DNA, RNA, string, sequence, pattern analysis, LCS, similarity,
   AMS
%X Hargrave library Monash H MOS 517 M685S
   isbn:0 8218 1167 3

%A G. M. Landau
%A U. Vishkin
%A R. Nussinov
%T An efficient string matching algorithm with k substitutions
%J J. Theor. Biol.
%V 126
%P 483-490
%D 1987
%K JTB, c1987, c198x, c19xx, DNA, approximate string matching, match,
   pattern, mismatches
%X text length n, pattern length m, <= k substitutions, not indels
   time O(k(m log m  + n))   space O(nk).
   Also see  L and V in Theor. Comp. Sci.  V.43 p.239 1986.
   [Also search for: Ukkonen approximate matching].

%A G. M. Landau
%A U. Vishkin
%T Efficient string matching with k mismatches
%J TCS
%V 43
%P 239
%D 1986
%K jrnl, TCS, c1986, c198x, c19xx, approximate string matching, match, pattern,
   kDifferences, mismatch, mismatches
%X k substitutions, not indels.
   Also see  L, V and N in J Theo Bio V.126 p.483-490 1987.
   [Also search for: Ukkonen approximate matching].

%A H. M. Martinez
%T An efficient method for finding repeats in molecular sequences
%J NAR
%V 11
%N 13
%P 4629-4634
%D 1983
%K jrnl, NAR, c1983, c198x, c19xx, MolBio, DNA, repeat, repeats, sequence

%A W. R. Pearson
%A D. J. Lipman
%T Improved tools for biological sequence comparison
%J Proc. Natl. Acad. Sci (USA).
%V 85
%N 8
%P 2444-2448
%M APR
%D 1988
%K jrnl, PNSA, c1988, c198x, c19xx, FASTA, MolBio, DNA, protein, local,
   FASTA, FASTA2, FASTP, LFASTA, similarity, homology, k tuple, tuples
%X heuristics, score regions of exact matches, ktuples,
   concentrate on these regions.
   Protein data strings:
      RWMSAV T-cell receptor
      v. RWHUAV T-cell receptor alpha-chain  -- best
         K1HURE Ig kappa chain V-I region
         KVMS50 Ig kappa chain V region
         KVMSM6 Ig kappa chain precursor V regions
   DNA data strings:
      RATTGFA rat transforming growth factor (? 816 bases)
      v. HUMTFGAM human TGF mRNA          --best
         HUMTGFA2 human TGF gene (exon 2)
         HUMTGFA1 human TGF gene 5' end

%A G. M. Landua
%A U. Vishkin
%T Fast string matching with k differences
%J J. of Computer and System Science
%V 37
%N 1
%P 63-78
%M AUG
%D 1988
%K LCS, LCSS, JCSS, c1988, c198x, c19xx, match, approximate
%X (several papers with similar titles).

%A M. D. Hendy
%A D. Penny
%T Branch and bound algorithms to determine minimal evolutionary trees
%J Mathematical Biosciences
%V 59
%P 277-290
%D 1982
%K MolBio, jrnl, c1982, c198x, c19xx, parsimony, family, phylogenetic, tree,
   trees, branch and bound, DNA
%X minimum weighted trees

%A W. M. Fitch
%T On the problem of discovering the most parsimonious tree
%J The American Naturalist
%V 111
%N 978
%D 1977
%P 223-257
%K MolBio, parsimony, phylogenetic tree, minimal spanning tree, DNA, family
%X minimum weighted trees

%A O. Owolabi
%A D. R. McGregor
%T Fast approximate string matching
%J SPE
%V 18
%N 4
%M APR
%D 1988
%P 387-393
%K jrnl, SPE, c1988, c198x, c19xx, string, matching, similarity, LCS,
   Levenshtein, distance, Levenstein metric, n-gram, n-tuple, tuples
%X uses n-grams to quickly find roughly similar strings
   inverted files
   binary -> bin ina nar ary  for trigrams
   intended for short words (I think).

%A J. S. Farris
%T Estimating phylogenetic trees from distance matrices
%J The American Naturalist
%V 106
%N 957
%M SEP-OCT
%D 1972
%P 645-668
%K MolBio, DNA, phylogenetic, tree, taxonomy

%A R. Lipton
%A D. Lopresti
%T Comparing long strings on a short systolic array
%J First International Workshop on Systolic Arrays
%W Oxford
%M JUL
%D 1986
%E W. Moore
%E A. McCabe
%E R. Urquhart
%P 181-190
%K LCS, LCSS, longest common subsequence, VLSI, partition, approximate match

%A J. Deken
%T Probabilistic behaviour of longest-common-subsequence length
%B Time Warps, String Edits and Macromolecules
%E D. Sankoff
%E J. B. Kruskal
%I AddisonWesley
%D 1983
%P 359-362
%K LCS, LCSS, longest common subsequence, sequence
%X bounds for ck = |LCS|/n
   alphabet size   lower bnd    upper bnd
            2      .7615        .8602 (.8575)
            3      .6153        .7769
            4      .5454        .7181
           15      .3273        .4650
   also try in files under Sankoff.

%A N. Jardine
%A R. Sibson
%T Mathematical Taxonomy
%I Wiley
%D 1971
%K book, text, MolBio, class, classification, hierarchical, ancestor,
   family tree, phylogeny, ultra metric, ultrametric, infer, inference,
   cluster analysis, stratified, patrician
%X 1. Kinds of similarity and dissimilarity;
   2. Information Theory;                  3: K-dissimilarity;
   4: Correlation & Weighting Attributes;  5: Other Measures...;
   6: Form and Analysis of Data;           7: Hierarchic Cluster Methods;
   8: Non Hierarchic (overlapping) Stratified Methods;
   9: Axiomatic Approach to Cluster A';   10: Flat Cluster Methods;
  11: Eval'n of Clusterings;              12: Other Approaches to C' A';
  13: .. Biological Taxonomy;             14: Auto' Class'n as a Res' Tool;
  15: Applications...;  uk us isbn:0 471 44050 7;
      uniform rate of evolution implies
      ultrametric inequality: for all A B C
                              d(A,B) <= max( d(A,C), d(B,C) ),
      so all triangles isosceles and odd side is shortest:
         A            eg.tree:   ?    ultrametric:   (patrician)
        . .                    1. .          d(AB)=1
       .   .                   ?   .2        d(AC)=d(AC)=2
       B...C                  . .   .
                            1.   .1  .
                             A   B   C
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>] research.)

%A G. G. Langdon
%T An introduction to arithmetic coding
%J IBM J. Res. Develop
%V 28
%N 2
%P 135-149
%M MAR
%D 1984
%K arithmetic coding, arithmeticCoding, encoding, code, data, text, string,
   compression, compress, algorithm, c1984, c198x, c19xx
%X "...creating a code string which represents a fractional value on the number
   line between 0 and 1. The coding algorithm is symbolwise recursive; i.e., it
   operates upon and encodes (decodes) one data symbol per iteration or
   recursion. On each recursion, the algorithm successively partitions an
   interval of the number line between 0 and 1, and retains one of the
   partitions as the new interval. ..."
   -- [<A HREF="http://domino.research.ibm.com/tchjr/journalindex.nsf/0/aa3c6bd1731fbf0485256bfa0067f5bb?OpenDocument">@ibm</A>]['05]
   [Also search for: arithmeticCoding].

%A I. H. Witten
%A R. M. Neal
%A J. G. Cleary
%T Arithmetic coding for data compression
%J CACM
%V 30
%N 6
%M JUN
%D 1987
%P 520-540
%K arithmetic coding, arithmeticCoding, encoding, code, data, text, string,
   model, compress, algorithm, jrnl, CACM, c1987, c198x, c19xx
%X "The state of the art in data compression is arithmetic coding, not the
   better-known Huffman method. Arithmetic coding gives greater compression, is
   faster for adaptive models, & clearly separates the model from the channel
   encoding."
   -- [<A HREF="http://doi.acm.org/10.1145/214762.214771">doi:10.1145/214762.214771</A>]['05].
   [Also search for: arithmeticCoding].

%A T. A. Reichert
%A D. N. Cohen
%A A. K. C. Wong
%T An application of information theory to genetic mutations
   and the matching of polypeptide sequences
%J J. Theor. Biol.
%V 42
%D 1973
%P 245-261
%K MolBio, amino acid, protein, DNA, mutate, information, code, coding, bits,
   JTB, minimum message length, MML, alignment, MDL
%X 4 operations allowed
      insert(position, "string")
      delete(position, length)
      substitute(position, "string")    this is equal length subs
      UnequalReplace(position, length, "string")
   estimates probabilities, uses LOC(l) = log2( l(l+1) ) for lengths and posns
   Talks about editing (Turing or FSA) machine and tape but at the crunch
   just assumes given operations are optimal.

%A A. K. C. Wong
%A T. A. Reichert
%A D. N. Cohen
%A B. O. Aygun
%T A generalized method of matching informational macromolecular
   coding sequences
%J Comput. Biol. Med.
%V 4
%D 1974
%P 43-57
%K MolBio, information theory, code, coding, bits, DNA, protein, amino acid,
   mutate, minimum message length, MML, alignment, MDL
%X minimum information path (message length)
   non-linear gap weights => backtracking
   tries to estimate prob of various edit ops
   assymetric, ancestor -> child
   Talks about editing (Turing etc) machine but at the crunch just assumes the
   given operations are optimal.

%A D. N. Cohen
%A T. A. Reichert
%A A. K. C. Wong
%T Matching code sequences utilizing context free quality measures
%J Mathematical Biosciences
%V 24
%D 1975
%P 25-30
%K MolBio, information theory, code, coding, bits, DNA, protein,
   amino acid, mutate, alignment, minimum message length, MML, MDL
%X attempts to get polynomial deterministic algorithm by restricting
   the gap costs to 'context free' type.
   get O(N^2 M^2) algorithm  v. O(MN) for usual metrics
   their information theory costs are nearly context free.

%A D. Sankoff
%T Matching sequences under deletion/insertion constraints
%J Proc. Natl. Acad. Sci. (USA)
%V 69
%N 1
%P 4-6
%D 1972
%K MolBio, DNA, alignment, LCS, homology, delete, insert, PNAS
%X O(MN) algorithm for Needleman Wunsch type alignments or edit distance
   metric.  linear gap costs.

%A R. W. Hamming
%T Error detecting and error correcting codes
%J Bell Syst. Tech. Jrnl.
%V 29
%D 1950
%P 147-160
%K code, coding, error, detect, correct, c1950, c195x, c19xx
%X classic stuff, includes Hamming distance = number of mismatched bits

%A W. J. Hsu
%A M. W. Du
%T Computing a longest common subsequence for a set of strings
%J Bit
%V 24
%P 45-59
%D 1984
%K jrnl, Bit, c1984, c198x, c19xx, DNA, LCS, homology, similarity, multiple,
   alignment, string, problem, LCSS, strings, sequence
%X preprocessing linear in total input length
   processing proportional to
      number of strings  K and
      number of matches between them
   good for large alphabets, maybe could do wilbur lipman trick for small
   ones, tuples

%A G. J. Chaitin
%T On the length of programs for computing finite binary sequences
%J JACM
%V 13
%N 4
%P 547-569
%M OCT
%D 1966
%K Turing machine, random string, sequence, randomness, complexity, Kolmogorov,
   information theory, minimum message length, MML, encoding, description,
   inductive inference, jrnl, JACM, II, MDL, Solomonoff, c1966, c196x, c19xx
%X "The use of Turing machines for calculating finite binary sequences is
   studied from the pt of view of info. theory & the theory of recursive fns.
   Various results are obtained concerning the # of instructions in programs.
   A modified form of Turing machine is studied from the same point of view.
   An application to the problem of defining a patternless sequence is
   proposed in terms of the concepts here developed."
   -- [<A HREF="http://doi.acm.org/10.1145/321356.321363">doi:10.1145/321356.321363</A>]['09].
   (Also see  S o l o m o n o f f,  K o l m o g o r o v, and
   [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A A. N. Kolmogorov
%T Three approaches to the quantitative definition of information
%J Problems of Information and Transmission (Problemy Peredachi Informatsii)
%V 1
%N 1
%P 1-7
%D 1965
%K jrnl, c1965, c196x, c19xx, Kolmogorov, kolmogoroff, complexity,
   information theory, inductive inference, II, minimum message length encoding,
   MML, description, MDL, Chaitin, Solomonoff, random, sequence, randomness
%X "There are two common approaches to the definition of 'information':
   combinatorial and probabilistic. The author briefly describes the major
   features of these approaches and introduces a new algorithmic approach that
   uses the theory of recursive functions."
   (Reprinted later: $$$@[<A HREF="http://dx.doi.org/10.1080/00207166808803030">doi:10.1080/00207166808803030</A>]['14].)
   (Also see  S o l o m o n o f f,   C h a i t i n,  and
   [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A A. N. Kolmogorov
%T Logical basis for information theory and probability theory
%J Info. Theory
%I IEEE
%V 14
%N 5
%P 662-664
%M SEP
%D 1968
%K jrnl, c1968, c196x, c19xx, complexity, random, probability
%X "A new logical basis for information theory as well as probability theory
   is proposed, based on computing complexity."
   -- [<A HREF="http://dx.doi.org/10.1109/TIT.1968.1054210">doi:10.1109/TIT.1968.1054210</A>]['14].
   (Also see  S o l o m o n o f f)
   [Also search for: Kolmogorov complexity c196x].

%A A. N. Kolmogorov
%A V. A. Uspenskii
%T Algorithms and randomness
%J Theoria Veroyatnostey i ee Primeneniya
 = Theory of Probability and its Applications
%V 3
%N 32
%P 389-412
%D 1987
%K jrnl, c1987, c198x, c19xx, inductive inference, II, algorithmic probablility,
   Kolmogorov complexity, minimum message length, MML, description, MDL,
   history, Maths, CS, CSci, information theory, randomness, zz1198
%X via <!-- Lnd@bu.edu --> - Leonid (Levin) 11/1998

%A J. Rissanen
%T A universal prior for integers and estimation by minimum description length
%J Annals of Statistics
%V 11
%N 2
%P 416-431
%D 1983
%K jrnl, c1983, c198x, c19xx, MML, MDL, minimum message length, code,
   coding theory, logstar, log star, log*, description encoding,
   inductive inference II, integer, intCodes, intCode
%X "... universal prior is P(n) = 2^-log*(n) closest possible to 1/n, this leads
   to use of log*(n) = log(n)+log^2(n)+... (+ve terms only) bits to code n.
   ... SUM_{n > 0} 2^{-log*(n)} ~ 2.865064 (p.424). ..."
   See [<A HREF="http://www.allisons.org/ll/MML/Discrete/">Discrete</A>]-codes.
   Note, the mean of the distribution is infinite - so it
   "may" not be appropriate if you expect a finite mean!
   -- 2240558@[<A HREF="http://www.jstor.org/stable/2240558">Jstor</A>]['17].
   [Also search for: integer code]  and  [also search for: intCodes],
   (and for Elias code c1975).

%A R. Solomonoff
%T A formal theory of inductive inference, I and II
%J Information and Control
%V 7
%N 1
%P 1-22 and 224-254
%M MAR
%D 1964
%K MML, minimum message length encoding, description, MDL,
   inductive inference, II, Kolmogorov, Chaitin, algorithmic probability,
   complexity, c1964, c196x, c19xx, Bayesian, universal Turing machine
%X A general paper on inductive inference,
   various methods including probability and ~MML or ~MDL.
   "In Part I, four ostensibly different theoretical models of induction are
   presented, in which the problem dealt with is the extrapolation of a very
   long sequence of symbols - presumably containing all of the information to be
   used in the induction. Almost all, if not all problems in induction can be
   put in this form. ...
   ... In Part II these models are applied to the solution of three problems -
   prediction of the Bernoulli sequence, extrapolation of a certain kind of
   Markov chain, and the use of phrase structure grammars for induction. Though
   some approximations are used, the 1st of these problems is treated most
   rigorously. The result is Laplace's rule of succession. ..."
   -- [<A HREF="http://dx.doi.org/10.1016/S0019-9958(64)90223-2">doi:10.1016/S0019-9958(64)90223-2</A>]['14].
   [Also search for: MML] and see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A P. H. Sellers
%T An algorithm for the distance between two finite sequences
%J J. of Combinatorial Theory
%V 16
%D 1974
%P 253-258
%K jrnl, MolBio, c1974, c197x, c19xx, edit distance, LCS, LCSS, homology,
   similarity, string, sequence, alignment, dynamic programming algorithm, DPA
%X Also see Levenshtein

%A O. Gotoh
%T An improved algorithm for matching biological sequences
%J J. Mol. Biol.
%V 162
%P 705-708
%D 1982
%K MolBio, JMB, jrnl, c1982, c198x, c19xx, DNA, homology, similarity, string,
   sequence, edit distance, DPA, linear, gap cost, costs, indel
%X O(m n) time algorithm for gap costs (indels)  w=u.length+v,  u,v>=0
   also piecewise linear costs.
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">alignment</A>].)

%A P. Taylor
%T A fast homology program for biological sequences
%J NAR
%V 12
%N 1
%D 1984
%P 447-455
%K NAR, MolBio, DNA, homology, similarity, string, sequence, edit distance,
   alignment
%X O(m n) time for linear gap (indel) costs
   but in fact it uses a limit on gap lengths and some crafty bit manip.

%A M. S. Waterman
%T Efficient sequence alignment algorithms
%J J. Theor. Biol.
%D 1984
%V 108
%P 333-337
%K JTB, MolBio, DNA, homology, similarity, string, sequence, edit distance
%X CONJECTURED O(m n) time algorithm for concave gap weight functions
   but it isn't; see Miller & Myers '88.

%A W. Miller
%A E. W. Myers
%T Sequence comparison with concave weighting functions
%J Bull. Math. Biol.
%V 50
%N 2
%P 97-120
%D 1988
%K MolBio, similarity, homology, alignment, LCS, LCSS, DNA, concave, linear,
   affine, string strings sequence, BMB, gap weight, block insert,
   dynamic programming algorithm DPA
%X O(m*n) if w(k)=w(k+a)+b solvable for k given a, b in O(1)
   O(m*n*(log n + log m)) otherwise
   also includes Hirschberg linear space technique

%A S. F. Altschul
%A B. W. Erickson
%T Optimal sequence alignment using affine gap costs
%J Bull. Math. Biol.
%V 48
%N 5-6
%P 603-616
%D 1986
%K BMB, MolBio, linear gap cost, weight, alignment homology, DNA, string strings
   sequence, Gotoh, DPA
%X affine=linear.   O(mn) time.
   corrects error in traceback in Gotoh algorithm
   DNA data strings: human IL-2   murine IL-2.
   By the way, suggests  indel(k)=2.5+k/2 cost.

%A R. L. Blanken
%A L. C. Klotz
%A A. G. Hinnenbusch
%T Computer comparison of new and existing criteria for constructing
   evolutionary trees from sequence data
%J J. Mol. Evol.
%V 19
%P 9-19
%D 1982
%K JME, MolBio, DNA, phylogenetic, family tree, trees
%X requested i.l.l.

%A J. Felsenstein
%T Inferring evolutionary trees from DNA sequences
%P 133-150
%B Statistical Analysis of DNA Sequence Data
%E B. Weir
%I Dekker
%D 1983
%K MolBio, c1983, c198x, c19xx, DNA, phylogenetic, family tree, trees,
   inference, parsimony, maximum likelihood, quote, quotable
%X Monash bio lib 574.873282028 W425S.
   Quote:
  "parsimony and maximum likelihood do become the same when rates of change
   become vary small"  and
  "extreme empirical bias of molecular biologists, who have little patience
   for discussions of the methodology of data analysis."

%A P. Hogeweg
%A B. Hesper
%T The alignment of sets of sequences and the construction of phyletic trees:
   an integrated method
%J J. Mol. Evol.
%V 20
%P 175-186
%D 1984
%K JME, MolBio, DNA, phylogenetic, evolutionary, family tree, trees
%X DNA data strings used prokaryotic 5S rRNA sequences
      chloroplasts and bacteria
      duckweed chloroplast,  broadbean chloroplast,  anacysttis nidulans,
      e.coli, proteus vulgaris   etc.
      NOTE very few indels,  give n-way alignments
   Argue that multiple alignment must use a tree.

%A L. C. Klotz
%A R. L. Blanken
%T A practical method for calculating evolutionary trees from sequence data
%J J. Theor. Biol.
%V 91
%P 261-272
%D 1981
%K JTB, MolBio, DNA, phylogenetic, family tree, trees

%A Y. Tateno
%A M. Nei
%A F. Tajima
%T Accuracy of estimated phylogenetic trees from molecular data. I,
   distantly related species
%J J. Mol. Evol.
%V 18
%P 387-404
%D 1982
%K JME, MolBio, DNA, phylogenetic, evolutionary, family tree, trees

%A M. Nei
%A F. Tajima
%A Y. Tateno
%T Accuracy of estimated phylogenetic trees from molecular data. II,
   gene frequency data
%J J. Mol. Evol.
%V 19
%P 153-170
%D 1983
%K JME, MolBio, DNA, evolutionary, phylogenetic, family tree, trees

%A D. Sankoff
%A R. J. Cedergren
%T Simultaneous comparison of three or more sequences related by a tree
%P 253-263
%B Time Warps, String Edits and Macromolecules: the Theory and Practice
   of Sequence Comparison
%E D. Sankoff
%E J. B. Kruskall
%I AddisonWesley
%D 1983
%K MolBio, DNA, phylogenetic, evolutionary, family tree, trees, parsimony,
   set, sets
%X tree with minimum number of mutations,
   uses sets of chars ~ fuzzy string.

%A E. W. Myers
%A W. Miller
%T Row replacement algorithms for screen editors
%J TOPLAS
%V 11
%N 1
%M JAN
%D 1989
%P 33-56
%K LCS, similarity, homology, string comparison, alignment, diff,
   edit distance, linear, cost
%X costs for n-char operation  a+b*n  for constants a and b
   algorithm O(cost*(M+N)) time
   see also Ukkonen '83

%A E. W. Myers
%A W. Miller
%T Optimal alignment in linear space
%J CABIOS
%V 4
%N 1
%D 1988
%P 11-17
%X see also  papers in Bull. Math. Bio. (BMB)  and  Toplas

%A L. Goldstein
%A M. S. Waterman
%T Mapping DNA by stochastic relaxation
%J Advances in Applied Mathematics
%V 8
%P 194-207
%D 1987
%K MolBio, RSM, DNA, dna, restriction site mapping, plasmid, map,
   SA, simulated annealing
%X also show RSM is NP-complete

%A W. H. Li
%A K. H. Wolfe
%A J. Sourdis
%A P. M. Sharp
%T Reconstruction of phylogenetic trees and estimation of
   divergence times under nonconstant rates of evolution
%J Symposia on Quantitative Biology
%V L11
%D 1987
%K MolBio, phylogenetic, family, evolutionary, tree, DNA
%X DNA data strings used   10.2 kb non coding from the n-globin
   pseudo-gene of human, chimpanzee, gorilla, orangutan
   or which two parts 5.3 kb also from rhesus and
   new world monkeys (owl monkey).
   When all compared:  used (1) the n-globin locus 2.2 kb (see Koop)
                            (2) 3.1 kb of n-d globin intergenic region (Maeda)
   Human allele used is latter region of the T allele.
   Excluded some poly-A in ALus, a polypyrimidine and some ambiguous regions.

%A B. F. Koop
%A M. Goodman
%A P. Xu
%A K. Chan
%A J. L. Slightom
%T Primate n-globin DNA sequences and man's place among the great apes
%J Nature
%P 234-238
%V 319
%D 1986
%K MolBio, DNA, gene, globin, data, string, psi, eta, globin, pseudo gene,
   family, evolutionary, phlogenetic, tree, trees
%X DNA data strings:
    alignment given of human, chimp, gorilla, orang utan,
    rhesus monkey, owl monkey and goat psi-eta globin pseudo gene
    2200 bp some longish indels.

%A N. Maeda
%A J. B. Bliska
%A O. Smithies
%T Recombination and balanced chromosome polymorphism suggested by DNA
   sequences 5' to the human delta-globin gene
%J Proc. Natl. Acad. Sci. (USA)
%V 80
%P 5012
%K MolBio, PNAS, DNA, gene, globin, data, string

%A J. S. Farris
%A A. G. Kluge
%A M. J. Eckardt
%T A numerical approach to phylogenetic systematics
%J Systematic Zoology
%V 19
%D 1970
%P 172-189
%K MolBio, family, evolutionary, wagner, phylogenetic, tree, trees,
   class, classification

%A R. W. Hamming
%T Coding and Information Theory
%I PrenticeHall
%D 1980
%K text, book, c1980, c198x, c19xx, data, compression, correction, model, code,
   error correcting codes
%X 1st ed 1980.
   2nd ed 1986.

%A M. Zuker
%T On finding all suboptimal foldings of an RNA molecule
%J Science
%V 244
%P 48-52
%M APR
%D 1989
%K MolBio, DNA, RNA, SS, secondary, structure, fold, folding

%T Computational Molecular Biology: Sources and Methods for Sequence
   Analysis
%E A. M. Lesk
%I OUP
%D 1988
%K MolBio, OUP, DNA, homology, similarity, alignment, string, text, book
%X via enews:
   have just read the review by Gunnar von Heijne in Nature 338:388

%A J. Felsenstein
%T Evolutionary trees from DNA sequences: A maximum likelihood approach
%J J. Mol. Evol.
%V 17
%N 6
%P 368-376
%D 1981
%K JME, MolBio, jrnl, c1981, c198x, c19xx, family, phylogenetic tree, trees,
   evolutionary, maximum likelihood, inference, II, DNA, sequence
%X "... M. L. techniques [for] est. of evolutionary trees from [DNA] seq. data
   is discussed. A computationally feasible method for finding such m. l. ests.
   is developed, & a computer program is available. ... has advantages over the
   traditional parsimony algs., which can give misleading results if rates of
   evolution differ in different lineages. It also allows the testing of
   hypotheses about the constancy of evolutionary rates by l.-ratio tests, &
   gives rough indication of the error of the est. of the tree."
   pdf@[<A HREF="http://dx.doi.org/10.1007/BF01734359">doi:10.1007/BF01734359</A>]['09],
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/7288891">ncbi</A>].
   Allows for non equal rates of evolution.
   NOTE did not deal with indels, changes only.
   DNA data strings: applied to 5 vertebrates' 5S RNA  gives a tree, not seq's
       salmo, chicken, turtle, iguana, xenopus 5S RNA 120bp.
   [Also search for: inference phylogenetic tree MolBio].

%A nosillA L
%T L. A l l i s o n
%D ?
%X See [<A HREF="http://www.allisons.org/ll/Computing/">a l l i s o n s . o r g</A>] and the [<A HREF="https://www.cantab.net/users/mmlist/">mmlist</A>].

%A W. R. Taylor
%A J. M. Thornton
%T Recognition of super-secondary structure in proteins
%J J. Mol. Biol.
%V 173
%P 487-514
%D 1984
%K JMB, MolBio, jrnl, c1984, c198x, c19xx, DNA, protein, secondary, structure,
   SS, prediction, folding, fold, alpha, beta, helix, sheet
%X templates from known super-secondary structures;
   find probable sites;
   beta-alpha-beta units of beta/alpha type  75% accuracy.
   Refine Garnier et al by 8.8% to get 83% secondary structure;
   assignment correct in 14 proteins.
   -- [<A HREF="https://doi.org/10.1016/0022-2836(84)90393-0">doi:10.1016/0022-2836(84)90393-0</A>]['22].

%A J. Felsenstein
%T Confidence limits on phylogenies with a molecular clock
%J Syst. Zool.
%V 34
%N 2
%P 152-161
%D 1985
%K MolBio, phylogenetic, family, tree, inductive inference
%X 3 species case
   discusses possible extension to n > 3.

%A J. Felsenstein
%T Confidence limits on phylogenies: an approach using the bootstrap
%J Evolution
%V 39
%N 4
%D 1985
%P 783-791
%K MolBio, c1985, c198x, c19xx, phylogenetic, family, tree, inductive inference

%A J. Felsenstein
%T Phylogenies and quantitative characters
%J Ann. Rev. Ecol. Syst.
%V 19
%P 445-471
%D 1988
%K MolBio, c1988, c198x, c19xx, phylogenetic, family, tree, inductive inference

%A J. F. Collins
%A A. F. W. Coulson
%T Applications of parallel processing algorithms for DNA sequence analysis
%J NAR
%V 12
%N 1
%D 1984
%P 181-192
%K MolBio, NAR, DNA, homology, LCS, string comparison, DAP, parallel processor
%X used the DAP at Edinburgh,  authors in Dept Mol Bio, Kings Bldgs
   DNA data strings human mitochondria MIHSXX and mouse MITOMM   from EMBL
                    these are 16000 bases
   MIGG45 Gorilla 896 bases,  MIHL45 Gibbon 896 bases,
   MIHS01 Human 608 bases,    MIHSRN Human 1164 bases,  and several others.

%A C. E. Shannon
%T A mathematical theory of communication
%J Bell Syst. Technical Jrnl.
%V 27
%N 3, 4
%P 379-423, 623-656
%M JUL, OCT
%D 1948
%K jrnl, Bell, information theory, MML, MDL, data, channel, telecommunications,
   minimum message length, description, encoding, c1948, c194x, c19xx
%X "The recent development of various methods of modulation such as PCM & PPM
   which exchange bandwidth for signal-to-noise ratio has intensified the
   interest in a general theory of communication. A basis for such a theory is
   contained in the important papers of Nyquist & Hartley on this subject. In
   the present paper we will extend the theory to include a number of new
   factors, in particular the effect of noise in the channel, & the savings
   possible due to the statistical structure of the original message & due to
   the nature of the final destination of the information."
   -- pt_1@[<A HREF="http://dx.doi.org/10.1002/j.1538-7305.1948.tb01338.x">doi:10.1002/j.1538-7305.1948.tb01338.x</A>]['15].
   And,
   "In this final installment of the paper we consider the case where the
   signals or the messages or both are continuously variable, in contrast with
   the discrete nature assumed until now. To a considerable extent the
   continuous case can be obtained through a limiting process from the discrete
   case by dividing the continuum of messages & signals into a large but finite
   number of small regions & calculating the various parameters involved on a
   discrete basis. As the size of the regions is decreased these parameters in
   general approach as limits the proper values for the continuous case. There
   are, however, a few new effects that appear & also a general change of
   emphasis in the direction of specialization of the general results to
   particular cases."
   -- pt_2@[<A HREF="http://dx.doi.org/10.1002/j.1538-7305.1948.tb00917.x">doi:10.1002/j.1538-7305.1948.tb00917.x</A>]['15].
   pt_1 no_3 July 1948, pt_2 no_4 October 1948.
   (Also pdf@[<A HREF="https://people.math.harvard.edu/~ctm/home/text/others/shannon/entropy/entropy.pdf">harv'rd</A>]['24].
   And see MTC@[<A HREF="https://en.wikipedia.org/wiki/A_Mathematical_Theory_of_Communication">wikip</A>]['24].)
   See also Shannon and Weaver (book) '49.

%A C. E. Shannon
%A W. Weaver
%T The Mathematical Theory of Communication
%I U. of Illinois Press
%D 1949
%K text, book, information theory, code coding, c1949, c194x, c19xx
%X for basics of information theory.
   See also Shannon, Bell Tech J, v27, '48.

%T Collected Papers of Claude Shannon
%E N. J. A. Sloane
%A A. D. Wyner
%D 1993
%I IEEE Press
%K Shannon, works, papers, book, text, mathematical theory communication,
   code, coding, information theory
%X ref' in notes at phy.cam.ac.uk .

%A G. A. Miller
%A E. A. Friedman
%T The reconstruction of mutilated English texts
%J Information and Control
%V 1
%N ?
%P 38-55
%D 1958
%K jrnl, text, information theory, inductive inference, c1958, c195x, c19xx
%X Ref in  W o l f f  '93   -  Attributes:
      Samples of natural language - English, French etc. -
      are normally about 50% redundant (Miller and Friedman, 1958).

%A G. J. Chaitin
%T Randomness and Mathematical Proof
%J Scientific American
%V 232
%M MAY
%D 1975
%P 47-52
%K information theory, MML, MDL, c1975, c197x, c19xx

%A G. J. Chaitin
%T Algorithmic Information Theory
%J IBM J. Res.  Dev.
%V 21
%P 350-359
%D 1977
%K MML, MDL, II, c1977, c197x, c19xx, IBM, AIT, randomness
%X "... algorithmic information theory ... an attempt to apply info.-theoretic
   and probabilistic ideas to recursive fn theory. Typical concerns in this
   approach are, for example, the # of bits of info. required to specify an
   alg., or the prob. that a program whose bits are chosen by coin flipping
   produces a given output. During the past few years the definitions of
   [AIT] have been reformulated. The basic features of the new formalism are
   presented here and certain results of R. M. Solovay are reported."
   [Also search for: algorithmic information theory].
   (Also See: The J. of Symbolic Logic, 54(2), Jun.,1989, pp.624-627
    @[<A HREF="http://www.jstor.org/stable/2274882">Jstor</A>].)

%A G. J. Chaitin
%T Information, Randomness and Incompleteness
%I World Scientific Pub
%D 1987
%K Information theory, book, minimum message length encoding,
   inductive inference

%A Qian Ning
%A T. Sejnowski
%T Predicting the secondary structure of globular proteins using neural
   network models
%J J. Mol. Biol.
%D 1988
%V 202
%P 865-884.
%K JMB MolBio, protein structure, fold, folding, RNA, SS, NN ANN

%A A. Apostolico
%A C. Guerra
%T The longest common subsequence problem revisited
%J Algorithmica
%V 2
%P 315-336
%D 1987
%K jrnl, c1987, c198x, c19xx, LCS, LCSS, approximate string matching,
   edit distance, alignment, sequence, match
%X some improvements on Hunt Szymanski and others.

%A E. Ukkonen
%T Algorithms for approximate string matching
%J Information and Control
%V 64
%P 100-118
%D 1985
%K jrnl,  c1985, c198x, c19xx, string, LCS, edit distance, algorithm, match,
   DPA
%X O(D.min(M,N)) time and space   M=|A|, N=|B|, D=distance indel/change
   Variation case  O(D.min(M,N)) time,  O(D.min(D,M,N)) space when
   all mutations have same cost.
   * [Also search for: Ukkonen c1983].

%A E. Myers
%T An O(ND) difference algorithm and its variations
%J Algorithmica
%V 1
%P 251-266
%D 1986
%K jrnl, c1986, c198x, c19xx, LCS, LCSS, edit distance, string matching,
   strings, algorithm
%X O(ND) time and space algorithm
   N = |A| = |B|  and  D=length min edit script, single char change and indel
   has O(N+D^2) expected time under stochastic model.
   The algorithm described is simple, and has O(D^2 + N) expected time.
   Refinement O(N) space.
   Variation has O(D^2 + N log N) worst-case time using suffix trees.
   -- [<A HREF="http://dx.doi.org/10.1007/BF01840446">doi:0.1007/BF01840446</A>]['09].
   *** [Also search for: Ukkonen c1983].

%A Z. Galil
%A R. Giancarlo
%T Data structures and algorithms for approximate string matching
%J J. of Complexity
%V 4
%P 33-72
%D 1988
%K edit distance, approximate, match, string, KMP, BM, homology, LCS,
   string, strings, sequence, survey, parallel, dataStructure, DS, algorithm
%X via enews.

%A D. J. Bacon
%A W. F. Anderson
%T Multiple sequence alignment
%J J. Mol. Biol.
%V 191
%P 153-161
%K edit distance, approximate string matching, homology, alignment, string,
   JMB, strings, multiple sequence
%X polynomial in number of sequences
   for amino acid strings
   uses 8 attributes of AA's alpha-helix, beta-strand, beta turn,
                           hydrophobicity, polar, size, +ve -ve
   each AA has a value for each attribute, derive distance on AA's
   Uses a segment length 10-40 residues.
   Heaps of less than 1000 segment alignments.
   Iterative, get best seg alignments for 2 strings,
   bring in 3rd string, ... .

%A O. Berkman
%A D. Breslauer
%A Z. Galil
%A B. Schieber
%A U. Vishkin
%T Highly parallelizable problems
%J Proc. 21st Ann. ACM Symp. on Theory of Computing
%P 309-319
%D 1989
%K conf, lowest common ancestor, LCA, x1989, c198x, c19xx
%X Ref'd by  B e n d e r  &  F a r a c h-C o l t o n  c2000.

%A Z. Galil
%A R. Giancarlo
%T Speeding up dynamic programming with applications to molecular biology
%J Theor. Comp. Sci.
%V 64
%D 1989
%P 107-118
%K MolBio, dynamic programming, string, comparison, approximate, alignment,
   TCS, concave, convex, weight, cost, gap, 1D, 2D, edit distance, LCS, LCSS,
   sequence, algorithm DPA
%X Get 1-D dynamic programming to O(n log(n)) time,
   or O(n) for closest zero property (can solve equations quickly).
   Instance is least weight (sum) subsequence problem   and
   breaking paragraph into lines with concave penalty function.
   An instance of the 1-D problem is one row of the 2-D string matching
   algorithm.
   Gives them Miller and Myers alg (independently?)
   for concave downward cost functions.
   Also get one for convex case.

%A K. Zhang
%A D. Shasha
%T Simple fast algorithms for the editing distance between trees and
   related problems
%J SIAM J. Comput.
%V 18
%N 6
%P 1245-1262
%D 1989
%K jrnl, c1989, c198x, c19xx, ordered labeled tree, labelled, edit distance,
   algorithm, treeEdit
%X "Ordered labeled trees are trees in which the left-to-right order among
   siblings is significant. The dist. between 2 ordered trees is... the weighted
   number of edit operations (insert, delete, & modify) to transform one tree to
   another. The problem of approx. tree matching is also considered. ...,
   algs are designed to answer the following kinds of questions: 1. What is the
   dist between 2 trees?  2. What is the min dist between T1 & T2 when zero or
   more subtrees can be removed from T2?  3. Let the pruning of a tree at node
   n mean removing all the descendants of node n. The analogous Q for prunings
   as for subtrees is answered. A DPA is presented to solve the 3 Qs in
   sequential time O(|T1| x |T2| x min(depth(T1),leaves(T1)) x
   min(depth(T2),leaves(T2 ))) & space O(|T1| x |T2|) compared with
   O(|T1| x |T2 | x (depth(T1))^2 x (depth(T2 ))^2) for the best previous
   alg. due to Tai [JACM 26 '79), pp.422-433]. Further [our] alg can be
   parallelized to give time O(|T1| x |T2|)."  [16 refs].
   -- [<A HREF="http://dx.doi.org/10.1137/0218082">doi:10.1137/0218082</A>]['08]
   (Also see  J a n s s o n  and  L i n g a s, c2001, and  T o u z e t  c2005.)
   [Also search for: treeEdit].

%A M. Das
%A M. J. Paulik
%A N. K. Loh
%T A bivariate autoregressive modeling technique for analysis and
   classification of planar shapes
%J IEEE Trans. on Pattern Matching and Machine Intelligence
%V 12
%N 1
%M JAN
%D 1990
%P 97-103
%K planar, shape, 1D, curve, boundary, polygon, closed, similar, distance
%X bivariate = 2  eg, [x,y]
   convex and concave shapes

%A G. J. Barton
%A M. J. E. Sternberg
%T A strategy for the rapid alignment of protein sequences
%J J. Mol. Biol.
%V 198
%D 1987
%P 327-337
%K MolBio, string, strings, multiple alignment, protein, amino acid, acids,
   JMB
%X do all pairwise; then iterate
   not DNA but
   protein data strings include 128 globin seqs from PIR DB with DB codes
   Accurucay is tested by application to globins and checking that the
   secondary structures match up correctly.

%A S. F. Altschul
%A D. J. Lipman
%T Trees, stars and multiple biological sequence alignment
%J SIAM J. Appl. Math.
%V 49
%N 1
%P 197-209
%M FEB
%D 1989
%K SIAM, JAM, c1989, c198x, c19xx, MolBio, multiple string alignment, fast,
   heuristic, star, all pairs, k-way, tree, trees, phylogenetic, family, MSA
%X uses pairwise alignments to place an upper bound on the projections
   of the optimal multi alignment onto each pair
   thus restricting the volume in the k dimensional lattice
   that need be searched for that optimal k way alignment.
   -- [<A HREF="http://dx.doi.org/10.1137/0149012">doi:10.1137/0149012</A>]['08].
   See  C a r r i l l o  and  L i p m a n  in S.I.A.M.  J.A.M.  '88.

%A H. Carrillo
%A D. Lipman
%T The multiple sequence alignment problem in biology
%J SIAM J. Appl. Math.
%V 48
%N 5
%P 1073-1082
%M OCT
%D 1988
%K SIAM, JAM, MolBio, c1988, c198x, c19xx, Carrillo, Carillo,
   multiple sequence alignment, strings, all pairs cost, MSA, fast, heuristic,
   projection, projections
%X "... proved here that knowledge of the measure of an arbitrarily chosen
   alignment can be used in combination with information from the pairwise
   alignments to considerably restrict the size of the region of the lattice in
   consideration. This reduction implies fewer computations and less memory
   space needed to carry out the dynamic programming optimization."
   -- [<A HREF="http://dx.doi.org/10.1137/0148063">doi:10.1137/0148063</A>]['08].
   * Also see  A l t s c h u l & Lipman in S.I.A.M., J.A.M., '89.

%A D. J. Lipman
%A S. F. Altschul
%A J. D. Keceioglu
%T A tool for multiple sequence alignment
%J Proc. Natl. Acad. Sci. USA
%V 86
%P 4412-4415
%M JUN
%D 1989
%K MolBio, multiple string alignment, PNAS, MSA
%X protein data strings:
      bovine chymotrypsin, bovine trypsin, pig elastase  given and aligned.
      rat mast cell proteinase II, human plasma kallikrein,
      bovine chymotrypsin, bovine trypsin, pig elastase given and aligned.
   -- [<A HREF="http://www.cs.arizona.edu/people/kece/">Kececioglu</A>][10/'02].

%A S. F. Altschul
%A R. J. Carroll
%A D. J. Lipman
%T Weights for data related by a tree
%J J. Mol. Biol.
%V 207
%P 647-653
%D 1989
%K MolBio, phylogenetic family tree, JMB
%X protein data strings:
     15 HIV isolates: BH8, PV22, BH10, BRU, HXB, SF2, CDC, WMJ1, WMJ2,
                      WMJ3, RF, Z6, ELI, MAL, Z3
     ?are they data base identifiers?

%A S. F. Altschul
%A D. J. Lipman
%T Protein data base searches for multiple alignment
%J Proc. Natl. Acad. Sci. (USA)
%V 87
%P 5509-5513
%M JUL
%D 1990
%K jrnl, PNAS, c1990, c199x, c19xx, BLAST, BLAST3, MolBio, multiple, string,
   sequence alignment, database
%X given string, find pairs of strings in DB that give good triple alignment.
   Claim find subtle relationships:
   "... searching a database for multiple as opposed to pairwise alignments,
   distant relationships are much more easily distinguished from b/g noise. ..."
   Preprocessing, tables of words.

%A S. F. Altschul
%A W. Gish
%A W. Miller
%A E. W. Myers
%A D. J. Lipman
%T A basic local alignment search tool
%J J. Mol. Biol.
%V 215
%N 3
%P 403-410?
%M OCT
%D 1990
%K MolBio, JMB, c1990, 199x, c19xx, BLAST, multiple string sequence alignment,
   heuristic MSP, maximum segment pair, MSP, similarity, alignment, DNA
%X "A new approach to rapid seq. comparison, basic local al. search tool (BLAST)
   directly approx. alignments that opt. a measure of local similarity, the
   maximal segment pair (MSP) score. ... results on the stochastic properties of
   MSP scores allow an analysis of the performance of this method as well as the
   stat. sig. of alignments it generates. The basic alg. is simple & robust; ...
   ... implemented in a # of ways & applied in a variety of contexts inc.
   straightforward DNA & protein seq. DB searches, motif searches, gene
   identification searches, & in the analysis of multiple regions of similarity
   in long DNA seqs.. [and] its flexibility & tractability to math. analysis,
   BLAST is an order of magnitude faster than existing seq. comparison tools of
   comparable sensitivity."    (very heavily cited paper)
   -- [<A HREF="http://www.cs.umd.edu/~wu/paper/blast_ref.pdf">pdf@umd</A>]['07].
   [Also search for: sequence alignment].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">bio'nformatics</A>].)

%A S. F. Altschul
%T Gap costs for multiple sequence alignment
%J J. Theor. Biol.
%D 1989
%P 297-309
%V 138
%K JTB, c1989, c198x, c19xx, MolBio, multiple string alignment, gap cost, gaps,
   costs, indel, DNA
%X [Also search for: multiple alignment].

%A D. Sankoff
%T Minimal mutation trees of sequences
%J SIAM J. Appl. Math.
%V 28
%N 1
%M JAN
%D 1975
%P 35-42
%K jrnl, MolBio, c1975, c197x, c19xx, phylogenetic, family, tree, trees,
   Steiner, multiple, string, sequence, alignment, parsimony
%X Allows arbitrary inter character distances or costs;
   paper@[<A HREF="http://www.jstor.org/stable/2100459">Jstor</A>]['09].
   For a more readable introduction see Sankoff and Cedergren
   chapter 9 of the time warps book '83.

%A M. Maes
%T On a cyclic string to string correction problem
%J IPL
%V 35
%P 73-78
%D 1990
%M JUN
%K IPL, jrnl, c1990, c199x, c19xx, alignment, LCS, edit distance, string,
   sequence, cyclic, circular, DPA, LCSS, approximate, match, matching
%X O(m*n*log(m)) time.
   [Also search for: circular string distance].

%A J. Hein
%T A new method that simultaneously aligns and reconstructs ancestral sequences
   for any number of homologous sequences, when the phylogeny is given
%J Molecular Biology and Evolution
%P 649-668
%V 6
%D 1989
%K jrnl, MBE, MolBio, c1989, c198x, c19xx, multiple alignment, bioinformatics,
   string, family, phylogenetic, tree, trees, MBE, edit distance, sequence,
   ancestor, DPA, algorithm, DAG, partial order, graph, partial, poa, pog
%X Represents fuzzy strings as acyclic graphs, aligns graphs by DPA',
   approximate, can handle  > 100 sequences of 1000-2000 chars
   linear indel costs.
   [<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/2488477">pubmed</A>]['15],
   [<A HREF="http://mbe.oxfordjournals.org/content/6/6/649.abstract">oxf</A>]['15].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Multiple/">multiple</A>].)

%A J. Hein
%T A tree reconstruction method that is economical in the number of pairwise
   comparisons used
%J Molecular Biology and Evolution
%P 669-684
%V 6
%D 1989
%K MBE, MolBio, jrnl, c1989, c198x, c19xx, alignment, string, sequence, family,
   phylogenetic, evolutionary, tree, trees
%X directs his multiple alignment program (same volume)
   1. most informative [pairwise] distances
   2. a distance tree is constructed by adding seqs one by one to growing tree
   3. rearrangements to improve tree
   4. alignment done according to tree
   5. parsimony used to rearrange to improve tree.

%A J. Hein
%T TreeAlign
%J Methods in Molecular Biology, V25:
   Computer Analaysis of Sequence Data, Part II
%V 25
%P 349-364
%E A. M. Griffin
%E H. G. Griffin
%I Humana Press
%D 1994
%K TreeAlign, Tree Align, string, sequence, evolutionary, family,
   phylogenetic, trees, multiple alignment

%A E. Kishon
%A H. Wolfson
%T 3-D curve matching
%J AAAI Workshop on Spatial Reasoning and Multi-Sensor Fusion
%P 250-261
%D 1987
%K 3-D, three, dimensions, curve, curves, match, matching, subcurve,
   shape, geometric hashing, GH, hash
%X finds longest common subcurve of two 3-D curves.
   Represented by sequences of local, rotationally and translationally
   invariant shape signatures.
   Signatures compared using geometric hashing.
   Long candidate matches found.
   These analyzed with L2 metric. ???
   Longest matching curve with a good L2 match is chosen.
   Time is O(n) where n is # of sample points on the 2 curves.

%A O. Gotoh
%T Optimal sequence alignment allowing for long gaps
%J Bull. Math. Biol.
%V 52
%N 3
%P 359-374
%D 1990
%K MolBio, alignment, piece wise, piecewise linear, string, strings, sequence,
   BMB, concave, cost, weight, indel, DPA algorithm
%X time is O((L+C)MN)
   where C is a constant; L is # of piece wise segments, M=|A|, N=|B|.

%A Z. Galil
%A K. Park
%T An improved algorithm for approximate string matching
%J SIAM J. Comput.
%V 19
%N 6
%P 989-999
%M DEC
%D 1990
%K MolBio, approximate, string, pattern, match matching,
   edit distance, indel, sequence, algorithm, similarity, homology
%X |pat|=M, |text|=N,  practical time O(kN+M**2) space O(M**2),
   preprocessing contributes the M**2 time and space
       (using suffix tree   time O(kN+MlogM~) and space O(m) - not practical?)
   Given a text string, a pattern string, and an integer k,
   find all occurences of the pattern in the text with at most k differences.
   (A difference is a mismatch an insert or a delete (indel).)
   Both theoretical and practical variants of algorithm improve on
   previous best known.

%A O. Gotoh
%T Consistency of optimal sequence alignments
%J Bull. Math. Biol.
%V 52
%N 4
%P 509-525
%D 1990
%K multiple, string, sequence, alignment, homology, MolBio, consistent, BMB
%X pairwise optimal alignments between >= 3 sequences are not
   necessarily consistent [optimal?] as a whole.
   .. consistent and inconsistent residues usually clustered.
   Use consistent regions as "anchor" points
   to direct multiple alignment.

%A V. G. Timkovskii
%T Complexity of common subsequence and supersequence problems and related
   problems
%J Cybernetics
%V 25
%N 5
%P 565-580
%D 1989
%K complexity, LCS, SCSS, longest common subsequence, word, word problems
   NP, NPC

%A M. Maes
%T Polygonal shape recognition using string matching techniques
%J Pattern Recognition
%V 24
%N 5
%P 433-440
%D 1991
%K pattern recognition, shape, LCS, LCSS, circular, string, match, matching,
   PR, IP, time warps, warp, warping
%X Also see DTW@[<A HREF="https://en.wikipedia.org/wiki/Dynamic_time_warping">wikip</A>]['22].

%A F. Luccio
%A L. Pagli
%T An efficient algorithm for some tree matching problems
%J IPL
%P 51-57
%D 1991
%K jrnl, IPL, c1991, c199x, c19xx, tree, trees, approximate, match, matching,
   ranked trees, edit distance, problem, treeEdit
%X "... consider ordered h-ary trees, that is, trees whose nodes have exactly h
   sons; & ranked trees, where the number of sons depends on the node label. We
   define the subtree distance between two ordered h-trees T1, T2 as the # of
   subtrees to be inserted or deleted in T1 to obtain T2, & consider the problem
   of finding all the occurences, with bounded distance k, of an h-ary tree P as
   a subtree of another h-ary tree T. ... solved in time O(h|P|+max(h,k)|T|).
   We then study the classical problem of finding all the occurences of a ranked
   tree P in another tree T, where the two trees are labelled, & a special label
   v in the leaves of P stands for any subtree in T. An extension of the prev
   alg allows to solve this problem in time O(|P|+k|T|) where k is the # of
   labels v in P. ..."  [9 refs].
   -- [<A HREF="http://dx.doi.org/10.1016/0020-0190(91)90062-M">doi:10.1016/0020-0190(91)90062-M</A>]['08].
   [Also search for: treeEdit].

%A N. Duncan
%A D. T. Barnard
%T The document-to-document correction problem
%R TR 91-315
%I Dept. Computing and Information Science, Queen's University, Kingston,
   Ontario, Canada
%M JUL
%D 1991
%K edit distance, tree, trees, document, correction
%X 16 refs.

%A C. Lawrence
%A A. Reilly
%T Maximum likelihood estimation of subsequence conservation
%J J. Theor. Biol.
%V 113
%P 425-439
%D 1985
%K MolBio, statistics, maximum likelihood, inference, sequence, PAM matrix,
   JTB, protein multiple alignment, ML, string, HMM, Markov model
%X From lawrence@stat.ph.albany.edu Thu Oct 31 09:50:06 1991
   Estimates the power to which the PAM matrix should optimally be raised.

%A I. E. Auger
%A C. E. Lawrence
%T Algorithms for the Optimal Identification of Segment Neighbourhoods
%J Bull. Math. Biol.
%V 51
%P 39-54
%D 1989
%K MolBio, statistics, maximum likelihood, inference, string, sequence,
   BMB, pattern, HMM markov model
%X From lawrence@stat.ph.albany.edu Thu Oct 31 09:50:06 1991

%A I. E. Auger
%A C. Lawrence
%T Identification of the Most Significant Amphipathic Helix with
   Application to HIV and MHV Envelope Proteins
%J CABIOS
%V 6
%P 165-171
%D 1990
%K MolBio, statistics, maximum likelihood, inference, sequence,
%X From lawrence@stat.ph.albany.edu Thu Oct 31 09:50:06 1991

%A M. P. Berger
%A P. J. Munson
%T A novel randomized iterative strategy for aligning multiple protein
   sequences
%J CABIOS
%V 7
%N 4
%P 479-484
%M OCT
%D 1991
%K multiple alignment, similarity, homology, MolBio, protein,
   random, randomised
%X randomly partitions set of sequences
   uses repeated pairwise alignment of alignments.

%A J. L. Spouge
%T Speeding up dynamic programming algorithms for finding optimal lattice paths
%J SIAM J. Appl. Math.
%V 49
%N 5
%P 1552-1566
%M OCT
%D 1989
%K JAM, c1989, c198x, c19xx, multiple, alignment, dynamic programming algorithm,
   DPA, edit distance, fast
%X Upper and lower bounds on path distances derived from the problem domain can
   help to reduce the computational volume investigated by the DPA.  34 refs.

%A Z. Galil
%A K. Park
%T Dynamic programming with convexity, concavity and sparsity
%J Theor. Comp. Sci.
%V 92
%N 1
%P 49-76
%M JAN
%D 1992
%K TCS, jrnl, c1992, c199x, c19xx, dynamic programming algorithm, DPA, survey,
   convex, concave, sparse, sparsity
%X Classification/survey of DPAs.
   -- [<A HREF="http://dx.doi.org/10.1016/0304-3975(92)90135-3">doi:10.1016/0304-3975(92)90135-3</A>]['08].

%A R. E. Bellman
%T Dynamic Programming
%I PrincetonUP
%D 1957
%K text, book, c1957, c195x, c19xx, DPA, dynamic programming algorithm,
   computing, algorithms
%X us isbn:069107951X; us isbn13:978-0691079516.

%A R. E. Bellman
%T Frontiers of Modern Mathematics
%I ?
%D ?
%K dynamic programming algorithm, DPA, book, text
%X is the best overview I have read.
   - Phil Miller, PhD, Bioinformatics, Sequana Therapeutics
   <!-- email: phil@sequana.com  --> [5/'95].

%A Z. Galil
%A K. Park
%T A linear-time algorithm for concave one-dimensional dynamic programming
%J IPL
%D 90??
%V ??
%N ??
%M ???
%P ???-???
%K DPA, dynamic programming algorithm, concave cost function, indel, gap,
   edit distance, linear time, 1-D
%X Given real-valued fn w(i,j) for 0 <= i <= j <= n,
   compute E[j] = min(O <= i < j){D[i]+w(i,j)}, for 1 <= j <= n,
   where D[i] is computed from E[i] in const time (eg. E[i]=D[j]).
   We say w is concave if it satisfies the quadrangle inequality
     w(a,c)+w(b,d) <= w(b,c)+w(a,d), a <= b <= c <= d.

%A Z. Galil
%A K. Park
%T Parallel dynamic programming
%J ???
%I Columbia University
%D 92??
%M ???
%K dynamic programming algorithm, parallel, DPA

%A R. P. Boland
%A E. K. Brown
%A W. H. E. Day
%T Approximating minimum-length-sequence metrics: a cautionary note
%J Math. Social. Sci.
%V 4
%P 261-270
%D 1983
%K minimum length sequence metric metrics, nearest neighbour, interchange,
   metric, generator, shortest expression, set partition

%A R. L. Kashyap
%A B. J. Oomen
%T The noisy substring matching problem
%J IEEE Trans. S. W. Eng.
%V SE-9
%N 3
%P 365-370
%M MAY
%D 1983
%K approximate string match, matching

%A M. Hirosawa
%A M. Hoshida
%A M. Ishikawa
%A T. Toya
%T MASCOT: multiple alignment system for protein sequences based on 3-way
   dynamic programming
%I Institute for New Generation Computer Technology (ICOT)
%D 1992
%K MASCOT, MolBio, multiple alignment, 3, three way, simulated annealing

%A M. Ishikawa
%A T. Toya
%A M. Hoshida
%A K. Nitta
%A A. Ogiwara
%A M. Kanehisa
%T Multiple sequence alignment by parallel simulated annealing
%J Comp. Appl. BioSci
%V 9
%N 3
%P 267-273
%D 1993
%O TR-730, Institute for New Generation Computing (ICOT), 1992
%K MolBio, Bioinformatics, multiple alignment, simulated annealing, SA,
   string, strings, sequence
%X ...simulated annealing [for] multiple sequence alignment.
   ... [gave] optimal solution as confirmed by [full] DPA for 3-sequence[s].
   ... [use] a parallel computer. A sequential alg', a simple parallel alg' &
   the temperature parallel alg' were tested...  CABIOS now J. Bioinformatics
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/9/3/267">abs'</A>][7/'02].

%A E. N. Trifonov
%T Nucleotide sequences as a language: morphological classes of words
%B Classification and Related Methods of Data Analaysis
%E H. H. Bock
%I Elsevier
%D 1988
%P 57-64
%K MolBio, DNA, string, sequence, word, words, morphology, frequency
   language, code, message, information, repetition
%X at Dept Polmer Research, Weizmann Inst. of Sci., Rehovot 76100, Israel

%A Sun Wu
%A Udi Manber
%A Gene Myers
%A Webb Miller
%T An O(N*P) sequence comparison algorithm
%J IPL
%V 35
%N 6
%P 317-323
%D 1990
%K LCS, LCSS, longest common subsequence, edit distance, homology, string,
   strings, sequence, similarity
%X via enews
   P is # matches ?

%A Francis Y. L. Chin
%A C. K. Poon
%T A fast algorithm for computing longest common subsequences of small alphabet
   size
%J J. of Information Processing
%V 13
%N 4
%P 463-469
%D 1990
%K LCS, LCSS, longest common subsequence, edit distance, homology, string,
   strings, sequence, alignment, similarity, JIP, c1990, c199x, c19xx
%X via enews

%A D. S. Hirschberg
%A L. L. Larmore
%T The set-set LCS problem
%J Algorithmica
%V 4
%P 503-510
%D 1989
%K LCS, LCSS, longest common subsequence, edit distance, homology, string,
   alignment, strings, match, similarity, set-set, set, sets, to, set-to-set,
   music, melody, tune, musical accompaniment, chord, chords, polyphonic,
   computer, jrnl, c1989, c198x, c19xx
%X given a sequence of sets A=A1, ..., Ap
   a FLATTENING of A is a sequence alpha=a1..am
   if alpha is a concatenation of strings,
   the ith of which is a permutation of Ai.
   Given 2 sequences of sets A=A1...Ap and B=B1...Bq
   the SET-SET LCS problem is to find the LCS of alpha and beta
   where alpha ranges over flattenings of A and beta ... of B.
   Apparently useful in musical accompaniment
   where Ai and Bj could be chords.
   Gives an O(mn) time algorithm where m=sum cardinalities if Ai, n= ... of Bj.
   -- [<A HREF="http://dx.doi.org/10.1007/BF01553904">doi:10.1007/BF01553904</A>]['11].
   [Also search for: music match].

%A D. S. Hirschberg
%A L. L. Larmore
%T The set LCS problem
%J Algorithmica
%V 2
%P 91-95
%D 1987
%K LCS, LCSS, longest common subsequence, edit distance, homology, string,
   alignment, strings, similarity, set, sets, set-set, to, set-to-set,
   music, melody, tune, match, musical accompaniment, chord, chords
%X "An efficient alg. is presented that solves a generalization of the
   Longest Common Subseq. problem, in which one of the two input strings
   contains sets of symbols which may be permuted. [It] arises from a music
   application." via enews.
   -- [<A HREF="http://dx.doi.org/10.1007/BF01840351">doi:10.1007/BF01840351</A>]['15].
   [Also search for: music match].

%A E. Ukkonen
%T A linear time algorithm for finding approximate shortest common superstrings
%J Algorithmica
%V 5
%D 1990
%P 313-323
%K MolBio, c1990, c199x, c19xx, shortest common super string, strings,
   superstring, sequence assembly, SCSS, SCS, greedy
%X [Also search for: MolBio sequence assembly].

%A J. Turner
%T Approximation algorithms for the shortest common superstring problem
%J Inf. & Comput.
%V 83
%N 1
%P 1-20
%D 1989
%K MolBio, jrnl, c1989, c198x, c19xx, shortest common super string, strings,
   superstings, SCSS, SCS, greedy, approximation algorithm
%X "... The value of an aprox. soln to SCS is normally taken to be its length,
   & we seek algs. that make the length as small as possible. A different
   measure is given by the sum of the overlaps between consec. strings in a
   candidate soln. When considering this measure, the object is to find soln
   that make it as large as possible. ... We describe several approximation
   algs. that produce solns that are always within a factor of two of optimum
   wrt the overlap measure. ..."
   -- [<A HREF="https://doi.org/10.1016/0890-5401(89)90044-8">doi:10.1016/0890-5401(89)90044-8</A>]['21].
   [Also search for: MolBio sequence assembly].

%A A. Blum
%A T. Jiang
%A M. Li
%A J. Tromp
%A M. Yanakakis
%T Linear approximation of shortest superstrings
%J Proc. 23rd ACM Symp. on Theory of Computing
%D 1991
%P 328-336
%O same title: JACM 41(4) p630-647 JUL 1994
%K MolBio, shortest common super string, strings, superstring, SCSS, SCS,
   greedy, ACM, STC, TC, STC23, STC91
%X greedy algorithm gives a solution at most 4x longer than optimal,
   modification gives 3x.

%A T. Jiang
%A Ming Li
%T Approximating shortest common superstrings with constraints
%J Theor. Comput. Sci.
%V 134
%N 2
%P 473-491
%M NOV
%D 1994
%K shortest common super string, SCSS, SCS, TCS, jrnl, MolBio, zz0296
%X see Blum, Jiang et al 1991
   Modify previous alg's to allow negative strings that may not appear
   as substrings in the super-string, ...
   [I wonder why?]
   Review in Comp Rev p586 Nov 95

%A A. Apostolico
%A C. Iliopoulos
%A G. M. Landau
%A B. Schieber
%A U. Vishkin
%T Parallel construction of a suffix tree with applications
%J Algorithmica
%V 3
%D 1988
%P 347-365
%K MolBio, suffix, prefix, tree, trees, longest common string, strings,
   parallel algorithm, CRCW, RAM, online, on line, string search,
   repeated substring, data structure, dataStructure, DS
%X CRCW parallel RAM machine, string of n symbols,
   O(log n) time given n processors.
   O(n^2) space but this can be reduced to O(n^(1+e)) for any 0 < e <= 1 and
   slowing down proportional to 1/e.

%A D. Gusfield
%A G. M. Landau
%A B. Schieber
%T An efficient algorithm for the all pairs suffix-prefix problem
%J IPL
%V 41
%M MAR
%D 1992
%P 181-185
%K IPL, jrnl, MolBio, c1992, c199x, c19xx, all pairs, suffix prefix problem,
   suffix tree, string, strings, sequence, assembly
%X Given strings S1,...,Sk of total length m,
   find the longest suffix-prefix match for all k(k-1) ordered pairs
   of strings.
   Give algorithm  O(m+k^2) time for any fixed alphabet.
   Input  size ~ m, output size ~ k^2 so it is optimal.
   -- [<A HREF="http://dx.doi.org/10.1016/0020-0190(92)90176-V">doi:/10.1016/0020-0190(92)90176-V</A>]['08].

%A G. M. Landau
%A J. P. Schmidt
%A D. Sokol
%T An algorithm for approximate tandem repeats
%J Proc. 4th Annual Symp. Combinatorial Pattern Matching
%P 120-133
%I SpringerVerlag
%S LNCS
%V 684
%D 1993
%O Landau, Schmidt, Sokol, J. Comput. Biol., 8(1), pp.1-18, 2001
%K conf, MolBio, c1993, c199x, c19xx, CPM, CPM4, CPM93, repeat, string,
   strings, approximate tandem repeats, multiple, finding, zz0599
%X "A perfect single tandem repeat is defined as a nonempty string that can be
   divided into 2 identical substrings, e.g. abcabc. An approx. single tandem
   repeat is one in which the substrings are similar, but not identical, e.g.,
   abcdaacd. ... consider 2 criteria of similarity: the Hamming dist. (k
   mismatches) & the edit dist. (k diffs.). For a string S of length n & an
   integer k our alg. reports all locally optimal approx. repeats, r=uu', for
   which the Hamming distance of u and u' is at most k in O(nk log(n/k)) time,
   or all those for which the edit distance of u and u is at most k, in
   O(nk log k log(n/k)) time. ...  multiple tandem repeats ..."
   -- [<A HREF="http://www.cs.biu.ac.il/~sokold/ps/jcb.ps">.ps@biu.ac.il</A>]['08].

%A K. Zhang
%A R. Statman
%A D. Sasha
%T On the editing distance between unordered labeled trees
%J IPL
%V 42
%P 133-139
%M MAY
%D 1992
%K jrnl, IPL, c1992, c199x, c19xx, edit, editing, distance, unordered, label,
   labeled, labelled, tree, trees, similarity, comparison, match, matching, NP,
   NPC
%X Efficient (P) alg if one tree is a string OR has a bounded # of leaves.
   But in general, NPC even for binary trees and label alphabet of size 2.
   [7 refs].

%A S. Karlin
%A S. F. Altschul
%T Methods for assessing the statistical significance of molecular sequence
   features by using general scoring schemes
%J PNAS
%V 87
%M MAR
%D 1990
%P 2264-2268
%K PNAS, jrnl, c1990, c199x, c19xx, MolBio, statistics, PNAS,
   sequence alignment, feature, score
%X random models score contiguous subsequences
   try to find a ss with max score
   application to sequence alignment with no gaps.

%A R. Arratia
%A P. Morris
%A M. S. Waterman
%T Stochastic scrabble: large deviations for sequences with scores
%J J. Appl. Prob.
%V 25
%P 106-119
%D 1988
%K string, sequence, score, statistics, longest matching subsequence,
   alignment
%X a law of large numbers for the highest scoring matching subsequence
   is derived.
   Highest scoring matching subsequence (no gaps) between two sequences

%E Miyamoto
%E Cracraft
%T Phylogenetic Analysis of DNA Sequences
%I OUP
%D 1991
%K book, MolBio, phylogenetic, family, tree, trees, string, strings, sequence,
   evolutionary, multiple, alignment, DNA, protein

%A A. Konagaya
%A H. Kondou
%T Stochastic motif extraction using a genetic algorithm with the MDL principle
%J 26th Hawaii Int. Conf. Sys. Sci.
%M JAN
%D 1993
%P ???-???
%K HICSS, HICSS-26, HICSS-93, MDL, motif, MolBio, GA, minimum message,
   description length

%A K. Hakata
%A H. Imai
%T The longest common subsequence problem for small alphabet size between
   many strings
%J Proc. 3rd Int. Symp. on Algorithms and Computation
%W Nagoya.
%M DEC
%D 1992
%I SpringerVerlag
%S LNCS
%V ???
%P ???-???
%K MolBio, multiple alignment, LCSS, LCS, string, sequence,
   dominant match, matches
%X given d strings of length n over an alphabet of size s,
   O(nsd + Dsd(log^(d-3)(n) + log^(d-2)(s))) time algorithm
   where D is the # of "dominant matches" and is much less than n^d.

%A D. Eppstein
%A Z. Galil
%A R. Giancarlo
%A G. F. Italiano
%T Sparse dynamic programming I: linear cost functions
%J JACM
%V 39
%N 3
%M JUL
%D 1992
%P 519-545
%K JACM, ACM c1992, c199x, c19xx, MolBio, string, strings, sequence,
   edit distance, alignment, fast, match, matching, affine, DPA, DNA, RNA,
   secondary structure, SS, algorithm
%X Sparse DPA i.e. use matching fragments ~ Wilbur Lipman
   Strings of length m and n.
   (i) Alignment in O(n+m+M log log min(M, nm/M)) time
          where M <= nm is # of matching fragments found
          and   log x = log2(2+x) i.e. not negative for small x.
  (ii) LCS in O(n log s + d log log min(d, nm/d)) time
          where s = min of m and alphabet size
                d <= M is # of dominant matches (Hirsch'b77)
 (iii) RNA sec struct with linear cost fns on single loops
          O(n+M log log min(M, n^2/M)) time
          where n is seq' length
          and   M <= n^2 is # poss' base-pairs under consideration
   The terms  log min(M,x/M) degrade gracefully to O(1) for dense problems
   so our times always at least as good as previously best known algorithms;
   if M < mn (or n^2) better.  [29 refs] also see part-II.
   -- [<A HREF="http://doi.acm.org/10.1145/146637.146650">doi:10.1145/146637.146650</A>]['07].

%A D. Eppstein
%A Z. Galil
%A R. Giancarlo
%A G. F. Italiano
%T Sparse dynamic programming II: convex and concave cost functions
%J JACM
%V 39
%N 3
%M JUL
%D 1992
%P 546-567
%K MolBio, string, strings, sequence, edit distance, alignment, fast,
   match, matching, DPA, DNA, RNA, secondary structure, algorithm
%X 31 refs.

%A D. Harel
%A R. E. Tarjan
%T Fast algorithms for finding nearest common ancestors
%J SIAM J. Comput.
%V 13
%N 2
%P 338-355
%M MAY
%D 1984
%K jrnl, c1984, c198x, c19xx, tree, trees, lowest, nearest common ancestor,
   suffix, prefix, common substring, string, strings, NCA, LCA, algorithm
%X given a collection of rooted trees, n vertices in total,
   answer on-line queries of the form
   "what is the nearest common ancestor of vertices x and y?"
   Show any pointer machine that solves this problem requires
   omega(log log n) time per query in worst case.
   For a random access machine, give an algorithm that needs
 *** O(1) time per query and O(n) preprocessing time if trees static.
   With dynamic trees, give an almost linear time and space algorithm.
   -- [<A HREF="http://dx.doi.org/10.1137/0213024">doi:/10.1137/0213024</A>]['09].

%A B. Schieber
%A U. Vishkin
%T On finding lowest common ancestors: simplification and parallelization
%J SIAM J. Comput.
%V 17
%N 6
%M DEC
%D 1988
%P 1253-1262
%O TR 63/87, Comp. Sci., Tel Aviv University, Jan 1987
%K tree, trees, lowest, nearest common ancestor, suffix, prefix, parallel,
   concurrent, common substring, LCA, NCA, EREW, PRAM, algorithm
%X answer on-line queries for LCA of x and y.
   Give linear time and space preprocessing alg' as for H@rel and Tarj@n
   SIAM J Comput '84, but this one can be parallelised.
  ***  Resulting parallel preprocessing alg' runs in  log(n) time
  ***  using an optimal #,   n/log n,  processors  on an EREW PRAM.
  ***  Each query answered in O(1) time using a single processor.

%A M. Steel
%T The complexity of reconstructing trees from qualitative characters and
   subtrees
%J J. Classification
%V 9
%P 91-116
%D 1992
%K jrnl, c1992, c199x, c19xx, family, evolutionary, phylogenetic, tree, trees,
   cluster, clustering, consensus, NP, NPC
%X when can tree-like classifications of overlapping sets of labels be
   consistently combined into a parent tree?
   NP-complete in general, even for just 4 labels.
   But, for a set of rooted trees, an algorithm is described which
   constructs a "strict consensus tree" of all consistent parent trees
   (when they exist) in polynomial time.

%A S. Dress
%A M. Steel
%T Convex tree realizations of partitions
%J Appl. Math. Lett.
%V 5
%N 3
%P 3-6
%D 1992
%K AML, jrnl, c1992, c199x, c19xx, partition, family, evolutionary,
   phylogenetic, tree, trees
%X Given a collection P of partitions of a label set L a problem arising in
   biological and linguistic classification is deciding whether there is a
   tree structure on L which is compatible with P. While this problem is
   in general NP-complete, we show that it has a polynomial time solution
   if the number of sets in each partition is at most three.
   -- [<A HREF="http://dx.doi.org/10.1016/0893-9659(92)90026-6">doi:10.1016/0893-9659(92)90026-6</A>]['10].

%A M. A. Steel
%A M. D. Hendy
%A L. A. Szekely
%A P. L. Erdos
%T Spectral analysis and a closest tree method for genetic sequences
%J Appl. Math. Lett.
%V 5
%N 6
%P 63-67
%D 1992
%K AML, partition, family, evolutionary, phylogenetic, tree, trees
   Hadamard matrix, conjugate spectrum, Klein group Z2*Z2, DNA
%X We describe a new method for estimating the evolutionary tree linking a
   collection of species from their aligned four-state genetic sequences.
   This methods, which can be adapted to provide a branch and bound algorithm
   is statistically consistent provided the sequences have evolved
   according to a standard stochastic model of nucleotide mutation.
   Our approach exploits a recent group-theoretic description of this model.

%A H.-J. Bandelt
%A A. Dress
%T Reconstructing the shape of a tree from observed dissimilarity data
%J Adv. Appl. Math.
%V 7
%P 309-343
%D 1986
%K c1986, c198x, c19xx, family, evolutionary, phylogenetic, tree, trees,
   partition, split, bipartition

%A M. D. Penny
%A D. Penny
%A M. A. Steel
%T A discrete Fourier analysis for evolutionary trees
%J PNAS
%V 91
%P 3339-3343
%D 1994
%K PNAS, jrnl, MolBio, c1994, c199x, c19xx, family, evolutionary, phylogenetic,
   tree, trees, discrete Fourier analysis, DFT, transform, spectral, 3ST
%X "Discrete Fourier transfs. have recently been developed to model the
   evolution of 2-state characters (the Cavender/Farris model). We report here
   the ext'n ... to provide invertible relationships between a p.tree T
   (with 3 prob. params. of nucleotide subs'n on each edge corr. to Kimura's
   3ST model) & the expected freqs. of the nucleotide patterns in the seqs.. We
   refer to these rel'ns as spectral analysis. In either model with indep. &
   identically distributed site substitutions, spectral analysis allows a global
   correction for all multiple substitutions (2nd- & higher-order interactions),
   indep. of any particular tree. From these corrected data we use a least-
   -squares selection procedure, the closest tree alg., to infer an evol. tree.
   Other selection criteria such as parsimony or compatibility analysis could
   also be used; each of these criteria will be stat.consistent for these
   models. The closest tree alg. selects a unique best-fit p.tree [and] indep.
   edge length params. for each edge. ..."
   pdf@[<A HREF="http://www.pnas.org/content/91/8/3339.full.pdf">pnas</A>]['09],
   pdf@[<A HREF="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC43572/pdf/pnas01130-0470.pdf">pubmed</A>]['09].

%A S. Kannan
%A T. Warnow
%T Inferring evolutionary trees from DNA sequences
%J 31st Annual Symp. of Foundations of Computer Science
%I IEEE Press
%D 362-371
%D 1990
%K FOCS 31, FOCS31, FOCS90, c1990, c199x, c19xx, family, evolutionary,
   phylogenetic, tree, trees

%A A. V. Aho
%A Y. Savig
%A T. G. Szymanski
%A J. D. Ullman
%T Inferring a tree from the lowest common ancestors with an application to
   the optimization of relational expressions
%J SIAM J. Comput.
%V 10
%N 3
%P 405-421
%D 1981
%K SJC, jrnl, c1981, c198x, c19xx, family, evolutionary, phylogenetic, tree,
   trees, ancestor, LCA, expression, relation

%A D. Gusfield
%T Efficient algorithms for inferring evolutionary trees
%J Networks
%V 21
%P 19-28
%D 1991
%K family, evolutionary, phylogenetic, tree, trees, partition, bipartition

%A C. A. Meacham
%T A manual method for character compatibility analysis
%J Taxon
%V 30
%P 591-600
%D 1981
%K family, evolutionary, phylogenetic, tree, trees, partition, bipartition,
   qualitative character

%A J. Gregor
%A M. G. Thomason
%T Dynamic programming alignment of sequences representing cyclic patterns
%J IEEE Trans Pattern Analysis and Machine Intelligence
%V 15
%N 2
%M FEB
%D 1993
%P 129-135
%K TPAMI, PAMI, DPA, string sequence, similarity, homology, alignment, cyclic,
   circular, match, matching, concanavalin, con A, favin, MolBio
%X application to repetitive satellite DNA
   and cyclic shift mutation between concanavalin A (Con A) and favin A & B.
   12 refs

%A A. F. M. Smith
%A G. O. Roberts
%T Bayesian computation via the Gibbs sampler and related Markov chain
   Monte Carlo methods
%J J. Royal Stat. Soc. B
%V 55
%N 1
%P 3-23
%D 1993
%K JRSS, JRSSB, MolBio, map, mapping, Bayes, Gibbs, Gibb's, Gibbs' sampling,
   Monte-Carlo, inductive inference, II, estimation, probabilistic
%X applications:  Gene mapping
                  Image modelling with deformable templates

%A S. C. Chan
%A A. K. C. Wong
%T Synthesis and recognition of sequences
%J IEEE Trans. on Pattern Analysis and Machine Intelligence
%V 13
%N 12
%M DEC
%D 1991
%K MolBio, TPAMI, string, sequence, multiple alignment, tree, trees
%X then at Dept. Systems Design Engineering, Uni of Waterloo, Waterloo,
           Canada N2L 3G1
   Seems to be a join nearest neighbour iterative heuristic.

%A E. C. Tyler
%A M. R. Horton
%A P. R. Krause
%T A review of algorithms for molecular sequence comparison
%J Comp. & Biomed Res.
%V 24
%P 72-96
%D 1991
%K MolBio, CBR, string, sequence, alignment, similarity, homology, approximate
   match matching, survey
%X via enews.

%A R. Baeza-Yates
%A G. H. Gonnet
%T A new approach to text searching
%J CACM
%V 35
%N 10
%P 74-82
%M OCT
%D 1992
%O Preliminary version in Proc. 12th Annual ACM-SIGIR Conf. on Info. retrieval
   Cambridge Mass. 168-175 JUN 1989
%K string, strings, sequence, pattern, search, match matching, mismatch, change,
   approximate, wild card, wild-card, don't, dont care, dont-care, bit, bits,
   string, strings, algorithm, jrnl, CACM, c1992, c199x, c19xx
%X pattern length m, text length n.
   Pattern can contain wild-cards, sets of characters and complements
   so it is NOT just the k-mismatch problem.
   Solve for one or more patterns, with or without mismatches,
   in O(n) time for small (bounded by const) patterns.
   Uses simple bit operations.      [30 refs]
   pdf@[<A HREF="http://doi.acm.org/10.1145/135239.135243">doi:10.1145/135239.135243</A>]['05].
   Also see  W u  and  M a n b e r  same issue CACM '92.

%A Sun Wu
%A U. Manber
%T Fast text searching allowing errors
%J CACM
%V 35
%N 10
%P 83-91
%M OCT
%D 1992
%K string, pattern, search, match matching, mismatch, change, insert, delete,
   indel, approximate, k-mismatch, edit distance, wild card, wild-card,
   don't, dont care, dont-care, grep, agrep, regular expression, bit, bits,
   string, strings, algorithm, jrnl, CACM, c1992, c199x, c19xx
%X Extends  B a e z a - Y a t e s  and  G o n n e t  same issue CACM '92
   to allow indels.    This includes the k-mismatch problem.  [25 refs]
   Basic idea in case of exact matching:
      R[1..m] is a bit array
      Let R< j > be the value of R after the 1st j chars of text are processed.
      R< j >[i]=1 iff the the 1st i chars of pattern p< 1..j > match
                the last i chars of text upto and including j: t< j-i+1..j >.
      Initially R< 0 >[k]=0 for all k 1 <= k <= m,
      Generally R< j+1 >[i]=1 if R< j >[i-1]=1 and p< i >=t< j+1 >
                           =0 otherwise.
      If R< j+1 >[m]=1 then we have a match at  j-m+2.
   Now R< j+1 > can be computed from R< j > by simple bit operations:
      Alphabet S=s< 1 >...s< |S| >
      for each letter s< i > construct bit array S< i >[r]=(p< r >=s< i >)
      Then R< j+1 > = (R< j > SHIFT 1) AND S< i >  where s< i >=t< j+1 >
      SHIFT is right [LA:?] shift and fills 1st posn with a 1.
   (B-Y&G use 0 with OR not AND in case there are only 0-fill shifts: C)
   Approximate matching:
      Let R{d}, 1 <= d <= k, store possible matches with <= d errs (chng/indel)
      R{d}< 0 >   = 11...1100...000   d ones
      R{d}< j+1 > = Rshift[R{d}< j >] AND S< c > OR  -- match
                  Rshift[R{d-1}< j >]   OR           -- change p< i >, t< j+1 >
                  Rshift[R{d-1}< j+1 >] OR           -- delete p< i >
                  R{d-1}< j >                        -- insert t< j+1 >
                = Rshift[R{d}< j >] AND S< c > OR
                  Rshift[R{d-1}< j > OR R{d-1}< j+1 >] OR R{d-1}< j >
   matching time O(n.k.ceiling(m/w)),  O(n.k) if m <= word size w.
      They go on to sets of chars, wild cards, combination exact and
   approx matching, non-uniform costs, sets of patterns, long patterns,
   regular expressions.  ftp agrep from cs.arizona.edu (IP 192.12.69.5)
   pdf [<A HREF="http://doi.acm.org/10.1145/135239.135244">doi:10.1145/135239.135244</A>]['05].

%A C. S. Iliopoulos
%A W. F. Smyth
%T Optimal algorithms for computing the canonical form of a circular string
%J TCS
%V 92
%N 1
%P 87-105
%M JAN
%D 1992
%K jrnl, TCS, c1992, c199x, c19xx, canonical, circular, string, strings
%X "An O(log n) time CRCW PRAM alg. for computing the least lexicographic
   rotation of a circular string (of length n) over a fixed alphabet ...
   logarithmic running time is achieved by using O(n/log n) processors & its
   space complexity is linear. A 2nd alg. for unbounded alphabets requires
   O(log n log log n) units of time, also using O(n/log n) processors."
   -- [<A HREF="http://dx.doi.org/10.1016/0304-3975(92)90137-5">doi:10.1016/0304-3975(92)90137-5</A>]['09].

%A H. Bunke
%A J. Csirik
%T An algorithm for matching run-length coded strings
%J Computing
%V 50
%P 297-314
%D 1993
%K string, sequence, run length encoding RLC RLE, low information content,
   repeat, repetitive, edit distance ED, longest common subsequence,
   LCS, LCSS, alignment, approximate match, matching, pattern, similarity,
   MolBio, jrnl, c1993, c199x, c19xx, Chung, Freschi, Bogliolo, encoded
%X string lengths m and n worst-case time O(m.n),
   k and l are # runs of identical chars, best-case time O(k.l) ah, ha!
   [also search for: match run length].

%A K-L. Chung
%T Fast string matching algorithms for run length coded strings
%J Computing
%V 54
%P 119-125
%D 1995
%K string, sequence, run length encoding RLC RLE, approximate match, matching,
   search, pattern, text, MolBio, c1995, c199x, c19xx, algorithm
%X r.l. coded text, length n;  r.l. coded pattern, length m;  m << n;
   (i)  O(n+m) time seq' algorithm
   (ii) O(1)   time parallel alg' on 2D mesh with reconfig bus
   [See Bunke and Csirik, Computing, '93]

%A N. S. V. Rao
%A Ching Luo
%T On similarity of polynomial configurations
%J IPL
%V 47
%N 5
%P 231-236
%M OCT
%D 1993
%K polynomial, polygon, similarity, match, matching, comparison, shape, FFT,
   point set, affine, transformation, translate, rotate, scale, mirror
%X A polynomial configuration is a set of polynomial curves in the plane.
   Degree of a config' = sum of degrees of its polynomials.
   (NB. a point is a trivial polynomial.)
   Done in optimal theta(n log n) time;  16 refs

%A A. Apostilico
%A A. Ehrenfeucht
%T Efficient detection of quasiperiodicities in strings
%J TCS
%V 119
%N 2
%P 247-265
%M OCT
%D 1993
%K TCS, string sequence, quasi periodic period, repeat, repetitive, pattern,
   low information content, Thue, squares
%X z is q.p. if there exists w!=z s.t. occurrences of w in z cover z entirely
   ie. every position of z falls within some occurrence of z.
   All maximal q.p. substrings of a string x of n symbols
   are found in O(n log^2 n) time.
   Axel Thue studied `squares',
   eg. 213 is a square (immediate repeat) in 12132131

%A A. Califano
%A I. Rigoutsos
%T FLASH: a fast look-up algorithm for string homology
%J Proc. IEEE Conf. Computer Vision and Pattern Recognition
%W New York City
%P 353-359
%M JUN
%D 1993
%K conf, c1993, c199x, c19xx, geometric hashing, hash key, keys, GH, strings,
   sequence, lookup, search, approximate, match, matching, alignment, data base,
   database, BLAST, FASTA, FASTP, MolBio, DNA, protein, Genbank, IBM, dFLASH,
   locality, sensitive, hash, hashing, LSH, neighbourhood, CVPR CVPR93, tuple,
   tuples, gap, gapped, spaced, seed, seeds
%X [10 refs].  acal at watson.ibm.com & rigoutso at watson.ibm.com
   ... implemented for genome of E.coli (2m bases) ... but goal is all Genbank
   (100m bases), so parameters were chosen for that:
    . k-tuples, k=13 [visible] nucleotides from sub-seg of length r=40, say,
    . density d = 40 [overlapping] indices per position,
    . required storage for 100m bases is ~ 18 G-bytes,
    . optimal threshhold is n0=3 [filters out noise],
    . prob' of missing a match on 100 base string with 30 mutations is < 1%,
      [LA: does the "30" include indels???]
    . search time is 10-20 secs on a workstation (~ IBM RS/6000, 530).
   -- [<A HREF="http://dx.doi.org/10.1109/CVPR.1993.341106">doi:10.1109/CVPR.1993.341106</A>]['09].
 * There seem to be two "similar" papers with the same title(!), i.e., also...
 * Proc. ISMB-93, pp.56-64 1993, pdf@[<A HREF="http://www.aaai.org/Papers/ISMB/1993/ISMB93-007.pdf">aaai</A>][10/'09].
   [Also search for: MolBio FLASH].

%A I. Rigoutsos
%A A. Califano
%T dFLASH: a distributed fast look-up algorithm for string homology
%I IBM T. J. Watson Research Centre
%D 1993
%K geometric hashing, hash, GH, string, sequence, lookup, search, approximate,
   strings, match, matching, alignment, data base database,
   TR, MolBio, c1993, c199x, c19xx, DNA, protein, Genbank, IBM, FLASH
%X [18 refs]. rigoutso of watson.ibm.com & acal of watson.ibm.com
   Idea: Consider a DNA database.  A 10-tuple will occur about every 10^6
   positions on average, if we built a hash-table of all 10-tuples and in each
   bucket listed all strings containing it (and where) then a new string could
   be matched by scanning its 10-tuples and counting votes for matching strings
   in the DB.  HOWEVER if S and S' differed in only every 10th position then we
   would never find this match.  So, consider words of length L, and have
   various patterns or rules to select B letters out of L,
   eg., 1101110111011 etc. This gives more hash entries per string. So mut'ns
   can't, or are v. unlikely to, hit them all.
   The parallelism is straightforward.
   [Also search for: MolBio FLASH].

%A E. Ukkonen
%T Constructing suffix trees on-line in linear time
%J Information Processing '92, Proc. IFIP 12th World Comp. Congress
%V 1, Algorithms, Software and Architecture
%W Madrid
%I Elsevier
%E J. v. Leeuwen
%P 484-492
%M SEP
%D 1992
%O TR A-1993-1, Dept. Comp. Sci., U. of Helsinki, Finland (revised)
%K conf, c1992, c199x, c19xx, IFIP92, suffix, tree, online, string, strings,
   searching, search, zz0499
%X (IFIP trans' A: Comp. Sci. and Tech. vol A-12)
   Ref' in  G i e g e r i c h  and  K u r t z  '97.
 NB. Ukkonen, Algorithmica 95, fixes an "inaccuracy" in this earlier paper.(*)
   Hint [Also search for: suffix tree].
   (See [<A HREF="http://www.allisons.org/ll/AlgDS/Tree/Suffix/">www</A>].)

%A E. Ukkonen
%T On-line construction of suffix-trees
%J Algorithmica
%V 14
%N 3
%P 249-260
%D 1995
%O TR A-1993-1, Dept. Comp. Sci., U. of Helsinki, Finland.
%K jrnl, zz0499, c1995, c199x, c19xx, suffix tree, prefix, online, on line,
   incremental, left to right, text, linear time, search, searching, string,
   strings, sequence
%X Corrects an "inaccuracy"(!) in
   Ukkonen "Constructing suffix trees on-line in linear time", IFIP, Sept. 92.
   [Also search for: suffix tree linear time].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Tree/Suffix/">www</A>].)

%A M. Nelson
%T Fast string searching with suffix trees
%J Dr. Dobbs Journal
%M AUG
%D 1996
%P ?-?
%K suffix trees
%X 2 refs:  M c C r e i g h t '76  and  U k k o n e n '95.   Gives C++ code.

%A E. Ukkonen
%A D. Wood
%T Approximate string matching with suffix automata
%J Algorithmica
%V 10
%N 5
%P 353-364
%M NOV
%D 1993
%K sub substring, strings, sequence, match, search, word, noise noisy,
   c1993, c199x, c19xx, algorithm

%A J. Y. Kim
%A J. Shawe-Taylor
%T Fast string matching using an n-gram algorithm
%J SPE
%V 24
%N 1
%P 79-88
%M JAN
%D 1994
%K substring, strings, sequence, search, match, ngram, Shawe Taylor

%A M. Mongeau
%A D. Sankoff
%T Comparison of musical sequences
%J Computers and the Humanities
%V 24
%P 161-175
%D 1990
%K CH, similarity, alignment, music, melody, tune, note, notes, pitch,
   approximate string matching, match, DPA
%X It makes use of the dynamic programming array concept, D[], and the weights
   that are used for computation of D[] are calculated from a combination of
   the relative interval between adjacent notes and the duration of the notes.
   It is well worth a read because it addresses the problem of musical notes
   having two components; pitch values and note duration.  Operations allowed
   in the algorithm are:
        deletion of one note (sequence A)
        insertion of one note (sequence B)
        replacement of one note (mismatch style seuquencing operation)
        fragmentation of one note into many (eg. from semibreve to 4 crotchets)
        consolidation of many notes into one (ie. the reverse of fragmentation)
   There are a few references listed at the end of the article which are not
   related to dynamic programing but do discuss some alternative techniques
   that can be used for comparing musical sequences.
      Hope this is of use, Shane Cook   [April '94]
      Internet:  ssc at waikato.ac.nz
      Comp. Sci. Dept, U. of Waikato, Private Bag, Hamilton, New Zealand.
   [Also search for: music match].

%A T. Jiang
%A E. L. Lawler
%A L. Wang
%T Aligning sequences via an evolutionary tree: complexity and approximation
%J Symposium on Theory of Computing
%P 760-769
%D 1994
%K conf, STOCS, c1994, c199x, c19xx, multiple alignment, phylogenetic, Steiner,
   tree, trees, P, NP, NPC approximation algorithm, family, evolutionary
%X tree alignment is NP-hard
   generalised tree alignment is MAX SNP-hard  (must construct hypothetical
   sequences too)
   authors at: CSci McMaster U.; CSci. U.C.Berkeley & Elec & Comp Eng  McMaster
   31 refs
   -- [<A HREF="http://doi.acm.org/10.1145/195058.195454">doi:10.1145/195058.195454</A>]['09]; isbn:0897916638.

%A E. Chow
%A et al.
%T Biological information signal processing
%J Proc. Intl. Conf. on Application-Specific Array Processors
%P ??-??
%M SEP
%D 1991
%E M. Valero
%I IEEE computer society press, la.
%K string, sequence, alignment, match, matching, approximate, BISP, chip,
   Leroy Hood
%X From: Tim Hunkapiller (tim@mbt.washington.edu)     4/94

%A E. Chow
%A et al.
%T A systolic array processor for biological information signal processing
%J Proc. Int. Conf. on Supercomputing
%P ??-??
%M JUN
%D 1991
%K string, sequence, alignment, match, matching, approximate, BISP, chip,
   Leroy Hood
%X From: Tim Hunkapiller (tim@mbt.washington.edu)     4/94

%A R. A. Baeza-Yates
%A G. H. Gonnet
%T Fast string matching with mismatches
%J Information and Computation
%V 108
%N 2
%P 187-199
%M FEB
%D 1994
%K jrnl, c1994, c199x, c19xx, strings, sequence, IC, sub string, substring,
   search, match, matching, approximate, mismatch, change, FSM, algorithm
%X [Also search for: Gonnet Baeza Yates].

%A D. Gusfield
%T Efficient methods for multiple sequence alignment with guaranteed error
   bounds
%J Bull. Math. Biol.
%V 55
%N 1
%P 141-154
%D 1993
%K MolBio, BMB, string, sequence, multiple alignment, evolutionary, family,
   phylogenetic, tree, trees, DPA, approximation algorithm, bound
%X Guaranteed to find alignment within a factor of 2 of best al'.
   (Factor is 1.33 for 3 strings).

%A S. C. Chan
%A A. K. C. Wong
%A D. K. Y. Chiu
%T A survey of multiple sequence comparison methods
%J Bull. Math. Biol.
%V 54
%N 4
%P 563-598
%D 1992
%K MolBio, BMB, string, sequence, multiple alignment, evolutionary family
   phylogenetic, tree, trees, DNA, RNA, 5S 5SRNA, entropy, introduction,
   tree costs, all pairs, DPA

%A T. J. Warnow
%T Tree compatibility and inferring evolutionary history
%J J. Algorithms
%V 16
%N 3
%P 388-407
%M MAY
%D 1994
%K JA, MolBio, family, evolutionary, phylogenetic, tree, trees, compatible,
   perfect phylogeny, problem, character
%X given a lot of subtrees, are they compatible with a tree over
   all of the items?

%A R. W. Irving
%A C. B. Fraser
%T Two algorithms for the longest common subsequence of three (or more) strings
%J Proc. Third Annual Symp. on Comb. Patt. Matching.
%P 214-229
%I SpringerVerlag
%S LNCS
%V 644
%D 1992
%K 3rd, SCPM, CPM, MolBio, LCS, LCSS, combinatorial pattern match,
   multiple alignment, 3, similarity, homology
%X ref by  R. G. Downey,  downey@math.vuw.ac.nz         ('94)
   [Also search for: three alignment].

%A J. Hein
%T An algorithm combining DNA and protein alignment
%J J. Theor. Biol.
%V 167
%P 169-174
%D 1994
%K MolBio, JTB, DPA, alignment, similarity, homology, string, sequence,
   reading frame
%X An algorithm is presented that aligns two DNA sequences minimizing
   the overall amount of evolution that the associated proteins have
   experienced. It is generalized to minimizing a weighted average of
   protein and DNA evolution.

%A R. K. Singh
%A S. G. Tell
%A C. T. White
%A D. Hoffman
%A V. L. Chi
%A B. W. Erickson
%T A scalable systolic multiprocessor for analysis of biological sequences
%J Proc. Symp. on Integrated Systems
%W Seattle
%P 168-182
%M MAR
%D 1993
%I MIT-Press
%K MolBio, string, sequence, comparison, alignment, hardware, VLSI
%X <A HREF="http://www.cs.unc.edu/bioscan/bioscan.html">BioScan</A>  (9/'94)

%A G. A. Stephen
%T String Searching Algorithms
%I World-Scientific-Publishing
%S Lecture-Notes-Series-on-Computing
%P 250
%M OCT
%D 1994
%K text, book, string, substring, sequence, search, find, finding, approximate,
   c1994, c199x, c19xx, strings
%X via enews,        email: graham@sees.bangor.ac.uk (Graham A Stephen) (9/'94)
      This book presents a bibliographic overview of the field and an anthology
      of detailed descriptions of the principal algorithms available.
   Contents: Introduction; String Matching; String Distance and
             Common Sequences; Suffix Trees; Approximate String Matching;
             Repeated Substrings.
   uk us isbn:981-02-1829-X;   US$ 34 / UK pounds 25.
   [<A HREF="ftp://venus.sees.bangor.ac.uk/pub/graham/BOOK">Contents-Bangor</A>].

%A D. Gusfield
%T Faster implementation of a shortest superstring approximation
%J IPL
%V 51
%N 5
%P 271-274
%M SEP
%D 1994
%K IPL, common, SCSS, sequence assembly
%X 6 refs,  author at U. Cal. at Davis
   [Also search for: MolBio sequence assembly].

%A W. H. E. Day
%A F. R. McMorris
%T Alignment, comparison and consensus of molecular sequences
%I Int. Federation of Class'n. Soc's.
%M SEP
%D 1993
%K MolBio, bibliography, alignment, string, sequence, edit distance,
   approximate, match, matching, similarity, computer algorithm
%X version 2.0 - bibliography of 600 entries
   email: whday@ac.dal.ca      email: frmcmo01@ulkyvx.louisville.edu  ('93)

%A E. R. Fiala
%A D. H. Greene
%T Data compression with finite windows
%J CACM
%V 32
%N 4
%P 490-505
%D 1989
%K data compress compression

%A D. Sankoff
%A Y. Abel
%A J. Hein
%T A tree . a window . a hill; generalization of nearest-neighbour interchange
   in phylogenetic optimization
%J J. Classification
%V 11
%N ?
%P 209-232
%M ?
%D 1994
%K MolBio, family, phylogenetic, evolutionary, tree, trees, NNI, local, minima,
   rearrangement
%X ... The NNI methods tend to be trapped in poor local minima because,
   relatively speaking, there are not many trees accessible in one step
   from any given tree. (p215)
   ... To get around this we propose at each step of a local improvement
   algorithm to examine an entire binary k-subtree of the [complete] n-tree.
   [that's the window]
   ... k=8, say, requires only the moderate computing power described ...
   [simulations are given for 40 terminal nodes, length=100, and k=4..8]

%A R. Cole
%T Tight bounds on the complexity of the Boyer-Moore string matching algorithm
%J SIAM J. Comput.
%V 23
%N 5
%P 1075-1091
%M OCT
%D 1994
%K SIAM, jrnl, text, substring, sub string, match, matching, search,
   strings, comparisons, bound
%X pattern length m, text length n,
   upper bound = 3n-3(n-m+1)/m+2 comparisons
   lower bound = 3n(1-o(1))      as n/m -> infinity, n -> infinity

%A M Crochemore
%A A. Czumaj
%A L. Gasieniec
%A S. Jarominek
%A T. Lecroq
%A W. Plandowski
%A W. Rytter
%T Speeding up two string-matching algorithms
%J Algorithmica
%V 12
%N 4/5
%P 247-267
%M OCT/NOV
%D 1994
%K string, strings, match, matching, search, speed, fast

%A R. A. Baeza-Yates
%A C. Choffrut
%A G. H. Gonnet
%T On Boyer-Moore automata
%J Algorithmica
%V 12
%N 4/5
%P 268-292
%M OCT/NOV
%D 1994
%K string, strings, match, matching, search

%A F. Chin
%A C. K. Poon
%T Performance analysis of some simple heuristics for computing longest common
   subsequences
%J Algorithmica
%V 12
%N 4/5
%P 293-311
%M OCT/NOV
%D 1994
%K string, strings, sequence, alignment, approximate, match, matching,
   LCS, LCSS, edit distance

%A D. Gusfield
%A K. Balasubramanian
%A D. Naor
%T Parametric optimization of sequence alignment
%J Algorithmica
%V 12
%N 4/5
%P 312-326
%M OCT/NOV
%D 1994
%K string, strings, approximate, match, matching

%A E. W. Myers
%T A sublinear algorithm for approximate key word searching
%J Algorithmica
%V 12
%N 4/5
%P 345-374
%M OCT/NOV
%D 1994
%K jrnl, string, strings, search, match, matching, c1994, c199x, c19xx, keyword
%X [<A HREF="http://www.cs.arizona.edu/people/gene/PAPERS/sublinear.ps">sublinear.ps@cs.arizona.edu</A>]['04].

%A G. M. Landau
%A U. Vishkin
%T Pattern matching in a digitized image
%J Algorithmica
%V 12
%N 4/5
%P 375-408
%M OCT/NOV
%D 1994
%K string, strings, image, images, processing, IP, match

%A A. S. Fraenkel
%A S. T. Klein
%T Complexity aspects of guessing prefix codes
%J Algorithmica
%V 12
%N 4/5
%P 409-?
%M OCT/NOV
%D 1994
%K jrnl, c1994, c199x, c19xx, string, strings, code

%A J. D. Kececioglu
%A E. W. Myers
%T Combinatorial algorithms for DNA sequence assembly
%J Algorithmica
%V 13
%N 1/2
%M JAN/FEB
%D 1995
%P 7-51
%K MolBio, shortest common super string, superstring, SCS, SCSS, noise, error,
   sequence assembly, c1995, c199x, c19xx
%X Can handle 10% error rate on *** non repetitive *** DNA.
   In special issue on computational molecular biology.
   -- [<A HREF="http://www.cs.arizona.edu/people/kece/">Kececioglu</A>][10/'02].
   [Also search for: MolBio sequence assembly].

%A D. Sankoff
%A G. Sundaram
%A J. D. Kececioglu
%T Steiner points in the space of genome rearrangements
%J Int.  J. of Foundations of Comp. Sci.
%V 7
%N 1
%P 1-9
%D 1996
%K MolBio, jrnl, sorting, reversals, phylogenetic, evolutionary, tree, trees
%X [<A HREF="http://www.cs.arizona.edu/people/kece/Research/papers/SSK96.ps.Z">paper</A>][10/'02],
   -- [<A HREF="http://www.cs.arizona.edu/people/kece/">Kececioglu</A>][10/'02],
   [also search for: sorting reversals] and
   [also search for: evolutionary tree].

%A F. Alizadeh
%A R. M. Karp
%A L. A. Newberg
%A D. K. Weisser
%T Physical mapping of chromosomes: a combinatorial problem in molecular
   biology
%J Algorithmica
%V 13
%N 1/2
%M JAN/FEB
%D 1995
%P 52-76
%K MolBio, map, maps, mapping, DNA, probe, clone
%X probe data about clones.
   In special issue on computational molecular biology.

%A P. A. Pevzner
%T DNA physical mapping and alternating Eulerian cycles in coloured graphs
%J Algorithmica
%V 13
%N 1/2
%M JAN/FEB
%D 1995
%P 77-105
%K MolBio, map, maps, mapping, DNA, RSM, restriction, site, double, digest,
   Eulerian cycle, cycles, graph
%X In special issue on computational molecular biology.

%A Kun-Mao Chao
%A W. Miller
%T Linear-space algorithms that build local alignments from fragments
%J Algorithmica
%V 13
%N 1/2
%M JAN/FEB
%D 1995
%P 106-134
%K MolBio, alignment
%X In special issue on computational molecular biology.

%A V. Bafna
%A E. L. Lawler
%A P. A. Pevzner
%T Approximation algorithms for multiple sequence alignment
%J Theor. Comp. Sci.
%V 182
%N 1-2
%P 233-244
%M AUG
%D 1997
%K jrnl, TCS, MolBio, c1997, c199x, c19xx, protein, zz0898
%X multiple alignment of k protein sequences of length n,
   performance guarantee  2-1/k
   see A.C.M. Comp. Rev. p216 APR '98

%A P. A. Pevzner
%A M. S. Waterman
%T Multiple filtration and approximate pattern matching
%J Algorithmica
%V 13
%N 1/2
%M JAN/FEB
%D 1995
%P 135-154
%M MolBio, pattern, match
%X In special issue on computational molecular biology.

%A M. Farach
%A S. Kannan
%A T. Warnow
%T A robust model for finding optimal evolutionary trees
%J Algorithmica
%V 13
%N 1/2
%M JAN/FEB
%D 1995
%P 155-179
%K MolBio, family, phylogenetic, evolutionary, tree, trees
%X In special issue on computational molecular biology.

%A J. Kececioglu
%A D. Sankoff
%T Exact and approximation algorithms for sorting by reversals, with
   application to genome rearrangement
%J Algorithmica
%V 13
%N 1/2
%M JAN/FEB
%D 1995
%P 180-210
%K MolBio, genome, DNA, inversion, reverse, reversal,
   unsigned, permutation, group
%X *unsigned* permutation ~ gene order, sorting by reversals ...
   1. greedy approximation algorithm O(n**2)-time, worst-case approximation
      factor is x2, and is usually much better;
   2. exact branch and bound algorithm can solve random perms to n~30.
   -- In special issue on computational molecular biology.
   As of 1993 in Proc. 4th Ann' Symp' Comb' Pattern Matching LNCS #684 87-105
   they had an approx' alg' for sorting by reversals with perf' guarantee 2.
   -- [<A HREF="http://www.cs.arizona.edu/people/kece/Research/papers/KS95.ps.Z">paper</A>][10/'02],
      [<A HREF="http://www.cs.arizona.edu/people/kece/">Kececioglu</A>][10/'02].

%A J. R. Knight
%A E. W. Myers
%T Super-pattern matching
%J Algorithmica
%V 13
%N 1/2
%M JAN/FEB
%D 1995
%P 211-?
%K MolBio, pattern, match
%X In special issue on computational molecular biology.

%A A. V. Aho
%A B. W. Kernighan
%A P. J. Weinberger
%T The AWK Programming Language
%I AddisonWesley
%D 1988
%P 210
%K book, text, unix, c1988, c198x, c19xx, computing, AWK, true,
   string processing language
%X pb, us$76, uk us isbn:020107981X, uk us isbn13:978-0201079814.
   -- [<A HREF="http://www.cs.princeton.edu/~bwk/btl.mirror/">@princeton</A>]['08].
      [<A HREF="http://cm.bell-labs.com/cm/cs/awkbook/">@bell-labs</A>]['08].
   From  <!-- email: fil@cea.berkeley.edu --> Fil Machi [3/'95].

%A G. Myers
%T Approximately matching context free-languages
%J IPL
%V 54
%N 2
%P 85-92
%M APR
%D 1995
%K context free language, CFL, match, jrnl, IPL, CSci, zz0595

%A H. Bunke
%A J. Csirik
%T An improved algorithm for computing the edit distance of run-length
   encoded strings
%J IPL
%V 54
%N 2
%P 93-96
%M APR
%D 1995
%K approximate match, ED, similarity, sequence, coding, coded, sequence,
   jrnl, IPL, CSci, zz0595

%A B. W. Watson
%T Taxonomies and Toolkits of Regular Language Algorithms
%I Faculty of Computing Science, Eindhoven University of Technology
%D 1995
%K PhD thesis, keyword, FA, FSA, DFA, zz0895
%X - Bruce (email: watson@win.tue.nl)  [8/'95]

%A T. Akutsu
%T Approximate string matching with don't care characters
%J IPL
%V 55
%N 5
%P 235-239
%M SEP
%D 1995
%K string matching, match, dont care, wild card character, IPL, jrnl, zz1095
%X O(sqrt(kmn)polylog(m)) time algorithm
   where k is # diffs, m patt' length, n text length,
   wild cards can be in pattern and/or text

%A S. Wu
%A U. Manber
%A E. Myers
%T A subquadratic algorithm for approximate regular expression matching
%J J. of Algorithms
%V 19
%N 3
%P 346-360
%M NOV
%D 1995
%K jrnl, strings, string, regular expression, approximate matching, match,
   zz1195, c1995, c199x, c19xx
%X O(nm/log(n)) time, where the log base is d+2 and d errors are allowed.

%A H. Soldano
%A A. Viari
%A M. Champesme
%T Searching for flexible repeated patterns using a non-transitive similarity
   relation
%J Patt. Recog. Lett.
%V 16
%N 3
%P 233-246
%M MAR
%D 1995
%K Patt, Recog, Lett, PRL, jrnl, approximate, similar, pattern, strings, string,
   substring, repeat, repetitive, clique, CSci, zz1295
%X Caulfield_serials  06.405 PAT
   ... two objects of size k are related if, at each position, their symbols
   are related. ... we are interested in maximal subsets of related objects.
   ... and propose algorithms for identifying them in the particular case
   of k-length substrings in a string. ...     [3 refs].

%A T. Jiang
%A L. Wang
%A K. Zhang
%T Alignment of trees: an alternative to tree edit
%J Theor. Comp. Sci.
%V 143
%N 1
%P 137-148
%M JUL
%D 1995
%K TCS, jrnl, c1995, c199x, c19xx, tree, edit distance, treeEdit, alignment,
   treeAlignment
%X [<A HREF="http://dx.doi.org/10.1016/0304-3975(95)80015-8">doi:10.1016/0304-3975(95)80015-8</A>]['08].
   [Also search for: treeEdit].

%A A. Landraud
%A J. F. Avril
%A P. Chretienne
%T An algorithm for finding a common structure shared by a family of strings
%J IEEE Trans. Patt. Anal. and Mach. Intell.
%V 11
%P 890-895
%D 1989
%K TPAML, jrnl, block, motif, substring, approximate, string
%X starts by finding words w, such that w occurs exactly in "enough"
   of the strings and occurs approximately "enough" in the others.

%T Pacific Symposium on Biocomputing '96
%E L. Hunter
%E T. E. Klein
%W Hawaii
%P 776
%M JAN
%D 1996
%I World Scientific
%K MolBio, PSB, PSB96, conf, molecular biology, computing, zz0196
%X Conf: Hawaii, 3-6 Jan 1996
   isbn:981-02-2578-4;   US$96
   [see also BioComp stream of HICSS '95 and prior]

%T Pacific Symposium on Biocomputing '97
%E R. B. Altman
%E A. K. Dunker
%E L. Hunter
%E T. E. Klein
%I World Scientific
%M JAN
%D 1997
%P 750 approx
%K MolBio, PSB, PSB97, conf, molecular biology, computing, zz0297
%X isbn:981-02-3005-2;   US$128
   [see also PSB96 and BioComp stream of HICSS '95 and prior].

%A M. Crochemore
%A W. Rytter
%T Text Algorithms
%I OUP
%D 1994
%K book, text, OUP, c1994, c199x, c19xx, text, strings, string, algorithm,
   search, searching, pattern match, matching, 1D, 2D, CS, CSci, zz0796
%X 1st ed 1994; us$95; uk us isbn:0 19 508609 0.
   Reviewed in Comp Rev, p.241, May '96;
   see also  Stephen's `String Searching Algorithms'.

%A R. A. Baeza-Yates
%A C. H. Perlberg
%T Fast and practical approximate string matching
%J IPL
%V 59
%N 1
%P 21-27
%M JUL
%D 1996
%O Proc. 3rd Annual Symp. on Combinatorial Pattern Matching,
   LNCS vol.644, pp.185-192, 1992
%K IPL, jrnl, approximate string matching, match, strings, search, counting,
   mismatches, errors, grep, zz0996, c1996, c199x, c19xx
%X 2 algs: 1. O(n) worst case, indep' of k (# mismatches)
           2. O(n) expected time, bound on k similar to Chang & Lawler 1990.
   33 refs.
   -- [<A HREF="http://dx.doi.org/10.1016/0020-0190(96)00083-X">doi:10.1016/0020-0190(96)00083-X</A>]['09].

%A C. S. Iliopoulos
%A D. W. G. Moore
%A K. Park
%T Covering a string
%J Algorithmica
%V 16
%P 289-297
%M SEP
%D 1996
%K jrnl, c1996, c199x, c19xx, seed, cover, strings, period, repeat, zz0996,
   algorithm
%X A string w 'covers' a string x if there exists a superstring of x
   which is made up of concatenations and superpositions of w.
   A substring w of x is a 'seed' of x if w covers. x.
   Paper gives an O(n log n) algorithm to find all seeds of a string.

%A R. Giancarlo
%T A generalization of the suffix tree to square matrices, with applications
%J SIAM J. Comput.
%V 24
%N 3
%P 520-562
%M JUN
%D 1995
%K jrnl, matrix, Lcharacters, Lsuffix, 2D, two dimensional,
   image processing, IP, zz1196
%X review in Comp Rev p420 Aug 96 by W F S m y t h ...
   An Lchar is a string of length 2j-1 determined by row j and column j.
   Lsuffix tree used for 2D dictionary matching.

%A R. de la Briandais
%T File searching using variable length keys
%J AFIPS Western JCC
%D 1959
%P 295-298
%K conf, trie, tries, test, strings, string, search, searching,
   match, text, delaBriandais, c1959, c195x, c19xx
%X B a e z a - Y a t e s  and  G o n n e t  (96) say R de la B
   invented tries, see also Fredkin 1960

%A E. Fredkin
%T Trie memory
%J CACM
%V 3
%N 9
%P 490-499
%M SEP
%D 1960
%K jrnl, CACM, test, strings, string, search, searching, match,
   tree, trie, tries, c1960, c196x, c19xx
%X B a e z a - Y a t e s  and  G o n n e t  (96) say EF
   suggested the name `trie', see also de la Briandais 1959.
   -- [<A HREF="http://doi.acm.org/10.1145/367390.367400">doi:10.1145/367390.367400</A>]['06].

%A R. A. Baeza-Yates
%A G. H. Gonnet
%T Fast text searching for regular expressions or automaton searching on tries
%J JACM
%V 43
%N 6
%P 915-936
%M NOV
%D 1996
%K jrnl, JACM, text, search, pattern, suffix, prefix, Patricia, tree, trie,
   finite automata, string, strings, match, sistring
%X search for a regular expression on _preprocessed_ text,
   using a Patricia Tree as a logical model for the index.
   Runs in logarithmic exprected time in the size of the text
   for a "wide class of" regular expressions and in sublinear expected time
   for any regexp.
   Interested in (i) location of an occurrence (esp' the first),
   (ii) the number of occurrences and (iii) all the occurrences of the regexp.

%A E. Ukkonen
%T Approximate string matching over suffix trees
%J CPM93
%S LNCS
%V 684
%I SpringerVerlag
%P 228-242
%W Padova
%D 1993
%K conf, CMP, CMP4, CPM93, tree, prefix, approximate, string matching, DPA
%X Search for approximate instances P' of pattern string P in text T.
   Use suffix tree of T.  Apply dynamic programming over the tree.
   uk us isbn:3-540-56764-X;   [H 005.730151 C731/4].

%A S. Giegerich
%A S. Kurtz
%T From Ukkonen to McCreight and Weiner: a unifying view of linear-time
   suffix tree construction
%J Algorithmica
%V 19
%N 3
%P 331-353
%D 1997
%K jrnl, c1997, c199x, c19xx, jrnl, trees, prefix, computer algorithm,
   suffix tree, strings, string, search, fast, online, on line
%X Compares the algorithms of Weiner '73, McCreight '76, and Ukkonen '92.
   [26 refs]  Authors at techfak.uni-bielefeld.de .
   [Also search for: suffix tree linear time].

%A R. D. M. Page
%T Forum: On consensus, confidence, and "total" evidence
%J Cladistics
%V 12
%P 83-92
%D 1996
%K family, phylogenetic, tree, trees, total evidence, c1996, c199x, c19xx,
   MolBio, biol, taxonomic congruence, gene, genes, species, consensus, combine
%X "... is it best to combine separate data sets (total evidence) or to
   combine trees (taxonomic congruence) ... implications of the differences
   between gene trees and species trees for the concept of total evidence. ..."
   -- [<A HREF="http://taxonomy.zoology.gla.ac.uk/rod/papers/total.pdf">.pdf</A>][4/'03].

%A S.W. Perrey
%A J. Stoye
%T Fast approximation to the NP-hard problem of multiple sequence alignment
%J Information and Math. Sciences Reports
%S B
%R 96/06
%M MAY
%D 1996
%K MolBio, strings, c1996, c199x, c19xx, complexity, NP, NP-hard, heuristic
%X "...has been shown that multiple seq' alignment with the sum-of-pairs score
   is NP-hard. Recently a fast heurstic method was proposed based on a
   Divide-and-Conquer technique. Recursively, all sequences were cut at some
   suitable positions. ... eventually, the sets of subsequences were aligned
   optimally. In general, the time-complexity of searching for good cutting
   points is O(l n) (n the number and l the maximal length of the sequences
   involved). By a simple (n \Delta l)-time technique, the base l was reduced,
   leading to a reasonable fast alignment algorithm for up to n=7 and l~500.
   We refine the base-reducing technique by spending computational time
   quadratic in n (and still linear in l). This improves the alignment
   procedure regarding the # of seq's managable up to n=9 (of same length l)."
   -- [<A HREF="http://www.dkfz-heidelberg.de/tbi/people/stoye/reports/reportB:96-06.ps.gz">.ps.gz@dkfz-heidelberg.de</A>]['04].

%T Pattern Matching Algorithms
%E A. Apostolico
%E Z. Galil
%I OUP
%M SEP
%D 1997
%P 400
%K book, text, c1997, c199x, c19xx, OUP, strings, string, matrix, tree, match,
   search, CSci, CompSci, dataStructure, DS, algorithm, zz0698
%X uk us isbn:0195113675;   price $65 U.S.;  on-order for Hargrave as of 6/'98;
    1 offline serial exact searching            (by Crochemore)
    2 offline parallel exact searching             (Galil and Yudkiewicz)
    3 online string searching                      (Apostolico)
    4. serial computation of Levenshtein distances (Hirschberg)
    5. parallel computation of L' distances        (Apostolico and Atallah)
    6. approximate string searching                (Landau and Vishkin)
    7. dynamic programming: special cases          (Giancarlo)
    8. shortest common superstrings (SCSS)         (Li and Jiang)
    9. 2D matching                                 (Amir and Farach)
   10. suffix tree data structures for matrices    (Giancarlo and Grossi)
   11. tree pattern matching                       (Zhang and Shasha).

%A H. G. Mairson
%T Generating words in a context-free language uniformly at random
%J IPL
%V 49
%P 95-99
%D 1994
%K jrnl, c1994, c199x, c19xx, IPL, generate, word, grammar, CFG, uar
%X Given an unambiguous CFG ...  2 algorithms:
   1) generates a word uar in O(n^2) time using O(n) space
   2) generates a word uar in O(n) time using O(n^2) space.
   Preprocessing  builds data-structure - time complexity not given. ...
   4 refs.  Author at Comp Sci, Brandeis Uni, USA.

%A J. F. Gentleman
%A R. C. Mullins
%T The distribution of frequency of occurence of
   nucleotide subsequences, based on their overlap capability
%J Biometrics
%V 45
%P 35-52
%D 1989
%K jrnl, strings, sequences, word, words, overlaps, probability, DNA
%X see also Gentleman, Appl Stats, Algorithm AS 291, '94
   See also  A t t e s o n  in  ISMB'98 for prob regular exp'ns.

%A J. F. Gentleman
%T The distribution of the frequency of subsequences in alphabetic
   sequences, as exemplified by deoxyribonucleic acid
%J Applied Stats.
%V 43
%P ?-?
%D 1994
%K jrnl, strings, probability, word, words, overlap, DNA
%X Algorithm AS 291
   author at Canadian Centre for Health Info., Stat's Canada, Ottowa K1A 0T6
   See also Gentleman and Mullins, Biometrics, 45, p35-52, '89
   See also  A t t e s o n  in  ISMB'98 for prob regular exp'ns.

%A P. M. Mcilroy
%A K. Bostic
%A M. D. Mcilroy
%T Engineering radix sort
%J Computing Sys.
%V 6
%N 1
%P 5-27
%D 1993
%K jrnl, c1993, c199x, c19xx, zz0409, radix sort, sorting, algorithm,
   American flag, string, strings
%X "Radix sorting methods have excellent asymptotic performance on string data,
   for which comparison is not a unit-time operation. Attractive for use in
   large byte addressable memories ... have nevertheless long been eclipsed by
   more easily programmed algs.. Three ways to sort strings by bytes left to
   right - a stable list sort, a stable two-array sort, & an in-place 'American
   flag' sort - are illustrated with practical C programs. For heavy-duty
   sorting, all 3 perform comparably, usually running at least 2x as fast as a
   good quicksort. We recommend American flag sort for general use."
   ps@[<A HREF="http://www.bostic.com/radix.paper.ps">bostic.com</A>]['09],
   -- [<A HREF="http://www.bostic.com/keith.html">bostic.com</A>]['09],
   [Also search for: engineering radix sort].

%A I. M. Gessel
%A C. Reutenauer
%T Counting permutations with given cycle structure and descent set
%J J. Combinatorial Theory, Series A
%V 64
%N 2
%P 189-215
%M NOV
%D 1993
%K jrnl, JCT, c1993, c199x, c19xx, zz0909, string, text, permutations,
   standard, permutation, cycle, cycles, involution, involutions,
   derangement, derangements, descent set, sets
%X "The # of permutations with given cycle structure & descent set is shown to
   be equal to the scalar product of 2 special chars. of the symmetric group.
   Enumerative applications are given to cycles, involutions & derangements."
   -- [<A HREF="http://dx.doi.org/10.1016/0097-3165(93)90095-P">doi:/10.1016/0097-3165(93)90095-P</A>]['09].

%A C. Lefevre
%A Joh-E Ikeda
%T The position end-set tree: a small automaton for word recognition in
   biological sequences
%J CABIOS
%V 9
%N 3
%P 343-348
%D 1993
%K jrnl, MolBio, CABIOS, FSM, FSA, words, word, automaton, PESTRY, trees
%X "We consider the basic function which locates a specific string of symbols
   within a longer sequence. When one is expecting to do many substring
   searches it is worthwhile to build an auxiliary index to the sequence to aid
   in the search. We propose a method to generate a compact index that can be
   viewed as a small (partial) deterministic finite automaton recognizing the
   subword structure of a sequence. We present an algorithm for its
   construction on-line in linear time. Such a data structure permits the
   efficient localization of subwords in a sequence and can be used in the
   development of interactive sequence analysis software."
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/9/3/343">abs</A>][3/'04]
   Also see  B l u m e r et al, Theor. Comput. Sci. '85.

%A C. Lefevre
%A Joh-E. Ikeda
%T A fast word search algorithm for the representation of
   sequence similarity in genomic DNA
%J Nucl. Acids. Res.
%P 404-411
%V 22
%N 3
%D 1994
%K MolBio, jrnl, NAR, dot plot, repetition, zz1198, position tree, trees,
   words, pestry, automaton
%X ... preprocessing of the data into an automaton recognizing the word
   structure of a sequence. ... eliminate the repetitions during word
   comparison. ...  [22 refs]
   Their `position tree' seems to be related to tries & `suffix/prefix trees'.

%A N. J. Larsson
%A A. Moffat
%T Offline dictionary-based compression
%J DCC
%P 296
%D 1999
%K conf, DCC, DCC99, c1999, c199x, c19xx, zz0415, RE-PAIR, REPAIR, grammar,
   CF grammar, string, compress, compression
%X "Dictionary-based modelling is the mechanism used in many practical
   compression schemes. We use the full message (or a large block of it) to
   infer a complete dictionary in advance, & include an explicit repn of the
   d. as part of the compressed msg. Intuitively, the advantage of this offline
   approach is that with the benefit of having access to all of the message, it
   should be possible to optimize the choice of phrases so as to maximize
   compression performance. Indeed, we demonstrate that v.g. compression can be
   attained by an offline method without compromising the fast decoding that is
   a distinguishing characteristic of d.-based techniques. Several nontrivial
   sources of overhead, in terms of both compn resources required to perform the
   compression, & bits generated into the compressed msg, have to be carefully
   managed as part of the offline process. To meet this challenge, we have
   developed a novel phrase derivation method & a compact d. encoding. In
   combination these two techniques produce the compression scheme RE-PAIR,
   which is highly efficient, particularly in decompression"
   -- [<A HREF="http://dx.doi.org/10.1109/DCC.1999.755679">doi:10.1109/DCC.1999.755679</A>]['15].
   [Also search for: smallest grammar problem].

%A J.-F. Myoupo
%A D. Seme
%T Time-efficient parallel algorithms for the longest common subsequence and
   related problems
%J J. Parallel and Distributed Computing
%V 57
%N 2
%P 212-223
%M MAY
%D 1999
%K jrnl, LCS, BSR, parallel algorithm, zz0599
%X Broadcast with parallel reduction (BSR) model of parallel computing.
   Of theoretical interest only;  via p.e.t.:  H 4.3505 J86

%A G. Myers
%T A fast bit-vector algorithm for approximate string matching based on dynamic
   programming
%J JACM
%V 46
%N 3
%M MAY
%D 1999
%P 395-415
%K jrnl, JACM, c1999, c199x, c19xx, grep, agrep, strings, DPA, bit, substring,
   zz1199
%X Substring search: Find (short) word of length m in a text of
   length n (n > > m), with k or fewer differences.
   "... present a [simple] algorithm ... O(nm/w) time..."
   Then because indep' of k, ... blocks ... as in 4-Russians ... leads to
   O(kn/w) expected-time alg for the case where m may be arb' large.
   (Where w is the machine word size, e.g., 32 or 64.)
   [Also search for: bit string DPA].
   (Also see
   [<A HREF="http://www.allisons.org/ll/Publications/1986IPL/">IPL'86</A>] or
   [<A HREF="/~lloyd/tildeStrings/Alignment/86.IPL.html">csse</A>]
   for a bit vector LCS algorithm.)

%A R. Steuer
%A L. Molgedey
%A W. Ebeling
%A M. A. Jimenez-Montano
%T Entropy and optimal partition for data analysis
%J Euro. Physical J. E
%P ?-?
%M FEB
%D 2001 ?
%K jrnl, time series, strings, sequences, n-gram, ngram, complexity,
   compression, zz0401
%X ... partitions to obtain coarse-grained symbolic sequences. ...
   commonly introduces a homogeneous partition which ensures roughly
   equidistributed symbols. ... may lead to spurious results for the
   est' entropy ...  [via M. A. J-M.]

%A E. L. L. Sonnhammer
%A R. Durbin
%T A dot-matrix program with dynamic threshold control suited for
   genomic DNA and protein sequence analysis
%J Gene
%V 167
%P GC1-10
%D 1995
%K MolBio, jrnl, Gene COMBIS, DOTTER, dot plot, zz0501
%X [<A HREF="http://www.elsevier.com/homepage/sah/genecombis/jnl/articles/0378111995007148/Menu.html">paper</A>][5/'01]
   -- [<A HREF="http://www.cgr.ki.se/cgr/groups/sonnhammer/Dotter.html">www</A>][5/01]

%A W. N. Grundy
%A T. L. Bailey
%A C. P. Elkan
%A M. E. Baker
%T Meta-MEME: Motif-based hidden Markov models of protein families
%J Comp. Appl. in the Biol. Sci. (CABIOS)
%V 13
%N 4
%P 397-406
%D 1997
%K J. Bioinformatics, CABIOS, MolBio, meme, pattern, HMM, model, family
%X [<A HREF="http://www.sdsc.edu/~tbailey/papers/metameme-cabios97.ps">ps@uq</A>][05], Bailey @ UQ as of '05.

%A M. Farach
%T Optimal suffix tree construction with large alphabets
%J Proc. of the 38th Annual Symp. on Foundations of Comp. Sci.
%P 137
%D 1997
%K conf, FOCS, c1997, c199x, c19xx, suffix tree, integer alphabet, linear time
%X "... For integer alphabets, a substantial gap remains between the known upper
   & lower bounds, & closing this gap is the main open question in the
   construction of suffix trees. There is no super-linear lower bound, & the
   fastest known alg was the O(n log n) time comparison based alg.  We settle
   this open problem by closing the gap: we build suffix trees in linear time
   for integer alphabet."    (NB. integer alphabet.)
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/SFCS.1997.646102">doi:10.1109/SFCS.1997.646102</A>]['09].

%A B. Baker
%A U. Manber
%T Deducing similarities in Java sources from bytecode
%J 1998 USENIX Technical Conf.
%W New Orleans
%P ?-?
%M JUN
%D 1998
%K conf, plagiarism, copying, program, source code, cheat, cheats, cheating,
   cheater checker, computer programming, byte code, Udi
%X Several techniques for detecting similarities of Java programs from bytecode
   files, without access to the source, are introduced in this paper. These
   techniques can be used to compare two files, to find similarities among
   thousands of files, or to compare one new file to an index of many old ones.
   Experimental results indicate that these techniques can be very effective.
   Even changes of 30% to the source file will usually result in bytecode that
   can be associated with the original. Several applications are discussed.
   -- [<A HREF="http://webglimpse.org/javadup.html">paper</A>][12/'02] [34 refs]

%A K. Iguchi
%T A toy model for understanding the conceptual framework of protein folding:
   Rubik's magic snake model
%J Modern Physics Letters
%V B12
%N 13
%P 499-506
%D 1998
%K jrnl, MPLB, Rubik, Rubik's, Rubiks, magic snake, protein folding, fold,
   3D structure, toys, MolBio, zz0202
%X via Louis Cuccia, Concordia, Ca  [2/'02]
   subscribers:[<A HREF="http://www.worldscinet.com/mplb/1213/0014.html">pdf</A>][2/'02]
    - [<A HREF="mailto:kazumoto@stannet.ne.jp">author</A>][<A HREF="http://www.stannet.ne.jp/kazumoto/">home</A>][2/'02]
   (Picture of a snake [<A HREF="/~lloyd/tildeStrings/#Protein">here</A>].)

%A R. Giegerich
%A S. Kurtz
%A G. F. Weiller
%T An algebraic dynamic programming approach to the analysis of
   recombinant DNA sequences
%J Proc. Workshop on Algorithmic Aspects of Advanced Prog. Lang.
%P ?-?
%M SEP
%D 1999
%K wShop, WAAAPL, MolBio, DPA, recombination, strings, functional programming,
   FP, alignment, dynamic programming algorithm
%X [<A HREF="www.zbh.uni-hamburg.de/ staff/kurtz/papers/GieKurWei1999.pdf">pdf@zbh.uni-hamburg.de</A>][7/'04]

%A T. Tsunoda
%A M. Fukagawa
%A T. Takagi
%T Time and memory efficient algorithm for extracting palindromic and
   repetitive subsequences in nucleic acid sequences
%J Pacific Symp. on Biocomputing
%V 4
%P 202-213
%D 1999
%K conf, PSB, PSB99, MolBio, DNA, c1999, c199x, c19xx, palindrome, palindromes,
   repeat, repeats
%X "... propose an algorithm to identify the maximum match sequence at each
   position with a calculation cost [?time?] of O(N log N) and memory space
   of O(N).  Applying of it to some sequences, we found unexpectedly large
   palindromes and repeats in DNA."  [...]
   "Algorithm of extracting subsequences common in two sequences ...
   (a) Substring sorting in each text ...  (b) To each combination for
   comparison...  (c) Scanning each line of the row of the source of the
   result of (b)...  (d) We combine the sorted sequences processed at (a)..."
   -- [<A HREF="http://helix-web.stanford.edu/psb99/Tsunoda.pdf">pdf@psb99</A>]['01]

%A K. Iguchi
%T Exactly solvable model of protein folding: Rubik's magic snake model
%J Int. J. Mod. Phys.
%V B13
%N 4
%P 325-361
%M FEB
%D 1999
%K jrnl, IJMPB, Rubik, Rubik's, Rubiks, magic snake, protein folding, fold,
   3D structure, toys, MolBio, zz0202
%X via Louis Cuccia, Concordia, Ca [2/'02]
   subscribers:[<A HREF="http://www.worldscinet.com/ijmpb/13/1304/S0217979299000205.html">pdf</A>][2/'02]
   [...] conceptual framework of protein folding considering an exactly
   solvable model - the Rubik's magic snake model. [...] math rep'n of the
   model, the model Levinthal paradox, the non-unique compact folded structure,
   the function of the chain, the ground state energy, the commensurability
   between the folded structure and the potential sequence, the relationship
   between the unique ground state and broken symmetry in this model and
   the dual model and the inflation of the magic snake chain, respectively.
    - [<A HREF="mailto:kazumoto@stannet.ne.jp">author</A>][<A HREF="http://www.stannet.ne.jp/kazumoto/">home</A>][2/'02]
   (Picture of a snake [<A HREF="/~lloyd/tildeStrings/#Protein">here</A>].)

%A W. L. Ruzzo
%A M. Tompa
%T A linear time algorithm for finding all maximal scoring subsequences
%J 7th Int. Conf. on Intelligent Systems for Molecular Biology
%P 234-241
%M AUG
%D 1999
%K conf, MolBio, ISMB, sequence, c1999, c199x, c19xx, interval, segment
%X "Given a seq. of real numbers (scores), we present a practical linear time
   algorithm to find those nonoverlapping, *contiguous* subsequences having
   greatest total scores. This improves on the best previously known alg., which
   requires quadratic time in the worst case. The problem arises in biological
   seq. analysis, where the high-scoring subsequences corr. to regions of
   unusual composition in a nucleic acid or protein sequence. ..."
   [http://www.cs.washington.edu/homes/ruzzo/papers/maxseq.pdf">pdf@wash</A>]['06]

%A M. A. Bender
%A M. Farach-Colton
%T The LCA problem revisited
%J Proc. of the 4th Latin American Symp. on Theoretical Informatics
%I SpringerVerlag
%S LNCS
%V 1776
%P 88-94
%D 2000
%K conf, c2000, c200x, c20xx, least, lowest common ancestor, LCA, ancestors,
   tree, trees, nearest, RMQ, 1RMQ, RMQ1, range minimization query, cartesian,
   minimisation, minimum, algorithm, practical, implementable, minimum, element,
   FarachColton
%X "... simple alg for the [LCA] problem. We thus dispel the frequently held
   notion that an optimal LCA computation is unwieldy and umimplementable.
   Interestingly this alg' is a sequentialization of a prev' known PRAM
   alg' of Berkman, Breslauer, Galil, Schieber and Vishkin." [c1989].
   (linear-time preprocessing, constant time per LCA query)
   -- [<A HREF="http://www.cs.iastate.edu/~cs548/references/bender00lca.pdf">pp.pdf@iastate.edu</A>]['04],
      [<A HREF="http://portal.acm.org/citation.cfm?id=690192">ref@acm.org</A>]['04], isbn:3540673067.
   Uses RMQ problem: Given numbers A[1..n]. Query: Given i,j, what is
      the index of the smallest element in A[i..j]?   ...
   Obs'n 4: The LCA of nodes u and v is the shallowest node encountered
      between visits to u and v in a depth-1st trav' of [the tree].  ...
   Fast ( < than n**2 ) RMQ by "blocking" in sizes 1, 2, 4, 8, ..., + tricks.
   (Lowest|least common ancestor).

%A T. L. Bailey
%A M. Gribskov
%T Concerning the accuracy of MAST E-values
%J J. Bioinformatics
%V 16
%N 5
%P 488-489
%M MAY
%D 2000
%K MolBio, e-value, Evalue, motif, pattern, motifs
%X [<A HREF="http://www3.oup.co.uk/bioinformatics/hdb/Volume_16/Issue_05">pdf</A>]['05]
   [<A HREF="http://research.imb.uq.edu.au/~tbailey/">Bailey@uq</A>['05]

%A H. L. Bodlaender
%A M. R. Fellows
%A M. T. Hallett
%A H. T. Wareham
%A T. J. Warnow
%T The hardness of perfect phylogeny, feasible register assignment and
   other problems on thin colored graphs
%J Theor. Comp. Sci.
%V 244
%N 1-2
%P 167-188
%M AUG
%D 2000
%K jrnl, TCS, c2000, c200x, c20xx, MolBio, phylogenetic tree, trees, graph,
   coloured, width
%X [<A HREF="http://dx.doi.org/10.1016/S0304-3975(98)00342-9">doi:10.1016/S0304-3975(98)00342-9</A>]['05]

%A M. Farach-Colton
%A P. Ferragina
%A S. Muthukrishnan
%T On the sorting-complexity of suffix tree construction
%J JACM
%V 47
%N 6
%P 987-1011
%M NOV
%D 2000
%K jrnl, JACM, c2000, c200x, c20xx, suffix tree, sorting complexity
%X "... recursive technique for building suffix trees that yields optimal algs
   in different computational models. ... For *integer* alphabets ... no
   super-linear lower bound is known. ...  [give] a linear time reduction to
   sorting for building suffix trees. ...   [And] All previously known algs for
   building s.ts. exhibit a marked absence of locality of reference ... We give
   a linear-I/O reduction to sorting for s.t. construction. Since sorting is a
   trivial I/O-lower bound for building s.ts., our alg. is I/O-optimal."
   -- [<A HREF="http://doi.acm.org/10.1145/355541.355547">doi:10.1145/355541.355547</A>]['09].

%A R. Grossi
%A J. S. Vitter
%T Compressed suffix arrays and suffix trees with applications to text
   indexing and string matching
%J STOC
%P 397-406
%D 2000
%O (SameTitle), SIAM J. Comput., 35(2), pp.378-407, 2005
%K conf, c2000, c200x, c20xx, string, strings, match, matching, search,
   searching, indexing, compressed index, suffix, array, arrays, tree, trees
%X Also see [<A HREF="http://dx.doi.org/10.1137/S0097539702402354">SIAM J. Comput.</A>]['09] ...
   "... goal is to support fast online queries for searching any string pattern
   $P$ of $m$ symbols, with $T$ being fully scanned only once, ... [Published]
   schemes...are greedy in terms of space usage: they require $\Omega(n \lg n)$
   additional bits of space in the worst case. ... These indexes are larger than
   the text itself by a mult.factor of $\Omega(\smash{\lg_{|\Sigma|} n})$, ...
   [But] these indexes support fast searching, ...  We present a new text index
   that is based upon compressed representations of suffix arrays & suffix
   trees. ... fast $\smash{O(m /\lg_{|\Sigma|} n + \lg_{|\Sigma|}^\epsilon n)}$
   search time in the worst case, for any constant $0 < \epsilon \leq 1$, using
   at most $\smash{\bigl(\epsilon^{-1} + O(1)\bigr) \, n \lg |\Sigma|}$ bits of
   storage. Our result thus presents for the 1st time an efficient index whose
   size is provably linear in the size of the text in the worst case, & for many
   scenarios, the space is actually sublinear in practice..."
   [Also search for: compressed index].

%A P. Ferragina
%A G. Manzini
%T Opportunistic data structures with applications
%J Proc. 41st Annual Symp. on Foundations of Comp. Sci.
%P 390
%D 2000
%K conf, FoCS, c2000, c200x, c20xx, zz0109, FOCS, FOCS41, FOCS00, opportunistic,
   dataStructure, DS, compressed index, self, indexing, search, strings, string,
   text, entropy, BW, BWT, FM, FMindex
%X "... compressing & indexing data. We devise a data struct.(DS) whose space
   occupancy is a fn of the entropy of the underlying data set. We call the
   [DS] opportunistic since its space occupancy is decreased when the
   input is compressible & this space reduction is achieved at no sig.slowdown
   ... its space occupancy is optimal in an info.-content sense because text
   T[1,u] is stored using O(H/sub k/(T))+o(1) bits/ input symbol in the worst
   case, where H/sub k/(T) is the kth order empirical entropy of T (the bound
   holds for any fixed k). Given an arbitrary string P[1,p], the opportunistic
   [DS] allows to search for the occurrences of P in T in
   O(p+occlog/sup /spl epsiv//u) time (for any fixed /spl epsiv/<0). If data are
   uncompressible we achieve the best space bound currently known (Grossi &
   Vitter, 2000); on compressible data our solution improves the succinct suffix
   array of (Grossi & Vitter, 2000) & the classical suffix tree & suffix array
   data structures either in space or in query time or both. We also study our
   opportunistic [DS] in a dynamic setting & devise a variant achieving
   effective search & update time bounds. Finally, we show how to plug our
   opportunistic [DS] into the Glimpse tool (Manber & Wu, 1994). The result is
   an indexing tool which achieves sublinear space & sublinear query time..."
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/SFCS.2000.892127">doi:/10.1109/SFCS.2000.892127</A>]['09].
   (FM from the auths, but a.k.a. "BW index".)
   [Also search for: compressed index] and [also search for: BWT text].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/BWT/">BWT</A>].)

%A R. Spang
%A M. Vingron
%T Limits of homology detection by pairwise sequence comparison
%J J. Bioinformatics
%V 17
%N 4
%P 338-342
%D 2001
%K jrnl, Molbio, alignment, similarity, sequence, string
%X a ref'

%A A. N. Arslan
%A O. Egecioglu
%A P. A. Pevzner
%T A new approach to sequence comparison: normalized sequence alignment
%J J. Bioinformatics
%V 17
%N 4
%P 327-337
%M APR
%D 2001
%K jrnl, Zhang, local alignment, maximum, maximal, similarity, zz0302
%X Find substrings I and J s.t. L = |I|+|J| >= T and s(I,J)/L is maximized.
   ...the existing notion of local similarity has a serious flaw: it does not
   discard poorly conserved intermediate segments.  The Smith-Waterman alg.
   finds the local alignment with maximal score but it is unable to find local
   alignment with max. degree of similarity (e.g. maximal percent of matches).
   Moreover, there is still no efficient alg. that answers the following natural
   question: do 2 seqs. share a (sufficiently long) fragment with more than 70%
   of similarity? As a result, the local al. sometimes produces a mosaic of
   well-conserved fragments artificially connected by poorly-conserved or even
   unrelated fragments. This may lead to problems in comparison of long genomic
   seqs. & comparative gene prediction as recently pointed out by Zhang et al.
   (Bioinf. 15, 1012-1019, '99). ... we propose a new ... algorithm
   (normalized local alignment) [for] regions with max. degree of similarity.
   ... based on fractional programming time is O(n**2 log n).
   In practice, [it] is only 3-5 x slower than the std Smith-Waterman alg..
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/17/4/327">paper</A>][2/'02].
   [Also search for: alignment].

%A J. Hein
%T An algorithm for statistical alignment of sequences related by a binary tree
%J PSB
%V 6
%P 179-190
%D 2001
%K PSB, conf, MolBio, c2001, c200x, c20xx, multiple, trees, probability, model,
   models
%X [<A HREF="http://www-smi.stanford.edu/projects/helix/psb01/">proc</A>][7/'02]
   [<A HREF="http://psb.stanford.edu/psb-online/">PSB</A>][7/'02]
   [Also search for: multiple alignment]

%A S. Rajasekan
%A X. Jin
%A J. L. Spouge
%T The efficient computation of position-specific match scores with the
   fast Fourier transform
%J J. Comput. Biol.
%V 9
%N 1
%D 2002
%P 23-33
%K jrnl, JCB, MolBio, strings, string, sequence, matching, protein,
   PSSM, matrix, FFT, zz0702
%X Also see  F i s c h e r  and  P a t e r s o n  '74.
   Turns an |alphabet|**2 multiplicative factor into just |alphabet|,
   i.e. of order 20x faster than before for protein sequences.
   -- [<A HREF="http://www.liebertpub.com/CMB/">JCB</A>][7/'02]

%A I. Rigoutsos
%A A. Floratos
%T Combinatorial pattern discovery in biological sequences: the
   TEIRESIAS algorithm
%J J. Bioinformatics
%V 14
%N 1
%P 55-67
%M JAN
%D 1998
%K TEIRESIAS, jrnl, c1998, c199x, c19xx, MolBio, sequence, pattern discovery,
   maximal patterns, motif, motifs, zz0802, motif, IBM
%X "...discovery of motifs in [] seqs. is an important problem. [] presents a
   new alg. for the discovery of rigid patterns (motifs) in biological seqs..
   [] method is combinatorial [] & able to produce all patterns that appear in
   at least a (user-defined) min' # of seqs., [but] efficient by avoiding the
   enumeration of the entire pattern space. [] reported patterns are maximal:
   any reported pattern cannot be made more specific & still keep on appearing
   at the exact same posns within the input seqs.. [...] running time is
   quasi-linear to the size of the generated output."
   "... 2 phases: scanning & convolution. During the scanning phase, elementary
   patterns with sufficient support are identified. ... combined into
   progressively larger & larger patterns until all the existing, maximal
   patterns have been gen. ..."
   -- [<A HREF="http://bioinformatics.oupjournals.org/cgi/content/abstract/14/1/55">article</A>][8/'02],
      [<A HREF="http://cbcsrv.watson.ibm.com/Tspd.html">IBM</A>][8/'02].

%A I. Rigoutsos
%A A. Floratos
%T Motif discovery without alignment or enumeration
%J Proc. 2nd Annual ACM Int. Conf. on Computational Molecular Biol. (RECOMB 98)
%M MAR
%D 1998
%K TEIRESIAS, conf, c1998, c199x, c19xx, MolBio, zz0802
%X [<A HREF="http://cbcsrv.watson.ibm.com/Tspd.html">www</A>][8/'02].

%A M. Schindler
%T A fast block-sorting algorithm for lossless data compression
%J DCC
%P 469-?
%D 1997
%K conf, DCC, DCC97, c1997, c199x, c19xx, Sort Transform, ST, string, sequence,
   strings, BWT
%X Summary only:  "... new trans. for block-sorting data compression methods.
   ... similar to the one presented by [BW], but avoids the drawbacks of
   uncertain runtime & low performance with large blocks. The cost is a small
   compression loss & a slower back transformation.  ... the original t. sorts
   on unlimited context, whereas this t. sorts on limited context (typically a
   few bytes) & uses the position in the input block to determine the sort order
   in the case of equal contexts."
   -- [<A HREF="http://dx.doi.org/10.1109/DCC.1997.582137">.doi:10.1109/DCC.1997.582137</A>]['09] $ $ieee$.
   [Also search for: Sort Transform ST sequence].

%A L. A. Goldberg
%A P. W. Goldberg
%A C.A.Phillips,  G.B.Sorkin
%T Constructing computer virus phylogenies
%J J. Algorithms
%V 26
%N 1
%P 188-208
%M JAN
%D 1998
%K jrnl, c1998, c199x, c19xx, malware, evolutionary, tree, phylogenetic, trees,
   phylogeny, worm, worms
%X [<A HREF="http://dx.doi.org/10.1006/jagm.1997.0897">doi:10.1006/jagm.1997.0897</A>]['06] [20 refs]

%A J. E. Atkins
%A E. G. Bowman
%A B. Hendrickson
%T A spectral algorithm for seriation and the consecutive ones problem
%J SIAM J. Comput
%V 28
%N 1
%P 297-310
%D 1998
%K jrnl, c1998, c199x, c19xx, spectral, analysis, graph, graphs, theory,serial,
   serialisation, seriation, sequence, eigenvector, Fiedler vector,
   C1P, consecutive ones property, problem
%X "In applicns ranging from DNA seq'ing through archeological dating to sparse
   matrix reordering, a recurrent problem is the sequencing of elts [s.t.]
   highly correlated pairs of elts are near each other. That is, given a
   correlation fn f reflecting the desire for each pair of elts to be near each
   other, find all perms pi with the property that if pi(i) < pi(j) < pi(k) then
   f(i,j) >= f(i,k) and f(j,k) >= f(i,k). This seriation problem is a gen. of
   the well-studied consecutive ones problem. We present a spectral alg. for
   this problem that has a # of interesting features. Whereas most previous
   applic'ns of spectral techniques provide only bounds or heuristics, [here]
   an alg. that correctly solves a nontrivial combinatorial problem. [And]
   spectral methods are being successfully applied as heuristics to a variety of
   sequ'ing problems, & our result helps explain & justify these applications."
   -- [<A HREF="http://dx.doi.org/10.1137/S0097539795285771">doi:10.1137/S0097539795285771</A>]['08], or ...
      [<A HREF="http://www.sandia.gov/~egboman/papers/seriation_sicomp.pdf">pdf@sandia</A>]['09].

%A L. J. Billera
%A S. P. Holmes
%A K. Vogtmann
%T Geometry of the space of phylogenetic trees
%J Advances in Applied Mathematics
%V 27
%N 4
%P 733-767
%D 2001
%K jrnl, MolBio, family, evolutionary, tree, semi-labelled, associahedron,
   consensus, bootstrap, zz0304
%X "... continuous space which models the set of all ... trees having a fixed
   set of leaves. ... natural metric ... non +ve curvature ..."
   -- [<A HREF="http://www.math.cornell.edu/~billera/research.html">~billera inc .ps</A>][3/'04],
      [<A HREF="http://www-stat.stanford.edu/~susan/">sph home</A>][3/'04].

%A J. Seward
%T Space-time tradeoffs in the inverse B-W transform
%J DCC
%P 439-448
%M MAR
%D 2001
%K conf, c2001, c200x, c20xx, zz1109, DCC, DCC01, BW Transform, BWT,
   space, time, tradeoff
%X "... presents a # of ways to implement the inverse [BWT], giving a useful
   range of speed-memory tradeoffs. We show that, at one extreme, it is possible
   to invert the BWT, slowly, using just one byte per block-byte. At the other
   extreme, we argue that the max. speed of BWT decompression is unavoidably
   constrained by the rate at which cache misses are serviced."
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/DCC.2001.917175">doi:10.1109/DCC.2001.917175</A>]['09] $ieee$,
   copy@[<A HREF="http://www.research.microsoft.com/~simonpj/papers/ibwt_sub.ps.gz">msft.com</A>][11/'09],
   & [<A HREF="http://citeseer.ist.psu.edu/381988.html">cite seer</A>].
   (BTW, auth@MicrosftResCambridge.)
   [Also search for: Burrows Wheeler BWT].

%A M. Crochemore
%A C. S. Iliopoulos
%A Y. J. Pinzon
%A J. F. Reid
%T A fast and practical bit-vector algorithm for the longest common
   subsequence problem
%J IPL
%V 80
%N 6
%P 279-285
%D 2001
%K jrnl, IPL, c2001, c200x, c20xx, bit string, LCS, LCSS, DPA, zz1102
%X [<A HREF="http://dx.doi.org/10.1016/S0020-0190(01)00182-X">doi:10.1016/S0020-0190(01)00182-X</A>].
   Also see
   [<A HREF="http://www.allisons.org/ll/Publications/1986IPL/">IPL'86</A>] or
   [<A HREF="/~lloyd/tildeStrings/Alignment/86.IPL.html">csse</A>]
   for a bit vector algorithm.
   [Also search for: bit string DPA].

%A W. Li
%T New stopping criteria for segmenting DNA sequences
%J Phys. Rev. Lett.
%V 86
%N 25
%P 5815-5818
%M JUN
%D 2001
%K MolBio, segmentation, segment, sequence, string, BIC, c2001, c200x, c20xx,
   telomere, S. cerevisiae, E. coli, strength, criteria, zzOSP, zOSP04
%X "... propose a solution on the stopping criterion in segmenting inhomogeneous
   DNA sequences with complex statistical patterns. [It] is based on Bayesian
   information criterion ... . When this criterion is applied to telomere of
   S. cerevisiae & the complete sequence of E. coli, borders of biologically
   meaningful units were identified, & a more reasonable number of domains was
   obtained. We also introduce a measure called segmentation strength which can
   be used to control the delineation of large domains. The relationship
   between the average domain size & the threshold of segmentation strength is
   determined for several genome sequences."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevLett.86.5815">doi:10.1103/PhysRevLett.86.5815</A>][7/'04],
   &  [<A HREF=" http://link.aps.org/abstract/PRL/v86/p5815">abs</A>][7/'04].
   [Also search for: segmentation].

%A T. Kasai
%A G. Lee
%A H. Arimura
%A S. Arikawa
%A K. Park
%T Linear-time longest-common-prefix computation in suffix arrays and
   its applications
%J Proc. of the 12th Annual Symp. on Combinatorial Pattern Matching
%I SpringerVerlag
%S LNCS
%V 2089/2001
%P 181-192
%D 2001
%K conf, CPM, CPM01, c2001, c200x, c20xx, string, strings, algorithm,
   suffix array, longest common prefix, suffixes
%X "... linear-time alg. to compute the longest common prefix information in
   suffix arrays.  As 2 applics. ... show that our alg. is crucial to the
   effective use of block-sorting compression, & we present a linear-time alg.
   to simulate the bottom-up traversal of a suffix tree with a suffix array
   combined with the longest common prefix information."
   -- [<A HREF="http://dx.doi.org/10.1007/3-540-48194-X_17">doi:10.1007/3-540-48194-X_17</A>]['09],
   ref@[<A HREF="http://portal.acm.org/citation.cfm?id=736222">acm.org</A>]['04].

%A A. Robbins
%T Effective AWK Programming
%I OReilly
%P 452
%M MAY
%D 2001
%K book, text, c2001, c200x, c20xx, AWK, gawk 3.1, gawk3.1, string processing,
   pattern matching, strings
%X 3rd ed, uk us isbn:0596000707; uk is isbn13:978-0596000707.
   [Also search for: AWK].

%A J. Jansson
%A A. Lingas
%T A fast algorithm for optimal alignment between similar ordered trees
%J Proc. of the 12th Annual Symposium on Combinatorial Pattern Matching
%I SpringerVerlag
%S LNCS
%V 2089
%P 232-240
%D 2001
%K conf, c2001, c200x, c20xx, labelled, ordered, tree, edit, treeAlignment,
   treeEdit, approximate match, matching, similar, Zhang, Shasha
%X "... a linear alg for comparing 2 similar ordered rooted trees with node
   labels. The method for comparing trees is the usual tree edit distance. We
   show that an optimal mapping which uses at most k insertions or deletions
   can then be constructed in O(n k^3) where n is the size of the trees. The
   approach is inspired by the Zhang-Shasha alg. for tree edit distance in
   combination with an adequate pruning of the search space."
   pdf: [<A HREF="http://dx.doi.org/10.1007/3-540-48194-X_22">doi:10.1007/3-540-48194-X_22</A>]['08](???),
        [<A HREF="http://www.springerlink.com/content/l968r62xcta1fk2y/">springer</A>][6/'08].
   (Also see  T o u z e t  c2005.)  uk us isbn:3540422714.
   [Also search for: treeEdit].

%A R. K. Azad
%A P. Bernaola-Galvan
%A R. Ramaswamy
%A J. Subba Rao
%T Segmentation of genomic DNA through entropic divergence: Power laws and
   scaling
%J Physical Review E
%V 65
%D 2002
%K molbio, segment
%X "Genomic DNA is fragmented into segments using the Jensen-Shannon
   divergence. ... results in the fragments being entropically homogeneous to
   within a predefined level of statistical significance. Application of this
   procedure is made to complete genomes of organisms from archaebacteria,
   eubacteria, & eukaryotes. The distribution of fragment lengths in bacterial
   & primitive eukaryotic DNAs shows two distinct regimes of power-law scaling.
   The characteristic length separating these two regimes appears to be an
   intrinsic property of the sequence rather than a finite-size artifact, & is
   independent of the significance level used in segmenting a given genome.
   Fragment length distributions obtained in the segmentation of the genomes of
   more highly evolved eukaryotes do not have such distinct regimes of
   power-law behavior."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevE.65.051909">doi:10.1103/PhysRevE.65.051909</A>][7/'04]

%A I. Grosse
%A P. Bernaola-Galvan
%A P. Carpena
%A R. Roman-Roldan
%A J. Oliver
%A H. E. Stanley
%T Analysis of symbolic sequences using the Jensen-Shannon divergence
%J Physical Review E
%V 65
%D 2002
%X "...Jensen-Shannon divergence D, which quantifies the difference between
   probability distributions, and which has been widely applied to analyses of
   symbolic sequences. We present 3 interpretations of D in the framework of
   statistical physics, information theory, and mathematical statistics, and
   obtain approximations of the mean, the variance, and the probability
   distribution of D in random, uncorrelated sequences. We present a
   segmentation method based on D that is able to segment a nonstationary
   symbolic sequence into stationary subsequences, and apply this method to DNA
   sequences, which are known to be nonstationary on a wide range of different
   length scales."
   -- [<A HREF="http://dx.doi.org/10.1103/PhysRevE.65.041905">doi:10.1103/PhysRevE.65.041905</A>][7/'04].

%A S. P. Holmes
%T Statistics for phylogenetic trees
%J Theor. Population Biol.
%V 63
%P 17-32
%D 2002
%K jrnl, MolBio, tree, family, evolutionary, stats, susan holmes
%X [<A HREF="http://www-stat.stanford.edu/~susan/">sph home</A>][3/'04]

%A L. Q. Ha
%A E. I. Sicilia-Garcia
%A J. Ming
%A F. J. Smith
%T Extension of Zipf's law to words and phrases
%J Int. Conf. on Computational Linguistics (COLING'2002)
%W Taipei, Taiwan
%P 315-320
%M AUG
%D 2002
%K conf, language, word, phrase, English, Mandarin, Chinese, frequency,
   frequencies, n-gram, ngram, n-grams, ngrams, Simon, c2002, c200x, c20xx
%X also includes Mandarin corpora, unigrams, bigrams, trigrams
   -- [<A HREF="http://acl.ldc.upenn.edu/coling2002/proceedings/data/area-04/co-305.pdf">.pdf</A>][7/'03]
   (authors at Queens U of Be1fast)

%A A. H. L. Porto
%A V. C. Barbosa
%T Finding approximate palindromes in strings
%J Pattern Recognition
%V 35
%P 2581-2591
%D 2002
%K jrnl, palindrome, string, sequence, c2002, c200x, c20xx, k errors
%X "... novel definition of approximate palindromes in strings, and provide an
   algorithm to find all maximal approximate palindromes in a string with up to
   k errors. Our definition is based on the usual edit operations of approx'
   pattern matching, & the algorithm we give, for a string of size n on a fixed
   alphabet, runs in O(k^2 n)-time. We also discuss 2 implementation-related
   improvements to the alg', & demonstrate their efficacy in practice by means
   of both experiments and an average-case analysis."  [valmir at cos ufrj br]
   -- [<A HREF="http://arxiv.org/abs/cs.DS/0309043">@arxiv.org</A>][7/'04]
   abs: [<A HREF="http://dx.doi.org/10.1016/S0031-3203(01)00179-0">doi:10.1016/S0031-3203(01)00179-0</A>][7/'04]
   [Also search for: approximate palindrome].

%A A. Bookstein
%A V. A. Kulyukin
%A T. Raita
%T Generalized Hamming distance
%J Inf. Retr.
%V 5
%N 4
%P 353-375
%M OCT
%D 2002
%K jrnl, c2002, c200x, c20xx, zz1015, generalized Hamming distance, GHD, DPA,
   similarity, bit, bits, string, vector
%X "... distance or similarity between objects that, most frequently, are
   represented as vectors. ... considers vectors of bits. ... a popular distance
   measure is the Hamming distance. ... it counts only exact matches, whereas
   in information retrieval, corresponding bits that are close by can still be
   considered to be almost identical. We define a 'Generalized Hamming distance'
   that extends the H. concept to give partial credit for near misses, & suggest
   a dynamic programming alg. that permits it to be computed efficiently. ...
   -- [<A HREF="http://dx.doi.org/10.1023/A:1020499411651">doi:10.1023/A:1020499411651</A>]['15].
   [Also search for: similarity bits].

%T Tangled Trees: Phylogeny, Cospeciation, and Coevolution
%E R. D. M. Page
%I U. ChicagoPress
%P 378
%M NOV
%D 2002
%K book, text, MolBio, Bioinformatics, family, evolutionary, phylogenetic, tree,
   c2002, c200x, c20xx, zz1203, trees, coevolution
%X 2002 us$28; isbn:226644677.

%A M. Lothaire
%T Algebraic Combinatorics on Words
%I CUP
%P 518
%D 2002
%K book, text, CUP, c2002, c200x, c20xx, string, strings, text, word, words,
   combinatorics, combinatorial, algebra
%X 1st ed 2002, hb us$130; uk us isbn:0521812208; uk us isbn13:978-0521812207.

%A T. L. Bailey
%T Discovering novel sequence motifs with MEME
%J Current Protocols in Bioinformatics
%E A. D. Baxevanis
%E D. B. Davison
%I JohnWiley
%D 2002
%K MolBio, MEME, motif, pattern
%X 2.4.1-2.4.32.  Auth@uq as of '05.

%A R. Baeza-Yates
%A G. Navarro
%T New and faster filters for multiple approximate string matching
%J Random Structures and Algorithms
%V 20
%N 1
%P 23-49
%M JAN
%D 2002
%K jrnl, c2002, c200x, c20xx, string, strings, sequence, approximate match,
   filter, error, errors, multiple strings, BaezaYates
%X "... 3 new algs. for on-line multiple string matching allowing errors. ...
   extensions of previous algs. that search for a single pattern. The avg.
   running time achieved is in all cases linear in the text size for moderate
   error level, pattern length, & number of patterns. They adapt (with higher
   costs) to the other cases. However, the algs. differ in speed & thresholds of
   usefulness ... The only prev.soln for this problem allows only 1 error. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/rsa.10014">doi:10.1002/rsa.10014</A>]['09],
   auth1@[<A HREF="http://www.dcc.uchile.cl/~rbaeza/">uchile</A>]['09].

%A W. Gibson
%T Pattern Recognition
%I Viking
%P 368
%M APR
%D 2003
%K book, SciFi, coolhunter, cool hunter, logo, logos, nologo, Cayce Pollard,
   fiction, garage Kubrick, William Gibson, c2003, c200x, c20xx, zz0603
%X Science fiction.  isbn:0670875597.  about stg$16

%A V. Makinen
%A E. Ukkonen
%A G. Navarro
%T Approximate matching of run-length compressed strings
%J Algorithmica
%V 35
%N 4
%P 347-369
%M MAR
%D 2003
%O Proc. 12th Annual Symp. Combinatorial Pattern Matching (CPM 2001),
   Springer Verlag, LNCS 2089, pp.31-49, July 2001
%K jrnl, conf, CPM12, edit distance, longest common subsequence, LCS, LCSS,
   string, sequence, match, runs, coded, encoded, zz0203
%X "We focus on the problem of approximate matching of strings that have been
   compressed using run-length encoding.  Previous studies have concentrated
   on the problem of computing the longest common subsequence (LCS) between two
   strings of length m and n, compressed to m' and n' runs. We extend an
   existing algorithm for the LCS to the Levenshtein distance achieving
   O(m'n+n'm) complexity. Furthermore, we extend this algorithm to a weighted
   edit distance model, where the weights of the three basic edit operations
   can be chosen arbitrarily. [...] also an algorithm for approximate searching
   of a pattern of m letters (m' runs) in a text of n letters (n' runs) in
   O(mm'n') time. Then we propose improvements for a greedy algorithm for the
   LCS, and conjecture that the improved algorithm has O(m'n') expected case
   complexity. Experimental results [...] support the conjecture."
   author 1 [<A HREF="http://www.cs.Helsinki.FI/u/vmakinen/">vmakinen</A>][2/'03],
   author 2 [<A HREF="http://www.dcc.uchile.cl/~gnavarro/">gnavarro</A>][2/'03]
   -- [<A HREF="http://dx.doi.org/10.1007/s00453-002-1005-2">doi:10.1007/s00453-002-1005-2</A>]['05],
      [<A HREF="http://www.dcc.uchile.cl/~gnavarro/ps/algor02.ps.gz">.ps</A>][2/'03].

%A V. Makinen
%A G. Navarro
%A E. Ukkonen
%T Algorithms for transposition invariant string matching
%J Proc. STACS'03
%P ?-?
%D 2003
%O J. Algs., 2OO5
%K conf, STAC03, transpose, transposition, music, melody, tune, musical,
   computer, key, shift, pitch, transformation, approximate, match, sequence,
   edit distance, similarity, LCS, LCSS, c2003, c200x, c20xx
%X Given strings A and B over an alphabet S subset of U where U is some
   numerical universe closed under addition and subtraction, and a
   distance function d(A,B) that gives the score of the best (partial)
   matching of A and B the transposition invariant distance is
   min{d(A+t,B), t in U} where A+t = (a(1)+t)(a(2)+t)...(a(m)+t).
   ... problem of computing the transposition invariant distance for various
   distance (and similarity) [fn's] d that are different versions of edit
   distance.  ... give algorithms whose time complexities are close to the
   known upper bounds without transposition invariance. ...we show how
   sparse dynamic programming ... solve[s] transposition invariant problems.
   -- [<A HREF="http://dx.doi.org/10.1016/j.jalgor.2004.07.008">doi:10.1016/j.jalgor.2004.07.008</A>]['05],
   author 1 [<A HREF="http://www.cs.Helsinki.FI/u/vmakinen/">vmakinen</A>][2/'03],
   author 2 [<A HREF="http://www.dcc.uchile.cl/~gnavarro/">gnavarro</A>][2/'03],
   .ps@[<A HREF="http://www.dcc.uchile.cl/~gnavarro/ps/stacs03.ps.gz">uchile</A>][2/'03].
   [Also search for: music match].

%A D. Caramelli
%A C. Lalueza-Fox, C. Vernesi, M. Lari, A. Casoli, F. Mallegni, B. Chiarelli,
   I. Dupanloup, J. Bertranpetit, G. Barbujani
%A G. Bertorelle
%T Evidence for a genetic discontinuity between Neandertals and
   24,000-year-old anatomically modern Europeans
%J PNAS
%P 6593-?
%V 100
%M MAY
%D 2003
%K jrnl, PNAS, MolBio, Neandertal, Neanderthal, out of Africa, evolution, human,
   Pleistocene, ancient, old, mt DNA sequences, mtDNA, Cro-Magnon, CroMagnon,
   Homo sapiens sapiens, man, Eve, tree, Adam, out of Africa,
   c2003, c200x, c20xx, zz0603
%X During the late Pleistocene, early anatomically modern humans coexisted in
   Europe with the anatomically archaic Neandertals for some thousand years.
   Under the recent variants of the multiregional model of human evolution,
   modern and archaic forms were different but related populations within a
   single evolving species, and both have contributed to the gene pool of
   current humans. Conversely, the Out-of-Africa model considers the transition
   between Neandertals and anatomically modern humans as the result of a
   demographic replacement, and hence it predicts a genetic discontinuity
   between them. Following the most stringent current standards for validation
   of ancient DNA sequences, we typed the mtDNA hypervariable region I of two
   anatomically modern Homo sapiens sapiens individuals of the Cro-Magnon type
   dated at about 23 and 25 thousand years ago. Here we show that the mtDNAs of
   these individuals fall well within the range of variation of today's humans,
   but differ sharply from the available sequences of the chronologically
   closer Neandertals. This discontinuity is difficult to reconcile with the
   hypothesis that both Neandertals and early anatomically modern humans
   contributed to the current European gene pool.
   -- [<A HREF="http://www.pnas.org/cgi/doi/10.1073/pnas.1130343100">doi/10.1073/pnas.1130343100</A>][5/'03].
   (NB. The mt DNA root, "Eve", is thought to be ~200,000+/- years ago,
        as of '87.)
   [Also search for: MolBio Eve human evolution].

%A S. W. Kim
%T Linear-time algorithm for finding a maximum-density segment of a sequence
%J IPL
%V 86
%N 6
%P 339-342
%M JUN
%D 2003
%K jrnl, IPL, MolBio, interval, bias, At-rich, zz0703
%X A=(a1, a2, ..., an) a seq of numbers,  i<=j,  interval (ai,...,aj),
   the density mu(i,j) = (a1+...+aj)/(j-i+1),  L <= (j-i+1) <= U,
   Find the maximum density segment with length at least L and at most U.
   If U=n, there is an O(n log L)-time algorithm.
   We transform problem to a geometric one and show that the
   transformed problem can be solved in O(n)-time by geometric algorithms.
   [Also see: longest biased interval]

%A A. Torsello
%A E. R. Hancock
%T Tree edit distance from information theory
%B Graph Based Representations in Pattern Recognition
%E E. Hancock
%E M. Vento
%I Springer
%S LNCS
%V 2726
%P ?-?
%D 2003
%K conf, similarity, matching, correction, trees, c2003, c200x, c20xx, zz0803,
   treeEdit, problem
%X "...a method for est. the cost of tree edit operations. ... poses the problem
   as that of estimating a generative model for a set of tree samples. The
   generative model uses the tree-union as the structural archetype for every
   tree in the distribution and assigns to each node in the archetype the
   probability that the node is present in a sample. A minimum descriptor length
   formulation is then used to estimate the structure & parameters of this tree
   model as well as the node-correspondences between trees in the sample-set &
   the tree model."
   pdf: [<A HREF="http://dx.doi.org/10.1007/3-540-45028-9_7">doi:10.1007/3-540-45028-9_7</A>]['08].
   went on display 30/7/03 - mispell Riss@nen,  one of the authors is also
   an ed. for the conf. proc.,  H 6.42 G291 2003.    -- via p.e.t.
   [Also search for: treeEdit].

%A G. Lunter
%A I. Miklos
%A A. Drummond
%A J. L. Jensen
%A J. Hein
%T Bayesian phylogenetic inference under a statistical insertion-deletion model
%B Algorithms in Bioinformatics
%E G. Benson
%E R. Page
%I Springer
%S LNBI
%V 2812
%P 228-244
%D 2003
%K MolBio, c2003, c200x, c20xx, tree, Miklos, trees, indel, zz1103
%X "... [typically] this problem is tackled stepwise, with phylogenetic
   reconstruction dependent on an initial multiple sequence alignment step.
   However these two steps are fundamentally interdependent. ...
   ... [e.g.,] ten globin protein sequences."
   pdf@[<A HREF="http://www.springerlink.com/index/CGHTUJBXN3KGBC9A.pdf">springer</A>]['09].
   [Also search for: Bayesian phylogenetic tree MolBio].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Trees/">Trees</A>].)

%A J. A. Cotton
%A R. D. M. Page
%T Gene tree parsimony vs. uninode coding for phylogenetic reconstruction
%J Molec. Phylogenetics and Evolution
%P 298-308
%V 29
%N 2
%M NOV
%D 2003
%K jrnl, MolBio, MPE, tree, trees, evolutionary, total evidence, gene,
   GeneTree, parsimony, Simmons, Freudenstein, c2003, c200x, c20xx, zz0404
%X "[S & f suggested] weaknesses of gene tree parsimony in reconstructing
   phylogeny in the face of gene duplication, weaknesses that are addressed by
   method of uninode coding. Here, we discuss Simmons & Freudenstein's
   criticisms & suggest a number of reasons why gene tree parsimony is
   preferable to uninode coding.  During this discussion we introduce a number
   of recent developments of gene tree parsimony methods overlooked by Simmons
   & Freudenstein. Finally, we present a re-analysis of data from that produces
   a more reasonable phylogeny than that found by Simmons & Freudenstein,
   suggesting that gene tree parsimony outperforms uninode coding, at least on
   these data."              J@mes.A.C. was at gl@sgow, then N@t Hist Mus' '04.
   -- [<A HREF="http://taxonomy.zoology.gla.ac.uk/~jcotton/MPE2003.pdf">.pdf</A>]['03]

%A G. Ganapathy
%A V. Ramachandran
%A T. Warnow
%T Better hill-climbing searches for parsimony
%B Algorithms in Bioinformatics
%E G. Benson
%E R. Page
%I Springer
%S LNBI
%V 2812
%P 245-258
%D 2003
%K MolBio, phylogenetic, family, tree, trees, zz1103
%X - appeared in new monographs section, Oct 30, 2003,
   Springer Lecture Notes in Bioinformatics,
   H 570.285 I61.1 2003; us$81; isbn:3540200762;  via p.e.t.
   [Also search for: phylogenetic tree]  and also see
   [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].

%A M. Mohri
%T Edit-distance of weighted automata
%I Springer
%S LNCS
%V 2608
%P 1-23
%M JAN
%D 2003
%K jrnl, IJFCS, FSA, FSM, automaton, machine, PFSA, PFSM, algorithm, set, sets,
   distributions, string, strings, MolBio, zz1203, c2003, c200x, c20xx,
   similarity
%X "...[edit distance] is used ... to give a measure of the difference ...
   between 2 strings. ... [extend] to ... similarity between 2 sets of strings.
   ... when ... sets are represented by automata, their edit-distance can be
   computed using the general algorithm of composition of weighted transducers
   combined with a single-source shortest-paths algorithm. ... the strings may
   represent a range of alternative hypotheses with assoc' prob's. ...
   introduce ... edit-distance of 2 distributions of strings given by 2
   weighted automata. ..."
   issn:03029743; [<A HREF="http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=2608&spage=1">article</A>][12/'03].
   Auth' at AT & T Labs, NJ.   Also see:
     "Edit-distance of weighted automata: General definitions and algorithms."
     Int. J. of Foundations of Comp. Sci., 14(6), pp.957-982, DEC 2003.
     On display 11/12/03 H 4.05 I61 -- via p.t..

%A Y. Gao
%A J. Wu
%A R. Niewiadomski
%A Y. Wang
%A Z.-Z. Chen
%A G. Lin
%T A space efficient algorithm for sequence alignment with inversions
%J 9th Int. Computing and Combinatorics Conf. (COCOON)
%W Big Sky, M T
%P 57-67
%M JUL
%D 2003
%I SpringerVerlag
%S LNCS
%V 2697
%K conf, COCOON, COCOON9, Schoniger, Waterman, c2003, c200x, c20xx, strings,
   Molbio, inversion, DPA, zz1004
%X "A [DPA] to find an optimal alignment for [2] DNA seq's has been described
   by Schoniger & Waterman. The alignments use not only substitutions,
   insertions, and deletions of single nucleotides, but also inversions, which
   are the reversed complements, of substrings of the sequences. With the
   restriction that the inversions are pairwise non-intersecting, their
   proposed alg' runs in O(n^2 m^2) time and consumes O(n^2 m^2) space, where
   n and m are the lengths of the input sequences respectively. We develop a
   space efficient algorithm [...] consumes only O(n m) space within the same
   amount of time. Our algorithm enables the computation for a pair of DNA
   sequences of length up to 10,000 to be [done]on an ordinary desktop [mc].
   [used] to verify some biological facts about gene shuffling across species."
   issn:0302-9743. [<A HREF="http://springerlink.metapress.com/openurl.asp?genre=article&issn=0302-9743&volume=2697&spage=57">openUrl</A>]['04]
   -- [<A HREF="http://springerlink.metapress.com/link.asp?id=catdg3ggkpt8ukhp">met@press</A>]['04]

%A A. Bergeron
%A J. Stoye
%T On the similarity of sets of permutations and its applications to genome
   comparison
%J 9th Int. Computing and Combinatorics Conf. (COCOON)
%W Big Sky, M T
%P 68-79
%M JUL
%D 2003
%I SpringerVerlag
%S LNCS
%V 2697
%K conf, COCOON, COCOON9, set, MolBio, match, matching, c2003, c200x, c20xx,
   permutation, perm, conserved interval
%X "The comparison of genomes with the same gene content relies on our ability
   to compare permutations, either by measuring how much they differ, or by
   measuring how much they are alike. With the notable exception of the
   breakpoint distance, which is based on the concept of conserved adjacencies,
   measures of distance do not generalize easily to sets of more than 2 perms.
   ... present a basic unifying notion,  conserved intervals, as a powerful
   generalization of adjacencies, and as a key feature of genome rearrangement
   theories. We also show that sets of conserved intervals have elegant nesting
   and chaining properties that allow the development of compact graphic
   representations, and linear time algorithms to manipulate them."
   -- [<A HREF="http://springerlink.metapress.com/openurl.asp?genre=article&issn=0302-9743&volume=2697&spage=68">openURL</A>]['04
      [<A HREF="http://springerlink.metapress.com/link.asp?id=9dc558me955ym49k">met@press</A>]['04].
   [Also search for: sorting reversals]

%A W. Fu
%A W.-K. Hon
%A W.-K. Sung
%T On all-substring alignment problems
%J 9th Int. Computing and Combinatorics Conf. (COCOON)
%W Big Sky, M T
%P 80-89
%M JUL
%D 2003
%I SpringerVerlag
%S LNCS
%V 2697
%K conf, COCOON, COCOON9, MolBio, DPA, problem, c2003, c200x, c20xx, problem
%X "Consider 2 strings A and B of lengths n and m respectively, with n < < m.
   ... computing global & local alignments between A and all m^2 substrings of
   B can be solved by the classical Needleman-Wunsch & Smith-Waterman alg's,
   respectively, which takes O(m^2 n) time and O(m^2) space. ...propose faster
   alg's that take O(m n^2) time and O(mn) space. The improvement stems from a
   compact way to represent all the alignment scores."
   -- [<A HREF="http://springerlink.metapress.com/openurl.asp?genre=article&issn=0302-9743&volume=2697&spage=80">openURL</A>]['04],
      [<A HREF="http://springerlink.metapress.com/link.asp?id=9vnv54uc6pueq11c">met@press</A>]['04].

%A J. Karkkainen
%A P. Sanders
%T Simple linear work suffix array construction
%J Int. Colloquium on Automata, Languages and Programming
%I SpringerVerlag
%S LNCS
%V 2719
%P 943-955
%D 2003
%K conf, c2003, c200x, c20xx, arrays, prefix, string, strings, linear time, DC3,
   difference cover, skew algorithm, sort, suffix
%X "... introduce the skew alg. for suffix array construction over int.alphabets
   that can be implemented to run in linear time using integer sorting as its
   only nontrivial subroutine: 1. recursively sort suffixes beginning at posns
   i mod 3 = 0;  2. sort the remaining suffixes using the info. obtained
   in step one;  3. merge the two sorted seqs. obtained in steps 1 & 2.  The
   alg. is much simpler than previous linear time algs. that are all based on
   the more complicated suffix tree data struct..  Since sorting is a well
   studied problem, we obtain optimal algs. for several other models of
   computation, e.g. external memory with parallel disks, cache oblivious, &
   parallel. The adaptations for BSP & EREW-PRAM are asymptotically faster than
   the best previously known algorithms."            (Also see JACM'06).
   auth1@[<A HREF="http://www.cs.helsinki.fi/u/tpkarkka/">helsin...</A>]['09],
   also a JACM paper '06.
   [Also search for: suffix array time complexity],
   [or for: suffix array linear time].

%A D. K. Kim
%A J. S. Sim
%A H. Park
%A K. Park
%T Linear-time construction of suffix arrays
%J Proc. Annual Symp. on Combinatorial Pattern Matching
%I SpringerVerlag
%S LNCS
%V 2676
%P 186-199
%D 2003
%K conf, c2003, c200x, c20xx, array, prefix, string, strings
%X [Also search for: linear time suffix array].

%A P. Ko
%A S. Aluru
%T Space efficient linear time construction of suffix arrays
%J Proc. Annual Symposium on Combinatorial Pattern Matching
%I SpringerVerlag
%V 2676
%P 200-210
%D 2003
%K conf, c2003, c200x, c20xx, array, prefix, string, strings, suffix array,
   space, time, complexity
%X pdf@[<A HREF="http://ko.pang.cn.googlepages.com/CPM_2003_linear_SA.pdf">cn.googlepages.com</A>]   (* later publ. in J. Disc. Alg. '05. *).
   [Also search for: suffix array linear time].

%A A. Torsello
%A E. R. Hancock
%T Computing approximate tree edit distance using relaxation labeling
%J Pattern Recognition Letters
%V 24
%N 8
%P 1089-1097
%M MAY
%D 2003
%K jrnl, c2003, c200x, c20xx, approximate, tree, trees, edit distance, treeEdit,
   relaxation labeling, labelling
%X (in a Special issue: Graph-based representations in pattern recognition)
   "... new method for computing the tree edit distance problem with uniform
   edit cost. We commence by showing that any tree obtained with a sequence of
   cut operations is a subtree of the transitive closure of the original tree
   [then] the necessary condition for any subtree to be a soln can be reduced
   to a clique problem in a derived structure. ... transform the problem of
   computing tree edit dist. into a series of maximum wt clique problems.
   [last] use relaxation labeling to find an approx. to the tree edit dist.."
   -- [<A HREF="http://dx.doi.org/10.1016/S0167-8655(02)00255-6">doi:10.1016/S0167-8655(02)00255-6</A>]['08].
   [Also search for: treeEdit].

%A S. Burkhardt
%A J. Karkkainen
%T Better filtering with gapped q-grams
%J Fundamenta Informaticae
%V 56
%P 51-70
%D 2003
%O also 12th Annual Symp. Comb. Patt. Matching, LNCS 2089, 2001, pp.73-85
%K jrnl, c2003, c200x, c20xx, gapped, spaced, seed, seeds, gram, mer, string,
   strings, approximate match, search, mismatch, mismatches, filter, filters,
   filtering
%X "A popular & well-studied class of filters for approx. string matching
   compares substrings of length q, the q-grams, in the pattern & the text to
   identify text areas that contain potential matches. A generalization ...
   uses gapped q-grams instead of contiguous substrings is mentioned a few times
   in literature but has never been analyzed in any depth.  ... report the 1st
   results of a study on gapped q-grams. We show that gapped q-grams can provide
   orders of mag. faster &/or more efficient filtering than contiguous q-grams.
   ... [the gaps &] a filter param. called threshold have to be optimized. Both
   of these tasks are nontrivial combinatorial optimization problems for which
   we present efficient solns. We concentrate on the k mismatches problem, i.e,
   approximate string matching with the Hamming distance."
   pdf@[<A HREF="http://iospress.metapress.com/content/8ad9p3mqeday8vt5/">jrnl</A>]['09],
   preprint@[<A HREF="http://www.cs.helsinki.fi/juha.karkkainen/publications/fundamenta-revised02.ps.gz">helsinki</A>]['09],
   symp .ps@[<A HREF="http://www.mpi-sb.mpg.de/~stburk/PAPERS/cpm_01.ps">.mpg.de</A>]['09].

%A R. Grossi
%A A. Gupta
%A J. S. Vitter
%T High-order entropy-compressed text indexes
%J Symp. on Discrete Algorithms
%I ACM, SIAM
%P 841-850
%D 2003
%K conf, SoDA, SoDA03, SoDA, wavelet tree, trees, c2003, c200x, c20xx, string,
   strings, sequence, compressed index, suffix array
%X "... novel implementation of compressed suffix arrays ... new tradeoffs
   between search time & space occupancy for a given text of n symbols over an
   alphabet sigma, where each symbol is encoded by lg|sigma| bits.
   We show that compressed suffix arrays use just nHh+sigma bits,
   while retaining full text indexing functionalities, such as searching any
   pattern seq. of length m in O(m lg |Ï| + polylog(n))
   time. The term Hh â¤ lg |Ï| denotes the
   hth-order empirical entropy of the text, which means that our index is nearly
   optimal in space apart from lower-order terms, achieving asymptotically the
   empirical entropy of the text (with a mult. const. 1). If the text
   is highly compressible so that Hn=o(1) & the |sigma| is small, we obtain a
   text index with o(m) search time that requires only o(n) bits. ..."
   -- pdf@[<A HREF="http://portal.acm.org/citation.cfm?id=644250&dl=GUIDE&coll=GUIDE&CFID=53949138&CFTOKEN=49820040">acm</A>]['09], in, isbn:0898715385;
   or pdf@[<A HREF="http://www.di.unipi.it/~grossi/PAPERS/sodaconf03FINAL-LATEST.pdf">unipi.it</A>]['09].

%A C. Hohlweg
%A C. Reutenauer
%T Lyndon words, permutations and trees
%J J. Theor. Comp. Sci.
%V 307
%N 1
%P 173-178
%M SEP
%D 2003
%K jrnl, TCS, c2003, c200x, c20xx, Lyndon word, factors, string, strings,
   permutation, tree, LyndonWord
%X -- [<A HREF="http://dx.doi.org/10.1016/S0304-3975(03)00099-9">doi:10.1016/S0304-3975(03)00099-9</A>]['13],
   pdf@[<A HREF="http://www.lacim.uqam.ca/~christo/PubliÃ©s/2003/LyndonPermPreprint.pd">uquam</A>]['13].
   [Also search for: Lyndon word string].

%A Y.-T. Tsai
%T The constrained longest common subsequence problem
%J IPL
%V 88
%N 4
%P 173-176
%M NOV
%D 2003
%K jrnl, IPL, c2003, c200x, c20xx, CLCS, LCS, LCSS, algorithm, constrained,
   constraint, seq-ic-lcs, STR-IC-LCS, string, strings, sequence
%X "... constrained version of LCS problem for 2 strings. Given ... S1, S2 & P,
   the constrained LCS problem for S1 & S2 wrt P is to find a LCS lcs of S1 & S2
   s.t. P is a subseq. of this lcs. An O(m^2 m^2)-time alg. based upon the DP
   technique is proposed ... where n, m & r are lengths of S1, S2 & P, resp."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2003.07.001">doi:10.1016/j.ipl.2003.07.001</A>]['12].
   (NB. P is a subSEQ. of the lcs.)

%A H. Hyyro
%A G. Navarro
%T A practical index for searching the human genome
%J Proc. SPIRE'03 (short paper)
%S LNCS
%V 2857
%P ?-?
%D 2003
%K conf, c2003, c200x, c20xx, zz0106, MolBio, DNA, string, strings, sequence,
   time, space, fast, qGram, neighbourhood, hierarchical verification,
   approximate, indexing, mismatch, search, searching, SPIRE03
%X "Several proposals exist for indexed approximate string matching. It is
   known that these approaches are, in principle, well suited to computational
   biology tasks, but in most cases no effort has been made to apply them.
   [here] choose some of the principles behind these previous indices, and tune
   them to suit the real case of searching the human genome. ... pay attention
   to issues such as secondary memory and uneven distribution, which are
   disregarded in many proposals, but have significance when indexing the human
   genome. Unique features of our index are: optimized of selection of pattern
   pieces, bidirectional text verification, and optimized piece neighborhood
   generation. We find empirically our index to be 2 to 10 x faster than the
   best previous approach when the index fits in memory."
   -- [<A HREF="http://www.dcc.uchile.cl/~gnavarro/ps/spire03.7.ps.gz">.ps@uchile</A>]['06]
   [It's an inverted index on q-grams; k-difference neighbourhoods; verify.]
   [Also search for: approximate indexing].

%A R. Hall
%A L. Stern
%T A rapid method for illustrating features in both coding and
   non-coding regions of a genome
%J J. Bioinformatics
%P 982-983
%V 20
%N 6
%M APR
%D 2004
%K jrnl, MolBio, DNA, coding, nonCoding, region, gene, genes, zz0304,
   c2004, c200x, c20xx
%X "A bitmap display of the Fourier spectra has been developed which allows
   convenient whole chromosome scanning for genes and other features. Use of a
   limited sliding window gives rapid visualisation and localisation of coding
   regions in the chromosomes, as well as non-coding features such as
   repetitive DNA. The method works particularly well on organisms with a
   skewed base composition, to provide an overview of genomic features."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bth042">doi:10.1093/bioinformatics/bth042</A>][2/'04] (on-line before print)
      [<A HREF="http://www.bioinformatics.oupjournals.org/cgi/content/abstract/bth042v1">abs' bth042v1</A>][3/'04].
   Also see: H. and S., "A rapid method of whole genome visualisation
             illustrating features in both coding and non-coding regions",
             Proc. 2nd conf. on Asia-Pacific bioinformatics, 285-290, 2004,
             [<A HREF="http://portal.acm.org/ft_gateway.cfm?id=976558&type=pdf&coll=GUIDE&dl=ACM&CFID=26292330&CFTOKEN=11396916">portal.acm.org</A>][8/'04].

%T Compact Handbook of Computational Biology
%E A. K. Konopka
%E M. J. C. Crabbe
%I MarcelDekker N.Y.
%M SEP
%D 2004
%K book, MolBio, bioinformatics, bio, biol, c2004, c200x, c20xx, zz1004
%X <!-- A.K. Konopka; akk AT BLINGUA org --> hb, us$85; isbn:0824709829.

%A N. C. Jones
%A P. A. Pevzner
%T An Introduction to Bioinformatics Algorithms
%I MITpress
%P 448
%D 2004
%K book, text, MolBio, algorithm, c2004, c200x, c20xx, zz0305, uniCSD,
   spectral alignment
%X 1st ed 2004 hb us$55; uk us isbn:0262101068; uk us isbn13:978-0262101066.
   -- [<A HREF="http://www.bioalgorithms.info">more</A>]['05].

%A M. I. Abouelhoda
%A S. Kurtz
%A E. Ohlebusch
%T Replacing suffix trees with enhanced suffix arrays
%J J. Discrete Algorithms
%V 2
%N 1
%P 53-86
%M MAR
%D 2004
%K jrnl, c2004, c200x, c20xx, zz0106, tree, array, time, space, lcp interval,
   intervals, prefix, string, strings, MolBio, repeats, repeat, substring,
   substrings, short, shortest unique, algorithm, link table, Gusfield
%X "...show how every algorithm that uses a suffix tree as data structure can
   systematically be replaced with an a. that uses an enhanced suffix array and
   solves the same problem in the same time complexity ... Our new algss are not
   only more space efficient than previous ones, but they are also faster and
   easier to implement."
   -- [<A HREF="http://dx.doi.org/10.1016/S1570-8667(03)00065-0">doi:10.1016/S1570-8667(03)00065-0</A>]['06], 34 refs
   [Also search for: unique substring].

%A G. Manzini
%A P. Ferragina
%T Engineering a lightweight suffix array construction algorithm
%J Algorithmica
%V 40
%N 1
%P 33-50
%M JUN
%D 2004
%O ESA'02, LNCS, Vol.2461, pp.698-710, 2002
%K jrnl, c2004, c200x, c20xx, arrays, string, strings, suffixes, deep, shallow,
   indexing, text, search, FM index, FMindex, BW, BWT
%X "... use a shallow sorter for the suffixes with a short common prefix and a
   deep ... long ... uses very small space in addition to the space required by
   the suffix array itself. ... alg is fast even when the input contains many
   repetitions ... extensive experiments ... C library ... GNU GPL."
   [i.e. claim small and fast in practice.]
   -- [<A HREF="http://dx.doi.org/10.1007/s00453-004-1094-1">doi:10.1007/s00453-004-1094-1</A>]['06]
   Also see [<A HREF="http://www.mfn.unipmn.it/~manzini/papers/esa02.html">unipmn.it</A>]['08].

%A A. Amir
%A M. Lewenstein
%A E. Porat
%T Faster algorithms for string matching with k mismatches
%J J. Algorithms
%V 50
%N 2
%P 257-275
%D 2004
%K jrnl, c2004, c200x, c20xx, strings, string, match, mismatches, algorithm,
   search
%X "The string matching with mismatches problem is that of finding the # of
   mismatches between a pattern P of length m & every length m substring of the
   text T. Currently, the fastest algs. for this problem are the following. The
   Galil-Giancarlo algorithm finds all locns where the patt. has at most k
   errors ... in time O(nk). The Abrahamson alg. finds the # of mismatches at
   every location in time O(n sqrt(m log m)). We present an alg. that is faster
   than both. ... finds all locns where the patt. has at most k errors in time
   O(n sqrt(k log k)). We also show an alg. that solves the above prob. in time
   O((n + (n k**3)/m) log k)."
   -- [<A HREF="http://dx.doi.org/10.1016/S0196-6774(03)00097-X">doi:10.1016/S0196-6774(03)00097-X</A>]['09].

%A F. Bassino
%A J. Clement
%A C. Nicaud
%T The standard factorization of Lyndon words: an average point of view
%J Discrete Maths.
%V 290
%N 1
%P 1-25
%M JAN
%D 2005
%K jrnl, c2005, c200x, c20xx, standard factorization, right, factor, factorize,
   factorise, factorizing, Lyndon word, LyndonWord, words, suffix, suffixes
%X "A non-empty word w is a Lyndon word iff it is strictly smaller for the
   lex.order than any of its proper suffixes. Such a word w is either a letter
   or admits a Standard Factorization uv where v is its smallest proper suffix.
   For any Lyndon word v, we show that the set of Lyndon words having v as
   right factor of the standard factorization is regular & compute explicitly
   the assoc. generating fn. Next, considering the Lyndon words of length n over
   a 2-letter alphabet, we establish that for the uniform distribution, the avg.
   length of the right factor v of the std factor'n is asymptotically 3n/4."
   -- [<A HREF="http://dx.doi.org/10.1016/j.disc.2004.11.002">doi:10.1016/j.disc.2004.11.002</A>]['09].
   (Also look for  D u v a l,  J. Algs.,  '83.)

%A G. Navarro
%T Indexing text using the Ziv-Lempel trie
%J J. Discrete Algorithms
%V 2
%N 1
%P 87-114
%M MAR
%D 2004
%K jrnl, c2004, c200x, c20xx, zz0106, index, search, searching, tries, LZ78, LZ,
   ZL, string, strings, sequence, sequence, dataStructure, DS
%X "Let a text of u chars over an alphabet of size sigma be compressible to n
   phrases by the LZ78 alg.. We show how to build a data structure based on the
   Ziv-Lempel trie, called the LZ-index, that takes 4n log2(n(1+o(1))) bits of
   space (that is, 4 times the entropy of the text for ergodic sources) &
   reports the R occurrences of a pattern of length m in worst case time
   O(m**3 log(sigma) + (m+R)log n). We present a practical implementation of
   the LZ-index, which is faster than current alternatives when we take into
   consideration the time to report the positions or text contexts of the
   occurrences found."
   -- [<A HREF="http://dx.doi.org/10.1016/S1570-8667(03)00066-2">doi:10.1016/S1570-8667(03)00066-2</A>]['06]
   [Also search for: string index search].

%A A. S. Konagurthu
%A J. C. Whisstock
%A P. J. Stuckey
%T Progressive multiple alignment using sequence triplet optimizations and
   three-residue exchange costs
%J J. Bioinformatics and Comp. Biol.
%V 2
%N 4
%P 719-745
%M DEC
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, sequence, alignment, triplet, three,
   Carrillo, Lipman, bounds
%X "... construct progressive multiple alignments using seq. triplet
   optimizations rather than a conventional p-wise approach. ... provides a
   scope for the synthesis of a 3-residue exchange amino acid substn matrix. We
   develop such a 20x20x20 matrix for the 1st time & demo. how its use in
   optimal seq. triplet alignments increases the sensitivity of building
   multiple alignments. Various comparisons were made between al's gen. using
   the ... method & the conventional progressive p-wise proc.. ... the triplet
   based approaches generate more accurate seq.als. than the trad. p-wise based
   procedures, especially between more divergent sets of sequences."
   -- [<A HREF="http://dx.doi.org/10.1142/S0219720004000831">doi:10.1142/S0219720004000831</A>]['09].
   [Also search for: multiple sequence alignment MolBio].

%A S. Lee
%A K. Park
%T Efficient implementations of suffix array construction algorithms
%J Proc. 15th Australasian Workshop on Combinatorial Algorithms
%P 64-72
%D 2004
%K wShop, c2004, c200x, c20xx, string, strings, suffix array, arrays,
   linear time
%X "... consider efficient implementations of 3 s.array construction algs. ...
   due to Manber-Myers, Karkkainen-Sanders & Ko-Aluru. The K.-S. & Ko-Aluru
   algs. both run in linear time in the worst case. The Manber-Myers alg. runs
   in linear time on average and O(n log n) time in the worst case. All 3 use
   linear space in the worst case. We developed several techniques to optimize
   implementations as much as possible. ... experiments to compare ... the 3
   algs. ...  K.-S. & Ko-Aluru algs. perform much better for DNA seqs. than
   the M.-M. alg., which is competitive, however, for random inputs. ...
   Ko-Aluru performs better than Karkkainen-Sanders in our implementations"
   -- .ps@[<A HREF="http://www.computing.edu.au/~smyth/lp04.ps">computing.edu.au</A>]['09].
   (Also see [<A HREF="http://doi.acm.org/10.1145/1242471.1242472">doi:10.1145/1242471.1242472</A>].)
   [Also search for: suffix array linear time].

%A G. Korodi
%A I. Tabus
%T An efficient normalized maximum likelihood algorithm for
   DNA sequence compression
%J ACM Trans. on Inf. Sys.
%V 23
%N 1
%P 3-34
%M JAN
%D 2005
%K jrnl, compress, MolBio, c2005, c200x, c20xx, strings, string, sequence, NML
%X "... achieves the best compression ratios reported over a test set commonly
   used for evaluating DNA compression programs. ... introduces many refinements
   to a compression method that combines: (1) encoding by a simple (NML) model
   for discrete regression, through reference to preceding approximate matching
   blocks, (2) encoding by a 1st order context coding & (3) representing strings
   in clear, to make efficient use of the redundancy sources in DNA data, under
   fast execution times. One of the main algorithmic features is the constraint
   on the matching blocks to include reasonably long contiguous matches, ...
   ...handles the changing statistics of DNA data in an adaptive way ..."
   -- [<A HREF="http://doi.acm.org/10.1145/1055709.1055711">doi:10.1145/1055709.1055711</A>]['05],
      [<A HREF="http://sigwww.cs.tut.fi/~tabus/genome.htm">tabus</A>]['05].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">compression</A>].)

%A W. H. Majoros
%A M. Pertea
%A S. L. Salzberg
%T Efficient implementation of a generalized pair hidden Markov model for
   comparative gene finding
%J J. Bioinformatics
%V 21
%N 9
%P 1782-1788
%D 2005
%K jrnl, GPHMM, HMM, gene prediction, genes, predicting, c2005, c200x, c20xx,
   MolBio, TWAIN, gene prediction
%X "...open-source GPHMM gene finder, TWAIN, which performs very well on 2 rel.
   Aspergillus species, A.fumigatus and A.nidulans, finding 89% of the exons &
   predicting 74% of the gene models ... in a test set of 147 conserved gene
   pairs. We describe the implementation of this GPHMM & we explicitly address
   the assumptions & limitations of the system. ... possible ways of relaxing
   those assumptions to improve the utility of the system without sacrificing
   efficiency beyond what is practical."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti297">doi:10.1093/bioinformatics/bti297</A>]['05]

%A B. Lazareva-Ulitsky
%A K. Diemer
%A P. D. Thomas
%T On the quality of tree-based protein classification
%J J. Bioinformatics
%V 21
%N 9
%P 1876-1890
%D 2005
%K jrnl, trees, evolutionary, hierarchical, c2005, c200x, c20xx, zz0605,
   MolBio, TIPS, UPGMA
%X "... Given a ref. class'n or group memb. lables for a set of
   related prot. seqs. as well as a tree describing the relationships ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti244">doi:10.1093/bioinformatics/bti244</A>]['05]

%A V. Freschi
%A A. Bogliolo
%T Using sequence compression to speedup probabilistic profile matching
%J J. Bioinformatics
%V 21
%N 10
%P 2225-2229
%D 2005
%K jrnl, MolBio, c2005, c200x, c20xx, compress, match, run length encoding,
   speed-up, profiles, RLE
%X "... exploit string compression techniques to speedup brute-force profile
   matching.  ... 2 algs., based on run-length & LZ78 encodings, that reduce
   computational complexity by the compression factor of the encoding."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti323">doi:10.1093/bioinformatics/bti323</A>]['05]
   [Also look for:  match run length]

%A A. McCallum
%A K. Bellare
%A F. Pereira
%T A conditional random field for discriminatively-trained finite-state
   string edit distance
%J Conf. on Uncertainty in AI
%P ?-?
%M JUL
%D 2005
%K conf, UAI, UAI21, molbio, strings, sequence, c2005, c200x, c20xx, citations,
   addresses, names
%X "Train a string edit distance function from both positive & negative egs of
   string pairs (matching & mismatching). Significantly, the model designer is
   free to use arbitrary, fancy features of both strings, & also very flexible
   edit operations. This model is an example of an increasingly popular
   interesting class - conditionally-trained models with latent variables.
   Positive results on citations, addresses & names."            [8 pages]
   -- [<A HREF="http://www.cs.umass.edu/~mccallum/papers/crfstredit-uai05.pdf">pdf</A>]['05]

%A D. Lupyan
%A A. Leo-Macias
%A A. R. Ortiz
%T A new progressive-iterative algorithm for multiple structure alignment
%J J. Bioinformatics
%V 21
%N 15
%P 3255-3263
%M AUG
%D 2005
%K jrnl, MolBio, protein, c2005, c200x, c20xx, 3D, MAMMOTH-mult
%X "...Typical alignments take only a median time of 5 CPU seconds in a
   single R12000 processor. ..."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/bti527">doi:10.1093/bioinformatics/bti527</A>]['05]
   [Also search for: MolBio protein structure alignment].

%A E. Mossel
%A E. Vigoda
%T Phylogenetic MCMC algorithms are misleading on mixtures of trees
%J Science
%V 309
%N 5744
%P 2207-2209
%M SEP
%D 2005
%K jrnl, family, evolutionary, tree, c2005, c200x, c20xx, MolBio, zz1005,
   algorithm, mixture, convergence
%X "... theoretical analysis of the rate of convergence of many of the widely
   used Markov chains. For N chars. generated from a uniform mixture of 2 trees
   ... Markov chains take an exponentially long (in N) # of iterations to
   converge to the posterior distrib.. [but] likelihood plots for sample runs
   of the Markov chains deceivingly suggest that the chains converge rapidly to
   a unique tree. ... novel mathematical understanding of the log-likelihood
   function on the space of phylogenetic trees. ... implications of our work
   are that Bayesian MCMC methods can be misleading when the data are generated
   from a mixture of trees. Thus, in cases of data containing potentially
   conflicting phylogenetic signals, phylogenetic reconstruction should be
   performed separately on each signal."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1115493">doi:10.1126/science.1115493</A>]['05]

%A P. Ko
%A S. Aluru
%T Space efficient linear time construction of suffix arrays
%J J. Discrete Algorithms
%V 3
%N 2-4
%P 143-156
%M JUN
%D 2005
%K jrnl, array, prefix, c2005, c200x, c20xx, zz0106, string,strings, substring,
   LCP, suffix array, space, time, complexity
%X "We present a linear time alg. to sort all the suffixes of a string over a
   large alphabet of integers.  ... Our result is one of the first linear time
   suffix array construction a's, ...  can also be used to derive a different
   linear time construction a. for suffix trees. Apart from being simple and
   applicable for alphabets not necessarily of fixed size, this method of
   constructing suffix trees is more space efficient."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jda.2004.08.002">doi:10.1016/j.jda.2004.08.002</A>]['06] (online 9/'04),
   (* earlier publ in a '03 conf *)
   [Also search for: suffix array linear time]  (space looks like 8n, table 2).

%A S. J. Puglisi
%A W. F. Smyth
%A A. Turpin
%T The performance of linear time suffix sorting algorithms
%J Data Compression Conf.
%P 358-367
%D 2005
%K conf, DCC, DCC05, c2005, c200x, c20xx, array, arrays, algorithm, BW index,
   strings, string, text
%X "Sorting all the suffixes of a string x = x[1..n] into lexicographical order
   is the most computationally expensive step in the Burrows-Wheeler
   transformation for lossless compression. One tool for achieving a suffix
   sort is the suffix array. Suffix arrays are also the basis for a variety of
   compressed text indexing systems that allow arbitrary queries, for example
   the scheme of Grossi and Vitter."      A.Turpin is @rmit('06),
   -- [<A HREF="http://www.computing.edu.au/~smyth/pst.ps">.ps</A>]['06],
   ... direct comparison algs O(n**2 log n) worst case but often fast in
   practice. Doubling algorithms ... double the depth on each pass, log # of
   passes, O(n log n) worst case assuming (say) radix sort. Then ... separate
   suffixes into 2 groups, use a recursive ordering of 1 group to order all s.
   ... Manzini & Ferragina c2004 (non lin-time worst-case) fastest in practice.
   auth1@[<A HREF="http://goanna.cs.rmit.edu.au/~sjp/">rmit</A>]['09].

%A M. E. Karim
%A A. Walenstein
%A A. Lakhotia
%A L. Parida
%T Malware phylogeny generation using permutations of code
%J J. in Computer Virology
%V 1
%N 1
%P 13-23
%D 2005
%K jrnl, c2005, c200x, c20xx, zz1206, permutation, phylogenetic, virus, worm,
   evolution, tree, trees, program
%X "... constructing a phylogeny model is expected to be helpful for analyzing
   new malware & for establishing a principled naming scheme. Matching
   permutations of code may help build better models in cases where malware
   evolution does not keep things in the same order. We describe methods for
   constructing phylogeny models that uses features called n-perms to match
   possibly permuted codes. An experiment was performed to compare the relative
   effectiveness of vector similarity measures using n-perms & n-grams when
   comparing permuted variants of programs. The similarity measures using
   n-perms maintained a greater separation between the similarity scores of
   permuted families of specimens versus unrelated specimens. A subsequent study
   using a tree generated through n-perms suggests that phylogeny models based
   on n-perms may help forensic analysts investigate new specimens, & assist in
   reconciling malware naming inconsistencies."  --via CharlesT.
   -- [<A HREF="http://dx.doi.org/10.1007/s11416-005-0002-9">doi:10.1007/s11416-005-0002-9</A>]['06],
      [<A HREF="http://www.cacs.louisiana.edu/labs/SRL/publications/2005-jicv-karim-walenstein-lakhotia-parida.pdf">pdf@cacs</A>]['06].

%A A. Lakhotia
%A Md. E. Karim
%A A. Walenstein
%A L. Parida
%T Malware phylogeny using maximal pi-patterns
%J EICAR
%P 167-174
%D 2005
%K conf, EICAR, pattern, c2005, c200x, c20xx, virus, worm
%X [<A HREF="http://www.cacs.louisiana.edu/labs/SRL/publications/2005-eicar-lakhotia-karim-walenstein-parida.pdf">pdf@cacs</A>]['06]
   also see j. paper.

%A K-Y Chen
%A K-M Chao
%T Optimal algorithms for locating the longest and shortest segments satisfying
   a sum or an average constraint
%J IPL
%V 96
%N 6
%P 197-201
%M DEC
%D 2005
%K jrnl, IPL, MolBio, c2005, c200x, c20xx, interval, segment
%X "We study several fundamental problems arising from biological seq. analysis.
   Given a seq. of real numbers, we present 2 linear-time algs, one for
   locating the "longest" sum-constrained segment, & the other for locating the
   "shortest" sum-constrained segment. These 2 algs are based on the same
   framework & run in an online manner, hence they are capable of handling data
   stream inputs. Our algs also yield online linear-time solutions for finding
   the longest & shortest average-constrained segments by a simple reduction."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2005.08.006">doi:10.1016/j.ipl.2005.08.006</A>]['05]
   [Also search for: longest interval]

%A D. Fukagawa
%A T. Akutsu
%T Fast algorithms for comparison of similar unordered trees
%J Algorithms and Computation
%I Springer
%S LNCS
%V 3341
%P 452-463
%D 2005
%K conf, c2005, c200x, c20xx, labelled, unordered, rooted, unrooted, tree,
   treeEdit, treeAlignment, largest common subtree, LCST
%X "...computing the largest common subtree (LCST) & the optimal alignment when
   2 similar unordered trees are given. We present an O(4^K n) time alg for the
   LCST problem for rooted trees, where n is the max size of 2 input trees & K
   is the min number of edit operations to obtain LCST. We extend this alg to
   unrooted trees & obtain an O(K 4^K n) time alg. We also show that the
   alignment problem for rooted & unordered trees of bounded degree can be
   solved in linear time if K is bounded by a constant."
   In [<A HREF="http://dx.doi.org/10.1007/b104582">doi:10.1007/b104582</A>]['08].
   [Also search for: treeEdit].

%A E. R. Hancock
%A A. Robles-Kelly
%T Graph edit distance from spectral seriation
%J IEEE Trans. on Pattern Analysis and Machine Intelligence
%V 27
%N 3
%M MAR
%D 2005
%P 365-378
%D 2005
%K jrnl, c2005, c200x, c20xx, graph edit distance, GED, graphs, spectral,
   analysis, seriation, eigenvectors, eigenvector, uniYork
%X "... [a criticism of] existing methods for ... graph edit dist. is that
   they lack some of the formality & rigor of ... string e.d.. Hence, our
   aim is to convert graphs to string seqs. so that string matching techniques
   can be used. ... use a graph spectral seriation method to convert the
   adjacency matrix into a string or seq order. We show how the serial ordering
   can be estab. using the leading eigenvector of the graph adjacency matrix.
   We pose the problem of graph-matching as a max. a posteriori prob. (MAP)
   alignment of the seriation seqs. for pairs of graphs. ... leads to an
   expression in which the edit cost is the -ve log of the a posteriori seq.
   alignment prob.. We compute the edit dist. by finding the seq. of string edit
   ops. which min. the cost of the path traversing the edit lattice. The edit
   costs are determined by the components of the leading eigenvectors of the
   adjacency matrix and by the edge densities of the graphs being matched. We
   demonstrate the utility ... on a number of graph clustering problems."
   -- [<A HREF="http://dx.doi.org/10.1109/TPAMI.2005.56">doi:10.1109/TPAMI.2005.56</A>]['08],
      [<A HREF="http://www.cs.york.ac.uk/~erh/rae/pami05.pdf">pdf@york</A>]['08],
   &  [<A HREF="http://www.cs.york.ac.uk/~erh/">auth1@york</A>]['08].
   [Also search for: graph edit distance GED].

%A H. Touzet
%T A linear tree edit distance algorithm for similar ordered trees
%J CPM
%I SpringerVerlag
%S LNCS
%V 3537
%P 334-345
%D 2005
%K conf, CPM, CPM05, c2005, c200x, c20xx, labelled, ordered, trees, treeEdit,
   Zhang, Shasha
%X "... linear alg for comparing 2 similar ordered rooted trees with node
   labels. The method for comparing trees is the usual tree edit distance. We
   show that an optimal mapping which uses at most k insertions or deletions can
   then be constructed in O(n k^3) where n is the size of the trees. The
   approach is inspired by the Zhang-Shasha algorithm for tree edit distance
   in combination with an adequate pruning of the search space."
   -- [<A HREF="http://dx.doi.org/10.1007/11496656_29">doi:10.1007/11496656_29</A>]['08]
   (also see  J a n s s o n  and  L i n g a s  c2001.)
   [Also search for: treeEdit].

%A B. Brejova
%A D. G. Brown
%A T. Vinar
%T Vector seeds: An extension to spaced seeds
%J JCSS
%V 70
%N 3
%P 364-380
%D 2005
%K jrnl, JCSS, c2005, c200x, c20xx, string, strings, DNA, sequence,
   spaced, vector, seed, mismatches
%X "... improved techniques for finding homologous regions in DNA & protein
   seqs.. ... focuses on the core regions of a local pairwise alignment; ...
   new ways to characterize these regions ... For any such characterization,
   which we call a vector seed, we give an efficient alg. that estimates the
   specificity & sensitivity of that seed under reasonable probabilistic models
   of sequence. We also characterize the probability of a match when an
   alignment is required to have multiple hits before it is detected. Our
   extensions fit well with existing approaches to seq.al., ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jcss.2004.12.008">doi:10.1016/j.jcss.2004.12.008</A>]['09].
   [Also search for: spaced seed].

%A A. Firth
%A T. Bell
%A A. Mukherjee
%A D. Adjeroh
%T A comparison of BWT approaches to string pattern matching
%J SPE
%V 35
%N 13
%P 1217-1258
%D 2005
%K jrnl, SPE, c2005, c200x, c20xx, text, string, approach, sequence, search,
   searching, index, indexing, compressed, Burrows Wheeler transform, BWT,
   FM, FMindex, strings
%X "Recently a number of algs. have been developed to search files compressed
   with the BWT without the need for full decompression first. This allows the
   storage requirement of data to be reduced ... while allowing fast access to
   the information for searching by taking advantage of the sorted nature of
   BWT files. We provide a detailed description of 5 of these algs.: BWT-based
   Boyer-Moore, Binary Search, Suffix Arrays, q-grams and the FM-index, & also
   present results from a set of extensive experiments that were performed to
   evaluate & compare the algs.. ... introduce a technique to improve the search
   times of Binary Search ...& q-grams by 22% on avg., as well as reduce the
   memory requirement of the latter two by 40% & 31%, resp.. ... indicate that,
   while the compressed files of the FM-index are larger than those of the other
   approaches, it is able to perform searches with considerably less memory.
   [and] when only counting the occurrences of a pattern, or when locating the
   posn of a small # of matches, it is the fastest alg.. For larger searches
   Binary Search ... fastest ...  Comparative results ... "
   -- [<A HREF="http://dx.doi.org/10.1002/spe.669">doi:10.1002/spe.669</A>]['09].
   [Also search for: FM index]  and  [also search for: Burrows Wheeler BWT].

%A M. Crochemore
%A J. Desarmenien
%A D. Perrin
%T A note on the Burrows-Wheeler transformation
%J TCS
%V 332
%N 1-3
%P 567-572
%M FEB
%D 2005
%K jrnl, TCS, c2005, c200x, c20xx, Burrows Wheeler transform, BW, BWT,
   string, strings, text, Gessel Reutenauer
%X "We relate the Burrows-Wheeler transformation with a result in combinatorics
   on words known as the Gessel-Reutenauer transformation."
   -- pdf@[<A HREF="http://dx.doi.org/10.1016/j.tcs.2004.11.014">doi:/10.1016/j.tcs.2004.11.014</A>][8/'09].
   [Also search for: BWT string] and  [also search for: Gessel Reutenauer].

%A G. Kucherov
%A L. Noe
%A M. Roytberg
%T Multiseed lossless filtration
%J Trans. on Computational Biology and Bioinformatics
%I ACM/IEEE
%V 2
%N 1
%P 51-61
%D 2005
%K MolBio, TCBB, c2005, c200x, c20xx, gapped, spaced, seed, seeds, multiple,
   filter, filters, filtering, strings, approximate matching
%X "... method of seed-based lossless filtration for approx. string matching ...
   ... based on a simultaneous use of several spaced seeds rather than a single
   seed as studied by Burkhardt & Karkkainen. We present algs.to compute several
   important params. of seed families, study their combinatorial properties, &
   describe several techniques to construct efficient families. We also report
   a large-scale application ... oligonucleotide sel'n for an EST seq. DB."
   -- [<A HREF="http://dx.doi.org/10.1109/TCBB.2005.12">doi:10.1109/TCBB.2005.12</A>]['09].

%A S. Mantaci
%A A. Restivo
%A G. Rosone
%A M. Sciortino
%T An extension of the Burrows Wheeler transform and applications to sequence
   comparison and data compression
%J Combinatorial Pattern Matching
%I SpringerVerlag
%S LNCS
%V 3537
%P 178-179
%D 2005
%O M, Re & S,  'An Extension of the Burrows Wheeler Transform to k Words',
      DCC05, pp.469-469, 2005, and
   M, R, R, S, 'An extension of the Burrows-Wheeler Transform',
      TCS, 387(3), pp.298-312, '07.
%K conf, c2005, c200x, c20xx, CPM, extended, BWT, EBWT, multiset, set, string,
   strings, multiple, sequences
%X "... generalization of the (BWT) that can be applied to a multiset of words.
   The extended transformation, denoted by E, is reversible, but, differently
   from BWT, it is also surjective. The E transformation allows to give a
   defn of distance between 2 seqs., that we apply here to the problem of the
   whole mitochondrial genome phylogeny. ..."
    -- [<A HREF="http://dx.doi.org/10.1007/11496656_16">doi:10.1007/11496656_16</A>]['09], also
   DCC [<A HREF="http://dx.doi.org/10.1109/DCC.2005.13">doi:10.1109/DCC.2005.13</A>]['09], and
   TCS [<A HREF="http://dx.doi.org/10.1016/j.tcs.2007.07.014">doi:10.1016/j.tcs.2007.07.014</A>]['09].

%A M. Charikar
%A E. Lehman
%A D. Liu
%A R. Panigrahy
%A M. Prabhakaran
%A A.Sahai
%A A. Shelat
%T The smallest grammar problem
%J IEEE Trans. Info. Theory
%V 51
%N 7
%P 2554-2576
%M JUL
%D 2005
%K jrnl, c2005, c200x, c20xx, zz0415, re pair, repair, string, CF grammar, CFG,
   smallest context free grammar, SCFG, problem, infer, inferring, generate
%X "... What is the smallest context-free grammar that generates exactly one
   given string sigma? ... Due to the problem's inherent complexity, our
   objective is to find an approxn alg. which finds a small grammar for the
   input string. We focus attention on the approxn ratio of the alg. (&
   implicitly, the worst case behavior) to establish provable performance
   guarantees & to address shortcomings in the classical measure of redundancy
   ... . Our first results are concern the hardness of approximating the
   smallest grammar problem. ... show that every efficient alg. for the smallest
   grammar problem has approxn ratio >=8569/8568 unless P=NP. We then bound
   approxn ratios for several of the best known grammar-based compression
   algs., inc. LZ78, B ISECTION, SEQUENTIAL, LONGEST MATCH, GREEDY, & RE-PAIR.
   Among these, the best upper bound we show is O(n12/). We finish by presenting
   two novel algs. with exponentially better ratios of O(log^3 n) & O(log(n/m*))
   where m* is the size of the smallest grammar for that input. The latter alg.
   highlights a connection between grammar-based compression & LZ77."
   -- [<A HREF="http://dx.doi.org/10.1109/TIT.2005.850116">doi:10.1109/TIT.2005.850116</A>]['15].
   (NB. "CFG that generates exactly one given string")
   [Also search for: RE PAIR REPAIR]  and  [also search for: SCFG]  and
   [also search for: infer grammar] and [also search for: infer automaton].

%A P. Bille
%T A survey on tree edit distance and related problem
%J Theor. Comp. Sci.
%V 337
%P 217-239
%D 2005
%K jrnl, TCS, c2005, c200x, c20xx, intro, survey, tree, trees, edit, distance,
   treeEdit, alignment, treeAlignment, label, labeled, labelled
%X "... comparing labeled trees based on simple local operations of deleting,
   inserting, and relabeling nodes. These operations lead to the tree edit
   distance, alignment distance, and inclusion problem. For each problem we
   review the results available and present, in detail, one or more of the
   central algorithms for solving the problem."   -- via Alex S.
   -- [<A HREF="http://dx.doi.org/10.1016/j.tcs.2004.12.030">doi:10.1016/j.tcs.2004.12.030</A>]['08].
   [Also search for: treeEdit].

%A M. G. Maass
%T Matching statistics: efficient computation and a new practical algorithm for
   the multiple common substring problem.
%J SPE
%V 36
%N 3
%P 305-331
%D 2006
%K jrnl, SPE, c2006, c200x, c20xx, string, strings, suffix array, arrays, tree
%X "...new algs. for computing matching statistics with suffix arrays. We show
   how the Multiple Common Substring Problem can be solved efficiently in
   practice with a new approach using matching statistics. ... finding the
   common substrings of a set of strings. For the computation of matching
   statistics we compare 7 different methods based on suffix trees & suffix
   arrays. Most of the suffix array algorithms have an inferior asymptotic
   worst case running time but a very low memory overhead & small constants in
   the running time complexity. Our exps. show a good performance in practice."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.698">doi:10.1002/spe.698</A>]['06]
   (online Nov '05)

%A D. C. Atkinson
%A W. G. Griswold
%T Effective pattern matching of source code using abstract syntax patterns
%J SPE
%V 36
%N 4
%P 413-447
%D 2006
%K jrnl, SPE, c2006, c200x, c20xx, zz0306, AWK, TAWK, syntax tree
%X "... extend the pattern syntax of AWK to support matching of abstract
   syntax trees, as demonstrated in a tool called TAWK. Its pattern syntax is
   language-independent, based on abstract tree patterns. As in AWK, patterns
   can have associated actions, which in TAWK are written in ..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.704">doi:10.1002/spe.704</A>]['06]

%A A. Gambin
%A J. Tiuryn
%A J. Tyszkiewicz
%T Alignment with context dependent scoring function
%J J. of Computational Biology
%V 13
%N 1
%P 81-101
%M JAN
%D 2006
%K jrnl, c2006, c200x, c20xx, MolBio, context, score, scoring
%X [Also search for: alignment low information].

%A F. Armougom
%A S. Moretti
%A V. Keduas
%A C. Notredame
%T The iRMSD: a local measure of sequence alignment accuracy using structural
   information
%J J. Bioinformatics
%V 22
%N 14
%P e35-e39
%D 2006
%K MolBio, c2006, c200x, c20xx, RMSD, iRMSD, c2006, c200x, c20xx, quality,
   alignment, protein, structure, iRMSD, Prefab
%X "... iRMSD, a new type of RMSD, indep. from any structure superposition and
   suitable for evaluating seq. alignments of proteins with known structures.
   Results: [show] iRMSD is equivalent to the standard RMSD although much
   simpler to compute and ... it is suitable for comparing seq. alignments &
   benchmarking multiple seq. alignment methods. We tested the iRMSD score on 6
   established multiple sequence alignment packages and found the results to be
   consistent with those obtained using an established reference alignment
   collection like Prefab"
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl218">doi:10.1093/bioinformatics/btl218</A>]['06].
   [Also search for: MolBio protein structure alignment].

%A S. Roch
%T A short proof that phylogenetic tree reconstruction by maximum likelihood is
   hard
%J IEEE/ACM Trans. on Comp. Biol.
%V 3
%N 1
%P 92-94
%M JAN-MAR
%D 2006
%K MolBio, c2006, c200x, c20xx, phylogenetic tree, family, evolutionary trees,
   maximum likelihood, inference, NP hard, NPH, complexity
%X "Maximum likelihood is one of the most widely used techniques to infer
   evolutionary histories. Although it is thought to be intractable, a proof of
   its hardness has been lacking. Here, we give a short proof that computing the
   max. l.h. tree is NP-hard by exploiting a connection between likelihood &
   parsimony observed by Tuffley and Steel."  [18 refs].
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/TCBB.2006.4">doi:10.1109/TCBB.2006.4</A>]['09].
   [Also search for: inference phylogenetic tree MolBio].

%A N. C. Jones
%A P. A. Pevzner
%T Comparative genomics reveals unusually long motifs in mammalian genomes
%J J. Bioinformatics
%V 22
%N 14
%P e236-e242
%D 2006
%K MolBio, c2006, c200x, c20xx, motif, genome, mammal, mammals,
   Neuron Restrictive Silencer Element
%X "...existing comparative genomics approaches (e.g. phylogenetic footprinting)
   rely on alignments of orthologous regions across multiple genomes. This
   approach, while extremely valuable, is not suitable for finding motifs with
   highly diverged "non-alignable" flanking regions. Here we show that several
   unusually long & well conserved motifs can be discovered de novo through a
   comparative genomics approach that does not require an alignment of
   orthologous upstream regions. These motifs, including Neuron Restrictive
   Silencer Element, were missed in recent comparative genomics studies that
   rely on phylogenetic footprinting. While the functions of these motifs remain
   unknown, we argue that some may represent biologically important sites."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl265">doi:10.1093/bioinformatics/btl265</A>]['06]

%A B. B. Zhou
%A M. Tarawneh, D. Chu, P. Wang, C. Wang, A. Y. Zomaya
%A R. P. Brent
%T On a new quartet-based phylogeny reconstruction algorithm
%J Proc. Int. Conf. on Bioinformatics and Computational Biology (BIOCOMP06)
%W Las Vegas
%P 87-93
%M JUN
%D 2006
%K conf, MolBio, c2006, c200x, c20xx, evolutionary, tree, trees,
   maximum likelihood, ML, ANUni
%X "... [earlier] algorithm constructs a limited number of trees for a given
   set of DNA or protein seqs. & the initial experimental results show that the
   prob. for the correct tree to be included in this small set of trees is very
   high. ... further extend the idea. We first discuss a revision to the
   original algorithm to reduce the number of trees generated, while keeping the
   high probability for the correct tree to be included. We then deal with the
   issue of how to retrieve the correct tree from the set of generated trees.
   Our current approach is to calculate the likelihood values of these trees &
   select a few which have the highest likelihood values. Though the
   experimental results are comparable to those obtained from currently popular
   ML-based algs., we find that it is common that certain incorrect trees can
   have likelihood values at least as large as that of the correct tree. ..."
   -- [<A HREF="http://wwwmaths.anu.edu.au/~brent/pub/pub223.html">abs & pdf</A>]['07]
   (RPB @ MSI ANU '06)

%A B. B. Zhou
%A M. Tarawneh
%A D. Chu, P. Wang, C. Wang, A. Zomaya, R. P. Brent
%T Evidence of multiple maximum likelihood points for a phylogenetic tree
%J Proc. Sixth IEEE Symp. on Bioinformatics and Bioengineering (BIBE06)
%W Arlington
%P 193-197
%M OCT
%D 2006
%K conf, MolBio, c2006, c200x, c20xx, FASTDNAML, PHYML, evolutionary, tree,
   trees, ANUni
%X "...Steel [] presented a simple analytical results to argue that the ML point
   is not unique. .... many researchers believe that multiple ML pts may exist
   ... existing phylogenetic construction programs only produce a single best
   tree under the ML criterion & in practice many researchers still use only the
   ML values to make a judgment on the quality of different trees for a given
   problem. ... present some experimental results from a large # of synthetic
   test data sets & show that it is quite common that certain incorrect trees
   can have likelihood values at least as large as that of the correct tree. A
   sig. implication of this is that even if we are able to find a globally
   optimal tree under the ML criterion, this tree is not necessarily the correct
   [one]. ... also show that our newly developed algorithm ..."
   -- [<A HREF="http://wwwmaths.anu.edu.au/~brent/pub/pub227.html">abs & pdf</A>]['07]
   (RPB @ MSI ANU '06).

%A J. Karkkainen
%A P. Sanders
%A S. Burkhardt
%T Linear work suffix array construction
%J JACM
%V 53
%N 6
%P 918-936
%M NOV
%D 2006
%K JACM, jrnl, c2006, c200x, c20xx, zz0409, suffix arry, linear work, time,
   complexity, fast, DC3, difference cover
%X "... a simple linear-time construction alg for suffix arrays. ...  C++ ...
   50 effective lines of code ... called DC3, ... central underlying concept of
   difference cover. ... leads to a generalized alg, DC, that allows a space-
   -efficient implementation & ... supports the choice of a space-time tradeoff.
   For any v in  [1,&nradic;], it runs in O(vn) time using O(n/&vradic;) space
   in addition to the input string & the suffix array. We also present variants
   of the alg for several parallel & hierarchical memory models of comp'n. The
   algs for BSP & EREW-PRAM models are asymptotically faster than all previous
   s.tree or array constr. algs." (version of conf. paper)
   -- [<A HREF="http://doi.acm.org/10.1145/1217856.1217858">doi:/10.1145/1217856.1217858</A>]['09],
   auth1@[<A HREF="http://www.cs.helsinki.fi/u/tpkarkka/">helsin...</A>]['09],
   also see a conf paper (without B.) in '03.
   [Also search for: suffix array linear time].

%A P. Ferragina
%A R. Giancarlo
%A G. Manzini
%T The myriad virtues of wavelet trees
%J Proc. 33rd Int. Colloquium on Automata and Languages (ICALP)
%I Springerverlag
%S LNCS
%N 4051
%P 561-572
%D 2006
%O Info. & Comp'n, 207(8), pp.849-866, Aug. 2009.
%K conf, ICALP, c2006, c200x, c20xx, string, strings, sequence, wavelet tree,
   trees, compressed index, FM
%X "Wavelet Trees have been introduced by Grossi et al. in SoDA03 ...
   ... compressed full-text indexes & data compression algs.. Although several
   papers have investigated the properties & usefulness of this data struct. ...
   its impact on data compression has not been fully explored. ... we provide a
   throughout theoretical analysis of a wide class of compression algs. based on
   WTs. ... propose a novel framework, called Pruned Wavelet Trees, that aims
   for the best combination of WTs of properly-designed shapes & compressors
   either binary (~ Run-Length encoders) or non-binary (~ Huffman & Arithmetic
   encoders)."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ic.2008.12.010">I+C</A>]['09],
   conf paper pdf@[<A HREF="http://web.unipmn.it/~manzini/papers/icalp06.pdf">unipmn.it</A>]['09].

%A A. S. Konagurthu
%A P. J. Stuckey
%T Optimal sum-of-pairs multiple sequence alignment using incremental Carrillo
   and Lipman bounds
%J J. of Computational Biology
%V 13
%N 3
%P 668-685
%M APR
%D 2006
%K jrnl, MolBio, c2006, c200x, c20xx, ArunK, multiple sequence alignment,
   strings, projection, projections, Carrillo, Lipman, bound, bounded
%X "... we generalize Carrillo & Lipman bounds & demonstrate a novel approach
   for finding optimal sum-of-pairs multiple alignments that allows incremental
   pruning of the optimal alignment search space. ... can result in a drastic
   pruning of the final search space polytope (where we search for the optimal
   alignment) when compared to C. & L.'s approach & hence allows many runs that
   are not feasible with the original method."
   pdf@[<A HREF=""http://dx.doi.org/10.1089/cmb.2006.13.668">doi:10.1089/cmb.2006.13.668</A>]['09],
   abs@[<A HREF="http://www.ncbi.nlm.nih.gov/pubmed/16706718">ncbi</A>]['09].
   [Also search for: multiple sequence alignment MolBio].

%A J. Kornblum
%T Identifying almost identical files using context triggered piecewise hashing
%J Digital Investigation
%V 3
%P 91-97
%M SEP
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0514, ssdeep, approximate, hash, hashing, CTPH,
   neighbourhood, context triggered, similar, file, match, matching, fuzzy
%X "Homologous files share identical sets of bits in the same order. Because
   such files are not completely identical, trad. techniques such as
   cryptographic hashing cannot be used to identify them. ... introduces a new
   technique for constructing hash signatures by combining a # of trad. hashes
   whose boundaries are determined by the context of the input. These sigs. can
   be used to identify modified versions of known files even if data has been
   inserted, modified, or deleted in the new files. The descn ... is followed by
   a brief analysis of its performance & some sample applns to comp. forensics."
   -- [<A HREF="http://dx.doi.org/10.1016/j.diin.2006.06.015">doi:10.1016/j.diin.2006.06.015</A>]['14],
      ssdeep@[<A HREF="http://ssdeep.sourceforge.net/">s'rcef'rge</A>]['14].
   [Also search for: hashing neighbourhood] and
   [also search for: approximate indexing].

%A S. Foret
%A M. R. Kantorovitz
%A C. J Burden
%T Asymptotic behaviour and optimal word size for exact and
   approximate word matches between random sequences
%J BMC Bioinformatics
%V 7 (suppl 5):S21
%M DEC
%D 2006
%O APBioNet - 5th Int. Conf. on Bioinformatics (InCoB2006)
%K proc, conf, MolBio, c2006, c200x, c20xx, k words, kWords, word, D2 statistic,
   probability distribution, match, matches, sequence, ANuni, ANU, Sylvain Foret
%X "The number of k-words shared between two sequences is a simple & efficient
   alignment-free sequence comparison method. This statistic, D2, ...  We have
   computed the D2 optimal word size for various sequence lengths, & for both
   perfect & approx. word matches. Kolmogorov-Smirnov tests show D2 to have a
   compound Poisson distribution at the optimal word size for small seq. lengths
   (< 400) & a normal distribution at the optimal word size for large seq.
   lengths ( > 1600). We find that the D2 statistic outperforms BLAST in the
   comparison of artificially evolved seqs., & performs similarly to other
   methods based on exact word matches. These results obtained with randomly
   generated seqs. are also valid for seqs. derived from human genomic DNA...."
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-7-S5-S21">doi:10.1186/1471-2105-7-S5-S21</A>]['07] auth1 and 3 @ CBIS MSI ANU c2007.

%A D. Okanohara
%A K. Sadakane
%T Practical entropy-compressed rank/select dictionary
%J Proc. Workshop on Algorithm Engineering and Experiments
%W New Orleans
%I SIAM
%P 60-70
%M JAN
%D 2007
%K wShop, ALENEX, ALENEX07, c2007, c200x, c20xx, zz0610, rank, select,
   compressed, succinct, data structure, esp, recrank, vcode, sdarray,
   ordered set, string, index, search
%X "... ordered set S ...  rank(x,S) = # elts in S <= x,
   select(i,s) get ith smallest elt in S ...
   propose 4 R/S dicts ... close to n H0(S) ..."
   -- pdf@[<A HREF="http://www.siam.org/proceedings/alenex/2007/alx07_006okanoharad2.pdf">siam</A>]['10].
   Also see [<A HREF="http://arxiv.org/abs/cs.DS/0610001">arXiv:cs/0610001v1</A>]['10].
   [Also search for: rank select data structure].

%A K. Katoh
%A H. Toh
%T PartTree: An algorithm to build an approximate tree from a large number of
   unaligned sequences
%J J. Bioinformatics
%V 23
%N 3
%P 372-374
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, phylogenetic, evolutionary, tree, trees,
   guide, PartTree, multiple sequence alignment, MSA, zz0207
%X "... To construct a multiple sequence alignment (MSA) of a large number
   (> ~10,000) seqs., the calc. of a guide tree with a complexity of O(N**2)
   to O(N**3), where N is the # of seqs., is the most time-consuming process.
   ...To overcome this limitation, we have developed an approx. alg., PartTree,
   to construct a guide tree with an avg. time complexity of O(N log N). ...
   ...can align ~60,000 seqs. in several minutes on a standard desktop computer.
   The loss of accuracy in MSA caused by this approximation was estimated to be
   several percent in benchmark tests using Pfam."
   -- [<A HREF="http://dx.doi.org/10.1093/bioinformatics/btl592">doi:10.1093/bioinformatics/btl592</A>]['07].

%A K.-B. Schumann
%A J. Stoye
%T An incomplex algorithm for fast suffix array construction
%J SPE
%V 37
%N 2
%P 309-329
%M MAR
%D 2007
%K jrnl, SPE, c2007, c200x, c20xx, string, strings, prefix
%X "... practical alg. for suffix array construction that consists of two
   easy-to-implement components. First it sorts the suffixes with respect to a
   fixed length prefix; then it refines each bucket of suffixes sharing the same
   prefix using the order of already sorted suffixes. Other suffix array
   construction algorithms follow more complex strategies. Moreover, we achieve
   a very fast construction for common strings as well as for worst case strings
   by enhancing our algorithm with further techniques."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.768">doi:10.1002/spe.768</A>]['07].

%A A. Bakalis
%A C. S. Iliopoulos1
%A C. Makris
%A S. Sioutas
%A E. Theodoridis
%A A. Tsakalidis
%A K. Tsichlas
%T Locating maximal multirepeats in multiple strings under various constraints
%J COMPJ
%V 50
%N 2
%P 178-185
%D 2007
%K COMPJ, jrnl, c2007, c200x, c20xx, zz0407, MolBio, bioinformatics, string,
   repeat, multirepeat, tandem array
%X "A multirepeat in a string is a substring (factor) that appears a predefined
   # of times. A multirepeat is maximal if it cannot be extended either to the
   right or to the left & produce a multirepeat. ...present algs for 2 different
   versions of the problem of finding maximal multirepeats in a set of strings.
   In the case of arbitrary gaps, we propose an algorithm with
   O(sigma N**2 n + alpha) time complexity. When the gap is bounded in a small
   range c, we propose an alg. with O((c**2 + sigma**2)m N**2 n log(Nn) + alpha)
   time complexity. Here, N is the # of strings, n the mean length of each
   string, m the multiplicity of the multirepeat & alpha the # of reported
   occurrences. ... extend previous work by considering sets of strings as well
   as by generalizing pairs to multirepeats."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxl058">doi:10.1093/comjnl/bxl058</A>]['07].

%A K.-S. Huang
%A C.-B. Yang
%A K.-T. Tseng
%A Y.-H. Peng
%A H.-Y. Ann
%T Dynamic programming algorithms for the mosaic longest common subsequence
%J IPL
%V 102
%N 1-2
%P 99-103
%M APR
%D 2007
%K jrnl, IPL, c2007, c200x, c20xx, zz0908, mosaic, LCS, LCSS, MLCS, algorithm
%X "... For finding the relationship between 1 seq. & a set of seqs., we cannot
   apply the traditional LCS algs. immediately. ... define the mosaic LCS (MLCS)
   problem of finding a mosaic seq. C, composed of repeatable k seqs. in source
   seq. set S, such that the LCS of C & the target seq. T is maximal. Based on
   the concept of break points in seq. T, we first propose a divide-and-conquer
   alg. with O(n^2 m|S|+n^3 log k) time for solving this problem, where n & m
   are the len. of T & the maximal len. of seqs. in S, respectively. Furthermore
   an improved alg. with O(n(m+k)|S|) time is proposed by applying an efficient
   preprocessing for the MLCS problem."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2006.11.006">doi:10.1016/j.ipl.2006.11.006</A>]['08].

%A J. Ronnblom
%T High-error approximate dictionary search using estimate hash comparisons
%J SPE
%V 37
%N 10
%P 1047-1059
%M JUL
%D 2007
%K jrnl, SPE, c2007, c200x, c20xx, zz0807, edit distance, approximate, indexing,
   string matching, strings, dictionary, hash, hashing, neighbourhood,
   k mismatch, mismatches, difference, differences, comparison
%X "...finding all matches in a pre-processed dictionary for a query string q
   & with at most k differences ... . A very fast constant-time estimate using
   hashes is presented. A tree structure is used to minimize the # of estimates
   made. [test show] the estimate can filter out 99% of the full comparisons for
   40% error rates & dictionaries of up to 4 million words. The tree is found to
   be efficient up to a 50% error rate."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.797">doi:10.1002/spe.797</A>]['07]
   [Also search for: approximate indexing]  and
   [also search for: hashing neighbourhood].

%A G. Chen
%A S. J. Puglisi
%A W. F. Smyth
%T Fast & practical algorithms for computing all the runs in a string
%J Proc. 18th Annual Symp. on Combinatorial Pattern Matching
%P 307-315
%D 2007
%K conf, CPM, CPM07, c2007, c200x, c20xx, MolBio, string, strings, run, runs,
   will, bill
%X auth2@rmit ['08].
   -- [<A HREF="http://www.cas.mcmaster.ca/~bill/">auth3</A>]['08] & sometimes Curtin.

%A M. Farach-Colton
%A G. M. Landau
%A S. C. Sahinalp
%A D. Tsur
%T Optimal spaced seeds for faster approximate string matching
%J JCSS
%V 73
%N 7
%P 1035-1044
%M NOV
%D 2007
%K jrnl, JCSS, c2007, c200x, c20xx, gapped, spaced, seed, seeds, indexing,
   mismatch, mismatches, approximate, similar, strings
%X "... In filtering, a quick 1st step is used to rule out almost all posns of a
   text as possible starting posns for a pattern. [eg] finding the exact matches
   of small parts of the pattern. [then] a slow method is used to verify or
   eliminate each remaining posn. ... spaced seed is a recently introduced type
   of filter pattern that allows ...do not cares in the small sub-pattern to be
   searched for. Spaced seeds promise to yield a much lower false +ve rate, ...
   extensively studied [but] only heuristically or statistically. ... show how
   to design almost optimal spaced seeds that yield no false -ves."
   -- [<A HREF="http://dx.doi.org/10.1016/j.jcss.2007.03.007">doi:/10.1016/j.jcss.2007.03.007</A>]['08].
   [Also search for: spaced seed].

%A J. Karkkainen
%T Fast BWT in small space by blockwise suffix sorting
%J Theor. Comput. Sci.
%V 387
%N 3
%P 249-257
%M NOV
%D 2007
%K jrnl, TCS, c2007, c200x, c20xx, Burrows Wheeler transform, BW, BWT,
   algorithm, block, blocks, sort, string, strings, text
%X "... new space- and time-efficient alg. for computing the [BWT]. For any
   choice of a parameter v@?[3,n^2^/^3], the computation of BWT for a text of
   length n takes O(nlogn+vn) worst-case time & O(nlogn+vn) average-case time
   using O(nlogn/v) bits of space in addition to the text & the BWT. [E.g], if
   v=log^2n, the time is O(nlog^2n) in the worst case & O(nlogn) on an average
   with the additional space requirement of O(n) bits. The alg. is alphabet-
   -independent: it uses only character comparisons, & the complexities do not
   depend on the alphabet size unless v does. A practical implementation is 2-3
   times slower than one of the fastest & most space-efficient previous algs.
   while needing only 1/3 of the main memory. ... based on suffix arrays, but
   unlike any other alg., it can construct the suffix array a small block at a
   time without storing the rest of the suffix array anywhere."
   -- [<A HREF="http://dx.doi.org/10.1016/j.tcs.2007.07.018">doi:10.1016/j.tcs.2007.07.018</A>],
   auth@[<A HREF="http://www.cs.helsinki.fi/u/tpkarkka/">helsin...</A>]['09].

%A G. Navarro
%A V. Makinen
%T Compressed full-text indexes
%J ACM Comp. Surveys
%V 39
%N 1
%P Article 2
%D 2007
%K jrnl, c2007, c200x, c20xx, text, string, strings, self index, indexing,
   search, searching, compressed, survey, intro
%X "... fast substring search over large text collections. ... space
   consumption. ... [now] function of the compressed text length. ... evolved
   into self-indexes, which in addition contain enough information to reproduce
   any text portion, so they replace the text.  ... nowadays are able to obtain
   almost optimal space and search time simultaneously.  ... present the main
   concepts ... Then we cover the most relevant self-indexes ..."
   -- [<A HREF="http://doi.acm.org/10.1145/1216370.1216372">doi:10.1145/1216370.1216372</A>]['09],
      [<A HREF="http://www.cs.helsinki.fi/u/vmakinen/papers/survey.pdf">preprint</A>]['09].
   [Also search for: compressed index].

%A P. Ferragina
%A G. Manzini
%A V. Makinen
%A G. Navarro
%T Compressed representations of sequences and full-text indexes
%J ACM Trans. on Algorithms
%V 3
%N 2
%P (article 20)
%M MAY
%D 2007
%K jrnl, TALG, ToA, c2007, c200x, c20xx, representation, sequence, string,
   strings, index, indexing, compressed, text, search, searching, BW, BWT,
   FM index, FMindex
%X "... seq. S = s1s2 ... sn of ints, < r = O(polylog(n)), we show how S can
   be rep. using n.H[0](S)+o(n) bits, so that we can know any s[q], as well as
   answer rank & select queries on S, in const.time. H0(S) is the 0-order
   empirical entropy of S & n.H[0](S) provides an info.-theor. lwb to the bit
   storage of any S via a fixed enc. of its symbols. This extends prev. res. on
   binary seqs., & improves prev. res. on general seqs. where those queries are
   answered in O(log r) time. For larger r, we can still represent S in
   n.H[0](S)+o(n log r) bits & answer queries in O(log r/log log n) time.
   ... combine our compressed rep. of int. seqs. with a compression boosting
   techn. to design compressed full-text indexes that scale well with the size
   of the input alphabet Sigma. ...design a variant of the FM-index that indexes
   a string T[1, n] within n.H[k](T)+o(n) bits, where Hk(T) is the kth-order...
   This space bound holds simultaneously for all k <= alpha log|Sigma| n,
   const. 0 < alpha < 1, & |Sigma| = O(polylog(n)). This index counts the
   occurrences of an arb. patt. P[1,p] as a substring of T in O(p) time; it
   locates each pattern occurrence in O(log**(1+eps) n) time for any const.
   0 < eps < 1, & reports a text substr. of len. l in O(l+log**(1+eps) n) time.
   [c.f.] previous works, our index is the 1st that removes the alphabet-size
   dependance from all query times, in particular counting time is linear in the
   pattern length. Still, our index uses essentially the same space of the
   kth-order entropy of the text T, which is the best space obtained in previous
   work. We can also handle larger alphabets of size |Sigma| = O(n**beta), for
   any 0 < beta < 1, by paying o(n log|Sigma|) extra space & multiplying all
   query times by O(log|Sigma|/log log n)."
   -- [<A HREF="http://doi.acm.org/10.1145/1240233.1240243">doi:10.1145/1240233.1240243</A>]['08],
      [<A HREF="http://www.cs.helsinki.fi/u/vmakinen/papers/talg07.pdf">preprint</A>]['09].
   auth4@[<A HREF="http://www.cs.helsinki.fi/u/vmakinen/">helsink'</A>]['09].
   [Also search for: compressed index].

%A S. Lee
%A K. Park
%T Dynamic rank-select structures with applications to run-length encoded texts
%J 18th Annual Symp. on Combinatorial Pattern Matching (CPM)
%I SpringerVerlag
%S LNCS
%V 4580
%P 95-106
%M JUL
%D 2007
%K conf, CPM, c2007, c200x, c20xx, string, strings, sequence, text, BWT,
   dynamic rank select structure, DRS, dictionary, DRSD, DRSS, compressed index
%X |text|=n, |alphabet|=sigma "propose dynamic rank-select struct. that supports
   O((1+log sigma/log log n) log n)-time operations in n log sigma space.
 * If sigma < log n, then the operation time is O(log n). [And] consider both
   static & dynamic rank-select structures on the run-length encoding (RLE) of
   a text. For an n'-length RLE of an n-length text, we present a static struct.
   that gives O(1)-time select and O(log log sigma)-time rank using
   n' log sigma + O(n) bits and a dynamic struct. that provides
   O((1 + log sigma / log log n) log n)-time ops. in
   n' log sigma + o(n' log sigma) + O(n) bits."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-73437-6_12">doi:10.1007/978-3-540-73437-6_12</A>]['09],
   .ppt@[<A HREF="http://www.cs.ucr.edu/~stelo/cpm/cpm07/dynamic_rank_select_lee.ppt">cpm07</A>]['09].
     . rank(T,c,i)   returns # of 'c's in T[0..i];
     . select(T,c,k) returns pos'n of the kth 'c';
     . insert(T,c,i) inserts a 'c' between T[i] and T[i+1];
     . delete(T,i)   deletes T[i].
   [Also search for: dynamic compressed index].

%A N. J. Larsson
%A K. Sadakane
%T Faster suffix sorting
%J Theor. Comp. Sci.
%V 387
%N 3
%P 258-272
%M NOV
%D 2007
%O TR LU-CS-TR:99-214, Lund Uni., '99
%K jrnl, TCS, c2007, c200x, c20xx, strings, string, suffix, sort, sorting,
   array, fast, faster, time complexity, space, work
%X "... fast & memory-efficient alg. for lexicographically sorting the suffixes
   of a string, ...  eliminates much of the overhead of previous specialized
   approaches while maintaining their robustness for degenerate inputs. For
   input size n, our alg. operates in only 2 integer arrays of size n, & has
   worst-case time complexity O(n log n). ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.tcs.2007.07.017">doi:10.1016/j.tcs.2007.07.017</A>]['09],
   TR pdf@[<A HREF="http://www.larsson.dogma.net/ssrev-tr.pdf">dogma.net</A>]['09].
   [Also search for: suffix array time complexity].

%A J. Berstel
%A D. Perrin
%T The origins of combinatorics on words
%J Euro. J. of Combinatorics
%V 28
%N 3
%P 996-1022
%M APR
%D 2007
%K jrnl, c2007, c200x, c20xx, history, survey, intro, combinatorics, word,
   problems, words, strings, Maths, square free, Sturmian, necklace, Lyndon,
   LyndonWord, factors, de Bruijn, deBruijn
%X "We investigate the historical roots of the field of combinatorics on words.
   They comprise applications & interpretations in algebra, geometry &
   combinatorial enumeration. These considerations gave rise to early results
   such as those of Axel Thue at the beginning of the 20th C.. Other early
   results were obtained as a by-product of investigations on various
   combinatorial objects. For example, paths in graphs are encoded by words in
   a natural way, & conversely, the Cayley graph of a group or a semigroup
   encodes words by paths. We give in this text an account of this two-sided
   interaction."  [144 refs].
   -- [<A HREF="http://dx.doi.org/10.1016/j.ejc.2005.07.019">doi:10.1016/j.ejc.2005.07.019</A>]['11].

%A W.-K. Hon
%A T.-W. Lam
%A K. Sadakane
%A W.-K. Sung
%A S.-M. Yiu
%T A space and time efficient algorithm for constructing compressed suffix
   arrays
%J Algorithmica
%V 48
%N 1
%P 23-36
%M MAY
%D 2007
%K jrnl, MolBio, c2007, c200x, c20xx, suffix array, BWT, compressed index,
   space, time, complexity, incremental, string, strings, text
%X "... [here] study of constructing compressed suffix arrays directly from the
   text. ... construction alg. that uses only O(n) bits of working memory, & the
   time complexity is O(n log n). ... alg. is also time & space efficient for
   texts with large alphabets such as Chinese or Japanese. ... when the alphabet
   size is |S|, the working space is O(n log |S|) bits, & the time complexity
   remains O(n log n), which is indep. of |S|."
   -- [<A HREF="http://dx.doi.org/10.1007/s00453-006-1228-8">doi:10.1007/s00453-006-1228-8</A>]['09],
   -- pdf@[<A HREF="http://www.cs.nthu.edu.tw/~wkhon/papers/HLSSY05.pdf">nthu.edu.tw</A>]['09],
   -- [<A HREF="http://www.cs.nthu.edu.tw/~wkhon/">auth1</A>]['09].
   Batch incremental, right-to-left.    [Also search for: compressed index].

%A J. Gramm
%A A. Nickelsen
%A T. Tantau
%T Fixed-parameter algorithms in phylogenetics
%J COMPJ
%V 51
%N 1
%P 79-101
%M JAN
%D 2008
%K jrnl, COMPJ, MolBio, c2008, c200x, c20xx, evolutionary, phylogenetic,
   tree, trees, phylogeny, algorithm, FPT, fixed parameter
%X "...fixed-parameter algs. in ... phylogenetics ... . ... the reconstruction
   of the evolutionary history of biological species, but its methods also apply
   to linguistics, philology or architecture. A basic computational problem is
   the reconstruction of a likely phylogeny (genealogical tree) for a set of
   species based on observed differences in the phenotype like color or form of
   limbs, based on differences in the genotype like mutated nucleotide positions
   in the DNA seq., or based on given partial phylogenies. Ideally, one would
   like to construct so called perfect phylogenies, which arise from a very
   simple evolutionary model, but in practice one must often be content with
   phylogenies whose 'distance from perfection' is as small as possible. The
   computation of phylogenies has applications in seemingly unrelated areas such
   as genomic sequencing & finding & understanding genes. The numerous comp.
   problems arising in phylogenetics often are NP-complete, but for many natural
   parametrizations they can be solved using fixed-parameter algs.."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxm049">doi:10.1093/comjnl/bxm049</A>]['08]  [80 refs].

%A J. Karkkainen
%A T. Rantala
%T Engineering radix sort for strings
%J Proc. of the 15th Int. Symp. on String Processing and Info. Retrieval
%I SpringerVerlag
%S LNCS
%V 5280
%P 3-14
%D 2008
%K conf, c2008, c200x, c20xx, zz0409, radix sort, sorting, strings,
   cache conscious
%X "We describe new implementations of MSD radix sort for efficiently sorting
   large collections of strings. ... significantly faster than previous MSD
   radix sort implementations, & in fact faster than any other string sorting
   alg. on several data sets. We also describe a new variant that achieves high
   space-efficiency at a small additional cost on runtime."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-89097-3_3">doi:10.1007/978-3-540-89097-3_3</A>]['09].
   [Also search for: engineering radix sort] and
   [also search for: sort cache conscious].

%A M. Crochemore
%A L. Ilie
%T Computing longest previous factor in linear time and applications
%J IPL
%V 106
%N 2
%P 75-80
%M APR
%D 2008
%K jrnl, IPL, c2008, c200x, c20xx, zz1009, string, strings, sequence,
   longest, previous, factor, LPF, factors, substring
%X "... 2 optimal linear-time algs. for computing the Longest Previous
   Factor (LPF) array corr.to a string w. For any posn i in w, LPF[i] gives the
   length of the longest factor of w starting at position i that occurs
   previously in w. ... properties & applics. of LPF are investigated ... inc.
   computing the Lempel-Ziv factorization of a string & detecting all
   repetitions (runs) in a string in linear time indep.of ... alphabet size."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2007.10.006">doi:10.1016/j.ipl.2007.10.006</A>]['09],
   pdf@[<A HREF="http://www.csd.uwo.ca/faculty/ilie/IPL07.pdf">uwo.ca</A>]['09].
   [Also search for: longest previous factor].

%A M. A. Maniscalco
%A S. J. Puglisi
%T An efficient, versatile approach to suffix sorting
%J ACM J. of Experimental Algorithmics
%V 12
%P Article 1.2
%M JUN
%D 2008
%K jrnl, c2008, c200x, c20xx, algorithm, suffix, array, arrays, sort, search,
   string, strings, BW indexing
%X "Sorting the suffixes of a string into lex. order ... . Most approaches ...
   produce a sorted array of s. directly, continually moving s. into their
   final place in the array until the ordering is complete. ... we describe a
   novel & resource-efficient (time & memory) approach to suffix sorting, which
   works in a complementary way - by assigning each s. its rank in the final
   ordering, before converting to a sorted array, if nec., once all s. are
   ranked. We layer several powerful extensions on this basic idea & show
   experimentally that our approach is superior to other leading algs. in a
   variety of real-world contexts."
   -- [<A HREF="http://doi.acm.org/10.1145/1227161.1278374">doi:10.1145/1227161.1278374</A>],
   auth2@[<A HREF="http://goanna.cs.rmit.edu.au/~sjp/">rmit</A>]['09].

%A D. Marx
%T Closest substring problems with small distances
%J SIAM J. Comput.
%V 38
%N 4
%P 1382-1410
%M AUG
%D 2008
%K jrnl, c2008, c200x, c20xx, string, strings, substrings, CS, problem,
   distance, consensus pattern, parameterized complexity
%O 46th IEEE Symp. on Foundations of Computer Science (FOCS'05), pp.63-72
%X "... two pattern matching problems that are motivated by applications in
   computational biology. In the Closest Substring problem k strings s_1,...,
   s_k  are given, & the task is to find a string s of length L such that each
   string s_i has a consecutive substring of length L whose distance is at most
   d from s. We present 2 algs. that aim to be efficient for small fixed values
   of d & k: for some functions f & g, the algs. have running time
   f(d).n^O(log d) and g(d,k).n^O(log log k), resp.. The 2nd alg. is based on
   connections with the extremal combinatorics of hypergraphs. The Closest
   Substring problem is also investigated from the parameterized complexity
   point of view. ... "
   -- [<A HREF="http://dx.doi.org/10.1137/060673898">doi:10.1137/060673898</A>]['08],
   (and [<A HREF="http://doi.ieeecomputersociety.org/10.1109/SFCS.2005.70">FOCS version</A>]['05]).

%A R. Sinha
%A A. Wirth
%T Engineering Burstsort: Towards fast in-place string sorting
%J 7th Int. Workshop WEA 2008
%P 14-27
%D 2008
%K wShop, c2008, c200x, c20xx, burst sort, burstsort, strings, sort, sorting,
   algorithm
%X "Burstsort ... distributes strings into small buckets whose contents are
   then sorted in cache. ... introduce improvements that reduce by a sig.margin
   the memory requirements of burstsort. ... now less than 1% > than an in-place
   alg.. ... Significantly, the overall impact on the speed of b.s. by combining
   these memory usage improvements is not unfavourable on real-world string
   collections. [and] during the bucket-sorting phase, the string suffixes are
   copied to a small buffer to improve their spatial locality, lowering the
   running time of burstsort by up to 30%."                 (auths@unimelb)
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-68552-4_2">doi:10.1007/978-3-540-68552-4_2</A>]['09].

%A H. Hyyro
%T Improving the bit-parallel NFA of Baeza-Yates and Navarro for approximate
   string matching
%J IPL
%V 108
%N 5
%P 313-319
%M NOV
%D 2008
%K jrnl, IPL, c2008, c200x, c20xx, string, strings, search, searching, BPD,
   approximate, k mismatch, mismatches, errors, matching, bit, bits
%X "... new variant of the bit-parallel NFA of Baeza-Yates & Navarro (BPD) for
   approx. str. matching. ... BPD is one of the most practical approx. str.
   m. algs. under moderate pattern lengths and error levels ... Given a
   length-m pattern & an error threshold k ... BPD requires (m-k)(k+2) bits of
   space to rep. an NFA with (m-k)(k+1) states. [here] remove redundancy from
   the original NFA representation ... requires (m-k)(k+1) bits of space ...
   optimal in the sense that exactly 1 bit/state ... achieved by using an
   alt. ... simulation alg. for the bit-parallel NFA. ...  new variant is more
   efficient than the original BPD ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2008.05.026">doi:10.1016/j.ipl.2008.05.026</A>]['08].

%A J. Siren
%A N. Valimaki
%A V. Makinen
%A G. Navarro
%T Run-length compressed indexes are superior for highly repetitive sequence
   collections
%J Proc. 15th Symp. on String Processing and Information Retrieval
%I SpringerVerlag
%S LNCS
%V 5280
%P 164-175
%M NOV
%D 2008
%K conf, SPIRE, SPIRE08, c2008, c200x, c20xx, text, string, strings, index,
   compressed, self, indexing, search, collection
%X "A repetitive seq. coll'n is one where portions of a base seq. of length n
   are repeated many times with small variations, ... total length N. Examples
   of such collections are version control data & genome seqs. of individuals,
   ... ways to store massive sets of highly repetitive seq.coll'ns in space-
   -efficient manner so that retrieval ... time-efficiently. We show that the
   state-of-the-art entropy-bound full-text self-indexes do not yet provide
   satisfactory space bounds for this specific task. We engineer some new
   structures that use run-length encoding & give empirical evidence that these
   structures are superior to the current structures. "
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-89097-3_17">doi:10.1007/978-3-540-89097-3_17</A>]['09].
   auth3@[<A HREF="http://www.cs.helsinki.fi/u/vmakinen/">helsink'</A>]['09].
   [Also search for: compressed index].

%A D. Okanohara
%A K. Sadakane
%T An online algorithm for finding the longest previous factors
%J 16th Annual European Symp. on Algorithms (ESA)
%I SpringerVerlag
%S LNCS
%V 5193/2008
%P 696-707
%M SEP
%D 2008
%K conf, ESA 16, ESA08, ESA16, c2008, c200x, c20xx, zz1009, algorithm, string,
   strings, sequence, factors, longest, previous, factor, LPF, last, substring,
   online, on line, incremental, BWT, prefix
%X "... novel alg. for finding the longest factors in a text, for which the
   working space ~ the history text size. ... [alg] online & exact; in that,
   unlike the prev. batch algs. which needs to read the entire input beforehand,
   our alg. reports the longest match just after reading each character. ... can
   be directly used for data compression, pattern analysis, & data mining. ...
   also supports the window buffer, in that we can bound the working space by
   discarding the history from the oldest char.. Using the dynamic rank/select
   dictionary, [we] require n log sigma + O(n log sigma)+O(n) bits of working
   space, & O(log**3 n) time/ char., O(n log**3 n) total time, n is the length
   of the history, and sigma is the alphabet size. ... compared it with the
   recent algs. ...  alg. can work with a smaller working space, < 1/2 of those
   for the prev. methods ... with a reasonable decline in speed." (via SJP '09).
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-540-87744-8_58">doi:10.1007/978-3-540-87744-8_58</A>]['09],
   pdf@[<A HREF="http://www-tsujii.is.s.u-tokyo.ac.jp/~hillbig/papers/esa2008_okanohara.pdf">u-tokyo.ac.jp</A>]['09],
   auth1@[<A HREF="http://www-tsujii.is.s.u-tokyo.ac.jp/members/wiki/wiki.cgi?page=Daisuke+Okanohara">u-tokyo.ac.jp</A>]['09].
     Keeps prefix-array, not suffix-a., Dynamic Rank Select Dictionary
     (DRSD, see DRSD c2007), Range Minimum Query (RMQ),
     (implicit) prefix-BWT (rev lex order),
   Longest Previous Factor: Given a history T[0,i-1] & next char T[i]=c,
     find the longest substring (factor) that occurs in the history,
     T[j,...,j+l-1]=T[i-l+1,...,i].
   [Also search for: longest previous factor].

%A P. Ferragina
%A T. Gagie
%A G. Manzini
%T Space-conscious data indexing and compression in a streaming model
%I Comp. Sci. Dept, Univ. Piemonte Orientale
%R TR-INF-2008-02-01-UNIPMN
%D 2008
%K TR, c2008, c200x, c20xx, string, strings, sequence, online, compressed index,
   stream, streaming
%X "... Surprisingly, algs. for building compressed indexes (or files) are
   space-ineff't &/or incompatible with a streaming setting. Space-conscious
   streaming algs. are crucial ... . For the 1st time ... we investigate string
   problems in the streaming model & prove upper & lower bounds on the
   complexity of building compressed indexes & compressing data in terms of the
   classic product: (internal memory space) x (number of passes)."
   -- pdf@[<A HREF="http://www.di.unipmn.it/TechnicalReports/TR-INF-2008-02-01-UNIPMN.pdf">unipmn.it</A>]['09] (via SJP '09).
   [Also search for: compressed index].

%A V. Makinen
%A G. Navarro
%T Dynamic entropy-compressed sequences and full-text indexes
%J ACM Trans. on Algorithms
%V 4
%N 3
%P ?-?
%D 2008
%K jrnl, TALG, c2008, c200x, c20xx, algorithm, text, sequence, string, strings,
   search, searching, self text, indexing, dictionary, compressed, index,
   dynamic, update
%X Article #32.
   "We give new solutions to the Searchable Partial Sums with Indels problem.
   Given a sequence of n k-bit numbers, we present a structure taking
   kn+o(kn) bits of space, able of performing operations sum, search, insert,
   and delete, all in O(log n) worst-case time, for any k = O(log n). ..."
   -- [<A HREF="http://www.cs.helsinki.fi/u/vmakinen/papers/talg08.pdf">preprint</A>]['09],
   or [<A HREF="http://doi.acm.org/10.1145/1367064.1367072">doi:10.1145/1367064.1367072</A>]['09]
   (at [<A HREF="http://portal.acm.org/browse_dl.cfm?linked=1&part=transaction&idx=J982&coll=portal&dl=ACM">TALG</A>]['09]).
   [Also search for: dynamic compressed index].

%A J. Y. Gil
%A D. A. Scott
%T A bijective string sorting transform
%I submitted
%M JUL
%D 2009
%K TR, c2009, c200x, c20xx, string, strings, text, BW, BWT, sort, transform,
   transformation, Kufleitner
%X "... [BWT] rearranges the characters in [a string] so as to produce another
   string of the same length which is more amenable to compression techniques
   such as [MTF], run-length encoding ...  present a variant of the transform
   which gives rise to similar or better comp'n value, but, unlike the original,
   ... is bijective, in that the inverse trans'n exists for all strings. Our
   experiments indicate that using our variant of the t. gives rise to better
   compression ratio than the original [BW]. We also show that both the
   transform & its inv. can be computed in linear time & ... lin.storage."
   -- pdf@[<A HREF="http://bijective.dogma.net/00yyy.pdf">dogma.net</A>]['09].
   [Also search for: BWT string] and
   [also search for: bijective string transform].

%A M. Salson
%A T. Lecroq
%A M. Leonard
%A L. Mouchard
%T A four-stage algorithm for updating a Burrows-Wheeler transform
%J TCS
%V ?
%N ?
%P ?-?
%D 2009
%O Stringology '08
%K jrnl, TCS, c2009, c200x, c20xx, zz0809, Burrows Wheeler transform, BWT,
   dynamic, edit, update, updating, modify, modifying, change, changing,
   compressed, index, string, strings, text
%X "... when this text is modified. The BWT is used by many text compression
   applications and ...  how standard edit operations (insertion, deletion,
   substitution of a letter or a factor) that transform a text T into T' impact
   bwt(T).  ... alg. that directly converts bwt(T) into bwt(T'). ... also sketch
   a method for converting the suffix array of T into the suffix array of T'.
   ... experiments ... this alg., whose worst-case time complexity is
   O(|T|log|T|(1+log sigma/loglog|T|)), performs really well in practice &
   replaces advantageously the traditional approach."  (online Aug '09.)
   -- [<A HREF="http://dx.doi.org/10.1016/j.tcs.2009.07.016">doi:10.1016/j.tcs.2009.07.016</A>]['09],
   pdf@[<A HREF="www-igm.univ-mlv.fr/~lecroq/articles/tcs2009.pdf">univ-mlv.fr</A>]['09],
   .ps.gz@[<A HREF="http://www.stringology.org/event/2008/psc08p02_ps.gz">stringology '08</A>]['09].
   [Also search for: dynamic compressed index].

%A M. Kufleitner
%T On bijective variants of the Burrows-Wheeler transform
%J arXiv
%D 2009
%K c2009, c200x, c20xx, variant, string, strings, sequence, text,
   Sort Transform, ST, inverse, bijective, Burrows Wheeler transform, BW, BWT
%X "The sort transform (ST) is a mod. of ...(BWT). Both transformations map an
   arb. word of length n to a pair consisting of a word of length n & an index
   between 1 & n. ... the ST of order k only uses the first k letters for
   sorting all such conjugates. If 2 conjugates start with the same prefix
   of length k, then the indices of the rotations are used for tie-breaking.
   Both transforms o/p the seq. of the last letters of the sorted list & the
   index of the input within the sorted list. ... discuss a bijective variant of
   the BWT (due to Scott), proving its correctness & reln to other results due
   to Gessel & Reutenauer ('93), & Crochemore, Desarmenien & Perrin ('05).
   Further, we present a novel bijective variant of the ST."
   -- pdf@[<A HREF="http://arxiv.org/abs/0908.0239">arXiv</A>][8/'09].
   [Also search for: BWT string], and
   [also search for: bijective string transform].

%A S. Deorowicz
%T Solving longest common subsequence and related problems on
   graphical processing units
%J SPE
%V 40
%N 8
%P 673-700
%M JUL
%D 2010
%K jrnl, SPE, c2010, c201x, c20xx, edit distance, longest common subsequence,
   LCS, LCSS, strings, string, sequence, unit, GPU, GpGPU, parallel
%X "Modern graphical processing units (GPUs) offer much more comp.power than
   modern [CPUs]. Therefore, it is natural that GPUs are applied not only for
   their original purposes, but also for general processing (GPGPU). ...
   ... examine the possibility of speeding up the algs. computing some of them.
   We chose three measures useful in different situations. The experimental
   results show that the GPU versions of the examined algs. are faster than
   their serial counterparts by a factor between 4 and 65"
   -- [<A HREF="http://dx.doi.org/10.1002/spe.976">doi:10.1002/spe.976</A>]['10].

%A R. Groulta
%A E. Prieurb
%A G. Richomme
%T Counting distinct palindromes in a word in linear time
%V 110
%N 20
%P 908-912
%M SEP
%D 2010
%K IPL, jrnl, c2010, c201x, c20xx, zz0810, palindrome, count, all, string,
   strings, palindromic richness, fullness, algorithm
%X "... alg. to count the # of distinct palindromes in a word w in time O(|w|),
   by adapting an alg. to detect all occurrences of maximal ps. in a given word
   & using the longest previous factor array. [So] this shows that the pal'ic
   richness (or fullness) of a word can be checked in linear time"
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2010.07.018">doi:10.1016/j.ipl.2010.07.018 </A>]['10].

%A M. Barsky
%A U. Stege
%A A. Thomo
%T A survey of practical algorithms for suffix tree construction in external
   memory
%J SPE
%V 40
%N 11
%P 965-988
%M OCT
%D 2010
%K jrnl, SPE, c2010, c201x, c20xx, zz1010, suffix tree, trees, survey,
   strings, string, index
%X "... suffix trees in secondary storage was considered impractical due to its
   excessive I/O cost. Algs. developed in the last decade show that a ST can
   efficiently be built in secondary storage for inputs which fit the main
   memory. ... we analyze the details of alg. approaches to the external memory
   ST construction & compare the performance & scalability of existing
   state-of-the-art s/w based on these algs.."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.960">doi:10.1002/spe.960</A>]['10].

%A M. Crochemore
%A G. Tischler
%T Computing longest previous non-overlapping factors
%J IPL
%V 111
%N 6
%P 291-295
%M FEB
%D 2011
%K jrnl, IPL, c2011, c201x, c20xx, zz0211, strings, string, longest previous,
   non-overlapping, nonoverlapping, factor, factors, LPnF, LPF
%X "The Longest Previous non-overlapping Factor table (LPnF) stores for each
   posn of a string the maximal length of factors occurring both there & in the
   preceding part of the string. The notion is a slight variant of the LPF table
   described before & used for text compression. The LPnF table is an essential
   elt for the design of efficient algs. on strings as it is related to a
   certain type of Ziv-Lempel factorisation used for this purpose.
   We show how to compute the LPnF table in linear time from the suffix array of
   the string when it is drawn from an integer alphabet. The alg. is a
   non-immediate extension of the LPF computation & it does not require any
   other sophisticated data struct. than the suffix array of the input string."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2010.12.005">doi:10.1016/j.ipl.2010.12.005</A>]['11].
   [Also search for: string factor].

%A C. Boucher
%A B. Ma
%T Closest string with outliers
%J BMC Bioinformatics
%V 12 (suppl.1)
%P i188-i196
%M FEB
%D 2011
%K jrnl, eJrnl, MolBio, c2011, c201x, c20xx, zz1012, CSWO, string, strings,
   sequence, centre, center, close, problem, outlier, small, distance, stats,
   representative
%X "Given n strings s1,...,sn each of length L & a nonneg. int. d, the CLOSEST
   STRING problem asks to find a center string s s.t. none of the input strings
   has Hamming dist. greater than d from s. Finding a common pattern in many
   -- but not necessarily all -- input strings is an important task that plays
   a role in many applications in bioinformatics.
   Although ... robust to the oversampling of strings in the input, it is
   severely affected by the existence of outliers. We propose a refined model,
   the CLOSEST STRING WITH OUTLIERS (CSWO) problem, ... asks for a center string
   s that is within Hamming dist. d to at least n-k of the n input strings,
   where k is a param. describing the max. # of outliers. ... provides the
   center string [and] reveals the outliers of the set.
   We provide fixed parameter algs. for CSWO when d & k are param., for both
   bounded & unbounded alphabets. ... show that when the alphabet is unbounded
   the problem is W[1]-hard wrt n-k, L, & d.  ..." [24 refs] [via TS].
   -- [<A HREF="http://dx.doi.org/10.1186/1471-2105-12-S1-S55">doi:10.1186/1471-2105-12-S1-S55</A>]['12],
   or [<A HREF="http://christinaboucher.com/research/publications/closest-string-with-outliers">www</A>]['12]
   at [<A HREF="http://christinaboucher.com/research/publications/">c'b'</A>]['12].
   [Also search for: stats outlier].

%A F. Petitjean
%A A. Ketterlin
%A P. Gancarski
%T A global averaging method for dynamic time warping, with applications to
   clustering
%J Pattern Recognition
%V 44
%N 3
%P 678-693
%M MAR
%D 2011
%K jrnl c2011, c201x, c20xx, zz2022, dynamic time warping, warp, warps,
   numerical, sequence averaging
%X "... the computation of an average of a set of seqs.. ... develop a global
   technique for averaging a set of seqs.. This technique is original in that it
   avoids using iterative pairwise averaging. It is thus insensitive to ordering
   effects. Second, we describe a new strategy to reduce the length of the
   resulting avg sequence. ..."
   Also see DTW@[<A HREF="https://en.wikipedia.org/wiki/Dynamic_time_warping">wikip</A>]['22].

%A S. Grabowski
%A S. Faro
%A E. Giaquinta
%T String matching with inversions and translocations in
   linear average time (most of the time)
%J IPL
%V 111
%N 11
%P 516-520
%M MAY
%D 2011
%K jrnl, IPL, c2011, c201x, c20xx, zz0511, strings, string, pattern, inversion,
   translocation
%X "... alg. for finding all approx. occurrences of a given pattern p of length
   m in a text t of length n allowing for translocations of equal length [???]
   adjacent factors and inversions of factors. ... based on an efficient
   filtering method & has an  O(nm max(alpha,beta))-time complexity in the
   worst case  & O(max(alpha,beta,sigma))-space complexity, where alpha & beta
   are resp. the max. length of the factors involved in any translocation &
   inversion, and sigma is the alphabet size. ... show that our alg. has an
   O(n)-avg.time complexity, whenever sigma=Omega(log m/log log^(1-eps) m), for
   eps > 0 ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2011.02.015">doi:10.1016/j.ipl.2011.02.015</A>]['11].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/">strings</A>].)

%A G. Fici
%T A classification of trapezoidal words
%J arXiv
%M AUG
%D 2011
%O 8th Int. Conf. WORDS 2011, EPTCS 63, 2011, pp. 129-137,
%K TR, c2011, c201x, c20xx, zz0922, closed string, strings, defn, trapezoidal,
   word, open, Sturmian, palindrome
%X "Trapezoidal words are finite words having at most n+1 distinct factors of
   length n, for every n >= 0. They encompass finite Sturmian words. We
   distinguish t.words into two disjoint subsets: open & closed t.words. A
   t.word is closed if its longest repeated prefix has exactly two occurrences
   in the word, the second one being a suffix of the word. Otherwise it is open.
   We show that open t.words are all primitive & that closed t.words are all
   Sturmian. We then show that t.palindromes are closed (& therefore Sturmian).
   This allows us to characterize the special factors of Sturmian palindromes.
   We end with several open problems."
   -- 1108.3629v1@[<A HREF="https://arxiv.org/abs/1108.3629v1">arXiv</A>]['22],
      [<A HREF="http://dx.doi.org/10.4204/EPTCS.63">doi:10.4204/EPTCS.63</A>]['22].
   [Also search for: closed string].

%A J.-J. Liu
%A W. C.-K. Yen
%A Y.-J. Chen
%T An optimal algorithm for untangling binary trees via rotations
%J COMPJ
%V 54
%N 11
%P 1838-1844
%M NOV
%D 2011
%K jrnl, COMPJ, c2011, c201x, c20xx, zz1111, rooted binary tree,
   distance, treeEdit, tree, edit, difference, rotate, rotation, untangle
%X "There are various ways to measure the shape diff. between two n-node rooted
   binary trees ... A rotation on a binary tree is a local restructuring that
   changes the tree into another one preserving the in-order seq.. The rotn
   distance between two binary trees is the min. # of rotns needed to transform
   one into another. Till now, no polynomial-time alg. exists ... . Recently,
   Lucas (Compj, 47, 259-269, '04) presented an O(n^2)-time alg. ... , where
   the source tree is a degenerate tree and the dest'n tree is an angle tree.
   This paper improves the time-complexity to O(n) under this constraint."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxr021">doi:10.1093/comjnl/bxr021</A>]['11].
   (NB. "under this constraint".)
   [Also search for: treeEdit distance].

%A S. Deorowicz
%T Quadratic-time algorithm for a string constrained LCS problem
%J IPL
%V 112
%N 11
%M 423-426
%M JUN
%D 2012
%K jrnl, IPL, c2012, c201x, c20xx, zz0612, CLCS, LCS, LCSS, STR-IC-LCS,
   strings, string, sequence
%X "... with some constraint that must be a substring of the result (STR-IC-LCS)
   was formulated recently ... a variant of the constrained longest common
   subseq. problem. As the known algs. for the STR-IC-LCS problem are
   cubic-time, [new] quadratic-time alg. is sig. faster."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2012.02.007">doi:10.1016/j.ipl.2012.02.007</A>]['12].
   (NB. P is a subSTRING of the lcs.)

%A Z. Duric
%A D. Gasevic
%T A source code similarity system for plagiarism detection
%J COMPJ
%V 56
%N 1
%P 70-86
%M JAN
%D 2013
%K jrnl, COMPJ, c2013, c201x, c20xx, zz0113, computer, program, source code,
   programs, similarity, plagiarism, copy, copying, cheating, comparison, JPlag
%X "... designed & developed the source code similarity system for plagiarism
   detection. ... that the proposed sys. has the desired effectiveness, we
   performed a well-known conformism test. ... showed promising results as
   compared with the JPlag system in detecting s.code similarity when various
   lexical or structural mods. are applied to plagiarized code. [And] an
   indep. samples t-test revealed that there was a stat.sig. difference between
   avg. values of F-measures for the test sets that we used & for the
   experiments that we have done in the practically usable range of cut-off
   threshold values of 35-70%."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxs018">doi:10.1093/comjnl/bxs018</A>]['13].

%A J. Kim
%A et al
%T Order preserving matching
%J arXiv
%M FEB
%D 2013
%O Theo Murphy Int. Sci. Mtg of the Royal Soc. on Storage & Indexing of
   Massive Data, Feb 2013
%K TR, c2013, c201x, c20xx, zz1022, Puglisi, string, order preserving matching,
   match, OPM, music, melody, stock price, numerical, numbers
%X "We introduce a new string matching problem called order-preserving matching
   on numeric strings where a pattern matches a text if the text contains a
   substring whose relative orders coincide with those of the pattern. ... stock
   price analysis & musical melody matching in which the order relations should
   be matched instead of the strings themselves. ... We define prefix repn &
   nearest neighbor repn, which lead to efficient algs. for [OPM]. ... efficient
   algs. for single & multiple pattern cases. For the single pattern case, we
   give an O(n log m) time alg. & optimize it further to obtain O(n+m log m)
   time. For the multiple pattern case, we give an O(n log m) time alg."
   -- 1302.4064@[<A HREF="https://arxiv.org/abs/1302.4064">arXiv</A>]['22].
   [Also search for: music match].

%A A. Amir
%A H. Paryenty
%A L. Roditty
%T On the hardness of the Consensus String problem
%J IPL
%V 113
%N 10-11
%P 371-374
%M MAY-JUN
%D 2013
%K jrnl, IPL, c2013, c201x, c20xx, zz0413, consensus string problem, strings,
   Hamming, swap metric, reversal metric
%X "... formally defined as follows: given a set of strings S={s1,...,,sk}
   & a const. d, find, if it exists, a string s* s.t. the dist. of s* from each
   of the strings does not exceed d. ... The stringology community researched
   this problem under the Hamming distance. In that metric the problem is
   NP-hard. A lot of work has been also done in the Euclidean metric. ...
   we consider the ... problem under other string metrics ... show that
   [it] is NP-hard for the swap metric & APX-hard for the reversal metric."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2013.02.016">doi:10.1016/j.ipl.2013.02.016</A>]['13].

%A E. Giaquinta
%A S. Grabowski
%A K. Fredriksson
%T Approximate pattern matching with k-mismatches in packed text
%J IPL
%V 113
%N 19-21
%P 693-697
%M SEP-OCT
%D 2013
%K jrnl, IPL, c2013, c201x, c20xx, string, strings, approximate matching,
   Hamming distance, mismatch, AC0, word RAM
%X "Given strings P [pattern] of length m & T of length n over an alphabet of
   size s, the ... problem is to find the posns of all the substrings in T that
   are at Hamming dist. <= k from P. If T can be read only one char. at the time
   the best known bds are O(n sqrt(k log k)) & O(n+n sqrt(k/(w log k))) in the
   word-RAM mdl with word len w. In the RAM models (inc. AC0AC0 & word-RAM) it
   is poss. to read up to floor(w/log s) chars in const.time if the chars of T
   are encoded using ceil(log s) bits. The only soln for k-m.m. in packed text
   works in O((nlog s / log n)ceil(m log(k+log n / log s)/w+n**eps) time, for
   any eps>0. We present an alg. that runs in time
   O(n/floor(w/(m log?)) (1+logmin(k, s)log m / log s)) in the AC0AC0 model if
   m=O(w/log s) & T is given packed. [&] a simpler variant that runs in time
   O(n/floor(w/(m log ?) logmin(m,log w / log s)) in the word-RAM model. The
   algs improve the existing bnd for w=Omega(log**(1+eps) n), for any eps>0.
   ... [&] algs for several other approx. m. problems."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2013.07.002">doi:10.1016/j.ipl.2013.07.002</A>]['13].
   [Also search for: string approximate matching].

%A S. Bonomo
%A S. Mantaci
%A A. Restivo
%A G. Rosone
%A M. Sciortino
%T Suffixes, conjugates and Lyndon words
%J Developments in Language Theory
%S LNCS
%V 7907
%P 131-142
%D 2013
%K conf, c2013, c201x, c20xx, Lyndon word, LyndonWord, string, strings, suffix,
   conjugate, array, factors, factorization, BWT, order
%X "... study of the comb. aspects connecting 3 important constructions in the
   field of string algs.: the suffix array, the Burrows-Wheeler transform (BWT)
   and the extended Burrows-Wheeler transform (EBWT). Such constructions involve
   the notions of suffixes and conjugates of words and are based on two
   different order relns, denoted by < lex and < omega, that, even if strictly
   connected, are quite different from the computational point of view. ...
   important role is played by Lyndon words. ... improve the upper bound on the
   # of symbol comparisons needed to establish the < omega order between two
   primitive words by using a preliminary knowledge of the < lex order of the
   corr. Lyndon conjugates. [&] propose an alg. that efficiently sorts,
   according to the < omega order, the list of conjugates of a multiset of
   L.words. Finally, we show that the L.factorization of a word helps the
   construction of its suffix array, allowing a reduction of the # of symbol
   comparisons needed to lexicographically sort the suffixes of the word."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-38771-5_13">doi:10.1007/978-3-642-38771-5_13</A>]['13].
   [Also search for: Lyndon word string].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/Factors/">Factors</A>].)

%A J. Dhaliwal
%T Faster semi-external suffix sorting
%J IPL
%V 114
%N 4
%P 174-178
%M APR
%D 2014
%K IPL, jrnl, c2014, c201x, c20xx, zz0214, string, strings, suffixes,
   sort, sorting, suffix array, construction
%X "Suffix array (SA) construction is a time-and-memory bottleneck in many
   string processing applications. ... improve the runtime of a small-space -
   semi-external -  SA constn alg. by Karkkainen (TCS, 2007). We achieve
   a speedup in practice of 2-4 times, without increasing memory usage. Our
   main contribution is a way to implement the 'pointer copying' heuristic,
   used in less space-efficient SA constn algs., in a memory-efficient way."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2013.11.017">doi:10.1016/j.ipl.2013.11.017</A>]['14].  (auth@RMIT)

%A A. Golovnev
%A A. S. Kulikov
%A I. Mihajlin
%T Solving SCS for bounded length strings in fewer than 2^n steps
%J IPL
%V 114
%N 8
%P 421-425
%M AUG
%D 2014
%K jrnl, IPL, c2014, c201x, c20xx, zz0514, shortest common superstring, problem,
   NPhard, algorithm, SCS, SCSS, string, strings, travelling, traveling salesman
%X "It is still not known whether a shortest common superstring (SCS) of n
   input strings can be found faster than in O*(2^n),  (O*(.) suppresses
   polynomial factors of the input length). ... we show that for any constant r,
   SCS for strings of len. <= r can be solved in time O*(2^((1-c(r))n))
   where c(r)=(1+2r2)^-1.  ... introduce so-called hierarchical graphs that
   allow us to reduce SCS on strings of length <= r to the directed rural
   postman problem on a graph with at most k=(1-c(r))n weakly connected
   components. One can then use a recent O*(2^k) time alg. by Gutin, Wahlstron
   & Yeo."  [24 refs.]
   "The main result is randomized 2^(n(1-Omega(r^-2)))-time alg for r-SCS."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2014.03.004">doi:10.1016/j.ipl.2014.03.004</A>]['14].

%A K. Shin
%T Tree edit distance and maximum agreement subtree
%J IPL
%V 115
%N 1
%P 69-73
%M SEP
%D 2014
%K jrnl, IPL, c2014, c201x, c20xx, zz1014, tree, edit distance, treeEdit, Tai,
   trees, maximum agreement subtree, MAST, forest, MASF, MAAST
%X "... reln between the Maximum Agreement Subtree (MAST) problem & the Tree
   Edit Dist. (TED) problem ... show that, for an arb. tree edit dist. metric
   that is a derivative of the Tai tree edit dist. metric, there exists a
   MAST-like pattern extraction problem, named Mostly Adjusted Sub-Forest (MASF)
   problem, s.t. computing a dist. between trees x & y is equiv. to finding an
   opt. pattern shared between x & y. The MASF problem is different from the
   MAST problem in: (1) A pattern of the MASF problem may be a forest instead of
   a tree; (2) Instead of requiring exact match of labels, a pattern of a MASF
   problem is multi-labeled, & our flexible matching rule only requires that the
   label set of a vertex of a pattern inc. the label of the corr. vertex in a
   target tree; (3) To control ambiguity of matching caused by the flexible
   rule, the objective fn includes a penalty fn. As an applicn of this generic
   framework, we equate the Lu* tree edit dist. metric with a pattern extraction
   problem, named the Mostly Adjusted Agreement Sub-Tree (MAAST) problem. The
   MAAST problem aims to find optimal agreement subtrees under the flexible
   matching rule & is solved in O(n^2 sqrt(d) log d)-time, where n & d are the
   size & the min. degree of the input trees. [MAST] requires O(n&2.5)-time ..."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2014.09.002">doi:10.1016/j.ipl.2014.09.002</A>]['14].
   [Also search for: treeEdit].

%A B. Saha
%T The Dyck language edit distance problem in near-linear time
%J IEEE
%M OCT
%D 2014
%K conf, c2014, c201x, c20xx, zz0223, string, strings, Dyck, grammar, CFG,
   language edit distance, algorithm, LEDistance
%X "Given a string s over alphabet S & a grammar G defined over the same
   alphabet, how many minimum # of repairs (insertions, deletions & subst'n) are
   required to map s into a valid member of G? ... Our main result is an alg.
   for edit distance comp'n to DYCK(s) for any +ve integer s that runs in
   O(n 1+e polylog(n)) time & achieves an approximation factor of
   O(1/eb(n) log |OPT|), for any e>0. ... b(n) is the best approx'n factor known
   for the simpler problem of stringED ..."
   -- [<A HREF="https://doi.org/10.1109/FOCS.2014.71">doi:10.1109/FOCS.2014.71</A>]['23].
   Also see, "... Language edit distance, ..."
   -- ED@[<A HREF="https://en.wikipedia.org/wiki/Edit_distance">wikip</A>]['23].

%A S. Gog
%A M. Petri
%T Optimized succinct data structures for massive data
%J SPE
%V 44
%N 11
%P 1287-1314
%M NOV
%D 2014
%K jrnl, SPE, c2014, c201x, c2011, zz1114, data structure, dataStructure, DS,
   FM index, FMindex, rank, select, bitVector, cache, bigData
%X "... present a cache-optimal, uncompressed bitvector representation that
   outperforms all existing approaches. Next, we improve, in both space &
   time, on a recent result by Navarro & Providel on compressed bitvectors.
   Last, we show techniques to perform rank & select on 64-bit words that are
   up to 3x faster than existing methods. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.2198">doi:10.1002/spe.2198</A>]['14].
   [Also search for: FMindex].

%A C. Boucher
%A A. Bowe
%A T. Gagie
%A S. J. Puglisi
%A K. Sadakane
%T Variable-order de Bruijn graphs
%J arXiv
%M NOV
%D 2014
%K arXiv, TR, c2014, c201x, c20xx, zz1114, maths, graph, deBruijn, deBruijn,
   variable order, sequence assembly
%X "... represents overlaps between all the K-length substrings of S.
   Construction & navigation of the graph is a space & time bottleneck in
   practice & the main hurdle for assembling large, eukaryote genomes. This
   problem is compounded by the fact that state-of-the-art assemblers do not
   build the ... graph for a single order ... but for multiple values of K.
   ... i.e., GK1, GK2, ..., GKd. ... increases the quality of the assembly
   produced, it increases the memory by a factor of d in most cases. ...  we
   show how to augment a succinct de Bruijn graph repn by Bowe et al. (Proc.
   WABI, 2012) to support new operations that let us change order on the fly,
   effectively representing all de Bruijn graphs of order up to some max. K in
   a single data struct.. Our experiments show our [method] only modestly
   increases space usage, construction time, & navigation time [v.] a single
   order graph."
   -- 1411.2718@[<A HREF="http://arxiv.org/abs/1411.2718">arXiv</A>]['14].
   [Also search for: sequence assembly MolBio].

%A C. Barton
%A A. Heliou
%A L. Mouchard
%A S. P. Pissis
%T Linear-time computation of minimal absent words using suffix array
%J BMC Bioinformatics
%V 15
%P e388
%M DEC
%D 2014
%K jrnl, MolBio, c2014, c201x, c20xx, zz1214, string, strings, word, words,
   absent, missing, substring, MAW, short, minimal, nullomer, factors,
   DNA, Crochemore, Pinho
%X "... minimal absent word if all its proper factors occur in y. Min.absent
   words have been computed in genomes of organisms from all domains of life;
   their comp. also provides a fast alt. for measuring approx. in seq.
   comparison. There exists an O(n)-time & O(n)-space algs. for comp. all min.
   absent words on a fixed-sized alphabet based on the construction of suffix
   automata (Crochemore et al., 1998). No implementation of this alg. is
   pub.available. There also exists an O(n2)-time & O(n)-space alg. for the
   same problem based on the constn of suffix arrays (Pinho et al., 2009). An
   implementation of this alg. was also provided by the authors & is currently
   the fastest available. ... first, we bridge this unpleasant gap by presenting
   an O(n)-time & O(n)-space alg. ... based on the construction of suffix
   arrays; & second, we provide the respective implementation of this alg..
   Exp.results, using real & synthetic data, show that this impln outperforms
   the one by Pinho et al. The open-source code ... is ... at
   [<A HREF="http://github.com/solonas13/maw">github</A>]['14]. ..."
   -- [<A HREF="http://dx.doi.org/10.1186/s12859-014-0388-9">doi:10.1186/s12859-014-0388-9</A>]['14].
   [Also search for: missing substring]  and [also search for: nullomer].

%A J.-J. Liu
%A Y.-L. Wang
%A Y.-S. Chiu
%T Constrained longest common subsequences with run-length-encoded strings
%J COMPJ
%V 58
%N 5
%P 1074-1084
%M MAY
%D 2015
%K jrnl, COMPJ, cc2015, c201x, c20xx, LCS, LCSS, constrained, string
%X "... seek Z = LCS of X and Y, s.t. P is a subseq. of Z ...
   propose an O(r.min{mN,nM})-time alg. for solving this problem, where m,
   n and r are the lengths of X, Y and P, respectively, & M & N are the # of
   runs of the run-length-encoded strings of X & Y, resp.. "
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxu012">doi:10.1093/comjnl/bxu012</A>]['15].
   [Also search for: constrained longest common subsequence].

%A M. Crochemore
%A G. Fici
%A R. Mercas
%A S. P. Pissis
%T Linear-time sequence comparison using minimal absent words & applications
%J arXiv
%M JUN
%D 2015
%K TR, c2015, c201x, c20xx, zz0615, absent, word, words, string, strings,
   q-gram, alignment free, similarity
%X "Seq. comp. ... is often realised by seq. alignment techniques, which are
   computationally expensive. This has led to increased research into al. free
   techniques, which are based on measures referring to the composition of seqs.
   in terms of their constituent patterns. These measures, such as q-gram
   distance, can usually be computed in time linear w.r.t. the length of the
   seqs.. ... focus on the complementary idea: how two seqs. can be efficiently
   compared based on info. about what does not occur in the sequences. ...
   present a linear-time & linear-space alg. to compare two seqs. by considering
   all their minimal absent words. An absent word is minimal if all its proper
   factors occur in the seq.. ... present some results of combinatorial interest
   & also extend the proposed techniques to circular sequences."
   -- 1506.04917@[<A HREF="http://arxiv.org/abs/1506.04917">arXiv</A>]['15].
   [Also search for: absent word].

%A M. Han
%A M. Kang
%A S. Cho
%A G. Gu
%A J. S. Sim
%A K. Park
%T Fast multiple order-preserving matching algorithms
%J arXiv
%M JUN
%D 2015
%K TR, c2015, c201x, c20xx, zz0615, match, order preserving matching, algorithm,
   Kubica, Kim, sequence, substring, string, strings, music, melody, tune
%X "Given a text T & a pattern P, the order-preserving matching problem is to
   find all substrings in T which have the same relative orders as P.
   Order-preserving matching ... was introduced by Kubica et al. & Kim et al..
   ... we present two algs. for the ... problem, one of which runs in sublinear
   time on avg & the other in linear time on avg. Both algs. run much faster
   than the previous algs.."
      "... e.g., given T=(10,15,20,25,15,30,20,25,30,35) & P=(35,40,30,45,35),
      P has the same rel. orders as the substring T=(20,25,15,30,20) of T. In T
      (resp. P), the 1st char. 20 (resp. 35) is the 2nd smallest number, ..."
   -- 1506.05203@[<A HREF="http://arxiv.org/abs/1506.05203">arXiv</A>]['15].
   {?Said to be useful in stock price analysis & music melody matching?}
   [Also search for: order preserving matching] and
   [also search for: music match].

%A T. Takagi
%A S. Inenaga
%A H. Arimura
%T Fully-online construction of suffix trees and DAWGs for multiple texts
%J arXiv
%P 22p
%M JUL
%D 2015
%K TR, c2015, c201x, c20xx, zz0815, online, suffix tree, DAWG, text, string
%X "... consider fully-online construction of indexing data structs. for
   multiple texts. Let T=T1,...,Tk be a colln of texts. By fully on-line, we
   mean that a new char. can be appended to any text in T at any time. ... a
   natural generalization of semi-online constn of indexing data structs. for
   multiple texts in which, after a new char. is appended to the kth text Tk,
   then its previous texts T1,...,T[k-1] will remain static. Our fully online
   scenario arises when we index multi-sensor data. We propose fully online
   algs. which construct the directed acyclic word graph (DAWG) & the
   generalized s.tree (GST) for T in O(Nlog sigma) time & O(N) space, where
   N & sigma denote the total length of texts in T & the alphabet size, resp."
   -- 1507.07622@[<A HREF="http://arxiv.org/abs/1507.07622">arXiv</A>]['15].
   [Also search for: suffix tree].

%A D. Belazzougui
%A S. J. Puglisi
%T Range predecessor and Lempel-Ziv parsing
%J arXiv
%M JUL
%D 2015
%K TR, c2015, c201x, c20xx, zz0815, LZ, LZ77, string, text, compression,
   2D orthogonal range
%X "... show that the LZ parsing of a string of length n on an alphabet of size
   sigma can be computed in O(n log log sigma) time (O(n) time if we allow
   randomization) using O(n log sigma) bits of working space; that is, using
   space proportional to that of the input string in bits. The prev. fastest
   alg. using O(n log sigma) space takes O(n(log sigma + log log n)) time. ...
   [&] rightmost variant of the problem ... most recent occurence ... We solve
   this problem in O(n(1+(log sigma / sqrt log n) time ... same working space
   ... The prev. best ... O(n(1+log sigma /log log n)) time and O(n log n)
   space. As a bonus, in our solution for rightmost parsing we provide a faster
   construction method for efficient 2D orthogonal range reporting, which is of
   indep. interest."
   -- 1507.07080@[<A HREF="http://arxiv.org/abs/1507.07080">arXiv</A>]['15].
   [Also search for: Lempel Ziv string].

%A D. Zhu
%A L. Wang
%A Y. Wu
%A X. Wang
%T A practical O(R log log n+n) time algorithm for computing the longest
   common subsequence
%J arXiv
%M AUG
%D 2015
%K TR, c2015, c201x, c20xx, zz0915, string, LCS, algorithm, Iliopoulos, Rahman
%X "... based on the alg. of Iliopoulos & Rahman for solving the LCS problem, we
   have suggested 3 new improved algs.. We first reformulate the problem in a
   very succinct form. ... LCS is abstracted to an ADT DS on an ordered +ve
   integer set with a special operation Update(S,x). For the two input seqs. X &
   Y of equal length n, the first improved alg. uses a van Emde Boas tree for DS
   & its time & space complexities are O(R log log n+n) & O(R), where R is the
   # of matched pairs of the two input seqs.. The 2nd alg. uses a balanced
   binary search tree for DS & its time & space complexities are O(R log L+n) &
   O(R), where L is the length of the LCS of X & Y. The 3rd alg. uses an ordered
   vector for DS & its time & space complexities are O(nL) & O(R)."
   -- 1508.05553@[<A HREF="http://arxiv.org/abs/1508.05553">arXiv</A>]['15].

%A S. Huntsman
%A A. Rezaee
%T De Bruijn entropy and string similarity
%J arXiv
%M SEP
%D 2015
%K TR, conf, WORDS, c2015, c201x, c20xx, zz0915, deBruijn, string similarity,
   Eulerian quiver
%X "We introduce the notion of de Bruijn entropy of an Eulerian quiver & show
   how the corresponding relative entropy can be applied to practical string
   similarity problems. This approach explicitly links the combinatorial &
   information-theoretical properties of words & its performance is superior to
   edit distances in many respects & competitive in most others. The comp.
   complexity of our current impln is parametrically tunable between linear &
   cubic, & we outline how an optimized lin. alg. subroutine can reduce the
   cubic complexity to ~ linear. Numerous examples are provided, inc. a
   realistic applicn to molecular phylogenetics."
   -- 1509.02975@[<A HREF="http://arxiv.org/abs/1509.02975">arXiv</A>]['15].

%A R. M. Hierons
%A U. Cengiz Turker
%T Incomplete distinguishing sequences for finite state machines
%J COMPJ
%V 58
%N 11
%P 3089-3113
%M NOV
%D 2015
%K jrnl, COMPJ, c2015, c201x, c20xx, zz1115, finite state machine, automaton,
   automata, FSM, FSA, distinguish, states, sequence, string
%X "Given a finite state machine (FSM) M, a distinguishing sequence (DS) is a
   test that identifies the state of M. While there are two types of DSs,
   preset DSs (PDSs) & adaptive DSs (ADSs), not all FSMs possess a DS. ...
   examine the problem of finding incomplete PDSs & ADSs, exploring associated
   optimization problems: finding a largest set of states that has a DS &
   finding a smallest set of DSs that, between them, distinguish all of the
   states. We also propose a greedy alg. to produce a small set of incomplete
   ADSs & use experiments to compare this with two previously published algs.
   for generating state identifiers. We show that the optimization problems
   related to incomplete ADSs & PDSs are PSPACE-complete as are corr.
   approximation problems. ... found that incomplete ADSs produced by the
   proposed greedy alg. led to relatively compact state identifiers."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/bxv041">doi:10.1093/comjnl/bxv041</A>]['15].

%A M. Dumitran
%A P. Gawrychowski
%A F. Manea
%T Longest gapped repeats and palindromes
%J arXiv
%M NOV
%D 2015
%K TR, c2015, c201x, c20xx, zz1115, string, factor, repeat, gap, palindrome
%X "A gapped repeat (resp., palindrome) occurring in a word w is a factor uvu
   (resp., uRvu) of w. ... u is called the arm of the repeat ..., while v is
   called the gap. We show how to compute efficiently, for every posn i of the
   word w, the longest gapped r. & p. occurring at that posn, provided that the
   length of the gap is subject to various types of restrictions. ... that for
   each posn i we compute the longest prefix u of w[i..n] s.t. uv (resp., uRv)
   is a suffix of w[1..i-1] (defining thus a gapped r. uvu - resp., p. uRvu), &
   the length of v is subject to the aforementioned restrictions."
   -- 1511.07180@[<A HREF="http://arxiv.org/abs/1511.07180">arXiv</A>]['15].
   (An extension of conf papers.)

%A T. Beller
%A E. Ohlebusch
%T A representation of a compressed de Bruijn graph for pan-genome analysis that
   enables search
%J arXiv
%M FEB
%D 2016
%K TR, MolBio, c2016, c201x, c20xx, zz0216, compressed, de Bruijn, deBruijn,
   graph, similar genomes
%X "Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed
   deB. graph to describe the relationship between the genomes of many
   individuals/strains of the same or closely related species. They devised an
   O(n log g) time algorithm called splitMEM that constructs this g. directly
   (i.e., without using the uncompressed de Bruijn graph) based on a suffix
   tree, where n is the total length of the genomes & g is the length of the
   longest genome. ... we present a constn alg. that outperforms their alg. in
   theory & in practice. [&] propose a new space-efficient repn of the
   compressed deB. g. that adds the possibility to search for a pattern (e.g. an
   allele - a variant form of a gene) within the pan-genome."
   -- 1602.03333@[<A HREF="http://arxiv.org/abs/1602.03333">arXiv</A>]['16].

%A A. Case
%A J. H. Lutz
%T Mutual dimension and random sequences
%J arXiv
%M MAR
%D 2016
%O 40th Int. Symp. on Mathematical Foundations of Comp. Sci. (FOCS)
%K TR, c2016, c201x, c20xx, zz0416, mutual dimension, sequence, mdim,
   Billingsley, Mayordomo, random
%X "If S & T are infinite seqs. over a finite alphabet, then the lower & upper
   mutual dimensions mdim(S:T) & Mdim(S:T) are the upper & lower densities of
   the algorithmic information that is shared by S & T. ... we investigate the
   relationships between mutual d. & coupled randomness, which is the
   algorithmic randomness of two seqs. R1 & R2 wrt probability measures that may
   be dependent on one another. For a restricted but interesting class of
   coupled probability measures we prove an explicit formula for the mutual ds.
   mdim(R1:R2) & Mdim(R1:R2), & we show that the condition Mdim(R1:R2)=0 is
   necessary but not sufficient for R1 & R2 to be indep. random.  We also
   identify conditions under which Billingsley generalizations of the mutual ds.
   mdim(S:T) & Mdim(S:T) can be meaningfully defined; we show that under these
   conditions these generalized mutual ds. have the 'correct' relationships with
   the Billingsley generalizations of dim(S), Dim(S), dim(T), & Dim(T) that were
   developed & applied by Lutz & Mayordomo; & we prove a divergence formula for
   the values of these generalized mutual ds.."
   -- 1603.09390@[<A HREF="http://arxiv.org/abs/1603.09390">arXiv</A>]['16].

%A D. Chakraborty
%A E. Goldenberg
%A M. Koucky
%T Streaming algorithms for computing edit distance without exploiting suffix
   trees
%J arXiv
%M JUL
%D 2016
%K TR, c2016, c201x, c20xx, zz0716, strings, edit distance, similarity,
   streaming, algorithm, bounded
%X "... study the computational problem of computing the edit distance between a
   pair of strings where their distance is bounded by a parameter k << n. We
   present two streaming algs. for computing edit distance: One runs in time
   O(n+k^2) and the other n+O(k^3). ... the running time does not depend on the
   alphabet size, & the alg. should[?] be easy to implement. ... The best
   off-line alg. runs in time O(n+k^2) (Landau et al., 1998) which is known to
   be optimal under the Strong Exponential Time Hypothesis."
   -- 1607.03718@[<A HREF="http://arxiv.org/abs/1607.03718">arXiv</A>]['16].
   [Also search for: strings edit distance algorithm].

%A J. Radoszewski
%A T. Starikovskaya
%T Streaming k-mismatch with data recovery and applications
%J arXiv
%M JUL
%D 2016
%K TR, c2016, c201x, c20xx, zz0716, string, strings, sequence, Hamming distance,
   mismatch, match, search, errors, pattern, algorithm
%X "... Given a pattern of length m & a text of length n ... find all m-length
   substrings of the text that are at the Hamming dist. at most k from the
   pattern. ... two new streaming algs. for the k-mismatch problem.  1) For k=1,
   we give an O(polylogm)-space alg. that uses O(polylogm) worst-case time per
   arriving symbol; 2) For k>=2, the problem can be solved in O(k^2 polylogm)
   space & O(k polylogm) worst-case time per arriving symbol. ... & our algs.
   are enhanced with an important new feature which we call Data Recovery: For
   each alignment where the Hamming dist. is at most k, the algs. output the
   difference of symbols of the pattern & of the text in the mismatching posns.
   This is a particularly surprising feature as we are not allowed to store a
   copy of the pattern or the text in the streaming setting.  Armed with this
   new feature, we develop the first streaming algs. for pattern matching on
   weighted strings. Unlike regular strings, a wtd string is not a seq. of
   symbols but rather a seq. of probability distributions on the alphabet. In
   the Weighted Pattern Matching problem we are given a text & a pattern, both
   of which can be either wtd or regular strings, & must find all alignments of
   the text & of the pattern where they match with probability above a given
   threshold.  The algs. presented in the paper are randomised & correct with
   high probability."
   -- 1607.05626@[<A HREF="http://arxiv.org/abs/1607.05626">arXiv</A>]['16].
   [Also search for: strings mismatch algorithm].

%A P. Bonizzoni
%A G. Della Vedova
%A S. Nicosia
%A M. Previtali
%A R. Rizzi
%T A new lightweight algorithm to compute the BWT and the LCP array of a set of
   strings
%J arXiv
%M JUL
%D 2016
%K TR, c2016, c201x, c20xx, zz0816, algorithm, strings, BWT, LCP,
   longest common prefix
%X "... The best current lightweight approach to compute BWT & LCP array on a
   set of m strings, each one k characters long, has I/O complexity that is
   O(m k^2 log|alphabet|) ...  thus it is not optimal. ... we propose a novel
   approach to build BWT and LCP array (simultaneously) with
   O(k m L(log k+log s) I/O complexity, where L is the length of longest
   substring that appears at least twice in the input strings."
   -- 1607.08342@[<A HREF="http://arxiv.org/abs/1607.08342">arXiv</A>]['16].

%A P. Siyari
%A M. Galle
%T The generalized smallest grammar problem
%J arXiv
%M AUG
%D 2016
%K TR, c2016, c201x, c20xx, zz0916, string, strings, generate,
   smallest, context free grammar, problem, infer, inferring, SCFG, CFG
%X "The Smallest Grammar Problem ... finding the smallest context-free grammar
   that generates exactly one given seq. -- has never been successfully applied
   to grammatical inference. We investigate the reasons & propose an extended
   formulation that seeks to minimize non-recursive grammars, instead of
   straight-line programs. [&] provide v.efficient algs. that approx. the
   minimization problem of this class of grammars. Our empirical evaluation
   shows that we are able to find smaller models than the current best
   approximations to the Smallest Grammar Problem on std benchmarks, & that the
   inferred rules capture much better the syntactic structure of nat. language."
   -- 1608.08927@[<A HREF="http://arxiv.org/abs/1608.08927">arXiv</A>]['16].
   [Also search for: SCFG]  and  [also search for: infer grammar].

%A D. Belazzougui
%A F. Cunial
%A J. Karkkainen
%A V. Makinen
%T Linear-time string indexing and analysis in small space
%J arXiv
%P 52pp
%M SEP
%D 2016
%K TR, c2016, c201x, c20xx, zz0916, string, strings, BWT, CSA, CST,
   compressed suffix tree, index, succinct data structure
%X "... report the following advances in string indexing & analysis. We show
   that the BWT of a string T in {1, ..., s}^n can be built in deterministic
   O(n) time using just O(n log s) bits of space, where s <= n. Within the same
   time & space budget, we can build an index based on the BWT that allows one
   to enumerate all the internal nodes of the suffix tree of T. Many fundamental
   string analysis problems can be mapped to such enumeration, & can thus be
   solved in deterministic O(n) time & in O(n log s) bits of space from the
   input string. We also show how to build many of the existing indexes based on
   the BWT, such as the CSA, the compressed suffix tree (CST), & the
   bidirectional BWT index, in randomized O(n) time & in O(n log s) bits of
   space. The previously fastest construction algs. for BWT, CSA & CST, which
   used O(n log s) bits of space, took O(n log log s) time for the first two
   structures, & O(n log^eps n) time for the third, where eps is any +ve const..
   Contrary to the state of the art, our bidirectional BWT index supports every
   operation in constant time per element in its output."
   -- 1609.06378@[<A HREF="http://arxiv.org/abs/1609.06378">arXiv</A>]['16].

%A J. Fischer
%A F. Kurpicz
%A P. Sanders
%T Engineering a distributed full-text index
%J arXiv
%M OCT
%D 2016
%K TR, c2016, c201x, c20xx, zz1016, text, string, index, strings, indexing
%X "... a distributed full-text index for big data applications in a distributed
   environment. The index can be used to answer different types of pattern
   matching queries (existential, counting and enumeration) and also be extended
   to answer document retrieval queries (counting, retrieve and top-k). ..."
   -- [<A HREF="https://arxiv.org/abs/1610.03332">arXiv</A>]['16].

%A F. A. Louza
%A S. Gog
%A G. P. Telles
%T Optimal suffix sorting and LCP array construction for constant alphabets
%J IPL
%V 118
%P 30-34
%M FEB
%D 2017
%K jrnl, IPL, c2016, c201x, c20xx, zz1016, string, suffix array, alphabet,
   longest common prefix, LCP, SACA K, SACAK, Nong, Fischer
%X "...  the longest common prefix (LCP) array can be generated as a by-product
   of the suffix array construction algorithm SACA-K (Nong, 2013). Our alg.
   builds on Fischer's proposal (F., WADS'11), & also runs in linear time, but
   uses only constant extra memory for constant alphabets."  [online 10/'16.]
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2016.09.010">doi:10.1016/j.ipl.2016.09.010</A>]['16].

%A M. Nicolae
%A S. Rajasekaran
%T On pattern matching with k mismatches and few don't cares
%J IPL
%V 118
%N ?
%P 78-82
%M FEB
%D 2017
%K IPL, jrnl, c2016, c201x, c20xx, zz1116, strings, string search, dont care,
   wildcard, dontCare, mismatch, mismatches, errors, algorithm
%X "... Input: text T of length n, pattern P of length m, with don't cares, &
   integer k. ..."  "... alg. whose runtime increases with the # of don't cares.
   We define an island to be a maximal length substring of P that does not
   contain don't cares. Let q be the # of islands in P. ... alg. that runs in
   O(n sqrt(k log m) + n min( (q k log^2 m)^(1/3), sqrt(q log m))).  If the #
   of islands q is O(k) this runtime becomes O(n sqrt(k log m)), which
   essentially matches the best known runtime for pattern matching with k
   mismatches without don't cares. If the # of islands q is O(k^2), this alg. is
   asymptotically faster than the prev. best alg. for pattern matching with k
   mismatches with don't cares in the pattern."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2016.10.003">doi:10.1016/j.ipl.2016.10.003</A>]['16].
   [Also search for: string search mismatch].

%A K. Bringmann
%A P. Gawrychowski
%A S. Mozes
%A O. Weimann
%T Tree edit distance cannot be computed in strongly subcubic time (unless
   APSP can)
%J arXiv
%M MAR
%D 2017
%K TR, c2017, c201x, c20xx, zz0417, tree edit distance, DPA,
   all pairs shortest paths, APSP
%X "The edit distance between two rooted ordered trees with n nodes labeled from
   an alphabet S is the minimum cost of transforming one tree into the other by
   a seq. of elementary opns consisting of deleting & relabeling existing nodes,
   [&] inserting new nodes. [It] is a well known generalization of string edit
   distance. The fastest known alg. for TED runs in cubic O(n^3) time ...
   we show that a truly subcubic O(n^(3âeps)) time alg. for TED is
   unlikely: For |S|=Omega(n), a truly subcubic alg. for TED implies a truly
   subcubic alg. for the all pairs shortest paths problem. For |S|=O(1), a truly
   ... for TED implies an O(n^(kâeps) alg. for finding a max. weight k-clique.
   in terms of lower bounds string ED exhibits the hardness of the strong
   exponential time hypothesis [Backurs, Indyk STOC'15] whereas TED exhibits the
   hardness of all pairs shortest paths. Our result provides a matching
   conditional lower bound for one of the last remaining classic dynamic
   programming problems."
   -- 1703.08940@[<A HREF="https://arxiv.org/abs/1703.08940">arXiv</A>]['17].
   [Also search for: tree edit distance].

%A N. T. Janakiraman
%A A. Vem
%A K. R. Narayanan
%A J.-Francois Chamberland
%T Sub-string/pattern matching in sub-linear time Using a sparse Fourier
   transform approach
%J arXiv
%M APR
%D 2017
%K TR, c2017, c201x, c20xx, zz0417, string, strings, pattern, matching, search,
   match, matching, approximate
%X "... querying a string ... off length N bits to determine all the locns where
   a substring (query) of length M appears either exactly or is within a
   Hamming distance of K from the query. We assume that sketches of the original
   signal can be computed off line & stored. Using the sparse Fourier transform
   computation based approach introduced by Pawar & Ramchandran, we show that
   all such matches can be determined with high prob. in sub-linear time. ...
   if ... M=O(N^mu) & the # of matches L=O(N^lambda), we show that for
   lambda < 1-mu all the matching posns can be determined with a prob. that
   approaches 1 as N  -> infin for K <= M/6. ... our scheme has a worst-case
   comp.complexity that is only O(max{N^(1âmu.log^2(N), N^(mu+lambda).log N}),
   [so] can recover all the matching posns in sub-linear time for lambda < 1-mu.
   ... a substantial improvement over the best known comp.complexity of
   O(N^(1â0.359 mu)) for recovering one matching posn by Andoni et al.(2013).
   [&] the # of FT coeffs that need to be computed, stored & accessed, i.e., the
   sketching complexity of this alg. is only O(N^(1âmu) log N). ..."
   -- 1704.07852@[<A HREF="https://arxiv.org/abs/1704.07852">arXiv</A>]['17].

%A T. Gagie
%A G. Navarro
%A N. Prezza
%T Fast locating with the RLBWT
%J arXiv
%M MAY
%D 2017
%K TR, c2017, c201x, c20xx, zz0617, strings, strings, BWT, RLBWT, index,
   find, locate, search
%X "... FM-index based on the run-length compressed Burrows-Wheeler Transform
   (RLBWT) of the text, which achieves excellent compression in practice &
   allows us, given a pattern, to count its occurrences in the text quickly. ...
   to be able to locate those occurrences quickly, however, the std soln is for
   us to augment the RLBWT with a large sample of the suffix array (SA).
   Recently, Policriti & Prezza (DCC 2016; Algorithmica, to appear) showed how
   we can store O(r) SA values, where r is the # of runs in the BWT, s.t., while
   counting the occurrences, we can locate at least one of them. ... we show how
   we can store O(r) SA values such that, knowing the location of one occurrence
   we can locate the others quickly. In other words, we show how to support fast
   locating with the RLBWT."
   -- 1705.10382@[<A HREF="https://arxiv.org/abs/1705.10382">arXiv</A>]['17].

%A T. Nakamura
%A S. Inenaga
%A H. Bannai
%A M. Takeda
%T Order preserving pattern matching on trees and DAGs
%J arXiv
%M JUN
%D 2017
%K TR, c2017, c201x, c20xx, zz0617, search, match, matching, pattern, string,
   tree, DAG, OPPM
%X "The order preserving pattern matching (OPPM) problem is, given a pattern
   string p & a text string t, find all substrings of t which have the same
   relative orders as p. ... we consider two variants of the OPPM problem where
   a set of text strings is given as a tree or a DAG. We show that the OPPM
   problem for a single pattern p of length m & a text tree T of size N can be
   solved in O(m+N) time if the characters of p are drawn from an integer
   alphabet of polynomial size. The time complexity becomes O(m log m + N) if
   the pattern p is over a general ordered alphabet. We then show that the OPPM
   problem for a single pattern & a text DAG is NP-complete."
   -- 1706.00148@[<A HREF="https://arxiv.org/abs/1706.00148">arXiv</A>]['17].
   [Also search for: order preserving matching].

%A J. W. Daykin
%A et al ...
%A B. Watson
%T Efficient pattern matching in degenerate strings with the Burrows-Wheeler
   transform
%J arXiv
%M AUG
%D 2017
%O IPL, 147, pp.82-87, July 2019
%K TR, c2017, c201x, c20xx, zz0817, string, search, BWT, degenerate, string,
   dString, fuzzy, indeterminate, ambiguous, sequence, sets, subsets, charSets,
   profile
%X "A degenerate or indeterminate string on an alphabet S is a seq. of non-empty
   subsets of S. Given a degenerate string t of length n, we present a new
   method based on the BWT for searching for a degenerate pattern of length m
   in t running in O(mn) time on a constant size alphabet S. Furthermore, it is
   a hybrid pattern-matching technique that works on both regular & degenerate
   strings. A degenerate string is said to be conservative if its # of non-solid
   letters is upper-bounded by a fixed +ve constant q; in this case we show that
   the search complexity time is O(qm^2). Experimental results show that our
   method performs well in practice."
   --  1708.01130@[<A HREF="https://arxiv.org/abs/1708.01130">arXiv</A>]['17],
   IPL [<A HREF="https://doi.org/10.1016/j.ipl.2019.03.003">doi:10.1016/j.ipl.2019.03.003</A>]['19].
   [Also search for: indeterminate dString].

%A D. Kosolobov
%A A. M. Shur
%T Comparison of LZ77-type parsings
%J arXiv
%M AUG
%D 2017
%K TR, c2017, c201x, c20xx, zz0817, AMShur, string, strings, LZ, LZ77
%X "... relations between different variants of the LZ77 parsing ...
   All of them are defined as greedily constructed parsings encoding each
   phrase by reference to a string occurring earlier in the input. They differ
   by the phrase encodings: encoded by pairs (length + posn of an earlier occ.)
   or by triples (length + posn of an earlier occ. + the letter following the
   earlier occurring part); & they differ by allowing or not allowing overlaps
   between the phrase & its earlier occ.. For a given string of length n over an
   alphabet of size s, denote the numbers of phrases in the parsings
   allowing (resp., not allowing) overlaps by z (resp., z'), for "pairs", & by
   z3 (resp., z3'), for "triples". We prove the following bounds & provide
   series of examples showing that these bounds are tight:
   . z <= z' <= z.O(log(n/(z log_s z)) and
     z3 <= z3' <= z3.O(log(n/(z3 log_s z3));
   . (1/2)z' <= z3' <= z' and (1/2)z < z3 <= z."
   -- 1708.03558@[<A HREF="https://arxiv.org/abs/1708.03558">arXiv</A>]['17].

%A N. Prezza
%T String attractors
%J arXiv
%M SEP
%D 2017
%K TR, c2017, c201x, c20xx, zz0622, string, strings, attractor, compression,
   dictionary, repetition, repetitiveness
%X "Let S be a string of length n. ... we introduce the notion of string
   attractor: a subset of the S's positions [1,n] s.t. every distinct substring
   of S has an occurrence crossing one of the attractor's elts. We first show
   that the minimum attractor's size yields upper-bounds to the string's
   repetitiveness as measured by its linguistic complexity & by the length of
   its longest repeated substring. We then prove that all known compressors for
   rep.strings induce a string attractor whose size is bounded by their assoc.
   repetitiveness measure, & can therefore be considered as approximations of
   the smallest one. ... present a universal compressed data struct. for text
   extraction that improves existing strategies simultaneously for all known
   dictionary compressors & that, by recent lower bounds, almost matches the
   optimal running time within the resulting space. ... we consider
   generalizations of string attractors to labeled graphs, show that the
   attractor problem is NP-complete on trees, & provide a logarithmic
   approximation computable in polynomial time."
   -- 1709.05314@[<A HREF="https://arxiv.org/abs/1709.05314">arXiv</A>]['22].

%A X. He
%A N. Huang
%A X. Sun
%T On the decision tree complexity of string matching
%J arXiv
%M DEC
%D 2017
%K TR, c2017, c201x, c20xx, zz0118, Rivest, Tuza, Skolem, problem, strings,
   match, search, pattern, comparisons, character queries
%X "... A natural problem is to find the # of characters that need to be queried
   (i.e. the decision tree complexity) in a string in order to determine whether
   this string contains a certain pattern. Rivest showed that for every pattern
   p, in the worst case any deterministic algorithm needs to query at least
   n-|p|+1 chars, where n is the length of the string and |p| is the length
   of the pattern. He further conjectured that these bounds are tight. By using
   adversary methods, Tuza disproved this conjecture and showed that more than
   half of binary patterns are evasive, i.e. any algorithm needs to query all
   the characters. ... we give a new sufficient condn for the evasiveness of
   patterns, which reveals an interesting connection to Skolem's Problem."
   -- 1712.09738@[<A HREF="https://arxiv.org/abs/1712.09738">arXiv</A>]['17].

%A U. Baier
%T On undetected redundancy in the Burrows-Wheeler transform
%J arXiv
%M APR
%D 2018
%K TR, c2018, c201x, c20xx, zz0418, string, strings, BWT,
   Burrows Wheeler transform, compression
%X "...  present a new technique to reduce the size of a BWT using its
   combinatorial properties, while keeping it invertible. The technique can be
   applied to any BWT-based compressor, and, as experiments show, is able to
   reduce the encoding size by 8-16% on average and up to 33-57% in the best
   cases (depending on the BWT-compressor used), making BWT-based compressors
   competitive or even superior to today's best lossless compressors."
   -- 1804.01937@[<A HREF="https://arxiv.org/abs/1804.01937">arXiv</A>]['18].
   [Also search for: BWT string].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/BWT/">BWT</A>].)

%A L. Fleischer
%A M. Kufleitner
%T Testing Simon's congruence
%J arXiv
%M APR
%D 2018
%L TR, c2018, c201x, c20xx, zz0823, Simons, Simon's congruence, string, strings,
   piecewise testable language, regular, languages
%X "Piecewise testable languages are a subclass of the regular languages. There
   are many equivalent ways of defining them; Simon's congruence ~k is one of
   the most classical approaches. Two words are ~k-equivalent if they have the
   same set of (scattered) subwords of length at most k. A language L is
   piecewise testable if there exists some k such that L is a union of
   ~k-classes. ...  If the alphabet is fixed, the running time of our alg. is
   linear in the size of the input word. ..."
   -- 1804.10459@[<A HREF="https://arxiv.org/abs/1804.10459">arXiv</A>]['23].

%A E. F. O. Sandes
%A G. L. M. Teodoro
%A M. Emilia
%A M. T. Walter
%A X. Martorell
%A E. Ayguade
%A A. C. M. A. Melo
%T Formalization of block pruning: Reducing the number of cells computed in
   exact biological sequence comparison algorithms
%J COMPJ
%V 61
%N 5
%P 687-713
%M MAY
%D 2018
%K Compj, jrnl, c2018, c201x, c20xx, zz0518, sequence comparison algorithm,
   alignment, dynamic programming, 2D, DPA, fast, prune, cell
%X "... The DP matrix H is calculated with a recurrence relation in which the
   value of each cell Hi,j is the result of a maximum operation on the cellsâ
   values Hiâ1,jâ1, Hiâ1,j and Hi,jâ1 added or subtracted by a constant value.
   ... define a generic pruning method which determines the cells that can
   pruned (i.e. no need to be computed since they will not contribute to the
   final solution), accelerating the computation but keeping the guarantee that
   the optimal result will be produced. The goal of this paper is thus to
   investigate and formalize properties of the DP matrix in order to estimate
   and increase the pruning method efficiency. We also show that the pruning
   efficiency depends mainly on three characteristics: (a) the order in which
   the cells of H are calculated, (b) the values of the parameters used in the
   recurrence relation and (c) the contents of the sequences compared."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxx090">doi:10.1093/comjnl/bxx090</A>]['18].
   [Also search for: fast DPA].

%A A. Farruggia
%A T. Gagie
%A G. Navarro
%A S. J. Puglisi
%A J. Siren
%T Relative suffix trees
%J COMPJ
%V 61
%N 5
%P 773-788
%M MAY
%D 2018
%K jrnl, COMPJ, c2018, c201x, c20xx, zz0618, compressed data structure,
   suffix tree, index, strings, sequences, genomes
%X "... take a new approach to compressed suffix trees for repetitive sequence
   collections, such as collections of individual genomes. We compress the
   suffix trees of individual seqs. relative to the suffix tree of a ref.seq..
   These relative data structures provide competitive time/space trade-offs,
   being almost as small as the smallest compressed suffix trees for repetitive
   collections, and competitive in time with the largest and fastest compressed
   suffix trees."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxx108">doi:10.1093/comjnl/bxx108</A>]['18].

%A K. Iwama
%A J. Teruyama
%A S. Tsuyama
%T Reconstructing strings from substrings: Optimal randomized and average-case
   algorithms
%J arXiv
%M AUG
%D 2018
%K TR, c2018, c201x, c20xx, zz0818, string, strings, substrings, queries,
   reconstruct, reconstruction, problem, sequencing, DNA, sequence assembly,
   MolBio, oracle, algorithm
%X "... 'String reconstruction from substrings' is a math. model of sequencing
   by hybridization that plays an important role in DNA seq.. ... we are given a
   blackbox oracle holding an unknown string X & are required to obtain
   (reconstruct) X through 'substring queries' Q(S). Q(S) is given to the oracle
   with a string S & the answer of the oracle is Yes if X includes S as a
   substring & No otherwise. Our goal is to minimize the # of queries for the
   reconstruction. ... we deal with only binary strings for X whose length n is
   given in advance by using a seq. of good S's. In 1995, Skiena & Sundaram
   first studied this problem & obtained an alg. whose query complexity is
   n+O(log n). Its information theoretic lower bound is n, & they posed an
   obvious open question; if we can remove the O(log n) additive term. No
   progress has been made until now. This paper gives two partially positive
   answers to this open question. One is a randomized alg. whose query
   complexity is n+O(1) with high probability & the other is an avg-case alg.
   also having a query complexity of n+O(1) on avg. The n lower bound is still
   true for both cases, & hence they are optimal up to an additive constant."
   -- 1808.00674@[<A HREF="https://arxiv.org/abs/1808.00674">arXiv</A>]['18].
   [Also search for: MolBio sequence assembly].

%A A. N. Arslan
%T A fast algorithm for all-pairs Hamming distances
%J IPL
%V 139
%P 49-52
%M ?
%D 2018
%K jrnl, IPL, c2018, c201x, c20xx, zz0818, strings, Hamming distance,
   AllPairsHamDist, all pairs, allPairs, algorithm
%X "AllPairsHamDist is introduced as the problem of computing Hamming distances
   for all pairs in two given sets. Solving an instance of AllPairHamDist yields
   a distance matrix that can be used for hierarchical clustering of biological
   sequences. For AllPairsHamDist, there exists a fast alg. based on fast
   matrix multiplication."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2018.07.006">doi:10.1016/j.ipl.2018.07.006</A>]['18].

%A T. Gagie
%A G. Gourdel
%A G. Navarro
%A J. Simpson
%T The read-optimized Burrows-Wheeler transform
%M SEP
%D 2018
%K TR, c2018, c201x, c20xx, zz0918, BWT, MolBio, FM index, FMindex
%X "The advent of high-throughput sequencing has resulted in massive genomic
   datasets, some consisting of assembled genomes but others consisting of raw
   reads. We consider how to reduce the amount of space needed to index a set of
   reads, in particular how to reduce the number of runs in the Burrows-Wheeler
   Transform (BWT) that is the basis of FM-indexing. The best current
   fully-functional index for repetitive collections (Gagie et al., SODA 2018)
   uses space proportional to this number.
   -- 1809.07320@[<A HREF="https://arxiv.org/abs/1809.07320">arXiv</A>]['18].

%A A. Clare
%A J. W. Daykin
%T Enhanced string factoring from alphabet orderings
%J IPL
%V 143
%P 4-7
%M MAR
%D 2019
%K jrnl, IPL, c2019, c201x, c20xx, zz0219, string, strings, Lyndon word, words,
   LyndonWord, algorithm, factoring, AClare, Parikh
%X "... consider the concept of alphabet ordering in the context of string
   factoring. We propose a greedy alg. that produces Lyndon factorizations with
   small #s of factors which can be modified to produce large #s of factors. For
   the technique we introduce the Exponent Parikh vector. Applications &
   research directions derived from circ-UMFFs are discussed."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2018.10.011">doi:10.1016/j.ipl.2018.10.011</A>]['19].
   [Also search for: Lyndon factorization]  &  [also search for: Lyndon words].
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Strings/Factors/">Factors</A>].)

%A H. Yamamoto
%T A faster algorithm for finding shortest substring matches of a
   regular expression
%J IPL
%V 143
%P 56-60
%M MAR
%D 2019
%K jrnl, IPL, c2019, c201x, c20xx, zz0219, string, regular expression, regexp,
   match, NFA, NFSA, NFSM, algorithm, text, search, searching,
   Thompson automaton
%X "Consider a reg.exp. r of length m & a text string T of length n over an
   alphabet S. Then, the RE shortest substring search problem is to find all
   shortest substrings of T matching r. The previous alg. proposed by Clarke &
   Cormack uses an eps-free nondeterministic finite automaton (NFA) & runs in
   O(ksn) time and O(s) space, where k is the max. # of outgoing transitions for
   any state & symbol, & s is the # of states. Generally, an eps-free NFA
   obtained from a regexp. has s=O(m) & k=O(m); thus the alg. takes O(m^2n) time
   & O(m) space. We propose a faster alg. that runs in O(mn) time O(m) space.
   [It] is based on a Thompson automaton which is an NFA with eps-transitions."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2018.12.001">doi:10.1016/j.ipl.2018.12.001</A>]['19].
   [Also search for: regular expression].

%A T. Nishimoto
%A Y. Tabei
%T Conversion from RLBWT to LZ77
%J arXiv
%M FEB
%D 2019
%K TR, c2019, c201x, c20xx, zz0219, compressed, string, strings, conversion,
   LZ, LZ77, BWT, RLBWT, Policriti, Prezza, Kempa
%X "Converting a compressed format of a string into another compressed format
   without an explicit decompression ... We discuss the problem of converting
   the run-length Burrows-Wheeler Transform (RLBWT) of a string to Lempel-Ziv 77
   (LZ77) phrases of the reversed string. The 1st results with Policriti &
   Prezza's conversion alg. [Algorithmica 2018] were O(n log r) time & O(r)
   working space for length of the string n, # of runs r in the RLBWT, & # of
   LZ77 phrases z. Recent results with Kempa's conversion alg. [SODA 2019] are
   O(n/log n + r log^9(n)+z log^9(n)) time & O(n/log_s(n)+rlog^8(n)) working
   space for the alphabet size Ï of the RLBWT. ... we present a new c.alg. by
   improving P & P's c.alg. where dynamic data structures for general purpose
   are used. We argue that these dynamic DSs can be replaced & present new data
   structures for faster conversion. The time & working space of our c.alg. with
   new data structures are O(n min(log log n, sqrt((log r)/(log log r))))
   & O(r), resp.."
   -- 1902.05224@[<A HREF="https://arxiv.org/abs/1902.05224">arXiv</A>]['19].

%A M. Gonen
%A D. Shapira
%A J. A Storer
%T Edit distance with multiple block operations
%J COMPJ
%V 62
%N 5
%P 657-669
%M MAY
%D 2019
%K jrnl, COMPJ, c2019, c201x, c20xx, zz0519, string, strings, edit distance,
   similarity, block moves, move
%X "... consider the edit distance with block moves, block copies & block
   deletions, which is shown to be NP-hard, & employ a simple left-to-right
   greedy sliding window algorithm that achieves a constant factor approximation
   ratio of 5. This is an improvement on the constant approximation of 12
   presented by Ergun & Sahinalp (ErgÃ¼n, F., Muthukrishnan, S., & Sahinalp,
   S. C. Comparing sequences with segment rearrangements. FST TCS 2003:
   Foundations of Software Technology & Theor. C. Sci.), & is achieved by a
   proof that introduces two non-trivial kinds of substrings for different
   purposes, so recursive & non-recursive ops can be treated at the same time."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxy066">doi:10.1093/comjnl/bxy066</A>]['19].
   [Also search for: strings block moves].

%A A. Nellore
%A A. Nguyen
%A R. F. Thompson
%T A multidimensional analog to the Burrows-Wheeler transform
%J arXiv
%M MAY
%D 2019
%K TR, c2019, c201x, c20xx, zz0519, strings, BWT, search, indexing, 2D, grid,
   pattern, text
%X "We show how to perform multidimensional pattern matching over an
   n-dimensional grid of text spanning a total of s characters with nength, an
   analog to the Burrows-Wheeler transform. Nength exploits a Fourier duality
   between two kinds of grid products to map a search problem that naively takes
   O(s^2) arithmetic ops to an equivalent problem that takes O(s log s)
   arithmetic operations."
   -- 1905.03424@[<A HREF="https://arxiv.org/abs/1905.03424">arXiv</A>]['19].
   ?where is it useful?

%A R. Janssen
%A J. Klawitter
%T Rearrangement operations on unrooted phylogenetic networks
%J arXiv
%M JUN
%D 2019
%K TR, MolBio, c2019, c201x, c20xx, zz0619, unrooted, phylogenetic, tree,
   network, distance, operation, NNI, SPR, TBR
%X "Rearrangement operations transform a phylogenetic tree into another one &
   hence induce a metric on the space of p.trees. Popular ops. for unrooted
   p.trees are NNI (nearest neighbour interchange), SPR (subtree prune &
   regraft), & TBR (tree bisection & reconnection). Recently, these ops. have
   been extended to unrooted phylogenetic n/wks, which are generalisations of
   p.trees that can model reticulated evolutionary relationships. Here, we study
   global & local properties of spaces of phylogenetic n/wk under these three
   operations. ... prove connectedness & asymptotic bounds on the diameters of
   spaces of different classes of phylogenetic n/wk, inc. tree-based & level-k
   n/wks. We also examine the behaviour of shortest TBR-sequence between two
   phylogenetic n/wks in a class, & whether the TBR-dist. changes if
   intermediate n/wks from other classes are allowed: e.g., the space of
   p.trees is an isometric subgraph of the space of phylogenetic n/wks under
   TBR. Lastly, we show that computing the TBR-distance & the PR-distance of
   two phylogenetic n/wks is NP-hard."
   -- 1906.04468@[<A HREF="https://arxiv.org/abs/1906.04468">arXiv</A>]['19].

%A S. McCauley
%T Approximate similarity search under edit distance using locality-sensitive
   hashing
%J arXiv
%M JUL
%D 2019
%K TR, c2019, c201x, c20xx, zz0719, string, strings, edit distance, match,
   matching, search, retrieval, locality, sensitive, hash, hashing, LSH, speed,
   approximate nearest neighbor problem
%X "... preprocess n strings of length d to quickly answer queries q of the
   form: if there is a database string within edit distance r of q, return a
   DB string within ED cr of q. ... In this work we achieve the first bounds for
   any approximation factor c, via a simple & easy-to-implement hash fn. This
   gives a running time of O~(d3^rn^{1/c}), with space O~(3^rn^{1+1/c}+dn). We
   show how to apply these ideas to the closely-related Approximate Nearest
   Neighbor problem for edit distance, obtaining similar time bounds."
   -- 1907.01600@[<A HREF="https://arxiv.org/abs/1907.01600">arXiv</A>]['19].
   [Also search for: locality sensitive hashing].

%A R. Giancarlo
%A G. Manzini
%A A. Restivo
%A G. Rosone
%A M. Sciortino
%T The alternating BWT: an algorithmic perspective
%J arXiv
%M JUL
%D 2019
%K TR, c2019, c201x, c20xx, zz0719, Alternating Burrows-Wheeler Transform, ABWT,
   BWT, string, strings, alternating lexicographical order, algorithm, Gessel
%X "The Burrows-Wheeler Transform (BWT) ... The Alternating Burrows-Wheeler
   Transform (ABWT) is another transformation recently introduced in [Gessel et
   al. 2012] & studied in the field of Combinatorics on Words. It is analogous
   to the BWT, except that it uses an alternating lexicographical order instead
   of the usual one. Building on results in [Giancarlo et al. 2018], where we
   have shown that BWT & ABWT are part of a larger class of reversible
   transformations, here we provide a combinatorial & algorithmic study of the
   novel transform ABWT. We establish a deep analogy between BWT & ABWT by
   proving they are the only ones in the above mentioned class to be
   rank-invertible, a novel notion guaranteeing efficient invertibility. [&] we
   show that the backward-search procedure can be efficiently generalized to the
   ABWT; this result implies that also the ABWT can be used as a basis for
   efficient compressed full text indices. Finally, we prove that the ABWT can
   be efficiently computed by using a combination of the Difference Cover suffix
   sorting algorithm [Karkkainen et al., 2006] with a linear time alg. for
   finding the minimal cyclic rotation of a word wrt the alt.lex. order."
   -- 1907.02308@[<A HREF="https://arxiv.org/abs/1907.02308">arXiv</A>]['19].

%A P. Bille
%A I. Li Gortz
%A T. Anna Steiner
%T String indexing with compressed patterns
%J arXiv
%M SEP
%D 2019
%J TR, c2019, c201x, c20xx, zz1019, string, strings, substring, match, index,
   query, pattern, search, compressed, LZ 77, LZ77, trie, algorithm,
   data structure
%X "Given a string S of length n, the classic string indexing problem is to
   preprocess S into a compact data struct. that supports efficient subsequent
   pattern queries. ... we consider the basic variant where the pattern is given
   in compressed form and the goal is to achieve query time that is fast in
   terms of the compressed size of the pattern. ... consider how to efficiently
   process the compressed query directly. Our main result is a novel linear
   space DS that achieves near-optimal query time for patterns compressed with
   the classic Lempel-Ziv compression scheme. [&] develop several data
   structural techniques of indep. interest, inc. a novel DS that compactly
   encodes all LZ77 compressed suffixes of a string in linear space & a general
   decomposition of tries that reduces the search time from logarithmic in the
   size of the trie to logarithmic in the length of the pattern."
   -- 1909.11930@[<A HREF="https://arxiv.org/abs/1909.11930">arXiv</A>]['19].

%A P. Charalampopoulos
%A T. Kociumaka
%A S. P. Pissis
%A J. Radoszewski
%A W. Rytter
%A J. Straszynski
%A T. Walen
%A W. Zuba
%T Weighted shortest common supersequence problem revisited
%J arXiv
%M SEP
%D 2019
%K TR, c2019, c201x, c20xx, zz1019, weighted shortest common supersequence,
   WSCS, SCS, SCSS, problem, NPC, weighted longest common subsequence, WLCS,
   Amir, fuzzy, character, probability, degenerate, dString, indeterminate,
   string, strings, algorithm
%X "A weighted string, also known as a position weight matrix, is a seq. of
   prob. distns over some alphabet. We revisit the Weighted Shortest Common
   Supersequence (WSCS) problem, introduced by Amir et al. [SPIRE 2011], that
   is, the SCS problem on weighted strings. .. we are given two weighted strings
   W1 and W2 and a threshold Freq on probability, and we are asked to compute
   the shortest (std) string S such that both W1 and W2 match subseqs. of S
   (not nec. the same) with prob. at least Freq. Amir et al. showed that this
   problem is NPC if the probs., inc. the threshold Freq, are represented by
   their logarithms (encoded in binary). We present an alg. that solves the WSCS
   problem for two wtd strings of length n over a const.-sized alphabet in
   O(n^2 sqrt(z) log(z)) time. Notably, our upper bound matches known cond.
   lower bounds stating that the WSCS problem cannot be solved in O(n^(2-e))
   time or in O^*(z^(0.5-e)) time unless there is a breakthrough improving upon
   long-standing upbs for fundamental NPH problems (CNF-SAT & Subset Sum,
   resp.). We also discover a fundamental difference between the WSCS problem &
   the WLCS problem, intr. by Amir et al. [JDA 2010]. We show that the WLCS
   problem cannot be solved in O(n^f(z)) time, for any fn f(z), unless P=NP."
   -- 1909.11433@[<A HREF="https://arxiv.org/abs/1909.11433">arXiv</A>]['19].
   [Also search for: indeterminate dString].

%A D. Kempa
%A T. Kociumaka
%T Resolution of the Burrows-Wheeler Transform conjecture
%J arXiv
%M OCT
%D 2019
%K TR, c2019, c201x, c20xx, zz1019, BWT, indexing, search, compression,
   string, strings, LZ, LZ77
%X "...  The compression ratio of BWT-based compressors, such as bzip2, is
   quantified by the # 'r' of maximal equal-letter runs in the BWT. ... we show
   that every text satisfies r=O(z log^2 n). This result has a # of immediate
   implications: (1) it proves that a large body of work related to BWT
   automatically applies to the so-far disjoint field of Lempel-Ziv indexing &
   compression, e.g., it is possible to obtain full functionality of the suffix
   tree & the suffix array in O(z polylog n) space; (2) it lets us relate the
   # of runs in the BWT of the text & its reverse; (3) it shows that many
   fundamental text processing tasks can be solved in the optimal time assuming
   that the text is compressible by a suff. large polylogn factor using LZ77."
      ('z' is "the size of Lempel-Ziv (LZ77) parsing of the text")
   -- 1910.10631@[<A HREF="https://arxiv.org/abs/1910.10631">arXiv</A>]['19].
   [Also search for: BWT].

%A Y. Sakai
%T Maximal common subsequence algorithms
%J TCS
%V 793
%P 132-139
%M NOV
%D 2019
%K jrnl, TCS, c2019, c201x, c20xx, zz0920, maximal common subsequence, MCS,
   MCSS, LCS, algorithm, string, strings
%X "A common subseq. of two strings is maximal if inserting any char. into it
   no longer yields a common subseq.. ... proposes a (sub)linearithmic-time,
   linear-space alg. for finding a MCS of two strings & a linear-time alg. for
   determining if a common subseq. of two strings is maximal."
   -- [<A HREF="https://doi.org/10.1016/j.tcs.2019.06.020">doi:10.1016/j.tcs.2019.06.020</A>]['20].

%A B. Cazaux
%A E. Rivals
%T Hierarchical overlap graph
%J IPL
%V 155
%N ?
%P ?-?
%M MAR
%D 2020
%K jrnl, IPL, c2020, c202x, c20xx, zz0120, graph, maths, algorithm, MolBio,
   sequence assembly, hierarchical, overlap, overlaps, HOG, strings, words,
   super string
%X "Given a set of finite words, the Overlap Graph (OG) is a complete weighted
   digraph where each word is a node & where the wt of an arc equals the length
   of the longest overlap of one word onto the other (Overlap is an asymmetric
   notion). The OG serves to assemble DNA fragments or to compute shortest
   superstrings, which are a compressed repn of the input. The OG requires space
   that is quadratic in the # of words, which limits its scalability. The
   Hierarchical Overlap Graph (HOG) is an alternative graph that also encodes
   all maximal overlaps, but uses space that is linear in the sum of the lengths
   of the input words. We propose the first alg. to build the HOG in linear
   space for words of equal length."
   -- [<A HREF="https://doi.org/10.1016/j.ipl.2019.105862">doi:10.1016/j.ipl.2019.105862</A>]['20],
   or 1802.04632@[<A HREF="https://arxiv.org/abs/1802.04632">arXiv</A>][2/'18].

%A M. Caceres
%A S. J. Puglisi
%A B. Zhukova
%T Fast indexes for gapped pattern matching
%J arXiv
%M FEB
%D 2020
%K TR, c2020, c202x, c20xx, zz0320, pattern, string, search, gap, gaps
%X "... indexes for searching large data sets for variable-length-gapped (VLG)
   patterns. ... composed of two or more subpat's, between each adjacent pair
   of which is a gap-constraint spec. upper & lower bds on the dist. allowed
   between subpat's. ... applic'ns in comp. biol. (motif search), info. ret.
   (e.g., for lang.models, snippet gen'n, m/c transl'n) & capture a useful
   subclass of the reg.exps. commonly used in practice for searching src code.
   Our best approach ... speeds several times faster than prior art across a
   broad range of pats & txts.
   -- 2002.12662@[<A HREF="https://arxiv.org/abs/2002.12662">arXiv</A>]['20].

%A H. Naganuma
%A D. Hendrian
%A R. Yoshinaka
%A A. Shinohara
%A N. Kobayashi
%T Grammar compression with probabilistic context-free grammar
%J arXiv
%M MAR
%D 2020
%K TR, c2020, c202x, c20xx, zz0420, text compression, CFG, PCFG, string,
   probabilistic context free grammar, compress, straight line program,
   straightLineProgram, SLP
%X "We propose a new approach for universal lossless text comp., based on
   grammar comp.. In the lit., a target string T has been compressed as a CFG G
   in Chomsky normal form satisfying L(G)={T}. Such a g. is often called a
   straight-line program (SLP). ... we consider a prob. gram. G that generates
   T, but not nec. as a unique elt of L(G). In order to recover the original
   text T unambiguously, we keep both the grammar G & the derivation tree of T
   from the start symbol in G, in compressed form. We show some simple evidence
   that our proposal is indeed more efficient than SLPs for certain texts, both
   from theoretical & practical points of view."
   -- 2003.08097@[<A HREF="https://arxiv.org/abs/2003.08097">arXiv</A>][18/3/2020].
   (Also see SLP@[<A HREF="https://en.wikipedia.org/wiki/Straight-line_program">wikip</A>]['21].)

%A G. Navarro
%T Indexing highly repetitive string collections
%J arXiv
%M APR
%D 2020
%K TR, c2020, c202x, c20xx, zz0420, strings, index, indexing, repetitive,
   repetition, repeats, data structure, compress, MolBio, bioinformatics
%X "Two decades ago, a breakthrough in indexing string collections ...
   [but] the string collections experienced a growth that outperforms Moore's
   Law ... [however] many of these rapidly growing string collections are highly
   repetitive ...  a new set of techniques has been developed in order to
   properly exploit [repetition]. ...  In this survey we cover the algorithmic
   developments that have led to these data structures. We describe the distinct
   compression paradigms that have been used to exploit repetitiveness ..."
   -- 2004.02781@[<A HREF="https://arxiv.org/abs/2004.02781">arXiv</A>][6/4/2020].
   [Also search for: string index].

%A L. M. S. Russo
%A A. P. Francisco
%A T. Rocher
%T Incremental multiple longest common subsequences
%J arXiv
%M MAY
%D 2020
%K TR, c2020, c202x, c20xx, zz0520, string, strings, LCS, LCSS, incremental,
   alignment, sub sequence, subsequence
%X "... a way to maintain this information when the underlying sequences are
   subject to modifications, namely when letters are added and removed from the
   extremes of the sequence. ..."
   -- 2005.02725@[<A HREF="https://arxiv.org/abs/2005.02725">arXiv</A>]['20].

%A A. Andoni
%A N. S. Nosatzki
%T Edit distance in near-linear time: It's a constant factor
%J arXiv
%M MAY
%D 2020
%K TR, c2020, c202x, c20xx, zz0520, string, strings, sequence,
   approximate, approximation, edit distance, algorithm, Chakraborty, Saks
%X "... alg. for approximating the edit distance between two strings of
   length n in time n^{1+e}, for any e > 0, up to a const. factor. ... completes
   the research dirn set forth in ... [Chakraborty-Das-Goldenberg-Koucky-Saks,
   FOCS18], which showed the first const.-factor approx. alg. with a
   (strongly) sub-quadratic running time. Several recent results have shown
   near-linear complexity under different restrictions on the inputs (eg, when
   the ED is close to maximal, or when one of the inputs is pseudo-random).
   ... our alg. obtains a constant-factor approx. in near-linear running time
   for any input strings."
   -- 2005.07678@[<A HREF="https://arxiv.org/abs/2005.07678">arXiv</A>]['20].
   [Also search for: strings approximation algorithm].

%A P. Charalampopoulos
%A P. Gawrychowski
%A K. Pokorski
%T Dynamic longest common substring in polylogarithmic time
%J arXiv
%M JUN
%D 2020
%K TR, c2020, c202x, c20xx, zz0620, dynamic longest common substring, DLCS,
   algorithm, string, strings
%X "...  the dynamic variant of this problem, in which we are to maintain two
   dynamic strings S & T, each of length at most n, that undergo substitutions
   of letters, in order to be able to return a LC-substring after each subs'n.
   Recently, Amir et al. [ESA 2019] presented a soln ... needs only O((n^{2/3})
   time per update. ... [we] designing a sig. faster alg. that processes each
   subsn in amortized log^(O(1)}(n) time with high prob.. ... relies on
   exploiting the local consistency of the parsing of a collection of dynamic
   strings due to Gawrychowski et al. [SODA 2018], & on maintaining two dynamic
   trees with labeled bicolored leaves, so that after each update we can report
   a pair of nodes, one from each tree, of maximum combined weight, which have
   >= 1 common leaf-descendant of each color. We complement this with a lwb of
   Omega(logn/loglogn) for the update time of any polynomial-size data structure
   that maintains the LCS of two dynamic strings, & the same lwb for the update
   time of any data structure of size Obar(n) that maintains the LCS of a static
   & a dynamic string. Both lwbs hold even allowing amortization &
   randomization."
   -- 2006.02408@[<A HREF="https://arxiv.org/abs/2006.02408">arXiv</A>]['20].
   [Also search for: longest common substring].
   (NB. subSTRING not seq.)

%A C. Boucher
%A et al ...
%A M. Rossi
%T PFP Data Structures
%J arXiv
%M JUN
%D 2020
%K TR, c2020, c202x, c20xx, zz0620, prefix free parsing, BWT, repetitive,
   string, strings, genomic database, dataStructure, DS
%X "Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a
   preprocessing step to ease the computation of BWT (BWTs) of genomic DBs.
   ... produces a dictionary D and a parse P of overlapping phrases such that
   BWT(S) can be computed from D and P in time & workspace bounded in terms of
   their combined size |PFP(S)|. In practice D & P are sig. smaller than S ...
   provide experimental evidence that the PFP [DS] can be efficiently
   constructed for v.large repetitive datasets: it takes one hour & 54GB peak
   memory for 1000 variants of human chr.19, initially occupying ~ 56GB."
   -- 2006.11687@[<a HREF="https://arxiv.org/abs/2006.11687">arXiv</A>]['20].
   [Also search for: strings BWT].

%A Jin Cao
%A Dewei Zhong
%T A fast randomized algorithm for finding the maximal common subsequences
%J arXiv
%M SEP
%D 2020
%K TR, c2020, c202x, c20xx, zz0920, multiple, string, strings,
   maximal common subsequence, MCS, MCSS, LCS
%X "... we develop a randomized alg., referred to as Random-MCS, for finding a
   random inst. of [MCS] of multiple strings. ... We show the complexity of our
   alg. is linear in L [# strings], & therefore is suitable for large L. ...
   study the occurrence prob. for a single instance of MCS & demo. via both
   theor. and exp. studies that the LCS from multiple runs of  Random-MCS often
   yields a solution to LCS."
   -- 2009.03352@[<A HREF="https://arxiv.org/abs/2009.03352">arXiv</A>]['20].
   [Also search for: string MCS algorithm]  (or try MCS -> LCS).

%A L. Jordon
%A P. Moser
%T A normal sequence compressed by PPM* but not by Lempel-Ziv 78
%J arXiv
%M SEP
%D 2020
%K TR, c2020, c202x, c20xx, zz0920, string, compression, PPM, PPM*, LZ78
%X "... compare the difference in performance of two of the Prediction by
   Partial Matching (PPM) family of compressors (PPM* and the original Bounded
   PPM alg.) & the Lempel-Ziv 78 (LZ) alg.. We construct an infinite binary seq.
   whose worst-case compression ratio for PPM* is 0, while Bounded PPM's & LZ's
   best-case comp.ratios are at least 1/2 & 1 resp.. This seq. is an enum. of
   all binary strings in order of length, i.e. all strings of length 1 followed
   by all strings of length 2 & so on. It is therefore normal, & is built using
   repetitions of deBruijn strings of increasing order."
   -- 2009.04827@[<A HREF="https://arxiv.org/abs/2009.04827">arXiv</A>]['20].

%A M. Lily
%A A. Clare
%A et al
%T Evaluation of a permutation-based evolutionary framework for
   Lyndon factorizations
%J Parallel Problem Solving from Nature - PPSN XVI
%P 390-403
%M SEP
%D 2020
%K conf, c2020, c202x, c20xx, zz1221, MolBio, AClare, Lyndon factorization,
   LyndonWord, word, words, string, strings, alphabet, ordering
%X "String factorization is an important tool for partitioning data for parallel
   proc. & other alg.techniques ... . Duval's well-known alg. uniquely factors
   a string over an ordered alphabet into Lyndon words, i.e., patterned strings
   which are strictly smaller than all of their cyclic rotations. While D's alg.
   produces a pre-determined factorization, modern applications motivate the
   demand for fs. with specific properties, e.g., those that minimize the # of
   factors or consist of factors with similar lengths. ... we consider the
   problem of finding an alphabet ordering that yields a Lyndon f. with such
   properties. We introduce a flexible evolutionary f/wk & evaluate it on
   biol. seq. data. For the minimization case, we also propose a new
   problem-specific heuristic, Flexi-Duval, & a problem-specific mutation
   operator for Lyndon f.. Our results show that our f/wk is competitive with
   Flexi-Duval for minimization & yields high quality & robust solns for
   balancing where no problem-specific alg. is available."
   -- pdf@[<A HREF="https://pure.aber.ac.uk/portal/files/38779287/PPSN_2020_Lyndon_Factorization.pdf">AberU</A>]['21],
      [<A HREF="https://doi.org/10.1007/978-3-030-58112-1_27">doi:10.1007/978-3-030-58112-1_27</A>]['21].
   [Also search for: Lyndon factorization].

%A D. Chakraborty
%A D. Das
%T Approximating edit distance within constant factor in truly sub-quadratic
   time
%J JACM
%V 67
%N 6
%P 1-22
%M NOV
%D 2020
%K jrnl, JACM, c2020, c202x, c20xx, zz0721, approximate, edit distance,
   approximation algorithm, strings
%X "... Andoni, Krauthgamer, & Onak (2010) gave a nearly linear time alg. that
   approx. ED within approx. factor poly(log n). ... we provide an alg. with
   running time O~(n^{2-2/7}) that approx. the ED within a const. factor."
   -- [<A HREF-:https://doi.org/10.1145/3422823">doi:10.1145/3422823</>]['21].
   [Also search for: strings approximation algorithm].

%A D. S. N. Nunes
%A et al ...
%A G. Navarro
%A Grammar compression by induced suffix sorting
%J arXiv
%M NOV
%D 2020
%K TR, c2020, c202x, c20xx, zz1120, compress, compression, algorithm, GCIS,
   grammar, SAIS, Gzip, 7zip, RePair, suffix sort
%X "A grammar compression alg., called GCIS, is introduced in this work. GCIS is
   based on the induced suffix sorting alg. SAIS, presented by Nong et al. in
   2009. ... experiments on regular & repetitive, moderate & very large texts,
   show that GCIS stands as a very convenient choice compared to well-known
   compressors such as Gzip, 7-Zip, & RePair, the gold standard in grammar
   compression. ..."
   -- 2011.12898@[<A HREF="https://arxiv.org/abs/2011.12898">arXiv</A>][25/11/'20].
   [Also search for: grammar compress].

%A T. Gagie
%A G. Navarro
%A N. Prezza
%T Fully functional suffix trees and optimal text searching in BWT-runs bounded
   space
%J JACM
%V 67
%N 1
%P 1-54
%M JAN
%D 2020
%K Jrnl, JACM, c020, c202x, c20xx, zz0321, run length FM index, FMindex, BWT,
   RLBWT, suffix tree, repetitive strings, stringology
%X "Indexing highly repetitive text - such as genomic databases, s/w
   repositories & versioned text collections ... One of the earliest indexes for
   rep.collections, the Run-Length FM-index, used O(r) space & was able to
   efficiently count the # of occurrences of a pattern of length m in a text of
   length n (in O(m log log n) time, with current techniques). However, it was
   unable to locate the posns of those occurrences efficiently within a space
   bounded in terms of r. ... we close this long-standing problem, showing how
   to extend the Run-Length FM-index so that it can locate the occ occurrences
   efficiently (in O(occ log log n) time) within O(r) space. By raising the
   space to O(r log log n), our index counts the occurrences in optimal time,
   O(m), & locates them in optimal time as well, O(m+occ). By further raising
   the space by an O(w/log s) factor, where s is the alphabet size &
   w=Omega(log n) is the RAM machine size in bits, we support count & locate in
   O(ceil(m log (s)/w)) & O(ceil(m log (s)/w)+occ) time, which is optimal in the
   packed setting & had not been obtained before in compressed space. We also
   describe a structure using O(r log (n/r)) space that replaces the text &
   extracts any text substring of length L in the almost-optimal time
   O(log (n/r)+L log (s)/w). Within that space, we similarly provide access to
   arbitrary suffix array, inverse suffix array, & longest common prefix array
   cells in time O(log(n/r)), and extend these capabilities to full suffix tree
   functionality, typically in O(log(n/r)) time per operation. Our experiments
   show that our O(r)-space index outperforms the space-competitive alternatives
   by 1 to 2 orders of magnitude in time. Competitive implementations of the
   original FM-index are outperformed by 1 to 2 orders of magnitude in space
   &/or 2 to 3 in time.
   -- [<A HREF="https://doi.org/10.1145/3375890">doi:10.1145/3375890</A>]['21].

%A P. Niroula
%A Yunseong Nam 
%T A quantum algorithm for string matching
%J NPI Quantum Info.
%V 7
%N #37
%M FEB
%D 2021
%K jrnl, eJrnl, c2021, c202x, c20xx, zz0324, string, pattern, search, algorithm,
   quantum computing, strings
%X "Algs. that search for a pattern within a larger data-set ... we present an
   explicit, circuit-level implementation of a q. pattern-matching alg. that
   matches a search string (pattern) of length M inside a longer text of length
   N. ... has a time complexity of ~O(sqrt N), while the space complexity
   remains modest at O(N+M). We report the q.gate counts relevant for both
   pre-fault-tolerant & fault-tolerant regimes."
   -- [<A HREF="https://doi.org/10.1038/s41534-021-00369-3">doi:10.1038/s41534-021-00369-3</A>]['24].
   [Also search for: quantum algorithm strings].

%A S. J. Puglisi
%A B. Zhukova
%T Smaller RLZ-compressed suffix arrays
%J Data Comp. Conf. (DCC)
%I IEEE
%M MAR
%D 2021
%K conf, c2021, c202x, c20xx, zz0321, DCC, DCC21, DCC2021, Snowbird, strings,
   suffix array, index, RLZ, RLZSA, SAdiff
%X "Recently it was shown (auths SPIRE, 2020) that the suffix array (SA) data
   structure can be effectively compressed with relative Lempel-Ziv (RLZ)
   dictionary comp'n in such a way that arbitrary subarrays can be rapidly
   decompressed, thus facilitating compressed indexing. ... we describe
   optimizations to RLZ-compressed SAs, including generation of more effective
   dictionaries & compact encodings of index components, both of which reduce
   index size without adversely affecting subarray access speeds relative to
   other compressed indexes. Our experimental analysis also elucidates the
   relationship between subarray size and per elt access time.
   -- [<A HREF="https://doi.org/0.1109/DCC50243.2021.00029">doi:0.1109/DCC50243.2021.00029</A>]['21].
   [Also search for: DCC21].

%A T. Akutsu
%A T. Mori
%A N. Nakamura
%A S. Kozawa
%A Y. Ueno
%A T. N. Sato
%T Tree edit distance with variables. Measuring the similarity between
   mathematical formulas
%J arXiv
%M MAY
%D 2021
%K TR, c2021, c202x, c20xx, zz0521, mathematical formula, tree edit distance,
   parse tree, variable, similarity, similar, formulae
%X "... propose tree edit dist. with variables, which is an extn of the [TED]
   to handle trees with variables & has a potential application to measuring the
   similarity between math. formulas, esp., those appearing in math. models of
   biol. sys.. ... show that the problem is NP-complete for ordered trees. [&]
   show for unordered trees that the problem of deciding whether or not the
   distance is 0 is graph isomorphism complete but can be solved in polynomial
   time if the max. outdegree of input trees is bounded by a constant. This
   distance model is then extended for measuring the difference/similarity
   between two systems of differential equns, for which results of preliminary
   computational experiments using biological models are provided."
   -- 2105.04802@[<A HREF="https://arxiv.org/abs/2105.04802">arXiv</A>]['21].

%A M. Boroujeni
%A S. Ehsani
%T Approximating edit distance in truly subquadratic time: Quantum and mapReduce
%J JACM
%V 68
%N 3
%P 1-41
%M MAY
%D 2021
%K jrnl, JACM, c2021, c202x, c20xx, zz0721, approximate, edit distance,
   quantum computing, approximation algorithm, strings
%X "... Our main result is a quantum constant approx. alg. for computing the
   ED in truly subquadratic time. More precisely, we give an q.alg. that
   approximates the ED within a factor of 3. We further extend this result to an
   q.alg. that approximates the ED within a larger constant factor. ... further
   show that this f/wk enables us to approx. ED in distributed settings. To this
   end, we provide a MapReduce alg. to approx. ED within a factor of ??, with
   sublinearly many machines & sublinear memory. Also, our alg. runs in a
   logarithmic number of rounds."
   -- [<A HREF="https://doi.org/10.1145/3456807">doi:10.1145/3456807</A>]['21].
   [Also search for: strings approximation algorithm].

%A K. Bringmann
%A V. Cohen-Addad
%A D. Das
%T A linear-time n^{0.4}-approximation for longest common subsequence
%J arXiv
%M JUN
%D 2021
%K TR, c2021, c202x, c20xx, zz0621, longest common subsequence, LCS, LCSS,
   strings, approximation algorithm, Abboud
%X "... While a simple quadratic alg. has been known ... for more than 40 years,
   no faster alg. has been found despite an extensive effort. The lack of
   progress on the problem has recently been explained by Abboud, Backurs, &
   Vassilevska Williams [FOCS'15] & Bringmann & Kunnemann [FOCS'15] who proved
   that there is no subquadratic alg. unless the Strong Exponential Time
   Hypothesis fails. ... we provide an alg. that in time O(n^{2âe}) computes an
   ~O(n^{2e/5})-apprxn with high prob., for any 0 < e <= 1. Our result (1) gives
   an ~O(n^{0.4})-apprxn in linear time, improving upon the bound of Hajiaghayi,
   Seddighin, Seddighin, & Sun, (2) provides an alg. whose apprxn scales with
   any subquadratic running time O(n^{2-e}), improving upon the naive bound of
   O(n^{e/2}) for any e, & (3) instead of only in expectation, succeeds with
   high prob.."
   -- 2106.08195@[<A HREF="https://arxiv.org/abs/2106.08195">arXiv</A>]['21].
   [Also search for: strings approximation algorithm].

%A M. Khan
%A A. Miranskyy
%T String comparison on a quantum computer using Hamming distance
%J arXiv
%M JUN
%D 2021
%K TR, c2021, c202x, c20xx, zz0721, Hamming distance, quantum computing,
   algorithm, strings, QisKit
%X "... we extend an existing alg. for computing the H.dist.. ... can compare
   strings with symbols drawn from an arbitrary-long alphabet (which the
   orig. alg. could not). We implement our extended alg. using the QisKit
   f/wk to be executed by a programmer without the knowledge of a QC (the code
   is publicly available). We then provide four pedagogical examples: two from
   the field of bioinf. & two from the field of SWEng. We finish by discussing
   resource requirements & the time horizon of the QCs becoming practical for
   string comp.."
   -- 2106.16173@[<A HREF="https://arxiv.org/abs/2106.16173">arXiv</A>]['21].
   [Also search for: quantum algorithm strings].

%A Y. Galluzzo
%A R. Giancarlo
%A M. Randazzo
%A S. E. Rombo
%T Burrows Wheeler transform on a large scale: Algorithms implemented in
   Apache Spark
%J arXiv
%M JUL
%D 2021
%K TR, c2021, c202x, c20xx, zz0721, strings, Burrows Wheeler Transform, BWT,
   parallel, cloud, distributed, Apache Spark, Hadoop
%X "With the rapid growth of Next Generation Sequencing (NGS) technologies,
   large amounts of "omics" data are daily collected & need to be processed. ...
   Here we propose algs. for the comp'n of BWT relying on Big Data tech., i.e.,
   Apache Spark & Hadoop. Our algs. are the first ones that distribute the
   index comp'n & not only the input dataset, allowing to fully benefit of the
   available cloud resources."
   -- 2107.03341@[<A HREF="https://arxiv.org/abs/2107.03341">arXiv</A>]['21].

%A M. Kosche
%A T. Koss
%A F. Manea
%A S. Siemer
%T Absent subsequences in words
%J arXiv
%M AUG
%D 2021
%O ext. abs. in Proc. 15th Int. Conf. on Reachability Problems RP2021
%K TR, c2021, c202x, c20xx, zz0921, strings, word, absent subsequence, shortest,
   minimal, missing, substring, algorithm
%X "An absent factor of a string w is a string u which does not occur as a
   contiguous substring ... We extend this ... & define absent subsequences: a
   string u is an absent subseq. of a string w if ... Of particular interest to
   us are minimal absent subseqs., i.e., absent subseq. whose every subseq. is
   not absent, & shortest absent subseq. ... For instance: we give combinatorial
   characterisations of the sets of minimal & shortest ... as well as compact
   representations of these sets; ... we can test efficiently if a string is a
   shortest or minimal absent subseq. ... give efficient algs. computing the
   lexicographically smallest [AS] of each kind; also, we show how a data
   structure for answering [SAS]-queries for the factors of a given string can
   be efficiently computed."
   -- 2108.13968@[<A HREF="https://arxiv.org/abs/2108.13968">arXiv</A>]['21].
   [Also search for: string absent].

%A Shyan Akmal
%A Ce Jin
%T Near-optimal quantum algorithms for string problems
%K arXiv
%M OCT
%D 2021
%K TR, c2021, c202x, c20xx, zz1021, string, strings, substring,
   quantum algorithm, Lyndon word, LyndonWord
%X "We study q.algs. for several fundamental string problems, inc. Longest
   Common Substring, Lexicographically Minimal String Rotation, & Longest
   Square Substring. ... known to be solvable by near-linear time classical
   algs.. ... Longest Square Substring can be solved by a q.alg. in
   ~O(n^{2/3}) time. ... is an adaptation of the alg. by Le Gall & Seddighin
   (2020) for the Longest Palindromic Substring problem, but uses additional
   techniques to overcome the difficulty that binary search no longer applies.
   Our techniques naturally extend to other related string problems, such as
   Longest Repeated Substring, Longest Lyndon Substring, & Minimal Suffix."
   -- 2110.09696@[<A HREF="https://arxiv.org/abs/2110.09696">arXiv</A>]['21].
   [Also search for: strings quantum algorithm].

%A Xiao Mao
%T Breaking the cubic barrier for (unweighted) tree edit distance
%J FOCS
%D 2021
%O SIAM J. Comput., 53(1), 2024
%K conf, FOCS, c2021, c202x, c20xx, zz0224, unweighted, tree edit distance,
   treeEdit, maxPlus, algorithm
%X "... In this paper, we break the cubic barrier by showing an time alg. for
   the unweighted tree ED problem. We consider an equivalent maximization
   problem & use a DP scheme involving matrices with many special properties. By
   using a decomposition scheme as well as several combinatorial techniques, we
   reduce TED to the max-plus product of bounded-difference matrices, which can
   be solved in truly subcubic time ..."
   -- [<A HREF="https://doi.org/10.1137/22M1480719">doi:10.1137/22M1480719</A>]['24].
   [Also search for: treeEdit].

%A H. Bannai
%A Tomohiro I
%A T. Kociumaka
%A D. Koppl
%A S. J. Puglisi
%T Computing longest (common) Lyndon subsequences
%J arXiv
%M JAN
%D 2022
%K TR, c2022, c202x, c20xx, zz0122, Lyndon, word, words, LyndonWord, factors,
   subsequence, string, strings, longest common Lyndon subsequence, LCLS,
   algorithm
%X "Given a string T with length n whose characters are drawn from an ordered
   alphabet of size s, its longest Lyndon subsequence is a longest subseq. of
   T that is a Lyndon word. We propose algs. for finding such a subseq. in
   O(n^3) time with O(n) space, or online in O(n^3s) space & time. Our 1st
   result can be extended to find the longest common L. subseq. of two strings
   of length n in O(n^4s) time using O(n^3) space.
   -- 2201.06773@[<A HREF="https://arxiv.org/abs/2201.06773">arXiv</A>]['22].
   [Also search for: LyndonWord].

%A D. Cenzato
%A Z. Liptak
%T A theoretical and experimental analysis of BWT variants for
   string collections
%J arXiv
%M FEB
%D 2022
%K TR, c2022, c202x, c20xx, zz0322, BWT, strings, collection, index, eBWT,
   omega order
%X "The extended Burrows-Wheeler-Transform (eBWT), introduced by Mantaci et al.
   is a generalization of the (BWT) to multisets of strings. While the original
   BWT is based on the lexicographic order, the eBWT uses the omega-order, which
   differs from the lexicographic order in important ways. ... we review the
   differences between ... BWT variants, both from a theor. & from a practical
   pt of view, comparing them on several real-life datasets with different
   characteristics. We find that the differences can be extensive, depending on
   the dataset characteristics, & are largest on collections of many highly
   similar short sequences. The widely-used param. r, the # of runs of the BWT,
   also shows notable var'n between the different BWT variants; on our datasets,
   it varied by a multiplicative factor of up to 4.2."
   -- 2202.13235@[<A HREF="https://arxiv.org/abs/2202.13235">arXiv</A>]['22].
   [Also search for: strings eBWT].

%A R. Giancarlo
%A G. Manzini
%A A. Restivo
%A G. Rosone
%A M. Sciortino
%T A new class of string transformations for compressed text indexing
%J arXiv
%M APR
%D 2022
%K TR, c2022, c202x, c20xx, zz0522, BWT, ABWT, string transformation, strings,
   invertible, index
%X "... Among the known BWT variants, the only one that has been recently shown
   to be a valid alternative to BWT is the Alternating BWT (ABWT), another
   invertible string transformation ... Lyndon words. ... we introduce a whole
   class of new string transformations, called local orderings-based trans.,
   which have all the myriad virtues of BWT. We show that this new family is a
   special case of a much larger class of trans., based on context adaptive
   alphabet orderings, that includes BWT & ABWT. Although all trans. support
   pattern search, we show that, in the general case, the trans. within our
   larger class may take quadratic time for inversion & pattern search. As a
   further result, we show that the local orderings-based trans. can be used for
   the construction of the recently introduced r-index, which makes them
   suitable also for highly repetitive collections. In this context, we consider
   the problem of finding, for a given string, the BWT variant that minimizes
   the # of runs in the transformed string, & we provide an alg. solving this
   problem in linear time."
   -- 2205.05643@[<A HREF="https://arxiv.org/abs/2205.05643">arXiv</A>]['22].
   [Also search for: BWT string].

%A G. Bernardini
%A P. Gawrychowski
%A N. Pisanti
%A S. P. Pissis
%A G. Rosone
%T Elastic-degenerate string matching via fast matrix multiplication
%J SIAM J. Comp.
%V 51
%N 3
%P ?-?
%M JUN
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0622, elastic degenerate string, dString,
   EDstring, problem, indeterminate, strings, EDSM, matching, search, pattern
%X "... An elastic-degenerate (ED) string is a seq. of n sets of strings of
   total length N ... to model a set of similar seqs.. The ED string matching
   (EDSM) problem is to find all occurrences of a pattern of length m in an ED
   text ... Our main technical contrib. is that we successfully combine these
   tools with fast matrix mult. to design a noncombinatorial ~O(nm^{omega-1}+N)-
   time alg. for EDSM, where omega denotes the matrix mult. exponent & the
   ~O(...)$ notation suppresses polylog factors. ..."
   -- [<A HREF="https://doi.org/10.1137/20M1368033">doi:10.1137/20M1368033</A>]['22], and
      1905.02298@[<A HREF="https://arxiv.org/abs/1905.02298">arXiv</A>]['22].

%A A. Abdi
%A M. Hooshmand
%T Longest common subsequence: Tabular vs. closed-form equation computation of
   subsequence probability
%J arXiv
%M JUN
%D 2022
%K TR, c2022, c202x, c20xx, zz0622, LCS, LCSS, multiple alignment,
   tabular random, heuristic
%X "... The LCS problem is an NP-hard problem ... heuristics methods. The
   baseline for most famous heuristics fns is a tabular random, probabilistic
   approach. This approach approximates the length of the LCS in each iteration.
   ... we introduce a closed-form eqn of the probabilistic table calculation for
   the 1st time. Moreover, we present other corr. forms of the closed-form
   eqn & prove all of them. ..."
   -- 2206.11726@[<A HREF="https://arxiv.org/abs/2206.11726">arXiv</A>]['22].

%A Z. Liptak
%A F. Masillo
%A S. J. Puglisi
%T Suffix sorting via matching statistics
%J arXiv
%M JUL
%D 2022
%K TR, c2022, c202x, c20xx, zz0722, generalised suffix array, similar strings,
   string, sacamats, heuristic
%X "We introduce a new algorithm for constructing the generalized suffix array
   of a collection of highly similar strings. ..."
   -- [<A HREF="https://doi.org/10.48550/arXiv.2207.00972">doi:10.48550/arXiv.2207.00972</A>]['22] (arXiv).

%A P. Gawrychowski
%A F. Manea
%A S. Siemer
%T Matching patterns with variables under edit distance
%J arXiv
%M JUL
%D 2022
%K TR, c2022, c202x, c20xx, zz0722, stringology, pattern match, variable,
   edit distance
%X "... say that 'a' matches a word w, consisting only of terminal letters, if
   w can be obtained by replacing the variables of 'a' by terminal words. ...
   NP-complete in general, but can be solved efficiently for classes of patterns
   with restricted structure. ... interested in what is the minimum Hamming
   distance between w & any word u obtained by replacing the variables of 'a' by
   terminal words ... Moreover, under Hamming distance, if a variable occurs
   more than once & its occurrences can be interleaved arbitrarily with those of
   other vars., even if each of these occurs just once, the matching problem is
   intractable. In this paper, we consider the problem of matching patterns with
   vars. under edit distance. We still obtain efficient algs. & matching
   conditional lower bounds for the class of regular patterns, but show that the
   problem becomes, in this case, intractable already for unary patterns,
   consisting of repeated occurrences of a single var. interleaved with
   terminals."
   -- 2207.07477@[<A HREF="https://arxiv.org/abs/2207.07477">arXiv</A>]['22].

%A P. Charalampopoulos
%A et al
%T Approximate circular pattern matching
%J arXiv
%M AUG
%D 2022
%K TR, c2022, c202x, c20xx, zz0822, circular pattern, match, CPM, string,
   substring, cyclic, edit distance
%X "... under the Hamming & edit dist. ... we are to report all starting posns
   of fragments of T (called occurrences) that are at distance at most k from
   some cyclic rotation of P. ... For the reporting version of the approx. CPM
   problem, under the Hamming dist. we improve upon the main alg. of [CKP+,
   JCSS'21] from O((n+(n/m)âk^4) to O((n+(n/m)âk^3 log log k) time; for the edit
   dist., we give an O(nk^2)-time alg.. We also consider the decision version of
   the approx. CPM problem. Under the Hamming dist., we obtain an
   O(n+(n/m)âk^2 log(k)/log(log(k)))-time alg., which nearly matches the alg. by
   Chan et al. ..."
   -- 2208.08915@[<A HREF="https://arxiv.org/abs/2208.08915">arXiv</A>]['22].
   (NB. circular pattern not circular text.)
   [Also search for: circular string distance].

%A G. Badkobeh
%A A. De Luca
%A G. Fici
%A S. Puglisi
%T Maximal closed substrings
%K arXiv
%M SEP
%D 2022
%K TR, c2011, c201x, c20xx, zz0922, maximal closed substring, MCS, string,
   strings, run, repeat
%X "A string is closed if it has length 1 or has a nonempty border without
   internal occurrences. ... we introduce the defn of a maximal closed substring
   (MCS) ... an occurrence of a closed substring that cannot be extended to the
   left nor to the right into a longer ... MCSs with exponent at least 2 are
   commonly called runs; those with exponent < 2, instead, are particular cases
   of maximal gapped repeats. We show that a string of length n contains
   O(n^{1.5}) MCSs. We also provide an output-sensitive alg. that, given a
   string of length n over a constant-size alphabet, locates all m MCSs the
   string contains in O(n.log(n)+m) time."
   -- 2209.00271@[<A HREF="https://arxiv.org/abs/2209.00271">arXiv</A>]['22].
   [Also search for: closed string].

%A D. Das
%A et al ...
%A H. Saleh
%T O(n+poly(k))-time algorithm for bounded tree edit distance
%J arXiv
%M SEP
%d 2022
%K TR, c2022, c202x, c20xx, bounded tree edit distance, BTED, algorithm
%X "... Given a param. k as an upb on the dist., an O(n+k^2)-time alg. for edit
   distance has been known since the 1980s due to the works of Myers (... '86) &
   Landau & Vishkin (JCSS'88). The existence of an ~O(n+poly(k))-time alg. for
   TED has been posed as an open Q., e.g., by Akmal & Jin (ICALP'21), who gave a
   state-of-the-art ~O(nk^2)-time alg.. ... we answer this Q positively."
   -- 2209.07524@[<A HREF="https://arxiv.org/abs/2209.07524">arXiv</A>]['22].

%A K. Chowdhury
%T Designing a parallel suffix sort
%j arXiv
%M OCT
%D 2022
%K TR, c2022, c202x, c20xx, zz1022, string, suffix array, sort, algorithm,
   generalized polynomial factorization
%X "... The sorting alg. becomes tricky when we have lot of repeated chars. in
   the string for a given radix. ... present here an analysis that uses a
   concept around generalized polynomial factorization to sort these suffixes.
   ... The set of distinct factors & their order are known beforehand, & this
   helps us to sort the polynomials (equivalent of strings) accordingly."
   -- 2210.01475@[<A HREF="https://arxiv.org/abs/2210.01475">arXiv</A>]['22].
   [Also search for: string suffix array].

%A E. Goldenberg
%A T. Kociumaka
%A R. Krauthgamer
%A B. Saha
%T An algorithmic bridge between Hamming and Levenshtein distances
%J arXiv
%M NOV
%D 2022
%K TR, c2022, c202x, c20xx, zz1122, string, edit distance, algorithm,
   indel, indels
%X "... in many real-life scenarios, insertions & deletions (indels) appear
   freq. but sig. less so than substitutions. ... consider substitutions being
   cheaper than indels, with cost 1/a for a parameter a>=1. [ED_a] ... first
   present a simple deterministic exact alg. for ED_a & further prove that it is
   near-optimal assuming the Orthogonal Vectors Conjecture. Our main result is a
   randomized alg. computing a (1+e)-approx. of ED_a(X,Y), given strings X,Y of
   total length n & a bound k>=ED_a(X,Y) ..."
   -- 2211.12496[<A HREF="https://arxiv.org/abs/2211.12496">arXiv</A>]['22].

%A D. Cenzato
%A V. Guerrini
%A Z. LiptÃ¡k
%A G. Rosone
%T Computing the optimal BWT of very large string collections
%J arXiv
%M DEC
%D 2022
%K TR, c2022, c202x, c20xx, zz1222, optBWT, BWT, string, strings, many,
   collection, letter runs, SAIS, BCR, SAP
%X "It is known that the exact form of the ... (BWT) of a string coll'n depends,
   in most implementations, on the input order of the strings in the coll'n.
   Reordering strings of an input coll'n affects the # of equal-letter runs r
   ... we present the first tool that guarantees a BWT with minimum # of runs
   (optBWT), by combining i) an alg. that builds the BWT from a string coll'n
   (either SAIS-based ...] or BCR ...; ii) the SAP array data structure
   introduced in [...]; & iii) the alg. by Bentley et al. ..."
   -- 2212.01156@[<A HREF="https://arxiv.org/abs/2212.01156">arXiv</A>]['22].
   [Also search for: BWT]  and  [also search for: BWT collection].

%A S. Faro
%A T. Lecroq
%A K. Park
%A S. Scafiti
%T On the longest common Cartesian substring problem
%J COMPJ
%V 66
%N 4
%P 907-923
%M APR
%D 2023
%K jrnl, COMPJ, c2023, c202x, c20xx, zz0523, cartesian substring problem, heap,
   algorithm, LCCS, string, strings, range search
%X "... the Cartesian tree matching problem appeared very recently. It consists
   in finding all substrings of given text, which have the same Cartesian tree
   as that of a given pattern. ... we address the problem of computing the
   longest common Cartesian substrings of two strings & present three methods
   for such problem ... From our experimental results, it turns out that our
   2nd soln runs faster than the std suffix tree soln for short strings, whereas
   our 3rd soln is more suitable for large strings, when storing a full suffix
   tree becomes prohibitive."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxab204">doi:10.1093/comjnl/bxab204</A>]['23].
   (Also see, "... seq. of distinct numbers ... A symmetric (in-order) traversal
   of the tree results in the original seq. ..."
   -- C.Tree@[<A HREF="https://en.m.wikipedia.org/wiki/Cartesian_tree">wikip</A>]['23].)

%A Md. Rabiul Islam Khan
%A S. Shahriar
%A S. Farhan Rafid
%T A linear time quantum algorithm for pairwise sequence alignment
%J arXiv
%M JUL
%D 2023
%K TR, MolBio, c2023, c202x, c20xx, zz0723, strings, sequence alignment,
   quantum, computing, algorithm, Grover search
%X "... a q.alg. for finding the optimal alignment between DNA seqs. [is]
   demonstrated which works by mapping the seq. alignment problem into a
   path-searching problem through a 2D graph. ... based on a proposed oracle for
   profit calculation. ..."
   -- 2307.04479@[<A HREF="https://arxiv.org/abs/2307.04479">arXiv</A>]['23].
   [Also search for: quantum algorithm strings].

%A M. Hirota
%A Y. Sakai
%T Efficient algorithms for enumerating maximal common subsequences of
   two strings
%J arXiv
%M JUL
%D 2023
%K TR, c2023, c202x, c20xx, zz0723, long, longest, maximal common subsequence,
   string, algorithm, enumerate
%X "... One alg. prepares a cubic-space data structure in cubic time to output
   each MCS in linear time. ... Another prepares a quadratic-space [DS] in
   quadratic time to output each MCS in linear time, & the other prepares a
   linear-space [DS] in quad.time to output each MCS in linearithmic time."
   -- 2307.10552@[<A HREF="https://arxiv.org/abs/2307.10552">arXiv</A>]['23].
      "... maximal, if there exists no common subseq. that is longer than it
      & has it as a subseq. ..."

%A R. Li
%A et al
%T An algorithm for the constrained longest common subsequence and substring
   problem
%J arXiv
%M AUG
%D 2023
%K TR, c2023, c202x, c20xx, zz0823, constrained string, CLCS, CLCSS
%X "Let S be an alphabet. For two strings X, Y, & a constrained string P over
   ... S, the constrained LCS & substring problem for two strings X & Y wrt
   P is to find a longest string Z which is a subseq. of X, a substring of Y, &
   has P as a subseq.. ... we propose an alg. for the constrained longest common
   subseq. & substring problem for two strings with a constrained string."
   -- 2308.01322@[<A HREF="https://arxiv.org/abs/2308.01322">arXiv</A>]['23].
   [Also search for: constrained longest common subsequence].

%A M. N. Palmer
%A S. Faro
%A S. Scafiti
%T Efficient online string matching through linked weak factors
%J arXiv
%M OCT
%D 2023
%K TR, c2023, c202x, c20xx, zz1023, string, algorithm, match, matching, online,
   hashing, hashChain
%X "... presents Hash Chain, a new alg. based on a robust weak factor
   recognition approach that connects adjacent factors through hashing. Despite
   its O(nm) complexity, [it] exhibits a sublinear behavior in practice &
   achieves superior performance compared to the most effective algs.."
   -- [<A HREF="https://arxiv.org/abs/2310.15711">arxiv:2310.15711</A>]['23].

%A G. Bathie
%A et al
%T Pattern matching with mismatches and wildcards
%J arXiv
%M FEB
%D 2024
%K TR, c2024, c202x, c20xx, zz0224, algorithm, string, strings, mismatch,
   wildcard, pattern matching, match
%X "... approximate pattern matching with wildcards. Given a pattern P of length
   m containing D wildcards, a text T of length n, & an int. k, ... identify
   all fragments of T within Hamming distance k from P. Our primary contrib'n is
   an alg. with runtime O(n+(D+k)(G+k).n/m). Here, G <= D represents the # of
   maximal wildcard fragments in P. ..."
   -- [<A HREF="https://arxiv.org/abs/2402.07732">arxiv:2402.07732</A>]['24]. 
   [Also search for: string pattern matching].

%A D. Hendrian
%A D. Koppl
%A R. Yoshinaka
%A A. Shinohara
%T Algorithms for Galois words: Detection, factorization, and rotation
%M MAR
%D 2024
%K TR, c2024, c202x, c20xx, zz0324, combinatorial, Galos word, alternating,
   Lyndon, strings
%X "... a Galois word exhibits the same property by exchanging the lexicographic
   order with the alternating order. Unfortunately, this exchange has a large
   impact on the properties G.words exhibit, which makes it a nontrivial task to
   translate results from Lyndon words to Galois words. Up until now, it has
   only been conjectured that linear-time algs. with constant additional working
   space in the spirit of Duval's alg. are possible for computing the Galois
   factorization or the Galois rotation. ..."
   -- [<A HREF="https://arxiv.org/abs/2403.02636">arxiv:2403.02636</A>]['24].

%A T. Kociumaka
%A J. Nogler
%A P. Wellnitz
%T On the communication complexity of approximate pattern matching
%K arXiv
%M MAR
%D 2024
%K TR, c2024, c202x, c20xx, zz0324, communication complexity, match, strings,
   communicationComplexity, edits
%X "The decades-old Pattern Matching with Edits problem, given a length-n string
   T, a length-m string P, & a +ve int. k (the threshold), asks to list all
   fragments of T that are at edit distance at most k from P. The one-way
   communication complexity of this problem is the minimum amount of space
   needed to encode the answer so that it can be retrieved without accessing the
   input strings P and T. The closely related Pattern Matching with Mismatches
   problem (defined in terms of the Hamming distance instead of the ED) is
   already well understood from the communication complexity perspective ...
   we prove an upper bound of O(n/m.k log^2 m) bits ..."
   -- [<A HREF="https://arxiv.org/abs/2403.18812">arxiv:2403.18812</A>]['24].
   (Also see CommComp@[<A HREF="https://en.wikipedia.org/wiki/Communication_complexity">wikip</A>]['24].)

%A T. Nishimoto
%A Y. Tabei
%T Dynamic suffix array in optimal compressed space
%J arXiv
%M APR
%D 2024
%K TR, c2024, c202x, c20xx, zz0424, suffix array, data structure 
%X "... We present the first dynamic compressed data structure that supports the
   SA query & update in polylogarithmic time and d-optimal space. More precisely
   it can answer SA queries & perform updates in O(log^7(n)) & expected
   O(log^8(n)) time, resp., using an expected d-optimal space.
   -- [<A HREF="https://arxiv.org/abs/2404.07510">arxiv:2404.07510</A>]['24].
   ('n' string length.  'd' is "substring complexity")
   [Also search for: suffix array].

%A B. Marchand
%A N. Tahiri
%A O. Tremblay-Savard
%A M. Lafond
%T Finding maximum common contractions between phylogenetic networks
%J arXiv
%M MAY
%D 2024
%K TR, c2024, c202x, c20xx, zz0624, phylogenetic, tree, network, distance,
   algorithm, edge, contraction, expansion, graph
%X "... comparison of phylogenetic n/wks based on edge contractions & expansions
   as edit operations ... define an operational distance on this space, as the
   minimum # of contractions & expansions required to transform one n/wk into
   another. We highlight the difference between this distance & the computation
   of the maximum common contraction between two n/wks. ... prove that computing
   a maximum common contraction between two n/wks is NP-hard ... Nonetheless,
   we do provide a polynomial-time alg. for weakly-galled n/wks, a
   generalization of galled trees."
   -- [<A HREF="https://arxiv.org/abs/2405.16713">arxiv:2405.16713</A>]['24].


%A T. R. Gruber
%T A translation approach to portable ontologies
%J Knowledge Acquisition
%V 5
%N 2
%P 199-220
%M JUN
%D 1993
%K ontology, c1993, c199x, c19xx, TRGruber, Ontolingua
%X [<A HREF="http://ksl-web.stanford.edu/KSL_Abstracts/KSL-92-71.html">pp.ps@stanf</A>]['05],
   [<A HREF="http://www-ksl.stanford.edu/kst/what-is-an-ontology.html">what...</A>]['05].

%A Y. Wand
%A R. Weber
%T An ontological model of an information system
%J IEEE Trans. on Software Eng.
%V 16
%N 11
%P 1282-1292
%D 1990
%K jrnl, SWE, Ron, ronald, RWeber, c1990, c199x, c19xx

%A B. Liskov
%A J. M. Wing
%T A behavioural notion of subtyping
%J TOPLAS
%I ACM
%V 16
%N 6
%P 1811-1841
%M NOV
%D 1994
%K jrnl, TOPLAS, subtype, OO, OOP, c1994, c199x, c19xx, object, inheritance,
   behaviour, substitution principle, subtype, subtyping, JMWing, BLiskov
%X "The use of hierarchy is an important component of OO design. H. allows the
   use of type families, in which higher level supertypes capture the behavior
   that all of their subtypes have in common. For this methodology to be
   effective, it is necessary to have a clear understanding of how subtypes and
   supertypes are related. This paper takes the position that the relationship
   should ensure that any property proved about supertype objects also holds
   for its subtype objects. It presents 2 ways of defining the subtype rel.,
   each of which meets this criterion, & each of which is easy for programmers
   to use. The subtype relation is based on the specs. of the sub- & supertypes;
   ..."  pdf: [<A HREF="http://doi.acm.org/10.1145/197320.197383">doi:10.1145/197320.197383</A>]['05]
   Also see: JMWing c1997

%A D. R. Hanson
%T C Interfaces and Implementations: Techniques for Creating Reusable Software
%I AddisonWesley
%P 544
%D 1996
%K book, text, c1996, c199x, c19xx, user interface, API, UI, interfaces, SWE,
   computer programming, software engineering, reuse
%X 1st ed 1996; pb us$39; uk us isbn:0201498413; uk us isbn13:978-0201498417.

%A S. Pan
%A R. G. Dromey
%T Beyond structured programming
%J Proc. 18th Int. Conf. on Software Engineering
%P 268-277
%D 1996
%K conf, ICSE, ICSE18, SWE, c1996, c199x, c19xx
%X "Structured programming principles are not strong enough to control
   complexity and guarantee high reliability of software at the module level.
   Stronger organizing principles and stronger properties of components are
   needed to make significant gains in the quality of software. Practical
   proposals, based on the definition of normal forms which have a mathematical/
   logical foundation, are suggested as a vehicle for constructing software that
   is both simpler and of higher quality with regard to clearly defined and
   justifiable criteria."
   [<A HREF="http://csdl.computer.org/comp/proceedings/icse/1996/7246/00/72460268abs.htm">subsc'n</A>]['05].
   (auth @ griffith U., .au)

%A H. Pennington
%T GTK+/Gnome Application Development
%I NewRiders
%D 1999
%K book, text, GTK, plus, GTKplus, Gnome, glib, Gnu, object, OO, OOP,
   c1999, c199x, c19xx, widget, widgets, Linux, software, developers
%P 528
%X maybe us$28, isbn:0735700788.
   Also see [<A HREF="http://developer.gnome.org/doc/books/">gnome.org</A>][10/'03]
        and [<A HREF="http://developer.gnome.org/doc/GGAD/">gnome.org</A>][10/'03].

%A E. Harlow
%T Developing Linux Applications with GTK+ and GDK
%I Que ?
%D 1999
%K book, text, GTK, plus, GTKplus, GDK, gnome, Gnu, object, OO, OOP,
     c199x, c19xx, c1999, widget, widgets, software, developers
%X about us$25, isbn:0735700214.
   Also see [<A HREF="http://developer.gnome.org/doc/books/">gnome.org</A>][10/'03]

%A R. A. Weber
%T Information Systems Control and Audit
%I PrenticeHall
%D 1999
%P 1027
%K book, software, auditing, ron, RWeber, c1999, c199x, c19xx
%X about us$141;  isbn:0139478701.

%A Y. Wand
%A V. C. Storey
%A R. Weber
%T An ontological analysis of the relationship construct in conceptual modeling
%J TODS
%V 24
%N 4
%P 494-528
%M DEC
%D 1999
%K jrnl, TODS, c1999, c199x, c19xx, Ron, RWeber, ontology, database management,
   entity, diagrams, modeling, DBMS
%X "... Often, however, rigorous definitions of ... are missing.
   ... occurs especially in the case of the relationship construct. Empirical
   evidence shows that use of relationships is often problematical as a way of
   communicating the meaning of an application domain. [e.g.] users of
   conceptual modeling methodologies are frequently confused about whether to
   show an association between things via a relationship, an entity, or an
   attribute. Because conceptual models are intended to capture knowledge about
   a real-world domain, we take the view that the meaning of modeling
   constructs should be sought in models of reality. Accordingly, we use
   ontology [...] to analyze the meaning of common conceptual modeling
   constructs. ... provides a precise defn of several conceptual modeling
   constructs. ... we derive rules for the use of relationships in entity-
   relationship conceptual modeling. Moreover, we show how the rules resolve
   ambiguities that exist in current practice and how they can enrich the
   capacity of an entity-relationship conceptual model to capture knowledge
   about an application domain."
   -- [<A HREF="http://doi.acm.org/10.1145/331983.331989">doi:10.1145/331983.331989</A>]['05].

%A Wei-Lung Wang
%T Viewpoint: Beware the engineering metaphor
%J CACM
%V 45
%N 5
%P 27-29
%M MAY
%D 2002
%K cacm, viewpoint, software engineering, SWE, SWEng, engineer, maths,
   programming, program, programmer, quote, zz1002, c2002, c200x, c20xx
%X "There are great similarities between the work of the software developer
   and the work of the mathematician."   ...
      "While the engineering approach has its place, it is important to
   realize the work of building software in not an engineering task.
   E' is the work of applying scientific and mathematical principles to
   practical ends.  SWE, on the other had, is the use of engineering practices
   to craft mathematical rigor.  As SWE's, we do not engineer software,
   we merely adopt E' practices when building software."  ...

%A S. Adams
%T Dilbert and the Way of the Weasel: A Guide to Outwitting Your Boss,
   Your Coworkers, and the Other Pants-Wearing Ferrets in Your Life
%I HarperBusiness
%P 350
%M OCT
%D 2003
%K book, c2003, c200x, c20xx, funny, haha, ha ha, SWE, software engineering
%X us$11; uk us isbn:006052149X.
   (Also see [<A HREF="http://www.dilbert.com/">dilbert</A>]['12].)

%A G. Shanks
%A E. Tansley
%A R. Weber
%T Using ontology to validate conceptual models
%J CACM
%V 46
%N 10
%P 85-89
%M OCT
%D 2003
%K jrnl, CACM, Ron, RWeber, c2003, c200x, c20xx, conceptual
%X "...Unfortunately, little is known about how to validate conceptual models
   effectively and efficiently. ... Perhaps the best way IS professionals can
   facilitate the validation of conceptual models is to generate high-quality
   conceptual models from the outset. Theories of ontology help ensure they
   select a conceptual modeling grammar needed to produce high-quality models
   of the focal domain. They can help guide how the grammar is used to generate
   clear, complete descriptions of the domain. And they can be used to help
   make sense of ambiguous semantics in conceptual models that need to be
   validated."
   -- [<A HREF="http://doi.acm.org/10.1145/944217.944244">doi:10.1145/944217.944244</A>]['05].

%A L. Wen
%A R. G. Dromey
%T From requirements change to design change: A formal path
%J 2nd Int. Conf. on Software Engineering and Formal Methods (SEFM)
%I IEEE
%P 104-113
%M SEP
%D 2004
%K conf, SWE, behavior tree, trees, c2004, c200x, c20xx, SEFM2, SEFM04,
   component, components, Geoff
%X "... change in the FR for a sys. ... can quickly determine (1) where to make
   the change (2) how the c. affects the arch. of the existing sys. (3) which
   components of the sys. are affected by the c. (4) and, what behavioral c.
   will need to be made to the components ... complicated because reqs. changes
   are specified in the problem domain, whereas the design response and the
   implementation changes that need to be made are in the solution domain. ...
   ... we use a formal component-state rep. called behavior trees ..."
   -- [<A HREF="http://doi.ieeecomputersociety.org/10.1109/SEFM.2004.20">doi:10.1109/SEFM.2004.20</A>]['05] subscr'n!.
   uk us isbn:076952222X. auths @ Griffith U., .au ['05].

%T First Joint IEEE/IFIP Symposium on Theoretical Aspects of
   Software Engineering (TASE 2007)
%W Shanghai
%I IEEE
%P 508
%D 2007
%K conf, symp, TASE, SWE, SWEng, c2007, c200x, c200x, proc, theory
%X 46 papers, us$240, isbn:0769528564.

%A J. Palfrey
%A U. Gasser
%T Interop: The Promise and Perils of Highly Interconnected Systems
%I BasicBooks
%P 304
%D 2012
%K book, text, c2012, c201x, c20xx, zz0612, interoperability, risks, open,
   standards, standardization
%X 1st ed 2012; hb us$18; uk us isbn:0465021972; uk us isbn13:978-0465021970.
   "... interoperability is a critical aspect of any successful system ...
   flow of information across systems is crucial ...  also consider its
   potential negative effects, especially with respect to privacy, security,
   and co-dependence of states ..."

%A Yanhong Annie Liu
%T Systematic Program Design: From Clarity to Efficiency
%I CUP
%P 253
%M MAY
%D 2013
%K book, text, CUP, c2013, c201x, c20xx, zz0214, computer programming, coding,
   step-wise, transformation
%X 1st ed 2013; pb us$35; uk us isbn:1107610796; uk us isbn13:978-1107610798.
   "... starts with a clear specification of a computation & derives an
   efficient implementation by step-wise program analysis & transformations. The
   method applies to problems specified in imperative, database, functional,
   logic, & object-oriented programming languages with different data, control,
   & module abstractions. Designed for courses or self-study ..."


%A K. Godel
%T On Formally Undecidable Propositions of Principia Mathematica and
   Related Systems
   (Uber formal unentscheidbare Satze der Principia Mathematica und
   verwandter Systeme I)
%J Monatshefte fur Mathematik und Physik
%D 1931
%K c1931, c193x, c19xx, maths, logic, theory, decision problem, decidability,
   incompleteness, undecidable, unprovable, theorem, arithmetization
%X -- [<A HREF="https://doi.org/10.1007%2FBF01700692">doi:10.1007%2FBF01700692</A>]['24].
   Also see, M.Davis, ed. 1965, The Undecidable: Basic Papers on Undecidable
     Propositions, Unsolvable Problems and Computable Functions, Raven, N.Y.,
     reprint, Dover, 2004. uk us isbn:0486432289
     [<A HREF="https://archive.org/details/undecidablebasic0000mart/page/n7/mode/1up">archive.org</A>]['24].

%A E. Post
%T A variant of a recursively unsolvable problem
%J Bulletin of the American Math. Soc.
%V 52
%P 264-268
%D 1946
%K jrnl, c1946, c194x, c19xx, decidability, computability, uncomputable,
   undecidable, Post correspondence problem, problems, PCP, csci, theory, math
%X Given a set of pairs of strings, find a seq. of pairs s.t. the concatenation
   of all the 1st members of the pairs is the same string as the concatenation
   of all 2nd members. This is undecidable.
   -- [<A HREF="http://dx.doi.org/10.1090/S0002-9904-1946-08555-9">doi:10.1090/S0002-9904-1946-08555-9</A>]['15].

%A J. Cocke
%A M. Minsky
%T Universality of tag systems with P=2
%J JACM
%V 11
%N 1
%P 15-20
%M JAN
%D 1964
%K jrnl, jacm, system, small, smallest, math, csci, theory, Post canonical,
   system, UTM, c1964, c196x, c19xx
%X "...shown that computations done by Turing machines can be duplicated by a
   very simple symbol manipulation process. The process is described by a
   simple form of Post canonical system with some very strong restrictions.
   This system is monogenic: each formula (string of symbols) of the system can
   be affected by one & only one production (rule of inference) to yield a
   unique result. Accordingly, if we begin with a single axiom (initial string)
   the system generates a simply ordered sequence of formulas, & this
   operation of a monogenic system brings to mind the idea of a machine. The
   Post canonical system is further restricted to the `Tag' variety, described
   briefly below. It was shown in that Tag sys. are equivalent to T. machines.
   The proof in [1] is very complicated & uses lemmas concerned
   with a variety of two-tape nonwriting TMs. The proof here avoids
   these otherwise interesting machines & strengthens the main result;
   obtaining the theorem with a best possible deletion number P=2..."
   -- [<A HREF="http://doi.acm.org/10.1145/321203.321206">doi:10.1145/321203.321206</A>][6/'04].

%A J. Hartmanis
%A R. E.Stearns
%T On the computational complexity of algorithms
%J Trans. Amer. Math. Soc.
%V 117
%P 285-306
%D 1965
%K jrnl, c1965, c196x, c19xx, zz1213, CSci, algorithm, complexity
%X [<A HREF="http://dx.doi.org/10.1090/S0002-9947-1965-0170805-7">doi:10.1090/S0002-9947-1965-0170805-7</A>]['13].

%A J. S. Royer
%A J. Case
%T Subrecursive Programming Systems: Complexity and Succinctness
%I Birkhauser
%D 1994
%K book, text, recursion, complexity, theory, computer science, CSci, computing
%X uk us isbn:0-8176-3767-2.
   This monograph develops general purpose recursion and complexity theoretic
   tools for working with low level subrecursive programming systems.
   The table of contents and introductory chapter are available on the WWW via
   <A HREF="file://top.cis.syr.edu/html/people/royer/royer.html">here</A>
   and by ftp via      site: top.cis.syr.edu   (128.230.31.4)
                       file: /users/royer/rc1.dvi
   <!-- email: royer@top.cis.syr.edu --> (Jim Royer  1/'95)

%A P. van Emde Boas
%T Another NP-complete partition problem and the complexity of computing
   shortest vectors in a lattice
%R MI/UVA 81-04
%I Univ-Amsterdam
%M APR
%D 1981
%K TR, NP, NPC, complete, CSci, computing, theory, vanEmdeBoas, van EmdeBoas,
   c1981, c198x, c19xx, zz1020, shortest vector problem, SVP, lattice, lattices,
   short vectors, SVP
%X -- [<A HREF="http://staff.science.uva.nl/~peter/vectors/mi8104c.html">www</A>]['20]
   Also see
   LP@[<A HREF="https://en.wikipedia.org/wiki/Lattice_problem">wikip</A>]['20].
   [Also search for: shortest vector lattice].

%A B. S.Majewski
%A G. Havas
%T The complexity of greatest common divisor computations
%J Proceedings First Algorithmic Number Theory Symposium
%I SpringerVerlag
%S LNCS
%V 877
%P 184-193
%D 1994
%K GCD, CSci, computing, theory, conf, proc
%X George Havas   <!-- email: havas@cs.uq.oz.au -->    (1/'95)

%A C. H. Papadimitriou
%T Computational Complexity
%I AddisonWesley
%D 1994
%K book, text, complexity, P, NP, NPC, theory, CSci, computing
%X enews from email: archie@qin.CS.Berkeley.EDU (Archie Cobbs 2/95)

%A D. Bovet
%A P. Crescenzi
%T Introduction to the Theory of Complexity
%I PrenticeHall
%D 1994
%K book, text, complexity, NP, NPC, theory, computer science, CSci, computing
%X via Alf-Christian Achilles <!-- email: achilles@ira.uka.de --> [2/'95]

%A M. Minsky
%T Universality of (p=2) tag systems and a
   4 symbol, 7 state, universal Turing machine
%J Computation
%I PrenticeHall
%P ?-?
%D 1967
%O MIT, AI memo 33, AIM33
%K UTM, small, smallest, four, seven, CSci, theory, c1967, c196x, c19xx,
   small, smallest, system
%X ?or was this (in) a book  Computation: Finite and Infinite Machines'?
   "This report describes (1) an improvement & great simplification of the
   proof that the "Tag" systems of Post can represent any computable process,
   & (2) a UTM with just four symbols and seven states - the smallest yet
   reported."
   -- [<A HREF="ftp://publications.ai.mit.edu/ai-publications/pdf/AIM-033.pdf">AIM-33 .pdf</A>][6/'04].
   (Also see JACM 1964 [<A HREF="https://doi.org/10.1145/321203.321206">www</A>]['24].)

%A S. Aanderaa
%T A universal Turing machine
%B Computer Science Logic
%S LNCS ?
%V ?
%P 1-4
%D 1993
%K c1993, c199x, c19xx, UTM, TM, CSci, theory, machines
%X S. Aanderaa  <!-- email: staal.aanderaa@math.uio.no --> .
   It is a short paper. Please compare it with the version given by
   Minsky in his 1967's book, "Computation: Finite and Infinite Machines".
   Hope this helps, -- Xin Wang  <!-- email: xwang@cs.ucla.edu --> [2/'95].

%A P. Flajolet
%A B. Salvy
%A P. Zimmermann
%T Automatic average-case analysis of algorithms
%J Theor. Comp. Sci.
%V 79
%P 37-109
%D 1991
%K jrnl, program, algorithm analysis, complexity, TCS, CSci
%X via Claude Chaunier <!-- email: cchaunie@bat710.univ-lyon1.fr --> [6/'95]

%A T. Hickey
%A J. Cohen
%T Automating program analysis
%J JACM
%V 35
%N 1
%P 185-220
%M JAN
%D 1988
%K JACM, ACM, automatic, algorithm analysis, complexity, jrnl, CSci
%X via Claude Chaunier <!-- email: cchaunie@bat710.univ-lyon1.fr --> [6/'95]

%A P. Flajolet
%A A. M. Odlyzko
%T The average height of binary trees and other simple trees
%J J. Comp. and Sys. Sci.
%V 25
%P 171-213
%D 1982
%K binary, tree, height, JCSS, jrnl, CSci
%X via Claude Chaunier <!-- email: cchaunie@bat710.univ-lyon1.fr --> [6/'95]

%T The Universal Turing Machine. A Half-Century Survey
%E R. Herken
%I OUP
%P 676
%D 1991
%K book, text, TM, UTM, theory, CSci, c1991, c199x, c19xx, zz1095
%X uk us isbn:0198537743; uk us isbn13:978-0198537748.

%A A. Arnold
%A A. Dicky
%A M. Nivat
%T A note about minimal non-deterministic automata
%J Bulletin of the EATCS
%V 47
%M JUN
%D 1992
%P 166-169
%K jrnl, EATCS, FSA, NDFSA, NFSA, small, theory, CSci, zz1095
%X <!-- email: oma@informatik.uni-kiel.de --> Oliver Matz [10/95]

%A O. Matz
%A A. Potthoff
%T Computing small nondeterministic automata
%J Proc. Workshop on Tools and Alg's for the Cons'n and Analysis of Sys's.
%E U. H. Engberg
%E K. G. Larsen
%E A. Skou
%S BRICS Notes
%M MAY
%D 1995
%K wShop, FSA, NDFSA, NFSA, non deterministic, minimal, theory, CSci, zz1095
%X <!-- email: oma@informatik.uni-kiel.de --> Oliver Matz [10/95].
   ISSN 0909-3206.

%E L. Brim
%E J. Gruka
%E J. Zlatuska
%T Mathematical Foundations of Computer Science 1998
%P 846
%D 1998
%I Springer
%S LNCS
%V 1450
%K proc, conf, MFCS, MFCS98, MFCS23, zz0199
%X uk us isbn:3-540-64827-5;   dm148, au$147 as of 11/98

%A J. E. Hopcroft
%A R. Motwani
%A J. D. Ullman
%T Introduction to Automata Theory, Languages, and Computation
%I AddisonWesley
%P 521
%D 2001
%K book, text, computer, computing, science, theory, maths, finite state, FSA,
   machine, FSM, language, CFG, decidability, complexity, P, NP, NPC, zz0501
%X 2nd ed, uk us isbn:0201441241;
   1st edn ~c1979(?).
   [<A HREF="http://www-db.stanford.edu/~ullman/ialc.html">home page</A>][5/01].

%A M. Sipser
%T Introduction to the Theory of Computation
%I CourseTechnology
%P 456
%D 2005
%K book, text, c2005, c200x, c20xx, computer science, computing, theory,
   maths, computability, L4Ref, L5Ref
%X "Intended as an upper-level undergraduate or introductory graduate text in
   computer science theory, this book lucidly covers the key concepts and
   theorems of the theory of computation. ..."
   2nd ed 2005; hb us$97; us isbn:0534950973; us isbn13:978-0534950972.

%A O. Finkel
%T The exact complexity of the infinite Post correspondence problem
%J IPL
%V 115
%N 6-8
%P 609-611
%M JUN-AUG
%D 2015
%K jrnl, IPL, c2015, c201x, c20xx, zz0515, Post correspondence problem, PCP,
   theory, strings, computability, undecidable, Simonnet
%X "... PCP ... is PI^0_1-complete. Surprisingly, .. the infinite PCP is not
   'more complex' than the PCP, which is known to be SIGMA^0_1-complete, but has
   the exact dual complexity. This gives an answer to a question of Simonnet."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2015.02.009">doi:10.1016/j.ipl.2015.02.009</A>]['15].
   [Also search for: Post correspondence problem].


%A W. E. Bowman
%T The Ascent of Rum Doodle
%I Max Parrish, London
%D 1956
%K wanted, collectable, book, Nepal, Himalaya, Mount Mt Everest,
   mountaineering, climbing, joke, spoof, funny, haha ha ha
%X new ed 2001, pb, stg6.00; uk isbn:071266808X; uk isbn13:978-0712668088.

%A Margaret D. Williamson
%T Memoirs of a Political Officer's Wife in Tibet, Sikkim and Bhutan
%D 1906-
%K book, travel, Tibet, Sikkim, Bhutan, Himalaya, mountain
%X Main library Monash: 915.49804 N731M (Main Collection).
   Highly recommended. This book is a surprise, because I expected the usual
   English preoccupation with ceremony, manners, status etc. which bores me
   silly. However, the author seems a `free spirit' and is lots of fun.
   -- Rohan.


%A T. Pennello
%A F. DeRemer
%A R. Meyers
%T A simplified operator identification scheme for ADA
%J ACM SIGPLAN Notices
%V 15
%N 7-8
%P 82-87
%D 1980
%K c1980, c198x, c19xx, type, types, check, checking, inference, ad hoc,
   polymorphism, overloading, method, method, OO, OOP
%X from the H@sekll mail list 21/7/'03.

%A N. McCracken
%T The typechecking of programs with implicit type structure
%P 301-315
%B Semantics of Data Types
%S LNCS
%V 173
%I SpringerVerlag
%W Sophia-Antipolis
%M JUN
%D 1984
%E G. Kahn
%E D. B. MacQueen
%E G. Plotkin
%K type, check, checker, checking, inference, polymorphism, polymorphic,
   functional, applicative, lambda calculus

%A J. C. Reynolds
%T Towards a theory of type structure
%P 408-425
%B Programming Symposium
%S LNCS, vol.19, pp.408-425
%D 1974
%W Paris
%I SpringerVerlag
%K conf, 1974, c197x, c19xx, type, types, datatype, check, checking, CSci,
   computing, inference, polymorphic, polymorphism, applicative, functional,
   system F, systemF
%X "... introduce an extension of the typed lambda calculus which permits
   user-defined types and polymorphic fns, & show that the semantics of this
   language satisfies a representation theorem which embodies our notion of a
   "correct" type structure. ..."
   --  [<A HREF="https://doi.org/10.1007/3-540-06859-7_148">doi:10.1007/3-540-06859-7_148</A>]['24].
   [Also search for: typed lambda calculus].
   Also see System F @ [<A HREF="https://en.wikipedia.org/wiki/System_F">wikip</A>]['24].

%A R. Milner
%T A theory of type polymorphism in programming
%J J. of Computer and System Sciences
%V 17
%P 348-375
%M DEC
%D 1978
%K JCSS, polymorphic, functional, applicative, ML, type, c1978, c197x, c19xx,
   datatype, check, types, checking, inference, CSci, computing, L4REF
%X -- [<A HREF="https://doi.org/10.1016/0022-0000(78)90014-4">doi:10.1016/0022-0000(78)90014-4</A>]['24],
    & [<A HREF="https://homepages.inf.ed.ac.uk/wadler/papers/papers-we-love/milner-type-polymorphism.pdf">ed.ac.uk</A>['24].

%A L. Damas
%A R. Milner
%T Principal type-schemes for functional programs
%J 9th Annual ACM Symposium on Principles of Programming Languages
%W Albuquerque
%P 207-212
%M JAN
%D 1982
%K polymorphic, polymorphism, functional, applicative, programming, FP,
   inference, datatype, type, types, POPL, check, checking, CSci, computing,
   c1982, c198x, c19xx

%A D. B. MacQueen
%A R. Sethi
%T A semantic model of types for applicative languages
%J ACM Symposium on Lisp and Functional Programming
%W Pittsburgh
%P 243-252
%M AUG
%D 1982
%K semantic, theory, lattice, type, datatype, check, inference, model,
   functional, applicative programming, FP

%A D. B. MacQueen
%A G. D. Plotkin
%A R. Sethi
%T An ideal model for recursive polymorphic types
%J Information and Control
%V 71
%P 95-130
%M NOV
%D 1986
%K jrnl, c1986, c198x, c19xx, type, datatype, polymorphic, CSci, computing,
   ideal, domain, lattice theory, denotational
%O expanded version of paper in POPL 84
%X -- [<A HREF="https://doi.org/10.1016/S0019-9958(86)80019-5">doi:10.1016/S0019-9958(86)80019-5</A>]['24].

%A D. B. MacQueen
%A G. D. Plotkin
%A R. Sethi
%T An ideal model for recursive polymorphic types
%J POPL
%D 1984
%K POPL, ideal, semantics, theory, polymorphic, types, type, CSci, computing
%O see Information and Control V71 p95 1986
%X -- [<A HREF="https://doi.org/10.1145/800017.800528">doi:10.1145/800017.800528</A>]['24].

%A M. Wand
%T A types as sets semantics for Milner style polymorphism
%J 11th Annual ACM Symposium on Principles of Programming Languages
%W Salt Lake City
%P 158-164
%M JAN
%D 1984
%K type, semantic, theory, lattice, type, datatype, check, inference, model,
   POPL, set, sets, datatype, polymorphism, polymorphic

%A J. C. Mitchell
%T Coercion and type inference
%J 11th Annual ACM Symposium on Principles of Programming Languages
%W Salt Lake City
%P 175-185
%M JAN
%D 1984
%K coercion, type, types, datatype, check, checking, inference, polymorphism,
   POPL, POPL11, POPL84, polymorphic

%A D. Leivant
%T Polymorphic type inference
%J 10th Annual ACM Symposium on Principles of Programming Languages
%W Austin
%P 88-98
%M JAN
%D 1983
%K POPL, polymorphic, polymorphism, type, datatype, check, checking, inference,
   POPL10, POPL83

%A D. Leivant
%T Structural semantics for polymorphic data types
%P 155-166
%J 10th Annual ACM Symposium on Principles of Programming Languages
%W Austin
%M Jan
%D 1983
%K POPL, polymorphic, polymorphism, type, datatype, semantics, POPL10, POPL83

%A B. W. Lampson
%A E. Schmidt
%T Practical use of a polymorphic applicative language
%P 237-255
%J 10th Annual ACM Symposium on Principles of Programming Languages
%W Austin
%M Jan
%D 1983
%K POPL, polymorphic, polymorphism, type, datatype, check, checking, inferences,
   POPL10, POPL83, CSci

%A L. Meertens
%T Incremental polymorphic typechecking in B
%P 265-275
%J 10th Annual ACM Symposium on Principles of Programming Languages
%W Austin
%M Jan
%D 1983
%K POPL, polymorphic, polymorphism, type, datatype, check, checking, inferences,
   POPL10, POPL83, BB, B, c1983, c198x, c19xx
%X "The prog. lang. B has been designed for personal computing. ... variables
   need not be declared, nor formal parameters specified. Nevertheless, B is
   strongly typed. All type requirements can be checked statically. To signal
   type violations on the spot during editing, the computations can be organized
   so that local the source text require a modest amount of recomputation."
   -- [<A HREF="https://doi.org/10.1145/567067.567092">doi:10.1145/567067.567092</A>].
   (There are other laguage(s) called 'B'.)

%A A. Mycroft
%T Polymorphic type schemes and recursive definitions
%J 6th Int. Symp. on Programming
%W Toulouse
%D 1984
%K polymorphic, polymorphism, type, datatype, check, checking, inference,
   recursive, recursion

%A M. Coppo
%T On the semantics of polymorphism
%J Acta Informatica
%V 20
%N 2
%P 159-170
%D 1983
%K polymorphism, polymorphic, type, datatype, check, checking, theory, lattice,
   model, CSci, computing

%A M. Coppo
%T An extended polymorphic type system for applicative languages
%B Mathematical Foundations of Computer Science
%I SpringerVerlag
%S LNCS
%V 88
%P 194-204
%D 1980
%K MFCS, polymorphic, type, datatype, checking, check, inference, CSci,
   computing

%A S. Fortune
%A D. Leivant
%A M. O'Donnell
%T The expressiveness of simple and second-order type structures
%J JACM
%V 30
%N 1
%P 151-185
%M JAN
%D 1983
%K lambda calculus, type, datatype, simple, theory, polymorphism,
   recursion, recursive, CSci, computing

%A H. B. Curry
%T Some philosophical aspects of combinatory logic
%B The Kleene Symposium
%E J. Barwise
%E J. Keisler
%E K. Kunen
%I NorthHolland
%P 85-101
%D 1980
%K combinatory logic, maths, mathematics, combinator, Schonfinkel, currying,
   curried, functions, FP, c1980, c198x, c19xx
%X Attributes currying to Schonfinkel - Schonfinkelling?
   -- [<AHREF="https://doi.org/10.1016/S0049-237X(08)71254-0">doi:10.1016/S0049-237X(08)71254-0</A>]['24].
   [Also search for: Schonfinkel c1924].

%A M. Schonfinkel
%T Uber die Bausteine der Mathematische Logik
%J Math. Ann.
%V 92
%P 305-316
%D 1924
%K jrnl, mathematics, theory, maths, FP, curried, currying, function,
   functions, logic, c1924, c192x, c19xx
%X S t r a c h e y  ('67) gives this ref for "curried" functions.
   Use  f x y == (f x)y,  rather than f'(x,y).

%A A. Mycroft
%A R. A. O'Keefe
%T A polymorphic type system for Prolog
%J Artificial Intelligence
%P 295-307
%V 23
%D 1984
%K polymorphic, polymorphism, type, datatype, check, checking, inference,
   LP, Prolog,, OKeefe

%A R. L. Constable
%A D. R. Zlatin
%T The type theory of PL/CV3
%J TOPLAS
%V 6
%N 1
%P 94-117
%M Jan
%D 1984
%K type, datatype, theory, PL/CV3

%A A. J. Cowling
%T Type checking in polymorphic languages
%J COMPJ
%V 29
%N 6
%P 538-544
%D 1986
%K polymorphic, polymorphism, type, datatype, check, checking, inference

%A H. I. E. Gunn
%A D. M. Harland
%T Polymorphic programming II. An orthogonal tagged high level
   architecture abstract machine
%J SPE
%V 14
%N 11
%P 1021-1046
%M NOV
%D 1984
%K polymorphism, polymorphic, machine, architecture, datatype, type

%A L. Cardelli
%T Basic polymorphic typechecking
%J Science of Computer Programming
%V 8
%N 2
%P 147-172
%M APR
%D 1987
%K jrnl, c1987, c198x, c19xx, type, types, polymorphism, parameter, typecheck,
   inference, datatype, ML, Hope, SML, functional programming, FP, CSci,
   computing
%X nice overview and introduction to polymorphic type systems.
   Includes a Modula-2 implementation.

%A K. B. Bruce
%A R. Meyer
%T The semantics of second order polymorphic lambda calculus
%B Semantics of Data Types
%S LNCS
%V 173
%I SpringerVerlag
%D 1984
%K functional programming, FP, data type, types, check, checking,
   c1984, c198x, c19xx

%A R. Hindley
%T The principal type scheme of an object in combinatory logic
%J Trans. American Mathematical Society
%V 146
%P 29-60
%M DEC
%D 1969
%K polymorphic,  polymorphism, combinator, logic, CSci, computing,
   CS, type, types, check, checking, c1969, c196x, c19xx

%A H. Barendregt
%T A filter lambda model and the completeness of type assignment
%J The J. of Symbolic Logic
%V 48
%N 4
%M DEC
%D 1985
%K type, types, data, datatype, assignment, inference, polymorphic,
   polymorphism, conjunction, complete

%A J.-Y. Girard
%T The system F of variable types, fifteen years later
%J Theor. Comp. Sci.
%V 45
%P 159-192
%D 1986
%K jrnl, TCS, c1986, c198x, c19xx, zz0224, typed lambda calculus, type, types,
   system F, systemF
%X "The semantic study of system F stumbles on the problem of variable types
   for which there was no convincing interpretation; we develop here a semantics
   based on the category-theoretic idea of direct limit, so that the behaviour
   of a variable type on any domain is determined by its behaviour on finite
   ones, thus getting rid of the circularity of variable types. To do so, one
   has first to simplify somehow the extant semantic ideas, replacing Scott
   domains by the simpler & more finitary qualitative domains. The interp'n
   obt. is extremely compact, as shown on simple examples. ... also contains the
   defn of a very small 'universal model' of lambda-calculus, & investigates the
   concept totality."
   -- [<A HREF="https://doi.org/10.1016/0304-3975(86)90044-7">doi:10.1016/0304-3975(86)90044-7</A>]['24].
   [Also search for: systemF]  and  [also search for: typed lambda calculus].
   (Also see system F @ [<A HREF="https://en.wikipedia.org/wiki/System_F">wikip</A>]['24].)

%A R. Ghosh-Roy
%T Conjunctional Polymorphism
%J ACSC 10
%W Geelong, Australia
%M FEB
%D 1987
%K c1987, c198x, c19xx, type, types, data, datatype, inference, polymorphic,
   conjunction, assignment
%X fun g f a b c = f( f(a,b), c)   g is not typed in ML because f has 2 types
   this is allowed in conjunction types
   g treated like
      g' f1 f2 a b c = f2( f1(a,b), c)                  NB. g(g) gets involved.
   eg. g' cons cons 1 [2,3] [4,5] = [[1,2,3], 4, 5]
      g': ('a->'b->'s) ->('s->'c->'t) -> 'a -> 'b -> 'c -> 't
   in conjunctional polymorphism have
      g :(('a->'b->'s) & ('s->'c->'t) -> 'a -> 'b -> 'c -> 't
          ----f1----     ----f2----      a     b     c    result
   fun twice f x = f(f x)
       twice: ('a->'b)&('b->'c) -> 'a -> 'c
   twice hd :list(list('t))->'t
   twice twice : ('a->'b1)&('b1->'b2)&('b2->'b3)&('b3->'c) -> 'a->'c
   fun selfapply x = x x
       selfapply: ('s->'t)&'s -> 't
   Gives an algorithm R claimed sound and complete.
   refers to Barendregt, Cardelli, Coppo, Damas, Milner
 [ ? NB. There are questions about the correctness of the conclusions ? ]

%A P. Martin-Lof
%T Constructive mathematics and computer programming
%B Mathematical Logic and Programming Languages
%E C. A. R. Hoare
%E J. C. Shepherdson
%I Prentice Hall
%P 167-184
%D 1986
%K constructive mathematics, logic, type, types, propositions as types,
   theory, CSci, computing, c1986, c198x, c19xx

%A P. Martin-Lof
%T Mathematics of infinity
%J Int. Conf. on Computer Logic
%E P. Martin-Lof
%E G. Mints
%I SpringerVerlag
%S LNCS
%V 417
%P 146-197
%D 1990
%K COLOG-88, conf, proc, theory, CSci, c1990, c199x, c19xx
%X from enews:  conf p12-16 1988, book p146-197 1990 ?

%A A. J. Kfoury
%A J. Tiuryn
%A P. Urzyczyn
%T On the computational power of universally polymorphic recursion
%J 3rd Annual Symposium on Logic in Computer Science
%P 72-81
%M JUL
%D 1988
%K ML, ML+, data type, datatype

%A K. B. Bruce
%A W. College
%A G. Longo
%T A modest model of records, inheritance and bounded quantification
%J 3rd Annual Symposium on Logic in Computer Science
%P 38-50
%M JUL
%D 1988
%K conf, object oriented, data type, datatype

%A L. Cardelli
%T A semantics of multiple inheritance
%J Proc. International Symposium on the Semantics of Data Types
%S LNCS
%V 173
%E Kahn
%E MacQueen
%E Plotkin
%P 51-67
%D 1984
%O Information and Computation, 88
%K object oriented, OO, OOP, OOPS, data type, datatype, CSci, computing,
   c1984, c198x, c19xx

%A S. Danforth
%A C. Tomlinson
%T Type theories and object-oriented programming
%J Computing Surveys
%V 20
%N 1
%P 29-72
%M MAR
%D 1988
%K data type, datatype, object oriented, OOP, subtype, inheritance, survey

%A Simona Ronchi Della Rocca
%T An unification semi-algorithm for intersection type schemes
%S LNCS
%I SpringerVerlag
%V 249
%P ???-???
%D 1988 ?
%K type, data type, datatype, polymorphism
%X via Tony Davie, St Andrews.

%A M. Gerritsen
%T Type Assignment Functions
%I University of Twente
%D 1988
%K type, types, datatype, intersection, conjunction, polymorphism,
   PhD thesis, theory, CSci, computing
%X She built a type inference algorithm where the occurrences of variables
   not necessarily have the same type.
   Instead she uses `conjuction types': *a & *b .
   (\x.x o x) has the type ((*b->*c)&(*a->*b))->*a->*c which says that x
   must be
   instantiatable as *a->*b and as *b->*c .
   Application of (\x.x o x) to hd yields the equations:
          *a->*b = List *d->*d  (and so: *a=List *d,   *b=*d)
          *b->*c = List *e->*e  (and so: *b=List *e,   *c=*e)
   The two occurrences of x have types List *d->*d and List *e->*e
   respectively.
   Solving the equations yields:
          *a=List (List *e)
          *b=List *e
          *c=*e
          *d=List *e
   and so (\x.x o x) hd::*a->*c = List (List *e)->*e
   In this type inference system there is no more need for an explicit
   let-construct.
   postal address:
      Functional Programming Group, Comp. Sc.,   University of Twente,
      postbus 217, 7500 AE  ENSCHEDE, the Netherlands
   proves Milner/Hindley typing is still completely covered.
   Furthermore, she shows how to build an efficient implementation.

%A J. C. Mitchell
%A G. D. Plotkin
%T Abstract types have existential type
%J TOPLAS
%V 10
%N 3
%P 470-502
%M JUL
%D 1988
%K data type, datatype, algebra, SOL, ML, polymorphism, lambda calculus
%O Proc. 12th ACM Symposium on Principles of Programming Languages, 85.

%A A. Lalita
%A Jategaonkar
%A J. C. Mitchell
%T ML with extended pattern matching and subtypes
%J Proc. 1988 Conf. on LISP and Functional Programming
%D 1988
%K c1988, c198x, c19xx, type, checking, ML, SML, LAFP, LFP

%A J. C. Mitchell
%T Polymorphic Type Inference
%J Information and Computation
%V 76
%N 2/3
%D 1988
%K jrnl, type check, checking, CSci, computing

%A P. Wadler
%A S. Blott
%T How to make ad-hoc polymorphism less ad hoc
%J 16th Symposium on Principles of Programming Languages (POPL)
%I ACM Press
%P 60-76
%M JAN
%D 1989
%K POPL, c1989, c198x, c19xx, FP, functional programming, type, types, adhoc,
   polymorphic, Haskell, class, overload, overloading, over loading, operator,
   OOP, object oriented, SML, classes
%X This paper presents type classes, a new approach to ad-hoc polymorphism.
   Type classes permit overloading of arithmetic operators such
   as multiplication, and generalise the ``eqtype variables'' of
   Standard ML. Type classes extend the Hindley-Milner polymorphic type
   system, and provide a new approach to issues that arise in
   object-oriented programming, bounded type quantification, and abstract
   data types. This paper provides an informal introduction to type classes,
   and defines them formally by means of type inference rules.
   -- [<A HREF="https://doi.org/10.1145/75277.75283">doi:10.1145/75277.75283</A>]['24].
   dvi and ps@[<A HREF="http://www.cs.bell-labs.com/who/wadler/topics/type-classes.html">www</A>][7/'01].

%A P. Wadler
%T Comprehending monads
%I U. Glasgow
%D 1991
%O Math. Structure in Comp. Sci., 2, pp.461-493, 1992, and also
   ACM Conf. Lisp and Functional Programming, Nice, pp.61-78, June 1990.
%K c1991, c199x, c19xx, monad, list comprehension, unit, map, join, triple,
   CSci, MSCS, LFP, LFP91, FP, functional programming, type, array,
   destructive update, state, exception, parse, parser, continuation
%X -- [<A HREF="https://doi.org/10.1145/91556.91592">doi:10.1145/91556.91592</A>]['24].

%A L. Cardelli
%A P. Wegner
%T On understanding types, data abstraction and polymorphism
%J Computing Surveys
%V 17
%N 4
%M DEC
%D 1985
%K jrnl, c1985, c198x, c19xx, data, type, types, datatype, abstraction,
   polymorphism, inheritance, check, checking, inference, survey, CSci,
   computing, c1985, c198x, c19xx, L4REF

%A H. J. Boehm
%T Type inference in the presence of type abstraction
%J SIGPLAN '89 Conference on Programming Language Design and Implementation
%D 1989
%K SIGPLAN, type, types, inference, abstract, abstraction, checking, datatype
%X via enews

%A M. Wand
%D 1986
%T Finding the source of type errors
%J 13th POPL
%P 38-43
%D 1986
%K conf, FP, c1986, c198x, c19xx, functional programming, type, types,
   error, errors, message, POPL13, POPL86
%X It is a truism that most bugs are detected only at a great
   distance from their source.  Although polymorphic type-checking
   systems like those in ML help greatly by detecting potential
   run-time type errors at compile-time, such systems are still not ...
   ... The alg. works by keeping track of the reasons the checker makes
   deductions about the types of variables.
   -- [<A HREF="https://doi.org/10.1145/512644.512648">doi:10.1145/512644.512648</A>]['24].

%A G. F. Johnson
%A J. A. Walz
%T A maximum-flow approach to anomaly isolation in unification-based
   incremental type inference
%T 13th POPL
%P 44-57
%D 1986
%K FP, functional programming, type, types, error, errors, message
   POPL13, POPL86
%X  We report here on a language-based editor for a variant of ML
    that uses a novel approach to the isolation of the likely causes
    of user errors.  As the user edits and manipulates his or her
    program, unification is incrementally applied to determine its
    type correctness.  If a type inconsistency arises, a maximum flow
    technique is applied to the set of type equations to determine the
    most likely source of error.  In this way a determination can be
    made as to the relative strengths with which the set of type
    equations asserts multiple contradictory hypotheses.
   via enews

%A B. A. Davey
%A H. A. Priestley
%T Introduction to Lattices and Order
%I CUP
%D 1990
%K book, text, c1990, c199x, c19xx, domain, lattice, complete partial order,
   CUP, CPO, denotational semantics, CUP, CSci, computing, algebraic, types
%X 2nd ed 2002; pb us$57; uk us isbn:0521784514; uk us isbn13:978-0521784511.
   "Ordered structures have been increasingly recognized in recent years due
   to an explosion of interest in theoretical computer science and all areas
   of discrete mathematics. ... ordered sets and lattices. A key feature of
   ordered sets, ..., is that they can be represented pictorially. Lattices
   are also considered as algebraic structures and hence a purely algebraic
   study is used to reinforce the ideas of homomorphisms and of ideals
   encountered in group theory and ring theory. Exposure to elementary
   abstract algebra and the rotation of set theory are the only prerequisites
   for this text. ..."
   1st ed 1990, from enews.

%A G. Saake
%A R. Jungclaus
%A C. Sernadas
%T Abstract data type semantics for many-sorted object query algebras
%B 3rd Symposium on Mathematical Foundations of Data Bases and Knowledge
   Base Systems.
%I SpringerVerlag
%S LNCS
%V 495
%P 291-307
%D 1991
%K DB, data base, database, type, types, many sorted, many-sorted, algebra,
   algebras, datatype, semantics, query

%A K. Chen
%A P. Hudak
%A M. Odersky
%T Parametric type classes (ext. abs.)
%J ACM Conf. Lisp and Functional Programming
%P 170-181
%M JUN
%D 1992
%K conf, FP, parametric, parameterised, parameterized, class, type, types,
   PTC, check, checking, multi parameter classes, c1992, c199x, c19xx
%X We propose a generalization to Haskell's type classes where a class can have
   type parameters besides the placeholder variable. We show that this
   generalization is essential to represent container classes with overloaded
   data constructor and selector operations. We also show that the resulting
   type system has principal types and present unification and type
   reconstruction algorithms.     isbn:0897914813.
   [<A HREF="http://doi.acm.org/10.1145/141471.141536">paper</A>][11/'02]
   (also see Jones 9th ESOP '00.)

%A J. R. Hindley
%T Types with intersection, an introduction
%J Formal Aspects of Computing.
%V 4
%N 5
%P 470-486
%D 1992
%K intersection, conjunction, data type, types, datatype, polymorphism,
   check, checking, inference, c1992, c199x, c19xx

%A S. Thompson
%T Type Theory and Functional Programming
%I AddisonWesley
%S Int. Comp. Sci. Series
%D 1991
%K text, book, c1991, c199x, c19xx, data type, datatype, types, FP, CSci,
   computing
%X [<A HREF="http://www.cs.kent.ac.uk/people/staff/sjt/TTFP/">online</A>][10/'03].
   uk us isbn:0201416670.

%A D. A. Wright
%T An intensional type discipline
%J Australian Computer Science Communications
%V 15
%P ??-??
%M JAN
%D 1992
%K ACSC, conf, c1992, c199x, c19xx, ACSC15, ACSC92, FP, functional programming,
   types

%A R. F. C. Walters
%T Categories and Computer Science
%I CUP
%S Cambridge Computer Science Texts
%P 176
%D 1992
%K book, text, CUP, c1992, c199x, c19xx, data type, types, FP,
   category theory
%X pb, us$27, uk us isbn:0521422264; uk us isbn13:978-0521422260.
   Hint [also search for: category type]

%A X. Leroy
%A M. Mauny
%T Dynamics in ML
%J JFP
%V 3
%N 4
%P 431-463
%D 1993
%K jrnl, JFP, FP, ML, SML, dynamic, data, type, types, c1993, c199x, c19xx
%X via H@skell m@il list 6/12/03.

%A D. A. Wright
%A C. A. Baker-Finch
%T Usage Analysis using Natural Reduction Types
%J Static Analysis '93
%I SpringerVerlag
%S LNCS
%V 724
%P ??-??
%W Padova
%M SEP
%D 1993
%K conf, c1993, c199x, c19xx, LNCS724, FP, functional programming

%A B. C. Pierce
%A D. N. Turner
%T Simple type-theoretic foundations for object-oriented programming
%J JFP
%V 4
%N 2
%P 207-247
%D 1994
%K jrnl, JFP, data type, types, datatype, high, higher rank, FP, OO, OOP, zz0903
%X via the H@ske.ll m@il list 11/9/'03

%A R. T. House
%T A proposal for an extended form of type checking of expressions
%J COMPJ
%V 26
%N 4
%P 366-374
%D 1983
%K COMPJ, c1983, c198x, c19xx, Pascal, dimension, type, types, static, check,
   checking, data, unit
%X via enews.

%A M. Wand
%A P. M. O'Keefe
%T Automatic dimensional inference
%P ??-??
%B Computational Logic: Essays in Honor of Alan Robinson.
%E J.-L. Lassez
%E G. Plotkin
%I MITpress
%D 1991
%K c1991, c199x, c19xx, dimension, type, types, unit, check, data,
   functional programming, FP
%X via enews

%A B. C. Pierce
%T Basic Category Theory for Computer Scientists
%I MITpress
%D 1991
%P 114
%K book, text, c1991, c199x, c19xx, type, types, Math, Maths, CSci,
   L4Ref, L5Ref, domain theory
%X "... important tool in theoretical computer science, especially in
   programming language semantics, domain theory, and concurrency, where it is
   a standard language of discourse. ..."
   1st ed 1991; pb, us$25; isbn:0262660717; isbn13:978-0262660716.

%A A. J. Kennedy
%T Dimension types
%J Proc. 5th European Symp. on Programming
%I SpringerVerlag
%S LNCS
%V 788
%D 1994
%K conf, c1994, c199x, c19xx, ESP, ESP5, ESP94, dimension, unit, type, types,
   check, data, functional programming, FP
%X via enews

%A M. Beaven
%A R. Stansifer
%T Explaining type errors in polymorphic languages
%J ACM Lett. Prog. Lang and Sys.
%V 2
%N 1-4
%P 17-30
%M MAR-DEC
%D 1993
%K LPLS, PLS, data, type, types, check, checking, error, diagnose, diagnosis
%X authors at Purdue and U. North Texas.

%A H. Seidl
%T Haskell overloading is DEXPTIME complete
%J IPL
%V 52
%N 2
%P 57-60
%M OCT
%D 1994
%K Haskell, functional programming, FP, type, types, check, checking,
   overload, over load, exptime, exp time

%A D. A. Schmidt
%T The Structure of Typed Programming Languages
%I MITpress
%D 1994
%K type, types, theory, CSci, computing, book, text, c1994, c199x, c19xx
%X isbn:0-262-19349-3;  (in Hargrave)

%E M. Dezani-Ciancaglini
%E G. Plotkin
%T Typed Lambda-Calculi and Applications
%J SpringerVerlag
%S LNCS
%V 902
%D 1995
%K book, text, lambda calculus, functional programming, FP,
   TLCA, TLCA95, type, types, check, checking, theory, CSci, zz0795
%X proc of TLCA conf' Edinburgh.

%E C. Gunter
%E J. Mitchell
%T Theoretical Aspects of Object-Oriented Programming: Types, Semantics,
   and Language Design
%I MITpress
%D 1994
%K text, book, OO, OOP, programming language, type, types, CS, CSci, zz1195
%X via Stephen Pipkin <!-- email: pipkin@cs.umbc.edu --> [11/'95]

%A M. P. Jones
%T A system of constructor classes: overloading and implicit higher-order
   polymorphism
%J J. of Functional Programming
%V 5
%N 1
%P 1-35
%M JAN
%D 1995
%O FPCA '93: Conf. on Func. Prog. Lang's. and Comp. Arch.,
   Copenhagen, Denmark, 1993  (short form)
%K jrnl, JFP, FP, class, type, types, monad, check, checking, OO, OOP,
   c1995, c199x, c19xx
%X This paper describes a flexible type system that combines overloading and
   higher-order polymorphism in an implicitly typed language using a system of
   constructor classes-a natural generalisation of type classes in Haskell. ...
   ... The underlying type system permits higher-order polymorphism but retains
   many of the attractive features that have made Hindley/Milner type systems
   so popular. In particular, there is an effective algorithm that can be used
   to calculate principal types without the need for explicit type or kind
   annotations. A prototype implementation has been developed providing,
   amongst other things, the first concrete implementation of monad
   comprehensions known to us at the time of writing.
   -- [<A HREF="http://www.cse.ogi.edu/~mpj/pubs/fpca93.html">FPCS93</A>][11/'02].
   (Also see Jones, 9th ESOP '00, LNCS 1782.)

%A R. Di Cosmo
%T Isomorphisms of Types: From Lambda-Calculus to Information Retrieval and
   Language Design
%I Birkauser Verlag
%D 235
%D 1995
%K FP, book, text, data type types, CAML, c1995, c199x, c19xx
%X review in Comp Rev p100 Feb '96.

%A K. Laufer
%T Type classes with existential types
%J J. of Functional Programming
%V 6
%N 3
%P 485-517
%M MAY
%D 1996
%K jrnl, type, exists, check, checking, class, FP, Haskell, c1996, c199x, c19xx
%X ... Adding existential types to an existing functional language that already
   features type classes requires only a minor syntactic extension. We first
   demonstrate how to provide existential quantification over type classes by
   extending the syntax of algebraic data type definitions and give examples of
   possible uses. We then develop a type system and a type inference algorithm
   for the resulting language. Finally, we present a formal semantics by
   translation to an implicitly-typed second-order lambda-calculus and show
   that the type system is semantically sound. Our extension has been
   implemented in the Chalmers Haskell B. system...
   [<A HREF="http://www.dcs.gla.ac.uk/jfp/bibliography/References/laufer1996:485.html">abs</A>][2/'03],
   [<A HREF="http://www.math.luc.edu/~laufer/papers/">.pdf@laufer</A>][2/03].

%A M. Odersky
%A P. Wadler
%T Pizza into Java: translating theory into practice
%J Proc. 24th ACM Symp. Principles of Prog. Langs.
%W Paris
%P ?-?
%M JAN
%D 1997
%K Pizza, Java, conf, POPL, POPL24, POPL97, parametric polymorphism,
   type, types, datatypes, date, OO, OOP, programming languages, zz1297
%X Pizza = Java + parametric polymorphism
         + high order functions + algebraic data types.

%A C. Bentley Dornan
%T Type-Secure Meta-Programming
%I Fac. Eng., U. Bristol, UK
%D 1998
%K PhD thesis, types, data, functional programming, FP, check, checking
%X via H@skell m@il list 6/12/03.

%A M. Phil
%T Dynamic types and type dependent functions
%B Implementation of Functional Languages
%E K. Hammond, A. Davie and C. Clack
%I Springer
%S LNCS
%V 1595
%P 169-185
%D 1998
%K conf, dynamics, functional programming, FP, overloading, overload
%X via H@skell m@il list 6/12/'03.

%E X. Leroy
%E A. Ohori
%T Types in compilation
%I Springer
%S LNCS
%V 1473
%P 299
%D 1998
%K proc, conf, c1998, c199x, c19xx, TIC2, TIC98, TIC, type, datatype, compiler
%X 2nd Int. workshop, Kyoto March 98,  13 sel' papers + 3 invited;
   dm74, au$73 at 11/98; uk us isbn:3-540-64925-5.

%A M. Karr
%A D. B. Loveman III
%T Incorporation of units into programming languages
%J CACM
%V 21
%N 5
%P 385-391
%M MAY
%D 1978
%K jrnl, CACM, c1978, c197x, c19xx, unit, dimension, dimensions, length, mass,
   type, types, check, checking
%X ref in  v a n D e l f t  SPE '99;  see also  H o u s e '83.

%A R. T. House
%T A proposal for an extended form of type checking of expressions
%J COMPJ
%V 26
%N 4
%P 366-374
%D 1983
%K jrnl, c1983, c198x, c19xx, COMPJ, unit, units, dimension, dimensions, types,
   type, length, mass
%X ref in  v a n D e l f t  SPE '99.

%A A. J. Kennedy
%T Dimension types
%J Proc. 5th European Symp. on Programming.
%S LNCS
%V 788
%I SpringerVerlag
%P 348-362
%D 1994
%K conf, c1994, c199x, c19xx, type, types, dimension, dimensions, unit, units,
   length, mass
%X ref in  v a n D e l f t  SPE '99;  see K e n n e d y  '95.

%A A. J. Kennedy
%T Programming Languages and Dimensions
%I Comp. Lab., Univ. of Cambridge
%D 1995
%O TR 391
%K PhD thesis, TR391, unit, units, type, types, check, checking,
   length, mass, dimension, dimensions
%X ref in  v a n D e l f t  SPE '99;   see K e n n e d y '84.
   [Also search for: dimension unit type].

%A L. Prechelt
%A W. F. Tichy
%T A controlled experiment to assess the benefits of procedure argument type
   checking
%J IEEE Trans. Software Eng.
%V 24
%N 4
%P 302-312
%M APR
%D 1998
%K jrnl, c1998, c199x, c19xx, types, check, static, strong, benefit, zz0407,
   SWE, error, errors, ANSI C, cc, programming languages, language
%X " ... experiment to assess the defect-detection capabilities of static,
   intermodule type checking. ... uses ANSI C & Kernighan & Ritchie (K & R) C.
   ... ANSI C compiler checks module interfaces (i.e., the param. lists calls to
   external fns), whereas K & R C does not. The experiment employs a
   counterbalanced design in which each of the 40 subjects, most of them CS PhD
   students, writes 2 nontrivial programs that interface with a complex library
   (Motif). Each subject writes 1 program in ANSI C & one in K & R C. The input
   to each compiler run is saved & manually analyzed for defects. Results
   indicate that delivered ANSI C programs contain significantly fewer interface
   defects than delivered K & R C programs. Furthermore, after subjects have
   gained some familiarity with the interface they are using, ANSI C programmers
   remove defects faster & are more productive (measured in both delivery time &
   functionality implemented)."
   -- [<A HREF="http://dx.doi.org/10.1109/32.677186">doi:10.1109/32.677186</A>]['07].

%A M. Jones
%T Typing Haskell in Haskell
%J Haskell Workshop
%P ?-?
%D 1999
%K wShop, L4Ref, L5Ref, functional programming, language, FP, data type, types,
   typed, inference, check, checking, polymorphic, system, c1999, c199x, c19xx,
   kind, kinds, class, classes, implementation, compiler, definition
%X "H benefits from a sophisticated type sys, but implementors, programmers,
   & researchers suffer because it has no formal description. To remedy this
   shortcoming, we present a H program that implements a H typechecker, thus
   providing a mathematically rigorous specification in a notation that is
   familiar to H users. We expect this program to fill a serious gap in current
   descriptions of H, both as a starting point for discussions about existing
   features of the type sys, & as a platform ... to explore new proposals."
  <!-- mpj @t cse ogi edu --> --[<A HREF="http://www.cse.ogi.edu/~mpj/thih/">inc revised.pdf@cse.ogi.edu</A>][10/'04].

%A R. Bird
%A R. Paterson
%T de Bruijn notation as a nested datatype
%J J. of Functional Programming
%V 9
%N 1
%P 77-91
%D 1999
%K jrnl, deBruijn, types, data type, FP, higher rank, zz0903
%X via the H@ske.ll m@il list 11/9/'03.

%A A. van Delft
%T A Java extension with support for dimensions
%J SPE
%V 29
%N 7
%P 605-616
%D 1999
%K jrnl, SPE, c1999, c199x, c19xx, programming language, type, types, check,
   checking, dimension, quantity, length, mass, time, electric current,
   temperature, mole, luminosity, luminous intensity, light, brightness,
   unit, units, SI, vanDelft, zz1199
%X length (meter),  mass (kg),  time (second),  electricCurrent (amp),
   temperature (K, Kelvin),     amountOfSubstance (mole),
   luminousIntensity (candela) --  7 base dimns. for physics def. in
   Int. Sys, of units (SI) --p.605.     [13 refs]
   -- [<A HREF="http://dx.doi.org/10.1002/(SICI)1097-024X(199906)">doi</A>]['06],
   [<A HREF="mailto:delft@delftware.nl">author</A>[11/99].
   [Also search for: dimension unit type].

%A R. L. Crole
%T Categories for Types
%I CUP
%S Math. Textbooks
%P 353
%D 1994
%K book, text, c1994, c199x, c19xx, category theory, data type, types,
   datatype, L4Ref, L5Ref
%X pb, us$47; uk us isbn:0521457017; uk us isbn13:978-0521457019.

%A C. Hall
%A K. Hammond
%A S. Peyton Jones
%A P. Wadler
%T Type classes in Haskell
%J European Symp. On Programming
%S LNCS
%I SpringerVerlag
%P 241-256
%M APR
%D 1994
%K conf, FP, functional programming, adhoc, ad hoc polymorphism, class,
   OOP, Haskell, type, types, classes, object oriented, OOP, OO,
   operator, overload, overloading, c1994, c199x, c19xx, zz0701
%X This paper defines a set of type inference rules for
   resolving overloading introduced by type classes.
   Programs including type classes are transformed into ones
   which may be typed by the Hindley-Milner inference rules.
   In contrast to an other work on type classes, the rules
   presented here relate directly to user programs. An innovative
   aspect of this work is the use of second-order lambda calculus
   to record type information in the program.
   Also see Wadler and Blott '89.
   dvi and ps@[<A HREF="http://www.cs.bell-labs.com/who/wadler/topics/type-classes.html">www</A>][7/'01].

%A M. Odersky
%A P. Wadler
%T A second look at overloading
%J 7th Int. Conf. on Functional Programming and Comp. Arch.
%I ACM Press
%W San Diego, California
%M JUN
%D 1995
%K conf, c1995, c199x, c19xx, FPCS, FPCS95, FPCS7, FP, functional programming,
   adhoc, ad hoc polymorphism, class, OOP, Haskell, type, types, records,
   classes, object oriented, OO, operator, overload, overloading,  zz0701
%X We study a minimal extension of the Hindley / Milner system that
   supports overloading and polymorphic records. We show that the
   type system is sound with respect to a standard untyped compositional
   semantics. We also show that every typable term in this system has a
   principal type and give an algorithm to reconstruct that type.
   See also Wadler and B l o t t '89.
   dvi ps@[<A HREF="http://www.cs.bell-labs.com/who/wadler/topics/type-classes.html">www</A>][7/'01].

%A A. D. Gordon
%T Notes on nominal calculi for security and mobility
%J Foundations of Security Analysis and Design
%E R. Focardi
%E R. Gorrieri
%I SpringerVerlag
%P 262-330
%S LNCS
%V 2171
%D 2001
%K mobile, agent, ambient calculus, pi, spi, c2001, c200x, c20xx, zz0204,
   introduction, agents, notes
%X "There is great interest in applying nominal calculi--computational
   formalisms that include dynamic name generation--to the problems of
   programming, specifying, & verifying secure & mobile computations. These
   notes introduce three nominal calculi - the pi calculus, the spi calculus, &
   the ambient calculus. We describe some typical techniques, & survey related
   work." isbn:3540428968.
   -- [<A HREF="   http://www.springerlink.com/openurl.asp?genre=article&issn=0302-9743&volume=2171&spage=262">openurl</A>][2/'04],
      [<A HREF="http://www.springerlink.com/link.asp?id=8anjyr6umbpwf23q">met@press</A>][2/'04],
      [<A HREF="http://research.microsoft.com/~adg/Publications/details.htm#nominal">adg</A>][2/'04].

%T Typed Lambda Calculi and Applications
%E S. Abramsky
%J LNCS
%I SpringerVerlag
%V 2044
%P 429
%D 2001
%K conf, c2001, c200x, c20xx, TLCA, calculus, type, types, check, checking,
   FP, pi-calculus, zz0801
%X 5th Int. Conf. TLCA.   [Also search for: type FP].
   About au$98 [8/'01]; uk us isbn:3-540-41960-8.

%A L. Cardelli
%A G. Ghelli
%A A. Gordon
%T Types for the ambient calculus
%J J. of Information and Computation
%P 160-194
%N 2
%V 177
%M SEP
%D 2002
%K jrnl, in, out, open, distributed, concurrent, mobile, ambients,
   c2002, c200x, c20xx, Luca, zz0204, agent, agents, process, processes,
   type, typing
%X "... a concurrent calculus where the unifying notion of `ambient' is used to
   model many different constructs for distributed & mobile computation. We
   study a type system that describes several properties of ambient behavior.
   The type system allows ambients to be partitioned in disjoint sets (groups),
   according to the intended design of a system, in order to specify both the
   communication & the mobility behavior of ambients."
   -- [<A HREF="http://dx.doi.org/10.1006/inco.2001.3121">doi:10.1006/inco.2001.3121</A>][2/'04],
      [<A HREF="http://www.luca.demon.co.uk/">Luca</A>][2/'04],
      [<A HREF="http://tql.di.unipi.it/papers.html">Ghelli</A>][2/'04],
      [<A HREF="http://research.microsoft.com/~adg/">Gordon</A>][2/'04].

%A Y. Jun
%A G. Michaelson
%A P. Trinder
%T Explaining polymorphic types
%J COMPJ
%V 45
%N 4
%D 2002
%P 436-452
%K jrnl, Compj, polymorphism, type, check, checking, ML, SML, FP,
   introduction, human factors, HCI, zz0802
%X [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_45/Issue_04/">jrnl</A>][8/'02].

%A P. J. Stuckey
%A M. Sulzmann
%T A theory of overloading
%J Proc. 7th ACM SIGPLAN Int. Conf. on Functional Programming
%P 167-178
%D 2002
%K conf, c2002, c200x, c20xx, type, types, overload, overloaded, uniMelb
%X "...a minimal extension of the Hindley/Milner system to allow for
   overloading of identifiers. ... relies on a combination of the HM(X) type
   sys. framework with Constraint Handling Rules (CHRs). CHRs are a declarative
   language for writing incremental constraint solvers. CHRs allow us to
   precisely describe the relationships among overloaded identifiers. Under
   some sufficient conditions on the CHRs we achieve decidable type inference &
   the semantic meaning of programs is unambiguous. Our approach allows us to
   combine open & closed world overloading. We also show how to deal with
   overlapping definitions."
   -- [<A HREF="http://doi.acm.org/10.1145/581478.581495">doi:10.1145/581478.581495</A>]['05] auths@uniMelb.

%A J. Cheney
%A R. Hinze
%T A lightweight implementation of generics and dynamics
%J Proc. of the ACM Sigplan workshop on Haskell
%I ACM_Press
%P 90-104
%D 2002
%K functional programming, FP, c2002, c200x, c20xx, zz0203, conf, Haskell,
   generic, values, dynamic, typecase, cast, type, types, representable,
   typerep, typing, polytypic, polyp, existential, template
%X "[recently] a number of proposals for extending statically typed languages
   by dynamics or generics. Most proposals -- if not all -- require significant
   extensions to the underlying language. [...] we show that this need not be
   the case. We propose a particularly lightweight extension that supports both
   dynamics & generics. Furthermore, the two features are smoothly integrated:
   dynamic values, for instance, can be passed to generic functions. Our
   proposal makes do with a standard Hindley-Milner type system augmented by
   existential types. Building upon these ideas we have implemented a small
   library that is readily usable both with Hugs & [ghc]". isbn:1581136056;
   -- [<A HREF="http://doi.acm.org/10.1145/581690.581698">www</A>][2/03].
   [Also search for: template Haskell], etc..

%A A. Baars
%A S. Doaitse Swierstra
%T Typing dynamic typing
%J ICFP
%P ?-?
%D 2002
%K conf, ICFP, type, types, check, static, c2002, c200x, c20xx, unsafeCoerce,
   check, checking, functional programming, FP
%X "Even ... in a statically typed l. we every now & then encounter statically
   untypable values ... result from interpreting values or from communicating
   with the outside world. To cope with this problem most ls. include some form
   of dynamic types. It may be that the core l. has been explicitly extended
   with such a type, or that one is allowed to live dangerously by using
   functions like unsafeCoerce. We show how, by a careful use of existentially
   & universally quantified types, one may achieve the same effect, without
   extending the l. with new or unsafe features. The techniques explained are
   universally applicable, provided the core l. is expressive enough; this is
   the case for the common implementations of Haskell. The techniques are used
   in the description of a type checking compiler that, starting from an
   expression term, constructs a typed function representing the semantics of
   that expression. In this function the overhead associated with the type
   checking is only once being paid for; in this sense we have thus achieved
   static type checking."
   -- [<A HREF="http://www.cs.uu.nl/people/arthurb/dynamic.html">paper</A>]['05].

%A B. C. Pierce
%T Types and Programming Languages
%I MITpress
%M FEB
%D 2002
%P 645
%K book, text, c2002, c200x, c20xx, type, language, check, checking,
   polymorphism, subtype, subtyping, bounded quantification, kind, kinds
%X hb, us$57, isbn:0262162091; isbn13:978-0262162098.
   [<A HREF="http://www.cis.upenn.edu/~bcpierce/tapl/">bcpierce</A>]['05].

%A M. Viroli
%T A type-passing approach for the implementation of parametric methods in Java
%J COMPJ
%V 46
%N 3
%P 263-294
%M MAY
%D 2003
%K jrnl, COMPJ, java, computer programming language, polymorphism, polymorphic,
   ad hoc, adhoc, parametric, generic, type, types, method, methods, Pizza, GJ,
   erasure, code expansion, dynamic dispatch, virtual, CC, c#, C++,
   OO, OOP, object, oriented, c2003, c200x, c20xx, zz0603
%X Parametric methods ... reusing code and augmenting the expressiveness
   of an [OO] language providing parametric classes. ... focuses on their
   implementation techniques for Java.  Existing proposals for extending Java
   with parametric polymorphism are outlined, [...] : type-erasure,
   code-expansion and type-passing.  ... only type-erasure and code-expansion
   have been exploited for the implementation of parametric methods, but they
   suffer from some problems.  ...type-erasure is unable to support parametric
   types at run-time, while code-expansion generally leads to significant
   increase of both disk and memory overhead. [here] study a type-passing
   approach aimed at tackling these issues. This is based on the management
   of method descriptors, which are objects passed to the method bodies at
   invocation-time, and which carry information on the instantiation of the
   method's type parameters.  Run-time efficiency is guaranteed thanks to a
   special treatment of descriptors deferring their creation at load-time.
   Dynamic dispatching of method calls is supported by exploiting a data
   structure called the Virtual Parametric Methods Table, resembling Virtual
   Methods Tables of C++. The approach here presented turns out to be a
   significant alternative to the existing proposals for implementing generics
   in Java, supporting parametric types at run-time without unnecessary code
   footprint.
   -- [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_46/Issue_03/460263.sgm.abs.html">abs</A>][5/'03].

%A R. Lammel
%A S. Peyton-Jones
%T Scrap your boilerplate: A practical design pattern for generic programming
%J ACM SIGPLAN Workshop on Types in Language Design and Implementation
%I ACM Press
%P 26-37
%D 2003
%O ACM SIGPLAN Notices
%K conf, functional programming, FP, Haskell, data type, types, boiler-plate,
   generics, Strafunski, rank-2 polymorphism, zz1003, c2003, c200x, c20xx,
   TLDI, rank2, traverse, traversal, data structures, OO, OOP, classes
%X "We describe a design pattern for writing programs that traverse data
   structures built from rich mutually-recursive data types. [They] often have
   a great deal of "boilerplate" code that simply walks the structure, hiding a
   small amount of "real" code that constitutes the reason for the traversal.
   Our technique allows most of this boilerplate to be written once and for
   all, or even generated mechanically, leaving the programmer free to
   concentrate on the important part of the algorithm.  These generic programs
   are much more adaptive when faced with data structure evolution because they
   contain many fewer lines of type-specific code. Our approach is simple to
   understand, reasonably efficient, and it handles all the data types found
   in conventional functional programming languages. It makes essential use of
   rank-2 polymorphism, an extension found in some implementations of Haskell.
   Further it relies on a simple type-safe cast operator."
   See [<A HREF="http://www.cs.vu.nl/boilerplate/">cs.vu.nl</A>][10/'03],
    & [<A HREF="http://haskell.org/ghc/docs/latest/html/base/">Haskell libs</A>][10/'03],
    & [<A HREF="http://doi.acm.org/10.1145/604174.604179">doi:10.1145/604174.604179</A>][10/'03].

%A O. Kiselyov
%A R. Lammel
%A K. Schupke
%T Strongly typed heterogeneous collections
%J Haskell Workshop
%W Snowbird
%P 96-107
%D 2004
%K wShop, HList, functional programming, FP, class, classes, type, types,
   two class trick, heterogeneous list, collection, overlapping instances,
   dynamic, database, data base, c2004, c200x, c20xx
%X "A heterogeneous collection is a datatype that is capable of storing data of
   different types. Such a datatype provides operations for look-up, update,
   iteration, and others. There are various kinds of heterogeneous collections,
   differing in representation, invariants, and access operations. We describe
   HList -- a Haskell-based library for strongly typed heterogeneous
   collections. We illustrate heterogeneous collections in the context of
   type-safe database access in Haskell. The development of HList relies on
   some common extensions of Haskell 98, and it raises some interesting issues
   regarding Haskell's type system."
   [<A HREF="http://homepages.cwi.nl/~ralf/HList/">cwl.nl</A>][6/'04],
   [<A HREF="http://doi.acm.org/10.1145/1017472.1017488">doi:10.1145/1017472.1017488</A>]['05].

%A R. Hinze
%T Generics for the masses
%J 9th ACM Sigplan Int. Conf. Functional Programming
%W Snowbird
%P 236-243
%M SEP
%D 2004
%K conf, ICFP, ICFP9, FP, generic function, type, types, c2004, c200x, c20xx,
   Haskell 98, class, classes
%X "A generic function is a function that can be instantiated on many [DTs] ...
   ... show that one can, in fact, program generically within Haskell-98
   obviating to some extent the need for fancy type systems or separate tools.
   [H]'s type classes are at the heart of this approach;..."
   [<A HREF="http://www.informatik.uni-bonn.de/~ralf/publications/ICFP04.pdf">paper.pdf@.uni-bonn.de</A>]['04],
   [<A HREF=" http://doi.acm.org/10.1145/1016850.1016882">doi:10.1145/1016850.1016882</A>]['04].

%A M. Erwig
%A D. Ren
%T Monadification of functional programs
%J Sci. of Computer Programming
%V 52
%N 1-3
%P 101-129
%D 2004
%K jrnl, SCP, monad, monads, FP, c2004, c200x, c20xx, program
%X "... integration of many different features by just changing the defn of the
   monad & not the rest of the program, which is a desirable feature from a
   SWE & software maintenance point of view. We describe an alg. for the
   automatic transformation of a group of fns into such a monadic form. We
   identify 2 correctness criteria & argue that the proposed transformation is
   at least correct in the sense that transformed programs yield the same
   results as the original programs modulo monad constructors. ..."
   [<A HREF="http://web.engr.oregonstate.edu/~erwig/papers/Monadify_SCP04.pdf">pdf</A>]['05].

%A I. Lynagh
%T Typing template Haskell: Soft types
%I Oxford U., Computing Lab.
%P 22
%M AUG
%D 2004
%K RR-04-19
%K TR, TR19, template Haskell, c2004, c200x, c20xx, soft type, types, check,
   compile time, meta-programming, zz0705
%X "... give the motivation for an improved type system for Template Haskell, a
   recent compile-time meta-programming extension for H., & explain what
   properties we would like the type system to have & why. ... present a type
   system, based on soft types, for a simplified Template Haskell-like language
   that has these properties. We prove that it has principal types & describe
   an algorithm that implements type inference for this type system."
   [<A HREF="http://web.comlab.ox.ac.uk/oucl/publications/tr/rr-04-19.html">tr.ps@ox.ac</A>]['05].

%A B. C. Pierce
%T Advanced Topics in Types and Programming Languages
%I MITpress
%P 588
%D 2004
%K book, text, c2004, c200x, c20xx, L4Ref, L5Ref, langyage, type, check,
   checking
%X hb us$47; uk us isbn:0262162288; uk us isbn13:978-0262162289.

%A O. Kiselyov
%A R. Lammel
%T Haskell's overlooked object system
%I ?
%M SEP
%D 2005
%O submitted '05
%K TR, OOHaskell, library, OO, OOP, c2005, c200x, c20xx, oriented, overriding,
   inheritance, subtyping, type, types, checking, functional programming, FP,
   class, classes, zz0905
%X "H. provides type-class-bounded & parametric polymorphism [v.] subtype
   polymorphism of object-oriented languages such as Java & OCaml. ...
   contentious question whether H. 98 without extensions, or with common
   extensions, or with new extensions can fully support conventional object-
   oriented programming with encapsulation, mutable state, inheritance,
   overriding, statically checked implicit & explicit subtyping, & so on. We
   [show] H. 98, with some common extensions, supports all the conventional OO
   features plus more advanced ones, inc.  1st-class lexically scoped classes,
   implicitly polymorphic classes, flexible multiple inheritance, safe downcasts
   & safe co-variant arguments.  H. indeed can support width & depth,
   structural & nominal subtyping. We address the particular challenge to
   preserve H.'s type inference even for objects & object-operating functions.
   The OO features are introduced in H.  as the OOHaskell library. OOHaskell
   lends itself as a sandbox for typed OO language design."
   [<A HREF="http://arxiv.org/abs/cs.PL/0509027">arxiv.org</A>]['05],
   [<A HREF="http://homepages.cwi.nl/~ralf/OOHaskell/">cwi.nl</A>]['05].

%A M. Chakravarty
%A G. Keller
%A S. Peyton Jones
%A S. Marlow
%T Associated types with class
%J ACM Conf. on Principles of Programming Languages
%P 1-13
%M JAN
%D 2005
%K conf, POPL, type, FP, c2005, c200x, c20xx, check, checking
%X "...extension to Haskell type classes that allows a type class declaration
   to define data types as well as values (or methods). Similarly, an instance
   declaration gives a witness for such data types, as well as a witness for
   each method. It turns out that this extension directly supports the idea of
   a type-indexed type, and is useful in many applications, especially for
   self-optimising libraries that adapt their data representations and
   algorithms in a type-directed manner. ..."
   -- [<A HREF="http://research.microsoft.com/~simonpj/papers/assoc-types/">paper</A>]['06].

%A M. Sulzmann
%A P. J. Stuckey
%T HM(X) type inference is CLP(X) solving
%J J. Functional Programiing
%V ?
%N ?
%P ?
%D 2007 to appear
%K jrnl, JFP, FP, LP, c2007, c200x, c20xx, type, types, check, checking,
   CLP, CLPx, constraint, constraints, solve, solver, zz1007
%X "The HM(X) sys. is a generalization of the H'-M' system param. in the
   constraint domain X. Type inf. is performed by generating constraints out of
   the program text, which are then solved by the domain-specific constraint
   solver X. The solver has to be invoked at the latest when type inference
   reaches a let node so that we can build a polymorphic type. A typical eg.,
   of such an inference approach is Milner's alg. W. We formalize an inference
   approach where the HM(X) type inference problem is first mapped to a CLP(X)
   program.  ... The CLP(X) style inf. sys., where X is def. by Constraint
   Handling Rules, is implemented as part of the Chameleon system."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796807006569">doi:10.1017/S0956796807006569</A>]['07].

%A J. Cooper
%A S. McKeever
%T A model-driven approach to automatic conversion of physical units
%J SPE
%V 38
%N 4
%P 337-359
%M APR
%D 2008
%K jrnl, SPE, c2008, c200x, c20xx, zz0308, unit, dimension, dimensions,
   length, mass, type, types
%X "When physical quantities are used in programs ... CellML, developed at
   the U. Auckland ... an intuitive alg. for performing automatic conversions
   between quantities measured in different units. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.828">doi:10.1002/spe.828</A>]['08],
   [also search for: dimension unit type].

%A A. Loh
%A C. McBride
%A W. Swierstra
%T A tutorial implementation of a dependently typed lambda calculus
%J Fundamenta Informaticae
%I IOSpress
%V 102
%N 2
%P 177-207
%D 2010
%K jrnl, FP, c2010, c201x, c20xx, zz1113, Loeh, dependent type, types,
   dependently typed, system, check, checker, checking, lambda calculus,
   LambdaPi, dependentType
%X "We present the type rules for a dependently-typed core calculus together
   with a straightforward implementation in Haskell. We explicitly highlight the
   changes necessary to shift from a simply-typed l.calculus to the dep.-typed
   l.calculus. We also describe how to extend our core language with data types
   & write several small example programs. The paper is accompanied by an
   executable interpreter & example code that allows immediate experimentation
   with the system we describe."
   -- [<A HREF="http://dx.doi.org/10.3233/FI-2010-304">doi:10.3233/FI-2010-304</A>]['13],
    & auth1@[<A HREF="http://www.andres-loeh.de/LambdaPi/">.de</A>]['13].
   [Also search for: dependent type].

%A S. Lindley
%A P. Wadler
%A J. Yallop
%T The arrow calculus
%J JFP
%V 20
%P 51-69
%D 2010
%K jrnl, JFP, FP, c2010, c201x, c20xx, zz0210, arrow, arrows, type, types,
   monad, monads, Hughes, Paterson, Moggi
%X "We introduce the arrow calculus, a metalanguage for manipulating Hughes's
   arrows with close relations both to Moggi's metalanguage for monads and to
   Paterson's arrow notation. Arrows are classically defined by extending lambda
   calculus with three constructs satisfying nine (somewhat idiosyncratic) laws;
   in contrast, the arrow calculus adds four constructs satisfying five laws
   (which fit two well-known patterns). The five laws were previously known to
   be sound; we show that they are also complete, and hence that the five laws
   may replace the nine."
   -- [<A HREF="http://dx.doi.org/10.1017/S095679680999027X">doi:10.1017/S095679680999027X</A>]['10].
   [Also search for: FP arrows].

%A D. Vytiniotis
%A S. Weirich
%T Parametricity, type equality, and higher-order polymorphism
%J JFP
%V 20
%N 2
%P 175-210
%M MAR
%D 2010
%K jrnl, JFP, c2010, c201x, c20xx, zz0510, FP, high order, polymorphism, type,
   equality, equal, GADTs, types, polymorphic, parametric
%X "... show that two examples of type equality propositions actually do reflect
   type equality; they are only inhabited when their arguments are equal and
   their proofs are unique (up to equivalence.) We show this result in the
   context of a strongly normalizing language with higher-order polymorphism and
   primitive recursion over runtime-type representations by proving Reynolds's
   abst'n thm. We then use this thm to derive "free" thms about equality types."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796810000079">doi:10.1017/S0956796810000079</A>]['10].

%A I. Sergey
%A D. Clarke
%T A correspondence between type checking via reduction and type checking via
   evaluation
%J IPL
%V 112
%N 1-2
%P 13-20
%M JAN
%D 2012
%K jrnl, IPL, c2012, c201x, c20xx, zz1111, type, types, check, checking,
   checker, inter-derivation, reduction, evaluation
%X "... consider a reduction-based type checking & a trad. recursive descent.
   # A correspondence is provided by the construction & inter-derivation.
   # Soundness is a corollary of the correctness of the inter-derivation.
   # The transformations we use are off-the-shelf."  [online Oct 2011].
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2011.10.008">doi:10.1016/j.ipl.2011.10.008</A>]['11].

%A G. M. Bierman
%A A. D. Gordon
%A C. Hritcu
%A D. Langworthy
%T Semantic subtyping with an SMT solver
%J JFP
%V 22
%N 1
%P 31-105
%M JAN
%D 2012
%K jrnl, JFP, FP, c2012, c201x, c20xx, zz0412, type, types, check, checking,
   subtype, subtyping, logic, Satisfiability Modulo Theories, SMT, solver,
   refinement type, type test, intersection, union, negation, singleton,
   nullable, variant
%X "... a 1st-order func.lang. ... combination of the ideas of refinement type
   (the subset of a type to satisfy a Boolean expn) & type-test (a B.expn
   testing whether a value belongs to a type). Our core calculus can express a
   rich variety of typing idioms; [eg] intersection, union, negation, singleton,
   nullable, variant, & algebraic types are all derivable. We formulate a
   semantics in which expns denote terms, & types are interpreted as 1st-order
   logic formulas. Subtyping is def. as valid implication between the semantics
   of types. The formulas are interpreted in a specific model that we axiomatize
   using std 1st-order theories. ... present a novel type-checking alg. able to
   eliminate many dynamic tests & to detect many errors statically. The key idea
   is to rely on a Satisfiability Modulo Theories solver to compute subtyping
   efficiently. [&] using a satisfiability modulo theories solver allows us to
   show the uniqueness of normal forms for non-deterministic expns, provide
   precise counterexamples when type-checking fails, detect empty types, &
   compute instances of types statically & at run-time."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796812000032">doi:10.1017/S0956796812000032</A>]['12].

%A B. Pientka
%T An insider's look at LF type reconstruction: Everything you (n)ever wanted
   to know
%J JFP
%V 23
%N 1
%P 1-37
%M JAN
%D 2013
%K jrnl, JFP, FP, c2013, c201x, c20xx, zz0113, type, contextual modal types,
   LF, type reconstruction, Beluga, Twelf, checking, programming languages
%X "... discuss a one-pass type reconstruction for objects in the logical
   framework LF, describe formally the type reco. process using the framework of
   contextual modal types, & prove correctness of type reco.. Since type
   reco. will find most general types & may leave free variables, we in addition
   describe abstraction which will return a closed object where all free
   variables are bound at the outside. We also implemented our algs. as part of
   the Beluga language, & the performance of our type reco. alg. is comparable
   to type reco. in existing systems such as the logical framework Twelf."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796812000408">doi:10.1017/S0956796812000408</A>]['13].

%A P.-E. Dagand
%A C. McBride
%T Transporting functions across ornaments
%J JFP
%V ?
%P 1-68 ?
%M APR
%D 2014
%K jrnl, JFP, FP, c2014, c201x, c20xx, zz0514, dependent type, dependant, types,
   function, ornament, invariant, generic programming
%X "Programming with dependent types is a blessing & a curse. It is a blessing
   to be able to bake invariants into the defn of datatypes: We can finally
   write correct-by-construction s/w. However, this extreme accuracy is also a
   curse: A datatype is the combination of a structuring medium together with a
   special purpose logic. These domain-specific logics hamper any attempt to
   reuse code across similarly structured data. ... we capitalise on the
   structural invariants of datatypes. To do so, we first adapt the notion of
   ornament to our universe of inductive families. We then show how code reuse
   can be achieved by ornamenting functions. Using these functional ornaments,
   we capture the relationship between fns such as the addition of natural
   numbers & the concat. of lists. With this knowledge, we demo. how the
   implementation of the former informs the implementation of the latter: The
   users can ask the defn of addition to be lifted to lists & they will only be
   asked the details nec. to carry on adding lists rather than numbers. Our
   presentation is formalised in the type theory with a universe of datatypes &
   all our constructions have been implemented as generic programs, requiring
   no extension to the type theory."  [online 23 Apr. 2014.]
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796814000069">doi:10.1017/S0956796814000069</A>]['14].

%A J. Breitner
%A R. A. Eisenberg
%A S. Peyton Jones
%A S. Weirich
%T Safe zero-cost coercions for Haskell
%J JFP
%V 26
%P e15 (pp.79)
%M JUL
%D 2016
%K jrnl, JFP, FP, c2016, c201x, c20xx, zz0816, data type, types, coercion,
   coercible, Haskell, ghc, programming languages
%X "Generative type abstractions -  present in Haskell, OCaml, & other languages
   - are useful concepts to help prevent programmer errors. They serve to create
   new types that are distinct at compile time but share a run-time
   representation with some base type. We present a new mechanism that allows
   for zero-cost conversions between generative type abstractions & their
   representations, even when such types are deeply nested. We prove type safety
   in the presence of these conversions and have implemented our work in GHC."
   -- [<A HREF="http://dx.doi.org/10.1017/S0956796816000150">doi:10.1017/S0956796816000150</A>]['16].

%A K.-B. Hou
%A N. Benton
%A R. Harper
%T Correctness of compiling polymorphism to dynamic typing
%J JFP
%V 27
%N ?
%P ?-?
%M DEC
%D 2016
%J jrnl, FP, JFP, c2016, c201x, c20xx, zz1117, type, types, lambda, calculus,
   typed, dynamic, polymorphic, Curry, Bracha, Scala, System F, SystemF, Moggi
%X "The connection between polymorphic & dynamic typing was originally
   considered by Curry et al. (1972, Combinatory Logic, vol. ii) in the form of
   'polymorphic type assignment' for untyped lambda-terms. ... in modern
   terminology, a dynamic language. Interest in type assignment was revitalized
   by the proposals of Bracha et al. (1998, OOPSLA) & Bank et al. (1997, POPL)
   to enrich Java with polymorphism (generics), which in turn sparked ...
   such as Scala, with similar combinations of features. In such a setting,
   where the target language already has a monomorphic type system, it is
   desirable to compile polymorphism to dynamic typing in such a way that as
   much static typing as possible is preserved, relying on dynamics only
   insofar as genericity is actually required. The basic approach is to compile
   polymorphism using embeddings from each type into a universal 'top' type, ID,
   & partial projections that go in the other direction. ... intuitively
   reasonable, &, indeed, has been used in practice many times. ... studies the
   compilation of System F to an extension of Moggi's computational
   meta-language with a dynamic type & shows how the compilation may be proved
   correct using a logical relation."  [online Dec 2017.]
   -- [<A HREF="https://doi.org/10.1017/S0956796816000265">doi:10.1017/S0956796816000265</A>]['17].
   [Also search for: typed lambda calculus].

%A O. Dardha
%A D. Gorla
%A D. Varacca
%T Semantic subtyping for objects and classes
%J COMPJ
%V 60
%N 5
%P 636-656
%M APR
%D 2017
%K jrnl, COMPJ, c2017, c201x, c20xx, zz0517, type, types, typing, check,
   checking, programming languages, OOP, object, class
%X "... propose an integration of structural subtyping with boolean connectives
   & semantic subtyping to define a Java-like prog. lang. that exploits the
   benefits of both techniques. Semantic subtyping is an approach for defining
   subtyping relation based on set-theoretic models, rather than syntactic
   rules. ... While semantic subtyping is naturally linked to the structural
   one, we show how our framework can also accommodate the nominal subtyping.
   Several [egs] show the expressivity & the practical advantages ..."
   -- [<A HREF="https://doi.org/10.1093/comjnl/bxw080">doi:10.1093/comjnl/bxw080</A>]['17].

%A A. Stump
%T The calculus of dependent lambda eliminations
%J JFP
%V 27
%M e14
%M MAY
%D 2017
%K jrnl, JFP, FP, type, types, typing, c2017, c201x, c20xx, zz0617, dependent,
   calculus of dependent lambda eliminations, Cedille
%X Modern  constructive  type  theory  is  based  on  pure  dependently  typed
   lambda calculus, augmented with user-defined datatypes. ... presents an
   alternative called the Calculus of Dependent Lambda Eliminations, based
   on pure lambda encodings with no auxiliary datatype system. New typing
   constructs are defined that enable induction, as well as large eliminations
   with lambda encodings. These constructs are constructor-constrained recursive
   types, and a lifting operation to lift simply typed terms to the type level.
   Using a lattice-theoretic denotational semantics for types, the language is
   proved logically consistent. The power of CDLE is demonstrated through
   several examples, which have been checked with a prototype implementation
   called Cedille."
   -- [<A HREF="https://doi.org/10.1017/S0956796817000053">doi:10.1017/S0956796817000053</A>]['17].

%A S. Cheng
%A M. Erwig
%T Systematic identification and communication of type errors
%J JFP
%V 28
%P e2
%M JAN
%D 2018
%K jrnl, JFP, c2018, c201x, c20xx, zz0218, FP, type, inference, types, check,
   checking, error, errors, variational typing
%X "... often difficult to pinpoint the cause of the type error among many
   potential candidates. ... employing the idea of variational typing that
   systematically reuses computations for shared parts and generates all
   messages by typing the whole ill-typed expression only once. We have
   evaluated our approach over a large set of examples collected from previous
   publications in the literature. The evaluation result shows that our approach
   outperforms previous approaches and is computationally feasible."
   -- [<A HREF="https://doi.org/10.1017/S095679681700020X">doi:10.1017/S095679681700020X</A>]['18].

%A J. Cockx
%A D. Devriese
%T Proof-relevant unification: Dependent pattern matching with only the
   axioms of your type theory
%J JFP
%V 20
%N e12
%M MAY
%D 2018
%K jrnl, JFP, c2018, c201x, c20xx, zz0518, functional programming language, FP,
   type, types, check, checking, axiom, proof, logic, dependent pattern,
   unification, dependencies, Agda, Coq, Idris, eta equality, record, records
%X "Dependently typed languages such as Agda, Coq, & Idris use a syntactic
   first-order unification alg. to check definitions by dependent pattern
   matching. ... proposes a proof-relevant framework for reasoning formally
   about unification in a dependently typed setting. In this framework,
   unification rules compute not just a unifier but also a corresponding
   soundness proof in the form of an equivalence between two sets of equations.
   By rephrasing the standard unification rules in a proof-relevant manner, they
   are guaranteed to preserve soundness of the theory. [&] it enables us to
   safely add new rules that can exploit the dependencies between the types of
   equns, such as rules for eta-equality of record types & higher dimensional
   unification rules for solving equns between equality proofs. ... implemented
   a complete overhaul of the unification algorithm used by Agda. ..."
   -- [<A HREF="https://doi.org/10.1017/S095679681800014X">doi:10.1017/S095679681800014X</A>]['18].

%A T. A. K. Zakian
%A T. L. Mcdonell
%A M. Cimini
%A R. R. newton
%T Ghostbuster: A tool for simplifying and converting GADTs
%J JFP
%V 28
%P e16
%M JUN
%D 2018
%K jrnl, eJrnl, JFP, c2018, c201x, c20xx, zz0718, datatype, type, types, check,
   checking, GADT, GADTs, Generalized Algebraic Data Type, Ghostbuster
%X "... GADTs, can encode non-trivial properties in the types of the
   constructors. ... however, all code manipulating that datatype must provide
   proof that it maintains these properties in order to typecheck. ... take a
   step toward gradualizing these obligations. We introduce a tool, Ghostbuster,
   that produces simplified versions of GADTs which elide selected type params,
   thereby weakening the guarantees of the simplified datatype in exchange for
   reducing the obligations necessary to manipulate it. Like ornaments, these
   simplified datatypes preserve the recursive structure of the original, but
   unlike ornaments, we focus on information-preserving bidirectional
   transformations. Ghostbuster generates type-safe conversion fns between the
   original & simplified datatypes, which we prove are the identity fn when
   composed. We evaluate a prototype tool for Haskell against thousands of GADTs
   found on the Hackage package database, generating simpler Haskell98 datatypes
   & round-trip conversion functions between the two."  (online 22/6/2018.)
   -- [<A HREF="https://doi.org/10.1017/S0956796818000114">doi:10.1017/S0956796818000114</A>]['18].

%A S. Maguire
%T Thinking with Types. Type-Level Programming in Haskell
%I LeanPub
%M JAN
%D 2019
%K book, ebook, c2019, c201x, c20xx, zz0320, type, types, check, checking,
   FP, Haskell, computer programming, dependent types
%X "This book aims to be the comprehensive manual for type-level programming.
   It's about getting you from here to there - from a competent Haskell
   programmer to one who convinces the compiler to do their work for them."
   -- [<A HREF="https://leanpub.com/thinking-with-types">leanPub</A>]['20].

%A T. Schrijvers
%A B. C. D. S. Oliveira
%A P. Wadler
%T K. Marntirosian
%T COCHIS: Stable and coherent implicits
%J JFP
%V 29
%P e3
%M FEB
%D 2019
%K jrnl, JFP, c2019, c201x, c20xx, zz0219, Oliveira, data type, types, checking,
   implicit, overlapping, coherent, implicits, programming languages,
   COCHIS, Haskell, classes, Scala, Agda, Coq, Rust
%X "Implicit programming (IP) mechanisms infer values by type-directed
   resolution, making programs more compact & easier to read. Examples of IP
   mechanisms include Haskell's type classes, Scala's implicits, Agda's instance
   arguments, Coq's type classes & Rust's traits. ... heated debate: proponents
   of one school argue for the desirability of strong reasoning properties,
   while proponents of another school argue for the power & flexibility of local
   scoping or overlapping instances. The current state of affairs seems to
   indicate that the two goals are at odds ... presents COCHIS, the Calculus Of
   CoHerent ImplicitS, an improved variant of the implicit calculus that offers
   flexibility while preserving two key properties: coherence & stability of
   type substitutions. COCHIS supports polymorphism, local scoping, overlapping
   instances, 1st-class instances & higher-order rules, while remaining
   type-safe, coherent & stable under type substitution. ..."
   -- [<A HREF="https://doi.org/10.1017/S0956796818000242">doi:10.1017/S0956796818000242</A>]['19].

%A B. Greenman
%A A. Takikawa
%A M. S. New
%A D. Feltey
%T How to evaluate the performance of gradual type systems
%J JFP
%V 29
%P e4
%M FEB
%D 2019
%K jrnl, JFP, c2019, c201x, c20xx, zz0219, gradual type, types, check, checking,
   Racket
%X "A sound gradual type system ensures that untyped components of a program can
   never break the guarantees of statically typed components. This assurance
   relies on runtime checks, which in turn impose performance overhead in
   proportion to the freq. & nature of interaction between typed & untyped
   components. The literature on gradual typing lacks rigorous description ...
   presents the 1st method for evaluating the performance of sound gradual type
   systems. The method quantifies both the absolute performance of a gradual
   type system & the relative performance of two implementations of the same
   gradual type system. To validate the method, the paper reports on its
   application to 20 programs & 3 implementations of Typed Racket."
   -- [<A HREF="https://doi.org/10.1017/S0956796818000217">doi:10.1017/S0956796818000217</A>]['19].
   [Also search for: gradual type].

%A V. Lanvin
%A M. Laurent
%A K. Nguyen
%A G. Castagna
%T Revisiting occurrence typing
%J arXiv
%M JUL
%D 2019
%K TR, c2019, c201x, c20xx, zz0719, FP, gradual type, types, occurrence typing,
   check, checking, programming language
%X "... [OT] a technique to refine the type of vars occurring in type-cases and,
   thus, capture some programming patterns used in untyped languages. Although
   occurrence typing was tied from its inception to set-theoretic types-union
   types, in particular-it never fully exploited the capabilities of these
   types. Here we show how, by using set-theoretic types, it is possible to
   develop a general typing framemork that encompasses and generalizes several
   aspects of current occurrence typing proposals and that can be applied to
   tackle other problems such as the inference of intersection types for
   functions & the optimization of the compilation of gradually typed langs."
   -- 1907.05590@[<A HREF="https://arxiv.org/abs/1907.05590">arXiv</A>]['19].
   [Also search for: gradual type].

%A Yangpen Yang
%A B. C. D. S. Oliveira
%T Pure iso-type systems
%J JFP
%V 29
%P #e14
%M OCT
%D 2019
%K jrnl, JFP, FP, c2019, c201x, c20xx, zz0120, type, iso, types, isoTypes,
   PITS, PITSs, dependent, dependently typed, programming languages
%X "... many dependently typed languages use a unified syntax that accounts for
   both terms & types. Unified syntax has some interesting advantages over
   separate syntax, inc. less duplication of concepts, & added expressiveness.
   However, integrating unrestricted general recursion in calculi with unified
   syntax is challenging when some level of type-level computation is present,
   since properties such as decidable type-checking are easily lost. This paper
   presents a family of calculi called pure iso-type systems (PITSs), which
   employs unified syntax, supports general recursion & preserves decidable
   type-checking. PITS is comparable in simplicity to pure type systems (PTSs),
   & is useful to serve as a foundation for F.languages that stand in-between
   traditional ML-like languages & fully blown dependently typed languages. In
   PITS, recursion & recursive types are completely unrestricted & type equality
   is simply based on alpha-equality, just like trad. ML-style languages.
   However, like most dependently typed languages, PITS uses unified syntax,
   naturally supporting many advanced type system features. Instead of implicit
   type conversion, PITS provides a generalization of iso-recursive types called
   iso-types. Iso-types replace the conversion rule typically used in
   dependently typed calculus & make every type-level computation explicit via
   cast operators. Iso-types avoid the complexity of explicit equality proofs
   employed in other approaches with casts. We study three variants of PITS that
   differ on the redn strategy employed by the cast operators: call-by-name,
   call-by-value & parallel redn. One key finding is that while using
   call-by-value or call-by-name redn in casts loses some expressive power, it
   allows those variants of PITS to have simple & direct operational semantics
   & proofs. In contrast, the variant of PITS with parallel redn retains the
   exp.power of PTS conversion, at the cost of a more complex metatheory."
   -- [<A HREF="https://doi.org/10.1017/S0956796819000108">doi:10.1017/S0956796819000108</A>]['20].

%A J. Cockx
%A A. Abel
%T Elaborating dependent (co)pattern matching: No pattern left behind
%J JFP
%V 30
%P #e2
%M JAN
%D 2020
%K jrnl, JFP, c2020, c202x, c20xx, zz0220, FP, programing languages, types,
   dependent, typed, type, check, checking, co pattern, copattern, Agda
%X "... dependently typed language, we can guarantee correctness of our
   programmes by providing formal proofs. To check them, the typechecker
   elaborates these programs and proofs into a low-level core language. However,
   this core language is by nature hard to understand by mere humans, so how can
   we know we proved the right thing? ...  A definition by copattern matching
   consists of a list of clauses that are elaborated to a case tree ...  present
   an algorithm elaborating definitions by dependent copattern matching to a
   core language with inductive data types, coinductive record types, an
   identity type, and constants defined by well-typed case trees. ...
   reimplement the alg. used by Agda to check left-hand sides of defns by
   pattern matching. ...  Thus, we take another step towards the formally
   verified implementation of a practical dependently typed language.
   -- [<A HREF="https://doi.org/10.1017/S0956796819000182">doi:10.1017/S0956796819000182</A>]['20].

%A S. Stucki
%A P. G. Giarrusso
%T A theory of higher-order subtyping with type intervals
%J arXiv
%P 73
%M JUL
%D 2021
%O 26th ACM SIGPLAN Int. Conf. on Func. Prog. (ICFP) 2021
%K TR, FP, c2021, c202x, c20xx, zz0721, type, types, kind, kinds, Scala, Agda,
   high order, Dependent Object Types, subtype, subtypes, Fomega, check,
   checking, normalization
%X "... we propose F^w.., a rigorous theor. foundation for Scala's
   higher-kinded types. F^w.. extends F^w_{<:} with interval kinds, which afford
   a unified treatment of important type- & kind-level abstraction mechanisms
   found in Scala, such as bounded quantification, bounded operator
   abstractions, translucent type definitions & first-class subtyping
   constraints. The result is a flexible & general theory of higher-order
   subtyping. We prove type & kind safety of F^w.., as well as weak
   normalization of types & undecidability of subtyping. All our proofs are
   mechanized in Agda using a fully syntactic approach based on hereditary
   substitution."
  -- 2107.01883@[<A HREF="https://arxiv.org/abs/2107.01883">arXiv</A>]['21].
  [Also search for: dependent type].

%A J. Sterling
%A R. Harper
%T Logical relations as types: Proof-relevant parametricity for program modules
%J JACM
%V 68
%N 6
%P 1-47
%M DEC
%D 2021
%K jrnl, JACM, c2021, c202x, c20xx, zz1021, dependent type, checking, types,
   logic, proof
%X "The theory of program modules ... we contribute a new synthetic approach to
   phase separated parametricity based on the slogan logical relations as types,
   by iterating our modal account of the phase distinction. We axiomatize a
   dependent type theory of parametricity structures using two pairs of
   complementary modalities (syntactic, semantic) & (static, dynamic),
   substantiated using the topos theoretic Artin gluing construction. Then, to
   construct a simulation between two implementations of an abstract type, one
   simply programs a third implementation whose type component carries the
   representation invariant."  [online Nov 2021].
   -- [<A HREF="https://doi.org/10.1145/3474834">doi:10.1145/3474834</A>]['21].
   !?-)

%A J. G. Siek
%A P. Thiemann
%A P. Wadler
%T Blame and coercion: Together again for the first time
%J JFP
%V 31
%M OCT
%D 2021
%K jrnl, JFP, c2021, c202x, c20xx, zz1021, data type, types, static, dynamic,
   gradual typing, coercion, cast, Csharp, Dart, Pyret, Racket, VB, lambdaS,
   lambdaT, programming language
%X "C#, Dart, Pyret, Racket, TypeScript, VB: many recent languages integrate
   dynamic & static types via gradual typing. We systematically develop four
   calculi for gradual typing & the rel'ns between them ... Together, lambdaB,
   lambdaC, lambdaS & lambdaT provide a coherent foundation for design,
   implementation, & optimization of gradual types. We define translations from
   lambdaB to lambdaC, from lambdaC to lambdaS, & from lambdaS to lambdaT, ..."
   -- [<A HREF="https://doi.org/10.1017/S0956796821000101">doi:10.1017/S0956796821000101</A>]['21].
   [Also search for: gradual type].

%A P. Baillot
%A A. Ghyselen
%T Types for complexity of parallel computation in Pi-calculus
%J TOPLAS
%V 44
%N 3
%P #15
%M JUL
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0822, type, types, FP, parallel, PFP, process,
   Pi calculus, PiCalculus, time, complexity, span
%X "... Two notions of time complexity are given: the total comp'n time without
   parallelism (the work) & the comp.time under maximal parallelism (the span).
   We define operational semantics to capture those two notions & present two
   type systems from which one can extract a complexity bound on a process. ..."
   -- [<A HREF="https://doi.org/10.1145/3495529">doi:/10.1145/3495529</A>]['22].
   [Also search for: parallel PFP].

%A K. Maillard
%A M. Lennon-Bertrand
%A N. Tabareau
%A E. Tanter
%T A reasonably gradual type theory
%J arXiv
%M SEP
%D 2022
%K TR, c2022, c202x, c20xx, zz0922, gradual type, types, datatype, theory, Coq,
   Calculus of Inductive Constructions, CIC, GCIC, CastCIC, GRIP, Agda, FP
%X "Gradualizing the Calculus of Inductive Constructions (CIC) involves dealing
   with subtle tensions between normalization, graduality, & conservativity with
   respect to CIC. ... We develop the metatheory of GRIP using a model
   formalized in Coq, & provide a prototype implementation of GRIP in Agda."
   -- 2209.00975@[<A HREF="https://arxiv.org/abs/2209.00975">arXiv</A>]['22].
   [Also search for: gradual type].

%A Yaoda Zhou
%A Jinxu Zhao
%A C. D. S. Oliveira
%T Revisiting iso-recursive subtyping
%J TOPLAS
%V 44
%N 4
%P #24
%M DEC
%D 2022
%K jrnl, TOPLAS, c2022, c202x, c20xx, zz0922, data type types, isorecursive,
   Amber, FP, Cardelli, subtype, subtypes, unfolding
%X "... This article aims to revisit the problem of subtyping iso-recursive
   types. We start by introducing a novel declarative spec. for Amber-style
   iso-recursive subtyping. Informally, the spec. states that two recursive
   types are subtypes if all their finite unfoldings are subtypes. The Amber
   rules are shown to have equivalent expressive power to this declarative
   spec.. We then show two variants of sound, complete & decidable algorithmic
   formulations of subtyping wrt the declarative spec., which employ the idea
   of double unfoldings. ..."
   -- [<A HREF="https://doi.org/10.1145/3549537">doi:10.1145/3549537</A>]['22], online Sept 2022.

%A G. Castagna
%A M. Laurent
%A K. Nguyen
%T Polymorphic type inference for dynamic languages
%J arXiv
%M NOV
%D 2023
%K TR, c2023, c202x, c20xx, zz1123, datatype, type, types, check, checking,
   polymorphism, intersection, union, subtype, subtyping, programming language
%X "We present a type system that combines, in a controlled way, first-order
   polymorphism with intersection types, union types, & subtyping, & prove its
   safety. We then define a type reconstruction alg. that is sound & terminating
   ..."
   -- [<A HREF="https://arxiv.org/abs/2311.10426">arxiv:2311.10426</A>]['23].
   [Also search for: polymorphic type].

%A Shuai Fu
%A T. Dwyer
%A P. J. Stuckey
%A J. Grundy
%T Goanna: Resolving Haskell type errors with minimal correction subsets
%J arXiv
%M MAY
%D 2024
%K TR, FP, data type, types, c2024, c202x, c20xx, zz0524, polymorphic, check,
   checking, error, correction, Goanna
%X "... Haskell, known for its expressive & strict type system, poses challenges
   for inexperienced programmers in learning & using its type system, esp. in
   debugging type errors. We introduce Goanna, a novel tool that serves as a
   type checker & an interactive type error debugging tool for H.. When
   encountering type errors, G. identifies a comprehensive list of potential
   causes & resolutions based on the minimum correction subsets (MCS)
   enumeration ..."
   -- [<A HREF="https://arxiv.org/abs/2405.12697">arxiv:2405.12697</A>]['24].
   [Also search for: FP type error].

%A A. Timany
%A et al
%T A logical approach to type soundness
%J JACM
%V 71
%N 6
%P #40 1-75
%M DEC
%D 2024
%K jrnl, c2024, c202x, c20xx, zz1124, sound, data type, logic, semantic
%X "... we argue that prog. lang. researchers should no longer be satisfied
   with proving syntactic type soundness & should instead start proving
   semantic type soundness ..."
   -- [<A HREF="https://doi.org/10.1145/3676954">doi:10.1145/3676954</A>]['24].
 

%A C. S. Wallace
%T Statistical and Inductive Inference by Minimum Message Length
%I SpringerVerlag
%S Information Science and Statistics
%P 432
%M MAY
%D 2005
%K Wal05, W05, zzMML, c2005, c200x, c20xx, CSW, CSWallace, Chris, CSSE, Monash,
   book, text, description, MML, II, AI, AIC,BIC,NML, stats, theory, MDL, Snob,
   machine learning, compression, compact coding, Kolmogorov complexity,
   algorithmic complexity, Bayesian, model, models, selection, MML87, SMML,
   MMLa, CSci, L4ref, L5ref, Occam's, Ockham's razor, information theory, IT,
   criterion, encoding, coding, uncertainty, estimate, estimation, estimator,
   theoretical, stochastic, statistics, entropy, minimum message length,
   feathers on the arrow of time
%X "Since 1965, Prof. Wallace & others have been developing an approach
   to statistical estimation, hypothesis testing, model selection & their
   applications in the [AI] field of Machine Learning. The approach is based
   on Information Theory, using concepts from classical Shannon theory & more
   recent work on Algorithmic Complexity. The new approach has come to be
   called the Minimum Message Length principle, since it is based on the idea
   of constructing a message which concisely encodes the available data.
   Although a range of jrnl & conf. papers has been published on the principle
   & its application, & several computer programs applying it have been shown
   to perform well & have been fairly widely used, there is no text providing
   a thorough treatment of the principle or giving general guidance for its
   application."  [-- until now.]
   1st ed 2005; hb us$80; uk us isbn:038723795X; uk us isbn13:9780387237954;
   [<A HREF="http://www.allisons.org/ll/MML/2005book.html">book-page</A>][10/'04],
   [<A HREF="https://doi.org/10.1007/0-387-27656-4">doi:10.1007/0-387-27656-4</A>]['17].
   (Note, Chapter_8, 'The Feathers on the Arrow of Time.')
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>], and
   the [<A HREF="http://www.allisons.org/ll/MML/Entropy/Gas/">Ideal_Gas</A>].)

%A C. S. Wallace
%A M. B. Dale
%T Hierarchical clusters of vegetation types
%J Commun. Ecol.
%I Akademiai Kiado
%V 6
%N 1
%P 57-74
%M JUN
%D 2005
%K jrnl, CSW, CSWallace, MBDale, c2005, c200x, c20xx, ecology, type, cluster,
   Minimum Message Length, MML, description, MDL, stats, hierarchic,
   clustering, mixture model, classification, Snob
%X "... a hierarchical solution was not as efficient as a nonhierarchical one.
   However, the hierarchical solution seems to provide a more comprehensible
   solution, separating first isolated types, probably caused from unusual
   contingent events, then subdividing the more diverse areas before finally
   subdividing the less diverse. By presenting this in 3 stages, the complexity
   of the non-hierarchical result is avoided. The result also suggests that a
   hierarchical analysis may be useful in determining homogeneous areas."
   issn:1585-8553.
   Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A C. S. Wallace
%T A Brief History of MML (Seminar)
%M NOV
%D 2003
%K CSW, CSWallace, c2003, c200x, c20xx, seminar, minimum message length, MML,
   minimum description length, MDL, NML, development, introduction, beginnings,
   origin, history, survey, AIC, BIC, complexity, comparison, compare, L3ref,
   Wal03, zMML, Bayesian, inductive inference, L4ref, II, AI, stats, statistics,
   CSci, machine learning, csse, monash university, algorithmic,
   research, computer science, Comp Sci, CompSci, CSci, talk, lecture, seminars
%X [<A HREF="http://www.allisons.org/ll/MML/20031120e/">transcribed</A>]['04].
   [Also search for: MML] and [also search for: CSWallace seminar].

%A C. S. Wallace
%A D. L. Dowe
%T MML clustering of multi-state, Poisson, von Mises circular and
   Gaussian distributions
%J Statistics and Computing
%V 10
%N 1
%P 73-83
%M JAN
%D 2000
%K jrnl, SNOB, minimum message length MML, inductive inference II, description,
   Normal, vonMises, classification, cluster, mixture, modelling, MDL,
   multistate, stats, AI, learning, data mining, CSW, CSWallace, DLD, zz1299,
   c2000, c200x, c20xx
%X Hint, [also search for: Snob]  or  more generally [also search for: MML];
   see [<A HREF="http://www.allisons.org/ll/MML/">MML page</A>].
   von Mises, probability density:
     f(x | mu, kappa) = (1/(2.pi.I0(kappa))).exp(kappa.cos(x-mu))
     where I0(kappa) is a normalisation constant.
   Its Fisher information
     F(mu,kappa) = N**2.kappa.A(kappa).{1-A(kappa)/kappa-(A(kappa))**2}
     where I1(kappa) = d I0(kappa)/d kappa
     and   A(kappa) = I1(kappa)/I0(kappa).
   -- [<A HREF="http://dx.doi.org/10.1023/A:1008992619036">doi:10.1023/A:1008992619036</A>][11/'04] (subscr'n?).
   Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW's publications</A>].

%A C. S. Wallace
%T Minimum description length
%B The MIT Encyclopedia of the Cognitive Science
%E R. A. Wilson
%E F. C. Keil
%I MITpress
%P 550-551
%D 1999
%K CSW, CSWallace, review, MDL, AI, II, c1999, c199x, c19xx
%X (from list prep by G.G. 12/'04.)  In, isbn:026273124X.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A C. S. Wallace
%A D. L. Dowe
%T Minimum message length and Kolmogorov complexity
%J COMPJ
%V 42
%N 4
%P 270-283
%D 1999
%K CSW, CSWallace, DLD, COMPJ, jrnl, MML, SMML, minimum description length,
   algorithmic complexity, AC, Kolmogorov complexity, KC, probability,
   prediction, predict, predicting, MDL, statistical inference,
   inductive inference, II, induction, AI, UTM, machine learning, Rissanen,
   Snob, CS, CSci, Monash, zz1099, c1999, c199x, c19xx
%X In a special issue of the Computer Journal (so is Solomonoff)
   on minimum length methods for machine learning.  [36 refs]
     1. Intro: (a) Kolmogorov '65, Lof, Chaitin '66, ...
               (b) Solomonoff '64, ...
               (c) Wallace & Boulton '68, ...; Rissanen '78, ...;
     2. Tech Details;  3. Data and Hypotheses;  4. 2-Part Encoding;
     5. Expected and Actual Lengths;  6. Choosing a Decoder;
     7. Terms of `order one';  8. Prediction and Induction;  9. Conclusion
   See also discussion
     by  `D a w i d' p323-326,   by `R i s s a n e n' p327-329,
     by  `C l a r k e' p338-339, by `S h e n' p340-342',
     and `Refinements of MDL and MML coding' by `W and D' p330-337,
     a reply to J. J. Rissanen's article, pp330-337,
     and a rejoinder by R p343-344, and one by `W and D' p345-347.
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/42.4.270">doi:10.1093/comjnl/42.4.270</A>]['05].
   Also see the [<A HREF="http://www.allisons.org/ll/MML/">MML page</A>].

%A C. S. Wallace
%T On the selection of the order of a polynomial model
%J Proc. of the 14th Biennial Australian Statistical Conf.
%E W. Robb
%W Queensland
%P 145
%M JUL
%D 1998
%O Royal Holloway College, London, '97
%K conf, minimum message length, MML, CSW, CSWallace, c1998, c199x, c19xx, MDL,
   stats, regression, description, polynomials, polynomial fitting, degree,
   function approximation, Vapnik-Chervonenkis VC dimension
%X "A report by Cherkassy, Mulier & Vapnik has compared the performance of
   several methods of selecting the order of a polynomial approximation to a
   fn t(x) given only the values of t(x) for some set of x-values, where the
   given values are corrupted by i.i.d. Gaussian noise of unknown variance. They
   compare various "classical" methods with a new method based on the
   Vapnik-Chervonenkis (VC) dimension, & conclude that the latter gives the most
   reliable prediction of the value of t(x) at unseen values of x. This work
   replicates their investigation & extends it by including a method based on
   Minimum Message Length (MML) estimation. The results largely confirm the
   previous results, but show that MML is generally superior to the VC method in
   terms of average squared prediction error."  (unref conf paper)
   -- [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/Polynomial/">more</A>].
   Also see sec.6.7.2, pp.272-275 in: [also search for: CSWallace MML book].

%A C. S. Wallace
%T A Monash FIT Graduation Address
%M APR
%D 1998
%K CSWallace, CSW, Monash, Faculty, FIT, ceremony, c1998, c199x, c19xx,
   altruism, computing, commercial, ethics, tragedy of the commons,
   open source, openSource, software
%X "First of all, let me congratulate you on your success. [...]
   I would like to offer you one final notion before you go, whether grain or
   chaff is for you to decide. There is a story told in economics called
   "The Tragedy of the Commons." [...]
   Considering the commercial importance and scale of the computing industry,
   a surprising number of the seminal developments in its technology have come
   from non-commercial sources. [...]"
   -- [<A HREF="/~gopal/cswgraduation.html">29 April 1998</A>],
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A C. S. Wallace
%T MML inference of predictive trees, graphs and nets
%J Proc. Applied Decision Technologies 1995 Conf.,
   Stream 1: Computational Learning and Probabilistic Reasoning
%W London
%P 101-115
%D 1995
%K conf, MML, minimum message length, description, inductive inference, MDL,
   II, AI, predict, prediction, expert systems, decision, classification,
   DTree, tree, net, graph, c1995, c199x, c19xx, graph, net, CSW, CSWallace
%X via GF. Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T How to do Inductive Inference using Information Theory (Seminar)
%D 1993
%K Wal93,zzMML, seminar, c1993, c199x, c19xx, CSW, CSWallace, Monash, MML, MDL,
   AIC, AI, II, minimum message length, description, explanation, mmld, stats,
   statistics, Bayesian inference, universal TM, UTM, machine learning,
   total ignorance, prior, priors, computer science, Comp Sci, CompSci,
   talk, lecture, seminars
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/1993-08-10/">transcribed</A>]['11].
   [Also search for: CSWallace seminar].

%A J. Oliver
%A D. L. Dowe
%A C. S. Wallace
%T Inferring Decision Graphs Using the Minimum Message Length Principle
%J Proc. of the 1992 Aust. Joint Conf. on Artificial Intelligence
%W Hobart, Tasmania
%P 361-367
%M SEP
%D 1992
%K conf, Monash, CSW, AJCAI AJCAI92, minimum message length MML, encoding,
   description, MDL, inductive inference, II,
   decision, graph, tree, CSW, CSWallace, c1992, c199x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].
   [Also search for: Dgraph decision].

%A C. E. Chew
%A C. S. Wallace
%T An Inter-Bus Connection for a Capability Based Multiprocessor
%J Proc. of 14th Australian Computer Science Conf.
%W Sydney,
%O Australian Computer Science Communications, Vol.13, No.1, 30/1-10,
%D 1991
%K Monash, CSW, ACSC, ACSC14, ACSC91, multi processor, bus, CSW, CSWallace,
   computer architecture, hardware, c1991, c199x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%A R. D.  Pose
%T Charging in a Secure Environment
%E J. Rosenberg
%E J. L. Keedy
%J Security and Persistance
%W Bremen
%D 1990
%I SpringerVerlag
%P 85-97
%K CSW, CSWallace, Monash, operating system, OS, charge, money, persistence,
   conf, capability, persistant, multiprocessor, computer, multi, security,
   c1990, c199x, c19xx
%X "The Monash Multiprocessor Architecture incorporates a monetary system at the
   lowest kernel level, integrated with a password capability scheme. Although
   the capability scheme is quite flexible, providing support for non-hierarchic
   security & access policies, abstract type management & information
   confinement, we show that it is possible for service providers to command
   use-based fees for service. The fee charging protocols must be designed with
   some care to avoid breaching required information confinement constraints
   when user & provider are mutually suspicious, but need not be v.complicated"
   -- [<A HREF="https://doi.org/10.1007/978-1-4471-3178-6_6">doi:10.1007/978-1-4471-3178-6_6</A>]['17].
   Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. E. Chew
%A C. S. Wallace
%T De-Bruijn interconnection networks
%R 90/139
%I Dept Computer Science, Monash University, Melbourne
%P 20
%D 1990
%K TR, TR139, c1990, c199x, c19xx, deBruijn network, computer architecture,
   Walnut, communication, multiprocessor system
%X "De-Bruijn networks are examined with a view to using them to interconnect
   a set of capability based Multiprocessor systems. The networks are described
   and a survey made of recent work by Pradhan (11), Esfahanian (5) and
   Imase (7, 8). Three classes of de-Bruijn networks are established based on
   the direction of message routing within the network. Class 2 networks route
   messages strictly along or strictly opposing the directed edges. A routing
   algorithm is described which will generate the shortest path in a class 2
   de-Bruijn network of arbitrary size. Two schemes for enhancing the node
   connectivity of 2 degree class 2 networks are examined.:
   -- abs@[<A HREF="http://www.csse.monash.edu.au/publications/1990/tr-cs90-139-abs.ps.gz">csse</A>]['11].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A E. D. Cathro
%A C. S. Wallace
%A M. S. Anderson
%T An I/O Subsystem for a Multiprocessor
%J Proc. of the 12th Australian Computer Science Conf.
%V 11
%N 1
%P 275-285
%M FEB
%D 1989
%K CSW, CSWallace, Monash, ACSC ACSC12 ACSC89, multi processor, input, output,
   computer architecture, IO, c1989, c198x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%A et al (Multi Group)
%T Using a Unix System as a Multiprocessor Frontend
%J AUUGN
%V 7
%N 2-3
%P 15-21
%D 1988 ???
%K conf, CSW, CSWallace, Monash, multi processor, c1988, c198x, c19xx,
   operating system, OS
%X date ~ c198x. [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A M. S. Anderson
%A C. S. Wallace
%T Some Comments on the Implementation of Capabilities
%J The Australian Computer Journal
%V 20
%N 3
%P 122-133
%M AUG
%D 1988
%K jrnl, CSW, CSWallace, ACJ, Monash, capability, operating system OS,
   c1988, c198x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A R. D. Pose
%A M. S. Anderson
%A C. S. Wallace
%T Implementation of a Tightly-Coupled Multiprocessor
%J Proc. ACSC-10
%V 9
%N 1
%P 330-342
%M FEB
%D 1987
%K conf, CSW, CSWallace, Monash, ACSC ACSC10 ACSC87, multi processor,
   computer architecture, c1987, c198x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T An improved program for classification
%J Proc. of ACSC-9
%V 8
%N 1
%P 357-366
%M FEB
%D 1986
%O C. S. Wallace, "An improved program for classification",
      Monash U., Comp. Sci., TR47, 1984
%K CSW, conf, Monash, ACSC, ACSC9, ACSC86, class, classify, classification,
   coding, unsupervised, mixture model, modelling, cluster, clustering, SNOB,
   bit borrowing, hard, fractional, soft assignment, II, minimum message length,
   MML, MDL, bits back, borrow, description, Hinton, Camp, COLT, encoding,
   Snob2, dld, SMEM, EM algorithm, c1986, c198x, c19xx, TR47,c1984, CSWallace
%X The first description of the bit-borrowing coding technique later called
   bits-back by G. E. Hinton & D. van Camp, COLT '93, (COLT93) 1993.
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)
   [Also search for: Wallace ICCI].

%A R. D. Pose
%A M. S. Anderson
%A C. S. Wallace
%T Aspects of a Multiprocessor Architecture
%J Proc. Workshop on Future Directions in Computer Architecture and Software
%W Charlston
%P 293-295
%M MAY
%D 1986
%K CSW, Monash, multi processor, CSWallace, c1986, c198x, c19xx, computer,
   wShop
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A Wallace C.S,
%A Koch D.,
%T TTL - Compatible Multiport Bus
%J Computer Systems Science and Engineering
%V 1
%N 1
%P 47-52
%M OCT
%D 1985
%K CSW, CSWallace, Monash, multi processor, c1985, c198x, c19xx,
   computer architecture
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A G. K. Gupta
%A C. S. Wallace
%T A New Step-Size Changing Technique for Multistep Methods
%J Mathematics of Computation
%V 33
%N 145
%P 125-138
%M JAN
%D 1979
%K jrnl, CSW, CSWallace, Monash, multi, step, size, c1979, c197x, c19xx,
   numerical analysis, methods
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T Memory and Addressing Extensions to a HP2100A
%J Proc. 8th Australian Computer Conf.
%V 4
%P 1796-1811
%M AUG-SEP
%D 1978
%K CSW, CSWallace, Monash, c1978, c197x, c19xx, computer architecture
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T Computing Research in Australia
%J The Australian Computer Journal
%V 9
%N 1
%P 21-24
%M MAR
%D 1977
%K jrnl, CSW, CSWallace, Monash, ACJ, c1977, c197x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A R. A. Hagan
%A C. S. Wallace
%T A Virtual Memory System for the HP2100A
%J Computer Architecture News
%V 6
%N 5
%P 5-13
%D 1977
%K jrnl, CSW, computer architecture, CSWallace, Monash, c1977, c197x, c19xx,
   virtual memory, paged, paging
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T Transformed rejection generators for Gamma and Normal pseudorandom variables
%J The Australian Computer Journal
%V 8
%N 3
%P 103-105
%M NOV
%D 1976
%K jrnl, CSW, CSWallace, Monash, pseudo random number generator, RNG, PRNG,
   gamma, normal, Gaussian, probability distributions, c1976, c197x, c19xx, ACJ
%X (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A C. S. Wallace
%A D. Harper
%A R. A. Hagan
%T A Discrete System Simulation Package for a Mini Computer
%J ACM Simuletter
%V 7
%N 1
%P 9-13
%D 1976
%K CSW, CSWallace, Monash, c1976, c197x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A D. M. Boulton
%A C. S. Wallace
%T An information measure for single-link classification
%J COMPJ
%V 18
%N 3
%P 236-238
%M AUG
%D 1975
%K jrnl, CSW, CSWallace, Monash, class, classify, classification, cluster,
   clustering, stats, SNOB, minimum message length, MML, encoding, description,
   minimum spanning tree, trees, linkage, MST, MDL, c1975, c197x, c19xx
%X "The information measure is an objective measure of the quality of a
   classification and results from an information transmission view of the
   classification problem. So far information measures have only been derived
   for the case where an explicit assumption is made about the form of the
   distribution of attribute values within a class. One important method which
   involves no such explicit assumption is single link. In this paper we derive
   a new information measure which is optimised by classifications produced by
   the single link method. By investigating the properties of this information
   measure we are able to gain more insight into the single link method and
   also determine the type of problem to which it best applies."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/18.3.236">doi:10.1093/comjnl/18.3.236</A>]['05].
   Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].
   [Also search for: single link]  and  [also search for: MML].

%A G. K. Gupta
%A C. S. Wallace
%T Some New Multistep Methods for Solving Ordinary Differential Equations
%J Proc. of ANZAAS Conf.
%D 1973
%O Math. of Comp., 29, 130, pp.489-500, April 1975
%K CSW, CSWallace, Monash, multi step, ODE, ODEs, c1973, c197x, c19xx,
   numerical methods, analysis
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%A D. M. Boulton
%T An invariant Bayes method for point estimation
%J Classification Society Bulletin
%V 3
%N 3
%P 11-34
%D 1975
%K jrnl, CSW, WB75, Monash, Bayes, Bayesian, statistics, minimum message length,
   MML, SMML, encoding, description, MDL, stats, c1975, c197x, c19xx, CSWallace,
   estimate, model, II, inference
%X "We consider the problem of forming a point estimate of an unknown
   parameter, based on the result of an experiment, & using, via Bayes' theorem,
   prior information about the parameter. ..."
   Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%A G. K. Gupta
%T General Linear Multistep Methods to Solve Ordinary Differential Equations
%J The Australian Computer Journal
%V 5
%N 2
%P 62-69
%M MAY
%D 1973
%K jrnl, CSW, CSWallace, Monash, multi step, ODE, ODEs, c1973, c197x, c19xx,
   ACJ, numerical methods, analysis
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A D. M. Boulton
%A C. S. Wallace
%T A comparison between information measure classification
%J Proc. of ANZAAS Congress
%W Perth
%M AUG
%D 1973
%K CSW, Monash, class, classify, classification, cluster, clustering, SNOB,
   mixture model, modelling, minimum message length, MML, encoding, MDL,
   CSWallace, c1973, c197x, c19xx, conf
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A D. M. Boulton
%A C. S. Wallace
%T Occupancy of a rectangular array
%J COMPJ
%V 16
%N 1
%P 57-63
%D 1973
%K jrnl, compj, chi squre, squared, association, rectangle, arrays, Bell,
   integer, CSW, Monash, c1973, c197x, c19xx, CSWallace
%X "The problem addressed is: the occupancy, by non-negative integers, of a
   rectangular array of given size when the row sums and column sums are all
   fixed. In general, a single expression for the number of array element
   combinations which covers all combinations of row and column sums cannot
   be found. Thus two algorithms which systematically count all element
   combinations are presented, the first applying to arrays with only two
   columns and the second to arrays with any number of rows and columns.
   The two-column algorithm is then used to derive expressions for the number
   of array element combinations of arrays having three rows and two columns.
   Five different expressions are required to cover all combinations of row and
   column totals."
   [<A HREF="http://dx.doi.org/10.1093/comjnl/16.1.57">doi:10.1093/comjnl/16.1.57</A>]['05]
   Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T Simulation of a two-dimensional gas
%J Proc. of ANZAAS Conf.
%W Perth
%P 19
%M AUG
%D 1973
%K CSW, CSWallace, Monash, 2D, two dimensional, gas, c1973, c197x, c19xx,
   thermodynamics, entropy, physics, theory, law
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/Entropy/Gas/">gas</A>]['01] simulation.)

%A P. S. Roberts
%A C. S. Wallace
%T A Microprogrammed Lexical Processor
%J Information Processing 71
%P 577-581
%D 1972
%K CSW, CSWallace, Monash, c1972, c197x, c19xx, computer hardware, firmware,
   conf, microprogramming, architecture
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A A. Y. Montgomery
%A C. S. Wallace
%T Evaluation and Design of Random Access Files
%J Proc. 5th Australian Computer Conf.
%W Brisbane
%P 142-150
%M MAY
%D 1972
%K CSW, CSWallace, Monash, ACC, ACC5, ACC72, c1972, c197x, c19xx, file system
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T Simulation Studies in File Structures
%J A.C.S Victorian Branch Professional Development Workshop
%P 16
%M FEB
%D 1971
%K wShop, CSW, CSWallace, Monash, c1971, c197x, c19xx, file system, structure
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A D. M. Boulton
%A C. S. Wallace
%A A program for numerical classification
%J COMPJ
%V 13
%N 1
%P 63-69
%M FEB
%D 1970
%K jrnl, COMPJ, c1970, c197x, c19xx, CSWallace, CSW, Monash, class, classify,
   classification, cluster, clustering, mixture modelling, model, stats, SNOB,
   BW60, minimum message length, II, MML, encoding, MDL, bit, nit, nat, ban,
   information theory
%X "In a previous paper (W & B '68) the information measure was derived. It is
   designed to measure the objective goodness of a nonhierarchical taxonomic
   classification & can be used to choose the best of a number of different
   classifications of the one data set. The information measure can also form
   the basis of a classification alg. which searches directly for that
   classification with the best information measure. ... such a classification
   alg. is described together with an ALGOL program called Snob ..."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/13.1.63">doi:10.1093/comjnl/13.1.63</A>]['05];
   see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>],
   [also search for: MML].

%A C. S. Wallace
%A A. M. Jessup
%A A Simple Graphic Input/Output Device
%J The Australian Computer Journal
%V 2
%N 1
%P 39-40
%M FEB
%D 1970
%K jrnl, CSW, CSWallace, Monash, ACJ, input output, c1970, c197x, c19xx,
   computer architecture, hardware, graphics
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A G. M. Clarke
%A C. S. Wallace
%T Analysis of Nasal Support
%J Archives of Otolaryngology
%V 92
%P 118-129
%M AUG
%D 1970
%K jrnl, CSW, CSWallace, Monash, nose, nasal, medical, c1970, c197x, c19xx
%X (!).  [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T A Digital Logic Simulator for Teaching Purposes
%J Proc. of the 4th Australian Computer Conf.
%P 215-219
%D 1969
%K CSW, CSWallace, Monash, ACC, ACC4, ACC69, c1969, c196x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A T. J. McQuade
%A D. Race
%A C. S. Wallace
%T Storage and Retrieval of Medical Information
%J Proc. of the 4th Australian Computer Conf.
%P 539-544
%D 1969
%K CSW, CSWallace, Monash, ACC ACC4 ACC69, medical informatics,
   c1969, c196x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T Control Systems
%J The Fourth Australian Computer Conf.
%V 2
%N 4
%P ?-?
%M AUG
%D 1969
%K CSW, CSWallace, Monash, c1969, c196x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A A. M. Jessup
%A C. S. Wallace
%T A Cheap Graphic Input Device
%J Aust. Comp. J.
%V 1
%P 2
%M MAY
%D 1968
%K jrnl, CSW, CSWallace, Monash, ACJ, c1968, c196x, c19xx, computer graphics
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%A B. G. Rowswell
%T Competition for memory access in the KDF9
%J COMPJ
%V 10
%N 1
%P 64-68
%M MAY
%D 1967
%K COMPJ, jrnl, CSW, CSWallace, KDF9, KDF 9, operating system, OS, usage, use,
   round robin, first come first served, priority, c1967, c196x, c19xx,
   computer architecture, hardware
%X "The I/O control of a computer may adopt various strategies for serving
   competing requests from peripheral channels for access to a single core
   memory. The strategy adopted places some limit on the peripheral
   configurations which may be simultaneously active. An "ideal" strategy is
   exhibited which imposes no constraint other than that implied by the finite
   speed of the core memory, but it is expensive to implement. Limits on
   configurations are derived for the ideal, first come-first served,
   round-robin & priority systems. It is shown that the first come-first served
   & round-robin systems have little or no advantage over a random choice. The
   KDF9 at the U. of Sydney, which was delivered with a first come-first
   served system, has been modified to incorporate a priority system. The
   new system uses 48 fewer circuit boards, but allows the attachment of
   high-rate channels which otherwise could not be accommodated."
   -- [<A HREF="http://dx.doi.org/10.1093/comjnl/10.1.64">doi:10.1093/comjnl/10.1.64</A>]['05],
   and [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].
   [Also search for: KDF9].

%A C. S. Wallace
%A O. Longe
%T Reading gapless tapes
%J IEEE Trans. Elec. Comp.
%V EC-16
%N 4
%P 517-518
%M AUG
%D 1967
%K jrnl, magnetic tape, computer hardware, CSW, CSWallace, c1967, c196x, c19xx,
   EC16, KDF 9, KDF9
%X "Field-recorded data are often most conveniently recorded on magnetic tapes
   without interblock gaps. Gapless tapes cannot be read by certain types of
   computers. A simple modification to a KDF 9 computer enables it to transcribe
   from gapless to conventional format as a time-shared monitor operation. The
   counter which increases peripheral transfer addresses and detects the
   completion of a block is time-shared by all channels on the KDF 9. It was
   modified so that for any channel which, in requesting a core memory access,
   indicates that it is engaged in a gapless read" carries out of the 64's digit
   of the counter are suppressed, and any change of the 64's digit causes an
   interrupt to the permanently resident monitor program (Director). Thus, if
   an input transfer is set up on a channel with initial core memory address an
   exact multiple of 128, and the channel is made to signal that it is reading
   gapless tape, the reading will proceed indefinitely, repeatedly cycling over
   the same 128 word core area, and causing an entry to Director after every 64
   words."
   -- [<A HREF="http://dx.doi.org/10.1109/PGEC.1967.264681">doi:10.1109/PGEC.1967.264681</A>]['11].
   [Also search for: KDF9].
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A C. S. Wallace
%T Digital Computers
%P ?-?
%B Atoms to Andromeda
%E S. T. Butler
%E H. Messel
%I ShakespeareHead, Sydney
%D 1966
%K CSW, CSWallace, c1966, c196x, c19xx, c1966, c196x, c19xx, chapter, computer
%X "selected lectures on theoretical physics, high-energy nuclear and
   cosmic ray research, plasma and thermonuclear physics, astronomy,
   astrophysics and electronic computing."   Also see
   [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A Boden
%A Branagan
%A Davies
%A Gould
%A Graham
%A Kelly
%A Mercer
%A Ross
%A Strahan
%A Wallace
%T Advancing with Science
%I Science Press, Sydney
%D 1966
%K CSW, CSWallace, c1966, c196x, c19xx, chapter
%X (This is a textbook for secondary schools, of which csw wrote one chapter
   and contributed substantially to four others.)
   [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A J. M. Bennett
%A C. S. Wallace
%A J. W. Winings,
%T Software and Hardware Contributions to Efficient Operating on a Limited
   Budget
%J Proc. 3rd Australian Comp. Conf.
%W Canberra
%P ?-?
%D 1966
%K conf, CSW, CSWallace, ACC, ACC3, ACC66, c1966, c196x, c19xx, computing
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A I. C. A. Martin
%A C. S. Wallace
%T Impedance change frequency of diluted ram semen recorded on a digital scaler
%J J. Reprod. Fertil.
%V 10
%P 425-437
%M JAN
%D 1965
%K jrnl, CSW, CSWallace, biology, biol, c1965, c196x, c19xx, reproductive,
   reproduction, animal fertility, sheep
%X The title says it all,
   [<A HREF="https://doi.org/10.1530/jrf.0.0100425">doi:10.1530/jrf.0.0100425</A>]['24].
   Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T A suggestion for a fast multiplier
%J IEEE Trans. on Electronic Comp.
%V EC-13
%N 1
%P 14-17
%D 1964
%O Univ' Illinois, TR UIUCDCS-R-63-133, '63
%K CSW, CSWallace, Wallace Tree multiplier, multiply, multiplication, CPU, ALU,
   computer hardware, architecture, circuit, arithmetic, algorithm, square root,
   W64, c1964, c196x, c19xx, jrnl
%X "It is suggested that the economics of present large-scale sci. computers
   could benefit from a greater investment in h/w to mechanize multiplication
   and division than is now common. As a move in this direction, a design is
   developed for a multiplier which generates the product of two numbers using
   purely combinational logic, i.e., in one gating step. Using straightforward
   diode-transistor logic, it appears presently possible to obtain products in
   under 1, mu-sec, and quotients in 3 mu-sec. A rapid square-root process is
   also outlined. Approximate component counts are given for the proposed
   design, and it is found that the cost of the unit would be about 10 per cent
   of the cost of a modern large-scale computer."
   -- [<A HREF="https://doi.org/10.1109/PGEC.1964.263830">doi:10.1109/PGEC.1964.263830</A>]['17].
   Reduces the problem of multiplying two n-bit numbers to one of
   summing two O(n)-bit numbers.
   Also see
   [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>], and
   w.t.@[<A HREF="http://en.wikipedia.org/wiki/Wallace_tree">wikip</A>]['11].
   [Also search for: Wallace multiplier].

%A C. S. Wallace
%T Correlated round-off errors in digital integrating differential analyzers
%J COMPJ
%V 7
%N 2
%P 131-134
%M JUL
%D 1964
%K jrnl, compj, architecture, hardware, error, analyzer, c1964, c196x, c19xx,
   CSW, CSWallace, computer, hadware, integration
%X "The integration method used in digital differential analyzers suffers from
   both truncation and round-off errors. It is shown that, if trapezoidal
   corrections are employed, the latter dominates. The round-off errors in
   successive steps of the integration are shown to be correlated whenever the
   function being integrated has a slope which passes through a rational
   fraction of small denominator. However, an analysis is presented to show
   that in general the correlation does not greatly affect the total round-off
   error. Some special cases are shown to suffer from anomalously high
   round-off error."
   [<A HREF="http://dx.doi.org/10.1093/comjnl/7.2.131">doi:10.1093/comjnl/7.2.131</A>]['05],
   [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A J. Malos
%A D. D. Millar
%A C. S. Wallace
%T Cerenkov radiation from E.A.S.
%J J. Phys. Soc. Japan
%V 17 Supplement A - III
%P ?-?
%D 1962
%K jrnl, physics, EAS, CSW, CSWallace, c1962, c196x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T Comparison between the response of Geiger and scintillation counters to
   the air shower flux
%J Proc. of Moscow Cosmic Ray Conf.
%V II
%P 316
%D 1960
%K conf, rays, CSW, CSWallace, physics, c1960, c196x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%T Counter Experiments on Extensive Cosmic Ray Air Showers
%I U. Sydney
%D 1960
%K PhD Thesis, physics, CSW, CSWallace, c1960, c196x, c19xx, rays, shower

%A C. S. Wallace
%T The determination of the radial distribution of electrons, and the size
   spectrum of extensive air showers
%J Proc. of A.A.E.C. Symp.
%W Sydney
%P ?-?
%D 1958
%K conf, AAEC, physics, CSW, CSWallace, c1958, c195x, c19xx,
   cosmic ray, shower
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A M. H. Brennan
%A J. A. Lehane
%A J. Malos
%A D. D. Millar
%A C. S. Wallace
%A M. M. Winn
%T The Sydney air shower experiment
%J N.2 del Supplemento al Vol. 8, Serie X del Nuovo Cimento
%P 653-661
%D 1958 ?
%K physics, cosmic ray, rays, shower, CSW, CSWallace, c1958, c195x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A M. H. Brennan
%A J. Malos
%A D. D.  Millar
%A C. S. Wallace
%T Cerenkov light from air showers
%J N2 del Supplemento al vol.8, Serie X, del Nuovo Cimento
%P 662-664
%D 1958 ?
%K physics, cosmic ray, rays, shower, CSW, CSWallace, c1958, c195x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%A M. M. Winn
%A K. K. Ogilvie
%T Dependence of the nucleonic component of cosmic ray air showers on radius
%J Nature
%N 182
%N 4650
%P 1653-1654
%M DEC
%D 1958
%K jrnl, physics, c1958, c195x, c19xx, CSW, CSWallace, cosmic ray, rays,
   shower
%X [<A HREF="http://dx.doi.org/10.1038/1821653a0">doi:10.1038/1821653a0</A>]['07],
   [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A M. H. Brennan
%A D. D. Millar
%A C. S. Wallace
%T Air showers of size greater than 10**5 particles - (1) core location and
   shower size determination
%J Nature
%V 182
%P 905-911
%M OCT
%D 1958
%K jrnl, physics, c1958, c195x, c19xx, CSW, CSWallace, cosmic ray, rays,
   shower
%X [<A HREF="http://dx.doi.org/10.1038/182905a0">doi:10.1038/182905a0</A>]['07],
   [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A M. H. Brennan
%A J. Malos
%A D. D. Millar
%A M. H. Rathgeber
%A C. S.  Wallace
%T Air showers of size greater than 10**5 particles - (2) Cerenkov radiation
   accompanying the showers
%J Nature
%V 182
%P 973-977
%M OCT
%D 1958
%K jrnl, physics, cosmic ray, rays, CSW, CSWallace, c1958, c195x, c19xx
%X [<A HREF="http://dx.doi.org/10.1038/182973a0">doi:10.1038/182973a0</A>]['07],
   [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A M. H. Brennan
%A D. D. Millar
%A M. H. Rathgebar
%A C. S. Wallace
%T Air showers of size greater than 10**5 particles - (3) comparison
   between the response of Geiger and scintillation counters
%J Nature
%V 182
%M OCT
%D 1958
%P 1053-1054
%K jrnl, physics, CSW, CSWallace, c1958, c195x, c19xx
%X [<A HREF="http://dx.doi.org/10.1038/1821053a0">doi:10.1038/1821053a0</A>]['07],
   [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A B. J. O'Brien
%A C. S. Wallace
%T Ettingshausen effect and thermomagnetic cooling
%J J. of Applied Physics
%V 29
%P 1010-1012
%M JUL
%D 1958
%K jrnl, physics, efects, CSW, CSWallace, c1958, c195x, c19xx, thermo-magnetic
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A C. S. Wallace
%A M. H. Brennan
%T The automatic digital recording of information from cosmic ray air showers
%J Proc. of Salisbury Conf. on Computing, W.R.E., Salisbury, S.A.
%P ?-?
%M JUN
%D 1957
%K conf, physics, hardware, cosmic rays, CSW, CSWallace, c1957, c195x, c19xx,
   shower, ray
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A B. J. O'Brien
%A C. S. Wallace
%A K. Landecker
%T The cascading of Peltier-couples for thermo-electric cooling
%J J. of Applied Physics
%V 27
%P 820-823
%M JUL
%D 1956
%K jrnl, physics, thermoelectric, CSW, CSWallace, c1956, c195x, c19xx, couple,
   Peltier effect, refrigeration
%X <!-- from dept record --> [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].


%A J. C. Mallery
%T A common Lisp hypermedia server
%J Proc. 1st Int. Conf. on the World-Wide Web.
%W Geneva, CERN
%M MAY
%D 1994
%P ?-?
%K Lisp, document retrieval, W3, c1994, c199x, c19xx,
   HTML, HTML+, CLIM, www, http
%X <A HREF="http://www.ai.mit.edu/projects/iiip/doc/cl-http/server.html">here (11/'94)</A>
   <A HREF="http://www.ai.mit.edu/">AI at MIT</A>
   email: JCMA@AI.MIT.EDU (11/'94)

%A S. Harris
%A G. Kidder
%T Netscape Quick Tour
%I Ventana Press
%P 152
%M MAR
%D 1995
%K book, computing, browser, explorer, mozilla, InterNet, world wide web, www
%X <A HREF="http://wwwnt.thegroup.net/harris/sgbook.htm">blurb</A>
   from Stuart Harris,   email: sirrah@cg57.esnet.com [3/'95].

%A E. van Herwijnen
%T Practical SGML 2nd edn
%I Kluwer
%D 1994
%K book, text, SGML, standard generalized markup language, markup, mark up,
   HTML, hypertext, internet, computing, www, vanHerwijnen, zz0895
%X (in Hargrave)

%A C. Bowman
%A P. B. Danzig
%A U. Manber
%A M. F. Schwartz
%T Scalable internet resource discovery: research problems and approaches
%J CACM
%V 37
%N 8
%P 98-107
%M AUG
%D 1994
%K internet, CACM, jrnl, world wide web, c1994, c199x, c19xx,
   search engine, harvest, zz1095
%X <A HREF="http://harvest.cs.colorado.edu/harvest/papers.html">[harvest home]</A> [10/95]

%A M. Pesce
%T VRML Browsing and Building Cyberspace
%I New Riders
%D 1996?
%K book, text, 3D, 3-D, VRML, VRML1, www, zz0696
%X from enews:   isbn:1562054988.
   author was an initiator of VRML
   published by NewRiders <A HREF="http://www.mcp.com/newriders">[web]</A>

%A J. Vacca
%T VRML: Bringing Virtual Reality to the Internet
%I AcademicPress
%D 1996
%K book, text, VRML 1, VRML1, 3D, 3-D, www, zz0996
%X isbn:0127099107;    $35 US

%A A. L. Ames
%A D. R. Nadeau
%A J. L. Moreland
%T VRML Sourcebook
%I Wiley
%D 1996
%K book, text, VRML, VRML1, 3D, 3-D, www, zz0996
%X isbn:0471141593;   $30 US
   reference, source code
   VRML 2.0 Sourcebook planned for ?Oct 1996?

%E E. Barrett
%T The Society of Text - Hypertext, Hypermedia and the Social Construction of
   Information
%I MIT
%D 1989
%K hyper text, essays, www, zz1196
%X form  A l p h a  L a u 's  report '96

%A J. Hartman
%A J. Wernecke
%T The VRML 2.0 Handbook, Building Moving Worlds on the Web
%I AddisonWesley
%D 1996
%K VRML, VRML2, java script, Javascript, book, text, 3D world
%X isbn:0201479443.

%A S. Brand
%T The Media Lab: Inventing the future at MIT
%I Penguin
%D 1987
%K media laboratory, internet, www, text, book

%A T. Forester
%A P. Morrison
%T Computer Ethics, Cautionary Tales and Ethical Dilemmas in Computing
%I MITpress
%D 1990, 1994
%K computing, moral, text, book, privacy, risk, abuse, social, society,
   professional, crime, privacy
%X 2nd edition 1994, isbn:0262061643; (hb), isbn:0262560739; (pb)
   Hargrave H 174.90904 F717C2

%A H. Rheingold
%T The Virtual Community: Homesteading on the Electronic Frontier
%I AddisonWesley
%D 1993
%K text, book, internet, inter net, well, cyberspace, cyber culture
%X <A HREF="http://kafka.uvic.ca/~svanmoss/FA345/Virtual.Community.HTML">**</A>
   [4/'97]

%T Rogue Programs: Viruses, Worms and Trojan Horses
%E L. J. Hoffman
%I Van Nostrand Reinhold
%P 384
%D 1990
%K book, text, c1990, c199x, c19xx, computer, virus, worm, Trojan horse,
   hacker, hacking, society, crime
%X 1st ed 1990; pb; uk us isbn:0442004540; uk us isbn13:978-0442004545.
   'Experts in the field of "mischevious" programs are collected here in papers
   that cover all aspects of viruses - workings, protection, legal and ethical
   implications - all in nuts-and-bolts language designed to inform both
   technical and non-technical readers.'
   (ref in   F o r e s t e r's   'HighTechHype' paper '92.)

%A J. A. Barry
%T Technobabble
%I MITpress
%D 1991
%K book, text, techno babble, computer, society, social effects,
   prediction, future, c1991, c199x, c19xx
%X (ref in   F o r e s t e r's   HighTechHype paper '92.)

%A K. Mullet
%A D. Sano
%T Designing Visual Interfaces
%I Sunsoft Press (Prentice Hall)
%D 1995
%K book, graphics, graphical user interface, GUI, GUIs,
   interface, design, taste, zz0597
%X isbn:0133033899.

%A E. Humphries
%T Security and the Internet, Rules and Best Practice
%I Blackell
%D 1996
%P 320
%K Internet, www, book, zz0697
%X stg35; uk us isbn:1855548070.

%A H. W. Lie
%A B. Bos
%T Cascading Style Sheets: Designing for the Web
%I Addison Wesley
%D 1997
%K book, stylesheets, Internet, www, CSS, HTML, cascaded, sheet, zz1197
%X isbn:020141998X;   $29.95 US

%A I. S. Graham
%T HTML Stylesheet Sourcebook
%I Wiley
%M SEP
%D 1997
%P 416
%K style sheets, sheet, cascaded, web, www, format, layout, markup, HTML, book
%X isbn:0471196649;     price $24.99 U.S.
   See also    L i e and B o s  '97.

%A A. Blum
%T ActiveX Web Programming
%I Wiley
%D 1997
%P 400
%K active-x, ms, microsoft, web
%X uk us isbn:0471161772;  price us$25.

%A S. Brin
%A L. Page
%T Anatomy of a large-scale hypertextual web search engine
%J Proc. 7th Int. World Wide Web Conf
%W Brisbane
%P 107-117
%M APR
%D 1998
%K conf, www7, www98, c1998, c199x, c19xx, www, hyper text, hypertext, html,
   google, page rank, ranking, authoritative sources, links, BackRub, engines,
   pages, retrieval, query, relevance, relevant, network, importance,
   PageRank, origins
%X "... addresses this question of how to build a practical large-scale system
   which can exploit the additional information present in hypertext. Also we
   look at the problem of how to effectively deal with uncontrolled hypertext
   collections where anyone can publish anything they want." ...
   "...assume page A has pages T1...Tn which point to it (i.e., are citations).
   The parameter d is a damping factor which can be set between 0 and 1. We
   usually set d to 0.85. There are more details about d in the next section.
   Also C(A) is defined as the number of links going out of page A. The
   PageRank of a page A is given as follows:
       PR(A) = (1-d) + d (PR(T1)/C(T1) + ... + PR(Tn)/C(Tn))
   Note that the PageRanks form a probability distribution over web pages, so
   the sum of all web pages' PageRanks will be one.
   PageRank or PR(A) can be calculated using a simple iterative alg., & corr.
   to the principal eigenvector of the normalized link matrix of the web. Also,
   a PageRank for 26 million web pages can be computed in a few hours on a
   medium size workstation. ..."
   -- [<A HREF="http://www-db.stanford.edu/~backrub/google.html">@stanford</A>]['05].
   It became [<A HREF="http://www.google.com/">google</A>]['05].
   (Also see discussion @[<A HREF="http://www.ams.org/samplings/feature-column/fcarc-pagerank">AMS</A>]['15].)
   (Also see pagerank@[<A HREF="https://en.wikipedia.org/wiki/PageRank">wikip</A>]['20].)
   [Also search for: Kleinberg c1998].

%A L. A. Davidson
%A K. Douglas
%T Digital Object Identifiers:  Promise and problems for scholarly publishing
%J J. Electronic Publishing
%V 4
%N 2
%M DEC
%D 1998
%K jrnl, online, DOI, org, www, HREF, http, c1998, c199x, c19xx, academic,
   scientific, literature, papers, indexes, indexing, addresses, web, links
%X [<A HREF="http://www.press.umich.edu/jep/04-02/davidson.html">@jep</A>][10/'04].
   Also see [<A HREF="http://www.doi.org/">doi.org</A>]['04].

%A C. Lee Giles
%A K. D. Bollacker
%A S. Lawrence
%T CiteSeer: An automatic citation indexing system
%J 3rd ACM Conf. on Digital Libraries
%P 89-98
%D 1998
%K conf, CiteSeer, world wide web, www,HREF,http,spider,crawler, citations,
   cience, scientific literature, database,, online, index, bib
%X "...CiteSeer: an autonomous citation indexing system which indexes academic
   literature ...  CiteSeer provides most of the advantages of trad. (manually
   constructed) citation indexes (e.g. the ISI citation indexes) ..."
   -- [<A HREF="http://doi.acm.org/10.1145/276675.276685">doi:/10.1145/276675.276685</A>]['04] inc' pdf,
   isbn:0897919653. [<A HREF="http://citeseer.ist.psu.edu/">citseer</A>][10/'04]

%A J. W. Palmer
%A D. A. Griffith
%T An emerging model of web site design for marketing
%J CACM
%P 44-51
%M MAR
%D 1998
%K CACM, world wide web, www, marketting, sales, selling, zz0398
%X some stat's on  audio/ frame/ free eval'n/ free software/
                   java/ prizes/ online slaes/ SW download/ tech support/
                   video/ graphics/ links/ naviagtion/ text   (12 refs).

%A R. J. Hall
%T How to avoid unwanted email
%J CACM
%P 88-95
%M MAR
%D 1998
%K CACM, internet, www, electronic mail, email, e_mail, e-mail,
   address, channel, junk, spam, spamming, zz0398, mail filter
%X The multiple email addresses / channels idea with the consequences
   carefully thought out.  12 refs.
   [Also search for: spam email].

%A B. Pfaffenberger
%T Discovering HTML 4
%I APprofessional
%M JUL
%D 1998
%P 350
%K book, text, HTML, HTML4, internet, world wide web, zz0698
%X isbn:0125531672;   au$52.50.

%A T. Dell
%T Dynamic HTML for Webmasters
%I APprofessional
%M APR
%D 1998
%P 350
%K book, text, HTML, DHTML, world wide wed, zz0698
%X isbn:0122090659;   au$67.50

%A D. Busch
%T Cascading Style Sheets
%I McGrawHill
%M MAR
%D 1998
%P 512
%K book, text, sheet, stylesheets, HTML, world wide web, zz0698
%X isbn:0079137032;  us$44.95

%A S. Holzner
%T XML Complete
%I McGrawHill
%D 1997
%P 600
%K book, text, HTML, XML, extensible markup language, SGML, world wide web,
   mathematical notation, mathML, zz0698
%X isbn:0079137024;       us$44.95

%A P. Wadler
%T A formal semantics of patterns in XSLT
%I Markup Technologies, Philadelphia
%M DEC
%D 1999
%O Revised version is in  `Markup Languages', MIT Press, June '01
%K XML, XSLT, HTML, SGML, world wide web
%X ...a formal semantics of the pattern language from the 16 December '98
   draft of XSLT. The semantics is clear and concise, summarizing in 1 page
   of formulas what required about 10 pages of prose to describe. With the
   aid of the semantics one can rigorously state and prove properties of the
   language; these properties helped to guide future development of the XSLT
   design. The semantics was developed using standard techniques from the
   programming language community...
   [<A HREF="http://www.research.avayalabs.com/user/wadler/papers/xsl-semantics/xsl-semantics.pdf">.pdf</A>][5/'04]

%A H. Williamson
%T XML: The Complete Reference
%I Osbourne/ McGrawHill
%M MAR
%D 2001
%P 1008
%K book, text, XML, XSL, DTD, xHTML, extensible HTML, www
%X isbn:0072127341;  about au$90;  [also search for: XML].

%A S. J. DeRose
%T The SGML FAQ Book: Understanding the Foundations of HTML and SGML
%I Kluwer
%D 1997
%P 250
%K book, text, SGML, FAQ, de Rose, ISO 8879, ISO8879
%X isbn:0792399439.

%A S. F. Goldfarb
%T The SGML Handbook
%I OUP
%P 688
%K book, text, standard, spec, SGML
%X isbn:0198537371.

%A I. S. Graham
%A L. Quin
%T XML Specification Guide
%I JohnWiley
%M FEB
%D 1999
%P 432
%K book, text, XML, SGML
%X uk us isbn:0471327530.
   <A HREF="http://www.groveware.com/xmlbook/">[web]</A> [5/1999].

%A R. Jelliffe
%T The XML and SGML Cookbook: Recipes for Structured Information
%I PrenticeHall
%P 650
%D 1998
%K book, text, XML, SGML, HTML, design, www
%X isbn:0136142230;

%A P. Spencer
%T XML Design and Implementation
%I WroxPress
%M JUN
%D 1999
%P 400
%K book, text, XML, HTML, extensible matkup language, zz1299
%X US$40, Au$63, isbn:1861002289.

%A S. St. Laurent
%T Inside XML DTDs
%I McGrawHill
%P 512
%D 1999
%K book, text, XML, SGML, extensible markup language, DTD, MathML, MolBio,
   Bioinformatic Sequence Language, Chemical, scientific, StLaurent, zz1299
%X US$50, Au$78, isbn:007134621X.

%A A. Broder
%A et al
%T Graph structure of the web
%I IBM
%M MAY
%D 2000
%K TR, c2000, c200x, c20xx, zz0500, graphs, world wide web, www, diameter, size
%X [<A HREF="http://www.almaden.ibm.com/cs/k53/www9.final/">at ibm</A>][5/'00],
   [<A HREF="/~lloyd/tildeMisc/Local/2000www.html">local</A>] only.

%A M. Pohl
%A P. Purgathofer
%T Analysis of the authoring process of hypertext documents
%J Proc. 11th ACM Conf. on Hypertext and Hypermedia
%D 2000
%K conf, c2000, c200x, c20xx, zz0413, hypertext, hyperlinks, HTML, link, links,
   document, style, styles, organization, heirarchical, education, teaching
%X "Hypertext & Hypermedia systems are used increasingly in educational
   environments. The active participation of students is generally supposed to
   be one of the major advantages of hypermedia systems. Nevertheless,
   inexperienced users of such systems still have many problems with them,
   esp. when authoring. Our experience shows that these problems can be
   alleviated by the intro. of an authoring tool tailored to the specific needs
   of the user. To develop such a tool, a systematic analysis of the authoring
   process is necessary. The methods used in the study described in the
   following text were a content analysis & an automatic monitoring system which
   yields a dynamic view of the authoring process. ... our study indicate that
   inexperienced authors of h.systems need special support to create
   non-hierarchical relationships & an adequate layout in their h.doc.."
   -- [<A HREF="http://dx.doi.org/10.1145/336296.336400">doi:10.1145/336296.336400</A>]['13],
   free [<A HREF="http://igw.tuwien.ac.at/igw/menschen/pohl/yorkzwo.html">tuwien</A>]['13];
   uk us isbn:1581132271.

%A M. W. Berry
%A B. Hendrickson
%A P. Raghavan
%T Sparse matrix reordering schemes for browsing hypertext
%B The Mathematics of Numerical Analysis
%S Lect. in Applied Math.
%V 32
%P 99-123
%E J. Renegar
%E M. Shub
%E S. Smale
%D 1996
%I Am. Math. Soc.
%K c1996, c199x, c19xx, chapter, HREF, www, hyper text, browse, similar, like,
   pages, reverse Cuthill McKee, RCM, zz0500
%X <A HREF="http://www.cs.utk.edu/~berry/order/index.html">[www]</A>[5'00]
   matrix:  documents x terms.  Perm' rows and cols to get a
   narrow banded form, read off ?clusters.
   [Also search for: sparse matrix]

%A S. Lawrence
%A C. Lee Giles
%T Accessibility of information on the web
%J Nature
%V 400
%P 107-109
%D 1999
%O Intelligence, was SIGART bulletin 11(1) 32-39, '00.
%K world wide web, www, size, internet, search engine, engines,
   coverage, page, pages, bias, zz1100, c1999, c199x, c19xx
%X Feb 1999:  Estimate 16 million web servers, 2.8 million "proper.
   Est' 800 million publicly accessible web pages (can have mult' sites).
   Est' major search engines each index 3 to 17% of these pages.
   Altavista & Northern Light index size 100 - 130M pages.
   ... we can see a trend where popular pages become more popular,
   while new, unlinked pages have an increasingly difficult time
   becoming visible in search engine listings.
   [Also search for: tall poppy].
   [<A HREF="http://www.nature.com/cgi-taf/dynapage.taf?file=/nature/journal/v400/n6740/abs/400107a0_fs.html">nature</A>][8/'04].

%A A. Reka
%A H. Jeong
%A A.-L. Barabasi
%T The diameter of the world wide web
%J Nature
%V 401
%P 130-131
%D 1999
%K jrnl, c1999, c199x, c19xx, www, network, size, graph, graphs,
   scale free, scalefree, power law
%X "... find that both P_out(k) and P_in(k) follow a power law over several
   orders of magnitude, remarkably different not only from the Poisson distn
   predicted by the classical theory of random graphs, but also from the
   bounded distribution found in models of random networks. ..."  [8 refs].
   -- [<A HREF="http://arxiv.org/abs/cond-mat/9907038">@arxiv</A>]['08],
      pdf@[<A HREF="http://www.nd.edu/%7Ealb/Publication06/062%20Diameter%20of%20the%20world%20wide%20web/Diameter%20of%20the%20world%20wide%20web.pdf">nd</A>]['08],
      alb@[<A HREF="http://www.nd.edu/~alb/">nd</A>]['08].
   [Also search for: graphModel]  and  [also search for: graphModel].

%A S. Lawrence
%T Online or invisible?
%J Nature
%V 411
%N 6837
%P 521
%D 2001
%K jrnl, citeseer, www, world wide web, papers, publications, online,
   ejournals, citations, cited, impact factor, c2001, c200x, c20xx
%X "...analyzed 119,924 conference articles in computer science and related
   disciplines, obtained from DBLP (dblp.uni-trier.de). In computer science,
   conference articles are typically formal publications and are often more
   prestigious than journal articles, with acceptance rates at some conferences
   below 10%. Citation counts and online availability were estimated using
   ResearchIndex...."
   -- [<A HREF="https://doi.org/10.1038/35079151">doi:10.1038/35079151</A>]['22].

%A A. C. Kaporis
%A L. M. Kirousis
%A E. Kranakis
%A D. Krizanc
%A Y. C. Stamatiou
%A E. C. Stavropoulos
%T Locating information with uncertainty in fully interconnected
   networks with applications to world wide web information retrieval
%J COMPJ
%V 44
%N 4
%P 221-229
%D 2001
%K jrnl, COMPJ, world wide web, www, computer network, IR, search, find
%X [<A HREF="http://www.oup.co.uk/computer_journal/hdb/Volume_44/Issue_04/440221.sgm.abs.html">www</A>][10/'01].
   ... search algorithm that is only allowed to transfer a
   fixed amount of memory along communication links as it
   visits the network nodes. The algorithm is, however,
   allowed to use one bit of memory at each node as an
   'already visited' flag ...

%A M. Adler
%A M. Mitzenmacher
%T Towards compressing web graphs
%J Proc. Data Compression Conf.
%P 203
%D 2001
%K conf, DCC, DCC01, c2001, c200x, c20xx, web, graph, www, compress,
   compression, hyper links
%X "... efficient algs. for such compression that are motivated by recently
   proposed random graph models for describing the Web. ... based on reducing
   the compression problem to the problem of finding a minimum spanning tree in
   a directed graph related to the original link graph. The performance of the
   alg. on graphs generated by the random graph models suggests that by taking
   advantage of the link structure of the Web, one may achieve sig. better
   compression than natural Huffman-based schemes. ..."
   -- pdf@[<A HREF="http://www.eecs.harvard.edu/~michaelm/postscripts/dcc2001b.pdf">harvard</A>]['08].
   [Also search for: compress graph].

%T Beginning PHP4 Databases
%I WroxPress
%D 2002
%K book, text, PHP, www, world wide web, database, data base, DBMS
%X hypertext preprocessor, open source, about us$40.  isbn:1861007825.

%A Y. Gil
%A C. Ratnakar
%T Trusting information sources one citizen at a time
%J Int. Semantic Web Conf. (ISWC)
%P ?-?
%M JUN
%D 2002
%K conf, world wide web, internet, trust, credibility, authentic, advogato,
   reputation, social, society, peer, relationships, http, HREF, www, zz1003
%X a ref in an online [<A HREF="http://www.mindswap.org/papers/Trust.pdf">paper</A>][10/'03]
   (also see [<A HREF="http://www.advogato.org/">www.advogato.org</A>][10/'03])

%A E. T. Ray
%A J. McIntosh
%T Perl and XML
%I O'Reilly
%P 216
%M APR
%D 2002
%K book, text, programming language, HTML, www, c2002, c200x, c20xx
%X about us$35.   isbn:059600205X.

%A B. Hopkins
%A R. Antony
%T Bluetooth for Java
%I Apress
%P 336
%M NOV
%D 2002
%K book, text, radio communications, wireless, c2002, c200x, c20xx,
   portable devices, protocol
%X about au$80.  isbn:1590590783.

%A J. R. Rusch
%T The social psychology of computer viruses and worms
%J INET 2002
%P ?-?
%M JUN
%D 2002
%K conf, internet, virus, worm, threat, hacker, c2002, c200x, c20xx, zz0204,
   scam, scams, con, conn, deceit, deceptive, spam, mail, email, attachment,
   attachments, trust, context confusion, Kournikova, sulfnbk, exe, w32,
   leaveb, reezak, computer security, inet2002
%X [<A HREF="http://inet2002.org/CD-ROM/lu65rw2n/papers/g10-c.pdf">.pdf</A>]2/'04]
   [<A HREF="http://inet2002.org/CD-ROM/lu65rw2n/govn.htm#g10">conf</A>][2/'04].
   auth' @ Ge0rgetown U.  L@w Center.
   [Also search for: spam email].

%A R. Blood
%T The Weblog Handbook: Practical Advice on Creating and Maintaining Your Blog
%I BasicBooks
%P 144
%D 2002
%K book, c2002, c200x, c20xx, web blog, weblog, blogging, blogger, www, html
%X 1st ed 2002, pb us$12; isbn:073820756X; isbn13:978-0738207568.

%A W. Kelly
%A P. Roe
%T Donating cycles over the internet using web services
%J 8th Australian World Wide Web Conf.
%W SunshineCoast (.au)
%P ?-?
%M JUL
%D 2002
%K conf, soap, .net, jvm, service, c2002, c200x, c20xx, grid, G2, www, www8,
   parallel, workstation, farm
%X "...We, ... proposing to use the web service model to create a parallel
   comp. framework based around cycle donation. Our framework is identical to
   web services in respect to both the programming model exposed to application
   programmers & the underlying communication mechanisms used. Compared to
   other parallel programming frameworks our framework is designed to be simple
   & lightweight. For application programmers, exploiting the additional
   computation power provided by a dynamically changing set of volunteer
   machines is no more complex that exploiting a simple web service. By hosting
   volunteer components in a web browser, volunteers are able to donate cycles
   with a minimum of pain - absolutely no special software needs to be pre-
   installed on the volunteer machines. The use of open standards such as SOAP
   & HTTP means that components created on different platforms, such as .NET or
   the JVM, can be freely substituted."
   [<A HREF="http://g2.fit.qut.edu.au/G2/HomePage/AusWeb02/auswebv5.htm">g2.fit.qut.edu.au</A>]['05], auths @ qut ['05]

%A L. Graham
%A P. T. Metaxas
%T "Of course it's true; I saw it on the Internet!": critical thinking in
   the Internet era
%J CACM
%V 46
%N 5
%P 70-75
%M MAY
%D 2003
%K jrnl, CACM, www, internet, http, HREF, c2003, c200x, c20xx, zz0903,
   students, source, information, research, trust, gullible, microsoft,
   spin, pr, ads, adverts, advertisment, advertising, think
%X "Students use the Net as a primary source of information, usually with
   little or no regard as to the accuracy of that information." issn:00010782.
   [<A HREF="http://dx.doi.org/10.1145/769800.769804">doi:10.1145/769800.769804</A>][8/'03]

%A A. Huang
%T Hacking the Xbox
%I NoStarchPress
%P 288
%M JUL
%D 2003
%K book, Microsoft X-Box, Xbox, hack, chip, digital millenium copyright act,
   hardware, closed, open, reverse engineering, disassembly, c2003, c200x,
   c20xx, MS, bunnie, game console, intellectual properity, IP, security, zzLaw,
   modify, modifications
%X "... Xbox security mechanisms and other advanced hacking topics, with an
   emphasis on educating the readers on the important subjects of computer
   security ..."
   us$17, isbn:1593270291.
   -- [<A HREF="http://hackingthexbox.com/">hackingthexbox.com</A>][4/'04],
      [<A HREF="http://www.nostarch.com/frameset.php?startat=xbox">nostarch.com</A>][4/'04].

%A S. Byers
%A et al
%T Analysis of security vulnerabilities in the movie production and
   distribution process
%J Workshop on Digital Rights Management (DRM)
%I ACM
%P ?-?
%M OCT
%D 2003
%K DRM, ACM, SIGSAC, DRM, movie, movies, film, films, copyright, copying, law,
   wShop, MPAA, internet, file sharing, bootleg, c2003, c200x, c20xx, zz1003,
   DVD, copy, copies
%X "... Our research attempts to determine the source of unauthorized copies by
   studying the availability and characteristics of recent popular movies in
   file sharing networks. We developed a data set of 312 popular movies and
   located one or more samples of 183 of these movies on file sharing networks,
   for a total of 285 movie samples. 77% of these samples appear to have been
   leaked by industry insiders. Most of our samples appeared on file sharing
   networks prior to their official consumer DVD release date. Indeed, of the
   movies that had been released on DVD as of the time of our study, only 5%
   first appeared after their DVD release date on a web site that indexes file
   sharing networks ..."
   [<A HREF="http://lorrie.cranor.org/pubs/drm03.html">abs &  pdf</A>]['05]
   in a workshop at 10th ACM conf on Comp'r and Comm'n Security.
   [<A HREF="mailto:byers OF research att com">authors</A>][10/'03] at AT&T Labs-Research.
   Also see [<A HREF="http://www.cnn.com/2003/TECH/biztech/10/23/film.leaks.reut/">CNN</A>][10/'03]

%A P. Murray-Rust
%A H. S. Rzepa
%T Chemical Markup, XML, and the World Wide Web. 4. CML Schema
%J J. Chem. Inf. Comput. Sci.
%V 43
%N 3
%P 757-772
%D 2003
%K jrnl, JCICS, c2003, c200x, c20xx, chemical markup language, CML, XML,
   CMLCore, chemical compound, structural formula
%X "A revision to Chemical Markup Language (CML) is presented as a XML Schema
   compliant form, modularized into nonchemical & chemical components. STMML
   contains generic concepts for numeric data & scientific units, while
   CMLCore retains most of the chemical functionality of the original CML 1.0
   & extends it by adding handlers for chemical substances, extended bonding
   models & names. We propose extension via new namespaced components for
   chemical queries, reactions, spectra, & computational chemistry. The
   conformance with XML schemas allows much greater control over datatyping,
   document validation, & structure."
   -- [<A HREF="http://dx.doi.org/10.1021/ci0256541">doi:10.1021/ci0256541</A>]['08]
   Also see [<A HREF="http://en.wikipedia.org/wiki/Structural_formula">wikip</A>]['08]
   [also search for: structural formula]

%A B. Basham
%A K. Sierra
%A B. Bates
%T Head First Servlets and JSP
%I O'Reilly
%P 854
%D 2004
%K book, text, c2003, c200x, c20xx, zz0508, Java server pages, page, JSP,
   world wide web, site, www, developer, JSTL
%X "... dynamically generate HTML, XML or other types of documents in response
   to a Web client request. The technology allows Java code and certain
   pre-defined actions to be embedded into static content. ..." -- wikip.
   uk us isbn:0596005407; uk us isbn13:978-0596005405.
   [<A HREF="http://java.sun.com/products/jsp/">jsp@sun</A>]['08]

%A J. C. Mogul
%T Clarifying the fundamentals of HTTP
%J SPE
%V 34
%N 2
%P 103-134
%D 2004
%K jrnl, SPE, type, types, access, name space, web, www, hyper-text,
   protocol, implementation, standards, zz0204
%X "...explains that HTTP needs a clean and consistent data-type model, and
   in particular needs an explicit instance data type; that HTTP needs a clear
   data access model, and that resources and instances should carry explicit
   access-model labels; and that HTTP needs a simple name space for
   implementations to declare sets of supported extensions."
   [<A HREF="http://dx.doi.org/10.1002/spe.573">doi:10.1002/spe.573</A>][2/'04]

%A R. Lake
%A D. Burggraf
%A M. Trninic
%A L. Rae
%T Geography Mark-up Language
%I Wiley
%P 384
%D 2004
%K book, text, GML, mark up, markup language, geographical, GIS, zz0504,
   GML2, GML3, c2004, c200x, c20xx
%X hb,  uk stg75, isbn:0470871539;
   ppb, uk stg32, isbn:0470871547;  authors @ Galdos Sys Inc USA.

%A L. Lessig
%T Free Culture: How Big Media Uses Technology and the Law to
   Lock Down Culture and Control Creativity
%I Penguin
%M MAR
%D 2004
%P 345
%K book, text, intellectual property, IP, copyright, law, legal, Micky Mouse,
   zzLaw, act, music, film, films, movie, movies, software, authors, publishers,
   Creative Commons licensing, media, copy-right, c2004, c200x, c20xx, zz0504
%X St@nford L@w Prof.   us$17, uk us isbn:1594200068.
   [<A HREF="http://www.lessig.org/">lessig.org</A>][5/'04].
   [Also search for: zzLaw].

%A B. Klimt
%A Y. Yang
%T Introducing the ENRON corpus
%J 1st Conf. on Email and Anti-Spam (CEAS)
%P -
%D 2004
%K conf, CEAS mail, email, spam, spamming, c2004, c200x, c20xx, nonSpam,
   data set, dataSet, CALO, Federal Energy Regulatory Commission, zz0805
%X 619,446 messages to 158 users, cleaned 200,339 msgs, avg 757/user.
   [<A HREF="http://www.ceas.cc/papers-2004/168.pdf">pdf@ceas</A>]['05],
   [<A HREF="http://www.cs.cmu.edu/~enron/">DataSet</A>]['05].
   [Also search for: spam email].

%A C. Jacobs
%A W. li
%A E. Scrier
%A D. Bargeron
%A D. Salesin
%T Adaptive document layout
%J CACM
%P 60-66
%V 47
%N 8
%M AUG
%D 2004
%K acm, cacm, document, size, resolution, text, images, format, formatting,
   c2004, c200x, c20xx, markup, mark-up, languages, templates, constraint,
   programming, XSL, style-sheet, stylesheet, typesetting
%X "How to automatically reformat, resize & paginate electronic text & graphics
   so documents look as good on displays of any size as they do on paper." ...
   "We can expect even greater proliferation of different-size reading devices,
   along with the need for documents that adapt to them."
   -- [<A HREF="http://doi.acm.org/10.1145/1012037.1012063">doi:10.1145/1012037.1012063</A>][8/'04].

%A E.Crawford
%A I. Koprinska
%A J. Patrick
%T Phrases and feature selection in e-mail classification
%J Proc. 9th Australasian Document Computing Symp. (ADCS'04)
%W Melbourne
%P ?-?
%D 2004
%X conf, ADCS, ADCS04, email, spam, scam, c2004, c200x, c20xx, text, features,
   phrase
%X "...study the effectiveness of using a phrase-based representation in e-mail
   classification, & the effect this approach has on a # of machine learning
   algs..  ...evaluate various feature selection methods & reduction levels
   for the bag-of-words representation on several learning algs. & corpora. ...
   show that the phrase-based rep. & feature selection methods can be used to
   increase the performance of e-mail class'n."
   [<A HREF="http://www.cs.mu.oz.au/~alistair/adcs2004/papers/paper09.pdf">pdf</A>]['05],
   [<A HREF="http://www.it.usyd.edu.au/~irena/">IK @ uSyd</A>]['05].
   [Also search for: spam email].

%A D. S. McFarland
%T Dreamweaver MX 2004: The Missing Manual
%I Pogue
%P 800
%D 2004
%K book, text, c2004, c200x, c20xx, Dreamweaver, dream weaver, www, web page,
   pages, site, design, multimedia, Macromedia, MX2004, XHTML, CSS
%X 3rd ed 2003, pb us$23; uk us isbn:0596006314; uk us isbn13:978-0596006310.

%A I. Androutsopoulos
%A E. F. Magirou
%A D. K. Vassilakis
%T A game theoretic model of spam e-mailing
%J Proc. 2nd Conf. on Email and Anti-Spam (CEAS)
%W Stanford U.
%P ?-?
%M JUL ?
%D 2005
%K CESA, CEAS2, spam, email, mail, emailing, spamming, internet, game theory
%X [<A HREF="http://www.aueb.gr/users/ion/docs/ceas2005_paper.pdf">pdf@aueb.gr</A>]['05]
   [<A HREF="http://www.ceas.cc/papers-2005/113.pdf">pdf@ceas.cc</A>]['05]
   [<A HREF="http://www.ceas.cc/">ceas.cc</A>]['05].
   [Also search for: spam email].

%A J. Hau
%A W. Lee
%A J. Darlington
%T A semantic similarity measure for semantic web services
%J Web Service Semantics Workshop
%P ?-?
%D 2005
%K wShop, WWW2005, c2005, c200x, c20xx, service, similar, OWL, Lite, OWLs, www
%X "... annotated with OWL ontology.  Similarity is calculated by defining the
   intrinsic information value of a service description based on the
   `inferencibility' of each OWL Lite construct. ..."
   [<A HREF="http://www.ai.sri.com/WSS2005/final-versions/WSS2005-Hau-Final.pdf">pdf</A>]['06]

%A K. Bryan
%A T. Leise
%T The $25,000,000,000 Eigenvector: The linear algebra behind Google
%J SIAM Review
%V 48
%N 3
%P 569-581
%D 2006
%K jrnl, c2006, c200x, c20xx, zz0415, google, pagerank, survey, intro, web,
   page, ranking, importance, links, search engine, Eigenvector
%X "... ranks the importance of web pages according to an eigenvector of a
   weighted link matrix. Analysis of the PageRank formula provides a wonderful
   applied topic for a linear algebra course. Instructors may assign this
   article as a project to more advanced students or spend one or two lectures
   presenting the material ..."
   -- [<A HREF="http://dx.doi.org/10.1137/050623280">doi:10.1137/050623280</A>]['15].
   (Also see pagerank@[<A HREF="https://en.wikipedia.org/wiki/PageRank">wikip</A>]['20].)

%A E. Meyer
%T CSS: The Definitive Guide
%I OReilly
%P 536
%D 2006
%K book, text, c2006, c200x, c20xx, cascaded style sheets, sheet, CSS, html,
   www, web page, pages, site, design, CSS2.1, explorer
%X 3rd ed 2006, pb us$30, uk us isbn:0596527330; uk us isbn13:978-0596527334.

%A D. Goodman
%T Dynamic HTML: The Definitive Reference
%I OReilly
%P 1322
%D 2006
%K book, text, c2006, c200x, c20xx, HTML, DHTML, www, web page, pages, design,
   xhtml, document object model, AJAX
%X 3rd ed 2006, pb, us$38, uk us isbn:0596527403; uk us isbn13:978-0596527402.

%A A. Ramachandran
%A N. Feamster
%T Understanding the network-level behaviour of spammers
%J Proc. ACM SIGCOMM
%P ?-?
%M SEP
%D 2006
%K SIG, c2006, c200x, c20xx, spam, spamming, spammer, email, TCP IP, bot, bots
%O Georgia Tech. Technical Report GT-CSS-2006-001
%X "... find that most spam is being sent from a few regions of IP address space
  & that spammers appear to be using transient bots that send only a few pieces
  of email over very short periods of time. Finally, a small, yet non-negligible
  amount of spam is received from IP addresses that correspond to short-lived
  BGP routes, typically for hijacked prefixes. These trends suggest that
  developing algorithms to identify botnet membership, filtering email messages
  based on network-level properties (which are less variable than email content)
  & improving the security of the Internet routing infrastructure, may prove to
  be extremely effective for combating spam."
  -- [<A HREF="http://www.cc.gatech.edu/~feamster/papers/p396-ramachandran.pdf">pdf</A>]['06].
   [Also search for: spam email].

%A K. Breitman
%A M.A. Casanova
%A W. Truszkowski
%T Semantic Web: Concepts, Technologies and Applications
%I SpringerVerlag
%S NASA Monographs in Systems and Software Engineering
%V XIV
%P 330
%D 2007
%K book, text, c2007, c200x, c20xx, www, ontology, web services, service
%X euro60; hb; uk us isbn13:978-1846285813.

%A P. Holme
%A J. Karlin
%A S. Forrest
%T Radial structure of the internet
%J Proc. Royal Soc. A
%V ?
%P ?
%D 2007
%K jrnl, PRSS, c2007, c200x, c20xx, www, web, internet, network, graph, graphs
%X "... Common vertex-specific quantities are plotted against this metric to
   reveal distinctive characteristics of central and peripheral vertices. Two
   datasets are analysed using these measures as well as two common generative
   models (Barabasi-Albert and Inet). We find a clear distinction between the
   highly connected core and a sparse periphery. We also find that the periphery
   has a more complex structure than that predicted by degree distribution or
   the two generative models."
   -- [<A HREF="http://dx.doi.org/10.1098/rspa.2007.1820">doi:10.1098/rspa.2007.1820</A>]['07].
   [Also search for: graphModel].

%A D. S. Anderson
%A C. Fleizach
%A S. Savage
%A G. M. Voelker
%T Spamscatter: Characterizing internet scam hosting infrastructure
%J 16th Usenix Security Symp.
%P ?-?
%M AUG
%D 2007
%K conf, c2007, c200x, c20xx, spam, scam, www, email, phishing, phish,
   security, risks, bot, bots, zombies, relay, relays
%X ... embedded link structure ... identified 2000+ scams on 7000+servers.
   [<A HREF="http://www.cs.ucsd.edu/~voelker/pubs/spamscatter-security07.pdf">pdf@ucsd</A>]['07].
   [Also search for: spam email].

%A T. Segaran
%T Programming Collective Intelligence: Building Smart Web 2.0 Applications
%I OReilly
%P 360
%M AUG
%D 2007
%K book, text, c2007, c200x, c20xx, world wide web, www, web2, www2,
   application
%X "... Collaborative filtering techniques ... clustering ... PageRank ..."
   pb, us$27, uk us isbn:0596529325; uk us isbn13:978-0596529321.

%A D. Crane
%A B. Bibeault
%A J. Sonneveld
%A T. Goddard
%A C. Gray
%A R. Venkataraman
%A J. Walker
%T Ajax in Practice
%I Manning Publ.
%P 456
%D 2007
%K Ajax, book, text, c2007, c200x, c20xx, web, www, Asynchronous JavaScript
%X pb us$33, uk us isbn:1932394990; uk us isbn13:978-1932394993.

%A N. C. Zakas
%A J. McPeak
%A J. Fawcett
%T Professional Ajax
%I Wrox
%P 624
%D 2007
%K Ajax, book, text, c2007, c200x, c20xx, pro, dot net, .net, web, www, jQuery
%X pb us$26, uk us isbn:0470109491; uk us isbn13:978-0470109496.

%A L. Richardson
%A S. Ruby
%T RESTful Web Services
%I OReilly
%P 446
%D 2007
%K book, c2007, c200x, c20xx, REST, restful, restfull, http, www,
   service, design
%X pb us$24, uk us isbn:0596529260; uk us isbn13:978-0596529260.

%A G. S. Manku
%A A. Jain
%A A. D. Sarma
%T Detecting near-duplicates for web crawling
%J Proc. of the 16th Int. Conf. on World Wide Web
%P 141-150
%D 2007
%K conf, c2007, c200x, c20xx, google labs, near duplicate, similar, simhash,
   hash, hashing, close, retrieval, neighbourhood, www, crawler, web page,
   pages, adverts, ads, Charikar fingerprinting, fingerprint,
   pigeonhole principle
%X "... 2 such docs. differ from each other in a very small portion that
   displays ad's, for example. ... [diffs] irrelevant for web search. So the
   quality of a web crawler increases if it can assess whether a newly crawled
   web page is a near-duplicate of a previously crawled web page or not.
   ... multi-billion page repository, we make 2 research contributions.  1. we
   demo. that Charikar's fingerprinting technique is appropriate for this goal.
   2. we present an alg. technique for id'ing existing f-bit fingerprints that
   differ from a given fingerprint in at most k bit-positions, for small k.
   Our technique is useful for both online queries (single fingerprints) & all
   batch queries (multiple fingerprints). ..."   [53 refs], Auth1,2@google.com.
 p.142 on simhash:
      "1. web page -> vector of wtd features; 2. v := 0...0;  -- f ints
       3. for each feature g do
            h := f_bit_hash(g);
            for i=0..f-1 do if h[i] == 1 then v[i] += wt(g) else v[i] -= wt(g);
       4.fingerprint[i] = if v[i] > 0 then 1 else 0
       with 8 billion (8B) web pages, 64-bit fingerprints suffice ..."
    on near-duplicate detection
       "... f.prints that differ it <= 3 bit posns ... 1B queries/day ..."
   pdf: [<A HREF="http://doi.acm.org/10.1145/1242572.1242592">doi:10.1145/1242572.1242592</A>]['08],
   pdf@[<A HREF="http://www2007.org/papers/paper215.pdf">www2007.org</A>]['08].
   [Also search for: hashing neighbourhood].

%T Web Search
%E A. Spink
%E M. Zimmer
%I SpringerVerlag
%S Information Science and Knowledge Management
%P 352
%D 2008
%K book, text, c2008, c200x, c20xx, zz0208, www, web, search engine, engines
%X hb., eu.89.95; isbn:3540758280; isbn13:978-3540758280.

%A A. T. Holdener III
%T Ajax: The Definitive Guide
%I OReilly
%P 980
%D 2008
%K Ajax, book, text, c2008, c200x, c20xx, programming, web, www, jSon,
   Asynchronous JavaScript and XML, css
%X "... How to connect server-side backend components to user interfaces in the
   browser Loading and manipulating XML documents, and how to replace XML with
   JSON Manipulating the Document Object Model (DOM) ..."
   pb us$31, uk us isbn:0596528388; uk us isbn13:978-0596528386.

%A E. R. Harold
%T Refactoring HTML: Improving the Design of Existing Web Applications
%I AddisonWesley
%P 368
%D 2008
%K book, text, c2008, c200x, c20xx, CSS, HTML, www, refactor, redesign, update,
   modify, programming
%X hb, us$32, uk us isbn:0321503635; uk us isbn13:978-0321503633.

%A J. A. Evans
%T Electronic publication and the narrowing of science and scholarship
%J Science
%V 321
%N 5887
%P 395-399
%M JUL
%D 2008
%K jrnl, c2008, c200x, c20xx, zz0708, web, www, online journals, papers,
   publications, cite, citation, citations, citing, references, narrow,
   academia, scholarship, scientific research, groupThink
%X "... show that as more journal issues came online, the articles referenced
   tended to be more recent, fewer journals & articles were cited, & more of
   those citations were to fewer journals & articles. The forced browsing of
   print archives may have stretched scientists & scholars to anchor findings
   deeply into past & present scholarship. Searching online is more efficient &
   following hyperlinks quickly puts researchers in touch with prevailing
   opinion, but this may accelerate consensus & narrow the range of findings &
   ideas built upon."
   [<A HREF="http://dx.doi.org/10.1126/science.1150473">doi:10.1126/science.1150473</A>]['08].

%A S. Begall
%A J. Cerveny
%A J. Neef
%A O. Vojtcch
%A H. Burda
%T Magnetic alignment in grazing and resting cattle and deer
%J PNAS
%V ?
%N ?
%P ?
%M ?
%D 2008
%K jrnl, PNAS, biol, c2008, c200x, c20xx, zz0908, cow, cows, north, south,
   orientation, compass, magnetic field, google earth
%X "We demonstrate by means of simple, noninvasive methods (analysis of
   satellite images, field observations, and measuring "deer beds" in snow) that
   domestic cattle (n=8,510 in 308 pastures) across the globe, & grazing &
   resting red & roe deer (n=2,974 at 241 localities), align their body axes in
   roughly a north-south direction. Direct obs. of roe deer revealed that
   animals orient their heads northward when grazing or resting. ..."
   (online Aug 2008) [<A HREF="http://dx.doi.org/10.1073/pnas.0803650105">doi:10.1073/pnas.0803650105</A>]['08].

%A J. S. Kong
%A N. Sarshar
%A V. P. Roychowdhury
%T Experience versus talent shapes the structure of the web
%J PNAS
%V ?
%P ?
%D 2008
%K PNAS, jrnl, c2008, c200x, c20xx, www, world wide web, new page, pages, graph,
   link, links
%X "...the overall structure of the web is defined by an intricate interplay
   between experience or entitlement of the pages (as measured by the # of
   inbound hyperlinks a page already has), inherent talent or fitness of the
   pages (as measured by the likelihood that someone visiting the page would
   give a hl. to it), & the continual high rates of birth & death of pages
   ...the web is conservative in judging talent & the overall fitness distn is
   exponential, showing low variability. The small variance in talent, however,
   is enough to lead to experience distributions with high variance: The
   preferential attachment mechanism amplifies these small biases & leads to
   heavy-tailed power-law (PL) inbound degree distributions ...  [as] we observe
   in high-mobility & meritocratic societies: People with entitlement continue
   to have access to the best resources, but there is just enough screening for
   fitness that allows for talented winners to emerge & join the ranks of the
   leaders. ... the fitness estimates have potential practical applications in
   ranking query results."  Online Sep 2008,
   [<A HREF="http://dx.doi.org/10.1073/pnas.0805921105">doi:10.1073/pnas.0805921105</A>]['08].

%A Z. Wu
%A H. Chen
%T Semantic Grid: Model, Methodology, and Applications
%I SpringerVerlag
%S Adv. Topics in Sci. and Technology in China
%P 500
%D 2008
%K book, c2008, c200x, c20xx, web, grid, computing
%X 1st ed, us$212 ; uk us isbn:3540794530; uk us isbn13:978-3540794530.

%A B. A. Huberman
%A D. M. Romero
%A F. Wu
%T Crowdsourcing, attention and productivity
%M SEP
%D 2008
%K TR, c2008, c200x, c20xx, zz1008, YouTube, You Tube, uTube, crowd sourcing,
   crowdsourcing, video, videos, upload, uploading, human behaviour, society,
   social web site, sites, community, glory, fame, www
%X "The tragedy of the digital commons does not prevent the copious voluntary
   production of content that one witnesses in the web. We show through an
   analysis of a massive data set from YouTube that the productivity exhibited
   in crowdsourcing exhibits a strong positive dependence on attention, measured
   by the # of downloads. Conversely, a lack of attention leads to a decrease
   in the # of videos uploaded & the consequent drop in productivity, which in
   many cases asymptotes to no uploads whatsoever. Moreover, uploaders compare
   themselves to others when having low productivity & to themselves when
   exceeding a threshold."
   [<A HREF="http://arxiv.org/abs/0809.3030v1">@arxiv</A>]['08].
   [<A HREF="http://www.hpl.hp.com/research/idl/people/huberman/">auth1@hp</A>]['08].

%A C. Kanich
%A C. Kreibich
%A K. Levchenko
%A B. Enright
%A G. M. Voelker
%A V. Paxson
%A S. Savage
%T Spamalytics: An empirical analysis of spam marketing conversion
%J CACM
%V 52
%N 9
%P 99-107
%M SEP
%D 2009
%K jrnl, cacm, c2009, c200x, c20xx, zz0310, spam, ad, ads, advert, marketing,
   click through, conversion rate, junk email, mail, filter, botnet, botnets,
   zombie, trojan, malware
%X "... Using a parasitic infiltration of an existing botnet's infrastructure,
   we analyze two spam campaigns: one designed to propagate a malware Trojan,
   the other marketing online pharmaceuticals. For nearly a half billion spam
   emails we identify the number that are successfully delivered, the number
   that pass through popular antispam filters, the number that elicit user
   visits to the advertised sites, and the number of "sales" and "infections"
   produced."
   -- [<A HREF="http://dx.doi.org/10.1145/1562164.1562190">doi:10.1145/1562164.1562190</A>]['10].
   [Also search for: spam email].

%A D. Hansen
%A B. Shneiderman
%A M. A. Smith
%T Analyzing Social Media Networks with NodeXL: Insights from a
   Connected World
%I MorganKaufmann
%P 304
%M SEP
%D 2010
%K book, text, c2010, c201x, c20xx, zz1210, NodeXL, Excel, Microsoft,
   SNA, analysis, www, web, social media, network
%X "... Microsot's NodeXL is a free, open-source SNA plug-in for use with
   Excel. It provides graphical representation of relationships of complex
   networked data. ..."
   1st ed 2010; pb us$30; uk us isbn:0123822297; uk us isbn13:978-0123822291.
   (And nodeXL@[<A HREF="http://nodexl.codeplex.com/">codeplex</A>][11'10].)

%A J. Bollen
%A H. Mao
%A X.-J. Zeng
%T Twitter mood predicts the stock market
%J arXiv
%M OCT
%D 2010
%O J. Comp. Sci., 2(1), 1-8, March 2011
%K TR, c2010, c201x, c20xx, zz0512, Twitter, tweet, tweets, www, web, internet,
   social media, stock market, share, shares, investment, investing, prediction,
   Dow Jones Industrial Average, DJIA, mood, moods, OpinionFinder, GPOMS
%X "... investigate whether measurements of collective mood states derived from
   large-scale Twitter feeds are correlated to the value of the Dow Jones
   Industrial Average (DJIA) over time. ...  ... investigate the hypothesis that
   public mood states, as measured by the OpinionFinder and GPOMS mood time
   series, are predictive of changes in DJIA closing values. ... indicate that
   the accuracy of DJIA predictions can be sig. improved by the inclusion of
   specific public mood dimensions but not others. We find an accuracy of 87.6%
   in predicting the daily up and down changes in the closing values of the
   DJIA and a reduction of the Mean Average Percentage Error by more than 6%."
   -- 1010.3003@[<A HREF="http://arxiv.org/abs/1010.3003">arXiv</A>]['12], and
   JCS [<A HREF="http://dx.doi.org/10.1016/j.jocs.2010.12.007">doi:10.1016/j.jocs.2010.12.007</A>]['12].

%A J. Brockman
%T Is the Internet Changing the Way You Think?: The Net's Impact on
   Our Minds and Future
%I Harper
%P 448
%D 2011
%K book, text, c2011, c201x, c20xx, zz0211, internet, www, web, think, thought,
   human behaviour, technology, society, social
%X 1st ed 2011; pb us$9; uk us isbn:0062020447; uk us isbn13:978-0062020444.
   "... [Q] posed to more than 150 of the world's most influential minds. ..."

%A M. Chorvost
%T World Wide Mind: The Coming Integration of Humanity, Machines, and
   the Internet
%K FreePress
%P 256
%D 2011
%K book, c2011, c201x, c20xx, www, web, internet, cyber, human, future, implant,
   computers
%X 1st ed 2011; hb us$15; uk us isbn:1439119147; uk us isbn13:978-1439119143.

%A N. Naveed
%A T. Gottron
%A J. e Kunegis
%A A. C. Alhadi
%T Bad news travel fast: A content-based analysis of interestingness on Twitter
%J WebSci '11
%I ACM
%P ?
%M JUN
%D 2011
%K conf, WebSci, WebSci11, www, c2011, c201x, c20xx, zz0711, twitter, twit, web,
   tweet, tweets, retweet, Xtwitter, forward, tweeting, news, interesting
%X "...  analyze a set of high- and low-level content-based features on several
   large collections of Twitter messages. We train a prediction model to
   forecast for a given tweet its likelihood of being retweeted based on its
   contents. From the parameters learned by the model we deduce what are the
   influential content features that contribute to the likelihood of a retweet.
   As a result we obtain insights into what makes a message on Twitter worth
   retweeting and, thus, interesting."
   -- [<A HREF="http://www.websci11.org/fileadmin/websci/Papers/50_paper.pdf">www</A>]['11].

%A S. Fulton
%A J. Fulton
%T HTML5 Canvas
%I OReilly
%P 652
%D 2011
%K book, text, c2011, c201x, c20xx, HTML, HTML5, canvas, SVG, drawing, media,
   interactive, animation, graphics, web page, www, markup, language,
   web design, PhoneGap
%X 1st ed 2011; pb us$22; uk us isbn:144939390X; uks us isbn13:978-1449393908.
   " . Create and modify 2D drawings, text, and bitmap images
     . Incorporate and manipulate video, and add audio
     . Build a basic framework for creating a variety of games on Canvas
     . Use bitmaps and tile sheets to develop animated game graphics
     . Go mobile: port Canvas applications to iPhone with PhoneGap
     . Explore ways to use Canvas for 3D and multiplayer game applications ..."
   [Also search for: HTML5 www].

%A R. Cecco
%T Supercharged JavaScript Graphics: with HTML5 canvas, jQuery, and More
%I OReilly
%P 280
%M AUG
%D 2011
%K book, text, c2011, c201x, c20xx, HTML, HTML5, canvas, SVG, drawing, media,
   JavaScript, DHTML, jQuery, PhoneGap, www, markup, web
%X 1st ed 2011; pb us$22; uk us isbn:1449393632; uk us isbn13:978-1449393632.
   " . Tackle JavaScript optimization and understand how it impacts performance
     . Create fast-moving graphics by combining old-school DHTML with jQuery
     . Learn advanced UI techniques using the jQuery UI and Ext JS libraries
     . Build games with collision detection, object handling, and
       JavaScript scrolling techniques
     . Master HTML5 Canvas basics for drawings, fills, bitmaps, animation, ...
     . Create applications for the small screen with jQuery Mobile & PhoneGap
     . Use Google's data visualization tools [for] interactive dashboards ..."
   [Also search for: HTML5 www].

%A C. Chen
%A K. Wu
%A V. Srinivasan
%A X. Zhang
%T Battling the internet water army: Detection of hidden paid posters
%J arXiv
%M NOV
%D 2011
%K report, TR, c2011, c201x, c20xx, zz0112, www, internet, web, astroturfing,
   water army, reports, recommendations, product, fake, review, reviews,
   comments, scam, scams, paid, online, posters, China, Chinese, PRC, .cn
%X "... study to help distinguish a special group of online users, called hidden
   paid posters, or termed "Internet water army" in China, from the legitimate
   ones  ...  may create a sig. -ve effect on the online communities ..."
   -- [<A HREF="http://arxiv.org/abs/1111.4297">arXiv</A>]['12].
   [Also search for: fake review www].

%T The Reputation Society: How Online Opinions Are Reshaping the Offline World
%E H Massum
%E M. Tovey
%I MITpress
%P 208
%M JAN
%D 2012
%K book, c2012, c201x, c20xx, zz0212, reputation, opinion, influence, internet,
   www, review, sentiment, open access, privacy, facebook, profile
%X 1st ed 2012, hb us$28; uk us isbn:0262016648; uk us isbn13:978-0262016643.
   "... online reputation systems serve as filters for information overload. ...
   experts discuss the benefits & risks of such online tools. ... perspectives
   that range from philanthropy & open access to science & law, addressing
   reputation systems in theory & practice. ..."
   [Also search for: influence network].

%A H. Rheingold
%T Net Smart: How to Thrive Online
%I MITpress
%P 272
%M MAR
%D 2012
%K book text, c2012, c201x, c20xx, zz0612, internet, www, web, online,
   infobabble, social media
%X 1st ed 2012; hb us$16; uk us isbn:0262017458; uk us isbn13:978-0262017459.
   "... outlines five fundamental digital literacies, online skills that will
   help us do this: attention, participation, collaboration, critical
   consumption of information, and network smarts. ..."

%A J. Ugander
%A L. Backstrom
%A C. Marlow
%A J. Kleinberg
%T Structural diversity in social contagion
%J PNAS
%V 109
%N 14
%P ?-?
%M APR
%D 2012
%K jrnl, PNAS, c2012, c201x, c20xx, zz0412, social, society, media, facebook,
   viral, influence, spread, www, web, network, internet, human behaviour,
   structural diversity
%X "... Trad.models of social contagion have been based on physical analogies
   with biological contagion, in which the prob. that an individual is affected
   by the contagion grows monotonically with the size of his or her 'contact
   neighborhood' - the # of affected individuals ... in contact. ...
   Here we study this question by analyzing the growth of Facebook, a rare e.g.
   of a social process with genuinely global adoption. We find that the prob.
   of contagion is tightly controlled by the # of connected components in an
   individual's contact n.hood, rather than by the actual size of the n.hood.
   Surprisingly, once this 'structural diversity' is controlled for, the size of
   the contact n.hood is in fact generally a -ve predictor of contagion. More
   broadly ... show how data at the size & resolution of the FB n/wk make
   poss. the identification of subtle structural signals that go undetected
   at smaller scales yet hold pivotal predictive roles for the outcomes of
   social processes."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1116502109">doi:10.1073/pnas.1116502109</A>]['12].
   [Also search for: influence network].

%A M. Ott
%A C. Cardie
%A J. Hancock
%T Estimating the prevalence of deception in online review communities
%J World Wide Web Conf
%W Lyon, .fr
%P ?-?
%M APR
%D 2012
%K conf, c2012, c201x, c20xx, fake, review, water army, bot, bots,
   posters, comments, spam, www, web
%X [<A HREF="http://www2012.wwwconference.org/">conf</A>][16-20/4/2012].
   [Also search for: fake review www].

%A A. Mukherjee
%A B. Liu
%T Spotting fake reviewer groups in consumer reviews
%J World Wide Web Conf
%W Lyon, .fr
%I ACM
%P ?-?
%M APR
%D 2012
%K conf, c2012, c201x, c20xx, zz0412, fake, review, water army, bot, bots,
   posters, comments, spam, www, web
%X "... method 1st uses a frequent itemset mining method to find a set of
   candidate groups. It then uses several behavioral models derived from the
   collusion phenomenon among fake reviewers & relation models based on the
   relationships among groups, individual reviewers, & products they reviewed
   to detect fake reviewer grps. Additionally, we also built a labeled dataset
   of fake reviewer grps. Although labeling individual fake reviews & reviewers
   is v.hard, to our surprise labeling fake reviewer grps is much easier. ..."
   -- [<A HREF="http://dx.doi.org/10.1145/2187836.2187863">doi:10.1145/2187836.2187863</A>]['12],
   in [<A HREF="http://www2012.wwwconference.org/">conf</A>][16-20/4/2012],
   uk us isbn13:978-1450312295.
   [Also search for: fake review www].

%A S. Aral
%A D. Walker
%T Identifying influential and susceptible members of social networks
%J Science
%M JUN
%D 2012
%K c2012, c201x, c20xx, zz0712, social media, facebook, influence, marketing,
   susceptibility, men, women
%X "Identifying social influence in networks is critical to understanding how
   behaviors spread. ...  Estimation in a representative sample of 1.3 million
   Facebook users showed that younger users are more susceptible than older
   users, men are more influential than women, women influence men more than
   they influence other women, and married individuals are the least susceptible
   to influence in the decision to adopt the product we studied. Analysis of
   influence and susceptibility together with network structure reveals that
   influential individuals are less susceptible to influence than non-
   -influential individuals and that they cluster in the network, which suggests
   that influential people with influential friends help spread this product."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1215842">doi:10.1126/science.1215842</A>]['12], 32 refs.
   [Also search for: influence network].

%A P. Ciancarini
%A A. Di Iorio
%A L. Furini
%A F. Vitali
%T High-quality pagination for publishing
%J SPE
%V 42
%N 6
%P 733-751
%M JUN
%D 2012
%K jrnl, SPE, c2012, c201x, c20xx, zz0812, pagination, page, pages, break,
   breaks, document, formatting, www, XSL FO, XSLFO, FOP, FOPplus, diIorio
%X "... presents a page-breaking alg. that extends the original Knuth & Plass
   line-breaking approach & produces high-quality documents without unwanted
   empty areas. ... delaying the definitive choice of breaks in the line-
   -breaking process in order to provide a larger set of alternatives ...
   The alg. also allows users to decide the set of properties to be adjusted for
   pagination & their variation ranges. An application of the alg. to XSL-FO is
   also presented, with an extension of the language that allows users to drive
   the pagination process. The tool, named FOP+, is a customized version of the
   open-source Apache Formatting Objects Processor formatter."   [32 refs].
   -- [<A HREF="http://dx.doi.org/10.1002/spe.1096">doi:10.1002/spe.1096</A>]['12].
   [Also search for: Knuth Plass].

%A P. Olson
%T We Are Anonymous: Inside the Hacker World of LulzSec, Anonymous, and the
   Global Cyber Insurgency
%I LittleBrown
%P 512
%M JUN
%D 2012
%K book, c2012, c201x, c20xx, zz1113, hackers, hacking, anonymous, lulzsec,
   computer, networks, internet, web, www, security, 4Chan, wikileaks,
   hacked, scientology
%X 1st ed 2012; hb us$18; uk us isbn:0316213543; uk us isbn13:978-0316213547.
   "... how a loosely assembled group of hackers scattered across the globe
   formed a new kind of insurgency, seized headlines, and tortured the feds -
   and the ultimate betrayal that would eventually bring them down.  ... goes
   behind the headlines and into the world of Anonymous and LulzSec with
   unprecedented access, drawing upon hundreds of conversations with the hackers
   themselves, including exclusive interviews with all six core members of
   LulzSec. ..."

%A J. M. Rao
%A D. H. Reiley
%T The economics of spam
%J J. Economic Perspectives
%V 26
%N 3
%P 87-110
%D 2012
%K jrnl, c2012, c201x, c20xx, zz0713, spam, scam, email, web, www, spammer,
   botnets, internet, spamming, cost, costs, nigerian
%X "We est. that American firms & consumers experience costs of almost
   $20 billion annually due to spam. ... spammers ... collect gross worldwide
   revenues on the ~ $200 million pa. Thus, the 'externality ratio' of external
   costs to internal benefits for spam is ~ 100:1. ... we start by describing
   the history of the market for spam, highlighting the strategic cat-&-mouse
   game between spammers & email providers. ... market structure for spamming
   has evolved from a diffuse n/wk of indep. spammers running their own online
   stores to a highly specialized industry featuring a well-organized n/wk of
   merchants, spam distributors (botnets), & spammers (or 'advertisers'). ...
   put the spam market's externality ratio of 100 into context by comparing it
   to other activities with -ve externalities. ... evaluate various policy
   proposals designed to solve the spam problem, cautioning that these proposals
   may err in assuming away the spammers' ability to adapt."
   -- [<A HREF="http://dx.doi.org/10.1257/jep.26.3.87">doi:10.1257/jep.26.3.87</A>]['13].
   [Also search for: spam email].

%A M. Chiang
%T Networked Life: 20 Questions and Answers
%I CUP
%P 488
%M SEP
%D 2012
%K book, text, CUP, c2012, c201x, c20xx, zz1212, network, internet, www, web,
   computing, online, wireless, communications, technology
%X 1st ed 2012; hb us$38; uk us isbn:1107024943; uk us isbn13:978-1107024946.
   "... explores the technology behind the multi-trillion dollar Internet
   and wireless industries. ..."

%A M. Kosinski
%A D. Stillwell
%A T. Graepel
%T Private traits and attributes are predictable from digital records of human
   behavior
%J PNAS
%V ?
%P ?-?
%D 2013
%K jrnl, PNAS, c2013, c201x, c20xx, zz0418, facebook, like, likes, behaviour,
   trait, personality, social media, privacy
%X "Likes, can be used to automatically and accurately predict a range of
   highly sensitive personal attributes including: sexual orientation,
   ethnicity, religious and political views, personality traits, intelligence,
   happiness, use of addictive substances, parental separation, age, and gender.
   The analysis presented is based on a dataset of over 58,000 volunteers who
   provided their Facebook Likes, detailed demographic profiles, and the results
   of several psychometric tests. The proposed model uses dimensionality
   reduction for preprocessing the Likes data, which are then entered into
   logistic/linear regression to predict individual psychodemographic profiles
   from Likes. The model correctly discriminates between homosexual and
   heterosexual men in 88% of cases, African Americans and Caucasian Americans
   in 95% of cases, and between Democrat and Republican in 85% of cases. For
   the personality trait 'Openness,' prediction accuracy is close to the
   test - retest accuracy of a std personality test. We give examples of
   associations between attributes and Likes and discuss implications for
   online personalization and privacy."  (online Mar 2013)
   -- [<A HREF="https://doi.org/10.1073/pnas.1218772110">doi:10.1073/pnas.1218772110</A>]['18].
   [Also search for: facebook Kogan].

%A R. Stone
%T A Call to Cyber Arms
%J Science
%V 339
%N 6123
%P 1026-1027
%M MAR
%D 2013
%K news, c2013, c201x, c20xx, zz0313, cyber, warfare, cyberweapon, espionage,
   threat, threats, eWarfare, army, mil, defense, spying, China, PLA, PRC, cn,
   USA, internet, hackers, rootkit, exploit, exploits
%X "China's extensive cyber research activities and allegations over cyber
   espionage have put the United States on high alert. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.339.6123.1026">doi:10.1126/science.339.6123.1026</A>]['13].

%A H. Lakkaraju
%A J. McAuley
%A J. Leskovec
%T What's in a name? Understanding the interplay between titles, content, and
   communities in social media
%J Proc. 7th Int. AAAI Conf. on Weblogs and Social Media
%I AAAI
%P ?-?
%M JUL
%D 2013
%K conf, c2013, c201x, c20xx, zz0713, www, internet, hit, blog, weblog, viral,
   content, title, description, interest, reddit, resubmissions
%X "Creating, placing, & presenting social media content is a difficult problem.
   ... the quality of the content itself, several factors such as the way the
   content is presented (title), the community it is posted to, whether it has
   been seen before, & the time it is posted determine its success. ...
   interactions between these factors. [Eg] the language of the title should be
   targeted to the community where the content is submitted, yet it should also
   highlight the distinctive nature of the content. ... examine how ... interact
   to determine the popularity of social media content. ... studying
   resubmissions, i.e., content that has been submitted multiple times, with
   multiple titles, to multiple different communities. Such data allows us to
   'tease apart' the extent to which each factor influences the success of that
   content. ..."
   -- pdf@[<A HREF="http://www.aaai.org/ocs/index.php/ICWSM/ICWSM13/paper/view/6085">conf</A>]['13].

%A L. Muchnik
%A S. Aral
%A S. J. Taylor
%T Social influence bias: A randomized experiment
%J Science
%V 341
%N 6146
%P 647-651
%M AUG
%D 2013
%K jrnl, c2013, c201x, c20xx, zz0813, social media, internet, www, web site,
   aggregation, Reddit, like, likes, dislike, upVote, downVote, rating, ratings,
   voting, positive herding, herd, effect, sockpuppet, bias, human beahviour
%X "... aggregated opinions of others to make decisions. ... designed & analyzed
   a large-scale randomized exp. on a social news aggregation Web site to
   investigate whether knowledge of such aggregates distorts decision-making.
   Prior ratings created sig.bias in individual rating behavior, & +ve & -ve
   social influences created asymmetric herding effects. Whereas -ve social i.
   inspired users to correct manipulated ratings, +ve social i. increased the
   likelihood of +ve ratings by 32% & created accumulating +ve herding that
   increased final ratings by 25% on avg.. This +ve herding was topic-dependent
   & affected by whether individuals were viewing the opinions of friends or
   enemies. A mixture of changing opinion & greater turnout under both
   manipulations together with a natural tendency to up-vote on the site
   combined to create the herding effects. ..."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1240466">doi:10.1126/science.1240466</A>]['13].
   And, "The final score of a post on an aggregation site was increased by an
   average of 25% if it got a single, random up-vote when first published."
   -- [<A HREF="http://www.theguardian.com/science/2013/aug/08/snowball-effect-skews-rating-systems">The G</A>]['13].

%A E. Kross
%A et al ...
%A O. Ybarra
%T Facebook use predicts declines in subjective well-being in young adults
%J PLoS ONE
%V 8
%N 8
%P e69841
%M AUG
%D 2013
%K jrnl, eJrnl, c2013, c201x, c20xx, zz0813, internet, www, Facebook, use,
   social media, online, networks, psychology, happiness, well being, wellbeing
%X "... addressed this issue using experience-sampling, the most reliable method
   for measuring in-vivo behavior and psychological experience. We text-messaged
   people five times per day for two-weeks to examine how Facebook use
   influences the two components of subjective well-being: how people feel
   moment-to-moment and how satisfied they are with their lives. Our results
   indicate that Facebook use predicts negative shifts on both of these
   variables over time. The more people used Facebook at one time point, the
   worse they felt the next time we text-messaged them; the more they used
   Facebook over two-weeks, the more their life satisfaction levels declined
   over time. Interacting with other people 'directly' did not predict these
   negative outcomes. ..."
   -- [<A HREF="http://dx.doi.org/10.1371/journal.pone.0069841">doi:10.1371/journal.pone.0069841</A>]['13].
   [Also search for: internet well being].

%A D. Eggers
%T The Circle
%I KnopfPubl
%P 504
%M OCT
%D 2013
%K book, novel, c2013, c201x, c20xx, zz0114, fiction, scifi, internet, www,
   theCircle, TruYou, zings, social media, meta, facebook, likes, posts,
   twitter, workplace, privacy, theft, secrecy, secret, secrets, lies,
   Silicon valley, the hive, film, movie
%X [Secrets are lies. Sharing is caring. Privacy is theft.]
   1st ed 2013; hb us$14; uk us isbn:0385351399; uk us isbn13:978-0385351393.
   '... When Mae Holland takes a job at the Circle, a tech giant with a utopian
   culture & cultlike following (Eggers didn't call it Schmoogle, but may as
   well have), she quickly loses sight of her friends, family, & sense of self
   in favor of professional success & social acceptance. As her Circle star
   rises, Mae succumbs to the corporate code of full disclosure, eventually
   agreeing to "go transparent" & let the public watch - & comment on - her
   every move. "Privacy is theft," decrees the company motto; "Secrets are
   lies." It's not subtle, but neither were "Harrison Bergeron" & 1984, and in
   its best moments The Circle is equally terrifying. Let's just hope it's not
   prescient. -- Mia Lipman'.
   And a review by Margaret Attwood [<A HREF="https://www.nybooks.com/articles/2013/11/21/eggers-circle-when-privacy-is-theft/">www</A>]['18].
   Also a film (2017).
   (As of 2018: Some of the ideas have come to pass or are coming, esp with
   cn's 'social credit' system, but the author didn't forsee Putin & Trump.)

%A I. Eyal
%A E. G. Sirer
%T Majority is not enough: Bitcoin mining is vulnerable
%J arXiv
%M NOV
%D 2013
%K arXiv, TR, c2013, c201x, c20xx, zz1113, bitcoin, bitcoins, virtual currency,
   digital, network, mining, miners, security, cryptocurrency, protocol,
   incentive compatible, attack, selfish, collusion
%X "The Bitcoin cryptocurrency records its transactions in a public log called
   the blockchain. Its security rests critically on the distributed protocol
   that maintains the b., run by participants called miners. Conventional wisdom
   asserts that the protocol is incentive-compatible & secure against colluding
   minority groups, i.e., it incentivizes miners to follow the protocol as
   prescribed.  We show that the Bitcoin protocol is not incentive-compatible.
   We present an attack with which colluding miners obtain a revenue larger than
   their fair share. This attack can have sig. consequences for Bitcoin:
   Rational miners will prefer to join the selfish miners, & the colluding group
   will increase in size until it becomes a majority. At this point, the Bitcoin
   system ceases to be a decentralized currency.  Selfish mining is feasible for
   any group size of colluding miners. We propose a practical mod. to the B.
   protocol that protects against selfish mining pools that command less than
   1/4 of the resources. This threshold is lower than the wrongly assumed 1/2
   bound, but better than the current reality where a group of any size can
   compromise the system."
   -- 1311.0243@[<A HREF="http://arxiv.org/abs/1311.0243">arXiv</A>]['13].
   Also see [<A HREF="http://bitcoin.org/en/">bitcoin.org</A>]['13],
   bitcoin@[<A HREF="http://en.wikipedia.org/wiki/Bitcoin">wikip</A>]['13],
   [<A HREF="http://www.bbc.co.uk/news/technology-24818975">bbc</A>][5/11/2013].

%A A. E. Maewick
%T Status Update
%I YaleUP
%P 368
%M NOV
%D 2013
%K book, text, c2013, c201x, c20xx, zz0514, internet, web 2.0, 2, web2, web2.0,
   social media, facebook, twitter, tweet, app, apps, self-promotion, fame,
   micro-celebrity, celebrity, attention seeking, human behaviour, ethnography,
   culture, gender, online, tech
%X 1st ed 2013; hb us$20; us isbn:0300176724; us isbn13:978-0300176728.
   "... web 2.0 only encouraged a preoccupation with status & attention. ...
   explores the culture & ideology of San Francisco's tech community in the
   period between the dot com boom & the App store ...  argues that early
   revolutionary goals have failed to materialize: while many continue to view
   social media as democratic, these technologies instead turn users into
   marketers & self-promoters, & leave technology companies poised to violate
   privacy & to prioritize profits over participation. ...  self-branding,
   micro-celebrity, & life-streaming - ... did not provide a cultural revoln,
   but only furthered inequality & reinforced traditional social stratification,
   demarcated by race, class, & gender."

%A L. Olejnik
%A T. Minh-Dung
%A C. Castelluccia
%T Selling off privacy at auction
%I hal inria
%R hal-00915249
%M DEC
%D 2019
%K TR, c2013, c201x, c20xx, zz0919, social media, google, privacy, advertising,
   ads, adverts, user, data, protection, targetting, targetted,
   real time bidding, RTB, cookies, www, HREF, web, tracking, users, internet
%X "Real-Time Bidding (RTB) and Cookie Matching(CM) are transforming the
   advertising landscape to an extremely dynamic market and make targeted
   advertising considerablypermissive. The emergence of these technologies
   allows companies to exchange user data ... We expose a design characteristic
   of RTB systems to observe the prices which advertisers pay for serving ads to
   Web users.We leverage this feature and provide important insights into these
   prices by analyzing different user profiles and visiting contexts. Our study
   shows the variation of prices accordingto context information including
   visiting site, time and user's physical location. ... We show that user's
   browsing history elts are routinely being sold off for less than $0.0005."
   -- [<A HREF="https://hal.inria.fr/file/index/docid/915249/filename/SellingOffPrivacyAtAuction.pdf">inria</A>]['19].
   Also see [<A HREF="https://lukaszolejnik.com/rtbdesc">www</A>]['19]
   and the [<A HREF="https://www.bbc.com/news/technology-49593830">bbc</A>][6/9/2019].
   [Also search for: internet privacy].

%A Y.-H. Eom
%A P. Aragon
%A D. Laniado
%A A. Kaltenbrunner
%A S. Vigna
%A D. L. Shepelyansky
%T Interactions of cultures and top people of Wikipedia from ranking of
   24 language editions
%J arXiv
%P 31
%M MAY
%D 2014
%K arXiv, TR, c2014, c201x, c20xx, zz0614, google, PageRank, 2DRank, CheiRank,
   web, www, network, influential, influence, fame, famous, people, cultural,
   culture, society, gender, wikipedia, edition
%X "... investigate interwinements between cultures. ... apply two methods,
   Markov chains & Google matrix, for the analysis of the hyperlink networks
   of 24 Wikipedia language editions ... construct a n/wk of cultures &
   identify the most influential cultures according to such n/wk." [41 refs.]
      "Table 2, English wikip:
         PageRank, 1 Napoleon, 2 Barack Obama, 3 Carl Linnaeus.
         2Drank,   1 Frank Sinatra, 2 Michael Jackson, ... ."
   -- 1405.7183@[<A HREF="http://arxiv.org/abs/1405.7183">arXiv</A>]['14].

%A A. D. I. Kramer
%A J. E. Guillory
%A J. T. Hancock
%T Experimental evidence of massive-scale emotional contagion through
   social networks
%J PNAS
%V 111
%N 24
%P 8788-8790
%M JUN
%D 2014
%K jrnl, PNAS, c2014, c201x, c20xx, zz0714, social media, www, internet, web,
   Facebook, network, posts, news feed, mood, emotion, experiment, stats,
   research, ethics, psychological, manipulation
%X "Emotional states can be transferred to others via emotional contagion,
   leading people to experience the same emotions without their awareness. ...
   In an experiment with people who use Facebook, we test whether e.c. occurs
   outside of in-person interaction between individuals by reducing the amount
   of emotional content in the News Feed. When +ve expressions were reduced,
   people produced fewer +ve posts & more -ve posts; when -ve expressions were
   reduced, the opposite pattern occurred. ... indicate that emotions expressed
   by others on Facebook influence our own emotions, constituting experimental
   evidence for massive-scale c. via social n/ws. ... also suggests that, in
   contrast to prevailing assumptions, in-person interaction & nonverbal cues
   are not strictly nec. for emotional contagion, & that the observation of
   others' +ve experiences constitutes a +ve experience for people."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1320040111">doi:10.1073/pnas.1320040111</A>]['14],
      [<A HREF="http://www.pnas.org/content/111/24/8788.full">pnas</A>]['14].
   (Was this experiment ethical? Also see The G. [<A HREF="http://www.theguardian.com/technology/2014/jun/29/facebook-users-emotions-news-feeds">www</A>]['14].)
   [Also search for: influence network].

%A G. Acar
%A C. Eubank
%A S. Englehardt
%A M. Juarez
%A A. Narayanan
%A C. Diaz
%T The Web never forgets: Persistent tracking mechanisms in the wild
%I kuleuven.be & Princeton U.
%M JUL
%D 2014
%K TR, c2014, c201x, c20xx, zz0714, internet, www, privacy, security, tracking,
   web, browser, browsing, history, canvas fingerprinting, evercookie,
   evercookies, cookie, cookies, syncing, evercookies, respawning,
   Adobe Flash, LSOs, localStorage, IndexDB, addThis, weibo, sina, yandex
%X "... studies of three advanced web tracking mechanisms - canvas
   fingerprinting, evercookies & use of 'cookie syncing' in conjunction with
   evercookies. ... a single lapse in judgement can shatter privacy defenses.
   This suggests that even sophisticated users face great difficulties in
   evading tracking techniques." [47 refs.]
   -- pdf@[<A HREF="https://securehomes.esat.kuleuven.be/~gacar/persistent/the_web_never_forgets.pdf">k'leuven.be</A>]['14],
      auth1@[<A HREF="https://securehomes.esat.kuleuven.be/~gacar/persistent/">k'leuven.be</A>]['14].
   [Adobe Flash really is a bad thing!]

%A X. Dong
%A E. Gabrilovich
%A G. Heitz
%A W. Horn
%A N. Lao
%A K. Murphy
%A T. Strohmann
%A S. Sun
%A W. Zhang
%T Knowledge vault: A web-scale approach to probabilistic knowledge fusion
%J KDD
%M AUG
%D 2014
%K conf, KDD, c2014, c201x, c20xx, zz0814, knowledge vault, data mining, AI, II,
   google
%X "... we need to explore automatic methods for constructing knowledge bases.
   Previous approaches have primarily focused on text-based extraction, which
   can be v.noisy. ... introduce Knowledge Vault, a Web-scale probabilistic
   knowledge base that combines extractions from Web content (obtained via
   analysis of text, tabular data, page structure, & human annotations) with
   prior knowledge derived from existing knowledge repositories. We employ
   supervised m/c learning methods for fusing these distinct info. sources. The
   Knowledge Vault is substantially bigger than any prev. published structured
   knowledge repository, & features a probabilistic inference system that
   computes calibrated probabilities of fact correctness. We report the results
   of multiple studies that explore the relative utility of the different
   information sources & extraction methods"
   -- pdf@[<A HREF="http://www.cs.cmu.edu/~nlao/publication/2014.kdd.pdf">cmu</A>]['14].

%A G. King
%A J. Pan
%A M. E. Roberts
%T Reverse-engineering censorship in China: Randomized experimentation and
   participant observation
%J Science
%V 345
%N 6199
%P ?-?
%M AUG
%D 2014
%K jrnl, c2014, c201x, c20xx, zz0814, China, Chinese, state, communist party,
   PRC, censorship, censor, great firewall, government, social media, blog,
   blogs, texts, posts, internet, www, politics
%X "... We conducted the first large-scale experimental study of censorship by
   creating accounts on numerous social media sites, randomly submitting
   different texts, & observing from a worldwide n/wk of computers which texts
   were censored & which were not. We also supplemented interviews with
   confidential sources by creating our own social media site, contracting with
   Chinese firms to install the same censoring technologies as existing sites, &
   - with their s/w, documentation, & even customer support - reverse-eng. how
   it all works. Our results offer rigorous support for the recent hyp. that
   criticisms of the state, its leaders, & their policies are published, whereas
   posts about real-world events with collective action potential are censored."
   -- [<A HREF="http://dx.doi.org/10.1126/science.1251722">doi:10.1126/science.1251722</A>]['14].

%A E. Uzun
%A E. S. Guner
%A Y. Kilicaslan
%A T. Yerlikaya
%A H. V. Agun
%T An effective and efficient Web content extractor for optimizing the
   crawling process
%J SPE
%V 44
%N 10
%P 1181-1199
%M OCT
%D 2014
%K jrnl, SPE, c2014, c201x, c20xx, zz1014, web, www, html, page, pages,
   iCrawler, bot, crawler, crawling, content
%X "...  iCrawler (intelligent crawler), the backbone of which is a Web content
   extractor that automatically pulls content out of seven different blocks:
   menus, links, main texts, headlines, summaries, additional necessaries, and
   unnecessary texts from Web pages. ..."
   -- [<A HREF="http://dx.doi.org/10.1002/spe.2195">doi:10.1002/spe.2195</A>]['14].

%A D. Keats Citron
%T Hate Crimes in Cyberspace
%I HarvardUP
%P 352
%M SEP
%D 2014
%K book, text, c2014, c201x, c20xx, zz1114, internet, nasty, hate, social media,
   troll, trolls, women, rights, bullying, mysogyny, threats, abuse,
   harrassment, crime, law, legal, online
%X "... investigation of a problem that is too often trivialized by lawmakers
   and the media, D.K.C. exposes the startling extent of personal cyber-attacks
   and proposes practical, lawful ways to prevent and punish online
   harassment. ..."
   1st ed 2014; hb us$22; uk us isbn:0674368290; uk us isbn13:978-0674368293.
   [Also search for: nasty social media].

%A J. Mervis
%T An internet research project draws conservative ire
%J Science
%V 346
%N 6210
%P 686-687
%M NOV
%D 2014
%K news, views, c2014, c201x, c20xx, zz1114, Truthy, internet, www, web, HREF,
   online, social media, project, memes, virality, Twitter, tweet, tweets,
   spread, trend, trends
%X "A 4-year-old academic study of how info. spreads on Twitter has become the
   target of withering attacks from conservative bloggers & politicians. The
   Truthy project, by researchers at Indiana U. (IU), Bloomington, is part of a
   growing body of work on how online memes - messages about ideas, issues, &
   events - can shape phenomena ranging from protest movements to outbreaks of
   disease. The [NSF] is a major funder of the project, which is one elt in a
   broader initiative to understand complex, nonlinear feedback systems. But
   critics, who cite the project as an unwise use of taxpayer dollars, say
   Truthy is really an attempt by the U.S. gvmt to monitor & restrict free
   speech. IU scientists say that is a gross distortion of what they have been
   doing. "
   -- [<A HREF="http://dx.doi.org/10.1126/science.346.6210.686">doi:10.1126/science.346.6210.686</A>]['14],
      Truthy@[<A HREF="http://truthy.indiana.edu/">IU</A>]['14].

%A W. Youyou
%A M. Kosinski
%A D. Stillwell
%T Computer-based personality judgments are more accurate than those made by
   humans
%J PNAS
%V 112
%N 4
%P 1036-1040
%M JAN
%D 2015
%K jrnl, PNAS, c2015, c201x, c20xx, zz0115, Facebook, likes, digital footprint,
   social media, human, personality, traits, myPersonality, app
%X "... compares the accuracy of human & computer-based personality judgments,
   using a sample of 86,220 volunteers who completed a 100-item personality
   questionnaire. We show that (i) computer predictions based on a generic
   digital footprint (Facebook Likes) are more accurate (r=0.56) than those
   made by the participants' Facebook friends using a personality questionnaire
   (r=0.49); (ii) computer models show higher interjudge agreement; &
   (iii) computer personality judgments have higher external validity when
   predicting life outcomes such as substance use, political attitudes, &
   physical health; for some outcomes, they even outperform the self-rated
   personality scores ..."
   -- [<A HREF="http://dx.doi.org/10.1073/pnas.1418680112">doi:10.1073/pnas.1418680112</A>]['15] online Jan 2015,
   or [<A HREF="http://www.pnas.org/content/early/2015/01/07/1418680112">early</A>]['15].
   (auth2@[<A HREF="http://www.michalkosinski.com/">www</A>]['15].)
   [Also search for: myPersonality] and [also search for: facebook Kogan].

%A X. L. Dong
%A E. Gabrilovich
%A K. Murphy
%A V. Dang
%A W. Horn
%A C. Lugaresi
%A S. Sun
%A W. Zhang
%T Knowledge-based trust: Estimating the trustworthiness of web sources
%J arXiv
%M FEB
%D 2015
%K TR, c2015, c20x, c20xx, zz0415, www, web, site, google, page, rank, ranking,
   source, trust, trustworthiness, fact, correct, false, knowledge, KBT, search
%X "The quality of web sources has been traditionally evaluated using exogenous
   signals such as the hyperlink structure of the graph. We propose a new
   approach that relies on endogenous signals, namely, the correctness of
   factual information provided by the source. A source that has few false facts
   is considered to be trustworthy. The facts are automatically extracted from
   each source by information extraction methods commonly used to construct
   knowledge bases. We propose a way to distinguish errors made in the
   extraction process from factual errors in the web source per se, by using
   joint inference in a novel multi-layer probabilistic model. We call the
   trustworthiness score we computed Knowledge-Based Trust (KBT). On synthetic
   data, we show that our method can reliably compute the true trustworthiness
   levels of the sources. We then apply it to a database of 2.8B facts extracted
   from the web, & thereby estimate the trustworthiness of 119M webpages. Manual
   evaluation of a subset of the results confirms the effectiveness of the
   method."  [33 refs].
   -- 1502.03519@[<A HREF="http://arxiv.org/abs/1502.03519">arXiv</A>]['15].
   auths@google.
   (Also see pagerank@[<A HREF="https://en.wikipedia.org/wiki/PageRank">wikip</A>]['20].)

%A V. Grolmusz
%T A note on the PageRank of undirected graphs
%J IPL
%V 115
%N 5-6
%P 633-634
%M JUN-AUG
%D 2015
%K jrnl, IPL, c2015, c201x, c20xx, zz0515, Pagerank, page rank, undirected,
   graph, network, degree
%X "... PageRank is defined for directed graphs, but in some special cases
   applications for undirected gs. occur. ... it is widely - but not exclusively
   - noted that the PR for undirected gs. is proportional to the degrees of the
   vertices of the graph. We prove that statement for a particular
   personalization vector in the definition of the PR, & we also show that in
   general, the PR of an undirected g. is not exactly proportional to the degree
   distn of the g.: ... give an upper & a lower bound to the L1 norm of the
   difference of the PR & the degree distn vectors. A necessary & sufficient
   condn is also given for the PR for being proportional to the degree."
   -- [<A HREF="http://dx.doi.org/10.1016/j.ipl.2015.02.015">doi:10.1016/j.ipl.2015.02.015</A>]['15].

%A E. Bakshy
%A S. Messing
%A L. Adamic
%T Exposure to ideologically diverse news and opinion on Facebook
%J Science
%V 348
%N 6239
%P 1130-1132
%M MAY
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0515, politics, opinions, web, Facebook,
   social media, www, web, internet, ideology, news feed, filter
%X "... examined how 10.1 million U.S. Facebook users interact with socially
   shared news. We directly measured ideological homophily in friend n/ws, &
   examine the extent to which heterogeneous friends could potentially expose
   individuals to cross-cutting content. We then quantified the extent to which
   individuals encounter comparatively more or less diverse content while
   interacting via FB's algorithmically ranked News Feed, & further studied
   users' choices to click through to ideologically discordant content. Compared
   to alg. ranking, individuals' choices about what to consume had a stronger
   effect limiting exposure to cross-cutting content. "
   -- [<A HREF="http://dx.doi.org/10.1126/science.aaa1160">doi:10.1126/science.aaa1160</A>]['15].
   (There was some controversy about the method.)

%A A. Agarwal
%A et al
%T Key female characters in film have more to talk about besides men:
   Automating the Bechdel test
%J Human Language Tech.: 2015 Annual Conf. the N.Amer. Ch. of the ACL
%P 830-840
%W Denver
%M MAY
%D 2015
%K conf, c2015, c201x, c20xx, zz0322, film, movie, movies, media, www, script,
   scripts, screenplay, Hollywood, actor, women, sex, gender, role,
   Alison Bechdel, Wallace, test, bechdeltest.com
%X "The Bechdel test is a sequence of three questions designed to assess the
   presence of women in movies. ...  we present a computational approach to
   automate the task of finding whether a movie passes or fails the B.test. ...
   confirm that in movies that fail the test, women are in fact portrayed as
   less-central and less-important characters."
   -- pdf@[<A HREF="https://aclanthology.org/N15-1084.pdf">www</A>]['22].
   (Also see Alison Bechdel@[<A HREF="https://en.wikipedia.org/wiki/Alison_Bechdel">wikip</A>]['22].)

%A S. Pfeiffer
%A T. Green
%T Beginning HTML5 Media: Make the most of the new video and audio standards for
   the Web
%I Apress
%P 304
%M JUN
%D 2015
%K book, text, c2015, c201x, c20xx, zz0715, web, www, HTML, HTML5, video, audio,
   canvas, CSS, WebM, Ogg Theora codec, page, browser
%X 1st ed 2015; pb us$35; uk us isbn:1484204611; uk us isbn13:978-1484204610.
   *1. Encoding Media.
   *2. Using and Manipulating Media Elements.
   *3. The JavaScript API.
   *4. Accessibility and Internationalization of HTML5 Media.
   *5. Manipulating Media via Canvas.
   *6. Manipulating Audio Through the WebAudio API.
   [Also search for: HTML5 www].

%A R. I. M. Dunbar
%A V. Arnaboldi
%A V. Arnaboldi
%A M. Conti
%A A. Passarella
%T The structure of online social networks mirrors those in the offline world
%J Social Networks
%V 43
%P 39-47
%M OCT
%D 2015
%K c2015, c201x, c20xx, zz0116, www, web, social media, network, networks,
   facebook, like, twitter, friend, friends, acquaintance, ego, alters, layer,
   layers, Dunbar, Dunbars number
%X "We use data on frequencies of bi-directional posts to define edges (or
   relationships) in two Facebook datasets & a Twitter dataset & use these to
   create ego-centric social networks. We explore the internal structure ...
   ... The two Facebook datasets are best described by a four-layer structure &
   the Twitter dataset by a five-layer structure. The absolute sizes of these
   layers & the mean frequencies of contact with alters within each layer match
   very closely the observed values from offline networks. In addition, all
   three datasets reveal the existence of an innermost network layer at ~1.5
   alters. ..."
   -- [<A HREF="http://www.psy.ox.ac.uk/publications/524828">ox.ac</A>]['16],
      auth1@[<A HREF="https://www.psy.ox.ac.uk/team/robin-dunbar">ox.ac.uk</A>]['16],
      auth1@[<A HREF="https://en.wikipedia.org/wiki/Robin_Dunbar">wikip</A>]['16].
   (Also see,
      "... Limitations on brain capacity and free time mean
      humans can nurture no more than about 150 true friendships
      on social media, just as in real life ..."
   -- [<A HREF="http://www.abc.net.au/news/2016-01-20/150-is-the-limit-of-real-facebook-friends/7101588">abc</A>][20/1/2016].)

%A P. Turchin
%A et al
%T Seshat: The global history databank
%J Cliodynamics: The J. of Quantitative and Cultural Evol.
%V 6
%P 77-107
%D 2015
%K c2015, c201x, c20xx, zz1016, Seshat, social, history, database, project
%X "The vast amount of knowledge about past human societies has not been
   systematically organized &, therefore, remains inaccessible for empirically
   testing theories about cultural evolution & historical dynamics. [eg] what
   evolutionary mechanisms were involved in the transition from the small-scale,
   uncentralized societies, in which humans lived 10,000 years ago, to the
   large-scale societies with an extensive division of labor, great
   differentials in wealth & power, & elaborate governance structures of today?
   Why do modern states sometimes fail to meet the basic needs of their
   populations? Why do economies decline, or fail to grow? In this article, we
   describe the structure & uses of a massive databank of historical &
   archaeological information, Seshat: The Global History Databank. The data
   that we are currently entering in Seshat will allow us & others to test
   theories explaining how modern societies evolved from ancestral ones, & why
   modern societies vary so much in their capacity to satisfy their members'
   basic human needs."
   -- [<A HREF="https://escholarship.org/uc/item/9qx38718">www</A>]['16];
    & [<A HREF="http://seshatdatabank.info/">seshatdatabank.info</A>]['16].
   (Also see S@[<A HREF="https://en.wikipedia.org/wiki/Seshat_(project)">wikip</A>]['16].)

%A L. Rosner
%A N. C. Kramer
%T Verbal venting in the social web: effects of anonymity and group norms on
   aggressive language use in online comments
%J Social Media & Society
%V 2
%N 3
%P ?-?
%M AUG
%D 2016
%K jrnl, c2016, c201x, c20xx, zz1221, social media, twitter, tweet, facebook,
   blog, blogging, comments, anonymity, anonymous, identity, aggression,
   aggressive, rude, rudeness, nasty, incivility, uncivil, abuse, bullying,
   troll, trolling
%X "... Drawing on the social identity & deindividuation effects (SIDE) model,
   ... conducts a lab. experiment with a 2 (anonymity vs. no anonymity) x2
   (aggressive norm vs. non-aggressive norm) between-subjects design in order to
   disentangle the effects of anonymity, social group norms, & their
   interactions on aggressive language use in online comments. Results reveal
   that participants used more aggressive expressions in their comments when
   peer comments on a blog included aggressive wording (i.e., the social grp
   norm was aggressive). Anonymity had no direct effect; however, we found a
   tendency that users' conformity to an aggressive social norm of commenting is
   stronger in an anonymous environment."
   -- [<A HREF="https://doi.org/10.1177%2F2056305116664220">doi:10.1177%2F2056305116664220</A>]['21].
   [Also search for: nasty social media].

%A A. Mann
%T The power of prediction markets
%J Nature
%V 538
%N 7625
%P 308-310
%M OCT
%D 2016
%K news, views, c2016, c201x, c20xx, zz1016, Dreber, Reproducibility Project,
   SciCast, Metaculus, prediction, predict, market, wisdom of crowds,
   poll, polls, polling, gambling, gamble, wager
%X "Scientists are beginning to understand why these 'mini Wall Streets' work so
   well at forecasting election results - and how they sometimes fail. ...
   When the Reproducibility Project revealed last year that it had been able to
   replicate fewer than half of the studies examined, Dreber found that her
   experts hadn't done much better than chance with their individual
   predictions. But working collectively through the markets, they had correctly
   guessed the outcome 71% of the time. ...
   -- [<A HREF="http://dx.doi.org/10.1038/538308a">doi:10.1038/538308a</A>]['16].

%A M. H. Yearwood
%A et al ...
%A A. Spectre [Kogan]
%T On wealth and the diversity of friendships: High social class people around
   the world have fewer international friends
%J Personality and Individual Differences
%V 87
%P 224-229
%M DEC
%D 2015
%K jrnl, c2015, c201x, c20xx, zz0418, facebook, app, ads, Kogan, internet,
   social media, personality, traits, friends, likes, privacy, controversy,
   controversial, GSR, SCL, Cambridge Analytica, This Is Your Digital Life app
%X "... , we found that among individuals in the United States, social class
   was negatively related to percentage of friends on Facebook that are outside
   the United States. In Study 2, we extended these findings to the global level
   by analyzing country-level data on Facebook friends formed in 2011 (nearly
   50 billion friendships) across 187 countries. We found that people from
   higher social class countries (as indexed by GDP per capita) had lower levels
   of internationalism - that is, they made more friendships domestically than
   abroad."  (online Aug 2015.)
   -- [<A HREF="https://doi.org/10.1016/j.paid.2015.07.040">doi:10.1016/j.paid.2015.07.040</A>]['18].
   (*Note, A.Spectre = A.Kogan, also see
   [<A HREF="http://www.cam.ac.uk/notices/news/statement-from-the-university-of-cambridge-about-dr-aleksandr-kogan">CamU</A>][11/4/'18] on Facebook & Kogan,
   and [<A HREF="http://www.bbc.com/news/technology-43752340">bbc</A>][13/4/2018].*)

%A A. Nordrum
%T Alarming security defects in SS7, the global cellular network - and how to
   fix them
%J IEEE Spectrum
%M APR
%D 2016
%K news, views, c2016, c201x, c20xx, zz1024, mobile, cellular, phone, network,
   phones, security, hack, hacking, vulnerability, surveillance, SS7, banking,
   flaw, eavesdrop, twoFactor, 2factor, Karsten Nohl, Tobias Engel
%X -- [<A HREF="https://spectrum.ieee.org/alarming-security-defects-in-ss7-the-global-cellular-networkand-how-to-fix-them">www</A>][11/24].
   Also see [<A HREF="https://www.youtube.com/watch?v=wVyu7NB7W6Y">www</A>][10/'24] -- via AK.

%A A. Ezrachi
%A M. E. Stucke
%T Virtual Competition: The Promise and Perils of the Algorithm-Driven Economy
%I HarvardUP
%P 368
%M NOV
%D 2016
%K book, text, c2016, c201x, c20xx, zz1116, web, www, capitalism, internet,
   shopping, economics, market, competition, anti-competitive
%X 1st ed 2016; hb us$30; uk us isbn:0674545478; uk us isbn13:978-0674545472.
   "... look at today's app-assisted paradise of digital shopping. While
   consumers reap many benefits from online purchasing, the sophisticated
   algs. & data-crunching that make browsing so convenient are also changing the
   nature of market competition, and not always for the better. ..."

%A C. Cadwalladr
%A Google, democracy and the truth about internet search
%J The Guardian
%M DEC
%D 2016
%K news, views, Grauniad, c2016, c201x, c20xx, zz1216, internet, web, www, HREF,
   google, search engine, facebook, social media, altRight, hate, fake news,
   fakeNews, post truth, postTruth, society, politics, election, US, USA,
   right wing, far, altRight, yahoo, Breibart, gender, race, propaganda
%X "Here's what you don't want to do late on a Sunday night. You do not want to
   type seven letters into Google. That's all I did. I typed: 'a-r-e'. And then
   'j-e-w-s'. Since 2008, Google has attempted to predict what question you
   might be asking and offers you a choice. And this is what it did. It offered
   me a choice of potential questions it thought I might want to ask: 'are jews
   a race?', 'are jews white?', 'are jews christians?', and finally, 'are jews
   evil?' ..."
   -- [<A HREF="https://www.theguardian.com/technology/2016/dec/04/google-democracy-truth-internet-search-facebook">www</A>]['16].

%A M. De Domenico
%A A. Arenas
%T Modeling structure and resilience of the dark network
%J Phys. Rev. E
%V 95
%N 2
%P 022313
%M FEB
%D 2017
%K jrnl, eJrnl, c2017, c201x, c20xx, zz0317, internet, darknet, web, www,
   denial of service attack, networks, DeDomenico
%X "While the statistical & resilience properties of the Internet are no longer
   changing significantly across time, the Darknet, a n/w devoted to keep
   anonymous its traffic, still experiences rapid changes to improve the
   security of its users. [find] its topology is rather peculiar, being
   characterized by a nonhomogeneous distribution of connections, typical of
   scale-free n/ws; v.short path lengths & high clustering, typical of
   small-world n/ws; & lack of a core of highly connected nodes. We propose a
   model to reproduce such features, demonstrating that the mechanisms used to
   improve cybersecurity are responsible for the observed topology. Unexpectedly
   we reveal that its peculiar structure makes the Darknet much more resilient
   than the Internet (used as a benchmark for comparison at a descriptive level)
   to random failures, targeted attacks, & cascade failures, as a result of
   adaptive changes in response to the attempts of dismantling the n/w across
   time."
   -- [<A HREF="https://doi.org/10.1103/PhysRevE.95.022313">doi:10.1103/PhysRevE.95.022313</A>]['17].

%A K. A. Zweig
%T Watching the watchers: Epstein and Robertson's "Search Engine Manipulation
   Effect"
%I AlgorithmWatch
%M APR
%D  2017
%K TR, c2017, c201x, c20xx, zz0821, Epstein, Robertson, web, www, internet,
   google, search engine, results, rank, ranking, bias, society, social,
   politics, election, news, curating
%X "... In July, 2015, Epstein & Robertson published a widely acknowledged study
   on how much a biased search engine result ranking can shift undecided voters
   towards one candidate ... In this article, I will show that the results are
   strongly exaggerated because they are based on a measure which sums up the
   effects of biasing the results for all candidates instead of averaging them
   or stating the range of possible effects. In the most realistic of the three
   studies conducted by E&R, the single effects are within the range of 2-4%.
   This is still an important effect, especially for elections which are as
   close as the ones often seen in the USA but less worrying for European
   countries with multiple parties."
   -- [<A HREF="https://algorithmwatch.org/en/watching-the-watchers-epstein-and-robertsons-search-engine-manipulation-effect/">www</A>]['21]
   Also see the ABC@[<A HREF="https://www.abc.net.au/news/science/2021-08-05/google-curating-covid-search-results-algorithm-project-finds/100343284">www</A>][5/8/2021].
   [Also search for: society web].

%A J. Y. Halpern
%A R. Pass
%T A knowledge-based analysis of the blockchain protocol
%J arXiv
%M JUL
%D 2017
%K TR, c2017, c201x, c20xx, zz0717, blockchain, block chain, protocol,
   bitCoin, bitCoins, virtual currency
%X "At the heart of the Bitcoin is a blockchain protocol, a protocol for
   achieving consensus on a public ledger that records bitcoin transactions. To
   the extent that a blockchain protocol is used for applications such as
   contract signing and making certain transactions (such as house sales)
   public, we need to understand what guarantees the protocol gives us in terms
   of agents' knowledge. Here, we provide a complete characterization of agent's
   knowledge when running a blockchain protocol using a variant of common
   knowledge that takes into account the fact that agents can enter and leave
   the system, it is not known which agents are in fact following the protocol
   (some agents may want to deviate if they can gain by doing so), and the fact
   that the guarantees provided by blockchain protocols are probabilistic. We
   then consider some scenarios involving contracts and show that this level of
   knowledge suffices for some scenarios, but not others."
   -- 1707.08751@[<A HREF="https://arxiv.org/abs/1707.08751">arXiv</A>]['17].

%A M. Pielot
%A L. Rello
%T Productive, anxious, lonely - 24 hours without push notifications
%J Proc. Mobile HCI
%P ?-?
%M SEP
%D 2017
%K conf, c2017, c201x, c20xx, zz0817, mobileHCI, social media, mobile device,
   phone, email, SMS, smartphone, www, tablet, facebook, notification,
   do not disturb, doNotDisturb, challenge, messaging, human behaviour,
   well being, wellBeing, anxiety, distraction, productivity
%X "We report from the Do Not Disturb Challenge where 30 volunteers disabled
   notification alerts for 24 hours across all devices. The effect of the
   absence of notifications on the participants was isolated through an
   experimental study design: we compared self-reported feedback from the day
   w/o not'ns v. a baseline day. ... indicates that not'ns have locked us in a
   dilemma: without notifications, participants felt less distracted & more
   productive.  But, they also felt no longer able to be as responsive as
   expected, which made some participants anxious. And, they felt less connected
   with one's social group. In contrast to prev. reports, ~ two third of the
   participants expressed the intention to change how they manage notifications.
   Two years later, half of the participants are still following through with
   their plans."
   -- [<A HREF="https://doi.org/10.1145/3098279.3098526">doi:10.1145/3098279.3098526</A>]['17],
      [<A HREF="http://pielot.org/pubs/PielotRello2017-MHCI-DoNotDisturb.pdf">www</A>][8/'17].

%A E. Losh
%T MOOCs and Their Afterlives
%I U. of Chicago Press
%D 2017
%K book, text, c2017, c201x, c20xx, zz0817, tertiary, university, higher,
   education, fad, hype, MOOC, MOOCs, SPOC, web, www, online courses, teaching
%X 1st ed 2017; hb us$110; uk us isbn: 022646931X; uk us isbn13:9780226469317.
   "... At the beginning of the 2010s, MOOCs, or Massive Open Online Courses,
   seemed poised to completely revolutionize higher education. But now, just a
   few years into the revolution, educators' enthusiasm seems to have cooled.
   As advocates and critics try to make sense of the rise and fall of these
   courses, both groups are united by 1 question: Where do we go from here? ..."

%A L. Harding
%T Collusion: How Russia Helped Trump Win the White House
%I GuardianBooks
%P 368
%M NOV
%D 2017
%K book, c2017, c201x, c20xx, zz1117, America, American, election, USA, Russia,
   Moscow, Clinton, Donald Trump, zzTrump, Putin, Manafort, Flynn, Kushner,
   Papadopoulos, zzTrump, facebook, fake news, fakeNews, Wikileaks,
   Julian Assange, social media, internet, www, the Guardian
%X 1st ed 2017; pb us$10, uk us isbn:0525562516, uk us isbn13:978-0525562511.
   "... Between 2007 and 2011, [H] was the Guardian's Moscow bureau chief. The
   Kremlin expelled him from the country in the first case of its kind since
   the Cold War. ..."

%A N. Smith
%A T. Graham
%T Mapping the anti-vaccination movement on Facebook
%J Info., Commn and Society
%V ?
%P ?-?
%M DEC
%D 2017
%K jrnl, eJrnl, c2017, c201x, c20xx, zz0118, web, www, href, social media,
   Facebook, network, filter bubble, science, fake news, fakeNews,
   anti-vaccination, antiVaccination, anti vax, antiVax, antiVaxxer,
   misinformation, conspiracy, myth, Tenpenny
%X "... examine the characteristics of & the discourses present within six
   popular anti-vaccination Facebook pages. We examine these large-scale
   datasets using a range of methods, inc. social n/wk analysis, gender
   prediction using historical census data, & generative statistical models for
   topic analysis (Latent Dirichlet allocation). We find that present-day
   discourses centre around moral outrage & structural oppression by
   institutional government & the media, suggesting a strong logic of
   'conspiracy-style' beliefs & thinking. Furthermore, anti-vaccination pages
   on [FB] reflect a highly 'feminised' movement - the vast majority of
   participants are women. Although anti-vaccination n/wks on [FB] are large &
   global in scope, the comment activity sub-n/wks appear to be 'small world'.
   This suggests that social media may have a role in spreading anti-vaccination
   ideas & making the movement durable on a global scale." (online Dec 2017)
   -- [<A HREF="https://doi.org/10.1080/1369118X.2017.1418406">doi:10.1080/1369118X.2017.1418406</A>]['18].
   [Also search for: fakeNews].
   (Also see [<A HREF="http://www.abc.net.au/news/science/2018-01-17/what-anti-vaccination-groups-reveal-about-facebook-filter-bubble/9324876">abc</A>][1/2018].)

%A S. C. Matz
%A M. Kosinski
%A G. Nave
%A D. J. Stillwell
%T Psychological targeting as an effective approach to digital mass persuasion
%J PNAS
%P ?-?
%M NOV
%D 2017
%K jrnl, PNAS, c2017, c201x, c20xx, zz0318, web, www, href, social media, meta,
   app, facebook, marketting, influence, persuasion, bias, manipulation, change,
   opinion, privacy, scandal, myPersonality, app, Kosinski, Cambridge Analytica,
   Aggregate IQ, AggregateIQ, Trump, zzTrump, Brexit, fake news, fakeNews,
   likes, tweets, SCL Elections, twitter, internet, controversial, controversy,
   Auspex International, Emerdata, mypersonality, psychometric quiz, META
%X "... Recent research, however, shows that people's psychological
   characteristics can be accurately predicted from their digital footprints,
   such as their Facebook Likes or Tweets. Capitalizing on this form of
   psychological assessment from digital footprints, we test the effects of
   psychological persuasion on people's actual behavior in an ecologically
   valid setting. In three field experiments that reached over 3.5 million
   individuals with psychologically tailored advertising, we find that matching
   the content of persuasive appeals to individuals' psychological
   characteristics significantly altered their behavior as measured by clicks &
   purchases. Persuasive appeals that were matched to people's extraversion or
   openness-to-experience level resulted in up to 40% more clicks & up to 50%
   more purchases than their mismatching or unpersonalized counterparts. Our
   findings suggest that the application of psychological targeting makes it
   possible to influence the behavior of large groups of people by tailoring
   persuasive appeals to the psychological needs of the target audiences. We
   discuss both the potential benefits of this method for helping individuals
   make better decisions & the potential pitfalls related to manipulation &
   privacy."
   -- [<A HREF="https://doi.org/10.1073/pnas.1710966114">doi:10.1073/pnas.1710966114</A>]['18].
   (Also see
    auth2@[<A HREF="https://scholar.google.com/citations?user=01-XV0YAAAAJ">sclr</A>]['18],
    auth4@[<A HREF="https://scholar.google.com.au/citations?user=z9CoSJMAAAAJ">schlr</A>]['18],
    myPersonality.org[<A HREF="http://mypersonality.org/">www</A>]['18] and
    myPersonality@[<A HREF="https://www.gsb.stanford.edu/sites/gsb/files/conf-presentations/stillwell_and_kosinski_2012.pdf">Stanf</A>]['18].
    And, "Data row ... 270,000 people took the [personality] quiz the data of
    some 50 million users, mainly in the US, was harvested without their
    explicit consent via their friend networks. ..."
    -- [<A HREF="http://www.bbc.com/news/uk-43554135">bbc</A>][28/3/2018].
    And, "Cambridge Analytica's parent company SCL Elections Ltd has been fined
    stg.15,000 plus costs for failing to hand over the personal data of a
    US citizen. ..."
    -- [<A HREF="https://www.bbc.com/news/technology-46822439">bbc</A>][10/1/2019].)
   [Also search for: facebook Kogan], [also search for: zzTrump] or try Brexit.
   (NB. "Former staff from scandal-hit Cambridge Analytica (CA) have
        set up another data analysis company [Auspex International]. ..."
   -- [<A HREF="https://www.bbc.com/news/technology-44807093">bbc</A>][12/7/2018].)
   (Also see, 'Facebook bans second Cambridge psychometric quiz app,'
   -- [<A HREF="https://www.bbc.com/news/technology-45282845">bbc</A>][23/8/2018].)
   "Meta settles Cambridge Analytica scandal case for $725m"
   -- [<A HREF="https://www.bbc.com/news/technology-64075067">bbc</A>][29/12/2022].

%A K. Muller
%A C. Schwarz
%T Fanning the Flames of Hate: Social Media and Hate Crime
%J SSRN
%M DEC
%D 2017
%K TR, c2017, c2017, c20xx, zz0818, internet, www, social network, media,
   meta, facebook, troll, hate, nasty, crime, Germany, politics, refugee,
   refugees, Alternative fur Deutschland, AfD, right, rightWing
%X "... investigates the link between social media & hate crime using Facebook
   data. We study the case of Germany, where the recently emerged right-wing
   party Alternative fur Deutschland (AfD) has developed a major social media
   presence. We show that right-wing anti-refugee sentiment on F. predicts
   violent crimes against refugees in otherwise similar municipalities with
   higher social media usage. To further establish causality, we exploit
   exogenous variation in major internet & F. outages, which fully undo the
   correlation between social media & hate crime. We further find that the
   effect decreases with distracting news events; increases with user network
   interactions; & does not hold for posts unrelated to refugees. Our results
   suggest that social media can act as a propagation mechanism between online
   hate speech & real-life violent crime."
   -- [<A HREF="https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3082972">www</A>]['18].

%A S. Umoja Noble
%T Algorithms of Oppression: How Search Engines Reinforce Racism
%I NYUpress
%P 246
%M FEB
%D 2018
%K book, text, c2018, c201x, c20xx, zz1121, internet, web, www, social media,
   race, racism, sexism, discrimination, society, search engine
%X 1st ed 2018; pb us$43; uk us isbn:1479837245; uk us isbn13:978-1479837243.
   "A revealing look at how negative biases against women of color are embedded
   in search engine results and algorithms ..."

%A L. Farach-Coulton
%A et al ...
%A M. Mosteiro
%T Closure operators and spam resistance for PageRank
%J arXiv
%M MAR
%D 2018
%K TR, c2018, c201x, c20xx, zz0418, www, HREF, web, internet, spam resistance,
   spamming, resistant, pagerank, ranking, rank, pages, graph, network, links,
   hub, hubs, Min-k-PRR, MinkPRR
%X "We study the spammablility of ranking fns on the web. Although
   graph-theoretic ranking fns, such as Hubs & Authorities & PageRank exist,
   there is no graph theoretic notion of how spammable such fns are.  We
   introduce a very general cost model that only depends on the observation that
   changing the links of a page that you own is free, whereas changing the links
   on pages owned by others requires effort or money. We define spammability to
   be the ratio between the amount of benefit one receives for one's spamming
   efforts & the amount of effort/money one must spend to spam. The more
   effort/money it takes to get highly ranked, the less spammable the fn.  Our
   model helps explain why both hubs & authorities & standard PageRank are very
   easy to spam. Although standard PageRank is easy to spam, we show that there
   exist spam-resistant PageRanks. Specifically, we propose a ranking method,
   Min-k-PPR, that is the component-wise min of a set of personalized PageRanks
   centered on k trusted sites. Our main results are that Min-k-PPR is, itself,
   a type of PageRank & that it is expensive to spam.  We elucidate a
   surprisingly elegant algebra for PageRank. We define the space of all
   possible PageRanks & show that this space is closed under some operations.
   Most notably, we show that PageRanks are closed under (normalized)
   component-wise min, which establishes that (normalized) Min-k-PPRis a
   PageRank. This algebraic structure is also key to demonstrating the spam
   resistance of Min-k-PPR."
   -- 1803.05001@[<A HREF="https://arxiv.org/abs/1803.05001">arXiv</A>]['18].

%A E. Ormsby
%T Darkest Web: Drugs, death and destroyed lives ... the inside story of the
   internet's evil twin
%I AllenAndUnwin
%M MAR
%D 2018
%K book, c2018, c201x, c20xx,  zz0418, internet, web, dark web, darkweb,
   drugs, Silk Road, SilkRoad, crime, hitmen, hitman, vice, porn,
   Daisy's Destruction, hurtcore, red room, rooms, 419, scam, scams, fraud,
   bitcoin, Dread Pirate Roberts, Variety Jones, deep web, deepweb
%X 1st ed 2018; pb us$26; uk us isbn:1760297852; uk us isbn13:978-1760297855.
   "Hitmen for hire, drugs for sale. Inside the dangerous world that lurks
   beneath the bright, friendly light of your internet screen Dark..."
   (The author was interviewed on ABC radio
   [<A HREF="http://www.abc.net.au/radionational/programs/bigideas/darkest-web/9640824">www</A>][17/4/2018].
   Drugs? -- yes.  Hitmen? -- mostly (all?) cons.
   Also see [<A HREF="https://en.wikipedia.org/wiki/All_Things_Vice">wikip</A>]['18].)

%T General Data Protection Regulation (GDPR)
%I EU
%M MAY
%D 2018
%K law, regulation, c2018, c201x, c20xx, zz0518, internet, data, privacy,
   personal, protection, GDPR, Europe, European, EU, UK, www, website, HREF,
   opt in, out, optin, optout, consent, conditions of use
%X "... the official PDF of the Regulation (EU) 2016/679 (General Data
   Protection Regulation) ..."
   -- [<A HREF="https://gdpr-info.eu/">www</A>]['5/2018].
   (Also see the [<A HREF="http://www.bbc.com/news/world-europe-44248448">bbc</A>][25/5/2018].)
   [Also search for: internet privacy].

%A M. Roberts
%T Censored: Distraction and Diversion Inside China's Great Firewall
%I PrincetonUP
%D 2018
%K book, text, c2018, c201x, c20xx, zz0618, China, Chinese, PRC, Great Firewall,
   censor, censorship, internet, web, www, fake news, influence, propaganda,
   manipulation, communist party, CCP, authoritarian, politics, political,
   right wing, social credit, control
%X 1st ed 2018; hb us$30; uk us isbn:0691178860; uk us isbn13:978-0691178868.
   "As authoritarian governments around the world develop sophisticated
   technologies for controlling information ... Roberts demonstrates that even
   censorship that is easy to circumvent can still be enormously effective.
   Taking advantage of digital data harvested from the Chinese Internet and
   leaks from China's Propaganda Department, this important book sheds light on
   how and when censorship influences the Chinese public. ... subtler censorship
   such as burying search results or introducing distracting information on the
   web, is more effective because users are less aware of it. ..."
   [Also search for: great firewall].
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/1984/">1984</A>].)

%A E. E. Bruch
%A M. E. J. Newman
%T Aspirational pursuit of mates in online dating markets
%J Sci. Adv.
%V 4
%N 5
%P eaap9815
%M AUG
%D 2018
%K jrnl, eJrnl, c2018, c201x, c20xx, zz0818, www, web, internet dating site,
   sites, men, women, attractiveness, desirability, mate selection, matching,
   messaging, pagerank, stats, US, eHarmony, courtship
%X "...  an empirical analysis of heterosexual dating markets in four large U.S.
   cities using data from a popular, free online dating service. ... competition
   for mates creates a pronounced hierarchy of desirability that correlates
   strongly with user demographics & is remarkably consistent across cities. We
   find that both men & women pursue partners who are on avg about 25% more
   desirable than themselves by our measures & that they use different messaging
   strategies with partners of different desirability. We also find that the
   probability of receiving a response to an advance drops markedly with
   increasing difference in desirability between the pursuer & the pursued.
   Strategic behaviors can improve one's chances of attracting a more desirable
   mate, although the effects are modest."
      "... The most popular individual in our four cities, a 30 y.o. woman
      living in New York, received 1504 messages during the period of
      observation, equivalent to one message every 30min, day & night, for the
      entire month. ..."
   -- [<A HREF="https://doi.org/10.1126/sciadv.aap9815">doi:10.1126/sciadv.aap9815</A>]['18].
   Also see Courtship@[<A HREF="https://en.wikipedia.org/wiki/Courtship">wikip</A>]['21].

%A C. Lagorio-Chafkin
%T We Are the Nerds: The Birth and Tumultuous Life of Reddit, the
   Internet's Culture Laboratory
%I HachetteBooks
%M OCT
%D 2018
%K book, c2018, c201x, c20xx, zz1018, Reddit, internet, www, HREF, news, rating,
   social media, subreddit, reddits, redditor, Snoo, web.py, Huffman, Ohanian
%X "... Reddit hails itself as 'the front page of the Internet.' It's the
   third most-visited website in the United States ..."
   1st ed 2018; hb us$18; uk us isbn:0316435376; uk us isbn13:978-0316435376.
   (Also see reddit@[<A HREF="https://en.wikipedia.org/wiki/Reddit">wikip</A>]['18].)

%A C. Kopp
%A K. B. Korb
%A B. I. Mills
%T Information-theoretic models of deception: Modelling cooperation and
   diffusion in populations exposed to "fake news"
%J PLoS One
%V 13
%N 11
%P e0207383
%M NOV
%D 2018
%K jrnl, eJrnl, c2018, c201x, c20xx, zz1118, internet, facebook, social media,
   fake news, fakeNews, lies, deception, disinformation, misinformation,
   corruption, information war, warfare, Trump, politics, Qanon, USA,
   post truth, postTruth, aLife, prisoners dilemma, IPD, game theory
%X "The modelling of deceptions in game theory and decision theory has not been
   well studied ... This paper presents an improved formulation of the extant
   information-theoretic models of deceptions, a framework for incorporating
   these models of deception into game & decision theoretic models of deception,
   & applies these models & this framework in an agent based evolutionary
   simulation that models two very common deception types employed in 'fake
   news' attacks. The simulation results for both deception types modelled show,
   as observed empirically in many social systems subjected to 'fake news'
   attacks, that even a very small population of deceivers that transiently
   invades a much larger population of non-deceiving agents can strongly alter
   the equilibrium behaviour of the population in favour of agents playing an
   always defect strategy. The results also show that the ability of a
   population of deceivers to establish itself or remain present in a population
   is highly sensitive to the cost of the deception, as this cost reduces the
   fitness of deceiving agents when competing against non-deceiving agents. ..."
   -- [<A HREF="https://doi.org/10.1371/journal.pone.0207383">doi:10.1371/journal.pone.0207383</A>]['18]  (102 refs).

%A N. Grinberg
%A K. Joseph
%A L. Friedland
%A B. Swire-Thompson
%A D. Lazer
%T Fake news on Twitter during the 2016 U.S. presidential election
%J Science
%V 363
%N 6425
%P 374-378
%M JAN
%D 2019
%K jrnl, c2019, c201x, c20xx, zz0119, social media, twitter, facebook,
   internet, www, Russia, Trump, zzTrump, Trumpery, POTUS, president, US, USA,
   election, politics, fake news, fakeNews, lies, Xtwitter
%X "... We examined exposure to & sharing of fake news by registered voters on
   Twitter & found that engagement with fake news sources was extremely
   concentrated. Only 1% of individuals accounted for 80% of fake news source
   exposures, & 0.1% accounted for nearly 80% of fake news sources shared.
   Individuals most likely to engage with fake news sources were conservative
   leaning, older, & highly engaged with political news. A cluster of fake news
   sources shared overlapping audiences on the extreme right, but for people
   across the political spectrum, most political news exposure still came from
   mainstream media outlets."
   (And, "... the strongest predictors of the proportion of fake news sources
      in an individual's feed were the individual's age & # of political URLs
      in the individual's feed ...")
   -- [<A HREF="https://doi.org/10.1126/science.aau2706">doi:10.1126/science.aau2706</A>]['19].

%A G. Gorman
%T Troll Hunting. Inside the World of online hate and its human fallout
%I HardieGrant
%P 304
%D 2019
%K book, text, c2019, c201x, c20xx, zz0219, internet, www, social media, nasty,
   troll, trolls, trolling, hate, cyberhate, threat, mysogyny, bully, bullying,
   altright, meepsheep, meta, facebook, twitter
%X 1st ed 2019; pb us$20; uk us isbn:1743794355; uk us isbn13:978-1743794357.
   "... What she discovered was both profoundly shocking and fascinating.
   Syndicates of highly organised predator trolls across the globe
   systematically set out to disrupt and disturb. Some want to highlight the
   media's alleged left-wing bias, some want to bring down capitalism, and
   some just want to have fun. Even if it means destroying someone's life..."
   [Also search for: trolling].

%A J. Griffith
%T The Great Firewall of China: How to Build and Control an
   Alternative Version of the Internet
%I ZedBooks
%P 288
%M MAR
%D 2019
%K book, c2019, c201x, c20xx, zz0319, internet, www, web, censor, censorship,
   China, Chinese, Xi Jinping, Great Firewall, state control, surveillance,
   communist party, PRC, CCP, autocrat, Orwellian, big brother, social media,
   press, freedom, nineteen eighty four, 1984, Winnie the Pooh, Weixin, WeChat
%X 1st ed 2019; hb us$20; uk us isbn:1786995352; uk us isbn13:978-1786995353.
   "... C. influence around the globe is tied to an increasing worldwide
   crackdown in online freedom. One of C's most insidious exports are its
   censorship techniques, and its Firewall is an inspiration for aspiring
   autocrats the world over. ..."
   (Also see [<A HREF="http://www.allisons.org/ll/Computing/Misc/1984/">1984</A>].)

%T Operation soft cell: A worldwide campaign against
   telecommunications providers
%I Cyberreason
%M JUN
%D 2019
%K TR, c2019, c201x, c20xx, zz0719, cell, phone, cellular, mobile phones, hack,
   hacking, hackers, networks, internet, security, threat, risks, China,
   Chinese, APT10, chopper, w3wp.exe, nbtscan, mimikatz, softcell,
   web, www, HREF, servers
%X "... In 2018, the Cybereason Nocturnus team identified an advanced,
   persistent attack targeting global telecommunications providers carried out
   by a threat actor using tools and techniques commonly associated with the
   Chinese-affiliated threat actor APT10.  This multi-wave attacks focused on
   obtaining data of specific, high-value targets and resulted in a complete
   takeover of the network ..."
   --  cybereason[<A HREF="https://www.cybereason.com/blog/operation-soft-cell-a-worldwide-campaign-against-telecommunications-providers">25/6/2019</A>]['19].
   (Also see the bbc[<A HREF="https://www.bbc.com/news/technology-48756030">25/6/2019</A>]['19].)

%A J. E. Grant
%A K. Lust
%A S. R. Chamberlain
%T Problematic smartphone use associated with greater alcohol consumption,
   mental health issues, poorer academic performance, and impulsivity
%J J. of Behavioral Addictions
%V 8
%N 2
%M JUL
%D 2019
%K jrnl, eJrnl, c2019, c201x, c20xx, zz0719, human, social media, smartphone,
   iphone, university student, students, use, usage, addiction, addictive,
   addict, drinking, alcohol, problems, risks, society, public, mental health,
   behaviour, internet, www
%X "... A 156-item anonymous online survey was distributed via email to a
   sample of 9,449 university students. ... A total of 31,425 participants were
   included in the analysis, of whom 20.1% reported problematic smartphone use.
   Problematic use of smartphones was associated with lower grade point averages
   and with alcohol use disorder symptoms. It was also sig. assoc. with
   impulsivity (Barratt scale and ADHD) and elevated occurrence of PTSD,
   anxiety, and depression. Finally, those with current problems with smartphone
   use were significantly more sexually active. ..."
   -- [<A HREF="https://akademiai.com/doi/full/10.1556/2006.8.2019.32">doi:10.1556/2006.8.2019.32</A>]['19].

%T WT Social
%D 2019
%K news, c2019, c201x, c20xx, zz1119, WikiTribune, WTsocial, social network,
   media, news, facebook, twitter, Jimmy Wales, privacy, www, web, HREF, http
%X WT.Social[<A HREF="https://wt.social/">www</A>]['19].
   Jimmy Wales is founder of wikipedia.
   Subs are stg.10 per month or stg.80 per year (us$13 / us$100).
   "Thousands flock to Wikipedia founder's 'Facebook rival' ..."
   -- [<A HREF="https://www.bbc.com/news/technology-50460243">bbc</A>][18/11/2019].
   It will take more than thousands to rival Facebook.

%A S. Cipolla
%A F. Durastante
%A F. Tudisco
%T Nonlocal pagerank
%J arXiv
%M JAN
%D 2020
%K TR, c2020, c202x, c20xx, zz0220, PageRank, non local, page rank, importance,
   ranking, ranks
%X "... introduce & study a nonlocal version of the PageRank. ... the random
   walker explores the graph using longer excursions than just moving between
   neighboring nodes. [So] the corr. ranking of the nodes, which takes into
   account a long-range interaction between them, does not exhibit concentration
   phenomena typical for spectral rankings taking into account just local
   interactions. We show that the predictive value of the rankings obtained
   using our proposals is considerably improved on different real world
   problems."
   -- 2001.10421@[<A HREF="https://arxiv.org/abs/2001.10421">arXiv</A>]['20].
   [Also search for: pagerank].

%A A. Bruns
%A S. Harrington
%A E. Hurcombe
%T 'Corona? 5G? or both?': The dynamics of COVID-19/5G conspiracy theories on
   Facebook
%J Media Int. Au.
%M AUG
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0920, covid 19, 5G, fiveG, altright, QAnon,
   conspiracy theory, Trumpery, Trumpistan, misinformation, disinformation,
   spread, rumour, rumours, denier, Facebook, Twitter, social media, www
%X "... Drawing on a mixture of quantitative & qualitative methods inc.
   time-series analysis, n/wk analysis & in-depth close reading, our analysis
   shows the dissemination of the rumour on Facebook from its obscure origins
   in pre-existing conspiracist groups through greater uptake in more diverse
   communities to substantial amplification by celebrities, sports stars & media
   outlets. The in-depth tracing of COVID-related mis- & disinformation across
   social n/wks offers important new insights into the dynamics of online ..."
   -- [<A HREF="https://doi.org/10.1177/1329878X20946113">doi:10.1177/1329878X20946113</A>]['20].  (auth1@QUT.)

%A K. P. Madore
%A et al
%T Memory failure predicted by attention lapsing and media multitasking
%J Nature
%M OCT
%D 2020
%K c2020, c202x, c20xx, zz1020, mobile digital media, online, screens, memory,
   lapses, attention, concentration, remembering, multitasking
%X "... Here we examine whether spontaneous attention lapses - in the moment,
   across individuals & as a fn of everyday media multitasking - negatively
   correlate with remembering ... we show that tonic lapses in attention in the
   moment before remembering, assayed by posterior alpha power & pupil diameter,
   were correlated with reductions in neural signals of goal coding & memory,
   along with behavioural forgetting. ... Attention lapses partially account for
   why we remember or forget in the moment, & why some individuals remember
   better than others. Heavier media multitasking is assoc. with a propensity to
   have attention lapses & forget."  [online 28 Oct 2020]
   -- [<A HREF="https://doi.org/10.1038/s41586-020-2870-z">doi:10.1038/s41586-020-2870-z</A>]['20].

%A C. Bergstrom
%A J. D. West
%T Calling Bullshit
%I RandomHouse
%D 2020
%K book, c2020, c202x, c20xx, zz0322, bullshit, lies, misinformation,
   disinformation, Qanon, Trumpism, antivax, social media, tweet, twitter,
   facebook, Xtwitter
%X 1st ed 2020; hb u$38; uk us isbn:0525509186; isbn13:978-0525509189.
   "... and fake news abound and it's increasingly difficult to know what's
   true. Our media environment has become hyperpartisan. Science is conducted
   by press release. Startup culture elevates bullshit to high art. ..."

%A N. Johannes
%A M. Vuorre
%A A. K. Przybylski
%T Video game play is positively correlated with well-being
%J PsyArXiv
%D 2021
%O Royal Soc. Open Sci., [<A HREF="https://doi.org/10.1098/rsos.202049">doi:10.1098/rsos.202049</A>]['22], Feb. 2021.
%K TR, c2021, c202x, c20xx, zz0722, psychology, mental health, video games,
   gaming, www, web, Nintendo, UniOxford
%X "... surveyed players of Plants vs. Zombies: Battle for Neighborville &
   Animal Crossing: New Horizons for their well - being , motivations, & need
   satisfaction during play & merged their responses with telemetry data (i.e.,
   logged game play). Contrary to many fears that excessive play time will lead
   to addiction & poor mental health, we found a small +ve reln between game
   play & affective well-being. Need satisfaction & motivations during play did
   not interact with play time but were instead indep.rel. to well-being. ..."
   -- [<A HREF="https://psyarxiv.com/qrjza">psyarxiv</A>]['22].
   [Also search for: video game gaming].

%A A. Papasavva
%A J. Blackburn
%A G. Stringhini
%A S. Zannettou
%A E. De Cristofaro
%T "Is it a Qoincidence?": An exploratory study of QAnon on Voat
%J Proc. the Web Conf.
%P 460-471
%M APR
%D 2021
%K conf, c2021, c202x, c20xx, zz0821, web, www, internet, social media, Voat,
   voat.co, QQ, Qanon, drops, Trumpery, pizzaGate, 4Chan, greatAwakening,
   awakening, conspiracy theory, theories, USA, fake news, fakeNews
%X "Online fringe communities offer fertile grounds to users seeking & sharing
   ideas fueling ... & conspiracy theories. ... the QAnon conspiracy theory
   emerged in 2017 on 4chan, broadly supporting the idea that powerful
   politicians, aristocrats, & celebrities are closely engaged in a global
   pedophile ring. Simultaneously, governments are thought to be controlled by
   'puppet masters,' as democratically elected officials serve as a fake
   showroom of democracy."
   -- [<A HREF="https://doi.org/10.1145/3442381.3450036">doi:10.1145/3442381.3450036</A>]['21] and
      2009.04885@[<a HREF="https://arxiv.org/abs/2009.04885">arXiv</A>]['21].
   [Also search for: conspiracy theory].

%T The online information environment: Understanding how the internet shapes
   people's engagement with scientific information
%I The Royal Soc.
%M JAN
%D 2022
%K report , news, views, c2022, c202x, c20xx, zz0122, internet, www, twitter,
   meta, facebook, reddit, social media, fake news, fakeNews, misinformation,
   malinformation, lies, deepfake, removal, dePlatform, deplatforming, Trumpery,
   altRight, 4chan, QQ, Qanon, antivax, Xtwitter
%X uk us isbn13:9781782525677.
   "How are digital technologies changing the way people interact with
   information?  What technologies are there that can fabricate & detect
   misinformation? And what role does technology have to play in creating a
   better information environment? ..."
   -- [<A HREF="https://royalsociety.org/online-information-environment">www</A>]['22].
   (Also see [<A HREF="https://www.bbc.com/news/technology-60036861">bbc</A>][19/1/2022].)

%A D. Kekulluoglu
%A W. Magdy
%A K. Vaniea
%T From an authentication question to a public social event: Characterizing
   birthday sharing on Twitter
%J arXiv
%M JAN
%d 2022
%K TR, c2022, c202x, c20xx, zz0222, social media, facebook, twitter,
   identity theft, privacy, security, DOB, birthday
%X "... Over 45 days, we collected over 2.8M tweets wishing happy birthday to
   724K Twitter accounts. For 50K accounts, their age was likely mentioned
   revealing their DOB, and 10% were protected accounts. ... the use of DOB in
   authentication process is no longer considered best practice."
   -- [<A HREF="https://arxiv.org/abs/2201.10655">arXiv</A>]['22].

%A S. Jain
%A et al
%T FUSED-PAGERANK: Loop-fusion based approximate PageRank
%J arXiv
%M MAR
%D 2022
%K TR, c2022, c202x, c20xx, zz0322, fused PageRank algorithm, network, graph,
   centrality, importance, www
%X "PageRank is a graph centrality metric that gives the importance of each node
   in a given g.. ... an iterative alg. that ranks the nodes in each iteration
   until all the node values converge. The [PR] alg. is implemented using
   sparse storage format, which results in irregular memory accesses ... we
   propose FUSED-PAGERANK ... improving its locality ..."
   -- 2203.09284@[<A HREF="https://arxiv.org/abs/2203.09284">arXiv</A>]['22].

%A S. Brown
%T Get Rich or Lie Trying: Ambition and Deceit in the New Influencer Economy
%I AtlanticBooks
%M MAR
%D 2022
%K book, c2022, c202x, c20xx, zz0322, social media, web, www, meta, facebook,
   instagram, OnlyFans, scams, frauds, influencer, followers
%X 1st ed 2002; pb us$33; uk us isbn:1838950281; uk us isbn13:978-1838950286.
   "... explores ... the reality is much murkier. From IRL streamers in LA to
   Brazilian butt lifts, from sex workers on OnlyFans to fraudulent
   cryptocurrency schemes, these are the incredible stories that lurk behind the
   filtered selfies and gleaming smiles. ..."

%A H. Iqbal
%A U. M. Khan
%A H. A. Khan
%A M. Shahzad
%T A peek into the political biases in email spam filtering algorithms during
   US election 2020
%J arXiv
%M MAR
%D 2022
%K TR, c2022, c2022, c20xx, zz0822, web, www, internet, email, political spam,
   filter, filtering, USA, politics, election, Republican, GOP, RNC, Democrat,
   google, gmail, yahoo, outlook
%X "... we conducted a large-scale study of the campaign emails of the US
   elections 2020 by subscribing to a large number # Presidential, Senate, &
   House candidates using over a hundred email accounts on Gmail, Outlook, &
   Yahoo. We analyzed the biases in the SFAs towards the left & the right
   candidates & further studied the impact of the interactions (such as reading
   or marking emails as spam) of email recipients on these biases. We observed
   that the SFAs of different email services indeed exhibit biases towards
   different political affiliations. ..."
   -- 2203.16743@[<A HREF="https://arxiv.org/abs/2203.16743">arXiv</A>]['22].
   (It could be down to the preferences of the users of the mail servers.)

%T Webarchive
%K webarchive, way back machine, wayback, www, HREF, web, wwweb
%X netpreserve[<A HREF="https://netpreserve.org/">www</A>]['22],
   archive.arg[<A HREF="https://archive.org/">www</A>]['22] wayback mc,
   bl.uk[<A HREF="https://www.bl.uk/collection-guides/uk-web-archive#">www</A>]['22],
   webarchive.org.uk[<A HREF="https://www.webarchive.org.uk/">www</A>]['22].

%T The biggest data breach. ICCL report on scale of Real-Time Bidding data
   broadcasts in the U.S. and Europe
%I Irish Council for Civil Liberties (ICCL)
%M MAY
%D 2022
%K TR, c2022, c202x, c20xx, zz0522, web, www, website, app, internet, privacy,
   data protection, tracking, RTB, real time bidding, USA, Europe
%X "Real-Time Bidding (RTB) operates behind the scenes on websites & apps. It
   tracks what you are looking at, no matter how private or sensitive, & it
   records where you go. Every day it broadcasts this data about you to a host
   of companies continuously, enabling them to profile you. This report presents
   the scale of this data breach for the first time. RTB is the biggest data
   breach ever recorded. It tracks & shares what people view online & their
   real-world location 294 billion times in the U.S. & 197 billion times in
   Europe every day ..."
   -- [<A HREF="https://www.iccl.ie/wp-content/uploads/2022/05/Mass-data-breach-of-Europe-and-US-data-1.pdf">iccl.ie</A>][16/5/2022].
   (Also see the [<A HREF="https://www.bbc.com/news/technology-61465973">bbc</A>]['16/5/2022].)
   [Also search for: internet privacy].

%A C. H. Chang
%A P. R. Armsworth
%A Y. J. Masuda
%T Twitter data reveal six distinct environmental personas
%J Frontiers in Ecology and the Environment
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0622, tweet, twitter, social media, www,
   concern, marketting, Xtwitter
%X "... the first systematic characterization of environmental personas on
   social media. Beginning with 1 million environmental nongovernmental
   organization (NGO) followers on Twitter, of which 500,000 users met data
   quality criteria, we identified six personas that differ in their expression
   of 21 environmental issues. ..."
   -- [<A HREF="https://doi.org/10.1002/fee.2510">www</A>].

%A M. Eisenstein
%T Need web data? Here's how to harvest them
%J Nature
%V 607
%P 200-201
%M JUL
%D 2022
%K news, views, c2022, c202x, c20xx, zz0722, internet, web, page, pages, www,
   Webscraping, scraping, data, HTML, XML, Selenium, Mozenda, ScrapeSimple,
   rvest, rSelenium, covidScraper
%X "Webscraping is a useful tool for gathering data from public websites, but
   researchers must develop some fundamental software skills to use it. ..."
   -- [<A HREF="https://doi.org/10.1038/d41586-022-01830-9">doi:10.1038/d41586-022-01830-9</A>]['22].

%A M. Vuorreâ 
%A N. Johannesâ 
%A K. Magnusson
%A A. K. Przybylski
%T Time spent playing video games is unlikely to impact well-being
%J Royal Soc. Open Sci.
%M JUL
%D 2022
%K jrnl, eJrnl, c2022, c202x, c20xx, zz0722, www, internet, video game, gaming,
   play well being, mental health
%X "... We addressed this disconnect by linking six weeks of 38,935 players'
   objective game-behaviour data, provided by seven global game publishers, with
   three waves of their self-reported well-being that we collected. We found
   little to no evidence for a causal connection between game play & well-being.
   However, results suggested that motivations play a role in players'
   well-being. For good or ill, the avg effects of time spent playing video
   games on players' well-being are probably v.small, & further industry data
   are required to determine potential risks & supportive factors to health."
   -- [<A HREF="https://doi.org/10.1098/rsos.220411">doi:10.1098/rsos.220411</A>]['22].
   [Also search for: video game gaming].
   (Also see the [<A HREF="https://www.bbc.com/news/technology-62293235">bbc</A>][27/7/2022].)

%A J. Clayton
%T Meta's chatbot says the company 'exploits people'
%I BBC
%M AUG
%D 2022
%K news, c2022, c202x, c20xx, zz0822, Meta, Facebook, social media, Twitter, AI,
   chatbot, BlenderBot 3, BlenderBot3, Zuckerberg, Microsoft, Bing, Tay
%X '... When asked about Mark Zuckerberg, the chatbot told the BBC: "He did a
   terrible job at testifying before congress. It makes me concerned about our
   country." ... His company exploits people for money and he doesn't care. It
   needs to stop!" it said. ...'
   -- [<A HREF="https://www.bbc.com/news/technology-62497674">bbc</A>][11/8/2022].
   (Also see,
   'Tay, Microsoft's AI chatbot gets a crash course in racism from Twitter',
   The G, [<A HREF="https://www.theguardian.com/technology/2016/mar/24/tay-microsofts-ai-chatbot-gets-a-crash-course-in-racism-from-twitter">24/5/2016</A>].)
   [Also search for: chatbot].

%A M. A. Hossain
%A et al
%T Are you a cyberbully on social media? Exploring the personality traits using
   a fuzzy-set configurational approach
%J Int. J. Info. Mgmt
%V 66
%P #102537
%M OCT
%D 2022
%K jrnl, c2022, c202x, c20xx, zz0123, nasty, social media, email, bully,
   bullying, human behaviour, online, cyberbullying, trolling, study,
   USA, India, RMIT, dark4, big5
%X "... Our all-inclusive model reveals that social media bullies, regardless of
   their gender, marital status, & social media experience, are young, educated,
   neurotic, conscientious, psychopathic, & sadistic with high Machiavellianism
   & low agreeableness. ..."
   -- [<A HREF="https://doi.org/10.1016/j.ijinfomgt.2022.102537">doi:10.1016/j.ijinfomgt.2022.102537</A>]['23].
   [Also search for: nasty social media].

%A M. Vuorre
%A A. K. Przybylski
%T Global well-being and mental health in the internet age
%I OSF
%D 2022
%O Clinical Psych, Sci, Nov 2023, doi:10.1177/21677026231207791
%K TR, c2022, c202x, c20xx, zz0524, www, HREF, http, web, internet,
   social media, twitter, Xtwitter, facebook, psychology, happiness
%X "... We show that the past two decades have seen only small & inconsistent
   changes in global well-being & mental health that are not suggestive of the
   idea that the adoption of internet & mobile broadband is consistently linked
   to -ve psychological outcomes. Further investigation of this topic requires
   transparent study of online behaviours where they occur, namely on online
   platforms. We call for increased collaborative efforts between independent
   scientists & the internet technology sector."
     "... for the avg country, life satisfaction had remained relatively stable,
     whereas both -ve & +ve experiences had increased ... although prev. reports
     have suggested increasing mental-health problems specific to young females
     we did not find support for such changes for the avg country ..."
   -- [<A HREF="https://doi.org/10.31234/osf.io/9tbjy">doi:10.31234/osf.io/9tbjy</A>]['22].
   [Also search for: internet well being].
   (Also see the [<A HREF="https://www.bbc.com/news/articles/c89z2v0pjl3o">bbc</A>][13/5/2024].)

%A A. M. Guess
%A et al
%T How do social media feed algorithms affect attitudes and behavior in an
   election campaign?
%J Science
%V 381
%N 6656
%P 398-404
%M JUL
%D 2023
%K jrnl, c2023, c202x, c20xx, zz0723, www, seb, social media, internet,
   Meta, Facebook, Instagram, USA, politics, election
%X "We investigated the effects of Facebook's & Instagram's feed algs. during
   the 2020 US election ... Moving users out of alg.feeds substantially
   decreased the time they spent on the platforms & their activity. The
   chronological feed also affected exposure to content: The amount of political
   & untrustworthy content they saw increased on both platforms, the amount of
   content classified as uncivil or containing slur words they saw decreased on
   FB, & the amount of content from moderate friends & sources with
   ideologically mixed audiences they saw increased on FB ... did not sig. alter
   levels of issue polarization, affective polarization, political knowledge, or
   other key attitudes during the 3-month study period."
   -- [<A HREF="https://doi.org/10.1126/science.abp9364">doi:10.1126/science.abp9364</A>]['23] (a spec. issue).
   [Also search for: social media politics].

%A D. Guilbeault
%A et al
%T Online images amplify gender bias
%J Nature 
%V 626
%P 1049-1055
%M FEB
%D 2024
%K jrnl, c2024, c202x, c20xx, zz1124, internet, www, image, google, googling,
   search results, stereotype, gender bias, social media
%X "... we show that the rise of images online sig. exacerbates gender bias, 
   both in its statistical prevalence and its psychological impact. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07068-x">doi:10.1038/s41586-024-07068-x</A>]['24].

%A M. Vuorre
%A A. K. Przybylski
%T A multiverse analysis of the associations between internet use and well-being
%J Tech., Mind and Behaviour
%V 5
%N 2
%M MAY
%D 2024
%K www, internet, jrnl, c2024, c202x, c20xx, zz0624, social media, well being,
   GWP, psychology, HREF, www,  facebook, twitter, Xtwitter, young women,
   bullying, cyberbullying
%X "... Of these, 84.9% resulted in positive and statistically sig. associations
   between internet connectivity and well-being. These results indicate that
   internet access and use predict well-being positively and independently from
   a set of plausible alternatives."
   -- [<A HREF="https://doi.org/10.1037/tmb0000127">doi:10.1037/tmb0000127</A>]['24].
   "... negative associations were specific to young (15-24-year-old) women's
   reports of community well-being. ..."
   [Also search for: internet well being].

%A S. D. McCabe
%A et al
%T Post-January 6th deplatforming reduced the reach of misinformation on Twitter
%J Nature
%M JUN
%D 2024
%K jrnl, c2024, c202x, c20xx, zz0624, deplatform, social media, www, twitter,
   Xtwitter, USA, Capitol, politics, Trump, insurrection, fake news, fakenews,
   lies
%X "... we evaluate the effect of the decision by Twitter to suddenly deplatform
   70,000 misinformation traffickers in response to the violence at the US
   Capitol on 6 Jan. 2021 ... Using a panel of more than 500,000 active Twitter
   users & natural experimental designs we evaluate the effects of this
   intervention on the circulation of misinformation on Twitter. We show that
   the intervention reduced circulation of misinformation by the deplatformed
   users as well as by those who followed [them], though we cannot identify the
   magnitude of the causal estimates owing to the co-occurrence of the
   deplatforming intervention with the events surrounding Jan.6th. We also find
   that many of the misinformation traffickers who were not deplatformed left
   Twitter following the intervention. ..."
   -- [<A HREF="https://doi.org/10.1038/s41586-024-07524-8">doi:10.1038/s41586-024-07524-8</A>]['24].
   [Also search for: twitter fakenews].


%A O. Jones
%T Introduction to the X Window System
%I PrenticeHall
%D 1989
%K text, book, X, X10 X11, window, windows, Xwindows, GUI, GUIs, computing
%X isbn:0-13-499997-5.

%A D. Heller
%T Motif Programming Manual
%I O'Reilly and Assoc.
%S The Definitive Guides to the X Windows System
%V 6
%D 1991
%K book, text, Motif, toolkit, OSF, XWindows, X windows window, manager, mwm,
   GUI, GUIs, widget, widgets, computing
%X isbn:0-937175-70-6.

%A W. A. Parrette
%T Motif Programming in the X Windows System Environment
%I McGrawHill
%P 466
%D 1993
%K book, text, Motif, XWindows X windows window, GUI, GUIs,
   widget, widgets, computing
%X isbn:0-07-031722-4; (hb);  isbn:0-07-031723-2; (pb).


%A J. Nedelman
%A P. Heagerty
%A C. Lawrence
%T Quantitative PCR with internal controls
%R #2
%D 1990
%I Dept. Biometry and Statistics, University at Albany, School of Public Health.
%K MolBio, PCR, polymerase chain reaction, control
%X estimate the initial copy number of the target in PCR.
   Show to design a series of PCR's to attain optimal precision of the estimate.
   (Real reactions eventually depart from expected exponential growth.)

%A C. Lawrence
%A A. Reilly
%T Misaligned (shuffled) data analysis with application to gene regulation
%R #3
%D 1990
%I Dept. Biometry and Statistics, University at Albany, School of Public Health.
%K MolBio, gene, genes, genetics, shuffle, permutation,
   misaligned, multiple alignment, site sites, ML, maximum likelihood
%X shuffle of indices in multivariate data
   can be due to error or inherent in data
   general technique to deal with problem.

%A J. Nedelman
%A P. Heagerty
%A C. Lawrence
%T Quantitative PCR: procedures and precisions
%R #4
%D 1990
%I Dept. Biometry and Statistics, University at Albany, School of Public Health.
%K MolBio, PCR, polymerase chain reaction, control
%X apply statistical model to three methods for estimating the initial
   number of target molecules present in a PCR.


%A A. Tridgell
%A P. Mackerras
%T The rsync algorithm
%I Dept. Comp. Sci., Australian National University
%R CS-96-05
%D 1996
%K TR, TR9605, ANU, c1996, c199x, c19xx, rsync, rsynch, rdiff, file, files,
   distributed, system, synchronise, update, updating, rolling checksum,
   MD4, mirroring, remote, network
%X [<A HREF="http://cs.anu.edu.au/techreports/1996/TR-CS-96-05.pdf">TR-96-05</A>]['06]
   "...algorithm for updating a file on one machine to be identical to a file
   on another machine. We assume that the two machines are connected by a
   low-bandwidth high-latency bi-directional communications link. The algorithm
   identifies parts of the source file which are identical to some part of the
   destination file, & only sends those parts which cannot be matched in this
   way. Effectively, the algorithm computes a set of differences without having
   both files on the same machine. The algorithm works best when the files are
   similar, but will also function correctly & reasonably efficiently when the
   files are quite different."
   -- [<A HREF="http://www.samba.org/rsync/tech_report/">TR@samba.org</A>]['06].
   "...The recipient splits its copy of the file into fixed-size non-overlapping
   chunks, say of size S, & computes two checksums for each chunk: the MD4
   hash, & a weaker 'rolling checksum'. It sends these checksums to the sender.
   The sender computes the rolling checksum for every chunk of size S in its own
   version of the file, even overlapping chunks. ... The sender then compares
   its rolling checksums with the set sent by the recipient to determine if any
   matches exist. If they do, it verifies the match by computing the MD4
   checksum for the matching block & by comparing it with the MD4 checksum
   sent by the recipient. ..." --wikip..


%A G. A. Stephen
%T String search
%R TR-92-gas-01
%I School of Electronic Engineering Science, University College of N. Wales.
%M OCT
%D 1992
%P 103
%K string, strings, find, search, pattern, match, matching, edit distance,
   LCS, LCSS, longest common subsequence, sequence, similarity, repeat,
   survey, TR9201, c1992, c199x, c19xx
%X 8 pages of references.   LA has a copy.
   [Also search for: string search algorithm].


%A R. Giegerich
%T Declarative approach to the development of dynamic programming algorithms
%I University of Bielefeld, Technische Fakultat
%D 1998
%R 98-02
%K TR 98 02, TR9802, DPA, RNA tRNA, grammar, grammars, functional programming,
   FP, Agpi, pi, ags, c1998, c199x, c19xx
%X [<A HREF="http://www.techfak.uni-bielefeld.de/techfak/ags/pi/Agpi/publications.html">publications</A>],
   [<A HREF="http://www.techfak.uni-bielefeld.de/">Techfak, Uni Bielefeld</A>][6/'00].


%A A. J. Martin
%T A message-passing model for highly concurrent computation
%R CS-TR-88-13
%I Comp. Sci. Dept., Caltech
%D 1988
%K TR, TR13, parallelism, concurrency, c1988, c198x, c19xx
%X L.A. has a copy.

%A A. J. Martin
%A S. M. Burns
%A T. K. Lee
%A D. Borkovic
%A P. J. Hazewindus
%T The first asynchronous microprocessor: The test results
%R CS-TR-89-6
%I Comp. Sci. Dept., Caltech
%M APR
%D 1989
%K TR, TR6, micro processor, hardware, architecture, c1989, c198x, x19xx
%X L.A. has a copy.


%A B. K. Boguraev
%T Automatic resolution of linguistic ambiguities
%R TR-11
%I Computer Laboratory, University of Cambridge
%M Aug
%D 1979
%K English, natural language, ambiguity, ambiguous, PhD thesis
%O (LA has)

%A B. K. Boguraev
%A K. Sparck Jones
%A J. I. Tait
%T Three papers on parsing
%R TR-17
%I Computer Laboratory, University of Cambridge
%D 1982
%K English, natural language, parse, parser, parsing, AI
%O (LA has)

%A K. Sparck Jones
%T Compound noun interpretation problems
%R TR-45
%I Computer Laboratory, University of Cambridge
%M Jul
%D 1983
%K AI, English, natural language, compound noun

%A W. R. Stoye
%A T. J. W. Clarke
%A A. C. Norman
%T Some practical methods for rapid combinator reduction
%I Computer Laboratory, Cambridge University
%D 1984
%K functional programming, FP, applicative, implementation

%A J. Fairbairn
%T Ponder and its type system
%R TR-31
%I Computer Laboratory, Cambridge University
%D 1982
%M Nov
%K c1982, c198x, c19xx, Ponder, SKI, FP, functional, applicative,
   programming language, type, data, datatype, check, checker

%A J. Fairbairn
%T A new type-checker for a functional language
%R TR-53
%I Computer Laboratory, University of Cambridge
%D 1984
%K data type, checker, Ponder, applicative, functional, inference, polymorphic,
   programming, FP, polymorphism
%O (LA has)

%A J. Fairbairn
%T Design and implementation of a simple typed language
   based on the lambda calculus
%R TR-75
%I Computer Laboratory, Cambridge University
%M May
%D 1985
%K functional,  applicative, Ponder,  polymorphism, polymorphic, data type,
   types, typed,  programming, FP
%O PhD thesis (LA has)

%A J. Fairbairn
%A S. W. Wray
%T Optimisations for lazy evaluators
%I Computer Laboratory, Cambridge University
%D 1984
%K functional programming, FP, applicative, optimise, optimization

%A M. Gordon
%T HOL a machine oriented formulation of higher order logic
%R TR-68
%I Computer Laboratory, Cambridge University
%M Jul
%D 1985
%K high, high-order, logic

%A S. C. Wray
%T Implementation techniques for functional programs
%R
%I Computer Laboratory, Cambridge University
%O PhD thesis
%D 1986
%K FP, functional, applicative, program, programming, style, technique,
   implement

%A G. Winskel
%T Using information systems to solve recursive domain equations effectively
%R TR-51
%I Computer Laboratory, University of Cambridge
%D 1984
%K lattice theory, CPO
%O (LA has)

%A G. Winskel
%T Categories of models for concurrency
%I Computer Laboratory, Cambridge University
%R 58
%D 1984
%K model, category theory, parallel, communication, concurrent
%O (LA has)

%A D. C. J. Matthews
%T Introduction to Poly
%R TR-29
%I Computer Laboratory, University of cambridge
%M May
%D 1982
%K polymorphism, polymorphic, programming language, type, types, datatype

%A D. C. J. Matthews
%T Poly report
%R TR-28
%I Computer Laboratory, University of Cambridge
%M Aug
%D 1982
%K polymorphic, polymorphism, programming language, types, datatype, type

%A D. C. J. Matthews
%T Programming language design with polymorphism
%I Computer Laboratory, University of Cambridge
%R TR-49
%D 1983
%K polymorphism, poly polymorphic, language, type, types, datatype

%A M. A. Johnson
%T Exception handling in domain based systems
%R TR-27
%I Computer Laboratory, University of Cambridge
%M Sep
%D 1981
%K exception, raise, handle, catch, throw

%A B. Moszkowski
%T Executing temporal logic programs
%R TR-55
%I Computer Laboratory, University of Cambridge
%M Aug
%D 1984

%A W. Stoye
%T The implementation of functional languages using custom hardware
%R TR-81
%I Computer Laboratory, University of Cambridge
%M Dec
%D 1985
%K functional programming, FP, applicative, language, S, K, I,
   SKIM, implementation
%X PhD thesis
   1 Introduction
   2 combinator reduction
   3 microcode
   4 optimisation
   5 director strings
   6 problems
   7 functional programming
   8 input and output
   9 operating systems
   10 conclusions
   A timeslicer implementation
   B Miranda
   C a functional program

%A I. D. Wilson
%T Operating System Design for Large Personal Workstations
%R TR-83
%I Computer Laboratory, University of Cambridge
%M Jul
%D 1985
%K operating system, systems, work station, workstation, personal computer,
   BCPL, Tripos
%X PhD thesis

%A W. Stoye
%T A new scheme for writing functional operating systems
%R TR-56
%I Computer Laboratory, University of Cambridge
%K functional programming, FP, applicative, OS, operating system,
   s, k, i, ski, skim, machine, message passing

%A D. C. J. Matthews
%T A persistent storage system for Poly and ML
%M Jan
%D 1987
%R TR-102
%I Computer Laboratory, University of Cambridge
%K persistent storage, object, workspace, storage, store,
   Poly, ML, SML

%A S. R. Eddy
%R R. Durbin
%T RNA sequence analysis using covariance models
%I MRC Laboratory of Molecular Biology, Cambridge, UK
%M APR
%D 1994
%O Nucl. Acids Res. 22(11) 2079-2088 1994
%K MolBio, RNA, secondary structure, tRNA, statistics, model,
   stochastic, context free, context-free, grammar, CFG, SCFG, HMM,
   multiple alignment, NAR, jrnl
%X We describe a general approach to several RNA sequence analysis problems
   using probabilistic models that flexibly describe the secondary structure
   and primary sequence consensus of an RNA sequence family.
   ... We also describe an algorithm for learning a model ...
   sre@mrc-lmb.cam.ac.uk   rd@mrc-lmb.cam.ac.uk .


%A M. Steel
%T Recovering a tree from the leaf colourations it generates under a Markov
   model
%I Dept. Mathematics & Statistics, University of Canterbury, Christchurch, NZ.
%R 103
%M MAY
%D 1993
%K TR, c1993, c199x, c19xx, MolBio, evolutionary, family, phylogenetic tree,
   trees
%X "we describe a simple transformation that allows for the fast recovery of a
   tree from the probabilities such a tree induces on the colourations of its
   leaves under a simple Markov process (with unknown parameters). This
   generalizes earlier results by not requiring the transition matrices
   associated with the edge of the tree to be of a particular form,
   or to be related to some fixed rate matrix, and by not insisting on a
   particular distribution of colours at the root of the tree. Applications
   to taxonomy are outlined briefly in three corollaries."  [9 refs].


%A R. J. van Glabbeek
%T Notes on the methodology of CCS and CSP
%R CS-R8624
%M Aug
%D 1986
%I Centre for Mathematics and Computer Science, Amsterdam
%K CCS, CSP, methodology, concurrent, parallel, process,
   communicate, communication,
   message,  process, algebra, concurrency
%X methodology of concurrency CCS CSP
   representation of processes
   identification issue
   nondeterminism communication recursion abstraction divergence
   deadlock dead lock

%A J. K. Lenstra
%A A. H. G. Rinnooy Kan
%T Computational complexity of discrete optimization problems
%I Mathematisch Centrum, Amsterdam
%R BW 77/77
%D 1977
%K optimisation problem, complexity, time, space, P, NP, NPC

%A P. R. H. Hendriks
%T Type-checking mini-ML: an algebraic specification with user-defined syntax
%I Centre for Mathematics and Computer Science, Amsterdam
%R CS-R8737
%M Aug
%D 1987
%K ML, mini ML, algebraic formal specification, polymorphism, type, datatype
%X really about application of formal specification to the case
   of polymorphic type checker.

%A P. America
%A J. W. de Bakker
%T Designing equivalent semantic models for process creation
%R CS-R8732
%M Jul
%D 1987
%I Centre for Mathematics and Computer Science, Amsterdam
%K uniform, non-uniform, static, dynamic

%A J. A. Bergstra
%A J. W. Klop
%T A convergence theorem in process algebra
%R CS-R8733
%M Jul
%D 1987
%I Centre for Mathematics and Computer Science, Amsterdam
%K model theory, recursion, merge, left merge

%A K. R. Apt
%A L. Bouge
%A Ph. Clermont
%T Two normal form theorems for CSP programs
%R CS-R8735
%M Jul
%D 1987
%I Centre for Mathematics and Computer Science, Amsterdam
%X first  form - each process has only one I/O repetitive command and
      all its I/O commands appear as guards in this command
   second - moreover required that all guards of this I/O repetitive command
      are in fact I/O guards.
   Transformation is given.
   Also shown no transform into second normal form can preserve
   freedom from deadlock.

%A J. A. Bergstra
%A J. W. Klop
%A E.-R. Olderog
%T Readies and failures in the algebra of communicating processes (revised)
%R CS-R8748
%M Oct
%D 1987
%I Centre for Mathematics and Computer Science, Amsterdam
%K process, ready, failure, ACP, CCS, CSP


%A G. Winskel
%T A note on powerdomain and modality
%M SEP
%D 1983
%R CMU-CS-83-150
%I Dept Computer Science, Carnegie-Mellon University
%K powerdomain, power domain, modal logic,
   CMU, TR-83-150, TR-150, TR 150
%O LNCS  Foundations of Computer Science Sweden Aug 1983

%A G. Jacobson
%T Succinct static data structures
%R CMU-CS-89-112
%I Dept Comp. Sci., Carnegie-Mellon U.
%K CMU, TR-89-112, TR112, TR 112, PhD thesis, c1989, c198x, c19xx, compression,
   list, binary, tree, planar graph, information theory, compress, compressed,
   compress, compact, succinct, data structure, structures
%P 101
%M JAN
%D 1989
%X PhD thesis;
     compress data structures so that operations can still
     be carried out efficiently, e.g., traversal.
     Trees by balanced brackets not perfect as language allows unbalanced
     but asymptotically efficient.
     Number of balanced strings of 2n brackets is the nth Catalan number
     C(n) = (2n,n)/(n+1)
     by Stirling's approx C(n) = 4**n Theta(n**(-3/2))
     take log2,  log2(C(n)) = 2n+o(n)     asymptotic need 2 bits per node.
     Another 2 bit per node representation
     is called  marked preorder sequential;
     store in preorder a pair of bits (left empty?, right empty?).
 * Also see: G. Jacobson, 'Space-efficient static trees and graphs',
     FOCS, pp.549-554, Nov 1989.
     "D.S. that rep. static unlabeled trees & planar graphs are developed. ...
     more space efficient than conventional pointer-based ..., but (to within a
     const.factor) ... just as time efficient for traversal ops. For trees, the
     D.S. described are asymptotically optimal: there is no other struct. that
     encodes n-node trees with fewer bits per node, as N grows without bound.
     For planar graphs (& all g. of bounded page #), the D.S. described uses
     lin.-space: it is within a const.factor of the most succinct repn"
     -- [<A HREF="http://dx.doi.org/10.1109/SFCS.1989.63533">doi:10.1109/SFCS.1989.63533</A>]['10].
   [Also search for: succinct data structure].

%A D. Tarditi
%A A. Acharya
%A P. Lee
%T No assembly required: compiling standard ML to C
%R CMU-CS-90-187
%I School of Computer Science, Carnegie Mellon University
%M NOV
%D 1990
%K standard, ML, SML, C, CC, functional, applicative, programming language,
   MLtoC, SMLtoC, implementation, compile, compiler, translation, intermediate,
   CMU, TR-90-187, TR187, TR 187
%X Translate SML to C.
   Claim preserve tail recursive properties
   and code a factor of 2 slower than best native code compiler.
   LA got a copy from Roland Yap.

%A J. C. Reynolds
%T Preliminary design of the programming language Forsythe
%R CMU-CS-88-159
%I School of Computer Science, Carnegie Mellon University
%P 49
%M JUN
%D 1988
%K CMU, Forsythe, programming language, Algol 60 Algol60, call by name,
   TR-88-159, TR159, TR 159
%X This is a preliminary description of the programming language Forsythe,
   which is a descendant of Algol 60 intended to be as uniform and general
   as possible, while retaining the basic character of its progenitor.
   10 refs.

%A J. C. Reynolds
%T Replacing complexity with generality: the programming language Forsythe
%I School of Computer Science, Carnegie Mellon University
%P 11
%M APR
%D 1991
%O based on lectures at DARPA/ISTO Software Principal Investigators Mtg, Feb 91
%K CMU, Forsythe, programming language, Algol 60, Algol60, call by name,
   high order, intersection type, types
%X By using concepts of modern programming-language theory, such as high-order
   procedures and intersection types, it is possible to design a programming
   language that is extremely general without being complicated. This thesis
   is illustrated by the Algol-like language Forsythe.

%A J. R. Shewchuk
%T An introduction to the conjugate gradient method without the agonizing pain,
   edition 1 1/4
%I School of Comp. Sci., Carnegie Mellon University
%M AUG
%D 1994
%K TR, CMW, intro, c1994, c199x, c19xx, zz0812, numerical methods, algorithm,
   quadratic forms, conjugate directions, gradients, CG, optimization,
   preconditioning, steepest descent, linear equations, minimization
%X "... quadratic forms ... steepest descent ... conjugate directions ...
   conjugate gradients ... preconditioning ...
   solve  A x = b, where x an unknown vector, b known vector,
   A known square, symmetric positive definite (or pos-indef) matrix. ...
   Quadratic form  f(x) = 0.5 x' A x - b' x + c   [[x' is transpose of x]] ...
   if A is symm and +ve-def the f(x) is minimized by the soln to Ax=b. ..."
   64pp., 16 refs.   (via Tom C.)
   -- pdf@[<A HREF="http://www.cs.cmu.edu/~quake-papers/painless-conjugate-gradient.pdf">cmu</A>]['12],
   auth@[<A HREF="http://www.cs.cmu.edu/~jrs/jrspapers.html">cmu</A>]['12].

%A J. M. Wing
%T Subtyping for distributed object stores (extended abstract)
%R CMU-CS-97-121
%I School of Comp. Sci., Carnegie Mellon U.
%M APR
%D 1997
%P 11
%K TR121, CMU, CMUCS97121, store, c1997, c199x, c19xx, OO, OOP, Liskov,
   subtype, inheritance, mutable objects, change, JMWing, BLiskov
%X "I review the Liskov and Wing subtype definition that takes into
   consideration the problem of subtyping in the presence of mutable objects.
   I then show how this notion of subtyping is relevant to the design of the
   TOM object repository whose main application today is a data type conversion
   service accesssible through the Web."
   [<A HREF="http://reports-archive.adm.cs.cmu.edu/anon/1997/abstracts/97-121.html">TR</A>]['05]
   [NB. "mutable objects"].   Also see: Wing T0PLAS '94.

%A B. Barthomieu
%T Programming with behaviours in an ML framework.  The syntax and semantics
   of LCS.
%I Laboratoire d'Automatique et d'Analys des Systemes du CNRS
%M APR
%D 1993
%K LCS, asynchronous parallel programming language, concurrent,
   message based, CSP, CCS, LAAS, CNR
%X extends standard ML with primitives for concurrency based on
   a higher order extension of the CCS formalism.
   Typechecking - communications and behaviours.
   Bernard.Berthomieu@laas.fr  (as of '93)


%A P. Sestoft
%A H. Sondergaard
%T Non-determinacy in a functional language
%I Univ. of Copenhagen, Universitetsparken 1, DK-2100 Copenhagen 0, Denmark
%R DIKU 86/12
%D 1986
%K functional programming, FP, applicative,
   alternation, nondeterminism, nondeterminacy,   bounded, unbounded,
   infinite choice, fairness, fair,  angelic, demonic, erratic,  chaotic,
   bounded, Power domain, denotational semantics, DS, theory, lattice
%X introduces a boundedly non-deterministic operator   exp|exp
   in a simple functional language
   pgm ::= f(x,y)=exp; f(int,int)
   exp ::= int | x | y | exp+exp | (exp->exp,exp) | f(exp,exp) |
           exp '|' exp
   12 semantics: {strict,lazy} x {angelic,demonic,erratic} x {singular,plural}
   Hoare, Plotkin, Smyth powerdomains
   Also discusses fairness.
   Specifications.

%A N. D. Jones
%A P. Sestoft
%A H. Sondergaard
%T Mix: a self-applicable partial evaluator for experiments in compiler
   generation
%I DIKU, University of Copenhagen
%M Jun
%D 1987
%R DIKU 87/8
%O submitted to Jrnl of Lisp and Symbolic Computation
%K Mix, compiler, compiler-compiler, partial evaluation,
   autoprojector, mixed computation,  symbolic evaluation,  unfolding

%A D. Sands
%T A naive time analysis and its theory of cost equivalence
%I DIKU, University of Copenhagen
%S TOPPS report
%R D-173
%D 1993
%O The Jrnl of Logic and Computation, OUP, to appear as of 1995
%K functional programming, FP, lazy evaluation, time, complexity, speed,
   analysis, sort, sorting, zz0995
%X via enews 9/93 and 8/95
   ftp.diku.dk in
   /pub/diku/semantics/papers/D-173.ps.Z D-173.dvi.Z
   Other papers relating to this area are available by anon ftp from
   theory.doc.ic.ac.uk in directory papers/Sands


%A P. van Emde Boas
%T An O(n log log n) on-line Algorithm for the insert-extract min problem
%R TR 74-221
%I Dept Computer Science, Cornell University
%M Dec
%D 1974
%K set, algorithm, priority queue, binary tree, trees
%X (LA has)
   [Also search for: van Emde Boas].

%A R. L. Constable
%T The nearly ultimate Pearl
%R TR 83-551
%I Dept Computer Science, Cornell University
%M Jan
%D 1984
%K Pearl, theory, type, datatype, programming language, types

%A A. Moitra
%T Automatic construction of CSP programs from sequential
   non-deterministic programs
%M Mar
%D 1984
%R 84-597
%I Dept Computer Science, Cornell University
%K CSP, CCS, parallel, algorithm, transformation
%X (LA has)

%A D. Bitton
%A D. J. DeWitt
%A D. K. Hsiao
%A J. Menon
%T A taxonomy of parallel sorting
%R TR 84-601
%I Dept Computer Science, Cornell University
%M Apr
%D 1984
%K parallel sort sorting algorithm

%A R. L. Constable
%A N. P. Mendler
%T Recursive definitions in type theory
%R TR 85-659
%I Dept Computer Science, Cornell University
%M Jan
%D 1985
%K type, types, datatype, theory, recursive, recursion, logic, domain,
   semantics
%X (LA has)

%A B. Natarajan
%T The homogeneous capture of random strings
%R TR 85-672
%M Apr
%D 1985
%I Dept Computer Science, Cornell University
%K c1985, c198x, c19xx, random string, Kolmogorov, theory, complexity

%A R. W. Harper
%T Aspects of the implementation of type theory
%R TR 85-675
%I Dept Computer Science, Cornell University
%M Apr
%D 1985
%K type, types, datatype, theory, recursive, recursion, logic, domain,
   semantics, implementation
%X PhD thesis (LA has)

%A H-J. Boehm
%T A logic for the Russell programming language
%R TR-84-593
%M Feb
%D 1984
%I Dept Computer Science, Cornell University
%K Russell, theory, axiom, axiomatisation
%X PhD thesis

%A K. Pingali
%T Lazy evaluation and the logic variable
%R 87-877
%I Dept Computer Science, Cornell University
%M Nov
%D 1987
%K c1987, c198x, c19xx, lazy evaluation, functional, applicative, programming,
   FP, LP, FLP, logic, variable, unify, unification, data flow, dataflow,
   demand propagation
%X gives implementation of lazy functional programming in data flow,
   uses demand propagation "signals".


%A A. J. Miller
%T Some notes on statistical packages for PCs
%I CSIRO Division of Mathematics & Statistics, Melbourne
%M OCT
%D 1992
%P 55
%K c1992, c199x, c19xx, maths, stats, package, language, survey,
   S, Splus S-plus, S+, SAS

%A G. Turner
%T A comparison of 'The Limits to Growth' with thirty years of reality
%I CSIRO
%P 55
%M JUN
%D 2008
%O Global Environmental Change, 18(3), pp.397-411, Aug., 2008.
%K TR, c2008, c200x, c20xx, zz1208, limit, limits, growth, sustainability,
   resources, sustainable, ecosystems, ecology, pollution, oil, energy, metals,
   food, economics, dynamics, collapse, report, Club of Rome, Meadows,
   zzPrediction
%X "In 1972, the Club of Rome's infamous report 'The Limits to Growth'
   (Meadows et al., 1972) presented some challenging scenarios for global
   sustainability, based on a system dynamics computer model to simulate the
   interactions of 5 global economic subsystems, namely: population, food
   production, industrial production, pollution, & consumption of non-renewable
   natural resources. Contrary to popular belief, The Limits to Growth scenarios
   by the team of analysts from the MIT did not predict world collapse by the
   end of 20C. This paper focuses on a comparison of recently collated
   historical data for 1970-2000 with scenarios presented in [LtoG]. ... shows
   that 30 years of historical data compares favorably with key features of a
   business-as-usual scenario called the 'standard run' scenario, which results
   in collapse of the global system midway through the 21C. The data does not
   compare well with other scenarios involving comprehensive use of tech. or
   stabilizing behaviour & policies. The results indicate the particular
   importance of understanding & controlling global pollution."
   GEC, [<A HREF="http://dx.doi.org/10.1016/j.gloenvcha.2008.05.001">doi:10.1016/j.gloenvcha.2008.05.001</A>]['08];
   55 pages, was www.csiro.au/files/files/plje.pdf 2008.
   [Also search for: limits growth resources].

%A K. R. Apt
%A R. N. Bol
%T Logic programming and negation: a survey
%R CS-R9402
%I CWI
%D 1994
%P 62
%K LP, prolog, not, CSci
%X f 20.00
   CWI, Centrum voor Wiskunde en Informatica
        Centre for Mathematics and Computer Science
   Library, P.O. Box 94079, 1090 GB  Amsterdam, The Netherlands
   email: ay@cwi.nl
   ftp: ftp.cwi.nl; directory pub/CWIreports; get the INDEX file first.

%A M. Holsheimer
%A A. P. J. M. Siebes
%T Data mining; the search for knowledge in databases
%R CS-R9406
%I CWI
%D 1994
%P 78
%K data base, mine, mining, discovery
%X f 24.00
   CWI, Centrum voor Wiskunde en Informatica
        Centre for Mathematics and Computer Science
   Library, P.O. Box 94079, 1090 GB  Amsterdam, The Netherlands
   email: ay@cwi.nl
   ftp: ftp.cwi.nl; directory pub/CWIreports; get the INDEX file first.

%A M. L. Kersten
%A C. A. van den Berg
%A A. P. J. M. Siebes,
%A C. J. E. Thieme
%A M. H. van der Voort
%T The Goblin database programming language
%R CS-R9407
%I CWI
%D 1994
%P 37
%K data base, Goblin
%X f 16.00
   CWI, Centrum voor Wiskunde en Informatica
        Centre for Mathematics and Computer Science
   Library, P.O. Box 94079, 1090 GB  Amsterdam, The Netherlands
   email: ay@cwi.nl
   ftp: ftp.cwi.nl; directory pub/CWIreports; get the INDEX file first.

%A M. Holsheimer
%A M. L. Kersten
%T Architectural support for data mining
%R CS-R9429
%I CWI
%D 1994
%P 12
%K data base, mine, mining, discovery
%X f 12.00
   CWI, Centrum voor Wiskunde en Informatica
        Centre for Mathematics and Computer Science
   Library, P.O. Box 94079, 1090 GB  Amsterdam, The Netherlands
   email: ay@cwi.nl
   ftp: ftp.cwi.nl; directory pub/CWIreports; get the INDEX file first.

%A K. R. Apt
%A F. Teusink
%T Comparing negation in logic programming and in Prolog
%R CS-R9468
%I CWI
%D 1994
%P 18
%K LP, not, CSci
%X f 12.00
   CWI, Centrum voor Wiskunde en Informatica
        Centre for Mathematics and Computer Science
   Library, P.O. Box 94079, 1090 GB  Amsterdam, The Netherlands
   email: ay@cwi.nl
   ftp: ftp.cwi.nl; directory pub/CWIreports; get the INDEX file first.


%A T. S. Ray
%T Evolution and optimization of digital organisms
%I School of Life and Health Sciences,
   University of Delaware, Newark, Delaware 19716, USA
%D 1991
%K Tierra, genetic, algorithm, evolution, mutation, adaption, optimise, digital,
   Alife, artificial life, parasites, replication, diversity, coevolution,
   c1991, c199x, c19xx
%X Programs mutate and evolve.
   The machine code uses pattern matching rather than addresses.
   Limited instruction set (~ 32).
   Claims this reduces brittleness of organisms -
   higher fraction of descendants are viable.
   Parasites evolve, then resistance, then hyper parasites ...
   Existence of parasites seems to encourage diversity amongst organisms.
   Social organisms evolve, sex?
   email: ray@brahms.udel.edu.


%A A. Bundy
%A B. Du Boulay
%A J. Howe
%A G. Plotkin
%T The researchers' bible
%R DAI occasional paper 10
%M SEP
%D 1978
%I Dept. Artificial Intelligence, University of Edinburgh
%O Modified for Computer Science at TCD by V.Gledhill, 1999 (etc.)
%K c1978, c197x, c19xx, TR 10, TR10, PhD, MSc, masters, degree, university,
   sage advice, pitfall, project, thesis, write, writing,
   postgraduate, supervisor, research student
%X "Getting a Ph.D. or M.Sc is hard work. This document gives advice about
   various aspects of the task. Section 1 describes the problem -- what is a
   thesis? Section 2 suggests ways to choose a topic. Sections 3 and 4 describe
   some of the pitfalls and hurdles which students have encountered. Sections 5
   and 6 advise about research support and then executing a research project.
   Sections 7, 8 and 9 deal with two of the three Râs: reading and writing.
   Section 10 describes the examination for a research degree, and how to cope
   with it."
   -- pdf@[<A HREF="https://sweb.inf.ed.ac.uk/bundy/how-tos/resbible.html">ed.ac</A>]['18],
   or pdf@[<A HREF="http://www.ifs.tuwien.ac.at/~silvia/research-tips/researchers_bible-1999.pdf">tuwien</A>]['18],
   or pdf@[<A HREF="http://www.cs.otago.ac.nz/research/resources-for-pgs/resbible.pdf">Otago</A>]['18], etc..

%A M. F. McCollum
%T Using natural language to interrogate a database
%R DAI working paper 122
%I Dept Artificial Intelligence, University of Edinburgh
%D Oct
%D 1982
%K AI, English, natural language, grammar, data base, database

%A A. Ramsay
%T Understanding English descriptions of programs
%R DAI Research Paper 140
%D 1980
%I Dept Artificial Intelligence, University of Edinburgh
%O Proc AISB 1980 Conf' on AI
%K AI, English, natural language, program, paraphrase, understand

%A A. Ramsay
%T Parsing English text
%R DAI Research Paper 139
%D 1980
%I Dept Artificial Intelligence, University of Edinburgh
%O Proc AISB Conf on AI 1980
%K c1980, c198x c19xx, English, natural language, parse, parser, parsing,
   grammar, AI

%A A. Mycroft
%T Abstract interpretation and optimising transformations for applicative
   programs
%I Dept Computer Science, University of Edinburgh
%R CST-15-81 (PhD thesis)
%M Dec
%D 1981
%K PhD thesis, c1981, c198x, c19xx, computer program, static analysis, strict,
   strictness, destructive operators,  symbolic execution, FP, functional,
   applicative, programming, optimise, optimisation, optimization
%X [Also search for: static analysis program].

%A K. Mitchell
%T A user's guide to PFL
%I Dept Computer Science, University of Edinburgh
%D 1984
%K c1984, c198x, c19xx,FP, parallel, CCS, CSP, communication, ML, applicative,
   PFL, process, processes, functional programming
%X (Also see [<A HREF="http://www.allisons.org/ll/FP/LambdaCCS/">PFL</A>].)

%A K. Mitchell
%T Implementation of process synchronisation and their analysis
%I Dept Computer Science, University of Edinburgh
%R CST-38-86 (PhD thesis)
%M Jul
%D 1986
%K c1986, c198x, c19xx, FP, applicative, functional programming, CCS, PFL,
   parallel, communication, ML
%X (Also see [<A HREF="http://www.allisons.org/ll/FP/LambdaCCS/">PFL</A>].)

%A L. M. M. Damas
%T Type assignment in programming languages
%R CST-33-85
%I Dept Computer Science, University of Edinburgh
%M Apr
%D 1985
%K data types, datatype, type inference
%X (LA has)

%A R. deNicola
%T Two complete axiom systems for a theory of communicating sequential processes
%R CSR-154-83
%I Dept Computer Science, University of Edinburgh
%M Dec
%D 1983
%K theory, axiom, CCS, CSP

%A R. Milner
%T Is computing an experimental science
%R ECS-LFCS-86-1
%M Aug
%D 1986
%I Dept Computer Science, University of Edinburgh
%X opening address for new laboratory

%A R. Milner
%T The standard ML core language
%I Dept Computer Science, University of Edinburgh
%K ML, functional, applicative programming, FP, language
%D 1984

%A R. Milner
%T A proposal for standard ML
%I Dept Computer Science, University of Edinburgh
%K ML, functional, applicative programming, FP, language
%M Dec
%D 1983
%R CSR-157-83

%A F. V. Jensen
%T Inductive inference in reflexive domains
%R CSR-86-81
%M May
%D 1981
%I Dept Computer Science, University of Edinburgh
%K data type, types, inference, recursion, recursive, reflexive

%A R. Milner
%A L. Morris
%A M. Newey
%T A logic for computable functions with reflexive and polymorphic types
%R LCF TR-1
%I Dept Computer Science, University of Edinburgh
%M Jan
%D 1975
%K LCF, c1975, c197x, c19xx
%X [Also search for: theorem proving].

%A L. G. Valiant
%T Negation can be exponentially powerful
%R CSR-39-79
%M Apr
%D 1979
%I Dept Computer Science, University of Edinburgh
%K complexity, NP, NPC, P
%O 11 ACM Symposium on Theory of Computing, Atlanta, Apr 1979

%A L. G. Valiant
%T Completeness classes in algebra
%M Apr
%D 1979
%I Dept Computer Science, University of Edinburgh
%R CSR-40-79
%K NP, P, NPC, complexity
%O 11 ACM Symposium on Theory of Computing, Atlanta, Apr 1979

%A L. G. Valiant
%T The complexity of combinatorial computations: an introduction
%R CSR-30-78
%M Oct
%D 1978
%I Dept Computer Science, University of Edinburgh
%K P, NP, NPC

%A L. Sterling
%T Impress: meta-level concepts in theorem proving
%R DAI working paper No 119
%I Dept of Artificial Intelligence, University of Edinburgh
%M Aug
%D 1982
%K meta level, metalevel, automatic, automated, theorem proving, prover,
   LP, prolog, logic programming
%X [Also search for: theorem proving].

%A D. H. D. Warren
%T An improved Prolog implementation which optimises tail recursion
%R DAI research paper 141
%I Dept of Artificial Intelligence, University of Edinburgh
%D 1980
%K prolog, logic programming, LP, optimisation, optimization, tail recursion

%A B. Ritchie
%T Othello - a strategy based outlook
%R DAI working paper 69
%I Dept of Artificial Intelligence, University of Edinburgh
%M Jul
%D 1980
%K TR, c1980, c198x, c19xx, board game, Othello, AI, strategy
%X [Also search for: Othello game].

%A R. Milner
%T A complete axiomatisation for observational congruence of finite-state
   behaviours
%R ECS-LFCS-86-8
%I Laboratory for Foundations of Computer Science, Edinburgh University
%M Aug
%D 1986
%O Information and Computation, 81, pp.227-247, 1989
%K c1986, c198x, c19xx, TR, CCS, axiom, theory, finite state, process,
   bisimulation, behaviour
%X "Finite state automata, with non-determinism & silent transitions, can be
   interpreted not as subsets of the free monoid as in classical automata theory
   but as congruence classes under a congruence relation based upon the idea of
   bisimulation due to Park. In this paper a complete axiomatisation for this
   congruence is presented. It extends the previously known complete
   axiomatisation by Hennessy & Milner for finite automata (no cycles); the
   extension consists of file recursion rules."
   [<A HREF="http://www.lfcs.inf.ed.ac.uk/reports/86/ECS-LFCS-86-8/">TR</A>]['07],
   [<A HREF="http://dx.doi.org/10.1016/0890-5401(89)90070-9">doi:10.1016/0890-5401(89)90070-9</A>]['07].

%A R. Harper
%T Modules and Persistence in Standard ML
%I Laboratory for Foundations of Computer Science, Edinburgh University
%R ECS-LFCS-86-11
%M Sep
%D 1986
%K module, ML, SML, functional, applicative programming, FP

%A R. M. Burstall
%T Research in interactive theorem proving at Edinburgh University
%I Laboratory for Foundations of Computer Science, Edinburgh University
%R ECS-LFCS-86-12
%M Oct
%D 1986
%K LCF, c1986, c198x, c19xx, prove, prover, automatic, automated,
   theorem proving, prover
%X [Also search for: theorem proving].

%A R. Harper
%T Introduction the standard ML
%I Laboratory for Foundations of Computer Science, Edinburgh University
%R ECS-LFCS-86-14
%O CSR-220-86
%M Nov
%D 1986
%K ML, SML, functional, applicative programming, FP
%X (Also see [<A HREF="http://www.allisons.org/ll/FP/SML/">SML</A>].)

%A J. Parrow
%T Verifying a CSMA/CD-protocol with CCS
%I Laboratory for Foundations of Computer Science, Edinburgh University
%R ECS-LFCS-87-18
%O CSR-224-87
%M Jan
%D 1987
%K CCS, CSMA, CD, protocol, parallel, concurrent, verification

%A D. Walker
%T Introduction to a calculus of communicating systems
%I Laboratory for Foundations of Computer Science, Edinburgh University
%R ECS-LFCS-87-22
%O CSR-227-87
%M MAR
%D 1987
%K TR, c1987, c198x, c19xx, FP, PFP, CCS, CSP, process, model,
   finite state behaviour, parallel, concurrent, programming language
%X "... The bulk of the material presented was drawn from a set of lecture notes
   written by Milner in the autumn of 1986, these being a development and
   refinement of their author's monograph ``A Calculus of Communicating
   Systems'' published by Springer-Verlag in 1980 ..."
   -- [<A HREF="https://www.lfcs.inf.ed.ac.uk/reports/87/ECS-LFCS-87-22/">ed.as.uk</A>]['22].
   [Also search for: CCS].

%A R. Milner
%T Changes to the standard ML core language
%I Laboratory for Foundations of Computer Science, Edinburgh University
%R ECS-LFCS-87-33
%O CSR-240-87
%M Aug
%D 1987
%K c1987, c198x, c19xx, TR, ML, SML, functional, applicative programming, FP
%X datatypebinding withtype typebinding;
   numeric record labels modified;
   polymorphic equality and < > - basically if no -> involved;
   polymorphic :=
   polymorphic exceptions

%A R. Harper
%A R. Milner
%A M. Tofte
%T The semantics of standard ML version 1
%I Laboratory for Foundations of Computer Science, Edinburgh University
%R ECS-LFCS-87-36
%O CSR-244-87
%M Aug
%D 1987
%K ML, SML, functional, applicative programming, FP

%A L. G. Valiant
%T Negative results on counting
%R CSR-38-79
%M Apr
%D 1979
%I Dept. Computer Science, Edinburgh University

%A L. G. Valiant
%T The complexity of enumeration and reliability problems
%R CSR-15-77
%M Oct
%D 1977
%I Dept. Computer Science, Edinburgh University

%A L. G. Valiant
%T The complexity of computing the permanent
%R CSR-14-77
%M Jun
%D 1977
%I Dept. Computer Science, Edinburgh University

%A R. Burstall
%T Programming with modules as typed functional programming
%I Dept. Computer Science, University of Edinburgh
%D 1984
%O International Conference on 5th Generation Computer Systems,
   Tokyo, 84
%K type, module, Pebble, functional


%A M. Tofte
%T Four Lectures on Standard ML
%R LFCS Report ECS-LFCS-89-73
%I Laboratory for Foundations of Computer Science
   Department of Computer Science
   University of Edinburgh
%M MAR
%D 1989
%K ML, SML, FP, functional, applicative, programming language
%X The following report is available from the LFCS (mail Dorothy McKie,
   dam@ecsvax.ed.ac.uk) and is free.  It includes an introduction to Standard ML
   and three lectures on the module system.

%A N. Royal
%T An introduction to VAX/VMS
%I Dept. Computer Science, University of Edinburgh
%R CSR-93-81
%M SEP
%D 1981
%K VAX, VMS, operating system

%A A. Mycroft
%T The theory and practice of transforming call-by-need into call-by-value
%I Dept. Computer Science, University of Edinburgh
%R CSR-88-81
%M JUL
%D 1981
%K c1981, c198x, c19xx, computer program, static analysis, lazy, call by need,
   functional programming, FP
%X [Also search for: FP lazy value].

%A A. Mycroft
%T Call-by-need = call-by-value + conditional
%I Dept. Computer Science, University of Edinburgh
%R CSR-78-81
%M JUL
%D 1981
%K c1981, c198x, c19xx, computer program, static analysis, lazy, call by need,
   evaluation, functional programming, FP
%X [Also search for: FP lazy need].


%A N. Wirth
%T Modula-2
%I Eidgenossische Technische Hochschule, Zurich, Switzerland
%M Mar
%D 1980
%K ETH, ETHZ, c1980, c198x, c19xx, Modula, Modula2, Modula-II, module,
   programming language

%A G. H. Gonnet
%T A tutorial introduction to computational biochemistry using Darwin
%M NOV
%D 1992
%I Informatik Eidgenossische Technische Hochschule, Zurich, Switzerland
%P 180
%K ETH, ETHZ, MolBio, c1992, c199x, c19xx, sequence, string, analysis,
   comparison, homology, alignment, substitution matrix, PAM, protein,
   alignment, clustering, family, phylogenetic, evolutionary tree, trees
%X An interactive package.
   "Darwin resembles Maple more than superficially".

%A L. J. Knecht
%A G. H. Gonnet
%T Alignment of nucleotide with peptide sequences
%R 184
%I Inst. for Scientific Computing, E.T.H. Zurich
%M SEP
%D 1992
%K TR 184, TR184, ETH, ETHZ, MolBio, c1992, c199x, c19xx, sequence, align, DNA,
   protein, alignment, reading frame, shift, frames, frameshift, DPA,
   algorithm
%X "The alignment of a nucleotide (DNA/RNA) with a peptide seq. (protein) is
   usually computed by translating the ORFs of the n.seq. into hypothetical
   proteins, then aligning each protein with the peptide seq.. ... cannot
   properly handle base indels or introns that change the n.'s reading frame.
   The DPA presented here simult. translates the n.seq. & aligns it to the
   peptide seq. thereby considering all reading frames in every step & in effect
   finds the optimal reading frames. ... can be efficiently implemented.  With a
   n.seq. of m bases & a peptide seq. of n AAs, its time complexity is O(mn).
   ...applied to searching for similarities b/w yeast chr III & known proteins.
   This alg. is implemented & available in the Darwin system."
   scanned pdf@[<A HREF="ftp://ftp.inf.ethz.ch/pub/publications/tech-reports/1xx/184.pdf">ethz</A>]['08].
   [<A HREF="http://mendel.ethz.ch:8080/Research/Publications/">list</A>]['08].

%A S. Holmstrom
%T PFL: a functional language for parallel programming and its implementation
%I Programming Methodology Group, University of Goteborg
   and Chalmers University of Technology
%R 7
%M SEP
%D 1983
%K PFL, CCS, CSP, parallel functional language, concurrent, applicative,
   FP, synchronise, synchronized, unbuffered message passing,
   communication channel, PMG, TR7 TR, Sweden
%O in Declarative Programming Workshop, 114-139, UCL 1983
%X PFL parallel based on ML
   similar to CCS but behaviours and channels are first class objects.
   <A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A>  ('94)

%A L. Augustsson
%T Small - a small interactive functional system
%I Programming Methodology Group, University of Goteborg
   and Chalmers University of Technology
%R 28
%M Dec
%D 1986
%K PMG, TR28, TR 28, Small,  functional, applicative language, FP, combinator,
   s, k, i, ski,   implementation, implement, lazy, need, normal order
%X Small is an interactive system for functional programming.
   The language is untyped, lazy and side-effect free.
   The small system is written in small.
   It resembles Lisp-kit but is less Lisp inspired.
   Implemented on Turner style combinators.
   The combinator interpreter is written in C.
   <A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A>  ('94)

%A T. Johnsson
%T Target code generation from the G-machine code
%I Programming Methodology Group, University of Goteborg
   and Chalmers University of Technology
%R 39
%M Feb
%D 1987
%K lazy, functional, applicative, programming, implementation,
   graph reduction, compile, compiler, PMG, TR39, TR 39, lazy ML, LML, FP,
   Gmachine, G-machine
%X G machine is a stack machine for von-Neumann-like execution of lazy
   functional languages using graph reduction. Paper describes
   target code generation from G-machine code in a compiler for lazy-ML.
   2 methods: (a) generates naive code like macro expansion
              (b) better, avoids redundant operations.
   Code generation expressed as an attribute grammar over G-machine
   code sequences.
   <A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A>  ('94)
%O Part of the PhD thesis: Compiling Lazy Functional Languages, 1987.
   Presented at the Graph Reduction Workshop, Santa Fe, Sep 1986.

%A T. Johnsson
%T Efficient compilation of lazy evaluation
%I Programming Methodology Group, University of Goteborg and
   Chalmers University of Technology
%R 40
%M Feb
%D 1987
%K lazy, functional, applicative, programming, compile, combinator, graph,
   PMG, TR40, TR 40, reduction, ML, LML, FP, G-machine, Gmachine,
   c1987, c198x, c19xx
%X compiling code for ordinary computers.
   combinator like graph reduction.
   each user function used as a rewrite rule for the graph.
   Claims speed improved by 2 orders of magnitude over previous lazy
   evaluators. Some performance figures are given.
   <A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A>  ('94)
%O Presented at SIGPLAN 1984 Symposium on Compiler Construction, Montreal.
   Part of the PhD thesis, Compiling Lazy Functional Languages, 1987.
   Issued Jun 1984, revised Feb 1987.

%A T. Johnsson
%T Attribute grammars as a functional programming paradigm
%I Programming Methodology Group, University of Goteborg and
   Chalmers University of Technology
%R 42
%M SEP
%D 1987
%O Functional Programming Languages and Computer Architecture (FPCA),
   p154-173, SEP 1987, LNCS 274.
%K PMG, TR42 TR 42, attribute grammar, functional programming, FP,
   lazy, circular program, lazy ML, LML, c1987, c198x, c19xx
%X Evaluate attributes of a parse tree in "one pass"
   Apparently technique used in LML compiler.
   <A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A>  ('94)
   [Also search for: circular program FP].

%A G. O. Uddeborg
%T A functional parser generator
%I Programming Methodology Group, University of Goteborg and
   Chalmers University of Technology
%R 43
%M FEB
%D 1988
%K PMG, TR43, TR 43, functional programming, FP, lazy,
   parser generator, FPG, LML, ML
%X A parser generator, written in LML, to accept attribute grammars.

%A B. Nordstrom
%T Terminating general recursion
%I Programming Methodology Group, University of Goteborg and
   Chalmers University of Technology
%R 46
%M JUN
%D 1988
%O BIT 28 p605-619 1988
%K PMG, TR46, TR 46, recursion, termination, proof rule, type theory

%A A. Aasa
%A K. Petersson
%A D. Synek
%T Concrete syntax for data objects in functional languages
%I Programming Methodology Group, University of Goteborg and
   Chalmers University of Technology
%R 47
%M MAR
%D 1988
%O 1988 ACM Conf. on Lisp and Functional Programming (LFP)
%K PMG, TR47, TR 47, functional programming languages, FP, concrete,
   syntax, lazy ML, LML

%A B. Bjerner
%A S. Holmstrom
%T A compositional approach to time analysis of first order lazy functional
   programs.
%I Programming Methodology Group, University of Goteborg and
   Chalmers University of Technology
%R 50
%M JUN
%D 1989
%O 4th Int. Conf. on Functional Programming Languages and Computer Architecture
   (FPCA), 1989.
%K PMG, TR50, TR 50, time complexity, analysis, compositional, lazy,
   functional, FP, program

%A U. Holmer
%T Translating static CCS agents into regular form
%I Programming Methodology Group, University of Goteborg and
   Chalmers University of Technology
%R 51
%M MAR
%D 1989
%K static, CCS, CSP, parallel, concurrent, theory, agent, agents, process,
   algebra, bisimulation equivalence, protocol
%X alternating bit protocol

%A P. Dybjer
%A L. Hallnas
%A B. Nordstrom
%A K. Petersson
%A J. M. Smith
%T Proc. of the workshop on Programming Logic
%I Programming Methodology Group, University of Goteborg and
   Chalmers University of Technology
%M MAY
%D 1989
%R 54

%A P. Dybjer
%A H. P. Sander
%T A functional programming approach to the specification and
   verification of concurrent systems.
%I Programming Methodology Group, University of Goteborg and
   Chalmers University of Technology
%R 56
%M SEP
%D 1989
%O Formal Aspects of Computing, 1, p303-319, 1989
%K PMG, TR56, TR 56, parallel, concurrent, system, systems, specification,
   verification, FP, functional programming, mu calculus, non determinism,
   alternating bit protocol

%A P. Dybjer
%T Inverse image analysis generalises strictness analysis
%I Programming Methodology Group, University of Goteborg and
   Chalmers University
%R 60
%M FEB
%D 1991
%O Information and Computation, 90(2), 194-216 FEB 1991
%K PMG, TR60 TR 60, functional programming, FP, strict, strictness analysis,
   lazy, optimise

%A A. Jeffrey
%T A linear time process algebra
%I Programming Methodology Group, University of Goteborg and
   Chalmers University
%R 61
%M APR
%D 1991
%O Computer Aided Verification, 1991
%K CCS, CSP, concurrent, parallel, communicating, process, processes, model,
   PMG, TR61, TR 61, real time, real-time, calculus

%A G. Hutton
%T Higher-order functions for parsing
%J J. Func. Prog.
%V 2
%N 3
%P 323-343
%M JUL
%D 1992
%O Chalmers University of Technology, March '92
%K JFP, PMG functional programming, FP, high order, combinator,
   parse, parser, parsing, backtracking, non-determinism,
   white space, off side, offside rule, c1992, c199x, c19xx
%X [<A HREF="http://www.cs.nott.ac.uk/~gmh/parsing.pdf">.pdf</A>][5/'04]
   Also see a later paper on mon@dic p@rsing JFP Jul '98.

%A H. Kuchen
%T Distributed memory implementation of a data parallel functional language
%R 76
%I Programming Methodology Group, University of Goteborg and
   Chalmers University
%M OCT
%D 1993
%K PMG, TR76, TR 76, functional programming, FP, SIMD, MIMD, array, arrays,
   communication, single thread
%X ... discuss why MIMD implementations of FP are not as fast as required.
   ... provide set of primitives on arrays ... control parallelism and
   communication ...  The single threaded use will be checked by the compiler.
   <A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A>  ('94)

%A T. Coquand
%A B. Nordstrom
%A J. M. Smith
%A B. von Sydow
%T Type theory and programming
%R 81
%I Programming Methodology Group, University of Goteborg and
   Chalmers University
%M JUN
%D 1994
%K ALF, PMG, TR81, TR 81, type theory, proof, proofs, constructive,
   intuitionistic mathematics
%X 48 refs
   <A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A>  ('94)

%A M. Rittri
%T Semi-unification of two terms in abelian groups
%R 83
%I Programming Methodology Group, University of Goteborg and
   Chalmers University
%P 13
%D 1995
%K PMG, TR83, TR 83, unification, term, logic, maths, group, theory, CSci
%X The Programming Methodology Group's Report Series.
   <A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A>  ('94)

%A S. B. Jones
%T An experiment in compile time garbage collection
%R 84
%I Programming Methodology Group, University of Goteborg and
   Chalmers University
%P 35
%D 1995
%K PMG, TR84, TR 84, garbage collection, GC, CSci
%X The Programming Methodology Group's Report Series.
   <A HREF="http://cs.chalmers.se/welcome.eng.html">CSci Chalmers</A>  ('94)


%A M. Houseman
%A D. Minor
%T Toxic workers
%I Harvard Business School
%R 16-057
%M NOV
%D 2015
%K TR, c2015, c201x, c20xx, zz1215, toxic worker, workplace, office, offices,
   human resources, behaviour, management, misconduct, ethics, Machiavellian,
   employee, business, risks, trouble
%X "While there has been a strong focus in past research on discovering &
   developing top performers in the workplace, less attention has been paid to
   the q. of how to manage those workers on the opposite side of the spectrum:
   those who are harmful to organizational performance. In extreme cases, aside
   from hurting performance, such workers can generate enormous regulatory &
   legal fees & liabilities for the firm. We explore a large novel dataset of
   over 50,000 workers across 11 diffeerent firms to document a variety of
   aspects of workers' characteristics & circumstances that lead them to engage
   in what we call 'toxic' behavior.  ... explore the relationship between
   toxicity & productivity, & the ripple eÂ¤ect that a toxic worker has on her
   peers. Finally, we find that avoiding a toxic worker (or converting him to
   an average worker) enhances performance to a much greater extent than
   replacing an average worker with a superstar worker."
   -- pdf@[<A HREF="http://www.hbs.edu/faculty/Publication%20Files/16-057_d45c0b4f-fa19-49de-8f1b-4b12fe054fea.pdf">hbs</A>]['15].
   (Also see [<A HREF="http://www.abc.net.au/news/2015-12-16/toxic-workers-ooze-condidence-productivity-and-do-gooder-nature/7033458">abc</A>][16/12/15].)


%A M. O. Stitson
%A J. A. E. Weston
%A A. Gammerman
%A V. Vovk
%A V. Vapnik
%T Theory of support vector machines
%I Royal Holloway U. London
%R CSD-TR-96-17
%M DEC
%D 1996
%K TR17, TR 17, RH, RHBNC, SVM, machine, method, supervised classification,
   VC dimension, decision function, separating hyperplane, zz0798,
   c1996, c199x, c19xx
%X ... svm's perform structural risk minimisation.
   ... linear separating hyperplane ... higher dimensional feature space.
   28 pages. 10 refs.
   -- [<A HREF="http://www.cs.rhbnc.ac.uk/">cSci at rhbnc</A>][7/1998].


%A J. J. Rissanen
%T Generalized Kraft inequality and arithmetic coding
%J IBM J. Res. and Dev.
%V 20
%N 3
%P 198-203
%M MAY
%D 1976
%K codes, coding, encoding, encode, data compression, c1976, c197x, c19xx,
   entropy, arithmetic, arithmeticCoding
%X "Algorithms for encoding & decoding finite strings over a finite alphabet
   are described. The coding operations are arithmetic involving rational
   numbers l[i] as parameters such that SUM i 2**(-l[i]) <= 2**(-epsilon).
   ... requires no blocking, & the per-symbol length of the encoded string
   approaches the associated entropy within epsilon. The coding speed is
   comparable to that of conventional coding methods."
   -- [<A HREF="http://www.research.ibm.com/journal/rd/203/ibmrd2003B.pdf">pdf</A>]['06],
      [<A HREF="http://dx.doi.org/10.1147/rd.203.0198">doi:10.1147/rd.203.0198</A>]['14].
   [Also search for: Pasco c1976] and [also search for: arithmeticCoding].

%A M. J. Maher
%T Algorithmic logic programming
%R RC 12428 (#55829)
%I IBM Yorktown Heights
%M DEC
%D 1986
%K IBM TR, LP, logic programming, prolog, c1986, c198x, c19xx

%A C. A. Pickover
%T Mathematics and Beauty: time discrete phase planes associated
   with the cyclic system, x(t)=-f(y(t)), y.(t)=f(x(t))
%I IBM Yorktown Heights
%R RC 11971 (#53875)
%D 1986
%K TR, picture, pictures, c1986, c198x, c19xx

%A C. A. Pickover
%T Computers, Pattern, Chaos and Beauty
%I IBM Yorktown Heights
%D 1986
%K TR, patern, patterns, graphics, c1986, c198x, c19xx

%A C. A. Pickover
%T Mathematics and Beauty III: Texture and tiling patterns
   computed from truncated sinusoids
%I IBM Yorktown Heights
%D 1986
%R 12282 (#55061)
%K TR, patter, pictures

%A C. A. Pickover
%T Mathematics and Beauty V: Turbulent complex curls
%R RC 12377 (#55593)
%I IBM Yorktown Heights
%M NOV
%D 1986
%K graphics, chaotic, chaos, turbulent, turbulence, pretty picture,
   pictures, TR, curl

%A C. A. Pickover
%T Mathematics and Beauty VIII: Tesselation automata derived from a single
   defect
%M APR
%D 1987
%R RC 12699 (#57118)
%I IBM Yorktown Heights
%K Graphics, chaotic, chaos, automata, pattern, tiling, patterns

%A P. Heidelberger
%A A. Norton
%A J. T. Robinson
%T Parallel Quicksort using Fetch-and-Add
%R RC 12576 (#56561)
%D 1987
%I IBM Yorktown Heights
%X parallel algorithm shared memory multiprocessor
   fetch and add instruction
   in place quicksort quick sort
   O(log(N)) on N processors.

%A C. A. Pickover
%T Mathematics and Beauty IV:
   Computer graphics and wild monopodial tendril plant growth
%R RC 12334 (#55282)
%I IBM Yorktown Heights
%D 1986
%K TR, coral, jungle, like, forms, fractal, image, images, graphics

%A C. A. Pickover
%T Overrelaxation
%I IBM Yorktown Heights
%R RC 12863 (#57791)
%M NOV
%D 1987
%K TR, graphics, chaos, pretty pictures, over relaxation
%X overrelaxed Halley's method for 1 parameter rational functions
   of form  x^a - 1 =0
   patterns indicating behaviour ranging from stable attractive points to chaos.

%A C. A. Pickover
%T Charged curves
%I IBM Yorktown Heights
%R RC 12864 (#57792)
%M NOV
%D 1987
%K graphics, voltage potential
%X voltage potentials around a charged folium of Descartes
   using Laplace's equation.

%A R. Schlichting
%A F. Cristian
%A T. D. M. Purdin
%T Mechanisms for failure handling in distributed programming languages
%R RJ 5713 (57692)
%D 1987
%K IBM TR, failure, exception, parallel, distributed system, concurrent
%X treat failure like any other event.
   add linguistic features for this.
   Paper uses SR distributed prog lang.
   ex: replicated directory management,
       and two phase commit.
   the class of failures are those suffered by fail-stop processors.

%A J. M. Stone
%T A graphical representation of concurrent processes
%R RC 13662 (#61133)
%M DEC
%D 1988
%P 10
%I IBM Yorktown Heights
%K IBM TR, parallel, concurrent, process

%A V. Nguyen
%A R. Strom
%T Process semantics: global axioms, compositional rules and applications
%R RC 13723 (#61517)
%M NOV
%D 1988
%P 40
%I IBM Yorktown Heights
%K IBM TR, parallel, concurrent, process, axiom, rule, csp, CSP
%X Process is defined by a set of partially ordered traces on ports.
   Global axioms rule out pathological processes.
   Compositional rules for joining processes together.
   Show global rules preserved by compositional rules.
   Sound and complete proof system given.
   Finally define a concurrent language with dynamic process creation
   and dynamic port bindings.

%A C. Lassez
%A K. McAloon
%A R. Yap
%T Constraint logic programming and option trading
%I IBM Yorktown Heights
%M Apr
%D 1987
%O IEEE Expert ?
%K IBM TR, option trading, options, stock market, LP, CLP CLP(R), CLPR

%A G. M. Kuper
%A K. W. McAloon
%A K. V. Palem
%A K. J. Perry
%T An efficient algorithm for anti-unification
%I IBM Yorktown Heights
%R RC 14065
%M Feb
%D 1988
%K IBM TR, c1988, c198x, c19xx, anti, unify, unification,
   most specialised generaliser, parallel, least general, LGG, MSG,
   most specific, logic programming, LP
%X returns most specific term having two given terms as instances.
   O(log^2(n)) time on n processors.

%A R. S. Cahn
%T An algorithm to draw networks and graphs
%I IBM Yorktown Heights
%R RC 14126
%D 1988
%K IBM TR, graph, planar, draw, display, format, layout, embed

%A C. A. Pickover
%T DNA vectorgrams: representation of cancer and other gene
   sequences as movements in a 2-D lattice
%I IBM Yorktown Heights
%R RC 11919 (#53685)
%M MAR
%D 1986

%A C. A. Pickover
%T Computer experiments in molecular evolution
%I IBM Yorktown Heights
%R RC 14467 (#64758)
%M FEB
%D 1989
%K DNA, secondary structure
%X simulates mutations of RNA, draws secondary structure
   constraints: no pairs bond if less than 5 bases apart - too strained
                planar
                G-C and A-U
                G-C 2 points, A-U 1 point, need 6 point cooperation to stick;
   paper not relevant.

%A D. Sheinwald
%A A. Lempel
%A J. Ziv
%T Two-dimensional encoding by finite state encoders
%I IBM Yorktown Heights
%R RJ 7242 (68009)
%D 1990
%K IBM TR, 2D, two dimensional, image, compression, compress, finite state,
   finite-state

%A C. C. Tappert
%A H. H. Jeanty
%T A study of several accuracy-improvement methods for a handwriting
   recognition system
%I IBM Yorktown Heights
%R RC 15373 (68416)
%D 1990
%K hand writing, recognition

%A P. Raghavan
%T Lecture Notes on Randomized Algorithms
%I IBM Yorktown Heights
%R RC 1540 (68237)
%D 1990
%P 170
%K IBM TR, random, randomized, algorithm, algorithms
   <A HREF="http://www.watson.ibm.com:8080/">[reports web]</A>.

%A A. Califano
%A I. Rigoutsos
%T Flash: a fast lookup algorithm for string homology
%I IBM Yorktown Heights
%R RC 18791 (82158)
%M MAR
%D 1993
%P 26
%K IBM TR, c1993, c199x, c19xx, string, sequence, homology, approximate, match,
   matching, search, dFlash, FLASH, database, MolBio, data base, geometric hash,
   hashing, GH, gapped, spaced, seed, seeds
%X [15 refs].
   [<A HREF="http://www.watson.ibm.com:8080/">reports web</A>]['93].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Alignment/">alignment</A>].)
   [Also search for: MolBio FLASH].

%A J. Rissanen
%T Fisher information and stochastic complexity
%I IBM Yorktown Heights
%R RJ 9547 (83553)
%M OCT
%D 1993
%O Fisher information and stochastic complexity.
   IEEE Transactions on Information Theory, 42(1), pp.40-47, Jan., 1996
%K IBM TR, minimum description, encoding, MDL, probability, information theory,
   NML, c1996, c1993, c199x, c19xx
%X 19 refs; also see [15] Rissanen          JRSB 49(3) 223-239 l987
                 and      Wallace & Freeman JRSB 49(3) 240-265 l987
   [also search for: MML Fisher] and [also search for: MDL Fisher].
   "By taking into account the F.info. & removing an inherent redundancy in
   earlier 2-part codes, a sharper code length as the stochastic complexity &
   the assoc. universal process are derived for a class of parametric processes.
   The main condn req. is that the max.-LH ests. satisfy the Central Limit Thm.
   The same code len. is also obtained from the so-called max.-LH code."
   -- [<A HREF="http://dx.doi.org/10.1109/18.481776">doi:10.1109/18.481776</A>]['06].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A C. C. Palmer
%A A. Kershenbaum
%T Representing trees in genetic algorithms
%R RC 19394
%P 6
%M ?
%D 1994 ?
%I IBM T.J.Watson Research Centre, Yorktown Heights
%K IBM TR, RC 19394, genetic algorithm, GA, tree, trees
%X 7 refs
   ftp://software.watson.ibm.com  --> pub  --> tjw.reports
   rc19394.ps.Z  -  longer version of WCCI EC paper
   cpthesis.ps.Z -  dissertation
   email: cpalmer@watson.ibm.com            (9/'94)
   <A HREF="http://www.watson.ibm.com:8080/">[reports web]</A>.

%A G. J. Chaitin
%T A new version of algorithmic information theory
%I IBM T.J.Watson Research Centre, Yorktown Heights
%R RC 20092
%P 12
%M JUN
%D 1995
%K IBM, TR20092, TR 20092, computer science, CSci, maths, mathematics, theory,
   algorithmic information theory, AIT, Berry, Berry's paradox, Berrys, zz0795,
   omega, c1995, c199x, c19xx
%X pdf@[<A HREF="http://arxiv.org/abs/chao-dyn/9506003">arxiv</A>]['09];
   7 refs.  See [<A HREF="http://xyz.lanl.gov/">xyz.lanl.gov</A>]['95],
   [<A HREF="http://www.watson.ibm.com:8080/">reports web</A>]['95].

%A S. Banerjee
%A W. Niblack
%A M. Flickner
%T A minimum description length polygonal approximation method
%I IBM T.J.Watson Research Centre, Yorktown Heights
%R RJ 10007 (89096)
%P 19
%M JAN
%D 1996
%K c1996, c199x, c19xx, polygon, fit, fitting, image processing, MDL, TR,
   point, sequence
%X "Given a seq. of pts in 2D, obtained by sampling the perimeter of a planar
   region, it is often of interest to approx. this set by piecewise linear
   curves or polygons. ... we take a [MDL] approach to this problem. ... The
   exec'n time & space requirements of our alg. are both O(n^2), where n is the
   # of pts. ..." [10 refs].
   -- [<A HREF="https://mp7.watson.ibm.com/5ed6fcf3463e124685256593006fe72d.html">ibm</A>]['22].
   [Also search for: MML].
   (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/Java/PolyFit/">demo</A>].)

%A N. Megiddo
%A S. Mizuno
%A T. Tsuchiya
%T A modified layered-step interior-point algorithm for linear programming
%I IBM Res' Divn, Almaden Res.
%R RJ 10028 (90524)
%M JUN
%D 1996
%K TR, linear programming, LP, layered step, interior point, CS, CSci,
   algorithm, Vavasis, Ye, zz0796
%X ... accelerates the path following interior point algorithm.
   ... we propose a modified ...
   same complexity is V' and Y', simpler, does not require a certain large
   unknown constant in computing the search direction.
   14 refs
   <A HREF="http://www.watson.ibm.com:8080/">[reports web]</A>.

%A A. Gupta
%T Graph partitioning based on sparse matrix orderings for interior-point
   algorithms
%I IBM T.J.Watson Research Centre, Yorktown Heights
%R RC 20467 (90480)
%M MAY
%D 1996
%K TR, c1996, c199x, c19xx, interior point, linear programming, LP,
   sparse matrix, multiple minimum degree, MMD, zz0796
%X Claims graph partitioning gives a better heuristic than
   MMD as normally used in LP,   26 refs.
   [<A HREF="http://www.watson.ibm.com:8080/">reports web</A>],
   [<A HREF="mailto:reports@watson.ibm.com">reports email</A>][2/'97].

%A G. J. Chaitin
%T Meta-mathematics and the foundations of mathematics
%R CDMTCS-182
%I IBM T. J. Watson Res. Center, N.Y.
%M MAY
%D 2002
%K TR 182, TR182, c2002, c200x, c20xx, algorithmic information theory,
   omega, theory, maths, CSci
%X [Also search for: MML].


%A S. Fong
%A J. Pitt
%A R. J. Cunningham
%T Parsing English with traditional grammar
%R TR 84-26
%I Department of Computing, Imperial College
%M Dec
%D 1984
%K English, natural language, parse, parser, parsing, grammar
%X (LA has)

%A P. G. Harrison
%T Optimisation of FP programs by linearisation
%R DoC 85/2
%I Department of Computing, Imperial College
%M Feb
%D 1985
%K applicative, functional programming, algebra, linear, transformation

%A R. A. Kowalski
%T Prolog as a logic programming language
%R DOC 81/26
%I Department of Computing, Imperial College
%M Jul
%D 1981
%K LP, Prolog, logic programming
%X [Also search for: Prolog book].

%A C. D. S. Moss
%T A formal definition of Asple using predicate logic
%R DOC 80/18
%I Department of Computing, Imperial College
%M Oct
%D 1980
%K Prolog, semantics, definition, asple

%A M. J. Sergot
%A F. Sadri
%A R. A. Kowalski
%A F. Kriwaczek
%A P. Hammond
%A H. T. Curry
%T The British nationality act as a logic program
%R DOC 86/10
%I Department of Computing, Imperial College
%M Nov
%D 1985
%X British nationality act 1981 translated to Horn clause logic extended
   by negation as failure.
%K Prolog, LP, case study, legal, act, rule based systems, expert system,
   legislation, British citizenship

%A K. L. Clark
%A S. Gregory
%T Parlog: a parallel logic programming language
%R DOC 83/5
%I Department of Computing, Imperial College
%K logic programming, LP, prolog, parlog, parallel, and-parallelism,
   or-parallelism

%A R. Ennals
%T Teaching logic as a computer language in schools
%M Apr
%D 1983
%I Department of Computing, Imperial College
%O First International Logic Programming Conference, Marseilles 1982
%K logic programming, LP, prolog,  teaching, school, schools, education,
   child, children

%A K. L. Clark
%A F. G. McCabe
%T The control facilities of IC-Prolog
%R TOC 79/43
%I Department of Computing, Imperial College
%M Jul
%D 1979
%K prolog, icprolog, ic-prolog, logic programming, LP,
   control, annotation

%A D. R. Brough
%A C. J. Hogger
%T Compiling associativity into logic programs
%R DoC 87/2
%I Department of Computing, Imperial College
%M Feb
%D 1987
%K logic program, programming, LP, prolog, transformation, transform
%X simple but important class of recursive logic programs
   transform mechanically  associativity of auxiliary relations.
   improve efficiency  introduce tail recursion

%A G. L. Burn
%T Using projection analysis in compiling lazy functional programs
%R DOC 90/3
%I Department of Computing, Imperial College
%D 1990
%O '90 ACM Conf on Lisp and Functional Programming
%K strict, strictness analysis, functional, lazy, programming, FP, IC

%A S. Hunt
%T PERs generalise projections for strictness analysis
%R DOC 90/14
%I Department of Computing, Imperial College
%M OCT
%D 1990
%K PER, PERs, strict, strictness analysis, functional, lazy, programming,
   FP, IC

%A G. L. Burn
%T The evaluation transformer model of reduction and its correctness
%R DOC 90/19
%I Department of Computing, Imperial College
%M OCT
%D 1990
%O TAPSOFT91
%K TAPSOFT 91, lazy, functional programming, FP, evaluation transformer, IC

%A M. D. Cripps
%T On the measurement of distribution of academic staff load
%R DOC 90/23
%I Department of Computing, Imperial College
%M SEP
%D 1989
%K staff load, IC, academics, work
%X extra data 1990

%A B. Thomsen
%T A calculus of higher order communicating systems
%J Proc. ACM Conf. Principles of Programming Languages
%P 143-154
%D 1989
%O TR 88/11 Department of Computing, Imperial College 1988
%K calculus, theory, semantics, parallel, communication, concurrent,
   system, process, FP, PFL, PFP, CCS, CSP, CHOCS, Imperial, IC,
   POPL, POPL89, port, channel
%X see also Milner  pi-calculus.

%A D. C. Dracopoulos
%T The connection machine implementation and programming
%R DoC 92/5
%M FEB
%D 1992
%I Department of Computing, Imperial College
%K IC, TR92/5, TR 92/5, CM, CM2, CM-2, *Lisp, *C

%A D. W. N. Sharp
%A A. J. Field
%A H. Khoshnevisan
%T An execise in the synthesis of parallel functional programs for message
   passing architectures
%B Parallel Computing: From Theory to Sound Practice
%E W. Joosen
%E E. Milgrom
%I IOS Press
%D 1992
%P 452-463
%O TR DoC 92/27, Dept. of Computing, Imperial College Nov '92
%K functional, applicative programming, parallel, concurrent, FP,
   IC, TR92/27, TR 92/27
%X Specify target architecture as a program skeleton (a high order fn)
   and use transformation to marry the algorithm to the skeleton.


%A C. S. Wallace
%T Suggested design for a very fast multiplier
%R UIUCDCS-R-63-133
%D 1963
%I Dept Computer Science, University of Illinois at Urbana-Champaign
%P 25
%O IEEE Trans. Comput, V 13, N ?, p ??-??, '64
%K CSW, CSWallace, hardware, fast, multiplier, multiplication, Wallace,
   multiply, computer, algorithm, arithmetic, integer, tree, trees,
   TR, TR 63 133, TR133, c1963, c196x, c19xx
%X [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>],
   [also search for: Wallace multiplier].

%A U. S. Reddy
%T Logic languages based on functions, semantics and implementation
%M AUG
%D 1986
%I Dept Computer Science, University of Illinois at Urbana-Champaign
%R UIUCDCS-R-86-1305
%K logic functional programming, LP, FP, FLP, narrowing, TR 86 1305, TR1305,
   c1986, c198x, c19xx, narrowing, PhD thesis, functional programming,
   logic programming, language, reduce, reducing, solving, narrowing


%A J. Rees
%A W. Clinger
%T Revised report on the algorithmic language Scheme
%R TR 174
%I Computer Science Department, Indiana University
%M Dec
%D 1986
%K scheme, lisp, functional, applicative programming, FP, language
%X scheme is statically scoped and tail recursive

%A M. Felleisen
%T Recursion and circularity - extended puzzle with solution
%R TR 201
%D 1986
%M Oct
%I Computer Science Department, Indiana University
%K lambda calculus, assignment
%X lambda calculus with assignment proof theory

%A M. Gasser
%A D. Eck
%A R. Port
%T Meter as mechanism: A neural network that learns metrical patterns
%I Cognitive Science Program, Indiana U.
%R 180
%D 1996
%K TR 180, TR180, ann, nn, music, rythm, pattern, metrical, computer,
   time signature, c1996, c199x, c19xx
%X "One kind of prosodic structure that apparently underlies both music & lang.
   is meter. ... nested periodicities that define metrical structure are noisy
   in some sense. What kind of system could produce or perceive such variable
   metrical timing? And what would it take to store particular metrical
   patterns in the long-term memory of the system? ... developed a network of
   coupled oscillators that both produces & perceives metrical patterns of
   pulses. In addition, beginning with an initial state with no biases, it
   learns to prefer 3-beat patterns (like waltzes) over 2-beat patterns. Models
   of this general class could learn to entrain to musical patterns. And given
   a way to process speech to extract appropriate pulses, the model should be
   applicable to metrical structure in speech as well."
   [<A HREF="http://www.cogs.indiana.edu/Publications/techreps1996/180.html">cogs.indiana</A>]['05] via C.T.
   [<A HREF="http://www.cogs.indiana.edu/people/homepages/gasser.html">~gasser</A>]['05]
   [<A HREF="http://www.iro.umontreal.ca/~eckdoug/">~eck</A>]['05].


%A N. A. Smith
%A R. W. Tromble
%T Sampling uniformly from the unit simplex
%I Centre for Lang. and Speech Proc., John Hopkins U.
%M AUG
%D 2004
%K TR, c2004, c200x, c20xx, zz1013, generate, sample, random, Simplex, member,
   draw, point picking, Kraemer, algorithm, RNG, PRNG
%X "We address the problem of selecting a point from a unit simplex, uniformly
   at random.  ... important, for instance, when random multinomial probability
   distributions are required. We show that a prev. proposed alg. is incorrect,
   & demonstrate a corrected alg.."
   Kraemer (modified):
      Pick x[1], ..., x[K-1] unif. in open(!) (0, 1).  x[0]=0 and x[K]=1.
      Sort the x[i]. 0=x[0] < x[1] < ... < x[K]=1.  Let y[i] = x[i[-x[i-1].
      Note, SUM y[i]=1.  (y[1], ..., y[K]) is uniform random in the K-Simplex.
   See pdf@[<A HREF="http://www.cs.cmu.edu/~nasmith/papers/smith+tromble.tr04.pdf">cmu</A>]['13].
  (OR...
      Generate K random values x[1], ..., x[K] from the unit (neg-) exponential.
      (i.e., gen. z[i] uniform in [0,1], x[i]=-ln(z[i]).)
      Set X=SUM x[i].  Then (x[1]/X, ..., x[K]/X) is uniform random in the S..
   -- [<A HREF="http://en.wikipedia.org/wiki/User:Skinnerd/Simplex_Point_Picking">wikip</A>]['13].)


%A S. L. Meira
%T Optimized combinatoric code for applicative language implementation
%R 20
%I Computing Laboratory, University of Kent
%M Apr
%D 1984
%K functional, applicative programming, FP, S, K, I, ski, combinator

%A R. Jones
%T Flex an experience of Miranda
%R 38
%I Computing Laboratory, University of Kent
%M Jun
%D 1985
%K functional, applicative programming, FP, application,
   Miranda,  Lex
%X implements Lex in Miranda

%A S. Thompson
%T Writing interactive programs in Miranda
%R 40
%I Computing Laboratory, University of Kent
%M Jul
%D 1986
%K c1986, c198x, c19xx, functional, applicative programming, FP, Miranda,
   high-order, high order, interact, input, output, IO, stream, lazy evaluation,
   need, denotational semantics
%X [Also search for: functional FP IO].

%A R. D. Lins
%T Categorical multi-combinators
%R 41
%M Sep
%D 1986
%I Computing Laboratory, University of Kent
%K category, categorical, combinator, lambda calculus, combinatorial logic,
   s, k, i, ski,
   functional, applicative programming, FP

%A M. Longley
%T Type checking Miranda
%D 1987
%M Apr
%R 44
%I Computing Laboratory, University of Kent
%K c1987, c198x, c19xx, data type, checking, check, types, polymorphic, Miranda,
   inference, functional programming, FP

%A S. J. Thompson
%T Interactive functional programs: a method and a formal semantics
%I Computing Laboratory, University of Kent
%M Nov
%D 1987
%R 48
%K c1987, c198x, c19xx, interactive, functional, applicative, programming, FP,
   lazy, stream, streams, trace, traces, input, output, IO, Miranda, interact
%X can use lazy lists to model streams.
   Second half uses traces, to explain input and output formally.
   [<A HREF="http://www.cs.kent.ac.uk/pubs/1987/142/">bib</A>][10/'03],
   [<A HREF="http://www.cs.kent.ac.uk/people/staff/sjt/Pubs/yoptrace.ps">updated .ps</A>][10/'03].
   [Also search for: functional FP IO].

%A A. J.Telford
%A D. A. Turner
%T A hierarchy of elementary languages with strong normalisation properties
%I U. of Kent Computing Laboratory
%R TR 2-00,
%P 75
%M FEB
%D 2000
%K TR, total functional programming language, c2000, c200x, c20xx, FP,
   termination, productive, ESFP, partial, function, codata, corecursion
%X "...type distinction between data which is known to be finite & codata which
   is (potentially) infinite. To ensure termination, recursion over data must
   be well-founded, & corecursion (the definition schema for codata) must be
   productive, & both of these restrictions must be enforced automatically by
   the compiler. In our previous work we used abstract interpretation to
   establish the productivity of corecursive definitions in an elementary
   strong F. lang.. ... similar ideas can be applied in the dual case to check
   whether recursive function definitions are strongly normalising. We thus
   exhibit a powerful termination analysis technique which we demonstrate can
   be extended to partial functions."
   -- [<A HREF="http://www.cs.kent.ac.uk/pubs/2000/964/">TR 2-00 inc .ps</A>][12/'04],
      [<A HREF="http://www.cs.mdx.ac.uk/staff/profiles/d_turner.html">DAT</A>][12/'04].
   Also see corecursion@[<A HREF="https://en.wikipedia.org/wiki/Corecursion">wikip</A>]['23].
   [Also search for: corecursion].


%A S. Muggleton
%A Luc De Raedt
%T Inductive logic programming: theory and methods
%I Dept. Computing Science, Katholieke Universiteit Leuven,
   200A Celestijnenlaan, B-3001, Heverlee, Belgium
%R CW 178
%P 60
%M MAY
%D 1993
%K ILP, LP, TR TR178, CW178, KUL, survey, golem
%X 134 refs


%A P. Watson
%T The parallel reduction of lambda calculus expressions
%I Dept. Computer Science, University of Manchester
%R UMCS-87-2-1
%M JUL
%D 1986
%K PhD thesis, parallel, evaluation, execution, functional, applicative,
   programming, FP, graph reduction, beta conversion, garbage collection

%A P. A. Lindsay
%A R. C. Moore
%A B. Ritchie
%T Review of existing theorem provers
%I Dept. Computer Science, University of Manchester
%R UMCS-87-8-2
%M DEC
%D 1986
%K theorem prover provers, LCF, NuPRL, Veritas, Isabelle, Affirm,
    Boyer Moore, Boyer-Moore, Gypsy, CSG, REVE, IOTA, HDM, NEVER, FDM, HOL,
    review, survey

%A I. J. Hayes
%A C. B. Jones
%T Specifications are not (necessarily) executable
%I Dept. Computer Science, University of Manchester
%R UMCS-89-12-1
%M DEC
%D 1989
%O I.J.Hayes, C.B.Jones. Specifcations are not (necessarily) executable.
   Softw. Eng. J., 6, pp.320-338, 1989.
%K TR, jrnl, specification, prototype, requirements, c1989, c198x, c19xx, SWE

%A C. B. Jones
%T Interference resumed
%I Dept. Computer Science, University of Manchester
%R UMCS-91-5-1
%D 1991
%K concurrent, parallel, program, programming, composition

%A H. Kingdon
%A D. R. Lester
%A G. L. Burn
%T The HDG-machine: a highly distributed graph-reducer for a
   transputer network
%R UMCS-91-4-3
%I Dept. Computer Science, University of Manchester
%D 1991
%K parallel machine, functional, applicative programming language, FP,
   graph reduction, reduce, Esprit-415, transputer

%A J. Sargeant
%T UFO - United Functions and Objects Draft Language Description
%R UMCS-92-4-3
%I Dept. Computer Science, University of Manchester
%D 1992
%K functional, object oriented programming language, module, type, types,
   module, OO, OOPS, UFO

%A C. B. Jones
%T The search for tractable ways of reasoning about programs
%R UMCS-92-4-4
%I Dept. Computer Science University of Manchester
%D 1992
%O La Verifica dei programmi in Volume Logica of Storia del XX Secola.
%K program proof, verification, correctness
%X From: brendan@cs.uq.oz.au (Brendan Mahony)
   It discusses a flow-diagram proof of Turing, some work by von
   Neumann, the work of Floyd and Naur, Hoare, and Dijkstra and is an
   invaluable reference work for those interested in program verification.


%A L. Naish
%T Mu-Prolog 2.4 reference manual
%I Dept Computer Science, University of Melbourne
%M Jul
%D 1982
%K Prolog, logic programming, LP, reference manual, muprolog, Mu-Prolog

%A L. Naish
%T Mu-Prolog 3.0 reference manual
%I Dept Computer Science, University of Melbourne
%M Jul
%D 1983
%K Prolog, Mu-Prolog, muprolog, manual, logic programming, LP

%A L. Naish
%T Automatic generation of control for logic programs
%R TR 83/6
%I Dept Computer Science, University of Melbourne
%D 1983
%K Prolog, muprolog, mu-prolog, logic programming, LP,
   annotation, wait, declaration

%A L. Naish
%T An introduction to Mu-Prolog
%R TR 82/2
%I Dept Computer Science, University of Melbourne
%D 1982
%K prolog, muprolog, Mu-Prolog, wait, control, annotation, logic programming,
   LP

%A J-L. Lassez
%A M. J. Maher
%T Closure and fairness in the semantics of programming logic
%I Dept Computer Science, University of Melbourne
%D 1984
%K logic programming, LP, prolog, semantics, chaotic, iterations,
   SLD resolution, finite failure

%A J-L. Lassez
%A M. J. Maher
%T Optimal fixedpoints of logic programs
%I Dept Computer Science, University of Melbourne
%D 1983
%K logic programming, LP, semantics, optimal, fixedpoint, fixed point

%A J. W. Lloyd
%T Foundations of logic programming
%R TR 82/7
%I Dept Computer Science, University of Melbourne
%M Aug
%D 1982
%K TR 7, TR7, JWLloyd, theory, logic programming, LP

%A J. W. Lloyd
%T Declarative error diagnosis
%R TR 86/3
%I Dept Computer Science, University of Melbourne
%M May
%D 1986
%K declarative, error diagnosis, debugging, Prolog, logic programming, LP,
   TR 3, TR3, JWLloyd, debug, debugging, error diagnosis

%A T. Y. Chen
%A J-L. Lassez
%A G. S. Port
%T Maximal unifiable subsets and minimal non-unifiable subsets
%R TR 84/16
%I Dept Computer Science, University of Melbourne
%K theory, logic programming, LP, Prolog,  intelligent, selective, backtracking

%A W. D. Bray
%T A Prolog implementation of a data manipulation language
%I Dept Computer Science, University of Melbourne
%D 1982
%X logic programming - deductive databases
   SQL optimization
%K data, database, enquiry, SQL, Prolog, logic programming, LP

%A Z. Somogyi
%T A system of precise modes for logic programs
%I Dept. of Computer Science, University of Melbourne
%D 1987
%K prolog, mode, modes, instantiate, data structure, logic programming, LP
%X mode system precise and can handle partially instantiated
   data structures. binding smallest possible unit
   relies on a type system to keep binding patterns regular.

%A B. D. McKay
%T Backtrack programming and isomorph rejection on ordered subsets
%I School of Mathematical Sciences, University of Melbourne
%R 45
%D 1976
%O Ars Combinatoria, vol.5, pp.65-99, 1978
%K TR 45, TR45, c1976, c197x, c19xx, maths, isomorph rejection, symmetry,
   permutation, perm, representative, group, graph isomorphism, nauty
%X "Let V be a finite set, where |V| = n > 0 and let Q[n] denote a set of seqs.
   of n distinct elts [i.e., perms] of V. Suppose X is a subset of Q[n] which
   is invariant under the action of a permutation group G acting on V.  We
   consider the application of backtrack programming to the problem of finding
   a traversal of the action of G on X. Effective methods are devised which
   require no info. about G other than a procedure for recognising whether or
   not a given perm. is in G. We show that these algs. find a small set of
   generators for G. An applic. to graph isomorphism is mentioned."
   (w.l.o.g., V = {1,2,...,n}.)
   -- 78.pdf@[<A HREF="http://cs.anu.edu.au/~bdm/papers/backtrack1978.pdf">anu</A>]['10].
   [Also search for: isomorph rejection] and
   [also search for: nauty maths graph].

%A K. Marriott
%A H. Sondergaard
%T Bottom-up abstract interpretation of logic programs
%I Dept. of Computer Science, University of Melbourne
%R 88/10
%D 1988
%O Proc. 5th Int. Conf. Symp. Logic Programming, MIT Press '88
%K static analysis, collecting semantics, LP

%A K. Marriott
%A H. Sondergaard
%T On describing success patterns of logic programs
%I Dept. of Computer Science, University of Melbourne
%R 88/12
%D 1988
%K abstract interpretation, dataflow analysis, logic programming, LP

%A A. Davison
%T Programming with HTML forms
%I Dept. of Computer Science, University of Melbourne
%M APR
%D 1995
%R 95/8
%K TR 95/8, TR95/8, HTML, Form, www, cgi, cgi-bin, cgibin
%X <A HREF="http://www.cs.mu.oz.au/~ad">[A.D.]</A>

%A Seng Wai Loke
%A A. Davison
%A L. Sterling
%T CiFi: An intelligent agent for citation finding on the world wide web
%I Dept. of Computer Science, University of Melbourne
%R 96/4
%D 1996
%K TR 96/4, TR96/4, logicWeb, search
%X tries for 1. HTML version of paper (via Lycos search engine)
             2. search from author's home page
             3. search from University CS Dept home page
             4. search tech rep archives


%A R. J. Koester
%T Virginia dataset on lost-person behaviour
%I ?
%D 2001
%K search, rescue, data set, people, cause, effect, causal, prediction, USA,
   missing person, c2001, c200x, c20xx, ctwardy
%X Exce1 file to Ch@rles T' @ csse.mon@sh, c2001.
   R.J.K. at [<A HREF="http://www.dbs-sar.com/">dbs-sar.com</A>]['04].
   (Also see [<A HREF="http://www.allisons.org/ll/Publications/2006ACSC/">MP-net</A>]['06].)


%A J. McCarthy
%T A new eval function
%I MIT
%D 1961 or 1962
%K TR 34, TR34, MIT, AI, AIM, AIM34, CSAIL, c196x, c19xx, zz1213, LISP,
   versions, S-expression, Sexpression, property list, FP, eval, lambda,
   evaluation
%X "The actual working definition of eval describes how the LISP system
   determines what, if anything, is denoted by a given S-expression. As things
   now stand, there are two versions of eval: the theor.version, given in RFSE,
   & the system version. Neither of these behaves in the most desirable way; &
   there exist S-exps. which will be handled correctly by the theor.version but
   not by the system version, & conversely. The chief defect of the system eval
   lies in its handling of functional arguments; the chief defect of the RFSE
   eval lies in its ignorance of property lists. If we wish to have a theory
   about how LISP really works, then it is necessary to have a version of eval
   which is satisfactory both theoretically & practically. I will propose a
   definition for eval, & then illustrate how this eval differs from the
   existing system & RFSE definitions by means of examples."
   -- [<A HREF="http://publications.csail.mit.edu/ai/browse/0000browse.shtml">AI</A>]['13],
      34.[<A HREF="ftp://publications.ai.mit.edu/ai-publications/0-499/AIM-034.ps">.ps</A>]['13],
      34.[<A HREF="ftp://publications.ai.mit.edu/ai-publications/pdf/AIM-034.pdf">pdf</A>]['13].
   [Also search for: FP evaluation] and [also search for: Lisp FP].

%A M. Beeler
%A R. W. Gosper
%A R. Schroeppel
%T "HAKMEM"
%R Memo 239
%I Artificial Intelligence Laboratory, MIT
%P 107
%M FEB
%D 1972
%K TR 239, TR239, c1972, c197x, c19xx, HAKMEM, Geometry, Algebra, Calculus,
   Recurrence Relations, Boolean Algebra, Random Numbers, Number Theory,
   Primes, Probability, Automata Theory,  games, Continued Fractions,
   Group Theory, series, relation, fraction, AI Lab MIT
%X [<A HREF="ftp://publications.ai.mit.edu/ai-publications/pdf/AIM-239.pdf">pdf</A>]['08] (scan).
   [<A HREF="http://home.pipeline.com/~hbaker1/hakmem/hakmem.html">html</A>]['08].

%A J. B. Dennis
%T First version of a data flow procedure language
%I Laboratory for Computer Science, MIT
%R MIT/LCS/TM-61
%M May
%D 1975
%K data flow, dataflow

%A E. W. Stark
%T Foundations of a Theory of Specification for Distributed Systems
%R MIT/LCS/TR-341
%I Laboratory for Computer Science, MIT
%M Aug
%D 1984
%K state transition, specification, verification, concurrency, hierarchy,
   modularity, temporal logic, safety, liveness
%X PhD thesis

%A R. C. Waters
%T Obviously synchronisable series expressions:
   part II: overview of the theory and implementation
%I Artificial Intelligence Laboratory, MIT
%R AI Memo 959a
%M Mar
%D 1988
%K functional, applicative, programming, language,
   list, less, vector, stream, series,
   intermediate data structure removal,
   listless, listlessness
%X curious paper, discusses listless programs, then lots on some Lisp
   macros. Hard to read if not a lisp er.

%A T. D. Sanger
%T Optimal unsupervised learning in feedforward neural networks
%R TR 1086
%I Artificial Intelligence Laboratory, MIT
%M JAN
%D 1989
%P 129
%K neural, net, network, learn, learning, feed forward, feedforward, NN
%X MSc thesis

%A W. E. L. Grimson
%A D. P. Huttenlocher
%T On the verification of hypothesized matches in model-based recognition
%R A.I. Memo 1110
%I Artificial Intelligence Laboratory, MIT
%M MAY
%D 1989
%P 22
%K model, based, image, recognition

%A N. H. Margolus
%T Physics and Computation
%I MIT Laboratory for Computer Science
%R MIT/LCS/TR-415
%P 188
%M MAR
%D 1988
%K physics, computation, computing information, modeling, cellular automata,
   reversibility, quantum mechanics, time, PhD thesis, TR415, TR 415

%A M. Biafore
%T Few-body Cellular Automata
%R MIT Laboratory for Computer Science
%R MIT/LCS/TR-597
%P 186
%M DEC
%D 1993
%K Cellular Automata, Quantum Computation, computing, Nanoelectronics,
   Nanotechnology, TR597, TR 597

%A C. Kemp
%A T. L. Griffiths
%A J. B. Tenenbaum
%T Discovering latent classes in relational data
%I MIT
%R AI Memo 2004-019
%D 2004
%K TR, c2004, c200x, c20xx, classification, class, category, kinship, kin,
   cause, causal, relation, AI, II, Dspace
%X "... based on a generative relational model with latent classes, &
   simultaneously determines the kinds of entities that exist in a domain, the
   # of latent classes, & the relations between classes that are possible or
   likely. This model goes beyond previous psychological models of category
   learning, which consider attributes assoc. with individual categories but not
   relationships between categories. We apply this domain-general framework to
   2 specific problems: learning the structure of kinship systems, & learning
   causal theories."
   -- [<A HREF="http://hdl.handle.net/1721.1/30489">hdl.handle.net/1721.1/30489</A>]['07],
      [<A HREF="http://www.mit.edu/~ckemp/">ckemp@mit</A>]['07].


%A J. D. Patrick
%T An Information Measure Comparative Analysis of Megalithic Geometries
%I Dept. Comp. Sci., Monash Uni.
%D 1979
%K Monash, PhD thesis, megalithic, stone, circle, circles, henge, stonehenge,
   yard, age, Thom, minimum message length, MML, encoding, description, MDL,
   inductive inference, II, hypothesis, theory, c1979, c197x, c19xx
%X Surveyed many stone circles, mostly in Eire.
   Null hypothesis: They are more or less (in)accurate circles as
     dictated by the lie of the land and ``technology'' of the time.
   Complex hypothesis: They fit one of a number of elaborate geometries
     and were made with the aid of an accurate megalithic-yard (which would
     have had to be maintained over several centuries.)
   Conclusion: Null hypothesis wins out.   [A good read.]
   -- [<A HREF="https://doi.org/10.26180/14875200.v1">doi:10.26180/14875200.v1</A>]['24].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. Jaffar
%A P. Stuckey
%T Canonical greatest fixpoints of logic programs
%R 55
%I Dept. Comp. Sci., Monash Uni.
%M JUN
%D 1985
%K Prolog, LP, logic programming, program, theory, fixed point

%A N. Heintze
%A J. Jaffar
%A C. S. Lim
%A S. Michaylov
%A P. Stuckey
%A R. Yap
%A C. N. Yee
%T The CLP programmer's manual
%I Dept. Comp. Sci., Monash Uni.
%M JUN
%D 1986
%K CLP, CLP(R), CLPR, constraint, LP, logic programming, Prolog,
   logic program, programming, inequality, unequation, c1986, c198x, c19xx
%X (Also see [<A HREF="http://www.allisons.org/ll/Logic/Prolog/">Prolog</A>].)

%A R. W. Topor
%T Functional programs for generating permutations
%J COMPJ
%M MAY
%D 1982
%V 25
%N 2
%P 257-263
%O TR 17 Dept. Comp. Sci., Monash Uni., July, '81
%K FP, functional programming, applicative, program, algorithm, permutation,
   generator, jrnl, COMPJ, linked lists, c1982, c198x, c19xx, TR17
%X "... presents several functional programs for generating perms. rep. as
   linear linked lists. Exact formulas for the storage used by some of these
   programs are derived & compared with the theoretical lower bound. 2 different
   programs are shown to be optimal with respect to this measure. Problems
   considered include generation of all N! perms. of N distinct elements,
   generation of all perms. of length k <= N, & generation of all distinct
   permutations of a multiset of N elements."
   -- [<A HREF="http://comjnl.oupjournals.org/cgi/reprint/25/2/257">pdf</A>]['05].

%A C. S. Wallace
%T A long-period pseudo-random generator
%R 89/123,
%I Dept. Comp. Sci., Monash Uni.
%M FEB
%D 1989
%K TR 123, TR123, CSW, CSWallace, PRNG, RNG, number, numbers,
   c1989, c198x, c19xx
%X (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A I. Cosic
%A M. T. W. Hearn
%T Hot spot amino acid distribution in Ha-ras oncogene product p21:
   relationship to guanine binding site
%J J. Mol. Recognition
%V 4
%P 57-62
%D 1991
%K JMR, jrnl, MolBio, binding site, protein, EIIP, biochemistry
%X 1. amino acid seq -> electron-ion interaction potentials (EIIP)
   2. do Fourier analysis of this numerical series

%A I. Cosic
%A A. N. Hodder
%A M-I. Aguilar
%A M. T. W. Hearn
%T Resonant recognition model and protein topography.  Model studies with
   myoglobin, hemoglobin and lysozyme
%J Eur. J. Biochem.
%V 198
%P 113-119
%D 1991
%K EJB, jrnl, MolBio, Monash, protein

%A I. Cosic
%A M. T. W. Hearn
%T Studies on protein-DNA interactions using the resonant recognition
   model.  Application to repressors and transforming proteins
%J Eur. J. Biochem.
%V 205
%P 613-619
%D 1992
%K EJB, jrnl, Monash, MolBio, protein

%A P Tischer
%T Optimal predictors for image compression
%R 93/189
%D 1993
%I Dept. Comp. Sci., Monash Uni.
%K TR 189, TR189, processing, IP, DPMC, predictor, error function, estimators,
   entropy
%X Discrete pulse code modulation (DPMC) ...   least squares
   criterion is often used  to select predictor coeff's. ...
   show LS not necc' optimal ... show how other criteria for
   ... technique for selecting the predictor coeffs in a way
   which minimises the entropy of the prediction error dist'n.
   ... show how LS can still be used to gen' predictors which
   are near optimal.

%A K. Marriott
%A H. Sondergaard
%T Precise and efficient groundness analysis for logic programs
%R 93/184
%M MAY
%D 1993
%I Dept. Comp. Sci., Monash Uni.
%K TR 93 179, TR179, logic programming LP, ground

%A C. S. Wallace
%T Fast pseudo-random generators for Normal and Exponential variates
%J ACM Trans. Math. Software
%V 22
%N 1
%P 119-127
%M MAR
%D 1996
%O TR 94/197, May 1994, Dept. Comp. Sci., Monash Uni.
%K jrnl, TOMS, c1996, c199x, c19xx, CSW, CSWallace, Monash, RNG, PRNG,
   pseudo random number generator, algorithm, numbers, normal, probability,
   distribution, variate, Gaussian, distribution, TR 94 197, TR197, generate
%X "Fast algorithms for generating pseudorandom numbers from the unit-normal and
   unit-exponential distributions are described. The methods are unusual in that
   they do not rely on a source of uniform random numbers, but generate the
   target distributions directly by using their maximal-entropy properties. The
   algorithms are fast. The normal generator is faster than the commonly used
   Unix library uniform generator 'random' when the latter is used to yield real
   values. Their statistical properties seem satisfactory, but only a limited
   suite of tests has been conducted. They are written in C and as written
   assume 32-bit integer arithmetic. The code is publicly available as C source
   and can easily be adopted for longer word lengths and/or vector processing."
   -- [<A HREF="http://dx.doi.org/10.1145/225545.225554">doi:10.1145/225545.225554</A>]['11];
   also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW publications</A>],
   [<A HREF="ftp://ftp.csse.monash.edu.au/pub/csw">CSW ftp</A>]['96].

%A D. M. Platt
%A T. I. Dix
%T Stochastic assembly of genomic restriction maps
%R 94/210
%I Dept. Comp. Sci.,
   Monash Uni., Australia 3168
%D 1994
%O 28th Hawaii Int. Conf. Sys. Sci., vol 5, 155-164, Jan 1995
%K MolBio, TR210 TR 210, map, maps, mapping, HICSS, HICSS28, HICSS95, conf,
   DMPlatt, TIDix
%X (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].)

%A J. P. McCormack
%T New Trends in Computer Graphics
%J New Media Technologies
%E R. Harley
%P 13-33
%I Australian Film, Television and Radio School
%C Sydney
%D 1993
%K jonmc, Monash
%X [<A HREF="/~jonmc/">jonmc</A>] home page (11/'94).

%A J. P. McCormack
%T Interactive evolution of L-System grammars for computer graphics modelling
%B Complex Systems: from biology to computation
%E D. G. Green
%E T. Bossomaier
%P 118-130
%I ISO Press
%C Amsterdam
%D 1993
%K jonmc, Monash, L systems, Lsystem, CompArt
%X [<A HREF="/~jonmc/">jonmc</A>] home page (11/'94).

%A J. P. McCormack
%T Interactive evolution of forms
%J 3rd Int. Symp. on Electronic Art (TISEA)
%W Sydney
%P 197
%M ?
%D 1992
%K jonmc, computer art, CompArt, Monash
%X [<A HREF="/~jonmc/">jonmc</A>] home page (11/'94).

%A J. J. Oliver
%A R. A. Baxter
%T MML and Bayesianism: Similarities and differences
   (Introduction to Minimum Encoding Inference, Part II)
%R 94/206
%D 1994
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%K TR 206, TR206, c1994, c199x, c19xx, intro, minimum message length, MML,
   description, encoding, MDL, comparison, introduction,
   inductive inference, II, Bayesian, RABaxter, JJOliver, jono
%X "... continues the intro. to minimum encoding inference given by O.&H.. This
   series of papers were written with the objective of providing an introduction
   ... examine the relationship between Bayesianism & Minimum Message Length
   (MML) inference. We argue that MML augments Bayesian methods by providing a
   sound B.method for point estimation which is invariant under non-linear
   transformations. We explore the issues of invariance of estimators under
   non-linear transformations, the role of the Fisher Info. matrix in MML
   inference, & the apparent similarity between MML & the adoption of a
   Jeffreys' Prior. We then compare MML to an approx. method of Bayesian Model
   Class Seln. Despite apparent similarities in their expressions, the
   properties of the two approaches can be different."
   -- cached@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.7367">c'teseer</A>]['21].
   Also see TR205, TR207
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A R. A. Baxter
%A J. J. Oliver
%T MDL and MML: Similarities and differences
   (Intro. to Minimum Encoding Inference - Part III)
%R 94/207
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%M JAN
%D 1995
%K TR 207, TR207, c1995, c199x, c19xx, minimum message length, MML, description,
   encoding, MDL, comparison, compared, compare, introduction, similarity,
   difference, inductive inference, II, Bayesian,
   RABaxter, JJOliver, jono, Rissanen
%X '... MDL Principle [Ris89 p.9]: "We may take it as an axiom that a model
           or model class which permits the shortest encoding of the data,
           captures best all the properties in the data we wish to learn."
        (In practice we note MDL methods have concentrated on
        selecting model classes rather than models.)
        MML principle (paraphrasing [WB68] & [WF87]): For each model in the
           set of models considered, we consider the message consisting of a
           description of a model, followed by the data under the assumption
           that the model is true. The preferred model amongst a set of
           competing models will be the one with the shortest two part message
           length of this structure. ...
        The MDL message may, but need not be, two part. ...'  -- p.4.
   Cached@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.8802">c'tseer</A>]['14].
   Also see TR205, TR206.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. J. Oliver
%A D. J. Hand
%T On pruning and averaging decision trees
%I Dept. Comp. Sci.,
   Monash Uni., Australia 3168
%R 95/219
%M APR
%D 1995
%K TR 219, TR219, Monash, JJOliver, jono, classification, decision tree, DTree,
   DJHand, MML, minimum message length, inductive inference, II
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].)

%A M. Castro
%T The Walnut Kernel: User Level Programmer's Guide
%I Dept. Comp. Sci.,
   Monash Uni., Australia 3168
%R 95/222
%M MAY
%D 1995
%O revised Nov 1995
%K Monash, c1995, c199x, c19xx, operating system, OS, multi,
   TR 222, TR222, zz0595

%A G. Pringle
%T Colour Correction of Spatial Image Sequences
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%M MAY ?
%D 1995
%K MComp thesis, c1995, c199x, c19xx, masters, color, computing, CSci,
   graphics, zz0595

%A A. D. Kelly
%A K. Marriott
%A A. Macdonald
%A H. Sondergaard
%A P. J. Stuckey
%A R. H. C. Yap
%T An optimizing compiler for CLP(R)
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 95/226
%M JUL
%D 1995
%K TR 226, TR226, logic programming, LP, CLP, CLPR, constraint, optimise,
   optimize, CSci, zz0895

%A M. Castro
%A G. Pringle
%A C. S. Wallace
%T The Walnut kernel: program implementation under the Walnut kernel
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 95/230
%M AUG
%D 1995
%K TR 230, TR230, csw, operating system, OS, secure, security, capability,
   object, walnut, kernel, CSci, zz0995, c1995, c199x, c19xx, CSW, CSWallace
%X Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A R. Rendell
%T Constraint programming in several domains
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 95/231
%M AUG
%D 1995
%K TR 231, TR231, constraint, programming, language, CSci, zz0895

%A D. Albrecht
%A J. N. Crossley
%A J. S. Jeavons
%T Program extraction for full linear logic
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 95/232
%M AUG
%D 1995
%K TR 232, TR232, jnc, logic, maths, theory, zz0995

%A Y. G. Ventsov
%A J. N. Crossley
%T Polynomial-time computable logic programs
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 95/233
%M AUG
%D 1995
%K TR 233, TR233, jnc, LP

%A D. L. Dowe
%A J. J. Oliver
%A R. A. Baxter
%A C. S. Wallace
%T Bayesian estimation of the Von Mises concentration parameter
%J Proc. 15th Int. Workshop on Maximum Entropy and Bayesian Methods, Santa Fe
%P 51-60
%M JUL
%D 1995
%O TR 95/236, Dept. Comp. Sci., Monash Uni., Sept 1995
%K TR 236, TR236, vonMises, vM, circle, circular, probability distribution,
   inductive inference, II, MML, CSW, CSWallace, DLD, jono, MaxEnt, Max Ent,
   c1995, c199x, c19xx, zz0995
%X "... examine a variety of Bayesian estimation techniques by examining the
   posterior distn in both polar & Cartesian co-ordinates. We compare the MML
   est. with these fellow B.techniques, & a range of Classical ests.. We find
   that the B. ests. outperform the Classical ests.."
   -- [<A HREF="https://doi.org/10.1007/978-94-011-5430-7_6">doi:10.1007/978-94-011-5430-7_6</A>]['19].
   (Later MML research: [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A D. M. Platt
%T Algorithms for Assembling Genomic Restriction Maps
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%D 1995
%K daz, Monash, PhD, thesis, MolBio, mapping, RSM, genome, digest, clone,
   clone order, contigs, contig, yac, assembly, c1995, c199x, c19xx, zz0995
%X 45 refs.
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].)

%A M. Saleeba
%T DRAMA: Dynamically reconfigurable abstract machine architecture
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 95/238
%M OCT
%D 1995
%K TR 238, TR238, DRAMA, computer architecture, zz1095

%A M. Saleeba
%A R. Pose
%T Fast prime number generation with reconfigurable logic
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 95/239
%M OCT
%D 1995
%K TR 239, TR239, zz1095, generate, primes, numbers

%A C. N. Yee
%A T. I. Dix
%T A platform for restriction mapping
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 95/241
%M NOV
%D 1995
%K TR 241, TR241, Monash, MolBio, genetic, map, mapping, site, RSM, zz1195
%X (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinformatics</A>].)

%A K. E. Macphee
%A T. I. Dix
%T Generic C++ classes for customised C pointers and arrays
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 95/243
%M NOV
%D 1995
%K TR 243, TR243, Monash, TIDix, zz1195,
   C plus plus, CplusPlus, C++, cc, safe C, safeC, programming language

%A R. A. Baxter
%T Finding overlapping distributions with MML
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 95/244
%M NOV
%D 1995
%K TR 244, TR244, Monash, RABaxter, minimum message length, MML, MDL,
   inductive inference, II, statistics, estimation, mixture modelling, model,
   class, classification, cluster, clustering, zz1195, c1995, c199x, c19xx
%X Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].

%A A. J. Hurst
%T A general purpose filing system literate program
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 95/246
%M DEC
%D 1995
%K TR 246, TR246, Monash, zz1295

%A N. Jitnah
%A A. E. Nicholson
%T Belief network inference algorithms: a study of performance based on domain
   characterisation
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/249
%M AUG
%D 1996
%K TR 249, TR249, belief networks, Bayesian, inductive inference, II,
   belief update, updating, stochastic sampling, Likelihood Weighting,
   Logic Sampling, Jensen, AI, annn, zz0896
%X "... There are a number of exact & approximate inference algorithms
   available for performing belief updating, however in general the task is
   NP-hard. To overcome the problems of computational complexity that occur
   when modelling larger, real-world problems, researchers have developed
   variants of stochastic simulation approximation algorithms, & a number of
   other approaches involve approximating the model or limiting belief updating
   to nodes of interest.  Typically comparisons are made of only a few
   algorithms, & on a particular example network. We survey the belief network
   algorithms & propose a system for domain characterisation as a basis for
   algorithm comparison. We present performance results using this framework
   from three sets of experiments: (1) on the Likelihood Weighting (LW) & Logic
   Sampling (LS) stochastic simulation algorithms; (2) on the performance of LW
   & Jensen's algorithms on state-space abstracted networks, (3) some
   comparisons of the time performance of LW, LS & the Jensen algorithm. Our
   results indicate that domain characterisation may be useful for predicting
   inference algorithm performance on a belief network for a new application
   domain."
   -- [<A HREF="/publications/1996/tr-1996-249-full.ps">.ps</A>][2/'04].
   Refd to in K & N p77 '04: ... faster convergence of [likelihood weighting]
   compared to [logic sampling] ... stochastic sampling methds... .
   [Also search for: Bnets II].

%A A. E. Nicholson
%T A case study in dynamic belief networks: monitoring walking, fall prediction
   and detection
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/251
%M AUG
%D 1996
%K TR 251, TR251, walk, patient, annn, zz1296
%X aka Bayesian networks.

%A J. Neil
%A K. B. Korb
%T The MML evolution of classification graphs
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/252
%M JAN
%D 1996
%K TR 252, TR252, Monash, decision graph, classification graph, KBKorb,
   minimum message length, MML, description, MDL, genetic algorithm, GA, zz0196
%X NB. what is commonly called a decision [tree|graph] is more
       correctly called  a classification [tree|graph] (as here).
   [Also search for: Dgraph decision].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>.)

%A C. S. Wallace
%A K. Korb
%A H. Dai
%T Causal discovery via MML
%J Proc. 13th Int. Conf. on Machine Learning
%E L. Saitta
%I MorganKaufmann
%P 516-524
%D 1996
%O TR 96/254, Dept. Comp. Sci., Monash Uni., Australia 3168,
   Feb 1996
%K conf, ICML, ICML13, causal net, nets, cause and effect, inductive inference,
   II, description, TR 254, TR254, minimum message length, MML, MDL, KBKorb,
   CSW, CSWallace, model, models, zz0296, c1996, c199x, c19xx
%X Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].
   [Also search for: II Bnets].

%A Y. Han
%A I. Zukerman
%T A mechanism for multimodal presentation planning based on agent cooperation
   and negotiation
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/257
%K TR 257, TR257, plan, agent, cooperate, negotiate, Monash, zz0296
%M JAN
%D 1996

%A D. Albrecht
%A J. N. Crossley
%A J. Jeavons
%T A functional language for full linear logic
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/259
%M FEB
%D 1996
%K TR259, TR 259, FP, maths, theory, zz0296

%A J. N. Crossley
%A L. Mandel
%A M. Wirsing
%T First-order constrained lambda calculus
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/261
%M MAR
%D 1996
%K TR261, TR 261, constraint, functional programming, FP, zz0396
%X (Also see [<A HREF="http://www.allisons.org/ll/FP/Lambda/">lambda calculus</A>].)

%A A. C. Bulhak
%T On the simulation of postmodernism and mental debility using recursive
   transition networks
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/264
%M APR
%D 1996
%K TR 264, TR264, c1996, c199x, c19xx, postmodern, post modern, postmodernism,
   grammar, generator, essay, paper, random, transition network, Dada engine,
   pomo, spoof, bogus, scam, fun, funny, scigen, mathgen, ha ha, haha,
   andrew, Monash, MonashUni, zz0496
%X pomo@[<A HREF="http://www.elsewhere.org/pomo/">www</A>]['08],
   [<A HREF="http://dev.null.org/">www</A>]['08].
   It is also mentioned by Richard Dawkins in 'Postmodernism disrobed'
   (a review of 'Intellectual Impostures,' Alan Sokal & Jean Bricmont, 1998),
   Nature, 394, pp.141-143, 9 July 1998
   -- [<A HREF="http://dx.doi.org/10.1038/28089">doi:10.1038/28089</A>]['15].

%A D. Conway
%T MAESTRO: A system for visual experimentation
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/265
%M APR
%D 1996
%K TR 265, TR265, computer graphics, CG, zz0496

%A A. D. Kelly
%A A. Macdonald
%A K. Marriott
%A P. J. Stuckey
%A R. H. C. Yap
%T A comparison of the effectiveness of optimizations in a CLP(R) compiler
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/267
%M MAY
%D 1996
%K TR 267, TR267, constraint, logic programming, LP, CLP, CLPR, zz0596

%A L. Crnogorac
%A A. D. Kelly
%A H. Sondergaard
%T A comparison of three occur-check analysers
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/268
%M MAY
%D 1996
%K TR 268, TR268, logic programming, LP, occurs check, analysis, zz0596

%A A. J. Hurst
%T Literate programming as an aid to marking student assignments
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/269
%M MAY
%D 1996
%K ajh, TR 269, TR269, teach, teaching, CSci, zz0696

%A K. Marriott
%A M. Odersky
%T A confluence calculus for concurrent constraint programming
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/270
%M JUL
%D 1996
%K TR270, TR 270, concurrent, parallel, CSci, zz0796

%A C. Kopp
%T The E-bomb - a weapon of electrical mass destruction
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%P 29
%M JUL
%D 1996
%K Carlo, c1996, c199x, c19xx, conf, e-bomb, ebomb, electronic war-fare,
   warfare, bombs, electromagnetic pulse, zz0796
%X [<A HREF="/~carlo">carlo</A>]['96]. 42 refs.

%A D. Albrecht
%A J. N. Crossley
%T Program extraction, simplified proof-terms and realizability
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R TR 96/271
%M JUL
%D 1996
%K TR 271, TR271, logic, programs as proofs, term, realizability,
   theory, CSci, zz0796

%A A. D. Kelly
%A K. Marriott
%A H. Sondergaard
%A P. J. Stuckey
%T A generic object-oriented incremental analyser for constraint logic programs
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/274
%M AUG
%D 1996
%K TR 274, TR274, oo, oop, CLP CLP(R), CLPR, zz0896

%A D. Albrecht
%A J. N. Crossley
%T Extracting simple programs from second order proofs
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/275
%M AUG
%D 1996
%K TR 275, TR275, logic, proof, zz0896

%A C. Wilson
%A B. Srinivasan
%A S. Ray
%T Comparison of the quadtree and ternary tree representations of binary
   hyperimages
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/281
%M OCT
%D 1996
%K TR281, TR 281, hyper image, quad-tree, zz1096

%A T. Lindarto
%T MML Segmentation-Based Image Coding
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%M NOV
%D 1996
%K MComp, thesis, segment, encoding, image processing, IP, zz1196
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A D. Conway
%A S. Welsh
%T A facial motion synthesiser for text-to-speech systems
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/283
%M NOV
%D 1996
%K TR 283, TR283, face, mouth, zz1196

%A D. R. Wood
%T On higher-dimensional orthogonal graph drawing
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/286
%M NOV
%D 1996
%K TR 286, TR286, graphs, zz1196

%A V. J. Fazio
%T Minimizing static route hot-spots for the Monash secure RISC multiprocessor
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/288
%M NOV
%D 1996
%K TR288, TR 288, multi processor, computer architecture, zz1196

%A W. He
%A K. Marriott
%T Constrained graph layout
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/289
%M NOV
%D 1996
%K TR289, TR 289, constraint programming, zz1196

%A H. Dai
%A K. Korb
%A C. Wallace
%T A study of causal discovery with weak links and small samples
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/298
%M DEC
%D 1996
%O Intelligent Information Systems, pp.27-30, 1996,
   Australian and New Zealand conf.
%K conf, TR 298, TR298, CSW, CSWallace, cause, effect, network, MML, MDL,
   KBKorb, machine learning, AI, inductive inference, II,
   zz1296, c1996, c199x, c19xx
%X "... examines the influence of sample size on the discovery of causal models.
   The experimental results illustrate the effect of larger sample sizes for
   reliably discovering causal models and the relevance of the strength of
   causal links and the complexity of the original causal model. They present
   indicative evidence of the superior robustness of MML methods to standard
   significance tests in the recovery of causal links. The comparative results
   show that the MML ..."
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A T. Seeman
%A P. Tischer
%T Generalized locally adaptive DPCM
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 97/301
%M MAR
%D 1997
%K TR 301, TR301, data, image, compression, compress, local, DPCM, PCM

%A G. W. Rumantir
%T Atlantic tropical cyclone intensity forecasting via the
   minimum message length principle: a preliminary result
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 97/303
%M OCT
%D 1997
%K TR303, TR 303, MML, description, weather, forecast, climate,
   hurricane, MDL, zz1097
%X date really is Oct 97.

%A K. B. Korb
%T Probabilistic causal structure
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 97/305
%M JUN
%D 1997
%K TR 305, TR305, cause, effect, machine learning, inductive inference, II,
   artificial intelligence, KBKorb, AI, zz0697
%X [Also search for: Bnet II].

%A N. Jitnah
%A A. E. Nicholson
%T Weight-Directed Search for Anytime Evaluation of Belief Networks
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 97/309
%M MAY
%D 1997
%K TR 309, TR309, AI, annn, network, zz0597
%X AKA Bayesian networks.   [Also search for: CaMML].

%A C. S. Wallace
%A K. B. Korb
%T Learning linear causal models by MML sampling
%B Causal Models and Intelligent Data Management
%E A. Gammerman
%I SpringerVerlag
%P 89-111
%D 1999
%O TR 97/310, Dept. Comp. Sci., Monash Uni., Australia, June '97
%K TR310, TR 310, model, cause, effect, inductive inference, MML, MDL, zz0697,
   conf, CSW, CSWallace, AI, learning, CS, CSci, minimum message length, MCMC,
   KBKorb, CaMML, causal network, machine learning, AI, II, net, nets, network,
   TETRAD, Madigan, description, zz1098, c1999, c199x, c19xx
%X "We combine [MML] evaln of linear causal models with Monte Carlo sampling to
   produce a program that, given ordinary joint sample data, reports the
   posterior probs. of equiv. classes of causal models & their member models.
   We compare our program with TETRAD II [7.15] & the Bayesian MCMC program of
   Madigan et al. [7.11]. Our approach differs from that of M. et al. [7.11]
   particularly in not assigning equal prior probs. to equiv. classes of causal
   models & in merging models from distinct equiv. classes when the causal links
   are suff. weak that the sample data available could not be expected to
   distinguish between them (which we call 'small effect equivalence')."
   -- [<A HREF="http://dx.doi.org/10.1007/978-3-642-58648-4_7">doi:10.1007/978-3-642-58648-4_7</A>]['14] (1999).
   See [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].
   [Tech report #310 June 1997, conf '98? / book 1999.]

%A M. S. Collins
%A J. J. Oliver
%T Automaton inference using MML principle - part II- MML measure development
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 96/312
%M MAR
%D 1997
%K TR 312, TR312, II, infer, finite state, machine, automaton, FSM, FSA, PFSA,
   HMM, MDL, AI, jono, zz0397
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)
   [Also search for: infer finite state automaton].

%A K. B. Korb
%A C. S. Wallace
%T In search of the philosopher's stone: Remarks on Humphreys and
   Freedman's critique of causal discovery
%J British Jrnl. for the Philosophy of Science
%P 543-553
%D 1999
%O TR 97/315, Mar 1997, Dept. Comp. Sci., Monash Univ., Australia 3168
%K TR 315, TR315, CSW, CSWallace, causal, cause and effect, CaMML, AI, zz0397,
   c1999, c199x, c19xx, KBKorb
%X See [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A R. Baxter
%T Minimum Message Length Inductive Inference - Theory and Applications
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%M DEC
%D 1996
%K Rohan Baxter, PhD, Thesis, minimum message length, MML, description,
   Inductive Inference, II, AI, machine learning, encoding, MDL,
   stochastic complexity, SC, Rissanen, Akaike, AIC, BIC, over fitting,
   complexity, Bayesian, model, zz1197, c1996, c199x, c19xx
%X Thesis submitted Dec 1996, passed July '97.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A M. S. Collins
%A J. J. Oliver
%T Efficient induction of finite state automata
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 97/320
%M JUL
%D 1997
%O UAI-97
%K c1997, c199x, c19xx, TR 320, TR320, UAI97, UAI, conf, Inductive Inference,
   II, AI, jono, k tails, k tail, ktails, ktail, machine learning, FSA, FSM,
   PFSA, PFSM, HMM, infer, inference, learn, learning, algorithm, MML, MDL,
   information, strings, automaton, zz0797
%X "... introduces a new alg. for the induction if complex finite state automata
   from samples of behavior. ... is based on information theoretic principles.
   ... reduces the search space by many orders of magnitude over what was prev.
   thought possible. We compare [it] with some existing induction techniques for
   finite state automata & show that [it] is much superior in both run time &
   quality of inductions."
   -- 1302.1530@[<A HREF="http://arxiv.org/abs/1302.1530">arXiv</A>]['16].
   [Also search for: infer finite state automaton].

%A J. J. Oliver
%A K. B. Korb
%T A Bayesian analysis of the doomsday argument
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 97/323
%M DEC
%D 1997
%K TR 323, TR323, dooms day, doom, zz1297, KBKorb

%A J. McCormack
%A A. Sherstyuk
%T Creating and rendering convolution surfaces
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 97/324
%M SEP
%D 1997
%K TR324, TR 324, computer graphics, render, surface, zz0997
%X [<A HREF="/~jonmc/">jonmc</A>].

%A S. Ray
%A R. Shakya
%A B. Srinivasan
%T New approaches to image segmentation based on probabilistic distance
   criteria
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 97/325
%M OCT
%D 1997
%K TR325, TR 325, images, image processing, IP, zz1097

%A R. H. Turi
%A S. Ray
%T Clustering-based colour image segmentation using inter-cluster distance
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 97/329
%M OCT
%D 1997
%K TR329, TR 329, processing, IP, zz1097

%A K. Marriott
%T Abstract interpretation: A theory of approximate computation
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 97/333
%M OCT
%D 1997
%K TR333, TR 333, zz1197

%A J. J. Oliver
%A C. S. Forbes
%T Bayesian approaches to segmenting a simple time series
%I Dept. Comp. Sci., Monash Uni., Australia 3168
%R 97/336
%M DEC
%D 1997
%K TR 336, TR336, segment, zz1297
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].)

%A D. R. Wood
%T Two-bend three-dimensional orthogonal grid drawing of maximum degree five
   graphs
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%M MAR
%D 1998
%R 98/03
%K TR 3, TR3, maths, graph, 3D, 3-D, zz0498

%A V. J. Fazio
%T A Routing System for the Monash Secure RISC Multiprocessor
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%D 1998
%K PhD thesis, computer architecture, multi-processor, walnut, zz0498
%X <!-- supervisor: Ron Pose --> .

%A J. Baum
%T Investigation of modifications of HINT image compression
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%M APR
%D 1998
%K MComp, masters thesis, compress, images, HINT, zz0498

%A A. Dorin
%T Physically based, self-organizing cellular automata
%R 98/08
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%M JUN
%D 1998
%K TR8, TR 08, artificial life, AL, complex systems, cellular automata, zz0698

%A S. Welsh
%A D. Conway
%T Encoding video narration as text
%D 1998
%R TR10, TR 10, 98/10, talking head, heads, zz0698
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168

%A M. Mitchell
%T A hierarchical concept learner
%R 98/11
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%M JUN
%D 1998
%K TR11, TR 11, AI

%A D. Conway
%T An algorithmic approach to English pluralization
%R 98/12
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%M JUN
%D 1998
%K TR12, TR 12, natural language

%A D. Conway
%T Declarative command-line interfaces
%R 98/13
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%M JUN
%D 1998
%K TR13, TR 13, interface, shell

%A J. R. Neil
%A K. B. Korb
%T The MML evolution of causal models
%R 98/17
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%M AUG
%D 1998
%K TR 17, TR17, Minimum Message Length, MML, inductive inference, II, MDL,
   model, cause, effect, AI, GA, description, zz0898, KBKorb
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. Baum
%A A. E. Nicholson
%T Dynamic non-uniform abstractions for approximate planning in large
   structured stochastic domains
%R 98/18
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%M AUG
%D 1998
%K TR 18, TR18, plan, planning, AI, annn, zz0898

%A R. H. Turi
%A S. Ray
%T K-means clustering for colour image segmentation with automatic
   detection of K
%R 98/21
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%M AUG
%D 1998
%K TR 21, TR21, kMeans, cluster, processing, segmenting, zz0898

%A H. Leroux
%A M. Hassan
%T On the inter-arrival distribution of FGN arrival processes
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%R 98/26
%M NOV
%D 1998
%K TR 26, TR26, zz1198

%A J. R. Neil
%A K. B. Korb
%T The evolution of causal models: A comparison of Bayesian metrics and
   structure priors
%J Methodologies for Knowledge Discovery and Data Mining PAKDD-99
%I SpringerVerlag
%W Beijing
%P 432-437
%M APR
%D 1999
%O TR 1999/27 Mar 1999, School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%K conf, PAKDD99, TR27, TR 27, cause, CaMML, Bayes, model, AI, II, MML, MDL,
   Bnet, KBKorb, JRNeil, zz0399
%X PAKD; uk us isbn:3540658661.
   [Also search for: Bnet II]  and  [also search for: CaMML].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. R. Neil
%A C. S. Wallace
%A K. B. Korb
%T Bayesian networks with non-interacting causes
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%R 1999/28
%M SEP
%D 1999
%K TR28, TR 28, network, cause, causal, effect, model, AI, MML, MDL, zz0999,
   CSW, CSWallace, KBKorb, JRNeil, c1999, c199x, c19xx
%X (that's right, Sept '99.)
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].)

%A K. Edwards
%A G. Farr
%T Fragmentability of graphs
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%R 1999/34
%M APR
%D 1999
%K TR 34, TR34, maths, graph, fragment, zz0599

%A D. R. Wood
%T Multi-dimensional orthogonal graph drawing in the general position model
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%R 1999/38
%M SEP
%D 1999
%K TR38, TR 38, graph, graphs, draw, drawing, 2D, 3D, orthogonal, zz0999

%A C. Mingins
%A Y. Liu
%T From UML to Design by Contract
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%R 1999/45
%M AUG
%D 1999
%K TR 45, TR45, UML, programming, zz1099

%A M. S. Collins
%T Induction of Finite State Models for Autonomous Agents
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%M NOV
%D 1999
%K PhD Thesis, Matt, Mat, jono, FSA, FSM, PFSA, PFSM, Inductive Inference, II,
   model, automaton, automata, machine, machines, Markov, HMM, AI,
   minimum description message length, MML, MDL, zz1199
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>] research.)

%A B. Demoen
%A M. Garcia de la Banda
%A P. J. Stuckey
%T Type constraint solving for parametric and ad-hoc polymorphism
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%R 1999/47
%M DEC
%D 1999
%K TR47, TR 47, CLP, LP, types, check, checking

%A B. Demoen
%A M. Garcia de la Banda
%A W. Harvey
%A K. Marriott
%A P. J. Stuckey
%T Herbrand constraint solving in HAL
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%R 1999/49
%M DEC
%D 1999
%K TR49, TR 49, CLP, LP

%A B. Demoen
%A M. Garcia de la Banda
%A W. Harvey
%A K. Marriott
%A P. J. Stuckey
%T An overview of HAL
%I School of Comp. Sci. & Software Engineering,
   Monash Uni., Australia 3168
%R 1999/50
%M DEC
%D 1999
%K TR50, TR 50, CLP, LP

%A J. N. Crossley
%A M. Wirsing
%T Programs from specification proofs
%R 2000/54
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%M JAN
%D 2000
%K TR54, TR 54, zz0100

%A J. Jeavons
%A I. Poernomo
%A B. Basit
%A J. N. Crossley
%T A layered approach to extracting programs from proofs with an
   application in graph theory
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2000/55
%M JAN
%D 2000
%K TR55, TR 55, zz0100

%A J. N. Crossley
%A I. Poernomo
%A M. Wirsing
%T Extraction of structured programs from specification proofs
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2000/56
%M JAN
%D 2000
%K TR56, TR 56, zz0100

%A J. Jeavons
%A I. Poernomo
%A J. N. Crossley
%A B. Basit
%T Fred: An implementation of a layered approach to extracting programs from
   proofs.  Part I: an application in Graph Theory
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2000/57
%M JAN
%D 2000
%K TR57, TR 57, zz0100

%A I. Poernomo
%A J. N. Crossley
%T Correct interaction between programs and proofs
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2000/58
%M JAN
%D 2000
%K TR58, TR 58, zz0100

%A M. V. Ramakrishna
%A S. Nepal
%T Similarity query processing in image data
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2000/61
%M FEB
%D 2000
%K TR61, TR 61, images, retrieval, retrieve, similar, zz0200

%A K. B. Korb
%A N. R. Thomason
%T The declining significance of significance
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2000/62
%M FEB
%D 2000
%K TR 62, TR62, significance testing, inductive inference, stats, statistics,
   hypothesis, test, KBKorb, thomson, zz0200
%X A title to die for.

%A N. Jitnah
%T Using Mutual Information for Approximate Evaluation of Bayesian Networks
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%M MAR
%D 2000
%K PhD thesis, net work, network, artificial intelligence,
   inductive inference, AI, II, zz0300, c2000, c200x, c20xx
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>] research.)

%A I. Davidson
%T Markov Chain Monte Carlo Sampling and the
   Minimum Message Length Principle: Application and Uses
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%M MAR
%D 2000
%K PhD thesis, MML, chains, MDL, AI, II, description, zz0300
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>] research.)

%A J. Chua
%T Fast Full-Search Equivalent Nearest-Neighbour Search Algorithms
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%M MAR
%D 2000
%K MComputing, MComp, masters thesis, searching, retrieval, retrieve, zz0300
%X This thesis was retrieved from the Caulfield campus.

%A A. Arslanov
%T On elementary computability-theoretic properties of algorithmic randomness
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2000/74
%M AUG
%D 2000
%K TR74, TR 74, minimum message length, description, MML, MDL, complexity,
   random, information content, theory, zz0800
%X (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>] research.)

%A J. W. Breen
%T A WWW Japanese dictionary
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2000/75
%M SEP
%D 2000
%K TR75, TR 75, Japan, natural language, zz0900

%A D. R. Wood
%T Three-Dimensional Orthogonal Graph Drawing
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%M OCT
%D 2000
%K PhD thesis, graphs, draw, 3D, three dimension, zz1000, c2000, c200x, c20xx
%X (One of  G r a h a m  F a r r's  grad' students.)

%A J. Neil
%T MML Discovery of Causal Models
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%M MAR
%D 2001
%K PhD thesis, minimum message length, MML, minimum description length, MDL,
   model, cause, effect, Julian, Jules, zz0301
%X supervisor: K e v i n  K o r b.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].)
   [Also search for: CaMML].

%A S. Mascaro
%A K. B. Korb
%A A. E. Nicholson
%T Suicide as an evolutionarily stable strategy
%J Adv. in Artificial Life (ECAL 6)
%E J. Kelemen
%E P. Sosik
%I SpringerVerlag
%S LNAI
%V 2159
%P 120-132
%M SEP
%D 2001
%O TR2001/89, School of Comp. Sci. and Software Eng., Monash Uni.
%K conf, ECAL, ECAL6, ECAL2001, TR89, TR 89, game, games, Alife, zz0301, c2001,
   c200x, c20xx, altruism, ethics, ESS, evolutionary programming, KBKorb, annn,
   artificial life
%X Ethics has traditionally been the domain of philosophers, pursuing their
   investigations a priori, since social experimentation is not an option.
   After Axelrod's work, artificial life (ALife) methods have been applied to
   social simulation. Here we use an ALife simulation to pursue experiments
   with ethics. We use a utilitarian model for assessing what is ethical, as it
   offers a computationally clear means of measuring ethical value, based on
   the utility of outcomes. We investigate the particular action of altruistic
   suicide fostering the survival of others, demonstrating that suicide can be
   an evolutionarily stable strategy (ESS).
   [<A HREF="http://link.springer.de/link/service/series/0558/papers/2159/21590120.pdf">pdf</A>][11/'02]

%A J. N. Crossley
%T Structures with features
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2001/91
%M APR
%D 2001
%K feature set theory, cognitive psychology, abstraction, formal, zz0401
%X paper presented at the International Conference
   in Honor of Fr. B.F. Nebres, Manila, 2/01

%A L. McIver
%T Syntactic and Semantic Issues in Introductory Programming Education
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%M AUG
%D 2001
%K PhD thesis, syntax, Mkiver, Maciver, zz0801

%A J. W. Breen
%T Software tools for text analysis
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2001/101
%M NOV
%D 2001
%K TR101, TR 101, zz1101

%A M. Stillwell
%T Studies in Evolutionary Algorithms
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%M NOV
%D 2001
%K Masters thesis, evolutionary program, programming, genetic algorithm, GA,
   programs, zz1101
%X (KK + LA)

%A R. Buyya
%A K. Branson
%A J. Giddy
%A D. A. Abramson
%T The virtual laboratory: Enabling molecular modeling for drug design on
   the world wide grid
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2001/103
%M DEC
%D 2001
%K TR103, TR 103, MolBio, WWG, zz1201

%A G. E. Farr
%T Some results on generalised Whitney functions
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2001/104
%M DEC
%D 2001
%K TR104, TR 104, GFarr, function, zz1201, c2001, c200x, c20xx

%A T. Sargeant
%T Decaf: Confluent Concurrent Programming in Java
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%M JAN
%D 2002
%K MComp, Masters, thesis, Java, language, parallel, zz0102

%A M. Holzl
%A J. N. Crossley
%T Constraint-lambda calculi
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2002/106
%M FEB
%D 2002
%K TR106, TR 106, constraint programming, lambda calculus, zz0202
%X (Also see [<A HREF="http://www.allisons.org/ll/FP/Lambda/">lambda</A>].)

%A S. Mascaro
%A K. B. Korb
%A A. E. Nicholson
%T Parental investment and reproductive strategies
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2002/112
%M JUL
%D 2002
%O S. Mascaro, K. B. Korb and A. E. Nicholson.
   ALife investigation of parental investment in reproductive strategies.
   Proc. of the 8th Int. Conf. on Artificial Life (Alife VIII),
   NSW, Australia, 9-13 Dec. 2002, MIT Press, pp.358-361
%K TR112, TR 112, strategy, simulation, parents, parent, invest, child, KBKorb,
   annn, children, strategy, resources, conf, Alife8, zz1203
%X [<A HREF="/publications/2002/tr-2002-112-full.ps">.ps</A>][12/'03]
   Conf paper in: us isbn:0262692813.

%A S. Welsh
%T Shape preserving linear interpolation (SPLINT)
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2002/113
%M MAY
%D 2002
%K computer graphics, TR113, TR 113, shape, morph, morphing, image, zz0602

%A S. Welsh
%T Pseudo-3D image morphing
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2002/114
%M MAY
%D 2002
%K computer graphics, TR114, TR 114, morph, shape, image, zz0602

%A I. Poernomo
%A J. N. Crossley
%T The Curry-Howard isomorphism adapted for imperative program
   synthesis and reasoning
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2002/117
%M JUN
%D 2002
%K TR 117, TR117, logic, theory, maths, zz0602

%A C. R. Twardy
%A K. B. Korb
%T Causal interaction in Bayesian networks
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2002/118
%M JUL
%D 2002
%K TR118, TR 118, network, net work, cause, effect, model, KBKorb,
   inductive inference, II, zz0702
%X (Also see [<A HREF="http://www.allisons.org/ll/Publications/2006AI/">Bayesian networks</A>].)

%A K. Edwards
%A G. Farr
%T An algorithm for finding 2-colourings with small monochromatic
   components in graphs of maximum degree 4
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2002/122
%M SEP
%D 2002
%K TR 122, TR122, GFarr, graph, colouring, two colours, colour, colors, color,
   component, max, coloring, zz1002, c2002, c200x, c20xx

%A A. Dorin
%T Artefact and artifice: Views on Life
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2002/126
%M NOV
%D 2002
%K TR 126, TR126, multi-media, multimedia, computer graphics, view, zz1102

%A D. R. Powell
%T Algorithms for Sequence Alignment
%I School of Comp. Sci. and Software Engineering, Monash Uni.,
   Australia 3168
%M DEC
%D 2002
%K PhD thesis, MolBio, c2002, c200x, c20xx, zz1202, bioinformatics, DNA, biol,
   hidden Markov model, HMM, alignment, pair, pairs, three, multiple, sequence,
   analysis, sequences, genetic, PHMM, homology, dynamic programming, DPA,
   algorithm
%X "Sequence alignment is an important tool for describing relationships between
   sequences.  Many sequence alignment algorithms exist, differing in efficiency
   and in their models of the sequences and of the relationship between
   sequences. The focus of this thesis is on algorithms for the optimal
   alignment of two or three sequences of biological data, particularly DNA
   sequences. The algorithms are discussed with particular emphasis on space
   and time complexity ..."
   -- thesis@[<A HREF="http://arrow.monash.edu.au/vital/access/services/Download/monash:6032/SOURCE2">mon@sh</A>][12/'11].
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Three/">Bioinformatics</A>].)

%A K. B. Korb
%A M. Stillwell
%T The story of the hot hand: Powerful myth or powerless critique?
%J 4th Int. Conf. on Cognitive Science (ICCS)
%I Elsevier
%D 2003
%O TR 2002/130, School of Comp. Sci. and Software Eng.,
   Monash Uni., Dec., 2002
%K conf, ICCS, c2002, c200x, c20xx, TR 130, TR130, player, skill, sport, score,
   scoring, hot hands, basketball, random sequence, stats, model, modelling,
   sports, basketball, run of success, goals, form slump, cut point,
   segmentation, II, significance tests, MML, mdl, Gilovich, Tversky, Vallone,
   Gould, KBKorb, stilwell, law of small numbers
%X "Thomas Gilovich & Amos Tversky famously claimed that the belief in the Hot
   Hand in basketball is a cognitive illusion, an instance of the belief in the
   Law of Small Numbers. They supported this claim with a variety of orthodox
   stat. tests failing to show any clear evidence of a Hot Hand phenomenon.
   These researchers neglected to perform any power analysis on this test. Here
   we show that their belief in having demonstrated the illusory status of the
   Hot Hand is itself an illustration of the Law of Small Numbers."
  -- pdf@[<A HREF="http://www.csse.monash.edu.au/~korb/iccs.pdf">iccs</A>]['12].
   -- [<A HREF="/publications/2002/tr-2002-130-abs.html">abs'</A>][12/'02],
   [Also search for: hot hand stats].

%A Y. Yang
%A G. I. Webb
%T Discretization for naive-Bayes learning:  Managing discretization bias
   and variance
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2003/131
%M APR
%D 2003
%K TR131, TR 131, AI
%X [Also search for: discretization].

%A H. Armstrong
%A K. B. Korb
%T Minimal I-map DAGs: Necessary and sufficient conditions
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2003/132
%M APR
%D 2003
%K TR132, c2003, c200x, c20xx, TR 132, KBKorb, Imap, DAG
%X [<A HREF="/publications/2003/tr-2003-132-full.ps">.ps</A>][12/'03].

%A A. Oboler
%A D. McG Squire
%A K. B. Korb
%T Why don't we practice what we teach?  Engineering software for
   computer science research in academia
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2003/139
%M DEC
%D 2003
%K TR139, TR 139, KBKorb, SWE, CS, CSci, Comp Sci, zz1203
%X Dec(!) [<A HREF="/publications/2003/tr-2003-132-full.ps">.ps</A>][12/'03].


%A G. E. Farr
%T The complexity of counting colourings of subgraphs of the grid
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2003/143
%M JUL
%D 2003
%K TR143, TR 143, GFarr, graph, graphs, colours, subgraph, zz0703

%A K. Edwards
%A G. E. Farr
%T Planarization and fragmentability of some classes of graphs
%I School of Comp. Sci. and Software Engineering,
   Monash Uni., Australia 3168
%R 2003/144
%M JUL
%D 2003
%K TR144, TR 144, GFarr, graph, graphs, planar, planarity, fragment, zz0703

%A Ying Yang
%T Discretization for Naive-Bayes Learning
%I School of Comp. Sci. and Software Engineering, Monash Uni., Australia 3800
%M AUG
%D 2003
%K PhD thesis, AI, zz0803
%X <!-- sup' G. W e b b --> .

%A K. van Haaster
%T Providing opportunities to demonstrate mastery rather than memory:
   Testing programming skills in a programming encironment
%I School of Comp. Sci. and Software Engineering, Monash Uni., Australia 3800
%R 2003/146
%M OCT
%D 2003
%K TR, TR146, education, comp sci, teaching, test, skill, ability,
   exam, examining, vanHaaster, zz1003

%A J. McCormack
%T A method for generating phyliotaxis over surfaces of revolution
%I School of Comp. Sci. and Software Engineering, Monash Uni., Australia 3800
%R 2003/149
%M DEC
%D 2003
%K TR 149, TR149, computer generated image, images, cgi, phylotaxis, zz1203
   [<A HREF="/~jonmc/">~jonmc</A>][12/'03]

%A A. Dorin
%T Artifact and artifice: Building artificial life for play
%I School of Comp. Sci. and Software Engineering, Monash Uni., Australia 3800
%R 2003/150
%M DEC
%D 2003
%K TR150, TR 150, computer generated image, images, cgi, zz1203
%X [<A HREF="/~aland/">~aland</A>][12/'03]

%A K. B. Korb
%A A. E. Nicholson
%T Bayesian Artificial Intelligence
%I ChapmanAndHall / CRC
%P 392
%D 2004
%K book, text, AI, II, machine learning, nets, zz1203, c2004, c200x, c20xx,
   network, networks, Bnet, probability, statistics, stats, causal, model,
   inverse, monash, annn, KBKorb, bai, L4Ref, L5Ref
%X Mostly about 'Bayesian networks' / `causal models', not all of B A I.
   uk us isbn:1584883871.
   (Also see [<A HREF="http://www.allisons.org/ll/Publications/2006AI/">b.nets</A>].)

%A Grace W. Rumantir
%T Minimum Message Length Criterion for Second-order Polynomial Model
   Selection Applied to Tropical Cyclone Intensity Forecasting
%I School of Comp. Sci. and Software Engineering, Monash Uni., Australia 3800
%M MAR
%D 2004
%K PhD thesis, MML, minimum message description length, MDL, polynomial, II,
   weather, model, models, modelling, criteria, zz0304, anti, forecast,
   meteorology
%X <!-- Sup'rvisors:  C S W@llace and P E Tisch'r --> .
   [Also search for: polynomial MML].

%A S. K. Chong
%A G. E. Farr
%A L. Frost and S. Hawley
%T Pedagogically sound examples in public-key cryptography
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%R TR 2004/155
%M JUN
%D 2004
%K TR 155, TR155, GFarr, security, example, zz0604

%A G. E. Farr
%T Cost-effectiveness of algorithms
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%R TR 2004/157
%M JUL
%D 2004
%K TR 157, TR157, zz0704, cost effective, algorithm, time, quality, solution,
   optimisation problem, maximum matching, graph colouring, Kolmogorov,
   complexity, c2004, c200x, c20xx, GFarr
%X "... how to assess the performance of algorithms for optimisation problems
   in a way that balances solution quality & time. We propose measures of
   cost-effectiveness of such algorithms. These measures give the gain in
   solution quality per time unit over a sequence of inputs, & give a basis for
   deciding which alg' to use when aiming for best accumulated solution quality
   for a given time investment over such an input sequence. Cost-effectiveness
   measures can be defined for both average-case & worst-case performance.
   [applied]  to 3 problems: maximum matching, graph colouring & Kolmogorov
   complexity. For the latter, we propose a cost-effectiveness measure for the
   time-bounded complexity Kt(x), & argue that it can be used to measure the
   cost-effectiveness both of finding a short program to output x & of
   generating x from such a program. Under mild assumptions, we show that
   (roughly speaking) if the time-bounded complexity Kt(x) is to be [a ?]
   cost-effective approximation to K(x) then t(n) = O(n**2)."
   [<A HREF="/publications/2004/tr-2004-157-abs.html">abs</A>][7/'04]

%A J. McCormack
%T The Application of L-systems and Developmental Models to Computer Art,
   Animation, and Music Synthesis
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%R 2004/158
%M AUG
%D 2004
%K PhD thesis, Lsystems, system, model, c2004, c200x, c20xx, Jon McCormack,
   generation, production, aesthetics, CSSE
%X staff candidate! [<A HREF="/~jonmc/">~jonmc</A>][8/'04]

%A L. J. Fitzgibbon
%T Message from Monte Carlo: A Framework for Minimum Message Length
   Inference using Markov Chain Monte Carlo Methods
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%M OCT
%D 2004
%K PhD thesis, c2004, c200x, c20xx, description, CSSE, MML, MCMC, MDL, zz1004,
   inductive inference, II, AI, method, Leigh Fitzgibbon, leighf, csse,
   reversible jump
%X [<A HREF="/publications/2004/leigh-abs.html">abs+pdf</A>]['05]
   Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>], (sup. L.A., assoc. sup. d.l.d)

%A B. Macmillan
%T MML Analysis of Melody
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%M OCT
%D 2004
%K MComp, masters, thesis, music, minimum message length, description, MDL,
   c2004, c200x, c20xx, zz1004
%X Brendan was sup' by the late csw.

%A C. Kopp
%A C. S. Wallace
%T TROPPO - A tropospheric propagation simulator
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%R 2004/161
%M NOV
%D 2004
%K TR 161, TR161, CSW, CSWallace, troposphere, data communications, comms,
   radio, zz1104
%X CK with the late [<A HREF="http://www.allisons.org/ll/Images/People/Wallace/">CSW</A>].

%A L. R. Hope
%A K. B. Korb
%T A Bayesian metric for evaluating machine learning algorithms
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%R 2004/163
%M NOV
%D 2004
%K TR 163, TR163, zz1104, AI, criterion, KBKorb

%A G. K. Gupta
%T Computer science curriculum developments in the USA in the 1960s
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%R 2004/164
%M DEC
%D 2004
%K TR 164, TR164, CSci, comp sci, education, history, development, teaching

%A C. R. Twardy
%A A. E. Nicholson
%A K. B. Korb
%A J. McNeil
%T Data mining cardiovascular Bayesian networks
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%R 2004/165
%M APR
%D 2005
%K TR 165, TR165, network, cardio-vascular, heart, medical, annn, zz0405
%X the announcement of 4/2OO5 said TR 2OO4/165.

%A S. Boyd
%T Computational Modelling and Prediction of Protease Specificity
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%M JUN
%D 2005
%K PhD thesis, MolBio, bioinformatics, c2005, c200x, c20xx, model, zz0705
%X <!-- sup  M. G de la B.,  R. P i k e,  J. W h i s s t o c k --> .

%A M. M. Holzl
%A J. N. Crossley
%T Disjunctive constraint lambda calculi
%R 2005/171
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%M JUL
%D 2005
%K TR 171, TR171, FP, lambda calculus, c2005, c200x, c20xx, zz0705,
   constraints, programming
%X also search for: lambda calculus

%A L. Kornienko
%T Implementing a Support Vector Machine in a Message Length Framework
%I School of Computer Science and Software Engineering,
   Monash Uni., Australia 3800
%M OCT
%D 2005
%K Masters, M.I.T., SVM, SVMs, MML, MDL, c2005, c200x, c20xx, Lara Kornienko,
   classifier, supervised classification, linear
%X <!-- sup: D. A l b r e c h t and D. D o w e -->
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].)

%A L. R. Hope
%A K. B. Korb
%T An information-theoretic approach to causal power
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2005/176
%M DEC (!)
%D 2005
%K TR 176, TR176, LRHope, KBKorb, cause, theory
%X Dec 2005.

%A J. N. Crossley
%T From the imaginary to the real:  The triumph of Rome
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2005/181
%M NOV
%D 2005
%K TR 181, TR181

%A J. Comley
%T Machine Learning with Generalised Tree-based Bayesian Networks,
   Decision Trees and MML
%I Monash Uni., Australia 3800
%M NOV
%D 2005
%K PhD, thesis, computer science, CSci, csse, c2005, c200x, c20xx, trees,
   network, dTree, MDL, minimum message length, MML, description
%X Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].
   Supervisors [<A HREF="http://www.allisons.org/ll/">L.A.</A>] & d.d.
   [Also search for: Dtree]  [also search for: MML]  and
   [also search for: CaMML].

%A J. N. Crossley
%T Raymond Llull's contributions to Computer Science
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2005/182
%M DEC
%D 2005
%K TR182, TR 182, contribution, Raymond Llull

%A K. B. Korb
%A C. R. Twardy
%A T. Handfield
%A G. Oppy
%T Causal reasoning with causal models
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2005/183
%M DEC
%D 2005
%K TR 183, TR183, model, cause, effect, csse, zz1205, KBKorb, CRTwardy,
   causality, c2005, c200x, c20xx
%X [Also search for: CaMML].

%A G. I. Webb
%A Y. Yang
%A J.R.Boughton, K.B.Korb, K.M.Ting
%T Classifying under computational resource constraints:  Anytime
   classification using probabilistic estimators
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2005/185
%M DEC
%D 2005
%K TR 185, TR185, GIWebb, KBKorb

%A R. T. O'Donnell
%A A. E. Nicholson
%A B.Han,  K.B.Korb,  M.J.Alam,
%A L.R.Hope
%T Incorporating expert elicited structural information in the
   CaMML causal discovery program
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2006/194
%M NOV
%D 2006
%K TR 194, TR194, MML, MDL, Bayesian net, nets, model, c2006, c200x, c20xx,
   KBKorb, annn, Bnet
%X yes, Nov. [<A HREF="/publications/2006/tr-2006-194-full.pdf">pdf</A>]['06]
   [Also search for: CaMML].

%A T. Dwyer
%A K. Marriott
%A M. Wybrow
%T Integrating edge routing into force-directed layout
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2006/195
%M OCT
%D 2006
%K TR195, TR 195, graphs, graph, layout, drawing

%A K. Morgan
%A G. Farr
%T Approximation algorithms for the maximum induced planar and outerplanar
   subgraph problems
%I Caulfield School of I.T., Monash Uni., Australia
%R 2006/197
%K TR197, TR 197, graph, graphs, GFarr, KMorgan, algorithm, c2006, c200x, c20xx

%A G. Farr
%A J. Schmidt
%T On the number of GO positions on lattice graphs
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2006/198
%M NOV
%D 2006
%K TR198, TR 198, GFarr, c2006, c200x, c20xx, game, position, count, counting,
   graph

%A G. K. Gupta
%A A. Singla
%T Using fingerprints based on the sequence of a set of selected words in
   a document for 1-to-n similarity analaysis
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2006/199
%M NOV
%D 2006
%K TR199, TR 199, word, c2006, c200x, c20xx, similar, files, file

%A E. Makalic
%A D. F. Schmidt
%T Efficient linear regression by minimum message length
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2006/201
%M NOV
%D 2006
%K TR201, TR 201, c2006, c200x, c20xx, MML, description, message, model,
   linear regression, MDL
%X [Also search for: Makalic Schmidt MML].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A E. P. Nyberg
%A K. B. Korb
%T Informative interventions
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2007/204
%M FEB
%D 2007
%K TR 204, TR204, KBKorb, intervene, causal model, causality, AI, II
%X issued Feb 2007

%A D. F. Schmidt
%T Minimum message length inference and parameter estimation of
   autoregressive and moving average models
%I Clayton School of I.T., Monash Uni., Australia 3800
%R 2006/206
%M FEB
%D 2007
%K TR 206, TR206, c2007, c200x, c20xx, zz0207, MML, description, II, MDL, model,
   time series, timeSeries, analysis, autoregression, ARMA
%X "This TR presents a formulation of the parameter estimation and model
   selection problem for Autoregressive (AR) and Moving Average (MA) models in
   the Minimum Message Length (MML) framework. In particular, it examines
   suitable priors for both classes of models, and subsequently derives message
   length expressions based on the MML87 approximation. Empirical results
   demonstrate the new MML estimators outperform several benchmark parameter
   estimation and model selection criteria on various prediction metrics."
   [Also search for: Schmidt thesis monash].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A D. Mossop
%T Security and the Password-Capability System
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M MAR
%D 2007
%K PhD thesis, CSC, CS, CSci, c2007, c200x, c20xx, operating systems, zz0407,
   capabilities, OS
%X <!-- sup  R o n a l d  P o s e  &  G r a h a m  F a r r --> .

%A J. Baum
%T Dynamic Non-Uniform Abstractions for Approximate Planning in Large
   Structured Stochastic Domains.
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M APR
%D 2007
%K PhD thesis, CS, CSC, CSci, c2007, c200x, c20xx, plan
%X J.Baum<!-- sup: A n n  N i c h o l s o n, &  T r e v o r  D i x --> .

%A E. Makalic
%T Minimum Message Length Inference of Artificial Neural Networks
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M JUN
%D 2007
%K enesm, PhD thesis, c2007, c200x, c20xx, MML, MDL, zz0707, ANN, network,
   CS, CSci, AI, II, description
%X <!-- sup: L. A l l i s o n and APP --> .
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)
   [Also search for: Makalic MML].

%A A. Dorin
%A K. B. Korb
%T Building virtual ecosystems from artificial chemistry
%R 2007/212
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M AUG
%D 2007
%K TR 212, TR212, c2007, c200x, c20xx, zz0807, ecosystem, Alife, Achemistry,
   ADorin, KBKorb
%X "... propose that limitations of the simulations in [Alife, ecology] can be
   overcome by simulating ecosystems from the level of artificial chemistry. We
   demonstrate the approach's feasibility by describing several virtual
   organisms represented at this level. The organisms naturally fall into
   trophic levels, generate energy from chemical bonds & transform material
   elements in the process. Virtual organisms may interact with one another &
   their abiotic environment using the same chemistry. Biosynthesis & decay
   may also be simulated through this mechanism."
   [<A HREF="/publications/2007/tr-2007-212-abs.html">abs@monash</A>]['07]
   [<A HREF="/publications/2007/tr-2007-212-full.pdf">pdf@monash</A>]['07]

%A T. Dwyer
%A N. Hurst
%A D. Merrick
%T A fast and simple heuristic for metro map path simplification
%R 2007/216
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M SEP
%D 2007
%O Proc 4th Int. Symp. on Advances in Visual Computing, pt.2 (ISVC), 2008
%K TR 216, TR216, city maps, layout, drawing, diagram, diagrams, njHurst, njh,
   underground, tube, metro, c2007, c200x, c20xx, zz0907
%X "We give a heuristic for simplifying a path def. by a given seq. of pts. ...
   seeks to fit the pts with a set of line segs. aligned with a limited set of
   possible directions. Such "schematic path simplification" has application in
   automatically drawing simplified metro maps from geographic data. We show
   that a simple version of our alg. produces reasonable results against
   real-world data & runs in linear time with respect to the number of pts
   (assuming a small fixed number of possible directions). We then give some
   refinements to the alg. which may improve the quality of the results but
   which significantly increase the worst-case time complexity." --
   conf:[<A HREF="http://dx.doi.org/10.1007/978-3-540-89646-3_3">doi:10.1007/978-3-540-89646-3_3</A>]['10],
   & TR:[<A HREF="/publications/2007/tr-2007-216-full.pdf">pdf@monash.edu.au</A>]['07].
   (NB. "limited set of possible directions" as in underground maps.)

%A D. F. Schmidt
%A E. Makalic
%T MMLD inference of the Poisson and geometric models
%R 2008/220
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M JAN
%D 2008
%K TR 220, TR220, c2008, c200x, c20xx, zz0108, minimum message length, MML,
   II, description, mmld, model, MDL, enesm, MML87, d.l.dowe, dld, dldowe,
   risk, model, bias, hypothesis testing, probability distribution
%X "... MMLD-based approx. for the inference of 2 univariate probability
   densities: the geometric distribution, parameterised in terms of a mean
   parameter, & the Poisson d.. The focus is on both parameter est. & hypothesis
   testing properties of the approx.. The new parameter estimators are
   compared to the MML87 estimators in terms of bias, squared error risk &
   KL divergence risk. Empirical experiments demonstrate that
   the MMLD parameter ests. are more biased, & feature higher
   squared error risk than the corr. MML87 est..  In contrast, the 2 criteria
   are virtually indistinguishable in the hypothesis testing experiment."
   -- [<A HREF="/publications/2008/tr-2008-220-full.pdf">pdf</A>]['08]
   [Also search for: message MML].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Discrete/Integers/Geometric/">Geom. & P.</A>].)

%A K. Morgan
%A G. Farr
%T Chromatic factorisations
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%R 2008/222
%M FEB
%D 2008
%K TR 222, TR222, c2008, c200x, c20xx, zz0208, graph, graphs, color, coloring,
   colour, colouring, chromatic, polynomial, factorisation, GFarr, KMorgan
%X [<A HREF="http://www.csse.monash.edu.au/publications/2008/tr-2008-222-full.pdf">pdf@monash</A>]['08]

%A S. Wijewickrema
%T Reconstruction of Quadrics from Two Silhouettes
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M FEB
%D 2008
%K PhD thesis, quadric, silhouette, c2008, c200x, c20xx, reconstruct
%X wikip: "... a quadric, or quadric surface, is any D-dimensional
   hypersurface defined as the locus of zeros of a quadratic polynomial. ...
   SUM[i,j=0..D] Q[i,j].x[i].x[j] + SUM[i=0..D] P[i].x[i] + R = 0  ..."

%A L. Hope
%T Information Measures for Causal Explanation and Prediction
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M MAY
%D 2008
%K PhD thesis, c2008, c200x, c20xx, zz0508, AI, machine learning, II,
   cause, effect, measure
%X Lucas Hope<!-- sup kk and annn --> .

%A T. Dwyer
%A K. Marriott
%A M. Wybrow
%T Topology preserving constrained graph layout
%R 2008/227
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%K JUN
%D 2008
%K TR 227, TR227, graphs, pretty printing, constraint programming

%A D. F. Schmidt
%A E. Makalic
%T Shrinkage and denoising by Minimum Message Length
%R 2008/230
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M SEP
%D 2008
%K TR 230, TR230, c2008, c200x, c20xx, zz0908, enesm, description, MML, MDL,
   NML, wavelet, de noise, denoise, orthonormal regression, stats
%X "... orthonormal regression & wavelet denoising within [MML] framework. A
   criterion for hard thresholding that naturally incorporates param. shrinkage
   is derived from a hierarchical Bayes approach. Both params. & hyperparams.
   are jointly est. from the data directly by minimisation of a 2-part message
   length, & the threshold implied by the new criterion is shown to have good
   asymptotic optimality properties with respect to zero-one loss under certain
   conditions. Empirical comparisons made against similar criteria derived from
   the MDL principle demonstrate that the MML procedure is competitive in terms
   of squared-error loss."
   -- [<A HREF="http://www.csse.monash.edu.au/publications/2008/tr-2008-230-full.pdf">pdf@monash</A>]['08],
   (also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>])
   [also search for: shrinkage stats],  [also search for: MML message].

%A C. Guttmann
%T Collective Iterative Allocation
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M SEP
%D 2008
%K PhD thesis, FIT, model, finance
%X <!-- sup  M. G e o r g e f f,  I. Z u k e r m a n,  S r i n i --> .

%A R. Rafeh
%T The Modelling Language Zinc
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M OCT
%D 2008
%K PhD thesis, Zinc

%A A. Bickerstaffe
%T Minimum Message Length Analysis of Discrete Sequential Data
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M FEB
%D 2009
%K PhD thesis, c2009, c200x, c20xx, MML, MDL
%X (For more on MML see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A D. Schmidt
%T Minimum Message Length Inference of Autoregressive Moving Average Models
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M MAR
%D 2009
%K PhD thesis, Daniel, c2009, c200x, c20xx, MML, MDL, time series, timeSeries,
   model, description, dowe, ARMA
%X [Also search for: Schmidt MML].
   (For more on MML see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A N. J. Hurst
%T Better automatic layout of documents
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M JUN
%D 2009
%K PhD thesis, njh, c2009, c200x, c20xx, zz0709, document, layout, constraint,
   constraints, programming
%X see njh@[<A HREF="http://www.njhurst.com/">njhurst.com</A>]<!-- sup: Kim.M@rriott --> .

%A A. Mani
%T Correlation inequalities for Tutte polynomials
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M APR
%D 2010
%K PhD thesis, ArunM, c2010, c201x, c20xx, zz0510, graph theory, graphs,
   Tutte polynomial, inequality
%X Arun Man,  sup G. F a r r.

%A Sk. M. Rokonuzzaman
%T Quality of service aware topology control for wireless ad hoc networks using
   smart antennas
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M JUN
%D 2010
%K PhD thesis, c2010, c201x, c20xx, zz0610, wireless, network, adhoc, ad hoc,
   computer, antenna
%X <!-- sup  R o n  P o s e  & I q b a l  G o n d a l -->("Rokon").

%A C. Mears
%T Automatic Symmetry Detection and Dynamic Symmetry Breaking for Constraint
   Programming
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M JUL
%D 2010
%K PhD thesis, c2010, c201x, c20xx, constraints
%X "Chris Mears".

%A J. Bernal
%T Models for Hepatitis B Virus Antiviral Drug Therapies and the
   Emergence of Drug Resistant Viral Strains
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M AUG
%D 2010
%K masters, Mcomp, thesis, MolBio, c2010, c201x, c20xx, zz0810, julie, jBernal,
   HBV, model, therapy, resistance, strain
%X "Julie Bernal"<!-- notif'n 5 Aug 2010; sup L Allison, T I Dix -->.
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/">Bioinf</A>].)

%A R. O'Donnell
%T Flexible Causal Discovery with MML
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M SEP
%D 2010
%K PhD thesis, c2010, c201x, c20xx, zz1010, Bayesian, network, net, nets, Bnet,
   Bnets, II, AI, causal discovery, minimum message length, MML, mdl, AIC,
   CaMML, CKL, desciption, hybrid, stats, model, rodo, Rodney ODonnell
%X pdf@[<A HREF="http://arrow.monash.edu.au/hdl/1959.1/123041">mon@sh</A>]['14].
   (AKA "rodo" <!-- sup. KK and LA --> .-)
   [Also search for: CaMML].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/Structured/">MML</A>].)

%A K. Morgan
%T Algebraic Aspects of the Chromatic Polynomial
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M SEP
%D 2010
%K PhD thesis, c2010, c201x, c20xx, zz1010, Kerri, maths, graph, graphs,
   chromatic polynomial
%X "Kerri Morgan"<!-- sup: G. F a r r -->.

%A Minh Duc Cao
%T Information Theoretic Approaches To Biological Sequence Analyses
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M SEP
%D 2010
%K PhD thesis, Minh Duc Cao, c2010, c201x, c20xx, zz1010,
   MolBio, Bioinformatics, information content, MML, MDL, sequence alignment,
   analysis, local genome, compress, XM, eXpert Model, DNA, homology,
   similarity, protein, stats, data compression, compressible, discovery
%X [Also search for: Minh Cao MolBio]<!-- sup. L. A l l i s o n & T. I. D i x -->.
   (Also see [<A HREF="http://www.allisons.org/ll/Bioinformatics/Compress/">Bioinformatics</A>].)

%A R. Myers
%T The intelligent integration and querying of bioinformatic data sources
%I Faculty of Info. Tech. (Clayton),
   Monash Uni., Australia 3800
%M Oct
%D 2010
%K PhD thesis, c2010, c201x, c20xx, zz1010, bioinformatics, query,
   Robert, Bob, Myers
%X "Bob Myers"<!-- sup: T. I. D i x,  R.C. & D.G.  -->.

%A D. Thiruvady
%T Hybrids of Stochastic Metaheuristics and Constraint Programming for
   Combinatorial Optimization
%I Faculty of Info. Tech.,
   Monash Uni., Australia 3800
%M FEB
%D 2012
%K PhD thesis, c2012, c201x, c20xx, zz0212, metaheuristic, heuristic
%X Dhananjay Thiruvady<!-- sup: B e r n d  &  A n d r e a s -->.


%A T. Jones
%T Evolutionary Algorithms, Fitness Landscapes and Search
%R 95-05-048
%I Dept. Computer Science, University of New Mexico, Albuquerque NM 87131
%M MAY
%D 1995
%K thesis, SFI, genetic, evolutionary, algorithms, GA, TR48, TR 48
%X email: terry@santafe.edu  [5/'95]
   <A HREF="ftp:ftp.santafe.edu">FTP</A> in the directory pub/terry/phd.
   The entire dissertation is in the file phd.ps.gz. 5MB when uncompressed.
   Hardcopy of the dissertation by requesting SFI TR 95-05-048 from
   email: mat@santafe.edu .


%A M. H. Kalos
%T The NYU Ultracomputer
%I New York University, Courant Inst. of Math. Sci., Divn of Computer Science
%R Ultracomputer Note # 48
%M APR
%D 1983
%O 1983 Maths and Comp Topic l Meeting of American Nuclear Society
%K ultra, ultracomputer, NYU, MIMD, parallel
%X MIMD parallel machine
   thousands of independently programmable fast processing elements
   large shared memory
   switching network
   geometry of an omega network
   bandwith proportional to number of processors
   (LA has)

%A A. Gottlieb
%A B. D. Lubachevsky
%A L. Rudolph
%T Basic techniques for the efficient coordination of
   vary large numbers of cooperating sequential processors
%I New York University, Courant Inst. of Math. Sci., Divn of Computer Science
%R Ultracomputer Note # 16
%M APR
%D 1983
%K ultra, ultracomputer, NYU, MIMD, parallel, computer, machine,
   replace, add,  replace-add,  synchronization,  omega network
%O TOPLAS V5 N2 Apr 1983 P164-189
%X implement several basic operating system primitives using a
   replace-add operation, supersedes test and set

%A G. M. Landau
%A U. Vishkin
%A R. Nussinov
%T An efficient string matching algorithm with
   k differences for nucleotide and amino acid sequences
%R TR 168
%I Dept Computer Science, Courant Institute of Mathematical Sciences,
   New York University.
%M JUL
%D 1985
%O Nucleic Acids Research V14 N1 Jan 1986 P 31-46
%K TR 168, TR168, NYU, DNA, edit distance, similarity, string, mismatch,
   delete, deletion, insert, insertion, amino acid, base, ACGT, nucleotide,
   codon, protein, kDifferences
%X strings of lengthn m and n
   most algorithms time O(m*n)
   k differences allowed
   this algorithm time O(k*k*n)

%A G. M. Landau
%A U. Vishkin
%T Efficient string matching with k differences
%R TR 186
%I Dept Comp. Sci., Courant Inst. of Math. Sciences, New York U.
%M OCT
%D 1985
%K TR 186, TR186, NYU, DNA, nucleotide, base, codon, edit distance, string,
   similarity, delete, deletion, insert, insertion, mismatch, change,
   kDifferences
%X text of length n    a pattern of length m     k differences
   finds all occurences of pattern with at most k differences
   in O(m+k*k*n) for fixed alphabet
   O(m log m + k*k*n) for arbitrary alphabet
   space O(m)

%A T. Schlick
%A C. Peskin
%A S. Broyde
%A M. Overton
%T Development of a new computational approach to prediction of
   nucleic acid structure by potential energy methods: I. Deoxyribose
%R TR 264
%I Dept Computer Science, Courant Institute of Mathematical Sciences,
   New York University
%M DEC
%D 1986
%K NYU, DNA, base, nucleic acid, ACGT,  structure, shape

%A T. Schlick
%A M. Overton
%T A powerful truncated Newton method for potential energy minimization
%R TR 265
%M DEC
%D 1986
%I Dept Computer Science, Courant Institute of Mathematical Sciences,
   New York University
%K NYU, newton, minimum, approximation,
   bond length, angle, torsion

%A T. Schlick
%T A modular strategy for generating starting conformations and data structures
   of polynucleotide helices for potential energy calculations
%R 348
%I Dept Computer Science, Courant Institute of Mathematical Sciences,
   New York University.
%M FEB
%D 1988
%K DNA, tertiary, structure

%A P. Caianiello
%T Inductive inference and encoding
%R 372
%P 11
%I Dept Computer Science, Courant Institute of Mathematical Sciences,
   New York University.
%M MAY
%D 1988
%K inductive inference, II, MML, MDL, grammar, learning
%X about learning grammars.
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)


%A J. J. Oliver
%A D. Hand
%T Fanned decision trees
%I Statistics Dept., Open University
%R 5-94
%M JUN
%D 1994
%K TR5, TR 5, Monash, jono, DTree, tree, c1994, c199x, c19xx,
   minimum message length encoding, MML, description, MDL,
   inductive inference, II
%X [<A HREF="http://www.cs.monash.edu.au/">CSci Monash home</A>]['94],
   [<A HREF="http://www.cs.monash.edu.au/~jono">Jono home</A>]['94].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. J. Oliver
%A D. Hand
%T Introduction to minimum encoding inference
%I Statistics Dept., Open University
%R 4-94
%M SEP
%D 1994
%K TR4, TR 4, TR205 205, OpenU, Monash, jono, minimum message length, MML,
   description, MDL, Rissanen, compared, compare, comparison, Bayesian,
   inductive inference, II, c1994, c199x, c19xx
%O TR 95/205 Computer Science, Monash University
%X "... examines the minimum encoding approaches to inference, Minimum Message
   Length (MML) and Minimum Description Length (MDL). ... written with the
   objective of providing an introduction to this area for statisticians. We
   describe coding techniques for data, and examine how these techniques can be
   applied to perform inference and model selection."
   -- Cached@[<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.7292">c'teseer</A>]['14].
   [Also search for: MML 1994 TR206] and [also search for: MML 1995 TR207].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)

%A J. J. Oliver
%A D. J. Hand
%T Mixture modelling using MML
%I Statistics Dept., Open University
%R TR3-93
%D 1993 ?
%K TR3 TR 3, minimum message length, MML, description, MDL, classification,
   model, multivariate, stats, statistics, inductive inference, II
%X <A HREF="http://www.cs.monash.edu.au/">CSci Monash home</A>,
   <A HREF="http://www.cs.monash.edu.au/~jono">Jono home</A> ('94).
   [Also search for: MML mixture model].
   (Also see [<A HREF="http://www.allisons.org/ll/MML/">MML</A>].)


%A D. Scott
%T Outline of a mathematical theory of computation
%R PRG-2
%I Programming Research Group, Oxford University
%M Nov
%D 1970
%K PRG, PRG2, DS, denotational semantics, lattice theory, c1970, c197x, c19xx
%X (Also see [<A HREF="http://www.allisons.org/ll/Semantics/">den.sem.</A>].)

%A D. Scott
%A C. Strachey
%T Towards a mathematical semantics for computer languages
%R PRG-6
%D ?
%I Programming Research Group, Oxford University
%K DS, denotational semantics,  PRG, PRG6, c1971, c197x, c19xx
%X ? '70 or '71 ?
   (Also see [<A HREF="http://www.allisons.org/ll/Semantics/">den.sem.</A>].)

%A D. Scott
%T Continuous lattices
%R PRG-7
%I Programming Research Group, Oxford University
%M Aug
%D 1971
%K PRG, PRG7,  CPO, DS, denotational semantics, lattice, c1971, c197x, c19xx
%O (LA has)

%A C. P. Wadsworth
%T Semantics and pragmatics of the lambda calculus
%R PhD thesis
%I Programming Research Group, Oxford University
%M Sep
%D 1971
%K PRG, functional programming, FP, DS, denotational semantics, lattice,
   PhD thesis, c1971, c197x, c19xx
%O (have bits)

%A C. Strachey
%A C. P. Wadsworth
%T Continuations: a mathematical semantics for handling full jumps
%R PRG-11
%I Programming Research Group, Oxford University
%M Jan
%D 1974
%K PRG,  DS, denotational semantics, jump, sequencer, goto, valof, resultis,
   return, cont, kont, control, c1974, c197x, c19xx
%O (LA has)

%A P. Mosses
%T The mathematical semantics of Algol 60
%R PRG-12
%I Programming Research Group, Oxford University
%M Jan
%D 1974
%K PRG,  DS, denotational, programming language definition, algol 60, A60,
   algol60, c1974, c197x, c19xx
%X (Also see [<A HREF="http://www.allisons.org/ll/ProgLang/Algol60/">Algol60</A>] page.)

%A R. Milne
%T The formal semantics of computer languages and their implementation
%R PRG-13
%I Programming Research Group, Oxford University
%D 1974
%K PRG, DS, denotation, denotational semantics, theory,
   standard semantics,  store,  stack, c1974, c197x, c19xx
%X Milne's PhD thesis

%A R. D. Tennent
%T A denotational semantics of the programming language Pascal
%M Apr
%D 1978
%I Programming Research Group, Oxford University
%K PRG, Pascal, DS, denotational semantics, definition,
   context sensitive syntax, c1978, c197x, c19xx
%X (LA has)

%A J. Hughes
%T Graph reduction with super combinators
%R PRG-28
%I Programming Research Group, Oxford University
%M Jun
%D 1982
%K PRG,  FP, functional programming,  combinator,  supercombinator
%X (LA has)

%A S. B. Jones
%T Abstract machine support for purely functional operating systems
%I Programming Research Group, Oxford University
%R PRG-34
%M Aug
%D 1983
%O (LA has) also a Stirling TR-15 Sep 1984
%K PRG, functional programming, FP, OS, SECD, SECDM, SECD-M

%A R. Bird
%T A calculus of functions for program derivation
%I Programming Research Group, Oxford University
%R PRG-64
%M Dec
%D 1987
%K PRG, functional, applicative, programming, program transformation,
   FP, leery, greedy, c1987, c198x, c19xx

%A K. Paliwoda
%A J. W. Sanders
%T The sliding-window protocol
%I Programming Research Group, Oxford University
%R PRG-66
%M Mar
%D 1988
%K PRG, CSP, sliding window, communications, buffer,
   specification, Occam, verification
%X formal spec of sliding window in CSP
   a. stop and wait   protocol defined
   b. alternating bit protocol  defined and proved

%A J. W. Sanders
%T An introduction to CSP
%I Programming Research Group, Oxford University
%R PRG-65
%M Mar
%D 1988
%K CSP, CCS, process, parallel, concurrent, calculus communicating systems,
   PRG, c1988, c198x, c19xx

%A M. P. Jones
%T Computing with lattices: an application of type classes
%I Programming Research Group, Oxford University
%R PRG-TR-11-90
%P 34
%M JUN
%D 1990
%O J. Functional Programming, 2(4), pp.475-503, Oct '92.
%K PRG, TR, Gofer, functional programming language, FP, lazy, type, types,
   jrnl, JFP, class, lattice, c1990, c199x, c19xx
%X "...a simple framework for performing calculations with the elements of
   (finite) lattices. ... [uses] type classes to enable the use of overloaded
   function symbols within a strongly typed language. Prev. applications of
   type classes have been in areas that are of most interest to language
   implementors. This paper suggests that type classes might also be useful as
   a general tool in the development of clear and modular programs."
   [cse ogi edu / ~mpj -- 0regon He@lth & Sci Uni][10/'04]

%A J. Gibbons
%T Algebras for Tree Algorithms
%I Programming Research Group, Oxford University
%R PRG-94
%D 1991
%K D. Phil., DPhil, thesis, PRG 94, PRG94, algenra, trees, algorithm,
   accumulation, upward, downward, FP, functional programming,
   hip trees, catamorphisms, catamorphism, c1991, c199x, c19xx
%X ...present three different tree algebras: two kinds of binary tree & a kind
   of general tree. One of the binary tree algebras, called `hip trees', is
   new. Instead of being built with a single ternary operator, hip trees are
   built with two binary operators which respectively add left & right
   children to trees which do not already have them... Each of these algebras
   brings with it with a class of `structure-respecting' functions called
   catamorphisms; the definition of a catamorphism... upwards' & `downwards'
   accumulations...
   (From the H@skell m@il list 2/'04. Available as Technical Monograph PRG-94.
   [<A HREF="http://web.comlab.ox.ac.uk/oucl/work/jeremy.gibbons/publications/index.html#algebras">.ox.ac.uk</A>][2/'04].)

%A M. P. Jones
%T Towards a theory of qualified types
%I Programming Research Group, Oxford University
%R PRG-TR-6-91
%M APR
%D 1991
%K PRG, TR, Gofer, functional programming language, FP, lazy, data type, types,
   class

%A M. P. Jones
%T Type inference for qualified types
%I Programming Research Group, Oxford University
%R PRG-TR-10-91
%M JUN
%D 1991
%K PRG, TR, Gofer, functional programming language, FP, lazy, type, types,
   class, zz0296

%A M. P. Jones
%T Qualified Types: Theory and Practice
%I Programming Research Group, Oxford University
%P 176
%M JUL
%D 1992
%K PRG, Gofer, PhD thesis, functional programming, FP, c1992, c199x, c19xx,
   class, overloading, type, types, zz0296, computing, CSci
%X c.f. Haskell.

%A W. Penny
%A S. Roberts
%T Variational Bayes for generalised autoregressive models
%R PARG-00-12
%I Dept. Eng. Sci., U. Oxford
%M OCT
%D 2000
%K TR 12, TR12, auto regressive, regression, model, c2000, c200x, c20xx,
   VB, VBI, inference, stats, AR, zz0205
%X "... a Variational Bayes (VB) learning algorithm for Generalised
   Autoregressive (GAR) models. The noise is modelled as a Mixture of Gaussians
   rather than the usual single Gaussian. This allows different data points to
   be associated with different noise levels and effectively provides a robust
   estimation of AR coefficients. The VB framework is used to prevent
   overfitting and provides model order selection criteria both for AR order
   and noise model order. ..."
   ([<A HREF="/~lloyd/tildeMisc/Local/2000penny.ps">local</A>].)
   (Also see [<A HREF="http://www.allisons.org/ll/Images/People/Bayes/">T.Bayes</A>].)
   [Also search for: VBI variational stats].


%A R. Bagnara
%A P. M. Hill
%A E. Zaffanella
%T Applications of polyhedral computations to the analysis and verification of
   hardware and software systems.
%R Quaderno 458
%I Dipartimento di Matematica, Universita di Parma (.it)
%D 2007
%K TR, TR458, Parma polyhedra library, polyhedron, constraint programming,
   c2007, c200x, c20xx, finite powerset, powersets, convex, NNC, PPL, uniParma
%X "Convex polyhedra are the basis for several abstractions used in static
   analysis & computer-aided verification of complex & sometimes mission
   critical systems. ... identification of an appropriate complexity-precision
   trade-off is a particularly acute problem, so that the availability of a wide
   spectrum of alternative solutions is mandatory. We survey the range of
   applications of polyhedral computations in this area; give an overview of the
   different classes of polyhedra that may be adopted; outline the main
   polyhedral operations required by automatic analyzers & verifiers; & look at
   some possible combinations of polyhedra with other numerical abstractions
   that have the potential to improve the precision of the analysis. Areas
   where further theoretical investigations can result in important
   contributions are highlighted."
   [<A HREF="http://www.cs.unipr.it/ppl/Documentation/BagnaraHZ07TR.pdf">pdf@unipr</A>]['07]
   Also arXiv:cs.CG/0701122, [<A HREF="http://arxiv.org/">arxiv</A>]['07]
   [<A HREF="http://www.cs.unipr.it/ppl/">ppl@unipr</A>]['07]


%A S. Gorn
%T Self-annihilating sentences, Saul Gorn's compendium of rarely used cliches
%R MS-CIS-85-03
%M Jan
%D 1985
%I Computer and Information Science Department, Uni. of Pennsylvania
%K self annihilating cliche, cliches, phrase, saying, tautology, contradiction,
   c1985, c198x, c19xx
%X This book fills a much needed gap.

%A D. Miller
%T Pi-calculus as a theory in linear logic: preliminary results
%R MS-CIS-92-48
%M JUN
%D 1992
%I Computer and Information Science Department,
   University of Philadelphia
%K pi calculus, piCalculus, c1992, c199x, c19xx, CCS, CSP, agent,
   process, parallel, concurrent, TR-92-48, TR 92 48, TR-48
%X (Also see [<A HREF="http://www.allisons.org/ll/FP/LambdaCCS/">CCS</A>].)


%A R. Duke
%A G. Rose
%T A complete Z specification of an interactive program editor
%R 71
%I Dept. of Computer Science, University of Queensland
%M Jun
%D 1986

%A J. Staples
%A P. J. Robinson
%T Efficient unification of quantified terms
%R 73
%I Dept. of Computer Science, University of Queensland
%M Oct
%D 1986
%K unify, unification, quantifier, logic

%A J. Staples
%A P. J. Robinson
%T Structure sharing for quantified terms
%R 74
%I Dept. of Computer Science, University of Queensland
%M Dec
%D 1986
%K quantifier, logic, unify

%A J. Staples
%T Delaying unification for lambda calculii
%R 75
%I Dept. of Computer Science, University of Queensland
%M Dec
%D 1986
%K FP, unify, lambda calculus

%A P. A. Bailes
%A E. J. Salzman
%T Software development by functional language prototyping
%R 79
%I Dept. of Computer Science, University of Queensland
%M Apr
%D 1987
%K FP, prototype

%A I. S. Fogg
%T Distributed scheduling algorithms: a survey
%R 81
%I Dept. of Computer Science, University of Queensland
%M Jun
%D 1987
%K scheduler, algorithm
%X 1. pairing
   2. bidding
   3. vector
   4. SLA stochastic learning automaton
   5. BDT Bayesian decision theory

%A P. A. Bailes
%T A tour through the G type mechanism
%R 87
%I Dept. of Computer Science, University of Queensland
%M Oct
%D 1987
%K type, datatype, polymorphic, dynamic

%A P. Pritchard
%T A sublinear additive sieve for finding prime numbers
%R 10
%D 1979
%M Dec
%I Dept. of Computer Science, University of Queensland
%K TR10, c1979, c197x, c19xx, number, primes
%X see his Comm. ACM paper

%A M. E. Orlowska
%A K. G. Jeffery
%T A functional method of data processing based on relational algebra
%I Dept. Computer Science, University of Queensland
%R 194
%M DEC
%D 1990
%K functional, FP, data base, database, DB, relational algebra


%A S. Abramsky
%T On semantic foundations for applicative multiprogramming
%R TR-338
%I Dept. Computer Science, Queen Mary College
%K FP, functional, parallel
%M Apr
%D 1983
%X (LA has)

%A S. Abramsky
%T SECD-M: a virtual machine for applicative multiprogramming
%R TR-339
%I Dept. Computer Science, Queen Mary College
%K FP, functional, parallel
%M Nov
%D 1982
%X (LA has)

%A C. T. Burton
%T A methodology for transforming functional programs (draft version)
%D 1987?
%I Dept. Computer Science, Queen Mary College
%K FP, functional, applicative, program, transformation
%X simulation proposed unify transformation
   examples minimax and alpha beta algorithms and O(n) search.

%A S. Reeves
%T Propositions as types - tutorial notes
%R TR-397
%M Nov
%D 1986
%I Dept. Computer Science, Queen Mary College
%K type, datatype, intuitionistic
%X Per Martin-Lof's intuitionistic type theory (ITT)
   type datatype.

%A J. Hill
%A R. Bornat
%T A data-parallel lazy language in which speculation is free
%I Dept. Computer Science, Queen Mary College
%R TR-573
%M NOV
%D 1991
%K functional programming language, FP, data parallel, SIMD, POD,
   speculative evaluation
%X POD == Parallel Object with arbitrary Dimension
   POD-1 == vector   < (index1, data1), ... >,
   POD-2 == matrix.

%A A. I. Comport
%T Robust Real-Time 3D Tracking of Rigid and Articulated Objects for
   Augmented Reality and Robotics.
%I Universite de Rennes 1, Mention informatique, .Fr
%M SEP
%D 2005
%K PhD thesis, Andrew Comport, object, c2005, c200x, c20xx, 3D motion, virtual,
   models, servoing, image processing, pose estimation
%X [<A HREF="http://www.irisa.fr/lagadic/pdf/2005_these_comport.pdf">pdf</A>]['05]
   Was an u/g @ Mon@sh, B.Sc(cs) c1997, B.Eng. c2000+/-.


%A W. Schreiner
%T ADAM and EVE an abstract dataflow machine and its programming language
%R 90-42.0
%I Research Institute for Symbolic Computation
   Johannes Kepler University, A4040 Linz, Austria
%M OCT
%D 1990
%K TR, RISC-Linz, adam, dataflow, machine,
   eve, functional programming language, FP
%X an Austrian diploma thesis.

%A H. W. Loidl
%T Circular programs on compound data structures
%R 92-06
%I Research Institute for Symbolic Computation,
   Johannes Kepler University, A4040 Linz, Austria
%M JAN
%D 1992
%K TR, FP, lazy, functional programming, circular program, recursion,
   data structure, list, lists, by need, non-strict,
   Fibonacci, Hamming, primes sieve, partition, survey, RISC-Linz, Linz
%X (hwloidl of risc.uni-linz.ac.at, '92.)
   [Also search for: circular program FP].

%A R. Newman-Wolfe
%T Observations on multi-peg towers of Hanoi
%R TR 187
%M Jul
%D 1986
%I Dept. of Computer Science, University of Rochester, NY.
%K tower, towers hanoi, peg, pegs, multipeg, multi,
   recursion, recursive program

%A D. Baldwin
%T Why we can't program multiprocessors
   the way we're trying to do it now
%I Dept. of Computer Science, University of Rochester, NY.
%R TR 224
%M Aug
%D 1987
%K multi, data parallel

%A R. Socher
%T An optimized transformation into conjunctive (or disjunctive) normal form
%R SR-87-13
%P 14
%M Dec
%D 1987
%I Fachbereich Informatik,
   Universitat Kaiserslautern
%K propositional logic, CNF, DNF, prime implicant, clause form, clausal
%X avoids generation of redundant clauses.
   clauses generated are prime implicants of the given formula.
   If "usual" algorithm produces contradictory clauses, this one
   generates the empty clause.

%A M. Tanik
%T A comparative study of synchronization models exploitable for
   real-time software development environment design and testing
%I Department of Computer Science and Engineering,
   Southern Methodist University, Dallas, Texas
%M Jan
%D 1987
%R 87-CSE-1
%K synchronise, parallel, process, task
%X 1. task system model, deadlock, routed network model, petri nets,
      semaphores, general resource systems, claim limited systems,
   2. Reachability systems
   3. dining philosophers


%A K. Birman
%A T. Joseph
%T Exploiting Virtual Synchrony in Distributed Systems
%P 123-138
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5

%A A. Birrell
%A J. Guttag
%A J. Horning
%A R. Levin
%T Synchronization Primitives for a Multiprocessor: A Formal Specification
%P 94-102
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5

%A A. Birrell
%A M. Jones
%A E. Wobber
%T A Simple and Efficient Implementation of a Small Database
%P 149-154
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5

%A A. Chang
%A M. Mergen
%T 801 Storage: Architecture and Programming
%J ACM TOCS
%D to appear
%O Originally presented at the
   Eleventh ACM Symposium on Operating Systems Principles,
   Austin, TX,
   8-11 November
   1987

%A R. Finlayson
%A D. Cheriton
%T Log Files: An Extended File Service Exploiting Write-Once Storage
%P 139-148
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5

%A R. Hagmann
%T Reimplementing the Cedar File System Using Logging and Group Commit
%P 155-162
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5

%A R. Haskin
%A Y. Malachi
%A W. Sawdon
%A G. Chan
%T Recovery Management in QuickSilver
%J ACM TOCS
%D to appear
%O Originally presented at the
   Eleventh ACM Symposium on Operating Systems Principles,
   Austin, TX,
   8-11 November 1987

%A J. Howard
%A M. Kazar
%A S. Menees
%A D. Nichols
%A M. Satyanarayanan
%A R. Sidebotham
%A M. West
%T Scale and Performance in a Distributed File System
%J ACM TOCS
%D to appear
%O Originally presented at the
   Eleventh ACM Symposium on Operating Systems Principles,
   Austin, TX,
   8-11 November 1987

%A D. Jefferson
%A B. Beckman
%A F. Wieland
%A L. Blume
%A M. DiLoreto
%A P. Hontalas
%A P. Laroche
%A K. Sturdevant
%A J. Tupman
%A V. Warren
%A J. Wedel
%A H. Younger
%A S. Bellenot
%T Time Warp Operating System
%P 77-93
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5

%A E. Jul
%A H. Levy
%A N. Hutchinson
%A A. Black
%T Fine-Grained Mobility in the Emerald System
%J ACM TOCS
%D to appear
%O Originally presented at the
   Eleventh ACM Symposium on Operating Systems Principles,
   Austin, TX,
   8-11 November 1987

%A B. Liskov
%A D. Curtis
%A P. Johnson
%A R. Scheifler
%T Implementation of Argus
%P 111-122
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5

%A J. Mogul
%A R. Rashid
%A M. Accetta
%T The Packet Filter: An Efficient Mechanism for User-level Network Code
%P 39-51
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5

%A M. Nelson
%A B. Welch
%A J. Ousterhout
%T Caching in the Sprite network file system
%J ACM TOCS
%D 1988
%O Originally presented at the 11th ACM Symp. on Operating Systems Principles,
   Austin, TX, 8-11 Nov. 1987
%K jrnl, TOCS, c1988, c198x, c19xx, Sprite, file system
%X "The Sprite network OS uses large main-memory disk block caches to achieve
   high performance in its file system. It provides non-write-through file
   caching on both client and server machines. A simple cache consistency
   mechanism permits files to be shared by multiple clients without danger of
   stale data. In order to allow the file cache to occupy as much memory as
   possible, the file system of each machine negotiates with the virtual memory
   system over physical memory usage and changes the size of the file cache
   dynamically. Benchmark programs indicate that client caches allow diskless
   Sprite workstations to perform within O-12% of workstations with disks. In
   addition, client caching reduces server loading by 50% & n/w traffic by 90%"
   [<A HREF="http://doi.acm.org/10.1145/35037.42183">doi:10.1145/35037.42183</A>]['09].

%A D. Nichols
%T Using Idle Workstations in a Shared Computing Environment
%P 5-12
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5

%A M. Schwartz
%A J. Zahorjan
%A D. Notkin
%T A Name Service for Evolving Heterogeneous Systems
%P 52-62
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5

%A D. Terry
%A D. Swinehart
%T Managing Stored Voice in the Etherphone System
%J ACM TOCS
%D to appear
%O Originally presented at the
   Eleventh ACM Symposium on Operating Systems Principles,
   Austin, TX,
   8-11 November 1987

%A G. Varghese
%A T. Lauck
%T Hashed and Hierarchical Timing Wheels: Data Structures for the Efficient
   Implementation of a Timer Facility
%P 25-38
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5.

%A M. Young
%A A. Tevanian
%A R. Rashid
%A D. Golub
%A J. Eppinger
%A J. Chew
%A W. Bolosky
%A D. Black
%A R. Baron
%T The Duality of Memory and Communication in the Implementation of a
   Multiprocessor Operating System
%P 63-76
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5

%A E. Zayas
%T Attaching the Process Migration Bottleneck
%P 13-24
%J Proceedings of the Eleventh ACM Symposium on Operating Systems Principles
%K sosp
%C Austin, TX
%M 8-11 November
%D 1987
%O In ACM Operating Systems Review 21:5


%A M. H. Brown
%A R. A. Shillner
%T DeckScape: An Experimental Web Browser
%R #135a
%I SRC/DEC
%M MAR
%D 1995
%P 13
%K SRC, DEC, TR135, world wide web browser, client, computing
%X Video  #135b, March 1, 1995, 07:00 minutes
   ... web browser based on a "deck" metaphor. A deck consists of a
   collection of Web pages, and multiple decks can exist on the screen at
   once. As the user traverses links, new pages appear on top of the
   current deck.  Retrievals are done using a background thread, so all
   visible pages in any deck are active at all times. Users can move and
   copy pages between decks, and decks can be used as a general-purpose
   way to organize material, such as hotlists, query results, and
   breadth-first expansions.
   -- [<A HREF="http://www.research.digital.com/SRC/publications/src-rr.html">wwweb</A>],
   Anonymous ftp: [<A HREF="ftp://gatekeeper.dec.com">FTP</A>] (16.1.0.2).
   /pub/DEC/SRC/research-reports/ .

%A Z. Manna
%A R. Waldinger
%T Deductive synthesis of the unification algorithm
%R Technical Note 246
%I SRI International
%M Jul
%D 1981
%K unify, unification, program synthesis, derivation

%A R. C. Moore
%T Automatic deduction for commonsense reasoning: an overview
%R Technical Note 239
%I SRI International
%M Apr
%D 1981
%O in The Handbook of Artificial Intelligence, A. Barr, E. A. Feigenbaum eds.
   (William Kaufman) 1982
%K AI, expert system, reasoning

%A R. C. Moore
%T The role of logic in knowledge representation and commonsense reasoning
%R Technical Note 264
%I SRI International
%M Jun
%D 1982
%O Proceedings of the National Conference on Artificial Intelligence
%K AI, logic, reasoning, expert system


%A R. Morrison
%A C. J. Barter
%A A. L. Brown
%A R. Carrick
%A R. Connor
%A A. Dearle
%A A. J. Hurst
%A M. J. Livesey
%T Polymorphic persistent processes
%I Dept. Comp. Sci.,  U. of St. Andrews
%R 39
%M JUN
%D 1987
%K TR 39, TR39, c1987, c198x, c19xx, persistence, process, object, store,
   concurrent, concurrency, Napier, StAndrews
%X see ajh.


%A R. C. Pasco
%T Source Coding Algorithms for Fast Data Compression
%I Stanford University
%M MAY
%D 1976
%K PhD Dissertation, Pasco, Pascoe, scaffdc, c1976, c197x, c19xx,
   arithmetic encoding, coding, arithmeticCoding, range, code, data compression
%X (Credited with early *practical* arithmetic coding.)
   Thesis at [<A HREF="http://www.richpasco.org/">richpasco.org</A>]['15],
   Richard Clark Pasco.
   [Also search for: arithmeticCoding] and [also search for: Rissanen c1976].

%A J. McCarthy
%T Colouring maps and the Kowalski doctrine
%R STAN-CS-82-903
%O AIM-346
%I Dept Computer Science, Stanford University
%M APR
%D 1982
%K graph, map colouring, prolog, logic programming, LP

%A C. Goad
%T Computational uses of the manipulation of formal proofs
%R CS-80-819
%M AUG
%D 1980
%I Department of Computer Science, Stanford University
%K proof
%X PhD thesis
   1 Introduction
   2 Normalization and puning of natural deduction proofs
   3 efficient implementation of operations on proofs
   4 specialization of a bin packing algorithm
   5 other applications
   A1 comparison to extraction methods from proof theory
   A2 content and form in proof manipulation - an example.

%A B. G. Buchanan
%A E. A. Feigenbaum
%T Dendral and meta-dendral: their applications dimension
%R CS-78-649
%I Stanford University
%M FEB
%D 1978
%K dendral, chemist, artificial intelligence, heuristic, c1978, c197x, c19xx

%A M. Plass
%T Optimal pagination techniques for automatic typesetting systems
%I Dept. of Comp. Sci., Stanford U.
%R STAN-CS-81-870
%D 1981
%K TR, TR870, c1981, c198x, c19xx, text, document, page, format, formatting,
   layout, setting, markup
%X also see  K n u t h  and  P l a s s, c1981.

%A D. S. Rosenblum
%T Design and verification of distributed tasking supervisors for
   concurrent programming languages
%R CSL-TR-88-357
%M MAR
%D 1988
%K thesis, Ada

%A K. Gopinath
%A J. L. Hennessy
%T Copy elimination in functional languages
%R CSL-TR-88-370
%P 12
%I Stanford University
%M NOV
%D 1988
%K optimise, functional, applicative, programming, FP, abstract interpretation,
   share, sharing
%X applied to some sorting algorithms
   introduce destructive array operations
   gives timings v. Pascal.

%A P. Schnorf
%A M. Ganapathi
%A J. Hennessy
%T Design and implementation of an optimizing compiler for a single assignment
   language
%R CSL-TR-90-452
%I Stanford University
%M NOV
%D 1990
%K SISAL, compiler, programming language implementation
%X some at least produces C code.

%A J. P. Singh
%A J. L. Hennessey
%T Automatic and explicit parallelisation of an n-body simulation
%R CSL-TR-91-462
%I Stanford University
%M MAR
%D 1991
%K parallel concurrent, n body, n-body

%A J. Mitchell
%A S. Meldal
%A N. Madhav
%T An extension of standard ML modules with subtyping and inheritance
%R CSL-TR-91-472
%I Stanford University
%M MAY
%D 1991
%K type, types, check, checking, subtype, sub-type, inheritance, module,
   SML, functional programming, FP, OO, OOP, OOPS

%E O. Danvy
%E C. Talcott
%T Proceddings of the ACM Sigplan workshop on continuations CW92
%R STAN-CS-92-1426
%I Dept. Computer Science, Stanford University
%M JUN
%D 1992
%K continuation, Sigplan, CW92, 1426

%A Andrew Barron
%T Logically smooth density estimation
%M AUG
%D 1985
%P 98
%I Stanford Dept. of E. E.
%K PhD thesis, inductive inference, II, minimum message length encoding, MML,
   Bayes, Bayesian, prior, probability distribution, estimate, model,
   description, linear, regression, MDL, c1985, c198x, c19xx
%X Supervisor: Tom Cover (A.B. acknowledges the influence of this father,
   Roger Barron, on his approach.  His father is a prominent worker in
   regression and polynomial learning networks. Don't confuse them...)
   Overview:
      1. Gives a principle for statistical inference based on the shortest
      complete description of random samples.  The complete description of the
      data requires two stages: first a candidate distribution P is described
      using the shortest length computer program P, second the optimal Shannon
      code for data based on the distribution P.
      2. Logically smooth estimators nearly achieve the minimum two-stage
      description length. Many standard estimators give numerical smoothing,
      but not logical smoothing, hence the thesis title.
      Cover, Rissanen and Sorkin have presented similar estimators
      (Wallace omitted).
      3. The convergence properties of these estimators are analyzed for
      parametric and non-parametric cases.
      4. The estimators here may be regarded as using a Bayes rule. However
      the motivation is the minimization of description length and not any
      Bayesian inclinations.
   Chapter 2: Coin tossing example      [try also keyword `multistate' in bib']
      This is a straightforward exposition of the MML estimator
      for the bias in a coin. Includes derivation of Fisher information term
      as the desired interval in parameter space. Also gives one-part
      description lengths and compares with the optimal two-part one.
   Chapter 3: Data Compression
      A review of Shannon coding and coding methods. The main result
      is that two-part description lengths are shown to have redundacy
      of o(n) for various computable distributions and non-computable
      distributions that can be approximated by computable ones.
      I guess the bottom line of these results is that asymptotically
      two-part messages do as good as any one-part messages...
   Chapter 4: Inference             [keywords `inductive inference II' in bib']
      The efficacy of two-part description lengths in inference is shown in
      this chapter. Description length estimates are shown to be accurate
      estimates of the true distribution in the computable, parametric and
      non-parametric cases.
      The derivation of the two-part description length expression:
         -log p(D|theta) + 1/2 log |Fisher(theta)| - log p(theta)
      is achieved by using Laplace's method to approximate the
      evidence, p(D) = sum p(D|theta) d theta, and then observing
      that this has a message length interpretation if we use the Fisher
      information, rather than just the plain second derviatives of p(D|theta).
   Further work Suggested:
      1. determine rates of convergence (this was done in Thomas and Cover('91)
      2. investigate logically smooth regression (re: Barron's work on
         neural networks (ANN) in late 80s)
      3. search for more feasible estimators achieving nearly minimal
         description length (re: Wallace's Factor Analysis and von Mises stuff).
   [via Roh@n B@xter].

%A M. A. Musen
%T Ontology oriented design and programming
%I Stanford Medical Informatics, Stanford U.
%R 2000-833
%D 2000
%K TR, TR833, c2000, c200x, c20xx, zzOSP, zOSP04, ontological, concepts, AI,
   KADS, formal, formalism, abstraction, quote, quotation, quotable, rule,
   rules, based
%X "...workers in AI also have had a history of getting themselves into
   trouble by not recognizing the central importance of <I>software</I> to
   the AI enterprise itself."
   "The developers of the first knowledge-based system ... faltered as they
   attempted to scale up their work."
   "Although an official claim was often made that rules such as those in
   MYCIN are `independent and modular' it became clear that developers
   needed to view prod'n rules as elements of a very high-level prog' lang'."
   "If a diagnostic task is to be solved using heuristic classification [say]
   different domain knowledge is required than if that task is to be solved
   using Bayesian reasoning."
   "[Production] rules ... may encode considerable control-flow information"
   [<A HREF="http://www-smi.stanford.edu/pubs/SMI_Reports/SMI-2000-0833.pdf">tr.pdf@stanford.edu.au</A>][8/'04] via L@riss@ So1d@tov@.

%A P. Henderson
%T Purely functional operating systems
%B Functional Programming and its Applications
%I Cambridge University Press
%D 1982
%P 177-189
%K FP, operating system, OS

%A R. G. Clark
%T PASCAL-ST: the implementation of a Pascal system
%I U. of Stirling, Dept of Computer Science
%R TR 1
%M July
%D 1980
%K Pascal

%A L. B. Wilson
%A J. S. Clowes
%A I. Mitrani
%T The enumeration of level number sequences for binary trees
%I U. of Stirling, Dept of Computer Science
%R TR 2
%M July
%D 1980
%K binary tree

%A T. Rus
%A C. M. I. Rattray
%T Abstract data type implementation for ADA-like languages
%I U. of Stirling, Dept of Computer Science
%R TR 3
%K Ada, datatype type types
%M Sep
%D 1980

%A T. Rus
%A C. M. I. Rattray
%T The ADA-Spirit: and algebraic view of ADA-like languages
%I U. of Stirling, Dept of Computer Science
%R TR 4
%M Sep
%D 1980
%K Ada

%A L. B. Wilson
%T A survey of the stable marriage assignment problem
%I U. of Stirling, Dept of Computer Science
%R TR 5
%M Aug
%D 1980
%K assignment problem,  combinatorics,  stable marriage assignment,
   room mates, match, matching
%X reviews progress in stable marriage assignment
      1. dynamic arrival and departure,
      2. equality in choice lists,
      3. the two sets are not disjoint.
   (Also see [<A HREF="http://www.allisons.org/ll/AlgDS/Graph/Stable/">stable-marriage</A>].)

%A W. B. Samson
%T Indexing on secondary keys in the PRECI data base
%I U. of Stirling, Dept of Computer Science
%R TR 6
%K database
%D 1984

%A P. A. Collier
%T An introduction to PDP-11 Prolog through graduated examples
%I U. of Stirling, Dept of Computer Science
%R TR 7
%M Feb
%D 1982
%K logic programming, LP

%A D. Budgen
%T Combining MASCOT with Modula-2 to aid the engineering of real-time systems
%I U. of Stirling, Dept of Computer Science
%R TR 8
%M Aug
%D 1982

%A D. Budgen
%T An introduction to the Oggin machine
%I U. of Stirling, Dept of Computer Science
%R TR 9
%M Jan
%D 1983

%A C. M. I. Rattray
%T HAS - hierarchy construction: a tool for abstraction, specification and
   implementation
%I U. of Stirling, Dept of Computer Science
%R TR 10
%M Jan
%D 1985

%A C. M. I. Rattray
%T Abstract specification relative to categories or graphs:
   a concept of dimension in formal languages
%I U. of Stirling, Dept of Computer Science
%R TR 11

%A R. G. Clark
%T SATS: the Stirling ADA-like teaching system
%I U. of Stirling, Dept of Computer Science
%R TR 12
%M May
%D 1984
%K Ada

%A L. B. Wilson
%A R. G. Clark
%T An historical survey of the development of programming languages
%I U. of Stirling, Dept of Computer Science
%R TR 13
%M Sep
%D 1984

%A C. Minkowitz
%T A methodology for the prototyping of software design
%I U. of Stirling, Dept of Computer Science
%R TR 14
%M Jul
%D 1984

%A S. B. Jones
%T Abstract machine support for purely functional operating systems
%I U. of Stirling, Dept of Computer Science
%R TR 15
%M Sep
%D 1984
%O also same title, prg-34 Oxford University Aug 1983
%K programming, FP, OS, SECD, SECDM, SECD-M, PRG34

%A S. B. Jones
%T A range of operating systems written in a purely functional style
%I U. of Stirling, Dept of Computer Science
%R TR 16
%M Sep
%D 1984
%O PRG42, Oxford Univ. Comp. Lab.
%K functional programming, FP, OS, TR16, PRG42

%A V. M. Jones
%T A resource management and planning system,
   a practical application of semantic network databases
%I U. of Stirling, Dept of Computer Science
%R TR 17
%K data base,  database
%M Nov
%D 1984

%A C. Minkowitz
%T Specification to prototype -
   a comparison of two formal methods of software design
%I U. of Stirling, Dept of Computer Science
%R TR 18
%M Jan
%D 1985

%A C. M. I. Rattray
%A L. B. Wilson
%T Expert systems
%I U. of Stirling, Dept of Computer Science
%R TR 19
%M Jan
%D 1985

%A V. M. Jones
%A S. B. Jones
%A C. Minkowitz
%T A formal specification of an expert system shell
%I U. of Stirling, Dept of Computer Science
%R TR 20
%M Mar
%D 1985

%A R. G. Clark
%T ADA as a complement to Lispkit for the prototyping of software design
%I U. of Stirling, Dept of Computer Science
%R TR 21
%M Apr
%D 1985

%A W. B. Boland
%T DROSS: an adaption of the -ms macro option of nroff to use on the QME daisy
   wheel printer
%I U. of Stirling, Dept of Computer Science
%R TR 22
%M Jun
%D 1985

%A L. S. Smith
%T On the relationship between stimulus and information
%I U. of Stirling, Dept of Computer Science
%R TR 23
%M Jun
%D 1985

%A A. G. Hamilton
%T Program construction in Martin-Lof type theory
%I U. of Stirling, Dept of Computer Science
%R TR 24
%K data type,  types, datatype
%M Jun
%D 1985

%A D. McArthur
%T SPECTRE: a specification translation and retrieval expert
%I U. of Stirling, Dept of Computer Science
%R TR 25
%M Jul
%D 1985

%A H. Alexander
%T Formal specification and rapid prototyping techniques
   for human-computer interaction
%I U. of Stirling, Dept of Computer Science
%R TR 26
%M Aug
%D 1985

%A C. Minkowitz
%T A formal design of a decision analysis system
%I U. of Stirling, Dept of Computer Science
%R TR 27
%M Jan
%D 1986

%A J. C. McLachlan
%T A HOPE specification of the blackboard model
%I U. of Stirling, Dept of Computer Science
%R TR 28
%M Jan
%D 1986

%A D. McArthur
%T A system to aid the construction of intelligent software tools
%I U. of Stirling, Dept of Computer Science
%R TR 29
%M Jan
%D 1986

%A R. G. Clark
%T ADA programs from me-too specifications
%I U. of Stirling, Dept of Computer Science
%R TR 30

%A V. Jones
%A K. Davies
%T A taxonomy of application areas for expert systems in business
%I U. of Stirling, Dept of Computer Science
%R TR 31
%M Jun
%D 1986

%A H. A. Alexander
%T SPI: specifying and prototyping interaction
%I U. of Stirling, Dept of Computer Science
%R TR 32
%M Dec
%D 1986
%K SPI

%A M. Thomas
%T Implementing algebraically specified abstract data types in an
   imperative programming language
%I U. of Stirling, Dept of Computer Science
%R TR 33
%K data type,  datatype
%M Dec
%D 1986

%A S. P. Finn
%T Lazy evaluation in a cold climate
%I U. of Stirling, Dept of Computer Science
%R TR 34
%M Jan
%D 1987
%K functional programming, FP, lazy, need, normal order

%A H. Alexander
%T Formally-based tools and techniques for human-computer dialogues
%I U. of Stirling, Dept of Computer Science
%R TR 35
%M Jan
%D 1987

%A P. Henderson
%A S. B. Jones
%T Shells of functional operating systems
%I Computing Science Dept., University of Stirling
%R FPN-4
%M Jun
%D 1984
%O SERC Distributed Computer Systems (Ch 17),
   D. A. Duce (ed)  Peter Peregrinus Ltd.
%K shell, shells, command interpreter, language,
   functional programming, FP, applicative, OS, operating system

%A P. Henderson
%T Process Combinators
%I Computing Science Dept., University of Stirling
%R FPN-7
%M Aug
%D 1984
%K functional, applicative language, programming, concurrent, parallel, network
%X notation allows expression of networks of processes.
   combinators for sequential, iterative and parallel composition.
   sequential combinator generalises the Unix pipe.

%A P. Henderson
%T Communicating functional programs
%I Computing Science Dept., University of Stirling
%R FPN-8
%M Sep
%D 1984
%K applicative, functional programming, FP, concurrent, parallel, CSP, CCS
%X deterministic version of CSP used to describe protocols
   connecting modules of communicating functional programs.
   rules to transform this subset of CSP into recursive equations.


%A D. Carmel
%A S. Markovitch
%T Learning models of opponent's strategy in game playing
%R CIS #9305
%M JAN
%D 1993
%I Centre for Intelligent Systems, Technion - Israel Inst. Technology,
   Haifa 32000 Israel
%K AI, 9305 TR9305, c1993, c199x, c19xx, game, checkers, chequers, tic tac toe,
   tictactoe, opponent, play


%A E. Erdem
%T Theory and applications of Answer Set Programming
%I Dept. Comp. Sci., U.Texas
%D 2002
%K PhD thesis, ASP, AI, program ,c2002, c200x, c20xx, application
%X [<A HREF="http://www.cs.utexas.edu/users/UTCS/techreports/tr02-69.pdf">pdf@utexas</A>]['05], sup. V. L i f s c h i t z.

%A D. H. Redelmeier
%T Towards Practical Functional Programming
%R CSRG-158
%I Computer Systems Research Group, University of Toronto
%M May
%D 1984
%K functional, applicative programming, FP, lazy, need, name,
   abstract data type, types, datatypes, datatype,
   exception, raise, handle, catch, throw
%X PhD thesis
   present evolution of a functional language from a conventional language
   ( algol like ).
   simplicity formal semantics.
   program transformation, language embedded in logic.
   techniques of efficient implementation.
   data abstraction and exception handling mechanism described.
   interactive functional programs.


%A K. Murphy
%T Conjugate Bayesian analysis of the univariate Gaussian: a tutorial
%I UBC
%M SEP
%D 2007
%K TR, UBC, c2007, c200x, c20xx, Gaussian, Normal, probability distribution,
   marginal likelihood, prior, posterior, parameters, conjugate
%X "The Gaussian or normal distribution is one of the most widely used in
   statistics. Estimating its params. using Bayesian inference & conjugate
   priors is also widely used. The use of c.priors allows all the results to be
   derived in closed form. Unfortunately, different books use different
   conventions on how to parameterize the various distns (e.g., put the prior
   on the precision or the variance, use an inverse gamma or inverse
   chi-squared, etc), which can be very confusing for the student. ... we
   summarize all of the most commonly used forms. We provide detailed
   derivations for some of these results; the rest can be obtained by simple
   reparameterization. See the appendix for the definition the distributions
   that are used."
   -- pdf@[<A HREF="http://www.cs.ubc.ca/~murphyk/Papers/bayesGauss.pdf">ubc</A>]['13],
      pdf@[<A HREF="http://www.ai.mit.edu/~murphyk/Papers/bayesGauss.pdf">mit</A>]['13],
      auth@[<A HREF="http://www.cs.ubc.ca/~murphyk/mypapers.html">ubc</A>]['13]
      (joined google in 2012).
   (Also see MargLH@[<A HREF="https://en.wikipedia.org/wiki/Marginal_likelihood">wikip</A>]['13].)


%A F. Douglis
%T Process migration in the Sprite operating system
%I Comp. Sci. Divn, University of California, Berkeley
%R UCB/CSD/ 87/343
%M Feb
%D 1987
%K 343, process, migration sprite, operating system, OS, OpSys, network, home
%X each process has a special home node.
   home node provides kernel services to process for its life.
   system calls that depend on a process' location are forwarded
   to its home node.
   remote execution is efficient as long as the no of sys calls that must
   be forwarded home is small.
   this appears to be the case as long as file system related calls
   can be handled without the home node.
   The cost of a process migrating varies from a fraction of a sec to
   a few secs.
   Measurements done on Sun 2 workstations.

%A J. R. Larus
%T Curare: restructuring Lisp programs for concurrent execution
%I Comp. Sci. Divn, University of California, Berkeley
%R UCB/CSD 87/344
%M Feb
%D 1987
%K 344, parallel, transformation, Lisp
%X tries to eliminate control and data dependencies that prevent
   concurrent execution of invocations of recursive functions.
   Also inserts synchronization devices to ensure unmovable dependencies
   do not change program effect.

%A C. F. Olson
%T Fast alignment by eliminating unlikely matches
%R UCB/CSD 92/704
%I Comp. Sci. Divn, University of California, Berkeley
%M NOV
%D 1992
%K 704, image processing, IP, machine vision, geometric hashing, GH

%A C. F. Olsen
%T Probabilistic indexing: recognising 3D objects from 2D images using the
   probabilistic peaking effect
%R UCB/CSD 93/733
%I Comp. Sci. Divn, University of California, Berkeley
%M MAY
%D 1993
%K 733, image processing, IP, machine vision, geometric hashing, GH

%A D. Gusfield
%A J. Stoye
%T Linear time algorithms for finding and representing all tandem repeats in
   a string.
%I Comp. Sci. Dept., U. California, Davis
%R CSE-98-4
%D 1998
%O J. Comp. Syst. Sci. (JCSS), 69, pp.525-546, 2004
%K TR 98 4, TR984, TR4, c1998, c199x, c19xx, algorithm, tandem repeat, square,
   squares, sequence
%X "A tandem repeat (or square) is a string αα where α
   is a non-empty string. ... suffix tree T(S) or S ..."
   O(|S|)-time, finds and marks end-points of every tandem repeat in S.
   [<A HREF="http://wwwcsif.cs.ucdavis.edu/~gusfield/lineartime.pdf">pdf@ucdavis</A>][7/'04]


%A M. J. Beal
%T Variational algorithms for approximate Bayesian Inference
%I UCL, U.London
%M MAY
%D 2003
%K PhD thesis, UCL, c2003, c200x, c20xx, algorithm, zz0805, KL distance,
   VB, VBI, inference, AI, stats, HMM, UCL
%X "... derive & apply the VB EM alg. to 3 commonly-used & important models:
   mixtures of factor analysers, linear dynamical systems, & hidden Markov
   models. It is shown how model selection tasks such as determining the
   dimensionality, cardinality, or number of variables are possible using VB
   approx.. Also explored are methods for combining sampling procedures with
   variational approxs., to estimate the tightness of VB bounds & to obtain
   more effective sampling algs.. Chapter 6 applies VB learning to a long-
   standing problem of scoring discrete-variable directed acyclic graphs, &
   compares the performance to annealed importance sampling amongst other
   methods. Throughout, the VB approx. is compared to other methods inc.
   sampling, Cheeseman-Stutz, & asymptotic approxs. such as BIC...."
   Ch 1: Introduction,       Ch 2: Variational Bayesian Theory,
   Ch 3: Variational Bayesian Hidden Markov Models,
   Ch 4: Variational Bayesian Mixture of Factor Analysers,
   Ch 5: Variational Bayesian Linear Dynamical Systems,
   Ch 6: Learning the structure of discrete-variable graphical models with
         hidden variables,   Ch 7: Conclusion
   -- [<A HREF="http://www.cse.buffalo.edu/faculty/mbeal/papers.html">auth. inc. thesis</A>]['05].
   (NB. Useful table of KL distances etc. in an appendix A.)
   [also search for: FactorAnalysis],  [also search for: Bayesian].
   (Also see VB@[<A HREF="https://en.wikipedia.org/wiki/Variational_Bayesian_methods">wikip</A>]['21].)

%A R. Dechter
%A J. Pearl
%T A problem simplification approach that generates heuristics for constraint
   satisfaction problems
%I Computer Science Dept., U.C.L.A.
%R CSD-850014
%M Apr
%D 1985
%K constraint satisfaction problem,  graph, width, decompose,  decomposition


%A M. Zhang (Chang)
%T The jpeg and image data compression algorithms
%R UCSC-CRL-90-68
%I U. California at Santa Cruz
%M DEC
%D 1990
%K TR, UCSC, jpeg, jpg, images, file, files, compress, algorithm

%A A. D. Milosavljevic
%T Categorization of macromolecular sequences by minimal length encoding
%R UCSC-CRL-90-41
%M SEP
%D 1990
%I U. California at Santa Cruz
%K PhD thesis, c1990, c199x, c19xx, MolBio, macro-molecule,
   minimum message length encoding, description, MML, MDL, inductive inference,
   string, classification, class, classes, clustering, phylogenetic, family,
   evolutionary, tree, trees
%X PhD thesis.

%A A. Zandi
%A G. C. Langdon_jr
%T Bayesian approach to early probability estimation in binary adaptive coding
%R UCSC-CRL-91-11
%I U. California at Santa Cruz
%M MAY
%D 1991
%K Bayes, binary adaptive code, coding, compression

%A D. Haussler
%A A. Krogh
%A S. Mian
%A K. Sjolander
%T Protein modeling using hidden Markov models: analysis of globins
%R UCSC-CRL-92-23
%I University of California at Santa Cruz,
   Dept of Comp. and Information Sci.
%M JUN
%D 1992
%O available electronically as ucsc-crl-92-23.ps.Z
%K MolBio, UCSC, UC, protein, amino acid, AA, multiple alignment,
   hidden Markov model, models, HMM, EM, globin globins, HICSS, HICSS-26
%X (Shorter version will appear in Proc. of 26th Hawaii Int. Conf. on System
   Sciences, Biocomputing technology track, Jan. 5-8, 1993)
   We apply Hidden Markov Models (HMMs) to the problem of
   statistical modeling and multiple alignment of protein families.
   ... we have taken 625 unaligned globin sequences from the Swiss Protein
   database, and produced a statistical model entirely automatically from the
   primary (unaligned) sequences using no prior knowledge of globin structure.
      Order paper copies from:  Technical Library, Baskin Center for Computer
      Engineering & Information Sciences, UCSC, Santa Cruz  CA  95064.


%A Belew
%A McInerney
%A Schraudolph
%T Evolving networks: Using the genetic algorithm with connectionist learning
%D 1990
%I UCSD
%R CSE Technical Report #CS90-174
%K TR 174, TR174, c1990, c199x, c19xx, neural network, NN, ANN,
   genetic algorithm, GA
%X via enews.


%A R. H. Berry
%A D. Trigueiros
%T Using the ID3 algorithm to interpret the results of financial models
%I School of Information Systems, University of East Anglia
%M JAN
%D 1991
%K UEA, East Anglia, decision tree, ID3, expert systems, finance

%A R. H. Berry
%A G. Erdogan
%A D. Trigueiros
%T Using the ID3 algorithm to interpret the results of financial models:
   experiments and developments
%I School of Information Systems, University of East Anglia
%M JAN
%D 1991
%K UEA, East Anglia, decision tree, ID3, expert systems, finance

%A R. H. Berry
%A G. Erdogan
%A D. Trigueiros
%T Rule induction for data modelling and model representation
%I School of Information Systems, University of East Anglia
%M NOV
%D 1991
%K UEA, East Anglia, decision tree, ID3, expert systems, finance

%A R. H. Berry
%A D. Trigueiros
%T Applying neural networks to the extraction of knowledge from accounting
   reports: a classification study
%I School of Information Systems, University of East Anglia
%M JUN
%D 1991
%O Neural Networks in Business, Trippi & Turban (eds) 1992?
%K UEA, East Anglia, expert systems, finance, NN ANN


%A R. E. Buckley
%T Performance of sorting algorithms in a lazy functional language
%I Uni. of South Australia, School of Comp. and Inf. Sci.
%R CIS-94-008
%M APR
%D 1994
%K TR, Uni SA, programming, FP, sort, sorts, sorting, lazy evaluation,
   algorithm, speed
%X [<A HREF="ftp://lux.levels.unisa.edu.au/pub/techreps/CIS-94-008.ps.Z">ftp</A>].

%A R. E. Buckley
%A M. J. Oudshoorn
%T Building efficient two-stack parsers: One-symbol look-ahead parsing for
   a broad class of context free grammars
%I Uni. of South Australia, School of Comp. and Inf. Sci.
%R CIS-94-022
%D 1994
%K TR, Uni SA, parser, parsing, LR, LR(k), lookahead, CFG
%X [<A HREF="ftp://lux.levels.unisa.edu.au/pub/techreps/CIS-94-022.ps.Z">ftp</A>]

%A R. Buckley
%A M. J. Oudshoorn
%T Beyond LR(1). Using a two-stack (bottom-up) parser with
   zero backtracking as an alternative to LR(k)
%J Aust. Comp. Sci. Comm.
%V 17
%N 1
%M FEB
%D 1995
%P 52-60
%K ACSC, LR, LR1, LRk, LR(k), stacks, CFG, paresers, parsing, look-ahead,
   lookahead, backtrack
%X [<A HREF="http://www.cs.adelaide.edu.au/~michael/">Oudshoorn</A>][7/'02]


%A P. A. Whigham
%T Grammatical genetic learning and schemata: restated
%I Dept. Comp. Sci.,  Univ. College,  Univ. of New South Wales,
   Aust. Defence Force Academy
%R CS13/95
%D 1995
%K TR 13, TR13, UNSW, adfa, genetic algorithm, GA, grammar, CFG, zz0895
%X 7 refs


%A U. Ekstrom
%T Design Patterns for Simulations in Erlang/OTP
%I Comp. Sci. Dept., Uppsala U.
%D 2000
%K masters thesis, discrete event simulation, c2000, c200x, c20xx, Erlang
%X "The growing field of Design Patterns offers hope of controlling the
   omplexities associated with the development of large software applications.
   The arch. of a sys. can be expressed at a higher level of abstraction, which
   allows the designer to concentrate on the specifics of the application
   rather than having to deal with low-level issues. Simulations are today an
   essential tool for research & training in areas such as national defense,
   where simulations are a cheaper (and sometimes the only possible)
   alternative. This work has focused on finding design patterns for simulation
   s/w & provides an implementation of the discovered patterns in Erlang/OTP as
   something called behaviours. The main simulation s/w in this study is Sim94 -
   A concurrent simulator for plan-driven troops, written in the Erlang
   programming language at the CS Dept of Uppsala U. in l994. This paper also
   investigates patterns in general as well as the relationship between
   behaviours & design patterns."
   -- [<A HREF="http://ftp.csd.uu.se/pub/papers/masters-theses/0178-ekstrom.pdf">pdf</A>]['05].


%A R. R. Bouckaert
%T Bayesian Belief Networks: From Construction to Inference
%I U. Utrecht
%D 1995
%K PhD thesis, c1995, c199x, c19xx, network, net, AI, II
%X Auth. @ U.W@ik@to working on Weka ~['04].


%A C. McDonald
%T A functional UNIX command interpreter
%R TR 86/7
%I Dept Computer Science, University of Western Australia
%C Perth
%D 1986
%K UWA, functional, applicative, operating system, shell

%A D. H. Kieronska
%T Practical implementation of restriction site mapping
%I Dept Computer Science, University of Western Australia
%R Honours Report
%M NOV
%D 1986
%K UWA, plasmid mapping, dna, restriction site, enzyme, molecular biology,
   single, double digest

%A T. I. Dix
%A D. H. Kieronska
%T Tree pruning in restriction site mapping
%R TR 86/8
%D 1986
%I Dept Computer Science, University of Western Australia
%O ACSC 10, pp37-45, Deakin University, Victoria, Australia, Feb 1987
%O Australian Computer Science Communications V9 N1 1987
%K UWA, restriction site, plasmid mapping, DNA

%A C. McDonald
%A L. Allison
%T Denotational semantics of a command interpreter and
   their implementation in standard ML
%I Dept. Computer Science, University of Western Australia
%R TR 88/7
%M JUL
%D 1988
%K UWA, unix, shell, command language, SML, LAllison, c1988, c198x, c19xx
%X significant subset of the Unix shell
   See: The Computer Journal V32 No5 pp422-431 1989.

%A T. D. Gedeon
%A J. S. Rohl
%T Non-recursive algorithms for drawing space-filling curves
%R TR 86/6
%I Dept. Computer Science, University of Western Australia
%M NOV
%D 1986
%K UWA, recursion, removal, curve

%A T. D. Gedeon
%T Recursion elimination by automatic schema generation
%R TR 89/2
%I Dept. Computer Science, University of Western Australia
%D 1989
%K UWA, recursion, removal, schema, program transformation

%A T. Mark Ellison
%T Discovering planar segregations
%R TR 90/5
%D 1990
%I Dept. Computer Science, University of Western Australia
%O Proc. of AAAI Spring Symp. on Machine Learning of
   Natural Language and Ontology, pp.42-47, 1991
%K UWA, natural language, vowel, consonant, phoneme, inductive inference II,
   information theory, MML, MDL, Occam, computational linguistics, languages,
   algorithmic complexity, c1990, c199x, c19xx, zz0419
%X (simulated annealing, classifies letters / phonemes into
   vowel / consonant / ... and infers patterns for words.)
   "this report I present an algorithm for finding planar segregations of
   phonemes for particular languages. This algorithm requires no domain-specific
   knowledge of phonology or phonetics. Despite this lack of knowledge, the
   implemented algorithm has identified the structurally significant
   segregations for thirty languages"
   -- [<A HREF="http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.17.4595">cites'er</A>]['19],
      [<A HREF="https://www.researchgate.net/publication/277298949_Discovering_planar_segregations">res.g.</A>]['19].
   [Also search for: natural language information].

%A R. Owens
%T On the primal sketch and feature-free profiles
%R TR 91/3
%I Dept. Computer Science, University of Western Australia
%M MAY
%D 1991
%K UWA, image processing, IP, local energy model, noise, feature, features

%A T. M. Ellison.
%T The Machine Learning of Phonological Structure
%I University of Western Australia
%D 1992
%K PhD thesis, c1992, c199x, c19xx, Mark Ellison, marke, UWA, Perth,
   computational linguistics, linguistic, natural language, MML, MDL,
   phonology, vowel, vowels, consonant, consonants
%X (?back in Perth c2008?)


%A P. G. K. Reiser
%T Evolutionary algorithms for learning formulae in first order logic
%I University of Wales, UK
%D 1999
%K PhD Thesis, program, programs, genetic, c1999, c199x, c19xx, algorithm,
   Aberystwyth, Phil, predicate logic, prolog, LP, zzOSP, zOSP04
%X [<A HREF="http://www.stancomb.co.uk/~prr/">~prr</A>][8/'04] [ps, pdf].


%A R. R. Bouckaert
%T Bayesian network classifiers in Weka
%R 14/2004
%D 2004
%I Comp. Sci. Dept.. U. of Waikato.
%M SEP
%D 2004
%K TR 14, TR14, networks, net, nets, inductive inference, II, machine learning,
   Weka, classifier, AI, c2004, c200x, c20xx
%X "... A [BN] is a DAG and a set of prob. tables.
   ... All BN algorithms implemented in Weka assume the
   following of a data set:
    . all variables are discrete finite [else ... Discretize]
    . no missing values [else ...ReplaceMissingValues filter]
   "Currently all search algs. assume that all variables are discrete." p22.
   "A limitation of the current classes is that they assume that there are
   no missing values." p23.
   -- [<A HREF="http://www.cs.waikato.ac.nz/~remco/weka.bn.pdf">pdf</A>][/'04].
   (Also see [<A HREF="http://www.allisons.org/ll/Publications/2006ACSC/">IP</A>].)


%A Shufen Kuo
%A George Cross
%T An improved algorithm to find the length of the longest common
   subsequence of two strings
%D 1987
%R CS-87-178
%I Dept of Computer Science,
   Washington State University.
%K longest common subsequence, homology, LCS, similarity, edit distance, DNA

%A B. N. Freeman-Benson
%T Constraint Imperative Programming
%I Dept. Computer Science and Engineering,  University of Washington, Seattle.
%D 1991
%M AUG
%R 91-07-02
%K constraint imperative programming language, CIP
%X PhD thesis. A. Borning was supervisor.

%A A. Borning
%A B. Freeman-Benson
%A M. Wilson
%T Constraint hierarchies
%D 1992
%I Dept. Computer Science and Engineering,  University of Washington, Seattle.
%K constraint programming language, hiererchical constraints
%X sub. to Lisp and Symbolic Computation.

%A B. N. Freeman-Benson
%A A. Borning
%T Integrating constraints with an object-oriented language
%I Dept. Computer Science and Engineering,  University of Washington, Seattle.
%D 1992
%K constraint programming language, object oriented
%X sub to ECOOP 92

%A M. Wilson
%A A. Borning
%T Hierarchical constraint logic programming
%I Dept. Computer Science and Engineering,  University of Washington, Seattle.
%D 1991
%K hierarchical, constraint, programming, language, logic, LP
%X sub to The J of Logic Prog

%A M. H. van Emden
%T An algorithm for interpreting Prolog programs
%R CS-81-28
%I Dept Computer Science, University of Waterloo
%M Sep
%D 1981
%K Prolog, logic program, implementation, interpreter

%A M. P. W. Mutrie
%A B. W. Char
%A R. H. Bartels
%T Expression optimization using high-level knowledge
%R CS-87-09
%M Feb
%D 1987
%I Dept Computer Science, University of Waterloo
%K optimise, optimize, symbolic expression, algebra,
   improve,   differentiate, Taylor series,  integrate
%X uses high level knowledge applied while output expressions are generated.


%A F. Frayman
%T Solving large scale interdependent constraint-satisfaction problems
%I Intelligent Systems Laboratory, Xerox Parc CA
%D ???
%O PROTO: an approach for determining protein structures from nuclear magnetic
   resonance data: an exercise in large scale interdependent
   constraint-satisfaction.
   PhD thesis, NorthWestern University Dept. Comp Sci 1985
%K ISL, constraint satisfaction problem CS, NMR, protein structure


%A ???
%T Yale Haskell
%D 1994
%K Yale, Haskell, ftp, functional programming language FP, implementation
%X  Site     Host name              Raw IP address
    Yale     nebula.cs.yale.edu     128.36.13.1
   All files are in the directory pub/haskell/yale.  Consult the README
   in this directory for further details.
   To obtain Yale Haskell via ftp:
  - Move to the directory where you intend to place Yale Haskell
  - Ftp to nebula and login anonymously
  - cd to pub/haskell/yale
  - Get the tar file: get haskell-2.1-?.tar.gz
  - Unzip the file: (your zip utility may have a different name)
           gzip -d *.gz
  - Untar the file: tar xf *.tar
  - Consult the documentation for further instructions.  The manual
    is provided in Postscript form as doc/manual/haskell.ps.
   Please send any comments or questions to
   email:  haskell-request@cs.yale.edu
   <A HREF="http://www.cs.yale.edu/HTML/YALE/CS/haskell/yale-fp.html">FP at Yale</A>   (8/'94)


%A C. Runciman
%A D. Wakeling
%T Heap profiling of lazy functional programs
%R 172
%M APR
%D 1992
%I Dept. Computer Science, University of York
%K FP, LML, lazy, functional programming, heap, space, profile, uniYork

%A D. M. Cattral
%A C. Runciman
%T A relational programming language with logical and functional aspects
%M FEB
%D 1992
%I Dept. Computer Science, University of York
%K functional, relational programming, FP, language, uniYork
%X draft

%A C. Ho-Stuart
%T Let's Party: Process algebra with real-time from York
%M APR
%D 1992
%I Dept. Computer Science, University of York
%K real time, process algebra, CSP, CCS, York, uniYork, Ho Stuart
%X draft


%A N. E. Fuchs
%A H. F. Hofmann
%A R. Schwitter
%T Specifying logic programs in controlled natural language
%R 94.17
%I Department of Computer Science, University of Zurich
%M NOV
%D 1994
%K logic programming, LP
%X ... we propose controlled natural language as a declarative and
   application-specific specification language. Controlled natural language is
   a subset of natural language that can be accurately and efficiently
   processed by a computer, but is expressive enough to allow natural usage by
   non-specialists. Specifications in controlled natural language are
   automatically translated into Prolog clauses, hence become formal and
   executable. The translation uses a definite clause grammar enhanced by
   feature structures. ...
   email: fuchs@ifi.unizh.ch (Norbert E. Fuchs  11/'94)
   Organization: IFI University of Zurich

%A N. E. Fuchs
%A M. P. J. Fromherz
%T Transformational development of logic programs from executable
   specifications - schema-based visual and textual composition of
   logic programs
%P ?-?
%B Development, Test and Maintenance of Declarative AI Programs
%E C. Beckstein
%E U. Geske
%V 238
%S GMD Studien
%D 1994
%I Gesellschaft fr Informatik und Datenverarbeitung (GMD)
%K logic programming, LP
%X email: fuchs@ifi.unizh.ch (Norbert E. Fuchs  11/'94)
   Organization: IFI University of Zurich